pmid title sentence year journal region virus mutation mutation_start mutation_end gene gene_start gene_end disease disease_start disease_end 32464271 Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? 2020 International journal of infectious diseases Title SARS_CoV_2 D614G 10 15 S;S 47;54 52;55 COVID-19 91 99 32464271 Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? The increasing number of deaths due to the COVID-19 pandemic has raised serious global concerns. 2020 International journal of infectious diseases Title SARS_CoV_2 D614G 10 15 S;S 47;54 52;55 COVID-19;COVID-19 91;154 99;162 32464271 Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality. 2020 International journal of infectious diseases Title SARS_CoV_2 D614G 10 15 32587973 The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. 2020 bioRxiv Title SARS_CoV_2 D614G 4 9 S 37 42 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. 2020 bioRxiv Title SARS_CoV_2 D614G 42 47 S 59 64 32676618 D614G Spike Variant Does Not Alter IgG, IgM, or IgA Spike Seroassay Performance. D614G Spike Variant Does Not Alter IgG, IgM, or IgA Spike Seroassay Performance. 2020 medRxiv Title SARS_CoV_2 D614G 0 5 S;S 6;52 11;57 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. 2020 Cell Title SARS_CoV_2 D614G 52 57 S 31 36 COVID-19 87 95 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. 2020 Cell Title SARS_CoV_2 D614G 31 36 COVID-19 51 59 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. 2020 bioRxiv Title SARS_CoV_2 D614G 4 9 32743581 The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State. The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State. 2020 bioRxiv Title SARS_CoV_2 D614G 29 34 32779780 Atomistic simulation reveals structural mechanisms underlying D614G spike glycoprotein-enhanced fitness in SARS-COV-2. Atomistic simulation reveals structural mechanisms underlying D614G spike glycoprotein-enhanced fitness in SARS-COV-2. 2020 Journal of computational chemistry Title SARS_CoV_2 D614G 62 67 S 68 86 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. 2020 Scientific reports Title SARS_CoV_2 D614G 51 56 S 57 62 32905045 Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. 2020 Cell reports. Medicine Title SARS_CoV_2 D614G 95 100 S 101 106 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. 2020 bioRxiv Title SARS_CoV_2 D614G 15 20 S 0 5 32934770 Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity. Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity. 2020 ACS medicinal chemistry letters Title SARS_CoV_2 D614G 30 35 S 50 55 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. 2020 Cell Title SARS_CoV_2 D614G 42 47 S 59 64 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. 2020 ACS chemical neuroscience Title SARS_CoV_2 D614G 96 101 S 102 107 COVID-19 28 36 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. 2020 bioRxiv Title SARS_CoV_2 D614G 11 16 33052347 D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction. D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction. 2020 bioRxiv Title SARS_CoV_2 D614G 0 5 S 33 38 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. 2021 International journal of infectious diseases Title SARS_CoV_2 D614G 66 71 S;S 55;48 56;53 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. 2020 NPJ vaccines Title SARS_CoV_2 D614G 85 90 S 114 119 33083806 Structural impact on SARS-CoV-2 spike protein by D614G substitution. Structural impact on SARS-CoV-2 spike protein by D614G substitution. 2020 bioRxiv Title SARS_CoV_2 D614G 49 54 S 32 37 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. Spike mutation D614G alters SARS-CoV-2 fitness. 2021 Nature Title SARS_CoV_2 D614G 15 20 S 0 5 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. 2020 bioRxiv Title SARS_CoV_2 D614G 17 22 S 11 16 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. 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Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. 2021 Biochemical and biophysical research communications Title SARS_CoV_2 D614G 29 34 S 62 67 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. 2020 Nature communications Title SARS_CoV_2 D614G 25 30 S;S 11;57 16;62 33253058 A Gapless, Unambiguous RNA Metagenome-Assembled Genome Sequence of a Unique SARS-CoV-2 Variant Encoding Spike S813I and ORF1a A859V Substitutions. A Gapless, Unambiguous RNA Metagenome-Assembled Genome Sequence of a Unique SARS-CoV-2 Variant Encoding Spike S813I and ORF1a A859V Substitutions. 2021 Omics Title SARS_CoV_2 A859V;S813I 126;110 131;115 ORF1a;S 120;104 125;109 33257936 Effect of D614G Spike Variant on Immunoglobulin G, M, or A Spike Seroassay Performance. 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D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. 2021 Cell reports Title SARS_CoV_2 D614G 0 5 S 33 38 33442691 Neutralization of N501Y mutant SARS-CoV-2 by BNT162b2 vaccine-elicited sera. Neutralization of N501Y mutant SARS-CoV-2 by BNT162b2 vaccine-elicited sera. 2021 bioRxiv Title SARS_CoV_2 N501Y 18 23 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. 2021 bioRxiv Title SARS_CoV_2 P681H 121 126 S 48 49 33447831 Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces shedding of SARS-CoV-2 D614G in rhesus macaques. 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SARS-CoV-2 genetic diversity in Venezuela: Predominance of D614G variants and analysis of one outbreak. 2021 PloS one Title SARS_CoV_2 D614G 59 64 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. 2021 Cell Title SARS_CoV_2 N439K 29 34 S 23 28 33628442 Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. 2021 Clinical & translational immunology Title SARS_CoV_2 D614G;D614G 118;57 123;62 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. 2021 Virus research Title SARS_CoV_2 E484K 26 31 33636719 SARS-CoV-2 spike D614G change enhances replication and transmission. SARS-CoV-2 spike D614G change enhances replication and transmission. 2021 Nature Title SARS_CoV_2 D614G 17 22 S 11 16 33671631 Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants. Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants. 2021 Microorganisms Title SARS_CoV_2 D614G 127 132 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. 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The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. 2021 The Journal of biological chemistry Title SARS_CoV_2 Y453F 15 20 33718878 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawai'i Reveals the Worldwide Emerging P681H Mutation. Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawai'i Reveals the Worldwide Emerging P681H Mutation. 2021 Hawai'i journal of health & social welfare Title SARS_CoV_2 P681H 122 127 S 48 49 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. Structural impact on SARS-CoV-2 spike protein by D614G substitution. 2021 Science (New York, N.Y.) Title SARS_CoV_2 D614G 49 54 S 32 37 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. 2021 FEBS letters Title SARS_CoV_2 N501Y 24 29 S 49 54 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. 2021 Microbiology resource announcements Title SARS_CoV_2 N439K 86 95 S 52 57 33750399 Modelling the association between COVID-19 transmissibility and D614G substitution in SARS-CoV-2 spike protein: using the surveillance data in California as an example. Modelling the association between COVID-19 transmissibility and D614G substitution in SARS-CoV-2 spike protein: using the surveillance data in California as an example. 2021 Theoretical biology & medical modelling Title SARS_CoV_2 D614G 64 69 S 97 102 COVID-19 34 42 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. 2021 Journal of cellular physiology Title SARS_CoV_2 E484K;K417N;K417T;N501Y 78;69;69;89 83;76;76;94 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. The N501Y spike substitution enhances SARS-CoV-2 transmission. 2021 bioRxiv Title SARS_CoV_2 N501Y 4 9 S 10 15 33758861 Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-Cov-2 variants. Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-Cov-2 variants. 2021 bioRxiv Title SARS_CoV_2 L452R 19 24 S 67 72 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. 2021 medRxiv Title SARS_CoV_2 L452R 114 119 S 120 125 33767200 The effect of SARS-CoV-2 D614G mutation on BNT162b2 vaccine-elicited neutralization. The effect of SARS-CoV-2 D614G mutation on BNT162b2 vaccine-elicited neutralization. 2021 NPJ vaccines Title SARS_CoV_2 D614G 25 30 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. 2021 Journal of virological methods Title SARS_CoV_2 N501Y 66 71 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. 2021 Infection, genetics and evolution Title SARS_CoV_2 D614G 55 60 S 83 84 33788036 New study on prevalence of anosmia in COVID-19 implicates the D614G virus mutation as a major contributing factor to chemosensory dysfunction. New study on prevalence of anosmia in COVID-19 implicates the D614G virus mutation as a major contributing factor to chemosensory dysfunction. 2021 Eur Arch Otorhinolaryngol Title SARS_CoV_2 D614G 62 67 Anosmia;COVID-19 27;38 34;46 33788923 Estimation of Secondary Household Attack Rates for Emergent Spike L452R Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants Detected by Genomic Surveillance at a Community-Based Testing Site in San Francisco. Estimation of Secondary Household Attack Rates for Emergent Spike L452R Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants Detected by Genomic Surveillance at a Community-Based Testing Site in San Francisco. 2022 Clinical infectious diseases Title SARS_CoV_2 L452R 66 71 S 60 65 COVID-19 79 119 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. 2021 Infection, genetics and evolution Title SARS_CoV_2 P504L;Y541C 106;116 111;121 Nsp13 123 128 COVID-19 146 154 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. 2021 Microorganisms Title SARS_CoV_2 N501Y 11 16 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. 2021 bioRxiv Title SARS_CoV_2 P681H 29 34 S 113 118 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. The SARS-CoV-2 Spike variant D614G favors an open conformational state. 2021 Science advances Title SARS_CoV_2 D614G 29 34 S 15 20 33880475 Generation of a novel SARS-CoV-2 sub-genomic RNA due to the R203K/G204R variant in nucleocapsid: homologous recombination has potential to change SARS-CoV-2 at both protein and RNA level. Generation of a novel SARS-CoV-2 sub-genomic RNA due to the R203K/G204R variant in nucleocapsid: homologous recombination has potential to change SARS-CoV-2 at both protein and RNA level. 2021 bioRxiv Title SARS_CoV_2 R203K;G204R 60;66 65;71 N 83 95 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. 2021 The journal of physical chemistry. B Title SARS_CoV_2 N501Y 77 82 S 56 61 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. 2021 Proc Natl Acad Sci U S A Title SARS_CoV_2 D614G;N501Y 50;56 55;61 33900193 Introduction of ORF3a-Q57H SARS-CoV-2 Variant Causing Fourth Epidemic Wave of COVID-19, Hong Kong, China. Introduction of ORF3a-Q57H SARS-CoV-2 Variant Causing Fourth Epidemic Wave of COVID-19, Hong Kong, China. 2021 Emerging infectious diseases Title SARS_CoV_2 Q57H 22 26 ORF3a 16 21 COVID-19 78 86 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. 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Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. 2021 Microorganisms Title SARS_CoV_2 N501Y 132 137 S 117 122 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. 2021 Viruses Title SARS_CoV_2 E484K 68 73 S 81 86 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. 2021 Molecules (Basel, Switzerland) Title SARS_CoV_2 D936Y 0 5 S 63 68 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. 2021 Journal of medical virology Title SARS_CoV_2 T478K 98 103 S 83 88 COVID-19 29 69 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. 2021 Emerging microbes & infections Title SARS_CoV_2 E484K;N501Y 65;75 70;80 33991677 Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage. Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage. 2021 Clinical microbiology and infection Title SARS_CoV_2 N501Y 30 35 S 36 41 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. 2021 EBioMedicine Title SARS_CoV_2 Q498H;Q493K 10;0 15;5 S 33 38 34011523 Mutation-Specific SARS-CoV-2 PCR Screen: Rapid and Accurate Detection of Variants of Concern and the Identification of a Newly Emerging Variant with Spike L452R Mutation. Mutation-Specific SARS-CoV-2 PCR Screen: Rapid and Accurate Detection of Variants of Concern and the Identification of a Newly Emerging Variant with Spike L452R Mutation. 2021 Journal of clinical microbiology Title SARS_CoV_2 L452R 155 160 S 149 154 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. 2021 Journal of medical virology Title SARS_CoV_2 D614G 124 129 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. 2021 Infection, genetics and evolution Title SARS_CoV_2 E484K;E484K 87;0 92;5 S 93 98 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. 2021 Microbial pathogenesis Title SARS_CoV_2 E484K 18 23 34060425 Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: reconciling functional mechanisms through allosteric model of spike regulation. Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: reconciling functional mechanisms through allosteric model of spike regulation. 2021 Journal of biomolecular structure & dynamics Title SARS_CoV_2 D614G 137 142 S;S 131;213 136;218 34061792 Severe systemic thrombosis in a young COVID-19 patient with a rare homozygous prothrombin G20210A mutation. Severe systemic thrombosis in a young COVID-19 patient with a rare homozygous prothrombin G20210A mutation. 2021 Le infezioni in medicina Title SARS_CoV_2 G20210A 90 97 COVID-19 38 46 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. 2021 Biochemical and biophysical research communications Title SARS_CoV_2 L84S 132 136 ORF8 82 86 34073577 Kinetics of Neutralizing Antibodies of COVID-19 Patients Tested Using Clinical D614G, B.1.1.7, and B 1.351 Isolates in Microneutralization Assays. Kinetics of Neutralizing Antibodies of COVID-19 Patients Tested Using Clinical D614G, B.1.1.7, and B 1.351 Isolates in Microneutralization Assays. 2021 Viruses Title SARS_CoV_2 D614G 79 84 COVID-19 39 47 34086878 Emergence of the E484K Mutation in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Lineage B.1.1.345 in Upstate New York. Emergence of the E484K Mutation in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Lineage B.1.1.345 in Upstate New York. 2022 Clinical infectious diseases Title SARS_CoV_2 E484K 17 22 COVID-19 35 82 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. 2021 Bioinformation Title SARS_CoV_2 D614G 0 5 S 85 90 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. 2021 Open forum infectious diseases Title SARS_CoV_2 D614G 52 57 COVID-19 94 102 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. 2021 PLoS pathogens Title SARS_CoV_2 W152L;E484K;G769V 105;111;117 110;116;122 S 91 96 COVID-19 32 72 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. 2021 medRxiv Title SARS_CoV_2 E484K 120 125 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. 2021 Journal of virology Title SARS_CoV_2 V367F 0 5 S;RBD 29;35 34;38 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. 2021 Journal of veterinary diagnostic investigation Title SARS_CoV_2 G142D;N501T 53;43 58;48 S 10 15 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. 2021 Frontiers in cellular and infection microbiology Title SARS_CoV_2 E484K;K417N;N501Y 70;59;42 75;64;47 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. 2021 Emerging microbes & infections Title SARS_CoV_2 D178H;V70L 99;126 104;130 Membrane;S 109;85 117;90 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. 2021 Journal of medical virology Title SARS_CoV_2 N501Y 35 40 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. 2021 Cell host & microbe Title SARS_CoV_2 L452R 17 22 S 11 16 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. 2021 ACS omega Title SARS_CoV_2 D614G 176 181 S 100 105 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. 2021 Journal of clinical virology Title SARS_CoV_2 N501Y 139 144 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. V483A: an emerging mutation hotspot of SARS-CoV-2. 2021 Future virology Title SARS_CoV_2 V483A 0 5 34197265 Comparison of SARS-CoV-2 Variants of Concern 202012/01 (U.K. Variant) and D614G Variant Transmission by Different Routes in Syrian Hamsters. Variant) and D614G Variant Transmission by Different Routes in Syrian Hamsters. 2021 Vector borne and zoonotic diseases (Larchmont, N.Y.) Title SARS_CoV_2 D614G 13 18 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. 2021 Vaccines Title SARS_CoV_2 P681H 34 39 S 20 25 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. 2021 Biomolecules Title SARS_CoV_2 P323L 110 115 RdRP 74 102 34223909 Limited Neutralization of Authentic Severe Acute Respiratory Syndrome Coronavirus 2 Variants Carrying E484K In Vitro. Limited Neutralization of Authentic Severe Acute Respiratory Syndrome Coronavirus 2 Variants Carrying E484K In Vitro. 2021 The Journal of infectious diseases Title SARS_CoV_2 E484K 102 107 COVID-19 36 83 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. 2022 bioRxiv Title SARS_CoV_2 P681R 61 66 S 0 5 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. 2021 Open forum infectious diseases Title SARS_CoV_2 E484K 41 46 34260717 SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion. SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion. 2021 The Journal of infectious diseases Title SARS_CoV_2 E484Q;L452R 39;29 44;34 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. 2021 Frontiers in medicine Title SARS_CoV_2 E484K;L249S 81;71 86;76 S 51 56 34268528 SARS-CoV-2 Infections in mRNA Vaccinated Individuals are Biased for Viruses Encoding Spike E484K and Associated with Reduced Infectious Virus Loads that Correlate with Respiratory Antiviral IgG levels. SARS-CoV-2 Infections in mRNA Vaccinated Individuals are Biased for Viruses Encoding Spike E484K and Associated with Reduced Infectious Virus Loads that Correlate with Respiratory Antiviral IgG levels. 2021 medRxiv Title SARS_CoV_2 E484K 91 96 S 85 90 COVID-19 0 21 34274369 A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. 2021 Journal of virological methods Title SARS_CoV_2 E484K;N501Y 102;112 107;117 S 118 123 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. 2021 The Lancet regional health. Europe Title SARS_CoV_2 E484K 17 22 34289053 The virological impacts of SARS-CoV-2 D614G mutation. The virological impacts of SARS-CoV-2 D614G mutation. 2021 Journal of molecular cell biology Title SARS_CoV_2 D614G 38 43 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. 2021 Meta gene Title SARS_CoV_2 D614G 52 57 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. 2021 Informatics in medicine unlocked Title SARS_CoV_2 C241T 61 66 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. 2021 mBio Title SARS_CoV_2 D614G 0 5 S;S 33;121 38;126 34314668 Emergence of SARS-COV-2 Spike Protein Escape Mutation Q493R after Treatment for COVID-19. Emergence of SARS-COV-2 Spike Protein Escape Mutation Q493R after Treatment for COVID-19. 2021 Emerging infectious diseases Title SARS_CoV_2 Q493R 54 59 S 24 29 34315826 Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces viral shedding after SARS-CoV-2 D614G challenge in preclinical models. Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces viral shedding after SARS-CoV-2 D614G challenge in preclinical models. 2021 Science translational medicine Title SARS_CoV_2 D614G 87 92 34351228 Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia. Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia. 2021 Microbiology resource announcements Title SARS_CoV_2 D614G 72 77 34352360 A discernable increase in the severe acute respiratory syndrome coronavirus 2 R.1 lineage carrying an E484K spike protein mutation in Japan. A discernable increase in the severe acute respiratory syndrome coronavirus 2 R.1 lineage carrying an E484K spike protein mutation in Japan. 2021 Infection, genetics and evolution Title SARS_CoV_2 E484K 102 107 S 108 113 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. 2021 Microorganisms Title SARS_CoV_2 E484Q;L452R;P681R;T478K 42;28;52;35 47;33;57;40 S 11 16 COVID-19 81 89 34362872 Phylogenomic analysis of SARS-CoV-2 from third wave clusters in Malaysia reveals dominant local lineage B.1.524 and persistent spike mutation A701V. Phylogenomic analysis of SARS-CoV-2 from third wave clusters in Malaysia reveals dominant local lineage B.1.524 and persistent spike mutation A701V. 2021 Tropical biomedicine Title SARS_CoV_2 A701V 142 147 S 127 132 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. 2021 Virus research Title SARS_CoV_2 D614G 81 86 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. 2021 Journal of clinical microbiology Title SARS_CoV_2 L452R 19 24 S 67 72 34384810 Infection-enhancing anti-SARS-CoV-2 antibodies recognize both the original Wuhan/D614G strain and Delta variants. A potential risk for mass vaccination? Infection-enhancing anti-SARS-CoV-2 antibodies recognize both the original Wuhan/D614G strain and Delta variants. 2021 The Journal of infection Title SARS_CoV_2 D614G 81 86 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. 2021 Frontiers in cell and developmental biology Title SARS_CoV_2 N439K 0 5 S 17 22 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. 2021 eLife Title SARS_CoV_2 N501Y 0 5 S 18 23 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. 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The low contagiousness and new A958D mutation of SARS-CoV-2 in children: An observational cohort study. 2021 International journal of infectious diseases Title SARS_CoV_2 A958D 31 36 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. 2022 Journal of medical virology Title SARS_CoV_2 D614G 36 41 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. 2021 bioRxiv Title SARS_CoV_2 P681R 12 17 S 6 11 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. 2021 Meta gene Title SARS_CoV_2 V90T 91 95 S;S 25;128 45;148 34473242 Association of E484K spike protein mutation with SARS-CoV-2 infection in vaccinated persons---Maryland, January - May 2021. Association of E484K spike protein mutation with SARS-CoV-2 infection in vaccinated persons---Maryland, January - May 2021. 2021 Clinical infectious diseases Title SARS_CoV_2 E484K 15 20 S 21 26 COVID-19 49 69 34482844 Case report: hepatitis in a child infected with SARS-CoV-2 presenting toll-like receptor 7 Gln11Leu single nucleotide polymorphism. 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Nucleic acids Title SARS_CoV_2 D614G 0 5 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin. 2021 Molecular therapy. Nucleic acids Title SARS_CoV_2 D614G 0 5 34493762 Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. 2021 Scientific reports Title SARS_CoV_2 N501Y 117 122 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. 2021 Journal of virology Title SARS_CoV_2 D614G 122 127 S 42 47 34495709 Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. 2021 Journal of clinical microbiology Title SARS_CoV_2 E484K 58 63 S 80 85 34499599 Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. 2021 Emerging infectious diseases Title SARS_CoV_2 E484K 27 32 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. 2021 Heliyon Title SARS_CoV_2 D614G 38 43 S 24 29 34516024 Computational decomposition reveals reshaping of the SARS-CoV-2-ACE2 interface among viral variants expressing the N501Y mutation. Computational decomposition reveals reshaping of the SARS-CoV-2-ACE2 interface among viral variants expressing the N501Y mutation. 2021 Journal of cellular biochemistry Title SARS_CoV_2 N501Y 115 120 34518554 Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. 2021 Scientific reports Title SARS_CoV_2 D614G 59 64 S 45 50 34531369 S19W, T27W, and N330Y mutations in ACE2 enhance SARS-CoV-2 S-RBD binding toward both wild-type and antibody-resistant viruses and its molecular basis. S19W, T27W, and N330Y mutations in ACE2 enhance SARS-CoV-2 S-RBD binding toward both wild-type and antibody-resistant viruses and its molecular basis. 2021 Signal transduction and targeted therapy Title SARS_CoV_2 N330Y;T27W;S19W 16;6;0 21;10;4 RBD;S 61;59 64;60 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. 2021 ACS chemical neuroscience Title SARS_CoV_2 D614G 4 9 COVID-19 45 53 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. 2021 Cell Title SARS_CoV_2 N501Y 65 70 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. 2021 Pathogens & immunity Title SARS_CoV_2 R203K;G204R 60;66 65;71 N 83 95 34545803 Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA. Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA. 2021 Emerging infectious diseases Title SARS_CoV_2 E484K 33 38 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. 2022 Briefings in bioinformatics Title SARS_CoV_2 E484K 61 66 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. 2021 PeerJ Title SARS_CoV_2 D614G 61 66 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. 2021 Journal of molecular graphics & modelling Title SARS_CoV_2 E484K 0 5 RBD 29 32 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. 2021 The Journal of biological chemistry Title SARS_CoV_2 D614G 0 5 S 33 38 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. 2021 Viruses Title SARS_CoV_2 L452R;T478K;E484Q 84;94;100 89;99;105 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. 2021 Viruses Title SARS_CoV_2 Q675H;Q677H 60;70 65;75 S 76 81 34594910 Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. 2021 China CDC weekly Title SARS_CoV_2 D614G 50 55 COVID-19 68 76 34602531 A rapid screening assay for L452R and T478K spike mutations in SARS-CoV-2 Delta variant using high-resolution melting analysis. A rapid screening assay for L452R and T478K spike mutations in SARS-CoV-2 Delta variant using high-resolution melting analysis. 2021 The Journal of toxicological sciences Title SARS_CoV_2 L452R;T478K 28;38 33;43 S 44 49 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. 2021 mBio Title SARS_CoV_2 Q677H 59 64 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. 2021 BMC infectious diseases Title SARS_CoV_2 D614G 130 135 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. 2022 Journal of virological methods Title SARS_CoV_2 N501Y 101 106 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. 2021 Frontiers in public health Title SARS_CoV_2 L452R 62 67 S 56 61 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. 2021 Journal of medical virology Title SARS_CoV_2 N501Y 49 54 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. 2021 Frontiers in cellular and infection microbiology Title SARS_CoV_2 N501Y;N501Y 40;53 45;58 S 62 67 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. 2022 Glycobiology Title SARS_CoV_2 D614G 125 130 S 69 74 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. 2021 PLoS pathogens Title SARS_CoV_2 Y453F 9 14 S 22 27 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. 2021 Applied microbiology and biotechnology Title SARS_CoV_2 D614G 0 5 S 41 42 34756912 RT-qPCR detection of SARS-CoV-2 mutations S 69-70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples. RT-qPCR detection of SARS-CoV-2 mutations S 69-70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples. 2022 The Science of the total environment Title SARS_CoV_2 D3L;N501Y 69;57 72;62 N;S;S 67;42;55 68;43;56 34758391 SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance. SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance. 2022 International journal of infectious diseases Title SARS_CoV_2 T135I 25 30 N 31 43 34763050 Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation. Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation. 2021 Infection, genetics and evolution Title SARS_CoV_2 D614A 136 141 S 133 134 COVID-19 67 75 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. 2021 International journal of biological macromolecules Title SARS_CoV_2 A94S;N65S;S46A;V35T 103;89;79;69 111;97;87;77 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. 2022 Virus research Title SARS_CoV_2 E484K;L249S 84;78 89;83 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. 2022 Journal of cellular biochemistry Title SARS_CoV_2 N501Y 55 60 S 11 16 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. 2021 ACS synthetic biology Title SARS_CoV_2 E484K 58 63 34783635 Identification of the SARS-CoV-2 Delta variant C22995A using a high-resolution melting curve RT-FRET-PCR. Identification of the SARS-CoV-2 Delta variant C22995A using a high-resolution melting curve RT-FRET-PCR. 2022 Emerging microbes & infections Title SARS_CoV_2 C22995A 47 54 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. 2021 Virology journal Title SARS_CoV_2 E661D 55 60 S 53 54 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. 2021 Immune network Title SARS_CoV_2 T478K 47 52 S 97 102 34806876 N501Y and K417N Mutations in the Spike Protein of SARS-CoV-2 Alter the Interactions with Both hACE2 and Human-Derived Antibody: A Free Energy of Perturbation Retrospective Study. N501Y and K417N Mutations in the Spike Protein of SARS-CoV-2 Alter the Interactions with Both hACE2 and Human-Derived Antibody: A Free Energy of Perturbation Retrospective Study. 2021 Journal of chemical information and modeling Title SARS_CoV_2 K417N;N501Y 10;0 15;5 S 33 38 34809492 Functional Antibodies Against SARS-CoV-2 Receptor Binding Domain Variants with Mutations N501Y or E484K in Human Milk from COVID-19-Vaccinated, -Recovered, and -Unvaccinated Women. Functional Antibodies Against SARS-CoV-2 Receptor Binding Domain Variants with Mutations N501Y or E484K in Human Milk from COVID-19-Vaccinated, -Recovered, and -Unvaccinated Women. 2022 Breastfeeding medicine Title SARS_CoV_2 E484K;N501Y 98;89 103;94 RBD 41 64 COVID-19 123 131 34818667 The N501Y spike substitution enhances SARS-CoV-2 infection and transmission. The N501Y spike substitution enhances SARS-CoV-2 infection and transmission. 2022 Nature Title SARS_CoV_2 N501Y 4 9 S 10 15 COVID-19 38 58 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. 2021 Analytical chemistry Title SARS_CoV_2 N501Y 151 156 S 145 150 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. 2021 Cell host & microbe Title SARS_CoV_2 R203K;G204R 23;29 28;34 N 0 12 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. 2022 Nature Title SARS_CoV_2 P681R 60 65 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. 2021 Reproductive sciences (Thousand Oaks, Calif.) Title SARS_CoV_2 N501Y 4 9 S 33 38 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. 2021 Microbial genomics Title SARS_CoV_2 S194L 192 197 N 170 182 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. 2021 Frontiers in genetics Title SARS_CoV_2 D614G 56 61 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. 2021 Frontiers in chemistry Title SARS_CoV_2 D614G 120 125 S 55 60 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. 2021 Scientific reports Title SARS_CoV_2 D614G 49 54 S;N 43;0 48;1 34878296 Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. 2021 Microbiology spectrum Title SARS_CoV_2 G142D 106 111 S 143 148 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. 2021 Euro surveillance Title SARS_CoV_2 E484K 99 104 34886945 Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020. Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020. 2021 Euro surveillance Title SARS_CoV_2 D614G 45 50 34904526 Elucidating the role of N440K mutation in SARS-CoV-2 spike - ACE-2 binding affinity and COVID-19 severity by virtual screening, molecular docking and dynamics approach. Elucidating the role of N440K mutation in SARS-CoV-2 spike - ACE-2 binding affinity and COVID-19 severity by virtual screening, molecular docking and dynamics approach. 2021 Journal of biomolecular structure & dynamics Title SARS_CoV_2 N440K 24 29 S 53 58 COVID-19 88 96 34909610 Functional evaluation of the P681H mutation on the proteolytic activation of the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Functional evaluation of the P681H mutation on the proteolytic activation of the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. 2022 iScience Title SARS_CoV_2 P681H 29 34 S 116 121 34909775 Intranasal immunization with a vaccinia virus vaccine vector expressing pre-fusion stabilized SARS-CoV-2 spike fully protected mice against lethal challenge with the heavily mutated mouse-adapted SARS2-N501Y MA30 strain of SARS-CoV-2. Intranasal immunization with a vaccinia virus vaccine vector expressing pre-fusion stabilized SARS-CoV-2 spike fully protected mice against lethal challenge with the heavily mutated mouse-adapted SARS2-N501Y MA30 strain of SARS-CoV-2. 2021 bioRxiv Title SARS_CoV_2 N501Y 202 207 S 105 110 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. 2022 International immunopharmacology Title SARS_CoV_2 N501Y;E484K 10;0 15;5 S 27 32 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. 2022 Travel medicine and infectious disease Title SARS_CoV_2 N501Y 8 13 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. 2021 PloS one Title SARS_CoV_2 N501Y 57 62 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. 2021 Journal of clinical medicine Title SARS_CoV_2 N501Y 53 58 34949225 Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N. Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N. 2021 BMC research notes Title SARS_CoV_2 H245N 101 106 S 86 91 34959053 Isolation of SARS-CoV-2 B.1.1.28.2 (P2) variant and pathogenicity comparison with D614G variant in hamster model. Isolation of SARS-CoV-2 B.1.1.28.2 (P2) variant and pathogenicity comparison with D614G variant in hamster model. 2022 Journal of infection and public health Title SARS_CoV_2 D614G 82 87 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. 2021 Viruses Title SARS_CoV_2 Q675H 8 13 S 47 52 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. 2021 Frontiers in molecular biosciences Title SARS_CoV_2 N121Q;R190K 57;47 62;52 S 91 96 34995777 A CLUSTER OF SARS-COV-2 DELTA VARIANT OF CONCERN ADDITIONALLY HARBORING F490S, NORTHERN LOMBARDY, ITALY. A CLUSTER OF SARS-COV-2 DELTA VARIANT OF CONCERN ADDITIONALLY HARBORING F490S, NORTHERN LOMBARDY, ITALY. 2022 International journal of infectious diseases Title SARS_CoV_2 F490S 72 77 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. 2022 Microbiology spectrum Title SARS_CoV_2 G29195T 18 25 N 11 12 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. 2021 Frontiers in public health Title SARS_CoV_2 E484K;N501Y;K417N;K417T 167;178;158;158 172;183;165;165 COVID-19 85 93 35072475 R346K Mutation in the Mu Variant of SARS-CoV-2 Alters the Interactions with Monoclonal Antibodies from Class 2: A Free Energy Perturbation Study. R346K Mutation in the Mu Variant of SARS-CoV-2 Alters the Interactions with Monoclonal Antibodies from Class 2: A Free Energy Perturbation Study. 2022 Journal of chemical information and modeling Title SARS_CoV_2 R346K 0 5 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Pro108Ser mutation of SARS-CoV-2 3CLpro reduces the enzyme activity and ameliorates the clinical severity of COVID-19. 2022 Scientific reports Title SARS_CoV_2 P108S 0 9 COVID-19 109 117 35083577 Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France. Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France. 2022 Archives of virology Title SARS_CoV_2 E484K 31 36 S 25 30 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. 2022 Computational and structural biotechnology journal Title SARS_CoV_2 D614G;S939F 47;53 52;58 S 32 37 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. 2022 bioRxiv Title SARS_CoV_2 E406W 43 48 S 37 42 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. 2022 Computational and structural biotechnology journal Title SARS_CoV_2 D155Y 0 5 ORF3a 33 38 35130474 Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA. Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA. 2022 Emerging infectious diseases Title SARS_CoV_2 P681R 64 69 35136839 Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike. Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike. 2022 Translational medicine communications Title SARS_CoV_2 T500S 59 64 S;RBD;S 128;17;44 133;20;45 35139811 Linked nosocomial COVID-19 outbreak in three facilities for people with intellectual and developmental disabilities due to SARS-CoV-2 variant B.1.1.519 with spike mutation T478K in the Netherlands. Linked nosocomial COVID-19 outbreak in three facilities for people with intellectual and developmental disabilities due to SARS-CoV-2 variant B.1.1.519 with spike mutation T478K in the Netherlands. 2022 BMC infectious diseases Title SARS_CoV_2 T478K 172 177 S 157 162 COVID-19 18 26 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. 2022 Infection and drug resistance Title SARS_CoV_2 E484K 11 16 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. 2022 Gene reports Title SARS_CoV_2 T1117I 27 33 S 41 46 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. 2022 Microbiology spectrum Title SARS_CoV_2 N501Y 63 68 S 85 90 35178586 Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. 2022 Archives of virology Title SARS_CoV_2 E484K;N501Y 83;73 88;78 S 110 115 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. 2022 Scientific reports Title SARS_CoV_2 E484K 98 103 COVID-19 33 41 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. 2022 Vaccine Title SARS_CoV_2 E484K 18 23 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. 2022 Diagnostic microbiology and infectious disease Title SARS_CoV_2 C379W;Y380Q 90;0 95;5 S 62 67 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. 2022 Diagnostic microbiology and infectious disease Title SARS_CoV_2 E484K 50 55 35257681 Simultaneous detection of SARS-CoV-2 and identification of spike D614G mutation using point-of-care real-time polymerase chain reaction. Simultaneous detection of SARS-CoV-2 and identification of spike D614G mutation using point-of-care real-time polymerase chain reaction. 2022 Journal of virological methods Title SARS_CoV_2 D614G 65 70 S 59 64 35262011 Use of amplicon melt temperature to detect SARS-CoV-2 Lineage B.1.1.7 variant through the G28048T mutation in the ORF 8 gene. Use of amplicon melt temperature to detect SARS-CoV-2 Lineage B.1.1.7 variant through the G28048T mutation in the ORF 8 gene. 2021 Journal of clinical virology plus Title SARS_CoV_2 G28048T 90 97 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. 2022 bioRxiv Title SARS_CoV_2 S371F;S371L 89;89 96;96 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. 2022 3 Biotech Title SARS_CoV_2 L452R;E484Q 88;94 93;99 S 55 73 35273335 The SARS-CoV-2 Alpha variant exhibits comparable fitness to the D614G strain in a Syrian hamster model. The SARS-CoV-2 Alpha variant exhibits comparable fitness to the D614G strain in a Syrian hamster model. 2022 Communications biology Title SARS_CoV_2 D614G 64 69 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. 2022 Emerging microbes & infections Title SARS_CoV_2 R203M 41 46 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. 2022 Life science alliance Title SARS_CoV_2 E156Delta;E156G 17;17 22;22 S 11 16 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). 2022 PloS one Title SARS_CoV_2 L452R 32 37 S 38 43 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. 2022 Viruses Title SARS_CoV_2 P681R 19 24 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. 2022 Viruses Title SARS_CoV_2 E484Q 79 84 S 77 78 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. 2022 Biochemical and biophysical research communications Title SARS_CoV_2 D796Y;G339D 106;96 111;101 S 82 87 35377633 Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614G Mutant: Conformational Plasticity and Frustration-Induced Allostery as Energetic Drivers of Highly Transmissible Spike Variants. Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614G Mutant: Conformational Plasticity and Frustration-Induced Allostery as Energetic Drivers of Highly Transmissible Spike Variants. 2022 Journal of chemical information and modeling Title SARS_CoV_2 D614G 122 127 S;S 116;241 121;246 35396165 A self-amplifying RNA vaccine protects against SARS-CoV-2 (D614G) and Alpha variant of concern (B.1.1.7) in a transmission-challenge hamster model. A self-amplifying RNA vaccine protects against SARS-CoV-2 (D614G) and Alpha variant of concern (B.1.1.7) in a transmission-challenge hamster model. 2022 Vaccine Title SARS_CoV_2 D614G 59 64 35398602 SARS-CoV-2 infections in mRNA vaccinated individuals are biased for viruses encoding spike E484K and associated with reduced infectious virus loads that correlate with respiratory antiviral IgG levels. SARS-CoV-2 infections in mRNA vaccinated individuals are biased for viruses encoding spike E484K and associated with reduced infectious virus loads that correlate with respiratory antiviral IgG levels. 2022 Journal of clinical virology Title SARS_CoV_2 E484K 91 96 S 85 90 COVID-19 0 21 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. 2022 EBioMedicine Title SARS_CoV_2 R346K 37 42 35416767 Expansion of L452R-Positive SARS-CoV-2 Omicron Variant, Northern Lombardy, Italy. Expansion of L452R-Positive SARS-CoV-2 Omicron Variant, Northern Lombardy, Italy. 2022 Emerging infectious diseases Title SARS_CoV_2 L452R 13 18 35436320 Occurrence of a novel cleavage site for cathepsin G adjacent to the polybasic sequence within the proteolytically sensitive activation loop of the SARS-CoV-2 Omicron variant: The amino acid substitution N679K and P681H of the spike protein. Occurrence of a novel cleavage site for cathepsin G adjacent to the polybasic sequence within the proteolytically sensitive activation loop of the SARS-CoV-2 Omicron variant: The amino acid substitution N679K and P681H of the spike protein. 2022 PloS one Title SARS_CoV_2 N679K;P681H 203;213 208;218 S 226 231 32300673 Genomic characterization of a novel SARS-CoV-2. We found 116 mutations, the three most common mutations were 8782C>T in ORF1ab gene, 28144T>C in ORF8 gene and 29095C>T in the N gene. 2020 Gene reports Abstract SARS_CoV_2 T28144C;C29095T;C8782T 85;111;61 93;119;68 ORF1ab;ORF8;N 72;97;127 78;101;128 32357545 Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment. Among such variants, 23403A>G variant (p.D614G) in spike protein B-cell epitope is observed frequently in European countries, such as the Netherlands, Switzerland, and France, but seldom observed in China. 2020 Pathogens (Basel, Switzerland) Abstract SARS_CoV_2 A23403G;D614G 21;39 29;46 S 51 56 32422894 A Novel Synonymous Mutation of SARS-CoV-2: Is This Possible to Affect Their Antigenicity and Immunogenicity? These two subtypes were divided by a novel synonymous mutation of D614G. 2020 Vaccines Abstract SARS_CoV_2 D614G 66 71 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. RNA sequencing using NGS in case 1 revealed mutations most consistent with Western European Clade A2a with ORF1a L3606F mutation. 2020 American journal of clinical pathology Abstract SARS_CoV_2 L3606F 113 119 ORF1a 107 112 32461321 Porcine Epidemic Diarrhea Virus Deficient in RNA Cap Guanine-N-7 Methylation Is Attenuated and Induces Higher Type I and III Interferon Responses. However, recombinant rPEDV-D350A with a single mutation (D350A) in nsp14, which retained 29.0% of G-N-7 MTase activity, was viable. 2020 Journal of virology Abstract SARS_CoV_2 D350A;D350A 57;27 62;32 32461321 Porcine Epidemic Diarrhea Virus Deficient in RNA Cap Guanine-N-7 Methylation Is Attenuated and Induces Higher Type I and III Interferon Responses. Notably, rPEDV-D350A induced significantly higher expression of both type I and III interferons in IPEC-DQ cells than the parental rPEDV. 2020 Journal of virology Abstract SARS_CoV_2 D350A 15 20 32461321 Porcine Epidemic Diarrhea Virus Deficient in RNA Cap Guanine-N-7 Methylation Is Attenuated and Induces Higher Type I and III Interferon Responses. Recombinant rPEDV-D350A formed a significantly smaller plaque and had significant defects in viral protein synthesis and viral replication in Vero CCL-81 cells and intestinal porcine epithelial cells (IPEC-DQ). 2020 Journal of virology Abstract SARS_CoV_2 D350A 18 23 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. INTERPRETATION & CONCLUSIONS: SARS-CoV-2 belonging to the A2a type possesses a non-synomymous variant (D614G) that possibly eases the entry of the virus into the lung cells of the host. 2020 The Indian journal of medical research Abstract SARS_CoV_2 D614G 103 108 32478289 The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey. All three viral genomes carried the D614G variant (G clade according to GISAID classification) with implications for the origin of a spread first through China to Europe then to Istanbul. 2020 Northern clinics of Istanbul Abstract SARS_CoV_2 D614G 36 41 32492203 Structural variations and expression profiles of the SARS-CoV-2 host invasion genes in lung cancer. p.H34N on the RBD binding residues for SARS-CoV-2 was determined in our LUAD patient group. 2020 Journal of medical virology Abstract SARS_CoV_2 H34N 0 6 RBD 14 17 32511374 An insertion unique to SARS-CoV-2 exhibits superantigenic character strengthened by recent mutations. Further examination revealed that this interaction between the virus and human T cells is strengthened in the context of a recently reported rare mutation (D839Y/N/E) from a European strain of SARS-CoV-2. 2020 bioRxiv Abstract SARS_CoV_2 D839E;D839N;D839Y 156;156;156 165;165;165 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. G1124V in Spike (S) protein, R203K, and G204R in the nucleocapsid (N) protein. 2020 Journal of biosciences Abstract SARS_CoV_2 G204R;R203K;G1124V 40;29;0 45;34;6 N;S;N;S 53;10;67;17 65;15;68;18 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. More importantly, the possible implications of mutation D614G (in SD domain) and G1124V (in S2 subunit) on the structural stability of S protein have also been discussed. 2020 Journal of biosciences Abstract SARS_CoV_2 D614G;G1124V 56;81 61;87 S 135 136 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. Specific mutations, characteristic of the A2a clade, were also detected, which included the P323L in RNA-dependent RNA polymerase and D614G in the Spike glycoprotein. 2020 Journal of biosciences Abstract SARS_CoV_2 D614G;P323L 134;92 139;97 RdRp;S 101;147 129;165 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Genomes of 5 strains sequenced from clustered infections were classified into a new clade with ORF1ab-V378I mutation, in addition to 3 dominant clades ORF8-L84S, ORF3a-G251V and S-D614G. 2020 Emerging microbes & infections Abstract SARS_CoV_2 D614G;G251V;L84S;V378I 180;168;156;102 185;173;160;107 ORF1ab;ORF3a;ORF8;S 95;162;151;178 101;167;155;179 32577641 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Several Spike-protein mutations, including D614G, which has been associated with increased transmission, disrupt otherwise-perfectly-conserved amino acids, and could be novel adaptations to human hosts. 2020 bioRxiv Abstract SARS_CoV_2 D614G 43 48 S 8 13 32577644 Beyond Shielding: The Roles of Glycans in SARS-CoV-2 Spike Protein. This finding is corroborated by biolayer interferometry experiments, which show that deletion of these glycans through N165A and N234A mutations significantly reduces binding to ACE2 as a result of the RBD conformational shift towards the "down" state. 2020 bioRxiv Abstract SARS_CoV_2 N165A;N234A 119;129 124;134 RBD 202 205 32587973 The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. SARS coronavirus 2 (SARS-CoV-2) isolates encoding a D614G mutation in the viral spike (S) protein predominate over time in locales where it is found, implying that this change enhances viral transmission. 2020 bioRxiv Abstract SARS_CoV_2 D614G 52 57 S;S 80;87 85;88 32595352 An updated analysis of variations in SARS-CoV-2 genome. Despite some variations being in low frequency rate in some continents, C14408T and A23403G variations on Nsp12 and S protein, respectively, observed to be the most prominent variations all over the world, in general, and both cause missense mutations. 2020 Turkish journal of biology Abstract SARS_CoV_2 A23403G;C14408T 84;72 91;79 Nsp12;S 106;116 111;117 32595352 An updated analysis of variations in SARS-CoV-2 genome. It is also notable that most of isolates carry C14408T and A23403 variations simultaneously and also nearly all isolates carrying the G25563T variation on ORF3a, also carry C14408T and A23403 variations, although their location distributions are not similar. 2020 Turkish journal of biology Abstract SARS_CoV_2 C14408T;C14408T;G25563T 47;173;134 54;180;141 ORF3a 155 160 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. When the mutations were evaluated, C3037T, C14408T and A23403G were found to be the most common nucleotide substitutions among the viral isolates in Turkey, which are mostly seen as linked mutations and are part of a haplotype observed high in Europe. 2020 Turkish journal of biology Abstract SARS_CoV_2 A23403G;C14408T;C3037T 55;43;35 62;50;41 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Assessment of the S protein trimer by cryo-electron microscopy showed that D614G disrupts a critical interprotomer contact and that this dramatically shifts the S protein trimer conformation toward an ACE2-binding and fusion-competent state. 2020 bioRxiv Abstract SARS_CoV_2 D614G 75 80 S;S 18;161 19;162 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and cells rendered permissive by ectopic expression of various mammalian ACE2 orthologs. 2020 bioRxiv Abstract SARS_CoV_2 D614G 18 23 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Nonetheless, D614G affinity for ACE2 was reduced due to a faster dissociation rate. 2020 bioRxiv Abstract SARS_CoV_2 D614G 13 18 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide in a matter of months. 2020 bioRxiv Abstract SARS_CoV_2 D614G 41 46 S;S 15;22 20;23 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. These results indicate that D614G adopts conformations that make virion membrane fusion with the target cell membrane more probable but that D614G retains susceptibility to therapies that disrupt interaction of the SARS-CoV-2 S protein with the ACE2 receptor. 2020 bioRxiv Abstract SARS_CoV_2 D614G;D614G 28;141 33;146 Membrane;Membrane;S 72;109;226 80;117;227 32641486 Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico. We also found evidence for early local transmission of strains with a H49Y mutation in the Spike protein, which could be further used as a molecular marker to follow viral spread within the country and the region. 2020 Journal of virology Abstract SARS_CoV_2 H49Y 70 74 S 91 96 32641486 Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico. Within this local transmission cluster, we also identified an H49Y amino acid change in the Spike protein. 2020 Journal of virology Abstract SARS_CoV_2 H49Y 62 66 S 92 97 32676618 D614G Spike Variant Does Not Alter IgG, IgM, or IgA Spike Seroassay Performance. Emergence of a new variant of spike protein (D614G) with increased infectivity and transmissibility has prompted many to analyze the potential role of this variant in the SARS-CoV-2 pandemic. 2020 medRxiv Abstract SARS_CoV_2 D614G 45 50 S 30 35 32693089 Mortality in COVID-19 disease patients: Correlating the association of major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants. Assuming the ORF8 (L84S) mutation is biologically significant, selective pressure from MHC class II alleles may select for viral varients and subsequently shape the quality and quantity of cellular immune responses aginast SARS-CoV-2. 2020 International journal of infectious diseases Abstract SARS_CoV_2 L84S 19 23 ORF8 13 17 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. 2020 Cell Abstract SARS_CoV_2 D614G 66 71 S 34 39 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. Although clinical and in vitro data suggest that D614G changes the virus phenotype, the impact of the mutation on transmission, disease, and vaccine and therapeutic development are largely unknown. 2020 Cell Abstract SARS_CoV_2 D614G 49 54 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. found that a SARS-CoV-2 variant in the spike protein D614G rapidly became dominant around the world. 2020 Cell Abstract SARS_CoV_2 D614G 53 58 S 39 44 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. In BCG-vaccinated countries, the frequency of the S 614G variant had a trend of association with the higher fatality rate. 2020 Journal of human genetics Abstract SARS_CoV_2 S614G 50 56 S 50 51 32699850 Bivalent binding of a fully human IgG to the SARS-CoV-2 spike proteins reveals mechanisms of potent neutralization. Furthermore, 5A6 is insensitive to several spike mutations identified in clinical isolates, including the D614G mutant that has become dominant worldwide. 2020 bioRxiv Abstract SARS_CoV_2 D614G 106 111 S 43 48 32701194 Emergence of European and North American mutant variants of SARS-CoV-2 in South-East Asia. Group 2 strains characterized by two co-evolving NS mutants which alter in RdRp (P323L) and spike (S) protein (D614G) were found to be common in Europe and North America. 2021 Transboundary and emerging diseases Abstract SARS_CoV_2 D614G;P323L 111;81 116;86 S;RdRP;S 92;75;99 97;79;100 32703419 Proteasome activator PA28gamma-dependent degradation of coronavirus disease (COVID-19) nucleocapsid protein. Overexpression of PA28gamma enhanced proteolysis of nCoV N compared to that in PA28gamma-N151Y cells containing a dominant-negative PA28gamma mutation, which reduced this process. 2020 Biochemical and biophysical research communications Abstract SARS_CoV_2 N151Y 89 94 N 57 58 32705298 [The virology of SARS-CoV-2]. The D614G mutation in the S spikes seems to cause a higher infectiosity. 2020 Der Internist Abstract SARS_CoV_2 D614G 4 9 S;S 28;26 34;27 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. D614G, along with several variants containing both D614G and another amino acid change, were significantly more infectious. 2020 Cell Abstract SARS_CoV_2 D614G;D614G 51;0 56;5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Interestingly, N234Q was markedly resistant to neutralizing antibodies, whereas N165Q became more sensitive. 2020 Cell Abstract SARS_CoV_2 N165Q;N234Q 80;15 85;20 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Most variants with amino acid change at receptor binding domain were less infectious, but variants including A475V, L452R, V483A, and F490L became resistant to some neutralizing antibodies. 2020 Cell Abstract SARS_CoV_2 A475V;F490L;L452R;V483A 109;134;116;123 114;139;121;128 RBD 40 63 32732280 Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. In particular, the N501Y mutation is located at the receptor binding domain (RBD) of the spike protein. 2020 Science (New York, N.Y.) Abstract SARS_CoV_2 N501Y 19 24 RBD;S;RBD 52;89;77 75;94;80 32735992 Design of an engineered ACE2 as a novel therapeutics against COVID-19. The Asp427Arg mutation was done to decrease the flexibility of the region with high B factor. 2020 Journal of theoretical biology Abstract SARS_CoV_2 D427R 4 13 32735992 Design of an engineered ACE2 as a novel therapeutics against COVID-19. The obtained resulted revealed that the Arg273Gln and Thr445Gly mutation have drastically reduced the binding affinity of the angiotensin-II into the active site of ACE2. 2020 Journal of theoretical biology Abstract SARS_CoV_2 T445G 54 63 32735992 Design of an engineered ACE2 as a novel therapeutics against COVID-19. The Pro451Met mutation along with the Gly448Trp mutation was predicted to increase the thermodynamic stability and thermostability of the ACE2. 2020 Journal of theoretical biology Abstract SARS_CoV_2 G448W;P451M 38;4 47;13 32735992 Design of an engineered ACE2 as a novel therapeutics against COVID-19. The Thr27Arg mutation was determined to be the most potent mutation to increase the binding affinity. 2020 Journal of theoretical biology Abstract SARS_CoV_2 T27R 4 12 32742035 Variant analysis of SARS-CoV-2 genomes. CONCLUSION: We found that several variants of the SARS-CoV-2 genome exist and that the D614G clade has become the most common variant since December 2019. 2020 Bulletin of the World Health Organization Abstract SARS_CoV_2 D614G 87 92 32742035 Variant analysis of SARS-CoV-2 genomes. The most common variants were the synonymous 3037C > T (6334 samples), P4715L in the open reading frame 1ab (6319 samples) and D614G in the spike protein (6294 samples). 2020 Bulletin of the World Health Organization Abstract SARS_CoV_2 C3037T;D614G;P4715L 45;127;71 54;132;77 S 140 145 32742035 Variant analysis of SARS-CoV-2 genomes. We identified six major clades, (that is, basal, D614G, L84S, L3606F, D448del and G392D) and 14 subclades. 2020 Bulletin of the World Health Organization Abstract SARS_CoV_2 D448del;D614G;G392D;L3606F;L84S 70;49;82;62;56 77;54;87;68;60 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. It is possible that 14408C>T mutation may have contributed to the dominance of its co-mutations in Europe and elsewhere. 2020 PeerJ Abstract SARS_CoV_2 C14408T 20 28 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. Our results indicate that 14408C>T mutation increases the mutation rate, while the third-most common RdRp mutation, 15324C>T, has the opposite effect. 2020 PeerJ Abstract SARS_CoV_2 C14408T;C15324T 26;116 34;124 RdRP 101 105 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. Therefore, we sought to understand the effects of mutations in RNA-dependent RNA polymerase (RdRp), particularly the common 14408C>T mutation, on mutation rate and viral spread. 2020 PeerJ Abstract SARS_CoV_2 C14408T 124 132 RdRp;RdRP 63;93 91;97 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. Here, we synthesized and expressed the WT and D614G variant SARS-Cov2 Spike protein, and report that using a SARS-CoV2 Spike protein pseudotyped lentiviral vector we observe that the D614G variant Spike has >1/2 log10 increased infectivity in human cells expressing the human ACE2 protein as the viral receptor. 2020 bioRxiv Abstract SARS_CoV_2 D614G;D614G 46;183 51;188 S;S;S 70;119;197 75;124;202 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. Most prominent among these is the D614G amino acid substitution in the SARS-CoV2 Spike protein, which mediates viral entry. 2020 bioRxiv Abstract SARS_CoV_2 D614G 34 39 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. The D614G substitution, however, is in linkage disequilibrium with the ORF1b P314L mutation where both mutations almost invariably co-occur, making functional inferences problematic. 2020 bioRxiv Abstract SARS_CoV_2 D614G;P314L 4;77 9;82 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. The increased binding/fusion activity of the D614G Spike protein was corroborated in a cell fusion assay using Spike and ACE2 proteins expressed in different cells. 2020 bioRxiv Abstract SARS_CoV_2 D614G 45 50 S;S 51;111 56;116 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. These results are consistent with the possibility that the Spike D614G mutant increases the infectivity of SARS-CoV2. 2020 bioRxiv Abstract SARS_CoV_2 D614G 65 70 S 59 64 32743581 The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State. Here we show that changes in the inter-protomer energetics due to the D614G substitution favor a higher population of infection-capable (open) states. 2020 bioRxiv Abstract SARS_CoV_2 D614G 70 75 32743581 The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State. The COVID-19 pandemic underwent a rapid transition with the emergence of a SARS-CoV-2 variant that carried the amino acid substitution D614G in the Spike protein that became globally prevalent. 2020 bioRxiv Abstract SARS_CoV_2 D614G 135 140 COVID-19 4 12 32756549 SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness. Here we show that mRNA-1273 induces potent neutralizing antibody responses to both wild-type (D614) and D614G mutant2 SARS-CoV-2 as well as CD8+ T cell responses, and protects against SARS-CoV-2 infection in the lungs and noses of mice without evidence of immunopathology. 2020 Nature Abstract SARS_CoV_2 D614G 104 109 COVID-19 184 204 32758336 Avoiding COVID-19 complications with diabetic patients could be achieved by multi-dose Bacillus Calmette-Guerin vaccine: a case study of beta cells regeneration. As the diabetic MODY-5 patient (mutation of HNF1B, Val2Leu) was on low dose Riometwhile eliminating insulin gradually, a simple analytical method for metformin assay was recommended to ensure its concentration before use as it is not approved yet by the Egyptian QC labs. 2020 Die Pharmazie Abstract SARS_CoV_2 V2L 51 58 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. Y449A, N487A, Y489A, N501A and Y505A in the receptor binding motif (RBM) of the ACE2-RBD SARS-CoV-2 complex (PDB: 6M0J). 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 N487A;N501A;Y489A;Y505A;Y449A 7;21;14;31;0 12;26;19;36;5 RBD 85 88 32763945 Genome Sequences of Six SARS-CoV-2 Strains Isolated in Morocco, Obtained Using Oxford Nanopore MinION Technology. Mutation analysis revealed the presence of the spike D614G mutation in all six genomes, which is widely present in several genomes around the world. 2020 Microbiology resource announcements Abstract SARS_CoV_2 D614G 53 58 S 47 52 32764372 Comprehensive Analyses of SARS-CoV-2 Transmission in a Public Health Virology Laboratory. Complete SARS-CoV-2 genomes were sequenced and mutation analyses showed inclusion of all samples to clades 20B and 20C, possessing the spike mutation D614G. 2020 Viruses Abstract SARS_CoV_2 D614G 150 155 S 135 140 32779445 Profiling of Initial Available SARS-CoV-2 Sequences from Iranian Related COVID-19 Patients. R207C, V378I, M2796I, L3606F, and A6407V in ORF1ab were common mutations in these sequences. 2020 Cell journal Abstract SARS_CoV_2 A6407V;L3606F;M2796I;V378I;R207C 34;22;14;7;0 40;28;20;12;5 ORF1ab 44 50 32779780 Atomistic simulation reveals structural mechanisms underlying D614G spike glycoprotein-enhanced fitness in SARS-COV-2. D614G spike glycoprotein (sgp) mutation in rapidly spreading severe acute respiratory syndrome coronavirus-2 (SARS-COV-2) is associated with enhanced fitness and higher transmissibility in new cases of COVID-19 but the underlying mechanism is unknown. 2020 Journal of computational chemistry Abstract SARS_CoV_2 D614G 0 5 S 6 24 COVID-19;COVID-19 68;202 108;210 32779780 Atomistic simulation reveals structural mechanisms underlying D614G spike glycoprotein-enhanced fitness in SARS-COV-2. These data provide evidence that D614G sgp mutant is more available for receptor binding, cellular invasion and reduced antibody interaction; thus, providing framework for enhanced fitness and higher transmissibility in D614G SARS-COV-2 mutant. 2020 Journal of computational chemistry Abstract SARS_CoV_2 D614G;D614G 33;220 38;225 32779784 Mutational spectra of SARS-CoV-2 orf1ab polyprotein and signature mutations in the United States of America. Four significant mutations T265I (nsp 2), P4715L (nsp 12), and P5828L and Y5865C (both at nsp 13) were identified in important nonstructural proteins, which function either as replicase or helicase. 2021 Journal of medical virology Abstract SARS_CoV_2 P4715L;P5828L;T265I;Y5865C 42;63;27;74 48;69;32;80 Helicase 189 197 32780783 Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2. Along with 241C>T change the important 5'-UTR change identified was 187A>G, while 29734G>C, 29742G>A/T and 29774C>T were the most familiar variants of 3'UTR among most of the continents. 2020 PloS one Abstract SARS_CoV_2 A187G;C241T;G29734C;C29774T 68;11;82;107 74;17;90;115 3'UTR 151 156 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. In particular, clade G, prevalent in Europe, carries a D614G mutation in the Spike protein, which is responsible for the initial interaction of the virus with the host human cell. 2020 Frontiers in microbiology Abstract SARS_CoV_2 D614G 55 60 S 77 82 32818213 Characterizing SARS-CoV-2 mutations in the United States. We identify that one of the top mutations, 27964C>T-(S24L) on ORF8, has an unusually strong gender dependence. 2020 Research square Abstract SARS_CoV_2 C27964T;S24L 43;53 51;57 ORF8 62 66 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. We also applied structural bioinformatics to assess the potential impact of D614G on the virulence and epidemiology of SARS-CoV-2. 2020 Scientific reports Abstract SARS_CoV_2 D614G 76 81 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. We identified a missense mutation, D614G, in the spike protein of SARS-CoV-2, which has emerged as a predominant clade in Europe (954 of 1,449 (66%) sequences) and is spreading worldwide (1,237 of 2,795 (44%) sequences). 2020 Scientific reports Abstract SARS_CoV_2 D614G 35 40 S 49 54 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. One viral strain presented a previously unreported mutation in the Nsp2 gene, namely K489E. 2020 Life (Basel, Switzerland) Abstract SARS_CoV_2 K489E 85 90 Nsp2 67 71 32837710 Structural insights into the mechanism of RNA recognition by the N-terminal RNA-binding domain of the SARS-CoV-2 nucleocapsid phosphoprotein. Our analyses suggest that residues T57A, H59A, S105A, R107A, F171A, and Y172A significantly affected the dynamics and binding of RNA. 2020 Computational and structural biotechnology journal Abstract SARS_CoV_2 F171A;H59A;R107A;S105A;T57A;Y172A 61;41;54;47;35;72 66;45;59;52;39;77 32839745 miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East. The exciting findings here that the nucleotide substitution 1841A > G at the viral genomic RNA level, which is an amino acid substation D614G at the spike protein level showed a change in the predicted miRNA sequence from hsa-miR-4793-5p to hsa-miR-3620-3p with an increase in the target score from 91 to 92. 2020 Non-coding RNA research Abstract SARS_CoV_2 A1841G;D614G 60;136 69;141 S 149 154 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. In our study, several mutations like R408I, L455Y, F486L, Q493N, Q498Y, N501T of RBD (319-591), and A930V, D936Y of HR1 (912-984) have been studied to examine its role on the spike glycoprotein native structure. 2022 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 A930V;D936Y;F486L;L455Y;N501T;Q493N;Q498Y;R408I 100;107;51;44;72;58;65;37 105;112;56;49;77;63;70;42 S;RBD 175;81 193;84 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). However, we report the following new findings from the variants: (1) Residues GLY15, VAL157, and PRO184 have mutated more than once in SARS CoV-2; (2) the D48E variant has lead to a novel "TSEEMLN"" loop at the binding pocket; (3) inactive apo Mpro does not show signs of dissociation in 100 ns MD; (4) a non-canonical pose for PHE140 widens the substrate binding surface; (5) dual allosteric pockets coinciding with various stabilizing and functional components of the substrate binding pocket were found to display correlated compaction dynamics; (6) high betweenness centrality values for residues 17 and 128 in all Mpro samples suggest their high importance in dimer stability-one such consequence has been observed for the M17I mutation whereby one of the N-fingers was highly unstable. 2020 Journal of chemical information and modeling Abstract SARS_CoV_2 D48E;M17I 155;728 159;732 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. We find limited diversity across SARS-CoV-2 genomes: Only 11 sites show polymorphisms in >5% of sequences; yet two mutations, including the D614G mutation in Spike, have already become consensus. 2020 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 D614G 140 145 S 158 163 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. While the rapid spread of the D614G mutation warrants further study, our results indicate that drift and bottleneck events can explain the minimal diversity found among SARS-CoV-2 sequences. 2020 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 D614G 30 35 32869023 SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution. Four genetically linked mutations known as the globally dominant SARS-CoV-2 haplotype (C241T, C3037T, C14408T and A23403G) were found in the majority of consensus sequences. 2020 bioRxiv Abstract SARS_CoV_2 A23403G;C14408T;C3037T;C241T 114;102;94;87 121;109;100;92 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. This allowed the identification of specific nucleotide variants including those coding for D614G and clades defining mutations. 2020 medRxiv Abstract SARS_CoV_2 D614G 91 96 32870641 Prevalence of Chemosensory Dysfunction in COVID-19 Patients: A Systematic Review and Meta-analysis Reveals Significant Ethnic Differences. A virus mutation (D614G) may cause differing infectivity, while at the host level genetic, ethnicity-specific variants of the virus-binding entry proteins may facilitate virus entry in the olfactory epithelium and taste buds. 2020 ACS chemical neuroscience Abstract SARS_CoV_2 D614G 18 23 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. Among them, 14408 C>T and 23403 A>G mutations in RdRp and S, respectively, became dominant in Europe and the US, which led to debates regarding their effects on the mutability and transmissibility of the virus. 2020 PeerJ Abstract SARS_CoV_2 C14408T;A23403G 12;26 21;35 RdRP;S 49;58 53;59 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. Second, this pattern was much delayed or even non-existent for the "mutant" (MT) strain that harbored both 14408 C>T and 23403 A>G mutations. 2020 PeerJ Abstract SARS_CoV_2 C14408T;A23403G 107;121 116;130 32880929 Molecular dynamics study with mutation shows that N-terminal domain structural re-orientation in Niemann-Pick type C1 is required for proper alignment of cholesterol transport. Also, the simulation indicates the possible re-orientation of the N-terminal domain with both the wild and the R518W-mutated NPC1 after receiving the cholesterol from the NPC2 that align to form an internal tunnel, which is a possible pose for further action in cholesterol trafficking. 2021 Journal of neurochemistry Abstract SARS_CoV_2 R518W 111 116 N 66 67 32880929 Molecular dynamics study with mutation shows that N-terminal domain structural re-orientation in Niemann-Pick type C1 is required for proper alignment of cholesterol transport. In this study, we report the extensive molecular dynamics simulations in order to gain insight into the structure and the dynamics of NPC1 lumenal domain for the cholesterol transport and the disease behind the mutation (R518W). 2021 Journal of neurochemistry Abstract SARS_CoV_2 R518W 221 226 32880929 Molecular dynamics study with mutation shows that N-terminal domain structural re-orientation in Niemann-Pick type C1 is required for proper alignment of cholesterol transport. The mutation R518W or R518Q on the NPC1 is one of the type of disease-related mutation that causes cholesterol transports to be cut in half, which results in the accumulation of cholesterol and lipids in the late endosomal/lysosomal compartment of the cell. 2021 Journal of neurochemistry Abstract SARS_CoV_2 R518Q;R518W 22;13 27;18 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. Indian strain showed mutation in spike glycoprotein at R408I and in replicase polyprotein at I671T, P2144S and A2798V. 2020 PloS one Abstract SARS_CoV_2 A2798V;I671T;P2144S;R408I 111;93;100;55 117;98;106;60 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. It was found that the R60C mutation in Mpro affects the protein dynamics, thereby, affecting the binding of inhibitor within its active site. 2020 PloS one Abstract SARS_CoV_2 R60C 22 26 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. While the spike protein of Spain & South Korea carried F797C and S221W mutation, respectively. 2020 PloS one Abstract SARS_CoV_2 F797C;S221W 55;65 60;70 S 10 15 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. Moreover, A930V and D936Y mutations were observed in the heptad repeat domain and one mutation D1168H was noted in heptad repeat domain 2. 2020 Journal of laboratory physicians Abstract SARS_CoV_2 A930V;D1168H;D936Y 10;95;20 15;101;25 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. Other mutations observed within RBD exhibiting low antigenicity were T323I, A344S, R408I, G476S, V483A, H519Q, A520S, A522S and K529E. 2020 Journal of laboratory physicians Abstract SARS_CoV_2 A344S;A520S;A522S;G476S;H519Q;K529E;R408I;T323I;V483A 76;111;118;90;104;128;83;69;97 81;116;123;95;109;133;88;74;102 RBD 32 35 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. The RBD T323I, A344S, V367F, A419S, A522S and K529E are novel mutations reported first time in this study. 2020 Journal of laboratory physicians Abstract SARS_CoV_2 A344S;A419S;A522S;K529E;T323I;V367F 15;29;36;46;8;22 20;34;41;51;13;27 RBD 4 7 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. The significant variations in the predicted epitopes showing high antigenicity were A348V, V367F and A419S in receptor binding domain (RBD). 2020 Journal of laboratory physicians Abstract SARS_CoV_2 A348V;A419S;V367F 84;101;91 89;106;96 RBD;RBD 110;135 133;138 32895623 Crystal structure of SARS-CoV-2 papain-like protease. We determined the unliganded structure of SARS-CoV-2 PLpro mutant C111S, which shares many structural features of SARS-CoV PLpro. 2021 Acta pharmaceutica Sinica. B Abstract SARS_CoV_2 C111S 66 71 32895643 Genomic characterization of SARS-CoV-2 identified in a reemerging COVID-19 outbreak in Beijing's Xinfadi market in 2020. It is noteworthy that there is an amino acid D614G mutation caused by nt23403 substitution in all six genomes, which may enhance the virus's infectivity in humans and help it become the leading strain of the virus to spread around the world today. 2020 Biosafety and health Abstract SARS_CoV_2 D614G 45 50 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. NSP13-Y541C was crucial substitution which might affect the unwinding activity of the viral helicase. 2020 Sustainable cities and society Abstract SARS_CoV_2 Y541C 6 11 Helicase;Nsp13 92;0 100;5 32905045 Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. Furthermore, the D614G spike mutant dominates the pandemic and it is unclear how serological tests designed to detect anti-spike antibodies perform against this variant. 2020 Cell reports. Medicine Abstract SARS_CoV_2 D614G 17 22 S;S 23;123 28;128 32905045 Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. The combined point of care antibody test and rapid NAAT is not affected by D614G and results in very high sensitivity for COVID-19 diagnosis with very high specificity. 2020 Cell reports. Medicine Abstract SARS_CoV_2 D614G 75 80 COVID-19 122 130 32905045 Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. We assess the diagnostic accuracy of combined rapid antibody point of care (POC) and nucleic acid assays for suspected COVID-19 disease due to either wild-type or the D614G spike mutant SARS-CoV-2. 2020 Cell reports. Medicine Abstract SARS_CoV_2 D614G 167 172 S 173 178 COVID-19 119 135 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. A spike protein mutation D614G became dominant in SARS-CoV-2 during the COVID-19 pandemic. 2020 bioRxiv Abstract SARS_CoV_2 D614G 25 30 S 2 7 COVID-19 72 80 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. A spike protein mutation D614G emerged and became dominant soon after the pandemic started. 2020 bioRxiv Abstract SARS_CoV_2 D614G 25 30 S 2 7 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. By engineering the D614G mutation into an authentic wild-type SARS-CoV-2 strain, we demonstrate the importance of this mutation to (i) enhanced viral replication on human lung epithelial cells and primary human airway tissues, (ii) improved viral fitness in the upper airway of infected hamsters, and (iii) increased susceptibility to neutralization. 2020 bioRxiv Abstract SARS_CoV_2 D614G 19 24 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Here we engineer the D614G mutation in the SARS-CoV-2 USA-WA1/2020 strain and characterize its effect on viral replication, pathogenesis, and antibody neutralization. 2020 bioRxiv Abstract SARS_CoV_2 D614G 21 26 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. The D614G mutation significantly enhances SARS-CoV-2 replication on human lung epithelial cells and primary human airway tissues, through an improved infectivity of virions with the spike receptor-binding domain in an "up" conformation for binding to ACE2 receptor. 2020 bioRxiv Abstract SARS_CoV_2 D614G 4 9 S 182 187 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. The hamster results confirm clinical evidence that the D614G mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increases transmission. 2020 bioRxiv Abstract SARS_CoV_2 D614G 55 60 COVID-19 125 133 32917283 Analysis of ACE2 genetic variants in 131 Italian SARS-CoV-2-positive patients. RESULTS: We identified three different germline variants: one intronic c.439+4G>A and two missense c.1888G>C p.(Asp630His) and c.2158A>G p.(Asn720Asp) in a total of 131 patients with a similar frequency in male and female. 2020 Human genomics Abstract SARS_CoV_2 G1888C;A2158G;N720D;D630H 99;127;140;112 108;136;149;121 32917283 Analysis of ACE2 genetic variants in 131 Italian SARS-CoV-2-positive patients. Thus far, only the c.1888G>C p.(Asp630His) variant shows a statistically different frequency compared to the ethnically matched populations. 2020 Human genomics Abstract SARS_CoV_2 G1888C;D630H 19;32 28;41 32933378 Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach. Sequence analysis revealed that 70.42% of Nsp12 sequences showed conserved P323L mutation, located in the Nsp8 binding cleft. 2022 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 P323L 75 80 Nsp12;Nsp8 42;106 47;110 32934770 Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity. Mutation D614G in the spike (S) protein has become dominant, and recent evidence suggests it yields a more stable phenotype with higher transmission efficacy. 2020 ACS medicinal chemistry letters Abstract SARS_CoV_2 D614G 9 14 S;S 22;29 27;30 32934770 Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity. The D614G substitution creates a sticky packing defect in subunit S1, promoting its association with subunit S2 as a means to stabilize the structure of S1 within the S1/S2 complex. 2020 ACS medicinal chemistry letters Abstract SARS_CoV_2 D614G 4 9 32935099 SARS-CoV-2 infection severity is linked to superior humoral immunity against the spike. Additionally, we revealed that antibodies against the spike are still capable of binding the D614G spike mutant and cross-react with the SARS-CoV-1 receptor binding domain. 2020 bioRxiv Abstract SARS_CoV_2 D614G 93 98 RBD;S;S 148;54;99 171;59;104 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. Moreover, earlier claims that the D614G mutation is associated to higher transmissibility is not consistent with the very high prevalence of COVID-19 in Spain when compared to other countries with lower disease incidence but much higher frequency of this mutation (56.4% in Spain vs. 2020 Zoological research Abstract SARS_CoV_2 D614G 34 39 COVID-19 141 149 32937868 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. Among those sites, the D936Y substitution in the viral Spike protein was under positive selection. 2020 Viruses Abstract SARS_CoV_2 D936Y 23 28 S 55 60 32937868 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. Mutational profiles 3 (B.1.1) and 6 (B.1), which contain the D936Y mutation, became the predominant profiles over time, spreading from Stockholm to other Swedish regions during April and the beginning of May. 2020 Viruses Abstract SARS_CoV_2 D936Y 61 66 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Only a single mutant was viable, likely because its E191D substitution is highly conservative. 2020 Journal of virology Abstract SARS_CoV_2 E191D 52 57 32941419 Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization. Through ISM compression, we find that certain distant nucleotide variants covary, including non-coding and ORF1ab sites covarying with the D614G spike protein mutation which has become increasingly prevalent as the pandemic has spread. 2020 PLoS computational biology Abstract SARS_CoV_2 D614G 139 144 ORF1ab;S 107;145 113;150 32943587 Impact of Circulating SARS-CoV-2 Mutant G614 on the COVID-19 Pandemic. A SARS-CoV-2 variant encoding a D614G mutation in the viral spike (S) protein has now become the most prevalent form of the virus worldwide, suggesting a fitness advantage for the mutant. 2020 Iranian journal of kidney diseases Abstract SARS_CoV_2 D614G 32 37 S;S 60;67 65;68 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. A similar replacement pattern was observed with R203K/G204R although more marked in Chile, Argentina and Brazil, suggesting similar introduction history and/or control strategies of SARS-CoV-2 in these countries. 2020 Infection, genetics and evolution Abstract SARS_CoV_2 R203K;G204R 48;54 53;59 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. The substitutions D614G in S and R203K/G204R in N were the most frequent in South America, observed in 83% and 34% of the sequences respectively. 2020 Infection, genetics and evolution Abstract SARS_CoV_2 D614G;R203K;G204R 18;33;39 23;38;44 N;S 48;27 49;28 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. The infamous D614G variant has spread worldwide with ever-rising dominance and across regions with different climatic conditions alongside L5F and D936Y mutants, which have been documented throughout all regions and climate zones, respectively. 2021 Transboundary and emerging diseases Abstract SARS_CoV_2 D614G;D936Y;L5F 13;147;139 18;152;142 32964802 Identification of destabilizing SNPs in SARS-CoV2-ACE2 protein and spike glycoprotein: implications for virus entry mechanisms. The mutations W461R, G405E and F588S in ACE2 receptor protein and population specific mutations P391S, C12S and G1223A in the spike glycoprotein were predicted as highly destabilizing to the structure of the bound complex. 2022 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 C12S;F588S;G1223A;G405E;P391S;W461R 103;31;112;21;96;14 107;36;118;26;101;19 S 126 144 32967693 A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual. Whole genome sequencing of the persistently replicating SARS-CoV-2 GZ69 has shown that this strain differs from the early AP66 variant in 9 nucleotide positions (C2939T; C3828T; G21784T; T21846C; T24631C; G28881A; G28882A; G28883C; G29810T) which lead to 6 non-synonymous substitutions spanning on ORF1ab (P892S; S1188L), S (K74N; I95T) and N (R203K, G204R) proteins. 2020 Journal of translational medicine Abstract SARS_CoV_2 C3828T;G204R;G21784T;G28881A;G28882A;G28883C;G29810T;I95T;S1188L;T21846C;T24631C;C2939T;K74N;P892S;R203K 170;351;178;205;214;223;232;331;313;187;196;162;325;306;344 176;356;185;212;221;230;239;335;319;194;203;168;329;311;349 ORF1ab;N;S 298;341;322 304;342;323 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. Here we demonstrate that the S861G mutation in RdRp eliminates chain termination, which confirms the existence of a steric clash between Ser-861 and the incorporated RDV-TP. 2020 The Journal of biological chemistry Abstract SARS_CoV_2 S861G 29 34 RdRP 47 51 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. The adjacent Val-557 is in direct contact with the template base, and the V557L mutation is implicated in low-level resistance to RDV. 2020 The Journal of biological chemistry Abstract SARS_CoV_2 V557L 74 79 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. We further show that the V557L mutation in RdRp lowers the nucleotide concentration required to bypass this template-dependent inhibition. 2020 The Journal of biological chemistry Abstract SARS_CoV_2 V557L 25 30 RdRP 43 47 32970329 Genomic and proteomic mutation landscapes of SARS-CoV-2. Nucleocapsid exhibited the highest mutation density among the structural proteins while the spike D614G was the most common, occurring mostly in genomes outside China and United States. 2021 Journal of medical virology Abstract SARS_CoV_2 D614G 98 103 N;S 0;92 12;97 32972934 Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh. We have identified a unique mutation (NSP2_V480I) in one of the sequenced genomes (isolate hCoV-19/Bangladesh/BCSIR-NILMRC-006/2020) compared to the sequences available in the Global Initiative on Sharing All Influenza Data (GISAID) database. 2020 Microbiology resource announcements Abstract SARS_CoV_2 V480I 43 48 Nsp2 38 42 32972948 Whole-Genome Sequence of SARS-CoV-2 Isolate Siena-1/2020. The isolate belongs to the B1.1 lineage, which is prevalent in Europe, and contains a mutation in the spike protein coding sequence leading to the D614G amino acid change. 2020 Microbiology resource announcements Abstract SARS_CoV_2 D614G 147 152 S 102 107 32975856 Evolution of SARS-CoV-2 genome from December 2019 to late March 2020: Emerged haplotypes and informative Tag nucleotide variations. A variation that causes an Asp614Gly near the receptor-binding domain of S were found at a high frequency, and it was considered that this may contribute to the rapid spread of viruses with this variation. 2021 Journal of medical virology Abstract SARS_CoV_2 D614G 27 36 S 73 74 32980406 Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13). Incidence of C17747T and A17858G mutations were observed to be much higher than others and they were on Nsp13, a vital enzyme of SARS-CoV-2. 2020 International journal of biological macromolecules Abstract SARS_CoV_2 A17858G;C17747T 25;13 32;20 Nsp13 104 109 32984400 Understanding Selenium and Glutathione as Antiviral Factors in COVID-19: Does the Viral M(pro) Protease Target Host Selenoproteins and Glutathione Synthesis? Thus, it is highly significant that cytosolic GPX1 has been shown to interact with an inactive C145A mutant of Mpro, the main cysteine protease of SARS-CoV-2, but not with catalytically active wild-type Mpro. 2020 Frontiers in nutrition Abstract SARS_CoV_2 C145A 95 100 32986807 Emerging RNA-Dependent RNA Polymerase Mutation in a Remdesivir-Treated B-cell Immunodeficient Patient With Protracted Coronavirus Disease 2019. We report the occurrence of a mutation in RdRP (D484Y) following treatment with remdesivir in a 76-year-old female with post-rituximab B-cell immunodeficiency and persistent SARS-CoV-2 viremia. 2021 Clinical infectious diseases Abstract SARS_CoV_2 D484Y 48 53 RdRP 42 46 32989130 Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation. This interaction between the virus and human T cells could be strengthened by a rare mutation (D839Y/N/E) from a European strain of SARS-CoV-2. 2020 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 D839E;D839N;D839Y 95;95;95 104;104;104 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Assessment of the S protein trimer by cryo-electron microscopy showed that D614G disrupts an interprotomer contact and that the conformation is shifted toward an ACE2 binding-competent state, which is modeled to be on pathway for virion membrane fusion with target cells. 2020 Cell Abstract SARS_CoV_2 D614G 75 80 Membrane;S 237;18 245;19 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. D614G did not alter S protein synthesis, processing, or incorporation into SARS-CoV-2 particles, but D614G affinity for ACE2 was reduced due to a faster dissociation rate. 2020 Cell Abstract SARS_CoV_2 D614G;D614G 101;0 106;5 S 20 21 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and on cells rendered permissive by ectopic expression of human ACE2 or of ACE2 orthologs from various mammals, including Chinese rufous horseshoe bat and Malayan pangolin. 2020 Cell Abstract SARS_CoV_2 D614G 18 23 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide, reaching near fixation in a matter of months. 2020 Cell Abstract SARS_CoV_2 D614G 41 46 S;S 15;22 20;23 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. CR3022 does not neutralize SARS-CoV-2, but the increased affinity to SARS-CoV-2 P384A mutant now enables neutralization with a similar potency to SARS-CoV. 2020 bioRxiv Abstract SARS_CoV_2 P384A 80 85 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. Using x-ray crystallography, mutagenesis, and binding experiments, we illustrate that of four amino acid differences in the CR3022 epitope between SARS-CoV-2 and SARS-CoV, a single mutation P384A fully determines the affinity difference. 2020 bioRxiv Abstract SARS_CoV_2 P384A 190 195 32995830 Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report. We sequenced viruses from two distinct episodes of symptomatic COVID-19 separated by 144 days in a single patient, to conclusively describe reinfection with a new strain harboring the spike variant D614G. 2020 medRxiv Abstract SARS_CoV_2 D614G 198 203 S 184 189 COVID-19 63 71 32995830 Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report. With antibody and B cell analytics, we show correlates of adaptive immunity, including a differential response to D614G. 2020 medRxiv Abstract SARS_CoV_2 D614G 114 119 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. Here, we discuss recent genetic and epidemiological data on the D614G spike protein variant and assess whether current evidence is consistent with the notion that this single nucleotide polymorphism augments chemosensory impairments in COVID-19 patients. 2020 ACS chemical neuroscience Abstract SARS_CoV_2 D614G 64 69 S 70 75 COVID-19 236 244 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. We analyzed 384 experimentally verified S missense variations and revealed that the dominant pandemic form, D614G, can stabilize the entire S protein. 2021 Briefings in bioinformatics Abstract SARS_CoV_2 D614G 108 113 S;S 40;140 41;141 33007039 Brief Report: Hydroxychloroquine does not induce hemolytic anemia or organ damage in a "humanized" G6PD A- mouse model. STUDY DESIGN AND METHODS: Recently, we created a novel "humanized" mouse model containing the G6PD deficiency A- variant (Val68Met) using CRISPR technology. 2020 PloS one Abstract SARS_CoV_2 V68M 122 130 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. A total of 228 sequences of variants had multiple variations, of note, most of them harboring the D614G mutation. 2020 Frontiers in immunology Abstract SARS_CoV_2 D614G 98 103 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. Among the predicted 69 linear B cell epitopes, 175 discontinuous B cell epitopes and 41 cytotoxic T lymphocyte epitopes in the viral S protein, we found that the protein structure and its potential function of some sites changed, such as the linear epitope length shortened and discontinuous epitope disappeared of G476S. 2020 Frontiers in immunology Abstract SARS_CoV_2 G476S 315 320 S 133 134 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. The most prominent sequence variation was observed on the spike protein, resulting in the substitution D614G, with a prevalence of 56.2%. 2020 Heliyon Abstract SARS_CoV_2 D614G 103 108 S 58 63 33024144 Molecular epidemiology of the first wave of severe acute respiratory syndrome coronavirus 2 infection in Thailand in 2020. The results indicated local transmission (type T, Spike protein (A829T)) and imported cases (types L, GH, GR and O) during the first wave in Thailand. 2020 Scientific reports Abstract SARS_CoV_2 A829T 65 70 S 50 55 33024961 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Several Spike-protein mutations, including D614G, which has been associated with increased transmission, disrupt otherwise-perfectly-conserved amino acids, and could be novel adaptations to human hosts. 2020 Research square Abstract SARS_CoV_2 D614G 43 48 S 8 13 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. However, the D614G variant exhibited significantly faster droplet transmission between hamsters than the WT virus, early after infection. 2020 bioRxiv Abstract SARS_CoV_2 D614G 13 18 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Infection of human ACE2 transgenic mice and Syrian hamsters with the WT or D614G viruses produced similar titers in respiratory tissue and pulmonary disease. 2020 bioRxiv Abstract SARS_CoV_2 D614G 75 80 Lung diseases 139 156 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Our study demonstrated the SARS-CoV2 D614G substitution enhances infectivity, replication fitness, and early transmission. 2020 bioRxiv Abstract SARS_CoV_2 D614G 37 42 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. The D614G substitution in the S protein is most prevalent SARS-CoV-2 strain circulating globally, but its effects in viral pathogenesis and transmission remain unclear. 2020 bioRxiv Abstract SARS_CoV_2 D614G 4 9 S 30 31 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. The D614G variant replicates more efficiency in primary human proximal airway epithelial cells and is more fit than wildtype (WT) virus in competition studies. 2020 bioRxiv Abstract SARS_CoV_2 D614G 4 9 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. We engineered SARS-CoV-2 variants harboring the D614G substitution with or without nanoluciferase. 2020 bioRxiv Abstract SARS_CoV_2 D614G 48 53 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. With similar morphology to the WT virion, the D614G virus is also more sensitive to SARS-CoV-2 neutralizing antibodies. 2020 bioRxiv Abstract SARS_CoV_2 D614G 46 51 33028676 Remdesivir targets a structurally analogous region of the Ebola virus and SARS-CoV-2 polymerases. We found that a single amino acid substitution, F548S, in the Ebola virus polymerase conferred low-level reduced susceptibility to remdesivir. 2020 Proceedings of the National Academy of Sciences of the United States of America Abstract SARS_CoV_2 F548S 48 53 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. It is evident that the D614G mutation in spike glycoprotein and P4715L in RdRp is the important determinant of SARS-CoV-2 evolution since its emergence. 2020 Microbes and infection Abstract SARS_CoV_2 D614G;P4715L 23;64 28;70 RdRp;S;RdRp 41;41;74 59;59;78 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. P4715L in RdRp, G251V in ORF3a and S1498F of Nsp3 is associated with the epitope loss that may influence pathogenesis caused by antibody escape variants. 2020 Microbes and infection Abstract SARS_CoV_2 G251V;S1498F;P4715L 16;35;0 21;41;6 ORF3a;Nsp3;RdRP 25;45;10 30;49;14 33052347 D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction. Despite a low mutation rate, isolates with the D614G substitution in the S protein appeared early during the pandemic, and are now the dominant form worldwide. 2020 bioRxiv Abstract SARS_CoV_2 D614G 47 52 S 73 74 33052347 D614G mutation alters SARS-CoV-2 spike conformational dynamics and protease cleavage susceptibility at the S1/S2 junction. Here, we analyze the D614G mutation in the context of a soluble S ectodomain construct. 2020 bioRxiv Abstract SARS_CoV_2 D614G 21 26 S 64 65 33067385 Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals. Similarly, we observed a significant decrease in the capacity of convalescent plasma to neutralize pseudoparticles bearing wild-type SARS-CoV-2 S or its D614G variant. 2020 mBio Abstract SARS_CoV_2 D614G 153 158 S 144 145 33072699 Geographical Distribution of Genetic Variants and Lineages of SARS-CoV-2 in Chile. Complete genome analysis of 141 viral samples from different regions of Chile revealed a predominance of variant D614G like in Europe and the USA and the major presence of lineage B.1. 2020 Frontiers in public health Abstract SARS_CoV_2 D614G 113 118 33073198 Therapeutically Targeted Destabilization of the Quaternary Structure of the Spike Protein in the Dominant G614 Strain of SARS-CoV-2. With a more stable phenotype, mutation D614G has become dominant. 2020 ACS pharmacology & translational science Abstract SARS_CoV_2 D614G 39 44 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. CONCLUSIONS: The D614G substitution in the G clade induced flexibility of the S protein, resulting in increased furin binding, which may enhance S protein cleavage and infiltration of host cells. 2021 International journal of infectious diseases Abstract SARS_CoV_2 D614G 17 22 S;S 78;145 79;146 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. METHODS: The effect of D614G substitution on the structure and thermodynamic stability of the S protein was analyzed with use of DynaMut and SCooP. 2021 International journal of infectious diseases Abstract SARS_CoV_2 D614G 23 28 S 94 95 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. RESULTS: The D614G substitution in the G clade of SARS-CoV-2 strains introduced structural mobility and decreased the thermal stability of the S protein (DeltaDeltaG = -0.086 kcal mol-1). 2021 International journal of infectious diseases Abstract SARS_CoV_2 D614G 13 18 S 143 144 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. The aim of this study was to characterize the D614G substitution in the severe acute respiratory syndome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S protein), which may affect viral infectivity. 2021 International journal of infectious diseases Abstract SARS_CoV_2 D614G 46 51 S;S 132;152 150;153 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. The results were corroborated by molecular dynamics simulations demonstrating higher binding energy of furin and the S protein D614G mutant (-61.9 kcal mol-1 compared with -56.78 kcal mol-1 for wild-type S protein). 2021 International journal of infectious diseases Abstract SARS_CoV_2 D614G 127 132 S;S 117;204 118;205 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Therefore, the SARS-CoV-2 D614G substitution may result in a more virulent strain. 2021 International journal of infectious diseases Abstract SARS_CoV_2 D614G 26 31 33080267 Designed variants of ACE2-Fc that decouple anti-SARS-CoV-2 activities from unwanted cardiovascular effects. Three mutants, R273A, H378A and E402A, completely lost their enzymatic activity for either surrogate or physiological substrates. 2020 International journal of biological macromolecules Abstract SARS_CoV_2 E402A;H378A;R273A 32;22;15 37;27;20 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. The 'D614G' mutation (Aspartate-to-Glycine change at position 614) of the SARS-CoV-2 spike protein has been speculated to adversely affect the efficacy of most vaccines and countermeasures that target this glycoprotein, necessitating frequent vaccine matching. 2020 NPJ vaccines Abstract SARS_CoV_2 D614G;D614G 22;5 65;10 S 85 90 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. Through this approach, supported by biomolecular modelling of this mutation and the commonly-associated P314L mutation in the RNA-dependent RNA polymerase, we have shown that there is no experimental evidence to support this speculation. 2020 NPJ vaccines Abstract SARS_CoV_2 P314L 104 109 RdRp 126 154 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. We additionally demonstrate that the putative elastase cleavage site introduced by the D614G mutation is unlikely to be accessible to proteases. 2020 NPJ vaccines Abstract SARS_CoV_2 D614G 87 92 33083498 Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies. By integrating genetics, biophysics, deep learning, and algebraic topology, we deduce that some of the mutations such as M153I, S254F, and S255F may weaken the binding of S protein and antibodies, and potentially disrupt the efficacy and reliability of antibody therapies and vaccines in the development. 2020 ArXiv Abstract SARS_CoV_2 M153I;S254F;S255F 121;128;139 126;133;144 S 171 172 33083804 Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2. The initial period of rapid diversification into region-specific phylogenies that ended in February 2020 was followed by a major extinction event and global homogenization concomitant with the spread of D614G in the spike protein, ending in March 2020. 2021 bioRxiv Abstract SARS_CoV_2 D614G 203 208 S 216 221 33083806 Structural impact on SARS-CoV-2 spike protein by D614G substitution. Substitution for aspartic acid by glycine at position 614 in the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the ongoing pandemic, appears to facilitate rapid viral spread. 2020 bioRxiv Abstract SARS_CoV_2 D614G 17 57 S;S 65;72 70;73 COVID-19 93 133 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. In addition, the hot spots within these docking mutant complexes were altered, among which the mutation Q57H was involved in both Orf3a-S and Orf3a-Orf8 protein interactions. 2021 Journal of medical virology Abstract SARS_CoV_2 Q57H 104 108 ORF3a;ORF3a;ORF8;S 130;142;148;136 135;147;152;137 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. Notably, the incidences of R203K/G204R in N and Q57H in Orf3a were both over 50% in some countries. 2021 Journal of medical virology Abstract SARS_CoV_2 Q57H;R203K;G204R 48;27;33 52;34;38 ORF3a;N 56;42 61;43 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. The results showed that four types of mutations caused dramatic changes in protein structures (RMSD >= 5.0 A), which were Q57H and G251V in open-reading frames 3a (ORF3a), S194L, and R203K/G204R in nucleocapsid (N). 2021 Journal of medical virology Abstract SARS_CoV_2 G251V;Q57H;R203K;S194L;G204R 131;122;183;172;189 136;126;188;177;194 ORF3a;N;ORF3a;N 140;198;164;212 162;210;169;213 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. A previously reported variant, 23403A > G, in the spike protein S2 was mostly seen. 2021 Genomics Abstract SARS_CoV_2 A23403G 31 41 S 50 55 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. Among those, a frame shift (8651A>) in NSP4, a stop codon 6887A > T in NSP3 and two missense mutations in spike S2 were found. 2021 Genomics Abstract SARS_CoV_2 A6887T 58 67 S;Nsp3;Nsp4 106;71;39 111;75;43 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. Two other known mutations 25563G > T in ORF3a and 14408C > T in ORF1ab were detected respectively in 6 and 8 out of the 11 isolates. 2021 Genomics Abstract SARS_CoV_2 C14408T;G25563T 50;26 60;36 ORF1ab;ORF3a 64;40 70;45 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. Mutation analysis showed the presence of the D614G mutation in the spike protein in 22 of 23 genomes. 2020 Microbiology resource announcements Abstract SARS_CoV_2 D614G 45 50 S 67 72 33095454 Evolutionary dynamics of SARS-CoV-2 nucleocapsid protein and its consequences. Remarkably, we observed that a high frequency (67.94% of mutated sequences) co-occuring mutations (R203K and G204R) destabilized and decreased overall structural flexibility. 2021 Journal of medical virology Abstract SARS_CoV_2 G204R;R203K 109;99 114;104 33097660 SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling. In addition, we show that a methionine-to-arginine substitution at residue 58 impairs Orf6 binding to the Nup98-Rae1 complex and abolishes its IFN antagonistic function. 2020 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 M58R 28 77 ORF6 86 90 33101829 In silico analysis of ACE2 orthologues to predict animal host range with high susceptibility to SARS-CoV-2. Furthermore, we identified a specific substitution of tyrosine to histidine at position 41 in ACE2 that likely reduces the affinity to SARS-CoV-2 in horses and greater horseshoe bats. 2020 3 Biotech Abstract SARS_CoV_2 Y41H 54 90 33105685 Viewpoint: Origin of SARS-CoV-2. The SARS-CoV-2 does not appear to present a mutational "hot spot" as only the D614G mutation has been identified from clinical isolates. 2020 Viruses Abstract SARS_CoV_2 D614G 78 83 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. Hamsters infected with SARS-CoV-2 expressing spike(D614G) (G614 virus) produced higher infectious titres in nasal washes and the trachea, but not in the lungs, supporting clinical evidence showing that the mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increase transmission. 2021 Nature Abstract SARS_CoV_2 D614G 51 56 S 45 50 COVID-19 270 278 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. Here we engineered the spike D614G substitution in the USA-WA1/2020 SARS-CoV-2 strain, and found that it enhances viral replication in human lung epithelial cells and primary human airway tissues by increasing the infectivity and stability of virions. 2021 Nature Abstract SARS_CoV_2 D614G 29 34 S 23 28 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein substitution D614G became dominant during the coronavirus disease 2019 (COVID-19) pandemic1,2. 2021 Nature Abstract SARS_CoV_2 D614G 92 97 S 65 70 COVID-19;COVID-19;COVID-19 125;11;151 149;51;159 33106822 COVID-19 neutralizing antibodies predict disease severity and survival. In addition to neutralization of wild-type SARS-CoV-2, patient sera were also able to neutralize the recently emerged SARS-CoV-2 mutant D614G, suggesting protection from reinfection by this strain. 2020 medRxiv Abstract SARS_CoV_2 D614G 136 141 33108902 ACE2 and TMPRSS2 Potential Involvement in Genetic Susceptibility to SARS-COV-2 in Cancer Patients. Variants were present at low frequency (range 0% to 3%) and among those with the highest frequency, the variant S19P belongs to the SARS-CoV-2 spike protein binding site and it was exclusively present in Africans with a frequency of 0.2%.The mechanisms of ACE2 and TMPRSS2 regulation could be targeted for preventive and therapeutic purposes in the whole population and especially in cancer patients.Further studies are needed to show a direct correlation of ACE2 and TMPRSS2 expressions in cancer patients and the incidence of COVID-19. 2020 Cell transplantation Abstract SARS_CoV_2 S19P 112 116 S 143 148 COVID-19 528 536 33109270 Molecular detection of drug resistant polymorphisms in Plasmodium falciparum isolates from Southwest, Nigeria. The Pfk13 C580Y mutant allele was suspected by allelic discrimination in two samples with mixed genotypes although this could not be validated with independent isolation or additional methods. 2020 BMC research notes Abstract SARS_CoV_2 C580Y 10 15 33109270 Molecular detection of drug resistant polymorphisms in Plasmodium falciparum isolates from Southwest, Nigeria. There was one synonymous (S679S) and two non-synonymous (M699V, S769M) mutations in the PATPase6 gene, while Pfcrt genotype (CVIET), had a prevalence of 45%. 2020 BMC research notes Abstract SARS_CoV_2 S769M;M699V;S679S 64;57;26 69;62;31 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. 57% of strains carry the spike D614G variant, which is associated with higher genome copy numbers, and its prevalence expands with time. 2020 Cell reports Abstract SARS_CoV_2 D614G 31 36 S 25 30 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. This study contributes to the understanding of COVID-19 through an extensive set of genomes from a non-urban setting and informs vaccine design by defining D614G as a dominant and emergent SARS-CoV-2 isolate in the United States. 2020 Cell reports Abstract SARS_CoV_2 D614G 156 161 COVID-19 47 55 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. In vitro assays showed an enhanced infectivity of pseudotyped virions displaying the G614 substitution compared with those having D614, suggesting a fitness advantage of D614G.IMPORTANCE Multiple SARS-CoV-2 introductions have been detected in Spain, and at least four resulted in the emergence of locally transmitted clusters that originated not later than mid-February, with further dissemination to many other countries around the world, and a few weeks before the explosion of COVID-19 cases detected in Spain during the first week of March. 2021 Journal of virology Abstract SARS_CoV_2 D614G 170 175 COVID-19 480 488 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. Most sequences from Spain were distributed in clades characterized by a D614G substitution in the S gene (20A, 20B, and 20C) and an L84S substitution in ORF8 (19B) with 163 and 118 sequences, respectively, with the remaining sequences branching in 19A. 2021 Journal of virology Abstract SARS_CoV_2 D614G;L84S 72;132 77;136 ORF8;S 153;98 157;99 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Despite huge differences in genome sampling worldwide, SARS-CoV-2 Spike D839Y has been detected in 13 countries in four continents, supporting the need for close surveillance and functional assays of Spike variants. 2020 Emerging microbes & infections Abstract SARS_CoV_2 D839Y 72 77 S;S 66;200 71;205 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Here, we track the geotemporal spread of a SARS-CoV-2 variant with a mutation (D839Y) in a potential host-interacting region involving the Spike fusion peptide, which is a target motif of anti-viral drugs that plays a key role in SARS-CoV-2 infectivity. 2020 Emerging microbes & infections Abstract SARS_CoV_2 D839Y 79 84 S 139 144 33132795 [The virology of SARS-CoV-2]. The D614G mutation in the S spikes seems to cause a higher infectiosity. 2020 Der Pneumologe Abstract SARS_CoV_2 D614G 4 9 S;S 28;26 34;27 33140034 Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein. This finding is corroborated by biolayer interferometry experiments, which show that deletion of these glycans through N165A and N234A mutations significantly reduces binding to ACE2 as a result of the RBD conformational shift toward the "down" state. 2020 ACS central science Abstract SARS_CoV_2 N165A;N234A 119;129 124;134 RBD 202 205 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. During the evolution of SARS-CoV-2 in humans a D614G substitution in the spike (S) protein emerged and became the predominant circulating variant (S-614G) of the COVID-19 pandemic 1 . 2020 bioRxiv Abstract SARS_CoV_2 D614G 47 52 S;S;S 80;147;73 81;148;78 COVID-19 162 170 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. A 75-year-old patient with severe disease had a mutation, G22017T, identified in the second specimen. 2021 Clinical microbiology and infection Abstract SARS_CoV_2 G22017T 58 65 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. DISCUSSION: A spike protein amino acid mutation W152L located within a neutralizing epitope has appeared naturally in a patient. 2021 Clinical microbiology and infection Abstract SARS_CoV_2 W152L 48 53 S 14 19 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. G22017T corresponds to W152L amino acid mutation in the spike protein which was only found in <0.03% of the sequences deposited into a public database. 2021 Clinical microbiology and infection Abstract SARS_CoV_2 W152L;G22017T 23;0 28;7 S 56 61 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. The difference in G22017T frequency was also confirmed by Sanger sequencing. 2021 Clinical microbiology and infection Abstract SARS_CoV_2 G22017T 18 25 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. The frequency of G22017T increased from <=5% (nanopore: 3.8%; Illumina: 5%) from the first respiratory tract specimen (sputum) to >=60% (nanopore: 67.7%; Illumina: 60.4%) in the second specimen (saliva; collected 2 days after the first specimen). 2021 Clinical microbiology and infection Abstract SARS_CoV_2 G22017T 17 24 33144890 [The virology of SARS-CoV-2]. The D614G mutation in the S spikes seems to cause a higher infectiousness. 2020 Der Gastroenterologe Abstract SARS_CoV_2 D614G 4 9 S;S 28;26 34;27 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. Mutation entropy decreased between March and April of 2020 after steady increases at several sites, including the D614G mutation site of the spike (S) protein that was previously found associated with higher case fatality rates and at sites of the NSP12 polymerase and the NSP13 helicase proteins. 2020 Evolutionary bioinformatics online Abstract SARS_CoV_2 D614G 114 119 Helicase;S;Nsp13;Nsp12;S 279;141;273;248;148 287;146;278;253;149 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. Notable expanding mutations include R203K and G204R of the nucleocapsid (N) protein inter-domain linker region and G251V of the viroporin encoded by ORF3a between March and April. 2020 Evolutionary bioinformatics online Abstract SARS_CoV_2 G204R;G251V;R203K 46;115;36 51;120;41 N;ORF3a;N 59;149;73 71;154;74 33157300 SARS-CoV-2 spread across the Colombian-Venezuelan border. Additionally, three mutations (R203K/G204R substitution) were present in the nucleocapsid (N) gene of one Venezuelan genome. 2020 Infection, genetics and evolution Abstract SARS_CoV_2 R203K;G204R 31;37 36;42 N;N 77;91 89;92 33157300 SARS-CoV-2 spread across the Colombian-Venezuelan border. We observed a point mutation in the Spike protein gene (D614G substitution), previously reported to be associated with increased infectivity, in all three Venezuelan genomes. 2020 Infection, genetics and evolution Abstract SARS_CoV_2 D614G 56 61 S 36 41 33159417 Humanized COVID-19 decoy antibody effectively blocks viral entry and prevents SARS-CoV-2 infection. The impairment of viral entry was not affected by virus variants, since efficient inhibition was also observed in six SARS-CoV-2 clinical strains, including the D614G variants which have been shown to exhibit increased infectivity. 2021 EMBO molecular medicine Abstract SARS_CoV_2 D614G 161 166 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. A single point mutation in S gene leading to an amino acid substitution at codon 614 from an aspartic acid 614 into glycine (D614G) resulted in greater infectivity compared to the wild type SARS-CoV2. 2020 Immune network Abstract SARS_CoV_2 D614G;D614G 93;125 123;130 S 27 28 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. New mutation sites were found in the critical receptor binding domain (RBD) of S gene, which is adjacent to the aforementioned D614G mutation residue. 2020 Immune network Abstract SARS_CoV_2 D614G 127 132 RBD;RBD;S 46;71;79 69;74;80 33163695 Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh. Genome-wide annotations revealed 256 mutations, of which 10 were novel (NSP3, RdRp, Spike) in Bangladeshi strains where I120F(NSP2), P323L(RdRp), D614G (Spike), R203K, G204R(N) are the most prominent. 2020 Gene reports Abstract SARS_CoV_2 D614G;G204R;I120F;P323L;R203K 146;168;120;133;161 151;173;125;138;166 S;S;Nsp2;Nsp3;RdRP;RdRP;N 84;153;126;72;78;139;174 89;158;130;76;82;143;175 33163955 Hereditary haemochromatosis, haemophagocytic lymphohistiocytosis and COVID-19. Results returned after his death showed homozygous C282Y mutation of the HFE gene consistent with a diagnosis of HH. 2020 Clinical infection in practice Abstract SARS_CoV_2 C282Y 51 56 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. Regarding the high price and low availability of sequencing techniques in developing countries, here we describe a rapid and inexpensive method for the detection of D614G mutation in SARS-CoV-2. 2020 Infection, genetics and evolution Abstract SARS_CoV_2 D614G 165 170 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. Using bioinformatics databases and software, we designed the PCR-RFLP method for D614G mutation detection. 2020 Infection, genetics and evolution Abstract SARS_CoV_2 D614G 81 86 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. We have little information about the prevalence of D614G mutation, and it seems that the reason is the lack of cheap and fast methods. 2020 Infection, genetics and evolution Abstract SARS_CoV_2 D614G 51 56 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. We hope that this method will provide more information on the prevalence and epidemiology of D614G mutations worldwide. 2020 Infection, genetics and evolution Abstract SARS_CoV_2 D614G 93 98 33170884 Static all-atom energetic mappings of the SARS-Cov-2 spike protein and dynamic stability analysis of "Up" versus "Down" protomer states. We conducted preliminary molecular dynamics simulations across 0.1 mu seconds to see if this latch provided structural stability and indeed found that a single point mutation (Q564G) resulted in the latch releasing transforming the protomer from the Down to the Up state conformation. 2020 PloS one Abstract SARS_CoV_2 Q564G 176 181 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. The phylogentic analysis identified two major Clades C1 and C2 harboring mutations L3606F and G614D, respectively and both emerging for the first time in China. 2020 PloS one Abstract SARS_CoV_2 G614D;L3606F 94;83 99;89 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Artificial intelligence, sequence alignment, and network analysis are applied to show that NSP6 mutation L37F may have compromised the virus's ability to undermine the innate cellular defense against viral infection via autophagy regulation. 2020 The journal of physical chemistry letters Abstract SARS_CoV_2 L37F 105 109 Nsp6 91 95 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. By analyzing the distribution of 11083G>T in various countries, we unveil that 11083G>T may correlate with the hypotoxicity of SARS-CoV-2. 2020 The journal of physical chemistry letters Abstract SARS_CoV_2 G11083T;G11083T 33;79 41;87 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Moreover, we show a global decaying tendency of the 11083G>T mutation ratio indicating that 11083G>T hinders the SARS-CoV-2 transmission capacity. 2020 The journal of physical chemistry letters Abstract SARS_CoV_2 G11083T;G11083T 52;92 60;100 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. On the basis of the genotyping of 75775 SARS-CoV-2 genome isolates, we reveal that asymptomatic infection is linked to SARS-CoV-2 11083G>T mutation (i.e., L37F at nonstructure protein 6 (NSP6)). 2020 The journal of physical chemistry letters Abstract SARS_CoV_2 G11083T;L37F 130;155 138;159 Nsp6;Nsp6 163;187 185;191 33181224 Molecular docking simulation reveals ACE2 polymorphisms that may increase the affinity of ACE2 with the SARS-CoV-2 Spike protein. HDOCK and FireDock simulations identified 6 ACE2 missense variants (I21T, A25T, K26R, E37K, T55A, E75G) with higher affinity for SARS-CoV-2 Spike protein receptor binding domain (RBD) with respect to wild type ACE2, and 11 variants (I21V, E23K, K26E, T27A, E35K, S43R, Y50F, N51D, N58H, K68E, M82I) with lower affinity. 2021 Biochimie Abstract SARS_CoV_2 A25T;E23K;E35K;E37K;E75G;K26E;K26R;K68E;M82I;N51D;N58H;S43R;T55A;Y50F;I21T;I21V 74;239;257;86;98;245;80;287;293;275;281;263;92;269;68;233 78;243;261;90;102;249;84;291;297;279;285;267;96;273;72;237 RBD;S;RBD 154;140;179 177;145;182 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. Later SNVs such as G28881A, G28882A, and G28883C have emerged with strong allelic associations, forming new subtypes. 2020 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 G28881A;G28882A;G28883C 19;28;41 26;35;48 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. Since C241T is in the 5' UTR with uncertain significance and the characteristics can be captured by the other three strongly associated SNVs, we focus on the other three. 2020 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 C241T 6 11 5'UTR 22 28 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. To date, type VI, characterized by the four signature SNVs C241T (5'UTR), C3037T (nsp3 F924F), C14408T (nsp12 P4715L), and A23403G (Spike D614G), with strong allelic associations, has become the dominant type. 2020 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 A23403G;C14408T;C241T;C3037T;D614G;F924F;P4715L 123;95;59;74;138;87;110 130;102;64;80;143;92;116 S;5'UTR;Nsp12;Nsp3 132;66;104;82 137;71;109;86 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. However, the D614G variant transmits significantly faster and displayed increased competitive fitness than the wild-type virus in hamsters. 2020 Science (New York, N.Y.) Abstract SARS_CoV_2 D614G 13 18 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. The spike aspartic acid-614 to glycine (D614G) substitution is prevalent in global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains, but its effects on viral pathogenesis and transmissibility remain unclear. 2020 Science (New York, N.Y.) Abstract SARS_CoV_2 D614G;D614G 10;40 38;45 S 4 9 COVID-19 90 130 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. These data show that the D614G substitution enhances SARS-CoV-2 infectivity, competitive fitness, and transmission in primary human cells and animal models. 2020 Science (New York, N.Y.) Abstract SARS_CoV_2 D614G 25 30 33185784 Comparison of Binding Site of Remdesivir and Its Metabolites with NSP12-NSP7-NSP8, and NSP3 of SARS CoV-2 Virus and Alternative Potential Drugs for COVID-19 Treatment. A recent study reported that the D614G mutation in the SARS-CoV-2 virus spike protein reduces S1 shedding and increases infectivity of SARS COV-2 virus. 2020 The protein journal Abstract SARS_CoV_2 D614G 33 38 S 72 77 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. A point mutation in the spike protein, D614G, emerged as the virus spread from Asia into Europe and the USA, and has rapidly become the dominant form worldwide. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 D614G 39 44 S 24 29 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. Here we review how the D614G variant was identified and discuss recent evidence about the effect of the mutation on the characteristics of the virus, clinical outcome of infection and host immune response. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 D614G 23 28 33200118 Copper(II) Inhibition of the SARS-CoV-2 Main Protease. We also started studying the Spike Protein, PDB ID: 6VXX and the region around the D614G mutant. 2020 ChemRxiv Abstract SARS_CoV_2 D614G 83 88 S 29 34 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. The prevalence of the former reflected probable European origin of viruses, and the transition D614G was dominant in Vietnam. 2020 PloS one Abstract SARS_CoV_2 D614G 95 100 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. The three most common variants were linked, and included C3037T, C14408T (nsp12: P323L) and A23403G (S: D614G) mutations. 2020 PloS one Abstract SARS_CoV_2 A23403G;C14408T;C3037T;D614G;P323L 92;65;57;104;81 99;72;63;109;86 Nsp12;S 74;101 79;102 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. This group of mutations often accompanied variant C241T (39/44 genomes) or GGG 28881..28883 AAC (33/44 genomes). 2020 PloS one Abstract SARS_CoV_2 C241T 50 55 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. Further investigation of orf3b deletion and spike D614G substitution on virulence and infectivity respectively will provide important insights into SARS-CoV-2 evolution. 2020 Emerging microbes & infections Abstract SARS_CoV_2 D614G 50 55 ORF3b;S 25;44 30;49 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. Interestingly, the loss of 3b coincides with the emergence of spike D614G substitution. 2020 Emerging microbes & infections Abstract SARS_CoV_2 D614G 68 73 S 62 67 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. The genome of SARS-CoV-2 continues to evolve during the global transmission with the notable emergence of the spike D614G substitution that enhances infectivity. 2020 Emerging microbes & infections Abstract SARS_CoV_2 D614G 116 121 S 110 115 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. The loss of 3b is caused by the presence of an early stop codon which is created by an orf3a Q57H substitution. 2020 Emerging microbes & infections Abstract SARS_CoV_2 Q57H 93 97 ORF3a 87 92 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. We have determined X-ray crystallographic structures of this cysteine protease in its wild-type free active site state at 1.8 A resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 A resolution and in its product bound state at 2.0 A resolution by employing an active site mutation (C145A). 2020 Nature communications Abstract SARS_CoV_2 C145A 337 342 33208827 Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19. In addition, the antibodies elicited were able to cross-neutralize pseudovirus containing the spike protein of the D614G variant, indicating the potential for broad spectrum protection. 2020 Scientific reports Abstract SARS_CoV_2 D614G 115 120 S 94 99 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. The spike protein D614G substitution that defines the clade "G" emerged in reinfection, while mutations that characterize the clade "V" (ie, nsp6 L37F and ORF3a G251V) were present at initial infection. 2021 Clinical infectious diseases Abstract SARS_CoV_2 D614G;G251V;L37F 18;161;146 23;166;150 S;ORF3a;Nsp6 4;155;141 9;160;145 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Compared to the reference strain of SARS-CoV-2, the majority of currently circulating isolates possess an S protein variant characterized by an aspartic acid-to-glycine substitution at amino acid position 614 (D614G). 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 D614G;D614G 144;210 208;215 S 106 107 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. This review summarizes and synthesizes the epidemiological and functional observations of the D614G spike mutation, with focus on the biochemical and cell-biological impact of this mutation and its consequences for S protein function. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 D614G 94 99 S;S 100;215 105;216 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. Among the 9 SNVs found on 4 conserved domains, the frequency of 15438G > T was highest (n = 34) and was predominantly found in Europe. 2020 Virology journal Abstract SARS_CoV_2 G15438T 64 74 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Our data suggest that here, positive selection in index cats followed by a narrow transmission bottleneck may have instead accelerated the fixation of S H655Y, a potentially beneficial SARS-CoV-2 variant. 2021 bioRxiv Abstract SARS_CoV_2 H655Y 153 158 S 151 152 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. We further identify a notable variant at amino acid position 655 in Spike (H655Y), which was previously shown to confer escape from human monoclonal antibodies. 2021 bioRxiv Abstract SARS_CoV_2 H655Y 75 80 S 68 73 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. However, D614G does not alter S-protein binding to ACE2 or neutralization sensitivity of pseudoviruses. 2020 Nature communications Abstract SARS_CoV_2 D614G 9 14 S 30 31 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. SARS-CoV-2 variants with spike (S)-protein D614G mutations now predominate globally. 2020 Nature communications Abstract SARS_CoV_2 D614G 43 48 S;S 25;32 30;33 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Thus, D614G may increase infectivity by assembling more functional S protein into the virion. 2020 Nature communications Abstract SARS_CoV_2 D614G 6 11 S 67 68 33252670 SARS-CoV-2 Among Military and Civilian Patients, Metro Manila, Philippines. Sequencing results showed the presence of the D614G mutation in the spike protein in a majority of specimens collected from the end of June to July 2020. 2021 Military medicine Abstract SARS_CoV_2 D614G 46 51 S 68 73 33252670 SARS-CoV-2 Among Military and Civilian Patients, Metro Manila, Philippines. Twenty-two of the 23 sequences collected after June 25, 2020, contained the D614G mutation. 2021 Military medicine Abstract SARS_CoV_2 D614G 76 81 33253058 A Gapless, Unambiguous RNA Metagenome-Assembled Genome Sequence of a Unique SARS-CoV-2 Variant Encoding Spike S813I and ORF1a A859V Substitutions. Although the genome, named CU_S3, belongs to the prevalent global genotype, marked by the D614G spike variation, the combined variations in the spike proteins and ORF1a do not co-occur in any of the 197,000 genomes reported to date. 2021 Omics Abstract SARS_CoV_2 D614G 90 95 ORF1a;S;S 163;96;144 168;101;149 33253058 A Gapless, Unambiguous RNA Metagenome-Assembled Genome Sequence of a Unique SARS-CoV-2 Variant Encoding Spike S813I and ORF1a A859V Substitutions. However, three mutations are worth highlighting and future tracking: a synonymous mutation causing a rare spike S813I variation and two less frequent ones leading to an A41V variation in NSP3, encoded by ORF1a (ORF1a A895V), and a Q677H variation in the spike protein. 2021 Omics Abstract SARS_CoV_2 A41V;A895V;Q677H;S813I 169;217;231;112 173;222;236;117 ORF1a;ORF1a;S;S;Nsp3 204;211;106;254;187 209;216;111;259;191 33253226 SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia. We also report a nsp3-C6310A substitution found in 47.3% of global B.6 sequences which was associated with reduced sensitivity using a commercial diagnostic real-time PCR assay. 2020 PLoS neglected tropical diseases Abstract SARS_CoV_2 C6310A 22 28 Nsp3 17 21 33257936 Effect of D614G Spike Variant on Immunoglobulin G, M, or A Spike Seroassay Performance. Emergence of a new spike protein variant (D614G) with increased infectivity has prompted many to analyze its role in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. 2021 The Journal of infectious diseases Abstract SARS_CoV_2 D614G 42 47 S 19 24 COVID-19 128 168 33259879 Evolution and genetic diversity of SARS-CoV-2 in Africa using whole genome sequences. CONCLUSION: This study has revealed a rapidly diversifying viral population with the G614G spike protein variant dominatinge advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARS-CoV-2 in Africa. 2021 International journal of infectious diseases Abstract SARS_CoV_2 G614G 85 90 S 91 96 33259879 Evolution and genetic diversity of SARS-CoV-2 in Africa using whole genome sequences. There was a high prevalence of the D614G spike protein amino acid mutation 59/69 (82.61%) among the African strains. 2021 International journal of infectious diseases Abstract SARS_CoV_2 D614G 35 40 S 41 46 33262895 Genomic characterization of SARS-CoV-2 in Egypt. Conclusion: The whole genomic sequence of SARS-CoV2 showed 204 variations in the genomes of the Egyptian isolates, where the Asp614Gly (D614G) substitution is the most common among the samples (60/61). 2021 Journal of advanced research Abstract SARS_CoV_2 D614G;D614G 125;136 134;141 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. A348T, G476S, and V483A variants display reduced affinity to ACE2 in comparison to the Wuhan SARS-CoV2 spike protein. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 G476S;V483A;A348T 7;18;0 12;23;5 S 103 108 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Evolutionary analysis reveals five RBD variants A348T, V367F, G476S, V483A, and S494P are under strong positive selection bias. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 A348T;G476S;S494P;V367F;V483A 48;62;80;55;69 53;67;85;60;74 RBD 35 38 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. On the other hand, the enhanced binding affinity of S494P is attributed to strong interfacial complementarity between the RBD and ACE2. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 S494P 52 57 RBD 122 125 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Reorientation of several crucial residues at the RBD-ACE2 interface facilitates additional hydrogen bond formation for the V367F variant which enhances the binding energy during ACE2 recognition. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 V367F 123 128 RBD 49 52 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. While the V367F and S494P population variants display a higher binding affinity towards human ACE2. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 S494P;V367F 20;10 25;15 33274614 Origin, evolution and global spread of SARS-CoV-2. These are generally neutral and have no impact on virulence and severity, but some appear to influence infectivity, notably the D614G mutation of the Spike protein. 2020 Comptes rendus biologies Abstract SARS_CoV_2 D614G 128 133 S 150 155 33275493 Multiscale Feedback Loops in SARS-CoV-2 Viral Evolution. First, we observe differences in mutational signals for geospatially separated populations such as the prevalence of A23404G in CA versus NY and WA. 2021 Journal of computational biology Abstract SARS_CoV_2 A23404G 117 124 33275493 Multiscale Feedback Loops in SARS-CoV-2 Viral Evolution. Namely, when C14408T first appeared in the viral population, the frequency of A23404G spiked in the subsequent week. 2021 Journal of computational biology Abstract SARS_CoV_2 A23404G;C14408T 78;13 85;20 33275493 Multiscale Feedback Loops in SARS-CoV-2 Viral Evolution. Third, we identify a noncoding mutation, G29540A, within the segment between the coding gene of the N protein and the ORF10 gene, which is largely confined to NY (>95%). 2021 Journal of computational biology Abstract SARS_CoV_2 G29540A 41 48 N 100 101 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. CR3022 does not neutralize SARS-CoV-2, but the increased affinity to SARS-CoV-2 P384A mutant now enables neutralization with a similar potency to SARS-CoV. 2020 PLoS pathogens Abstract SARS_CoV_2 P384A 80 85 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. Using x-ray crystallography, mutagenesis, and binding experiments, we illustrate that of four amino acid differences in the CR3022 epitope between SARS-CoV-2 and SARS-CoV, a single mutation P384A fully determines the affinity difference. 2020 PLoS pathogens Abstract SARS_CoV_2 P384A 190 195 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. 2021 Cell Abstract SARS_CoV_2 D614G 82 87 S 60 65 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. 2021 Cell Abstract SARS_CoV_2 D614G 62 67 S 56 61 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. Intriguingly, a SARS-CoV-2 isolate containing an amino acid substitution at site 614 of the spike protein (mutation D614G) replicated at higher magnitude in ex vivo tissues of both ruminant species, supporting previous results obtained using human cells. 2021 Veterinary microbiology Abstract SARS_CoV_2 D614G 116 121 S 92 97 33292056 Sensing the interactions between carbohydrate-binding agents and N-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies. Interestingly, stable BanLec mutant (H84T) also showed similar docking affinity and interactions as compared to wild-type BanLec, thus, confirming that uncoupling the mitogenic activity did not alter the lectin binding activity of BanLec. 2020 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 H84T 37 41 33298875 Initial whole-genome sequencing and analysis of the host genetic contribution to COVID-19 severity and susceptibility. The p.Val197Met missense variant that affects the stability of the TMPRSS2 protein displays a decreasing allele frequency among the severe patients compared to the mild and the general population. 2020 Cell discovery Abstract SARS_CoV_2 V197M 4 15 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. Molecular Dynamics simulations of SARS-CoV-2 wild-type and G502P mutant show that the affinity for the human receptor of the mutant is drastically diminished. 2020 bioRxiv Abstract SARS_CoV_2 G502P 59 64 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. Our analysis of 1000 S protein sequences from field isolates collected globally over the past few months identified three recurrent point mutations including L5F, D614G and G1124V. 2020 PloS one Abstract SARS_CoV_2 D614G;G1124V;L5F 163;173;158 168;179;161 S 21 22 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. In our cohort, lethal outcome of SARS-CoV-2 infection significantly correlated with arterial hypertension, kidney failure, and ICU admission (FDR < 0.01), but not with any mutation in a structural or non-structural protein, such as the spike D614G mutation. 2021 Emerging microbes & infections Abstract SARS_CoV_2 D614G 242 247 S 236 241 Hypertension;kidney failure;COVID-19 84;107;33 105;121;53 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. Based on these findings, the D614G mutation is not expected to be an obstacle for current vaccine development. 2021 Cell host & microbe Abstract SARS_CoV_2 D614G 29 34 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein acquired a D614G mutation early in the pandemic that confers greater infectivity and is now the globally dominant form. 2021 Cell host & microbe Abstract SARS_CoV_2 D614G 90 95 S 65 70 COVID-19 11 51 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. To determine whether D614G might also mediate neutralization escape that could compromise vaccine efficacy, sera from spike-immunized mice, nonhuman primates, and humans were evaluated for neutralization of pseudoviruses bearing either D614 or G614 spike. 2021 Cell host & microbe Abstract SARS_CoV_2 D614G 21 26 S;S 118;249 123;254 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Apparently, these two features of the SARS-CoV-2 S glycoprotein, the furin cleavage site and D614G, have evolved to balance virus infectivity, stability, cytopathicity and antibody vulnerability. 2020 Journal of virology Abstract SARS_CoV_2 D614G 93 98 S 49 63 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Here we identify key features of the spike glycoprotein, including the furin cleavage site and the D614G natural mutation, that modulate viral cytopathic effects, infectivity and sensitivity to inhibition. 2020 Journal of virology Abstract SARS_CoV_2 D614G 99 104 S 37 55 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Notably, the D614G change found in globally predominant SARS-CoV-2 strains increased infectivity, modestly enhanced responsiveness to the ACE2 receptor and susceptibility to neutralizing sera, and tightened association of the S1 subunit with the trimer. 2020 Journal of virology Abstract SARS_CoV_2 D614G 13 18 33319124 Mutational insights into the envelope protein of SARS-CoV-2. Furthermore, this study revealed the V25A mutation in the transmembrane domain which is a key factor for the homopentameric conformation of E protein. 2021 Gene reports Abstract SARS_CoV_2 V25A 37 41 E 140 141 33319124 Mutational insights into the envelope protein of SARS-CoV-2. Our analysis also observed a triple cysteine motif harboring mutation (L39M, A41S, A41V, C43F, C43R, C43S, C44Y, N45R) which may hinder the binding of E protein with spike glycoprotein. 2021 Gene reports Abstract SARS_CoV_2 A41S;A41V;C43F;C43R;C43S;C44Y;N45R;L39M 77;83;89;95;101;107;113;71 81;87;93;99;105;111;117;75 S;E 166;151 184;152 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. The microbody inhibits the entry of beta coronaviruses and virus with the variant D614G spike. 2020 Cell reports Abstract SARS_CoV_2 D614G 82 87 S 88 93 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. At the same time, 20A and 20B clades depicted prevalence of four common mutations 241 C > T in 5' UTR, P4715L, F942F along with D614G in the Spike protein. 2020 Frontiers in microbiology Abstract SARS_CoV_2 C241T;D614G;F942F;P4715L 82;128;111;103 91;133;116;109 5'UTR;S 95;141 101;146 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. D614G mutation has been reported to increase virus shedding and infectivity. 2020 Frontiers in microbiology Abstract SARS_CoV_2 D614G 0 5 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. Our molecular modeling and docking analysis identified that D614G mutation resulted in enhanced affinity of Spike S1-S2 hinge region with TMPRSS2 protease, possibly the reason for increased shedding of S1 domain in G614 as compared to D614. 2020 Frontiers in microbiology Abstract SARS_CoV_2 D614G 60 65 S 108 113 33330626 Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM. Besides, Computational Alanine Scanning (CAS) mutagenesis was performed, which revealed hotspot mutants, namely I40A, V104A, and R86A for the dimer association. 2020 Frontiers in molecular biosciences Abstract SARS_CoV_2 I40A;R86A;V104A 112;129;118 116;133;123 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. The spike D614G mutation increases SARS-CoV-2 infectivity, viral load, and transmission but the molecular mechanism underlying these effects remains unclear. 2020 bioRxiv Abstract SARS_CoV_2 D614G 10 15 S 4 9 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. These results are consistent with a lysosomal pathway of coronavirus biogenesis and raise the possibility that a common mechanism may underly the D614G mutation's effects on spike protein trafficking in infected cells and the accelerated entry of SARS-CoV-2 into uninfected cells. 2020 bioRxiv Abstract SARS_CoV_2 D614G 146 151 S 174 179 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. We report here that spike is trafficked to lysosomes and that the D614G mutation enhances the lysosomal sorting of spike and the lysosomal accumulation of spike-positive punctae in SARS-CoV-2-infected cells. 2020 bioRxiv Abstract SARS_CoV_2 D614G 66 71 S;S;S 20;115;155 25;120;160 33335073 Cross-species recognition of SARS-CoV-2 to bat ACE2. Notably, the Y41H mutant, which exists in many bats, attenuates the binding capacity of bACE2-Rm, indicating the central roles of Y41 in the interaction network. 2021 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 Y41H 13 17 33335187 CoV2-ID, a MIQE-compliant sub-20-min 5-plex RT-PCR assay targeting SARS-CoV-2 for the diagnosis of COVID-19. Finally, we have designed an assay for the detection of the D614G mutation and show that all of the samples isolated in the Chelmsford, Essex area between mid-April and June 2020, have the mutant genotype whereas a sample originating in Australia was infected with the wild type genotype. 2020 Scientific reports Abstract SARS_CoV_2 D614G 60 65 33336251 Multisystem Inflammatory Syndrome in Children in February 2020 and Implications of Genomic Sequencing for SARS-CoV-2. Our patient's SARS-CoV-2 infection was caused by an emerging lineage with the D614G variant in the spike protein. 2021 Journal of the Pediatric Infectious Diseases Society Abstract SARS_CoV_2 D614G 78 83 S 99 104 COVID-19 14 34 33344912 Defusing SARS-CoV-2: Emergency Brakes in a Vaccine Failure Scenario. The timing and locus for the therapeutic intervention are dictated by the cell entry mechanism and by the selective advantage of the dominant D614G mutation. 2020 ACS pharmacology & translational science Abstract SARS_CoV_2 D614G 142 147 33347622 Comparative insight into the genomic landscape of SARS-CoV-2 and identification of mutations associated with the origin of infection and diversity. We found 11 common nonsynonymous mutations; among them, two novel effective mutations were identified in ORF9 (S194L and S202N). 2021 Journal of medical virology Abstract SARS_CoV_2 S202N;S194L 121;111 126;116 ORF9 105 109 33350913 Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China. By using phylogenetic analysis, we attributed the community outbreak to 2 lineages; 1 harbored a common mutation, Orf3a-G251V, and accounted for 88.0% of the cases in our study. 2021 Emerging infectious diseases Abstract SARS_CoV_2 G251V 120 125 ORF3a 114 119 33353101 SARS-CoV-2 Spike Alterations Enhance Pseudoparticle Titers and Replication-Competent VSV-SARS-CoV-2 Virus. Additionally, we engineered a replication-competent VSV (rVSV) virus to produce the S-D614G variant with a truncated cytoplasmic tail. 2020 Viruses Abstract SARS_CoV_2 D614G 86 91 S 84 85 33353101 SARS-CoV-2 Spike Alterations Enhance Pseudoparticle Titers and Replication-Competent VSV-SARS-CoV-2 Virus. While the particles can be used to assess S entry requirements, the rVSV G/SMet1D614G 21 virus has a poor specific infectivity (particle to infectious titer ratio). 2020 Viruses Abstract SARS_CoV_2 D614G 80 85 S 42 43 33357220 Malaria and COVID-19: unmasking their ties. The variable distribution of the ACEI/D and the ACE2 (C1173T substitution) polymorphisms has been postulated to explain this variable prevalence. 2020 Malaria journal Abstract SARS_CoV_2 C1173T 54 60 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Functional predictions from structural analyses indicate that, contrary to previous reports, the Asp614Gly mutation in the spike glycoprotein (S) likely reduced transmission and the subsequent Pro323Leu mutation in the RNA-dependent RNA polymerase led to the precipitous spread of the virus. 2020 Genome biology Abstract SARS_CoV_2 D614G;P323L 97;193 106;202 RdRp;S;S 219;123;143 247;141;144 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. A unique mutation, I280V, was first reported in Oman and was associated with a rare lineage, B.1.113 (10.6%). 2021 International journal of infectious diseases Abstract SARS_CoV_2 I280V 19 24 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. FINDINGS: The study found that P323L (94.7%) is the most common mutation, followed by D614G (92.6%) Spike protein mutation. 2021 International journal of infectious diseases Abstract SARS_CoV_2 D614G;P323L 86;31 91;36 S 100 105 33359807 SARS-Cov-2 ORF3a: Mutability and function. Within the entire sample, the five most frequent mutations are V13L, Q57H, Q57H + A99V, G196V and G252V. 2021 International journal of biological macromolecules Abstract SARS_CoV_2 A99V;G196V;G252V;Q57H;Q57H;V13L 82;88;98;69;75;63 86;93;103;73;79;67 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. Dynamic tracking of SARS-CoV-2 showed that the D614G variant became predominant after emergence in Europe and North America, but not in China. 2020 Genes Abstract SARS_CoV_2 D614G 47 52 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) glycoprotein D614G mutation became the predominant globally circulating variant after its emergence in the early coronavirus disease 2019 (COVID-19) pandemic. 2020 Genes Abstract SARS_CoV_2 D614G 88 93 S;S 65;72 70;73 COVID-19;COVID-19;COVID-19 188;11;214 212;51;222 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. This study suggests that the dynamics of the SARS-CoV-2 D614G mutation during the early-to-mid pandemic is associated with enhanced transmission efficiency in populations with lower ACE2 expression. 2020 Genes Abstract SARS_CoV_2 D614G 56 61 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. This supports the idea that lower ACE2 expression is a driving force in the positive selection for the D614G mutation. 2020 Genes Abstract SARS_CoV_2 D614G 103 108 33377145 Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2. The N501T mutation in SARS-CoV-2-CTD furnishes better support to hotspot 353 in comparison with SARS-CoV and shows higher affinity for receptor binding. 2021 Briefings in bioinformatics Abstract SARS_CoV_2 N501T 4 9 33377359 The British variant of the new coronavirus-19 (Sars-Cov-2) should not create a vaccine problem. In today's pandemic, the D614G mutation of the amino acid of corronavirus-19, which emerged in Europe in February 2020 is the most frequent form and causes high viral growth. 2021 Journal of biological regulators and homeostatic agents Abstract SARS_CoV_2 D614G 25 30 33377359 The British variant of the new coronavirus-19 (Sars-Cov-2) should not create a vaccine problem. Recent studies suggest that coronavirus-19 variation occurs at the level N501Y of the spike protein and involves 23 separate mutations on the spike, 17 of which are linked to the virus proteins, thus giving specific characteristics to the virus. 2021 Journal of biological regulators and homeostatic agents Abstract SARS_CoV_2 N501Y 73 78 S;S 86;142 91;147 33377359 The British variant of the new coronavirus-19 (Sars-Cov-2) should not create a vaccine problem. The previously infrequent D614G mutation is now globally dominant. 2021 Journal of biological regulators and homeostatic agents Abstract SARS_CoV_2 D614G 26 31 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. RESULTS: Results on the whole GISAID sequence dataset at the time of the writing (October 2020) reveals an emerging mutation, S477N, located on the central part of the Spike protein Receptor Binding Domain, the Receptor Binding Motif. 2020 Journal of translational medicine Abstract SARS_CoV_2 S477N 126 131 RBD;S 182;168 205;173 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. In the cat, two unique amino acid substitutions were discovered in the N (T247I) and matrix (T175M) proteins. 2020 PeerJ Abstract SARS_CoV_2 T175M;T247I 93;74 98;79 N 71 72 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. In the mouse, the S protein had two amino acid substitutions, one in the RBM (Q498H) and the other (N969S) in the heptad repeat 1. 2020 PeerJ Abstract SARS_CoV_2 N969S;Q498H 100;78 105;83 S 18 19 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. SARS-CoV-2 isolates from minks exhibited two amino acid substitutions (G261D, A262S) in the N-terminal domain of S protein and four (L452M, Y453F, F486L, N501T) in the receptor-binding motif (RBM). 2020 PeerJ Abstract SARS_CoV_2 A262S;F486L;N501T;Y453F;G261D;L452M 78;147;154;140;71;133 83;152;159;145;76;138 N;S 92;113 93;114 33385461 Development of new vaccine target against SARS-CoV2 using envelope (E) protein: An evolutionary, molecular modeling and docking based study. Four novel mutations (T55S, V56F, E69R and G70del) were observed in E-protein of SARS-CoV2 after evolutionary analysis. 2021 International journal of biological macromolecules Abstract SARS_CoV_2 E69R;G70del;V56F;T55S 34;43;28;22 38;49;32;26 E 68 69 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. BACKGROUND: Recently, SARS-CoV-2 virus with the D614G mutation has become a public concern due to rapid dissemination of this variant across many countries. 2020 PeerJ Abstract SARS_CoV_2 D614G 48 53 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. CONCLUSION: These findings indicate that SARS-CoV-2 with the D614G mutation appears to become the major circulating virus in Indonesia, concurrent with the COVID-19 situation worldwide. 2020 PeerJ Abstract SARS_CoV_2 D614G 61 66 COVID-19 156 164 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. Using full-length sequences available in the GISAID EpiCoV Database, 39 of 60 SARS-CoV-2 (65%) from Indonesia harbor the D614G mutation. 2020 PeerJ Abstract SARS_CoV_2 D614G 121 126 33398275 An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. Variant N501Y in the RBD, which has emerged in a rapidly spreading lineage (B.1.1.7) in England, enhances affinity for wild type ACE2 20-fold but remains tightly bound to engineered sACE22.v2.4. 2020 bioRxiv Abstract SARS_CoV_2 N501Y 8 13 RBD 21 24 33398278 SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma. At day 73, an E484K substitution in the receptor-binding domain (RBD) occurred, followed at day 80 by an insertion in the NTD N5 loop containing a new glycan sequon, which generated a variant completely resistant to plasma neutralization. 2020 bioRxiv Abstract SARS_CoV_2 E484K 14 19 RBD 65 68 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. Although little change was observed in the overall viral population structure following two courses of remdesivir over the first 57 days, N501Y in Spike was transiently detected at day 55 and V157L in RdRp emerged. 2020 medRxiv Abstract SARS_CoV_2 N501Y;V157L 138;192 143;197 S;RdRP 147;201 152;205 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. D796H appeared to be the main contributor to decreased susceptibility, but incurred an infectivity defect. 2020 medRxiv Abstract SARS_CoV_2 D796H 0 5 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. However, following convalescent plasma we observed large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and Delta H69/ Delta V70 in the S1 N-terminal domain NTD of the Spike protein. 2020 medRxiv Abstract SARS_CoV_2 D796H 145 150 S;N 221;192 226;193 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. In vitro, the Spike escape double mutant bearing Delta H69/ Delta V70 and D796H conferred decreased sensitivity to convalescent plasma, whilst maintaining infectivity similar to wild type. 2020 medRxiv Abstract SARS_CoV_2 D796H 74 79 S 14 19 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. The Delta H69/ Delta V70 single mutant had two-fold higher infectivity compared to wild type and appeared to compensate for the reduced infectivity of D796H. 2020 medRxiv Abstract SARS_CoV_2 D796H 151 156 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Efficient detection of the SARS-CoV-2 D614G mutant by biosensing technologies is therefore crucial for the control of the pandemic. 2021 Trends in genetics Abstract SARS_CoV_2 D614G 38 43 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. The emergence of a mutant strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with an amino acid change from aspartate to a glycine residue at position 614 (D614G) has been reported and this mutant appears to be now dominant in the pandemic. 2021 Trends in genetics Abstract SARS_CoV_2 D614G 176 181 COVID-19 43 83 33407987 Impact of population density and weather on COVID-19 pandemic and SARS-CoV-2 mutation frequency in Bangladesh. About 82% of Bangladeshi isolates had D614G at spike protein. 2021 Epidemiology and infection Abstract SARS_CoV_2 D614G 38 43 S 47 52 33408342 A longitudinal study of SARS-CoV-2-infected patients reveals a high correlation between neutralizing antibodies and COVID-19 severity. Finally, we found that the D614G mutation in the spike protein, which has recently been identified as the current major variant in Europe, does not allow neutralization escape. 2021 Cellular & molecular immunology Abstract SARS_CoV_2 D614G 27 32 S 49 54 33410223 A main event and multiple introductions of SARS-CoV-2 initiated the COVID-19 epidemic in Greece. A dominant variant, encompassing the G614D amino acid substitution, spread through a major virus dispersal event, and sporadic introductions of rare variants characterized the local initiation of the epidemic. 2021 Journal of medical virology Abstract SARS_CoV_2 G614D 37 42 33412089 COVID-19-neutralizing antibodies predict disease severity and survival. In addition to neutralization of wild-type SARS-CoV-2, patient sera were also able to neutralize the recently emerged SARS-CoV-2 mutant D614G, suggesting cross-protection from reinfection by either strain. 2021 Cell Abstract SARS_CoV_2 D614G 136 141 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. Among the numerous mutations detected, 14,408C>T and 23,403A>G mutations resulting in RNA-dependent RNA polymerase (RdRp) P323L and spike protein D614G mutations, respectively, were found predominantly in severely affected group (>82%) compared with mildly affected group (<46%, p < 0.001). 2020 Genomics & informatics Abstract SARS_CoV_2 D614G;P323L;A403G;C408T 146;122;56;42 151;127;62;48 RdRp;S;RdRP 86;132;116 114;137;120 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. The 241C>T mutation in the non-coding region of the genome was also found predominantly in severely affected group (p < 0.001). 2020 Genomics & informatics Abstract SARS_CoV_2 C241T 4 10 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. The 3,037C>T, a silent mutation, also appeared in relatively high frequency in severely affected group compared with mildly affected group, but the difference was not statistically significant (p = 0.06). 2020 Genomics & informatics Abstract SARS_CoV_2 C037T 6 12 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. We concluded that spike protein D614G and RdRp P323L mutations in SARS-CoV-2 are associated with severity of COVID-19. 2020 Genomics & informatics Abstract SARS_CoV_2 D614G;P323L 32;47 37;52 S;RdRP 18;42 23;46 COVID-19 109 117 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. Spike D614G (and nsp12 L314P) mutations were most frequent (> 86%), whilst spike A222V/L18F have recently increased. 2021 Genome medicine Abstract SARS_CoV_2 A222V;D614G;L314P;L18F 81;6;23;87 86;11;28;91 S;S;Nsp12 0;75;17 5;80;22 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. Two new SARS-CoV-2 lineages with the N501Y mutation in the receptor-binding domain of the spike protein spread rapidly in the United Kingdom. 2021 Euro surveillance Abstract SARS_CoV_2 N501Y 37 42 S 90 95 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Despite a low mutation rate, isolates with the D614G substitution in the S protein appeared early during the pandemic and are now the dominant form worldwide. 2021 Cell reports Abstract SARS_CoV_2 D614G 47 52 S 73 74 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Here, we explore S conformational changes and the effects of the D614G mutation on a soluble S ectodomain construct. 2021 Cell reports Abstract SARS_CoV_2 D614G 65 70 S;S 17;93 18;94 33418186 Mutation analysis of the spike protein in Italian feline infectious peritonitis virus and feline enteric coronavirus sequences. Mutation M1058L was detected in 16/18 FCoV-I and 1/1 FCoV-II strains associated with FIP, while change S1060A was presented by two FIPV strains. 2021 Research in veterinary science Abstract SARS_CoV_2 M1058L;S1060A 9;103 15;109 33418186 Mutation analysis of the spike protein in Italian feline infectious peritonitis virus and feline enteric coronavirus sequences. Recently, two amino acid substitutions, M1058L and S1060A, within the spike protein have been associated to the FECV/FIPV virulence change. 2021 Research in veterinary science Abstract SARS_CoV_2 M1058L;S1060A 40;51 46;57 S 70 75 33429204 PfAgo-based detection of SARS-CoV-2. Moreover, this platform was also applied to identify SARS-CoV-2 D614G mutant due to its single-nucleotide specificity. 2021 Biosensors & bioelectronics Abstract SARS_CoV_2 D614G 64 69 33433004 Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) has been identified to be a mutation hot spot, with the P323L mutation being commonly observed in viral genomes isolated from North America. 2021 Journal of medical virology Abstract SARS_CoV_2 P323L 153 158 RdRp;RdRP 61;91 89;95 COVID-19 0 47 33436577 A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein. The CT-P59 mAb potently neutralizes SARS-CoV-2 isolates including the D614G variant without antibody-dependent enhancement effect. 2021 Nature communications Abstract SARS_CoV_2 D614G 70 75 33441410 An Observational Laboratory-Based Assessment of SARS-CoV-2 Molecular Diagnostics in Benin, Western Africa. Genomic surveillance showed near-simultaneous introduction of distinct SARS-CoV-2 lineages termed A.4 and B.1, including the D614G spike protein variant potentially associated with higher transmissibility from travelers from six different European and African countries during March-April 2020. 2021 mSphere Abstract SARS_CoV_2 D614G 125 130 S 131 136 33441410 An Observational Laboratory-Based Assessment of SARS-CoV-2 Molecular Diagnostics in Benin, Western Africa. SARS-CoV-2 genomic surveillance confirmed a high genomic diversity in Benin introduced by travelers returning from Europe and other African countries, including early circulation of the D614G spike mutation associated with potentially higher transmissibility. 2021 mSphere Abstract SARS_CoV_2 D614G 186 191 S 192 197 33442690 Landscape analysis of escape variants identifies SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Some variants ( e.g ., S477N) were resistant to neutralization by multiple mAbs, whereas others ( e.g ., E484K) escaped neutralization by convalescent sera, suggesting some humans induce a narrow repertoire of neutralizing antibodies. 2021 bioRxiv Abstract SARS_CoV_2 E484K;S477N 105;23 110;28 33442691 Neutralization of N501Y mutant SARS-CoV-2 by BNT162b2 vaccine-elicited sera. Rapidly spreading variants of SARS-CoV-2 that have arisen in the United Kingdom and South Africa share the spike N501Y substitution, which is of particular concern because it is located in the viral receptor binding site for cell entry and increases binding to the receptor (angiotensin converting enzyme 2). 2021 bioRxiv Abstract SARS_CoV_2 N501Y 113 118 S 107 112 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Further, we decoded 13 single nucleotide polymorphisms across 13 unique SARS-CoV-2 genomes within this region of the S gene, with one non-synonymous mutation (P681H) found in the two Hawaii strains. 2021 bioRxiv Abstract SARS_CoV_2 P681H 159 164 S 117 118 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The P681H mutation has unique and emerging characteristics with a significant exponential increase in worldwide frequency when compared to the plateauing of the now universal D614G mutation. 2021 bioRxiv Abstract SARS_CoV_2 D614G;P681H 175;4 180;9 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The P681H mutation is also characteristic of the new SARS-CoV-2 variants from the United Kingdom and Nigeria. 2021 bioRxiv Abstract SARS_CoV_2 P681H 4 9 33447831 Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces shedding of SARS-CoV-2 D614G in rhesus macaques. Here we investigate whether intranasally administered ChAdOx1 nCoV-19 reduces shedding, using a SARS-CoV-2 virus with the D614G mutation in the spike protein. 2021 bioRxiv Abstract SARS_CoV_2 D614G 122 127 S 144 149 33458832 World-wide tracking of major SARS-CoV-2 genome haplotypes in sequences of June 1 to November 15, 2020 and discovery of rapid expansion of a new haplotype. Also, 23403A>G that causes p. 2021 Journal of medical virology Abstract SARS_CoV_2 A23403G 6 14 33458832 World-wide tracking of major SARS-CoV-2 genome haplotypes in sequences of June 1 to November 15, 2020 and discovery of rapid expansion of a new haplotype. Asp614Gly in the spike protein and is one of the defining variations of the haplotype group H1, was becoming increasingly prevalent. 2021 Journal of medical virology Abstract SARS_CoV_2 D614G 0 9 S 17 22 33458832 World-wide tracking of major SARS-CoV-2 genome haplotypes in sequences of June 1 to November 15, 2020 and discovery of rapid expansion of a new haplotype. Consistent with the reports on 23403A>G, H1 haplotype frequency increased world-wide; among August to November sequences, only 0.3% were associated with non-H1 haplotypes. 2021 Journal of medical virology Abstract SARS_CoV_2 A23403G 31 39 33458832 World-wide tracking of major SARS-CoV-2 genome haplotypes in sequences of June 1 to November 15, 2020 and discovery of rapid expansion of a new haplotype. The new sub-haplotype is defined by seven sequence variations, one of which causes Ala222Val in the spike protein. 2021 Journal of medical virology Abstract SARS_CoV_2 A222V 83 92 S 100 105 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. BACKGROUND: In the initial few months of the COVID-19 pandemic, two distinct strains of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) were identified (L and S strain) based on a tightly linked SNP between two widely separated nucleotides at location 8782 (ORF1ab T8517C) and position 28,144 (ORF8: C251T, codon S84L). 2021 Indian journal of medical microbiology Abstract SARS_CoV_2 C251T;S84L;T8517C 313;326;278 318;330;284 ORF1ab;ORF8;S 271;307;172 277;311;173 COVID-19;COVID-19 95;45 135;53 33467732 Intranasal Infection of Ferrets with SARS-CoV-2 as a Model for Asymptomatic Human Infection. Viral genomic sequence analysis in samples from three animals identified the Y453F nucleotide substitution relative to the inoculum. 2021 Viruses Abstract SARS_CoV_2 Y453F 77 82 33468688 Engineering a Reliable and Convenient SARS-CoV-2 Replicon System for Analysis of Viral RNA Synthesis and Screening of Antiviral Inhibitors. Some viral variations, such as 5'UTR-C241T and ORF8-(T28144C) L84S mutation, also exhibit their different impact upon viral replication. 2021 mBio Abstract SARS_CoV_2 L84S;T28144C;C241T 62;53;37 66;60;42 5'UTR;ORF8 31;47 36;51 33468695 SARS-CoV-2 Infection Severity Is Linked to Superior Humoral Immunity against the Spike. Additionally, we revealed that antibodies against the spike are still capable of binding the D614G spike mutant and cross-react with the SARS-CoV-1 receptor binding domain. 2021 mBio Abstract SARS_CoV_2 D614G 93 98 RBD;S;S 148;54;99 171;59;104 33468702 SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia. We found that all of our isolates contained the D614G substitution in the viral spike and belong to lineages variously designated B.1, Nextstrain clade 20A or 20C, and GISAID clade G or GH. 2021 mBio Abstract SARS_CoV_2 D614G 48 53 S 80 85 33469576 Neutralization of N501Y mutant SARS-CoV-2 by BNT162b2 vaccine-elicited sera. Rapidly spreading variants of SARS-CoV-2 that have arisen in the United Kingdom and South Africa share the spike N501Y substitution, which is of particular concern because it is located in the viral receptor binding site for cell entry and increases binding to the receptor. 2021 Research square Abstract SARS_CoV_2 N501Y 113 118 S 107 112 33469580 CAR-NK Cells Effectively Target the D614 and G614 SARS-CoV-2-infected Cells. Here, we improve upon a novel approach for the generation of CAR-NK cells for targeting SARS-CoV-2 and its D614G mutant. 2021 bioRxiv Abstract SARS_CoV_2 D614G 107 112 33469580 CAR-NK Cells Effectively Target the D614 and G614 SARS-CoV-2-infected Cells. S309-CAR-NK cells can specifically bind to pseudotyped SARS-CoV-2 virus and its D614G mutant. 2021 bioRxiv Abstract SARS_CoV_2 D614G 80 85 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. Remarkably, a mutation that leads to an I300F change in the nsp2 protein and a mutation leading to D614G change in the spike protein were prevalent in SARS-CoV-2 genomic sequences, and might have influenced the epidemiological properties of the virus in Bangladesh. 2021 PloS one Abstract SARS_CoV_2 D614G;I300F 99;40 104;45 S;Nsp2 119;60 124;64 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. D614G as a spike mutant of SARS-CoV-2 previously identified as an associated risk factor with a high mortality rate of this virus. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 D614G 0 5 S 11 16 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. Using structural bioinformatics, our group determined that D614G mutation could cause extensive changes in SARS-CoV-2 behavior including the secondary structure, receptor binding pattern, 3D conformation, and stability of it.Communicated by Ramaswamy H. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 D614G 59 64 33476695 The 442th amino acid residue of the spike protein is critical for the adaptation to bat hosts for SARS-related coronaviruses. On the contrary, the reverse substitution in WIV1 S (S442Y) significantly attenuated the pseudovirus utilization of bat, civet and human ACE2s for cell entry, and reduced its binding affinity with the three ACE2s. 2021 Virus research Abstract SARS_CoV_2 S442Y 53 58 S 50 51 33476695 The 442th amino acid residue of the spike protein is critical for the adaptation to bat hosts for SARS-related coronaviruses. The results showed that the single amino acid substitution Y442S in the RBD of BJ01 S enhanced its utilization of bat ACE2 and its binding affinity to bat ACE2. 2021 Virus research Abstract SARS_CoV_2 Y442S 59 64 RBD;S 72;84 75;85 33477951 Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. Evolutionary and spatial analyses revealed clustering in the GH clade, characterized by three amino acid substitutions in spike gene (D614G), RdRp (P323L) and NS3 (Q57H). 2021 Viruses Abstract SARS_CoV_2 D614G;P323L;Q57H 134;148;164 139;153;168 S;RdRP;NS3 122;142;159 127;146;162 33477951 Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. P323L causes conformational change near nsp8 binding site that might affect virus replication and transcription. 2021 Viruses Abstract SARS_CoV_2 P323L 0 5 Nsp8 40 44 33478625 Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020. This approach revealed mutations co-occurring with DeltaH69/DeltaV70 including S:N501Y in the VOC. 2021 Euro surveillance Abstract SARS_CoV_2 N501Y 81 86 S 79 80 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. Genetic diversity analysis showed two main regions that harbor L84S and S24L. 2021 Gene reports Abstract SARS_CoV_2 L84S;S24L 63;72 67;76 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. L84S is by far the most predominant mutation, followed by S24L that appeared first in USA. 2021 Gene reports Abstract SARS_CoV_2 S24L;L84S 58;0 62;4 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. Phylogenetic analysis of ORF8 variants revealed the appearance of small clades with that of L84S being closer to bats. 2021 Gene reports Abstract SARS_CoV_2 L84S 92 96 ORF8 25 29 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. A significant increase in the proportion of D614G was noticed from (63.0%) in February 2020, to (98.5%) in June 2020 (p < 0.001). 2021 Heliyon Abstract SARS_CoV_2 D614G 44 49 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. CONCLUSIONS: The D614G mutation appeared to be taking over the COVID-19 infections in the MENA. 2021 Heliyon Abstract SARS_CoV_2 D614G 17 22 COVID-19 63 71 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. RESULT: A total of 553 MENA sequences were analyzed and the most frequent S gene mutations included: D614G = 435, Q677H = 8, and V6F = 5. 2021 Heliyon Abstract SARS_CoV_2 D614G;Q677H;V6F 101;114;129 106;119;132 S 74 75 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. This study aimed to identify mutations in the S gene among SARS-CoV-2 sequences collected in the Middle East and North Africa (MENA), focusing on the D614G mutation, that has a presumed fitness advantage. 2021 Heliyon Abstract SARS_CoV_2 D614G 150 155 S 46 47 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. All the minor group mutations, except 11083G>T (L37F, NSP6 gene), were unique to the Indian isolates. 2020 JMIR bioinformatics and biotechnology Abstract SARS_CoV_2 G11083T;L37F 38;48 46;52 Nsp6 54 58 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. The secondary structure of the RNA-dependent RNA polymerase/nonstructural protein NSP12 was predicted with respect to the novel A97V mutation. 2020 JMIR bioinformatics and biotechnology Abstract SARS_CoV_2 A97V 128 132 RdRP;Nsp12 31;60 59;87 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. We highlight two interesting mutations found in genes N (P13L) and ORF3a (Q57H). 2021 PloS one Abstract SARS_CoV_2 P13L;Q57H 57;74 61;78 ORF3a;N 67;54 72;55 33498225 Biological and Clinical Consequences of Integrin Binding via a Rogue RGD Motif in the SARS CoV-2 Spike Protein. The highly infectious variant, B.1.1.7 (or VUI 202012/01), includes a receptor-binding domain amino acid replacement, N501Y, that could potentially provide the RGD motif with enhanced access to cell-surface integrins, with consequent clinical impacts. 2021 Viruses Abstract SARS_CoV_2 N501Y 118 123 33501442 mRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants. Geometric mean titer (GMT) of human sera from clinical trial participants in VSV PsVN assay using D614G spike was 1/1852. 2021 bioRxiv Abstract SARS_CoV_2 D614G 98 103 S 104 109 33501442 mRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants. Here, using two orthogonal VSV and lentivirus PsVN assays expressing spike variants of 20E (EU1), 20A.EU2, D614G-N439, mink cluster 5, B.1.1.7, and B.1.351 variants, we assessed the neutralizing capacity of sera from human subjects or non-human primates (NHPs) that received mRNA-1273. 2021 bioRxiv Abstract SARS_CoV_2 D614G 107 112 S 69 74 33501442 mRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants. Similarly, sera from NHPs immunized with 30 or 100mug of mRNA-1273 had VSV PsVN GMTs of ~ 1/323 or 1/404, respectively, against the full B.1.351 spike variant with a ~ 5 to 10-fold reduction compared to D614G. 2021 bioRxiv Abstract SARS_CoV_2 D614G 203 208 S 145 150 33501442 mRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants. VSV pseudoviruses with spike containing K417N-E484K-N501Y-D614G and full B.1.351 mutations resulted in 2.7 and 6.4-fold GMT reduction, respectively, when compared to the D614G VSV pseudovirus. 2021 bioRxiv Abstract SARS_CoV_2 D614G;K417N;D614G;E484K;N501Y 170;40;58;46;52 175;45;63;51;57 S 23 28 33501451 mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. However, activity against SARS-CoV-2 variants encoding E484K or N501Y or the K417N:E484K:N501Y combination was reduced by a small but significant margin. 2021 bioRxiv Abstract SARS_CoV_2 E484K;K417N;N501Y;E484K;N501Y 55;77;64;83;89 60;82;69;88;94 33501451 mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. However, neutralization by 14 of the 17 most potent mAbs tested was reduced or abolished by either K417N, or E484K, or N501Y mutations. 2021 bioRxiv Abstract SARS_CoV_2 E484K;K417N;N501Y 109;99;119 114;104;124 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. Interestingly, one mutation in the receptor binding domain of the S protein results in the change of an asparagine to tyrosine residue at position 501 (N501Y). 2021 medRxiv Abstract SARS_CoV_2 N501Y 152 157 RBD;S 35;66 58;67 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. We show that human convalescent and post vaccination sera can neutralize the newly emerging N501Y virus variant with similar efficiency as that of the reference USA-WA1/2020 virus, suggesting that current SARS-CoV-2 vaccines will protect against the 20B/501Y.V1 strain. 2021 medRxiv Abstract SARS_CoV_2 N501Y 92 97 33502471 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Replication and Tropism in the Lungs, Airways, and Vascular Endothelium of Patients With Fatal Coronavirus Disease 2019: An Autopsy Case Series. The D614G variant was detected in 9 RT-PCR-positive case patients. 2021 The Journal of infectious diseases Abstract SARS_CoV_2 D614G 4 9 33503420 The immunodominant and neutralization linear epitopes for SARS-CoV-2. We find that the immunodominant epitopes of individuals with domestic (China) SARS-CoV-2 are different from those of individuals with imported (Europe) SARS-CoV-2, which may be caused by mutations on the S (G614D) and N proteins. 2021 Cell reports Abstract SARS_CoV_2 G614D 207 212 N;S 218;204 219;205 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. CONCLUSION: Our results have shown low mutational sensitivity in all variants except to D614G the one with the most likely neutral mutational sensitivity that all variants might not explicitly affect the function of spike glycoprotein. 2021 Biochemistry and biophysics reports Abstract SARS_CoV_2 D614G 88 93 S 216 234 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. GENERAL SIGNIFICANCE: Studying mutations such as D614G in deep is essential to control the pandemic in terms of immune systems, antibodies, or even vaccines. 2021 Biochemistry and biophysics reports Abstract SARS_CoV_2 D614G 49 54 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. However, D614G might change the viral conformational plasticity and hence a potential viral fitness gain but one must be cautious about drawing any concrete conclusions about the severity of symptoms and viral transmission from genomic data only. 2021 Biochemistry and biophysics reports Abstract SARS_CoV_2 D614G 9 14 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. The second and the dominant variant, represented by 62%, showed aspartate a coil amino acid substitution to glycine an extracellular amino acid at D614G located in the spike recognition binding site. 2021 Biochemistry and biophysics reports Abstract SARS_CoV_2 D614G 147 152 S 168 173 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. The third variant, represented by 5%, showed aspartate substitution to tyrosine at D1139Y, and the fourth variant, represented by 5% glycine substitution to serine at G1167S. 2021 Biochemistry and biophysics reports Abstract SARS_CoV_2 D1139Y;G1167S 83;167 89;173 33506644 Genotype-phenotype correlation identified a novel SARS-CoV-2 variant possibly linked to severe disease. A missense (Q271R) and synonymous (R41R) mutation in the S and N proteins, respectively, were identified in 2/27 patients with severe COVID-19 but not in patients with mild or moderate disease (0/86; p = .05, Fisher's Exact Test). 2022 Transboundary and emerging diseases Abstract SARS_CoV_2 Q271R;R41R 12;35 17;39 N;S 63;57 64;58 COVID-19 134 142 33506644 Genotype-phenotype correlation identified a novel SARS-CoV-2 variant possibly linked to severe disease. Majority of sequenced strains (N = 60, 52%) were from the European cluster consistent with the higher infectivity rates associated with the D614G mutation carried by most strains in this cluster. 2022 Transboundary and emerging diseases Abstract SARS_CoV_2 D614G 140 145 33508515 Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. A total of 26,642 high quality SARS-CoV-2 sequences were included and the A23,403G (S:D614G) variant was found to be in linkage disequilibrium with C14,408 U (RdRp: P323L). 2021 Infection, genetics and evolution Abstract SARS_CoV_2 P323L;D614G 165;86 170;91 RdRP;S 159;84 163;85 33508515 Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. Network analysis revealed the presence of two major clusters of viral haplotypes, namely, clade-G and a variant of clade L [Lv] having the RdRp:A97V amino acid change. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 A97V 144 148 RdRP 139 143 33509990 Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq. There was a D614G mutation in the spike protein-coding sequence. 2021 Microbiology resource announcements Abstract SARS_CoV_2 D614G 12 17 S 34 39 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. Particularly, it allowed us to strictly discriminate key mutation of the SARS-CoV-2 variant, D614G, which may induce higher epidemic and pathogenetic risk. 2021 Analytical chemistry Abstract SARS_CoV_2 D614G 93 98 33513449 Different SARS-CoV-2 haplotypes associate with geographic origin and case fatality rates of COVID-19 patients. Using an new alternative bioinformatics approach we were able to confirm that the presence of the D614G mutation correlates with increased case severity in a sample of 127 sequences from a shared geographic origin in the US (p = 0.018). 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G 98 103 33515713 Mannose binding lectin gene 2 (rs1800450) missense variant may contribute to development and severity of COVID-19 infection. DNAs of all patients and controls were examined for the codon 54 A/B (gly54asp: rs1800450) variation in exon 1 of the MBL2 gene. 2021 Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases Abstract SARS_CoV_2 G54D 70 78 Exon 104 108 33524589 A global analysis of replacement of genetic variants of SARS-CoV-2 in association with containment capacity and changes in disease severity. CONCLUSIONS: SARS-CoV-2 variant lineage G* (S-D614G) replaced older lineages more efficiently in countries with lower containment capacity, and its possible association with increased disease severity deserves further investigation. 2021 Clinical microbiology and infection Abstract SARS_CoV_2 D614G 46 51 S 44 45 33524589 A global analysis of replacement of genetic variants of SARS-CoV-2 in association with containment capacity and changes in disease severity. RESULTS: At the global level, variant lineage G*, characterized by the S-D614G mutation, replaced the older lineages L and S in March 2020. 2021 Clinical microbiology and infection Abstract SARS_CoV_2 D614G 73 78 S 71 72 33524990 BNT162b vaccines protect rhesus macaques from SARS-CoV-2. BNT162b2 encodes the full-length transmembrane S glycoprotein, locked in its prefusion conformation by the substitution of two residues with proline (S(K986P/V987P); hereafter, S(P2) (also known as P2 S)). 2021 Nature Abstract SARS_CoV_2 K986P;S986P;V987P 152;152;158 157;157;163 S;S;S 47;150;177 61;151;178 33525415 Chloroquine and Hydroxychloroquine Interact Differently with ACE2 Domains Reported to Bind with the Coronavirus Spike Protein: Mediation by ACE2 Polymorphism. The frequencies of these allele variants range from 3.88 x 10-3 to 5.47 x 10-6 for rs4646116 (K26R) and rs1238146879 (P426A), respectively. 2021 Molecules (Basel, Switzerland) Abstract SARS_CoV_2 K26R;P426A 94;118 98;123 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Among the 12 mutations, three mutations (Y160H, D210Y and S171L) also lead to alterations in secondary structure and protein disorder parameters of the Orf3a protein. 2021 Biochemistry and biophysics reports Abstract SARS_CoV_2 D210Y;S171L;Y160H 48;58;41 53;63;46 ORF3a 152 157 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. Three S protein variants: Wuhan reference, D614G, and Y28H were identified predicted to possess different binding affinities to host ACE2. 2021 PloS one Abstract SARS_CoV_2 D614G;Y28H 43;54 48;58 S 6 7 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? As anticipated, our calculations capture previously reported mutations that arose in the first months of the pandemic, such as D614G (Spike), P323L (NSP12), and R203K/G204R (Nucleocapsid), but they also identify more recent mutations, such as A222V and L18F (Spike) and A220V (Nucleocapsid), among others. 2021 Biology Abstract SARS_CoV_2 A220V;A222V;D614G;L18F;P323L;R203K;G204R 270;243;127;253;142;161;167 275;248;132;257;147;166;172 N;N;S;S;Nsp12 174;277;134;259;149 186;289;139;264;154 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. We determined the high resolution structure of wild-type PLpro, the active site C111S mutant, and their complexes with inhibitors. 2021 Nature communications Abstract SARS_CoV_2 C111S 80 85 33531709 Sixteen novel lineages of SARS-CoV-2 in South Africa. The newly identified C lineage of SARS-CoV-2, C.1, which has 16 nucleotide mutations as compared with the original Wuhan sequence, including one amino acid change on the spike protein, D614G (ref. 2021 Nature medicine Abstract SARS_CoV_2 D614G 185 190 S 170 175 33532652 ACE2 and FURIN variants are potential predictors of SARS-CoV-2 outcome: A time to implement precision medicine against COVID-19. We identified two activating variants (K26R and N720D) in the ACE2 gene that are more common in Europeans than in the Middle Eastern, East Asian, and African populations. 2021 Heliyon Abstract SARS_CoV_2 N720D;K26R 48;39 53;43 33532652 ACE2 and FURIN variants are potential predictors of SARS-CoV-2 outcome: A time to implement precision medicine against COVID-19. We postulate that K26R can activate ACE2 and facilitate binding to S-protein RBD while N720D enhances TMPRSS2 cutting and, ultimately, viral entry. 2021 Heliyon Abstract SARS_CoV_2 K26R;N720D 18;87 22;92 RBD;S 77;67 80;68 33532763 Increased Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7 to Antibody Neutralization. Considerable viral evolution has occurred since, including variants with a D614G mutation that have become dominant. 2021 Research square Abstract SARS_CoV_2 D614G 75 80 33532763 Increased Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7 to Antibody Neutralization. Findings on B.1.351 are more worrisome in that this variant is not only refractory to neutralization by most NTD mAbs but also by multiple potent mAbs to the receptor-binding motif on RBD, largely due to an E484K mutation. 2021 Research square Abstract SARS_CoV_2 E484K 207 212 RBD 184 187 33532768 Genetic and structural basis for recognition of SARS-CoV-2 spike protein by a two-antibody cocktail. Nonetheless, both COV2-2196 and COV2130 showed strong neutralizing activity against SARS-CoV-2 strain with recent variations of concern including E484K, N501Y, and D614G substitutions. 2021 bioRxiv Abstract SARS_CoV_2 D614G;E484K;N501Y 164;146;153 169;151;158 33532771 Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera. We engineered three SARS-CoV-2 viruses containing key spike mutations from the newly emerged United Kingdom (UK) and South African (SA) variants: N501Y from UK and SA; 69/70-deletion+N501Y+D614G from UK; and E484K+N501Y+D614G from SA. 2021 bioRxiv Abstract SARS_CoV_2 E484K;N501Y;D614G;D614G;N501Y;N501Y 208;146;189;220;183;214 213;151;194;225;188;219 S 54 59 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. Findings on B.1.351 are more worrisome in that this variant is not only refractory to neutralization by most NTD mAbs but also by multiple individual mAbs to the receptor-binding motif on RBD, largely due to an E484K mutation. 2021 bioRxiv Abstract SARS_CoV_2 E484K 211 216 RBD 188 191 33532796 The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. For some of the convalescent donor sera with low or moderate IgG against the SARS-CoV-2 spike, the drop in neutralization efficiency resulted in neutralization ID50 values similar to negative control samples, with low or even absence of neutralization of the E484K rSARS-CoV-2. 2021 medRxiv Abstract SARS_CoV_2 E484K 259 264 S 88 93 33532796 The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. However, human sera with high neutralization titers against the USA-WA1/2020 strain were still able to neutralize the E484K rSARS-CoV-2. 2021 medRxiv Abstract SARS_CoV_2 E484K 118 123 33532796 The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. Serum neutralization efficiency was lower against the E484K rSARS-CoV-2 (vaccination samples: 3.4 fold; convalescent low IgG: 2.4 fold, moderate IgG: 4.2 fold and high IgG: 2.6 fold) compared to USA-WA1/2020. 2021 medRxiv Abstract SARS_CoV_2 E484K 54 59 33532796 The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. The glutamate (E) to Lysine (K) substitution at position 484 (E484K) in the receptor binding domain (RBD) of the spike protein is present in the rapidly spreading variants of concern belonging to the B.1.351 and P.1 lineages. 2021 medRxiv Abstract SARS_CoV_2 E484K 62 67 RBD;S;RBD 76;113;101 99;118;104 33532796 The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. We performed in vitro microneutralization assays with both the USA-WA1/2020 virus and a recombinant (r)SARS-CoV-2 virus that is identical to USA-WA1/2020 except for the E484K mutation introduced in the spike RBD. 2021 medRxiv Abstract SARS_CoV_2 E484K 169 174 S;RBD 202;208 207;211 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Some variants (e.g., S477N) were resistant to neutralization by multiple mAbs, whereas others (e.g., E484K) escaped neutralization by convalescent sera. 2021 Cell host & microbe Abstract SARS_CoV_2 E484K;S477N 101;21 106;26 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. All seven GR strains were D614G variants with R202K and G203R mutations in N. 2021 PloS one Abstract SARS_CoV_2 D614G;G203R;R202K 26;56;46 31;61;51 N 75 76 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. Comparing the first- and second-wave GR strains, mutation rate was 1.17-1.36 x 10-3 base substitutions per site per year; in addition, amino acid changes occurred at S1361P and P3371S in ORF1a, A314V in ORF1b, and P151L in N. 2021 PloS one Abstract SARS_CoV_2 A314V;P151L;P3371S;S1361P 194;214;177;166 199;219;183;172 ORF1a;N 187;223 192;224 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. The predominant D614G variants and a new form of ORF8 deletion in Hiroshima provide the clue for role of viral factor in local outbreaks of SARS-CoV-2. 2021 PloS one Abstract SARS_CoV_2 D614G 16 21 ORF8 49 53 33545711 SARS-CoV-2 evolution during treatment of chronic infection. However, after convalescent plasma therapy, we observed large, dynamic shifts in the viral population, with the emergence of a dominant viral strain that contained a substitution (D796H) in the S2 subunit and a deletion (DeltaH69/DeltaV70) in the S1 N-terminal domain of the spike protein. 2021 Nature Abstract SARS_CoV_2 D796H 180 185 S;N 275;250 280;251 33545711 SARS-CoV-2 evolution during treatment of chronic infection. In vitro, the spike double mutant bearing both DeltaH69/DeltaV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, while maintaining infectivity levels that were similar to the wild-type virus.The spike substitution mutant D796H appeared to be the main contributor to the decreased susceptibility to neutralizing antibodies, but this mutation resulted in an infectivity defect. 2021 Nature Abstract SARS_CoV_2 D796H;D796H 69;248 74;253 S;S 14;222 19;227 33545711 SARS-CoV-2 evolution during treatment of chronic infection. The spike deletion mutant DeltaH69/DeltaV70 had a twofold higher level of infectivity than wild-type SARS-CoV-2, possibly compensating for the reduced infectivity of the D796H mutation. 2021 Nature Abstract SARS_CoV_2 D796H 170 175 S 4 9 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. In addition, among the sequence variants observed in >=0.5% clinical isolates, including P323L, none were located near the established polymerase active site or sites critical for the RDV mechanism of inhibition. 2021 Antiviral research Abstract SARS_CoV_2 P323L 89 94 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. Overall, low genetic variation was observed with only 12 amino acid substitutions present in the entire RNA replication complex in >=0.5% of analyzed sequences with the highest overall frequency (82.2%) observed for nsp12 P323L that consistently increased over time. 2021 Antiviral research Abstract SARS_CoV_2 P323L 222 227 Nsp12 216 221 33551188 Fast and cost-effective screening for SARS-CoV-2 variants in a routine diagnostic setting. In case of a positive test for SARS-CoV-2 and corresponding clinical and anamnestic indications, a second qPCR for the mutation N501Y can follow and deliver the result to public health authorities and to the treating physician within a few hours. 2021 Dental materials Abstract SARS_CoV_2 N501Y 128 133 33551188 Fast and cost-effective screening for SARS-CoV-2 variants in a routine diagnostic setting. METHODS: A rapid procedure using qPCR is described to provide clinicians with information about the two currently most prevalent variants (B1.1.7 and B1.351) that harbour receptor binding domain mutation N501Y. 2021 Dental materials Abstract SARS_CoV_2 N501Y 204 209 RBD 171 194 33551188 Fast and cost-effective screening for SARS-CoV-2 variants in a routine diagnostic setting. The N501Y specific assay only delivers an amplification signal if the Y501 variant is present. 2021 Dental materials Abstract SARS_CoV_2 N501Y 4 9 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. Two evolved subtypes (A2 and A2a) carry a non-synonymous Spike protein mutation (D614G). 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G 81 86 S 57 62 33556653 The G614 pandemic SARS-CoV-2 variant is not more pathogenic than the original D614 form in adult Syrian hamsters. Dynamic tracking of variant frequencies among viruses circulating in the global pandemic has revealed the emergence and dominance of a D614G mutation in the SARS-CoV-2 spike protein. 2021 Virology Abstract SARS_CoV_2 D614G 135 140 S 168 173 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. The most prevalent aa changes were D614G (81.5%) in the spike protein, followed by the R203K and G204R combination (37%) in the nucleocapsid protein. 2021 Viruses Abstract SARS_CoV_2 D614G;G204R;R203K 35;97;87 40;102;92 N;S 128;56 140;61 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Among S variants, the D614G mutant shows the highest cell entry, as supported by structural and binding analyses. 2021 Nature communications Abstract SARS_CoV_2 D614G 22 27 S 6 7 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Nevertheless, the D614G mutation does not affect neutralization by antisera against prototypic viruses. 2021 Nature communications Abstract SARS_CoV_2 D614G 18 23 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Taken together, we conclude that the D614G mutation increases cell entry by acquiring higher affinity to ACE2 while maintaining neutralization susceptibility. 2021 Nature communications Abstract SARS_CoV_2 D614G 37 42 33558635 Potent neutralization of clinical isolates of SARS-CoV-2 D614 and G614 variants by a monomeric, sub-nanomolar affinity nanobody. Furthermore, W25 potently neutralizes SARS-CoV-2 wild type and the D614G variant with IC50 values in the nanomolar range, demonstrating its potential as antiviral agent. 2021 Scientific reports Abstract SARS_CoV_2 D614G 67 72 33558724 Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K and N501Y variants by BNT162b2 vaccine-elicited sera. We engineered three severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viruses containing key spike mutations from the newly emerged United Kingdom (UK) and South African (SA) variants: N501Y from UK and SA; 69/70-deletion + N501Y + D614G from UK; and E484K + N501Y + D614G from SA. 2021 Nature medicine Abstract SARS_CoV_2 D614G;D614G;E484K;N501Y;N501Y;N501Y 243;278;262;196;235;270 248;283;267;201;240;275 S 104 109 COVID-19 27 67 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. The mutations NSP10_R134S, NSP15_D335N, NSP16_I169L, NSP3_L431H, NSP3_P1292L and Spike_V6F occurred once in Moroccan sequences, with no record in other sequences worldwide. 2021 Biosafety and health Abstract SARS_CoV_2 D335N;I169L;L431H;P1292L;R134S 33;46;58;70;20 38;51;63;76;25 S;Nsp3;Nsp3 81;53;65 86;57;69 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. The mutations Spike_D614G and NSP12_P323L were present in all the 22 analyzed sequences, followed by N_G204R and N_R203K, which occurred in 9 among the 22 sequences. 2021 Biosafety and health Abstract SARS_CoV_2 D614G;G204R;P323L;R203K 20;103;36;115 25;108;41;120 S;Nsp12 14;30 19;35 33564768 Neutralization of viruses with European, South African, and United States SARS-CoV-2 variant spike proteins by convalescent sera and BNT162b2 mRNA vaccine-elicited antibodies. Analysis by antibody neutralization of pseudotyped viruses showed that convalescent sera from patients infected prior to the emergence of the variant viruses neutralized viruses with the B.1.1.7, B.1.351, COH.20G/677H Columbus Ohio, 20A.EU2 Europe and mink cluster 5 spike proteins with only a minor decrease in titer compared to that of the earlier D614G spike protein. 2021 bioRxiv Abstract SARS_CoV_2 D614G 350 355 S;S 267;356 272;361 33564768 Neutralization of viruses with European, South African, and United States SARS-CoV-2 variant spike proteins by convalescent sera and BNT162b2 mRNA vaccine-elicited antibodies. Serum specimens from individuals vaccinated with the BNT162b2 mRNA vaccine neutralized D614G virus with titers that were on average 7-fold greater than convalescent sera. 2021 bioRxiv Abstract SARS_CoV_2 D614G 87 92 33564768 Neutralization of viruses with European, South African, and United States SARS-CoV-2 variant spike proteins by convalescent sera and BNT162b2 mRNA vaccine-elicited antibodies. The B.1.1.7 and B.1.351 viruses were not more infectious than D614G on ACE2.293T cells in vitro but N501Y, an ACE2 contacting residue present in the B.1.1.7, B.1.351 and COH.20G/677H spike proteins caused higher affinity binding to ACE2, likely contributing to their increased transmissibility. 2021 bioRxiv Abstract SARS_CoV_2 D614G;N501Y 62;100 67;105 S 183 188 33564768 Neutralization of viruses with European, South African, and United States SARS-CoV-2 variant spike proteins by convalescent sera and BNT162b2 mRNA vaccine-elicited antibodies. The reduction in titer was attributable to the E484K mutation in the RBD. 2021 bioRxiv Abstract SARS_CoV_2 E484K 47 52 RBD 69 72 33564768 Neutralization of viruses with European, South African, and United States SARS-CoV-2 variant spike proteins by convalescent sera and BNT162b2 mRNA vaccine-elicited antibodies. These findings suggest that antibodies elicited by primary infection and by the BNT162b2 mRNA vaccine are likely to maintain protective efficacy against B.1.1.7 and most other variants but that the partial resistance of virus with the B.1.351 spike protein could render some individuals less well protected, supporting a rationale for the development of modified vaccines containing E484K. 2021 bioRxiv Abstract SARS_CoV_2 E484K 383 388 S 243 248 33564768 Neutralization of viruses with European, South African, and United States SARS-CoV-2 variant spike proteins by convalescent sera and BNT162b2 mRNA vaccine-elicited antibodies. Vaccine elicited antibodies neutralized virus with the B.1.1.7 spike protein with titers similar to D614G virus and neutralized virus with the B.1.351 spike with, on average, a 3-fold reduction in titer (1:500), a titer that was still higher than the average titer with which convalescent sera neutralized D614G (1:139). 2021 bioRxiv Abstract SARS_CoV_2 D614G;D614G 100;306 105;311 S;S 63;151 68;156 33564771 The basis of a more contagious 501Y.V1 variant of SARS-COV-2. Modeling analysis showed that the N501Y mutation would allow a potential aromatic ring-ring interaction and an additional hydrogen bond between the RBD and ACE2. 2021 bioRxiv Abstract SARS_CoV_2 N501Y 34 39 RBD 148 151 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. Here we used the experimental structure of the Spike RBD domain co-crystallized with part of the ACE2 receptor, several in silico methods and numerous experimental data reported recently to analyze the possible impacts of three amino acid replacements (Spike K417N, E484K, N501Y) with regard to ACE2 binding. 2021 International journal of molecular sciences Abstract SARS_CoV_2 E484K;K417N;N501Y 266;259;273 271;264;278 S;S;RBD 47;253;53 52;258;56 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. If indeed the South African strain has a high transmission level, this could be due to the N501Y replacement and/or to substitutions in regions located outside the direct Spike-ACE2 interface but not so much to the K417N and E484K replacements. 2021 International journal of molecular sciences Abstract SARS_CoV_2 E484K;K417N;N501Y 225;215;91 230;220;96 S 171 176 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. It is unclear if the N501Y substitution in the South African strain could counterbalance the K417N and E484K Spike replacements with regard to ACE2 binding. 2021 International journal of molecular sciences Abstract SARS_CoV_2 E484K;K417N;N501Y 103;93;21 108;98;26 S 109 114 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. We found that the N501Y replacement in this region of the interface (present in both the UK and South African strains) should be favorable for the interaction with ACE2, while the K417N and E484K substitutions (South African strain) would seem neutral or even unfavorable. 2021 International journal of molecular sciences Abstract SARS_CoV_2 E484K;K417N;N501Y 190;180;18 195;185;23 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Prediction results suggest that mutation D614G in the virus spike protein, which has attracted much attention from researchers, is unlikely to make changes in protein secondary structure and relative solvent accessibility. 2021 Scientific reports Abstract SARS_CoV_2 D614G 41 46 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. A novel variant of the SARS-CoV-2 virus carrying a point mutation in the Spike protein (D614G) has recently emerged and rapidly surpassed others in prevalence. 2021 eLife Abstract SARS_CoV_2 D614G 88 93 S 73 78 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. Furthermore, trans-complementation of SARS-CoV-2 virus with Spike D614G showed an increased infectivity in human cells. 2021 eLife Abstract SARS_CoV_2 D614G 66 71 S 60 65 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. Here, we perform site-directed mutagenesis on wild-type human-codon-optimized Spike to introduce the D614G variant. 2021 eLife Abstract SARS_CoV_2 D614G 101 106 S 78 83 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. The increased transduction with Spike D614G ranged from 1.3- to 2.4-fold in Caco-2 and Calu-3 cells expressing endogenous ACE2 and from 1.5- to 7.7-fold in A549ACE2 and Huh7.5ACE2 overexpressing ACE2. 2021 eLife Abstract SARS_CoV_2 D614G 38 43 S 32 37 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. This mutation is in linkage disequilibrium with an ORF1b protein variant (P314L), making it difficult to discern the functional significance of the Spike D614G mutation from population genetics alone. 2021 eLife Abstract SARS_CoV_2 D614G;P314L 154;74 159;79 S 148 153 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. Using multiple human cell lines, including human lung epithelial cells, we found that the lentiviral particles pseudotyped with Spike D614G are more effective at transducing cells than ones pseudotyped with wild-type Spike. 2021 eLife Abstract SARS_CoV_2 D614G 134 139 S;S 128;217 133;222 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. There were associations of P323L, D614G, R203K and G204R substitutions with disease severity. 2021 Pathogens (Basel, Switzerland) Abstract SARS_CoV_2 D614G;G204R;P323L;R203K 34;51;27;41 39;56;32;46 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. 2021 Pathogens (Basel, Switzerland) Abstract SARS_CoV_2 A23403G;C14408T;D614G;P323L 31;13;39;21 38;20;44;26 S;Nsp12 71;61 76;66 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein, emerged recently and have spread in Oceania and Europe. 2021 Pathogens (Basel, Switzerland) Abstract SARS_CoV_2 A1163T;G22992A;I120F;S477N 21;46;28;54 27;53;33;59 S;Nsp2 67;37 72;41 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. Mutational analysis revealed the presence of the D614G substitution in both the isolates. 2021 Microbiology resource announcements Abstract SARS_CoV_2 D614G 49 54 33579701 Insights into neutralizing antibody responses in individuals exposed to SARS-CoV-2 in Chile. We also identified samples with decreased or enhanced neutralization activity against the D614G spike variant compared with the wild type, indicating the relevance of this variant in host immunity. 2021 Science advances Abstract SARS_CoV_2 D614G 90 95 S 96 101 33579792 The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2. The majority of currently circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viruses have mutant spike glycoproteins that contain the D614G substitution. 2021 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 D614G 156 161 S 119 138 COVID-19 45 85 33580132 Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada. A heterozygous variant (C9994A) was detected by both sequencing platforms but filtered by the ARTIC network bioinformatic pipeline suggesting that heterozygous variants may be underreported in the SARS-CoV-2 literature. 2021 Scientific reports Abstract SARS_CoV_2 C9994A 24 30 33580132 Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada. The D614G point mutation was the predominate viral strain in our cohort (92.6%). 2021 Scientific reports Abstract SARS_CoV_2 D614G 4 9 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. As a result, we observed five dominant mutations involving three nonsynonymous mutations C28144T, C14408T and A23403G and two synonymous mutations T8782C, and C3037T. 2021 Briefings in bioinformatics Abstract SARS_CoV_2 A23403G;C14408T;C28144T;C3037T 110;98;89;159 117;105;96;165 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. Besides, we also observed two potential dominant nonsynonymous mutations C1059T and G25563T, which occurred in most of the strains in April 2020. 2021 Briefings in bioinformatics Abstract SARS_CoV_2 C1059T;G25563T 73;84 79;91 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. In addition, the A23403G mutation increases the spike-ACE2 interaction and finally leads to the enhancement of its infectivity. 2021 Briefings in bioinformatics Abstract SARS_CoV_2 A23403G 17 24 S 48 53 33587268 Making sense of spike D614G in SARS-CoV-2 transmission. Here we summarize the recent progress on the role of the D614G mutation in viral replication, pathogenesis, transmission, and vaccine and therapeutic antibody development. 2021 Science China. Life sciences Abstract SARS_CoV_2 D614G 57 62 33587268 Making sense of spike D614G in SARS-CoV-2 transmission. One prominent adaptive mutation is the asparagine-to-glycine substitution at amino acid position 614 in the viral spike protein (D614G), which has become dominant in the currently circulating virus strains. 2021 Science China. Life sciences Abstract SARS_CoV_2 N614G;D614G 39;129 100;134 S 114 119 33587268 Making sense of spike D614G in SARS-CoV-2 transmission. Since spike protein determines host ranges, tissue tropism, and pathogenesis through binding to the cellular receptor of angiotensin converting enzyme 2 (ACE2), the D614G mutation is hypothesized to enhance viral fitness in human host, leading to increased transmission during the global pandemic. 2021 Science China. Life sciences Abstract SARS_CoV_2 D614G 165 170 S 6 11 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. The most common, high impact variants were 10818delTinsG, 2772delCinsC, 14159delCinsC and 2789delAinsA. 2021 Microbial pathogenesis Abstract SARS_CoV_2 10818delTinsG;2789delAinsA 43;90 56;102 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. One of the top mutations, 27964C > T-(S24L) on ORF8, has an unusually strong gender dependence. 2021 Communications biology Abstract SARS_CoV_2 C27964T;S24L 26;38 36;42 ORF8 47 51 33594356 SARS-CoV-2 variants show resistance to neutralization by many monoclonal and serum-derived polyclonal antibodies. Several highly neutralizing mAbs engaging the receptor binding domain (RBD) or N-terminal domain (NTD) lost inhibitory activity against Wash SA-B.1.351 or recombinant variants with an E484K spike mutation. 2021 Research square Abstract SARS_CoV_2 E484K 184 189 RBD;S;RBD;N 46;190;71;79 69;195;74;80 33594365 Transformations, Lineage Comparisons, and Analysis of Down to Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein Including the UK Variant B.1.1.7. For the B.1.1.7 variant, we demonstrated the critical importance of D614G and N5017 on the structure and binding, respectively, of the Spike protein. 2021 bioRxiv Abstract SARS_CoV_2 D614G 68 73 S 135 140 33594365 Transformations, Lineage Comparisons, and Analysis of Down to Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein Including the UK Variant B.1.1.7. In addition, we demonstrate that the mutation N501Y may significantly increase the Spike protein binding to hACE2 cell receptors through its interaction with Y41 of hACE2 forming a potentially strong hydrophobic residue binding pair. 2021 bioRxiv Abstract SARS_CoV_2 N501Y 46 51 S 83 88 33594365 Transformations, Lineage Comparisons, and Analysis of Down to Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein Including the UK Variant B.1.1.7. The mutant D614G is a structure breaking Glycine mutation demonstrating a relatively more distal Down state RBD and a more stable conformation in general. 2021 bioRxiv Abstract SARS_CoV_2 D614G 11 16 RBD 108 111 33594365 Transformations, Lineage Comparisons, and Analysis of Down to Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein Including the UK Variant B.1.1.7. We note that these two key mutations, D614G and N501Y, are also found in the so-called South African (SA; B.1.351) variant of SARS-CoV-2. 2021 bioRxiv Abstract SARS_CoV_2 D614G;N501Y 38;48 43;53 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Independent genomic surveillance programs based in New Mexico and Louisiana contemporaneously detected the rapid rise of numerous clade 20G (lineage B.1.2) infections carrying a Q677P substitution in S. 2021 medRxiv Abstract SARS_CoV_2 Q677P 178 183 S 200 201 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Phylogenetic analyses revealed the independent evolution and spread of at least six distinct Q677H sub-lineages, with first collection dates ranging from mid-August to late November 2020. 2021 medRxiv Abstract SARS_CoV_2 Q677H 93 98 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Q677P cases have been detected predominantly in the south central and southwest United States; as of 03 Feb 2021, GISAID data show 499 viral sequences of this variant from the USA. 2021 medRxiv Abstract SARS_CoV_2 Q677P 0 5 33595922 Detection of the SARS-CoV-2 D614G mutation using engineered Cas12a guide RNA. Overall, we have developed the symRNA-Cas12a method to specifically, sensitively and rapidly detect the SARS-CoV-2 D614G mutation. 2021 Biotechnology journal Abstract SARS_CoV_2 D614G 115 120 33595922 Detection of the SARS-CoV-2 D614G mutation using engineered Cas12a guide RNA. The D614G mutation in the SARS-CoV-2 spike protein is known to markedly enhance viral infectivity but is difficult to detect. 2021 Biotechnology journal Abstract SARS_CoV_2 D614G 4 9 S 37 42 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. A348T, G476S, and V483A variants display reduced affinity to ACE2 in comparison to the Wuhan SARS-CoV2 spike protein. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 G476S;V483A;A348T 7;18;0 12;23;5 S 103 108 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Evolutionary analysis reveals five RBD variants A348T, V367F, G476S, V483A, and S494P are under strong positive selection bias. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 A348T;G476S;S494P;V367F;V483A 48;62;80;55;69 53;67;85;60;74 RBD 35 38 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. On the other hand, the enhanced binding affinity of S494P is attributed to strong interfacial complementarity between the RBD and ACE2. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 S494P 52 57 RBD 122 125 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Reorientation of several crucial residues at the RBD-ACE2 interface facilitates additional hydrogen bond formation for the V367F variant which enhances the binding energy during ACE2 recognition. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 V367F 123 128 RBD 49 52 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. While the V367F and S494P population variants display a higher binding affinity towards human ACE2. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 S494P;V367F 20;10 25;15 33605869 Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil. We describe a case of reinfection from distinct virus lineages in Brazil harboring the E484K mutation, a variant associated with escape from neutralizing antibodies. 2021 Emerging infectious diseases Abstract SARS_CoV_2 E484K 87 92 33606828 SARS-CoV-2 genetic diversity in Venezuela: Predominance of D614G variants and analysis of one outbreak. In conclusion, a high diversity of SARS-CoV-2 isolates were found circulating in Venezuela, with predominance of the D614G mutation. 2021 PloS one Abstract SARS_CoV_2 D614G 117 122 33606828 SARS-CoV-2 genetic diversity in Venezuela: Predominance of D614G variants and analysis of one outbreak. Ten out of 11 isolates (6 complete genomes and 4 partial spike genomic regions) belonged to lineage B, bearing the D614G mutation in the Spike protein. 2021 PloS one Abstract SARS_CoV_2 D614G 115 120 S;S 57;137 62;142 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. Possible novel mutations were also detected in the S gene (G1167V), ORF1ab (A6269S and P3371S), ORF7b (T28I), and ORF8 (G96R). 2020 Frontiers in genetics Abstract SARS_CoV_2 P3371S;A6269S;G1167V;G96R;T28I 87;76;59;120;103 93;82;65;124;107 ORF1ab;ORF7b;ORF8;S 68;96;114;51 74;101;118;52 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. Previously reported mutations including D614G in S gene, P4715L in ORF1ab, S194L, R203K, and G204R in N gene were identified in the genomes sequenced in this study. 2020 Frontiers in genetics Abstract SARS_CoV_2 D614G;G204R;P4715L;R203K;S194L 40;93;57;82;75 45;98;63;87;80 ORF1ab;N;S 67;102;49 73;103;50 33618621 Structural stability predictions and molecular dynamics simulations of RBD and HR1 mutations associated with SARS-CoV-2 spike glycoprotein. We have studied the impact of mutations such as A348T, N354D, D364Y, G476S, V483A, S494D in the RBD (319-591), and S939F, S940T, T941A, S943P (912-984) in the HR1 domains of spike glycoprotein. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 A348T;D364Y;G476S;N354D;S494D;S939F;S940T;S943P;T941A;V483A 48;62;69;55;83;115;122;136;129;76 53;67;74;60;88;120;127;141;134;81 S;RBD 174;96 192;99 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. Therefore, using MD simulations, we have investigated the role of S477 and its two frequent mutations (S477G and S477N) at the RBD during the binding to hACE2. 2021 Scientific reports Abstract SARS_CoV_2 S477N;S477G 113;103 118;108 RBD 127 130 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. We found that the amino acid exchanges S477G and S477N strengthen the binding of the SARS-COV-2 spike with the hACE2 receptor. 2021 Scientific reports Abstract SARS_CoV_2 S477G;S477N 39;49 44;54 S 96 101 33619479 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to Bamlanivimab in vitro. We found that the mutant RBD with K417N, E484K, and N501Y exchanges has higher binding affinity to the human receptor compared to the wildtype RBD. 2021 bioRxiv Abstract SARS_CoV_2 E484K;K417N;N501Y 41;34;52 46;39;57 RBD;RBD 25;143 28;146 33619480 A Combination Adjuvant for the Induction of Potent Antiviral Immune Responses for a Recombinant SARS-CoV-2 Protein Vaccine. The combination adjuvant with spike protein antigen elicited robust responses to SARS-CoV-2 in mice, with markedly enhanced T H 1-biased cellular responses and high virus-neutralizing antibody titers towards both homologous SARS-CoV-2 and a variant harboring the N501Y mutation shared by B1.1.7, B.1.351 and P.1 variants. 2021 bioRxiv Abstract SARS_CoV_2 N501Y 263 268 S 30 35 33619484 Decreased neutralization of SARS-CoV-2 global variants by therapeutic anti-spike protein monoclonal antibodies. The failure of REGN10933 to neutralize B.1.351 is caused by the K417N and E484K mutations in the receptor binding domain; the failure to neutralize the mink cluster 5 spike protein is caused by the Y453F mutation. 2021 bioRxiv Abstract SARS_CoV_2 E484K;K417N;Y453F 74;64;198 79;69;203 RBD;S 97;167 120;172 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. However, their binding and neutralization are abrogated by either the E484K or K417N mutation, whereas nAbs to the cross-reactive CR3022 and S309 sites are largely unaffected. 2021 bioRxiv Abstract SARS_CoV_2 E484K;K417N 70;79 75;84 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Five of the 10 pseudoviruses, harboring receptor-binding domain mutations, including K417N/T, E484K, and N501Y, were highly resistant to neutralization. 2021 medRxiv Abstract SARS_CoV_2 E484K;K417N;K417T;N501Y 94;85;85;105 99;92;92;110 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. E484K emergence on a B.1.1.7 background represents a threat to the vaccine BNT162b. 2021 medRxiv Abstract SARS_CoV_2 E484K 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Introduction of the E484K mutation in a B.1.1.7 background to reflect newly emerging viruses in the UK led to a more substantial loss of neutralising activity by vaccine-elicited antibodies and mAbs (19 out of 31) over that conferred by the B.1.1.7 mutations alone. 2021 medRxiv Abstract SARS_CoV_2 E484K 20 25 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. Here, we describe case studies in which users can interrogate (1) SNVs in the SARS-CoV-2 spike receptor binding domain (RBD) across different geographical regions to inform the design and testing of therapeutics, (2) SNVs that may impact the sensitivity of commonly used diagnostic primers, and (3) the emergence of a dominant lineage harboring an S477N RBD mutation in Australia in 2020. 2021 eLife Abstract SARS_CoV_2 S477N 348 353 RBD;S;RBD;RBD 95;89;120;354 118;94;123;357 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Here, we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is a highly variable region of S and provide epidemiological, clinical, and molecular characterization of a prevalent, sentinel RBM mutation, N439K. 2021 Cell Abstract SARS_CoV_2 N439K 237 242 S;S;S 56;63;126 61;64;127 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics. 2021 Cell Abstract SARS_CoV_2 N439K 69 74 S 104 105 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. We demonstrate N439K S protein has enhanced binding affinity to the hACE2 receptor, and N439K viruses have similar in vitro replication fitness and cause infections with similar clinical outcomes as compared to wild type. 2021 Cell Abstract SARS_CoV_2 N439K;N439K 15;88 20;93 S 21 22 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. We show the N439K mutation confers resistance against several neutralizing monoclonal antibodies, including one authorized for emergency use by the US Food and Drug Administration (FDA), and reduces the activity of some polyclonal sera from persons recovered from infection. 2021 Cell Abstract SARS_CoV_2 N439K 12 17 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. Docking highlighted mutation (D614G) caused reduction in binding of spike proteins with angiotensin-converting enzyme 2 (ACE2), but it also showed better interaction with the TMPRSS2 receptor contributing to high transmissibility among U.S. 2021 mSystems Abstract SARS_CoV_2 D614G 30 35 S 68 73 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. T1103P mutation in Nsp3 was predicted to increase protein stability in 238 strains except for 6 strains which were marked as ancestral type, whereas co-mutation (P409L and Y446C) in Nsp13 were found in 64 genomes from the United States highlighting its 100% co-occurrence. 2021 mSystems Abstract SARS_CoV_2 Y446C;P409L;T1103P 172;162;0 177;167;6 Nsp13;Nsp3 182;19 187;23 33628442 Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. Methods: Antibody profiling against the SARS-CoV-2 S protein of the D614 variant by flow cytometry and assessment of neutralising antibody titres using pseudotyped lentiviruses expressing the SARS-CoV-2 S protein of either the D614 or G614 variant tagged with a luciferase reporter were performed on plasma samples from COVID-19 patients with known D614G status (n = 44 infected with D614, n = 6 infected with G614, n = 7 containing all other clades: O, S, L, V, G, GH or GR). 2021 Clinical & translational immunology Abstract SARS_CoV_2 D614G 349 354 S;S;S 51;203;454 52;204;455 COVID-19 320 328 33628442 Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. Objectives: The emergence of a SARS-CoV-2 variant with a point mutation in the spike (S) protein, D614G, has taken precedence over the original Wuhan isolate by May 2020. 2021 Clinical & translational immunology Abstract SARS_CoV_2 D614G 98 103 S;S 79;86 84;87 33628442 Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. Of clinical importance, patients infected with either the D614 or G614 clade elicited a similar degree of neutralisation against both pseudoviruses, suggesting that the D614G mutation does not impact the neutralisation capacity of the elicited antibodies. 2021 Clinical & translational immunology Abstract SARS_CoV_2 D614G 169 174 33629236 A Biochemical Perspective of the Nonstructural Proteins (NSPs) and the Spike Protein of SARS CoV-2. Additionally, other emerging strains called "501Y.V1" and "501Y.V2" have several differences in the receptor binding domain of the spike protein (N501Y) as well as other locations. 2021 The protein journal Abstract SARS_CoV_2 N501Y 146 151 RBD;S 100;131 123;136 33629236 A Biochemical Perspective of the Nonstructural Proteins (NSPs) and the Spike Protein of SARS CoV-2. One strain, called "D614G", possesses a glycine (G) instead of an aspartate (D) at position 614 of the spike protein. 2021 The protein journal Abstract SARS_CoV_2 D614G 20 25 S 103 108 33630820 Detection of B.1.351 SARS-CoV-2 Variant Strain - Zambia, December 2020. The variant included a mutation (N501Y) associated with increased transmissibility. 2021 MMWR. Morbidity and mortality weekly report Abstract SARS_CoV_2 N501Y 33 38 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. In light of the evidence for E484K dispersion, co-infection and emergence of VUI-NP13 L in Rio Grande do Sul, we reaffirm the importance of establishing strict and effective social distancing measures to counter the spread of potentially more hazardous SARS-CoV-2 strains. 2021 Virus research Abstract SARS_CoV_2 E484K 29 34 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Most samples sequenced belonged to the B.1.1.28 (E484K) lineage, demonstrating its widespread dispersion. 2021 Virus research Abstract SARS_CoV_2 E484K 49 54 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Nevertheless, the spread of B.1.1.28 (E484K) and other variants in Brazil is still unknown. 2021 Virus research Abstract SARS_CoV_2 E484K 38 43 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Recent reports of novel variants in the United Kingdom, South Africa and Brazil (B.1.1.28-E484K) have raised intense interest because of a possible higher transmission rate or resistance to the novel vaccines. 2021 Virus research Abstract SARS_CoV_2 E484K 90 95 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. We were the first to identify two independent events of co-infection caused by the occurrence of B.1.1.28 (E484K) with either B.1.1.248 or B.1.91 lineages. 2021 Virus research Abstract SARS_CoV_2 E484K 107 112 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. To date, there have been described three lineages of SARS-CoV-2 circulating worldwide, two of them are found among Mexican population, within these, we observed three mutations of spike (S) protein located at amino acids H49Y, D614G, and T573I. 2021 Scientific reports Abstract SARS_CoV_2 D614G;H49Y;T573I 227;221;238 232;225;243 S;S 180;187 185;188 33634309 A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. It is suggested that D398 in particular contributes to a pH-dependence of the open/closed equilibrium, potentially coupled to the effects of linoleic acid binding and D614G mutation, and possibly also A570D mutation. 2021 Briefings in bioinformatics Abstract SARS_CoV_2 A570D;D614G 201;167 206;172 33634309 A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. The D614G mutation is known to modulate the balance of closed to open trimer. 2021 Briefings in bioinformatics Abstract SARS_CoV_2 D614G 4 9 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Our data suggest that here, positive selection in index cats followed by a narrow transmission bottleneck may have instead accelerated the fixation of S H655Y, a potentially beneficial SARS-CoV-2 variant. 2021 PLoS pathogens Abstract SARS_CoV_2 H655Y 153 158 S 151 152 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. We further identify a notable variant at amino acid position 655 in Spike (H655Y), which was previously shown to confer escape from human monoclonal antibodies. 2021 PLoS pathogens Abstract SARS_CoV_2 H655Y 75 80 S 68 73 33636719 SARS-CoV-2 spike D614G change enhances replication and transmission. During the evolution of SARS-CoV-2 in humans, a D614G substitution in the spike glycoprotein (S) has emerged; virus containing this substitution has become the predominant circulating variant in the COVID-19 pandemic1. 2021 Nature Abstract SARS_CoV_2 D614G 48 53 S;S 74;94 92;95 COVID-19 199 207 33636719 SARS-CoV-2 spike D614G change enhances replication and transmission. Here we use isogenic SARS-CoV-2 variants to demonstrate that the variant that contains S(D614G) has enhanced binding to the human cell-surface receptor angiotensin-converting enzyme 2 (ACE2), increased replication in primary human bronchial and nasal airway epithelial cultures as well as in a human ACE2 knock-in mouse model, and markedly increased replication and transmissibility in hamster and ferret models of SARS-CoV-2 infection. 2021 Nature Abstract SARS_CoV_2 D614G 87 95 S 87 88 COVID-19 415 435 33636719 SARS-CoV-2 spike D614G change enhances replication and transmission. Our data show that the D614G substitution in S results in subtle increases in binding and replication in vitro, and provides a real competitive advantage in vivo-particularly during the transmission bottleneck. 2021 Nature Abstract SARS_CoV_2 D614G 23 28 S 45 46 33636719 SARS-CoV-2 spike D614G change enhances replication and transmission. Our data therefore provide an explanation for the global predominance of the variant that contains S(D614G) among the SARS-CoV-2 viruses that are currently circulating. 2021 Nature Abstract SARS_CoV_2 D614G 99 107 S 99 100 33639276 The role of A-to-I RNA editing in infections by RNA viruses: Possible implications for SARS-CoV-2 infection. A single nucleotide substitution can have dramatic effects on SARS-CoV-2 infectivity as shown by the D614G(A-to-G) substitution in the spike protein. 2021 Clinical immunology (Orlando, Fla.) Abstract SARS_CoV_2 D614G 101 106 S 135 140 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. In the present study we identified important active site mutations within the SARS-CoV-2 Mpro (Y54C, N142S, T190I and A191V). 2021 Saudi journal of biological sciences Abstract SARS_CoV_2 A191V;N142S;T190I;Y54C 118;101;108;95 123;106;113;99 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. While PF-03715455 (Y54C), Salvianolic acid A (N142S and T190I), and Montelukast (A191V) were found to be most active against the other selected mutants. 2021 Saudi journal of biological sciences Abstract SARS_CoV_2 T190I;A191V;N142S;Y54C 56;81;46;19 61;86;51;23 33653892 Introduction of Two Prolines and Removal of the Polybasic Cleavage Site Lead to Higher Efficacy of a Recombinant Spike-Based SARS-CoV-2 Vaccine in the Mouse Model. While all versions of the protein were able to induce neutralizing antibodies, only the antigen with both a deleted cleavage site and the K986P and V987P (PP) mutations completely protected from challenge in this mouse model.IMPORTANCE A vaccine for SARS-CoV-2 is urgently needed. 2021 mBio Abstract SARS_CoV_2 K986P;V987P 138;148 143;153 33655250 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. Additionally, the L452R mutation in the B.1.429 lineage escapes LY-CoV555. 2021 bioRxiv Abstract SARS_CoV_2 L452R 18 23 33655250 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. Individual mutations that escape binding by each antibody are combined in the circulating B.1.351 and P.1 SARS-CoV-2 lineages (E484K escapes LY-CoV555, K417N/T escape LY-CoV016). 2021 bioRxiv Abstract SARS_CoV_2 K417N;K417T;E484K 152;152;127 159;159;132 33655251 SARS-CoV-2 B.1.1.7 and B.1.351 Spike variants bind human ACE2 with increased affinity. The B.1.351 variant harboring three mutations, (E484K, N501Y, and K417N) binds the ACE2 at nearly five-fold greater affinity than the original SARS-COV-2 RBD. 2021 bioRxiv Abstract SARS_CoV_2 K417N;N501Y;E484K 66;55;48 71;60;53 RBD 154 157 33655254 Reduced binding and neutralization of infection- and vaccine-induced antibodies to the B.1.351 (South African) SARS-CoV-2 variant. In acutely-infected (5-19 days post-symptom onset), convalescent COVID-19 individuals (through 8 months post-symptom onset) and mRNA-1273 vaccinated individuals (day 14 post-second dose), we observed an average 4.3-fold reduction in antibody titers to the B.1.351-derived receptor binding domain of the spike protein and an average 3.5-fold reduction in neutralizing antibody titers to the SARS-CoV-2 B.1.351 variant as compared to the B.1 variant (spike D614G). 2021 bioRxiv Abstract SARS_CoV_2 D614G 455 460 RBD;S;S 272;303;449 295;308;454 COVID-19 65 73 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. Here, we report the emergence of variant lineage B.1.526 that contains E484K and its alarming rise to dominance in New York City in early 2021. 2021 medRxiv Abstract SARS_CoV_2 E484K 71 76 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. Such transmission dynamics, together with the relative antibody resistance of its E484K sub-lineage, likely contributed to the sharp rise and rapid spread of B.1.526. 2021 medRxiv Abstract SARS_CoV_2 E484K 82 87 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. Two signature mutations of concern are E484K, which plays a crucial role in the loss of neutralizing activity of antibodies, and N501Y, a driver of rapid worldwide transmission of the B.1.1.7 lineage. 2021 medRxiv Abstract SARS_CoV_2 E484K;N501Y 39;129 44;134 33660619 Lethal zoonotic coronavirus infections of humans - comparative phylogenetics, epidemiology, transmission, and clinical features of coronavirus disease 2019, The Middle East respiratory syndrome and severe acute respiratory syndrome. The emergence of genetic variants, such as D614G, N501Y (variants 1 and 2), has led to an increase in transmissibility and raises concern about the possibility of re-infection and impaired vaccine response. 2021 Current opinion in pulmonary medicine Abstract SARS_CoV_2 D614G;N501Y 43;50 48;55 33662015 Genomic characterization and evolution of SARS-CoV-2 of a Canadian population. Analysis of these substitutions indicated that P1427I (ORF1b), Y1464C (ORF1b), and Q57H (ORF3a) might affect functions of the corresponding SARS-CoV-2 encoded proteins. 2021 PloS one Abstract SARS_CoV_2 P1427I;Q57H;Y1464C 47;83;63 53;87;69 ORF3a 89 94 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Many highly neutralizing mAbs engaging the receptor-binding domain or N-terminal domain and most convalescent sera and mRNA vaccine-induced immune sera showed reduced inhibitory activity against viruses containing an E484K spike mutation. 2021 Nature medicine Abstract SARS_CoV_2 E484K 217 222 S;N 223;70 228;71 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. The most potent monoclonal antibody, engineered to reduce the risk of antibody-dependent enhancement and prolong half-life, neutralized the authentic wild-type virus and emerging variants containing D614G, E484K, and N501Y substitutions. 2021 Cell Abstract SARS_CoV_2 D614G;E484K;N501Y 199;206;217 204;211;222 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. Our previous findings had shown that the two most frequently observed mutations in the SARS-CoV-2 genome, 14408C>T in the RdRp coding region, and 23403A>G in the S gene, are correlated with higher mutation density over time. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 C14408T;A23403G 106;146 114;154 RdRP;S 122;162 126;163 33671631 Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants. In parallel with the B lineages and sublineages, the D614G mutation in the Spike protein sequence was detected soon after the detection of the first coronavirus disease 19 (COVID-19) case in Madrid and in two weeks became dominant, being found in 80% of the samples and remaining at this level during all the study periods. 2021 Microorganisms Abstract SARS_CoV_2 D614G 53 58 S 75 80 COVID-19;COVID-19 149;173 168;181 33672021 Molecular Epidemiological Investigation of a Nosocomial Cluster of C. auris: Evidence of Recent Emergence in Italy and Ease of Transmission during the COVID-19 Pandemic. All isolates were resistant to amphotericin B, voriconazole, and fluconazole at high-level, owing to mutations in ERG11(K143R) and TACB1(A640V). 2021 Journal of fungi (Basel, Switzerland) Abstract SARS_CoV_2 A640V;K143R 137;120 142;125 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. Although less frequent, HV69-70del and L5F spike mutations occurred in the background of six different ORF8 nonsense mutations. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 L5F 39 42 S;ORF8 43;103 48;107 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. However, VOC-202012/01 has also a mutation (Q27stop) that truncates the ORF8, a likely immune evasion protein. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 Q27X 44 51 ORF8 72 76 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The widespread D614G spike mutation was found in most ORF-deficient lineages. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 D614G 15 20 S 21 26 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Interestingly, subclade 2B with the amino acid changes at nsp2 T85I, Spike D614G, and ORF3a Q57H was firstly reported on March 4, 2020 in United States of America, becoming the most frequent sub-haplogroup in the world (36.21%) and America (45.81%). 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G;Q57H;T85I 75;92;63 80;96;67 S;ORF3a;Nsp2 69;86;58 74;91;62 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Phylogenetic tree analysis with Neighbor-Joining and Maximum-Parsimony methods indicated that the haplotypes of SARS-CoV-2 genome sequences were classified into four clades with the unique nucleotide and amino acid changes: T27879C (ORF8 L84S) in clade 1 (25.34%), A23138G (spike D614G) in clade 2 (63.54%), G10818T (nsp6 L37F), C14540T (nsp12 T442I), and G25879T (ORF3a V251F) in clade 3 (2.58%), and miscellaneous changes in clade 4 (8.54%). 2021 Infection, genetics and evolution Abstract SARS_CoV_2 A23138G;C14540T;D614G;G10818T;G25879T;L37F;L84S;T27879C;T442I;V251F 265;329;280;308;356;322;238;224;344;371 272;336;285;315;363;326;242;231;349;376 S;ORF3a;Nsp12;Nsp6;ORF8 274;365;338;317;233 279;370;343;321;237 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Subclade 1C with the amino acid changes at nsp13 P504L and ORF8 L84S was becoming the second most frequent sub-haplogroup in the world (19.91%) and America (26.29%). 2021 Infection, genetics and evolution Abstract SARS_CoV_2 L84S;P504L 64;49 68;54 ORF8;Nsp13 59;43 63;48 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Subclade 2A with the amino acid changes in Spike D614G and Nucleocapsid R203K and G204R was highly prevalent in Asia (18.82%) and Europe (29.72%). 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G;G204R;R203K 49;82;72 54;87;77 S;N 43;59 48;71 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. D614G mutation in Pahang/IIUM91 Spike protein increases viral stability and flexibility, hence render higher infectivity. 2022 Materials today. Proceedings Abstract SARS_CoV_2 D614G 0 5 S 32 37 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. Here we reported that the virus with D614G mutation in Spike protein circulates in a few Malaysia states before the Sivagangga cluster announced in Kedah in July 2020. 2022 Materials today. Proceedings Abstract SARS_CoV_2 D614G 37 42 S 55 60 33681755 The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant. Recently, a new strain is reported in the UK that includes a mutation (N501Y) in the RBD, that is possibly increasing the infection rate. 2021 Medicine in drug discovery Abstract SARS_CoV_2 N501Y 71 76 RBD 85 88 33683658 Isolation and genetic characterization of SARS-CoV-2 from Indian patients in a single family without H/O travel abroad. On comparison with Wuhan strain, 3 unique mutations were identified in nsp3 (A1812D), exonuclease (P1821S) of Orf1ab and spike protein (Q677H) regions, respectively. 2021 Virus genes Abstract SARS_CoV_2 A1812D;P1821S;Q677H 77;99;136 83;105;141 Exonuclease;ORF1ab;S;Nsp3 86;110;121;71 97;116;126;75 33684923 Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7. The B.1.351 variant is not only refractory to neutralization by most monoclonal antibodies against the N-terminal domain but also by multiple individual monoclonal antibodies against the receptor-binding motif of the receptor-binding domain, which is mostly due to a mutation causing an E484K substitution. 2021 Nature Abstract SARS_CoV_2 E484K 287 292 N 103 104 33688650 Ultrapotent miniproteins targeting the receptor-binding domain protect against SARS-CoV-2 infection and disease in mice. Importantly, LCB1v1.3 protected in vivo against a historical strain (WA1/2020), an emerging B.1.1.7 strain, and a strain encoding key E484K and N501Y spike protein substitutions. 2021 bioRxiv Abstract SARS_CoV_2 E484K;N501Y 134;144 139;149 S 150 155 33688659 Multimeric nanobodies from camelid engineered mice and llamas potently neutralize SARS-CoV-2 variants. The second group is almost exclusively focused to the RBD-ACE2 interface and fails to neutralize pseudoviruses carrying the E484K or N501Y substitutions. 2021 bioRxiv Abstract SARS_CoV_2 E484K;N501Y 124;133 129;138 RBD 54 57 33688664 Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. 2021 medRxiv Abstract SARS_CoV_2 E484K;N501Y;K417T 268;278;261 273;283;266 S 246 251 33688689 Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. Certain viral lineages bearing spike mutations, defined in part by L452R, S13I, and W152C, comprised 54.9% of the total sequences from January, compared to 15.7% in November. 2021 medRxiv Abstract SARS_CoV_2 L452R;S13I;W152C 67;74;84 72;78;89 S 31 36 33690265 Detection of a SARS-CoV-2 variant of concern in South Africa. Here we describe a newly arisen lineage of SARS-CoV-2 (designated 501Y.V2; also known as B.1.351 or 20H) that is defined by eight mutations in the spike protein, including three substitutions (K417N, E484K and N501Y) at residues in its receptor-binding domain that may have functional importance3-5. 2021 Nature Abstract SARS_CoV_2 E484K;N501Y;K417N 200;210;193 205;215;198 S 147 152 33692211 SARS-CoV-2 rapidly adapts in aged BALB/c mice and induces typical pneumonia. Deep sequencing showed a panel of mutations potentially associated with the enhanced infection in aged BALB/c mice, such as the Q498H mutations which are located at the receptor binding domain (RBD) of the spike (S) protein. 2021 Journal of virology Abstract SARS_CoV_2 Q498H 128 133 RBD;S;RBD;S 169;206;194;213 192;211;197;214 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Two unique mutations such as W6152R and N5928H found in exonuclease of Surat (GBRC275b) and Gandhinagar (GBRC239) isolates. 2021 Computers in biology and medicine Abstract SARS_CoV_2 N5928H;W6152R 40;29 46;35 Exonuclease 56 67 33706364 Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Introduction of the mutation that encodes the E484K substitution in the B.1.1.7 background to reflect a newly emerged variant of concern (VOC 202102/02) led to a more-substantial loss of neutralizing activity by vaccine-elicited antibodies and monoclonal antibodies (19 out of 31) compared with the loss of neutralizing activity conferred by the mutations in B.1.1.7 alone. 2021 Nature Abstract SARS_CoV_2 E484K 46 51 33706364 Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. The emergence of the E484K substitution in a B.1.1.7 background represents a threat to the efficacy of the BNT162b2 vaccine. 2021 Nature Abstract SARS_CoV_2 E484K 21 26 33707329 Coding-Complete Genome Sequences and Mutation Profiles of Nine SARS-CoV-2 Strains Detected from COVID-19 Patients in Bangladesh. We have identified the E484K escape mutation and the S359T mutation within the spike protein coding region of the sequenced genomes. 2021 Microbiology resource announcements Abstract SARS_CoV_2 E484K;S359T 23;53 28;58 S 79 84 33714462 Pyrococcus furiosus Argonaute coupled with modified ligase chain reaction for detection of SARS-CoV-2 and HPV. PLCR can detect DNA or RNA without PCR at attomolar sensitivities, distinguish single base mutation between the genome of wild type SARS-CoV-2 and its mutant spike D614G, effectively distinguish the novel coronavirus from other coronaviruses and finally achieve multiplexed detection in 70 min. 2021 Talanta Abstract SARS_CoV_2 D614G 164 169 S 158 163 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. Here we present functional data on the cluster-five variant, which contains a mutation resulting in a Y453F residue change in the receptor-binding domain (RBD) of the spike protein. 2021 The Journal of biological chemistry Abstract SARS_CoV_2 Y453F 102 107 S;RBD 167;155 172;158 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. Using an ELISA-based angiotensin-converting enzyme-2/RBD inhibition assay, we show that the Y453F variant does not decrease established humoral immunity from previously infected individuals or affect the neutralizing antibody response in a vaccine mouse model based on the original Wuhan strain RBD or spike as antigens. 2021 The Journal of biological chemistry Abstract SARS_CoV_2 Y453F 92 97 S;RBD;RBD 302;53;295 307;56;298 33718878 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawai'i Reveals the Worldwide Emerging P681H Mutation. Further, we decoded 13 single nucleotide polymorphisms across 13 unique SARS-CoV-2 genomes within this region of the S gene, with 1 non-synonymous mutation (P681H) found in the 2 Hawai'i strains. 2021 Hawai'i journal of health & social welfare Abstract SARS_CoV_2 P681H 157 162 S 117 118 33718878 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawai'i Reveals the Worldwide Emerging P681H Mutation. The P681H mutation has unique and emerging characteristics with a significant exponential increase in worldwide frequency when compared to the plateauing of the now universal D614G mutation. 2021 Hawai'i journal of health & social welfare Abstract SARS_CoV_2 D614G;P681H 175;4 180;9 33718878 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawai'i Reveals the Worldwide Emerging P681H Mutation. The P681H mutation is also characteristic of the new SARS-CoV-2 variants from the United Kingdom and Nigeria. 2021 Hawai'i journal of health & social welfare Abstract SARS_CoV_2 P681H 4 9 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. The Spike protein has different hotspots of mutation and deletion, the most dangerous for immune escape being the ones within the receptor binding domain (RBD), such as K417N/T, N439K, L452R, Y453F, S477N, E484K, and N501Y. 2021 Reviews in medical virology Abstract SARS_CoV_2 E484K;K417N;K417T;L452R;N439K;N501Y;S477N;Y453F 206;169;169;185;178;217;199;192 211;176;176;190;183;222;204;197 RBD;S;RBD 130;4;155 153;9;158 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. In majority (above 10%) of virus population, the most frequent and common mutation points between global excluding India and India are L37F, P323L, F506L, S507G, D614G and Q57H in NSP6, RdRp, Exon, Spike and ORF3a respectively. 2021 Briefings in bioinformatics Abstract SARS_CoV_2 D614G;F506L;L37F;P323L;Q57H;S507G 162;148;135;141;172;155 167;153;139;146;176;160 S;ORF3a;Exon;Nsp6;RdRP 198;208;192;180;186 203;213;196;184;190 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. While for India, the other most frequent mutation points are T1198K, A97V, T315N and P13L in NSP3, RdRp, Spike and ORF8 respectively. 2021 Briefings in bioinformatics Abstract SARS_CoV_2 A97V;P13L;T1198K;T315N 69;85;61;75 73;89;67;80 S;Nsp3;ORF8;RdRP 105;93;115;99 110;97;119;103 33725432 Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. Serum samples obtained from 25 participants after the second dose were tested by pseudovirus and live-virus neutralization assays against the original D614G virus and the B.1.351 variant. 2021 The New England journal of medicine Abstract SARS_CoV_2 D614G 151 156 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Conclusion The results of this study indicate that SII above 40% is associated with the emergence of SARS-CoV-2 E484K variants and P.1 lineage in the state of Amazonas, which was not observed in overall Brazil. 2021 Cureus Abstract SARS_CoV_2 E484K 112 117 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Conversely, in overall Brazil, correlations between SII and P.1 lineage and E484K variants were weaker and shorter, or negative, respectively. 2021 Cureus Abstract SARS_CoV_2 E484K 76 81 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Data regarding demographics, lineage, and prevalence of P.1 lineage and E484K mutations were obtained. 2021 Cureus Abstract SARS_CoV_2 E484K 72 77 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. In the state of Amazonas, SII on a given week was positively, significantly, and moderately or strongly (r > 0.6) correlated with the prevalence of both P.1 lineage and other E484K variants in the six following weeks after the SII on a given week. 2021 Cureus Abstract SARS_CoV_2 E484K 175 180 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Our objective is to determine if social isolation is associated with the emergence of new SARS-CoV-2 variants, particularly the P.1 lineage and E484K mutants, in Brazil and in the state of Amazonas. 2021 Cureus Abstract SARS_CoV_2 E484K 144 149 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. SII was correlated with the prevalence P.1 lineage and E484K mutations in the eight following weeks. 2021 Cureus Abstract SARS_CoV_2 E484K 55 60 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. When SII was above 40%, apparently exponential positive correlations between SII and prevalence of both P.1 lineage and E484K variants were observed. 2021 Cureus Abstract SARS_CoV_2 E484K 120 125 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. When SII was below 40%, P.1 lineage or E484K variants were not detected in the following weeks. 2021 Cureus Abstract SARS_CoV_2 E484K 39 44 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. The N501Y mutation within the receptor-binding domain (RBD) of the spike protein of these SARS-CoV-2 variants may enhance binding to the human angiotensin-converting enzyme 2 (hACE2). 2021 FEBS letters Abstract SARS_CoV_2 N501Y 4 9 S;RBD 67;55 72;58 33729394 Immunity, virus evolution, and effectiveness of SARS-CoV-2 vaccines. During the global pandemic, COVID-19 patients were identified with non-synonymous substitution of G614D in the spike protein, indicating virus co-evolution in host cells. 2021 Brazilian journal of medical and biological research Abstract SARS_CoV_2 G614D 98 103 S 111 116 COVID-19 28 36 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. The receptor-binding domain mutations provide tighter ACE2 binding and widespread escape from monoclonal antibody neutralization largely driven by E484K, although K417N and N501Y act together against some important antibody classes. 2021 Cell Abstract SARS_CoV_2 E484K;K417N;N501Y 147;163;173 152;168;178 33731300 Genetic modification to design a stable yeast-expressed recombinant SARS-CoV-2 receptor binding domain as a COVID-19 vaccine candidate. METHOD: We constructed three variants of the recombinant receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein (residues 331-549) in yeast as follows: (1) a "wild type" RBD (RBD219-WT), (2) a deglycosylated form (RBD219-N1) by deleting the first N-glycosylation site, and (3) a combined deglycosylated and cysteine-mutagenized form (C538A-mutated variant (RBD219-N1C1)). 2021 Biochimica et biophysica acta. General subjects Abstract SARS_CoV_2 C538A 345 350 S;RBD;RBD;RBD;RBD;RBD;N;S 105;82;181;186;225;368;258;112 110;85;184;189;228;371;259;113 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. Interestingly, a non-negligible number of mis-sense variations were predicted to enhance ACE2/S-RBDCoV-2 binding, including the variants Q24T, T27D/K/W, D30E, H34S7T/K, E35D, Q42K, L79I/W, R357K, and R393K on ACE2 and L455D/W, F456K/W, Q493K, N501T, and Y505W on S-RBDCoV-2, respectively. 2021 ACS nano Abstract SARS_CoV_2 L455D;L455W;L79I;L79W;N501T;Q493K;Y505W 218;218;181;181;243;236;254 225;225;187;187;248;241;259 S;S 94;263 95;264 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. The neutralization resistance was mainly caused by E484K and N501Y mutations in the receptor-binding domain of spike. 2021 Cell Abstract SARS_CoV_2 E484K;N501Y 51;61 56;66 S 111 116 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. All genomes carried the spike mutation D614G and were classified as part of the GH clade. 2021 International journal of infectious diseases Abstract SARS_CoV_2 D614G 39 44 S 24 29 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. In line with the global trend, D614G mutation in spike glycoprotein was predominantly high (98 %) in Bangladeshi isolates. 2021 Virus research Abstract SARS_CoV_2 D614G 31 36 S 49 67 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. Previously reported frequent mutations, such as R203K, D614G, G204R, P4715L and I300F at protein levels were also prevalent in Bangladeshi isolates. 2021 Virus research Abstract SARS_CoV_2 D614G;G204R;I300F;P4715L;R203K 55;62;80;69;48 60;67;85;75;53 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. The sequence, which was obtained using Ion Torrent technology, is valuable as it carries a recently described deletion (His69-Val70) and substitution (Asn439Lys). 2021 Microbiology resource announcements Abstract SARS_CoV_2 N439K 151 160 33738124 SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity. Four genetically linked mutations known as the globally dominant SARS-CoV-2 haplotype (C241T, C3037T, C14408T and A23403G) were found in the majority of consensus sequences. 2021 Virus evolution Abstract SARS_CoV_2 A23403G;C14408T;C3037T;C241T 114;102;94;87 121;109;100;92 33738620 Clinical characteristics of SARS-CoV-2 by re-infection vs. reactivation: a case series from Iran. The sequencing of SARS-CoV-2 sample obtained from two cases revealed a D614G mutation of S gene from the second isolated sample strengthens the case for the re-infection. 2021 European journal of clinical microbiology & infectious diseases Abstract SARS_CoV_2 D614G 71 76 S 89 90 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. Importantly, the number of patients infected with the V354F and V470A mutants has increased with the development of the SARS-CoV-2 pandemic. 2021 Zoological research Abstract SARS_CoV_2 V354F;V470A 54;64 59;69 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. We identified two spike-S1 point mutations (V354F and V470A) by receptor-ligand docking and binding enzyme-linked immunosorbent assays. 2021 Zoological research Abstract SARS_CoV_2 V470A;V354F 54;44 59;49 S 18 23 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. We infer the origin of B.1-C15324T to mid-February in our tri-national region. 2021 PLoS pathogens Abstract SARS_CoV_2 C15324T 27 34 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. Within B.1, 68 2% of our samples fall within a clade defined by the SNP C15324T ('Basel cluster'), including 157 identical sequences at the root of the 'Basel cluster', some of which we can specifically trace to regional spreading events. 2021 PLoS pathogens Abstract SARS_CoV_2 C15324T 72 79 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Five of the 10 pseudoviruses, harboring receptor-binding domain mutations, including K417N/T, E484K, and N501Y, were highly resistant to neutralization. 2021 Cell Abstract SARS_CoV_2 E484K;K417N;K417T;N501Y 94;85;85;105 99;92;92;110 33743891 Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera. Variant B.1.1.7, now dominant in the UK, with increased transmission, harbors 9 amino acid changes in the spike, including N501Y in the ACE2 interacting surface. 2021 Cell Abstract SARS_CoV_2 N501Y 123 128 S 106 111 33743891 Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera. We map the impact of N501Y by structure/function analysis of a large panel of well-characterized monoclonal antibodies. 2021 Cell Abstract SARS_CoV_2 N501Y 21 26 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. On the other hand, during almost all months analyzed, OTU_5 characterized by the mutation T85I in nsp2 is the most frequent in North America. 2021 Frontiers in microbiology Abstract SARS_CoV_2 T85I 90 94 Nsp2 98 102 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. OTU_3 characterized by mutations R203K and G204R is currently the most frequent haplotype circulating in four of the six continents analyzed (South America, North America, Europe, Asia, Africa, and Oceania). 2021 Frontiers in microbiology Abstract SARS_CoV_2 G204R;R203K 43;33 48;38 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Some novel mutations [NSP2 (D268del), NSP5 (N228K), and NS3 (F105S)] and specific characters have been detected in the coding regions, which may affect viral transmission, epidemiology, and disease severity. 2021 ACS omega Abstract SARS_CoV_2 DEL268D;F105S;N228K 28;61;44 35;66;49 Nsp2;Nsp5;NS3 22;38;56 26;42;59 33750399 Modelling the association between COVID-19 transmissibility and D614G substitution in SARS-CoV-2 spike protein: using the surveillance data in California as an example. CONCLUSIONS: Our findings show a link between the molecular-level mutation activity of SARS-CoV-2 and population-level transmission of COVID-19 to provide further evidence for a positive association between the D614G substitution and Rt. 2021 Theoretical biology & medical modelling Abstract SARS_CoV_2 D614G 211 216 COVID-19 135 143 33750399 Modelling the association between COVID-19 transmissibility and D614G substitution in SARS-CoV-2 spike protein: using the surveillance data in California as an example. RESULTS: We found a significant positive association between population-level COVID-19 transmissibility and the D614G substitution on the SARS-CoV-2 spike protein. 2021 Theoretical biology & medical modelling Abstract SARS_CoV_2 D614G 112 117 S 149 154 COVID-19 78 86 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Herein, using structural and biophysical approaches, we explored that the specific mutations in the UK (N501Y), South African (K417N-E484K-N501Y), Brazilian (K417T-E484K-N501Y), and hypothetical (N501Y-E484K) variants alter the binding affinity, create new inter-protein contacts and changes the internal structural dynamics thereby increases the binding and eventually the infectivity. 2021 Journal of cellular physiology Abstract SARS_CoV_2 K417N;K417T;N501Y;N501Y;E484K;E484K;E484K;N501Y;N501Y 127;158;104;196;133;164;202;139;170 132;163;109;201;138;169;207;144;175 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Our investigation highlighted that the South African (K417N-E484K-N501Y), Brazilian (K417T-E484K-N501Y) variants are more lethal than the UK variant (N501Y). 2021 Journal of cellular physiology Abstract SARS_CoV_2 K417N;K417T;N501Y;E484K;E484K;N501Y;N501Y 54;85;150;60;91;66;97 59;90;155;65;96;71;102 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The behavior of the wild type and N501Y is comparable. 2021 Journal of cellular physiology Abstract SARS_CoV_2 N501Y 34 39 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. Notably, we have found a D614G (aspartic acid to glycine) mutation in spike protein of the sequences from the GH clade. 2021 PloS one Abstract SARS_CoV_2 D614G 25 30 S 70 75 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. The G614 variant carrying the characteristic D614G mutation has been shown to be more infectious that lead to its rapid spread worldwide. 2021 PloS one Abstract SARS_CoV_2 D614G 45 50 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. SARS-CoV-2 E-SLiM binds to the human target protein with a higher affinity compared to SARS-CoV-1, showing a difference significantly greater than previously reported using the F318W mutant of PALS1 protein and shorter target peptides. 2021 Computational and structural biotechnology journal Abstract SARS_CoV_2 F318W 177 182 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Computational docking and molecular dynamics simulation analysis of N439K mutation with respect to ACE 2 binding and reactivity with RBM targeted antibodies viz., B38, BD23, CB6, P2B-F26 and EY6A suggests that variant have relatively higher affinity with ACE 2 receptor which may support higher infectivity. 2021 Heliyon Abstract SARS_CoV_2 N439K 68 73 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Indian isolates did not reported prevalence of N439K mutation in receptor binding motif (RBM) as compared to global isolates (0.54%). 2021 Heliyon Abstract SARS_CoV_2 N439K 47 52 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. The study suggests that SARS-CoV-2 genomes from India share consensus with global trends with respect to D614G as most prevalent mutational event (81.66% among 2525 Indian isolates). 2021 Heliyon Abstract SARS_CoV_2 D614G 105 110 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. As suggested by its convergent evolution in Brazil and South Africa, our results indicate that N501Y substitution is a major adaptive spike mutation of major concern. 2021 bioRxiv Abstract SARS_CoV_2 N501Y 95 100 S 134 139 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Here, using a reverse genetics approach, we show that, of the 8 individual spike protein substitutions, only N501Y exhibited consistent fitness gains for replication in the upper airway in the hamster model as well as primary human airway epithelial cells. 2021 bioRxiv Abstract SARS_CoV_2 N501Y 109 114 S 75 80 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Mechanistically, the N501Y substitution improved the affinity of the viral spike protein for cellular receptors. 2021 bioRxiv Abstract SARS_CoV_2 N501Y 21 26 S 75 80 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. The N501Y substitution recapitulated the phenotype of enhanced viral transmission seen with the combined 8 UK spike mutations, suggesting it is a major determinant responsible for increased transmission of this variant. 2021 bioRxiv Abstract SARS_CoV_2 N501Y 4 9 S 110 115 33758837 Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice. Chimeric spike mRNA vaccines efficiently neutralized D614G, UK B.1.1.7., mink cluster five, and the South African B.1.351 variant of concern. 2021 bioRxiv Abstract SARS_CoV_2 D614G 53 58 S 9 14 33758838 Effect of natural mutations of SARS-CoV-2 on spike structure, conformation and antigenicity. HIGHLIGHTS: Cryo-EM structures reveal changes in SARS-CoV-2 S protein during inter-species transmission or immune evasion.Adaptation to mink resulted in increased ACE2 binding and spike destabilization.B.1.1.7 S mutations reveal an intricate balance of stabilizing and destabilizing effects that impact receptor and antibody binding.E484K mutation in B.1.351 and B.1.1.28 S proteins drives immune evasion by altering RBD conformation.S protein uses different mechanisms to converge upon similar solutions for altering RBD up/down positioning. 2021 bioRxiv Abstract SARS_CoV_2 E484K 333 338 S;RBD;RBD;S;S;S;S 180;417;518;60;210;372;434 185;420;521;61;211;373;435 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. Polyclonal antibodies elicited by both vaccines are resilient to most RBD mutations tested, but the E484K substitution has similar negative consequences for neutralization, and exhibit modest but comparable neutralization breadth against distantly related sarbecoviruses. 2021 bioRxiv Abstract SARS_CoV_2 E484K 100 105 RBD 70 73 33758853 Recombinant SARS-CoV-2 genomes are currently circulating at low levels. Recombinant genomes were also found to contain substitutions of concern for elevated transmissibility and lower vaccine efficacy, including D614G, N501Y, E484K, and L452R. 2021 bioRxiv Abstract SARS_CoV_2 D614G;E484K;L452R;N501Y 140;154;165;147 145;159;170;152 33758860 Yeast surface display-based identification of ACE2 mutations that modulate SARS-CoV-2 spike binding across multiple mammalian species. Gln42Leu increased ACE2-spike binding for human and four of four other mammalian ACE2s; Leu79Ile had a effect for human and three of three mammalian ACE2s. 2022 bioRxiv : the preprint server for biology Abstract SARS_CoV_2 L79I;Q42L 88;0 96;8 S 24 29 33758861 Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-Cov-2 variants. According to the phylogenetic analysis, however, emergence of CAL.20C was also specifically triggered by acquisition of the L452R mutation. 2021 bioRxiv Abstract SARS_CoV_2 L452R 124 129 33758861 Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-Cov-2 variants. Further analysis of GISAID-deposited genomes revealed that several independent L452R-carrying lineages have recently emerged across the globe, with over 90% of the isolates reported between December 2020 - February 2021. 2021 bioRxiv Abstract SARS_CoV_2 L452R 79 84 33758861 Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-Cov-2 variants. If true, this in turn might lead to significantly increased infectivity of the L452R variants, warranting their close surveillance and in-depth functional studies. 2021 bioRxiv Abstract SARS_CoV_2 L452R 79 84 33758861 Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-Cov-2 variants. In contrast to CAL.20C that carries two additional to L452R mutations in the Spike protein, L452R is the only mutation found in CAL.20A. 2021 bioRxiv Abstract SARS_CoV_2 L452R;L452R 54;92 59;97 S 77 82 33758861 Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-Cov-2 variants. In some samples, however, we found a distinct L452R-carrying variant of the virus that, upon detailed analysis of the GISAID database genomes, is also circulating primarily in California, but emerged even more recently. 2021 bioRxiv Abstract SARS_CoV_2 L452R 46 51 33758861 Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-Cov-2 variants. Taken together, these results indicate that the L452R mutation alone is of significant adaptive value to SARS-CoV-2 and, apparently, the positive selection for this mutation became particularly strong only recently, possibly reflecting viral adaptation to the containment measures or increasing population immunity. 2021 bioRxiv Abstract SARS_CoV_2 L452R 48 53 33758861 Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-Cov-2 variants. We found that samples isolated since November have an increased number of amino acid mutations in the region, with L452R being the dominant mutation. 2021 bioRxiv Abstract SARS_CoV_2 L452R 115 120 33758861 Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-Cov-2 variants. While the functional impact of L452R has not yet been extensively evaluated, leucine-452 is positioned in the receptor-binding motif of RBD, in the interface of direct contact with the ACE2 receptor. 2021 bioRxiv Abstract SARS_CoV_2 L452R 31 36 RBD 136 139 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. Neutralizing activity of NTD mAbs but not RBD mAbs against a clinical viral isolate carrying E484K as well as extensive changes in the NTD was abolished, suggesting that a proportion of vaccine induced RBD binding antibodies may provide substantial protection against viral variants carrying single E484K RBD mutations. 2021 medRxiv Abstract SARS_CoV_2 E484K;E484K 93;299 98;304 RBD;RBD;RBD 42;202;305 45;205;308 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. METHODS: RT-PCR primers and four sloppy molecular beacon (SMB) probes were designed to amplify and detect the SARS-CoV-2 N501Y (A23063T) and E484K (G23012A) mutations and their corresponding wild type sequences. 2021 medRxiv Abstract SARS_CoV_2 E484K;N501Y;A23063T;G23012A 141;121;128;148 146;126;135;155 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. The assay was 100% sensitive and 100% specific for identifying the N501Y and E484K mutations in cultured virus and in clinical samples as confirmed by Sanger sequencing. 2021 medRxiv Abstract SARS_CoV_2 E484K;N501Y 77;67 82;72 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Our analyses revealed 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation found in the B.1.1.7, B.1.351, and P.1 variants. 2021 medRxiv Abstract SARS_CoV_2 L452R;N501Y 92;213 97;218 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. The variant carries 3 mutations in the spike protein, including an L452R substitution. 2021 medRxiv Abstract SARS_CoV_2 L452R 67 72 S 39 44 33760807 SARS-CoV-2 variants reveal features critical for replication in primary human cells. Notably, naturally occurring variants in Orf3a (Q57H) and nsp2 (T85I) were associated with poor replication in Vero-CCL81 cells but not in BEpCs, while SARS-CoV-2 isolates expressing the Spike D614G variant generally exhibited enhanced replication abilities in BEpCs. 2021 PLoS biology Abstract SARS_CoV_2 D614G;Q57H;T85I 193;48;64 198;52;68 S;ORF3a;Nsp2 187;41;58 192;46;62 33761008 Diverse SARS-CoV-2 variants preceded the initial COVID-19 outbreak in Croatia. Interestingly, we identified a unique mutation resulting in a V13I substitution in Nsp5A, the main viral protease, in a patient who had not received antiviral therapy. 2021 Archives of virology Abstract SARS_CoV_2 V13I 62 66 33767200 The effect of SARS-CoV-2 D614G mutation on BNT162b2 vaccine-elicited neutralization. Here, we report that the D614G mutation modestly reduced (1.7-2.4-fold) SARS-CoV-2 neutralization by BNT162b2 vaccine-elicited mouse, rhesus, and human sera, concurring with the 95% vaccine efficacy observed in clinical trial. 2021 NPJ vaccines Abstract SARS_CoV_2 D614G 25 30 33767200 The effect of SARS-CoV-2 D614G mutation on BNT162b2 vaccine-elicited neutralization. However, the virus has since accumulated mutations, among which the spike D614G is dominant in circulating virus, raising questions about potential virus escape from vaccine-elicited immunity. 2021 NPJ vaccines Abstract SARS_CoV_2 D614G 74 79 S 68 73 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. For instance, mutations Pro462Ala and Leu472Phe resulted in the altered binding energy from - 2 kcal mol-1 in SARS-COV to - 6 kcal mol-1 in SARS-COV-2. 2021 Scientific reports Abstract SARS_CoV_2 L472F;P462A 38;24 47;33 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. Seven of the human mAbs also neutralized (with IC50 < 6.7 x 10-12 M) viruses pseudotyped with mutant spike proteins (including receptor-binding domain mutants and the S1 C-terminal D614G mutant). 2021 JCI insight Abstract SARS_CoV_2 D614G 181 186 S 101 106 33772244 Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies. Sera from 19 individuals vaccinated twice with Pfizer Cominarty, longitudinally tested up to 6 weeks after vaccination, were similarly potent against B.1.1.7 but less efficacious against B.1.351, when compared to D614G. 2021 Nature medicine Abstract SARS_CoV_2 D614G 213 218 33772244 Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies. Sera from 58 convalescent individuals collected up to 9 months after symptoms, similarly neutralized B.1.1.7 and D614G. 2021 Nature medicine Abstract SARS_CoV_2 D614G 113 118 33772244 Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies. We examined sensitivity of the two variants to SARS-CoV-2 antibodies present in sera and nasal swabs from individuals infected with previously circulating strains or who were recently vaccinated, in comparison with a D614G reference virus. 2021 Nature medicine Abstract SARS_CoV_2 D614G 217 222 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. In order to discriminate N501Y variants quickly, a single nucleotide polymorphism (SNP) discrimination assay was designed and validated. 2021 Journal of virological methods Abstract SARS_CoV_2 N501Y 25 30 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. N501Y was found in 206 (27.4 %) of the samples: 94 (28.2 %) men and 112 (26.85 %) women (p = 0.73). 2021 Journal of virological methods Abstract SARS_CoV_2 N501Y 0 5 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. The N501Y mutation in SARS-CoV-2 variants found in several strains from the UK, South Africa and Brazil has been linked to increased transmission. 2021 Journal of virological methods Abstract SARS_CoV_2 N501Y 4 9 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. In this study, we used molecular dynamics simulation and MM-PBSA binding energy analysis to provide insights into the behaviour of the D614G S-protein at the molecular level and describe the neutralization mechanism of this variant. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G 135 140 S 141 142 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Our results show that the D614G S-protein adopts distinct conformational dynamics which is skewed towards the open-state conformation more than the closed-state conformation of the wild-type S-protein. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G 26 31 S;S 32;191 33;192 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The D614G variant of SARS-CoV-2 S-protein emerged in early 2020 and quickly became the dominant circulating strain in Europe and its environs. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G 4 9 S 32 33 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The results of this study have shed insights into the behaviour of the D614G S-protein at the molecular level and provided a glimpse of the neutralization mechanism of this variant. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G 71 76 S 77 78 33777333 Specific epitopes form extensive hydrogen-bonding networks to ensure efficient antibody binding of SARS-CoV-2: Implications for advanced antibody design. Subsequently, mutations of VH V98E and VL G68D in CC12.1, which could significantly enhance the binding affinity of the antibody, were also proposed. 2021 Computational and structural biotechnology journal Abstract SARS_CoV_2 G68D;V98E 42;30 46;34 33778179 Mutational analysis of structural proteins of SARS-CoV-2. Based on structural analysis, our study revealed that the D614G mutation in the S protein diminished the interaction with T859 and K854 of adjacent chains. 2021 Heliyon Abstract SARS_CoV_2 D614G 58 63 S 80 81 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Hence, we developed a PCR-based method to rapidly detect the 6 mutational hotspots (H49Y, G476S, V483A, H519Q, A520S, and D614G) in the S protein and applied this method to analyze the hotspots in the viral isolates from different geographical origins. 2021 Gene reports Abstract SARS_CoV_2 A520S;D614G;G476S;H519Q;V483A;H49Y 111;122;90;104;97;84 116;127;95;109;102;88 S 136 137 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Here, we identified that there was only the D614G mutation in the viral isolates. 2021 Gene reports Abstract SARS_CoV_2 D614G 44 49 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Our results support recent epidemiological and genomic data demonstrating that the viral infectivity and transmission are enhanced by the S protein D614G mutation. 2021 Gene reports Abstract SARS_CoV_2 D614G 148 153 S 138 139 33780970 Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Although we tested only one plasma sample from an individual infected with a SARS-CoV-2 variant with only the E484K substitution, this plasma sample potently neutralized both variants. 2021 Nature Abstract SARS_CoV_2 E484K 110 115 33780970 Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Sequencing demonstrated that infections of plasma donors from the first wave were with viruses that did not contain the mutations associated with 501Y.V2, except for one infection that contained the E484K substitution in the receptor-binding domain. 2021 Nature Abstract SARS_CoV_2 E484K 199 204 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. As a consequence, T85I, Q57H and R203M in NSP2, ORF3a and Nucleocapsid respectively are found to be responsible for Cluster 1 as they are damaging and unstable non-synonymous signature SNPs. 2021 Virus research Abstract SARS_CoV_2 Q57H;R203M;T85I 24;33;18 28;38;22 N;ORF3a;Nsp2 58;48;42 70;53;46 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. Similarly, F506L and S507C in Exon are responsible for both Clusters 3 and 4 while Clusters 2 and 5 do not exhibit such behaviour due to the absence of any non-synonymous signature SNPs. 2021 Virus research Abstract SARS_CoV_2 F506L;S507C 11;21 16;26 Exon 30 34 33785459 Emergence and outcomes of the SARS-CoV-2 'Marseille-4' variant. One leads to an S477N substitution in the receptor binding domain of the spike protein targeted by current vaccines. 2021 International journal of infectious diseases Abstract SARS_CoV_2 S477N 16 21 RBD;S 42;73 65;78 33788923 Estimation of Secondary Household Attack Rates for Emergent Spike L452R Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants Detected by Genomic Surveillance at a Community-Based Testing Site in San Francisco. Certain viral lineages bearing spike mutations, defined in part by L452R, S13I, and W152C, comprised 54.4% of the total sequences from January, compared to 15.7% in November. 2022 Clinical infectious diseases Abstract SARS_CoV_2 L452R;S13I;W152C 67;74;84 72;78;89 S 31 36 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Contribution of single or combined spike mutations to neutralization and infectivity were monitored, highlighting mechanisms by which viral infectivity and neutralization resistance are enhanced by N501Y or E484K/K417N mutations. 2021 Cell host & microbe Abstract SARS_CoV_2 E484K;N501Y;K417N 207;198;213 212;203;218 S 35 40 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. However, while wild-type and UK-N501Y pseudoviruses were similarly neutralized, those displaying SA-N501Y/K417N/E484K spike mutations moderately resist neutralization. 2021 Cell host & microbe Abstract SARS_CoV_2 E484K;K417N;N501Y;N501Y 112;106;32;100 117;111;37;105 S 118 123 33789940 Stability of SARS-CoV-2 Spike G614 Variant Surpasses That of the D614 Variant after Cold Storage. A SARS-CoV-2 S-D614G variant is currently the most dominant variant in circulation and is associated with enhanced infectivity. 2021 mSphere Abstract SARS_CoV_2 D614G 15 20 S 13 14 33789940 Stability of SARS-CoV-2 Spike G614 Variant Surpasses That of the D614 Variant after Cold Storage. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) carrying the D614G mutation on the spike protein is the predominant circulating variant and is associated with enhanced infectivity. 2021 mSphere Abstract SARS_CoV_2 D614G 74 79 S 96 101 COVID-19 0 47 33791698 B.1.526 SARS-CoV-2 variants identified in New York City are neutralized by vaccine-elicited and therapeutic monoclonal antibodies. The E484K version was neutralized with a 12-fold decrease in titer by the REGN10933 monoclonal antibody but the combination cocktail with REGN10987 was fully active. 2021 bioRxiv Abstract SARS_CoV_2 E484K 4 9 33791698 B.1.526 SARS-CoV-2 variants identified in New York City are neutralized by vaccine-elicited and therapeutic monoclonal antibodies. Two versions of the variant were identified, both with the prevalent D614G mutation in the spike protein together with four novel point mutations and with an E484K or S477N mutation in the receptor binding domain, raising concerns of possible resistance to vaccine-elicited and therapeutic antibodies. 2021 bioRxiv Abstract SARS_CoV_2 D614G;E484K;S477N 69;158;167 74;163;172 RBD;S 189;91 212;96 33791698 B.1.526 SARS-CoV-2 variants identified in New York City are neutralized by vaccine-elicited and therapeutic monoclonal antibodies. We report that convalescent sera and vaccine-elicited antibodies retain full neutralizing titer against the S477N B.1.526 variant and neutralize the E484K version with a modest 3.5-fold decrease in titer as compared to D614G. 2021 bioRxiv Abstract SARS_CoV_2 D614G;E484K;S477N 219;149;108 224;154;113 33791700 Factors Associated with Emerging and Re-emerging of SARS-CoV-2 Variants. Additionally, we show that new SARS-CoV-2 variants emerged in the background of D614G in Spike protein and P323L in RNA polymerase. 2021 bioRxiv Abstract SARS_CoV_2 D614G;P323L 80;107 85;112 S 89 94 33791702 Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2. Moreover, the entry characteristics of B.1.1.7 were distinct from that of its predecessor strain containing the D614G mutation. 2021 bioRxiv Abstract SARS_CoV_2 D614G 112 117 33791722 SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis. All genomes presented differences in the S gene compared to the Wuhan reference strain, being the D614G amino acid replacement the most common change. 2021 medRxiv Abstract SARS_CoV_2 D614G 98 103 S 41 42 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. NMA, C-alpha DMD and all-atom MD suggested some mutations to have stabilizing roles (P13L, S197L and R203K in N protein) where remaining ones were predicted to destabilize mutant protein. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 R203K;S197L;P13L 101;91;85 106;96;89 N 110 111 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. PredictSNP predictor suggested that four mutations (L37H in E, R203K and P344S in N and D614G in S) out of seven were predicted to be neutral whilst the remaining ones (P13L, S197L and G204R in N) were predicted to be deleterious in nature thereby impacting protein functionality. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 D614G;G204R;P344S;R203K;S197L;L37H;P13L 88;185;73;63;175;52;169 93;190;78;68;180;56;173 E;N;N;S 60;82;194;97 61;83;195;98 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. A possible reason behind this phenomenon can be that V843F is a conserved residue of PLPro which damaged the protease structure, but A889V, a less conserved residue, presumably neutralized that damage. 2021 Journal, genetic engineering & biotechnology Abstract SARS_CoV_2 A889V;V843F 133;53 138;58 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. G1691C can decrease the flexibility of the protein. 2021 Journal, genetic engineering & biotechnology Abstract SARS_CoV_2 G1691C 0 6 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. However, V843F+A889V double mutant exhibited the same binding affinity as wild type PLPro. 2021 Journal, genetic engineering & biotechnology Abstract SARS_CoV_2 V843F;A889V 9;15 14;20 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. RESULTS: Using different computational tools, we have found V121D substitution has the potential to destabilize the non-structural protein-1 (NSP-1). 2021 Journal, genetic engineering & biotechnology Abstract SARS_CoV_2 V121D 60 65 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. The genome has four novel non-synonymous mutations in V121D, V843F, A889V, and G1691C positions. 2021 Journal, genetic engineering & biotechnology Abstract SARS_CoV_2 A889V;G1691C;V121D;V843F 68;79;54;61 73;85;59;66 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. V843F and A889V might change the binding pattern and efficacy of SARS-CoV-2 papain-like protease (PLPro) inhibitor GRL0617. 2021 Journal, genetic engineering & biotechnology Abstract SARS_CoV_2 A889V;V843F 10;0 15;5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. V843F substitution in PLPro was the most prevalent mutation in the clinical samples. 2021 Journal, genetic engineering & biotechnology Abstract SARS_CoV_2 V843F 0 5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. V843F, A889V, and G1691C are all located in nonstructural protein-3 (NSP-3). 2021 Journal, genetic engineering & biotechnology Abstract SARS_CoV_2 A889V;G1691C;V843F 7;18;0 12;24;5 33798491 Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant. We compared antibody binding and live virus neutralization of sera from naturally infected and Moderna-vaccinated individuals against two SARS-CoV-2 variants: B.1 containing the spike mutation D614G and the emerging B.1.351 variant containing additional spike mutations and deletions. 2021 Cell host & microbe Abstract SARS_CoV_2 D614G 193 198 S;S 178;254 183;259 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Haplotype maps and phylogenetic tree analysis showed that amino acid variations in ORF1ab (p.5828P > L and p.5865Y > C, also NSP13: P504L and NSP13: Y541C) were the important characteristics of such clade. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 P504L;Y541C 132;149 137;154 ORF1ab;Nsp13;Nsp13 83;125;142 89;130;147 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. While the N501Y mutation was observed in all three lineages, the 501Y.V1 and P.1 accumulated a different set of mutations in the S protein. 2021 Viruses Abstract SARS_CoV_2 N501Y 10 15 S 129 130 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. Of concern are immune escape mutations acquired by the VOC: E484K, F490S, S494P (in the receptor binding motif of spike) and Q677H, Q675H (in the proximity of the polybasic cleavage site at the S1/S2 boundary). 2021 Viruses Abstract SARS_CoV_2 E484K;F490S;Q675H;Q677H;S494P 60;67;132;125;74 65;72;137;130;79 S 114 119 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The L18F substitution is of significance because it has been found to compromise binding of neutralizing antibodies. 2021 Viruses Abstract SARS_CoV_2 L18F 4 8 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. We have estimated growth rates of expanding mutations acquired by the VOC lineage to find that the L18F substitution in spike has initiated a fast growing VOC substrain. 2021 Viruses Abstract SARS_CoV_2 L18F 99 103 S 120 125 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. A total of 739 N501Y positive genomes were analysed and show a broad range of introduction events to Switzerland. 2021 Microorganisms Abstract SARS_CoV_2 N501Y 15 20 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. In January 2021, we validated and implemented an N501Y-specific PCR to rapidly screen for VoCs, which are then confirmed using amplicon sequencing or whole genome sequencing (WGS). 2021 Microorganisms Abstract SARS_CoV_2 N501Y 49 54 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. In this paper, we describe the nationwide coordination and implementation process across laboratories, public health institutions, and researchers, the first results of our N501Y-specific variant screening, and the phylogenetic analysis of all available WGS data in Switzerland, that together identified the early introduction events and subsequent community spreading of the VoCs. 2021 Microorganisms Abstract SARS_CoV_2 N501Y 173 178 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations for lineage specific surveillance. 2021 Microorganisms Abstract SARS_CoV_2 N501Y;N501Y;N501Y 139;53;91 144;58;96 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. In the spike gene region, the molecular signature for B.1.1.312 was the non-synonymous mutation A24432T resulting in a deleterious amino acid substitution (Q957L), while the molecular signature for B.1.36.10 was the synonymous mutation C22444T. 2021 Pathogens (Basel, Switzerland) Abstract SARS_CoV_2 A24432T;C22444T;Q957L 96;236;156 103;243;161 S 7 12 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. The amino acid substitution D614G in the spike glycoprotein was exclusively present in the country from July 2020 onwards. 2021 Pathogens (Basel, Switzerland) Abstract SARS_CoV_2 D614G 28 33 S 41 59 33810168 Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa. In addition, a new mutation, 5209A>G, emerged within the Cape Town cluster. 2021 Viruses Abstract SARS_CoV_2 A5209G 29 36 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. Among the missense mutations present in the Gujarat SARS-CoV-2 genomes, C28854T (Ser194Leu) had an allele frequency of 47.62 and 7.25% in deceased patients from the Gujarat and global datasets, respectively. 2021 Frontiers in genetics Abstract SARS_CoV_2 C28854T;S194L 72;81 79;90 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. The other deleterious variant identified in deceased patients from Gujarat (p-value of 0.355) and the world (p-value of 2.43E-06) is G25563T, which is located in Orf3a and plays a potential role in viral pathogenesis. 2021 Frontiers in genetics Abstract SARS_CoV_2 G25563T 133 140 ORF3a 162 167 33821264 An MHV macrodomain mutant predicted to lack ADP-ribose binding activity is severely attenuated, indicating multiple roles for the macrodomain in coronavirus replication. D1329A and N1347A both replicated poorly in bone-marrow derived macrophages (BMDMs), were inhibited by PARP enzymes, and were highly attenuated in vivo . 2021 bioRxiv Abstract SARS_CoV_2 N1347A;D1329A 11;0 17;6 33821264 An MHV macrodomain mutant predicted to lack ADP-ribose binding activity is severely attenuated, indicating multiple roles for the macrodomain in coronavirus replication. However, D1329A was significantly more attenuated than N1347A in all cell lines tested that were susceptible to MHV infection. 2021 bioRxiv Abstract SARS_CoV_2 D1329A;N1347A 9;55 15;61 33821264 An MHV macrodomain mutant predicted to lack ADP-ribose binding activity is severely attenuated, indicating multiple roles for the macrodomain in coronavirus replication. In addition, D1329A retained some ability to block IFN-beta transcript accumulation compared to N1347A, indicating that these two mutants impacted distinct Mac1 functions. 2021 bioRxiv Abstract SARS_CoV_2 D1329A;N1347A 13;96 19;102 33821264 An MHV macrodomain mutant predicted to lack ADP-ribose binding activity is severely attenuated, indicating multiple roles for the macrodomain in coronavirus replication. To determine if Mac1 ADP-ribose binding separately contributes to CoV replication, we compared the replication of a murine hepatitis virus (MHV) Mac1 mutant predicted to dramatically reduce ADP-ribose binding, D1329A, to the previously mentioned asparagine mutant, N1347A. 2021 bioRxiv Abstract SARS_CoV_2 D1329A;N1347A 210;265 216;271 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. Furthermore, a bispecific antibody that neutralized B.1.351 protected against SARS-CoV-2 expressing the crucial E484K mutation in the hamster model. 2021 bioRxiv Abstract SARS_CoV_2 E484K 112 117 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. Unlike other natural cysteine variants, a Cys15Phe (C15F) mutant retained partial, but unstable, infectivity. 2021 bioRxiv Abstract SARS_CoV_2 C15F;C15F 42;52 50;56 33821281 SARS-CoV-2 immune evasion by variant B.1.427/B.1.429. Furthermore, we observed a complete loss of B.1.427/B.1.429 neutralization for a panel of mAbs targeting the N-terminal domain due to a large structural rearrangement of the NTD antigenic supersite involving an S13I-mediated shift of the signal peptide cleavage site. 2021 bioRxiv Abstract SARS_CoV_2 S13I 211 215 N 109 110 33821281 SARS-CoV-2 immune evasion by variant B.1.427/B.1.429. It is unclear whether antibody responses to SARS-CoV-2 infection or to the prototypic Wuhan-1 isolate-based vaccines will be impacted by the three B.1.427/B.1.429 S mutations: S13I, W152C and L452R. 2021 bioRxiv Abstract SARS_CoV_2 L452R;S13I;W152C 192;176;182 197;180;187 S 163 164 COVID-19 44 64 33821281 SARS-CoV-2 immune evasion by variant B.1.427/B.1.429. The RBD L452R mutation reduced or abolished neutralizing activity of 14 out of 35 RBD-specific monoclonal antibodies (mAbs), including three clinical-stage mAbs. 2021 bioRxiv Abstract SARS_CoV_2 L452R 8 13 RBD;RBD 4;82 7;85 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. We find evidence for strong selection favoring the D614G spike mutation and B.1.1.7 (Alpha), weaker selection favoring B.1.351 (Beta), and no advantage of R.1 after it spreads beyond Japan. 2021 medRxiv Abstract SARS_CoV_2 D614G 51 56 S 57 62 33834012 Comparison of Clinical Features and Outcomes of Medically Attended COVID-19 and Influenza Patients in a Defined Population in the 2020 Respiratory Virus Season. In addition, the S477N and N439K mutations on spike may affect the affinity with receptor ACE2. 2021 Frontiers in public health Abstract SARS_CoV_2 N439K;S477N 27;17 32;22 S 46 51 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. Here, we show that despite the decrease in binding affinity (1.48 kcal/mol) between RBD and ACE2, the K417N mutation abolishes a buried interfacial salt bridge between the RBD and neutralizing antibody CB6. 2022 Journal of medicinal chemistry Abstract SARS_CoV_2 K417N 102 107 RBD;RBD 84;172 87;175 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. However, the K417N mutation appears to be unfavorable as it removes one interfacial salt bridge. 2022 Journal of medicinal chemistry Abstract SARS_CoV_2 K417N 13 18 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. It is known that N501Y and E484K can enhance binding between the coronavirus receptor domain (RBD) and human ACE2. 2022 Journal of medicinal chemistry Abstract SARS_CoV_2 E484K;N501Y 27;17 32;22 RBD 94 97 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. The highly infectious SARS-CoV-2 variant B.1.351 that first emerged in South Africa with triple mutations (N501Y, K417N, and E484K) is globally worrisome. 2022 Journal of medicinal chemistry Abstract SARS_CoV_2 E484K;K417N;N501Y 125;114;107 130;119;112 33835028 Human airway cells prevent SARS-CoV-2 multibasic cleavage site cell culture adaptation. Here, we report that propagating SARS-CoV-2 on the human airway cell line Calu-3 - that expresses serine proteases - prevents cell culture adaptations in the MBCS and directly adjacent to the MBCS (S686G). 2021 eLife Abstract SARS_CoV_2 S686G 198 203 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Remarkably, variation tracking of the virus indicated the increase in frequency of D614G mutation, along with B.1* lineages, which showed continuity till October 2020. 2022 Transboundary and emerging diseases Abstract SARS_CoV_2 D614G 83 88 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. The increase in frequency of D614G mutation and B.1* lineages from mid-May onwards predicts a rapid viral transmission that may push the country into a critical health situation followed by a considerable change in composition of viral lineages circulating in the country. 2022 Transboundary and emerging diseases Abstract SARS_CoV_2 D614G 29 34 33836314 Implementation of an in-house real-time reverse transcription-PCR assay for the rapid detection of the SARS-CoV-2 Marseille-4 variant. In our geographical area a viral variant we named Marseille-4 harbors a S477 N substitution in this RBD. 2021 Journal of clinical virology Abstract SARS_CoV_2 S477N 72 78 RBD 100 103 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. Among the 100,849 genome variants of SARS-CoV-2 in the GISAID database, we identify that ~37% (36,941) of the genomes contain a specific trio-nucleotide polymorphism (GGG-to-AAC) in the coding sequence of N, which leads to the amino acid substitutions, R203K/G204R. 2021 Nature communications Abstract SARS_CoV_2 R203K;G204R 253;259 258;264 N 205 206 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. Interestingly, NR203K/G204R exhibits a higher propensity to undergo LLPS and a greater effect on IFN inhibition. 2021 Nature communications Abstract SARS_CoV_2 G204R;N203K;R203K 22;16;16 27;21;21 33838638 Free SARS-CoV-2 Spike Protein S1 Particles May Play a Role in the Pathogenesis of COVID-19 Infection. the wild type D614 protein), and lack of increased severity of the COVID-19 infection caused by the mutant (D614G) SARS-CoV-2 strain, despite its higher infectivity and higher in vivo viral load. 2021 Biochemistry. Biokhimiia Abstract SARS_CoV_2 D614G 108 113 COVID-19 67 85 33838638 Free SARS-CoV-2 Spike Protein S1 Particles May Play a Role in the Pathogenesis of COVID-19 Infection. This hypothesis also suggests the association between less pronounced shedding of the S1 particles reported for the S protein carrying the D614G mutation (vs. 2021 Biochemistry. Biokhimiia Abstract SARS_CoV_2 D614G 139 144 S 116 117 33840632 Association of SARS-CoV-2 clades with clinical, inflammatory and virologic outcomes: An observational study. 29 (9%) were infected with clade S, 90 (28%) with clade L/V, 96 (30%) with clade G (containing D614G variant), and 104 (33%) with other clades 'O' were assigned to lineage B.6. 2021 EBioMedicine Abstract SARS_CoV_2 D614G 95 100 S 33 34 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. Through haplotype subgroup epidemic trends analysis of 131,576 genome sequences, the great significance of the previous 4 specific sites (C241T, C3037T, C14408T and A23403G) was further revealed, and 6 new mutation sites of highly linked (T445C, C6286T, C22227T, G25563T, C26801G and G29645T) were discovered for the first time that might be related to the infectivity, pathogenicity or host adaptability of SARS-CoV-2. 2021 Computational and structural biotechnology journal Abstract SARS_CoV_2 A23403G;C14408T;C22227T;C26801G;C3037T;C6286T;G25563T;G29645T;C241T;T445C 165;153;254;272;145;246;263;284;138;239 172;160;261;279;151;252;270;291;143;244 33842902 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. In addition, the L452R mutation in the B.1.429 lineage escapes LY-CoV555. 2021 Cell reports. Medicine Abstract SARS_CoV_2 L452R 17 22 33842902 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. Individual mutations that escape binding by each antibody are combined in the circulating B.1.351 and P.1 SARS-CoV-2 lineages (E484K escapes LY-CoV555, K417N/T escapes LY-CoV016). 2021 Cell reports. Medicine Abstract SARS_CoV_2 K417N;K417T;E484K 152;152;127 159;159;132 33851149 Deletion of ER-retention Motif on SARS-CoV-2 Spike Protein Reduces Cell Hybrid During Cell-cell Fusion. Comparison of cell fusion occurring via Delta19-S expressing cells shows defective nuclear fusion and syncytia formation compared to WT-S. 2021 Research square Abstract SARS_CoV_2 Delta19-S 40 47 S;S 48;136 49;137 33851149 Deletion of ER-retention Motif on SARS-CoV-2 Spike Protein Reduces Cell Hybrid During Cell-cell Fusion. Recently, the Delta19-S variant is being widely used to increase SARS-CoV-2 pseudovirus production for in vitro assays. 2021 Research square Abstract SARS_CoV_2 Delta19-S 14 21 S 22 23 33851149 Deletion of ER-retention Motif on SARS-CoV-2 Spike Protein Reduces Cell Hybrid During Cell-cell Fusion. These cell lines were stably transduced with either wild-type (WT-S) S protein or a mutated variant where the ER-retention motif was removed (Delta19-S), or human ACE2 vectors. 2021 Research square Abstract SARS_CoV_2 Delta19-S 142 149 S;S;S 66;69;150 67;70;151 33851149 Deletion of ER-retention Motif on SARS-CoV-2 Spike Protein Reduces Cell Hybrid During Cell-cell Fusion. This distinction between the Delta19-S variant and WT-S protein may have downstream implications for studies that utilize pseudovirus-based entry assays. 2021 Research square Abstract SARS_CoV_2 Delta19-S 29 36 S;S 37;54 38;55 33851150 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. The same set of sera efficiently neutralized S from B.1.1.7 and showed only moderately reduced activity against S carrying the E484K substitution alone. 2021 Research square Abstract SARS_CoV_2 E484K 127 132 S;S 45;112 46;113 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Functional assays using pseudoparticles harboring SARS-CoV-2 spikes and cell-to-cell fusion assays demonstrated no differences between Wuhan-Hu-1, B.1.1.7 or a P681H point mutant. 2021 bioRxiv Abstract SARS_CoV_2 P681H 160 165 S 61 67 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Here, we studied the role of the P681H mutation in B.1.1.7 cell entry. 2021 bioRxiv Abstract SARS_CoV_2 P681H 33 38 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Our findings suggest that while the B.1.1.7 P681H mutation may slightly increase S1/S2 cleavage this does not significantly impact viral entry or cell-cell spread. 2021 bioRxiv Abstract SARS_CoV_2 P681H 44 49 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. SARS-CoV-2 B.1.1.7 (Alpha), a WHO variant of concern (VOC) first identified in the UK in late 2020, contains several mutations including P681H in the spike S1/S2 cleavage site, which is predicted to increase cleavage by furin, potentially impacting the viral cell entry. 2021 bioRxiv Abstract SARS_CoV_2 P681H 137 142 S 150 155 33851157 Regulation of the Dimerization and Activity of SARS-CoV-2 Main Protease through Reversible Glutathionylation of Cysteine 300. Proteolytic digestions of Mpro revealed Cys300 as a primary target of glutathionylation, and experiments using a C300S Mpro mutant revealed that Cys300 is required for inhibition of activity upon Mpro glutathionylation. 2021 bioRxiv : the preprint server for biology Abstract SARS_CoV_2 C300S 113 118 33851162 A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. We report a SARS-CoV-2 lineage that shares N501Y, P681H, and other mutations with known variants of concern, such as B.1.1.7. 2021 bioRxiv Abstract SARS_CoV_2 N501Y;P681H 43;50 48;55 33851214 Nosocomial Outbreak of Coronavirus Disease 2019 by Possible Airborne Transmission Leading to a Superspreading Event. The outbreak strains belong to SARS-CoV-2 lineage B.1.36.27 (GISAID clade GH) with the unique S-T470N mutation on WGS. 2021 Clinical infectious diseases Abstract SARS_CoV_2 T470N 96 101 S 94 95 33851216 Sera Neutralizing Activities Against Severe Acute Respiratory Syndrome Coronavirus 2 and Multiple Variants 6 Months After Hospitalization for Coronavirus Disease 2019. In addition, sera collected at 6 months were tested against multiple SARS-CoV-2 variants and showed efficient neutralizing effects against the D614G, B.1.1.7, and P.1 variants but significantly weaker activity against the B.1.351 variant. 2021 Clinical infectious diseases Abstract SARS_CoV_2 D614G 143 148 33851216 Sera Neutralizing Activities Against Severe Acute Respiratory Syndrome Coronavirus 2 and Multiple Variants 6 Months After Hospitalization for Coronavirus Disease 2019. Our results indicate a sustained humoral response against the ancestral strain and the D614G, B.1.1.7, and P.1 variants for at least 6 months in patients previously hospitalized for COVID-19. 2021 Clinical infectious diseases Abstract SARS_CoV_2 D614G 87 92 COVID-19 182 190 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. All have mutations in the ACE2 binding site, with P.1 and B.1.351 having a virtually identical triplet (E484K, K417N/T, and N501Y), which we show confer similar increased affinity for ACE2. 2021 Cell Abstract SARS_CoV_2 K417N;K417T;N501Y;E484K 111;111;124;104 118;118;129;109 33853970 Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. 2021 Science (New York, N.Y.) Abstract SARS_CoV_2 E484K;N501Y;K417T 81;92;74 86;97;79 S 59 64 33855313 Phylogenetic estimates of SARS-CoV-2 introductions into Washington State. Lineages with the Spike D614G variant accounted for the majority (88%) of introductions. 2021 medRxiv Abstract SARS_CoV_2 D614G 24 29 S 18 23 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. In contrast, mutation Y453F reduces neutralization by an antibody with emergency use authorization for coronavirus disease 2019 (COVID-19) therapy and sera/plasma from COVID-19 patients. 2021 Cell reports Abstract SARS_CoV_2 Y453F 22 27 COVID-19;COVID-19;COVID-19 103;129;168 122;137;176 33860605 Polysulfates Block SARS-CoV-2 Uptake through Electrostatic Interactions*. Furthermore, in molecular dynamics simulations, we verified that LPGS can bind more strongly to the spike protein than heparin, and that LPGS can interact even more with the spike protein of the new N501Y and E484K variants. 2021 Angewandte Chemie (International ed. in English) Abstract SARS_CoV_2 E484K;N501Y 209;199 214;204 S;S 100;174 105;179 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. The COVID-19 (coronavirus disease 2019) pandemic underwent a rapid transition with the emergence of a dominant viral variant (from the "D-form" to the "G-form") that carried an amino acid substitution D614G in its "Spike" protein. 2021 Science advances Abstract SARS_CoV_2 D614G 201 206 S 215 220 COVID-19;COVID-19 14;4 33;12 33868743 COVID-19 and mutations a threat level assessment. E484K being the most concerning as it aids in immune evasion and drastically causes the efficacy of the current vaccines to be reduced by large margins. 2021 Nepal journal of epidemiology Abstract SARS_CoV_2 E484K 0 5 33868743 COVID-19 and mutations a threat level assessment. It is evident that the SARS-CoV-2 variants pose an international health risk, the mutations of E484K and N501Y are the two most implicated mutations. 2021 Nepal journal of epidemiology Abstract SARS_CoV_2 E484K;N501Y 95;105 100;110 33875719 Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology. Chronological analysis revealed expansion in SARS-CoV-2 clades carrying D614G mutations with the predominance of the newest clade, GV, in the last three months. 2021 Scientific reports Abstract SARS_CoV_2 D614G 72 77 33875719 Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology. D614G clades prevail in countries with more COVID-19 cases. 2021 Scientific reports Abstract SARS_CoV_2 D614G 0 5 COVID-19 44 52 33880470 Revealing the threat of emerging SARS-CoV-2 mutations to antibody therapies. We unveil, for the first time, that high-frequency mutations R346K/S, N439K, G446V, L455F, V483F/A, E484Q/V/A/G/D, F486L, F490L/V/S, Q493L, and S494P/L might compromise some of mAbs in clinical trials. 2021 bioRxiv Abstract SARS_CoV_2 E484A;E484D;E484G;E484Q;E484V;F486L;F490L;F490S;F490V;G446V;L455F;N439K;Q493L;R346K;R346S;S494L;S494P;V483A;V483F 100;100;100;100;100;115;122;122;122;77;84;70;133;61;61;144;144;91;91 113;113;113;113;113;120;131;131;131;82;89;75;138;68;68;151;151;98;98 33880475 Generation of a novel SARS-CoV-2 sub-genomic RNA due to the R203K/G204R variant in nucleocapsid: homologous recombination has potential to change SARS-CoV-2 at both protein and RNA level. In this study, we examined the adjacent amino acid polymorphisms in the nucleocapsid (R203K/G204R) of SARS-CoV-2 that arose on the background of the spike D614G change and describe how strains harboring these changes became dominant circulating strains globally. 2021 bioRxiv Abstract SARS_CoV_2 D614G;R203K;G204R 155;86;92 160;91;97 N;S 72;149 84;154 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. A recently identified variant of SARS-CoV-2 virus, known as the United Kingdom (UK) variant (lineage B.1.1.7), has an N501Y mutation on its spike protein. 2021 The journal of physical chemistry. B Abstract SARS_CoV_2 N501Y 118 123 S 140 145 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. Here, we report an efficient computational approach, including the simple energy minimizations and binding free energy calculations, starting from an experimental structure of the binding complex along with experimental calibration of the calculated binding free energies, to rapidly and reliably predict the binding affinities of the N501Y mutant with human ACE2 (hACE2) and recently reported miniprotein and hACE2 decoy (CTC-445.2) drug candidates. 2021 The journal of physical chemistry. B Abstract SARS_CoV_2 N501Y 335 340 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. It has been demonstrated that the N501Y mutation markedly increases the ACE2-spike protein binding affinity (Kd) from 22 to 0.44 nM, which could partially explain why the UK variant is more infectious. 2021 The journal of physical chemistry. B Abstract SARS_CoV_2 N501Y 34 39 S 77 82 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. The miniproteins are predicted to have ~10,000- to 100,000-fold diminished binding affinities with the N501Y mutant, creating a need for design of novel therapeutic candidates to overcome the N501Y mutation-induced drug resistance. 2021 The journal of physical chemistry. B Abstract SARS_CoV_2 N501Y;N501Y 103;192 108;197 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. The N501Y mutation is also predicted to decrease the binding affinity of a hACE2 decoy (CTC-445.2) binding with the spike protein by ~200-fold. 2021 The journal of physical chemistry. B Abstract SARS_CoV_2 N501Y 4 9 S 116 121 33882219 Vaccine Breakthrough Infections with SARS-CoV-2 Variants. Viral sequencing revealed variants of likely clinical importance, including E484K in 1 woman and three mutations (T95I, del142-144, and D614G) in both. 2021 The New England journal of medicine Abstract SARS_CoV_2 D614G;E484K;T95I 136;76;114 141;81;118 33883059 Severe Acute Respiratory Syndrome Coronavirus 2 P.2 Lineage Associated with Reinfection Case, Brazil, June-October 2020. Of note, P.2 corresponds to an emergent viral lineage in Brazil that contains the mutation E484K in the spike protein. 2021 Emerging infectious diseases Abstract SARS_CoV_2 E484K 91 96 S 104 109 33883466 Pandemic analysis of infection and death correlated with genomic open reading frame 10 mutation in severe acute respiratory syndrome coronavirus 2 victims. A8F expressed highly dominant in Japan (over 80%) and German (around 40%) coming to the end of 2020, but no significant finding in other countries. 2021 Journal of the Chinese Medical Association : JCMA Abstract SARS_CoV_2 A8F 0 3 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. By applying molecular docking using both Z-Dock and Haddock software we found that multiple mutations, including A475V, V455E, V445L, and V445I, resulted in the higher binding free energy as compared to the wild type (WT) spike protein, thus had a destabilizing effect on the binding to ACE2. 2021 EXCLI journal Abstract SARS_CoV_2 A475V;V445I;V445L;V455E 113;138;127;120 118;143;132;125 S 222 227 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. On the other hand, several mutants, including the most prevalent N501Y and B.1.1.7 variants, as well as the K444R, L455F, Q493R, and Y505W variants exhibited lower binding free energy as compared to the WT spike. 2021 EXCLI journal Abstract SARS_CoV_2 K444R;L455F;N501Y;Q493R;Y505W 108;115;65;122;133 113;120;70;127;138 S 206 211 33884270 In Silico Analysis of High-Risk Missense Variants in Human ACE2 Gene and Susceptibility to SARS-CoV-2 Infection. Six ACE2 high-risk pathogenic nsSNPs (D427Y, R514G, R708W, R710C, R716C, and R768W) were found to be the most damaging by at least six software tools (cumulative score between 6 and 7) and exert deleterious effect on the ACE2 protein structure and likely function. 2021 BioMed research international Abstract SARS_CoV_2 R514G;R708W;R710C;R716C;R768W;D427Y 45;52;59;66;77;38 50;57;64;71;82;43 33885735 New framework for recombination and adaptive evolution analysis with application to the novel coronavirus SARS-CoV-2. Clustering results show that the novel coronavirus has diverged into several clusters that cocirculate over time in various regions and that several mutations across the genome are fixed during transmission throughout the human population, including D614G in the S gene and two accompanied mutations in ORF1ab. 2021 Briefings in bioinformatics Abstract SARS_CoV_2 D614G 250 255 ORF1ab;S 303;263 309;264 33886690 The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways. Finally, we demonstrate that the D614G mutation increases SARS-CoV-2 stability, particularly at 37 C, and, enhances its use of the cathepsin L pathway. 2021 PLoS pathogens Abstract SARS_CoV_2 D614G 33 38 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. Here, we report the near-complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harboring the N501Y mutation assigned to the B.1.1.7 lineage. 2021 Microbiology resource announcements Abstract SARS_CoV_2 N501Y 176 181 COVID-19 108 148 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Nanobody-Fc fusions of the four most potent nanobodies blocked ACE2 engagement with RBD variants present in human populations and potently neutralized both wild-type SARS-CoV-2 and the N501Y D614G variant at concentrations as low as 0.1 nM. 2021 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 D614G;N501Y 191;185 196;190 RBD 84 87 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Prophylactic administration of either single nanobody-Fc or as mixtures reduced viral loads by up to 104-fold in mice infected with the N501Y D614G SARS-CoV-2 virus. 2021 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 D614G;N501Y 142;136 147;141 33893880 Combined RT-qPCR and pyrosequencing of a Spike glycoprotein polybasic cleavage motif can uncover pediatric SARS-CoV-2 infections associated with heterogeneous presentation. Moreover, due to the incremental transmission of SARS-CoV-2 variants of concern, we note that the used strategy can uncover (Spike) P681H allowing the pre-selection of SARS-CoV-2 B.1.1.7 candidate specimens for deep sequencing. 2021 Molecular and cellular pediatrics Abstract SARS_CoV_2 P681H 132 137 S 125 130 33894500 Screening of potent phytochemical inhibitors against SARS-CoV-2 protease and its two Asian mutants. Docking of Kazinol T with two Asian mutants (R60C and I152V) showed variations in binding and energy parameters. 2021 Computers in biology and medicine Abstract SARS_CoV_2 I152V;R60C 54;45 59;49 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. A similar increase in incidence was also noted in another related mutation, V70L, also within the TM2 transmembrane helix. 2021 Emerging microbes & infections Abstract SARS_CoV_2 V70L 76 80 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. The rapid emergence of this B.1.I82T clade, recently named Pangolin B.1.575 lineage, suggests that this M gene mutation is more biologically fit, perhaps related to glucose uptake during viral replication, and should be included in ongoing genomic surveillance efforts and warrants further evaluation for potentially increased pathogenic and therapeutic implications. 2021 Emerging microbes & infections Abstract SARS_CoV_2 I82T 32 36 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. This is associated with emergence of a new sub-B.1 clade, B.1.I82T, defined by the previously unreported M:I82T mutation within TM3, the third of three membrane spanning helices implicated in glucose transport. 2021 Emerging microbes & infections Abstract SARS_CoV_2 I82T;I82T 62;107 66;111 Membrane 152 160 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. While constituting 0.7% of the isolates overall, M:I82T sub-B.1 lineage accounted for 14.4% of B.1 lineage isolates in February 2021, similar to the rapid initial increase previously seen with the B.1.1.7 and B.1.429 lineages, which quickly became the dominant lineages in Europe and California over a period of several months. 2021 Emerging microbes & infections Abstract SARS_CoV_2 I82T 51 55 33897278 The dual role of the immune system in the course of COVID-19. The fatal impact of the aging immune system. Moreover, the current, more contagious pathogen carrying the D614G mutation has become the globally dominant form of SARS-CoV-2. 2021 Central-European journal of immunology Abstract SARS_CoV_2 D614G 61 66 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. in 2020 identified the P323L mutation in the RdRp protein of SARS-CoV-2. 2021 Frontiers in molecular biosciences Abstract SARS_CoV_2 P323L 23 28 RdRP 45 49 33900165 Susceptibility to SARS-CoV-2 of Cell Lines and Substrates Commonly Used to Diagnose and Isolate Influenza and Other Viruses. Moreover, a D614G mutation in the spike protein did not appear to affect SARS-CoV-2 cell tropism. 2021 Emerging infectious diseases Abstract SARS_CoV_2 D614G 12 17 S 34 39 33900193 Introduction of ORF3a-Q57H SARS-CoV-2 Variant Causing Fourth Epidemic Wave of COVID-19, Hong Kong, China. The virus has an ORF3a-Q57H mutation, causing truncation of ORF3b. 2021 Emerging infectious diseases Abstract SARS_CoV_2 Q57H 23 27 ORF3b;ORF3a 60;17 65;22 33900328 N-Glycosylated Ganoderma lucidum immunomodulatory protein improved anti-inflammatory activity via inhibition of the p38 MAPK pathway. Four proteins, including FIP-glu (WT) and its mutants N31S, T36N and N31S/T36N, were successfully expressed in P. 2021 Food & function Abstract SARS_CoV_2 N31S;N31S;T36N;T36N 54;69;60;74 58;73;64;78 33900328 N-Glycosylated Ganoderma lucidum immunomodulatory protein improved anti-inflammatory activity via inhibition of the p38 MAPK pathway. pastoris, of which T36N and N31S/T36N were glycoproteins. 2021 Food & function Abstract SARS_CoV_2 N31S;T36N;T36N 28;19;33 32;23;37 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. Conclusions and Relevance: Within weeks of SARS-CoV-2 circulation, a profound shift toward 23403A>G (D614G) specific genotypes occurred. 2021 JAMA network open Abstract SARS_CoV_2 A23403G;D614G 91;101 99;106 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. Infection by strains lacking the 23403A>G variant showed higher mortality in multivariable analysis (odds ratio [OR], 22.4; 95% CI, 0.6 to 5.6; P = .01). 2021 JAMA network open Abstract SARS_CoV_2 A23403G 33 41 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. Several variants were associated with lower hospitalization rate, and those containing 23403A>G (D614G Spike) were associated with increased survival when the patient was hospitalized (64 of 74 patients [86.5%] vs 10 of 17 patients [58.8%]; chi21 = 6.907; P = .009). 2021 JAMA network open Abstract SARS_CoV_2 A23403G;D614G 87;97 95;102 S 103 108 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. E484D also emerged in Vero E6-cultured viruses that became viable in A549 cells. 2021 Antimicrobial agents and chemotherapy Abstract SARS_CoV_2 E484D 0 5 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. The adapted virus exhibited mutations in the spike protein, including a 9-amino-acid deletion and 3 amino acid changes (E484D, P812R, and Q954H). 2021 Antimicrobial agents and chemotherapy Abstract SARS_CoV_2 P812R;Q954H;E484D 127;138;120 132;143;125 S 45 50 33905891 Spike protein mutational landscape in India during the complete lockdown phase: Could Muller's ratchet be a future game-changer for COVID-19? For this, we analyzed the sequences of 630 Indian isolates as available in GISAID database till June 07, 2020 (during the time-period before the start of Unlock 1.0 in India on and from June 08, 2020), and detected the spike protein variants to emerge from two major ancestors - Wuhan-Hu-1/2019 and its D614G variant. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G 303 308 S 219 224 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. In conclusion, genome analyses of the SARS-CoV-2 sequences over the course of the COVID-19 pandemic in Costa Rica suggest the introduction of lineages from other countries and the detection of mutations in line with other studies, but pointing out the local increase in the detection of Spike-T1117I variant. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 T1117I 293 299 S 287 292 COVID-19 82 90 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Interestingly, the frequency of mutation T1117I in the Spike has increased during the current pandemic wave beginning in May 2020 in Costa Rica, reaching 29.2% detection in the full genome analyses in November 2020. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 T1117I 41 47 S 55 60 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Structural modeling of the Spike protein with the T1117I mutation suggests a potential effect on the viral oligomerization needed for cell infection, but no differences with other genomes on transmissibility, severity nor vaccine effectiveness are predicted. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 T1117I 50 56 S 27 32 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. The prevalence of worldwide-found variant D614G in the Spike (98.9% in Costa Rica), ORF8 L84S (1.1%) is similar to what is found elsewhere. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G;L84S 42;89 47;93 S;ORF8 55;84 60;88 33906967 Noncanonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9. LEOPARD allowed simultaneous detection of RNAs from different viruses in one test and distinguished severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its D614G (Asp614 Gly) variant with single-base resolution in patient samples. 2021 Science (New York, N.Y.) Abstract SARS_CoV_2 D614G;D614G 169;176 174;186 COVID-19 107 147 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? In this review, we summarized the current understanding on five notable genetic variants, i.e., D614G, Cluster 5, VOC 202012/01, 501Y.V2 and P.1, and discussed the potential impact of these variants on the virus transmission, pathogenesis and vaccine efficacy. 2021 International journal of biological sciences Abstract SARS_CoV_2 D614G 96 101 33907518 SARS-CoV-2 main protease suppresses type I interferon production by preventing nuclear translocation of phosphorylated IRF3. NSP5 variants G15S and K90R commonly seen in circulating strains of SARS-CoV-2 retained the IFN-antagonizing property. 2021 International journal of biological sciences Abstract SARS_CoV_2 G15S;K90R 14;23 18;27 Nsp5 0 4 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Phylodynamic inference confirmed the rapid growth of the B.1.526 lineage in NYC, notably the sub-clade defined by the spike mutation E484K, which has outpaced the growth of other variants in NYC. 2021 bioRxiv Abstract SARS_CoV_2 E484K 133 138 S 118 123 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The most common sets of spike mutations in this lineage (now designated as B.1.526) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V. 2021 bioRxiv Abstract SARS_CoV_2 A701V;D253G;D614G;E484K;L5F;S477N;T95I 133;99;122;106;88;115;93 138;104;127;111;91;120;97 S 24 29 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. Comparative genomics of all currently available high coverage B.1.1.7+E484K genomes (n=235) available on GISAID suggested the existence of 7 distinct groups or clonal complexes (CC; as defined by GNUVID) bearing the E484K mutation raising the possibility of 7 independent acquisitions of the E484K spike mutation in each background. 2021 bioRxiv Abstract SARS_CoV_2 E484K;E484K;E484K 216;292;70 221;297;75 S 298 303 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. Here we report the genome of a virus isolated in Pennsylvania in March 2021 that was identified as lineage B.1.1.7 (VOC-202012/01) that also harbors the E484K spike mutation, which has been shown to promote "escape" from neutralizing antibodies in vitro . 2021 bioRxiv Abstract SARS_CoV_2 E484K 153 158 S 159 164 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. Phylogenetic analysis suggested the presence of at least 3 distinct clades of B.1.1.7+E484K circulating in the US, with the Pennsylvanian isolates belonging to two distinct clades. 2021 bioRxiv Abstract SARS_CoV_2 E484K 86 91 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. We compare this sequence to the only 5 other B.1.1.7+E484K genomes from Pennsylvania, all of which were isolated in mid March. 2021 bioRxiv Abstract SARS_CoV_2 E484K 53 58 33907767 Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. Chart extraction of demographic and clinical information was performed, and available specimens meeting cycle threshold value criteria were tested for L452R, N501Y and E484K mutations by RT-PCR. 2021 medRxiv Abstract SARS_CoV_2 E484K;L452R;N501Y 168;151;158 173;156;163 33907767 Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. Of 115 samples available for mutation testing, 42 were positive for L452R alone, presumptive of B.1.427/B.1.429; three had N501Y mutation alone and none were found with E484K mutation. 2021 medRxiv Abstract SARS_CoV_2 E484K;L452R;N501Y 169;68;123 174;73;128 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. Cluster mutations namely N501Y (45%), E484K (30%), N439K (16%), K417N (6%) and T478I (3%) at spike protein have increased during January to February 2021. 2021 Epidemiology and infection Abstract SARS_CoV_2 E484K;K417N;N439K;N501Y;T478I 38;64;51;25;79 43;69;56;30;84 S 93 98 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. Here, we assessed the neutralizing activity and binding affinity of a panel of 12 monoclonal antibodies against the wild type and N501Y mutant SARS-CoV-2 pseudovirus and RBD protein, respectively. 2021 Virology journal Abstract SARS_CoV_2 N501Y 130 135 RBD 170 173 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. The N501Y substitution is the only mutation in the interface between the RBD of B.1.1.7 and ACE2, raising concerns that its recognition by neutralizing antibodies may be affected. 2021 Virology journal Abstract SARS_CoV_2 N501Y 4 9 RBD 73 76 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. We found that the neutralization activity and binding affinity of most detected antibodies (10 out of 12) were unaffected, although the N501Y substitution decreased the neutralizing and binding activities of CB6 and increased that of BD-23. 2021 Virology journal Abstract SARS_CoV_2 N501Y 136 141 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. Using the landscape, we searched through 7.5 million possible 2-point mutation combinations and report that the (R355D K424E) mutation produces one of the strongest spike proteins that therapeutic efforts should investigate for the sake of developing effective vaccines. 2021 Scientific reports Abstract SARS_CoV_2 K424E;R355D 119;113 124;118 S 165 170 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. The recently reported "UK variant" (B.1.1.7) of SARS-CoV-2 is thought to be more infectious than previously circulating strains as a result of several changes, including the N501Y mutation. 2021 PLoS biology Abstract SARS_CoV_2 N501Y 174 179 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. This additional interaction provides a structural explanation for the increased ACE2 affinity of the N501Y mutant, and likely contributes to its increased infectivity. 2021 PLoS biology Abstract SARS_CoV_2 N501Y 101 106 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. We present a 2.9-A resolution cryo-electron microscopy (cryo-EM) structure of the complex between the ACE2 receptor and N501Y spike protein ectodomains that shows Y501 inserted into a cavity at the binding interface near Y41 of ACE2. 2021 PLoS biology Abstract SARS_CoV_2 N501Y 120 125 S 126 131 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Interestingly, K417N and E484K mutations dramatically enhanced cell-cell fusion than N501Y even though their infectivity were similar, suggesting that K417N and E484K mutations harboring SARS-CoV-2 variant might be more transmissible than N501Y mutation containing SARS-CoV-2 variant. 2021 Viruses Abstract SARS_CoV_2 E484K;E484K;K417N;K417N;N501Y;N501Y 25;161;15;151;85;239 30;166;20;156;90;244 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Remarkably, Imdevimab effectively neutralized B.1.351 lineage pseudoviruses containing N501Y, K417N, and E484K mutations, while Casirivimab partially affected them. 2021 Viruses Abstract SARS_CoV_2 E484K;K417N;N501Y 105;94;87 110;99;92 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. We here tested infectivity and neutralization efficiency of SARS-CoV-2 spike pseudoviruses bearing particular mutations of the receptor-binding domain (RBD) derived either from the Wuhan strains (referred to as D614G or with other sites) or the B.1.351 lineage (referred to as N501Y, K417N, and E484K). 2021 Viruses Abstract SARS_CoV_2 D614G;E484K;K417N;N501Y 211;295;284;277 216;300;289;282 S;RBD 71;152 76;155 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. As COVID-19 is posing a serious threat to global health, the emerging mutation in SARS-CoV-2 genomes, for example, N501Y substitution, is one of the major challenges against control of the pandemic. 2021 Viruses Abstract SARS_CoV_2 N501Y 115 120 COVID-19 3 11 33918332 Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. One sequence in lineage B.1.1.70 had an N501Y substitution while lacking the Delta69/70 in S. 2021 Microorganisms Abstract SARS_CoV_2 N501Y 40 45 S 91 92 33918332 Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. RESULTS AND CONCLUSION: We found 28 different lineages of SARS-CoV-2 circulating during the study period, including the variant of concern B.1.1.7 (Delta69/70, N501Y). 2021 Microorganisms Abstract SARS_CoV_2 N501Y 160 165 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. Here we report the identification of a new SARS-CoV-2 VOI within lineage B.1.1.33 that also harbors mutation S:E484K and was detected in Brazil between November 2020 and February 2021. 2021 Viruses Abstract SARS_CoV_2 E484K 111 116 S 109 110 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. Lineage P.1 is considered a Variant of Concern (VOC) because of the presence of multiple mutations in the S protein (including K417T, E484K, N501Y), while lineage P.2 only harbors mutation S:E484K and is considered a Variant of Interest (VOI). 2021 Viruses Abstract SARS_CoV_2 E484K;K417T;N501Y;E484K 134;127;141;191 139;132;146;196 S;S 106;189 107;190 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. This VOI displayed four non-synonymous lineage-defining mutations (NSP3:A1711V, NSP6:F36L, S:E484K, and NS7b:E33A) and was designated as lineage N.9. 2021 Viruses Abstract SARS_CoV_2 A1711V;E33A;E484K;F36L 72;109;93;85 78;113;98;89 Nsp7b;Nsp3;Nsp6;S 104;67;80;91 108;71;84;92 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. Among 25,629 amino acid substitutions at 8484 polymorphic sites across the coding region of the SARS-CoV-2 genome, the D614G (93.88%) variant in spike and the P323L (93.74%) variant in RNA-dependent RNA polymerase were the dominant variants on six continents. 2021 Biomedicines Abstract SARS_CoV_2 D614G;P323L 119;159 124;164 RdRp;S 185;145 213;150 33922914 Dieckol and Its Derivatives as Potential Inhibitors of SARS-CoV-2 Spike Protein (UK Strain: VUI 202012/01): A Computational Study. The UK SARS-CoV-2 variant possesses D614G mutation in the Spike protein, which impart it a high rate of infection. 2021 Marine drugs Abstract SARS_CoV_2 D614G 36 41 S 58 63 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Combining molecular interaction modeling and the free energy of binding (FEB) calculations for VOC, it can be assumed that the mutation N501Y has the highest binding affinity in RBD for all VOC, followed by E484K (only for BR-VOC), which favors the formation of a stable complex. 2021 Microorganisms Abstract SARS_CoV_2 E484K;N501Y 207;136 212;141 RBD 178 181 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. However, mutations at the residue K417N/T are shown to reduce the binding affinity. 2021 Microorganisms Abstract SARS_CoV_2 K417N;K417T 34;34 41;41 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Notable nonsynonymous mutations in RBD of VOC include the E484K and K417N/T that can be seen in South African and Brazilian variants, and N501Y and D614G that can be seen in all VOC. 2021 Microorganisms Abstract SARS_CoV_2 D614G;E484K;K417N;K417T;N501Y 148;58;68;68;138 153;63;75;75;143 RBD 35 38 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. To better understand and maximize the infectivity of SARS-CoV-2 PsV, we generated PsV carrying spike protein variants known to have varying human ACE2 binding properties, including 19 deletion (19del) and 19del + D614G. 2021 Journal of biomedical science Abstract SARS_CoV_2 19del;D614G;19del 205;213;194 210;218;199 S 95 100 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Spike protein and RNA-dependent RNA polymerase variants, D614G and P323L in combination became dominant world-wide. 2021 Epidemiology and infection Abstract SARS_CoV_2 D614G;P323L 57;67 62;72 RdRp;S 18;0 46;5 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. Compared with pseudovirus D614, pseudovirus with D614G mutation had decreased shedding and higher density of S1 protein present on particles. 2021 Emerging microbes & infections Abstract SARS_CoV_2 D614G 49 54 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. The 50% neutralization titers to pseudoviruses D614 or D614G correlated with the plaque reduction neutralization titers to live SARS-CoV-2. 2021 Emerging microbes & infections Abstract SARS_CoV_2 D614G 55 60 33930563 Assessment of basic reproduction number (R0), spatial and temporal epidemiological determinants, and genetic characterization of SARS-CoV-2 in Bangladesh. Alternatively, I120F in NSP2 protein, R203K and G204R in nucleocapsid protein, and P323L in RdRp were more recurrent. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 G204R;I120F;P323L;R203K 48;15;83;38 53;20;88;43 N;Nsp2;RdRP 57;24;92 69;28;96 33930563 Assessment of basic reproduction number (R0), spatial and temporal epidemiological determinants, and genetic characterization of SARS-CoV-2 in Bangladesh. In spike (S) protein, 355 predominant mutations were recorded, highest in D614G. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G 74 79 S;S 3;10 8;11 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. CONCLUSIONS: The most common mutations, D614G/spike-glycoprotein and P4715L/RNA-dependent-RNA-polymerase, were linked to transmissibility regardless of symptom variability. 2021 Biochimica et biophysica acta. Molecular basis of disease Abstract SARS_CoV_2 D614G;P4715L 40;69 45;77 RdRp;S 76;46 104;64 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. E3909G-nsp7 could explain why children recover so quickly. 2021 Biochimica et biophysica acta. Molecular basis of disease Abstract SARS_CoV_2 E3909G 0 6 Nsp7 7 11 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. However, the E3909G-nsp7 variant was more common in children (2-13 years old) and was associated with a shorter duration of symptoms. 2021 Biochimica et biophysica acta. Molecular basis of disease Abstract SARS_CoV_2 E3909G 13 19 Nsp7 20 24 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. Nsp6-L3606fs, spike-glycoprotein-V6fs, and nsp13-S5398L variants may be linked to clinical symptom worsening. 2021 Biochimica et biophysica acta. Molecular basis of disease Abstract SARS_CoV_2 L3606fs;S5398L;V6fs 5;49;33 12;55;37 S;Nsp13;Nsp6 14;43;0 32;48;4 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. S5398L nsp13-helicase was linked to an increased risk of fever duration and progression. 2021 Biochimica et biophysica acta. Molecular basis of disease Abstract SARS_CoV_2 S5398L 0 6 Nsp13;Helicase 7;14 12;22 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. The duration of fever was significantly reduced with E1363D-nsp3 and E3073A-nsp4. 2021 Biochimica et biophysica acta. Molecular basis of disease Abstract SARS_CoV_2 E1363D;E3073A 53;69 59;75 Nsp3;Nsp4 60;76 64;80 33936746 Extensive genetic diversity with novel mutations in spike glycoprotein of severe acute respiratory syndrome coronavirus 2, Bangladesh in late 2020. A P681R substitution adjacent to the furin cleavage site was detected in one sample. 2021 New microbes and new infections Abstract SARS_CoV_2 P681R 2 7 33936746 Extensive genetic diversity with novel mutations in spike glycoprotein of severe acute respiratory syndrome coronavirus 2, Bangladesh in late 2020. A total of 133 mutations were detected in 15 samples, with D614G being present in all the samples; 53 were novel mutations as of January 2021. 2021 New microbes and new infections Abstract SARS_CoV_2 D614G 59 64 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. Overall, this suggests that with regard to D614G, the behavior of individuals has been more important in shaping the course of the pandemic in Washington State than this variant of the virus. 2021 Science translational medicine Abstract SARS_CoV_2 D614G 43 48 33945070 Longitudinal virological changes and underlying pathogenesis in hospitalized COVID-19 patients in Guangzhou, China. Furthermore, the viral shedding time significantly decreased when the A1,430G or C12,473T mutation occurred (P<0.01 and FDR<0.01) and increased when G227A occurred (P<0.05 and FDR<0.05). 2021 Science China. Life sciences Abstract SARS_CoV_2 G227A 149 154 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. The most frequent of them, D936Y, was present in 17% of sequences from Finland and 12% of sequences from Sweden. 2021 Molecules (Basel, Switzerland) Abstract SARS_CoV_2 D936Y 27 32 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. These were S929T, D936Y, and S949F, all in the N-terminal half of the HR1 fusion core segment and particularly spread in Europe and USA. 2021 Molecules (Basel, Switzerland) Abstract SARS_CoV_2 D936Y;S929T;S949F 18;11;29 23;16;34 N 47 48 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. We investigated the effect of the D936Y mutation on the pre-fusion and post-fusion state of the protein by using molecular dynamics, showing how it especially affects the latter one. 2021 Molecules (Basel, Switzerland) Abstract SARS_CoV_2 D936Y 34 39 33948590 A broadly neutralizing antibody protects against SARS-CoV, pre-emergent bat CoVs, and SARS-CoV-2 variants in mice. Here, we demonstrate the neutralization of SARS-CoV, bat CoVs WIV-1 and RsSHC014, and SARS-CoV-2 variants D614G, B.1.1.7, B.1.429, B1.351 by a receptor-binding domain (RBD)-specific antibody DH1047. 2021 bioRxiv Abstract SARS_CoV_2 D614G 106 111 RBD 168 171 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. In this study, we analyzed more than 1,000,000 SARS-CoV-2 genomic sequences deposited up to April 27, 2021, on the GISAID public repository, and identified a novel T478K mutation located on the SARS-CoV-2 Spike protein. 2021 Journal of medical virology Abstract SARS_CoV_2 T478K 164 169 S 205 210 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. We show that T478K has appeared and risen in frequency since January 2021, predominantly in Mexico and the United States, but we could also detect it in several European countries. 2021 Journal of medical virology Abstract SARS_CoV_2 T478K 13 18 33956645 Whole Genome Sequencing and Phylogenetic Analysis of SARSCoV2 strains in Turkey. In all samples c.1-25C>T (5'UTR), c.14144C>T (ORF1ab), c.2772C>T (ORF1ab) and c.1841A>G(S) mutations were detected. 2021 Journal of infection in developing countries Abstract SARS_CoV_2 C14144T;A1841G;C2772T;1-25C>T 34;78;55;17 44;87;64;24 ORF1ab;ORF1ab;5'UTR;S 46;66;26;88 52;72;31;89 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. We determined that the single nucleotide polymorphisms (SNPs) 1,059.C > T and 25,563.G > T were significantly associated with approximately half of the North American SARS-CoV-2 isolates that accumulated largely during March 2020. 2021 Transboundary and emerging diseases Abstract SARS_CoV_2 C059T;G563T 64;81 73;90 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. In contrast, the heparin chain bound the furin cleavage site and surrounding glycosylation structures, but not S247R. 2021 Computational and structural biotechnology journal Abstract SARS_CoV_2 S247R 111 116 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. The heparan sulfate chain bridged the gap, binding the furin cleavage site and S247R. 2021 Computational and structural biotechnology journal Abstract SARS_CoV_2 S247R 79 84 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. We hypothesized that GAGs of a sufficient length might bridge the gap between this site and the PRRARS furin cleavage site, including the mutation S247R. 2021 Computational and structural biotechnology journal Abstract SARS_CoV_2 S247R 147 152 33968806 SARS CoV-2 Nucleoprotein Enhances the Infectivity of Lentiviral Spike Particles. Importantly, this improvement in infectivity is observed with both wild-type spike protein as well as the D614G mutant. 2021 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 D614G 106 111 S 77 82 33968834 Myelodysplastic syndrome in a 30-year-old man with coronavirus disease 2019 (COVID-19): a diagnostic challenge. Next generation sequencing demonstrated SF3B1 K700E mutation. 2021 Autopsy & case reports Abstract SARS_CoV_2 K700E 46 51 33969329 Interferon antagonism by SARS-CoV-2: a functional study using reverse genetics. We did a luciferase-based interferon-stimulated response element promotor activation assay to evaluate the antagonistic capacity of SARS-CoV-2 wild-type ORF6 constructs and three mutants (Gln51Glu, Gln56Glu, or both) that represent amino acid substitutions between SARS-CoV and SARS-CoV-2 protein 6 in the carboxy-terminal domain. 2021 The Lancet. Microbe Abstract SARS_CoV_2 Q56E;Q51E 198;188 206;196 ORF6 153 157 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. Although this property is suspected to result from a specific mutation in the spike glycoprotein, D614G, there are 9 mutations that distinguish the UK variant B.1.1.7 from Wuhan-Hu-1 yet to be evaluated for functional effects. 2021 Journal of cellular immunology Abstract SARS_CoV_2 D614G 98 103 S 78 96 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. N501Y increased affinity between the spike protein and ACE2. 2021 Journal of cellular immunology Abstract SARS_CoV_2 N501Y 0 5 S 37 42 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. The D614G mutation, associated with enhanced virus transmissibility, opens a potentially druggable structural pocket at the interface between spike glycoprotein subunits S1 and S2. 2021 Journal of cellular immunology Abstract SARS_CoV_2 D614G 4 9 S 142 160 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. The mutations at A570D, D614G and S982A reduced contact between individual chains of the trimeric spike protomer, potentially enhancing cleavage into S1 and S2 subunits, dynamic structural rearrangement and host cell fusion mechanisms. 2021 Journal of cellular immunology Abstract SARS_CoV_2 A570D;D614G;S982A 17;24;34 22;29;39 S 98 103 33970798 A higher flexibility at the SARS-CoV-2 main protease active site compared to SARS-CoV and its potentialities for new inhibitor virtual screening targeting multi-conformers. A higher hydration propensity for the MCoV2pro S2 loop with the A46S substitution seems to exercise a key role. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 A46S 64 68 33972947 LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants. In pseudovirus neutralization studies, LY-CoV1404 retains potent neutralizing activity against numerous variants including B.1.1.7, B.1.351, B.1.617.2, B.1.427/B.1.429, P.1, B.1.526, B.1.1.529, and the BA.2 subvariant and retains binding to spike proteins with a variety of underlying RBD mutations including K417N, L452R, E484K, and N501Y. 2022 bioRxiv Abstract SARS_CoV_2 E484K;K417N;L452R;N501Y 323;309;316;334 328;314;321;339 S;RBD 241;285 246;288 33972947 LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants. Notably, the binding and neutralizing activity of LY-CoV1404 is unaffected by the most common mutations at these positions (N439K and N501Y). 2022 bioRxiv Abstract SARS_CoV_2 N501Y;N439K 134;124 139;129 33975021 A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern. Here we propose a rapid and accessible protocol based on Sanger sequencing of a single PCR fragment that is able to identify and discriminate all SARS-CoV-2 variants of concern (VOCs) identified so far, according to each characteristic mutational profile at the Spike-RBD region (K417N/T, E484K, N501Y, A570D). 2021 Infection, genetics and evolution Abstract SARS_CoV_2 A570D;E484K;N501Y;K417N;K417T 303;289;296;280;280 308;294;301;287;287 S;RBD 262;268 267;271 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? Furthermore, mutations such as N501Y, E484K, and K417N in the S protein may affect viral fitness and transmissibility. 2021 Journal of Korean medical science Abstract SARS_CoV_2 E484K;K417N;N501Y 38;49;31 43;54;36 S 62 63 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? The common feature of these variants is that they share the N501Y mutation involving the SARS-CoV-2 spike (S) protein, which is precisely the target of most COVID-19 vaccines. 2021 Journal of Korean medical science Abstract SARS_CoV_2 N501Y 60 65 S;S 100;107 105;108 COVID-19 157 165 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Evolutionary histories of residues disrupted by spike-protein substitutions D614G, N501Y, E484K, and K417N/T provide clues about their biology, and we catalog likely-functional co-inherited mutations. 2021 Nature communications Abstract SARS_CoV_2 D614G;E484K;K417N;K417T;N501Y 76;90;101;101;83 81;95;108;108;88 S 48 53 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. In response to the unmet need for a fast and efficient screening tool, we developed a single-tube duplex molecular assay for rapid and simultaneous identification of E484K and N501Y mutations from nasopharyngeal swab (NS) samples within 2.5 h from sample preparation to report. 2021 Emerging microbes & infections Abstract SARS_CoV_2 E484K;N501Y 166;176 171;181 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. Our data revealed dramatic increases in the frequencies of both E484K and N501Y over time, underscoring the need for continuous epidemiological monitoring. 2021 Emerging microbes & infections Abstract SARS_CoV_2 E484K;N501Y 64;74 69;79 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. Spike protein mutations E484K and N501Y carried by SARS-CoV-2 variants have been associated with concerning changes of the virus, including resistance to neutralizing antibodies and increased transmissibility. 2021 Emerging microbes & infections Abstract SARS_CoV_2 E484K;N501Y 24;34 29;39 S 0 5 33983915 Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant - New York City, New York, January 1-April 5, 2021. Two predominant subclades within the B.1.526 lineage have been identified, one containing the E484K mutation in the receptor-binding domain (1,2), which attenuates in vitro neutralization by multiple SARS-CoV-2 antibodies and is present in variants of concern (VOCs) first identified in South Africa (B.1.351) (4) and Brazil (P.1).* The NYC Department of Health and Mental Hygiene (DOHMH) analyzed laboratory and epidemiologic data to characterize cases of B.1.526 infection, including illness severity, transmission to close contacts, rates of possible reinfection, and laboratory-diagnosed breakthrough infections among vaccinated persons. 2021 MMWR. Morbidity and mortality weekly report Abstract SARS_CoV_2 E484K 94 99 33990523 The Longest Infectious Virus Shedding in a Child Infected With the G614 Strain of SARS-CoV-2. A missense mutation, D614G, in the spike protein of SARS-CoV-2, which has emerged as a predominant clade in Europe and is spreading worldwide that can result in higher viral loads in patients. 2021 The Pediatric infectious disease journal Abstract SARS_CoV_2 D614G 21 26 S 35 40 33990523 The Longest Infectious Virus Shedding in a Child Infected With the G614 Strain of SARS-CoV-2. Herein, we described the longest infectious virus shedding in a previously healthy child infected with SARS-CoV-2 expressing spike D614G substitution. 2021 The Pediatric infectious disease journal Abstract SARS_CoV_2 D614G 131 136 S 125 130 33991677 Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage. RESULTS: We identified that SARS-CoV-2 genomes from four patients diagnosed in our institute harboured a new set of amino acid substitutions including L18F, L452R, N501Y, A653V, H655Y, D796Y, G1219V +- Q677H. 2021 Clinical microbiology and infection Abstract SARS_CoV_2 A653V;D796Y;G1219V;H655Y;L18F;L452R;N501Y;Q677H 171;185;192;178;151;157;164;202 176;190;198;183;155;162;169;207 33991677 Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage. These spike N501Y genomes are the first of Nextstrain clade 19B. 2021 Clinical microbiology and infection Abstract SARS_CoV_2 N501Y 12 17 S 6 11 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Applying structural analysis to highly transmissible variants, we find that circulating point mutations S477N, E484K and N501Y form high-affinity complexes (~40% more than wild-type). 2021 Journal of molecular biology Abstract SARS_CoV_2 E484K;N501Y;S477N 111;121;104 116;126;109 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. By combining predicted affinities and available antibody escape data, we show that fast-spreading viral variants exploit combinatorial mutations possessing both enhanced affinity and antibody resistance, including S477N/E484K, E484K/N501Y and K417T/E484K/N501Y. 2021 Journal of molecular biology Abstract SARS_CoV_2 E484K;K417T;S477N;E484K;E484K;N501Y;N501Y 227;243;214;220;249;233;255 232;248;219;225;254;238;260 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. By focusing on natural variants at the Spike-hACE2 interface and assessing over 700 mutant complexes, our analysis reveals that high-affinity Spike mutations (including N440K, S443A, G476S, E484R, G502P) tend to cluster near known human ACE2 recognition sites (K31 and K353). 2021 Journal of molecular biology Abstract SARS_CoV_2 E484R;G476S;G502P;N440K;S443A 190;183;197;169;176 195;188;202;174;181 S;S 39;142 44;147 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. INTERPRETATION: We found for the first time that the Q493K and Q498H mutations in the RBD of WBP-1 enhanced its interactive affinities with mACE2. 2021 EBioMedicine Abstract SARS_CoV_2 Q493K;Q498H 53;63 58;68 RBD 86 89 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. We characterized the dynamics of the adaptive mutations in SARS-CoV-2 and demonstrated that Q493K and Q498H in RBD significantly increased its binding affinity towards mouse ACE2. 2021 EBioMedicine Abstract SARS_CoV_2 Q493K;Q498H 92;102 97;107 RBD 111 114 33999091 Key residues of the receptor binding domain in the spike protein of SARS-CoV-2 mediating the interactions with ACE2: a molecular dynamics study. This is in line with recent findings that it is mutated by lysine (E484K mutation) in the rapidly spreading variants of COVID-19 belonging to the B.1.351 and P.1 lineages. 2021 Nanoscale Abstract SARS_CoV_2 E484K 67 72 COVID-19 120 128 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. An N15A mutation increased the production of virus-like particles, induced significant chemical shift changes from residues in the inhibitor binding site, and abolished HMA binding, suggesting that Asn15 plays a key role in maintaining the protein conformation near the binding site. 2021 PLoS pathogens Abstract SARS_CoV_2 N15A 3 7 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. A list of most likely vaccine escape mutations is given, including S494P, Q493L, K417N, F490S, F486L, R403K, E484K, L452R, K417T, F490L, E484Q, and A475S. 2021 Genomics Abstract SARS_CoV_2 A475S;E484K;E484Q;F486L;F490L;F490S;K417N;K417T;L452R;Q493L;R403K;S494P 148;109;137;95;130;88;81;123;116;74;102;67 153;114;142;100;135;93;86;128;121;79;107;72 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Among these RBD mutations, L452R is also now known as part of the California variant B.1.427. 2021 Genomics Abstract SARS_CoV_2 L452R 27 32 RBD 12 15 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. In particular, we discover new fast-growing RBD mutations N439K, S477N, S477R, and N501T that also enhance the RBD and ACE2 binding. 2021 Genomics Abstract SARS_CoV_2 N439K;N501T;S477N;S477R 58;83;65;72 63;88;70;77 RBD;RBD 44;111 47;114 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Mutation T478K appears to make the Mexico variant B.1.1.222 the most infectious one. 2021 Genomics Abstract SARS_CoV_2 T478K 9 14 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. We further unveil that mutation N501Y involved in United Kingdom (UK), South Africa, and Brazil variants may moderately weaken the binding between the RBD and many known antibodies, while mutations E484K and K417N found in South Africa and Brazilian variants, L452R and E484Q found in India variants, can potentially disrupt the binding between the RBD and many known antibodies. 2021 Genomics Abstract SARS_CoV_2 E484K;E484Q;K417N;L452R;N501Y 198;270;208;260;32 203;275;213;265;37 RBD;RBD 151;349 154;352 34011523 Mutation-Specific SARS-CoV-2 PCR Screen: Rapid and Accurate Detection of Variants of Concern and the Identification of a Newly Emerging Variant with Spike L452R Mutation. The S-L450R assay, designed to detect the B.1.427/429 VOC, also identified multiple isolates of a newly emerging multiply mutated B.1.526.1 variant that is now rapidly increasing in the eastern United States. 2021 Journal of clinical microbiology Abstract SARS_CoV_2 L450R 6 11 S 4 5 34011523 Mutation-Specific SARS-CoV-2 PCR Screen: Rapid and Accurate Detection of Variants of Concern and the Identification of a Newly Emerging Variant with Spike L452R Mutation. The screening results were compared to the whole-genome sequencing (WGS) and showed 100% concordance for strain typing for B.1.1.7 (n = 25) and P.1 (n = 5) variants using spike (S) mutation S-N501Y, S-E484K, and S-H69-V70del assays. 2021 Journal of clinical microbiology Abstract SARS_CoV_2 E484K;N501Y;H69-V70del 199;192;214 206;197;224 S;S;S;S;S 171;178;190;199;212 176;179;191;200;213 34011547 Unique Mutations in the Murine Hepatitis Virus Macrodomain Differentially Attenuate Virus Replication, Indicating Multiple Roles for the Macrodomain in Coronavirus Replication. Conversely, D1329A retained some ability to block beta interferon (IFN-beta) transcript accumulation compared to N1347A, indicating that these mutations have different effects on Mac1 functions. 2021 Journal of virology Abstract SARS_CoV_2 D1329A;N1347A 12;113 18;119 34011547 Unique Mutations in the Murine Hepatitis Virus Macrodomain Differentially Attenuate Virus Replication, Indicating Multiple Roles for the Macrodomain in Coronavirus Replication. Interestingly, D1329A was also significantly more attenuated than N1347A in all cell lines tested. 2021 Journal of virology Abstract SARS_CoV_2 D1329A;N1347A 15;66 21;72 34011547 Unique Mutations in the Murine Hepatitis Virus Macrodomain Differentially Attenuate Virus Replication, Indicating Multiple Roles for the Macrodomain in Coronavirus Replication. N1465A had no effect on MHV replication or pathogenesis, while D1329A and N1347A both replicated poorly in bone marrow-derived macrophages (BMDMs), were inhibited by PARP enzymes, and were highly attenuated in vivo. 2021 Journal of virology Abstract SARS_CoV_2 D1329A;N1347A;N1465A 63;74;0 69;80;6 34011547 Unique Mutations in the Murine Hepatitis Virus Macrodomain Differentially Attenuate Virus Replication, Indicating Multiple Roles for the Macrodomain in Coronavirus Replication. To determine if additional Mac1 activities contribute to CoV replication, we compared the replication of murine hepatitis virus (MHV) Mac1 mutants, D1329A and N1465A, to the previously mentioned asparagine mutant, N1347A. 2021 Journal of virology Abstract SARS_CoV_2 D1329A;N1347A;N1465A 148;214;159 154;220;165 34011679 Shedding of Viable Virus in Asymptomatic SARS-CoV-2 Carriers. Genome sequence analysis of SARS-CoV-2 samples consecutively obtained from a person who shed viable virus for 15 days identified the emergence of two novel single nucleotide variants (C8626T transition and C18452T transition) in the sample collected on day 15, with the latter corresponding to an amino acid substitution in nonstructural protein 14. 2021 mSphere Abstract SARS_CoV_2 C18452T;C8626T 206;184 213;190 34013259 In vivo monoclonal antibody efficacy against SARS-CoV-2 variant strains. Although some individual mAbs showed reduced or abrogated neutralizing activity against B.1.351 and B.1.1.28 viruses with E484K spike protein mutations in cell culture, low prophylactic doses of mAb combinations protected against infection in K18-hACE2 transgenic mice, 129S2 immunocompetent mice, and hamsters without emergence of resistance. 2021 Research square Abstract SARS_CoV_2 E484K 122 127 S 128 133 34013280 Impact of BNT162b first vaccination on the immune transcriptome of elderly patients infected with the B.1.351 SARS-CoV-2 variant. The B.1.351 variant carrying the escape mutation E484K in the receptor binding domain is of particular concern due to reduced immunological protection following vaccination. 2021 medRxiv Abstract SARS_CoV_2 E484K 49 54 RBD 62 85 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. According to the result of MM-PBSA binding free energy calculations, we found that V367F and N354D/D364Y mutant types showed enhanced binding affinities with hACE2 compared to the prototype. 2021 Briefings in bioinformatics Abstract SARS_CoV_2 N354D;V367F;D364Y 93;83;99 98;88;104 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. Mutations on RBD have been observed in different countries and classified into nine types: A435S, D364Y, G476S, N354D/D364Y, R408I, V341I, V367F, V483A and W436R. 2021 Briefings in bioinformatics Abstract SARS_CoV_2 A435S;D364Y;G476S;N354D;R408I;V341I;V367F;V483A;W436R;D364Y 91;98;105;112;125;132;139;146;156;118 96;103;110;117;130;137;144;151;161;123 RBD 13 16 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. Our computational protocols were validated by the successful prediction of relative binding free energies between prototype and three mutants: N354D/D364Y, V367F and W436R. 2021 Briefings in bioinformatics Abstract SARS_CoV_2 N354D;V367F;W436R;D364Y 143;156;166;149 148;161;171;154 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. The B.1.351 and P.1 variants also display the E484K mutation which decreases binding of neutralizing antibodies, leading to partial immune escape; this favours reinfections, and decreases the in vitro efficacy of some antibody therapies or vaccines. 2021 Clinical microbiology and infection Abstract SARS_CoV_2 E484K 46 51 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. The emergence of the E484K mutation independently in different parts of the globe may reflect the adaptation of SARS-CoV-2 to humans against a background of increasing immunity. 2021 Clinical microbiology and infection Abstract SARS_CoV_2 E484K 21 26 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. The N501Y mutation is shared by the three main VOCs: B.1.1.7, first identified in the United Kingdom, P.1, originating from Brazil, and B.1.351, first described in South Africa. 2021 Clinical microbiology and infection Abstract SARS_CoV_2 N501Y 4 9 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. E484K was found in two genomes from mid-October, which is the earliest description of this mutation in Southern Brazil. 2021 BMC genomics Abstract SARS_CoV_2 E484K 0 5 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. RESULTS: We provided a comprehensive view of mutations from a representative sampling from May to October 2020, highlighting two frequent mutations in spike glycoprotein (D614G and V1176F), an emergent mutation (E484K) in spike Receptor Binding Domain (RBD) characteristic of the B.1.351 and P.1 lineages, and the adjacent replacement of 2 amino acids in Nucleocapsid phosphoprotein (R203K and G204R). 2021 BMC genomics Abstract SARS_CoV_2 G204R;V1176F;D614G;E484K;R203K 394;181;171;212;384 399;187;176;217;389 RBD;S;N;S;RBD 228;151;355;222;253 251;169;367;227;256 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Binding and neutralization of the two most frequently elicited antibody families (IGHV3-53/3-66 and IGHV1-2), which can both bind the RBS in alternative binding modes, are abrogated by K417N, E484K, or both. 2021 Science (New York, N.Y.) Abstract SARS_CoV_2 E484K;K417N 192;185 197;190 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. We analyzed their effects on angiotensin-converting enzyme 2 binding, as well as the effects of two of these mutations (K417N and E484K) on nAbs isolated from COVID-19 patients. 2021 Science (New York, N.Y.) Abstract SARS_CoV_2 E484K;K417N 130;120 135;125 COVID-19 159 167 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. Introducing the Q498H substitution found in pangolin CoVs into the SARS-CoV-2 RBD expands its binding capacity to ACE2 homologs of mouse, rat, and European hedgehog. 2021 The EMBO journal Abstract SARS_CoV_2 Q498H 16 21 RBD 78 81 34019466 Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. Although we do not have any knowledge upon the nucleotide sequences of the primers and probe adopted by this kit, it is likely that N gene dropout only occurs when 28948C > T is coupled with 28932C > T, this latter present, in turn, in all B.1.177.75 sequences available on public databases. 2021 Emerging microbes & infections Abstract SARS_CoV_2 C28932T;C28948T 191;164 201;174 N 132 133 34019466 Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. By sequencing, a unique mutation, synonymous 28948C > T, was found in the N-negative B.1.177.75 strains. 2021 Emerging microbes & infections Abstract SARS_CoV_2 C28948T 45 55 N 74 75 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. Among 86 potent NAbs identified by high-throughput single-cell VDJ sequencing of peripheral blood mononuclear cells from vaccinees and convalescents, near half anti-RBD NAbs showed major neutralization reductions against the K417N/E484K/N501Y mutation combination, with E484K being the dominant cause. 2021 Cell research Abstract SARS_CoV_2 E484K;K417N;E484K;N501Y 270;225;231;237 275;230;236;242 RBD 165 168 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. Plasma of convalescents and CoronaVac vaccinees displayed comparable neutralization reductions against pseudo- and authentic 501Y.V2 variants, mainly caused by E484K/N501Y and 242-244Delta, with the effects being additive. 2021 Cell research Abstract SARS_CoV_2 E484K;N501Y 160;166 165;171 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. VH3-53/VH3-66 recurrent antibodies respond differently to RBD variants, and K417N compromises the majority of neutralizing activity through reduced polar contacts with complementarity determining regions. 2021 Cell research Abstract SARS_CoV_2 K417N 76 81 RBD 58 61 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. Among these mutations are amino acid changes N501Y (lineage B.1.1.7, first identified in the UK), and the combination N501Y, E484K, K417N (B.1.351, first identified in South Africa), all located at the interface on the receptor binding domain (RBD). 2021 Journal of molecular biology Abstract SARS_CoV_2 E484K;K417N;N501Y;N501Y 125;132;45;118 130;137;50;123 RBD;RBD 219;244 242;247 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. As a result, RBD from B.1.351 containing all three mutations binds 3-fold stronger to hACE2 than wild type RBD but 2-fold weaker than N501Y. 2021 Journal of molecular biology Abstract SARS_CoV_2 N501Y 134 139 RBD;RBD 13;107 16;110 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. However, the recently emerging double mutant E484K/N501Y binds even stronger than N501Y. 2021 Journal of molecular biology Abstract SARS_CoV_2 E484K;N501Y;N501Y 45;82;51 50;87;56 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. The E484K mutation only slightly enhances the affinity for the receptor, while K417N attenuates affinity. 2021 Journal of molecular biology Abstract SARS_CoV_2 E484K;K417N 4;79 9;84 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. We experimentally establish that RBD containing the N501Y mutation results in 7-fold stronger binding to the hACE2 receptor than wild type RBD. 2021 Journal of molecular biology Abstract SARS_CoV_2 N501Y 52 57 RBD;RBD 33;139 36;142 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. Clinical and pseudovirus experimental studies have demonstrated that the spike protein D614G mutation alters the virus phenotype. 2021 Frontiers in medicine Abstract SARS_CoV_2 D614G 87 92 S 73 78 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. Recently, an amino acid aspartate (D) to glycine (G) (D614G) mutation due to an adenine to guanine nucleotide change at position 23,403 at the 614th amino-acid position of the spike protein in the original reference genotype has been identified. 2021 Frontiers in medicine Abstract SARS_CoV_2 D614G 54 59 S 176 181 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. The D614G mutation has been found to be associated with 3 other mutations in the spike protein. 2021 Frontiers in medicine Abstract SARS_CoV_2 D614G 4 9 S 81 86 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. The SARS-CoV-2 viruses that carry the spike protein D614G mutation have become dominant variant around the world. 2021 Frontiers in medicine Abstract SARS_CoV_2 D614G 52 57 S 38 43 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. They are B.1.1.7 (UK) variant, B.1.351 (N501Y.V2, South African) variant and B.1.1.28 (Brazilian) variant. 2021 Frontiers in medicine Abstract SARS_CoV_2 N501Y 40 45 34029587 Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication. Methylation of R95 regulated the ability of N protein to suppress the formation of SGs, as R95K substitution or MS023 treatment blocked N-mediated suppression of SGs. 2021 The Journal of biological chemistry Abstract SARS_CoV_2 R95K 91 95 N;N 44;136 45;137 34029937 Corilagin prevents SARS-CoV-2 infection by targeting RBD-ACE2 binding. RESULTS: Corilagin preferentially binds to a pocket that contains residues Cys 336 to Phe 374 of spike-RBD with a relatively low binding energy of -9.4 kcal/mol. 2021 Phytomedicine Abstract SARS_CoV_2 C336F 75 89 S;RBD 97;103 102;106 34030593 Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis. The positive selection analysis of the SARS-CoV-2 genome uncovered the positive selected amino acid G251V on ORF3a. 2021 Virulence Abstract SARS_CoV_2 G251V 100 105 ORF3a 109 114 34033650 SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. In addition, we structurally modelled the two most common mutations, Spike_D614G and Nsp12_P314L, which suggested that these linked mutations may enhance viral entry and replication, respectively. 2021 PloS one Abstract SARS_CoV_2 D614G;P314L 75;91 80;96 S;Nsp12 69;85 74;90 34037430 Multiplex SARS-CoV-2 Genotyping Reverse Transcriptase PCR for Population-Level Variant Screening and Epidemiologic Surveillance. The assay revealed the rapid emergence of the L452R variant in our population, with a prevalence of 24.8% in December 2020 that increased to 62.5% in March 2021. 2021 Journal of clinical microbiology Abstract SARS_CoV_2 L452R 46 51 34037430 Multiplex SARS-CoV-2 Genotyping Reverse Transcriptase PCR for Population-Level Variant Screening and Epidemiologic Surveillance. We designed and analytically validated a one-step multiplex allele-specific reverse transcriptase PCR (RT-qPCR) to detect three nonsynonymous spike protein mutations (L452R, E484K, N501Y). 2021 Journal of clinical microbiology Abstract SARS_CoV_2 E484K;N501Y;L452R 174;181;167 179;186;172 S 142 147 34037430 Multiplex SARS-CoV-2 Genotyping Reverse Transcriptase PCR for Population-Level Variant Screening and Epidemiologic Surveillance. We detected 1,567 L452R mutations (38.7%), 34 N501Y mutations (0.84%), 22 E484K mutations (0.54%), and 3 (0.07%) E484K plus N501Y mutations. 2021 Journal of clinical microbiology Abstract SARS_CoV_2 E484K;E484K;L452R;N501Y;N501Y 74;113;18;46;124 79;118;23;51;129 34039497 An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose. D614G genotype of SARS-CoV-2 virus is highly infectious and responsible for almost all infection for 2nd wave. 2021 Vaccine Abstract SARS_CoV_2 D614G 0 5 34039497 An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose. Here we report the development of an mRNA-LNP vaccine with D614G variant and characterization in animal model. 2021 Vaccine Abstract SARS_CoV_2 D614G 59 64 34039497 An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose. However, there are currently no reports with D614G as vaccine candidate. 2021 Vaccine Abstract SARS_CoV_2 D614G 45 50 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. The D614G mutation, first detected in March 2020, was identified in 18 strains and was more likely associated with a lower cycle threshold (<25) in real-time reverse-transcription polymerase chain reaction diagnostic tests than the original D614 (prevalence ratio = 2.75; 95% confidence interval, 1.19-6.38). 2021 Journal of medical virology Abstract SARS_CoV_2 D614G 4 9 34043733 Molecular dynamics analysis of N-acetyl-D-glucosamine against specific SARS-CoV-2's pathogenicity factors. Furthermore, computational analysis against the D614G mutant of the virus has shown that N-acetyl-D-glucosamine affinity and its binding potential were not affected by the mutations occurring in the virus' receptor binding domain. 2021 PloS one Abstract SARS_CoV_2 D614G 48 53 RBD;N 206;89 229;90 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. A lower rate of hospitalization was associated with N501YV infection compared with 20AS and M4V (aOR 0.33, p < 0.0001 and aOR 0.27, p < 0.0001, respectively). 2021 Clinical microbiology and infection Abstract SARS_CoV_2 M4V 92 95 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. Compared with 20AS, patients infected with M1V were less likely to report dyspnoea (adjusted odds ratio (OR) 0.50, p 0.04), rhinitis (aOR 0.57, p 0.04) and to be hospitalized (aOR 0.22, p 0.002). 2021 Clinical microbiology and infection Abstract SARS_CoV_2 M1V 43 46 Rhinitis 124 132 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. M1V reached a very weak peak, then disappeared after six weeks. 2021 Clinical microbiology and infection Abstract SARS_CoV_2 M1V 0 3 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. M4V appeared in July presented an atypical wave form for 7 months. 2021 Clinical microbiology and infection Abstract SARS_CoV_2 M4V 0 3 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. Patients infected with M4V were more likely to report fever than those with 20AS and M1V (aOR 2.49, p < 0.0001 and aOR 2.30, p 0.007, respectively) and to be hospitalized than those with M1V (aOR 4.81, p 0.003). 2021 Clinical microbiology and infection Abstract SARS_CoV_2 M1V;M1V;M4V 85;187;23 88;190;26 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. RESULTS: A total of 254 patients were infected with clade 20A (20AS), 85 with Marseille-1 (M1V), 190 with Marseille-4 (M4V) and 211 with N501Y (鈮) variants. 2021 Clinical microbiology and infection Abstract SARS_CoV_2 N501Y 137 142 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. RESULTS: A total of 254 patients were infected with clade 20A (20AS), 85 with Marseille-1 (M1V), 190 with Marseille-4 (M4V) and 211 with N501Y (N501YV) variants. 2021 Clinical microbiology and infection Abstract SARS_CoV_2 N501V;N501Y;M1V;M4V 137;137;91;119 142;142;94;122 34044153 SARS-CoV-2 N gene dropout and N gene Ct value shift as indicator for the presence of B.1.1.7 lineage in a commercial multiplex PCR assay. The N gene coding sequence of SARS-CoV-2 with and without the D3L mutation (specific for B.1.1.7) was cloned into pCR II-TOPOvectors to validate polymorphism-dependent N gene dropout with the AllplexSARS-CoV-2/FluA/FluB/RSVPCR assay. 2021 Clinical microbiology and infection Abstract SARS_CoV_2 D3L 62 65 N;N 4;168 5;169 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. From October 2020, more than 40% of the sequenced genomes present the E484K mutation, which was identified in three different lineages (P.1, P.2 and B.1.1.33 - posteriorly renamed as N.9) in four Brazilian regions. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 E484K 70 75 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Since the second semester of 2020, the mutation E484K has been progressively found in the Brazilian territory, composing different lineages over time. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 E484K 48 53 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. To better characterize the current scenario we performed genomic and phylogenetic analyses of the E484K mutated genomes sequenced from Brazilian samples in 2020. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 E484K 98 103 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. We also evaluated the presence of E484K associated mutations and identified selective pressures acting on the spike protein, leading us to some insights about adaptive and purifying selection driving the virus evolution. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 E484K 34 39 S 110 115 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. The new strain 501.V2 in South Africa bears three mutations in the spike receptor-binding domain (RBD); K417 N, E484K, and N501Y, while the Brazilian B.1.1.248 lineage has 12 mutations. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 E484K;K417N;N501Y 112;104;123 117;110;128 S;RBD 67;98 72;101 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. The results showed that E484K and N501Y are critical in viral spike recognition through either ACE2 or CS-GRP78. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 E484K;N501Y 24;34 29;39 S 62 67 34059617 A core-shell structured COVID-19 mRNA vaccine with favorable biodistribution pattern and promising immunity. Extensive evaluations in mice and nonhuman primates revealed strong immunogenicity of SW0123, represented by induction of Th1-polarized T cell responses and high levels of antibodies that were capable of neutralizing not only the wild-type SARS-CoV-2, but also a panel of variants including D614G and N501Y variants. 2021 Signal transduction and targeted therapy Abstract SARS_CoV_2 D614G;N501Y 291;301 296;306 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Similarly, antibodies elicited by Pfizer BNT162b2 vaccination neutralized B.1.351 and B.1.1.248 with only a 3-fold decrease in titer, an effect attributable to E484K. 2021 mBio Abstract SARS_CoV_2 E484K 160 165 34060425 Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: reconciling functional mechanisms through allosteric model of spike regulation. By combining functional dynamics analysis and ensemble-based alanine scanning of the SARS-CoV-2 spike proteins we found that the D614G mutation can improve stability of the spike protein in both closed and open forms, but shifting thermodynamic preferences towards the open mutant form. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 D614G 129 134 S;S 96;173 101;178 34060425 Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: reconciling functional mechanisms through allosteric model of spike regulation. In this study, we used an integrative computational approach to examine molecular mechanisms underlying functional effects of the D614G mutation by exploring atomistic modeling of the SARS-CoV-2 spike proteins as allosteric regulatory machines. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 D614G 130 135 S 195 200 34060425 Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: reconciling functional mechanisms through allosteric model of spike regulation. Our results revealed that the D614G mutation can promote the increased number of stable communities and allosteric hub centers in the open form by reorganizing and enhancing the stability of the S1-S2 inter-domain interactions and restricting mobility of the S1 regions. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 D614G 30 35 34060425 Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: reconciling functional mechanisms through allosteric model of spike regulation. This study provides atomistic-based view of allosteric communications in the SARS-CoV-2 spike proteins, suggesting that the D614G mutation can exert its primary effect through allosterically induced changes on stability and communications in the residue interaction networks.Communicated by Ramaswamy H. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 D614G 124 129 S 88 93 34060425 Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: reconciling functional mechanisms through allosteric model of spike regulation. Through distance fluctuations communication analysis, we probed stability and allosteric communication propensities of protein residues in the native and mutant SARS-CoV-2 spike proteins, providing evidence that the D614G mutation can enhance long-range signaling of the allosteric spike engine. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 D614G 216 221 S;S 172;282 177;287 34060900 Emergence of Resistance to Novel Cephalosporin-beta-Lactamase Inhibitor Combinations through the Modification of the Pseudomonas aeruginosa MexCD-OprJ Efflux Pump. Whole-genome sequencing revealed that the strain, belonging to ST274, had acquired a nonsense mutation leading to truncated carbapenem porin OprD (W277X), a 7-bp deletion (nt213Delta7) in NfxB (negative regulator of the efflux pump MexCD-OprJ), and two missense mutations (Q178R and S133G) located within the first large periplasmic loop of MexD. 2021 Antimicrobial agents and chemotherapy Abstract SARS_CoV_2 S133G;Q178R;W277X 283;273;147 288;278;152 34061377 Inhibitory effect on SARS-CoV-2 infection of neferine by blocking Ca(2+) -dependent membrane fusion. Neferine effectively protected HEK293/hACE2 and HuH7 cell lines from infection by different coronaviruses pseudovirus particles (SARS-CoV-2, SARS-CoV-2 [D614G, N501Y/D614G, 501Y.V1, 501Y.V2, 501Y.V3 variants], SARS-CoV, MERS-CoV) in vitro, with median effect concentration (EC50 ) of 0.13-0.41 muM. 2021 Journal of medical virology Abstract SARS_CoV_2 N501Y;D614G;D614G 160;166;153 165;171;158 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Although clinical reports indicate that ORF8 variant strains (Delta382 and L84S variants) are less likely to cause severe illness, functional differences between wild-type and variant ORF8 are unknown. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 L84S 75 79 ORF8;ORF8 40;184 44;188 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. In this study, the physicochemical properties of the wild-type ORF8 and its L84S variant were analyzed and compared. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 L84S 76 80 ORF8 63 67 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Interestingly, the L84S variant exhibited greater solubility than wild-type ORF8 under acidic conditions. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 L84S 19 23 ORF8 76 80 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Our data suggested that the wild-type and L84S variant ORF8 structures are highly stable over a wide temperature range. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 L84S 42 46 ORF8 55 59 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Using the tobacco BY-2 cell production system, which has been successfully used to produce the wild-type ORF8 protein with a single conformation, was used to successfully produce the ORF8 L84S variant protein at the same level as wild-type ORF8. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 L84S 188 192 ORF8;ORF8;ORF8 105;183;240 109;187;244 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Comparative coarse-grained molecular dynamic simulations indicated that T307I and D614G belong to a previously unrecognized dynamic domain, interfering with the mobility of the receptor binding domain of the spike. 2021 Viruses Abstract SARS_CoV_2 D614G;T307I 82;72 87;77 RBD;S 177;208 200;213 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. The emergence of SARS-CoV-2 variants, as observed with the D614G spike protein mutant and, more recently, with B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1) lineages, represent a continuous threat and might lead to strains of higher infectivity and/or virulence. 2021 Viruses Abstract SARS_CoV_2 D614G 59 64 S 65 70 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. The T307I mutation showed a synergistic effect with the D614G. 2021 Viruses Abstract SARS_CoV_2 D614G;T307I 56;4 61;9 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. We report on the occurrence of a SARS-CoV-2 haplotype with nine mutations including D614G/T307I double-mutation of the spike. 2021 Viruses Abstract SARS_CoV_2 D614G;T307I 84;90 89;95 S 119 124 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. However, the introduction of lineage B.1.1.7 (UK variant/S_N501Y) and S_E484K mutation in lineage B.1.1.25 in a few sequences reported in late December 2020 is of particular concern. 2021 Microorganisms Abstract SARS_CoV_2 E484K;N501Y 72;59 77;64 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. In particular, the D614G mutation in the spike protein (S_D614G) was found in 97% of the sequences. 2021 Microorganisms Abstract SARS_CoV_2 D614G;D614G 19;58 24;63 S 41 46 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. Amino acid exchanges within the SARS-CoV-2 spike protein variant of B.1.1.7 affect inter-monomeric contact sites within the trimer (A570D and D614G) as well as the ACE2-receptor interface region (N501Y), which comprises the receptor-binding domain (RBD) of the spike protein. 2021 Biomedicines Abstract SARS_CoV_2 D614G;A570D;N501Y 142;132;196 147;137;201 S;S;RBD 43;261;249 48;266;252 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. Furthermore, we found increased flexibility in direct spatial proximity of the fusion peptide due to salt bridge rearrangements induced by the D614G mutation in B.1.1.7. 2021 Biomedicines Abstract SARS_CoV_2 D614G 143 148 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. This study also implies a reduced binding affinity for B.1.1.7 with ACE2, as the N501Y mutation restructures the RBD-ACE2 interface, significantly decreasing the linear interaction energy between the RBD and ACE2. 2021 Biomedicines Abstract SARS_CoV_2 N501Y 81 86 RBD;RBD 113;200 116;203 34067745 An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. These sequences also revealed the presence of single independent mutations-E484Q and N440K-from Maharashtra (first observed in March 2020) and Southern Indian States (first observed in May 2020), respectively. 2021 Viruses Abstract SARS_CoV_2 N440K;E484Q 85;75 90;80 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Applying our simulated results, we illustrate how the recently prevalent N501Y mutation may alter specific interactions with host ACE2 that facilitate the virus-host binding. 2021 Viruses Abstract SARS_CoV_2 N501Y 73 78 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. The D614G mutation is the hallmark of all variants, as it promotes viral spread by increasing the number of open spike protomers in the homo-trimeric receptor complex. 2021 Viruses Abstract SARS_CoV_2 D614G 4 9 S 113 118 34073577 Kinetics of Neutralizing Antibodies of COVID-19 Patients Tested Using Clinical D614G, B.1.1.7, and B 1.351 Isolates in Microneutralization Assays. We applied neutralization tests to paired recoveree sera (n = 38) using clinical isolates representing the first wave (D614G), VoC1, and VoC2 lineages (B.1.1.7 and B 1.351). 2021 Viruses Abstract SARS_CoV_2 D614G 119 124 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. Mutation of E484K leads to the loss of bamlanivimab binding to RBD, although this mutation does not affect the binding between RBD and ACE2. 2021 mAbs Abstract SARS_CoV_2 E484K 12 17 RBD;RBD 63;127 66;130 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. We found that the mutations K417N, E484K, and N501Y within the receptor-binding domains (RBDs) of the virus could confer ~2-fold higher binding affinity to the human receptor, angiotensin converting enzyme 2 (ACE2), compared to the wildtype RBD. 2021 mAbs Abstract SARS_CoV_2 E484K;K417N;N501Y 35;28;46 40;33;51 RBD;RBD 89;241 93;244 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. About 94% (16/17) of the virus samples showed D614G on spike protein and 56% of these (9/16) showed other various amino acid mutations on this protein, including L5F, V83L, V213A, W258R, Q677H, and N811I. 2021 BMC medical genomics Abstract SARS_CoV_2 D614G;L5F;N811I;Q677H;V213A;V83L;W258R 46;162;198;187;173;167;180 51;165;203;192;178;171;185 S 55 60 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. All samples from this family cluster revealed a combination of spike protein mutations of D614G and V213A. 2021 BMC medical genomics Abstract SARS_CoV_2 D614G;V213A 90;100 95;105 S 63 68 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Virus samples from family cluster-2 (n = 3) also belonged to the clade GH and showed other spike protein mutations of L5F alongside the D614G mutation. 2021 BMC medical genomics Abstract SARS_CoV_2 D614G;L5F 136;118 141;121 S 91 96 34075330 A variant in TMPRSS2 is associated with decreased disease severity in COVID-19. V160M). 2021 Meta gene Abstract SARS_CoV_2 V160M 0 5 34075375 Evaluation of mRNA-1273 against SARS-CoV-2 B.1.351 Infection in Nonhuman Primates. RESULTS: Eight weeks post-boost, 100 microg x2 of mRNA-1273 induced reciprocal ID 50 neutralizing geometric mean titers against live SARS-CoV-2 D614G and B.1.351 of 3300 and 240, respectively, and 430 and 84 for the 30 microg x2 group. 2021 bioRxiv Abstract SARS_CoV_2 D614G 144 149 34081630 Epitope-specific antibody responses differentiate COVID-19 outcomes and variants of concern. Moreover, we found that the P681H and S235F mutations associated with the coronavirus variant of concern B.1.1.7 altered the specificity of the corresponding epitopes.CONCLUSIONEpitope-resolved antibody testing not only affords a high-resolution alternative to conventional immunoassays to delineate the complex humoral immunity to SARS-CoV-2 and differentiate between neutralizing and non-neutralizing antibodies, but it also may potentially be used to predict clinical outcome. 2021 JCI insight Abstract SARS_CoV_2 P681H;S235F 28;38 33;43 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. Lastly, the energetics of emerging SARS-CoV-2 mutations were studied, showing that the affinity of the RBD for ACE2 is increased by N501Y and E484K mutations but is slightly decreased by K417N. 2021 The journal of physical chemistry letters Abstract SARS_CoV_2 E484K;K417N;N501Y 142;187;132 147;192;137 RBD 103 106 34086878 Emergence of the E484K Mutation in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Lineage B.1.1.345 in Upstate New York. A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.345 variant carrying the E484K mutation was detected in 4 patients with no apparent epidemiological association from a hospital network in upstate New York. 2022 Clinical infectious diseases Abstract SARS_CoV_2 E484K 94 99 COVID-19 9 49 34087220 Synthetic proteins for COVID-19 diagnostics. Variants of JS7, such as E484K or N501Y, can be quickly synthesized in pure form in large quantities by automated methods. 2021 Peptides Abstract SARS_CoV_2 E484K;N501Y 25;34 30;39 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. Currently, the D614G substitution in the spike protein has become dominant worldwide. 2021 Bioinformation Abstract SARS_CoV_2 D614G 15 20 S 41 46 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. These results suggest that the D614G substitution modulates the flexibility of spike protein and confers enhanced thermodynamic stability irrespective of conformational states. 2021 Bioinformation Abstract SARS_CoV_2 D614G 31 36 S 79 84 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. This data concurs with the known information demonstrating increased availability of the functional form of spikeprotein trimer upon D614G substitution. 2021 Bioinformation Abstract SARS_CoV_2 D614G 133 138 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. Thus, the thermodynamic stability has increased upon D614G substitution. 2021 Bioinformation Abstract SARS_CoV_2 D614G 53 58 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. We demonstrate using Gaussian network model-based normal mode analysis that the D614G substitution occurs at the hinge region that facilitates domain-domain motions between receptor binding domain and S2 region of the spike protein. 2021 Bioinformation Abstract SARS_CoV_2 D614G 80 85 RBD;S 173;218 196;223 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. CONCLUSIONS: Genomic evaluation demonstrated greater than expected genetic diversity, presence of the D614G mutation, increased mutation rate, and evidence of multiple introductions of SARS-CoV-2 into Southern California. 2021 Open forum infectious diseases Abstract SARS_CoV_2 D614G 102 107 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. The calculated viral mutational rate of 22.2 substitutions/year contrasts the 13.5 substitutions/year observed in California isolates without the D614G mutation. 2021 Open forum infectious diseases Abstract SARS_CoV_2 D614G 146 151 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. The D614G mutation in the spike protein was present in 99.3% of the isolates. 2021 Open forum infectious diseases Abstract SARS_CoV_2 D614G 4 9 S 26 31 34097003 Detecting SARS-CoV-2 and its variant strains with a full genome tiling array. From the tiling array analysis results, we identified the D614G mutation in the spike protein in four of the eight samples, suggesting the widespread distribution of this variant at the early stage of the outbreak in the United States. 2021 Briefings in bioinformatics Abstract SARS_CoV_2 D614G 58 63 S 80 85 34097003 Detecting SARS-CoV-2 and its variant strains with a full genome tiling array. Two additional nonsynonymous mutations were identified in one sample in the nucleocapsid protein (P13L and S197L), which may complicate future vaccine development. 2021 Briefings in bioinformatics Abstract SARS_CoV_2 S197L;P13L 107;98 112;102 N 76 88 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. In January 2021, three family members (one aged in their 40s and two aged under 10 years old) were found to be infected with SARS-CoV-2 harboring W152L/E484K/G769V mutations. 2021 PLoS pathogens Abstract SARS_CoV_2 W152L;E484K;G769V 146;152;158 151;157;163 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. R.1 lineage SARS-CoV-2 has potential escape mutations in the spike protein RBD (E484K) and N-terminal domain (W152L); therefore, it will be necessary to continue to monitor the R.1 lineage as it spreads around the world. 2021 PLoS pathogens Abstract SARS_CoV_2 E484K;W152L 80;110 85;115 S;RBD;N 61;75;91 66;78;92 34098567 Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. Group 2 is almost exclusively focused to the RBD-ACE2 interface and does not neutralize SARS-CoV-2 variants that carry E484K or N501Y substitutions. 2021 Nature Abstract SARS_CoV_2 E484K;N501Y 119;128 124;133 RBD 45 48 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. In contrast, only 3 pigs (3/4, 75%) in the E191A-P1 group shed low levels of viral RNA and 2 pigs had moderate diarrhea at acute infection phase. 2021 Cell & bioscience Abstract SARS_CoV_2 E191A 43 48 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Only one mutant E191A with a mutation in the Mg2+-binding site was rescued using the infectious clone of PEDV PC22A strain (icPC22A). 2021 Cell & bioscience Abstract SARS_CoV_2 E191A 16 21 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Pigs in the E191A-P1 group had less severe diarrhea and no pigs died. 2021 Cell & bioscience Abstract SARS_CoV_2 E191A 12 17 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Sanger sequencing analysis revealed that the viral genome in the fecal sample of one E191A-P1-inoculated pig and the P4 virus passaged in vitro lost the E191A mutation, suggesting the genetic instability of the E191A mutant. 2021 Cell & bioscience Abstract SARS_CoV_2 E191A;E191A;E191A 85;153;211 90;158;216 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. The passage no.1-3 (P1-3) of E191A grew to very low titers in Vero cells. 2021 Cell & bioscience Abstract SARS_CoV_2 E191A 29 34 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. To evaluate the pathogenesis of the E191A, 4 or 5-day-old gnotobiotic pigs were inoculated orally with 100 TCID50/pig of the E191A-P1, icPC22A, or mock. 2021 Cell & bioscience Abstract SARS_CoV_2 E191A;E191A 36;125 41;130 34099945 First importations of SARS-CoV-2 P.1 and P.2 variants from Brazil to Spain and early community transmission. The exportation of the P.2 variant, carrying the E484K mutation, deserves attention. 2022 Enfermedades infecciosas y microbiologia clinica Abstract SARS_CoV_2 E484K 49 54 34100009 Impact of BNT162b First Vaccination on the Immune Transcriptome of Elderly Patients Infected with the B.1.351 SARS-CoV-2 Variant. The B.1.351 variant carrying the escape mutation E484K in the receptor binding domain is of particular concern due to reduced immunological protection following vaccination. 2021 Research square Abstract SARS_CoV_2 E484K 49 54 RBD 62 85 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Acquisition of the E484K substitution in the B.1.1.7 background elicits an altered immune response, which could impact disease progression. 2021 medRxiv Abstract SARS_CoV_2 E484K 19 24 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. B.1.1.7 (VOC-202012/01) has become the predominant variant in many countries and a new lineage (VOC-202102/02) harboring the E484K escape mutation in the B.1.1.7 background emerged in February 2021 1 . 2021 medRxiv Abstract SARS_CoV_2 E484K 125 130 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Here, we investigate differences in the immune transcriptome in hospitalized patients infected with either B.1.1.7 (n=28) or B.1.1.7+E484K (n=12). 2021 medRxiv Abstract SARS_CoV_2 E484K 133 138 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Longitudinal transcriptome studies demonstrated a delayed dampening of interferon-activated pathways in B.1.1.7+E484K patients. 2021 medRxiv Abstract SARS_CoV_2 E484K 112 117 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Prior vaccination with BNT162b vaccine (n=8 one dose; n=1 two doses) reduced the transcriptome inflammatory response to B.1.1.7+E484K infection relative to unvaccinated patients. 2021 medRxiv Abstract SARS_CoV_2 E484K 128 133 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. RNA-seq conducted on PBMCs isolated within five days after the onset of COVID symptoms demonstrated elevated activation of specific immune pathways, including JAK-STAT signaling, in B.1.1.7+E484K patients as compared to B.1.1.7. 2021 medRxiv Abstract SARS_CoV_2 E484K 190 195 COVID-19 72 77 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. From missense mutations found from Gujarat SARS-CoV-2 genomes, C28854T, deleterious mutation in the nucleocapsid (N) gene was significantly associated with patients' mortality. 2021 European journal of medical research Abstract SARS_CoV_2 C28854T 63 70 N;N 100;114 112;115 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. Studies have demonstrated that the C14408T and A23403G alterations in the Nsp12 and S proteins are the most prominent alterations in the world, leading to life-threatening mutations.The spike D614G amino acid change has become the most common variant since December 2019. 2021 European journal of medical research Abstract SARS_CoV_2 A23403G;C14408T;D614G 47;35;192 54;42;197 S;Nsp12;S 186;74;84 191;79;85 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. The other significant deleterious variant (G25563T) is found in patients located in Orf3a and has a potential role in viral pathogenesis. 2021 European journal of medical research Abstract SARS_CoV_2 G25563T 43 50 ORF3a 84 89 34104863 Unexpected acute pulmonary embolism in an old COVID-19 patient with warfarin overdose: a case report. The combination of azithromycin intake, a known inhibitor of CYP2C9, with the presence of CYP2C9*2 and -1639G>A VKORC1, two variants associated with warfarin hypersensitivity, have likely contributed to explain the warfarin overdose and the difficulty to reverse warfarin effect in this patient. 2021 European heart journal. Case reports Abstract SARS_CoV_2 G1639A 103 111 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Phylogenetic analysis of the genomes of V367F mutants showed that during the early transmission phase, most V367F mutants clustered more closely with the SARS-CoV-2 prototype strain than the dual-mutation variants (V367F+D614G), which may derivate from recombination. 2021 Journal of virology Abstract SARS_CoV_2 V367F;V367F;V367F;D614G 40;108;215;221 45;113;220;226 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The mutant type V367F continuously circulating worldwide displayed higher binding affinity to human ACE2 due to the enhanced structural stabilization of the RBD beta-sheet scaffold. 2021 Journal of virology Abstract SARS_CoV_2 V367F 16 21 RBD 157 160 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. The design principle can be rapidly adapted for other mutations (as shown also for E484K and T716I) highlighting the advantages of quick optimization and roll-out of CRISPR diagnostics (CRISPRDx) for disease surveillance even beyond COVID-19. 2021 eLife Abstract SARS_CoV_2 E484K;T716I 83;93 88;98 COVID-19 233 241 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. We report the detection of the S gene mutation N501Y (present across multiple variant lineages of SARS-CoV-2) within an hour using lateral flow paper strip chemistry. 2021 eLife Abstract SARS_CoV_2 N501Y 47 52 S 31 32 34106944 Identification and evaluation of the inhibitory effect of Prunella vulgaris extract on SARS-coronavirus 2 virus entry. In this study, we established a sensitive SCoV-2 Spike glycoprotein (SP), including an SP mutant D614G, pseudotyped HIV-1-based vector system and tested their ability to infect ACE2-expressing cells. 2021 PloS one Abstract SARS_CoV_2 D614G 97 102 S;S;S 49;69;87 67;71;89 34107326 SARS-CoV-2 reinfection with a virus harboring mutation in the Spike and the Nucleocapsid proteins in Panama. The virus associated with the reinfection, from an endemic lineage containing the S:L452R immune escape mutation, was circulating in Panama at the time. 2021 International journal of infectious diseases Abstract SARS_CoV_2 L452R 84 89 S 82 83 34107326 SARS-CoV-2 reinfection with a virus harboring mutation in the Spike and the Nucleocapsid proteins in Panama. We report a case of reinfection by SARS-CoV-2 with the second virus harboring amino acid changes in the Spike protein (141-143del, D215A, ins215AGY, L452R, D614G), orf1a, helicase, orf3a, and Nucleocapside. 2021 International journal of infectious diseases Abstract SARS_CoV_2 D215A;D614G;ins215AGY;L452R 131;156;138;149 136;161;147;154 Helicase;ORF1a;S;ORF3a 171;164;104;181 179;169;109;186 34109031 SARS-CoV-2 Brazil variants in Latin America: More serious research urgently needed on public health and vaccine protection. The essential modifications located in the spike glycoprotein RBD include E484K, K417T and N501Y. 2021 Annals of medicine and surgery (2012) Abstract SARS_CoV_2 E484K;K417T;N501Y 74;81;91 79;86;96 S;RBD 43;62 61;65 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. (173,277) SARS-CoV2 sequences deposited in GISAID from December 2019 to March 12, 2021, and identified 2 dominant novel variants, the N501T-G142D variant and N501T-G142D-F486L variant, in the U.S. 2021 Journal of veterinary diagnostic investigation Abstract SARS_CoV_2 N501T;N501T;F486L;G142D;G142D 134;158;170;140;164 139;163;175;145;169 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. Large numbers of mink have been infected with SARS-CoV2 containing the spike protein Y453F mutation in Europe, causing zoonosis concerns. 2021 Journal of veterinary diagnostic investigation Abstract SARS_CoV_2 Y453F 85 90 S 71 76 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. The N501T mutation occurred 2 mo earlier in humans than in mink in the United States, and the novel N501T-G142D and N501T-G142D-F486L variants were found in humans prior to mink. 2021 Journal of veterinary diagnostic investigation Abstract SARS_CoV_2 N501T;N501T;N501T;F486L;G142D;G142D 4;100;116;128;106;122 9;105;121;133;111;127 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. The Y453F mutation was not identified in the mink-derived sequences in the United States and Canada. 2021 Journal of veterinary diagnostic investigation Abstract SARS_CoV_2 Y453F 4 9 34114829 Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study. Our most promising stapled peptides presented a stable profile and could retain important interactions with the RBD in the presence of the E484K RBD mutation. 2021 The journal of physical chemistry. B Abstract SARS_CoV_2 E484K 139 144 RBD;RBD 112;145 115;148 34119826 Therapeutic effect of CT-P59 against SARS-CoV-2 South African variant. CT-P59 showed reduced binding affinity against a RBD (receptor binding domain) triple mutant containing mutations defining B.1.351 (K417N/E484K/N501Y) also showed reduced potency against the SA variant in live virus and pseudovirus neutralization assay systems. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 K417N;E484K;N501Y 132;138;144 137;143;149 RBD;RBD 54;49 77;52 34119951 Examining the interactions scorpion venom peptides (HP1090, Meucin-13, and Meucin-18) with the receptor binding domain of the coronavirus spike protein to design a mutated therapeutic peptide. The results revealed that the A9T mutation had more effective interaction with the RBD domain than the meucin-18 and was able to inhibit spike protein's interaction with ACE2 receptor. 2021 Journal of molecular graphics & modelling Abstract SARS_CoV_2 A9T 30 33 S;RBD 137;83 142;86 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. Notably, 1H1 was able to neutralize all 6 emerging SARS-CoV-2 variants tested including D614G, B.1.1.7, B.1.429, P.1, B.1.526, and B.1.351 variants, and 5E1 could neutralize against the above 5 variants except P.1. 2021 Emerging microbes & infections Abstract SARS_CoV_2 D614G 88 93 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Although huge number of mutations are detected (more than 70 in Asia) by regions, according to bioinformatics tools, some of them which are G75V (isolated from North America), T95I (isolated from South Korea), G143V (isolated from North America), M177I (isolated from Asia), L293M (isolated from Asia), P295H (isolated from Asia), T393P (isolated from Europe), P507S (isolated from Asia), and D614G (isolated from all regions) (These color used only make correct) predicted a damage to spike' protein structure. 2021 Bioinformatics and biology insights Abstract SARS_CoV_2 D614G;G143V;G75V;L293M;M177I;P295H;P507S;T393P;T95I 393;210;140;275;247;303;361;331;176 398;215;144;280;252;308;366;336;180 S 486 491 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Methods: Targeting spike (S) gene mutations of SARS-CoV-2 (N501Y, 69-70del, K417N, and E484K), specific primers, and probes for three specific quantitative reverse transcription PCR (RT-qPCR) assays were designed, and validated using Sanger sequencing. 2021 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 E484K;K417N;N501Y 87;76;59 92;81;64 S;S 19;26 24;27 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. The N501Y, 69-70del, K417N, and E484K SARS-CoV-2 mutations have been documented among the most relevant due to their potential pathogenic biological effects. 2021 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 E484K;K417N;N501Y 32;21;4 37;26;9 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. The screening of samples of COVID-19 patients allowed the identification of the E484K mutation in nine individuals and the identification of P.2 Brazilian variant in Mexico. 2021 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 E484K 80 85 COVID-19 28 36 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. This strategy allowed the detection of E484K mutation and P.2 variant for the first time in samples from the Mexican population. 2021 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 E484K 39 44 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. It is defined by the N501Y mutation in the receptor-binding domain (RBD) of the Spike (S) protein, and a few other mutations. 2021 Emerging microbes & infections Abstract SARS_CoV_2 N501Y 21 26 S;RBD;S 80;68;87 85;71;88 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Structural analysis revealed that the S:D178H mutation is in the NTD of the S protein and close to two other signature mutations of B.1.1.7, HV69-70del and Y144del. 2021 Emerging microbes & infections Abstract SARS_CoV_2 Y144del;D178H 156;40 163;45 S;S 38;76 39;77 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. These include two mutations in the N terminal domain (NTD) of the S protein, HV69-70del and Y144del (also known as Y145del due to the presence of tyrosine at both positions). 2021 Emerging microbes & infections Abstract SARS_CoV_2 Y144del;Y145del 92;115 99;122 N;S 35;66 36;67 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. We now identify a sub-lineage of B.1.1.7 that emerged through sequential acquisitions of M:V70L in November 2020 followed by a novel S:D178H mutation first observed in early February 2021. 2021 Emerging microbes & infections Abstract SARS_CoV_2 D178H;V70L 135;91 140;95 S 133 134 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. We recently identified several emerging SARS-CoV-2 variants of concerns, characterized by Membrane (M) protein mutations, including I82T and V70L. 2021 Emerging microbes & infections Abstract SARS_CoV_2 I82T;V70L 132;141 136;145 Membrane 90 98 34127980 2020 SARS-CoV-2 diversification in the United States: Establishing a pre-vaccination baseline. In Phase 1 (winter/spring), sequences were already dominated by the D614G Spike mutation and by Phase 3 (fall), genetic diversity of the viral population had tripled and at least 54 new amino acid changes had emerged at frequencies above 5%, several of which were within known antibody epitopes. 2021 medRxiv Abstract SARS_CoV_2 D614G 68 73 S 74 79 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. We show that ES can provide an early warning of VOCs becoming prevalent in the population and that, as well as B.1.1.7, our method can detect VOCs B.1.351 and P.1, first identified in South Africa and Brazil, respectively, and other viruses carrying critical spike mutation E484K, known to have an effect on virus antigenicity. 2021 mSystems Abstract SARS_CoV_2 E484K 274 279 S 259 264 34129519 Association of Sickle Cell Trait with Risk and Mortality of COVID-19: Results from the United Kingdom Biobank. Sickle cell trait (SCT) carriers inherit one copy of the Glu6Val mutation in the hemoglobin gene and is particularly common in Black individuals (5-10%). 2021 The American journal of tropical medicine and hygiene Abstract SARS_CoV_2 E6V 57 64 34129831 Antibody Responses After mRNA-Based COVID-19 Vaccination in Residential Older Adults: Implications for Reopening. Pseudovirus neutralization titer levels were strongly correlated (P < .001) with Beckman Coulter antibody levels [D614 G NT50, rs = 0.91; B.1.1.7 (UK) NT50, rs = 0.91]. 2021 Journal of the American Medical Directors Association Abstract SARS_CoV_2 D614G 114 120 34132301 Molecular insights into the binding variance of the SARS-CoV-2 spike with human, cat and dog ACE2 proteins. In accordance with the binding free energies and residue interactions, the spike RBD has respective binding specificities with cACE2, dACE2 and hACE2, and the binding affinities decrease in the order of hACE2, cACE2, dACE2, mainly due to changes in the amino acids Q24L, H34Y, and M82T in cACE2 or dACE2. 2021 Physical chemistry chemical physics : PCCP Abstract SARS_CoV_2 H34Y;M82T;Q24L 271;281;265 275;285;269 S;RBD 75;81 80;84 34134034 Rapid and simultaneous identification of three mutations by the Novaplex SARS-CoV-2 variants I assay kit. Of them, two harbored both H69/V70 deletion and N501Y substitution, whereas two harbored E484K substitution alone. 2021 Journal of clinical virology Abstract SARS_CoV_2 E484K;N501Y 89;48 94;53 34134034 Rapid and simultaneous identification of three mutations by the Novaplex SARS-CoV-2 variants I assay kit. The variant with E484K substitution alone ("R.1") has been now categorized as a variant of interest in Japan. 2021 Journal of clinical virology Abstract SARS_CoV_2 E484K 17 22 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. Based on the partial sequencing of SGTF samples 93.5% (n = 29/31) showed the characteristic N501Y, A570D, P681H, and T716I mutations found in the B.1.1.7 variant. 2021 Frontiers in public health Abstract SARS_CoV_2 A570D;N501Y;P681H;T716I 99;92;106;117 104;97;111;122 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. Several mutations have been reported in the genome of the B.1.1.7 variant including the N501Y and 69-70deletion in the Spike region that has implications on virus transmissibility and diagnostics. 2021 Frontiers in public health Abstract SARS_CoV_2 N501Y 88 93 S 119 124 34137759 Quantitative analysis of ACE2 binding to coronavirus spike proteins: SARS-CoV-2 vs. SARS-CoV and RaTG13. Both calculations confirmed a significant increase of the binding affinity of the N501Y mutant to ACE2 and explained its molecular mechanism. 2021 Physical chemistry chemical physics Abstract SARS_CoV_2 N501Y 82 87 34137759 Quantitative analysis of ACE2 binding to coronavirus spike proteins: SARS-CoV-2 vs. SARS-CoV and RaTG13. We also calculated an important mutation of N501Y in SARS-CoV-2 using both alanine scanning calculation and a thermodynamic integration (TI) method. 2021 Physical chemistry chemical physics Abstract SARS_CoV_2 N501Y 44 49 34137815 Post-Vaccination Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infections and Incidence of the Presumptive B.1.427/B.1.429 Variant Among Healthcare Personnel at a Northern California Academic Medical Center. Available specimens were tested for L452R, N501Y, and E484K mutations using reverse-transcription polymerase chain reaction. 2022 Clinical infectious diseases Abstract SARS_CoV_2 E484K;L452R;N501Y 54;36;43 59;41;48 34137815 Post-Vaccination Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infections and Incidence of the Presumptive B.1.427/B.1.429 Variant Among Healthcare Personnel at a Northern California Academic Medical Center. Of 261 available samples from vaccinated and unvaccinated HCP, 103 (39.5%), including 42 PVSCs (36.5%), had the L452R mutation presumptive of B.1.427/B.1.429. 2022 Clinical infectious diseases Abstract SARS_CoV_2 L452R 112 117 34138474 High-resolution melting curve FRET-PCR rapidly identifies SARS-CoV-2 mutations. Reverse transcription fluorescence resonance energy transfer-polymerase chain reaction (FRET-PCRs) were designed against the two most common mutations in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) (A23403G in the spike protein; C14408T in the RNA-dependent RNA polymerase). 2021 Journal of medical virology Abstract SARS_CoV_2 C14408T;A23403G 246;216 253;223 RdRp;S 261;231 289;236 COVID-19 161 201 34140350 Characterization of a new SARS-CoV-2 variant that emerged in Brazil. However, the effect was less pronounced against the P.1 variant than the S-614G strain. 2021 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 S614G 73 79 S 73 74 34140350 Characterization of a new SARS-CoV-2 variant that emerged in Brazil. In addition, passive transfer of neutralizing antibodies to hamsters infected with the P.1 variant or the S-614G strain led to reduced virus replication in the lower respiratory tract. 2021 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 S614G 106 112 S 106 107 34140350 Characterization of a new SARS-CoV-2 variant that emerged in Brazil. In contrast, the S-614D and S-614G strains were less well recognized than the P.1 variant by serum from a P.1-infected patient. 2021 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 S614D;S614G 17;28 23;34 S;S 17;28 18;29 34140350 Characterization of a new SARS-CoV-2 variant that emerged in Brazil. Prior infection with S-614D or S-614G strains efficiently prevented the replication of the P.1 variant in the lower respiratory tract of hamsters upon reinfection. 2021 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 S614D;S614G 21;31 27;37 S;S 21;31 22;32 34140350 Characterization of a new SARS-CoV-2 variant that emerged in Brazil. Sera and/or plasma from convalescent patients and BNT162b2 messenger RNA vaccinees showed comparable neutralization titers across the P.1 variant, S-614D, and S-614G strains. 2021 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 S614D;S614G 147;159 153;165 S;S 147;159 148;160 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. The ACE2 Triple Decoy maintains high affinity for mutated S RBD, displays enhanced affinity for S RBD N501Y or L452R, and has the highest affinity for S RBD with both E484K and N501Y mutations, making it a viable therapeutic option for the prevention or treatment of SARS-CoV-2 infection with a high likelihood of efficacy against variants. 2021 Scientific reports Abstract SARS_CoV_2 E484K;L452R;N501Y;N501Y 167;111;102;177 172;116;107;182 RBD;RBD;RBD;S;S;S 60;98;153;58;96;151 63;101;156;59;97;152 COVID-19 267 287 34141447 Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2. However, multiple sequence alignment reveals that the majority of SARS-CoV-2 possesses a variant RSM harboring SL5b C241U, and intriguingly, several variations in the coding sequences of viral proteins, such as Nsp12 P323L, S protein D614G, and N protein R203K-G204R, are concurrently found with such variant RSM. 2021 Virus evolution Abstract SARS_CoV_2 D614G;P323L;R203K;G204R 234;217;255;261 239;222;260;266 Nsp12;N;S 211;245;224 216;246;225 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Among these mutations, the most representative ones are substitution mutations such as D614G, N501Y, Y453F, N439K/R, P681H, K417N/T, and E484K, and deletion mutations of DeltaH69/V70 and Delta242-244, which confer the virus with enhanced infectivity, transmissibility, and resistance to neutralization. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G;E484K;K417N;K417T;N439K;N439R;N501Y;P681H;Y453F 87;137;124;124;108;108;94;117;101 92;142;131;131;115;115;99;122;106 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Among the 7 highly recurring (percentage frequency>=10%) mutations (Nsp2:T85I, Nsp6:L37F, Nsp12:P323L, Spike:D614G, ORF3a:Q57H, N protein:R203K and N protein:G204R), N protein:R203K and N protein: G204R are co-occurring (dependent) mutations. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 G204R;D614G;G204R;L37F;P323L;Q57H;R203K;R203K;T85I 197;109;158;84;96;122;138;176;73 202;114;163;88;101;126;143;181;77 S;ORF3a;Nsp12;Nsp2;Nsp6;N;N;N;N 103;116;90;68;79;128;148;166;186 108;121;95;72;83;129;149;167;187 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Further, the occurrence of ORF3a:Q57H&Nsp2:T85I, ORF3a:Q57H and N protein:R203K&G204R along with Nsp12:P323L&Spike:D614G has led to 3 additional sub-clades. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 G204R;D614G;P323L;Q57H;Q57H;R203K;T85I 80;115;103;55;33;74;43 85;120;108;59;42;79;47 ORF3a;ORF3a;Nsp12;Nsp2;N 27;49;97;38;64 32;54;102;42;65 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Intriguingly, ORF3a:G251V and ORF8:L84S are found to occur independent of Nsp12:P323L and Spike:D614G mutations. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G;G251V;L84S;P323L 96;20;35;80 101;25;39;85 S;ORF3a;Nsp12;ORF8 90;14;74;30 95;19;79;34 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Nonetheless, ORF8:L84S does not occur along with ORF3a:G251V or Nsp6:L37F. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 G251V;L37F;L84S 55;69;18 60;73;22 ORF3a;Nsp6;ORF8 49;64;13 54;68;17 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Nsp12:P323L and Spike:D614G often appear simultaneously. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G;P323L 22;6 27;11 S;Nsp12 16;0 21;5 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Similarly, occurrence of Nsp6:L37F and ORF3a:G251V together has led to the emergence of a sub-clade. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 G251V;L37F 45;30 50;34 ORF3a;Nsp6 39;25 44;29 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. The highly recurring Spike:D614G, Nsp12:P323L and Nsp6:L37F as well as moderately recurring (percentage frequency between >=1 and <10%) ORF3a:G251V and ORF8:L84S mutations have led to4 major clades in addition to a clade that lacks high recurring mutations. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G;G251V;L37F;L84S;P323L 27;142;55;157;40 32;147;59;161;45 S;ORF3a;Nsp12;Nsp6;ORF8 21;136;34;50;152 26;141;39;54;156 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. Notably, the optimized antibodies possess potential neutralizing activity against the alarming SARS-CoV-2 variant of N501Y. 2021 Computers in biology and medicine Abstract SARS_CoV_2 N501Y 117 122 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. Two potent P2B-2F6 mutants, namely H:V106R and H:V106R/H:P107Y, were found to possess higher binding affinities with the RBD domain of SARS-CoV-2 than others. 2021 Computers in biology and medicine Abstract SARS_CoV_2 P107Y;V106R;V106R;V106H 57;37;49;49 62;42;56;56 RBD 121 124 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Of 9 single RBD mutants evaluated, K417T, E484K, and N501Y disrupted binding of 65% of the NAbs evaluated, consistent with the assignment of the SARS-CoV-2 P.1 Japan/Brazil strain as a variant of concern (VoC). 2021 Frontiers in immunology Abstract SARS_CoV_2 E484K;K417T;N501Y 42;35;53 47;40;58 RBD 12 15 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. RBD variants E484K and N501Y exhibited ACE2 binding equivalent to a Wuhan-1 reference SARS-CoV-2 RBD. 2021 Frontiers in immunology Abstract SARS_CoV_2 E484K;N501Y 13;23 18;28 RBD;RBD 0;97 3;100 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Thus, the L452R mutant, associated with the SARS-CoV-2 California VoC (B.1.427/B.1.429-California), has evolved to enhance ACE2 binding, while simultaneously disrupting C1 and C2 NAb classes. 2021 Frontiers in immunology Abstract SARS_CoV_2 L452R 10 15 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. While slightly less disruptive to NAb binding, L452R enhanced ACE2 binding affinity. 2021 Frontiers in immunology Abstract SARS_CoV_2 L452R 47 52 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. METHODS: We investigated five mutation sites, A23403G, G25563T, G26144T, T28144C, and G28882A, which are known strain determinants according to GISAID clades (L, S, V, G, GH, and GR). 2021 Journal of infection and chemotherapy Abstract SARS_CoV_2 A23403G;G25563T;G26144T;G28882A;T28144C 46;55;64;86;73 53;62;71;93;80 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. All SARS-CoV-2 strains showed a high genetic similarity with the parent Wuhan strain, but Saudi Arabian, South African, USA, Russia and New Zealand strains carry 3 additional genetic variations like P333L (RNA -dependant RNA polymerase), D614G (spike), and P4715L (ORF1ab). 2021 Computers in biology and medicine Abstract SARS_CoV_2 D614G;P333L;P4715L 238;199;257 243;204;263 ORF1ab;S 265;245 271;250 34158771 Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study. RESULTS: Some mutations were determined, where only one (D614G) had a high prevalence. 2021 Ethiopian journal of health sciences Abstract SARS_CoV_2 D614G 57 62 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. In this study, African green monkeys were infected intranasally with either a contemporary D614G or the UK B.1.1.7 variant. 2021 bioRxiv Abstract SARS_CoV_2 D614G 91 96 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. Interestingly, D614G infected animals showed significantly higher levels of viral RNA and infectious virus in rectal swabs and gastrointestinal tract tissues. 2021 bioRxiv Abstract SARS_CoV_2 D614G 15 20 34159336 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. Structural modeling supported potential functional impact of the D1118H and L452R mutations. 2021 bioRxiv Abstract SARS_CoV_2 D1118H;L452R 65;76 71;81 34159627 Genome-wide association analysis of COVID-19 mortality risk in SARS-CoV-2 genomes identifies mutation in the SARS-CoV-2 spike protein that colocalizes with P.1 of the Brazilian strain. The locus at 25,088 bp is located in the P.1 strain, which later (April 2021) became one of the distinguishing loci (precisely, substitution V1176F) of the Brazilian strain as defined by the Centers for Disease Control. 2021 Genetic epidemiology Abstract SARS_CoV_2 V1176F 141 147 34160124 Preliminary Structural Data Revealed That the SARS-CoV-2 B.1.617 Variant's RBD Binds to ACE2 Receptor Stronger Than the Wild Type to Enhance the Infectivity. In this study, we used structural and biomolecular simulation techniques to explore the impact of specific mutations (L452R-E484Q) in the B.1.617 variant on the binding of RBD to the host receptor ACE2. 2021 Chembiochem Abstract SARS_CoV_2 L452R;E484Q 118;124 123;129 RBD 172 175 34160124 Preliminary Structural Data Revealed That the SARS-CoV-2 B.1.617 Variant's RBD Binds to ACE2 Receptor Stronger Than the Wild Type to Enhance the Infectivity. L452R-E484Q, may play a different role in the B.1.617 (also known as G/452R.V3) variant's pathogenicity and better survival compared to the wild type. 2021 Chembiochem Abstract SARS_CoV_2 E484Q;L452R 6;0 11;5 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. Here, all-atom molecular dynamics simulations and dynamical network theory of the wild-type and mutant RBD/ACE2 adducts disclose that while the N501Y mutation (UK variant) enhances the Spike's binding affinity toward ACE2, the concomitant N501Y, E484K, and K417N mutations (South African variant) aptly adapt to increase SARS-CoV-2 propagation via a two-pronged strategy: (i) effectively grasping ACE2 through an allosteric signaling between pivotal RBD structural elements and (ii) impairing the binding of antibodies elicited by infected or vaccinated patients. 2021 The journal of physical chemistry letters Abstract SARS_CoV_2 E484K;K417N;N501Y;N501Y 246;257;144;239 251;262;149;244 S;RBD;RBD 185;103;450 190;106;453 34161337 SARS-CoV-2 uses major endothelial integrin alphavbeta3 to cause vascular dysregulation in-vitro during COVID-19. A unique K403R spike protein substitution encodes an Arg-Gly-Asp (RGD) motif, introducing a potential role for RGD-binding host integrins. 2021 PloS one Abstract SARS_CoV_2 K403R 9 14 S 15 20 34162440 Deletion of ER-retention motif on SARS-CoV-2 spike protein reduces cell hybrid during cell-cell fusion. Comparison of cell fusion occurring via Delta19-S expressing cells shows defective nuclear fusion and syncytia formation compared to WT-S. 2021 Cell & bioscience Abstract SARS_CoV_2 Delta19-S 40 47 S;S 48;136 49;137 34162440 Deletion of ER-retention motif on SARS-CoV-2 spike protein reduces cell hybrid during cell-cell fusion. CONCLUSIONS: This distinction between the Delta19-S variant and WT-S protein may have downstream implications for studies that utilize pseudovirus-based entry assays. 2021 Cell & bioscience Abstract SARS_CoV_2 Delta19-S 42 49 S;S 50;67 51;68 34162440 Deletion of ER-retention motif on SARS-CoV-2 spike protein reduces cell hybrid during cell-cell fusion. Delta19-S mRNA may represent a safer mRNA vaccine design in the future. 2021 Cell & bioscience Abstract SARS_CoV_2 Delta19-S 0 7 S 8 9 34162440 Deletion of ER-retention motif on SARS-CoV-2 spike protein reduces cell hybrid during cell-cell fusion. Recently, the Delta19-S variant is being widely used to increase SARS-CoV-2 pseudovirus production for in vitro assays. 2021 Cell & bioscience Abstract SARS_CoV_2 Delta19-S 14 21 S 22 23 34162440 Deletion of ER-retention motif on SARS-CoV-2 spike protein reduces cell hybrid during cell-cell fusion. These cell lines were transduced with either wild-type (WT-S) S protein or a mutated variant where the ER-retention motif was removed (Delta19-S), as well as human ACE2 expression vectors. 2021 Cell & bioscience Abstract SARS_CoV_2 Delta19-S 135 142 S;S;S 59;62;143 60;63;144 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Alpha variant B.1.1.7 spike mediates faster kinetics of cell-cell fusion than wild-type Wuhan-1 D614G, dependent on DeltaH69/V70. 2021 Cell reports Abstract SARS_CoV_2 D614G 96 101 S 22 27 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. DeltaH69/V70 is able to partially rescue infectivity of spike proteins that have acquired N439K and Y453F escape mutations by increased spike incorporation. 2021 Cell reports Abstract SARS_CoV_2 N439K;Y453F 90;100 95;105 S;S 56;136 61;141 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike DeltaH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase binding affinity to the ACE2 receptor and confer antibody escape. 2021 Cell reports Abstract SARS_CoV_2 N439K;Y453F 205;215 210;220 S 71 76 COVID-19 17 57 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. This resistance hierarchy corresponded with Y144del and 242-244del mutations in the N-terminal domain and K417N/T, E484K, and N501Y mutations in the receptor-binding domain (RBD) of SARS-CoV-2. 2021 Immunity Abstract SARS_CoV_2 E484K;K417N;K417T;N501Y 115;106;106;126 120;113;113;131 RBD;N 174;84 177;85 34168071 Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity. A local destabilizing effect of the RBD E484K mutation was implicated in resistance of the B.1.1.28/P.1 (Brazil) and B.1.351 (South Africa) variants to neutralizing antibodies. 2021 Science (New York, N.Y.) Abstract SARS_CoV_2 E484K 40 45 RBD 36 39 34168138 The architecture of the SARS-CoV-2 RNA genome inside virion. Unexpectedly, the D614G and the other two accompanying mutations may remodel duplexes into more stable forms. 2021 Nature communications Abstract SARS_CoV_2 D614G 18 23 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. Genotyping by RT-ddPCR offers an alternative to rapidly detect VOCs through discrimination of specific alleles such as N501Y, which is associated with increased transmissibility and virulence. 2021 Journal of medical virology Abstract SARS_CoV_2 N501Y 119 124 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. Real-time epidemiological tracking of variants of concern (VOCs) can help limit the spread of more contagious forms of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), such as those containing the N501Y mutation. 2021 Journal of medical virology Abstract SARS_CoV_2 N501Y 210 215 COVID-19 126 166 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. S gene target failures (SGTF) were subsequently assayed by RT-ddPCR to confirm four mutations within the S gene associated with the B.1.1.7 lineage: a deletion at amino acid (AA) 69-70 (ACATGT), deletion at AA 145, (TTA), N501Y mutation (TAT), and S982A mutation (GCA). 2021 Journal of medical virology Abstract SARS_CoV_2 N501Y;S982A 222;248 227;253 S 105 106 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Here, we demonstrate that two recently emerging mutations in the receptor-binding domain of the SARS-CoV-2 spike protein, L452R (in B.1.427/429 and B.1.617) and Y453F (in B.1.1.298), confer escape from HLA-A24-restricted cellular immunity. 2021 Cell host & microbe Abstract SARS_CoV_2 L452R;Y453F 122;161 127;166 S 107 112 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Notably, the L452R mutation increases spike stability, viral infectivity, viral fusogenicity, and thereby promotes viral replication. 2021 Cell host & microbe Abstract SARS_CoV_2 L452R 13 18 S 38 43 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. All six SARS-CoV-2 positive clinical specimens available in our laboratory with a D399N nucleocapsid mutation and CT < 31 were not detected by the Sofia 2 but detected by the Abbott BinaxNOW COVID-19 Ag Card, while clinical specimens with the T205I mutation were detected by both assays. 2021 Journal of clinical virology Abstract SARS_CoV_2 D399N;T205I 82;243 87;248 N 88 100 COVID-19 191 199 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Testing of recombinant SARS-CoV-2 nucleocapsid with these variants demonstrated an approximate 1000-fold loss in sensitivity for the Quidel Sofia SARS Antigen FIA test associated with the D399N mutation, while the BinaxNOW and Quidel Quickvue SARS Antigen tests were unaffected by the mutation. 2021 Journal of clinical virology Abstract SARS_CoV_2 D399N 188 193 N 34 46 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. The D399N nucleocapsid mutation has been relatively uncommon to date, appearing in only 0.02% of genomes worldwide at time of writing. 2021 Journal of clinical virology Abstract SARS_CoV_2 D399N 4 9 N 10 22 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Whole genome sequencing of the specimen uncovered two mutations, T205I and D399N, present in the nucleocapsid protein of the isolate. 2021 Journal of clinical virology Abstract SARS_CoV_2 D399N;T205I 75;65 80;70 N 97 109 34179048 Poikiloderma With Neutropenia and Mastocytosis: A Case Report and a Review of Dermatological Signs. Here, we present the case of a patient, the only child of apparently unrelated Serbian parents, affected by PN resulting from the homozygous mutation NM_024598.3:c.243G>A (p.Trp81Ter) of USB1; early onset of poikiloderma (1 year of age) was associated with cutaneous mastocytosis. 2021 Frontiers in medicine Abstract SARS_CoV_2 W81X;G243A 172;162 182;170 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. All-atom molecular dynamics simulations are combined with deep mutational scanning and analysis of the residue interaction networks to investigate conformational landscapes and energetics of the SARS-CoV-2 spike proteins in different functional states of the D614G mutant. 2021 ACS omega Abstract SARS_CoV_2 D614G 259 264 S 206 211 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. The network community analysis of the SARS-CoV-2 spike proteins showed that the D614G mutation can enhance long-range couplings between domains and strengthen the interdomain interactions in the open form, supporting the reduced shedding mechanism. 2021 ACS omega Abstract SARS_CoV_2 D614G 80 85 S 49 54 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. The results suggest that the D614G mutation can induce the increased stability of the open form acting as a driver of conformational changes, which may result in the increased exposure to the host receptor and promote infectivity of the virus. 2021 ACS omega Abstract SARS_CoV_2 D614G 29 34 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. We developed and applied a computational approach to simulate functional effects of the global circulating mutation D614G of the SARS-CoV-2 spike protein. 2021 ACS omega Abstract SARS_CoV_2 D614G 116 121 S 140 145 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. CONCLUSION: We describe here a highly sensitive, fully automated multiplex PCR assay for the simultaneous detection of the del-HV69/70 and N501Y mutations that can distinguish between B.1.1.7 and other lineages. 2021 Journal of clinical virology Abstract SARS_CoV_2 N501Y 139 144 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. LoDs were slightly higher for detection of the HV69/70 deletion (85.92, CI: 61-194.41) and the N501Y SNP (105.99 cp/ml, CI: 81.59 - 183.66). 2021 Journal of clinical virology Abstract SARS_CoV_2 N501Y 95 100 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. METHODS: A set of RT-qPCR assays was modified for a diagnostic SARS-CoV-2 multiplex assay including detection of the del-HV69/70 and N501Y mutations on the cobas6800 platform. 2021 Journal of clinical virology Abstract SARS_CoV_2 N501Y 133 138 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. Here we show, that after the second dose, the sera of BNT162b2-vaccinated health care workers (n = 180) effectively neutralize the SARS-CoV-2 variant with the D614G substitution and the B.1.1.7 variant, whereas the neutralization of the B.1.351 variant is five-fold reduced. 2021 Nature communications Abstract SARS_CoV_2 D614G 159 164 34184982 Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. Our analysis: identified a discrete sublineage associated with six care facilities; found no evidence of reinfection in longitudinal samples; ruled out a nosocomial outbreak; identified 16 lineages in key workers which were not in patients, indicating infection control measures were effective; and found the D614G spike protein mutation which is linked to increased transmissibility dominates the samples and rapidly confirmed relatedness of cases in an outbreak at a food processing facility. 2021 Microbial genomics Abstract SARS_CoV_2 D614G 309 314 S 315 320 34188167 Activation of NF-kappaB and induction of proinflammatory cytokine expressions mediated by ORF7a protein of SARS-CoV-2. The viral sequence from infected zoo lions belonged to clade V, and a single mutation of G251V is found for ORF3a gene compared to all other clades. 2021 Scientific reports Abstract SARS_CoV_2 G251V 89 94 ORF3a 108 113 34188776 Evolution, correlation, structural impact and dynamics of emerging SARS-CoV-2 variants. However, reported greater binding affinity of N501Y Spike with ACE2 does not seem to be entirely due to increased hydrophobic interactions, given that Spike mutation R417T in P.1 or K417N in B.1.351 results in the loss of a salt-bridge interaction between ACE2 and S-RBD. 2021 Computational and structural biotechnology journal Abstract SARS_CoV_2 K417N;N501Y;R417T 182;46;166 187;51;171 S;S;RBD;S 52;151;267;265 57;156;270;266 34188776 Evolution, correlation, structural impact and dynamics of emerging SARS-CoV-2 variants. Structural analysis indicated that the N501Y mutation may increase hydrophobic interactions at the ACE2/Spike interface. 2021 Computational and structural biotechnology journal Abstract SARS_CoV_2 N501Y 39 44 S 104 109 34188776 Evolution, correlation, structural impact and dynamics of emerging SARS-CoV-2 variants. Using a combination of bioinformatics and structural analyses, we show that the new SARS-CoV-2 variants emerged in the background of an already known Spike protein mutation D614G together with another mutation P323L in the RNA polymerase of SARS-CoV-2. 2021 Computational and structural biotechnology journal Abstract SARS_CoV_2 D614G;P323L 173;210 178;215 S 150 155 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. Importantly, LCB1v1.3 protected in vivo against a historical strain (WA1/2020), an emerging B.1.1.7 strain, and a strain encoding key E484K and N501Y spike protein substitutions. 2021 Cell host & microbe Abstract SARS_CoV_2 E484K;N501Y 134;144 139;149 S 150 155 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. Neutralizing activity of NTD mAbs but not RBD mAbs against a clinical viral isolate carrying E484K as well as extensive changes in the NTD was abolished, suggesting that a proportion of vaccine-induced RBD binding antibodies may provide substantial protection against viral variants carrying single E484K RBD mutations. 2021 Cell Abstract SARS_CoV_2 E484K;E484K 93;299 98;304 RBD;RBD;RBD 42;202;305 45;205;308 34193667 Less Frequent Sequence Mismatches in Variants of Concern (VOCs) of SARS-CoV-2 in the Real-Time RT-PCR Assays Developed by the National Institute of Infectious Diseases, Japan. The frequency of mismatched sequences in three variants (GRY/VOC202012/01, GH/N501Y.V2, and GR/N501Y.V3) was lower than that in all SARS-CoV-2 sequences. 2022 Japanese journal of infectious diseases Abstract SARS_CoV_2 N501Y;N501Y 78;95 83;100 34193667 Less Frequent Sequence Mismatches in Variants of Concern (VOCs) of SARS-CoV-2 in the Real-Time RT-PCR Assays Developed by the National Institute of Infectious Diseases, Japan. The mismatch, that G to C substitution at nucleotide 8 in reverse primer of S2 set, elevated to about 16.3% in G/L452R.V3, however the substitution did not affect the analytical sensitivity of assay. 2022 Japanese journal of infectious diseases Abstract SARS_CoV_2 G8C;G452R;L452R 19;111;113 54;118;118 34193667 Less Frequent Sequence Mismatches in Variants of Concern (VOCs) of SARS-CoV-2 in the Real-Time RT-PCR Assays Developed by the National Institute of Infectious Diseases, Japan. The variant containing L to R substitution at position 452 in the S protein G/L452R.V3 (B1.617) was endemic to India. 2022 Japanese journal of infectious diseases Abstract SARS_CoV_2 G452R;L452R 76;78 83;83 S 66 67 34193667 Less Frequent Sequence Mismatches in Variants of Concern (VOCs) of SARS-CoV-2 in the Real-Time RT-PCR Assays Developed by the National Institute of Infectious Diseases, Japan. The variants GRY/VOC202012/01 (B1.1.7), GH/N501Y.V2 (B1.351), and GR/N501Y.V3 (P1) are characterized by N to Y amino acid substitution at position 501 in the S protein. 2022 Japanese journal of infectious diseases Abstract SARS_CoV_2 N501Y;N501Y 43;69 48;74 S 158 159 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. One of the many mutations that have occurred in the viral genome is the V483A mutation, which is a part of the receptor-binding motif present in the S1 domain of the spike protein. 2021 Future virology Abstract SARS_CoV_2 V483A 72 77 S 166 171 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. This review compares the wild-type and the V483A mutants to analyze certain factors like the interaction between the virus and host-cell interface, binding affinity, stability, partition energy, hydrophobicity, occurrence rate and transmissibility. 2021 Future virology Abstract SARS_CoV_2 V483A 43 48 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. V483A mutant virus is popular in North America with 36 cases so far and frequently occurring in recent days. 2021 Future virology Abstract SARS_CoV_2 V483A 0 5 34197265 Comparison of SARS-CoV-2 Variants of Concern 202012/01 (U.K. Variant) and D614G Variant Transmission by Different Routes in Syrian Hamsters. and D614G variants of SARS-CoV-2 in Syrian hamsters in the given conditions. 2021 Vector borne and zoonotic diseases (Larchmont, N.Y.) Abstract SARS_CoV_2 D614G 4 9 34197265 Comparison of SARS-CoV-2 Variants of Concern 202012/01 (U.K. Variant) and D614G Variant Transmission by Different Routes in Syrian Hamsters. variant) and D614G variant in the hamster model, we observed higher viral RNA shedding through nasal wash in the case of U.K. 2021 Vector borne and zoonotic diseases (Larchmont, N.Y.) Abstract SARS_CoV_2 D614G 13 18 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. Herein we report a novel local variant with a non-synonymous mutation in the spike (S) protein P681H. 2021 Vaccines Abstract SARS_CoV_2 P681H 95 100 S;S 77;84 82;85 34203844 SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence. To date, most studies showed that the viral mutations, especially the D614G variant, correlate with a higher infectivity than the wild-type virus. 2021 Journal of clinical medicine Abstract SARS_CoV_2 D614G 70 75 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. Here we tested the neutralizing activity of infected and/or vaccinated individuals against pseudoviruses expressing the spike of the original SARS-CoV-2 isolate Wuhan-Hu-1 (WH1), the D614G mutant and the B.1.1.7 variant. 2021 Viruses Abstract SARS_CoV_2 D614G 183 188 S 120 125 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. Uninfected vaccinees showed a small reduction in neutralization against the B.1.1.7 variant compared to both the WH1 strain and the D614G mutant. 2021 Viruses Abstract SARS_CoV_2 D614G 132 137 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. During the spread of the virus, the RdRp has developed several mutations, with the most frequent being A97V and P323L. 2021 Biomolecules Abstract SARS_CoV_2 A97V;P323L 103;112 107;117 RdRP 36 40 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Results showed that RDV that bound to WT- and A97V-RdRp had a similar dynamic motion and internal residue fluctuations, whereas RDV interaction with P323L-RdRp exhibited a tighter molecular conformation, with a high internal motion near the active site. 2021 Biomolecules Abstract SARS_CoV_2 A97V;P323L 46;149 50;159 RdRP;RdRP 51;155 55;159 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. The current study sought to investigate whether A97V and P323L mutations influence the binding of RDV to the RdRp of SARS-CoV-2 compared to wild-type (WT). 2021 Biomolecules Abstract SARS_CoV_2 A97V;P323L 48;57 52;62 RdRP 109 113 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. The interaction of RDV with WT-, A97V-, and P323L-RdRp were measured using molecular dynamic (MD) simulations, and the free binding energies were extracted. 2021 Biomolecules Abstract SARS_CoV_2 A97V;P323L 33;44 38;54 RdRP 50 54 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. This study provides insight into the potential significance of administering RDV to patients carrying the SARS-CoV-2 P323L-RdRp mutation, which may have a more favourable chance of alleviating the SARS-CoV-2 illness in comparison to WT-RdRp carriers, thereby suggesting further scientific consensus for the usage of Remdesivir as clinical candidate against COVID-19. 2021 Biomolecules Abstract SARS_CoV_2 P323L 117 127 RdRP;RdRP 123;236 127;240 COVID-19;COVID-19 357;197 365;215 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. This was further corroborated with RDV showing a higher binding affinity to P323L-RdRp (-24.1 kcal/mol) in comparison to WT-RdRp (-17.3 kcal/mol). 2021 Biomolecules Abstract SARS_CoV_2 P323L 76 86 RdRp;RdRp 82;124 86;128 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The newly recognized VOC Delta or lineage B.1.617.2, as well as locally accepted VOCs (Epsilon or B.1.427/29-US and B1.1.7 with the E484K-UK) are indicating the necessity of close monitoring of new variants on a global level. 2021 Viruses Abstract SARS_CoV_2 E484K 132 137 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. The first relevant event in this context was the occurrence of the mutant D614G in the Spike gene. 2021 Viruses Abstract SARS_CoV_2 D614G 74 79 S 87 92 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. Genetic analysis of whole SARS-CoV-2 genomic sequences of the aforementioned lineages revealed the presence of mutations within the S protein (L18F, DeltaH69/V70, S898F, DeltaY144, S162G, A222V, N439K, N501Y, A570D, D614G, P681H, S982A and D1118H) that confer higher transmissibility and/or antibody escape (immune evasion) upon the virus. 2021 Viruses Abstract SARS_CoV_2 A222V;A570D;D1118H;D614G;DeltaY144;N439K;N501Y;P681H;S162G;S898F;S982A;L18F 188;209;240;216;170;195;202;223;181;163;230;143 193;214;246;221;179;200;207;228;186;168;235;147 S 132 133 34208912 Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. The potential contributions of the mutations (N501Y, E484K, and K417N/T) contained in these variants' RBDs to the antibody pairing capability, neutralization activity, and therapeutic antibody targeting strategy are discussed. 2021 Diagnostics (Basel, Switzerland) Abstract SARS_CoV_2 E484K;K417N;K417T;N501Y 53;64;64;46 58;71;71;51 RBD 102 106 34210893 SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern. A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429), which was originally detected in California, carries spike glycoprotein mutations S13I in the signal peptide, W152C in the N-terminal domain (NTD), and L452R in the receptor-binding domain (RBD). 2021 Science (New York, N.Y.) Abstract SARS_CoV_2 L452R;S13I;W152C 218;148;176 223;152;181 S;RBD;N 119;256;189 137;259;190 34210893 SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern. The L452R mutation reduced neutralizing activity in 14 of 34 RBD-specific monoclonal antibodies (mAbs). 2021 Science (New York, N.Y.) Abstract SARS_CoV_2 L452R 4 9 RBD 61 64 34210893 SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern. The S13I and W152C mutations resulted in total loss of neutralization for 10 of 10 NTD-specific mAbs because the NTD antigenic supersite was remodeled by a shift of the signal peptide cleavage site and the formation of a new disulfide bond, as revealed by mass spectrometry and structural studies. 2021 Science (New York, N.Y.) Abstract SARS_CoV_2 S13I;W152C 4;13 8;18 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Our results suggest that the P323L mutation, located in the interface domain of the RNA-dependent RNA polymerase, is a necessary alteration that led to the epidemiological success of the present variant of SARS-CoV-2. 2021 Scientific reports Abstract SARS_CoV_2 P323L 29 34 RdRp 84 112 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. The D614G mutation in the Spike protein of the SARS-CoV-2 has effectively replaced the early pandemic-causing variant. 2021 Scientific reports Abstract SARS_CoV_2 D614G 4 9 S 26 31 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. To explain the epidemiological success of D614G, we analysed the evolution of 27,086 high-quality SARS-CoV-2 genome sequences from GISAID. 2021 Scientific reports Abstract SARS_CoV_2 D614G 42 47 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Using pseudotyped lentivectors, we confirmed that the aspartate replacement by glycine in position 614 is markedly more infectious. 2021 Scientific reports Abstract SARS_CoV_2 D614G 54 102 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. We observed striking coevolution of D614G with the P323L mutation in the viral polymerase. 2021 Scientific reports Abstract SARS_CoV_2 D614G;P323L 36;51 41;56 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. These sequences were highly diverse in the G clade with nine novel amino acid mutations including NSP12-M755I and ORF8-V117F. 2021 Scientific reports Abstract SARS_CoV_2 M755I;V117F 104;119 109;124 Nsp12;ORF8 98;114 103;118 34211709 The emerging SARS-CoV-2 variants of concern. These mutations carry a lineage from N501Y, D614G, N439K, Y453F, and others, which are globally dominated by clades 20A, 20B, and 20C. 2021 Therapeutic advances in infectious disease Abstract SARS_CoV_2 D614G;N439K;N501Y;Y453F 44;51;37;58 49;56;42;63 34214046 Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice. Chimeric spike mRNA vaccines efficiently neutralized D614G, mink cluster five, and the UK B.1.1.7 and South African B.1.351 variants of concern. 2021 Science (New York, N.Y.) Abstract SARS_CoV_2 D614G 53 58 S 9 14 34214142 ACE2-lentiviral transduction enables mouse SARS-CoV-2 infection and mapping of receptor interactions. Transduction of non-permissive cell lines with hACE2 imparted replication competence, and transduction with mACE2 containing N30D, N31K, F83Y and H353K substitutions, to match hACE2, rescued SARS-CoV-2 replication. 2021 PLoS pathogens Abstract SARS_CoV_2 F83Y;H353K;N30D;N31K 137;146;125;131 141;151;129;135 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Anti-S monoclonal antibodies differentially neutralize SARS-CoV-2 E484D S in H522 cells as compared to ACE2-expressing cells. 2021 Cell reports Abstract SARS_CoV_2 E484D 66 71 S;S 5;72 6;73 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Remarkably, H522 infection requires the E484D S variant; viruses expressing wild-type S are not infectious. 2021 Cell reports Abstract SARS_CoV_2 E484D 40 45 S;S 46;86 47;87 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. These findings establish an alternative SARS-CoV-2 host cell receptor for the E484D SARS-CoV-2 variant, which may impact tropism of SARS-CoV-2 and consequently human disease pathogenesis. 2021 Cell reports Abstract SARS_CoV_2 E484D 78 83 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The hotspot stabilizing residue mutations N501I, N501Y, Q493L, Q493H and K417R, strengthen the RBD-ACE2 complex by modulating the interaction statistics at the interface. 2021 Virology Abstract SARS_CoV_2 K417R;N501I;N501Y;Q493H;Q493L 73;42;49;63;56 78;47;54;68;61 RBD 95 98 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. However, the convalescent sera, inactivated virus vaccine-elicited sera, mRNA vaccine-elicited sera, spike DNA-elicited sera, and recombinant RBD protein-elicited sera could still neutralize these variants (within three-fold changes compared to the reference D614G variant). 2021 Frontiers in immunology Abstract SARS_CoV_2 D614G 259 264 S;RBD 101;142 106;145 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. The N501Y, N439K, and S477N mutations caused immune escape from nine of 18 mAbs. 2021 Frontiers in immunology Abstract SARS_CoV_2 N439K;N501Y;S477N 11;4;22 16;9;27 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. To determine whether the neutralization activity of monoclonal antibodies, convalescent sera and vaccine-elicited sera was affected by the top five epidemic SARS-CoV-2 variants in the UK, including D614G+L18F+A222V, D614G+A222V, D614G+S477N, VOC-202012/01(B.1.1.7) and D614G+69-70del+N439K, a pseudovirus-neutralization assay was performed to evaluate the relative neutralization titers against the five SARS-CoV-2 variants and 12 single deconvolution mutants based on the variants. 2021 Frontiers in immunology Abstract SARS_CoV_2 D614G;D614G;D614G;D614G;A222V;A222V;L18F;N439K;S477N 198;216;229;269;209;222;204;284;235 203;221;234;274;214;227;208;289;240 34220870 Declining Levels of Neutralizing Antibodies Against SARS-CoV-2 in Convalescent COVID-19 Patients One Year Post Symptom Onset. However, neutralizing capacities, in particular against an E484K-mutated VOC were only detectable in a minority of patients one year after symptomatic COVID-19. 2021 Frontiers in immunology Abstract SARS_CoV_2 E484K 59 64 COVID-19 151 159 34220870 Declining Levels of Neutralizing Antibodies Against SARS-CoV-2 in Convalescent COVID-19 Patients One Year Post Symptom Onset. When neutralization tests against the E484K-mutated variant of concern (VOC) B.1.351 (initially identified in South Africa) were performed among patients who neutralize the original virus, the capacity to neutralize was even further diminished to 22.6% of donors. 2021 Frontiers in immunology Abstract SARS_CoV_2 E484K 38 43 34222046 SARS-CoV-2: Origin, Evolution, and Targeting Inhibition. Moreover, we analyzed the structural differences between SARS-CoV-2 ancestral S protein and D614G mutant, which led to a second wave of infection during the recent pandemic. 2021 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 D614G 92 97 S 78 79 34223589 Corilagin and 1,3,6-Tri-O-galloy-beta-D-glucose: potential inhibitors of SARS-CoV-2 variants. In addition to the wild-type RBD, we also study numerically three RBD mutations (E484K, N501Y and E484K/N501Y) found in the main SARS-CoV-2 variants of concerns. 2021 Physical chemistry chemical physics Abstract SARS_CoV_2 E484K;N501Y;E484K;N501Y 98;88;81;104 103;93;86;109 RBD;RBD 29;66 32;69 34223589 Corilagin and 1,3,6-Tri-O-galloy-beta-D-glucose: potential inhibitors of SARS-CoV-2 variants. We find that corilagin could be as effective for RBD/E484K but less effective for the RBD/N501Y and RBD/E484K-N501Y mutants, while TGG strongly binds at relevant locations to all three mutants, demonstrating the significant interest of these molecules as potential inhibitors for variants of SARS-CoV-2. 2021 Physical chemistry chemical physics Abstract SARS_CoV_2 E484K;E484K;N501Y;N501Y 53;104;90;110 58;109;95;115 RBD;RBD;RBD 49;86;100 52;89;103 34223909 Limited Neutralization of Authentic Severe Acute Respiratory Syndrome Coronavirus 2 Variants Carrying E484K In Vitro. We show that authentic SARS-CoV-2 carrying E484K were resistant against bamlanivimab and less susceptible to casirivimab, convalescent and vaccine-elicited sera. 2021 The Journal of infectious diseases Abstract SARS_CoV_2 E484K 43 48 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. Importantly, these two antibodies also showed efficient neutralizing activities to the variants including B.1.1.7 and B.1.351, and reacted with mutations of N501Y, E484K, and L452R, indicated that it may also neutralize the recent India endemic strain B.1.617. 2021 Virologica Sinica Abstract SARS_CoV_2 E484K;L452R;N501Y 164;175;157 169;180;162 34225487 Replicative Fitness of a SARS-CoV-2 20I/501Y.V1 Variant from Lineage B.1.1.7 in Human Reconstituted Bronchial Epithelium. Here, we analyze the replication ability of this new variant in different cellular models using for comparison an ancestral D614G European strain (lineage B1). 2021 mBio Abstract SARS_CoV_2 D614G 124 129 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. In the current study, we formulated protein subunit vaccines with AS03 adjuvant and recombinant proteins of S1 subunit of SARS-CoV-2 (S1-WT) and S1 variant (K417N, E484K, N501Y, and D614G) subunit (S1-Mut), and immunized transgenic mice that express human angiotensin-converting enzyme 2 (hACE2). 2021 MedComm Abstract SARS_CoV_2 D614G;E484K;N501Y;K417N 182;164;171;157 187;169;176;162 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. Neutralization potency was retained for S variants including S477N, E484K, and N501Y, substitutions present in recent variants of concern. 2021 Human vaccines & immunotherapeutics Abstract SARS_CoV_2 E484K;N501Y;S477N 68;79;61 73;84;66 S 40 41 34229570 Comparative analysis of SARS-CoV-2 envelope viroporin mutations from COVID-19 deceased and surviving patients revealed implications on its ion-channel activities and correlation with patient mortality. F4F, R69I, P71L, L73F) with patient mortalities were also observed, based on the patient data available for 18,691 SARS-CoV-2-genomes in the GISAID database till 30 April 2021. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 L73F;P71L;R69I;F4F 17;11;5;0 21;15;9;3 34230926 Natural isolate and recombinant SARS-CoV-2 rapidly evolve in vitro to higher infectivity through more efficient binding to heparan sulfate and reduced S1/S2 cleavage. The S686G mutation also transforms the FCS into the heparin-binding peptide. 2021 bioRxiv Abstract SARS_CoV_2 S686G 4 9 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. However, these changes in infectivity were not reproduced in the original Wuhan-Hu-1 spike bearing only the P681R substitution. 2022 bioRxiv Abstract SARS_CoV_2 P681R 108 113 S 85 90 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. Our findings suggest that while A.23.1 has increased furin-mediated cleavage linked to the P681R substitution, which may affect viral infection and transmissibility, this substitution alone is not sufficient and needs to occur on the background of other spike protein changes to enable its full functional consequences. 2022 bioRxiv Abstract SARS_CoV_2 P681R 91 96 S 254 259 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. The A.23 viral lineage, characterized by three spike mutations F157L, V367F and Q613H, was first identified in COVID-19 cases from a Ugandan prison in July 2020, and then was identified in the general population with additional spike mutations (R102I, L141F, E484K and P681R) to comprise lineage A.23.1 by September 2020, with this virus being designated a variant of interest (VOI) in Africa and with subsequent spread to 26 other countries. 2022 bioRxiv Abstract SARS_CoV_2 E484K;F157L;L141F;P681R;Q613H;V367F;R102I 259;63;252;269;80;70;245 264;68;257;274;85;75;250 S;S 47;228 52;233 COVID-19 111 119 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. The P681R spike substitution of the A.23.1 VOI is of note as it increases the number of basic residues in the sub-optimal SARS-CoV-2 spike protein furin cleavage site; as such, this substitution may affect viral replication, transmissibility or pathogenic properties. 2022 bioRxiv Abstract SARS_CoV_2 P681R 4 9 S;S 10;133 15;138 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. The same P681R substitution has also appeared in B.1.617 variants, including B.1.617.2 (Delta). 2022 bioRxiv Abstract SARS_CoV_2 P681R 9 14 34234758 A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3' Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity. Almost all VOC-containing genomes possess one stop codon in ORF8 gene (Q27*), however, 13% of these genomes also contains another stop codon (K68*), suggesting that ORF8 loss does not interfere with SARS-CoV-2 spread and may play a role in its increased virulence. 2021 Frontiers in microbiology Abstract SARS_CoV_2 K68X;Q27X 142;71 146;75 ORF8;ORF8 60;165 64;169 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. In contrast, single mutation E484K had almost no impact on the binding kinetics, but essentially abolished recognition of RBD by convalescent sera. 2022 Allergy Abstract SARS_CoV_2 E484K 29 34 RBD 122 125 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. Interestingly, combining mutations E484K, K417N, and N501Y resulted in a RBD with both features: enhanced receptor binding and abolished immune recognition. 2022 Allergy Abstract SARS_CoV_2 E484K;K417N;N501Y 35;42;53 40;47;58 RBD 73 76 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. METHODS: We produced wild type RBD, RBD with single mutations (E484K, K417N, or N501Y) or with all three mutations combined and tested their binding to ACE2 by biolayer interferometry (BLI). 2022 Allergy Abstract SARS_CoV_2 K417N;N501Y;E484K 70;80;63 75;85;68 RBD;RBD 31;36 34;39 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. RESULTS: We demonstrated that single mutation N501Y increased binding affinity to ACE2 but did not strongly affect its recognition by convalescent sera. 2022 Allergy Abstract SARS_CoV_2 N501Y 46 51 34241897 Genomic monitoring unveil the early detection of the SARS-CoV-2 B.1.351 (beta) variant (20H/501Y.V2) in Brazil. Our analysis allowed also the detection, for the first time in Brazil, the South African B.1.351 (beta) variant of concern, B.1.351 (501Y.V2) (0.5%), characterized by the following mutations: ORF1ab: T265I, R724K, S1612L, K1655N, K3353R, SGF 3675_F3677del, P4715L, E5585D; spike: D80A, D215G, L242_L244del, A262D, K417N, E484K, N501Y, D614G, A701V, C1247F; ORF3a: Q57H, S171L, E: P71L; ORF7b: Y10F, N: T205I; ORF14: L52F. 2021 Journal of medical virology Abstract SARS_CoV_2 A262D;A701V;C1247F;D215G;D614G;D80A;E484K;E5585D;K1655N;K3353R;K417N;L52F;N501Y;P4715L;P71L;Q57H;R724K;S1612L;S171L;T205I;T265I;Y10F 307;342;349;286;335;280;321;265;222;230;314;416;328;257;380;364;207;214;370;402;200;393 312;347;355;291;340;284;326;271;228;236;319;420;333;263;384;368;212;220;375;407;205;397 ORF1ab;ORF7b;S;ORF3a;E;N 192;386;273;357;377;399 198;391;278;362;378;400 34241906 Genomic characterization of SARS-CoV-2 isolates from patients in Turkey reveals the presence of novel mutations in spike and nsp12 proteins. Novel mutations were found in nsp12 (V111A, H133R, Y453C, M626K) and ORF2/S (R995G, V1068L). 2021 Journal of medical virology Abstract SARS_CoV_2 H133R;M626K;V1068L;Y453C;R995G;V111A 44;58;84;51;77;37 49;63;90;56;82;42 Nsp12 30 35 34241906 Genomic characterization of SARS-CoV-2 isolates from patients in Turkey reveals the presence of novel mutations in spike and nsp12 proteins. The most frequent mutations were P323L (nsp12), D614G (ORF2/S), and 2421C>T (5'-untranslated region) found simultaneously in all sequences. 2021 Journal of medical virology Abstract SARS_CoV_2 C2421T;D614G;P323L 68;48;33 75;53;38 Nsp12 40 45 34242876 Energetic and structural basis for the differences in infectivity between the wild-type and mutant spike proteins of SARS-CoV-2 in the Mexican population. To date, there have been several lineages of SARS-CoV-2 worldwide; in the Mexican population, two variants of the spike protein (S-protein) are found, localized at H49Y and D614G, which have been related to increased infectivity with respect to the wild-type S-protein. 2021 Journal of molecular graphics & modelling Abstract SARS_CoV_2 D614G;H49Y 173;164 178;168 S;S;S 114;129;259 119;130;260 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. However, virus escape analysis identifies a single natural mutation in RBD, namely K417N found in B.1.351 variant from South Africa, abolished the neutralizing activity of these public antibodies. 2021 Nature communications Abstract SARS_CoV_2 K417N 83 88 RBD 71 74 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Apart from that the group of SNVs became dominant, which is represented by two nonsynonymous mutations A23403G (S:D614G) and C14408T (ORF1ab:P4715L), a few emerging groups of SNVs were recognized with sharply increased monthly incidence ratios of up to 70% in November 2020. 2021 Journal of medical virology Abstract SARS_CoV_2 A23403G;C14408T;D614G;P4715L 103;125;114;141 110;132;119;147 ORF1ab;S 134;112 140;113 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Our logistic regression model explored features contributing to mortality status, including three critical SNVs, G25088T(S:V1176F), T27484C (ORF7a:L31L), and T25A (upstream of ORF1ab), ages above 40 years old, and the male gender. 2021 Journal of medical virology Abstract SARS_CoV_2 G25088T;T25A;T27484C;L31L;V1176F 113;158;132;147;123 120;162;139;151;129 ORF1ab;ORF7a;S 176;141;121 182;146;122 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. CONCLUSION: The findings indicate that the 11083G > T mutation of SARS-CoV-2 spread during shipboard quarantine and arose through de novo RNA recombination under positive selection pressure. 2021 Bulletin of the World Health Organization Abstract SARS_CoV_2 G11083T 43 53 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. FINDINGS: The SARS-CoV-2 outbreak in the cruise most likely originated from either a single person infected with a virus variant identical to the WIV04 isolates, or simultaneously with another primary case infected with a virus containing the 11083G > T mutation. 2021 Bulletin of the World Health Organization Abstract SARS_CoV_2 G11083T 243 253 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. Linkage disequilibrium analysis confirmed that ribonucleic acid (RNA) recombination with the11083G > T mutation also contributed to the increase of mutations among the viral progeny. 2021 Bulletin of the World Health Organization Abstract SARS_CoV_2 G11083T 92 102 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. Potential alterations in antigenicity conferred by amino acid changes in the spike protein that include three substitutions (Y453F, I692V, and M1229I) and a loss of two amino acid residues 69 and 70 (DeltaH69/V70), were evaluated in a virus microneutralization assay. 2021 Frontiers in microbiology Abstract SARS_CoV_2 I692V;M1229I;Y453F 132;143;125 137;149;130 S 77 82 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. All substitutions tested (H41A, H41D, H41E, C145A, and C145S) resulted in a complete inactivation of 3CLpro, even when amino acids with a similar catalytic function to that of the original residues were used. 2021 Frontiers in chemistry Abstract SARS_CoV_2 C145A;C145S;H41D;H41E;H41A 44;55;32;38;26 49;60;36;42;30 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. C145A, but not the other substitutions, shifted the oligomeric state of the enzyme from dimeric to a higher oligomeric state. 2021 Frontiers in chemistry Abstract SARS_CoV_2 C145A 0 5 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. Finally, the thermodynamic stability of 3CLpro H41A, H41D, and C145S variants was reduced relative the wild-type enzyme, with a similar stability of the H41E and C145A variants. 2021 Frontiers in chemistry Abstract SARS_CoV_2 C145A;C145S;H41A;H41D;H41E 162;63;47;53;153 167;68;51;57;157 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. We describe the enhanced affinity of RBD variants N439K, S477N, Q493L, S494P, and N501Y to the ACE2 receptor and demonstrate the ability of this assay to bridge a major gap for SARS-CoV-2 research, informing selection of complementary monoclonal antibody candidates and the rapid identification of immune escape to emerging RBD variants following vaccination or natural infection. 2021 JCI insight Abstract SARS_CoV_2 N439K;N501Y;Q493L;S477N;S494P 50;82;64;57;71 55;87;69;62;76 RBD;RBD 37;324 40;327 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Besides, mutations in SR-rich region of N protein and P323L in RDRP were also present. 2021 Virus genes Abstract SARS_CoV_2 P323L 54 59 RdRP;N 63;40 67;41 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. However, along with D614G mutation, more than 20 different mutations in the Spike protein were detected basically in the S2 domain. 2021 Virus genes Abstract SARS_CoV_2 D614G 20 25 S 76 81 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Analyses showed the existence of at least 4 distinct clades of this variant circulating in the United States and the possibility of at least 59 independent acquisitions of the E484K mutation. 2021 Open forum infectious diseases Abstract SARS_CoV_2 E484K 176 181 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. We report the genome of a B.1.1.7+E484K severe acute respiratory syndrome coronavirus 2 from Southeastern Pennsylvania and compare it with all high-coverage B.1.1.7+E484K genomes (n = 235) available. 2021 Open forum infectious diseases Abstract SARS_CoV_2 E484K;E484K 34;165 39;170 COVID-19 47 87 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. The comprehensive mutagenesis of guide-target interaction demonstrated that single-nucleotide mismatches does not impair the capacity of a potent single crRNA to simultaneously suppress ancestral and mutated SARS-CoV-2 strains in infected mammalian cells, including the Spike D614G mutant. 2021 Nature communications Abstract SARS_CoV_2 D614G 276 281 S 270 275 34258267 Relevant SARS-CoV-2 Genome Variation through Six Months of Worldwide Monitoring. Four hotspot mutations were found in all geographical locations at least once: T265I (NSP2), P314L (NSP12), D614G (S), and Q57H (ORF3a). 2021 BioMed research international Abstract SARS_CoV_2 D614G;P314L;Q57H;T265I 108;93;123;79 113;98;127;84 ORF3a;Nsp12;Nsp2;S 129;100;86;115 134;105;90;116 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Different genetic polymorphisms, particularly P681H and A688V, were detected in the FCS, mainly in human isolates, and otherwise, only pangolin and bat sequences had these mutations. 2021 Archives of virology Abstract SARS_CoV_2 A688V;P681H 56;46 61;51 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Here, we analyzed the frequency of Q677P/H and FCS point mutations in 1,144,793 human and 1042 animal spike protein sequences and from those of the emergent variants B.1.1.7, B.1.351, P.1, B.1.429 + B.1.427, and B.1.525, which were deposited in the database of the GISAID Initiative. 2021 Archives of virology Abstract SARS_CoV_2 Q677H;Q677P 35;35 42;42 S 102 107 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. On the other hand, analysis of FCS from emergent variants showed no deletions in the FCS except for spike P681del, which was detected in seven B.1.1.7 isolates from the USA. 2021 Archives of virology Abstract SARS_CoV_2 DEL681P 106 113 S 100 105 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Spike Q677P was detected only once in variant, B.1.1.7, whereas Q677H was detected in all variants, i.e., B.1.1.7 (n = 1938), B.1.351 (n = 28), P.1 (n = 9), B.1.429 + B.1.427 (n = 132), and B.1.525 (n = 1584). 2021 Archives of virology Abstract SARS_CoV_2 Q677H;Q677P 64;64 69;69 S 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Taken together, our results show that Q677H and FCS point mutations are prevalent and may have various biological effects on the circulating variants. 2021 Archives of virology Abstract SARS_CoV_2 Q677H 38 43 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. The SARS-CoV-2 spike protein Q677P/H mutation and furin cleavage site (FCS) have been shown to affect cell tropism and virus transmissibility. 2021 Archives of virology Abstract SARS_CoV_2 Q677H;Q677P 29;29 36;36 S 15 20 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? This variant has 13 amino acid changes, three in its spike protein, which are currently of particular concern: E484Q, L452R, and P681R. 2021 Journal of medical virology Abstract SARS_CoV_2 E484Q;L452R;P681R 111;118;129 116;123;134 S 53 58 34260717 SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion. The effect is similar in magnitude to the loss of sensitivity conferred by L452R or E484Q alone. 2021 The Journal of infectious diseases Abstract SARS_CoV_2 E484Q;L452R 84;75 89;80 34260717 SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion. There have been fears that 2 key mutations seen in the receptor-binding domain, L452R and E484Q, would have additive effects on evasion of neutralizing antibodies. 2021 The Journal of infectious diseases Abstract SARS_CoV_2 E484Q;L452R 90;80 95;85 34260717 SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion. These data demonstrate reduced sensitivity to vaccine-elicited neutralizing antibodies by L452R and E484Q but lack of synergistic loss of sensitivity. 2021 The Journal of infectious diseases Abstract SARS_CoV_2 E484Q;L452R 100;90 105;95 34260717 SARS-CoV-2 B.1.617 Mutations L452R and E484Q Are Not Synergistic for Antibody Evasion. We report that spike bearing L452R and E484Q confers modestly reduced sensitivity to BNT162b2 mRNA vaccine-elicited antibodies following either first or second dose. 2021 The Journal of infectious diseases Abstract SARS_CoV_2 E484Q;L452R 39;29 44;34 S 15 20 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. The amino acid changes L249S and E484K located at the CTD and RBD of the Spike protein could be of special interest due to their potential biological role in the virus-host relationship. 2021 Frontiers in medicine Abstract SARS_CoV_2 E484K;L249S 33;23 38;28 S;RBD 73;62 78;65 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. One B.1.1.7 sequence contained two additional mutations, F318N and V320F, with V320F located in the receptor binding domain of the S1 subunit. 2021 Microbiology resource announcements Abstract SARS_CoV_2 F318N;V320F;V320F 57;67;79 62;72;84 RBD 100 123 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. Based on these findings, available experimental data showing that bile acids reduce the binding affinity of wild-type RBD to the ACE2 receptor, and the data suggesting that the respiratory tract microbiota affect viral infection we put forward the following proposal: mutations such as N501Y enable the RBD to bind to the ACE2 receptor more effectively in the presence of NPs produced by the respiratory tract bacteria thereby, increasing the infectivity rate of the virus. 2021 Chembiochem Abstract SARS_CoV_2 N501Y 286 291 RBD;RBD 118;303 121;306 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. N501Y mutation, which is present in many of the emerging variants of the virus, abolishes the predicted binding pocket of bile acids and NRPs. 2021 Chembiochem Abstract SARS_CoV_2 N501Y 0 5 34267528 Detection of Representative Mutant Strains and a Case of Prolonged Infection by SARS-CoV-2 with Spike 69/70 Deletion in Japan. The mutants of the spike region of SARS-CoV-2, such as N501Y, E484K, P681H, and deletion H69/V70 (del 69/70), were studied in 25 COVID-19 patients admitted from December 2020 to April 2021; there were no patients with N501Y and P681H, but nine patients had E484K alone. 2021 Infection and drug resistance Abstract SARS_CoV_2 E484K;E484K;N501Y;N501Y;P681H;P681H 62;257;55;218;69;228 67;262;60;223;74;233 S 19 24 COVID-19 129 137 34268505 Impact of temperature on the affinity of SARS-CoV-2 Spike for ACE2. Interestingly, the RBD N501Y mutation, present in emerging variants of concern (VOCs) that are fueling the pandemic worldwide, bypassed this requirement. 2021 bioRxiv Abstract SARS_CoV_2 N501Y 23 28 RBD 19 22 34268505 Impact of temperature on the affinity of SARS-CoV-2 Spike for ACE2. This data suggests that the acquisition of N501Y reflects an adaptation to warmer climates, a hypothesis that remains to be tested. 2021 bioRxiv Abstract SARS_CoV_2 N501Y 43 48 34268527 Durable Humoral and Cellular Immune Responses Following Ad26.COV2.S Vaccination for COVID-19. We also report neutralizing antibody responses against the parental SARS-CoV-2 WA1/2020 strain as well as against the SARS-CoV-2 variants D614G, B.1.1.7 (alpha), B.1.617.1 (kappa), B.1.617.2 (delta), P.1 (gamma), B.1.429 (epsilon), and B.1.351 (beta). 2021 medRxiv Abstract SARS_CoV_2 D614G 138 143 34268528 SARS-CoV-2 Infections in mRNA Vaccinated Individuals are Biased for Viruses Encoding Spike E484K and Associated with Reduced Infectious Virus Loads that Correlate with Respiratory Antiviral IgG levels. The predominant virus variant was the alpha (B.1.1.7), however a significant association between lineage B.1.526 and amino acid change S: E484K with positives after vaccination was noted when genomes were compared to a large control cohort from a matched time frame. 2021 medRxiv Abstract SARS_CoV_2 E484K 138 143 S 135 136 34270613 Mutants of human ACE2 differentially promote SARS-CoV and SARS-CoV-2 spike mediated infection. The panel of ACE2 mutants also revealed altered ACE2 surface dependencies by the N501Y spike variant, including a near-complete utilization of the K353D ACE2 variant, despite decreased infection mediated by the parental SARS-CoV-2 spike. 2021 PLoS pathogens Abstract SARS_CoV_2 K353D;N501Y 147;81 152;86 S;S 87;231 92;236 34270613 Mutants of human ACE2 differentially promote SARS-CoV and SARS-CoV-2 spike mediated infection. While ACE2 mutants D355N, R357A, and R357T abrogated entry by both SARS-CoV and SARS-CoV-2 spike proteins, the Y41A mutant inhibited SARS-CoV entry much more than SARS-CoV-2, suggesting differential utilization of the ACE2 side-chains within the largely overlapping interaction surfaces utilized by the two CoV spike proteins. 2021 PLoS pathogens Abstract SARS_CoV_2 D355N;R357A;R357T;Y41A 19;26;37;111 24;31;42;115 S;S 91;311 96;316 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. The D614G is the first and most frequently established mutation in different regions including Europe, Asia, America, Africa and Australia with the number of mutations of 49, 33, 17, 16 and 4, respectively. 2021 Biomedical journal Abstract SARS_CoV_2 D614G 4 9 34271432 Natto extract, a Japanese fermented soybean food, directly inhibits viral infections including SARS-CoV-2 in vitro. In addition, RBD protein carrying a point mutation (UK variant N501Y) was also degraded by the natto extract. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 N501Y 63 68 RBD 13 16 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. A significant increase in the B.1.1.7 lineage (alpha variant) in March 2021 as well as a transient circulation of regional variants that carried both the concerning S: E484K and S: P681H substitutions were noted. 2022 Clinical infectious diseases Abstract SARS_CoV_2 E484K;P681H 168;181 173;186 S;S 165;178 166;179 34273397 Revealing the Threat of Emerging SARS-CoV-2 Mutations to Antibody Therapies. We unveil, for the first time, that high-frequency mutations R346K/S, N439K, G446V, L455F, V483F/A, F486L, F490L/S, Q493L, and S494P might compromise some of mAbs in clinical trials. 2021 Journal of molecular biology Abstract SARS_CoV_2 F486L;F490L;F490S;G446V;L455F;N439K;Q493L;R346K;R346S;S494P;V483A;V483F 100;107;107;77;84;70;116;61;61;127;91;91 105;114;114;82;89;75;121;68;68;132;98;98 34273991 Estimating COVID-19 cases infected with the variant alpha (VOC 202012/01): an analysis of screening data in Tokyo, January-March 2021. BACKGROUND: In Japan, a part of confirmed patients' samples have been screened for the variant of concern (VOC), including the variant alpha with N501Y mutation. 2021 Theoretical biology & medical modelling Abstract SARS_CoV_2 N501Y 146 151 34274369 A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. The emergence of SARS-CoV-2 mutations resulting in the S protein amino-acid substitutions N501Y and E484K, which have been associated with enhanced transmissibility and immune escape, respectively, necessitates immediate actions, for which their rapid identification is crucial. 2021 Journal of virological methods Abstract SARS_CoV_2 E484K;N501Y 100;90 105;95 S 55 56 34274478 No association between the SARS-CoV-2 variants and mortality rates in the Eastern Mediterranean Region. Two substitutions, spike_D614G and NSP12_P323L, were predominantly concurrent in most countries. 2021 Gene Abstract SARS_CoV_2 D614G;P323L 25;41 30;46 S;Nsp12 19;35 24;40 34274478 No association between the SARS-CoV-2 variants and mortality rates in the Eastern Mediterranean Region. While the single incidence of NSP12_P323L was positively correlated with higher case fatality rates in EMR, no such association was established for the double (spike_D614G and NSP12_P323L) concurrent variant across the region. 2021 Gene Abstract SARS_CoV_2 D614G;P323L;P323L 166;36;182 171;41;187 S;Nsp12;Nsp12 160;30;176 165;35;181 34278277 SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high risk variants into the United Kingdom. A high diversity of 49 different SARS-CoV-2 variants were identified, including the VOCs B.1.1.7 (Kent; 80.6%), B.1.351 (South Africa; 4.2%), B.1.617.2 (India; 1.7%), P.1 (Brazil; 0.4%) and B.1.1.7 with E484K (Bristol; 0.2%). 2021 EClinicalMedicine Abstract SARS_CoV_2 E484K 203 208 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. Given that the E484K mutation can hamper natural immunity, the effectiveness of vaccination as well as antibody-based therapies, these findings may have important implications not only for individual treatment decisions but may also pose a risk to general prevention and treatment strategies. 2021 The Lancet regional health. Europe Abstract SARS_CoV_2 E484K 15 20 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. In these five patients, the E484K substitution - known to confer immune escape - was detected at the time of viral rebound but not before bamlanivimab treatment. 2021 The Lancet regional health. Europe Abstract SARS_CoV_2 E484K 28 33 34278671 Efficient Inhibition of SARS-CoV-2 Using Chimeric Antisense Oligonucleotides through RNase L Activation*. In pseudovirus infection models, chimera-S4 achieved potent and broad-spectrum inhibition of SARS-CoV-2 and its N501Y and/or DeltaH69/DeltaV70 mutants, indicating a promising antiviral agent based on the nucleic acid-hydrolysis targeting chimera (NATAC) strategy. 2021 Angewandte Chemie (International ed. in English) Abstract SARS_CoV_2 DeltaH69;N501Y;DeltaV70 125;112;134 133;117;142 34280951 Broad sarbecovirus neutralization by a human monoclonal antibody. Furthermore, deep-mutational scanning and in vitro escape selection experiments demonstrate that S2X259 possesses an escape profile that is limited to a single substitution, G504D. 2021 Nature Abstract SARS_CoV_2 G504D 174 179 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. In addition, a retention of Q57H (B.1.X), R203K/G204R (B.1.1.X), T85I (B.1.2-B.1.3), G15S+T428I (C.X), and I120F (D.X) variations was observed. 2021 mBio Abstract SARS_CoV_2 G15S;I120F;Q57H;R203K;T85I;G204R;T428I 85;107;28;42;65;48;90 89;112;32;47;69;53;95 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. We recorded persistence of D614G, S477N, A222V, and V1176F variants and a global expansion of the PANGOLIN variant B.1. 2021 mBio Abstract SARS_CoV_2 A222V;D614G;S477N;V1176F 41;27;34;52 46;32;39;58 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. Here, we report the biophysical properties of the SARS-CoV-2 spike variants D614G, B.1.1.7, B.1.351, and P.1 with affinities to the ACE2 receptor and infectivity capacity, revealing weaknesses in the developed neutralizing antibody approaches. 2021 Journal of virology Abstract SARS_CoV_2 D614G 76 81 S 61 66 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. RT-PCR primers and four sloppy molecular beacon (SMB) probes were designed to amplify and detect the SARS-CoV-2 N501Y (A23063T) and E484K (G23012A) mutations and their corresponding wild-type sequences. 2021 Journal of clinical microbiology Abstract SARS_CoV_2 E484K;N501Y;A23063T;G23012A 132;112;119;139 137;117;126;146 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. The assay was 100% sensitive and 100% specific for identifying the N501Y and E484K mutations in cultured virus and in clinical samples, as confirmed by Sanger sequencing. 2021 Journal of clinical microbiology Abstract SARS_CoV_2 E484K;N501Y 77;67 82;72 34289053 The virological impacts of SARS-CoV-2 D614G mutation. The current prevalent D614G variant, with glycine substituted for aspartic acid at position 614 in the spike glycoprotein, is one of such variants that became the main circulating strain worldwide in a short period of time. 2021 Journal of molecular cell biology Abstract SARS_CoV_2 D614G;G614D 22;42 27;95 S 103 121 34289053 The virological impacts of SARS-CoV-2 D614G mutation. This review aims at presenting an overall picture of the impacts of D614G mutation on virus transmission, elucidating the underlying mechanisms of D614G in virus pathogenicity, and providing insights into the development of effective therapeutics. 2021 Journal of molecular cell biology Abstract SARS_CoV_2 D614G;D614G 68;147 73;152 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. As predicted, T372A RBD bound hACE2 with higher affinity in experimental binding assays. 2021 Cell Abstract SARS_CoV_2 T372A 14 19 RBD 20 23 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. We engineered the reversion mutant (A372T) and found that A372 (wild-type [WT]-SARS-CoV-2) enhanced replication in human lung cells relative to its putative ancestral variant (T372), an effect that was 20 times greater than the well-known D614G mutation. 2021 Cell Abstract SARS_CoV_2 D614G;A372T 239;36 244;41 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. We scanned more than 182,000 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes for selective sweep signatures and found a distinct footprint of positive selection located around a non-synonymous change (A1114G; T372A) within the spike protein receptor-binding domain (RBD), predicted to remove glycosylation and increase binding to human ACE2 (hACE2), the cellular receptor. 2021 Cell Abstract SARS_CoV_2 T372A;A1114G 230;222 235;228 S;RBD 248;287 253;290 COVID-19 36 76 34292870 Inhalable nanocatchers for SARS-CoV-2 inhibition. The hACE2-containing NCs, derived from the cellular membrane of genetically engineered cells stably expressing hACE2, exhibited excellent neutralization ability against pseudoviruses of both wild-type SARS-CoV-2 and the D614G variant. 2021 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 D614G 220 225 Membrane 52 60 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. The initial period of rapid diversification into region-specific phylogenies that ended in February 2020 was followed by a major extinction event and global homogenization concomitant with the spread of D614G in the spike protein, ending in March 2020. 2021 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 D614G 203 208 S 216 221 34294374 Computational study of the therapeutic potentials of a new series of imidazole derivatives against SARS-CoV-2. The compounds interacted with HIS 41 - CYS 145 and GLU 288 - ASP 289 - GLU 290 of Mpro, ASN 501 of Spro receptor binding motif and some active site amino acids of RdRp. 2021 Journal of pharmacological sciences Abstract SARS_CoV_2 D289E 61 74 RdRP 163 167 34302370 Neutralization of SARS-CoV-2 by highly potent, hyperthermostable, and mutation-tolerant nanobodies. We constructed nanobody tandems and identified nanobody monomers that tolerate the K417N/T, E484K, N501Y, and L452R immune-escape mutations found in the Alpha, Beta, Gamma, Epsilon, Iota, and Delta/Kappa lineages. 2021 The EMBO journal Abstract SARS_CoV_2 E484K;K417N;K417T;L452R;N501Y 92;83;83;110;99 97;90;90;115;104 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. Eleven B.1.1.7 genomes had an E484K replacement in spike protein, a change also identified in other SARS-CoV-2 lineages. 2021 The American journal of pathology Abstract SARS_CoV_2 E484K 30 35 S 51 56 34304682 An overview of the preclinical discovery and development of bamlanivimab for the treatment of novel coronavirus infection (COVID-19): reasons for limited clinical use and lessons for the future. Expectations related to its use in COVID-19 patients as a single agent have been largely disregarded, especially against E484K-carrying SARS-CoV-2 variants.Areas covered: In this drug discovery case history, the development of the drug is described starting from the identification and selection of the antibody, from the pre-clinical and clinical trials up to the post-authorization phase.Expert opinion: Bamlanivimab has shown some efficacy in patients with mild to moderate COVID-19. 2021 Expert opinion on drug discovery Abstract SARS_CoV_2 E484K 121 126 COVID-19;COVID-19 35;477 43;485 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Most Suceava genomes contained mutations common to European lineages, such as A20268G, however, approximately 10% of samples were missing such mutations, indicating a possible different arrival route. 2021 Frontiers in microbiology Abstract SARS_CoV_2 A20268G 78 85 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Non-synonymous mutations, such as T987N (Thr987Asn in NSP3a domain), associated with changes in a protein responsible for decreasing viral tethering in human host were also present. 2021 Frontiers in microbiology Abstract SARS_CoV_2 T987N;T987N 34;41 39;50 Nsp3a 54 59 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Patients with diabetes and hypertension exhibited higher risk ratios (RR) of acquiring severe forms of the disease and these were mainly related to A105V mutation. 2021 Frontiers in microbiology Abstract SARS_CoV_2 A105V 148 153 Hypertension 27 39 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. While overall genome regions ORF1ab, S, and ORF7 were subject to most mutations, several recurring mutations such as A105V were identified, and these were mainly present in severe forms of the disease. 2021 Frontiers in microbiology Abstract SARS_CoV_2 A105V 117 122 ORF1ab;ORF7;S 29;44;37 35;48;38 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. A common mutation has occurred in the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), known as D614G (A23403G). 2021 Meta gene Abstract SARS_CoV_2 D614G;A23403G 126;133 131;140 S 38 43 COVID-19 62 102 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. This study aims to develop three fast economical assays for prompt identifications of the D614G mutation including Taqman probe-based real-time reverse transcriptase polymerase chain reaction (rRT PCR), an amplification refractory mutation system (ARMS) RT and restriction fragment length polymorphism (RFLP), in nasopharyngeal swab samples. 2021 Meta gene Abstract SARS_CoV_2 D614G 90 95 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. In the mutational analysis, we found 639 mutations in the spike protein sequence of SARS-CoV-2 and identified/highlighted 20 common mutations L5F, T22I, T29I, H49Y, L54F, V90F, S98F, S221L, S254F, V367F, A520S, T572I, D614G, H655Y, P809S, A879S, D936Y, A1020S, A1078S, and H1101Y. 2021 Virusdisease Abstract SARS_CoV_2 A1020S;A1078S;A520S;A879S;D614G;D936Y;H1101Y;H49Y;H655Y;L54F;L5F;P809S;S221L;S254F;S98F;T22I;T29I;T572I;V367F;V90F 253;261;204;239;218;246;273;159;225;165;142;232;183;190;177;147;153;211;197;171 259;267;209;244;223;251;279;163;230;169;145;237;188;195;181;151;157;216;202;175 S 58 63 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. In the present study, the effect of the C241T mutation has been studied with respect to the changes in RNA structure and its interaction with the host replication factors MADP1 Zinc finger CCHC-type and RNA-binding motif 1 (hnRNP1). 2021 Informatics in medicine unlocked Abstract SARS_CoV_2 C241T 40 45 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. One of the most frequent 5' UTR variants in the SARS-CoV-2 genome is the C241T, with a global frequency of more than 95 %. 2021 Informatics in medicine unlocked Abstract SARS_CoV_2 C241T 73 78 5'UTR 25 31 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. The results obtained from molecular docking and molecular dynamics simulation indicated weaker interaction of C241T mutant stem-loops with the host transcription factor MADP1, indicating a reduced replication efficiency. 2021 Informatics in medicine unlocked Abstract SARS_CoV_2 C241T 110 115 34309648 Impact of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variant-Associated Receptor Binding Domain (RBD) Mutations on the Susceptibility to Serum Antibodies Elicited by Coronavirus Disease 2019 (COVID-19) Infection or Vaccination. RBD with E484K or E484Q mutation, either alone or in combination with other mutations, showed greatest reduction in serum IgG binding. 2022 Clinical infectious diseases Abstract SARS_CoV_2 E484K;E484Q 9;18 14;23 RBD 0 3 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. IMPORTANCE Analysis of viral genomes and monitoring of the evolutionary trajectory of SARS-CoV-2 over time has identified the D614G substitution in spike (S) as the most prevalent expanding variant worldwide, which might confer a selective advantage in transmission. 2021 mBio Abstract SARS_CoV_2 D614G 126 131 S;S 148;155 153;156 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. Our study pointed to the impact of the D614G substitution on syncytium formation through enhanced furin-mediated S cleavage, which might increase the transmissibility and infectivity of SARS-CoV-2 strains containing S-G614. 2021 mBio Abstract SARS_CoV_2 D614G 39 44 S;S 113;216 114;217 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. Several studies showed that the D614G variant replicates and transmits more efficiently than the wild-type virus, but the mechanism is unclear. 2021 mBio Abstract SARS_CoV_2 D614G 32 37 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. Since the D614G substitution in the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged, the variant strain has undergone a rapid expansion to become the most abundant strain worldwide. 2021 mBio Abstract SARS_CoV_2 D614G 10 15 S;S 36;43 41;44 COVID-19 64 104 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. The effect of the D614G substitution on furin-mediated S cleavage and the resulting enhancement of the syncytium phenotype has been validated in S-expressing cells. 2021 mBio Abstract SARS_CoV_2 D614G 18 23 S;S 55;145 56;146 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. The enhancement of the D614G substitution in the cleavage of the S protein and in syncytium formation has been validated in cells expressing S protein. 2021 mBio Abstract SARS_CoV_2 D614G 23 28 S;S 65;141 66;142 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. This study suggests a possible effect of the D614G substitution on S of SARS-CoV-2; the antiviral effect through targeting furin protease is worthy of being investigated in proper animal models. 2021 mBio Abstract SARS_CoV_2 D614G 45 50 S 67 68 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. One of the Regeneron therapeutic monoclonal antibodies was less effective against the B.1.526 (E484K) variant but the two-antibody combination cocktail was fully active. 2021 mBio Abstract SARS_CoV_2 E484K 95 100 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. The E484K version was neutralized with a 12-fold decrease in titer by the REGN10933 monoclonal antibody, but the combination cocktail with REGN10987 was fully active. 2021 mBio Abstract SARS_CoV_2 E484K 4 9 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. The findings should assuage concerns that current vaccines will be ineffective against the B.1.526 (E484K) variant and suggest the importance of continued widespread vaccination. 2021 mBio Abstract SARS_CoV_2 E484K 100 105 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. Two versions of the variant were identified, both with the prevalent D614G mutation in the spike protein, together with four novel point mutations and with an E484K or S477N mutation in the receptor-binding domain, raising concerns of possible resistance to vaccine-elicited and therapeutic antibodies. 2021 mBio Abstract SARS_CoV_2 D614G;E484K;S477N 69;159;168 74;164;173 S 91 96 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. We report that convalescent-phase sera and vaccine-elicited antibodies retain full neutralizing titer against the S477N B.1.526 variant and neutralize the E484K version with a modest 3.5-fold decrease in titer compared to D614G. 2021 mBio Abstract SARS_CoV_2 D614G;E484K;S477N 222;155;114 227;160;119 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. The same set of sera efficiently neutralize S from B.1.1.7 and exhibit only moderately reduced activity against S carrying the E484K substitution alone. 2021 Nature communications Abstract SARS_CoV_2 E484K 127 132 S;S 44;112 45;113 34314050 SARS-CoV-2 R.1 lineage variants that prevailed in Tokyo in March 2021. Clinical parameters such as mortality and admission to the intensive care unit were analyzed to examine the association between increased disease severity and the E484K mutation. 2021 Journal of medical virology Abstract SARS_CoV_2 E484K 163 168 34314050 SARS-CoV-2 R.1 lineage variants that prevailed in Tokyo in March 2021. The samples were analyzed using reverse transcription-PCR with melting curve analysis to detect the N501Y and E484K mutations. 2021 Journal of medical virology Abstract SARS_CoV_2 E484K;N501Y 110;100 115;105 34314050 SARS-CoV-2 R.1 lineage variants that prevailed in Tokyo in March 2021. Therefore, we began testing all patients with COVID-19 for the N501Y and E484K mutations by using polymerase chain reaction (PCR)-based methods. 2021 Journal of medical virology Abstract SARS_CoV_2 E484K;N501Y 73;63 78;68 COVID-19 46 54 34314668 Emergence of SARS-COV-2 Spike Protein Escape Mutation Q493R after Treatment for COVID-19. We report in vivo selection of a severe acute respiratory syndrome coronavirus 2 spike mutation (Q493R) conferring simultaneous resistance to bamlanivimab and etesivimab. 2021 Emerging infectious diseases Abstract SARS_CoV_2 Q493R 97 102 S 81 86 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. The P681H mutation in the "PRRAR" furin cleavage site might affect the binding affinity to furin enzyme and hence its infectivity. 2021 Virus research Abstract SARS_CoV_2 P681H 4 9 34315826 Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces viral shedding after SARS-CoV-2 D614G challenge in preclinical models. Here, we investigated whether intranasally administered ChAdOx1 nCoV-19 reduces detection of virus in nasal swabs after challenging vaccinated macaques and hamsters with SARS-CoV-2 carrying a D614G mutation in the spike protein. 2021 Science translational medicine Abstract SARS_CoV_2 D614G 192 197 S 214 219 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. Among the 15 single-nucleotide polymorphisms (SNPs) (11 leading to amino acid alterations) and 3 deletions accumulated during this long-term infection, four amino acid changes (V3G, S50L, N87S, and A222V) and two deletions (18-30del and 141-144del) occurred in the virus Spike protein. 2021 mSphere Abstract SARS_CoV_2 A222V;N87S;S50L;V3G 198;188;182;177 203;192;186;180 S 271 276 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. We used in silico mutagenesis approach to design more peptides from the native wild peptide, which revealed that substitutions (T2W, T2Y, L3R, and A5W) could increase the binding affinity of the peptide towards the 3CLpro. 2021 Interdisciplinary sciences, computational life sciences Abstract SARS_CoV_2 A5W;L3R;T2Y;T2W 147;138;133;128 150;141;136;131 34326308 Structural and functional basis for pan-CoV fusion inhibitors against SARS-CoV-2 and its variants with preclinical evaluation. They are also effective against infection of pseudotyped SARS-CoV-2 variants B.1.1.7 (Alpha) and B.1.1.248 (Gamma) as well as those with mutations in S protein, including N417T, E484K, N501Y, and D614G, which are common in South African and Brazilian variants. 2021 Signal transduction and targeted therapy Abstract SARS_CoV_2 D614G;E484K;N417T;N501Y 196;178;171;185 201;183;176;190 S 150 151 34332998 The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another. From week 18 we used in addition the new NovaplexSARS-CoV-2 Variants II Assay for samples with no targets found with the Variants I assay or with the mutation E484K alone, in order to screen the mutations L452R, K417N/T and W152C. 2021 Journal of virological methods Abstract SARS_CoV_2 E484K;K417N;K417T;L452R;W152C 159;212;212;205;224 164;219;219;210;229 34332998 The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another. Of these, 47 had the L452R mutation without the W152C mutation, typical in the B.1.617 variant. 2021 Journal of virological methods Abstract SARS_CoV_2 L452R;W152C 21;48 26;53 34332998 The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another. Target sought were deletion H69/V70 and mutations N501Y and E484K. 2021 Journal of virological methods Abstract SARS_CoV_2 E484K;N501Y 60;50 65;55 34333122 SARS-CoV-2 in Transit: Characterization of SARS-CoV-2 Genomes From Venezuelan Migrants in Colombia. A mutation (L18F) in the N-terminal domain of the spike protein that has been associated with compromised binding of neutralizing antibodies was found in 2 of 30 (6.6%) genomes. 2021 International journal of infectious diseases Abstract SARS_CoV_2 L18F 12 16 S;N 50;25 55;26 34335010 Double masking protection vs. comfort-A quantitative assessment. The virus responsible for causing COVID-19 has undergone several mutations in the recent past, including B.1.1.7, B.1.351, P.1, and N501Y, B.1.617, with a higher infectious rate. 2021 Physics of fluids (Woodbury, N.Y. Abstract SARS_CoV_2 N501Y 132 137 COVID-19 34 42 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. Among all the reported mutations, W45L was found to bind most stringently to IRF3. 2021 Frontiers in microbiology Abstract SARS_CoV_2 W45L 34 38 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. Since several mutations in ORF8 have been observed, therefore, in the present study, we adapted structural and biophysical analysis approaches to explore the impact of various mutations of ORF8, such as S24L, L84S, V62L, and W45L, the recently circulating mutant in Pakistan, on its ability to bind IRF3 and to evade the host immune system. 2021 Frontiers in microbiology Abstract SARS_CoV_2 L84S;S24L;V62L;W45L 209;203;215;225 213;207;219;229 ORF8;ORF8 27;189 31;193 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. We quantitatively determined the degrees of binding affinity caused by different S glycoprotein mutations, and the result indicated that the 501Y.V1 variant yielded the highest enhancements in binding affinity (increased by 36.8%), followed by the N439K variant (increased by 29.5%) and the 501Y.V2 variant (increased by 19.6%). 2021 Computational and structural biotechnology journal Abstract SARS_CoV_2 N439K 248 253 S 81 95 34336597 Lack of N2-gene amplification on the Cepheid Xpert Xpress SARS-CoV-2 assay and potential novel causative mutations: A case series from Auckland, New Zealand. We describe three cases with viral strains that demonstrate impaired N2-gene detection on the Cepheid Xpert Xpress SARS-CoV-2 assay, with two previously undescribed single nucleotide polymorphisms (SNPs): C29197T and G29227T. 2021 IDCases Abstract SARS_CoV_2 C29197T;G29227T 205;217 212;224 34336597 Lack of N2-gene amplification on the Cepheid Xpert Xpress SARS-CoV-2 assay and potential novel causative mutations: A case series from Auckland, New Zealand. We propose that these SNPs are likely responsible since they are in close proximity to the previously described C29200T/C29200A SNPs, already shown to abolish N2-gene detection by the Xpert assay. 2021 IDCases Abstract SARS_CoV_2 C29200A;C29200T 112;112 119;119 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. The most common mutations that were detected at the C-terminal domain, Ser68Phe, Pro71Ser, and Leu73Phe, were examined through molecular dynamics (MD) simulations for a 100ns period. 2021 Informatics in medicine unlocked Abstract SARS_CoV_2 L73F;P71S;S68F 95;81;71 103;89;79 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. The results of root mean square deviation, fluctuations, radius of gyration, and free energy landscape show that Ser68Phe, Pro71Ser, and Leu73Phe are exhibiting a more stabilizing effect. 2021 Informatics in medicine unlocked Abstract SARS_CoV_2 L73F;P71S;S68F 137;123;113 145;131;121 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The concordance and rigidity ratios of multiple mutation strains such as B.1.617.2 against the wild-type one at the receptor-binding domain (RBD) and receptor-binding motif (RBM) regions provide a good indication of the transmissibility and neutralization escape ability except for binding affinity of mutation sites such as N501Y. 2021 ACS omega Abstract SARS_CoV_2 N501Y 325 330 RBD 141 144 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The conformational variability of the mutation sites for B.1.617.2 (Delta), B.1.617.1 (kappa), B.1.427/429 (epsilon), P.1 (gamma), B.1.351 (beta), B.1.1.7 (alpha), S477N, and the wild-type strain has been assessed using a deep neural-network-based prediction program of conformational flexibility or rigidity in proteins (SSSCPreds). 2021 ACS omega Abstract SARS_CoV_2 S477N 164 169 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The increased rigidity of the amino acid sequence YRYRLFR from the SSSCPreds data of B.1.427/429 near the L452R mutation site contributes to the 2-fold increased B.1.427/B.1.429 viral shedding in vivo and the increase in transmissibility relative to wild-type circulating strains in a similar manner to D614G. 2021 ACS omega Abstract SARS_CoV_2 D614G;L452R 303;106 308;111 34341401 Computational design of SARS-CoV-2 peptide binders with better predicted binding affinities than human ACE2 receptor. Molecular dynamics show that predicted binding affinities of three peptides (SPB25Q22R, SPB25F8R/K11W/L25R and SPB25F8R/K11F/Q22R/L25R) are better than ACE2. 2021 Scientific reports Abstract SARS_CoV_2 K11F;L25R;L25R;Q22R 120;102;130;125 124;106;134;129 34341790 Protection of human ACE2 transgenic Syrian hamsters from SARS CoV-2 variants by human polyclonal IgG from hyper-immunized transchromosomic bovines. For the聽in vivo聽studies, we used a new human ACE2 (hACE2) transgenic Syrian hamster model that exhibits lethality after SARS-Cov-2 challenge and the Munich, UK, SA and 螖144-146 variants. 2021 bioRxiv Abstract SARS_CoV_2 Delta144-146 168 176 34341790 Protection of human ACE2 transgenic Syrian hamsters from SARS CoV-2 variants by human polyclonal IgG from hyper-immunized transchromosomic bovines. The Ab preparation was tested for neutralization against five variant SARS-CoV-2 strains: Munich (Spike D614G), UK (B.1.1.7), Brazil (P.1) and SA (B.1.3.5) variants, and a variant isolated from a chronically infected immunocompromised patient (Spike Delta144-146). 2021 bioRxiv Abstract SARS_CoV_2 D614G;Delta144-146 104;250 109;262 S;S 98;244 103;249 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. Among all variants investigated in this work, the RBD of the Epsilon (L452R) variant is relatively easily detached from ACE2. 2021 bioRxiv Abstract SARS_CoV_2 L452R 70 75 RBD 50 53 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. We report that the RBD of the Alpha (N501Y) variant requires the highest amount of force initially to be detached from ACE2 due to the N501Y mutation in addition to the role of N90-glycan, followed by Beta/Gamma (K417N/T, E484K, and N501Y) or Delta (L452R and T478K) variant. 2021 bioRxiv Abstract SARS_CoV_2 E484K;N501Y;N501Y;T478K;K417N;K417T;L452R;N501Y 222;135;233;260;213;213;250;37 227;140;238;265;220;220;255;42 RBD 19 22 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Further, the molecular dynamics simulation (MDS) approach reveals the structural transition of mutants (N501Y and D614G) S-protein. 2021 Computers in biology and medicine Abstract SARS_CoV_2 D614G;N501Y 114;104 119;109 S 121 122 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Using the extensive bioinformatics pipeline, we screened the destabilizing (L8V, L8W, L18F, Y145H, M153T, F157S, G476S, L611F, A879S, C1247F, and C1254F) and stabilizing (H49Y, S50L, N501Y, D614G, A845V, and P1143L) nonsynonymous mutations in the S-protein. 2021 Computers in biology and medicine Abstract SARS_CoV_2 A845V;A879S;C1247F;C1254F;D614G;F157S;G476S;L18F;L611F;L8W;M153T;N501Y;P1143L;S50L;Y145H;H49Y;L8V 197;127;134;146;190;106;113;86;120;81;99;183;208;177;92;171;76 202;132;140;152;195;111;118;90;125;84;104;188;214;181;97;175;79 S 247 248 34346744 SARS-CoV-2 Quasispecies Provides an Advantage Mutation Pool for the Epidemic Variants. The later predominant substitution D614G existed in the minor mutants of more than one early patient. 2021 Microbiology spectrum Abstract SARS_CoV_2 D614G 35 40 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. For the B.1.1.7 variant, we demonstrated the critical importance of mutations D614G and N501Y on the structure and binding, respectively, of the Spike protein. 2021 Microbiology spectrum Abstract SARS_CoV_2 D614G;N501Y 78;88 83;93 S 145 150 34351228 Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia. Here, we report the nearly complete genome sequences of nine severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with the D614G mutation. 2021 Microbiology resource announcements Abstract SARS_CoV_2 D614G 140 145 COVID-19 68 108 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Our results correctly model an increase in open-state occupancy for the more infectious D614G via an increase in flexibility of the closed-state and decrease of flexibility of the open-state. 2021 PLoS computational biology Abstract SARS_CoV_2 D614G 88 93 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. We predict the same effect for several mutations on glycine residues (404, 416, 504, 252) as well as residues K417, D467 and N501, including the N501Y mutation recently observed within the B.1.1.7, 501.V2 and P1 strains. 2021 PLoS computational biology Abstract SARS_CoV_2 N501Y 145 150 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. In silico analysis provided an explanation for E484K immune evasion. 2021 PLoS pathogens Abstract SARS_CoV_2 E484K 47 52 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. Using the already circulating mutation S494P, we found that it reduces antibody neutralization of convalescent and post-immunization sera, particularly when combined with E484K and with mutations able to increase binding to ACE2, such as N501Y. 2021 PLoS pathogens Abstract SARS_CoV_2 E484K;N501Y;S494P 171;238;39 176;243;44 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. We confirmed that E484K evades antibody neutralization elicited by infection or vaccination, a capacity augmented when complemented by K417N and N501Y mutations. 2021 PLoS pathogens Abstract SARS_CoV_2 E484K;K417N;N501Y 18;135;145 23;140;150 34352360 A discernable increase in the severe acute respiratory syndrome coronavirus 2 R.1 lineage carrying an E484K spike protein mutation in Japan. E484K could be a pivotal amino acid substitution with the potential to mediate immune escape; thus, more attention should be paid to such potential variants of concern to avoid the emergence of mutants of concern. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 E484K 0 5 34352360 A discernable increase in the severe acute respiratory syndrome coronavirus 2 R.1 lineage carrying an E484K spike protein mutation in Japan. Recently, in addition to the B.1.1.7 lineage, which shows 25% abundance, an R.1 lineage carrying the E484K mutation in the spike protein was found to show up to 40% predominance. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 E484K 101 106 S 123 128 34354142 Entropy based analysis of SARS-CoV-2 spread in India using informative subtype markers. Moreover, we analysed the RGD motif and D614G mutation in the spike protein of SARS-CoV-2. 2021 Scientific reports Abstract SARS_CoV_2 D614G 40 45 S 62 67 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. Among the identified mutations, NSP2_T153M, NSP14_I42V and Spike_L18F mutations showed a positive correlation to CFR. 2021 Genes Abstract SARS_CoV_2 I42V;L18F;T153M 50;65;37 54;69;42 S;Nsp2 59;32 64;36 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. In contrast, NS8_L84S and NSP12_A97V mutations showed a negative correlation to the number of cases per million. 2021 Genes Abstract SARS_CoV_2 A97V;L84S 32;17 36;21 Nsp12 26 31 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The mutations having the highest frequencies among different continents were Spike_D614G and NSP12_P323L. 2021 Genes Abstract SARS_CoV_2 D614G;P323L 83;99 88;104 S;Nsp12 77;93 82;98 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NSP12_P323L and Spike_D614G mutations showed a positive correlation to the number of cases per million. 2021 Genes Abstract SARS_CoV_2 D614G;P323L 26;10 31;15 S;Nsp12 20;4 25;9 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NSP3_T1198K, NS8_L84S and NSP12_A97V mutations showed a significant negative correlation to deaths per million. 2021 Genes Abstract SARS_CoV_2 A97V;L84S;T1198K 36;21;9 40;25;15 Nsp12;Nsp3 30;4 35;8 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The Spike_D614G and NSP12_P323L mutations showed a positive correlation to deaths per million. 2021 Genes Abstract SARS_CoV_2 D614G;P323L 10;26 15;31 S;Nsp12 4;20 9;25 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. While the NSP13_Y541C, NSP3_T73I and NSP3_Q180H mutations demonstrated a negative correlation to CFR. 2021 Genes Abstract SARS_CoV_2 Q180H;T73I;Y541C 42;28;16 47;32;21 Nsp13;Nsp3;Nsp3 10;23;37 15;27;41 34358019 Antibodies Targeting Two Epitopes in SARS-CoV-2 Neutralize Pseudoviruses with the Spike Proteins from Different Variants. Antibodies against these two epitopes could effectively neutralize SARS-CoV-2 pseudoviral particles with the spike proteins from not only the original strain (basal; wild-type), but also a strain with a single point mutation (D614G), and two other emerging variants (the Alpha and Beta variants) prevalent around the world, but not from SARS-CoV. 2021 Pathogens (Basel, Switzerland) Abstract SARS_CoV_2 D614G 226 231 S 109 114 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. The data obtained indicate no significant differences in VNA against B.1.1.7, B.1.617.3 and local genetic lineages B.1.1.141 (T385I), B.1.1.317 (S477N, A522S) with RBD mutations. 2021 Vaccines Abstract SARS_CoV_2 A522S;S477N;T385I 152;145;126 157;150;131 RBD 164 167 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. Virus-neutralizing activity (VNA) of sera obtained from people vaccinated with Sputnik V in relation to internationally relevant genetic lineages B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3 and Moscow endemic variants B.1.1.141 (T385I) and B.1.1.317 (S477N, A522S) with mutations in the RBD domain has been assessed. 2021 Vaccines Abstract SARS_CoV_2 A522S;S477N;T385I 258;251;229 263;256;234 RBD 287 290 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Since January 2021, the diffusion of the most propagated SARS-CoV-2 variants in France (UK variant 20I/501Y.V1 (lineage B.1.1.7), 20H/H501Y.V2 (lineage B.1.351) and 20J/H501Y.V3 (lineage P.1)) were urgently screened, needing a surveillance with an RT-PCR screening assay. 2021 Diagnostics (Basel, Switzerland) Abstract SARS_CoV_2 H501Y;H501Y 134;169 139;174 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. The thirteen with the UK variant presented one mutation in the S-gene, near the DeltaH69/DeltaV70 deletion (S71F or A67S), which impacted the detection of DeltaH69/DeltaV70 deletion. 2021 Diagnostics (Basel, Switzerland) Abstract SARS_CoV_2 A67S;S71F 116;108 120;112 S 63 64 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Thirteen samples belonged to the UK variant (B.1.1.7), and two to A.27 with N501Y mutation. 2021 Diagnostics (Basel, Switzerland) Abstract SARS_CoV_2 N501Y 76 81 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Using another screening kit (PKampVariantDetect SARS-CoV-2 RT-PCR combination 1 and 3PerkinElmer, Waltham, MA, USA) on the misidentified samples, we observed that the two mutations, S71F or A67S, did not impact the detection of the UK variant. 2021 Diagnostics (Basel, Switzerland) Abstract SARS_CoV_2 A67S;S71F 190;182 194;186 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The signature mutations possessed by these strains were L452R, T478K, E484Q, D614G and P681R in the spike protein, including within the receptor-binding domain (RBD). 2021 Microorganisms Abstract SARS_CoV_2 D614G;E484Q;L452R;P681R;T478K 77;70;56;87;63 82;75;61;92;68 S;RBD 100;161 105;164 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The structural analysis of RBD mutations L452R, T478K and E484Q revealed that these may possibly result in increased ACE2 binding while P681R in the furin cleavage site could increase the rate of S1-S2 cleavage, resulting in better transmissibility. 2021 Microorganisms Abstract SARS_CoV_2 E484Q;L452R;P681R;T478K 58;41;136;48 63;46;141;53 RBD 27 30 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The two RBD mutations, L452R and E484Q, indicated decreased binding to select monoclonal antibodies (mAbs) and may affect their neutralization potential. 2021 Microorganisms Abstract SARS_CoV_2 E484Q;L452R 33;23 38;28 RBD 8 11 34362872 Phylogenomic analysis of SARS-CoV-2 from third wave clusters in Malaysia reveals dominant local lineage B.1.524 and persistent spike mutation A701V. This lineage contains another spike mutation A701V that co-exists with the D614G spike mutation that was predominant in most of the third-wave clusters. 2021 Tropical biomedicine Abstract SARS_CoV_2 A701V;D614G 45;75 50;80 S;S 30;81 35;86 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. By targeting SARS-CoV-2 D614G mutation, synthetic mismatch crRNAs were designed from -3 to +3 position around the mutation site. 2021 Virus research Abstract SARS_CoV_2 D614G 24 29 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Herein, we report a dual synthetic mismatches CRISPR/Cas12a (dsmCRISPR) method to detect the SARS-CoV-2 D614G mutation with high sensitivity and specificity. 2021 Virus research Abstract SARS_CoV_2 D614G 104 109 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. SARS-CoV-2 variant carrying D614G amino acid change at the spike protein is the most dominant strain in the pandemic. 2021 Virus research Abstract SARS_CoV_2 D614G 28 33 S 59 64 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Therefore, efficient detection of the SARS-CoV-2 variants including D614G mutation is critical to control the COVID-19 pandemic. 2021 Virus research Abstract SARS_CoV_2 D614G 68 73 COVID-19 110 118 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Therefore, the dsmCRIPSR method has significant potential to serve as a sensitive and specific assay for SARS-CoV-2 D614G detection and could be further extended for the detection of other SARS-CoV-2 variants of interest. 2021 Virus research Abstract SARS_CoV_2 D614G 116 121 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. This method can detect the SARS-CoV-2 D614G mutation nucleic acid with high sensitivity, which was validated with synthetic SARS-CoV-2 D614G RNA. 2021 Virus research Abstract SARS_CoV_2 D614G;D614G 38;135 43;140 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. To improve the sensitivity and specificity, a synthetic mismatch primer with a 3'-terminal base complementary to the D614G point mutation and a mismatch next to 3'-terminal base was used to specifically amplify the D614G mutation site with higher annealing temperature. 2021 Virus research Abstract SARS_CoV_2 D614G;D614G 117;215 122;220 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. When combined with mismatch primer to amplify D614G mutation, the fluorescence ratio of G614/D164 template detected was increased by 73.53% to 23.12. 2021 Virus research Abstract SARS_CoV_2 D614G 46 51 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. g., E484K, N501Y) draws attention due to their association with immune evasion and enhanced receptor binding affinity. 2021 Virus research Abstract SARS_CoV_2 E484K;N501Y 4;11 9;16 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. Furthermore, a single dose immunization of D330A or Y414A can induce long-term humoral immune responses and robust CD4+ and CD8+ T cell responses, which can provide full protection against the challenge of a lethal-dose of MHV-A59. 2021 Emerging microbes & infections Abstract SARS_CoV_2 D330A;Y414A 43;52 48;57 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. Using murine hepatitis virus strain A59 (MHV-A59), a representative and well-studied model of coronaviruses, we constructed N7-MTase-deficient recombinant MHV D330A and Y414A. 2021 Emerging microbes & infections Abstract SARS_CoV_2 D330A;Y414A 159;169 164;174 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. S309-CAR-NK cells can specifically bind to pseudotyped SARS-CoV-2 virus and its D614G, N501Y, and E484K mutants. 2021 Frontiers in immunology Abstract SARS_CoV_2 D614G;E484K;N501Y 80;98;87 85;103;92 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Detection of N501Y was possible in samples with mixtures of WT with low proportions of B.1.351 (0.5%) and could accurately determine the proportion of N501Y and WT in mixtures of SARS-CoV-2 RNA. 2021 The Science of the total environment Abstract SARS_CoV_2 N501Y;N501Y 13;151 18;156 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. In this study, we demonstrate the use of RT-ddPCR on wastewater samples for specific detection of mutation N501Y. 2021 The Science of the total environment Abstract SARS_CoV_2 N501Y 107 112 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. It also indicates that RT-ddPCR could be used for sensitive and accurate monitoring of current (like K417N, K417T, E484K, L452R) or future mutations present in SARS-CoV-2 variants of concern. 2021 The Science of the total environment Abstract SARS_CoV_2 E484K;K417N;K417T;L452R 115;101;108;122 120;106;113;127 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. The emergence of N501Y in Amsterdam and Utrecht wastewater aligned with the emergence of B.1.1.7 as causative agent of COVID-19 in the Netherlands, indicating that RT-ddPCR of wastewater samples can be used to monitor the emergence of the N501Y mutation in the community. 2021 The Science of the total environment Abstract SARS_CoV_2 N501Y;N501Y 17;239 22;244 COVID-19 119 127 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. Expansion in variant diversity was observed since September 2020 with increasing frequency of the number in spike substitutions, mainly H69V70 deletion, P681H, N439K, and S98F. 2021 Viruses Abstract SARS_CoV_2 N439K;P681H;S98F 160;153;171 165;158;175 S 108 113 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The most common sets of spike mutations in this lineage (now designated as B.1.526) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V. 2021 Nature communications Abstract SARS_CoV_2 A701V;D253G;D614G;E484K;L5F;S477N;T95I 133;99;122;106;88;115;93 138;104;127;111;91;120;97 S 24 29 34374354 Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay. This SNV, G29179T, is the most prevalent in Korea and is associated with the B.1.497 virus lineage, which is dominant in Korea. 2022 Annals of laboratory medicine Abstract SARS_CoV_2 G29179T 10 17 34374354 Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay. We report a single-nucleotide variant (SNV) in the nucleocapsid (N) gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), i.e., G29179T, which impairs the diagnostic sensitivity of the Xpert Xpress SARS-CoV-2 assay (Cepheid, Sunnyvale, CA, USA). 2022 Annals of laboratory medicine Abstract SARS_CoV_2 G29179T 144 151 N;N 51;65 63;66 COVID-19 83 123 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. The H69/V70 deletion and N501Y mutation assays demonstrated accuracies of 98.3% (95% CI 93.8 to 99.8) and 100% (95% CI 96.8 to 100), limits of detection of 1,089 and 294 copies/ml, and percent coefficients of variation of 0.08 to 1.16% and 0 to 2.72% for the two gene targets, respectively. 2021 Microbiology spectrum Abstract SARS_CoV_2 N501Y 25 30 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. To rapidly detect VOCs, two real-time reverse transcriptase PCR assays were designed and implemented, targeting the spike gene H69/V70 deletion and the N501Y mutation. 2021 Microbiology spectrum Abstract SARS_CoV_2 N501Y 152 157 S 116 121 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. Most importantly, the antibodies from Bin2 showed stronger binding affinity or ability to mutant RBDs (N501Y, W463R, R408I, N354D, V367F, and N354D/D364Y) derived from different SARS-CoV-2 strains as well, suggesting the great potential of these antibodies in preventing infection of SARS-CoV-2 and its mutations. 2021 Biotechnology journal Abstract SARS_CoV_2 N354D;N354D;R408I;V367F;W463R;N501Y;D364Y 124;142;117;131;110;103;148 129;147;122;136;115;108;153 RBD 97 101 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Based on genome-wide phylogenetic analysis, emergence of both viral variants was specifically triggered by acquisition of L452R, suggesting a strong positive selection for this mutation. 2021 Journal of clinical microbiology Abstract SARS_CoV_2 L452R 122 127 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. By PCR amplification and Sanger sequencing of a 541-base fragment coding for amino acids 414 to 583 of the RBD from a collection of clinical specimens, we identified a separate L452R variant that also recently emerged in California but derives from the lineage B.1.232, clade 20A (named CAL.20A). 2021 Journal of clinical microbiology Abstract SARS_CoV_2 L452R 177 182 RBD 107 110 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Global analysis revealed that L452R is nearly omnipresent in a dozen independently emerged lineages, including the most recent variants of concern/interest delta, kappa, epsilon and iota, with the lambda variant carrying L452Q. 2021 Journal of clinical microbiology Abstract SARS_CoV_2 L452Q;L452R 221;30 226;35 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. It was reported that the L452R mutation is associated with immune escape and could result in a stronger cell attachment of the virus, with both factors likely increasing viral transmissibility, infectivity, and pathogenicity. 2021 Journal of clinical microbiology Abstract SARS_CoV_2 L452R 25 30 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. The massive emergence of L452R variants was first linked to lineage B.1.427/B.1.429 (clade 21C) that has been spreading in California since November and December 2020, originally named CAL.20C and currently variant of interest epsilon. 2021 Journal of clinical microbiology Abstract SARS_CoV_2 L452R 25 30 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Unlike the epsilon variant that carries two additional mutations in the N-terminal domain of spike protein, L452R is the only mutation found in the spike proteins of CAL.20A. 2021 Journal of clinical microbiology Abstract SARS_CoV_2 L452R 108 113 S;S;N 93;148;72 98;153;73 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. We report that there is a recent global expansion of numerous independent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with mutation L452R in the receptor-binding domain (RBD) of the spike protein. 2021 Journal of clinical microbiology Abstract SARS_CoV_2 L452R 158 163 S;RBD 208;196 213;199 COVID-19 81 121 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Here, we studied the pathogenicity of variants of concern (VOC) B.1.1.7 and B.1.351 in rhesus macaques and compared it to a recent clade B.1 SARS-CoV-2 isolate containing the D614G substitution in the spike protein. 2021 bioRxiv Abstract SARS_CoV_2 D614G 175 180 S 201 206 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. In bronchoalveolar lavages, cytokines and chemokines were upregulated on day 4 in animals inoculated with D614G and B.1.1.7 but not in those inoculated with B.1.351. 2021 bioRxiv Abstract SARS_CoV_2 D614G 106 111 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. In nasal samples, we did not detect upregulation of cytokines and chemokines in D614G or B.1.351-inoculated animals. 2021 bioRxiv Abstract SARS_CoV_2 D614G 80 85 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. The B.1.1.7 VOC behaved similarly to the D614G with respect to clinical disease, virus shedding and virus replication in the respiratory tract. 2021 bioRxiv Abstract SARS_CoV_2 D614G 41 46 34384810 Infection-enhancing anti-SARS-CoV-2 antibodies recognize both the original Wuhan/D614G strain and Delta variants. A potential risk for mass vaccination? As the NTD is also targeted by neutralizing antibodies, our data suggest that the balance between neutralizing and facilitating antibodies in vaccinated individuals is in favor of neutralization for the original Wuhan/D614G strain. 2021 The Journal of infection Abstract SARS_CoV_2 D614G 218 223 34384810 Infection-enhancing anti-SARS-CoV-2 antibodies recognize both the original Wuhan/D614G strain and Delta variants. A potential risk for mass vaccination? However, this study was performed with the original Wuhan/D614G strain. 2021 The Journal of infection Abstract SARS_CoV_2 D614G 58 63 34384810 Infection-enhancing anti-SARS-CoV-2 antibodies recognize both the original Wuhan/D614G strain and Delta variants. A potential risk for mass vaccination? Using molecular modeling approaches, we show that enhancing antibodies have a higher affinity for Delta variants than for Wuhan/D614G NTDs. 2021 The Journal of infection Abstract SARS_CoV_2 D614G 128 133 34385423 Potent prophylactic and therapeutic efficacy of recombinant human ACE2-Fc against SARS-CoV-2 infection in vivo. hACE2-Fc also neutralized various SARS-CoV-2 strains with enhanced infectivity including D614G and V367F mutations, as well as the emerging SARS-CoV-2 variants, B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.1 (Kappa), and B.1.617.2 (Delta), demonstrating its potent and broad-spectrum antiviral effects. 2021 Cell discovery Abstract SARS_CoV_2 D614G;V367F 89;99 94;104 34385690 Effect of SARS-CoV-2 B.1.1.7 mutations on spike protein structure and function. The B.1.1.7-specific A570D mutation introduces a molecular switch that could modulate the opening and closing of the RBD. 2021 Nature structural & molecular biology Abstract SARS_CoV_2 A570D 21 26 RBD 117 120 34385690 Effect of SARS-CoV-2 B.1.1.7 mutations on spike protein structure and function. The N501Y mutation introduces a pi-pi interaction that enhances RBD binding to ACE2 and abolishes binding of a potent neutralizing antibody (nAb). 2021 Nature structural & molecular biology Abstract SARS_CoV_2 N501Y 4 9 RBD 64 67 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. In addition, although the binding free energy at this point increased after the mutation of N354D, the conformation of the random coil (Pro384-Asp389) was looser than that of other systems, and the combined effect weakened the binding free energy between RBD and ACE2. 2021 Frontiers in molecular biosciences Abstract SARS_CoV_2 N354D 92 97 RBD 255 258 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. In particular, the D364Y and V367F systems showed a higher affinity for ACE2 owing to their electrostatic interactions and polar solvation energy changes. 2021 Frontiers in molecular biosciences Abstract SARS_CoV_2 D364Y;V367F 19;29 24;34 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The binding free energy of the non-RBM mutant group at the binding loop had positive and negative changes, and these changes were more obvious than that of the Q498A system. 2021 Frontiers in molecular biosciences Abstract SARS_CoV_2 Q498A 160 165 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. To unravel how mutations in the non-RBM regions impact the interaction between RBD and ACE2, we selected three non-RBM mutant systems (N354D, D364Y, and V367F) from the documented clinical cases, and the Q498A mutant system located in the RBM region served as the control. 2021 Frontiers in molecular biosciences Abstract SARS_CoV_2 D364Y;Q498A;V367F;N354D 142;204;153;135 147;209;158;140 RBD 79 82 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. The high frequency S477N mutation is present in 6.7% of all SARS-CoV-2 sequences, co-occurs with D614G, and is currently present in 14 countries. 2021 Antibody therapeutics Abstract SARS_CoV_2 D614G;S477N 97;19 102;24 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. We report high frequency mutations with improved binding affinity to ACE2 including S477N, N439K, V367F, and N501Y and address the potential impact of RBD mutations on antibody binding. 2021 Antibody therapeutics Abstract SARS_CoV_2 N439K;N501Y;S477N;V367F 91;109;84;98 96;114;89;103 RBD 151 154 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. GB-2 can inhibit the binding between ACE2 and RBD with K417N-E484K-N501Y mutation in a dose-dependent manner. 2021 Biomedicine & pharmacotherapy Abstract SARS_CoV_2 K417N;E484K;N501Y 55;61;67 60;66;72 RBD 46 49 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. GB-2 inhibited the binding between ACE2 and the RBD with a single mutation (K417N or N501Y or L452R) except the E484K mutation. 2021 Biomedicine & pharmacotherapy Abstract SARS_CoV_2 E484K;L452R;N501Y;K417N 112;94;85;76 117;99;90;81 RBD 48 51 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. N501Y, K417N and E484K, in the receptor binding domain (RBD) region may induce a conformational change of the spike protein and subsequently increase the infectivity of the beta variant. 2021 Biomedicine & pharmacotherapy Abstract SARS_CoV_2 E484K;K417N;N501Y 17;7;0 22;12;5 RBD;S;RBD 31;110;56 54;115;59 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Our results suggest that GB-2 could be a potential candidate for the prophylaxis of some SARS-CoV-2 variants infection in the further clinical study because of its inhibition of binding between ACE2 and RBD with K417N-E484K-N501Y mutations or L452R mutation. 2021 Biomedicine & pharmacotherapy Abstract SARS_CoV_2 K417N;L452R;E484K;N501Y 212;243;218;224 217;248;223;229 RBD 203 206 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. The L452R mutation in the epsilon variant (the B.1.427/B.1.429 variants) also reduced neutralizing activity of monoclonal antibodies. 2021 Biomedicine & pharmacotherapy Abstract SARS_CoV_2 L452R 4 9 34389380 EGCG as an anti-SARS-CoV-2 agent: Preventive versus therapeutic potential against original and mutant virus. Molecular modeling experiments revealed N501Y-specific stacking interactions in the RBD-ACE2 complex and provided insight into EGCG interference with the complex formation. 2021 Biochimie Abstract SARS_CoV_2 N501Y 40 45 RBD 84 87 34389380 EGCG as an anti-SARS-CoV-2 agent: Preventive versus therapeutic potential against original and mutant virus. We complemented that finding with a detailed investigation of EGCG interactions with viral S-protein subunits, including S2, RBD, and the RBD mutant harboring the N501Y mutation. 2021 Biochimie Abstract SARS_CoV_2 N501Y 163 168 RBD;RBD;S 125;138;91 128;141;92 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. A new mutation was identified in ORF1a (A1146T), which was only present in the Delta Plus variant with ~58 % prevalence. 2021 Journal of autoimmunity Abstract SARS_CoV_2 A1146T 40 46 ORF1a 33 38 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Based on the results presented here, it is clear that the Delta and Delta Plus variants have unique mutation profiles, and the Delta Plus variant is not just a simple addition of K417N to the Delta variant. 2021 Journal of autoimmunity Abstract SARS_CoV_2 K417N 179 184 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Furthermore, five key mutations (T95I, A222V, G142D, R158G, and K417N) were significantly more prevalent in the Delta Plus than in the Delta variant. 2021 Journal of autoimmunity Abstract SARS_CoV_2 A222V;G142D;K417N;R158G;T95I 39;46;64;53;33 44;51;69;58;37 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Signature mutations in Spike (G142D, A222V, and T95I) existed at a more significant percentage in the Delta Plus variant than the Delta variant. 2021 Journal of autoimmunity Abstract SARS_CoV_2 A222V;T95I;G142D 37;48;30 42;52;35 S 23 28 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Three mutations in Spike (K417N, V70F, and W258L) were exclusively present in the Delta Plus variant. 2021 Journal of autoimmunity Abstract SARS_CoV_2 V70F;W258L;K417N 33;43;26 37;48;31 S 19 24 34399368 Controversy surrounding the Sputnik V vaccine. Furthermore, there is emerging documentation that Sputnik V has a reduced neutralizing capacity against the Beta variant and all variants with the spike protein carrying the E484K substitution. 2021 Respiratory medicine Abstract SARS_CoV_2 E484K 174 179 S 147 152 34399606 Regulation of the Dimerization and Activity of SARS-CoV-2 Main Protease through Reversible Glutathionylation of Cysteine 300. Tryptic and chymotryptic digestions of Mpro as well as experiments using a C300S Mpro mutant revealed that Cys300, which is located at the dimer interface, is a primary target of glutathionylation. 2021 mBio Abstract SARS_CoV_2 C300S 75 80 34400835 SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution. Further in vitro evolution increased binding by 1,000-fold and identified mutations that may be more infectious if they evolve in the circulating viral population, for example, Q498R is epistatic to N501Y. 2021 Nature microbiology Abstract SARS_CoV_2 N501Y;Q498R 199;177 204;182 34400835 SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution. We found that mutations present in more transmissible viruses (S477N, E484K and N501Y) were preferentially selected in our high-throughput screen. 2021 Nature microbiology Abstract SARS_CoV_2 E484K;N501Y;S477N 70;80;63 75;85;68 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. CONCLUSIONS: Four rRT-PCR assays (RdRp, N, S484K, and S501Y) were used to detect SARS-CoV-2 variants, and these assays were shown to be effective in screening for multiple virus strains. 2021 Chinese medical journal Abstract SARS_CoV_2 S484K;S501Y 43;54 48;59 RdRP;N 34;40 38;41 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. In addition, the S484K and S501Y assays were combined with the ORF1ab assay, respectively. 2021 Chinese medical journal Abstract SARS_CoV_2 S484K;S501Y 17;27 22;32 ORF1ab 63 69 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. In addition, we also developed two rRT-PCR assays (S484K and S501Y) targeting the spike gene, which when combined with the open reading frames (ORF)1ab assay, respectively, to form duplex rRT-PCR assays, were able to detect SARS-CoV-2 VOCs (lineages B.1.351 and B.1.1.7). 2021 Chinese medical journal Abstract SARS_CoV_2 S501Y;S484K 61;51 66;56 S 82 87 34403732 Identification of natural compounds as SARS-CoV-2 entry inhibitors by molecular docking-based virtual screening with bio-layer interferometry. The EGCG was further validated with no observable animal toxicity and certain antiviral effect against SARS-CoV-2 pseudovirus mutants (D614G, N501Y, N439K & Y453F). 2021 Pharmacological research Abstract SARS_CoV_2 N439K;N501Y;Y453F;D614G 149;142;157;135 154;147;162;140 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. This strategy allowed us to identify the emergence of the B.1.621 lineage, considered a variant of interest (VOI) with the accumulation of several substitutions affecting the Spike protein, including the amino acid changes I95I, Y144T, Y145S and the insertion 146 N in the N-terminal domain, R346K, E484K and N501Y in the Receptor binding Domain (RBD) and P681H in the S1/S2 cleavage site of the Spike protein. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 E484K;I95I;N501Y;P681H;R346K;Y144T;Y145S 299;223;309;356;292;229;236 304;227;314;361;297;234;241 RBD;S;S;RBD;N;N 322;175;396;347;264;273 345;180;401;350;265;274 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. The S686G mutation also transforms the FCS into the heparin-binding peptide. 2021 Journal of virology Abstract SARS_CoV_2 S686G 4 9 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. Our analysis suggests that B.1.1.7, B.1.351, and P.1 are more easily spreading than other variants, and the key mutations of S protein, including N501Y, E484K, and K417N/T, have high mutant frequencies, which may have become the main genotypes for the spread of SARS-CoV-2. 2021 Frontiers in public health Abstract SARS_CoV_2 E484K;K417N;K417T;N501Y 153;164;164;146 158;171;171;151 S 125 126 34410361 Post-vaccination COVID-19: A case-control study and genomic analysis of 119 breakthrough infections in partially vaccinated individuals. Genomic analysis identified one post-vaccination case harboring the E484K vaccine escape mutation (B.1.525 lineage). 2021 Clinical infectious diseases Abstract SARS_CoV_2 E484K 68 73 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. Furthermore, prediction of secondary structure, protein modeling and its dynamics were performed which revealed that seven mutations (R118C, T148I, Y149C, E802A, Q822H, V880I and D893Y) significantly altered the stability and flexibility of RdRp protein. 2021 Archives of microbiology Abstract SARS_CoV_2 D893Y;E802A;Q822H;T148I;V880I;Y149C;R118C 179;155;162;141;169;148;134 184;160;167;146;174;153;139 RdRP 241 245 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. According to the molecular dynamics simulation, a key mutation N439K in the SARS-CoV-2 RBD region created a new salt bridge with Glu329 of hACE2, which resulted in greater electrostatic complementarity, and created a weak salt bridge with Asp442 of RBD. 2021 Frontiers in cell and developmental biology Abstract SARS_CoV_2 N439K 63 68 RBD;RBD 87;249 90;252 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. Furthermore, the N439K-mutated RBD bound hACE2 with a higher affinity than wild-type, which may lead to more infectious. 2021 Frontiers in cell and developmental biology Abstract SARS_CoV_2 N439K 17 22 RBD 31 34 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. In addition, the N439K-mutated RBD was markedly resistant to the SARS-CoV-2 neutralizing antibody REGN10987, which may lead to the failure of neutralization. 2021 Frontiers in cell and developmental biology Abstract SARS_CoV_2 N439K 17 22 RBD 31 34 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Molecular dynamics simulations of RBD-ACE2 complexes indicated that the N501Y mutation introduced additional pi-pi and pi-cation interactions that could explain the changes observed by force microscopy. 2021 eLife Abstract SARS_CoV_2 N501Y 72 77 RBD 34 37 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Recently, several variants such as B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma), which share a key mutation N501Y on the receptor-binding domain (RBD), appear to be more infectious to humans. 2021 eLife Abstract SARS_CoV_2 N501Y 112 117 RBD 150 153 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Remarkably, RBD with the N501Y mutation exhibited a considerably stronger interaction, with a faster association rate and a slower dissociation rate. 2021 eLife Abstract SARS_CoV_2 N501Y 25 30 RBD 12 15 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Taken together, these results suggest that the reinforced RBD-ACE2 interaction that results from the N501Y mutation in the RBD should play an essential role in the higher rate of transmission of SARS-CoV-2 variants, and that future mutations in the RBD of the virus should be under surveillance. 2021 eLife Abstract SARS_CoV_2 N501Y 101 106 RBD;RBD;RBD 58;123;249 61;126;252 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. People with HIV and HIV-negative participants showed vaccine-induced serum IgG responses against wild-type Wuhan-1 Asp614Gly (also known as D614G). 2021 The lancet. HIV Abstract SARS_CoV_2 D614G;D614G 115;140 124;145 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. People with HIV showed cross-reactive binding antibodies to the beta variant and Asp614Gly wild-type, and high responders retained neutralisation against beta. 2021 The lancet. HIV Abstract SARS_CoV_2 D614G 81 90 34417165 Effectiveness of BNT162b2 and mRNA-1273 covid-19 vaccines against symptomatic SARS-CoV-2 infection and severe covid-19 outcomes in Ontario, Canada: test negative design study. After two doses, high vaccine effectiveness was observed against variants with the E484K mutation. 2021 BMJ (Clinical research ed.) Abstract SARS_CoV_2 E484K 83 88 34417349 SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. At day 73, an E484K substitution in the receptor-binding domain (RBD) occurred, followed, at day 80, by an insertion in the NTD N5 loop containing a new glycan sequon, which generated a variant completely resistant to plasma neutralization. 2021 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 E484K 14 19 RBD 65 68 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. Two doses of 100 microg of mRNA-1273 induced 50% inhibitory reciprocal serum dilution neutralizing antibody titers against live SARS-CoV-2 p.Asp614Gly and B.1.351 of 3,300 and 240, respectively. 2021 Nature immunology Abstract SARS_CoV_2 D614G 139 150 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. In more than ten countries, the frequencies of the isolates with E484K and S477N increased significantly. 2021 Infectious diseases of poverty Abstract SARS_CoV_2 E484K;S477N 65;75 70;80 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. Of all predicted mutants, the number of E484K was the largest one with 86 585 sequences, followed by S477N with 55 442 sequences worldwide. 2021 Infectious diseases of poverty Abstract SARS_CoV_2 E484K;S477N 40;101 45;106 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. SARS-CoV-2 with V367F was more sensitive to the S1-targeting neutralizing antibody than the wild-type counterpart (P < 0.001). 2021 Infectious diseases of poverty Abstract SARS_CoV_2 V367F 16 21 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. V367F and N354D mutations increased the infectivity of SARS-CoV-2 pseudoviruses (P < 0.001). 2021 Infectious diseases of poverty Abstract SARS_CoV_2 N354D;V367F 10;0 15;5 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. B117-1 and B117-2 differ by only 3 amino acids (nsp2-S512Y, nsp13-K460R, spike-A1056V). 2021 EBioMedicine Abstract SARS_CoV_2 A1056V;K460R;S512Y 79;66;53 85;71;58 S;Nsp13;Nsp2 73;60;48 78;65;52 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. BACKGROUND: Several SARS-CoV-2 lineages with spike receptor binding domain (RBD) N501Y mutation have spread globally. 2021 EBioMedicine Abstract SARS_CoV_2 N501Y 81 86 S 45 50 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Enzyme immunoassay using 272 convalescent sera showed reduced binding of anti-RBD IgG to N501Y or N501Y-E484K-K417N when compared with that of wild-type RBD (mean difference: 0.1116 and 0.5613, respectively; one-way ANOVA). 2021 EBioMedicine Abstract SARS_CoV_2 N501Y;N501Y;E484K;K417N 89;98;104;110 94;103;109;115 RBD;RBD 78;153 81;156 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. FINDINGS: The microneutralization antibody (MN) titers of convalescent sera from 9 recovered COVID-19 patients against B117-1 (geometric mean titer[GMT],80; 95% CI, 47-136) were similar to those against the non-N501Y viruses. 2021 EBioMedicine Abstract SARS_CoV_2 N501Y 211 216 COVID-19 93 101 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. However, MN titer of these serum against B117-2 (GMT, 20; 95% CI, 11-36) was statistically significantly reduced when compared with non-N501Y viruses (P < 0.01; one-way ANOVA). 2021 EBioMedicine Abstract SARS_CoV_2 N501Y 136 141 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. METHODS: The susceptibility to neutralization by COVID-19 patients' convalescent sera from Hong Kong were compared between two SARS-CoV-2 isolates (B117-1/B117-2) from the alpha variant with N501Y and 4 non-N501Y isolates. 2021 EBioMedicine Abstract SARS_CoV_2 N501Y;N501Y 191;207 196;212 COVID-19 49 57 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Of 7 anti-N-IgG positive sera from patients infected with N501Y variants (collected 9-14 days post symptom onset), 6 (85.7%) tested negative for a commercially-available anti-S1-IgG assay. 2021 EBioMedicine Abstract SARS_CoV_2 N501Y 58 63 N 10 11 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. The effect of N501Y on antibody binding was assessed. 2021 EBioMedicine Abstract SARS_CoV_2 N501Y 14 19 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. The performance of commercially-available IgG assays was determined for patients infected with N501Y variants. 2021 EBioMedicine Abstract SARS_CoV_2 N501Y 95 100 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. We evaluated the impact of N501Y on neutralizing activity of COVID-19 convalescent sera and on anti-RBD IgG assays. 2021 EBioMedicine Abstract SARS_CoV_2 N501Y 27 32 RBD 100 103 COVID-19 61 69 34423327 Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing. In January, a localized emergence of a variant (Spike:A522S) of the B.1.1.7 lineage occurred in one neighborhood. 2021 The Lancet regional health. Europe Abstract SARS_CoV_2 A522S 54 59 S 48 53 34423763 Severe Acute Respiratory Syndrome Coronavirus 2 in Farmed Mink (Neovison vison), Poland. We verified this finding by sequencing full viral genomes and confirmed a virus variant that has sporadic mutations through the full genome sequence in the spike protein (G75V and C1247F). 2021 Emerging infectious diseases Abstract SARS_CoV_2 C1247F;G75V 180;171 186;175 S 156 161 34424256 Emergence of the First Strains of SARS-CoV-2 Lineage B.1.1.7 in Romania: Genomic Analysis. Mutations in nonstructural protein 3 (Nsp3; N844S and D455N) and ORF3a (L15F) were also detected, indicating common ancestry with UK strains as well as remote connections with strains from Nagasaki, Japan. 2021 JMIRx med Abstract SARS_CoV_2 D455N;N844S;L15F 54;44;72 59;49;76 ORF3a;Nsp3 65;38 70;42 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. Genomic analysis identified that primoinfection was caused by the endemic lineage B.1.1.33 while reinfection by the lineage B.1.1.44, a lineage with an additional V1176F mutation in S protein. 2021 Diagnostic microbiology and infectious disease Abstract SARS_CoV_2 V1176F 163 169 S 182 183 34426813 Protection against SARS-CoV-2 Beta Variant in mRNA-1273 Boosted Nonhuman Primates. Reciprocal ID 50 pseudovirus neutralizing antibody geometric mean titers (GMT) against live SARS-CoV-2 D614G and the beta variant, were 4700 and 765, respectively, at week 6, the peak of primary response, and 644 and 553, respectively, at a 5-month post-vaccination memory time point. 2021 bioRxiv Abstract SARS_CoV_2 D614G 103 108 34428371 Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation. In the Beta variant, K417N reduces the binding, E484K slightly enhances it, and N501Y significantly increases it as in Alpha. 2021 Journal of chemical information and modeling Abstract SARS_CoV_2 E484K;K417N;N501Y 48;21;80 53;26;85 34428371 Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation. RBD with Alpha and Beta variants has slightly different interacting AAs due to N501Y mutation. 2021 Journal of chemical information and modeling Abstract SARS_CoV_2 N501Y 79 84 RBD 0 3 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Here we report the emergence of the variant lineage B.1.526 (also known as the Iota variant5), which contains E484K, and its rise to dominance in New York City in early 2021. 2021 Nature Abstract SARS_CoV_2 E484K 110 115 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. These transmission dynamics, together with the relative antibody resistance of its E484K sub-lineage, are likely to have contributed to the sharp rise and rapid spread of B.1.526. 2021 Nature Abstract SARS_CoV_2 E484K 83 88 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Two signature spike mutations of concern are E484K, which has a crucial role in the loss of neutralizing activity of antibodies, and N501Y, a driver of rapid worldwide transmission of the B.1.1.7 lineage. 2021 Nature Abstract SARS_CoV_2 E484K;N501Y 45;133 50;138 S 14 19 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. Significant reduction of hCoV-2IG binding was observed to RBD-E484K followed by RBD-N501Y (but not RBD-K417N). 2021 iScience Abstract SARS_CoV_2 E484K;K417N;N501Y 62;103;84 67;108;89 RBD;RBD;RBD 58;80;99 61;83;102 34431691 Emergence of Multiple SARS-CoV-2 Antibody Escape Variants in an Immunocompromised Host Undergoing Convalescent Plasma Treatment. We identified a mixed viral population with five different S protein mutations (141 to 144 deletion, 243 to 244 deletion, E484K, Q493K, and Q493R) at the NTD or RBD region from the second tracheal aspirate sample (day 21) and a predominance of the S protein 141 to 144 LGVY deletion and E484K mutant on day 27. 2021 mSphere Abstract SARS_CoV_2 E484K;E484K;Q493K;Q493R 122;287;129;140 127;292;134;145 RBD;S;S 161;59;248 164;60;249 34432488 Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern. A single primer pair was designed to amplify a 348-bp region of spike, and probes were initially designed to detect K417, E484K, and N501Y. 2021 Journal of clinical microbiology Abstract SARS_CoV_2 E484K;N501Y 122;133 127;138 S 64 69 34432488 Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern. Subsequently, a fourth probe was designed to detect L452R. 2021 Journal of clinical microbiology Abstract SARS_CoV_2 L452R 52 57 34433426 Investigation of Interaction between the Spike Protein of SARS-CoV-2 and ACE2-Expressing Cells Using an In Vitro Cell Capturing System. Furthermore, spike S1 protein variant with D614G mutant show a higher cell capturing ability than wild type spike S1 protein and stronger binding capacity of its receptor ACE2. 2021 Biological procedures online Abstract SARS_CoV_2 D614G 43 48 S;S 13;108 18;113 34433803 ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker. Here we report a human angiotensin-converting enzyme 2 (ACE2)-targeting monoclonal antibody, 3E8, blocked the S1-subunits and pseudo-typed virus constructs from multiple coronaviruses including SARS-CoV-2, SARS-CoV-2 mutant variants (SARS-CoV-2-D614G, B.1.1.7, B.1.351, B.1.617.1, and P.1), SARS-CoV and HCoV-NL63, without markedly affecting the physiological activities of ACE2 or causing severe toxicity in ACE2 "knock-in" mice. 2021 Signal transduction and targeted therapy Abstract SARS_CoV_2 D614G 245 250 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. For example, the B.1.1.7 lineage has a mutation (N501Y) in its Spike RBD that enhances binding to ACE2. 2021 eLife Abstract SARS_CoV_2 N501Y 49 54 S;RBD 63;69 68;72 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Here we perform a detailed affinity and kinetics analysis of the effect of five common RBD mutations (K417N, K417T, N501Y, E484K, and S477N) and two common ACE2 mutations (S19P and K26R) on the RBD/ACE2 interaction. 2021 eLife Abstract SARS_CoV_2 E484K;K26R;K417T;N501Y;S477N;K417N 123;181;109;116;134;102 128;185;114;121;139;107 RBD;RBD 87;194 90;197 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Taken together with other studies, our results suggest that the N501Y and S477N mutations enhance transmission primarily by enhancing binding, the K417N/T mutations facilitate immune escape, and the E484K mutation enhances binding and immune escape. 2021 eLife Abstract SARS_CoV_2 E484K;K417N;K417T;N501Y;S477N 199;147;147;64;74 204;154;154;69;79 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. The exceptions were mutations K417N/T, which decreased the affinity. 2021 eLife Abstract SARS_CoV_2 K417N;K417T 30;30 37;37 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. The N501Y mutation, which is associated with three variants of concern, was identified in samples from July 2020, but not detected in January 2021 samples. 2021 The Science of the total environment Abstract SARS_CoV_2 N501Y 4 9 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. We identify four signature mutations in the surface glycoprotein (spike) gene that are associated with the following variants of interest or concern, VOI or VOC (listed in parenthesis): S477N (B.1.526, Iota), T478K (B.1.617.2, Delta), D614G (present in all VOC as of May 2021), and H655Y (P.1, Gamma). 2021 The Science of the total environment Abstract SARS_CoV_2 D614G;H655Y;S477N;T478K 235;282;186;209 240;287;191;214 S;S 44;66 64;71 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Additionally, E484Q, which could favor the up conformation of the RBD, may help in enhanced hACE2 binding and immune escape. 2021 Biomolecules Abstract SARS_CoV_2 E484Q 14 19 RBD 66 69 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. L452R introduces a charged patch near the binding surface that permits increased electrostatic attraction between the proteins. 2021 Biomolecules Abstract SARS_CoV_2 L452R 0 5 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Our results indicate that the E484Q mutation disrupts the conserved salt bridge formed between Lys31 of hACE2 and Glu484 of S protein. 2021 Biomolecules Abstract SARS_CoV_2 E484Q 30 35 S 124 125 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. The rapidly spreading B.1.617 lineage harbors two key mutations-L452R and E484Q-in the receptor binding domain (RBD) of its spike (S) protein. 2021 Biomolecules Abstract SARS_CoV_2 E484Q;L452R 74;64 79;69 RBD;S;RBD;S 87;124;112;131 110;129;115;132 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. To understand the impact and structural dynamics of the variations in the interface of S protein and its host factor, the human angiotensin-converting enzyme 2 (hACE2), triplicate 500 ns molecular dynamics simulations were performed using single (E484Q or L452R) and double (E484Q + L452R) mutant structures and compared to wild type simulations. 2021 Biomolecules Abstract SARS_CoV_2 L452R;L452R;E484Q;E484Q 256;283;247;275 261;288;252;280 S 87 88 34442775 Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally. Furthermore, a significant number of amino acid substitutions were found in environmental strains where the D614G was found in 83.8% of the sequences. 2021 Microorganisms Abstract SARS_CoV_2 D614G 108 113 34442775 Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally. However, the key mutations-N501Y (44.6%), S982A (44.4%), A570D (43.3%), T716I (40.4%), and P681H (40.1%) were also recorded in spike protein. 2021 Microorganisms Abstract SARS_CoV_2 A570D;P681H;S982A;T716I;N501Y 57;91;42;72;27 62;96;47;77;32 S 127 132 34442817 Impact of Full Vaccination with mRNA BNT162b2 on SARS-CoV-2 Infection: Genomic and Subgenomic Viral RNAs Detection in Nasopharyngeal Swab and Saliva of Health Care Workers. Moreover, concordance was observed between NPS and saliva in the detection of viral mutations, and both N501Y and 69/70del (associated with the B.1.1.7 variant) were detected in the majority 6/8 (75%) of subjects, while the K417T mutation (associated with the P.1-type variants) was detected in 2/8 (25%) individuals. 2021 Microorganisms Abstract SARS_CoV_2 K417T;N501Y 224;104 229;109 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. A mutational analysis indicated the prevalence of D614G (S) and P323L (RdRP) variants, as well as of the Beta.1.1.7/alpha variant of concern, in agreement with the frequency of Beta.1.1.7/alpha variant in clinical samples of the same period of the third pandemic wave at the national level. 2021 International journal of molecular sciences Abstract SARS_CoV_2 D614G;P323L 50;64 55;69 RdRP;S 71;57 75;58 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. D614G mutant of CT2 domain, showing to be the most prevalent in the global pandemic, showed higher stability in all open-complex forms than the wild type and other mutants. 2021 International journal of molecular sciences Abstract SARS_CoV_2 D614G 0 5 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. In this study, Korean mutants for spike protein (D614G and D614A-C terminal domain, L455F and F456L-RBD, and Q787H-S2 domain) were investigated in patients. 2021 International journal of molecular sciences Abstract SARS_CoV_2 D614A;F456L;L455F;Q787H;D614G 59;94;84;109;49 64;99;89;114;54 S;RBD 34;100 39;103 34445669 Molecular Masks for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. ACE2P1D1 and ACE2P2D1 also blocked infection by a D614G mutant pseudovirus. 2021 International journal of molecular sciences Abstract SARS_CoV_2 D614G 50 55 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. In the present work, we report the identification of a potential variant of interest, harboring the mutations T478K, P681H, and T732A in the spike protein, within the newly named lineage B.1.1.519, that rapidly outcompeted the preexisting variants in Mexico and has been the dominant virus in the country during the first trimester of 2021. 2021 Archives of virology Abstract SARS_CoV_2 P681H;T478K;T732A 117;110;128 122;115;133 S 141 146 34449757 An Autochthonous Outbreak of the SARS-CoV-2 P.1 Variant of Concern in Southern Italy, April 2021. It is characterized by the E484K mutation in the receptor-binding domain, which could contribute to the evasion from neutralizing antibodies. 2021 Tropical medicine and infectious disease Abstract SARS_CoV_2 E484K 27 32 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. The previous most prevalent lineages in the state of Rio Grande do Sul (RS, Southern Brazil), B.1.1.28 and B.1.1.33, were rapidly replaced by P.1 and P.2, two B.1.1.28-derived lineages harboring the E484K mutation. 2021 Pathogens (Basel, Switzerland) Abstract SARS_CoV_2 E484K 199 204 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. In this study, we report a novel variant carrying the L452R mutation that emerged from a local B.1.362 lineage, B.1.362+L452R. 2021 Vaccines Abstract SARS_CoV_2 L452R;L452R 54;120 59;125 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Indeed, the B.1.362+L452R variant demonstrated a X4-fold reduction in neutralization capacity of sera from BNT162b2-vaccinated individuals compared to a wild-type strain. 2021 Vaccines Abstract SARS_CoV_2 L452R 20 25 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. The L452R mutation is associated with the Delta and Epsilon variants and was shown to cause increased infection and reduction in neutralization in pseudoviruses. 2021 Vaccines Abstract SARS_CoV_2 L452R 4 9 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. This study demonstrates an independent, local emergence of a variant carrying a critical mutation, L452R, which may have the potential of becoming a variant of concern and emphasizes the importance of routine surveillance and detection of novel variants among efforts undertaken to prevent further disease spread. 2021 Vaccines Abstract SARS_CoV_2 L452R 99 104 34452356 Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. Among those, L18F, L452R and N501Y are located in the epitope regions of the N-terminal- (NTD) or receptor binding domain (RBD) and have been suggested to result in immune escape and higher transmissibility. 2021 Viruses Abstract SARS_CoV_2 L18F;L452R;N501Y 13;19;29 17;24;34 RBD;RBD;N 98;123;77 121;126;78 34452356 Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. In addition, A.27 does not show the D614G mutation typical for all VOIs/VOCs from the B lineage. 2021 Viruses Abstract SARS_CoV_2 D614G 36 41 34452371 Intravenous, Intratracheal, and Intranasal Inoculation of Swine with SARS-CoV-2. For this study, a SARS-CoV-2 isolate obtained from a tiger which is identical to human SARS-CoV-2 isolates detected in New York City and contains the D614G S mutation was utilized for inoculation. 2021 Viruses Abstract SARS_CoV_2 D614G 150 155 S 156 157 34452390 The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect. Additionally, a connection between Algeria_EPI_ISL_420037 and sequences originating from the USA was observed through a USA characteristic amino-acid replacement T1004I in the nsp3 gene, found in the aforementioned Algerian sequence. 2021 Viruses Abstract SARS_CoV_2 T1004I 162 168 Nsp3 176 180 34452390 The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect. Our results revealed individual amino-acid replacements such as the deleterious replacement A23T in the orf3a gene in Algeria_EPI_ISL_418241. 2021 Viruses Abstract SARS_CoV_2 A23T 92 96 ORF3a 104 109 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. The emergence of E484K mutants was observed in five out of six patients, and the last patient presented a Q496R mutation potentially associated with resistance. 2021 Viruses Abstract SARS_CoV_2 E484K;Q496R 17;106 22;111 34452511 Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. We report here on the emergence of two variants of concern, B.1.1.7 (Alpha) and P.1 (Gamma), and their displacement of the D614G B.1 variant in a Missouri sewershed. 2021 Viruses Abstract SARS_CoV_2 D614G 123 128 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. BACKGROUND: Emerged mutations can be attributed to increased transmissibility of the B.1.617 and B.1.36 Indian delta variants of SARS-CoV-2, most notably substitutions L452R/E484Q and N440K, respectively, which occur in the receptor-binding domain (RBD) of the Spike (S) fusion glycoprotein. 2022 Allergy Abstract SARS_CoV_2 L452R;N440K;E484Q 168;184;174 173;189;179 S;RBD;S 261;249;268 266;252;269 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. Meanwhile, the anti-RBD IgG titration resulted in lower recognition of mutants E484K and L452R/E484Q by infection-induced antibodies, whereas only mutant E484K was recognized less by antibodies induced by vaccination. 2022 Allergy Abstract SARS_CoV_2 E484K;E484K;L452R;E484Q 79;154;89;95 84;159;94;100 RBD 20 23 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. METHODS: To this end, we produced recombinant wild-type RBD, as well as RBD containing each of the mutations L452R/E484Q, N440K, or E484K (the latest present in variants of concern B.1.351 and P.1), as well as the ectodomain of ACE2. 2022 Allergy Abstract SARS_CoV_2 E484K;L452R;N440K;E484Q 132;109;122;115 137;114;127;120 RBD;RBD 56;72 59;75 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. More interestingly, sera from convalescent as well as immunized subjects showed reduced ability to block the interaction between ACE2 and RBD mutants E484K and L452R/E484Q, as shown by the inhibition assays. 2022 Allergy Abstract SARS_CoV_2 E484K;L452R;E484Q 150;160;166 155;165;171 RBD 138 141 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. OBJECTIVE: We aimed to assess the effects of mutations L452R/E484Q and N440K (as well as the previously studied mutation E484K present in variants B.1.351 and P.1) on the affinity of RBD for ACE2, SARS-CoV-2 main receptor. 2022 Allergy Abstract SARS_CoV_2 E484K;L452R;N440K;E484Q 121;55;71;61 126;60;76;66 RBD 183 186 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. RESULTS: The binding assays showed L452R/E484Q double-mutant RBD to interact with ACE2 with higher affinity (KD= 4.6 nM) than wild-type (KD= 21.3 nM) or single mutants N440K (KD= 9.9 nM) and E484K (KD= 19.7 nM) RBDs. 2022 Allergy Abstract SARS_CoV_2 E484K;L452R;N440K;E484Q 191;35;168;41 196;40;173;46 RBD;RBD 61;211 64;215 34454120 The low contagiousness and new A958D mutation of SARS-CoV-2 in children: An observational cohort study. The new A958D mutation is a potential reason for its long residence in the intestine. 2021 International journal of infectious diseases Abstract SARS_CoV_2 A958D 8 13 34454120 The low contagiousness and new A958D mutation of SARS-CoV-2 in children: An observational cohort study. We obtained SARS-CoV-2 sequences from the same infant's throat and fecal samples at a two-month interval and found that the new spike protein A958D mutation detected in the stool improved thermostability theoretically. 2021 International journal of infectious diseases Abstract SARS_CoV_2 A958D 142 147 S 128 133 34455390 Evolution of antibody responses up to 13 months after SARS-CoV-2 infection and risk of reinfection. Live-virus neutralization assay revealed that after one year, variants D614G and B.1.1.7, but less so B.1.351, were sensitive to anti-RBD antibodies at 1.4 log BAU/mL, while IgG >= 2.0 log BAU/mL strongly neutralized all three variants. 2021 EBioMedicine Abstract SARS_CoV_2 D614G 71 76 RBD 134 137 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. The most frequent mutation that occurred in 98% isolates was 3037C>T which is a synonymous change that usually accompanied 3 other mutations that include 241C>T, 14408C>T (P323L in RdRp) and 23403A>G (D614G in spike protein). 2021 Heliyon Abstract SARS_CoV_2 C14408T;A23403G;C241T;C3037T;D614G;P323L 162;191;154;61;201;172 170;199;160;68;206;177 S;RdRP 210;181 215;185 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. The P323L was reported to increase mutation rate and D614G is associated with increased viral replication and currently most prevalent variant circulating all over the world. 2021 Heliyon Abstract SARS_CoV_2 D614G;P323L 53;4 58;9 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. We identified multiple missense mutations in B-cell and T-cell predicted epitope regions and/or PCR target regions (including R203K and G204R that occurred in 86% of the isolates) that may impact immunogenicity and/or RT-PCR based diagnosis. 2021 Heliyon Abstract SARS_CoV_2 G204R;R203K 136;126 141;131 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. Plasma showed lower neutralization with alpha (geometric mean titer [GMT] = 18.5) and gamma (GMT = 10.0) variants than with D614G (GMT = 75.1) variant. 2022 Journal of medical virology Abstract SARS_CoV_2 D614G 124 129 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. To understand the impact of these variants, we report the neutralization potency against alpha, gamma, and D614G SARS-CoV-2 variants in 44 individuals that received two doses of CoronaVac vaccine, an inactivated SARS-CoV-2 vaccine. 2022 Journal of medical virology Abstract SARS_CoV_2 D614G 107 112 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Collectively, our results indicate P681R as a key mutation in enhancing Delta variant replication via increased S1/S2 cleavage. 2021 bioRxiv Abstract SARS_CoV_2 P681R 35 40 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Here we report that Delta spike mutation P681R plays a key role in the Alpha-to-Delta variant replacement. 2021 bioRxiv Abstract SARS_CoV_2 P681R 41 46 S 26 31 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. In contrast, the Alpha spike also has a mutation at the same amino acid (P681H), but the spike cleavage from purified Alpha virions was reduced compared to the Delta spike. 2021 bioRxiv Abstract SARS_CoV_2 P681H 73 78 S;S;S 23;89;166 28;94;171 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Mechanistically, the Delta P681R mutation enhanced the cleavage of the full-length spike to S1 and S2, leading to increased infection via cell surface entry. 2021 bioRxiv Abstract SARS_CoV_2 P681R 27 32 S 83 88 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Reverting the P681R mutation to wild-type P681 significantly reduced the replication of Delta variant, to a level lower than the Alpha variant. 2021 bioRxiv Abstract SARS_CoV_2 P681R 14 19 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. The Delta spike has accumulated mutation P681R located at a furin cleavage site that separates the spike 1 (S1) and S2 subunits. 2021 bioRxiv Abstract SARS_CoV_2 P681R 41 46 S;S 10;99 15;104 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Chondramide C (2) on the other hand exhibited strong affinity against spike variants identified in the United Kingdom (N501Y), South Africa (N501Y, E484K, K417N) and Brazil (N501Y, E484K, K417T). 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 E484K;E484K;K417N;K417T;N501Y;N501Y;N501Y 148;181;155;188;119;141;174 153;186;160;193;124;146;179 S 70 75 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. The most frequent mutations were 5' UTR 241C > T, Spike glycoprotein D614G, RNA dependent RNA polymerase (RdRp) P4715L and Orf3a Q57H. 2021 PloS one Abstract SARS_CoV_2 C241T;D614G;P4715L;Q57H 40;69;112;129 48;74;118;133 RdRp;S;5'UTR;ORF3a;RdRP 76;50;33;123;106 104;68;39;128;110 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. 2C08 reduced lung viral load and morbidity in hamsters challenged with the WA1/2020 D614G, B.1.351, or B.1.617.2 strains. 2021 Immunity Abstract SARS_CoV_2 D614G 84 89 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. Here, we analyzed receptor binding domain-binding monoclonal antibodies derived from SARS-CoV-2 mRNA vaccine-elicited germinal center B cells for neutralizing activity against the WA1/2020 D614G SARS-CoV-2 strain and variants of concern. 2021 Immunity Abstract SARS_CoV_2 D614G 189 194 RBD 18 41 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. Of five monoclonal antibodies that potently neutralized the WA1/2020 D614G strain, all retained neutralizing capacity against the B.1.617.2 variant, four also neutralized the B.1.1.7 variant, and only one, 2C08, also neutralized the B.1.351 and B.1.1.28 variants. 2021 Immunity Abstract SARS_CoV_2 D614G 69 74 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. Suspected and non-suspected cases of VOC B.1.1.7 were defined according to the VirSNiP assay, which detects N501Y and deletion H69-V70. 2021 Diagnostic microbiology and infectious disease Abstract SARS_CoV_2 N501Y 108 113 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. The study also evaluated the mutational landscape and important spike protein mutations (E484K, K417T/N, N501Y, and D614G) of all of the above variants. 2021 mBio Abstract SARS_CoV_2 D614G;K417N;K417T;N501Y;E484K 116;96;96;105;89 121;103;103;110;94 S 64 69 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. We also critically evaluated the above emerging variants mutational landscape and significant spike protein mutations (E484K, K417T/N, N501Y, and D614G) impacting public health. 2021 mBio Abstract SARS_CoV_2 D614G;K417N;K417T;N501Y;E484K 146;126;126;135;119 151;133;133;140;124 S 94 99 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Interestingly, the SARS2-S D614G mutant, a more infectious variant, shows 3-time stronger force-dependent ACE2 binding and 35-time faster force-induced S1/S2 detachment. 2021 Cell research Abstract SARS_CoV_2 D614G 27 32 S 25 26 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Unreported V90T SARS-CoV-2 surface glycoprotein mutation was also identified, that contributes towards escaping 2-51 neutralizing antibody. 2021 Meta gene Abstract SARS_CoV_2 V90T 11 15 S 27 47 34466655 Furin and the adaptive mutation of SARS-COV2: a computational framework. The viral fusion process is linked with the furin enzyme and the adaptation is linked with the mutation, called D614G mutation. 2021 Modeling earth systems and environment Abstract SARS_CoV_2 D614G 112 117 34467913 An innovative approach for the non-invasive surveillance of communities and early detection of SARS-CoV-2 via solid waste analysis. Amino acid substitutions already reported in SARS-CoV-2 sequences circulating in Italy (A222V and P521S) were detected in two positive samples. 2021 The Science of the total environment Abstract SARS_CoV_2 P521S;A222V 98;88 103;93 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. We recover known epitopes on the reference D614G sequence. 2021 Journal of chemical information and modeling Abstract SARS_CoV_2 D614G 43 48 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. Anti-S/N IgG/IgM levels, blood group A + , cardiovascular and tumour disease, NSP12 Q444H and ORF3a S177I were independent predictors of clinical characteristics with anti-S/N IgM being associated with the need for hospitalization (multivariate regression, P < 0.05, respectively). 2021 GeroScience Abstract SARS_CoV_2 Q444H;S177I 84;100 89;105 ORF3a;Nsp12 94;78 99;83 Cardiovascular and tumour disease 43 76 34471122 Targeting SARS-CoV-2 receptor-binding domain to cells expressing CD40 improves protection to infection in convalescent macaques. Vaccine-elicited antibodies cross-neutralize different SARS-CoV-2 variants, including D614G, B1.1.7 and to a lesser extent B1.351. 2021 Nature communications Abstract SARS_CoV_2 D614G 86 91 34472141 Pseudoephedrine and its derivatives antagonize wild and mutated severe acute respiratory syndrome-CoV-2 viruses through blocking virus invasion and antiinflammatory effect. These mutations were noticed to happen in the receptor-binding domain of spike protein (S-RBD), especially mutations N501Y, E484Q, E484K, K417N, K417T, and L452R. 2021 Phytotherapy research Abstract SARS_CoV_2 E484K;E484Q;K417N;K417T;L452R;N501Y 131;124;138;145;156;117 136;129;143;150;161;122 S;RBD;S 73;90;88 78;93;89 34473242 Association of E484K spike protein mutation with SARS-CoV-2 infection in vaccinated persons---Maryland, January - May 2021. Among 9,048 people infected with SARS-CoV-2 between January-May, 2021 in Maryland, in regression-adjusted analysis, SARS-CoV-2 viruses carrying the spike protein mutation E484K were disproportionately prevalent among persons infected after full vaccination against COVID-19 as compared to infected persons who were not fully vaccinated (aOR 1.96, 95% CI, 1.36 to 2.83). 2021 Clinical infectious diseases Abstract SARS_CoV_2 E484K 171 176 S 148 153 COVID-19 265 273 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. Interestingly, the RBD N501Y mutation, present in emerging variants of concern (VOCs) that are fueling the pandemic worldwide (including the B.1.1.7 (alpha) lineage), bypassed this requirement. 2021 The Journal of biological chemistry Abstract SARS_CoV_2 N501Y 23 28 RBD 19 22 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. This data suggests that the acquisition of N501Y reflects an adaptation to warmer climates, a hypothesis that remains to be tested. 2021 The Journal of biological chemistry Abstract SARS_CoV_2 N501Y 43 48 34482844 Case report: hepatitis in a child infected with SARS-CoV-2 presenting toll-like receptor 7 Gln11Leu single nucleotide polymorphism. CASE PRESENTATION: We identified a 5-year-old-male child with gastrointestinal symptoms and fever presenting acholic stool and jaundice, who was positive for SARS-CoV-2 IgM, IgA, and IgG and presenting the Gln11Leu rs 179008 in tlr-7. 2021 Virology journal Abstract SARS_CoV_2 Q11L;Q11L 206;206 214;215 34482844 Case report: hepatitis in a child infected with SARS-CoV-2 presenting toll-like receptor 7 Gln11Leu single nucleotide polymorphism. CONCLUSION: To our knowledge, this is the first report of a SARS-CoV-2 caused hepatitis in a male child that has the tlr-7 Gln11Leu rs 179008, which could impair an efficient initial immune response. 2021 Virology journal Abstract SARS_CoV_2 Q11L;Q11L 123;123 131;132 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. A475V and E484Q mutants are highly resistant to neutralization by mAb B38 and 2-4, suggesting that some crucial mutations in spike protein might evolve SARS-CoV-2 variants capable of escaping humoral immune response. 2021 Frontiers in immunology Abstract SARS_CoV_2 E484Q;A475V 10;0 15;5 S 125 130 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. Three of 24 SARS-CoV-2 pseudoviruses containing different mutations in spike protein, including D614G, A475V, and E484Q, consistently showed an altered sensitivity to neutralization by convalescent plasmas. 2021 Frontiers in immunology Abstract SARS_CoV_2 A475V;D614G;E484Q 103;96;114 108;101;119 S 71 76 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? One mutation, D614G, is very prominent in all VOI and VOC in SARS-CoV-2. 2021 Molecular therapy. Nucleic acids Abstract SARS_CoV_2 D614G 14 19 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? This paper attempts to answer the question of whether the mutation (D614G) occurs due to positive selection or not. 2021 Molecular therapy. Nucleic acids Abstract SARS_CoV_2 D614G 68 73 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? With the help of this mutation (D614G), the SARS-CoV-2 variants have gained viral fitness to enhance viral replication and increase transmission. 2021 Molecular therapy. Nucleic acids Abstract SARS_CoV_2 D614G 32 37 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. 2021 Nature Abstract SARS_CoV_2 D614G 208 213 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. AREAS COVERED: The evolution of the Delta variant is reviewed, including an overview of the Delta Plus variant with a K417N mutation in the RBD, which may confer an improved immune evasion ability. 2021 Expert review of vaccines Abstract SARS_CoV_2 K417N 118 123 RBD 140 143 34492088 Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination. The viral strains belonged to lineages B.1.1.218 and B.1.1.305, possessing the mink-specific S-Y453F substitution. 2021 PLoS pathogens Abstract SARS_CoV_2 Y453F 95 100 S 93 94 34493762 Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. Finally, taking N501Y mutation as representative of high-frequency mutations, we showed that level of control measure stringency negatively correlates with the effective reproduction number of SARS-CoV-2 with high-frequency or not-high-frequency and both follows similar trends in different levels of stringency. 2021 Scientific reports Abstract SARS_CoV_2 N501Y 16 21 34494022 Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid and Potential Utility for SARS-CoV-2 Detection. E-beacon prepared for the E484K variant of SARS-CoV-2 functioned with similar sensitivity. 2021 bioRxiv Abstract SARS_CoV_2 E484K 26 31 34494022 Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid and Potential Utility for SARS-CoV-2 Detection. These E-beacons could discriminate their complementary target from nucleic acid encoding the E484Q mutation of the SARS-CoV-2 Kappa variant. 2021 bioRxiv Abstract SARS_CoV_2 E484Q 93 98 34495697 A Bifluorescent-Based Assay for the Identification of Neutralizing Antibodies against SARS-CoV-2 Variants of Concern In Vitro and In Vivo. Here, we report the generation and use of a recombinant (r)SARS-CoV-2 USA/WA1/2020 (WA-1) strain expressing Venus and an rSARS-CoV-2 strain expressing mCherry and containing mutations K417N, E484K, and N501Y found in the receptor binding domain (RBD) of the spike (S) glycoprotein of the South African (SA) B.1.351 (beta [beta]) VoC in bifluorescent-based assays to rapidly and accurately identify human monoclonal antibodies (hMAbs) able to neutralize both viral infections in vitro and in vivo. 2021 Journal of virology Abstract SARS_CoV_2 E484K;K417N;N501Y 191;184;202 196;189;207 RBD;S;RBD;S 221;258;246;265 244;263;249;266 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. However, our studies have shown that such effects can also mask the phenotype of the D614G mutation in the ectodomain of the protein, which was a dominant variant arising early in the COVID-19 pandemic. 2021 Journal of virology Abstract SARS_CoV_2 D614G 85 90 COVID-19 184 192 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. In addition, we analyzed the effect of the D614G mutation, which became a dominant SARS-CoV-2 variant early in the pandemic. 2021 Journal of virology Abstract SARS_CoV_2 D614G 43 48 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. Our studies revealed that, similar to the tail truncation, D614G independently increases Spike incorporation and vector titers, but this effect is masked by also including the cytoplasmic tail truncation. 2021 Journal of virology Abstract SARS_CoV_2 D614G 59 64 S 89 94 34495709 Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. Of the 200 samples belonging to the B.1.575 lineage, 194 (97%) corresponded to the B.1.575.2 sublineage, which was related to the presence of the E484K mutation. 2021 Journal of clinical microbiology Abstract SARS_CoV_2 E484K 146 151 34495709 Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. We report the emergence and spread of a new SARS-CoV-2 variant within the B.1.575 lineage, containing the E484K mutation in the spike protein (named B.1.575.2), in a region in northern Spain in May and June 2021. 2021 Journal of clinical microbiology Abstract SARS_CoV_2 E484K 106 111 S 128 133 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Based on docking binding affinities and free energy calculations the E484K, N501Y and triple mutant variants were found to interact stronger with the ACE2 than the wild-type spike. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 E484K;N501Y 69;76 74;81 S 174 179 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Interestingly, molecular dynamics and MM-PBSA results showed that E484K and spike triple mutant complexes were more stable than the N501Y one. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 E484K;N501Y 66;132 71;137 S 76 81 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Moreover, SARS-CoV-2 still continues to evolve, and specifically the E484K, N501Y, and South Africa triple (K417N + E484K + N501Y) spike protein mutants remain as the 'escape' phenotypes. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 E484K;E484K;N501Y;N501Y;K417N 69;116;76;124;108 74;121;81;129;113 S 131 136 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Moreover, the E484K and South Africa triple mutants triggered greater conformational changes in the spike glycoprotein than N501Y. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 E484K;N501Y 14;124 19;129 S 100 118 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). The aim of this study was to compare the interaction between the receptor binding domain (RBD) of the E484K, N501Y and South Africa triple spike variants and ACE2 with the interaction between wild-type spike RBD-ACE2 and to show whether the obtained binding affinities and conformations corraborate clinical findings. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 E484K;N501Y 102;109 107;114 RBD;S;S;RBD;RBD 65;139;202;90;208 88;144;207;93;211 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). The E484K variant alone, or the combination of K417N + E484K + N501Y mutations induce significant conformational transitions in the spike glycoprotein, while increasing the spike-ACE2 binding affinity.Communicated by Ramaswamy H. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 E484K;E484K;K417N;N501Y 4;55;47;63 9;60;52;68 S;S 132;173 150;178 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). The structures of the RBDs of the E484K, N501Y and South Africa triple variants were generated with DS Studio v16 and energetically minimized using the CHARMM22 force field. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 E484K;N501Y 34;41 39;46 RBD 22 26 34499599 Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. We report a case cluster caused by Delta sublineage B.1.617.2 harboring the mutation E484K in Italy during July 11-July 29, 2021. 2021 Emerging infectious diseases Abstract SARS_CoV_2 E484K 85 90 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. In the case of Kappa and Delta variants, the mutations at L452R, T478K and E484Q increased the stability and intra-chain interactions in the spike protein, which may change the interaction ability of neutralizing antibodies to these spike variants. 2021 International journal of molecular sciences Abstract SARS_CoV_2 E484Q;L452R;T478K 75;58;65 80;63;70 S;S 141;233 146;238 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. To understand the biophysical perspective, we have performed molecular dynamic simulations of four different spikes (receptor binding domain)-hACE2 complexes, namely wildtype (WT), Alpha variant (N501Y spike mutant), Kappa (L452R, E484Q) and Delta (L452R, T478K), and compared their dynamics, binding energy and molecular interactions. 2021 International journal of molecular sciences Abstract SARS_CoV_2 E484Q;T478K;L452R;L452R;N501Y 231;256;224;249;196 236;261;229;254;201 RBD;S;S 117;109;202 140;115;207 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. In conclusion, a new design for the current vaccines to include at least the mutation D614G is immediately needed. 2021 Biochimie Abstract SARS_CoV_2 D614G 86 91 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The prediction results of this study have exhibited the stabilizing role of the globally dominant variant, the D614G; clade 20A, and other variants in addition to their role in increasing the flexibility of the spike protein of the virus. 2021 Biochimie Abstract SARS_CoV_2 D614G 111 116 S 211 216 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The presence of D614G in any clade or subclade, such as 20A, B.1.1.7 (20I/501Y.V1) or Alpha, B.1.351 (20H/501Y.V2) or Beta, P.1 (20J/501Y.V3) or Gamma, B.1.617.2 (21A/478K.V1) or Delta, has increased its stability and flexibility and unified the superimposition among all clades which might impact the virus ability to escape the antibodies neutralization by changing the antigenicity drift of the protein three-dimensional (3D) structure from the wild type clade 19A; this is in agreement with previous study. 2021 Biochimie Abstract SARS_CoV_2 D614G 16 21 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The SuperPose findings have revealed a conformational change impact of D614G in allowing the polybasic Furin cleavage site (682RRAR S686) to be closer to the receptor-binding domain (RBD) and hence more exposed to cleavage. 2021 Biochimie Abstract SARS_CoV_2 D614G 71 76 RBD 183 186 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. We found that the N501Y locus was almost completely linked to the other 16 loci in SARS-CoV-2 genomes from the UK and Europe. 2021 Computational and structural biotechnology journal Abstract SARS_CoV_2 N501Y 18 23 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. It was found that the mutations, Leu452Arg, Thr478Lys, and Glu484Gln in the spike protein increase the affinity for the hACE2 receptor, which explains the greater infectivity of the SARS-Cov-2 B.1.617 (Indian Variant). 2021 Cureus Abstract SARS_CoV_2 E484Q;L452R;T478K 59;33;44 68;42;53 S 76 81 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. CONCLUSIONS: This study demonstrated a sensitive method that can identify the D614G mutation by a simple two-step RT-qPCR-HRM assay procedure analysis, which can be useful for active surveillance of the transmission of a specific mutation. 2021 Heliyon Abstract SARS_CoV_2 D614G 78 83 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. METHODS: Six SARS-CoV-2 RNA samples were synthesized into cDNA and analyzed with the qPCR-HRM method in order to detect the D614G mutation in Spike protein of SARS-CoV-2. 2021 Heliyon Abstract SARS_CoV_2 D614G 124 129 S 142 147 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. The primers are designed to target the specific Spike region containing the D614G mutation. 2021 Heliyon Abstract SARS_CoV_2 D614G 76 81 S 48 53 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. Therefore, a rapid and accurate method that can reliably detect the D614G mutation will be beneficial. 2021 Heliyon Abstract SARS_CoV_2 D614G 68 73 34515998 The first Italian outbreak of SARS-CoV-2 B.1.1.7 lineage in Corzano, Lombardy. The genomic sequencing revealed, for the first time, the presence of the V551F mutation in the B.1.1.7 lineage in Italy. 2022 Journal of medical virology Abstract SARS_CoV_2 V551F 73 78 34516024 Computational decomposition reveals reshaping of the SARS-CoV-2-ACE2 interface among viral variants expressing the N501Y mutation. Altogether, we provide extensive data on all N501Y expressing SARS-CoV-2 variants of concern with respect to their interaction with ACE2 and how this induces reshaping of the RBD-ACE2 interface. 2021 Journal of cellular biochemistry Abstract SARS_CoV_2 N501Y 45 50 34516024 Computational decomposition reveals reshaping of the SARS-CoV-2-ACE2 interface among viral variants expressing the N501Y mutation. However, especially the N501Y exchange increased contact formation for this residue and also induced some local conformational changes. 2021 Journal of cellular biochemistry Abstract SARS_CoV_2 N501Y 24 29 34516024 Computational decomposition reveals reshaping of the SARS-CoV-2-ACE2 interface among viral variants expressing the N501Y mutation. These SARS-Cov-2 variants comprise the two Alpha variants (B.1.1.7, United Kingdom and B.1.1.7 with the additional E484K mutation), the Beta variant (B.1.351, South Africa), and the Gamma variant (P.1, Brazil). 2021 Journal of cellular biochemistry Abstract SARS_CoV_2 E484K 115 120 34516024 Computational decomposition reveals reshaping of the SARS-CoV-2-ACE2 interface among viral variants expressing the N501Y mutation. Variants of concern of the SARS-CoV-2 virus with an asparagine-to-tyrosine substitution at position 501 (N501Y) in the receptor-binding domain (RBD) show enhanced infectivity compared to wild-type, resulting in an altered pandemic situation in affected areas. 2021 Journal of cellular biochemistry Abstract SARS_CoV_2 N501Y;N501Y 52;105 103;110 RBD 144 147 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Finally, we have identified the co-mutations that have the great likelihood of becoming dominant: [A411S, L452R, T478K], [L452R, T478K, N501Y], [V401L, L452R, T478K], [K417N, L452R, T478K], [L452R, T478K, E484K, N501Y], and [P384L, K417N, E484K, N501Y]. 2021 ArXiv Abstract SARS_CoV_2 E484K;E484K;K417N;L452R;L452R;L452R;N501Y;N501Y;N501Y;T478K;T478K;T478K;T478K;T478K;A411S;K417N;L452R;L452R;P384L;V401L 205;239;232;106;152;175;136;212;246;113;129;159;182;198;99;168;122;191;225;145 210;244;237;111;157;180;141;217;251;118;134;164;187;203;104;173;127;196;230;150 34519222 Improved SARS-CoV-2 PCR detection and genotyping with double-bubble primers. Additionally, these primers were used to positively confirm the N501Y mutation from nasopharyngeal swabs. 2021 BioTechniques Abstract SARS_CoV_2 N501Y 64 69 34519517 Bispecific antibodies targeting distinct regions of the spike protein potently neutralize SARS-CoV-2 variants of concern. Furthermore, a bispecific antibody that neutralized the Beta variant protected hamsters against SARS-CoV-2 expressing the E484K mutation. 2021 Science translational medicine Abstract SARS_CoV_2 E484K 122 127 34526000 Case Report:clinical experience of bilateral giant pediatric Testicular adrenal rest tumors with 3 Beta-Hydroxysteroid Dehydrogenase-2 family history. The C.674 T>A inherited from mother and cannot found in gene library and may related to TARTs. 2021 BMC pediatrics Abstract SARS_CoV_2 C674A;C674T;T674A 4;4;4 13;13;13 34526000 Case Report:clinical experience of bilateral giant pediatric Testicular adrenal rest tumors with 3 Beta-Hydroxysteroid Dehydrogenase-2 family history. The C.776 C>T is from father and has been reported. 2021 BMC pediatrics Abstract SARS_CoV_2 C776C;C776T;C776T 4;4;6 13;13;13 34526000 Case Report:clinical experience of bilateral giant pediatric Testicular adrenal rest tumors with 3 Beta-Hydroxysteroid Dehydrogenase-2 family history. The gene analysis reported two novel mutations C.776 C>T and C.674 T>A. 2021 BMC pediatrics Abstract SARS_CoV_2 C674A;C674T;T674A;C776C;C776T;C776T 61;61;61;47;47;49 70;70;70;56;56;56 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. All boosters, including mRNA-1273, numerically increased neutralization titers against the wild-type D614G virus compared to peak titers against wild-type D614G measured 1 month after the primary series; significant increases were observed for mRNA-1273 and mRNA-1273.211 (P < 0.0001). 2021 Nature medicine Abstract SARS_CoV_2 D614G;D614G 101;155 106;160 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. and B.1.617.2, that were statistically equivalent to peak titers measured after the primary vaccine series against wild-type D614G virus, with superior titers against some VOIs. 2021 Nature medicine Abstract SARS_CoV_2 D614G 125 130 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Immediately before the booster dose, neutralizing antibodies against wild-type D614G virus had waned (P < 0.0001) relative to peak titers against wild-type D614G measured 1 month after the primary series, and neutralization titers against B.1.351 (Beta), P.1 (Gamma) and B.1.617.2 (Delta) VOCs were either low or undetectable. 2021 Nature medicine Abstract SARS_CoV_2 D614G;D614G 79;156 84;161 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. Specific S477N, N501Y, K417N, K417T, E484K mutations in the receptor binding domain (RBD) of the spike protein in the wild type SARS-COV-2 virus have resulted, among others, in the following variants: B.1.160 (20A or EU2, first reported in continental Europe), B1.1.7 (alpha or 20I501Y.V1, first reported in the United Kingdom), B.1.351 (beta or 20H/501Y.V2, first reported in South Africa), B.1.1.28.1 (gamma or P.1 or 20J/501Y.V3, first reported in Brazil), and B.1.1.28.2 (zeta, or P.2 or 20B/S484K, also first reported in Brazil). 2022 Chembiochem Abstract SARS_CoV_2 E484K;K417N;K417T;N501Y;S477N;S484K 37;23;30;16;9;496 42;28;35;21;14;501 RBD;S;RBD 60;97;85 83;102;88 34530915 Association of HLA genotypes, AB0 blood type and chemokine receptor 5 mutant CD195 with the clinical course of COVID-19. A suggestive association of a heterozygous CCR5 delta 32 mutation status with prolonged disease duration was implied by univariate analyses but could not be confirmed by hierarchical multivariate testing. 2021 European journal of medical research Abstract SARS_CoV_2 delta 32 48 56 34531369 S19W, T27W, and N330Y mutations in ACE2 enhance SARS-CoV-2 S-RBD binding toward both wild-type and antibody-resistant viruses and its molecular basis. Here we show that mutations of S19W, T27W, and N330Y in ACE2 could individually enhance SARS-CoV-2 S-RBD binding. 2021 Signal transduction and targeted therapy Abstract SARS_CoV_2 N330Y;S19W;T27W 47;31;37 52;35;41 RBD;S 101;99 104;100 34531369 S19W, T27W, and N330Y mutations in ACE2 enhance SARS-CoV-2 S-RBD binding toward both wild-type and antibody-resistant viruses and its molecular basis. Taken together, our biochemical and structural data have delineated the basis for the elevated S-RBD binding associated with S19W, T27W, and N330Y mutations in ACE2, paving the way for potential application of these mutants in clinical treatment of COVID-19. 2021 Signal transduction and targeted therapy Abstract SARS_CoV_2 N330Y;S19W;T27W 141;125;131 146;129;135 RBD;S 97;95 100;96 COVID-19 249 257 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. In contrast, while E484K mutation did not highly change the binding affinity, it still escaped antibody inhibition likely due to changes in the epitope recognized by the antibody. 2021 Scientific reports Abstract SARS_CoV_2 E484K 19 24 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. Studying the effect of RBD mutations on ACE2 binding showed that the N501Y mutation increased RBD apparent affinity toward ACE2 tenfold that resulted in escaping inhibition by some anti-RBD antibodies. 2021 Scientific reports Abstract SARS_CoV_2 N501Y 69 74 RBD;RBD;RBD 23;94;186 26;97;189 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. At the level of the virus, the D614G mutation enhances virus entry to the host cell. 2021 ACS chemical neuroscience Abstract SARS_CoV_2 D614G 31 36 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. The new virus strains that have additional mutations on the background of the D614G mutation can be expected to cause a similarly increased prevalence of chemosensory dysfunctions. 2021 ACS chemical neuroscience Abstract SARS_CoV_2 D614G 78 83 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. We conclude that the D614G mutation is a major contributing factor that increases the prevalence of anosmia in COVID-19, and that this enhanced effect on olfaction constitutes a previously unrecognized phenotype of the D614G mutation. 2021 ACS chemical neuroscience Abstract SARS_CoV_2 D614G;D614G 21;219 26;224 Anosmia;COVID-19 100;111 107;119 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. Introduction of the NSP12 E802D mutation into our SARS-CoV-2 reverse genetics backbone confirmed its role in decreasing RDV sensitivity in vitro. 2021 PLoS pathogens Abstract SARS_CoV_2 E802D 26 31 Nsp12 20 25 34535691 Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020. Specifically, we employ a recently developed phylogeographic workflow to infer the regional dispersal history of viral lineages associated with three specific mutations on the spike protein (S98F, A222V and S477N) and to quantify their relative importance through time. 2021 Scientific reports Abstract SARS_CoV_2 A222V;S477N;S98F 197;207;191 202;212;195 S 176 181 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Finally, we made the interesting observation that the Spikes from tested emerging variants bind better to ACE2 at 37 C compared to the D614G variant. 2021 Virology Abstract SARS_CoV_2 D614G 135 140 S 54 60 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. The dissociation constant (KD) values obtained by surface plasmon resonance of the wildtype SARS-CoV-2 spike (S)-protein receptor-binding domain (RBD) and N501Y mutant RBD in interactions with the heparin-immobilized sensor chip were 94 and 1.8 x 103 nM, respectively. 2021 The Journal of biological chemistry Abstract SARS_CoV_2 N501Y 155 160 S;RBD;RBD;S 103;146;168;110 108;149;171;111 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. Assessment of H655Y (n = 139) yielded a 100.0% concordance when applied in the proposed algorithm. 2022 Clinical microbiology and infection Abstract SARS_CoV_2 H655Y 14 19 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. METHODS: PCR SNP assays targeting SARS-CoV-2 S-gene mutations DeltaH69-V70, L452R, E484K, N501Y, H655Y and P681R using melting curve analysis were performed on 567 samples in which SARS-CoV-2 viral RNA was detected by a multiplex PCR. 2022 Clinical microbiology and infection Abstract SARS_CoV_2 E484K;H655Y;L452R;N501Y;P681R 83;97;76;90;107 88;102;81;95;112 S 45 46 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. RESULTS: The N501Y-specific assay (n = 567) had an overall percentage agreement (OPA) of 98.5%. 2022 Clinical microbiology and infection Abstract SARS_CoV_2 N501Y 13 18 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. The DeltaH69-V70-specific (n = 178) and E484K-specific (n = 401) assays had OPA of 96.6% and 99.7%, respectively. 2022 Clinical microbiology and infection Abstract SARS_CoV_2 E484K 40 45 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. The L452R-specific (n = 67) and P681R-specific (n = 62) assays had an OPA of 98.2% and 98.1%, respectively. 2022 Clinical microbiology and infection Abstract SARS_CoV_2 L452R;P681R 4;32 9;37 34537363 Influence of treatment with neutralizing monoclonal antibodies on the SARS-CoV-2 nasopharyngeal load and quasispecies. The fourth patient harboured a variant with a Q493K spike mutation 7 days post-treatment, and the fifth patient had a variant with a E484K spike mutation on day 21. 2022 Clinical microbiology and infection Abstract SARS_CoV_2 E484K;Q493K 133;46 138;51 S;S 52;139 57;144 34537363 Influence of treatment with neutralizing monoclonal antibodies on the SARS-CoV-2 nasopharyngeal load and quasispecies. Two patients harboured SARS-CoV-2 variants with a Q493R spike mutation 7 days after administration, as did a third patient 14 days after administration. 2022 Clinical microbiology and infection Abstract SARS_CoV_2 Q493R 50 55 S 56 61 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. Compared with XG81, XG83 exhibited a higher RBD binding affinity and neutralization potency against wild-typed pseudovirus, variant pseudoviruses with mutated spike proteins, such as D614G, E484Q, and A475V, as well as the authentic SARS-CoV-2 virus. 2021 Frontiers in immunology Abstract SARS_CoV_2 A475V;D614G;E484Q 201;183;190 206;188;195 S;RBD 159;44 164;47 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Beside D614G mutation, we report three unique mutations: A352S, S477I, and Q677H. 2021 Iranian journal of microbiology Abstract SARS_CoV_2 A352S;D614G;Q677H;S477I 57;7;75;64 62;12;80;69 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Besides, some mutations were also detected in two domains that were expected to be conserved region, the main viral proteases: PLpro (P77L and V205I), 3CLpro (M49I and L50F). 2021 Iranian journal of microbiology Abstract SARS_CoV_2 L50F;V205I;M49I;P77L 168;143;159;134 172;148;163;138 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. RESULTS: In total WGS from Indonesia, we found 5 major clades, which dominated as G clade, where the mutation of D614G was found. 2021 Iranian journal of microbiology Abstract SARS_CoV_2 D614G 113 118 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The prevalence of D614G over the time in different locations, indicating that changes in this mutation may related to host infection and the viral transmission. 2021 Iranian journal of microbiology Abstract SARS_CoV_2 D614G 18 23 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. This D614G was identified as much as 59%, which mostly reported in late samples submitted. 2021 Iranian journal of microbiology Abstract SARS_CoV_2 D614G 5 10 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. Next, using spike sequencing of twenty-eight strains and whole genome sequencing of thirteen strains, we found that Nexstrain clades 20A and 20B with a typically European D614G substitution in the spike and a frequent P2633L substitution in nsp16 were the dominant viruses during the first epidemic wave, while the clade 20H South African variants spread during the second wave characterized by an increase in the number of severe forms of COVID-19. 2021 Frontiers in medicine Abstract SARS_CoV_2 D614G;P2633L 171;218 176;224 S;S 12;197 17;202 COVID-19 440 448 34541054 Optimised Method for the Production and Titration of Lentiviral Vectors Pseudotyped with the SARS-CoV-2 Spike. High titers (>1.00 E+06 infectious units/ml) are produced using codon-optimized CoV-2 S, harbouring the prevalent D614G mutation and lacking its ER retention signal. 2021 Bio-protocol Abstract SARS_CoV_2 D614G 114 119 S 86 87 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. In this study, we examined the adjacent amino acid polymorphisms in the nucleocapsid (R203K/G204R) of SARS-CoV-2 that arose on the background of the spike D614G change and describe how strains harboring these changes became dominant circulating strains globally. 2021 Pathogens & immunity Abstract SARS_CoV_2 D614G;R203K;G204R 155;86;92 160;91;97 N;S 72;149 84;154 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. High-affinity RBD-specific antibodies exhibited high potency in neutralizing both live and pseudotype SARS-CoV-2 viruses and the SARS-CoV-2 pseudovirus particle containing the spike protein S-RBDV367F mutant (SARS-CoV-2(V367F)). 2021 MedComm Abstract SARS_CoV_2 V367F 220 225 S;RBD;RBD;S 176;14;192;190 181;17;195;191 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Compared with the wildtype, four mutants (K417N, Y453F, N501Y, and K417T/E484K/N501Y) had weaker affinity for the CC12.1 antibody, whereas two (S477N and S494P) had similar affinity, and two (T478I and E484K) had stronger affinity than the wildtype. 2021 The Journal of biological chemistry Abstract SARS_CoV_2 E484K;K417T;N501Y;S494P;Y453F;K417N;S477N;T478I;E484K;N501Y 202;67;56;154;49;42;144;192;73;79 207;72;61;159;54;47;149;197;78;84 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Of the eight best-expressed mutants, two (N501Y and K417T/E484K/N501Y) showed stronger affinity to angiotensin-converting enzyme 2 compared with the wildtype, whereas four (Y453F, S477N, T478I, and S494P) had similar affinity and two (K417N and E484K) had weaker affinity than the wildtype. 2021 The Journal of biological chemistry Abstract SARS_CoV_2 E484K;K417T;S477N;S494P;T478I;K417N;N501Y;Y453F;E484K;N501Y 245;52;180;198;187;235;42;173;58;64 250;57;185;203;192;240;47;178;63;69 34544043 Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants. Among the sequences were three novel viral variants: BV-1 with a B.1.1.7/20I genetic background and an additional spike mutation Q493R, associated with a mild but longer-than-usual COVID-19 case in a college-age person, BV-2 with a T478K mutation on a 20B genetic background, and BV-3, an apparent recombinant lineage. 2021 The American journal of tropical medicine and hygiene Abstract SARS_CoV_2 Q493R;T478K 129;232 134;237 S 114 119 COVID-19 181 189 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. We found that the Alpha variant (B.1.1.7) increased competitive fitness over earlier parental D614G lineages in in-vitro and in-vivo systems. 2021 Communications biology Abstract SARS_CoV_2 D614G 94 99 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. Accordingly, mAb1 failed to inhibit the ACE2-RBD interaction while mAb2 inhibited the ACE2-RBD interactions for all RBD mutants, except mutant E484K, which only displayed partial blocking. 2022 Journal of pharmaceutical analysis Abstract SARS_CoV_2 E484K 143 148 RBD;RBD;RBD 45;91;116 48;94;119 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. All mAb-RBD mutant proteins displayed a reduction in binding affinities relative to the original RBD, except for the E484K-mAb1 interaction. 2022 Journal of pharmaceutical analysis Abstract SARS_CoV_2 E484K 117 122 RBD;RBD 8;97 11;100 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. Compared to the original RBD, the Y453F and N501Y mutants displayed a significant increase in ACE2 binding affinity, whereas D614G had a substantial reduction in binding affinity. 2022 Journal of pharmaceutical analysis Abstract SARS_CoV_2 D614G;N501Y;Y453F 125;44;34 130;49;39 RBD 25 28 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. In addition, the interactions of the ACE2 receptor, an anti-spike mAb (mAb1), a neutralizing mAb (mAb2), the original spike RBD sequence, and mutants D614G, N501Y, N439K, Y453F, and E484K were assessed. 2022 Journal of pharmaceutical analysis Abstract SARS_CoV_2 D614G;E484K;N439K;N501Y;Y453F 150;182;164;157;171 155;187;169;162;176 S;S;RBD 60;118;124 65;123;127 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. However, we reveal that antibody-disruptive co-mutations [Y449S, N501Y] debuted as a new vaccine-resistant transmission pathway of viral evolution in highly vaccinated populations a few months ago. 2021 ArXiv Abstract SARS_CoV_2 N501Y;Y449S 65;58 70;63 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. We predict that RBD co-mutation [A411S, L452R, T478K], [L452R, T478K, N501Y], [L452R, T478K, E484K, N501Y], [K417N, L452R, T478K], and [P384L, K417N, E484K, N501Y] will have high chances to grow into dominating variants due to their high infectivity and/or strong ability to break through current vaccines, calling for the development of new vaccines and antibody therapies. 2021 ArXiv Abstract SARS_CoV_2 E484K;E484K;K417N;L452R;L452R;N501Y;N501Y;N501Y;T478K;T478K;T478K;T478K;A411S;K417N;L452R;L452R;P384L 93;150;143;40;116;70;100;157;47;63;86;123;33;109;56;79;136 98;155;148;45;121;75;105;162;52;68;91;128;38;114;61;84;141 RBD 16 19 34545362 Rapid Identification of Neutralizing Antibodies against SARS-CoV-2 Variants by mRNA Display. A potent ACE2-blocking nAb was further engineered to sustain binding to S RBD with the E484K and L452R substitutions found in multiple SARS-CoV-2 variants. 2021 bioRxiv Abstract SARS_CoV_2 E484K;L452R 87;97 92;102 RBD;S 74;72 77;73 34545803 Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA. While conducting genomic surveillance (1,663 cases) from December 2020-April 2021 in Arizona, USA, we detected an emergent E484K-harboring variant, B.1.243.1. 2021 Emerging infectious diseases Abstract SARS_CoV_2 E484K 123 128 34547443 Characterisation of SARS-CoV-2 clades based on signature SNPs unveils continuous evolution. As a consequence, for global dataset without Indian sequences, G251V in ORF3a in clade 19A, F308Y and G196V in NSP4 and ORF3a in 19B are the unique amino acid changes which are responsible for defining each clade as they are all deleterious and unstable. 2021 Methods (San Diego, Calif.) Abstract SARS_CoV_2 F308Y;G196V;G251V 92;102;63 97;107;68 ORF3a;ORF3a;Nsp4 72;120;111 77;125;115 34547443 Characterisation of SARS-CoV-2 clades based on signature SNPs unveils continuous evolution. Such changes which are common for both global dataset without Indian and dataset of exclusive Indian sequences are R203M in Nucleocapsid for 20B, T85I and Q57H in NSP2 and ORF3a respectively for 20C while for exclusive Indian sequences such unique changes are A97V in RdRp, G339S and G339C in NSP2 in 19A and Q57H in ORF3a in 20A. 2021 Methods (San Diego, Calif.) Abstract SARS_CoV_2 A97V;G339C;G339S;Q57H;Q57H;R203M;T85I 260;284;274;155;309;115;146 264;289;279;159;313;120;150 N;ORF3a;ORF3a;Nsp2;Nsp2;RdRP 124;172;317;163;293;268 136;177;322;167;297;272 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. Yet, it remains uncertain to exert the antiviral effect of CT-P59 on Gamma, Delta and its associated variants (L452R). 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 L452R 111 116 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. Two mutations were identified including D108G and A249V and shown to increase the molecular flexibility of PLPro protein and alter the protein stability, particularly with D108G mutation. 2022 Saudi journal of biological sciences Abstract SARS_CoV_2 A249V;D108G;D108G 50;40;172 55;45;177 34549097 Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran. There were seven single nucleotide variations (SNVs) in common in all samples and only one of the sequenced genomes showed the D614G amino acid substitution. 2021 Heliyon Abstract SARS_CoV_2 D614G 127 132 34549097 Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran. Three SNVs, 1397 G > A, 28688T > C, 29742 G > T, which had already been reported in February, were found with high frequency in all the sequenced genomes in this study, implying that viral diversity reflected in the early stages of viral transmission in Iran were established in the second wave. 2021 Heliyon Abstract SARS_CoV_2 G1397A;T28688C;G29742T 12;24;36 22;34;47 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Results showed minimal, statistically nonsignificant effects on neutralization titers against the B.1.1.7 (Alpha) variant (1.2-fold reduction compared with D614G); other VOCs, such as B.1.351 (Beta, including B.1.351-v1, B.1.351-v2, and B.1.351-v3), P.1 (Gamma), and B.1.617.2 (Delta), showed significantly decreased neutralization titers ranging from 2.1-fold to 8.4-fold reductions compared with D614G, although all remained susceptible to mRNA-1273-elicited serum neutralization. 2021 Journal of virology Abstract SARS_CoV_2 D614G;D614G 156;398 161;403 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Sera from participants immunized on a prime-boost schedule with the mRNA-1273 COVID-19 vaccine were tested for neutralizing activity against several SARS-CoV-2 variants, including variants of concern (VOCs) and variants of interest (VOIs), compared to neutralization of the wild-type SARS-CoV-2 virus (designated D614G). 2021 Journal of virology Abstract SARS_CoV_2 D614G 313 318 COVID-19 78 86 34550770 Discovery and Evaluation of Entry Inhibitors for SARS-CoV-2 and Its Emerging Variants. Our data showed that mutation N501Y (present in B.1.351 variant) alters the binding mode of MU-UNMC-2 such that it is partially exposed to the solvent and has reduced polar contacts. 2021 Journal of virology Abstract SARS_CoV_2 N501Y 30 35 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Although the current coronavirus disease 2019 (COVID-19) vaccines have been used worldwide to halt spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the emergence of new SARS-CoV-2 variants with E484K mutation shows significant resistance to the neutralization of vaccine sera. 2022 Briefings in bioinformatics Abstract SARS_CoV_2 E484K 221 226 COVID-19;COVID-19;COVID-19 21;120;47 40;160;55 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Binding free energy decomposition revealed that the residue E484 forms attraction with most antibodies, while the K484 has repulsion from most antibodies, which should be the main reason of the weaker binding affinities of E484K mutant to most antibodies. 2022 Briefings in bioinformatics Abstract SARS_CoV_2 E484K 223 228 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Impressively, a monoclonal antibody (mAb) combination was found to have much stronger binding affinity with E484K mutant than WT, which may work well against the mutated virus. 2022 Briefings in bioinformatics Abstract SARS_CoV_2 E484K 108 113 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. The results showed that most antibodies (~85%) have weaker binding affinities to the E484K mutated spike protein than to the WT, indicating the high risk of immune evasion of the mutated virus from most of current antibodies. 2022 Briefings in bioinformatics Abstract SARS_CoV_2 E484K 85 90 S 99 104 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. To better understand the resistant mechanism, we calculated the binding affinities of 26 antibodies to wild-type (WT) spike protein and to the protein harboring E484K mutation, respectively. 2022 Briefings in bioinformatics Abstract SARS_CoV_2 E484K 161 166 S 118 123 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. RESULTS: The D614G mutation was identified in imported cases, which separated into two clusters related to viruses originally detected in the USA. 2021 PeerJ Abstract SARS_CoV_2 D614G 13 18 34558408 A major outbreak of COVID-19 at aresidential care home. and phylogenetic analysis demonstrated a dominant outbreak lineage belonging to Global Lineage B.1.1.29 containing the mutation I233V in the S gene. 2021 Danish medical journal Abstract SARS_CoV_2 I233V 128 133 S 141 142 34560289 SARS-CoV-2 B.1.1.7 lineage rapidly spreads and replaces R.1 lineage in Japan: Serial and stationary observation in a community. After the emerging of the R.1 lineage harboring E484K variant (designated VOI in Japan), the prevalent B.1.1.214 lineage were no longer identified. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 E484K 48 53 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. Importantly, ADCC activities were mediated by a diversity of epitopes in SARS-COV-2-infected mice and induced to comparable levels against SARS-CoV-2 variants of concern (VOCs) (B.1.1.7, B.1.351, and P.1) as that against the D614G mutant in human patients and vaccinated mice. 2021 Signal transduction and targeted therapy Abstract SARS_CoV_2 D614G 225 230 34561887 Proteolytic activation of SARS-CoV-2 spike protein. All four variants of concern carry the D614G mutation, which indirectly enhances S1/S2 cleavability by furin. 2022 Microbiology and immunology Abstract SARS_CoV_2 D614G 39 44 34561887 Proteolytic activation of SARS-CoV-2 spike protein. The P681R mutation of the delta variant directly increases S1/S2 cleavability, enhancing membrane fusion and SARS-CoV-2 virulence. 2022 Microbiology and immunology Abstract SARS_CoV_2 P681R 4 9 Membrane 89 97 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Among the various naturally-occurring mutations, the E484K mutation shared by many variants attracted serious concerns, which may potentially enhance the receptor binding affinity and reduce the immune response. 2021 Journal of molecular graphics & modelling Abstract SARS_CoV_2 E484K 53 58 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Besides that, the E484K mutation also causes the conformational rearrangements of the loop region containing the mutant residue, which leads to tighter binding interface of RBD with hACE2 and formation of some new hydrogen bonds. 2021 Journal of molecular graphics & modelling Abstract SARS_CoV_2 E484K 18 23 RBD 173 176 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In addition, six neutralizing antibodies and nanobodies complexed with RBD were selected to explore the effects of E484K mutation on the recognition of these antibodies to RBD. 2021 Journal of molecular graphics & modelling Abstract SARS_CoV_2 E484K 115 120 RBD;RBD 71;172 74;175 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In the present study, the molecular mechanism behind the impacts of E484K mutation on the binding affinity of the receptor-binding domain (RBD) with the receptor human angiotensin-converting enzyme 2 (hACE2) was investigated by using the molecular dynamics (MD) simulations combined with the molecular mechanics-generalized Born surface area (MMGBSA) method. 2021 Journal of molecular graphics & modelling Abstract SARS_CoV_2 E484K 68 73 RBD 139 142 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Our results indicate that the E484K mutation results in more favorable electrostatic interactions compensating the burial of the charged and polar groups upon the binding of RBD with hACE2, which significantly improves the RBD-hACE2 binding affinity. 2021 Journal of molecular graphics & modelling Abstract SARS_CoV_2 E484K 30 35 RBD;RBD 174;223 177;226 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Our studies revealed that the E484K mutation may improve the binding affinity between RBD and the receptor hACE2, implying more transmissibility of the E484K-containing variants, and weaken the binding affinities between RBD and the studied neutralizing antibodies/nanobodies, indicating reduced effectiveness of these antibodies/nanobodies. 2021 Journal of molecular graphics & modelling Abstract SARS_CoV_2 E484K;E484K 30;152 35;157 RBD;RBD 86;221 89;224 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The simulation results show that the E484K mutation significantly reduces the binding affinities to RBD for most of the studied neutralizing antibodies/nanobodies, and the decrease in the binding affinities is mainly owing to the unfavorable electrostatic interactions caused by the mutation. 2021 Journal of molecular graphics & modelling Abstract SARS_CoV_2 E484K 37 42 RBD 100 103 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Here we demonstrated by cryo-electron microscopy that the D614G mutation resulted in increased propensity of multiple receptor-binding domains (RBDs) in an upward conformation poised for host receptor binding. 2021 The Journal of biological chemistry Abstract SARS_CoV_2 D614G 58 63 RBD 144 148 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Our findings shed light on how the D614G mutation enhances the infectivity of SARS-CoV-2 through a stabilizing mutation and suggest an approach for better design of spike protein-based conjugates for vaccine development. 2021 The Journal of biological chemistry Abstract SARS_CoV_2 D614G 35 40 S 165 170 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. The D614G mutation in the spike protein of SARS-CoV-2 alters the fitness of the virus, leading to the dominant form observed in the COVID-19 pandemic. 2021 The Journal of biological chemistry Abstract SARS_CoV_2 D614G 4 9 S 26 31 COVID-19 132 140 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. The D614G spike variant also exhibited exceptional long-term stability when stored at 37C for up to 2 months. 2021 The Journal of biological chemistry Abstract SARS_CoV_2 D614G 4 9 S 10 15 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. However, S477N and L452R RBDs were observed to increase the flexibility of the RBM region while maintaining similar flexibility in other RBD regions in comparison to WT RBD. 2021 Biomolecules Abstract SARS_CoV_2 L452R;S477N 19;9 24;14 RBD;RBD;RBD 25;137;169 29;140;172 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Interestingly, N501Y, N439K, and E484K mutations were observed to increase the rigidity in some RBD regions while increasing the flexibility of the receptor-binding motif (RBM) region, suggesting a compensation of the entropy penalty. 2021 Biomolecules Abstract SARS_CoV_2 E484K;N439K;N501Y 33;22;15 38;27;20 RBD 96 99 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. The destabilizing effect of S477N RBD was consistent with previous work on S477N mutation. 2021 Biomolecules Abstract SARS_CoV_2 S477N;S477N 28;75 33;80 RBD 34 37 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Therefore, both mutations (especially S477N) might destabilize the RBD structure, as loose conformation compactness was observed. 2021 Biomolecules Abstract SARS_CoV_2 S477N 38 43 RBD 67 70 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. To understand the molecular structural link between RBD mutations and infectivity, the top five mutant RBDs (i.e., N501Y, E484K L452R, S477N, and N439K) were selected based on their recorded case numbers. 2021 Biomolecules Abstract SARS_CoV_2 E484K;L452R;N439K;N501Y;S477N 122;128;146;115;135 127;133;151;120;140 RBD;RBD 52;103 55;107 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. The results of the MD simulations showed that the conformation and configuration of the ligand was changed for mutants H163A and E166A, although the structure of the whole protein and of the catalytic dyad did not change significantly, suggesting that mutations in His163 and Glu166 may be linked to drug resistance. 2021 International journal of molecular sciences Abstract SARS_CoV_2 E166A;H163A 129;119 134;124 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. We examined structural alterations at the RNA and protein levels as a result of three of these mutations: A26194T, T28854T, and C25611A, present in the Orf3a and N protein. 2021 Pathogens (Basel, Switzerland) Abstract SARS_CoV_2 A26194T;C25611A;T28854T 106;128;115 113;135;122 ORF3a;N 152;162 157;163 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Both B.1.617 variants Kappa (+E484Q) and Delta (+T478K) were less susceptible to either casirivimab or imdevimab. 2021 Viruses Abstract SARS_CoV_2 E484Q;T478K 30;49 35;54 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. We found that authentic SARS-CoV-2 variants harboring L452R had reduced susceptibility to convalescent and vaccine-elicited sera and mAbs. 2021 Viruses Abstract SARS_CoV_2 L452R 54 59 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. We performed a cell culture-based neutralization assay focusing on authentic SARS-CoV-2 variants B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.427/B.1.429 (Epsilon), all harboring the spike substitution L452R. 2021 Viruses Abstract SARS_CoV_2 L452R 199 204 S 180 185 34578354 SARS-CoV-2 Delta Variant Pathogenesis and Host Response in Syrian Hamsters. The pathogenicity of B.1.617.2 (Delta) and B.1.617.3 lineage of SARS-CoV-2 was evaluated and compared with that of B.1, an early virus isolate with D614G mutation in a Syrian hamster model. 2021 Viruses Abstract SARS_CoV_2 D614G 148 153 34578363 Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India. Sub-lineage I had mutations in ORF1ab A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, and A6319V, and in N G215C; Sub-lineage II had mutations in ORF1ab P309L, A3209V, V3718A, G5063S, P5401L, and ORF7a L116F; Sub-lineage III had mutations in ORF1ab A3209V, V3718A, T3750I, G5063S, and P5401L and in spike A222V; Sub-lineage IV had mutations in ORF1ab P309L, D2980N, and F3138S and spike K77T. 2021 Viruses Abstract SARS_CoV_2 A1306S;A222V;A3209V;A3209V;A6319V;D2980N;F3138S;G215C;G5063S;G5063S;G5063S;K77T;L116F;P2046L;P2287S;P309L;P309L;P5401L;P5401L;P5401L;T3255I;T3446A;T3750I;V2930L;V3718A;V3718A 38;321;176;265;106;374;386;123;86;192;289;403;218;46;54;169;367;94;200;301;70;78;281;62;184;273 44;326;182;271;112;380;392;128;92;198;295;407;223;52;60;174;372;100;206;307;76;84;287;68;190;279 ORF1ab;ORF1ab;ORF1ab;ORF1ab;ORF7a;S;S;N 31;162;258;360;212;315;397;121 37;168;264;366;217;320;402;122 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Although P.6 was replaced by the variant of concern (VOC) P.1 as the predominant lineage in Uruguay since April 2021, the monitoring of the concurrent emergence of Q675H + Q677H in VOCs should be of worldwide interest. 2021 Viruses Abstract SARS_CoV_2 Q675H;Q677H 164;172 169;177 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. The more efficient dissemination of lineage P.6 with respect to P.2 and P.7 and the presence of mutations (Q675H and Q677H) in the proximity of the key cleavage site at the S1/S2 boundary suggest that P.6 may be more transmissible than other lineages co-circulating in Uruguay. 2021 Viruses Abstract SARS_CoV_2 Q677H;Q675H 117;107 122;112 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. We identified that the most prevalent viral variant during the first epidemic wave in Uruguay (December 2020-February 2021) was a B.1.1.28 sublineage carrying Spike mutations Q675H + Q677H, now designated as P.6, followed by lineages P.2 and P.7. 2021 Viruses Abstract SARS_CoV_2 Q675H;Q677H 175;183 180;188 S 159 164 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. Deep sequencing identified three amino acid substitutions, N501Y, Q493H, and K417N, at the receptor binding domain (RBD) of MASCp36, during in vivo passaging. 2021 Nature communications Abstract SARS_CoV_2 K417N;N501Y;Q493H 77;59;66 82;64;71 RBD;RBD 91;116 114;119 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. N501Y and Q493H enhance the binding affinity to hACE2, whereas triple mutations at N501Y/Q493H/K417N decrease affinity and reduce infectivity of MASCp36. 2021 Nature communications Abstract SARS_CoV_2 N501Y;Q493H;K417N;Q493H;N501Y 83;10;95;89;0 88;15;100;94;5 34587819 COVID-19 and anosmia: The story so far. The D614G spike variant may also play a role in the increased number of anosmia patients. 2021 Ear, nose, & throat journal Abstract SARS_CoV_2 D614G 4 9 S 10 15 Anosmia 72 79 34591922 Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example. A number of topologically similar examples are then analyzed in detail, some of them are even better candidates for a bifurcation hot-spot than D614G. 2021 PloS one Abstract SARS_CoV_2 D614G 144 149 34591922 Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example. It is observed that the notorious D614G substitution of the spike protein is a good example of a bifurcation hot-spot. 2021 PloS one Abstract SARS_CoV_2 D614G 34 39 S 60 65 34591922 Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example. The local topology of the more recently observed N501Y substitution is also inspected, and it is found that this site is proximal to a different kind of local topology changing bifurcation. 2021 PloS one Abstract SARS_CoV_2 N501Y 49 54 34592572 SARS-CoV-2 spike protein receptor-binding domain N-glycans facilitate viral internalization in respiratory epithelial cells. In this study, we expressed and purified N331 and N343 N-glycosite mutants of SARS-CoV-2 RBD. 2021 Biochemical and biophysical research communications Abstract SARS_CoV_2 N343N 50 56 RBD;N 89;55 92;56 34594910 Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. Background: COVID-19 infection is a major public health problem worldwide, and the D614G mutation enhances the infectivity of COVID-19. 2021 China CDC weekly Abstract SARS_CoV_2 D614G 83 88 COVID-19;COVID-19 12;126 30;134 34594910 Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. Conclusions: A rapid, convenient, sensitive, and specific method to detect D614G mutation was developed, which offers a useful tool to monitor mutations in COVID-19 virus RNA. 2021 China CDC weekly Abstract SARS_CoV_2 D614G 75 80 COVID-19 156 164 34594910 Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. Methods: A probe-directed recombinase amplification (PDRA) assay was discussed to detect the D614G mutation at 39 C for 30 min. 2021 China CDC weekly Abstract SARS_CoV_2 D614G 93 98 34595399 Genomic epidemiological analysis of SARS-CoV-2 household transmission. However, a divergent viral sub-lineage was recovered from the infant and another child, each harbouring a distinguishing spike substitution (N30S). 2021 Access microbiology Abstract SARS_CoV_2 N30S 141 145 S 121 126 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Delta, Y144Delta, and LLA241/243Delta. 2021 Nature communications Abstract SARS_CoV_2 E484K;S477N 209;216 214;221 S 134 139 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Alpha and Beta replicated similarly to D614G strain in Vero, Caco-2, Calu-3, and primary airway cells. 2021 The EMBO journal Abstract SARS_CoV_2 D614G 39 44 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Alpha, Beta, and D614G fusion was similarly inhibited by interferon-induced transmembrane proteins (IFITMs). 2021 The EMBO journal Abstract SARS_CoV_2 D614G 17 22 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Here, we first assessed Alpha (B.1.1.7) and Beta (B.1.351) spread and fusion in cell cultures, compared with the ancestral D614G strain. 2021 The EMBO journal Abstract SARS_CoV_2 D614G 123 128 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Variant spike proteins displayed higher ACE2 affinity compared with D614G. 2021 The EMBO journal Abstract SARS_CoV_2 D614G 68 73 S 8 13 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. We further show that Delta spike also triggers faster fusion relative to D614G. 2021 The EMBO journal Abstract SARS_CoV_2 D614G 73 78 S 27 32 34602531 A rapid screening assay for L452R and T478K spike mutations in SARS-CoV-2 Delta variant using high-resolution melting analysis. In addition, HRM analysis distinguished the T478K mutant from the wild-type T478. 2021 The Journal of toxicological sciences Abstract SARS_CoV_2 T478K 44 49 34602531 A rapid screening assay for L452R and T478K spike mutations in SARS-CoV-2 Delta variant using high-resolution melting analysis. In this assay, we determined L452R and T478K, among which T478K is an identifier of the Delta variant since L452R is seen in other strains (Kappa and Epsilon variants). 2021 The Journal of toxicological sciences Abstract SARS_CoV_2 L452R;L452R;T478K;T478K 29;108;39;58 34;113;44;63 34602531 A rapid screening assay for L452R and T478K spike mutations in SARS-CoV-2 Delta variant using high-resolution melting analysis. Our method discriminated between the L452R mutant and wild-type L452. 2021 The Journal of toxicological sciences Abstract SARS_CoV_2 L452R 37 42 34602531 A rapid screening assay for L452R and T478K spike mutations in SARS-CoV-2 Delta variant using high-resolution melting analysis. Seven clinical samples containing the Delta variant were successfully identified as L452R/T478K mutants. 2021 The Journal of toxicological sciences Abstract SARS_CoV_2 L452R;T478K 84;90 89;95 34603303 A Combination Adjuvant for the Induction of Potent Antiviral Immune Responses for a Recombinant SARS-CoV-2 Protein Vaccine. The combination adjuvant with spike protein antigen elicited robust responses to SARS-CoV-2 in mice, with markedly enhanced TH1-biased cellular responses and high virus-neutralizing antibody titers towards both homologous SARS-CoV-2 and a variant harboring the N501Y mutation shared by B1.1.7, B.1.351 and P.1 variants. 2021 Frontiers in immunology Abstract SARS_CoV_2 N501Y 261 266 S 30 35 34604978 Variants of SARS-CoV-2, their effects on infection, transmission and neutralization by vaccine-induced antibodies. Deadly K417N+E484K+N501Y triplet mutations found in B.1.351 and P.1 have increased the transmission ability of these strains by 50% leading to greater COVID-19 hospitalization, ICU admissions and deaths. 2021 European review for medical and pharmacological sciences Abstract SARS_CoV_2 K417N;E484K;N501Y 7;13;19 12;18;24 COVID-19 151 159 34604978 Variants of SARS-CoV-2, their effects on infection, transmission and neutralization by vaccine-induced antibodies. S477N, E484K, Q677H, E484Q, L452R, K417T, K417N and N501Y. 2021 European review for medical and pharmacological sciences Abstract SARS_CoV_2 E484K;E484Q;K417N;K417T;L452R;N501Y;Q677H;S477N 7;21;42;35;28;52;14;0 12;26;47;40;33;57;19;5 34604978 Variants of SARS-CoV-2, their effects on infection, transmission and neutralization by vaccine-induced antibodies. The variant, B.1.617 circulating in India and many other countries (double variant) having E484Q and L452R mutations, has raised the infection rate and decreased the neutralization capacity of the vaccine-induced antibodies. 2021 European review for medical and pharmacological sciences Abstract SARS_CoV_2 E484Q;L452R 91;101 96;106 34604978 Variants of SARS-CoV-2, their effects on infection, transmission and neutralization by vaccine-induced antibodies. These mutations are relevant for different characteristics and are present in newly evolved strains of SARS-CoV-2 like E484K in B.1.526, B.1.525, P.2, B.1.1.7, P.1 and B.1.351. 2021 European review for medical and pharmacological sciences Abstract SARS_CoV_2 E484K 119 124 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. Comparative analyses of the viral sequences reveal the prevalence P4715L and D614G mutations as the most recurrent and concurrent in Africa (97.20%), Europe (89.83%) and moderately in Asia (61.60%). 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G;P4715L 77;66 82;72 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. High recurrent mutations, namely: T265I in non-structural protein 2 (nsp2), L3606F in nsp6, P4715L in RNA-dependent RNA polymerase (RdRp), D614G in spike glycoprotein, R203K and G204R in nucleocapsid phosphoprotein and Q57H in ORF3a with well-conserved envelope and membrane proteins, 3CLpro and spike S2 domains across regions were observed. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614G;G204R;L3606F;P4715L;Q57H;R203K;T265I 139;178;76;92;219;168;34 144;183;82;98;223;173;39 RdRp;S;N;Membrane;S;ORF3a;Nsp2;Nsp6;RdRP 102;148;187;266;296;227;69;86;132 130;166;199;274;301;232;73;90;136 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Here, we examine the role of the non-RBD Q677H mutation arising in many SARS-CoV-2 lineages, including VOCs. 2021 mBio Abstract SARS_CoV_2 Q677H 41 46 RBD 37 40 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Our work highlights the importance of epistatic interactions between SARS-CoV-2 spike mutations and the continued need to monitor Q677H-bearing VOCs. 2021 mBio Abstract SARS_CoV_2 Q677H 130 135 S 80 85 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. The effect on neutralization of Q677H was determined in the context of the RBD mutations and in the background of major VOCs, including B.1.1.7 (United Kingdom, Alpha), B.1.351 (South Africa, Beta), and P1-501Y-V3 (Brazil, Gamma). 2021 mBio Abstract SARS_CoV_2 Q677H 32 37 RBD 75 78 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. The sensitivity of SARS-CoV-2 variants of concern (VOCs) to neutralizing antibodies has largely been studied in the context of key receptor binding domain (RBD) mutations, including E484K and N501Y. 2021 mBio Abstract SARS_CoV_2 E484K;N501Y 182;192 187;197 RBD;RBD 131;156 154;159 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. We demonstrate that the Q677H mutation enhances viral infectivity and confers neutralizing antibody resistance, particularly in the background of other SARS-CoV-2 VOCs. 2021 mBio Abstract SARS_CoV_2 Q677H 24 29 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. We demonstrate that the Q677H mutation increases viral infectivity and syncytium formation, as well as enhancing resistance to neutralization for VOCs, including B.1.1.7 and P1-501Y-V3. 2021 mBio Abstract SARS_CoV_2 Q677H 24 29 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. We now investigate the neutralization sensitivity of variants containing the non-RBD mutation Q677H, including B.1.525 (Nigerian isolate) and Bluebird (U.S. 2021 mBio Abstract SARS_CoV_2 Q677H 94 99 RBD 81 84 34607456 A Combination of Receptor-Binding Domain and N-Terminal Domain Neutralizing Antibodies Limits the Generation of SARS-CoV-2 Spike Neutralization-Escape Mutants. As seen with some of the natural VOC, the neutralization potencies of COVID-19 convalescent-phase sera were reduced by 4- to 16-fold against rVSV-SARS2 bearing Y145D, K150E, or W152R spike mutations. 2021 mBio Abstract SARS_CoV_2 K150E;W152R;Y145D 167;177;160 172;182;165 S 183 188 COVID-19 70 78 34607791 BNT162b2 vaccine-induced humoral and cellular responses against SARS-CoV-2 variants in systemic lupus erythematosus. In responders, serum neutralisation activity decreased against VOCs bearing the E484K mutation but remained detectable in a majority of patients. 2022 Annals of the rheumatic diseases Abstract SARS_CoV_2 E484K 80 85 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. BACKGROUND: Between February and June 2021, the initial wild-type strains of SARS-CoV-2 were supplanted in Ontario, Canada, by new variants of concern (VOCs), first those with the N501Y mutation (i.e., Alpha/B1.1.17, Beta/B.1.351 and Gamma/P.1 variants) and then the Delta/B.1.617 variant. 2021 CMAJ Abstract SARS_CoV_2 N501Y 180 185 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. Compared with non-VOC SARS-CoV-2 strains, the adjusted elevation in risk associated with N501Y-positive variants was 52% (95% confidence interval [CI] 42%-63%) for hospitalization, 89% (95% CI 67%-117%) for ICU admission and 51% (95% CI 30%-78%) for death. 2021 CMAJ Abstract SARS_CoV_2 N501Y 89 94 34611654 Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein. Using SARS-CoV-1 and bat RaTG13-CoV as comparisons, we identified two molecular switches that regulate the conformations of SARS-CoV-2 spike protein: (i) a furin motif loop turns SARS-CoV-2 spike from a closed conformation to a mixture of open and closed conformations, and (ii) a K417V mutation turns SARS-CoV-2 spike from mixed conformations to an open conformation. 2021 Research square Abstract SARS_CoV_2 K417V 281 286 S;S;S 135;190;313 140;195;318 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. In a single assay, we combined four reactions-one that detects SC-2 RNA independently of the strain, one that detects the D3L mutation, which is specific to variant B.1.1.7, one that detects the 242 to 244 deletion, which is specific to variant B.1.351, and the fourth reaction, which identifies the human RNAseP gene, serving as an endogenous control for RNA extraction integrity. 2021 Microbiology spectrum Abstract SARS_CoV_2 D3L 122 125 34613786 Highly Efficient SARS-CoV-2 Infection of Human Cardiomyocytes: Spike Protein-Mediated Cell Fusion and Its Inhibition. A spike mutant with the single amino acid change R682S that disrupts the multibasic furin cleavage motif was fusion inactive. 2021 Journal of virology Abstract SARS_CoV_2 R682S 49 54 S 2 7 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. Residues involved in the most ubiquitous D614G mutation and the A570D mutation of the highly contagious UK SARS-CoV-2 variant are predicted ab initio from our model. 2021 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 A570D;D614G 64;41 69;46 34615860 Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil. In summary, we report that ChAdOx1 nCoV-19 protects against emerging variants in Brazil despite the presence of the spike protein mutation E484K. 2021 Nature communications Abstract SARS_CoV_2 E484K 139 144 S 116 121 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. Mink-selected SARS-CoV-2 variants carrying the Y453F/D614G mutations display an increased affinity for human ACE2 and can escape neutralization by one monoclonal antibody. 2021 Frontiers in microbiology Abstract SARS_CoV_2 Y453F;D614G 47;53 52;58 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. BACKGROUND: The COVID-19 pandemic poses serious threats to global health, and the emerging mutation in SARS-CoV-2 genomes, e.g., the D614G substitution, is one of the major challenges of disease control. 2021 BMC infectious diseases Abstract SARS_CoV_2 D614G 133 138 COVID-19 16 24 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. CONCLUSIONS: We reported an evidence of transmission advantage associated with D614G substitution, and highlighted the real-time estimating potentials of modelling framework. 2021 BMC infectious diseases Abstract SARS_CoV_2 D614G 79 84 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. We find a significant transmission advantage of COVID-19 associated with the D614G substitution, which increases the infectivity by 54% (95%CI: 36, 72). 2021 BMC infectious diseases Abstract SARS_CoV_2 D614G 77 82 COVID-19 48 56 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. Results: Spike gene analysis of three samples (#6, #11, #35) found that the D614G mutation was detected in all isolates, although one isolate exhibited the D215Y and E484D mutation. 2021 F1000Research Abstract SARS_CoV_2 D215Y;D614G;E484D 156;76;166 161;81;171 S 9 14 34624095 The Ethics of Human Challenge Trials Using Emerging Severe Acute Respiratory Syndrome 2 Variants. The world's first coronavirus disease 2019 human challenge trial using the D614G strain of severe acute respiratory syndrome 2 (SARS-CoV-2) is underway in the United Kingdom. 2022 The Journal of infectious diseases Abstract SARS_CoV_2 D614G 75 80 COVID-19 18 37 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). OBJECTIVE: This study evaluated the clinical and analytical performance of the Seegene AllplexSARS-CoV-2 Variants I assay, which detects the HV69/70 deletion, N501Y and E484K mutations of the S gene. 2021 Journal of clinical virology Abstract SARS_CoV_2 E484K;N501Y 169;159 174;164 S 192 193 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). RESULTS: The clinical study revealed sensitivity of 100% (95% CI 99.27%-100%) and specificity of 100% (95% CI 98.99%-100%) for HV69/70 deletion, sensitivity of 100% (95% CI 99.55%-100%) and specificity of 100% (95% CI 93.73% - 100%) for N501Y, and sensitivity of 100% (95% CI 98.94% - 100%) and specificity of 98.10% (95% CI 96.53% - 99.08%) for E484K mutation. 2021 Journal of clinical virology Abstract SARS_CoV_2 E484K;N501Y 346;237 351;242 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). The E484Q mutation was detected in 10 specimens of the Kappa variant (B.1.627.1). 2021 Journal of clinical virology Abstract SARS_CoV_2 E484Q 4 9 34630410 A Barcoded Flow Cytometric Assay to Explore the Antibody Responses Against SARS-CoV-2 Spike and Its Variants. However, we find a reduce expression of the chimeric RBD-CD8 carrying the point mutation N501Y and E484K characteristic for the alpha and beta variant, respectively. 2021 Frontiers in immunology Abstract SARS_CoV_2 E484K;N501Y 99;89 104;94 RBD 53 56 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. A recently reported mutation in the protease, P108S, may be responsible for milder symptoms observed in COVID-19 patients in Tokyo. 2021 Biophysics and physicobiology Abstract SARS_CoV_2 P108S 46 51 COVID-19 104 112 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Further studies are certainly necessary to quantitively understand the relationships between the P108S mutation and physical properties of the main protease, but the results of our study will immediately inform development of new protease inhibitors. 2021 Biophysics and physicobiology Abstract SARS_CoV_2 P108S 97 102 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Our computational results suggest a link between the mutation P108S and dynamics of the catalytic sites in the main protease: The catalytic dyad become considerably inaccessible to substrates in the P108S mutant. 2021 Biophysics and physicobiology Abstract SARS_CoV_2 P108S;P108S 62;199 67;204 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Starting from a crystal structure of the SARS-CoV-2 main protease in the dimeric form, we performed triplicate 5.0-mus molecular dynamics simulations of the wild-type and P108S mutant. 2021 Biophysics and physicobiology Abstract SARS_CoV_2 P108S 171 176 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. In the fourth wave, sera-neutralizing activity against B.1.1.7 was significantly higher than that against any other variants, including D614G. 2021 Open forum infectious diseases Abstract SARS_CoV_2 D614G 136 141 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. METHODS: We investigated the neutralizing potency of 81 coronavirus disease 2019 (COVID-19) patients' sera from the first to fourth waves of the pandemic against SARS-CoV-2 D614G, B.1.1.7, P.1, and B.1.351 variants using their authentic viruses. 2021 Open forum infectious diseases Abstract SARS_CoV_2 D614G 173 178 COVID-19;COVID-19 56;82 75;90 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. RESULTS: Most sera had neutralizing activity against all variants, showing similar activity against B.1.1.7 and D614G, but lower activity especially against B.1.351. 2021 Open forum infectious diseases Abstract SARS_CoV_2 D614G 112 117 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. The high neutralizing activity specific to B.1.1.7 in the fourth wave suggests that mutations in the virus might cause conformational change of its spike protein, which affects immune recognition of D614G. 2021 Open forum infectious diseases Abstract SARS_CoV_2 D614G 199 204 S 148 153 34633892 Mutational profile confers increased stability of SARS-CoV-2 spike protein in Brazilian isolates. Most of the SARS-CoV-2 isolates belongs to the G clade and showed a large occurrence of D614G, N501Y and L18F substitutions. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 D614G;L18F;N501Y 88;105;95 93;109;100 34633892 Mutational profile confers increased stability of SARS-CoV-2 spike protein in Brazilian isolates. Mutations E484K, N501Y and K417N belong to several SARS-CoV-2 variants of concern such as Alpha, Beta, Gamma and Delta, and showed high incidence among Brazilian isolates. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 E484K;K417N;N501Y 10;27;17 15;32;22 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. In this study, plaque reduction neutralization assays demonstrated that mAb 1741-LALA neutralizes SARS-CoV-2 strains B.1.351, D614 and D614G. 2021 Antiviral research Abstract SARS_CoV_2 D614G 135 140 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. MAbs S1D2-hIgG1 and S1D2-LALA mutant (STI-1499-LALA) did not neutralize B.1.351, but did neutralize SARS-CoV-2 strains D614 and D614G. 2021 Antiviral research Abstract SARS_CoV_2 D614G 128 133 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. In addition, three antibody clones retained in vitro blocking activity when the E484K spike protein mutant was used. 2021 FASEB journal Abstract SARS_CoV_2 E484K 80 85 S 86 91 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. Of those, 10 showed an ability to block both the spike protein receptor binding domain from the Wuhan variant and the N501Y mutant from interacting with recombinant angiotensin-converting enzyme 2 (ACE2) receptor in vitro. 2021 FASEB journal Abstract SARS_CoV_2 N501Y 118 123 RBD;S 63;49 86;54 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The analysis highlighted that the mutations C14408T and C14805T played an important role in clusters selection and further virus spread. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 C14408T;C14805T 44;56 51;63 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. These include mutations S13I and W152C, decreasing antibody binding, N460K, increasing RDB affinity, or Q498R, positively affecting both properties. 2021 International journal of molecular sciences Abstract SARS_CoV_2 N460K;Q498R;S13I;W152C 69;104;24;33 74;109;28;38 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. The main findings from this study show that, compared to the wild-type SARS-CoV-2 spike protein, mutations E484A/G/K/Q/R/V, Q493K/L/R, S494A/P/R, L452R and F490S are predicted to be markedly resistant to neutralization by LY-CoV555, while mutations K417E/N/T, D420A/G/N, N460I/K/S/T, T415P, and Y489C/S are predicted to confer LY-CoV016 escaping advantage to the viral protein. 2021 Scientific reports Abstract SARS_CoV_2 D420A;D420G;D420N;E484A;E484G;E484K;E484Q;E484R;E484V;F490S;K417E;K417N;K417T;L452R;N460I;N460K;N460S;N460T;Q493K;Q493L;Q493R;S494A;S494P;S494R;T415P;Y489C;Y489S 260;260;260;107;107;107;107;107;107;156;249;249;249;146;271;271;271;271;124;124;124;135;135;135;284;295;295 269;269;269;122;122;122;122;122;122;161;258;258;258;151;282;282;282;282;133;133;133;144;144;144;289;302;302 S 82 87 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Specifically, vaccine-resistant mutation Y449S in the spike (S) protein receptor-bonding domain (RBD), which occurred in co-mutation [Y449S, N501Y], has reduced infectivity compared to the original SARS-CoV-2 but can disrupt existing antibodies that neutralize the virus. 2021 ArXiv Abstract SARS_CoV_2 N501Y;Y449S;Y449S 141;41;134 146;46;139 S;RBD;S 54;97;61 59;100;62 34643437 Shared Mutations in Emerging SARS-CoV-2 Circulating Variants May Lead to Reverse Transcription-PCR (RT-PCR)-Based Misidentification of B.1.351 and P.1 Variants of Concern. We evaluated an assay targeting E484K/N501Y to identify B.1.351/P1. 2021 Microbiology spectrum Abstract SARS_CoV_2 E484K;N501Y 32;38 37;43 34644287 Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. We also identified the occurrence of a new lineage descending from B.1.1.33 that convergently carries the E484K mutation, N.9. 2021 PLoS neglected tropical diseases Abstract SARS_CoV_2 E484K 106 111 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. However, the resistance to neutralization by convalescent serum or vaccines elicited serum is mainly caused by the E484K mutation. 2021 Communications biology Abstract SARS_CoV_2 E484K 115 120 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Our study provides insights regarding therapeutic antibodies and vaccines, and highlights the importance of E484K mutation. 2021 Communications biology Abstract SARS_CoV_2 E484K 108 113 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. RBD amino acid mutations comprising K417T/N, L452R, Y453F, S477N, E484K, and N501Y cause significant immune escape from 11 of 13 monoclonal antibodies. 2021 Communications biology Abstract SARS_CoV_2 E484K;K417N;K417T;L452R;N501Y;S477N;Y453F 66;36;36;45;77;59;52 71;43;43;50;82;64;57 RBD 0 3 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. The K417N/T, N501Y, or E484K-carrying variants exhibit significantly increased abilities to infect mouse ACE2-overexpressing cells. 2021 Communications biology Abstract SARS_CoV_2 E484K;K417N;K417T;N501Y 23;4;4;13 28;11;11;18 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. The newly emerging Kappa, Delta, and Lambda SARS-CoV-2 variants are worrisome, characterized with the double mutations E484Q/L452R, T478K/L452R, and F490S/L452Q, respectively, in their receptor binding domains (RBDs) of the spike proteins. 2021 Journal of chemical information and modeling Abstract SARS_CoV_2 E484Q;F490S;T478K;L452Q;L452R;L452R 119;149;132;155;138;125 124;154;137;160;143;130 RBD;S;RBD 185;224;211 209;229;215 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. To verify simulation results, we further carried out experiments with both pseudovirions- and live virus-based neutralization assays and demonstrated that LY-CoV555 completely lost neutralizing activity against the L452R/E484Q mutant. 2021 Journal of chemical information and modeling Abstract SARS_CoV_2 L452R;E484Q 215;221 220;226 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Using all-atom molecular dynamics (MD) simulation, here, we show that the E484Q/L452R mutations significantly reduce the binding affinity between the RBD of the Kappa variant and the antibody LY-CoV555 (also named as Bamlanivimab), which was efficacious for neutralizing the wild-type SARS-CoV-2. 2021 Journal of chemical information and modeling Abstract SARS_CoV_2 E484Q;L452R 74;80 79;85 RBD 150 153 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Here, we demonstrate that the N501Y variant permits respiratory infection in unmodified mice. 2021 Cell reports Abstract SARS_CoV_2 N501Y 30 35 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Immune escape of the K417N + E484K variant is observed because infection can be appreciated in the nasopharynx, but not lungs, of mice transferred with low-antibody-tier plasma. 2021 Cell reports Abstract SARS_CoV_2 E484K;K417N 29;21 34;26 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. We utilize N501Y to survey in vivo pseudovirus infection dynamics and susceptibility to reinfection with the L452R (Los Angeles), K417N + E484K (South Africa), and L452R + K417N + E484Q (India) variants. 2021 Cell reports Abstract SARS_CoV_2 E484K;E484Q;K417N;K417N;L452R;L452R;N501Y 138;180;130;172;109;164;11 143;185;135;177;114;169;16 34649268 Genomic reconstruction of the SARS-CoV-2 epidemic in England. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. 2021 Nature Abstract SARS_CoV_2 E484K 60 65 S 54 59 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Conversely, double mutations E484Q and L452R present in B.1.617.1 variant show partial antibody evasion with no evidence for an additive effect. 2021 Genome medicine Abstract SARS_CoV_2 E484Q;L452R 29;39 34;44 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Furthermore, we showed that RBD co-mutations K417N, E484K, and N501Y present in B.1.351 appear more resistant to NAbs and human convalescent plasma from the early stage of the pandemic, possibly due to an additive effect. 2021 Genome medicine Abstract SARS_CoV_2 E484K;K417N;N501Y 52;45;63 57;50;68 RBD 28 31 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Of note, these escape mutations could not affect the ACE2 binding affinity of RBD, among which L452R even enhanced binding. 2021 Genome medicine Abstract SARS_CoV_2 L452R 95 100 RBD 78 81 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. The comprehensive escape mutation map not only confirms the widely circulating strains carrying important immune escape RBD mutations such as K417N, E484K, and L452R, but also facilitates the discovery of new immune escape-enabling mutations such as F486L, N450K, F490S, and R346S. 2021 Genome medicine Abstract SARS_CoV_2 E484K;F486L;F490S;K417N;L452R;N450K;R346S 149;250;264;142;160;257;275 154;255;269;147;165;262;280 RBD 120 123 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. More patients tested positive for G769 V plus C1248F, A352S, and R158G and C1248F, respectively. 2021 Emerging microbes & infections Abstract SARS_CoV_2 A352S;C1248F;C1248F;G769V;R158G 54;46;75;34;65 59;52;81;40;70 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. Two patients (one of them vaccinated) tested positive for a Delta sublineage harbouring S71F, T250I, T572I and K854N. 2021 Emerging microbes & infections Abstract SARS_CoV_2 K854N;S71F;T250I;T572I 111;88;94;101 116;92;99;106 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. In this study, we computationally analyzed the N439K, S477 N, and T478K variants for their ability to bind Angiotensin-converting enzyme 2 (ACE2). 2021 Computers in biology and medicine Abstract SARS_CoV_2 N439K;S477N;T478K 47;54;66 52;60;71 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. The net binding energy of the systems was -31.86 kcal/mol for the wild-type-ACE2 complex, -67.85 kcal/mol for N439K, -69.82 kcal/mol for S477 N, and -69.64 kcal/mol for T478K. 2021 Computers in biology and medicine Abstract SARS_CoV_2 N439K;S477N;T478K 110;137;169 115;143;174 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. The stability and binding energies of N439K, S477 N, and T478K variants were enhanced compared to the wild-type-ACE2 complex. 2021 Computers in biology and medicine Abstract SARS_CoV_2 N439K;S477N;T478K 38;45;57 43;51;62 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. A total of 31 PANGO lineages were identified from 168 SARS-CoV-2 positive cases, in which 34 samples belonged to N501Y variants, including B.1.1.7 (n = 20), B.1.351 (n = 12) and P.3 (n = 2). 2022 Journal of virological methods Abstract SARS_CoV_2 N501Y 113 118 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. In this study, we developed an in-house TaqMan minor groove binder (MGB) probe-based one-step RT-qPCR assay to detect the presence of N501Y mutation in SARS-CoV-2. 2022 Journal of virological methods Abstract SARS_CoV_2 N501Y 134 139 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. It enables robust high-throughput screening for surveillance of SARS-CoV-2 variants of concern harbouring N501Y mutation. 2022 Journal of virological methods Abstract SARS_CoV_2 N501Y 106 111 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. N501Y mutation was successfully detected at an allele frequency as low as 10 % in a sample with mixed SARS-CoV-2 lineage. 2022 Journal of virological methods Abstract SARS_CoV_2 N501Y 0 5 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. The analytical sensitivity and the ability of the assay to detect low frequency of N501Y variants were also evaluated. 2022 Journal of virological methods Abstract SARS_CoV_2 N501Y 83 88 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. The increasing prevalence of N501Y variants of SARS-CoV-2 has kindled global concern due to their enhanced transmissibility. 2022 Journal of virological methods Abstract SARS_CoV_2 N501Y 29 34 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. The N501Y RT-qPCR correctly identified all 34 samples as N501Y-positive and the other 134 samples as wildtype. 2022 Journal of virological methods Abstract SARS_CoV_2 N501Y;N501Y 4;57 9;62 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. The N501Y RT-qPCR is simple and inexpensive (US$1.6 per sample). 2022 Journal of virological methods Abstract SARS_CoV_2 N501Y 4 9 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. While performing epidemiological and genomic surveillance of SARS-CoV-2 in samples from Porto Ferreira-Sao Paulo-Brazil, we identified sequences classified by pangolin as B.1.1.28 harboring Spike L452R mutation, in the RBD region. 2021 Frontiers in public health Abstract SARS_CoV_2 L452R 196 201 S;RBD 190;219 195;222 34663909 SARS-CoV-2 promotes RIPK1 activation to facilitate viral propagation. Furthermore, NSP12 323L variant, encoded by the SARS-CoV-2 C14408T variant first detected in Lombardy, Italy, that carries a Pro323Leu amino acid substitution in NSP12, showed increased ability to activate RIPK1. 2021 Cell research Abstract SARS_CoV_2 C14408T;P323L 59;125 66;134 Nsp12;Nsp12 13;162 18;167 34668773 Susceptibilities of Human ACE2 Genetic Variants in Coronavirus Infection. We identified an ACE2 SNP, D355N, that restricts the spike protein-ACE2 interaction and consequently has the potential to protect individuals against SARS-CoV-2 infection. 2022 Journal of virology Abstract SARS_CoV_2 D355N 27 32 S 53 58 COVID-19 150 170 34668773 Susceptibilities of Human ACE2 Genetic Variants in Coronavirus Infection. We identified the ACE2 D355N variant that restricts the spike protein-ACE2 interaction and consequently limits infection both in vitro and in vivo. 2022 Journal of virology Abstract SARS_CoV_2 D355N 23 28 S 56 61 34668780 SARS-CoV-2 Causes Lung Infection without Severe Disease in Human ACE2 Knock-In Mice. Because the entry mechanisms of SARS-CoV-2 in mice remain uncertain, we evaluated the impact of the naturally occurring, mouse-adapting N501Y mutation by comparing infection of hACE2 KI, K18-hACE2 Tg, ACE2-deficient, and wild-type C57BL/6 mice. 2022 Journal of virology Abstract SARS_CoV_2 N501Y 136 141 34668780 SARS-CoV-2 Causes Lung Infection without Severe Disease in Human ACE2 Knock-In Mice. Overall, our study highlights the hACE2 KI mice as a model of mild SARS-CoV-2 infection and disease and clarifies the requirement of the N501Y mutation in mice. 2022 Journal of virology Abstract SARS_CoV_2 N501Y 137 142 COVID-19 67 87 34668780 SARS-CoV-2 Causes Lung Infection without Severe Disease in Human ACE2 Knock-In Mice. The N501Y mutation minimally affected SARS-CoV-2 infection in hACE2 KI mice but was required for viral replication in wild-type C57BL/6 mice in a mACE2-dependent manner and augmented pathogenesis in the K18-hACE2 Tg mice. 2022 Journal of virology Abstract SARS_CoV_2 N501Y 4 9 COVID-19 38 58 34668780 SARS-CoV-2 Causes Lung Infection without Severe Disease in Human ACE2 Knock-In Mice. Thus, the N501Y mutation likely enhances interactions with mACE2 or hACE2 in vivo. 2022 Journal of virology Abstract SARS_CoV_2 N501Y 10 15 34671769 A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. We selected 2-36-escape viruses in vitro and confirmed that K378T in SARS-CoV-2 RBD led to viral resistance. 2021 bioRxiv Abstract SARS_CoV_2 K378T 60 65 RBD 80 83 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. Importantly, the R203K+G204R mutation increases nucleocapsid phosphorylation and confers resistance to inhibition of the GSK-3 kinase, providing a molecular basis for increased virus replication. 2022 bioRxiv Abstract SARS_CoV_2 R203K;G204R 17;23 22;28 N 48 60 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. Recreating a mutation found in the alpha and omicron variants in an early pandemic (WA-1) background, we find that the R203K+G204R mutation is sufficient to enhance replication, fitness, and pathogenesis of SARS-CoV-2. 2022 bioRxiv Abstract SARS_CoV_2 R203K;G204R 119;125 124;130 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. Recreating the prominent nucleocapsid R203K+G204R mutation in an early pandemic background, we show that this mutation is alone sufficient to enhance SARS-CoV-2 replication and pathogenesis. 2022 bioRxiv Abstract SARS_CoV_2 R203K;G204R 38;44 43;49 N 25 37 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. The R203K+G204R mutant corresponds with increased viral RNA and protein both in vitro and in vivo . 2022 bioRxiv Abstract SARS_CoV_2 R203K;G204R 4;10 9;15 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. This mutant was found to mimic R203K+G204R, suggesting augmentation of infection occurs by disrupting the ancestral sequence. 2022 bioRxiv Abstract SARS_CoV_2 R203K;G204R 31;37 36;42 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. We also link augmentation of SARS-CoV-2 infection by the R203K+G204R mutation to its modulation of nucleocapsid phosphorylation. 2022 bioRxiv Abstract SARS_CoV_2 R203K;G204R 57;63 62;68 N 99 111 COVID-19 29 49 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The N501Y mutation was detected in patients with positive Covid-19 PCR test results. 2021 Journal of medical virology Abstract SARS_CoV_2 N501Y 4 9 COVID-19 58 66 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. We aimed to evaluate the N501Y mutation rate in randomly chosen positive patients with the polymerase chain reaction (PCR). 2021 Journal of medical virology Abstract SARS_CoV_2 N501Y 25 30 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. Another silent 5'-UTR:C241T mutation might affect translational efficiency and viral packaging. 2021 Journal of medical virology Abstract SARS_CoV_2 C241T 22 27 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. GV-clade viruses seemingly gained the evolutionary advantage of the confounding factors; nevertheless, N:p.A220V might modulate RNA binding with no phenotypic effect. 2021 Journal of medical virology Abstract SARS_CoV_2 A220V 105 112 N 103 104 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. RdRp mutation p.P323L significantly increased genome-wide mutations (p < 0.0001), allowing for more flexible RdRp (mutated)-NSP8 interaction that may accelerate replication. 2021 Journal of medical virology Abstract SARS_CoV_2 P323L 14 21 Nsp8;RdRP;RdRP 124;0;109 128;4;113 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. Sentinel GH-clade ORF3a:p.Q57H variants constricted the ion-channel through intertransmembrane-domain interaction of cysteine(C81)-histidine(H57). 2021 Journal of medical virology Abstract SARS_CoV_2 Q57H 24 30 ORF3a 18 23 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. Superior RNA stability and structural variation at NSP3:C241T might impact protein, RNA interactions, or both. 2021 Journal of medical virology Abstract SARS_CoV_2 C241T 56 61 Nsp3 51 55 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. B.1.1.7 behaved similarly to D614G with respect to clinical disease and replication in the respiratory tract. 2021 Science advances Abstract SARS_CoV_2 D614G 29 34 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Here, we compared variants of concern (VOC) B.1.1.7 and B.1.351 to a recent B.1 SARS-CoV-2 isolate containing the D614G spike substitution in the rhesus macaque model. 2021 Science advances Abstract SARS_CoV_2 D614G 114 119 S 120 125 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. In bronchoalveolar lavages, cytokines and chemokines were up-regulated on day 4 in animals inoculated with D614G and B.1.1.7 but not with B.1.351. 2021 Science advances Abstract SARS_CoV_2 D614G 107 112 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. As proof-of-concept, a multiplex-test was compiled and validated (SCOV2-617VOC-UCT) including SNP-detection for L452R, P681R, E484K, and E484Q to provide rapid screening capabilities for the novel B.1.617 lineages. 2021 Diagnostics (Basel, Switzerland) Abstract SARS_CoV_2 E484K;E484Q;L452R;P681R 126;137;112;119 131;142;117;124 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. METHODS: We created a broad set of single nucleotide polymorphism (SNP)-assays including del-Y144/145, E484K, E484Q, P681H, P681R, L452R, and V1176F based on a highly specific multi-LNA (locked nucleic acid)-probe design to maximize mismatch discrimination. 2021 Diagnostics (Basel, Switzerland) Abstract SARS_CoV_2 E484K;E484Q;L452R;P681H;P681R;V1176F 103;110;131;117;124;142 108;115;136;122;129;148 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. RESULTS: For the multiplex-test (SCOV2-617VOC-UCT), the analytic lower limit of detection was determined as 182 IU/mL for L452R, 144 IU/mL for P681R, and 79 IU/mL for E484Q. 2021 Diagnostics (Basel, Switzerland) Abstract SARS_CoV_2 E484Q;L452R;P681R 167;122;143 172;127;148 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. This could be shown for the wild type and mutant forms (D614G, N501Y, and a mix of K417N, E484K, and N501Y) in human HEK293-hACE2 kidney and A549-hACE2-TMPRSS2 lung cells. 2021 Pharmaceuticals (Basel, Switzerland) Abstract SARS_CoV_2 E484K;K417N;N501Y;N501Y;D614G 90;83;63;101;56 95;88;68;106;61 34683466 SARS-CoV-2 Evolution among Oncological Population: In-Depth Virological Analysis of a Clinical Cohort. We identified amino acid changes D614G and P4715L as well as mutations at nucleotide positions 241 and 3037 in all samples. 2021 Microorganisms Abstract SARS_CoV_2 D614G;P4715L 33;43 38;49 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. The most frequently occurring mutation in the 180-amino-acid Nsp1 protein was R24C (n = 1122), followed by D75E (n = 890), D48G (n = 881), H110Y (n = 860), and D144A (n = 648). 2021 Pathogens (Basel, Switzerland) Abstract SARS_CoV_2 D144A;D48G;D75E;H110Y;R24C 160;123;107;139;78 165;127;111;144;82 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. Here, the blood coagulation effect is tested after exposure to Spike protein in nanoparticles and Spike variant D614G in viral vectors and the results are corroborated using live SARS-CoV-2. 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Abstract SARS_CoV_2 D614G 112 117 S;S 63;98 68;103 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. FINDINGS: We tested seven currently circulating viral variants of concern/interest, including the three Iota sublineages, Alpha (E484K), Beta, Delta and Lambda in neutralization assays. 2021 EBioMedicine Abstract SARS_CoV_2 E484K 129 134 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. The reduction was stronger against a sub-variant of Lambda, followed by Beta and Alpha (E484K). 2021 EBioMedicine Abstract SARS_CoV_2 E484K 88 93 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. Prior infection significantly boosts spike-binding antibodies, antibody-dependent cellular cytotoxicity, and neutralizing antibodies against D614G, Beta, and Delta; however, neutralization cross-reactivity varied by wave. 2021 Cell host & microbe Abstract SARS_CoV_2 D614G 141 146 S 37 42 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. We compared participants who were SARS-CoV-2 naive with those either infected with the ancestral D614G virus or infected in the second wave when Beta predominated. 2021 Cell host & microbe Abstract SARS_CoV_2 D614G 97 102 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. Further, a novel mutation NSP13:G206F mapping to NSP13 region was observed from wastewater. 2022 The Science of the total environment Abstract SARS_CoV_2 G206F 32 37 Nsp13;Nsp13 26;49 31;54 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. Notably, S:P1140del mutation was detected in December 2020 samples while it was reported in February 2021 from clinical data, indicating the instrumentality of wastewater data in early detection. 2022 The Science of the total environment Abstract SARS_CoV_2 P1140del 10 19 S 9 10 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. The study also revealed four mutations; S:N801, S:C480R, NSP14:C279F and NSP3:L550del not currently reported from wastewater or clinical data in India but reported worldwide. 2022 The Science of the total environment Abstract SARS_CoV_2 C279F;C480R;L550del 63;50;78 68;55;85 Nsp3;S;S 73;40;48 77;41;49 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. FINDINGS: Our results reveal that B.1.1.7 and other N501Y-carrying variants but not WT SARS-CoV-2 can infect wildtype mice. 2021 EBioMedicine Abstract SARS_CoV_2 N501Y 52 57 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. INTERPRETATION: Our study provides direct evidence that the SARS-CoV-2 variant, B.1.1.7, as well as other N501Y-carrying variants including B.1.351 and P.3, has gained the capability to expand species tropism to murines and public health measures including stringent murine control should be implemented to facilitate the control of the ongoing pandemic. 2021 EBioMedicine Abstract SARS_CoV_2 N501Y 106 111 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. Although we can't conclude the properties of all the mutants including N501Y thoroughly, it merits focusing on their spread epidemically and biologically. 2021 Frontiers in microbiology Abstract SARS_CoV_2 N501Y 71 76 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. Besides the well known substitutions of L452R, P681R and deletions of E156 and F157, as well as the potential biological significance, structural analysis in this study still indicated that new amino acid changes in B.1.617, such as E484Q and N501Y, had reshaped the viral bonding network, and increasingly sequenced N501Y mutant with a potential enhanced binding ability was detected in many other countries in the follow-up monitoring. 2021 Frontiers in microbiology Abstract SARS_CoV_2 E484Q;L452R;N501Y;N501Y;P681R 233;40;243;317;47 238;45;248;322;52 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. E484K and N501Y result in gain-of-function with two different outcomes: The N501Y confers a ten-fold affinity increase towards ACE-2, but a modest antibody evasion potential of plasma from convalescent or vaccinated individuals, whereas the E484K displays a significant antibody evasion capacity without a major impact on affinity. 2021 Frontiers in immunology Abstract SARS_CoV_2 E484K;N501Y;N501Y;E484K 241;10;76;0 246;15;81;5 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. On the other hand, the two different 417 substitutions severely impair the RBD/ACE-2 affinity, but in the combined P.1 and B.1.351 RBD variants, this effect is partly counterbalanced by the effect of the E484K and N501Y. 2021 Frontiers in immunology Abstract SARS_CoV_2 E484K;N501Y 204;214 209;219 RBD;RBD 75;131 78;134 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. The same three positions in the receptor-binding domain (RBD) are affected in both variants, but where the 417 substitution differs, the E484K/N501Y have co-evolved by convergent evolution. 2021 Frontiers in immunology Abstract SARS_CoV_2 E484K;N501Y 137;143 142;148 RBD 57 60 34693968 Anti-Severe Acute Respiratory Syndrome Coronavirus 2 Hyperimmune Immunoglobulin Demonstrates Potent Neutralization and Antibody-Dependent Cellular Cytotoxicity and Phagocytosis Through N and S Proteins. METHODS: Functional characterization of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hyperimmune immunoglobulin (hIG) from human convalescent plasma was performed by different virus neutralization methodologies (plaque reduction, virus-induced cytotoxicity, median tissue culture infectious dose [TCID50] reduction, and immunofluorimetry) at different laboratories using geographically different SARS-CoV-2 isolates (USA [1], Italy [1], and Spain [2]; 2 containing the D614G mutation). 2022 The Journal of infectious diseases Abstract SARS_CoV_2 D614G 490 495 COVID-19 40 92 34693968 Anti-Severe Acute Respiratory Syndrome Coronavirus 2 Hyperimmune Immunoglobulin Demonstrates Potent Neutralization and Antibody-Dependent Cellular Cytotoxicity and Phagocytosis Through N and S Proteins. Neutralization capacity against the original Wuhan SARS-CoV-2 strain and variants (D614G mutant, B.1.1.7, P.1, and B.1.351) was evaluated using a pseudovirus expressing the corresponding spike (S) protein. 2022 The Journal of infectious diseases Abstract SARS_CoV_2 D614G 83 88 S;S 187;194 192;195 34695371 Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data. 151 (97%) of 156 had the Asp614Gly mutation in the spike protein. 2021 The Lancet. Global health Abstract SARS_CoV_2 D614G 25 34 S 51 56 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure, indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation (G8371T in ORF1ab) of this cluster. 2021 Genomics, proteomics & bioinformatics Abstract SARS_CoV_2 G8371T 284 290 ORF1ab 294 300 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. In the case of prolonged infections' mutations (long-term SARS-CoV-2 infections), V483A (0.009%) was found to be dominant followed by Q493R (0.009%), while other mutations were found in less than 0.007% of the studied sequences. 2021 Viruses Abstract SARS_CoV_2 Q493R;V483A 134;82 139;87 COVID-19 58 79 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Irrespective of the geographical region, in the case of the adaptive mutations, N501Y (48.38%) was found to be the dominant mutation followed by L452R (17.52%), T478K (14.31%), E484K (4.69%), S477N (3.29%), K417T (1.64%), N439K (0.7%) and S494P (0.7%). 2021 Viruses Abstract SARS_CoV_2 E484K;K417T;L452R;N439K;N501Y;S477N;S494P;T478K 177;207;145;222;80;192;239;161 182;212;150;227;85;197;244;166 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Since the last two months, there has been a massive increase of L452R and T478K mutations (delta variant) in certain areas. 2021 Viruses Abstract SARS_CoV_2 L452R;T478K 64;74 69;79 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. Mutation K417N was detected only in three samples. 2021 Viruses Abstract SARS_CoV_2 K417N 9 14 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. The relative proportion of N501Y positive virus samples increased continually to 68% of weekly samples. 2021 Viruses Abstract SARS_CoV_2 N501Y 27 32 34696495 High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses. The clade for pangolin lineage B that contains certain distant variants, including P4715L in ORF1ab, Q57H in ORF3a, and S84L in ORF8 covarying with the D614G spike protein mutation, were the most prevalent early in the pandemic in Georgia, USA. 2021 Viruses Abstract SARS_CoV_2 D614G;P4715L;Q57H;S84L 152;83;101;120 157;89;105;124 ORF1ab;S;ORF3a;ORF8 93;158;109;128 99;163;114;132 34696839 HCV RdRp, sofosbuvir and beyond. The ternary crystal structure of HCV RdRp, primer/template, and incoming nucleotide showed the interaction between the nucleotide analog and the 2'-hydroxyl binding pocket and how an unfit mutation of serine 282 to threonine results in resistance by interacting with the uracil base and modified 2'-position of the analog. 2021 The Enzymes Abstract SARS_CoV_2 S282T 201 224 RdRP 37 41 34698407 SARS-CoV-2 variant with mutations in N gene affecting detection by widely used PCR primers. Mutations in the N gene causing diagnostic resistance and on the other hand E484K mutation in the causing altered infectivity warrants careful inspection on virus variants that might get underdiagnosed. 2021 Journal of medical virology Abstract SARS_CoV_2 E484K 76 81 N 17 18 34698407 SARS-CoV-2 variant with mutations in N gene affecting detection by widely used PCR primers. This strain shares with the Beta variant the S gene E484K mutation linked to impaired vaccine protection, but differs from this variant in several other ways, for example by deletions in the N gene region. 2021 Journal of medical virology Abstract SARS_CoV_2 E484K 52 57 N;S 191;45 192;46 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Finally, we predicted that the yet-to-be-identified hypothetical N439S, T478S, and N501K mutations could confer an even greater binding affinity to hACE2 and evade host immune surveillance more efficiently than the respective native variants. 2021 mBio Abstract SARS_CoV_2 N439S;N501K;T478S 65;83;72 70;88;77 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Through in silico protein structure prediction and immunoinformatics tools, we discovered D614G is the key determinant to S protein conformational change, while variations of N439K, T478I, E484K, and N501Y in S1-RBD also had an impact on S protein binding affinity to hACE2 and antigenicity. 2021 mBio Abstract SARS_CoV_2 D614G;E484K;N439K;N501Y;T478I 90;189;175;200;182 95;194;180;205;187 RBD;S;S 212;122;238 215;123;239 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. In June 2021 all variants carried the D614G amino acid substitution. 2021 Scientific reports Abstract SARS_CoV_2 D614G 38 43 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. Until April 2020, variants carrying the crucial Europe-associated D614G amino acid change were predominantly found in Senegal and Gambia, and combinations of late variants with and early variants without D614G in Ghana and Nigeria. 2021 Scientific reports Abstract SARS_CoV_2 D614G;D614G 66;204 71;209 34704098 SARS-CoV-2 variants associated with vaccine breakthrough in the Delaware Valley through summer 2021. Viral point substitutions could also be associated with vaccine breakthroughs, notably the N501Y substitution found in the alpha, beta and gamma variants (odds ratio 2.04; 95% credible interval of 1.25-3.18). 2021 medRxiv Abstract SARS_CoV_2 N501Y 91 96 34705425 Gold-Nanostar-Chitosan-Mediated Delivery of SARS-CoV-2 DNA Vaccine for Respiratory Mucosal Immunization: Development and Proof-of-Principle. The immune response to IN delivery of this SC2-spike DNA vaccine transported on a modified gold-chitosan nanocarrier shows a strong and consistent surge in antibodies (IgG, IgA, and IgM) and effective neutralization of pseudoviruses expressing S proteins of different SC2 variants (Wuhan, beta, and D614G). 2021 ACS nano Abstract SARS_CoV_2 D614G 299 304 S;S 47;244 52;245 34717972 Allosteric Regulation of 3CL Protease of SARS-CoV-2 and SARS-CoV Observed in the Crystal Structure Ensemble. The T285A mutation from SARS-CoV 3CLpro to SARS-CoV-2 3CLpro significantly closes the interface of the domain III dimer and allosterically stabilizes the active conformation of the C-loop via hydrogen bonds with Ser1 and Gly2; thus, SARS-CoV-2 3CLpro seems to have increased activity relative to that of SARS-CoV 3CLpro. 2021 Journal of molecular biology Abstract SARS_CoV_2 T285A 4 9 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. Analysis of the intermolecular interactions revealed that T27A (ACE2), G476S (receptor-binding domain [RBD] of the spike protein), C297T (TMPRSS2), and P812S (cleavage site for TMPRSS2) coding variants may render resistance in viral infection, whereas Q493L (RBD), S477I (RBD), P681R (cleavage site for FURIN), and P683W (cleavage site for FURIN) may lead to increase viral infection. 2021 Bioinformatics and biology insights Abstract SARS_CoV_2 G476S;Q493L;S477I 71;252;265 76;257;270 S;RBD;RBD;RBD 115;103;259;272 120;106;262;275 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Here, with a vesicular stomatitis virus (VSV)-based pseudotype system, we demonstrated that the pseudovirus bearing N501Y.V2 S protein has higher infection efficiency than pseudovirus with wildtype (WT) and D614G S protein. 2021 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 D614G;N501Y 207;116 212;121 S;S 125;213 126;214 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. However, the pseudovirus bearing N501Y.V1 or N501Y.V2 S protein has similar sensitivity to inhibitors of protease and endocytosis with WT and D614G. 2021 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 D614G;N501Y;N501Y 142;33;45 147;38;50 S 54 55 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Moreover, pseudovirus with N501Y.V1 or N501Y.V2 S protein has better thermal stability than WT and D614G, suggesting these mutations of variants may increase the stability of SARS-CoV-2 S protein and virion. 2021 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 D614G;N501Y;N501Y 99;27;39 104;32;44 S;S 48;186 49;187 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. The newly emerging variants N501Y.V1 (B.1.1.7) and N501Y.V2 (B.1.351), first reported in the United Kingdom and South Africa respectively, raised concerns due to the unusually rapid global spread. 2021 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 N501Y;N501Y 28;51 33;56 34723159 Partial resistance of SARS-CoV-2 Delta variants to vaccine-elicited antibodies and convalescent sera. Highly transmissible SARS-CoV-2 variants identified in India and designated B.1.617, Kappa (B.1.617.1), Delta (B.1.617.2), B.1.618, and B.1.36.29 contain spike mutations L452R, T478K, E484K, E484Q, and N440K located within the spike receptor-binding domain and thus could contribute to increased transmissibility and potentially allow re-infection or cause resistance to vaccine-elicited antibody. 2021 iScience Abstract SARS_CoV_2 E484K;E484Q;L452R;N440K;T478K 184;191;170;202;177 189;196;175;207;182 S;S 154;227 159;232 34723159 Partial resistance of SARS-CoV-2 Delta variants to vaccine-elicited antibodies and convalescent sera. Neutralization resistance to serum antibodies and monoclonal antibodies was mediated by L452R mutation. 2021 iScience Abstract SARS_CoV_2 L452R 88 93 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. In this study, we compared African green monkeys infected intranasally with either the UK B.1.1.7 (Alpha) variant or its contemporary D614G progenitor. 2021 Emerging microbes & infections Abstract SARS_CoV_2 D614G 134 139 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Interestingly, D614G infected animals showed significantly higher levels of viral RNA and infectious virus in rectal swabs and gastrointestinal tissues. 2021 Emerging microbes & infections Abstract SARS_CoV_2 D614G 15 20 34725366 Association between prognostic factors and the outcomes of patients infected with SARS-CoV-2 harboring multiple spike protein mutations. Besides the D614G mutation, we found L5F (18.8%), V213A (18.8%), and S689R (8.3%). 2021 Scientific reports Abstract SARS_CoV_2 D614G;L5F;S689R;V213A 12;37;69;50 17;40;74;55 34726473 A broadly cross-reactive antibody neutralizes and protects against sarbecovirus challenge in mice. Here, we demonstrate the neutralization of SARS-CoV; bat coronaviruses WIV-1 and RsSHC014; and SARS-CoV-2 variants D614G, B.1.1.7, B.1.351, P.1, B.1.429, B.1.526, B.1.617.1, and B.1.617.2 by a receptor binding domain (RBD)-specific human antibody, DH1047. 2022 Science translational medicine Abstract SARS_CoV_2 D614G 115 120 RBD;RBD 193;218 216;221 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Furthermore, in the beta variant, two significant rare non-synonymous spike mutations (A879S and K444R) were also reported. 2021 Journal of medical virology Abstract SARS_CoV_2 K444R;A879S 97;87 102;92 S 70 75 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Notably, two rare mutations (E484Q and L5F) were found in the delta variant. 2021 Journal of medical virology Abstract SARS_CoV_2 L5F;E484Q 39;29 42;34 34728625 Potent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants. Surprisingly, structural analysis has revealed that 58G6 and 13G9 both recognize the steric region S470-495 on the RBD, overlapping the E484K mutation presented in B.1.351. 2021 Nature communications Abstract SARS_CoV_2 E484K 136 141 RBD 115 118 34729465 The impact of viral mutations on recognition by SARS-CoV-2 specific T cells. Complete loss of T cell responsiveness was seen due to Q213K in the A*01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B*27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A*03:01/A*11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. 2021 iScience Abstract SARS_CoV_2 P13L;P13S;P13T;P365S;Q213K;T362I 131;137;147;240;55;230 135;141;151;245;60;235 N;N;ORF3a 183;285;92 195;297;97 34729560 A humanized nanobody phage display library yields potent binders of SARS CoV-2 spike. Molecular dynamics simulations provide a structural basis for understanding the neutralization process of nanobodies exclusively focused on the spike-ACE2 interface with and without the N501Y mutation on RBD. 2022 bioRxiv Abstract SARS_CoV_2 N501Y 186 191 S;RBD 144;204 149;207 34729560 A humanized nanobody phage display library yields potent binders of SARS CoV-2 spike. The most potent nanobody, RBD-1-2G(NCATS-BL8125), tolerates the N501Y RBD mutation and remains capable of neutralizing the B.1.1.7 (Alpha) variant. 2022 bioRxiv Abstract SARS_CoV_2 N501Y 64 69 RBD;RBD 26;70 29;73 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. From 720 SARS-CoV-2 genome sequences, we found few sites under positive selection pressure, such as the D614G (98.5 %) in the spike, that has replaced the old variant; the V1167F in the spike (41 %), identified in the P.2 variant that emerged from Brazil during the period of analysis; and I292T (39 %) in the N protein. 2021 Microbial genomics Abstract SARS_CoV_2 D614G;I292T;V1167F 104;290;172 109;295;178 S;S;N 126;186;310 131;191;311 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. Binding assay and pseudovirus neutralization assay show no evasion of recently prevalent SARS-CoV-2 lineages, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2) for n3113.1-Fc with Y58L mutation, demonstrating the potential of n3113.1-Fc (Y58L) as a promising candidate for clinical development to treat COVID-19. 2021 Signal transduction and targeted therapy Abstract SARS_CoV_2 Y58L;Y58L 208;266 212;270 COVID-19 331 339 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. D614G, Q57H, and S194L mutations were correlated with mild and severe outcome with high prevalence. 2021 Frontiers in microbiology Abstract SARS_CoV_2 Q57H;S194L;D614G 7;17;0 11;22;5 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. The mutations associated with asymptomatic outcome were mainly in open reading frame 1ab (ORF1ab) and N genes; especially R6997P and V30L mutations occurred together and were correlated with asymptomatic outcome with high prevalence. 2021 Frontiers in microbiology Abstract SARS_CoV_2 R6997P;V30L 122;133 128;137 ORF1ab;N 90;102 96;103 34735219 Rapid assessment of SARS-CoV-2-evolved variants using virus-like particles. In SC2-VLPs, four nucleocapsid (N) mutations found universally in more-transmissible variants independently increased messenger RNA delivery and expression ~10-fold, and in a reverse genetics model, the serine-202 arginine (S202R) and arginine-203 methionine (R203M) mutations each produced >50 times as much virus. 2021 Science (New York, N.Y.) Abstract SARS_CoV_2 R203M;S202R;R203M;S202R 235;203;260;224 258;222;265;229 N;N 18;32 30;33 34735219 Rapid assessment of SARS-CoV-2-evolved variants using virus-like particles. SC2-VLPs provide a platform for rapid testing of viral variants outside of a biosafety level 3 setting and demonstrate N mutations and particle assembly to be mechanisms that could explain the increased spread of variants, including B.1.617.2 (Delta, which contains the R203M mutation). 2021 Science (New York, N.Y.) Abstract SARS_CoV_2 R203M 270 275 N 119 120 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. Despite maintaining an overall similar structural conformation, our mass spectrometry-based site-specific glycosylation analyses of similarly produced spike proteins with and without the D614G and Alpha variant mutations reveal a significant shift in the processing state of N-glycans on one specific NTD site. 2022 Glycobiology Abstract SARS_CoV_2 D614G 187 192 S;N 151;275 156;276 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. The Alpha variant derived from the D614G lineage is distinguished from others by having deletion mutations located right within an immunogenic supersite of the spike N-terminal domain (NTD) that make it refractory to most neutralizing antibodies directed against this domain. 2022 Glycobiology Abstract SARS_CoV_2 D614G 35 40 S;N 160;166 165;167 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Clustering results suggested that a proportion of people (2.46%) was infected with a distinct subtype of the B.1.1.7 variant, which contained four to six additional mutations (G28881A, G28882A, G28883S, A23403G, A28095T, G25437T). 2021 Computers in biology and medicine Abstract SARS_CoV_2 A23403G;A28095T;G25437T;G28882A;G28883S;G28881A 203;212;221;185;194;176 210;219;228;192;201;183 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. Three (2%) were B.1.526, and 17 (11.3%) have a mutation in D614G. 2021 Infection and drug resistance Abstract SARS_CoV_2 D614G 59 64 34739037 Evaluating the Neutralizing Ability of a CpG-Adjuvanted S-2P Subunit Vaccine Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants of Concern. In humans, vaccinated phase 1 subjects still showed appreciable neutralization abilities against the D614G, Alpha, and Beta variants, although neutralizing titers were significantly reduced against the Beta variant. 2021 Clinical infectious diseases Abstract SARS_CoV_2 D614G 101 106 34739037 Evaluating the Neutralizing Ability of a CpG-Adjuvanted S-2P Subunit Vaccine Against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants of Concern. The neutralizing titers of serum antibodies were assayed with pseudoviruses coated with the SARS-CoV-2 spike protein of the wild-type (WT), D614G, Alpha, or Beta variants. 2021 Clinical infectious diseases Abstract SARS_CoV_2 D614G 140 145 S 103 108 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. The genotypes of three isolates such as Bra/1236/2021 (G15), Bra/MASP2C844R2/2020 (G11), and Bra/RJ-DCVN5/2020 (G9) have a unique mutant in NSP4 (S184N), 2'O-Mutase (R216N), membrane protein (A2V) and Envelope protein (V5A). 2022 Virus research Abstract SARS_CoV_2 A2V;R216N;S184N;V5A 192;166;146;219 195;171;151;222 Membrane;Nsp4 174;140 182;144 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. We found that the combination of mutations K417N, E484K, L452R, and T478K produced higher binding energy to ACE2 than the wild type, suggesting higher efficiency to enter host cells. 2021 Scientific reports Abstract SARS_CoV_2 E484K;K417N;L452R;T478K 50;43;57;68 55;48;62;73 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. While Class I enhances the binding avidity in the presence of N501Y mutation, class II antibodies showed a sharp decline in the binding affinity. 2021 Scientific reports Abstract SARS_CoV_2 N501Y 62 67 34744053 Recruitment for Remote Decentralized Studies in Parkinson's Disease. research participants carrying the LRRK2 G2019S variant with and without PD (n = 277); and AT-HOME PD, a longitudinal study of former phase III clinical trial participants with PD (n = 226). 2022 Journal of Parkinson's disease Abstract SARS_CoV_2 G2019S 41 47 34745450 A spatial multi-scale fluorescence microscopy toolbox discloses entry checkpoints of SARS-CoV-2 variants in Vero E6 cells. Given the cell-entry scenario dominated by the endosomal "late pathway", the faster internalization of B.1.1.7 could be directly related to the N501Y mutation in the S protein, which is known to strengthen the binding of Spike receptor binding domain with ACE2. 2021 Computational and structural biotechnology journal Abstract SARS_CoV_2 N501Y 144 149 RBD;S;S 227;221;166 250;226;167 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. Compared with D614G, the emerging variants exhibited an increased affinity for the receptor, ACE2, and increased ability to infect cells with low ACE2 levels. 2021 iScience Abstract SARS_CoV_2 D614G 14 19 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. We compared the functional properties of spike (S) glycoproteins from the original SARS-CoV-2 strain (D614) (Wuhan, China), the globally dominant D614G strain, and emerging geographic variants: B.1.1.7 (United Kingdom), B.1.351 (South Africa), P.1 (Brazil), and B.1.1.248 (Brazil/Japan). 2021 iScience Abstract SARS_CoV_2 D614G 146 151 S;S 41;48 46;49 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. Of the two viruses that were sequenced and were of the B.1 and B.4 lineages with one carrying the D614G mutation. 2021 PloS one Abstract SARS_CoV_2 D614G 98 103 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. Since the majority of those who were in this underserved settlement were not infected despite circulation of the D614G variant, it would be important to further study environmental and host factors that lead to disease severity and transmission. 2021 PloS one Abstract SARS_CoV_2 D614G 113 118 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Additionally, the Y453F spike exhibited resistance to convalescent serum, posing a risk for vaccine development. 2021 PLoS pathogens Abstract SARS_CoV_2 Y453F 18 23 S 24 29 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. In this study, we found that the Y453F mutation located in the RBD domain of miSARS-CoV-2 is an adaptive mutation that enhances binding to mink ACE2 and other orthologs of Mustela species without compromising, and even enhancing, its ability to utilize human ACE2 as a receptor for entry. 2021 PLoS pathogens Abstract SARS_CoV_2 Y453F 33 38 RBD 63 66 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Structural analysis suggested that despite the similarity in the overall binding mode of SARS-CoV-2 RBD to human and mink ACE2, Y34 of mink ACE2 was better suited to interact with a Phe rather than a Tyr at position 453 of the viral RBD due to less steric clash and tighter hydrophobic-driven interaction. 2021 PLoS pathogens Abstract SARS_CoV_2 Y453F 182 219 RBD;RBD 100;233 103;236 34749522 Structural analysis of SARS-Cov-2 nonstructural protein 1 polymorphisms found in the Brazilian Amazon. However, the NSP1 C-terminal region (residues 145 to 180) was severely affected in the delKSF and R29H mutants. 2021 Experimental biology and medicine (Maywood, N.J.) Abstract SARS_CoV_2 R29H 98 102 34749522 Structural analysis of SARS-Cov-2 nonstructural protein 1 polymorphisms found in the Brazilian Amazon. The delKSF was found in 47 samples, whereas R29H and R43C were found in two samples, one for each mutation. 2021 Experimental biology and medicine (Maywood, N.J.) Abstract SARS_CoV_2 R29H;R43C 44;53 48;57 34749522 Structural analysis of SARS-Cov-2 nonstructural protein 1 polymorphisms found in the Brazilian Amazon. The NSP1 structures carrying the mutations R43C and R29H on the N-terminal portion (e.g. 2021 Experimental biology and medicine (Maywood, N.J.) Abstract SARS_CoV_2 R29H;R43C 52;43 56;47 N 64 65 34749522 Structural analysis of SARS-Cov-2 nonstructural protein 1 polymorphisms found in the Brazilian Amazon. Three mutations were detected in the SARS-CoV-2 NSP1 gene: deletion of the amino acids KSF from positions 141 to 143 (delKSF), SARS-CoV-2, lineage B.1.195; and two substitutions, R29H and R43C, SARS-CoV-2 lineage B.1.1.28 and B.1.1.33, respectively. 2021 Experimental biology and medicine (Maywood, N.J.) Abstract SARS_CoV_2 R29H;R43C 179;188 183;192 34751271 Algorithm for the Quantitation of Variants of Concern for Rationally Designed Vaccines Based on the Isolation of SARS-CoV-2 Hawai'i Lineage B.1.243. The tenth, D614G, has a prevalence >99% and r -value of 0.67. 2021 bioRxiv Abstract SARS_CoV_2 D614G 11 16 34751522 Inadequate design of mutation detection panels prevents interpretation of variants of concern: results of an external quality assessment for SARS-CoV-2 variant detection. For five samples containing the VoC Alpha + E484K, Beta, Gamma, Delta, or B.1.1.318 (as a variant of interest), 848 results for SARS-2-CoV mutation detection were reported, 824 (97.2%, range per sample 88-100%) of which were correct. 2022 Clinical chemistry and laboratory medicine Abstract SARS_CoV_2 E484K 44 49 34753092 RT-qPCR assays for SARS-CoV-2 variants of concern in wastewater reveals compromised vaccination-induced immunity. RT-qPCR assays for the Original (D614G), Alpha and Beta variants had been previously developed and are being employed for wastewater surveillance. 2021 Water research Abstract SARS_CoV_2 D614G 33 38 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. The most frequently mutations occurred at the D614G (87/91), followed by S982A (50/91), and A570D (48/91), respectively. 2022 Gene reports Abstract SARS_CoV_2 A570D;D614G;S982A 92;46;73 97;51;78 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. Twenty-two distinct mutations were identified within the spike protein regions which were: L5F, L18F, T19R, S151T, G181A, A222V, A348S, L452 (Q or M), T478K, N501Y, A520S, A522V, A570D, S605A, D614G, Q675H, N679K, P681H, T716I, S982A, A1020S, D1118H. 2022 Gene reports Abstract SARS_CoV_2 A1020S;A222V;A348S;A520S;A522V;A570D;D1118H;D614G;G181A;L18F;L5F;N501Y;N679K;P681H;Q675H;S151T;S605A;S982A;T19R;T478K;T716I 235;122;129;165;172;179;243;193;115;96;91;158;207;214;200;108;186;228;102;151;221 241;127;134;170;177;184;249;198;120;100;94;163;212;219;205;113;191;233;106;156;226 S 57 62 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Here, we have tried to illustrate a novel direction for future researchers to develop effective therapeutic approaches and counterweight strategies to minimize the spread of COVID-19.Key pointsD614G mutation arises within the S-glycoprotein of significant SARS-CoV-2 variants.The D614G mutation affects infection, re-infection, cleavage patterns of S-glycoprotein, and replication fitness of SARS-CoV-2 variants.The D614G mutation influences the immunity and partial vaccine escape. 2021 Applied microbiology and biotechnology Abstract SARS_CoV_2 D614G;D614G 280;416 285;421 S;S 226;349 240;363 COVID-19 174 182 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The D614G mutation in the S-glycoprotein of SARS-CoV-2 variants has shown the most efficient interaction with the ACE2 receptor of the cells. 2021 Applied microbiology and biotechnology Abstract SARS_CoV_2 D614G 4 9 S 26 40 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. This review will also effectively emphasize the mechanism of action of D614G mutant variants, immune escape, and partial vaccine escape of this virus. 2021 Applied microbiology and biotechnology Abstract SARS_CoV_2 D614G 71 76 34755818 SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil. BACKGROUND: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.33-derived lineage named N.9 was described recently in Brazil and it's considered a potential variant of interest (VOI) due to the presence of E484K substitution at the receptor-binding domain (RBD) of the Spike (S) protein. 2021 Memorias do Instituto Oswaldo Cruz Abstract SARS_CoV_2 E484K 226 231 S;RBD;S 289;277;296 294;280;297 COVID-19 23 63 34755818 SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil. One of them had only the E484K substitution of the six N.9 lineage-defining mutations. 2021 Memorias do Instituto Oswaldo Cruz Abstract SARS_CoV_2 E484K 25 30 34755818 SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil. These four strains are grouped within the B.1.1.33 lineage and basal to the N.9 lineage in our phylogenetic analysis, and we call them "N.9-like/B.1.1.33 + E484K". 2021 Memorias do Instituto Oswaldo Cruz Abstract SARS_CoV_2 E484K 156 161 34756912 RT-qPCR detection of SARS-CoV-2 mutations S 69-70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples. In this work we present a national wastewater survey of the distribution of three SARS-CoV-2 mutations found in the B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma) VoC, namely the S-gene 69-70 deletion, N501Y mutation, and N-gene D3L. 2022 The Science of the total environment Abstract SARS_CoV_2 D3L;N501Y 231;204 234;209 N;S 224;181 225;182 34757622 Neurological pathophysiology of SARS-CoV-2 and pandemic potential RNA viruses: a comparative analysis. We present new insight into key mutations in SARS-CoV-2 variants B.1.1.7 (P681H) and B.1.617.2 (P681R), which may impact on neuropilin 1 (NRP1) binding and CNS invasion. 2021 FEBS letters Abstract SARS_CoV_2 P681H;P681R 74;96 79;101 34757638 Changing predominant SARS-CoV-2 lineages drives successive COVID-19 waves in Malaysia, February 2020 to March 2021. It is due to lineage B.1.524 viruses containing spike mutations D614G and A701V. 2021 Journal of medical virology Abstract SARS_CoV_2 A701V;D614G 74;64 79;69 S 48 53 34758391 SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance. The T135I mutation was also identified in one variant case in which the rapid antigen test and RT-PCR test were discordantly negative and positive, respectively. 2022 International journal of infectious diseases Abstract SARS_CoV_2 T135I 4 9 34758391 SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance. These findings suggest that the variants undetected by the Panbio COVID-19 rapid antigen test may be due to the T135I mutation in the N protein, posing a potential diagnostic risk for commercially available antigen tests. 2022 International journal of infectious diseases Abstract SARS_CoV_2 T135I 112 117 N 134 135 COVID-19 66 74 34758391 SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance. These isolates belonged to the B.1.1.7 variant, exhibiting several amino acid substitutions, including D3L, R203K, G204R, and S235F N protein mutations. 2022 International journal of infectious diseases Abstract SARS_CoV_2 D3L;G204R;R203K;S235F 103;115;108;126 106;120;113;131 N 132 133 34759999 Epidemiology of COVID-19: An updated review. On the other hand, among 14 detected mutations in the SARS-CoV-2 S protein that provide advantages to virus for transmission and evasion form treatment, the D614G mutation (substitution of aspartic acid [D] with glycine [G] in codon 614 was particular which could provide the facilitation of the transmission of the virus and virulence. 2021 Journal of research in medical sciences Abstract SARS_CoV_2 D614G 157 162 S 65 66 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. Of 359 mutations detected, 60.5% of which were non-synonymous, the most frequent were in the ORF1ab (P4715L), S (D614G and A701V) and N (S194L) genes. 2021 PeerJ Abstract SARS_CoV_2 A701V;D614G;P4715L;S194L 123;113;101;137 128;118;107;142 ORF1ab;N;S 93;134;110 99;135;111 34760721 Host Response to SARS-CoV2 and Emerging Variants in Pre-Existing Liver and Gastrointestinal Diseases. The mutations in the spike protein of VOC are implicated for increased receptor binding (N501Y, P681R) and immune escape (L452R, E484K/Q, T478K/R) to host response. 2021 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 E484K;E484Q;P681R;T478K;T478R;L452R;N501Y 129;129;96;138;138;122;89 136;136;101;145;145;127;94 S 21 26 34763050 Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation. Two Gamma lineage consensus sequences presented a new S:D614A mutation. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 D614A 56 61 S 54 55 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. A new B.1.524(G) lineage with S-D614G mutation was detected in Sabah, East Malaysia and Selangor, Peninsular Malaysia on 7th October 2020 and 14th October 2020, respectively. 2021 Scientific reports Abstract SARS_CoV_2 D614G 32 37 S 30 31 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. The new B.1.524(G) carried a set of genetic variations, including A701V (position variant frequency = 0.0007) in Spike protein and a novel G114T mutation at the 5'UTR. 2021 Scientific reports Abstract SARS_CoV_2 A701V;G114T 66;139 71;144 S;5'UTR 113;161 118;166 34766651 SARS-CoV-2 AY.4.2 variant circulating in Italy: Genomic preliminary insight. AY.4.2, a recently detected Delta variant sublineage, is considered a new variant under investigation (VUI) as it carries specific genetic signatures present in the spike protein, called Y145H and A222V. 2022 Journal of medical virology Abstract SARS_CoV_2 A222V;Y145H 197;187 202;192 S 165 170 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. While sharing the N501T mutation which is common in mink, the Utah strains did not share other spike RBD mutations Y453F and F486L found in nearly all mink from the United States. 2021 PLoS pathogens Abstract SARS_CoV_2 F486L;N501T;Y453F 125;18;115 130;23;120 S;RBD 95;101 100;104 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Here we report that ouabain, digitoxin, and digoxin, as well as sugar-free derivatives digitoxigenin and digoxigenin, are high-affinity competitive inhibitors of ACE2 binding to the Original [D614] S1 and the alpha/beta/gamma [D614G] S1 proteins. 2021 Scientific reports Abstract SARS_CoV_2 D614G 227 232 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. These drugs also inhibit ACE2 binding to the Original RBD, as well as to RBD proteins containing the beta [E484K], Mink [Y453F] and alpha/beta/gamma [N501Y] mutations. 2021 Scientific reports Abstract SARS_CoV_2 E484K;N501Y;Y453F 107;150;121 112;155;126 RBD;RBD 54;73 57;76 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. Val35Thr, Ser46Ala, Asn65Ser, Ala94Ser mutations were not included in that analysis, since they are located far from the catalytic tetrad. 2021 International journal of biological macromolecules Abstract SARS_CoV_2 A94S;N65S;S46A;V35T 30;20;10;0 38;28;18;8 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. We previously found that the Val86Leu, Lys88Arg, Phe134His, and Asn180Lys mutations in these enzymes can change the orientation of the N- and C-terminal domains of 3CLpro relative to each other, which leads to a change in catalytic activity. 2021 International journal of biological macromolecules Abstract SARS_CoV_2 N180K;K88R;F134H;V86L 64;39;49;29 73;47;58;37 N 135 136 34780358 Sequencing of SARS-CoV-2 in local transmission cases through Oxford Nanopore MinION platform from Karachi Pakistan. All the isolates belonged to GH clade and shared missense mutation D614G in spike protein linked to increased transmission rate worldwide. 2021 Journal of infection in developing countries Abstract SARS_CoV_2 D614G 67 72 S 76 81 34780358 Sequencing of SARS-CoV-2 in local transmission cases through Oxford Nanopore MinION platform from Karachi Pakistan. Another spike protein mutation A222V coexisted with D614G in the virus from the second wave of COVID-19. 2021 Journal of infection in developing countries Abstract SARS_CoV_2 A222V;D614G 31;52 36;57 S 8 13 COVID-19 95 103 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. The virus responsible had a deletion of nucleotides encoding residues H69 and V70 within the spike protein gene as well as the A22920T mutation, resulting in the Y453F substitution within this protein, seen previously in mink. 2021 PLoS pathogens Abstract SARS_CoV_2 A22920T;Y453F 127;162 134;167 S 93 98 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. In this work, the B.1 + L249S+E484K lineage was isolated along with A.1, B.1.420, and B.1.111 SARS-CoV-2 lineages without the E484K mutation and the neutralizing titer of convalescent sera was compared using microneutralization assays. 2022 Virus research Abstract SARS_CoV_2 E484K;L249S;E484K 126;24;30 131;29;35 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. The E484K mutation at the SARS-CoV-2 Spike protein emerged independently in different variants around the world and has been widely associated with immune escape from neutralizing antibodies generated during previous infection or vaccination. 2022 Virus research Abstract SARS_CoV_2 E484K 4 9 S 37 42 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. This study supports the capability of new variants with the E484K mutation to be resistant to neutralization by humoral immunity, and therefore the need to intensify surveillance programs to determine if these lineages represent a risk for public health. 2022 Virus research Abstract SARS_CoV_2 E484K 60 65 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. While no significant differences in the neutralizing antibody titers were found between A.1 and B.lineages without the E484K mutation, the neutralizing titers against B.1 + L249S+E484K were 1.5, 1.9, 2.1, and 1.3-fold lower than against A.1, B.1.420, B.1.111-I, and B.1.111-II, respectively. 2022 Virus research Abstract SARS_CoV_2 E484K;L249S;E484K 119;173;179 124;178;184 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Moreover, following the N501Y mutation secondary structure and folding of the spike protein changed dramatically. 2022 Journal of cellular biochemistry Abstract SARS_CoV_2 N501Y 24 29 S 78 83 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Our group utilizes computational biology approaches such as immunoinformatics, protein-protein interaction analysis, molecular dynamics, free energy computation, and tertiary structure analysis to disclose the consequences of N501Y mutation at the molecular level. 2022 Journal of cellular biochemistry Abstract SARS_CoV_2 N501Y 226 231 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. There is a lot of focus on RBD mutations, especially the displacement of N501Y which is observed in the UK/Kent, South Africa, and Brazilian lineages of SARS-CoV-2. 2022 Journal of cellular biochemistry Abstract SARS_CoV_2 N501Y 73 78 RBD 27 30 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. Here, we applied the CRISPR-Cas12a system to detect, without the need of sequencing, SARS-CoV-2 genomes harboring the E484K mutation, first identified in the Beta variant and catalogued as an escape mutation. 2021 ACS synthetic biology Abstract SARS_CoV_2 E484K 118 123 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. The E484K mutation creates a canonical protospacer adjacent motif for Cas12a recognition in the resulting DNA amplicon, which was exploited to obtain a differential readout. 2021 ACS synthetic biology Abstract SARS_CoV_2 E484K 4 9 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. We analyzed a series of fecal samples from hospitalized patients in Valencia (Spain), finding one infection with SARS-CoV-2 harboring the E484K mutation, which was then confirmed by sequencing. 2021 ACS synthetic biology Abstract SARS_CoV_2 E484K 138 143 34784198 Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study. A mutation (R167E) was introduced across all three PLpro to study the effect of mutation on the protein-protein binding. 2021 Journal of chemical information and modeling Abstract SARS_CoV_2 R167E 12 17 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. In parallel, we identify organ-specific SARS-CoV-2 genome diversity and mutations of concern N501Y, T1027I, and Y453F, while the patient had died long before reported emergence of VOCs. 2021 Nature communications Abstract SARS_CoV_2 N501Y;T1027I;Y453F 93;100;112 98;106;117 34786352 Gasless laparoendoscopic single-site surgery for management of unruptured tubal pregnancy in a woman with moderate COVID-19 pneumonia after administration of remdesivir and casirivimab-imdevimab: A case report. Real-time reverse transcription-polymerase chain reaction assay detected SARS-CoV-2, which was subsequently identified to be an L452R variant. 2022 Case reports in women's health Abstract SARS_CoV_2 L452R 128 133 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. Our findings support the high level of protection provided by full vaccination despite a steep increase in the prevalence of polymorphisms associated with increased transmission potential (N501Y) and immune evasion (E484K) in the nonvaccinated population. 2021 Microbiology spectrum Abstract SARS_CoV_2 E484K;N501Y 216;189 221;194 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. There was an upward trend from January to April for E484K/Q (3% to 26%) and N501Y (1% to 49%). 2021 Microbiology spectrum Abstract SARS_CoV_2 E484K;E484Q;N501Y 52;52;76 59;59;81 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. VOC screening from 16 fully vaccinated HCPs identified 6 (38%) harboring N501Y and 1 (6%) with E484K polymorphisms; percentage of concurrent nonvaccinated samples was 37% (523/1,404) and 20% (284/1,394), respectively. 2021 Microbiology spectrum Abstract SARS_CoV_2 E484K;N501Y 95;73 100;78 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. Here, we report two single-point mutations in the N gene of SARS-CoV-2 associated with N gene target detection failures in the Cepheid Xpert Xpress SARS-CoV-2 assay, the first a C to T mutation at position 29197, found in five patients, and the second a C to T mutation at position 29200, found in eight patients. 2021 Microbiology spectrum Abstract SARS_CoV_2 C29197T;C29200T 178;254 211;287 N;N 50;87 51;88 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. Our results indicated that the CRISPR-Cas12a assay could readily detect the signature spike protein mutations (K417N/T, L452R/Q, T478K, E484K/Q, N501Y, and D614G) to distinguish alpha, beta, gamma, delta, kappa, lambda, and epsilon variants of SARS-CoV-2. 2021 Microbiology spectrum Abstract SARS_CoV_2 D614G;E484K;E484Q;L452Q;L452R;N501Y;T478K;K417N;K417T 156;136;136;120;120;145;129;111;111 161;143;143;127;127;150;134;118;118 S 86 91 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. Using the nucleic acid sequence of a SARS-CoV-2 nonvariant and a synthetic SARS-CoV-2 variant-carrying plasmid, a matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) method based on the single-base mass probe extension of multiplex PCR amplification products was established to detect 9 mutation types in 7 mutated sites (HV6970del, N501Y, K417N, P681H, D614G, E484K, L452R, E484Q, and P681R) in the receptor-binding domain of the spike protein of SARS-CoV-2 variants. 2021 Microbiology spectrum Abstract SARS_CoV_2 D614G;E484K;E484Q;K417N;L452R;N501Y;P681H;P681R;HV6970del 394;401;415;380;408;373;387;426;362 399;406;420;385;413;378;392;431;371 S 471 476 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. Additionally, a new mutation (E661D) in the spike (S) protein has been identified in nearly 10% of the genomes classified as the VOC Gamma from Parana in March and April 2021.Finally, we analyzed the correlation between the lineage and the Gamma variant frequency, age group (patients younger or older than 60 years old) and the clinical data of 86 cases from the state of Parana. 2021 Virology journal Abstract SARS_CoV_2 E661D 30 35 S;S 44;51 49;52 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. CONCLUSIONS: Our results provided a reliable picture of the evolution of the SARS-CoV-2 pandemic in the state of Parana characterized by the dominance of the Gamma strain, as well as a high frequencies of the Gamma-like-II lineage and the S:E661D mutation. 2021 Virology journal Abstract SARS_CoV_2 E661D 241 246 S 239 240 34790342 On the association between SARS-COV-2 variants and COVID-19 mortality during the second wave of the pandemic in Europe. The average proportion of EU2 variant (S:477 N) was a significant predictor of cumulative COVID-19 deaths in the pre-peak period. 2021 Journal of market access & health policy Abstract SARS_CoV_2 S477N 39 46 S 39 40 COVID-19 90 98 34790979 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Here, using single-molecule Forster resonance energy transfer (smFRET) imaging we report the effects of ACE2 and antibody binding on the conformational dynamics of S from the Wuhan-1 strain and the B.1 variant (D614G). 2021 bioRxiv Abstract SARS_CoV_2 D614G 211 216 S 164 165 34790979 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. We find that D614G modulates the energetics of the RBD position in a manner similar to ACE2 binding. 2021 bioRxiv Abstract SARS_CoV_2 D614G 13 18 RBD 51 54 34790980 SARS-COV-2 Delta variant displays moderate resistance to neutralizing antibodies and spike protein properties of higher soluble ACE2 sensitivity, enhanced cleavage and fusogenic activity. Against AY.1 pseudoviruses, the L452R and K417N substitutions accounted for the loss of neutralization by four antibodies and one antibody, respectively, whereas one antibody lost potency that could not be fully accounted for by a single RBD substitution. 2021 bioRxiv Abstract SARS_CoV_2 K417N;L452R 42;32 47;37 RBD 238 241 34790980 SARS-COV-2 Delta variant displays moderate resistance to neutralizing antibodies and spike protein properties of higher soluble ACE2 sensitivity, enhanced cleavage and fusogenic activity. Finally, the spike proteins of B.1.617 variants are more efficiently cleaved due to the P681R substitution, and the spike of Delta variants exhibited greater sensitivity to soluble ACE2 neutralization, as well as fusogenic activity, which may contribute to enhanced spread of Delta variants. 2021 bioRxiv Abstract SARS_CoV_2 P681R 88 93 S;S 13;116 18;121 34790980 SARS-COV-2 Delta variant displays moderate resistance to neutralizing antibodies and spike protein properties of higher soluble ACE2 sensitivity, enhanced cleavage and fusogenic activity. Four of twenty-three therapeutic neutralizing antibodies showed either complete or partial loss of neutralization against B.1.617.2 pseudoviruses due to the L452R substitution, whereas six of twenty-three therapeutic neutralizing antibodies showed either complete or partial loss of neutralization against B.1.617.1 pseudoviruses due to either the E484Q or L452R substitution. 2021 bioRxiv Abstract SARS_CoV_2 E484Q;L452R;L452R 348;157;357 353;162;362 34790980 SARS-COV-2 Delta variant displays moderate resistance to neutralizing antibodies and spike protein properties of higher soluble ACE2 sensitivity, enhanced cleavage and fusogenic activity. The spike proteins of B.1.617.1, B.1.617.2, and AY.1 variants have several substitutions in the receptor binding domain (RBD), including L452R+E484Q, L452R+T478K, and K417N+L452R+T478K, respectively, that could potentially reduce effectiveness of therapeutic antibodies and current vaccines. 2021 bioRxiv Abstract SARS_CoV_2 K417N;L452R;L452R;E484Q;L452R;T478K;T478K 167;137;150;143;173;156;179 172;142;155;148;178;161;184 RBD;S;RBD 96;4;121 119;9;124 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Interestingly, this beneficial Asp17Leu mutation is present in the N-terminal caps of three of the five DARPin domains of ensovibep, a SARS-CoV-2 entry inhibitor currently in clinical development, indicating this mutation could be partly responsible for the very high melting temperature (>90C) of this promising anti-COVID-19 drug. 2022 The Journal of biological chemistry Abstract SARS_CoV_2 D17L 31 39 N 67 68 COVID-19 318 326 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Molecular dynamics simulations showed that the Asp17Leu mutation reduces electrostatic repulsion and improves van-der-Waals packing, rendering the DARPin domain less flexible and more stable. 2022 The Journal of biological chemistry Abstract SARS_CoV_2 D17L 47 55 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. We then transferred the Asp17Leu mutation to various backgrounds, including clinically validated DARPin domains, such as the vascular endothelial growth factor-binding domain of the DARPin abicipar pegol. 2022 The Journal of biological chemistry Abstract SARS_CoV_2 D17L 24 32 34794434 SARS-CoV-2 exposure in Malawian blood donors: an analysis of seroprevalence and variant dynamics between January 2020 and July 2021. In a subset, we also assessed in vitro neutralisation against the original variant (D614G WT) and the Beta variant. 2021 BMC medicine Abstract SARS_CoV_2 D614G 84 89 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. Recently, SARS-CoV-2 delta variant prevails over different countries that have 3 unique mutation sites: E156del/R158G in the N-terminal domain and T478K in a crucial receptor binding domain. 2021 Immune network Abstract SARS_CoV_2 T478K;R158G 147;112 152;117 RBD;N 166;125 189;126 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Complete genome sequencing of these cases allowed us to identify E484K mutation in association with Gamma VOC and other lineages. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 E484K 65 70 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. In addition to the Gamma VOC, other isolates carrying the mutation E484K were also detected. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 E484K 67 72 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. The frequency of this mutation has been increasing worldwide, as shown in a survey of sequences carrying E484K mutation in GISAID, and was detected in Venezuela in many probable cases of reinfection. 2021 Infection, genetics and evolution Abstract SARS_CoV_2 E484K 105 110 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Within the furin cleavage site of the spike protein, a high degree of conservation was observed, but the P681H mutation was observed in 10.47% of sequences analyzed. 2022 Infection, genetics and evolution Abstract SARS_CoV_2 P681H 105 110 S 38 43 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. This article highlights the pressures that facilitate the rise of new SARS-CoV-2 variants and the key mutations of the viral spike protein - L452R, E484K, N501Y and D614G- that promote immune escape mechanism and warrant a cautionary point for clinical and public health responses in terms of re-infection, vaccine breakthrough infection and therapeutic values. 2021 Frontiers in immunology Abstract SARS_CoV_2 D614G;E484K;L452R;N501Y 165;148;141;155 170;153;146;160 S 125 130 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. Here, a 2.0 A resolution room-temperature X-ray crystal structure is reported of a Michaelis-like complex of Mpro harboring a single inactivating mutation C145A bound to the octapeptide Ac-SAVLQSGF-CONH2 corresponding to the nsp4/nsp5 autocleavage site. 2021 IUCrJ Abstract SARS_CoV_2 C145A 155 160 Nsp4;Nsp5 225;230 229;234 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. Notably, each RBD mutation acted like a positive allosteric modulator; nevertheless, K417N was shown to have the largest effects among all of the mutations on the allostery and thereby holds the highest binding affinity with ACE2. 2021 ACS omega Abstract SARS_CoV_2 K417N 85 90 RBD 14 17 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. To address this question, here we have individually assessed the effects of SARS-CoV-2 variant-specific spike (S) protein receptor-binding domain (RBD) mutations E484K, K417N, L452Q, L452R, N501Y, and T478K that characterize and differentiate several emerging variants. 2021 ACS omega Abstract SARS_CoV_2 E484K;K417N;L452Q;L452R;N501Y;T478K 162;169;176;183;190;201 167;174;181;188;195;206 S;RBD;S 104;147;111 109;150;112 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Extensive molecular dynamics simulations of D614G mutant spike structure with hACE2 further revealed dynamic features with 47.7% of mutations mapping on flexible regions of spike protein. 2021 Current research in structural biology Abstract SARS_CoV_2 D614G 44 49 S;S 57;173 62;178 34806722 Mechanistic insights into the effects of key mutations on SARS-CoV-2 RBD-ACE2 binding. In this study, we provide atomic-level insights into the binding of the receptor binding domain (RBD) of the wild-type SARS-CoV-2 spike protein and its single (N501Y), double (E484Q, L452R) and triple (N501Y, E484Q, L452R) mutated variants to the human ACE2 receptor. 2021 Physical chemistry chemical physics Abstract SARS_CoV_2 E484Q;L452R;L452R;E484Q;N501Y;N501Y 209;183;216;176;160;202 214;188;221;181;165;207 RBD;S;RBD 72;130;97 95;135;100 34806722 Mechanistic insights into the effects of key mutations on SARS-CoV-2 RBD-ACE2 binding. We find higher binding affinities for the double (E484Q, L452R) and triple (N501Y, E484Q, L452R) mutated variants than for the wild type and the N501Y variant, which could contribute to the higher transmissibility of recent variants containing these mutations. 2021 Physical chemistry chemical physics Abstract SARS_CoV_2 E484Q;L452R;L452R;N501Y;E484Q;N501Y 83;57;90;145;50;76 88;62;95;150;55;81 34806876 N501Y and K417N Mutations in the Spike Protein of SARS-CoV-2 Alter the Interactions with Both hACE2 and Human-Derived Antibody: A Free Energy of Perturbation Retrospective Study. However, Lys417Asn seems to have a compensatory mechanism of action increasing the S1 RBD-ACE2 free energy of binding. 2021 Journal of chemical information and modeling Abstract SARS_CoV_2 K417N 9 18 RBD 86 89 34806876 N501Y and K417N Mutations in the Spike Protein of SARS-CoV-2 Alter the Interactions with Both hACE2 and Human-Derived Antibody: A Free Energy of Perturbation Retrospective Study. The K417N mutation in a combination with N501Y fully abolished the antibody effect. 2021 Journal of chemical information and modeling Abstract SARS_CoV_2 K417N;N501Y 4;41 9;46 34806876 N501Y and K417N Mutations in the Spike Protein of SARS-CoV-2 Alter the Interactions with Both hACE2 and Human-Derived Antibody: A Free Energy of Perturbation Retrospective Study. The N501Y and K417N mutations in the spike protein of SARS-CoV-2 and their combination gave rise to questions, but the data on their mechanism of action at the molecular level were limited. 2021 Journal of chemical information and modeling Abstract SARS_CoV_2 K417N;N501Y 14;4 19;9 S 37 42 34809492 Functional Antibodies Against SARS-CoV-2 Receptor Binding Domain Variants with Mutations N501Y or E484K in Human Milk from COVID-19-Vaccinated, -Recovered, and -Unvaccinated Women. Results: The titers of human milk IgG against N501Y were higher in the COVID-19 vaccine group than in the no-vaccine group but comparable with the COVID-19 PCR group. 2022 Breastfeeding medicine Abstract SARS_CoV_2 N501Y 46 51 COVID-19;COVID-19 71;147 79;155 34809492 Functional Antibodies Against SARS-CoV-2 Receptor Binding Domain Variants with Mutations N501Y or E484K in Human Milk from COVID-19-Vaccinated, -Recovered, and -Unvaccinated Women. The titers and NAbs of secretory IgA (SIgA)/IgA, secretory IgM (IgM)/IgM, and IgG against SARS-CoV-2 RBD with mutations N501Y or E484K were measured by using ELISA and a surrogate virus neutralization assay. 2022 Breastfeeding medicine Abstract SARS_CoV_2 E484K;N501Y 129;120 134;125 RBD 101 104 34809492 Functional Antibodies Against SARS-CoV-2 Receptor Binding Domain Variants with Mutations N501Y or E484K in Human Milk from COVID-19-Vaccinated, -Recovered, and -Unvaccinated Women. The titers of SIgM/IgM and the inhibition of NAbs were higher against the mutation E484K than N501Y. 2022 Breastfeeding medicine Abstract SARS_CoV_2 E484K;N501Y 83;94 88;99 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. Conversely, D3L, L5F, and S97I were found to largely increase the structural stability of the corresponding proteins. 2021 Informatics in medicine unlocked Abstract SARS_CoV_2 D3L;L5F;S97I 12;17;26 15;20;30 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. D1118H, S194L, R262H, M809L, P314L, A8D, S220G, A890D, G1433C, T1456I, R233C, F263S, L111K, A54T, A74V, L183A, A316T, V212F, L46C, V48G, Q57H, W131R, G172V, Q185H, and Y206S missense mutations were found to largely decrease the structural stability of the corresponding proteins. 2021 Informatics in medicine unlocked Abstract SARS_CoV_2 A316T;A54T;A74V;A890D;A8D;F263S;G1433C;G172V;L111K;L183A;L46C;M809L;P314L;Q185H;Q57H;R233C;R262H;S194L;S220G;T1456I;V212F;V48G;W131R;Y206S;D1118H 111;92;98;48;36;78;55;150;85;104;125;22;29;157;137;71;15;8;41;63;118;131;143;168;0 116;96;102;53;39;83;61;155;90;109;129;27;34;162;141;76;20;13;46;69;123;135;148;173;6 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. D416G, F106F, P314L, UTR:C241T, L93L, A222V, A199A, V30L, and A220V mutations were found as the most frequent mutations. 2021 Informatics in medicine unlocked Abstract SARS_CoV_2 A199A;A220V;A222V;F106F;L93L;P314L;V30L;C241T;D416G 45;62;38;7;32;14;52;25;0 50;67;43;12;36;19;56;30;5 34816264 Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro. Analysis of the 2.14 A resolution crystal structure of 3CLpro C145S bound to NEMO 226-235 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. 2021 bioRxiv : the preprint server for biology Abstract SARS_CoV_2 C145S 62 67 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. Unlike other natural cysteine variants, a Cys15Phe (C15F) mutant retained partial, but unstable, infectivity. 2022 Journal of virology Abstract SARS_CoV_2 C15F;C15F 42;52 50;56 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Single mutation analysis revealed that this reduction in neutralization was caused by L452Q and F490S mutations. 2022 Emerging microbes & infections Abstract SARS_CoV_2 F490S;L452Q 96;86 101;91 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. The variant harbours two mutations in the receptor binding domain, L452Q and F490S, which may change its infectivity and antigenicity to neutralizing antibodies. 2022 Emerging microbes & infections Abstract SARS_CoV_2 F490S;L452Q 77;67 82;72 RBD 42 65 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. We found that compared with the D614G reference strain, Lambda demonstrated enhanced infectivity of Calu-3 and LLC-MK2 cells by 3.3-fold and 1.6-fold, respectively. 2022 Emerging microbes & infections Abstract SARS_CoV_2 D614G 32 37 34818667 The N501Y spike substitution enhances SARS-CoV-2 infection and transmission. As suggested by its convergent evolution in Brazil, South Africa and elsewhere2,3, our results indicate that N501Y substitution is an adaptive spike mutation of major concern. 2022 Nature Abstract SARS_CoV_2 N501Y 109 114 S 143 148 34818667 The N501Y spike substitution enhances SARS-CoV-2 infection and transmission. Here, using a reverse genetics approach, we show that of the 8 individual spike protein substitutions, only N501Y resulted in consistent fitness gains for replication in the upper airway in a hamster model as well as in primary human airway epithelial cells. 2022 Nature Abstract SARS_CoV_2 N501Y 108 113 S 74 79 34818667 The N501Y spike substitution enhances SARS-CoV-2 infection and transmission. Mechanistically, the N501Y substitution increased the affinity of the viral spike protein for cellular receptors. 2022 Nature Abstract SARS_CoV_2 N501Y 21 26 S 76 81 34818667 The N501Y spike substitution enhances SARS-CoV-2 infection and transmission. The N501Y substitution recapitulated the enhanced viral transmission phenotype of the eight mutations in the Alpha spike protein, suggesting that it is a major determinant of the increased transmission of the Alpha variant. 2022 Nature Abstract SARS_CoV_2 N501Y 4 9 S 115 120 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. Wild-type or spike N501Y can be detected with a limit of detection of 10 copies/muL (wild-type) even at a 1% ratio level on the background (spike N501Y). 2021 Analytical chemistry Abstract SARS_CoV_2 N501Y;N501Y 19;146 24;151 S;S 13;140 18;145 34820854 Analysis of BNT162b2- and CVnCoV-elicited sera and of convalescent sera toward SARS-CoV-2 viruses. The significance of common VOC mutations K417N, E484K, or N501Y focused on linear epitopes was analyzed using a peptide array approach. 2021 Allergy Abstract SARS_CoV_2 E484K;K417N;N501Y 48;41;58 53;46;63 34821383 Association of polymorphisms in tumor necrosis factors with SARS-CoV-2 infection and mortality rate: A case-control study and in silico analyses. The tetra-amplification refractory mutation system polymerase chain reaction technique was recruited to detect -308G>A TNFalpha and +252A>G TNFbeta polymorphisms among the Iranian subjects. 2022 Journal of medical virology Abstract SARS_CoV_2 A252G;G308A 132;111 139;118 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. The incidence domination was likely due to a fitness advantage that could be driven by the receptor-binding domain (RBD) residue change (N501Y), which also emerged independently in other variants of concern such as the beta/B.1.351 and gamma/P.1 strains. 2021 eLife Abstract SARS_CoV_2 N501Y 137 142 RBD 116 119 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. When challenged with sera from convalescent individuals or anti-RBD monoclonal antibodies, the N501Y variant showed a minor, but significant elevated evasion potential of ACE-2/RBD antibody neutralization. 2021 eLife Abstract SARS_CoV_2 N501Y 95 100 RBD;RBD 64;177 67;180 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Previous work found that the co-occurring mutations R203K/G204R on the SARS-CoV-2 nucleocapsid (N) protein are increasing in frequency among emerging variants of concern or interest. 2021 Cell host & microbe Abstract SARS_CoV_2 R203K;G204R 52;58 57;63 N;N 82;96 94;97 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Through a combination of in silico analyses, this study demonstrates that R203K/G204R are adaptive, while large-scale phylogenetic analyses indicate that R203K/G204R associate with the emergence of the high-transmissibility SARS-CoV-2 lineage B.1.1.7. 2021 Cell host & microbe Abstract SARS_CoV_2 R203K;R203K;G204R;G204R 74;154;160;80 79;159;165;85 34822912 Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR. 25 samples (3.9 %) detected N501Y, with K417 were considered as the alpha variant. 2022 Journal of virological methods Abstract SARS_CoV_2 N501Y 28 33 34822912 Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR. RESULTS: Of the 664/934 that were subjected to the multiplex qRT-PCR, 638 (96.1 %) detected L452R and K417 in the channels and were identified as the delta variant. 2022 Journal of virological methods Abstract SARS_CoV_2 L452R 92 97 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. Nation-wide mutational analysis depicted >0.5 million mutation events with four major mutations in >19,300 genomes, including two mutations in coding (spike (D614G), and NSP 12b (P314L) of rdrp), one silent mutation (NSP3 F106F) and one extragenic mutation (5' UTR 241). 2022 Virus research Abstract SARS_CoV_2 F106F;D614G;P314L 222;158;179 227;163;184 5'UTR;S;Nsp3;RdRP 258;151;217;189 264;156;221;193 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Moreover, we demonstrate that the P681R-bearing virus exhibits higher pathogenicity compared with its parental virus. 2022 Nature Abstract SARS_CoV_2 P681R 34 39 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Our data suggest that the P681R mutation is a hallmark of the virological phenotype of the B.1.617.2/Delta variant and is associated with enhanced pathogenicity. 2022 Nature Abstract SARS_CoV_2 P681R 26 31 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. The P681R mutation in the spike protein, which is highly conserved in this lineage, facilitates cleavage of the spike protein and enhances viral fusogenicity. 2022 Nature Abstract SARS_CoV_2 P681R 4 9 S;S 26;112 31;117 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Conversely, mutation of R403T in the SARS-CoV-2 S reduces pseudoparticle infection and viral replication. 2021 Nature communications Abstract SARS_CoV_2 R403T 24 29 S 48 49 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Here, we show that a single T403R mutation increases binding of RaTG13 S to human ACE2 and allows VSV pseudoparticle infection of human lung cells and intestinal organoids. 2021 Nature communications Abstract SARS_CoV_2 T403R 28 33 S 71 72 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. The T403R RaTG13 S is neutralized by sera from individuals vaccinated against COVID-19 indicating that vaccination might protect against future zoonoses. 2021 Nature communications Abstract SARS_CoV_2 T403R 4 9 S 17 18 COVID-19 78 86 34828410 Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India. This relative consolidation of the kappa variant was significant, since it shared 3 of the 4 signature mutations (L452R, E484Q and P681R) observed in the spike protein of delta variant and thus was likely to be the precursor in its evolution. 2021 Genes Abstract SARS_CoV_2 E484Q;P681R;L452R 121;131;114 126;136;119 S 154 159 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. Among the N501Y-containing mutants formerly designated as VOCs (alpha, beta, and gamma), a previously described mAb, CB6, can distinguish beta from alpha and gamma. 2021 Diagnostics (Basel, Switzerland) Abstract SARS_CoV_2 N501Y 10 15 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. As delta is currently the predominant variant globally, they will be useful for POC testing to identify N501Y meta-signature variants, protect individuals in high-risk settings, and help detect epidemiological shifts among SARS-CoV-2 variants. 2021 Diagnostics (Basel, Switzerland) Abstract SARS_CoV_2 N501Y 104 109 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. The 2E8 mAb can distinguish the delta VOC from variants with the N501Y meta-signature, which is characterized by convergent mutations that contribute to increased virulence and evasion of host immunity. 2021 Diagnostics (Basel, Switzerland) Abstract SARS_CoV_2 N501Y 65 70 34829998 SARS-CoV-2 Variants, RBD Mutations, Binding Affinity, and Antibody Escape. The variant-induced risk of breakthrough infections in vaccinated people is attributed to the L452R mutation's reduction of the binding affinity of many antibodies. 2021 International journal of molecular sciences Abstract SARS_CoV_2 L452R 94 99 34833135 Emerging Mutations Potentially Related to SARS-CoV-2 Immune Escape: The Case of a Long-Term Patient. The viral isolate was assigned to lineage B.1.177.51 through whole-genome sequencing (WGS) and harbored a novel set of mutations on the Spike protein (V143D, del144/145 and E484K); furthermore, seroneutralization assays showed impaired response of the surveyed strain to BNT162b2 (Comirnaty) Pfizer/BioNTech vaccine-induced (average reduction of 70%) and convalescent sera (average reduction of 19.04%), when compared to VOC P.1. 2021 Life (Basel, Switzerland) Abstract SARS_CoV_2 E484K;V143D 173;151 178;156 S 136 141 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. Curcumin also inhibited D614G strain by pre-infection and post-infection treatment. 2021 Molecules (Basel, Switzerland) Abstract SARS_CoV_2 D614G 24 29 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. In addition, curcumin showed a virucidal effect against D614G strain and Delta variant. 2021 Molecules (Basel, Switzerland) Abstract SARS_CoV_2 D614G 56 61 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. The D614G strain and Delta variant of SARS-CoV-2 were used, and the viral titer was quantified by plaque assay. 2021 Molecules (Basel, Switzerland) Abstract SARS_CoV_2 D614G 4 9 34834948 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a Dog in Connecticut in February 2021. It contained both the D614G in spike and P323L in nsp12 substitutions, which have become the dominant mutations in the United States. 2021 Viruses Abstract SARS_CoV_2 D614G;P323L 22;41 27;46 S;Nsp12 31;50 36;55 34834983 High Individual Heterogeneity of Neutralizing Activities against the Original Strain and Nine Different Variants of SARS-CoV-2. In France, most cases were due to spike D641G-harbouring viruses that descended initially from the Wuhan strain, then by the variant of B.1.160 lineage we called Marseille-4 since the summer of 2020, which was followed by the Alpha and Beta variants in early 2021, then the Delta variant currently. 2021 Viruses Abstract SARS_CoV_2 D641G 40 45 S 34 39 34834984 Macrophages and Monocytes: "Trojan Horses" in COVID-19. We aimed to explore whether variants of SARS-CoV-2 (Chinese-derived strain (D614, lineage A), Italian strain PV10734 (D614G, lineage B.1.1) and Alpha strain (lineage B.1.1.7)) were able to infect monocytes (MN) and monocyte-derived macrophages (MDM) and whether these infected cells may, in turn, be vectors of infection. 2021 Viruses Abstract SARS_CoV_2 D614G 118 123 34834987 The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City. It is characterized by three amino acid changes in the spike protein: T478K, P681H, and T732A. 2021 Viruses Abstract SARS_CoV_2 P681H;T478K;T732A 77;70;88 82;75;93 S 55 60 34835101 Impact of the Double Mutants on Spike Protein of SARS-CoV-2 B.1.617 Lineage on the Human ACE2 Receptor Binding: A Structural Insight. The novel variants harbored by the B.1.617 lineage (kappa and delta) carry mutations within the receptor-binding domain of spike (S) protein (L452R + E484Q and L452R + T478K), the region binding to the host receptor. 2021 Viruses Abstract SARS_CoV_2 E484Q;L452R;T478K;L452R 150;160;168;142 155;165;173;147 S;S 123;130 128;131 34835288 Antibody Titer Kinetics and SARS-CoV-2 Infections Six Months after Administration with the BNT162b2 Vaccine. Neutralization activity against the D614G, B.1.1.7, and B.1.351 variants were also analyzed. 2021 Vaccines Abstract SARS_CoV_2 D614G 36 41 34836485 A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. We selected 2-36-escape viruses in vitro and confirmed that K378 T in SARS-CoV-2 RBD led to viral resistance. 2022 Emerging microbes & infections Abstract SARS_CoV_2 K378T 60 66 RBD 81 84 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. Also, eight genomes were classified in the A.27/Marseille-501 lineage which was first detected in our institute in January 2021 and which either harboured or did not harbour the Q677H substitution. 2022 Virus genes Abstract SARS_CoV_2 Q677H 178 183 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. At the end of 2020, an increasing incidence of spike substitutions Q677H/P was described in the USA, which involved six independent lineages. 2022 Virus genes Abstract SARS_CoV_2 Q677H;Q677P 67;67 74;74 S 47 52 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. In seven genomes (0.2%), we found a deletion of five amino acids at spike positions 675-679 (QTQTN) including Q677, and in 76 genomes (2.3%) we found a Q677H substitution. 2022 Virus genes Abstract SARS_CoV_2 Q677H 152 157 S 68 73 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. The Q677H substitution was found in genomes all obtained from respiratory samples collected from 19 January 2021 and were classified in seven different lineages. 2022 Virus genes Abstract SARS_CoV_2 Q677H 4 9 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. Thus, the spike Q677H substitution should be considered as another example of convergent evolution, as it is the case of spike substitutions L18F, E484K, L452R, and N501Y which also independently appeared in various lineages. 2022 Virus genes Abstract SARS_CoV_2 E484K;L18F;L452R;N501Y;Q677H 147;141;154;165;16 152;145;159;170;21 S;S 10;121 15;126 34840498 Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021. Furthermore, it also found that D614G mutation appeared in 103 Indonesian SARS-CoV-2 isolates. 2021 Bulletin of the National Research Centre Abstract SARS_CoV_2 D614G 32 37 34841034 Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2. Second, the host-specific D614G mutation becomes prevalent starting from March 2020. 2021 One health (Amsterdam, Netherlands) Abstract SARS_CoV_2 D614G 26 31 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Most common and frequent mutations in the South Asian countries are 241C > T, 3037C > T, 14408C > T, and 23403A > G and about 85% SNPs are localized in ORF1ab, spike protein, and nucleocapsid. 2021 Current research in microbial sciences Abstract SARS_CoV_2 C14408T;A23403G;C241T;C3037T 89;105;68;78 99;115;76;87 N;ORF1ab;S 179;152;160 191;158;165 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Surprisingly, one missense mutation (1163A > T) in ORF1ab gene became dominant only in Bangladesh (78.8%), which led to debates regarding effects on the pathogenicity and transmissibility of the virus. 2021 Current research in microbial sciences Abstract SARS_CoV_2 A1163T 37 46 ORF1ab 51 57 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. While analyzing transmission source in terms of geolocation, the largest clustered group from the South Asian countries was based on the G-clade (D614G) (81.7%; 335/410 samples), tracing the inception and transmission of SARS-CoV-2 infections in the South Asian countries from European regions. 2021 Current research in microbial sciences Abstract SARS_CoV_2 D614G 146 151 COVID-19 221 242 34842496 A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). Almost all (96.4%) were carrying D614G mutation in the S protein, with additional mutations that define lineages or variants. 2022 Emerging microbes & infections Abstract SARS_CoV_2 D614G 33 38 S 55 56 34842496 A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). But some mutations of concern, such as E484K from B.1.351 and P.1 lineages are currently under monitoring, together with those observed in the receptor-binding domain or N-terminal domain, such as L452R and T478K from B.1.617.2 lineage. 2022 Emerging microbes & infections Abstract SARS_CoV_2 E484K;L452R;T478K 39;197;207 44;202;212 N 170 171 34842604 Fc-Independent Protection from SARS-CoV-2 Infection by Recombinant Human Monoclonal Antibodies. The Fc of these antibodies was engineered to include the triple mutation N297G/S298G/T299A that eliminates glycosylation and the binding to FcgammaR and to the complement system activator C1q. 2021 Antibodies (Basel, Switzerland) Abstract SARS_CoV_2 N297G;S298G;T299A 73;79;85 78;84;90 34843105 SARS-CoV-2 Neutralization in Convalescent Plasma and Commercial Lots of Plasma-Derived Immunoglobulin. METHODS: Final containers of IVIG/SCIG and CP donations were analyzed by commercial ELISA for anti-SARS-CoV-2 S1-receptor binding domain (RBD) IgG as well as microneutralization assay using a patient-derived SARS-CoV-2 (D614G) isolate. 2022 BioDrugs Abstract SARS_CoV_2 D614G 220 225 RBD;RBD 113;138 136;141 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. Upon reverse engineering of these mutations into different betacoronavirus genomes, we identified two substitutions (R310A and F426A in SARS-CoV nsp14) abrogating virus viability and one mutation (H424A) yielding a crippled phenotype across all viruses tested. 2021 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 F426A;H424A;R310A 127;197;117 132;202;122 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. Our most successful design encodes I358F, Y365W, T430I, and I513L RBD mutations, maintains recognition by the receptor ACE2 and a panel of different anti-RBD monoclonal antibodies, is between 1-2 C more thermally stable than the original RBD using a thermal shift assay, and is less proteolytically sensitive to chymotrypsin and thermolysin than the original RBD. 2021 bioRxiv Abstract SARS_CoV_2 I358F;I513L;T430I;Y365W 35;60;49;42 40;65;54;47 RBD;RBD;RBD;RBD 66;154;238;359 69;157;241;362 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. To further characterize the mechanism, we tested a natural ORF3a Beta variant, Q57H, and a mutant with deletion of the highly conserved residue, DeltaG188. 2021 bioRxiv Abstract SARS_CoV_2 Q57H 79 83 ORF3a 59 64 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. Furthermore, the mean spindle length and the plate width were significantly increased in the N501Y-treated group compared to the control group. 2021 Reproductive sciences (Thousand Oaks, Calif.) Abstract SARS_CoV_2 N501Y 93 98 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. The purpose of this study was to investigate the effect of N501Y mutant spike protein of SARS-Cov-2 on oocyte maturation. 2021 Reproductive sciences (Thousand Oaks, Calif.) Abstract SARS_CoV_2 N501Y 59 64 S 72 77 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. We demonstrated that the N501Y mutant of SARS-CoV-2 spike protein impaired the mouse oocyte maturation accompanied by abnormal spindle assembly. 2021 Reproductive sciences (Thousand Oaks, Calif.) Abstract SARS_CoV_2 N501Y 25 30 S 52 57 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. A real-time quantitative PCR screening and phylogenomic reconstructions directed at sequence/structure analysis of the spike glycoprotein revealed mutation of concern E484K in genomes from central Mexico, in addition to the nationwide prevalence of the imported variant 20C/S:452R (B.1.427/9). 2021 Microbial genomics Abstract SARS_CoV_2 E484K 167 172 S 119 137 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. P681R/H, T732A), and at the basis of the protein, V1176F, raising concerns about the lack of phenotypic and clinical data available for the variants of interest we postulate: 20B/478K.V1 (B.1.1.222 or B.1.1.519) and 20B/P.4 (B.1.1.28.4). 2021 Microbial genomics Abstract SARS_CoV_2 T732A;V1176F;P681H;P681R 9;50;0;0 14;56;7;7 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. R190M), in the receptor-binding motif. 2021 Microbial genomics Abstract SARS_CoV_2 R190M 0 5 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. T478K, E484K), within the S1-S2 subdomains. 2021 Microbial genomics Abstract SARS_CoV_2 E484K;T478K 7;0 12;5 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. We identified the mutation N:S194L of the nucleocapsid protein associated with symptomatic patients. 2021 Microbial genomics Abstract SARS_CoV_2 S194L 29 34 N;N 42;27 54;28 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. In addition, the profiling of sub-haplotypes indicated that sub-haplotype 2A_1 with the mutations at N501Y, A570D, D614G, P681H, T716I, S982A, and D118H in Spike was over 58% in May 2021 in the high partly vaccinated rate group (US, Canada, and Germany). 2022 Infection, genetics and evolution Abstract SARS_CoV_2 A570D;D118H;D614G;N501Y;P681H;S982A;T716I 108;147;115;101;122;136;129 113;152;120;106;127;141;134 S 156 161 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Meanwhile, the new haplotype 2C_3 bearing the mutations at EFR156-158del, T19R, A222V, L452R, T478K, and D614G in Spike occupied over 54.8% in May 2021 in the low partly vaccinated rate group (India, Malaysia, Taiwan, and Vietnam). 2022 Infection, genetics and evolution Abstract SARS_CoV_2 A222V;D614G;L452R;T19R;T478K 80;105;87;74;94 85;110;92;78;99 S 114 119 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Phylogenetic tree analysis of the proteomes of SARS-CoV-2 variants with Neighbor-Joining and Maximum Parsimony methods indicated that haplotype 2 variant with nsp12 P323L and Spike D614G was dominant (98.81%), including new sub-haplotypes 2A_1 to 2A_3, 2B_1 to 2B_3, and 2C_1 to 2C_2 emerged post-one-year COVID-19 outbreak. 2022 Infection, genetics and evolution Abstract SARS_CoV_2 D614G;P323L 181;165 186;170 S;Nsp12 175;159 180;164 COVID-19 306 314 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. While the N501Y and E484Q mutations are particularly important for the greater stability, the N501Y mutation is unlikely to significantly affect antibody neutralization. 2021 Nature communications Abstract SARS_CoV_2 E484Q;N501Y;N501Y 20;10;94 25;15;99 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. Our diagnostic assays detect the E484K and N501Y single-nucleotide polymorphisms (SNPs) as well as a spike gene deletion (HV69/70) and can be run on standard laboratory equipment or on the portable rapid diagnostic technology platform peakPCR. 2021 Analytical chemistry Abstract SARS_CoV_2 E484K;N501Y 33;43 38;48 S 101 106 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. Two nonsense mutations in open reading frame 3a (ORF3a) (G254*) and ORF8 (K68*) were found in the alpha variant sequences. 2021 Microbiology resource announcements Abstract SARS_CoV_2 G254X;K68X 57;74 62;78 ORF3a;ORF8 49;68 54;72 34855904 Niclosamide shows strong antiviral activity in a human airway model of SARS-CoV-2 infection and a conserved potency against the Alpha (B.1.1.7), Beta (B.1.351) and Delta variant (B.1.617.2). Furthermore, niclosamide remains its potency against the D614G, Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2) variants. 2021 PloS one Abstract SARS_CoV_2 D614G 57 62 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. Among all variants investigated in this work, RBD of the Epsilon (L452R) variant is relatively easily detached from ACE2. 2021 Journal of chemical theory and computation Abstract SARS_CoV_2 L452R 66 71 RBD 46 49 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. We report that RBD of the Alpha (N501Y) variant requires the highest amount of force initially to be detached from ACE2 due to the N501Y mutation in addition to the role of N90-glycan, followed by Beta/Gamma (K417N/T, E484 K, and N501Y) or Delta (L452R and T478 K) variants. 2021 Journal of chemical theory and computation Abstract SARS_CoV_2 E484K;N501Y;N501Y;T478K;K417N;K417T;L452R;N501Y 218;131;230;257;209;209;247;33 224;136;235;263;216;216;252;38 RBD 15 18 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Furin inhibitor prevented infection by 682-686-deleted SARS-CoV-2 in 293T-ACE2-furin cells, but not the K814A mutant. 2022 Emerging microbes & infections Abstract SARS_CoV_2 K814A 104 109 34856891 A second functional furin site in the SARS-CoV-2 spike protein. However, K814A mutation eliminated the enhancing effect of furin on virus infection. 2022 Emerging microbes & infections Abstract SARS_CoV_2 K814A 9 14 34856891 A second functional furin site in the SARS-CoV-2 spike protein. K814A mutation did not affect the activity of TMPRSS2 and cathepsin L but did impact the cleavage of S2 into S2' and cell-cell fusion. 2022 Emerging microbes & infections Abstract SARS_CoV_2 K814A 0 5 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. The immune response elicited by this vaccine has been described against the first SARS-CoV-2 strain isolated from Wuhan, China and the D614G strain (lineage B). 2021 Frontiers in immunology Abstract SARS_CoV_2 D614G 135 140 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. We also observed that antibodies from vaccinated subjects were able to neutralize the infection of variants D614G, Alpha, Gamma and Delta in a conventional microneutralization assay. 2021 Frontiers in immunology Abstract SARS_CoV_2 D614G 108 113 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. The D614G variant in spike protein is reported to have a very high frequency of >95% globally followed by the L452R and P681R, thus getting significant attention. 2021 Frontiers in genetics Abstract SARS_CoV_2 D614G;L452R;P681R 4;110;120 9;115;125 S 21 26 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. Thus, the D614G is the cause for higher viral antigenicity, however, it has not been reported to be effective to be causing more deaths. 2021 Frontiers in genetics Abstract SARS_CoV_2 D614G 10 15 34859134 Production, Titration, Neutralisation, Storage and Lyophilisation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Lentiviral Pseudotypes. This protocol details a rapid and reliable method for the production and titration of high-titre viral pseudotype particles with the SARS-CoV-2 spike protein (and D614G or other variants of concern, VOC) on a lentiviral vector core, and use for neutralisation assays in target cells expressing angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). 2021 Bio-protocol Abstract SARS_CoV_2 D614G 163 168 S 144 149 34863783 Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay. Five unique nucleotide mutations were identified in ORF1ab: C11450A (nsp10) C14178T (RdRp), G15006T (RdRp), G18394T (Hel), and G20995T (Hel). 2022 Journal of virological methods Abstract SARS_CoV_2 C11450A;C14178T;G15006T;G18394T;G20995T 60;76;92;108;127 67;83;99;115;134 ORF1ab;RdRP;RdRP 52;85;101 58;89;105 34866979 Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study. The most frequently changed nucleotide was C3037T (silent mutation) and A23403G (D614G), each of which occurred in 57 variants out of 58 followed by C14408T (P4715L) and C241T (5'UTR) which were found in 56 and 55 variants respectively. 2021 Saudi journal of biological sciences Abstract SARS_CoV_2 A23403G;C14408T;C241T;C3037T;D614G;P4715L 72;149;170;43;81;158 79;156;175;49;86;164 5'UTR 177 182 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Comparison of the whole cell-derived WA1 and D614G spike proteins revealed that N-glycosites local to the mutation site appeared to be more readily detected, hinting that these sites are more exposed to glycosylation machinery. 2021 Frontiers in chemistry Abstract SARS_CoV_2 D614G 45 50 S;N 51;80 56;81 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Moreover, recombinant HEK293-derived S1 was occupied almost completely with complex glycan, while both WA1 and D614G derived from the Vero E6 cell whole virus were predominantly high-mannose glycans. 2021 Frontiers in chemistry Abstract SARS_CoV_2 D614G 111 116 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. The Vero cell-derived spike from the WA1 strain and a D614G variant was analyzed. 2021 Frontiers in chemistry Abstract SARS_CoV_2 D614G 54 59 S 22 27 34869681 Arterial and Venous Thrombosis Complicated in COVID-19: A Retrospective Single Center Analysis in Japan. SARS-CoV-2 variants of concern/interest (VOC/VOI) carrying the spike protein mutants E484K, N501Y, or L452R were identified by PCR-based analysis. 2021 Frontiers in cardiovascular medicine Abstract SARS_CoV_2 E484K;L452R;N501Y 85;102;92 90;107;97 S 63 68 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. There was less surface hydrophilicity increase in the Asp614Gly mutation, which exhibits a more compact conformation around the ACE-2 receptor binding domain region, rendering the structure in a "down" conformation. 2021 PloS one Abstract SARS_CoV_2 D614G 54 63 RBD 134 157 34871906 Highly sensitive and specific detection of the SARS-CoV-2 Delta variant by double-mismatch allele-specific real time reverse transcription PCR. The technique exploits allele-specific primers, targeting two spike gene mutations, L452R and T478K, within the same amplicon. 2022 Journal of clinical virology Abstract SARS_CoV_2 L452R;T478K 84;94 89;99 S 62 67 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Specifically, vaccine-resistant mutation Y449S in the spike (S) protein receptor-binding domain, which occurred in co-mutations Y449S and N501Y, has reduced infectivity compared to that of the original SARS-CoV-2 but can disrupt existing antibodies that neutralize the virus. 2021 The journal of physical chemistry letters Abstract SARS_CoV_2 N501Y;Y449S;Y449S 138;41;128 143;46;133 S;S 54;61 59;62 34874953 1H, 13C and 15N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution. Validation of assignment have been done by using two different mutants, H81P and K129E/D48E as well as by amino acid specific experiments. 2021 PloS one Abstract SARS_CoV_2 H81P;K129E;D48E 72;81;87 76;86;91 34876033 Emergence of SARS-CoV-2 resistance mutations in a patient who received anti-SARS-COV2 spike protein monoclonal antibodies: a case report. CASE PRESENTATION: We here report the case of an immunosuppressed patient infected with a B.1.1.7 variant, who received a combination of monoclonal antibodies, and subsequently selected mutations K417N, E484K and Q493R on Spike protein of SARS-CoV-2. 2021 BMC infectious diseases Abstract SARS_CoV_2 E484K;K417N;Q493R 203;196;213 208;201;218 S 222 227 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. All the glycosylation sites with altered patterns were in the spike head while the glycosylation of three sites in the stalk remained unchanged between S-614G and S-614D proteins. 2021 Scientific reports Abstract SARS_CoV_2 S614D;S614G 163;152 169;158 S;S;S 62;152;163 67;153;164 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. In this report, we used mass spectrometry techniques to characterize and compare the N-glycosylation of the wild type (S-614D) or variant (S-614G) SARS-CoV-2 spike glycoproteins prepared under identical conditions. 2021 Scientific reports Abstract SARS_CoV_2 S614D;S614G 119;139 125;145 S;N;S;S 158;85;119;139 177;86;120;140 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. The data showed that half of the N-glycosylation sequons changed their distribution of glycans in the S-614G variant. 2021 Scientific reports Abstract SARS_CoV_2 S614G 102 108 N;S 33;102 34;103 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. The first major SARS-CoV-2 variant carries a D614G substitution in the spike (S-D614G) that has been associated with altered conformation, enhanced ACE2 binding, and increased infectivity and transmission. 2021 Scientific reports Abstract SARS_CoV_2 D614G;D614G 45;80 50;85 S;S 71;78 76;79 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. The S-614G variant showed a decrease in the relative abundance of complex-type glycans (up to 45%) and an increase in oligomannose glycans (up to 33%) on all altered sequons. 2021 Scientific reports Abstract SARS_CoV_2 S614G 4 10 S 4 5 34877393 Reduced neutralization of SARS-CoV-2 B.1.617 variant by convalescent and vaccinated sera. Our results showed that, compared to D614G and B.1.1.7 variants, B.1.617 shows enhanced viral entry and membrane fusion, as well as more resistant to antibody neutralization. 2021 Genes & diseases Abstract SARS_CoV_2 D614G 37 42 Membrane 104 112 34877674 Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multitarget approach. Of specimens with N3 target dropout, 57% harbored an A28095T substitution that is highly specific for the Alpha (B.1.1.7) variant of concern. 2022 Journal of medical virology Abstract SARS_CoV_2 A28095T 53 60 34878296 Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. Due to the prior release and widespread use of the ARTIC V3 primers during the initial surge of the Delta variant, it is likely that the G142D amino acid substitution is substantially underrepresented among early Delta variant genomes deposited in public repositories. 2021 Microbiology spectrum Abstract SARS_CoV_2 G142D 137 142 34878296 Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. Importantly, we also find nearly universal presence of spike protein substitution G142D in Delta-lineage samples. 2021 Microbiology spectrum Abstract SARS_CoV_2 G142D 82 87 S 55 60 34878296 Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. We observe general improvements in sequencing depth and quality, and improved resolution of the SNP causing the D950N variation in the spike protein. 2021 Microbiology spectrum Abstract SARS_CoV_2 D950N 112 117 S 135 140 34880295 Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal. Amongst these genomes, new combinations of SARS-CoV-2 spike mutations were identified, with E484K + N501T, L452R + N501Y, and L452M + S477N exclusively found in second wave specimens. 2021 Scientific reports Abstract SARS_CoV_2 E484K;L452M;L452R;N501T;N501Y;S477N 92;126;107;100;115;134 97;131;112;105;120;139 S 54 59 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. The most often observed were positive mutations, especially D614G and E484K, located in the region of S1/S2 junction, and in the receptor-binding domain (RBD), respectively. 2021 Infection and drug resistance Abstract SARS_CoV_2 D614G;E484K 60;70 65;75 RBD 154 157 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. Conversely, the less prevalent B.1.617.2 with E484K showed a significant more than 4-fold reduction in neutralisation that warrants surveillance of strains with the acquired E484K mutation. 2021 Euro surveillance Abstract SARS_CoV_2 E484K;E484K 46;174 51;179 34886945 Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020. By June 2021, all the emerging variants of concern carried the D614G mutation. 2021 Euro surveillance Abstract SARS_CoV_2 D614G 63 68 34886945 Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020. IntroductionThe SARS-CoV-2 lineages carrying the amino acid change D614G have become the dominant variants in the global COVID-19 pandemic. 2021 Euro surveillance Abstract SARS_CoV_2 D614G 67 72 COVID-19 121 129 34886945 Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020. The rapid spread of the G614 mutant suggests that it may have a transmission advantage over the D614 wildtype.AimOur objective was to estimate the transmission advantage of D614G by integrating phylogenetic and epidemiological analysis.MethodsWe assume that the mutation D614G was the only site of interest which characterised the two cocirculating virus strains by June 2020, but their differential transmissibility might be attributable to a combination of D614G and other mutations. 2021 Euro surveillance Abstract SARS_CoV_2 D614G;D614G;D614G 173;271;459 178;276;464 34888394 A Multidimensional Cross-Sectional Analysis of Coronavirus Disease 2019 Seroprevalence Among a Police Officer Cohort: The PoliCOV-19 Study. Serum neutralization titers toward the wild-type SARS-CoV-2 spike protein (expressing D614G) and the Alpha and Beta variants were measured in seropositive study participants. 2021 Open forum infectious diseases Abstract SARS_CoV_2 D614G 86 91 S 60 65 34888860 Unusual pattern of thrombotic events in young adult non-critically ill patients with COVID-19 may result from an undiagnosed inherited and acquired form of thrombophilia. The presence of JAK2-V617F, and FII-G20210A mutations was linked with SVT. 2022 British journal of haematology Abstract SARS_CoV_2 G20210A;V617F 36;21 43;26 34888860 Unusual pattern of thrombotic events in young adult non-critically ill patients with COVID-19 may result from an undiagnosed inherited and acquired form of thrombophilia. We found a 55% prevalence of TGs mainly heterozygous coagulation factor II, thrombin (FII)-G20210A, Janus kinase 2 (JAK2)-V617F, protein-S, and antithrombin III deficiency with a high (76 9%) prevalence of venous UTEs, multiple vessels thrombosis, and recurrence rate among the TG versus non-TG subcohort. 2022 British journal of haematology Abstract SARS_CoV_2 G20210A;V617F 91;122 98;127 S 137 138 34889898 A Comparative Study between Spanish and British SARS-CoV-2 Variants. In particular, the N501Y substitution, situated in the RBD of the spike of the British variant, might be the reason for its extraordinary infective potential. 2021 Current issues in molecular biology Abstract SARS_CoV_2 N501Y 19 24 S;RBD 66;55 71;58 34890095 Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid. Both E-beacons could discriminate their target from the E484Q mutation of the SARS-CoV-2 Kappa variant. 2022 Chembiochem Abstract SARS_CoV_2 E484Q 56 61 34890095 Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid. E-beacon prepared for the SARS-CoV-2 E484K variant functioned with similar sensitivity. 2022 Chembiochem Abstract SARS_CoV_2 E484K 37 42 34890524 The significant immune escape of pseudotyped SARS-CoV-2 variant Omicron. Our results indicated that the mean neutralization ED50 of these sera against Omicron decreased to 66, which is about 8.4-folds compared to the D614G reference strain (ED50 = 556), whereas the neutralization activity of other VOC and VOI pseudotyped viruses decreased only about 1.2-4.5-folds. 2022 Emerging microbes & infections Abstract SARS_CoV_2 D614G 144 149 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. We used a Cas12a-based RT-PCR combined with CRISPR on-site rapid detection system (RT-CORDS) platform to detect the key mutations in SARS-CoV-2 variants, such as 69/70 deletion, N501Y, and D614G. 2022 Biosensors & bioelectronics Abstract SARS_CoV_2 D614G;N501Y 189;178 194;183 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. However, some of the Delta variants in Iran carry an additional mutation, namely E1202Q in the HR2 subdomain that might confer an advantage to viral/cell membrane fusion process. 2022 Gene Abstract SARS_CoV_2 E1202Q 81 87 Membrane 154 162 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. We also observed some more common mutations such as an N-terminal domain (NTD) deletion at position I210 and P863H in fusion peptide-heptad repeat 1 span region in Iranian SARS-COV-2. 2022 Gene Abstract SARS_CoV_2 P863H 109 114 N 55 56 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. CONCLUSIONS: The D614G, P618H and E484K mutations have previously been reported to favor increased transmissibility, enhanced infectivity, and immune invasion, respectively. 2022 Journal of infection and public health Abstract SARS_CoV_2 D614G;E484K;P618H 17;34;24 22;39;29 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Out of these 129 sequences, 27 sequences also harbored E484K mutation in S glycoprotein. 2022 Journal of infection and public health Abstract SARS_CoV_2 E484K 55 60 S 73 87 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. The V1230L mutation, present within the TM domain of S glycoprotein, might strengthen the interaction of S glycoprotein with the viral envelope and increase S glycoprotein deposition to the virion, resulting in more infectious virion. 2022 Journal of infection and public health Abstract SARS_CoV_2 V1230L 4 10 S;S;S 53;105;157 67;119;171 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Therefore, the new variant having D614G, P618H, V1230L, and E484K may have higher infectivity, transmissibility, and immune invasion characteristics, and thus need to be monitored closely. 2022 Journal of infection and public health Abstract SARS_CoV_2 D614G;E484K;P618H;V1230L 34;60;41;48 39;65;46;54 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. This novel variant encompasses 129 SARS-CoV-2 strains which are characterized by the presence of 11 coexisting mutations including D614G, P681H, and V1230L in S glycoprotein. 2022 Journal of infection and public health Abstract SARS_CoV_2 D614G;P681H;V1230L 131;138;149 136;143;155 S 159 173 34898481 Emergence of Novel SARS-CoV-2 variants in India: second wave. The remaining sequences were assigned to clade 20H, 20J, 20D, 20C, 20G,20E,19A and 19B.The spike mutation frequencies of L452R, E484Q and P681R in Indian state of Maharashtra were 62.4%, 66.5% and 61.5% respectively. 2021 Journal of infection in developing countries Abstract SARS_CoV_2 E484Q;L452R;P681R 128;121;138 133;126;143 S 91 96 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. Recently, a new strain is reported in India that includes a mutation (T478K, and L452R) in the RBD, that is possibly increasing the infection rate. 2021 Medicine in drug discovery Abstract SARS_CoV_2 L452R;T478K 81;70 86;75 RBD 95 98 34904526 Elucidating the role of N440K mutation in SARS-CoV-2 spike - ACE-2 binding affinity and COVID-19 severity by virtual screening, molecular docking and dynamics approach. The frequency of N440K variant was higher during the second wave in South India. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 N440K 17 22 34904526 Elucidating the role of N440K mutation in SARS-CoV-2 spike - ACE-2 binding affinity and COVID-19 severity by virtual screening, molecular docking and dynamics approach. The N440K strain escapes from antibody neutralization, which might increase reinfection and decrease vaccine efficiency. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 N440K 4 9 34904526 Elucidating the role of N440K mutation in SARS-CoV-2 spike - ACE-2 binding affinity and COVID-19 severity by virtual screening, molecular docking and dynamics approach. To find a potential inhibitor against mutant N440K SARS-CoV-2, a virtual screening process was carried out and found ZINC169293961, ZINC409421825 and ZINC22060839 as the best binding energy compounds. 2021 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 N440K 45 50 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. harboring the Spike glycoprotein p.E484K mutation). 2021 PloS one Abstract SARS_CoV_2 E484K 33 40 S 14 32 34905589 Development of an efficient Sanger sequencing-based assay for detecting SARS-CoV-2 spike mutations. Here, we developed five SARS-CoV-2 spike gene primer pairs (5-SSG primer assay; 69S, 144S, 417S, 484S, and 570S) and verified their ability to detect nine key spike mutations (DeltaH69/V70, T95I, G142D, DeltaY144, K417T/N, L452R, E484K/Q, N501Y, and H655Y) using a Sanger sequencing-based assay. 2021 PloS one Abstract SARS_CoV_2 DeltaY144;E484K;E484Q;G142D;H655Y;K417N;K417T;L452R;N501Y;T95I 203;230;230;196;250;214;214;223;239;190 212;237;237;201;255;221;221;228;244;194 S;S 35;159 40;164 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. All strains other than the delta mutant are often found with the N501Y mutation situated on the RBD, resulting in higher binding between the spike protein and angiotensin-converting enzyme 2 (ACE2) receptors, enhanced viral adhesion, and following the entrance to host cells. 2022 Biomedicine & pharmacotherapy Abstract SARS_CoV_2 N501Y 65 70 S;RBD 141;96 146;99 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. We find evidence for strong selection favoring the D614G spike mutation and B.1.1.7 (Alpha), weaker selection favoring B.1.351 (Beta), and no advantage of R.1 after it spreads beyond Japan. 2021 Nature communications Abstract SARS_CoV_2 D614G 51 56 S 57 62 34909459 Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M(pro). Since examined adamantly-isothiourea derivatives (1-4) shown broad-spectrum of antibacterial activity and significant in vitro cytotoxic effects against five human tumor cell lines and shown similarity in structure with opaganib, it was of interest to study their inhibitory potency toward some SARS-CoV-2 proteins such as SARS-CoV-2 main protease Mpro and mutation of SARS-CoV-2 Spike (S) Protein D614G. 2021 ChemistrySelect Abstract SARS_CoV_2 D614G 398 403 S;S 380;387 385;388 34909459 Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M(pro). The results of molecular docking simulations indicate compound 1 as the most prominent candidate of inhibition of SARS-CoV-2 main protease Mpro ( Gbind=11.24 kcal/mol), while almost the same inhibition potency of all studied compounds is exhibited toward D614G. 2021 ChemistrySelect Abstract SARS_CoV_2 D614G 255 260 34909573 Ventricular fibrillation arrest due to Brugada syndrome in a coronavirus disease 2019 patient with negative procainamide challenge: a case report. He later underwent genetic testing and was found to be heterozygous for c.844C>G (p.Arg282Gly) mutation in the SCN5A gene. 2021 European heart journal. Case reports Abstract SARS_CoV_2 C844G;R282G 72;82 80;93 34909610 Functional evaluation of the P681H mutation on the proteolytic activation of the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Functional assays using pseudoparticles harboring SARS-CoV-2 spikes and cell-to-cell fusion assays demonstrated no differences between Wuhan-Hu-1, B.1.1.7, or a P681H point mutant. 2022 iScience Abstract SARS_CoV_2 P681H 161 166 S 61 67 34909610 Functional evaluation of the P681H mutation on the proteolytic activation of the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Here, we studied the role of the P681H mutation in B.1.1.7 cell entry. 2022 iScience Abstract SARS_CoV_2 P681H 33 38 34909610 Functional evaluation of the P681H mutation on the proteolytic activation of the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Our findings suggest that, although the B.1.1.7 P681H mutation may slightly increase S1/S2 cleavage, this does not significantly impact viral entry or cell-cell spread. 2022 iScience Abstract SARS_CoV_2 P681H 48 53 34909610 Functional evaluation of the P681H mutation on the proteolytic activation of the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. SARS-CoV-2 B.1.1.7 (Alpha), a WHO variant of concern first identified in the United Kingdom in late 2020, contains several mutations including P681H in the spike S1/S2 cleavage site, which is predicted to increase cleavage by furin, potentially impacting the viral cell entry. 2022 iScience Abstract SARS_CoV_2 P681H 143 148 S 156 161 34909634 Severe breakthrough COVID-19 with a heavily mutated variant in a multiple myeloma patient 10 weeks after vaccination. RESULTS: Sequencing of the viral isolate revealed an extensively mutated variant with 10 spike protein mutations, including E484Q and N440K. 2022 Clinical infection in practice Abstract SARS_CoV_2 E484Q;N440K 124;134 129;139 S 89 94 34909634 Severe breakthrough COVID-19 with a heavily mutated variant in a multiple myeloma patient 10 weeks after vaccination. Viral variants with immune escape mutations such as N440K, also seen independently in the SARS-CoV-2 Omicron variant (B.1.1.529) and in viral passaging experiments, likely require a higher level of anti-spike antibodies to prevent severe COVID-19. 2022 Clinical infection in practice Abstract SARS_CoV_2 N440K 52 57 S 203 208 COVID-19 238 246 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. We note certain RBD mutations that might further enhance Omicron's escape, and in particular advise careful surveillance of two subclades bearing R346S/K mutations with relevance for certain therapeutic antibodies. 2021 bioRxiv Abstract SARS_CoV_2 R346K;R346S 146;146 153;153 RBD 16 19 34909775 Intranasal immunization with a vaccinia virus vaccine vector expressing pre-fusion stabilized SARS-CoV-2 spike fully protected mice against lethal challenge with the heavily mutated mouse-adapted SARS2-N501Y MA30 strain of SARS-CoV-2. In this manuscript we show that intranasal immunization with a pre-fusion stabilized Washington strain spike, expressed from a highly attenuated, replication-competent vaccinia virus construct, NYVAC-KC, fully protected mice against disease and death from SARS2-N501Y MA30 . 2021 bioRxiv Abstract SARS_CoV_2 N501Y 262 267 S 103 108 34909775 Intranasal immunization with a vaccinia virus vaccine vector expressing pre-fusion stabilized SARS-CoV-2 spike fully protected mice against lethal challenge with the heavily mutated mouse-adapted SARS2-N501Y MA30 strain of SARS-CoV-2. The mouse-adapted strain of SARS-CoV-2, SARS2-N501Y MA30 , contains a spike that is also heavily mutated, with mutations at 4 of the 5 positions in Omicron spike associated with neutralizing antibody escape (K417, E484, Q493 and N501). 2021 bioRxiv Abstract SARS_CoV_2 N501Y 46 51 S;S 70;156 75;161 34909775 Intranasal immunization with a vaccinia virus vaccine vector expressing pre-fusion stabilized SARS-CoV-2 spike fully protected mice against lethal challenge with the heavily mutated mouse-adapted SARS2-N501Y MA30 strain of SARS-CoV-2. This data demonstrates that Washington strain spike, when expressed from a highly attenuated, replication-competent poxvirus, administered without parenteral injection can fully protect against the heavily mutated mouse-adapted SARS2-N501Y MA30 . 2021 bioRxiv Abstract SARS_CoV_2 N501Y 234 239 S 46 51 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. To address this, we examined the neutralizing antibody (nAb) response against four major SARS-CoV-2 variants-D614G, Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2)-in health care workers (HCWs) at pre-vaccination, post-first and post-second mRNA vaccine dose, and six months post-second mRNA vaccine dose. 2021 bioRxiv Abstract SARS_CoV_2 D614G 109 114 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. We observed an increase of the Delta sublineage AY.25, its spike mutation S112L, and nsp12 mutation F192V in breakthroughs. 2021 medRxiv Abstract SARS_CoV_2 F192V;S112L 100;74 105;79 S;Nsp12 59;85 64;90 34909788 SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection. Neutralization capacity of the D614G virus was much higher in infected and vaccinated versus vaccinated only participants but both groups had 22-fold Omicron escape from vaccine elicited neutralization. 2021 medRxiv Abstract SARS_CoV_2 D614G 31 36 34909788 SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection. We isolated and sequence confirmed live Omicron virus from an infected person in South Africa and compared plasma neutralization of this virus relative to an ancestral SARS-CoV-2 strain with the D614G mutation, observing that Omicron still required ACE2 to infect. 2021 medRxiv Abstract SARS_CoV_2 D614G 195 200 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Indeed, over 90% of Delta samples in Russia are characterized by the nsp2:K81N+ORF7a:P45L pair of mutations which is rare outside Russia, putting them in the AY.122 sublineage. 2021 medRxiv Abstract SARS_CoV_2 K81N;P45L 74;85 78;89 ORF7a;Nsp2 79;69 84;73 34910734 Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. In dog, cat, gorilla, lion, and tiger, Y505H and Y453F were the common mutations followed by Y145del, Y144del, and V70I in S protein. 2021 PloS one Abstract SARS_CoV_2 V70I;Y144del;Y145del;Y453F;Y505H 115;102;93;49;39 119;109;100;54;44 S 123 124 34910734 Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. The highest mutations observed in mink where the substitution of D614G in spike (95.2%) and P323L in NSP12 (95.2%) protein. 2021 PloS one Abstract SARS_CoV_2 D614G;P323L 65;92 70;97 S;Nsp12 74;101 79;106 34910734 Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. The mink variant mutation (spike_Y453F) was detected in both humans and domestic cats. 2021 PloS one Abstract SARS_CoV_2 Y453F 33 38 S 27 32 34912372 Hotspot Mutations in SARS-CoV-2. In addition to this, SSIPe is used to report the binding affinity between the receptor-binding domain of Spike protein and human ACE2 protein by considering L452R, T478K, E484Q, and N501Y hotspot mutations in that region. 2021 Frontiers in genetics Abstract SARS_CoV_2 E484Q;L452R;N501Y;T478K 171;157;182;164 176;162;187;169 S 105 110 34914115 Omicron and Delta variant of SARS-CoV-2: A comparative computational study of spike protein. Based on docking studies, the Q493R, N501Y, S371L, S373P, S375F, Q498R, and T478K mutations contribute significantly to high binding affinity with human ACE2. 2022 Journal of medical virology Abstract SARS_CoV_2 N501Y;Q493R;Q498R;S371L;S373P;S375F;T478K 37;30;65;44;51;58;76 42;35;70;49;56;63;81 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Given that the D614G SARS-CoV-2 variant that rapidly spread from Europe to predominate in the USA during the first wave of the outbreak was not present in the initial China outbreak, we hypothesized that this mutation might affect symptom order. 2021 PLoS computational biology Abstract SARS_CoV_2 D614G 15 20 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Supporting this notion, we found that as SARS-CoV-2 in Japan shifted from the original Wuhan reference strain to the D614G variant, symptom order shifted to the USA pattern. 2021 PLoS computational biology Abstract SARS_CoV_2 D614G 117 122 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. These findings indicate that symptom order can change with mutation in viral disease and raise the possibility that D614G variant is more transmissible because infected people are more likely to cough in public before being incapacitated with fever. 2021 PLoS computational biology Abstract SARS_CoV_2 D614G 116 121 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. In contrast, the Epsilon variants (B.1.427/429) lack the N501Y mutation yet exhibit antibody evasion. 2021 Cell reports Abstract SARS_CoV_2 N501Y 57 62 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. The recently emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Beta (B.1.351) and Gamma (P.1) variants of concern (VoCs) include a key mutation (N501Y) found in the Alpha (B.1.1.7) variant that enhances affinity of the spike protein for its receptor, angiotensin-converting enzyme 2 (ACE2). 2021 Cell reports Abstract SARS_CoV_2 N501Y 164 169 S 238 243 COVID-19 28 68 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. B.1.135 and P.1 lineages have another mutation, E484K. 2022 International immunopharmacology Abstract SARS_CoV_2 E484K 48 53 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. SARS-CoV2 mutants B.1.1.7, B.1.351, and P.1 contain a key mutation N501Y. 2022 International immunopharmacology Abstract SARS_CoV_2 N501Y 67 72 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The higher binding affinity of the E484K mutant is caused due to the formation of additional hydrogen bond and salt-bridge interactions with ACE2. 2022 International immunopharmacology Abstract SARS_CoV_2 E484K 35 40 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The N501Y RBD mutant binds to ACE2 with higher affinity due to improved pi-pi stacking and pi-cation interactions. 2022 International immunopharmacology Abstract SARS_CoV_2 N501Y 4 9 RBD 10 13 34915551 Neutralization of SARS-CoV-2 Omicron variant by sera from BNT162b2 or Coronavac vaccine recipients. METHODS: Omicron variant strains HKU691 and HKU344-R346K were isolated from patients using TMPRSS2-overexpressing VeroE6 cells. 2021 Clinical infectious diseases Abstract SARS_CoV_2 R346K 51 56 34915551 Neutralization of SARS-CoV-2 Omicron variant by sera from BNT162b2 or Coronavac vaccine recipients. Only 20% and 24% of BNT162b2 recipients had detectable neutralizing antibody against the Omicron variant HKU691 and HKU344-R346K, respectively, while none of the Coronavac recipients had detectable neutralizing antibody titer against either Omicron isolate. 2021 Clinical infectious diseases Abstract SARS_CoV_2 R346K 123 128 34915551 Neutralization of SARS-CoV-2 Omicron variant by sera from BNT162b2 or Coronavac vaccine recipients. RESULTS: The Omicron variant strain HKU344-R346K has an additional spike R346K mutation, which is present in 8.5% of strains deposited in GISAID database. 2021 Clinical infectious diseases Abstract SARS_CoV_2 R346K;R346K 73;43 78;48 S 67 72 34915551 Neutralization of SARS-CoV-2 Omicron variant by sera from BNT162b2 or Coronavac vaccine recipients. The additional R346K mutation did not affect the neutralization susceptibility. 2021 Clinical infectious diseases Abstract SARS_CoV_2 R346K 15 20 34915551 Neutralization of SARS-CoV-2 Omicron variant by sera from BNT162b2 or Coronavac vaccine recipients. There was no significant difference in the GMT between HKU691 and HKU344-R346K. 2021 Clinical infectious diseases Abstract SARS_CoV_2 R346K 73 78 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. After March 11, 2020, the Chinese domestic clade was naturally divided into the imported SARS-CoV-2 D614G mutant strain and evolutionarily-related similar sequences and that of sequences collected in the original Wuhan area. 2021 Frontiers in medicine Abstract SARS_CoV_2 D614G 100 105 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. As expected, the identified sequence was closely related to the evolution of the SARS-CoV-2 D614G mutant strain circulating in Spain. 2021 Frontiers in medicine Abstract SARS_CoV_2 D614G 92 97 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. In this study, we conducted transcriptome sequencing on respiratory throat swabs from the subject and found that the dominant SARS-CoV-2 sequence (Gene Bank ID: MW301121) was a spike protein D614G mutant strain, which is currently popular throughout world. 2021 Frontiers in medicine Abstract SARS_CoV_2 D614G 191 196 S 177 182 34920116 Zoonotic spill-over of SARS-CoV-2: mink-adapted virus in humans. RESULTS: In an isolate obtained from an asymptomatic patient testing positive for SARS-CoV-2, we found four distinguishing mutations in the S gene that gave rise to the mink-adapted variant (G75V, M177T, Y453F, and C1247F) and others. 2022 Clinical microbiology and infection Abstract SARS_CoV_2 C1247F;M177T;Y453F;G75V 215;197;204;191 221;202;209;195 S 140 141 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. There is a major response to N501Y, including a public IgVH4-39 sequence, with E484K and K417N also targeted. 2022 Cell host & microbe Abstract SARS_CoV_2 E484K;K417N;N501Y 79;89;29 84;94;34 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Two of these RBD-binding mAbs recognize a neutralizing epitope conserved between SARS-CoV-1 and -2, while 18 target mutated residues in Beta: K417N, E484K, and N501Y. 2022 Cell host & microbe Abstract SARS_CoV_2 E484K;K417N;N501Y 149;142;160 154;147;165 RBD 13 16 34923570 Heterologous prime-boost immunizations with chimpanzee adenoviral vectors elicit potent and protective immunity against SARS-CoV-2 infection. Potent neutralizing antibodies produced against the highly transmissible SARS-CoV-2 variants B.1.1.7 lineage (also known as N501Y.V1) and B.1.351 lineage (also known as N501Y.V2) were detectable in mouse sera over 6 months after prime immunization. 2021 Cell discovery Abstract SARS_CoV_2 N501Y;N501Y 124;169 129;174 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Mutations have been reported in NSP13; hence, in the current study, biophysical and structural modeling methodologies were adapted to dissect the influence of major mutations in NSP13, i.e., P77L, Q88H, D260Y, E341D, and M429I, on its binding to the TBK1 and to escape the human immune system. 2021 Frontiers in microbiology Abstract SARS_CoV_2 D260Y;E341D;M429I;P77L;Q88H 203;210;221;191;197 208;215;226;195;201 Nsp13;Nsp13 32;178 37;183 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Glycan-masking of Ad-S-D428N in the RBD resulted in a 3.0-fold and 2.0-fold increase in the IC-50 neutralization titer against the Alpha (B.1.1.7) and Beta (B.1.351) variants, respectively. 2021 Frontiers in immunology Abstract SARS_CoV_2 D428N 23 28 RBD;S 36;21 39;22 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Our results demonstrated that the use of glycan-masking Ad-S-R158N/Y160T in the NTD elicited a 2.8-fold, 6.5-fold, and 4.6-fold increase in the IC-50 NT titer against the Alpha (B.1.1.7), Beta (B.1.351) and Delta (B.1.617.2) variants, respectively. 2021 Frontiers in immunology Abstract SARS_CoV_2 Y160T;R158N 67;61 72;66 S 59 60 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The use of glycan-masking in Ad-S-R158N/Y160T and Ad-S-D428N antigen design may help develop universal COVID-19 vaccines against current and future emerging SARS-CoV-2 variants. 2021 Frontiers in immunology Abstract SARS_CoV_2 Y160T;D428N;R158N 40;55;34 45;60;39 S;S 32;53 33;54 COVID-19 103 111 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. Given kinases might be elevated in cancer patients, the N501Y mutation containing lineages may be possibly much more infectious and additional care for cancer management might be taken into consideration by precision prevention, therapy or recovery. 2022 Travel medicine and infectious disease Abstract SARS_CoV_2 N501Y 56 61 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. However, the potential interactions with host cells linking N501Y mutation to pathogenic relevance remain elusive. 2022 Travel medicine and infectious disease Abstract SARS_CoV_2 N501Y 60 65 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. To our surprise, the Omicron receptor binding domain harboring N501Y mutation did not enhance binding to EGFR which might be due to the mutations of charged polar to uncharged polar side chains located on the interaction interfaces. 2022 Travel medicine and infectious disease Abstract SARS_CoV_2 N501Y 63 68 RBD 29 52 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. Variants of SARS-CoV-2 lineages including the most recently circulated Omicron, and previous pandemic B.1.351, B.1.1.7, which have been public concerns, contain a N501Y mutation located in the spike receptor binding domain. 2022 Travel medicine and infectious disease Abstract SARS_CoV_2 N501Y 163 168 RBD;S 199;193 222;198 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. We found kinases such as EGFR might potentially act as new factors involving the N501Y mutation binding through possible phosphorylation at Y501 and enhanced affinity in certain variants. 2022 Travel medicine and infectious disease Abstract SARS_CoV_2 N501Y 81 86 34931119 Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences. On the other hand, the P681H mutation contributed to the increased cavity size and relatively higher residue depth. 2022 International journal of peptide research and therapeutics Abstract SARS_CoV_2 P681H 23 28 34931119 Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences. The obtained results revealed that the N501Y substitution has altered the interaction orientation, augmented the number of interface bonds, and increased the affinity against the ACE2. 2022 International journal of peptide research and therapeutics Abstract SARS_CoV_2 N501Y 39 44 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Many of these substitutions have previously been found to independently dampen or even ablate antibody binding, and perhaps mediate antibody-mediated neutralization escape ( e.g ., K417N). 2021 bioRxiv Abstract SARS_CoV_2 K417N 181 186 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. Omicron was 41-84-fold less sensitive to neutralization than D614G and 5.3-7.4-fold less sensitive than Beta when assayed with serum samples obtained 4 weeks after 2 standard inoculations with 100 mug mRNA-1273. 2021 medRxiv Abstract SARS_CoV_2 D614G 61 66 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. To assess the potential risk of this variant to existing vaccines, serum samples from mRNA-1273 vaccine recipients were tested for neutralizing activity against Omicron and compared to neutralization titers against D614G and Beta in live virus and pseudovirus assays. 2021 medRxiv Abstract SARS_CoV_2 D614G 215 220 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. In the latter, we identified mutations E484K, L18F, and D614G. 2022 Infection, genetics and evolution Abstract SARS_CoV_2 D614G;E484K;L18F 56;39;46 61;44;50 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. Simulations of the D614G mutant show differences in behaviour between these clinical variants of the spike: the D614G mutant shows a significantly different conformational response for some structural motifs relevant for binding and fusion. 2021 Computational and structural biotechnology journal Abstract SARS_CoV_2 D614G;D614G 19;112 24;117 S 101 106 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. By contrast, Beta was outcompeted by Alpha and wt-S614G in hamsters and in mice expressing human ACE2. 2022 Nature Abstract SARS_CoV_2 S614G 50 55 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Here we show that the spike protein (S) from Alpha (also known as B.1.1.7) and Beta (B.1.351) VOCs had a greater affinity towards the human angiotensin-converting enzyme 2 (ACE2) receptor than that of the progenitor variant S(D614G) in vitro. 2022 Nature Abstract SARS_CoV_2 D614G 226 231 S;S;S 22;37;224 27;38;225 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. In hamsters, which support high viral replication levels, Alpha and wt-S614G showed similar fitness. 2022 Nature Abstract SARS_CoV_2 S614G 71 76 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. In vivo, competition experiments showed a clear fitness advantage of Alpha over wt-S614G in ferrets and two mouse models-the substitutions in S were major drivers of the fitness advantage. 2022 Nature Abstract SARS_CoV_2 S614G 83 88 S 142 143 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Our study highlights the importance of using multiple models to characterize fitness of VOCs and demonstrates that Alpha is adapted for replication in the upper respiratory tract and shows enhanced transmission in vivo in restrictive models, whereas Beta does not overcome Alpha or wt-S614G in naive animals. 2022 Nature Abstract SARS_CoV_2 S614G 285 290 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Progenitor variant virus expressing S(D614G) (wt-S614G) and the Alpha variant showed similar replication kinetics in human nasal airway epithelial cultures, whereas the Beta variant was outcompeted by both. 2022 Nature Abstract SARS_CoV_2 D614G;S614G 38;49 43;54 S 36 37 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. Nevertheless, the binding constant of PF-00835231 toward C145A Mpro is still good enough to inhibit the enzyme. 2021 Frontiers in pharmacology Abstract SARS_CoV_2 C145A 57 62 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. The C145A Mpro mutant interacts with PF-00835231 approximately 100-fold less effectively. 2021 Frontiers in pharmacology Abstract SARS_CoV_2 C145A 4 9 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. We examined the kinetic mechanism of peptide substrate binding and cleavage by wild-type Mpro and by its catalytically inactive mutant C145A. 2021 Frontiers in pharmacology Abstract SARS_CoV_2 C145A 135 140 34939673 Genomic characterization of the dominating Beta, V2 variant carrying vaccinated (Oxford-AstraZeneca) and nonvaccinated COVID-19 patient samples in Bangladesh: A metagenomics and whole-genome approach. Noteworthily, the receptor binding domain (RBD) region of S protein of all the isolates harbored similar substitutions including K417N, E484K, and N501Y that signify the Beta, while D614G, D215G, D80A, A67V, L18F, and A701V substitutions were commonly found in the non-RBD region of Spike proteins. 2022 Journal of medical virology Abstract SARS_CoV_2 A67V;A701V;D215G;D614G;D80A;E484K;K417N;L18F;N501Y 202;218;189;182;196;136;129;208;147 206;223;194;187;200;141;134;212;152 RBD;S;RBD;RBD;S 18;283;43;269;58 41;288;46;272;59 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Some concerning mutations associated with an impact on viral fitness have been described in the Spike protein, such as D614G, N501Y, E484K, K417N/T, L452R, and P681R, among others. 2021 Journal of developmental biology Abstract SARS_CoV_2 D614G;E484K;K417N;K417T;L452R;N501Y;P681R 119;133;140;140;149;126;160 124;138;147;147;154;131;165 S 96 101 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. The Delta variant has a particular genetic profile, bearing unique mutations, such as T478K in the spike protein and M203R in the nucleocapsid. 2021 Journal of developmental biology Abstract SARS_CoV_2 M203R;T478K 117;86 122;91 N;S 130;99 142;104 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. The first known mutation associated with higher transmissibility, D614G, was detected in early 2020. 2021 Journal of developmental biology Abstract SARS_CoV_2 D614G 66 71 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. Here, we report for the first time that chimeric crRNA could be critical in enhancing the specificity of CRISPR-Cas12a detecting of N501Y, which is shared by Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2 without compromising its sensitivity. 2021 PloS one Abstract SARS_CoV_2 N501Y 132 137 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. 9659 in ORF-10, 8782C > T in ORF-1ab, or 28144T > C in ORF-8, have been proposed for altering SARS-CoV-2 virulence and pathogenicity. 2021 Biology Abstract SARS_CoV_2 T28144C;C8782T 41;16 51;25 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. Therefore, in this study, we focused on A105V mutation of SARS-CoV-2 ORF7a accessory protein, which has been associated with severe COVID-19 clinical manifestation. 2021 Biology Abstract SARS_CoV_2 A105V 40 45 ORF7a 69 74 COVID-19 132 140 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. Well-characterized mutations in the spike protein, such as D614G, N439K, Delta69-70, E484K, or N501Y, are currently defining specific variants; however, some less studied mutations outside the spike region, such as p. 2021 Biology Abstract SARS_CoV_2 D614G;E484K;N439K;N501Y 59;85;66;95 64;90;71;100 S;S 36;193 41;198 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. Recently, a new variant, B.1620, with mutations (S477N-E484K) in the spike protein's receptor-binding domain (RBD) has been reported in Europe. 2021 Biology Abstract SARS_CoV_2 S477N;E484K 49;55 54;60 S;RBD 69;110 74;113 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. The current findings based on protein complex modeling and bio-simulation methods revealed the atomic features of the B.1.620 variant harboring S477N and E484K mutations in the RBD and the basis for infectivity. 2021 Biology Abstract SARS_CoV_2 E484K;S477N 154;144 159;149 RBD 177 180 34943523 Low Represented Mutation Clustering in SARS-CoV-2 B.1.1.7 Sublineage Group with Synonymous Mutations in the E Gene. Interestingly, these samples also harbored three other mutations (S137L-Orf1ab; N439K-S gene; A156S-N gene), which had a very low diffusion rate worldwide. 2021 Diagnostics (Basel, Switzerland) Abstract SARS_CoV_2 A156S;N439K;S137L 94;80;66 99;85;71 ORF1ab;N;S 72;100;86 78;101;87 34943523 Low Represented Mutation Clustering in SARS-CoV-2 B.1.1.7 Sublineage Group with Synonymous Mutations in the E Gene. Our sequencing data revealed the presence of a synonymous mutation (c.26415 C > T, TAC > TAT) in the E gene of all four samples showing the dropout in RT-qPCR. 2021 Diagnostics (Basel, Switzerland) Abstract SARS_CoV_2 C26415T 68 81 E 101 102 34943523 Low Represented Mutation Clustering in SARS-CoV-2 B.1.1.7 Sublineage Group with Synonymous Mutations in the E Gene. Within our database, one sample showed the synonymous mutation (c.26415 C > T, TAC > TAT) in the E gene. 2021 Diagnostics (Basel, Switzerland) Abstract SARS_CoV_2 C26415T 64 77 E 97 98 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. The clinical characteristics of patients with N501Y mutation in SARS-CoV-2 variants (N501YV) is not fully understood, especially in the setting of general practice. 2021 Journal of clinical medicine Abstract SARS_CoV_2 N501Y 46 51 34949225 Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N. These analyses revealed a unique spike mutation H245N that has never been reported before. 2021 BMC research notes Abstract SARS_CoV_2 H245N 48 53 S 33 38 34953513 Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. We analyzed longitudinal humoral responses against the D614G strain and variants of concern for SARS-CoV-2 in a cohort of SARS-CoV-2-naive and previously infected individuals who received the BNT162b2 mRNA vaccine with sixteen weeks between doses. 2022 Cell host & microbe Abstract SARS_CoV_2 D614G 55 60 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. Protein-protein docking and Molecular mechanics with generalised Born and surface area solvation (MM/GBSA) binding free energy analysis reveal that the spike mutants-L452R, T478K and N501Y have a higher binding affinity to human ACE2 as compared to the native spike protein. 2022 Journal of King Saud University. Science Abstract SARS_CoV_2 N501Y;T478K;L452R 183;173;166 188;178;171 S;S 152;260 157;265 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The present study is aimed at understanding the impact of the major mutations (L452R, T478K and N501Y) in the receptor-binding domain (RBD) of spike protein and their consequences on the binding affinity to human ACE2 through protein-protein docking and molecular dynamics simulation approaches. 2022 Journal of King Saud University. Science Abstract SARS_CoV_2 N501Y;T478K;L452R 96;86;79 101;91;84 S;RBD 143;135 148;138 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. Therefore, the findings of this study unravel plausible molecular mechanisms of increase in binding affinity of spike mutants (L452R, T478K and N501Y) to human ACE2 leading to higher virulence and infectivity of emerging SARS-CoV-2 variants. 2022 Journal of King Saud University. Science Abstract SARS_CoV_2 N501Y;T478K;L452R 144;134;127 149;139;132 S 112 117 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. Neutralizing activity of day 29 sera from bamlanivimab monotherapy cohorts against both spike E484Q and beta variant (B.1.351) were slightly reduced compared with placebo (by a factor of 3.1, p=0.001, and 2.9, p=0.002, respectively). 2021 Frontiers in immunology Abstract SARS_CoV_2 E484Q 94 99 S 88 93 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. Titer change from baseline against a receptor-binding domain mutant (Spike-RBD E484Q), as well as N-terminal domain (Spike-NTD) and nucleocapsid protein (NCP) epitopes were 1.4 to 4.1 fold lower at day 15-85 in mAb recipients compared with placebo. 2021 Frontiers in immunology Abstract SARS_CoV_2 E484Q 79 84 N;S;S;RBD;N 132;69;117;75;98 144;74;122;78;99 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. For example, G839W of SARS-CoV-1 corresponds to G857W of SARS-CoV-2, which decrease the stability of their S glycoproteins. 2021 Frontiers in molecular biosciences Abstract SARS_CoV_2 G839W;G857W 13;48 18;53 S 107 122 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. In addition, the mutations of L472P and F360S destabilized the 2003-2004 viral isolate. 2021 Frontiers in molecular biosciences Abstract SARS_CoV_2 F360S;L472P 40;30 45;35 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. The viral mutation analysis of the two different SARS-CoV-1 isolates showed that mutations, T487S and L472P, weakened the S-hACE2 binding of the 2003-2004 SARS-CoV-1 isolate. 2021 Frontiers in molecular biosciences Abstract SARS_CoV_2 L472P;T487S 102;92 107;97 S 122 123 34957346 Ultra-sensitive and fast optical detection of the spike protein of the SARS-CoV-2 using AgNPs/SiNWs nanohybrid based sensors. The study deliberately projects the factors that influence the growth of silicon nanowires, uniform decoration of AgNPs onto the SiNWs matrix along with detection of Rhodamine-6G (R6G) to optimize the best conditions for enhanced sensing of the spike protein. 2021 Surfaces and interfaces Abstract SARS_CoV_2 R6G 180 183 S 245 250 34957346 Ultra-sensitive and fast optical detection of the spike protein of the SARS-CoV-2 using AgNPs/SiNWs nanohybrid based sensors. Tremendous increase in sensitivity of R6G detection was perceived on SiNWs etched for 2 min (length=0.90 microm), followed by 30s of immersion time for their optimal decoration by AgNPs. 2021 Surfaces and interfaces Abstract SARS_CoV_2 R6G 38 41 34959053 Isolation of SARS-CoV-2 B.1.1.28.2 (P2) variant and pathogenicity comparison with D614G variant in hamster model. The sera from B.1.1.28.2 infected hamsters efficiently neutralized the D614G variant virus whereas 6-fold reduction in the neutralization was seen in case of D614G variant infected hamsters' sera with the B.1.1.28.2 variant. 2022 Journal of infection and public health Abstract SARS_CoV_2 D614G;D614G 71;158 76;163 34959053 Isolation of SARS-CoV-2 B.1.1.28.2 (P2) variant and pathogenicity comparison with D614G variant in hamster model. We report herewith the isolation of the P.2 variant (B.1.1.28.2) from international travelers and further its pathogenicity evaluation and comparison with D614G variant (B.1) in hamster model. 2022 Journal of infection and public health Abstract SARS_CoV_2 D614G 155 160 34960156 The Impact of Mutations on the Pathogenic and Antigenic Activity of SARS-CoV-2 during the First Wave of the COVID-19 Pandemic: A Comprehensive Immunoinformatics Analysis. The D614G mutation in spike and the P323Lmutation in RdRp are the globally dominant variants with a high frequency. 2021 Vaccines Abstract SARS_CoV_2 D614G 4 9 S;RdRP 22;53 27;57 34960694 Semi-Supervised Pipeline for Autonomous Annotation of SARS-CoV-2 Genomes. We observed 3362 non-redundant sequences per protein on average within this corpus and described key D614G and N501Y variants spatiotemporally in the initial genome corpus. 2021 Viruses Abstract SARS_CoV_2 D614G;N501Y 101;111 106;116 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Finally, the P681R substitution confers efficient cleavage of B.1.617 variants' spike proteins and the spike of Delta variants exhibited greater sensitivity to soluble ACE2 neutralization, as well as fusogenic activity, which may contribute to enhanced spread of Delta variants. 2021 Viruses Abstract SARS_CoV_2 P681R 13 18 S;S 80;103 85;108 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. As a consequence, Q675H mutation could confer a fitness advantage to SARS-CoV-2 by promoting a more efficient viral entry. 2021 Viruses Abstract SARS_CoV_2 Q675H 18 23 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. At the same time, it may suggest Q675H spike mutation involvement in SARS-CoV-2 evolution. 2021 Viruses Abstract SARS_CoV_2 Q675H 33 38 S 39 44 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Furin was predicted to have a greater affinity for Q675H than Q675 substrate conformations. 2021 Viruses Abstract SARS_CoV_2 Q675H 51 56 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Genotype screening was implemented in Italy and showed a significant prevalence of new SARS-CoV-2 mutants carrying Q675H mutation, near the furin cleavage site of spike protein. 2021 Viruses Abstract SARS_CoV_2 Q675H 115 120 S 163 168 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. In silico data show that the Q675H mutation gives rise to a hydrogen-bonds network in the spike polar region. 2021 Viruses Abstract SARS_CoV_2 Q675H 29 34 S 90 95 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Interestingly, here we have shown that Q675H spike mutation is documented in all the VOCs. 2021 Viruses Abstract SARS_CoV_2 Q675H 39 44 S 45 50 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Our studies reveal that Q675H spike mutation is the result of parallel evolution because it arose independently in separate evolutionary clades. 2021 Viruses Abstract SARS_CoV_2 Q675H 24 29 S 30 35 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Therefore, we performed phylogenetic and biocomputational analysis to better understand SARS-CoV-2 Q675H mutants' evolutionary relationships with other circulating lineages and Q675H function in its molecular context. 2021 Viruses Abstract SARS_CoV_2 Q675H;Q675H 99;177 104;182 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. These missing positions included mutations that are decisive for lineage assignation, such as G142D (n = 11), N501Y (n = 6), or E484K (n = 2). 2021 Viruses Abstract SARS_CoV_2 E484K;G142D;N501Y 128;94;110 133;99;115 34962614 Discovery of potential anti-SARS-CoV-2 drugs based on large-scale screening in vitro and effect evaluation in vivo. Seven compounds reduced weight loss and promoted weight regain of hamsters infected not only with the original strain but also the D614G variant. 2021 Science China. Life sciences Abstract SARS_CoV_2 D614G 131 136 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. Crystal and electron cryo-microscopy (cryo-EM) structure analyses revealed that P36-5D2 targeted to a conserved epitope on the receptor-binding domain of the spike protein, withstanding the three key mutations-K417N, E484K, and N501Y-found in the variants that are responsible for escape from many potent neutralizing mAbs, including some already approved for emergency use authorization (EUA). 2021 Frontiers in immunology Abstract SARS_CoV_2 E484K;N501Y;K417N 217;228;210 222;233;215 S 158 163 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. For the N121Q mutation, Gln121 still maintained a hydrogen bond with biliverdin; nevertheless, the overall binding mode deviated significantly under the reversal of the side chain of Phe175. 2021 Frontiers in molecular biosciences Abstract SARS_CoV_2 N121Q 8 13 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. In addition, N121Q significantly promoted the gate loop deviating to the biliverdin binding site and compressed the site. 2021 Frontiers in molecular biosciences Abstract SARS_CoV_2 N121Q 13 18 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. Our simulations indicated that the R190K mutation causes Lys190 to form six hydrogen bonds, guided by Asn99 and Ile101, which brings Lys190 closer to Arg102 and Asn121, thereby weakening the interaction energy between biliverdin and Ile101 as well as Lys190. 2021 Frontiers in molecular biosciences Abstract SARS_CoV_2 R190K 35 40 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. Two single-site mutations, R190K and N121Q, were deemed to weaken the binding affinity of biliverdin although the underlying molecular mechanism is still unknown. 2021 Frontiers in molecular biosciences Abstract SARS_CoV_2 N121Q;R190K 37;27 42;32 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. In this study, we use pseudoviruses and reveal that the spike protein of the Lambda variant is more infectious than that of other variants due to the T76I and L452Q mutations. 2022 Cell reports Abstract SARS_CoV_2 L452Q;T76I 159;150 164;154 S 56 61 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Furthermore, the binding strength of different MTs along with WT (wildtype) was revealed that MTs showed differential binding affinities to host protein with high binding strength exhibited by V367F and V483A MTs. 2022 Computer methods and programs in biomedicine Abstract SARS_CoV_2 V367F;V483A 193;203 198;208 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The spike protein mutations D614G-S943T-V622F (-75.17 kcal/mol), D614G-Q677H (-75.78 kcal/mol), and N74K-D614G (-73.84 kcal/mol) exhibit stronger binding energy than the wild type (-66.34 kcal/mol), thus increasing infectivity. 2022 Computers in biology and medicine Abstract SARS_CoV_2 D614G;D614G;N74K;D614G;Q677H;S943T;V622F 28;65;100;105;71;34;40 33;70;104;110;76;39;45 S 4 9 34968879 SARS-CoV-2 wastewater surveillance in Germany: Long-term RT-digital droplet PCR monitoring, suitability of primer/probe combinations and biomarker stability. The occurrence of the N501Y mutation in the wastewater of Karlsruhe was consistent with the occurrence of the alpha-variant (B.1.1.7) in the corresponding individual clinical tests. 2022 Water research Abstract SARS_CoV_2 N501Y 22 27 34968879 SARS-CoV-2 wastewater surveillance in Germany: Long-term RT-digital droplet PCR monitoring, suitability of primer/probe combinations and biomarker stability. This methodology was used to determine the SARS-CoV-2 concentration and the proportion of N501Y mutation in raw sewage of the wastewater treatment plant of the city of Karlsruhe in south-western Germany over a period of 1 year (June 2020 to July 2021). 2022 Water research Abstract SARS_CoV_2 N501Y 90 95 34975266 SARS-CoV-2 Variants: Mutations and Effective Changes. Certain mutations (D614G, E484K, N501Y, K417N, L452R and P681R) have appeared across several different strains, often accompanied by others that may be complementary working together to confer increased infectivity, fitness, or resistance to neutralization. 2021 Biotechnology and bioprocess engineering Abstract SARS_CoV_2 E484K;K417N;L452R;N501Y;P681R;D614G 26;40;47;33;57;19 31;45;52;38;62;24 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Consequently, we reported three variants N501I, N501T, and N501V could worsen the situation further if they emerged. 2022 Computers in biology and medicine Abstract SARS_CoV_2 N501I;N501T;N501V 41;48;59 46;53;64 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Our analysis revealed that N501I, N501T, and N501V increase the binding affinity and alter the intra and inter-residue bonding networks. 2022 Computers in biology and medicine Abstract SARS_CoV_2 N501I;N501T;N501V 27;34;45 32;39;50 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The N501T has shown strong positive selection and fitness in other animals. 2022 Computers in biology and medicine Abstract SARS_CoV_2 N501T 4 9 34981057 SARS-CoV-2 Omicron neutralization by therapeutic antibodies, convalescent sera, and post-mRNA vaccine booster. A booster vaccination significantly increased titers against Omicron to levels comparable to those seen against the ancestral (D614G) variant after two immunizations. 2021 bioRxiv Abstract SARS_CoV_2 D614G 127 132 34981064 Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. Upon training a TLmutation model on the effects of single mutations, we identified several ACE2 double mutants that bind to RBD with tighter affinity as compared to the wild type, most notably, L79V;N90D that binds RBD with similar affinity to ACE2 2 .v.2.4. 2021 bioRxiv Abstract SARS_CoV_2 L79V;N90D 194;199 198;203 RBD;RBD 124;215 127;218 34982246 Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing. Among the 10 genetic variants, 1 missense mutation (c.1139A > G, p.Lys292Glu) in the Open Reading Frame 1ab (ORF1ab) positioned at 112 in the non-structural protein 2 (NSP2) was found to be unique. 2022 Current microbiology Abstract SARS_CoV_2 K292E;A1139G 65;53 76;63 ORF1ab;Nsp2 109;168 115;172 34982509 Engineered small extracellular vesicles displaying ACE2 variants on the surface protect against SARS-CoV-2 infection. Furthermore, engineered sEVs inhibit the entry of wild-type (WT), the globally dominant D614G variant, Beta (K417N-E484K-N501Y) variant, and Delta (L452R-T478K-D614G) variant SARS-CoV-2 pseudovirus, and protect against authentic SARS-CoV-2 and Delta variant infection. 2022 Journal of extracellular vesicles Abstract SARS_CoV_2 D614G;K417N;L452R;D614G;E484K;N501Y;T478K 88;109;148;160;115;121;154 93;114;153;165;120;126;159 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. Among them, mutations C1709A (a change of C to A at position 1709) and C56G, respectively, were found in more than 99% of the genomes of Alpha and Delta variants and were specific to them. 2022 Microbiology spectrum Abstract SARS_CoV_2 C1709A;C1709A;C56G 42;22;71 65;28;75 34985974 Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2. As a proof of concept, the fusion protein-coated cellulose substrates exhibited enhanced capture efficiency against SARS-CoV-2 pseudovirus of both the wild type and the D614G variant, the latter of which has been shown to confer higher infectivity. 2022 Applied and environmental microbiology Abstract SARS_CoV_2 D614G 169 174 34985974 Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2. The immobilization of the fusion proteins on cellulose substrates enhanced the capture efficiency of Nbs against SARS-CoV-2 pseudoviruses of the wild type and the D614G variant, the latter of which has been shown to confer higher infectivity. 2022 Applied and environmental microbiology Abstract SARS_CoV_2 D614G 163 168 34987509 An Intranasal OMV-Based Vaccine Induces High Mucosal and Systemic Protecting Immunity Against a SARS-CoV-2 Infection. We developed an intranasal COVID-19 subunit vaccine, based on a recombinant, six-proline-stabilized, D614G spike protein (mC-Spike) of SARS-CoV-2 linked via the LPS-binding peptide sequence mCramp (mC) to outer membrane vesicles (OMVs) from Neisseria meningitidis. 2021 Frontiers in immunology Abstract SARS_CoV_2 D614G 101 106 Membrane;S;S 211;107;125 219;112;130 COVID-19 27 35 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Interestingly, 8 months after inoculation with the D614G-specific vaccine, a new boost with this bivalent vaccine potently elicits cross-neutralizing antibodies for SARS-CoV-2 variants in rhesus macaques. 2022 Cell reports Abstract SARS_CoV_2 D614G 51 56 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. We developed a bivalent nanoparticle vaccine that displays the receptor binding domains (RBDs) of the D614G and B.1.351 strains. 2022 Cell reports Abstract SARS_CoV_2 D614G 102 107 RBD;RBD 63;89 87;93 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. We suggest that the D614G/B.1.351 bivalent vaccine could be used as an initial single dose or a sequential enforcement dose to prevent infection with SARS-CoV-2 and its variants. 2022 Cell reports Abstract SARS_CoV_2 D614G 20 25 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. With a prime-boost or a single-dose strategy, this vaccine elicits a robust neutralizing antibody and full protection against infection with the authentic D614G or B.1.351 strain in human angiotensin-converting enzyme 2 transgene mice. 2022 Cell reports Abstract SARS_CoV_2 D614G 155 160 34993157 Clinical, Virological, Immunological, and Genomic Characterization of Asymptomatic and Symptomatic Cases With SARS-CoV-2 Infection in India. The D614G mutation in spike protein is linked with higher virus replication efficiency and severe SARS-CoV-2 infection as three patients had higher viral load, and among them, two patients with this mutation passed away. 2021 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 D614G 4 9 S 22 27 COVID-19 98 118 34995777 A CLUSTER OF SARS-COV-2 DELTA VARIANT OF CONCERN ADDITIONALLY HARBORING F490S, NORTHERN LOMBARDY, ITALY. In this article, we report a cluster caused by B.1.617.2 harboring the additional mutation of concern (MOC) F490S. 2022 International journal of infectious diseases Abstract SARS_CoV_2 F490S 108 113 34995777 A CLUSTER OF SARS-COV-2 DELTA VARIANT OF CONCERN ADDITIONALLY HARBORING F490S, NORTHERN LOMBARDY, ITALY. The immune escape mutation F490S, first identified in the Lambda VOI, appears to impair vaccine efficacy and is rapidly increasing in prevalence worldwide. 2022 International journal of infectious diseases Abstract SARS_CoV_2 F490S 27 32 34997207 SARS-CoV-2 non-structural protein 6 triggers NLRP3-dependent pyroptosis by targeting ATP6AP1. L37F NSP6 variant, which was associated with asymptomatic COVID-19, exhibited reduced binding to ATP6AP1 and weakened ability to impair lysosome acidification to induce pyroptosis. 2022 Cell death and differentiation Abstract SARS_CoV_2 L37F 0 4 Nsp6 5 9 COVID-19 58 66 34998405 Different decay of antibody response and VOC sensitivity in naive and previously infected subjects at 15 weeks following vaccination with BNT162b2. By means of ELISA and pseudotyped-neutralization assays, we investigated the kinetics of developed IgG-RBD and their neutralizing activity against both the ancestral D614G and the SARS-CoV-2 variants of concern emerged later, respectively. 2022 Journal of translational medicine Abstract SARS_CoV_2 D614G 166 171 RBD 103 106 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Concurrent with the upsurge of the second wave in March 2021, 73% (33/45) of RBD sequences harboured L452R/E484Q mutations characteristic of the Kappa variant. 2022 Archives of virology Abstract SARS_CoV_2 L452R;E484Q 101;107 106;112 RBD 77 80 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. In April 2021, co-circulation of Kappa (37%) and Delta (L452R/T478K, 59%) variants was recorded. 2022 Archives of virology Abstract SARS_CoV_2 L452R;T478K 56;62 61;67 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. A point mutation (H84T) divorces BanLec mitogenicity from antiviral activity. 2021 Frontiers in immunology Abstract SARS_CoV_2 H84T 18 22 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. H84T-Banana Lectin (BanLec) CAR-NK cells bind high mannose glycosites that decorate the SARS-CoV-2 envelope, thereby decreasing cellular infection in a model of SARS-CoV-2. 2021 Frontiers in immunology Abstract SARS_CoV_2 H84T 0 4 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. H84T-BanLec CAR-NK cells are a promising cell therapy for further testing against wild-type SARS-CoV-2 virus in models of SARS-CoV-2 infection. 2021 Frontiers in immunology Abstract SARS_CoV_2 H84T 0 4 COVID-19 122 142 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. H84T-BanLec CAR-NK cells are innate effector cells, activated by virus. 2021 Frontiers in immunology Abstract SARS_CoV_2 H84T 0 4 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. H84T-BanLec CAR-NK cells reduced S-protein pseudotyped lentiviral infection of 293T cells expressing ACE2, the receptor for SARS-CoV-2. 2021 Frontiers in immunology Abstract SARS_CoV_2 H84T 0 4 S 33 34 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. Our H84T-BanLec CAR was devised to specifically direct NK cell binding of SARS-CoV-2 envelope glycosites to promote viral clearance. 2021 Frontiers in immunology Abstract SARS_CoV_2 H84T 4 8 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. The H84T-BanLec CAR was stably expressed at high density on primary human NK cells during two weeks of ex vivo expansion. 2021 Frontiers in immunology Abstract SARS_CoV_2 H84T 4 8 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. We designed a chimeric antigen receptor (CAR) that incorporates H84T-BanLec as the extracellular moiety. 2021 Frontiers in immunology Abstract SARS_CoV_2 H84T 64 68 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. Approximately, 20% of SNP changes occurred in spike glycoprotein (S) gene, such as p.Asp501Tyr, p.Pro681His, and p.Pro681Arg. 2021 Frontiers in public health Abstract SARS_CoV_2 D501Y;P681R;P681H 83;113;96 94;124;107 S;S 46;66 64;67 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. It is worth mentioning that amino acid substitution of p.Asp614Gly was significantly positively correlated with the clinical severity of patients. 2021 Frontiers in public health Abstract SARS_CoV_2 D614G 55 66 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. The amino acid replacements of p.Ser316Thr and p.Lu484Lys were significantly negatively correlated with the course of disease. 2021 Frontiers in public health Abstract SARS_CoV_2 S316T 31 42 35007661 A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: Effects on proteolytic cleavage and ACE2 binding. Using a series of innovative ELISA-based assays, this furin site blocking antibody displayed high sensitivity and specificity for the S1/S2 furin cleavage site, including with a P681R mutation, and demonstrated effective blockage of both enzyme-mediated cleavage and spike-ACE2 interaction. 2022 Immunology letters Abstract SARS_CoV_2 P681R 178 183 S 267 272 35008446 Analysis of Immune Escape Variants from Antibody-Based Therapeutics against COVID-19: A Systematic Review. While the former is mainly associated with specific single amino acid mutations at residues within the receptor-binding domain (e.g., E484K/Q, Q493R, and S494P), a few cases of immune evasion after CCP were associated with recurrent deletions within the N-terminal domain of the spike protein (e.g., DeltaHV69-70, DeltaLGVY141-144 and DeltaAL243-244). 2021 International journal of molecular sciences Abstract SARS_CoV_2 E484K;E484Q;Q493R;S494P 134;134;143;154 141;141;148;159 S;N 279;254 284;255 35012335 Alpha-Soluble NSF Attachment Protein Prevents the Cleavage of the SARS-CoV-2 Spike Protein by Functioning as an Interferon-Upregulated Furin Inhibitor. IMPORTANCE Some key mutations of SARS-CoV-2 spike protein, such as D614G and P681R mutations, increase the transmission or pathogenicity by enhancing the cleavage efficacy of spike protein by furin. 2022 mBio Abstract SARS_CoV_2 D614G;P681R 67;77 72;82 S;S 44;175 49;180 35013591 Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California. Vaccine breakthrough infections were more commonly associated with circulating antibody-resistant variants carrying >=1 mutation associated with decreased antibody neutralization (L452R/Q, E484K/Q and/or F490S) than infections in unvaccinated individuals (78% versus 48%, P = 1.96 x 10-8). 2022 Nature microbiology Abstract SARS_CoV_2 E484K;E484Q;F490S;L452Q;L452R 189;189;204;180;180 196;196;209;187;187 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. By using our pipeline, we built 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for the VoC B.1.1.7-United Kingdom (carrying the mutations of concern/interest N501Y, S494P, E484K at the RBD), P.1-Japan/Brazil (RBD mutations: K417T, E484K, N501Y), B.1.351-South Africa (RBD mutations: K417N, E484K, N501Y), B.1.427/B.1.429-California (RBD mutations: L452R), the B.1.141 (RBD mutations: N439K), and the recent B.1.617.1-India (RBD mutations: L452R; E484Q) and the B.1.620 (RBD mutations: S477N; E484K). 2022 The EPMA journal Abstract SARS_CoV_2 E484K;E484K;E484K;E484K;E484Q;K417N;K417T;L452R;L452R;N439K;N501Y;N501Y;N501Y;S477N;S494P 198;257;316;518;472;309;250;374;465;410;184;264;323;511;191 203;262;321;523;477;314;255;379;470;415;189;269;328;516;196 S;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD 72;78;211;235;294;359;395;450;496 77;81;214;238;297;362;398;453;499 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Conversely, it was also observed that the replacement of a single acidic/hydrophilic residue with a basic residue (E484K or N439K) at the "stern" or "bow" regions, of the boat-shaped receptor binding motif on the RBD, appears to determine an interaction energy with ACE2 receptor higher than that observed with single mutations occurring at the "hull" region or with other multiple mutants. 2022 The EPMA journal Abstract SARS_CoV_2 N439K;E484K 124;115 129;120 RBD 213 216 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Notably, the P.1 Japan/Brazil variant present three mutations, K417T, E484K, N501Y, located along the entire receptor binding motif, which apparently determines the highest interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein-protein interface, among those calculated. 2022 The EPMA journal Abstract SARS_CoV_2 E484K;K417T;N501Y 70;63;77 75;68;82 S;RBD 210;216 215;219 35013735 Phylogenetic estimates of SARS-CoV-2 introductions into Washington State. Lineages with the Spike D614G variant accounted for the majority (88%) of introductions. 2021 Lancet Regional Health. Americas Abstract SARS_CoV_2 D614G 24 29 S 18 23 35014989 COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis. Most (291/299, 97.3%) of our samples were dominated by the spike protein D614G substitution and were from SARS-CoV-2 B.1 lineage or one of 37 different B.1 sublineages, with none representing more than 8.7% (26/299) of the cases. 2021 JMIRx med Abstract SARS_CoV_2 D614G 73 78 S 59 64 35014989 COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis. Multiple SARS-CoV-2 lineages were distributed in patients in New England early in the COVID-19 era, mostly related to viruses from New York State with D614G mutation. 2021 JMIRx med Abstract SARS_CoV_2 D614G 151 156 COVID-19 86 94 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Antibodies in group E (for example, S309)6 and group F (for example, CR3022)7, which often exhibit broad sarbecovirus neutralizing activity, are less affected by Omicron, but a subset of neutralizing antibodies are still escaped by G339D, N440K and S371L. 2022 Nature Abstract SARS_CoV_2 G339D;N440K;S371L 232;239;249 237;244;254 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Specifically, neutralizing antibodies in groups A-D, the epitopes of which overlap with the ACE2-binding motif, are largely escaped by K417N, G446S, E484A and Q493R. 2022 Nature Abstract SARS_CoV_2 E484A;G446S;K417N;Q493R 149;142;135;159 154;147;140;164 35016198 Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2. Moreover, we also identified four new spike mutations (S371L, N440K, G446S and Q493R) that confer greater antibody resistance on B.1.1.529. 2022 Nature Abstract SARS_CoV_2 G446S;N440K;Q493R;S371L 69;62;79;55 74;67;84;60 S 38 43 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. D614G is the commonest and predominant mutation found among the S-protein followed by L54F. 2021 Journal of global infectious diseases Abstract SARS_CoV_2 L54F;D614G 86;0 90;5 S 64 65 35018385 Integrin/TGF-beta1 inhibitor GLPG-0187 blocks SARS-CoV-2 Delta and Omicron pseudovirus infection of airway epithelial cells which could attenuate disease severity. Omicron pseudovirus infected normal human small airway epithelial (HSAE) cells significantly less than D614G or Delta variant pseudovirus, and GLPG-0187 effectively blocked SARS-CoV-2 pseudovirus infection in a dose-dependent manner across multiple viral variants. 2022 medRxiv Abstract SARS_CoV_2 D614G 103 108 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. Because the G29195T mutation occurs within a region probed by a commonly referenced U.S. 2022 Microbiology spectrum Abstract SARS_CoV_2 G29195T 12 19 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. CDC N gene reverse transcription (RT)-PCR assay, we hypothesize that the G29195T mutation rendered the N gene target of a proprietary commercial assay undetectable. 2022 Microbiology spectrum Abstract SARS_CoV_2 G29195T 73 80 N;N 4;103 5;104 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. Potential diagnostic escapes, such as those of clinical samples harboring the G29195T mutation, may result in false-negative SARS-CoV-2 RT-PCR results. 2022 Microbiology spectrum Abstract SARS_CoV_2 G29195T 78 85 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. The putative diagnostic escape G29195T mutation demonstrates the need for nearly real-time surveillance, as emergence of a novel SARS-CoV-2 variant with the potential to escape diagnostic tests continues to be a threat. 2022 Microbiology spectrum Abstract SARS_CoV_2 G29195T 31 38 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. Notably, analysis of the plasma neutralization activity against these variants showed that the L1197I mutation at the S2 subunit of the spike can affect the plasma neutralization activity. 2022 PLoS pathogens Abstract SARS_CoV_2 L1197I 95 101 S 136 141 35022734 But Mouse, You Are Not Alone: On Some Severe Acute Respiratory Syndrome Coronavirus 2 Variants Infecting Mice. This effect could be enhanced by mutations in positions 417, 484, and 493 (especially K417N, E484K, Q493K, and Q493R), and to a lesser extent by mutations in positions 486 and 499 (such as F486L and P499T). 2022 ILAR journal Abstract SARS_CoV_2 E484K;F486L;K417N;P499T;Q493K;Q493R 93;189;86;199;100;111 98;194;91;204;105;116 35025877 A short plus long-amplicon based sequencing approach improves genomic coverage and variant detection in the SARS-CoV-2 genome. Analysis showed 26 SARS-CoV-2 lineage defining mutations including 4 known variants of concern K417N, E484K, N501Y, P618H in spike gene. 2022 PloS one Abstract SARS_CoV_2 E484K;K417N;N501Y;P618H 102;95;109;116 107;100;114;121 S 125 130 35025877 A short plus long-amplicon based sequencing approach improves genomic coverage and variant detection in the SARS-CoV-2 genome. For example, G172V mutation in the ORF3a protein and A2A mutation in Membrane protein were missed by the ARTIC assay. 2022 PloS one Abstract SARS_CoV_2 A2A;G172V 53;13 56;18 Membrane;ORF3a 69;35 77;40 35026305 SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021. We evaluated Allplex SARS-CoV-2 Master Assay and Variants I Assay to detect HV69/70 deletion, Y144 deletion, E484K, N501Y, and P681H spike mutations in 248 positive samples collected in Kuala Lumpur, Malaysia, between January and May 2021. 2022 Journal of virological methods Abstract SARS_CoV_2 E484K;N501Y;P681H 109;116;127 114;121;132 S 133 138 35028838 SARS-CoV-2 phase I transmission and mutability linked to the interplay of climatic variables: a global observation on the pandemic spread. The onset of the D614G mutation and subsequent changes to D614 before March, later G614 in mid-March, and S943P, A831V, D839/Y/N/E in April were observed in Asian and European countries. 2022 Environmental science and pollution research international Abstract SARS_CoV_2 A831V;D614G;S943P 113;17;106 118;22;111 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. A single mutant of A520S, V367F, and S494P in the above three VOCs enhanced infectivity in ACE2-overexpressing 293T cells of different species, LLC-MK2 and Vero cells. 2022 Journal of medical virology Abstract SARS_CoV_2 A520S;S494P;V367F 19;37;26 24;42;31 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Regarding neutralization, it is noteworthy that E484K, N501Y, K417N, and N439K predispose to monoclonal antibodies (mAbs) protection failure in the 15 high-frequency mutations. 2022 Journal of medical virology Abstract SARS_CoV_2 E484K;K417N;N439K;N501Y 48;62;73;55 53;67;78;60 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. Gene sequencing showed mutation within ORF1b at position P314L. 2022 New microbes and new infections Abstract SARS_CoV_2 P314L 57 62 35041639 A 48-Year-Old Immunocompetent Female Resident of Southern Florida with Confirmed Reinfection with P.1 (Gamma) Variant of SARS-CoV-2. Whole-genome sequencing (WGS) of viral RNA from the patient's second infection confirmed that the viral strain was P.1 variant containing the E484K spike protein substitution. 2022 The American journal of case reports Abstract SARS_CoV_2 E484K 142 147 S 148 153 35042962 Two short low complexity regions (LCRs) are hallmark sequences of the Delta SARS-CoV-2 variant spike protein. The presence of the medically-important point mutations P681R and D950N in these LCRs, combined with the ubiquity of these regions in the highly contagious Delta variant opens the possibility that they may play a role in its rapid spread. 2022 Scientific reports Abstract SARS_CoV_2 D950N;P681R 66;56 71;61 35044933 SARS-CoV-2 genetic diversity and variants of concern in Saudi Arabia. D614G was associated with higher morbidities than the wild-type virus, including higher rates of death and hospitalization. 2021 Journal of infection in developing countries Abstract SARS_CoV_2 D614G 0 5 35044933 SARS-CoV-2 genetic diversity and variants of concern in Saudi Arabia. Risk of death was highest with the NSP12_P323L mutation (OR = 1.84; 95% CI = 0.37-9.30) and lowest with the NS3_Q57H mutation (OR = 0.43; 95% CI = 0.25-0.727). 2021 Journal of infection in developing countries Abstract SARS_CoV_2 P323L;Q57H 41;112 46;116 Nsp12;NS3 35;108 40;111 35044933 SARS-CoV-2 genetic diversity and variants of concern in Saudi Arabia. The most common variants detected were the NSP12_P323L mutation 94.9%, followed by the D614G mutation (76%) and the NS3_Q57H mutation (71.4%). 2021 Journal of infection in developing countries Abstract SARS_CoV_2 D614G;P323L;Q57H 87;49;120 92;54;124 Nsp12;NS3 43;116 48;119 35044933 SARS-CoV-2 genetic diversity and variants of concern in Saudi Arabia. The NS3_Q57H mutation was the only variant associated with better patient outcome than the wild type. 2021 Journal of infection in developing countries Abstract SARS_CoV_2 Q57H 8 12 NS3 4 7 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. In SARS-CoV-2 variant detection, RAT had a 42.8% detection sensitivity in samples with RT-qPCR amplification range 20 <= Cq <25 containing the single nucleotide polymorphisms (SNP) K417N/T, N501Y and E484K, associated with beta or gamma SARS-CoV-2 variants. 2021 Frontiers in public health Abstract SARS_CoV_2 E484K;K417N;K417T;N501Y 200;181;181;190 205;188;188;195 35047533 Differences in Clinical Characteristics Between Delta Variant and Wild-Type SARS-CoV-2 Infected Patients. Methods: We reported one cohort of 341 wild-type patients with COVID-19 admitted at Wuhan, China in 2020 and the other cohort of 336 delta variant patients with COVID-19 admitted at Yangzhou, China in 2021, with comparisons of their demographic information, medical history, clinical manifestation, and hematological data. 2021 Frontiers in medicine Abstract SARS_CoV_2 336 del 129 138 COVID-19;COVID-19 63;161 71;169 35051442 Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests. Whole genome sequencing on a subset of patient samples identified a highly conserved G15451A, non-synonymous mutation exclusively within the RdRp gene of Delta variants, which may cause reduced RT-PCR amplification efficiency. 2022 Journal of virological methods Abstract SARS_CoV_2 G15451A 85 92 RdRP 141 145 35055023 Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors. The MD investigations reveal that the H3 truncation results in a small inhibitor with a -1.5 kcal/mol tighter binding to RBD than original LCB1, while the best miniprotein with higher binding affinity involves D17R or E11V + D17R mutation. 2022 International journal of molecular sciences Abstract SARS_CoV_2 D17R;D17R;E11V 210;225;218 214;229;222 RBD 121 124 35056548 Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan. Phylogenetic and haplotype network analysis indicated that the CA strains were derived from a common ancestral strain introduced on the CA cruise ship and spread in a superspreading event-like manner, resulting in several mutations that might have affected viral characteristics, including the P681H substitution in the spike protein. 2022 Microorganisms Abstract SARS_CoV_2 P681H 294 299 S 320 325 35056592 SARS-CoV-2 Evolution and Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIV Immune Suppression. SARS-CoV-2 was identified as variant Alpha (PANGO lineage B.1.1.7) with mutation S:E484K. 2022 Microorganisms Abstract SARS_CoV_2 E484K 83 88 S 81 82 35060147 SARS-CoV-2 intralineage variation and temporal patterns of COVID-19 risk factors in three cities of southeastern Brazil: Age, sex, and race. Intralineage variation revealed a significant amino-acid substitution in the ORF3a encoding protein (A33S) present in four out of six (67%) P.1 Maua isolates. 2022 Journal of medical virology Abstract SARS_CoV_2 A33S 101 105 ORF3a 77 82 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. The neutralization assay testing the Wuhan convalescents' sera one-year post-infection showed a more dramatic reduction (10.15 fold) of neutralization against the Omicron variant than the Delta variant (1.79 fold) compared with the original strain with D614G. 2022 Emerging microbes & infections Abstract SARS_CoV_2 D614G 253 258 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. In addition to the well-known single mutation in the RBD, the recent new mutation strains with an RBD "double mutation" are causing new outbreaks globally, as represented by the delta strain containing RBD L452R/T478K. 2021 Viruses Abstract SARS_CoV_2 L452R;T478K 206;212 211;217 RBD;RBD;RBD 53;98;202 56;101;205 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. Using the methods of molecular dynamics simulation, superimposed structural comparison, free binding energy estimation, and antibody escaping, we investigated the relationship between the ACE2 receptor and the RBD double mutants of L452R/T478K (delta), L452R/E484Q (kappa), and E484K/N501Y (beta, gamma). 2021 Viruses Abstract SARS_CoV_2 E484K;L452R;L452R;E484Q;N501Y;T478K 278;232;253;259;284;238 283;237;258;264;289;243 RBD 210 213 35062211 SARS-CoV-2 Spike Expression at the Surface of Infected Primary Human Airway Epithelial Cells. Human airway epithelial cells (pAECs) were infected with authentic SARS-CoV-2 D614G or Alpha variants. 2021 Viruses Abstract SARS_CoV_2 D614G 78 83 35062214 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. Structural modeling supported a potential functional impact of the D1118H and L452R mutations. 2021 Viruses Abstract SARS_CoV_2 D1118H;L452R 67;78 73;83 35062281 Intra-Host SARS-CoV-2 Evolution in the Gut of Mucosally-Infected Chlorocebus aethiops (African Green Monkeys). Three amino acid changes were also identified; ORF 1a S2103F, and spike D215G and H655Y, which were detected in rectal swabs from all sampled animals. 2022 Viruses Abstract SARS_CoV_2 D215G;H655Y;S2103F 72;82;54 77;87;60 S 66 71 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. Mathematical, statistical, and bioinformatic analyses demonstrated that our choice allowed us to identify all variants even without looking for all related mutations, as some of them are shared by different variants (e.g., N501Y is found in the Alpha, Beta, and Gamma variants) whereas others, that are more informative, are unique (e.g., A57 distinctive to the Alpha variant). 2022 Viruses Abstract SARS_CoV_2 N501Y 223 228 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. Similarly, the L452R mutation of B.1.617.2 (Delta) variant is present in A.2.5. 2022 Viruses Abstract SARS_CoV_2 L452R 15 20 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. Some of the pivotal mutations such as N501Y and E484K in the receptor-binding domain (RBD) detected in B.1.1.7 (Alpha), B.1.351 (Beta) and P.1 (Gamma) are now present within the Mu variant. 2022 Viruses Abstract SARS_CoV_2 E484K;N501Y 48;38 53;43 RBD 86 89 35062734 Immunogenicity of a Heterologous Prime-Boost COVID-19 Vaccination with mRNA and Inactivated Virus Vaccines Compared with Homologous Vaccination Strategy against SARS-CoV-2 Variants. Three groups showed reduced neutralizing activity against D614G, beta, theta and delta variants. 2022 Vaccines Abstract SARS_CoV_2 D614G 58 63 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Delta variant spike mutation of T19R, G142D, E156G, L452R, and deletion (F157 and R158) helps in escaping antibody response, T478K and D614G enhance viral affinity with ACE2 receptor while P681R and D950N result in higher replication and transmissibility by cleaving S1/S2 at furin site. 2022 Microbial pathogenesis Abstract SARS_CoV_2 D614G;D950N;E156G;G142D;L452R;P681R;T19R;T478K 135;199;45;38;52;189;32;125 140;204;50;43;57;194;36;130 S 14 19 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. Strikingly, in hamsters that had been infected with the omicron variant, a 3 log10 lower viral RNA load was detected in the lungs as compared to animals infected with D614G and no infectious virus was detectable in this organ. 2022 Antiviral research Abstract SARS_CoV_2 D614G 167 172 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. We here wanted to explore the infectivity of the omicron variant in comparison to the ancestral D614G strain in the hamster model. 2022 Antiviral research Abstract SARS_CoV_2 D614G 96 101 35067489 Simultaneous Screening of SARS-CoV-2 Omicron and Delta Variants Using High-Resolution Melting Analysis. In this study, we successfully developed a novel screening assay using high-resolution melting analysis, in which two genotypes at G446/L452 and S477/T478 RBD were determined (G446S/L452 and S477N/T478K for Omicron; G446/L452R and S477/T478K for Delta). 2022 Biological & pharmaceutical bulletin Abstract SARS_CoV_2 S477N;G446L;G446S;L452R;T478K;T478K 191;176;176;221;197;236 196;181;181;226;202;241 RBD 155 158 35070322 Sequence analysis for SNP detection and phylogenetic reconstruction of SARS-cov-2 isolated from Nigerian COVID-19 cases. CONCLUSION AND RECOMMENDATION: There was a preponderance of L lineage (to include the new lineage scheme) and D614G mutants. 2022 New microbes and new infections Abstract SARS_CoV_2 D614G 110 115 35070322 Sequence analysis for SNP detection and phylogenetic reconstruction of SARS-cov-2 isolated from Nigerian COVID-19 cases. Majority (72.2%) of viruses in Nigeria are of L lineage with preponderance of D614G mutation which accounted for 11 (61.1%) out of the 18 viral sequences. 2022 New microbes and new infections Abstract SARS_CoV_2 D614G 78 83 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. Signature substitution at positions S:L452R, S:P681R, and S:D614G were commonly detected in the Delta, Delta AY.1, and Kappa variants whereas S:T19R and S:T478K were confined to Delta and Delta AY.1 variants only. 2021 Frontiers in medicine Abstract SARS_CoV_2 D614G;L452R;P681R;T19R;T478K 60;38;47;144;155 65;43;52;148;160 S;S;S;S;S 36;45;58;142;153 37;46;59;143;154 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. Vaccine breakthrough infections showed unique mutational changes at position S:D574Y in the case of the Delta variant, whereas position S:T95 was conserved among Kappa variants compared to the Wuhan isolate. 2021 Frontiers in medicine Abstract SARS_CoV_2 D574Y 79 84 S;S 77;136 78;137 35071665 Infection spread simulation technology in a mixed state of multi variant viruses. (2) The rate of increase will be mainly by d strain (L452R) virus, while the increase by a strain (N501Y) virus will be suppressed. 2022 AIMS public health Abstract SARS_CoV_2 L452R;N501Y 53;99 58;104 35072475 R346K Mutation in the Mu Variant of SARS-CoV-2 Alters the Interactions with Monoclonal Antibodies from Class 2: A Free Energy Perturbation Study. For comparison, the addition of the K417N mutation, present in the newly registered Mu variant in July 2021 in the U.K., affected the class 1 mAbs by strongly reducing the binding by 1.29 kcal/mol or about 10-fold. 2022 Journal of chemical information and modeling Abstract SARS_CoV_2 K417N 36 41 35072475 R346K Mutation in the Mu Variant of SARS-CoV-2 Alters the Interactions with Monoclonal Antibodies from Class 2: A Free Energy Perturbation Study. In particular, special attention was given to the R346K mutation located in the receptor binding domain (RBD). 2022 Journal of chemical information and modeling Abstract SARS_CoV_2 R346K 50 55 RBD;RBD 80;105 103;108 35072475 R346K Mutation in the Mu Variant of SARS-CoV-2 Alters the Interactions with Monoclonal Antibodies from Class 2: A Free Energy Perturbation Study. Our results show that R346K affects class 2 antibodies but its effect is not so significant (0.66 kcal/mol), i.e., it reduces the binding with antibodies by about 3-fold. 2022 Journal of chemical information and modeling Abstract SARS_CoV_2 R346K 22 27 35072475 R346K Mutation in the Mu Variant of SARS-CoV-2 Alters the Interactions with Monoclonal Antibodies from Class 2: A Free Energy Perturbation Study. Thus, the resistance effect of the R346K mutation on the Mu variant is possible but not so significant and is due to the additional decrease of antibody neutralization based on the reduced binding of class 2 antibodies. 2022 Journal of chemical information and modeling Abstract SARS_CoV_2 R346K 35 40 35073390 Predicting spike protein NTD mutations of SARS-CoV-2 causing immune evasion by molecular dynamics simulations. Binding free energy calculations and an interaction mechanism study reveal that R246I, which is present in the Beta (B.1.351/501Y.V2) variant, may have various impacts on current NTD antibodies through abolishing the hydrogen bonds and electrostatic interaction with the antibodies or affecting other interface residues. 2022 Physical chemistry chemical physics Abstract SARS_CoV_2 R246I 80 85 35073761 N7-Methylation of the Coronavirus RNA Cap Is Required for Maximal Virulence by Preventing Innate Immune Recognition. A Y414A substitution in nsp14 of the coronavirus mouse hepatitis virus (MHV) significantly decreased N7-methyltransferase activity and reduced guanine N7-methylation of the 5' cap in vitro. 2022 mBio Abstract SARS_CoV_2 Y414A 2 7 35073761 N7-Methylation of the Coronavirus RNA Cap Is Required for Maximal Virulence by Preventing Innate Immune Recognition. Infection of myeloid cells with recombinant MHV harboring the nsp14-Y414A mutation (rMHVnsp14-Y414A) resulted in upregulated expression of IFN-I and ISG15 mainly via MDA5 signaling and in reduced viral replication compared to that of wild-type rMHV. 2022 mBio Abstract SARS_CoV_2 Y414A;Y414A 68;94 73;99 35073761 N7-Methylation of the Coronavirus RNA Cap Is Required for Maximal Virulence by Preventing Innate Immune Recognition. Moreover, infection with rSARS-CoV-2nsp14-Y420A conferred complete protection against subsequent and otherwise lethal SARS-CoV-2 infection in mice, indicating the vaccine potential of this mutant. 2022 mBio Abstract SARS_CoV_2 Y420A 42 47 COVID-19 118 138 35073761 N7-Methylation of the Coronavirus RNA Cap Is Required for Maximal Virulence by Preventing Innate Immune Recognition. rMHVnsp14-Y414A replicated to lower titers in livers and brains and exhibited an attenuated phenotype in mice. 2022 mBio Abstract SARS_CoV_2 Y414A 10 15 35073761 N7-Methylation of the Coronavirus RNA Cap Is Required for Maximal Virulence by Preventing Innate Immune Recognition. This attenuated phenotype was IFN-I dependent because the virulence of the rMHVnsp14-Y414A mutant was restored in Ifnar-/- mice. 2022 mBio Abstract SARS_CoV_2 Y414A 85 90 35073761 N7-Methylation of the Coronavirus RNA Cap Is Required for Maximal Virulence by Preventing Innate Immune Recognition. We further found that the comparable mutation (Y420A) in SARS-CoV-2 nsp14 (rSARS-CoV-2nsp14-Y420A) also significantly decreased N7-methyltransferase activity in vitro, and the mutant virus was attenuated in K18-human ACE2 transgenic mice. 2022 mBio Abstract SARS_CoV_2 Y420A;Y420A 47;92 52;97 35074352 Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. The circulation of the Alpha VOC in the area under study was confirmed, and additionally two combinations of mutations in the S glycoprotein (T73A and D253N, and S477N and A522S) that could affect antibody binding were identified. 2022 Environmental research Abstract SARS_CoV_2 A522S;D253N;S477N;T73A 172;151;162;142 177;156;167;146 S 126 140 35075065 COVID-19 Delta variation; more contagious or more pernicious? More detailed analysis disclosed that the prevailing lineage in distribution is a novel identified lineage B.1.617 holding in common signature mutations D111D, G142D, L452R, E484Q, D614G, and P681R, in the spike protein, containing within the receptor-binding domain (RBD) [2, 3]. 2022 Acta bio-medica Abstract SARS_CoV_2 D111D;D614G;E484Q;G142D;L452R;P681R 153;181;174;160;167;192 158;186;179;165;172;197 S;RBD 206;268 211;271 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. The haplotype included a synonymous change N73N in endoRNase, and three non-synonymous changes coding residues R203K, R203S and G204R in the nucleocapsid protein. 2022 Scientific reports Abstract SARS_CoV_2 G204R;N73N;R203K;R203S 128;43;111;118 133;47;116;123 N;EndoRNAse 141;51 153;60 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. FINDINGS: AX290 and AX677, two monoclonal antibodies with non-overlapping epitopes, exhibit subnanomolar or nanomolar affinities to the receptor binding domain of the viral Spike protein carrying amino acid substitutions N501Y, N439K, E484K, K417N, and a combination N501Y/E484K/K417N found in the circulating virus variants. 2022 EBioMedicine Abstract SARS_CoV_2 E484K;K417N;N439K;N501Y;N501Y;E484K;K417N 235;242;228;221;267;273;279 240;247;233;226;272;278;284 RBD;S 136;173 159;178 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Lending support to this critically important result of the aforementioned trial, we demonstrated in our study that patients infected with a SARS-Cov-2 sub-lineage (B.1.1.284) carrying the Pro108Ser mutation in 3CLpro tended to have a comparatively milder clinical course (i.e., a smaller proportion of patients required oxygen supplementation during the clinical course) than patients infected with the same sub-lineage of virus not carrying the mutation. 2022 Scientific reports Abstract SARS_CoV_2 P108S 188 197 35079901 Trypsin enhances SARS-CoV-2 infection by facilitating viral entry. During 50 serial passages without the addition of trypsin, a specific R685S mutation occurred in the S1/S2 FCS (681PRRAR685) that was completely conserved but accompanied by several mutations in the S2 fusion subunit in the presence of trypsin. 2022 Archives of virology Abstract SARS_CoV_2 R685S 70 75 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. The concentrations of antibodies against RBD, D614G, N501Y, E484K, and L452R/E484Q-mutants after two doses of vaccines are 6.6 +- 3.6, 8.7 +- 4.6, 3.4 +- 2.8, 3.8 +- 2.8, and 2.8 +- 2.3 ng/mL, respectively. 2022 Analytical chemistry Abstract SARS_CoV_2 D614G;E484K;L452R;N501Y;E484Q 46;60;71;53;77 51;65;76;58;82 RBD 41 44 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. This suggests that neutralizing activities against N501Y, E484K, and L452R/E484Q-mutants were less effective than RBD and D614G-mutant. 2022 Analytical chemistry Abstract SARS_CoV_2 D614G;E484K;L452R;N501Y;E484Q 122;58;69;51;75 127;63;74;56;80 RBD 114 117 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. In this study, an epidemiological investigation of SARS-CoV-2 in Portugal was performed, and the VSV-DeltaG-G* pseudovirus system was used to construct 12 spike protein epidemic mutants, D614G, A222V+D614G, B.1.1.7, S477N+D614G, P1162R+D614G+A222V, D839Y+D614G, L176F+D614G, B.1.1.7+L216F, B.1.1.7+M740V, B.1.258, B.1.258+L1063F, and B.1.258+N751Y. 2022 Archives of virology Abstract SARS_CoV_2 A222V;D614G;D839Y;L176F;P1162R;S477N;A222V;D614G;D614G;D614G;D614G;D614G;L1063F;L216F;M740V;N751Y 194;187;249;262;229;216;242;200;222;236;255;268;322;283;298;342 199;192;254;267;235;221;247;205;227;241;260;273;328;288;303;347 S 155 160 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. Neutralization resistance was mainly caused by the mutations S477N, N439K, and N501Y in the spike-receptor binding domain. 2022 Archives of virology Abstract SARS_CoV_2 N439K;N501Y;S477N 68;79;61 73;84;66 RBD;S 98;92 121;97 35083577 Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France. We detected SARS-CoV-2 of PANGO lineage R.1 with the spike substitution E484K in three patients. 2022 Archives of virology Abstract SARS_CoV_2 E484K 72 77 S 53 58 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. The spike protein mutation D614G was observed across all the sequenced strains. 2022 Microbiology resource announcements Abstract SARS_CoV_2 D614G 27 32 S 4 9 35090164 Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants. Atomic structures of the Omicron spike protein in complex with three classes of antibodies that were active against all five variants of concern defined the binding and neutralizing determinants and revealed a key antibody escape site, G446S, that confers greater resistance to a class of antibodies that bind on the right shoulder of the receptor-binding domain by altering local conformation at the binding interface. 2022 Nature Abstract SARS_CoV_2 G446S 236 241 S 33 38 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. Among participants naive to SARS-CoV-2 at day 36, 158 (98%) of 162 in the low-dose group, 166 (99%) of 168 in the medium-dose group, and 163 (98%) of 166 in the high-dose group had at least a two-fold increase in neutralising antibody titres to the D614G variant from baseline. 2022 The Lancet. Infectious diseases Abstract SARS_CoV_2 D614G 249 254 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. The primary immunogenicity objective was to describe the neutralising antibody titres to the D614G variant 14 days after the second vaccination (day 36) in participants who were SARS-CoV-2 naive who received both injections, provided samples at day 1 and day 36, did not have protocol deviations, and did not receive an authorised COVID-19 vaccine before day 36. 2022 The Lancet. Infectious diseases Abstract SARS_CoV_2 D614G 93 98 COVID-19 331 339 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Furthermore, we risk assess these mutations and conclude mink-adapted viruses are unlikely to pose an increased threat to humans, as Y453F attenuates the virus replication in human cells and all three mink adaptations have minimal antigenic impact. 2022 Cell reports Abstract SARS_CoV_2 Y453F 133 138 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Here we investigate the molecular basis of mink and ferret adaptation and demonstrate the spike mutations Y453F, F486L, and N501T all specifically adapt SARS-CoV-2 to use mustelid ACE2. 2022 Cell reports Abstract SARS_CoV_2 F486L;N501T;Y453F 113;124;106 118;129;111 S 90 95 35093484 Comparative analyses of IgG/IgA neutralizing effects induced by three COVID-19 vaccines against variants of concern. Interestingly, all 3 vaccines could neutralize all tested variants of concern in addition to WT virus, but in some individuals, only low or no neutralization, especially against Alpha-E484K and the Delta variant, was detected. 2022 The Journal of allergy and clinical immunology Abstract SARS_CoV_2 E484K 184 189 35093484 Comparative analyses of IgG/IgA neutralizing effects induced by three COVID-19 vaccines against variants of concern. We also determined the neutralization ability against SARS-CoV-2 WT and B.1.1.7 (Alpha), B1.1.7 E484K (Alpha-E484K), B.1.351 (Beta), and B.1.617.2 (Delta) variants. 2022 The Journal of allergy and clinical immunology Abstract SARS_CoV_2 E484K;E484K 96;109 101;114 35095027 Development of new SNP genotyping assays to discriminate the Omicron variant of SARS-CoV-2. In addition, a sensitivity test showed that the G339D and T547K assays detected at least 2.60 and 3.36 RNA copies of the Omicron variant, respectively, and 1.59 RNA copies of the Delta variant. 2022 Japanese journal of infectious diseases Abstract SARS_CoV_2 G339D;T547K 48;58 53;63 35095027 Development of new SNP genotyping assays to discriminate the Omicron variant of SARS-CoV-2. In this study, we describe our development of two single nucleotide polymorphism (SNP) genotyping assays targeting the G339D or T547K mutation of the spike protein for screening of the Omicron variant. 2022 Japanese journal of infectious diseases Abstract SARS_CoV_2 G339D;T547K 119;128 124;133 S 150 155 35095814 A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands. Additional spike mutations were rarely documented with the exception of mutation S:Q613H which has been detected in several genomes (n = 25) since July 2021. 2021 Frontiers in microbiology Abstract SARS_CoV_2 Q613H 83 88 S;S 11;81 16;82 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. The frequency of variant Y144F in the spike protein deviated from global values with higher prevalence of this mutation in the island. 2021 Frontiers in microbiology Abstract SARS_CoV_2 Y144F 25 30 S 38 43 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. RESULTS: Retrospective sequencing analysis revealed a double Spike D614G/S939F mutation in COVID-19 positive subjects present in Ostia while D614G mutation was evidenced in those based in Fiumicino. 2022 Computational and structural biotechnology journal Abstract SARS_CoV_2 D614G;D614G;S939F 67;141;73 72;146;78 S 61 66 COVID-19 91 99 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Unlike D614G, S939F mutation affects immune response by the slight but significant modulation of T-cell propensity and the selective enrichment of potential binding epitopes for some HLA alleles. 2022 Computational and structural biotechnology journal Abstract SARS_CoV_2 D614G;S939F 7;14 12;19 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. The data support the notion that a third vaccination is key to boosting existing titers and improving the breadth of antibodies to address variants of concern, including those with an E484K mutation in the Receptor Binding Domain (RBD) (Beta, Gamma). 2022 Vaccine Abstract SARS_CoV_2 E484K 184 189 RBD;RBD 206;231 229;234 35104067 Neutralizing Antibodies and Cytokines in Breast Milk After Coronavirus Disease 2019 (COVID-19) mRNA Vaccination. Milk samples were tested for the presence of neutralizing antibodies against the spike and four variants of concern: D614G, Alpha (B.1.1.7), Beta (B.1.351), and Gamma (P.1). 2022 Obstetrics and gynecology Abstract SARS_CoV_2 D614G 117 122 S 81 86 35104836 SARS-CoV-2 Omicron variant replication in human bronchus and lung ex vivo. Here we compared the replication competence and cellular tropism of the wild-type virus and the D614G, Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2) and Omicron (B.1.1.529) variants in ex vivo explant cultures of human bronchi and lungs. 2022 Nature Abstract SARS_CoV_2 D614G 96 101 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Here, we provide crucial information in linking the R203K/G204R mutations in the N protein to modulations of host-virus interactions and underline the potential of the nucleocapsid protein as a drug target during infection. 2022 Nature communications Abstract SARS_CoV_2 R203K;G204R 52;58 57;63 N;N 168;81 180;82 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. We show that two consecutive mutations (R203K/G204R) in the nucleocapsid (N) protein are associated with higher viral loads in COVID-19 patients. 2022 Nature communications Abstract SARS_CoV_2 R203K;G204R 40;46 45;51 N;N 60;74 72;75 COVID-19 127 135 35109768 Mutations in the receptor-binding domain of human SARS CoV-2 spike protein increases its affinity to bind human ACE-2 receptor. Here, we use the crystal structure of the RBD in complex with ACE-2 available in the public domain and analyse the 250 ns molecular dynamics (MD) simulations of wild-type and mutants; K417N, K417T, N440K, N501Y, L452R, T478K, E484K and S494P. 2022 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 E484K;K417N;K417T;L452R;N440K;N501Y;S494P;T478K 226;184;191;212;198;205;236;219 231;189;196;217;203;210;241;224 RBD 42 45 35113647 Divergent SARS-CoV-2 Omicron-reactive T and B cell responses in COVID-19 vaccine recipients. Here, we studied neutralizing antibodies and T cell responses targeting SARS-CoV-2 D614G [wild type (WT)] and the Beta, Delta, and Omicron variants of concern in a cohort of 60 health care workers after immunization with ChAdOx-1 S, Ad26.COV2.S, mRNA-1273, or BNT162b2. 2022 Science immunology Abstract SARS_CoV_2 D614G 83 88 S;S 230;243 231;244 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. Further, we engineer a potent ACE2-blocking nAb to sustain binding to S RBD with the E484K and L452R substitutions found in multiple SARS-CoV-2 variants. 2022 Cell reports Abstract SARS_CoV_2 E484K;L452R 85;95 90;100 RBD;S 72;70 75;71 35114688 ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. However, the effects of individual mutations can differ considerably between viruses, as shown by the N501Y mutation, which enhances the human ACE2-binding affinity of several SARS-CoV-2 variants of concern12 but substantially decreases it for SARS-CoV-1. 2022 Nature Abstract SARS_CoV_2 N501Y 102 107 35115239 Persistent viral shedding of severe acute respiratory syndrome coronavirus 2 after treatment with bendamustine and rituximab: A case report. The first nasopharyngeal specimen (NPS) for the SARS-CoV-2 polymerase chain reaction assay tested positive for the N501Y variant five weeks before admission. 2022 Journal of infection and chemotherapy Abstract SARS_CoV_2 N501Y 115 120 35115523 Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. These lineages contain mutations that had been rarely observed in clinical samples, including Q493K, Q498Y, E484A, and T572N and share many mutations with the Omicron variant of concern. 2022 Nature communications Abstract SARS_CoV_2 E484A;Q493K;Q498Y;T572N 108;94;101;119 113;99;106;124 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. Although vaccine-elicited neutralizing antibody titers are decreased similarly against the E406 mutant and the Delta or Epsilon variants, broadly neutralizing sarbecovirus mAbs, including a clinical mAb, inhibit the E406W spike mutant. 2022 bioRxiv Abstract SARS_CoV_2 E406W 216 221 S 222 227 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. The SARS-CoV-2 receptor-binding domain (RBD) E406W mutation abrogates neutralization mediated by the REGEN-CoV therapeutic monoclonal antibody (mAb) COVID-19 cocktail and the cilgavimab (AZD1061) mAb. 2022 bioRxiv Abstract SARS_CoV_2 E406W 45 50 RBD 40 43 COVID-19 149 157 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. We report that the Omicron brings an enhanced RBD-ACE2 interface through N501Y, Q493K/R, and T478K mutations; the changes further lead to unique interaction patterns, reminiscing the features of previously dominated variants, Alpha (N501Y) and Delta (L452R and T478K). 2022 bioRxiv Abstract SARS_CoV_2 N501Y;Q493K;Q493R;T478K;T478K;L452R;N501Y 73;80;80;93;261;251;233 78;87;87;98;266;256;238 RBD 46 49 35118474 Breadth of SARS-CoV-2 Neutralization and Protection Induced by a Nanoparticle Vaccine. The Omicron variant was neutralized by RBD-scNP-induced serum antibodies with a mean of 10.6-fold reduction of ID50 titers compared to SARS-CoV-2 D614G. 2022 bioRxiv Abstract SARS_CoV_2 D614G 146 151 RBD 39 42 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. CONCLUSIONS: A two-dose regimen of 100 microg mRNA-1273 in adolescents and of 50 microg in children elicited neutralization responses against the Omicron variant that were reduced compared with the wild-type D614G, and numerically higher than those in adults. 2022 medRxiv Abstract SARS_CoV_2 D614G 208 213 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. In adolescents (12-17 years), the GMT was 11.8-fold lower than D614G, 4 weeks after a second dose of mRNA-1273 (100 microg), and compared with adults, were 1.5- and 3.8-fold higher for D614G and the Omicron variant, respectively. 2022 medRxiv Abstract SARS_CoV_2 D614G;D614G 63;185 68;190 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. In children (6-<12 years), 4 weeks post-second dose of 50 microg mRNA-1273, Omicron GMTs were reduced 22.1-fold versus D614G and were 2.0-fold higher for D614G and 2.5-fold higher for Omicron compared with adults. 2022 medRxiv Abstract SARS_CoV_2 D614G;D614G 119;154 124;159 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. Neutralizing antibody geometric mean ID50 titers (GMT) were measured using a lentivirus-based pseudovirus neutralizing assay at day 1 and 4 weeks (day 57) following the second mRNA-1273 dose, compared with wild-type (D614G). 2022 medRxiv Abstract SARS_CoV_2 D614G 217 222 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. RESULTS: At 4 weeks following a second dose of mRNA-1273 (100 microg), the GMT was reduced 28.8-fold compared with D614G in adults (>=18 years). 2022 medRxiv Abstract SARS_CoV_2 D614G 115 120 35123044 Clinical and genomic data of sars-cov-2 detected in maternal-fetal interface during the first wave of infection in Brazil. Genomes recovered from two placentas belong to the B.1.1.28 and B.1.1.33 lineages and present nonsynonymous mutations associated with virus fitness and infectivity; other not frequently reported mutations (B.1.1.33: NSP3 V2090G, M A2S and ORF3ab S253P and Y264N; B.1.1.28: NSP3 E995D, NSP12 R240K, NSP14 H1897Y and in ORF7b V21F) were found in proteins involved in viral replication, viral induction of apoptosis, viral interference on interferon and on NF-Kappabeta pathways. 2022 Microbes and infection Abstract SARS_CoV_2 A2S;E995D;H1897Y;R240K;S253P;V2090G;V21F;Y264N 231;278;304;291;246;221;324;256 234;283;310;296;251;227;328;261 ORF7b;Nsp12;Nsp3;Nsp3 318;285;216;273 323;290;220;277 35123263 The function of SARS-CoV-2 spike protein is impaired by disulfide-bond disruption with mutation at cysteine-488 and by thiol-reactive N-acetyl-cysteine and glutathione. We showed that the substitution of Cys-488 with alanine impaired pseudotyped SARS-CoV-2 infection, syncytium formation, and cell-cell fusion triggered by SARS-CoV-2 spike expression. 2022 Biochemical and biophysical research communications Abstract SARS_CoV_2 C488A 35 55 S 165 170 COVID-19 77 97 35126106 Antidepressant and Antipsychotic Drugs Reduce Viral Infection by SARS-CoV-2 and Fluoxetine Shows Antiviral Activity Against the Novel Variants in vitro. Furthermore, fluoxetine remained effective against pseudoviruses with common receptor binding domain mutations, N501Y, K417N, and E484K, as well as B.1.1.7 (alpha), B.1.351 (beta), and B.1.617.2 (delta) variants of SARS-CoV-2. 2021 Frontiers in pharmacology Abstract SARS_CoV_2 E484K;K417N;N501Y 130;119;112 135;124;117 RBD 77 100 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. In this work, we have studied the effect of one of the most frequently occurring mutants, D155Y of ORF3a protein, found in Indian COVID-19 patients. 2022 Computational and structural biotechnology journal Abstract SARS_CoV_2 D155Y 90 95 ORF3a 99 104 COVID-19 130 138 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. Protein-protein docking using HADDOCK analysis revealed that substitution D155Y weakened the binding affinity of ORF3a with caveolin-1 compared with the other substitutions, suggesting its importance in the overall stability of ORF3a-caveolin-1 complex, which may modulate the virulence property of SARS-CoV-2. 2022 Computational and structural biotechnology journal Abstract SARS_CoV_2 D155Y 74 79 ORF3a;ORF3a 113;228 118;233 35128118 SARS-CoV-2 in Egypt: epidemiology, clinical characterization and bioinformatics analysis. The most predominant subclade was D614G/Q57H/V5F/G823S. 2022 Heliyon Abstract SARS_CoV_2 D614G;G823S;Q57H;V5F 34;49;40;45 39;54;44;48 35129839 Vaccination of COVID-19 convalescent plasma donors increases binding and neutralizing antibodies against SARS-CoV-2 variants. STUDY DESIGN/METHODS: In this study, paired-samples from 11 CCP donors collected before and after vaccination was tested to measure binding antibody levels and neutralization activity against the ancestral Wuhan-Hu-1 and SARS-CoV-2 variants (Wuhan-Hu-1 with D614G, alpha, beta, gamma, delta, epsilon) on the Ortho Vitros Spike Total Ig and IgG assays, the MSD V-PLEX SARS-CoV-2 arrays for IgG binding and ACE2 inhibition, and variant-specific Spike Reporter Viral Particle Neutralization (RVPN) assays. 2022 Transfusion Abstract SARS_CoV_2 D614G 258 263 S;S 321;443 326;448 35130474 Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA. Of 379 severe acute respiratory syndrome coronavirus 2 samples collected in New York, USA, we detected 86 Omicron variant sequences containing Delta variant mutation P681R. 2022 Emerging infectious diseases Abstract SARS_CoV_2 P681R 166 171 35130474 Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA. Repeated library preparation with fewer cycles showed the P681R calls were artifactual. 2022 Emerging infectious diseases Abstract SARS_CoV_2 P681R 58 63 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. Our best estimate is a 3-fold enrichment for some lineages of delta among breakthroughs, and enrichment of a notable spike substitution, N501Y. 2022 mBio Abstract SARS_CoV_2 N501Y 137 142 S 117 122 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. Viral point substitutions could also be associated with vaccine breakthroughs, notably the N501Y substitution found in the alpha, beta and gamma variants (odds ratio 2.04; 95% credible interval of1.25-3.18). 2022 mBio Abstract SARS_CoV_2 N501Y 91 96 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Finally, we identify sets of comutations that have a high likelihood of massive growth: [A411S, L452R, T478K], [L452R, T478K, N501Y], [V401L, L452R, T478K], [K417N, L452R, T478K], [L452R, T478K, E484K, N501Y], and [P384L, K417N, E484K, N501Y]. 2022 ACS infectious diseases Abstract SARS_CoV_2 E484K;E484K;K417N;L452R;L452R;L452R;N501Y;N501Y;N501Y;T478K;T478K;T478K;T478K;T478K;A411S;K417N;L452R;L452R;P384L;V401L 195;229;222;96;142;165;126;202;236;103;119;149;172;188;89;158;112;181;215;135 200;234;227;101;147;170;131;207;241;108;124;154;177;193;94;163;117;186;220;140 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Unexpectedly, Kappa variant spike trimers form a structural head-to-head dimer-of-trimers assembly, which we demonstrate is a result of the E484Q mutation and with unknown biological implications. 2022 Nature communications Abstract SARS_CoV_2 E484Q 140 145 S 28 33 35139271 Final Analysis of Efficacy and Safety of Single-Dose Ad26.COV2.S. Efficacy in the United States, primarily against the reference strain (B.1.D614G) and the B.1.1.7 (alpha) variant, was 69.7% (95% CI, 60.7 to 76.9); efficacy was reduced elsewhere against the P.1 (gamma), C.37 (lambda), and B.1.621 (mu) variants. 2022 The New England journal of medicine Abstract SARS_CoV_2 D614G 75 80 35139368 Long-term, infection-acquired immunity against the SARS-CoV-2 Delta variant in a hamster model. Here, we use a live virus neutralization assay with sera from Pfizer- and Moderna-vaccinated individuals to examine neutralizing antibody titers against SARS-CoV-2 and observe a 3.9- and 2.7-fold reduction, respectively, in neutralizing antibody titers against the Delta variant compared with an early isolate bearing only a D614G substitution in its spike protein. 2022 Cell reports Abstract SARS_CoV_2 D614G 325 330 S 351 356 35139811 Linked nosocomial COVID-19 outbreak in three facilities for people with intellectual and developmental disabilities due to SARS-CoV-2 variant B.1.1.519 with spike mutation T478K in the Netherlands. Little is known about variant B.1.1.519 with spike mutation T478K, dominant in Mexico. 2022 BMC infectious diseases Abstract SARS_CoV_2 T478K 60 65 S 45 50 35139987 Prolonged SARS-CoV-2 RNA shedding in a young man recovering from traumatic pneumothorax. Genotyping revealed canonical beta-variant E484K and N501Y mutations at earlier time points. 2022 South African medical journal Abstract SARS_CoV_2 E484K;N501Y 43;53 48;58 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K has rapidly emerged and has frequently been detected in several SARS-CoV-2 variants of concern. 2022 Infection and drug resistance Abstract SARS_CoV_2 E484K 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. In this study, we review the epidemiology and impact of E484K, its effects on neutralizing effect of several monoclonal antibodies, convalescent plasma, and post-vaccine sera. 2022 Infection and drug resistance Abstract SARS_CoV_2 E484K 56 61 35140714 Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. Notably, three substitutions, i.e., T478K, Q493K, and Q498R, significantly contribute to the binding energies and almost doubled the electrostatic potential (ELE) of the RBDOmic-ACE2 complex. 2021 Frontiers in immunology Abstract SARS_CoV_2 Q493K;Q498R;T478K 43;54;36 48;59;41 35140714 Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. Omicron also harbors E484A substitution instead of the E484K that helped neutralization escape of Beta, Gamma, and Mu variants. 2021 Frontiers in immunology Abstract SARS_CoV_2 E484A;E484K 21;55 26;60 35140714 Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. Together, T478K, Q493K, Q498R, and E484A substitutions contribute to a significant drop in the ELE between RBDOmic-mAbs, particularly in etesevimab, bamlanivimab, and CT-p59. 2021 Frontiers in immunology Abstract SARS_CoV_2 E484A;Q493K;Q498R;T478K 35;17;24;10 40;22;29;15 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. Moreover, individual mutations such as Spike N501Y and Nucleocapsid D138Y were predicted to have an overall stronger affinity through HLA-I than the reference sequence while Spike E484K shows signs of evasion. 2022 Infection, genetics and evolution Abstract SARS_CoV_2 D138Y;E484K;N501Y 68;180;45 73;185;50 N;S;S 55;39;174 67;44;179 35150193 Severe relapse of SARS-CoV-2 infection in a kidney transplant recipient with negative nasopharyngeal SARS-CoV-2 RT-PCR after rituximab. However, it had an acquired G142D mutation and a larger deletion of 3-amino-acids at position 143-145. 2022 American journal of transplantation Abstract SARS_CoV_2 G142D 28 33 35151002 Rapid biosensing SARS-CoV-2 antibodies in vaccinated healthy donors. The protocol for the detection of BAbs could be utilized for detection of the RBD-N501Y variant with equal sensitivity and speed. 2022 Biosensors & bioelectronics Abstract SARS_CoV_2 N501Y 82 87 RBD 78 81 35155280 The Impact of Accumulated Mutations in SARS-CoV-2 Variants on the qPCR Detection Efficiency. It was found that detection sensitivity of G28916T mutant was 2.35 and 1.74 times less than that of the wt sequence and detection limit was reduced from 1 copy/mul to 10 copies/mul for the commercially available CP3 and CP4 primer/probe sets. 2022 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 G28916T 43 50 35155280 The Impact of Accumulated Mutations in SARS-CoV-2 Variants on the qPCR Detection Efficiency. We also found that the G28916T mutation of the N gene accounts for 78.78% sequenced genomes of Delta variant. 2022 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 G28916T 23 30 N 47 48 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. In Costa Rica during the year 2020, a predominant genotype carrying the mutation T1117I in the spike (S:T1117I) was previously identified. 2022 Gene reports Abstract SARS_CoV_2 T1117I;T1117I 81;104 87;110 S;S 95;102 100;103 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. Results of the phylogeny of sequences carrying the S:T1117I worldwide showed a polyphyletic group, with the emergence of local lineages. 2022 Gene reports Abstract SARS_CoV_2 T1117I 53 59 S 51 52 35156077 Rapid detection of multiple SARS-CoV-2 variants of concern by PAM-targeting mutations. Here, we describe a CRISPR-based assay that detects mutations in spike gene CRISPR PAM motif or seed regions to identify a pan-specific VOC single-nucleotide polymorphism (SNP)) ((D614G) and Alpha- and Delta-specific (S982A and D950N) SNPs. 2022 Cell reports methods Abstract SARS_CoV_2 D950N;D614G;S982A 228;180;218 233;185;223 S 65 70 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. Six highly prevalent missense mutations in the viral life cycle-associated Membrane (I82T), Nucleocapsid (R203M, D377Y), NS3 (S26L), and NS7a (V82A, T120I) proteins are almost exclusive to the Delta variant compared to other variants of concern (mean prevalence across genomes: Delta = 99.74%, Alpha = 0.06%, Beta = 0.09%, and Gamma = 0.22%). 2022 Molecular systems biology Abstract SARS_CoV_2 D377Y;T120I;I82T;R203M;S26L;V82A 113;149;85;106;126;143 118;154;89;111;130;147 Membrane;NS3 75;121 83;124 35157870 Detection of SARS-CoV-2 RNA in wastewater, river water, and hospital wastewater of Nepal. One influent sample was positive for N501Y mutation using the mutation-specific qPCR, highlighting a need for further typing of water samples to detect Variants of Concern. 2022 The Science of the total environment Abstract SARS_CoV_2 N501Y 37 42 35162151 Shorter Incubation Period among Unvaccinated Delta Variant Coronavirus Disease 2019 Patients in Japan. The incubation periods were calculated and compared by Mann-Whitney U test for Delta (with L452R mutation) and non-Delta cases. 2022 International journal of environmental research and public health Abstract SARS_CoV_2 L452R 91 96 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. We employed the efficient and accurate coarse-grained (CG) simulations of multiple functional states of the D614G mutant, B.1.1.7 and B.1.351 spike variants to characterize conformational dynamics of the SARS-CoV-2 spike proteins and identify dynamic signatures of the functional regions that regulate transitions between the closed and open forms. 2022 International journal of molecular sciences Abstract SARS_CoV_2 D614G 108 113 S;S 142;215 147;220 35164548 Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. To further characterize the mechanism, we tested a natural ORF3a Beta variant, Q57H, and a mutant with deletion of the highly conserved residue, DeltaG188. 2022 mBio Abstract SARS_CoV_2 Q57H 79 83 ORF3a 59 64 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. Here, we report single-molecule Forster resonance energy transfer (smFRET) studies of critical mutations observed in VOCs, including D614G and E484K, in the context of virus particles. 2022 mBio Abstract SARS_CoV_2 D614G;E484K 133;143 138;148 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. Among 48 mutant isolates, 26 were B.1.1.7 (Alpha), 7 were E484K single mutation and the rest were other types of mutation. 2022 Scientific reports Abstract SARS_CoV_2 E484K 58 63 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. Moreover, 5 cluster cases with single mutation at N501S were firstly reported in Hiroshima. 2022 Scientific reports Abstract SARS_CoV_2 N501S 50 55 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. Several mutations were identified in the FCS region, i.e., D614G, Q675H, Q677H, S680P, and silent mutation in 235.57 C > T. 2022 International microbiology Abstract SARS_CoV_2 D614G;Q675H;Q677H;S680P 59;66;73;80 64;71;78;85 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. The data indicated there is evolutionary advantage of the D614G mutation in the FCS region of the spike protein of SARS-CoV-2 circulating in the Special Region of Yogyakarta and Central Java provinces in Indonesia. 2022 International microbiology Abstract SARS_CoV_2 D614G 58 63 S 98 103 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. The most important mutation in the FCS region is D614G. 2022 International microbiology Abstract SARS_CoV_2 D614G 49 54 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. To address this, we examined the neutralizing antibody response against the spike protein of five major SARS-CoV-2 variants, D614G, Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529), in health care workers (HCWs) vaccinated with SARS-CoV-2 mRNA vaccines. 2022 Science translational medicine Abstract SARS_CoV_2 D614G 125 130 S 76 81 35168024 Development of SARS-CoV-2 variant protein microarray for profiling humoral immunity in vaccinated subjects. To meet this need, the present study developed a SARS-CoV-2 variant (CoVariant) array which consists of the extracellular domain of spike variants, e.g., wild-type, D614G, B.1.1.7, B.1.351, P.1, B.1.617, B.1.617.1, B.1.617.2, and B.1.617.3. 2022 Biosensors & bioelectronics Abstract SARS_CoV_2 D614G 165 170 S 132 137 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Collectively, increased propensity for more RBD-up states and the affinity-enhancing T478K substitution together contribute to increased ACE2 binding, providing structural basis of rapid spread of Delta. 2022 Nature communications Abstract SARS_CoV_2 T478K 85 90 RBD 44 47 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Moreover, we identify a previously generated MAb 8D3 as a cross-variant broadly neutralizing antibody and reveal that 8D3 binding induces a large K478 side-chain orientation change, suggesting 8D3 may use an "induced-fit" mechanism to tolerate Delta T478K mutation. 2022 Nature communications Abstract SARS_CoV_2 T478K 250 255 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Noteworthy, we find the Delta T478K substitution plays a vital role in stabilizing and reshaping the RBM loop473-490, enhancing interaction with ACE2. 2022 Nature communications Abstract SARS_CoV_2 T478K 30 35 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. N-G215C exhibits substantially stronger self-association, shifting the unliganded protein from a dimeric to a tetrameric oligomeric state, which leads to enhanced co-assembly with nucleic acids. 2022 bioRxiv Abstract SARS_CoV_2 G215C 2 7 N 0 1 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. One of these conserved regions is in the central disordered linker proximal to the N-G215C mutation that has become dominant in the Delta variant, outcompeting G215 variants without further spike or N-protein substitutions. 2022 bioRxiv Abstract SARS_CoV_2 G215C 85 90 S;N;N 190;83;199 195;84;200 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. Structural models suggest that the G215C mutation stabilizes conserved transient helices in the disordered linker serving as protein-protein interaction interfaces. 2022 bioRxiv Abstract SARS_CoV_2 G215C 35 40 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. A total of 160 clinical specimens positive for SARS-CoV-2 were characterized as mutant (N501Y) or N501 wild type by Sanger sequencing and were subsequently tested with the N501Y single nucleotide polymorphism real-time reverse transcriptase PCR assay. 2022 Microbiology spectrum Abstract SARS_CoV_2 N501Y;N501Y 172;88 177;93 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Our assay, compared to Sanger sequencing for single nucleotide polymorphism detection, demonstrated positive percent agreement of 100% for all 57 specimens displaying the N501Y mutation, which were confirmed by Sanger sequencing to be typed as A23063T, including one specimen with mixed signal for wild type and mutant. 2022 Microbiology spectrum Abstract SARS_CoV_2 A23063T;N501Y 244;171 251;176 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Our real-time RT-PCR assay helps with surveillance by providing an easy method to quickly survey SARS-CoV-2 specimens for VOCs carrying the N501Y single nucleotide polymorphism (SNP). 2022 Microbiology spectrum Abstract SARS_CoV_2 N501Y 140 145 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Samples that test positive for the N501Y mutation in the spike gene with our assay can be sequenced to identify the lineage. 2022 Microbiology spectrum Abstract SARS_CoV_2 N501Y 35 40 S 57 62 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The identification of circulating SARS-CoV-2 lineages carrying an N501Y mutation is critical for surveillance purposes. 2022 Microbiology spectrum Abstract SARS_CoV_2 N501Y 66 71 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The N501Y amino acid mutation caused by a single point substitution A23063T in the spike gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is possessed by three variants of concern (VOCs), B.1.1.7, B.1.351, and P.1. 2022 Microbiology spectrum Abstract SARS_CoV_2 A23063T;N501Y 68;4 75;9 S 83 88 COVID-19 104 144 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. We developed and validated a single nucleotide polymorphism real-time reverse transcription PCR assay using allelic discrimination of the spike gene N501Y mutation to screen for potential variants of concern and differentiate them from SARS-CoV-2 lineages without the N501Y mutation. 2022 Microbiology spectrum Abstract SARS_CoV_2 N501Y;N501Y 149;268 154;273 S 138 143 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. All the P.1 sequences included other important mutations, such as P314L and R203K/G204R, and revealed a high genetic diversity in the phylogenetic tree. 2022 Microbiology spectrum Abstract SARS_CoV_2 P314L;R203K;G204R 66;76;82 71;81;87 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. Notably, we found the most frequent variant, the previously reported missense p.Asp614Gly in the S protein, as a single mutation in only three patients, whereas in the large majority of cases it occurs in concomitance with three other variants, suggesting a high linkage and that this variant alone might not provide a significant selective advantage to the virus. 2022 PloS one Abstract SARS_CoV_2 D614G 78 89 S 97 98 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. The C29197T mutation is one of 4 point mutations known to cause N-gene target failure (NGTF) in the Xpert Xpress SARS-CoV-2 and Xpert Omni SARS-CoV-2 assays from Cepheid (Sunnyvale, CA). 2022 PloS one Abstract SARS_CoV_2 C29197T 4 11 N 64 65 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. We describe a high local prevalence in January of 8.5% (CI 4.9-14.2%) for the C29197T mutation, which was over 3-fold higher than the prevalence estimated statewide in California during the same time frame, 2.5% (CI 2.1-2.8%). 2022 PloS one Abstract SARS_CoV_2 C29197T 78 85 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. Our data showed that N501Y RBD had fivefold higher ACE2 binding than the original variant. 2022 Scientific reports Abstract SARS_CoV_2 N501Y 21 26 RBD 27 30 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. While some antisera from naturally infected subjects had substantially reduced neutralization ability against N501Y RBD, all blood samples from vaccinated individuals were highly effective in neutralizing it. 2022 Scientific reports Abstract SARS_CoV_2 N501Y 110 115 RBD 116 119 35174856 Yeast surface display-based identification of ACE2 mutations that modulate SARS-CoV-2 spike binding across multiple mammalian species. Gln42Leu increased ACE2-spike binding for human and four of four other mammalian ACE2s; Leu79Ile had an effect for human and three of three mammalian ACE2s. 2022 Protein engineering, design & selection Abstract SARS_CoV_2 L79I;Q42L 88;0 96;8 S 24 29 35176330 Evolutionary shift from purifying selection towards divergent selection of SARS-CoV2 favors its invasion into multiple human organs. Evolution of a critical entry-point residue Y493Q needs two substitutions with an intermediate virus carrying Y493H (Y>H>Q) but has not been identified in known twenty-nine bat CoV virus. 2022 Virus research Abstract SARS_CoV_2 Y493H;Y493Q 110;44 115;49 35176774 Characterization of the immune resistance of SARS-CoV-2 Mu variant and the robust immunity induced by Mu infection. Here we reveal that the two mutations in the SARS-CoV-2 Mu spike protein, YY144-145TSN and E484K, are responsible for the resistance to COVID-19 convalescent sera during early 2020 and vaccine sera. 2022 The Journal of infectious diseases Abstract SARS_CoV_2 E484K 91 96 S 59 64 COVID-19 136 144 35178586 Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. Fourteen of the amino acid substitutions, including N501Y and E484K, and nine deletions are located in the spike protein. 2022 Archives of virology Abstract SARS_CoV_2 E484K;N501Y 62;52 67;57 S 107 112 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Additionally, longitudinal transcriptome analyses revealed a more persistent retention of immune signatures in Alpha+E484K patients throughout the entire course of COVID-19 disease and convalescence. 2022 Scientific reports Abstract SARS_CoV_2 E484K 117 122 COVID-19 164 180 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Our study offers insights into distinct molecular immune responses elicited by SARS-CoV-2 variants carrying the E484K escape mutation throughout the COVID-19 disease. 2022 Scientific reports Abstract SARS_CoV_2 E484K 112 117 COVID-19 149 165 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. The E484K signature was enriched for genes preferentially expressed in monocytes and linked to severe viral infection. 2022 Scientific reports Abstract SARS_CoV_2 E484K 4 9 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. To test this, we generated and investigated the transcriptomes in BCs from hospitalized patients infected with either the Alpha variant (n = 36) or with the Alpha variant that had acquired the E484K escape mutation (Alpha+E484K) (n = 13). 2022 Scientific reports Abstract SARS_CoV_2 E484K;E484K 193;222 198;227 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. We identified a gene module preferentially activated in patients infected with the Alpha+E484K variant and in patients infected with the Beta (n = 9) and Gamma (n = 3) variants that also carry by the E484K escape mutation. 2022 Scientific reports Abstract SARS_CoV_2 E484K;E484K 200;89 205;94 35182772 Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir. We expressed Mpro of six SARS-CoV-2 lineages (C.37 Lambda, B.1.1.318, B.1.2, B.1.351 Beta, B.1.1.529 Omicron, P.2 Zeta), each of which carries a strongly prevalent missense mutation (G15S, T21I, L89F, K90R, P132H, L205V). 2022 Bioorganic & medicinal chemistry letters Abstract SARS_CoV_2 K90R;L205V;L89F;P132H;T21I;G15S 201;214;195;207;189;183 205;219;199;212;193;187 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. 1.351 (beta variant) containing the E484K and N501Y mutations is well known. 2022 Vaccine Abstract SARS_CoV_2 E484K;N501Y 36;46 41;51 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. Although further investigations with other variant strains and serum samples are essential, our results imply that the weakened humoral response is not caused solely by the E484K mutation. 2022 Vaccine Abstract SARS_CoV_2 E484K 173 178 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. The E484K mutation in SARS-CoV-2 is thought to be responsible for weakened humoral immunity. 2022 Vaccine Abstract SARS_CoV_2 E484K 4 9 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. Vaccine efficacy against the R.1 lineage, which contains the E484K mutation but not the N501Y mutation, is uncertain. 2022 Vaccine Abstract SARS_CoV_2 E484K;N501Y 61;88 66;93 35187580 Impaired detection of omicron by SARS-CoV-2 rapid antigen tests. We examined a total of 115 SARS-CoV-2 PCR-negative and 166 SARS-CoV-2 PCR-positive respiratory swab samples (101 omicron, 65 delta (B.1.617.2)) collected from October 2021 until January 2022 as well as cell culture-expanded clinical isolates of both VoCs. 2022 Medical microbiology and immunology Abstract SARS_CoV_2 65delta 122 130 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. All patients presented the same 6 major SNVs: D614G in the S gene; P4715L, ntC3037T (F924F) and S5398P in Orf1ab gene; ntC26681T (F53F) in the M gene; and ntC241T in the non-coding UTR region. 2022 Infection, genetics and evolution Abstract SARS_CoV_2 D614G;C241T;C26681T;C3037T;P4715L;S5398P;F53F;F924F 46;155;119;75;67;96;130;85 51;162;128;83;73;102;134;90 ORF1ab;S 106;59 112;60 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. Further, we showed that most of the RBD mutations increased the binding affinity of ACE2 in the absence of heparin, with the maximum increase observed for N501Y (-13.7 kcal/mol). 2022 Process biochemistry (Barking, London, England) Abstract SARS_CoV_2 N501Y 155 160 RBD 36 39 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. Herein, using the molecular docking and interaction energy analysis, we showed that N501Y, L452R-E484Q, and E484K mutations bind strongly with heparin in the range of - 7.4 to - 8.0 kcal/mol. 2022 Process biochemistry (Barking, London, England) Abstract SARS_CoV_2 E484K;L452R;N501Y;E484Q 108;91;84;97 113;96;89;102 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The strong RBD/ACE2 interaction was observed in case of triple variants (-11.3 kcal/mol) whereas, N501Y showed weakest binding of RBD/ACE2 in the presence of heparin (-9.2 kcal/mol). 2022 Process biochemistry (Barking, London, England) Abstract SARS_CoV_2 N501Y 98 103 RBD;RBD 11;130 14;133 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The triple mutations, K417N-E484K-N501Y, and K417T-E484K-N501Y displayed weaker binding affinity to heparin (-6.6 kcal/mol). 2022 Process biochemistry (Barking, London, England) Abstract SARS_CoV_2 K417N;K417T;E484K;E484K;N501Y;N501Y 22;45;28;51;34;57 27;50;33;56;39;62 35194575 SARS-CoV-2 variant B.1.1.7 caused HLA-A2(+) CD8(+) T cell epitope mutations for impaired cellular immune response. Our results further showed that at least two site mutations in B.1.1.7 resulted in a decrease in CD8+ T cell activation and a possible immune evasion, namely A1708D mutation in ORF1ab1707-1716 and I2230T mutation in ORF1ab2230-2238. 2022 iScience Abstract SARS_CoV_2 A1708D;I2230T 158;197 164;203 ORF1ab;ORF1ab 177;216 183;222 35194576 Impact of new variants on SARS-CoV-2 infectivity and neutralization: A molecular assessment of the alterations in the spike-host protein interactions. The substitutions T478K and L452R in the Delta variant enhance associations with ACE2, whereas P681R promotes recognition by proteases, thus facilitating viral entry. 2022 iScience Abstract SARS_CoV_2 L452R;P681R;T478K 28;95;18 33;100;23 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. We describe three cases in which a Mu strain containing the mutation K417N was initially misclassified as the Beta variant. 2022 Archives of virology Abstract SARS_CoV_2 K417N 69 74 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. We recommend the detection of P681H to distinguish between these two variants. 2022 Archives of virology Abstract SARS_CoV_2 P681H 30 35 35196496 Listeria toxin promotes phosphorylation of the inflammasome adaptor ASC through Lyn and Syk to exacerbate pathogen expansion. Furthermore, the virulence of LLO T223A mutant is markedly attenuated in vivo due to impaired ability to activate the inflammasome. 2022 Cell reports Abstract SARS_CoV_2 T223A 34 39 35196496 Listeria toxin promotes phosphorylation of the inflammasome adaptor ASC through Lyn and Syk to exacerbate pathogen expansion. Notably, a Listeria mutant expressing LLO T223A is impaired in inducing ASC phosphorylation and inflammasome activation. 2022 Cell reports Abstract SARS_CoV_2 T223A 42 47 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. As lineages P.1.4 (S:N679K) and P.1.6 (S:P681H) expanded (Re > 1) from March to July 2021, the lineage P.1 declined (Re < 1) and the median Ct value of SARS-CoV-2 positive cases in Amazonas significantly decreases. 2022 Microbiology spectrum Abstract SARS_CoV_2 N679K;P681H 21;41 26;46 S;S 19;39 20;40 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Our study reveals a sharp increase in the relative prevalence of Gamma plus (P.1+) variants, designated Pango Lineages P.1.3 to P.1.6, harboring two types of additional Spike changes: deletions in the N-terminal (NTD) domain (particularly Delta144 or Delta141-144) associated with resistance to anti-NTD neutralizing antibodies or mutations at the S1/S2 junction (N679K or P681H) that probably enhance the binding affinity to the furin cleavage site, as suggested by our molecular dynamics simulations. 2022 Microbiology spectrum Abstract SARS_CoV_2 P681H;N679K 373;364 378;369 S;N 169;201 174;202 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. This multiplex PCR typing method was established to detect 9 mutations with specific primers and probes (DeltaHV 69/70, K417T, K417N, L452R, E484K, E484Q, N501Y, P681H, and P681R) against the receptor-binding domain of the spike protein of SARS-CoV-2 variants. 2022 Microbiology spectrum Abstract SARS_CoV_2 E484K;E484Q;K417N;K417T;L452R;N501Y;P681H;P681R 141;148;127;120;134;155;162;173 146;153;132;125;139;160;167;178 S 223 228 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. This PCR typing strategy allowed the detection of five major variants of concern and also provided an open-source PCR assay which could rapidly be deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, P.1, and B.1.617.2 variants and of four Omicron mutations on the spike protein (DeltaHV 69/70, K417N, N501Y, P681H). 2022 Microbiology spectrum Abstract SARS_CoV_2 K417N;N501Y;P681H 364;371;378 369;376;383 S 334 339 35197485 An adjuvanted subunit SARS-CoV-2 spike protein vaccine provides protection against Covid-19 infection and transmission. In mice, NARUVAX-C19 vaccine administered intramuscularly twice at 21-day interval elicited balanced Th1/Th2 humoral and T-cell responses with high titers of neutralizing antibodies against wild-type (D614G) and delta (B.1.617.2) variants. 2022 NPJ vaccines Abstract SARS_CoV_2 D614G 201 206 35197485 An adjuvanted subunit SARS-CoV-2 spike protein vaccine provides protection against Covid-19 infection and transmission. In Syrian hamsters, NARUVAX-C19 provided complete protection against wild-type (D614G) infection and prevented its transmission to naive animals (n = 2/group) placed in the same cage as challenged animals (n = 6/group). 2022 NPJ vaccines Abstract SARS_CoV_2 D614G 80 85 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. Additionally, A22D and A36V mutation in E protein were first reported in our study, which potentially contributed to the virulence difference between the two variants. 2022 Frontiers in immunology Abstract SARS_CoV_2 A22D;A36V 14;23 18;27 E 40 41 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. Q489H substitution in the receptor-binding domain (RBD) of BMA8 and C57MA14 variants results in the receptors of SARS-CoV-2 switching from human angiotensin-converting enzyme 2 (hACE2) to murine angiotensin-converting enzyme 2 (mACE2). 2022 Frontiers in immunology Abstract SARS_CoV_2 Q489H 0 5 RBD 51 54 35205855 A Brazilian Inter-Hospital Candidemia Outbreak Caused by Fluconazole-Resistant Candida parapsilosis in the COVID-19 Era. Unprecedentedly, most of the FRCP isolates from the cardiology center presented the same genetic profile and Erg11-Y132F mutation detected in the strain that has been causing the persistent outbreak in the cancer center, highlighting the uninterrupted horizontal transmission of clonal isolates in our hospitals during the COVID-19 pandemic. 2022 Journal of fungi (Basel, Switzerland) Abstract SARS_CoV_2 Y132F 115 120 COVID-19 323 331 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. Interactions between mutated residues and RBD have been demonstrated by structural modelling of variants including D614G, B.1.1.7, B1.351, P.1, P2; other genomic variants allow escape from antibodies generated by vaccines. 2022 International journal of environmental research and public health Abstract SARS_CoV_2 D614G 115 120 RBD 42 45 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. Molecular docking analysis revealed that G462D/G462S variants were predicted to be protective variants, whereas Q438E and S339F variants were predicted to increase susceptibility. 2022 Life (Basel, Switzerland) Abstract SARS_CoV_2 G462D;G462S;Q438E;S339F 41;41;112;122 46;46;117;127 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. Our structural analysis revealed that G462D, C297S and S460R variants had possibly altered the interactions with the protease inhibitors. 2022 Life (Basel, Switzerland) Abstract SARS_CoV_2 C297S;G462D;S460R 45;38;55 50;43;60 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. Methods: Competitive allele-specific primers and universal primers were designed for the key gene mutation sites N501Y, E484K, L452R, and K417N of SARS-CoV-2 VOCs, respectively.Using the principle of allele-specific polymerase chain reaction and fluorescence energy resonance transfer, different VOCs can be differentiated. 2022 Micromachines Abstract SARS_CoV_2 E484K;K417N;L452R;N501Y 120;138;127;113 125;143;132;118 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. Then, specimens were screened for the detection of L452R, W152C, K417T, K417N, E484Q, E484K and N501Y mutations using the SARS-CoV-2 Variants II Assay Allplex, UltraGene Assay SARS-CoV-2 452R & 484K & 484Q Mutations V1, COVID-19 Ultra Variant Catcher, SARS-CoV-2 Extended ELITe MGB and Simplexa SARS-CoV-2 Variants Direct. 2022 Microorganisms Abstract SARS_CoV_2 E484K;E484Q;K417N;K417T;L452R;N501Y;W152C 86;79;72;65;51;96;58 91;84;77;70;56;101;63 COVID-19 220 228 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? In addition, mutations affecting other viral proteins appeared frequently including; N:RG203KR, N:G212V, NSP3:T428I, ORF3a:Q57H, S:N501Y, M:I82T and E:V5F. 2022 Microorganisms Abstract SARS_CoV_2 G212V;I82T;N501Y;Q57H;T428I;V5F 98;140;131;123;110;151 103;144;136;127;115;154 ORF3a;Nsp3;E;N;N;S 117;105;149;85;96;129 122;109;150;86;97;130 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? Lower prevalence was noted for GRY (variant S-N501Y) (5.1%), S (variant ORF8-L84S) (3.1%) and GV (variant of the ORF3a coding protein NS3-G251V) (2.0%). 2022 Microorganisms Abstract SARS_CoV_2 G251V;L84S;N501Y 138;77;46 143;81;51 ORF3a;ORF8;NS3;S;S 113;72;134;44;61 118;76;137;45;62 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? Phylogenetic analysis of SARS-CoV-2 genomes revealed the existence of eleven GISAID clades with GR (variant of the spike protein S-D614G and nucleocapsid protein N-G204R), GH (variant of the ORF3a coding protein ORF3a-Q57H) and GK (variant S-T478K) being the most common with 25.9%, 19.9%, and 19.6%, respectively, followed by their parent clade G (variant S-D614G) (10.3%). 2022 Microorganisms Abstract SARS_CoV_2 D614G;D614G;G204R;Q57H;T478K 131;359;164;218;242 136;364;169;222;247 N;S;ORF3a;ORF3a;N;S;S;S 141;115;191;212;162;129;240;357 153;120;196;217;163;130;241;358 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? The effect of mutations in SAR-CoV-2 genomes highlighted similar profiles with D614G spike (S) and ORF1b-P314L variants as the most changes found in 95.3% and 87.9% of total sequences, respectively. 2022 Microorganisms Abstract SARS_CoV_2 D614G;P314L 79;105 84;110 S;S 85;92 90;93 35211985 Detection and isolation of SARS-CoV-2 Eta variant from the international travelers and local residents of India. The detection of this variant with lethal E484K mutation across the globe and India necessitates persistent genomic surveillance of the SARS-CoV-2 variants, which would aid in taking preventive action. 2022 Journal of medical virology Abstract SARS_CoV_2 E484K 42 47 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Mutational analysis showed presence of unique G1223C missense mutation in transmembrane domain of the spike protein. 2022 PloS one Abstract SARS_CoV_2 G1223C 46 52 S 102 107 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. The selected SARS-CoV-2 isolates were then sequenced, characterized and analyzed along with 986 sequences of the dominant lineages of D614G variants currently circulating throughout Malaysia. 2022 PloS one Abstract SARS_CoV_2 D614G 134 139 35215765 Versatile SARS-CoV-2 Reverse-Genetics Systems for the Study of Antiviral Resistance and Replication. We found that putative coronavirus remdesivir resistance-associated substitutions F480L and V570L-and naturally found polymorphisms A97V, P323L, and N491S, all in nsp12-did not decrease SARS-CoV-2 susceptibility to remdesivir. 2022 Viruses Abstract SARS_CoV_2 A97V;F480L;N491S;P323L;V570L 132;82;149;138;92 136;87;154;143;97 35215781 Structure Based Affinity Maturation and Characterizing of SARS-CoV Antibody CR3022 against SARS-CoV-2 by Computational and Experimental Approaches. It was found that the binding affinity of the CR3022 antibody could be significantly enhanced more than ten times after the introduction of the S103F/Y mutation in HCDR-3 and the S33R mutation in LCDR-1. 2022 Viruses Abstract SARS_CoV_2 S103F;S103Y;S33R 144;144;179 151;151;183 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. Four out of the 13 patients acquired a mutation during follow-up; two mutations (G1204E and E406G) appeared as a mixture without clinical impact, while the Q493R mutation emerged in two patients (one receiving bamlanivimab and one receiving bamlanivimab/etesevimab) with fatal outcomes. 2022 Viruses Abstract SARS_CoV_2 E406G;Q493R;G1204E 92;156;81 97;161;87 35215823 Characterization of a Broadly Neutralizing Monoclonal Antibody against SARS-CoV-2 Variants. Based on our in vitro escape mutant studies, we proved that the mutations V483F and Y489H within the RBD were involved in ACE2 binding and caused the neutralizing evasion of the virus from mAb 9G8. 2022 Viruses Abstract SARS_CoV_2 V483F;Y489H 74;84 79;89 RBD 101 104 35215911 Ferristatin II Efficiently Inhibits SARS-CoV-2 Replication in Vero Cells. The findings were well confirmed by the significant inhibition of the SARS-CoV-2 infection of Vero cells by ferristatin II with IC50 values of 27 microM (for Wuhan D614G virus) and 40 microM (for Delta virus). 2022 Viruses Abstract SARS_CoV_2 D614G 164 169 COVID-19 70 90 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Furthermore, comparison of both Vero-grown isolates on WD-PNECs disclosed marked growth attenuation mapping to the loss of the polybasic cleavage site (PBCS) in Spike, while the strain with mutations in Nsp12 (T293I), Spike (P812R) and a truncation of Orf7a remained viable in WD-PNECs. 2022 Viruses Abstract SARS_CoV_2 P812R;T293I 225;210 230;215 ORF7a;S;S;Nsp12 252;161;218;203 257;166;223;208 35215963 Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic. Interestingly, four SARS-CoV-2 isolates, carrying the D614G substitution originally associated with increased transmissibility, were more susceptible (2.4-fold) to a commercial monoclonal antibody targeting the spike glycoprotein than the wild-type viruses. 2022 Viruses Abstract SARS_CoV_2 D614G 54 59 S 211 229 35215988 Influenza A(H1N1)pdm09 Virus but Not Respiratory Syncytial Virus Interferes with SARS-CoV-2 Replication during Sequential Infections in Human Nasal Epithelial Cells. We have evaluated the interactions between SARS-CoV-2 (D614G mutant) and influenza A(H1N1)pdm09 or respiratory syncytial virus (RSV) in the nasal human airway epithelium (HAE) infected simultaneously or sequentially (24 h apart) with virus combinations. 2022 Viruses Abstract SARS_CoV_2 D614G 55 60 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. Here we report the analysis of 87 viral genomes, which revealed that the unique ancestor haplotype introduced in Vo' belongs to lineage B, carrying the mutations G11083T and G26144T. 2022 Viruses Abstract SARS_CoV_2 G11083T;G26144T 162;174 169;181 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. The mutational scanning analysis supported the notion that E484A mutation can have a significant detrimental effect on nanobody binding and result in Omicron-induced escape from nanobody neutralization. 2022 International journal of molecular sciences Abstract SARS_CoV_2 E484A 59 64 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. Omicron Spike is recognized less efficiently than D614G, Alpha, Beta, Gamma, and Delta Spikes. 2022 Cell reports Abstract SARS_CoV_2 D614G 50 55 S;S 8;87 13;93 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. The RBD novel mutation (Y380Q) was found in one sample occurring simultaneously with C379W and V395A, and the B.1.91 lineage in the spike protein. 2022 Diagnostic microbiology and infectious disease Abstract SARS_CoV_2 C379W;V395A;Y380Q 85;95;24 90;100;29 S;RBD 132;4 137;7 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. The Y380Q and C379W may interfere with the binding of neutralizing antibodies (CR3022, EY6A, H014, S304). 2022 Diagnostic microbiology and infectious disease Abstract SARS_CoV_2 C379W;Y380Q 14;4 19;9 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. Whole genome sequencing of 46 randomly selected samples validated the strains identified as positive and negative for the B.1.617.2 (Delta) variant and confirmed the S gene deletion in addition to B.1.617.2 characteristic mutations including L452R, T478K, P681R and D950N located in the spike protein. 2022 Pathology Abstract SARS_CoV_2 D950N;L452R;P681R;T478K 266;242;256;249 271;247;261;254 S;S 287;166 292;167 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Simultaneously we have discussed the significant mutations related to emerging variants and immune escape, such as mutations in the RBD region (N439K, L452R, E484K, N501Y, K444R) and other parts (D614G, P681R) of the S-glycoprotein. 2022 Frontiers in immunology Abstract SARS_CoV_2 E484K;K444R;L452R;N501Y;P681R;D614G;N439K 158;172;151;165;203;196;144 163;177;156;170;208;201;149 S;RBD 217;132 231;135 35223905 Molecular and Epidemiological Characterization of Emerging Immune-Escape Variants of SARS-CoV-2. We found that the Mu variant and a derivative of the Delta strain with E484K and N501Y mutations significantly evaded vaccine-elicited neutralizing antibodies. 2022 Frontiers in medicine Abstract SARS_CoV_2 E484K;N501Y 71;81 76;86 35227008 Variants of SARS CoV-2: mutations, transmissibility, virulence, drug resistance, and antibody/vaccine sensitivity. Mutations in the S protein that are common among several of the variants include D614G that increases transmissibility and viral load and is often associated with P323L on the RNA dependent RNA polymerase. 2022 Frontiers in bioscience (Landmark edition) Abstract SARS_CoV_2 D614G;P323L 81;163 86;168 RdRp;S 176;17 204;18 35227008 Variants of SARS CoV-2: mutations, transmissibility, virulence, drug resistance, and antibody/vaccine sensitivity. N501Y is a mutation in the receptor binding domain of the S protein that increases binding to the ACE-2 receptor on the human host cells by 10 fold. 2022 Frontiers in bioscience (Landmark edition) Abstract SARS_CoV_2 N501Y 0 5 RBD;S 27;58 50;59 35228982 Coexistence of Chronic Myelomonocytic Leukemia and Ulcerative Colitis With Rapid Progression to Acute Myelomonocytic Leukemia: A Case Report. Next-generation DNA sequencing of a bone marrow sample demonstrated mutations of the TET2, ASXL1, NRAS, and SRSF2 genes along with low-level JAK2^V617F mutation. 2022 Cureus Abstract SARS_CoV_2 V617F 146 151 35229308 SARS-COV-2 genomic monitoring in the state of Sao Paulo unveils two emerging AY.43 sublineages. These sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a:T14I for the AY.43.1 and ORF1ab:G1155C for the AY.43.2 and our analysis reveals that they might have a likely-Brazilian origin. 2022 Journal of medical virology Abstract SARS_CoV_2 A4133V;G1155C;T14I 94;143;111 100;149;115 ORF1ab;ORF1ab;ORF3a 87;136;105 93;142;110 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. Here we describe a newly acquired spike E484K mutation detected within the B.1.311 lineage. 2022 Diagnostic microbiology and infectious disease Abstract SARS_CoV_2 E484K 40 45 S 34 39 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. The timing and patterns of spread were consistent with de novo emergence of this E484K variant in the bamlanivimab-treated index patient. 2022 Diagnostic microbiology and infectious disease Abstract SARS_CoV_2 E484K 81 86 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. The most frequent non-synonymous mutation 486/546 (89.01%) occurred in the S gene (structural gene) at position 23,403 where A changed to G leading to the replacement of aspartic acid by glycine in position (D614G). 2022 Saudi journal of biological sciences Abstract SARS_CoV_2 D614G 208 213 S 75 76 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. Furthermore, Beta and Delta infection trigger responses with significantly improved Fc cross-reactivity against global VOCs compared with D614G-infected or Ad26.COV2.S-vaccinated individuals. 2022 Cell reports. Medicine Abstract SARS_CoV_2 D614G 138 143 S 166 167 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. Here, we demonstrate that the Beta VOC partially evades Fc effector activity in individuals infected with the original (D614G) variant. 2022 Cell reports. Medicine Abstract SARS_CoV_2 D614G 120 125 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. To build an investigative framework, we have applied an unsupervised machine learning approach to 4296 Omicron viral genomes collected and deposited to GISAID as of December 14, 2021, and have identified a core haplotype of 28 polymutants (A67V, T95I, G339D, R346K, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, K796Y, N856K, Q954H, N69K, L981F) in the spike protein and a separate core haplotype of 17 polymutants in non-spike genes: (K38, A1892) in nsp3, T492 in nsp4, (P132, V247, T280, S284) in 3C-like proteinase, I189 in nsp6, P323 in RNA-dependent RNA polymerase, I42 in Exonuclease, T9 in envelope protein, (D3, Q19, A63) in membrane glycoprotein, and (P13, R203, G204) in nucleocapsid phosphoprotein. 2022 Research square Abstract SARS_CoV_2 D614G;E484A;G339D;G446S;G496S;H655Y;K417N;K796Y;L981F;N440K;N501Y;N679K;N69K;N764K;N856K;P681H;Q493R;Q498R;Q954H;R346K;S371L;S373P;S375F;S477N;T478K;T547K;T95I;Y505H;A67V 371;322;252;301;336;378;287;406;433;294;350;385;427;399;413;392;329;343;420;259;266;273;280;308;315;364;246;357;240 376;327;257;306;341;383;292;411;438;299;355;390;431;404;418;397;334;348;425;264;271;278;285;313;320;369;250;362;244 RdRp;N;Exonuclease;Membrane;S;S;Nsp3;Nsp4;Nsp6 635;775;672;727;447;516;545;559;621 663;787;683;735;452;521;549;563;625 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. Two emerging mutations may be of particular concern: the N1192S mutation in spike protein locates in an extremely highly conserved region of all human coronaviruses that is integral to the viral fusion process, and the F694Y mutation in the RNA polymerase may induce conformational changes that could impact Remdesivir binding. 2022 Research square Abstract SARS_CoV_2 F694Y;N1192S 219;57 224;63 S 76 81 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. Using these core haplotypes as reference, we have identified four newly emerging polymutants (R346, A701, I1081, N1192) in the spike protein (p-value=9.37*10 -4 , 1.0*10 -15 , 4.76*10 -7 and 1.56*10 -4 , respectively), and five additional polymutants in non-spike genes (D343G in nucleocapsid phosphoprotein, V1069I in nsp3, V94A in nsp4, F694Y in the RNA-dependent RNA polymerase and L106L/F of ORF3a) that exhibit significant increasing trajectories (all p-values < 1.0*10 -15 ). 2022 Research square Abstract SARS_CoV_2 F694Y;L106F;L106L;V1069I;V94A;D343G 339;385;385;309;325;271 344;392;392;315;329;276 RdRp;N;S;S;ORF3a;Nsp3;Nsp4 352;280;127;258;396;319;333 380;292;132;263;401;323;337 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. Among the SARS-CoV-2 related sarbecoviruses, it is found that the genetically more distant bat RaTG13 and pangolin GX-P5L sarbecoviruses had less neutralization escape than Omicron. 2022 Research square Abstract SARS_CoV_2 P5L 118 121 35233570 VE607 Stabilizes SARS-CoV-2 Spike In the "RBD-up" Conformation and Inhibits Viral Entry. The IC 50 values are in the low micromolar range for pseudoparticles derived from SARS-CoV-2 Wuhan/D614G as well as from variants of concern (Alpha, Beta, Gamma, Delta and Omicron), suggesting that VE607 has potential for the development of drugs against SARS-CoV-2 infections. 2022 bioRxiv Abstract SARS_CoV_2 D614G 99 104 COVID-19 255 276 35233612 Deep learning based on biologically interpretable genome representation predicts two types of human adaptation of SARS-CoV-2 variants. The identified adaptive determinants included D1118H and A570D mutations and local DNTs. 2022 Briefings in bioinformatics Abstract SARS_CoV_2 A570D;D1118H 57;46 62;52 35233783 Active surveillance and early detection of community transmission of SARS-CoV-2 Mu variant (B.1.621) in the Brazilian Amazon. Two infected individuals from different households caring viruses with additional amino acid substitutions ORF7a P45L and ORF1a T1055A compared to the Mu virus reference sequence. 2022 Journal of medical virology Abstract SARS_CoV_2 P45L;T1055A 113;128 117;134 ORF1a;ORF7a 122;107 127;112 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. Cases were classified as N501Y-positive VOC, probable Delta VOC, or VOC undetected. 2022 Clinical infectious diseases Abstract SARS_CoV_2 N501Y 25 30 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. RESULTS: Infection with either N501Y-positive or Delta VOCs was associated with significant elevations in risk of hospitalization, ICU admission, and death across age groups, compared to infections where a VOC was not detected. 2022 Clinical infectious diseases Abstract SARS_CoV_2 N501Y 31 36 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. We constructed age-specific logistic regression models to evaluate associations between N501Y-postive or Delta VOC infections and infection severity, using hospitalization, intensive care unit (ICU) admission, and death as outcome variables. 2022 Clinical infectious diseases Abstract SARS_CoV_2 N501Y 88 93 35235585 Travel ban effects on SARS-CoV-2 transmission lineages in the UAE as inferred by genomic epidemiology. The study comprehensively characterized the genomic aspects of the virus and its spread within the UAE and identified that the prevalence shift of the D614G mutation was due to the later introductions of the G-variant associated with international travel, rather than higher local transmissibility. 2022 PloS one Abstract SARS_CoV_2 D614G 151 156 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. In addition, the neutralization efficacy of authentic SARS-CoV-2 wild type (D614G), Delta, and Omicron by sera from 2x or 3x BNT162b2-vaccinated persons was analyzed. 2022 BMC medicine Abstract SARS_CoV_2 D614G 76 81 35238382 Safety of the BNT162b2 mRNA COVID-19 vaccine in patients with familial Mediterranean fever. Patients with a more active FMF disease and patients harboring the M694V mutation had a significantly higher rate of post-vaccination systemic side effects and attacks. 2022 Rheumatology (Oxford, England) Abstract SARS_CoV_2 M694V 67 72 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. BA.2 also exhibited marked resistance to 17 of 19 neutralizing monoclonal antibodies tested, including S309 (sotrovimab)7, which had retained appreciable activity against BA.1 and BA.1+R346K (refs. 2022 Nature Abstract SARS_CoV_2 R346K 185 190 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. Continuing surveillance of the evolution of Omicron has since revealed the rise in prevalence of two sublineages, BA.1 with an R346K alteration (BA.1+R346K, also known as BA.1.1) and B.1.1.529.2 (BA.2), with the latter containing 8 unique spike alterations and lacking 13 spike alterations found in BA.1. 2022 Nature Abstract SARS_CoV_2 R346K;R346K 127;150 132;155 S;S 239;272 244;277 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. Polyclonal sera from patients infected by wild-type SARS-CoV-2 or recipients of current mRNA vaccines showed a substantial loss in neutralizing activity against both BA.1+R346K and BA.2, with drops comparable to that already reported for BA.1 (refs. 2022 Nature Abstract SARS_CoV_2 R346K 171 176 35240804 Estimating the transmissibility of SARS-CoV-2 VOC 202012/01 in Japan using travel history information. The variant of concern (VOC) 202012/01 (B.1.1.7, also known as the alpha variant) bearing the N501Y mutation emerged in late 2020. 2022 Mathematical biosciences and engineering Abstract SARS_CoV_2 N501Y 94 99 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. Variant A.27 is characterized by a mutational pattern in the spike gene that includes the L18F, L452R and N501Y spike amino acid substitutions found in various variants of concern but lacks the globally dominant D614G. 2022 Nature communications Abstract SARS_CoV_2 D614G;L18F;L452R;N501Y 212;90;96;106 217;94;101;111 S;S 61;112 66;117 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. The N440K change was detected in 45/162 (27.7%) of the sequences, 37 of these were in the B.1.36 lineage (37/65, 56.92%) Conclusions: Our data support the idea that variants of concern spread by travel. 2021 Wellcome open research Abstract SARS_CoV_2 N440K 4 9 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. In the Beta variant spike, the presence of a new substitution, K417N (also observed in the Omicron variant), in combination with the D614G, stabilises a more open spike trimer, a conformation required for receptor binding. 2022 Nature communications Abstract SARS_CoV_2 D614G;K417N 133;63 138;68 S;S 20;163 25;168 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. Spikes of both variants have the same mutation, N501Y, in the receptor-binding domains. 2022 Nature communications Abstract SARS_CoV_2 N501Y 48 53 S 0 6 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. This substitution confers tighter ACE2 binding, dependent on the common earlier substitution, D614G. 2022 Nature communications Abstract SARS_CoV_2 D614G 94 99 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. This results in the prediction that the H80R variant is a solid new candidate for potential new testing. 2022 Informatics in medicine unlocked Abstract SARS_CoV_2 H80R 40 44 35255849 Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. During a separate outbreak within a skilled nursing facility, genomic surveillance data were used to rule out the putative index case, detect the emergence of an independent Spike:N501Y substitution, and verify that the outbreak had been brought under control. 2022 BMC public health Abstract SARS_CoV_2 N501Y 180 185 S 174 179 35257681 Simultaneous detection of SARS-CoV-2 and identification of spike D614G mutation using point-of-care real-time polymerase chain reaction. Here, we developed a multiplex real-time reverse transcription PCR (rRT-PCR) analysis that not only detects SARS-CoV-2 but also D614G strains with higher contagiousness than wild types among SARS-CoV-2 mutants using probe-based rRT-PCR. 2022 Journal of virological methods Abstract SARS_CoV_2 D614G 128 133 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. Furthermore, we examined the effect of significant antibody-binding mutations (K417N, T478K, E484A, and N501Y) on antibody affinity, stability to ACE2 interaction, and possibility of amino acid substitution. 2022 GeroScience Abstract SARS_CoV_2 E484A;N501Y;T478K;K417N 93;104;86;79 98;109;91;84 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. New mutations were found in the NTD (Delta143-145, A67V, T95I, L212I, and Delta211) including one new mutation in fusion peptide (D796Y). 2022 GeroScience Abstract SARS_CoV_2 A67V;L212I;T95I;D796Y 51;63;57;130 55;68;61;135 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. There are several mutations in the antibody-binding region including K417N, E484A, Q493K, Q498R, N501Y, and Y505H and several near the antibody-binding region (S477N, T478K, G496S, G446S, and N440K). 2022 GeroScience Abstract SARS_CoV_2 E484A;G446S;G496S;K417N;N440K;N501Y;Q493K;Q498R;T478K;Y505H;S477N 76;181;174;69;192;97;83;90;167;108;160 81;186;179;74;197;102;88;95;172;113;165 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. Various new receptor-binding domain mutations were detected, including Q493K, G496S, Q498R, S477N, G466S, N440K, and Y505H. 2022 GeroScience Abstract SARS_CoV_2 G466S;G496S;N440K;Q493K;Q498R;S477N;Y505H 99;78;106;71;85;92;117 104;83;111;76;90;97;122 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. We also evaluated mutations in the antibody-binding regions and observed some important mutations overlapping those of previous variants including N501Y, D614G, H655Y, N679K, and P681H. 2022 GeroScience Abstract SARS_CoV_2 D614G;H655Y;N501Y;N679K;P681H 154;161;147;168;179 159;166;152;173;184 35262011 Use of amplicon melt temperature to detect SARS-CoV-2 Lineage B.1.1.7 variant through the G28048T mutation in the ORF 8 gene. It was confirmed that these carried the G28048T mutation. 2021 Journal of clinical virology plus Abstract SARS_CoV_2 G28048T 40 47 35262011 Use of amplicon melt temperature to detect SARS-CoV-2 Lineage B.1.1.7 variant through the G28048T mutation in the ORF 8 gene. The objective of this study was to determine if the recently identified mutation in ORF8 (G28048T) in the B.1.1.7. 2021 Journal of clinical virology plus Abstract SARS_CoV_2 G28048T 90 97 ORF8 84 88 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. and Iketani et al., we propose a mechanism to explain S371L/F escape according to a perturbation of spike trimer conformational dynamics that has not yet been described for any SARS-CoV-2 escape mutation. 2022 bioRxiv Abstract SARS_CoV_2 S371L;S371F 54;54 61;61 S 100 105 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. observed a profoundly broad escape effect for the individual mutations S371L and S371F. 2022 bioRxiv Abstract SARS_CoV_2 S371F;S371L 81;71 86;76 35262087 Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites. The SNP assays (K417T, E484K, E484Q, L452R) demonstrated 99.20%, 96.40%, 99.60%, and 96.80% accuracies, respectively. 2022 medRxiv Abstract SARS_CoV_2 E484K;E484Q;L452R;K417T 23;30;37;16 28;35;42;21 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. Variants D614G, Alpha, and Eta are neutralized by sera of 100% of vaccinees, whereas neutralization of Delta is 3.8-fold reduced and neutralization of Beta is 5.8-fold reduced compared to D614G. 2022 Microbiology spectrum Abstract SARS_CoV_2 D614G;D614G 9;188 14;193 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. A recent study reported a double mutant of SARS-CoV-2, L452R-E484Q, located in the RBD region. 2022 3 Biotech Abstract SARS_CoV_2 L452R;E484Q 55;61 60;66 RBD 83 86 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. Thus, this study employed various computational algorithms and methods to understand the structural impact of both individual variants L452R, E484Q, and the double mutant L452R-E484Q on the native RBD of spike glycoprotein. 2022 3 Biotech Abstract SARS_CoV_2 E484Q;L452R;L452R;E484Q 142;135;171;177 147;140;176;182 S;RBD 204;197 222;200 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. Furthermore, the P681R mutation leads to enhanced spike cleavage, which could facilitate viral entry. 2022 mBio Abstract SARS_CoV_2 P681R 17 22 S 50 55 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. In addition, Kappa, Delta, and B.1.618 exhibit a reduced sensitivity to neutralization by convalescent-phase sera due to the mutation E484Q, T478K, Delta145-146, or E484K, but remain sensitive to entry inhibitors such as ACE2-Ig decoy receptor. 2022 mBio Abstract SARS_CoV_2 E484K;E484Q;T478K 165;134;141 170;139;146 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. The spike protein of Kappa contains the four mutations E154K, L452R, E484Q, and P681R, and Delta contains L452R, T478K, and P681R, while B.1.618 spike harbors mutations Delta145-146 and E484K. 2022 mBio Abstract SARS_CoV_2 E154K;E484K;E484Q;L452R;L452R;P681R;P681R;T478K 55;186;69;62;106;80;124;113 60;191;74;67;111;85;129;118 S;S 4;145 9;150 35266944 Tetra-primer ARMS-PCR combined with dual-color fluorescent lateral flow assay for the discrimination of SARS-CoV-2 and its mutations with a handheld wireless reader. Herein, we report a low-cost, facile, and highly sensitive diagnostic platform that can simultaneously distinguish wild-type (WT) SARS-CoV-2 and its two mutations, namely, D614G and N501Y, within 2 h. 2022 Lab on a chip Abstract SARS_CoV_2 D614G;N501Y 172;182 177;187 35266944 Tetra-primer ARMS-PCR combined with dual-color fluorescent lateral flow assay for the discrimination of SARS-CoV-2 and its mutations with a handheld wireless reader. The limits of detection (LODs) for the WT and M D614G were estimated as 78.91 and 33.53 copies per muL, respectively. 2022 Lab on a chip Abstract SARS_CoV_2 D614G 48 53 35266944 Tetra-primer ARMS-PCR combined with dual-color fluorescent lateral flow assay for the discrimination of SARS-CoV-2 and its mutations with a handheld wireless reader. The WT and M viruses were indicated and were strictly discriminated by the presence of a green or red band on test line 1 for the D614G site and test line 2 for the N501Y site. 2022 Lab on a chip Abstract SARS_CoV_2 D614G;N501Y 130;165 135;170 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. The P.1.2 exclusive haplotype H_5 originated from a non-synonymous mutational step (H3509Y) in H_1 of ORF1a. 2022 Genetics and molecular biology Abstract SARS_CoV_2 H3509Y 84 90 ORF1a 102 107 35271728 Rapid spread of SARS-CoV-2 Omicron subvariant BA.2 in a single-source community outbreak. All individuals in the STY cluster had the unique mutation C12525T. 2022 Clinical infectious diseases Abstract SARS_CoV_2 C12525T 59 66 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. We screened the mutations of del69-70, E484K, E484Q, D614G, L452R, and T478K in 100 cases from SARS-COV-2 positive patients in Kurdistan- Iran population. 2022 Journal of virological methods Abstract SARS_CoV_2 D614G;E484K;E484Q;L452R;T478K 53;39;46;60;71 58;44;51;65;76 35273217 A SARS-CoV-2 Wuhan spike virosome vaccine induces superior neutralization breadth compared to one using the Beta spike. In addition, neutralizing activity against the D614G, Alpha and Delta variants was also significantly lower after Beta spike vaccination than after Wuhan spike vaccination. 2022 Scientific reports Abstract SARS_CoV_2 D614G 47 52 S;S 119;154 124;159 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Specific amino acid substitutions such as D614G and N501Y were found to alter the transmissibility and virulence of the virus. 2022 Frontiers in medicine Abstract SARS_CoV_2 D614G;N501Y 42;52 47;57 35277343 A prospective evaluation of diagnostic performance of a combo rapid antigen test QuickNavi-Flu+COVID19 Ag. METHODS: We included those who were suspected of contracting coronavirus disease 2019 (COVID-19) and were referred to a PCR center at Ibaraki prefecture in Japan, between August 2, 2021 to September 13, 2021, when the variant carrying L452R spike mutation of SARS-CoV-2 were prevalent. 2022 Journal of infection and chemotherapy Abstract SARS_CoV_2 L452R 235 240 S 241 246 COVID-19;COVID-19 61;87 80;95 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. In addition, GB-1 inhibited the binding between ACE2 and RBD with a single mutation (E484K or N501Y), except the K417N mutation. 2022 Biomedicine & pharmacotherapy Abstract SARS_CoV_2 K417N;N501Y;E484K 113;94;85 118;99;90 RBD 57 60 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. In the compositions of GB-1, glycyrrhizic acid can inhibit the binding between ACE2 and RBD with Wuhan type, except K417N-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Abstract SARS_CoV_2 K417N;E484K;N501Y 116;122;128 121;127;133 RBD 88 91 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. In this study, we discovered that GB-1, developed from Chiehyuan herbal formula which obtained from Tian Shang Sheng Mu of Chiayi Puzi Peitian Temple, can inhibit the binding between ACE2 and RBD with Wuhan type, K417N-E484K-N501Y and L452R-T478K mutation. 2022 Biomedicine & pharmacotherapy Abstract SARS_CoV_2 K417N;L452R;E484K;N501Y;T478K 213;235;219;225;241 218;240;224;230;246 RBD 192 195 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. N501Y, E484K, K417N, K417T, L452R and T478K in the receptor binding domain (RBD) region may increase the infectivity in several variants of SARS-CoV-2. 2022 Biomedicine & pharmacotherapy Abstract SARS_CoV_2 E484K;K417N;K417T;L452R;T478K;N501Y 7;14;21;28;38;0 12;19;26;33;43;5 RBD;RBD 51;76 74;79 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Our results suggest that GB-1 could be a potential candidate for the prophylaxis of different variants of SARS-CoV-2 infection because of its inhibition of binding between ACE2 and RBD with different mutations (L452R-T478K, K417N-E484K-N501Y, N501Y or E484K). 2022 Biomedicine & pharmacotherapy Abstract SARS_CoV_2 E484K;K417N;N501Y;L452R;E484K;N501Y;T478K 252;224;243;211;230;236;217 257;229;248;216;235;241;222 RBD 181 184 COVID-19 106 126 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The neutralizing antibody titer against D614G significantly decreased in sera of 6-8 months post onset compared to those of 1-3 months post onset. 2022 Frontiers in immunology Abstract SARS_CoV_2 D614G 40 45 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. Then, a virus neutralization assay against SARS-CoV-2 variants (D614G mutation as conventional strain; B.1.1.7, P.1, and B.1.351 as VOCs) was performed using authentic viruses. 2022 Frontiers in immunology Abstract SARS_CoV_2 D614G 64 69 35283546 SARS-CoV-2 infection after vaccination in Italian health care workers: a case report. Their genotyping performed on RNA extracts highlighted the presence of del69/70, N501Y, A570D, and 1841A > G (D614G) sequence variants, all indicative of VOC 202012/01-lineage B.1.1.7, suggesting a common source of infection. 2022 National Academy science letters. National Academy of Sciences, India Abstract SARS_CoV_2 A1841G;A570D;N501Y;D614G 99;88;81;110 108;93;86;115 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. Using next-generation sequencing (NGS) of the spike (S) gene amplicons of the Delta variant-dominant samples, we found six mutations exclusive to the Delta variant (S:T19R, S:Delta156/157, S:L452R, S:T478K, S:P681R, and S:D950N). 2022 Applied and environmental microbiology Abstract SARS_CoV_2 D950N;L452R;P681R;T19R;T478K 222;191;209;167;200 227;196;214;171;205 S;S;S;S;S;S;S;S 46;53;165;173;189;198;207;220 51;54;166;174;190;199;208;221 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. The Alpha reaction targets the D3L substitution in the N gene, and the Delta reaction targets the spike gene 156 to 158 mutations. 2022 Microbiology spectrum Abstract SARS_CoV_2 D3L 31 34 S;N 98;55 103;56 35286152 Risk and Outcome of Breakthrough COVID-19 Infections in Vaccinated Patients With Cancer: Real-World Evidence From the National COVID Cohort Collaborative. METHODS: We used the National COVID Cohort Collaborative (N3C) to identify breakthrough infections between December 1, 2020, and May 31, 2021. 2022 Journal of clinical oncology : official journal of the American Society of Clinical Oncology Abstract SARS_CoV_2 N3C 58 61 35286152 Risk and Outcome of Breakthrough COVID-19 Infections in Vaccinated Patients With Cancer: Real-World Evidence From the National COVID Cohort Collaborative. RESULTS: A total of 6,860 breakthrough cases were identified within the N3C-vaccinated population, among whom 1,460 (21.3%) were patients with cancer. 2022 Journal of clinical oncology : official journal of the American Society of Clinical Oncology Abstract SARS_CoV_2 N3C 72 75 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. The AY.4.2 spike displays three additional mutations (T95I, Y145H and A222V) in the N-terminal domain when compared to the original Delta variant (B.1.617.2) and remains poorly characterized. 2022 EBioMedicine Abstract SARS_CoV_2 A222V;Y145H;T95I 70;60;54 75;65;58 S;N 11;84 16;85 35293190 [Detection SARS-CoV-2 (Coronaviridae: Coronavirinae: Betacoronavirus: Sarbecovirus) in children with acute intestinal infection in Nizhny Novgorod during 2020-2021]. Analysis of the S-protein amino acid sequence of the strains studied showed the absence of the N501Y mutation in the 2020 samples, which is a marker for variants with a high epidemic potential, called variants of concern (VOC) according to the World Health Organization (WHO) definition (lines Alpha B.1.1.7, Beta B.1.351, Gamma P.1). 2022 Voprosy virusologii Abstract SARS_CoV_2 N501Y 95 100 S 16 17 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. B.1.617 variants did not exhibit significant enhanced infectivity in human cells, but mutations T478K and E484Q in the receptor binding domain led to enhanced infectivity in mouse ACE2-overexpressing cells. 2022 Emerging microbes & infections Abstract SARS_CoV_2 E484Q;T478K 106;96 111;101 RBD 119 142 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Furthermore, B.1.617 variants escaped neutralization by several mAbs, mainly because of mutations L452R, T478K, and E484Q in the receptor binding domain. 2022 Emerging microbes & infections Abstract SARS_CoV_2 E484Q;L452R;T478K 116;98;105 121;103;110 RBD 129 152 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. The neutralization activities of sera from convalescent patients, inactivated vaccine-immunized volunteers, adenovirus vaccine-immunized volunteers, and SARS-CoV-2 immunized animals against pseudotyped B.1.617 variants were reduced by approximately twofold, compared with the D614G variant. 2022 Emerging microbes & infections Abstract SARS_CoV_2 D614G 276 281 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. R203M in the N gene of SARS-CoV-2 was chosen as the Delta variant-specific mutation for genotyping. 2022 Emerging microbes & infections Abstract SARS_CoV_2 R203M 0 5 N 13 14 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. To target the R203M-harboring region and the conserved sequence of the N gene, two sets of primers were designed, and a Cq (quantification cycle) ratio-based RT-LAMP for SARS-CoV-2 and R203M detection was developed by analyzing the significant discrepancy in amplification efficiency of the two sets of primers. 2022 Emerging microbes & infections Abstract SARS_CoV_2 R203M;R203M 14;185 19;190 N 71 72 35293850 Immune escape facilitation by mutations of epitope residues in RdRp of SARS-CoV-2. The mutation P323L in RdRp is associated with the loss of a particular epitope (321-327) from this protein. 2022 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 P323L 13 18 RdRP 22 26 35293850 Immune escape facilitation by mutations of epitope residues in RdRp of SARS-CoV-2. We consider the effects of mutations in some of the epitope region including the naturally occurring mutation P323L on the structure of the epitope and their interface with paratope using all-atom molecular dynamics (MD) simulation studies. 2022 Journal of biomolecular structure & dynamics Abstract SARS_CoV_2 P323L 110 115 35294336 Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variant genome assemblies produced by next-generation sequencing. Additionally, one sample had the Y508F mutation and four samples the S477N. 2022 Microbial genomics Abstract SARS_CoV_2 S477N;Y508F 69;33 74;38 35294336 Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variant genome assemblies produced by next-generation sequencing. We applied the primer set and wet-laboratory protocol to sequence 222 samples that were missing positions with key mutations K417N, E484K, and N501Y due to poor coverage after NGS sequencing. 2022 Microbial genomics Abstract SARS_CoV_2 E484K;K417N;N501Y 132;125;143 137;130;148 35294336 Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variant genome assemblies produced by next-generation sequencing. We successfully sequenced 153 samples of 222 (69 %) using Sanger sequencing and confirmed the occurrence of key beta variant mutations (K417N, E484K, N501Y) in the S genes of 142 of 153 (93 %) samples. 2022 Microbial genomics Abstract SARS_CoV_2 E484K;N501Y;K417N 143;150;136 148;155;141 S 164 165 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Delineating the functional impact of spike mutations revealed that N-terminal domain (NTD)-specific E156G/Delta157-158 contributed to increased infectivity and reduced sensitivity to vaccine-induced antibodies. 2022 Life science alliance Abstract SARS_CoV_2 E156Delta;E156G 100;100 105;105 S;N 37;67 42;68 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Notably, E156G/Delta157-158 was present in more than 90% of the sequences reported from the USA and UK in October 2021. 2022 Life science alliance Abstract SARS_CoV_2 E156Delta;E156G 9;9 14;14 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. The spike-pseudotyped viruses bearing a combination of E156G/Delta157-158 and L452R exhibited higher infectivity and reduced sensitivity to neutralization. 2022 Life science alliance Abstract SARS_CoV_2 E156Delta;E156G;L452R 55;55;78 60;60;83 S 4 9 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. We confirmed the presence of E156G/Delta157-158 from cases concurrently screened, in addition to other circulating spike (S1) mutations such as T19R, T95I, L452R, E484Q, and D614G. 2022 Life science alliance Abstract SARS_CoV_2 D614G;E156Delta;E156G;E484Q;L452R;T19R;T95I 174;29;29;163;156;144;150 179;34;34;168;161;148;154 S 115 120 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. When the spike harbored E156G/Delta157-158 along with L452R and E484Q, increased cell-to-cell fusion was also observed, suggesting a combinatorial effect of these mutations. 2022 Life science alliance Abstract SARS_CoV_2 E156Delta;E156G;E484Q;L452R 24;24;64;54 29;29;69;59 S 9 14 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Although the fitness cost observed in vitro may limit the risk posed by E802D, this case illustrates the importance of monitoring for remdesivir resistance and the potential benefit of combinatorial therapies in immunocompromised patients with SARS-CoV-2 infection. 2022 Nature communications Abstract SARS_CoV_2 E802D 72 77 COVID-19 244 264 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Whole genome sequencing identified a mutation, E802D, in the nsp12 RNA-dependent RNA polymerase, which was not present in pre-treatment specimens. 2022 Nature communications Abstract SARS_CoV_2 E802D 47 52 RdRp;Nsp12 67;61 95;66 35301412 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. This variant belongs to Pango lineage B.1.1291, which also contains the D614G mutation in the Spike (S) gene. 2022 Scientific reports Abstract SARS_CoV_2 D614G 72 77 S;S 94;101 99;102 35304093 Tracking SARS-CoV-2 variants by entire S-gene analysis using long-range RT-PCR and Sanger sequencing. RESULTS: The S:D614G mutation was found in all samples. 2022 Clinica chimica acta; international journal of clinical chemistry Abstract SARS_CoV_2 D614G 15 20 S 13 14 35304531 In vitro evaluation of therapeutic antibodies against a SARS-CoV-2 Omicron B.1.1.529 isolate. Using a clinical strain of the Omicron variant, we analyzed the neutralizing power of eight currently used monoclonal antibodies compared to the ancestral B.1 BavPat1 D614G strain. 2022 Scientific reports Abstract SARS_CoV_2 D614G 167 172 35305699 Neutralisation sensitivity of the SARS-CoV-2 omicron (B.1.1.529) variant: a cross-sectional study. However, S309, the parent of sotrovimab, retained most of its activity, with only an approximately two-fold reduction in potency against the omicron variant compared with ancestral D614G SARS-CoV-2 (IC50 0 1-0 2 mug/mL). 2022 The Lancet. Infectious diseases Abstract SARS_CoV_2 D614G 181 186 35307848 Low-frequency variants in mildly symptomatic vaccine breakthrough infections presents a doubled-edged sword. Low-frequency mutations were observed, which have been more recently identified as mutations of interest owing to their location within targeted immune epitopes (P812L) and association with increased replicative capacity (L18F). 2022 Journal of medical virology Abstract SARS_CoV_2 L18F;P812L 222;162 226;167 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. Some of these changes, such as the E484Q, were mutations of concern as defined by WHO. 2022 Frontiers in microbiology Abstract SARS_CoV_2 E484Q 35 40 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? Emphasizing the potential benefits of surveillance, low-frequency mutations, D144H in the N gene and D138Y in the S gene, were observed to potentially alter the protein secondary structure with possible influence on viral characteristics. 2022 Frontiers in microbiology Abstract SARS_CoV_2 D138Y;D144H 101;77 106;82 N;S 90;114 91;115 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. For general application illustrations, HBV genotyping and SARS-CoV-2 D614G mutant biosensing platforms are developed to validate the enhanced Cas12a's specificity. 2022 Chemical science Abstract SARS_CoV_2 D614G 69 74 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. For this, we succeeded in sequencing 44 per cent of all reported cases from Basel-City and performed phylogenetic clustering and compartmental modelling based on the dominating viral variant (B.1-C15324T; 60 per cent of cases) to identify drivers and patterns of transmission. 2022 Virus evolution Abstract SARS_CoV_2 C15324T 196 203 35311662 Reduced DMPC and PMPC in lung surfactant promote SARS-CoV-2 infection in obesity. DMPC and PMPC markedly inhibited wild type and D614G mutant SARS-CoV-2 infection in HEK293T-ACE2 and Vero-E6 cells. 2022 Metabolism Abstract SARS_CoV_2 D614G 47 52 COVID-19 60 80 35311662 Reduced DMPC and PMPC in lung surfactant promote SARS-CoV-2 infection in obesity. Lipid extract from BALF of trimyristin-treated obese mice mitigated the elevated wild type and D614G mutant SARS-CoV-2 infection. 2022 Metabolism Abstract SARS_CoV_2 D614G 95 100 COVID-19 108 128 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. S375F was found to be a mutation that majorly changed the binding affinity of the spike protein to hACE2 and the eight monoclonal antibodies. 2022 Journal of chemical information and modeling Abstract SARS_CoV_2 S375F 0 5 S 82 87 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). A single missense mutation of U to G at nucleotide position 1355 (U1355G) in the spike (S) gene changes leucine to arginine (L452R) in the spike protein. 2022 PloS one Abstract SARS_CoV_2 L452R 125 130 S;S;S 81;139;88 86;144;89 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). Furthermore, using a peptide nucleic acid (PNA) probe, the RT-LAMP-BART method correctly identified the L452R spike mutation. 2022 PloS one Abstract SARS_CoV_2 L452R 104 109 S 110 115 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). Therefore, we established a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay plus a bioluminescent assay in real-time (BART) to detect SARS-CoV-2 and the L452R spike mutation. 2022 PloS one Abstract SARS_CoV_2 L452R 182 187 S 188 193 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. In addition, mutations to the class 1 epitope (e.g., K417N) tend to have larger effects on antibody binding and neutralization in the Delta spike than in the D614G spike, both for vaccine- and Delta-infection-elicited antibodies. 2022 bioRxiv Abstract SARS_CoV_2 D614G;K417N 158;53 163;58 S;S 140;164 145;169 35314694 Genetic alteration of human MYH6 is mimicked by SARS-CoV-2 polyprotein: mapping viral variants of cardiac interest. Interestingly, analysis of protein-coding mutations from 141,456 individuals showed that one of these 8-mers from the SARS-CoV-2 Replicase polyprotein 1a/1ab (KIALKGGK) is identical to an MYH6 peptide encoded by the c.5410 C > A (Q1804K) genetic variation, which has been observed at low prevalence in Africans/African Americans (0.08%), East Asians (0.3%), South Asians (0.06%), and Latino/Admixed Americans (0.003%). 2022 Cell death discovery Abstract SARS_CoV_2 C5410A;Q1804K 216;230 228;236 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Some noticeable mutations, including K417N, T478K, N501Y, and P681H, are shared with the previous VOCs Alpha, Beta, Gamma, or Delta variants and have been proven to be associated with higher transmissibility, viral infectivity, and immune evasion potential. 2022 MedComm Abstract SARS_CoV_2 K417N;N501Y;P681H;T478K 37;51;62;44 42;56;67;49 35317858 SARS-CoV-2 NSP13 helicase suppresses interferon signaling by perturbing JAK1 phosphorylation of STAT1. Nucleic acid binding-defective mutant K345A K347A and NTPase-deficient mutant E375A of NSP13 were found to have largely lost the ability to suppress IFN-beta-induced STAT1 phosphorylation and transcriptional activation, indicating the requirement of the helicase activity for NSP13-mediated inhibition of STAT1 phosphorylation. 2022 Cell & bioscience Abstract SARS_CoV_2 E375A;K345A;K347A 78;38;44 83;43;49 Helicase;Nsp13;Nsp13 254;87;276 262;92;281 35321260 Heat Treatment Promotes Ubiquitin-Mediated Proteolysis of SARS-CoV-2 RNA Polymerase and Decreases Viral Load. A mild daily heat treatment maintains low levels of both wild-type and P323L mutant of NSP12, suggesting clinical potential. 2022 Research (Washington, D.C.) Abstract SARS_CoV_2 P323L 71 76 Nsp12 87 92 35321260 Heat Treatment Promotes Ubiquitin-Mediated Proteolysis of SARS-CoV-2 RNA Polymerase and Decreases Viral Load. Here, we reveal a potential mechanism by which mild heat treatment destabilizes the wild-type RNA-dependent RNA polymerase (also known as nonstructural protein 12 (NSP12)) of SARS-CoV-2 as well as the P323L mutant commonly found in SARS-CoV-2 variants, including omicron and IHU. 2022 Research (Washington, D.C.) Abstract SARS_CoV_2 P323L 201 206 RdRp;Nsp12 94;164 122;169 35321335 Omicron Variant of SARS-CoV-2 Virus: In Silico Evaluation of the Possible Impact on People Affected by Diabetes Mellitus. In the Omicron variant, Lys417 mutates into an asparagine, preventing the possible non-enzymatic glycation of this residue. 2022 Frontiers in endocrinology Abstract SARS_CoV_2 K417N 24 57 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Here, using single-molecule Forster resonance energy transfer (smFRET) imaging, we report the effects of ACE2 and antibody binding on the conformational dynamics of S from the Wuhan-1 strain and in the presence of the D614G mutation. 2022 eLife Abstract SARS_CoV_2 D614G 218 223 S 165 166 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. We find that D614G modulates the energetics of the RBD position in a manner similar to ACE2 binding. 2022 eLife Abstract SARS_CoV_2 D614G 13 18 RBD 51 54 35324468 First detection of SARS-CoV-2 lineage A.27 in Sardinia, Italy. Among the key mutations identified in the spike protein, the N501Y and the L452R deserve attention as considered likely vaccine escape mutations. 2022 Annali dell'Istituto superiore di sanita Abstract SARS_CoV_2 L452R;N501Y 75;61 80;66 S 42 47 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. Molecular clock analysis results suggested that the subclade 6B.1A5A + 156K emerged in Denmark, Australia, or the United States in July 2019, while subclades 6B.1A5A + 187V/A and 6B.1A5A + 156K with K209M emerged in East Asia in April and September 2019, respectively. 2022 Tropical medicine and infectious disease Abstract SARS_CoV_2 K209M 199 204 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. On the other hand, sequence analysis of NA segments showed that the viruses lacked the H275Y mutation that confers oseltamivir resistance. 2022 Tropical medicine and infectious disease Abstract SARS_CoV_2 H275Y 87 92 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. Sequence analysis of the HA segments of the virus strains isolated from the clinical specimens and the subsequent phylogenic analyses of the obtained sequences revealed that all of the H1N1pdm recent subclades 6B.1A5A + 187V/A, 6B.1A5A + 156K, and 6B.1A5A + 156K with K209M were already present in Bangladesh in January 2020. 2022 Tropical medicine and infectious disease Abstract SARS_CoV_2 K209M 268 273 35325236 Stabilization of the SARS-CoV-2 receptor binding domain by protein core redesign and deep mutational scanning. Our most successful design encodes I358F, Y365W, T430I, and I513L receptor binding domain mutations, maintains recognition by the receptor ACE2 and a panel of different anti-receptor binding domain monoclonal antibodies, is between 1 and 2 C more thermally stable than the original receptor binding domain using a thermal shift assay, and is less proteolytically sensitive to chymotrypsin and thermolysin than the original receptor binding domain. 2022 Protein engineering, design & selection Abstract SARS_CoV_2 I358F;I513L;T430I;Y365W 35;60;49;42 40;65;54;47 RBD;RBD;RBD;RBD 66;174;282;423 89;197;305;446 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Mutation's spike_F157del, spike_P681R, spike_T478K, spike_T19R, spike_L452R, spike_D614G, spike_G142D, spike_E156G, and spike_R158del have been detected in all samples where K1086Q, E554K, and C1250W were unique in spike protein. 2022 Genes Abstract SARS_CoV_2 C1250W;E554K;K1086Q;D614G;E156G;F157del;G142D;L452R;P681R;R158del;T19R;T478K 193;182;174;83;109;17;96;70;32;126;58;45 199;187;180;88;114;24;101;75;37;133;62;50 S;S;S;S;S;S;S;S;S;S 11;26;39;52;64;77;90;103;120;215 16;31;44;57;69;82;95;108;125;220 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The most common were NSP3_P1469S (N = 17), NSP3_A488S (N = 17), NSP3_P1228L (N = 17), NSP4_V167L (N = 17), NSP4_T492I (N = 17), NSP6_T77A (N = 17), NSP14_A394V (N = 17), NSP12_G671S (N = 18), and NSP13_P77L (N = 18). 2022 Genes Abstract SARS_CoV_2 A394V;A488S;G671S;P1228L;P1469S;P77L;T492I;T77A;V167L 154;48;176;69;26;202;112;133;91 159;53;181;75;32;206;117;137;96 Nsp13;Nsp12;Nsp3;Nsp3;Nsp3;Nsp4;Nsp4;Nsp6 196;170;21;43;64;86;107;128 201;175;25;47;68;90;111;132 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The mutation, F313Y in NSP12, detected in the current study, was found in a single isolate from Belgium. 2022 Genes Abstract SARS_CoV_2 F313Y 14 19 Nsp12 23 28 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. Using pseudotyped virus, we examine the capacity of convalescent sera, from a well-defined cohort of healthcare workers (HCW) and Patients infected during the first wave from a national critical care centre in the UK to neutralise B.1.1.298, variants of interest (VOI) B.1.617.1 (Kappa), and four VOCs, B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) and B.1.617.2 (Delta), including the B.1.617.2 K417N, informally known as Delta Plus. 2022 Frontiers in immunology Abstract SARS_CoV_2 K417N 395 400 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. None of the mutations increased but several decreased S protein cleavage at the S1/S2 site, including S686G and P681H, the latter of which is found in variants of concern B.1.1.7 (Alpha variant) and B.1.1.529 (Omicron variant). 2022 PloS one Abstract SARS_CoV_2 P681H;S686G 112;102 117;107 S 54 55 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. The effects of mutation S686G on viral entry were cell-type dependent and could be linked to the availability of cathepsin L for S protein activation. 2022 PloS one Abstract SARS_CoV_2 S686G 24 29 S 129 130 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). CONCLUSIONS: SARS-CoV-2 variants carrying the B.1.258 ( H69/ V70) and S477N substitutions were reported here in a pediatric population for the first time. 2022 Microorganisms Abstract SARS_CoV_2 S477N 70 75 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). Of the 32 isolates, 4 (12.5%) carried a nonsynonymous nucleotide mutation leading to the N439K (3/4), lineage B.1.258 ( H69/ V70), and S477N (1/4) substitution. 2022 Microorganisms Abstract SARS_CoV_2 N439K;S477N 89;135 94;140 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). The D614G amino acid substitution was detected in all isolated and amplified viral strains. 2022 Microorganisms Abstract SARS_CoV_2 D614G 4 9 35336868 Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens. The genome analysis revealed the presence of L212C mutation, Tyrosine 69 deletion, and C25000T nucleotide change in spike gene of hamster passage sequences and an absence of V17I mutation in E gene in hamster passage sequences, unlike human clinical specimen and Vero CCL-81 passages. 2022 Viruses Abstract SARS_CoV_2 C25000T;L212C;V17I 87;45;174 94;50;178 S;E 116;191 121;192 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. Here, using ultra large-scale ab initio computational modeling, we study the P681R and D614G mutations in the SD2-FP domain, including the effect of double mutation, and compare the results with the wild type. 2022 Viruses Abstract SARS_CoV_2 D614G;P681R 87;77 92;82 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. In particular, an especially dangerous mutation P681R close to the furin cleavage site has been identified as responsible for increasing the infection rate. 2022 Viruses Abstract SARS_CoV_2 P681R 48 53 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. Together with the earlier reported mutation D614G in the same domain, it offers an excellent instance to investigate the nature of mutations and how they affect the interatomic interactions in the spike protein. 2022 Viruses Abstract SARS_CoV_2 D614G 44 49 S 197 202 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. Even within the Omicron wave, the B.1.617.2 + S:E484Q variant appeared in community samples in Sweden, as it seems that this combination has an evolutionary gain compared to other B.1.617.2 lineages. 2022 Viruses Abstract SARS_CoV_2 E484Q 48 53 S 46 47 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. In Sweden, at least 10% of all positive SARS-CoV-2 samples were sequenced in each county; the B.1.717.2 + S:E484Q combination was not detected in Sweden before and was imported within the scenario described in this report. 2022 Viruses Abstract SARS_CoV_2 E484Q 108 113 S 106 107 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. The high transmission rate of the delta lineage combined with the S:E484Q mutation, associated with immune escape in other lineages, makes this specific genetic combination a possible threat to the global fight against the COVID-19 pandemic. 2022 Viruses Abstract SARS_CoV_2 E484Q 68 73 S 66 67 COVID-19 223 231 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. We describe a flight-associated infection scenario of seven individuals with a B.1.617.2 (Delta) lineage, harbouring an S:E484Q point mutation. 2022 Viruses Abstract SARS_CoV_2 E484Q 122 127 S 120 121 35336922 Multiorgan and Vascular Tropism of SARS-CoV-2. More specifically, mutations of the spike protein, i.e., V341A (18.3%), E654 (44%) and H655R (30.8%), were detected in the inferior vena cava. 2022 Viruses Abstract SARS_CoV_2 H655R;V341A 87;57 92;62 S 36 41 35336952 Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. We explored the R346K substitution, prevalent in 42% of Omicron variants, known to be associated with immune escape by monoclonal antibodies. 2022 Viruses Abstract SARS_CoV_2 R346K 16 21 35337002 Protective Immunity of the Primary SARS-CoV-2 Infection Reduces Disease Severity Post Re-Infection with Delta Variants in Syrian Hamsters. The Delta AY.1 variant produced mild disease in the hamster model and did not show any evidence of neutralization resistance due to the presence of the K417N mutation, as speculated. 2022 Viruses Abstract SARS_CoV_2 K417N 152 157 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. Analytic sensitivity was determined as 19.0 IU/mL (CI95%: 12.9-132.2 IU/mL) for the A67V + del-HV69-70 target, 193.9 IU/mL (CI95%: 144.7-334.7 IU/mL) for the E484A target, 35.5 IU/mL (CI95%: 23.3-158.0 IU/mL) for the N679K + P681H target and 105.0 IU/mL (CI95%: 80.7-129.3 IU/mL) for the P681R target. 2022 Viruses Abstract SARS_CoV_2 A67V;E484A;N679K;P681H;P681R 84;158;217;225;288 88;163;222;230;293 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. Key mutations were targeted in the different VOC strains, including SDelta69/70 deletion, N501Y, SDelta241 and SDelta157. 2022 Viruses Abstract SARS_CoV_2 N501Y 90 95 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. Docking of the four possible monosulfated BoSG disaccharides in interactions with the N501Y mutant S-protein predicted potential binding poses of the BoSG constructs and favorable binding in close proximity to the 501Y residue. 2022 The Journal of biological chemistry Abstract SARS_CoV_2 N501Y 86 91 S 99 100 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. We observed distinct affinities of BoSG derivatives for the S-proteins of different SARS-CoV-2 strains, including WT, N501Y (Alpha), K417T/E484K/N501Y (Gamma), and L542R (Delta) mutants, and stronger affinity for the N501Y-containing variants. 2022 The Journal of biological chemistry Abstract SARS_CoV_2 K417T;L542R;N501Y;N501Y;E484K;N501Y 133;164;118;217;139;145 138;169;123;222;144;150 S 60 61 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Discussion: Molecular dynamics simulations followed by Poisson-Boltzmann calculations corroborate the higher complementarity to the receptor and lower to the antibodies for the K417T/E484K/N501Y (Gamma) mutant compared to the wild-type strain, as pointed by E-Volve, as well as an intensification of this effect by changes at the protein conformational equilibrium in solution. 2022 PeerJ Abstract SARS_CoV_2 K417T;E484K;N501Y 177;183;189 182;188;194 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Results: The results found in this study depict the highly frequent interface changes made by the entire set of mutations, mainly conducted by N501Y and E484K. 2022 PeerJ Abstract SARS_CoV_2 E484K;N501Y 153;143 158;148 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. Additionally, the S_T19R, S_E156G, S_F157del, S_R158del, S_L452R, S_T478K, S_D950N and S_V1264L changes were only detected in Delta variants, consistent with those changes being characteristic of Delta variants in general. 2022 PeerJ Abstract SARS_CoV_2 F157del;R158del;D950N;E156G;L452R;T19R;T478K;V1264L 36;47;77;28;59;20;68;89 44;55;82;33;64;24;73;95 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. In the spike protein gene, S_D614G and S_P681R changes were dominant in both B.1.466.2 and Delta variants, while N439K was only observed in B.1.466.2 (n = 44) and B.1.470 (n = 1). 2022 PeerJ Abstract SARS_CoV_2 N439K;D614G;P681R 113;29;41 118;34;46 S 7 12 35341060 An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. 2022 PeerJ Abstract SARS_CoV_2 Q27X 35 42 ORF8 62 66 COVID-19 150 158 35341060 An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. 2022 PeerJ Abstract SARS_CoV_2 Q27X 74 81 ORF8;ORF8 42;59 46;63 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. A naturally occurring ORF8 L84S variant that was highly associated with mild COVID-19 showed reduced hIL-17RA binding and attenuated inflammatory responses. 2022 mBio Abstract SARS_CoV_2 L84S 27 31 ORF8 22 26 COVID-19 77 85 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. Moreover, the neutralising antibody titre reduction of the recovered patient plasma against the delta variant was similar to that of the D614G variant and lower than that of the beta variant. 2022 The Lancet. Microbe Abstract SARS_CoV_2 D614G 137 142 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. Moreover, we evaluated both antibody and T-cell responses to the D614G, beta, and delta viral strains. 2022 The Lancet. Microbe Abstract SARS_CoV_2 D614G 65 70 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. Neutralising antibodies against the original SARS-CoV-2 strain, and the D614G, beta (B.1.351), and delta (B.1.617.2) variants were analysed using a microneutralisation assay in a subset of plasma samples. 2022 The Lancet. Microbe Abstract SARS_CoV_2 D614G 72 77 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. Neutralising antibodies to the D614G, beta, and delta viral strains were reduced compared with those for the original strain, and were diminished in general. 2022 The Lancet. Microbe Abstract SARS_CoV_2 D614G 31 36 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. The degree of reduced in-vitro neutralising antibody responses to the D614G and delta variants, but not to the beta variant, was associated with the neutralising antibody titres after SARS-CoV-2 infection. 2022 The Lancet. Microbe Abstract SARS_CoV_2 D614G 70 75 COVID-19 184 204 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. The anti-RBD IgG antibodies from these vaccinated individuals were broadly cross-reactive against multiple VOCs and had neutralisation potency against original D614G, beta, and delta variants. 2022 BMC medicine Abstract SARS_CoV_2 D614G 160 165 RBD 9 12 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. High-resolution melting (HRM) analysis was performed to detect G339D and D796Y variations in the SARS-CoV-2 Omicron variant spike protein. 2022 Biochemical and biophysical research communications Abstract SARS_CoV_2 D796Y;G339D 73;63 78;68 S 124 129 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. The melting temperatures (Tm) of the amplicon from the cDNA of the Omicron variant receptor binding domain (RBD) were 73.1C (G339D variation) and 75.1C (D796Y variation), respectively. 2022 Biochemical and biophysical research communications Abstract SARS_CoV_2 D796Y;G339D 153;125 158;130 RBD;RBD 83;108 106;111 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. Results: Beta+R346K, which was identified in the Philippines in August 2021, exhibited the highest vaccine resistance among the tested mutants. 2022 Future microbiology Abstract SARS_CoV_2 R346K 14 19 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. Surprisingly, Mu+K417N mutant exhibited almost no decrease in neutralization. 2022 Future microbiology Abstract SARS_CoV_2 K417N 17 22 35355624 Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. Altogether, these hot spots/epitopes identified between S-protein and ACE2/B38 Fab antibody may provide useful information for future antibody design, evaluation of the binding property of the SARS-CoV-2 variants including its N501Y, and small or medium drug design against the SARS-CoV-2. 2021 Chemical science Abstract SARS_CoV_2 N501Y 227 232 S 56 57 35364605 Insights from computational analysis: how does the SARS-CoV-2 Delta (B.1.617.2) variant hijack ACE2 more effectively? The results showed that the existence of L452R and T478K mutations can trigger the effective hijacking of ACE2 by the Delta variant through the following three ways: (i) these two mutations can significantly enhance the electrostatic energy of the system by the introduction of two positively charged amino acids (Arg and Lys), thereby increasing the binding affinity of RBD and ACE2, (ii) the Loops 1, 3, and 4 in the receptor-binding motif (RBM) of RBD form a tighter conformation under the dominance of the T478K mutation, allowing ACE2 to be captured more effectively than the wild-type system, and (iii) these conformational changes lead to a more stable hydrogen bond in the Delta variant, which further ensures the stability of the binding. 2022 Physical chemistry chemical physics Abstract SARS_CoV_2 L452R;T478K;T478K 41;51;510 46;56;515 RBD;RBD 371;451 374;454 35365787 Differential neutralizing antibody responses elicited by CoronaVac and BNT162b2 against SARS-CoV-2 Lambda in Chile. Comparative analyses among the spike structures of the different variants suggest that mutations in the spike protein from the Lambda variant, including the 246-252 deletion in an antigenic supersite at the N-terminal domain loop and L452Q/F490S within the receptor-binding domain, may account for immune escape. 2022 Nature microbiology Abstract SARS_CoV_2 L452Q;F490S 234;240 239;245 S;S;N 31;104;207 36;109;208 35365787 Differential neutralizing antibody responses elicited by CoronaVac and BNT162b2 against SARS-CoV-2 Lambda in Chile. Compared with the ancestral virus, neutralization against D614G, Alpha, Gamma, Lambda and Delta variants was reduced by between 0.93- and 4.22-fold for CoronaVac, 1.04- and 2.38-fold for BNT162b2, and 1.26- and 2.67-fold for convalescent plasma. 2022 Nature microbiology Abstract SARS_CoV_2 D614G 58 63 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. Mutational analysis detected 18,261 mutations in the omicron variant, majority of which were non-synonymous mutations in spike (A67, T547K, D614G, H655Y, N679K, P681H, D796Y, N856K, Q954H), followed by RNA dependent RNA polymerase (rdrp) (A1892T, I189V, P314L, K38R, T492I, V57V), ORF6 (M19M) and nucleocapsid protein (RG203KR). 2022 Virus research Abstract SARS_CoV_2 D614G;D796Y;H655Y;I189V;K38R;N679K;N856K;P314L;P681H;Q954H;T492I;T547K;V57V;A1892T;M19M 140;168;147;247;261;154;175;254;161;182;267;133;274;239;287 145;173;152;252;265;159;180;259;166;187;272;138;278;245;291 RdRp;N;S;ORF6;RdRP 202;297;121;281;232 230;309;126;285;236 35369437 Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China. A total of 328 nucleotide mutation sites were found in 42 genomes, among which A23403G mutation (D614G amino acid change in the spike protein) was the most common substitution. 2022 Frontiers in microbiology Abstract SARS_CoV_2 A23403G;D614G 79;97 86;102 S 128 133 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. In addition, ATV showed an antiviral effect against the D614G strain independent of the cell line (EC50 of 7.4 muM in Caco-2). 2022 Frontiers in microbiology Abstract SARS_CoV_2 D614G 56 61 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. Our study demonstrated the in vitro antiviral activity of atorvastatin against the ancestral SARS-CoV-2 D614G strain and two emerging variants (Delta and Mu), with an independent effect of the cell line. 2022 Frontiers in microbiology Abstract SARS_CoV_2 D614G 104 109 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. This compound showed antiviral activity against SARS-CoV-2 D614G strain in Vero E6 with median effective concentrations (EC50s) of 15.4, 12.1, and 11.1 muM by pre-post, pre-infection, and post-infection treatments, respectively. 2022 Frontiers in microbiology Abstract SARS_CoV_2 D614G 59 64 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. METHODS: To address this, we performed molecular dynamics (MD) simulation on B.1.617 along with K417G variants and other RBD variants. 2022 Indian journal of medical microbiology Abstract SARS_CoV_2 K417G 96 101 RBD 121 124 35370361 CRISPR-Cas13a cascade-based viral RNA assay for detecting SARS-CoV-2 and its mutations in clinical samples. In addition, the Cas13C assay could be able to discriminate single-nucleotide mutation, which was proven with N501Y in SARS-Cov-2 variant. 2022 Sensors and actuators. B, Chemical Abstract SARS_CoV_2 N501Y 110 115 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. We found that some SARS-CoV-2 variants have changed significantly in viral infectivity; especially, B.1.617.2 is more likely to infect less susceptible cells than D614G, and the virus infection process can be completed in a shorter time. 2022 Frontiers in immunology Abstract SARS_CoV_2 D614G 163 168 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Indeed, over 90 per cent of Delta samples in Russia are characterized by the nsp2:K81N + ORF7a:P45L pair of mutations which is rare outside Russia, putting them in the AY.122 sublineage. 2022 Virus evolution Abstract SARS_CoV_2 K81N;P45L 82;95 86;99 ORF7a;Nsp2 89;77 94;81 35373411 Association of tumor necrosis factor alpha -308 single nucleotide polymorphism with SARS CoV-2 infection in an Iraqi Kurdish population. A single-nucleotide polymorphism (SNP) in a promoter region of tumor necrosis factor alpha (TNF-alpha) gene, TNF-alpha -308G>A, increases expression of TNF-alpha protein against infectious diseases leading to immune dysregulations and organ damage. 2022 Journal of clinical laboratory analysis Abstract SARS_CoV_2 G308A 119 126 35373411 Association of tumor necrosis factor alpha -308 single nucleotide polymorphism with SARS CoV-2 infection in an Iraqi Kurdish population. This study aims to discover associations between TNF-alpha -308G>A SNP and Covid-19 infection. 2022 Journal of clinical laboratory analysis Abstract SARS_CoV_2 G308A 59 66 35373411 Association of tumor necrosis factor alpha -308 single nucleotide polymorphism with SARS CoV-2 infection in an Iraqi Kurdish population. This suggests that TNF-alpha -308G>A SNP might be associated with Covid-19 infections. 2022 Journal of clinical laboratory analysis Abstract SARS_CoV_2 G308A 29 36 35373810 Origin of the tight binding mode to ACE2 triggered by multi-point mutations in the omicron variant: a dynamic insight. Multi-point mutations in the Omicron variant RBD could cause the conformation shift in the large Loop (where T478K and E484A are located), which makes it easier to wrap the N-terminal helix of ACE2 and form tighter contacts. 2022 Physical chemistry chemical physics Abstract SARS_CoV_2 E484A;T478K 119;109 124;114 RBD;N 45;173 48;174 35373810 Origin of the tight binding mode to ACE2 triggered by multi-point mutations in the omicron variant: a dynamic insight. This was due to the large number of positively charged patches (N440K, T478K, Q493R, Q498R, and Y505H) formed by the substitution of neutral amino acids at multiple sites. 2022 Physical chemistry chemical physics Abstract SARS_CoV_2 Q493R;Q498R;T478K;Y505H;N440K 78;85;71;96;64 83;90;76;101;69 35377298 SARS-CoV-2 variants of concern alpha, beta, gamma and delta have extended ACE2 receptor host ranges. All four VOCs were able to overcome a previous restriction for mouse ACE2, with demonstrable differences also seen for individual VOCs with rat, ferret or civet ACE2 receptors, changes that we subsequently attributed to N501Y and E484K substitutions within the spike RBD. 2022 The Journal of general virology Abstract SARS_CoV_2 E484K;N501Y 230;220 235;225 S;RBD 261;267 266;270 35377633 Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614G Mutant: Conformational Plasticity and Frustration-Induced Allostery as Energetic Drivers of Highly Transmissible Spike Variants. In this study, we employed efficient and accurate coarse-grained simulations of multiple structural substates of the D614G spike trimers together with the ensemble-based mutational frustration analysis to characterize the dynamics signatures of the conformational landscapes. 2022 Journal of chemical information and modeling Abstract SARS_CoV_2 D614G 117 122 S 123 128 35377633 Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614G Mutant: Conformational Plasticity and Frustration-Induced Allostery as Energetic Drivers of Highly Transmissible Spike Variants. The recent structural and biophysical studies provided important evidence about multiple conformational substates of the D614G spike protein. 2022 Journal of chemical information and modeling Abstract SARS_CoV_2 D614G 121 126 S 127 132 35377633 Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614G Mutant: Conformational Plasticity and Frustration-Induced Allostery as Energetic Drivers of Highly Transmissible Spike Variants. The results suggest that the D614G mutant may employ a hinge-shift mechanism in which the dynamic couplings between the site of mutation and the interprotomer hinge modulate the interdomain interactions, global mobility change, and the increased stability of the open form. 2022 Journal of chemical information and modeling Abstract SARS_CoV_2 D614G 29 34 35377633 Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614G Mutant: Conformational Plasticity and Frustration-Induced Allostery as Energetic Drivers of Highly Transmissible Spike Variants. The structural and functional studies of the SARS-CoV-2 spike protein variants revealed an important role of the D614G mutation that is shared across many variants of concern (VOCs), suggesting the effect of this mutation on the enhanced virus infectivity and transmissibility. 2022 Journal of chemical information and modeling Abstract SARS_CoV_2 D614G 113 118 S 56 61 35377633 Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614G Mutant: Conformational Plasticity and Frustration-Induced Allostery as Energetic Drivers of Highly Transmissible Spike Variants. We found that the D614G mutation may induce a considerable conformational adaptability of the open states in the SARS-CoV-2 spike protein without compromising the folding stability and integrity of the spike protein. 2022 Journal of chemical information and modeling Abstract SARS_CoV_2 D614G 18 23 S;S 124;202 129;207 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. A booster vaccination increased titers more than 30-fold against Omicron to values comparable to those seen against the D614G variant after two immunizations. 2022 Science translational medicine Abstract SARS_CoV_2 D614G 120 125 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. Of these, only three retained potencies comparable to the D614G variant. 2022 Science translational medicine Abstract SARS_CoV_2 D614G 58 63 35380892 Structural basis for replicase polyprotein cleavage and substrate specificity of main protease from SARS-CoV-2. Substrate selectivity is revealed using structures of the H41A mutant in complex with six individual native cleavage substrates. 2022 Proc Natl Acad Sci U S A Abstract SARS_CoV_2 H41A 58 62 35382714 Mutational Analysis of Interleukin-11 and its Consequences on Cancer and COVID-19 Related Cytokine Storm -An Extensive Molecular Dynamics Study. CONCLUSION Mutation R190E led to the formation of a less stable complex than the wild-type which suggests a decrease in the binding affinity between IL11 and IL11Ralpha. 2022 Protein and peptide letters Abstract SARS_CoV_2 R190E 20 25 35382714 Mutational Analysis of Interleukin-11 and its Consequences on Cancer and COVID-19 Related Cytokine Storm -An Extensive Molecular Dynamics Study. Moreover, mutation R135E led to an increase in the binding affinity of IL11 with IL11Ralpha and the formation of a more stable complex in comparison to the wild-type protein with its receptor. 2022 Protein and peptide letters Abstract SARS_CoV_2 R135E 19 24 35382714 Mutational Analysis of Interleukin-11 and its Consequences on Cancer and COVID-19 Related Cytokine Storm -An Extensive Molecular Dynamics Study. OBJECTIVE: This study aimed to evaluate the impact of the two point mutations- R135E and R190E on the stability of IL11 and their effect on the binding affinity of IL11 with its receptor IL11Ralpha. 2022 Protein and peptide letters Abstract SARS_CoV_2 R135E;R190E 79;89 84;94 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. Importantly, we observed the mutation S194* within the recovered to be comparatively unstable, hence showing a low global frequency, as we observed. 2022 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 S194X 38 43 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. In addition, we found the mutation S194L to have the most significant occurrence in the mortality group, suggesting its role toward a severe disease progression. 2022 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 S194L 35 40 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. To understand the possible mechanism, we performed molecular dynamics (MD) simulations of nucleocapsid mutations, S194L and S194*, from the mortality and recovered patients, respectively, to examine its impacts on protein structure and stability. 2022 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 S194X;S194L 124;114 129;119 N 90 102 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. In conclusion, within the limitations of phylogeographical reconstruction, the estimated ancestral scenario suggests an important role of China and Italy in the widespread diffusion of the D614G variant in Europe in the early phase of the pandemic and more dispersed exchanges involving several European countries from the second half of March 2020. 2022 Scientific reports Abstract SARS_CoV_2 D614G 189 194 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. Furthermore, SARS-CoV-2 nsp5 exhibited stronger inhibition of Sendai virus (SEV)-induced interferon beta (IFN-beta) production than SARS-CoV-2 nsp5 (S46A), while introduction of the A46S substitution in SARS-CoV nsp5 enhanced suppression of SEV-induced IFN-beta production. 2022 Journal of virology Abstract SARS_CoV_2 A46S;S46A 182;149 186;153 Nsp5;Nsp5;Nsp5 24;143;212 28;147;216 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. Mutagenesis experiments showed that SARS-CoV-2 nsp5 (S46A) exhibited poorer cleavage of NEMO than SARS-CoV-2 nsp5 wild type (WT), while SARS-CoV nsp5 (A46S) showed enhanced NEMO cleavage compared with the WT protein. 2022 Journal of virology Abstract SARS_CoV_2 A46S;S46A 151;53 155;57 Nsp5;Nsp5;Nsp5 47;109;145 51;113;149 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. Purified recombinant SARS-CoV-2 nsp5 WT and SARS-CoV nsp5 (A46S) proteins exhibited higher hydrolysis efficiencies than SARS-CoV-2 nsp5 (S46A) and SARS-CoV nsp5 WT proteins in vitro. 2022 Journal of virology Abstract SARS_CoV_2 A46S;S46A 59;137 63;141 Nsp5;Nsp5;Nsp5;Nsp5 32;53;131;156 36;57;135;160 35396511 Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage. Like Beta and Delta, C.1.2 shows significantly reduced neutralization sensitivity to plasma from vaccinees and individuals infected with the ancestral D614G virus. 2022 Nature communications Abstract SARS_CoV_2 D614G 151 156 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Based on previous reports and our observations, we can conclude that the occurrence of one of two mutations D614G or Y453F is sufficient for infection of minks by SARS-CoV-2 from humans. 2022 Journal of applied genetics Abstract SARS_CoV_2 D614G;Y453F 108;117 113;122 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Unfortunately, D614G is observed in the world's most common line of virus B.1.1.7 and the latest SARS-CoV-2 variants B.1.617.1, B.1.617.2, and B.1.617.3 too. 2022 Journal of applied genetics Abstract SARS_CoV_2 D614G 15 20 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Here, we reconstituted an in vitro pseudovirus-liposome fusion reaction and report that SARS-CoV-2 wild-type spike is a dynamic Ca2+ sensor, and D614G mutation enhances dynamic calcium sensitivity of spike protein for facilitating membrane fusion. 2022 Cell reports Abstract SARS_CoV_2 D614G 145 150 Membrane;S;S 231;109;200 239;114;205 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Mutations in the spike protein generated a highly infectious and transmissible D614G variant, which is present in newly evolved fast-spreading variants. 2022 Cell reports Abstract SARS_CoV_2 D614G 79 84 S 17 22 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. The D614G, Alpha, Beta, and Delta spike variants of SARS-CoV-2 appear to expedite membrane fusion process for entry, but the mechanism of spike-mediated fusion is unknown. 2022 Cell reports Abstract SARS_CoV_2 D614G 4 9 Membrane;S;S 82;34;138 90;39;143 35398519 Immune evasion and chronological decrease in titer of neutralizing antibody against SARS-CoV-2 and its variants of concerns in COVID-19 patients. We enrolled 146 COVID-19 patients, who were thought to be infected with Wuhan-hu-1 or D614G strains, and examined the time course of neutralizing titers against six concerning strains (Wuhan-hu-1, Alpha, Beta, Gamma, Kappa, and Delta) using newly developed ELISA. 2022 Clinical immunology (Orlando, Fla.) Abstract SARS_CoV_2 D614G 86 91 COVID-19 16 24 35398602 SARS-CoV-2 infections in mRNA vaccinated individuals are biased for viruses encoding spike E484K and associated with reduced infectious virus loads that correlate with respiratory antiviral IgG levels. The predominant virus variant was the Alpha (B.1.1.7), however a significant association between lineage B.1.526 and amino acid change S: E484K with positives after vaccination was noted. 2022 Journal of clinical virology Abstract SARS_CoV_2 E484K 138 143 S 135 136 35399222 The status and analysis of common mutations found in the SARS-CoV-2 whole genome sequences from Bangladesh. Scattered Single Nucleotide Polymorphisms (SNPs) were identified throughout the genome of variants and common SNPs such as: 241:C>T in the 5'UTR of Open Reading Frame 1A (ORF1A), 3037: C>T in Non-structural Protein 3 (NSP3), 14,408: C>T in ORF6 and 23,402: A>G, 23,403: A>G in Spike Protein (S) were observed, but all of them were synonymous mutations. 2022 Gene reports Abstract SARS_CoV_2 A403G 265 273 ORF1a;S;5'UTR;ORF6;Nsp3;S 171;277;139;240;218;292 176;282;144;244;222;293 35399374 Unique peptide signatures of SARS-ComicronV-2 virus against human proteome reveal variants' immune escape and infectiveness. Extensive analysis has indicated that the critical P681R mutation produces new C/H-CrUPs around the R685 cleavage site, while the L452R mutation causes loss of antigenicity of the NF9 peptide and strong(er) binding of the virus to its ACE2 receptor protein. 2022 Heliyon Abstract SARS_CoV_2 L452R;P681R 130;51 135;56 35401825 Inhibitor screening using microarray identifies the high capacity of neutralizing antibodies to Spike variants in SARS-CoV-2 infection and vaccination. In addition, similar results were obtained using a SARS-CoV-2 pseudovirus neutralization assay specific for wild-type S and five prevalent S variants (D614G, B.1.1.7, B.1.351, P.1, B.1.617.2), thus demonstrating that high antibody diversity is associated with high NAb titers. 2022 Theranostics Abstract SARS_CoV_2 D614G 151 156 S;S 118;139 119;140 35403431 Cocktail of REGN Antibodies Binds More Strongly to SARS-CoV-2 Than Its Components, but the Omicron Variant Reduces Its Neutralizing Ability. Consistent with recent experimental reports, our results confirmed that the Omicron variant reduces the neutralizing activity of REGN10933, REGN10987, and REGN10933+REGN10987 with the K417N, N440K, L484A, and Q498R mutations playing a decisive role, while the Delta variant slightly changes their activity. 2022 The journal of physical chemistry. B Abstract SARS_CoV_2 K417N;L484A;N440K;Q498R 184;198;191;209 189;203;196;214 35403837 Potent Anti-SARS-CoV-2 Efficacy of COVID-19 Hyperimmune Globulin from Vaccine-Immunized Plasma. Pseudotyped and authentic virus-based assays show that COVID-HIG displays broad-spectrum neutralization effects on a wide variety of SARS-CoV-2 variants, including D614G, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Kappa (B.1.617.1), Delta (B.1.617.2), and Omicron (B.1.1.529) in vitro. 2022 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Abstract SARS_CoV_2 D614G 164 169 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. FINDINGS: The disease characteristics of the Omicron (R346K) variant were found to be similar to that of the Delta variant infection in hamsters like viral replication in the respiratory tract and interstitial pneumonia. 2022 EBioMedicine Abstract SARS_CoV_2 R346K 54 59 Pneumonia 197 219 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. INTERPRETATION: This preliminary data shows that Omicron (R346K) variant infection can produce moderate to severe lung disease similar to that of the Delta variant and the neutralizing antibodies produced in response to Omicron (R346K) variant infection shows poor neutralizing ability against other co-circulating SARS-CoV-2 variants like Delta which necessitates caution as it may lead to increased cases of reinfection. 2022 EBioMedicine Abstract SARS_CoV_2 R346K;R346K 58;229 63;234 Lung diseases 114 126 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Neutralizing antibody response against Omicron (R346K) variant was detected from day 5 and the cross-neutralization titre of the sera against other variants showed severe reduction ie., 7 fold reduction against Alpha and no titers against B.1, Beta and Delta. 2022 EBioMedicine Abstract SARS_CoV_2 R346K 48 53 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. The Omicron (R346K) infected hamsters demonstrated lesser body weight reduction and viral RNA load in the throat swab and nasal wash samples in comparison to the Delta variant infection. 2022 EBioMedicine Abstract SARS_CoV_2 R346K 13 18 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. The viral load in the lungs and nasal turbinate samples and the lung disease severity of the Omicron (R346K) infected hamsters were found comparable with that of the Delta variant infected hamsters. 2022 EBioMedicine Abstract SARS_CoV_2 R346K 102 107 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. We assessed the pathogenicity and immune response generated by BA.1.1 sub-lineage of SARS-CoV-2 [Omicron (R346K) variant] in 5 to 6-week old Syrian hamsters and compared the observations with that of Delta variant infection. 2022 EBioMedicine Abstract SARS_CoV_2 R346K 106 111 35408761 Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor. Our results indicate that mutations E484K and K417T compensate each other in terms of binding affinity, while the mutation N501Y promotes a more convoluted effect. 2022 Molecules (Basel, Switzerland) Abstract SARS_CoV_2 E484K;K417T;N501Y 36;46;123 41;51;128 35408761 Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor. This variant contains the N501Y, E484K and K417T mutations in the receptor binding domain (RBD) of the spike protein. 2022 Molecules (Basel, Switzerland) Abstract SARS_CoV_2 E484K;K417T;N501Y 33;43;26 38;48;31 RBD;S;RBD 66;103;91 89;108;94 35409572 Increased Secondary Attack Rate among Unvaccinated Household Contacts of Coronavirus Disease 2019 Patients with Delta Variant in Japan. We studied household contacts of index cases of COVID-19 infected with Delta (L452R mutation), Alpha (N501Y mutation), and wild strain from December 2020 through November 2021 in Itako, Japan. 2022 International journal of environmental research and public health Abstract SARS_CoV_2 L452R;N501Y 78;102 83;107 COVID-19 48 65 35412379 Differences in Transmission between SARS-CoV-2 Alpha (B.1.1.7) and Delta (B.1.617.2) Variants. In index cases, Spike gene target failure (TaqPath) was used as a proxy of Alpha variant and the L452R mutation (TaqMan) for Delta variant. 2022 Microbiology spectrum Abstract SARS_CoV_2 L452R 97 102 S 16 21 35416390 Development of antibody resistance in emerging mutant strains of SARS CoV-2: Impediment for COVID-19 vaccines. Lower than expected inhibitory activity of antibodies was reported against viruses with E484K Spike mutation, including B.1.1.7 (UK), P.1 (Brazil), B.1.351 (South African), and new Omicron variant (B.1.1.529) with E484A mutation. 2022 Reviews in medical virology Abstract SARS_CoV_2 E484A;E484K 214;88 219;93 S 94 99 35416767 Expansion of L452R-Positive SARS-CoV-2 Omicron Variant, Northern Lombardy, Italy. Many laboratories are using previously developed L452R-specific PCRs to discriminate Omicron from Delta mutations, but these tests may be unreliable. 2022 Emerging infectious diseases Abstract SARS_CoV_2 L452R 49 54 35416767 Expansion of L452R-Positive SARS-CoV-2 Omicron Variant, Northern Lombardy, Italy. We report 25 cases of infection with SARS-CoV-2 Omicron variant containing spike protein L452R mutation in northern Lombardy, Italy. 2022 Emerging infectious diseases Abstract SARS_CoV_2 L452R 89 94 S 75 80 35419205 Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. Methodology: We performed experimental evolution with two strains of SARS-CoV-2, one carrying the originally described spike protein (CoV-2-D) and another carrying the D614G mutation that has spread worldwide (CoV-2-G). 2022 Evolution, medicine, and public health Abstract SARS_CoV_2 D614G 168 173 S 119 124 35421378 Efficacy of vaccination and previous infection against the Omicron BA.1 variant in Syrian hamsters. While the Moderna mRNA vaccine reduces viral loads in the respiratory tissues upon challenge with an early S-614G isolate, the vaccine efficacy is not as pronounced after infection with the Omicron variant. 2022 Cell reports Abstract SARS_CoV_2 S614G 107 113 S 107 108 35421842 Split T7 promoter-based isothermal transcription amplification for one-step fluorescence detection of SARS-CoV-2 and emerging variants. Moreover, we provide experimental evidence of the broad applicability of this assay through the multiplex detection of SARS-CoV-2 variants (D614G mutation) and direct detection of bacterial 16S rRNA. 2022 Biosensors & bioelectronics Abstract SARS_CoV_2 D614G 140 145 35422572 Multi-factorial Mechanism Behind COVID-19 Related Thrombosis. Thrombophilic mutations, mainly factor V Leiden and prothrombin G20201A mutations, can be a contributing factor in the development of thrombosis in COVID-19 patients, and they are associated with increased disease severity and pulmonary embolism. 2022 Medical archives (Sarajevo, Bosnia and Herzegovina) Abstract SARS_CoV_2 G20201A 64 71 COVID-19 148 156 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. First, we served comparative genomics, such as genome sequence submission patterns, mutational landscapes, and structural landscapes of significant mutations (N501Y, D614G, L452R, E484Q, and P681R). 2022 Infection, genetics and evolution Abstract SARS_CoV_2 D614G;E484Q;L452R;P681R;N501Y 166;180;173;191;159 171;185;178;196;164 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. The structural pattern was analyzed in the N501Y, D614G L452R, E484Q, and P681R mutations. 2022 Infection, genetics and evolution Abstract SARS_CoV_2 D614G;E484Q;L452R;N501Y;P681R 50;63;56;43;74 55;68;61;48;79 35430092 Prolonged shedding of infectious viruses with haplotype switches of SARS-CoV-2 in an immunocompromised patient. Seven haplotypes were identified and the non-synonymous mutations accumulated in the spike gene which included E484Q and S494P. 2022 Journal of infection and chemotherapy Abstract SARS_CoV_2 E484Q;S494P 111;121 116;126 S 85 90 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. Soon after the first outbreak due to the wild-type strain in December 2019, a genetic variant D614G emerged in late January to early February 2020 and became the dominant genotype worldwide. 2022 Frontiers in cellular and infection microbiology Abstract SARS_CoV_2 D614G 94 99 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Among them, D614G, B.1.640.1, and B.1.630 formed a cluster, C.1.2 and B.1.640.2 formed a cluster, and BA.1, BA.2, and BA.3 formed a cluster. 2022 MedComm Abstract SARS_CoV_2 D614G 12 17 35434714 Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern. Bioinformatics analysis revealed that the D614G mutation led to formation of a protruding spike (S) in the tertiary structure of spike protein, which could be responsible for the enhanced binding to angiotensin-converting enzyme 2 (ACE2) receptor. 2022 MedComm Abstract SARS_CoV_2 D614G 42 47 S;S;S 90;129;97 95;134;98 35438777 USA SARS-CoV-2 Epsilon Variant: Though Highly Transmissible has an Adjusted Muted Host T-Cell Response. BACKGROUND: The multiple mutations comprising the epsilon variant demonstrates the independent convergent evolution of SARS-CoV-2, with its spike protein mutation L452R present in the delta (L452R), kappa(L452R) and lambda (L452Q) variants. 2022 Clinical infectious diseases Abstract SARS_CoV_2 L452R;L452Q;L452R;L452R 163;224;191;205 168;229;196;210 S 140 145 35441172 Receptor binding domain of SARS-CoV-2 is a functional alphav-integrin agonist. Among the novel mutations distinguishing SARS-CoV-2 from similar respiratory coronaviruses is a K403R substitution in the receptor-binding domain (RBD) of the viral spike (S) protein within its S1 region. 2022 bioRxiv Abstract SARS_CoV_2 K403R 96 101 S;RBD;S 165;147;172 170;150;173 35441368 Identification of SARS-CoV-2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021. Of the positive samples received, 11.0% (175/1589) were randomly selected to assess if SGTF and genotyping assays, that detect del69/70 and K417N mutations, could identify Omicron BA.1. 2022 Journal of medical virology Abstract SARS_CoV_2 K417N 140 145 35441368 Identification of SARS-CoV-2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021. Our data shows that genotyping for the detection of the del69/70 and K417N coupled with SGTF is efficient to exclude Alpha and Beta variants and rapidly detect Omicron BA.1. 2022 Journal of medical virology Abstract SARS_CoV_2 K417N 69 74 35441368 Identification of SARS-CoV-2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021. SARS-CoV-2 genotyping assays were used for the detection of del69/70 and K417N mutation. 2022 Journal of medical virology Abstract SARS_CoV_2 K417N 73 78 35441368 Identification of SARS-CoV-2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021. We identified SGTF in 98.9% (173/175) of samples, of which 88.0% (154/175) had both the del69/70 and K417N mutation. 2022 Journal of medical virology Abstract SARS_CoV_2 K417N 101 106 35442417 Life-threatening viral disease in a novel form of autosomal recessive IFNAR2 deficiency in the Arctic. The affected individuals bore the same homozygous IFNAR2 c.157T>C, p.Ser53Pro missense variant. 2022 The Journal of experimental medicine Abstract SARS_CoV_2 T157C 57 65 35454022 Unusual N Gene Dropout and Ct Value Shift in Commercial Multiplex PCR Assays Caused by Mutated SARS-CoV-2 Strain. All the isolates harbored three non-synonymous mutations in the N gene, which resulted in four amino acid changes (R203K, G204R, A208G, Met234I). 2022 Diagnostics (Basel, Switzerland) Abstract SARS_CoV_2 A208G;G204R;M234I;R203K 129;122;136;115 134;127;143;120 N 64 65 35454161 Mutational Effect of Some Major COVID-19 Variants on Binding of the S Protein to ACE2. Our calculations show that five major mutations (N501Y, E484K, L452R, T478K and K417N), first reported in Alpha, Beta, Gamma and Delta variants, all increase the binding of the S protein to ACE2 (except K417N), consistent with the experimental findings. 2022 Biomolecules Abstract SARS_CoV_2 E484K;K417N;K417N;L452R;T478K;N501Y 56;80;203;63;70;49 61;85;208;68;75;54 S 177 178 35454161 Mutational Effect of Some Major COVID-19 Variants on Binding of the S Protein to ACE2. Our study showed that most of these mutations (except Y505H and G446S) enhance the binding of the S protein to ACE2. 2022 Biomolecules Abstract SARS_CoV_2 G446S;Y505H 64;54 69;59 S 98 99 35455241 Durability and Cross-Reactivity of SARS-CoV-2 mRNA Vaccine in Adolescent Children. We tested the durability and cross-reactivity of anti-SARS-CoV-2 serologic responses over a six-month time course in vaccinated adolescents against the SARS-CoV-2 D614G ("wild type") and Omicron antigens. 2022 Vaccines Abstract SARS_CoV_2 D614G 163 168 35456137 Comparative Evaluation of Six SARS-CoV-2 Real-Time RT-PCR Diagnostic Approaches Shows Substantial Genomic Variant-Dependent Intra- and Inter-Test Variability, Poor Interchangeability of Cycle Threshold and Complementary Turn-Around Times. We comparatively assessed the variability of Ct values generated by six diagnostic approaches by testing serial dilutions of well-characterized isolates of 10 clinically most relevant SARS-CoV-2 genomic variants: Alpha, Beta, Gamma, Delta, Eta, Iota, Omicron, A.27, B.1.258.17, and B.1 with D614G mutation. 2022 Pathogens (Basel, Switzerland) Abstract SARS_CoV_2 D614G 291 296 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. We show that a constellation of mutational sites (G496S, Q498R, N501Y and Y505H) correspond to key binding energy hotspots and also contribute decisively to the key interfacial communities that mediate allosteric communications between S-RBD and ACE2. 2022 International journal of molecular sciences Abstract SARS_CoV_2 N501Y;Q498R;Y505H;G496S 64;57;74;50 69;62;79;55 RBD;S 238;236 241;237 35458400 Longitudinal Analysis of Neutralizing Potency against SARS-CoV-2 in the Recovered Patients after Treatment with or without Favipiravir. These subjects participated in the longitudinal (>6 months) analysis of (i) SARS-CoV-2 spike protein's receptor-binding domain IgG, (ii) virus neutralization assay using authentic virus, and (iii) neutralization potency against original (WT) SARS-CoV-2 and cross-neutralization against B.1.351 (beta) variant carrying triple mutations of K417N, E484K, and N501Y. 2022 Viruses Abstract SARS_CoV_2 E484K;N501Y;K417N 345;356;339 350;361;343 S 87 92 35458508 Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements. Lineage and phylogenetic analyses of two periods defined by the Delta variant outbreak reveal that: (1) B.1.466.2 variants were the most predominant in Indonesia before the Delta variant outbreak, having a unique spike gene mutation N439K at more than 98% frequency, (2) Delta variants AY.23 sub-lineage took over after June 2021, and (3) the highest rate of virus transmissions between Indonesia and other countries was through interactions with Singapore and Japan, two neighbouring countries with a high degree of access and travels to and from Indonesia. 2022 Viruses Abstract SARS_CoV_2 N439K 233 238 S 213 218 35458530 Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice. We show that mice immunised with these vaccine formulations elicit high titres of antibodies that neutralise SARS-CoV-2 variants VIC31 (with Spike: D614G mutation), Delta and Omicron (BA.1.1) VOC. 2022 Viruses Abstract SARS_CoV_2 D614G 148 153 S 141 146 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. However, when in conjunction with the RBD-N501Y mutation, viral infectivity is enhanced. 2022 Viruses Abstract SARS_CoV_2 N501Y 42 47 RBD 38 41 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. Our functional analysis demonstrates that single, P681H, P681R or A701V-FCS mutations do not play a role in viral infectivity and neutralization potential. 2022 Viruses Abstract SARS_CoV_2 A701V;P681H;P681R 66;50;57 71;55;62 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. Similarly, combining the E484K-RBD mutation to the spike that carries FCS mutations reduces neutralization sensitivity with no effects on viral infectivity. 2022 Viruses Abstract SARS_CoV_2 E484K 25 30 S;RBD 51;31 56;34 35461042 Increased resistance of SARS-CoV-2 Lambda variant to antibody neutralization. F490S contributed more than L452Q in affecting the neutralization. 2022 Journal of clinical virology Abstract SARS_CoV_2 L452Q;F490S 28;0 33;5 35461042 Increased resistance of SARS-CoV-2 Lambda variant to antibody neutralization. The combination of two substitutions appearing in the RBD of spike protein (L452Q and F490S) resulted in noticeably reduced neutralization against Lambda variant. 2022 Journal of clinical virology Abstract SARS_CoV_2 F490S;L452Q 86;76 91;81 S;RBD 61;54 66;57 35461811 Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. These VOC/VOI carry prevalent mutations at varying frequencies in the Mpro specifically for: alpha, beta, gamma (K90R), lambda (G15S) and omicron (P132H). 2022 The Journal of biological chemistry Abstract SARS_CoV_2 G15S;K90R;P132H 128;113;147 132;117;152 35461811 Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. We found that nirmatrelvir has similar potency against each mutant Mpro including P132H that is observed in the Omicron variant with a Ki of 0.635 nM as compared to a Ki of 0.933 nM for wildtype. 2022 The Journal of biological chemistry Abstract SARS_CoV_2 P132H 82 87 35464398 Case Report: X-Linked SASH3 Deficiency Presenting as a Common Variable Immunodeficiency. Genetic testing using an NGS-based custom-targeted gene panel revealed a novel hemizygous loss-of-function variant in the SASH3 gene (c.505C>T/p.Gln169*). 2022 Frontiers in immunology Abstract SARS_CoV_2 C505T;N169X 134;147 142;152 35464418 Decreased and Heterogeneous Neutralizing Antibody Responses Against RBD of SARS-CoV-2 Variants After mRNA Vaccination. The most significant increase was observed in variants Epsilon and Delta, containing mutation L452R. 2022 Frontiers in immunology Abstract SARS_CoV_2 L452R 94 99 35464418 Decreased and Heterogeneous Neutralizing Antibody Responses Against RBD of SARS-CoV-2 Variants After mRNA Vaccination. Variants Gamma and Kappa encompassing RBD E484K/Q mutations presented the highest neutralizing resistance. 2022 Frontiers in immunology Abstract SARS_CoV_2 E484K;E484Q 42;42 49;49 RBD 38 41 35465708 Evaluation of a Rapid and Accessible Reverse Transcription-Quantitative PCR Approach for SARS-CoV-2 Variant of Concern Identification. We designed and analytically validated a two-reaction multiplex reverse transcription-quantitative PCR (RT-qPCR) assay targeting spike protein mutations L452R, E484K, and N501Y in reaction 1 and del69-70, K417N, and T478K in reaction 2. 2022 Journal of clinical microbiology Abstract SARS_CoV_2 E484K;K417N;L452R;N501Y;T478K 160;205;153;171;216 165;210;158;176;221 S 129 134 35467423 Evidence for an ACE2-Independent Entry Pathway That Can Protect from Neutralization by an Antibody Used for COVID-19 Therapy. Notably, mutation E484D largely rescued Huh-7 but not Vero cell entry from blockade by the neutralizing antibody Imdevimab and rendered Huh-7 cell entry ACE2-independent. 2022 mBio Abstract SARS_CoV_2 E484D 18 23 35467423 Evidence for an ACE2-Independent Entry Pathway That Can Protect from Neutralization by an Antibody Used for COVID-19 Therapy. SARS-CoV-2 variants of concern (VOC) acquired mutations in the spike (S) protein, including E484K, that confer resistance to neutralizing antibodies. 2022 mBio Abstract SARS_CoV_2 E484K 92 97 S;S 63;70 68;71 35467423 Evidence for an ACE2-Independent Entry Pathway That Can Protect from Neutralization by an Antibody Used for COVID-19 Therapy. These results suggest that the naturally occurring mutation E484D allows SARS-CoV-2 to employ an ACE2-independent mechanism for entry that is largely insensitive against Imdevimab, an antibody employed for COVID-19 therapy. 2022 mBio Abstract SARS_CoV_2 E484D 60 65 COVID-19 206 214 35467423 Evidence for an ACE2-Independent Entry Pathway That Can Protect from Neutralization by an Antibody Used for COVID-19 Therapy. We report that mutation E484D markedly increased SARS-CoV-2 S-driven entry into the hepatoma cell line Huh-7 and the lung cell NCI-H1299 without augmenting ACE2 binding. 2022 mBio Abstract SARS_CoV_2 E484D 24 29 S 60 61 35468331 Risk of hospitalisation associated with infection with SARS-CoV-2 omicron variant versus delta variant in Denmark: an observational cohort study. Compared with delta infection, omicron infection was associated with an adjusted RR of hospitalisation of 0 64 (95% CI 0 56-0 75; 222 [0 6%] of 38 669 omicron cases admitted to hospital vs 2213 [1 5%] of 150 311 delta cases). 2022 The Lancet. Infectious diseases Abstract SARS_CoV_2 311 delta 208 217 35474581 T-cell responses to SARS-CoV-2 Omicron spike epitopes with mutations after the third booster dose of an inactivated vaccine. Interestingly, compared with the ancestral peptides, only the peptides with the G339D or N440K mutation were detected to significantly destabilize the T-cell response. 2022 Journal of medical virology Abstract SARS_CoV_2 G339D;N440K 80;89 85;94 35474907 SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants. In the spike protein, Q493R and Q498R substitutions from passaged viruses were consistent with those in the B.1.1.529 (Omicron) variant. 2022 Computational and structural biotechnology journal Abstract SARS_CoV_2 Q493R;Q498R 22;32 27;37 S 7 12 35474907 SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants. Y144del and H655Y substitutions from passaged viruses were also reported in B.1.1.7 (Alpha), P.1 (Gamma), and B.1.1.529 (Omicron) variants. 2022 Computational and structural biotechnology journal Abstract SARS_CoV_2 H655Y;Y144del 12;0 17;7 35480056 Safety and Immunogenicity of Inactivated COVID-19 Vaccines Among People Living with HIV in China. Additionally, compared to HDs (Geomean titers (GMT) of 165 for D614G and GMT of 72 for delta), the neutralizing antibody titers against the two variants in PLWH (GMT of 43 for D614G and GMT 13 for delta) were decreased significantly (p = 0.018 and p < 0.001, respectively). 2022 Infection and drug resistance Abstract SARS_CoV_2 D614G;D614G 63;176 68;181 SARS-CoV-2-HIV coinfections 156 160 35480056 Safety and Immunogenicity of Inactivated COVID-19 Vaccines Among People Living with HIV in China. SARS-CoV-2 IgG and neutralizing antibody responses to the D614G variant and delta variant were measured for immune response assessment. 2022 Infection and drug resistance Abstract SARS_CoV_2 D614G 58 63 35480256 The SARS-CoV-2 B.1.618 variant slightly alters the spike RBD-ACE2 binding affinity and is an antibody escaping variant: a computational structural perspective. Our results revealed that the E484K mutation in the RBD slightly altered the binding affinity through affecting the hydrogen bonding network. 2021 RSC advances Abstract SARS_CoV_2 E484K 30 35 RBD 52 55 35480256 The SARS-CoV-2 B.1.618 variant slightly alters the spike RBD-ACE2 binding affinity and is an antibody escaping variant: a computational structural perspective. The recently reported variant B.1.618, which possesses the E484K mutation specific to the receptor-binding domain (RBD), as well as two deletions of Tyr145 and His146 at the N-terminal binding domain (NTD) of the spike protein, must be studied in depth to devise new therapeutic options. 2021 RSC advances Abstract SARS_CoV_2 E484K 59 64 S;RBD;N 213;115;174 218;118;175 35481766 Binding Interactions between Receptor-Binding Domain of Spike Protein and Human Angiotensin Converting Enzyme-2 in Omicron Variant. Other mutations, such as K417N, G446S, and Y505H, decrease the ACE2 binding, whereas S447N, Q493R, G496S, Q498R, and N501Y tend to increase it. 2022 The journal of physical chemistry letters Abstract SARS_CoV_2 G446S;G496S;K417N;N501Y;Q493R;Q498R;S447N;Y505H 32;99;25;117;92;106;85;43 37;104;30;122;97;111;90;48 35481766 Binding Interactions between Receptor-Binding Domain of Spike Protein and Human Angiotensin Converting Enzyme-2 in Omicron Variant. Some of the OV RBD mutations are predicted to affect the antibody neutralization either through their role in the S-protein conformational changes, such as S371L, S373P, and S375F, or through changing its surface charge distribution, such as G339D, N440K, T478K, and E484A. 2022 The journal of physical chemistry letters Abstract SARS_CoV_2 E484A;G339D;N440K;S371L;S373P;S375F;T478K 267;242;249;156;163;174;256 272;247;254;161;168;179;261 RBD;S 15;114 18;115 35482820 Mutations in the SARS-CoV-2 RNA dependent RNA polymerase confer resistance to remdesivir by distinct mechanisms. Biochemical analysis of SARS-CoV-2 RdRp encoding S759A demonstrated a roughly 10-fold decreased preference for RDV-triphosphate (RDV-TP) as a substrate, whereas nsp12-V792I diminished the uridine-triphosphate (UTP) concentration needed to overcome template-dependent inhibition associated with RDV. 2022 Science translational medicine Abstract SARS_CoV_2 S759A;V792I 49;167 54;172 Nsp12;RdRP 161;35 166;39 35482820 Mutations in the SARS-CoV-2 RNA dependent RNA polymerase confer resistance to remdesivir by distinct mechanisms. In one lineage, the V792I substitution emerged first, then combined with S759A. 2022 Science translational medicine Abstract SARS_CoV_2 S759A;V792I 73;20 78;25 35482820 Mutations in the SARS-CoV-2 RNA dependent RNA polymerase confer resistance to remdesivir by distinct mechanisms. Introduction of S759A and V792I substitutions at homologous nsp12 positions in murine hepatitis virus (MHV) demonstrated transferability across betacoronaviruses; introduction of these substitutions resulted in up to 38-fold RDV resistance and a replication defect. 2022 Science translational medicine Abstract SARS_CoV_2 S759A;V792I 16;26 21;31 Nsp12 60 65 35482820 Mutations in the SARS-CoV-2 RNA dependent RNA polymerase confer resistance to remdesivir by distinct mechanisms. Sequence analysis identified non-synonymous mutations in nonstructural protein 12 RNA-dependent RNA polymerase (nsp12-RdRp): V166A, N198S, S759A, V792I and C799F/R. 2022 Science translational medicine Abstract SARS_CoV_2 C799F;C799R;N198S;S759A;V166A;V792I 156;156;132;139;125;146 163;163;137;144;130;151 RdRp;Nsp12;RdRP 82;112;118 110;117;122 35482820 Mutations in the SARS-CoV-2 RNA dependent RNA polymerase confer resistance to remdesivir by distinct mechanisms. Two lineages encoded the S759A substitution at the RdRp Ser759-Asp-Asp active motif. 2022 Science translational medicine Abstract SARS_CoV_2 S759A 25 30 RdRP 51 55 35486915 Biomechanical Dependence of SARS-CoV-2 Infections. Given the recent data highlighting the importance of alternative virulent strains, we included both the native strain identified in early 2020 and an early S protein variant (D614G) that was shown to increase the viral infectivity markedly. 2022 ACS applied bio materials Abstract SARS_CoV_2 D614G 175 180 S 156 157 35486915 Biomechanical Dependence of SARS-CoV-2 Infections. Our results show that cells on softer and sparser scaffolds, closer resembling younger lungs, exhibit higher infection rates by the WT and D614G variant. 2022 ACS applied bio materials Abstract SARS_CoV_2 D614G 139 144 35489692 RBD-mRNA vaccine induces broadly neutralizing antibodies against Omicron and multiple other variants and protects mice from SARS-CoV-2 challenge. The RBD-mRNA-induced antibodies exerted moderate neutralization against authentic B.1.617.2 and B.1.1.529 variants, and pseudotyped B.1.351 and P.1 lineage variants containing K417N/T, E484K, and N501Y mutations, the B.1.617.2 lineage variant harboring L452R, T478K, and P681R mutations, and the B.1.1.529 lineage variant containing 38 mutations in the S protein. 2022 Translational research Abstract SARS_CoV_2 E484K;K417N;K417T;L452R;N501Y;P681R;T478K 185;176;176;253;196;271;260 190;183;183;258;201;276;265 RBD;S 4;353 7;354 35489692 RBD-mRNA vaccine induces broadly neutralizing antibodies against Omicron and multiple other variants and protects mice from SARS-CoV-2 challenge. The vaccine induced durable antibodies that potently neutralized prototypic strain and B.1.1.7 lineage variant pseudoviruses containing N501Y or D614G mutations alone or in combination with a N439K mutation (B.1.258 lineage), with a L452R mutation (B.1.427 or B.1.429 lineage), or a L452R-E484Q double mutation (B.1.617.1 variant), although neutralizing activity against B.1.1.7 lineage variant containing 10 amino acid changes in the S protein was slightly reduced. 2022 Translational research Abstract SARS_CoV_2 D614G;L452R;L452R;N439K;N501Y;E484Q 145;233;283;192;136;289 150;238;288;197;141;294 S 435 436 35490276 Lipopolysaccharide Responsive Beige-like Anchor Protein Deficiency in a Patient with Autoimmune Lymphoproliferative Syndrome-like Disease Phenotype: A Case Report and Literature Review. Due to recurrent infections and worsening gastrointestinal symptoms, whole-exome sequencing was conducted and revealed a novel homozygous pathogenic variant in the LRBA gene (c.534del; p.9Asp179IIef*16). 2022 Iranian journal of allergy, asthma, and immunology Abstract SARS_CoV_2 534del 175 183 35493173 Theoretical insights into the effect of halogenated substituent on the electronic structure and spectroscopic properties of the favipiravir tautomeric forms and its implications for the treatment of COVID-19. The variant analyzed for RdRp (Y176C) decreases the affinity of the keto form of the compounds in the active site, and prevented the ligands from interacting with RNA. 2021 RSC advances Abstract SARS_CoV_2 Y176C 31 36 RdRP 25 29 35494175 Emergence and spread of a sub-lineage of SARS-CoV-2 Alpha variant B.1.1.7 in Europe, and with further evolution of spike mutation accumulations shared with the Beta and Gamma variants. Thereby we identified a new B.1.1.7 sub-lineage carrying additional mutations of nucleoprotein G204P and open-reading-frame-8 K68stop. 2022 Virus evolution Abstract SARS_CoV_2 G204P;K68X 95;126 100;133 35494175 Emergence and spread of a sub-lineage of SARS-CoV-2 Alpha variant B.1.1.7 in Europe, and with further evolution of spike mutation accumulations shared with the Beta and Gamma variants. We have also detected its further evolution with extra spike mutations D138Y and A701V, which are signature mutations shared with the Gamma and Beta variants, respectively. 2022 Virus evolution Abstract SARS_CoV_2 A701V;D138Y 81;71 86;76 S 55 60 35496653 Genetic differentiation and diversity of SARS-CoV-2 omicron variant in Its early outbreak. Three of them are on the S protein, including S_A701V, S_L1081V, and S_R346K, which belong to the receptor-binding domain (RBD). 2022 Biosafety and health Abstract SARS_CoV_2 A701V;L1081V;R346K 48;57;71 53;63;76 RBD;S 123;25 126;26 35497518 Thermodynamics and kinetics in antibody resistance of the 501Y.V2 SARS-CoV-2 variant. Three substitutions in the RBD including K417N, E484K, and N501Y alter the free energy landscape, binding pose, binding free energy, binding kinetics, hydrogen bonding, nonbonded contacts, and unbinding pathway of RBD + NAb complexes. 2021 RSC advances Abstract SARS_CoV_2 E484K;K417N;N501Y 48;41;59 53;46;64 RBD;RBD 27;214 30;217 35497643 The twin-beginnings of COVID-19 in Asia and Europe-one prevails quickly. The first wave is a group of four mutations (C241T, C3037T, C14408T and A23403G [this being the amino acid change D614G]; all designated 0 to 1 below). 2022 National science review Abstract SARS_CoV_2 A23403G;C14408T;C3037T;D614G;C241T 72;60;52;114;45 79;67;58;119;50 35497643 The twin-beginnings of COVID-19 in Asia and Europe-one prevails quickly. This DG (D614G) group, fixed at the start of the pandemic, is the foundation of all subsequent waves of strains. 2022 National science review Abstract SARS_CoV_2 D614G 9 14 35499274 Investigation of changes in protein stability and substrate affinity of 3CL-protease of SARS-CoV-2 caused by mutations. Changes in the 3CLpro structure induced by the mutations Met49Thr, Leu167Ser, and Val202Ala resulted in significant levels of instability (-2.029,-2.612,-2.177 kcal.mol-1, respectively). 2022 Genetics and molecular biology Abstract SARS_CoV_2 L167S;M49T;V202A 67;57;82 76;65;91 35499994 Whole genome sequencing of SARS-CoV2 strains circulating in Iran during five waves of pandemic. There were different mutations in all parts of the genomes but Spike-D614G, NSP12-P323L, N-R203K and N-G204R were the most frequent mutants in these studied viruses. 2022 PloS one Abstract SARS_CoV_2 D614G;G204R;P323L;R203K 69;103;82;91 74;108;87;96 S;Nsp12;N;N 63;76;89;101 68;81;90;102 35502206 Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules. Specifically, we predicted a dramatical decline in binding affinity of HLA-DRB1*03:01 and this peptide both because of the Omicron BA.1 mutations (N211 deletion, L212I substitution and EPE 212-214 insertion) and the Omicron BA.2 mutations (V213G substitution). 2022 PeerJ Abstract SARS_CoV_2 L212I;V213G 162;240 167;245 35505068 COVID-19 patient serum less potently inhibits ACE2-RBD binding for various SARS-CoV-2 RBD mutants. ACE2 binding inhibition was reduced for ten out of eleven variants examined compared to wild-type, especially for those displaying the E484K mutation such as VOCs beta and gamma. 2022 Scientific reports Abstract SARS_CoV_2 E484K 135 140 35505237 Pseudotyped Bat Coronavirus RaTG13 is efficiently neutralised by convalescent sera from SARS-CoV-2 infected patients. Moreover, introducing the 484 K mutation into RaTG13 resulted in increased neutralisation, in contrast to the same mutation in SARS-CoV-2 (E484K). 2022 Communications biology Abstract SARS_CoV_2 E484K 139 144 35505237 Pseudotyped Bat Coronavirus RaTG13 is efficiently neutralised by convalescent sera from SARS-CoV-2 infected patients. This is despite E484K having a well-documented role in immune evasion in variants of concern (VOC) such as B.1.351 (Beta). 2022 Communications biology Abstract SARS_CoV_2 E484K 16 21 35507895 Delta variant (B.1.617.2) of SARS-CoV-2: Mutations, impact, challenges and possible solutions. The enhanced transmissibility of Delta variant has been associated with critical mutations such as D614G, L452R, P681R, and T478K in the S-protein. 2022 Human vaccines & immunotherapeutics Abstract SARS_CoV_2 D614G;L452R;P681R;T478K 99;106;113;124 104;111;118;129 S 137 138 35511584 Convergent Evolution of Multiple Mutations Improves the Viral Fitness of SARS-CoV-2 Variants by Balancing Positive and Negative Selection. Compared to the wild-type, K417T escapes Class 1 antibodies and has increased stability and expression; however, it has decreased receptor binding. 2022 Biochemistry Abstract SARS_CoV_2 K417T 27 32 35511584 Convergent Evolution of Multiple Mutations Improves the Viral Fitness of SARS-CoV-2 Variants by Balancing Positive and Negative Selection. E484K escapes Class 2 antibodies; however, it has decreased receptor binding, stability, and expression. 2022 Biochemistry Abstract SARS_CoV_2 E484K 0 5 35511584 Convergent Evolution of Multiple Mutations Improves the Viral Fitness of SARS-CoV-2 Variants by Balancing Positive and Negative Selection. N501Y increases receptor binding; however, it has decreased stability and expression. 2022 Biochemistry Abstract SARS_CoV_2 N501Y 0 5 35511584 Convergent Evolution of Multiple Mutations Improves the Viral Fitness of SARS-CoV-2 Variants by Balancing Positive and Negative Selection. Triple mutant K417T/E484K/N501Y has increased receptor binding, escapes both Class 1 and Class 2 antibodies, and has similar stability and expression as that of the wild-type. 2022 Biochemistry Abstract SARS_CoV_2 K417T;E484K;N501Y 14;20;26 19;25;31 35511584 Convergent Evolution of Multiple Mutations Improves the Viral Fitness of SARS-CoV-2 Variants by Balancing Positive and Negative Selection. We examined the physical mechanisms underlying the convergent evolution of three mutations K417T/E484K/N501Y by delineating the individual and collective effects of mutations on binding to angiotensin converting enzyme 2 receptor, immune escape from neutralizing antibodies, protein stability, and expression. 2022 Biochemistry Abstract SARS_CoV_2 K417T;E484K;N501Y 91;97;103 96;102;108 32422894 A Novel Synonymous Mutation of SARS-CoV-2: Is This Possible to Affect Their Antigenicity and Immunogenicity? If the mutation of D614G plays a crucial role in the positive selection process, SARS-CoV-2b will be the dominant type of SARS-CoV-2 in the future. 2020 Vaccines Introduction SARS_CoV_2 D614G 19 24 32422894 A Novel Synonymous Mutation of SARS-CoV-2: Is This Possible to Affect Their Antigenicity and Immunogenicity? Since no amino acid changes were found in this area other than the change of D614G, it is believed that this amino acid change alters the conformation of these immunogenic determinants; consequently, this region is expected to no longer act as a B-cell epitope in SARS-CoV-2b. 2020 Vaccines Introduction SARS_CoV_2 D614G 77 82 32422894 A Novel Synonymous Mutation of SARS-CoV-2: Is This Possible to Affect Their Antigenicity and Immunogenicity? The results of the antigenic index analysis showed severely reduced indexes of amino acids 615-617 in the SARS-CoV-2b strains compared to SARS-CoV-2a; it is predicted that the change of D614G affects the antigenicity of this region (Figure 1F). 2020 Vaccines Introduction SARS_CoV_2 D614G 186 191 32464271 Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? For example, a substantial number of strains with the S-D614G variant are from the countries Belgium, Spain, Italy, France, Netherlands, and Switzerland that top the death toll (Figure 1B) (https://www.worldometers.info/coronavirus/; last accessed May 2, 2020); while Germany and Kuwait, with a lower death toll, constitute most strains with the wild-type 614D at S (Figure 1B). 2020 International journal of infectious diseases Introduction SARS_CoV_2 D614G 56 61 S;S 54;364 55;365 32464271 Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? Overall, our observation speculates that the S-D614G strains may be more virulent, increasing the severity in infected individuals, especially in Europe where this mutation is prominent. 2020 International journal of infectious diseases Introduction SARS_CoV_2 D614G 47 52 S 45 46 32464271 Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? Strikingly, we observed that the variant S-D614G distinguishes the SARS-CoV-2 strains (Figure 1A) that may have caused fatal infections in European populations (Figure 1B). 2020 International journal of infectious diseases Introduction SARS_CoV_2 D614G 43 48 S 41 42 32464271 Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? The SARS-CoV-2 genomes with the S-D614G variant have been classified under a larger phylogenetic clade G constituting most strains from Europe (Figure 1 A). 2020 International journal of infectious diseases Introduction SARS_CoV_2 D614G 34 39 S 32 33 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. Although the effect of the D614G mutation is unclear, this mutation is located in the S1-S2 junction near the furin recognition site (R667) for the cleavage of S protein that is required for the entry of the virion into the host cell. 2020 The Indian journal of medical research Introduction SARS_CoV_2 D614G 27 32 S 160 161 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. Another mutation, A23403G, located in the gene encoding the spike glycoprotein results in an amino acid change (D614G) from aspartic acid to glycine. 2020 The Indian journal of medical research Introduction SARS_CoV_2 A23403G;D614G 18;112 25;117 S 60 78 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Moreover, a highlighted clade with ORF1ab-V378I mutation was observed in addition to the three major clades designated by the GISAID. 2020 Emerging microbes & infections Introduction SARS_CoV_2 V378I 42 47 ORF1ab 35 41 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Three major clades, including clade G (with G variant at position 614 within the spike protein, as S-D614G), clade S (ORF8-L84S), and clade V (ORF3a-G251V), were designated by the GISAID (https://www.gisaid.org/hcov-19-analysis-update/). 2020 Emerging microbes & infections Introduction SARS_CoV_2 D614G;G251V;L84S 101;149;123 106;154;127 S;ORF3a;ORF8;S;S 81;143;118;99;115 86;148;122;100;116 32587973 The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. Instead, these data show there is more S1 domain in the SG614-expressing cells, a result again consistent with the observation that the D614G mutation reduces S1 shedding. 2020 bioRxiv Introduction SARS_CoV_2 D614G 136 141 32587973 The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. It has also been speculated that the D614G mutation would promote, not limit, shedding of the S1 domain, based on the hypothetical loss of a hydrogen bond between D614 in S1 and T859 in S2. 2020 bioRxiv Introduction SARS_CoV_2 D614G 37 42 32587973 The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. It has previously been speculated that D614G mutation promotes an open configuration of the S protein that is more favorable to ACE2 association. 2020 bioRxiv Introduction SARS_CoV_2 D614G 39 44 S 92 93 32587973 The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. One of these variations encodes a S-protein mutation, D614G, in the carboxy(C)-terminal region of the S1 domain. 2020 bioRxiv Introduction SARS_CoV_2 D614G 54 59 S 34 35 32587973 The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. The strong phenotypic difference we observe here between D614 and G614 suggests that more study on the impact of the D614G mutation on the course of disease is warranted. 2020 bioRxiv Introduction SARS_CoV_2 D614G 117 122 32587973 The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. Therefore, the D614G mutation may have emerged to compensate for this newly acquired furin site. 2020 bioRxiv Introduction SARS_CoV_2 D614G 15 20 32587973 The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. Thus, the D614G mutation enhances virus infection through two related mechanisms: It reduces S1 shedding and increases total S protein incorporated into the virion. 2020 bioRxiv Introduction SARS_CoV_2 D614G 10 15 S 125 126 32587973 The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. To determine if the D614G mutation alters the properties of the S-protein in a way that could impact transmission or replication, we assessed its role in viral entry. 2020 bioRxiv Introduction SARS_CoV_2 D614G 20 25 S 64 65 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Here we investigate the potential consequences of one of these variants, the Spike protein variant D614G. 2020 bioRxiv Introduction SARS_CoV_2 D614G 99 104 S 77 82 32693089 Mortality in COVID-19 disease patients: Correlating the association of major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants. European HPV-16 E6 variants, such as the E6 variant L83V (at the nucleotide position 350) is associated with increased risk of HPV infection and progression to malignant transformation. 2020 International journal of infectious diseases Introduction SARS_CoV_2 L83V 52 56 32693089 Mortality in COVID-19 disease patients: Correlating the association of major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants. For MHC class I, starting with a peptide with the mutation site in the middle (flanked by seven amino acid residues to the left and right, resulting in a 15mer peptide) for ORF8 (L84S) (GNYTVSCLPFTINCQ and GNYTVSCSPFTINCQ) and for ORF3a (G251V) (VQIHTIDGSSGVVNP and VQIHTIDVSSGVVNP), we tested all possible combinations of length from 8 to 14 residues for MHC class I binding, For MHC class II, starting with a peptide with 33 residues with the mutation site in the middle for ORF8 (L84S) (KSPIQYIDIGNYTVSCL/SPFTINCQEPKLGSLVV) and for ORF3a (G251V) (KIVDEPEEHVQIHTIDG/VSSGVVNPVMEPIYDEP), we tested all possible combinations to bind to MHC class II alleles listed in the supplementary data set since MHC class II molecules can accommodate longer peptides, and nominal epitopes may 'glide' within the MHC class II peptide binding cleft. 2020 International journal of infectious diseases Introduction SARS_CoV_2 G251V;G251V;L84S;L84S 238;542;179;483 243;547;183;487 ORF3a;ORF3a;ORF8;ORF8 231;535;173;477 236;540;177;481 32693089 Mortality in COVID-19 disease patients: Correlating the association of major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants. From the countries that have submitted more than 100 sequences, there are four where the distribution of ORF8 (L84S) is different from the worldwide trend: in China, 38% SARS-CoV-2 sequences account for ORF8 (L84S), in Spain 43%, in the USA 32% and in Canada 31% (Figure 1 ). 2020 International journal of infectious diseases Introduction SARS_CoV_2 L84S;L84S 111;209 115;213 ORF8;ORF8 105;203 109;207 32693089 Mortality in COVID-19 disease patients: Correlating the association of major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants. In contrast, one of the Flu variant (T314K) peptides does not bind to to HLA-DRB1*04:01 (Table 1). 2020 International journal of infectious diseases Introduction SARS_CoV_2 T314K 37 42 32693089 Mortality in COVID-19 disease patients: Correlating the association of major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants. In contrast, the ORF8 L84S variant annuls binding to two MHC class II alleles that the wildtype virus allows: HLA-DPA1*01:03/DPB1*02:01 and DRB1*15:01. 2020 International journal of infectious diseases Introduction SARS_CoV_2 L84S 22 26 ORF8 17 21 32693089 Mortality in COVID-19 disease patients: Correlating the association of major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants. In order to test this possibility, we analyzed the most frequent MHC class I and II alleles in Europe, Asia, and Africa for binding to the mutations in ORF8 (L84S) and ORF3a (G251V) (see supplementary data sets). 2020 International journal of infectious diseases Introduction SARS_CoV_2 G251V;L84S 175;158 180;162 ORF3a;ORF8 168;152 173;156 32693089 Mortality in COVID-19 disease patients: Correlating the association of major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants. Most likely, there is selective pressure from MHC class II alleles regarding the binding of the ORF8 (L84S) variants, assuming that this mutation may be biologically relevant. 2020 International journal of infectious diseases Introduction SARS_CoV_2 L84S 102 106 ORF8 96 100 32693089 Mortality in COVID-19 disease patients: Correlating the association of major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants. Thus, ORF8 L84S variant in SARS-CoV-2, but not the wildtype, can be accommodated by DRB1*0401, which has been reported to be associated with susceptibility to HPV infections, Multiple Sclerosis, Rheumatoid Arthritis, type 1 diabetes, and Lyme disease-induced arthritis. 2020 International journal of infectious diseases Introduction SARS_CoV_2 L84S 11 15 ORF8 6 10 SARS-CoV-2-HPV infections;Multiple sclerosis;Rheumatoid Arthritis;Diabetes mellitus type 1 159;175;195;217 173;193;215;232 32693089 Mortality in COVID-19 disease patients: Correlating the association of major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants. We could not identify differences in MHC class I or class II binding characteristics (see Appendix- supplementary data sets Tables S1, S2 and S3) except for three MHC class II alleles, i.e., DRB3*02:02, DRB1*09:01, and DRB1*04:01, that do not allow binding of the wildtype, but accommodate the SARS-CoV-2 ORF8 (L84S) variant (Table 1 ) and also two MHC class II alleles HLA-DPA1*01:03/DPB1*02:01 that do the opposite: they accommodate the wildtype but not the SARS-CoV-2 ORF8 (L84S) variant (Table 1). 2020 International journal of infectious diseases Introduction SARS_CoV_2 L84S;L84S 311;477 315;481 ORF8;ORF8 305;471 309;475 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. By early April 2020, it was clear that the Spike D614G mutation exhibited this behavior, and G614 has since become the dominant form in the pandemic. 2020 Cell Introduction SARS_CoV_2 D614G 49 54 S 43 48 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. D480A/G escapes neutralizing antibody 80R, and immune pressure from 80R in vitro could recapitulate emergence of the D480 mutation. 2020 Cell Introduction SARS_CoV_2 D480A;D480G 0;0 7;7 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Notably, a single SARS-CoV-1 amino acid change, Spike D480A/G in the receptor binding domain (RBD), arose in infected humans and civets and became the dominant variant among 2003/2004 viruses. 2020 Cell Introduction SARS_CoV_2 D480A;D480G 54;54 61;61 RBD;S;RBD 69;48;94 92;53;97 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. Although the D614G mutation is located in the virus's external spike protein that receives a lot of attention from the human immune system, and thus could have an influence on the ability of SARS-CoV-2 to evade vaccine-induced immunity, we think that it's unlikely for these reasons. 2020 Cell Introduction SARS_CoV_2 D614G 13 18 S 63 68 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. And because of that, many questions remain on the potential impacts, if any, that D614G has on the COVID-19 pandemic. 2020 Cell Introduction SARS_CoV_2 D614G 82 87 COVID-19 99 107 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. Because the specific effect of D614G on spike function in entry and fusion is unknown, the impact of this mutation on therapeutic entry inhibitors is unknown. 2020 Cell Introduction SARS_CoV_2 D614G 31 36 S 40 45 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. D614G is not in the receptor-binding domain (RBD) of the spike protein, but in the interface between the individual spike protomers that stabilize its mature trimeric form on the virion surface through hydrogen bonding. 2020 Cell Introduction SARS_CoV_2 D614G 0 5 S;S;RBD 57;116;45 62;121;48 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. However, until we better understand the role of D614G during natural SARS-CoV-2 infection, the mutation should be taken into consideration for any vaccine or therapeutic design. 2020 Cell Introduction SARS_CoV_2 D614G 48 53 COVID-19 69 89 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. The current evidence suggests that D614G is less important for COVID-19 than other risk factors, such as age or comorbidities. 2020 Cell Introduction SARS_CoV_2 D614G 35 40 COVID-19 63 71 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. The D614G mutation is therefore unlikely to have a major impact on the efficacy of vaccines currently in the pipeline, some of which exclusively target the RBD. 2020 Cell Introduction SARS_CoV_2 D614G 4 9 RBD 156 159 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. The work by provides an early base for more extensive epidemiological, in vivo experimental, and diverse clinical investigations to fill in the many critical gaps in how D614G impacts the pandemic. 2020 Cell Introduction SARS_CoV_2 D614G 170 175 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. They present compelling data that an amino acid change in the virus's spike protein, D614G, emerged early during the pandemic, and viruses containing G614 are now dominant in many places around the world. 2020 Cell Introduction SARS_CoV_2 D614G 85 90 S 70 75 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. Will D614G Impact Therapeutic and Vaccine Designs? 2020 Cell Introduction SARS_CoV_2 D614G 5 10 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. Will D614G Impact Therapeutic and Vaccine Designs. 2020 Cell Introduction SARS_CoV_2 D614G 5 10 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. Will D614G Make Infections More Severe? 2020 Cell Introduction SARS_CoV_2 D614G 5 10 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. Will D614G Make Infections More Severe. 2020 Cell Introduction SARS_CoV_2 D614G 5 10 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. Will D614G Make Outbreaks Harder to Control? 2020 Cell Introduction SARS_CoV_2 D614G 5 10 32697970 Making Sense of Mutation: What D614G Means for the COVID-19 Pandemic Remains Unclear. Will D614G Make Outbreaks Harder to Control. 2020 Cell Introduction SARS_CoV_2 D614G 5 10 32705298 [The virology of SARS-CoV-2]. Fur D614G wird aktuell keine Auswirkung auf Diagnostik, Impfstoff- oder DAA-Wirksamkeit befurchtet. 2020 Der Internist Introduction SARS_CoV_2 D614G 4 9 32705298 [The virology of SARS-CoV-2]. Zu vorherrschenden Linien entwickelten sich dabei solche SARS-CoV-2-Viren, die auf den prominent aus dem Virus herausragenden ,,S spikes" die Mutation D614G tragen. 2020 Der Internist Introduction SARS_CoV_2 D614G 151 156 S;S 130;128 136;129 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. For example, A226V of Chikungunya virus E1 protein facilitated its adaptability in the vector Aedesalbopictus, resulting in an increased transmissibility. 2020 Cell Introduction SARS_CoV_2 A226V 13 18 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Moreover, the highly pathogenic avian influenza H5N1 with 4 amino acid changes demonstrated enhanced transmission, whereas in H7N9, the combined amino acid change A143V/R148K of hemagglutinin decreased the sensitivity of the virus to neutralizing antibodies by more than 10 times. 2020 Cell Introduction SARS_CoV_2 A143V;R148K 163;169 168;174 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Preliminary study suggested that the increased fatality rate may be associated with the most dominant variant D614G. 2020 Cell Introduction SARS_CoV_2 D614G 110 115 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Similarly, A82V of Ebola virus GP protein led to increased viral infectivity and mortality. 2020 Cell Introduction SARS_CoV_2 A82V 11 15 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. Although the higher number of mutations in genomes with RdRp 14408C>T mutation was suggested to be caused by lower fidelity of the mutant enzyme, it could also be due to many other epidemiological factors, such as worse containment of the mutant strain compared to others, more frequent introduction of the mutant strain into high-risk and/or higher-transmitting populations by chance, etc. 2020 PeerJ Introduction SARS_CoV_2 C14408T 61 69 RdRP 56 60 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. Key among them is the 14408C>T transition, identified in over 7,000 isolates across multiple continents. 2020 PeerJ Introduction SARS_CoV_2 C14408T 22 30 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. The proline to leucine substitution (P323L) caused by the 14408C>T mutation has been suggested to rigidify the RdRp protein structure, which may exert its effects through altered interaction with other components of the replication/transcription machinery or with the RNA template, thereby resulting in an altered mutation rate. 2020 PeerJ Introduction SARS_CoV_2 C14408T;P323L 58;37 66;42 RdRP 111 115 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. After the appearance of the Spike D614G variant in the latter course of the Chinese epidemic, over time in most examined local epidemics an enrichment of the 614G Spike protein variant over the original 614D variant has been observed, leading to the hypothesis that the Spike D614G mutation is positively selected (Supplemental movie, https://nextstrain.org/ncov/global?c=gt-S_614). 2020 bioRxiv Introduction SARS_CoV_2 D614G;D614G 34;276 39;281 S;S;S 28;163;270 33;168;275 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. By the time the epidemic reached Europe, a variant strain had appeared that carried a missense mutation in the Spike glycoprotein that substituted the aspartate at position 614 for a glycine in isolates identified in Germany, Italy and Mexico. 2020 bioRxiv Introduction SARS_CoV_2 G614D 151 190 S 111 129 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. Here, we present evidence that the D614G Spike mutant displays a slightly increased infectivity (~5X) in ACE2-expressing cells without a contribution of the ORF1b P314L mutation, when tested in pseudotyped lentiviral vectors. 2020 bioRxiv Introduction SARS_CoV_2 D614G;P314L 35;163 40;168 S 41 46 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. In almost all cases ORF1b P314L and Spike D614G variants co-occur. 2020 bioRxiv Introduction SARS_CoV_2 D614G;P314L 42;26 47;31 S 36 41 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. This mutation is in linkage disequilibrium with the ORF1b gene P314L substitution. 2020 bioRxiv Introduction SARS_CoV_2 P314L 63 68 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. This result provides a plausible mechanism for the increased observed infectivity inferred from epidemiological observations and is consistent with the positive selection hypothesis of the D614G mutation. 2020 bioRxiv Introduction SARS_CoV_2 D614G 189 194 32756549 SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness. Pseudovirus neutralizing activity in 1 mug mRNA-1273-immunized mice was similar comparing homotypic Wuhan-1 pseudovirus expressing spike with the S D614G substitution, which has recently become dominant around the world (Extended Data. 2020 Nature Introduction SARS_CoV_2 D614G 148 153 S;S 131;146 136;147 32756549 SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness. SARS-CoV-2 MA contains RBD substitutions Q498Y/P499T generated via site-directed mutagenesis in an infectious clone. 2020 Nature Introduction SARS_CoV_2 Q498Y;P499T 41;47 46;52 RBD 23 26 32763945 Genome Sequences of Six SARS-CoV-2 Strains Isolated in Morocco, Obtained Using Oxford Nanopore MinION Technology. All the genomes shared four mutations, namely, two synonymous (F924F and L4715L), one nonsynonymous (D614G), and one intergenic (241C>T). 2020 Microbiology resource announcements Introduction SARS_CoV_2 L4715L;C241T;D614G;F924F 73;129;101;63 79;135;106;68 32763945 Genome Sequences of Six SARS-CoV-2 Strains Isolated in Morocco, Obtained Using Oxford Nanopore MinION Technology. Only one nonsynonymous mutation was detected (D614G) in the spike protein, which is known as the most prevalent variant worldwide, and it is also associated with the emergence of clade A2, which includes all Moroccan strains sequenced in this study. 2020 Microbiology resource announcements Introduction SARS_CoV_2 D614G 46 51 S 60 65 32764372 Comprehensive Analyses of SARS-CoV-2 Transmission in a Public Health Virology Laboratory. For example, using Nextstrain's nomenclature, there are currently five major clades: 19A (the root clade) and 19B, and clades 20A, B and C that are widespread in Europe and include a mutation in the spike protein, D614G, that is associated with increased infectivity and higher viral loads. 2020 Viruses Introduction SARS_CoV_2 D614G 214 219 S 199 204 32779445 Profiling of Initial Available SARS-CoV-2 Sequences from Iranian Related COVID-19 Patients. The number of mutation events depicts that some of these mutations occurred more than three times among these 20 sequences such as R207C, V378I, M2796I, L3606F and A6407V in ORF1ab which are highlighted in the light orange columns in Figure 1B. 2020 Cell journal Introduction SARS_CoV_2 A6407V;L3606F;M2796I;R207C;V378I 164;153;145;131;138 170;159;151;136;143 ORF1ab 174 180 32779445 Profiling of Initial Available SARS-CoV-2 Sequences from Iranian Related COVID-19 Patients. The results showed some significant mutations such as R207C, V378I, M2796I, L3606F, and A6407V in ORF1ab which occur more than three times among these 20 Iranian related sequences. 2020 Cell journal Introduction SARS_CoV_2 A6407V;L3606F;M2796I;R207C;V378I 88;76;68;54;61 94;82;74;59;66 ORF1ab 98 104 32779780 Atomistic simulation reveals structural mechanisms underlying D614G spike glycoprotein-enhanced fitness in SARS-COV-2. A major finding from a recent study is guanine-to-adenine transition in position 23,403 in the Wuhan reference strain leading to aspartate-to-glycine mutation in spike glycoprotein residue 614 (D614G). 2020 Journal of computational chemistry Introduction SARS_CoV_2 D614G 194 199 S 162 180 32779780 Atomistic simulation reveals structural mechanisms underlying D614G spike glycoprotein-enhanced fitness in SARS-COV-2. Notably, at 75 ns, the G614-T859 inter-residue distance further increased to ~2.5 nm and was maintained till about 135 ns but moved back to its initial state of 1.0 nm at the end of the simulation; thus, providing the first evidence in support of S1 shedding from viral-membrane-bound S2 following D614G mutation (Figure 1a). 2020 Journal of computational chemistry Introduction SARS_CoV_2 D614G 298 303 Membrane 270 278 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. According to data from the public database of the Global Initiative on Sharing All Influenza Data (GISAID), three major clades of SARS-CoV-2 can be identified (Forster et al.,), that have been subsequently named as clade G (variant of the spike protein S-D614G), clade V (variant of the ORF3a coding protein NS3-G251), and clade S (variant ORF8-L84S). 2020 Frontiers in microbiology Introduction SARS_CoV_2 D614G;L84S 255;345 260;349 S;ORF3a;ORF8;NS3;S;S 239;287;340;308;253;329 244;292;344;311;254;330 32818213 Characterizing SARS-CoV-2 mutations in the United States. Among them, mutations 17858A>G-(Y541C), 17747C>T-(P504L), and 27964C>T-(S24L) were originated and prevalent mainly in the US, attributing to the unique characteristics of COVID-19 in the US. 2020 Research square Introduction SARS_CoV_2 C17747T;A17858G;C27964T;P504L;S24L;Y541C 40;22;62;50;72;32 48;30;70;55;76;37 COVID-19 171 179 32818213 Characterizing SARS-CoV-2 mutations in the United States. Based on co-mutation and time evolution analysis, we hypothesize that three concurrent mutations 17747C>T-(P504L), 17858A>G-(Y541C), and 28144T>C tend to fade out, while the other five concurrent mutations can enhance the infectivity of SARS-CoV-2. 2020 Research square Introduction SARS_CoV_2 C17747T;A17858G;T28144C;P504L;Y541C 97;115;137;107;125 105;123;145;112;130 32818213 Characterizing SARS-CoV-2 mutations in the United States. Based on genotyping results, top eight missense mutations (i.e., 14408C>T-(P323L), 23403A>G-(D614G), 25563G>T-(Q57H), 1059C>T-(T85I), 28144T>C-(L84S), 17858A>G-(Y541C), 17747C>T-(P504L), and 27964C>T-(S24L)) are identified, in addition to three synonymous mutations (i.e., 3037C>T-(F106F), 8782C>T-(S76S), and 18060C>T-(L7L)) that do not change SARS-CoV-2 proteins. 2020 Research square Introduction SARS_CoV_2 C1059T;C14408T;C17747T;A17858G;C18060T;A23403G;G25563T;C27964T;T28144C;C3037T;C8782T;D614G;F106F;L7L;L84S;P323L;P504L;Q57H;S24L;S76S;T85I;Y541C 118;65;169;151;310;83;101;191;134;273;290;93;282;320;144;75;179;111;201;299;127;161 125;73;177;159;318;91;109;199;142;280;297;98;287;323;148;80;184;115;205;303;131;166 32818213 Characterizing SARS-CoV-2 mutations in the United States. Employing the Jaccard distance-based genotyping, topological data analysis, artificial intelligence, flexibility-rigidity index (FRI), and network models, we show that 23403A>G-(D614G) and 27964C>T-(S24L) strengthen the folding stability of the spike protein and ORF8 protein. 2020 Research square Introduction SARS_CoV_2 A23403G;C27964T;D614G;S24L 168;189;178;199 176;197;183;203 S;ORF8 245;263 250;267 32818213 Characterizing SARS-CoV-2 mutations in the United States. Moreover, by analyzing the gender disparity, we find that a US-unique mutation, 27964C>T-(S24L), shows an interesting female-dominated pattern. 2020 Research square Introduction SARS_CoV_2 C27964T;S24L 80;90 88;94 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. 3B), but further analyses would be required to assess whether the D614G mutation has an effect on the way the S protein changes its conformation after interaction with ACE2. 2020 Scientific reports Introduction SARS_CoV_2 D614G 66 71 S 110 111 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. A comparison against the previous set of genomes collected for our phylogenetic and molecular dating analysis revealed that for samples submitted during the period from March 17-30, 2020, the D614G clade became increasingly prevalent worldwide, expanding from 22 to 42 countries. 2020 Scientific reports Introduction SARS_CoV_2 D614G 192 197 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. Accordingly, it was not possible to draw any conclusions regarding the clinical phenotype of the D614G clade and there is no evidence at this time to suggest this clade is associated with any differences in disease phenotype. 2020 Scientific reports Introduction SARS_CoV_2 D614G 97 102 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. Although the mutation appears to be clade-specific, we noted that D614G also arose another time in a single isolate belonging to a distinct lineage, Wuhan/HBCDC-HB-06/2020 (EPI 412982), collected on 7 February 2020. 2020 Scientific reports Introduction SARS_CoV_2 D614G 66 71 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. As of 30 March 2020, the D614G clade includes 954 of 1,449 (66%) of European specimens and 1,237 of 2,795 (44%) worldwide sequenced specimens. 2020 Scientific reports Introduction SARS_CoV_2 D614G 25 30 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. At the time of our study, the D614G mutation was at particularly high frequency 20/23 (87%) among Italian SARS-CoV-2 sequenced specimens, which was then emerging as the most severely affected country outside of China, with an overall case fatality rate of 7.2%. 2020 Scientific reports Introduction SARS_CoV_2 D614G 30 35 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. Finally, the global spread of the D614G mutation may have nothing to do with viral biology but may simply be a consequence of the high level of interconnectedness of Europe to the rest of the world. 2020 Scientific reports Introduction SARS_CoV_2 D614G 34 39 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. For example, most strains of the D614G clade also harbor a mutation (P4715L) in orf1ab and a subclade processes three nucleotide changes in the nucleoprotein (N) gene (GGG to AAC; G204R), which plays diverse roles in virion assembly as well as genome transcription and translation. 2020 Scientific reports Introduction SARS_CoV_2 D614G;G204R;P4715L 33;180;69 38;185;75 ORF1ab;N 80;159 86;160 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. From our findings of the recent emergence of the D614G clade and the increasing number of specimens harboring the mutation identified worldwide, we sought to investigate the potential significance of the mutation on clinical disease severity phenotypes. 2020 Scientific reports Introduction SARS_CoV_2 D614G 49 54 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. Given the high degree of nucleotide identity of the D614G clade (~ 99.6%), we expect that future tMRCA estimates will not differ substantially. 2020 Scientific reports Introduction SARS_CoV_2 D614G 52 57 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. However, at the time of the study, the mutation D614G was only found in one sequence from Germany (collected on 28 January, 2020). 2020 Scientific reports Introduction SARS_CoV_2 D614G 48 53 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. However, using country-wide crude case fatality data for countries from which sequencing data was available, there was no significant correlation between proportion of D614G clade sequences and crude case fatality rate as of 30 March 2020 (Spearman's rank correlation coefficient, r 0.22, 95% CI - 0.12 to 0.51). 2020 Scientific reports Introduction SARS_CoV_2 D614G 168 173 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. In addition, on analysis of crude case fatality rate by age-group (available for China, Italy, South Korea, Spain, and Canada) there was no significant correlation with proportion of D614G clades in the sequences analysed for these countries (Supplementary Table 2). 2020 Scientific reports Introduction SARS_CoV_2 D614G 183 188 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. In spite of the lack of evidence for phenotypic differences, it is interesting that in a short period of time since its emergence the D614G clade has become widespread all around the world. 2020 Scientific reports Introduction SARS_CoV_2 D614G 134 139 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. Most recently, it has been suggested that D614G introduces a new elastase cleavage site that may be differentially activated by host genomic mutations thereby facilitating spike processing, and entry into host cells in some host populations but not others. 2020 Scientific reports Introduction SARS_CoV_2 D614G 42 47 S 172 177 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. Notably, four inter-chain destabilizing (i.e., hydrophobic-hydrophilic) contacts are lost with residues of an adjacent chain upon D614G mutation (see Table 1 and. 2020 Scientific reports Introduction SARS_CoV_2 D614G 130 135 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. Our results are consistent with the work by Wrapp and colleagues, where they identified nine missense mutations (including D614G) in the spike protein that were thought to be relatively conservative and thus unlikely to affect protein function. 2020 Scientific reports Introduction SARS_CoV_2 D614G 123 128 S 137 142 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. The possibility that the D614G mutation may still have a potential impact on the function of the SARS-CoV-2 spike protein could not be excluded. 2020 Scientific reports Introduction SARS_CoV_2 D614G 25 30 S 108 113 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. Therefore, we investigated the potential functional and epidemiological consequences of the D614G mutation with structural modeling of the SARS-CoV-2 spike (S) protein and its interaction with the angiotensin-converting enzyme 2 (ACE2) receptor. 2020 Scientific reports Introduction SARS_CoV_2 D614G 92 97 S;S 150;157 155;158 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. Thus, the emergence of the D614G clade may be explained by a founder event and subsequent clonal expansion in Europe that led to its spreading worldwide. 2020 Scientific reports Introduction SARS_CoV_2 D614G 27 32 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. Upon further investigation, we found that these strains are distinguished by a derived missense mutation in the spike protein (S-protein) encoding gene, resulting in an amino acid change from an aspartate to a glycine residue at position 614 (D614G). 2020 Scientific reports Introduction SARS_CoV_2 D614G;D614G 195;243 241;248 S;S 112;127 117;128 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. We employed molecular dating to estimate the time of emergence of the D614G clade. 2020 Scientific reports Introduction SARS_CoV_2 D614G 70 75 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. reported various mutations on spike glycoprotein and also highlighted the importance of R408I mutation responsible for lower ACE2 binding which revealed a higher risk of COVID-19 pandemic (Jia et al.,). 2022 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 R408I 88 93 S 30 48 COVID-19 170 178 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The important RBD mutations like R408I, L455Y, F486L, Q493N, Q498Y, N501T and the mutations A930V, D936Y mapped on HR1 domain were derived due to its significant role in protein de-stabilization (Brielle et al.,; Lokman et al.,; Perilla et al.,; Shang et al.,). 2022 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 A930V;D936Y;F486L;L455Y;N501T;Q493N;Q498Y;R408I 92;99;47;40;68;54;61;33 97;104;52;45;73;59;66;38 RBD 14 17 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The mutations were analyzed using various computational algorithms and MD simulations enabled to predict the impact of the deleterious mutations R408I, L455Y, F486L, Q493N, Q498Y, N501T of RBD and HR1 associated A930V, D936Y mutations in the prefusion SARS-CoV-2 spike glycoprotein (Adzhubei et al.,; Rodrigues et al.,; Worth et al.,). 2022 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 A930V;D936Y;F486L;L455Y;N501T;Q493N;Q498Y;R408I 212;219;159;152;180;166;173;145 217;224;164;157;185;171;178;150 S;RBD 263;189 281;192 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). Homodimerization plays an important role in the catalytic activity of Mpro, as reported in the case of the SARS-CoV Mpro homolog, where the G11A mutation completely abolished its activity by interfering with the insertion of the N-finger region (residues 1-9). 2020 Journal of chemical information and modeling Introduction SARS_CoV_2 G11A 140 144 N 229 230 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. This isolate contains an amino acid change in residue P323L/F of RdRp (nsp12). 2020 medRxiv Introduction SARS_CoV_2 P323F;P323L 54;54 61;61 Nsp12;RdRP 71;65 76;69 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. Claims of increased transmissibility of this new strain due to spike D614G mutation by were met with caution, as other factors such as founder effect, drift etc. 2020 PeerJ Introduction SARS_CoV_2 D614G 69 74 S 63 68 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. However, animal studies will be required to further test the effects of the D614G mutation to reach a more definitive conclusion. 2020 PeerJ Introduction SARS_CoV_2 D614G 76 81 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. In our previous study, where we analyzed 11,208 SARS-CoV-2 genome sequences, we showed that RdRp mutations, particularly the 14408 C>T mutation, were associated with SARS-CoV-2 genome evolution and higher mutation density. 2020 PeerJ Introduction SARS_CoV_2 C14408T 125 134 RdRP 92 96 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. In the current study, we analyzed the time-dependent changes in the mutation densities of several SARS-CoV-2 genes and asked whether the patterns of change were different between the strain with the 14408 C>T / 23403 A>G mutations compared to those without either mutation. 2020 PeerJ Introduction SARS_CoV_2 C14408T;A23403G 199;211 208;220 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. In this respect, a series of reports from several labs has lent support to the increased transmissibility hypothesis for viruses carrying the 23403 A>G mutation: pseudotyped lenti- and retro-viruses with the mutant spike protein infect human cells in culture more efficiently, compared to those with the wild-type spike. 2020 PeerJ Introduction SARS_CoV_2 A23403G 142 151 S;S 215;314 220;319 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. Our previous study suggested that RdRp 14408 C>T mutation is associated with SARS-CoV-2 genome evolution and could even be working synergistically with the 23403 A>G (D614G) mutation. 2020 PeerJ Introduction SARS_CoV_2 C14408T;A23403G;D614G 39;156;167 48;165;172 RdRP 34 38 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. Soon after its spread to Europe and the US, a strain of SARS-CoV-2 with two non-synonymous mutations in the RNA-dependent RNA polymerase (RdRp) and spike (S) proteins, namely 14408 C>T (P323L) and 23403 A>G (D614G), became the dominant form particularly in Europe, and to some extent in the US, as well. 2020 PeerJ Introduction SARS_CoV_2 C14408T;A23403G;D614G;P323L 175;197;208;186 184;206;213;191 RdRp;S;RdRP;S 108;148;138;155 136;153;142;156 32895643 Genomic characterization of SARS-CoV-2 identified in a reemerging COVID-19 outbreak in Beijing's Xinfadi market in 2020. Although there is no evidence from available epidemiological and clinical data that the mutation of S protein D614G leads to increased pathogenicity or virulence of the virus, whether the transmission of the virus is enhanced still needs to be examined by systematic global assessment. 2020 Biosafety and health Introduction SARS_CoV_2 D614G 110 115 S 100 101 32895643 Genomic characterization of SARS-CoV-2 identified in a reemerging COVID-19 outbreak in Beijing's Xinfadi market in 2020. Finally, we also need to note whether the epidemic of D614G mutant SARS-CoV-2 is random or naturally selected, as the virus is circulating globally at present. 2020 Biosafety and health Introduction SARS_CoV_2 D614G 54 59 32895643 Genomic characterization of SARS-CoV-2 identified in a reemerging COVID-19 outbreak in Beijing's Xinfadi market in 2020. In a recent study, researchers found that a D614G mutation in the SARS-CoV-2 genome enhances the virus's ability to infect human cells, helping it to become the leading strain of the virus spreading around the world today. 2020 Biosafety and health Introduction SARS_CoV_2 D614G 44 49 32895643 Genomic characterization of SARS-CoV-2 identified in a reemerging COVID-19 outbreak in Beijing's Xinfadi market in 2020. It is worth noting that there is an amino acid D614G mutation caused by nt23403 substitution in all six genomes of SARS-CoV-2 found in Xinfadi market. 2020 Biosafety and health Introduction SARS_CoV_2 D614G 47 52 32895643 Genomic characterization of SARS-CoV-2 identified in a reemerging COVID-19 outbreak in Beijing's Xinfadi market in 2020. The research team also proposed that D614G mutation pseudovirus was associated with higher infectivity. 2020 Biosafety and health Introduction SARS_CoV_2 D614G 37 42 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. In addition, the non-synonymous substitutions of ORF3a-G251V and ORF8-L84S both cause the changes of amino acid (aa) polarity, which may affect the conformation of the protein and lead to function alteration. 2020 Sustainable cities and society Introduction SARS_CoV_2 G251V;L84S 55;70 60;74 ORF3a;ORF8 49;65 54;69 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. Recently, 7 substitution hotspots in SARS-CoV-2, ORF1ab-G10818T (ORF1ab-L3606F), ORF1ab-C8517T, ORF3a-G752T (ORF3a-G251V) S-A1841G (D614G), G171T (Q57H), ORF8-T251C (ORF8-L84S) and N-GGG608_609_610AAC (N-RG203_204KR) have been reported. 2020 Sustainable cities and society Introduction SARS_CoV_2 G171T;D614G;Q57H;A1841G;C8517T;G10818T;G251V;G752T;L3606F;L84S;T251C 140;132;147;124;88;56;115;102;72;171;159 145;137;151;130;94;63;120;107;78;175;164 32905045 Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. Given that POC antibody tests were designed to detect antibodies to the wild-type S protein, we also aimed to investigate whether SARS-CoV-2 infections with D614G Spike mutant virus could be diagnosed by POC antibody tests. 2020 Cell reports. Medicine Introduction SARS_CoV_2 D614G 157 162 S;S 163;82 168;83 COVID-19 130 151 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. For SARS-CoV-2, analyses of over 28,000 spike protein gene sequences in late May 2020 revealed a D614G amino acid substitution that was rare before March but increased in frequency as the pandemic spread, reaching over 74% of all published sequences by June 2020. 2020 bioRxiv Introduction SARS_CoV_2 D614G 97 102 S 40 45 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Initial phenotypic characterizations of the D614G spike substitution were performed using pseudotyped viruses, whereby vesicular stomatitis virus (VSV) and lentiviral particles incorporating the SARS-CoV-2 spike protein alone were studied by replication kinetics. 2020 bioRxiv Introduction SARS_CoV_2 D614G 44 49 S;S 50;206 55;211 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. The association of spike protein amino acid substitutions with coronavirus transmissibility suggested that the D614G substitution was critical to this putative selective sweep. 2020 bioRxiv Introduction SARS_CoV_2 D614G 111 116 S 19 24 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. The D614G substitution was accompanied by three other mutations: a C-to-T mutation in the 5' untranslated genome region at position 241, a synonymous C-to-T mutation at position 3,037, and a nonsynonymous C-to-T mutation at position 14,408 in the RNA-dependent RNA polymerase gene. 2020 bioRxiv Introduction SARS_CoV_2 D614G 4 9 RdRp 247 275 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Therefore, using an infectious cDNA clone for SARS-CoV-2, we generated the D614G substitution in the January 2020 USA-WA1/2020 strain and performed experimental comparisons using in vitro cell culture, a primary human 3D airway tissue, and a hamster infection model. 2020 bioRxiv Introduction SARS_CoV_2 D614G 75 80 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Using the reporter SARS-CoV-2 viruses, we analyzed the effect of D614G mutation on susceptibility to neutralization. 2020 bioRxiv Introduction SARS_CoV_2 D614G 65 70 32934770 Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity. A biophysical/structural analysis of the impact of the D614G substitution on the S1/S2 interface supports this picture, yet as shown subsequently, the analysis needs to go beyond mere structural considerations (cf. 2020 ACS medicinal chemistry letters Introduction SARS_CoV_2 D614G 55 60 32934770 Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity. A conservative estimate drawn from experimental data on the cost of unwrapping the BHB (ref Figure 3) gives 3 x 8 kJ/mol = 5.73 kcal/mol as the thermodynamic cost of destabilizing the S1 structure resulting from depriving the BHB 614-647 of three wrapping carbonaceous groups due to the D614G substitution. 2020 ACS medicinal chemistry letters Introduction SARS_CoV_2 D614G 287 292 32934770 Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity. A more thorough analysis of the impact of the D614G substitution takes into account the epistructure of the interacting S1 and S2 domains. 2020 ACS medicinal chemistry letters Introduction SARS_CoV_2 D614G 46 51 32934770 Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity. because the substitution D614G would eliminate altogether the postulated hydrogen bond across the S1/S2 interface; hence, the SG614 phenotype would be characterized by more S1 shedding compared with SD614. 2020 ACS medicinal chemistry letters Introduction SARS_CoV_2 D614G 25 30 32934770 Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity. In other words, the D614G mutation promotes the S1/S2 association because (a) it destabilizes the free (uncomplexed) S1 structure through the enhanced exposure of the BHB pairing residues G614 and A647 and (b) it stabilizes the S1/S2 interface as the D614G substitution decreases the intramolecular wrapping of the G614-A647 dehydron, thereby further promoting its intermolecular wrapping via the contribution from S2 residue P862 (Figure 1d). 2020 ACS medicinal chemistry letters Introduction SARS_CoV_2 D614G;D614G 20;251 25;256 32934770 Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity. provided epidemiological evidence that the amino acid substitution D614G in SARS-CoV-2 spike protein is rapidly becoming dominant, suggesting that the G614 mutant may entail a significant fitness advantage. 2020 ACS medicinal chemistry letters Introduction SARS_CoV_2 D614G 67 72 S 87 92 32934770 Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity. Structural and Mechanistic Impact of the D614G Mutation. 2020 ACS medicinal chemistry letters Introduction SARS_CoV_2 D614G 41 46 32934770 Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity. The effect results from two contributions: (a) Mutation D614G eliminates the salt bridge that hampers the S1/S2 association as it improves the wrapping of the dehydron pairing residues at locations 614 and 647. 2020 ACS medicinal chemistry letters Introduction SARS_CoV_2 D614G 56 61 32934770 Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity. The substitution D614G has a major impact on the epistructure of S1, vis-a-vis the previous considerations. 2020 ACS medicinal chemistry letters Introduction SARS_CoV_2 D614G 17 22 32934770 Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity. Thus, the net gain in stability (loss in free energy) for the S1/S2 complex resulting from the D614G mutation is significant and may be conservatively estimated at DeltaDeltaG = -5.73kcal/mol. 2020 ACS medicinal chemistry letters Introduction SARS_CoV_2 D614G 95 100 32935099 SARS-CoV-2 infection severity is linked to superior humoral immunity against the spike. 5a), suggesting the D614G epitope was not a major antigenic site. 2020 bioRxiv Introduction SARS_CoV_2 D614G 20 25 32935099 SARS-CoV-2 infection severity is linked to superior humoral immunity against the spike. SARS-CoV-2 has acquired a D614G mutation within the spike protein and viruses carrying this mutation have since become the dominant circulating strain globally as of early April. 2020 bioRxiv Introduction SARS_CoV_2 D614G 26 31 S 52 57 32935099 SARS-CoV-2 infection severity is linked to superior humoral immunity against the spike. These data indicate that the region that encompasses the D614G mutation is not immunodominant or does not affect the antigenicity of epitopes at or near this site. 2020 bioRxiv Introduction SARS_CoV_2 D614G 57 62 32935099 SARS-CoV-2 infection severity is linked to superior humoral immunity against the spike. We did not observe a difference in antibody titers against the WT and D614G spike antigens within our acute cohort. 2020 bioRxiv Introduction SARS_CoV_2 D614G 70 75 S 76 81 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. While completing our MERS-CoV nsp14 studies, given the developing pandemic, we also evaluated the impact of ExoN inactivation (using a D90A/E92A ExoN motif I double mutant) on SARS-CoV-2 replication and viability. 2020 Journal of virology Introduction SARS_CoV_2 D90A;E92A 135;140 139;144 Exon;Exon 108;145 112;149 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. F476L and V553L were shown to cause 2.4-fold resistance and 5.0-fold resistance, respectively. 2020 The Journal of biological chemistry Introduction SARS_CoV_2 V553L;F476L 10;0 15;5 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. The equivalent mutations F480L and V557L introduced together in SARS-CoV were also shown to confer low-level (6.0-fold) resistance to the drug. 2020 The Journal of biological chemistry Introduction SARS_CoV_2 F480L;V557L 25;35 30;40 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. The F476L+V553L double mutant showed 5.5-fold resistance to RDV. 2020 The Journal of biological chemistry Introduction SARS_CoV_2 F476L;V553L 4;10 9;15 32972934 Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh. A unique mutation (NSP2_V480I) was observed in the BCSIR-NILMRC-006 genome sequence compared to the genome sequences available in the GISAID CoVsurver (GISAID Initiative_CoVsurver_files). 2020 Microbiology resource announcements Introduction SARS_CoV_2 V480I 24 29 Nsp2 19 23 32972934 Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh. Compared with hCoV-19/Wuhan/WIV04/2019, for strain BCSIR-NILMRC-006, we found eight mutations, including NSP2_G339S, N_R203K, N_G204R, NSP3_Q172R, Spike_D614G, NSP2_I120F, NSP12_P323L, and NSP2_V480I. 2020 Microbiology resource announcements Introduction SARS_CoV_2 D614G;G204R;G339S;I120F;P323L;Q172R;R203K;V480I 153;128;110;165;178;140;119;194 158;133;115;170;183;145;124;199 S;Nsp12;Nsp2;Nsp2;Nsp2;Nsp3 147;172;105;160;189;135 152;177;109;164;193;139 32972934 Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh. In BCSIR-NILMRC-008, the genome mutations Spike_D614G, N_R203K, N_G204R, NSP2_I120F, NSP12_P323L, and NSP3_P822S were observed (Table 1). 2020 Microbiology resource announcements Introduction SARS_CoV_2 D614G;G204R;I120F;P323L;P822S;R203K 48;66;78;91;107;57 53;71;83;96;112;62 S;Nsp12;Nsp2;Nsp3 42;85;73;102 47;90;77;106 32972934 Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh. Six mutations were found in BCSIR-NILMRC-007, Spike_D614G, N_R203K, N_G204R, NSP12_K59N, NSP2_I120F, and NSP12_P323L. 2020 Microbiology resource announcements Introduction SARS_CoV_2 D614G;G204R;I120F;K59N;P323L;R203K 52;70;94;83;111;61 57;75;99;87;116;66 S;Nsp12;Nsp12;Nsp2 46;77;105;89 51;82;110;93 32972948 Whole-Genome Sequence of SARS-CoV-2 Isolate Siena-1/2020. Among the 5 single nucleotide changes, the one at position 23403 causes a change in the predicted amino acid sequence of the spike (S) protein (D614G), which is now the most common variant worldwide. 2020 Microbiology resource announcements Introduction SARS_CoV_2 D614G 144 149 S;S 125;132 130;133 32980406 Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13). Mutations on Nsp13 have been studied on a type of coronavirus called avian infectious bronchitis virus (IBV), specifically the lethal effect of Arg132/Pro mutation on IBV Nsp13 has been demonstrated. 2020 International journal of biological macromolecules Introduction SARS_CoV_2 R132P 144 154 Nsp13;Nsp13 13;171 18;176 32984400 Understanding Selenium and Glutathione as Antiviral Factors in COVID-19: Does the Viral M(pro) Protease Target Host Selenoproteins and Glutathione Synthesis? identified one other host protein (TRMT1) that bound only to the inactive Mpro C145A mutant, and concluded it was a likely Mpro substrate, because they were able to identify a putative Mpro cleavage site in the TRMT1 protein sequence (PRLQ/ANFT), where the slash (/) represents the cleavage site. 2020 Frontiers in nutrition Introduction SARS_CoV_2 C145A 79 84 32984400 Understanding Selenium and Glutathione as Antiviral Factors in COVID-19: Does the Viral M(pro) Protease Target Host Selenoproteins and Glutathione Synthesis? One of the interactions they identified involved the cytosolic form of the selenoprotein glutathione peroxidase, GPX1, which bound strongly to the inactive C145A Mpro mutant. 2020 Frontiers in nutrition Introduction SARS_CoV_2 C145A 156 161 32984400 Understanding Selenium and Glutathione as Antiviral Factors in COVID-19: Does the Viral M(pro) Protease Target Host Selenoproteins and Glutathione Synthesis? The study also included a catalytically inactive C145A Mpro mutant (lacking the active site cysteine), which was also used as a bait protein, in order to discriminate false positives that might bind non-specifically to the Mpro active site cysteine via disulfide bond formation. 2020 Frontiers in nutrition Introduction SARS_CoV_2 C145A 49 54 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Here, we investigate potential functional and structural consequences of one of these variants, the Spike protein variant D614G, which has been associated with increased viral load in people with COVID-19. 2020 Cell Introduction SARS_CoV_2 D614G 122 127 S 100 105 COVID-19 196 204 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. Moreover, CR3022 is now able to neutralize SARS-CoV-2 P384A with a similar potency to SARS-CoV. 2020 bioRxiv Introduction SARS_CoV_2 P384A 54 59 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. Another structural analysis corroborates with experimental data conclusions of Zhang and colleagues, showing that the D614G substitution promotes S1-S2 spike subunit association. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 118 123 S 152 157 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. As Indian and Australian populations have different genetic backgrounds than Chinese populations, this suggests that, in addition to host genetic factors, the D614G spike variant may also contribute to the frequency of chemosensory dysfunction. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 159 164 S 165 170 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. D614G Spike Variant as the First Putative Viral Factor Affecting Incidence of Anosmia. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 0 5 S 6 11 Anosmia 78 85 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. Further studies should establish the extent to which host genetic factors contribute to anosmia in COVID-19 as compared to viral factors such as the D614G variant. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 149 154 Anosmia;COVID-19 88;99 95;107 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. Geographical Prevalence of D614G Variant and Prevalence of Chemosensory Deficits. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 27 32 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. Homology modeling of the spike protein region spanning the FCS revealed that the D614G mutation affects the secondary structure at the FCS region and thus possibly modulates spike protein cleavage and in consequence protein stability and binding to hACE2. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 81 86 S;S 25;174 30;179 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. It must be emphasized that the D614G spike variant is not the only mechanism and that additional factors, such as the yet uncharacterized host genetic variants of ACE2 and TMPRSS2, may similarly contribute to the incidence of chemosensory deficits in COVID-19. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 31 36 S 37 42 COVID-19 251 259 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. Molecular modeling data shows that D614G is located on the surface of the spike protomer, and recent studies report that the amino acid substitution D614 to G614 favors the open conformational state of the spike protein. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 35 40 S;S 74;206 79;211 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. Taken together, the latest genetic and epidemiology data suggest that the D614G spike variant may be, in part, responsible for the increased frequency of the chemosensory dysfunction during the current pandemic. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 74 79 S 80 85 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. The above considerations prompt a mechanistic assessment of the impact of the D614G mutation on efficiency of virus binding and entry to ACE2-expressing cells in the olfactory epithelium. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 78 83 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. The recent work on viral genetics done by Korber and colleagues showed that, early in the pandemic, SARS-CoV-2 spike protein had amino acid D (aspartic acid) at position 614. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614D 139 174 S 111 116 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. The reduced cleavage and increased spike protein stability may be due to the D614G mutation's impact on the adjacent furin-cleavage site (FCS) located at the position near the 682-686 amino acids. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 77 82 S 35 40 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. The structural and functional consequences of the D614G mutation are not yet clear and are a topic of ongoing debate. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 50 55 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. The usage of appropriate animal models is another strategy to obtain insights about the role of the D614G variant in the incidence of chemosensory dysfunction. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 100 105 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. There are further similarities between the functional properties of the D614G spike variant and chemosensory dysfunction caused by the SARS-CoV-2 coronavirus. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 72 77 S 78 83 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. Thus, the usage of retrospective data and their reinterpretation in the context of the role of the D614G variant in chemosensory dysfunction is limited. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 99 104 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. Virus Binding to hACE2, a Critical Step Leading to Anosmia, Is Likely Affected by the D614G Spike Variant. 2020 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 86 91 S 92 97 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. Among these, F229E, HKU1, NL63 and OC43 coronaviruses are involved in flu-like disease in immune-competent individuals. 2020 Heliyon Introduction SARS_CoV_2 F229E 13 18 33024961 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. We use protein-level and nucleotide-level inter-strain constraint to analyze 1875 mutations from 2544 pandemic isolates, show gene-level and codon-level agreement between within-strain and across-strain selective pressures, reveal recent adaptive acceleration for N and surprising deceleration for S1 and nsp3, and flag mutations disrupting evolutionarily-conserved positions that may represent novel adaptations to human hosts, including Spike D614G. 2020 Research square Introduction SARS_CoV_2 D614G 445 450 S;Nsp3;N 439;305;264 444;309;265 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. After three continuous passages at 72h intervals, the D614G variant became dominant in the cultures regardless of whether the WT virus was at a 1:1 or 10:1 ratio over the isogenic D614G mutant. 2020 bioRxiv Introduction SARS_CoV_2 D614G;D614G 54;180 59;185 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Although the D614G variant showed similar or slightly higher titers at the early time point (8h), its peak titers were significantly lower than the WT virus in Vero-E6 and A549-ACE2 cell lines but not in Vero-81 and Huh7. 2020 bioRxiv Introduction SARS_CoV_2 D614G 13 18 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Both WT and D614G were transmitted efficiently to naive hamsters evident by positive nasal wash samples detected in all exposed animals at day 4. 2020 bioRxiv Introduction SARS_CoV_2 D614G 12 17 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Consistent with previous studies, we demonstrated the increased sensitivity of the SARS-CoV2 D614G-nLuc variant to the antisera from D-form spike (WT) vaccinated mice. 2020 bioRxiv Introduction SARS_CoV_2 D614G 93 98 S 140 145 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Cultures from the same donor were infected with either WT or D614G virus in triplicate. 2020 bioRxiv Introduction SARS_CoV_2 D614G 61 66 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Despite the presence of a CoV proof-reading function, recent reports identified an emergent D614G substitution in the spike glycoprotein of SARS-CoV-2 strains that is now the most prevalent form globally. 2020 bioRxiv Introduction SARS_CoV_2 D614G 92 97 S 118 136 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Direct competition experiments also demonstrate that the SARS-CoV2 D614G isogenic virus displays a significant advantage following passage in primary human large airway epithelial cells in vitro. 2020 bioRxiv Introduction SARS_CoV_2 D614G 67 72 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. However, five of eight hamsters exposed to the D614G-infected group showed infection and detectable viral shedding at day 2 while those exposed to the WT-infected group had no infection and viral shedding (p = 0.0256, Fisher exact test). 2020 bioRxiv Introduction SARS_CoV_2 D614G 47 52 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. However, our data are consistent with recent studies indicate that D614G alters spike trimer hydrogen-bond interactions, reorienting the RBD into an "up" conformation, increasing ACE2 receptor binding and infectivity. 2020 bioRxiv Introduction SARS_CoV_2 D614G 67 72 S;RBD 80;137 85;140 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. However, the D614G substitution has yet to be evaluated in the authentic SARS-CoV-2 infection models, and its function in viral pathogenesis and transmissibility remains unclear. 2020 bioRxiv Introduction SARS_CoV_2 D614G 13 18 COVID-19 73 93 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. However, the D614G-infected hamsters lost modestly more body weight than those infected with the WT virus. 2020 bioRxiv Introduction SARS_CoV_2 D614G 13 18 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. In accord with pseudovirus studies, the D614G-nLuc infection resulted in a 0.5 to 2-fold higher transgene expression as compared with WT-nLuc virus. 2020 bioRxiv Introduction SARS_CoV_2 D614G 40 45 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. In contrast, the isogenic D614G recombinant virus infection of hamsters resulted in significant differences in weight loss, but not pathology or virus replication in the lung and nasal turbinates. 2020 bioRxiv Introduction SARS_CoV_2 D614G 26 31 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. In transmission studies, the D614G isogenic was transmitted significantly faster to adjacent animals early in infection, demonstrating that the substitution preserved efficient transmission phenotypes in vivo. 2020 bioRxiv Introduction SARS_CoV_2 D614G 29 34 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Our data demonstrate that SARS-CoV2 D614G recombinant viruses are significantly more infectious in some continuous cells in culture, but more importantly, in multiple patient codes of nasal and large airway epithelial cells derived from the upper respiratory, but not lower respiratory tract. 2020 bioRxiv Introduction SARS_CoV_2 D614G 36 41 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Our data unilaterally support a critical role for the D614G mutation in enhanced virus infectivity, growth and fitness in human nasal and proximal airway epithelia, but not in the lower respiratory tract airway epithelium from multiple donors. 2020 bioRxiv Introduction SARS_CoV_2 D614G 54 59 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Our Western blot and SEM studies demonstrated no obvious differences in proteolytic processing or S incorporation into isogenic virions encoding the D614G mutations, perhaps reflecting differences in S trimer incorporation and presentation between authentic and pseuotyped viruses. 2020 bioRxiv Introduction SARS_CoV_2 D614G 149 154 S;S 98;200 99;201 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Paired t-test analysis suggests the D614G-infected HNE at 24, 48 and 72h, and LAE cultures at 48h exhibited significantly higher titers than cultures infected with the WT virus. 2020 bioRxiv Introduction SARS_CoV_2 D614G 36 41 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Patients infected with the D614G variant could not be conclusively linked to increased disease severity in humans. 2020 bioRxiv Introduction SARS_CoV_2 D614G 27 32 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Patients infected with the D614G-bearing SARS-CoV-2 are associated with higher viral loads in the upper respiratory tract, but not altered disease severity. 2020 bioRxiv Introduction SARS_CoV_2 D614G 27 32 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Replication kinetics comparing WT and D614G viruses were performed utilizing multi-step growth curves in cell lines (Fig 1C). 2020 bioRxiv Introduction SARS_CoV_2 D614G 38 43 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. SARS-CoV2 S pseudotyped viruses encoding the D614G mutation were reported to exhibit increased infectivity in continuous cells lines and increased sensitivity to neutralization. 2020 bioRxiv Introduction SARS_CoV_2 D614G 45 50 S 10 11 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Taken together, these data suggest the D614G substitution enhances SARS-CoV-2 replication fitness in the primary epithelial cells, with a marked advantage in the upper respiratory tract epithelial cells in nasal and large (proximal) airway epithelia. 2020 bioRxiv Introduction SARS_CoV_2 D614G 39 44 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Taking together, the D614G substitution marginally enhances SARS-CoV-2 pathogenesis in the hamster, but not mouse models. 2020 bioRxiv Introduction SARS_CoV_2 D614G 21 26 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. The effect of the D614G variant on vaccine efficacy has been of major concern. 2020 bioRxiv Introduction SARS_CoV_2 D614G 18 23 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. The emergent D614G mutation in the spike glycoprotein of SARS-CoV-2 strains has raised significant concerns about potential enhancements in transmissibility, antigenicity and/or pathogenesis. 2020 bioRxiv Introduction SARS_CoV_2 D614G 13 18 S 35 53 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. The infected groups at all three timepoints and the exposure groups at 4 and 6 dpi exhibit similar viral titers between WT and D614G viruses. 2020 bioRxiv Introduction SARS_CoV_2 D614G 127 132 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. The serum samples show 0.8 to 5.1-fold higher half-maximal inhibitory dilution (ID50) values against the D614G virus than the WT virus, suggesting the D614G substitution rendered SARS-CoV-2 more sensitive to neutralizing antibodies. 2020 bioRxiv Introduction SARS_CoV_2 D614G;D614G 105;151 110;156 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. These data suggest that the D614G substitution may modesty enhances SARS-CoV-2 entry and replication in some immortalized cell lines. 2020 bioRxiv Introduction SARS_CoV_2 D614G 28 33 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. These data suggest the D614G variant transmits significantly faster than the WT virus through droplets and aerosols between hamsters. 2020 bioRxiv Introduction SARS_CoV_2 D614G 23 28 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. These ex vivo human airway culture data are consistent with the moderately increased pathogenicity, as shown by body weight changes, and improved transmission of the D614G variant in the hamster models of human disease. 2020 bioRxiv Introduction SARS_CoV_2 D614G 166 171 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. To address the function of the D614G substitution in SARS-CoV-2 replication and transmissibility, we generated an isogenic variant containing the D614G mutation in the S glycoprotein, along with a second variant that contained the nanoLuciferease (nLuc) gene in place of the accessory gene 7a (Fig 1A). 2020 bioRxiv Introduction SARS_CoV_2 D614G;D614G 31;146 36;151 S 168 182 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. To compare antibody neutralization properties with reported pseudotyped virus assays, neutralization activity was measured in 10 serum samples from D614 (WT) spike-vaccinated mice using the nLuc-expressing recombinant SARS-CoV-2 encoding either WT or D614G spike. 2020 bioRxiv Introduction SARS_CoV_2 D614G 251 256 S;S 158;257 163;262 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. To evaluate the function of the D614G substitution in viral pathogenesis, hACE2 transgenic mice and Syrian hamsters were infected with equal plaque-forming units (PFU) of WT or D614G viruses. 2020 bioRxiv Introduction SARS_CoV_2 D614G;D614G 32;177 37;182 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. To evaluate the replication of SARS-CoV-2 D614G variant in the human respiratory tract, we compared WT and the D614G growth kinetics in primary human nasal epithelial (HNE) from five donors, large (proximal) airway epithelial (LAE) from four donors, and distal lung small airway epithelial (SAE) cells from three donors. 2020 bioRxiv Introduction SARS_CoV_2 D614G;D614G 42;111 47;116 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. To evaluate the role of the D614G substitution in SARS-CoV-2 respiratory droplet transmissibility, we set up eight pairs of hamsters for each virus as described previously. 2020 bioRxiv Introduction SARS_CoV_2 D614G 28 33 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. To examine whether the D614G substitution enhanced authentic SARS-CoV-2 entry, four susceptible cell lines were infected with wildtype (WT)-nLuc and D614G-nLuc viruses at an MOI of 0.1. 2020 bioRxiv Introduction SARS_CoV_2 D614G;D614G 23;149 28;154 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Together with similar neutralization properties against six SARS-CoV-2 mAbs, these data suggest that the current vaccine and mAb approaches directed against WT spike should be effective against the D614G strains. 2020 bioRxiv Introduction SARS_CoV_2 D614G 198 203 S 160 165 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Together, these data strongly support the role of the nasal epithelium and the D614G mutation in enhanced infectivity and transmission in human populations. 2020 bioRxiv Introduction SARS_CoV_2 D614G 79 84 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Two groups of hACE2 mice infected with WT and D614G viruses exhibited undetectable viral titers in nasal turbinates and similar lung viral titers at day 2 and 5 post infection. 2020 bioRxiv Introduction SARS_CoV_2 D614G 46 51 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Using authentic live recombinant viruses, the infectivity and fitness of D614G isogenic virus were compared in primary human cells and its pathogenesis and transmissibility were tested in hamsters and hACE2 mice. 2020 bioRxiv Introduction SARS_CoV_2 D614G 73 78 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Using pseudotype viruses, the D614G mutation has been suggested to increase proteolytic cleavage and S glycoprotein incorporation into virions, reduce S1 loss and promote enhanced infectivity in vitro. 2020 bioRxiv Introduction SARS_CoV_2 D614G 30 35 S 101 115 33067385 Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals. 1D, convalescent plasma from 96.8% of donors (all but one) recognized both SARS-CoV-2 S variants (wild type [WT] and D614G) at baseline. 2020 mBio Introduction SARS_CoV_2 D614G 117 122 S 86 87 33067385 Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals. Interestingly, the MFI values were almost identical for the cells expressing the WT S and those expressing the D614G variant S (7,206 and 7,024, respectively. 2020 mBio Introduction SARS_CoV_2 D614G 111 116 33067385 Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals. Moreover, while the loss of neutralizing activity on the WT and D614G pseudoparticles over time correlated with the loss of anti-RBD IgM, IgA, and IgG antibodies, the correlation was higher for IgM than for IgG and IgA. 2020 mBio Introduction SARS_CoV_2 D614G 64 69 RBD 129 132 33067385 Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals. Neutralizing activity against SARS-CoV-2 WT or D614G S glycoprotein, as measured by the neutralization half-maximum inhibitory dilution (ID50), was detected in 71% of patients 6 weeks after the onset of symptoms. 2020 mBio Introduction SARS_CoV_2 D614G 47 52 S 53 67 33067385 Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals. Of note, while we observed enhanced infectivity for the D614G variant compared to its WT SARS-CoV-2 S counterpart. 2020 mBio Introduction SARS_CoV_2 D614G 56 61 S 100 101 33067385 Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals. S2B), thus suggesting that the D614G change does not affect the overall conformation of the Spike, in agreement with recent findings. 2020 mBio Introduction SARS_CoV_2 D614G 31 36 S 92 97 33067385 Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals. Since the SARS-CoV-2 strain circulating in Europe and North America has the D614G mutation, we also evaluated recognition of this variant by flow cytometry. 2020 mBio Introduction SARS_CoV_2 D614G 76 81 33067385 Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals. The capacity to neutralize SARS-CoV-2 S WT- or D614G-pseudotyped particles significantly correlated with the presence of RBD-specific IgG, IgM, IgA, and anti-S antibodies. 2020 mBio Introduction SARS_CoV_2 D614G 47 52 RBD;S;S 121;38;158 124;39;159 33067385 Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals. We next measured the capacity of plasma samples to neutralize pseudoparticles bearing WT SARS-CoV-2 S, its D614G variant, or vesicular stomatitis virus G (VSV-G) glycoproteins using 293T cells stably expressing ACE2 as target cells. 2020 mBio Introduction SARS_CoV_2 D614G 107 112 S 100 101 33067385 Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals. While this percentage was found to have remained stable 4 weeks later, the level of recognition (mean fluorescence intensity [MFI]) was significantly diminished for both WT and D614G S-expressing cells, indicating that Spike-reactive antibodies were less abundant in convalescent plasma collected at this later time point. 2020 mBio Introduction SARS_CoV_2 D614G 177 182 S;S 219;183 224;184 33072699 Geographical Distribution of Genetic Variants and Lineages of SARS-CoV-2 in Chile. The genetic variants are located in the nucleotide positions 23,403, 26,144, and 28,144 based on the reference sequence NC_045512.2, and the variant's name is represented by a capital letter that corresponds to the amino acid substitution product of the SNP G: Spike:D614G, V: NS3:G251V, S: ORF8:L84S, respectively, and O for other strains that keep some of the nucleotide as the reference strain on that genome position that cannot be assigned to the previous described clades. 2020 Frontiers in public health Introduction SARS_CoV_2 D614G;G251V;L84S 267;281;296 272;286;300 S;ORF8;NS3;S 261;291;277;288 266;295;280;289 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Also, we model the binding of furin to the S protein, where we measured the binding affinities of furin for the S protein (WT and mutant) to understand further the high virulence associated with the D614G substitution. 2021 International journal of infectious diseases Introduction SARS_CoV_2 D614G 199 204 S;S 43;112 44;113 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Furthermore, D614G substitution demonstrated higher titers in pseudoviruses from in vitro assays, thus indicating that the D614G mutant is more infective than the wild type (WT). 2021 International journal of infectious diseases Introduction SARS_CoV_2 D614G;D614G 13;123 18;128 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. In this study, we further analyze the structure of the WT S protein (D614) and a mutant (D614G) to understand the stability of both states using an array of bioinformatics tools and molecular dynamics (MD) simulations. 2021 International journal of infectious diseases Introduction SARS_CoV_2 D614G 89 94 S 58 59 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Initially, the 23403A > G mutation (D614G) found in the G clade S protein was found in the European population. 2021 International journal of infectious diseases Introduction SARS_CoV_2 A23403G;D614G 15;36 25;41 S 64 65 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Recently, showed that patients infected with SARS-CoV-2 D614G mutant had higher levels of viral RNA. 2021 International journal of infectious diseases Introduction SARS_CoV_2 D614G 56 61 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. This mutation has resulted in a number of articles and preprints postulating that isolates containing this 'D614G' mutation have a structural advantage, including as a better substrate to the S1 furin cleavage domain, and are associated with an increase in: (a) transmissibility and viral loads; (b) transduction of human cells; (c) pathogenicity and case fatality. 2020 NPJ vaccines Introduction SARS_CoV_2 D614G 108 113 33083804 Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2. Although not considered a candidate for positive selection in our analysis due to its NCN context, ORF8 S84L is a hub in the larger epistatic network including all strongly associated residues. 2021 bioRxiv Introduction SARS_CoV_2 S84L 104 108 ORF8 99 103 33083804 Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2. Another mutation, S H49Y, less likely to evolve under positive selection but also epistatically linked to S D614G. 2021 bioRxiv Introduction SARS_CoV_2 D614G;H49Y 108;20 113;24 S;S 18;106 19;107 33083804 Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2. Conceivably, the D614G substitution in the spike protein opens up new adaptive routes for later steps in the viral lifecycle, but the specific mechanisms remain to be investigated experimentally. 2021 bioRxiv Introduction SARS_CoV_2 D614G 17 22 S 43 48 33083804 Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2. It is associated with ORF7a Q62*, one of the 6 stop mutations that are observed in at least 10 sequences (Table S5). 2021 bioRxiv Introduction SARS_CoV_2 Q62X 28 32 ORF7a 22 27 33083804 Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2. Spike D614G is thought to increase the infectivity of the virus, possibly, by increasing the binding affinity between the spike protein and the cell receptor. 2021 bioRxiv Introduction SARS_CoV_2 D614G 6 11 S;S 0;122 5;127 33083804 Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2. Strikingly, D614G in the spike protein is associated with exceptionally many interactions and is the main hub of the network. 2021 bioRxiv Introduction SARS_CoV_2 D614G 12 17 S 25 30 33083804 Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2. The majority of the mutations in the epistatic cluster of D614G are located in the non-structural polyprotein (orf1ab) and thus are even less amenable to direct interpretation. 2021 bioRxiv Introduction SARS_CoV_2 D614G 58 63 ORF1ab 111 117 33083804 Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2. The rest of the connections of S84L are with mutations in orf1ab which, as in the case of D614G, implies uncharacterized functional links between virus-host interactions and virus replication. 2021 bioRxiv Introduction SARS_CoV_2 D614G;S84L 90;31 95;35 ORF1ab 58 64 33083804 Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2. The well known D614G site in the spike protein is part of these signatures, and so are two adjacent sites in the nucleocapsid protein (see below). 2021 bioRxiv Introduction SARS_CoV_2 D614G 15 20 N;S 113;33 125;38 33083804 Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2. Two non-synonymous mutations linked to spike 614G in this network, S R21I and S L54H, are in the spike protein itself though we were unable to validate physical interaction through structural analysis. 2021 bioRxiv Introduction SARS_CoV_2 L54H;R21I 80;69 84;73 S;S;S;S 39;97;67;78 44;102;68;79 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. 4 Additionally, along with the occurrence of S139A and F140A mutations, the structure of SARS-CoV 3CLpro altered remarkably, followed by the decrease of its enzyme activity. 2021 Journal of medical virology Introduction SARS_CoV_2 F140A;S139A 56;46 61;51 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. Besides, mutations I529T and D510G in MERS-CoV S reduced the binding affinity of the receptor-binding domain (RBD)-CD26, respectively, which impaired the virulence of the virus. 2021 Journal of medical virology Introduction SARS_CoV_2 D510G;I529T 30;20 35;25 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. Five substitutions (ORF1a-R226K, ORF1a-E1126K, ORF1a-L3930F, S-V1176F, and ORF7b-V21I) were observed uniquely in 2 sequences of lineage B.1.1.28. 2020 Microbiology resource announcements Introduction SARS_CoV_2 E1126K;L3930F;R226K;V1176F;V21I 39;53;26;63;81 45;59;31;69;85 ORF1a;ORF1a;ORF1a;ORF7b;S 20;33;47;75;61 25;38;52;80;62 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. Four amino acid substitutions (ORF1b-P314L, S-D614G, N-R203K, and N-G204R) unique to clade GR (both lineages B.1.1 and B.1.1.28) were seen in all our sequences in this clade. 2020 Microbiology resource announcements Introduction SARS_CoV_2 D614G;G204R;P314L;R203K 46;68;37;55 51;73;42;60 N;N;S 53;66;44 54;67;45 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. From the same set of data, lineage B.1.1 containing D614G was found in a sample collected on 25 June 2020. 2020 Microbiology resource announcements Introduction SARS_CoV_2 D614G 52 57 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. None of the Philippine SARS-CoV-2 sequences in GISAID (accessed 22 August 2020) with a collection date before 25 June 2020 contained the D614G mutation. 2020 Microbiology resource announcements Introduction SARS_CoV_2 D614G 137 142 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. The D614G mutation is currently the most prevalent variant worldwide and is associated with higher viral RNA levels and titers of pseudoviruses. 2020 Microbiology resource announcements Introduction SARS_CoV_2 D614G 4 9 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. The D614G mutation is replacing and rapidly surpassing in prevalence the original strain circulating prior to June 2020 and may partially explain the rapid rise of cases in the Philippines. 2020 Microbiology resource announcements Introduction SARS_CoV_2 D614G 4 9 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. This observation coincides with our findings that the D614G mutation was observed in samples collected in June 2020. 2020 Microbiology resource announcements Introduction SARS_CoV_2 D614G 54 59 33105685 Viewpoint: Origin of SARS-CoV-2. Although human Coronaviruses frequently contain "hot spots" for non-synonymous amino acid replacements affecting host tropism/adaptation, resistance to neutralizing antibodies and immune evasion, only a single high-frequency non-synonymous mutation (D614G) has been identified from clinical SARS-CoV-2 isolates. 2020 Viruses Introduction SARS_CoV_2 D614G 250 255 33105685 Viewpoint: Origin of SARS-CoV-2. Furthermore, it has been demonstrated that the D614G mutation in the SARS-CoV-2 S protein reduced S1 shedding and increased infectivity. 2020 Viruses Introduction SARS_CoV_2 D614G 47 52 S 80 81 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. For SARS-CoV-2, analyses of over 28,000 spike gene sequences in May 2020 revealed a D614G amino acid substitution that was rare before March but increased in frequency as the pandemic spread, reaching over 74% of all published sequences by June 2020. 2021 Nature Introduction SARS_CoV_2 D614G 84 89 S 40 45 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. However, these results need to be confirmed in studies with authentic SARS-CoV-2 containing the D614G variant, and also using in vivo studies with a suitable animal model. 2021 Nature Introduction SARS_CoV_2 D614G 96 101 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. Initial phenotypic characterizations of the D614G spike substitution were performed using pseudotyped viruses, whereby vesicular stomatitis virus (VSV) and lentiviral particles incorporating the SARS-CoV-2 spike protein were studied by replication kinetics. 2021 Nature Introduction SARS_CoV_2 D614G 44 49 S;S 50;206 55;211 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. The association of spike amino acid substitutions with coronavirus transmissibility suggested that the D614G substitution was critical to this putative selective sweep. 2021 Nature Introduction SARS_CoV_2 D614G 103 108 S 19 24 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. The D614G substitution was accompanied by three other mutations: a C-to-T mutation in the 5' untranslated region at position 241, a synonymous C-to-T mutation at position 3,037, and a nonsynonymous C-to-T mutation at position 14,408 in the RNA-dependent RNA polymerase gene. 2021 Nature Introduction SARS_CoV_2 D614G 4 9 RdRp 240 268 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. Therefore, using an infectious cDNA clone for SARS-CoV-2, we generated the D614G substitution in the USA-WA1/2020 strain and performed experimental comparisons using in vitro cell culture, primary human 3D airway tissue, and a hamster infection model. 2021 Nature Introduction SARS_CoV_2 D614G 75 80 33106822 COVID-19 neutralizing antibodies predict disease severity and survival. One mutation, D614G, has rapidly become the predominant transmitted variant by outcompeting wildtype infections. 2020 medRxiv Introduction SARS_CoV_2 D614G 14 19 33109270 Molecular detection of drug resistant polymorphisms in Plasmodium falciparum isolates from Southwest, Nigeria. A single point mutation K76T, in codons 72-76 of the chloroquine resistance transporter gene (Pfcrt) has been the main cause of resistance to CQ, while mutations in the dihydrofolate reductase (DHFR) and dihydropteroate synthase (DHPS) were responsible for SP resistance in parasites. 2020 BMC research notes Introduction SARS_CoV_2 K76T 24 28 S 257 259 33109270 Molecular detection of drug resistant polymorphisms in Plasmodium falciparum isolates from Southwest, Nigeria. Alleles of Pfk13 propeller domain polymorphisms (Y493H, R539T, I543T, C580Y), and PfATPase6 (S679S, M699V, S769M) associated with delayed clearance were determined by Taqman allelic discrimination and sequencing and list of primers used provided in Additional file 1: (Tables S1, 2). 2020 BMC research notes Introduction SARS_CoV_2 C580Y;I543T;M699V;R539T;S769M;S679S;Y493H 70;63;100;56;107;93;49 75;68;105;61;112;98;54 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. Clade B was derived from clade A by a synonymous T8782C mutation in ORF1ab and a nonsynonymous C28144T mutation that changes a leucine to serine in ORF8. 2020 Cell reports Introduction SARS_CoV_2 C28144T;T8782C 95;49 102;55 ORF1ab;ORF8 68;148 74;152 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. Clade C was derived from clade B by a nonsynonymous G26144T mutation that changes a glycine to valine in ORF3a. 2020 Cell reports Introduction SARS_CoV_2 G26144T 52 59 ORF3a 105 110 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. Phylogenetic analyses established the dominance of the S protein D614G SNV among this population, which has been increasing over time through community spread and was introduced initially by a person returning from Europe. 2020 Cell reports Introduction SARS_CoV_2 D614G 65 70 S 55 56 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. According to Nextstrain, almost all sequences in clade 19B are characterized by the presence of L84S in ORF8 (GISAID clade S), whereas the clades that emerged in 2020 (20A, 20B, and 20C) are characterized by D614G in the S protein (GISAID clade G). 2021 Journal of virology Introduction SARS_CoV_2 D614G;L84S 208;96 213;100 ORF8;S;S 104;123;221 108;124;222 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. Three other clades appeared in 2020: 20A, distinguished from 19A by the substitutions C3037T, C14408T, and A23403G; 20B, characterized by three consecutive substitutions (G28881A, G28882A, and G28883C); and 20C, distinguished by the substitutions C1059T and G25563T. 2021 Journal of virology Introduction SARS_CoV_2 A23403G;C1059T;C14408T;C3037T;G25563T;G28882A;G28883C;G28881A 107;247;94;86;258;180;193;171 114;253;101;92;265;187;200;178 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. Two emerged in 2019: 19A, which is considered the root clade, and 19B, marked by substitutions C8782T and T28144C. 2021 Journal of virology Introduction SARS_CoV_2 C8782T;T28144C 95;106 101;113 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. A variant carrying the Spike D614G mutation stands out as a remarkable example, as it became dominant worldwide during the first months of the pandemic with recent studies suggesting that the G614 variant might be linked to an increased transmissibility but not pathogenicity. 2020 Emerging microbes & infections Introduction SARS_CoV_2 D614G 29 34 S 23 28 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. After the globally dispersed Spike D614G mutation, this is the first study reporting the superspread of a Spike variant with a tremendous epidemiological impact at country level. 2020 Emerging microbes & infections Introduction SARS_CoV_2 D614G 35 40 S;S 29;106 34;111 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Here, we evaluated the temporal and geographical spread of a SARS-CoV-2 variant carrying the Spike protein amino acid change D839Y that had a massive dissemination during the early COVID-19 epidemic in Portugal after its introduction from Italy in mid-late February. 2020 Emerging microbes & infections Introduction SARS_CoV_2 D839Y 125 130 S 93 98 COVID-19 181 189 33132795 [The virology of SARS-CoV-2]. Fur D614G wird aktuell keine Auswirkung auf Diagnostik, Impfstoff- oder DAA-Wirksamkeit befurchtet. 2020 Der Pneumologe Introduction SARS_CoV_2 D614G 4 9 33132795 [The virology of SARS-CoV-2]. Zu vorherrschenden Linien entwickelten sich dabei solche SARS-CoV-2-Viren, die auf den prominent aus dem Virus herausragenden ,,S spikes" die Mutation D614G tragen. 2020 Der Pneumologe Introduction SARS_CoV_2 D614G 151 156 S;S 130;128 136;129 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. S-D614G is a protein variant containing a substitution in the S protein outside of the RBD and is thought to cause a conformational change. 2020 bioRxiv Introduction SARS_CoV_2 D614G 2 7 RBD;S;S 87;0;62 90;1;63 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. The data show that the S-D614G substitution confers increased binding to the hACE2 receptor and increased replication in primary human airway epithelial cultures. 2020 bioRxiv Introduction SARS_CoV_2 D614G 25 30 S 23 24 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. To better address the role that the S-D614G substitution has played in the dissemination and predominance of this SARS-CoV-2 variant during the COVID-19 pandemic, we characterized S protein binding to human ACE2 (hACE2) and replication kinetics in vitro, and evaluated infection and transmission dynamics in vivo using three different animal models. 2020 bioRxiv Introduction SARS_CoV_2 D614G 38 43 S;S 36;180 37;181 COVID-19 144 152 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. For A(H1N1)pdm09 virus, the D225G substitution of haemagglutinin was more enriched in the lower respiratory tract specimens because this substitution enables the virus to bind more efficiently to alpha2,3 sialic acid receptors that are predominantly found in the alveoli. 2021 Clinical microbiology and infection Introduction SARS_CoV_2 D225G 28 33 33144890 [The virology of SARS-CoV-2]. Fur D614G wird aktuell keine Auswirkung auf Diagnostik, Impfstoff- oder DAA-Wirksamkeit befurchtet. 2020 Der Gastroenterologe Introduction SARS_CoV_2 D614G 4 9 33144890 [The virology of SARS-CoV-2]. Zur vorherrschenden Linie entwickelten sich dabei solche SARS-CoV-2-Viren, die auf den prominent aus dem Virus herausragenden S-Spikes die Mutation D614G tragen. 2020 Der Gastroenterologe Introduction SARS_CoV_2 D614G 148 153 S;S 128;126 134;127 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. From the beginning of the COVID-19 epidemic, many articles published on the evaluation of D614G mutation in SARS-CoV-2. 2020 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 90 95 COVID-19 26 34 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. Given that D614G is the most important among all detected mutations, here we evaluated and optimized a fast and inexpensive method for detection of this mutation in SARS-CoV-2 in clinical samples. 2020 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 11 16 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. One of the most critical mutations is D614G in the spike protein gene. 2020 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 38 43 S 51 56 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. 11083G>T was found in Vietnam 2 months after the first confirmed cases, which resulted in a low 11083G>T mutation ratio. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 96 104 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. A piece of recent news reported that half of the COVID-19 cases in Singapore are symptomless, which matches our finding that mutation 11083G>T-(L37F) is relevant to asymptomatic infections. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 134;144 142;148 COVID-19 49 57 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. After genotyping 537 sequences with asymptomatic and symptomatic records, we find that 11083G>T is significantly relevant to the asymptomatic infection. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 87 95 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. After that, fewer cases were collected in New York, and the 11083G>T mutation ratio decreased. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 60 68 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Almost all of the cases collected after the beginning of April have the 11083G>T mutation with asymptomatic infections recorded, which may be the most robust evidence to associate the SARS-CoV-2 11083G>T or L37F mutation on NSP6 with the asymptomatic infections. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;G11083T;L37F 72;195;207 80;203;211 Nsp6 224 228 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Also, the state of Washington had a small proportion of the 11083G>T mutation before May 26, 2020. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 60 68 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Although the 11083G>T mutation has arrived in the United States and the United Kingdom at a very early stage, different subtypes of SARS-CoV-2 spread vastly due to their large population, which makes the 11083G>T mutation nondominant. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;G11083T 13;204 21;212 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Among them, 241C>T, 3037C>T, 14408C>T, 23403A>G, 11083G>T, 28881G>A, 28882G>A, and 28883G>C have a frequency greater than 5000. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;C14408T;A23403G;C241T;G28881A;G28882A;G28883C;C3037T 49;29;39;12;59;69;83;20 57;37;47;18;67;77;91;27 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. As a result, mutation L37F can stiffen the NSP6 structure by the aromatic-aromatic, hydrophobic, or pi-stacking interactions. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 L37F 22 26 Nsp6 43 47 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. As shown in Table 4, a negative folding stability change DeltaDeltaG is found for the mutation, indicating a destabilizing mutation L37F for NSP6. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 L37F 132 136 Nsp6 141 145 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. At this stage, 728 genome isolates from the United States in our data set are relevant to 11083G>T. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 90 98 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. By analyzing the distribution of 11083G>T in various countries, we unveil that the 11083G>T mutation may be correlated with the asymptomatic infection and the hypotoxicity of SARS-CoV-2. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;G11083T 33;83 41;91 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. By employing the graph network analysis and topology-based mutation predictor, we find that 11083G>T-(L37F) destabilizes the structure of NSP6 proteinwise. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 92;102 100;106 Nsp6 138 142 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. By genotyping 537 genome samples, we find that mutation 11083G>T is significantly relevant to asymptomatic infection with a p-value being much smaller than 0.05. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 56 64 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. China's COVID-19 epicenter, Wuhan, implemented a lockdown on January 23, 2020, which explains why China has a relatively low ratio of the 11083G>T-(L37F) mutation. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 138;148 146;152 COVID-19 8 16 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Considering the sequence alignment in Figure 4(c), we have also carried out a similar calculation for the mutation of L37 V: DeltaDeltaG = -0.74 kcal/mol. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 L37V 118 123 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Figure 2 illustrates the number of complete SARS-CoV-2 sequences in our data set with 11083G>T-(L37F) detected versus the number of complete SARS-CoV-2 sequences without 11083G>T-(L37F) detected every 14 days in China, Japan, Singapore, India, the United Kingdom, Malaysia, the United States, Australia, and Spain as well as in two states in the United States: New York and Washington. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;G11083T;L37F;L37F 86;170;96;180 94;178;100;184 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Figure 3(a) generated by Highcharts illustrates the distribution and proportion of the 11083G>T-(L37F) mutation in the United States. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 L37F 97 101 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Figure 3(b) displays the potential age and gender disparities in mutation 11083G>T-(L37F). 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 74;84 82;88 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Figure 3(c) created by using Highcharts illustrates the distribution and proportion of the 11083G>T-(L37F) mutation in the world. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 91;101 99;105 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. For example, Japan has a relatively high ratio of 11083G>T-(L37F), while the death ratio is 1.77%. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 50;60 58;64 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. For example, Singapore has the second-highest 11083G>T-(L37F) mutation ratio as of 0.673. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 46;56 54;60 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. France is the next country that found the 11083G>T mutation at an early stage. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 42 50 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. From May 26 to June 09, 52 out of 695 genome sequences had mutation 11083G>T, which may indicate that the asymptomatic infection may be becoming increasingly prevalent in Washington. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 68 76 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Furthermore, the analysis of the distribution of 11083G>T for different ages and genders unveils that the 11083G>T-driven mutation does not exhibit host-dependent behavior. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;G11083T 49;106 57;114 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Furthermore, we track the global transmission pathways of the single mutation 11083G>T-(L37F) to understand its spread dynamics. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 78;88 86;92 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Globally, the ratio of samples with the 11083G>T mutation over all samples, shown in the middle chart of the last row in Figure 2, decays over time, suggesting that the mutation is unfavorable to viral transmission. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 40 48 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. However, except for 11083G>T, the other mutations that pass the multiple hypothesis test appear in only three sequences with asymptomatic labels. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 20 28 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. However, the first genome isolates related to mutation 11083G>T in our data set were collected on March 17, 2020. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 55 63 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. In Jordan, the earliest sequence released on GISAID was on March 16, 2020, with the 11083G>T mutation, which indicates the high 11083G>T ratio in Jordan. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;G11083T 84;128 92;136 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. In mutation 11083G>T-(L37F), both leucine and phenylalanine are alpha-amino acids and nonpolar. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 12;22 20;26 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. In the following sections, we investigate the relationship between mutation 11083G>T-(L37F) and asymptomatic infections using both gene-specific analysis and protein-specific analysis. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 76;86 84;90 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. In total, 65 genome samples are related to 11083G>T among 1512 samples that were collected before May 12 in New York. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 43 51 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. India is one of the countries that also have a large number of 11083G>T mutation cases. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 63 71 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Interestingly, the first genome sequence related to mutation 11083G>T-(L37F) was found in Singapore on January 29, 2020, only a few days after the first confirmed cases. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 61;71 69;75 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. It is of paramount importance to understand how NSP6 mutation L37F leads to COVID-19 asymptomatic transmission and reduced virulence. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 L37F 62 66 Nsp6 48 52 COVID-19 76 84 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. It was reported on June 1, 2020 that 80% of all COVID-19 patients in India were asymptomatic or showed mild symptoms, which supports our deduction that 11083G>T correlates with asymptomatic infection. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 152 160 COVID-19 48 56 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Moreover, one can see that mutation 11083G>T in China, the United Kingdom, and Australia is not as abundant as in Singapore, Japan, and South Korea. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 36 44 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Moreover, seven network models are utilized to analyze the L37F mutation in NSP6 as shown in Table 4. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 L37F 59 63 Nsp6 76 80 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Moreover, Singapore has the lowest death ratio as listed in Table 3, suggesting that single mutation 11083G>T-(L37F) may have weakened the SARS-CoV-2 virulence. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 101;111 109;115 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Moreover, the p-value is 5.42 x 10-56, which reveals the significant relevance between asymptomatic and single mutation 11083G>T-(L37F). 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 120;130 128;134 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Moreover, we track the dynamics of the 11083G>T mutation ratio globally and discover its decaying tendency, indicating that the 11083G>T mutation hinders SARS-CoV-2 transmission. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;G11083T 39;128 47;136 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Most of the other countries have a small proportion of mutation 11083G>T-(L37F). 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 64;74 72;78 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Mutation 11083G>T changes leucine (L) residue at position 37 of NSP6 to phenylalanine (F), denoted as L37F. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F;L37L 9;102;25 17;106;61 Nsp6 64 68 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Mutation 11083G>T was also detected in a commutation record [8782C>T, 11083G>T, 28144T>C] in Yunnan, China 1 day earlier than Chongqing's sequence, which indicates that the true ancestor of 11083G>T might have occurred earlier than January 18, 2020. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;G11083T;G11083T;T28144C;C8782T 9;70;190;80;61 17;78;198;88;68 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Mutation 11083G>T-(L37F) dominated in only a few countries such as Japan, Singapore, Pakistan, Jamaica, Kenya, Belarus, and Brunei. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 9;19 17;23 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Mutation 11083G>T-(L37F) first appeared in the United States on January 22, 2020 in Arizona in a 26-year-old male with comutations [8782C>T, 11083G>T, 28144T>C, 29095C>T], which is the descendant of [8782C>T, 11083G>T, 28144T>C] found in China. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;G11083T;G11083T;T28144C;T28144C;C29095T;L37F;C8782T;C8782T 9;141;209;151;219;161;19;132;200 17;149;217;159;227;169;23;139;207 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Next, we split our genotyping data set of 75 775 sequences into different countries and extract those records with the 11083G>T mutation. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 119 127 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Note that although Russia has the lowest 11083G>T-(L37F) mutation ratio lists in Table 3, its 1.72% death ratio caused by COVID-19 is also relatively low. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 41;51 49;55 COVID-19 122 130 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Note that in Figure 2 China, the United States, and Spain have relatively lower occurrences of 11083G>T, which may contribute to their relatively high death ratios. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 95 103 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. One can see that Alaska, Texas, Oregon, and Ohio have higher proportion of 11083G>T than do the other states. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 75 83 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. One may be due to the hypotoxicity of SARS-CoV-2 caused by mutation 11083G>T. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 68 76 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Overall, male cases have a slightly higher ratio of the 11083G>T-(L37F) mutation than female cases. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 56;66 64;70 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Red and blue represent the 11083G>T-(L37F) mutation and non-11083G>T mutations, respectively. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F;G11083T 27;37;60 35;41;68 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Similarly, the United Kingdom has the highest death ratio, but its ratio of mutation 11083G>T-(L37F) is not in the last echelon. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 85;95 93;99 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Since then, more records related to 11083G>T have appeared in the United States. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 36 44 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Singapore and Malaysia's plots show that 11083G>T was widely found after mid-March, which is consistent with the report saying that at least half of Singapore's newly discovered COVID-19 cases show no symptoms. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 41 49 COVID-19 178 186 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Table 3 suggests that the 11083G>T-(L37F) ratio may be one of the factors affecting the death ratio. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 26;36 34;40 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Table 3 summarizes the total number of sequences related to 11083G>T-(L37F), denoted as NL37F, the total number of sequences NS, the 11083G>T-(L37F) ratio, the number of total cases, the number of total deaths, and the death ratio of 20 countries up to October 19, 2020. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;G11083T;L37F;L37F 60;133;70;143 68;141;74;147 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. The 11083G>T mutation leads the leucine (L) residue at position 37 of NSP6, changing to phenylalanine (F). 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37L 4;31 12;67 Nsp6 70 74 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. The blue and red bars represent the 11083G>T-(L37F) counts and other mutation counts every 14-day period, respectively. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 36;46 44;50 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. The death ratios in the United Kingdom, Belgium, France, and Spain are even higher than 3%, which supports our assumption that mutation 11083G>T-(L37F) may weaken the SARS-CoV-2 virulence. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 136;146 144;150 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. The odds ratio and p-value are 33.39 and 8.45 x 10-35, which confirm the significant relevance between asymptomatic and single mutation 11083G>T-(L37F). 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 136;146 144;150 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. The prevalence of the 11083G>T-(L37F) mutation in Singapore's SARS-CoV-2 infections explains its low death ratio. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 22;32 30;36 COVID-19 62 83 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. The quadruplet phenylalanine resulting from mutation L37F can significantly reduce NSP6's interactions with ER. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 L37F 53 57 Nsp6 83 87 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. The relatively high 11083G>T-(L37F) mutation ratio (greater than 0.135) with a correspondingly low death ratio (less than 2.70%) further validates that 11083G>T-(L37F) may be relevant to the asymptomatic-induced hypotoxicity of SARS-CoV-2. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;G11083T;L37F;L37F 20;152;30;162 28;160;34;166 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. The statistical analysis shows that the Pearson correlation coefficient between asymptomatic records and 10083G>T is 0.61. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G10083T 105 113 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Therefore, the transmission of COVID-19 in Singapore in the initial stage contains a large proportion of the11083G>T-(L37F) mutation. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 L37F;G11083T 118;108 122;116 COVID-19 31 39 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Therefore, there will be four continuous phenylalanine amino acid FFFFs after the L37F mutation. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 L37F 82 86 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Therefore, this destabilized mutation may result in the inefficiency of NSP6 in participating in viral protein folding, viral assembly, and the replication cycle, which underpins our deduction that 11083G>T-(L37F) may be relevant to the asymptomatic infections and weaken the SARS-CoV-2 virulence. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 198;208 206;212 Nsp6 72 76 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Therefore, we conclude that mutation 11083G>T-(L37F) is quite evenly distributed over age and gender groups, implying that the mutation does not exhibit host-dependent behavior. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 37;47 45;51 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Therefore, we say that 11083G>T is the only mutation that has significant relevance to being asymptomatic. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T 23 31 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. This work parses 75 775 complete genome isolates of SARS-CoV-2 and for the first time reveals the relationship between asymptomatic cases and a single nucleotide mutation 11083G>T-(L37F) on NSP6. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 171;181 179;185 Nsp6 190 194 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. To further understand the impact of mutation L37F on NSP6, we carry out several theoretical analyses using AI, TDA, the flexibility and rigidity index (FRI), and a large number of other network theory models. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 L37F 45 49 Nsp6 53 57 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Together with the FRI rigidity index and the protein folding stability changes, these network assessments show that NSP6 becomes unstable and less functional after the L37F mutation. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 L37F 168 172 Nsp6 116 120 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Two abnormal peaks appearing on February 18 and June 9 in the ratio were due to the L37F mutation counts from Japan and Washington, respectively. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 L37F 84 88 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. Using artificial intelligence (AI), topological data analysis (TDA), and a variety of network models, we further demonstrate that mutation L37F disrupts the folding stability of NSP6. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 L37F 139 143 Nsp6 178 182 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. We also analyze the global transmission and find the decay tendency of NSP6 mutation L37F. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 L37F 85 89 Nsp6 71 75 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. We demonstrate that the evolutionary dynamics of L37F is age- and gender-independent. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 L37F 49 53 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. We found that the first genome containing single mutation 11083G>T-(L37F) was sequenced in Chongqing, China on January 18, 2020, which can be considered to be the ancestor of 11083G>T in our data set. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;G11083T;L37F 58;175;68 66;183;72 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. We reveal a significant correlation between asymptomatic infections and SARS-CoV-2 single mutation 11083G>T-(L37F) on NSP6. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 G11083T;L37F 99;109 107;113 Nsp6 118 122 33179934 Decoding Asymptomatic COVID-19 Infection and Transmission. We uncover the correlation between NSP6 mutation L37F and weakened SARS-CoV-2 virulence. 2020 The journal of physical chemistry letters Introduction SARS_CoV_2 L37F 49 53 Nsp6 35 39 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. After three continuous passages at 72h intervals, the D614G variant became dominant in the cultures regardless of whether the WT virus was at a 1:1 or 10:1 ratio over the isogenic D614G mutant. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G;D614G 54;180 59;185 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. After three continuous passages in naive animals at 3-day intervals, we observed the D614G became dominant in the lung tissues of animals after the 1st passage of all groups. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 85 90 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Although the D614G variant showed similar or slightly higher titers at the early time point (8h), its peak titers were ~0.5 logs lower than the ancestral WT virus in Vero-E6 and A549-ACE2 cell lines but not in Vero-81 and Huh7. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 13 18 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Both WT and D614G viruses were transmitted efficiently to naive hamsters evident by positive nasal wash samples detected in all exposed animals at day 4. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 12 17 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Consistent with previous pseudotype virus studies, our data show that the D614G recombinant virus enters immortalized cell lines more efficiently than the WT virus. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 74 79 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Consistent with previous studies, we showed overall equivalent sensitivity of the both luciferase reporter viruses to the 25 convalescent human sera and 6 RBD-binding mAbs, suggesting the D614G substitution does not significantly shift SARS-CoV-2 neutralization properties. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 188 193 RBD 155 158 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Cultures from the same donor were infected with either WT or D614G virus in triplicate. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 61 66 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Despite the presence of a CoV proof-reading function in viral replication, recent reports identified an emergent D614G substitution in the spike glycoprotein of SARS-CoV-2 strains that is now the most prevalent form globally. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 113 118 S 139 157 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Equivalent virus titers were measured in the lungs and nasal turbinates of all time points, and similar severity of lesions were observed in the histopathological samples, suggesting the D614G substitution doesn't significantly enhance the SARS-CoV-2 pathogenesis in both animal models, although this phenotype needs to be confirmed in both sexes of animals in future studies. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 187 192 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Further, we evaluated the neutralization properties of convalescent human serum samples (n=25) using the nLuc-expressing recombinant SARS-CoV-2 encoding either WT or D614G spike (Fig 2G and 2H). 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 166 171 S 172 177 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Growth curves comparing WT and D614G viruses were performed in those cell lines (Fig 1C). 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 31 36 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. However, five of eight hamsters exposed to the D614G-infected group showed infection and detectable viral shedding at day 2 while those exposed to the WT-infected group had no infection and viral shedding (p = 0.0256, Fisher exact test), supporting the hypothesis that the D614G variant transmits significantly faster than the WT virus between hamsters. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G;D614G 47;273 52;278 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. However, the D614G substitution has yet to be evaluated in the authentic SARS-CoV-2 infection models, and its functions in viral replication, pathogenesis and transmissibility remain unclear. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 13 18 COVID-19 73 93 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. However, the D614G-infected hamsters lost slightly more body weight than those infected with the WT virus. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 13 18 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. However, the increased weight loss and improved in vivo replication fitness in hamsters suggest the D614G variant may cause marginally enhanced disease outcomes. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 100 105 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. However, we didn't observe the enhancement of viral titers in continuous replication kinetics, suggesting the variable ACE2 and protease levels between different cell lines and the virion thermostability may also affect to the D614G replication in vitro. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 227 232 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Importantly, the efficient replication and fitness in our ex vivo models suggest that SARS-CoV-2 D614G isogenic virus displays a significant advantage in epithelial cells in the nose and upper respiratory tract. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 97 102 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Importantly, we demonstrate that the D614G variant transmits significantly faster between hamsters through aerosol and droplets. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 37 42 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. In accord with pseudovirus studies, the D614G-nLuc infection resulted in a 3.7 to 8.2-fold higher transgene expression as compared with WT-nLuc virus in different cell lines. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 40 45 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. In the backdrop of a full complement of SARS-CoV-2 structural proteins, our study demonstrated no obvious differences in proteolytic processing or S incorporation into isogenic virions encoding the D614G mutations, perhaps reflecting differences in S trimer incorporation and presentation between authentic and pseuotyped viruses; the latter lack a full component of virion proteins. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 198 203 S;S 147;249 148;250 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. In the hamster transmission study, the D614G isogenic transmitted significantly faster to adjacent animals early in infection, showing that the substitution preserved efficient transmission in vivo. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 39 44 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. In this study, we evaluated the pathogenesis of the D614G variants in both hACE2 mouse and hamster models. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 52 57 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Paired t-test analysis suggests the D614G-infected HNE at 24, 48 and 72 hours, and LAE cultures at 48 hours exhibited statistically higher titers than those infected with the WT virus. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 36 41 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Patients infected with the D614G variant are associated with higher upper respiratory tract viral loads than seen with the ancestral strain, but not altered disease severity. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 27 32 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Patients infected with the D614G virus have not been conclusively linked to increased disease severity. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 27 32 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Potential reasons for this phenotype could be that the D614G variant exhibits lower minimum infectious dose to animals and/or to subtle variations in virion stability in small/large droplets, which requires further mechanistic studies in the future. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 55 60 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Recent studies indicate that D614G alters spike trimer hydrogen-bond interactions, reorienting the RBD into an "up" conformation, increasing ACE2 receptor binding and infectivity. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 29 34 S;RBD 42;99 47;102 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. S2C and S2D), consistent with the phenotype of enhanced fitness of the D614G virus noted in the human LAE competition assay. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 71 76 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. SARS-CoV-2 S pseudotyped viruses encoding the D614G substitution were reported to exhibit increased infectivity in continuous cell lines and increased sensitivity to neutralization. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 46 51 S 11 12 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Taken together, these data suggest the D614G substitution enhances SARS-CoV-2 replication fitness in the primary epithelial cells, with an advantage in the upper respiratory tract epithelial cells in nasal and large (proximal) airway epithelia that express higher levels of hACE2 receptor. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 39 44 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. The effect of the D614G variant on vaccine efficacy has been of major concern. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 18 23 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. The emergent D614G mutation in the spike gene of SARS-CoV-2 strains has raised significant concerns about potential enhancements in transmissibility, antigenicity, and/or pathogenesis. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 13 18 S 35 40 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. The relationship between increased transmission and virulence remains complex and could be impacted by age, sex and other comorbidities, and it is unclear whether the minimum infectious dose may be lower for D614G in humans. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 208 213 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. These data also suggest that the current vaccine approaches directed against WT spike should be effective against the D614G strains. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 118 123 S 80 85 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. These data support the role of the nasal epithelium and the D614G substitution in enhanced infectivity and transmission in human populations. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 60 65 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. These studies indicate that the D614G substitution contributes to marginal enhancement of SARS-CoV-2 pathogenesis in hamsters, but not in hACE2 mice, and to improved competitive fitness in the hamster model. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 32 37 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. To address these questions, we generated an isogenic SARS-CoV-2 variant containing only the D614G substitution in the S glycoprotein, along with a second variant that contained the nanoLuciferease (nLuc) gene in place of accessory gene 7a (Fig 1A), using a D614-form SARS-CoV-2 strain WA1 as the backbone. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 92 97 S 118 132 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. To evaluate the impact of the D614G substitution in SARS-CoV-2 respiratory transmissibility, we set up eight pairs of hamsters for each virus similar to previously studies. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 30 35 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. To evaluate the replication of SARS-CoV-2 D614G variant in the human respiratory tract, we compared the multi-step growth kinetics (MOI = 0.1) of the WT and D614G viruses in ex vivo primary human nasal epithelial (HNE) cells from five donors, large (proximal) airway epithelial (LAE) cells from four donors, and distal lung small airway epithelial (SAE) cells from three donors. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G;D614G 42;157 47;162 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. To evaluate the role of the D614G substitution in viral pathogenesis, hACE2 transgenic mice and Syrian hamsters were infected with equal plaque-forming units (PFU) of WT or D614G viruses. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G;D614G 28;173 33;178 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. To evaluate the roles of the D614G variant replication fitness in vivo, we performed a competition assay in four independent lines of hamsters. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 29 34 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. To examine whether the D614G substitution enhances authentic SARS-CoV-2 entry, four susceptible cell lines were infected with the ancestral wild-type (WT)-nLuc and D614G-nLuc viruses and maintained in the medium containing neutralizing antibodies to limit viral spreading. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G;D614G 23;164 28;169 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Together, these data suggest that the D614G substitution doesn't alter significantly SARS-CoV-2 morphology, spike cleavage pattern and in vitro neutralization properties in the context of live virus. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 38 43 S 108 113 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Two groups of hACE2 mice infected with WT or D614G viruses exhibited undetectable viral titers in nasal turbinates and similar lung viral titers at day 2 and 5 post infection. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 45 50 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Using authentic SARS-CoV-2 isogenic variants, we show the role of the D614G substitution in enhancing viral infectivity in immortalized cell lines, growth, and fitness in primary human airway epithelial cells and hamsters, yet, it marginally alters viral pathogenesis in hamster and hACE2 mouse models. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 70 75 33184236 SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo. Using pseudotype viruses, the D614G substitution has been suggested to increase proteolytic cleavage and S glycoprotein incorporation into virions, reduce S1 loss and promote enhanced infectivity in vitro. 2020 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 30 35 S 105 119 33185784 Comparison of Binding Site of Remdesivir and Its Metabolites with NSP12-NSP7-NSP8, and NSP3 of SARS CoV-2 Virus and Alternative Potential Drugs for COVID-19 Treatment. It was reported that the D614G mutation reduces S1 shedding and increases infectivity. 2020 The protein journal Introduction SARS_CoV_2 D614G 25 30 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. Herein we discuss the importance of the Spike D614G mutation in terms of the epidemiology of SARS CoV-2 infection and its impact for the immune response and vaccine design. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 46 51 S 40 45 COVID-19 93 113 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. However, analysis of clinical data from the Sheffield cohort showed no relationship between the D614G mutation and disease severity (such as the need for hospital admission or transfer to the Intensive Care Unit). 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 96 101 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. However, antigenic drift is known to occur among the endemic human coronaviruses, and during the first SARS outbreak in 2003, a single amino acid mutation in SARS-CoV (D480 A/G) within the receptor binding domain (RBD) of the Spike (S) protein became the dominant variant due to its ability to escape from neutralising antibodies. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D480A;D480G 168;168 176;176 RBD;S;RBD;S 189;226;214;233 212;231;217;234 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. Identification of the D614G mutation and its clinical associations. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 22 27 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. Impact of the D614G mutation on spike protein structure and interactions with host cells. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 14 19 S 32 37 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. More recent studies suggest that the D614G variant is close to reaching fixation around the world. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 37 42 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. None of these epitopes spans the D614G position which might suggest that the mutation does not induce T cell escape, but more studies are needed to map T-cell epitopes in Spike in different populations with distinct HLA repertoires which may restrict epitopes in the vicinity of D614G. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G;D614G 33;279 38;284 S 171 176 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. report that the D614G spike mutation increases the susceptibility of SARS CoV-2 to neutralisation. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 16 21 S 22 27 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. showed that the increased infectivity of the D614G variant is not specific for the human ACE2 receptor but also increases the ability of the D614G strain to enter cells expressing equivalent receptors from a variety of mammalian species, suggesting that the mutation has not been selected by the spread of the virus within humans. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G;D614G 45;141 50;146 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. Similarly, in an extensive analysis of the antigenicity of spike mutations expressed in pseudoviruses, there was little evidence that the D614G substitution significantly affected neutralisation by a panel of monoclonal neutralising antibodies. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 138 143 S 59 64 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. Taken together these data suggest that the main effect of the D614G mutation is to increase the availability of spike trimer components in the conformation that permits the most efficient binding of the spike protein to ACE2. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 62 67 S;S 112;203 117;208 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. The accessibility of whole viral genome sequences collected around the world in the GISAID database enabled Korber and colleagues to develop a pipeline to identify Spike variants that were increasing in frequency across different geographic locations: this study highlighted the increasing dominance of a point mutation, D614G, in the Spike protein in viral isolates from the USA and Europe. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 321 326 S;S 164;335 169;340 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. The effects of the D614G mutation on the immune response towards the virus. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 19 24 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. The Sars-CoV2 Spike protein is heavily glycosylated, with 22 putative glycosylation sites, but only a few of them are documented as sites of mutations in the GISAID database to date (N74K, N149H, and T719A). 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 N149H;T719A;N74K 189;200;183 194;205;187 S 14 19 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. Their results showed that pseudotyped viruses expressing either the D614G single mutation or a combination of mutations that included D614G are more infectious than the reference strain, whereas no difference was found between single D614G and D614G combination variants, which suggests that the enhanced infectivity is most likely due to the presence of D614G itself. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G;D614G;D614G;D614G;D614G 68;134;234;244;355 73;139;239;249;360 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. They noted that this mutation is almost always accompanied by three other mutations: C241T is located in the 5'UTR region, there is a silent mutation, C3037T, and C14408T results in the P323L amino acid change in the RNA-dependent RNA polymerase (RdRp). 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 C14408T;C241T;C3037T;P323L 163;85;151;186 170;90;157;191 RdRp;5'UTR;RdRP 217;109;247 245;114;251 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. They went on to show that there was a substantial difference between the two variants in the presentation of the protomers in the "open" conformation that allows ACE2 binding, with D614G protomers being much more likely to assume this "open" conformation than the D614 variants. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 181 186 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. This analysis showed a correlation between the D614G mutation and the cycle threshold (CT) values from the real-time polymerase chain reaction (RT-PCR) used for clinical diagnosis, suggesting that the variant is associated with increased viral load - this could suggest that the D614G mutation makes the virus more infectious. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G;D614G 47;279 52;284 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. This led to the identification of variants carrying the D614G mutation in the Spike protein that were rapidly becoming the dominant viral strains across the world, even in regions where the D614 strain had initially caused infection. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 56 61 S 78 83 33199022 The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. used the available structures to map the D614G substitution to the surface of S1 in the spike protomer, where cryo-electron microscopy studies have showed that it forms a hydrogen bond with the T859 residue on S2 of the neighbouring protomer. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 41 46 S 88 93 33200118 Copper(II) Inhibition of the SARS-CoV-2 Main Protease. We are testing the proposal that cobalt(III) or copper(II) binding to these residues would partially unfold the protein, including the region around GLY 614 in the D614G mutant. 2020 ChemRxiv Introduction SARS_CoV_2 D614G 164 169 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. For instance, spike D614G substitution that arose in January has enhanced the virus transmissibility and infectivity. 2020 Emerging microbes & infections Introduction SARS_CoV_2 D614G 20 25 S 14 19 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. Taken together, our study indicates that there is increasing circulation of SARS-CoV-2 with the loss of orf3b in the ongoing pandemic, which coincides with the emergence of spike D614G virus strains. 2020 Emerging microbes & infections Introduction SARS_CoV_2 D614G 179 184 ORF3b;S 104;173 109;178 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. We showed that the Q57H amino acid substitution in SARS-CoV-2 orf3a gives rise to a premature stop codon in the reading frame for orf3b, and such genotype contributes to 23.82% of analysed sequences. 2020 Emerging microbes & infections Introduction SARS_CoV_2 Q57H 19 23 ORF3b;ORF3a 130;62 135;67 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Further, a product complex of the same substrate, captured at 2.0 A resolution using a Cys145Ala mutation, is also presented, providing further mechanistic and atomic information to inform future therapeutic design. 2020 Nature communications Introduction SARS_CoV_2 C145A 87 96 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. 2 ): the D614G mutation (a) modulates cleavage efficiency of S protein, (b) promotes a conformation favorable for RBD-ACE2 interaction ("openness" hypothesis), (c) facilitates more efficient S protein incorporation into the virion ("density" hypothesis), and (d) stabilizes the association of prefusion spike trimers ("stability" hypothesis). 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 9 14 S;RBD;S;S 303;114;61;191 308;117;62;192 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Another group used an independent software tool for prediction of protease cleavage sites and identified the same novel cleavage site introduced by the D614G substitution. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 152 157 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. By performing molecular dynamics simulations, Mansbach and colleagues predicted that the D614G mutation effects changes in intra-protomer energetics which favor a "one-up" conformation of the spike trimer - one of three protomers in open conformation. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 89 94 S 192 197 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Consistently, increased spike density associated with the D614G mutation was reproduced by Michaud et al. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 58 63 S 24 29 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Extensive efforts have been undertaken to ascertain how the D614G mutation increases infectivity of SARS-CoV-2 and S-pseudotyped vectors. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 60 65 S 115 116 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Further work has demonstrated a clear phenotypic advantage conferred by D614G, including our own observation of enhanced infectivity by PVs pseudotyped with S(G614) versus S(D614). 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 72 77 S;S 157;172 158;173 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Importantly, although direct inoculation did not reveal an appreciable effect of the D614G mutation, the G614 virus was remarkably more transmissible from infected hamsters to naive hamsters. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 85 90 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. In the initial absence of clear functional evidence for a phenotype of S(G614), independent epidemiological analyses using other methodologies concluded that the D614G mutation did not confer a transmissibility advantage. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 162 167 S 71 72 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Independent molecular dynamics simulations also support the hypothesis that the S(G614) variant favors an open conformation, specifically suggesting that the D614G mutation disrupts the formation of an inter-protomer D614-K835 salt bridge in the closed conformation. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 158 163 S 80 81 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Initial attention to the D614G mutation was prompted by a preprint from Korber et al. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 25 30 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Initial observations of the D614G effect from PV systems have now been borne out with live SARS-CoV-2 in cell culture and in animal models. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 28 33 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. It is noteworthy that the D614G mutation does not modulate the S protein binding affinity for ACE2; independent studies have found that monomers of S(D614) and S(G614) have similar affinity for ACE2 as measured by surface plasmon resonance or bio-layer interferometry. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 26 31 S;S;S 63;148;160 64;149;161 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Molecular mechanisms underlying the D614G effect are incompletely understood. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 36 41 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Moreover, computational models of evolutionary dynamics suggest that D614G is under strong selective pressure. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 69 74 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. On the contrary, several studies observed no effect of the D614G mutation on spike density, using lentiviral PV or live SARS-CoV-2. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 59 64 S 77 82 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. One aspect of the D614G mutation which has been investigated more extensively than the mechanism of increased infectivity is its impact on vaccines and antibodies. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 18 23 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. One non-synonymous mutation of S gene in particular, an aspartic acid-to-glycine substitution at amino acid position 614 (D614G), has attracted immense attention following reports of its enrichment discovered by epidemiological surveillance. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G;D614G 56;122 120;127 S 31 32 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. proposed that the D614G substitution introduces a cleavage site for elastase. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 18 23 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. The D614G mutation enhances the infectivity of pseudoviruses and live SARS-CoV-2. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 4 9 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. The effect of the D614G mutation in virus infectivity was durable in the presence or absence of TMPRSS2 overexpression and regardless of the modification of the S protein cytoplasmic domain, namely, full-length or C-terminally truncated S protein. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 18 23 S;S 161;237 162;238 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. The findings support the hypothesis that the D614G variant of S protein promotes transmissibility of the virus in mammals. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 45 50 S 62 63 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. The stability of S(G614) likely underlies observations that the D614G mutation decreases S1 shedding. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 64 69 S 17 18 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Therefore, the analyzed macromolecular structures were uncleaved and effects of D614G on intermolecular association between S1 and S2 of processed S protein trimers could not be ascertained. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 80 85 S 147 148 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. This review aims to assemble the work to date on the D614G mutation, including published studies as well as unreviewed manuscripts available in pre-print. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 53 58 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Various studies have identified co-segregation of changes in other viral genes along with the D614G mutation in spike, such as the P323L mutation in the viral polymerase RdRp which may attenuate replication to compensate for the increased transmissibility of D614G viruses. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G;D614G;P323L 94;259;131 99;264;136 S;RdRP 112;170 117;174 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Work by Michaud and colleagues further augmented observations on D614G with quantitatively focused approaches. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 65 70 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Yuan and Li employed in silico prediction of 12 linear and 53 discontinuous B-cell epitopes from the S protein and found that the D614G mutation had a negligible impact on predicted epitopes. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 130 135 S 101 102 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. At least two groups independently noted that D614G mutation correlated with increased viral loads in COVID-19 patients, but because this change is also associated with three or four other mutations in other viral proteins including nsp3 and RdRp, the role of the S protein in these observations remained undefined. 2020 Nature communications Introduction SARS_CoV_2 D614G 45 50 Nsp3;RdRP;S 232;241;263 236;245;264 COVID-19 101 109 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Here we show that the D614G mutation indeed increases pseudovirus (PV) infectivity and that reduced S1 shedding and increased S-protein density in the virion correlate with this increased infectivity. 2020 Nature communications Introduction SARS_CoV_2 D614G 22 27 S 126 127 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. One of these variations encodes an S-protein mutation, D614G, in the carboxy (C)-terminal region of the S1 domain. 2020 Nature communications Introduction SARS_CoV_2 D614G 55 60 S 35 36 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. Moreover, CR3022 is now able to neutralize SARS-CoV-2 P384A with a similar potency to SARS-CoV. 2020 PLoS pathogens Introduction SARS_CoV_2 P384A 54 59 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Considerable attention has focused on the D614G mutation in SARS-CoV-2, a non-synonymous mutation resulting in a replacement of aspartic acid with glycine at position 614 of the virus's spike protein (D614G). 2021 Cell Introduction SARS_CoV_2 D614G;D614G;D614G 128;42;201 170;47;206 S 186 191 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. First, experimental work using pseudotyped lentiviruses indicate that D614G increases infectivity in vitro. 2021 Cell Introduction SARS_CoV_2 D614G 70 75 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. In the United Kingdom, the first observation of a genome carrying the D614G mutation was in a sample collected on February 28 from a patient in Scotland who had recently traveled through Italy. 2021 Cell Introduction SARS_CoV_2 D614G 70 75 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. It is therefore likely that the D614G mutation occurred in China before being introduced on multiple occasions to European countries where it increased in frequency. 2021 Cell Introduction SARS_CoV_2 D614G 32 37 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Second, structural analysis suggests that D614G alters the receptor binding conformation, such that ACE2 binding and fusion is more likely. 2021 Cell Introduction SARS_CoV_2 D614G 42 47 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. The D614G mutation is associated with the B.1 lineage of SARS-CoV-2 (Figure 1), which now dominates the global pandemic, based upon global SARS-CoV-2 genome sequences shared via GISAID (https://cov-lineages.org/lineages/lineage_B.1.html). 2021 Cell Introduction SARS_CoV_2 D614G 4 9 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. The effect of the D614G replacement has been characterized in vitro with pseudotype virus and an in vivo in animal models, but this may not accurately recapitulate the effect of variants on virus transmissibility within the human population. 2021 Cell Introduction SARS_CoV_2 D614G 18 23 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. The putative importance of the D614G mutation is based on three distinct sets of observations. 2021 Cell Introduction SARS_CoV_2 D614G 31 36 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. There is currently no scientific consensus on the effect of the D614G mutation on SARS-CoV-2 infectivity and transmissibility, and there is some skepticism that it could produce a meaningful effect at the population level given that SARS-CoV-2 is already highly transmissible and rapidly spreading. 2021 Cell Introduction SARS_CoV_2 D614G 64 69 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. Analyses of over 28,000 S gene sequences in May 2020 revealed a D614G (23403A > G) amino acid substitution that was rare before March but increased in frequency as the pandemic spread, reaching over 74 % of all published sequences by June 2020. 2021 Veterinary microbiology Introduction SARS_CoV_2 D614G;A23403G 64;71 69;81 S 24 25 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. Importantly, however, the susceptibility of farm animals to SARS-CoV-2 remains largely unknown as well as the effect of D614G in animals. 2021 Veterinary microbiology Introduction SARS_CoV_2 D614G 120 125 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. Moreover, we show that a SARS-CoV-2 isolate which contains D614G in the S protein, mutation now widespread in the vast majority of globally SARS-CoV-2 currently circulating strains, replicates to higher titers than earlier SARS-CoV-2 variants that contain D614. 2021 Veterinary microbiology Introduction SARS_CoV_2 D614G 59 64 S 72 73 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. Notably, it has been proposed that D614G increases infectivity in cell assays in vitro and is also proposed to enhance viral transmissibility in nature. 2021 Veterinary microbiology Introduction SARS_CoV_2 D614G 35 40 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. The D614G substitution is accompanied by a set of mutations including 241C > T in the leader sequence, 3037C > T, and 14408C > T. 2021 Veterinary microbiology Introduction SARS_CoV_2 C14408T;C241T;C3037T;D614G 118;70;103;4 128;78;112;9 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. While 3037C > T causes a synonymous mutation in nsp3 (F105 F), 14408C > T is responsible for a substitution in the RNA primase (nsp 12, P323L). 2021 Veterinary microbiology Introduction SARS_CoV_2 C14408T;C3037T;P323L;F105F 63;6;136;54 73;15;141;60 Nsp3 48 52 33292056 Sensing the interactions between carbohydrate-binding agents and N-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies. H84T was also seen to interact with the S glycoprotein in both the complexes. 2020 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 H84T 0 4 S 40 54 33292056 Sensing the interactions between carbohydrate-binding agents and N-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies. Here, in this study, we selected lectins like NPA, UDA, GRFT and CV-N, Banana lectin (BanLec) wild-type and mutant (H84T mutant) type and non-peptidic mimic PRM-A based on their previously reported antiviral activity and availability of PDB structures. 2020 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 H84T 116 120 33292056 Sensing the interactions between carbohydrate-binding agents and N-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies. More specifically, we also analyzed the BanLec mutant lectin (H84T) where replacement of histidine with threonine at 84th position in BanLec abolishes its mitogenic activity while significantly retaining its broad-range antiviral activity. 2020 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 H84T 62 66 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. We surmise that G502 might play a critical role in the dissociation of the complex, and we tested this hypothesis by performing MD simulations of the G502P mutant. 2020 bioRxiv Introduction SARS_CoV_2 G502P 150 155 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. In addition, our analysis using a large number of S protein sequences derived from SARS-CoV-2 genomes revealed important mutations including L5F, D614G and G1124V that are although less likely driven by seasonal CoV derived cross-reactive CD8 T cells, may differentially impact CD8 T cell epitope generation by different HLA alleles. 2020 PloS one Introduction SARS_CoV_2 D614G;G1124V;L5F 146;156;141 151;162;144 S 50 51 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. Because this was the only difference between the pseudoviruses, any change in phenotype can be directly attributed to D614G. 2021 Cell host & microbe Introduction SARS_CoV_2 D614G 118 123 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. Early in the pandemic, the virus acquired a D614G mutation in the spike protein that rapidly increased in frequency and is now the dominant form of the virus globally. 2021 Cell host & microbe Introduction SARS_CoV_2 D614G 44 49 S 66 71 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Second, compared to the original source virus in Wuhan, China, the more prevalent SARS-CoV-2 variants emerging in the global pandemic substitute a glycine residue for aspartic acid 614 (D614G) in the S1 C-terminal domain (CTD2); the D614G change is associated with higher levels of virus replication in cultured human lung cells and in cells expressing human ACE2 and TMPRSS2. 2020 Journal of virology Introduction SARS_CoV_2 D614G;D614G;D614G 233;147;186 238;184;191 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. It was active against the D614G variant spike protein and against a panel of beta coronavirus spike proteins and protected human ACE2 transgenic mice against infection. 2020 Cell reports Introduction SARS_CoV_2 D614G 26 31 S;S 40;94 45;99 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. At the same time, it has been reported that D614G mutation co-occurs with three more mutations, i.e., 241 in UTR, 3307, and 14408. 2020 Frontiers in microbiology Introduction SARS_CoV_2 D614G 44 49 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. Moreover, we have analyzed the D614G mutations in the samples to obtain information on its evolution in Indian population. 2020 Frontiers in microbiology Introduction SARS_CoV_2 D614G 31 36 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. Protein-modeling analysis of D614G mutation was carried out to identify the impact on structural changes at protein levels. 2020 Frontiers in microbiology Introduction SARS_CoV_2 D614G 29 34 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. Recently, a predominant mutation, i.e., D614G in Spike protein, has been identified in virus strains sequenced from European population. 2020 Frontiers in microbiology Introduction SARS_CoV_2 D614G 40 45 S 49 54 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. There are several reports depicting that D614G mutation in Spike protein is associated with enhanced infectivity and spread of the virus owing to increased interaction with ACE2 receptor present on host cells. 2020 Frontiers in microbiology Introduction SARS_CoV_2 D614G 41 46 S 59 64 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. We further performed protein-protein docking simulation to predict the impact of D614G mutation on the interaction between of wild-type and mutated Spike protein with TMPRSS2 enzyme to assess its impact on binding and perhaps viral infectivity. 2020 Frontiers in microbiology Introduction SARS_CoV_2 D614G 81 86 S 148 153 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. Here we extend our understanding of the spike D614G mutation by demonstrating that it shifts spike protein trafficking towards the lysosome and away from organelles of the biosynthetic secretory pathway. 2020 bioRxiv Introduction SARS_CoV_2 D614G 46 51 S;S 40;93 45;98 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. Shortly after its entry into the human population, a variant strain of SARS-CoV-2 arose that displays multiple hallmarks of increased viral fitness, including a higher rate of transmission, elevated viral load in vivo, and enhanced infectivity in vitro This variant contains a mutation in the spike gene, D614G, that replaces the aspartate at position 614 with a glycine. 2020 bioRxiv Introduction SARS_CoV_2 D614G;D614G 330;305 370;310 S 293 298 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. The spike S1 domain binds SARS-CoV-2 receptors, primarily angiotensin converting enzyme-2 (ACE2) but also neuropilin-1, and yet, there is as yet no evidence that the D614G mutation alters the affinity of S1 for its receptors or for target cells. 2020 bioRxiv Introduction SARS_CoV_2 D614G 167 172 S 4 9 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. These and other results raise the possibility that that a single, lysosome-related mechanism may explain the pleiotropic effects of the D614G mutation on spike protein biogenesis, accelerated virus entry, and enhanced infectivity. 2020 bioRxiv Introduction SARS_CoV_2 D614G 136 141 S 154 159 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Based on our models, we find that a widely distributed mutation in the spike glycoprotein, Asp614Gly, likely alters its quaternary structure conformation and dynamics, and it only became pervasive after a subsequent mutation in the RNA-dependent RNA polymerase. 2020 Genome biology Introduction SARS_CoV_2 D614G 91 100 RdRp;S 232;71 260;89 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. A molecular virology study by Zhang and colleagues showed that the D614G mutation in the SARS-CoV-2 S glycoprotein can decrease S1 shedding and increase S glycoprotein incorporation into the virion, thereby enhancing SARS-CoV-2 infectivity. 2020 Genes Introduction SARS_CoV_2 D614G 67 72 S;S 100;153 114;167 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. Another study by Becerra-Flores and colleagues found that patients infected with SARS-CoV-2 containing the D614G mutation have a higher case fatality rate. 2020 Genes Introduction SARS_CoV_2 D614G 107 112 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. Genetic variations in ACE2 and its protein expression levels could provide the driving force for viral evolution, thereby causing the positive selection for D614G in the SARS-CoV-2 S glycoprotein. 2020 Genes Introduction SARS_CoV_2 D614G 157 162 S 181 195 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. However, according to a recent study, whether more S glycoprotein is incorporated into the SARS-CoV-2 D614G virion is still controversial. 2020 Genes Introduction SARS_CoV_2 D614G 102 107 S 51 65 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. Notably, the structure of the RBD in SARS-CoV-2 D614G variant displayed a more open conformation, which may increase the probability of ACE2 binding and fusion steps. 2020 Genes Introduction SARS_CoV_2 D614G 48 53 RBD 30 33 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. One of the predominant mutations, D614G, is located in the spike (S) glycoprotein in SARS-CoV-2 and was found by a current study to display increased virulence. 2020 Genes Introduction SARS_CoV_2 D614G 34 39 S;S 59;66 64;67 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. Our results strongly suggest a possible correlation between the SARS-CoV-2 S glycoprotein D614G mutation and diversity within ACE2 expression levels in human genetic populations. 2020 Genes Introduction SARS_CoV_2 D614G 90 95 S 75 89 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. The D614G mutation in the S glycoprotein can affect SARS-CoV-2 infectivity by affecting the RBD structure, S1/S2 subunit interaction, viral entry, and immune response. 2020 Genes Introduction SARS_CoV_2 D614G 4 9 S;RBD 26;92 40;95 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. These studies underline the importance of continuing to monitor the impact of the D614G mutation on the COVID-19 pandemic. 2020 Genes Introduction SARS_CoV_2 D614G 82 87 COVID-19 104 112 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. Nevertheless, some other reports stressed a possible selective pressure on the D614G variant, the only frequent variation of the spike protein, recently providing in-vivo evidence of its increased fitness . 2020 Journal of translational medicine Introduction SARS_CoV_2 D614G 79 84 S 129 134 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. Recently, SARS-CoV-2 with the D614G mutation became the most frequently detected globally, including South East Asia region. 2020 PeerJ Introduction SARS_CoV_2 D614G 30 35 33398275 An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. Another S variant (D839Y) became prevalent in Portugal, possibly due to a founder effect. 2020 bioRxiv Introduction SARS_CoV_2 D839Y 19 24 S 8 9 33398275 An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. To what extent this will occur as increasing numbers of people are infected and mount counter immune responses is unknown, but already a variant in the viral spike protein S (D614G) has rapidly emerged from multiple independent events and effects S protein stability and dynamics. 2020 bioRxiv Introduction SARS_CoV_2 D614G 175 180 S;S;S 158;172;247 163;173;248 33398278 SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma. Four plasma samples did not show neutralization activity against the SARS-CoV-2 WT and SARS-CoV-2 D614G variant. 2020 bioRxiv Introduction SARS_CoV_2 D614G 98 103 33398278 SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma. In contrast, the single mutation in the RBD (E484K) swaps the charge of the sidechain, which would significantly alter the electrostatic complementarity of antibody binding to this region. 2020 bioRxiv Introduction SARS_CoV_2 E484K 45 50 RBD 40 43 33398278 SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma. In the RBD, the possibility to escape is limited and the mutation E484K that we found is one of the most frequent mutations to escape monoclonal antibodies and among the most common RBD mutations described in experimental settings as well as in natural isolates posted in the GISAD database. 2020 bioRxiv Introduction SARS_CoV_2 E484K 66 71 RBD;RBD 7;182 10;185 33398278 SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma. Neutralization activity tested against the SARS-CoV-2 WT and D614G variant also showed variable titers. 2020 bioRxiv Introduction SARS_CoV_2 D614G 61 66 33398278 SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma. Sequence analyses revealed a deletion of the phenylalanine in position 140 (F140) on the S-protein NTD N3 loop in 36% of the virions. 2020 bioRxiv Introduction SARS_CoV_2 del 140F 29 74 S 89 90 33398278 SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma. The ability of the virus to adapt to the host immune system was also observed in clinical settings where an immunocompromised COVID-19 patient, after 154 days of infection, presented different variants of the virus including the E484K substitution. 2020 bioRxiv Introduction SARS_CoV_2 E484K 229 234 COVID-19 126 134 33398278 SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma. The E484K substitution was rapidly followed by a third and final change comprising an 11-amino-acid insertion between Y248 and L249 in the NTD N5 loop (248aKTRNKSTSRRE248k). 2020 bioRxiv Introduction SARS_CoV_2 E484K 4 9 33398278 SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma. These antibodies also showed a variable neutralization potency against the SARS-CoV-2 WT and D614G viruses ranging from 3.9 ng/mL to 500.0 ng/mL. 2020 bioRxiv Introduction SARS_CoV_2 D614G 93 98 33398278 SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma. This time, the glutamic acid in position 484 of the RBD was substituted with a lysine (E484K). 2020 bioRxiv Introduction SARS_CoV_2 E484K 87 92 RBD 52 55 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. Another European cluster in GISAID includes DeltaH69/DeltaV70 along with the RBD mutation N439K. 2020 medRxiv Introduction SARS_CoV_2 N439K 90 95 RBD 77 80 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. Here we document real time SARS-CoV-2 emergence of DeltaH69/DeltaV70 in combination with the S2 mutation D796H following convalescent plasma therapy in an immunocompromised human host, demonstrating selection and reduced phenotypic susceptiblility of selected mutations. 2020 medRxiv Introduction SARS_CoV_2 D796H 105 110 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. The capacity for successful adaptation is exemplified by the Spike D614G mutation, that arose in China and rapidly spread worldwide, now accounting for more than 90% of infections. 2020 medRxiv Introduction SARS_CoV_2 D614G 67 72 S 61 66 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. There it was associated with the RBD mutation Y453F in almost 200 individuals. 2020 medRxiv Introduction SARS_CoV_2 Y453F 46 51 RBD 33 36 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. A set of primers can be designed and optimized to specially identify the D614G mutant genotype. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 73 78 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Alternatively, biosensing based on aptamers, antibodies, or nanobodies can be designed to distinguish the S protein with or without the D614G mutation (Figure 2A). 2021 Trends in genetics Introduction SARS_CoV_2 D614G 136 141 S 106 107 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Although, the D614G point mutation is outside of the RBD (Figure 1C), it has been suggested to have an impact on the infectivity of the virus. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 14 19 RBD 53 56 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Aptamers, antibodies, and nanobodies specifically distinguishing D614G mutation within the S protein can be used as biorecognition elements and then incorporated into ELISA and lateral flow assays (Figure 2A). 2021 Trends in genetics Introduction SARS_CoV_2 D614G 65 70 S 91 92 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Besides using endonucleases for mutation site recognition, engineered pore-forming proteins could be applied directly to gene sequencing and D614G mutant detection. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 141 146 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Biosensing Technologies for the Detection of the SARS-CoV-2 D614G Mutation at Gene Level. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 60 65 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Biosensing Technologies for the Detection of the SARS-CoV-2 D614G Mutation at the Protein Level. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 60 65 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Clinical samples from patients infected with the D614G mutant were shown to have higher viral RNA levels and higher pseudovirus titers. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 49 54 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Consequently, the D614G mutation can be detected using restriction endonucleases to enzymatically cleave deoxynucleotides at this specific site, following double-stranded cDNA synthesis. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 18 23 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. D614G is a missense mutation where the amino acid change is caused by an A-to-G nucleotide mutation at genomic position 23 403. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 0 5 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Development of biosensing technologies for the efficient and rapid detection of SARS-CoV-2 and the D614G mutation is crucial for the control of the pandemic. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 99 104 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Due to the impact of the D614G mutation on SARS-CoV-2 biology, novel methods for its fast and reliable detection are of the highest importance. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 25 30 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Furthermore, current studies suggest that the D614G mutation retains similar sensitivity to antibodies that target the RBD. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 46 51 RBD 119 122 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Furthermore, the D614G mutation is located in the S1 subunit of the S protein, which is crucial for the entry of the SARS-CoV-2 virus into the host cell (Figure 1B,C). 2021 Trends in genetics Introduction SARS_CoV_2 D614G 17 22 S 68 69 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Hybridization techniques using point-mutated probes and corresponding perfect matching probes can be also confidently employed for the D614G mutation detection. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 135 140 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. In conjunction with DNA sequencing and different types of PCR-based techniques, capillary electrophoresis, surface-enhanced Raman spectroscopy (SERS), mass spectrometry (MS), and denaturing high performance liquid chromatography (dHPLC) can also be used to screen for the presence of the D614G mutation. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 288 293 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. LAMP is fast and its products can be detected with electrochemical and optical readouts, or even by the naked eye, making it suitable for point-of-care testing of the SARS-CoV-2 D614G mutation (Figure 2B). 2021 Trends in genetics Introduction SARS_CoV_2 D614G 178 183 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Novel biosensing technologies for rapid monitoring of D614G are therefore urgently needed. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 54 59 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. One such promising method, surface plasmon resonance (SPR), has been used to investigate the effect of the D614G mutation on the binding kinetics of the SARS-CoV-2 S protein with human ACE2. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 107 112 S 164 165 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Overall, despite the need for the conversion of an RNA single-stranded genome of SARS-CoV-2 into cDNA for detection purposes, biosensing technologies aimed at the detection of the D614G mutation at the gene level show much greater promise. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 180 185 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Similar CRISPR/Cas systems can be exploited for the accurate and scalable detection of the SARS-CoV-2 D614G mutation on a lateral flow strip using different signal readout based on electrochemical and optical techniques (Figure 2B). 2021 Trends in genetics Introduction SARS_CoV_2 D614G 102 107 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. The binding rates of the S protein with and without the D614G mutation were similar, but the dissociation rate of the D614G mutant was faster, which contributed to the decrease in binding affinity. 2021 Trends in genetics Introduction SARS_CoV_2 D614G;D614G 56;118 61;123 S 25 26 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. The D614G mutation corresponds to the alteration of an adenine to a guanine at genomic position 23 403 (Figure 1C). 2021 Trends in genetics Introduction SARS_CoV_2 D614G 4 9 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. The D614G mutation has been identified by phylogenetic analysis of over a thousand SARS-CoV-2 genomes. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 4 9 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. The D614G Mutation Increases SARS-CoV-2 Infectivity. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 4 9 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. The D614G point mutation is predominant amongst the SARS-CoV-2 genomes currently circulating in the population. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 4 9 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. The rapid spread of the D614G mutant version of the virus was hypothesized to correlate with the higher infectivity of SARS-CoV-2 harboring this mutation. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 24 29 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. The sequencing of thousands of SARS-CoV-2 genomes revealed a number of recurrent mutations, out of which an amino acid change from aspartate to a glycine residue at position 614 (D614G) in the S protein has gained most attention. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 179 184 S 193 194 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. The specific cleaving of the point mutation can be combined with suitable signal amplification strategies, such as rolling circle amplification (RCA), strand displacement amplification (SDA), and isothermal exponential amplification (EXPAR), for the optical and electrochemical detection of the D614G mutant version (Figure 2B). 2021 Trends in genetics Introduction SARS_CoV_2 D614G 295 300 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. This observation could be exploited for the engineering of an SPR-based biosensing platform employing ACE2 protein for SARS-CoV-2 D614G mutant protein detection (Figure 2A). 2021 Trends in genetics Introduction SARS_CoV_2 D614G 130 135 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Thus, the possibility of reliable detection of mutation-specific antibodies by D614G and D614 antigens will require further investigation. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 79 84 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. While the D614G mutation was relatively rare at the onset of the pandemic, by June 2020 this mutation was found in the majority of COVID-19 patients. 2021 Trends in genetics Introduction SARS_CoV_2 D614G 10 15 COVID-19 131 139 33408342 A longitudinal study of SARS-CoV-2-infected patients reveals a high correlation between neutralizing antibodies and COVID-19 severity. Finally, we found that the D614G mutation in the spike protein, recently identified as the major variant now found in Europe, did not induce nAb escape. 2021 Cellular & molecular immunology Introduction SARS_CoV_2 D614G 27 32 S 49 54 33412089 COVID-19-neutralizing antibodies predict disease severity and survival. One mutation, D614G, has rapidly become the predominant transmitted variant by outcompeting wild-type infections. 2021 Cell Introduction SARS_CoV_2 D614G 14 19 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. However, some studies suggested that D614G mutation in the spike protein may contribute to increased infectivity or transmissibility of SARS-CoV-2 leading to increased severity of COVID-19. 2020 Genomics & informatics Introduction SARS_CoV_2 D614G 37 42 S 59 64 COVID-19 180 188 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. The D614G mutation of the spike protein was observed sometimes in late January 2020 both in Europe and in China, but then this mutation spread first in the Europe and gradually globally. 2020 Genomics & informatics Introduction SARS_CoV_2 D614G 4 9 S 26 31 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. Thus the distribution of spike protein D614G mutation has temporal and geographical variation. 2020 Genomics & informatics Introduction SARS_CoV_2 D614G 39 44 S 25 30 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. Here we adopted our previous epidemiological framework for relative fitness inference of co-circulating pathogen strains, which has been applied on influenza viruses and SARS-CoV-2 D614G strains, to characterise the comparative transmissibility of the 501Y lineages. 2021 Euro surveillance Introduction SARS_CoV_2 D614G 181 186 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. The most concerning mutation is N501Y, which co-occurs with several mutations of potential biological importance, including P681H and deletion of the amino acid at the 69th and 70th residues (Delta69/Delta70) on the spike protein (Supplementary Table S1). 2021 Euro surveillance Introduction SARS_CoV_2 N501Y;P681H 32;124 37;129 S 216 221 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. Two new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages carrying the amino acid substitution N501Y in the receptor-binding domain (RBD) of the spike protein have spread rapidly in the United Kingdom (UK) during late autumn 2020. 2021 Euro surveillance Introduction SARS_CoV_2 N501Y 115 120 S;RBD 165;153 170;156 COVID-19 15 55 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. We assumed that the N501Y mutation and Delta69/Delta70 deletions characterise the three strains (501N, 501Y Variant 1 and 501Y Variant 2), but their differential transmissibility (if any) might be attributable to the combination of N501Y and other mutations acquired in the emergence of 501Y Variant 1 and 2 lineages (Table and Supplementary Table S1). 2021 Euro surveillance Introduction SARS_CoV_2 N501Y;N501Y 20;232 25;237 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Our results demonstrate the effect of the D614G substitution on S conformational diversity and furin cleavage susceptibility of the S ectodomain and reveal insights into the allostery between RBD motions and distal regions of the S protein. 2021 Cell reports Introduction SARS_CoV_2 D614G 42 47 RBD;S;S;S 192;64;132;230 195;65;133;231 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. The D614G mutation in particular has attracted attention because it has quickly become the dominant variant of SARS-CoV-2 circulating worldwide. 2021 Cell reports Introduction SARS_CoV_2 D614G 4 9 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. The D614G mutation of the S protein has been associated in numerous reports with increased fitness and/or infectivity of the virus. 2021 Cell reports Introduction SARS_CoV_2 D614G 4 9 S 26 27 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. To probe the effect of the D614G substitution on furin cleavage of the S protein, we either reinstated the native furin sequence or replaced it with an exogeneous HRV3C proteolysis cleavage site. 2021 Cell reports Introduction SARS_CoV_2 D614G 27 32 S 71 72 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. With the goal of investigating the biophysical and structural consequences of the D614G mutation and to prevent the engineered PP mutations from confounding our observations, we produced two SARS-CoV-2 S ectodomain constructs with the native K986 and V987 residues, incorporating either a D or a G at position 614 (Figure 1). 2021 Cell reports Introduction SARS_CoV_2 D614G 82 87 S 202 203 33433004 Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure. 2 In particular, a mutation at position 14408, which leads to an amino acid substitution (P323L) in RdRp, was identified as a mutation hotspot, and in silico analysis suggests that this change may affect stability of the tertiary complex of RdRp. 2021 Journal of medical virology Introduction SARS_CoV_2 P323L 91 96 RdRP;RdRP 101;242 105;246 33436577 A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein. Indeed, over time, SARS-CoV-2 isolates bearing D614G mutations in the viral S protein variant have emerged that enable more efficient cellular entry and ultimately lead to an enhanced viral transmission. 2021 Nature communications Introduction SARS_CoV_2 D614G 47 52 S 76 77 33441410 An Observational Laboratory-Based Assessment of SARS-CoV-2 Molecular Diagnostics in Benin, Western Africa. In sum, genomic analyses suggest multiple introductions of at least two globally circulating SARS-CoV-2 lineages as well as the D614G mutation into Africa before mid-April 2020, highlighting the value of closing borders to decrease virus importation into Benin and other African countries. 2021 mSphere Introduction SARS_CoV_2 D614G 128 133 33441410 An Observational Laboratory-Based Assessment of SARS-CoV-2 Molecular Diagnostics in Benin, Western Africa. Of note, all eight strains belonging to lineage B.1 harbored a nucleotide exchange resulting in the D614G spike protein variant, which may be associated with increased transmissibility. 2021 mSphere Introduction SARS_CoV_2 D614G 100 105 S 106 111 33442691 Neutralization of N501Y mutant SARS-CoV-2 by BNT162b2 vaccine-elicited sera. These rapidly spreading variants share the spike N501Y substitution. 2021 bioRxiv Introduction SARS_CoV_2 N501Y 49 54 S 43 48 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. Another recent study, based on presence of three mutations including one in the spike protein D614G (a A-to-G base change at position 23,403 with reference strain resulting in change of amino acid from Aspartic acid to Glycine) labeled as 'G' Clade has emerged as the dominant and highly transmissible strain replacing the other initial clades of the virus. 2021 Indian journal of medical microbiology Introduction SARS_CoV_2 D614G 94 99 S 80 85 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. in February 2020, analyzing 103 complete SARS-CoV-2 genomes, have found a tightly linked SNPs between two widely separated nucleotides at location 8782 (ORF1ab T8517C) and position 28,144 (ORF8: C251T, codon S84L). 2021 Indian journal of medical microbiology Introduction SARS_CoV_2 C251T;S84L;T8517C 195;208;160 200;212;166 ORF1ab;ORF8 153;189 159;193 33468702 SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia. All genomes contained the D614G spike substitution and the P314L RdRp substitution. 2021 mBio Introduction SARS_CoV_2 D614G;P314L 26;59 31;64 S;RdRP 32;65 37;69 33468702 SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia. One notable substitution encodes the spike protein (S) variant D614G. 2021 mBio Introduction SARS_CoV_2 D614G 63 68 S;S 37;52 42;53 33468702 SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia. The D614G substitution has been proposed to promote infection of human cells, and this variant has spread globally at the expense of other genotypes. 2021 mBio Introduction SARS_CoV_2 D614G 4 9 33468702 SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia. The D614G variant in recently isolated genomes often cooccurs with a mutation encoding P314L in the virus-encoded RNA-dependent RNA polymerase (RdRp) located on ORF1b. 2021 mBio Introduction SARS_CoV_2 D614G;P314L 4;87 9;92 RdRp;RdRP 114;144 142;148 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. So far, several mutants and spike variants such as V615L, D614G, F817L, and P812S have been identified. 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 D614G;F817L;P812S;V615L 58;65;76;51 63;70;81;56 S 28 33 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. The present study aims to investigate the structural and molecular properties of mutant D614G by employing bioinformatics and molecular dynamics (MD). 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 D614G 88 93 33478625 Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020. For 21 of the 36 samples, the S mutations co-occurring with DeltaH69/DeltaV70 were S477N and D614G; 10 of the 36 samples presented N439K and D614G mutations in addition to DeltaH69/DeltaV70. 2021 Euro surveillance Introduction SARS_CoV_2 D614G;D614G;N439K;S477N 93;141;131;83 98;146;136;88 S 30 31 33478625 Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020. The DeltaH69/DeltaV70 has also co-occurred with either one of two other noteworthy RBD mutations: N439K that is currently spreading in Europe and might also be related to reduced susceptibility to SARS-CoV-2 antibodies and N501Y that was identified for example in the SARS-CoV-2 variant of concern (VOC) 202012/01 recently detected in England. 2021 Euro surveillance Introduction SARS_CoV_2 N439K;N501Y 98;223 103;228 RBD 83 86 33478625 Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020. This cluster-5 variant carries a receptor binding domain (RBD) mutation Y453F and was associated with reduced susceptibility to neutralising antibodies of sera from recovered coronavirus disease (COVID-19) patients. 2021 Euro surveillance Introduction SARS_CoV_2 Y453F 72 77 RBD;RBD 33;58 56;61 COVID-19;COVID-19 175;196 194;204 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. Single Nucleotide Variations (SNVs) in ORF8 at 28144T>C (251T>C, L84S) characterize the SARS-CoV-2 S clade, leading to divergence of phylogenetic group. 2021 Gene reports Introduction SARS_CoV_2 T28144C;L84S;T251C 47;65;57 55;69;63 ORF8;S 39;99 43;100 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. In addition, we aimed to characterize the temporal changes of D614G mutation spread in the region. 2021 Heliyon Introduction SARS_CoV_2 D614G 62 67 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. Other mutations in the S gene have also been reported, with the most frequent including: D936Y/H, P1263L, and L5F. 2021 Heliyon Introduction SARS_CoV_2 D936H;D936Y;L5F;P1263L 89;89;110;98 96;96;113;104 S 23 24 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. Some of these mutations appeared to have a significant epidemiologic value, with the replacement of aspartic acid by glycine at position 614 of the spike glycoprotein (D614G), being associated with a higher viral shedding and increased infectivity. 2021 Heliyon Introduction SARS_CoV_2 D614G;D614G 100;168 140;173 S 148 166 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. We propose two interesting mutations found in the nucleocaspid (N) (P13L) and ORF3a (Q57H) genes; that appear to be significantly associated with either increased or decreased deaths and cases per million according to our GLMs. 2021 PloS one Introduction SARS_CoV_2 P13L;Q57H 68;85 72;89 ORF3a;N 78;64 83;65 33498225 Biological and Clinical Consequences of Integrin Binding via a Rogue RGD Motif in the SARS CoV-2 Spike Protein. The recurrent emergence of amino acid replacement N501Y, within the large surface loop, 437-508, has the potential for enhancing the flexibility of surface loops, thereby exposing the RGD motif to solvent in a way that is conducive to integrin-binding. 2021 Viruses Introduction SARS_CoV_2 N501Y 50 55 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. Finally, we show that human sera from convalescent and vaccinated individuals can neutralize both the reference USA-WA1/2020 strain and the mouse adapted strain that contains the N501Y spike mutation with similar efficiency. 2021 medRxiv Introduction SARS_CoV_2 N501Y 179 184 S 185 190 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. This mouse-adapted SARS-CoV-2 strain with N501Y mutation causes enhanced morbidity in mouse models for advanced age, obesity and obesity-associated type 2 diabetes mellitus. 2021 medRxiv Introduction SARS_CoV_2 N501Y 42 47 Diabetes mellitus type 2 148 172 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. We mapped mutations associated with mouse adaptation in the SARS-CoV-2 genome and observed that one of them is the N501Y mutation in the RBD from the spike protein that was also reported for the newly emerging SARS-CoV-2 variant (20B/501Y.V1 strain) with potentially enhanced human transmission potential. 2021 medRxiv Introduction SARS_CoV_2 N501Y 115 120 S;RBD 150;137 155;140 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. One of the most interesting amino acid variants in the spike protein of SARS-Cov-2 is the D614G due to a missense mutation. 2021 Biochemistry and biophysics reports Introduction SARS_CoV_2 D614G 90 95 S 55 60 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. The D614G mutation became an alarm due to it has been increasingly prevalent all over the world, which might be the new transmissible form of SARS-Cov-2, which has dismayed many scientists according to previous reports. 2021 Biochemistry and biophysics reports Introduction SARS_CoV_2 D614G 4 9 33509990 Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq. Among these changes, the following two infrequent amino acid changes were observed: NSP8-S76F, which has already been identified in three countries, and N-G215S, which has been identified in 10 countries to date. 2021 Microbiology resource announcements Introduction SARS_CoV_2 G215S;S76F 155;89 160;93 Nsp8;N 84;153 88;154 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. The missense mutation, D614G, in the spike protein of SARS-CoV-2 has been reported to endow the SARS-CoV-2 virus with 10-fold higher infectivity, and it is now emerging as a predominant clade in some regions such as Europe. 2021 Analytical chemistry Introduction SARS_CoV_2 D614G 23 28 S 37 42 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. We applied the RNA assays to profile the key mutation, D614G of SARS-CoV-2 variants, and detect SARS-CoV-2 infection in throat swab, serum samples, and SARS-CoV-2 contaminations in food packaging and seafood. 2021 Analytical chemistry Introduction SARS_CoV_2 D614G 55 60 COVID-19 96 116 33524589 A global analysis of replacement of genetic variants of SARS-CoV-2 in association with containment capacity and changes in disease severity. A recent report suggested that a mutation of the spike protein, S-D614G, could be associated with increased infectivity. 2021 Clinical microbiology and infection Introduction SARS_CoV_2 D614G 66 71 S;S 49;64 54;65 33532771 Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera. (i) Mutant N501Y virus contains the N501Y mutation that is shared by both the UK and SA variants. 2021 bioRxiv Introduction SARS_CoV_2 N501Y;N501Y 11;36 16;41 33532771 Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera. (ii) Mutant Delta69/70+N501Y+D614G virus contains two additional changes present in the UK variants: amino acid 69 and 70 deletion (Delta69/70) and D614G substitution. 2021 bioRxiv Introduction SARS_CoV_2 D614G;D614G;N501Y 148;29;23 153;34;28 33532771 Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera. (iii) Mutant E484K+N501Y+D614G virus additionally contains the E484K substitution, which is also located in the viral RBD. 2021 bioRxiv Introduction SARS_CoV_2 E484K;E484K;D614G;N501Y 13;63;25;19 18;68;30;24 RBD 118 121 33532771 Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera. 1b), whereas six out of the twenty sera had neutralization titers against mutant E484K+N501Y+D614G virus that were half their titers against the wild-type virus. 2021 bioRxiv Introduction SARS_CoV_2 E484K;D614G;N501Y 81;93;87 86;98;92 33532771 Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera. Consistent with other recent reports of the neutralization of SARS-CoV-2 variants or corresponding pseudoviruses by convalescent or post-immunization sera, the neutralization GMT of the serum panel against the virus with three mutations from the SA variant (E484K+N501Y+D614G) was slightly lower than the neutralization GMTs against the N501Y virus or the virus with three mutations from the UK variant (Delta69/70+N501Y+D614G). 2021 bioRxiv Introduction SARS_CoV_2 N501Y;E484K;D614G;D614G;N501Y;N501Y 337;258;270;421;264;415 342;263;275;426;269;420 33532771 Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera. Nevertheless, preserved neutralization of N501Y, Delta69/70+N501Y+D614G, and E484K+N501Y+D614G viruses by BNT162b2 vaccine-elicited human sera is consistent with preserved neutralization of a panel of 15 pseudoviruses bearing spikes with other single mutations found in circulating SARS-CoV-2 strains. 2021 bioRxiv Introduction SARS_CoV_2 E484K;N501Y;D614G;D614G;N501Y;N501Y 77;42;66;89;60;83 82;47;71;94;65;88 S 226 232 33532771 Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera. Notably, ten out of the twenty sera had neutralization titers against mutant Delta69/70+N501Y+D614G virus that were twice their titers against the wild-type virus. 2021 bioRxiv Introduction SARS_CoV_2 D614G;N501Y 94;88 99;93 33532771 Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera. The biological functions of N501Y and the other mutations (such as Delta69/70 and E484K) remain to be defined for viral replication, pathogenesis, and/or transmission in animal models. 2021 bioRxiv Introduction SARS_CoV_2 E484K;N501Y 82;28 87;33 33532771 Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera. The D614G mutation is dominant in circulating strains around the world. 2021 bioRxiv Introduction SARS_CoV_2 D614G 4 9 33532771 Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera. The E484K substitution alone confers resistance to several monoclonal antibodies. 2021 bioRxiv Introduction SARS_CoV_2 E484K 4 9 33532771 Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera. The emergence of the common mutation N501Y from different geographical regions, as well as the previously emerged globally dominant D614G mutation, suggest that these mutations may improve viral fitness, as recently demonstrated for the increased viral transmission by the D614G mutation in animal models. 2021 bioRxiv Introduction SARS_CoV_2 D614G;D614G;N501Y 132;273;37 137;278;42 33532771 Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera. The ratios of the neutralization GMTs of the sera against the N501Y, Delta69/70+N501Y+D614G, and E484K+N501Y+D614G viruses to their GMTs against the USA-WA1/2020 virus were 1.46, 1.41, and 0.81, respectively. 2021 bioRxiv Introduction SARS_CoV_2 E484K;N501Y;D614G;D614G;N501Y;N501Y 97;62;86;109;80;103 102;67;91;114;85;108 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. A structural explanation on how E484K disrupts the binding of 2-15, LY-CoV555, and REGN10933 is presented in Extended Data. 2021 bioRxiv Introduction SARS_CoV_2 E484K 32 37 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. Again, S982A seems to have a minor negative impact on the plasma neutralizing activity of every serum sample. 2021 bioRxiv Introduction SARS_CoV_2 S982A 7 12 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. Against SADelta9, the complete loss of activity of 2-15, LY-CoV555, and C121 is mediated by E484K; the complete loss for 910-30 is mediated by K417N; and the marked reduction for REGN10933 is mediated by K417N and E484K. 2021 bioRxiv Introduction SARS_CoV_2 E484K;E484K;K417N;K417N 92;214;143;204 97;219;148;209 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. Against UKDelta8, the decreased activity of 910-30 is mediated by N501Y, whereas the slightly impaired activity of S309 is unexplained. 2021 bioRxiv Introduction SARS_CoV_2 N501Y 66 71 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. B.1.1.7 contains 8 spike mutations in addition to D614G, including two deletions (69-70del & 144del) in NTD, one mutation (N501Y) in RBD, and one mutation (P681H) near the furin cleavage site. 2021 bioRxiv Introduction SARS_CoV_2 D614G;N501Y;P681H 50;123;156 55;128;161 S;RBD 19;133 24;136 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. B.1.351 contains 9 spike mutations in addition to D614G, including a cluster of mutations (e.g., 242-244del & R246I) in NTD, three mutations (K417N, E484K, & N501Y) in RBD, and one mutation (A701V) near the furin cleavage site. 2021 bioRxiv Introduction SARS_CoV_2 D614G;E484K;N501Y;R246I;A701V;K417N 50;149;158;110;191;142 55;154;163;115;196;147 S;RBD 19;168 24;171 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. It is evident that the resistance of UKDelta8 to most NTD mAbs is largely conferred by 144del, whereas the resistance of SADelta9 is largely conferred by 242-244del and/or R246I. 2021 bioRxiv Introduction SARS_CoV_2 144del;R246I 87;172 93;177 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. Lastly, we examined, in a single experiment, the neutralizing activity of mAb therapies in clinical use or under clinical investigation against UKDelta8, SADelta9, and D614G pseudoviruses. 2021 bioRxiv Introduction SARS_CoV_2 D614G 168 173 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. On the other hand, the loss of plasma neutralizing activity against SADelta9 could be largely attributed to E484K. 2021 bioRxiv Introduction SARS_CoV_2 E484K 108 113 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. S982A seems to have a discernible negative impact on the plasma neutralizing activity of 9 samples. 2021 bioRxiv Introduction SARS_CoV_2 S982A 0 5 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. The activity of CB6 is slightly impaired against UKDelta8, likely due to N501Y and/or S982A, but it is rendered inactive against SADelta9 because of K417N. 2021 bioRxiv Introduction SARS_CoV_2 K417N;N501Y;S982A 149;73;86 154;78;91 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. The loss of neutralizing activity against SADelta9 in vaccinee sera could be principally attributed to E484K. 2021 bioRxiv Introduction SARS_CoV_2 E484K 103 108 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. We first assayed the neutralizing activity of 12 RBD mAbs against UKDelta8, SADelta9, and WT (D614G) pseudoviruses in Vero E6 cells as previously described. 2021 bioRxiv Introduction SARS_CoV_2 D614G 94 99 RBD 49 52 33532796 The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. However, there remains concern about additional substitutions like E484K present in B.1.351 and P.1 lineages allowing escape from neutralizing antibodies, thereby potentially rendering vaccine-induced immunity less protective. 2021 medRxiv Introduction SARS_CoV_2 E484K 67 72 33532796 The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. In order to investigate the impact of the E484K mutation in the neutralizing activity of SARS-CoV-2 specific antisera, we performed in vitro microneutralization assays with both the USA-WA1/2020 virus and a recombinant (r)SARS-CoV-2 virus that is identical to USA-WA1/2020 except for the E484K mutation introduced in the spike RBD. 2021 medRxiv Introduction SARS_CoV_2 E484K;E484K 42;288 47;293 S;RBD 321;327 326;330 33532796 The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. The E484K mutant rSARS-CoV-2 was generated using previously described reverse genetics based on the use of a bacterial artificial chromosome (BAC). 2021 medRxiv Introduction SARS_CoV_2 E484K 4 9 33532796 The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. The same sera have been tested for neutralization studies with a N501Y SARS-CoV-2 variant in our recent report. 2021 medRxiv Introduction SARS_CoV_2 N501Y 65 70 33532796 The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. We and others have previously reported that the asparagine (N) to tyrosine (Y) substitution at position 501 (N501Y), present in variants of concern belonging to the B.1.1.7, B.1.351 and P.1 lineages, does not seem to affect in vitro neutralization of SARS-CoV-2 viruses by human sera from convalescent or vaccinated human donors. 2021 medRxiv Introduction SARS_CoV_2 N501Y 109 114 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Resistance to inhibition by soluble recombinant human ACE2, a candidate decoy molecule drug currently in clinical trials (NCT04375046 and NCT04287686), was observed with an F486S substitution. 2021 Cell host & microbe Introduction SARS_CoV_2 F486S 173 178 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. After 23 passages, two mutations were selected in the nsp12 polymerase at residues F476L and V553L. 2021 Antiviral research Introduction SARS_CoV_2 F476L;V553L 83;93 88;98 Nsp12 54 59 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. Compared with wild-type virus, recombinant MHV containing the F476L and V553L single mutation showed 2.4-fold and 5-fold reduced susceptibility to RDV, respectively, while the double mutant conferred 5.6-fold reduced susceptibility to RDV in vitro. 2021 Antiviral research Introduction SARS_CoV_2 F476L;V553L 62;72 67;77 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. The B.1.1.7 variant contained a signature of spike amino acid changes including H69/V70 deletion, Y144 deletion, N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H. 2021 Antiviral research Introduction SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 120;159;127;113;134;148;141 125;165;132;118;139;153;146 S 45 50 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. The B.1.351 variant also contains a signature of spike amino acid changes including K417N, E484K, and N501Y. 2021 Antiviral research Introduction SARS_CoV_2 E484K;K417N;N501Y 91;84;102 96;89;107 S 49 54 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. The substitution V557L was introduced in biochemical studies, where it was shown that the mutation impacted the template-dependent inhibition of RDV, but not RDV-TP incorporation or delayed chain termination. 2021 Antiviral research Introduction SARS_CoV_2 V557L 17 22 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. This was confirmed by an engineered S861G mutation, which eliminated the delayed chain termination of RDV-TP. 2021 Antiviral research Introduction SARS_CoV_2 S861G 36 41 33551188 Fast and cost-effective screening for SARS-CoV-2 variants in a routine diagnostic setting. Both the SARS-CoV-2 variant from South Africa and the UK harbor the receptor binding domain mutation N501Y, a spike protein that allows the virus to enter human cells. 2021 Dental materials Introduction SARS_CoV_2 N501Y 101 106 RBD;S 68;110 91;115 33551188 Fast and cost-effective screening for SARS-CoV-2 variants in a routine diagnostic setting. The lack of detection of the N501Y mutation in qPCR accordingly excludes the South African and UK variants quickly and does not require sequencing. 2021 Dental materials Introduction SARS_CoV_2 N501Y 29 34 33556653 The G614 pandemic SARS-CoV-2 variant is not more pathogenic than the original D614 form in adult Syrian hamsters. A very recent preprint reported that an engineered D614G mutation significantly enhances SARS-CoV-2 replication on human lung epithelial cells and primary human airway tissues, and there is as of yet limited literature on the effects of mutations on SARS-CoV-2 pathogenesis. 2021 Virology Introduction SARS_CoV_2 D614G 51 56 33556653 The G614 pandemic SARS-CoV-2 variant is not more pathogenic than the original D614 form in adult Syrian hamsters. described the emergence and dominance of a D614G mutation in the SARS-CoV-2 spike protein during the ongoing pandemic. 2021 Virology Introduction SARS_CoV_2 D614G 43 48 S 76 81 33556653 The G614 pandemic SARS-CoV-2 variant is not more pathogenic than the original D614 form in adult Syrian hamsters. However, there was no significant association between the D614G mutation and disease severity. 2021 Virology Introduction SARS_CoV_2 D614G 58 63 33556653 The G614 pandemic SARS-CoV-2 variant is not more pathogenic than the original D614 form in adult Syrian hamsters. Of concern, the D614G mutation was associated with elevated viral loads observed in infected patients and enhanced replication of pseudotyped virions. 2021 Virology Introduction SARS_CoV_2 D614G 16 21 33556653 The G614 pandemic SARS-CoV-2 variant is not more pathogenic than the original D614 form in adult Syrian hamsters. The question of whether the D614G mutation increases virulence or pathogenicity of SARS-CoV-2 in humans remains unanswered. 2021 Virology Introduction SARS_CoV_2 D614G 28 33 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. In this study, we analyze ACE2/TMPRSS2 usage of SARS-CoV S and SARS-CoV-2 S (referred to hereafter as SARS-S and SARS2-S, respectively), compare cell entry of natural SARS2-S variants, and focus on the D614G variant by investigating its structure, ACE2-binding affinity, and neutralization susceptibility. 2021 Nature communications Introduction SARS_CoV_2 D614G 202 207 S;S;S;S;S 57;74;107;119;173 58;75;108;120;174 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Our results indicate that the D614G mutation confers increased entry efficiency resulting from enhanced binding affinity for ACE2 with no influence on the antigenicity of the S protein. 2021 Nature communications Introduction SARS_CoV_2 D614G 30 35 S 175 176 33558635 Potent neutralization of clinical isolates of SARS-CoV-2 D614 and G614 variants by a monomeric, sub-nanomolar affinity nanobody. Interestingly, the S protein residue 614 is located in the interface between adjacent S protomers, and it has been hypothesized that amino acid exchange to glycine stabilizes the trimeric Spike protein architecture Accordingly, the D614G variant exhibits less S1 subunit shedding and improved Spike protein incorporation into virions. 2021 Scientific reports Introduction SARS_CoV_2 D614G 232 237 S;S;S;S 188;293;19;86 193;298;20;87 33558635 Potent neutralization of clinical isolates of SARS-CoV-2 D614 and G614 variants by a monomeric, sub-nanomolar affinity nanobody. Recent studies highlighted the emergence of the Spike protein variant D614G, which has become the dominant SARS-CoV-2 pandemic strain. 2021 Scientific reports Introduction SARS_CoV_2 D614G 70 75 S 48 53 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. These variants harbor one or several nonsynonymous spike mutations including amino acid replacements at key sites in the spike RBD domain (K417N, E484K, N501Y for the African strain and only N501Y in this region of the protein for the UK strain). 2021 International journal of molecular sciences Introduction SARS_CoV_2 E484K;N501Y;N501Y;K417N 146;153;191;139 151;158;196;144 S;S;RBD 51;121;127 56;126;130 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Among them, the mutations at position C8782T in the ORF1ab gene, T28144C in the ORF8 gene and C29095T in the N gene are common. 2021 Scientific reports Introduction SARS_CoV_2 C29095T;C8782T;T28144C 94;38;65 101;44;72 ORF1ab;ORF8;N 52;80;109 58;84;110 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Among them, there are three mutations occurring in the RBD region of the spike surface glycoprotein S, including N354D, D364Y and V367F, with the numbers showing amino acid (AA) positions in the protein. 2021 Scientific reports Introduction SARS_CoV_2 D364Y;N354D;V367F 120;113;130 125;118;135 S;S;RBD;S 79;73;55;100 99;78;58;101 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). They detected 14 mutations in the spike protein that are growing, especially the mutation D614G that rapidly becomes the dominant form when spread to a new geographical region. 2021 Scientific reports Introduction SARS_CoV_2 D614G 90 95 S 34 39 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Typically, the mutation D614G occurring in the spike protein is found prevalent in the European population. 2021 Scientific reports Introduction SARS_CoV_2 D614G 24 29 S 47 52 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. For example, neutralizing antibodies that target the receptor-binding domain seem largely unaffected in potency, but it remains to be seen whether the D614G variant alters neutralization sensitivity to other classes of anti-Spike antibodies . 2021 eLife Introduction SARS_CoV_2 D614G 151 156 S 224 229 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. Furthermore, in the A2a clade, this mutation is in linkage disequilibrium with a ORF1b protein variant (P314L) , making it difficult to discern the functional significance of the Spike D614G mutation from population genetics alone. 2021 eLife Introduction SARS_CoV_2 D614G;P314L 185;104 190;109 S 179 184 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. Here, we perform site-directed mutagenesis on a human-codon-optimized Spike protein to introduce the D614G variant and produce SARS-CoV-2-pseudotyped lentiviral particles (S-virus) with this variant and with D614 Spike. 2021 eLife Introduction SARS_CoV_2 D614G 101 106 S;S;S 70;214;173 75;219;174 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. Recently, a novel variant of the SARS-CoV-2 virus carrying a point mutation in the Spike protein (D614G) has emerged and rapidly surpassed others in prevalence, including the original SARS-CoV-2 isolate from Wuhan, China. 2021 eLife Introduction SARS_CoV_2 D614G 98 103 S 83 88 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. Using phylogenomic data, several groups have proposed that the D614G variant may confer increased transmissibility leading to positive selection , while others have claimed that currently available evidence does not support positive selection . 2021 eLife Introduction SARS_CoV_2 D614G 63 68 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. We show that in multiple cell lines, including human lung epithelial cells, that S-virus carrying the D614G mutation is up to eightfold more effective at transducing cells than wild-type S-virus. 2021 eLife Introduction SARS_CoV_2 D614G 102 107 S;S 81;187 82;188 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. In both of the isolates, the P314L (ORF1b), D614G (S), R203K (N), G50N (ORF14), and G204R (N) substitutions were found in common (Table 1). 2021 Microbiology resource announcements Introduction SARS_CoV_2 D614G;G204R;G50N;P314L;R203K 44;84;66;29;55 49;89;70;34;60 N;N;S 62;91;51 63;92;52 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. Of these variations, D614G is reported to be highly prevalent worldwide and is associated with higher viral load and titers of pseudoviruses. 2021 Microbiology resource announcements Introduction SARS_CoV_2 D614G 21 26 33579701 Insights into neutralizing antibody responses in individuals exposed to SARS-CoV-2 in Chile. Since the D614G virus is highly prevalent in Chile, we also assessed the ability of plasma samples to neutralize pseudotypes carrying this variant of the spike protein. 2021 Science advances Introduction SARS_CoV_2 D614G 10 15 S 154 159 33579701 Insights into neutralizing antibody responses in individuals exposed to SARS-CoV-2 in Chile. The spike variant D614G, which emerged in February 2020 and is highly prevalent in viral sequences obtained from Europe as well as North and South America, confers increased infectivity when assessed in different pseudotyped viruses. 2021 Science advances Introduction SARS_CoV_2 D614G 18 23 S 4 9 33579792 The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2. To better understand the impact of the D614G substitution we have now solved the cryo-electron microscopy (cryo-EM) structure of the G614 spike and compared it to that of the D614 spike recently solved by us and others. 2021 Proc Natl Acad Sci U S A Introduction SARS_CoV_2 D614G 39 44 S;S 138;180 143;185 33579792 The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2. Viruses that have spike proteins containing the amino acid substitution D614G are currently predominant in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, and it has recently been shown that G614 viruses have higher infectivity and produce higher viral loads than D614 viruses. 2021 Proc Natl Acad Sci U S A Introduction SARS_CoV_2 D614G 72 77 S 18 23 COVID-19;COVID-19 118;160 158;180 33579792 The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2. We have also shown that both furin cleavage and the presence of ACE2 increase the proportion of the spikes that adopt open conformations and suggested that the D614G substitution could also promote the spike's "opening". 2021 Proc Natl Acad Sci U S A Introduction SARS_CoV_2 D614G 160 165 S;S 100;202 106;207 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. analyzed 103 SARS-CoV-2 genomes and identified two complete linkage SNPs T8782C and C28144T. 2021 Briefings in bioinformatics Introduction SARS_CoV_2 C28144T 84 91 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. In total, both of these two researches support that T8782C and C28144T play important roles in the evolution of SARS-CoV-2. 2021 Briefings in bioinformatics Introduction SARS_CoV_2 C28144T 63 70 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. Though current discoveries about high CFR associated GAAL insertion in SARS-CoV-2 and evolution associated SNPs T8782C and C28144T, researchers did not investigate the functional alterations caused by these mutations, which could explain high CFR and reflect the evolutionary trends of SARS-CoV-2. 2021 Briefings in bioinformatics Introduction SARS_CoV_2 C28144T 123 130 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. Type B is derived from type A with T8782C and C28144T, and type C is derived from type B with one nonsynonymous mutation G26144T. 2021 Briefings in bioinformatics Introduction SARS_CoV_2 C28144T;G26144T 46;121 53;128 33583326 Structural genetics of circulating variants affecting the SARS-CoV-2 spike/human ACE2 complex. D614G does not fall within the putative RBD (AA ~330-530), but some studies suggest it may have a clinically relevant role: D614G is positively correlated with increased case fatality rate (Becerra-Flores & Cardozo,), and it shows increased transmissibility and infectivity compared to the reference genome (Korber,). 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 D614G;D614G 124;0 129;5 RBD 40 43 33583326 Structural genetics of circulating variants affecting the SARS-CoV-2 spike/human ACE2 complex. Despite these preliminary observations, there are still several doubts on the molecular effects of the D614G variant (Grubaugh et al.,). 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 D614G 103 108 33583326 Structural genetics of circulating variants affecting the SARS-CoV-2 spike/human ACE2 complex. In fact, the Spike D614G mutation gives the name to the most frequent viral clade (G), which was first detected in Europe at the end of January 2020, and is currently present in all continents, with increasing frequency over time (Mercatelli & Giorgi,). 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 D614G 19 24 S 13 18 33583326 Structural genetics of circulating variants affecting the SARS-CoV-2 spike/human ACE2 complex. In vitro studies show that viruses carrying the D614G Spike mutation have an increased viral load and cytopathic effect in cultured Vero cells (Tang et al.,). 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 D614G 48 53 S 54 59 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Additionally, three concurrent missense mutations 17747C>T-(P504L), 17858A>G-(Y541C), and 28144T>C-(L84S) tend to fade out, while the other eight concurrent mutations may enhance the infectivity of SARS-CoV-2. 2021 Communications biology Introduction SARS_CoV_2 C17747T;A17858G;T28144C;L84S;P504L;Y541C 50;68;90;100;60;78 58;76;98;104;65;83 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Finally, mutations 23403A>G-(D614G) and 27964C>T-(S24L) likely strengthen the folding stability of the spike protein and ORF8 protein. 2021 Communications biology Introduction SARS_CoV_2 A23403G;C27964T;D614G;S24L 19;40;29;50 27;48;34;54 S;ORF8 103;121 108;125 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Furthermore, the US SARS-CoV-2 strains that have 1059C>T-(T85I), 14408C>T-(P323L), 23403A>G-(D614G), 25563G>T-(Q57H), 28144T>C-(L84S), 28881G>A-(R203K), 28882G>A-(R203K), and 28883G>C-(G204R) mutations may become more infectious in the United States. 2021 Communications biology Introduction SARS_CoV_2 C1059T;C14408T;A23403G;G25563T;T28144C;G28881A;G28882A;G28883C;D614G;G204R;L84S;P323L;Q57H;R203K;R203K;T85I 49;65;83;101;118;135;153;175;93;185;128;75;111;145;163;58 56;73;91;109;126;143;161;183;98;190;132;80;115;150;168;62 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Moreover, a US-unique mutation, 27964C>T-(S24L), shows an interesting female-dominated pattern. 2021 Communications biology Introduction SARS_CoV_2 C27964T;S24L 32;42 40;46 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. A key concern is that certain polymorphisms may enhance SARS-CoV-2 infectivity or transmission, akin to what was seen for Spike D614G, which has overtaken the original D614 form of the virus that dominated at the outset of the pandemic. 2021 medRxiv Introduction SARS_CoV_2 D614G 128 133 S 122 127 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Given the broad detection of the lineages across multiple states and the apparent increase in frequency of detection, these novel emergent Q677H and Q677P lineages merit further study for potential differences in transmissibility. 2021 medRxiv Introduction SARS_CoV_2 Q677H;Q677P 139;149 144;154 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Missense mutations at other positions, for example S477N and N439K, have appeared multiple times in large infection clusters in Australia and Europe, and are associated with resistance to certain antibodies and/or increased affinity for ACE2. 2021 medRxiv Introduction SARS_CoV_2 N439K;S477N 61;51 66;56 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. One early mutation in Spike, D614G, quickly came to dominate the pandemic (currently accounting for >98% of sequences), at least in part because it promotes an S conformation that is more competent for binding to angiotensin-converting enzyme 2 (ACE2) and reduces shedding of the S1 subunit that contains the receptor binding domain. 2021 medRxiv Introduction SARS_CoV_2 D614G 29 34 RBD;S;S 309;22;160 332;27;161 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Such circumstances are thought to have contributed to the emergence of lineages B.1.351 and P.1 (501Y.V2 and 501Y.V3), which in addition to Spike N501Y, harbor at least two other non-synonymous substitutions, K417N/T and E484K, which have been found to confer escape from neutralizing antibodies. 2021 medRxiv Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 221;209;209;146 226;216;216;151 S 140 145 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. We further provide phylogenetic analyses that identify six independent Q677H sub-lineages and one Q677P sub-lineage that all appear to have emerged within the United States. 2021 medRxiv Introduction SARS_CoV_2 Q677H;Q677P 71;98 76;103 33605869 Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil. At least 3 main lineages harbor E484K: B.1.351, first identified in South Africa and widespread worldwide (H. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 32 37 33605869 Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil. Genomic evidence of SARS-CoV-2 reinfection involving E484K spike mutation, Brazil. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 53 58 33605869 Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil. In the first infection, the retrieved genome had the S:G1219C mutation, whereas the mutation S:E484K was observed in the second infection. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K;G1219C 95;55 100;61 S;S 53;93 54;94 33605869 Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil. Our report of SARS-CoV-2 reinfection with a E484K variant corroborates in vitro and in silico studies that estimated the potential of lineages carrying this mutation to escape from neutralizing antibodies (3; Z. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 44 49 33605869 Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil. Tegally et al.); P.1, recently described in Manaus, Brazil, which harbors a constellation of new mutations (including N501Y) (N.R. 2021 Emerging infectious diseases Introduction SARS_CoV_2 N501Y 118 123 33605869 Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil. The E484K mutation, located in the viral receptor binding domain, has been emerging independently in several SARS-CoV-2 variants, and its monitoring is of pivotal importance in the current stage of the pandemic. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 4 9 RBD 41 64 33605869 Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil. We report a case of reinfection from distinct SARS-CoV-2 lineages in Brazil harboring the E484K mutation, a variant associated with escape from neutralizing antibodies (2; A.J. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 90 95 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. D614G (Aspartate to Glycine) mutation in the S gene has been reported to result in increased transduction into human epithelial cells. 2020 Frontiers in genetics Introduction SARS_CoV_2 D614G 0 5 S 45 46 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. N gene mutations R203K and G204R are believed to increase viral fitness, survival and adaptation to humans. 2020 Frontiers in genetics Introduction SARS_CoV_2 G204R;R203K 27;17 32;22 N 0 1 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. P4715L in ORF1ab is believed to play a major role in interaction with other proteins that regulate RNA dependent RNA polymerase. 2020 Frontiers in genetics Introduction SARS_CoV_2 P4715L 0 6 RdRp;ORF1ab 99;10 127;16 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. SNPs in the genome that result in commonly reported non-synonymous mutations such as P4715L in ORF1ab, D614G in S gene, R203K, and G204R in N gene are some of the commonly reported. 2020 Frontiers in genetics Introduction SARS_CoV_2 D614G;G204R;P4715L;R203K 103;131;85;120 108;136;91;125 ORF1ab;N;S 95;140;112 101;141;113 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. Interestingly, S477N occurs very frequently alongside the D614G variant which has been reported to be associated with a very high viral load, structurally these two sites are located distinctly in the spike protein, but the very high frequency of co-occurrence among these two sites needs to be investigated. 2021 Scientific reports Introduction SARS_CoV_2 D614G;S477N 58;15 63;20 S 201 206 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. A few B.1.1.7 genomes with the E484K mutation have also recently been detected. 2021 bioRxiv Introduction SARS_CoV_2 E484K 31 36 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. All of these RBS-C antibodies also interact with E484 (Figure 4A), many with an Arg residue in CDR H3, suggesting that RBD-E484K may influence neutralization by RBS-C antibodies. 2021 bioRxiv Introduction SARS_CoV_2 E484K 123 128 RBD 119 122 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. As a result, IGHV1-2 antibodies [like IGHV3-53/66 ], can also engage the RBD in another example of two different binding modes, both of which are susceptible to escape by the E484K mutation, but not K417N (Figure 1C-D). 2021 bioRxiv Introduction SARS_CoV_2 E484K;K417N 175;199 180;204 RBD 73 76 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Consistently, binding and neutralization of IGHV3-53/3-66 antibodies with binding mode 2 (Figure S3) are abolished by E484K, but not K417N (Figure 1C-D, Figure S1). 2021 bioRxiv Introduction SARS_CoV_2 E484K;K417N 118;133 123;138 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Consistently, binding of IGHV3-53/3-66 and IGHV1-2 antibodies to RBD was abolished by either K417N or E484K mutations (Figure S1). 2021 bioRxiv Introduction SARS_CoV_2 E484K;K417N 102;93 107;98 RBD 65 68 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Furthermore, SARS-CoV-2 pseudovirus neutralization by two other highly potent antibodies CC6.29 and COVA2-15 was markedly reduced by the E484K mutation (Figure 1C). 2021 bioRxiv Introduction SARS_CoV_2 E484K 137 142 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. IGHV3-53 and IGHV3-66, which differ by only one conservative substitution V12I, and IGHV1-2 are the most enriched IGHV genes used among 1,593 RBD antibodies from 32 studies (Figure 1B). 2021 bioRxiv Introduction SARS_CoV_2 V12I 74 78 RBD 142 145 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Importantly, all of the IGHV3-53/3-66 antibodies that bind to the RBS-A epitope interact with K417 (and N501Y), consistent with our neutralization results (Figure 1C-D). 2021 bioRxiv Introduction SARS_CoV_2 N501Y 104 109 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Importantly, CV05-163 also extensively interacts with RBD-E484 via H-bonds (VH W50 and VH N58) and a salt bridge (VL R91) (Figure 3B) that explains why the binding and neutralization by CV05-163 were diminished by the E484K mutant (Figure 1C-D, Figure S1). 2021 bioRxiv Introduction SARS_CoV_2 E484K 218 223 RBD 54 57 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. In addition, neutralization by IGHV1-2 antibodies was strongly reduced in the E484K variant (Figure 1C-D). 2021 bioRxiv Introduction SARS_CoV_2 E484K 78 83 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. In addition, neutralization by REGN10933 was reduced by both K417N and E484K (Figure 1C), which is a potent antibody used for the therapeutic treatment of COVID-19. 2021 bioRxiv Introduction SARS_CoV_2 E484K;K417N 71;61 76;66 COVID-19 155 163 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. In particular, germline-encoded VH Y33 and VH N52 (somatically mutated to S52 in C121) and S54 are involved in polar interactions with the side chain of RBD-E484, where these H-bonds would be altered by substitution with Lys (Figure 3A) and diminish binding and neutralization of IGHV1-2 antibodies against E484K (Figure 1C-D, Figure S1). 2021 bioRxiv Introduction SARS_CoV_2 E484K 307 312 RBD 153 156 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Indeed, binding and neutralization of RBS-C antibody CV07-270 was abrogated by RBD-E484K (Figure S1 and Figure 1C). 2021 bioRxiv Introduction SARS_CoV_2 E484K 83 88 RBD 79 82 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. K417N/T would diminish such interactions and, therefore, affect antibody binding and neutralization. 2021 bioRxiv Introduction SARS_CoV_2 K417N;K417T 0;0 7;7 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Neutralization of four and five antibodies out of the 18 tested antibodies were abolished by K417N and E484K, respectively. 2021 bioRxiv Introduction SARS_CoV_2 E484K;K417N 103;93 108;98 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Overall, our results demonstrate that RBS mutations K417N and E484K can either abolish or extensively reduce the binding and neutralization of several major classes of SARS-CoV-2 RBD antibodies. 2021 bioRxiv Introduction SARS_CoV_2 E484K;K417N 62;52 67;57 RBD 179 182 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Strikingly, neutralization by all six highly potent IGHV3-53/3-66 antibodies that we tested was diminished for either K417N (binding mode 1) or E484K (binding mode 2) mutations (Figure 1C-D). 2021 bioRxiv Introduction SARS_CoV_2 E484K;K417N 144;118 149;123 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Such antigenic drift was also observed in at least one well-studied immunosuppressed COVID-19 patient, and included N501Y and E484K mutations. 2021 bioRxiv Introduction SARS_CoV_2 E484K;N501Y 126;116 131;121 COVID-19 85 93 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. The B.1.351 and B.1.1.28.1 lineages both share three mutations, namely K417N/T, E484K, and N501Y (which is also present in the UK B.1.1.7 lineage). 2021 bioRxiv Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 80;71;71;91 85;78;78;96 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. This observation provides a structural explanation for K417N escape in all tested IGHV3-53/3-66 antibodies with binding mode 1 (Figures 1C-D and 2B, Figure S3). 2021 bioRxiv Introduction SARS_CoV_2 K417N 55 60 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. To test the effect of the RBD-K417N and RBD-E484K mutations on neutralizing antibodies that target the S309 and CR3022 sites, we performed binding and neutralization assays on CV38-142 and COVA1-16. 2021 bioRxiv Introduction SARS_CoV_2 E484K;K417N 44;30 49;35 RBD;RBD 26;40 29;43 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Two of these three mutations, K417N and E484K, decrease the neutralizing activity of sera as well as of monoclonal antibodies isolated from COVID-19 convalescent plasma and vaccinated individuals. 2021 bioRxiv Introduction SARS_CoV_2 E484K;K417N 40;30 45;35 COVID-19 140 148 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. We tested the activity of a panel of 18 neutralizing antibodies isolated from COVID-19 patients or humanized mice against wild-type (Wuhan) SARS-CoV-2 pseudovirus, as well as single mutants K417N and E484K (Figure 1C). 2021 bioRxiv Introduction SARS_CoV_2 E484K;K417N 200;190 205;195 COVID-19 78 86 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Another variant that recently emerged in California, United States, designated as B.1.429, contains 4 missense mutations in spike, one of which is a single L452R RBD mutation. 2021 medRxiv Introduction SARS_CoV_2 L452R 156 161 S;RBD 124;162 129;165 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. B.1.1.7 harbors 3 amino acid deletions and 7 missense mutations in spike, including D614G as well as N501Y in the ACE2 receptor-binding domain (RBD), and has been reported to be more infectious than D614G. 2021 medRxiv Introduction SARS_CoV_2 D614G;D614G;N501Y 84;199;101 89;204;106 S;RBD 67;144 72;147 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Novel variants arising from the B.1.1.28 lineage first described in Brazil and Japan, termed P.2 (with 3 spike missense mutations) and P.1 (with 12 spike missense mutations), contain this E484K mutation, and P.1 in particular also contains K417T and N501Y mutations in RBD. 2021 medRxiv Introduction SARS_CoV_2 E484K;K417T;N501Y 188;240;250 193;245;255 S;S;RBD 105;148;269 110;153;272 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Of particular concern is an E484K mutation in RBD, which was recently identified through deep mutational scanning as a variant with the potential to evade monoclonal and serum antibody responses. 2021 medRxiv Introduction SARS_CoV_2 E484K 28 33 RBD 46 49 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. One of the earliest variants that emerged and rapidly became globally dominant was D614G. 2021 medRxiv Introduction SARS_CoV_2 D614G 83 88 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. There have also been reports of SARS-CoV-2 transmission between humans and minks in Denmark with a variant called mink cluster 5 or B.1.1.298, which harbors a 2-amino acid deletion and 4 missense mutations including Y453F in RBD. 2021 medRxiv Introduction SARS_CoV_2 Y453F 216 221 RBD 225 228 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. This lineage bears three RBD mutations, K417N, E484K, and N501Y, in addition to several mutations outside of RBD, and several reports have suggested that convalescent and vaccinee sera have decreased cross-neutralization of B.1.351 lineage variants. 2021 medRxiv Introduction SARS_CoV_2 E484K;K417N;N501Y 47;40;58 52;45;63 RBD;RBD 25;109 28;112 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. We find that although neutralization is largely preserved against many variants, those containing the K417N/T, E484K, and N501Y RBD mutations, namely, P.1 and B.1.351 variants, have significantly decreased neutralization even in fully vaccinated individuals. 2021 medRxiv Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 111;102;102;122 116;109;109;127 RBD 128 131 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. While several studies demonstrated that this strain is more infectious, we and others found that sera from convalescent individuals showed effective cross-neutralization of both wildtype and D614G variants. 2021 medRxiv Introduction SARS_CoV_2 D614G 191 196 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Concerns have been raised as to whether these vaccines will be effective against newly emergent SARS-CoV-2 variants, such as B.1.1.7 (N501Y.V1), B.1.351 (N501Y.V2) and P1 (N501Y.V3) that originated in the UK, South Africa, and Brazil and are now being detected all over the world. 2021 medRxiv Introduction SARS_CoV_2 N501Y;N501Y;N501Y 134;154;172 139;159;177 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Finally, we show that the recent emergence and transmission of B.1.1.7 viruses bearing the Spike E484K mutation results in significant additional loss of neutralisation by BNT162b2 mRNA-elicited antibodies, convalescent sera and mAbs. 2021 medRxiv Introduction SARS_CoV_2 E484K 97 102 S 91 96 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. In this study, we assess antibody responses against the the B.1.1.7 variant after vaccination with the first and second doses of BNT162b2, showing modest reduction in neutralisation against pseudoviruses bearing B.1.1.7 Spike mutations (DeltaH69/V70, Delta144, N501Y, A570D, P681H, T716I, S982A and D1118H). 2021 medRxiv Introduction SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;T716I 268;299;261;275;289;282 273;305;266;280;294;287 S 220 225 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. A SARS-CoV-2 S amino acid change, D614G, is now dominant in most places around the globe. 2021 Cell Introduction SARS_CoV_2 D614G 34 39 S 13 14 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Initial studies suggest that D614G viruses exhibit increased sensitivity to neutralizing antibodies, likely due to the effect of the mutation on the molecular dynamics of the S protein. 2021 Cell Introduction SARS_CoV_2 D614G 29 34 S 175 176 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. N439K provides a sentinel example of immune escape, indicating that RBM variants must be evaluated when considering vaccines and the therapeutic or prophylactic use of mAbs. 2021 Cell Introduction SARS_CoV_2 N439K 0 5 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. To understand the implications of this structural plasticity, which could allow the RBD to accommodate amino acids changes that could contribute to immune evasion, we defined the clinical and epidemiological impact, molecular features, and immune response to the RBM mutation N439K. 2021 Cell Introduction SARS_CoV_2 N439K 276 281 RBD 84 87 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. We find that the N439K mutation results in enhanced RBD affinity for hACE2, it is associated with a similar clinical spectrum of disease and slightly higher viral loads in vivo compared to viruses with the wild-type (WT) N439 residue, and it results in immune escape from polyclonal sera from a proportion of recovered individuals and some neutralizing mAbs. 2021 Cell Introduction SARS_CoV_2 N439K 17 22 RBD 52 55 33630820 Detection of B.1.351 SARS-CoV-2 Variant Strain - Zambia, December 2020. Spread of the B.1.351 variant is of public health concern because of the potential for increased transmissibility and, thus, increases in cases, hospitalizations, and deaths.*** The B.1.351 variant might be associated with higher viral loads and contains another spike protein mutation (E484K) that might hinder antibody binding, , which could blunt naturally developed immunity or reduce vaccine efficacy. 2021 MMWR. Morbidity and mortality weekly report Introduction SARS_CoV_2 E484K 287 292 S 263 268 33630820 Detection of B.1.351 SARS-CoV-2 Variant Strain - Zambia, December 2020. The variant included a mutation (N501Y) associated with increased transmissibility. 2021 MMWR. Morbidity and mortality weekly report Introduction SARS_CoV_2 N501Y 33 38 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. After the finding of a new variant of SARS-CoV-2 in Rio de Janeiro, we have made an effort to survey whether this new lineage harboring the E484K mutation could also be found in the second wave of COVID-19 affecting southern Brazil, and we aimed to investigate the presence of other possible lineages circulating in the state. 2021 Virus research Introduction SARS_CoV_2 E484K 140 145 COVID-19 197 205 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. The in silico results provide evidence of affectation in the binding affinity and the free energy binding values for the three different compounds on the S protein wild type (WT) and its mutants (H49Y, D614G, and T573I); these results supported by in silico studies should be further supported with experimental evidence. 2021 Scientific reports Introduction SARS_CoV_2 D614G;T573I;H49Y 202;213;196 207;218;200 S 154 155 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. The review and comparative assessment of sequences of S protein among available SARS-CoV-2 genomes in the GISAID database showed three major mutations (H49Y, D614G, and T573I) circulating among Mexican population. 2021 Scientific reports Introduction SARS_CoV_2 D614G;T573I;H49Y 158;169;152 163;174;156 S 54 55 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. To determine if the mutated S proteins found in Mexican population (H49Y, D614G, and T573I) could affect its 3D structure conformations, here we employed MD simulations for full-length atomistic models of S protein 3D structure and its mutants. 2021 Scientific reports Introduction SARS_CoV_2 D614G;T573I;H49Y 74;85;68 79;90;72 S;S 28;205 29;206 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Here we use a cat transmission model to show that SARS-CoV-2 genetic diversity is largely shaped by genetic drift and purifying selection, with the notable exception of a single variant in Spike at residue 655 (H655Y). 2021 PLoS pathogens Introduction SARS_CoV_2 H655Y 211 216 S 189 194 33639276 The role of A-to-I RNA editing in infections by RNA viruses: Possible implications for SARS-CoV-2 infection. Finally, the best-studied SARS-CoV-2 mutation to date leading to an amino-acid substitution (D614G) in the spike protein affecting viral binding to ACE2 and consequently cellular entry and virulence is indeed an A-to-G substitution. 2021 Clinical immunology (Orlando, Fla.) Introduction SARS_CoV_2 D614G 93 98 S 107 112 33655251 SARS-CoV-2 B.1.1.7 and B.1.351 Spike variants bind human ACE2 with increased affinity. The B.1.351 variant first identified in South Africa has 3 notable mutations in the Spike Receptor-Binding Domain (RBD), namely K417N, E484K and N501Y while the B.1.1.7 variant first identified in the UK carries the N501Y mutation. 2021 bioRxiv Introduction SARS_CoV_2 E484K;K417N;N501Y;N501Y 135;128;145;216 140;133;150;221 S;RBD 84;115 89;118 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. 1B), six cases with N501Y were identified as belonging to the B.1.1.7 lineage, two cases with E484K as P.2, and one sample as B.1.351, which harbored both N501Y and E484K based on our screening assay. 2021 medRxiv Introduction SARS_CoV_2 E484K;E484K;N501Y;N501Y 94;165;20;155 99;170;25;160 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. 2A) that initially lacked the L5F, D253G, and E484K mutations. 2021 medRxiv Introduction SARS_CoV_2 D253G;E484K;L5F 35;46;30 40;51;33 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. 2B shows that D253G resides in the antigenic supersite within the N-terminal domain, which is a target for neutralizing antibodies, whereas the E484K is situated at the RBD interface with the cellular receptor ACE2. 2021 medRxiv Introduction SARS_CoV_2 D253G;E484K 14;144 19;149 RBD;N 169;66 172;67 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. However, quite unexpectedly, the large majority (n=49) of the remaining cases with E484K fell within a single lineage, B.1.526. 2021 medRxiv Introduction SARS_CoV_2 E484K 83 88 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. Importantly, these effects were largely mediated by the E484K mutation. 2021 medRxiv Introduction SARS_CoV_2 E484K 56 61 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. In conclusion, we identified B.1.526 as a local lineage of concern due to E484K in particular, which could threaten the efficacy of current antibody therapies and vaccines. 2021 medRxiv Introduction SARS_CoV_2 E484K 74 79 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. Likewise, neutralizing activities of convalescent plasma or vaccinee sera are lower by 7.7-fold or 3.4-fold, respectively, against the E484K variant. 2021 medRxiv Introduction SARS_CoV_2 E484K 135 140 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. Moreover, it appears that the E484K mutation has emerged in at least 59 different lineages of SARS-CoV-2, a real testament to convergent evolution. 2021 medRxiv Introduction SARS_CoV_2 E484K 30 35 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. Nearly all of the newly identified B.1.526 variants have a set of common mutations in the spike protein: L5F, T95I, D253G, E484K, D614G, and A701V. 2021 medRxiv Introduction SARS_CoV_2 A701V;D253G;D614G;E484K;L5F;T95I 141;116;130;123;105;110 146;121;135;128;108;114 S 90 95 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. Patients with E484K variant viruses were comparable in gender, race and ethnicity to those with wildtype SARS-CoV-2, but on average were older (58.1 vs 52.4 years, p=0.049) and more likely to present to the ED or be admitted to the hospital (85.9% vs 70.8%, p=0.007, Table S1). 2021 medRxiv Introduction SARS_CoV_2 E484K 14 19 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. Reinfections with P.1, as well as with another related Brazilian variant P.2 that also harbors E484K, have been documented. 2021 medRxiv Introduction SARS_CoV_2 E484K 95 100 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. S2, the neutralizing activity of REGN10987 against E484K pseudovirus is unaltered, but the activities of REGN10933, CB6, and LY-CoV555 are either impaired or abolished. 2021 medRxiv Introduction SARS_CoV_2 E484K 51 56 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. Sequencing results verified the E484K and N501Y substitutions in all samples identified by our screening PCR assays. 2021 medRxiv Introduction SARS_CoV_2 E484K;N501Y 32;42 37;47 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. Subsequently, there was a substantial increase in E484K-positive cases over time. 2021 medRxiv Introduction SARS_CoV_2 E484K 50 55 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. The A701V mutation near the furin cleavage site is also shared with variant B.1.351. 2021 medRxiv Introduction SARS_CoV_2 A701V 4 9 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. The earliest case with E484K was collected in mid-November 2020. 2021 medRxiv Introduction SARS_CoV_2 E484K 23 28 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. The hallmark mutation of B.1.1.7, the first SARS-CoV-2 variant of concern that emerged in the UK, is N501Y located in the receptor-binding domain (RBD) of spike. 2021 medRxiv Introduction SARS_CoV_2 N501Y 101 106 S;RBD 155;147 160;150 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. The impact of the E484K mutation on antibody neutralization was assessed using 4 monoclonal antibodies with emergency use authorization, 10 convalescent plasma, and 10 vaccinee sera. 2021 medRxiv Introduction SARS_CoV_2 E484K 18 23 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. The majority of patients with E484K variants were geographically concentrated in two distinct neighborhoods in the catchment area of our hospital system, but many others were found scattered throughout the metropolitan area without evidence for a single outbreak. 2021 medRxiv Introduction SARS_CoV_2 E484K 30 35 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. The other variants of concern, B.1.351 (first detected in South Africa) and P.1 (first described in Brazilian travelers), share the N501Y mutation with B.1.1.7 but contain an E484K substitution in RBD. 2021 medRxiv Introduction SARS_CoV_2 E484K;N501Y 175;132 180;137 RBD 197 200 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. These were predominantly from samples collected in the Northeastern US, suggesting that E484K in the B.1.526 lineage is now widespread in the region, the original epicenter of COVID-19 in the US. 2021 medRxiv Introduction SARS_CoV_2 E484K 88 93 COVID-19 176 184 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. Viruses harboring N501Y also increased over time, from the earliest detection in mid-January to 2.6% of screened isolates by mid-February. 2021 medRxiv Introduction SARS_CoV_2 N501Y 18 23 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. We first developed rapid PCR-based, single-nucleotide-polymorphism assays to search for N501Y and E484K mutations (see schematic in. 2021 medRxiv Introduction SARS_CoV_2 E484K;N501Y 98;88 103;93 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. We found that 83 (9.0%) were positive for E484K and 17 (1.8%) were positive for N501Y. 2021 medRxiv Introduction SARS_CoV_2 E484K;N501Y 42;80 47;85 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. We then performed whole genome nanopore sequencing on samples flagged as potential N501Y- or E484K-harboring strains (n=65). 2021 medRxiv Introduction SARS_CoV_2 E484K;N501Y 93;83 98;88 33655278 Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York. We therefore began an effort to survey our patient population at the Columbia University Irving Medical Center in New York City for B.1.351 and other E484K variants such as P.1 and P.2. 2021 medRxiv Introduction SARS_CoV_2 E484K 150 155 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. In our follow-up study, we also identified the trend of a positive correlation between the presence of the 14408C>T mutation and increased mutation density in regions under low selective pressure persisted beyond our initial study. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 C14408T 107 115 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. One of the key mutations in the SARS-CoV-2 RdRp coding region is the 14408C>T mutation, responsible for the P323L aminoacid substitution, frequently co-occurring with the 23403A>G mutation of the S gene, responsible for the D614G substitution. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 C14408T;A23403G;D614G;P323L 69;171;224;108 77;179;229;113 RdRP;S 43;196 47;197 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. The mutation that most strongly affects the mutation density was the 14408C>T mutation, predicating it as a genotype of interest. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 C14408T 69 77 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. In particular, mutation N501Y has been shown to provide a more favourable interaction with the angiotensin-converting enzyme 2 (ACE2) in mice. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 N501Y 24 29 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. P681H is located immediately adjacent to the furin cleavage site of importance for infection and transmission and the HV 69-70 deletion has been described in the context of evasion to the human immune response. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 P681H 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Recently, the spike variant D614G has emerged, as the most prevalent clade at multiple geographic levels that represented up to 78%. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 28 33 S 14 19 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. A recent announcement by MOH revealed that five clusters in Malaysia, namely Benteng (23 viruses), Sivagangga (4 viruses), Tawar (3 viruses), Sungai (1 virus) and Bukit Tiram (1 virus); were found to display the D614G mutation in Spike protein. 2022 Materials today. Proceedings Introduction SARS_CoV_2 D614G 212 217 S 230 235 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. Analysis of more than 28,000 S gene sequence in May 2020 revealed that the variant carrying the D614G Spike mutation became the globally dominant form of SARS-CoV-2. 2022 Materials today. Proceedings Introduction SARS_CoV_2 D614G 96 101 S;S 102;29 107;30 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. Hence D614G genotype is likely to be more infectious, due to higher viral loads in COVID-19 patients infected with G614 variant. 2022 Materials today. Proceedings Introduction SARS_CoV_2 D614G 6 11 COVID-19 83 91 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. Nevertheless, it has been observed that the spike D614G substitution increases the susceptibility of G614 virus to neutralisation by antibodies, suggesting that the efficacy of vaccines, designed based on the original D614 spike sequence, could not be reduced. 2022 Materials today. Proceedings Introduction SARS_CoV_2 D614G 50 55 S;S 44;223 49;228 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. suggest that D614G mutation increased virus infectivity by assembling more functional Spike protein density in the virion, allowing more efficient person-to-person transmission. 2022 Materials today. Proceedings Introduction SARS_CoV_2 D614G 13 18 S 86 91 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. The frequency of D614G genotype expands by April to May 2020. 2022 Materials today. Proceedings Introduction SARS_CoV_2 D614G 17 22 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. They also show that the G614 variant retained higher infectivity at various temperature tested, thus suggesting a D614G mutation increase the stability of SARS-CoV-2. 2022 Materials today. Proceedings Introduction SARS_CoV_2 D614G 114 119 33681755 The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant. Experimental findings showed that the N501Y could enhance the binding affinity of SARS-CoV2 spike protein to ACE2. 2021 Medicine in drug discovery Introduction SARS_CoV_2 N501Y 38 43 S 92 97 33681755 The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant. In order to build the N501Y mutant, the sidechain of N501 is replaced by aromatic.sidechain of tyrosine using MCCE. 2021 Medicine in drug discovery Introduction SARS_CoV_2 N501Y 22 27 33681755 The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant. In summary, we showed that the binding affinity of SARS-CoV-2 to human ACE2 is higher in the N501Y mutated structure than that in WT because of the significant change in the electrostatic interactions. 2021 Medicine in drug discovery Introduction SARS_CoV_2 N501Y 93 98 33681755 The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant. In this study, we used a combined Molecular dynamic (MD) and Monte Carlo (MC) simulations to assess the molecular interactions between RBD of S-protein and ACE2 for the N501Y mutant and compared our results with the wild type. 2021 Medicine in drug discovery Introduction SARS_CoV_2 N501Y 169 174 RBD;S 135;142 138;143 33681755 The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant. Recently, it was shown that the spread rate of the virus has become much faster due to different genetic changes in the receptor-binding domain and the FURIN cleavage site.These changes include the mutation of Asparagine at position 501 to Tyrosine (N501Y), which is one of the residues in the RBD-ACE2 contact area. 2021 Medicine in drug discovery Introduction SARS_CoV_2 N501Y;N501Y 210;250 248;255 RBD 294 297 33681755 The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant. The N501Y mutant is shown to decrease the repulsion between carboxylate of ACE2-D355 and backbone oxygen of RBD-T500 RBD-T500 as the distance decreased from 3.81 to 3.42 A. 2021 Medicine in drug discovery Introduction SARS_CoV_2 N501Y 4 9 RBD;RBD 108;117 111;120 33681755 The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant. Then, MCCE is used to generate Boltzmann distribution for all conformer using MC sampling for the wild type and the N501Y mutant at pH 7. 2021 Medicine in drug discovery Introduction SARS_CoV_2 N501Y 116 121 33681755 The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant. Therefore, we herein study how the N501Y mutation in the RBD of the SARS-CoV2 can alter the binding of the virus to ACE2. 2021 Medicine in drug discovery Introduction SARS_CoV_2 N501Y 35 40 RBD 57 60 33681755 The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant. Upon N501Y mutation, RBD-K417 and ACE2-D30 exhibit less attraction than that for WT by ~1.57 Kcal/mol. 2021 Medicine in drug discovery Introduction SARS_CoV_2 N501Y 5 10 RBD 21 24 33688650 Ultrapotent miniproteins targeting the receptor-binding domain protect against SARS-CoV-2 infection and disease in mice. Most importantly, LCB1v1.3 protected animals against the currently emerging B.1.1.7 United Kingdom variant and a SARS-CoV-2 strain encoding key spike substitutions E484K and N501Y present in both the South Africa (B.1.351) and Brazil (B.1.1.248) variants of concern. 2021 bioRxiv Introduction SARS_CoV_2 E484K;N501Y 164;174 169;179 S 144 149 33688664 Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. Lineage P.1 contains 10 new amino acid mutations in the virus spike protein (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I) compared its immediate ancestor (B.1.1.28). 2021 medRxiv Introduction SARS_CoV_2 D138Y;E484K;H655Y;K417T;N501Y;P26S;R190S;T1027I;T20N;L18F 95;116;130;109;123;89;102;137;83;77 100;121;135;114;128;93;107;143;87;81 S 62 67 33688664 Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. Moreover, E484K has been associated with reduced antibody neutralisation and as RBD-presented epitopes account for ~90% of the neutralising activity of sera from individuals previously infected with SARS-CoV-2, tighter binding of P.1 viruses to hACE2 may further reduce the effectiveness of neutralizing antibodies that are competing with hACE2 to bind the RBD. 2021 medRxiv Introduction SARS_CoV_2 E484K 10 15 RBD;RBD 80;357 83;360 33688664 Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. Notably, the same three residues are mutated with the B.1.351 variant of concern, and N501Y is also present in the B.1.1.7 lineage. 2021 medRxiv Introduction SARS_CoV_2 N501Y 86 91 33688664 Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. The former two interact with human angiotensin-converting enzyme 2 (hACE2), whilst E484K is located in a loop region outside the direct hACE2 interface. 2021 medRxiv Introduction SARS_CoV_2 E484K 83 88 33688664 Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. Three key mutations present in P.1, N501Y, K417T and E484K, are located in the spike protein RBD. 2021 medRxiv Introduction SARS_CoV_2 E484K;K417T;N501Y 53;43;36 58;48;41 S;RBD 79;93 84;96 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. A fourth spike gene mutation that is shared by ~48% of V2 sequences and by all V3 sequences is L18F. 2021 medRxiv Introduction SARS_CoV_2 L18F 95 99 S 9 14 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. Almost all the spike genes of sequences in these lineages carry the N501Y mutation at a key receptor binding domain (RBD) site that increases the affinity of the spike protein for human ACE2 receptors by ~2.1-3.5 fold. 2021 medRxiv Introduction SARS_CoV_2 N501Y 68 73 RBD;S;S;RBD 92;15;162;117 115;20;167;120 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. Although both the K417N and K417T mutations can reduce the affinity of spike for ACE2, in conjunction with the N501Y and E484K mutations ACE2 binding is restored to that of wild-type Spike. 2021 medRxiv Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 121;18;28;111 126;23;33;116 S;S 71;183 76;188 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. Crucially, E484K and other mutations at S/484 also frequently confer protection from neutralization by both convalescent sera, vaccine elicited antibodies, and some monoclonal antibodies. 2021 medRxiv Introduction SARS_CoV_2 E484K 11 16 S 40 41 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. K417N and K417T also both have moderately positive impacts on spike expression and these and other mutations at S/417 provide modest protection from neutralization by some convalescent sera, vaccine induced antibodies and some neutralizing monoclonal antibodies. 2021 medRxiv Introduction SARS_CoV_2 K417T;K417N 10;0 15;5 S;S 62;112 67;113 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. Other than the early identification of the D614G substitution in the viral spike protein and P323L in the viral RNA dependent RNA polymerase protein, both of which may have increased viral transmissibility without impacting pathogenesis (reviewed in), few mutations were epidemiologically significant and the evolutionary dynamics of the virus were predominantly characterized by a mutational pattern of slow and selectively-neutral random genetic drift. 2021 medRxiv Introduction SARS_CoV_2 D614G;P323L 43;93 48;98 RdRp;S 112;75 140;80 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. The vast majority of V2 and V3 variants and ~0.3% of more recent samples of V1 variants also have a spike E484K mutation. 2021 medRxiv Introduction SARS_CoV_2 E484K 106 111 S 100 105 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. There is therefore increasing evidence that viruses carrying the E484K mutation (with or without 501Y) will be able to more frequently infect both previously infected and vaccinated individuals. 2021 medRxiv Introduction SARS_CoV_2 E484K 65 70 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. Viruses carrying the L18F mutation increased in prevalence from the start of the pandemic and now account for ~10% of sampled SARS-CoV-2 sequences. 2021 medRxiv Introduction SARS_CoV_2 L18F 21 25 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. Whereas V2 sequences generally carry a K417N mutation, V3 sequences carry a K417T mutation. 2021 medRxiv Introduction SARS_CoV_2 K417N;K417T 39;76 44;81 33688689 Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. The P.1/P.2 lineages originally discovered in Brazil harbor the E484K mutation within the spike protein which, along with other mutations, is associated with reduced neutralization in laboratory experiments. 2021 medRxiv Introduction SARS_CoV_2 E484K 64 69 S 90 95 33707329 Coding-Complete Genome Sequences and Mutation Profiles of Nine SARS-CoV-2 Strains Detected from COVID-19 Patients in Bangladesh. Additionally, we found cluster substitutions D614G, Q677H, and A871V in the spike protein of GRBL_S10. 2021 Microbiology resource announcements Introduction SARS_CoV_2 A871V;D614G;Q677H 63;45;52 68;50;57 S 76 81 33707329 Coding-Complete Genome Sequences and Mutation Profiles of Nine SARS-CoV-2 Strains Detected from COVID-19 Patients in Bangladesh. In this announcement, among the multitude of mutations, we are reporting two mutations, one at position 1450 from G (0 evidence) to A (267 evidence) in GRBL_S1, which results in the amino acid substitution of E484K, and one at position 1076 from G (0 evidence) to C (4,559 evidence) in GRBL_S9, which results in S359T in the spike protein region ("evidence" relates to area-wise coverage obtained by Snippy tools for short-read sequences generated by Illumina MiniSeq). 2021 Microbiology resource announcements Introduction SARS_CoV_2 E484K;S359T 209;312 214;317 S 325 330 33707329 Coding-Complete Genome Sequences and Mutation Profiles of Nine SARS-CoV-2 Strains Detected from COVID-19 Patients in Bangladesh. It is also noteworthy that in two samples, GRBL_S2 (2,446 evidence) and GRBL_S3 (68 evidence), the deletion of GATCAT and its subsequent replacement by G at nucleotide position 108 of ORF7b resulted in the introduction of a stop codon, ultimately resulting in a frameshift mutation and D36E substitution, potentially without any loss of function. 2021 Microbiology resource announcements Introduction SARS_CoV_2 D36E 286 290 ORF7b 184 189 33707329 Coding-Complete Genome Sequences and Mutation Profiles of Nine SARS-CoV-2 Strains Detected from COVID-19 Patients in Bangladesh. Substitutions pertaining to the nucleocapsid protein coding region were S327L, G18V, and A252S in samples GRBL_S1, GRBL_S11, and GRBL_S14, respectively. 2021 Microbiology resource announcements Introduction SARS_CoV_2 A252S;G18V;S327L 89;79;72 94;83;77 N 32 44 33707329 Coding-Complete Genome Sequences and Mutation Profiles of Nine SARS-CoV-2 Strains Detected from COVID-19 Patients in Bangladesh. The E484K substitution was observed in a cluster containing D614G, P681H, and S13I changes (GRBL_S1), while the S359T amino acid substitution was observed in a cluster containing D614G and A942V changes (GRBL_S9). 2021 Microbiology resource announcements Introduction SARS_CoV_2 A942V;D614G;D614G;E484K;P681H;S13I;S359T 189;60;179;4;67;78;112 194;65;184;9;72;82;117 33707329 Coding-Complete Genome Sequences and Mutation Profiles of Nine SARS-CoV-2 Strains Detected from COVID-19 Patients in Bangladesh. Within the open reading frame 1ab (ORF1ab) region, we observed amino acid substitutions of I1257S in GRBL_S1 and L151I and T275A in GRBL_S14. 2021 Microbiology resource announcements Introduction SARS_CoV_2 I1257S;L151I;T275A 91;113;123 97;118;128 ORF1ab 35 41 33714462 Pyrococcus furiosus Argonaute coupled with modified ligase chain reaction for detection of SARS-CoV-2 and HPV. There is a kind of mutant called spike D614G which reduces S1 shedding and increases infectivity. 2021 Talanta Introduction SARS_CoV_2 D614G 39 44 S 33 38 33714462 Pyrococcus furiosus Argonaute coupled with modified ligase chain reaction for detection of SARS-CoV-2 and HPV. There is a one-base difference in the genome between wild type SARS-CoV-2 and its mutant spike D614G. 2021 Talanta Introduction SARS_CoV_2 D614G 95 100 S 89 94 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. At present, two new RBD variants known as N439K and N501Y have been found in humans. 2021 The Journal of biological chemistry Introduction SARS_CoV_2 N439K;N501Y 42;52 47;57 RBD 20 23 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. However, we found a 4-fold affinity increase of the Y453F variant to the ACE-2 binding that could result in an enhanced spreading potential. 2021 The Journal of biological chemistry Introduction SARS_CoV_2 Y453F 52 57 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. One of these cluster variants, disclosed as "cluster five," has been discovered in Denmark and bears a tyrosine to phenylalanine substitution (Y453F) in the receptor-binding domain (RBD) of the spike protein. 2021 The Journal of biological chemistry Introduction SARS_CoV_2 Y453F 143 148 S;RBD 194;182 199;185 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. The Y453F variant did not alter the inhibition potency of sera from convalescent individuals exposed to the WT strain in the spring of 2020, nor did it challenge the humoral vaccine response in a mouse model immunized with WT RBD or prefusion-stabilized spike protein ectodomain. 2021 The Journal of biological chemistry Introduction SARS_CoV_2 Y453F 4 9 S;RBD 254;226 259;229 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. To address the biophysical characteristics and the impact of this variant on established immunity, we expressed recombinant SARS-CoV-2 RBD WT (WT, from the Wuhan-Hu-1/2019 isolate) and "cluster-five" Y453F and the ACE-2 ectodomain. 2021 The Journal of biological chemistry Introduction SARS_CoV_2 Y453F 200 205 RBD 135 138 33725432 Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. Another independent lineage of SARS-CoV-2 (P.1) also containing the E484K, K417N, and some B.1.351 NTD mutations has been identified in Brazil. 2021 The New England journal of medicine Introduction SARS_CoV_2 E484K;K417N 68;75 73;80 33725432 Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. Furthermore, we report on immunogenicity of ChAdOx1 nCoV-19 and on post hoc pseudovirus and live-virus neutralization assay investigations of the sensitivity of the original D614G virus and the B.1.351 variant to vaccine-elicited antibodies. 2021 The New England journal of medicine Introduction SARS_CoV_2 D614G 174 179 33725432 Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. In contrast, the E484K and K417N RBD mutations and mutations in the NTD have been associated with neutralizing antibody escape. 2021 The New England journal of medicine Introduction SARS_CoV_2 E484K;K417N 17;27 22;32 RBD 33 36 33725432 Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. The B.1.1.7 (N501Y.V1) lineage, first identified in the United Kingdom, includes the N501Y mutation, which has been associated with 53% increased transmissibility. 2021 The New England journal of medicine Introduction SARS_CoV_2 N501Y;N501Y 85;13 90;18 33725432 Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. The B.1.1.7 variant, however, has now evolved to include the E484K mutation in the United Kingdom. 2021 The New England journal of medicine Introduction SARS_CoV_2 E484K 61 66 33725432 Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. The B.1.351 (N501Y.V2) lineage first identified in South Africa contains the three RBD mutations and five additional NTD mutations. 2021 The New England journal of medicine Introduction SARS_CoV_2 N501Y 13 18 RBD 83 86 33725432 Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. The RBD mutations include the N501Y mutation, which is associated with increased affinity of SARS-CoV-2 to the angiotensin-converting enzyme 2 (ACE2) receptor. 2021 The New England journal of medicine Introduction SARS_CoV_2 N501Y 30 35 RBD 4 7 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. Although the viral evolution is slowed by the RNA proofreading capability of its replication machinery, a variant with a single-residue substitution (D614G) in its spike (S) protein rapidly became the dominant strain throughout the world. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 150 155 S;S 164;171 169;172 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. Here, we focus on the D614G mutation that is in all currently circulating strains of SARS-CoV-2. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 22 27 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. Likewise, a similar pattern was observed with these mutants in the cell-cell fusion assay, except that Y636A showed substantially weaker fusion activity than R634E. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 R634E;Y636A 158;103 163;108 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. The D614G change did not cause any large local structural rearrangements except for loss of the D614-K854 salt bridge and a small shift of residue 614 toward the three-fold axis. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 4 9 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. The D614G change has apparently also rigidified a neighboring segment of CTD2, residues 620 to 640, which we designate the 630 loop. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 4 9 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. The D614G substitution eliminates a salt bridge between D614 in CTD2 of one subunit and K854 in the FPPR of the adjacent subunit, but the FPPR in the three RBDdown conformation of the G614 trimer remains structured. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 4 9 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. The known S trimer structures indicate that the D614G change breaks a salt bridge between D614 and a lysine residue (K854) in the fusion peptideproximal region (FPPR), which may help clamp the RBD in the prefusion conformation. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 48 53 RBD;S 193;10 196;11 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. The mutant V635K had wild-type phenotypes in these assays, likely because V635 does not make any direct contact with the CTD2. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 V635K 11 16 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. The mutants R634E and Y636A showed intermediate levels of antibody binding because Y636 appears to contribute less to the 630 loopCTD2 interaction than W633, and R634 may help maintain the loops overall shape for inserting between domains. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 R634E;Y636A 12;22 17;27 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. This suggests that D614G has a notable effect on the stability of the SARS-CoV-2 S trimer. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 19 24 S 81 82 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. Thus, the D614G substitution has led to a slightly more open conformation than that of the D614 trimer, even when all three RBDs are down. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 10 15 RBD 124 128 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. To examine the structural changes resulting from the D614G substitution, we superposed the structures of the G614 trimer onto the D614 trimer in the closed conformation, aligning them by the invariant S2. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 53 58 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. To resolve these issues, we report the structural consequences of the D614G substitution in the context of the full-length S protein. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 70 75 S 123 124 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. To test the impact of the 630 loop on S1 shedding and membrane fusion, we generated five S mutants, each containing a single-residue change either in the 630 loop (W633A, R634E, V635K, and Y636A) or the CTD2 hydrophobic surface (V610K) in the G614 sequence. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 R634E;V635K;Y636A;V610K;W633A 171;178;189;229;164 176;183;194;234;169 Membrane;S 54;89 62;90 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. Unsurprisingly, the recent fast-spreading variantsincluding the B.1.1.7 (VUI202012/01; 501Y.V1) lineage from the United Kingdom, the B.1.351 (501Y.V2) lineage from South Africa, and the B.1.1.28 (484K.V2; P.1) lineage from Brazil all contain the D614G substitution (table S3), which suggests that the increased transmissibility of the G614 virus has led to a great number of replication events and to greater genetic diversity, despite a lower absolute mutation rate. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 D614G 246 251 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. When detected by monoclonal antibodies using flow cytometry, mutants V610K and W633A showed markedly lower binding of RBD-specific antibodies [REGN10933 and REGN10987; ] and of an NTD-specific antibody [4A8; ] than the parental G614 S, whereas binding to an S2-specific antibody [0304-3H3; ] was slightly higher. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 V610K;W633A 69;79 74;84 RBD;S 118;233 121;234 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. In this communication, we attempt to assess if social isolation into small family or groups is associated with the emergence of new severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) variants, particularly the P.1 lineage and E484K mutants, in Brazil and in the state of Amazonas. 2021 Cureus Introduction SARS_CoV_2 E484K 236 241 COVID-19 139 179 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. All three recently identified variant SARS-CoV-2 strains have acquired mutations in the ACE2 interaction surface of the RBD: N501Y in B.1.1.7; K417N, E484K, and N501Y in B.1.351; and K417T, E484K, and N501Y in P.1. 2021 Cell Introduction SARS_CoV_2 E484K;E484K;K417N;K417T;N501Y;N501Y;N501Y 150;190;143;183;125;161;201 155;195;148;188;130;166;206 RBD 120 123 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. Compared against the S protein of the 614G virus shows that 501Y.V2-3's S protein contains 8 mutations: four are located at the NTD (L18F, D80A, D215G, and Del242-244), three are in the viral RBD (K417N, E484K, and N501Y), and one is in the S2 region (A701V). 2021 Cell Introduction SARS_CoV_2 D215G;D80A;E484K;N501Y;A701V;K417N;L18F 145;139;204;215;252;197;133 150;143;209;220;257;202;137 RBD;S;S 192;21;72 195;22;73 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. For example, the D614G mutation in the S protein increases viral infectivity in susceptible cells by 8- to 10-fold, and both the infectivity and transmissibility of the D614G mutant virus are significantly elevated in a hamster model. 2021 Cell Introduction SARS_CoV_2 D614G;D614G 17;169 22;174 S 39 40 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. In the early stages of the second wave, 501Y.V2-1 was prevalent; it is identifiable by five amino acid mutations in the S protein (in addition to D614G), including D80A, D215G, E484K, N501Y, and A701V. 2021 Cell Introduction SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;N501Y 195;170;146;164;177;184 200;175;151;168;182;189 S 120 121 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. Subsequently, two further mutations arose in the S protein, L18F, and K417N, resulting in the emergence of variant 501Y.V2-2. 2021 Cell Introduction SARS_CoV_2 K417N;L18F 70;60 75;64 S 49 50 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. The only reported difference in the S protein amino acid sequences between these lineages and the Wuhan-1 strain is the D614G mutation. 2021 Cell Introduction SARS_CoV_2 D614G 120 125 S 36 37 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. Another reported mutation of ORF1ab is P4715 L linked with D614G, which is linked with higher fatality rates in 28 countries and 17 states of the United States. 2021 Virus research Introduction SARS_CoV_2 D614G;P4715L 59;39 64;46 ORF1ab 29 35 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. Out of these mutations, D614G mutation (causing aspartate to glycine at 614 in S protein) is reported to be the most prevalent mutations in Europe, Oceania, South America, Africa, Middle East, and India. 2021 Virus research Introduction SARS_CoV_2 D614G;D614G 48;24 75;29 S 79 80 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. Three other mutations namely C14408T (ORF1b), C241T (5' UTR), C3037T (ORF1a) are reported to be common and coexisting in the same genome, while G11083T has been found mostly in Asian countries. 2021 Virus research Introduction SARS_CoV_2 C14408T;C241T;C3037T;G11083T 29;46;62;144 36;51;68;151 5'UTR;ORF1a 53;70 59;75 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. We studied the frequency of mutations in different ORFs of SARS-CoV-2 genomes, having the mutation of D614G. 2021 Virus research Introduction SARS_CoV_2 D614G 102 107 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. The His69-Val70 deletion (spike N-terminal domain) cooccurring with the Asn439Lys mutation (spike receptor binding domain) in the studied case was not reported in Morocco previously. 2021 Microbiology resource announcements Introduction SARS_CoV_2 N439K 72 81 RBD;S;S;N 98;26;92;32 121;31;97;33 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. The His69-Val70 deletion is one of the mutations reported for new emergent lineages primarily identified in the United Kingdom, while Asn439Lys was primally reported in Scotland and is now spreading worldwide. 2021 Microbiology resource announcements Introduction SARS_CoV_2 N439K 134 143 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. The spike protein D614G mutation, for example, has been implicated in more effective transmission, although the actual impact may be through fixation in an expanding lineage rather than conferring increased transmissibility per se. 2021 PLoS pathogens Introduction SARS_CoV_2 D614G 18 23 S 4 9 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. We then probed the spike metastability by comparing two uncleaved spike antigens, S2P (K986P/V987P) and S2G (K986G/V987G). 2021 Science advances Introduction SARS_CoV_2 K986G;K986P;V987G;V987P 109;87;115;93 114;92;120;98 S;S 19;66 24;71 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Another variant that recently emerged in California, United States, designated as B.1.429, contains four missense mutations in spike, one of which is a single L452R RBD mutation. 2021 Cell Introduction SARS_CoV_2 L452R 159 164 S;RBD 127;165 132;168 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. B.1.1.7 harbors three amino acid deletions and seven missense mutations in spike, including D614G as well as N501Y in the ACE2 receptor-binding domain (RBD), and has been reported to be more infectious than D614G. 2021 Cell Introduction SARS_CoV_2 D614G;D614G;N501Y 92;207;109 97;212;114 S;RBD 75;152 80;155 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Novel variants arising from the B.1.1.28 lineage first described in Brazil and Japan, termed P.2 (with 3 spike missense mutations) and P.1 (with 12 spike missense mutations), contain this E484K mutation, and P.1 in particular also contains K417T and N501Y mutations in RBD. 2021 Cell Introduction SARS_CoV_2 E484K;K417T;N501Y 188;240;250 193;245;255 S;S;RBD 105;148;269 110;153;272 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Of particular concern is an E484K mutation in RBD, which was previously identified through in vitro selection experiments to escape from monoclonal antibodies and was also recently identified through deep mutational scanning as a variant with the potential to evade monoclonal and serum antibody responses. 2021 Cell Introduction SARS_CoV_2 E484K 28 33 RBD 46 49 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. One of the earliest variants that emerged and rapidly became globally dominant was D614G. 2021 Cell Introduction SARS_CoV_2 D614G 83 88 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. There have also been reports of SARS-CoV-2 transmission between humans and minks in Denmark with a variant called mink cluster 5 or B.1.1.298, which harbors a two-amino acid deletion and four missense mutations including Y453F in RBD. 2021 Cell Introduction SARS_CoV_2 Y453F 221 226 RBD 230 233 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. This lineage bears three RBD mutations, K417N, E484K, and N501Y, in addition to several mutations outside of RBD, and several reports have suggested that convalescent and vaccinee sera have decreased cross-neutralization of B.1.351 lineage variants. 2021 Cell Introduction SARS_CoV_2 E484K;K417N;N501Y 47;40;58 52;45;63 RBD;RBD 25;109 28;112 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. We find that although neutralization is largely preserved against many variants, those containing the K417N/T, E484K, and N501Y RBD mutations, namely, P.1 and B.1.351 variants, have significantly decreased neutralization even in fully vaccinated individuals. 2021 Cell Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 111;102;102;122 116;109;109;127 RBD 128 131 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. While several studies demonstrated that this strain is more infectious, we and others found that sera from convalescent individuals showed effective cross-neutralization of both wild type and D614G variants. 2021 Cell Introduction SARS_CoV_2 D614G 192 197 33750399 Modelling the association between COVID-19 transmissibility and D614G substitution in SARS-CoV-2 spike protein: using the surveillance data in California as an example. Early in February 2020, genetic variants with the D614G substitution on the SARS-CoV-2 spike (S) protein began to spread first in Europe and globally and were suspected to potentially affect viral transmission. 2021 Theoretical biology & medical modelling Introduction SARS_CoV_2 D614G 50 55 S;S 87;94 92;95 33750399 Modelling the association between COVID-19 transmissibility and D614G substitution in SARS-CoV-2 spike protein: using the surveillance data in California as an example. Here, 'D614G' denotes the amino acid substitution that changes aspartic acid (D) to glycine (G) on codon 614 of the S protein of SARS-CoV-2. 2021 Theoretical biology & medical modelling Introduction SARS_CoV_2 D614G 7 12 S 116 117 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Novel mutations in the spike protein of B.1.1.7 (deletion 69-70, 144 and substitution K417N, K417T, E484K, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, and many others) might have altered the SARS-CoV-2 ability to transmit and infect. 2021 Journal of cellular physiology Introduction SARS_CoV_2 A570D;D1118H;D614G;E484K;K417N;K417T;N501Y;P681H;S982A;T716I 114;149;121;100;86;93;107;128;142;135 119;155;126;105;91;98;112;133;147;140 S 23 28 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The mutation N501Y co-occurs with other mutations in the N, orf8, orf1a, and S glycoprotein in 501, involving two deletions Delta69 and Delta70. 2021 Journal of cellular physiology Introduction SARS_CoV_2 N501Y 13 18 S;ORF1a;ORF8;N 77;66;60;57 91;71;64;58 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The new variant of South Africa carries K417N-E484K-N501Y mutations amongst others (Kirby, 2021; Koyama et al., 2020). 2021 Journal of cellular physiology Introduction SARS_CoV_2 K417N;E484K;N501Y 40;46;52 45;51;57 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The substitution mutations N501Y, E484K, and others) within RBD of the UK and South African SARS-CoV-2 strains are now spreading unchecked. 2021 Journal of cellular physiology Introduction SARS_CoV_2 E484K;N501Y 34;27 39;32 RBD 60 63 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Therefore, in the present study, we employed the protein-protein docking methods with a biophysical investigation to examine the effect of K417N-E484K-N501Y, K417T-E484K-N501Y, E484K, N501Y, and E484K-N501Y mutations on the structure and binding of the ACE2 receptor and their correlation with infectivity of newly emerged strains of SARS-CoV-2. 2021 Journal of cellular physiology Introduction SARS_CoV_2 E484K;E484K;K417N;K417T;N501Y;E484K;E484K;N501Y;N501Y;N501Y 177;195;139;158;184;145;164;151;170;201 182;200;144;163;189;150;169;156;175;206 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. However, the role of D614G mutation in the emergence of a more transmissible variant of SARS-CoV-2 was first highlighted by Korber et al. 2021 PloS one Introduction SARS_CoV_2 D614G 21 26 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. Recently, the detection of a D614G mutation in the S protein of SARS-CoV-2 and subsequent global spread has received tremendous attention. 2021 PloS one Introduction SARS_CoV_2 D614G 29 34 S 51 52 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. Since the initial report, several studies on the role of D614G amino acid change in enhanced infectivity of SARS-CoV-2 have been documented. 2021 PloS one Introduction SARS_CoV_2 D614G 57 62 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. The D614G mutation has been shown to be present in the S2 domain of spike protein and is critical for cleavage of S1 facilitating the fusion of virus with host cell membrane. 2021 PloS one Introduction SARS_CoV_2 D614G 4 9 Membrane;S 165;68 173;73 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. At the same time, a 3-fold higher affinity for the SARS-CoV-2 peptide with respect to SARS-CoV-1 was experimentally measured by Toto et al, using a mutant of the human PALS1 protein (F318W) through equilibrium and ultra-fast kinetic binding measurements monitored by FRET, thus giving experimental support to our in silico model. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 F318W 183 188 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. The F318W mutant was selected for the FRET measurements due to the higher intrinsic fluorescence of the variant expressing tryptophan. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 F318W 4 9 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. Thus, in the present study, we compare the binding affinities to the SARS-CoV peptides of both the wild type and the F318W mutant PALS1 by using Surface Plasmon Resonance (SPR). 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 F318W 117 122 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Our results suggest that, consistent with its convergent evolution, the N501Y substitution is a critical spike protein determinant of enhanced infection of the upper airway and transmission. 2021 bioRxiv Introduction SARS_CoV_2 N501Y 72 77 S 105 110 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Since then, additional spike mutations have been identified, including an N501Y spike substitution that occurred convergently in the United Kingdom (UK), South Africa, and Brazil. 2021 bioRxiv Introduction SARS_CoV_2 N501Y 74 79 S;S 23;80 28;85 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. The first dominant mutation observed in SARS-CoV-2 encoded the spike protein D614G substitution, which enhances viral replication in human airway epithelial cells and viral transmission in animal models. 2021 bioRxiv Introduction SARS_CoV_2 D614G 77 82 S 63 68 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. Although we did not observe any reduction in neutralization titers towards the B.1.1.7 variant, similar to what was seen with the N501Y point mutant, animals vaccinated with RBD-NP or HexaPro had 5-fold reduced serum neutralizing Ab titers against the B.1.351 S variant using HIV pseudovirus (GMT 1x102. 2021 bioRxiv Introduction SARS_CoV_2 N501Y 130 135 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. Furthermore, we observed a nearly ten-fold reduction in potency in sera from individuals who received two doses of the Pfizer-BioNTech BNT162b2 mRNA vaccine when comparing serum neutralization titers against B.1.351 S (GMT 6.7x101) pseudotyped virus to wild-type (D614G) SARS-CoV-2 S (GMT 6x102). 2021 bioRxiv Introduction SARS_CoV_2 D614G 264 269 S;S 216;282 217;283 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. Most single-residue RBD mutations tested did not affect the serum neutralizing titers of NHPs vaccinated twice with RBD-NP or soluble HexaPro using an HIV pseudotyped virus compared to wild-type (D614G) SARS-CoV-2 S (GMT 5x102 and 7x102 for RBD-NP and HexaPro, respectively. 2021 bioRxiv Introduction SARS_CoV_2 D614G 196 201 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. The E484K mutation reduced serum neutralizing activity by ~5-fold and ~7-fold for RBD-NP and HexaPro (GMT 1x102) compared to wild-type (D614G) SARS-CoV-2 S, respectively, whereas the E484A and E484D mutations did not significantly affect the neutralizing activity induced by either immunogen. 2021 bioRxiv Introduction SARS_CoV_2 E484A;E484D;E484K;D614G 183;193;4;136 188;198;9;141 RBD;S 82;154 85;155 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. The N501Y substitution present in the B.1.1.7 and B.1.351 lineages, the mink-associated Y453F substitution, and the prevalent N439K mutation did not affect the neutralization potency of any RBD-NP- or HexaPro-elicited sera significantly, while these substitutions have been associated with loss of neutralization for some mAbs. 2021 bioRxiv Introduction SARS_CoV_2 N439K;N501Y;Y453F 126;4;88 131;9;93 RBD 190 193 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. The SARS-CoV-2 S D614G mutation has become globally dominant and is associated with enhanced viral transmission and replication but does not significantly affect Ab-mediated neutralization. 2021 bioRxiv Introduction SARS_CoV_2 D614G 17 22 S 15 16 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. These changes in neutralizing activity were presumably largely due to the E484K substitution albeit RBD-specific binding Ab titers were not markedly different compared to widtype RBD (Extended Data. 2021 bioRxiv Introduction SARS_CoV_2 E484K 74 79 RBD;RBD 100;179 103;182 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. This boost induced very high serum neutralizing activity against wild-type (D614G) SARS-CoV-2 (GMT 2x105) (Extended Data. 2021 bioRxiv Introduction SARS_CoV_2 D614G 76 81 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. To assess the neutralization breadth of RBD-NP-elicited Abs, we evaluated serum neutralizing activity against a panel of pseudotyped viruses comprising wild-type (D614G) SARS-CoV-2 S and nine single-residue SARS-CoV-2 RBD mutants detected in clinical isolates (G446S, Y453F, L455F, T478I, E484A/K, F486L, S494P, and N501Y) as well as the B.1.1.7 (H69-V70 deletion, Y144 deletion, N501Y, A570D, P681H, T716I, S982A, D1118H) and B.1.351 (L18F, D80A, D215G, L242-L244 deletion, R246I, K417N, E484K, N501Y, A701V) variants of concern that originated in the UK and South Africa, respectively. 2021 bioRxiv Introduction SARS_CoV_2 A570D;A701V;D1118H;D215G;D80A;E484A;E484K;E484K;F486L;K417N;L455F;N501Y;N501Y;N501Y;P681H;R246I;S494P;S982A;T478I;T716I;Y453F;D614G;G446S;L18F 387;503;415;448;442;289;289;489;298;482;275;316;380;496;394;475;305;408;282;401;268;163;261;436 392;508;421;453;446;296;296;494;303;487;280;321;385;501;399;480;310;413;287;406;273;168;266;440 RBD;RBD;S 40;218;181 43;221;182 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. All three of the major N501Y SARS-CoV-2 variants are circulating around the world. 2021 medRxiv Introduction SARS_CoV_2 N501Y 23 28 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. All three, B.1.1.7, B.1.352 and P.1 variants contain the N501Y mutation, while the South African and Brazilian variants additionally contain mutations in E484K and K417N. 2021 medRxiv Introduction SARS_CoV_2 E484K;K417N;N501Y 154;164;57 159;169;62 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. New SARS-CoV-2 variants have also been recently reported in the United States with evidence for convergent evolution at a Q667P mutation; however, the epidemiological and clinical importance of strains containing the Q667P mutation is not currently known. 2021 medRxiv Introduction SARS_CoV_2 Q667P;Q667P 122;217 127;222 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. The B.1.1.7 variant has a number of mutations in the spike protein including single nucleotide polymorphisms (SNPs) resulting in N501Y, A570D, D614G and P681H mutations, and deletions at amino acids 69-70 and 144Y. 2021 medRxiv Introduction SARS_CoV_2 A570D;D614G;N501Y;P681H 136;143;129;153 141;148;134;158 S 53 58 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. The N501Y (A23063T) mutation has been identified an important contributor to the worrisome phenotype. 2021 medRxiv Introduction SARS_CoV_2 N501Y;A23063T 4;11 9;18 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. Thus, the N501Y mutation appears to be an excellent marker for all three strains while the E484K mutation can be used to differentiate the other two strains from B.1.1.7. 2021 medRxiv Introduction SARS_CoV_2 E484K;N501Y 91;10 96;15 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Among numerous SARS-CoV-2 variants now circulating globally, those harboring a D614G mutation have predominated since June of 2020, possibly due to enhanced viral fitness and transmissibility. 2021 medRxiv Introduction SARS_CoV_2 D614G 79 84 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Here we used viral whole-genome sequencing of nasal/nasopharyngeal (N/NP) swab samples from multiple counties to characterize the emergence and spread of this L452R-carrying variant in California from September 1, 2020, to January 29, 2021. 2021 medRxiv Introduction SARS_CoV_2 L452R 159 164 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. In January 2021, we and others independently reported the emergence of a novel variant in California carrying an L452R mutation in the RBD of the spike protein. 2021 medRxiv Introduction SARS_CoV_2 L452R 113 118 S;RBD 146;135 151;138 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Multiple studies have reported that the E484K mutation in particular may confer resistance to antibody neutralization, potentially resulting in decreased efficacy of currently available vaccines. 2021 medRxiv Introduction SARS_CoV_2 E484K 40 45 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. The B.1.1.7 variant, originally detected in the United Kingdom (UK), has accumulated 17 lineage-defining mutations, including the spike protein N501Y mutation that confers increased transmissibility over other circulating viruses. 2021 medRxiv Introduction SARS_CoV_2 N501Y 144 149 S 130 135 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. The other two VOCs, B.1.351 detected in South Africa and P.1 first detected in Brazil, carry E484K and K417N/K417T in addition to N501Y mutations. 2021 medRxiv Introduction SARS_CoV_2 E484K;K417N;N501Y;K417T 93;103;130;109 98;108;135;114 33760807 SARS-CoV-2 variants reveal features critical for replication in primary human cells. An important example of this is the D614G substitution in S, which rapidly dominated SARS-CoV-2 sequences following its emergence, and is functionally linked to increased virus infectivity and replication capacity, potentially aiding virus spread throughout the population. 2021 PLoS biology Introduction SARS_CoV_2 D614G 36 41 S 58 59 33760807 SARS-CoV-2 variants reveal features critical for replication in primary human cells. Notably, SARS-CoV-2 isolates with naturally occurring Orf3a (Q57H) and nsp2 (T85I) substitutions exhibited a cell-specific replication phenotype, with efficient propagation restricted to primary human BEpCs. 2021 PLoS biology Introduction SARS_CoV_2 Q57H;T85I 61;77 65;81 ORF3a;Nsp2 54;71 59;75 33767200 The effect of SARS-CoV-2 D614G mutation on BNT162b2 vaccine-elicited neutralization. Collectively, the results indicate that the D614G substitution modestly reduces the inhibition of SARS-CoV-2 by antibodies elicited by the D614 spike antigen. 2021 NPJ vaccines Introduction SARS_CoV_2 D614G 44 49 S 144 149 33767200 The effect of SARS-CoV-2 D614G mutation on BNT162b2 vaccine-elicited neutralization. Mechanically, the D614G mutation promotes the spike receptor-binding domain (RBD) adopting an open conformation for binding the angiotensin-converting enzyme 2 (ACE2) receptor, resulting in a higher virion infectivity and thermal stability. 2021 NPJ vaccines Introduction SARS_CoV_2 D614G 18 23 S;RBD 46;77 51;80 33767200 The effect of SARS-CoV-2 D614G mutation on BNT162b2 vaccine-elicited neutralization. One prominent mutation in circulating SARS-CoV-2 is the spike D614G substitution. 2021 NPJ vaccines Introduction SARS_CoV_2 D614G 62 67 S 56 61 33767200 The effect of SARS-CoV-2 D614G mutation on BNT162b2 vaccine-elicited neutralization. Previous studies that examined the effect of spike D614G substitution on neutralization activities reached different conclusions. 2021 NPJ vaccines Introduction SARS_CoV_2 D614G 51 56 S 45 50 33767200 The effect of SARS-CoV-2 D614G mutation on BNT162b2 vaccine-elicited neutralization. Recent studies demonstrate that the D614G mutation does not enhance viral pathogenesis in animal models, but increases viral replication in the upper respiratory tract, and causes more efficient transmission. 2021 NPJ vaccines Introduction SARS_CoV_2 D614G 36 41 33767200 The effect of SARS-CoV-2 D614G mutation on BNT162b2 vaccine-elicited neutralization. Since the D164G substitution promotes an open conformation of spike RDB for binding to receptor ACE2, the modest difference in neutralization titer may be caused by the improved spike function (i.e., cellular attachment and virus entry) rather than antigenicity. 2021 NPJ vaccines Introduction SARS_CoV_2 D164G 10 15 S;S 62;178 67;183 33767200 The effect of SARS-CoV-2 D614G mutation on BNT162b2 vaccine-elicited neutralization. The D614G mutation was rare before March 2020, but became dominant as the pandemic continued, reaching >74% prevalence globally by June 2020. 2021 NPJ vaccines Introduction SARS_CoV_2 D614G 4 9 33767200 The effect of SARS-CoV-2 D614G mutation on BNT162b2 vaccine-elicited neutralization. Thus, the consensus appears to be that the effect of spike D614G mutation on neutralization is modest, small enough that different neutralization assays and laboratories can reach different conclusions about whether vaccine candidate-elicited or infection-elicited neutralization is greater against D614 or G614 virus. 2021 NPJ vaccines Introduction SARS_CoV_2 D614G 59 64 S 53 58 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. All three have the N501Y mutation, which is involved in the receptor-binding mechanism and may have clinical impacts. 2021 Journal of virological methods Introduction SARS_CoV_2 N501Y 19 24 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. In order to achieve a faster and cheaper method a new one-step variant discrimination real time PCR (VD RT-PCR) assay to detect the N501Y SARS-CoV-2 mutation was designed and developed, and then assayed in clinical samples. 2021 Journal of virological methods Introduction SARS_CoV_2 N501Y 132 137 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. The spike D614 G mutation of SARS-CoV-2 emerged in Europe in February 2020 and was linked to more serious infection and increased transmissibility. 2021 Journal of virological methods Introduction SARS_CoV_2 D614G 10 16 S 4 9 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. In this study, we used molecular dynamics simulation and MM-PBSA binding energy analysis to provide insights into the behaviour of the D614G S-protein and describe the neutralization interactions between the variant and neutralizing antibodies. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 135 140 S 141 142 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Our results show that the D614G S-protein adopts distinct conformational dynamics, which is skewed towards the open-state conformation more than the closed-state conformation of the wild-type S-protein. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 26 31 S;S 32;192 33;193 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The D614G mutation is caused by a substitution of an A to G at position 23,403 of the Wuhan reference sequence resulting in the replacement of aspartate with glycine at position 614 of the S-protein. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G;D614G 143;4 181;9 S 189 190 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The D614G variant has been characterized by higher viral load, which is not associated with disease severity, higher incorporation into virion, and high cell entry via ACE-2 and TMPRSS2. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 4 9 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The molecular features of the D614G S-protein conformational dynamics and its potential effect on the interactions with neutralizing antibodies have not been extensively looked at. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 30 35 S 36 37 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The period between the latter part of February and March 2020 saw the emergence of the SARS-CoV-2 S-protein D614G variant which distributed globally after dominating Europe. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 108 113 S 98 99 33777333 Specific epitopes form extensive hydrogen-bonding networks to ensure efficient antibody binding of SARS-CoV-2: Implications for advanced antibody design. Point mutations including VH V98E and VL G68D of CC12.1 were explored and proposed for advanced antibody design. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 G68D;V98E 41;29 45;33 33778179 Mutational analysis of structural proteins of SARS-CoV-2. An in depth molecular docking and dynamic simulation study demonstrated that a protein inhibitor DeltaABP-D25Y exclusively bound to the S protein ACE-2 binding site, thus the inhibitor could be a potential blocker of S protein and receptor binding domain (RBD) attachment. 2021 Heliyon Introduction SARS_CoV_2 D25Y 106 110 RBD;RBD;S;S 231;256;136;217 254;259;137;218 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Especially, the D614G mutation in the S protein, an A-to-G base change at the position 23,403 in the Wuhan reference strain, is closely related to the emergence of a more transmissible form of SARS-CoV-2. 2021 Gene reports Introduction SARS_CoV_2 D614G 16 21 S 38 39 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. In addition to the D614G, other mutations in the S gene region have recently been identified in isolates from different geographical origins. 2021 Gene reports Introduction SARS_CoV_2 D614G 19 24 S 49 50 33788036 New study on prevalence of anosmia in COVID-19 implicates the D614G virus mutation as a major contributing factor to chemosensory dysfunction. The D614G mutation, especially, is responsible for the enhanced cell entry or binding of the SARS-CoV-2 spike protein to the ACE2 protein. 2021 Eur Arch Otorhinolaryngol Introduction SARS_CoV_2 D614G 4 9 S 104 109 33788036 New study on prevalence of anosmia in COVID-19 implicates the D614G virus mutation as a major contributing factor to chemosensory dysfunction. To our knowledge, their study provides the most convincing argument for the D614G mutation leading to higher rates of anosmia. 2021 Eur Arch Otorhinolaryngol Introduction SARS_CoV_2 D614G 76 81 Anosmia 118 125 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Additional mutations in spike, three amino acid deletions and seven missense mutations, including N501Y in RBD, make B.1.1.7 more infectious than the wild-type or the D614G strain. 2021 Cell host & microbe Introduction SARS_CoV_2 D614G;N501Y 167;98 172;103 S;RBD 24;107 29;110 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. B.1.1.7 (501Y.V1) was first detected in the United Kingdom (UK) and displays the dominant early D614G mutation, which improves viral fitness and transmission. 2021 Cell host & microbe Introduction SARS_CoV_2 D614G 96 101 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Both wild-type and the UK-N501Y pseudoviruses were efficiently neutralized by tested sera. 2021 Cell host & microbe Introduction SARS_CoV_2 N501Y 26 31 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Early reports have indicated that while the N501Y spike mutation in B.1.1.7 does not compromise post-vaccine neutralization, E484K partly impairs neutralization resistance, potentially compromising vaccines effectiveness. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;N501Y 125;44 130;49 S 50 55 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Effects of spike RBD mutations, N501Y, K417N, and E484K (or their combinations) on viral infectivity (i.e., transduction and inhibition of viral entry) were also documented. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N;N501Y 50;39;32 55;44;37 S;RBD 11;17 16;20 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Finally, pseudoviruses with the K417N/E484K and the SA-N501Y/K417N/E484K spike mutations exhibited the highest neutralization resistance to post-vaccination sera, emphasizing the role of E484K mutation in neutralization resistance (Figure 2D). 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N;E484K;E484K;K417N;N501Y 187;32;38;67;61;55 192;37;43;72;66;60 S 73 78 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. However, pseudovirus carrying the SA-N501Y/K417N/E484K spike mutations moderately resisted neutralization by convalescent and post-vaccinated sera. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N;N501Y 49;43;37 54;48;42 S 55 60 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. However, pseudoviruses displaying the E484K and N501Y/E484K spike mutations partly resisted neutralization by vaccination sera. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;N501Y;E484K 38;48;54 43;53;59 S 60 65 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. However, SA-N501Y/K417N/E484K spike pseudovirus partly resisted neutralization by post-vaccinated sera, exhibiting 6.8-fold decrease in mean NT50 relative to wild-type SARS-CoV-2 spike pseudoviruses (Figure 2C). 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N;N501Y 24;18;12 29;23;17 S;S 30;179 35;184 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. However, the SA-N501Y/K417N/E484K pseudovirus was unique, as it exhibited high infectivity levels and exhibited moderate neutralization resistance from vaccination sera. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N;N501Y 28;22;16 33;27;21 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. In contrast, pseudovirus displaying E484K spike mutation, and to a lesser extent, K417N, partly resisted neutralization by post-vaccination sera. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N 36;82 41;87 S 42 47 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. In contrast, pseudovirus displaying the SA-N501Y/K417N/E484K spike mutations exhibited a moderate resistance to neutralization by convalescent sera, with a 6.8-fold decrease in mean NT50 value relative to the wild-type SARS-CoV-2 pseudovirus (Figure 2A). 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N;N501Y 55;49;43 60;54;48 S 61 66 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Indeed, a combined N501Y/E484K mutation led to a 13-fold increase in transduction levels relative to wild-type pseudovirus, similarly to that of the SA pseudovirus. 2021 Cell host & microbe Introduction SARS_CoV_2 N501Y;E484K 19;25 24;30 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Interestingly, pseudovirus that carried the UK-N501Y spike mutation was also efficiently neutralized by convalescent sera samples, exhibiting only a mean of 1.5-fold decrease in ability to neutralize viral entry relative to wild-type SARS-CoV-2 pseudovirus. 2021 Cell host & microbe Introduction SARS_CoV_2 N501Y 47 52 S 53 58 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Interestingly, pseudoviruses where the N501Y spike mutation was attached to either K417N or E484K mutations (i.e., N501Y/K417N or N501Y/E484K), exhibited high transduction rates, slightly higher than those of the UK-N501Y pseudovirus alone. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N;N501Y;N501Y;N501Y;E484K;K417N;N501Y 92;83;39;115;130;136;121;216 97;88;44;120;135;141;126;221 S 45 50 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Its spike harbors the N501Y mutation and includes an additional nine changes. 2021 Cell host & microbe Introduction SARS_CoV_2 N501Y 22 27 S 4 9 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Moreover, the SA-N501Y/K417N/E484K spike mutations further boosted transduction levels, up to 13-fold, relative to SARS-CoV-2 wild-type pseudovirus. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N;N501Y 29;23;17 34;28;22 S 35 40 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Moreover, when N501Y mutation within spike was combined with other mutations:K417N (N501Y/K417N), E484K (N501Y/E484K), or N501Y/K417N/E484K:enhancement of infectivity was documented relative to the wild-type SARS-CoV-2 pseudovirus. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;N501Y;N501Y;N501Y;N501Y;E484K;E484K;K417N;K417N;K417N 98;15;122;84;105;111;134;90;128;77 103;20;127;89;110;116;139;95;133;82 S 37 42 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. N501Y potentially enhances association of the virus with hACE2, leading to enhanced infectivity and spread. 2021 Cell host & microbe Introduction SARS_CoV_2 N501Y 0 5 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Neutralizing potency of convalescent or post-vaccination sera against pseudoviruses displaying UK-N501Y and SA-N501Y/K417N/E484K spike mutants. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N;N501Y;N501Y 123;117;111;98 128;122;116;103 S 129 134 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. One cluster includes four substitutions and a deletion (L18F, D80A, D215G, delta 242-244, and R246I), while a second cluster contains three RBD substitutions:K417N, E484K, and N501Y. 2021 Cell host & microbe Introduction SARS_CoV_2 D215G;D80A;E484K;N501Y;R246I;L18F;K417N 68;62;165;176;94;56;158 73;66;170;181;99;60;163 RBD 140 143 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Oppositely, resistance to neutralization seemed to be driven by the E484K, and to a lesser extent, on the K417N mutations. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N 68;106 73;111 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Our data also indicate that the Pfizer vaccine is moderately compromised against SA-N501Y/K417N/E484K pseudo-variants. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N;N501Y 96;90;84 101;95;89 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Our findings show that, relative to pseudovirus bearing wild-type SARS-CoV-2 spike, the ability of pseudovirus carrying the UK-N501Y mutation to transduce its target cells significantly increased, up to 9-fold. 2021 Cell host & microbe Introduction SARS_CoV_2 N501Y 127 132 S 77 82 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Our results show that pseudovirus carrying the UK-N501Y mutation is highly infectious, relative to pseudovirus bearing wild-type SARS-CoV-2 (Figure 2D). 2021 Cell host & microbe Introduction SARS_CoV_2 N501Y 50 55 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Pseudovirus carrying the E484K single mutation exhibited only a 2-fold increase in its ability to transduce cells, relative to SARS-CoV-2 wild-type pseudovirus. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K 25 30 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Pseudoviruses carrying K417N or E484K single mutations, or the combined K417N/E484K mutations, exhibited infectivity rates that were similar to the wild-type pseudovirus. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N;K417N;E484K 32;23;72;78 37;28;77;83 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Pseudoviruses carrying the E484K mutation alone, or the combined N501Y/E484K spike mutations, resisted neutralization to some extent. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;N501Y;E484K 27;65;71 32;70;76 S 77 82 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Pseudoviruses with K417N or N501Y/K417N mutations were also similarly neutralized by post-vaccination sera, similarly to that of wild-type pseudovirus. 2021 Cell host & microbe Introduction SARS_CoV_2 K417N;N501Y;K417N 19;28;34 24;33;39 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Pseudoviruses with UK-N501Y or SA-N501Y/K417N/E484K spike mutants were tested, as were pseudoviruses carrying single or combined RBD mutations:K417N, E484K, N501Y/E484K, N501Y/K417N, and K417N/E484K (Figure 2C). 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N;N501Y;N501Y;E484K;E484K;E484K;K417N;K417N;K417N;N501Y;N501Y 150;187;157;170;46;193;163;176;40;143;34;22 155;192;162;175;51;198;168;181;45;148;39;27 S;RBD 52;129 57;132 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Similarly, pseudovirus bearing the E484K/K417N mutations also resisted neutralization by post-vaccination sera relative to wild-type SARS-CoV-2 pseudovirus (Figure 2D). 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N 35;41 40;46 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Similarly, pseudovirus displaying the K417N single spike mutation, or K417N/E484K double mutations, also showed a 2-fold increase in transduction rates relative to the wild-type pseudovirus. 2021 Cell host & microbe Introduction SARS_CoV_2 K417N;K417N;E484K 38;70;76 43;75;81 S 51 56 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. These findings point to a high efficacy of the vaccine against the UK-N501Y strain. 2021 Cell host & microbe Introduction SARS_CoV_2 N501Y 70 75 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. These results suggest that the emergence and spread of viral variants may be driven by infectivity rather than resistance to neutralization, and highlight the contribution of the N501Y spike mutation for enhancement of viral infectivity into target cells (Figure 2C). 2021 Cell host & microbe Introduction SARS_CoV_2 N501Y 179 184 S 185 190 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Thus, in the context of N501Y spike mutation, the contribution of the E484K mutation to viral transduction was boosted. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;N501Y 70;24 75;29 S 30 35 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Tighter RBD-N501Y interactions with ACE2 are considered the driving force for the increased B.1.1.7 infectivity. 2021 Cell host & microbe Introduction SARS_CoV_2 N501Y 12 17 RBD 8 11 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Uniquely, pseudovirus displaying the SA-N501Y/K417N/E484K spike mutations exhibited both high infectivity levels and efficient neutralization resistance, raising concerns for vaccine efficiency. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N;N501Y 52;46;40 57;51;45 S 58 63 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. We conclude that pseudovirus displaying SA-N501Y/K417N/E484K spike mutations exhibits a moderately increased resistance to neutralization by both convalescent and Pfizer-vaccinated sera. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N;N501Y 55;49;43 60;54;48 S 61 66 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. We confirmed our results showing that pseudovirus with the UK-N501Y spike mutation exhibited similar neutralization potency between vaccinated sera and wild-type SARS-CoV-2 pseudovirus. 2021 Cell host & microbe Introduction SARS_CoV_2 N501Y 62 67 S 68 73 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. We further monitored the ability of our sera samples to neutralize entry of pseudoviruses carrying the UK-N501Y and the SA-N501Y/K417N/E484K spike mutations. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N;N501Y;N501Y 135;129;123;106 140;134;128;111 S 141 146 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. When combined with E484K or K417N mutations, an increase in neutralization resistance is also observed. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;K417N 19;28 24;33 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. While pseudovirus displaying the N501Y spike mutant exhibited high infectivity rates relative to wild-type SARS-CoV-2, it was efficiently neutralized by post-vaccinated sera. 2021 Cell host & microbe Introduction SARS_CoV_2 N501Y 33 38 S 39 44 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Wild-type or UK-N501Y SARS-CoV-2 spike pseudoviruses were comparably neutralized by sera from the second post-vaccination dose (Figure 2B). 2021 Cell host & microbe Introduction SARS_CoV_2 N501Y 16 21 S 33 38 33789940 Stability of SARS-CoV-2 Spike G614 Variant Surpasses That of the D614 Variant after Cold Storage. A SARS-CoV-2 S-D614G variant emerged in February 2020 in Europe and is currently the most dominant variant in circulation. 2021 mSphere Introduction SARS_CoV_2 D614G 15 20 S 13 14 33789940 Stability of SARS-CoV-2 Spike G614 Variant Surpasses That of the D614 Variant after Cold Storage. The rapid spread of the S-D614G variant quickly garnered attention and necessitated investigations to understand its effect on SARS-CoV-2 infectivity. 2021 mSphere Introduction SARS_CoV_2 D614G 26 31 S 24 25 33789940 Stability of SARS-CoV-2 Spike G614 Variant Surpasses That of the D614 Variant after Cold Storage. The reproductive number of the SARS-CoV-2 S-D614G variant increased by 31% compared with that of the wild-type SARS-CoV-2 S-D614. 2021 mSphere Introduction SARS_CoV_2 D614G 44 49 S;S 42;122 43;123 33789940 Stability of SARS-CoV-2 Spike G614 Variant Surpasses That of the D614 Variant after Cold Storage. The S-D614G variant showed no significant association with disease severity and no change in sensitivity to neutralizing antibodies compared with the wild type. 2021 mSphere Introduction SARS_CoV_2 D614G 6 11 S 4 5 33791702 Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2. For example, NSP6 Delta106-108 and NSP12 P323L are apparent in each of the three variants. 2021 bioRxiv Introduction SARS_CoV_2 P323L 41 46 Nsp12;Nsp6 35;13 40;17 33791702 Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2. The spike mutations observed in current variants can be broadly divided into three categories based on their locations: N-terminal domain (NTD) mutations including deletions found in both B.1.1.7 and B.1.351; receptor binding domain (RBD) mutations including N501Y (B.1.1.7, B.1.351 and P.1) and E484K (B.1.351 and P.1); and stalk/S2 mutations including P681H proximal to the polybasic S1/S2 cleavage site (B.1.1.7). 2021 bioRxiv Introduction SARS_CoV_2 E484K;N501Y;P681H 296;259;354 301;264;359 RBD;S;RBD;N 209;4;234;120 232;9;237;121 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Another group utilized computational methods to characterize D614G mutation in SARS-CoV-2 spike protein and observed that the mutation led to generation of serine protease cleavage site near S1-S2 junction (Bhattacharyya et al.,). 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 D614G 61 66 S 90 95 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Further characterization of this mutation revealed that pseudovirus containing spike protein with D614G mutation entered Angiotensin-converting enzyme 2 (ACE2) expressing cells more efficiently as well as higher incorporation of S protein in virion particles (Zhang et al.,). 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 D614G 98 103 S;S 79;229 84;230 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Further reports suggested that D614G spike mutation led to increased infectivity of the SARS-CoV-2 (Korber et al.,). 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 D614G 31 36 S 37 42 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Our extensive analysis of several mutations on SARS-CoV-2 structural proteins revealed that L37H mutation in E protein, G204R and P344S in N protein and D614G in S protein were destabilizing the parent protein whereas P13L, S197L, and R203K in N protein had stabilizing effect on the parent protein. 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 D614G;G204R;L37H;P13L;P344S;R203K;S197L 153;120;92;218;130;235;224 158;125;96;222;135;240;229 E;N;N;S 109;139;244;162 110;140;245;163 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. The members of this clade contain S-D614G and N-G204R mutations. 2021 Journal, genetic engineering & biotechnology Introduction SARS_CoV_2 D614G;G204R 36;48 41;53 N;S 46;34 47;35 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. We also explored how the loss and gain of Valine in V843F and A889V mutations respectively affect the binding of protease inhibitors GRL0617 and ISG-15 for their implication in new therapeutics development. 2021 Journal, genetic engineering & biotechnology Introduction SARS_CoV_2 A889V;V843F 62;52 67;57 33798491 Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant. In comparison to the D614G variant (GMT: 135; range: <20-836), we observed a significant reduction in the neutralization capacity of samples from the acutely infected cohort against the B.1.351 variant (GMT: 40; range: <20-433). 2021 Cell host & microbe Introduction SARS_CoV_2 D614G 21 26 33798491 Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant. One of these is a substitution of a Q677H, which has now been reported in multiple lineages of circulating variants of SARS-CoV-2 in the US population as early as mid-August 2020. 2021 Cell host & microbe Introduction SARS_CoV_2 Q677H 36 41 33798491 Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant. Relative to the deposited sequence on GISAID (EPI_ISL_678615), we identified two additional mutations within the spike protein at positions Q677H and R682W (Figure S1). 2021 Cell host & microbe Introduction SARS_CoV_2 Q677H;R682W 140;150 145;155 S 113 118 33798491 Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant. The B.1.351 RBD contains three mutations (K417N, E484K and N501Y) which reduces antibody binding. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;N501Y;K417N 49;59;42 54;64;47 RBD 12 15 33798491 Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant. The B.1.351 viral variant contains the following amino acid mutations within the viral spike protein: L18F, D80A, D215G, deletion at positions 242-244 (L242del, A243del, and L244del), K417N, E484K, N501Y, and D614G. 2021 Cell host & microbe Introduction SARS_CoV_2 A243del;D215G;D614G;D80A;E484K;K417N;L18F;L244del;N501Y;L242del 161;114;209;108;191;184;102;174;198;152 168;119;214;112;196;189;106;181;203;159 S 87 92 33798491 Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant. The emerging B.1.351 SARS-CoV-2 variant includes three mutations within the receptor-binding domain (K417N, E484K, and N501Y) and several additional mutations within the spike protein. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;N501Y;K417N 108;119;101 113;124;106 S 170 175 33798491 Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant. The other is a substitution (R682W) within the furin cleavage motif (PRRAR) located between the S1/S2 regions of the spike protein. 2021 Cell host & microbe Introduction SARS_CoV_2 R682W 29 34 S 117 122 33798491 Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant. This variant contains the D614G mutation within the spike protein. 2021 Cell host & microbe Introduction SARS_CoV_2 D614G 26 31 S 52 57 33798491 Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant. Within the the RBD, we and others have shown that the presence of N501Y mutation found in the B.1.1.7 UK variant does not affect the neutralizing ability of serum from either naturally infected or mRNA-1273 vaccinated individuals. 2021 Cell host & microbe Introduction SARS_CoV_2 N501Y 66 71 RBD 15 18 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. At the phylogeny of SARS-CoV-2, strains were identified as lineage A, B, and C according to variants, and the variant carrying the Y5865C mutation was associated with the lineage S or 19 B. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 Y5865C 131 137 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Based on the infection, fatality, and recovery rates, as well as dynamic curves for the emergence of genome variations, in different countries, we identified amino acid variations in ORF1ab at the 5828 and 5865 loci (NSP13: P504L and NSP13: Y541C) and gained insight into COVID-19 outcomes in the United States that contained different proportions of strains with these ORF1ab variations. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 P504L;Y541C 224;241 229;246 ORF1ab;ORF1ab;Nsp13;Nsp13 183;370;217;234 189;376;222;239 COVID-19 272 280 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. identified the potential relevance of amino acid Y5865C in ORF1ab, showing that this residue is experimenting directional selection. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 Y5865C 49 55 ORF1ab 59 65 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. In the correlation analysis, variants of S 614G was associated with case fatality rates (CRF) and median CFR in 12 countries, and variants ORF1ab 4715 L and S 614G were reported correlated with fatality rates in 28 countries and 17 states of the United States. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 S614G;S614G 41;157 47;163 ORF1ab;S;S 139;41;157 145;42;158 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Recent studies focused on the mutation of Spike protein and showed that variants carrying D614G have become the most prevalent worldwide, suggesting the fitness advantage for SARS-CoV-2. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 90 95 S 42 47 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. Another variant from Brazil (known as VOC202101/02 in UK), identified first in Japanese travelers from Brazil, shows seventeen unique mutations including the N501Y and E484K mutations. 2021 Viruses Introduction SARS_CoV_2 E484K;N501Y 168;158 173;163 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. The recent temporal analyses of SARS-CoV-2 epidemics highlighted selective global sweep of the D614G variant S protein (Clade G) over G251V in ORF3a (Clade V) and L84S in ORF 8 (Clade S) variants. 2021 Viruses Introduction SARS_CoV_2 D614G;G251V;L84S 95;134;163 100;139;167 ORF3a;S;S 143;109;184 148;110;185 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. The ubiquitous D614G variant of SARS-CoV-2 exhibits efficient replication in upper respiratory tract epithelial cells and higher transmissibility among humans, thereby conferring enhanced fitness. 2021 Viruses Introduction SARS_CoV_2 D614G 15 20 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. Both strains are independent substrains of a spike glycoprotein D614G variant that has spread in spring 2020 in England and worldwide, almost reaching fixation. 2021 Viruses Introduction SARS_CoV_2 D614G 64 69 S 45 63 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. In England, the VOC is currently replacing the recently dominant 20A.EU1 strain, characterized by A222V substitution in spike protein. 2021 Viruses Introduction SARS_CoV_2 A222V 98 103 S 120 125 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. In such approach, we analyze the progression of strains with increasing replication advantage: D614G 20A.EU1 the VOC. 2021 Viruses Introduction SARS_CoV_2 D614G 95 100 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The L18F mutation is of significance because when recently analyzed in the context of the South African strain 501Y.V2 it has been found to compromise binding of neutralizing antibodies. 2021 Viruses Introduction SARS_CoV_2 L18F 4 8 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The lineage, characterized by nine spike protein mutations (deletions: 69-70 HV, 145V; substitutions: N501Y, A570D, D614G, P681H, T716I, S982A, D1118H), started to spread rapidly in mid-October 2020 to constitute in January 2021 86% of all SARS-CoV-2 genomes sequenced in England. 2021 Viruses Introduction SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 109;144;116;102;123;137;130 114;150;121;107;128;142;135 S 35 40 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The VOC strain in the receptor-binding motif (RBM) of spike shares mutation N501Y with the 501Y.V2 and P.1 strains that are currently rapidly spreading in South Africa and Brazil, respectively. 2021 Viruses Introduction SARS_CoV_2 N501Y 76 81 S 54 59 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. Then, using the same approach, we estimated the replicative advantage of the 20A.EU1 strain in relation to previous D614G strains and the D614G strain in relation to the D614 strains (i.e., the strains with non-mutated residue 614). 2021 Viruses Introduction SARS_CoV_2 D614G;D614G 116;138 121;143 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. We have systematically estimated growth rates of spreading mutations acquired by the VOC lineage to find that spike L18F substitution has likely initiated a substrain of replicative advantage. 2021 Viruses Introduction SARS_CoV_2 L18F 116 120 S 110 115 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. In addition, the N484K mutants remain rare and we do not observe a strong selection pressure towards these variants. 2021 Microorganisms Introduction SARS_CoV_2 N484K 17 22 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. It is hypothesized that the viral variants B.1.1.7, B.1.351, and P.1 are more transmissible compared to other circulating variants, due to a higher affinity towards the angiotensin-converting enzyme 2 (ACE2) receptor resulting from the N501Y mutation and were defined as variants of concern (VoC). 2021 Microorganisms Introduction SARS_CoV_2 N501Y 236 241 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Most recently the P.1 lineage, exhibiting the N501Y and E484K mutations, among others, was described in Brazil and has also been found in Japan. 2021 Microorganisms Introduction SARS_CoV_2 E484K;N501Y 56;46 61;51 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Of particular concern is the spike glycoprotein E484K mutation, which has been shown to reduce binding affinities towards neutralizing antibodies. 2021 Microorganisms Introduction SARS_CoV_2 E484K 48 53 S 29 47 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Since December 2020, three emerging SARS-CoV-2 lineages:B.1.1.7 (N501Y.V1), B.1.351 (N501Y.V2), and P.1 (B.1.1.28.1; N501Y.V3):have generated concern in public and scientific communities. 2021 Microorganisms Introduction SARS_CoV_2 N501Y;N501Y;N501Y 117;65;85 122;70;90 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Some of the B.1.1.7 polymorphisms may modulate the protein's function, such as the N501Y mutation in the receptor binding domain, the HV 69-70 deletion, and the P681H mutation in the furin cleavage site. 2021 Microorganisms Introduction SARS_CoV_2 N501Y;P681H 83;161 88;166 RBD 105 128 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. The B.1.351 lineage was first detected in October 2020 in ZA (according to the GISAID database) and also shares the N501Y mutation, but has otherwise different lineage-determining polymorphisms (Table S1) and does not show a characteristic S gene dropout due to lack of the HV 69-70 deletion. 2021 Microorganisms Introduction SARS_CoV_2 N501Y 116 121 S 240 241 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. Another amino acid substitutions with potential significance include N501Y and E484K in the receptor binding domain of the spike glycoprotein. 2021 Pathogens (Basel, Switzerland) Introduction SARS_CoV_2 E484K;N501Y 79;69 84;74 RBD;S 92;123 115;141 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. The most notable example of such substitutions is the replacement of aspartic acid by glycine at position 614 of the spike glycoprotein of the virus (D614G). 2021 Pathogens (Basel, Switzerland) Introduction SARS_CoV_2 D614G;D614G 69;150 109;155 S 117 135 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. the UK variant of concern) that was detected in the UK in September 2020 with N501Y and P681H as the most notable amino acid substitutions; (5) lineage B.1.351 which dates back to December 2020 (the South African variant) with N501Y, K417N, and E484K as the most notable amino acid substitutions; and (6) lineage P.1 (the Brazilian variant) that was first detected in December 2020 with N501Y, and E484K as the most notable amino acid substitutions. 2021 Pathogens (Basel, Switzerland) Introduction SARS_CoV_2 E484K;E484K;K417N;N501Y;N501Y;N501Y;P681H 245;398;234;78;227;387;88 250;403;239;83;232;392;93 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. All the bispecific antibodies neutralized D614G with no loss of efficacy. 2021 bioRxiv Introduction SARS_CoV_2 D614G 42 47 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. Next, we tested the in vivo efficacy of a potent bispecific antibody that neutralized B.1351, CV503_521_GS, against SARS-CoV-2 carrying the critical E484K variant mutation, which reduces the neutralization potency of many mAbs and convalescent plasma. 2021 bioRxiv Introduction SARS_CoV_2 E484K 149 154 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. Surprisingly, our most potent antibody CV503 (RBS-specific) also retained binding to all variants tested, while CV1182 and CV1206, which share a bin with this antibody, failed to bind to B.1.351 due to the E484K mutation. 2021 bioRxiv Introduction SARS_CoV_2 E484K 206 211 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. To confirm the binding results, we tested the ability of nine bispecific antibodies to neutralize SARS-CoV-2 D614G, B.1.1.7 and B.1.351 pseudotyped virus in two independent labs. 2021 bioRxiv Introduction SARS_CoV_2 D614G 109 114 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. Several groups have investigated the selective advantage of particular SARS-CoV-2 variants, such as D614G and B.1.1.7, either qualitatively or quantitatively. 2021 medRxiv Introduction SARS_CoV_2 D614G 100 105 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. Specifically for the UK, the selection coefficient for the D614G variant has been estimated using various phylogenetic and phylodynamic methods. 2021 medRxiv Introduction SARS_CoV_2 D614G 59 64 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. The global spread of the D614G variant was first described by Korber et al. 2021 medRxiv Introduction SARS_CoV_2 D614G 25 30 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. The increased infectiousness of the D614G variant has also been functionally explained in terms of ACE2 receptor binding. 2021 medRxiv Introduction SARS_CoV_2 D614G 36 41 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. These changes to the SARS-CoV-2 phenotype embodied in D614G and B.1.1.7 likely represent only a small fraction of the phenotypic variability in the broader population. 2021 medRxiv Introduction SARS_CoV_2 D614G 54 59 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. Complementary to experimental efforts, all-atom molecular dynamics (MD) simulations with sophisticated and well-calibrated force fields have been widely used to image nanoscale events and investigate the molecular mechanism of proteins.- In this work, we conducted a computational analysis of the K417N mutation in the South Africa variant using MD simulations with explicit solvent, aiming to gain a better understanding of its underlying molecular mechanism. 2022 Journal of medicinal chemistry Introduction SARS_CoV_2 K417N 297 302 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. Here, we are motivated to investigate the molecular mechanism of the K417N mutation, to unveil its key benefits for the virus to evolve through this path. 2022 Journal of medicinal chemistry Introduction SARS_CoV_2 K417N 69 74 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. However, reflected in the paucity of existing work, the significance of the K417N mutation so far is still elusive, which prevents us from fully understanding the infection mechanism of these new variants. 2022 Journal of medicinal chemistry Introduction SARS_CoV_2 K417N 76 81 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. In addition to the N501Y mutation, the South Africa and Brazil variants also contain the K417N and E484K mutations. 2022 Journal of medicinal chemistry Introduction SARS_CoV_2 E484K;K417N;N501Y 99;89;19 104;94;24 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. Our results may help provide invaluable insights into why K417N has been selected during viral evolution and inspire a better design of more efficacious mAbs for treating COVID-19 patients infected with the new SARS-CoV-2 variants. 2022 Journal of medicinal chemistry Introduction SARS_CoV_2 K417N 58 63 COVID-19 171 179 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. Recent studies showed that the E484K mutation not only can enhance RBD-ACE2 binding but also can help the virus escape the therapeutically relevant mAbs. 2022 Journal of medicinal chemistry Introduction SARS_CoV_2 E484K 31 36 RBD 67 70 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. Thus, the K417N mutation resulting in the abolishment of this favorable interfacial interaction (i.e., reducing the RBD-ACE2 binding affinity as verified in experiment) is highly unintuitive. 2022 Journal of medicinal chemistry Introduction SARS_CoV_2 K417N 10 15 RBD 116 119 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. variant (with the N501Y mutation on the RBD), experimental studies have demonstrated that the reproductive number that measures its infectiousness is approximately 0.4-0.7 higher than those of other strains of the virus and determined recently it is unlikely to escape BNT162b2 vaccine-mediated protection. 2022 Journal of medicinal chemistry Introduction SARS_CoV_2 N501Y 18 23 RBD 40 43 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. revealed three major substitutions of G1397A, T28688C and G29742T in genomes of patients with travel history to Iran, which constitute a distinct clade representative of the specific viral diversity present in Iran at that time (Eden et al., 2020). 2022 Transboundary and emerging diseases Introduction SARS_CoV_2 G1397A;G29742T;T28688C 38;58;46 44;65;53 33836314 Implementation of an in-house real-time reverse transcription-PCR assay for the rapid detection of the SARS-CoV-2 Marseille-4 variant. One of them, we named Marseille-4, harbors a S477 N substitution in the spike RBD that has been associated with an improved binding affinity to ACE2 and a broad resistance to monoclonal neutralizing antibodies. 2021 Journal of clinical virology Introduction SARS_CoV_2 S477N 45 51 S;RBD 72;78 77;81 33836314 Implementation of an in-house real-time reverse transcription-PCR assay for the rapid detection of the SARS-CoV-2 Marseille-4 variant. Such SARS-CoV-2 variants include the 20I/501Y.V1, 20 H/501Y.V2, and 20 J/501Y.V3 strains that harbor a N501Y substitution in the spike RBD and were reported in the UK and in South Africa, as highly transmissible, and in Brazil, respectively. 2021 Journal of clinical virology Introduction SARS_CoV_2 N501Y 103 108 S;RBD 129;135 134;138 33840632 Association of SARS-CoV-2 clades with clinical, inflammatory and virologic outcomes: An observational study. A literature search was done through Medline up to October 23, 2020 with the following keywords: Coronavirus disease 2019; COVID-19; SARS-CoV-2; clade; lineage; D614G. 2021 EBioMedicine Introduction SARS_CoV_2 D614G 161 166 COVID-19;COVID-19 97;123 116;131 33840632 Association of SARS-CoV-2 clades with clinical, inflammatory and virologic outcomes: An observational study. The global initiative on sharing all influenza data (GISAID) nomenclature describes four major SARS-CoV-2 clades in the early outbreak: clade L, clade V (variant of the ORF3a coding protein NS3-G251), clade G (variant of the spike protein S-D614G with further subclades GR, GH and GV collectively called clade G here), and clade S (variant ORF8-L84S). 2021 EBioMedicine Introduction SARS_CoV_2 D614G;L84S 241;345 246;349 S;ORF3a;ORF8;NS3;S;S 225;169;340;190;239;329 230;174;344;193;240;330 33840632 Association of SARS-CoV-2 clades with clinical, inflammatory and virologic outcomes: An observational study. The global initiative on sharing all influenza data (GISAID) nomenclature describes the emergence of four major SARS-CoV-2 clades: clade L, clade V (variant of the ORF3a coding protein NS3-G251), clade G (variant of the spike protein S-D614G with further subclades GR, GH and GV collectively called clade G here), and clade S (variant ORF8-L84S). 2021 EBioMedicine Introduction SARS_CoV_2 D614G;L84S 236;340 241;344 S;ORF3a;ORF8;NS3;S;S 220;164;335;185;234;324 225;169;339;188;235;325 33840632 Association of SARS-CoV-2 clades with clinical, inflammatory and virologic outcomes: An observational study. Viruses containing the genetic variant D614G (clade G) have become the most common reported worldwide since March 2020, and in vitro and animal models suggest this virus may be more infectious. 2021 EBioMedicine Introduction SARS_CoV_2 D614G 39 44 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. In a previous study, we tracked the evolution trends of SARS-CoV-2 through linkage analysis and haplotype subgroup epidemic trends at three time points (March 22, 2020, April 6, 2020 and May 10, 2020), and found that the frequency of H1 haplotype with the 4 specific mutations (C241T, C3037T, C14408T and A23403G) increased over time, which indicated that they might be related to infectivity, pathogenicity or host adaptability of SARS-CoV-2. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 A23403G;C14408T;C3037T;C241T 305;293;285;278 312;300;291;283 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. Thereinto, the A23403G mutation, which resulted in amino acid change of D614G in the spike protein, had been proved to be related to infectivity by several in vitro experiments subsequently. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 A23403G;D614G 15;72 22;77 S 85 90 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. D614G has now become established in circulating B lineage viruses. 2021 bioRxiv Introduction SARS_CoV_2 D614G 0 5 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. For B.1.1.7 S, P681H (P5) may provide an additional basic residue (especially at low pH) and modulate S1/S2 cleavability by furin, and hence virus infection properties. 2021 bioRxiv Introduction SARS_CoV_2 P681H 15 20 S 12 13 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Here, we used a similar approach to study the role of the proteolytic activation of the spike protein in the context of the B.1.1.7 VOC, with a focus on the P681H point mutant. 2021 bioRxiv Introduction SARS_CoV_2 P681H 157 162 S 88 93 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. N501Y has subsequently been found in other VOCs circulating around the world, i.e., B.1.351 and B.1.1.28.1 (P.1) 2021 bioRxiv Introduction SARS_CoV_2 N501Y 0 5 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. N501Y has subsequently been found in other VOCs circulating around the world, i.e., B.1.351 and B.1.1.28.1 (P.1). 2021 bioRxiv Introduction SARS_CoV_2 N501Y 0 5 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Of particular note were nine mutations in the spike gene compared to prototype sequences; a 69-70 deletion (the cause of S-gene target failure), Y144 del, N501Y, A570D, D614G, P681H, T716I, S982A, and D118H, with seven of these distinct to B.1.1.7. 2021 bioRxiv Introduction SARS_CoV_2 A570D;D118H;D614G;N501Y;P681H;S982A;T716I;Y144 del 162;201;169;155;176;190;183;145 167;206;174;160;181;195;188;153 S;S 46;121 51;122 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. One of the more concerning mutations was N501Y, which was linked (along with D614G) to increased affinity of the spike protein to the SARS-CoV-2 receptor (ACE-2). 2021 bioRxiv Introduction SARS_CoV_2 D614G;N501Y 77;41 82;46 S 113 118 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. The B lineage has undergone significant diversification as it expanded, and in particular acquired an S gene mutation (D614G) that resulted in a more stabilized spike protein, which has been linked to increased transmissibility. 2021 bioRxiv Introduction SARS_CoV_2 D614G 119 124 S;S 161;102 166;103 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. The P681H mutation of B.1.1.7 is of note as it is part of a proteolytic cleavage site for furin and furin-like proteases at the junction of the spike protein receptor-binding (S1) and fusion (S2) domains. 2021 bioRxiv Introduction SARS_CoV_2 P681H 4 9 S 144 149 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. B.1.351 also has three changes in the RBD (K417N, E484K, and N501Y), whereas B.1.1.7 contains the single N501Y mutation. 2021 Cell Introduction SARS_CoV_2 E484K;N501Y;N501Y;K417N 50;61;105;43 55;66;110;48 RBD 38 41 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. P.1 has three changes in the RBD (K417T, E484K, and N501Y), which are a particular cause for concern. 2021 Cell Introduction SARS_CoV_2 E484K;N501Y;K417T 41;52;34 46;57;39 RBD 29 32 33853970 Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. In the mutants, other amino acids were substituted at certain locations; for example, K417T indicates that lysine at position 417 was replaced by threonine.) 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 K417T;K417T 86;107 91;155 33853970 Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. In the mutants, other amino acids were substituted at certain locations; for example, K417T indicates that lysine at position 417 was replaced by threonine.). 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 K417T 86 91 33853970 Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Lineage P.1 contains 10 lineage-defining amino acid mutations in the virus spike protein (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, and T1027I) compared with its immediate ancestor (B.1.1.28). 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 D138Y;E484K;H655Y;K417T;N501Y;P26S;R190S;T1027I;T20N;L18F 108;129;143;122;136;102;115;154;96;90 113;134;148;127;141;106;120;160;100;94 S 75 80 33853970 Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Moreover, E484K is associated with reduced antibody neutralization. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K 10 15 33853970 Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. The former two interact with human ACE2 (hACE2), whereas E484K is located in a loop region outside the direct hACE2 interface. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K 57 62 33853970 Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. The same three residues are mutated with the B.1.351 variant of concern, and N501Y is also present in the B.1.1.7 lineage. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 N501Y 77 82 33853970 Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Three key mutations present in P.1N501Y, K417T, and E484Kare in the spike protein RBD. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 K417T 41 46 S;RBD 68;82 73;85 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Here, we investigated whether S proteins harboring Y453F either alone or in conjunction with other mutations showed altered expression, host cell interactions, and susceptibility to antibody-mediated neutralization. 2021 Cell reports Introduction SARS_CoV_2 Y453F 51 56 S 30 31 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Moreover, SARS-CoV-2 containing a combination of five mutations (H69Delta/V70Delta/Y453F/I692V/M1229I) in their S protein have been observed, which gave rise to the designation cluster 5 variant. 2021 Cell reports Introduction SARS_CoV_2 I692V;M1229I;Y453F 89;95;83 94;101;88 S 112 113 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. The S protein of SARS-CoV-2 from farmed mink in Denmark and the Netherlands harbors different combinations of mutations relative to SARS-CoV-2 circulating in humans (; Figures 1B and 1C): a deletion of H69 (H69Delta) and V70 (V70Delta) in the S protein N terminus and amino acid exchanges Y453F in the RBD, I692V located downstream of the furin motif, S1147L in the S2 subunit, and M1229I in the transmembrane domain (Figures 1B and 1C). 2021 Cell reports Introduction SARS_CoV_2 I692V;M1229I;S1147L;Y453F 307;382;352;289 312;388;358;294 RBD;N;S;S 302;253;4;243 305;254;5;244 33860605 Polysulfates Block SARS-CoV-2 Uptake through Electrostatic Interactions*. [22] The E484K substitution is reported to enable the virus to escape from neutralizing antibodies. 2021 Angewandte Chemie (International ed. in English) Introduction SARS_CoV_2 E484K 10 15 33860605 Polysulfates Block SARS-CoV-2 Uptake through Electrostatic Interactions*. [22] The N501Y variant is reported to be more infectious than the wild-type virus, and a virus carrying this mutation was adapted to infect mice, which cannot be infected by wild-type SARS-CoV-2. 2021 Angewandte Chemie (International ed. in English) Introduction SARS_CoV_2 N501Y 10 15 33860605 Polysulfates Block SARS-CoV-2 Uptake through Electrostatic Interactions*. Moreover, we investigate the consequences of the N501Y and E484K mutations in the spike protein for the virus binding to HS. 2021 Angewandte Chemie (International ed. in English) Introduction SARS_CoV_2 E484K;N501Y 59;49 64;54 S 82 87 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. A viral variant has recently emerged, carrying a single amino acid substitution in Spike at residue 614 from an aspartic acid (D) to a glycine (G) (D614G). 2021 Science advances Introduction SARS_CoV_2 D614G 148 153 S 83 88 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. Although there have been several studies validating the increase on the infectivity and transmissibility of D614G substitution in laboratory settings, the transition from the ancestral to the D614G form at the population level is still being investigated. 2021 Science advances Introduction SARS_CoV_2 D614G;D614G 108;192 113;197 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. In addition, natural viruses that carry D614G are more infectious in primary human cells and are more infectious and outcompete the ancestral D614 form in animal models. 2021 Science advances Introduction SARS_CoV_2 D614G 40 45 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. We found that the D614G substitution was directly associated with far-reaching alterations in interactions between different protomers and indirectly associated with changes in binding site exposure. 2021 Science advances Introduction SARS_CoV_2 D614G 18 23 33868743 COVID-19 and mutations a threat level assessment. A study of the genome of this B.1.351 variant has revealed very similar mutations to those present in the P.1 Brazilian strain, namely mutations of E484K and N501Y glycoproteins are present. 2021 Nepal journal of epidemiology Introduction SARS_CoV_2 E484K;N501Y 148;158 153;163 33868743 COVID-19 and mutations a threat level assessment. At this current stage the South African variant B.1.351 poses the greatest risk to international health as it is the most widespread, most resistant to current vaccinations and harbours both the E484K and N501Y mutations. 2021 Nepal journal of epidemiology Introduction SARS_CoV_2 E484K;N501Y 195;205 200;210 33868743 COVID-19 and mutations a threat level assessment. It has now been established that the P.1, B.1.526 and B.1.351 variants pose the greatest risk to international health as they harbor the infamous E484K mutation, thereby enhancing the capability of the virus to escape the host immune response. 2021 Nepal journal of epidemiology Introduction SARS_CoV_2 E484K 146 151 33868743 COVID-19 and mutations a threat level assessment. It is poignant however to ensure that targeted vaccines are synthesized to combat the strains harbouring the E484K mutation as it confers the ability to escape the immune response and thus cause a more severe and life-threatening infection. 2021 Nepal journal of epidemiology Introduction SARS_CoV_2 E484K 109 114 33868743 COVID-19 and mutations a threat level assessment. It is thus evident that the P.1 strain has the mutations of both E484K and N501Y making it more virulent as well as more resistant to antibodies. 2021 Nepal journal of epidemiology Introduction SARS_CoV_2 E484K;N501Y 65;75 70;80 33868743 COVID-19 and mutations a threat level assessment. The B.1.526 variant has a mutation of the E484K conferring a greater resistance to antibodies and thus poses a great concern. 2021 Nepal journal of epidemiology Introduction SARS_CoV_2 E484K 42 47 33868743 COVID-19 and mutations a threat level assessment. The E484K mutation is found in the South African variant and confers greater resistance to antibodies, and thus poses a greater threat. 2021 Nepal journal of epidemiology Introduction SARS_CoV_2 E484K 4 9 33868743 COVID-19 and mutations a threat level assessment. The English or B.1.1.7 harbours the N501Y mutation which confers a higher transmissibility of the virus and greater shedding of virions. 2021 Nepal journal of epidemiology Introduction SARS_CoV_2 N501Y 36 41 33868743 COVID-19 and mutations a threat level assessment. The English variant contains a host of mutations but most poignant is the mutation of N501Y which confers a higher transmissibility of the virus, via increasing viral shedding and load. 2021 Nepal journal of epidemiology Introduction SARS_CoV_2 N501Y 86 91 33868743 COVID-19 and mutations a threat level assessment. The N501Y causes an asparagine tyrosine AA substitution at position 501 present in the S gene. 2021 Nepal journal of epidemiology Introduction SARS_CoV_2 N501Y 4 9 S 89 90 33868743 COVID-19 and mutations a threat level assessment. The N501Y mutation is shown to confer an enhanced virulence in animal study models using mice. 2021 Nepal journal of epidemiology Introduction SARS_CoV_2 N501Y 4 9 33868743 COVID-19 and mutations a threat level assessment. The P.1 and the B.1.526 variant discovered in New York also harbour the worrisome E484K mutation and thus also pose a great risk, however they are less quantified whence compared to the South African strain. 2021 Nepal journal of epidemiology Introduction SARS_CoV_2 E484K 82 87 33868743 COVID-19 and mutations a threat level assessment. There are a host of phenotypically important mutations namely some being mutations of E484K and N501Y both of which involve the glycoprotein spikes of the virus. 2021 Nepal journal of epidemiology Introduction SARS_CoV_2 E484K;N501Y 86;96 91;101 S 141 147 33875719 Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology. In addition to D614G, NS3-Q57H, N-G204R and S-A222V mutations characterize the clades GH, GR and GV, respectively. 2021 Scientific reports Introduction SARS_CoV_2 D614G;A222V;G204R;Q57H 15;46;34;26 20;51;39;30 NS3;N;S 22;32;44 25;33;45 33875719 Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology. Such changes include: L84S in NS8 for clade S; coexisting L37F and G251V mutations in NSP6 and NS3, respectively for clade V; D614G mutation in the spike protein (S) for clade G. 2021 Scientific reports Introduction SARS_CoV_2 D614G;G251V;L37F;L84S 126;67;58;22 131;72;62;26 S;Nsp6;NS3;S;S 148;86;95;44;163 153;90;98;45;164 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. Additionally, we have modeled the wild-type and N501Y mutant spike proteins with a truncated ACE2 peptide to investigate the potential impacts of the N501Y residue change of the spike protein on ACE2 mimicking therapeutics such as the aforementioned miniprotein drug candidates, demonstrating that the N501Y mutation significantly improves binding affinity to soluble ACE2 derivatives but diminishes affinity to miniprotein drug candidates. 2021 The journal of physical chemistry. B Introduction SARS_CoV_2 N501Y;N501Y;N501Y 48;150;302 53;155;307 S;S 61;178 66;183 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. However, these miniproteins mimic the alpha-helix binding domain of the ACE2 protein to bind with the same interface of the spike protein as ACE2 and are therefore not immune to the potential changes that the N501Y mutation on the spike protein might cause. 2021 The journal of physical chemistry. B Introduction SARS_CoV_2 N501Y 209 214 S;S 124;231 129;236 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. Of note with the UK variant is an N501Y mutation on the SARS-CoV-2 spike protein, which is responsible for the virus' identification and attachment to the target host cells. 2021 The journal of physical chemistry. B Introduction SARS_CoV_2 N501Y 34 39 S 67 72 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. To investigate the potential change in binding affinity associated with the N501Y mutation, we have modeled both the SARS-CoV-2 spike protein and its N501Y mutant binding with wild-type human ACE2 (hACE2) and a previously reported T27Y/L79T/N330Y mutant of ACE2 (known as ACE2.v2.4) which has a 40-fold increased binding affinity with the wild-type spike protein of SARS-CoV-2. 2021 The journal of physical chemistry. B Introduction SARS_CoV_2 N501Y;N501Y;L79T;N330Y 76;150;236;241 81;155;240;246 S;S 128;349 133;354 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. With the increase in infectivity that the UK SARS-CoV-2 variant displays, it is essential to know whether the N501Y mutation on the spike protein has compromised the binding affinities of the spike protein-targeted therapeutics that are currently being developed. 2021 The journal of physical chemistry. B Introduction SARS_CoV_2 N501Y 110 115 S;S 132;192 137;197 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. 1) The D614G mutation in the spike protein was first detected in Europe in the early phase of pandemic, and currently it is widely spread around the globe. 2021 EXCLI journal Introduction SARS_CoV_2 D614G 7 12 S 29 34 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. This linage also exhibited a change at the residue 681 (P681H), one of the four residues comprising the furin cleavage site located between S1 and S2 domains in the spike protein (Rambaut et al., 2020). 2021 EXCLI journal Introduction SARS_CoV_2 P681H 56 61 S 165 170 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. This mutation was found at low prevalence before March 2020, however, in June 2020 the occurrence of the D614G variant was reported in over 70 % of the SARS-CoV-2 published sequences (Bobay et al., 2020; Groves et al., 2021; Korber et al., 2020); 2) The B.1.1.7 linage that first appeared in the United Kingdom became rapidly worldwide distributed, reaching the United States in January 2021. 2021 EXCLI journal Introduction SARS_CoV_2 D614G 105 110 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. Thus, P681H residue substitution could additionally enhance this interaction. 2021 EXCLI journal Introduction SARS_CoV_2 P681H 6 11 33886690 The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways. Mutation D614G was already detected during the early phase of the pandemic and, after four months, the SG614 variant became globally predominant. 2021 PLoS pathogens Introduction SARS_CoV_2 D614G 9 14 33886690 The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways. The D614G mutation was also shown to enhance virus replication in cultured airway epithelial cells and increase infectivity of pseudovirus bearing SARS-CoV-2 S protein. 2021 PLoS pathogens Introduction SARS_CoV_2 D614G 4 9 S 158 159 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. The spike gene carries the mutation known as N501Y (Asn501Tyr; c.1501A>T). 2021 Microbiology resource announcements Introduction SARS_CoV_2 A1501T;N501Y;N501Y 63;45;52 72;50;61 S 4 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. This mutation cooccurs with several mutations, including missense mutations (A570D, P681H, T716I, S982A, and D1118H), as well as disruptive in-frame deletions (H69-V70 and Y145). 2021 Microbiology resource announcements Introduction SARS_CoV_2 D1118H;P681H;S982A;T716I;A570D 109;84;98;91;77 115;89;103;96;82 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. E484K has recently been demonstrated to reduce virus neutralization for several monoclonal antibodies and polyclonal human sera. 2021 Proc Natl Acad Sci U S A Introduction SARS_CoV_2 E484K 0 5 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. In particular, all three variants share one specific mutation called D614G, which replaced the initial SARS-CoV-2 strain to become the dominant form of the virus circulating globally and is thought to promote transmission of the virus but with no impact on pathogenesis. 2021 Proc Natl Acad Sci U S A Introduction SARS_CoV_2 D614G 69 74 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. N501 is one of six key contact residues within the RBD, and the N501Y mutation increases binding affinity to human and mouse ACE2. 2021 Proc Natl Acad Sci U S A Introduction SARS_CoV_2 N501Y 64 69 RBD 51 54 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Nanobody-Fc fusions effectively blocked ACE2 receptor engagement with naturally occurring RBD variants present in human populations, showed potent neutralization against wild-type (WT) SARS-CoV-2 and an N501Y D614G variant, and, when used prophylactically, protected mice infected with a SARS-CoV-2 N501Y D614G variant. 2021 Proc Natl Acad Sci U S A Introduction SARS_CoV_2 D614G;D614G;N501Y;N501Y 209;305;203;299 214;310;208;304 RBD 90 93 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Within the RBD, B.1.1.7 carries N501Y mutation; B.1.351 carries K417N, E484K, and N501Y mutations; and B.1.1.248 carries K417N/T, E484K, and N501Y mutations. 2021 Proc Natl Acad Sci U S A Introduction SARS_CoV_2 E484K;E484K;K417N;K417N;K417T;N501Y;N501Y;N501Y 71;130;64;121;121;32;82;141 76;135;69;128;128;37;87;146 RBD 11 14 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. This allowed us to identify SARS-CoV-2 haplotypes and their localized transmission patterns that arose early and became dominant, specifically the D614G S spike protein mutation that was unidentified prior to April but which was identified in 99.3% of viral isolates from our pediatric COVID-19 patients by June of 2020. 2021 Emerging microbes & infections Introduction SARS_CoV_2 D614G 147 152 S;S 155;153 160;154 COVID-19 286 294 33897278 The dual role of the immune system in the course of COVID-19. The fatal impact of the aging immune system. In particular, clade G, prevalent in Europe, carries a D614G mutation in the spike (S) protein, which is responsible for the initial interaction of the virus with the host human cell. 2021 Central-European journal of immunology Introduction SARS_CoV_2 D614G 55 60 S;S 77;84 82;85 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. in 2020 identified the P323L mutation in the RdRp protein of SARS-CoV-2, which may confer resistance to the drug. 2021 Frontiers in molecular biosciences Introduction SARS_CoV_2 P323L 23 28 RdRP 45 49 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. It has been shown that in the presence of GS-441524, there was 5.6-fold resistance in coronavirus mouse hepatitis virus, which was attributed to two mutations, F476L and V553L, in the coding region of nsp12 core polymerase (Agostini et al.,). 2021 Frontiers in molecular biosciences Introduction SARS_CoV_2 F476L;V553L 160;170 165;175 Nsp12 201 206 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. Similar findings were observed in SARS-CoV carrying the mutations F480L and V557L, which are not in the vicinity of the binding site of RdRp; thus, the exact mechanism behind the resistance remains undetermined (Agostini et al.,). 2021 Frontiers in molecular biosciences Introduction SARS_CoV_2 F480L;V557L 66;76 71;81 RdRP 136 140 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. Three clades (G, GH, and GR) contain the 23403A>G (D614G) variant within the gene that encodes the spike glycoprotein. 2021 JAMA network open Introduction SARS_CoV_2 A23403G;D614G 41;51 49;56 S 99 117 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Also, we report an increase in local detection of a variant with a Spike mutation T1117I not broadly reported elsewhere. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 T1117I 82 88 S 67 72 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? A competition assay comparing virus of D614G and D614 recovered the virus D614G /D614 ratio of 1.2 to 2.6, suggesting that D substitution by G at residue 614 of the S protein likely increases the virus fitness and transmission. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G;D614G 39;74 44;79 S 165 166 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? An enhanced entry of D614G was seen with pseudoviruses carrying D614G, which correlated with the observation of less S1 domain shedding and higher S protein incorporation into the virion. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G;D614G 21;64 26;69 S 147 148 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? By comparing the decay of infectivity of D614 and D614G virus over time at 33C, 37C and 42C, the D614G variant retained higher infectivity at all temperatures than the D614 virus. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G;D614G 50;97 55;102 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Consistently, patient infected by D614G did not show any altered disease severity. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 34 39 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Consistently, Weissman and colleagues evaluated the neutralization of pseudoviruses bearing either D614 or D614G spike by sera from spike-immunized mice, non-human primates or convalescent sera from people infected with either form of the virus. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 107 112 S;S 113;132 118;137 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Conversely, another group showed an enhanced binding of D614G variant to hACE2. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 56 61 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? D614G variant. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 0 5 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? demonstrated that sera from hamsters infected with D614 virus have modestly higher neutralization titers against D614G variant than that against D614 virus. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 113 118 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Different from N501Y and E484K, the mutation of K417 locates outside the RBM. 2021 International journal of biological sciences Introduction SARS_CoV_2 E484K;N501Y 25;15 30;20 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? examined D614G variant using more than 25,000 whole genome SARS-CoV-2 sequences from COG- UK dataset. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 9 14 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? examined the neutralization of convalescent plasma from patients infected by SARS-CoV-2 carrying D614G mutation but no mutation in RBD or NTD. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 97 102 RBD 131 134 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Except D614G, all the critical variants we reviewed here contain mutations in NTD: for example, L18F in variant 501.V2 and P.1, T20N and P26N in variant P.1, DeltaH69/DeltaV70 in Cluster 5 and VOC 202012/01, Y144 deletion in VOC 202012/01, 242-244 deletion and R246I in VOC 202012/01. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G;L18F;P26N;R246I;T20N 7;96;137;261;128 12;100;141;266;132 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Fortunately, the mutation in D614G variants seems not compromise the effectiveness of vaccines currently being developed against the ancestral SARS-COV-2. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 29 34 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? However, it is of note that the analysis of a dataset of 46,723 SARS-CoV-2 genomes isolated from patients worldwide did not find any evidence associate with significantly increased viral transmission of variant D614G. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 211 216 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? However, no increased COVID-19 mortality or clinical severity was found to be correlated with D614G. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 94 99 COVID-19 22 30 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? However, the neutralization by sera from participants vaccinated with BNT162b2 against N501Y, Delta69/Delta70+ N501Y + D614G and E484K+ N501Y+D614G pseudoviruses only demonstrated small effects of these mutations on neutralization. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G;E484K;N501Y;N501Y;N501Y;D614G 119;129;87;111;136;142 124;134;92;116;141;147 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? In addition, patients infected by the D614G variant demonstrated higher viral loads than that seen in the primary strain in the upper respiratory tract. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 38 43 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? In addition, the P681H mutation has appeared many times independently and has become dominant in the local epidemic in Hawaii. 2021 International journal of biological sciences Introduction SARS_CoV_2 P681H 17 22 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? In addition, the simultaneous mutations of DeltaH69/DeltaV70 and Y453F were also found in several other variants closely related to cluster 5 with high frequency. 2021 International journal of biological sciences Introduction SARS_CoV_2 Y453F 65 70 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? In contrast to the enhanced transmissibility, the mutation of D614G has little effect on the pathogenesis of SARS-CoV-2 in the hamster animal model. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 62 67 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? In the Syrian golden hamster model, hamsters infected by D614G variant produced higher infectious titers in the nasal washes and the trachea, but not in the lungs, compared to those infected by D614 viruses. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 57 62 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? In this variant, five mutations appeared on the S protein, including: Y453F, a H69/V70 deletion (DeltaH69/DeltaV70), I692V, S1147L and M1229I. 2021 International journal of biological sciences Introduction SARS_CoV_2 I692V;M1229I;S1147L;Y453F 117;135;124;70 122;141;130;75 S 48 49 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Indeed, N501Y has been shown to increase the affinity to hACE2 receptor. 2021 International journal of biological sciences Introduction SARS_CoV_2 N501Y 8 13 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Initial experimental study on the D614G was performed using pseudovirus. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 34 39 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Interestingly, structural and functional analysis on D614G found that this mutation did not alter S protein synthesis, processing, or incorporation into SARS-CoV-2 particles, whereas the affinity of D614G to ACE2 was significantly reduced due to a faster dissociation rate. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G;D614G 53;199 58;204 S 98 99 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? It is of note that D614G mutation has dominated the COVID-19 pandemic now (Table 2) and all the variants mentioned below (Cluster 5, VOC 202012/01, 501Y.V2 and P.1.) carry the D614G mutation (Table 1). 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G;D614G 19;176 24;181 COVID-19 52 60 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? It seems that variant D614G has enhanced abilities for infection and transmission. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 22 27 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Mechanism study on the enhanced vulnerability to neutralization by a negative stain electron microscopy revealed that the D614G spike has a higher percentage of the 1-RBD "up" conformation, which likely increases the epitope exposure to antibodies.Taken together, these results suggested that D614G mutation is unlikely reduce the ability of current vaccines to protect against COVID-19. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G;D614G 122;293 127;298 S;RBD 128;167 133;170 COVID-19 378 386 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Mutant N501Y has demonstrated significant increase in the binding affinity to ACE2. 2021 International journal of biological sciences Introduction SARS_CoV_2 N501Y 7 12 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? N501Y is also presented in the VOC 202012/01 variant. 2021 International journal of biological sciences Introduction SARS_CoV_2 N501Y 0 5 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? P.1 has three mutations in the RBD of S proteins: K417T, E484K and N501Y (Table 1). 2021 International journal of biological sciences Introduction SARS_CoV_2 E484K;K417T;N501Y 57;50;67 62;55;72 RBD;S 31;38 34;39 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Recently, Xie et al generated isogenic N501 and N501Y SARS-CoV-2 strains, and examined sera from participants vaccinated by mRNA-based COVID-19 vaccine BNT162b2 (Pfizer-BioNTech). 2021 International journal of biological sciences Introduction SARS_CoV_2 N501Y 48 53 COVID-19 135 143 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Similarly, the inactivated vaccine BBIBP-CorV and recombinant dimeric RBD vaccine ZF2001 were shown to largely preserve the neutralizing titers against 501Y.V2, with a slight reduction comparing to original strain or D614G strain (Table 3). 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 217 222 RBD 70 73 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Subsequently, Planete and colleague engineered a D614G variant in the USA-WA1/2020 strain and used the resultant virus to infect human lung epithelial cells and the primary human airway tissue. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 49 54 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? The 501Y.V2 variant is characterized by carrying nine mutations in S protein (L18F, D80A, D215G, R246I, Delta242-244, K417N, E484K, N501Y, A701V) (Table 1), three of which (K417N, E484K and N501Y) locate in the RBD of the S protein. 2021 International journal of biological sciences Introduction SARS_CoV_2 A701V;D215G;D80A;E484K;E484K;K417N;N501Y;N501Y;R246I;K417N;L18F 139;90;84;125;180;118;132;190;97;173;78 144;95;88;130;185;123;137;195;102;178;82 RBD;S;S 211;67;222 214;68;223 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? The function of mutation of P681H is unclear but it locates near the furin-cleavage site, which is important for SARS-CoV-2 entry. 2021 International journal of biological sciences Introduction SARS_CoV_2 P681H 28 33 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? The importance of the D614G mutation was quickly seen by the analysis of the frequency of the ancestral strain D614 and D614G variant over time. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G;D614G 22;120 27;125 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? The mutation I692V occurs seven amino acids downstream of the furin cleave site, whereas S1147L and M1229I locates on the S2 subunit (Table 1). 2021 International journal of biological sciences Introduction SARS_CoV_2 I692V;M1229I;S1147L 13;100;89 18;106;95 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? The mutation of D614G attracted considerable attention as such mutation potentially could alter the receptor binding affinity, thus the virus infectivity and the immunogenicity. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 16 21 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? The mutations of both N501Y and E484K locate in the receptor binding motif (RBM) in the RBD. 2021 International journal of biological sciences Introduction SARS_CoV_2 E484K;N501Y 32;22 37;27 RBD 88 91 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? The results showed that the neutralization activities of plasma from vaccinated individual to the pseudoviruses expressing N501Y, E484K or K417N:E484K:N510Y were significantly reduced. 2021 International journal of biological sciences Introduction SARS_CoV_2 E484K;K417N;N501Y;E484K;N510Y 130;139;123;145;151 135;144;128;150;156 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? The SARS-CoV-2 D614G variant, emerged at the end of January 2020, was first noticed in April 2020 in a preprint by Korber and colleagues, who warned of "D614G is increasing in frequency at an alarming rate". 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G;D614G 15;153 20;158 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? The studies found that the location initially reporting the D614 viruses in the pandemic were often dominated by D614G virus subsequently. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 113 118 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? The variant of D614G harbors a substitution of aspartic acid by a glycine at the position 614 of the virus spike glycoprotein, which helps virus particles to penetrate cells (Table 1). 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 15 20 S 107 125 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? The Y453F mutation locates in the RBD that directly contacts the host ACE2 at amino acid 34. 2021 International journal of biological sciences Introduction SARS_CoV_2 Y453F 4 9 RBD 34 37 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? These findings were echoed by another group, who used similar approach and concluded that D614G variant enhanced SARS-COV-2 infectivity, competitive fitness, and transmission in primary human cells and animal model. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 90 95 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? They found that D614G was associated with higher viral load and younger age of patients. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 16 21 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? They found that D614G was more susceptible to neutralization by all of the sera. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 16 21 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? They found that the mutation D614G enhanced viral replication through increasing the infectivity and stability of virions. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 29 34 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? They showed that the sera had equivalent neutralizing titers to the N501 and N501Y viruses. 2021 International journal of biological sciences Introduction SARS_CoV_2 N501Y 77 82 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Three mutations, namely N501Y, DeltaH69/DeltaV70 and P681H, locate in S protein. 2021 International journal of biological sciences Introduction SARS_CoV_2 N501Y;P681H 24;53 29;58 S 70 71 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? To accurately recapitulate the effect of D614G variant on the virus transmissibility and clinical severity, Volz et al. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 41 46 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? used convalescent human serum and neutralizing antibodies to examine their blockage on live viruses of D614G variant and did not find any significant difference, consistent with the results from a separated study. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 103 108 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? Vesicular stomatitis virus and lentiviral particles incorporating the D614G variant were used to study the replication kinetics, and D614G demonstrated significantly higher pseudovirus titers in multiple cell types. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G;D614G 70;133 75;138 33907511 The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic? VOC 202012/01 is highly transmissible compared to the parental strain of D614G. 2021 International journal of biological sciences Introduction SARS_CoV_2 D614G 73 78 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. After the early months of the SARS-CoV-2 pandemic in 2020, the vast majority of sequenced genomes contained the spike mutation D614G (along with 3 separate nucleotide changes). 2021 bioRxiv Introduction SARS_CoV_2 D614G 127 132 S 112 117 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. A temporal plot of the number of B.1.1.7+E484K isolates collected between December 2020 to March 2021 (2-week window) is shown in Figure 1B. 2021 bioRxiv Introduction SARS_CoV_2 E484K 41 46 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. For each of these CCs, representative sequences without the E484K mutation have been circulating since at least November 2020, predating the first E484K in each CC. 2021 bioRxiv Introduction SARS_CoV_2 E484K;E484K 60;147 65;152 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. Here we present a comparative analysis of the first SARS-CoV-2 B.1.1.7 isolates detected in PA that harbor the E484K spike mutation, a mutation that could be associated with reduced efficacy of both vaccine-induced and natural immunity. 2021 bioRxiv Introduction SARS_CoV_2 E484K 111 116 S 117 122 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. Here we report a B.1.1.7 isolate with the E484K spike mutation isolated in southeastern Pennsylvania (PA). 2021 bioRxiv Introduction SARS_CoV_2 E484K 42 47 S 48 53 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. However, in February 2021 Public Health England (PHE) published a concerning report of eleven B.1.1.7 genomes that had acquired the E484K spike mutation. 2021 bioRxiv Introduction SARS_CoV_2 E484K 132 137 S 138 143 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. Interestingly, one B.1.1.7 isolate carried the E484K spike mutation that is present in the South African and Brazilian lineages. 2021 bioRxiv Introduction SARS_CoV_2 E484K 47 52 S 53 58 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. It also shared with 9 other US isolates a stop mutation (A28095T) in ORF8 (Figure 2B). 2021 bioRxiv Introduction SARS_CoV_2 A28095T 57 64 ORF8 69 73 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. Lineages B.1.1.7, B.1.429 (California), B.1.526 (New York) and R.1 (International lineage with the E484K mutation) accounted for 69% of the sequenced genomes in March. 2021 bioRxiv Introduction SARS_CoV_2 E484K 99 104 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. Our analysis suggests that multiple lineages of B.1.1.7+E484K are circulating in the US, and that these lineages may have acquired E484K independently. 2021 bioRxiv Introduction SARS_CoV_2 E484K;E484K 131;56 136;61 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. Phylogenetic analysis of the 235 B.1.1.7+E484K GISAID isolates showed that US isolates are found in at least 3 different clades. 2021 bioRxiv Introduction SARS_CoV_2 E484K 41 46 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. Since the first report by PHE in February, a total of 253 B.1.1.7+E484K genomes have been uploaded to GISAID from England and 14 other countries (Germany, France, Italy, Poland, Sweden, Ireland, Netherlands, Portugal, Wales, Turkey, Slovakia, Austria, Czech Republic and USA) (as of 04/17/2021). 2021 bioRxiv Introduction SARS_CoV_2 E484K 66 71 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. This increase raises the concern that more B.1.1.7+E484K sequences may be emerging even as herd immunity increases by natural immunity and vaccines. 2021 bioRxiv Introduction SARS_CoV_2 E484K 51 56 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. This raises the possibility that the E484K mutation was acquired independently in each of these CCs in independent events. 2021 bioRxiv Introduction SARS_CoV_2 E484K 37 42 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. To better understand the relationship between this isolate and publicly available SARS-CoV-2 genomes, we compared it to all available B.1.1.7+E484K high coverage genomes available on GISAID (n=235). 2021 bioRxiv Introduction SARS_CoV_2 E484K 142 147 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. Two of these lineages, B.1.351 and P.1 were of specific concern because they harbor the mutation E484K, which has been shown to enhance escape from neutralizing antibody inhibition in vitro, and may be associated with reduced efficacy of the vaccine. 2021 bioRxiv Introduction SARS_CoV_2 E484K 97 102 33907767 Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. The B.1.427/B.1.429 variant, which carries a L452R substitution mutation in the spike protein, was first detected in October 2020 and by January 2021 accounted for 35% of all SARS-CoV-2 cases detected in California. 2021 medRxiv Introduction SARS_CoV_2 L452R 45 50 S 80 85 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. In addition, N501Y was also shared by another SARS-CoV-2 variant-N501Y.V2 reported from South Africa, also known as B.1.351 lineage containing three mutations (K417N, E484K, and N501Y) in the RBD. 2021 Virology journal Introduction SARS_CoV_2 E484K;N501Y;N501Y;K417N;N501Y 167;13;178;160;65 172;18;183;165;70 RBD 192 195 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. In this study, we further combined a RBD-specific monoclonal nAbs panel involving twelve published antibodies from different classes with diverse neutralizing epitopes, and measured their neutralizations and binding affinities against the wild type and N501Y mutant SARS-CoV-2, which will enrich the research in the field of viral escape and be crucial to the control of COVID-19. 2021 Virology journal Introduction SARS_CoV_2 N501Y 253 258 RBD 37 40 COVID-19 371 379 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. Indeed, a novel viral variant recently emerged in England, named N501Y.V1 (also known as VOC-202012/01 or B.1.1.7 lineage), which is up to 70% more transmissible. 2021 Virology journal Introduction SARS_CoV_2 N501Y 65 70 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. The N501Y.V1 variant usually maintained or partially affected the neutralizing sensitivity to most of nAbs, but N501Y.V2 could fully escaped from the neutralization of certain types of nAbs, which become a serious challenge to the current antibody and vaccine candidates. 2021 Virology journal Introduction SARS_CoV_2 N501Y;N501Y 4;112 9;117 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. There are seven substitutions (N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H) and three deletions (H69Del, V70Del, and Y144Del) in the spike of the N501Y.V1 variant comparing with the Wuhan-Hu-1 strain (wide type), with N501Y the only mutation in the ACE2 interface of the receptor binding domain (RBD). 2021 Virology journal Introduction SARS_CoV_2 A570D;D1118H;D614G;N501Y;N501Y;P681H;S982A;T716I;N501Y 38;77;45;155;227;52;66;59;31 43;83;50;160;232;57;71;64;36 RBD;S;RBD 280;142;305 303;147;308 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Despite being phylogenetically distinct, a common feature of both the UK and South African variants is the mutation of residue 501 in the RBD from Asn to Tyr (N501Y). 2021 PLoS biology Introduction SARS_CoV_2 N501Y 159 164 RBD 138 141 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Understanding the impact of N501Y on antibody neutralization, ACE2 binding, and viral entry is therefore of fundamental interest in the efforts to prevent the spread of COVID-19. 2021 PLoS biology Introduction SARS_CoV_2 N501Y 28 33 COVID-19 169 177 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. A SARS-CoV-2 variant with D614G substitution was shown to enhance transmissibility and competitive fitness in animal models and human cell cultures. 2021 Viruses Introduction SARS_CoV_2 D614G 26 31 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Among them, Delta69Delta70 and N501Y in B.1.1.7 lineage have been shown to cause a conformational change in the spike protein and have higher infectivity than D614G, suggesting that they may increase transmissibility and alter antigenicity. 2021 Viruses Introduction SARS_CoV_2 D614G;N501Y 159;31 164;36 S 112 117 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Fortunately, vaccines with verified efficacy against the ancestral SARS-CoV-2 are also efficacious against the D614G variant. 2021 Viruses Introduction SARS_CoV_2 D614G 111 116 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Furthermore, structural analysis elucidated that D614G mutation led to a conformational change of the receptor-binding domains (RBDs), indicating that enhanced the ability to attach to the ACE2, ultimately induced higher infectivity. 2021 Viruses Introduction SARS_CoV_2 D614G 49 54 RBD 128 132 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. In the case of B.1.1.7, a series of mutations in eight sites including D614G appeared in the spike protein: Delta69Delta70, Delta144Delta145, N501Y, A570D, P681H, T716I, S982A, and D1118H (; GISAID, accessed on 1 December 2020). 2021 Viruses Introduction SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 149;181;71;142;156;170;163 154;187;76;147;161;175;168 S 93 98 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Mounting results reported that pseudoviruses encoding D614G mutant show higher infectivity than the original strain. 2021 Viruses Introduction SARS_CoV_2 D614G 54 59 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Remarkably, B.1.351 contains additional two mutations, K417N and E484K, in receptor binding motif (RBM) of the RBD region and those may potentially induce a conformational change of the spike protein, and subsequently increase the infectivity of B.1.351 than other lineages. 2021 Viruses Introduction SARS_CoV_2 E484K;K417N 65;55 70;60 S;RBD 186;111 191;114 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. The first reported emerging SARS-CoV-2 mutation, D614G, has now become the most common form in the world. 2021 Viruses Introduction SARS_CoV_2 D614G 49 54 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. The patients who were infected with SARS-CoV-2 D614G strain were associated with higher viral loads but not disease severity and mortality. 2021 Viruses Introduction SARS_CoV_2 D614G 47 52 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. We show that SARS-CoV-2 B.1.351 variant harboring K417N and E484K mutations have naturally evolved to possess notable alterations in their infectivity and S1/S2 cleavage, leading to enhanced syncytium formation and antigenicity. 2021 Viruses Introduction SARS_CoV_2 E484K;K417N 60;50 65;55 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. A recent study adopted individual patients' data from more than 2 million SARS-CoV-2 infections in the UK, and found significant positive association of B.1.1.7 lineage (which is dominant by N501Y substitution) and the fatality risk in terms of the hazard and absolute risks. 2021 Viruses Introduction SARS_CoV_2 N501Y 191 196 COVID-19 74 95 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. Around September 2020, genetic variants carrying the N501Y substitution on the spike (S) protein of SARS-CoV-2 were first detected in the United Kingdom (UK), then spread to elsewhere globally, and trended to reach fixation rapidly in many places, for example, South Africa, Brazil, and the U.S. 2021 Viruses Introduction SARS_CoV_2 N501Y 53 58 S;S 79;86 84;87 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. By contrast, whether the N501Y substitution leads to a difference in disease severity among SARS-CoV-2 infections remains largely unassessed. 2021 Viruses Introduction SARS_CoV_2 N501Y 25 30 COVID-19 92 113 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. Classic epidemiological investigations, for example, cohort or case-control studies, using individual patients' information with a large sample size may explore the evidence about the association between severity of COVID-19 and N501Y directly. 2021 Viruses Introduction SARS_CoV_2 N501Y 229 234 COVID-19 216 224 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. On the other hand, together with some recent scientific preprints, the relevant peer-reviewed literature found either no significant evidence or a weakly positive association between clinical severity and N501Y. 2021 Viruses Introduction SARS_CoV_2 N501Y 205 210 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. Recent analyses reported evidence that the 501Y variants were associated with an increase in transmissibility of SARS-CoV-2 at population scale, and similar findings were also reported for the D614G substitution in previous studies. 2021 Viruses Introduction SARS_CoV_2 D614G 193 198 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. We reconstruct the real-time and variant-specific case fatality ratio (CFR) of COVID-19 empirically, and infer the change in fatality risk associated with N501Y substitution in SARS-CoV-2. 2021 Viruses Introduction SARS_CoV_2 N501Y 155 160 COVID-19 79 87 33918332 Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. A number of substitutions in S have been associated with immune escape (e.g., E484K, K417N), or increased binding to the ACE-2 receptor (e.g., N501Y). 2021 Microorganisms Introduction SARS_CoV_2 E484K;K417N;N501Y 78;85;143 83;90;148 S 29 30 33918332 Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. In particular, the D614G substitution in the Spike (S) protein, which arose early in the pandemic, is associated with higher transmissibility. 2021 Microorganisms Introduction SARS_CoV_2 D614G 19 24 S;S 45;52 50;53 33918332 Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. Lineage B.1.1.7 has seventeen lineage-defining mutations including a deletion at positions 69/70 (Delta69/70) and 144, and substitutions N501Y and P681H in S. 2021 Microorganisms Introduction SARS_CoV_2 N501Y;P681H 137;147 142;152 S 156 157 33918332 Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. The N501Y substitution in S, either alone or in combination with other mutations, was suggested to have an increased binding affinity to the human receptor ACE2, and B.1.1.7 was predicted to be more transmissible. 2021 Microorganisms Introduction SARS_CoV_2 N501Y 4 9 S 26 27 33918332 Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. The neutralization of B.1.1.7 S corresponding pseudoviruses was not affected by BNT162b2 (BioNTech/Pfizer) vaccine-elicited human sera, but studies using cDNA-based SARS-CoV-2 clones with spike Delta69/70, E484K and N501Y revealed moderately diminished protection. 2021 Microorganisms Introduction SARS_CoV_2 E484K;N501Y 206;216 211;221 S;S 188;30 193;31 33918332 Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. Viruses with D614G substitution are now the dominant circulating lineages. 2021 Microorganisms Introduction SARS_CoV_2 D614G 13 18 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. Here, we define the lineage N.9 within B.1.1.33 diversity that harbors mutation E484K in the S protein as was detected in different Brazilian states between November 2020 and February 2021. 2021 Viruses Introduction SARS_CoV_2 E484K 80 85 S 93 94 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. The VOC P.1, first described in January 2021, displayed an unusual number of lineage-defining mutations in the S protein (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I) and its emergence was associated with a second COVID-19 epidemic wave in the Amazonas state. 2021 Viruses Introduction SARS_CoV_2 D138Y;E484K;H655Y;K417T;N501Y;P26S;R190S;T1027I;T20N;L18F 140;161;175;154;168;134;147;182;128;122 145;166;180;159;173;138;152;188;132;126 S 111 112 COVID-19 237 245 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. The VOI P.2, first described in samples from October 2020 in the state of Rio de Janeiro, was distinguished by the presence of the S:E484K mutation in RBD and other four lineage-defining mutations outside the S protein. 2021 Viruses Introduction SARS_CoV_2 E484K 133 138 RBD;S;S 151;131;209 154;132;210 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. Nevertheless, some variants, such as D614G in spike, can escape proofreading and significantly shape the global dispersal of SARS-CoV-2 infections. 2021 Biomedicines Introduction SARS_CoV_2 D614G 37 42 S 46 51 COVID-19 125 146 33922914 Dieckol and Its Derivatives as Potential Inhibitors of SARS-CoV-2 Spike Protein (UK Strain: VUI 202012/01): A Computational Study. Of note, Tyr453Phe and Asn501Tyr mutations are located in the receptor-binding domain (RBD) of SARS-CoV-2. 2021 Marine drugs Introduction SARS_CoV_2 N501Y;Y453F 23;9 32;18 RBD 87 90 33922914 Dieckol and Its Derivatives as Potential Inhibitors of SARS-CoV-2 Spike Protein (UK Strain: VUI 202012/01): A Computational Study. The new variant is characterized by many mutations such as Delta69-70, Delta144, Tyr453Phe, Asn501Tyr, Ala570Asp, Asp614Gly, Phe681His, Thr716Ile, Ser982Ala, and Asp1118His in the spike protein. 2021 Marine drugs Introduction SARS_CoV_2 A570D;N501Y;D1118H;D614G;F681H;S982A;T716I;Y453F 103;92;162;114;125;147;136;81 112;101;172;123;134;156;145;90 S 180 185 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Based on GISAID classification, the clade L is considered as wild-type (WT) variant, which consists of initial isolates from China (including reference genome) or other countries mainly involved in the first stage of pandemic; the clade S is defined by L84S mutation in NS8; the clade V is defined by G251V mutation in NS3; the clade G is defined by D614G mutation in S-protein (dominant isolate since spring 2020). 2021 Microorganisms Introduction SARS_CoV_2 D614G;G251V;L84S 350;301;253 355;306;257 NS3;S;S 319;237;368 322;238;369 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Subsequently, three clades 'GH, GR, GV' descended from the clade G, while each one has identical mutations in addition to D614G. 2021 Microorganisms Introduction SARS_CoV_2 D614G 122 127 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Therefore, the clade GH is defined by Q57H mutation in NS3, the clade GR is defined by G204R mutation in N-protein; and the clade GV is defined by A222V mutation in S-protein. 2021 Microorganisms Introduction SARS_CoV_2 A222V;G204R;Q57H 147;87;38 152;92;42 NS3;N;S 55;105;165 58;106;166 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. Specifically, the 19del was demonstrated to permit significantly higher infection of SARS-CoV PsVs, and the D614G mutation emerged early in the COVID-19 pandemic, showed heightened infection potential, and quickly became the most common variant spreading. 2021 Journal of biomedical science Introduction SARS_CoV_2 19del;D614G 18;108 23;113 COVID-19 144 152 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. To better understand and maximize the infectivity of SARS-CoV-2 PsV, we generated PsV carrying spike protein variants known to have varying human ACE2 binding properties, including 19 deletion (19del) and 19del + D614G. 2021 Journal of biomedical science Introduction SARS_CoV_2 19del;D614G;19del 205;213;194 210;218;199 S 95 100 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. A total of 607 mutations are reported in RdRp of which 14408C>T (P323L) mutation which lies near the interface domain of RdRp showed highest frequency (10 925 times in 15 140 genotypes) (Table 2). 2021 Epidemiology and infection Introduction SARS_CoV_2 C14408T;P323L 55;65 63;70 RdRP;RdRP 41;121 45;125 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Among 51 non-synonymous mutations in ORF3a, Q57H (17.4%) and G251V (9.7%) were predominant ones of which Q57H mutation was found to cause disease severity in hospitalised. 2021 Epidemiology and infection Introduction SARS_CoV_2 G251V;Q57H;Q57H 61;44;105 66;48;109 ORF3a 37 42 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Among all S protein variants, D614G increased at an alarming rate which was observed 10 969 times in 15 140 genome isolates, suggesting a positive selection of this variant during the course of viral evolution. 2021 Epidemiology and infection Introduction SARS_CoV_2 D614G 30 35 S 10 11 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Among the accessory proteins, ORF3a and ORF8 are brought into limelight due to the rapid spread of cluster V (NSP3:F106F, RdRp:P323L, S:D614G and ORF3a:Q57H) and VI (NSP4:S76S and ORF8:L84S). 2021 Epidemiology and infection Introduction SARS_CoV_2 D614G;F106F;L84S;P323L;Q57H;S76S 136;115;185;127;152;171 141;120;189;132;156;175 ORF3a;ORF3a;Nsp3;Nsp4;ORF8;ORF8;RdRP;S 30;146;110;166;40;180;122;134 35;151;114;170;44;184;126;135 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Among the point mutations, L84S is the predominant one and associated with mild disease symptoms among the hospitalised individuals. 2021 Epidemiology and infection Introduction SARS_CoV_2 L84S 27 31 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Cluster I includes 3037C>T; NSP3:F106F (non-structural protein3:F106F) and 14408C>T; RdRp:P323L, cluster II includes 3037C>T, 14408C>T and 23403A>G; S:D614G, cluster III includes 14408C>T, cluster IV includes 3037C>T, 14408C>T, 23403A>G, 28881G>A; N:R203K, 28882G>A; N:R203K, 28883G>C; N:G204R, cluster V includes 3037C>T, 14408C>T, 23403A>G and 25563G>T; ORF3a:Q57H and cluster VI includes 8782C>T; NSP4:S76S, 28144T>C; ORF8:L84S. 2021 Epidemiology and infection Introduction SARS_CoV_2 C14408T;C14408T;C14408T;C14408T;C14408T;A23403G;A23403G;A23403G;G25563T;T28144C;G28881A;G28882A;G28883C;C3037T;C3037T;C3037T;C3037T;C8782T;D614G;F106F;F106F;G204R;L84S;P323L;Q57H;R203K;R203K;S76S 75;126;179;218;323;139;228;333;346;411;238;257;276;19;117;209;314;391;151;33;64;288;426;90;362;250;269;405 83;134;187;226;331;147;236;341;354;419;246;265;284;26;124;216;321;398;156;38;69;293;430;95;366;255;274;409 ORF3a;Nsp3;Nsp4;ORF8;RdRP;N;N;N;S 356;28;400;421;85;248;267;286;149 361;32;404;425;89;249;268;287;150 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. D614G variant was highly transmissible and became predominant in Europe, Canada, Australia and United States. 2021 Epidemiology and infection Introduction SARS_CoV_2 D614G 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. GR clade has a combination of spike D614G and nucleocapsid RG203KR mutations, prevalent in Europe and South America while GH comprises mutations in spike D614G and ORF3a Q57H which predominates in North America. 2021 Epidemiology and infection Introduction SARS_CoV_2 D614G;D614G;Q57H 36;154;170 41;159;174 N;S;S;ORF3a 46;30;148;164 58;35;153;169 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. In addition to these mutations, A570D (RBD), Delta144/145 (S1 subunit), T716I, S982A and D1118H (S2 subunit) are also reported in VUI202012/01. 2021 Epidemiology and infection Introduction SARS_CoV_2 A570D;D1118H;S982A;T716I 32;89;79;72 37;95;84;77 RBD 39 42 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. In addition to this co-mutation, a novel non-synonymous mutation NSP3:S1515F (4809C>T) was observed only in Indian strains early in March 2020. 2021 Epidemiology and infection Introduction SARS_CoV_2 C4809T;S1515F 78;70 85;76 Nsp3 65 69 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. In silico analysis predicted the docking site of anti-viral drugs within a hydrophobic cleft located near the 14408C>T mutation site. 2021 Epidemiology and infection Introduction SARS_CoV_2 C14408T 110 118 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. In silico analysis predicts V1176F variant could facilitate the interaction with ACE2 by stabilising spike protein trimeric complex. 2021 Epidemiology and infection Introduction SARS_CoV_2 V1176F 28 34 S 101 106 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Interestingly, 3037C>T, 14408C>T and 23403A>G co-mutations had the highest number of descendants world-wide indicating positive selection of this epidemiologically dominant SARS-CoV-2 variants. 2021 Epidemiology and infection Introduction SARS_CoV_2 C14408T;A23403G;C3037T 24;37;15 32;45;22 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Moreover, Q57H mutation co-occurred with either of W131C, L129F and D173Y second site mutations. 2021 Epidemiology and infection Introduction SARS_CoV_2 D173Y;L129F;Q57H;W131C 68;58;10;51 73;63;14;56 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Mutation in the catalytic domain of RdRp, D484Y resulted in remdesivir resistance, the first anti-viral drug used in the United States. 2021 Epidemiology and infection Introduction SARS_CoV_2 D484Y 42 47 RdRP 36 40 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. N501Y falls within the RBD and had been shown to enhance the binding affinity of S protein with human ACE2. 2021 Epidemiology and infection Introduction SARS_CoV_2 N501Y 0 5 RBD;S 23;81 26;82 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. NSP3:F106F (3037C>T) mutation co-evolved with RdRp:P323L, S:D614G, N:R203K, N:G204R and ORF3a:Q57H mutations and these strains with co-mutations were predominant in Russia, United States and Europe. 2021 Epidemiology and infection Introduction SARS_CoV_2 C3037T;D614G;F106F;G204R;P323L;Q57H;R203K 12;60;5;78;51;94;69 19;65;10;83;56;98;74 ORF3a;Nsp3;RdRP;N;N;S 88;0;46;67;76;58 93;4;50;68;77;59 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. P681H mutation lies near the furin cleavage site and might interfere with viral infectivity and transmission. 2021 Epidemiology and infection Introduction SARS_CoV_2 P681H 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. R203K, G204R, P13L, D128D, L139L, S188L, S202N, D103Y and I292T mutations are more frequently observed in N protein (Table 2). 2021 Epidemiology and infection Introduction SARS_CoV_2 D103Y;D128D;G204R;I292T;L139L;P13L;S188L;S202N;R203K 48;20;7;58;27;14;34;41;0 53;25;12;63;32;18;39;46;5 N 106 107 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. R408I mutation stabilising S protein was reported in an Indian strain. 2021 Epidemiology and infection Introduction SARS_CoV_2 R408I 0 5 S 27 28 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Several mutations including A475V, N439K, L452R, F490L, V483A and Y508H in S protein resulted in decreased sensitivity to mAb. 2021 Epidemiology and infection Introduction SARS_CoV_2 A475V;F490L;L452R;N439K;V483A;Y508H 28;49;42;35;56;66 33;54;47;40;61;71 S 75 76 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Since 3037C>T mutation is silent and does not have major impact on NSP3 protein per se, it may change codon usage and thereby might affect the translation efficiency of NSP3. 2021 Epidemiology and infection Introduction SARS_CoV_2 C3037T 6 13 Nsp3;Nsp3 67;169 71;173 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Structural analysis revealed D614G mutation favours open conformation of S protein which facilitates binding with the host receptor thereby enhances its infectivity. 2021 Epidemiology and infection Introduction SARS_CoV_2 D614G 29 34 S 73 74 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. The 14408C>T (P323L) mutation was found to be associated with increasing point mutations in viral isolates in Europe during the early phase of COVID-19 outbreak. 2021 Epidemiology and infection Introduction SARS_CoV_2 C14408T;P323L 4;14 12;19 COVID-19 143 151 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. The clade G, S and V comprise variants of S:D614G (23403A>G), ORF8:L84S (8782C>T) and ORF3a:G251V (26144G>T), respectively (Table 2). 2021 Epidemiology and infection Introduction SARS_CoV_2 A23403G;G26144T;C8782T;D614G;G251V;L84S 51;99;73;44;92;67 59;107;80;49;97;71 ORF3a;ORF8;S;S 86;62;13;42 91;66;14;43 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. The co-mutations D614G + V341I, D614G + K458R and D614G + I472V fall within the RBD of S protein and enhance the infectivity of virus by favouring binding with the host receptor. 2021 Epidemiology and infection Introduction SARS_CoV_2 D614G;D614G;D614G;I472V;K458R;V341I 17;32;50;58;40;25 22;37;55;63;45;30 RBD;S 80;87 83;88 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Two new variants, V1176F and S4777N are also associated with higher mortality and found to spread rapidly across the world. 2021 Epidemiology and infection Introduction SARS_CoV_2 S4777N;V1176F 29;18 35;24 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. V1176F arose independently and also co-occurred with D614G. 2021 Epidemiology and infection Introduction SARS_CoV_2 D614G;V1176F 53;0 58;6 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. VUI202012/01 had eight mutations in S protein of which N501Y, P681H, Delta69 and Delta70 have potential implications on viral infectivity. 2021 Epidemiology and infection Introduction SARS_CoV_2 N501Y;P681H 55;62 60;67 S 36 37 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. A variant SARS-CoV-2 containing a D614G substitution in the S1 subunit and three other associated mutations first reported in Europe has become the dominant strain globally. 2021 Emerging microbes & infections Introduction SARS_CoV_2 D614G 34 39 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. However, it remains unclear whether these population-level trends are due to higher transmissibility of the virus or simply due to founder effects owing to strong bottlenecks when SARS-CoV-2 spread globally, as the D614G variant was introduced early on in the European COVID-19 epidemic and spread from Europe to the rest of the world. 2021 Science translational medicine Introduction SARS_CoV_2 D614G 215 220 COVID-19 269 277 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. Last, we investigated whether the D614G amino acid substitution led to more severe disease in patients infected with SARS-CoV-2. 2021 Science translational medicine Introduction SARS_CoV_2 D614G 34 39 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. A search in such a resource showed a variable occurrence of mutations at different positions of the HR1 fusion core, with mutant D936Y being the most frequent, with 1296 occurrences, particularly in some European countries, especially Finland and Sweden. 2021 Molecules (Basel, Switzerland) Introduction SARS_CoV_2 D936Y 129 134 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. Therefore, we performed a comparative study of the wild-type S protein and the D936Y mutant, both in their pre-fusion and post-fusion conformations by molecular dynamics (MD). 2021 Molecules (Basel, Switzerland) Introduction SARS_CoV_2 D936Y 79 84 S 61 62 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. We also investigated the structural basis, both in the pre-fusion and post-fusion conformation as well as sequencing dates and geographical distribution of the other two most frequent HR1 mutations, S939F and S929T, with 1108 and 467 occurrences, respectively. 2021 Molecules (Basel, Switzerland) Introduction SARS_CoV_2 S929T;S939F 209;199 214;204 33948590 A broadly neutralizing antibody protects against SARS-CoV, pre-emergent bat CoVs, and SARS-CoV-2 variants in mice. Here, we demonstrate, using both pseudoviruses and live virus assays, that DH1047 neutralizes SARS-CoV, SARS-like bat viruses RsSHC014 and WIV-1, and SARS-CoV-2 D614G, B.1.1.7, B.1.429, B.1.351 variants. 2021 bioRxiv Introduction SARS_CoV_2 D614G 161 166 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. 11 Virtually all variants of concern contain mutations in the SARS-CoV-2 Spike protein, such as variant B.1.351 (Spike mutations K417N, E484K, N501Y, D614G, and A701V) and variants B.1.427/B.1.429 (Spike mutations S13I, W152C, L452R, and D614G), and many of these reside on the receptor-binding domain (RBD), a region located between residues 350-550 of Spike and directly binding to the human ACE2. 2021 Journal of medical virology Introduction SARS_CoV_2 A701V;D614G;D614G;E484K;K417N;L452R;N501Y;S13I;W152C 162;151;239;137;130;228;144;215;221 167;156;244;142;135;233;149;219;226 S;S;S;S;RBD 74;114;199;355;304 79;119;204;360;307 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. 8 , 14 , 15 , 16 A recently published clinical study 17 has shown also a decreased vaccine efficacy against the lineage B.1.351 (carrying Spike mutations E484K and N501Y), testifying the need to track and monitor all SARS-CoV-2 mutations, with a particular accent on those affecting the Spike RBD. 2021 Journal of medical virology Introduction SARS_CoV_2 E484K;N501Y 159;169 164;174 S;S;RBD 143;292;298 148;297;301 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. Another mutation in the Spike protein, D614G, was prevalent in early 2020 and is currently present in more than 90% of all circulating SARS-CoV-2s; this mutation is not located in the interaction domain with ACE2, but it has been associated with increased entry efficiency into human host cells. 2021 Journal of medical virology Introduction SARS_CoV_2 D614G 40 45 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. In this short communication, we will show a report on a novel SARS-CoV-2 Spike mutation, T478K, which is also located at the interface of the Spike/ACE2 interaction, and it is worryingly rising in prevalence among SARS-CoV-2 sequences collected since the beginning of 2021. 2021 Journal of medical virology Introduction SARS_CoV_2 T478K 89 94 S;S 73;142 78;147 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. N501Y is only one of the 9 Spike mutations of variant B.1.1.7, also characterized by mutations in polyprotein open reading frame (ORF1a), proteins ORF8, and nucleocapsid (N). 2021 Journal of medical virology Introduction SARS_CoV_2 N501Y 0 5 N;ORF1a;S;ORF8;N 157;130;27;147;171 169;135;32;151;172 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. One of these is the variant B.1.1.7, 5 characterized by 18 mutations over the reference genomic sequence (NCBI entry NC_045512.2, most notably a mutation A23063T, causing an aminoacidic change N501Y in the viral Spike protein interaction domain with human receptor angiotensin-converting enzyme 2 (ACE2). 2021 Journal of medical virology Introduction SARS_CoV_2 A23063T;N501Y 155;194 162;199 S 213 218 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. One mutation that has attracted interest is D614G. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 44 49 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. One such mutation - S247R - was documented in the first patient diagnosed with COVID-19 in Australia (GenBank: QHR84449.1). 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 S247R 20 25 COVID-19 79 87 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. We propose longer GAG molecules are able to bridge the gap between the PRRARS furin cleavage site and the 245H-246R site with the S247R mutation improving this binding. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 S247R 130 135 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. We then studied, in the presence of glycosylation, the interaction of HS and HP molecules with the S247R mutant protein, a variant of the S protein that first emerged in Melbourne, Australia (GenBank: QHR84449.1). 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 S247R 99 104 S 138 139 33968806 SARS CoV-2 Nucleoprotein Enhances the Infectivity of Lentiviral Spike Particles. Our observations implicated the N protein as an enhancer of viral infectivity for both the wild-type as well as the highly infectious D614G mutant of the spike glycoprotein. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G 134 139 S;N 154;32 172;33 33975021 A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern. Specific mutations, such as the N501Y and the E484K, in the receptor binding domain (RBD) of the Spike protein are recurrent across VOCs. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K;N501Y 46;32 51;37 RBD;S;RBD 60;97;85 83;102;88 33975021 A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern. The K417, E484 and N501Y mutations were identified in the samples assigned to P.1 with WGS and the E484K (in absence of the others) in the samples assigned to P.2 with WGS (Table 1). 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K;N501Y 99;19 104;24 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? The SARS-CoV-2 B.1.351 variant in South Africa has eight mutations involving the S protein (L18F, D80A, D215G, R246I, K417N, E484K, N501Y, and A701V). 2021 Journal of Korean medical science Introduction SARS_CoV_2 A701V;D215G;D80A;E484K;K417N;N501Y;R246I;L18F 143;104;98;125;118;132;111;92 148;109;102;130;123;137;116;96 S 81 82 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? The SARS-CoV-2 P.1 variant in Brazil harbors three S protein mutations E484K, K417N and N501Y in common with 20J/501Y.V2 (lineage B.1.351). 2021 Journal of Korean medical science Introduction SARS_CoV_2 E484K;K417N;N501Y 71;78;88 76;83;93 S 51 52 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? The UK SARS-CoV-2 B.1.1.7 variant is defined by multiple spike (S) protein changes (deletion 69-70, deletion 145, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H). 2021 Journal of Korean medical science Introduction SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 121;156;128;114;135;149;142 126;162;133;119;140;154;147 S;S 57;64 62;65 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. All N501Y cases except one are members of B.1.1.7 lineage. 2021 Emerging microbes & infections Introduction SARS_CoV_2 N501Y 4 9 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. All six samples carrying dual mutations of E484K and N501Y were from March. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K;N501Y 43;53 48;58 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. Amplicon sequencing verified that this sample carries an E484Q (GAA > CAA) mutation. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484Q 57 62 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. Another key spike mutation, N501Y, present in all three VOCs is considered to enhance the binding between spike and the ACE2 receptor in human cells, thus contributing to increased transmissibility and possibly virulence as well. 2021 Emerging microbes & infections Introduction SARS_CoV_2 N501Y 28 33 S;S 12;106 17;111 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. As shown in Figure 1, E484 WT is featured for a Tm at 54.85 +- 0.19 C, ~ 5 C higher than the Tm of E484K (49.81 +- 0.07 C). 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K 99 104 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. Dramatic increases in both E484K and N501Y prevalence over time were observed (Figure S1). 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K;N501Y 27;37 32;42 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. E484K climbed up swiftly from none in December (n = 28) and 3.2% (3/95) in January to 12.0% (29/242) in February and 22.4% (133/595) in March. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K 0 5 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. Genomic analysis (Figure S3) showed that the majority of the E484K cases (n = 19) fell within the B.1.526 lineage, a recent clone emerged from New York, and the rest belong to clade 20C B.1 lineage (n = 2), and clade 20B under R.1 (n = 2) and B.1.1.309 lineage (n = 1), respectively. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K 61 66 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. In a blinded fashion, this test correctly genotyped RNA samples extracted from six different reference viral strains, including one WT (SARS-CoV-2 USA WA1/2020), two B.1.1.7 variants (SARS-CoV-2 hCoV-19/USA/CA_CDC_5574/2020 and SARS-CoV-2 hCoV-19/England/204820464/2020), and two B.1.351 variants (SARS-CoV-2 hCoV-19/South Africa/KRISP-EC-K005321/2020 and SARS-CoV-2 hCoV-19/South Africa/KRISP-K005325/2020) purchased from BEI resources, and one E484K variant isolate recently obtained from our network hospital. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K 446 451 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. In addition, we discovered a new genotype at the 501-probe binding site from 12 samples (12/971, 1.2%), which thereafter was confirmed to be a N501T (AAT > ACT) mutation in subsequent sequencing. 2021 Emerging microbes & infections Introduction SARS_CoV_2 N501T 143 148 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. Moreover, the new variant of interest discovered in New York (B.1.526) also carries the E484K mutation, and alarmingly, fast-spreading over the past two months. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K 88 93 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. Our data revealed dramatic increases in the frequencies of both E484K and N501Y over time, underscoring the need for continuous epidemiological monitoring. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K;N501Y 64;74 69;79 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. Previously, E484K was only harboured by B.1.351 and P1 variants. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K 12 17 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. Similarly, the signature Tm for N501 WT was 59.97 +- 0.09 C, higher than 54.78 +- 0.12 C for N501Y. 2021 Emerging microbes & infections Introduction SARS_CoV_2 N501Y 93 98 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. Studies have shown that currently observed resistance to neutralizing antibodies is largely associated with the E484K mutation. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K 112 117 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. The assay can reliably identify as low as 200 copies of 484WT, 200 copies of E484K, 20 copies of 501WT, and 200 copies of N501Y per reaction, respectively. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K;N501Y 77;122 82;127 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. The melting profile of N501T is markedly different from that of WT and N501Y, with a signature Tm of 56.41 +- 0.15 C. 2021 Emerging microbes & infections Introduction SARS_CoV_2 N501T;N501Y 23;71 28;76 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. The most recent report found that the E484K has been successfully incorporated into some isolates of the B.1.1.7 variant. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K 38 43 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. The N501Y followed the same trend with even higher speed, rising sharply from < 4% in December and January to 11.2% (28/251) in February and 44.9% (267/595) in March. 2021 Emerging microbes & infections Introduction SARS_CoV_2 N501Y 4 9 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. The proportion of E484K was 17.2% (165/960), and it was 30.6% (297/971) for N501Y. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K;N501Y 18;76 23;81 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. There were six samples carrying both E484K and N501Y, and the remaining samples flagged as mutants only carry one of the two signature mutations. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K;N501Y 37;47 42;52 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. This has been well exemplified by our discovery of the N501T and E484Q mutations from the clinical specimens. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484Q;N501T 65;55 70;60 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. We also happened to capture one sample eliciting a distinct 484 Tm at 48.88 C ~ 1 C lower than E484K and ~6 C lower than 484WT. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K 95 100 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. While E484K occurrence in each hospital was very similar, N501Y varied between hospitals in a wide range from 20.2% to 47.1% yet lack of obvious concentration in a certain geographic area. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K;N501Y 6;58 11;63 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. While our screening efforts were continuing with newly collected March samples, we performed whole-genome sequencing (WGS) with a panel of 74 samples from earlier months representing different genotypes flagged by this screening tool, including 24 E484K, 25 N501Y, 5 N501T, and 20 WT at 484 and 501 loci. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K;N501T;N501Y 248;267;258 253;272;263 33983915 Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant - New York City, New York, January 1-April 5, 2021. Among 3,679 (38%) B.1.526 variant viruses identified, 2,050 (56%) carried the E484K mutation. 2021 MMWR. Morbidity and mortality weekly report Introduction SARS_CoV_2 E484K 78 83 33983915 Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant - New York City, New York, January 1-April 5, 2021. Among 32 fully vaccinated persons with sequenced viruses, eight (25%) were identified who were infected with the B.1.526 variant carrying the E484K mutation, three (9%) with the B.1.526 variant without the E484K mutation, seven (22%) with the B.1.1.7 variant, and 14 (44%) with non-VOI/VOC infections. 2021 MMWR. Morbidity and mortality weekly report Introduction SARS_CoV_2 E484K;E484K 142;206 147;211 33983915 Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant - New York City, New York, January 1-April 5, 2021. Among persons infected with the B.1.526 variant carrying the E484K mutation, previous seropositivity was slightly more common (1.3%) than that among persons infected with the B.1.526 variant without the E484K mutation (0.7%), with the B.1.1.7 variant (0.7%), and with other non-VOI/VOC infections (0.9%); however, the difference was not significant (p = 0.23). 2021 MMWR. Morbidity and mortality weekly report Introduction SARS_CoV_2 E484K;E484K 61;203 66;208 33983915 Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant - New York City, New York, January 1-April 5, 2021. No difference in rates of possible reinfection was found between persons infected with B.1.1.7 variants and those infected with B.1.526 variants with or without the E484K mutation (Supplementary Figure, https://stacks.cdc.gov/view/cdc/105634). 2021 MMWR. Morbidity and mortality weekly report Introduction SARS_CoV_2 E484K 165 170 33983915 Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant - New York City, New York, January 1-April 5, 2021. The proportion of B.1.526 variants with the E484K mutation increased more quickly and as of April 5 represented 25% of all sequenced SARS-CoV-2 viruses, compared with 16% of B.1.526 variants without the E484K mutation. 2021 MMWR. Morbidity and mortality weekly report Introduction SARS_CoV_2 E484K;E484K 44;203 49;208 33983915 Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant - New York City, New York, January 1-April 5, 2021. Two predominant subclades within the B.1.526 lineage have been identified, one containing the E484K mutation in the receptor-binding domain, which attenuates in vitro neutralization by multiple SARS-CoV-2 antibodies and is present in variants of concern (VOCs) first identified in South Africa (B.1.351) and Brazil (P.1).* The NYC Department of Health and Mental Hygiene (DOHMH) analyzed laboratory and epidemiologic data to characterize cases of B.1.526 infection, including illness severity, transmission to close contacts, rates of possible reinfection, and laboratory-diagnosed breakthrough infections among vaccinated persons. 2021 MMWR. Morbidity and mortality weekly report Introduction SARS_CoV_2 E484K 94 99 33991677 Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage. These variants include the Marseille-4 variant (Nexstrain clade 20A.EU1), which has been the most prevalent one between August 2020 and January 2021, and the rapidly-spreading variants 20I/501Y.V1, 20H/501Y.V2, and 20J/501Y.V3, which harbor in their spike the amino acid (aa) substitution N501Y. 2021 Clinical microbiology and infection Introduction SARS_CoV_2 N501Y 289 294 S 250 255 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. In addition, we provide structural/energetic analysis of the current fast-spreading L452R/E484Q variant in India and show that its spread is likely due to the variant's strong antibody escape mutations. 2021 Journal of molecular biology Introduction SARS_CoV_2 L452R;E484Q 84;90 89;95 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Interestingly, enhanced adaptation to hACE2 can be engineered by simultaneous Y442F and L472F mutations. 2021 Journal of molecular biology Introduction SARS_CoV_2 L472F;Y442F 88;78 93;83 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Significantly, we show that computed binding affinities for recent fast-spreading variants have high affinities (in decreasing order of affinity, S477N/E484K, E484K/N501Y, K417T/E484K/N501Y) and are resistant to neutralizing antibodies or overlap with their binding sites, consistent with their rapid spread and emergence of combinatorial mutations. 2021 Journal of molecular biology Introduction SARS_CoV_2 E484K;K417T;S477N;E484K;E484K;N501Y;N501Y 159;172;146;152;178;165;184 164;177;151;157;183;170;189 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Specifically, the recurring S mutations E484K, N501Y, D614G and their combinations have been implicated in increased viral transmission. 2021 Journal of molecular biology Introduction SARS_CoV_2 D614G;E484K;N501Y 54;40;47 59;45;52 S 28 29 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Structural modeling suggests that D614G promotes an open conformational state, making the S-protein available for receptor binding. 2021 Journal of molecular biology Introduction SARS_CoV_2 D614G 34 39 S 90 91 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The widespread S protein mutation, D614G, has also been found to increase viral infectivity in cell culture. 2021 Journal of molecular biology Introduction SARS_CoV_2 D614G 35 40 S 15 16 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. We found that 31 high-affinity S mutations, including N440K, S443A, G476S, E484R, G502P, are clustered in the vicinities of two known interaction hotspots of hACE2. 2021 Journal of molecular biology Introduction SARS_CoV_2 E484R;G476S;G502P;N440K;S443A 75;68;82;54;61 80;73;87;59;66 S 31 32 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. More importantly, we found for the first time that the Q493K and Q498H mutations in the RBD of WBP-1 enhanced its interactive affinities with mACE2, suggesting that WBP-1 is capable of using mACE2 to gain access to the host cells. 2021 EBioMedicine Introduction SARS_CoV_2 Q493K;Q498H 55;65 60;70 RBD 88 91 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. We characterized the dynamics of the adaptive mutations in SARS-CoV-2 and demonstrated that Q493K and Q498H in RBD significantly increased its binding affinity towards mouse ACE2. 2021 EBioMedicine Introduction SARS_CoV_2 Q493K;Q498H 92;102 97;107 RBD 111 114 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. The N15A and V25F mutations of the SARS-CoV-2 E protein have very different effects on the NMR spectra of the protein; the N15A mutation causes greater chemical shift perturbations over a larger region of the protein than the V25F mutation, which causes only minor changes near the site of the amino acid substitution. 2021 PLoS pathogens Introduction SARS_CoV_2 N15A;N15A;V25F;V25F 4;123;13;226 8;127;17;230 E 46 47 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. These mutations affect production of virus-like particle (VLP) and, in the case of N15A, the binding of HMA. 2021 PLoS pathogens Introduction SARS_CoV_2 N15A 83 87 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. In May 2020, an intensively validated topology-based neural network tree (TopNetTree) model was employed to predict certain RBD mutations, including E484K, L452R, and K417N, would strengthen SARS-CoV-2 infectivity. 2021 Genomics Introduction SARS_CoV_2 E484K;K417N;L452R 149;167;156 154;172;161 RBD 124 127 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Specifically, all three variants involve RBD mutation N501Y, whereas the South Africa and Brazil(ian) variants also contain RBD mutations E484K and K417N. 2021 Genomics Introduction SARS_CoV_2 E484K;K417N;N501Y 138;148;54 143;153;59 RBD;RBD 41;124 44;127 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. We show that in addition to mutations N501Y, E484K, and K417N in the UK, South Africa, and Brazil(ian) variants, L452R, E484Q in the India variants, N439K, S477N, S477R, and N501T are also fast-growing mutations in 31 pandemic-devastated countries in the past few months. 2021 Genomics Introduction SARS_CoV_2 E484K;E484Q;K417N;L452R;N439K;N501T;N501Y;S477N;S477R 45;120;56;113;149;174;38;156;163 50;125;61;118;154;179;43;161;168 34013280 Impact of BNT162b first vaccination on the immune transcriptome of elderly patients infected with the B.1.351 SARS-CoV-2 variant. The receptor-binding domain (RBD) mutation E484K provides tighter ACE2 binding and widespread escape from monoclonal antibody neutralization, a concern for a limited protection by some vaccines, and recent data from Qatar demonstrate a BNT162b vaccine effectiveness of 75% with the B.1.351 variant. 2021 medRxiv Introduction SARS_CoV_2 E484K 43 48 RBD 29 32 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. Strains of SARS-CoV-2 have been collected from multiple countries, and mutants have been detected and classified into nine types according to mutation positions on RBDs, including V341I, F342L, N354D/D364Y, V367F, R408I, A435S, W436R, G476S and V483A. 2021 Briefings in bioinformatics Introduction SARS_CoV_2 A435S;F342L;G476S;N354D;R408I;V341I;V367F;V483A;W436R;D364Y 221;187;235;194;214;180;207;245;228;200 226;192;240;199;219;185;212;250;233;205 RBD 164 168 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. To thoroughly study the only dual amino acids mutant, N354D/D364Y, single mutation models of N354D and D364Y were also built for the subsequent studies, including molecular dynamics (MD) simulations of the protein complexes, end-point molecular mechanics-Poisson Boltzmann surface area-weighted solvent accessible surface area (MM-PBSA-WSAS) binding free energy calculations, and end-point molecular mechanics generalized Born surface area (MM-GBSA) binding free energy decomposition analysis (see the Method section). 2021 Briefings in bioinformatics Introduction SARS_CoV_2 D364Y;N354D;N354D;D364Y 103;54;93;60 108;59;98;65 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. Early in the pandemic, the D614G mutation of S arose and is now found in nearly every sequence worldwide, likely due to epidemiological factors and a transmission advantage. 2021 Clinical microbiology and infection Introduction SARS_CoV_2 D614G 27 32 S 45 46 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. Search terms used in various combinations were as follows: "SARS-CoV-2", "variants", "variants of concern", "VOC", "variants of interest", "VOI", "mutations", "evolution", "B.1.1.7", "B.1.351", "P.1", "B.1.148", "B.1.1.28", "N501Y", "E484K", and "L452R". 2021 Clinical microbiology and infection Introduction SARS_CoV_2 E484K;L452R;N501Y 234;247;225 239;252;230 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. Furthermore, the E484K mutation was associated with immune evasion from neutralizing antibodies produced in response to currently available vaccines. 2021 BMC genomics Introduction SARS_CoV_2 E484K 17 22 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. The genetic diversity of SARS-CoV-2 has been extensively studied, evidencing the presence of recurrent mutations such as S: D614G, S:E484K, S:N501Y across the world, related to increased pathogenicity and transmissibility (higher viral loads, increased replication on lung epithelial cells, and enhanced binding affinity). 2021 BMC genomics Introduction SARS_CoV_2 D614G;E484K;N501Y 124;133;142 129;138;147 S;S;S 121;131;140 122;132;141 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. 3A) and thereby diminish binding and neutralization of IGHV1-2 antibodies against E484K. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K 82 87 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. 3B) that explains why CV05-163 binding and neutralization were diminished with E484K. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K 79 84 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Among 585,054 SARS-CoV-2 genome sequences in the GISAID database (March 5, 2021), about 95% of K417N/T mutations occur with N501Y, despite N501Y being present in only 21% of all analyzed sequences. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 K417N;K417T;N501Y;N501Y 95;95;124;139 102;102;129;144 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Binding and neutralization of four and five antibodies out of the 17 tested were abolished by K417N and E484K, respectively. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K;K417N 104;94 109;99 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Certain IGHV genes are highly enriched in the antibody response to SARS-CoV-2 infection, with IGHV3-53 and IGHV3-66, which differ by only one conservative substitution (V12I), and IGHV1-2 being the most enriched IGHV genes used among 1,593 RBD-targeting antibodies from 32 studies . 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 V12I 169 173 RBD 240 243 COVID-19 67 87 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Consistently, K417N/T mutations are associated with N501Y in naturally circulating SARS-CoV-2. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 K417N;K417T;N501Y 14;14;52 21;21;57 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. E484K has also been detected in a few B.1.1.7 genomes. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K 0 5 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. E484K slightly reduced binding (11.3 nM). 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K 0 5 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Here, we quantified binding of K417N, E484K, N501Y, and double and triple combinations in the RBD to ACE2 by biolayer interferometry. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K;K417N;N501Y 38;31;45 43;36;50 RBD 94 97 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Importantly, N501Y could rescue binding of K417N (9.0 nM), and the triple mutant K417N/E484K/N501Y (as in B.1.351) had similar binding (6.5 nM) to wild type. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 K417N;K417N;N501Y;E484K;N501Y 43;81;13;87;93 48;86;18;92;98 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. In addition, binding and neutralization of IGHV1-2 antibodies was severely reduced for the E484K mutation. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K 91 96 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. In addition, neutralization by REGN10933, a potent antibody used for therapeutic treatment, was reduced to a less extent by K417N and E484K. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K;K417N 134;124 139;129 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. In contrast, only 36% of E484K mutations occur with N501Y. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K;N501Y 25;52 30;57 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. In the receptor-binding site (RBS) of the spike (S) protein receptor-binding domain (RBD), the B.1.1.7 lineage has acquired an N501Y mutation, B.1.351 and P.1 lineages share this mutation along with K417N/T and E484K, whereas the California variants have an L452R mutation that is also present in the Indian variant B.1.617 with E484Q. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K;E484Q;K417N;K417T;L452R;N501Y 211;329;199;199;258;127 216;334;206;206;263;132 S;RBD;S 42;85;49 47;88;50 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Indeed, binding and neutralization by CV07-270 was abrogated by E484K. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K 64 69 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Interestingly, unlike most IGHV3-53 antibodies that are sensitive to K417N/T or E484K, a recently discovered IGHV3-53-encoded mAb-222, which binds RBS retains activity against P.1 and B.1.351. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K;K417N;K417T 80;69;69 85;76;76 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Intra-host antigenic drift has also been observed in an immunosuppressed COVID-19 patient who had low titers of neutralizing antibodies that allowed emergence of N501Y and E484K mutations. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K;N501Y 172;162 177;167 COVID-19 73 81 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. K417N and E484K in VOCs B.1.351 and P.1 have been reported to decrease the neutralizing activity of sera as well as neutralizing monoclonal antibodies isolated from COVID-19 convalescent plasma and vaccinated individuals. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K;K417N 10;0 15;5 COVID-19 165 173 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. K417N/T would diminish such interactions and, therefore, affect antibody binding and neutralization, providing a structural explanation for K417N escape in IGHV3-53/3-66 antibodies with binding mode 1. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 K417N;K417N;K417T 140;0;0 145;7;7 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. mainly through an arginine in CDRH3, suggesting that E484K may adversely impact RBS-C antibodies. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K 53 58 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. N501Y indeed increased RBD binding to ACE2 compared to wild-type RBD (KD 3.3 nM vs 7.0 nM), whereas K417N substantially reduced ACE2 binding (41.6 nM). 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 K417N;N501Y 100;0 105;5 RBD;RBD 23;65 26;68 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. N501Y was previously reported to enhance binding to human receptor ACE2. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 N501Y 0 5 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Overall, our results demonstrate that RBS mutations K417N and E484K can either abolish or extensively reduce the binding and neutralization of several major classes of SARS-CoV-2 RBD antibodies. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K;K417N 62;52 67;57 RBD 179 182 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. S4) are abolished by E484K, but not K417N. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K;K417N 21;36 26;41 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Strikingly, binding and neutralization by all six highly potent IGHV3-53 antibodies that we tested were abrogated by either K417N (RBS-A/class 1) or E484K (RBS-B/class 2). 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K;K417N 149;124 154;129 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. The mAb-222 light chain could largely restore the neutralization potency of other IGHV3-53 antibodies, suggesting that light-chain interactions can compensate for loss of binding of K417N/T by the heavy chain. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 K417N;K417T 182;182 189;189 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Thus, IGHV1-2 antibodies, akin to IGHV3-53/66, can engage the RBD in two different binding modes, both of which are susceptible to escape by E484K, but not by K417N. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K;K417N 141;159 146;164 RBD 62 65 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. To test the effect of the K417N and E484K mutations on nAbs that target the S309 and CR3022 sites, we assessed binding and neutralization by CV38-142 and COVA1-16 to SARS-CoV-2. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K;K417N 36;26 41;31 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. We tested the activity of a panel of nAbs against wild-type (Wuhan strain) SARS-CoV-2 pseudovirus and single mutants K417N and E484K. 2021 Science (New York, N.Y.) Introduction SARS_CoV_2 E484K;K417N 127;117 132;122 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. 501Y.V1 is associated with a set of mutations in its spike (S) protein, including DeltaH69/V70 and DeltaY144 in N-terminal domain (NTD), N501Y in receptor-binding domain (RBD), and P681H near the furin cleavage site. 2021 Cell research Introduction SARS_CoV_2 N501Y;P681H 137;181 142;186 S;RBD;N;S 53;171;112;60 58;174;113;61 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. 501Y.V2 is associated with multiple S mutations, which could be divided into two main subsets, one is clustered in NTD (L18F, D80A, D215G, 242-244Delta, and R246I), and the other is clustered in RBD (K417N, E484K, and N501Y). 2021 Cell research Introduction SARS_CoV_2 D215G;D80A;E484K;N501Y;R246I;K417N;L18F 132;126;207;218;157;200;120 137;130;212;223;162;205;124 RBD;S 195;36 198;37 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. 501Y.V3 shares multiple common mutations in the RBD region with 501Y.V2, including N501Y, E484K, and K417N, but lacks 242-244Delta and R246I in the NTD. 2021 Cell research Introduction SARS_CoV_2 E484K;K417N;N501Y;R246I 90;101;83;135 95;106;88;140 RBD 48 51 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. Another common mutation is N439K, which is located in the receptor binding domain and enhances affinity for the hACE2 receptor by creating a new salt-bridge across the binding interface. 2021 Journal of molecular biology Introduction SARS_CoV_2 N439K 27 32 RBD 58 81 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. B.1.1.7 contains a change from asparagine to tyrosine at position 501 (N501Y) in the receptor binding motif of the receptor binding domain (RBD) (Figure 1 (C)). 2021 Journal of molecular biology Introduction SARS_CoV_2 N501Y;N501Y 31;71 69;76 RBD;RBD 115;140 138;143 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. Furthermore, N501Y was identified as adaptive mutation during serial passaging of a clinical SARS-CoV-2 isolate in mice. 2021 Journal of molecular biology Introduction SARS_CoV_2 N501Y 13 18 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. One such mutation is D614G, which confers increased infectivity and transmissibility and has rapidly become the dominant global variant. 2021 Journal of molecular biology Introduction SARS_CoV_2 D614G 21 26 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. P.2 contains only the E484K change in its receptor binding domain. 2021 Journal of molecular biology Introduction SARS_CoV_2 E484K 22 27 RBD 42 65 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. SARS-CoV-2 N439K retains fitness and causes infections with similar clinical outcome, but also shows immune evasion. 2021 Journal of molecular biology Introduction SARS_CoV_2 N439K 11 16 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. The N501Y mutation is accompanied by two additional changes at the receptor binding interface in two of the other strains (Figure 1(C)); glutamate to lysine at position 484 (E484K) and lysine to asparagine or threonine at position 417 (K417N in B.1.351; K417T in P.1). 2021 Journal of molecular biology Introduction SARS_CoV_2 E484K;K417T;N501Y;E484K;K417N 137;254;4;174;236 172;259;9;179;241 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. (a) N501Y mutation, at the 501st amino-acid position of the spike protein, the amino acid asparagine is replaced by the amino acid tyrosine, is located within the RBD and can increase ACE2 receptor affinity. 2021 Frontiers in medicine Introduction SARS_CoV_2 N501Y 4 9 S;RBD 60;163 65;166 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. (b) P681H mutation located within the RBD and has biological significance. 2021 Frontiers in medicine Introduction SARS_CoV_2 P681H 4 9 RBD 38 41 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. A key question about D614G mutation is whether a single amino acid mutation could change viral fitness and transmissibility. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 21 26 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. A recent study on a sample of 25,000 whole genome sequences from the UK could not demonstrate the effect of D614G mutation on transmission. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 108 113 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. Additionally, the D614G mutation has been demonstrated to stabilize the interaction between the S1 and S2 domains and limit S1 shedding, resulting in increased overall infectivity. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 18 23 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. Additionally, the South African variant carries E484K and K417N mutations that can reduce the binding of antibodies to the virus. 2021 Frontiers in medicine Introduction SARS_CoV_2 E484K;K417N 48;58 53;63 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. Although clinical and in vitro data showed that the D614G mutation changes the virus phenotype, the impact of the mutation on viral fitness, transmission and clinical outcomes is still unclear. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 52 57 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. analyzed a data set including more than 46,700 SARS-CoV-2 assemblies sampled from 99 countries and found that the D614G mutation does not associated with significantly increased viral transmission. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 114 119 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. Both the B.1.351 variant and the B.1.1.28 variant have N501Y, E484K, and K417N mutations in the spike protein. 2021 Frontiers in medicine Introduction SARS_CoV_2 E484K;K417N;N501Y 62;73;55 67;78;60 S 96 101 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. Both the South African variant and the Brazilian variant have the N501Y mutation. 2021 Frontiers in medicine Introduction SARS_CoV_2 N501Y 66 71 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. Clinical and in vitro experiments suggest that the D614G mutation changes the virus phenotype and may have an impact on transmission and disease severity. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 51 56 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. Current findings suggested that D614G mutation does not have an impact on the neutralizing antibodies generated against the SARS-CoV-2. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 32 37 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. D480A/G variant has been shown to escape neutralizing antibody and immune pressure. 2021 Frontiers in medicine Introduction SARS_CoV_2 D480A;D480G 0;0 7;7 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. D614G mutation was first detected in viruses collected from China and Germany in late January. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 0 5 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. discovered spike protein D614G mutation in the SARS-CoV-2 genome and demonstrated that the G614 variant has become dominant genotype around the world. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 25 30 S 11 16 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. E484K and K417N mutation can reduce the binding of antibodies to the virus. 2021 Frontiers in medicine Introduction SARS_CoV_2 K417N;E484K 10;0 15;5 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. found the spike protein D614G mutation to be associated with higher levels of viral nucleic acid in the upper respiratory tract in COVID-19 patients and demonstrated that the G614 variant has become dominant genotype around the world. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 24 29 S 10 15 COVID-19 131 139 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. In RBD of the spike protein, D480A/G mutation has emerged in patients with SARS-CoV infection and has become the dominant variant among 2003/2004 viruses. 2021 Frontiers in medicine Introduction SARS_CoV_2 D480A;D480G 29;29 36;36 S;RBD 14;3 19;6 COVID-19 75 93 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. In some studies, N501Y mutation has been found to be associated with a higher viral load and faster spread, which may be concerning to higher transmissibility. 2021 Frontiers in medicine Introduction SARS_CoV_2 N501Y 17 22 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. investigated whether D614G mutation has an impact on replication fitness and clinical status of COVID-19 patients in Washington State. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 21 26 COVID-19 96 104 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. Like the South African variant, the Brazilian variant also has N501Y, E484K, and K417N mutations. 2021 Frontiers in medicine Introduction SARS_CoV_2 E484K;K417N;N501Y 70;81;63 75;86;68 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. N501Y mutation has been found to be associated with increased infectivity and virulence in mouse models. 2021 Frontiers in medicine Introduction SARS_CoV_2 N501Y 0 5 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. N501Y mutation have been independently reported in South Africa and Australia. 2021 Frontiers in medicine Introduction SARS_CoV_2 N501Y 0 5 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. N501Y mutation is altering an amino acid within six key residues in the RBD. 2021 Frontiers in medicine Introduction SARS_CoV_2 N501Y 0 5 RBD 72 75 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. One of the key findings of the study was that the D614G mutation has been shown to be to have a greater number of the interaction between the S1 and S2 domains and limit S1 shedding, resulting in better overall infectivity. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 50 55 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. Previous studies showed that D614G mutation is located in the external spike protein of SARS-CoV-2 that has strong immunogenicity therefore the mutation may contribute the virus to evade vaccine:induced immunity. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 29 34 S 71 76 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. proposed that the D614G mutation don't have a major impact on the efficacy of vaccines currently in the pipeline. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 18 23 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. Pseudoviruses do not carry the other three mutations that are almost always with the D614G mutation. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 85 90 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. Recently, researchers have identified novel variants of SARS-CoV-2 genome, named B.1.1.7 variant, B.1.351 (N501Y.V2) variant and B.1.1.28 variant. 2021 Frontiers in medicine Introduction SARS_CoV_2 N501Y 107 112 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. suggest that age and comorbidity are more significant than D614G mutation in determining clinical outcomes of COVID-19 patients. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 59 64 COVID-19 110 118 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. suggested that the G614 genotype has not been detected in February and D614G mutation has been observed in 70% of all viral sequences in May. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 71 76 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. The B.1.1.7 variant-specific non-synonymous mutations and deletions have been detected in the spike protein including deletion 69-70, deletion 144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H. 2021 Frontiers in medicine Introduction SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 155;190;162;148;169;183;176 160;196;167;153;174;188;181 S 94 99 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. The B.1.351 (South African) variant has the N501Y mutation in the spike protein. 2021 Frontiers in medicine Introduction SARS_CoV_2 N501Y 44 49 S 66 71 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. The D614G mutation has been found to be always associated with three other mutations. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 4 9 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. The D614G mutation is transmitted as a part of a haplotype comprising four genetic mutations. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 4 9 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. The other groups investigating the effect of the G614 variant on the transmission capacity of the virus using different pseudovirus systems, also demonstrated that viruses carrying spike protein D614G mutation infected cells faster, 10 times, than D614 variant. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 195 200 S 181 186 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. The viruses with a D614G mutation were detected in Europe in the early phase of the pandemic and have rapidly spread worldwide, especially to European and North American countries. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 19 24 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. They considered that the G614 variant provides a transmission advantage to the virus and suggested that the D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 108 113 S 141 146 34026780 Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. They showed that D614G mutation emerged early during ongoing pandemic and viruses with G614 variant spread rapidly worldwide and over the course of 1 month the variant has become the globally dominant variant. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 17 22 34029937 Corilagin prevents SARS-CoV-2 infection by targeting RBD-ACE2 binding. For instance, more contagious variants of SARS-CoV-2 with point mutations such as D614G, N501Y and E484K were identified with the abilities to induce immune escape. 2021 Phytomedicine Introduction SARS_CoV_2 D614G;E484K;N501Y 82;99;89 87;104;94 34033650 SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. Currently, the D614G mutation has become the focus of several studies addressing prospective drug targeting strategies. 2021 PloS one Introduction SARS_CoV_2 D614G 15 20 34033650 SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. We were the first to report the major role of D614G (23403A>G) mutation located at the S1-S2 proximal junction. 2021 PloS one Introduction SARS_CoV_2 D614G;A23403G 46;53 51;61 34039497 An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose. Currently, D614G is the most prevalent circulating isotype of SARS-CoV-2 worldwide (more than 95%). 2021 Vaccine Introduction SARS_CoV_2 D614G 11 16 34039497 An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose. The D614G amino acid change, among these, in the spike protein of Wuhan reference strain is caused by an A-to-G nucleotide substitution at position 23,403 of the relevant nucleotide sequence. 2021 Vaccine Introduction SARS_CoV_2 D614G 4 9 S 49 54 34039497 An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose. To address this, we have incorporated D614G variant-targeted nucleic acid sequence, as well as few other immunogen-enhancing aspects in our mRNA design consideration. 2021 Vaccine Introduction SARS_CoV_2 D614G 38 43 34039497 An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose. To date, there is no published report about the D614G-relevant vaccine development. 2021 Vaccine Introduction SARS_CoV_2 D614G 48 53 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. 6 Many mutations have been found amongst SARS-CoV-2 strains circulating around the world, particularly the D614G which has been shown to increase infectivity. 2021 Journal of medical virology Introduction SARS_CoV_2 D614G 108 113 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. Finally, the third episode due to N501Y variants (N501YV) previously identified in the UK, South Africa and Brazil started in early 2021. 2021 Clinical microbiology and infection Introduction SARS_CoV_2 N501Y 34 39 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. Marseille-4 variant (M4V) likely originating from a mink farm in the North of France was observed soon after, and became prevalent across most of Europe. 2021 Clinical microbiology and infection Introduction SARS_CoV_2 M4V 21 24 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. The second episode was linked to Marseille-1 variant (M1V), which had an African origin and specific clinical and epidemiological profiles. 2021 Clinical microbiology and infection Introduction SARS_CoV_2 M1V 54 57 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. To date, most studies showed that the viral mutations, especially the D614G mutation in the spike protein, correlated with a higher infectivity than the wild-type virus. 2021 Clinical microbiology and infection Introduction SARS_CoV_2 D614G 70 75 S 92 97 34044153 SARS-CoV-2 N gene dropout and N gene Ct value shift as indicator for the presence of B.1.1.7 lineage in a commercial multiplex PCR assay. B.1.1.7 has also a specific single nucleotide polymorphism in the N gene (D3L) which can be targeted by PCR assays. 2021 Clinical microbiology and infection Introduction SARS_CoV_2 D3L 74 77 N 66 67 34044153 SARS-CoV-2 N gene dropout and N gene Ct value shift as indicator for the presence of B.1.1.7 lineage in a commercial multiplex PCR assay. For example, amino acid exchange N501Y in the SARS-CoV-2 spike protein (S) is present in all three mentioned lineages, whereas the additional deletion H69/V70 in the same protein is present in B.1.1.7, but not in the other two VOCs B.1.351 and P.1. 2021 Clinical microbiology and infection Introduction SARS_CoV_2 N501Y 33 38 S;S 57;72 62;73 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Due to its rapid spread, the independent origins and the potential implications in vaccination and passive immune therapies, E484K has received particular attention ever since. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K 125 130 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Due to the independent origin of two current known lineages harboring E484K in Brazil, we aimed to describe the mutation patterns of these lineages, investigate phylogenetic relationships and perform positive selection tests to identify if adaptive evolution has acted as a major evolutionary force leading to the increase of amino acid variability in the RBD sites. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K 70 75 RBD 356 359 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. In January 2021, the E484K mutation was identified in several viral genomes from Brazil. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K 21 26 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Moreover, B.1.1.7, B.1.351, and P.1 also harbor N501Y mutation, which is associated with enhanced receptor affinity and increased infectivity and virulence in a mouse model. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 N501Y 48 53 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. N501Y is one of the key contact residues interacting with hACE2 and P681H is one of four residues comprising the insertion that creates a furin-like cleavage site between S1 and S2, which is not found in closely-related coronaviruses. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 P681H;N501Y 68;0 73;5 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Structural analysis points to E484K as potentially the most crucial mutation so far in brazilian SARS-CoV-2 genomes. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K 30 35 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The presence of E484K and N501Y substitutions in the same SARS-CoV-2 genome may be particularly relevant for viral evolution. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K;N501Y 16;26 21;31 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The second lineage probably emerged in South Africa in August 2020 and harbors three mutations in RBD: K417N, E484K, and N501Y. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K;K417N;N501Y 110;103;121 115;108;126 RBD 98 101 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. This combination was shown to induce more conformational changes than the N501Y mutant alone, potentially altering antibodies' complementarity to this region resulting in the above mentioned immune escape phenomena. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 N501Y 74 79 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Two substitutions present in this lineage deserve special attention: N501Y in the Receptor Binding Domain (RBD) of S1 and P681H near the polybasic RRAR sequence in the furin-like cleavage region. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 N501Y;P681H 69;122 74;127 RBD;RBD 82;107 105;110 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. We speculate that the consequent neutralization escape due to E484K alone or as a part of a larger array of distinct mutations might act as a common evolutionary solution for several different viral lineages. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K 62 67 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Without previous introductions in other Latin American countries, which have been affected by their own specific mutations, such as the convergent evolution of the S:T1117I in Costa Rica the E484K mutation arose independently in Brazil and was identified in the Rio de Janeiro state (Southeast Brazil) in early-October carried by the P.2 lineage. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K;T1117I 191;166 196;172 S 164 165 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. Despite its incorporation in the ACE2 binding surface, the N501Y mutation showed a remarkable increase in binding of the ACE2-spike RBD complex to the host-cell surface Glucose Regulated Protein 78 (CS-GRP78). 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 N501Y 59 64 S;RBD 126;132 131;135 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. On the other hand, the E484K is located at the spike RBD's binding motif (C480-C488 region) that we previously reported to be recognized by cell-surface GRP78. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 E484K 23 28 S;RBD 47;53 52;56 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. Some potential mutations found in the new variants of SARS-CoV-2 could be problematic owing to its viral-host cell recognition engagement, for example, the N501Y mutation, which is shared in the three variants, the South African (501.V2), Brazilian (B.1.1.248 lineage) and the UK (VOC-202012/01). 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 N501Y 156 161 34059617 A core-shell structured COVID-19 mRNA vaccine with favorable biodistribution pattern and promising immunity. In addition, it is becoming increasingly evident that an effective vaccine needs to elicit durable responses due to rapid waning immunity observed in COVID-19 patients, and in the meantime provides protection against emerging SARS-CoV-2 variants with increased infectivity and transmissibility such as the D614G variant. 2021 Signal transduction and targeted therapy Introduction SARS_CoV_2 D614G 306 311 COVID-19 150 158 34059617 A core-shell structured COVID-19 mRNA vaccine with favorable biodistribution pattern and promising immunity. Moreover, antibodies elicited by SW0123 demonstrated high neutralizing potency against a panel of SARS-CoV-2 variants including the D614G and N501Y mutant that has emerged as the dominant variant with increased infectivity. 2021 Signal transduction and targeted therapy Introduction SARS_CoV_2 D614G;N501Y 132;142 137;147 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. A variant with a D614G mutation in the spike protein was identified in January 2020, and by May, the variant had become the predominant strain worldwide, with a prevalence of >97%. 2021 mBio Introduction SARS_CoV_2 D614G 17 22 S 39 44 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Additional variants with increased transmissibility were subsequently identified, each containing D614G. 2021 mBio Introduction SARS_CoV_2 D614G 98 103 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. An analysis of the infectivity, thermostability, and ACE2 binding affinity showed that the variant spike proteins bound ACE2 with increased affinity and were more stable than the parental D614G. 2021 mBio Introduction SARS_CoV_2 D614G 188 193 S 99 104 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. E484K, like N501Y, lies in the receptor binding motif (RBM) that directly contacts specific ACE2 residues. 2021 mBio Introduction SARS_CoV_2 N501Y;E484K 12;0 17;5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. In addition, a variant found in domesticated minks in Denmark, designated mink cluster 5 (Delta69-70/Y453F/I692V/M1229I), has the potential for transfer to humans. 2021 mBio Introduction SARS_CoV_2 I692V;M1229I;Y453F 107;113;101 112;119;106 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. K417N, while not contributing to ACE2 binding, is an epitope for neutralizing antibodies, as is E484K, and thus may have been selected for evasion of the humoral response. 2021 mBio Introduction SARS_CoV_2 E484K;K417N 96;0 101;5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. N501Y is one of six ACE2 contact residues and has been shown to increase the affinity for ACE2 by forming a hydrogen bond with Y41, the Delta69-70 deletion in the N-terminal domain (NTD) is found in multiple independent lineages, and P681H lies adjacent to the furin cleavage site, suggesting a role in spike protein processing. 2021 mBio Introduction SARS_CoV_2 P681H;N501Y 234;0 239;5 S;N 303;163 308;164 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. REGN10987 retains most of its activity against the variants, and REGN10933 failed to neutralize B.1.351, B.1.1.248, or mink cluster 5 pseudotyped viruses, an effect that mapped to E484K and K417N. 2021 mBio Introduction SARS_CoV_2 E484K;K417N 180;190 185;195 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The B.1.1.7 lineage (VOC-202012/01) variant identified in patients in the United Kingdom encodes a spike protein with 8 mutations in addition to D614G (Delta69-70, Y144Del, N501Y, A570D, P681H, T716I, S982A, and D1118H). 2021 mBio Introduction SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 180;212;145;173;187;201;194 185;218;150;178;192;206;199 S 99 104 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The B.1.351 lineage variant identified in South Africa that has become the predominant genotype in that population is more heavily mutated than B.1.1.7, with 9 mutations (L18F, D80A, D215G, L242-244del, R246I, K417N, E484K, N501Y, and A701V), 3 of which (K417N, E484K, and N501Y) are in the receptor binding domain (RBD). 2021 mBio Introduction SARS_CoV_2 A701V;D215G;D80A;E484K;E484K;K417N;N501Y;N501Y;R246I;K417N;L18F 235;183;177;217;262;210;224;273;203;255;171 240;188;181;222;267;215;229;278;208;260;175 RBD;RBD 291;316 314;319 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The COH.20G/677H spike protein contains D614G, N501Y, and Q677H but lacks the mutations present in B.1.1.7 and B.1.351, suggesting an independent origin. 2021 mBio Introduction SARS_CoV_2 D614G;N501Y;Q677H 40;47;58 45;52;63 S 17 22 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The decreased neutralizing titers against B.1.351 were largely the result of the E484K mutation, an amino acid residue that serves as a contact point for ACE2. 2021 mBio Introduction SARS_CoV_2 E484K 81 86 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Furthermore, SARS-CoV-2 mutants carrying ORF8 variants (Delta382 variant and L84S variant) were reported to be less likely to cause severe disease. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 L84S 77 81 ORF8 41 45 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. In this study, we succeeded in the mass production of wild-type ORF8 and its L84S variant with a single conformation in tobacco BY-2 cells. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 L84S 77 81 ORF8 64 68 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. A comparative set of coarse-grained molecular dynamics simulations of WT, D614G, and T307I/D614G mutants pinpointed coordinated motions between the N-terminal and the Receptor Binding Domains of Spike protomers and identified a previously unrecognized dynamic domain containing the mutation positions 307 and 614, along with the furin cleavage site. 2021 Viruses Introduction SARS_CoV_2 D614G;T307I;D614G 74;85;91 79;90;96 RBD;S;N 167;195;148 191;200;149 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. During the SARS-CoV-2 pandemic, the dynamic tracking of variant frequencies revealed the emergence of a mutation (D614G), resulting in a worldwide shift of the structure of the spike protein. 2021 Viruses Introduction SARS_CoV_2 D614G 114 119 S 177 182 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. In the present study, we focus on the B.1.1.7 variant and use molecular dynamics (MD) simulations of S protein trimer to assess its dynamic behavior in terms of conformational stability as well as interaction of the isolated viral RBD in complex with human ACE2 to calculate linear interaction energies for wild type and mutated (N501Y) RBD-ACE2 complexes. 2021 Biomedicines Introduction SARS_CoV_2 N501Y 330 335 RBD;RBD;S 231;337;101 234;340;102 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. Interestingly, these three Variants of Concern (VOC) have the N501Y and D614G mutation in common. 2021 Biomedicines Introduction SARS_CoV_2 D614G;N501Y 72;62 77;67 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. Our data suggest increased flexibility around the fusion peptide induced by the D614G mutation and reduced binding affinity between RBD and ACE2 due to conformational reorganization of the RBD-ACE2 interface mediated by N501Y. 2021 Biomedicines Introduction SARS_CoV_2 D614G;N501Y 80;220 85;225 RBD;RBD 132;189 135;192 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. This variant is characterized by several amino acid deletions and exchanges, with most of the protein-coding mutations found within the surface-anchored spike (S) protein of the virus: del69-70HV, del144Y, N501Y, A570D, D614G, P681H, T761I, S982A, D1118H (Figure S1a). 2021 Biomedicines Introduction SARS_CoV_2 A570D;D1118H;D614G;del144Y;N501Y;P681H;S982A;T761I 213;248;220;197;206;227;241;234 218;254;225;204;211;232;246;239 S;S 153;160 158;161 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Specifically, we show that N501Y in RBD introduces additional stabilizing interactions with Y41 and K353 of ACE2, which can contribute to enhanced infectivity of the new variants that carry N501Y. 2021 Viruses Introduction SARS_CoV_2 N501Y;N501Y 27;190 32;195 RBD 36 39 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Using our simulated interactions as foundation, we evaluate the effect of N501Y, a recent mutation that accounts for the majority of new infections in South East England. 2021 Viruses Introduction SARS_CoV_2 N501Y 74 79 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. A ten-fold affinity gain is brought about by the N501Y mutation as Y501 interacts through a strong, aromatic stacking interaction with Y41 and forms two new hydrogen bonds with D38 and K353 in hAce2. 2021 Viruses Introduction SARS_CoV_2 N501Y 49 54 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. All variants of concern driving the recent waves of the COVID-19 (coronavirus disease 2019) pandemic are descendants of the D614G strain. 2021 Viruses Introduction SARS_CoV_2 D614G 124 129 COVID-19;COVID-19 66;56 85;64 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Allosteric key positions, like E484 or N501, possess sufficient structural freedom to accommodate new residues without significant affinity loss (sometimes even affinity gains, i.e., N501Y) while changing the surface of the binding site such that neutralising antibodies fail to bind. 2021 Viruses Introduction SARS_CoV_2 N501Y 183 188 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Although the B.1.526 NTD harbours with L5F, T95I, and D253G, three mutations which are distinct from B.1.429, the 3D model of B.1.526 spike predicts a similar structural rearrangement of loop N5 (245-264aa) (Figure 6d). 2021 Viruses Introduction SARS_CoV_2 D253G;L5F;T95I 54;39;44 59;42;48 S 134 139 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Although the P681H mutation at the furin cleavage site initially raised much interest, it has no significant impact on viral fitness and was only found to slightly increase S1/S2 cleavage in cell culture. 2021 Viruses Introduction SARS_CoV_2 P681H 13 18 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Although the substitution of the negatively charged aspartate-614 by the uncharged and smaller glycine (D614G) removes a salt bridge with lysine-854 (K854) and a bond with T859, both in another spike protomer of the trimer, the overall structural changes in spike itself are limited to a loop (620-640 aa) close to its furin site. 2021 Viruses Introduction SARS_CoV_2 D614G 104 109 S;S 194;258 199;263 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Antibodies and sera from vaccinated people are, however, able to neutralise a pseudotyped VSV virus carrying the B.1.617 spike with the mutations R21T, E154K, Q218H, L452R, E484Q, D614G, P681R, and H1101D (GISAID Accession ID: PI_ISL_1360382). 2021 Viruses Introduction SARS_CoV_2 D614G;E154K;E484Q;H1101D;L452R;P681R;Q218H;R21T 180;152;173;198;166;187;159;146 185;157;178;204;171;192;164;150 S 121 126 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. B.1.351 Spike contains also a consecutive deletion of the three amino acids L242, A243, and L244 immediately N-terminal to loop N5 (245-264aa) as well as the replacements D80A, D215G, and A701V. 2021 Viruses Introduction SARS_CoV_2 A701V;D215G;D80A 188;177;171 193;182;175 S;N 8;109 13;110 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. B.1.617 is currently not a defined variant, as it consolidates a group of sequence clusters within clade G that share the common signature mutations: G142D, L452R, E484Q, D614G, and P681R (Table 1) as well the silent mutation D111D. 2021 Viruses Introduction SARS_CoV_2 D111D;D614G;E484Q;G142D;L452R;P681R 226;171;164;150;157;182 231;176;169;155;162;187 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Both the K417T and K417N mutations abolish this bond and are therefore predicted to have a lower hAce2 affinity while helping to evade neutralizing antibodies. 2021 Viruses Introduction SARS_CoV_2 K417N;K417T 19;9 24;14 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. By June 2020, barely six months into the pandemic, the L clade dwindled to only 7% outside of Asia, and the dominating sequence group became the rapidly evolving G clade harbouring, amongst other changes, the D614G mutation in the viral spike protein (base change: A23403G, reference sequence: EPI_ISL_450201). 2021 Viruses Introduction SARS_CoV_2 A23403G;D614G 265;209 272;214 S 237 242 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Clade GR (D614G + G204R in the nucleocapsid (N) protein; reference sequence: EPI_ISL_850687) is currently dominating Africa (41.1%), Asia (52.7%), Oceania (74.8%), and South America (66.8%), while GH (D614G + Q57H in the NS3 protein; reference sequence: EPI_ISL_861025) reigns in North America (59.0%). 2021 Viruses Introduction SARS_CoV_2 G204R;Q57H;D614G;D614G 18;209;10;201 23;213;15;206 N;NS3;N 31;221;45 43;224;46 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. E484K is also the only shared mutation of both Brazilian variants (Table 1), which possess a similar resistance to neutralization after two doses of the BioNTech/Pfizer (BNT162b2) or two doses of the Moderna (mRNA-1273) vaccine. 2021 Viruses Introduction SARS_CoV_2 E484K 0 5 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. For example, a high in-host evolution rate was found over a period of 70 days in a cancer patient, and the spontaneous appearance of the RBD mutations E484K and N501Y were observed 75 days and 128 days post-diagnosis in a patient suffering from the immune disorder antiphospholipid syndrome. 2021 Viruses Introduction SARS_CoV_2 E484K;N501Y 151;161 156;166 RBD 137 140 Immune disorder antiphospholipid syndrome 249 290 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Furthermore, the D614G mutation reduces furin cleavage, thereby lowering the risk of premature S1 shedding, and it enhances thermal stability of spike. 2021 Viruses Introduction SARS_CoV_2 D614G 17 22 S 145 150 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. In conclusion, the adaptability of the viral genome and the continuous appearance of escape mutations, as illustrated by the recent appearance of N439K in Scotland or the dynamic evolution of B.1.617, suggest that SARS-CoV-2 has the potential to become a seasonal virus like influenza with the need of re-adjusting the vaccines. 2021 Viruses Introduction SARS_CoV_2 N439K 146 151 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. In January 2021, the mutation Q1071H emerged, giving rise to three new sub-clusters (B.1.617:A, B.1.617:B, B.1.617C). 2021 Viruses Introduction SARS_CoV_2 Q1071H 30 36 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. In late December 2020, the strain B.1.526 with the E484K mutation in Spike was identified in New York. 2021 Viruses Introduction SARS_CoV_2 E484K 51 56 S 69 74 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Interestingly, the replacement of arginine-246 by an isoleucine (R246I) at the beginning of loop N5 in Spike B.1.351-V3 suppresses this structural aberration (Figure 6g). 2021 Viruses Introduction SARS_CoV_2 R246I;R246I 34;65 63;70 S 103 108 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Intriguingly, recent data from England and Wales (February 2021) show the accumulation of E484K in the B.1.1.7 background, suggesting a selection of this mutation in the response to the vaccination program. 2021 Viruses Introduction SARS_CoV_2 E484K 90 95 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Intriguingly, the N501Y mutation evolved independently in the Brazilian P.1 and South African B.1.351 variants (Table 1) and was spontaneously selected when the Wuhan virus was repeatedly propagated in BALB/c mice. 2021 Viruses Introduction SARS_CoV_2 N501Y 18 23 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. It carries the Spike mutations T19R, G142D, L454R, E484Q, D614G, P681R, and D950N. 2021 Viruses Introduction SARS_CoV_2 D614G;D950N;E484Q;G142D;L454R;P681R;T19R 58;76;51;37;44;65;31 63;81;56;42;49;70;35 S 15 20 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Its spike protein carries the L452R replacement at the outer rim of its hAce2 binding site (Figure 4b). 2021 Viruses Introduction SARS_CoV_2 L452R 30 35 S 4 9 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Its Spike protein shares the three RBD mutations at the key residues K417, E484, and N501 (K417N, E484K, N501Y) with the Brazilian P.1 strain (please note the K417 is replaced by an asparagine in B.1.351 but a threonine in P.1) (Figure 2, Table 1). 2021 Viruses Introduction SARS_CoV_2 E484K;N501Y;K417N 98;105;91 103;110;96 S;RBD 4;35 9;38 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Moreover, Y501 destabilises the RBD-down conformation, thereby adding to the D614G effect of more open RBDs. 2021 Viruses Introduction SARS_CoV_2 D614G 77 82 RBD;RBD 32;103 35;107 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. P.1 Spike contains 12 amino acid changes of which K417T, E484K, and N501Y are key positions with a high degree of structural and energetic plasticity that can accommodate novel residues with altered Ace2-interaction potentials (Table 1). 2021 Viruses Introduction SARS_CoV_2 E484K;K417T;N501Y 57;50;68 62;55;73 S 4 9 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Since both interactions are absent in the E484K mutant, the S1 movements favour the RBD-up conformation. 2021 Viruses Introduction SARS_CoV_2 E484K 42 47 RBD 84 87 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. The D614G Mutation in Spike Facilitates SARS-CoV-2 Evolution. 2021 Viruses Introduction SARS_CoV_2 D614G 4 9 S 22 27 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. The E484K mutation attracted much attention due to its ability to prevent binding of neutralizing antibodies and to be selected as an escape mutation in the presence of neutralizing antibodies or plasma from immune humans in vitro. 2021 Viruses Introduction SARS_CoV_2 E484K 4 9 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. The emergence of the new variants was preceded by the global rise of the D614G mutation in spike that was first detected in January 2020 independently in China and Germany, outperforming the initial Wuhan virus by April/May 2020 (Figure 2). 2021 Viruses Introduction SARS_CoV_2 D614G 73 78 S 91 96 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. The European Centre for Disease Prevention and Control (ECDC) lists currently the following sub-variants: B.1.617.1 was detected in India in December 2020 (L452R, E484Q, D614G, P681R, Q1071H (some viruses also carry V382L)), B.1.617.2 was initially identified in India in December 2020 but is now on the rise in the UK (T19R, Delta157-158, L452R, T478K, D614G, P681R, D950N), and the rare variant B.1.617.3 (T19R, Delta157-158, L452R, E484Q, D614G, P681R, D950N) that was found in February 2021 in India. 2021 Viruses Introduction SARS_CoV_2 D614G;D614G;D614G;D950N;D950N;E484Q;E484Q;L452R;L452R;P681R;P681R;P681R;Q1071H;T478K;V382L;L452R;T19R;T19R 170;354;442;368;456;163;435;340;428;177;361;449;184;347;216;156;320;408 175;359;447;373;461;168;440;345;433;182;366;454;190;352;221;161;324;412 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. The fitness gain indicated by the convergent evolution of N501Y is supported in the mouse model, where Y501 promotes a higher infectivity in the lung, enhances morbidity in the case of obesity, and pronounces interstitial pneumonia. 2021 Viruses Introduction SARS_CoV_2 N501Y 58 63 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. The importance of this position is further underscored by the convergent appearance of the E484Q mutation in the Indian B.1.617 variant (Table 1). 2021 Viruses Introduction SARS_CoV_2 E484Q 91 96 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. The L452R mutation increases hAce2 affinity only slightly but results in much higher viral replication in non-human veroE6 cells suggesting a role for this site in animal reservoirs like the mink. 2021 Viruses Introduction SARS_CoV_2 L452R 4 9 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. The main impact of the K417N mutation seems to be its ability to destabilize the RBD-down conformation, thereby increasing the propensity of the open configuration. 2021 Viruses Introduction SARS_CoV_2 K417N 23 28 RBD 81 84 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. The so-called cluster 5 strain contains the same two N-terminal deletions (DeltaH69, DeltaV70) as the UK B.1.1.7 Spike as well as the three mutations Y453F, I692V, and M1229I in addition to D614G (Table 1). 2021 Viruses Introduction SARS_CoV_2 D614G;I692V;M1229I;Y453F 190;157;168;150 195;162;174;155 S;N 113;53 118;54 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. The two clades GR (35.5%) and GV (D614G + A222V in spike; reference sequence: EPI_ISL_724371) (34.6%) are co-dominant in Europe. 2021 Viruses Introduction SARS_CoV_2 A222V;D614G 42;34 47;39 S 51 56 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. The variant B.1.1.7 (clade GR) emerged in late September 2020 in England (Figure 2), harbouring three deletions and seven replacements, including D614G, in spike (Table 1). 2021 Viruses Introduction SARS_CoV_2 D614G 146 151 S 156 161 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. The Y453F mutation arose several times independently in different sub-lineages, was found as an escape mutant in in vitro experiments, and increases hAce2 affinity four-fold (Table 2). 2021 Viruses Introduction SARS_CoV_2 Y453F 4 9 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. There are seven additional mutations (T19R, K77T, T95I, E154K, N440K, T478K, H1101D) that occur with varying frequencies in the B.1.617 sequence background. 2021 Viruses Introduction SARS_CoV_2 E154K;H1101D;K77T;N440K;T478K;T95I;T19R 56;77;44;63;70;50;38 61;83;48;68;75;54;42 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. This aberrant modification is caused by the S13I mutation enabling B.1.429 to escape many anti-NTD antibodies. 2021 Viruses Introduction SARS_CoV_2 S13I 44 48 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. This aberration may be linked with the D253G replacement in this loop. 2021 Viruses Introduction SARS_CoV_2 D253G 39 44 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. This is probably the result of an increased number of open RBDs due to the D614G mutation combined with the N501Y replacement in the hAce2 binding site (Figure 4 and Figure 5) (Table 2). 2021 Viruses Introduction SARS_CoV_2 D614G;N501Y 75;108 80;113 RBD 59 63 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. This may explain why L452R emerged independently in the Indian B.1.617 variant (Table 1). 2021 Viruses Introduction SARS_CoV_2 L452R 21 26 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. This structural change is probably caused by a novel disulfide bond between C136 and the W152C mutation in loop N3 (140-158aa). 2021 Viruses Introduction SARS_CoV_2 W152C 89 94 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. This was shown for the E484K mutation that effects the epitope of the 80R antibody and the N501Y mutation that impairs binding of 80R and a second neutralising antibody, M396 (Figure 7). 2021 Viruses Introduction SARS_CoV_2 E484K;N501Y 23;91 28;96 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Variant B.1.351-V2 carries one additional N-terminal mutation, L18F, which is also present in the Brazilian P.1 virus, and variant B.1.351-V3, which harbours the R246I mutation in loop N5 but lacks the D215G replacement (Table 1). 2021 Viruses Introduction SARS_CoV_2 D215G;L18F;R246I 202;63;162 207;67;167 N 42 43 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. What is, however, worth noting is the convergent mutation of P681 to an arginine (P681R) in the Indian B.1.617 Spike (Table 1), implying a functional role for a positive charge at this position (histidine can also be positively charged at a lower pH value). 2021 Viruses Introduction SARS_CoV_2 P681R 82 87 S 111 116 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. Whether this applies also to the K417T mutation is not yet clear, but it is likely, as K417 is a major site in the RBD with long-range, inter-molecular links throughout spike (Table 2). 2021 Viruses Introduction SARS_CoV_2 K417T 33 38 S;RBD 169;115 174;118 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. While inter-person transmission becomes therefore more likely, neither disease progression nor neutralization by anti-spike antibodies are significantly affected by the D614G mutation. 2021 Viruses Introduction SARS_CoV_2 D614G 169 174 S 118 123 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. While the affinity of B.1.351-V1 for hAce2 increases 19-fold due to the three RBD mutations and D614G, its neutralization by serum from convalescent patients is on average 13-fold lower and is also reduced in serum from people vaccinated with Oxford-AstraZeneca AZD1222 (9-fold) or immunized with Pfizer-BioNTech BNT162b2 (7.6-fold). 2021 Viruses Introduction SARS_CoV_2 D614G 96 101 RBD 78 81 34071984 The Spike of Concern-The Novel Variants of SARS-CoV-2. While the data related to B.1.617 are still scarce, experiments with B.1.617.1 in the hamster model indicate a higher pathogenicity compared to the D614G variant. 2021 Viruses Introduction SARS_CoV_2 D614G 148 153 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. An N501Y variant of SARS-CoV-2 (B.1.1.7, 20I/501Y.V1) that first emerged in the United Kingdom is now spreading to the rest of the world, and it appears to be much more contagious than the original virus. 2021 mAbs Introduction SARS_CoV_2 N501Y 3 8 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. However, this same N501Y mutation is also found in a variant (B.1.351, 20 H/501Y.V2) with mutations of K417N, E484K, and N501Y from South Africa and a variant (P1, 20 J/501Y.V3) with K417T, E484K, and N501Y from Brazil with additional mutations within the RBD. 2021 mAbs Introduction SARS_CoV_2 E484K;E484K;K417N;K417T;N501Y;N501Y;N501Y 110;190;103;183;19;121;201 115;195;108;188;24;126;206 RBD 256 259 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. The two additional mutations, K417N/T and E484K, are also critical residues involved in the interactions between RBD and ACE2, as well as bamlanivimab. 2021 mAbs Introduction SARS_CoV_2 E484K;K417N;K417T 42;30;30 47;37;37 RBD 113 116 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. We found that this N501Y single mutation confers an ~10-fold increase in affinity between RBD and ACE2. 2021 mAbs Introduction SARS_CoV_2 N501Y 19 24 RBD 90 93 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. Although the K417N mutation was unfavorable for ACE2 binding, the effect was small (+0.4 kcal/mol) and could be compensated by decreased antibody binding. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 K417N 13 18 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. Among a number of mutations, one common to both is N501Y, which has now also been observed in a Brazilian variant (lineage P.1). 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 N501Y 51 56 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. As expected, several mutations that were observed initially yet never became widespread, namely, G476S, V483A, and V367F, had negligible or slightly detrimental effects on binding to ACE2 (Table 2). 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 G476S;V367F;V483A 97;115;104 102;120;109 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. As in previous computational and experimental studies, although most mutations from SARS-CoV to SARS-CoV-2 were favorable, there were several exceptions, notably N439R, Q498Y, and N501T. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 N439R;N501T;Q498Y 162;180;169 167;185;174 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. FEP indicates that the SARS-CoV residues are more favorable in both positions, by 4.0 kcal/mol (Q498Y) and 0.7 kcal/mol (N501T). 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 N501T;Q498Y 121;96 126;101 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. Finally, we considered the K417N mutation, found in the South African and Brazilian variants. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 K417N 27 32 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. However, K417N has been found in simulations to have an even more detrimental effect on monoclonal antibody binding. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 K417N 9 14 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. In agreement, experiments also demonstrate that both the L455Y point mutation and the F456L point mutation significantly diminish binding of the SARS-CoV-2 RBD to ACE2 by at least 75%. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 F456L;L455Y 86;57 91;62 RBD 156 159 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. In contrast, two of the widespread mutations found in several strains, N501Y and E484K, greatly enhanced binding to ACE2, by -4.5 and -1.3 kcal/mol, respectively. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 E484K;N501Y 81;71 86;76 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. Mutation of Leu455 to tyrosine disrupts the salt bridge between Lys417 in the RBD with Asp30 in ACE2. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 L455Y 12 30 RBD 78 81 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. Our FEP calculation also shows a decrease in binding free energy of -1.3 kcal/mol for E484K (Table 2). 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 E484K 86 91 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. Recent mutations of SARS-CoV-2 have increased infectivity, and many of them are believed to facilitate binding to ACE2.- Therefore, it is imperative to understand the mechanisms behind enhanced binding to ACE2 by SARS-CoV-2 RBD and how binding changes because of emerging mutations, notably K417N, E484K, and N501Y. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 E484K;K417N;N501Y 298;291;309 303;296;314 RBD 224 227 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. Some of these residues have been further mutated in new variants of SARS-CoV-2, e.g., N501Y. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 N501Y 86 91 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. Such is the case, for example, for G476S, V483A, and V367F. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 G476S;V367F;V483A 35;53;42 40;58;47 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. Supporting this conclusion, our FEP calculation shows a large decrease in binding free energy of -4.5 kcal/mol for N501Y (Table 2). 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 N501Y 115 120 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. The weaker effect of E484K compared to N501Y is also borne out by experimental binding assays in which N501Y improved affinity for ACE2 by a factor of 4, whereas E484K enhanced binding by a factor of only 1.5. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 E484K;E484K;N501Y;N501Y 21;162;39;103 26;167;44;108 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. We also examined the E484K mutation, which was originally identified in the South African variant 501Y.V2 and was later found in the Brazilian variant 501Y.V3. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 E484K 21 26 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. Early in the pandemic, the emergence of a new variant having D614G substitution in the spike protein was identified in China. 2021 Bioinformation Introduction SARS_CoV_2 D614G 61 66 S 87 92 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. Several studies in the past few months demonstrate that the D614G substitution enhances the infectivity and efficient replication of the virus . 2021 Bioinformation Introduction SARS_CoV_2 D614G 60 65 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. Therefore, it is of interest to document the effect of D614G substitution on the structural flexibility, inter-residue interaction energies and thermodynamic stability of the spike protein trimer. 2021 Bioinformation Introduction SARS_CoV_2 D614G 55 60 S 175 180 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. In this study, we conducted a genetic surveillance and identified the SARS-CoV-2 R.1 lineage, which harbors an E484K mutation in the RBD, via whole genome sequencing and TaqMan assay. 2021 PLoS pathogens Introduction SARS_CoV_2 E484K 111 116 RBD 133 136 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. The hallmark mutation shared by the B.1.1.7, B.1.351, and P.1 lineages is N501Y, located in the receptor-binding domain (RBD) of the spike protein. 2021 PLoS pathogens Introduction SARS_CoV_2 N501Y 74 79 S;RBD 133;121 138;124 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. The other hallmark mutation of the B.1.351 and P.1 lineages is E484K, which has been shown to reduce the neutralizing activity of antibodies, thus raising concerns about vaccine efficacy. 2021 PLoS pathogens Introduction SARS_CoV_2 E484K 63 68 34098567 Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. A second variant of concern is B.1.351, which combines N501Y with two additional RBD substitutions (K417N and E484K). 2021 Nature Introduction SARS_CoV_2 E484K;N501Y;K417N 110;55;100 115;60;105 RBD 81 84 34098567 Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. In contrast to their efficacy against the wild-type virus, Nb17, Nb19 and Nb56 were unable to neutralize viruses carrying the E484K substitution alone or in combination with K417N and N501Y. 2021 Nature Introduction SARS_CoV_2 E484K;K417N;N501Y 126;174;184 131;179;189 34098567 Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. Of particular interest is the B.1.1.7 variant (which contains an N501Y substitution) that caused an upsurge in COVID-19 cases in the UK. 2021 Nature Introduction SARS_CoV_2 N501Y 65 70 COVID-19 111 119 34098567 Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. P.1, a third variant that spread rapidly in Brazil, shows changes similar to those of B.1.1.7 and B.1.351: N501Y, K417T and E484K. 2021 Nature Introduction SARS_CoV_2 E484K;K417T;N501Y 124;114;107 129;119;112 34098567 Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. Similarly, Nb15 was ineffective against N501Y. 2021 Nature Introduction SARS_CoV_2 N501Y 40 45 34098567 Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. The R683G substitution, which increases infectivity in vitro was included as a control. 2021 Nature Introduction SARS_CoV_2 R683G 4 9 34098567 Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. Thus, the E484K and N501Y substitutions enable viral escape from monomeric, but not multimeric, nanobodies. 2021 Nature Introduction SARS_CoV_2 E484K;N501Y 10;20 15;25 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. confirmed that the mutation within the nsp14-ExoN motif III (D272A) of MHV made the virus susceptible to lethal mutagenesis, and the mutant showed increased sensitivity to IFN-beta pretreatment. 2021 Cell & bioscience Introduction SARS_CoV_2 D272A 61 66 Exon 45 49 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. suggested that SARS-CoV nsp14-ExoN with D242A mutation in motif II exhibited poor nucleolytic activity compared with wildtype in tube. 2021 Cell & bioscience Introduction SARS_CoV_2 D242A 40 45 Exon 30 34 34099945 First importations of SARS-CoV-2 P.1 and P.2 variants from Brazil to Spain and early community transmission. A recent alarm has raised in the UK due to the acquisition of the same E484K mutation in 28 cases infected with the B.1.1.7 variant. 2022 Enfermedades infecciosas y microbiologia clinica Introduction SARS_CoV_2 E484K 71 76 34099945 First importations of SARS-CoV-2 P.1 and P.2 variants from Brazil to Spain and early community transmission. However, P.2 carries the E484K substitution, shared by the P.1 and B.1.351 variants, which maps in the RBD (receptor binding domain) of the spike protein. 2022 Enfermedades infecciosas y microbiologia clinica Introduction SARS_CoV_2 E484K 25 30 RBD;S;RBD 108;140;103 131;145;106 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. However, it remains unclear whether the B1.1.7+E484K variant elicits a modified immune response in patients compared with the parent B.1.1.7 variant. 2021 medRxiv Introduction SARS_CoV_2 E484K 47 52 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. In February 2021 Public Health England (PHE) published a report of B.1.1.7 genomes with acquisition of the E484K spike mutation. 2021 medRxiv Introduction SARS_CoV_2 E484K 107 112 S 113 118 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Recent in vitro data demonstrated that introduction of the E484K mutation into the B.1.1.7 background led to a more-substantial loss of neutralizing activity by vaccine-elicited antibodies compared with the mutations in B.1.1.7 alone, suggesting that this variant represents a threat to the efficacy of the BNT162b2 vaccine. 2021 medRxiv Introduction SARS_CoV_2 E484K 59 64 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Since the PHE announcement a total of 1332 B.1.1.7+E484K genomes have been uploaded to GISAID from England and 14 other countries, including 203 from the United States where it was first detected in Oregon (as of 05/24/2021). 2021 medRxiv Introduction SARS_CoV_2 E484K 51 56 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Specifically, B.1.351 and P.1 were of particular concern because they carry the mutation E484K within the receptor binding domain (RBD), which has been demonstrated to enhance escape from neutralizing antibody inhibition in vitro and may be linked with reduced vaccination efficacy. 2021 medRxiv Introduction SARS_CoV_2 E484K 89 94 RBD;RBD 106;131 129;134 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. The new B.1.1.7+E484K variant (VOC 202102/02) is fast spreading, prompting interest in the response of both unvaccinated and vaccinated individuals to disease from this variant. 2021 medRxiv Introduction SARS_CoV_2 E484K 16 21 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. To obtain insight into the biological significance of the E484K mutation in the B.1.1.7 backbone, we investigated the transcriptome of a total of 40 hospitalized patients infected with either the B.1.1.7+E484K variant (n=12) or the B.1.1.7 parent strain (n=28). 2021 medRxiv Introduction SARS_CoV_2 E484K;E484K 58;204 63;209 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. In addition, experimental validation of the enhanced affinity and infectivity of the V367F mutant was performed. 2021 Journal of virology Introduction SARS_CoV_2 V367F 85 90 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. RAY can successfully detect both SARS-CoV-2 infection as well as the presence of the common N501Y mutation present across the majority of VOCs described so far and distinguish it from the parent CoV2 lineage. 2021 eLife Introduction SARS_CoV_2 N501Y 92 97 COVID-19 33 53 34109031 SARS-CoV-2 Brazil variants in Latin America: More serious research urgently needed on public health and vaccine protection. In this mutation, substitution has been noted at position 484 (Glutamate (E) to Lysine (K)) that causes E484K mutation in RBD. 2021 Annals of medicine and surgery (2012) Introduction SARS_CoV_2 E484K 104 109 RBD 122 125 34109031 SARS-CoV-2 Brazil variants in Latin America: More serious research urgently needed on public health and vaccine protection. noted that E484K mutation decrease neutralization in convalescent sera by polyclonal antibodies. 2021 Annals of medicine and surgery (2012) Introduction SARS_CoV_2 E484K 11 16 34109031 SARS-CoV-2 Brazil variants in Latin America: More serious research urgently needed on public health and vaccine protection. On the other hand, the occurrence of the E484K mutation may neutralize convalescent sera. 2021 Annals of medicine and surgery (2012) Introduction SARS_CoV_2 E484K 41 46 34109031 SARS-CoV-2 Brazil variants in Latin America: More serious research urgently needed on public health and vaccine protection. One of the significant mutations in N501Y was noted in RBD. 2021 Annals of medicine and surgery (2012) Introduction SARS_CoV_2 N501Y 36 41 RBD 55 58 34109031 SARS-CoV-2 Brazil variants in Latin America: More serious research urgently needed on public health and vaccine protection. Other considerable modifications are A570D, D614G, P681H, 144Y deletion, and 69/70 deletion. 2021 Annals of medicine and surgery (2012) Introduction SARS_CoV_2 A570D;D614G;P681H 37;44;51 42;49;56 34109031 SARS-CoV-2 Brazil variants in Latin America: More serious research urgently needed on public health and vaccine protection. Other than the E484K mutation, some different mutations are noted in the P.2 lineage. 2021 Annals of medicine and surgery (2012) Introduction SARS_CoV_2 E484K 15 20 34109031 SARS-CoV-2 Brazil variants in Latin America: More serious research urgently needed on public health and vaccine protection. reported ten unique mutations accrued in the spike protein, which comprises of E484K and N501K. 2021 Annals of medicine and surgery (2012) Introduction SARS_CoV_2 E484K;N501K 79;89 84;94 S 45 50 34109031 SARS-CoV-2 Brazil variants in Latin America: More serious research urgently needed on public health and vaccine protection. The essential mutations in the spike include the glycoprotein RBD, E484K, K417T, and N501Y. 2021 Annals of medicine and surgery (2012) Introduction SARS_CoV_2 E484K;K417T;N501Y 67;74;85 72;79;90 S;RBD 31;62 36;65 34109031 SARS-CoV-2 Brazil variants in Latin America: More serious research urgently needed on public health and vaccine protection. These mutations are D614G and V1176F. 2021 Annals of medicine and surgery (2012) Introduction SARS_CoV_2 D614G;V1176F 20;30 25;36 34109031 SARS-CoV-2 Brazil variants in Latin America: More serious research urgently needed on public health and vaccine protection. These mutations are L18F, T20N, P26S, D138Y, R190S, D614G H655Y, T1027I, and V1176F. 2021 Annals of medicine and surgery (2012) Introduction SARS_CoV_2 D138Y;D614G;H655Y;L18F;P26S;R190S;T1027I;T20N;V1176F 38;52;58;20;32;45;65;26;77 43;57;63;24;36;50;71;30;83 34109031 SARS-CoV-2 Brazil variants in Latin America: More serious research urgently needed on public health and vaccine protection. This is a sub-lineage of B.1.128 and its separately accrued one significant spike glycoprotein mutation called E484K. 2021 Annals of medicine and surgery (2012) Introduction SARS_CoV_2 E484K 111 116 S 76 94 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. Among 454 Danish mink SARS-CoV2 sequences, 3 had N501T mutations as described earlier, none had G142D or F486L mutations (Table 1, Suppl. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 F486L;G142D;N501T 105;96;49 110;101;54 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. Comparatively, the incidence of N501Y is much lower in the United States and Canada than globally. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501Y 32 37 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. During the revision of this manuscript, 4 more N501T-F486L-144-5del human-derived variant sequences collected in November 2020 from MI, and 4 D614G mink variant sequences (collected in November 2020 from Oregon) were deposited to GISAID in April 2021 (Table 1). 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 D614G;N501T;F486L 142;47;53 147;52;58 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. Furthermore, we identified N501T mutants without G142D and F486L in U.S. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 F486L;G142D;N501T 59;49;27 64;54;32 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. Hereafter, we designated the SARS-CoV2 with N501T and G142D, but without F486L, as the N501T-G142D variant (WI mink variant), and the ones with all 3 novel mutations as the N501T-G142D-F486L variant (MI mink variant). 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 F486L;G142D;N501T;N501T;N501T;F486L;G142D;G142D 73;54;44;87;173;185;93;179 78;59;49;92;178;190;98;184 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. However, it cannot be ruled out that the different time of introduction of N501Y and N501T (April 2020 vs. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501T;N501Y 85;75 90;80 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. In addition to the above 3 mutations and 1 deletion in S protein, G614D, the mutation that dominated the SARS-CoV2 sequences, existed in all U.S. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 G614D 66 71 S 55 56 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. In Canada, the N501T mutation only existed in human-derived sequences (Suppl. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501T 15 20 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. In the GISAID (Global Initiative on Sharing All Influenza Data, https://www.gisaid.org) database of SARS-CoV2 genomes as of March 17, 2021, 758,684 of 792,388 (95.7%) of the SARS-CoV2 genome had the D614G mutation in the S protein gene; and 178,186 of 792,388 (22%) had the N501Y mutation, which occurred in the more virulent U.K. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 D614G;N501Y 199;274 204;279 S 221 222 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. Interestingly, an N501T mutation was found in almost all U.S. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501T 18 23 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. It has been described that 486F of the SARS-CoV2 receptor binding motif (RBM) inserts into a hydrophobic pocket of M82 of ACE2 to further stabilize hotspot 31K, and the F486L mutation has the potential to change the RBD region protein structure. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 F486L 169 174 RBD 216 219 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. It is likely that the N501T mutation in mink SARS-CoV2 provides the binding affinity to host ACE2 in a similar manner. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501T 22 27 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. It was predicted that a single N501T mutation might significantly enhance the binding affinity between 2019-nCoV (SARS-CoV2) receptor-binding domain (RBD) and human angiotensin-converting enzyme 2 (ACE2), and researchers were urged to closely monitor the emergence of the novel mutations at the 501 position. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501T 31 36 RBD 150 153 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. Large numbers of mutants with Y453F mutations were found in infected mink in Denmark, which may have spread from human to animal and back to humans. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 Y453F 30 35 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. mink SARS-CoV2 sequences (100 of 101; 99%); furthermore, all N501T mutant sequences, except 2 of poor quality, had the G142D mutation (Suppl. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 G142D;N501T 119;61 124;66 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. mink-derived sequences as a result of the nucleotide T23047G mutation. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 T23047G 53 60 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. Multiple alignment of human and animal ACE2 and SARS-CoV2 protein sequences indicated that the hot spot amino acid 353 of ACE2, the binding site of SARS-CoV2 spike amino acid 501, is identical between humans and mink, and that the mink ACE2 G354H substitution could conserve the polar contacts between the mink ACE2 and SARS-CoV2 virus. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 G354H 241 246 S 158 163 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. No N501T-G142D or N501T-G142D-F486L variants were found in mink and other animals from Canada or other countries (Table 1). 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501T;N501T;F486L;G142D;G142D 3;18;30;9;24 8;23;35;14;29 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. Our analysis revealed that the N501T and G142DL mutations occurred in 99% of mink-derived sequences collected in the United States; all, except one with poor quality, mink sequences collected from MI also contained the F486L mutation. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 F486L;N501T 219;31 224;36 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. Our analysis suggested that the N501T mutants might have weaker transmissibility compared to the N501Y mutants, which include U.K. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501T;N501Y 32;97 37;102 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. Outside the United States, among 335 Netherlands mink-derived SARS-CoV2 S protein gene sequences, 5 collected from April-June 2020 had the N501T mutation without G142D or F486L mutations (Suppl. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 F486L;G142D;N501T 171;162;139 176;167;144 S 72 73 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. sequences had the N501Y and N501T maturation, respectively; and 315 of 19,529 (1.6%) and 12 of 19,529 (0.06%) of Canadian sequences had the N501Y and N501T mutation, respectively (Suppl. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501T;N501T;N501Y;N501Y 28;150;18;140 33;155;23;145 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. Table 3), which is consistent with a previous report on N501T in Netherlands mink-derived sequences. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501T 56 61 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. The actual effects of mink SARS-CoV2 spike protein mutations N501T, N501T-G142D, and N501T-G142D-F486L on virus-receptor interaction needs further investigation. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501T;N501T;N501T;F486L;G142D;G142D 61;68;85;97;74;91 66;73;90;102;79;96 S 37 42 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. The F486L mutation was unique to Netherlands mink-derived sequences caused by nucleotide mutation T23045C, different from the F486L mutation found in the U.S. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 F486L;F486L;T23045C 4;126;98 9;131;105 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. The global incidence of "N501T" was not determined because the query of substitution "N501T" was not available in GISAID. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501T;N501T 25;86 30;91 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. The global incidence of "N501Y" was determined using the "search" function with substitution "N501Y" in GISAID. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501Y;N501Y 25;94 30;99 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. The N501T mutation was described in 2 Italian human-derived sequences collected in August 2020. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501T 4 9 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. The N501Y mutation that was common to U.K., South African, and Brazilian variants, and the Y453F mutation that widely prevailed in COVID-19-positive mink in Denmark and the Netherlands were absent in all U.S. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501Y;Y453F 4;91 9;96 COVID-19 131 139 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. These variants were not identical to the N501T-G142D and N501T-F486L-G142D variants revealed in our study. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501T;N501T;F486L;G142D;G142D 41;57;63;47;69 46;62;68;52;74 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. Three WI N501T-G142D variant and 2 MI N501T-G142D-F486L variant sequences were identified only from the sequences collected from WI on October 3, 2020 and Michigan on October 6, and the sequences were identical to WI and MI mink variants, respectively, except that the MI human variants lacked the Y144 deletion in the S protein. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501T;N501T;F486L;G142D;G142D 9;38;50;15;44 14;43;55;20;49 S 319 320 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. To evaluate the transmissibility of N501T mutants, the incidence of N501T and N501Y mutants was enumerated from U.S. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501T;N501T;N501Y 36;68;78 41;73;83 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. variant lineage B.1.1.7, with transmissibility increased by 50% and potentially more virulence; a similar phenomenon was observed with the South African lineage B.1.351 and Brazilian lineage P.1 (B.1.1.28.1) variants, both of which have the N501Y mutation. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501Y 241 246 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. variant N501Y is an example. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501Y 8 13 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. We also found the F486L mutation in 204 of 335 (60%) Netherlands mink-derived SARS-CoV2 S protein gene sequences, none of which were N501T-G142D variants. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 F486L;N501T;G142D 18;133;139 23;138;144 S 88 89 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. We found that, except for 1 sequence with poor quality, all MI mink sequences had the F486L mutation and the Y144 deletion, in addition to the N501T and G142D mutations (Suppl. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 F486L;G142D;N501T 86;153;143 91;158;148 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. We therefore speculate that the N501T-G142D and N501T-F486L-G142D mutations may have evolved during human infection and were then transmitted to mink populations in the United States, and it is less likely that the mutations occurred in mink populations. 2021 Journal of veterinary diagnostic investigation Introduction SARS_CoV_2 N501T;N501T;F486L;G142D;G142D 32;48;54;38;60 37;53;59;43;65 34119826 Therapeutic effect of CT-P59 against SARS-CoV-2 South African variant. For instance, the B.1.1.7 (501Y.V1) variant first described in the UK, and containing a N501Y mutation in the spike protein has spread to more than 100 countries worldwide. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 N501Y 88 93 S 110 115 34119826 Therapeutic effect of CT-P59 against SARS-CoV-2 South African variant. In contrast, LY-CoV555 showed preserved activity against the UK variant but activity against the SA variant was completely abolished since LY-CoV555 cannot bind to triple mutant protein (K417N/E484K/N501Y) of RBD in SARS-CoV-2 SA variant. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 K417N;E484K;N501Y 187;193;199 192;198;204 RBD 209 212 34119826 Therapeutic effect of CT-P59 against SARS-CoV-2 South African variant. The second variant of concern (VOC), B.1.351 (501Y.V2) first discovered in South Africa variant, has 9 mutations (L18F, D80A, D215G, Delta242-244, K417N, E484K, N501Y, D614G, and A701V). 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;N501Y;L18F 179;126;168;120;154;147;161;114 184;131;173;124;159;152;166;118 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. B.1.1.7 contains D614G and N510Y in the RBD region, with only slightly neutralization resistance by convalescent individuals and vaccine recipients. 2021 Emerging microbes & infections Introduction SARS_CoV_2 D614G;N510Y 17;27 22;32 RBD 40 43 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. B.1.351 bears three RBD mutations (K417N, E484K, and N501Y), in addition to several mutations outside of RBD, leading to substantial or complete loss of neutralization potency from humoral immunity elicited by natural infection and vaccination. 2021 Emerging microbes & infections Introduction SARS_CoV_2 E484K;N501Y;K417N 42;53;35 47;58;40 RBD;RBD 20;105 23;108 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. D614G is one of the earliest variants that rapidly emerged and became globally dominant, while convalescent sera demonstrated efficient cross-neutralization for both wild-type strain and D614G variants. 2021 Emerging microbes & infections Introduction SARS_CoV_2 D614G;D614G 187;0 192;5 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. The B.1.429 variant, a lineage recently emerged in California, United States, contains 4 missense mutations in spike including a single L452R RBD mutation. 2021 Emerging microbes & infections Introduction SARS_CoV_2 L452R 136 141 S;RBD 111;142 116;145 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. The B.1.526 variant, another variant currently spreading alarmingly in New York, United States, shares the prevalent D614G and E484K mutation in the RBD region, raising the concerns of escaped immunity for neutralization activity. 2021 Emerging microbes & infections Introduction SARS_CoV_2 D614G;E484K 117;127 122;132 RBD 149 152 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. The recent circulating variants include the D614G variant, the B.1.1.7 variant in the United Kingdom, the B.1.351 variant in South Africa, the P.1 variant in Brazil, the B.1.429 variant in California, and the B.1.526 variant in New York. 2021 Emerging microbes & infections Introduction SARS_CoV_2 D614G 44 49 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Additionally, the 69-70del, K417N, and E484K mutations have been described as possible "escape mutations," in the context of their association with the humoral immune response evasion. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 E484K;K417N 39;28 44;33 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Four mutations (N501Y, 69-70del, K417N, and E484K) in the spike protein could explain the potential biological effects that have been described for these variants. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 E484K;K417N;N501Y 44;33;16 49;38;21 S 58 63 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Mutation N501Y has been found on the receptor-binding domain (RBD) and has been associated with an increase of binding affinity to the ACE2 receptor. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 N501Y 9 14 RBD 62 65 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. In the same study, we identified multiple other M mutations including V70L that are currently being encountered with significantly increased frequency. 2021 Emerging microbes & infections Introduction SARS_CoV_2 V70L 70 74 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. The B.1.1.7-M:V70L sub-lineage has been circulating at consistently moderate prevalence since November 2020. 2021 Emerging microbes & infections Introduction SARS_CoV_2 V70L 14 18 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. The Spike (S) protein N501Y mutation in the receptor-binding domain (RBD) confers higher binding affinity of the S protein for ACE2, while the other two deletions, HV69-70del and Y144del in the N-terminal domain (NTD) may also play a role in ACE2 receptor binding or neutralizing antibody escape. 2021 Emerging microbes & infections Introduction SARS_CoV_2 N501Y;Y144del 22;179 27;186 S;RBD;N;S;S 4;69;194;11;113 9;72;195;12;114 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. This allowed us to identify a new rapidly expanding SARS-CoV-2 lineage (B.1.575) with a signature mutation I82T in the M gene. 2021 Emerging microbes & infections Introduction SARS_CoV_2 I82T 107 111 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. This new B.1.1.7 sub-lineage, carrying both M:V70L and S:D178H mutations, appeared in February 2021 but by April 2021 quickly increased to account for 36.8% and 1.8% of all reported B.1.1.7 genomes in Washington and the US, respectively, This B.1.1.7-M:V70L-S:D178H sub-lineage is currently exclusive to the US as of 8 May 2021, and had been detected in 31 states, with the majority of cases found in Washington, California and Ohio. 2021 Emerging microbes & infections Introduction SARS_CoV_2 D178H;D178H;V70L;V70L 57;260;46;253 62;265;50;257 S;S 55;258 56;259 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Through continuous genomic surveillance, we identified the subsequent acquisition of yet another Spike mutation, D178H, within this lineage. 2021 Emerging microbes & infections Introduction SARS_CoV_2 D178H 113 118 S 97 102 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. We have identified the M:V70L mutation in multiple SARS-CoV-2 lineages but primarily in the B.1.1.7 lineage. 2021 Emerging microbes & infections Introduction SARS_CoV_2 V70L 25 29 34127980 2020 SARS-CoV-2 diversification in the United States: Establishing a pre-vaccination baseline. However, the G-based clades (G/GH/GR), defined by the D614G mutation in the Spike (S) gene, accounted for >99% of sequences by Phase 2. 2021 medRxiv Introduction SARS_CoV_2 D614G 54 59 S;S 76;83 81;84 34127980 2020 SARS-CoV-2 diversification in the United States: Establishing a pre-vaccination baseline. In particular, clade G mutation NS194L and clade GH ORF1aL3352F, ORF1bN1653D;R2613C increased more than 40% from Phase 1 to Phase 3. 2021 medRxiv Introduction SARS_CoV_2 R2613C 77 83 ORF1a 52 57 34127980 2020 SARS-CoV-2 diversification in the United States: Establishing a pre-vaccination baseline. Mutations defining the B.1.427/429 VOC (SS13I;W152C;L452R) which originated in the U.S., were only detected in a very small fraction of sequences in Dec 2020, possibily due to the lag between sample collection and sequence deposition and/or shallow Phase 3 sampling. 2021 medRxiv Introduction SARS_CoV_2 L452R;W152C 52;46 57;51 S 85 86 34127980 2020 SARS-CoV-2 diversification in the United States: Establishing a pre-vaccination baseline. SARS-CoV-2 variants with the D614G mutation have been shown to be more infectious and exhibit some degree of resistance to certain monoclonal antibodies, yet they maintain convalescent serum neutralization sensitivity and do not appear to worsen clinical outcomes. 2021 medRxiv Introduction SARS_CoV_2 D614G 29 34 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. Amino acid substitutions at residue 417, K417N in B.1.351 and K417T in P.1, appear to improve evasion from antibodies in combination with N501Y and E484K. 2021 mSystems Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 148;41;62;138 153;46;67;143 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. B.1.351 and P.1 variants have two more spike mutations of biological significance: E484K and K417N/T, both located in the RBD and both important for ACE-2 binding and antibody recognition. 2021 mSystems Introduction SARS_CoV_2 E484K;K417N;K417T 83;93;93 88;100;100 S;RBD 39;122 44;125 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. In addition, using next-generation sequencing (NGS) analysis of PCR amplicons generated from sewage concentrates, we were able to track changes in variant predominance during the first stages of the pandemic detecting variants that were particularly prevalent in the UK and the rapid expansion of D614G variant reaching nearly complete dominance in May 2020. 2021 mSystems Introduction SARS_CoV_2 D614G 297 302 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. More recently, mutation E484K has been identified in a small number of B.1.1.7 viruses in England, raising increased concerns about this variant. 2021 mSystems Introduction SARS_CoV_2 E484K 24 29 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. Mutation N501Y, located within the receptor-binding domain (RBD), can increase binding affinity to human and murine angiotensin-converting enzyme 2 (ACE-2) receptor and cell infectivity in mice. 2021 mSystems Introduction SARS_CoV_2 N501Y 9 14 RBD 60 63 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. Other VOCs have been identified recently, notably lineages B.1.351 and P.1, known to be circulating in South Africa since early October 2020 and in Brazil since early December 2020, respectively, and also containing complex mutation constellations, including an N501Y amino acid change. 2021 mSystems Introduction SARS_CoV_2 N501Y 262 267 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. Substitution P681H is immediately adjacent to the furin cleavage site, important for viral pathogenesis, whereas deletion of amino acids 69 and 70 has been identified in multiple lineages associated with different RBD mutations and has been related to the evasion to human immune response. 2021 mSystems Introduction SARS_CoV_2 del 69;P681H 113;13 139;18 RBD 214 217 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. This variant contains a mutation from A to G at nucleotide 23403, resulting in amino acid change from aspartic acid to glycine at residue 614 of the spike protein, which appeared to increase viral infectivity and transmissibility. 2021 mSystems Introduction SARS_CoV_2 A23403G;D614G 38;102 64;141 S 149 154 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. Variant D614G was first described in late February 2020 in Italy, rapidly expanding and becoming the dominant SARS-CoV-2 variant globally a few months later. 2021 mSystems Introduction SARS_CoV_2 D614G 8 13 34134034 Rapid and simultaneous identification of three mutations by the Novaplex SARS-CoV-2 variants I assay kit. All three VOCs listed above harbor the N501Y mutation; B.1.1.7 harbors an additional H69/V70 deletion; and the other two, the E484K substitution mutation. 2021 Journal of clinical virology Introduction SARS_CoV_2 E484K;N501Y 126;39 131;44 34134034 Rapid and simultaneous identification of three mutations by the Novaplex SARS-CoV-2 variants I assay kit. Among the various mutations emerging in SARS-CoV-2, those in the spike (S) protein, specifically the H69/V70 deletion and E484K N501Y substitution mutations, are important because the S protein is involved in infectivity to host cells via angiotensin-converting enzyme 2 and the main target of neutralizing antibodies induced by vaccines. 2021 Journal of clinical virology Introduction SARS_CoV_2 E484K;N501Y 122;128 127;133 S;S;S 65;72;184 70;73;185 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. Of particular note is the N501Y change in the receptor binding domain (RBD) that is directly involved in interactions with the human angiotensin-converting enzyme 2 (hACE2) receptor. 2021 Frontiers in public health Introduction SARS_CoV_2 N501Y 26 31 RBD;RBD 46;71 69;74 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. The B.1.1.7 harbors 17 amino acid changes mostly in the Spike (S) protein (69-70del, 144del, N501Y, A570D, P681H, T716I, S982A, and D1118H). 2021 Frontiers in public health Introduction SARS_CoV_2 144del;A570D;D1118H;N501Y;P681H;S982A;T716I 85;100;132;93;107;121;114 91;105;138;98;112;126;119 S;S 56;63 61;64 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. The N501Y mutation can lead to enhanced viral binding efficiency with hACE2 thus rendering the virus more transmissible. 2021 Frontiers in public health Introduction SARS_CoV_2 N501Y 4 9 34140350 Characterization of a new SARS-CoV-2 variant that emerged in Brazil. In addition, the E484K substitution has been shown to confer resistance to monoclonal and polyclonal neutralizing antibodies in COVID-19 convalescent and postvaccination sera. 2021 Proc Natl Acad Sci U S A Introduction SARS_CoV_2 E484K 17 22 COVID-19 128 136 34140350 Characterization of a new SARS-CoV-2 variant that emerged in Brazil. Previous studies suggest that both the E484K and N501Y mutations in the RBD may enhance the binding affinity of the S protein for hACE2. 2021 Proc Natl Acad Sci U S A Introduction SARS_CoV_2 E484K;N501Y 39;49 44;54 RBD;S 72;116 75;117 34140350 Characterization of a new SARS-CoV-2 variant that emerged in Brazil. S protein plays a key role in viral binding to host cell receptors (i.e., human angiotensin-converting enzyme 2 [hACE2]), and the P.1 variant has three mutations (K417T, E484K, and N501Y) in the receptor-binding domain (RBD). 2021 Proc Natl Acad Sci U S A Introduction SARS_CoV_2 E484K;N501Y;K417T 170;181;163 175;186;168 RBD;S 220;0 223;1 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. This ACE2 Triple Decoy not only maintained affinity for variant S RBD, it showed an increased affinity for S RBD expressing N501Y or L452R mutations. 2021 Scientific reports Introduction SARS_CoV_2 L452R;N501Y 133;124 138;129 RBD;RBD;S;S 66;109;64;107 69;112;65;108 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. We therefore assessed the affinity of our ACE2 decoy, as compared to wild type (WT) ACE2, for S RBD with a variety of single or multiple mutations associated with the currently predominant variants, including the B.1.351 variant expressing E484K, K417N, and N501Y mutations, the B.1.1.7 variant (N501Y), and the B.1.427/B.1.429 L452R variant. 2021 Scientific reports Introduction SARS_CoV_2 E484K;K417N;L452R;N501Y;N501Y 240;247;328;258;296 245;252;333;263;301 RBD;S 96;94 99;95 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. A recent paper identified a novel neutrophil elastase (ELANE) cleavage site near the S1-S2 junction of the spike protein in the SARS-CoV-2614G-mutant (D614G), which may be the reason for enhancing the spread of SARS-CoV-2 in high Alpha-anti-trypsin (AAT)-deficient regions. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 151 156 S 107 112 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Although some mutations, such as D796H, may lead to a decrease in infectivity, it seems the deletions of DeltaH69/DeltaV70 can enhance the viral infectivity by more than two times to compensate for this decrease, and finally resulting in a moderate decrease in sensitivity to convalescent plasma. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D796H 33 38 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Among the mutations in the B.1.1.7, nine mutations, including H69-V70 deletion (Delta69/Delta70), Y144 deletion (Delta144), N501Y, A570D, D614G, P681H, T716I, S982A, and D1119H, were located in the viral spike protein. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 A570D;D1119H;D614G;N501Y;P681H;S982A;T716I 131;170;138;124;145;159;152 136;176;143;129;150;164;157 S 204 209 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Another report showed that a deletion of F140 in the NTD N3 loop, an insertion of 11-aa peptides (KTRNKSTSRRE) containing a glycan sequon (NKS) at N248 in the NTD N5 loop, and an E484K substitution in the RBD lead to complete resistance to plasma neutralization. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K 179 184 RBD 205 208 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Compared with the spike protein of SARS-CoV-2 Wuhan-1 strain, the spike protein of 501Y V2-3 contains eight mutations: four mutations in NTD (L18F, D80A, D215G, and Delta242-244), three mutations in viral RBD (K417N, E484K, and N501Y), and one mutation in S2 region (A701V). 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D215G;D80A;E484K;N501Y;A701V;K417N;L18F 154;148;217;228;267;210;142 159;152;222;233;272;215;146 S;S;RBD 18;66;205 23;71;208 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Compared with wild-type viruses, the D614G mutation enhanced the ability of virus proliferation and transmission. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 37 42 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. D614G. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 0 5 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. found that the affinity between D614G strain and cellular ACE2 receptor was reduced due to the faster dissociation rate. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 32 37 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. found the virus population changed dynamically during convalescent plasma therapy, which was characterized by the emergence of a dominant virus carrying double mutates in the spike, including D796H in the S2 and DeltaH69/DeltaV70 in the N-terminal of the S1. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D796H 192 197 S;N 175;237 180;238 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. From early September 2020, a new SARS-CoV-2 variant, named 501Y Variant 1, or N501Y, was reported in United Kingdom. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 N501Y 78 83 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. From the end of January 2020, the SARS-CoV-2 D614G strain, characterized by D614G substitution in the viral spike protein, gradually replaced other subtypes and spread widely, becoming the main circulating strain of the COVID-19 pandemic. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G;D614G 45;76 50;81 S 108 113 COVID-19 220 228 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Further studies showed that D614G mutation changes the conformation of the SARS-CoV-2 spike and enhances protease cleavage at the S1/S2 junction. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 28 33 S 86 91 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Further studies showed that the N501Y mutation significantly increases RBD:ACE2 affinity, viral entry, and infection. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 N501Y 32 37 RBD 71 74 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Furthermore, a new mutation P681H was identified at the S1/S2 linkage site, which is adjacent to the furin cleavage site (682-685 aa). 2021 Infection, genetics and evolution Introduction SARS_CoV_2 P681H 28 33 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Furthermore, more than 1500 mutations in SARS-CoV-2 have been identified in Russia, and 18 mutations of SARS-CoV-2 were found in a Russian woman with low immunity, some of which are the same as the mutated virus appearing in Britain, and two others are consistent with the variant carried by Danish mink (Y453F and Delta69-70 HV). 2021 Infection, genetics and evolution Introduction SARS_CoV_2 Y453F 305 310 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Furthermore, residue K417N can bind to N501Y, thus increasing the binding between spike and ACE2 receptor in the variant. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 K417N;N501Y 21;39 26;44 S 82 87 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. However, whether P681H affects the recognition and cleavage of S1/S2 by furin protease remains to be further studied. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 P681H 17 22 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. In November 2020, another SARS-CoV-2 variant similar to the N501Y mutant was detected in South Africa, which was named 501Y V2 strain (or B.1.351 lineage). 2021 Infection, genetics and evolution Introduction SARS_CoV_2 N501Y 60 65 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. It is worth noting that N501Y mutation was detected in four SARS-CoV-2 mutants, which appeared almost simultaneously in different countries, including B.1.1.7 (UK, mid-December 2020), B.1.351 (South Africa, late December 2020), COH.20 g/N501Y (the USA, late December 2022) and P.1 strain (501Y V3, Brazil, January 2021), suggesting that this residue may play an important role for the virus evolution and transmission. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 N501Y;N501Y 24;237 29;242 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. It was reported that the human sera from people immunized with Pfizer BTN162b2 vaccine can neutralize three SARS-CoV-2 viruses containing key spike mutations, including N501Y, 69/70-deletion+N501Y + D614G, and E484K + N501Y + D614G, with neutralization geometric mean titers of 0.81-1.46 times of the parental virus. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G;D614G;E484K;N501Y;N501Y;N501Y 199;226;210;169;218;191 204;231;215;174;223;196 S 142 147 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Moreover, the South African variant 501Y V2-3 can escape the inhibition of convalescent plasma and cause reinfection, which may be mainly due to the E484K and N501Y mutations. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K;N501Y 149;159 154;164 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Moreover, to date, four mutations have been identified in amino acid 484 of spike protein, namely E484A, E484G, E484D, and E484K, and each mutation has partial resistance to the convalescent plasma, indicating that amino acid 484 is also one of the dominant epitopes of spike protein. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484A;E484D;E484G;E484K 98;112;105;123 103;117;110;128 S;S 76;270 81;275 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Mutations K417N and E484K may also reduce the sensitivity of the virus to neutralizing antibodies by more than 10 times. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K;K417N 20;10 25;15 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. N501Y. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 N501Y 0 5 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Several groups found that the D614G substitution of the viral spike protein enhances the affinity with host receptor ACE2 and susceptibility to neutralization, another group demonstrates the mutation does not alter spike protein binding to ACE2, while Yurkovetskiy et al. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 30 35 S;S 62;215 67;220 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. The 501Y V2-1 was the dominant variant in the early stage of the second wave of epidemic in South Africa, which enhances ACE2 affinity through seven mutations in spike protein, D614G, D80A, D215G, R246I, E484K, N501Y, and A701V. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;N501Y;R246I 222;190;177;184;204;211;197 227;195;182;188;209;216;202 S 162 167 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. The 501Y Variant 2 contains 17 mutations, including H69-V70 deletion (Delta69/Delta70), Y144 deletion (Delta144), N501Y, A570D, P681H, T716I, S982A, D1118H, T1001I, A1708D, I2230T, S3675-G3676-F3677 deletion, Q27stop, R52I, Y73C, D3L, and S325F. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 A1708D;A570D;D1118H;D3L;I2230T;N501Y;P681H;Q27X;R52I;S325F;S982A;T1001I;T716I;Y73C 165;121;149;230;173;114;128;209;218;239;142;157;135;224 171;126;155;233;179;119;133;216;222;244;147;163;140;228 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. The D614G mutation leads to increased replication and transmission in primary human cells and animal models but does not affect virus virulence. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 4 9 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. The first discovered strain N501Y (501Y Variant 1) has six mutations, namely T14I, N501Y, S944L, H2357Y, P3395L, and M6723I. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 H2357Y;M6723I;N501Y;N501Y;P3395L;S944L;T14I 97;117;28;83;105;90;77 103;123;33;88;111;95;81 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. The most representative ones in the spike protein are substitution mutations such as D614G, N501Y, Y453F, N439K/R, P681H, K417N/T, and E484K, and deletion mutations of DeltaH69/V70 and Delta242-244. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G;E484K;K417N;K417T;N439K;N439R;N501Y;P681H;Y453F 85;135;122;122;106;106;92;115;99 90;140;129;129;113;113;97;120;104 S 36 41 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. The N501Y strain has stronger transmission ability, which is 40-70% higher than the original strain, and the transmission index R0 of the 501Y Variant 1 and Variant 2 was 10% and 75% higher, respectively, than that of the parent strain 501 N, but the pathogenicity and reinfection rate is similar. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 N501Y 4 9 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. The N501Y strengthened the affinity with human ACE2 and the infectivity, while 501Y V2 variant is more resistant to multiple monoclonal antibodies, convalescent plasma, and vaccinee sera partly due to the E484K substitution. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K;N501Y 205;4 210;9 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. The sentinel mutation N439K in the viral receptor-binding motif endows the virus with enhanced binding affinity to human ACE2, resistance to several neutralizing monoclonal antibodies, and polyclonal sera from the recovered patients. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 N439K 22 27 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Then, a second N501Y mutant 501Y Variant 2 (also named 20B/501Y V1, SARS-CoV-2 VOC 202012/01, or lineage B.1.1.7) appeared in England in late September 2020 and became the dominant lineage in December 2020. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 N501Y 15 20 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Thereafter, two other mutations L18F and K417N were identified in 501Y V2-1, resulting in strain 501Y V2-2. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 K417N;L18F 41;32 46;36 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. These results indicate that Delta69/Delta70, N501Y, and P681H are three key mutations in the spike protein of the N501Y strain, and their effects on virus pathogenicity, transmission, and immune escape should be further evaluated. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 N501Y;N501Y;P681H 45;114;56 50;119;61 S 93 98 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. These results suggest that D614G mutation leads to allosteric effects of SD1 and SD2 domains, with a more open conformation of the S trimer, thus exposing neutralizing epitopes and ACE2 receptor binding residues on the RBD, and finally making S protein more sensitive to neutralizing antibodies and increasing the efficiency of membrane fusion. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 27 32 Membrane;RBD;S;S 328;219;131;243 336;222;132;244 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Among the mutations, Spike:D614G and Nsp12:P323L are occurring in nearly 75% of the sequences soon after their first appearance in January 2020 (GISAID ID: EPI_ISL_422425) indicating their evolutionary advantage. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 D614G;P323L 27;43 32;48 S;Nsp12 21;37 26;42 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Interestingly, R203K and G204R present in nucleoprotein are found to be co-occurring (dependent) mutations. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 G204R;R203K 25;15 30;20 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. Experimental data suggests mutation N501Y increases the binding affinity of the spike protein with human and murine ACE2. 2021 Computers in biology and medicine Introduction SARS_CoV_2 N501Y 36 41 S 80 85 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. It is estimated that the spread of SARS-CoV-2 N501Y variant is 70% faster than previous strains, indicating a much higher infectivity. 2021 Computers in biology and medicine Introduction SARS_CoV_2 N501Y 46 51 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. N501 of RBD is spatially distant from its interacting interface with P2B-2F6, and thereby the newly identified mutation N501Y is unlikely to affect the neutralizing activity of P2B-2F6. 2021 Computers in biology and medicine Introduction SARS_CoV_2 N501Y 120 125 RBD 8 11 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. These variants have an unusually large number of genetic changes, including the noteworthy spike protein mutation N501Y, one of the key residues in RBD domain interacting with ACE2. 2021 Computers in biology and medicine Introduction SARS_CoV_2 N501Y 114 119 S;RBD 91;148 96;151 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. Two potent P2B-2F6 mutants of H:V106R and H:V106 R/H:P107Y were found to have higher binding affinities with the RBD domain of SARS-CoV-2. 2021 Computers in biology and medicine Introduction SARS_CoV_2 P107Y;V106H;V106R;V106R 53;44;44;32 58;52;52;37 RBD 113 116 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. We hope that our proposed antibody mutants could be more efficient to combat SARS-CoV-2 as well as the more infectious N501Y variant. 2021 Computers in biology and medicine Introduction SARS_CoV_2 N501Y 119 124 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Another RBD variant, L452R, disrupted fewer NAbs, but exhibited 2-fold higher affinity for ACE2, suggesting this mutation may enhance viral fitness through increased affinity for ACE2, as well as disrupting the host NAb response. 2021 Frontiers in immunology Introduction SARS_CoV_2 L452R 21 26 RBD 8 11 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Furthermore, N501Y and E484K RBD variants exhibited essentially wild type (WT) affinity for ACE2, where WT is defined as the Wuhan-1 RBD sequence. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K;N501Y 23;13 28;18 RBD;RBD 29;133 32;136 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Of the nine RBD variants tested, N501Y, E484K, and K417T disrupted binding to 65% of the NAbs evaluated. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K;K417T;N501Y 40;51;33 45;56;38 RBD 12 15 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. Indeed, a mutant strain, D614G, carries a spike amino acid mutation and possesses higher infectivity towards human cells and in animal models. 2021 Journal of infection and chemotherapy Introduction SARS_CoV_2 D614G 25 30 S 42 47 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. Therefore, the rapid genotyping of SARS-CoV-2, especially to detect the D614G mutant, is now essential for tracing its infection source and reducing its further transmission. 2021 Journal of infection and chemotherapy Introduction SARS_CoV_2 D614G 72 77 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. A recent study posted on a preprint server examining SARS-CoV-2 variants in the rhesus macaque model showed no difference in viral replication nor disease between the D614G and B.1.1.7 variants. 2021 bioRxiv Introduction SARS_CoV_2 D614G 167 172 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. Although viral RNA was detectable throughout the study, infectious virus was only isolated from oral swabs at 1dpi with significantly higher titers for the D614G infected animals (Fig 1E). 2021 bioRxiv Introduction SARS_CoV_2 D614G 156 161 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. B.1.1.7 infected AGMs scored slightly higher earlier and peaked at 1dpi, whereas D614G infected animals scored higher later and peaked at 3dpi. 2021 bioRxiv Introduction SARS_CoV_2 D614G 81 86 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. B.1.1.7 replicated at higher levels in the respiratory tract resulting in lesions that were both more numerous and severe than seen for D614G infected animals. 2021 bioRxiv Introduction SARS_CoV_2 D614G 136 141 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. B.1.1.7 replication in the lower respiratory tract was increased compared to D614G. 2021 bioRxiv Introduction SARS_CoV_2 D614G 77 82 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. B.1.1.7 replication/shedding from the upper respiratory tract was increased compared to D614G. 2021 bioRxiv Introduction SARS_CoV_2 D614G 88 93 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. By 7dpi these animals were all shedding significantly more viral RNA than those infected with D614G (Fig 1F, G). 2021 bioRxiv Introduction SARS_CoV_2 D614G 94 99 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. Consistent with the viral RNA and infectious titer results, most animals (5 out of 6) infected with B.1.1.7 had inflammation of the trachea, with only 1 of 5 animals infected with the D614G variant having any similar observable lesion. 2021 bioRxiv Introduction SARS_CoV_2 D614G 184 189 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. D614G replication in the gastrointestinal (GI) tract was increased compared to B.1.1.7. 2021 bioRxiv Introduction SARS_CoV_2 D614G 0 5 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. Following infection with either variant, animals in both groups exhibited minor differences in disease progression but overall disease signs were similar with mild respiratory disease for both B.1.1.7 and D614G. 2021 bioRxiv Introduction SARS_CoV_2 D614G 205 210 Respiratory Disease 164 183 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. Following intranasal infection with 1x106 infectious particles of either the SARS-CoV-2 D614G (n=5) or the B.1.1.7 variant (n=6) (5x105 per naris) using a nasal atomization device, animals were monitored and scored daily for clinical signs of disease including changes in general appearance, respiration, food intake and fecal output and locomotion. 2021 bioRxiv Introduction SARS_CoV_2 D614G 88 93 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. In contrast, D614G replicated at higher levels in the GI tract and the associated pathology seen in these animals correlated with this difference in GI replication. 2021 bioRxiv Introduction SARS_CoV_2 D614G 13 18 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. In contrast, scores for the D614G animals increased slowly peaking at 4dpi and remained stable until euthanasia (Fig 1A, Table S1). 2021 bioRxiv Introduction SARS_CoV_2 D614G 28 33 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. In D614G infected animals, only one AGM presented with inflammation and a small amount of associated viral antigen in the cecum. 2021 bioRxiv Introduction SARS_CoV_2 D614G 3 8 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. In our current study, the AGM intranasal model of SARS-CoV-2 infection was used to assess differences between a contemporary SARS-CoV-2 D614G variant, which was circulating in the summer of 2020, and the B.1.1.7 VOC that emerged in the UK in late 2020. 2021 bioRxiv Introduction SARS_CoV_2 D614G 136 141 COVID-19 50 70 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. In the present study, we have used the AGM intranasal infection model to compare the B.1.1.7 VOC, a variant that emerged in the UK in September of 2020 and then quickly spread throughout the world, with a contemporary D614G variant, in terms of virus replication, shedding and disease severity. 2021 bioRxiv Introduction SARS_CoV_2 D614G 218 223 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. Levels of T cell chemo-attractants IP-10 (CXCL 10) (Fig S4B) and I-Tac (CXCL 11) (Fig S4) were also increased at 1dpi in the D614G group but were not sustained throughout the study. 2021 bioRxiv Introduction SARS_CoV_2 D614G 125 130 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. Levels of viral RNA corresponded to infectious virus with only D614G animals having detectable infectious SARS-CoV-2 in these two GI-derived tissues (Fig 4C). 2021 bioRxiv Introduction SARS_CoV_2 D614G 63 68 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. No differences were found in the hematology (Fig S2A-L), blood chemistry (Fig S2M-T) or coagulation assays (Fig S3) between the D614G and B.1.1.7 infected AGMs. 2021 bioRxiv Introduction SARS_CoV_2 D614G 128 133 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. Notably and in marked contrast to respiratory tissues, AGMs infected with D614G had significantly more total and sgRNA in the ileum and cecum than B.1.1.7 infected AGMs (Fig 4A, B). 2021 bioRxiv Introduction SARS_CoV_2 D614G 74 79 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. S4), IL6 was the only pro-inflammatory cytokine that was significantly different between the groups, with IL6 being elevated in the D614G group at 3dpi and 5dpi compared to B.1.1.7 infected animals (Fig S4A). 2021 bioRxiv Introduction SARS_CoV_2 D614G 132 137 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. sgRNA was recovered intermittently across the study (Fig 4E), but infectious virus was recovered from rectal swabs of only one D614G animal (Fig 4F). 2021 bioRxiv Introduction SARS_CoV_2 D614G 127 132 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. Similarly, gRNA in rectal swabs peaked and was significantly higher at 7dpi in D614G infected animals (Fig 4D). 2021 bioRxiv Introduction SARS_CoV_2 D614G 79 84 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. Similarly, lesions were found in 8 of 10 bronchi from B.1.1.7 infected AGMs compared to only 2 of 8 of D614G animals, with lesions corresponding to SARS-CoV-2 immunoreactivity by immunohistochemistry (IHC) (Fig 2G-N). 2021 bioRxiv Introduction SARS_CoV_2 D614G 103 108 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. This may indicate that D614G is more suited to replication in the digestive tract than other variants which is in line with clinical studies conducted in early to mid-2020 that reported GI symptoms in approximately 15-20% of COVID-19 patients. 2021 bioRxiv Introduction SARS_CoV_2 D614G 23 28 COVID-19 225 233 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. Total and sgRNA was significantly higher in the lungs of B.1.1.7- compared to D614G-infected animals (Fig 3A, B); however, elevated levels of infectious virus in B.1.1.7 animals remained just below statistical significance (Fig 3C). 2021 bioRxiv Introduction SARS_CoV_2 D614G 78 83 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. Total gRNA in oral swabs was significantly higher at 5dpi in B.1.1.7 compared to D614G infected animals; this difference between variants was maintained but dropped below significance by 7dpi (Fig 1C). 2021 bioRxiv Introduction SARS_CoV_2 D614G 81 86 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. Viral replication in the ileum was associated with inflammation in D614G infected AGMs and corresponded with detectable viral antigen by IHC (Fig 4G,H,K,L), while AGMs infected with the B.1.1.7 had no observable inflammation or viral antigen (Fig 4I,J,L,M). 2021 bioRxiv Introduction SARS_CoV_2 D614G 67 72 34159332 UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates. Viral RNA and infectious virus in the lower respiratory tract tissues were more prevalent in the animals infected with B.1.1.7 compared to D614G, especially at later timepoints suggesting the development of a stronger respiratory component associated with the emerging VOC (Figs 2, Fig 3). 2021 bioRxiv Introduction SARS_CoV_2 D614G 139 144 34160124 Preliminary Structural Data Revealed That the SARS-CoV-2 B.1.617 Variant's RBD Binds to ACE2 Receptor Stronger Than the Wild Type to Enhance the Infectivity. According to government officials, an increasing number of variants with mutations, specially E484Q and L452R, have been seen in samples collected from the western state of Maharashtra. 2021 Chembiochem Introduction SARS_CoV_2 E484Q;L452R 94;104 99;109 34160124 Preliminary Structural Data Revealed That the SARS-CoV-2 B.1.617 Variant's RBD Binds to ACE2 Receptor Stronger Than the Wild Type to Enhance the Infectivity. Accordingly, in this present study, our objective is to employ several computational techniques to decipher the impact of the newly emerged B.1.617 carrying L452R-E484Q mutations on the overall S protein structure and function, assessing the effect on binding with ACE2 and the overall impact on interactions network. 2021 Chembiochem Introduction SARS_CoV_2 L452R;E484Q 157;163 162;168 S 194 195 34160124 Preliminary Structural Data Revealed That the SARS-CoV-2 B.1.617 Variant's RBD Binds to ACE2 Receptor Stronger Than the Wild Type to Enhance the Infectivity. More worrisome is the continuous spread of new SARS-CoV-2 strains in South Africa (B.1.351) and the United Kingdom (B.1.1.7), carrying mutations of N501Y and E484 K within the RBD domain. 2021 Chembiochem Introduction SARS_CoV_2 E484K;N501Y 158;148 164;153 RBD 176 179 34160124 Preliminary Structural Data Revealed That the SARS-CoV-2 B.1.617 Variant's RBD Binds to ACE2 Receptor Stronger Than the Wild Type to Enhance the Infectivity. The wild-type spike protein sequence (PDB ID: 6M0J) was then accessed from the protein data bank (PDB) and, subsequently, used in the UCSF Chimera v.1.15 interactive visualization program to generate the desired E484Q-L452R mutant. 2021 Chembiochem Introduction SARS_CoV_2 E484Q;L452R 212;218 217;223 S 14 19 34160124 Preliminary Structural Data Revealed That the SARS-CoV-2 B.1.617 Variant's RBD Binds to ACE2 Receptor Stronger Than the Wild Type to Enhance the Infectivity. These mutations in this strain may enhance virus transmissibility and infectivity, including the deletion of residues 69-70 and 144 and the substitution of A570D, D614G, T716I, S982A, D1118H, P681H, K417N, K417T, E484 K and N501Y. 2021 Chembiochem Introduction SARS_CoV_2 A570D;D1118H;D614G;E484K;K417N;K417T;N501Y;P681H;S982A;T716I 156;184;163;213;199;206;224;192;177;170 161;190;168;219;204;211;229;197;182;175 34160124 Preliminary Structural Data Revealed That the SARS-CoV-2 B.1.617 Variant's RBD Binds to ACE2 Receptor Stronger Than the Wild Type to Enhance the Infectivity. Very recently, a novel B.1.617 variant with two mutations L452R and E484Q on the RBD domain was identified in India. 2021 Chembiochem Introduction SARS_CoV_2 E484Q;L452R 68;58 73;63 RBD 81 84 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. Although the total binding free energies (DeltaGb) of the distinct RBD/ACE2 adducts, calculated with the molecular mechanics/generalized born surface area (MM-GBSA) method, do not enable one to discriminate the subtle differences between WT and mutant RBD/ACE2 adducts (Table S3), a dissection of the per-residue amino acids DeltaGb contributions showed an increase, related to the N501Y substitution, with respect to the WT by 3.8 +- 2.0 and 4.4 +- 2.0 kcal/mol in SARBD/ACE2 and N501YRBD/ACE2, respectively (Figure S4), in agreement with recently reported theoretical and experimental evidence. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 N501Y;N501Y 382;481 387;486 RBD;RBD 67;252 70;255 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. As a result, we disclose that while N501Y (hallmark of the UK variant) enhances the binding affinity toward ACE2 and increases the alpha1-helix@ACE2 bending, the SA strain exploits a two-pronged strategy to more effectively infect the host cells by (i) increasing the allosteric signaling among the pivotal RBM loops, which acting as a tweezer more effectively grasp/bend alpha1-helix@ACE2 and (ii) hindering the interactions with class 1 and 2 mAbs (K417N and E484K, respectively) extracted from COVID-19 patients' sera (Figure 4 and Table S6). 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 E484K;N501Y;K417N 461;36;451 466;41;456 COVID-19 497 505 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. As an example, one of the first S-protein mutations, D614G, characterized by an enhanced transmissibility, has rapidly become dominant. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 D614G 53 58 S 32 33 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. As concerns the most prominent nonsynonymous mutations placed in the S-protein's RBD, most SARS-CoV-2 variants share the N501Y substitution (Figure 1), most likely implicated into an enhanced binding affinity toward ACE2,- although preliminary reports indicate that this variant retains vaccine efficacy. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 N501Y 121 126 RBD;S 81;69 84;70 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. As such, N501Y, present in the highly infective UK and SA variants, possibly increases the RBD binding affinity for ACE2. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 N501Y 9 14 RBD 91 94 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. E484, the most frequently mutated residue in COVID-19 patients, becomes E484K in the SA and BR and E484Q in the Indian strains. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 E484K;E484Q 72;99 77;104 COVID-19 45 53 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. Hence, K417N and E484K substitutions alter the electrostatic complementarity between the RBD and class 1 and 2 mAbs, respectively (Figure 4 and Table S6),- impairing mAbs binding and contributing to viral escape from vaccine/disease-induced immunity. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 E484K;K417N 17;7 22;12 RBD 89 92 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. Hence, the way K417N contributes to enhance the ACE2 sequestration remains elusive. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 K417N 15 20 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. In addition to N501Y, the SA variant also exhibits the E484K and K417N RBD mutations. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 E484K;K417N;N501Y 55;65;15 60;70;20 RBD 71 74 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. In the current set of MD simulations all the investigated systems evidence a similar RBMs flexibility, with small differences being restricted to Loop1 and 4 (L1/4, Figure S2), where N501Y is placed (Figure 1). 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 N501Y 183 188 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. In this scenario, it is tempting to argue that the BR variant, differing from the SA one only by the K417T@RBD substitution, may exploit the same strategy to foster viral propagation. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 K417T 101 106 RBD 107 110 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. Namely, we first built the adduct between ACE2 and RBD carrying the N501Y, E484K, and K417N substitutions of the SA lineage (hereafter termed SARBD/ACE2). 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 E484K;K417N;N501Y 75;86;68 80;91;73 RBD 51 54 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. Next, to inspect the role of each mutation, we built three distinct RBD/ACE2 models carrying N501Y (N501YRBD/ACE2 or UKRBD/ACE2), E484K (E484KRBD/ACE2), and K417N (K417NRBD/ACE2), ultimately comparing them with the WT RBD/ACE2 adduct (hereafter named RBD/ACE2). 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 E484K;K417N;N501Y;E484K;K417N;N501Y 130;157;93;137;164;100 135;162;98;142;169;105 RBD;RBD;RBD 68;218;251 71;221;254 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. No significant variation of the DeltaGb could be observed for K417NRBD/ACE2 and SARBD/ACE2 as compared to RBD/ACE2 (Figures S4 and S6), and K417N does not increase the alpha1-helix@ACE2 bending (Figure 2). 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 K417N;K417N 140;62 145;67 RBD 106 109 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. Remarkably, in N501Y(UK)RBD and SARBD these paths are shorter (the residues are more correlated, Figure 3F,H), suggesting a stronger signaling between the two RBM extremities, which may result in a more effective opening/closing of the L1/4 and L3. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 N501Y 15 20 RBD 24 27 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. Stunningly, the main actor in modulating the allosteric cross-talk among the RBD mutants appears to be K417N, whose role has remained so far elusive. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 K417N 103 108 RBD 77 80 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. The similar distribution observed for SARBD/ACE2 and K417NRBD/ACE2 indicates that K417N is primarily liable for the enhanced cross-talk between critical RBD recognition loops (Figure 3E,G). 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 K417N 82 87 RBD 153 156 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. This comes along with a more effective grasping and bending of the ACE2's alpha1-helix in both N501YRBD/ACE2 and SARBD/ACE2 models as compared to RBD/ACE2 (Figure 2). 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 N501Y 95 100 RBD 146 149 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. We also inspected the role of the E484K mutation common to the SA and BR variants for which no significant and reliable variation of the DeltaGb could be calculated (Figures S4 and S5) in SARBD/ACE2 and E484KRBD/ACE2, respectively. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 E484K;E484K 34;203 39;208 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. We finally assessed the role of K417, whose salt-bridge with Asp30@ACE2, present in half of the RBD/ACE2 MD trajectory, is lost upon K417N mutation (Table S1). 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 K417N 133 138 RBD 96 99 34161337 SARS-CoV-2 uses major endothelial integrin alphavbeta3 to cause vascular dysregulation in-vitro during COVID-19. However, a novel K403R mutation in the spike protein of SARS-CoV-2 forms a unique Arg-Gly-Asp (RGD) motif outside the ACE2 recognition site. 2021 PloS one Introduction SARS_CoV_2 K403R 17 22 S 39 44 34162440 Deletion of ER-retention motif on SARS-CoV-2 spike protein reduces cell hybrid during cell-cell fusion. 2) Interaction between the Delta19-S variant and ACE2 show defects in nuclear fusion during syncytia formation. 2021 Cell & bioscience Introduction SARS_CoV_2 Delta19-S 27 34 S 35 36 34162440 Deletion of ER-retention motif on SARS-CoV-2 spike protein reduces cell hybrid during cell-cell fusion. Different cell lines (293T, A549, K562 and SK-Hep1) expressing either S-WT-EGFP or S-Delta19-EGFP have been co-cultured with cells expressing ACE2-mCherry. 2021 Cell & bioscience Introduction SARS_CoV_2 Delta19 86 92 S;S 70;83 71;84 34162440 Deletion of ER-retention motif on SARS-CoV-2 spike protein reduces cell hybrid during cell-cell fusion. In Delta19-S, the 19 amino acids from the C terminus are deleted which results in the loss of S protein retention in the endoplasmic reticulum (ER). 2021 Cell & bioscience Introduction SARS_CoV_2 Delta19-S 3 10 S;S 11;94 12;95 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Functionally, we find that DeltaH69/V70 does increase spike infectivity and compensates for an infectivity defect resulting from the RBD replacements N439K and Y453F. 2021 Cell reports Introduction SARS_CoV_2 N439K;Y453F 150;160 155;165 S;RBD 54;133 59;136 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Here we analyze global SARS-CoV-2 data and find that DeltaH69/V70 occurs independently, often emerging after a significant RBD amino acid replacement, such as Y453F and N439K, which are known to facilitate neutralizing antibody escape or alter ACE2 binding while incurring an infectivity defect, according to some reports. 2021 Cell reports Introduction SARS_CoV_2 N439K;Y453F 169;159 174;164 RBD 123 126 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. In addition, a chronically infected immune-suppressed individual has been reported recently in Russia with emergence of Y453F along with DeltaH69/V70. 2021 Cell reports Introduction SARS_CoV_2 Y453F 120 125 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. A few mutations in the SD1-2 region near the Furin cleavage site are also identified, such as P681H in B.1.1.7 and A701V in B.1.351. 2021 Immunity Introduction SARS_CoV_2 A701V;P681H 115;94 120;99 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. B.1.351 and P.1 each have three mutation sites in common within the RBD:K417N/T, E484K, and N501Y:which may change their antigenic profile. 2021 Immunity Introduction SARS_CoV_2 E484K;N501Y;K417N;K417T 81;92;72;72 86;97;79;79 RBD 68 71 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Crystal structural analysis of the RBD carrying the triple K417N-E484K-N501Y mutation found in B.1.351 bound with the mAb P2C-1F11 revealed a molecular basis for antibody neutralization and escape. 2021 Immunity Introduction SARS_CoV_2 K417N;E484K;N501Y 59;65;71 64;70;76 RBD 35 38 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. For example, the S protein D614G mutation became dominant just a few months into the pandemic and is associated with greater infectivity and transmissibility as well as moderately decreased susceptibility to antibody neutralization. 2021 Immunity Introduction SARS_CoV_2 D614G 27 32 S 17 18 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. In addition, various deletion mutants are found in the NTD, such as 69-70del and Y144del in B.1.1.7 and 242-244del in B.1.351. 2021 Immunity Introduction SARS_CoV_2 Y144del 81 88 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Specifically, B.1.1.7, B.1.351, and P.1 share the N501Y mutation, shown previously to enhance binding affinity to ACE2. 2021 Immunity Introduction SARS_CoV_2 N501Y 50 55 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. These included 14 single mutations in the B.1.1.7, B.1.351, or P.1 variants, the K417N-E484K-N501Y mutation, and highly prevalent single mutations in the NTD, RBD, SD1-2, and S2 domains, identified across the entire S protein in the GISAID database (Figure 1 A). 2021 Immunity Introduction SARS_CoV_2 K417N;E484K;N501Y 81;87;93 86;92;98 RBD;S 159;216 162;217 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. Here we describe the first detection of B.1.1.7 lineages in Washington State by a novel reverse-transcription droplet digital-PCR (RT-ddPCR) assay that specifically detects four mutations associated with the B.1.1.7 variant, particularly N501Y. 2021 Journal of medical virology Introduction SARS_CoV_2 N501Y 238 243 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. This RT-ddPCR assay can distinguish SARS-CoV-2 positive samples that carry this important N501Y mutation, flagging clinically relevant potential VOCs for genetic sequencing. 2021 Journal of medical virology Introduction SARS_CoV_2 N501Y 90 95 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. A well-studied SARS-CoV-2 mutant harbors a D614G substitution in the spike (S) protein. 2021 Cell host & microbe Introduction SARS_CoV_2 D614G 43 48 S;S 69;76 74;77 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Furthermore, we artificially generated SARS-CoV-2 harboring these point mutations by reverse genetics and show that the L452R mutant enhances viral replication capacity. 2021 Cell host & microbe Introduction SARS_CoV_2 L452R 120 125 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. However, there is no evidence suggesting that the D614G variant is associated with viral pathogenicity or lethality. 2021 Cell host & microbe Introduction SARS_CoV_2 D614G 50 55 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. More intriguingly, the L452R and Y453F mutants enhance binding affinity for ACE2, and experiments using pseudoviruses show that the L452R substitution increases viral infectivity. 2021 Cell host & microbe Introduction SARS_CoV_2 L452R;L452R;Y453F 23;132;33 28;137;38 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Recent studies have revealed that the D614G mutation increases the binding affinity of SARS-CoV-2 to ACE2, the SARS-CoV-2 receptor; infectivity, fitness, and transmissibility in the human population are also enhanced. 2021 Cell host & microbe Introduction SARS_CoV_2 D614G 38 43 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. We demonstrate that at least two naturally occurring substitutions in the receptor-binding motif (RBM; residues 438-506) of the SARS-CoV-2 S protein, L452R and Y453F, which were identified in the two major variants, B.1.427/429 (L452R) and B1.1.298 (Y453F), can be resistant to cellular immunity in the context of HLA-A24, an allele of HLA-I. 2021 Cell host & microbe Introduction SARS_CoV_2 L452R;Y453F;L452R;Y453F 150;160;229;250 155;165;234;255 S 139 140 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. According to this investigation, the D614G mutation can shift the population of the SARS-CoV-2 S trimer from the closed form to an open topology of the "up" protomers with 39% of the population adopting two open protomers and 20% with all three protomers in the open conformation. 2021 ACS omega Introduction SARS_CoV_2 D614G 37 42 S 95 96 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Contrary to the original hypothesis, a detailed structural and functional analysis found that the D614G mutation does not appreciably affect S protein synthesis and incorporation into SARS-CoV-2 particles but could reduce the binding affinity to ACE2 and lead to faster dissociation rates. 2021 ACS omega Introduction SARS_CoV_2 D614G 98 103 S 141 142 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. D614G mutation is characterized by the enhanced transmissibility but this variant is not linked with the increased disease severity. 2021 ACS omega Introduction SARS_CoV_2 D614G 0 5 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. In this study, we examine molecular mechanisms underlying the functional effects of the D614G mutation by exploring conformational landscapes in different states of the SARS-CoV-2 S protein. 2021 ACS omega Introduction SARS_CoV_2 D614G 88 93 S 180 181 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Large-scale functional and clinical studies showed that the D614G mutation could be linked with the higher viral load and younger age of patients but does not result in the higher mortality. 2021 ACS omega Introduction SARS_CoV_2 D614G 60 65 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Other studies examined dynamics and energetics of the S-D614 and S-G614 proteins in the closed and partially open conformations, suggesting that the S-G614 mutant can improve the interprotomer interactions between S1 and S2 regions.- MD simulations of other circulating variants revealed that the N501Y mutation increases ACE2-binding affinity. 2021 ACS omega Introduction SARS_CoV_2 N501Y 297 302 S;S;S 54;65;149 55;66;150 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Other studies suggested that the D614G mutation increases entry efficiency with the enhanced ACE2-binding affinity by conferring the increased structural flexibility to S protein. 2021 ACS omega Introduction SARS_CoV_2 D614G 33 38 S 169 170 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Several computational studies examined the effects of global circulating mutations on dynamics and stability of the SARS-CoV-2 S proteins.- Microsecond all-atom simulations recently probed the effects of the D614G mutation showing a higher population of receptor-accessible open states in the S-G614 mutant forming through release of asymmetry present in the native interprotomer interactions. 2021 ACS omega Introduction SARS_CoV_2 D614G 208 213 S;S 127;293 128;294 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Structure-based protein design and cryo-EM structural determination established that D614G and D614N mutations can result in the increased stability due to a decrease in the premature shedding of the S1 domain. 2021 ACS omega Introduction SARS_CoV_2 D614G;D614N 85;95 90;100 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Th global circulating mutants of the SARS-CoV-2 S protein discovered through epidemiological surveillance prompted a significant effort in the biomedical community.- From studies of pseudotype viruses, it was initially conjectured that the D614G substitution can increase S glycoprotein incorporation into virions, reduce S1 loss, and promote enhanced infectivity. 2021 ACS omega Introduction SARS_CoV_2 D614G 240 245 S;S 272;48 286;49 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. The biochemical studies suggested a phenotypic advantage and the enhanced infectivity conferred by the D614G mutation. 2021 ACS omega Introduction SARS_CoV_2 D614G 103 108 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. The genomes of 5085 SARS-CoV-2 strains from two distinct COVID-19 disease waves were sequenced in the metropolitan Houston region, showing that strains with D614G mutation caused the vast majority of clinical cases in the massive second disease wave, likely due to the increased transmission. 2021 ACS omega Introduction SARS_CoV_2 D614G 157 162 COVID-19 57 73 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. The increased population of the 1 RBD-up open form compared to that of the closed state was also observed in the S-GSAS/D614G structure. 2021 ACS omega Introduction SARS_CoV_2 D614G 120 125 RBD;S 34;113 37;114 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. The landscape-based network community analysis of the SARS-CoV-2 spike proteins showed that the D614G mutation can enhance long-range couplings between domains and strengthen the interdomain interactions in the open form. 2021 ACS omega Introduction SARS_CoV_2 D614G 96 101 S 65 70 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. The results suggest that the D614G mutation can induce the increased stability of the open form acting as a driver of conformational changes, which may result in the increased exposure to the host receptor and promote infectivity of the virus. 2021 ACS omega Introduction SARS_CoV_2 D614G 29 34 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. The simplified physical model characterized the dynamics of the SARS-CoV-2 S protein and mutational variants, suggesting the increased population for the D614G mutation. 2021 ACS omega Introduction SARS_CoV_2 D614G 154 159 S 75 76 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. These structures confirmed that D614G eliminates a salt bridge between D614 of one subunit and K854 of the adjacent subunit but can promote ordering of the partly disordered loop (residues 620-640), which can strengthen the intra- and interdomain interactions and enhance the stability of the mutated S protein. 2021 ACS omega Introduction SARS_CoV_2 D614G 32 37 S 301 302 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. These studies advocated the mutation-induced shift to the open states favorable for the S-ACE2 interaction as primary mechanism associated with the increased infectivity of the D614G mutant. 2021 ACS omega Introduction SARS_CoV_2 D614G 177 182 S 88 89 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. This study provides a novel insight into the molecular mechanisms underlying the effect of the D614G mutation by examining the SARS-CoV-2 S protein as an allosteric regulatory machine. 2021 ACS omega Introduction SARS_CoV_2 D614G 95 100 S 138 139 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. While several alternative mechanisms were proposed to explain the experimental data, a consensus view on the mechanism underlying the functional effects and increased infectivity of the S-D614G spike mutant is yet to be established. 2021 ACS omega Introduction SARS_CoV_2 D614G 188 193 S;S 194;186 199;187 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. 3 of the 85 non-B.1.1.7 samples (B.1.258 lineage) were positive for del-HV69/70, but not N501Y, which was confirmed by the TIB MOL reference assays (Table 3 ). 2021 Journal of clinical virology Introduction SARS_CoV_2 N501Y 89 94 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. 50 B1.1.7 lineage samples were classified as positive for N501Y and del-HV69/70. 2021 Journal of clinical virology Introduction SARS_CoV_2 N501Y 58 63 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. Additionally, all samples were tested with a set of commercial assays to confirm the relevant mutations (TIB MOL, VirSNiP Spike N501Y and Del69/70, Berlin, Germany). 2021 Journal of clinical virology Introduction SARS_CoV_2 N501Y 128 133 S 122 127 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. An additional assay was designed (using Beacon designer and PrimerQuest software) and integrated into the multiplex to detect the N501Y SNP. 2021 Journal of clinical virology Introduction SARS_CoV_2 N501Y 130 135 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. Another variant of concern, B.1.351 (501Y.V2) first described in south Africa, are characterized by the same spike-gene mutation, along with E484K and others. 2021 Journal of clinical virology Introduction SARS_CoV_2 E484K 141 146 S 109 114 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. In particular, non-synonymous spike-gene mutations such as the N501Y SNP (single nucleotide polymorphism) may lead to changes in receptor binding properties. 2021 Journal of clinical virology Introduction SARS_CoV_2 N501Y 63 68 S 30 35 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. Limit for successful detection of an N501Y SNP was 105.99 cp/ml (CI: 81.59 - 183.66), indicating that the N501Y SNP-assay is less sensitive than the two diagnostic-grade SARS-CoV-2 assays. 2021 Journal of clinical virology Introduction SARS_CoV_2 N501Y;N501Y 37;106 42;111 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. One was detected as N501Y positive and del-HV69/70 negative (B.1.351). 2021 Journal of clinical virology Introduction SARS_CoV_2 N501Y 20 25 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. All four vaccines aim to generate spike protein-specific antibodies and all have been shown to induce anti-S IgG antibodies with neutralizing activity against the first pandemic SARS-CoV-2 Wuhan Hu-1 variant and the currently circulating D614G variants. 2021 Nature communications Introduction SARS_CoV_2 D614G 238 243 S;S 34;107 39;108 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. The second vaccine dose induces antibodies for efficient neutralization of D614G and B.1.1.7. 2021 Nature communications Introduction SARS_CoV_2 D614G 75 80 34184982 Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. It was through large-scale analysis of SARS-CoV-2 genomes that evidence of a mutation (D614G) in the spike protein was revealed; it is likely that this mutation is responsible for increased transmissibility of the virus. 2021 Microbial genomics Introduction SARS_CoV_2 D614G 87 92 S 101 106 34184982 Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. Our analysis: identified a sublineage associated with six care facilities; found no evidence of reinfection in longitudinal samples; ruled out a nosocomial outbreak; identified 16 lineages in key workers which were not in patients, indicating infection control measures were effective; and found the D614G spike protein mutation which is linked to increased transmissibility dominates the samples and rapidly confirmed relatedness of cases in an outbreak at a food processing facility. 2021 Microbial genomics Introduction SARS_CoV_2 D614G 300 305 S 306 311 34188167 Activation of NF-kappaB and induction of proinflammatory cytokine expressions mediated by ORF7a protein of SARS-CoV-2. According to additional mutation, the clade G can be split into three subclades, clade GH (Q57H variant of ORF3a), clade GR (RG203KR variant of the nucleocapsid protein), and GV (A222V variant of the spike protein). 2021 Scientific reports Introduction SARS_CoV_2 A222V;Q57H 179;91 184;95 N;S;ORF3a 148;200;107 160;205;112 34188167 Activation of NF-kappaB and induction of proinflammatory cytokine expressions mediated by ORF7a protein of SARS-CoV-2. According to the data from the Global Initiative on Sharing All Influenza Data (GISAID; https://www.gisaid.org), four major clades of SARS-CoV-2 have so far been identified and named clade L (prototype virus Wuhan-Hu-1; GenBank accession number NC_045512), clade G (D614G variant of the spike protein), clade V (G251V variant of ORF3a), and clade S (L84S variant of ORF8). 2021 Scientific reports Introduction SARS_CoV_2 D614G;G251V;L84S 266;312;350 271;317;354 S;ORF3a;ORF8;S 287;329;366;347 292;334;370;348 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. Most importantly, LCB1v1.3 protected animals against the currently emerging B.1.1.7 variant and a SARS-CoV-2 strain encoding key spike substitutions, E484K and N501Y, present in both B.1.351 and B.1.1.28 variants of concern. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K;N501Y 150;160 155;165 S 129 134 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. Apart from the primary (amino acid change) and secondary (loop structure) changes observed at the RBM of S protein due to V483A mutation, there are few gains in functions like higher solvent accessibility, tighter binding of the mutant protein to the receptor and aid in antibody escape mechanism that will be discussed in this review. 2021 Future virology Introduction SARS_CoV_2 V483A 122 127 S 105 106 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. In this review, we have singled out one such mutation, the V483A, which lies within the RBM of the RBD. 2021 Future virology Introduction SARS_CoV_2 V483A 59 64 RBD 99 102 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. It is a critical amino acid residue in the RBM region of the spike glycoprotein, where the valine (Val) at position 483 has changed to alanine (Ala) (Figure 2), making the viral genome a unique mutant strain. 2021 Future virology Introduction SARS_CoV_2 V483V 90 120 S 61 79 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. Therefore, the V483A mutation can become one of the virus's favorable mutations and increase the transmission rate. 2021 Future virology Introduction SARS_CoV_2 V483A 15 20 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. This review aims to comprise all currently available information of the V483A mutant type and its characteristics compared with the wild-type strain. 2021 Future virology Introduction SARS_CoV_2 V483A 72 77 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. V483A is a few mutations that can change the protein secondary structure and relative solvent accessibility in the RBM region. 2021 Future virology Introduction SARS_CoV_2 V483A 0 5 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. Additionally, the A.23.1 variant that has been reported as the dominant lineage in Uganda and the B.1.617 family of variants identified in India (not published) acquired the P681R mutation in the same position. 2021 Vaccines Introduction SARS_CoV_2 P681R 174 179 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. It is postulated that the P681H mutation enhances the transmissibility of the virus by facilitating a conformational change in the S protein following protease activity at the cell membrane. 2021 Vaccines Introduction SARS_CoV_2 P681H 26 31 Membrane;S 181;131 189;132 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. Mutations in the SARS-CoV-2 genome affecting the S protein have emerged in numerous differentially-reported variants, such as the N501Y mutation that is shared by the currently known VOCs, B.1.1.7, B.1.351, and P.1, and which increase the affinity of the S protein to its receptor binding domain (RBD). 2021 Vaccines Introduction SARS_CoV_2 N501Y 130 135 RBD;RBD;S;S 272;297;49;255 295;300;50;256 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. The P681H mutation was observed as early as March 2020 in samples worldwide, such as in Nigeria, Hawaii, and recently in three independent variants in New York, and also characterizes the globally spreading B.1.1.7 VOC. 2021 Vaccines Introduction SARS_CoV_2 P681H 4 9 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. This B.1.1.50 + P681H variant was identified in clinical samples in Israel between November 2020 and January 2021, whereas the P681H mutation had already been identified in Israel via sequencing of SARS-CoV-2 positive sewage samples in October 2020. 2021 Vaccines Introduction SARS_CoV_2 P681H;P681H 16;127 21;132 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. This variant is characterized by the non-synonymous S protein mutation P681H and four additional synonymous mutations. 2021 Vaccines Introduction SARS_CoV_2 P681H 71 76 S 52 53 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. Besides the D614G mutation, the B.1.1.7 variant contains six non-synonymous mutations and three deleted amino acids in the spike (S) protein (Figure 1A). 2021 Viruses Introduction SARS_CoV_2 D614G 12 17 S;S 123;130 128;131 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. The major changes are the mutation N501Y in the receptor-binding domain (RBD); the deletion 69-70 which may increase transmissibility and produces a false negative in certain RT-PCR-based diagnostic assays; and the mutation P681H, next to the furin cleavage site, that could impact antigenicity and enhance viral infectivity. 2021 Viruses Introduction SARS_CoV_2 N501Y;P681H 35;224 40;229 RBD 73 76 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. As such, our results gave an insight into the potential significance of administering RDV to patients carrying the SARS-CoV-2 P323L-RdRp mutation; thus, setting the path for initiating functional studies and future personalised medicine. 2021 Biomolecules Introduction SARS_CoV_2 P323L 126 131 RdRP 132 136 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Especially, P323L is the highest mutation in the US (5918) and the second highest mutation in the world (22018). 2021 Biomolecules Introduction SARS_CoV_2 P323L 12 17 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. In addition, we compared the binding free energies of RDV to the RdRp-wild type (WT) and mutants A97V and P323L. 2021 Biomolecules Introduction SARS_CoV_2 A97V;P323L 97;106 101;111 RdRP 65 69 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. In addition, when searching the GISAID database mutational statistics, which uses hCoV-19/Wuhan/WIV04/2019 EPI_ISL_402124 as a reference strain (COVserver tool), P323L presented a high percentage in Europe (61.7% n = 33480). 2021 Biomolecules Introduction SARS_CoV_2 P323L 162 167 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Moreover, the two most frequent mutations were A97V (14408C > T) and P323L (13730C > T) and were found predominantly in Europe, North America, and, more recently, in India. 2021 Biomolecules Introduction SARS_CoV_2 A97V;P323L;C13730T;C14408T 47;69;76;53 51;74;86;63 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Out of the top five, P323L (13730C > T), and A97V (14408C > T) presented amino acid mutations that could affect the structure of the protein. 2021 Biomolecules Introduction SARS_CoV_2 A97V;P323L;C13730T;C14408T 45;21;28;51 49;26;38;61 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. To elucidate the molecular mechanisms caused by RdRp mutations on the binding of RDV, we applied atomistic molecular dynamic (MD) simulations to predict the effect of A97V and P323L mutations on the stability and flexibility of RdRp in comparison to WT-RdRp in apo and complex with RDV. 2021 Biomolecules Introduction SARS_CoV_2 A97V;P323L 167;176 171;181 RdRP;RdRP;RdRP 48;228;253 52;232;257 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Whereby, 607 mutations were observed on the RdRp gene, with the top five with the highest frequency mutations on the RdRp gene being P323L (10925), Y455Y (1242), N628N (405), A97V (263), and Y32Y (121). 2021 Biomolecules Introduction SARS_CoV_2 A97V;N628N;P323L;Y32Y;Y455Y 175;162;133;191;148 179;167;138;195;153 RdRP;RdRP 44;117 48;121 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? A combination of del H69/V70 and N501Y was shown to increase infectivity in vitro. 2021 Viruses Introduction SARS_CoV_2 N501Y 33 38 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? A combination of E484K with various NTD mutations (particularly deletions) might prove to be even more effective in immune evasion, which is of the most significance in cases of both Beta variant and B1.1.7 with E484K. 2021 Viruses Introduction SARS_CoV_2 E484K;E484K 17;212 22;217 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? A similar change at position 478 (T478I) was previously selected in vitro and shown to exhibit reduced neutralization by monoclonal antibodies and human convalescent sera. 2021 Viruses Introduction SARS_CoV_2 T478I 34 39 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? All three sublineages of B.1.617 display P681R adjacent to the furin cleavage site and have enhanced S cleavage by furin, which is hypothesized to be enhancing transmissibility and pathogenicity. 2021 Viruses Introduction SARS_CoV_2 P681R 41 46 S 101 102 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? Another was acknowledged as VOC in the UK and by ECDC:B.1.1.7 with E484K and two others by the US:Epsilon or B.1.427/29. 2021 Viruses Introduction SARS_CoV_2 E484K 67 72 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? Five mutations are located within NTD (L18F, T20N, P26S, D138Y, R190S), three in RBD (K417T, E484K, N501Y), two in the C-terminal domain of S1 and near the furin cleavage site (D614G, H655Y), and one in S2 (T1027I) (Figure 3). 2021 Viruses Introduction SARS_CoV_2 D138Y;E484K;H655Y;N501Y;P26S;R190S;T20N;D614G;K417T;L18F;T1027I 57;93;184;100;51;64;45;177;86;39;207 62;98;189;105;55;69;49;182;91;43;213 RBD 81 84 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? However, a combination of K417N and N501Y was shown to enhance the binding with ACE2 and reduce binding with antibodies. 2021 Viruses Introduction SARS_CoV_2 K417N;N501Y 26;36 31;41 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? In addition, the combination of L452R and E484Q was not shown to have an additive effect; rather, the loss of sensitivity was similar to that observed with each mutation individually. 2021 Viruses Introduction SARS_CoV_2 E484Q;L452R 42;32 47;37 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? In February 2021, Public Health England (PHE) recognized B.1.1.7 with E484K mutation as a new VOC (VOC-202102/02), and it has since been identified in the US. 2021 Viruses Introduction SARS_CoV_2 E484K 70 75 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? In January 2021, the emergence of a novel variant in California carrying an L452R mutation in the RBD was reported. 2021 Viruses Introduction SARS_CoV_2 L452R 76 81 RBD 98 101 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? It enhances the binding affinity of N501Y for ACE2 still further but has been associated with immune escape from both mAbs and polyclonal sera as well. 2021 Viruses Introduction SARS_CoV_2 N501Y 36 41 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? It is characterized by spike mutations T19R, G142D, Delta157-158, L452R, T478K, D614G, P681R, and D950N (Figure 3). 2021 Viruses Introduction SARS_CoV_2 D614G;D950N;G142D;L452R;P681R;T19R;T478K 80;98;45;66;87;39;73 85;103;50;71;92;43;78 S 23 28 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? K417N was shown to be crucial to viral escape, effectively abrogating neutralization by some of the most common and potent neutralizing antibodies to SARS-CoV-2. 2021 Viruses Introduction SARS_CoV_2 K417N 0 5 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? Monoclonal antibodies were shown to lose almost 50% of neutralizing activity against B.1.1.7 carrying E484K. 2021 Viruses Introduction SARS_CoV_2 E484K 102 107 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? Mutation E484K, which emerged independently in over 50 lineages, also corresponds with improved binding to ACE2. 2021 Viruses Introduction SARS_CoV_2 E484K 9 14 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? N501Y probably does not impair neutralization on its own but rather in combination with other two, which were found to partially compromise neutralization generated by previous infection or vaccination. 2021 Viruses Introduction SARS_CoV_2 N501Y 0 5 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? Since then, the strain harboring D614G has become the dominant pandemic variant in most countries, possibly because the mutation enabled a relative fitness advantage to the original Wuhan strain and enhanced infectivity. 2021 Viruses Introduction SARS_CoV_2 D614G 33 38 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The B1.1.7 variant bearing the E484K mutation emerged and was recognized as a variant of concern in the UK and Europe, since it appears to be responsible for a significant additional loss of neutralization capacity of monoclonal and polyclonal antibodies. 2021 Viruses Introduction SARS_CoV_2 E484K 31 36 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The E484Q was found to have slightly milder impact but still corresponding to the effect of E484K, which is 10-fold reduction in the neutralization by sera of vaccine recipients. 2021 Viruses Introduction SARS_CoV_2 E484K;E484Q 92;4 97;9 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The earliest spike protein mutation D614G of SARS-CoV-2 in Europe was identified in January 2020 in Germany. 2021 Viruses Introduction SARS_CoV_2 D614G 36 41 S 13 18 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The extensively studied D614G was found to increase the ability of RBD to shift to the up position, which is necessary for interaction with ACE2. 2021 Viruses Introduction SARS_CoV_2 D614G 24 29 RBD 67 70 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The first variant Alpha or B.1.1.7 that raised global concerns about increased transmissibility and potential immune evasion harbors seven missense mutations (N501Y, A570D, D614G, P681H, T716I, S982A, D1118H) and three deletions in spike (69/70del and 144del) (Figure 3). 2021 Viruses Introduction SARS_CoV_2 A570D;D1118H;D614G;P681H;S982A;T716I;N501Y 166;201;173;180;194;187;159 171;207;178;185;199;192;164 S 232 237 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The impact on the immune escape capacity of three sublineages of B.1.617 is expected, owing to RBD mutations L452R, T478K, and E484Q and their combination with NTD mutations and deletions, particularly in the case of B.1.617.2. 2021 Viruses Introduction SARS_CoV_2 E484Q;L452R;T478K 127;109;116 132;114;121 RBD 95 98 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The other two sublineages have a similar mutational profile: B.1.617.1 is defined by the spike amino acid changes G142D, E154K, L452R, E484Q, D614G, P681R, and Q1071H, and B.1.617.3 is defined by T19R, L452R, E484Q, D614G, P681R, and D950N. 2021 Viruses Introduction SARS_CoV_2 D614G;D614G;D950N;E154K;E484Q;E484Q;G142D;L452R;L452R;P681R;P681R;Q1071H;T19R 142;216;234;121;135;209;114;128;202;149;223;160;196 147;221;239;126;140;214;119;133;207;154;228;166;200 S 89 94 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The P681H change is adjacent to the furin cleavage site and could potentially have an effect on S1/S2 cleavage and therefore on cell entry and infectivity. 2021 Viruses Introduction SARS_CoV_2 P681H 4 9 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The part of the diminished neutralizing effect of antibodies against the B.1.1.7 variant can be attributed to the only RBM mutation:N501Y. 2021 Viruses Introduction SARS_CoV_2 N501Y 132 137 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The presence of RBD mutations L452R, E484Q, and D614G in the C-terminal domain of S1 may result in the higher transmissibility of these sublineages due to their known impact on ACE2 binding and conformational changes important for ACE2 binding. 2021 Viruses Introduction SARS_CoV_2 D614G;E484Q;L452R 48;37;30 53;42;35 RBD 16 19 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The RBD mutation L452R, shared by these lineages, is not located in the part that directly interacts with ACE2, but it is speculated that it may cause structural changes in the region that promote the interaction between the spike protein and its ACE2 receptor. 2021 Viruses Introduction SARS_CoV_2 L452R 17 22 S;RBD 225;4 230;7 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The residue 484 can mutate into a diversity of different amino acids (E484A, E484G, E448D, and E484K) under the pressure of SARS-CoV-2 convalescent sera and exhibits resistance. 2021 Viruses Introduction SARS_CoV_2 E448D;E484G;E484K;E484A 84;77;95;70 89;82;100;75 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The resistance to antibody neutralization of the B.1.351 variant is mainly ascribed to three mutations within RBD (K417N, E484K, N501Y). 2021 Viruses Introduction SARS_CoV_2 E484K;N501Y;K417N 122;129;115 127;134;120 RBD 110 113 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The similar mechanism of RBD structural change due to L452R is offered in explanation of the reduced neutralization capacity of antibodies. 2021 Viruses Introduction SARS_CoV_2 L452R 54 59 RBD 25 28 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The three deleted residues are located within NTD, only one mutation (N501Y) is within RBM, three are displayed in the C-terminal domain (CTD) of S1, and three are displayed within S2. 2021 Viruses Introduction SARS_CoV_2 N501Y 70 75 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? The variant of the greatest concern in regard to immune escape, Beta or B.1.351, contains seven mutations (D80A, D215G, K417N, E484K, N501Y, D614G, A701V) and three deletions (241/242/243del) in the spike protein (Figure 3). 2021 Viruses Introduction SARS_CoV_2 A701V;D215G;D614G;E484K;K417N;N501Y;D80A 148;113;141;127;120;134;107 153;118;146;132;125;139;111 S 199 204 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? This resulted in the increased infectivity and transmissibility observed for the D614G variant relative to the original SARS-CoV-2 strains. 2021 Viruses Introduction SARS_CoV_2 D614G 81 86 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? This variant (Epsilon) comprises two separate lineages B.1.427 and B.1.429, the first carrying two spike mutations (L452R, D614G) and the second carrying four (S13I, W152C, L452R, D614G). 2021 Viruses Introduction SARS_CoV_2 D614G;D614G;L452R;W152C;L452R;S13I 123;180;173;166;116;160 128;185;178;171;121;164 S 99 104 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? Thus, the infectivity of pseudoviruses carrying L452R was shown to be higher than of the D614G variant but slightly reduced compared to that of N501Y variants. 2021 Viruses Introduction SARS_CoV_2 D614G;L452R;N501Y 89;48;144 94;53;149 34206453 Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? Two mutations (D80A, D215G) and three deleted residues are in the N-terminal domain of S1, one (A701V) is in loop 2 of S2 and 3 are at key residues in the RBD (K417N, E484K, N501Y). 2021 Viruses Introduction SARS_CoV_2 D215G;E484K;N501Y;A701V;D80A;K417N 21;167;174;96;15;160 26;172;179;101;19;165 RBD;N 155;66 158;67 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. Among these mutations, some are linked to the immune system, particularly when present in the RBD, such as E484K and S477N. 2021 Viruses Introduction SARS_CoV_2 E484K;S477N 107;117 112;122 RBD 94 97 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. analyzed the impact of the neutralization of several mAbs on a panel of variants, including an authentic chimeric variant named Wash SA B.13 51, which contains the 20H/501Y.V2 Spike gene with other additional mutations (D80A, 242-244 del, R246I, K417N, E484K, N501Y, D614G and A701V), in addition to a panel of isogenic recombinant mutant variants (69-70 Del, K417N, E484K, N501Y, and/or D614G). 2021 Viruses Introduction SARS_CoV_2 A701V;D614G;D614G;E484K;E484K;K417N;K417N;N501Y;N501Y;R246I;D80A 277;267;388;253;367;246;360;260;374;239;220 282;272;393;258;372;251;365;265;379;244;224 S 176 181 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. Based on Spike sequences available on April 06, 2020, the prevalence of the D614G variant has been reported to be significantly correlated with the COVID-19 fatality rate in different countries (Table 1). 2021 Viruses Introduction SARS_CoV_2 D614G 76 81 S 9 14 COVID-19 148 156 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. D614G Variant. 2021 Viruses Introduction SARS_CoV_2 D614G 0 5 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. However, an absence of neutralization reduction was observed in other monoclonal antibodies in the case of Wash SA-B.1351 compared to the E484K/N501Y/D614G mutants, which showed a reduction in neutralization. 2021 Viruses Introduction SARS_CoV_2 E484K;D614G;N501Y 138;150;144 143;155;149 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. However, the presence of L452R could be involved in the decrease in antibody activity, and the E484Q could affect vaccine efficiency. 2021 Viruses Introduction SARS_CoV_2 E484Q;L452R 95;25 100;30 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. In addition to Spike mutations, the ORF8 Q27stop mutation truncates the ORF8 protein and thus allows other downstream mutations to accumulate. 2021 Viruses Introduction SARS_CoV_2 Q27X 41 48 S;ORF8;ORF8 15;36;72 20;40;76 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. In January 2021, the British health authorities reported 11 cases that were infected with a 20I/501Y.V1 variant that had acquired the E484K mutation also present in the 20H/501Y.V2 and 20J/501Y.V3 variants. 2021 Viruses Introduction SARS_CoV_2 E484K 134 139 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. It carries E484K, D614G, and V1176F on Spike. 2021 Viruses Introduction SARS_CoV_2 D614G;E484K;V1176F 18;11;29 23;16;35 S 39 44 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. It carries mutations in NSPs and on some ORF proteins, in addition to two key mutations on RBD: L452R common to the CAL.20C variant and E484Q close to the E484K observed in some VOCs. 2021 Viruses Introduction SARS_CoV_2 E484K;E484Q;L452R 155;136;96 160;141;101 RBD 91 94 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. It carries Spike mutations including E484K, N501Y, D614G, P681H/R, and V1176F. 2021 Viruses Introduction SARS_CoV_2 D614G;E484K;N501Y;P681H;P681R;V1176F 51;37;44;58;58;71 56;42;49;65;65;77 S 11 16 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. It carries the N501Y mutation in the receptor-binding domain (RBD), and other mutations including the 69/70 deletion, which lead to a conformational change in the Spike protein and the P681H near the site of S1/S2 furin cleavage. 2021 Viruses Introduction SARS_CoV_2 N501Y;P681H 15;185 20;190 S;RBD 163;62 168;65 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. It derives from the B line (B.1.429 and B.1.427) and carries three mutations on the Spike: S13I, W152C, and, most notably, L452R, located in the RBD and potentially involved in mAbs neutralization escape (Table 1). 2021 Viruses Introduction SARS_CoV_2 L452R;S13I;W152C 123;91;97 128;95;102 S;RBD 84;145 89;148 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. It has also been shown that mutations in RNA-dependent RNA polymerase (RdRp), particularly the P323 mutation in Nsp12 initially observed in the D614G variant, accelerate RdRp, thus affecting its fidelity and promoting mutations in the viral structural proteins. 2021 Viruses Introduction SARS_CoV_2 D614G 144 149 RdRp;Nsp12;RdRP;RdRP 41;112;71;170 69;117;75;174 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. It is characterized by 17 non-synonymous mutations, including at least 3 of the 8 present in Spike that have a biological importance: (1) N501Y, which has a role in enhancing the binding affinity to ACE2R; (2) the P681H mutation, which is located near the furin cleavage site and absent in other group B coronaviruses, and is considered to be the key to SARS-CoV-2 pathogenesis because viral entry requires the processing of the S protein by cellular proteases, which are responsible for Spike cleavage at the S1/S2 site (the furin cleavage site); and (3) the 69/70 deletion, which is located in the N terminal domain (NTD) of Spike, and could promote the viral transmissibility and affect the performance of certain RT-PCR diagnostic tests, leading to a false negative result for the detection of the S gene (e.g., Thermo Fisher TaqPath COVID-19). 2021 Viruses Introduction SARS_CoV_2 N501Y;P681H 138;214 143;219 S;S;S;N;S;S 93;488;627;600;429;802 98;493;632;601;430;803 COVID-19 838 846 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. It is characterized by an insertion of three amino acids (Ins214TDR) and four mutations in the Spike gene: Q414K, N450K, D614G, and T716I. 2021 Viruses Introduction SARS_CoV_2 D614G;N450K;Q414K;T716I 121;114;107;132 126;119;112;137 S 95 100 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. It is characterized by four key mutations on Spike: L18F on N-Terminal-Domain (NTD); L452R on RBD, which could be involved in antibody neutralization escape and viral fitness improvement; N501Y (in common with 20I/501Y.V1); and H655Y (in common with 20J/501Y.V3), which could be involved in the Spike modulation and immune escape. 2021 Viruses Introduction SARS_CoV_2 H655Y;L18F;L452R;N501Y 228;52;85;188 233;56;90;193 S;S;RBD;N 45;295;94;60 50;300;97;61 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. It is characterized by nine mutations, and one deletion in the Spike, in particular H655Y, the 144 deletion (in common with 20I/501Y.V1), D215G (in common with 20H/501Y.V2), and V483A, near to the E484K residue in 20J/501Y.V3. 2021 Viruses Introduction SARS_CoV_2 D215G;E484K;H655Y;V483A 138;197;84;178 143;202;89;183 S 63 68 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. It is characterized by nine mutations, and one deletion in the Spike; in particular, these include H655Y, which is also present in the 20J/501Y.V3 and 19B/501Y variants; the Y144 deletion common with 20I/501Y.V1; the D215G mutation in common with the 20H/501Y.V2 variant; and the V483A close to the E484 residue mutated in the 20J/501Y.V3 variant (E484K), which may be involved in post-vaccine or post-infection immune escape or a decrease in the efficacy of monoclonal antibodies. 2021 Viruses Introduction SARS_CoV_2 D215G;H655Y;V483A;E484K 217;99;280;348 222;104;285;353 S 63 68 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. It is characterized by the presence of 18 substitutions, among which 7 or 8 are located on the Spike protein, including L18F in NTD and L452R in RBD, which are also present in 20J/501Y.V3, 20H/501Y.V2, and CAL.20C variants, respectively. 2021 Viruses Introduction SARS_CoV_2 L18F;L452R 120;136 124;141 S;RBD 95;145 100;148 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. It is characterized by three main mutations in the SARS-CoV-2 Spike protein: E484K could be involved in a structural modification of the Spike end, thus allowing a potential escape from antibody neutralization or vaccination targeting the Spike protein, and the K417N and N501Y mutations may be involved in enhancing Spike binding to ACE2R. 2021 Viruses Introduction SARS_CoV_2 E484K;K417N;N501Y 77;262;272 82;267;277 S;S;S;S 62;137;239;317 67;142;244;322 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. It presents mutations in common with the 20H/501Y.V2 variant located at the RBM of the S protein: N501Y and K417T, which may be involved in enhancing transmission, and E484K, which may be related to a slight improvement in receptor-binding affinity and immune escape (Table 1). 2021 Viruses Introduction SARS_CoV_2 E484K;K417T;N501Y 168;108;98 173;113;103 S 87 88 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. Like H665Y, the Q677H mutation is located near the furin cleavage site and may be involved in rapid virus replication, in addition to RBD-ACE2R binding. 2021 Viruses Introduction SARS_CoV_2 H665Y;Q677H 5;16 10;21 RBD 134 137 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. Moreover, certain mutations observed in emergent variants have been associated with receptor-binding improvement on Spike (Figure 4), such as theS477N mutation, observed in the 20A.(EU2) and the 20C/477N variants, and the H655Y mutation observed in 20J/501Y.V3, 19B/501Y, or 20C/655Y variants. 2021 Viruses Introduction SARS_CoV_2 H655Y 222 227 S 116 121 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. One branch has the S477N mutation (8.6% of B.1.526 viruses), which is found near the binding site of several antibodies and implicated in the enhancement of Spike-ACE2R interaction. 2021 Viruses Introduction SARS_CoV_2 S477N 19 24 S 157 162 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. Relatively early during the COVID-19 pandemic, in late January 2020, the D614G mutant was correlated with the viral fitness improvement. 2021 Viruses Introduction SARS_CoV_2 D614G 73 78 COVID-19 28 36 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. Some mutations could affect the activity of vaccines, leading to the generation of less effective post-vaccine antibodies against the mutated target Spike protein, such as the E484K substitution, which is involved in the vaccine immunity escape and is present in 20H/501Y.V2 and 20J/501Y.V3 variants. 2021 Viruses Introduction SARS_CoV_2 E484K 176 181 S 149 154 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. Studies have shown that B.1.351, P.1 lines, and B.1.1.7 with the E484K mutation are a source of concern in terms of vaccination, because of their potential resistance to sera from convalescents, immune sera from animals, and human sera from vaccinated patients (Pfizer-BioNTech, Astrazeneca, Johnson & Johnson, and Novavax vaccines) (Figure 2). 2021 Viruses Introduction SARS_CoV_2 E484K 65 70 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. The 20J/501Y.V3 variant and other variants containing the E484K mutation may have similar results (Figure 2). 2021 Viruses Introduction SARS_CoV_2 E484K 58 63 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. The 20J/501Y.V3 variant, in addition to other variants containing the E484K mutation, may have similar results as the 20H/501.V2 variant (Figure 2). 2021 Viruses Introduction SARS_CoV_2 E484K 70 75 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. The acquisition of the E484K mutation is a source of concern because of its involvement in vaccine and mAbs immune evasion (Figure 2). 2021 Viruses Introduction SARS_CoV_2 E484K 23 28 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. The combination of S309 with S2E12 showed reduced activity (almost ten-fold) against the E484K/N501Y/D614G strain, although it retained good activity against Wash SA-B.1.351 strain, thus leading to the suggestion that additional mutations, such as K417N, compensate for the loss of neutralization activity because of the E484K mutation. 2021 Viruses Introduction SARS_CoV_2 E484K;E484K;K417N;D614G;N501Y 89;321;248;101;95 94;326;253;106;100 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. The D614G mutation was first detected in late January in Germany and China. 2021 Viruses Introduction SARS_CoV_2 D614G 4 9 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. The first relevant event in this context was the occurrence of the D614G mutation in the Spike gene. 2021 Viruses Introduction SARS_CoV_2 D614G 67 72 S 89 94 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. The first two recombinations did not show any impact on the neutralization activity of three variants (20I/501Y.V1, D614G, and 20H/501Y.V2) (Figure 2), except that each of these potent combinations had a component that lost some neutralization activity, thus showing that one compensates for the loss of the activity of the other. 2021 Viruses Introduction SARS_CoV_2 D614G 116 121 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. The H665Y mutation observed in 20J/501Y.V3 was also identified in this variant; it can modulate the stability, immunogenicity, and interaction of Spike with ACE2R. 2021 Viruses Introduction SARS_CoV_2 H665Y 4 9 S 146 151 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. The presence of this double mutant (E484Q-L452R) could also promote transmission. 2021 Viruses Introduction SARS_CoV_2 E484Q;L452R 36;42 41;47 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. The second branch carries E484K common to 20H/501Y.V2 and the 20J/501Y.V3, and is present in 74% of B.1.526 viruses. 2021 Viruses Introduction SARS_CoV_2 E484K 26 31 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. The slight decrease in the neutralizing activity was linked to the S982A mutation located in the S2 domain of the Spike protein. 2021 Viruses Introduction SARS_CoV_2 S982A 67 72 S 114 119 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. The variant also carries N501Y in common with the UK strain or N501T common with the Mink strain. 2021 Viruses Introduction SARS_CoV_2 N501T;N501Y 63;25 68;30 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. Their study showed that the antigenic impact of the N501Y mutation was limited to a few mAbs targeting the internal or external side of the RBD (the 910-30 antibody and the S309 antibody, respectively). 2021 Viruses Introduction SARS_CoV_2 N501Y 52 57 RBD 140 143 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. They share mutations with the 20I/501Y.V1 variant, and particularly N501Y, but do not contain the 69/70 deletion. 2021 Viruses Introduction SARS_CoV_2 N501Y 68 73 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. They showed a decrease in neutralization activity by certain mAbs targeting RBM and NTD on the Spike protein, or even a loss of activity (half-maximal effective concentration (EC50) < 10,000 ng/mL) in the case of the Wash SA B.13 51 strain and the recombinant mutant with the E484K and N501Y mutations. 2021 Viruses Introduction SARS_CoV_2 E484K;N501Y 276;286 281;291 S 95 100 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. This is associated with the presence of a K417N compensatory mutation located at the extremity of RBM in Wash SA-B.1351. 2021 Viruses Introduction SARS_CoV_2 K417N 42 47 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. This lineage has increased rapidly and carries Spike mutations including: D253G reported as an antibody escape mutation against the N-terminal domain; D614G (in common with 20I/501Y.V1, 20H/501Y.V2, and 20J/501Y.V3); and A701V, in common with 20H/501Y.V2. 2021 Viruses Introduction SARS_CoV_2 A701V;D253G;D614G 221;74;151 226;79;156 S;N 47;132 52;133 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. This resistance is largely linked to the E484K mutation (Figure 2). 2021 Viruses Introduction SARS_CoV_2 E484K 41 46 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. This resistance is linked to the E484K mutation (Figure 2), which allowed the authors to suggest its location in an immunodominant epitope recognized by vaccines. 2021 Viruses Introduction SARS_CoV_2 E484K 33 38 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. This suggests a potential role of the Q27stop mutation in compensating for the reduction in vaccine or antibody activity, probably caused by certain mutations of the 20I/501Y.V1 variant. 2021 Viruses Introduction SARS_CoV_2 Q27X 38 45 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. This variant carries a nucleotide mutation at position 22920, leading to the Y453F substitution on the RBM of the Spike protein. 2021 Viruses Introduction SARS_CoV_2 Y453F 77 82 S 114 119 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. This variant shares the D614G and N501Y mutations with the 20I/501Y.V1 variant. 2021 Viruses Introduction SARS_CoV_2 D614G;N501Y 24;34 29;39 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. Two cases with S477N have been detected in Auvergne-Rhone-Alpes in France. 2021 Viruses Introduction SARS_CoV_2 S477N 15 20 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. By March 2020, the D614G substitution, along with other accompanying mutations, started to sporadically appear, and by June 2020, it was prevalent enough to be present in over 74% of all published sequences. 2021 Viruses Introduction SARS_CoV_2 D614G 19 24 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. Furthermore, mutations/deletions in the S-protein, such as L18F, DeltaH69/V70, S898F, DeltaY144, S162G, A222V, N439K, N501Y, A570D, D614G, P681H, S982A and D1118H, were discovered in the lineages identified in this study and have phenotypic and antigenic implications that may impact the spread of the virus, as well as the efficiency of current vaccines and diagnostic tests. 2021 Viruses Introduction SARS_CoV_2 A222V;A570D;D1118H;D614G;DeltaY144;L18F;N439K;N501Y;P681H;S162G;S898F;S982A 104;125;156;132;86;59;111;118;139;97;79;146 109;130;162;137;95;63;116;123;144;102;84;151 S 40 41 34208912 Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. Figure 1 summarizes currently circulating SARS-CoV-2 variants and their respective mutations within the spike RBD, which include the following: N501Y in the UK, SA, and BR-P.1 variants; E484K/Q in the SA, BR P.1, BR P.2, NY, and IN variants; K417N/T in the SA and BR P.1 variants; L452R in the CA and IN variants; S477N in some NY variants; and Y453F in the Denmark mink variant. 2021 Diagnostics (Basel, Switzerland) Introduction SARS_CoV_2 E484K;E484Q;K417N;K417T;L452R;N501Y;S477N;Y453F 186;186;242;242;281;144;314;345 193;193;249;249;286;149;319;350 S;RBD 104;110 109;113 34208912 Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. was able to demonstrate that the RBD containing the E484K mutation escapes the LY-CoV555 antibody, while the RBD containing the K417N/T mutations escapes the LY-CoV016 antibody. 2021 Diagnostics (Basel, Switzerland) Introduction SARS_CoV_2 E484K;K417N;K417T 52;128;128 57;135;135 RBD;RBD 33;109 36;112 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. The P323L mutation of the RdRp has received less attention; however, it has been suggested that this mutation might alter viral proofreading and thereby lead to an increased down-stream mutation rate. 2021 Scientific reports Introduction SARS_CoV_2 P323L 4 9 RdRP 26 30 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. The S-protein D614G mutation has received attention given that it could potentially alter the viral attachment, fusogenicity and/or immunogenicity. 2021 Scientific reports Introduction SARS_CoV_2 D614G 14 19 S 4 5 34211709 The emerging SARS-CoV-2 variants of concern. Currently, the N501Y variant has been detected in over 40 countries outside of the UK. 2021 Therapeutic advances in infectious disease Introduction SARS_CoV_2 N501Y 15 20 34211709 The emerging SARS-CoV-2 variants of concern. The 501Y.V2 variant has been detected in many countries outside of South Africa and is characterized by mutations in the S protein, including residues in the RBD:K417N, E484K, and N501Y. 2021 Therapeutic advances in infectious disease Introduction SARS_CoV_2 E484K;N501Y;K417N 169;180;162 174;185;167 RBD;S 158;121 161;122 34211709 The emerging SARS-CoV-2 variants of concern. This N501Y mutation became a growing concern due to the virus being able to adhere to the ACE2 receptor more strongly. 2021 Therapeutic advances in infectious disease Introduction SARS_CoV_2 N501Y 5 10 34211709 The emerging SARS-CoV-2 variants of concern. This strain had a similar mechanism of action to the N501Y in the UK. 2021 Therapeutic advances in infectious disease Introduction SARS_CoV_2 N501Y 53 58 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Strikingly, the E484D substitution within the receptor-binding domain (RBD) of S is required for H522 infection. 2021 Cell reports Introduction SARS_CoV_2 E484D 16 21 RBD;S 71;79 74;80 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. 20 J/501Y.V3) emerged in Brazil, contains mutations K417T, E484K and N501Y in the RBD with evidence to affect transmissibility and antigenic profile. 2021 Virology Introduction SARS_CoV_2 E484K;K417T;N501Y 59;52;69 64;57;74 RBD 82 85 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. 20H/501Y.V2) was identified in Nelson Mandela Bay, South Africa, with multiple S protein mutations, including K417N, E484K and N501Y. 2021 Virology Introduction SARS_CoV_2 E484K;K417N;N501Y 117;110;127 122;115;132 S 79 80 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. A variant named Delta plus or AY.1 has been identified in India with the point mutation K417N. 2021 Virology Introduction SARS_CoV_2 K417N 88 93 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. All these SARS-CoV-2 VOC carry a common mutation N501Y in the receptor binding domain (RBD) of the S protein. 2021 Virology Introduction SARS_CoV_2 N501Y 49 54 RBD;RBD;S 62;87;99 85;90;100 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Among all, the most common clade identified was the D614G variant in the spike (S) protein. 2021 Virology Introduction SARS_CoV_2 D614G 52 57 S;S 73;80 78;81 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Later, six major clades (basal, D614G, L84S, L3606F, D448del and G392D) and 14 subclades were identified by analyzing genome variants of SARS-CoV-2 from all over the world. 2021 Virology Introduction SARS_CoV_2 D448del;D614G;G392D;L3606F;L84S 53;32;65;45;39 60;37;70;51;43 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The lineage is B.1.617.2 (Delta) with mutations, L452R, T478K, D614G and P681R in the S protein. 2021 Virology Introduction SARS_CoV_2 D614G;L452R;P681R;T478K 63;49;73;56 68;54;78;61 S 86 87 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. VOC, 202012/01) with multiple S protein mutations (deletion 69-70, deletion 144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H) spread rapidly across South East England and London. 2021 Virology Introduction SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 88;123;95;81;102;116;109 93;129;100;86;107;121;114 S 30 31 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. As the recent SARS-CoV-2 variants contain a number of different mutations, we selected the five most frequent natural variants from the UK for further study, which included D614G+L18F+A222V, D614G+A222V, D614G+S477N, D614G+69-70del+N439K, and the VOC-202012/01 strain ( Figure 1B ). 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G;D614G;D614G;D614G;A222V;A222V;L18F;N439K;S477N 173;191;204;217;184;197;179;232;210 178;196;209;222;189;202;183;237;215 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. For example, D614G rapidly became the dominant strain, cluster 5 was transmitted between humans and mink, the 501Y.V1(VOC-202012/01, B.1.1.7) variant spread rapidly in the United Kingdom, the 501Y.V2(VOC-202012/01, B.1.351) variant appeared in South Africa, the 501Y.V3(P1, B.1.1.28.1) variant appeared in Brazil, and the COH.20G/677H variant appeared in the USA. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 13 18 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Neutralization activity was compared between the variants and the reference strain D614G. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 83 88 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Since December 2020, the VOC-202012/01 (VOC-202012/01 variant, including multiple mutations 69-70del, 144/145del, N501Y, A570D, P681H, T716I, S982A, and D1118H) has been increasing rapidly. 2021 Frontiers in immunology Introduction SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;T716I 121;153;114;128;142;135 126;159;119;133;147;140 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. The most common mutations were D614G, A222V, L18F, and S477N. 2021 Frontiers in immunology Introduction SARS_CoV_2 A222V;D614G;L18F;S477N 38;31;45;55 43;36;49;60 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. We constructed pseudoviruses corresponding to the five variants and 12 single deconvolution mutants of the variants in the D614G genetic background using the VSV vector system. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 123 128 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. We found that the D614G mutation increased the infectivity of SARS-CoV-2, but its antigenicity did not change. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 18 23 34220870 Declining Levels of Neutralizing Antibodies Against SARS-CoV-2 in Convalescent COVID-19 Patients One Year Post Symptom Onset. In particular the amino acid exchange E484K in the S protein. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K 38 43 S 51 52 34222046 SARS-CoV-2: Origin, Evolution, and Targeting Inhibition. As for the A23403G, it encodes the mutant D614G in Spike protein. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 A23403G;D614G 11;42 18;47 S 51 56 34222046 SARS-CoV-2: Origin, Evolution, and Targeting Inhibition. Because mutant D614G has association with a lower RT-PCR cycle threshold among patients, the upper respiratory tract has high viral load. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G 15 20 34222046 SARS-CoV-2: Origin, Evolution, and Targeting Inhibition. Besides, the ratio of the open conformations of mutant D614G increased up to 58% and is in sharp contrast in the ancestral SARS-CoV-2 virus, in which the ratio of RBDs in the open conformation is only 18%. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G 55 60 RBD 163 167 34222046 SARS-CoV-2: Origin, Evolution, and Targeting Inhibition. Compared with the virus strain provided by Wuhan, Spike mutant D614G is caused by the 23,403nucleotide mutation of SARS-CoV-2. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G 63 68 S 50 55 34222046 SARS-CoV-2: Origin, Evolution, and Targeting Inhibition. Hamsters infected with D614G have higher viral titers in the trachea and nasal wash than those in the lungs. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G 23 28 34222046 SARS-CoV-2: Origin, Evolution, and Targeting Inhibition. In comparison with the ancestral S protein in the closed state, the NTD and the INT domain of the S protein D614G shift by 4 A and 6 A, respectively. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G 108 113 S;S 33;98 34;99 34222046 SARS-CoV-2: Origin, Evolution, and Targeting Inhibition. In late January 2020, D614G was first discovered in the viral genomes. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G 22 27 34222046 SARS-CoV-2: Origin, Evolution, and Targeting Inhibition. In these SNPs, four SNPs, C3037U, C14408U, A23403G, and C241U, show high frequency. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 A23403G 43 50 34222046 SARS-CoV-2: Origin, Evolution, and Targeting Inhibition. Moreover, the NTD of the S protein D614G has a 3A shift in the open state ( Figure S1 ). 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G 35 40 S 25 26 34222046 SARS-CoV-2: Origin, Evolution, and Targeting Inhibition. This also supports the mutant D614G increase the load of virus in the Covid-19 patients' upper respiratory tract and might enhance the spread. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G 30 35 COVID-19 70 78 34222046 SARS-CoV-2: Origin, Evolution, and Targeting Inhibition. With the sequencing analysis, studies showed that the S mutant D614G is a pseudo-typed virion. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G 63 68 S 54 55 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. American variants (B.1.429 and B.1.427) containing L452R (Long et al.) show refractory to mAbs as well. 2021 Virologica Sinica Introduction SARS_CoV_2 L452R 51 56 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. SARS-CoV-2 variants isolated from minks and mouse harboring mutations G261D, A262S, L452M, Y453F, F486L, Q498H and N501T may cause potential cross-species transmission that worth closely monitor (Thomson et al.; Yao et al.). 2021 Virologica Sinica Introduction SARS_CoV_2 A262S;F486L;G261D;L452M;N501T;Q498H;Y453F 77;98;70;84;115;105;91 82;103;75;89;120;110;96 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. The D614G mutation in the S protein enhances viral transmission and overtakes the prime strain of SARS-CoV-2 (Zhang et al.; Li et al.). 2021 Virologica Sinica Introduction SARS_CoV_2 D614G 4 9 S 26 27 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. The recent emerging variants of concern observed in the United Kingdom (B.1.1.7 with mutations N501Y, A570D and del69/70), South Africa (B.1.351 with mutations K417N, E484K and N501Y), Brazil (P.1 and P.2 with mutations K417T, E484K and N501Y) (Long et al.) and India (B.1.617 with mutations L452R and E484Q) (Cherian et al.) initially respond more tightly to ACE2 and appear to be more infectious to human (Laffeber et al.; Tian et al.). 2021 Virologica Sinica Introduction SARS_CoV_2 A570D;E484K;E484K;E484Q;K417N;K417T;L452R;N501Y;N501Y;N501Y 102;167;227;302;160;220;292;95;177;237 107;172;232;307;165;225;297;100;182;242 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. Variants B.1.141 and B.1.258 with mutation N439K increase spike affinity for ACE2 and confer resistance to several mAbs (Thomson et al.). 2021 Virologica Sinica Introduction SARS_CoV_2 N439K 43 48 S 58 63 34225487 Replicative Fitness of a SARS-CoV-2 20I/501Y.V1 Variant from Lineage B.1.1.7 in Human Reconstituted Bronchial Epithelium. EPI_ISL_918165), using for comparison the lineage B.1 BavPat D614G strain that circulated in Europe in February/March of 2020. 2021 mBio Introduction SARS_CoV_2 D614G 61 66 34225487 Replicative Fitness of a SARS-CoV-2 20I/501Y.V1 Variant from Lineage B.1.1.7 in Human Reconstituted Bronchial Epithelium. In a few months, the D614G spike mutation was rapidly fixed in almost all circulating SARS-CoV-2 populations, without evidence of higher CoV disease 2019 (COVID-19) mortality or clinical severity. 2021 mBio Introduction SARS_CoV_2 D614G 21 26 S 27 32 COVID-19 155 163 34225487 Replicative Fitness of a SARS-CoV-2 20I/501Y.V1 Variant from Lineage B.1.1.7 in Human Reconstituted Bronchial Epithelium. Our results demonstrated that the 20I/501Y.V1 (B.1.1.7) variant is more fit than the lineage B.1 BavPat D614G strain in reconstituted bronchial human epithelium. 2021 mBio Introduction SARS_CoV_2 D614G 104 109 34225487 Replicative Fitness of a SARS-CoV-2 20I/501Y.V1 Variant from Lineage B.1.1.7 in Human Reconstituted Bronchial Epithelium. Similar observations have been made with the D614G mutation, with which the new G614 strains overcame the original D614 strains when put in competition. 2021 mBio Introduction SARS_CoV_2 D614G 45 50 34225487 Replicative Fitness of a SARS-CoV-2 20I/501Y.V1 Variant from Lineage B.1.1.7 in Human Reconstituted Bronchial Epithelium. This may be explained by the presence of the N501Y mutation in the receptor binding domain (RBD) of the spike protein, which enhances viral particle binding to the ACE2 receptor. 2021 mBio Introduction SARS_CoV_2 N501Y 45 50 RBD;S;RBD 67;104;92 90;109;95 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. In particular, B.1.351 variant as a dominant variant in South Africa, characterized by three amino acid mutations on the K417N, E484K, and N501Y in RBD accompanying with four substitutions and a deletion in the N-terminal domain (NTD), decreased neutralization activity of antibodies induced by non-B.1.351 SARS-CoV-2 infection or vaccination and increased transmissibility. 2021 MedComm Introduction SARS_CoV_2 E484K;K417N;N501Y 128;121;139 133;126;144 RBD;N 148;211 151;212 COVID-19 307 327 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. Distinct mutants to the Wuhan-Hu-1 virus strain, such as the D614G strain, and three newer mutants from the United Kingdom, South Africa, and Brazil, have arisen. 2021 Human vaccines & immunotherapeutics Introduction SARS_CoV_2 D614G 61 66 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. Genomic analysis of circulating SARS-CoV-2 variants has identified mutations in S including E484K that blunt the ability of multiple mAbs and convalescent plasma to neutralize virus in cell culture-based assays. 2021 Human vaccines & immunotherapeutics Introduction SARS_CoV_2 E484K 92 97 S 80 81 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. Substitutions N501Y (B.1.1.7) and E484K-N501Y (B.1.351) are present among variants of concern which also possess other mutations in the spike gene and elsewhere in the viral genome. 2021 Human vaccines & immunotherapeutics Introduction SARS_CoV_2 E484K;N501Y;N501Y 34;14;40 39;19;45 S 136 141 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. We demonstrate that SAB-185 retains potent neutralizing activity against the D614G, S477N, E484K, and N501Y S protein substitutions in cell culture-based assays and were unable to isolate escape variants. 2021 Human vaccines & immunotherapeutics Introduction SARS_CoV_2 D614G;E484K;N501Y;S477N 77;91;102;84 82;96;107;89 S 108 109 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. We, therefore, tested the ability of this Tc-hIgG-SARS-CoV-2 to neutralize SARS-CoV-2 (D614G variant) and several VSV-SARS-CoV-2 chimeric viruses in vitro. 2021 Human vaccines & immunotherapeutics Introduction SARS_CoV_2 D614G 87 92 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. Both lineages have undergone significant diversification as they expanded; with this expansion apparently linked to a key S gene mutation D614G in lineage B and Q613H in lineage A:an apparent example of convergent evolution that resulted in a more stabilized spike protein, with D614G linked to modest increase in virus transmissibility. 2022 bioRxiv Introduction SARS_CoV_2 D614G;D614G;Q613H 138;279;161 143;284;166 S;S 259;122 264;123 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. D614G/Q613H have now become established in circulating B/A lineage viruses. 2022 bioRxiv Introduction SARS_CoV_2 Q613H;D614G 6;0 11;5 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. For A.23.1 S, P681R (P5) provides an additional basic residue and may modulate S1/S2 cleavability by furin, and hence virus infection properties. 2022 bioRxiv Introduction SARS_CoV_2 P681R 14 19 S 11 12 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. Here, we used a similar approach to study the role of the proteolytic activation of the spike protein in the context of the A.23.1 lineage virus, with a focus on the P681R point mutant. 2022 bioRxiv Introduction SARS_CoV_2 P681R 166 171 S 88 93 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. The P681R mutation of A.23.1 is of note as it is part of a proteolytic cleavage site for furin and furin-like proteases at the junction of the spike protein receptor-binding (S1) and fusion (S2) domains. 2022 bioRxiv Introduction SARS_CoV_2 P681R 4 9 S 143 148 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. This lineage then spilled into the general population adding additional spike mutations (R102I, L141F, E484K and P681R, as well as in nsp6, ORF8 and ORF9:to comprise lineage A.23.1:by September 2020. 2022 bioRxiv Introduction SARS_CoV_2 E484K;L141F;P681R;R102I 103;96;113;89 108;101;118;94 S;Nsp6;ORF8;ORF9 72;134;140;149 77;138;144;153 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. Within lineage A, the A.23 viral lineage, was first identified in a Ugandan prison in July 2020, and was characterized by three spike mutations F157L, V367F and Q613H. 2022 bioRxiv Introduction SARS_CoV_2 F157L;Q613H;V367F 144;161;151 149;166;156 S 128 133 34234758 A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3' Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity. In fact, the Spike protein mutation D614G global transmission was discovered in this way and is associated with higher viral titers and increased fitness . 2021 Frontiers in microbiology Introduction SARS_CoV_2 D614G 36 41 34242876 Energetic and structural basis for the differences in infectivity between the wild-type and mutant spike proteins of SARS-CoV-2 in the Mexican population. In a recent computational study, it was identified that H49Y, D614G, and T573I mutations in the Mexican population differently impact the affinity of some potential inhibitors of the S-protein. 2021 Journal of molecular graphics & modelling Introduction SARS_CoV_2 D614G;H49Y;T573I 62;56;73 67;60;78 S 183 184 34242876 Energetic and structural basis for the differences in infectivity between the wild-type and mutant spike proteins of SARS-CoV-2 in the Mexican population. In addition, it has been reported that the H49Y mutation is linked to a reduction in total free energy, while the D614G substitution has a more stabilizing effect. 2021 Journal of molecular graphics & modelling Introduction SARS_CoV_2 D614G;H49Y 114;43 119;47 34242876 Energetic and structural basis for the differences in infectivity between the wild-type and mutant spike proteins of SARS-CoV-2 in the Mexican population. In this study, these two mutations (H49Y and D614G) of the S-protein of SARS-CoV-2, discovered among the Mexican population for which increased infectivity has been observed, were studied using a computational approach that combines molecular dynamics simulations and free energy calculation using the MMGB(PB)SA approach, here we attempt to discover the potential variations in their infectivity. 2021 Journal of molecular graphics & modelling Introduction SARS_CoV_2 D614G;H49Y 45;36 50;40 S 59 60 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Even though two dominant amino acid (AA) changes, ORF1ab:P4715L and S:D614G variants, were reported to be strongly correlated with mortality, their death rates have been relatively stable. 2021 Journal of medical virology Introduction SARS_CoV_2 D614G;P4715L 70;57 75;63 ORF1ab;S 50;68 56;69 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. The majority of SARS-CoV-2 genomes have evolved with a dominant SNV cluster represented by nonsynonymous mutations A23403G (S:D614G) and C14408T (ORF1ab:P4715L), in addition to C241T at the upstream of ORF1ab and another synonymous mutation C3037T on ORF1ab. 2021 Journal of medical virology Introduction SARS_CoV_2 A23403G;C14408T;C241T;C3037T;D614G;P4715L 115;137;177;241;126;153 122;144;182;247;131;159 ORF1ab;ORF1ab;ORF1ab;S 146;202;251;124 152;208;257;125 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. A temporal plot of the number of global B.1.1.7+E484K isolates collected between December 2020 and March 2021 (2-week window) is shown in Figure 1B (as of 04/17/2021). 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 48 53 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Although all 236 B.1.1.7+E484K genomes were typed as B.1.1.7 using Pangolin, a more granular view using our typing tool "GNUVID" shows that they belong to 7 different clonal complexes (CCs; 45062, 46649, 49676, 57630, 58534, 62415, and 67441) (Figure 1C; Supplementary Table 1). 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 25 30 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Another large clade of 75 B.1.1.7 isolates had 34 isolates that carry the E484K mutation; 30 of them are from the United States (CA, CT, FL, MA, NC, NH, NJ, NY, OR). 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 74 79 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. For each of these CCs, representative sequences without the E484K mutation have been circulating since at least November 2020, predating the first E484K in each CC. 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K;E484K 60;147 65;152 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Here we present a comparative analysis of the first SARS-CoV-2 B.1.1.7 isolates detected in PA that carry the E484K spike mutation, a mutation that could be associated with reduced efficacy of both vaccine-induced and natural immunity. 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 110 115 S 116 121 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Here we report a B.1.1.7 isolate with the E484K spike mutation isolated in Southeastern Pennsylvania (PA). 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 42 47 S 48 53 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. However, in February 2021 Public Health England (PHE) published a concerning report of 11 B.1.1.7 genomes that had acquired the E484K spike mutation. 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 128 133 S 134 139 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. In the phylogeny, 6 E484K clades were found in >1 country and 4 E484K clades in >1 US state, suggesting widespread dissemination of these viruses. 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K;E484K 20;64 25;69 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Interestingly, 1 B.1.1.7 isolate from this surveillance, collected on 3/24/2021 from a 52-year-old male, carried the E484K spike mutation that is present in the South African and Brazilian lineages. 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 117 122 S 123 128 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. It also shared with 9 other US isolates a stop mutation (A28095T) in ORF8 (Supplementary Figure 2). 2021 Open forum infectious diseases Introduction SARS_CoV_2 A28095T 57 64 ORF8 69 73 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Lineages B.1.1.7, B.1.429 (California), B.1.526 (New York), and R.1 (international lineage with the E484K mutation) accounted for 69% of the sequenced genomes in March. 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 100 105 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Our analysis shows that multiple lineages of B.1.1.7+E484K are circulating in the United States and globally and that these lineages have acquired the E484K mutation independently, which argues for strong selective pressure for this mutation. 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K;E484K 151;53 156;58 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Since the first report by PHE in February, a total of 253 B.1.1.7+E484K genomes have been uploaded to GISAID from England and 14 other countries (Germany, France, Italy, Poland, Sweden, Ireland, Netherlands, Portugal, Wales, Turkey, Slovakia, Austria, Czech Republic, and the United States). 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 66 71 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Since this analysis was completed and at the time of this submission (05/26/2021), there are 1400 B.1.1.7+E484K genomes on GISAID, which raises the concern that more B.1.1.7+E484K sequences may be emerging even as herd immunity increases by natural immunity and vaccines. 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K;E484K 106;174 111;179 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. The 9 other B.1.1.7+E484K isolates reported from PA were in a large clade containing US genomes (from CA, CO, FL, MA, MD, MI, NC, NE, NJ, NY, OR, TX, WA, WV). 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 20 25 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. The genome from PA presented here falls in a well-supported clade of 77 B.1.1.7 isolates, 48 of which have the E484K mutation. 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 111 116 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. This raised the possibility that the E484K mutation was acquired independently in each of these CCs in independent events. 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 37 42 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. To better understand the relationship between this isolate and publicly available severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes, we compared it with all available B.1.1.7+E484K high-coverage genomes available on the Global Initiative on Sharing All Influenza Data (GISAID; n = 235). 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 194 199 COVID-19 89 129 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. To test the hypothesis of multiple acquisitions in a rigorous phylogenetic framework, we queried the GISAID database for closely related genomes for each of the 236 high-quality B.1.1.7+E484K genomes and retrieved 354 closely related B.1.1.7 genomes. 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 186 191 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Two of these lineages, B.1.351 and P.1, were of specific concern because they have the mutation E484K, which has been shown to enhance escape from neutralizing antibody inhibition in vitro and may be associated with reduced efficacy of the vaccine. 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 96 101 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Using the phylogeny reconstructed from the combined data set, we performed an ancestral reconstruction using Fitch optimization, which revealed 59 de novo acquisitions of the E484K mutation in the B.1.1.7 lineage (Figure 2). 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 175 180 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. Here we report a reprogrammed CRISPR-pspCas13b that can efficiently suppress replication-competent SARS-CoV-2, including the ancestral virus, D614G and B.1.1.7 variants in monkey and human epithelial cells. 2021 Nature communications Introduction SARS_CoV_2 D614G 142 147 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. The SARS-CoV-2 D614G (Asp614Gly) variant was the first variant described. 2021 Nature communications Introduction SARS_CoV_2 D614G;D614G 15;22 20;31 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Here, we analyzed the evolutionary patterns of Q677P/H and FCS amino acids residues (amino acid positions 680-689) from all animal and human variants and five major emergent variants for which whole-genome SARS-CoV-2 sequences had been deposited in the GISAID Initiative database since the start of the COVID-19 pandemic. 2021 Archives of virology Introduction SARS_CoV_2 Q677H;Q677P 47;47 54;54 COVID-19 303 311 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Moreover, mutations in or close to the FCS, such as Q677P/H, are common in the course of coronaviruses evolution and adaptation, particularly when the virus adapts to a different host. 2021 Archives of virology Introduction SARS_CoV_2 Q677H;Q677P 52;52 59;59 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. The D614G mutation is thought to increase virus transmissibility, while the N501Y mutation has also been implicated in the rapid spread of SARS-CoV-2. 2021 Archives of virology Introduction SARS_CoV_2 D614G;N501Y 4;76 9;81 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? Currently, B.1.617 comprises three subvariants, B.1.617.1-3, with different distribution of the mutations P478K and E484Q (Public Health England). 2021 Journal of medical virology Introduction SARS_CoV_2 E484Q;P478K 116;106 121;111 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? Here, we focus on biochemical and biophysical changes conferred to the B.1.617+ VUI by the P478K and E484Q mutations. 2021 Journal of medical virology Introduction SARS_CoV_2 E484Q;P478K 101;91 106;96 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? Two of them, the E484Q (or the P478K) and the L452R, are located in the RBD region, and they are critical sites for the binding with ACE2. 2021 Journal of medical virology Introduction SARS_CoV_2 E484Q;L452R;P478K 17;46;31 22;51;36 RBD 72 75 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. Interestingly, a very high and increasing number of lineages containing the E484K substitution in the Spike protein have been reported to emerge independently at least 67 times and worldwide (Table 1). 2021 Frontiers in medicine Introduction SARS_CoV_2 E484K 76 81 S 102 107 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. The F318N mutation was located in an unknown function region between the N-terminal domain and the receptor binding domain, while the V320F mutation was located in the receptor binding domain in the S1 subunit. 2021 Microbiology resource announcements Introduction SARS_CoV_2 F318N;V320F 4;134 9;139 RBD;RBD;N 99;168;73 122;191;74 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. We compared the S gene mutations in our sequences with 542,800 B.1.1.7 and 14,359 B.1.351 GISAID sequences accessed on 8 May 2021 using outbreak.info, and one of our B.1.1.7 sequences (MZ068158) contained two unique mutations, F318N and V320F. 2021 Microbiology resource announcements Introduction SARS_CoV_2 F318N;V320F 227;237 232;242 S 16 17 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. Additionally, in the N501Y-RBD the predicted binding pocket of tauro-alpha-muricholic acid (Figure 3g), tilivalline (Figure 3h), and other bile acids and NRPs (Supporting Figures S6-S9) shifted. 2021 Chembiochem Introduction SARS_CoV_2 N501Y 21 26 RBD 27 30 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. Alternatively, it is possible that N501Y or other mutations of the RBD like those present in the B.1.617.2 variant (delta variant, which was first detected in India) increase the interactions of RBD with the ACE2 receptor and thus, improving its binding to the ACE2 receptor in the presence of microbial NPs (Figure 4a). 2021 Chembiochem Introduction SARS_CoV_2 N501Y 35 40 RBD;RBD 67;195 70;198 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. In summary, our in-silico studies revealed that NPs of commensal microbiota like bile acids and NRPs can bind to the WT-RBD of SARS-CoV-2 with a reasonable affinity and that N501Y mutation interferes with their binding to the RBD. 2021 Chembiochem Introduction SARS_CoV_2 N501Y 174 179 RBD;RBD 120;226 123;229 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. In the emerging variants with mutations such as N501Y, bile acids or NRPs cannot effectively interact with the RBD and thus, do not interfere with viral entry to host cells. 2021 Chembiochem Introduction SARS_CoV_2 N501Y 48 53 RBD 111 114 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. In this new binding pocket, the interference of NPs with the binding of N501Y-RBD to the ACE2 receptor is minimized (Figures 3g-h). 2021 Chembiochem Introduction SARS_CoV_2 N501Y 72 77 RBD 78 81 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. Molecular docking studies revealed that N501Y mutation abolishes the binding pocket of bile acids and NRPs observed in the WT-RBD (Supporting Table S1 and Figures 3e-f). 2021 Chembiochem Introduction SARS_CoV_2 N501Y 40 45 RBD 126 129 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. Molecular dynamics simulations suggest that the N501Y mutation may increase or decrease the binding affinity of RBD to the ACE2 receptor. 2021 Chembiochem Introduction SARS_CoV_2 N501Y 48 53 RBD 112 115 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. More recent data using hamster models and cell-based assays show that the replication rates of the N501Y variants increase in the upper respiratory airway. 2021 Chembiochem Introduction SARS_CoV_2 N501Y 99 104 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. N501Y mutation interferes with the binding of bile acids and NRPs to the RBD. 2021 Chembiochem Introduction SARS_CoV_2 N501Y 0 5 RBD 73 76 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. Next, we used MD simulations to study the conformational stability of tilivalline in the predicted binding site of glycosylated structures of WT-RBD and N501Y-RBD. 2021 Chembiochem Introduction SARS_CoV_2 N501Y 153 158 RBD;RBD 145;159 148;162 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. On the other hand, studies using pseudotyped viruses revealed that N501Y mutation does not increase the infectivity rate of variants of SARS-CoV-2 as compared to the wild-type (WT) virus in cell-based assays. 2021 Chembiochem Introduction SARS_CoV_2 N501Y 67 72 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. Since the predicted binding pocket for most of the NPs includes the amino acid Asn501 (Figures 3a-b and Supporting Figures S1-S4), which in many of the emerging variants of SARS-CoV-2 is replaced by a tyrosine (N501Y) (Figure 1c), we hypothesized that this mutation could interfere with the binding of bile acids and NRPs to the RBD. 2021 Chembiochem Introduction SARS_CoV_2 N501Y 211 216 RBD 329 332 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. The common mutation of the RBD among all these variants is the substitution of asparagine 501 by tyrosine (Asn501Tyr or N501Y) (Figure 1c). 2021 Chembiochem Introduction SARS_CoV_2 N501Y;N501Y;N501Y 79;120;107 105;125;116 RBD 27 30 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. The interaction energy between tillivaline and the RBD binding site averaged over the last 4 ns of the MDs simulations (Supporting Figure S12), was predicted to be as low as -10.26 kCal/mol for the N501Y-RBD and below -17.08 kCal/mol for the WT-RBD. 2021 Chembiochem Introduction SARS_CoV_2 N501Y 198 203 RBD;RBD;RBD 51;204;245 54;207;248 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. Therefore, we tested the binding of metabolites and NPs (Supporting Table S1) to the RBD of a variant harboring N501Y mutation (N501Y-RBD). 2021 Chembiochem Introduction SARS_CoV_2 N501Y;N501Y 112;128 117;133 RBD;RBD 85;134 88;137 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. This observation suggests that tillivaline will be easily displaced by the N501Y-RBD binding to the ACE2 receptor. 2021 Chembiochem Introduction SARS_CoV_2 N501Y 75 80 RBD 81 84 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. To further evaluate the results of molecular docking studies, we performed classical all atoms molecular dynamics (MD) simulations of glycosylated structures of WT-RBD and of the N501Y-RBD, both in complex with tilivalline. 2021 Chembiochem Introduction SARS_CoV_2 N501Y 179 184 RBD;RBD 164;185 167;188 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. When bound to the N501Y-RBD, tillivaline mostly interacts with the amino acid residues of RBD (Y501 and Y505) in such a way that it is positioned at the edge of the interface with the ACE2 receptor as revealed by close inspection of the MD trajectories (Supporting Figure S13). 2021 Chembiochem Introduction SARS_CoV_2 N501Y 18 23 RBD;RBD 24;90 27;93 34267528 Detection of Representative Mutant Strains and a Case of Prolonged Infection by SARS-CoV-2 with Spike 69/70 Deletion in Japan. E484K was found in South Africa and Brazil with the N501Y mutant, and they appear to be associated with decreased vaccine efficacy. 2021 Infection and drug resistance Introduction SARS_CoV_2 N501Y;E484K 52;0 57;5 34267528 Detection of Representative Mutant Strains and a Case of Prolonged Infection by SARS-CoV-2 with Spike 69/70 Deletion in Japan. However, the prevalence of other mutants, such as P681H and del69/70, is unknown. 2021 Infection and drug resistance Introduction SARS_CoV_2 P681H 50 55 34267528 Detection of Representative Mutant Strains and a Case of Prolonged Infection by SARS-CoV-2 with Spike 69/70 Deletion in Japan. In contrast, nine patients had the E484K mutation without N501Y and other mutants. 2021 Infection and drug resistance Introduction SARS_CoV_2 E484K;N501Y 35;58 40;63 34267528 Detection of Representative Mutant Strains and a Case of Prolonged Infection by SARS-CoV-2 with Spike 69/70 Deletion in Japan. In Japan, it has been reported that the N501Y mutant and severe COVID-19 patients had increased rapidly in the western area, including the Osaka City area, and that the E484K alone mutant appeared in the eastern area, especially around the Tokyo Metropolitan area in April 2021. 2021 Infection and drug resistance Introduction SARS_CoV_2 E484K;N501Y 169;40 174;45 COVID-19 64 72 34267528 Detection of Representative Mutant Strains and a Case of Prolonged Infection by SARS-CoV-2 with Spike 69/70 Deletion in Japan. In the B1.1.7 lineage, P681H and deletion of H69/V70 (del 69/70) were also reported to be resistant to the anti-viral agent remdesivir and to have an allosterically changed spike protein conformation, respectively. 2021 Infection and drug resistance Introduction SARS_CoV_2 P681H 23 28 S 173 178 34267528 Detection of Representative Mutant Strains and a Case of Prolonged Infection by SARS-CoV-2 with Spike 69/70 Deletion in Japan. It is important to be vigilant regarding the existence of mutant strains other than N501Y and E484K if patients show delayed improvement despite receiving appropriate treatment in Japan and other areas where the mutants are not highly prevalent. 2021 Infection and drug resistance Introduction SARS_CoV_2 E484K;N501Y 94;84 99;89 34267528 Detection of Representative Mutant Strains and a Case of Prolonged Infection by SARS-CoV-2 with Spike 69/70 Deletion in Japan. N501Y and E484K are representative and well-known mutant, but P681H and del69/70 are also important, because they could directly affect the treatment and pathophysiological features of the patients. 2021 Infection and drug resistance Introduction SARS_CoV_2 E484K;P681H;N501Y 10;62;0 15;67;5 34267528 Detection of Representative Mutant Strains and a Case of Prolonged Infection by SARS-CoV-2 with Spike 69/70 Deletion in Japan. N501Y was first reported from the United Kingdom as a representative mutant in the B1.1.7 lineage (now called Alpha variant), and it was suggested that it has increased infectivity. 2021 Infection and drug resistance Introduction SARS_CoV_2 N501Y 0 5 34267528 Detection of Representative Mutant Strains and a Case of Prolonged Infection by SARS-CoV-2 with Spike 69/70 Deletion in Japan. There has been a worldwide pandemic of coronavirus disease 2019 (COVID-19), including Japan, since February 2020, and the spread of mutant viral strains, such as N501Y and E484K, of the spike protein of SARS-CoV-2 has become a major issue. 2021 Infection and drug resistance Introduction SARS_CoV_2 E484K;N501Y 172;162 177;167 S 186 191 COVID-19;COVID-19 39;65 58;73 34267528 Detection of Representative Mutant Strains and a Case of Prolonged Infection by SARS-CoV-2 with Spike 69/70 Deletion in Japan. There were no patients with N501Y and P681H, though some patients showed severe disease and delayed improvement with administration of remdesivir. 2021 Infection and drug resistance Introduction SARS_CoV_2 N501Y;P681H 28;38 33;43 34267528 Detection of Representative Mutant Strains and a Case of Prolonged Infection by SARS-CoV-2 with Spike 69/70 Deletion in Japan. Therefore, the prevalence of these mutants was analyzed in 25 COVID-19 patients admitted to our hospital located in Tohoku rural area from December 2020 to April 2021 by polymerase chain reaction (PCR)-based detection kits (VirSNiP-SAS B1351 (484K+501Y), SARS-CoV-2 Spike P681Y, and del H69/N70, respectively; Roche, Basel, Switzerland). 2021 Infection and drug resistance Introduction SARS_CoV_2 P681Y 272 277 S 266 271 COVID-19 62 70 34268527 Durable Humoral and Cellular Immune Responses Following Ad26.COV2.S Vaccination for COVID-19. Excluding the three individuals who developed breakthrough SARS-CoV-2 infection or who received mRNA vaccines, and restricted to individuals who received the single-shot vaccine regimen, median neutralizing antibody titers on day 239 were 184, 158, 147, 171, 107, 129, 87, and 62 against the SARS-COV-2 variants WA1/2020, D614G, B.1.1.7 (alpha), B.1.617.1 (kappa), B.1.617.2 (delta), P.1 (gamma), B.1.429 (epsilon), and B.1.351 (beta), respectively. 2021 medRxiv Introduction SARS_CoV_2 D614G 322 327 COVID-19 59 79 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. For example, the P462L and D480 A/G mutations that occur in SARS-CoV induce viruses to escape to a monoclonal NAb. 2021 Biomedical journal Introduction SARS_CoV_2 D480A;D480G;P462L 27;27;17 35;35;22 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. Along with multiple mutations in the spike protein, there are 3 specific changes of particular concern: the S: N501Y, shown to enhance the binding affinity to angiotensin-converting enzyme 2 (ACE2), the S: 69-70del that could potentially cause immune escape, and the S: P681H that is close to the furin cleavage site. 2022 Clinical infectious diseases Introduction SARS_CoV_2 N501Y;P681H 111;270 116;275 S;S;S;S 37;108;203;267 42;109;204;268 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. Other S: N501Y emerging VOCs include B.1.351 (beta) and P.1 (gamma), which both carry S: E484K and became predominant in their countries of origin. 2022 Clinical infectious diseases Introduction SARS_CoV_2 E484K;N501Y 89;9 94;14 S;S 6;86 7;87 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. The aspartate-to-glycine change at position 614 (S: D614G) substitution in the spike (S) protein garnered much attention in mid-2020 and rapidly became globally predominant . 2022 Clinical infectious diseases Introduction SARS_CoV_2 D614G;D614G 4;52 47;57 S;S;S 79;49;86 84;50;87 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. These variants are characterized by the S: L452R, which could affect neutralization by monoclonal antibodies. 2022 Clinical infectious diseases Introduction SARS_CoV_2 L452R 43 48 S 40 41 34273991 Estimating COVID-19 cases infected with the variant alpha (VOC 202012/01): an analysis of screening data in Tokyo, January-March 2021. Japan intensified sequencing virus samples from late December both at border quarantine station and domestic testing centers, and also devised a real-time polymerase chain reaction (rt-PCR) technique to detect N501Y mutation as the screening method in each prefecture. 2021 Theoretical biology & medical modelling Introduction SARS_CoV_2 N501Y 210 215 34273991 Estimating COVID-19 cases infected with the variant alpha (VOC 202012/01): an analysis of screening data in Tokyo, January-March 2021. New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG) in the United Kingdom (UK) identified the common mutation N501Y in the variant alpha. 2021 Theoretical biology & medical modelling Introduction SARS_CoV_2 N501Y 126 131 34274369 A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. 484 K and 501Y phenotype (Texas Red/Cy5, such as Beta and Gamma variant strains), or a strain belonging to a different variant with only the E484K amino-acid substitution (Texas Red/HEX). 2021 Journal of virological methods Introduction SARS_CoV_2 E484K 141 146 34274369 A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. before the emergence of E484K and N501Y amino-acid substitutions in Greece were included. 2021 Journal of virological methods Introduction SARS_CoV_2 E484K;N501Y 24;34 29;39 34274369 A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. In all of these 3 VOCs, the N501Y amino-acid substitution (change of asparagine to tyrosine) is present at the position 501 of the S-protein (receptor-binding domain), which confers enhanced affinity for receptor binding. 2021 Journal of virological methods Introduction SARS_CoV_2 N501Y 28 33 S 131 132 34274369 A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. In conclusion, the typing real-time RT-PCR assay developed herein is able to accurately identify the mutations associated with the E484K and N501Y phenotypes of SARS-CoV-2 S protein, considered as MOCs. 2021 Journal of virological methods Introduction SARS_CoV_2 E484K;N501Y 131;141 136;146 S 172 173 34274369 A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. Most importantly, besides the aforementioned VOCs, the substitution E484K has been reported to emerge independently in several other SARS-CoV-2 lineages worldwide, such as in variants/lineages P.2 (20B), Eta (21D), Iota (21 F) and B.1.620 (20A/S:126A). 2021 Journal of virological methods Introduction SARS_CoV_2 E484K 68 73 34274369 A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. The two latter VOCs (Beta and Gamma) also possess the E484K amino-acid substitution (change from glutamate to lysine), which reduces the neutralization sensitivity to convalescent sera, and thus, possibly affecting the protection conferred by vaccine-derived antibodies, or antibodies produced in previous infections from non-carrying the E484K SARS-CoV-2 strains. 2021 Journal of virological methods Introduction SARS_CoV_2 E484K;E484K 54;339 59;344 34278277 SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high risk variants into the United Kingdom. 69-70del is thought to lead to increased transmissibility in combination with N501Y. 2021 EClinicalMedicine Introduction SARS_CoV_2 N501Y 78 83 34278277 SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high risk variants into the United Kingdom. A further VOC has recently been identified in India, designated B.1.617 and contains 3 clades with different mutation profiles; B.1.617.1 has a spike profile which includes L452R and E484Q; B.1.617.2 has a different profile without E484Q and appears to have undergone recent expansion; B.1.617.3 has L452R and E484Q but is distinct from B.1.617.1 and currently is only detected in a small proportion of sequences. 2021 EClinicalMedicine Introduction SARS_CoV_2 E484Q;E484Q;E484Q;L452R;L452R 183;232;310;173;300 188;237;315;178;305 S 144 149 34278277 SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high risk variants into the United Kingdom. A mutation of particular concern is E484K, which reduces antibody binding to the RBD, reducing neutralisation efficacy in some SARS-CoV-2 WT convalescent human sera by > 10-fold. 2021 EClinicalMedicine Introduction SARS_CoV_2 E484K 36 41 RBD 81 84 34278277 SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high risk variants into the United Kingdom. Indeed, evidence suggests both the Moderna and Pfizer vaccines are less effective at neutralising viruses with these mutations and of 17 vaccine-elicited antibodies tested, 9 were at least 10 times less effective against pseudotyped viruses containing E484K, 5 against K417N and 4 against N501Y. 2021 EClinicalMedicine Introduction SARS_CoV_2 E484K;K417N;N501Y 252;269;289 257;274;294 34278277 SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high risk variants into the United Kingdom. K417 has been found to be 60-100% buried in class 1 antibody paratopes and K417N has also been shown to significantly reduce sera neutralisation. 2021 EClinicalMedicine Introduction SARS_CoV_2 K417N 75 80 34278277 SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high risk variants into the United Kingdom. N501Y is found in the receptor binding domain (RBD) of the spike protein and has been shown to increase its binding affinity to human angiotensin-concerting enzyme 2 (ACE2), the virus' primary mode of entry into human cells. 2021 EClinicalMedicine Introduction SARS_CoV_2 N501Y 0 5 RBD;S;RBD 22;59;47 45;64;50 34278277 SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high risk variants into the United Kingdom. P681H is adjacent to the furin cleavage site, potentially affecting membrane fusion. 2021 EClinicalMedicine Introduction SARS_CoV_2 P681H 0 5 Membrane 68 76 34278277 SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high risk variants into the United Kingdom. The combination of nearby RBD mutations K417N/T, E484K and N501Y found in B.1.351 (South Africa) and P.1 (Brazil) make these particularly concerning variants. 2021 EClinicalMedicine Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 49;40;40;59 54;47;47;64 RBD 26 29 34278277 SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high risk variants into the United Kingdom. The E484K mutation has also been identified in B.1.1.7 variants, designated VOC-21FEB-02, as well as B.1.525, a strain first found in the UK, but thought to originate in Nigeria. 2021 EClinicalMedicine Introduction SARS_CoV_2 E484K 4 9 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. There are no clinical reports describing the emergence of the E484K mutant after treatment with bamlanivimab, with the exception of data from a pivotal large randomized trial (BLAZE-1), which reported low frequencies of newly detected bamlanivimab immune escape mutants in patients receiving different doses of bamlanivimab and significantly lower frequencies in patients in the placebo arm. 2021 The Lancet regional health. Europe Introduction SARS_CoV_2 E484K 62 67 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. We searched PubMed Central for articles published until April 27, 2021, using the key words "SARS-CoV-2'', "bamlanivimab", "E484K" and "immune escape". 2021 The Lancet regional health. Europe Introduction SARS_CoV_2 E484K 124 129 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. While it is known that escape mutations can evolve upon treatment with monoclonal antibodies, convalescent plasma, or under the selection pressure of natural immunity, our study provides, to our knowledge, for the first time data on a clinical constellation in which selection of the immune escape mutation E484K, which also occurs in epidemiologically important "variants of concern," occurs in a very high proportion of patients. 2021 The Lancet regional health. Europe Introduction SARS_CoV_2 E484K 307 312 34278671 Efficient Inhibition of SARS-CoV-2 Using Chimeric Antisense Oligonucleotides through RNase L Activation*. Mutations DeltaH69/DeltaV70 and N501Y on the spike protein of SARS-CoV-2 have been reported to cause S-gene target failure (SGTF) and greatly increase viral transmissibility. 2021 Angewandte Chemie (International ed. in English) Introduction SARS_CoV_2 N501Y 32 37 S;S 45;101 50;102 34278671 Efficient Inhibition of SARS-CoV-2 Using Chimeric Antisense Oligonucleotides through RNase L Activation*. One of these chimeras also effectively inhibited three SARS-CoV-2 pseudovirus mutants, including N501Y, DeltaH69/DeltaV70, and the recently discovered dual-site mutations with higher transmission ability. 2021 Angewandte Chemie (International ed. in English) Introduction SARS_CoV_2 N501Y 97 102 34278671 Efficient Inhibition of SARS-CoV-2 Using Chimeric Antisense Oligonucleotides through RNase L Activation*. Since mutation sites on S-RNA corresponding to N501Y and DeltaH69/DeltaV70 are not overlaid with targeted region of Chimera-S4, unaffected high potent inhibition of these mutants was still successfully achieved. 2021 Angewandte Chemie (International ed. in English) Introduction SARS_CoV_2 N501Y 47 52 S 24 25 34278671 Efficient Inhibition of SARS-CoV-2 Using Chimeric Antisense Oligonucleotides through RNase L Activation*. This chimeric sequence still showed robust inhibiting capability toward three highly transmissible SARS-CoV-2 mutants involving N501Y and DeltaH69/DeltaV70 mutations. 2021 Angewandte Chemie (International ed. in English) Introduction SARS_CoV_2 N501Y 128 133 34278671 Efficient Inhibition of SARS-CoV-2 Using Chimeric Antisense Oligonucleotides through RNase L Activation*. To assess the broad-spectrum inhibitory effect on SARS-CoV-2 mutants, Chimera-S4 was then co-transfected with pseudovirus packaging plasmids carrying DeltaH69/DeltaV70, N501Y or dual-site mutations into HEK293T packaging cells. 2021 Angewandte Chemie (International ed. in English) Introduction SARS_CoV_2 N501Y 169 174 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. Similarly, the hypothesis that rapid spread of the D614G variant of SARS-CoV-2 indicates a possible fitness advantage has been questioned. 2021 mBio Introduction SARS_CoV_2 D614G 51 56 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. Additionally, we report the biophysical characterization and ACE2 affinity measurements for the D614G, B.1.1.7, and B.1.351 SARS-CoV-2 S1 variants, with links to infective potency in a pseudotyped vector setting, with direct comparison to approved COVID-19 monoclonal antibodies. 2021 Journal of virology Introduction SARS_CoV_2 D614G 96 101 COVID-19 248 256 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. Of note is the identification of the D614G (clade 20A) that has rapidly become the dominant strain globally. 2021 Journal of virology Introduction SARS_CoV_2 D614G 37 42 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. The variants A222V (clade 20A.EU1) and S477N (clade 20A.EU2) emerged in the summer of 2020 in Spain and have rapidly shown diffusion within Europe. 2021 Journal of virology Introduction SARS_CoV_2 A222V;S477N 13;39 18;44 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. All three of the major SARS-CoV-2 N501Y variants are circulating around the world. 2021 Journal of clinical microbiology Introduction SARS_CoV_2 N501Y 34 39 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. All three variants, B.1.1.7, B.1.351, and P.1, contain the N501Y mutation, while the South African and Brazilian variants additionally contain mutations in E484K and K417N. 2021 Journal of clinical microbiology Introduction SARS_CoV_2 E484K;K417N;N501Y 156;166;59 161;171;64 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. Most of the new variants also have mutations at the 501 and/or 484 position, although additional mutations, such as L452R, have also been reported in more recent variants; however, the epidemiological and clinical relevance of these new variants are not well understood. 2021 Journal of clinical microbiology Introduction SARS_CoV_2 L452R 116 121 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. The B.1.1.7 variant has a number of mutations in the spike protein, including single-nucleotide polymorphisms (SNPs) resulting in N501Y, A570D, D614G, and P681H mutations and deletions at amino acids 69 and 70 and 144Y. 2021 Journal of clinical microbiology Introduction SARS_CoV_2 A570D;D614G;N501Y;P681H 137;144;130;155 142;149;135;160 S 53 58 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. The N501Y (A23063T) mutation has been identified as an important contributor to the worrisome phenotype. 2021 Journal of clinical microbiology Introduction SARS_CoV_2 N501Y;A23063T 4;11 9;18 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. Thus, the N501Y mutation appears to be an excellent marker for all three strains, while the E484K mutation can be used to differentiate the other two strains from B.1.1.7. 2021 Journal of clinical microbiology Introduction SARS_CoV_2 E484K;N501Y 92;10 97;15 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Although an individual mutation that likely increases replication of SARS-CoV-2 in humans has been identified:a single aspartic acid-to-glycine change at position 614 in the S protein :this occurred after emergence into humans, and the genetic determinants of SARS-CoV-2 expansion from an animal reservoir into humans remain entirely unknown. 2021 Cell Introduction SARS_CoV_2 D614G 119 166 S 174 175 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Ebola viruses' human adaptation following spillover from bats was at least partly mediated by a single alanine-to-valine mutation at position 82 in the glycoprotein. 2021 Cell Introduction SARS_CoV_2 A82V 103 144 34292870 Inhalable nanocatchers for SARS-CoV-2 inhibition. The spike aspartic acid-614 to glycine (D614G), the dominant SARS-CoV-2 mutational form globally, showed obviously increased binding efficiency with ACE2 receptor during the virus infection process. 2021 Proc Natl Acad Sci U S A Introduction SARS_CoV_2 D614G;D614G 10;40 38;45 S 4 9 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. Of the 3276 B.1.1.7 genomes, 11 (0.3%) had an E484K change in spike protein that reduces binding by some neutralizing antibodies. 2021 The American journal of pathology Introduction SARS_CoV_2 E484K 46 51 S 62 67 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. Subsequently, sequence analysis of 5085 genomes causing the first disease wave and massive second disease wave in Houston showed that all strains in the second wave had a D614G amino acid replacement in the spike protein. 2021 The American journal of pathology Introduction SARS_CoV_2 D614G 171 176 S 207 212 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. The D614G polymorphism increases human transmission and infectivity in vitro and in vivo in animal infection models. 2021 The American journal of pathology Introduction SARS_CoV_2 D614G 4 9 34304682 An overview of the preclinical discovery and development of bamlanivimab for the treatment of novel coronavirus infection (COVID-19): reasons for limited clinical use and lessons for the future. Efficacy of bamlanivimab was preserved against VOC alpha (also named B.1.1.7 by PANGOLIN and 20I/501Y.V1 by NextStrain), but was lost in the related E484K-positive eta VOI (also named B.1.525 in PANGOLIN and 21D in NextStrain). 2021 Expert opinion on drug discovery Introduction SARS_CoV_2 E484K 149 154 34304682 An overview of the preclinical discovery and development of bamlanivimab for the treatment of novel coronavirus infection (COVID-19): reasons for limited clinical use and lessons for the future. This evidence confirms that the E484K mutation, occurring in 64 out of the 800 clades reported as of March 2021 and hence being a dramatic example of convergent evolution, inevitably leads to full resistance to bamlanivimab as well as to many other class 2 RBD-directed mAbs. 2021 Expert opinion on drug discovery Introduction SARS_CoV_2 E484K 32 37 RBD 257 260 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. One of the most well-known mutations is in position 23404, changing an aspartate for a glycine at residue 614 in Spike protein and, presumably, offering an advantage in viral replication. 2021 Frontiers in microbiology Introduction SARS_CoV_2 G614D 71 109 S 113 118 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. A previous study mistakenly developed an RFLP method for identifying another mutation at residue 615 of the spike protein, but not D614G as commented by Niranji and Al-Jaf. 2021 Meta gene Introduction SARS_CoV_2 D614G 131 136 S 108 113 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. A study highlighted the necessity of SARS CoV-2 D614G mutant using biosensing and restriction enzyme methods including BtsCI endonuclease which can cleave the wild type D614 but do not cut G614 mutant. 2021 Meta gene Introduction SARS_CoV_2 D614G 48 53 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Few studies have conducted investigations of D614G mutation on in vitro viral pseudotype infected cells, laboratory animal models, and infected populations, suggesting increases in infectivity, viral loads (; L.), and fatality. 2021 Meta gene Introduction SARS_CoV_2 D614G 45 50 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. One of the most common mutations occurred, since its emergence, has been recognized as D614G (A23403) at amino acid number 614 in the spike protein sequence (nucleotide sequence number 23403) of the reference Wuhan SARS CoV-2 genome, when nucleotide A in GAT encoding aspartate residue (D) altered to G creating GGT, a codon for glycine. 2021 Meta gene Introduction SARS_CoV_2 D614G 87 92 S 134 139 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Overall, data indicated the viral adaptability to human cells as a result of D614G mutation. 2021 Meta gene Introduction SARS_CoV_2 D614G 77 82 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Since the emergence of the SARS CoV-2 D614G mutation, tracing back to January 2020 from China to Europe, and it is currently highly prevalent in all continents of the world, there have been controversial studies on impacts of this single nucleotide variation (SNV), D614G, on the viral survival fitness, immunogenicity and antigenic epitopes, antibody neutralizing sensitivity, infectivity, transmission and fatality. 2021 Meta gene Introduction SARS_CoV_2 D614G;D614G 38;266 43;271 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. The D614G mutation is located in the NTD of S1 that lies between RBD and S2 near the cleavage site, where both S1 and S2 are cleaved by TMPRSS2 and furin. 2021 Meta gene Introduction SARS_CoV_2 D614G 4 9 RBD 65 68 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Therefore, developing inexpensive and rapid methods for identifying SNVs, such as D614G, are essential for tracking this variant by epidemiologists, molecular virologists or immunologists collaborating with clinicians to compare Covid-19 patients with SARS CoV-2 D614 and G614 variants. 2021 Meta gene Introduction SARS_CoV_2 D614G 82 87 COVID-19 229 237 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Therefore, the purpose of this study is to develop three various methods such as Taqman probe-based rRT PCR, ARMS and RFLP to detect SARS CoV-2 D614G mutation in clinical nasal swab samples taken from Covid-19 patients. 2021 Meta gene Introduction SARS_CoV_2 D614G 144 149 COVID-19 201 209 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. They predicted spike protein destabilizing effect of the D614G mutation, leading to rapid S1 detachment with S2 causing more ACE2 attachments. 2021 Meta gene Introduction SARS_CoV_2 D614G 57 62 S 15 20 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. Overall, this work helps establish the interactions of host factors with viral 5'UTR stem-loops and understanding the effect of C241T mutation on the dynamics of SL1, SL2, SL3 SL4A, SL4B and SL5 with respect to host-factors. 2021 Informatics in medicine unlocked Introduction SARS_CoV_2 C241T 128 133 5'UTR 79 84 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. Though a lot of research has been performed about the missense variants of the genome, to the best of our knowledge, no detailed reports on the effect of the 5' UTR variant C241T on host factor binding are available. 2021 Informatics in medicine unlocked Introduction SARS_CoV_2 C241T 173 178 5'UTR 158 164 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. Top variants in the SARS-CoV-2 genome include high-frequency variants including C241T, C1059T, C3037T, C14408T, A23403G, G25563T, and G28883C, out of which the C241T variant had a 99 % frequency with 0.505 entropy by October 2020. 2021 Informatics in medicine unlocked Introduction SARS_CoV_2 A23403G;C1059T;C14408T;C241T;C241T;C3037T;G25563T;G28883C 112;87;103;80;160;95;121;134 119;93;110;85;165;101;128;141 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. Among the genetic variations that have evolved during the course of the SARS-CoV-2 outbreak, the D614G substitution in the spike (S) protein, which corresponds to a change of the A nucleotide at genome position 23403 to a G, has been identified as the signature of the A2a clade of SARS-CoV-2, the most prevalent clade. 2021 mBio Introduction SARS_CoV_2 D614G 97 102 S;S 123;130 128;131 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. As noted previously, the D614G substitution is located in the C-terminal region of the S1 domain of the S protein, close to the furin cleavage site (between amino acids [aa] 685 and 686). 2021 mBio Introduction SARS_CoV_2 D614G 25 30 S 104 105 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. Elucidating the molecular basis for the higher infectivity of the D614G virus is urgent to understand its predominance and to design an effective treatment strategy for patients. 2021 mBio Introduction SARS_CoV_2 D614G 66 71 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. It thus raised the possibility that the D614G substitution contributes to the increased accessibility of the S protein for cleavage by furin through a conformational change and thus increases the membrane fusion activity of the virus; this may be the basis for the increased infectivity, transmission capability, and virus titer of S-G614-containing SARS-CoV-2. 2021 mBio Introduction SARS_CoV_2 D614G 40 45 Membrane;S;S 196;109;332 204;110;333 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. Meanwhile, recent cryogenic electron microscopy (cryo-EM) studies suggested that the D614G substitution might induce conformational changes in the S protein. 2021 mBio Introduction SARS_CoV_2 D614G 85 90 S 147 148 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. The effects of the D614G substitution on enhanced S cleavage and syncytium formation were further quantitatively validated in cells expressing S protein. 2021 mBio Introduction SARS_CoV_2 D614G 19 24 S;S 50;143 51;144 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. These findings thus raised the possibility that the D614G substitution confers increased infectivity and transmissibility neither through an increased binding to ACE2 nor through increased escape of immune surveillance. 2021 mBio Introduction SARS_CoV_2 D614G 52 57 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. This cell-based assay system was further used to examine the critical role of furin-mediated S cleavage for the effect of the D614G substitution. 2021 mBio Introduction SARS_CoV_2 D614G 126 131 S 93 94 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. Analysis of the B.1.526 titers showed the S477N version was neutralized with a titer similar to D614G; neutralization titers of the E484K version were decreased by 3.6-fold, a titer similar to that of B.1.351. 2021 mBio Introduction SARS_CoV_2 D614G;E484K;S477N 96;132;42 101;137;47 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. Immunoblot analysis showed that both B.1.526 spike proteins were expressed and processed in transfected human 293T cells and that both were incorporated into virions at a level comparable to that of the wild-type (D614G) spike protein. 2021 mBio Introduction SARS_CoV_2 D614G 214 219 S;S 45;221 50;226 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. One version of B.1.526 also contains the E484K mutation, which is present in the B.1.351 and B.1.1.248 variant spike proteins and allows for partial escape from immune serum neutralization; the other lacks the E484K mutation but has a nearby S477N mutation, which lies within the receptor binding domain (RBD) and thus may influence affinity for the entry receptor ACE2. 2021 mBio Introduction SARS_CoV_2 E484K;E484K;S477N 41;210;242 46;215;247 RBD;S;RBD 280;111;305 303;116;308 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. Our results showed that REGN10987, which binds to the side of the RBD, maintains potent neutralizing activity against both versions of B.1.526 but that REGN10933, which binds to the top face of the RBD, that interacts with ACE2, loses 12-fold potency against the E484K version. 2021 mBio Introduction SARS_CoV_2 E484K 263 268 RBD;RBD 66;198 69;201 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. Previous studies have shown that the E484K mutation in the B.1.351 spike protein leads to a degree of resistance to neutralization by both infection- and vaccine-elicited antibodies, as well as to the REGN10933 therapeutic monoclonal antibody. 2021 mBio Introduction SARS_CoV_2 E484K 37 42 S 67 72 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. REGN10933 neutralized virus with the S477N B.1.526 spike protein with a high titer but was 12-fold less active against the E484K B.1.526 version. 2021 mBio Introduction SARS_CoV_2 E484K;S477N 123;37 128;42 S 51 56 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. The B.1.526 variant spike proteins contain the D614G mutation, a shared set of novel mutations (L5F, T95I, D253G, and A701V), and either E484K or S477N, both of which lie within the RBD. 2021 mBio Introduction SARS_CoV_2 A701V;D253G;D614G;E484K;S477N;T95I;L5F 118;107;47;137;146;101;96 123;112;52;142;151;105;99 S;RBD 20;182 25;185 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. The D253G mutation is located in the amino-terminal supersite that serves as a binding site for neutralizing antibodies, while A701V is located adjacent to the furin processing site. 2021 mBio Introduction SARS_CoV_2 A701V;D253G 127;4 132;9 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. The decrease in neutralizing titer was caused by the E484K mutation and is similar to the previously reported loss of titer against B.1.351, which also bears the mutation. 2021 mBio Introduction SARS_CoV_2 E484K 53 58 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. The E484K version of B.1.526 did show a significant, nearly 4-fold, decrease in neutralization by vaccine-elicited antibodies, but this represents a modest decrease in titer that is not expected to result in a significant decrease in the protection provided by vaccination and is not expected to result in an increased susceptibility to reinfection. 2021 mBio Introduction SARS_CoV_2 E484K 4 9 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. The PDB file of D614G SARS-CoV-2 spike protein (7BNM) was downloaded from the Protein Data Bank. 2021 mBio Introduction SARS_CoV_2 D614G 16 21 S 33 38 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. The REGN-COV2 cocktail potently neutralized the B.1.526 spike variants despite the partial loss of neutralizing activity against the E484K version of B.1.526. 2021 mBio Introduction SARS_CoV_2 E484K 133 138 S 56 61 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. The results showed that BNT162b2 vaccine serum-elicited antibodies neutralized the D614G and B.1.1.7 viruses with similarly high titers, while titer for neutralization of B.1.351 was decreased by 3.4-fold. 2021 mBio Introduction SARS_CoV_2 D614G 83 88 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. The results showed that neutralizing titers against the S477N B.1.526 variant were similar to that of D614G, while the neutralizing titers against the E484K B.1.526 variant decreased by 3.8-fold, a modest decrease that was attributed to the E484K mutation. 2021 mBio Introduction SARS_CoV_2 D614G;E484K;E484K;S477N 102;151;241;56 107;156;246;61 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. The S477N version was neutralized with no decrease in titer. 2021 mBio Introduction SARS_CoV_2 S477N 4 9 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. The vast majority of sequenced SARS-CoV-2 isolates contain a D614G mutation in the spike protein that increases viral infectivity and transmissibility and, subsequently, variants with multiple mutations in the spike protein and enhanced transmissibility have emerged in the United Kingdom, South Africa, Brazil, and the United States, raising concerns of diminished neutralization by immune sera-elicited antibodies and escape from therapeutic monoclonal antibodies. 2021 mBio Introduction SARS_CoV_2 D614G 61 66 S;S 83;210 88;215 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. To test the ability of convalescent-phase sera to neutralize the B.1.526 viruses, we determined the neutralizing antibody titers of sera from individuals who had been infected prior to April 2020 on viruses with D614G, B.1.526 and E484K spike proteins. 2021 mBio Introduction SARS_CoV_2 D614G;E484K 212;231 217;236 S 237 242 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. Two versions of B.1.526 were identified, both having the D614G and A701V mutations and, in addition, the mutations L5F, T95I, and D253G, which are not present in previously reported variants. 2021 mBio Introduction SARS_CoV_2 A701V;D253G;D614G;L5F;T95I 67;130;57;115;120 72;135;62;118;124 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. We found that the B.1.526 variant (S477N) was fully susceptible to neutralization, while the B.1.526 variant with the E484K mutation neutralized with a modest (3.5-fold) reduction in titer by convalescent and vaccine-elicited antibodies. 2021 mBio Introduction SARS_CoV_2 E484K;S477N 118;35 123;40 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. We report here that both S477N and E484K versions of B.1.526 were neutralized well by convalescent and vaccine-elicited antibodies. 2021 mBio Introduction SARS_CoV_2 E484K;S477N 35;25 40;30 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Although the Sputnik V vaccine has a reported vaccine efficacy of 91.6% in the interim analysis of Phase 3 trials held in Russia between September 7 and November 24, 2020, none of the VOC mentioned above nor independent lineages containing the E484K mutation were prevalent in Russia during this time period. 2021 Nature communications Introduction SARS_CoV_2 E484K 244 249 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Analyses of dose response curves indicate that S: B.1.351 exhibits resistance to neutralizing sera in a manner that is qualitatively different from the E484K mutant. 2021 Nature communications Introduction SARS_CoV_2 E484K 152 157 S 47 48 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. For example, a B.1.526 sub-lineage carrying E484K in recent weeks has expanded more rapidly than B.1.1.7, which may be indicative of the ability of S: E484K variants to penetrate herd immunity. 2021 Nature communications Introduction SARS_CoV_2 E484K;E484K 44;151 49;156 S 148 149 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Here, we generated isogenic replication-competent vesicular stomatitis virus bearing the prevailing wild-type (WT = D614G) SARS-CoV-2 S (rcVSV-CoV2-S), or the B.1.1.7 (alpha variant), B.1.351 (beta variant) or E484K mutant S and used them in a robust virus neutralization assay. 2021 Nature communications Introduction SARS_CoV_2 D614G;E484K 116;210 121;215 S;S;S 134;148;223 135;149;224 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. In contrast, the E484K polymorphism is recurrently emergent, and is found in a number of other lineages that are increasing in the U.S. 2021 Nature communications Introduction SARS_CoV_2 E484K 17 22 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Our work was spurred by Argentina's nascent genomic surveillance efforts, which detected multiple independent lineages with S: E484K (B.1.1.318 and P.2) and/or S: N501Y substitutions (B.1.1.7 and P.1) in common, just as Argentina had started rolling out its vaccination campaign, which commenced on December 29, 2020. 2021 Nature communications Introduction SARS_CoV_2 E484K;N501Y 127;163 132;168 S;S 124;160 125;161 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. S: E484K had already been identified in multiple independent laboratories to confer escape from convalescent sera and monoclonal antibodies. 2021 Nature communications Introduction SARS_CoV_2 E484K 3 8 S 0 1 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Since the Sputnik vaccine is now in use not only in Russia, but also in countries like Argentina, Mexico, and Hungary, where some of the VOC and emerging lineages bearing the E484K mutation are more widespread, it is critical to assess the neutralizing activity of Sputnik vaccine elicited antibody responses against these cognate VOC and mutant spikes. 2021 Nature communications Introduction SARS_CoV_2 E484K 175 180 S 346 352 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. The P.2 lineage, originally detected in Rio de Janeiro, carries only the E484K mutation in the RBD and has spread to other parts of South America, including Argentina. 2021 Nature communications Introduction SARS_CoV_2 E484K 73 78 RBD 95 98 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. The S genes of B.1.351 and P.1 viruses each carry a number of mutations, but include three in the receptor binding domain (RBD) that are particularly notable, the S: N501Y substitution, found in B.1.1.7, alongside polymorphisms at positions 417 and 484, K417N/T and E484K. 2021 Nature communications Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 266;254;254;166 271;261;261;171 RBD;RBD;S;S 98;123;4;163 121;126;5;164 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. The same sera, however, exhibited moderate and markedly reduced neutralization titers, respectively, against S: E484K and S: B.1.351. 2021 Nature communications Introduction SARS_CoV_2 E484K 112 117 S;S 109;122 110;123 34314050 SARS-CoV-2 R.1 lineage variants that prevailed in Tokyo in March 2021. Therefore, we began testing all samples from outpatients and inpatients who tested polymerase chain reaction (PCR)-positive for SARS-CoV-2 for its associated mutations, N501Y and E484K, using PCR-based melting curve analysis. 2021 Journal of medical virology Introduction SARS_CoV_2 E484K;N501Y 179;169 184;174 34314668 Emergence of SARS-COV-2 Spike Protein Escape Mutation Q493R after Treatment for COVID-19. Bamlanivimab has been recently withdrawn as a monotherapy because of treatment failure against E484K SARS-CoV-2 virus variants. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 95 100 34314668 Emergence of SARS-COV-2 Spike Protein Escape Mutation Q493R after Treatment for COVID-19. Emergence of SARS-COV-2 spike protein escape mutation Q493R after treatment for COVID-19. 2021 Emerging infectious diseases Introduction SARS_CoV_2 Q493R 54 59 S 24 29 COVID-19 80 88 34314668 Emergence of SARS-COV-2 Spike Protein Escape Mutation Q493R after Treatment for COVID-19. However, the May 3 specimen showed a secondary A1478G peak in the spike protein gene, corresponding to the spike Q493R mutation, which became predominant by May 8 (Ct 18; GenBank accession no. 2021 Emerging infectious diseases Introduction SARS_CoV_2 A1478G;Q493R 47;113 53;118 S;S 66;107 71;112 34314668 Emergence of SARS-COV-2 Spike Protein Escape Mutation Q493R after Treatment for COVID-19. In a flow cytometry competitive assay, Q493R reduces the 50% inhibitory concentration >100-fold for bamlanivimab and 42-fold for etesivimab. 2021 Emerging infectious diseases Introduction SARS_CoV_2 Q493R 39 44 34314668 Emergence of SARS-COV-2 Spike Protein Escape Mutation Q493R after Treatment for COVID-19. In pseudoviral neutralization assays, Q493R reduces susceptibility to bamlanivimab by >6,666-fold, to etesevimab by 232-fold, and to the combination of both drugs by >100-fold. 2021 Emerging infectious diseases Introduction SARS_CoV_2 Q493R 38 43 34314668 Emergence of SARS-COV-2 Spike Protein Escape Mutation Q493R after Treatment for COVID-19. Q493R has a frequency of 0.006% in the GISAID database (https://www.gisaid.org; 85 of 1,424,998 deposited sequences as of May 8, 2021; https://covid19dashboard.regeneron.com/?tab=Mutation_Details&subTab=Spike), making the occurrence of co-infection with a Q493R-positive strain extremely unlikely in our patient. 2021 Emerging infectious diseases Introduction SARS_CoV_2 Q493R;Q493R 256;0 261;5 S 203 208 34314668 Emergence of SARS-COV-2 Spike Protein Escape Mutation Q493R after Treatment for COVID-19. Q493R/K (which can be selected in vitro by bamlanivimab ) is to date the only mutation that causes resistance to bamlanivimab and etesivimab. 2021 Emerging infectious diseases Introduction SARS_CoV_2 Q493K;Q493R 0;0 7;7 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Furthermore, to understand the stability of the S-protein P681H mutation, compared the S-protein B.1.1.7 variant upon interaction with furin, both states were subjected to 100ns molecular dynamic (MD) simulations. 2021 Virus research Introduction SARS_CoV_2 P681H 58 63 S;S 48;87 49;88 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Hence, in this study, we compared the S-protein-B.1.1.7 variant structure in complex with furin with the S-protein P681H-furin complex to determine if the B.1.1.7 variant or the P681H mutation affected furin cleavage. 2021 Virus research Introduction SARS_CoV_2 P681H;P681H 115;178 120;183 S;S 38;105 39;106 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. In addition, we calculated the binding affinity of furin to S-protein-P681H and S-protein-B.1.1.7 variant using Generalized-Born surface area molecular mechanics (MM/GBSA). 2021 Virus research Introduction SARS_CoV_2 P681H 70 75 S;S 60;80 61;81 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Increased SARS-CoV-2 infectivity was observed with the S-protein-D614G mutation initially found in the European population. 2021 Virus research Introduction SARS_CoV_2 D614G 65 70 S 55 56 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Notably, the N501Y mutation is located in the receptor-binding domain (RBD), which interacts with ACE2 and the deletions present on the N-terminal domain (NTD) of the S-protein. 2021 Virus research Introduction SARS_CoV_2 N501Y 13 18 RBD;N;S 71;136;167 74;137;168 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. One of the notable mutations in the B.1.1.7 variant is the P681H, which is a substitution of proline (P) to histidine (H) on the S-protein "PRRAR" at furin cleavage site. 2021 Virus research Introduction SARS_CoV_2 P681H 59 64 S 129 130 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Patients infected with SARS-CoV-2 D614G mutation manifested higher viral RNA levels and demonstrated higher titers with pseudoviruses in vitro infection assays, indicating that the D614G mutation is more permissive than the wild type (WT) virus first discovered in Wuhan, China. 2021 Virus research Introduction SARS_CoV_2 D614G;D614G 34;181 39;186 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Recently it was shown that the D614G (European origin) substitution influenced the S-protein stability and enhanced binding of furin to S-protein "PRRAR" cleavage site as compared to the WT discovered in Wuhan, China (; Mohammad et al., 2020). 2021 Virus research Introduction SARS_CoV_2 D614G 31 36 S;S 83;136 84;137 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Since furin proteolysis occurs at a specific multi-basic sequence (R-[X]-(R/K)-R), the substitution of P681H on the furin cleavage site may affect the structure of S-protein, hence enhancing the infectivity of the new SARS-CoV-2 variant. 2021 Virus research Introduction SARS_CoV_2 P681H 103 108 S 164 165 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. The B.1.1.7 SARS-CoV-2 variant strain exhibits missense mutations (N501Y, A570D, P681H, D614G, T716I, S982A, D1118H) and three deletions in residues H69, V70, Y144. 2021 Virus research Introduction SARS_CoV_2 A570D;D1118H;D614G;P681H;S982A;T716I;N501Y 74;109;88;81;102;95;67 79;115;93;86;107;100;72 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. The B.1.1.7 strain consists of seven mutations and three residue deletions on the spike protein (S-protein) compared to the initial SARS-CoV-2 strain that was reported in Wuhan, China, and the D614G strain that originated in Europe. 2021 Virus research Introduction SARS_CoV_2 D614G 193 198 S;S 82;97 87;98 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Therefore, it would be of interest to ascertain if all the mutations and deletions present in the B.1.1.7 variant affect the binding to furin or just the P681H mutation. 2021 Virus research Introduction SARS_CoV_2 P681H 154 159 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Therefore, we utilized structural bioinformatics tools to decipher the binding differences and structural-dynamic variations of S-protein-P681H and the B.1.1.7 variant. 2021 Virus research Introduction SARS_CoV_2 P681H 138 143 S 128 129 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. Corroborating the potential biological relevance of those recurrent mutations, some of them are predicted to affect SARS-CoV-2 affinity to ACE-2 receptors (e.g., Y453F), to be potentially involved in immune evasion (e.g., E484K), or to increase entry efficiency (e.g., DeltaH69/DeltaV70). 2021 mSphere Introduction SARS_CoV_2 E484K;Y453F 222;162 227;167 34326308 Structural and functional basis for pan-CoV fusion inhibitors against SARS-CoV-2 and its variants with preclinical evaluation. Indeed, under the pressure of host immunity, some mutations, which have occurred in the RBD, such as N501Y, K417N, and E484K, are found in numerous variants, including B.1.1.248 and B.1.351 dominant variants. 2021 Signal transduction and targeted therapy Introduction SARS_CoV_2 E484K;K417N;N501Y 119;108;101 124;113;106 RBD 88 91 34332998 The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another. This is respectively the case for the E484K mutation, found in the B.1.351 and P.1 variants, and for the N501Y mutation found in these two VOCs as well as in the B.1.1.7. 2021 Journal of virological methods Introduction SARS_CoV_2 E484K;N501Y 38;105 43;110 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. Moreover, it has been found that V62L mutation was accompanied with L84S mutation. 2021 Frontiers in microbiology Introduction SARS_CoV_2 L84S;V62L 68;33 72;37 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. We found that mutations in ORF8, in particular W45L, increase the binding with IRF3, suggesting the important role of SARS-CoV-2 ORF8 in regulating innate immune response upon virus infection. 2021 Frontiers in microbiology Introduction SARS_CoV_2 W45L 47 51 ORF8;ORF8 27;129 31;133 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. (2) The root-mean-square deviations (RMSDs) and root-mean-square fluctuations (RMSFs) of the 501Y.V1, 501Y.V2, and N439K variants were all greater than those of wild-type SARS-CoV-2, indicating the increased flexibility of the SARS-CoV-2 residues after mutations and the enhanced binding affinities between the three variants and the hACE2 receptor. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 N439K 115 120 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. (3) The binding free energy calculations indicated that the 501Y.V1, 501Y.V2 and N439K variants all had significant increases in binding affinity, with enhancements of 36.8%, 19.6% and 29.5%, respectively, indicating the enhanced binding affinity of the SARS-CoV-2 variant. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 N439K 81 86 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. (5) The N501Y mutation waw present not only in the 501Y.V1 variant but also in the 501Y.V2 variant. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 N501Y 8 13 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. 1(a), the 501Y.V1 variant contains N501Y mutation in the RBD, the 501Y.V2 variant contains the mutations of K417N, E484K, and N501Y in the RBD, and the N439K variant contains the mutation of N439K in the RBD. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 E484K;K417N;N439K;N439K;N501Y;N501Y 115;108;152;191;35;126 120;113;157;196;40;131 RBD;RBD;RBD 57;139;204 60;142;207 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. For example, the 501Y.V1 and N439K variants were both capable of creating new hydrogen bonds, resulting in the enhancement of their binding affinities to hACE2. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 N439K 29 34 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. For example, the N439K variant, in which the ASN439 residue in the RBD is mutated to LYS439, first emerged in Scotland and spread widely in many European countries. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 N439K 17 22 RBD 67 70 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. However, the 501Y.V1 variant had a stronger binding affinity to hACE2 than the 501Y.V2 variant, suggesting that the K417N and E484K mutations in the 501Y.V2 variant weaken the binding affinity between the SARS-CoV-2 RBD and hACE2 compared to the 501Y.V1 variant by breaking hydrogen bonds. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 E484K;K417N 126;116 131;121 RBD 216 219 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. In this work, we studied the structures, chemical bond changes, binding free energies (enthalpy and entropy), and residue contribution decompositions of the three most widespread and important S glycoprotein variants (501Y.V1, 501Y.V2, N439K) of SARS-CoV-2. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 N439K 236 241 S 193 207 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. K417N refers to the residue mutation from LYS417 to ASN417, E484K represents the residue mutation from GLU484 to LYS484, and N501Y denotes the residue mutation from ASN501 to TYR501. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 N501Y;E484K;E484K;K417N;N501Y;K417N 165;60;103;42;125;0 181;65;119;58;130;5 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. N439K was reported to significantly enhance the binding affinity of S glycoprotein to the hACE2 receptor and influence the activity of neutralizing antibodies. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 N439K 0 5 S 68 82 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. The 501Y.V2 variant has three residue mutations in the S glycoprotein (K417N, E484K and N501Y mutations), which allow the virus to more easily bind to human cells. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 E484K;N501Y;K417N 78;88;71 83;93;76 S 55 69 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. In the CoV-2 E protein sequence, arginine is mutated by isoleucine, threonine, and lysine (R69I, R69T, and R69K) at the 69th position. 2021 Informatics in medicine unlocked Introduction SARS_CoV_2 R69K;R69T;R69I 107;97;91 111;101;95 E 13 14 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. In the current study, the most common mutations that were detected at the C-terminal (Ser68Phe, Pro71Ser, Leu73Phe) were exhibiting more stabilizing effect on E proteins structure. 2021 Informatics in medicine unlocked Introduction SARS_CoV_2 L73F;P71S;S68F 106;96;86 114;104;94 E 159 160 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. After March 2020, only two mutations, RNA-directed RNA polymerase P323L (ORF1ab P4715L, ORF1b P314L) and spike protein D614G had nearly overwhelmed the original mutation sites (). 2021 ACS omega Introduction SARS_CoV_2 D614G;P314L;P323L;P4715L 119;94;66;80 124;99;71;86 ORF1ab;S 73;105 79;110 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. Although B.1.427/429 exhibited an 18.6-24% increase in transmissibility relative to wild-type circulating strains, a quantitative deep mutational scanning of L452R indicated the constant binding affinity against the wild-type one in contrast with the high expression. 2021 ACS omega Introduction SARS_CoV_2 L452R 158 163 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. Although the high binding affinity of the mutation site such as N501Y in B.1.1.7 (alpha) expanded from UK and in B.1.351 (beta) circulated from South Africa, which was measured by the quantitative deep mutational scanning, can rationalize the increased infections, identifying the fundamental cause of vaccine nullification is difficult in general, and is a source of significant concern. 2021 ACS omega Introduction SARS_CoV_2 N501Y 64 69 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. As for the receptor-binding motif (RBM) of spike protein, before B.1.1.7, B.1.351, and P.1, the mutation of S477N has expanded in Australia and in Europe but has not led to an extension of the pandemic (). 2021 ACS omega Introduction SARS_CoV_2 S477N 108 113 S 43 48 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. B.1.1.7 is prevalent all over the world, but the N501Y frequency of phylogeny is about 60-70% (). 2021 ACS omega Introduction SARS_CoV_2 N501Y 49 54 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. In January 2021, novel strains B.1.427/429, which contain S13I, W152C, L452R, and D614G mutations in the spike protein, were found in California (Figure 1A). 2021 ACS omega Introduction SARS_CoV_2 D614G;L452R;S13I;W152C 82;71;58;64 87;76;62;69 S 105 110 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. On the other hand, P.1 that emerged in Brazil has K417T, E484K, N501Y, and D614G mutations (Figure 1B). 2021 ACS omega Introduction SARS_CoV_2 D614G;E484K;K417T;N501Y 75;57;50;64 80;62;55;69 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The main protein substitutions are L452R, E484Q (or T478K), D614G, and P681R. 2021 ACS omega Introduction SARS_CoV_2 D614G;E484Q;L452R;P681R;T478K 60;42;35;71;52 65;47;40;76;57 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. As shown in Figure 2B,C, Alpha and Beta variants include N501Y mutation, while Beta variant involves two additional mutations, K417N and E484K. 2021 bioRxiv Introduction SARS_CoV_2 E484K;K417N;N501Y 137;127;57 142;132;62 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. conducted an experimental and computational study to capture the role of N501Y mutation in Alpha, Beta, and Gamma variants. 2021 bioRxiv Introduction SARS_CoV_2 N501Y 73 78 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. Even though both Epsilon and Kappa/Delta variants share L452R mutation, Kappa and Delta variants show similar trends in force profiles to WT from D = 55 A to 75 A (Figure 1A). 2021 bioRxiv Introduction SARS_CoV_2 L452R 56 61 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. Gamma variant also shows decreased contact numbers similar to Beta due to its K417T mutation (Figure S2A). 2021 bioRxiv Introduction SARS_CoV_2 K417T 78 83 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. However, only the N501Y mutation was examined in their study, although other potentially important mutations have emerged. 2021 bioRxiv Introduction SARS_CoV_2 N501Y 18 23 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. In addition, Epsilon variant is likely to be relatively easily dissociated from ACE2 than others due to its destabilized RBD structure upon the L452R mutation. 2021 bioRxiv Introduction SARS_CoV_2 L452R 144 149 RBD 121 124 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. It should be noted that this difference between Kappa/Delta and Epsilon might stem from the limitation in our model in this study, as we only employed L452R mutation in RBD for Epsilon variant without D614G mutation. 2021 bioRxiv Introduction SARS_CoV_2 D614G;L452R 201;151 206;156 RBD 169 172 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. K417N. 2021 bioRxiv Introduction SARS_CoV_2 K417N 0 5 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. K417N/T mutations of Beta and Gamma appear to make the RBD-ACE2 interactions less strong compared to Alpha variant. 2021 bioRxiv Introduction SARS_CoV_2 K417N;K417T 0;0 7;7 RBD 55 58 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. Newly reported Kappa and Delta variants display the same L452R mutation as Epsilon, but each variant contains an additional mutation, E484Q (Kappa) or T478K (Delta). 2021 bioRxiv Introduction SARS_CoV_2 E484Q;L452R;T478K 134;57;151 139;62;156 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. Note that L450 and L492 are positioned in different beta-strands (Figure S4B,D colored in green and orange, respectively), and the L452R mutation makes the RBD-ACE2 interface unstable by shortening each beta-strand (i.e., the length of interacting beta-strands of Epsilon variant is decreased by almost half). 2021 bioRxiv Introduction SARS_CoV_2 L452R 131 136 RBD 156 159 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. Such contacts are decreased or even lost in the case of RBDWT or RBDEpsilon lacking the N501Y mutation (Figure 2A,D). 2021 bioRxiv Introduction SARS_CoV_2 N501Y 88 93 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. The only difference between Gamma and Beta is the K417 mutation, i.e., K417T vs. 2021 bioRxiv Introduction SARS_CoV_2 K417T 71 76 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. The weakened interactions of RBDBeta N417 and RBDGamma T417 could make them less contagious than the Alpha variant, while the N501Y mutation still allows them to have a strong enough potential to interact with ACE2. 2021 bioRxiv Introduction SARS_CoV_2 N501Y 126 131 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. They investigated each specific mutation, N501Y, K417N/T, and E484K, and reported that F486, Q498, T500, and Y505 in RBD are important residues across viral variants in the RBD-ACE2 interface. 2021 bioRxiv Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 62;49;49;42 67;56;56;47 RBD;RBD 117;173 120;176 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. To gain molecular insight into the difference of all variants that are classified as the variants of concern (Alpha (first identified in United Kingdom, B.1.1.7: N501Y), Beta (first identified in South Africa, B.1.351: K417N, E484K, N501Y), Gamma (first identified in Japan/Brazil, P.1: K417T, E484K, N501Y), and Delta (first identified in India, B.1.617.2: L452R, T478K)) and two additional variants of interest (Epsilon (first identified in US-California, B.1.427: L452R) and Kappa (first identified in India, B.1.617.1: L452R, E484Q)), pulling force analysis was performed on each RBD-ACE2 complex (Figure 1A) as a function of distance (D) between the centers of mass of RBD and ACE2 proteins. 2021 bioRxiv Introduction SARS_CoV_2 E484K;E484K;E484Q;K417N;K417T;L452R;L452R;L452R;N501Y;N501Y;N501Y;T478K 226;294;530;219;287;358;467;523;162;233;301;365 231;299;535;224;292;363;472;528;167;238;306;370 RBD;RBD 584;674 587;677 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. To investigate the mechanism behind such a big difference, the contact analysis in between RBD residues was performed, where the influence of the L452R mutation was examined by checking its contacts with surrounding residues, L450 and L492 (Figure S4). 2021 bioRxiv Introduction SARS_CoV_2 L452R 146 151 RBD 91 94 34341794 Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. Upon the T478K mutation, it requires the highest force for the RBD-ACE2 complex to be completely dissociated at D = 78 A (Figure 1A). 2021 bioRxiv Introduction SARS_CoV_2 T478K 9 14 RBD 63 66 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. found six distinct types of mutations namely, V367F, P384L, S438F, K439N, G476S, and V483A in RBD domain of the S-protein. 2021 Computers in biology and medicine Introduction SARS_CoV_2 G476S;K439N;P384L;S438F;V367F;V483A 74;67;53;60;46;85 79;72;58;65;51;90 RBD;S 94;112 97;113 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. MD simulation approach revealed the structural changes of mutant (N501Y and D614G) proteins. 2021 Computers in biology and medicine Introduction SARS_CoV_2 D614G;N501Y 76;66 81;71 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Mutation D614G was the most abundant mutation and showed the highly infectious A2 subtypes of SARS-CoV-2. 2021 Computers in biology and medicine Introduction SARS_CoV_2 D614G 9 14 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Recently, the mutation N501Y was observed in the RBD domain, which has spread rapidly in the UK and other countries. 2021 Computers in biology and medicine Introduction SARS_CoV_2 N501Y 23 28 RBD 49 52 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The mutation D614G, which originated either in China or Europe, and started to spread swiftly first in Europe and then throughout the world, is the focus of the current pandemic in a number of countries. 2021 Computers in biology and medicine Introduction SARS_CoV_2 D614G 13 18 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The mutation N501Y has augmented the many discussions and questions, but only a small amount of data relating to it is currently available. 2021 Computers in biology and medicine Introduction SARS_CoV_2 N501Y 13 18 34346744 SARS-CoV-2 Quasispecies Provides an Advantage Mutation Pool for the Epidemic Variants. The spike mutation of D614G is widely spread in infected patients, and its infection ability is 2.6 to 9.3 times stronger than the early ancestral haplotypes. 2021 Microbiology spectrum Introduction SARS_CoV_2 D614G 22 27 S 4 9 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. For example, the Spike protein mutation D614G has been associated with higher upper respiratory tract viral loads and appears to be omnipresent in recent genomic sequences across the globe. 2021 Microbiology spectrum Introduction SARS_CoV_2 D614G 40 45 S 17 22 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. For example, we previously identified D614 as a key glue point with neighboring protomer residues (Table S1 in the supplemental material) prior to its mutational emergence (as D614G) in current variants. 2021 Microbiology spectrum Introduction SARS_CoV_2 D614G 176 181 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. In addition, another variant called the UK variant or VOC 202012/01 or B.1.1.7 (classification system) has been identified as a highly transmittable variant and involves both deletions and mutations in the Spike protein of this virion, including D614G. 2021 Microbiology spectrum Introduction SARS_CoV_2 D614G 246 251 S 206 211 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. In addition, using these tools, we critically examine the UK variant B.1.1.7, including the D614G mutation, in order to discern key differences in protomer configurations that could potentially impact vaccine and therapeutic efforts aimed at the debilitation of the current pandemic. 2021 Microbiology spectrum Introduction SARS_CoV_2 D614G 92 97 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. We are able to demonstrate dynamic changes in the B.1.1.7 spike protein that can be traced to two key mutations, resulting in a more accessible RBD (D614G) and simultaneously stronger binding to ACE2 (N501Y). 2021 Microbiology spectrum Introduction SARS_CoV_2 D614G;N501Y 149;201 154;206 S;RBD 58;144 63;147 34351228 Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia. Of the nine strains sequenced, six were classified as the B.1.351 variant, which harbors the E484K and N501Y mutations commonly associated with increased transmission rate. 2021 Microbiology resource announcements Introduction SARS_CoV_2 E484K;N501Y 93;103 98;108 34351228 Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia. The COVID-19 D614G mutation was associated with higher risk of infection. 2021 Microbiology resource announcements Introduction SARS_CoV_2 D614G 13 18 COVID-19 4 12 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Experimental analysis of the effect of the SARS-CoV-2 Spike mutation D614G and the comparison between SARS-CoV and SARS-CoV-2 Spike proteins show unique dynamic characteristics that correlate with epidemiological and experimental data on infection. 2021 PLoS computational biology Introduction SARS_CoV_2 D614G 69 74 S;S 54;126 59;131 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. A two amino acid deletion in positions 69 and 70 of spike is observed in cluster 5 and lineages B.1.1.7, B.1.525 and B.1.258. 2021 PLoS pathogens Introduction SARS_CoV_2 del 69 2 41 S 52 57 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. For example, in B.1.351 and P.1 lineages, mutations in amino acid residues at positions 18 (L18F) and at position 417 (S417N, or S417T in some P.1 cases) were observed. 2021 PLoS pathogens Introduction SARS_CoV_2 S417T;L18F;S417N 129;92;119 134;96;124 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. In fact, the D614G mutation in the spike protein was amongst the few epidemiologically significant variants, resulting in increased transmissibility without affecting the severity of the disease. 2021 PLoS pathogens Introduction SARS_CoV_2 D614G 13 18 S 35 40 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. Interestingly, the reduction became substantial with the addition of synergetic mutations K417N/N501Y to E484K, or E484K/N501Y to S494P. 2021 PLoS pathogens Introduction SARS_CoV_2 E484K;E484K;K417N;S494P;N501Y;N501Y 105;115;90;130;96;121 110;120;95;135;101;126 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. It also suggests that the combination of these mutations with others that promote ACE2 binding, such as N501Y, increases their ability to escape neutralizing-antibody responses. 2021 PLoS pathogens Introduction SARS_CoV_2 N501Y 104 109 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. L452R and N439K are associated with a modest reduction in antibody-dependent neutralization by immune sera, whilst variants containing E484K display a reduction that is moderate to substantial. 2021 PLoS pathogens Introduction SARS_CoV_2 E484K;N439K;L452R 135;10;0 140;15;5 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. More recently, other lineages were added to this list: B.1.427, B.1.429 [California, United States of America (USA)], B.1.617 or B.1.617.1-3 (India), as well as several lineages of interest that carry the mutation E484K, including P.2 and B.1.1.7 containing E484K. 2021 PLoS pathogens Introduction SARS_CoV_2 E484K;E484K 214;258 219;263 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. The appearance of shared mutations in distinct and rapidly spreading SARS-CoV-2 lineages suggests that these mutations, either alone or in combination, may provide fitness advantage, as recently observed with the acquisition of S417N by B.1.617.2 lineage. 2021 PLoS pathogens Introduction SARS_CoV_2 S417N 228 233 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. Three mutations:D614G, N501Y and L452R - are associated with an increased ACE2 binding affinity in humans and increased viral transmission. 2021 PLoS pathogens Introduction SARS_CoV_2 L452R;N501Y;D614G 33;23;16 38;28;21 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. We found a moderate reduction in neutralizing potency of sera against SARS-CoV-2 spike-pseudotyped lentivirus containing single mutations at positions 484 (E484K) and 494 (S494P). 2021 PLoS pathogens Introduction SARS_CoV_2 E484K;S494P 156;172 161;177 S 81 86 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. Y453F was associated with a mink-to-human adaptation in cluster 5. 2021 PLoS pathogens Introduction SARS_CoV_2 Y453F 0 5 34354142 Entropy based analysis of SARS-CoV-2 spread in India using informative subtype markers. A study showed that the S-protein of SARS-CoV-2 produced an evolutionary mutation of K403R compared with the S-protein of SARS-CoV, thus forming an adjacent RGD motif at the interaction surface. 2021 Scientific reports Introduction SARS_CoV_2 K403R 85 90 S;S 24;109 25;110 34354142 Entropy based analysis of SARS-CoV-2 spread in India using informative subtype markers. Further, we investigate the progression of the major two strains (S-614G and S-614D) in different regions in India and other countries. 2021 Scientific reports Introduction SARS_CoV_2 S614D;S614G 77;66 83;72 S;S 66;77 67;78 34354142 Entropy based analysis of SARS-CoV-2 spread in India using informative subtype markers. However, one dominant mutation at position 614 of the S-protein (i.e., D614G mutation) is known to affect viral infectivity. 2021 Scientific reports Introduction SARS_CoV_2 D614G 71 76 S 54 55 34354142 Entropy based analysis of SARS-CoV-2 spread in India using informative subtype markers. Moreover, we perform geographical distribution and temporal dynamics analysis for the D614G mutation in order to understand the spread before and after mutation. 2021 Scientific reports Introduction SARS_CoV_2 D614G 86 91 34358019 Antibodies Targeting Two Epitopes in SARS-CoV-2 Neutralize Pseudoviruses with the Spike Proteins from Different Variants. Among these clades, the D614G clade has become a dominant strain type since December 2019. 2021 Pathogens (Basel, Switzerland) Introduction SARS_CoV_2 D614G 24 29 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. Assessment of individual mutation contributions shows the major impact of the E484K mutation. 2021 Vaccines Introduction SARS_CoV_2 E484K 78 83 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. These mutations are likely to include K417N, L452R, E484K, S494P and N501Y/T, based on molecular dynamics data. 2021 Vaccines Introduction SARS_CoV_2 E484K;K417N;L452R;N501T;N501Y;S494P 52;38;45;69;69;59 57;43;50;76;76;64 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. The first was the United Kingdom variant 20I/501Y.V1 (lineage B.1.1.7), followed by two other lineages: the South-African variant 20H/H501Y.V2 (lineage B.1.351) and the Brazilian variant 20J/H501Y.V3 (lineage P.1). 2021 Diagnostics (Basel, Switzerland) Introduction SARS_CoV_2 H501Y;H501Y 134;191 139;196 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Two of these lineages, B.1.351 and P.1, were of specific concern because they harbored the E484K mutation, which has been shown to enhance escape from neutralizing antibody inhibition in vitro, and may be associated with a reduced efficacy of the vaccine. 2021 Diagnostics (Basel, Switzerland) Introduction SARS_CoV_2 E484K 91 96 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Clades G/GH/GR/GV/GRY as per the Global Initiative on Sharing All Influenza Data (GISAID) database (, Accessed on 14 June 2021) possess a common mutation D614G in the spike protein. 2021 Microorganisms Introduction SARS_CoV_2 D614G 154 159 S 167 172 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. These variants are known to possess multiple mutations across the genome, including several in the S protein and its RBD, such as N501Y, E484K and K417N/T. 2021 Microorganisms Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 137;147;147;130 142;154;154;135 RBD;S 117;99 120;100 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Additionally, the mutations of L452R and E484Q within spike receptor-binding domain (RBD) were shown to have reduced susceptibility to monoclonal antibodies, including bamlanivimab, as well as convalescent plasma, even though the exact mechanism is not well-established. 2021 Virus research Introduction SARS_CoV_2 E484Q;L452R 41;31 46;36 S;RBD 54;85 59;88 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. D614G mutation is located at the S1 subunit of the S protein which mediates SARS-CoV-2 entry into cells. 2021 Virus research Introduction SARS_CoV_2 D614G 0 5 S 51 52 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Despite D614G mutation was only detected in January 2020, Korber and colleagues reported that the mutation is circulating in many places in the world. 2021 Virus research Introduction SARS_CoV_2 D614G 8 13 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Firstly, the method employed a mismatched crRNA, -3 to +3 position around the D614G site, to discriminate the wild type (D614) and the mutant (G614) virus based on the target efficiency score calculated by CRISPR-DT. 2021 Virus research Introduction SARS_CoV_2 D614G 78 83 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Hence, the D614G variant was speculated to be responsible for the high SARS-CoV-2 infectivity due to its high transmissibility. 2021 Virus research Introduction SARS_CoV_2 D614G 11 16 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. High viral RNA levels and pseudovirus titers were found in patients infected with the SARS-CoV-2 D614G variant. 2021 Virus research Introduction SARS_CoV_2 D614G 97 102 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. In this study, we developed a dual synthetic mismatches CRIPSR/Cas12a-based method (dsmCRISPR) to detect SARS-CoV-2 D614G mutation. 2021 Virus research Introduction SARS_CoV_2 D614G 116 121 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. The D614G mutation (aspartate change to glycine at position 614) in the spike (S) protein is the most prevalent variant resulting from an A-to-G nucleotide substitution at genomic position 234035. 2021 Virus research Introduction SARS_CoV_2 D614G;D614G 4;20 9;63 S;S 72;79 77;80 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. To sum up, the dsmCRIPSR method provides a novel approach to detect the D614G mutation of SARS-CoV-2 with high sensitivity and specificity, which could be extended to the detection of any other SARS-CoV-2 variants of interest. 2021 Virus research Introduction SARS_CoV_2 D614G 72 77 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. Importantly, B.1.351 and P.1 carry the E484K mutation associated with escape from neutralizing antibodies ( and). 2021 Virus research Introduction SARS_CoV_2 E484K 39 44 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. It has the same three mutations (except for K417T instead of K417N) in RBD as B.1.351, but it arose independently. 2021 Virus research Introduction SARS_CoV_2 K417N;K417T 61;44 66;49 RBD 71 74 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. L452R, E484K, N501Y, P681H/R) have been positively selected, since they may confer adaptive advantages leading to convergent evolution in different lineages spreading across multiple countries. 2021 Virus research Introduction SARS_CoV_2 E484K;N501Y;P681H;P681R;L452R 7;14;21;21;0 12;19;28;28;5 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. More recently, the B.1.617.2 lineage, first detected in India, has also been characterized as a VOC, primarily for carrying a constellation of mutations in the spike protein (especially L452R and P681R), its wide spread worldwide even outperforming other VOCs, and reduced antibody sensitivity in vaccinated individuals. 2021 Virus research Introduction SARS_CoV_2 L452R;P681R 186;196 191;201 S 160 165 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. Moreover, all three VOC lineages harbor N501Y mutation, already associated with enhanced receptor binding affinity, which could lead to increased infectiousness. 2021 Virus research Introduction SARS_CoV_2 N501Y 40 45 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. Recently, a E484K harboring virus was identified in a reinfected patient from Brazil, confirming the ability to evade naturally developed antibodies from previous infection as well. 2021 Virus research Introduction SARS_CoV_2 E484K 12 17 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. The former (B.1.1.7) emerged in England in mid-September 2020 and it is characterized by 14 lineage-specific amino acid substitutions, especially N501Y (a key contact residue interacting with hACE2) and P681H (one of four amino acids comprising the insertion that creates a novel furin cleavage site between S1 and S2). 2021 Virus research Introduction SARS_CoV_2 N501Y;P681H 146;203 151;208 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. The second (B.1.351) emerged in South Africa in October 2020 and harbor a constellation of mutations in the Receptor Binding Domain (RBD) (especially K417N, E484K, and N501Y). 2021 Virus research Introduction SARS_CoV_2 E484K;K417N;N501Y 157;150;168 162;155;173 RBD;RBD 108;133 131;136 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. Furthermore, we showed that a single dose of D330A or Y414A immunization could elicit long-term humoral immune responses that last for at least 48 weeks. 2021 Emerging microbes & infections Introduction SARS_CoV_2 D330A;Y414A 45;54 50;59 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. Here, we introduced single amino acid substitution at conserved position D330 or Y414 of MHV nsp14 and generated two MHV N7-MTase mutant virus D330A and Y414A by a reverse genetic system. 2021 Emerging microbes & infections Introduction SARS_CoV_2 D330A;Y414A 143;153 148;158 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. Here, we show that both the S309-CAR-NK-92MI cell line and primary S309-CAR-NK cells expanded from PB (hereinafter S309-CAR-NKprimary) cells effectively bind to SARS-CoV-2 pseudovirus and the D614G variant pseudovirus. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 192 197 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. Moreover, compared to the previously generated Spike-protein-targeting CR3022-CAR-NK cells, S309-CAR-NK cells show superior killing activities against target cells [e.g., A549, an epithelial carcinoma derived from a 58 year old Caucasian male with a non-small cell lung carcinoma ] expressing SARS-CoV-2 S protein and mutant S protein (hereinafter, A549-Spike and A549-Spike D614G, respectively) in vitro. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 375 380 S;S;S;S;S 47;354;369;304;325 52;359;374;305;326 Non-small cell lung carcinoma;Epithelial carcinoma 250;180 279;200 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. S309-CAR-NKprimary cells show increased productions of TNF-alpha and IFN-gamma when cocultured with A549-Spike and A549-Spike D614G target cells in comparison to CR3022-CAR-NKprimary. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 126 131 S;S 105;120 110;125 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. Since February 2020, the frequency of the SARS-CoV-2 D614G, N501Y, and E484K variants have increased significantly and has become the dominant variant over the course of the pandemic. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G;E484K;N501Y 53;71;60 58;76;65 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. The D614G variant is shown to associate with higher viral loads in patients, though there is currently insufficient scientific evidence showing the effect of D614G mutation in increased infectivity and transmissibility. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G;D614G 4;158 9;163 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Mutation N501Y was selected to study the possibilities to apply RT-ddPCR to monitor VoC signature mutations. 2021 The Science of the total environment Introduction SARS_CoV_2 N501Y 9 14 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. The N501Y mutation appears to influence binding of the spike protein to the human ACE2 receptor resulting in more efficient transmission. 2021 The Science of the total environment Introduction SARS_CoV_2 N501Y 4 9 S 55 60 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. This N501Y mutation is present in lineages B.1.1.7, B.1.351 and P.1 and started to emerge rapidly at the end of 2020. 2021 The Science of the total environment Introduction SARS_CoV_2 N501Y 5 10 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. Specific mutations, such as D614G, have been fixed in the circulating viral strains since the initial months of the pandemic, while others are common among the variants of increased virulence (e.g., N501Y, E484K). 2021 Viruses Introduction SARS_CoV_2 D614G;E484K;N501Y 28;206;199 33;211;204 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. Studies on the impact of the mutations on virus evolution are ongoing, and continuously identify novel variants and mutations, with the key recent ones being L452R, E484Q, and T478K from Indian isolate B.1.617-VOC Delta and Kappa. 2021 Viruses Introduction SARS_CoV_2 E484Q;L452R;T478K 165;158;176 170;163;181 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. After the early months of the SARS-CoV-2 pandemic in 2020, the vast majority of sequenced genomes contained the spike mutation D614G (along with three separate nucleotide changes). 2021 Nature communications Introduction SARS_CoV_2 D614G 127 132 S 112 117 34374354 Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay. Additionally, G29179T has been reported in Peru, Israel, Hong Kong, the United States, Congo, and several other countries, although the prevalence in these countries was significantly lower than that in Korea (Supplemental Data. 2022 Annals of laboratory medicine Introduction SARS_CoV_2 G29179T 14 21 34374354 Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay. Additionally, some B.1.497 strains reported in the GISAID database harbor SNVs, such as C26313A, in E. 2022 Annals of laboratory medicine Introduction SARS_CoV_2 C26313A 88 95 E 100 101 34374354 Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay. Although nearly 70% of GISAID sequences from Korea harbor G29179T, genomic surveillance data to accurately estimate the prevalence of B.1.497 in the country are lacking. 2022 Annals of laboratory medicine Introduction SARS_CoV_2 G29179T 58 65 34374354 Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay. G29179T is located in the 3 -end of the N2 forward primer of the CDC SARS-CoV-2 PCR protocol. 2022 Annals of laboratory medicine Introduction SARS_CoV_2 G29179T 0 7 34374354 Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay. In total, 1,740 sequences (69.9%) harbored G29179T. 2022 Annals of laboratory medicine Introduction SARS_CoV_2 G29179T 43 50 34374354 Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay. Most G29179T strains belonged to the PANGO lineage B.1.497 (Table 2, Supplemental Data. 2022 Annals of laboratory medicine Introduction SARS_CoV_2 G29179T 5 12 34374354 Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay. recently reported a similar phenomenon with the Xpert Xpress assay, which was caused by a different SNV, C29200T, in the N2 region of the CDC primers. 2022 Annals of laboratory medicine Introduction SARS_CoV_2 C29200T 105 112 34374354 Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay. Sanger sequencing revealed a G>T substitution at position 29,179 (G29179T GenBank: MN908947.3) in all five specimens. 2022 Annals of laboratory medicine Introduction SARS_CoV_2 G29179T;G29179T 29;66 64;73 34374354 Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay. The SNV identified, G29179T, is the most prevalent in Korea and is associated with the B.1.497 lineage, which is dominant in Korea. 2022 Annals of laboratory medicine Introduction SARS_CoV_2 G29179T 20 27 34374354 Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay. The SNVs that define B.1.497 include C241T, C1059T, C11916T, C14408T, C16560T, A20675T, A23403G, G25563T, and G29179T. 2022 Annals of laboratory medicine Introduction SARS_CoV_2 A20675T;A23403G;C1059T;C11916T;C14408T;C16560T;C241T;G25563T;G29179T 79;88;44;52;61;70;37;97;110 86;95;50;59;68;77;42;104;117 34374354 Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay. These results suggested that G29179T was responsible for the Ct value discrepancies between E and N. 2022 Annals of laboratory medicine Introduction SARS_CoV_2 G29179T 29 36 E;N 92;98 93;99 34374354 Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay. To estimate the prevalence of G29179T in Korea, we analyzed 2,489 SARS-CoV-2 sequences from isolates collected in Korea up to February 28, 2021 and stored in the Global Initiative on Sharing All Influenza Data (GISAID) database. 2022 Annals of laboratory medicine Introduction SARS_CoV_2 G29179T 30 37 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. For example, B.1.1.7 is characterized by a number of mutations in the S gene, including the H69/V70 and Y144 deletions, N501Y, and P681H, among a number of other changes. 2021 Microbiology spectrum Introduction SARS_CoV_2 N501Y;P681H 120;131 125;136 S 70 71 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. Sera from patients immunized with the Moderna or Pfizer-BioNTech mRNA vaccines exhibited a 1- to 3-fold decrease in neutralization activity against B.1.351, which carries both N501Y and E484K, which may indicate a degree of immune escape by this VOC. 2021 Microbiology spectrum Introduction SARS_CoV_2 E484K;N501Y 186;176 191;181 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. The E484K mutation (found in B.1.1.7 + E484K, B.1.351, and P.1) confers resistance to some neutralizing and commercial monoclonal antibody preparations directed against the S protein. 2021 Microbiology spectrum Introduction SARS_CoV_2 E484K;E484K 4;39 9;44 S 173 174 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. The N501Y mutation (found in all VOCs except B.1.617.2) is found in the receptor-binding domain of the S protein and may confer elevated affinity for its receptor. 2021 Microbiology spectrum Introduction SARS_CoV_2 N501Y 4 9 S 103 104 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. To date, there are four variants of concern (VOCs) that have been declared as such by the World Health Organization (WHO): B.1.1.7 (Alpha) (with and without the spike [S] gene E484K mutation), B.1.351 (Beta), P.1 (Gamma), and more recently B.1.617.2 (Delta). 2021 Microbiology spectrum Introduction SARS_CoV_2 E484K 176 181 S;S 161;168 166;169 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. Notably, new SARS-CoV-2 lineages carrying the mutation N501Y in the RBD of the spike protein which are more transmissible spread rapidly in the United Kingdom (UK). 2021 Biotechnology journal Introduction SARS_CoV_2 N501Y 55 60 S;RBD 79;68 84;71 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. Several neutralizing human antibodies were then identified and characterized with the ability to bind with RBD and its mutants (N501Y, R408I, W463R, N354D, V367F and N354D/D364Y) and block the interaction with hACE2. 2021 Biotechnology journal Introduction SARS_CoV_2 N354D;N354D;R408I;V367F;W463R;N501Y;D364Y 149;166;135;156;142;128;172 154;171;140;161;147;133;177 RBD 107 110 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Because of the important functional and antigenic properties of the RBD, structural changes in this domain deserve special attention and have already been highlighted by such notorious RBD mutations as E484K (e.g., found in B.1.1.28, also known as the "Brazil" variant or VOI zeta) and N501Y (found in B.1.1.7, also known as the "British" variant or VOC alpha, and in B.1.351, also known as the "South African" variant or VOC beta). 2021 Journal of clinical microbiology Introduction SARS_CoV_2 E484K;N501Y 202;286 207;291 RBD;RBD 68;185 71;188 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. In the process of region 414 to 583 analysis, we noted a high prevalence of samples that carried nCoV variants with an L452R mutation. 2021 Journal of clinical microbiology Introduction SARS_CoV_2 L452R 119 124 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. This prompted us to perform an in-depth follow-up analysis of the L452R-carrying nCoV strains in our samples and a determination of their prevalence and clonal origin on a global scale using publicly available nCoV genomes and analytical tools of GISAID and Nextstrain databases. 2021 Journal of clinical microbiology Introduction SARS_CoV_2 L452R 66 71 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Therefore, we studied the pathogenesis of B.1.1.7 and B.1.351 in rhesus macaques and compared it to a recent SARS-CoV-2 isolate containing the D614G substitution in spike that rapidly became dominant globally in March 2020 due to its' increased transmissibility. 2021 bioRxiv Introduction SARS_CoV_2 D614G 143 148 S 165 170 34384810 Infection-enhancing anti-SARS-CoV-2 antibodies recognize both the original Wuhan/D614G strain and Delta variants. A potential risk for mass vaccination? - G142D/E154K (B.1.617.1). 2021 The Journal of infection Introduction SARS_CoV_2 G142D;E154K 2;8 7;13 34384810 Infection-enhancing anti-SARS-CoV-2 antibodies recognize both the original Wuhan/D614G strain and Delta variants. A potential risk for mass vaccination? - T19R/E156G/del157/del158/A222V (B.1.617.2). 2021 The Journal of infection Introduction SARS_CoV_2 T19R;A222V;E156G 2;27;7 6;32;12 34384810 Infection-enhancing anti-SARS-CoV-2 antibodies recognize both the original Wuhan/D614G strain and Delta variants. A potential risk for mass vaccination? Each mutational pattern was introduced in the original Wuhan/D614G strain, submitted to energy minimization, and then tested for antibody binding. 2021 The Journal of infection Introduction SARS_CoV_2 D614G 61 66 34384810 Infection-enhancing anti-SARS-CoV-2 antibodies recognize both the original Wuhan/D614G strain and Delta variants. A potential risk for mass vaccination? The energy of interaction (DeltaG) of the reference pdb file #7LAB (Wuhan/D614G strain) in the NTD region was estimated to -229 kJ/mol-1. 2021 The Journal of infection Introduction SARS_CoV_2 D614G 74 79 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. A previous study showed that the D614G mutation in the Spike protein could increase viral infectivity. 2021 Frontiers in molecular biosciences Introduction SARS_CoV_2 D614G 33 38 S 55 60 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Finally, it has been reported that the antibody neutralization sensitivity of some RBD mutants including A475V, F490L, and V483A (among others) is reduced, suggesting that SARS-CoV-2 is mutating to evade neutralization/RBD binding. 2021 Antibody therapeutics Introduction SARS_CoV_2 A475V;F490L;V483A 105;112;123 110;117;128 RBD;RBD 83;219 86;222 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Mutational analyses led to the discovery of a D614G mutation found on the S protein that was later shown to be responsible for higher infectivity in a pseudotyped viral infection assay, showed higher Ct values in patients, and was shown to enhance viral load in the upper respiratory tract of patients. 2021 Antibody therapeutics Introduction SARS_CoV_2 D614G 46 51 S 74 75 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. We found four high frequency variants with improved binding to ACE2:S477N, N439K, V367F, and N501Y and cross-referenced antibody interaction data with RBD mutations. 2021 Antibody therapeutics Introduction SARS_CoV_2 N439K;N501Y;V367F;S477N 75;93;82;68 80;98;87;73 RBD 151 154 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Among them, N501Y, K417N, and E484K in the receptor binding motif of the RBD region may induce a conformational change in the spike protein and subsequently increase the infectivity of beta variant. 2021 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 E484K;K417N;N501Y 30;19;12 35;24;17 S;RBD 126;73 131;76 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Moreover, beta variant is resistant to neutralization by most monoclonal antibodies against the N-terminal domain and multiple individual monoclonal antibodies against the receptor-binding motif of the RBD due to E484K mutation. 2021 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 E484K 213 218 RBD;N 202;96 205;97 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Moreover, L452R mutation in spike protein of epsilon variant could increase infectivity in vitro and loss neutralizing activity of monoantibodies. 2021 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 L452R 10 15 S 28 33 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. The SARS-CoV-2 beta variant contains nine mutations in the spike protein: D614G, Delta242-Delta244, and R246I in the N-terminal domain; three mutations (K417N, E484K, and N501Y) in the RBD; and one mutation (A701V) near the furin cleavage site. 2021 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 D614G;E484K;N501Y;R246I;A701V;K417N 74;160;171;104;208;153 79;165;176;109;213;158 S;RBD;N 59;185;117 64;188;118 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. 14 out of 15 Delta variant sequences that contained E465A were from the state of Missouri. 2021 Journal of autoimmunity Introduction SARS_CoV_2 E465A 52 57 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. 1b that all viruses that have G142D also have R158G mutation. 2021 Journal of autoimmunity Introduction SARS_CoV_2 G142D;R158G 30;46 35;51 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. 1b), all mutations co-exist at ~100 % frequency, except T95I and G142D. 2021 Journal of autoimmunity Introduction SARS_CoV_2 G142D;T95I 65;56 70;60 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. According to the United States (US) Center for Disease Control (CDC), signature Spike mutations in the aggregated Delta and Delta Plus variant include T19R, (V70F*), T95I, G142D, E156-, F157-, R158G, (A222V*), (W258L*), (K417N*), L452R, T478K, D614G, P681R, and D950N. 2021 Journal of autoimmunity Introduction SARS_CoV_2 D614G;D950N;G142D;L452R;P681R;R158G;T19R;T478K;T95I;A222V;K417N;V70F;W258L 244;262;172;230;251;193;151;237;166;201;221;158;211 249;267;177;235;256;198;155;242;170;206;226;162;216 S 80 85 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Additionally, our data indicate that Delta and Delta Plus variants have two additional mutations (T95I and W258L) with significant prevalence (~40 % in Delta Plus). 2021 Journal of autoimmunity Introduction SARS_CoV_2 W258L;T95I 107;98 112;102 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Additionally, the conformation R258 is nearly identical, as seen in the W258L mutation. 2021 Journal of autoimmunity Introduction SARS_CoV_2 W258L 72 77 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Additionally, we found that nsp4 A446V (ORF1a: A3209V) is almost always (~90 %) present in sequences that had the spike mutation D950N (Delta signature mutation). 2021 Journal of autoimmunity Introduction SARS_CoV_2 A3209V;A446V;D950N 47;33;129 53;38;134 ORF1a;S;Nsp4 40;114;28 45;119;32 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. and nsp4 A446V mutation (ORF1a: A3209V), suggesting that all sequences that contained W258L also had all mutations shown in. 2021 Journal of autoimmunity Introduction SARS_CoV_2 A3209V;A446V;W258L 32;9;86 38;14;91 ORF1a;Nsp4 25;4 30;8 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. For example, A328T in nsp3 (ORF1a: A1146T) was only present in Delta Plus (58 %). 2021 Journal of autoimmunity Introduction SARS_CoV_2 A1146T;A328T 35;13 41;18 ORF1a;Nsp3 28;22 33;26 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. For example, we found that a Spike mutation E465A was present in 15 sequences of the Delta variant. 2021 Journal of autoimmunity Introduction SARS_CoV_2 E465A 44 49 S 29 34 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. For SARS-CoV-2, it has been shown that D164G mutation enhances viral fitness. 2021 Journal of autoimmunity Introduction SARS_CoV_2 D164G 39 44 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Four additional mutations: nsp3:P822L (ORF1a:P1604L), nsp4:A446V (ORF1a:A3209V), nsp6:V149S (ORF1a: V3718S), and nsp6:T181I (ORF1a:T3750I) are present at 58 % in Delta Plus, and only at 16 % in Delta except nsp6:T181I, which was only 9 % (Table 1). 2021 Journal of autoimmunity Introduction SARS_CoV_2 V3718S;A3209V;A446V;P1604L;P822L;T181I;T181I;T3750I;V149S 100;72;59;45;32;118;212;131;86 106;78;64;51;37;123;217;137;91 ORF1a;ORF1a;ORF1a;ORF1a;Nsp3;Nsp4;Nsp6;Nsp6;Nsp6 39;66;93;125;27;54;81;113;207 44;71;98;130;31;58;85;117;211 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Hence, as noted above, the Delta Plus variant is not just a variant of Delta signified by the K417N mutation but has additional mutations that need to be considered. 2021 Journal of autoimmunity Introduction SARS_CoV_2 K417N 94 99 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Hence, we propose including these mutations as signature mutations of Delta (T95I) and Delta Plus (T95I + W258L) in understanding the pathogenic mechanisms associated with these viruses. 2021 Journal of autoimmunity Introduction SARS_CoV_2 W258L;T95I;T95I 106;77;99 111;81;103 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Importantly, sequences that contained Spike mutation W258L almost always included G142D, T95I, nsp4 A446V (ORF1a: A3209V). 2021 Journal of autoimmunity Introduction SARS_CoV_2 A3209V;A446V;G142D;T95I;W258L 114;100;82;89;53 120;105;87;93;58 ORF1a;S;Nsp4 107;38;95 112;43;99 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. In the Delta Plus variant, the sequences containing W258L, which exists in ~40 % of all sequences, also had a strong correlation with all listed Spike mutations. 2021 Journal of autoimmunity Introduction SARS_CoV_2 W258L 52 57 S 145 150 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. It appears that the virus evolved to overcome the clash by mutating R158G, which is in accordance with the correlation data shown in. 2021 Journal of autoimmunity Introduction SARS_CoV_2 R158G 68 73 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. It is clear from this figure that W258L mutation reorients the R246 sidechain such that the interaction with E31 and G26 of antibody heavy chain would be weakened due to longer interaction distance (3.5 and 3.0 A verses 4.2 and 4.4 A). 2021 Journal of autoimmunity Introduction SARS_CoV_2 W258L 34 39 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. It was previously reported that D614G and P323L were present in all SARS-CoV-2 sequences by the summer of 2020. 2021 Journal of autoimmunity Introduction SARS_CoV_2 D614G;P323L 32;42 37;47 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. It was recently demonstrated that monoclonal antibodies, convalescent, and vaccine sera reduce the neutralization of the Delta variant containing T478K or L452R/T478K mutations compared with Wuhan-related virus. 2021 Journal of autoimmunity Introduction SARS_CoV_2 L452R;T478K;T478K 155;146;161 160;151;166 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Mutation G142D causes a steric clash with the sidechain of R158 (shown as a dotted line of 1.6 A length). 2021 Journal of autoimmunity Introduction SARS_CoV_2 G142D 9 14 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Mutation K417N will result in a loss of this interaction and thereby reduced binding of the antibody with the Spike. 2021 Journal of autoimmunity Introduction SARS_CoV_2 K417N 9 14 S 110 115 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Similar structural data for T95I, G142D, and W258L is not available. 2021 Journal of autoimmunity Introduction SARS_CoV_2 G142D;T95I;W258L 34;28;45 39;32;50 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Similarly, T95I was 37 % in Delta Plus and 22 % in Delta. 2021 Journal of autoimmunity Introduction SARS_CoV_2 T95I 11 15 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. T95I occurs at a frequency of 20-30 % in the background of other mutations, whereas G142D co-exists at a frequency of ~50 % in the background of other mutations. 2021 Journal of autoimmunity Introduction SARS_CoV_2 G142D;T95I 84;0 89;4 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. The criterion used to classify the Delta Plus variant was based on the K417N mutation in the parent Delta Variant. 2021 Journal of autoimmunity Introduction SARS_CoV_2 K417N 71 76 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. The effect of G142D and R158G mutation is shown in. 2021 Journal of autoimmunity Introduction SARS_CoV_2 G142D;R158G 14;24 19;29 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. The effect of the W258A mutation is shown in. 2021 Journal of autoimmunity Introduction SARS_CoV_2 W258A 18 23 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. The rationale behind selecting these mutations was that they were unique (e.g., K417N) or highly correlated with another mutation in other variants (e.g., T95I being variably associated with other Spike protein mutations). 2021 Journal of autoimmunity Introduction SARS_CoV_2 K417N;T95I 80;155 85;159 S 197 202 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. The temporal analysis showed that while W258L and T95I are highly correlated, the actual prevalence of both W258L and T95I mutations has decreased over time in our analysis. 2021 Journal of autoimmunity Introduction SARS_CoV_2 T95I;T95I;W258L;W258L 50;118;40;108 54;122;45;113 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Therefore, to get insight into the impact of mutations (e.g., D142G, R158G, W258L, and K417N), we analyzed available structures in the Protein Data Bank (PDB, www.rcsb.org) and assessed the impact of mutations. 2021 Journal of autoimmunity Introduction SARS_CoV_2 D142G;K417N;R158G;W258L 62;87;69;76 67;92;74;81 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. These include mutation A222V was 58 % in Delta Plus, whereas only 9 % in Delta. 2021 Journal of autoimmunity Introduction SARS_CoV_2 A222V 23 28 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. These include V70F and W258L, which were present in Delta Plus at the prevalence of 52 % and 39 %, respectively. 2021 Journal of autoimmunity Introduction SARS_CoV_2 V70F;W258L 14;23 18;28 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. These results further justify our conclusion, as mentioned earlier, that the Delta Plus variant is more than just an additional mutation (K417N). 2021 Journal of autoimmunity Introduction SARS_CoV_2 K417N 138 143 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. To assess how Delta Plus was evolving from Delta, we determined the prevalence of six key mutations (T95I, G142D, R158G, L452R, T478K, and K417N) at different time points. 2021 Journal of autoimmunity Introduction SARS_CoV_2 G142D;K417N;L452R;R158G;T478K;T95I 107;139;121;114;128;101 112;144;126;119;133;105 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. To assess if mutations change sidechain conformation, we generated mutations W258A, G142D and R158G using Prime software of Schrodinger Suite (Schrodinger LLC, NY). 2021 Journal of autoimmunity Introduction SARS_CoV_2 G142D;R158G;W258A 84;94;77 89;99;82 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. To further investigate the correlation between W258L and T95I in Delta Plus. 2021 Journal of autoimmunity Introduction SARS_CoV_2 T95I;W258L 57;47 61;52 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. We also included G142D and R158G since these mutations occurred at high prevalence (69-100 %). 2021 Journal of autoimmunity Introduction SARS_CoV_2 G142D;R158G 17;27 22;32 34399368 Controversy surrounding the Sputnik V vaccine. A small, independent Argentinean study by Ikegame and colleagues has shed light on this fundamental aspect revealing the worrying possibility that the Beta variant, and to a lesser extent, any variant carrying the E484K substitution may escape the neutralizing antibody responses that this immunisation elicits. 2021 Respiratory medicine Introduction SARS_CoV_2 E484K 214 219 34399368 Controversy surrounding the Sputnik V vaccine. Also, Kappa variant has four S mutations of interest, L452R, E484Q, D614G, and P681R. 2021 Respiratory medicine Introduction SARS_CoV_2 D614G;E484Q;L452R;P681R 68;61;54;79 73;66;59;84 S 29 30 34399368 Controversy surrounding the Sputnik V vaccine. Delta variant shows four key mutations in sequence encoding S protein: L452R, T478K, D614G, P681R. 2021 Respiratory medicine Introduction SARS_CoV_2 D614G;L452R;P681R;T478K 85;71;92;78 90;76;97;83 S 60 61 34399368 Controversy surrounding the Sputnik V vaccine. E484Q mutation shares antibody-escape features like those of E484K mutation. 2021 Respiratory medicine Introduction SARS_CoV_2 E484K;E484Q 61;0 66;5 34399368 Controversy surrounding the Sputnik V vaccine. Gamma variant has three changes in the S RBD (K417T, E484K, and N501Y). 2021 Respiratory medicine Introduction SARS_CoV_2 E484K;N501Y;K417T 53;64;46 58;69;51 RBD;S 41;39 44;40 34399368 Controversy surrounding the Sputnik V vaccine. N501Y enhances receptor binding domain/angiotensin-converting enzyme 2 (ACE2) receptor binding affinity while also disrupting the binding of potent neutralizing antibodies and is the major S determinant driving increased transmission of these variants. 2021 Respiratory medicine Introduction SARS_CoV_2 N501Y 0 5 RBD;S 15;189 38;190 34399368 Controversy surrounding the Sputnik V vaccine. One serum had little to no detectable neutralizing activity against Beta variant, E484K and even wild type, but neutralized Alpha variant effectively. 2021 Respiratory medicine Introduction SARS_CoV_2 E484K 82 87 34399368 Controversy surrounding the Sputnik V vaccine. The B.1.1.7 variant, now labelled Alpha variant, carries the N501Y mutation in the S receptor-binding domain (RBD) whereas the B.1.351 variant, labelled Beta variant, has three notable mutations in the S RBD, namely, K417 N, E484K, and N501Y. 2021 Respiratory medicine Introduction SARS_CoV_2 E484K;K417N;N501Y;N501Y 225;217;61;236 230;223;66;241 RBD;RBD;S;S 110;204;83;202 113;207;84;203 34399368 Controversy surrounding the Sputnik V vaccine. The D614G mutation is the hallmark of all variants, as it promotes viral spread by increasing the number of open S protomers in the homo-trimeric receptor complex. 2021 Respiratory medicine Introduction SARS_CoV_2 D614G 4 9 S 113 114 34399368 Controversy surrounding the Sputnik V vaccine. The E484K mutation can help virus variants to escape neutralization by serum antibodies from recovered COVID-19 patients. 2021 Respiratory medicine Introduction SARS_CoV_2 E484K 4 9 COVID-19 103 111 34399368 Controversy surrounding the Sputnik V vaccine. The important information is that 8 out of 12 (67%) serum samples from a cohort of recipients of Sputnik V vaccine showed dose response curve slopes indicative of failure to neutralize Beta variant, but antibodies from people who had received both doses of Sputnik V were effective against the Alpha variant and D614G variant and showed only moderately reduced activity against S carrying the E484K substitution alone. 2021 Respiratory medicine Introduction SARS_CoV_2 D614G;E484K 312;393 317;398 S 378 379 34399368 Controversy surrounding the Sputnik V vaccine. The L452R mutation increases protein stability, viral infectivity, and potentially promotes viral replication. 2021 Respiratory medicine Introduction SARS_CoV_2 L452R 4 9 34399368 Controversy surrounding the Sputnik V vaccine. The L452R mutation is within the S RBD, and thus may be relevant to transmissibility or immune escape. 2021 Respiratory medicine Introduction SARS_CoV_2 L452R 4 9 RBD;S 35;33 38;34 34399368 Controversy surrounding the Sputnik V vaccine. Ultimately, sera from Sputnik vaccine recipients had a median 6.1-fold and 2.8-fold reduction in neutralizing potency against Beta variant and all variants with the S protein carrying the E484K substitution, respectively, although resistance of the E484K mutant was competitive and was absent at higher serum concentrations. 2021 Respiratory medicine Introduction SARS_CoV_2 E484K;E484K 188;249 193;254 S 165 166 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. In this study, we report the development of rRT-PCR assays (RNA-dependent RNA polymerase [RdRp], nucleocapsid [N], S484K, and S501Y) to detect SARS-CoV-2 variants. 2021 Chinese medical journal Introduction SARS_CoV_2 S484K;S501Y 115;126 120;131 RdRp;N;RdRP;N 60;97;90;111 88;109;94;112 34403732 Identification of natural compounds as SARS-CoV-2 entry inhibitors by molecular docking-based virtual screening with bio-layer interferometry. Recently, the D614G and N501Y mutants were discovered in Northern Europe and Africa, whereas N439K is commonly found in over 300 countries. 2021 Pharmacological research Introduction SARS_CoV_2 D614G;N439K;N501Y 14;93;24 19;98;29 34403732 Identification of natural compounds as SARS-CoV-2 entry inhibitors by molecular docking-based virtual screening with bio-layer interferometry. The Y453F mutant was originated from mammal mink and has infectivity on humans. 2021 Pharmacological research Introduction SARS_CoV_2 Y453F 4 9 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. However, a lineage turnover accompanied the third epidemic peak during March and April 2021, involving the emergence of B.1 lineage descendants with high mutation accumulation (B.1.621 and the provisionally assigned B.1 + L249S + E484K), as well as the introduction of the B.1.1.7, P.1 and VOI in Magdalena, Atlantico, Bolivar, Bogota D.C, and Santander. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K;L249S 230;222 235;227 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. In this study, we reported the emergence and spread of the novel B.1.621 lineage of SARS-CoV-2, a new VOI with the insertion 146 N and several amino acid substitutions in the Spike protein (Y144T, Y145S, R346K, E484K, N501Y and P681H). 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K;N501Y;P681H;R346K;Y145S;Y144T 211;218;228;204;197;190 216;223;233;209;202;195 S;N 175;129 180;130 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. Here, we evaluated genomic sequences of SARS-CoV-2 and observed a high frequency (0.72%) mutation occurring in the RBM region, N439K, which was first sampled in March 2020 in Scotland from lineage B.1 on the background of D614G, has arisen independently multiple times. 2021 Frontiers in cell and developmental biology Introduction SARS_CoV_2 D614G;N439K 222;127 227;132 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. On the other hand, N439K reduced the sensitivity to neutralizing antibodies which are mainly attributed to polar solvation and electrostatic interactions. 2021 Frontiers in cell and developmental biology Introduction SARS_CoV_2 N439K 19 24 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. Study have demonstrated that N439K S protein enhances binding affinity to the hACE2 receptor and reduces the neutralization activity of monoclonal antibodies. 2021 Frontiers in cell and developmental biology Introduction SARS_CoV_2 N439K 29 34 S 35 36 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. Taken together, the SARS-CoV-2 spike protein with N439K may be more infectious and become resistant to some SARS-CoV-2 neutralizing antibodies. 2021 Frontiers in cell and developmental biology Introduction SARS_CoV_2 N439K 50 55 S 31 36 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. The structure of N439K-mutated RBD-hACE2 complexes show a new salt bridge and local interaction. 2021 Frontiers in cell and developmental biology Introduction SARS_CoV_2 N439K 17 22 RBD 31 34 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. There are 930 naturally occurring missense mutations in SARS-CoV-2 spike protein that had been reported in the GISAID database (Supplementary Table 1), and a key mutation from ASP614 to GLY614 (D614G) in SARS-CoV-2 spike protein confer the SARS-CoV-2 more infectious than the original strain. 2021 Frontiers in cell and developmental biology Introduction SARS_CoV_2 D614G;D614G 176;194 192;199 S;S 67;215 72;220 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. To further provide insights into the infection and neutralization processes of N439K at the molecular level, we present performed molecular dynamics (MD) simulations of the binary complexes of the RBD domain with the common receptor hACE2 and the neutralizing monoclonal antibody (mAb) CB6/REGN10987, respectively. 2021 Frontiers in cell and developmental biology Introduction SARS_CoV_2 N439K 79 84 RBD 197 200 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Both of these mutants carry an N501Y mutation, and the B.1.351 lineage has two additional mutations (K417N and E484K) within the RBD region (Figure 1B,C). 2021 eLife Introduction SARS_CoV_2 E484K;N501Y;K417N 111;31;101 116;36;106 RBD 129 132 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Our results reveal the molecular mechanism that underlies the increased transmissibility of two SARS-CoV-2 variants by identifying the key mutation N501Y. 2021 eLife Introduction SARS_CoV_2 N501Y 148 153 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. Acquisition of amino acid substitutions in the S RBD- namely K417N, E484K, and N501Y:and in the NTD, such as L18F, D80A, D215G, and Delta242-244, is associated with increased transmissibility and reduction in neutralization sensitivity. 2021 Nature immunology Introduction SARS_CoV_2 D215G;D80A;E484K;K417N;L18F;N501Y 121;115;68;61;109;79 126;119;73;66;113;84 RBD;S 49;47 52;48 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. Additionally, it was reported that sera from mRNA-1273-immunized human and nonhuman primates (NHP) showed the greatest reduction of neutralization against B.1.351 compared to B.1.1.7, P.1, B.1.427/B.1.429, and B.1.1.7+E484K variants. 2021 Nature immunology Introduction SARS_CoV_2 E484K 218 223 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. In UK- or US-based clinical studies, NVX-CoV2373 (Novavax), AZD1222 (University of Oxford/AstraZeneca), and Ad26.COV2.S (Janssen/Johnson & Johnson) vaccines show between ~70 and 90% protection against the circulating D614G or B.1.1.7 variants, and vaccine efficacy against mild symptomatic COVID-19 caused by B.1.351 was up to 60% for Ad26.CoV2 and NVX-CoV2373 and ~10% for AZD122. 2021 Nature immunology Introduction SARS_CoV_2 D614G 217 222 S 118 119 COVID-19 290 298 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. Soon after the outbreak, SARS-CoV-2 mutations including D614G appeared. 2021 Infectious diseases of poverty Introduction SARS_CoV_2 D614G 56 61 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. All three variants contain spike N501Y mutation. 2021 EBioMedicine Introduction SARS_CoV_2 N501Y 33 38 S 27 32 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Clinicians and clinical microbiologists should also be alerted to the possible reduced sensitivity of currently available anti-RBD IgG assays which are designed based on non-N501Y virus. 2021 EBioMedicine Introduction SARS_CoV_2 N501Y 174 179 RBD 127 130 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Furthermore, sera from patients infected with N501Y variant (either B.1.1.7 or B.1.351 lineage) are often negative for anti-RBD IgG even when the anti-nucleocapsid IgG is positive. 2021 EBioMedicine Introduction SARS_CoV_2 N501Y 46 51 N;RBD 151;124 163;127 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Furthermore, we assessed the difference in antibody against wild type and N501Y mutant RBD with a large serum panel consisting of > 250 patients. 2021 EBioMedicine Introduction SARS_CoV_2 N501Y 74 79 RBD 87 90 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. SARS-CoV-2 variants with spike protein N501Y mutation are of particular concern as they are associated with increased transmissibility, higher mortality, or reduced susceptibility to neutralization by antibody induced after natural infection or COVID-19 vaccination. 2021 EBioMedicine Introduction SARS_CoV_2 N501Y 39 44 S 25 30 COVID-19 245 253 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Spike D614G affects the transmissibility of the virus, and SARS-CoV-2 with D614G mutation has been found in reinfection cases. 2021 EBioMedicine Introduction SARS_CoV_2 D614G;D614G 6;75 11;80 S 0 5 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. The B.1.351 and P.1 variants also contain mutation at the spike amino acid position 484 (E484K) and at position 417 (K417N for B.1.351; K417T for P.1). 2021 EBioMedicine Introduction SARS_CoV_2 K417T;E484K;K417N 136;89;117 141;94;122 S 58 63 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. The first major mutation was the spike D614G, which first emerged in February 2020 and then dominated the world. 2021 EBioMedicine Introduction SARS_CoV_2 D614G 39 44 S 33 38 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. This is unlike sera from patients infected with non-N501Y lineages, for whom the anti-RBD IgG is often positive when the anti-N IgG is positive. 2021 EBioMedicine Introduction SARS_CoV_2 N501Y 52 57 RBD;N 86;126 89;127 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. We searched PubMed without language restrictions on 5th April 2021 for articles using the terms "COVID-19" or "SARS-CoV-2" and the terms "N501Y", "variant", or "antibody assay". 2021 EBioMedicine Introduction SARS_CoV_2 N501Y 138 143 COVID-19 97 105 34424256 Emergence of the First Strains of SARS-CoV-2 Lineage B.1.1.7 in Romania: Genomic Analysis. Among the most notable mutations is N501Y, within the S protein, which corresponds to the receptor binding domain of the virus, where attachment to the host ACE2 enzyme takes place. 2021 JMIRx med Introduction SARS_CoV_2 N501Y 36 41 RBD;S 90;54 113;55 34428371 Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation. The RBD with the Alpha variant contains a mutation of asparagine to tyrosine at position 501 (N501Y), while the Beta variant has two new mutations, K417N and E484K, in addition to N501Y. 2021 Journal of chemical information and modeling Introduction SARS_CoV_2 N501Y;E484K;K417N;N501Y;N501Y 54;158;148;180;94 92;163;153;185;99 RBD 4 7 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. 1) to identify N501Y and E484K mutations in SARS-CoV-2-positive clinical samples stored at the Columbia University Biobank. 2021 Nature Introduction SARS_CoV_2 E484K;N501Y 25;15 30;20 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. 2b shows the localization of signature B.1.526-E484K and B.1.526-S477N mutations within the spike protein. 2021 Nature Introduction SARS_CoV_2 E484K;S477N 47;65 52;70 S 92 97 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. 3c) showed that antibody resistance of B.1.526-E484K is probably lower than that of B.1.351 and closer to that of P.1. 2021 Nature Introduction SARS_CoV_2 E484K 47 52 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. A significantly higher proportion of patients infected with B.1.526-E484K were admitted to hospital or presented to the emergency department (P = 0.037). 2021 Nature Introduction SARS_CoV_2 E484K 68 73 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. B.1.526-E484K and B.1.526-S477N share the characteristic spike protein mutations L5F, T95I, D253G, D614G and either A701V or Q957R, along with either E484K or S477N. 2021 Nature Introduction SARS_CoV_2 A701V;D253G;D614G;E484K;L5F;Q957R;S477N;T95I;E484K;S477N 116;92;99;150;81;125;159;86;8;26 121;97;104;155;84;130;164;90;13;31 S 57 62 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. D253G resides in the antigenic supersite in the N-terminal domain, which is a target for neutralizing antibodies, whereas E484K is situated at the RBD interface with the cellular receptor ACE2. 2021 Nature Introduction SARS_CoV_2 E484K;D253G 122;0 127;5 RBD;N 147;48 150;49 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Demographic and clinical features, including clinical outcomes, were largely similar in patients infected with viruses containing E484K versus those without the signature E484K or N501Y mutations, and between patients with B.1.526-E484K versus those with non-variant lineages (Extended Data Table 1). 2021 Nature Introduction SARS_CoV_2 E484K;E484K;N501Y;E484K 130;171;180;231 135;176;185;236 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. However, significantly lower Ct values were associated with both E484K (29.49 versus 30.71, P = 0.013) and B.1.526-E484K (27.65 versus 28.81 in non-variant lineages, P = 0.015), indicating a modestly higher viral load in these variant samples. 2021 Nature Introduction SARS_CoV_2 E484K;E484K 65;115 70;120 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. However, the activities of several antibodies:including REGN10933 and LY-CoV555, which are already in clinical use:were either impaired or lost when tested against E484K and NYDelta5(E484K) pseudoviruses. 2021 Nature Introduction SARS_CoV_2 E484K;E484K 164;183 169;188 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. However, unexpectedly, the large majority of PCR-screened cases with E484K (98 out of 128 (77%)) were from the B.1.526 lineage. 2021 Nature Introduction SARS_CoV_2 E484K 69 74 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Isolates subsequently branched into four sub-lineages, with two major groups B.1.526-E484K and B.1.526-S477N containing A701V, and a smaller sub-lineage B.1.526-S477N containing Q957R. 2021 Nature Introduction SARS_CoV_2 A701V;Q957R;E484K;S477N;S477N 120;178;85;103;161 125;183;90;108;166 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Neutralization studies on the authentic B.1.526-E484K virus yielded similar results, although the magnitudes of resistance to convalescent plasma and vaccinee sera were slightly lower at 2.6-fold and 1.8- to 2.0-fold, respectively. 2021 Nature Introduction SARS_CoV_2 E484K 48 53 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Non-spike mutations widely shared by B.1.526-E484K and B.1.526-S477N isolates include: T85I in ORF1a-nsp2; L438P in ORF1a-nsp4, a 9-base pair (bp) deletion (Delta106-108) in ORF1a-nsp6; P323L in ORF1b-nsp12; Q88H in ORF1b-nsp13; Q57H in ORF3a; and P199L and M234I in the N gene. 2021 Nature Introduction SARS_CoV_2 L438P;M234I;P199L;P323L;Q57H;Q88H;T85I;E484K;S477N 107;258;248;186;229;208;87;45;63 112;263;253;191;233;212;91;50;68 ORF1a;ORF1a;ORF1a;S;ORF3a;Nsp13;Nsp12;Nsp2;Nsp4;Nsp6;N 95;116;174;4;237;222;201;101;122;180;271 100;121;179;9;242;227;206;105;126;184;272 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Of note, these effects were mediated in part by the E484K mutation. 2021 Nature Introduction SARS_CoV_2 E484K 52 57 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Of the sequenced N501Y isolates, 31 out of 41 (76%) were consistent with the B.1.1.7 lineage. 2021 Nature Introduction SARS_CoV_2 N501Y 17 22 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Overall, these results demonstrate the need to modify the antibody therapies currently in use and to monitor the efficacy of current vaccines in regions where B.1.526-E484K is prevalent. 2021 Nature Introduction SARS_CoV_2 E484K 167 172 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Phylogenetic examination showed that the B.1.526 lineage comprises two closely related sub-lineages harbouring either E484K (B.1.526-E484K; defined as Pangolin lineage B.1.526) or S477N (B.1.526-S477N; Pangolin lineage B.1.526.2), and the additional sub-lineage B.1.526.1, harbouring the L452R substitution (B.1.526-L452R). 2021 Nature Introduction SARS_CoV_2 E484K;L452R;S477N;E484K;L452R;S477N 118;288;180;133;316;195 123;293;185;138;321;200 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Pseudoviruses were constructed containing S477N or E484K alone, or containing all five signature mutations (L5F, T95I, D253G, A701V and E484K or S477N) (NYDelta5(E484K) or NYDelta5(S477N)), and analysed in a neutralization assay with 12 monoclonal antibodies (including 5 with emergency use authorization), 20 plasma samples from patients who had recovered from SARS-CoV-2 infection and 22 sera from vaccinated individuals. 2021 Nature Introduction SARS_CoV_2 A701V;D253G;E484K;E484K;S477N;S477N;T95I;E484K;L5F;S477N 126;119;51;136;42;145;113;162;108;181 131;124;56;141;47;150;117;167;111;186 COVID-19 362 382 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Reinfections with P.1 and another related Brazilian variant P.2 harbouring E484K have been documented. 2021 Nature Introduction SARS_CoV_2 E484K 75 80 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Samples that harboured both N501Y and E484K were genotyped as P.1 (n = 6), B.1.351 (n = 1) and B.1.623 (n = 1). 2021 Nature Introduction SARS_CoV_2 E484K;N501Y 38;28 43;33 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Sequencing results verified the E484K and N501Y substitutions in all samples identified by PCR screening. 2021 Nature Introduction SARS_CoV_2 E484K;N501Y 32;42 37;47 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Similarly, neutralizing activities of convalescent plasma or vaccinee sera were reduced by 4.1-fold or 3.3- to 3.6-fold, respectively, against NYDelta5(E484K). 2021 Nature Introduction SARS_CoV_2 E484K 152 157 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. The A701V mutation near the furin cleavage site is also shared with variant B.1.351. 2021 Nature Introduction SARS_CoV_2 A701V 4 9 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. The B.1.526-L452R lineage:which emerged in parallel with these:is related to B.1.526-E484K and B.1.526-S477N, but forms a distinct phylogenetic branch (Extended Data. 2021 Nature Introduction SARS_CoV_2 E484K;L452R;S477N 85;12;103 90;17;108 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. The earliest sample containing E484K was collected in mid-November 2020. 2021 Nature Introduction SARS_CoV_2 E484K 31 36 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. The frequency of viruses harbouring N501Y also increased over time, from the earliest detection in mid-January to 5.3% of screened isolates by the beginning of March. 2021 Nature Introduction SARS_CoV_2 N501Y 36 41 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. The hallmark mutation of B.1.1.7:a SARS-CoV-2 variant of concern first identified in the UK:is N501Y, located in the receptor-binding domain (RBD) of spike. 2021 Nature Introduction SARS_CoV_2 N501Y 95 100 S;RBD 150;142 155;145 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. The neutralizing activities of 12 monoclonal antibodies covering a range of epitopes on RBD were essentially unaltered against the S477N and NYDelta5(S477N) pseudoviruses (Extended Data. 2021 Nature Introduction SARS_CoV_2 S477N;S477N 131;150 136;155 RBD 88 91 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. The proportion of samples containing E484K increased substantially from 1.8% between 1 and 15 December 2020 to 26.1% between 1 and 15 March 2021. 2021 Nature Introduction SARS_CoV_2 E484K 37 42 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. This mutation appears to render the virus more transmissible and virulent, perhaps owing to a higher binding affinity of N501Y for the ACE2 receptor or a greater propensity to evade host innate immune responses. 2021 Nature Introduction SARS_CoV_2 N501Y 121 126 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. This suggests that B.1.526:and B.1.526-E484K in particular:became widespread in the region, the original epicenter of COVID-19 in the United States, although the lineage has also grown in states outside the northeastern United States (for example, North Carolina). 2021 Nature Introduction SARS_CoV_2 E484K 39 44 COVID-19 118 126 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. To further investigate the evolutionary history of B.1.526, we performed phylogenetic analyses on genomes in this collection and in the GISAID collection harbouring the ORF1a-nsp6 deletion Delta106-108, along with the mutation A20262G that uniquely defines the parent clade containing B.1.526 and related viruses. 2021 Nature Introduction SARS_CoV_2 A20262G 227 234 ORF1a;Nsp6 169;175 174;179 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Two other variants of concern, B.1.351 and P.1, also harbour the N501Y mutation, in addition to an E484K substitution in the RBD. 2021 Nature Introduction SARS_CoV_2 E484K;N501Y 99;65 104;70 RBD 125 128 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. We genotyped 1,533 samples between 1 November 2020 and 15 March 2021; 169 (11%) contained E484K, 43 (2.8%) contained N501Y and 1 sample contained both mutations. 2021 Nature Introduction SARS_CoV_2 E484K;N501Y 90;117 95;122 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. We observed a stepwise emergence of the key lineage-defining mutations, with T95I, D253G and L5F appearing in the earliest phylogenetic nodes. 2021 Nature Introduction SARS_CoV_2 D253G;L5F;T95I 83;93;77 88;96;81 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. While B.1.526-L452R isolates shared a number of mutations across the genome in ORF-1ab, ORF-3ab, ORF-8 and N, they did not share characteristic spike mutations with B.1.526-E484K and B.1.526-S477N. 2021 Nature Introduction SARS_CoV_2 E484K;L452R;S477N 173;14;191 178;19;196 S;N 144;107 149;108 34431691 Emergence of Multiple SARS-CoV-2 Antibody Escape Variants in an Immunocompromised Host Undergoing Convalescent Plasma Treatment. Four severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) VOCs, i.e., B.1.1.7 (20I/501Y.V1, alpha), B.1.351 (20H/501Y.V2, beta), P1 (20J/501Y.V3, gamma), and B.1.617.2 (delta), carrying the spike protein N501Y mutation emerged in the United Kingdom, South Africa, Brazil, Japan, and India and have been associated with high transmissibility due to increased affinity to the angiotensin-converting enzyme 2 (ACE2) receptor. 2021 mSphere Introduction SARS_CoV_2 N501Y 212 217 S 198 203 COVID-19 12 52 34431691 Emergence of Multiple SARS-CoV-2 Antibody Escape Variants in an Immunocompromised Host Undergoing Convalescent Plasma Treatment. In each of these viruses, the spike protein contains clustered mutations in the N-terminal domain (NTD) and the receptor-binding domain (RBD) (e.g., E484K) regions. 2021 mSphere Introduction SARS_CoV_2 E484K 149 154 S;RBD;N 30;137;80 35;140;81 34432488 Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern. These lineages, many of which share common mutations in the spike protein (e.g., N501Y, E484K and L452R), have been declared variants of concern (VOC) by public health authorities (https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html). 2021 Journal of clinical microbiology Introduction SARS_CoV_2 E484K;L452R;N501Y 88;98;81 93;103;86 S 60 65 34433803 ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker. Analyses of over 28,000 gene sequences of SARS-CoV-2 spike protein (S-protein) in May 2020 revealed a D614G amino acid substitution (SARS-CoV-2-D614G) that was rare before March 2020, but increased greatly in frequency as the pandemic spread worldwide, reaching over 74% of all published sequences by June 2020 and 81% by May 2021 (GISAID). 2021 Signal transduction and targeted therapy Introduction SARS_CoV_2 D614G;D614G 102;144 107;149 S;S 53;68 58;69 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. A later mutation, N501Y, which has appeared in multiple lineages, lies within the RBD, and increases its affinity for ACE2. 2021 eLife Introduction SARS_CoV_2 N501Y 18 23 RBD 82 85 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Although the K417N/T mutations found in the South African (B.1.351) and Brazilian (P.1) variants both decreased the affinity, the affinity-enhancing N501Y and E484K mutations that are also present in both variants confer a net ~4-fold increase in the affinity of their RBDs for ACE2. 2021 eLife Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 159;13;13;149 164;20;20;154 RBD 269 273 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Both mutations of ACE2 (S19P, K26R) and most of the mutations of RBD (N501Y, E484K, and S477N) enhanced the interaction, with one RBD mutation (N501Y) increasing the affinity by ~10-fold. 2021 eLife Introduction SARS_CoV_2 E484K;K26R;S477N;N501Y;N501Y 77;30;88;70;144 82;34;93;75;149 RBD;RBD 65;130 68;133 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Increased binding was the result of decreases in dissociation rate constants (N501Y, S477N) and/or increases in association rate constants (N501Y, E484K). 2021 eLife Introduction SARS_CoV_2 E484K;S477N;N501Y;N501Y 147;85;78;140 152;90;83;145 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. One that emerged early in Europe, D614G, and quickly became dominant globally, increases the density of intact Spike trimer on the virus surface by preventing premature dissociation of S1 from S2 following cleavage. 2021 eLife Introduction SARS_CoV_2 D614G 34 39 S 111 116 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. The N501Y mutation is of functional significance because it is located in the receptor-binding domain of the spike protein. 2021 The Science of the total environment Introduction SARS_CoV_2 N501Y 4 9 S 109 114 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. These three variants of concern, commonly referred to as the UK (World Health Organization label Alpha), South African (Beta), and Brazilian (Gamma) variants, share several mutations, such as the spike protein mutation from asparagine to tyrosine (N501Y). 2021 The Science of the total environment Introduction SARS_CoV_2 N501Y 248 253 S 196 201 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. We report the detection of the N501Y mutation in wastewater as early as July 2020, as well as other mutations, some of which are present in variants of interest or concern. 2021 The Science of the total environment Introduction SARS_CoV_2 N501Y 31 36 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Both variants (B.1.351 and B.1.1.7) share the N501Y mutation that aids in increased binding affinity and immune escape. 2021 Biomolecules Introduction SARS_CoV_2 N501Y 46 51 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Here, we extend this to investigate the structural stability, binding affinity and intermolecular polar and hydrophobic contacts in the S protein RBD of the B.1.617 variant:E484Q and L452R independently and in combination (E484Q + L452R):using multiple 500 ns molecular dynamics (MD) simulations and binding free energy calculations. 2021 Biomolecules Introduction SARS_CoV_2 L452R;L452R;E484Q;E484Q 183;231;223;173 188;236;228;178 RBD;S 146;136 149;137 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. However, in April 2020, the original SARS-CoV-2 virus acquired the D614G mutation in the S protein. 2021 Biomolecules Introduction SARS_CoV_2 D614G 67 72 S 89 90 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Of these, N501Y appeared to be the major mutation in the RBD of the S protein. 2021 Biomolecules Introduction SARS_CoV_2 N501Y 10 15 RBD;S 57;68 60;69 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Of these, the combination of E484Q and L452R is of particular concern as they are positioned in the receptor-binding motif (RBM) of the S protein (Figure 1B,C). 2021 Biomolecules Introduction SARS_CoV_2 E484Q;L452R 29;39 34;44 S 136 137 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Sequencing analysis identified several mutations in the spike region including D614G. 2021 Biomolecules Introduction SARS_CoV_2 D614G 79 84 S 56 61 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. The now ubiquitous D614G variant exhibited higher transmissibility and infectivity with efficient replication. 2021 Biomolecules Introduction SARS_CoV_2 D614G 19 24 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. The South African variant B.1.351 or 20H/501Y is characterized by three mutations in the RBD region of the S protein:K417N, E484K, and N501Y. 2021 Biomolecules Introduction SARS_CoV_2 E484K;N501Y;K417N 124;135;117 129;140;122 RBD;S 89;107 92;108 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. The variant P.1, originally reported in Brazil, harbors N501Y, E484K, K417T mutations in the S protein. 2021 Biomolecules Introduction SARS_CoV_2 E484K;K417T;N501Y 63;70;56 68;75;61 S 93 94 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. This lineage includes three main subtypes (B1.617.1, B.1.617.2, and B.1.617.3) harboring several mutations in the S protein, including the synonymous D111D variation and the nonsynonymous G142D, L452R, E484Q, D614G and P681R variations. 2021 Biomolecules Introduction SARS_CoV_2 D111D;D614G;E484Q;G142D;L452R;P681R 150;209;202;188;195;219 155;214;207;193;200;224 S 114 115 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. From April 2020, the D614G mutation of the S protein exhibited major variation, and D614G has since become the dominant mutant form of the S protein in the pandemic. 2021 International journal of molecular sciences Introduction SARS_CoV_2 D614G;D614G 21;84 26;89 S;S 43;139 44;140 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. Mutations such as D614G cannot be explained using only research into RBDs, as D614G is positioned at the CT2 domain, not at RBD. 2021 International journal of molecular sciences Introduction SARS_CoV_2 D614G;D614G 18;78 23;83 RBD;RBD 69;124 73;127 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. The D614 residue is located in the CT2 domain of the S1 region, as before-mentioned, and the L455F and F456L residues are in the RBD region of the S1 domain. 2021 International journal of molecular sciences Introduction SARS_CoV_2 F456L;L455F 103;93 108;98 RBD 129 132 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. Variants in the S protein, such as D614G, D614A, L455F, F456L, and Q787H, have been identified. 2021 International journal of molecular sciences Introduction SARS_CoV_2 D614A;D614G;F456L;L455F;Q787H 42;35;56;49;67 47;40;61;54;72 S 16 17 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. A phylogenomic analysis of genomic sequences using the Nextstrain tool showed that the viruses in the lineage B.1.1.519 (B.1.1.1.222+T478K+P681H+T732A) group independently of the lineage B.1.1.222 sequences, strongly suggesting that this variant should be classified as a variant of interest (VOI). 2021 Archives of virology Introduction SARS_CoV_2 P681H;T478K;T732A 139;133;145 144;138;150 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. A striking observation was the detection of the B.1.1.519 lineage in the USA, derived from B.1.1.222, which harbors the mutation T478K in the spike protein. 2021 Archives of virology Introduction SARS_CoV_2 T478K 129 134 S 142 147 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. An in silico analysis using different potent structures of related strains suggested that the position of the T478K mutation in the S protein is involved in antibody recognition and the receptor binding site. 2021 Archives of virology Introduction SARS_CoV_2 T478K 110 115 S 132 133 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. Finally, two variants with interesting features were identified in this study: first, 13 sequences belonging to the B.1.1.222 lineage without the T478K mutation, but harboring the T732A mutation and the 69-70 deletion in the spike protein, the latter being a characteristic mutation of the B.1.1.7 VOC first detected in the UK; and second, 11 sequences corresponding to four lineages differing from B.1.1.519 (B.1, B.1.1.222, B.1.1.322, and B.1.323) but containing the same T478K, P681H, and T732A mutations in the spike glycoprotein that are present in the variant B.1.1.519. 2021 Archives of virology Introduction SARS_CoV_2 P681H;T478K;T478K;T732A;T732A 481;146;474;180;492 486;151;479;185;497 S;S 515;225 533;230 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. Here, we report the identification of a potential VOI harboring the mutations T478K, P681H, and T732A in the spike protein, within the newly named lineage B.1.1.519, derived from the B.1.1.222 lineage, that rapidly outcompeted the preexisting variants in Mexico and has been the dominant virus in the country during 2021. 2021 Archives of virology Introduction SARS_CoV_2 P681H;T478K;T732A 85;78;96 90;83;101 S 109 114 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. However, the presence of the mutations T478K, P681H, and T732A clearly differentiated it from this lineage, which does not contain these mutations, giving rise to the B.1.1.519 lineage. 2021 Archives of virology Introduction SARS_CoV_2 P681H;T478K;T732A 46;39;57 51;44;62 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. In a deep mutational scanning of the SARS-CoV-2 receptor binding domain, the T478K mutation did not have a significant effect on folding or binding to human angiotensin-converting enzyme 2 (ACE2). 2021 Archives of virology Introduction SARS_CoV_2 T478K 77 82 RBD 48 71 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. Notably, a T478K mutation is present in the receptor binding domain (RBD), where mutations have been shown to reduce the activity of some monoclonal antibodies. 2021 Archives of virology Introduction SARS_CoV_2 T478K 11 16 RBD;RBD 44;69 67;72 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. The P681H mutation is one of the mutations found in the B.1.1.7 variant detected in the UK. 2021 Archives of virology Introduction SARS_CoV_2 P681H 4 9 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. These SARS-CoV-2 VOCs have acquired some of the same spike protein mutations independently, particularly E484K, N501Y, S477N, and K417T, which have been associated with increased viral transmission and/or decreased sensitivity to antibody neutralization. 2021 Archives of virology Introduction SARS_CoV_2 E484K;K417T;N501Y;S477N 105;130;112;119 110;135;117;124 S 53 58 34449757 An Autochthonous Outbreak of the SARS-CoV-2 P.1 Variant of Concern in Southern Italy, April 2021. Cases of reinfection caused by SARS-CoV-2 strains carrying the E484K mutation have been described. 2021 Tropical medicine and infectious disease Introduction SARS_CoV_2 E484K 63 68 34449757 An Autochthonous Outbreak of the SARS-CoV-2 P.1 Variant of Concern in Southern Italy, April 2021. The 501Y.V2 and P.1 variants are both characterized by the E484K mutation in the RBD, which could contribute to the evasion from neutralizing antibodies. 2021 Tropical medicine and infectious disease Introduction SARS_CoV_2 E484K 59 64 RBD 81 84 34449757 An Autochthonous Outbreak of the SARS-CoV-2 P.1 Variant of Concern in Southern Italy, April 2021. These amino acid changes are L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I, and V1176F. 2021 Tropical medicine and infectious disease Introduction SARS_CoV_2 D138Y;E484K;H655Y;K417T;L18F;N501Y;P26S;R190S;T1027I;T20N;V1176F 47;68;82;61;29;75;41;54;89;35;101 52;73;87;66;33;80;45;59;95;39;107 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. However, these previous lineages were rapidly replaced by P.1 and P.2 in late 2020 and early 2021, which are both derived from the common ancestor B.1.1.28 and harbor concerning mutations in the spike protein (e.g., E484K and N501Y). 2021 Pathogens (Basel, Switzerland) Introduction SARS_CoV_2 E484K;N501Y 216;226 221;231 S 195 200 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. Since the P.1 variant carries multiple mutations of potential biological significance (especially E484K, K417T, and N501Y in the receptor-binding domain (RBD) of the spike protein): (i) some key substitutions may lead to the immunity evasion; (ii) higher transmissibility when compared with pre-existing lineages has been characterized; (iii) this VOC has been the focus of increased surveillance and deserves being studied in greater detail. 2021 Pathogens (Basel, Switzerland) Introduction SARS_CoV_2 E484K;K417T;N501Y 98;105;116 103;110;121 S;RBD 166;154 171;157 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Accordingly, independent estimation of the Epsilon variants B.1.429 and B.1.427 carrying the L452R mutation showed a 6.7-fold and a 5.3-fold median reduction in neutralization, respectively, in comparison to the WT strain. 2021 Vaccines Introduction SARS_CoV_2 L452R 93 98 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Amongst the mutations characterizing various globally circulating variants, the L452R mutation has been recently revealed as one of the mutations associated with the most recently denoted new VOC, Delta. 2021 Vaccines Introduction SARS_CoV_2 L452R 80 85 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Data analysis performed on GISAID-deposited genomes revealed that most lineages including the L452R mutation have independently emerged in recent months (since December 2020), suggesting that this mutation may significantly contribute to the adaptiveness of the virus, possibly reflecting adaptation for increasing immunity against the virus within the population. 2021 Vaccines Introduction SARS_CoV_2 L452R 94 99 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Identification of this locally emerging B.1.362+L452R variant carrying a mutation known to have increased infectivity and/or reduced neutralization emphasizes the importance of routine surveillance of emerging variants, which is crucial to control further spread of SARS-CoV-2. 2021 Vaccines Introduction SARS_CoV_2 L452R 48 53 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. In this study, we describe a novel emerging variant carrying the L452R mutation that emerged from a local B.1.362 lineage, which was widespread in Israel prior to the entrance of the Alpha variant in December 2020. 2021 Vaccines Introduction SARS_CoV_2 L452R 65 70 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Indeed, the L452R mutation is also associated with other known variants such as the A.27.1 variant identified in Mayotte and the B.1.427/B.1.429 (Epsilon) variant identified in California, US. 2021 Vaccines Introduction SARS_CoV_2 L452R 12 17 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Pseudoviruses carrying the L452R mutation were shown to be resistant to some neutralizing antibodies. 2021 Vaccines Introduction SARS_CoV_2 L452R 27 32 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Pseudoviruses with the L452R mutation were shown to have a X5.8:a 22.5-fold increase in cell entry compared to wild-type (WT) pseudoviruses, which was slightly lower compared to the X11.4:a 30.9-fold increase observed in N501Y compared to WT pseudoviruses. 2021 Vaccines Introduction SARS_CoV_2 L452R;N501Y 23;221 28;226 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Recently, the Delta variant carrying the L452R mutation was shown to have a 5.8-fold reduction in neutralization compared to the WT strain. 2021 Vaccines Introduction SARS_CoV_2 L452R 41 46 34452371 Intravenous, Intratracheal, and Intranasal Inoculation of Swine with SARS-CoV-2. This isolate is identical to other human SARS-CoV-2 isolates detected in New York City at the time of the outbreak and it contains the D614G mutation in the S protein. 2021 Viruses Introduction SARS_CoV_2 D614G 135 140 S 157 158 34452390 The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect. Furthermore, mutation-based tracing could be established; for instance, a relationship to the USA sequences was confirmed by identifying the USA characteristic amino-acid replacement T1004I (nsp3) in Algeria_EPI_ISL_420037. 2021 Viruses Introduction SARS_CoV_2 T1004I 183 189 Nsp3 191 195 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. Moreover, bamlanivimab demonstrated a strongly decreased in vitro neutralization activity against SARS-CoV-2 variants harboring the E484K mutation. 2021 Viruses Introduction SARS_CoV_2 E484K 132 137 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. Several case reports have demonstrated such selection, especially the E484K mutation, in patients treated with convalescent plasma or monoclonal antibody therapy. 2021 Viruses Introduction SARS_CoV_2 E484K 70 75 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. In contrast, variants lacking the E484K mutation (e.g., UK B.1.1.7) are well recognized by convalescent and immunized sera, with the RBD-ACE2 interaction barely affected by these antibodies. 2022 Allergy Introduction SARS_CoV_2 E484K 34 39 RBD 133 136 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. The importance of RBD/RBM is underlined by the observation that prominent variants of concern (e.g., South Africa B.1.351 and Brazil P.1) show strongly reduced susceptibility to neutralizing antibodies due to equally reduced recognition by serum antibodies caused by E484K mutation located in the RBM. 2022 Allergy Introduction SARS_CoV_2 E484K 267 272 RBD 18 21 34454120 The low contagiousness and new A958D mutation of SARS-CoV-2 in children: An observational cohort study. For example, researchers have found that the Europe-prevalent D614G mutation of the S protein may increase the infectivity of SARS-CoV-2. 2021 International journal of infectious diseases Introduction SARS_CoV_2 D614G 62 67 S 84 85 34455390 Evolution of antibody responses up to 13 months after SARS-CoV-2 infection and risk of reinfection. We found that anti-N antibodies dramatically decreased whereas anti-RBD IgG persist for up to 13 months at a level that neutralizes infectious variants D614G, B.1.1.7 but less B. 2021 EBioMedicine Introduction SARS_CoV_2 D614G 152 157 RBD;N 68;19 71;20 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. The objective of our study was to determine in CoronaVac-vaccinated people in Chile, with a complete two-dose schedule, the levels of neutralizing antibodies against D614G, alpha, and gamma variants. 2022 Journal of medical virology Introduction SARS_CoV_2 D614G 166 171 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. The top-binding ligands were additionally screened against biologically significant SARS-CoV-2 mutations occurring in the RBD of the S protein such as N501Y, E484K, K417N/T, A475V, I472V, L452R, V483A, F490L, S477N and N439K along with the United Kingdom, South African and Brazilian SARS-CoV-2 variants. 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 A475V;E484K;F490L;I472V;K417N;K417T;L452R;N439K;N501Y;S477N;V483A 174;158;202;181;165;165;188;219;151;209;195 179;163;207;186;172;172;193;224;156;214;200 RBD;S 122;133 125;134 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. 2C08 reduced lung viral load and morbidity in hamsters challenged with the WA1/2020 D614G, B.1.351, or B.1.617.2 strains. 2021 Immunity Introduction SARS_CoV_2 D614G 84 89 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. One mAb, 2C08, potently neutralized the WA1/2020 D614G SARS-CoV-2 strain and also neutralized the B.1.351 and B.1.1.28 variants. 2021 Immunity Introduction SARS_CoV_2 D614G 49 54 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. Although there are some mutations in VOC B.1.1.7, detection of the N501Y mutation and H69-V70 deletion could be a good strategy to screen for this variant and serve as a proxy to identify the B.1.1.7 lineage. 2021 Diagnostic microbiology and infectious disease Introduction SARS_CoV_2 N501Y 67 72 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. The European Centre for Disease Prevention and Control (ECDC) recommends that laboratories should consider implementing pre-screening reverse transcription PCR (RT-PCR) approaches in samples where SARS-CoV-2 has been detected to detect S-gene dropout (deletion H69-V70), or a screening method to detect the N501Y mutation in variant viruses. 2021 Diagnostic microbiology and infectious disease Introduction SARS_CoV_2 N501Y 307 312 S 236 237 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. The most unusual and concerning single mutation in this cluster is N501Y in the spike protein, which has been associated with increasing binding affinity to human ACE2. 2021 Diagnostic microbiology and infectious disease Introduction SARS_CoV_2 N501Y 67 72 S 80 85 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. The N501Y mutation has been detected in other emerging variants, such as B.1.351, detected mainly in South Africa, and P.1, which is now spreading across Brazil and has been found in 24 other countries. 2021 Diagnostic microbiology and infectious disease Introduction SARS_CoV_2 N501Y 4 9 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. used the combination of N501Y and H69/V70 as surrogate markers of VOC B.1.1.7. 2021 Diagnostic microbiology and infectious disease Introduction SARS_CoV_2 N501Y 24 29 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Reports also showed that some crucial mutations, such as D614G in some variants, might be responsible for enhanced infectivity. 2021 mBio Introduction SARS_CoV_2 D614G 57 62 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. We also assessed the significant mutations (E484K, K417T/N, N501Y, and D614G) in emerging variants that may concern public health. 2021 mBio Introduction SARS_CoV_2 D614G;K417N;K417T;N501Y;E484K 71;51;51;60;44 76;58;58;65;49 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. A D614G variation of SARS2 spike enhances force-dependent spike recognition of ACE2 and speeds up the follow-up S1/S2 detachment simultaneously. 2021 Cell research Introduction SARS_CoV_2 D614G 2 7 S;S 27;58 32;63 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. A93Y is identified for the first time among the European population and V90T for the first time globally. 2021 Meta gene Introduction SARS_CoV_2 V90T;A93Y 72;0 76;4 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Estimated negative change in binding affinity of -0.040 kcal/mol indicated that V90T mutation contributes minimally towards escaping 2-51 neutralizing antibody. 2021 Meta gene Introduction SARS_CoV_2 V90T 80 84 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Exploring computed variants, rare missense mutations: A93Y and V90T were identified. 2021 Meta gene Introduction SARS_CoV_2 A93Y;V90T 54;63 58;67 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. N501Y mutation in the receptor-binding domain has been identified as the key mutation that increases virus binding affinity to human angiotensin-converting enzyme 2 (hACE2). 2021 Meta gene Introduction SARS_CoV_2 N501Y 0 5 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. P681H mutation, that is found next to the furin cleavage site, enhances virus transmission by facilitating spike protein conformational change. 2021 Meta gene Introduction SARS_CoV_2 P681H 0 5 S 107 112 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Some B.1.1.7 surface glycoprotein mutations, such as: N501Y, P681H,HV [69-70],Y144 attracted special attention, as they have been associated to specific properties. 2021 Meta gene Introduction SARS_CoV_2 N501Y;P681H 54;61 59;66 S 13 33 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. The impact of the novel V90T mutation on N-terminal domain biding affinity towards 2-51 neutralizing antibody was inspected by mCSM-PPI2 web server. 2021 Meta gene Introduction SARS_CoV_2 V90T 24 28 N 41 42 34466655 Furin and the adaptive mutation of SARS-COV2: a computational framework. D614G mutation neither increases S protein affinity for ACE2 nor makes viral particle more resistant to neutralization and that TMPRSS2 and Furin of all species studied can cleave the SARS-CoV-2 S glycoprotein in a similar way, provided that they are well conserved proteases among many species Brooke and Prischi. 2021 Modeling earth systems and environment Introduction SARS_CoV_2 D614G 0 6 34466655 Furin and the adaptive mutation of SARS-COV2: a computational framework. (A) Acquisition of the adaptive mutation D614G; (B) Structural adaptive modification for the furin cleavage site; (C) Protein S structured from the complex of adaptive modifications that improves the rate of viral infection. 2021 Modeling earth systems and environment Introduction SARS_CoV_2 D614G 41 46 S 126 127 34466655 Furin and the adaptive mutation of SARS-COV2: a computational framework. It is important to consider this characteristic because it implies a greater speed of action of SARS-CoV2 than, for example, SARS-CoV, so much so that some adaptive mutations such as D614G seem to carry out structural changes that more expose the cut site for furin Korber et al. 2021 Modeling earth systems and environment Introduction SARS_CoV_2 D614G 183 188 34466655 Furin and the adaptive mutation of SARS-COV2: a computational framework. This fact, in addition to enhancing the viral pathogenic aspect, also seems to be responsible for the speed of infection, especially in connection with the presence of an adaptive mutation "D614G". 2021 Modeling earth systems and environment Introduction SARS_CoV_2 D614G 190 195 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. All such sequences contain various mutations due to nonsynonymous nucleotide changes in the receptor-binding domain (RBD), including E484K, N501Y, and/or K417N. 2021 Journal of chemical information and modeling Introduction SARS_CoV_2 E484K;K417N;N501Y 133;154;140 138;159;145 RBD 117 120 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. Several studies showed how some of these circulating variants may have reduced sensitivity to neutralizing antibodies targeting the RBD or to the NTD.- In this context, polyclonal antibodies contained in convalescent plasma (CP) from individuals infected with the D614G-containing SARS-CoV-2, showed reduced potency in neutralizing 501Y.V2/B.1.351 virus isolates. 2021 Journal of chemical information and modeling Introduction SARS_CoV_2 D614G 264 269 RBD 132 135 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. This S variant features the additional mutations L18F (in common with P.1) and R246I but does not feature the Delta241-243 deletion, whose existence was still debated when the authors released their study in January 2021. 2021 Journal of chemical information and modeling Introduction SARS_CoV_2 L18F;R246I 49;79 53;84 S 5 6 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. While for almost one year the only notable mutation in S has been the D614G (Asp614 Gly), which increases affinity for the cell receptor ACE2 and has immediately become dominant, novel S protein variants reported of late may pose new potential challenges for efficacy of vaccination, antibody-based therapies and viral diffusion control. 2021 Journal of chemical information and modeling Introduction SARS_CoV_2 D614G;D614G 70;77 75;89 S;S 55;187 56;188 34472141 Pseudoephedrine and its derivatives antagonize wild and mutated severe acute respiratory syndrome-CoV-2 viruses through blocking virus invasion and antiinflammatory effect. These lineages of viruses have many mutations in receptor-binding domain (RBD) of S1 subunit of SARS-CoV-2, especially mutations N501Y, E484Q, E484K, L452R, K417N, and K417T (Ostrov, ; Verghese et al., ). 2021 Phytotherapy research Introduction SARS_CoV_2 E484K;E484Q;K417N;K417T;L452R;N501Y 143;136;157;168;150;129 148;141;162;173;155;134 RBD 74 77 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. This was linked to Spike stability, which was enhanced by the introduction of the D614G mutation but also enhanced its use of cell surface and endosomal proteases (, ). 2021 The Journal of biological chemistry Introduction SARS_CoV_2 D614G 82 87 S 19 24 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. During the SARS epidemic in 2003, the single amino acid mutation D480A/G in the RBD domain of SARS-CoV spike protein gradually became dominant, and subsequent study confirmed that this mutation occurred in a critical site and enabled the mutant escaping neutralizing antibodies. 2021 Frontiers in immunology Introduction SARS_CoV_2 D480A;D480G 65;65 72;72 S;RBD 103;80 108;83 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. In addition, several recent studies have focused on the neutralizing activity of vaccine-elicited humoral immunity against new circulating mutant lineages, including B.1.1.7 (United Kingdom, bearing mutations 69-70 del, 144 del, N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H in the spike protein), B.1.429 (United States, bearing mutations S13I, W152C, L452R, and D614G in the spike protein), B.1.351(South Africa, bearing mutations D80A, D215G, K417N, E484K, N501Y D614G, and A701V in the spike protein), and P.1 and P.2 (Brazil, bearing certain mutations E484K, D614G, and V1176F, etc. 2021 Frontiers in immunology Introduction SARS_CoV_2 A570D;A701V;D1118H;D215G;D614G;D614G;D614G;D614G;D80A;E484K;E484K;K417N;L452R;N501Y;N501Y;P681H;S13I;S982A;T716I;V1176F;W152C 236;484;275;446;243;371;473;571;440;460;564;453;360;229;467;250;347;264;257;582;353 241;489;281;451;248;376;478;576;444;465;569;458;365;234;472;255;351;269;262;588;358 S;S;S 289;384;497 294;389;502 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. In contrast, early in the COVID-19 pandemic, SARS-CoV-2 spike mutation D614G rapidly became globally dominant. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 71 76 S 56 61 COVID-19 26 34 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. Several studies demonstrated that the D614G mutation enhanced the replication of the mutated virus in the lung epithelial cells. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 38 43 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? A classic example is the D614G mutated variant of SARS-CoV-2 that has become so dominant in all variants of concern (VOC) and variants of interest (VOI) globally (Figure 1). 2021 Molecular therapy. Nucleic acids Introduction SARS_CoV_2 D614G 25 30 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? However, we conclude from our analysis that the D614G mutation is not at all a vibrant outcome of genetic drift, and instead, it appears to be part of positive selection. 2021 Molecular therapy. Nucleic acids Introduction SARS_CoV_2 D614G 48 53 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? proposed a hypothesis that the D614G variants got a selective advantage due to structural changes in the furin-like domain in S-glycoprotein. 2021 Molecular therapy. Nucleic acids Introduction SARS_CoV_2 D614G 31 36 S 126 140 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? reported that the D614G mutation might alter the viral fitness of SARS-CoV-2. 2021 Molecular therapy. Nucleic acids Introduction SARS_CoV_2 D614G 18 23 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? Thus, further exploration of D614G mutation will certainly contribute to better understanding of the molecular evolution of emerging variants of SARS-CoV-2. 2021 Molecular therapy. Nucleic acids Introduction SARS_CoV_2 D614G 29 34 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? With the help of the mutation (D614G), the SARS-CoV-2 variants are gaining viral fitness to improve replication and increase transmission. 2021 Molecular therapy. Nucleic acids Introduction SARS_CoV_2 D614G 31 36 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Cases of the B.1.1.7 Alpha variant, introduced by travel from the UK in late 2020, expanded in the north of India, and it is known to be more transmissible than previous versions of the virus bearing the D614G spike substitution, while maintaining sensitivity to vaccine-elicited neutralizing antibodies. 2021 Nature Introduction SARS_CoV_2 D614G 204 209 S 210 215 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. followed by B.1.617.2, both bearing the L452R spike receptor-binding motif (RBM) substitution also observed in B.1.427/B.1.429 (refs. 2021 Nature Introduction SARS_CoV_2 L452R 40 45 S 46 51 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. The B.1.617.1 and B.1.617.2 spike proteins mediated higher fusion activity and syncytium formation than WT, probably mediated by P681R (Extended Data. 2021 Nature Introduction SARS_CoV_2 P681R 129 134 S 28 33 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. These experiments showed a loss of sensitivity for B.1.617.2 compared with WT Wuhan-1 bearing D614G of around eightfold for both sets of vaccine sera and reduction against B.1.1.7 that did not reach statistical significance. 2021 Nature Introduction SARS_CoV_2 D614G 94 99 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. These sera were tested for their ability to neutralize a B.1.617.2 viral isolate, in comparison with a B.1.1.7 variant isolate and a wild-type (WT) Wuhan-1 virus bearing D614G in spike. 2021 Nature Introduction SARS_CoV_2 D614G 170 175 S 179 184 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. We also used a pseudotyped virus (PV) system to test the neutralization potency of a larger panel of 65 vaccine-elicited sera, this time against B.1.617.1 as well as B.1.617.2 spike compared with Wuhan-1 D614G spike. 2021 Nature Introduction SARS_CoV_2 D614G 204 209 S;S 176;210 181;215 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. We investigated the role of the B.1.617.2 spike as an escape mechanism by testing 33 spike-specific monoclonal antibodies with an in vitro PV neutralization assay using Vero E6 target cells expressing transmembrane protease serine 2 (TMPRSS2) and the Wuhan-1 D614G SARS-CoV-2 spike or the B.1.617.2 spike (Extended Data. 2021 Nature Introduction SARS_CoV_2 D614G 259 264 S;S;S;S 42;85;276;299 47;90;281;304 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. We previously showed that B.1.1.7 spike, bearing P681H, had significantly higher fusogenic potential than a D614G Wuhan-1 virus. 2021 Nature Introduction SARS_CoV_2 D614G;P681H 108;49 113;54 S 34 39 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. A pseudovirus neutralization test showed that the D614G/P681R virus has partial (1.2-1.5 times) resistance to three monoclonal antibodies against the RBD of SARS-CoV-2 S protein. 2021 Expert review of vaccines Introduction SARS_CoV_2 D614G;P681R 50;56 55;61 RBD;S 150;168 153;169 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. A study in Ontario, Canada found that compared with non-VOC SARS-CoV-2 strains, the adjusted risk associated with Delta variant increases 120% (93-153%) for hospitalization, 287% (198-399%) for ICU admission, and 137% (50-230%) for death, compared with 59% (49-69%) for hospitalization, 105% (82-134%) for ICU admission, and 61% (40-87%) for death for N501Y-positive variants. 2021 Expert review of vaccines Introduction SARS_CoV_2 N501Y 352 357 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. An in vitro study has shown that the P681R mutation does not increase infectivity; however, the mutant virus shows higher pathogenicity than that of the parent SARS-CoV-2 virus in infected hamsters. 2021 Expert review of vaccines Introduction SARS_CoV_2 P681R 37 42 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. By analyzing the global GISAID database up to 27 April 2021, it was found that the rapid increase in the T478K mutation frequency in North America and some European countries may indicate that the adaptability of SARS-CoV-2 variants carrying the mutation increased. 2021 Expert review of vaccines Introduction SARS_CoV_2 T478K 105 110 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. Compared with D614G, the immune serum neutralizing antibody titer against the Delta variant after two shots decreased by 2.10-3.80 times, greater than the decrease for the Alpha variant (1.20 times) and smaller than that for the Beta variant (2.20-8.40 times). 2021 Expert review of vaccines Introduction SARS_CoV_2 D614G 14 19 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. Compared with D614G, the immune serum neutralizing antibody titer of inactivated vaccine BBV152 developed in India against Delta live virus decreased by 2.7 times, which was less than the decrease in neutralizing antibody titers against the Beta variant (3.0 times) used in the same study. 2021 Expert review of vaccines Introduction SARS_CoV_2 D614G 14 19 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. Compared with the D614G mutation alone, the ability of a pseudovirus carrying the L452R mutation to infect 293T cells increases by 6.7-22.5 times and the ability to infect HAO-ACE2 cells increases by 5.8-14.7 times. 2021 Expert review of vaccines Introduction SARS_CoV_2 D614G;L452R 18;82 23;87 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. Compared with WT/D614G, the immune serum neutralizing antibody titer against the Delta variant after one shot decreased by 1.72-3.40 times, which was greater than the decreases for the Alpha variant (0.90-1.25 times) and Gamma variant (1.45-1.60 times) and lower than that for the Beta variant (2.97-3.60 times). 2021 Expert review of vaccines Introduction SARS_CoV_2 D614G 17 22 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. Covishield, a similar vaccine produced by AstraZeneca in India, had a 3.28-fold decrease in immune serum neutralizing ability after two shots against the Delta variant as compared with D614G, consistent with the trend for ChAdOx1. 2021 Expert review of vaccines Introduction SARS_CoV_2 D614G 185 190 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. For the vast majority of vaccines approved and distributed in many countries, Phase II/III clinical studies were completed before the Delta variant outbreak, and their efficacies were mainly based on populations exposed to the D614G, Alpha, Beta, and Gamma variants. 2021 Expert review of vaccines Introduction SARS_CoV_2 D614G 227 232 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. Furthermore, K452R is the only mutation in CAL.20A (B.1.232). 2021 Expert review of vaccines Introduction SARS_CoV_2 K452R 13 18 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. In addition to the three important mutation sites mentioned above, the Delta-AY.1 variant has the K417N mutation, which has potentially serious consequences. 2021 Expert review of vaccines Introduction SARS_CoV_2 K417N 98 103 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. In addition, the P681R mutation promoted the cleavage of the spike protein (S protein) mediated by furin and accelerated cell-cell fusion. 2021 Expert review of vaccines Introduction SARS_CoV_2 P681R 17 22 S;S 61;76 66;77 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. It should be noted that the detection method used in this study was quite different from those in other studies, and the convalescent serum of D614G-infected patients detected using the Delta variant decreased by 33.69 times, which exceeded that of CoronaVac vaccine immune serum. 2021 Expert review of vaccines Introduction SARS_CoV_2 D614G 143 148 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. K417N was first reported in the RBD region of the Beta variant and can bind to N501Y, thus increasing the binding between spike proteins and ACE2 receptors in the variant and possibly reducing the susceptibility of the virus to neutralizing antibodies by more than 10 times. 2021 Expert review of vaccines Introduction SARS_CoV_2 N501Y;K417N 79;0 84;5 S;RBD 122;32 127;35 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. L452R is also the main mutation in the "Epsilon variant" B.1.429 and is related to an increase in the viral load and an approximately 20% increase in transmissibility. 2021 Expert review of vaccines Introduction SARS_CoV_2 L452R 0 5 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. P681R/P681H also exists in several variants under investigation in the United Kingdom, including A.23.1/E484K, B.1.1.7, and B1.318. 2021 Expert review of vaccines Introduction SARS_CoV_2 E484K;P681H;P681R 104;6;0 109;11;5 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. Several independent lineages carrying L452R have been reported in the global GISAID database, suggesting that the L452R mutation alone is of significant adaptive value to SARS-CoV-2. 2021 Expert review of vaccines Introduction SARS_CoV_2 L452R;L452R 38;114 43;119 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. Studies have shown that compared with the original strain WT/D614G, the serum neutralizing antibody titers against the Delta variant after inoculation with the Pfizer vaccine are 1.41-11.30 times lower. 2021 Expert review of vaccines Introduction SARS_CoV_2 D614G 61 66 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. T478K is located at the interface of Spike/ACE2 interactions. 2021 Expert review of vaccines Introduction SARS_CoV_2 T478K 0 5 S 37 42 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. The Delta variant contains L452R, T478K, D614G, and P681R (Delta-AY.1 with additional K417N mutation) mutations in the S protein domain; these mutations have been detected in other VOCs/VOIs and may affect the infectivity of viruses or resistance to specific antibodies. 2021 Expert review of vaccines Introduction SARS_CoV_2 D614G;K417N;L452R;P681R;T478K 41;86;27;52;34 46;91;32;57;39 S 119 120 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. The immune serum neutralizing antibody after two or three shots of another vaccine, ZF2001, developed in China decreased by 1.37-3.08 times compared with D614G, which was greater than the decrease for the Alpha variant (1.03-1.80 times) used in the same study. 2021 Expert review of vaccines Introduction SARS_CoV_2 D614G 154 159 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. The K417N mutation, together with the conserved L452R mutation in the Delta variant (also found in the CAL.20C/B.1.427/B.1.429 epsilon variant detected in California), may increase vaccine escape by Delta-AY.1. 2021 Expert review of vaccines Introduction SARS_CoV_2 K417N;L452R 4;48 9;53 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. The location of T478K in the interaction complex with human ACE2 may affect the affinity with human cells, thus affecting the infectivity of the virus. 2021 Expert review of vaccines Introduction SARS_CoV_2 T478K 16 21 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. The neutralizing antibody titer of immune serum induced by the BNT162b2 vaccine against the D614G/P681R virus decreased significantly (p < 0.0001). 2021 Expert review of vaccines Introduction SARS_CoV_2 D614G;P681R 92;98 97;103 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. The P681R mutation can cause a partial decrease in neutralizing antibodies. 2021 Expert review of vaccines Introduction SARS_CoV_2 P681R 4 9 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. The P681R mutation is located in close proximity to the furin cleavage site (FCS; residues RRAR positioned between 682 and 685) of the SARS-CoV-2 S protein; it increases the number of basic residues in the sub-optimal SARS-CoV-2 spike protein furin cleavage site. 2021 Expert review of vaccines Introduction SARS_CoV_2 P681R 4 9 S;S 229;146 234;147 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. used the Delta pseudovirus to detect the immune serum neutralizing antibody levels after two shots of CoronaVac and found that compared with D614G, the neutralizing titer decreased by 2.47 times, which was greater than the decrease for the Alpha variant (1.62 times). 2021 Expert review of vaccines Introduction SARS_CoV_2 D614G 141 146 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. Using the pseudovirus to test the immune serum after two shots of BNT162b2, its neutralizing antibody titer against the Delta variant decreased by 2.83-11.30 times compared with that against WT/D614G, consistent with the results obtained using live virus. 2021 Expert review of vaccines Introduction SARS_CoV_2 D614G 194 199 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. When Muecksch treated SARS-CoV-2 virus culture with weakly active neutralizing antibody in vitro, the T478K/R variant was enriched, suggesting that the mutation at this site may be related to immune evasion. 2021 Expert review of vaccines Introduction SARS_CoV_2 T478K;T478R 102;102 109;109 34493762 Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. use phylogenetic methods to estimate the importance of SARS-CoV-2 introductions on increasing the relative frequency of the D614G mutation, implicitly showing that international movement can affect the relative frequency of mutations. 2021 Scientific reports Introduction SARS_CoV_2 D614G 124 129 34494022 Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid and Potential Utility for SARS-CoV-2 Detection. A second E-beacon was prepared for detecting the E484K mutation, which is present in certain alpha and all beta and gamma strains of SARS-CoV-2. 2021 bioRxiv Introduction SARS_CoV_2 E484K 49 54 34494022 Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid and Potential Utility for SARS-CoV-2 Detection. Here Eb.19 (E484K) was mixed with either E484K target oligo (Figure 3C, top trace), with random oligonucleotide, E484 (WT) or an oligo corresponding to E484Q of the SARS-CoV-2 Kappa variant. 2021 bioRxiv Introduction SARS_CoV_2 E484K;E484Q;E484K 41;152;12 46;157;17 34494022 Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid and Potential Utility for SARS-CoV-2 Detection. In Figure 3C, we present selectivity data for Eb.19 (E484K) in the form of comparative bioluminescence spectra. 2021 bioRxiv Introduction SARS_CoV_2 E484K 53 58 34494022 Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid and Potential Utility for SARS-CoV-2 Detection. Nonetheless, samples of Eb.1 with G1 and G2F, compared to samples with Eb.1 plus the complementary oligo were easily distinguished. 2021 bioRxiv Introduction SARS_CoV_2 G2F 41 44 34494022 Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid and Potential Utility for SARS-CoV-2 Detection. Once again, although some unquenching is apparent with base variants, signal of Eb.19 (E484K) was greatest with the fully complementary target, E484K (6-8 fold). 2021 bioRxiv Introduction SARS_CoV_2 E484K;E484K 144;87 149;92 34494022 Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid and Potential Utility for SARS-CoV-2 Detection. Similar behavior was observed with Eb.19 (E484K) (Supporting Figure 3). 2021 bioRxiv Introduction SARS_CoV_2 E484K 42 47 34494022 Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid and Potential Utility for SARS-CoV-2 Detection. This Eb.19(E484K) carried the hairpin oligo: (sterol)-5'-CGCTCTGGTGTTAAAGGTTTGAGCG-3'-(dabcyl). 2021 bioRxiv Introduction SARS_CoV_2 E484K 11 16 34494022 Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid and Potential Utility for SARS-CoV-2 Detection. To assess specificity, we compared signal from samples of Eb.19 (WT) mixed with the target oligo to signal from samples of Eb.19 (WT) mixed with the random oligo and the E484K variant oligo (single base-pair mismatch). 2021 bioRxiv Introduction SARS_CoV_2 E484K 170 175 34494022 Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid and Potential Utility for SARS-CoV-2 Detection. Unquenching of 15-20% of Eb.1 was observed when mixed with oligo G2F, carrying (T-to-G) mismatches to the probe region at both the 3' and the 5' flanks. 2021 bioRxiv Introduction SARS_CoV_2 G2F 65 68 34494022 Enzymatic Beacons for Specific Sensing of Dilute Nucleic Acid and Potential Utility for SARS-CoV-2 Detection. Unquenching of Eb.19 (WT) did become apparent in samples containing the E484K oligo when added >10-8 M, although bioluminescence remained below samples with the fully complementary target oligo (Figure 3B, compare squares and circles). 2021 bioRxiv Introduction SARS_CoV_2 E484K 72 77 34495697 A Bifluorescent-Based Assay for the Identification of Neutralizing Antibodies against SARS-CoV-2 Variants of Concern In Vitro and In Vivo. Using this strategy, we have successfully rescued Venus-and mCherry-expressing rSARS-CoV-2 USA/WA1/2020 (WA-1) and a new rSARS-CoV-2 strain expressing mCherry and containing mutations K417N, E484K, and N501Y present in the receptor binding domain (RBD) of the viral spike (S) glycoprotein of the South Africa (SA) B.1.351 (beta [beta]) VoC. 2021 Journal of virology Introduction SARS_CoV_2 E484K;K417N;N501Y 191;184;202 196;189;207 RBD;S;RBD;S 223;266;248;273 246;271;251;274 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. An optimized system based on VSV vectors was used to assess the impact of the Spike mutation D614G and to assess neutralizing activity in convalescent serum. 2021 Journal of virology Introduction SARS_CoV_2 D614G 93 98 S 78 83 34495709 Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. Initially, the B.1.1.7 lineage had mutations N501Y and D614G and the characteristic DeltaH69/DeltaV70 deletion in the spike protein; in early 2021, however, Public Health England reported the first B.1.1.7 SARS-CoV-2 cases that had acquired the E484K mutation. 2021 Journal of clinical microbiology Introduction SARS_CoV_2 D614G;E484K;N501Y 55;245;45 60;250;50 S 118 123 34495709 Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. Lineages B.1.351 and P.1 are of specific concern because they present the spike mutation E484K, which has been associated with reduced neutralizing activity of antibodies and may be associated with reduced efficacy of vaccines. 2021 Journal of clinical microbiology Introduction SARS_CoV_2 E484K 89 94 S 74 79 34495709 Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. The B.1.575.1 sublineage was classified in the Phylogenetic Assignment of Named Global Outbreak (PANGO) lineage system as a Spanish sublineage of B.1.575 with spike mutations P681H, S494P, and T716I, and the B.1.575.2 sublineage, whose main characteristic is the presence of the E484K spike mutation, also originated in Spain. 2021 Journal of clinical microbiology Introduction SARS_CoV_2 E484K;P681H;S494P;T716I 279;175;182;193 284;180;187;198 S;S 159;285 164;290 34495709 Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. This study identified the emergence and spread of the E484K spike mutation within the SARS-CoV-2 B.1.575.2 lineage, which increased in the circulating virus population in Pamplona, Spain, between May and June 2021. 2021 Journal of clinical microbiology Introduction SARS_CoV_2 E484K 54 59 S 60 65 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). A recurrent emergence and significant onward transmission of a mutation in the spike gene which result in loss of H69/V70 has recently been reported to co-occur with the receptor binding motif (RBM) amino acid substitutions N501Y, N439K and Y453F (Kemp et al.,). 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 N439K;N501Y;Y453F 231;224;241 236;229;246 S 79 84 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). For this purpose: i) two single mutants (N501Y and E484K) and a multiple-mutant (K417N + N501Y + E484K) were constructed on the initial crystallographic structure of the spike protein, ii) the obtained mutant structures were submitted to energy minimization, iii) protein-protein dockings were performed on the HADDOCK server, iv) the docked spike/ACE2 conformations with the most negative binding energy (including control) were subjected to 200-nanosecond long molecular dynamics simulations in order to observe the stability of these interactions and, v) the binding free energies of all complexes were calculated using the endpoint MM-PBSA method. 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 E484K;E484K;N501Y;K417N;N501Y 51;97;89;81;41 56;102;94;86;46 S;S 170;342 175;347 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Furthermore, vaccines manufactured by Novavax and Johnson & Johnson which have been tested in recent clinical trials were reported to be less effective against South African variants (B.1.351) harboring the E484K mutation than UK (B.1.1.7) and US (B.1.427 and B.1.429) lineages (Wise,). 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 E484K 207 212 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). In addition to the N501Y and E484K mutations, the substitution that is at least as effective in the escape of SARS-CoV-2 from antibodies and causes greater conformational changes when found in combination with other mutations is the K417N mutation (Nelson et al.,). 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 E484K;K417N;N501Y 29;233;19 34;238;24 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). It has been reported that the experimental induction of E484K mutation alone can provide resistance to many monoclonal antibodies, and is associated with complete elimination of neutralization capacity in convalescent sera tested in some SARS-CoV-2 lineages (Ferrareze et al.,; Jangra et al.,; Xie et al.,). 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 E484K 56 61 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). It has been reported that the N501Y mutation affects the receptor binding affinity of the spike protein and increases the infectivity of the virus alone or together with the 69/70 deletion in the N-terminal domain of the protein. 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 N501Y 30 35 S;N 90;196 95;197 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Mechanistically, the E484K mutation in the flexible loop region of the SARS-CoV-2 receptor binding domain (RBD) causes the formation of novel favorable contacts in the RBD/ACE2 interface (Nelson et al.,) and more specifically, it ends up with a stronger ionic interaction between the residue GLU75 of ACE2 and the LYS484 of RBD (Franceschi, Caldana et al.,). 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 E484K 21 26 RBD;RBD;RBD;RBD 82;107;168;324 105;110;171;327 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Recently, just after N501Y, one of the mutations with the highest frequency nearly in all SARS-CoV-2 variants is the E484K. 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 E484K;N501Y 117;21 122;26 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). The aim of this study was therefore to compare these mutant (N501Y, E484K, K417N) spike glycoprotein/ACE2 interactions with the wild-type RBD/ACE2 interaction and to investigate whether the obtained binding conformations correlate with the clinical data. 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 E484K;K417N;N501Y 68;75;61 73;80;66 S;RBD 82;138 100;141 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Thus, these three mutations (K417N, E484K, N501Y), alone or in combination, most likely play a role as key mutational factors in the virulence and escape potential of the SARS-CoV-2. 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 E484K;N501Y;K417N 36;43;29 41;48;34 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Today, there are a total of 32 recorded variants of the SARS-CoV-2 and three of these variants (B.1.351 [South Africa], B.1.351 + P384L [South Africa], B.1.351 + E516Q [South Africa]) still maintain their importance in terms of public health, as they are 'escape mutants' (Variants of Concern) (European Centre for Disease Prevention and Control (ECDC),),). 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 E516Q;P384L 162;130 167;135 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). While the K417N mutation alone cannot give the virus the ability to escape from neutralization significantly, it causes a 5- to 12-fold decrease in serum neutralization when found in combination with E484K and N501Y mutations (Chen et al.,; Fratev,). 2021 Journal of biomolecular structure & dynamics Introduction SARS_CoV_2 E484K;K417N;N501Y 200;10;210 205;15;215 34499599 Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. As of August 12, 2021, GISAID reported E484K in 52 of 408,781 B.1.617.2 sequences, 2 of 549 AY.1 sequences, and 32 of 19,996 AY.3 (Delta) sequences; none of these reports were in Italy. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 39 44 34499599 Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. Breakthrough infections of E484K-harboring SARS-CoV-2 Delta variant, Lombardy, Italy. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 27 32 34499599 Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. E484K causes resistance to many class 2 RBD-directed antibodies, including bamlanivimab. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 0 5 RBD 40 43 34499599 Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. E484K has been additionally reported in 1 of 6,011 B.1.617.1 (Kappa variant) sequences. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 0 5 34499599 Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. E484K is the hallmark MOC of VOCs Beta and Gamma, in addition to having been reported in a minor sublineage of VOC Alpha, in variants of interest Eta and Iota, and at frequencies >50% in 38 more strains. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 0 5 34499599 Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. E484K mutation represents a critical evolutionary event that leads to immune escape, although its consequences on viral fitness are unclear. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 0 5 34499599 Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. He fully recovered without need for hospital admission; whole-genome sequencing confirmed B.1.617.2 that harbored E484K. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 114 119 34499599 Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. However, given the widespread convergent evolution of the spike protein observed across clades, the occurrence of MOC E484K and its widespread circulation is largely expected. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 118 123 S 58 63 34499599 Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. None of the 5 sublineages are to date characterized by the occurrence of the other MOC E484K, which causes resistance to monoclonal antibodies and reduced vaccine efficacy. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 87 92 34499599 Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. The most potent mRNA vaccine-elicited monoclonal antibodies were >10-fold less effective against pseudotyped viruses carrying the E484K mutation (Z. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 130 135 34499599 Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. This variant of concern (VOC) was renamed Delta by the World Health Organization and consists to date of 5 different sublineages (B.1.617.2, AY.1, AY.2, AY.3, and AY.3.1, according to PANGOLIN phylogeny) that share T478K and L452R as the main mutations of concern (MOCs) within the spike protein. 2021 Emerging infectious diseases Introduction SARS_CoV_2 L452R;T478K 225;215 230;220 S 282 287 34499599 Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. We report a cluster of B.1.617.2 and E484K occurring in Lombardy, Italy. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 37 42 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. All these lineages have conserved L452R, D614G and P681R (accessed on 6 June 2021). 2021 International journal of molecular sciences Introduction SARS_CoV_2 D614G;L452R;P681R 41;34;51 46;39;56 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. As in lineage B.1.617, Kappa and B.1.617.3 have same L452R and E484Q mutation in RBD of spike, while Delta has L452R and T478K, we have only considered Kappa and Delta in this study. 2021 International journal of molecular sciences Introduction SARS_CoV_2 E484Q;L452R;L452R;T478K 63;53;111;121 68;58;116;126 S;RBD 88;81 93;84 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. Further, the B.1.618 (triple mutant), recently detected in the four Indian states (Maharashtra, Delhi, West Bengal and Chhattisgarh), has been characterized by the deletion of Tyr145 and His146 as well as E484K and D614G mutation in the spike protein (accessed on 10 July 2021). 2021 International journal of molecular sciences Introduction SARS_CoV_2 D614G;E484K 215;205 220;210 S 237 242 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. In another study, it has been reported that N501Y mutation increases (dissociation constant: 22 nM to 0.44 nM) the binding affinity with hACE2. 2021 International journal of molecular sciences Introduction SARS_CoV_2 N501Y 44 49 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. In October 2020, B.1.351 (Beta variant) was detected in the South African population, which could infect more younger people and had three primary mutations in the RBD of spike protein, namely, N501Y, K417N and E484K. 2021 International journal of molecular sciences Introduction SARS_CoV_2 E484K;K417N;N501Y 211;201;194 216;206;199 S;RBD 171;164 176;167 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. In our previous study, we had reported that N501Y mutation could enhance the ACE2 affinity and possibly confer resistance towards the antibodies. 2021 International journal of molecular sciences Introduction SARS_CoV_2 N501Y 44 49 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. It contains same mutations as Delta variant and two other mutations:K417N and W258L in the spike glycoprotein. 2021 International journal of molecular sciences Introduction SARS_CoV_2 W258L;K417N 78;68 83;73 S 91 109 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. Our results also indicated the reinfection potential of P1 and N501Y.V2 variants. 2021 International journal of molecular sciences Introduction SARS_CoV_2 N501Y 63 68 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. Similarly, the lineage P.1 (Gamma variant) detected in January 2021 in the Brazilian population had three mutations of concern in spike RBD, namely, N501Y, K417T and E484K. 2021 International journal of molecular sciences Introduction SARS_CoV_2 E484K;K417T;N501Y 166;156;149 171;161;154 S;RBD 130;136 135;139 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. The Kappa is characterized by E154K, L452R, E484Q, D614G, P681R, Q1071H mutations in the spike protein and Delta by T19R, L452R, T478K, D614G, P681R, D950N mutations while the B.1.617.3 lineage has T19R, L452R, E484Q, D614G, P681R mutations in the spike protein. 2021 International journal of molecular sciences Introduction SARS_CoV_2 D614G;D614G;D614G;D950N;E154K;E484Q;E484Q;L452R;L452R;L452R;P681R;P681R;P681R;Q1071H;T19R;T19R;T478K 51;136;218;150;30;44;211;37;122;204;58;143;225;65;116;198;129 56;141;223;155;35;49;216;42;127;209;63;148;230;71;120;202;134 S;S 89;248 94;253 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. The loss of E484Q mutation and gain of T478K in the B.1.617.2 lineage directly correlated with increase in the positivity rate. 2021 International journal of molecular sciences Introduction SARS_CoV_2 E484Q;T478K 12;39 17;44 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. This variant increased the transmissibility by 40-80% and has been partially correlated with N501Y mutation in the receptor binding domain (RBD) of spike protein (Figure 1A). 2021 International journal of molecular sciences Introduction SARS_CoV_2 N501Y 93 98 RBD;S;RBD 115;148;140 138;153;143 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. While in this study we have focused on the mutations within the RBD of spike protein, the D614G mutation (present outside the RBD region) has already been reported to increase the binding affinity with hACE2 and is susceptible to neutralization by antibodies. 2021 International journal of molecular sciences Introduction SARS_CoV_2 D614G 90 95 S;RBD;RBD 71;64;126 76;67;129 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. In addition, it has been reported that D614G had increased viral titers and viral replication in the upper respiratory airway in the human epithelial cells. 2021 Biochimie Introduction SARS_CoV_2 D614G 39 44 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. In this study, we studied variants of interest or concern in terms of mutational sensitivity utilizing Phyre2 and prediction of stability changes in the spike protein of SARS-CoV-2 upon mutations using DynaMut by Normal Mode Analysis (NMA) considering the clade 20A, which bears the D614G the new global dominant variant, as a new reference sequence instead of the clade 19A due to the fact that all other clades and subclades have been derived from the clade 20A. 2021 Biochimie Introduction SARS_CoV_2 D614G 283 288 S 153 158 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. One of the most well-studied emerging and globally distributed mutations in the spike protein of the SARS-CoV-2 virus is D614G which now occupies the first rank in terms of the total mutation frequency (frequency = 1349735 counts, the last update on 08.08.2021). 2021 Biochimie Introduction SARS_CoV_2 D614G 121 126 S 80 85 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. PANGO reports, which are available online, currently include five linages; B.1.1.7 or known as UK linage (N501Y, P681H and other mutations), B.1.351 or known as South Africa linage (501Y.v2), P.1 or known as Brazil linage (E484K, N501Y and K417T), A.23.1 linage (F157L, V367F, Q613H and P681R) and B.1.525 linage (E484K, Q677H, F888L). 2021 Biochimie Introduction SARS_CoV_2 F888L;K417T;N501Y;P681H;P681R;Q613H;Q677H;V367F;E484K;E484K;F157L;N501Y 328;240;230;113;287;277;321;270;223;314;263;106 333;245;235;118;292;282;326;275;228;319;268;111 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. Previous reports have hypothesized that the mutation D614G impacts the viral fitness and infectivity. 2021 Biochimie Introduction SARS_CoV_2 D614G 53 58 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. Since its discovery in Wuhan in December 2019 (named Wuhan-Hu-1 or WA1), SARS-CoV-2, the wild type clade, has been called 19A, without any amino acid changes in the spike protein and 19B; without D614G but other changes in the spike protein. 2021 Biochimie Introduction SARS_CoV_2 D614G 196 201 S;S 165;227 170;232 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The clade 19A has evolved into several co-circulating variants presently the major clades from 2020 until now are: 20A: basal pandemic lineage bearing spike protein mutation D614G that is globally distributed, 20B: derived from 20A, 20C: derived from 20A, 20D: derived from 20B, 20E: derived from 20A, 20F: derived from 20B, 20G: derived from 20C, 20H/501Y.V2: derived from 20C, 20I/501Y.V1: derived from 20B. 2021 Biochimie Introduction SARS_CoV_2 D614G 174 179 S 151 156 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. However, it is reported that N501Y mutation in the spike protein may reduce the neutralization sensitivity of antibodies, and may influence the effectiveness of some vaccines. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 N501Y 29 34 S 51 56 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. In our previous work, we found 9 candidate key mutations, including A23403G causing D614G amino acid change on the S protein, which has been proved to increase the infectivity of SARS-CoV-2 by several in vitro experiences. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 A23403G;D614G 68;84 75;89 S 115 116 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. We further found that the 4 highly linked sites (C241T, C3037T, C14408T and A23403G) of the previous 9 candidate key mutations have been almost fixed in the virus population, and the other 5 mutations disappeared gradually. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 A23403G;C14408T;C241T;C3037T 76;64;49;56 83;71;54;62 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. An in-silico molecular dynamics study on the protein structure of spike has predicted that the T478K mutation may significantly alter the electrostatic surface of the protein, and therefore, the interaction with ACE2, drugs, or antibodies, and that the effect can be increased if combined by other co-occurring spike mutations. 2021 Cureus Introduction SARS_CoV_2 T478K 95 100 S;S 66;311 71;316 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. However, it does not have the E484Q mutation. 2021 Cureus Introduction SARS_CoV_2 E484Q 30 35 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. In the Delta variant, the mutations found in its RBD are L452R and T478K. 2021 Cureus Introduction SARS_CoV_2 L452R;T478K 57;67 62;72 RBD 49 52 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. In the present study, we have focused on the Delta and Kappa variants and utilized homology modeling (HM) simulations of S protein trimer to assess its dynamic behavior in terms of conformational stability as well as the interaction of isolated viral RBD in complex with human ACE2 to probe the specific interactions emanating from the double mutations (L452R/E484Q in Kappa and L452R/T478K in Delta) in the RBD-ACE2 complexes. 2021 Cureus Introduction SARS_CoV_2 L452R;L452R;E484Q;T478K 379;354;360;385 384;359;365;390 RBD;RBD;S 251;408;121 254;411;122 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. Moreover, it was found that the L452R mutation strengthens virus-cell attachment and, thus, increases infectiousness. 2021 Cureus Introduction SARS_CoV_2 L452R 32 37 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. Mutations at this same position (E484K) have been observed in the variants Gamma and Zeta, as well as in the variant Beta. 2021 Cureus Introduction SARS_CoV_2 E484K 33 38 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. Mutations in the Beta and Gamma variants, including E484K and K417N/T, are of high concern since they partly compromise neutralization generated by previous infection or vaccination or affect viral stability. 2021 Cureus Introduction SARS_CoV_2 E484K;K417N;K417T 52;62;62 57;69;69 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. T478K mutation has appeared and risen in frequency since January 2021, predominantly in Mexico and the USA in variant B.1.1.519. 2021 Cureus Introduction SARS_CoV_2 T478K 0 5 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. The E484Q mutation is known to participate in the partial immune escape post-infection and post-vaccination and is responsible for resistance to certain monoclonal antibodies. 2021 Cureus Introduction SARS_CoV_2 E484Q 4 9 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. The L425R mutation, present in the variants Epsilon, Delta, and Kappa, reduces the spike protein reactivity with the virus-neutralizing antibodies and sera from convalescent patients. 2021 Cureus Introduction SARS_CoV_2 L425R 4 9 S 83 88 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. The RBD mutation N501Y, which increases affinity to ACE2 and is present in the Alpha, Beta, and Gamma variants, does not have any effect on post-vaccine serum neutralization. 2021 Cureus Introduction SARS_CoV_2 N501Y 17 22 RBD 4 7 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. The variant kappa contains two mutations in the RBD, L452R, and E484Q, which had never been observed together before the emergence of this variant. 2021 Cureus Introduction SARS_CoV_2 E484Q;L452R 64;53 69;58 RBD 48 51 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. They share an L452R mutation on the spike protein, which may be associated with increased transmissibility of the virus. 2021 Cureus Introduction SARS_CoV_2 L452R 14 19 S 36 41 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. Another study illustrated that the Biosensing approach was also reliable in detecting the D614G mutation. 2021 Heliyon Introduction SARS_CoV_2 D614G 90 95 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. Furthermore, this is the first study that describes the reliability of the qPCR-HRM assay for the detection of D614G mutations in SARS-CoV-2 and provides a model that can be developed for the detection of other mutations in SARS-CoV-2. 2021 Heliyon Introduction SARS_CoV_2 D614G 111 116 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. Several approaches have been developed to rapidly detect the D614G mutation. 2021 Heliyon Introduction SARS_CoV_2 D614G 61 66 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. The PCR-RFLP method has also been described to detect the D614G mutation, but the data were ultimately misinterpreted. 2021 Heliyon Introduction SARS_CoV_2 D614G 58 63 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. The RT-qPCR assay was also specially developed to perform a D614G genotyping that could distinguish the two variants. 2021 Heliyon Introduction SARS_CoV_2 D614G 60 65 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. This mutation is known as the D614G, which has been shown to affect the infectivity of SARS-CoV-2 in vitro and in vivo. 2021 Heliyon Introduction SARS_CoV_2 D614G 30 35 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. This study developed a sensitive method for the detection of the D614G mutation of SARS-CoV-2. 2021 Heliyon Introduction SARS_CoV_2 D614G 65 70 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. This suggests that SNP genotyping by RT-qPCR-HRM analysis can detect the D614G mutation in SARS-CoV-2. 2021 Heliyon Introduction SARS_CoV_2 D614G 73 78 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. By analyzing the frequency, binding free energy (BFE) changes, and antibody disruption counts of RBD co-mutations, we reveal that nine RBD co-mutation sets, namely [L452R, T478K], [L452Q, F490S], [E484K, N501Y], [F490S, N501Y], [S494P, N501Y], [K417T, E484K, N501Y], [K417N, L452R, T478K], [K417N, E484K, N501Y], and [P384L, K417N, E484K, N501Y], may strongly disrupt existing vaccines and mAbs with relatively high infectivity and transmissibility among the populations. 2021 ArXiv Introduction SARS_CoV_2 E484K;E484K;E484K;F490S;K417N;L452R;N501Y;N501Y;N501Y;N501Y;N501Y;N501Y;T478K;T478K;E484K;F490S;K417N;K417N;K417T;L452Q;L452R;P384L;S494P 252;298;332;188;325;275;204;220;236;259;305;339;172;282;197;213;268;291;245;181;165;318;229 257;303;337;193;330;280;209;225;241;264;310;344;177;287;202;218;273;296;250;186;170;323;234 RBD;RBD 97;135 100;138 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Nonetheless, near 700 non-degenerate mutations are observed on RBD, contributing many key mutations in emerging variants, i.e., N501Y for Alpha, K417N, E484K, and N501Y for Beta, K417T, E484K, and N501Y for Gamma, L452R and T478K for Delta, L452Q and F490S for Lambda, etc. 2021 ArXiv Introduction SARS_CoV_2 E484K;E484K;F490S;K417N;K417T;L452Q;L452R;N501Y;N501Y;N501Y;T478K 152;186;251;145;179;241;214;128;163;197;224 157;191;256;150;184;246;219;133;168;202;229 RBD 63 66 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. The associated new mutations, P384L, V401L, and A411S, call for the new design of boosting vaccines and mAbs. 2021 ArXiv Introduction SARS_CoV_2 A411S;P384L;V401L 48;30;37 53;35;42 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. We predict that low-frequency co-mutation sets [A411S, L452R, T478K], [L452R, T478K, N501Y], [V401L, L452R, T478K], and [L452R, T478K, E484K, N501Y] are on the path to become dangerous new variants. 2021 ArXiv Introduction SARS_CoV_2 E484K;L452R;L452R;N501Y;N501Y;T478K;T478K;T478K;T478K;A411S;L452R;L452R;V401L 135;55;101;85;142;62;78;108;128;48;71;121;94 140;60;106;90;147;67;83;113;133;53;76;126;99 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. However, the reduction of in vitro neutralizing antibody titers against variants relative to the wild-type D614G virus raises the possibility of breakthrough infections and waning efficacy for the current SARS-CoV-2 vaccines. 2021 Nature medicine Introduction SARS_CoV_2 D614G 107 112 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. The most parsimonious interpretation of these data is that the D614G mutation plays a significant, and apparently the most important, role in causing an increased prevalence of anosmia in COVID-19 patients. 2021 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 63 68 Anosmia;COVID-19 177;188 184;196 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. The pandemic started in East Asia with the less infectious D614 virus strain, but when COVID-19 reached Europe and North America and the rest of the world, the virus with a D614G mutation in the spike protein rapidly replaced the original D614 virus. 2021 ACS chemical neuroscience Introduction SARS_CoV_2 D614G 173 178 S 195 200 COVID-19 87 95 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. For example, the N501Y substitution that was first observed in the B.1.1.7 lineage and provides enhanced ACE2 binding, is now present in B.1.351, P.1, and P.3 lineages. 2021 Virology Introduction SARS_CoV_2 N501Y 17 22 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Similarly, the E484K and K417N/T mutations in the RBD that were first described in the B.1.351 and P.1 lineages likely due to immune evasion from vaccine or natural infection-elicited antibodies, are now present in several other lineages. 2021 Virology Introduction SARS_CoV_2 E484K;K417N;K417T 15;25;25 20;32;32 RBD 50 53 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. The first identified D614G mutation in the Spike glycoprotein became dominant among the rapidly spreading emerging variants. 2021 Virology Introduction SARS_CoV_2 D614G 21 26 S 43 61 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. A fourth spike gene mutation that is shared by ~48% of V2 sequences and by all V3 sequences is L18F. 2021 Cell Introduction SARS_CoV_2 L18F 95 99 S 9 14 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Almost all the spike genes of sequences in these lineages carry the N501Y mutation at a key receptor binding domain (RBD) site that increases the affinity of the Spike protein for human ACE2 receptors by ~2.1- to 3.5-fold. 2021 Cell Introduction SARS_CoV_2 N501Y 68 73 RBD;S;S;RBD 92;15;162;117 115;20;167;120 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Although both the K417N and K417T mutations can reduce the affinity of Spike for ACE2, in conjunction with the N501Y and E484K mutations, ACE2 binding is restored to that of wild-type Spike. 2021 Cell Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 121;18;28;111 126;23;33;116 S;S 71;184 76;189 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Crucially, E484K and other mutations at S/484 also frequently confer protection from neutralization by both convalescent sera, vaccine-elicited antibodies, and some monoclonal antibodies. 2021 Cell Introduction SARS_CoV_2 E484K 11 16 S 40 41 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. K417N and K417T also both have moderately positive impacts on Spike expression, and these and other mutations at S/417 provide modest protection from neutralization by some convalescent sera, vaccine-induced antibodies, and some neutralizing monoclonal antibodies. 2021 Cell Introduction SARS_CoV_2 K417T;K417N 10;0 15;5 S;S 62;113 67;114 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Other than the early identification of the D614G substitution in the viral Spike protein and P323L in the viral RNA-dependent RNA polymerase protein, both of which may have increased viral transmissibility without impacting pathogenesis, few mutations were epidemiologically significant and the evolutionary dynamics of the virus were predominantly characterized by a mutational pattern of slow and selectively neutral random genetic drift. 2021 Cell Introduction SARS_CoV_2 D614G;P323L 43;93 48;98 RdRp;S 112;75 140;80 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. The vast majority of V2 and V3 variants and ~0.3% of more recent samples of V1 variants also have a Spike E484K mutation. 2021 Cell Introduction SARS_CoV_2 E484K 106 111 S 100 105 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. There is therefore increasing evidence that viruses carrying the E484K mutation (with or without 501Y) will be able to more frequently infect both previously infected and vaccinated individuals. 2021 Cell Introduction SARS_CoV_2 E484K 65 70 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Viruses carrying the L18F mutation increased in prevalence from the start of the pandemic and now account for ~10% of sampled SARS-CoV-2 sequences. 2021 Cell Introduction SARS_CoV_2 L18F 21 25 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Whereas V2 sequences generally carry a K417N mutation, V3 sequences carry a K417T mutation. 2021 Cell Introduction SARS_CoV_2 K417N;K417T 39;76 44;81 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. All the glycans also exhibited strong binding to S-protein N501Y mutant. 2021 The Journal of biological chemistry Introduction SARS_CoV_2 N501Y 59 64 S 49 50 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. The emergence of new SARS-CoV-2 variants with a key N501Y mutation in S-protein receptor binding domain (RBD) may lead to tighter binding to ACE2 receptor, thus causing higher infectivity and increased human to human transmissibility. 2021 The Journal of biological chemistry Introduction SARS_CoV_2 N501Y 52 57 RBD;RBD;S 80;105;70 103;108;71 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. N501Y, E484K/Q, L452R...), or were associated with diagnostic failure (DeltaH69-V70). 2022 Clinical microbiology and infection Introduction SARS_CoV_2 E484K;E484Q;L452R;N501Y 7;7;16;0 14;14;21;5 34537363 Influence of treatment with neutralizing monoclonal antibodies on the SARS-CoV-2 nasopharyngeal load and quasispecies. The full spectrum of key spike mutations associated with resistance to mAbs is not yet established, but mutations K417N, E484D/K/Q, Q493R/K and S494P seem to be involved in virus escape and resistance to mAbs. 2022 Clinical microbiology and infection Introduction SARS_CoV_2 E484D;E484K;E484Q;K417N;Q493K;Q493R;S494P 121;121;121;114;132;132;144 130;130;130;119;139;139;149 S 25 30 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. A475V variant at RBD has also been reported to become resistant to some nAbs. 2021 Frontiers in immunology Introduction SARS_CoV_2 A475V 0 5 RBD 17 20 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. Moreover, the recombined antibodies (rAbs) with heavy and light chains from different nAbs produced some new antibodies with a higher neutralization potency against E484Q or A475V mutations which showed immune escape from the original nAbs. 2021 Frontiers in immunology Introduction SARS_CoV_2 A475V;E484Q 174;165 179;170 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. Previous report suggested that D614G altered SARS-CoV-2 fitness and neutralization susceptibility, and that might be a challenge for therapeutic antibodies or vaccines. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 31 36 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. Recently, the mutation E484Q found in India variant (B.1.617) could escape the vaccine-induced humoral immune response. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484Q 23 28 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. SARS-CoV-2 D614G variant, which could produce higher infectious titers, has become dominant during the COVID-19 pandemic. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 11 16 COVID-19 103 111 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. Two nAbs, XG81 and XG83, were identified showing a high neutralization potency against different SARS-CoV-2 variants, including the ones with D614G, E484Q, or A475V mutations. 2021 Frontiers in immunology Introduction SARS_CoV_2 A475V;D614G;E484Q 159;142;149 164;147;154 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The type A was ancestral of the group based on the bat outgroup coronavirus, recognized by mutation T29095C. 2021 Iranian journal of microbiology Introduction SARS_CoV_2 T29095C 100 107 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Type B was derived from type A by two mutations: T8782C and C28144T, while type C was different from its parents type B, noticed by mutation G26144T, major found in Europeans. 2021 Iranian journal of microbiology Introduction SARS_CoV_2 C28144T;G26144T;T8782C 60;141;49 67;148;55 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. During the spring of 2020, a non-synonymous mutation leading to a spike protein substitution D614G became dominant in the reported sequences of SARS-CoV-2 and was found to enhance viral replication as a result of higher affinity for the ACE2 receptor. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 93 98 S 66 71 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. A SARS-CoV-2 variant in the spike protein, D614G (B.1 lineage), emerged early in the epidemic and has rapidly became dominant in virtually all areas of the world where it has circulated. 2021 Pathogens & immunity Introduction SARS_CoV_2 D614G 43 48 S 28 33 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. Here we examined a variant of SARS-CoV-2 that emerged within the subset of sequences harboring the D614G variant and contains 3 adjacent nucleotide changes spanning 2 residues of the nucleocapsid protein (R203K/G204R; B.1.1 lineage), which has resulted in a novel sub-genomic RNA transcript. 2021 Pathogens & immunity Introduction SARS_CoV_2 D614G;R203K;G204R 99;205;211 104;210;216 N 183 195 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. Overall, these antibodies recognize four distinct epitopes on the RBD, and cocktails containing mAbs targeting different antigenic sites showed higher potency to neutralize the SARS-CoV-2 virus and SARS-CoV-2(V367F) pseudovirus particle. 2021 MedComm Introduction SARS_CoV_2 V367F 209 214 RBD 66 69 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. These antibodies exhibited a higher binding affinity to the RBD and high potency to neutralize both live and pseudotype SARS-CoV-2 viruses and SARS-CoV-2(V367F) pseudovirus. 2021 MedComm Introduction SARS_CoV_2 V367F 154 159 RBD 60 63 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. These include 9 single site mutations K417N, N439K, Y453F, S477N, S477I, T478I, E484K, S494P and N501Y (Alpha variant), a double mutant (E484K/N501Y) and two triple mutants (K417N/E484K/N501Y (Beta variant) and K417T/E484K/N501Y (Gamma variant)). 2021 The Journal of biological chemistry Introduction SARS_CoV_2 E484K;K417N;K417T;N439K;N501Y;S477I;S477N;S494P;T478I;Y453F;E484K;K417N;E484K;E484K;N501Y;N501Y;N501Y 80;38;211;45;97;66;59;87;73;52;137;174;180;217;143;186;223 85;43;216;50;102;71;64;92;78;57;142;179;185;222;148;191;228 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. Interestingly, two other VOCs, P1 and B.1.351, also contain the N501Y mutation. 2021 Communications biology Introduction SARS_CoV_2 N501Y 64 69 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. Moreover, with low dose inocula, the Alpha variant initiates more robust infectious in the upper respiratory tracts of hamsters and transmits more efficiently than earlier D614G variants. 2021 Communications biology Introduction SARS_CoV_2 D614G 172 177 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. The aim of this study is to provide experimental evidence to explain why the Alpha variant has increased transmissibility among the human population, compared to earlier D614G variants. 2021 Communications biology Introduction SARS_CoV_2 D614G 170 175 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. These spike mutations include the deletion H69/ V70, which has arisen in multiple independent lineages and is suggested to associate with increased infectivity and evasion of the immune response; the substitution N501Y, which enhances binding affinity for the human ACE2 receptor and might affect viral transmissibility; and the mutation P681H, which is adjacent to the S1/S2 furin cleavage site in spike and might have an impact on viral infectivity. 2021 Communications biology Introduction SARS_CoV_2 N501Y;P681H 214;339 219;344 S;S 6;400 11;405 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. E484K is known as an escape mutant in which antibodies targeting the original RBD protein sequence may fail to recognize this particular mutation, leading to consequences regarding the effectiveness of neutralizing antibodies as therapies or the efficacy of existing vaccines targeting the original sequence. 2022 Journal of pharmaceutical analysis Introduction SARS_CoV_2 E484K 0 5 RBD 78 81 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. For example, mutation N501Y, which occurs in a position within the RBD, was identified as a key contributor to increased binding affinity with ACE2 associated with increased transmission of the virus. 2022 Journal of pharmaceutical analysis Introduction SARS_CoV_2 N501Y 22 27 RBD 67 70 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. However, mutation D614G, which occurs outside the RBD, may cause a moderate increase in transmissibility. 2022 Journal of pharmaceutical analysis Introduction SARS_CoV_2 D614G 18 23 RBD 50 53 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. Some mutations (N501Y and E484K) have been found in multiple variants, such as the Beta (B.1.351) and Gamma (P.1/B.1.1.28) variants. 2022 Journal of pharmaceutical analysis Introduction SARS_CoV_2 E484K;N501Y 26;16 31;21 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. The previously identified high frequency variants, such as mutation N439K and Y453F (mink mutation), were also of significant concern as the antibodies raised after exposure to the original strain spike protein may not neutralize the virus containing these spike variants. 2022 Journal of pharmaceutical analysis Introduction SARS_CoV_2 N439K;Y453F 68;78 73;83 S;S 197;257 202;262 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. This variant is defined as lineage B.1.1.7 and has multiple spike protein amino acid deletions and mutations, such as deletion 69-70, deletion 144, and mutations N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H. 2022 Journal of pharmaceutical analysis Introduction SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 169;208;176;162;183;197;190 174;214;181;167;188;202;195 S 60 65 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. To understand the impact of RBD mutations on ACE2 and anti-spike mAb binding activities, the binding kinetics (association (kon), dissociation (koff) rates, and the equilibrium dissociation constant (KD)) of the SARS-CoV-2 RBD (original isolated RBD sequence) protein and the selected RBD mutants (D614G, N501Y, N439K, Y453F, E484K) against ACE2 and two different antibodies, anti-spike S1 antibody (mAb1) and anti-spike neutralizing antibody (mAb2), were investigated. 2022 Journal of pharmaceutical analysis Introduction SARS_CoV_2 E484K;N439K;N501Y;Y453F;D614G 326;312;305;319;298 331;317;310;324;303 S;S;S;RBD;RBD;RBD;RBD 59;381;415;28;223;246;285 64;386;420;31;226;249;288 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. A list of vaccine-escape (vaccine-breakthrough) mutations was tabulated in our early work, including S494P, Q493L, K417N, F490S, F486L, R403K, E484K, L452R, K417T, F490L, E484Q, and A475S. 2021 ArXiv Introduction SARS_CoV_2 A475S;E484K;E484Q;F486L;F490L;F490S;K417N;K417T;L452R;Q493L;R403K;S494P 182;143;171;129;164;122;115;157;150;108;136;101 187;148;176;134;169;127;120;162;155;113;141;106 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. Additionally, although their frequencies are relatively low at present, co-mutation sets [L452R, T478K, E484K, N501Y] and [P384L, K417N, E484K, N501Y] have very high BFE changes (i.e., 2.22 and 1.07 kcal/mol, respectively) and very high antibody disruption counts (i.e., 75 and 101, respectively). 2021 ArXiv Introduction SARS_CoV_2 E484K;E484K;K417N;N501Y;N501Y;T478K;L452R;P384L 104;137;130;111;144;97;90;123 109;142;135;116;149;102;95;128 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. Additionally, our prediction indicates that T478K increases the RBD-ACE2 BFE by 1.00 kcal/mol. 2021 ArXiv Introduction SARS_CoV_2 T478K 44 49 RBD 64 67 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. Based on this observation, we anticipate that co-mutation sets [A411S, L452R, T478K], [L452R, T478K, N501Y] and [K417N, L452R, T478K] are on the path to becoming emerging SARS-CoV-2 variants. 2021 ArXiv Introduction SARS_CoV_2 L452R;L452R;N501Y;T478K;T478K;T478K;A411S;K417N;L452R 71;120;101;78;94;127;64;113;87 76;125;106;83;99;132;69;118;92 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. However, Eli Lilly mAbs were allowed to return to the market in September because they are quite effective on the Delta variant [452R, T478K]. 2021 ArXiv Introduction SARS_CoV_2 T478K 135 140 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. In the next few months, the Delta variant, involving RBD mutation L452R and T478K, had rapidly fueled a new wave of COVID-19 infections around the world. 2021 ArXiv Introduction SARS_CoV_2 L452R;T478K 66;76 71;81 RBD 53 56 COVID-19 116 124 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. Indeed, Eli Lilly mAbs were taken off the market in March due to Beta [K417N, E484K, N501Y] and Gamma [K417T, E484K, N501Y] variants. 2021 ArXiv Introduction SARS_CoV_2 E484K;E484K;N501Y;N501Y;K417N;K417T 78;110;85;117;71;103 83;115;90;122;76;108 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. Many of these co-mutation sets involve vaccine-escape mutations predicted in our early work: S494P, Q493L, K417N, F490S, F486L, R403K, E484K, L452R, K417T, F490L, E484Q, and A475S. 2021 ArXiv Introduction SARS_CoV_2 A475S;E484K;E484Q;F486L;F490L;F490S;K417N;K417T;L452R;Q493L;R403K;S494P 174;135;163;121;156;114;107;149;142;100;128;93 179;140;168;126;161;119;112;154;147;105;133;98 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. Many potential factors, such as the insertion of multi-basic residues at the S1/S2 subunit cleavage site, the high-frequency mutation D614G, temperature and pH conditions, and numerous other hypotheses, have been extensively studied in the literature since the outbreak of the pandemic. 2021 ArXiv Introduction SARS_CoV_2 D614G 134 139 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. The combined effect of L452R and T478K makes the Delta variant the most infectious variant among all variants formally named by the World Health Organization (WHO). 2021 ArXiv Introduction SARS_CoV_2 L452R;T478K 23;33 28;38 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. Their RBD (co-)mutations are [N501Y], [K417N, E484K, N501Y], and [K417T, E484K, N501Y], respectively. 2021 ArXiv Introduction SARS_CoV_2 E484K;E484K;N501Y;N501Y;K417N;K417T;N501Y 46;73;53;80;39;66;30 51;78;58;85;44;71;35 RBD 6 9 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. We noted that L452R, V483F/A, E484K/Q, F486L, F490L/S, Q493K/R, and S494P could disrupt Eli Lilly mAbs. 2021 ArXiv Introduction SARS_CoV_2 E484K;E484Q;F486L;F490L;F490S;L452R;Q493K;Q493R;S494P;V483A;V483F 30;30;39;46;46;14;55;55;68;21;21 37;37;44;53;53;19;62;62;73;28;28 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. We postulated that an alternative transmission pathway had led to the occurrence of co-mutation set [Y449S, N501Y]. 2021 ArXiv Introduction SARS_CoV_2 N501Y;Y449S 108;101 113;106 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. Worth noting that the co-mutation set [Y449S, N501Y] has a negative BFE change of -0.26 kcal/mol, highlighting its infectivity weakening characteristic. 2021 ArXiv Introduction SARS_CoV_2 N501Y;Y449S 46;39 51;44 34545803 Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA. E484K variants have also been identified in reinfection cases, suggesting a role in breakthrough infections; these findings indicate the need to monitor for SARS-CoV-2 variants in real time. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 0 5 34545803 Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA. Genomic sequencing of SARS-CoV-2 E484K variant B.1.243.1, Arizona, USA. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 33 38 34545803 Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA. In contrast, the 2 additional B.1.243 cases bearing the E484K mutation alone were phylogenetically distinct from the B.1.243.1 clade, suggesting that those isolates had evolved independently. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 56 61 34545803 Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA. Several of these VOCs and VOIs (e.g., Beta/B.1.351, Gamma/P.1, Delta/B.1.617.2) harbor the E484K mutation in the spike glycoprotein gene. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 91 96 S 113 131 34545803 Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA. Studies have demonstrated that the E484K mutation reduces antibody neutralization. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 35 40 34545803 Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA. Targeted sampling efforts, such as prescreening samples for the E484K mutation by PCR-based assays, would complement random sampling for genomic sequencing surveillance. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 64 69 34545803 Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA. The B.1.243 parent lineage encodes the spike gene D614G substitution but none of the other concerning mutations (Appendix Table 3, Figure 1). 2021 Emerging infectious diseases Introduction SARS_CoV_2 D614G 50 55 S 39 44 34545803 Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA. The novel variant had 11 lineage-defining mutations, including V213G and E484K in the spike gene, a 9-nt deletion in open reading frame (ORF) 1ab (DeltaSGF3675-77), a 3-nt insertion in the noncoding intergenic region upstream of the N gene, and other synonymous substitutions (Appendix Table 2, Figure 1). 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K;V213G 73;63 78;68 S;N 86;233 91;234 34545803 Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA. This new E484K-harboring variant has been officially designated as B.1.243.1 using the pangolin nomenclature system. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 9 14 34545803 Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA. We also identified 2 instances in which the parent B.1.243 lineage independently acquired the E484K mutation. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 94 99 34545803 Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA. We detected 8 genomes associated with a common B.1.243 variant that had acquired an E484K mutation in the spike protein. 2021 Emerging infectious diseases Introduction SARS_CoV_2 E484K 84 89 S 106 111 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. Delta and Kappa have a P681R mutation at furin cleavage sites (681PRRAR/S686). 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 P681R 23 28 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. In particular, three mutations (K417T, E484K, and N501Y) in RBD (Receptor Binding Domain) are common in Alpha (N501Y) and Beta (K417 N, E484K, and N501Y) which are associated with increased transmissibility, immune escape and pathogenicity. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 E484K;E484K;N501Y;N501Y;K417N;K417T;N501Y 39;136;50;147;128;32;111 44;141;55;152;134;37;116 RBD;RBD 65;60 88;63 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. One of Delta-associated variants, B.1.427 and B.1.429 also known as Epsilon have L452R mutation, causing reduction in antibody neutralization. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 L452R 81 86 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. Recent studies showed that P681R enhances spike cleavage and fusion for viral entry, suggesting augmented transmissibility and pathogenicity. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 P681R 27 32 S 42 47 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. T478K was a previously predominant variant in Mexico and located at the interface of RBD and ACE2 (Angiotensin-Converting Enzyme 2) interaction, thereby potentially impacting viral infection. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 T478K 0 5 RBD 85 88 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. The Delta has L452R, T478K and P681R in the spike protein (Table 1 ) which may contribute to increased infectivity, pathogenicity and immune evasion, resulting in re-infection or resistance to vaccine-elicited antibody and therapeutic antibodies. 2021 Biochemical and biophysical research communications Introduction SARS_CoV_2 L452R;P681R;T478K 14;31;21 19;36;26 S 44 49 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. Additionally, mutations, such as Y269T and Y268G, in SARS-CoV-2 PLPro strongly reduced the inhibitory effect of the putative antiviral agent, GRL0617 . 2022 Saudi journal of biological sciences Introduction SARS_CoV_2 Y268G;Y269T 43;33 48;38 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. Furthermore, Q233E PLPro favors a more robust deISGylase activity. 2022 Saudi journal of biological sciences Introduction SARS_CoV_2 Q233E 13 18 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. In SARS-CoV-2 PLPro, non-synonymous mutations (A889V and V843F) were recently found to alter the protein's flexibility and reduce the affinity for ISG-15 . 2022 Saudi journal of biological sciences Introduction SARS_CoV_2 V843F;A889V 57;47 62;52 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. Previously, R167E mutation in SARS CoV-1 PLPro significantly increases deubiquitinase activity and was nearly 20 times less efficient in hydrolyzing ISG15. 2022 Saudi journal of biological sciences Introduction SARS_CoV_2 R167E 12 17 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. Some of these mutations have relatively high incidences, such as a non-synonymous mutation (D614G) in the virus's S protein. 2022 Saudi journal of biological sciences Introduction SARS_CoV_2 D614G 92 97 S 114 115 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. A deep mutational scanning study revealed that the E484K mutant only leads to slightly increased ACE2 binding affinity of the mutated RBD. 2022 Briefings in bioinformatics Introduction SARS_CoV_2 E484K 51 56 RBD 134 137 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Additionally, a recent experimental study suggested that the E484K mutation impairs the efficacy of current mAbs targeting the angiotensin-converting enzyme 2 (ACE2) binding site, such as REGN10933. 2022 Briefings in bioinformatics Introduction SARS_CoV_2 E484K 61 66 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Considering that the RBD is a dominant target of neutralizing antibodies and its E484K mutation has led to unsettling immune evasion, it is of great importance to understand the underlying mechanism for better coping with the E484K mutation. 2022 Briefings in bioinformatics Introduction SARS_CoV_2 E484K;E484K 81;226 86;231 RBD 21 24 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Hence, the strong immune evasion of the E484K mutant is unlikely caused by its ACE2 binding affinity but by its mAb interaction. 2022 Briefings in bioinformatics Introduction SARS_CoV_2 E484K 40 45 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. In this paper, we calculated the binding affinities of current 26 mAbs to RBDWT and to RBDE484K, respectively, alarming that 22 mAbs have decreased binding affinity to the E484K mutant. 2022 Briefings in bioinformatics Introduction SARS_CoV_2 E484K 172 177 RBD 87 90 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Recently emerged SARS-CoV-2 variants B.1.1.33, P1 and P2 are also identified as the E484K mutant in the Brazilian territory, which are of serious concern due to the possibility of escaping from neutralizing antibodies. 2022 Briefings in bioinformatics Introduction SARS_CoV_2 E484K 84 89 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Recently, experiments in vitro have shown that E484K mutation occurs when SARS-CoV-2 was co-incubated in a highly neutralizing COVID-19 convalescent plasma. 2022 Briefings in bioinformatics Introduction SARS_CoV_2 E484K 47 52 COVID-19 127 135 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Several studies have shown that neutralization by some mAbs and immune sera was diminished against the SARS-CoV-2 variants, particularly for the B.1.351 harboring E484K. 2022 Briefings in bioinformatics Introduction SARS_CoV_2 E484K 163 168 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. The single mutation (E484K) residing in RBD makes the SARS-CoV-2 variant strongly resist to plasma neutralization, indicating that the survivors may be reinfected by the variants carrying with E484K mutation. 2022 Briefings in bioinformatics Introduction SARS_CoV_2 E484K;E484K 193;21 198;26 RBD 40 43 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Therefore, the E484K mutation has received particular attention among the SARS-CoV-2 variants due to its worrisome implications in vaccination and passive immune therapies. 2022 Briefings in bioinformatics Introduction SARS_CoV_2 E484K 15 20 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. The D614G mutation in the spike glycoprotein of SARS-CoV-2 was first detected at a significant level in early March 2020 and spread to global dominance over the following few months. 2021 PeerJ Introduction SARS_CoV_2 D614G 4 9 S 26 44 34560289 SARS-CoV-2 B.1.1.7 lineage rapidly spreads and replaces R.1 lineage in Japan: Serial and stationary observation in a community. We previously reported on the SARS-CoV-2 R.1 lineage harboring spike W152L, E484K and G769V mutations. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K;G769V;W152L 76;86;69 81;91;74 S 63 68 34561887 Proteolytic activation of SARS-CoV-2 spike protein. All of these VOCs have the D614G mutation (Figure 5). 2022 Microbiology and immunology Introduction SARS_CoV_2 D614G 27 32 34561887 Proteolytic activation of SARS-CoV-2 spike protein. As mentioned earlier, SARS-CoV-2 with the D614G mutation, which emerged early in the epidemic and has become a major cause of the global pandemic, has gained increased infectivity because of the D614G mutation. 2022 Microbiology and immunology Introduction SARS_CoV_2 D614G;D614G 42;195 47;200 34561887 Proteolytic activation of SARS-CoV-2 spike protein. Besides, the 614th amino acid is located in the vicinity of the S1/S2 cleavage site (Figure 7), and the D614G mutation increases S1/S2 cleavability by furin (Figure 5). 2022 Microbiology and immunology Introduction SARS_CoV_2 D614G 104 109 34561887 Proteolytic activation of SARS-CoV-2 spike protein. However, in that study, the P681R mutation alone was not sufficient to increase the infectivity of the original Wuhan SARS-CoV-2 strain. 2022 Microbiology and immunology Introduction SARS_CoV_2 P681R 28 33 34561887 Proteolytic activation of SARS-CoV-2 spike protein. However, there are conflicting observations that E484K and K417N/T are mutations acquired to escape from neutralizing antibodies and rather reduce binding to ACE2. 2022 Microbiology and immunology Introduction SARS_CoV_2 E484K;K417N;K417T 49;59;59 54;66;66 34561887 Proteolytic activation of SARS-CoV-2 spike protein. In fact, the D614G mutation is of great significance when the S protein contains an FCM. 2022 Microbiology and immunology Introduction SARS_CoV_2 D614G 13 18 S 62 63 34561887 Proteolytic activation of SARS-CoV-2 spike protein. Instead, it has L452R and T478K mutations. 2022 Microbiology and immunology Introduction SARS_CoV_2 L452R;T478K 16;26 21;31 34561887 Proteolytic activation of SARS-CoV-2 spike protein. It does not have mutations found in the aforesaid three VOCs, such as N501Y, E484K, and K417N/T. 2022 Microbiology and immunology Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 77;88;88;70 82;95;95;75 34561887 Proteolytic activation of SARS-CoV-2 spike protein. Nevertheless, given the effect of the D614G mutation and the characteristics of the delta variant, it is likely that cleavability by furin is deeply involved in the infectivity and transmissibility of SARS-CoV-2. 2022 Microbiology and immunology Introduction SARS_CoV_2 D614G 38 43 34561887 Proteolytic activation of SARS-CoV-2 spike protein. SARS-CoV-2 with the D614G mutation, which emerged early in the epidemic, has better infectivity and proliferative potential and has subsequently become the predominant strain in the pandemic worldwide. 2022 Microbiology and immunology Introduction SARS_CoV_2 D614G 20 25 34561887 Proteolytic activation of SARS-CoV-2 spike protein. Similar to the alpha variant, the S protein of the delta variant has the P681R mutation in addition to L452R and T478K (Figure 5). 2022 Microbiology and immunology Introduction SARS_CoV_2 L452R;P681R;T478K 103;73;113 108;78;118 S 34 35 34561887 Proteolytic activation of SARS-CoV-2 spike protein. The alpha variant also has an amino acid mutation, P681H, in the S1/S2 site (681-HRRAR S-686; the mutated amino acid is underlined; Figure 2). 2022 Microbiology and immunology Introduction SARS_CoV_2 P681H 51 56 S 87 88 34561887 Proteolytic activation of SARS-CoV-2 spike protein. The alpha-variant emerged in the United Kingdom in November 2020 and has an N501Y mutation that directly affects the interaction with ACE2, making it more contagious than previous strains (Figure 5). 2022 Microbiology and immunology Introduction SARS_CoV_2 N501Y 76 81 34561887 Proteolytic activation of SARS-CoV-2 spike protein. The beta and gamma variants emerged in South Africa and Brazil, respectively, and in addition to N501Y, they have mutations, K417N/T and E484K, which may directly affect the interaction with ACE2, resulting in enhanced ACE2 binding (Figure 5). 2022 Microbiology and immunology Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 137;125;125;97 142;132;132;102 34561887 Proteolytic activation of SARS-CoV-2 spike protein. The P681R mutation promotes furin-mediated S1/S2 cleavage and confers the strong membrane fusion activity characteristic of the delta variant, which has been shown to have increased virulence (Figure 5). 2022 Microbiology and immunology Introduction SARS_CoV_2 P681R 4 9 Membrane 81 89 34561887 Proteolytic activation of SARS-CoV-2 spike protein. The S protein with the D614G mutation, which therefore affects the interprotomer interactions between the S1 and S2 subunits, tends to adopt the up/open conformation (Figure 5). 2022 Microbiology and immunology Introduction SARS_CoV_2 D614G 23 28 S 4 5 34561887 Proteolytic activation of SARS-CoV-2 spike protein. The same mutation (P681R) has been found in another variant that is not a VOC, and a study with this variant has also demonstrated that the P681R mutation increases the cleavability of the S protein. 2022 Microbiology and immunology Introduction SARS_CoV_2 P681R;P681R 140;19 145;24 S 189 190 34561887 Proteolytic activation of SARS-CoV-2 spike protein. Thus, S protein that contains the D614G mutation may be more likely to adopt the up/open conformation (Figure 5). 2022 Microbiology and immunology Introduction SARS_CoV_2 D614G 34 39 S 6 7 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Experimental and simulation studies have revealed that the N501Y mutation improves the binding affinity of RBD to the receptor hACE2, which is believed to account for the more transmissibility of the 501Y.V1 variant than the original strain. 2021 Journal of molecular graphics & modelling Introduction SARS_CoV_2 N501Y 59 64 RBD 107 110 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Fortunately, the sera neutralization assay showed that the N501Y mutation has little effect on the neutralization of the human sera elicited by the BNT162b2 mRNA vaccine. 2021 Journal of molecular graphics & modelling Introduction SARS_CoV_2 N501Y 59 64 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In addition, for most of the studied neutralizing antibodies and nanobodies, the E484K mutation leads to reduced binding affinities between RBD and these antibodies/nanobodies mainly due to the mutation-caused disadvantage electrostatic interactions, which weakens the effectiveness of these antibodies and even evades the immune protect. 2021 Journal of molecular graphics & modelling Introduction SARS_CoV_2 E484K 81 86 RBD 140 143 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In the 501Y.V2 and 501Y.V3 variants, besides the N501Y mutation, two other mutations E484K and K417N (or K417T) occurred in RBD of the S protein, and it was revealed that the E484K mutation obviously enhances the binding affinity between RBD and hACE2. 2021 Journal of molecular graphics & modelling Introduction SARS_CoV_2 E484K;E484K;K417N;K417T;N501Y 85;175;95;105;49 90;180;100;110;54 RBD;RBD;S 124;238;135 127;241;136 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In the present work, all-atom molecular dynamics (MD) simulation combined with the molecular mechanics-generalized Born surface area (MMGBSA) method was employed to investigate the impacts of E484K mutation on the binding affinities of RBD with the receptor hACE2 as well as with the neutralizing antibodies and nanobodies. 2021 Journal of molecular graphics & modelling Introduction SARS_CoV_2 E484K 192 197 RBD 236 239 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. More importantly, growing evidences indicated that the E484K mutation shared by both the 501Y.V2 and 501Y.V3 variants, distinctly reduces the neutralization activity and even may escape from the neutralizing antibodies in the convalescent plasma of COVID-19 patients, which may weaken the effectiveness of the vaccines and the efficacy of the neutralizing antibody therapeutics in developments. 2021 Journal of molecular graphics & modelling Introduction SARS_CoV_2 E484K 55 60 COVID-19 249 257 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Our calculation results showed that the E484K mutation may improve the binding affinity of RBD to the receptor hACE2 owing to more favorable electrostatic forces and tighter binding interface caused by the mutation, which implies more transmissibility of the E484K-containing variants. 2021 Journal of molecular graphics & modelling Introduction SARS_CoV_2 E484K;E484K 40;259 45;264 RBD 91 94 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The 501Y.V1 strain carries the N501Y mutation in the RBM of the S protein. 2021 Journal of molecular graphics & modelling Introduction SARS_CoV_2 N501Y 31 36 S 64 65 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Understanding the molecular mechanism behind the effects of the E484K mutation on the RBD-hACE2 interactions as well as on the effectiveness of the neutralizing antibodies and nanobodies targeted at the wild-type RBD is of great significance for the development of the therapeutic antibodies and vaccine design. 2021 Journal of molecular graphics & modelling Introduction SARS_CoV_2 E484K 64 69 RBD;RBD 86;213 89;216 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Compared with the wild-type S (hereafter S-D614), the increased propensity of S-D614G in the RBD-up conformation implicated the facilitation of the binding to the receptor ACE2. 2021 The Journal of biological chemistry Introduction SARS_CoV_2 D614G 80 85 RBD;S;S;S 93;28;41;78 96;29;42;79 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Here, we demonstrated the structural dynamics of the D614G variant spike protein (hereafter S-D614G) by using cryo-EM with the aid of three-dimensional variability analysis (3DVA). 2021 The Journal of biological chemistry Introduction SARS_CoV_2 D614G;D614G 53;94 58;99 S;S 67;92 72;93 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Our study shows that the S protein with the D614G mutation is more thermally stable than S-D614, suggesting that S-D614G will be a new candidate for vaccine development. 2021 The Journal of biological chemistry Introduction SARS_CoV_2 D614G;D614G 44;115 49;120 S;S;S 25;89;113 26;90;114 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. The enhanced infectivity of the D614G variant is observed in cell cultures as well as animal models . 2021 The Journal of biological chemistry Introduction SARS_CoV_2 D614G 32 37 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. The last mutation corresponds to a missense D614G mutation in the spike (S) protein. 2021 The Journal of biological chemistry Introduction SARS_CoV_2 D614G 44 49 S;S 66;73 71;74 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. We further conducted the negative staining electronic microscopy (NSEM) analysis coupled with differential scanning calorimetry (DSC) and differential scanning fluorimetry (DSF) to reveal that the D614G mutation eliminates the cold sensitivity of the original D614 and confers the resistance to the high temperature. 2021 The Journal of biological chemistry Introduction SARS_CoV_2 D614G 197 202 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. For instance, according to a recent report, the N439K variant showed resistance against several neutralizing antibodies, including one authorized by the U.S. 2021 Biomolecules Introduction SARS_CoV_2 N439K 48 53 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. However, there have been several mutations reported in SARS-CoV-2 RBD, such as N501Y, L452R, S477N, E484K, A502S, N439K, S494P, T478K, K417N, and K417T. 2021 Biomolecules Introduction SARS_CoV_2 A502S;E484K;K417N;K417T;L452R;N439K;N501Y;S477N;S494P;T478K 107;100;135;146;86;114;79;93;121;128 112;105;140;151;91;119;84;98;126;133 RBD 66 69 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. One of the dominant variants during COVID-19 pandemic has been the D614G mutation (not in the RBD region) of S glycoprotein; several reports have claimed that this mutation is able to increase the infectivity and stability of SARS-CoV-2. 2021 Biomolecules Introduction SARS_CoV_2 D614G 67 72 S;RBD 109;94 123;97 COVID-19 36 44 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Therefore, in this study, mutant RBDs of SARS-CoV-2 were selected from the RBD mutation tracker website (CovMT); the following variants were selected: N501Y, L452R, S477N, N439K, and E484K. 2021 Biomolecules Introduction SARS_CoV_2 E484K;L452R;N439K;N501Y;S477N 183;158;172;151;165 188;163;177;156;170 RBD;RBD 33;75 37;78 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. For example, E166A mutant lacks the interaction between E166 and S1 at the homodimer interface, but shows enzymatic activity. 2021 International journal of molecular sciences Introduction SARS_CoV_2 E166A 13 18 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. In Delta, in close proximity to E484, a threonine is replaced by a positively charged lysine leading to T478K. 2021 Viruses Introduction SARS_CoV_2 T478K 104 109 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. In Kappa, but not Delta, E484 is substituted with a Glutamine (Q) and might confer immune escape similar to E484K. 2021 Viruses Introduction SARS_CoV_2 E484K 108 113 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. It has been shown that SARS-CoV-2 variants carrying E484K have limited susceptibility to convalescent and vaccine-elicited sera as well as monoclonal antibodies in vitro. 2021 Viruses Introduction SARS_CoV_2 E484K 52 57 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Little is known so far about the clinical relevance of the newly emerging T478K substitution. 2021 Viruses Introduction SARS_CoV_2 T478K 74 79 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Moreover, E484K located within the S-ACE2 interface contributes to increased affinity to ACE2 resulting in enhanced virulence of variant Beta and Gamma. 2021 Viruses Introduction SARS_CoV_2 E484K 10 15 S 35 36 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Whether T478K or E484Q, respectively, contribute to immune evasion similar to the E484K mutation is of great therapeutic importance as well as for evaluating the efficacy of currently approved vaccines. 2021 Viruses Introduction SARS_CoV_2 E484K;E484Q;T478K 82;17;8 87;22;13 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. While Alpha, Beta, and Gamma all harbor the N501Y substitution in S, Delta and many variants of interest (VOI) such as Epsilon or Zeta gained other mutations e.g., the L452R. 2021 Viruses Introduction SARS_CoV_2 L452R;N501Y 168;44 173;49 S 66 67 34578354 SARS-CoV-2 Delta Variant Pathogenesis and Host Response in Syrian Hamsters. The characteristic mutations reported in the spike gene of the B.1.617 lineage are D111D, L452R, D614G, P618R, and +-E484Q. 2021 Viruses Introduction SARS_CoV_2 D111D;D614G;L452R;P618R;E484Q 83;97;90;104;117 88;102;95;109;122 S 45 50 34578363 Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India. Since then, the virus has been continuously evolving, and the first major mutation was seen in its spike protein (D614G), which led to increased infectivity. 2021 Viruses Introduction SARS_CoV_2 D614G 114 119 S 99 104 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. One additional B.1.1.28 descendant clade that emerged in southern Brazil carrying mutation N:P13L was recently defined as a new Pango P.7 lineage. 2021 Viruses Introduction SARS_CoV_2 P13L 93 97 N 91 92 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Our study revealed that a novel B.1.1.28 clade harboring two nonsynonymous changes in the Spike protein: Q675H and Q677H, now designated as lineage P.6, was the most prevalent SARS-CoV-2 variant by the end of 2020 and beginning of 2021. 2021 Viruses Introduction SARS_CoV_2 Q675H;Q677H 105;115 110;120 S 90 95 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. The lineage P.3 (former VOI Theta) emerged in the Philippines, and it includes substitutions S:E484K/N501Y/P681H among the lineage-defining mutations; the first sample was collected on 8 January 2021, and later it further spread to the USA, Germany, and Malaysia, among other countries. 2021 Viruses Introduction SARS_CoV_2 N501Y;P681H;E484K 101;107;95 106;112;100 S 93 94 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. The lineages P.2, P.4, and P.5, carrying the concerning amino acid changes S:E484K, S:L452R, and S:E484Q/N501T, respectively, were also initially detected in samples from Brazil. 2021 Viruses Introduction SARS_CoV_2 N501T;E484K;E484Q;L452R 105;77;99;86 110;82;104;91 S;S;S 75;84;97 76;85;98 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. The Q675H and Q677H mutations are in the proximity of the polybasic cleavage site at the S1/S2 boundary, a region of biological relevance for virus replication, and also arose independently in many other SARS-CoV-2 VOIs circulating worldwide. 2021 Viruses Introduction SARS_CoV_2 Q675H;Q677H 4;14 9;19 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. The VOC P.1, which harbors the mutations of concern S:K417T/E484K/N501Y among its lineage defining mutations, originated in the Amazonas state in mid-November and rapidly spread across Brazil and to over 50 countries globally. 2021 Viruses Introduction SARS_CoV_2 E484K;N501Y;K417T 60;66;54 65;71;59 S 52 53 34591922 Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example. Apparently this mutation converted SARS-CoV-2 into a more transmissible form, and the D614G mutated virus now dominates in the global COVID-19 pandemic. 2021 PloS one Introduction SARS_CoV_2 D614G 86 91 COVID-19 134 142 34591922 Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example. Finally, the site of the N501Y substitution is identified as a different kind of hot-spot, and analyzed as an additional example of a bifurcation. 2021 PloS one Introduction SARS_CoV_2 N501Y 25 30 34591922 Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example. For the spike protein, the Protein Data Bank structures 6VXX (closed state) 6VYB (open state) and 6XS6 (D614G mutation) are used. 2021 PloS one Introduction SARS_CoV_2 D614G 104 109 S 8 13 34591922 Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example. It consists of backbone segments that surround a site that is proximal to a flattening point: The D614G substitution occurred at such a hot-spot, thus the details of the methodology are worked out with the site 614 of the spike protein as an example. 2021 PloS one Introduction SARS_CoV_2 D614G 98 103 S 222 227 34594910 Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. In this study, a PDRA method for simple and quick differentiation of D614G mutation in COVID-19 was reported. 2021 China CDC weekly Introduction SARS_CoV_2 D614G 69 74 COVID-19 87 95 34594910 Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. One of the most critical mutations was the D614G of the spike protein gene (S), which is a replacement of aspartic acid (D) with glycine (G). 2021 China CDC weekly Introduction SARS_CoV_2 D614G 43 48 S;S 56;76 61;77 34594910 Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. The D614G mutation brings new challenges to the prevention and control of the epidemic, and there are few reported molecular detection methods for D614G mutation. 2021 China CDC weekly Introduction SARS_CoV_2 D614G;D614G 4;147 9;152 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. During initial B.1.620 circulation in Lithuania the only other E484K-bearing lineages in Lithuania had been B.1.351 (one isolated case in Kaunas county, and 12 cases from a transmission chain centred in Vilnius county) and B.1.1.318 (one isolated case in Alytus county), none of which had been found in Utena county despite a high epidemic sequencing coverage in Lithuania. 2021 Nature communications Introduction SARS_CoV_2 E484K 63 68 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Starting April 2nd 2021, targeted E484K PCR confirmed a growing cluster of cases with this mutation in Anyksciai municipality in Utena county with a total of 43 E484K+ cases out of 81 tested by April 28th. 2021 Nature communications Introduction SARS_CoV_2 E484K;E484K 34;161 39;166 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. The first samples of B.1.620 in Lithuania were redirected to sequencing because they were flagged by occasional targeted PCR testing for SARS-CoV-2 spike protein mutation E484K repeated on PCR-positive samples. 2021 Nature communications Introduction SARS_CoV_2 E484K 171 176 S 148 153 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Up to this point, the Lithuanian genomic surveillance programme had sequenced over 10% of PCR-positive SARS-CoV-2 cases in Lithuania and identified few lineages with E484K circulating in Lithuania. 2021 Nature communications Introduction SARS_CoV_2 E484K 166 171 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Here, we compared the replication and syncytia forming potential of D614G, Alpha, and Beta viruses in human cell lines and primary airway cells. 2021 The EMBO journal Introduction SARS_CoV_2 D614G 68 73 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. One of the earliest identified variants contained the D614G mutation in S protein, which increased infectivity without significantly altering antibody neutralization (Yurkovetskiy et al,). 2021 The EMBO journal Introduction SARS_CoV_2 D614G 54 59 S 72 73 34603303 A Combination Adjuvant for the Induction of Potent Antiviral Immune Responses for a Recombinant SARS-CoV-2 Protein Vaccine. This reduction is especially prominent with the B.1.351 variant, which contains the N501Y mutation shared by the B.1.1.7 and P.1 variants, and two additional mutations (K417N, E484K) in the spike receptor binding domain (RBD). 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K;N501Y;K417N 176;84;169 181;89;174 RBD;S;RBD 196;190;221 219;195;224 34603303 A Combination Adjuvant for the Induction of Potent Antiviral Immune Responses for a Recombinant SARS-CoV-2 Protein Vaccine. We and others have shown that the E484K substitution alone, significantly reduces the neutralization capacity of human convalescent and post-vaccination sera, which may leave people that have low NAb titers against current strains unprotected against newly emerging variants. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K 34 39 34603303 A Combination Adjuvant for the Induction of Potent Antiviral Immune Responses for a Recombinant SARS-CoV-2 Protein Vaccine. We demonstrate that adjuvanting S1 with NE/IVT, markedly improves the magnitude and quality of the antibody responses towards both a homologous SARS-CoV-2 virus and a divergent mouse-adapted variant (MA-CoV2) harboring the N501Y substitution in the S protein found in the B.1.1.7, B.1.351, and P.1 variants. 2021 Frontiers in immunology Introduction SARS_CoV_2 N501Y 223 228 S 249 250 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. 2B04 exhibited an ~50% reduction in neutralization of Q677H relative to WT and of Q677H/D614G relative to D614G. 2021 mBio Introduction SARS_CoV_2 D614G;Q677H;Q677H;D614G 106;54;82;88 111;59;87;93 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Additionally, the Q677H mutation increased the pseudotyping viral infectivity of B.1.1.7 by 2.5-fold (P < 0.001) and of P1 by 26.3% (P < 0.001). 2021 mBio Introduction SARS_CoV_2 Q677H 18 23 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Again, all variants, including those containing Q677H, showed decreased neutralization compared with D614G. 2021 mBio Introduction SARS_CoV_2 D614G;Q677H 101;48 106;53 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Although the non-RBD mutation Q677H alone in SARS-CoV-2 spike led to only modest neutralization resistance, it increased viral infectivity and syncytium formation and, importantly, had an epistatic effect when paired with certain emerging RBD mutations present in VOCs. 2021 mBio Introduction SARS_CoV_2 Q677H 30 35 S;RBD;RBD 56;17;239 61;20;242 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Both the B.1.525 and Bluebird variants harbor a key S1 non-RBD mutation, Q677H, with the B.1.525 variant also possessing the E484K RBD mutation. 2021 mBio Introduction SARS_CoV_2 E484K;Q677H 125;73 130;78 RBD;RBD 59;131 62;134 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Future structural studies are required to determine the exact mechanisms by which Q677H impacts infectivity and spike conformation. 2021 mBio Introduction SARS_CoV_2 Q677H 82 87 S 112 117 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Given that neutralizing antibodies often target the receptor binding domain (RBD), recent studies on neutralizing antibody escape by VOCs, including the rapidly spreading B.1.1.7 (United Kingdom, Alpha), B.1.351 (South Africa, Beta), B.1.429 (United States), and P1 (P1-501Y-V3, Brazil, Gamma) variants, have focused on mutations in the RBD, including E484K, N501Y, and L452R, which have been shown to decrease the efficacy of mRNA vaccines to VOCs. 2021 mBio Introduction SARS_CoV_2 E484K;L452R;N501Y 352;370;359 357;375;364 RBD;RBD;RBD 52;77;337 75;80;340 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Given the impact and epistasis of the non-RBD mutation Q677H on infectivity and neutralization escape, we hypothesized that it may induce conformational changes in the spike protein. 2021 mBio Introduction SARS_CoV_2 Q677H 55 60 S;RBD 168;42 173;45 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Here, we examine the infectivity and neutralization of non-RBD Q677H-bearing variants and define its synergistic effects in the context of key RBD mutations. 2021 mBio Introduction SARS_CoV_2 Q677H 63 68 RBD;RBD 59;143 62;146 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Importantly, the Q677H mutation is also present in some isolates of VOCs, including B.1.1.7, B.1.351, and P1. 2021 mBio Introduction SARS_CoV_2 Q677H 17 22 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. In comparison, emerging B.1.525 (Nigeria) and Bluebird (United States) variants containing Q677H have received less attention, despite maintaining a strong prevalence in some parts of the United States, especially the Midwest and Southeast areas, as well as Nigeria. 2021 mBio Introduction SARS_CoV_2 Q677H 91 96 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. In examining the infectivity of the lentiviral pseudotypes (see Text S1 in the supplemental material), all D614G-containing variants showed enhanced infectivity, whereas E484K exhibited decreased infectivity (29%, P < 0.01) and B.1.525 showed an increase (41%, P < 0.01) compared to D614G. 2021 mBio Introduction SARS_CoV_2 D614G;D614G;E484K 107;283;170 112;288;175 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. In particular, B.1.525 and E484K/Q677H/D614G exhibited 36.5% (P < 0.001) and 46.5% (P < 0.001), respectively, decreased NT50 relative to D614G. 2021 mBio Introduction SARS_CoV_2 D614G;E484K;D614G;Q677H 137;27;39;33 142;32;44;38 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. In this study, we found that the E484K mutation had a greater impact on neutralization by convalescent-phase (~3.8-fold decrease) compared with vaccinee (~2-fold decrease) sera, consistent with recent reports. 2021 mBio Introduction SARS_CoV_2 E484K 33 38 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Interestingly, although the Q677H mutation exhibited no drastic effect on SARS-CoV-2 S cleavage. 2021 mBio Introduction SARS_CoV_2 Q677H 28 33 S 85 86 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Interestingly, no effect of Q677H on infectivity or neutralizing antibody resistance was observed for B.1.351. 2021 mBio Introduction SARS_CoV_2 Q677H 28 33 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Interestingly, we did not find increased infectivity and neutralizing antibody resistance for Q677H in the context of the B.1.351 variant, which could be due to its preexisting strong resistance to neutralization or due to the presence of other compensatory mutations. 2021 mBio Introduction SARS_CoV_2 Q677H 94 99 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. It is possible that the effect of Q677H is masked by the presence of other mutations, including D614G. 2021 mBio Introduction SARS_CoV_2 D614G;Q677H 96;34 101;39 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. likely because the D614G mutation stabilizes the "open" (RBD-exposed) spike conformation. 2021 mBio Introduction SARS_CoV_2 D614G 19 24 S;RBD 70;57 75;60 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Moderna versus Pfizer neutralization of Q677H-containing variants. 2021 mBio Introduction SARS_CoV_2 Q677H 40 45 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Moreover, we found that Q677H increased the infectivity and neutralizing antibody resistance of B.1.1.7 and P1 spike. 2021 mBio Introduction SARS_CoV_2 Q677H 24 29 S 111 116 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Neutralization of SARS-CoV-2 variants of concern harboring Q677H. 2021 mBio Introduction SARS_CoV_2 Q677H 59 64 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Notably, the single D614G mutant showed an increase in 50% neutralization titer (NT50) compared to WT. 2021 mBio Introduction SARS_CoV_2 D614G 20 25 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Of note, E484K, N501Y, and Q677H mutants conferred 38.3% (P < 0.001), 17.8%, and 11.1% decreased NT50, respectively, compared with D614G. 2021 mBio Introduction SARS_CoV_2 D614G;E484K;N501Y;Q677H 131;9;16;27 136;14;21;32 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Q677H enhances infectivity and neutralizing antibody resistance of prevalent VOCs. 2021 mBio Introduction SARS_CoV_2 Q677H 0 5 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Q677H enhances resistance to neutralizing antibodies. 2021 mBio Introduction SARS_CoV_2 Q677H 0 5 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Such mutations can have drastic effects on viral spread, as illustrated by the D614G mutation, which emerged early in the pandemic and is now present in nearly all circulating SARS-CoV-2 strains. 2021 mBio Introduction SARS_CoV_2 D614G 79 84 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. The Bluebird and B.1.525 variants exhibited ~2.2-fold (P < 0.01)- and ~3.6-fold (P < 0.01)-reduced NT50, respectively, compared with D614G for ICU patient samples. 2021 mBio Introduction SARS_CoV_2 D614G 133 138 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. The possible role of Q677H in modulating viral infectivity and SARS-CoV-2 sensitivity to antibody neutralization is currently unknown, a particular concern if it emerges in an existing VOC. 2021 mBio Introduction SARS_CoV_2 Q677H 21 26 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. These conclusions are further strengthened by the neutralization profiles of K484E and H677Q reversion mutants made in the backbone of B.1.525 and Bluebird variants, where a modest effect was observed for Q677H mutants compared to K484E. 2021 mBio Introduction SARS_CoV_2 H677Q;K484E;K484E;Q677H 87;77;231;205 92;82;236;210 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Thus, it is possible that Q677H might alter protease processing or spike conformation, as suggested by the increased syncytium formation and reduced neutralization by 2B04 of the D614G/Q677H spike compared to D614G; however, no dramatic effect of Q677H on furin cleavage was observed. 2021 mBio Introduction SARS_CoV_2 D614G;D614G;Q677H;Q677H;Q677H 179;209;26;247;185 184;214;31;252;190 S;S 67;191 72;196 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. To examine the impact of the Q677H mutation emerging in major VOCs, we examined its possible role in the backgrounds of the B.1.1.7, B.1.351, and P1 variants. 2021 mBio Introduction SARS_CoV_2 Q677H 29 34 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Unsurprisingly, spike proteins bearing the E484K mutation in the epitope of 2B04 were not neutralized by 2B04. 2021 mBio Introduction SARS_CoV_2 E484K 43 48 S 16 21 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. We first determined the neutralizing activity of sera from 9 intensive care unit (ICU) COVID-19 patients and 9 hospitalized non-ICU patients against SARS-CoV-2 USA-WA1/2020 (wild type [WT]), D614G, and a panel of variants harboring the Q677H mutation. 2021 mBio Introduction SARS_CoV_2 D614G;Q677H 191;236 196;241 COVID-19 87 95 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. We found that introduction of the Q677H mutation to the B.1.1.7 and P1 spike proteins further reduced the NT50 of sera from mRNA vaccinees (8 Moderna and 8 Pfizer) by ~21.9% (P < 0.05) and ~29.0% (P < 0.001), respectively. 2021 mBio Introduction SARS_CoV_2 Q677H 34 39 S 71 76 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. Although the increased virulence of strains with the N501Y mutation relative to strains that lack this mutation has been described, only limited information is available on the virulence of infection with the Delta variant, relative to earlier N501Y-positive VOCs (i.e., Alpha, Beta and Gamma). 2021 CMAJ Introduction SARS_CoV_2 N501Y;N501Y 53;244 58;249 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. Novel SARS-CoV-2 variants of concern (VOCs), including viral lineages carrying the N501Y (Alpha/B.1.1.7) or both the N501Y and E484K mutations (Beta/B.1.351 and Gamma/P.1), were first identified in Ontario, Canada, in December 2020. 2021 CMAJ Introduction SARS_CoV_2 E484K;N501Y;N501Y 127;83;117 132;88;122 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. Our objectives were to evaluate the virulence of N501Y-positive variants relative to earlier SARS-CoV-2 lineages and to evaluate the virulence of the Delta variant of SARS-CoV-2 relative to N501Y-positive VOCs using Ontario's COVID-19 case data. 2021 CMAJ Introduction SARS_CoV_2 N501Y;N501Y 49;190 54;195 COVID-19 226 234 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. An additional SC-2 VOC is the B.1.351 variant, which contains both B.1.351-unique mutations and mutations that are present in other notable VOC, such as the SGF deletion in the nsp6 gene and the N501Y substitution in the spike gene that is identified also in B1.1.7. 2021 Microbiology spectrum Introduction SARS_CoV_2 N501Y 195 200 S;Nsp6 221;177 226;181 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. In fact, the most ubiquitous spike protein mutation to date, the D614G, and the A570D mutation in the recently emerged highly contagious UK SARS-CoV-2 strain both appeared among our predicted set of residues, the latter having been discovered after the completion of our calculations. 2021 Proc Natl Acad Sci U S A Introduction SARS_CoV_2 A570D;D614G 80;65 85;70 S 29 34 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. This suggests a strong propensity to form new strains with higher virulence and more complicated epidemiology; the dominant D614G mutation and the recent B.1.1.7 mutant are notable examples. 2021 Proc Natl Acad Sci U S A Introduction SARS_CoV_2 D614G 124 129 34615860 Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil. Both the Gamma (P.1) and Zeta (P.2) sublineages harbour the E484K mutation in the receptor binding domain (RBD) of the spike protein. 2021 Nature communications Introduction SARS_CoV_2 E484K 60 65 RBD;S;RBD 82;119;107 105;124;110 34615860 Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil. E484K has been associated with in vitro immune escape from therapeutic monoclonal antibodies, prompting the withdrawal of the emergency use authorisation for bamlanivumab in the US. 2021 Nature communications Introduction SARS_CoV_2 E484K 0 5 34615860 Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil. The coincident emergence of N501Y, K417T/N and E484K mutations in Gamma (P.1) and Beta (B.1.351) is suggestive of convergent evolution. 2021 Nature communications Introduction SARS_CoV_2 E484K;K417T;K417N;N501Y 47;35;35;28 52;42;42;33 34615860 Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil. The E484K mutation is observed to have arisen independently in other variants such as Beta (B.1.351) and features as an additional mutation in recent samples of established VOCs such as Alpha (B.1.1.7). 2021 Nature communications Introduction SARS_CoV_2 E484K 4 9 34615860 Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil. Whilst P.2 harbours no other lineage-specific spike mutations, Gamma (P.1) has additional RBD mutations, most notably K417T and N501Y. 2021 Nature communications Introduction SARS_CoV_2 K417T;N501Y 118;128 123;133 S;RBD 46;90 51;93 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. A K359R mutation was observed at a position considered important for CendR binding but the charge (positive) remained unchanged. 2021 Frontiers in microbiology Introduction SARS_CoV_2 K359R 2 7 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. A mink-selected SARS-CoV-2 variant with four mutations H69del/V70del, Y453F, I692V, and M1229I, was found in humans in the northern region of Jutland. 2021 Frontiers in microbiology Introduction SARS_CoV_2 I692V;M1229I;Y453F 77;88;70 82;94;75 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. Based on the 3D modeling of the SARS-CoV-2 spike-human ACE2 interactions we visualized the location of amino acids described as major mutation sites in the SARS-CoV-2 variants infecting humans, i.e., the S477N, E484K, and N501Y/T mutations known to characterize the Marseille-4 variant (France), the 20I/501Y.V1 variant (United Kingdom), and the 20H/501Y.V2 variant (South Africa) (Figure 8A, left panel). 2021 Frontiers in microbiology Introduction SARS_CoV_2 E484K;N501T;N501Y;S477N 211;222;222;204 216;229;229;209 S 43 48 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. Open access tools make it possible to quickly visualize the evolution of strains such as the SARS-CoV-2 cluster 5 in minks carrying the Y453F mutation in the spike protein. 2021 Frontiers in microbiology Introduction SARS_CoV_2 Y453F 136 141 S 158 163 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. The D614G mutation was previously reported as a variant having emerged in humans and conferring higher affinity for the ACE2 receptor. 2021 Frontiers in microbiology Introduction SARS_CoV_2 D614G 4 9 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. The D614G mutation which became dominant in human SARS-CoV-2 isolates, was reported to increase viral infectivity. 2021 Frontiers in microbiology Introduction SARS_CoV_2 D614G 4 9 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. The most important changes were found in the 82-94 region with the N90D mutation changing the capacity for sugar modification and the L91P mutation in which a proline in the Mustelidae ACE2 sequence is likely to modify the 3D structure. 2021 Frontiers in microbiology Introduction SARS_CoV_2 L91P;N90D 134;67 138;71 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. These viruses, which expressed a wild type D614 and a mutated Y453F amino acid, could be considered as D clade viruses of human origin having been transferred to minks where they acquired the Y453F mutation and then re-infected humans with a conserved Y453F mutation. 2021 Frontiers in microbiology Introduction SARS_CoV_2 Y453F;Y453F;Y453F 62;192;252 67;197;257 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. They could be considered G clade viruses from human origin likely to have acquired the Y453F mutation under mink selection before being reintroduced into humans. 2021 Frontiers in microbiology Introduction SARS_CoV_2 Y453F 87 92 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. This D614G mutation would facilitate the formation of trimeric S protein complexes permitting thus a stable conformation which in turn led to a higher affinity for the ACE2 receptor. 2021 Frontiers in microbiology Introduction SARS_CoV_2 D614G 5 10 S 63 64 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. Y453F was the only mutation located in an RBD region which could directly change the affinity of the S protein-ACE2 interaction by reducing the clash of polar groups (Figure 8B). 2021 Frontiers in microbiology Introduction SARS_CoV_2 Y453F 0 5 RBD;S 42;101 45;102 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. In February 2020, genetic variants carrying the D614G substitution on the SARS-CoV-2 spike (S) protein began to spread first in Europe and otherwhere globally, reaching fixation in many places rapidly. 2021 BMC infectious diseases Introduction SARS_CoV_2 D614G 48 53 S;S 85;92 90;93 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. Recent modelling analysis reported statistical evidence that SARS-CoV-2 strains with D614G substitution are likely to have an increased infectivity retrospectively. 2021 BMC infectious diseases Introduction SARS_CoV_2 D614G 85 90 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. The D614G is potentially affecting viral transmission. 2021 BMC infectious diseases Introduction SARS_CoV_2 D614G 4 9 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. It is reported that at the population level, there is relatively insufficient herd immunity to drive significant mutation, and there are several spike mutations that increase virus transmission without changes in clinical significance such as D614G. 2021 F1000Research Introduction SARS_CoV_2 D614G 243 248 S 145 150 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). At the beginning of April 2020, a variant with the spike protein (S-protein) D614G mutation replaced the original SARS-CoV-2 strain in many areas of the world, as the mutation appears to improve the binding efficiency between the receptor binding domain (RBD) with the angiotensin-converting enzyme 2 (ACE2) receptor. 2021 Journal of clinical virology Introduction SARS_CoV_2 D614G 77 82 RBD;S;RBD;S 230;51;255;66 253;56;258;67 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). In September 2020, the B.1.1.7 lineage emerged as a variant of concern in the United Kingdom (UK), subsequently termed the alpha variant, with 9 spike protein mutations (del69/70HV, del144Y, N501Y, A570D, D614G, P681H, T761I, S982A, and D1118H). 2021 Journal of clinical virology Introduction SARS_CoV_2 A570D;D1118H;D614G;del144Y;N501Y;P681H;S982A;T761I 198;237;205;182;191;212;226;219 203;243;210;189;196;217;231;224 S 145 150 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). The assay targets the RNA-dependent RNA polymerase (RdRp) gene, the S-protein N501Y and E484K mutations and HV69/70 deletion, as well as an endogenous internal control. 2021 Journal of clinical virology Introduction SARS_CoV_2 E484K;N501Y 88;78 93;83 RdRp;RdRP;S 22;52;68 50;56;69 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). These mutations, specifically N501Y, A570D and D614G, appear to restructure the protein-protein interaction between the spike protein and the ACE2 receptor leading to an overall enhanced efficacy of cellular uptake. 2021 Journal of clinical virology Introduction SARS_CoV_2 A570D;D614G;N501Y 37;47;30 42;52;35 S 120 125 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). Two subsequent variants of concern, B.1.351 (beta variant), first identified in South Africa, and P.1 (gamma variant), first identified in Brazil, were found to harbor the D614G and N501Y mutations, as well as 2 additional key mutations in the receptor binding domain (RBD), K417N/T and E484K, which increase binding affinity to the ACE2 receptor. 2021 Journal of clinical virology Introduction SARS_CoV_2 D614G;E484K;K417N;K417T;N501Y 172;287;275;275;182 177;292;282;282;187 RBD;RBD 244;269 267;272 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). With ten different mutations in the S gene including L452R and D614G this variant showed an increased transmissibility and vaccine effectiveness is also reduced. 2021 Journal of clinical virology Introduction SARS_CoV_2 D614G;L452R 63;53 68;58 S 36 37 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Although further experimental characterization is necessary, this is the first report that links the mutation P108S to the dynamics of the dimeric SARS-CoV-2 main protease. 2021 Biophysics and physicobiology Introduction SARS_CoV_2 P108S 110 115 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. analyzed dynamics of the wild-type (WT) main protease and 50 natural variants, including P108S, in the dimeric form through a single 100-ns MD simulation of each mutant. 2021 Biophysics and physicobiology Introduction SARS_CoV_2 P108S 89 94 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Based on a crystal structure of the SARS-CoV-2 main protease, we performed triplicate 5.0-mus molecular dynamics simulations of the wild-type and mutant P108S protease. 2021 Biophysics and physicobiology Introduction SARS_CoV_2 P108S 153 158 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Based on visual inspection, the authors argued that mutations located in a hinge region that connects rigid and flexible regions, such as the P108S mutation, control regulatory motions of the main protease. 2021 Biophysics and physicobiology Introduction SARS_CoV_2 P108S 142 147 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. However, the impacts of the P108S mutation on dynamics and substrate recognition of the main protease were unclear. 2021 Biophysics and physicobiology Introduction SARS_CoV_2 P108S 28 33 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. In this study, our computational results demonstrated that the systems studied are stabilized only after 4.0 mus of simulation, after which different dynamics between the WT protease and the P108S mutant emerged. 2021 Biophysics and physicobiology Introduction SARS_CoV_2 P108S 191 196 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. In this study, we employed triplicate 5.0-mus MD simulations to investigate effects of the non-synonymous mutation, P108S, on dynamics of the SARS-CoV-2 main protease. 2021 Biophysics and physicobiology Introduction SARS_CoV_2 P108S 116 121 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. The authors further demonstrated in vitro that the P108S mutation reduced the enzymatic activity. 2021 Biophysics and physicobiology Introduction SARS_CoV_2 P108S 51 56 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. The mutation P108S is located in domain II. 2021 Biophysics and physicobiology Introduction SARS_CoV_2 P108S 13 18 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Their phylogenetic analysis identified four non-synonymous mutations in the viral genome sequence inversely correlated with COVID-19 severity, and subsequent sequence comparison and structure-based prediction suggested that two mutations, P108S and P151L, in the main protease and the nucleocapsid protein, respectively, contribute to a milder clinical course of COVID-19. 2021 Biophysics and physicobiology Introduction SARS_CoV_2 P108S;P151L 239;249 244;254 N 285 297 COVID-19;COVID-19 124;363 132;371 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. Among the 9 mutations in the spike gene in this variant, there are 3 biologically important mutations: K417N, E484K, and N501Y. 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K;K417N;N501Y 110;103;121 115;108;126 S 29 34 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. By the beginning of April 2020, a variant bearing a D614G mutation with evidence of increased infectivity had become dominant. 2021 Open forum infectious diseases Introduction SARS_CoV_2 D614G 52 57 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. In addition to D614G and several mutations in other areas of the genome, B.1.1.7 bears 8 mutations in the spike gene including deletions in the N-terminal domain ( H69/ V70, 144) and amino acid substitutions in the receptor binding domain (N501Y). 2021 Open forum infectious diseases Introduction SARS_CoV_2 D614G;N501Y 15;241 20;246 RBD;S;N 216;106;144 239;111;145 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. In addition, the B.1.351 and P.1 variants carry the E484K mutation, which is responsible for evasion from the monoclonal antibody against the original SARS-CoV-2, further compromising the currently available therapy against this virus. 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K 52 57 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. In this study, we investigated the neutralizing potency of serum from patients infected during the first to fourth waves of the pandemic against the SARS-CoV-2 variants D614G, B.1.1.7, B.1.351, and P1, using authentic virus. 2021 Open forum infectious diseases Introduction SARS_CoV_2 D614G 169 174 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. It bears 12 mutations in the spike gene, including K417T, E484K, and N501Y, which are the same 3 amino acid substitutions found in B.1.351. 2021 Open forum infectious diseases Introduction SARS_CoV_2 E484K;K417T;N501Y 58;51;69 63;56;74 S 29 34 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. SARS-CoV-2 genome surveillance has revealed that D614G_KR and its lineages were the predominating circulating viruses responsible for the first to third waves of the pandemic in Japan, but the introduction of the R1 and B.1.1.7 variants in late 2020 has replaced the previously existing strains and may be responsible for the fourth wave. 2021 Open forum infectious diseases Introduction SARS_CoV_2 D614G 49 54 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. Clones STI-1499-LALA and S1D2-hIgG1 did not neutralize B.1.351, but did neutralize strains D614 and D614G. 2021 Antiviral research Introduction SARS_CoV_2 D614G 100 105 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. Our plaque reduction neutralization assays demonstrate that clone 1741-LALA neutralizes SARS-CoV-2 strains B.1.351, D614, and D614G. 2021 Antiviral research Introduction SARS_CoV_2 D614G 126 131 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. All 10 clones retained high affinity binding and blocking activity against the S1-RBD N501Y mutant, and 3 showed neutralizing activity against the S1-RBD E484K mutant. 2021 FASEB journal Introduction SARS_CoV_2 E484K;N501Y 154;86 159;91 RBD;RBD 82;150 85;153 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. As mentioned in Ref., RBD mutations such as E484K/A, Y489H, Q493K, and N501Y found in late-stage evolved S variants "confer resistance to a common class of SARS-CoV-2 neutralizing antibodies", which suggests the viral evolution is also regulated by vaccine-resistant mutations. 2021 ArXiv Introduction SARS_CoV_2 E484K;E484A;N501Y;Q493K;Y489H 44;44;71;60;53 51;51;76;65;58 RBD;S 22;105 25;106 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Furthermore, the vaccination rates of 12 countries where Y449S is distributed are also analyzed, which provides a reliable explanation of the relation between the emergence of vaccine-resistant mutations and the vaccination rate. 2021 ArXiv Introduction SARS_CoV_2 Y449S 57 62 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. In early January 2021, we have predicted that RBD mutations W353R, I401N, Y449D, Y449S, P491R, P491L, Q493P, etc., will weaken most antibody bindings to the S protein. 2021 ArXiv Introduction SARS_CoV_2 I401N;P491L;P491R;Q493P;W353R;Y449D;Y449S 67;95;88;102;60;74;81 72;100;93;107;65;79;86 RBD;S 46;157 49;158 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Later on, we have provided a list of most likely vaccine escape RBD mutations with high frequency, including S494P, Q493L, K417N, F490S, F486L, R403K, E484K, L452R, K417T, F490L, E484Q, and A475S. 2021 ArXiv Introduction SARS_CoV_2 A475S;E484K;E484Q;F486L;F490L;F490S;K417N;K417T;L452R;Q493L;R403K;S494P 190;151;179;137;172;130;123;165;158;116;144;109 195;156;184;142;177;135;128;170;163;121;149;114 RBD 64 67 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Moreover, vaccine-resistant RBD mutation Y449S that has been found in more than 1000 isolates will be discussed. 2021 ArXiv Introduction SARS_CoV_2 Y449S 41 46 RBD 28 31 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Moreover, we have pointed out that Y449S and Y449H are two vaccine-resistant mutations, and "Y449S, S494P, K417N, F490S, L452R, E484K, K417T, E484Q, L452Q, and N501Y" are the top 10 mutations that will disrupt most antibodies with high-frequency. 2021 ArXiv Introduction SARS_CoV_2 E484K;E484Q;F490S;K417N;K417T;L452Q;L452R;N501Y;S494P;Y449H;Y449S;Y449S 128;142;114;107;135;149;121;160;100;45;35;93 133;147;119;112;140;154;126;165;105;50;40;98 34643437 Shared Mutations in Emerging SARS-CoV-2 Circulating Variants May Lead to Reverse Transcription-PCR (RT-PCR)-Based Misidentification of B.1.351 and P.1 Variants of Concern. For the remaining cases, for which the RT-PCR-based prescreening did not detect the E484K/N501Y mutations, three (33.33%) corresponded to B.1.617.2, a VOC. 2021 Microbiology spectrum Introduction SARS_CoV_2 E484K;N501Y 84;90 89;95 34643437 Shared Mutations in Emerging SARS-CoV-2 Circulating Variants May Lead to Reverse Transcription-PCR (RT-PCR)-Based Misidentification of B.1.351 and P.1 Variants of Concern. In five cases (41.67%), the E484K mutation was wrongly assigned by RT-PCR, corresponding to E484Q (B.1 and B.1.280 variants; Table 1). 2021 Microbiology spectrum Introduction SARS_CoV_2 E484K;E484Q 28;92 33;97 34643437 Shared Mutations in Emerging SARS-CoV-2 Circulating Variants May Lead to Reverse Transcription-PCR (RT-PCR)-Based Misidentification of B.1.351 and P.1 Variants of Concern. It harbors several mutations affecting the spike protein, including E484K and N501Y. 2021 Microbiology spectrum Introduction SARS_CoV_2 E484K;N501Y 68;78 73;83 S 43 48 34643437 Shared Mutations in Emerging SARS-CoV-2 Circulating Variants May Lead to Reverse Transcription-PCR (RT-PCR)-Based Misidentification of B.1.351 and P.1 Variants of Concern. Of these candidates, 121 (85.21%) harbored the E484K and N501Y mutations (B.1.351/P1 candidates as per commercial kit indications), 12 (8.45%) harbored the E484K mutation (B.1.525 candidates), and none of the previous mutations were found in the remaining nine (6.34%) cases (Table 1). 2021 Microbiology spectrum Introduction SARS_CoV_2 E484K;E484K;N501Y 47;156;57 52;161;62 34643437 Shared Mutations in Emerging SARS-CoV-2 Circulating Variants May Lead to Reverse Transcription-PCR (RT-PCR)-Based Misidentification of B.1.351 and P.1 Variants of Concern. Similarly, other RT-PCR-based assays have been developed by other companies to screen two new worrying VOCs, B.1.351 and P.1, targeting the E484K and N501Y mutations in the S-gene, which are considered markers for these VOCs. 2021 Microbiology spectrum Introduction SARS_CoV_2 E484K;N501Y 140;150 145;155 S 173 174 34643437 Shared Mutations in Emerging SARS-CoV-2 Circulating Variants May Lead to Reverse Transcription-PCR (RT-PCR)-Based Misidentification of B.1.351 and P.1 Variants of Concern. The emergent presence of the B.1.621 VOI, sharing the two E484K/N501Y mutations with P.1/B.1.351, is mainly responsible for the incorrect assignments in our study. 2021 Microbiology spectrum Introduction SARS_CoV_2 E484K;N501Y 58;64 63;69 34644287 Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. Both lineages evolved within the B.1.1.28 clade and convergently carried the E484K mutation in the receptor-binding domain (RBD) of the Spike protein. 2021 PLoS neglected tropical diseases Introduction SARS_CoV_2 E484K 77 82 S;RBD 136;124 141;127 34644287 Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. In addition to E484K, P.1 harbors the N501Y and K417T mutations in the RBD region. 2021 PLoS neglected tropical diseases Introduction SARS_CoV_2 E484K;K417T;N501Y 15;48;38 20;53;43 RBD 71 74 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Additionally, a new variant B.1.1.318 recently appeared in the United Kingdom; this variant requires close attention because of its E484K mutation. 2021 Communications biology Introduction SARS_CoV_2 E484K 132 137 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. B.1.351(beta or 501Y.V2) first appeared in South Africa and leads to immune escape of the spike protein because of mutation E484K in the RBD; this variant may influence the efficacies of vaccines and therapeutic monoclonal antibodies (mAbs) and sera. 2021 Communications biology Introduction SARS_CoV_2 E484K 124 129 S;RBD 90;137 95;140 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Beginning in March 2020, the D614G mutant strain became the dominant strain globally, and the current prevalence has exceeded 95%. 2021 Communications biology Introduction SARS_CoV_2 D614G 29 34 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. We compared infectivity, host tropism, and neutralization characteristics with the D614G reference strain, with the aim of providing clues for the prevention and control of COVID-19, particularly with respect to designing mAbs and vaccines. 2021 Communications biology Introduction SARS_CoV_2 D614G 83 88 COVID-19 173 181 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Also, the E484Q mutation is similar to E484K found in the Beta and Gamma variants. 2021 Journal of chemical information and modeling Introduction SARS_CoV_2 E484K;E484Q 39;10 44;15 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Because the virus surface spike protein plays an important role in mediating SARS-CoV-2 entry into human cells and is the target for vaccine and therapeutic development, any mutations on this region may have biological significance, as it could affect the viral infectivity and antigenicity.- Indeed, experimental studies showed that the D614G mutation discovered at the earlier stage of the pandemic enhances the virus fitness and increases its transmission. 2021 Journal of chemical information and modeling Introduction SARS_CoV_2 D614G 338 343 S 26 31 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. For example, the L452R mutation has been spotted in the B.1.427/B.1.429 variant, which is known to be more contagious and is capable of escaping antibody neutralization. 2021 Journal of chemical information and modeling Introduction SARS_CoV_2 L452R 17 22 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Recently, a variant named B.1.617.1 (Kappa) that carries two mutations including L452R and E484Q has been designated as a variant of interest (VOI) by the World Health Organization (WHO), suggesting that this variant potentially could have higher transmissibility and severity or reinfection risk and is required continuous monitoring. 2021 Journal of chemical information and modeling Introduction SARS_CoV_2 E484Q;L452R 91;81 96;86 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Similarly, the N501Y mutation found in the B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.1.28.1 (Gamma) variants has been demonstrated to increase the binding affinity between the receptor-binding domain (RBD) and its human receptor ACE2 (hACE2), making these variants more transmissible.- Moreover, experimental and computational studies have showed that K417N and E484K found in the Beta variant could evade neutralization by many monoclonal antibodies (mAbs). 2021 Journal of chemical information and modeling Introduction SARS_CoV_2 E484K;K417N;N501Y 361;351;15 366;356;20 RBD 200 203 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. For example, the D614G mutation displayed heightened infectivity and quickly became the most prevalent form spreading early in the COVID-19 pandemic. 2021 Cell reports Introduction SARS_CoV_2 D614G 17 22 COVID-19 131 139 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Recently, SARS-CoV-2 variants that carry the N501Y mutation have been spreading in the United Kingdom, Brazil, South Africa, and India and appear to have heightened transmissibility in humans. 2021 Cell reports Introduction SARS_CoV_2 N501Y 45 50 34649268 Genomic reconstruction of the SARS-CoV-2 epidemic in England. A phylogeographical analysis establishing the most parsimonious sets of monophyletic and exclusively domestic clades, which can be interpreted as individual introductions, confirmed that A.23.1 with E484K (1 clade) probably has a domestic origin as no genomes of the same clade were observed internationally (Methods. 2021 Nature Introduction SARS_CoV_2 E484K 199 204 34649268 Genomic reconstruction of the SARS-CoV-2 epidemic in England. An initial sign was the emergence and global spread of the spike protein variant D614G in the second quarter of 2020. 2021 Nature Introduction SARS_CoV_2 D614G 81 86 S 59 64 34649268 Genomic reconstruction of the SARS-CoV-2 epidemic in England. However, the underlying biological mechanism is unclear as the characteristic A222V spike variant is not believed to confer a growth advantage. 2021 Nature Introduction SARS_CoV_2 A222V 78 83 S 84 89 34649268 Genomic reconstruction of the SARS-CoV-2 epidemic in England. In contrast to other VOCs, Delta/Kappa do not contain N501Y or E484K mutations, but their L452R mutation may reduce antibody recognition and P681R enhances furin cleavage, similar to the P681H mutation of Alpha. 2021 Nature Introduction SARS_CoV_2 E484K;L452R;N501Y;P681H;P681R 63;90;54;187;141 68;95;59;192;146 34649268 Genomic reconstruction of the SARS-CoV-2 epidemic in England. Refractory variants with E484K mutations. 2021 Nature Introduction SARS_CoV_2 E484K 25 30 34649268 Genomic reconstruction of the SARS-CoV-2 epidemic in England. The AY.1 lineage, derived from Delta and containing an additional K417N mutation, appeared only transiently. 2021 Nature Introduction SARS_CoV_2 K417N 66 71 34649268 Genomic reconstruction of the SARS-CoV-2 epidemic in England. The growth advantage is thought to stem, at least in part, from spike mutations that facilitate ACE2 receptor binding (N501Y) and furin cleavage (P681H). 2021 Nature Introduction SARS_CoV_2 N501Y;P681H 119;146 124;151 S 64 69 34649268 Genomic reconstruction of the SARS-CoV-2 epidemic in England. The proportion of these E484K-containing variants was consistently 0.3-0.4% from January to early April 2021. 2021 Nature Introduction SARS_CoV_2 E484K 24 29 34649268 Genomic reconstruction of the SARS-CoV-2 epidemic in England. The variants B.1.525/Eta, B.1.526/Iota, B.1.1.318 and P.2/Zeta also harbour E484K spike mutations as per their lineage definition, and sublineages of Alpha and A.23.1 that acquired E484K were found in England. 2021 Nature Introduction SARS_CoV_2 E484K;E484K 76;181 81;186 S 82 87 34649268 Genomic reconstruction of the SARS-CoV-2 epidemic in England. These include the VOCs B.1.351/Beta and P.1/Gamma, which carry the spike variant N501Y that is also found in B.1.1.7/Alpha and a similar pair of mutations (K417N/T and E484K) that were each shown to reduce the binding affinity of antibodies from vaccine-derived or convalescent sera . 2021 Nature Introduction SARS_CoV_2 E484K;N501Y;K417N;K417T 168;81;156;156 173;86;163;163 S 67 72 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Among the SARS-CoV-2 variants of concern, Beta B.1.351 (RBD-K417N/E484K/N501Y) discovered in South Africa and Gamma P.1 (RBD-K417T/E484K/N501Y) discovered in Brazil have been demonstrated to have high potential to reduce the efficacy of some vaccines. 2021 Genome medicine Introduction SARS_CoV_2 E484K;E484K;N501Y;N501Y;K417N;K417T 66;131;72;137;60;125 71;136;77;142;65;130 RBD;RBD 56;121 59;124 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Recently, the B.1.617 variant carrying two RBD mutations (E484Q and L452R) emerged in India has become a variant of interest for its high transmission rate and ability to evade immune responses. 2021 Genome medicine Introduction SARS_CoV_2 L452R;E484Q 68;58 73;63 RBD 43 46 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. The Delta VOC, identified in October 2020 in India, consists of 41 different sublineages sharing additional T19R, del157/158, T478K, and D950N in Spike protein and I82T in M protein compared to B.1. 2021 Emerging microbes & infections Introduction SARS_CoV_2 D950N;I82T;T19R;T478K 137;164;108;126 142;168;112;131 S 146 151 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. A detailed, systematic, and comprehensive investigation is essential to determine how the N439K, S477 N, and T478K substitutions affect the binding of the spike protein with the ACE2 receptor and initiate structural and functional changes. 2021 Computers in biology and medicine Introduction SARS_CoV_2 N439K;S477N;T478K 90;97;109 95;103;114 S 155 160 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. In the present study, we used different theoretical and computational methods such as protein-protein docking, molecular dynamics simulations, and binding free energy calculations to investigate the structural changes that (1) alter the binding between RDB and ACE2 receptor as a result of N439K, S477 N, and T478K mutations, and (2) increase the infectivity rates. 2021 Computers in biology and medicine Introduction SARS_CoV_2 N439K;S477N;T478K 290;297;309 295;303;314 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. The novel mutations N439K, S477 N, and T478K were recently reported to increase the binding affinity and impact the infectivity. 2021 Computers in biology and medicine Introduction SARS_CoV_2 N439K;S477N;T478K 20;27;39 25;33;44 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. 3 copies/reaction) and is capable of detecting minor N501Y variant at 10 % frequency. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 53 58 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. All platforms could consistently identify N501Y variant at a concentration as low as 1.5 copies/muL, which was therefore considered as the limit of detection (LoD) of the assay. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 42 47 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. Although the utilisation of whole genome surveillance remains a necessity to classify the lineage of SARS-CoV-2, the application of N501Y RT-qPCR screening for early identification of these highly contagious variants may help the health authorities to better plan for enhanced infection control measures. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 132 137 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. Among 134 samples without N501Y, majority of them were genotyped as B.1.36.27 (n = 39, 30 %) and B.1.1.63 (n = 23, 17.7 %) (Table S1, Supplemental Material). 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 26 31 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. As N501Y has started to dominate the current circulating viral population in Asia, health authorities surge the development of alternative assay to expand screening capacity with reduced time and cost. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 3 8 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. Currently, in Hong Kong, all cases tested positive for N501Y variants on hospital admission would be arranged under single airborne infection isolation room isolation until discharge. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 55 60 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. For determination of analytical sensitivity, one sample of B.1.1.7 (N501Y variant) and B.1.36.27 (non-N501Y variant) were quantified with SARS-CoV-2 Droplet Digital PCR (ddPCR) Kit (BIO-RAD, US) and were normalized to 1500 copies/muL respectively, followed by serially diluted down to 0.15 copies/muL. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y;N501Y 68;102 73;107 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. In addition, the ability of our assay to identify low-frequency N501Y variants was evaluated by mixing B.1.1.7 SARS-CoV-2 RNA with B.1.36.27 SARS-CoV-2 RNA at ratios from 9:1 (allele frequency = 90 %) to 1:9 (allele frequency = 10 %). 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 64 69 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. In conclusion, the N501Y RT-qPCR can be rapidly implemented and widely adopted by clinical laboratories as it is simple and inexpensive to run robust high-throughput screening for surveillance of SARS-CoV-2 variants of concern harbouring N501Y mutation. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y;N501Y 19;238 24;243 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. In this study, we developed an in-house TaqMan MGB probe-based one-step RT-qPCR assay that can specifically and accurately detect the N501Y containing variants in SARS-CoV-2 positive samples. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 134 139 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. In this study, we present an in-house developed TaqMan MGB (minor groove binder) probe-based one-step RT-qPCR assay to detect the presence of N501Y mutation in SARS-CoV-2 positive specimens, providing analytical sensitivity as low as 1.5 copies/muL and result delivery within 40 min. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 142 147 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. Interestingly, N501Y mutation was successfully detected at an allele frequency as low as 10 % in the RNA mixtures. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 15 20 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. N501Y mutation is a surrogate marker of SARS-CoV-2 variants of concern, including lineages B.1.1.7, B.1.351 and P.1. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 0 5 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. N501Y was accurately discriminated regardless of the lineages of SARS-CoV-2 (Table S1, Supplemental Material). 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 0 5 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. Our laboratory is developing another TaqMan MGB probe-based one-step RT-qPCR assay to detect the presence of L452R mutation, which shall be used in conjunction with N501Y RT-qPCR. 2022 Journal of virological methods Introduction SARS_CoV_2 L452R;N501Y 109;165 114;170 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. Recently, several N501Y RT-qPCR kits are commercially available, such as Allplex SARS-CoV-2 Variants I Assay (SeeGene, Republic of Korea) and VirSNiP SARS-CoV-2 Spike N501Y (TIB Molbiol, Germany). 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y;N501Y 18;168 23;173 S 162 167 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. Regarding the diagnostic accuracy, the RT-qPCR results were in 100 % agreement with the WGS data, where all 34 samples were correctly identified as N501Y-positive, and the other 134 samples were indicated as wildtype. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 148 153 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. The increasing prevalence of N501Y containing variants has kindled global concern due to their heightened transmissibility and their potential to evade host immune responses and cause reinfection. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 29 34 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. The major limitation of the assay is its inability to detect the recently expanding SARS-CoV-2 variant of concern, B.1.617.2 lineage, (a.k.a G/452R.V3), which does not harbour N501Y mutation but E484Q and L452R instead. 2022 Journal of virological methods Introduction SARS_CoV_2 E484Q;L452R;N501Y 195;205;176 200;210;181 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. The N501Y mutation is also observed in other SARS-CoV-2 variants of concern, including B.1.351 and P.1, where a similar sharp increase in spread and frequency of the virus was noticed in their respective area of origin. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 4 9 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. Their highly mutated spike glycoprotein, especially the N501Y substitution, has been shown to enhance viral entry into the host cell. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 56 61 S 21 39 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. Therefore, N501Y RT-qPCR is being used as a reflex test for every sample which was tested positive for SARS-CoV-2, and subsequent WGS analysis is performed to determine the lineages and the phylogenetic relatedness of N501Y-positive samples. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y;N501Y 11;218 16;223 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. Thirty-four samples were confirmed to carry N501Y mutation, in which 20, 12 and 2 were classified as lineages B.1.1.7, B.1.351 and P.3 respectively. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y 44 49 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. Two MGB TaqMan probes, with FAM and VIC-labelled respectively, were used to differentiate the nucleotide A from T at position 23063, where the N501Y mutation is located. 2022 Journal of virological methods Introduction SARS_CoV_2 A23063T;N501Y 105;143 131;148 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. B.1.1.7 (Alpha), B.1.351 (Beta), Lineages P.1 (Gamma), and B.1.617.2 (Delta, a L452R mutant) are the current Variants of Concern (VOC). 2021 Frontiers in public health Introduction SARS_CoV_2 L452R 79 84 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. While doing epidemiological and genomic surveillance of SARS-CoV-2 in samples from the city of Porto Ferreira:SP:Brazil, using Sanger and NGS techniques, we detected a new lineage designated by Pango as P.4, harboring the L452R mutation, that is circulating in Sao Paulo state. 2021 Frontiers in public health Introduction SARS_CoV_2 L452R 222 227 S 110 112 34663909 SARS-CoV-2 promotes RIPK1 activation to facilitate viral propagation. In addition, the SARS-CoV-2 viral variants carrying P323L mutation in NSP12 and the associated D614G mutation in spike protein were reported to be enriched in severely affected group. 2021 Cell research Introduction SARS_CoV_2 D614G;P323L 95;52 100;57 S;Nsp12 113;70 118;75 34663909 SARS-CoV-2 promotes RIPK1 activation to facilitate viral propagation. The mechanism behind the apparent positive selection of the variant with C14408T mutation is unclear with most studies focused on the Spike protein. 2021 Cell research Introduction SARS_CoV_2 C14408T 73 80 S 134 139 34663909 SARS-CoV-2 promotes RIPK1 activation to facilitate viral propagation. The SARS-CoV-2 C14408T variant that carries a Pro323Leu amino acid substitution in RNA-dependent RNA polymerase (RdRp, NSP12), the central component of coronaviral replication and transcription machinery, was first detected in the early outbreak phase in Lombardy, Italy and quickly established as the dominant SARS-CoV-2 variant detected in between 50% and 70% of SARS-CoV-2 sequences around the world, particularly in Europe, North and South America, and Africa, with significantly higher infectivity and transmissibility than the original variant. 2021 Cell research Introduction SARS_CoV_2 C14408T;P323L 15;46 22;55 RdRp;Nsp12;RdRP 83;119;113 111;124;117 34671769 A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. As an example, a single mutation, E484K, found in several variants could knock out a class of antibodies binding the receptor binding motif (RBM) on the viral spike. 2021 bioRxiv Introduction SARS_CoV_2 E484K 34 39 S 159 164 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. Three prominent mutations occur in this region including R203K/G204R, a double substitution (KR mt) present in the alpha and gamma variants; T205I present in the beta variant; and R203M that occurs in the kappa and delta variants. 2022 bioRxiv Introduction SARS_CoV_2 R203K;R203M;T205I;G204R 57;180;141;63 62;185;146;68 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. For both variants, the mutation in the RBD region of SARS-CoV-2 is described by the N501Y mutation. 2021 Journal of medical virology Introduction SARS_CoV_2 N501Y 84 89 RBD 39 42 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. On the other hand, in B.1.351 lineage, the K417N, and E484K mutations are found in the RBD region. 2021 Journal of medical virology Introduction SARS_CoV_2 E484K;K417N 54;43 59;48 RBD 87 90 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. P681H is adjacent to the furin cleavage site, a location known to be of biological importance. 2021 Journal of medical virology Introduction SARS_CoV_2 P681H 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The N501Y is located in the receptor binding motif (RBM) of the C-terminal domain (CTD) and has been found to increase its binding affinity to human ACE2 receptor as shown in Figure 1. 2021 Journal of medical virology Introduction SARS_CoV_2 N501Y 4 9 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The SARS-CoV-2 Variant of Concern 202012/01 (VOC-202012/01), also known as strain B.1.1.7 and N501Y, associated with a significant increase in the rate of COVID-19 infection in the United Kingdom. 2021 Journal of medical virology Introduction SARS_CoV_2 N501Y 94 99 COVID-19 155 173 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Three mutations in the S protein of the novel variant (N501Y, HV69-70del, and P681H) have potential biological implications. 2021 Journal of medical virology Introduction SARS_CoV_2 P681H;N501Y 78;55 83;60 S 23 24 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Thus, with this study, we aim to evaluate the N501Y mutation rate in randomly chosen 13 972 positive COVID-19 PCR test result patients to contribute to the literature in the global pandemic that affects our society with a retrospective approach with the comparison of age, gender, and Cq scales of patients. 2021 Journal of medical virology Introduction SARS_CoV_2 N501Y 46 51 COVID-19 101 109 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. Also, N: A220V, ORF10: V30L and three other synonymous mutations T445C, C6286T, and C26801G are observed for this clade. 2021 Journal of medical virology Introduction SARS_CoV_2 A220V;C26801G;C6286T;T445C;V30L 9;84;72;65;23 14;91;78;70;27 N 6 7 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. Although the possible role of ORF3a:p.Q57H in the replication cycle has recently been investigated, the molecular perspective was not fully explored. 2021 Journal of medical virology Introduction SARS_CoV_2 Q57H;Q57H 38;36 42;42 ORF3a 30 35 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. Another derivative of G clade is GH or lineage B.1.*, characterized by an additional ORF3a:p.Q57H mutation. 2021 Journal of medical virology Introduction SARS_CoV_2 Q57H;Q57H 93;91 97;97 ORF3a 85 90 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. GISAID referred to these co-occurring mutations containing viruses as clade G (named after the spike D614G mutation) or PANGO (https://cov-lineages.org/) lineage B.1. 2021 Journal of medical virology Introduction SARS_CoV_2 D614G 101 106 S 95 100 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. The effects of 5'-UTR: C241T, Leader: T445C, NSP3: C318T, RdRp:p.P323L, N:p.RG203-203KR, and N:p.A220V are still being overlooked. 2021 Journal of medical virology Introduction SARS_CoV_2 C241T;C318T;T445C;A220V;P323L;A220V;P323L 23;51;38;97;65;95;63 28;56;43;102;70;102;70 Nsp3;RdRP;N;N 45;58;72;93 49;62;73;94 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. The GR clade or lineage B.1.1.* is classified with additional trinucleotide mutations at 28 881-28 883 (GGG>AAC), creating two consecutive amino acid (aa) changes, R203K and G204R, in N protein. 2021 Journal of medical virology Introduction SARS_CoV_2 G204R;R203K 174;164 179;169 N 184 185 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. The most frequently observed mutation is D614G of the S protein, which has direct roles in receptor binding and immunogenicity, thus viral immune-escape, transmission, and replication fitness. 2021 Journal of medical virology Introduction SARS_CoV_2 D614G 41 46 S 54 55 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. The variant GV or lineage B.1.177 featured an A222V mutation in the S protein and other mutations of the clade G. 2021 Journal of medical virology Introduction SARS_CoV_2 A222V 46 51 S 68 69 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. Yin reported that the 5'-untranslated region (5'-UTR) mutation 241C>T is co-occurring with three other mutations, 3037 C>T (NSP3: C318T), 14408C>T (RdRp: p.P323L), and 23403A>G (S: p.D614G). 2021 Journal of medical virology Introduction SARS_CoV_2 C14408T;A23403G;C241T;C3037T;C318T;D614G;P323L;D614G;P323L 138;168;63;114;130;181;154;183;156 146;176;69;122;135;188;161;188;161 Nsp3;RdRP;S 124;148;178 128;152;179 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Therefore, we studied the pathogenesis of B.1.1.7 and B.1.351 in rhesus macaques and compared it to a recent SARS-CoV-2 isolate containing the D614G substitution in spike that rapidly became dominant globally in March 2020 because of its increased transmissibility. 2021 Science advances Introduction SARS_CoV_2 D614G 143 148 S 165 170 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. RT-qPCR is the gold standard for detection of SARS-CoV-2 in clinical samples and has also been used for SARS-CoV-2 spike gene mutation detection in previous studies, often focusing on the HV69/70 deletion and the N501Y SNP (single nucleotide polymorphism) using various methods such as specific primers, simple probes, and melt curve analyses. 2021 Diagnostics (Basel, Switzerland) Introduction SARS_CoV_2 N501Y 213 218 S 115 120 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. Spike gene mutations such as N501Y, E484K/Q, L452R, and P681H/R have occurred independently in multiple VOCs and VOIs (variants of interest), enabling dynamic adaptation of existing assay designs to detect emerging SARS-CoV-2 variants. 2021 Diagnostics (Basel, Switzerland) Introduction SARS_CoV_2 E484K;E484Q;L452R;N501Y;P681H;P681R 36;36;45;29;56;56 43;43;50;34;63;63 S 0 5 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. found that the variants' spike P681R mutation augments spike processing, which leads to enhanced SARS-CoV-2 fitness over the Alpha variant. 2021 Pharmaceuticals (Basel, Switzerland) Introduction SARS_CoV_2 P681R 31 36 S;S 25;55 30;60 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. Free energy perturbation calculations for interactions of the N501Y and K417N mutations with both the ACE2 receptor and an antibody derived from COVID-19 patients raise important questions about the possible human immune response and the success of already-available vaccines. 2021 Pharmaceuticals (Basel, Switzerland) Introduction SARS_CoV_2 K417N;N501Y 72;62 77;67 COVID-19 145 153 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. Further, increased resistance of the variants Beta and Alpha to antibody neutralization has been reported; for the Beta variant this was largely due to the E484K mutation in the spike protein. 2021 Pharmaceuticals (Basel, Switzerland) Introduction SARS_CoV_2 E484K 156 161 S 178 183 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. Here we report on the inhibitory potential of dandelion on the binding of the spike S1 protein RBD to the hACE2 cell surface receptor and compare the effect of the original D614 spike protein to its D614G, N501Y, and mix (K417N, E484K, and N501Y) mutations. 2021 Pharmaceuticals (Basel, Switzerland) Introduction SARS_CoV_2 D614G;E484K;N501Y;N501Y;K417N 199;229;206;240;222 204;234;211;245;227 S;S;RBD 78;178;95 83;183;98 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. Most of these variants share the mutation N501Y in the spike protein and SARS-CoV-2 variants with spike protein D614G mutations now predominate globally. 2021 Pharmaceuticals (Basel, Switzerland) Introduction SARS_CoV_2 D614G;N501Y 112;42 117;47 S;S 55;98 60;103 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. Preliminary data suggest a possible association between the observed increased fatality rate and the mutation D614G and it is hypothesized that a conformational change in the spike protein results in increased infectivity. 2021 Pharmaceuticals (Basel, Switzerland) Introduction SARS_CoV_2 D614G 110 115 S 175 180 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. The Beta variant contains, besides D614G, other spike mutations, including three mutations (K417N, E484K, and N501Y) in the RBD. 2021 Pharmaceuticals (Basel, Switzerland) Introduction SARS_CoV_2 D614G;E484K;N501Y;K417N 35;99;110;92 40;104;115;97 S;RBD 48;124 53;127 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. At a shear stress of 25 dyne cm-2, we visualized and quantified the inflammatory cytokine-mediated microthrombosis upon exposure to the most common Spike mutation D614G (Asp614 Gly substitution in S1 subunit) using a viral vector, and we corroborated blood coagulation using the live SARS-CoV-2 virus. 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Introduction SARS_CoV_2 D614G;D614G 163;170 168;180 S 148 153 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. We performed countermeasure to reverse Spike-, and Spike mutation D614G-mediated blood coagulation by conjugating liposomes with human-ACE2 (Lipo-hACE2) as a competitive S protein decoy. 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Introduction SARS_CoV_2 D614G 66 71 S;S;S 39;51;170 44;56;171 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. Here, we tested the neutralizing activity of a panel of 30 post-mRNA SARS-CoV-2 vaccination sera against the seven emerging variants (three Iota sub-lineages, Alpha-E484K, Beta, Delta and a Lambda sub-variant) using a microneutralization assay designed to allow for multi-cycle replication with sera/antibodies being present in the overlay at all times to better mimic physiological conditions. 2021 EBioMedicine Introduction SARS_CoV_2 E484K 165 170 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. In comparison with the WA-1 wild type reference virus, we found that differences in neutralization activity were minimal for Delta and the three Iota sublineages with a greater reduction being observed for the Beta and Alpha (E484K) variants as well as for a Lambda subvariant. 2021 EBioMedicine Introduction SARS_CoV_2 E484K 226 231 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. These include Iota (B.1.526) which emerged in New York City and comprises three different sub-lineages, Epsilon (B.1.427/B.1.429) which emerged in California, Lambda (C.37) which emerged in Peru (preprint), Delta (B.1.617.2) and Kappa (B.1.617.1) which emerged in India, B.1.1.7 carrying E484K (Alpha+484K), which was detected in several countries, as well as A.23.1 which was first detected in Uganda. 2021 EBioMedicine Introduction SARS_CoV_2 E484K 288 293 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Considering the high susceptibility of mice to N501Y-carrying variants and the endogenous ACE2 expression in wildtype mice in comparison to the hACE2-transgenic mice, the N501Y-carrying variant infection model may represent a physiologically-relevant model for SARS-CoV-2 studies on pathogenesis, immunology, and antivirals. 2021 EBioMedicine Introduction SARS_CoV_2 N501Y;N501Y 47;171 52;176 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. High viral genome copies and high infectious virus particle titres are recovered from the nasal turbinate and lung of N501Y-carrying variants-inoculated mice for 4-to-7 days post infection. 2021 EBioMedicine Introduction SARS_CoV_2 N501Y 118 123 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. In addition, infection of N501Y-carrying variants is compatible with all existing knock-out and knock-in mouse models that will greatly facilitate further functional studies on host genes and pathways. 2021 EBioMedicine Introduction SARS_CoV_2 N501Y 26 31 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Interestingly, emerging SARS-CoV-2 variants, including B.1.1.7, B.1.351, P.1, and P.3, all contain the N501Y mutation in spike that has been suggested to be associated with mouse adaptation, raising the postulation that these emerging SARS-CoV-2 variants may have evolved to expand species tropism to mouse and possibly other murines. 2021 EBioMedicine Introduction SARS_CoV_2 N501Y 103 108 S 121 126 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Our results demonstrate that while wildtype mice are not permissive to WT SARS-CoV-2, B.1.1.7 and N501Y-carrying variants efficiently infect wildtype mice with production of infectious virus particles in the nasal turbinate and lung. 2021 EBioMedicine Introduction SARS_CoV_2 N501Y 98 103 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Our search did not reveal any report that performed comprehensive side-by-side investigations of the susceptibility of SARS-CoV-2 N501Y-carrying variants in murines in both in vitro and in vivo settings. 2021 EBioMedicine Introduction SARS_CoV_2 N501Y 130 135 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Our study reveals that B.1.1.7 and other variants carrying the N501Y mutation but not WT SARS-CoV-2 can infect wildtype mice. 2021 EBioMedicine Introduction SARS_CoV_2 N501Y 63 68 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. These findings indicate that B.1.1.7 and other N501Y-carrying variants have gained the capacity to expand species tropism to murine species and that public health control measures including stringent murine control should be implemented to facilitate the control of the ongoing pandemic. 2021 EBioMedicine Introduction SARS_CoV_2 N501Y 47 52 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. These findings provide direct evidence that B.1.1.7 and other N501Y-carrying variants have gained the capability to expand species tropism to murine species. 2021 EBioMedicine Introduction SARS_CoV_2 N501Y 62 67 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. To evaluate this possibility with major public health significance, we evaluated the capacity of SARS-CoV-2 wildtype (WT), B.1.1.7, and additional N501Y-carrying variants to infect mice (Mus musculus). 2021 EBioMedicine Introduction SARS_CoV_2 N501Y 147 152 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. For example, T478K aa change in the receptor-binding domain (RBD) and 156-157 deletions in the N-terminal domain (NTD) of the S protein are unique to B.1.617.2, while E154K and Q1071H substitutions exist only in the B.1.617.1 sublineage. 2021 Frontiers in microbiology Introduction SARS_CoV_2 E154K;Q1071H;T478K 167;177;13 172;183;18 RBD;N;S 61;95;126 64;96;127 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. It was observed that the variants carrying spike L452R change are likely to be more transmissible and infective and less susceptible to the neutralizing antibodies from convalescent patients and vaccine recipients. 2021 Frontiers in microbiology Introduction SARS_CoV_2 L452R 49 54 S 43 48 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. L452R is located in the RBD, and P681H or P681R is located in the furin cleavage site. 2021 Frontiers in microbiology Introduction SARS_CoV_2 P681H;P681R;L452R 33;42;0 38;47;5 RBD 24 27 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. Some of the aa changes or similar ones in B.1.617 were also identified in other circulating lineages: D614G was also found in B.1 lineage, L452R in B.1.526 (Iota), and P681H in B.1.1.7 (Alpha). 2021 Frontiers in microbiology Introduction SARS_CoV_2 D614G;L452R;P681H 102;139;168 107;144;173 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. The variant bearing P681R, such as B.1.617.2, has an increased furin-mediated cleavage at the S1/S2 cleavage site that would lead to enhanced viral fusogenicity and exhibit a higher pathogenicity. 2021 Frontiers in microbiology Introduction SARS_CoV_2 P681R 20 25 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. Though the amino acid (aa) changes of G142D, L452R, D614G, and P681R occurring in the spike (S) protein are signatures for B.1.617 and present in all the three sublineages, distinct mutation profiles were found in each of the sublineages. 2021 Frontiers in microbiology Introduction SARS_CoV_2 D614G;G142D;L452R;P681R 52;38;45;63 57;43;50;68 S;S 86;93 91;94 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. All three VOC B.1.1.7, B.1.351, and P.1 contain the residue substitution N501Y due to an asparagine to tyrosine exchange in position 501 in the RBD domain. 2021 Frontiers in immunology Introduction SARS_CoV_2 N501Y;N501Y 89;73 136;78 RBD 144 147 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. Combined in the B.1.351 and P.1 RBD variants, the two different K417 substitutions also lower the overall affinity, but the effect is in part counterbalanced by the E484K and N501Y gain-of-function changes. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K;N501Y 165;175 170;180 RBD 32 35 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. In contrast, the E484K displays a significant antibody evasion capacity without significantly impacting the affinity. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K 17 22 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. The N501Y substitution impacts transmissibility and disease severity. 2021 Frontiers in immunology Introduction SARS_CoV_2 N501Y 4 9 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. The substitution of lysine417 to either an asparagine (K417N) or a threonine (K417T) results in a significant reduction in RBD/ACE-2 affinity, while the N501Y confers a ten-fold affinity increase towards ACE-2. 2021 Frontiers in immunology Introduction SARS_CoV_2 N501Y;K417N;K417T 153;55;78 158;60;83 RBD 123 126 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. We found the prevalence of adaptive mutations in the global population to be quite significant, especially the N501Y, L452R, T478K, E484K and S477N mutations. 2021 Viruses Introduction SARS_CoV_2 E484K;L452R;N501Y;S477N;T478K 132;118;111;142;125 137;123;116;147;130 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Accumulated sequencing data on SARS-CoV-2 observed that a key amino acid mutation at position 614, from aspartic acid (D) to glycine (G) in the S protein (S-D614G) in late January 2020, started to spread globally and became dominance beginning in March 2020. 2021 mBio Introduction SARS_CoV_2 D614G 157 162 S;S 144;155 145;156 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Besides D614G, amino acid changes within S1-RBD, such as N439K, L452R, E484K/Q, and N501Y, also favor virus resistance to monoclonal antibody neutralization. 2021 mBio Introduction SARS_CoV_2 D614G;E484K;E484Q;L452R;N439K;N501Y 8;71;71;64;57;84 13;78;78;69;62;89 RBD 44 47 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Emerging evidence indicates that virus bearing the D614G mutation is associated with faster transmission, increased viral infectivity, and enhanced viral replication and host fitness, which is consistent with higher binding affinity due to a more open conformation toward an hACE2 binding-competent state ( to), suggestive of natural selection on an adaptive benefit. 2021 mBio Introduction SARS_CoV_2 D614G 51 56 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. Another interesting feature of the G clades is that the associated C14408T mutation adjacent to the RNA dependent RNA polymerase (RdRp) putatively increases the mutation rate as Pachetti et al. 2021 Scientific reports Introduction SARS_CoV_2 C14408T 67 74 RdRp;RdRP 100;130 128;134 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. Brufsky hypothesized that the higher number of deaths on the East coast of the United States compared to the West coast could be due to the higher prevalence of the D614G amino acid substitution on the East coast. 2021 Scientific reports Introduction SARS_CoV_2 D614G 165 170 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. In China, four early samples carried the D614G amino acid substitution. 2021 Scientific reports Introduction SARS_CoV_2 D614G 41 46 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. In Europe the first German sample from January 28th carried the A-to-G mutation at nucleotide position 23403 (D614G) mutation and the C-to-T mutation at position 3037, but not the mutation at position 14408. 2021 Scientific reports Introduction SARS_CoV_2 A23403G;C3037T;D614G 64;134;110 108;166;115 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. One sample from January 24th 2020 had only the A23403G (D614G) but not the C3037T and C14408T mutations which usually associate with A23403T in clade G. 2021 Scientific reports Introduction SARS_CoV_2 A23403G;A23403T;C14408T;C3037T;D614G 47;133;86;75;56 54;140;93;81;61 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. Previous studies reported the potential impact of the D614G amino acid substitution which is a result of the A23403G single nucleotide polymorphism (SNP) and associated with the branch of the phylogenetic tree referred to as clade G. 2021 Scientific reports Introduction SARS_CoV_2 A23403G;D614G 109;54 116;59 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. The D614G amino acid substitution has been suggested to affect the adherence of the virus to the cell membrane and consequently results in higher virulence. 2021 Scientific reports Introduction SARS_CoV_2 D614G 4 9 Membrane 102 110 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. The first sample carrying all of the above mentioned mutations plus the C241T in the Untranslated Region (UTR) was identified in Italy on February 20th, 2020. 2021 Scientific reports Introduction SARS_CoV_2 C241T 72 77 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. Three samples with the D614G were related to the first German sample. 2021 Scientific reports Introduction SARS_CoV_2 D614G 23 28 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. A701V, one of S protein mutation in N501Y.V2 lineage, become the dominant strain in the third wave in Malaysia, and may affect the infectivity of the virus. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 N501Y;A701V 36;0 41;5 S 14 15 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. As a common mutation of N501Y.V1 and N501Y.V2, N501Y mutation was first reported in a mouse model and hereafter identified in populations of many countries and regions. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 N501Y;N501Y;N501Y 24;37;47 29;42;52 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. E484K mutation was first identified in N501Y.V2, and was reported to be associated with escaping from neutralizing antibodies. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 N501Y;E484K 39;0 44;5 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. In addition, the P681H substitution in SARS-CoV-2 S protein is adjacent to the furin cleavage site, implying the potential influence on the infection tropism and efficiency of virus. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 P681H 17 22 S 50 51 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. In particular, D614G mutation was first identified in Europe, then replaced previously circulating lineages and led to a global pandemic. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G 15 20 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. In the mouse model, N501Y mutation enhances the binding affinity of SARS-CoV-2 S protein with mouse ACE2, and increase infectivity in mouse lung tissue. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 N501Y 20 25 S 79 80 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. In this study, we constructed pseudoviruses bearing SARS-CoV-2 S protein with mutations of N501Y.V1 and N501Y.V2 variants. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 N501Y;N501Y 91;104 96;109 S 63 64 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Interestingly, N501Y.V3 (also known as P.1) lineage in Brazil almost has the same three RBD mutations as N501Y.V2 lineage, except for the K417N/T substitution. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 K417N;K417T;N501Y;N501Y 138;138;15;105 145;145;20;110 RBD 88 91 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. N501Y.V2 lineage includes ten mutations in the S protein, and three of them are located in the receptor binding domain (RBD) (K417N, E484K and N501Y). 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 E484K;N501Y;K417N;N501Y 133;143;126;0 138;148;131;5 RBD;RBD;S 95;120;47 118;123;48 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Preliminary studies have shown that N501Y.V1 and N501Y.V2 lineages have high transmission efficiency and immune escape from neutralizing antibodies than the original strain. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 N501Y;N501Y 36;49 41;54 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. SARS-CoV-2 N501Y.V1 and N501Y.V2 lineages rapidly replaced the original strain, suggesting the mutations of these variants may be related to increased transmissibility. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 N501Y;N501Y 11;24 16;29 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Since December 2020, emergence of new SARS-CoV-2 variants N501Y.V1 (also known as B.1.1.7) in the United Kingdom and N501Y.V2 (also known as B.1.351) in South Africa aroused widespread concern because of their extensive mutations and enhanced transmissibility. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 N501Y;N501Y 58;117 63;122 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Studies show that the D614G substitution leads to the enhancement of viral replication and infectivity in human lung epithelial cells. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G 22 27 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. The SARS-CoV-2 N501Y.V1 lineage has 17 non-synonymous mutations and deletions, and many of them locate in the S protein. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 N501Y 15 20 S 110 111 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. We investigated the infectivity, S protein cleavage, thermal stability and drug inhibition properties of N501Y.V1 and N501Y.V2 pseudoviruses. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 N501Y;N501Y 105;118 110;123 S 33 34 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. In our current study, the AGM intranasal model of SARS-CoV-2 infection was used to assess differences between a contemporary progenitor SARS-CoV-2 variant (D614G), which was circulating in the summer of 2020, and the B.1.1.7 (Alpha) VOC that emerged from the D614G variant in the UK in late 2020. 2021 Emerging microbes & infections Introduction SARS_CoV_2 D614G;D614G 259;156 264;161 COVID-19 50 70 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. These variants were selected for direct comparison as they represent the two dominant SARS-CoV-2 variants circulating worldwide in late 2020 (D614G) and early 2021 (B.1.1.7). 2021 Emerging microbes & infections Introduction SARS_CoV_2 D614G 142 147 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Additionally, structural analysis of mutations (L452R and E484Q) in RBD and furin cleavage site (P681R) revealed increased ACE2 binding and cleavage rate resulting in increased transmissibility. 2021 Journal of medical virology Introduction SARS_CoV_2 E484Q;L452R;P681R 58;48;97 63;53;102 RBD 68 71 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Additionally, the beta and gamma variants may provide an immune escape mechanism from antibodies due to E484K mutation in the spike protein. 2021 Journal of medical virology Introduction SARS_CoV_2 E484K 104 109 S 126 131 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Interestingly, the gamma and beta lineages share three common mutations (K417N/T, E484K, and N501Y) in spike protein. 2021 Journal of medical virology Introduction SARS_CoV_2 E484K;N501Y;K417N;K417T 82;93;73;73 87;98;80;80 S 103 108 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Its sub-lineage, B.1.617.1, is defined by the presence of a constellation of mutations, L452R, P681R, and E484Q in the spike region, whereas B.1.617.2 is characterized by following spike mutations: L452R, P681R, and T478K. 2021 Journal of medical virology Introduction SARS_CoV_2 E484Q;L452R;L452R;P681R;P681R;T478K 106;88;198;95;205;216 111;93;203;100;210;221 S;S 119;181 124;186 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. The beta variant was first reported in South Africa in December, 2020 and is characterized by seven different lineage-defining mutations in the spike protein, with three significant mutations (N501Y, E484K, and K417N) in the receptor-binding domain (RBD). 2021 Journal of medical virology Introduction SARS_CoV_2 E484K;K417N;N501Y 200;211;193 205;216;198 S;RBD 144;250 149;253 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. The gamma variant was first detected in Manaus, Brazil in November, 2020 with the following lineage-defining mutations: E484K, K417T, and N501Y. 2021 Journal of medical virology Introduction SARS_CoV_2 E484K;K417T;N501Y 120;127;138 125;132;143 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. The K417N/T, E484K, and N501Y mutations significantly decreased the neutralizing activity of convalescent and messenger RNA vaccine-induced serum. 2021 Journal of medical virology Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 13;4;4;24 18;11;11;29 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. The RBD mutations enhance infectivity due to the presence of L452R and T478K by increasing the spike protein's affinity for human ACE2 receptor. 2021 Journal of medical virology Introduction SARS_CoV_2 L452R;T478K 61;71 66;76 S;RBD 95;4 100;7 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. There is an evidence that strains with N501Y substitution have increased transmissibility due to enhanced binding affinity with human angiotensin-converting enzyme 2 (ACE2) as determined by deep mutation scanning in a mouse model. 2021 Journal of medical virology Introduction SARS_CoV_2 N501Y 39 44 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. According to the new labels, VOCs Alpha, Beta, Gamma, and Delta correspond to, respectively, lineages B.1.1.7 (and B.1.1.7+E484K), B.1.351, P.1, and B.1.617.2. 2021 Microbial genomics Introduction SARS_CoV_2 E484K 123 128 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. Although the mutation V1176F it is not described by the WHO as a substitution of interest, its presence in the P.2 variant, and possibly in other variants under monitoring, has been drawing attention, since it interferes in the HR2 region of the spike, and may favour entry of the virus into the cell. 2021 Microbial genomics Introduction SARS_CoV_2 V1176F 22 28 S 246 251 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. Among them, the variants P.1 and P.2, first isolated in Brazil possess substitutions of interest in the S protein, including K417T, E484K, N501Y, D614G, and H655Y. 2021 Microbial genomics Introduction SARS_CoV_2 D614G;E484K;H655Y;K417T;N501Y 146;132;157;125;139 151;137;162;130;144 S 104 105 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. The most frequent substitutions identified have been described globally, such as the G614-carrying virus and V1176F, enhancing viral transmissibility and infectivity. 2021 Microbial genomics Introduction SARS_CoV_2 V1176F 109 115 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. Similarly, some mutations, such as S197L, S194L, and a 382-nucleotide deletion, were associated with clinical outcomes. 2021 Frontiers in microbiology Introduction SARS_CoV_2 S194L;S197L 42;35 47;40 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. suggested that the presence of P25L in ORF3a was a probable mechanism of immune evasion and likely contributes to enhanced virulence, which was associated with higher case fatality rates in SARS-CoV-2 infection. 2021 Frontiers in microbiology Introduction SARS_CoV_2 P25L 31 35 ORF3a 39 44 COVID-19 190 210 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. The D614G variant in the S glycoprotein was associated with increased transmissibility, infectivity, and viral loads but not with disease severity. 2021 Frontiers in microbiology Introduction SARS_CoV_2 D614G 4 9 S 25 39 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. The D614G mutation in the S protein was among the first identified in the early phase of the pandemic that became prevalent globally with increased infectivity. 2022 Glycobiology Introduction SARS_CoV_2 D614G 4 9 S 26 27 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. We found that the mutations of the D614G and Alpha variants did not impact significantly on the gross site-specific glycosylation pattern, consistent with no major change in the 3D conformation of their trimeric spike proteins as determined by cryo-EM, except for different proportion of their receptor-binding domains (RBD) found in either an open and upward or down and closed conformation. 2022 Glycobiology Introduction SARS_CoV_2 D614G 35 40 S;RBD 212;320 217;323 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. Additionally, mutations L452R and T478K, present in the delta variant (B.1.617.2), were also simulated in the RBD to compute the binding energy with the ACE2. 2021 Scientific reports Introduction SARS_CoV_2 L452R;T478K 24;34 29;39 RBD 110 113 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. We benchmarked five hNAbs (two in Classes I and II and one in Class III) with the RBD, including three mutations N501Y (MT1), E484K, and N501Y (MT2), and K417N, E484K, and N501Y (MT3). 2021 Scientific reports Introduction SARS_CoV_2 E484K;E484K;K417N;N501Y;N501Y;N501Y 126;161;154;113;137;172 131;166;159;118;142;177 RBD 82 85 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. Additional SARS-CoV-2 variants have emerged as descendants of this D614G strain, including B.1.1.7 (identified in the United Kingdom), B.1.351 (identified in South Africa), P.1 (prevalent in Brazil), and B.1.1.248 (identified in travelers to Japan from Brazil). 2021 iScience Introduction SARS_CoV_2 D614G 67 72 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. Shortly after the beginning of the COVID-19 pandemic, a SARS-CoV-2 strain with a D614G alteration in the S glycoprotein arose that exhibited greater S stability and infectivity than the original virus from Wuhan, China. 2021 iScience Introduction SARS_CoV_2 D614G 81 86 S;S 105;149 119;150 COVID-19 35 43 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The D614G variant quickly became globally dominant. 2021 iScience Introduction SARS_CoV_2 D614G 4 9 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. In this study, we demonstrate that the Y453F mutation in the miSARS-CoV-2 spike is an adaptive mutation that increases interaction with mink ACE2 without compromising utilization of human ACE2. 2021 PLoS pathogens Introduction SARS_CoV_2 Y453F 39 44 S 74 79 34753092 RT-qPCR assays for SARS-CoV-2 variants of concern in wastewater reveals compromised vaccination-induced immunity. First evidence for such an evolutionary event for the SARS-CoV-2 virus occurred in April 2020, when the D614G substitution enhanced infectivity and transmission. 2021 Water research Introduction SARS_CoV_2 D614G 104 109 34753092 RT-qPCR assays for SARS-CoV-2 variants of concern in wastewater reveals compromised vaccination-induced immunity. The D614G mutation lineage became the dominant SARS-CoV-2 variant form. 2021 Water research Introduction SARS_CoV_2 D614G 4 9 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. A variant that carries D614G mutation in the spike protein of the virus, also known as G clade or B.1, was diagnosed during the early days of the pandemic in the north of America, and then reported in many European countries. 2022 Gene reports Introduction SARS_CoV_2 D614G 23 28 S 45 50 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. Another variant possesses N439K mutation in the receptor-binding domain (RBD) of spike protein has also been reported independently in many countries in Europe and the USA. 2022 Gene reports Introduction SARS_CoV_2 N439K 26 31 S;RBD 81;73 86;76 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. Beta variant (B.1.351) lineage is another variant of concern (VOC), which was first reported in South Africa in October 2020, and characterized by eight mutations in the spike protein region, including K417N, E484K, and N501Y. 2022 Gene reports Introduction SARS_CoV_2 E484K;K417N;N501Y 209;202;220 214;207;225 S 170 175 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. The N439K variant has shown to have increased pathogenicity and can escape from neutralizing monoclonal antibodies and reducing the activities of some polyclonal responses. 2022 Gene reports Introduction SARS_CoV_2 N439K 4 9 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. The variant is characterized by having a deletion in the amino acid position of 69/70 (nucleotide number: 21765-21770), and 17 mutations in the total viral genome including N501Y in the receptor-binding domain of spike protein. 2022 Gene reports Introduction SARS_CoV_2 N501Y 173 178 S 213 218 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. There are other variants, such as P.1 (Gamma) lineage (20J/501Y.V3) which is mainly spread in Brazil, carrying 17 mutations; three of them are located in the spike protein regions (K417T, E484K, and N501Y). 2022 Gene reports Introduction SARS_CoV_2 E484K;N501Y;K417T 188;199;181 193;204;186 S 158 163 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. This variant is characterized by having several mutations in the spike proteins including L452R, T478K and P681R. 2022 Gene reports Introduction SARS_CoV_2 L452R;P681R;T478K 90;107;97 95;112;102 S 65 70 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. A research report supported the chances that the D614G nucleotide substitution confers higher infectivity and transmissibility without better binding affinities to ACE2 receptors or over increased escape of immune surveillance mechanisms (Cheng et al.). 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 49 54 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. A SARS-CoV-2 pp assay (spike-pseudotyped particle) was conducted to examine the chances of immune escape due to the emergence of the D614G mutation, which insinuated the neutralizing effect of the antibodies against this mutation. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 133 138 S 23 28 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Although the D614G mutation site is distant from the RBD, it still alters activity in the mutant variants. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 13 18 RBD 53 56 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Another extremely virulent strain with the presence of D614G mutation is B.1.1.7, and it was first reported in the UK (Peters et al.). 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 55 60 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Association of D614G in B.1.526 (iota) variant. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 15 20 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. At the same time, to illustrate the molecular mechanism of action of D614G mutant variants, we have presented some essential points which are first, D614G mutant and RBD conformation; second, S-protein cleavage pattern and D614G mutation; third, S-protein stability and D614G mutation; fourth, D614G mutation and S-protein volume; and fifth, D614G mutation activity on human ACE2 receptor protein. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G;D614G;D614G;D614G;D614G;D614G 69;149;223;270;294;342 74;154;228;275;299;347 RBD;S;S;S 166;192;246;313 169;193;247;314 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. D614G in the spike protein outside the RBD is also present (Harvey et al.; Wang et al.). 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 0 5 S;RBD 13;39 18;42 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. D614G mutation and human ACE2 receptor protein. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 0 5 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. D614G mutation and infectivity. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 0 5 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. D614G mutation and S-protein volume. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 0 5 S 19 20 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Due to the prevalence of the D614G mutation, there is an alteration in the RBD conformation, maintaining it in an open state and an increased affinity of the variant towards the ACE2 receptor contributes to its high transmission rate. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 29 34 RBD 75 78 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Effect of D614G in B.1.351 (beta) variant. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 10 15 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. experimented with the binding affinity of the ACE2 receptor and concluded that the D614G variant has a greater binding affinity than the wild-type strain. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 83 88 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Explaining the mechanism of higher infectivity by D614G mutation containing SARS-CoV-2 virus is critical to understanding the prevalence for developing an effective treatment approach for virus-infected patients. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 50 55 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. have investigated the structural stability of the spike protein in the D614G mutation using some in silico approaches and concluded that the replacement of the aspartic acid residue with glycine decreases the entropy and energy of the mutant strain compared to the wild type. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 71 76 S 50 55 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. However, the D614G mutation also accelerates the spike protein cleavage into S1 and S2 domains, hindering the contact between the separate chains of the spike protein complex. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 13 18 S;S 49;153 54;158 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Immune escape and D614G. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 18 23 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Impact of D614G in B.1.427/B.1.429 (epsilon) variant. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 10 15 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Implication of D614G in B.1.1.7 (alpha) variant. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 15 20 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Importance of D614G in P.1 (gamma) variant. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 14 19 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Importance of D614G in P.2 (zeta) variant. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 14 19 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. In this manuscript, we have discussed the D614G mutation using different points, such as the distribution of D614G mutation in all significant variants of this virus. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G;D614G 42;109 47;114 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. It has been reported that the D614G mutation does not possess greater severity of the disease, but it enhances viral fitness (Korber et al.; Zhang et al.). 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 30 35 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. It is also essential that multiple characteristic changes are observed in SARS-CoV-2 variants due to the D614G mutant (Table 1). 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 105 110 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. It shows a greater transmissibility rate and virulence, a common characteristic of the D614G mutation. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 87 92 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Mansbach and his colleagues have performed molecular dynamics simulation highlighting the D614G results in an open conformation of the RBD. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 90 95 RBD 135 138 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Molecular mechanism of action of D614G mutant variants. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 33 38 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Moreover, the increased volume of the spike glycoprotein in the D614G mutation gives it additional characteristic features, including transmissibility, virulence, antigenicity, immune escape, and partial vaccine escape. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 64 69 S 38 56 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Moreover, we have discussed the D614G mutation that helps in the infectivity and re-infectivity. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 32 37 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Notwithstanding the fact, we can conclude by seeing the characteristics of this variant that the D614G spike mutation plays a potential role in dominating these characteristics in this variant. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 97 102 S 103 108 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Partial vaccine escape and D614G. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 27 32 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. RBD conformation and D614G mutation. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 21 26 RBD 0 3 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. reported that the D614G alters the conformation of the spike glycoprotein towards an open state. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 18 23 S 55 73 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. S-protein cleavage pattern and D614G mutation. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 31 36 S 0 1 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. S-protein stability and D614G mutation. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 24 29 S 0 1 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Significance of D614G in B.1.525 (eta) variant. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 16 21 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The alteration and interaction of spike protein with antibodies suggest that the D614G mutation may elevate, drop, or bring no change in the neutralization effect as it is entirely controlled by the nature of the neutralizing antibody (Kwarteng et al.). 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 81 86 S 34 39 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The B.1.427 has a single mutation in the trimeric spike complex, namely, D614G, and it falls under the VOC category by the CDC and VOI by the WHO. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 73 78 S 50 55 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The B.1.429 variant had some other mutations in the spike protein besides D614G. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 74 79 S 52 57 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The D614G mutation does not increase the binding efficiency of the spike protein with the ACE2 receptor. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 4 9 S 67 72 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The D614G mutation in B.1.351 variant also alters its binding affinity with hACE2 (human angiotensin-converting enzyme 2) and brings about some changes in antibody neutralization (Zhou et al.). 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 4 9 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The D614G mutation in the S-protein is predominant in the virus inhabiting the upper respiratory tract. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 4 9 S 26 27 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The D614G mutation in the spike protein increases the host-invading capability of the virus due to the strong binding with the ACE2 receptor. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 4 9 S 26 31 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The D614G mutation results in forming a structural cavity between S1 and S2 interface in B.1.1.7 variant, contributing to its high transmission efficiency. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 4 9 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The D614G mutation site also serves as an effective tool for designing vaccines against B.1.1.7 strain with a very high transmissibility rate (Ostrov). 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 4 9 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The direct effect of the D614G mutation is yet to be explored. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 25 30 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The elucidated molecular mechanism lying behind the D614G mutation is yet to be explored. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 52 57 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The molecular mechanism of action of D614G mutant variants is illustrated very extensively. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 37 42 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The open-up conformation of the RBD in the D614G mutant strain contributes to its enhanced transmissibility into the host cells (Korber et al.). 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 43 48 RBD 32 35 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The presence of D614G far and wide. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 16 21 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The S-protein cleavage in the D614G strain interferes with the confirmation of the RBD, resulting in reduced shedding of the S1 subunit. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 30 35 RBD;S 83;4 86;5 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The site of the D614G mutation is situated in the carboxy-terminal of the S1 domain, which belongs to the exterior region of the RBD (Ogawa et al.). 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 16 21 RBD 129 132 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The zeta variant has few mutations, and D614G in the S-protein outside the RBD is common among them (Chakraborty et al.). 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 40 45 RBD;S 75;53 78;54 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. These are some of the standard features possessed by the D614G variant. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 57 62 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. These variants originating from a different country of SARS-CoV-2 have shown the sequence similarity of S-protein, which contains D614G mutation (Table 3). 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 130 135 S 104 105 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. This mutation also reduces the intermolecular attraction between the two subunits (S1 and S2) of the D614G strain. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 101 106 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. This strain also possesses several mutations, notably in the S-protein, of which D614G is common. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 81 86 S 61 62 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. This variant includes several mutations, including D614G. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 51 56 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. This, in turn, also contributes to the increase in S-glycoprotein stability in the D614G mutation (Mahmoudi Gomari et al.). 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 83 88 S 51 65 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Two patients in Iran were reinfected with the virus, and the genome sequencing results indicated the D614G mutation. 2021 Applied microbiology and biotechnology Introduction SARS_CoV_2 D614G 101 106 34755818 SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil. A novel variant of the virus emerged at the end of January 2020 in lineage B.1 presented the spike protein substitution D614G. 2021 Memorias do Instituto Oswaldo Cruz Introduction SARS_CoV_2 D614G 120 125 S 93 98 34755818 SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil. The lineage N.9 is also considered a potential VOI due to the presence of E484K amino acid substitution at the receptor-binding domain (RBD) of the Spike (S) protein. 2021 Memorias do Instituto Oswaldo Cruz Introduction SARS_CoV_2 E484K 74 79 S;RBD;S 148;136;155 153;139;156 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. Other prominent outbreaks included the Pesantren cluster in April that was linked to Malaysian students returning from a religious school in East Java, Indonesia, and the Sivaganga cluster in July-August that was traced to a Malaysian who returned from India carrying the D614G variant. 2021 PeerJ Introduction SARS_CoV_2 D614G 272 277 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. The best known variants with global spread since their introduction include the UK variant B.1.1.7 N501Y that has been shown to have higher transmissibility and risk of death than the wild-type virus, the S. 2021 PeerJ Introduction SARS_CoV_2 N501Y 99 104 S 205 206 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. Up to April 2021, five infections by B.1.1.7 N501Y and 21 by B.1.351 20H/501Y.V2 were reported by the Ministry of Health, Malaysia. 2021 PeerJ Introduction SARS_CoV_2 N501Y 45 50 34760721 Host Response to SARS-CoV2 and Emerging Variants in Pre-Existing Liver and Gastrointestinal Diseases. Additionally, this variant has P681R and L452R mutations in the RBD region, with L452R also present in B.1.427/B.1.429 variants found in California, USA, which have been associated with increased transmissibility of virus. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 L452R;L452R;P681R 41;81;31 46;86;36 RBD 64 67 34760721 Host Response to SARS-CoV2 and Emerging Variants in Pre-Existing Liver and Gastrointestinal Diseases. As of May 2021, three sublineages have been detected for this variant (B.1.617.1/2/3) with B.1.617.2 being the most dominant, having a unique T478K mutation absent in sublineages 1 and 3, serving as a possible route of immune evasion. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 T478K 142 147 34760721 Host Response to SARS-CoV2 and Emerging Variants in Pre-Existing Liver and Gastrointestinal Diseases. Further, L clade evolved to V (G11083T, G26144T, NSP6-L37F + NS3-G251V) and G (C241T, C3037T, A23403G, and S-D614G); and later G clade evolved into GH (C241T, C3037T, A23403G, G25563T includes S-D614G + NS3-Q57H), GR (C241T, C3037T, A23403G, G28882A includes S-D614G + N-G204R), GV (C241T, C3037T, A23403G, C22227T includes S-D614G + S-A222V), and GK. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 A23403G;A23403G;A23403G;A23403G;C22227T;C3037T;C3037T;C3037T;C3037T;G25563T;G26144T;G28882A;C241T;C241T;C241T;C241T;G11083T;A222V;D614G;D614G;D614G;D614G;G204R;G251V;L37F;Q57H 94;167;233;298;307;86;159;225;290;176;40;242;79;152;218;283;31;336;109;195;261;326;271;65;54;207 101;174;240;305;314;92;165;231;296;183;47;249;84;157;223;288;38;341;114;200;266;331;276;70;58;211 Nsp6;NS3;NS3;N;S;S;S;S;S 49;61;203;269;107;193;259;324;334 53;64;206;270;108;194;260;325;335 34760721 Host Response to SARS-CoV2 and Emerging Variants in Pre-Existing Liver and Gastrointestinal Diseases. It is important to note that the E484K mutation, termed as "escape mutation," which partially aids the virus to evade host immunity, is acquired either through natural infection or vaccines. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 E484K 33 38 34760721 Host Response to SARS-CoV2 and Emerging Variants in Pre-Existing Liver and Gastrointestinal Diseases. Lineage-A variants mostly harbor two unique mutations (8782 C>T and 28144 T>C), which are absent in Lineage-B variants. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 T28144C;C8782T 68;55 77;63 34760721 Host Response to SARS-CoV2 and Emerging Variants in Pre-Existing Liver and Gastrointestinal Diseases. Recently, GR into GRY (C241T,C3037T, 21765-21770del, 21991-21993del, A23063T, A23403G, G28882A includes S-H69del, S-V70del, S-Y144del, S-N501Y + S-D614G + N-G204R) along with GK. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 A23063T;A23403G;G28882A;V70del;Y144del;C241T;C3037T;D614G;G204R;H69del;N501Y 69;78;87;115;125;23;29;147;157;106;137 76;85;94;122;133;28;35;152;162;112;142 N;S;S;S;S;S 155;104;114;124;135;145 156;105;115;125;136;146 34760721 Host Response to SARS-CoV2 and Emerging Variants in Pre-Existing Liver and Gastrointestinal Diseases. Similar to E484K, another probable escape mutation, E484Q, has been observed in the delta variant (B.1.617, G/452R.V3) currently dominant in India and detected in more than 50 other nations. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 E484K;E484Q 11;52 16;57 34760721 Host Response to SARS-CoV2 and Emerging Variants in Pre-Existing Liver and Gastrointestinal Diseases. The early splits of phylogenetic clades were S (marker C8782T, T28144C and NS8-L84S) and L (C241, C3037, A23403, C8782, G11083, G26144, T28144). 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 C8782T;T28144C;L84S 55;63;79 61;70;83 S 45 46 34760721 Host Response to SARS-CoV2 and Emerging Variants in Pre-Existing Liver and Gastrointestinal Diseases. The emerging variants with D614G aa substitution in the spike protein are now dominant and circulating globally. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G 27 32 S 56 61 34760721 Host Response to SARS-CoV2 and Emerging Variants in Pre-Existing Liver and Gastrointestinal Diseases. The variants with D614G substitution do not cause severe illness but alter its infectivity, competitive fitness, and transmission as evident from laboratory studies. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G 18 23 34760721 Host Response to SARS-CoV2 and Emerging Variants in Pre-Existing Liver and Gastrointestinal Diseases. This variant of B.1.1.7 lineage harbors receptor-binding domain (RBD) N501Y mutation and other mutations including 69/70 deletion, spike P681H, and ORF8 stop codon (Q27stop) mutation.The beta variant (20H/501Y.V2) of B.1.351 lineage harbors spike N501Y, E484K, and K417N/T mutations without 69/70 deletion and is predicted to have emerged in South Africa during October 2020 with potential of global spread. 2021 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y;N501Y;P681H;Q27X 254;265;265;70;247;137;165 259;272;272;75;252;142;172 S;S;ORF8;RBD 131;241;148;65 136;246;152;68 34763050 Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation. Both lineages exhibit the E484K mutation and descendant of the B.1.1.28 strain . 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K 26 31 34766651 SARS-CoV-2 AY.4.2 variant circulating in Italy: Genomic preliminary insight. This new subvariant of the virus is distinguished by two mutations in its spike protein, called Y145H and A222V and it has been suggested that it might be 10%-15% more transmissible than the original strain. 2022 Journal of medical virology Introduction SARS_CoV_2 A222V;Y145H 106;96 111;101 S 74 79 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Additional mutations have been detected in the RBD, including the alpha/beta/gamma [N501Y]; [Y453F], the Mink mutation; and the beta [E484K]. 2021 Scientific reports Introduction SARS_CoV_2 E484K;N501Y;Y453F 134;84;93 139;89;98 RBD 47 50 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. The beta [E484K] mutation contributes to recent COVID-19 outbreaks in India in the B.1.116 lineage, and in Brazil as variants P.1 and P.2 within the B.1.1.33 lineage. 2021 Scientific reports Introduction SARS_CoV_2 E484K 10 15 COVID-19 48 56 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Using the WHO nomenclature, examples of such mutations in the spike include the mutation at residue 614, alpha/beta/gamma [D614G]. 2021 Scientific reports Introduction SARS_CoV_2 D614G 123 128 S 62 67 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. However, Val35Thr, Ser46Ala, Asn65Ser, Ala94Ser mutations were not included in the previous analysis, since they are located far from the catalytic tetrad. 2021 International journal of biological macromolecules Introduction SARS_CoV_2 A94S;N65S;S46A;V35T 39;29;19;9 47;37;27;17 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. In SARS-CoV 3CLpro, leucine replaces valine at position 86. 2021 International journal of biological macromolecules Introduction SARS_CoV_2 L86V 20 58 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. It was also found that the Val86Leu, Lys88Arg, Phe134His, and Asn180Lys mutations in these enzymes can change the orientation of the N- and C-terminal domains of 3CLpro relative to each other, which leads to a change in catalytic activity. 2021 International journal of biological macromolecules Introduction SARS_CoV_2 N180K;K88R;F134H;V86L 62;37;47;27 71;45;56;35 N 133 134 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. The inclusion of the four amino acids of the 102T-Core in the SCC composition made it possible to reveal one more important difference between the 3CLpro of SARS-CoV-2 and SARS-CoV: Lys88Arg. 2021 International journal of biological macromolecules Introduction SARS_CoV_2 K88R 182 190 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. The S-Core from the 3CLpro of SARS-CoV-2 and SARS-CoV are characterized by two amino acid differences: Phe134His and Asn180Lys. 2021 International journal of biological macromolecules Introduction SARS_CoV_2 N180K;F134H 117;103 126;112 S 4 5 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. These two viral proteases differ in their amino acid sequence at 12 positions: Thr35Val, Ala46Ser, Ser65Asn, Leu86Val, Arg88Lys, Ser94Ala, His134Phe, Lys180Asn, Leu202Val, Ala267Ser, Thr285Ala and Ile286Leu. 2021 International journal of biological macromolecules Introduction SARS_CoV_2 A267S;A46S;R88K;H134F;I286L;L202V;L86V;K180N;S65N;S94A;T285A;T35V 172;89;119;139;197;161;109;150;99;129;183;79 181;97;127;148;206;170;117;159;107;137;192;87 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. For this reason, it was proposed for lineage reassignment (B.1+L249S+E484K) and laboratory evaluation of neutralizing antibodies. 2022 Virus research Introduction SARS_CoV_2 E484K;L249S 69;63 74;68 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. In fact, the E484K mutation is a significant genetic marker, and its presence is considered enough to qualify a variant for VOI status. 2022 Virus research Introduction SARS_CoV_2 E484K 13 18 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. In February 2020, in the early stages of the pandemic, the B.1 lineage emerged in Europe with the characteristic D614G mutation in the S protein, which distinguishes it from the A and B ancestral lineages. 2022 Virus research Introduction SARS_CoV_2 D614G 113 118 S 135 136 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. In line with this, SARS-CoV-2 genomic surveillance at Colombia's National Institute of Health (INS), identified a highly divergent SARS-CoV-2 lineage characterized by the presence of 21 substitutions, including two amino acid changes in the S protein (L249S and E484K). 2022 Virus research Introduction SARS_CoV_2 E484K;L249S 262;252 267;257 S 241 242 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Later, the E484K mutation in the S protein emerged independently in different VOI and VOC, probably by evolutionary convergence (; "SARS-CoV-2 variants of concern as of 6 September 2021," n.d.) and was associated with reduced antibody neutralization, antiviral drug resistance (") and a slightly enhancing of ACE2 affinity (C et al., 2021). 2022 Virus research Introduction SARS_CoV_2 E484K 11 16 S 33 34 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Thus, in this work, we determined the neutralizing antibody titers in convalescent sera against B.1+L249S+E484K and three lineages (A.1, B.1.420, and B.1.111) without the E484K mutation using microneutralization assays to evaluate the potential impact of the E484K mutation in this new lineage on the sensitivity to convalescent neutralizing antibodies. 2022 Virus research Introduction SARS_CoV_2 E484K;E484K;E484K;L249S 171;259;106;100 176;264;111;105 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. An important mutation in the ACE2-binding domain is N501Y, which has been observed in the UK/Kent (B.1.1.7; N501Y.V1), South Africa (B.1.351; N501Y.V2), and Brazilian (B.1.1.28; P1; N501Y.V3) spike protein variants, generating the explanation of variants of concern and suggestion for lineage-specific surveillance. 2022 Journal of cellular biochemistry Introduction SARS_CoV_2 N501Y;N501Y;N501Y;N501Y 52;108;142;182 57;113;147;187 S 192 197 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Examination of other variants carrying the N501Y mutation, such as B.1.351 and B.1.1.28, have shown that the ability to escape from neutralizing antibodies responses increases in these lineages. 2022 Journal of cellular biochemistry Introduction SARS_CoV_2 N501Y 43 48 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. In addition to characterized lineages, the prevalence of unknown mutants of SARS-CoV-2 carrying the N501Y has been reported and raised concerns. 2022 Journal of cellular biochemistry Introduction SARS_CoV_2 N501Y 100 105 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. in an investigation that evaluated the transmission capability of the B.1.1.7 variant, they realized that N501Y substitution is the main factor in increasing the rate of transmission and spike affinity to its receptor. 2022 Journal of cellular biochemistry Introduction SARS_CoV_2 N501Y 106 111 S 187 192 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Regarding the importance of the N501Y mutation in the spike protein biological behavior, our group studied the structural characteristics of this variant using computational biology and structural bioinformatics approaches, such as immunoinformatics, docking, molecular dynamics (MD), and free energy computations. 2022 Journal of cellular biochemistry Introduction SARS_CoV_2 N501Y 32 37 S 54 59 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. SARS-CoV-2 linages that introduced K417N/E484K/N501Y spike mutations show a greater transmission and infectivity potency compared to the native form. 2022 Journal of cellular biochemistry Introduction SARS_CoV_2 K417N;E484K;N501Y 35;41;47 40;46;52 S 53 58 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. So far, many studies have evaluated the biological consequences of the N501Y mutation in SARS-CoV-2 behavior. 2022 Journal of cellular biochemistry Introduction SARS_CoV_2 N501Y 71 76 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. In this work, we applied the CRISPR-Cas12a system, in combination with reverse transcription polymerase chain reaction (RT-PCR), to identify infections caused by variants that harbor the E484K mutation without the need of sequencing. 2021 ACS synthetic biology Introduction SARS_CoV_2 E484K 187 192 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. One mutation in SARS-CoV-2 that has gained attention is E484K, a substitution of a glutamic acid by a lysine in the receptor-binding domain of the spike protein (at the position 484 of the protein). 2021 ACS synthetic biology Introduction SARS_CoV_2 E484K 56 61 S 147 152 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. The E484K mutation is an innovation that seems to be associated with an increased transmissibility and also with an escape from neutralizing antibodies. 2021 ACS synthetic biology Introduction SARS_CoV_2 E484K 4 9 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. Although we find steep increases in variants harboring E484K and N501Y among community samples, our early genomic assessment does not indicate specific variant enrichment among postvaccinated individuals. 2021 Microbiology spectrum Introduction SARS_CoV_2 E484K;N501Y 55;65 60;70 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. The mapping of specific mutations in the spike protein has revealed strong evidence of convergent evolution and particularly the E484K polymorphism, which is able to evade certain monoclonal therapy and is less responsive to neutralizing antibodies from recovered patients. 2021 Microbiology spectrum Introduction SARS_CoV_2 E484K 129 134 S 41 46 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. A mutation in the E gene (C26340T) has also been reported, resulting in failure to amplify this target in the cobas SARS-CoV-2 assay (cobas) (Roche, Basel, Switzerland). 2021 Microbiology spectrum Introduction SARS_CoV_2 C26340T 26 33 E 18 19 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. The first mutation, C29200T, was found in eight patients, and the second, C29197T, was found in five patients. 2021 Microbiology spectrum Introduction SARS_CoV_2 C29197T;C29200T 74;20 81;27 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. To date, three independent single-point mutations (C29200T, C29200A, and C29197T) in the N gene of the SARS-CoV-2 genome have been associated with failure to amplify the N2 gene target in the Xpert assay. 2021 Microbiology spectrum Introduction SARS_CoV_2 C29197T;C29200A;C29200T 73;60;51 80;67;58 N 89 90 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. Furthermore, N501Y mutation on the receptor binding domain (RBD) of SARS-CoV-2 S protein is associated with increased binding affinity to angiotensin-converting enzyme 2 (ACE2) receptor. 2021 Microbiology spectrum Introduction SARS_CoV_2 N501Y 13 18 RBD;RBD;S 35;60;79 58;63;80 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. have recently reported a multiplex SARS-CoV-2 genotyping assay by using reverse transcription-PCR (RT-PCR) to screen three mutations (L452R, E484K, and N501Y) in the S protein. 2021 Microbiology spectrum Introduction SARS_CoV_2 E484K;N501Y;L452R 141;152;134 146;157;139 S 166 167 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. It has been reported that D614G substitution in the S protein can affect viral infectivity and antigenicity. 2021 Microbiology spectrum Introduction SARS_CoV_2 D614G 26 31 S 52 53 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. It has been reported that variants with the deletion of amino acids Delta69 and 70 and K417N and E484K mutations in the SARS-CoV-2 S protein are linked to immune response evasion. 2021 Microbiology spectrum Introduction SARS_CoV_2 E484K;K417N 97;87 102;92 S 131 132 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. However, the number of people infected with the VOC Gamma (P.1), a ramification of the B.1.1.28 lineage first detected in Manaus (northern Brazil) that harbors the E484K and N501Y mutations in the spike (S) protein, has grown rapidly since December 2020 and was thought to be responsible for the deadly second wave of COVID 19 throughout Brazil. 2021 Virology journal Introduction SARS_CoV_2 E484K;N501Y 164;174 169;179 S;S 197;204 202;205 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. Notably, a new S:E661D mutation present in approximately 10% of the VOC Gamma genomes from March and April 2021 was identified. 2021 Virology journal Introduction SARS_CoV_2 E661D 17 22 S 15 16 34790342 On the association between SARS-COV-2 variants and COVID-19 mortality during the second wave of the pandemic in Europe. Besides newly identified mutations, it cannot be ignored that SARS-COV-2 variants developed during the first wave, such as 20A (mutation S:D614G), developed in February 2020 and dominant during the previous wave, can also have impact on the mortality during the second wave. 2021 Journal of market access & health policy Introduction SARS_CoV_2 D614G 139 144 S 137 138 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. It is likely that this improvement mainly arises from the Met24Leu-mutation present in N02, which removes the only methionine (besides the methionine encoded by the start codon) from the original DARPin sequence, and thereby also removes this hotspot for oxidation. 2022 The Journal of biological chemistry Introduction SARS_CoV_2 M24A;M24Delta;M24I;M24L;M24M;M24N;M24O;M24T;M24U 58;58;58;58;58;58;58;58;58 66;66;66;66;66;66;66;66;66 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. A single point mutation A701V presents in the S2 region that is distinct from SARS-CoV-2 alpha variant. 2021 Immune network Introduction SARS_CoV_2 A701V 24 29 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. Five mutation sites present in NTD with 3 serial deletions at L241del, L242del, and A243del. 2021 Immune network Introduction SARS_CoV_2 A243del;L241del;L242del 84;62;71 91;69;78 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. In addition, T478K mutation site in critical RBD was highlighted by yellow with bolded red letter (Table 1). 2021 Immune network Introduction SARS_CoV_2 T478K 13 18 RBD 45 48 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. Like SARS-CoV-2 beta variant, most mutation sites locate in S1 region of S gene except a single mutation site T1027I in Central helix domain of S2 region. 2021 Immune network Introduction SARS_CoV_2 T1027I 110 116 S 73 74 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. SARS-CoV-2 delta variant shares three common mutation sites, L452R, D614G, and P681R with SARS-CoV-2 kappa and B.1.617.3 variant (Table 1). 2021 Immune network Introduction SARS_CoV_2 D614G;L452R;P681R 68;61;79 73;66;84 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. Surprisingly, three K417T, E484K, and N501Y mutation sites in the critical RBD of S gene are identical to SARS-CoV-2 beta variant except K417 is substituted by T instead of N. 2021 Immune network Introduction SARS_CoV_2 E484K;K417T;N501Y 27;20;38 32;25;43 RBD;N;S 75;173;82 78;174;83 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. The alpha variant has 3 mutations, E484K, S494P, and N501Y in RBD, which is well characterized by protein structure utilizing diverse methods and the rest of mutation sites in S gene presents in functionally uncharacterized domain. 2021 Immune network Introduction SARS_CoV_2 E484K;N501Y;S494P 35;53;42 40;58;47 RBD;S 62;176 65;177 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. The comparison of SARS-CoV-2 delta variant with other variants revealed 3 unique mutation sites, E156del, R158G, and T478K, which were indicated by red letter (Table 1 and. 2021 Immune network Introduction SARS_CoV_2 E156del;R158G;T478K 97;106;117 104;111;122 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. The D614G mutation site exists all four SARS-CoV-2 variants of concern as well as all six SARS-CoV-2 variants of interest and alert. 2021 Immune network Introduction SARS_CoV_2 D614G 4 9 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. The L452R mutation site presents in three SARS-CoV-2 epsilon and iota variants from US. 2021 Immune network Introduction SARS_CoV_2 L452R 4 9 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. Two mutation sites, E484K and N501Y in critical RBD are identical to that of SARS-CoV-2 alpha variant, whereas K417N does not present in SARS-CoV-2 alpha variant. 2021 Immune network Introduction SARS_CoV_2 E484K;K417N;N501Y 20;111;30 25;116;35 RBD 48 51 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Delta VOC harbors several mutations, such as L452R and T478K, being the former associated with an increased transmission potential and reduced susceptibility to protective immunity, both at humoral and cellular level. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 L452R;T478K 45;55 50;60 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Mutation E484K, present in Beta an Gamma VOCs, has been frequently associated with reinfection cases and might reduce the neutralizing activity of antibodies produced by vaccination. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K 9 14 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Mutation N501Y, present in all except the Delta VOC, confers a higher affinity for the cellular ACE2 (Angiotensin-converting Enzyme 2) viral receptor and may be related to an increased transmissibility of VOCs carrying this mutation. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 N501Y 9 14 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Special attention was also paid to mutation E484K alone, in order to analyze its eventual association with cases of reinfection. 2021 Infection, genetics and evolution Introduction SARS_CoV_2 E484K 44 49 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The Iota variant contains the E484K mutation linked to antibody escape in the Beta and Gamma variants, suggesting it may similarly decrease the effectiveness of current vaccines. 2022 Infection, genetics and evolution Introduction SARS_CoV_2 E484K 30 35 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. A cohort study identified a slight reduction of protection by vaccines against subsequent infection with E484K-carrying Alpha and Beta variants of concern. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K 105 110 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. A report has demonstrated that N501Y mutation reduces the virus sensitivity to neutralising monoclonal antibodies and vaccine-induced polyclonal antibodies. 2021 Frontiers in immunology Introduction SARS_CoV_2 N501Y 31 36 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. A report of breakthrough infections in fully or partially vaccinated healthcare workers and a secondary infection with L452R-carrying variants have been described, highlighting the relevance of this mutation in mediating viral immune escape. 2021 Frontiers in immunology Introduction SARS_CoV_2 L452R 119 124 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. Additionally, in silico and cryo-EM studies have found that E484K mutation enhances the virus affinity for host ACE2 receptor binding which may account for the increased infectivity of these mutant variants. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K 60 65 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. Also gaining in frequency among circulating variant sequences is N501Y substitution that has been acquired by three VOCs Alpha, Beta and Gamma. 2021 Frontiers in immunology Introduction SARS_CoV_2 N501Y 65 70 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. Another mutation that has gained attention is L452R substitution which can resist neutralisation by monoclonal antibodies and vaccinee and convalescent sera. 2021 Frontiers in immunology Introduction SARS_CoV_2 L452R 46 51 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. Another report also documented an infection of a vaccinated individual with E484K-carrying variant. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K 76 81 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. D614G mutation is located outside of the RBD (Figure 1). 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 0 5 RBD 41 44 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. D614G variant bypassed natural bottlenecks due to its selective advantages that lead to improved viral infectivity and transmissibility and reduced viral sensitivity to neutralising convalescent sera. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 0 5 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. Downstream P681R mutation in furin cleavage site promotes cleavage and processing of the spike protein and hence the entry efficiency and infectivity of the virus in vitro. 2021 Frontiers in immunology Introduction SARS_CoV_2 P681R 11 16 S 89 94 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. E484K mutation first emerged in late 2020 and has now been gaining prevalence among the circulating strains. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K 0 5 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. Furthermore, several independent reports of breakthrough infections with N501Y-caryying variant had been reported in vaccinated individuals suggesting an evasion of humoral immunity. 2021 Frontiers in immunology Introduction SARS_CoV_2 N501Y 73 78 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. In another study, a full vaccination elicited a high level of neutralising antibodies that were capable of inhibiting an E484K variant in vitro but failed to pre-empt a high viral replication. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K 121 126 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. In contrast, the E484 residue in RBD engages more with antibodies than with ACE2 receptor, which may explain the relevance of E484K mutation in mediating antibody escape. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K 126 131 RBD 33 36 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. In vitro infection assay of murine ACE2-expressing HEK293T cells with N501Y-carrying pseudotyped virus also showed that this mutation caused a 5-fold increase in viral infectivity. 2021 Frontiers in immunology Introduction SARS_CoV_2 N501Y 70 75 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. In vitro studies showed that E484K mutation can significantly reduce binding and resist neutralisation by convalescent and vaccine-induced sera and monoclonal antibodies. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K 29 34 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. It is noteworthy to mention that five reinfection cases of E484K-carrying variants (Gamma and Zeta), which primary infections were of non-E484K variants, have been reported in Brazil as early as December 2020. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K;E484K 59;138 64;143 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. Its impact on infectivity in vitro has been revealed in an infection assay of murine ACE2-expressing HEK29T cells with E484K-carrying pseudotyped viruses whereby 3-fold more infection was observed. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K 119 124 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. L425R mutation has been identified in the circulating VOC Delta and other variants including Epsilon (B.1.427/B.1.429), Iota and Kappa. 2021 Frontiers in immunology Introduction SARS_CoV_2 L425R 0 5 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. N501Y-carrying variants (VOCs Alpha and Gamma) have been reported in four re-infection cases in which primary episode of infection agents were of non-N501Y-carrying variant. 2021 Frontiers in immunology Introduction SARS_CoV_2 N501Y;N501Y 0;150 5;155 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. Other mutations, in addition to L452R of the RBD, have been attributed to its explosive spread. 2021 Frontiers in immunology Introduction SARS_CoV_2 L452R 32 37 RBD 45 48 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. The growing relevance of a select spike mutations urges immediate investigation, particularly E484K, to discern whether it will become the next consensus sequence (as did D614G). 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G;E484K 171;94 176;99 S 34 39 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. The most profound mark of SARS-CoV-2 evolution is perhaps the D614G mutation that emerged as early as 6 months into the outbreak. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 62 67 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. The prevalence of E484K-carrying variants has been increasingly reported in viral isolates, presenting at low frequency in the circulating strain populations, likely due to the positive selection that provides for an immune escape and a greater transmissibility. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K 18 23 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. This is consistent with in vitro evolutionary studies that showed that E484K mutation is readily introduced in the viral genome when cultured in the presence of anti-SARS-CoV-2 neutralising antibodies or ACE2 receptor. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K 71 76 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. This is in agreement with an observation of pseudotyped viruses carrying N501Y mutation demonstrating a higher infectivity in vitro than those carrying E484K mutation. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K;N501Y 152;73 157;78 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. Two of the cases reported the presence of anti-SARS-CoV-2 IgG antibodies during re-infection suggesting the possibility of E484K mutation in aiding antibody evasion. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K 123 128 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. Upstream NTD mutation G142D has been shown to resist binding by monoclonal antibodies which may be mediated by the change of the conformation of the spike protein that deters antibody binding. 2021 Frontiers in immunology Introduction SARS_CoV_2 G142D 22 27 S 149 154 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. While E484K only mildly increases the affinity of the RBD for ACE2 receptor, N501Y appears to substantially enhance it by allowing it to engage the receptor for longer. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K;N501Y 6;77 11;82 RBD 54 57 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. (2020) have recently reported capturing a covalent acyl-enzyme intermediate using native enzyme and a product complex using the inactive C145A mutant. 2021 IUCrJ Introduction SARS_CoV_2 C145A 137 142 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. Based on the crystal structures of the closely related SARS-CoV Mpro inactive mutant H41A in complex with an 11-amino-acid peptide substrate (Xue et al., 2008) and SARS-CoV Mpro inactive mutant C145A containing a ten-residue C-terminal prosequence (Muramatsu et al., 2016), the Mpro active-site cavity located on the protein surface can accommodate up to nine substrate residues in positions P5 through P4' in the corresponding substrate-binding subsites S5 through S4'. 2021 IUCrJ Introduction SARS_CoV_2 C145A;H41A 194;85 199;89 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. This paper reports a room-temperature X-ray crystal structure of SARS-CoV-2 Mpro C145A mutant (Mpro/C145A) in complex with the octapeptide Ac-SAVLQSGF-CONH2 corresponding to the nsp4/nsp5 autocleavage site (henceforth referred to as Mpro/C145A-substrate), at 2.0 A resolution and pH 6.5. 2021 IUCrJ Introduction SARS_CoV_2 C145A;C145A;C145A 81;100;238 86;105;243 Nsp4;Nsp5 178;183 182;187 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. For example, the P.1 lineage detected first in Brazil is characterized by several amino acid (AA) substitutions mostly located either in RBD or in NTD: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, and T1027I, which are shown to reduce neutralization by some antibodies. 2021 ACS omega Introduction SARS_CoV_2 D138Y;E484K;H655Y;K417T;L18F;N501Y;P26S;R190S;T1027I;T20N 170;191;205;184;152;198;164;177;216;158 175;196;210;189;156;203;168;182;222;162 RBD 137 140 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. Here, we have considered prominent spike receptor-binding domain (RBD) mutations that are commonly observed among the VOI/VOC variants (Table 1), namely, E484K, K417N, L452Q, L452R, N501Y, and T478K. 2021 ACS omega Introduction SARS_CoV_2 E484K;K417N;L452Q;L452R;N501Y;T478K 154;161;168;175;182;193 159;166;173;180;187;198 S;RBD 35;66 40;69 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. In particular, the delta variant consisting of the RBD mutation K417N shows a strong long-range modulated allostery, resulting in higher interactions with ACE2. 2021 ACS omega Introduction SARS_CoV_2 K417N 64 69 RBD 51 54 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. Of these, T478K and K417N substitutions in the spike protein make it characteristically different from other VOIs. 2021 ACS omega Introduction SARS_CoV_2 K417N;T478K 20;10 25;15 S 47 52 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. A sub-lineage of Delta with an additional mutation, K417N is termed as AY.1 (Delta-plus). 2021 Current research in structural biology Introduction SARS_CoV_2 K417N 52 57 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Although it did not reveal greater clinical severity, structural features of mutant D614G spike showed interesting characteristics. 2021 Current research in structural biology Introduction SARS_CoV_2 D614G 84 89 S 90 95 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Another variant from South Africa (B.1.351) emerged independently with multiple mutations in the RBD (K417N and E484K) along with N501Y, however, lacked the 69/70 deletion mutations in the NTD segment. 2021 Current research in structural biology Introduction SARS_CoV_2 E484K;N501Y;K417N 112;130;102 117;135;107 RBD 97 100 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Compared to previous variants, the Alpha variant raised concern due to the presence of N501Y mutation in the RBD of the spike protein. 2021 Current research in structural biology Introduction SARS_CoV_2 N501Y 87 92 S;RBD 120;109 125;112 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Early analysis of viral variants revealed a single amino acid substitution D614G, which has now become a widespread dominant variant. 2021 Current research in structural biology Introduction SARS_CoV_2 D614G 75 80 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Extensive molecular dynamics simulations of the D614G mutant spike structure with hACE2 further revealed dynamic features that may play a key role in the conformational ensemble of the spike protein. 2021 Current research in structural biology Introduction SARS_CoV_2 D614G 48 53 S;S 61;185 66;190 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Particularly in spike, this variant emerged with several other mutations like 69/70 deletion and P681H mutation present in the N-terminal domain (NTD) and near S1/S2 site, respectively. 2021 Current research in structural biology Introduction SARS_CoV_2 P681H 97 102 S;N 16;127 21;128 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Recently, a rapidly transmitting variant emerged in India, namely- B.1.617.2 (Delta) with unique RBD mutations E484Q and L452R, two deletions (E156del and F157del) and a substitution (R158G) in the NTD, and 4 other mutations including D614G. 2021 Current research in structural biology Introduction SARS_CoV_2 D614G;E484Q;F157del;L452R;E156del;R158G 235;111;155;121;143;184 240;116;162;126;150;189 RBD 97 100 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. The lineage B.1.526 is classified as a Variant of Interest (VOI) which have multiple spike mutations with unique substitutions L5F, T95I, and, D253G, which were not present earlier in any other lineages. 2021 Current research in structural biology Introduction SARS_CoV_2 D253G;L5F;T95I 143;127;132 148;130;136 S 85 90 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. For instance, the D614G mutation in spike protein was figured out to be increasing in frequency in April 2020 and to have emerged several times globally. 2021 Informatics in medicine unlocked Introduction SARS_CoV_2 D614G 18 23 S 36 41 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. Several studies documented that D614G reveals a moderate benefit to SARS-CoV-2 for infectivity and transmissibility. 2021 Informatics in medicine unlocked Introduction SARS_CoV_2 D614G 32 37 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. In addition to D614G, the Lambda variant contains seven mutation sites in the S protein, including G75 V, T76I, Del246-252, D253N, L452Q, F490S, and T859N. 2022 Emerging microbes & infections Introduction SARS_CoV_2 D253N;D614G;F490S;G75V;L452Q;T76I;T859N 124;15;138;99;131;106;149 129;20;143;104;136;110;154 S 78 79 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. L452Q and F490S are mutationsin antigenic sites recognized by antibodies. 2022 Emerging microbes & infections Introduction SARS_CoV_2 F490S;L452Q 10;0 15;5 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Meanwhile, the F490L mutation is resistant to some neutralizing antibodies, and the F490S mutation may affect the efficiency of existing vaccines. 2022 Emerging microbes & infections Introduction SARS_CoV_2 F490L;F490S 15;84 20;89 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Of the Beta variants, the AY.1 and AY.2 lineages contain a K417N mutation, and the Gamma variant contains a K417 T mutation. 2022 Emerging microbes & infections Introduction SARS_CoV_2 K417T;K417N 108;59 114;64 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Specifically, D614G is the backbone of almost all variants, while N501Y is found in the Alpha, Beta and Gamma variants. 2022 Emerging microbes & infections Introduction SARS_CoV_2 D614G;N501Y 14;66 19;71 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. The L452R mutation found in the Delta, Kappa, and Epsilon variants has been reported to enhance viral infectivity and fusogenicity while promoting viral replication. 2022 Emerging microbes & infections Introduction SARS_CoV_2 L452R 4 9 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. For the B.1.1.7 variant, spike N501Y (A23063T in nucleic acid) is the main mutation point that needs rigorous monitoring. 2021 Analytical chemistry Introduction SARS_CoV_2 N501Y;A23063T 31;38 36;45 S 25 30 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. To solve the shortage of these five pathogen POCT diagnoses, including mutant SARS-CoV-2 spike N501Y, and at the same time develop a universally stable isothermal amplification platform (with low false-positive and high signal-background ratio), we developed a universally stable and precise CRISPR-LAMP detection platform (UCLD). 2021 Analytical chemistry Introduction SARS_CoV_2 N501Y 95 100 S 89 94 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. A large yeast two-hybrid study characterizing the mutational landscape of SARS-CoV-2 RBD indicated that the N501Y residue-change results in increased affinity towards ACE-2. 2021 eLife Introduction SARS_CoV_2 N501Y 108 113 RBD 85 88 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. A not-yet-peer reviewed publication on vaccine breakthrough, found that the N501Y mutation was associated with increased number of breakthrough infections. 2021 eLife Introduction SARS_CoV_2 N501Y 76 81 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Additionally, we present data suggesting a partial decrease in the antibody capacity to neutralize N501Y:ACE-2 interaction in vitro using sera from convalescent individuals (n = 140). 2021 eLife Introduction SARS_CoV_2 N501Y 99 104 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. In the present study, we have performed detailed biophysical characterization of the RBD variants N439K (the most prevalent RBD mutation to date) and N501Y (shared between the B.1.1.7, B.1.351, and P.1), showing that the 1:1 interaction affinity to human ACE-2 is two- and eightfold increased, respectively, compared to the original Wuhan RBD. 2021 eLife Introduction SARS_CoV_2 N439K;N501Y 98;150 103;155 RBD;RBD;RBD 85;124;339 88;127;342 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Some of these residue substitutions, including the N501Y mutation, seem to have arisen independently by convergent evolution and selection and are found in the B.1.1.7 (alpha), the South African B.1.351 (beta), and the Brazilian P.1 (gamma) variants of concern (VOC) as well as the variant of interest (VOI) B.1.621 (mu), first identified in Colombia, and the former VOI P.3 (theta) from The Philippines. 2021 eLife Introduction SARS_CoV_2 N501Y 51 56 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Two recent studies, one still non-peer reviewed, have focused on the N501Y mutation showing a variable impact on affinity (from 0.5 nM to sub pM). 2021 eLife Introduction SARS_CoV_2 N501Y 69 74 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Using a transgenic humanized ACE-2 mouse model we found that a lower infection dose was required to establish infection when challenged with the alpha/B.1.1.7 variant compared to an early 2020 isolate (differing at the N501Y position) and that the alpha variant resulted in increased disease severity. 2021 eLife Introduction SARS_CoV_2 N501Y 219 224 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. D614G mutants show a dramatically increased identified sample frequency (IF) and increases in fitness, infectivity and fatality. 2021 Cell host & microbe Introduction SARS_CoV_2 D614G 0 5 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. E484K has the ability to evade neutralization by most monoclonal antibodies. 2021 Cell host & microbe Introduction SARS_CoV_2 E484K 0 5 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Hence, we constructed an R203K/G204R mutant virus by site-directed mutagenesis. 2021 Cell host & microbe Introduction SARS_CoV_2 R203K;G204R 25;31 30;36 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. N501Y increases virus infectivity and confers high resistance to neutralization. 2021 Cell host & microbe Introduction SARS_CoV_2 N501Y 0 5 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. R203K/G204R are co-occurring mutations in the N protein (another structural protein of the virion) that are rapidly increasing in frequency and show a potential association with the infectivity of the virus. 2021 Cell host & microbe Introduction SARS_CoV_2 G204R;R203K 6;0 11;5 N 46 47 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. The R203K/G204R mutations are becoming dominant in the worldwide pandemic and may have positive effects on the fitness of SARS-CoV-2. 2021 Cell host & microbe Introduction SARS_CoV_2 R203K;G204R 4;10 9;15 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. These results indicated that the R203K/G204R N mutations, which may act in coordination with N501Y, are associated with the increased transmission and virulence of B.1.1.7 and P.1. 2021 Cell host & microbe Introduction SARS_CoV_2 N501Y;R203K;G204R 93;33;39 98;38;44 N 45 46 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Thus, a thorough evaluation of the evolutionary and functional effects of R203K/G204R is important for understanding the effects of N mutations and the contribution of N mutations to rapidly increasing lineages. 2021 Cell host & microbe Introduction SARS_CoV_2 R203K;G204R 74;80 79;85 N;N 132;168 133;169 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Thus, previous research has focused on adaptive SARS-CoV-2 mutants in S, such as D614G, N501Y, and E484K. 2021 Cell host & microbe Introduction SARS_CoV_2 D614G;E484K;N501Y 81;99;88 86;104;93 S 70 71 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Thus, the N protein R203K/G204R mutations deserve more attention during SARS-CoV-2 surveillance in the future. 2021 Cell host & microbe Introduction SARS_CoV_2 R203K;G204R 20;26 25;31 N 10 11 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. We continued tracking the evolution of R203K/G204R based on all documented SARS-CoV-2 genome sequences on a monthly basis and found that these mutations showed a second period of rapid expansion accompanying the emergence of B.1.1.7. 2021 Cell host & microbe Introduction SARS_CoV_2 R203K;G204R 39;45 44;50 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. 1d, the L452R and P681R mutations were highly conserved in the B.1.617 lineage and, notably, the P681R mutation (16,650 out of 16,759 sequences, 99.3%) was the most representative mutation in this lineage. 2022 Nature Introduction SARS_CoV_2 L452R;P681R;P681R 8;18;97 13;23;102 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. 2c) in the D614G/P681R-infected VeroE6/TMPRSS2 cells at 72 h.p.i. 2022 Nature Introduction SARS_CoV_2 D614G;P681R 11;17 16;22 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. 8a), suggesting that the P681R mutation facilitates furin-mediated cleavage of the SARS-CoV-2 S protein. 2022 Nature Introduction SARS_CoV_2 P681R 25 30 S 94 95 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. 8a), these results suggest that the P681R mutation facilitates S cleavage. 2022 Nature Introduction SARS_CoV_2 P681R 36 41 S 63 64 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Although the amounts of viral RNA in the culture supernatants of the D614G/P681R-infected Vero and VeroE6/TMPRSS2 cells were significantly lower compared with those of the D614G-infected cells at some timepoints, the growth of these two viruses was relatively comparable. 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 69;172;75 74;177;80 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Although the fusogenicity of S proteins of all VOCs tested was significantly greater than that of the parental D614G S, the B.1.617.2/Delta S exhibited the highest fusogenicity with statistical significance (Extended Data. 2022 Nature Introduction SARS_CoV_2 D614G 111 116 S;S;S 29;117;140 30;118;141 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Although the viral RNA levels of D614G/P681R virus gradually decreased after 5 d.p.i., plaque-like spots were observed after 7 d.p.i., and the sizes of these plaque-like spots in the culture of D614G/P681R infection were significantly larger than the plaque-like spots in the culture of parental D614G virus infection (Extended Data. 2022 Nature Introduction SARS_CoV_2 D614G;D614G;D614G;P681R;P681R 33;194;296;39;200 38;199;301;44;205 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. As the D614G mutation increases viral infectivity, fitness and interindividual transmissibility, the D614G-bearing variant quickly outcompeted the original strain. 2022 Nature Introduction SARS_CoV_2 D614G;D614G 7;101 12;106 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. As the P681R mutation is located in proximity to the furin cleavage site (FCS; residues RRAR positioned at 682-685) of the SARS-CoV-2 S protein, we hypothesized that the P681R mutation is responsible for the promotion of cell-cell fusion, leading to the formation of larger syncytia. 2022 Nature Introduction SARS_CoV_2 P681R;P681R 7;170 12;175 S 134 135 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. At 7 d.p.i., no differences in viral titres in the nasal turbinates were found between the two groups; however, the lung titres in the D614G/P681R-infected group were significantly higher than those in the D614G-infected group (P = 0.0013). 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 135;206;141 140;211;146 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. At 7 d.p.i., the D614G/P681R-infected hamsters had significantly higher PenH values than the D614G-infected hamsters (P = 0.043). 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 17;93;23 22;98;28 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. By contrast, all of the hamsters infected with the D614G/P681R virus experienced gradual body weight loss, and the hamsters showed a weight loss of 4.7-6.9% at 7 d.p.i., significantly greater compared with the weight loss of hamsters that were infected with the D614G virus (P = 0.011). 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 51;262;57 56;267;62 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. First, in spring 2020, a SARS-CoV-2 derivative containing a D614G mutation in its spike (S) protein emerged and quickly became predominant. 2022 Nature Introduction SARS_CoV_2 D614G 60 65 S;S 82;89 87;90 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Flow cytometry analysis showed that the surface expression level of D614G/P681R S was significantly lower than that of D614G S (Extended Data. 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 68;119;74 73;124;79 S;S 80;125 81;126 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Furthermore, neutralization experiments using 19 serum samples collected after two rounds of BNT162b2 vaccination showed that the D614G/P681R pseudovirus was significantly more resistant than the D614G pseudovirus to vaccine-induced neutralizing antibodies (P < 0.0001, Wilcoxon matched-pairs signed-rank test) (Extended Data. 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 130;196;136 135;201;141 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Furthermore, when we used targeted cells expressing TMPRSS2, both the fusion efficacy (about 1.2-fold) and initial fusion velocity (about 2.0-fold) were increased in both the D614G and D614G/P681R S proteins (Extended Data. 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 175;185;191 180;190;196 S 197 198 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. However, at 24 h.p.i., significantly larger GFP-positive adherent syncytia were observed in VeroE6/TMPRSS2 cells infected with the GFP-expressing D614G/P681R virus. 2022 Nature Introduction SARS_CoV_2 D614G;P681R 146;152 151;157 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. However, the relative infectivity of the D614G and D614G/P681R pseudoviruses was not altered by TMPRSS2 expression (Extended Data. 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 41;51;57 46;56;62 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. in the D614G/P681R-infected hamsters. 2022 Nature Introduction SARS_CoV_2 D614G;P681R 7;13 12;18 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. In the effector cells (that is, S-expressing cells), although the expression level of the D614G/P681R S protein was comparable to that of the D614G S protein, the level of the cleaved S2 subunit was significantly higher for the D614G/P681R mutant than for the D614G mutant. 2022 Nature Introduction SARS_CoV_2 D614G;D614G;D614G;D614G;P681R;P681R 90;142;228;260;96;234 95;147;233;265;101;239 S;S;S 32;102;148 33;103;149 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. in VeroE6/TMPRSS2 cells infected with GFP-expressing D614G/P681R virus were significantly larger (2.4-fold) in size compared with those of VeroE6/TMPRSS2 cells infected with GFP-expressing D614G virus (Extended Data. 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 53;189;59 58;194;64 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Infected hamsters of both groups showed increases in the lung PenH value, but the PenH values of D614G/P681R-infected hamsters were significantly higher than those of the D614G-infected hamsters on average across all timepoints (P = 0.038, multiple regression). 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 97;171;103 102;176;108 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Moreover, a mathematical modelling analysis of the fusion assay data showed that the initial fusion velocity of D614G/P681R S (0.83 +- 0.03 per hour) was significantly faster (2.8-fold) than that of D614G S (0.30 +- 0.03 per hour; P = 4.0 x 10-6, Welch's t-test) (Extended Data. 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 112;199;118 117;204;123 S;S 124;205 125;206 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Moreover, GFP-positive syncytia were observed in D614G/P681R-infected Calu-3 cells but not in D614G-infected Calu-3 cells at 72 h.p.i. 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 49;94;55 54;99;60 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Moreover, immunofluorescence assays showed that D614G/P681R-infected VeroE6/TMPRSS2 cells exhibited larger multinuclear cells than D614G-infected cells (Extended Data. 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 48;131;54 53;136;59 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Moreover, we demonstrate that the P681R mutation can partly explain the higher pathogenicity of the B.1.617.2/Delta variant in vivo. 2022 Nature Introduction SARS_CoV_2 P681R 34 39 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Neutralization of the P681R mutant. 2022 Nature Introduction SARS_CoV_2 P681R 22 27 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Nevertheless, the cell-based fusion assay using the target cells without TMPRSS2 demonstrated that D614G/P681R S is 2.1-fold more fusogenic than D614G S:a statistically significant difference (P = 0.0002, Welch's t-test). 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 99;145;105 104;150;110 S;S 111;151 112;152 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Notably, the viral RNA levels of D614G/P681R virus on the apical side of culture at 2 and 3 d.p.i. 2022 Nature Introduction SARS_CoV_2 D614G;P681R 33;39 38;44 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Pathogenicity of the P681R mutant. 2022 Nature Introduction SARS_CoV_2 P681R 21 26 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. The CT severity scores of the D614G-infected and D614G/P681R-infected hamsters ranged from 8 to 14, with an overall average CT severity score of 10.5 (median 9.5) (Extended Data. 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 30;49;55 35;54;60 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. The D614G-infected hamsters exhibited no weight loss, although a slight decrease in body weight by 7 d.p.i. 2022 Nature Introduction SARS_CoV_2 D614G 4 9 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. The D614G/P681R pseudovirus was partially resistant (1.2-1.5-fold) to three monoclonal antibodies targeting the receptor-binding domain of the SARS-CoV-2 S protein (Extended Data. 2022 Nature Introduction SARS_CoV_2 D614G;P681R 4;10 9;15 S 154 155 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. The D614G/P681R-infected hamsters had a higher CT severity score (mean 11 (range 9-14, median 10.5)), compared with the D614G-infected hamsters (mean 10 (range 8-13, median 9.5)). 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 4;120;10 9;125;15 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. The effect of the P681R mutation on viral fusion. 2022 Nature Introduction SARS_CoV_2 P681R 18 23 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. The infectivity of both the D614G and D614G/P681R pseudoviruses was increased approximately tenfold by the expression of TMPRSS2 in the target cells (Extended Data. 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 28;38;44 33;43;49 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. The P681R mutation enhances the cleavage of the SARS-CoV-2 S protein and enhances viral fusogenicity. 2022 Nature Introduction SARS_CoV_2 P681R 4 9 S 59 60 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. The P681R mutation in the S protein is a unique feature of the B.1.617 lineage, including the B.1.617.2/Delta variant. 2022 Nature Introduction SARS_CoV_2 P681R 4 9 S 26 27 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. The weight loss of D614G/P681R-infected hamsters was significantly greater compared with that of D614G-infected hamsters on average across all timepoints (P = 0.00015, multiple regression). 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 19;97;25 24;102;30 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. These data suggest that the P681R mutation accelerates viral replication in human primary nasal epithelial culture and produces large plaque-like spots, which could be formed by cell-to-cell infection as the case of plaque formation. 2022 Nature Introduction SARS_CoV_2 P681R 28 33 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. These data suggest that the P681R mutation does not affect the infectivity of the viral particles. 2022 Nature Introduction SARS_CoV_2 P681R 28 33 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. These data suggest that the P681R mutation enhances and accelerates SARS-CoV-2 S-mediated fusion. 2022 Nature Introduction SARS_CoV_2 P681R 28 33 S 79 80 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. These data suggest that the P681R mutation is a hallmark of the B.1.617 lineage. 2022 Nature Introduction SARS_CoV_2 P681R 28 33 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. These results suggest that the B.1.617.2/Delta variant promotes syncytium formation more strongly than the D614G-bearing B.1.1 virus as well as the B.1.1.7/Alpha and B.1.351/Beta VOCs. 2022 Nature Introduction SARS_CoV_2 D614G 107 112 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. These results suggest that the features of the B.1.617.2/Delta virus observed in in vitro cell culture experiments, particularly the formation of larger syncytia, are well reproduced by the insertion of the P681R mutation. 2022 Nature Introduction SARS_CoV_2 P681R 207 212 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. These results suggest that the P681R-bearing pseudovirus is relatively resistant to neutralizing antibodies. 2022 Nature Introduction SARS_CoV_2 P681R 31 36 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. These results suggest that TMPRSS2 facilitates the fusion mediated by SARS-CoV-2 S and human ACE2 and that this TMPRSS2-dependent acceleration and promotion of viral fusion is not specific for the P681R mutant. 2022 Nature Introduction SARS_CoV_2 P681R 197 202 S 81 82 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. To address this possibility, we generated a P681R-bearing artificial virus by reverse genetics (Extended Data. 2022 Nature Introduction SARS_CoV_2 P681R 44 49 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. To assess the effect of the P681R mutation on viral replication and the pathogenicity of SARS-CoV-2, we intranasally infected Syrian hamsters with the D614G and D614G/P681R viruses. 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R;P681R 151;161;28;167 156;166;33;172 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. To clearly observe syncytium formation, we further generated GFP-expressing replication-competent D614G and D614G/P681R viruses. 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 98;108;114 103;113;119 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. To determine whether the P681R mutation contributes to this virological phenotype, we performed a neutralization assay. 2022 Nature Introduction SARS_CoV_2 P681R 25 30 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. To directly investigate the effect of the P681R mutation on the cleavage of the SARS-CoV-2 S protein, we prepared an HIV-1-based pseudovirus carrying the P681R mutation. 2022 Nature Introduction SARS_CoV_2 P681R;P681R 42;154 47;159 S 91 92 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. To further investigate the effect of the P681R mutation, the GFP-expressing viruses were inoculated into human primary nasal epithelial culture. 2022 Nature Introduction SARS_CoV_2 P681R 41 46 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. To investigate the virological characteristics of the B.1.617.2/Delta variant, we conducted virological experiments using an isolate of B.1.617.2 (GISAID ID: EPI_ISL_2378732) as well as a D614G-bearing B.1.1 isolate (GISAID ID: EPI_ISL_479681) in Japan. 2022 Nature Introduction SARS_CoV_2 D614G 188 193 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Two of the D614G/P681R-infected hamsters developed a small-volume pneumomediastinum, probably secondary to severe pulmonary damage, micropulmonary rupture and gas tracking into the mediastinum. 2022 Nature Introduction SARS_CoV_2 D614G;P681R 11;17 16;22 Lung diseases 114 130 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. We also show that the P681R mutation in the S protein is a hallmark mutation of this lineage. 2022 Nature Introduction SARS_CoV_2 P681R 22 27 S 44 45 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. We next addressed the effect of the P681R mutation on viral fusogenicity by a cell-based fusion assay. 2022 Nature Introduction SARS_CoV_2 P681R 36 41 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. were 12.3-fold and 7.0-fold higher, respectively, than those of parental D614G virus with statistical significance, and the rapid growth of D614G/P681R virus was supported by the observation of GFP expression (Extended Data. 2022 Nature Introduction SARS_CoV_2 D614G;D614G;P681R 73;140;146 78;145;151 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. were significantly larger in size compared with the syncytia in the D614G-mutant-infected cells. 2022 Nature Introduction SARS_CoV_2 D614G 68 73 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Western blot analysis of the prepared pseudoviruses showed that the level of the cleaved S2 subunit was significantly increased in the presence of the P681R mutation (Extended Data. 2022 Nature Introduction SARS_CoV_2 P681R 151 156 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. An RBD mutation screen for high-affinity ACE2 binding repeatedly produced de novo N501Y mutants, consistent with the observed worldwide appearance of multiple independent N501Y-containing variants. 2021 Diagnostics (Basel, Switzerland) Introduction SARS_CoV_2 N501Y;N501Y 82;171 87;176 RBD 3 6 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. Both possess the N501Y and E484K mutations, which provide resistance to vaccine immunity and reduced neutralization by mAb therapeutics. 2021 Diagnostics (Basel, Switzerland) Introduction SARS_CoV_2 E484K;N501Y 27;17 32;22 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. N501Y is found in the alpha, beta, and gamma variants. 2021 Diagnostics (Basel, Switzerland) Introduction SARS_CoV_2 N501Y 0 5 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. N501Y provides a selective advantage over Wuhan-Hu-1 (L) by increasing the affinity of the RBD for ACE2 3- to 16-fold and collaborating with other RBD mutations (especially E484K) to increase binding and infectivity. 2021 Diagnostics (Basel, Switzerland) Introduction SARS_CoV_2 E484K;N501Y 173;0 178;5 RBD;RBD 91;147 94;150 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. Natural selection of N501Y-containing variants is predicted to increase infectivity in non-immune individuals and enable breakthrough infections in vaccine recipients. 2021 Diagnostics (Basel, Switzerland) Introduction SARS_CoV_2 N501Y 21 26 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. One of the most frequent changes is N501Y, which defines a meta-signature of 35 convergent mutations that are associated with increased virulence and evasion of host immunity. 2021 Diagnostics (Basel, Switzerland) Introduction SARS_CoV_2 N501Y 36 41 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. Two recently emerged variants further exemplify the threat posed by N501Y-containing SARS-CoV-2 variants, Mu (B.1.621) and C.1.2. 2021 Diagnostics (Basel, Switzerland) Introduction SARS_CoV_2 N501Y 68 73 34829998 SARS-CoV-2 Variants, RBD Mutations, Binding Affinity, and Antibody Escape. Although the RBD mutation at amino-acid position 498 is not a missense mutation that presented in one or more of the VOCs, the RBD mutation such as Q498A has also been reported. 2021 International journal of molecular sciences Introduction SARS_CoV_2 Q498A 148 153 RBD;RBD 13;127 16;130 34829998 SARS-CoV-2 Variants, RBD Mutations, Binding Affinity, and Antibody Escape. Surprisingly, the mutations of L452R, K417N, Y453F, E484K N501Y, and F490S transform the Ho-Hi interactions into Ho-Ho or ADD interactions at these positions, thus increasing the binding affinity with ACE2. 2021 International journal of molecular sciences Introduction SARS_CoV_2 E484K;F490S;K417N;L452R;N501Y;Y453F 52;69;38;31;58;45 57;74;43;36;63;50 34829998 SARS-CoV-2 Variants, RBD Mutations, Binding Affinity, and Antibody Escape. There have been a number of missense mutations observed in the receptor-binding domain (RBD) of the SARS-CoV-2 S protein, which have presented in one or more of the VOCs, including the N440K, G446V, L452R, Y453F, E484Q, F490S, N501Y, N501S, E484K, and K417N, most of which are located at the RBD-ACE2 interface. 2021 International journal of molecular sciences Introduction SARS_CoV_2 E484K;E484Q;F490S;G446V;K417N;L452R;N440K;N501S;N501Y;Y453F 241;213;220;192;252;199;185;234;227;206 246;218;225;197;257;204;190;239;232;211 RBD;RBD;S 88;292;111 91;295;112 34833135 Emerging Mutations Potentially Related to SARS-CoV-2 Immune Escape: The Case of a Long-Term Patient. In the past few months, emerging mutations in the spike (S) glycoprotein have been constantly under surveillance due to the prominent role of this protein in the viral infection, with special concern for S:E484K since it occurs in the receptor binding domain (RBD). 2021 Life (Basel, Switzerland) Introduction SARS_CoV_2 E484K 206 211 RBD;S;RBD;S;S 235;50;260;57;204 258;55;263;58;205 34833135 Emerging Mutations Potentially Related to SARS-CoV-2 Immune Escape: The Case of a Long-Term Patient. Therefore, it has been speculated that S:E484K could provide an evolutionary advantage for SARS-CoV-2 lineages to escape the host immune response. 2021 Life (Basel, Switzerland) Introduction SARS_CoV_2 E484K 41 46 S 39 40 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. For that, in this study, we investigated the antiviral and anti-inflammatory properties of curcumin against D614G strain and Delta variant of SARS-CoV-2 using in vitro models. 2021 Molecules (Basel, Switzerland) Introduction SARS_CoV_2 D614G 108 113 34834987 The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City. During the third epidemic peak between February and March 2021, we observed an increase in variant B.1.1.519, which possesses three substitutions in the spike protein (T478K, P681H, and T732A). 2021 Viruses Introduction SARS_CoV_2 P681H;T732A;T478K 175;186;168 180;191;173 S 153 158 34835101 Impact of the Double Mutants on Spike Protein of SARS-CoV-2 B.1.617 Lineage on the Human ACE2 Receptor Binding: A Structural Insight. Here in this study, we have investigated the impact of the double mutation (L452R + E484Q and L452R + T478K) carried by the B.1.617.1 (kappa variant) and the B.1.617.2 (delta variant), respectively, on the binding propensity of SARS-CoV-2 S protein with the human ACE2. 2021 Viruses Introduction SARS_CoV_2 E484Q;L452R;T478K;L452R 84;94;102;76 89;99;107;81 S 239 240 34835101 Impact of the Double Mutants on Spike Protein of SARS-CoV-2 B.1.617 Lineage on the Human ACE2 Receptor Binding: A Structural Insight. This variant harbors two mutations within the RBD (L452R, E484Q), the region responsible for the viral entry. 2021 Viruses Introduction SARS_CoV_2 E484Q;L452R 58;51 63;56 RBD 46 49 34836485 A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. As an example, a single mutation, E484 K, found in several variants could knock out a class of antibodies binding the receptor binding motif (RBM) on the viral spike. 2022 Emerging microbes & infections Introduction SARS_CoV_2 E484K 34 40 S 160 165 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. At the end of 2020, the incidence of variants carrying the Q677H, or Q677P substitutions in the spike increased, mainly in the USA, where the first sequences originated from Louisiana. 2022 Virus genes Introduction SARS_CoV_2 Q677H;Q677P 59;69 64;74 S 96 101 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. The variants recently considered to be of greatest concern are those carrying amino acid substitutions N501Y and/or E484K within the spike protein, as they have increased affinity for the ACE2 cellular receptor, decreased sensitivity to neutralising antibodies, and may escape the immune responses elicited by the vaccines currently used in Western countries. 2022 Virus genes Introduction SARS_CoV_2 E484K;N501Y 116;103 121;108 S 133 138 34840498 Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021. D614G mutation ever became the spotlight in the early time of COVID-19 pandemic and had a high correlation with the widespread infection and virulence besides the changes of antigenicity (Korber et al.; Nidom et al.). 2021 Bulletin of the National Research Centre Introduction SARS_CoV_2 D614G 0 5 COVID-19 62 70 34841034 Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2. Another amino acid variation of the spike protein, which appeared in mid-2020 and then became prevalent, is D614G. 2021 One health (Amsterdam, Netherlands) Introduction SARS_CoV_2 D614G 108 113 S 36 41 34841034 Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2. As reported by an in vitro neutralizing assay performed with pseudo-typed viruses, L452R increases resistance to some monoclonal antibodies, while in-field observations suggest that administering one dose of the BNT162b2 vaccine produces 5.8 times lower neutralizing activity for variant B.1.617.2 (delta) than for variant B.1.1.7 (alpha). 2021 One health (Amsterdam, Netherlands) Introduction SARS_CoV_2 L452R 83 88 34841034 Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2. In fact, N501Y influences protein S affinity for the receptor enhancing infectivity of the virus and, possibly, virulence, and all the most widespread variants in mid-2021 (June 2021), i.e., B.1.1.7 (alpha), B.1.351 (beta) and P.1 (gamma) show the N501Y mutation, despite their distinct geographical origin (United Kingdom, South Africa, and Brazil, respectively). 2021 One health (Amsterdam, Netherlands) Introduction SARS_CoV_2 N501Y;N501Y 9;248 14;253 S 34 35 34841034 Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2. In these frames, we used a docking method whereby the N501Y mutation is predicted to increase ACE2 binding energy by ~ -20 Kcal/mol. 2021 One health (Amsterdam, Netherlands) Introduction SARS_CoV_2 N501Y 54 59 34841034 Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2. P681R, which instead of operating on ACE2 receptor binding seems to primarily act on S1/S2 cleavage by furin. 2021 One health (Amsterdam, Netherlands) Introduction SARS_CoV_2 P681R 0 5 34841034 Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2. This variant does not have the amino acid substitution N501Y but exhibits two other substitutions: L452R and T478K. 2021 One health (Amsterdam, Netherlands) Introduction SARS_CoV_2 L452R;N501Y;T478K 99;55;109 104;60;114 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. For example, the mutation of asparagine at position 501 to tyrosine (N501Y), which is one of the residues in the RBD-ACE2 contact area, can enhance the binding affinity of SARS-CoV2 spike protein to ACE2 both in human and mouse. 2021 Reproductive sciences (Thousand Oaks, Calif.) Introduction SARS_CoV_2 N501Y;N501Y 29;69 67;74 S;RBD 182;113 187;116 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. The present study aims to evaluate the effects of N501Y variant of the SARS-CoV-2 spike protein on the in vitro maturation of mouse oocytes. 2021 Reproductive sciences (Thousand Oaks, Calif.) Introduction SARS_CoV_2 N501Y 50 55 S 82 87 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. We have investigated the nuclear and cytoplasmic maturation by examining the spindle assembly and mitochondrial distribution upon the treatment of N501Y spike protein. 2021 Reproductive sciences (Thousand Oaks, Calif.) Introduction SARS_CoV_2 N501Y 147 152 S 153 158 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Based on this, we identified mutation N:S194L of the nucleocapsid to be potentially associated with the development of symptoms. 2021 Microbial genomics Introduction SARS_CoV_2 S194L 40 45 N;N 53;38 65;39 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. E484K, are increasingly common worldwide as they are imported from their regions of origin into naive populations, but also as independent evolution converges to the same point mutations, such as in the recently reported VOI 20A/S.484K and 20C/S.484K (B.1.525/526, eta/iota, amongst others. 2021 Microbial genomics Introduction SARS_CoV_2 E484K 0 5 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. For instance, 20J/501Y.V3 or P.1 evolved in parallel with the 20B/S.484K or P.2 variant in Brazil, and they share the spike protein mutations E484K and V1176F, but not N501Y. 2021 Microbial genomics Introduction SARS_CoV_2 E484K;N501Y;V1176F 142;168;152 147;173;158 S 118 123 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Mutation D614G of the SARS-CoV-2 spike protein was the first mutation implicated in increased transmission and a more efficient viral replication in human cells. 2021 Microbial genomics Introduction SARS_CoV_2 D614G 9 14 S 33 38 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Shortly after the appearance of D614G, other mutations in the Receptor Binding Domain (RBD) of the spike protein appeared, including but not limited to K417N, L452R, E484K and N501Y. 2021 Microbial genomics Introduction SARS_CoV_2 D614G;E484K;K417N;L452R;N501Y 32;166;152;159;176 37;171;157;164;181 RBD;S;RBD 62;99;87 85;104;90 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. The convergence of K417N, E484K and N501Y in different geographical regions suggest that during the 'pre-vaccination stage' of the pandemic, similar selection pressures took place to increase the fitness of SARS-CoV-2. 2021 Microbial genomics Introduction SARS_CoV_2 E484K;K417N;N501Y 26;19;36 31;24;41 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Together with the P.1 closely related VOI P.2 (B.1.1.28.2, zeta) these VOC/VOI often share mutations E484K and/or N501Y. 2021 Microbial genomics Introduction SARS_CoV_2 E484K;N501Y 101;114 106;119 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Emerging SARS-CoV-2 variants in early 2021, including B.1.1.7/B.1.1.7 + E484K lineage (United Kingdom), B.1.351 lineage (South Africa), P.1 lineage (Brazil), and B.1.427/B.1.429 lineage (California) has rapidly become dominant in domestic and arousing global concerns. 2022 Infection, genetics and evolution Introduction SARS_CoV_2 E484K 72 77 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. The B.1.1.7 lineage harbors three amino acid deletions and seven missense mutations in spike protein, including D614G and N501Y in the ACE2 receptor-binding domain. 2022 Infection, genetics and evolution Introduction SARS_CoV_2 D614G;N501Y 112;122 117;127 S 87 92 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. The variations within the S protein-cell receptor interface is more vulnerable to viral infectivity, in which the variant with S D614G emerged is the most prevalent clade at multiple geographic areas. 2022 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 129 134 S;S 26;127 27;128 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. In this regard, some mutations in SARS-CoV-2 are responsible for large conformational changes that may enhance infection, such as those located in the distal region of the spike protein and near the fusion region as the well-known D614G. 2021 Nature communications Introduction SARS_CoV_2 D614G 231 236 S 172 177 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. N501Y, for example, present in the Alpha, Beta, and Gamma variants, increases ACE2 binding. 2021 Nature communications Introduction SARS_CoV_2 N501Y 0 5 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. One of the far-reaching consequences of this antigenic variation of the RBM was the withdrawal of Eli Lilly's mAb bamlanivimab from emergency use approval as monotherapy for the treatment of COVID-19 patients, because VoCs with E484K/Q mutations had become resistant. 2021 Nature communications Introduction SARS_CoV_2 E484K;E484Q 228;228 235;235 COVID-19 191 199 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. For example, the D614G variant has been shown to increase the viral load of infected patients and has replaced the original variant since June 2020 around the globe. 2021 Analytical chemistry Introduction SARS_CoV_2 D614G 17 22 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. The N501Y mutation is found in the Alpha, Beta, and Gamma VOCs, while the E484K mutation is restricted to Beta and Gamma variants. 2021 Analytical chemistry Introduction SARS_CoV_2 E484K;N501Y 74;4 79;9 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. G254* in ORF3a resulted in the predicted absence of 18 amino acid residues (positions 254 to 271) at the C terminus of the protein, located in a region thought to carry several B cell epitopes. 2021 Microbiology resource announcements Introduction SARS_CoV_2 G254X 0 5 ORF3a 9 14 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. K68* was reported previously. 2021 Microbiology resource announcements Introduction SARS_CoV_2 K68X 0 4 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. Two nonsense mutations, i.e., G254* and K68* in open reading frame 3a (ORF3a) and ORF8 genes, respectively, were not found in the first alpha variant virus in Thailand but were found in all alpha variant viruses in this study. 2021 Microbiology resource announcements Introduction SARS_CoV_2 G254X;K68X 30;40 35;44 ORF3a;ORF8 71;82 76;86 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. conducted an experimental and computational study to capture the role of the N501Y mutation in Alpha, Beta, and Gamma variants. 2021 Journal of chemical theory and computation Introduction SARS_CoV_2 N501Y 77 82 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. However, only the N501Y mutation was examined in their study, although other potentially important mutations have emerged. 2021 Journal of chemical theory and computation Introduction SARS_CoV_2 N501Y 18 23 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. They investigated each specific mutation, N501Y, K417N/T, and E484 K, and reported that F486, Q498, T500, and Y505 in RBDs are important residues across viral variants in the RBD-ACE2 interface. 2021 Journal of chemical theory and computation Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 62;49;49;42 68;56;56;47 RBD;RBD 118;175 122;178 34856891 A second functional furin site in the SARS-CoV-2 spike protein. During our study of furin in SARS-CoV-2 infection, based on bioinformatic prediction, in addition to the classical furin cleavage site (682-RRAR-685), we found a novel furin cleavage site (K814A) in the S protein of SARS-CoV-2. 2022 Emerging microbes & infections Introduction SARS_CoV_2 K814A 189 194 S 203 204 COVID-19 29 49 34856891 A second functional furin site in the SARS-CoV-2 spike protein. K814A mutation affects the cleavage of S2 into S2' and cell-cell fusion. 2022 Emerging microbes & infections Introduction SARS_CoV_2 K814A 0 5 34856891 A second functional furin site in the SARS-CoV-2 spike protein. K814A mutation does not affect the activity of TMPRSS2 and cathepsin L. 2022 Emerging microbes & infections Introduction SARS_CoV_2 K814A 0 5 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. Alpha (first identified in the UK), Beta (first identified in South Africa) and Gamma (first identified in Brazil) mutants share the N501Y mutation that has been linked with increased affinity of the Spike protein for the endogenous receptor human Angiotensin-converting enzyme 2 (hACE2). 2021 Frontiers in immunology Introduction SARS_CoV_2 N501Y 133 138 S 200 205 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. Although this mutant has been reported to be more infective, sera from convalescent patients and subjects vaccinated with mRNA vaccines are able to neutralize the D614G mutant to an extent similar to that of the ancestral strain. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 163 168 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. Beta and Gamma mutants exhibit the E484K mutation, associated with an increased evasion of neutralizing antibodies. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K 35 40 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. Delta exhibits unique mutations (L452R, T478K and P681R), which may increase viral infectivity and viral fusion. 2021 Frontiers in immunology Introduction SARS_CoV_2 P681R;T478K;L452R 50;40;33 55;45;38 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. Furthermore, Beta and Gamma exhibit mutations in the residue K417 of the RBD but differ in the amino acid substitutions (K417N for Beta and K417T for Gamma), which may affect antibody binding. 2021 Frontiers in immunology Introduction SARS_CoV_2 K417T;K417N 140;121 145;126 RBD 73 76 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. One of the most prevalent strains is the D614G, which displays a mutation in the C-terminal region of the Spike 1 (S1) domain outside the Receptor Binding Domain (RBD). 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 41 46 RBD;S;RBD 138;106;163 161;111;166 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. The neutralizing capacities of antibody were evaluated using a conventional plaque-reduction neutralization test (cVNT) for the D614G, Alpha, Gamma and Delta variants. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 128 133 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. In context to the same, here we assessed the antigenic propensity of the epitope encompassing the D614G mutation considering its high frequency and the segment being earlier reported as immune-dominant peptide in SARS-CoV. 2021 Frontiers in genetics Introduction SARS_CoV_2 D614G 98 103 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. There are a lot of variations observed in spike protein sequence, a major variation in spike protein is a non-synonymous D614G mutation (d-Aspartate, G-Glycine) which has received special attention by several groups due to its dominance. 2021 Frontiers in genetics Introduction SARS_CoV_2 D614G 121 126 S;S 42;87 47;92 34863783 Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay. By comparing the sequence of the SARS-CoV-2 variant with diminished amplification in the ORF1ab target to other SARS-CoV-2 sequences generated in our laboratory, we were able to identify 5 unique mutations which may have caused this amplification problem: C11450A (nsp10) C14178T (RdRp), G15006T (RdRp), G18394T (Hel), and G20995T (Hel) (Supplemental data. 2022 Journal of virological methods Introduction SARS_CoV_2 C11450A;C14178T;G15006T;G18394T;G20995T 256;272;288;304;323 263;279;295;311;330 ORF1ab;RdRP;RdRP 89;281;297 95;285;301 34863783 Diminished amplification of SARS-CoV-2 ORF1ab in a commercial dual-target qRT-PCR diagnostic assay. Five unique nucleotide mutations were identified in ORF1ab: C11450A (nsp10) C14178T (RdRp), G15006T (RdRp), G18394T (Hel), and G20995T (Hel) (Supplemental data. 2022 Journal of virological methods Introduction SARS_CoV_2 C11450A;C14178T;G15006T;G18394T;G20995T 60;76;92;108;127 67;83;99;115;134 ORF1ab;RdRP;RdRP 52;85;101 58;89;105 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Compared to strains containing the original D614, viruses with the D614G mutation have significantly higher infection titers as well as faster transmission but are less sensitive to spike-based SARS-CoV-2 vaccine sera produced in mice, non-human primates, and humans. 2021 Frontiers in chemistry Introduction SARS_CoV_2 D614G 67 72 S 182 187 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Given this conformational shift, it is of interest to examine glycosylation for possible changes in the D614G spike compared to its close progenitor, the WA1 strain, while keeping the viral propagation cell platform the same. 2021 Frontiers in chemistry Introduction SARS_CoV_2 D614G 104 109 S 110 115 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. SARS-CoV-2/Massachusetts/VPT1/2020 (MA/VPT1), containing the D614G mutation, was isolated in Vero E6 cells from a nasopharyngeal specimen collected in April 2020. 2021 Frontiers in chemistry Introduction SARS_CoV_2 D614G 61 66 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. The D614G mutation is also carried by the more recent and concerning SARS-CoV-2 variants, including B.1.1.7, B.1.351, P.1, and B.1.617 (https://www.cdc.gov/coronavirus/2019-ncov/variants/). 2021 Frontiers in chemistry Introduction SARS_CoV_2 D614G 4 9 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. The D614G mutation, which appeared in early 2020, has become dominant worldwide. 2021 Frontiers in chemistry Introduction SARS_CoV_2 D614G 4 9 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Therefore, in addition to analysis of recombinant spike constructs, we report the glycosylation patterns of spikes in WA1 and D614G strains produced by the whole virus in Vero E6 cells. 2021 Frontiers in chemistry Introduction SARS_CoV_2 D614G 126 131 S;S 50;108 55;114 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Thus, we compare the glycosylation of recombinant RBD and S1 to two intact viruses, the WA1 strain and a D614G variant, both produced in Vero E6 cells. 2021 Frontiers in chemistry Introduction SARS_CoV_2 D614G 105 110 RBD 50 53 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. For example, nucleotide mutations 14 408C>T. 2021 Microbial genomics Introduction SARS_CoV_2 C408T 37 43 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. the mutation D614G in the virus spike protein), which tended to be found together, were reported to show significant positive correlations with death, and to be found more frequently in severe cases than mild cases. 2021 Microbial genomics Introduction SARS_CoV_2 D614G 13 18 S 32 37 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. the mutation P323L in RNA-dependent RNA polymerase protein) and 23 403A>G. 2021 Microbial genomics Introduction SARS_CoV_2 A403G;P323L 67;13 73;18 RdRp 22 50 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. One of the first variations that spread vigorously across countries was Asp614Gly at the spike protein, with this mutation showing higher viral loads than the reference virus from Wuhan, China. 2021 PloS one Introduction SARS_CoV_2 D614G 72 81 S 89 94 34871906 Highly sensitive and specific detection of the SARS-CoV-2 Delta variant by double-mismatch allele-specific real time reverse transcription PCR. In contrast, the double-mismatch allele-specific real time RT-PCR (DMAS-RT-PCR) method that we describe here does not exhibit such non-specificity because it targets two separate Delta spike gene mutations, L452R and T478K, within the same amplicon. 2022 Journal of clinical virology Introduction SARS_CoV_2 L452R;T478K 207;217 212;222 S 185 190 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. A few vaccine-resistant mutations (S438F, I434K, Y505C, and Q506K) were detected before November 2020 with relatively low frequencies. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 I434K;Q506K;Y505C;S438F 42;60;49;35 47;65;54;40 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. After April 2021, the Y449S mutation quickly spread to 10 other countries. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 22 27 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. All of the Y449S-related cases are found in Europe and America, where the vaccination rates in those areas are relatively high. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 11 16 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Although DK has the smallest number of positive cases among 14 countries, the frequency of the Y449S mutation is the highest. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 95 100 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Among all of the vaccine-resistant mutations, the Y449S mutation has the highest frequency (1193). 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 50 55 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Among the 50 most observed RBD co-mutations, the Y449S and N501Y co-mutation is the only co-mutation with a significantly negative BFE change and an extremely high antibody disruption count (94). 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 N501Y;Y449S 59;49 64;54 RBD 27 30 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Among them, the total number of cases related to Y449S has a tendency to increase rapidly, especially in DK, the UK, and FR. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 49 54 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. As mentioned in ref, RBD mutations such as E484K/A, Y489H, Q493K, and N501Y found in late-stage evolved S variants "confer resistance to a common class of SARS-CoV-2 neutralizing antibodies", which suggests the viral evolution is also regulated by vaccine-resistant mutations. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 E484K;E484A;N501Y;Q493K;Y489H 43;43;70;59;52 50;50;75;64;57 RBD;S 21;104 24;105 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. As the most observed vaccine-resistant RBD mutation, Y449S has been detected in 14 countries, including Denmark (DK), the United Kingdom (UK), France (FR), Bulgaria (BG), the United States (US), Argentina (AR), Brazil (BR), Sweden (SE), Canada (CA), Switzerland (CH), Germany (DE), Spain (ES), Romania (RO), and Belgium (BE), as illustrated in Figure 4a. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 53 58 RBD 39 42 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. At the end of March 2021, vaccine-resistant mutation Y449D showed up with mutation N501Y in some genome isolates, resulting in a negative BFE change (-0.473 kcal/mol) and a high antibody disruption count (98) for a pair of RBD co-mutations (Y449D and N501Y). 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 N501Y;N501Y;Y449D;Y449D 83;251;53;241 88;256;58;246 RBD 223 226 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Figure 4b shows the time evolution of the vaccination ratio and the frequency of Y449S in the top 12 countries as mentioned above in 30-day periods. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 81 86 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Furthermore, the vaccination rates of 12 countries where Y449S is distributed are also analyzed, which provides a sound explanation of the relation between the emergence of vaccine-resistant mutations and the vaccination rate. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 57 62 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Here, 14 countries in which Y449S was found are colored blue. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 28 33 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. However, since late March 2021, once vaccines had provided protection to highly vaccinated populations, several vaccine-resistant mutations such as Y449S and Y449H have been observed relatively frequently. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449H;Y449S 158;148 163;153 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. However, the frequency of the Y449S mutation in BG and the US is quite low before April 2021. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 30 35 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. However, three RBD mutations (S477I, D427N, and Y449S) have negative BFE changes. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 D427N;Y449S;S477I 37;48;30 42;53;35 RBD 15 18 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. In addition, at residue 449, mutations Y449H, Y449N, and Y449D are all vaccine-resistant mutations that have been observed in more than 20 SARS-CoV-2 genome isolates. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449D;Y449H;Y449N 57;39;46 62;44;51 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. In addition, the Y449S mutation has a relatively high frequency. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 17 22 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. In early January 2021, we have predicted that RBD mutations W353R, I401N, Y449D, Y449S, P491R, P491L, Q493P, etc., will weaken the binding of most antibodies to the S protein. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 I401N;P491L;P491R;Q493P;W353R;Y449D;Y449S 67;95;88;102;60;74;81 72;100;93;107;65;79;86 RBD;S 46;165 49;166 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. It is worth mentioning that the frequency of the Y449S mutation is low in DE, ES, BE, etc., which is mainly due to the first Y449-related case in these countries being detected after June 2021. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 49 54 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Later, we provided a list of most likely vaccine escape RBD mutations with high frequency, including S494P, Q493L, K417N, F490S, F486L, R403K, E484K, L452R, K417T, F490L, E484Q, and A475S. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 A475S;E484K;E484Q;F486L;F490L;F490S;K417N;K417T;L452R;Q493L;R403K;S494P 182;143;171;129;164;122;115;157;150;108;136;101 187;148;176;134;169;127;120;162;155;113;141;106 RBD 56 59 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. More than 800 patients carry vaccine-resistant mutation Y449S in DK. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 56 61 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Moreover, from Figure 4, one can see that the frequency of the Y449S mutation has a tendency to increase similar to that of the fully vaccinated ratio, suggesting that the vaccine-resistant mutations will gradually become one of the main evolution-driving forces of SARS-CoV-2, especially in those areas with high vaccination rates. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 63 68 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Moreover, in May 2021, two vaccine-resistant mutations (Y449S and Y449H) came back to the top 100 most observed RBD mutation list. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449H;Y449S 66;56 71;61 RBD 112 115 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Moreover, vaccine-resistant RBD mutation Y449S that has been found in more than 1000 isolates is discussed. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 41 46 RBD 28 31 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Moreover, we have pointed out that Y449S and Y449H are two vaccine-resistant mutations, and "Y449S, S494P, K417N, F490S, L452R, E484K, K417T, E484Q, L452Q, and N501Y" are the top 10 mutations that will disrupt most antibodies with high frequency. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 E484K;E484Q;F490S;K417N;K417T;L452Q;L452R;N501Y;S494P;Y449H;Y449S;Y449S 128;142;114;107;135;149;121;160;100;45;35;93 133;147;119;112;140;154;126;165;105;50;40;98 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Notably, Gamma variants, one of the variants of concern (VOC), carry three co-mutations (K417T, E484K, and N501Y) on the RBD, which indicates that four vaccine-resistant co-mutations (K417T, Y449S, E484K, and N501Y) may be a potential threat in the future. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 E484K;E484K;N501Y;N501Y;Y449S;K417T;K417T 96;198;107;209;191;89;184 101;203;112;214;196;94;189 RBD 121 124 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Notably, the Y449S mutation has a significantly negative BFE change (-0.8112 kcal/mol) and a large antibody disruption count (85), revealing an atypical mechanism of mutagenesis. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 13 18 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Observing the evolution trajectory of Y449S and N501Y shows that the infectivity transmission pathway regulated by natural selection in the population level was the major evolution-driving force of SARS-CoV-2 mutagenesis before March 2021. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 N501Y;Y449S 48;38 53;43 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. One can see that the Y449S mutation was first found in BG and the US in December 2020. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 21 26 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Since late April 2021, vaccine-resistant mutation Y449S showed up with N501Y, making RBD co-mutations Y449S and N501Y some of the most prevament vaccine-resistant co-mutations. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 N501Y;N501Y;Y449S;Y449S 71;112;50;102 76;117;55;107 RBD 85 88 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. Since then, Delta variants dominated among the prevailing variants, which gave the Y449S mutation a limited chance to spread rapidly. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 83 88 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. The darker the blue, the higher the frequency of Y449S. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y449S 49 54 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. The left-hand side y-axis shows the frequency of Y499S (red lines), and the right-hand side y-axis shows the vaccination ratio. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 Y499S 49 54 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. There are no triple vaccine-resistant co-mutations at present, while a quadruple vaccine-resistant co-mutation (K417T, Y449S, E484K, and N501Y) appeared after late August 2021. 2021 The journal of physical chemistry letters Introduction SARS_CoV_2 E484K;N501Y;Y449S;K417T 126;137;119;112 131;142;124;117 34874953 1H, 13C and 15N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution. As a first step towards characterizing the structure and dynamics of the full-length SARS-CoV-2 nsp1 in neutral buffer by NMR spectroscopy, we herein report the almost complete 1H, 13C and 15N backbone and 13Cbeta side chain assignment of the wild type protein and two of its mutants: a single mutant H81P and a double mutant K129E, D48E. 2021 PloS one Introduction SARS_CoV_2 D48E;H81P;K129E 333;301;326 337;305;331 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. from molecular dynamic (MD) studies on the variant sequence and was supported by a recent cryo-EM study of S-D614G. 2021 Scientific reports Introduction SARS_CoV_2 D614G 109 114 S 107 108 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. Given the current predominance of the S-D614G variant and the apparent influence of this modification upon the structure and function of the S protein, it is important to understand how this substitution might influence the glycan complement. 2021 Scientific reports Introduction SARS_CoV_2 D614G 40 45 S;S 38;141 39;142 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. Here we use our previously described signature ion triggered electron-transfer/higher-energy collision dissociation (EThcD) approach for analyzing S proteins expressed in a human cell line (HEK 293) for a comparative glycoproteomics study of the S-D614G variant relative to the wild type S. 2021 Scientific reports Introduction SARS_CoV_2 D614G 248 253 S;S;S 147;246;288 148;247;289 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. indicated that the S-D614G variant significantly favored more "open" conformations compared to the wild type by disrupting interchain contacts stabilized by hydrogen bonding between D614 and residue T859 on an adjacent molecule. 2021 Scientific reports Introduction SARS_CoV_2 D614G 21 26 S 19 20 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. Of these, the substitution of aspartic acid (D) to glycine (G) at residue 614 of the spike protein (S-D614G) has been of highest prevalence, first being detected in early January 2020 in China and Europe and quickly spreading worldwide, being present in over 75% of sequenced samples from infected individuals by late 2020. 2021 Scientific reports Introduction SARS_CoV_2 D614G 102 107 S;S 85;100 90;101 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. Other studies reinforcing these observations found increased rates of viral replication in lung epithelial cells and tissues infected with the S-D614G virus. 2021 Scientific reports Introduction SARS_CoV_2 D614G 145 150 S 143 144 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. Similar enhanced rates of infection were also observed in a panel of S mutants in studies by Li et al and in another report using virus like particles (VLPs) expressing S-D614G. 2021 Scientific reports Introduction SARS_CoV_2 D614G 171 176 S;S 69;169 70;170 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. The preference for the open conformation in S-D614G was also postulated by Mansbach et al. 2021 Scientific reports Introduction SARS_CoV_2 D614G 46 51 S 44 45 34878296 Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. A fourth sample (MCoV-50188) differed only at positions 21,987 (G142D) and 24,410 (D950N). 2021 Microbiology spectrum Introduction SARS_CoV_2 D950N;G142D 83;64 88;69 34878296 Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. bearing resemblance to previous evolutionary sweeps, including the D614G substitution in 2020, B.1.1.7 (Alpha) last fall and winter, and Delta this spring and summer (GISAID acknowledgment table can be found at doi: https://doi.org/10.1101/2021.09.27.461949). 2021 Microbiology spectrum Introduction SARS_CoV_2 D614G 67 72 34878296 Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. Except for the ends of the assembled sequences which can be jagged, and therefore ambiguous, 3 samples (MCoV-49081, MCoV-50268 and MCoV-49000) differed only at position 21,987 (G142D) SNP in the V3 versus V4 assemblies. 2021 Microbiology spectrum Introduction SARS_CoV_2 G142D 177 182 34878296 Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. From June 2021 through August 2021, the rapid increase in the G142D amino acid substitution present in Delta variants in public repositories appeared to indicate a rapid evolutionary sweep. 2021 Microbiology spectrum Introduction SARS_CoV_2 G142D 62 67 34878296 Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. However, our data lead us to conclude that the sharp uptick in spike protein G142D was caused by community adoption of the V4 primers. 2021 Microbiology spectrum Introduction SARS_CoV_2 G142D 77 82 S 63 68 34878296 Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. In particular, there were spike protein amino acid changes common to the Beta, Delta, and Gamma variants that occurred in known V3 primer binding sites, including G142D (Delta) in the 2_Right primer, the 241/243del (Beta) that occurs in the 74_Left primer, and the K417N (Beta) or K417T (Gamma) which occur in the 76_Left primer (https://community.artic.network/t/sars-cov-2-version-4-scheme-release/312). 2021 Microbiology spectrum Introduction SARS_CoV_2 G142D;K417N;K417T 163;265;281 168;270;286 S 26 31 34878296 Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. Indeed, when we examine 12,441 samples from Houston Methodist patients collected since April of 2021, comparing the occurrence of G142D with L452R (another hallmark Delta substitution in spike), it becomes clear that the G142D uptick is an artifact that corresponds precisely with our adoption of the V4 primers in mid-July 2021. 2021 Microbiology spectrum Introduction SARS_CoV_2 G142D;G142D;L452R 130;221;141 135;226;146 S 187 192 34878296 Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. The most common nucleotide difference occurs at nucleotide position 21,987, which is the G to A transition that causes the G142D amino acid spike variant. 2021 Microbiology spectrum Introduction SARS_CoV_2 G142D 123 128 S 140 145 34878296 Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. The second most common SNP occurs in position 24,410, which causes the D950N amino acid variant. 2021 Microbiology spectrum Introduction SARS_CoV_2 D950N 71 76 34880295 Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal. Alarmingly, N = 2122 N501T strains were posted to GISAID from specimens collected in the months that followed the identification of this specimen in Senegal (January-April 2021) from countries in Africa, Europe, Asia, North America, and South America (GISAID, date of accession April 18th, 2021). 2021 Scientific reports Introduction SARS_CoV_2 N501T 21 26 34880295 Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal. All three of the genomes carrying the L452R/N501Y combination belonged to the A.27 lineage (clade 19B) and did not encode the D614G mutation that predominates most global infections today. 2021 Scientific reports Introduction SARS_CoV_2 D614G;L452R;N501Y 126;38;44 131;43;49 34880295 Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal. In addition to strains carrying L452R individually, variant strains carrying a combination of L452R + N501Y (3/117, 2.6%) were also identified. 2021 Scientific reports Introduction SARS_CoV_2 L452R;L452R;N501Y 32;94;102 37;99;107 34880295 Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal. In addition to the L452R + N501Y double mutant, a single genome was identified that carried a unique combination of E484K + N501T spike RBD mutations in a B.1 lineage genome (clade 20C) with D614G also present. 2021 Scientific reports Introduction SARS_CoV_2 D614G;E484K;L452R;N501T;N501Y 191;116;19;124;27 196;121;24;129;32 S;RBD 130;136 135;139 34880295 Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal. Likewise, the other lineage defining mutations for variants of concern were absent in the A.27 genomes, with the exception of L18F and H655Y, which are both present in the gamma lineage. 2021 Scientific reports Introduction SARS_CoV_2 H655Y;L18F 135;126 140;130 34880295 Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal. Notably, the E484K and L452R mutations in RBD had previously been demonstrated to confer immune escape in cell culture selection experiments, which is consistent with their increasing prevalence, possibly due to increased viral fitness. 2021 Scientific reports Introduction SARS_CoV_2 E484K;L452R 13;23 18;28 RBD 42 45 34880295 Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal. Strains harboring N501T first emerged in August of 2020 in Northern Italy and the N501T mutation has been found recently in an emerging Brazilian lineage that differs from B.1.501T.V1. 2021 Scientific reports Introduction SARS_CoV_2 N501T;N501T 18;82 23;87 34880295 Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal. Subsequent reports have demonstrated that increased transmissibility and immune escape are linked to these lineages, which are defined by spike receptor binding domain (RBD) mutations, including N501Y, K417N/T, L452R, and E484K. 2021 Scientific reports Introduction SARS_CoV_2 E484K;K417N;K417T;L452R;N501Y 222;202;202;211;195 227;209;209;216;200 RBD;S;RBD 144;138;169 167;143;172 34880295 Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal. The N501Y mutation confers higher affinity for the ACE2 receptor and is present in several variants of concern (alpha, beta, gamma) while L452R is a signature escape mutation found in the delta and epsilon lineages that also increases infectivity. 2021 Scientific reports Introduction SARS_CoV_2 L452R;N501Y 138;4 143;9 34880295 Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal. When classified by clade, all of the L452R mutations were exclusively found in 19B clade genomes whereas the L452M mutation appears to have emerged in wave two in the 20A clade (Supplemental Table 1). 2021 Scientific reports Introduction SARS_CoV_2 L452M;L452R 109;37 114;42 34880295 Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal. While E484K confers escape from neutralizing antibodies, the N501T mutation enhances the spike receptor binding domain (RBD) affinity for ACE2 in vitro and is predicted to enhance transmissibility, similar to N501Y. 2021 Scientific reports Introduction SARS_CoV_2 E484K;N501T;N501Y 6;61;209 11;66;214 RBD;S;RBD 95;89;120 118;94;123 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. A Delta strain bearing a known neutralisation-resistant mutation, E484K, has also established small clusters in the UK and contributed to breakthrough infections in Italy. 2021 Euro surveillance Introduction SARS_CoV_2 E484K 66 71 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. A functional consequence for Y145H remains to be established. 2021 Euro surveillance Introduction SARS_CoV_2 Y145H 29 34 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. and B.1.617.2 with E484K in Denmark. 2021 Euro surveillance Introduction SARS_CoV_2 E484K 19 24 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. Between 29 August and 15 November 2021, 56 cases of Delta strains with the E484K mutation have been identified in Denmark. 2021 Euro surveillance Introduction SARS_CoV_2 E484K 75 80 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. Here, we investigate the sensitivity of the Delta sub-lineage AY.4.2 and Delta lineage B.1.617 with the E484K mutation (+ E484K) to neutralisation by SARS-CoV-2 Comirnaty (BNT162b2 mRNA, BioNTech-Pfizer, Mainz, Germany/New York, United States (US)) vaccine-induced anti-sera. 2021 Euro surveillance Introduction SARS_CoV_2 E484K;E484K 104;122 109;127 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. In addition to Beta and Gamma, the E484K mutation has emerged in several different lineages, including Delta. 2021 Euro surveillance Introduction SARS_CoV_2 E484K 35 40 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. In contrast to AY.4.2, the B.1.617.2 strain with E484K had a significant reduction in virus neutralisation titres relative to D614G (4.0-fold) and all other Delta strains tested - B.1.617.2 (2.3-fold), AY.4 (2.3-fold), and AY.4.2 (1.7-fold) (p < 0.050 for all comparisons). 2021 Euro surveillance Introduction SARS_CoV_2 D614G;E484K 126;49 131;54 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. In contrast, the Delta lineage B.1.617.2 with the E484K neutralisation-resistant mutation (4.4-fold) approached the reduction in neutralisation titres observed for the Beta variant. 2021 Euro surveillance Introduction SARS_CoV_2 E484K 50 55 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. In the UK, 152 sequences of the Delta variant with E484K occurred by 8 November 2021, an increase of 59 cases since an earlier report on 15 October 2021. 2021 Euro surveillance Introduction SARS_CoV_2 E484K 51 56 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. Relative to the early pandemic strain (D614G), the AY.4.2 virus had a 2.3-fold reduction in median neutralisation titres (median titre: 199 vs 87; p < 0.001) (Figure 2). 2021 Euro surveillance Introduction SARS_CoV_2 D614G 39 44 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. Relative to the early pandemic strain (D614G), the reduction in the AY.4.2 sub-lineage-associated virus neutralisation (2.3-fold) was not as pronounced as observed for the Beta variant (4.9-fold). 2021 Euro surveillance Introduction SARS_CoV_2 D614G 39 44 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. The A222V mutation occurred in SARS-CoV-2 variants that emerged in June 2020, but has been shown not to contribute to increased transmissibility or immune escape in those variants. 2021 Euro surveillance Introduction SARS_CoV_2 A222V 4 9 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. The cohort (n = 30), vaccinated with two doses between 18 January and 15 May 2021, was selected to represent a broad age range (20-91 years; median: 42 years; interquartile range (IQR): 35-63; 7/30 donors were men) and varied neutralisation reactivity against an early pandemic strain that is highly homologous to the vaccine strain (D614G; Table). 2021 Euro surveillance Introduction SARS_CoV_2 D614G 334 339 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. The Delta sub-lineage AY.4.2 bears the same spike mutations as the Delta lineage AY.4 with the addition of Y145H and A222V in the N-terminal domain (Figure 1). 2021 Euro surveillance Introduction SARS_CoV_2 A222V;Y145H 117;107 122;112 S;N 44;130 49;131 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. We further evaluated a B.1.617.2 lineage isolate that contains the E484K amino acid substitution in the receptor-binding domain. 2021 Euro surveillance Introduction SARS_CoV_2 E484K 67 72 34886945 Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020. One of the notable variations, the D614G mutation, encodes a change from aspartic acid to glycine in the C-terminal region of the S1 domain of the viral spike protein of SARS-CoV-2. 2021 Euro surveillance Introduction SARS_CoV_2 D614G 35 40 S 153 158 34886945 Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020. Since late 2020, all emerging variants of concern (VOC) have carried the D614G mutation. 2021 Euro surveillance Introduction SARS_CoV_2 D614G 73 78 34886945 Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020. This hypothesis is corroborated by in vitro studies which showed that the D614G mutation is correlated with increased infectivity in cell models. 2021 Euro surveillance Introduction SARS_CoV_2 D614G 74 79 34888394 A Multidimensional Cross-Sectional Analysis of Coronavirus Disease 2019 Seroprevalence Among a Police Officer Cohort: The PoliCOV-19 Study. We also measured antibody titers of naturally acquired SARS-CoV-2 infection and correlated the results with the neutralizing capacity of the antibodies towards the "wild-type" SARS-CoV-2 spike (S) protein (expressing D614G) and the Alpha and Beta variants. 2021 Open forum infectious diseases Introduction SARS_CoV_2 D614G 217 222 S;S 187;194 192;195 COVID-19 55 75 34890524 The significant immune escape of pseudotyped SARS-CoV-2 variant Omicron. The neutralization sensitivity of PV-Omicron against serum samples from a panel of COVID-19 convalescent patients was tested, using PV-D614G (S protein from SARS-CoV-2 D614G strain) as the reference. 2022 Emerging microbes & infections Introduction SARS_CoV_2 D614G;D614G 168;135 173;140 S 142 143 COVID-19 83 91 34890524 The significant immune escape of pseudotyped SARS-CoV-2 variant Omicron. These mutations cover almost all the key mutations of the previous VOCs (Alpha, Beta, Gamma, and Delta), including K417N, E484A, and N501Y and other known mutations which are proved to change the sensitivity of the virus to neutralization by protective antibodies. 2022 Emerging microbes & infections Introduction SARS_CoV_2 E484A;K417N;N501Y 122;115;133 127;120;138 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. Because the spike protein mediates SARS-CoV-2 entry into the host and is also a significant target of neutralizing antibodies and vaccines, some key mutations of VOC occurring in the spike protein (e.g., D614G, N501Y and 69/70 deletion) have garnered significant scientific attention. 2022 Biosensors & bioelectronics Introduction SARS_CoV_2 D614G;N501Y 204;211 209;216 S;S 12;183 17;188 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. Clinical data indicate that N501Y-positive VOC significantly increase the risks of hospitalization (59% higher), intensive care unit admission (105% higher), and death (61% higher). 2022 Biosensors & bioelectronics Introduction SARS_CoV_2 N501Y 28 33 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. D614G, one of the key mutations, is a nonsynonymous amino acid change in the spike protein due to a 23,403 A>G single-base substitution in the SARS-CoV-2 reference sequence; the mutation was first identified in early 2020. 2022 Biosensors & bioelectronics Introduction SARS_CoV_2 A403G;D614G 103;0 110;5 S 77 82 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. Furthermore, the N501Y mutation exhibits poorer binding potential for 82.7% of the common alleles of the major histocompatibility complex than N501 and might escape immune defenses. 2022 Biosensors & bioelectronics Introduction SARS_CoV_2 N501Y 17 22 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. In addition, D614G variants have been demonstrated to increase the transmissibility in in vitro human cell models (from 1.3 to 7.7 folds) and in vivo animal models. 2022 Biosensors & bioelectronics Introduction SARS_CoV_2 D614G 13 18 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. N501Y is also a nonsynonymous amino acid change due to 23,063 A>T substitution in the SARS-CoV-2 reference sequence. 2022 Biosensors & bioelectronics Introduction SARS_CoV_2 N501Y 0 5 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. Recent evidence indicates that the N501Y mutation enhances the affinity to bind with the host angiotensin-converting enzyme 2 (ACE2) receptor by up to 7-fold more than that of the wild-type (WT) and also enhances viral transmission both in vivo (1.0-5.3 fold) and in vitro (1.3-5.4 fold). 2022 Biosensors & bioelectronics Introduction SARS_CoV_2 N501Y 35 40 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. The 69/70 deletion results from 204 to 209del in the S gene and has been found in both B.1.1.7 and B.1.526.1 variants. 2022 Biosensors & bioelectronics Introduction SARS_CoV_2 209del 39 45 S 53 54 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. The D614G mutation may alter proteolytic cleavage and further increase S1 shedding, or it could enhance the binding affinity between RBD and AEC2. 2022 Biosensors & bioelectronics Introduction SARS_CoV_2 D614G 4 9 RBD 133 136 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. Therefore, we assessed the detection of SARS-CoV-2 mutations of concern (69/70 deletion, N501Y, and D614G) using an improved Cas12a-based CRISPR on-site rapid detection system (CORDS) platform:a rapid, sensitive, and specific on-site biosensing system developed in our laboratory. 2022 Biosensors & bioelectronics Introduction SARS_CoV_2 D614G;N501Y 100;89 105;94 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. They reported that S mutation D614G increases infectivity. 2022 Gene Introduction SARS_CoV_2 D614G 30 35 S 19 20 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. While most of alterations in the receptor binding domain (RBD) reduce infectivity, A475V, L452R, V483A, and F490L variants induce resistance to some neutralizing antibodies. 2022 Gene Introduction SARS_CoV_2 A475V;F490L;L452R;V483A 83;108;90;97 88;113;95;102 RBD;RBD 33;58 56;61 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Along with the clade specific mutations, these variants have their own sets of characteristics mutations including several mutations in the S glycoprotein like Delta69-70, Delta144-145, N501Y, A570D, P681H, T716I, S982A, D1118H in the Alpha variant; D80A, D215G, Delta241-243, K417N, E484K, N501Y, A701V in the Beta variant; L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I in the Gamma variant; and T19R, E156G, Delta157-158, L452R, T478K, P681R, D950N in the Delta variant. 2022 Journal of infection and public health Introduction SARS_CoV_2 A570D;A701V;D1118H;D138Y;D215G;D80A;D950N;E156G;E484K;E484K;H655Y;K417N;K417T;L18F;L452R;N501Y;N501Y;N501Y;P26S;P681H;P681R;R190S;S982A;T1027I;T19R;T20N;T478K;T716I 193;298;221;343;256;250;466;424;284;364;378;277;357;325;445;186;291;371;337;200;459;350;214;385;418;331;452;207 198;303;227;348;261;254;471;429;289;369;383;282;362;329;450;191;296;376;341;205;464;355;219;391;422;335;457;212 S 140 154 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. B.1.617 is characterized by the S glycoprotein mutations L452R, D614G, and P681R. 2022 Journal of infection and public health Introduction SARS_CoV_2 D614G;L452R;P681R 64;57;75 69;62;80 S 32 46 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. It has three sublineages B.1.617.1/Kappa (S protein mutations: T95I, G142D, E154K, L452R, E484Q, D614G, P681R and Q1071H), B.1.617.2/Delta (S protein mutations: T19R, E156G, Delta157-158, L452R, T478K, D614G, P681R, D950N), and B.1.617.3 (S glycoprotein mutations: T19R, G142D, L452R, E484Q, D614G, P681R and D950N) (https://www.cdc.gov). 2022 Journal of infection and public health Introduction SARS_CoV_2 D614G;D614G;D614G;D950N;D950N;E154K;E156G;E484Q;E484Q;G142D;G142D;L452R;L452R;L452R;P681R;P681R;P681R;Q1071H;T19R;T19R;T478K;T95I 97;202;292;216;309;76;167;90;285;69;271;83;188;278;104;209;299;114;161;265;195;63 102;207;297;221;314;81;172;95;290;74;276;88;193;283;109;214;304;120;165;269;200;67 S;S;S 239;42;140 253;43;141 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. The D614G, the first mutation emerged within the S glycoprotein, has been shown to be responsible for better infectivity and transmissibility of the virus. 2022 Journal of infection and public health Introduction SARS_CoV_2 D614G 4 9 S 49 63 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. The second Indian variant, B.1.618, also known as triple mutant, has four mutations DeltaH146, DeltaY147, E484K, and D614G in the S glycoprotein. 2022 Journal of infection and public health Introduction SARS_CoV_2 D614G;E484K 117;106 122;111 S 130 144 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. This new variant is characterized by the presence of 12 co-existing mutations including E484K, D614G, P681H, and V1230L in the S glycoprotein. 2022 Journal of infection and public health Introduction SARS_CoV_2 D614G;E484K;P681H;V1230L 95;88;102;113 100;93;107;119 S 127 141 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. Besides, L452R mutation recently reported to enhance the viral replication by increasing the S protein stability and viral infectivity and viral fusogenicity. 2021 Medicine in drug discovery Introduction SARS_CoV_2 L452R 9 14 S 93 94 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. In contrary to T478K, the L452R variant is shown to enhance the total binding energy between RBD and ACE2 to be about 2.63 kcal/mol more negative than its value in WT protein. 2021 Medicine in drug discovery Introduction SARS_CoV_2 L452R;T478K 26;15 31;20 RBD 93 96 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. In this research, we study the effect of both of L452R and T478K variants in the RBD of the SARS-CoV2 on its binding to ACE2. 2021 Medicine in drug discovery Introduction SARS_CoV_2 L452R;T478K 49;59 54;64 RBD 81 84 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. In WT and protein with single mutation T478K, Maximum electrostatic interactions were reported between RBD-T500 and ACE2-D355 with ~ -2.94 and -2.8 kcal/mol, respectively. 2021 Medicine in drug discovery Introduction SARS_CoV_2 T478K 39 44 RBD 103 106 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. Mutations induced vdW interactions with maximum values between RBD- Q498 and ACE2- Y41 with ~ -1.97, -1.89 and -1.92 kcal/mol for double and single mutations T478K and L452R, respectively. 2021 Medicine in drug discovery Introduction SARS_CoV_2 L452R;T478K 168;158 173;163 RBD 63 66 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. Single and double mutations in RBD are shown to enhance the electrostatic energy between RBD-Q493 and ACE2-K31, where that L452R mutation induced the maximum increase in the electrostatic interaction energy with about -1.53 kcal/mol compared to its value in WT protein. 2021 Medicine in drug discovery Introduction SARS_CoV_2 L452R 123 128 RBD;RBD 31;89 34;92 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. Single mutations T478K and L452R induced an increase in the electrostatic interaction between RBD-R403 and ACE2-E37 with only ~0.1 kcal/mol. 2021 Medicine in drug discovery Introduction SARS_CoV_2 L452R;T478K 27;17 32;22 RBD 94 97 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. The mutation L452R have been reported to enhance the binding affinity to the host entry receptor ACE2, transmissibility, fitness, and infectivity and so improves the viral replication. 2021 Medicine in drug discovery Introduction SARS_CoV_2 L452R 13 18 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. This interaction is shown to be, slightly, reduced by the single mutation L452R to be 0.52 kcal/mol more positive compared to WT protein. 2021 Medicine in drug discovery Introduction SARS_CoV_2 L452R 74 79 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. Those changes include two mutations in the RBD; Leucine at position 452 to Arginine (L452R) and Threonine at position 478 to Lysine (T478K). 2021 Medicine in drug discovery Introduction SARS_CoV_2 L452R;T478K;L452R;T478K 48;96;85;133 83;131;90;138 RBD 43 46 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. To build both variants L452R and T478K, the sidechains of L452 and T478 were replaced by sidechains of Arginine and Lysine, respectively, using MCCE. 2021 Medicine in drug discovery Introduction SARS_CoV_2 L452R;T478K 23;33 28;38 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. A regular genome sequence is essential for viral specimens, particularly in the global context of a pandemic, since it aids to identify any emerging SARS-CoV-2 genetic strains, most importantly, with the development of the worldwide prevalence of D614G strain, which was linked with enhanced disease transmission however could not produce severe disease, the genetic transition was negligible at first. 2022 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 D614G 247 252 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. Consequently, ten mutations in the spike protein of B.1.617.2 strain, including T19R, (G142D*), 156/157del, R158G, L452R, T478K, D614G, P681R, and D950N were identified. 2022 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 D614G;D950N;L452R;P681R;R158G;T19R;T478K;G142D 129;147;115;136;108;80;122;87 134;152;120;141;113;84;127;92 S 35 40 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. Eight of these mutations are in the spike protein (S), including 69/70/144 deletion, N501Y, A570D, P681H, T716I, S982A, D1118H. 2022 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;T716I 92;120;85;99;113;106 97;126;90;104;118;111 S;S 36;51 41;52 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. Higher selectivity of the spike protein for ACE2 receptors is shown in N501Y, resulting in improved viral adhesion and the following entrance into host cells. 2022 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 N501Y 71 76 S 26 31 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. In the spike protein of the B.1.1.28 strain, there are eleven mutations, including L18F, T20N, P26S, D138Y, R190S, H655Y, T1027I, D614G, K417T, E484K, and N501Y. 2022 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 D138Y;D614G;E484K;H655Y;K417T;L18F;N501Y;P26S;R190S;T1027I;T20N 101;130;144;115;137;83;155;95;108;122;89 106;135;149;120;142;87;160;99;113;128;93 S 7 12 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. Strain B.1.351 contains nine mutations within spike protein, including the L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G, and A701V. 2022 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;L18F;N501Y;R246I 133;87;122;81;108;101;75;115;94 138;92;127;85;113;106;79;120;99 S 46 51 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. The binding affinity for the ACE2 receptors is increased by three mutations of K417N, E484K, and N501Y situated within RBD. 2022 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 E484K;K417N;N501Y 86;79;97 91;84;102 RBD 119 122 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. There are three mutations throughout the RBD that are comparable to the B.1.351 strain: L18F, K417N, and E484K. 2022 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 E484K;K417N;L18F 105;94;88 110;99;92 RBD 41 44 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. As discussed above, D614G and B.1.1.7 (Alpha) emerged relatively early and received much attention as they rapidly spread globally. 2021 Nature communications Introduction SARS_CoV_2 D614G 20 25 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. Specifically for the United Kingdom, the selection coefficient for D614G has been estimated using phylogenetic and phylodynamic methods, although the estimates from the various methods are highly variable. 2021 Nature communications Introduction SARS_CoV_2 D614G 67 72 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. The global spread of the D614G variant was first described by Korber et al. 2021 Nature communications Introduction SARS_CoV_2 D614G 25 30 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. The increased infectiousness of D614G has also been functionally explained in terms of ACE2-receptor binding. 2021 Nature communications Introduction SARS_CoV_2 D614G 32 37 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. These changes to the SARS-CoV-2 phenotype embodied in D614G, Alpha, and Delta likely represent only a small fraction of the phenotypic variability in the broader population. 2021 Nature communications Introduction SARS_CoV_2 D614G 54 59 34909459 Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M(pro). Further, some studies show that SARS-CoV-2 modification carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. 2021 ChemistrySelect Introduction SARS_CoV_2 D614G 101 106 S 69 74 34909459 Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M(pro). Further, the binding potential between OPG and the synthesized compounds 1 [4-bromobenzyl (Z)-N'-(adamantan-1-yl)-4-phenylpiperazine-1-carbothioimidate], 2 [3,5-bis(trifluoromethyl)benzyl (Z)-N'-(adamantan-1-yl)-4-phenylpiperazine-1-carbothioimidate], 3 [4-bromobenzyl (Z)-N-(adamantan-1-yl)morpholine-4-carbothioimidate] and 4 [3,5-bis(trifluoromethyl)benzyl (Z)-N-(adamantan-1-yl)morpholine-4-carbothioimidate] (Figure 1) towards SK, SARS-CoV-2 main protease Mpro and mutation of SARS-CoV-2 Spike (S) Protein D614G, is determined using molecular docking simulations regarding potential interactions between this compounds and targeted proteins. 2021 ChemistrySelect Introduction SARS_CoV_2 D614G 511 516 S;S 493;500 498;501 34909775 Intranasal immunization with a vaccinia virus vaccine vector expressing pre-fusion stabilized SARS-CoV-2 spike fully protected mice against lethal challenge with the heavily mutated mouse-adapted SARS2-N501Y MA30 strain of SARS-CoV-2. SARS2-N501YMA30 was generated by serially passaging through mice of Washington strain SARS-CoV-2 that had an N501Y spike mutation. 2021 bioRxiv Introduction SARS_CoV_2 N501Y 109 114 S 115 120 34909775 Intranasal immunization with a vaccinia virus vaccine vector expressing pre-fusion stabilized SARS-CoV-2 spike fully protected mice against lethal challenge with the heavily mutated mouse-adapted SARS2-N501Y MA30 strain of SARS-CoV-2. Thus, Washington strain spike, when expressed from a highly attenuated, replication-competent heat-stable poxvirus vector, administered without parenteral injection, can fully protect against challenge with the heavily mutated, mouse-adapted SARS2-N501YMA30 variant of SARS-CoV-2. 2021 bioRxiv Introduction SARS_CoV_2 N501Y 248 253 S 24 29 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. Another VOC to emerge at about the same time was Beta (B.1.351), which is characterized by other NTD mutations and deletions, as well as key RBD mutations, including K417N, E484K, and N501Y. 2021 bioRxiv Introduction SARS_CoV_2 E484K;K417N;N501Y 173;166;184 178;171;189 RBD 141 144 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. As a result, nearly all currently circulating SARS-CoV-2 strains bear the D614G mutation. 2021 bioRxiv Introduction SARS_CoV_2 D614G 74 79 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. Finally, Delta (B.1.617.2) is responsible for the most recent wave of the COVID-19 pandemic and is characterized by new NTD alterations, together with key RBD mutations (L452R and T478K). 2021 bioRxiv Introduction SARS_CoV_2 T478K;L452R 180;170 185;175 RBD 155 158 COVID-19 74 82 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. One VOC, Alpha (B.1.1.7), is characterized by N-terminal domain (NTD) deletions and a key N501Y mutation in its receptor-binding domain (RBD). 2021 bioRxiv Introduction SARS_CoV_2 N501Y 90 95 RBD;N 137;46 140;47 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. Very soon after zoonotic transmission, SARS-CoV-2 acquired a predominant D614G mutation in its spike (S) protein. 2021 bioRxiv Introduction SARS_CoV_2 D614G 73 78 S;S 95;102 100;103 34909788 SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection. Also, the R346K substitution in the isolate, a putative escape mutation which may confer additional antibody resistance (https://jbloomlab.github.io/SARS2_RBD_Ab_escape_maps/escape-calc/), is not found in the majority of Omicron genomes. 2021 medRxiv Introduction SARS_CoV_2 R346K 10 15 34909788 SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection. Fold-drop relative to the ancestral D614G virus was 4.3 for H1299-ACE2 and 5.0 for Vero E6. 2021 medRxiv Introduction SARS_CoV_2 D614G 36 41 34909788 SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection. H1299-ACE2 cells were similar to Vero E6 in the formation of infection foci in a live virus infection with ancestral D614G and Beta variant viruses but were considerably more sensitive relative to unmodified Vero E6 (Fig S2A-B). 2021 medRxiv Introduction SARS_CoV_2 D614G 117 122 34909788 SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection. Sequencing of the isolated virus confirmed it was the Omicron variant bearing the R346K mutation. 2021 medRxiv Introduction SARS_CoV_2 R346K 82 87 34909788 SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection. We then tested the ability of plasma from BNT162b2 vaccinated study participants to neutralize Omicron versus ancestral D614G virus in a live virus neutralization assay. 2021 medRxiv Introduction SARS_CoV_2 D614G 120 125 34912372 Hotspot Mutations in SARS-CoV-2. In December 2020, the variant B.1.351 was first detected in South Africa, with mutations such as K417N, E484K, N501Y, D614G, and A701V. 2021 Frontiers in genetics Introduction SARS_CoV_2 A701V;D614G;E484K;K417N;N501Y 129;118;104;97;111 134;123;109;102;116 34912372 Hotspot Mutations in SARS-CoV-2. In this regard, the variant B.1.1.7 was first identified in the United Kingdom, which contains E484K, N501Y, D614G, and P681H mutations in Spike glycoprotein. 2021 Frontiers in genetics Introduction SARS_CoV_2 D614G;E484K;N501Y;P681H 109;95;102;120 114;100;107;125 S 139 157 34912372 Hotspot Mutations in SARS-CoV-2. On the other hand, the variant B.1.617.2 was first identified in India with L452R, T478K, D614G, and P681R mutations in Spike glycoprotein. 2021 Frontiers in genetics Introduction SARS_CoV_2 D614G;L452R;P681R;T478K 90;76;101;83 95;81;106;88 S 120 138 34912372 Hotspot Mutations in SARS-CoV-2. The Brazilian variant P.1 also has almost the same mutations as the B.1.351 variant, but instead of A701V, the P.1 variant has H555Y mutation. 2021 Frontiers in genetics Introduction SARS_CoV_2 A701V;H555Y 100;127 105;132 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. The increasingly prevalent SARS-CoV-2 variant in North America and Europe during the timespan of the USA study was the D614G variant of the G clade, which did not progress in Asia until later. 2021 PLoS computational biology Introduction SARS_CoV_2 D614G 119 124 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. The most signifying characteristic of this early variant is the mutation in the spike protein S-D614G. 2021 PLoS computational biology Introduction SARS_CoV_2 D614G 96 101 S;S 80;94 85;95 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. To this end, we first analyzed a large dataset from the USA, that consists of approximately 70% of D614G variant cases at this time, to compare to our previous results that were calculated from a large dataset from China, that consists of approximately 2% of D614G variant cases at the time of data collection. 2021 PLoS computational biology Introduction SARS_CoV_2 D614G;D614G 99;259 104;264 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. We then analyzed other datasets to determine whether the D614G mutation is correlated with the predicted likely order of symptom onset. 2021 PLoS computational biology Introduction SARS_CoV_2 D614G 57 62 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Additionally, three of the four VoC RBD mutations (L452R, E484K, and N501Y) are located within the receptor binding motif (RBM), which comprises the interaction interface between the S protein and ACE2. 2021 Cell reports Introduction SARS_CoV_2 E484K;N501Y;L452R 58;69;51 63;74;56 RBD;S 36;183 39;184 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. The one RBD mutation occurring outside of the RBM, K417N/T, additionally exhibits ambiguity in mutation, with the P.1 strain mutated to threonine (K417T) and the B.1.351 strain mutated to asparagine (K417N) (Figure 1B). 2021 Cell reports Introduction SARS_CoV_2 K417N;K417T;K417N;K417T 51;51;200;147 58;58;205;152 RBD 8 11 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. (https://viralzone.expasy.org/9556) Among them, lineages B.1.1.7, B.1.351, and P.1 contain a key common RBM mutation, N501Y, which was experimentally shown to increase the ACE2 binding affinity. 2022 International immunopharmacology Introduction SARS_CoV_2 N501Y 118 123 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. A molecular-level insight is urgently required to quantitate the effect of both the N501Y and E484K RBD mutations on receptor recognition and therapeutic monoclonal antibody recognition. 2022 International immunopharmacology Introduction SARS_CoV_2 E484K;N501Y 94;84 99;89 RBD 100 103 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Also, the E484K variant caused a 3 4-fold decrease in the neutralization titer in five individuals who received two doses of the Pfizer-BioNTech vaccine. 2022 International immunopharmacology Introduction SARS_CoV_2 E484K 10 15 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Among these mutants, the N439K exhibits resistance to several mAbs and even escapes some polyclonal responses. 2022 International immunopharmacology Introduction SARS_CoV_2 N439K 25 30 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. An enhancement of -0.81 kcal/mol in the ACE2 binding free energy was reported for the N501Y mutant, which was attributed to the formation of favorable interactions with Tyr41 and Lys353 of ACE2. 2022 International immunopharmacology Introduction SARS_CoV_2 N501Y 86 91 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Analysis of the crystal structure of G485R RBD mutant-ACE2 complex (PDB ID: 7LO4) reveals that the residue 485 is not directly interacts with hACE2. 2022 International immunopharmacology Introduction SARS_CoV_2 G485R 37 42 RBD 43 46 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Currently, there are four variants of concerns: Alpha variant (B.1.1.7; RBD mutations: N501Y, A570D), Beta (B.1.351; RBD mutations: K417N, E484K, and N501Y), Gamma (P.1, B.1.1.28.1; RBD mutations: K417N/T, E484K, and N501Y) and Delta (B.1.617.2; RBD mutations: L452R, T478K). 2022 International immunopharmacology Introduction SARS_CoV_2 A570D;E484K;E484K;K417N;K417N;K417T;L452R;N501Y;N501Y;N501Y;T478K 94;139;206;132;197;197;261;87;150;217;268 99;144;211;137;204;204;266;92;155;222;273 RBD;RBD;RBD;RBD 72;117;182;246 75;120;185;249 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. E484K mutation may be accountable for evasion from neutralizing antibodies. 2022 International immunopharmacology Introduction SARS_CoV_2 E484K 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. G446V RBD mutation was reported to reduce ACE2 binding affinities, but S477N mutation strengthen the binding between SARS-CoV2 spike RBD and hACE2. 2022 International immunopharmacology Introduction SARS_CoV_2 S477N;G446V 71;0 76;5 S;RBD;RBD 127;6;133 132;9;136 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. G485R mutation leads to a rotation in the loop, affecting some interacting residues without significantly reducing the affinity. 2022 International immunopharmacology Introduction SARS_CoV_2 G485R 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Here, we critically decode the role of both the N501Y and E484K spike mutations on ACE2 and neutralization antibody recognition using extensive all-atom molecular dynamics simulation complimented with binding free energy simulations. 2022 International immunopharmacology Introduction SARS_CoV_2 E484K;N501Y 58;48 63;53 S 64 69 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. However, mouse-adapted SARS-CoV-2 N501Y strain can be effectively neutralized by vaccine-elicited sera. 2022 International immunopharmacology Introduction SARS_CoV_2 N501Y 34 39 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. However, surface plasmon resonance (SPR) binding assays revealed over ten times increment in binding affinity for Y501 RBD with ACE2, in comparison to the wild-type N501Y due to the formation of two new hydrogen bonds with the side chains of Asp38 and Lys353 of ACE2, in addition to the formation of a pi stacking interaction between Tyr501 of RBD and Tyr41 of ACE2. 2022 International immunopharmacology Introduction SARS_CoV_2 N501Y 165 170 RBD;RBD 119;344 122;347 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. However, the E484K RBD mutation diminishes its interaction with Bamlanivimab in vitro. 2022 International immunopharmacology Introduction SARS_CoV_2 E484K 13 18 RBD 19 22 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. In pseudoviruses carrying the N501Y mutation, a 10-fold decrease in efficacy was reported during the neutralization of mRNA vaccine-elicited mAbs. 2022 International immunopharmacology Introduction SARS_CoV_2 N501Y 30 35 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Initial modeling studies suggest enhancement of ACE2 binding affinity for E484K mutant due to the formation of additional hydrogen bond involving Lys484 of mutant RBD with ACE2 and gain in average solvation energy. 2022 International immunopharmacology Introduction SARS_CoV_2 E484K 74 79 RBD 163 166 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Later, it was demonstrated that the S494P caused a 3-5 fold decrease in neutralization titer and was reported in many cases in UK, USA, and Mexico. 2022 International immunopharmacology Introduction SARS_CoV_2 S494P 36 41 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. N439K, L452R, and Y453F showed an increase in ACE2 receptor binding ability. 2022 International immunopharmacology Introduction SARS_CoV_2 L452R;Y453F;N439K 7;18;0 12;23;5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. On the other hand, an ELISA-based ACE2/RBD inhibition assay reports Y453F RBD mutant does not decrease established humoral immunity from previously infected individuals or affect the neutralizing antibody response. 2022 International immunopharmacology Introduction SARS_CoV_2 Y453F 68 73 RBD;RBD 39;74 42;77 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. On the otherhand, G446V, S477N, G485R, and F490S RBD mutants demonstrated ~3-5 fold decrease in neutralization titer for few sera. 2022 International immunopharmacology Introduction SARS_CoV_2 F490S;G446V;G485R;S477N 43;18;32;25 48;23;37;30 RBD 49 52 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. performed 185ns equilibrium simulation and free energy calculation using the FEP (Free energy perturbation) method to evaluate the effect of N501Y mutation on ACE2 binding. 2022 International immunopharmacology Introduction SARS_CoV_2 N501Y 141 146 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Recent data suggest that N501Y mutation does not significantly alter the binding affinity with one of the mAb, Bamlanivimab. 2022 International immunopharmacology Introduction SARS_CoV_2 N501Y 25 30 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Recently, computational and experimental approaches have been adopted to understand the mechanism of increased transmissibility and the immune invasion ability of the N501Y spike mutant. 2022 International immunopharmacology Introduction SARS_CoV_2 N501Y 167 172 S 173 178 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Recently, in-vitro micro-neutralization assays revealed a significant reduction in neutralization efficiency for the recombinant (r)SARS-CoV-2 virus with E484K mutation compared to the control USA-WA1/2020 strain on 34 sera collected from different study participants. 2022 International immunopharmacology Introduction SARS_CoV_2 E484K 154 159 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. reported minor enhancement in the RBD-ACE2 interaction energies upon N501Y mutations using the molecular dynamics simulations. 2022 International immunopharmacology Introduction SARS_CoV_2 N501Y 69 74 RBD 34 37 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The F490S mutation on the other hand showed limited effects on ACE2 binding affinity. 2022 International immunopharmacology Introduction SARS_CoV_2 F490S 4 9 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The variant of interest P.2, first reported in Rio de Janeiro and then rapidly widespread in the northeast region of Brazil, contains only the E484K spike mutation. 2022 International immunopharmacology Introduction SARS_CoV_2 E484K 143 148 S 149 154 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. These include N440K, S443A, G476S, E484R, and G502P, which cluster near known human ACE2 recognition sites, Lys31 and Lys353. 2022 International immunopharmacology Introduction SARS_CoV_2 E484R;G476S;G502P;N440K;S443A 35;28;46;14;21 40;33;51;19;26 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. They observed an enhancement of 7 kcal/mol in ACE2 binding energy upon N501Y mutations. 2022 International immunopharmacology Introduction SARS_CoV_2 N501Y 71 76 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. This mutation itself and in combination with the N501Y mutation significantly enhance the ACE2 binding affinity, evident from SPR data. 2022 International immunopharmacology Introduction SARS_CoV_2 N501Y 49 54 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Two other rapidly emerging SARS-CoV2 variants (B.1.135 and P.1) contain another crucial RBM mutation, E484K. 2022 International immunopharmacology Introduction SARS_CoV_2 E484K 102 107 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Using a large-scale genomic screening pipeline, my group previously identified two spike mutants, V367F and S494P, with enhanced human ACE2 binding ability. 2022 International immunopharmacology Introduction SARS_CoV_2 S494P;V367F 108;98 113;103 S 83 88 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Verma et al., on the other hand, performed structural modeling using computation mutagenesis followed by energy minimization and binding free energy calculations using MM/GBSA (Molecular Mechanics/Generalized Born Surface Area) method to probe the effect of N501Y RBD mutation on the ACE2 binding affinity. 2022 International immunopharmacology Introduction SARS_CoV_2 N501Y 258 263 RBD 264 267 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. While, in vitro study demonstrates that reduced sensitivity of the L452R RBD mutant to BNT162b2 mRNA vaccine-elicited antibodies. 2022 International immunopharmacology Introduction SARS_CoV_2 L452R 67 72 RBD 73 76 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. In addition, an Nsp12 mutation (P323L) and N protein double mutations (R203K and G204R) were also found. 2021 Frontiers in medicine Introduction SARS_CoV_2 G204R;P323L;R203K 81;32;71 86;37;76 Nsp12;N 16;43 21;44 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. Mutant strains have appeared one after another around the world, currently mainly including D614G, B.1.1.207, 501Y.V2/B.1.351, B.1.1.7, B.1.429, P.1, and P.2, B.1.617, etc. 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 92 97 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. Unexpectedly, this sequence contained a spike protein mutation (D614G). 2021 Frontiers in medicine Introduction SARS_CoV_2 D614G 64 69 S 40 45 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. The majority of potent mAbs are directed to the mutations present in the Beta RBD, principally N501Y, and E484K, underscoring the small antigenic distance between Beta and Gamma, the larger distance between early pandemic strains and Beta, and interestingly, few anti-Beta mAbs can neutralize Delta, consistent with the extreme antigenic distance between Beta and Delta. 2022 Cell host & microbe Introduction SARS_CoV_2 E484K;N501Y 106;95 111;100 RBD 78 81 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. The RBD mutations found in Alpha (N501Y), Beta (K417N, E484K, and N501Y), Gamma (K417T, E484K, and N501Y), and Delta (L452R and T478K) are located in or closely adjacent to the ACE2-interacting surface where they have the potential to modulate ACE2 interaction or disrupt the binding of neutralizing mAbs. 2022 Cell host & microbe Introduction SARS_CoV_2 E484K;E484K;N501Y;N501Y;T478K;K417N;K417T;L452R;N501Y 55;88;66;99;128;48;81;118;34 60;93;71;104;133;53;86;123;39 RBD 4 7 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. The RBD mutations present in Beta (K417N, E484K, and N501Y) disrupt the binding of a number of potent neutralizing mAbs including some being developed for clinical use and likely, together with changes in the NTD, explain the antigenic distance between Beta and early SARS-CoV-2 strains. 2022 Cell host & microbe Introduction SARS_CoV_2 E484K;N501Y;K417N 42;53;35 47;58;40 RBD 4 7 34923570 Heterologous prime-boost immunizations with chimpanzee adenoviral vectors elicit potent and protective immunity against SARS-CoV-2 infection. However, the highly transmissible SARS-CoV-2 variants B.1.1.7 lineage (also known as N501Y.V1 or VOC-202012/01) and B.1.351 lineage (also known as N501Y.V2), discovered and reported in the United Kingdom and South Africa, respectively, carrying mutations in the RBD of spike have led to wide concerns. 2021 Cell discovery Introduction SARS_CoV_2 N501Y;N501Y 85;147 90;152 S;RBD 269;262 274;265 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. NC_045512), the mutations in NSP13 included P77L in Delta (B.1.617.2), Q88H in Iota (B.1.526), D260Y in Epsilon (B.1.429), E341D in Gamma (P.1.1), and M429I in Kappa (B.1.617.1). 2021 Frontiers in microbiology Introduction SARS_CoV_2 D260Y;E341D;M429I;P77L;Q88H 95;123;151;44;71 100;128;156;48;75 Nsp13 29 34 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. The mutations P504L and Y541C in NSP13 were important for different disease outcomes. 2021 Frontiers in microbiology Introduction SARS_CoV_2 P504L;Y541C 14;24 19;29 Nsp13 33 38 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The Alpha (B.1.1.7) variant encodes an S protein with nine mutations (del 69-70, Del 144, N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H), of which N501Y is in the receptor-binding domain (RBD). 2021 Frontiers in immunology Introduction SARS_CoV_2 A570D;D1118H;D614G;N501Y;N501Y;P681H;S982A;T716I 97;136;104;90;154;111;125;118 102;142;109;95;159;116;130;123 RBD;S 195;39 198;40 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The Beta (B.1.351) variant encodes an S protein with nine mutations (L18F, D80A, D215G, Del 241-243, K417N, E484K, N501Y, D614G and A701V, three of which (K417N, E484K and N501Y) are in the RBD. 2021 Frontiers in immunology Introduction SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;E484K;K417N;N501Y;N501Y;K417N;L18F 132;81;122;75;108;162;101;115;172;155;69 137;86;127;79;113;167;106;120;177;160;73 RBD;S 190;38 193;39 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The Delta (B.1.617.2) variant encodes an S protein with ten mutations (T19R, G142D, del 156, del 157, R158G, L452R, T478K, D614G, P681R, and D950N), two of which are in the RBD (L452R and T478K). 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G;D950N;G142D;L452R;P681R;R158G;T478K;T478K;L452R;T19R 123;141;77;109;130;102;116;188;178;71 128;146;82;114;135;107;121;193;183;75 RBD;S 173;41 176;42 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The Gamma P.1 variant encodes an S protein with 12 mutations (L18F, T20N, P26S, D138Y, R190S, K417N/T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F), two of which are in the RBD (E484K, and N501Y). 2021 Frontiers in immunology Introduction SARS_CoV_2 D138Y;D614G;E484K;H655Y;K417N;K417T;N501Y;N501Y;P26S;R190S;T1027I;T20N;V1176F;E484K;L18F 80;117;103;124;94;94;110;192;74;87;131;68;143;181;62 85;122;108;129;101;101;115;197;78;92;137;72;149;186;66 RBD;S 176;33 179;34 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The immunity-evading mutations in the Beta (B1.351) variant include E484K in the RBD of the S protein, while those in the Delta (B.167.2) variant include L19R, del 157, del 158, L452R, and T478K in the S protein. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K;L19R;L452R;T478K 68;154;178;189 73;158;183;194 RBD;S;S 81;92;202 84;93;203 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. All the three variants retain N501Y mutation on spike protein receptor binding domain (RBD) which is required for binding to human receptor ACE2 (hACE2) for viral entry to host cells. 2022 Travel medicine and infectious disease Introduction SARS_CoV_2 N501Y 30 35 RBD;S;RBD 62;48;87 85;53;90 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. However, not much are reported as an evidence of kinase or other signaling pathways resulting the severe complications or increased death rate by variant containing N501Y mutation has been concluded. 2022 Travel medicine and infectious disease Introduction SARS_CoV_2 N501Y 165 170 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. The B.1.1.7 is reported to be more infectious with higher spreading rate and increased binding affinity to ACE2 in particular due to N501Y, compared with other mutations such as E484K. 2022 Travel medicine and infectious disease Introduction SARS_CoV_2 E484K;N501Y 178;133 183;138 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. The N501Y mutation localizes at RBD that might help in attaining higher binding to host cells and result elevated transmission and infectious. 2022 Travel medicine and infectious disease Introduction SARS_CoV_2 N501Y 4 9 RBD 32 35 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. Therefore, we hypothesized that the N501Y mutation could be more prone to the host-kinases to be modified or phosphorylated. 2022 Travel medicine and infectious disease Introduction SARS_CoV_2 N501Y 36 41 34931119 Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences. The first mutation is the N501Y that is one of the six central contact residues in the receptor-binding domain (RBD) of the spike protein. 2022 International journal of peptide research and therapeutics Introduction SARS_CoV_2 N501Y 26 31 S;RBD 124;112 129;115 34931119 Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences. The third mutation, P681H, is located immediately near the furin cleavage site. 2022 International journal of peptide research and therapeutics Introduction SARS_CoV_2 P681H 20 25 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. A post-boost improvement in neutralization also was seen for Beta (3.4- and 2.6-fold less susceptible, respectively, than D614G). 2021 medRxiv Introduction SARS_CoV_2 D614G 122 127 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. A second subset of COVE samples having moderate titers against D614G was pre-selected to avoid potential bias of high titer sera. 2021 medRxiv Introduction SARS_CoV_2 D614G 63 68 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. Alpha and Delta were modest neutralization escape variants, being 2-3 fold less susceptible than D614G to neutralization by mRNA-1273 vaccine-induced antibodies and having little impact on mRNA-1273 vaccine efficacy. 2021 medRxiv Introduction SARS_CoV_2 D614G 97 102 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. An approximate 12-fold improvement in Omicron neutralization was seen after the 50 mug boost such that the variant was now only 6.5- and 4.2-fold less neutralization-susceptible, respectively, than D614G (Fig 1). 2021 medRxiv Introduction SARS_CoV_2 D614G 198 203 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. Both laboratories assayed D614G and Beta as comparators. 2021 medRxiv Introduction SARS_CoV_2 D614G 26 31 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. Compared to D614G, ID50 geometric mean titers (GMTs) after 2 doses of vaccine were 84-fold and 49-fold lower against Omicron in the VRC and Duke laboratories, respectively (Fig 1). 2021 medRxiv Introduction SARS_CoV_2 D614G 12 17 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. D614G spike binding and neutralizing antibodies also correlated with vaccine efficacy in the COVE study, further strengthening the utility of this spike as a reference standard. 2021 medRxiv Introduction SARS_CoV_2 D614G 0 5 S;S 6;147 11;152 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. ID50 titers 2 weeks after the second dose were highest against D614G and lowest against Omicron, where titers against Omicron were 35.1-fold lower and titers against Beta were 8.9-fold lower than D614G (Fig 2). 2021 medRxiv Introduction SARS_CoV_2 D614G;D614G 63;196 68;201 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. Importantly, D614G was dominant over the period of time when the Moderna mRNA-1273 vaccine demonstrated 94% efficacy in preventing symptomatic COVID-19 in the Coronavirus Efficacy (COVE) phase 3 trial, making D614G spike protein a primary reference standard. 2021 medRxiv Introduction SARS_CoV_2 D614G;D614G 13;209 18;214 S 215 220 COVID-19 143 151 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. In a separate analysis, sequential serum samples from the 7 participants who were vaccinated and boosted under EUA were tested against D614G, Beta and Omicron. 2021 medRxiv Introduction SARS_CoV_2 D614G 135 140 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. In contrast to the dramatic reduction in titers seen after the second dose, the post-boost ID50 GMT against Omicron showed a more modest 6.5-fold reduction compared to D614G, and the post-boost titers against Beta showed a 3.4-fold reduction compared to D614G, for all 7 participants combined. 2021 medRxiv Introduction SARS_CoV_2 D614G;D614G 168;254 173;259 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. Notably, D614G is one of the most neutralization-sensitive forms of the virus known to date. 2021 medRxiv Introduction SARS_CoV_2 D614G 9 14 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. One subset of samples from the COVE study was pre-selected as having high titers of neutralizing antibodies against D614G to enable detection of a wide range of titer reductions against Omicron. 2021 medRxiv Introduction SARS_CoV_2 D614G 116 121 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. The Beta variant contained spike mutations L18F, D80A, D215G, Delta242-244, R246I, K417N, E484K, N501Y and A701V. 2021 medRxiv Introduction SARS_CoV_2 A701V;D215G;D80A;E484K;K417N;L18F;N501Y;R246I 107;55;49;90;83;43;97;76 112;60;53;95;88;47;102;81 S 27 32 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. The earliest variant carried a single spike mutation, D614G, providing a fitness advantage for transmission and rapidly replacing the ancestral virus as the dominant pandemic variant by May, 2020. 2021 medRxiv Introduction SARS_CoV_2 D614G 54 59 S 38 43 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. The latter set specifically included the highest D614G responders. 2021 medRxiv Introduction SARS_CoV_2 D614G 49 54 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. The main purpose of this study was to gain an early understanding of the extent by which Omicron escapes vaccine-elicited neutralizing antibodies in comparison to D614G and Beta. 2021 medRxiv Introduction SARS_CoV_2 D614G 163 168 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. The Omicron spike in this study contained mutations A67V, Delta69-70, T95I, G142D, Delta143-145, Delta211, L212I, +214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F. 2021 medRxiv Introduction SARS_CoV_2 A67V;D614G;D796Y;E484A;G142D;G339D;G446S;G496S;H655Y;K417N;L212I;L981F;N440K;N501Y;N679K;N764K;N856K;N969K;P681H;Q493R;Q498R;Q954H;S371L;S373P;S375F;S477N;T478K;T547K;T95I;Y505H 52;235;270;186;76;123;165;200;242;151;107;298;158;214;249;263;277;291;256;193;207;284;130;137;144;172;179;228;70;221 56;240;275;191;81;128;170;205;247;156;112;303;163;219;254;268;282;296;261;198;212;289;135;142;149;177;184;233;74;226 S 12 17 34931200 Booster of mRNA-1273 Strengthens SARS-CoV-2 Omicron Neutralization. Together, these results suggest that neutralizing titers to Omicron are 49-84 times lower than neutralization titers to D614G after 2 doses of mRNA-1273, which could lead to an increased risk of symptomatic breakthrough infections. 2021 medRxiv Introduction SARS_CoV_2 D614G 120 125 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. A distribution of conformations taken from the equilibrium simulations of the locked form of the unglycosylated and uncleaved D614G spike with LA bound was used as the starting point for the dynamical-nonequilibrium simulations. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 126 131 S 132 137 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. An analogous analysis was performed on the D614G mutant to establish whether K854 makes alternative hydrogen-bond or salt-bridge contacts across the 3 subunit interfaces (averaged over 3 x 200 ns replicates) in the absence of a partnering D614 carboxylate. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 43 48 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. As noted above, the response of the D614G spike to LA is also less symmetrical than the wild-type. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 36 41 S 42 47 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. Dynamical-nonequilibrium simulations of the D614G variant were also performed to test whether the D614G mutation affects the response of the spike to LA. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G;D614G 44;98 49;103 S 141 146 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. For instance, the amplitude of the structural response of the V266-L629 and furin cleavage/recognition site regions in monomer C (Figure S33) of the D614G is substantially smaller than in monomers B and A. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 149 154 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. Furthermore, the region located upstream of the fusion peptide, namely D808-S813, also shows different rates of signal propagation between the wild-type and D614G proteins. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 157 162 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. Here, three equilibrium 200 ns MD simulations were performed for the locked form of the unglycosylated and uncleaved ectodomain region of the D614G spike modelled from a wild-type model based on the cryo-EM structure 6ZB5 with and without LA bound (see Supplementary Material). 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 142 147 S 148 153 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. However, the D614G mutation significantly affects inter-monomer communication, with reduction of signal transmission from the furin cleavage/recognition site and V622-L629 of one monomer to the FPPR of another. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 13 18 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. However, three of the four variants, involved in the April 2021 surge of cases in India as well as the B.1.617.2 (Delta) and B.1.1.529 (Omicron) variants do include D614G among the mutations (COVID-19 Genomics UK Consortium, https://www.cogconsortium.uk and https://www.ecdc.europa.eu/). 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 165 170 COVID-19 192 200 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. However, unlike the wild-type with or without LA, a single chain in one replicate of the D614G with LA bound exhibits greater fluctuation in the middle of the RBM corresponding to exposed loop residues Q474-N487 (Figure S21). 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 89 94 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. In the D614G spike, K854 fails to find any alternative salt-bridge and only occasionally comes within hydrogen-bonding distance of residues Q613 and N317 (Figure S24). 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 7 12 S 13 18 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. In the D614G spike, only minor deviations of the FPPR are observed. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 7 12 S 13 18 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. In the D614G variant, there is notably less symmetry across the monomers in the response of the spike to LA removal, compared to the wild-type. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 7 12 S 96 101 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. LA and the D614G mutation may affect glycosylation. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 11 16 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. Note that D614G has the same sequence as the wild-type except for the residue in position 614, which was mutated from an aspartate to a glycine. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 10 15 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. Root mean square fluctuation (RMSF) profiles from equilibrium MD for the wild-type and D614G apo spikes are similar (Figure S21). 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 87 92 S 97 103 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. Simulations of the D614G spike . 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 20 25 S 25 30 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. Simulations of the D614G spike. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 19 24 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. That a single amino acid replacement of the aspartate residue in position 614 by a glycine leads to more efficient viral transduction into host cells and greater infectivity is worthy of mechanistic exploration. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 44 90 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. The B.1.1.7 (also known as Alpha) variant, largely responsible for the surge in cases in the UK in the winter of 2020/21, has increased infectivity without the D614G mutation. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 160 165 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. The conformational response of the NTDs and RBDs to LA removal is generally similar in the wild-type and D614G spike. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 105 110 S;RBD 111;44 116;48 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. The conformational responses of the wild-type and D614G spikes can be directly compared because the same perturbation was used for both in the dynamical-nonequilibrium simulations. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 50 55 S 56 62 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. The D614G mutation is now dominant in SARS-CoV-2 lineages circulating worldwide and confers increased transmissibility. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 4 9 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. The differences identified here may relate to functionally important differences between the wild-type and D614G spikes. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 107 112 S 113 119 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. The Q474-N487 loop is interesting because, although the RBD in the closed conformation remains inaccessible for binding to ACE2, residues Q474-N487 of the RBM (shown in magenta in the insert in Figure S21F) it includes the epitope Y473-P479 (YQAGSTP), which may still provide a target for neutralizing antibodies in the closed conformation, depending on the degree of glycan shielding (being close to the S349 O-glycosylation site). 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 S21F 201 205 RBD 56 59 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. The results here show that the D614G mutation alters the allosteric networks connecting the FA site to the regions surrounding the FP, particularly the FPPR. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 31 36 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. There is reduced communication between the monomers in the D614G spike. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 59 64 S 65 70 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. This behaviour, albeit in a single chain of our equilibrium MD simulations of the unglycosylated, uncleaved wild-type and D614G LA-bound spikes, suggests that the D614G may influence mobility in this important region. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G;D614G 122;163 127;168 S 137 143 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. This corresponds to the observation that the D614G mutant was mostly in an open conformation on the EM grids and suggests that loss of the D614-K854 interaction somehow destabilises the closed conformation (e.g.). 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 45 50 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. This supports the inference drawn from cryo-EM structures of the head region of the D614G spike that this mutation disrupts the inter-monomer salt-bridge and hydrogen bond networks in this region, which may cause reduced stability of the trimer. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 84 89 S 90 95 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. We also performed equilibrium and dynamical-nonequilibrium simulations of the D614G mutant spike. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 78 83 S 91 96 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. wild-type and D614G spike) can be meaningfully compared. 2021 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G 14 19 S 20 25 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. 4c) and was highly efficient for Alpha and wt-S614G variants, which were both detected in nasal washes of almost all contact 1 hamsters. 2022 Nature Introduction SARS_CoV_2 S614G 46 51 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Alpha and wt-S614G outcompete Beta in hamsters. 2022 Nature Introduction SARS_CoV_2 S614G 13 18 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Alpha dominates wt-S614G in ferrets. 2022 Nature Introduction SARS_CoV_2 S614G 19 24 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Alpha dominates wt-S614G in K18Tg mice. 2022 Nature Introduction SARS_CoV_2 S614G 19 24 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Beta has nine mutations in S, including N501Y, and two in the S receptor-binding domain (RBD), K417N and E484K. 2022 Nature Introduction SARS_CoV_2 E484K;K417N;N501Y 105;95;40 110;100;45 RBD;S;S 89;27;62 92;28;63 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Beyond S(D614G), Alpha has 18 further mutations in its genome compared with the progenitor, with two deletions and six substitutions within the S gene. 2022 Nature Introduction SARS_CoV_2 D614G 9 14 S;S 7;144 8;145 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. By contrast, Beta showed reduced fitness compared with wt-S614G. 2022 Nature Introduction SARS_CoV_2 S614G 58 63 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Competition between Alpha and wt-S614G showed no clear difference in virus titres in nasal washes of donor hamsters, and both variants were detected at all time points in each donor with numbers of individual variants ranging from 105 to 109 gc ml-1. 2022 Nature Introduction SARS_CoV_2 S614G 33 38 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Competitive transmission experiments in Syrian hamsters showed similar replication and transmission of wt-S614G and Alpha, which both outcompeted Beta. 2022 Nature Introduction SARS_CoV_2 S614G 106 111 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Consequently, transmission of Beta was limited or undetectable in contact 1 and contact 2 hamsters compared with the competing variants wt-S614G. 2022 Nature Introduction SARS_CoV_2 S614G 139 144 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Correspondingly, the nasal concha of donor ferrets revealed high levels of replication in the nasal epithelium and up to 100-fold higher load of Alpha (up to 108.2 gc ml-1) than wt-S614G (up to 106.5 gc ml-1) (Extended Data. 2022 Nature Introduction SARS_CoV_2 S614G 181 186 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. E484K is thought to be responsible for the ability of Beta to escape neutralization by plasma from convalescent individuals. 2022 Nature Introduction SARS_CoV_2 E484K 0 5 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Finally, Alpha and a recombinant clone of progenitor virus expressing the Alpha S protein (wt-SAlpha) both outcompeted the parental wt-S614G strain, resulting in higher virus load in the upper respiratory tract (URT) of mice expressing human ACE2 instead of mouse ACE2 under the endogenous mouse Ace2 promoter (hACE2-KI mice). 2022 Nature Introduction SARS_CoV_2 S614G 135 140 S 80 81 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Here we investigate the fitness of Alpha and Beta VOCs relative to wt-S614G, the predominant parental strain containing the S(D614G) substitution:in relevant primary airway culture systems in vitro, and in ferrets, Syrian hamsters and two mouse models expressing human ACE2:to assess specific advantages in replication and transmission and to evaluate the effects of Alpha S mutations alone in vivo. 2022 Nature Introduction SARS_CoV_2 D614G;S614G 126;70 131;75 S;S 124;373 125;374 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. However, competitive experiments in ferrets and transgenic mice expressing human ACE2 controlled by the KRT18 promoter (hACE2-K18Tg), which overexpress human ACE2 in epithelial cells, showed increased fitness of Alpha compared with wt-S614G. 2022 Nature Introduction SARS_CoV_2 S614G 235 240 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. However, in direct competition experiments in AEC cultures, Alpha had no advantage over wt-S614G, whereas Beta was outcompeted by both Alpha and wt-S614G (Extended Data. 2022 Nature Introduction SARS_CoV_2 S614G;S614G 91;148 96;153 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. In a similar approach, we inoculated six donor ferrets with a mixture of wt-S614G and Alpha at equivalent numbers of genome copies and monitored sequential transmission in naive contact 1 and contact 2 ferrets (Extended Data. 2022 Nature Introduction SARS_CoV_2 S614G 76 81 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. In contrast to hACE2-K18Tg mice, hACE2-KI mice show physiological expression of human ACE2, with no ectopic expression of human ACE2 in the brain, and no expression of mouse ACE2, which has been shown to be permissive to the spike mutation N501Y contained in SAlpha. 2022 Nature Introduction SARS_CoV_2 N501Y 240 245 S 225 230 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. In donor and contact hamsters, viral genome loads in the URT (comprising nasal conchae and trachea) revealed increased replication of Alpha and wt-S614G compared with Beta (Extended Data. 2022 Nature Introduction SARS_CoV_2 S614G 147 152 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. In March 2020, a single amino acid change in the S protein at position 614 (S(D614G)) was identified in a small fraction of sequenced samples:this became the predominant variant worldwide within a few weeks. 2022 Nature Introduction SARS_CoV_2 D614G 78 83 S;S 49;76 50;77 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. In organ samples from the donor hamsters, the highest viral loads were found in the LRT, where Alpha was predominant (more than 66% of genome copies) overall with more than tenfold more viral genome copies than wt-S614G in 14 out of 18 lung samples from the 6 donor hamsters (Extended Data. 2022 Nature Introduction SARS_CoV_2 S614G 214 219 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. In two competition experiments, wt-S614G and Alpha outcompeted Beta, as indicated by nasal washes of the donor hamsters from 1 dpi until euthanasia at 4 dpi. 2022 Nature Introduction SARS_CoV_2 S614G 35 40 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Infections with Alpha and wt-S614G virus resulted in similar pathologies in all the in vivo models. 2022 Nature Introduction SARS_CoV_2 S614G 29 34 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Moreover, there were significantly higher numbers of viral genome copies of Alpha and wt-SAlpha in the nose at 2 dpi and in the olfactory bulb at 4 dpi compared with wt-S614G and Beta (Extended Data. 2022 Nature Introduction SARS_CoV_2 S614G 169 174 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Neither Alpha nor Beta showed enhanced replication in human airway epithelial cell (AEC) cultures compared with wt-S614G. 2022 Nature Introduction SARS_CoV_2 S614G 115 120 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Of note, Alpha was dominant over wt-S614G in the donor hamsters at 1 dpi, but these strains were balanced by the endpoint at 4 dpi. 2022 Nature Introduction SARS_CoV_2 S614G 36 41 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Of note, Beta replicated to high titres in the lower respiratory tract (LRT; comprising cranial, medial and caudal lung lobes) of donor hamsters, similar levels as observed for the competing Alpha and wt-S614G virus (Extended Data. 2022 Nature Introduction SARS_CoV_2 S614G 204 209 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Of note, viral titres in the nasal airways and lungs showed SARS-CoV-2 persistence at 4 dpi in 3 out of 4 mice infected with either Alpha or with wt-SAlpha, but not in mice inoculated with wt-S614G, whereas Beta persisted in the lungs of 2 out of 4 mice (Extended Data. 2022 Nature Introduction SARS_CoV_2 S614G 192 197 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Replication kinetics of Alpha, Beta and a wild-type clinical isolate with the S(D614G) mutation were similar in relation to viral copies and titres in AEC cultures incubated at 33 and 37 C (Extended Data. 2022 Nature Introduction SARS_CoV_2 D614G 80 85 S 78 79 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. S protein from Alpha (SAlpha) or Beta (SBeta) exhibited a fourfold higher affinity for human ACE2 than that of S(D614G) protein (Extended Data. 2022 Nature Introduction SARS_CoV_2 D614G 113 118 S;S 0;111 1;112 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Similar to results from AEC cultures, Beta showed lower fitness than wt-S614G in hACE2-KI mice. 2022 Nature Introduction SARS_CoV_2 S614G 72 77 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Some of the S mutations, such as N501Y and the H69/V70 deletion, have been hypothesized to enhance replication and transmission, but there is a lack of clear experimental evidence for this. 2022 Nature Introduction SARS_CoV_2 N501Y 33 38 S 12 13 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. The increased replicative fitness of Alpha over wt-S614G was further reflected throughout the respiratory tract, with higher numbers of genome copies in nose, lungs, olfactory bulb and most brain samples at 4 dpi. 2022 Nature Introduction SARS_CoV_2 S614G 51 56 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. The replicative advantage of wt-SAlpha was less clear in this experiment, and both wt-SAlpha and wt-S614G were present with similarly high numbers of viral genome copies in lung and brain samples. 2022 Nature Introduction SARS_CoV_2 S614G 100 105 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. The viral load reached 109 genome copies (gc) per ml for wt-S614G and Alpha, whereas Beta viral loads were tenfold lower at corresponding time points. 2022 Nature Introduction SARS_CoV_2 S614G 60 65 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. These results indicate that the SAlpha spike mutations contribute to the replication advantage of Alpha over wt-S614G in the URT of mice that express high levels of human ACE2. 2022 Nature Introduction SARS_CoV_2 S614G 112 117 S 39 44 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. To assess further adaptation of Alpha to human ACE2, four hACE2-K18Tg mice, which overexpress hACE2 in respiratory epithelium, were inoculated with a mixture of SARS-CoV-2 wt-S614G and Alpha with equivalent numbers of genomic copies. 2022 Nature Introduction SARS_CoV_2 S614G 175 180 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Together, the two mouse models support enhanced fitness of SARS-CoV-2 Alpha VOC over its progenitor wt-S614G with increased replication and persistence in the URT and more systemic spread, mediated in part by changes in the Alpha S sequence. 2022 Nature Introduction SARS_CoV_2 S614G 103 108 S 230 231 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. We inoculated 4 groups of hACE2-KI mice intranasally with 104 plaque-forming units (PFU) per mouse of either wt-S614G, Alpha, wt-SAlpha or Beta (n = 8 mice per group) as individual virus infections. 2022 Nature Introduction SARS_CoV_2 S614G 112 117 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. We inoculated groups of six Syrian hamsters intranasally with a mixture of two SARS-CoV-2 strains comprising equivalent numbers of genome copies in three one-to-one competition experiments: Alpha versus Beta, Beta versus wt-S614G, and Alpha versus wt-S614G. 2022 Nature Introduction SARS_CoV_2 S614G;S614G 224;251 229;256 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. We inoculated hACE2-K18Tg mice with an equal mixture of wt-SAlpha and wt-S614G and housed them with a contact hACE2-K18Tg mouse at 1 dpi. 2022 Nature Introduction SARS_CoV_2 S614G 73 78 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. We observed a complete predominance of Alpha and wt-SAlpha over wt-S614G. 2022 Nature Introduction SARS_CoV_2 S614G 67 72 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. We observed a twofold increase in in vitro binding affinity of recombinant trimeric SAlpha to hamster ACE2 compared with S(D614G) (Extended Data. 2022 Nature Introduction SARS_CoV_2 D614G 123 128 S 121 122 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. We observed significantly higher viral genome copy numbers in mice infected with Alpha, wt-SAlpha or Beta compared with wt-S614G in oropharyngeal swabs at 1 dpi (Extended Data. 2022 Nature Introduction SARS_CoV_2 S614G 123 128 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. We performed a similar competition experiment between wt-S614G and an isogenic recombinant virus expressing SAlpha (wt-SAlpha). 2022 Nature Introduction SARS_CoV_2 S614G 57 62 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Whereas all donor and contact 1 hamsters transmitted both viruses to their respective contacts, contact 2 hamsters mainly shed one variant at high levels in nasal washes, demonstrating similar transmission ability for wt-S614G and Alpha. 2022 Nature Introduction SARS_CoV_2 S614G 221 226 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. The strong reversible binding of PF-00835231 in the active site of C145A Mpro clearly indicates that potential inhibitors should have specific structural characteristics to finely fit into the pocket of the enzyme's active site even without covalent bond formation. 2021 Frontiers in pharmacology Introduction SARS_CoV_2 C145A 67 72 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. A new clade bearing mutation D614G, called A2a or Clade G, identified in February 2020, became the founder of the B1 lineage and spread globally. 2021 Journal of developmental biology Introduction SARS_CoV_2 D614G 29 34 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Although P681H initially raised much interest, it has not yet been found to significantly impact viral fitness (see Box 1). 2021 Journal of developmental biology Introduction SARS_CoV_2 P681H 9 14 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. As explained above, mutation N501Y lies in a critical contact residue in the RBD that enhances virus binding to human ACE2. 2021 Journal of developmental biology Introduction SARS_CoV_2 N501Y 29 34 RBD 77 80 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. As happened with N501Y, mutation E484K has emerged recurrently in many different lineages, such as Beta and Gamma, pointing out that this mutation is favored by evolution. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K;N501Y 33;17 38;22 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Chen and colleagues reported that sera from BNT162b2-vaccinated individuals showed decreased neutralizing potency against Alpha (2-fold), E484K + N501Y + D614G recombinant (4-fold), and two chimeric SARS-CoV-2 strains encoding Beta (10-fold) and Gamma (2.2-fold) compared to the D614G original. 2021 Journal of developmental biology Introduction SARS_CoV_2 D614G;D614G;E484K;N501Y 154;279;138;146 159;284;143;151 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Close to them within the RBD, K417N, and K417T mutations have been repeatedly described to protect against binding to certain monoclonal antibodies. 2021 Journal of developmental biology Introduction SARS_CoV_2 K417N;K417T 30;41 35;46 RBD 25 28 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Clustered in the NTD domain, the Delta156-157, Delta157-158, and G158R mutations, unique to the Delta variant, map to the same surface as the Delta144-145 and Delta241-243 deletions in the Alpha and Beta variants, respectively (Figure 2). 2021 Journal of developmental biology Introduction SARS_CoV_2 G158R 65 70 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Conversely, the analysis showed a decrease in titers of nAbs against the Alpha + E484K variant, Beta, Gamma and Epsilon variants. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K 81 86 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. D614G is located in an area where S1/S2 successive cleavages occur that are necessary for the entrance of the virus into the cell (Figure 1B). 2021 Journal of developmental biology Introduction SARS_CoV_2 D614G 0 5 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. D614G. 2021 Journal of developmental biology Introduction SARS_CoV_2 D614G 0 5 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Different mutations have been observed in this residue, such as the P681H mutation in the Alpha variant, P681R in Delta and DeltaP681 in the Indian lineage B.1.617 (Table 2). 2021 Journal of developmental biology Introduction SARS_CoV_2 P681H;P681R 68;105 73;110 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. E484K. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K 0 5 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Even though the S1 movements favor the RBD-up conformation in the E484K mutant, this mutation has shown neutral to very mild effects on RBD-ACE2 binding. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K 66 71 RBD;RBD 39;136 42;139 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Furthermore, the D614G mutation reduces furin cleavage, thereby lowering the risk of premature S1 shedding, and it enhances the thermal stability of the spike. 2021 Journal of developmental biology Introduction SARS_CoV_2 D614G 17 22 S 153 158 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. However, the detection in February 2021 of E484K acquisition in some Alpha sub-lineages raises concerns about this variant's capacity to overcome the attack of antibodies. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K 43 48 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. However, the neutralization activities of some antibodies directed against the Beta Spike were seriously impaired or even wholly abolished, which is attributed to the presence of the E484K mutation and, to a lesser extent, to the K417N substitution, both in the RBD. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K;K417N 183;230 188;235 S;RBD 84;262 89;265 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. In addition, convalescent plasma obtained six months after SARS-CoV-2 infection was 0.5- to 20.2-fold less effective at neutralizing the K417N + E484K + N501Y combination. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K;K417N;N501Y 145;137;153 150;142;158 COVID-19 59 79 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. In addition, mutation P681H, which is immediately adjacent to the furin S1/S2 cleavage site in spike, could facilitate the processing of the spike protein, and thus improve binding to ACE2. 2021 Journal of developmental biology Introduction SARS_CoV_2 P681H 22 27 S;S 95;141 100;146 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. In fact, it has been proposed that K417N could provide a slightly improved ACE2 binding compared to K417T. 2021 Journal of developmental biology Introduction SARS_CoV_2 K417N;K417T 35;100 40;105 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. In fact, N501Y has been shown experimentally to result in one of the highest increases in ACE2 affinity conferred by a single RBD mutation. 2021 Journal of developmental biology Introduction SARS_CoV_2 N501Y 9 14 RBD 126 129 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. In fact, the combination K417N + E484K + N501Y, considered the most efficient in terms of immune scape with the addition of R246I, makes this variant extremely dangerous. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K;K417N;N501Y;R246I 33;25;41;124 38;30;46;129 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. In fact, there is much evidence supporting the fact that the E484K mutation enables the virus to escape some people's immune responses, sometimes being impervious to convalescent's serum and escaping even a potent polyclonal serum targeting multiple neutralizing epitopes. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K 61 66 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. In some strains, it bears Q677H, whereas in others it is Q677P. 2021 Journal of developmental biology Introduction SARS_CoV_2 Q677H;Q677P 26;57 31;62 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Instead of E484Q, Delta bears T478K, which falls within the same epitope region that targets potent neutralizing monoclonal antibodies. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484Q;T478K 11;30 16;35 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. It carries E484K and Delta69-70 mutations. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K 11 16 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. It has been proposed that viruses bearing P681R fuse with the plasma membranes of uninfected cells, a critical step in disease, almost three times faster than control ones. 2021 Journal of developmental biology Introduction SARS_CoV_2 P681R 42 47 Membrane 69 78 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. It has recently been documented that P681R provides a pre-active state that could facilitate virus-cell binding and, in general, cell infection. 2021 Journal of developmental biology Introduction SARS_CoV_2 P681R 37 42 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. It is characterized by the L452R mutation, which was expected to give an advantage when spreading over other variants, being more contagious than earlier forms. 2021 Journal of developmental biology Introduction SARS_CoV_2 L452R 27 32 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. It is predicted that RBD altered conformation by N501Y explains the 5 to 10-fold higher affinity compared to N501 versions. 2021 Journal of developmental biology Introduction SARS_CoV_2 N501Y 49 54 RBD 21 24 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. It remains unclear whether the presence of T478K or P681R could be decisive, causing this variant's increased strength. 2021 Journal of developmental biology Introduction SARS_CoV_2 P681R;T478K 52;43 57;48 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Its appearance is recurrent and often co-occurs with N439K, Y453F, and N501Y mutations, suggesting a selective advantage and possible epistasis between mutations, which should be further examined. 2021 Journal of developmental biology Introduction SARS_CoV_2 N439K;N501Y;Y453F 53;71;60 58;76;65 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Its location and the recurrent appearance of N501Y in different virus strains suggests that it is a major determinant for the increased Alpha variant transmission. 2021 Journal of developmental biology Introduction SARS_CoV_2 N501Y 45 50 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. L452R, defined as an escape mutation, has been shown to promote a much higher viral replication in non-human cell cultures, which would correspond with the better fitness of the Delta variant observed in populations. 2021 Journal of developmental biology Introduction SARS_CoV_2 L452R 0 5 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Like many other B.1 lineages, the Gamma variant also has the B.1-defining mutation, D614G, related to increased spike on the virus surface. 2021 Journal of developmental biology Introduction SARS_CoV_2 D614G 84 89 S 112 117 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Like the Alpha variant, the Beta variant presents an enhanced system for the entry to the cell provided mostly by D614G and N501Y. 2021 Journal of developmental biology Introduction SARS_CoV_2 D614G;N501Y 114;124 119;129 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Moreover, an allosteric effect of the NTD mutations (L18F, D80A, D215G, Delta243-244 and R246) in the spike interaction with ACE2 has been suggested, because the binding of the Beta spike to the NTD-directed nAbs was dramatically reduced. 2021 Journal of developmental biology Introduction SARS_CoV_2 D215G;D80A;L18F 65;59;53 70;63;57 S;S 102;182 107;187 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Mutation Y453F, along with N439K, G446V, K444E, and S477N, among others, which are located at the interface between the S1 and ACE2, have been shown to partially interfere with antibody binding and neutralization. 2021 Journal of developmental biology Introduction SARS_CoV_2 G446V;K444E;N439K;S477N;Y453F 34;41;27;52;9 39;46;32;57;14 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. N439K has also been shown to enhance the binding affinity for the ACE2 receptor. 2021 Journal of developmental biology Introduction SARS_CoV_2 N439K 0 5 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. N501Y. 2021 Journal of developmental biology Introduction SARS_CoV_2 N501Y 0 5 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Nevertheless, both K417N and K417T are expected to moderately decrease ACE2-binding affinity. 2021 Journal of developmental biology Introduction SARS_CoV_2 K417N;K417T 19;29 24;34 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Nevertheless, researchers suggest that there must be more mutations to make the difference for Delta, because other variants carrying P681R, such as the Kappa variant, do not share this high efficiency during infection. 2021 Journal of developmental biology Introduction SARS_CoV_2 P681R 134 139 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Nevertheless, the E484K substitution alone has been shown to confer resistance to neutralization by several nAbs, and it is associated with immune evasion where neutralization by some plasma is considerably reduced. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K 18 23 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. P681R is located in the S1/S2 furin-cleavage site, the same residue affected in the P681H substitution found in the Alpha variant. 2021 Journal of developmental biology Introduction SARS_CoV_2 P681H;P681R 84;0 89;5 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Several studies point out that the combination of K417N + E484K + N501Y may cause a more significant decrease in neutralization than any single mutation by itself. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K;K417N;N501Y 58;50;66 63;55;71 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Starting in 2020, soon after the emergence of the zoonosis, the D614G mutation, where amino acid D (aspartic acid) was replaced by G (glycine), appeared to be associated with higher transmissibility. 2021 Journal of developmental biology Introduction SARS_CoV_2 D614G 64 69 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Still, it has been suggested that the great variability in the NTD between these variants, with allosteric influences from other mutations (T20N, P26S, D138Y, R190S; Table 2), could contribute to the observed differences. 2021 Journal of developmental biology Introduction SARS_CoV_2 D138Y;P26S;R190S;T20N 152;146;159;140 157;150;164;144 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. That is the case, for example, of variants Iota (lineage B.1.526), identified in New York in late December 2020 and Theta (lineage P.3), both bearing mutations E484K and D614G, among others. 2021 Journal of developmental biology Introduction SARS_CoV_2 D614G;E484K 170;160 175;165 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. The analysis of the S protein structure using both cryo-electron microscopy and computational modeling analysis found that bearing D614G favors an 'open' configuration that facilitates ACE2 binding and increases the spike density in the virion surface. 2021 Journal of developmental biology Introduction SARS_CoV_2 D614G 131 136 S;S 216;20 221;21 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. The ancestral lineage B.1.617 is not a variant but a cluster of sequences within clade G that share the common signature mutations: G142D, L452R, E484Q, D614G, and P681R. 2021 Journal of developmental biology Introduction SARS_CoV_2 D614G;E484Q;G142D;L452R;P681R 153;146;132;139;164 158;151;137;144;169 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. The D614G mutation is the hallmark of all variants (Table 2) and delimitates the founding of the B1 lineage. 2021 Journal of developmental biology Introduction SARS_CoV_2 D614G 4 9 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. The D950N mutation is mapped to the S trimer interface, suggesting that this mutation may contribute to the regulation of S protein dynamics. 2021 Journal of developmental biology Introduction SARS_CoV_2 D950N 4 9 S;S 36;122 37;123 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. The E484Q substitution, which may be functionally similar to E484K, is present in the B.1.617.1 (Kappa) and B.1.617.3 sublineages and the ancestral B.1.617 but is likely to have reverted and is absent in the Delta lineage. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K;E484Q 61;4 66;9 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. The genetic profile of the Delta variant is considerably particular, as it does not bear the typical mutations observed in other VOCs, except D614G (Figure 2). 2021 Journal of developmental biology Introduction SARS_CoV_2 D614G 142 147 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. The importance of this position is further underscored by the convergent appearance of the E484Q mutation in the Indian B.1.617 lineage (Table 2). 2021 Journal of developmental biology Introduction SARS_CoV_2 E484Q 91 96 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. The improved binding affinity of spike for the ACE2 receptor is one of the defining factors that explain the high cell infectivity of SARS-CoV-2 and the fast expansion of this N501Y in the population, a mutation that has appeared recurrently in many different strains and it is present in some of the most relevant variants. 2021 Journal of developmental biology Introduction SARS_CoV_2 N501Y 176 181 S 33 38 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. The increase has been mainly attributed to the N501Y mutation in both variants. 2021 Journal of developmental biology Introduction SARS_CoV_2 N501Y 47 52 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. The main impact of the K417N mutation seems to be its ability to destabilize the RBD-down conformation (Figure 1B), thereby increasing the propensity of the open configuration. 2021 Journal of developmental biology Introduction SARS_CoV_2 K417N 23 28 RBD 81 84 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. The residue 501 is at the RBD-ACE2 interface, and the N501Y change results in increased affinity of the S protein for the ACE2 receptors, enhancing the viral attachment and the subsequent entry into the host cells. 2021 Journal of developmental biology Introduction SARS_CoV_2 N501Y 54 59 RBD;S 26;104 29;105 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. The substitution L452R can impair neutralization by several nAbs and convalescent plasma and emerged independently in different lineages, such as the Delta and Epsilon variants. 2021 Journal of developmental biology Introduction SARS_CoV_2 L452R 17 22 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. The variant Zeta, or lineage P.2, which independently acquired the E484K mutation, has been detected in many locations in Brazil, including in Manaus. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K 67 72 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. These data fit with other data published for both mRNA vaccines tested, but they found no significant effect for K417N mutation alone. 2021 Journal of developmental biology Introduction SARS_CoV_2 K417N 113 118 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. This could destabilize the RBD-down conformation, thereby adding more open RBDs to the D614G effect. 2021 Journal of developmental biology Introduction SARS_CoV_2 D614G 87 92 RBD;RBD 27;75 30;79 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. This protein binds to the viral ssRNA after replication to form the vRNP (Figure 1D), and it has been suggested that the mutation N:R203M (Table 2) is involved in an improved assembly mechanism that would contribute to explaining the fast spread of the Delta variant. 2021 Journal of developmental biology Introduction SARS_CoV_2 R203M 132 137 N 130 131 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. This variant bears a few mutations that potentially affect viral function (Figure 2): D614G, N501Y, P681H and 69-70, among others. 2021 Journal of developmental biology Introduction SARS_CoV_2 D614G;N501Y;P681H 86;93;100 91;98;105 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. This variant shares with the Beta variant some mutations with functional significance, which were acquired independently: E484K, N501Y, and K417T (instead of K417N found in Beta) located in the RBD, and L18F in the NTD. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K;K417N;K417T;L18F;N501Y 122;158;140;203;129 127;163;145;207;134 RBD 194 197 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. Towards the end of 2020, rising concern was reported in South Africa regarding lineage B.1.351, which bears some worrying mutations in the spike gene:D614G, N501Y, E484K, and K417N (Figure 2):with proven functional significance. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K;K417N;N501Y;D614G 164;175;157;150 169;180;162;155 S 139 144 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. While inter-person transmission becomes more likely, neither disease progression nor neutralization by anti-spike antibodies are significantly affected by the D614G mutation. 2021 Journal of developmental biology Introduction SARS_CoV_2 D614G 159 164 S 108 113 34940505 The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. While it has been described that the combination of K417N + E484K + N501Y is the most resistant to nAbs, the Delta variant, lacking all three of them, has displaced all the other VOCs, becoming prevalent in most countries towards the mid of 2021. 2021 Journal of developmental biology Introduction SARS_CoV_2 E484K;K417N;N501Y 60;52;68 65;57;73 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. Detection of the N501Y plays a crucial role in identifying the Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2 as N501Y mutation is shared by these variants. 2021 PloS one Introduction SARS_CoV_2 N501Y;N501Y 17;116 22;121 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. However, the hurdle for designing crRNA with high specificity for detecting N501Y is primarily due to single nucleotide substituting wild-type SARS-CoV-2. 2021 PloS one Introduction SARS_CoV_2 N501Y 76 81 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. We report here a chimeric crRNA which could be efficiently used to detect N501Y with high specificity and sensitivity by CRISPR-Cas12a. 2021 PloS one Introduction SARS_CoV_2 N501Y 74 79 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. We have previously sequenced the SARS-CoV-2 viral genome isolated from a group of 62 Romanian patients during first COVID-19 outbreak and identified several mutations, one of which occurred at position 27,707 (C27707T) which leads to a substitution of alanine to valine (A105V) in the transmembrane domain of SARS-CoV-2 ORF7a. 2021 Biology Introduction SARS_CoV_2 A105V;C27707T 271;210 276;217 ORF7a 320 325 COVID-19 116 124 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. A report published in Cell reported that these mutations (S477N-E484K) in the RBD increase the binding affinity for the host receptor ACE2. 2021 Biology Introduction SARS_CoV_2 S477N;E484K 58;64 63;69 RBD 78 81 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. Another VOI known as Iota (iota) from lineage B.1.526, reported in New York City in early 2021, had the E484K mutation reported in the P.1 variant and was reported to partially or wholly escape the response from the two currently used therapeutic monoclonal antibodies (mAbs) and is less susceptible to neutralization. 2021 Biology Introduction SARS_CoV_2 E484K 104 109 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. Globally, most SARS-CoV-2 isolates have the D614G mutation. 2021 Biology Introduction SARS_CoV_2 D614G 44 49 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. In contrast, the delta+ variant acquired an additional mutation, the K417N mutation, alongside the L452R and T478K mutations. 2021 Biology Introduction SARS_CoV_2 K417N;L452R;T478K 69;99;109 74;104;114 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. Moreover, a novel VOI termed as C.37, or the Lambda/lambda variant, reported in Peru with mutations L452Q and F490S in the RBD was suspected to be associated with decreased antibody neutralization susceptibility, particularly due to the F490S mutation in the RBD. 2021 Biology Introduction SARS_CoV_2 F490S;F490S;L452Q 110;237;100 115;242;105 RBD;RBD 123;259 126;262 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. Recently, a new variant, B.1620, with mutations (S477N-E484K) in the RBD of the spike protein has been reported in Europe. 2021 Biology Introduction SARS_CoV_2 S477N;E484K 49;55 54;60 S;RBD 80;69 85;72 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. The E484K substitution in the P.1 variant has been reported to establish direct interaction with the host receptor hACE2. 2021 Biology Introduction SARS_CoV_2 E484K 4 9 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. The Kappa (kappa) variant, also known as B.1.617.1, first identified in India, and designated as a VOI, owns a single mutation, that is, L452R, which was suspected to be associated with reduced antibody neutralization by disrupting the respective conformational epitopes. 2021 Biology Introduction SARS_CoV_2 L452R 137 142 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. This variant harbors E484K, N501Y, and P681H mutations in the spike protein, while many other new mutations accompany these mutations, including R346K, Y144T, Y145S, and 146N insertion. 2021 Biology Introduction SARS_CoV_2 E484K;N501Y;P681H;R346K;Y144T;Y145S 21;28;39;145;152;159 26;33;44;150;157;164 S 62 67 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. To date, many variants have been reported, among which the VOC Delta (delta)+ (AY.1 or lineage B.1.617.2.1), which evolved from Delta, demonstrated a different mutational landscape by acquiring L452R and T478K mutations in the RBD. 2021 Biology Introduction SARS_CoV_2 L452R;T478K 194;204 199;209 RBD 227 230 34943523 Low Represented Mutation Clustering in SARS-CoV-2 B.1.1.7 Sublineage Group with Synonymous Mutations in the E Gene. Thus, the samples were sequenced, which revealed the presence of a synonymous mutation (c.26415 C > T, TAC > TAT, Reference Genome: NC_045512) in the E gene and three other mutations (S137L:Orf1ab gene, N439K:Spike gene, and A156S:Nucleocapsid gene) scattered throughout the genome in all samples carrying the E gene dropout. 2021 Diagnostics (Basel, Switzerland) Introduction SARS_CoV_2 A156S;N439K;C26415T;S137L 225;203;88;184 230;208;101;189 N;ORF1ab;S;E;E 231;190;209;150;310 243;196;214;151;311 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. Around the 9th week of 2021, Japan entered the fourth wave of the SARS-CoV-2 pandemic with a rapid replace of predominant strains with the B.1.1.7 lineage of SARS-CoV-2 with a N501Y replacement in the receptor binding domain (RBD) of spike (N501YV). 2021 Journal of clinical medicine Introduction SARS_CoV_2 N501Y 176 181 RBD;S;RBD 201;234;226 224;239;229 34949225 Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N. A spike mutation H245N was first reported in one of the Palestinian isolates. 2021 BMC research notes Introduction SARS_CoV_2 H245N 17 22 S 2 7 34949225 Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N. All ten study genome sequences contained the spike mutation D614G which is the most prevalent mutation (90.2%) reported in 132 countries which has been shown to increase infectivity of the virus by increasing cellular transduction. 2021 BMC research notes Introduction SARS_CoV_2 D614G 60 65 S 45 50 34949225 Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N. By the end of March 2021, 50 H245N mutations were reported worldwide with 11 in USA (9 in Florida, one in California, and one in Massachusetts). 2021 BMC research notes Introduction SARS_CoV_2 H245N 29 34 34949225 Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N. Eleven out of 18 genome sequences (61%) in cluster-III contained the unique Middle Eastern spike mutation H245N compared to one (14%) in cluster-II (red) and one (6%) in cluster-I (yellow). 2021 BMC research notes Introduction SARS_CoV_2 H245N 106 111 S 91 96 34949225 Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N. The first strain containing the unique spike mutation H245N (genotype: B 1.1.50) was isolated in Palestine in November 2020 (Genbank: MW419997, GISIAD: EPI_ISL_752605, hCoV-19/Palestine/AAS24/2020). 2021 BMC research notes Introduction SARS_CoV_2 H245N 54 59 S 39 44 34949225 Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N. The GISAID database showed that the spike mutation H245N first reported in a Palestinian patient early November 2020 was spread in five countries (PS, IT, IL, NZ, and US) (Additional file 2). 2021 BMC research notes Introduction SARS_CoV_2 H245N 51 56 S 36 41 34949225 Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N. The mutation (22295C > A) created a new potential N-glycosylation site at position 245 that changed the amino acid Histidine (H) in the reference strain to Asparagine (N) and this might influence the quality of antibody recognition in COVID-19 virus. 2021 BMC research notes Introduction SARS_CoV_2 C22295A 14 24 N;N 50;168 51;169 COVID-19 235 243 34953513 Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. For example, the mutation D614G in the S glycoprotein, which appeared very early in the pandemic, is now present in almost all circulating strains. 2022 Cell host & microbe Introduction SARS_CoV_2 D614G 26 31 S 39 53 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. Delta variant additionally has a unique mutation, T478K in addition to the two mutations listed above. 2022 Journal of King Saud University. Science Introduction SARS_CoV_2 T478K 50 55 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. Due to the E484K substitution, the 501Y.V2 variant is more resistant to multiple monoclonal antibodies, convalescent plasma, and vaccine sera, whereas the N501Y substitution enhanced the affinity to human ACE2 and infectivity. 2022 Journal of King Saud University. Science Introduction SARS_CoV_2 E484K;N501Y 11;155 16;160 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. In India's second COVID-19 wave, the newest significant variants, Delta and Kappa, were discovered to share two mutations: E484Q and L452R. 2022 Journal of King Saud University. Science Introduction SARS_CoV_2 E484Q;L452R 123;133 128;138 COVID-19 18 26 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. In the present studies, we have modelled the mutant structures of Spike protein-L452R, T478K and N501Y through in silico mutagenesis technique and evaluated their binding interactions with human ACE2 with respect to the native spike protein using protein-protein docking method. 2022 Journal of King Saud University. Science Introduction SARS_CoV_2 N501Y;T478K;L452R 97;87;80 102;92;85 S;S 66;227 71;232 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. Other than N501Y, both Beta and Gamma variants harbours additional substitutions. 2022 Journal of King Saud University. Science Introduction SARS_CoV_2 N501Y 11 16 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. Substitution mutations like D614G, N501Y, Y453F, N439K/R, P681H, K417N/T, and E484K, as well as deletion mutations like DeltaH69/V70 and Delta242-244 are the most common in the spike protein. 2022 Journal of King Saud University. Science Introduction SARS_CoV_2 D614G;E484K;K417N;K417T;N439K;N439R;N501Y;P681H;Y453F 28;78;65;65;49;49;35;58;42 33;83;72;72;56;56;40;63;47 S 177 182 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The Alpha variant features a N501Y mutation as well as a K417N mutation. 2022 Journal of King Saud University. Science Introduction SARS_CoV_2 K417N;N501Y 57;29 62;34 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The D614G mutation enhanced viral proliferation and transmission as compared to wild-type viruses. 2022 Journal of King Saud University. Science Introduction SARS_CoV_2 D614G 4 9 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The E484K mutation is present in the Beta variants, whereas the E484K and K417T mutations are present in the Gamma variants. 2022 Journal of King Saud University. Science Introduction SARS_CoV_2 E484K;E484K;K417T 4;64;74 9;69;79 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The E484K mutation is seen in an emerging variant variation derived from B.1.1.7. 2022 Journal of King Saud University. Science Introduction SARS_CoV_2 E484K 4 9 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. These variations all have the N501Y mutation in the SARS-CoV-2 spike (S) protein, which is the target of most COVID-19 vaccines. 2022 Journal of King Saud University. Science Introduction SARS_CoV_2 N501Y 30 35 S;S 63;70 68;71 COVID-19 110 118 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. We identified some target mutations D614G, N501Y, and K417N in the South Africa, United Kingdom, and Brazil variants, respectively. 2021 Frontiers in molecular biosciences Introduction SARS_CoV_2 D614G;K417N;N501Y 36;54;43 41;59;48 34959053 Isolation of SARS-CoV-2 B.1.1.28.2 (P2) variant and pathogenicity comparison with D614G variant in hamster model. During January 2021, lineage P.1, also known as Gamma variant, a VOC with 17 amino acid changes which includes N501Y, E484K, and K417N on the spike protein; ORF1b deletion outside the spike protein was detected in the travelers from Brazil at Japan. 2022 Journal of infection and public health Introduction SARS_CoV_2 E484K;K417N;N501Y 118;129;111 123;134;116 S;S 142;184 147;189 34959053 Isolation of SARS-CoV-2 B.1.1.28.2 (P2) variant and pathogenicity comparison with D614G variant in hamster model. Furthermore, Brazil reported another variant P.2 lineage, which has E484K mutation but not the N501Y and K417N amino acid changes in the spike protein. 2022 Journal of infection and public health Introduction SARS_CoV_2 E484K;K417N;N501Y 68;105;95 73;110;100 S 137 142 34959053 Isolation of SARS-CoV-2 B.1.1.28.2 (P2) variant and pathogenicity comparison with D614G variant in hamster model. Here, we report isolation and characterization of the P.2/Zeta (B.1.1.28.2) variant from clinical specimens of international travelers and its pathogenesis in Syrian hamsters in comparison with B.1 variant, an early virus isolate with D614G mutation. 2022 Journal of infection and public health Introduction SARS_CoV_2 D614G 235 240 34959053 Isolation of SARS-CoV-2 B.1.1.28.2 (P2) variant and pathogenicity comparison with D614G variant in hamster model. Subsequently, another variant B.1.351 (Beta variant) was identified in South Africa with 21 mutations, including N501Y, E484K, and K417N on the spike protein, and ORF1b deletion outside the spike protein. 2022 Journal of infection and public health Introduction SARS_CoV_2 E484K;K417N;N501Y 120;131;113 125;136;118 S;S 144;190 149;195 34959053 Isolation of SARS-CoV-2 B.1.1.28.2 (P2) variant and pathogenicity comparison with D614G variant in hamster model. This variant has about 17 mutations, including N501Y, P681H, 69-70 deletion; the ORF8 Q27stop mutation outside the spike protein and is adapted to be more transmissible. 2022 Journal of infection and public health Introduction SARS_CoV_2 N501Y;P681H;Q27X 47;54;86 52;59;93 S;ORF8 115;81 120;85 34960156 The Impact of Mutations on the Pathogenic and Antigenic Activity of SARS-CoV-2 during the First Wave of the COVID-19 Pandemic: A Comprehensive Immunoinformatics Analysis. Among these, the D614G mutation is responsible for increased transmissibility. 2021 Vaccines Introduction SARS_CoV_2 D614G 17 22 34960156 The Impact of Mutations on the Pathogenic and Antigenic Activity of SARS-CoV-2 during the First Wave of the COVID-19 Pandemic: A Comprehensive Immunoinformatics Analysis. However, few mutations, such as D614G in spike (S) and p323L in RdRp, have been rapidly evolving in SARS-CoV-2 genome. 2021 Vaccines Introduction SARS_CoV_2 D614G 32 37 S;RdRP;S 41;64;48 46;68;49 34960694 Semi-Supervised Pipeline for Autonomous Annotation of SARS-CoV-2 Genomes. Additionally, several variants of SARS-CoV-2 genomes have emerged, including the D614G variant, which appeared earlier in the pandemic, or the more recent B.1.1.7 (Alpha) or B.1.617.2 (Delta) variants, which represent the majority of new cases in the U.S.A. 2021 Viruses Introduction SARS_CoV_2 D614G 81 86 S 253 254 34960694 Semi-Supervised Pipeline for Autonomous Annotation of SARS-CoV-2 Genomes. Furthermore in a targeted analysis, we achieved greater than 97.9% sequence identity in spike glycoprotein domains and tracked the emergence of the D614G and N501Y spike glycoprotein variants over time and by region of exposure. 2021 Viruses Introduction SARS_CoV_2 D614G;N501Y 148;158 153;163 S;S 88;164 106;182 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. An additional substitution in RBD, K417N is also observed in the RBD of AY.1. 2021 Viruses Introduction SARS_CoV_2 K417N 35 40 RBD;RBD 30;65 33;68 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. B.1.617.1 contains additional substitutions in the NTD (T95I), the NTD antigenic supersite beta-hairpin (G142D and E154K), within the S1/S2 cleavage junction (P681R), and in the S2 subunit (Q1071H). 2021 Viruses Introduction SARS_CoV_2 E154K;G142D;P681R;Q1071H;T95I 115;105;159;190;56 120;110;164;196;60 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. E484Q was also previously identified as an RBD escape mutant for an RBD-specific mAb. 2021 Viruses Introduction SARS_CoV_2 E484Q 0 5 RBD;RBD 43;68 46;71 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Finally, we showed that the P681R substitution confers enhanced furin processing in spike protein of B.1.617 lineage variants that corresponded to enhanced cell-cell fusion activity. 2021 Viruses Introduction SARS_CoV_2 P681R 28 33 S 84 89 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. However, convalescent sera from individuals infected with an early viral isolate (Wuhan-Hu-1) effectively cross-neutralized D614G. 2021 Viruses Introduction SARS_CoV_2 D614G 124 129 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. In addition, the B.1.617.2 spike also has two substitutions in the receptor-binding domain (RBD) (L452R, T478K), one substitution proximal to S1/S2 cleavage site (P681R), and one in the S2 region (D950N). 2021 Viruses Introduction SARS_CoV_2 T478K;D950N;L452R;P681R 105;197;98;163 110;202;103;168 S;RBD 27;92 32;95 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. One of the earliest variants that is highly infectious and thus became globally dominant is B.1 (D614G). 2021 Viruses Introduction SARS_CoV_2 D614G 97 102 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Several studies have described a significant drop in the neutralization potency of convalescent and vaccine sera, as well as numerous therapeutic neutralizing antibodies that contacted the mutated sites in B.1.351, P.1, and B.1.526 lineages, particularly E484K. 2021 Viruses Introduction SARS_CoV_2 E484K 255 260 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The B.1.427/B.1.429 and B.1.617 lineage variants share the L452R substitution in RBD. 2021 Viruses Introduction SARS_CoV_2 L452R 59 64 RBD 81 84 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The E484K substitution found in B.1.351, B.1.526, P.1, P.3 (theta), and some B.1.617 variants confers some level of resistance to neutralization by convalescent sera, vaccine-elicited sera, and therapeutic neutralizing antibodies. 2021 Viruses Introduction SARS_CoV_2 E484K 4 9 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The E484K substitution in the RBD of B.1.351, P.1, R.1, and B.1.526 variants was previously identified among in vitro escape mutants selected against single antibody and antibody cocktails. 2021 Viruses Introduction SARS_CoV_2 E484K 4 9 RBD 30 33 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The E484Q along with L452R is present in the RBD of B.1.617 sublineages, B.1.617.1 and B.1.617.3. 2021 Viruses Introduction SARS_CoV_2 E484Q;L452R 4;21 9;26 RBD 45 48 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The L452R RBD substitution was shown to confer modest resistance to neutralization by convalescent sera, vaccine-elicited sera, and therapeutic neutralizing antibodies in the context of other variants of interest (VOI), such as B.1.427/B.1.429 and B.1.617.1. 2021 Viruses Introduction SARS_CoV_2 L452R 4 9 RBD 10 13 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The L452R substitution has been demonstrated to enhance ACE2 binding and pseudovirus infectivity and reduce or ablate the neutralizing potency of 10 out of 34 RBD-specific mAbs tested. 2021 Viruses Introduction SARS_CoV_2 L452R 4 9 RBD 159 162 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The spike protein of the B.1.617.2 variant contains nine substitutions and deletions compared to the early D614G variant used here as wild type (WT or D614G). 2021 Viruses Introduction SARS_CoV_2 D614G;D614G 107;151 112;156 S 4 9 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The three substitutions (T19R, G142D, and R158G) and two deletions (DeltaE156, DeltaF157) in NTD occur in the NTD antigenic supersite spanning between residues 14-20, 140-158, and 245-264. 2021 Viruses Introduction SARS_CoV_2 G142D;R158G;T19R 31;42;25 36;47;29 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. We found that resistance to convalescent and vaccine-elicited sera was predominantly conferred by RBD substitutions E484Q, T478K, and L452R. 2021 Viruses Introduction SARS_CoV_2 E484Q;L452R;T478K 116;134;123 121;139;128 RBD 98 101 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Altogether, our results suggest that Q675H spike mutation may enhance viral fitness by ensuring a more efficient spike proteolytic cleavage. 2021 Viruses Introduction SARS_CoV_2 Q675H 37 42 S;S 43;113 48;118 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Here, we describe the emergence of SARS-CoV-2 strains carrying mutation involving the substitution of a glutamine (Q) with a histidine (H) residue at position 675 (Q675H), within the polar region of spike proximal to the S1/S2 furin cleavage site. 2021 Viruses Introduction SARS_CoV_2 Q675H 164 169 S 199 204 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Moreover, we highlight that Q675H mutation is the result of a process of parallel evolution, and that multiple SARS-CoV-2 VOCs displaying the Q675H mutation have recently emerged. 2021 Viruses Introduction SARS_CoV_2 Q675H;Q675H 28;142 33;147 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. We also demonstrate that Q675H mutation contributes to the formation of a hydrogen bond (H-bond) network that facilitates the accessibility of the spike core region to the furin binding pocket and improves the orientation of arginine residues to increase furin binding strength to the viral substrate. 2021 Viruses Introduction SARS_CoV_2 Q675H 25 30 S 147 152 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. Another variant belonging to lineage B.1.160 (clade 20A, previously identified 20A.EU2) that has a S477N substitution in the spike protein was common in Autumn 2020 and early 2021 in some European countries, including France. 2021 Viruses Introduction SARS_CoV_2 S477N 99 104 S 125 130 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. For instance, the European lineage B.1.177 (clade 20E(EU1)) differs from ancestral sequences at 6 or more positions, including a A222V mutation in the spike protein. 2021 Viruses Introduction SARS_CoV_2 A222V 129 134 S 151 156 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. It harbors three aa deletions (69del-70del and 144del) and seven mutations in the spike protein, including D614G and N501Y. 2021 Viruses Introduction SARS_CoV_2 D614G;N501Y 107;117 112;122 S 82 87 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. One of the first notable variants had a D614G substitution in the S1 domain that increased the affinity of the virus for ACE2. 2021 Viruses Introduction SARS_CoV_2 D614G 40 45 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. The Gamma variants described in Brazil belonging to the lineage P.1 clade 20J also have the E484K mutation in addition to K417T and N501Y mutations in their RBD. 2021 Viruses Introduction SARS_CoV_2 E484K;K417T;N501Y 92;122;132 97;127;137 RBD 157 160 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. The latest variant of concern, variant Delta (lineage B.1.617.2, clades 21A, 21I and 21J), emerged in India in October 2020 and was later detected in France in May 2021, and has the L452R mutation that makes it more transmissible. 2021 Viruses Introduction SARS_CoV_2 L452R 182 187 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. Variants belonging to this lineage have three mutations in the RBD: K417N, E484K, and N501Y, and several others outside the RBD and are neutralized less efficiently by convalescent and vaccine sera. 2021 Viruses Introduction SARS_CoV_2 E484K;K417N;N501Y 75;68;86 80;73;91 RBD;RBD 63;124 66;127 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. Conserved among variants Alpha, Beta, and Gamma, the N501Y mutation was previously shown to enhance the binding affinity to ACE2. 2021 Frontiers in immunology Introduction SARS_CoV_2 N501Y 53 58 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. Most class I mAbs were largely disrupted by the K417N/T mutation and class II mAbs by the E484K mutation. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K;K417N;K417T 90;48;48 95;55;55 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. The Beta and Gamma variants each has three mutation sites in common within the RBD region:K417N/T, E484K, and N501Y:which change their antigenic profiles. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K;N501Y;K417N;K417T 99;110;90;90 104;115;97;97 RBD 79 82 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. The Delta variant contains the unique L452R and T478K mutations while sharing a common mutation with the Alpha and Gamma variants at P681 near the furin cleavage site. 2021 Frontiers in immunology Introduction SARS_CoV_2 L452R;T478K 38;48 43;53 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. Through crystal and electron cryo-microscopy (cryo-EM) structure analyses, P36-5D2 was found to target a conserved epitope on the RBD of the spike protein, bypassing the three key mutations (K417N, E484K, and N501Y) responsible for immune escape from many potent neutralizing mAbs. 2021 Frontiers in immunology Introduction SARS_CoV_2 E484K;N501Y;K417N 198;209;191 203;214;196 S;RBD 141;130 146;133 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. Various deletion mutants in the NTD have also been identified, such as 69-70del and Y144del in Alpha and 242-244del in Beta. 2021 Frontiers in immunology Introduction SARS_CoV_2 Y144del 84 91 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. Moreover, the binding affinity of biliverdin bound to SARS-CoV-2 S1 is profoundly affected by the R190K and N121Q amino acid substitutions, with the corresponding Kd values significantly weakening. 2021 Frontiers in molecular biosciences Introduction SARS_CoV_2 N121Q;R190K 108;98 113;103 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Another strain in which Asparagine positioned at 501 of RBD is substituted by Tyrosine (N501Y) arose in United Kingdom and South Africa. 2022 Computer methods and programs in biomedicine Introduction SARS_CoV_2 N501Y 88 93 RBD 56 59 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. In addition, mutations such as G476S (Glycine 476 to Serine) and V483A (Valine 483 to Alanine) were reported in the United States. 2022 Computer methods and programs in biomedicine Introduction SARS_CoV_2 G476S;V483A;G476S;V483A 31;65;38;72 36;70;59;93 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Moreover, RBD MTs such as V367F and V483A showed high binding affinities to the host ACE2 receptor protein. 2022 Computer methods and programs in biomedicine Introduction SARS_CoV_2 V367F;V483A 26;36 31;41 RBD 10 13 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Of these five, three mutations such as G476S, V483A and N501Y occur at the binding interface of RBD (C-terminal side) that interact with PD (peptidase domain) of the host ACE2 receptor. 2022 Computer methods and programs in biomedicine Introduction SARS_CoV_2 G476S;N501Y;V483A 39;56;46 44;61;51 RBD 96 99 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. R408I (Arginine 408 to Isoleucine) mutant isolated from India. 2022 Computer methods and programs in biomedicine Introduction SARS_CoV_2 R408I;R408I 7;0 33;5 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. The rest of mutations V367F and R408I, mostly affected the overall topology and stability of RBD as these mutations present at the loop regions of N-terminal and turn that connect beta-sheet3 and 4, respectively. 2022 Computer methods and programs in biomedicine Introduction SARS_CoV_2 R408I;V367F 32;22 37;27 RBD;N 93;147 96;148 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. These mutations (V367F, R408I, G476S, V483A and N501Y) indirectly assist in the stable binding of RBD to the host ACE2 receptor. 2022 Computer methods and programs in biomedicine Introduction SARS_CoV_2 G476S;N501Y;R408I;V483A;V367F 31;48;24;38;17 36;53;29;43;22 RBD 98 101 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. These mutations (V367F, R408I, G476S, V483A and N501Y) were mainly located in the SpikeS1 RBD domain. 2022 Computer methods and programs in biomedicine Introduction SARS_CoV_2 G476S;N501Y;R408I;V483A;V367F 31;48;24;38;17 36;53;29;43;22 S;RBD 82;90 87;93 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. V367F (Valine 367 to Phenylalanine) mutation in the RBD of SpikeS1 protein was reported from the strains found in Wuhan, Shenzhen, Hong Kong and France. 2022 Computer methods and programs in biomedicine Introduction SARS_CoV_2 V367F;V367F 7;0 34;5 S;RBD 59;52 64;55 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Some of the reported mutations also expedite the transmission of the virus i.e., D614G mutation in the spike protein has been reported to be associated with unusual increased in the transmission fitness of SARS-CoV-2. 2022 Computers in biology and medicine Introduction SARS_CoV_2 D614G 81 86 S 103 108 34968879 SARS-CoV-2 wastewater surveillance in Germany: Long-term RT-digital droplet PCR monitoring, suitability of primer/probe combinations and biomarker stability. All three VoCs have the mutation A23063T, also named N501Y, in common, which is involved in the receptor-binding mechanism and may have clinical impacts. 2022 Water research Introduction SARS_CoV_2 A23063T;N501Y 33;53 40;58 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. For instance, we previously reported that the E484K variant could be more devastating than anyone else and thus emerged as a Delta variant which is more lethal and contagious. 2022 Computers in biology and medicine Introduction SARS_CoV_2 E484K 46 51 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. These variants, such as B.1.17 (Alpha variant) harbouring a mutation N501Y reported in the UK, D614G variant, lineage B.1.1.207 with P681H replacement, lineage B.1.351 (Beta) with E484K mutation reported in South Africa (B.1.351) and P.1 variant reported in Brazil. 2022 Computers in biology and medicine Introduction SARS_CoV_2 D614G;E484K;N501Y;P681H 95;180;69;133 100;185;74;138 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. These VOCs harbour numerous mutations in the RBD domain, which includes N501Y, E484K and K417 N/T. 2022 Computers in biology and medicine Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 79;89;89;72 84;97;97;77 RBD 45 48 34981057 SARS-CoV-2 Omicron neutralization by therapeutic antibodies, convalescent sera, and post-mRNA vaccine booster. The predominant strain of Omicron has mutations in the spike gene encoding 15 amino acid changes in the receptor binding domain (RBD) of the spike surface protein (G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, and Y505H). 2021 bioRxiv Introduction SARS_CoV_2 E484A;G446S;G496S;K417N;N440K;N501Y;Q493R;Q498R;S371L;S373P;S375F;S477N;T478K;Y505H;G339D 227;206;241;192;199;255;234;248;171;178;185;213;220;266;164 232;211;246;197;204;260;239;253;176;183;190;218;225;271;169 RBD;S;S;RBD 104;55;141;129 127;60;146;132 34981057 SARS-CoV-2 Omicron neutralization by therapeutic antibodies, convalescent sera, and post-mRNA vaccine booster. We compared the magnitude of neutralization escape by Omicron to D614G (referred to as wild type, WT) and Delta SARS-CoV-2 variants to help inform public health decisions and offer further data toward correlate of protection research. 2021 bioRxiv Introduction SARS_CoV_2 D614G 65 70 34981064 Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. A recent in silico mutagenesis study employing the Rosetta based modeler for protein-protein association, Flex ddG, has successfully identified a quadruple ACE2 mutant, S19F;T27F;K31W;N330F, to exhibit nanomolar binding affinity similar to the sACE22.v2.4 designed mutant. 2021 bioRxiv Introduction SARS_CoV_2 S19F;K31W;N330F;T27F 169;179;184;174 173;183;189;178 34981064 Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. Double mutants containing the combination of sACE22.v2.4 mutations, T27Y;L79T, T27Y;N330Y, and L79T;N330Y, bound to RBD with greater affinity than the single mutant variants, and had similar affinity as sACE22.v2.4. 2021 bioRxiv Introduction SARS_CoV_2 L79T;L79T;N330Y;N330Y 95;73;84;100 99;77;89;105 RBD 116 119 34981064 Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. For the L91P;N330Y mutant, both single mutations exhibited a relative binding fold enhancement of under two; however, when expressed together, the relative binding increased over 2.5 fold. 2021 bioRxiv Introduction SARS_CoV_2 L91P;N330Y 8;13 12;18 34981064 Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. For the nine mutants that scored in the top 1% of the TLmutation predictions, three mutants D67A;N387N, A387N;S511Q, and N394D;S511Q failed to be distinguishable from the wild type. 2021 bioRxiv Introduction SARS_CoV_2 A387N;D67A;N394D;N387N;S511Q;S511Q 104;92;121;97;110;127 109;96;126;102;115;132 34981064 Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. Furthermore, the E484K mutation in the Beta and Gamma variants introduces new electrostatic interactions with neighboring acidic residues on ACE2. 2021 bioRxiv Introduction SARS_CoV_2 E484K 17 22 34981064 Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. Interestingly, L91P is not directly located on the ACE2 binding interface and may allosterically stabilize the alpha2 helix for favorable S binding. 2021 bioRxiv Introduction SARS_CoV_2 L91P 15 19 S 138 139 34981064 Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. The best performing double mutant, L79V;N90D (Figure 4B), bound RDB-sfGFP exceptionally well, equivalent to sACE22.v2.4. 2021 bioRxiv Introduction SARS_CoV_2 L79V;N90D 35;40 39;44 34981064 Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. The N501Y mutation identified in the Alpha, Beta, Gamma, and Omicron strains introduces additional pi-pi and cation-pi interactions with ACE2 residues that increase the binding affinity by 10-fold as compared to the wild-type RBD. 2021 bioRxiv Introduction SARS_CoV_2 N501Y 4 9 RBD 226 229 34981064 Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. They further characterized a sACE2 derivative containing the three mutations T27Y, L79T, and N330Y, referred to as sACE22.v2.4 (Figure 1A), to exhibit a 35-fold increase in binding affinity to SARS-CoV-2, and further tighter affinity for SARS-CoV-2 variants that contain the N501Y mutation. 2021 bioRxiv Introduction SARS_CoV_2 L79T;N330Y;N501Y 83;93;275 87;98;280 34981064 Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. We have previously conducted molecular dynamics simulations of sACE22.v2.4 with the RBD domain of SARS-CoV-2 and observed the N330Y mutation to interact with backbone carbonyls of P499 on RBD further to stabilize the associated complex (Figure 4A). 2021 bioRxiv Introduction SARS_CoV_2 N330Y 126 131 RBD;RBD 84;188 87;191 34981064 Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. When examining the in silico mutagenesis predictions for these double mutants, TLmutation score the sACE22.v2.4 double mutants in the top 14%, with T27Y;N330Y and L79T;N330Y scoring in the upper 5%. 2021 bioRxiv Introduction SARS_CoV_2 L79T;N330Y;N330Y 163;153;168 167;158;173 34982509 Engineered small extracellular vesicles displaying ACE2 variants on the surface protect against SARS-CoV-2 infection. Further, pseudoviruses of the B1.351 lineage, also known as Beta variant, containing S protein receptor-binding domain (RBD) mutations, including N501Y, E484K, and K417N, exhibited increased resistance to neutralization by therapeutic monoclonal antibodies and convalescent plasma (Wibmer et al.,). 2022 Journal of extracellular vesicles Introduction SARS_CoV_2 E484K;K417N;N501Y 153;164;146 158;169;151 RBD;S 120;85 123;86 34982509 Engineered small extracellular vesicles displaying ACE2 variants on the surface protect against SARS-CoV-2 infection. SARS-CoV-2 harbouring S glycoprotein substitution D614G became the most dominant variant and was reported to exhibit greater infectivity (Plante et al.,). 2022 Journal of extracellular vesicles Introduction SARS_CoV_2 D614G 50 55 S 22 36 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. After the emergence of the variant with the D614G mutation, it was reported that rapid transmission led by a SARS-CoV-2 variant was linked to infection among farmed minks. 2022 Microbiology spectrum Introduction SARS_CoV_2 D614G 44 49 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. Another study revealed that, due to mutations K417N, E484K, and N501Y in the spike protein of B.1.351, convalescent and some vaccine sera might only offer limited protection against B.1.351. 2022 Microbiology spectrum Introduction SARS_CoV_2 E484K;K417N;N501Y 53;46;64 58;51;69 S 77 82 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. Since there are multiple mutations in variants, the current ARMS-PCR methods for screening SARS-CoV-2 variants depend on the combination of multiple hot spot mutations, such as D614G and R203K. 2022 Microbiology spectrum Introduction SARS_CoV_2 D614G;R203K 177;187 182;192 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. Some related studies revealed that the substitution D614G could enhance the viral transmission and replication in human cells. 2022 Microbiology spectrum Introduction SARS_CoV_2 D614G 52 57 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. The first globally dominant mutation identified was D614G (a change of D to G at position 614) in the spike protein of SARS-CoV-2. 2022 Microbiology spectrum Introduction SARS_CoV_2 D614G;D614G 71;52 93;57 S 102 107 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. These B.1.351 strains were about 9.4-fold more refractory to neutralization by convalescent plasma, which was largely due to the E484K mutation in the spike protein. 2022 Microbiology spectrum Introduction SARS_CoV_2 E484K 129 134 S 151 156 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. Variants belonging to lineages B.1.1.7 and B.1.351 were found to have an N501Y amino acid substitution. 2022 Microbiology spectrum Introduction SARS_CoV_2 N501Y 73 78 34987509 An Intranasal OMV-Based Vaccine Induces High Mucosal and Systemic Protecting Immunity Against a SARS-CoV-2 Infection. In the present study, we developed an innovative subunit vaccine for COVID-19 in which a HexaPro spike protein containing the D614G mutation is associated with OMV, which serves as a carrier and adjuvant for the spike molecule, using the short amphipathic peptide sequence mCRAMP fused to the C-terminus. 2021 Frontiers in immunology Introduction SARS_CoV_2 D614G 126 131 S;S 97;212 102;217 COVID-19 69 77 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Because the mutants of B.1.351 exert the highest possibility of immune evasion so far, its RBD was chosen as the representative immunogen for E484K/Q mutant lineages. 2022 Cell reports Introduction SARS_CoV_2 E484K;E484Q 142;142 149;149 RBD 91 94 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Furthermore, 8 months after inoculation with the D614G-specific vaccine, a new boost with this bivalent vaccine potently elicited cross-nAbs for SARS-CoV-2 variants in rhesus macaques. 2022 Cell reports Introduction SARS_CoV_2 D614G 49 54 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Given that the B.1.351 and P.1 strains harbor K417N/T, E484K, and N501Y mutations in the RBD domain, B.1.526 harbors E484K, and B.1.617.1 harbors L452R and E484Q (Figure S4C), we wanted to develop a D614G- and E484K/Q-specific bivalent vaccine. 2022 Cell reports Introduction SARS_CoV_2 D614G;E484K;E484K;E484K;E484Q;E484Q;K417N;K417T;L452R;N501Y 199;55;117;210;210;156;46;46;146;66 204;60;122;217;217;161;53;53;151;71 RBD 89 92 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Importantly, compared with the D614 and D614G lineages, most of these variants, especially those harboring E484K/Q mutants, confer elevated resistance to neutralization from convalescent COVID-19 sera as well as many therapeutic monoclonal antibodies. 2022 Cell reports Introduction SARS_CoV_2 D614G;E484K;E484Q 40;107;107 45;114;114 COVID-19 187 195 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Recent clinical studies in South Africa, in parallel, confirmed reduced efficacy against symptomatic COVID-19 disease for various vaccines based on the original D614/D614G, including the NVX-CoV2373 (Novavax), BNT162b2 (Pfizer-BioNTech), AZD1222 (University of Oxford/AstraZeneca), and Ad26.COV2.S (Janssen/Johnson & Johnson) vaccines. 2022 Cell reports Introduction SARS_CoV_2 D614G 166 171 S 296 297 COVID-19 101 117 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Some recent studies also show that the protection efficiency of these vaccines against other variants harboring E484K/Q mutations, such as B1.617.1 harboring L452R/E484Q, is decreased. 2022 Cell reports Introduction SARS_CoV_2 E484K;E484Q;L452R;E484Q 112;112;158;164 119;119;163;169 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Therefore, strategies for developing updated vaccines against B.1.351 and other variants harboring E484K/Q mutations are urgently needed to avoid potential loss of clinical efficacy. 2022 Cell reports Introduction SARS_CoV_2 E484K;E484Q 99;99 106;106 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. To this end, a bivalent D614G/B.1.351 RBD nanoparticle vaccine was developed that comprises a 1:1 mix of D614G_RBD-NP (D614G RBD nanoparticle vaccine) and B.1.351_RBD-NP (B.1.351 RBD nanoparticle vaccine). 2022 Cell reports Introduction SARS_CoV_2 D614G;D614G;D614G 24;105;119 29;110;124 RBD;RBD;RBD 38;125;179 41;128;182 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. With a prime-boost or single-dose strategy, this bivalent vaccine elicited robust nAbs and full protection against infection with the authentic D614G or B.1.351 strains in human ACE2 (hACE2) transgene mice. 2022 Cell reports Introduction SARS_CoV_2 D614G 144 149 34995777 A CLUSTER OF SARS-COV-2 DELTA VARIANT OF CONCERN ADDITIONALLY HARBORING F490S, NORTHERN LOMBARDY, ITALY. As of September 10, 2021, GISAID reported F490S in 30 of 418,956 B.1.617.2 sequences, in 1 of 24,391 AY.3 sequences, in 2 of 2,926 AY.3.1 sequences, in 18 of AY.4 325,042 sequences, in 4 of 40,191 AY.12 sequences, and in 1 of 9,447 AY.20 sequences. 2022 International journal of infectious diseases Introduction SARS_CoV_2 F490S 42 47 34995777 A CLUSTER OF SARS-COV-2 DELTA VARIANT OF CONCERN ADDITIONALLY HARBORING F490S, NORTHERN LOMBARDY, ITALY. F490 is an O-linked glycan site; F490S causes resistance to convalescent sera and escape to several monoclonal antibodies (mAbs) (such as C121 but not C135 and C144) and nanobodies. 2022 International journal of infectious diseases Introduction SARS_CoV_2 F490S 33 38 34995777 A CLUSTER OF SARS-COV-2 DELTA VARIANT OF CONCERN ADDITIONALLY HARBORING F490S, NORTHERN LOMBARDY, ITALY. F490S had never been reported in Delta sequences in Italy before, but its frequency is increasing worldwide since the beginning of September 2021 (http://outbreak.info/situation-reports), recommending close monitoring and further investigations of vaccine efficacy. 2022 International journal of infectious diseases Introduction SARS_CoV_2 F490S 0 5 34995777 A CLUSTER OF SARS-COV-2 DELTA VARIANT OF CONCERN ADDITIONALLY HARBORING F490S, NORTHERN LOMBARDY, ITALY. F490S is the hallmark MOC of VOIs Lambda (C.37) and is also found at frequencies higher than 50% in Q.5 and B.1.1.456 lineages. 2022 International journal of infectious diseases Introduction SARS_CoV_2 F490S 0 5 34995777 A CLUSTER OF SARS-COV-2 DELTA VARIANT OF CONCERN ADDITIONALLY HARBORING F490S, NORTHERN LOMBARDY, ITALY. In this article, we report a cluster of B.1.617.2 + F490S occurring in 2 families living in the same small town in Northern Lombardy. 2022 International journal of infectious diseases Introduction SARS_CoV_2 F490S 52 57 34995777 A CLUSTER OF SARS-COV-2 DELTA VARIANT OF CONCERN ADDITIONALLY HARBORING F490S, NORTHERN LOMBARDY, ITALY. NGS analysis of the 6 SARS-CoV-2 strains revealed B.1.617.2 additionally harboring F490S mutation. 2022 International journal of infectious diseases Introduction SARS_CoV_2 F490S 83 88 34995777 A CLUSTER OF SARS-COV-2 DELTA VARIANT OF CONCERN ADDITIONALLY HARBORING F490S, NORTHERN LOMBARDY, ITALY. T478K and L452R are the main mutations of concern (MOC) within the Spike protein of Delta. 2022 International journal of infectious diseases Introduction SARS_CoV_2 L452R;T478K 10;0 15;5 S 67 72 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. BanLec mitogenicity can be divorced from antiviral activity via a single amino acid change (H84T). 2021 Frontiers in immunology Introduction SARS_CoV_2 H84T 92 96 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. Consequently, enhanced durability of H84T-BanLec treatments could potentially improve antiviral efficacy. 2021 Frontiers in immunology Introduction SARS_CoV_2 H84T 37 41 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. Glycosylation-directed CAR-NK cells such as H84T-BanLec CAR-NK are activated against SARS-CoV-2 and have the potential to blunt viral infection, potentially through clearance of virally-infected cells or prevention of viral entry. 2021 Frontiers in immunology Introduction SARS_CoV_2 H84T 44 48 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. H84T-BanLec chimeric antigen receptor natural killer (CAR-NK) cells diminished the potency of lentivirus pseudotyped with a SARS-CoV-2 spike protein (S-protein) envelope. 2021 Frontiers in immunology Introduction SARS_CoV_2 H84T 0 4 S;S 135;150 140;151 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. H84T-BanLec retains its binding capacity to HIV, influenza, and coronaviruses. 2021 Frontiers in immunology Introduction SARS_CoV_2 H84T 0 4 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. We designed a H84T-BanLec CAR containing the 4-1BB (CD137) and TCRzeta intracellular domains and expressed this artificial chimeric receptor at the NK cell membrane. 2021 Frontiers in immunology Introduction SARS_CoV_2 H84T 14 18 Membrane 156 164 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. We sought to improve H84T-BanLec antiviral activity by combining its exquisite viral targeting and the innate activity of primary NK cells. 2021 Frontiers in immunology Introduction SARS_CoV_2 H84T 21 25 35008446 Analysis of Immune Escape Variants from Antibody-Based Therapeutics against COVID-19: A Systematic Review. In vitro, continuous passaging of SARS-CoV-2 in the presence of a CCP unit with nAb titer >1:104 led to DeltaF140 spike mutation at day 45, followed by E484K at day 73, and an insertion in the N-terminal domain (NTD): these accumulating mutations led to complete immune escape. 2021 International journal of molecular sciences Introduction SARS_CoV_2 E484K 152 157 S;N 114;193 119;194 35008446 Analysis of Immune Escape Variants from Antibody-Based Therapeutics against COVID-19: A Systematic Review. Similarly, K417N, E484K, and N501Y mutations were selected when pseudotyped SARS-CoV-2 was cultured in the presence of vaccine-elicited mAbs. 2021 International journal of molecular sciences Introduction SARS_CoV_2 E484K;K417N;N501Y 18;11;29 23;16;34 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Africa, mutations of concern/interest: K417N, E484K, N501Y), B.1.427/B.1.429-California (mutations of concern/interest: L452R), the B.1.141 variant (mutations of concern/interest: N439K), the recent B.1.617.1-India (mutations of concern/interest: L452R; E484Q), and the B.1.620 (mutations of concern/interest: namely S477N; E484K). 2022 The EPMA journal Introduction SARS_CoV_2 E484K;E484K;E484Q;K417N;L452R;L452R;N439K;N501Y;S477N 46;324;254;39;120;247;180;53;317 51;329;259;44;125;252;185;58;322 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. As a consequence of the lower lethality, the spike D614G mutation is currently detectable in most of SARS-CoV-2 variants of concern (https://covdb.stanford.edu/page/mutation-viewer). 2022 The EPMA journal Introduction SARS_CoV_2 D614G 51 56 S 45 50 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Conversely, a lower virulence is often correlated with a higher transmissibility, as already observed for recent variants showing new mutations, i.e., D614G, at the SARS-CoV-2 spike protein (relatively far from the RBD region involved in direct interactions with the ACE2 receptor), which resulted in a less deadly virus. 2022 The EPMA journal Introduction SARS_CoV_2 D614G 151 156 S;RBD 176;215 181;218 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Thus, aiming to test our pipeline and to investigate the effect of amino acid replacement at the SARS-CoV-2 spike RBD, as observed within the most studied VoC, we built a 3D comparative model for each spike variant showing an amino acid replacement at the RBD positions K417; N439; L452, E484; S477; S494; N501, as highlighted in the SARS-CoV-2 VoC B.1.1.7-United Kingdom (UK, mutations of concern/interest at the RBD: N501Y, S494P, E484K), P.1-Japan/Brazil (K417T, E484K, N501Y), B.1.351-South Africa (S. 2022 The EPMA journal Introduction SARS_CoV_2 E484K;E484K;N501Y;N501Y;S494P;K417T 433;466;419;473;426;459 438;471;424;478;431;464 S;S;RBD;RBD;RBD;S 108;201;114;256;414;503 113;206;117;259;417;504 35014989 COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis. In the early era of COVID-19, there was significant concern about the D614G variant being more infectious, and SARS-CoV-2 with this mutation had been found to cause infections in New York State. 2021 JMIRx med Introduction SARS_CoV_2 D614G 70 75 COVID-19 20 28 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. 5d); specifically, by the K417N mutation (Extended Data. 2022 Nature Introduction SARS_CoV_2 K417N 26 31 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. 6c, 7c), such as the E484K mutation found in Beta. 2022 Nature Introduction SARS_CoV_2 E484K 21 26 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. A loop involving the RBD residues 371-375 lies in the ridge between the E and F sites; thus, a subset of group F antibodies:including some group E antibodies:could be affected by the S371L/S373P/S375F mutations if their epitopes extend to this region. 2022 Nature Introduction SARS_CoV_2 S371L;S373P;S375F 183;189;195 188;194;200 RBD;E;E 21;72;145 24;73;146 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. A subset of neutralizing antibodies in group B, such as AZD8895 and BD-836, could survive the Beta variant (Fig 2e); however, Omicron significantly reduced the binding affinity of group B neutralizing antibodies to the RBD, potentially as a result of S477N/T478K/E484A on their epitope (Extended Data. 2022 Nature Introduction SARS_CoV_2 S477N;E484A;T478K 251;263;257 256;268;262 RBD 219 222 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Also, for those antibodies that could tolerate a G446S single mutation, the N440K/G446S combination may considerably reduce their binding affinity, with the result that most group D antibodies are escaped by Omicron. 2022 Nature Introduction SARS_CoV_2 G446S;N440K;G446S 49;76;82 54;81;87 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Also, part of the epitope of group E antibodies would extend to the 440-449 loop, rendering them sensitive to the N440K mutation in Omicron. 2022 Nature Introduction SARS_CoV_2 N440K 114 119 E 35 36 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. For example, K417N and N501Y contribute to immune escape and higher infectivity.The functional effects of many other mutations still require investigation. 2022 Nature Introduction SARS_CoV_2 K417N;N501Y 13;23 18;28 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Group A neutralizing antibodies mainly comprise antibodies that are encoded by the VH3-53 and VH3-66 (also known as IGHV3-53 and IGHV3-66) germline genes; these are present at high levels in our present collection of SARS-CoV-2 neutralizing antibodies, including several antibodies that have obtained emergency use authorization (CB6/LY-CoV016) or that are currently being studied in clinical trials (P2C-1F11/BRII-196 and BD-604/DXP-604). 2022 Nature Introduction SARS_CoV_2 P2C 401 404 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. However, the IC50 of VIR-7831 is reduced to 181 ng ml-1, and may be subject to further reduction against Omicron with R346K. 2022 Nature Introduction SARS_CoV_2 R346K 118 123 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. However, the neutralization capability of these antibodies might be undermined by N501Y and Y505H in Omicron. 2022 Nature Introduction SARS_CoV_2 N501Y;Y505H 82;92 87;97 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. In addition, a subset of neutralizing antibodies of groups E and F are escaped by single mutations of G339D, N440K, S371L and S375F. 2022 Nature Introduction SARS_CoV_2 G339D;N440K;S371L;S375F 102;109;116;126 107;114;121;131 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Most neutralizing antibodies in group D remain active against Beta; however, G446S would substantially affect their neutralization capability against Omicron. 2022 Nature Introduction SARS_CoV_2 G446S 77 82 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Neutralizing antibodies that survived the Beta strain, such as BRII-196 and DXP-604, are insensitive to the K417N single-site change but could also be heavily affected by the combination of K417N and other RBD mutations located on their epitopes, such as S477N, Q493R, G496S, Q498R, N501Y and Y505H of Omicron, thus causing a loss or reduction of neutralization (Fig 2d, Extended Data. 2022 Nature Introduction SARS_CoV_2 G496S;K417N;K417N;N501Y;Q493R;Q498R;S477N;Y505H 269;108;190;283;262;276;255;293 274;113;195;288;267;281;260;298 RBD 206 209 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Notably, the frequency of Omicron with the R346K mutation is continuously increasing, which may severely affect the neutralization capacity of group E antibodies. 2022 Nature Introduction SARS_CoV_2 R346K 43 48 E 149 150 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Specifically, neutralizing antibodies in groups A-D, the epitopes of which overlap with the ACE2-binding motif, are largely escaped by the single mutations K417N, G446S, E484A, and Q493R. 2022 Nature Introduction SARS_CoV_2 E484A;G446S;K417N;Q493R 170;163;156;181 175;168;161;186 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. The E484A mutation that is seen in Omicron elicited a similar escaping effect, although the change to alanine is slightly subtler, and could be tolerated by certain antibodies in this group (Extended Data. 2022 Nature Introduction SARS_CoV_2 E484A 4 9 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. The G339D mutation would affect the neutralization performance of a subset of neutralizing antibodies. 2022 Nature Introduction SARS_CoV_2 G339D 4 9 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. The RBD, which is responsible for interacting with the angiotensin-converting enzyme 2 (ACE2) receptor, contains 15 of these mutations: G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y and Y505H. 2022 Nature Introduction SARS_CoV_2 E484A;G339D;G446S;G496S;K417N;N440K;N501Y;Q493R;Q498R;S371L;S373P;S375F;S477N;T478K;Y505H 199;136;178;213;164;171;227;206;220;143;150;157;185;192;237 204;141;183;218;169;176;232;211;225;148;155;162;190;197;242 RBD 4 7 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. VIR-7831 retains strong RBD-binding capability; although G339 is part of its epitope, the G339D mutation in Omicron does not appear to affect the binding of VIR-7831. 2022 Nature Introduction SARS_CoV_2 G339D 90 95 RBD 24 27 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. A point mutation, G29195T, was detected in the consensus sequences of SNDE1 and SNDE2 but not in other surveillance samples sequenced in our laboratory between June 2020 and October 2021 (n = 700). 2022 Microbiology spectrum Introduction SARS_CoV_2 G29195T 18 25 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. G29195T was suspected to affect N gene detection because this mutation lies within a region targeted by one of the U.S. 2022 Microbiology spectrum Introduction SARS_CoV_2 G29195T 0 7 N 32 33 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. Here, we report a novel N gene point mutation, G29195T, which affected the detection of the SARS-CoV-2 N gene by the Cepheid Xpert Xpress SARS-CoV-2 assay. 2022 Microbiology spectrum Introduction SARS_CoV_2 G29195T 47 54 N;N 24;103 25;104 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. This G29195T mutation is a novel mutation in Singapore and was first reported in the GISAID database (https://www.gisaid.org) in October 2021. 2022 Microbiology spectrum Introduction SARS_CoV_2 G29195T 5 12 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. Three N gene point mutations, i.e., C29200T, G29140U, and C29200A, and one N gene 6-nucleotide deletion at genome position 28889 have been reported to affect N gene detection in RT-PCR assays. 2022 Microbiology spectrum Introduction SARS_CoV_2 C29200A;C29200T 58;36 65;43 N;N;N 6;75;158 7;76;159 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. Interestingly, despite a much lower mutation rate, recent studies showed that SARS-CoV-2 has the potential to escape neutralizing antibodies, namely by introducing the E484K, N501Y or K417N/E484K spike mutations. 2022 PLoS pathogens Introduction SARS_CoV_2 E484K;K417N;N501Y;E484K 168;184;175;190 173;189;180;195 S 196 201 35026305 SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021. E484K and N501Y mutations are found in B.1.1.7, B.1.351 and P.1. 2022 Journal of virological methods Introduction SARS_CoV_2 N501Y;E484K 10;0 15;5 35026305 SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021. Notable spike (S) amino acid mutations are: HV69/70 deletion and P681H in B.1.1.7, K417N in B.1.351, and K417T in P.1. 2022 Journal of virological methods Introduction SARS_CoV_2 K417N;K417T;P681H 83;105;65 88;110;70 S;S 8;15 13;16 35026305 SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021. The most recent VOC B.1.617.2 contains L452R and P681R mutations. 2022 Journal of virological methods Introduction SARS_CoV_2 L452R;P681R 39;49 44;54 35028838 SARS-CoV-2 phase I transmission and mutability linked to the interplay of climatic variables: a global observation on the pandemic spread. Apart from this, L5F was also observed in 37 countries; Q239K, V483A, and D839Y/N/E in Europe; G476S and V483A in the USA; and P1263L in the UK. 2022 Environmental science and pollution research international Introduction SARS_CoV_2 D839E;D839N;D839Y;G476S;L5F;P1263L;Q239K;V483A;V483A 74;74;74;95;17;127;56;63;105 83;83;83;100;20;133;61;68;110 35028838 SARS-CoV-2 phase I transmission and mutability linked to the interplay of climatic variables: a global observation on the pandemic spread. Subsequent studies on the spike mutation (Korber et al.) indicated that D614G was the predominant spike protein observed globally. 2022 Environmental science and pollution research international Introduction SARS_CoV_2 D614G 72 77 S;S 26;98 31;103 35028838 SARS-CoV-2 phase I transmission and mutability linked to the interplay of climatic variables: a global observation on the pandemic spread. Though there are several spike proteins reported, D614G has resulted in the global pandemic, leading to a great impact on potential immunity due to its structure and mutation (Korber et al.). 2022 Environmental science and pollution research international Introduction SARS_CoV_2 D614G 50 55 S 25 30 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. All three VOCs contain the N501Y mutation that makes the virus more infectious. 2022 Journal of medical virology Introduction SARS_CoV_2 N501Y 27 32 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Another important amino acid mutant is E484K, reaching more than 5.7% of total sequences. 2022 Journal of medical virology Introduction SARS_CoV_2 E484K 39 44 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. As of March 2021, at the beginning of this study, the most widely spread single mutant variant was N501Y, accounting for more than 820 000 (46%) of the ~1.77 million SARS-CoV-2 sequences uploaded in the GISAID database (https://www.epicov.org). 2022 Journal of medical virology Introduction SARS_CoV_2 N501Y 99 104 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. As of March 2021, the 15 most commonly observed mutations in the RBD were as follows: V367F, P384L, K417N, N439K, L452R, Y453F, S477N, S477R, T478K, E484K, S494P, N501T, N501Y, A520S, and A522S, which were located at 13 sites in the RBD. 2022 Journal of medical virology Introduction SARS_CoV_2 A520S;A522S;E484K;K417N;L452R;N439K;N501T;N501Y;P384L;S477N;S477R;S494P;T478K;V367F;Y453F 177;188;149;100;114;107;163;170;93;128;135;156;142;86;121 182;193;154;105;119;112;168;175;98;133;140;161;147;91;126 RBD;RBD 65;233 68;236 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. For example, the RBD of spike protein in the Alpha variant has since evolved a new mutation E484K, which has also appeared in the Beta and Gamma variants. 2022 Journal of medical virology Introduction SARS_CoV_2 E484K 92 97 S;RBD 24;17 29;20 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Mutations such as N501Y, S477N, N439K, L452R, E484K, K417N, T478K, and K417T were observed in VOCs and VOIs, and these sites were listed as RBD high-frequency mutation sites, suggesting that these sites are mutation-prone. 2022 Journal of medical virology Introduction SARS_CoV_2 E484K;K417N;K417T;L452R;N439K;N501Y;S477N;T478K 46;53;71;39;32;18;25;60 51;58;76;44;37;23;30;65 RBD 140 143 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The amino acid change N501Y enhances the affinity of the RBD to ACE2 and is more transmissible than other mutant variants. 2022 Journal of medical virology Introduction SARS_CoV_2 N501Y 22 27 RBD 57 60 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. Analysis is also showing mutation within ORF1b at position P314L (P323L) in the initial swab sample in four out of five individuals. 2022 New microbes and new infections Introduction SARS_CoV_2 P314L;P323L 59;66 64;71 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. Fourth patient, we found substitution at ORF1b:P314L on the second swab. 2022 New microbes and new infections Introduction SARS_CoV_2 P314L 47 52 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. In the first patient, we found substitution at position N:S255A and S:N501Y on the first swab and revert back to its original sequence on the second swab and additional substitution at N:R203K and N:S235F. 2022 New microbes and new infections Introduction SARS_CoV_2 N501Y;R203K;S235F;S255A 70;187;199;58 75;192;204;63 N;N;N;S 56;185;197;68 57;186;198;69 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. Last patient, we found substitutions at N:D3Q and ORF1b:P314L on the first swab and reversion of both substitutions with addition substitution at N:R203K on the second swab. 2022 New microbes and new infections Introduction SARS_CoV_2 D3Q;P314L;R203K 42;56;148 45;61;153 N;N 40;146 41;147 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. Second patient, we found substitution at position N:R203K and N:S235F on the first swab, additional substitution at ORF1a:T1001I and S:N501Y on the second swab. 2022 New microbes and new infections Introduction SARS_CoV_2 N501Y;R203K;S235F;T1001I 135;52;64;122 140;57;69;128 ORF1a;N;N;S 116;50;62;133 121;51;63;134 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. Third patient, we found substitution at N:L139F, ORF1a:P1640L and ORF7a:L116F on the first swab and all substitution revert to original on the second swab. 2022 New microbes and new infections Introduction SARS_CoV_2 L116F;L139F;P1640L 72;42;55 77;47;61 ORF1a;ORF7a;N 49;66;40 54;71;41 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. We found reversion of all substitution except at ORF1a:T1001I on the third swab perform during recovery. 2022 New microbes and new infections Introduction SARS_CoV_2 T1001I 55 61 ORF1a 49 54 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. Interestingly, we determined that this antigen test loses sensitivity for detecting SARS-CoV-2 variants carrying the K417N/T, E484K and N501Y single nucleotide polymorphisms (SNPs). 2021 Frontiers in public health Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 126;117;117;136 131;124;124;141 35051442 Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests. Evidence including the RdRp target delay in Delta variants from this study, RdRp complete GTF in a minority of Beta variants and confirmation by Seegene that the G15451A mutation in Delta variants leads to a mismatch in the primer binding site, suggest that these diagnostic primers overlap with the WHO-recommended RT-PCR primer sets stemming from. 2022 Journal of virological methods Introduction SARS_CoV_2 G15451A 162 169 RdRP;RdRP 23;76 27;80 35051442 Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests. In addition, we previously found that a synonymous G15452C mutation (codon 671S) in a minority of Beta variant sequences (3'-end of this forward primer binding site) also affected RdRp gene target detection when using the Seegene, Allplex 2019-nCoV assay. 2022 Journal of virological methods Introduction SARS_CoV_2 G15452C 51 58 RdRP 180 184 35051442 Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests. This highly conserved G15451A mutation was present in 100 % (369/369) of Delta variant sequences and not observed in Alpha (n = 11), Beta (n = 749) or Eta (n = 5) variants sequenced between March 2020 and 19 August 2021. 2022 Journal of virological methods Introduction SARS_CoV_2 G15451A 22 29 35051442 Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests. To systematically assess the effect of this Delta variant G15451A mutation on Seegene assay RdRp target amplification efficiency relative to that of ancestral strain and Beta variant, we compared the median relative RdRp and E gene target Ct values (RDeltaE) among the different World Health Organisation SARS-CoV-2 designated variants detected in diagnostic samples over this time period. 2022 Journal of virological methods Introduction SARS_CoV_2 G15451A 58 65 RdRP;RdRP 92;216 96;220 35051442 Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests. We identified a non-synonymous G15451A mutation (codon 671S) within RdRp gene of Delta variants, potentially responsible for the reduced amplification efficiency of the assay RdRp target. 2022 Journal of virological methods Introduction SARS_CoV_2 G15451A 31 38 RdRP;RdRP 68;175 72;179 35056548 Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan. This extensive molecular surveillance of the virus has enabled researchers to identify critical mutations that might contribute to higher transmissibility or immune escape, such as D614G, N501Y, and E484K amino acid substitutions in the spike (S) protein. 2022 Microorganisms Introduction SARS_CoV_2 D614G;E484K;N501Y 181;199;188 186;204;193 S;S 237;244 242;245 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. Different spike mutations emerged and became dominant in the emerged variants of concern (VOC), such as the representative mutations D614G, N501Y, E484Q/K, L452R, P681R in the Alpha, Beta, Gamma, and Delta variants. 2022 Emerging microbes & infections Introduction SARS_CoV_2 D614G;E484K;E484Q;L452R;N501Y;P681R 133;147;147;156;140;163 138;154;154;161;145;168 S 10 15 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. For example, the "delta" strain, with the RBD mutation L452R/T478K, rapidly spread globally since it was identified in late 2020. 2021 Viruses Introduction SARS_CoV_2 L452R;T478K 55;61 60;66 RBD 42 45 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. However, the strains containing several RBD mutations, namely, L452R (epsilon), T478K, E484K, E484Q, and N501Y, were selected (Figure 1) and have caused multiple outbreaks, mostly due to the increased transmissibility of SARS-CoV-2 caused by these RBD mutations, (, accessed 15 December 2021). 2021 Viruses Introduction SARS_CoV_2 E484K;E484Q;L452R;N501Y;T478K 87;94;63;105;80 92;99;68;110;85 RBD;RBD 40;248 43;251 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. In this study, we investigated the changes in binding pattern and structural conformation between the ACE2 receptor and three major RBD double mutants of L452R/T478K (delta), L452R/E484Q (kappa) and E484K/N501Y (beta, gamma). 2021 Viruses Introduction SARS_CoV_2 E484K;L452R;L452R;E484Q;N501Y;T478K 199;154;175;181;205;160 204;159;180;186;210;165 RBD 132 135 35062281 Intra-Host SARS-CoV-2 Evolution in the Gut of Mucosally-Infected Chlorocebus aethiops (African Green Monkeys). Since the discovery of the D614G mutation, noted early in the pandemic and found to enable enhanced infection in cells and is now present in all sequenced isolates, several variants of interest and concern (as defined by the CDC) have arisen. 2022 Viruses Introduction SARS_CoV_2 D614G 27 32 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. Announced in December 2020 and probably emerging in November 2020, the Alpha variant, the most commonly isolated variant worldwide, is characterized by the presence of the N501Y, A570D, P681H, T716I, S982A, and D1118H substitutions and deletions at positions 69/70 and 144 in the S gene. 2022 Viruses Introduction SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;T716I 179;211;172;186;200;193 184;217;177;191;205;198 S 280 281 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. As an example of this, the strain that quickly became predominant during the first pandemic wave (March 2020) was characterized by the D614G substitution in the S gene. 2022 Viruses Introduction SARS_CoV_2 D614G 135 140 S 161 162 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. Last in order of arrival but certainly not least, the variant called Omicron (B.1.1.529) is characterized by more than thirty mutations on the spike gene only, many of these unique (E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, H655Y, and N679K) while others are shared with other lineages (for example T478K with Delta and P681H with Alpha and Mu). 2022 Viruses Introduction SARS_CoV_2 G496S;H655Y;N501Y;N679K;P681H;Q493R;Q498R;T478K;T547K;Y505H;E484A 196;231;210;242;327;189;203;306;224;217;182 201;236;215;247;332;194;208;311;229;222;187 S 143 148 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. Nowadays, new important SARS-CoV-2 variants descending from D614G and with increased transmissibility have been discovered. 2022 Viruses Introduction SARS_CoV_2 D614G 60 65 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. The Beta variant, discovered a few days after the Alpha in samples collected between March and November 2020, also carries the N501Y mutation (phylogenetically not related to the Alpha variant) and other peculiar substitutions in the S gene:D80A, D215G, E484K, N501Y, and A701V. 2022 Viruses Introduction SARS_CoV_2 A701V;D215G;E484K;N501Y;N501Y;D80A 272;247;254;127;261;241 277;252;259;132;266;245 S 234 235 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. The Gamma variant emerged in February 2020 and is associated with the E484K, K417N, N501Y, and H655Y mutations in the S gene. 2022 Viruses Introduction SARS_CoV_2 E484K;H655Y;K417N;N501Y 70;95;77;84 75;100;82;89 S 118 119 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. The Iota variant has six mutations on the spike gene (L5F, T95I, D253G, E484K, D614G, and A701V), whilst the Lambda variant is characterized by seven mutations on the same gene (G75V, T76I, del246/252, L452Q, F490S, D614G, and T859N). 2022 Viruses Introduction SARS_CoV_2 A701V;D253G;D614G;D614G;E484K;F490S;L452Q;T76I;T859N;T95I;G75V;L5F 90;65;79;216;72;209;202;184;227;59;178;54 95;70;84;221;77;214;207;188;232;63;182;57 S 42 47 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. The most recent variants, referred to as the Kappa and the Delta variants, are characterized by six mutations (E154K, L452R, E484Q, D614G, P681R, and Q1071H), and eight mutations (T19R, del156/157, R158G, L452R, T478K, P618R, D614G, and D950N) on the spike gene, respectively. 2022 Viruses Introduction SARS_CoV_2 D614G;D614G;D950N;E484Q;L452R;L452R;P618R;P681R;Q1071H;R158G;T478K;E154K;T19R 132;226;237;125;118;205;219;139;150;198;212;111;180 137;231;242;130;123;210;224;144;156;203;217;116;184 S 251 256 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. With respect to the other less common D614G-descending lineages, apart from several mutations occurring in other genomic regions, B.1.160 is characterized by a S477N mutation in the S gene and another one in the nucleocapsid (N) gene (A376T), whereas the Eta variant shares the E484K mutation with the Beta and Gamma variants and shows new peculiar mutations in the S gene, i.e., Q52R, A67V, Q677H, and F888L. 2022 Viruses Introduction SARS_CoV_2 A67V;D614G;E484K;F888L;Q52R;Q677H;S477N;A376T 386;38;278;403;380;392;160;235 390;43;283;408;384;397;165;240 N;N;S;S 212;226;182;366 224;227;183;367 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. Another variant, A.2.5, likely spread north from Central America to the Quebec province in Canada and accumulated deletions 141-143 at the NTD and the L452R mutations in RBD. 2022 Viruses Introduction SARS_CoV_2 L452R 151 156 RBD 170 173 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. Further analysis revealed the convergent acquisition of the D614G and L452R signature mutations of the B lineages and Delta variant, respectively, and a mutational jump of 23 mutations, a characteristic of most of the VOCs. 2022 Viruses Introduction SARS_CoV_2 D614G;L452R 60;70 65;75 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. The Spike of Mu accumulated the following mutations: insertion in 146N, T95I, Y144T and Y145S, in the N-terminal domain (NTD); R346K, E484K, N501Y in the receptor-binding domain (RBD) and P681H at the S1/S2 interface. 2022 Viruses Introduction SARS_CoV_2 E484K;N501Y;P681H;R346K;T95I;Y144T;Y145S 134;141;188;127;72;78;88 139;146;193;132;76;83;93 S;RBD;N 4;179;102 9;182;103 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. This variant belongs to the A.* lineages, which predominated early during the pandemic but were replaced by B lineages characterized by the D614G mutation on the Spike glycoprotein until becoming quasi-extinct in mid-2020. 2022 Viruses Introduction SARS_CoV_2 D614G 140 145 S 162 180 35062734 Immunogenicity of a Heterologous Prime-Boost COVID-19 Vaccination with mRNA and Inactivated Virus Vaccines Compared with Homologous Vaccination Strategy against SARS-CoV-2 Variants. A variant that detected a single mutant with D614G in the spike protein has shown a higher ability of transmission and replication. 2022 Vaccines Introduction SARS_CoV_2 D614G 45 50 S 58 63 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. A median viral RNA load of 4 x 106 RNA copies/mg of lung tissue was detected at 4 dpi in the lungs from the animals infected with the D614G strain. 2022 Antiviral research Introduction SARS_CoV_2 D614G 134 139 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. In another study, omicron-infected human ACE2 transgenic hamsters also showed reduced mortality and infectious virus loads in the lung compared to those infected with the D614G strain. 2022 Antiviral research Introduction SARS_CoV_2 D614G 171 176 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. In Brief, 6-8 weeks old female Syrian hamsters were intranasally infected with 50 muL containing approximately 103 TCID50 of either the ancestral strain (BavPat(D614G)) or the omicron VoC (B.1.1.529) SARS-CoV-2. 2022 Antiviral research Introduction SARS_CoV_2 D614G 161 166 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. Infectious virus titers in the lungs of D614G strain-infected animals were around 2 x 104 TCID50/mg of lung tissue. 2022 Antiviral research Introduction SARS_CoV_2 D614G 40 45 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. On the day of sacrifice, animals infected with the omicron variant had gained more body weight (average body weight change from d0 of 3.8%) than the D614G strain-infected animals (average body weight change from d0 of 0.65%), p = 0.0087, Mann-Whitney Test. 2022 Antiviral research Introduction SARS_CoV_2 D614G 149 154 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. P = 0022 compared to the D614G group, Mann-Whitney Test). 2022 Antiviral research Introduction SARS_CoV_2 D614G 25 30 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. P = 0022 compared to the D614G strain-infected group, Mann-Whitney Test). 2022 Antiviral research Introduction SARS_CoV_2 D614G 25 30 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. Taken together, these results clearly demonstrate that the omicron is not able to efficiently replicate in the lower respiratory tract of Syrian hamsters compared to the ancestral D614G strain and other variants of concerns. 2022 Antiviral research Introduction SARS_CoV_2 D614G 180 185 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. The calculated TCID50/mL values for the ancestral D614G strain and the omicron variant were 7.07 x 105 and 1.6 x 106, respectively. 2022 Antiviral research Introduction SARS_CoV_2 D614G 50 55 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. The median cumulative histopathological lung score of the D614G-infected hamsters was 7.5. 2022 Antiviral research Introduction SARS_CoV_2 D614G 58 63 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. The scored parameters, to which a cumulative score of 1-3 was attributed, were the following: congestion, intra-alveolar hemorrhagic, apoptotic bodies in bronchus wall, necrotizing bronchiolitis, perivascular oedema, bronchopneumonia, perivascular inflammation, peribronchial inflammation and vasculitis.Hematoxylin/eosin (H&E)-stained images of lungs of hamsters infected with the D614G strain revealed significant pathological signs including peri-bronchial inflammation, bronchopneumonia in the surrounding alveoli and perivascular inflammation with peri-vascular oedema. 2022 Antiviral research Introduction SARS_CoV_2 D614G 382 387 Bronchopneumonia;Bronchopneumonia 217;474 233;490 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. This strain carries a spike D614G substitution found in early European variants and linked to more efficient transmission. 2022 Antiviral research Introduction SARS_CoV_2 D614G 28 33 S 22 27 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. Unlike the D614G strain-infected group, no inflammation or disease signs were observed in the lungs of the omicron-infected animals on day 4 pi. 2022 Antiviral research Introduction SARS_CoV_2 D614G 11 16 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. We here compare the infectivity of the omicron variant versus the ancestral D614G strain in our Syrian hamster model. 2022 Antiviral research Introduction SARS_CoV_2 D614G 76 81 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. In January 2021, WHO included B.1.617.2 (Delta variant) as a VOC with spike double mutation E484Q and L452R have led to the second wave in India. 2021 Frontiers in medicine Introduction SARS_CoV_2 E484Q;L452R 92;102 97;107 S 70 75 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. Subsequently, in April 2021, Delta has been further substituted to Delta variants such as AY.1, AY.2, and AY.3 contains an additional spike protein substitution K417N. 2021 Frontiers in medicine Introduction SARS_CoV_2 K417N 161 166 S 134 139 35075065 COVID-19 Delta variation; more contagious or more pernicious? Based on new findings, strains that contain L452R mutation can evade host immune response by escaping both cell and humoral immune systems, so it can be concluded that this virus is more dangerous and deadly. 2022 Acta bio-medica Introduction SARS_CoV_2 L452R 44 49 35075065 COVID-19 Delta variation; more contagious or more pernicious? It was first classified in India in December 2020 and quickly established itself as the most common lineage within the country, leading to an ultimate increase in the number of cases and daily deaths and overburdening of health systems in April 2021 More detailed analysis disclosed that the prevailing lineage in distribution is a novel identified lineage B.1.617 holding in common signature mutations D111D, G142D, L452R, E484Q, D614G, and P681R, in the spike protein, containing within the receptor-binding domain (RBD). 2022 Acta bio-medica Introduction SARS_CoV_2 D111D;D614G;E484Q;G142D;L452R;P681R 403;431;424;410;417;442 408;436;429;415;422;447 S;RBD 456;518 461;521 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. In parallel with the clinical study, we conducted in vitro experiments to characterize Pro108Ser mutant 3CLpro enzyme from a biochemical standpoint. 2022 Scientific reports Introduction SARS_CoV_2 P108S 87 96 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Through molecular surveillance of patients infected in the Tokyo Metropolitan area, we found that in the summer of 2020, a sub-lineage of the virus with non-synonymous Pro108Ser mutation in the 3CLpro protein became relatively dominant. 2022 Scientific reports Introduction SARS_CoV_2 P108S 168 177 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. We hypothesized in our clinical study that the patient group infected with the SARS-Cov-2 sub-lineage (B.1.1.284) carrying the Pro108Ser mutation in 3CLpro tended to have a comparatively milder clinical course (i.e., a smaller proportion of patients required oxygen supplementation during the clinical course) than the patient group infected with the same sub-lineage not carrying the mutation. 2022 Scientific reports Introduction SARS_CoV_2 P108S 127 136 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. Each test can detect six targets (RBD, D614G, N501Y, E484K, L452R/E484Q-mutants, and 1 blank) of seven samples. 2022 Analytical chemistry Introduction SARS_CoV_2 D614G;E484K;L452R;N501Y;E484Q 39;53;60;46;66 44;58;65;51;71 RBD 34 37 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. The RBDs of SARS-CoV-2 spike protein and its variants (E484K, N501Y, D614G, and L452R/E484Q-mutants) were used as an ELISA antigen to enhance the specificity of our assay (Figure 1b). 2022 Analytical chemistry Introduction SARS_CoV_2 D614G;L452R;N501Y;E484K;E484Q 69;80;62;55;86 74;85;67;60;91 S;RBD 23;4 28;8 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. In this study, virus strains containing the N501Y mutation in Portugal were traced. 2022 Archives of virology Introduction SARS_CoV_2 N501Y 44 49 35083577 Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France. Here, we describe three infections with rare E484K-harboring SARS-CoV-2 containing three other amino acid substitutions in the spike, including W152L, which is located in the N-terminal domain (NTD) and possibly reduces sensitivity to neutralizing antibodies, and D614G and G679V, located in the S2 subunit. 2022 Archives of virology Introduction SARS_CoV_2 D614G;E484K;G679V;W152L 264;45;274;144 269;50;279;149 S;N 127;175 132;176 35083577 Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France. However, the loss of affinity of the W152L mutant for gangliosides is not anecdotical. 2022 Archives of virology Introduction SARS_CoV_2 W152L 37 42 35083577 Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France. Interestingly, the surface potential of the RBD was markedly increased by substitution E484K. 2022 Archives of virology Introduction SARS_CoV_2 E484K 87 92 RBD 44 47 35083577 Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France. Structural analysis of the Marseille-484K.V1 spike protein showed that amino acid substitutions G679V and D614G are at the same height in the spike protein, in a region considered to play a role in the conformational change required for demasking the RBD in the open state of the trimeric spike. 2022 Archives of virology Introduction SARS_CoV_2 D614G;G679V 106;96 111;101 S;S;S;RBD 45;142;289;251 50;147;294;254 35083577 Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France. The electrostatic surface potential of the NTD was also increased by the mutation W152L, but by an indirect mechanism of compaction of the domain that decreases the electronegative areas in favor of an enlarged electropositive surface. 2022 Archives of virology Introduction SARS_CoV_2 W152L 82 87 35083577 Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France. The low level of circulation of this variant in France and worldwide, with the notable exceptions of Japan and the USA, contrasts with the dramatic spread of other E484K-harboring viruses such as lineages B.1.351 and B.1.1.28/P.1. 2022 Archives of virology Introduction SARS_CoV_2 E484K 164 169 35083577 Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France. The Marseille-484K.V1, or R.1, lineage is another example of convergent evolution leading to the amino acid substitution E484K, as also observed for the substitutions L452R, N501Y, Q677H, and L18F, which have occurred independently in various SARS-CoV-2 lineages and geographical areas. 2022 Archives of virology Introduction SARS_CoV_2 E484K;L18F;L452R;N501Y;Q677H 121;192;167;174;181 126;196;172;179;186 35083577 Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France. These include viruses of PANGO lineages B.1.351 (WHO Beta variant) and B.1.1.28/P.1 (Gamma variant) that have spread worldwide, as well as the less-prevalent lineages B.1.525 (Eta variant) and B.1.1.345, all of which harbor the substitution E484K in their spike protein. 2022 Archives of virology Introduction SARS_CoV_2 E484K 241 246 S 256 261 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. The D614G mutation in the spike protein was observed in all the sequenced strains. 2022 Microbiology resource announcements Introduction SARS_CoV_2 D614G 4 9 S 26 31 35090164 Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants. Consistent with XGv289, the substitution of G446S alters the hydrophobic microenvironment generally established by RBD and a group of antibodies bound at the right shoulder, including XGv289 and XGv282, triggering a conformational shift on CDRs and disrupting antibody recognition (Extended Data. 2022 Nature Introduction SARS_CoV_2 G446S 44 49 RBD 115 118 35090164 Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants. Furthermore, mutations of N440K and Q498R, together with altered local conformation, also decrease hydrogen bonding formed by N439, K440, Y449, R498, T500 and Q506 from the Omicron RBD and D95, L98 from the light chain complementarity-determining regions (LCDRs) as well as Y59 and N62 from the HCDRs that would exist in the XGv289-WT S complex (Extended Data. 2022 Nature Introduction SARS_CoV_2 N440K;Q498R 26;36 31;41 RBD;S 181;335 184;336 35090164 Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants. However, substitutions of Y505H and K417N abolished three hydrogen bonds formed with K75, D31 and E104 from the heavy chain complementarity-determining regions (HCDRs), leading to conformational shifts in HCDR3 and the RBM tip (residues 470-490), which further perturbed six hydrogen bonds built by Y473, A475, S477, T478 and Q493 from WT RBD with T105, C107, A56, G55 and D109 from the HCDRs, albeit with an extra hydrogen bond established by the mutation Q493R and G55 from HCDR2 for Omicron (Extended Data. 2022 Nature Introduction SARS_CoV_2 K417N;Q493R;Y505H 36;457;26 41;462;31 RBD 339 342 35090164 Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants. In addition, the mutation E484A breaks the hydrogen bond with R74 from XGv282 HCDR2 and losses of charge interactions between R346 and K444 on WT RBD, and D56 and D58 on XGv265 LCDR2 owing to conformational alterations, further decreasing the binding of XGv282 and XGv265 to the Omicron S, respectively (Extended Data. 2022 Nature Introduction SARS_CoV_2 E484A 26 31 RBD;S 146;287 149;288 35090164 Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants. Overall XGv289, XGv282 and XGv265 bind patches surrounding the right shoulder of RBD with various orientations, but in a manner similar to those observed for LY-CoV1404, BD-812 and REGN10987:antibodies that are known to generally neutralize most VOCs with high potency:but showing decreased, to varying degrees, binding and neutralizing activities against Omicron owing to the presence of new N440K and G446S mutations. 2022 Nature Introduction SARS_CoV_2 G446S;N440K 403;393 408;398 RBD 81 84 35090164 Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants. Substitution of G446S disrupts the hydrophobic microenvironment, substantially decreasing hydrophobic interactions between Omicron S and XGv289. 2022 Nature Introduction SARS_CoV_2 G446S 16 21 S 131 132 35090164 Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants. The pattern of some of these alterations, similar to the those noted in previous VOCs, such as Delta69-70 in Alpha (B.1.1.7), N501Y in Alpha, Beta and Gamma (P.1), and P681H in Alpha and Delta (B.1.617.2), are associated with enhanced transmissibility, whereas many substitutions, including G142D/Delta143-145, ins214EPE, K417N, T478K, E484A, Q493R and N501Y, are closely linked with resistance to neutralizing antibodies and vaccine induced humoral immunity. 2022 Nature Introduction SARS_CoV_2 E484A;G142D;K417N;N501Y;N501Y;P681H;Q493R;T478K 336;291;322;126;353;168;343;329 341;296;327;131;358;173;348;334 35090164 Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants. Together, G446S, acting as a critical mutation site, can alter the local conformation at the binding interface, conferring greater resistance to a class of antibodies bound at the right shoulder of the RBD. 2022 Nature Introduction SARS_CoV_2 G446S 10 15 RBD 202 205 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. A similar mutation N501Y, which is also associated with increased human ACE2 binding, is often found upon mouse adaptation of SARS-CoV-2 and is present in several human SARS-CoV-2 variants of concern showing signs of higher transmissibility. 2022 Cell reports Introduction SARS_CoV_2 N501Y 19 24 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. During experimental infection of SARS-CoV-2 in ferrets, several groups have independently reported mink-associated spike mutations Y453F or N501T. 2022 Cell reports Introduction SARS_CoV_2 N501T;Y453F 140;131 145;136 S 115 120 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. From June to November 2020, an outbreak of SARS-CoV-2 infections occurred among farmed mink in Denmark, with continuous spillover to farm workers and local communities with viruses harboring Y453F. 2022 Cell reports Introduction SARS_CoV_2 Y453F 191 196 COVID-19 43 64 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Interestingly, both the Y453F and the N501T substitutions have also been associated with increased binding to human ACE2. 2022 Cell reports Introduction SARS_CoV_2 N501T;Y453F 38;24 43;29 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Of particular concern was the increased acquisition of spike mutations in mink-associated SARS-CoV-2 viruses, as demonstrated by the Cluster 5 variant identified in September 2020, which had several additional changes in the spike glycoprotein, including Delta69-70 in the N-terminal domain (NTD), and I692V and M1229I in S2. 2022 Cell reports Introduction SARS_CoV_2 I692V;M1229I 302;312 307;318 S;S;N 225;55;273 243;60;274 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Sequence analyses revealed several mutations in spike enriched after circulation in mink, most commonly the amino acid substitutions Y453F or N501T; residues that map to the RBD of spike protein. 2022 Cell reports Introduction SARS_CoV_2 N501T;Y453F 142;133 147;138 S;S;RBD 48;181;174 53;186;177 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Herein we identified by retrospective next-generation sequencing analysis a SARS-CoV-2 double Spike mutation D614G/S939F in 16 respiratory samples from occasionally employers within the Bangladeshi community present in Ostia. 2022 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G;S939F 109;115 114;120 S 94 99 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. SARS-CoV-2 Spike D614G mutation was evidenced in the members of the Bangladeshi community living in the close town Fiumicino who were frequently in contact with those members found positive for Spike D614G/S939F double mutation in Ostia. 2022 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G;D614G;S939F 17;200;206 22;205;211 S;S 11;194 16;199 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. We also found that unlike D614G, S939F mutation affects immune response through the slight but significant modulation of T-cell propensity and the selective enrichment of potential binding epitopes for some HLA alleles. 2022 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G;S939F 26;33 31;38 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. In addition to increased transmissibility due to the D614G mutation, both Beta and Gamma variants harbor key mutations such as K417N and E484K (or the functionally similar E484Q) in the Receptor Binding Domain (RBD) of the viral Spike protein, which account for the observed reduction in neutralizing potency of convalescent sera and post-vaccination immune sera. 2022 Vaccine Introduction SARS_CoV_2 D614G;E484K;E484Q;K417N 53;137;172;127 58;142;177;132 RBD;S;RBD 186;229;211 209;234;214 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. The question posed to vaccine researchers and developers is how to define vaccine candidates or compositions to best address the variants of concern already in circulation and those emerging in the future, especially viruses with the key E484K/Q mutation in the RBD resistant to neutralization by antibodies. 2022 Vaccine Introduction SARS_CoV_2 E484K;E484Q 238;238 245;245 RBD 262 265 35104067 Neutralizing Antibodies and Cytokines in Breast Milk After Coronavirus Disease 2019 (COVID-19) mRNA Vaccination. The D614G variant is associated with increased infectivity, the Alpha variant (B.1.1.7) is associated with enhanced transmissibility,6 and some reports suggest that the Beta and Gamma variants (B.1.351 and P.1) evade the natural immunity conferred by a prior SARS-CoV-2 infection. 2022 Obstetrics and gynecology Introduction SARS_CoV_2 D614G 4 9 COVID-19 259 279 35113647 Divergent SARS-CoV-2 Omicron-reactive T and B cell responses in COVID-19 vaccine recipients. Here, we analyzed humoral and cellular immune responses early and late (up to 6 months) after vaccination with ChAdOx-1, S, Ad26.COV2.S, mRNA-1273 or BNT162b2 and performed in-depth analyses of cross-reactivity of neutralizing antibodies and T-cells against against the D614G (wildtype, WT), B.1.351 (Beta), B.1.617.2 (Delta), and B.1.1.529 (Omicron) variants. 2022 Science immunology Introduction SARS_CoV_2 D614G 270 275 S;S 121;134 122;135 35113647 Divergent SARS-CoV-2 Omicron-reactive T and B cell responses in COVID-19 vaccine recipients. Indeed, there is a concerning reduction in neutralizing antibody titers against Omicron compared to D614G in convalescent and vaccinated individuals, which can be partially restored by booster vaccination. 2022 Science immunology Introduction SARS_CoV_2 D614G 100 105 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. This powerful technique enabled the rapid selection of a discovered SARS-CoV-2 nAb to extend its neutralizing capability to SARS-CoV-2 expressing the E484K and L452R S RBD mutations found in multiple SARS-CoV-2 variants. 2022 Cell reports Introduction SARS_CoV_2 E484K;L452R 150;160 155;165 RBD;S 168;166 171;167 35114688 ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. affinis ACE2s with avidity that is improved by the T498W mutation and, strikingly, the Khosta-2 RBD binds to human ACE2 even in the absence of mutations. 2022 Nature Introduction SARS_CoV_2 T498W 51 56 RBD 96 99 35114688 ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. affinis ACE2s, and the K493Y/T498W double mutant confers human ACE2 binding to the PRD-0038 RBD as it does for BtKY72. 2022 Nature Introduction SARS_CoV_2 K493Y;T498W 23;29 28;34 RBD 92 95 35114688 ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. Binding to human ACE2-Fc is not detectable with the parental BtKY72 RBD using BLI but is conferred by T498W and enhanced for the K493Y/T498W double mutant. 2022 Nature Introduction SARS_CoV_2 K493Y;T498W;T498W 129;102;135 134;107;140 RBD 68 71 35114688 ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. For example, the N501Y mutation increases human ACE2-binding affinity for SARS-CoV-2 where it has arisen in variants of concern, but the homologous mutation in the SARS-CoV-1 RBD (position 487) is highly deleterious for human ACE2 binding. 2022 Nature Introduction SARS_CoV_2 N501Y 17 22 RBD 175 178 35114688 ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. The RsYN04 RBD can also acquire binding to human ACE2 through the single T498W mutation. 2022 Nature Introduction SARS_CoV_2 T498W 73 78 RBD 11 14 35114688 ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. We detected robust spike-mediated entry for the K493Y/T498W double mutant but not the T498W single mutant. 2022 Nature Introduction SARS_CoV_2 K493Y;T498W;T498W 48;86;54 53;91;59 S 19 24 35114688 ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. We found that the mutation K493Y in AncSarbecovirus enables binding to human ACE2. 2022 Nature Introduction SARS_CoV_2 K493Y 27 32 35114688 ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. We validated that the mutations K493Y and T498W enable the RBD of the African sarbecovirus BtKY72 to interact with human ACE2 using purified recombinant proteins. 2022 Nature Introduction SARS_CoV_2 K493Y;T498W 32;42 37;47 RBD 59 62 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. Accordingly, we observed that the monomeric human ACE2 ectodomain bound with a 14-fold reduced affinity to immobilized SARS-CoV-2 E406W RBD (KD=1.34 muM) relative to wildtype (Wuhan-Hu-1) RBD (KD=93.9 nM) using biolayer interferometry (Figure S3a-c and Table S2). 2022 bioRxiv Introduction SARS_CoV_2 E406W 130 135 RBD;RBD 136;188 139;191 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. Although the E406W mutation promotes escape from REGEN-COV- and cilgavimab (AZD1061)-mediated neutralization, it requires multiple nucleotide substitutions from the Wuhan-Hu-1 spike sequence, has a strong deleterious effect on ACE2 binding and has not been detected in clinical isolates to date. 2022 bioRxiv Introduction SARS_CoV_2 E406W 13 18 S 176 181 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. Although the organization of residues 475-484 are only subtly different in the E406W RBD relative to apo S structures, it deviates markedly more from the ACE2-bound RBD structure or the REGEN-COV-bound RBD structure (Figure 1a). 2022 bioRxiv Introduction SARS_CoV_2 E406W 79 84 RBD;RBD;RBD;S 85;165;202;105 88;168;205;106 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. Casirivamab (REGN10933) interacts with residues 417, 453-456 and 475-490 (within antigenic site Ia) and the distinct conformation of the latter residues in the REGEN-COV-bound RBD and E406W apo S structures likely precludes mAb binding through steric clash with the mAb light chain (Figure 1c). 2022 bioRxiv Introduction SARS_CoV_2 E406W 184 189 RBD;S 176;194 179;195 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. Finally, we set out to assess the impact of the E406W mutation on vaccine-elicited plasma neutralizing activity using samples obtained from individuals who had received 2 doses of either Pfizer BNT162b2 or Moderna mRNA-1273 COVID-19 vaccine (Table S4). 2022 bioRxiv Introduction SARS_CoV_2 E406W 48 53 COVID-19 224 232 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. Imdevimab (REGN10987) recognizes an epitope residing at the interface between antigenic sites Ia and IIa and forms extensive interactions with residues 440-449 that would sterically clash with the mAb heavy chain in the E406W RBD structure (Figure 1b). 2022 bioRxiv Introduction SARS_CoV_2 E406W 220 225 RBD 226 229 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. Our data therefore shows that the E406W mutation disrupts the antigenic sites recognized by casirivamab (REGN10933) and imdevimab (REGN10987) allosterically, which are positioned 5 and 20A away, respectively. 2022 bioRxiv Introduction SARS_CoV_2 E406W 34 39 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. Several best-in-class broadly neutralizing sarbecovirus mAbs are unaffected by the E406W mutation and COVID-19 mRNA vaccine-elicited polyclonal antibodies retain a substantial fraction of their activity against this mutant, indicating several strategies are available should a E406W mutant virus emerge in the future. 2022 bioRxiv Introduction SARS_CoV_2 E406W;E406W 83;277 88;282 COVID-19 102 110 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. Similar to imdevimab, the loss of cilgavimab (AZD1061) binding to the E406W RBD is explained by the structural reorganization of residues 443-450 which are recognized by this mAb (Figure S2). 2022 bioRxiv Introduction SARS_CoV_2 E406W 70 75 RBD 76 79 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. The E406W substitution places the introduced side chain indol ring in a position sterically incompatible with the neighboring Y495 phenol side chain, inducing a rotameric rearrangement of the latter residue relative to the ACE2-bound RBD structure or apo S ectodomain trimer structures. 2022 bioRxiv Introduction SARS_CoV_2 E406W 4 9 RBD;S 234;255 237;256 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. These data indicate that the single E406W mutation leads to moderate erosion of vaccine-elicited polyclonal neutralizing antibodies, comparable to the SARS-CoV-2 Epsilon variant or the Delta variant. 2022 bioRxiv Introduction SARS_CoV_2 E406W 36 41 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. To understand the molecular basis of the E406W-mediated escape from the REGEN-COV cocktail and cilgavimab, we characterized the SARS-CoV-2 spike ectodomain trimer structure harboring the E406W mutation using single-particle cryo-electron microscopy. 2022 bioRxiv Introduction SARS_CoV_2 E406W;E406W 41;187 46;192 S 139 144 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. We previously mapped all possible RBD residue mutations that permit escape from the REGEN-COV mAb cocktail and the cilgavimab (AZD1061) mAb which led us to identify that the E406W substitution abrogated binding and neutralization of both REGEN-COV mAbs and the cocktail as well as binding of cilgavimab. 2022 bioRxiv Introduction SARS_CoV_2 E406W 174 179 RBD 34 37 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. Our study reveals that the Omicron mutations lead to an enhancement of binding between RBD and ACE2 by forming unique interaction patterns, which are caused mainly by N501Y, Q493K/R, and T478K mutations. 2022 bioRxiv Introduction SARS_CoV_2 N501Y;Q493K;Q493R;T478K 167;174;174;187 172;181;181;192 RBD 87 90 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. Compared with adults, GMTs in adolescents were 1.5- and 3.8-fold higher for D614G and the Omicron variant, respectively. 2022 medRxiv Introduction SARS_CoV_2 D614G 76 81 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. In children, at 4 weeks following a second dose of 50 mug mRNA-1273, Omicron neutralization was observed in 100% of participants and GMTs were reduced 22.1-fold versus D614G. 2022 medRxiv Introduction SARS_CoV_2 D614G 168 173 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. In this report, neutralization of the Omicron variant was compared with the prototypic wild-type (D614G) strain using serum samples obtained from twenty participants each in ongoing clinical trials that evaluated 2 doses of 100 mug mRNA-1273 in adults >=18 years (Coronavirus Efficacy [COVE]) and adolescents 12-17 years (TeenCOVE), and 2 doses of 50 mug mRNA in children 6-<12 years of age (KidCOVE) (Table S1). 2022 medRxiv Introduction SARS_CoV_2 D614G 98 103 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. Neutralizing titers in children were 2.0-fold higher for D614G and 2.5-fold higher for Omicron compared with those of adults. 2022 medRxiv Introduction SARS_CoV_2 D614G 57 62 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. Omicron neutralization titers in adolescents and children were also reduced less compared with D614G neutralization than those in adults. 2022 medRxiv Introduction SARS_CoV_2 D614G 95 100 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. Omicron neutralization was detected in 100% of adolescents, 4 weeks following a second dose of 100 mug of mRNA-1273, and Omicron GMTs were 11.8-fold lower than D614G titers (Fig 1B). 2022 medRxiv Introduction SARS_CoV_2 D614G 160 165 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. The geometric mean ID50 titer (GMT) was reduced 28.8-fold compared to D614G (Fig 1A). 2022 medRxiv Introduction SARS_CoV_2 D614G 70 75 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. These results indicate that D614G and Omicron neutralizing titers observed were numerically higher in adolescents and children than adults, 4 weeks following the second dose of a two-dose primary vaccination regimen of mRNA-1273. 2022 medRxiv Introduction SARS_CoV_2 D614G 28 33 35123263 The function of SARS-CoV-2 spike protein is impaired by disulfide-bond disruption with mutation at cysteine-488 and by thiol-reactive N-acetyl-cysteine and glutathione. The D614G mutation was identified during the initial global pandemic period of COVID-19 as the dominant SARS-CoV-2 variant, and multiple variants have been reported since then. 2022 Biochemical and biophysical research communications Introduction SARS_CoV_2 D614G 4 9 COVID-19 79 87 35126106 Antidepressant and Antipsychotic Drugs Reduce Viral Infection by SARS-CoV-2 and Fluoxetine Shows Antiviral Activity Against the Novel Variants in vitro. A common RBD mutation, N501Y, is shared by alpha, beta, and gamma, while K417N and E484K are found in beta and gamma. 2021 Frontiers in pharmacology Introduction SARS_CoV_2 E484K;K417N;N501Y 83;73;23 88;78;28 RBD 9 12 35126106 Antidepressant and Antipsychotic Drugs Reduce Viral Infection by SARS-CoV-2 and Fluoxetine Shows Antiviral Activity Against the Novel Variants in vitro. Moreover, infection by pseudotyped viruses carrying N501Y, K417N, or E484K single point mutations or triple mutation (N501Y/K417N/E484K) in the spike protein was shown to be reduced by fluoxetine. 2021 Frontiers in pharmacology Introduction SARS_CoV_2 E484K;K417N;N501Y;N501Y;E484K;K417N 69;59;52;118;130;124 74;64;57;123;135;129 S 144 149 35126106 Antidepressant and Antipsychotic Drugs Reduce Viral Infection by SARS-CoV-2 and Fluoxetine Shows Antiviral Activity Against the Novel Variants in vitro. The delta variant contains a non-RBD mutation, D614G, shared by alpha and gamma variants, as well as an RBD mutation, E484Q, which is similar to E484K in other variants. 2021 Frontiers in pharmacology Introduction SARS_CoV_2 D614G;E484K;E484Q 47;145;118 52;150;123 RBD;RBD 33;104 36;107 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. G251V and Q57H exhibit severe virulence property.Viral infection consists of several steps starting from viral entry, intracellular trafficking, replication, assembly and then release of the viral particles. 2022 Computational and structural biotechnology journal Introduction SARS_CoV_2 Q57H;G251V 10;0 14;5 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. Our study aims to understand the effect of one of the frequently occurring substitutions, D155Y, in the structural stability of the ORF3a protein and its ability to form complex with caveolin-1. 2022 Computational and structural biotechnology journal Introduction SARS_CoV_2 D155Y 90 95 ORF3a 132 137 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. The mutation patterns of ORF3a gene have been characterized as largely non-synonymous and increasingly deleterious (Q57H, H93Y, R126T, L127I, W128L, L129F, W131C, D155Y, D173Y, G196V, and G251V). 2022 Computational and structural biotechnology journal Introduction SARS_CoV_2 D155Y;D173Y;G196V;G251V;H93Y;L127I;L129F;R126T;W128L;W131C;Q57H 163;170;177;188;122;135;149;128;142;156;116 168;175;182;193;126;140;154;133;147;161;120 ORF3a 25 30 35130474 Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA. A total of 59 samples showed P681H on this repeated testing; only 2 still showed P681R, 1 at 0.52 frequency (down from 0.98) and 1 at 0.94, exactly as the previous sequence, suggesting a true P681R call, possibly co-infection with Delta, because the Ct for this sample was low (Ct = 17). 2022 Emerging infectious diseases Introduction SARS_CoV_2 P681H;P681R;P681R 29;81;192 34;86;197 35130474 Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA. Amplification artifact in SARS-CoV-2 Omicron sequences carrying P681R mutation, New York, USA. 2022 Emerging infectious diseases Introduction SARS_CoV_2 P681R 64 69 35130474 Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA. Closer examination indicated that the Omicron sequences with P681R contained varying numbers of P681H reads (median frequency of P681R call, a G at nucleotide position 23604, was 0.79 [range 0.43-0.98]). 2022 Emerging infectious diseases Introduction SARS_CoV_2 P681H;P681R;P681R 96;61;129 101;66;134 35130474 Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA. Of the 379 samples, amplified using 24 cycles regardless of cycle threshold (Ct), we detected 86 with P681R, a key Delta mutation associated with increased transmissibility, fusogenicity, and pathogenicity, distinct from the P681H mutation of Omicron. 2022 Emerging infectious diseases Introduction SARS_CoV_2 P681H;P681R 225;102 230;107 35130474 Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA. Repeating the library preparations and resequencing by different methods produced sequences with no P681R calls, except for 2 samples that showed P681R with 24 PCR cycles and P681H with 18 cycles (Table), indicating that a high number of PCR cycles can introduce false mutation calls. 2022 Emerging infectious diseases Introduction SARS_CoV_2 P681H;P681R;P681R 175;100;146 180;105;151 35130474 Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA. The presence of P681R in Omicron was cause for concern because it could be associated with higher pathogenicity/transmissibility. 2022 Emerging infectious diseases Introduction SARS_CoV_2 P681R 16 21 35130474 Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA. To investigate further, we repeated the library preparation and sequencing on 13 random samples previously assigned as P681R and 13 assigned as P681H as controls and changed 2 parameters: reverse transcriptase (RT) and PCR cycles. 2022 Emerging infectious diseases Introduction SARS_CoV_2 P681H;P681R 144;119 149;124 35130474 Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA. We also observed that sequences with P681R were from samples with higher Cts according to real-time detection assays compared with those with P681H, (open reading frame, TaqPath COVID-19 Combo Kit, Applied Biosystems, https://www.thermofisher.com) (median Ct = 22 for P681H and 28 for P681R; p<7.0803 x 10-37). 2022 Emerging infectious diseases Introduction SARS_CoV_2 P681H;P681H;P681R;P681R 142;268;37;285 147;273;42;290 COVID-19 178 186 35130474 Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA. We conclude that the foremost reason for detecting P681R in our Omicron samples was contamination with Delta amplicons and artifactual mixed base pair calls, resulting from preferential coverage of that specific position and amplicon in the context of Delta but not Omicron. 2022 Emerging infectious diseases Introduction SARS_CoV_2 P681R 51 56 35130474 Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA. We performed an additional RNA extraction, library preparation, and sequencing for this sample; the P681R persisted at frequency 0.84, suggesting that this sample represents co-infection. 2022 Emerging infectious diseases Introduction SARS_CoV_2 P681R 100 105 35130474 Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA. We then reprocessed the remaining 61 samples with P681R, using the xGen kit with 18 cycles of amplification. 2022 Emerging infectious diseases Introduction SARS_CoV_2 P681R 50 55 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. Some of the substitutions in these variants have been detected arising independently on multiple genetic backgrounds, such as the spike substitutions N501Y, E484K or the 69-70 deletion, supporting a model of convergent evolution. 2022 mBio Introduction SARS_CoV_2 E484K;N501Y 157;150 162;155 S 130 135 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. The amino acid substitution N501Y, found in the alpha, beta, and gamma variants, was also notably enriched in vaccine breakthrough samples. 2022 mBio Introduction SARS_CoV_2 N501Y 28 33 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. This was first documented for the D614G substitution, which spread around the world in the Spring of 2020 and displaced most strains lacking this substitution. 2022 mBio Introduction SARS_CoV_2 D614G 34 39 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. By analyzing the frequency, binding free energy (BFE) changes, and antibody disruption counts of RBD comutations, we reveal that nine RBD comutation sets, namely [L452R, T478K], [L452Q, F490S], [E484K, N501Y], [F490S, N501Y], [S494P, N501Y], [K417T, E484K, N501Y], [K417N, L452R, T478K], [K417N, E484K, N501Y], and [P384L, K417N, E484K, N501Y], may strongly disrupt existing vaccines and mAbs with relatively high infectivity and transmissibility among the populations. 2022 ACS infectious diseases Introduction SARS_CoV_2 E484K;E484K;E484K;F490S;K417N;L452R;N501Y;N501Y;N501Y;N501Y;N501Y;N501Y;T478K;T478K;E484K;F490S;K417N;K417N;K417T;L452Q;L452R;P384L;S494P 250;296;330;186;323;273;202;218;234;257;303;337;170;280;195;211;266;289;243;179;163;316;227 255;301;335;191;328;278;207;223;239;262;308;342;175;285;200;216;271;294;248;184;168;321;232 RBD;RBD 97;134 100;137 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Nonetheless, near 700 non-degenerate mutations are observed on RBD, contributing many key mutations in emerging variants, that is, N501Y for Alpha, K417N, E484K, and N501Y for Beta, K417T, E484K, and N501Y for Gamma, L452R and T478K for Delta, L452Q and F490S for Lambda, and so forth. 2022 ACS infectious diseases Introduction SARS_CoV_2 E484K;E484K;F490S;K417N;K417T;L452Q;L452R;N501Y;N501Y;N501Y;T478K 155;189;254;148;182;244;217;131;166;200;227 160;194;259;153;187;249;222;136;171;205;232 RBD 63 66 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. The associated new mutations, P384L, V401L, and A411S, call for the new design of boosting vaccines and mAbs. 2022 ACS infectious diseases Introduction SARS_CoV_2 A411S;P384L;V401L 48;30;37 53;35;42 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. We predict that low-frequency comutation sets [A411S, L452R, T478K], [L452R, T478K, N501Y], [V401L, L452R, T478K], and [L452R, T478K, E484K, N501Y] are on the path to become dangerous new variants. 2022 ACS infectious diseases Introduction SARS_CoV_2 E484K;L452R;L452R;N501Y;N501Y;T478K;T478K;T478K;T478K;A411S;L452R;L452R;V401L 134;54;100;84;141;61;77;107;127;47;70;120;93 139;59;105;89;146;66;82;112;132;52;75;125;98 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Finally, the P681R mutation (present in all B.1.617 lineages) immediately precedes the furin cleavage consensus sequence (682-RRSR/SVA-688), with initial reports suggesting that the P681R mutation enhances cleavage, and consequently S protein post-fusion transition. 2022 Nature communications Introduction SARS_CoV_2 P681R;P681R 13;182 18;187 S 233 234 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. In March 2021, genomic sequencing of SARS-CoV-2 samples in Maharashtra, India revealed an increased prevalence of E484Q, L452R and P681R co-mutation in the Spike glycoprotein (S protein). 2022 Nature communications Introduction SARS_CoV_2 E484Q;L452R;P681R 114;121;131 119;126;136 S;S 156;176 174;177 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The Delta variant contains a novel T478K mutation within the RBD - that is not present in previous variants of concern - with uncharacterised effect. 2022 Nature communications Introduction SARS_CoV_2 T478K 35 40 RBD 61 64 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The Kappa (B.1.617.1) lineage is a sub-lineage of the B.1.617 lineage, which is defined by L452R and P681R co-mutation. 2022 Nature communications Introduction SARS_CoV_2 L452R;P681R 91;101 96;106 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The S protein E484Q mutation in the Kappa variant was similarly found in the Beta (B.1.351) and Gamma (P.1) lineages, where residue 484 is mutated to lysine (E484K). 2022 Nature communications Introduction SARS_CoV_2 E484Q;E484K 14;158 19;163 S 4 5 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. While the Kappa variant contains only a single mutation (E154K) in N3, the Delta variant contains a mutation in N1 (T19R) and multiple mutations in N3 (Delta156/157, R158G). 2022 Nature communications Introduction SARS_CoV_2 R158G;E154K;T19R 166;57;116 171;62;120 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Within the receptor-binding domain (RBD) of the S protein, both the Kappa and Delta variants share an identical substitutional mutation (L452R) with the previously emerged variants of interest B.1.427/429 (Epsilon). 2022 Nature communications Introduction SARS_CoV_2 L452R 137 142 RBD;S 36;48 39;49 35136839 Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike. Selected amino acid T500 from the proposed RBD fraction was mutated and found that the conserved fraction CUT4 (from CUT 1, 2, 3 and 4) with T500S, Y489S, T500S and Y489S,Y453S,T500Y mutations have higher binding than the corresponding wild type fraction or the whole spike protein. 2022 Translational medicine communications Introduction SARS_CoV_2 T500S;T500S;Y489S;Y489S;T500Y;Y453S 141;155;148;165;177;171 146;160;153;170;182;176 S;RBD 268;43 273;46 35139368 Long-term, infection-acquired immunity against the SARS-CoV-2 Delta variant in a hamster model. The Delta variant is characterized by the spike protein amino acid mutations T19R, D614G, and D950N along with a deletion of two amino acids in the N-terminal domain at positions 157-158, antigenic mutations in the receptor binding domain (L452R and T478K), and a P681R mutation at the S1-S2 furin cleavage site. 2022 Cell reports Introduction SARS_CoV_2 D614G;D950N;P681R;T19R;T478K;L452R 83;94;264;77;250;240 88;99;269;81;255;245 RBD;S;N 215;42;148 238;47;149 35139811 Linked nosocomial COVID-19 outbreak in three facilities for people with intellectual and developmental disabilities due to SARS-CoV-2 variant B.1.1.519 with spike mutation T478K in the Netherlands. Additionally, B.1.1.519 shares the P681H mutation with the B.1.1.7 variant, which is near the furin-cleavage site and could have an effect on viral entry. 2022 BMC infectious diseases Introduction SARS_CoV_2 P681H 35 40 35139811 Linked nosocomial COVID-19 outbreak in three facilities for people with intellectual and developmental disabilities due to SARS-CoV-2 variant B.1.1.519 with spike mutation T478K in the Netherlands. Little information is available on the B.1.1.519 variant with spike mutation T478K which became dominant in Mexico over the course of a few months: in October 2020, 5% of sequenced specimens were reported to be B.1.1.519, whereas in February 2021, this percentage had increased to 87%. 2022 BMC infectious diseases Introduction SARS_CoV_2 T478K 77 82 S 62 67 35139811 Linked nosocomial COVID-19 outbreak in three facilities for people with intellectual and developmental disabilities due to SARS-CoV-2 variant B.1.1.519 with spike mutation T478K in the Netherlands. Spike mutation T478K lies within the interaction domain with the human receptor ACE2. 2022 BMC infectious diseases Introduction SARS_CoV_2 T478K 15 20 S 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. A few studies revealed an increased proportion of variants containing E484K (such as Beta and Gamma variants) in cases of breakthrough. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 70 75 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. A pseudovirus with the E484K mutation resulted in a 2-fold reduction individually. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 23 28 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. According to the data from Outbreak Information, the presence of the E484K mutation in the Gamma variant is 91%, compared with 86% in the Beta variant, and less than 0.5% in the Alpha variant. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 69 74 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Another study obtained mRNA-1273 post-vaccine sera and compared the neutralizing activity against VSV-pseudovirus of the Alpha variant and the Alpha+E484K variant, and a significant reduction in neutralizing titers was evident when the E484K mutation was present. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K;E484K 236;149 241;154 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Antibodies induced by NVX-CoV2373, a recombinant protein nanoparticle vaccine, reduced neutralization 14.5-fold against the Beta variant relative to D614G in a pseudovirus assay. 2022 Infection and drug resistance Introduction SARS_CoV_2 D614G 149 154 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Both the Beta and Gamma variants contain E484K, and Alpha variants do not. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 41 46 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Chen et al evaluated post-BNT162b vaccine sera using Vero-hACE2-TMPRSS2 cells and found E484K/N501Y mutation decreased neutralization fourfold compared to the WA1/2020 D614G variant. 2022 Infection and drug resistance Introduction SARS_CoV_2 D614G;E484K;N501Y 168;88;94 173;93;99 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Chen et al used Vero-hACE2-TMPRSS2 cells, and found neutralization titer of convalescent plasma decreased fivefold against E484K/N501Y compared with the WA1/2020 D614G virus. 2022 Infection and drug resistance Introduction SARS_CoV_2 D614G;E484K;N501Y 162;123;129 167;128;134 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Class 2 antibodies resist E484K mutations. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 26 31 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Collier et al found a similar result showing that the Alpha variant combined with E484K reduced the neutralization 11.4-fold in comparison with the wild-type spike protein. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 82 87 S 158 163 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Convalescence sera obtained from different countries and periods have consistently demonstrated that E484K or triple mutation (K417N/E484K/N501Y) decreased neutralization in pseudo-viral assays. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K;K417N;E484K;N501Y 101;127;133;139 106;132;138;144 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K and Vaccine Breakthrough Infection. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K Global Presence Rate. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K has been identified as an escape mutation that emerges during convalescent plasma. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K mutation prevalence rates over 50% in Southern America, according to data from Outbreak Information, were reported to be 62% in Suriname, 70% in French Guiana, 72% in Brazil, and 78% in both Trinidad and Tobago. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K Reduced Neutralization by Convalescence Sera. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K Reduced Neutralization by Post-Vaccination Sera. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K reduced susceptibility to casirivimab (25-fold). 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K reduces the convalescent sera antibody binding affinity by more than order of magnitude. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K together with other mutations, also decreased the neutralization effect of post-vaccine sera. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K, a mutation of one of the RBD residues, has a glutamate (E) to lysine (K) substitution at position 484. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 0 5 RBD 32 35 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Figure 1 summarizes the E484K global presence rate, and the world map is created by the Microsoft Excel on the Bing platform and reprinted under a CC BY license. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 24 29 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Gaebler et al and Wang et al obtained convalescent plasma at 1.3 months after infection, and the neutralization against the K417N/E484K/N501Y mutant was reduced 0.5- to 29-fold (P = 0.001). 2022 Infection and drug resistance Introduction SARS_CoV_2 K417N;E484K;N501Y 124;130;136 129;135;141 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Geographically, E484K mutations are highly prevalent in countries in Southern Africa and neighboring islands. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 16 21 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Greaney et al used lentiviral vector-based SARS-CoV-2 pseudoviruses and reported amino acid changes in E484 to K, P, or Q reduced binding of polyclonal convalescent plasma, and in some individuals, mutations at E484K could decrease neutralization by >100-fold. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 211 216 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Herein, we analyze the percentage of E484K present in the variants and the global prevalence based on geographic location in order to surveil the unfolding pandemic, comprehend the roles of epidemiological variables, identify SARS-CoV-2 variants and their genetic sequences, and recommend public health policy strategies. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 37 42 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. In a pseudovirus harboring the E484K substitution, bamlanivimab and etesevimab reduced susceptibility by 17-fold. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 31 36 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. In an escape mutation study, which using 19 monoclonal antibodies, substitutions were found at E484 with higher incidence than at any other residue, and four variants at this position (E484A, E484D, E484G, and E484K) exhibited resistance to each of the human convalescent sera tested. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484D;E484G;E484K;E484A 192;199;210;185 197;204;215;190 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. In conclusion, studies on post-vaccine sera showed that E484K alone, or combined with other mutations or variants containing E484K, reduced the neutralization titer, regardless of the vaccine platform used. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K;E484K 56;125 61;130 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. In contrast, imdevimab and casirivimab combined with imdevimab retained their activity against VSV pseudovirus with E484K. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 116 121 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. In one study, sera from individuals who received BNT162b2 vaccine were obtained, and the analysis found a 3.4-fold reduction in serum neutralization efficiency when E484K was present. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 165 170 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. In the SPR assay, class 2 antibodies lose binding affinity with E484K mutations. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 64 69 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. In this review, E484K mutations are discussed particularly in the context of observed frequencies in global sequence datasets. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 16 21 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. In this trial, 95% of the Covid-19 cases in South Africa were caused by the Beta variant, whereas 69% of the cases in Brazil were caused by the Zeta variant (P.2 lineage), and both carry the E484K mutation. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 191 196 COVID-19 26 34 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. In vitro assays have demonstrated that sotrovimab, AZD7442, regdanvimab, and REGN-CoV2 retained their activity against SARS-CoV-2 variants containing E484K, while bamlanivimab and etesevimab reduced neutralization. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 150 155 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. In vitro, AZD8895, AZD1061, and AZD8895+ AZD1061 reduced the inhibitory capacity slightly (2- to fivefold increases in IC50 values) when tested in recombinant isogenic SARS-CoV-2s possessing the E484K mutation. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 195 200 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Jangra et al compared the neutralization of the USA-WA1/2020 virus and a recombinant (r)SARS-CoV-2 virus with the E484K mutation, and found a 2 4-fold to 4 2-fold reduction in neutralization when E484K was present. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K;E484K 114;196 119;201 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Madhi et al investigated antibodies induced by ChAdOx1 nCoV-19 vaccine in a pseudovirus assay, and found that the geometric mean titers of the RBD triple mutant (K417N, E484K, and N501Y) decreased 3.49-fold relative to the original virus, and the live-virus assay showed lower neutralization than the pseudo-viral assay. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K;N501Y;K417N 169;180;162 174;185;167 RBD 143 146 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Moreover, it was reported that in patients with a high risk of severe Covid-19 treated with bamlanivimab, viral rebound was found in five of six severely immunodeficient patients, and E484K was found in the five patients. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 184 189 COVID-19 70 78 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Other studies using pseudovirus assay similarly proved class 2 antibodies conferred resistance to E484K mutation. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 98 103 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Post-vaccine sera of mRNA-1273 against recombinant SARS-CoV-2 pseudovirus containing RBD mutations (K417N-E484K-N501Y- D614G) in the Beta variant decreased neutralization 2.7-fold. 2022 Infection and drug resistance Introduction SARS_CoV_2 D614G;K417N;E484K;N501Y 119;100;106;112 124;105;111;117 RBD 85 88 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Prevalence of positive E484K mutation over 50% in all confirmed cases with genetic sequence is listed in descending order as follows: Mozambique 66%, Mauritius 65%, Reunion 63%, Malawi 61%, South Africa 54%, and Mayotte 51%. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 23 28 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Pseudotyped viruses carrying the E484K mutation reduced the effectiveness by at least tenfold against the 17 most potent antibodies selected from eight vaccinated individuals who received the mRNA-1273 or BNT162b2 vaccine. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 33 38 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Significance of E484K in SARS-CoV-2 Variant. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 16 21 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Studies evaluating the impact of E484K, as well as the mutations and variants of concern on post-vaccine sera are summarized in Table 3. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 33 38 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Studies on the neutralization of post-mRNA vaccine sera consistently demonstrated that variants containing E484K, such as the Beta and Gamma variants, decreased the neutralizing effects. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 107 112 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Table 1 illustrates the prevalence rates of E484K in the other variants. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 44 49 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Table 2 summarizes studies on the impact of E484K on the neutralization of convalescent sera. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 44 49 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Table 4 summarizes studies showing the impact of variants containing E484K on vaccine efficacy and effectiveness. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 69 74 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Table 6 summarizes monoclonal antibodies under Phase III clinical trials and the impact of E484K on neutralization of these monoclonal antibodies. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 91 96 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. The above studies verified that E484K decreased the neutralization in pseudovirus assays of post-mRNA-vaccine sera from human and macaque monkeys. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 32 37 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. The Alpha variant alone reduced neutralization 1.9-fold; when adding E484K to the Alpha variant, the neutralization was reduced 6.7-fold relative to the wild-type virus. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 69 74 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. The binding-strengthening mutations of E484K can play a vital role in the development of infectivity, transmissibility, and/or antigenicity, and therefore it is important to gain insights into the underlying mechanisms involved. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 39 44 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. The E484K mutation is present in several variants and popped up in rapid succession in different geographical regions of five continents, especially in Southern Africa and South America. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 4 9 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. The E484K mutation is present in Zeta variant (P.2) with a prevalence rate of 96%, compared to 85% in P.3. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 4 9 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. The E484K mutation was first identified in the Beta variant (B1.351) in South Africa and was also detected in the Alpha variant (B.1.1.7) in the United Kingdom, as well as in the Gamma variant (P.1) in Brazil, all of which are classified as SARS-CoV-2 variants of concern (VOC). 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 4 9 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. The Effects of E484K on Therapeutic Monoclonal Antibodies. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 15 20 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. The Impact of E484K on Vaccine Efficacy and Effectiveness. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 14 19 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. The neutralization decreased one- to three-fold when human immunodeficiency virus-1 (HIV-1) pseudoviruses possessed the E484K-, N501Y-, or K417N/E484K/N501-mutant. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K;K417N;N501Y;E484K 120;139;128;145 125;144;133;150 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. The prevalence of the E484K mutation in the Eta variant is 97%, compared with 43% in Iota, 1% in Lambda, and less than 0.5% in Kappa. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 22 27 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. The study revealed that the E484K escape mutation can develop during treatment with monoclonal antibodies. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 28 33 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. There is a gap in our current knowledge, with few available data on E484K mutations. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 68 73 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Therefore, these data collectively indicate that the primary determinant responsible for decreased neutralization is related to E484K. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 128 133 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Variants containing the E484K mutation, such as the Beta and Gamma variants, reduced neutralization of post-vaccine sera, whereas there was a minimal effect on the Alpha variant. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 24 29 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. We assessed the impact of E484K based on vaccine efficacy and effectiveness against variants containing the E484K mutation using real-world data. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K;E484K 26;108 31;113 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Whether variants possessing E484K play a role in breakthrough infection is not clear currently. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 28 33 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Whole viral genome sequencing found E484K along with other mutations. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K 36 41 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Wibmer et al obtained convalescent sera from blood donors in South Africa and discovered 27% of the samples lost neutralization against the pseudovirus containing K417N, E484K, and N501Y. 2022 Infection and drug resistance Introduction SARS_CoV_2 E484K;K417N;N501Y 170;163;181 175;168;186 35140714 Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. Omicron also had mutations in the other structural proteins, including Envelope (E) (T9I), Membrane (M) (D3G, Q19E, and A63T), and Nucleocapsid (N) (P13L, Delta31-33, R203K, G204R), further enhancing their infectivity. 2021 Frontiers in immunology Introduction SARS_CoV_2 A63T;G204R;Q19E;R203K;D3G;P13L;T9I 120;174;110;167;105;149;85 124;179;114;172;108;153;88 N;Membrane;E;N 131;91;81;145 143;99;82;146 35140714 Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. The non-structural proteins encoded by the ORF1ab contain mutations in the nsp3 (K38R, V1069I, Delta1265, L1266I, A1892T), nsp4 (T492I), nsp5 (P132H), nsp6 (Delta105-107, A189V), nsp12 (P323L), and nsp14 (I42V). 2021 Frontiers in immunology Introduction SARS_CoV_2 A1892T;A189V;L1266I;V1069I;I42V;K38R;P132H;P323L;T492I 114;171;106;87;205;81;143;186;129 120;176;112;93;209;85;148;191;134 ORF1ab;Nsp12;Nsp3;Nsp4;Nsp5;Nsp6 43;179;75;123;137;151 49;184;79;127;141;155 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. For other geographic locations, other lineages carrying the mutation S:T1117I have been reported but, unlike Costa Rica, with a frequency < 1% (https://www.gisaid.org/). 2022 Gene reports Introduction SARS_CoV_2 T1117I 71 77 S 69 70 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. In Costa Rica, during 2020 the predominant SARS-CoV-2 genome was a genotype carrying the mutation T1117I in the spike (S:T1117I), as we reported previously. 2022 Gene reports Introduction SARS_CoV_2 T1117I;T1117I 98;121 104;127 S;S 112;119 117;120 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. In the case of the mutation S:T1117I, despite being located between the HR1 and HR2 regions, predictions suggested possible effects on viral oligomerization needed for cell infection, and more studies were demanded to investigate the possible changes in transmissibility, severity, or vaccine effectiveness. 2022 Gene reports Introduction SARS_CoV_2 T1117I 30 36 S 28 29 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. To this end, this work aimed to study in-depth the biological effects of the mutation S:T1117I on the function of the spike protein. 2022 Gene reports Introduction SARS_CoV_2 T1117I 88 94 S;S 118;86 123;87 35157870 Detection of SARS-CoV-2 RNA in wastewater, river water, and hospital wastewater of Nepal. Since all three VOC display N501Y spike mutation, it was selected for mutation-specific quantitative polymerase chain reaction (qPCR) run. 2022 The Science of the total environment Introduction SARS_CoV_2 N501Y 28 33 S 34 39 35157870 Detection of SARS-CoV-2 RNA in wastewater, river water, and hospital wastewater of Nepal. The primary objective of this study was to determine the presence of SARS-CoV-2 RNA along with N501Y mutation in the collected water samples. 2022 The Science of the total environment Introduction SARS_CoV_2 N501Y 95 100 35162151 Shorter Incubation Period among Unvaccinated Delta Variant Coronavirus Disease 2019 Patients in Japan. SARS-CoV-2 VOCs bearing the L452R spike protein mutation demonstrate increased transmissibility, infectivity, and avoidance of antibody neutralization. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 L452R 28 33 S 34 39 35162151 Shorter Incubation Period among Unvaccinated Delta Variant Coronavirus Disease 2019 Patients in Japan. The proportion of SARS-CoV-2 virus strains with the L452R mutation was 89% in the week from 16 August to 22 August 2021. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 L452R 52 57 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Importantly, these variants of the SARS-CoV-2 share D614G mutation, which is also individually linked with the enhanced infectivity, following the evidence of the mutation enrichment via epidemiological surveillance. 2022 International journal of molecular sciences Introduction SARS_CoV_2 D614G 52 57 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. In particular, using an atomistic-based model of signal transmission in the SARS-CoV-2 S proteins, we determined that the D614G mutation can exert its effect through allosterically induced changes on stability and communications in the residue interaction networks. 2022 International journal of molecular sciences Introduction SARS_CoV_2 D614G 122 127 S 87 88 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Previous computational studies also identified residues that exhibit long-distance couplings with the RBD opening that included sites harboring functional mutations D614G and A570D shared across SARS-CoV-2 S protein variants. 2022 International journal of molecular sciences Introduction SARS_CoV_2 A570D;D614G 175;165 180;170 RBD;S 102;206 105;207 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. S-B.1.1.7 variant of the SARS-CoV-2 has 9 of the 17 mutations (Delta69-70 deletion, Delta144 deletion, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H) in the S protein, featuring N501Y mutation, which can increase binding affinity with ACE2 while eliciting immune escape from RBD-targeting antibodies. 2022 International journal of molecular sciences Introduction SARS_CoV_2 A570D;D1118H;D614G;N501Y;N501Y;P681H;S982A;T716I 110;145;117;103;181;124;138;131 115;151;122;108;186;129;143;136 RBD;S 278;160 281;161 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. S-B.1.351 variant is characterized by 21 mutations with 9 mutations (L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G, and A701V) in the spike protein, of which three mutations (K417N, E484K, and N501Y) are located in the RBD and increase the binding affinity for the ACE receptors and induce significant immune escape. 2022 International journal of molecular sciences Introduction SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;E484K;K417N;N501Y;N501Y;R246I;K417N;L18F 127;81;116;75;102;189;95;109;200;88;182;69 132;86;121;79;107;194;100;114;205;93;187;73 S;RBD 141;226 146;229 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. The cryo-EM structures of the S-GSAS/D614G mutant revealed the increased population of the 1-RBD-up open form as compared to the closed state in the S-GSAS/D614 structure. 2022 International journal of molecular sciences Introduction SARS_CoV_2 D614G 37 42 RBD;S;S 93;30;149 96;31;150 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. The detection of common mutational changes such as D614G, E484K, N501Y and K417N that are shared among major circulating variants B.1.1.7, B.1.351, and B.1.1.28/P.1 indicated that these positions can be particularly critical for modulation of the SARS-CoV-2 S protein responses and may induce immunity escape from vaccines and different classes of monoclonal antibodies. 2022 International journal of molecular sciences Introduction SARS_CoV_2 D614G;E484K;K417N;N501Y 51;58;75;65 56;63;80;70 S 258 259 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. The emergence of variants of concern (VOCs) with the enhanced transmissibility and infectivity profile, including D614G variant, B.1.1.7 (alpha), B.1.351 (beta), B.1.1.28/P.1 (gamma) and B.1.1.427/B.1.429 (epsilon) variants have attracted enormous attention in the scientific community and a considerable variety of the proposed mechanisms explaining functional observations from structural and biochemical perspectives. 2022 International journal of molecular sciences Introduction SARS_CoV_2 D614G 114 119 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. The increased stability of the D614G mutant was inferred from the recent cryo-EM structures of a full-length unmodified S-G614 trimer, which can reversibly adopt an all-down closed state and 1 RBD-up open conformation. 2022 International journal of molecular sciences Introduction SARS_CoV_2 D614G 31 36 RBD;S 193;120 196;121 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. The initial structural studies showed that the D614G mutation can act by shifting the population of the SARS-CoV-2 S trimer from the closed form (53% of the equilibrium) in the native spike protein to a widely-open topology of the "up" protomers in the D614G mutant, with 36% of the population adopting a single open protomer, 39% with two open protomers and 20% with all three protomers in the open conformation. 2022 International journal of molecular sciences Introduction SARS_CoV_2 D614G;D614G 47;253 52;258 S;S 184;115 189;116 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. The S-GSAS construct showed similar structural, antigenic, and stability behavior as the S-GSAS/PP construct, which included the K986P and V987P mutations. 2022 International journal of molecular sciences Introduction SARS_CoV_2 K986P;V987P 129;139 134;144 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. These studies suggested that the N501Y and S477N mutations enhance transmission primarily by enhancing binding, and that the K417N/T mutations facilitate immune escape, and the E484K mutation enhances binding and immune escape. 2022 International journal of molecular sciences Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y;S477N 177;125;125;33;43 182;132;132;38;48 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. This study showed that N501Y, E484K, and L452R mutations can modulate, either directly or allosterically, the increased ACE2 binding affinity, while E484K, L452R, and K417N/T mutations tend to primarily compromise productive antibody binding and induce immune escape. 2022 International journal of molecular sciences Introduction SARS_CoV_2 E484K;E484K;K417N;K417T;L452R;L452R;N501Y 30;149;167;167;41;156;23 35;154;174;174;46;161;28 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. D614G has been associated with increased infectivity and transmissibility of SARS-CoV-2. 2022 mBio Introduction SARS_CoV_2 D614G 0 5 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. E484K has been identified as an escape mutation that facilitates virus immune evasion. 2022 mBio Introduction SARS_CoV_2 E484K 0 5 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. E484K was first identified in South Africa (B.1.351) and Brazil (P.1), but it has also been gradually adopted by the U.K. 2022 mBio Introduction SARS_CoV_2 E484K 0 5 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. For instance, D614G is a spike variant that first emerged in January 2020 and became a dominant form as the pandemic spread, reaching >74% global prevalence by June 2020. 2022 mBio Introduction SARS_CoV_2 D614G 14 19 S 25 30 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. including the D614G (SG614), U.K. 2022 mBio Introduction SARS_CoV_2 D614G 14 19 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. Other mutations on S variants such as L452R, N501Y, and P681R also attracted research attention due to enhanced angiotensin-converting enzyme 2 (ACE2) interaction and partial escape from vaccine-elicited antibodies. 2022 mBio Introduction SARS_CoV_2 L452R;N501Y;P681R 38;45;56 43;50;61 S 19 20 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. Spike variants that contain our mutations of interest, D614G or/and E484K, as well as their parental strains were analyzed and compared side by side in this study. 2022 mBio Introduction SARS_CoV_2 D614G;E484K 55;68 60;73 S 0 5 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. Three notable SARS-CoV-2 variants were appeared since November 2020, sharing the same mutation of N501Y and are called B.1.1.7 (VOC Alpha GRY/501Y.V1), B1.351 (VOC Beta GH/501Y.V2) and P.1 (VOC Gamma GR/501Y.V3) which had high ACE2 binding affinity. 2022 Scientific reports Introduction SARS_CoV_2 N501Y 98 103 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. Moreover, the importance of D614G mutation in the evolutionary dynamics of SARS-CoV-2 is supported by the evidence that the increased proportion of G614 variant is consistent with an evolutionary selective advantage of the virus (Volz et al.). 2022 International microbiology Introduction SARS_CoV_2 D614G 28 33 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. One of the most important mutations in the FCS region is D614G, which is reported to spread globally and responsible for the rapid and massive transmission of SARS-CoV-2 (Korber et al.). 2022 International microbiology Introduction SARS_CoV_2 D614G 57 62 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. Our work showed that D614G was transmitted massively in Indonesia and might involve the founder effect of SARS-CoV-2 and be responsible for the high prevalence of COVID-19 in Indonesia. 2022 International microbiology Introduction SARS_CoV_2 D614G 21 26 COVID-19 163 171 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. The study of the biological effect of D614G mutation was facilitated by the development of SARS-CoV-2 pseudoviruses, in which the core (backbone) virus (such as retrovirus) was manipulated to express the S protein of SARS-CoV-2 (Chen and Zhang,). 2022 International microbiology Introduction SARS_CoV_2 D614G 38 43 S 204 205 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. Another VOC to emerge at about the same time was Beta (B.1.351), which is characterized by other NTD mutations and deletions, as well as crucial RBD mutations, including K417N, E484K, and N501Y. 2022 Science translational medicine Introduction SARS_CoV_2 E484K;K417N;N501Y 177;170;188 182;175;193 RBD 145 148 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. As a result, nearly all currently circulating SARS-CoV-2 strains bear the D614G mutation. 2022 Science translational medicine Introduction SARS_CoV_2 D614G 74 79 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. One VOC, Alpha (B.1.1.7), is characterized by N-terminal domain (NTD) deletions and a key N501Y mutation in its receptor-binding domain (RBD). 2022 Science translational medicine Introduction SARS_CoV_2 N501Y 90 95 RBD;N 137;46 140;47 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. Soon after initial identification, SARS-CoV-2 acquired a predominant D614G mutation in its spike protein. 2022 Science translational medicine Introduction SARS_CoV_2 D614G 69 74 S 91 96 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. The recently emerged Delta (B.1.617.2) variant is characterized by additional NTD alterations together with crucial RBD mutations (L452R and T478K). 2022 Science translational medicine Introduction SARS_CoV_2 T478K;L452R 141;131 146;136 RBD 116 119 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Importantly, our structural and biochemical data demonstrate that the Delta T478K substitution plays a vital role in stabilization and reshaping of the loop473-490 of the receptor binding motif (RBM), leading to enhanced interaction with ACE2. 2022 Nature communications Introduction SARS_CoV_2 T478K 76 81 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Our structural study reveals that the 8D3 epitope is located in the RBM loop473-490 region, and 8D3 binding induces a large side-chain orientation alternation of the substituted K478, suggesting 8D3 may use a unique "induced-fit" mechanism unreported for SARS-CoV-2 neutralizing antibodies to tolerate Delta T478K mutation. 2022 Nature communications Introduction SARS_CoV_2 T478K 308 313 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Previous studies have investigated the impact of such mutations on the spike structure, receptor binding, and antigenicity of the Alpha, Beta, Gamma, Epsilon (B.1.427/B.1.429), D614G, and N501Y variants as well as the partially mutated Delta RBDs. 2022 Nature communications Introduction SARS_CoV_2 D614G;N501Y 177;188 182;193 S;RBD 71;242 76;246 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. The Delta variant harbors multiple mutations in S protein, including two substitutions (L452R and T478K) in the RBD, the D614G substitution, a cluster of mutations in the N-terminal domain (NTD), and two more substitutions near the furin cleavage site and in the heptad repeat 1 (HR1). 2022 Nature communications Introduction SARS_CoV_2 D614G;T478K;L452R 121;98;88 126;103;93 RBD;N;S 112;171;48 115;172;49 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. Among those, mutation R203M was shown to significantly increase replication, but is similar to analogous N-protein mutations in all other SARS-CoV-2 variants of concern including the current Omicron variant. 2022 bioRxiv Introduction SARS_CoV_2 R203M 22 27 N 105 106 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. Conspicuously, the Delta variant containing the G215C mutation arose without accompanying changes in the spike protein (Nextstrain clade 21J) and has dramatically outperformed and virtually displaced other Delta variant clades, assuming worldwide dominance in 2021. 2022 bioRxiv Introduction SARS_CoV_2 G215C 48 53 S 105 110 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. Delta variant mutations in N-protein include D63G, R203M, D377Y, and in different clades additionally R385K and G215C, respectively. 2022 bioRxiv Introduction SARS_CoV_2 D377Y;D63G;G215C;R203M;R385K 58;45;112;51;102 63;49;117;56;107 N 27 28 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. In comparison with biophysical properties of the ancestral N-protein, the G215C mutant displays significant differences in secondary structure, self-association and co-assembly with nucleic acid, revealing a plasticity of protein biophysical properties that mirrors its remarkable sequence variability. 2022 bioRxiv Introduction SARS_CoV_2 G215C 74 79 N 59 60 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. In the present work, we observe a highly conserved region that reveals a possible role of the G215C mutation in enhancing interactions critical for assembly. 2022 bioRxiv Introduction SARS_CoV_2 G215C 94 99 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. This warrants a detailed study of the impact of the G215C mutation on protein structure and function. 2022 bioRxiv Introduction SARS_CoV_2 G215C 52 57 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Herein, we report the validation of a laboratory-developed SNP rRT-PCR protocol to detect the presence of N501Y, which can act as a screening tool for three circulating VOCs in Ontario (B.1.1.7, B.1.351, and P.1), as they all share this SNP. 2022 Microbiology spectrum Introduction SARS_CoV_2 N501Y 106 111 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Specimens with the N501Y mutation detected are subsequently submitted for WGS to confirm the presence of a VOC and identify the SARS-CoV-2 VOC lineage. 2022 Microbiology spectrum Introduction SARS_CoV_2 N501Y 19 24 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The E484K mutation has been observed in some B.1.1.7 genome sequences. 2022 Microbiology spectrum Introduction SARS_CoV_2 E484K 4 9 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The VOC first detected in the United Kingdom represents the B.1.1.7 lineage (also known as 20I/501Y.V1, VOC202012/010, and Alpha) and contains three key mutations in the spike (S) gene: 69 to 70 deletion, N501Y, and P681H. 2022 Microbiology spectrum Introduction SARS_CoV_2 N501Y;P681H 205;216 210;221 S;S 170;177 175;178 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. This lineage is characterized by several S gene SNPs, including L452R, T478K, E484Q, D614G, and P681R. 2022 Microbiology spectrum Introduction SARS_CoV_2 D614G;E484Q;L452R;P681R;T478K 85;78;64;96;71 90;83;69;101;76 S 41 42 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. This VOC has multiple mutations in the receptor-binding domain (RBD) of the S protein, including K417N, E484K, and N501Y. 2022 Microbiology spectrum Introduction SARS_CoV_2 E484K;K417N;N501Y 104;97;115 109;102;120 RBD;S 64;76 67;77 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. This VOC shares the S gene N501Y single nucleotide polymorphism (SNP) with B.1.1.7 and the E484K SNP with B.1.351; however, all three lineages arose independently. 2022 Microbiology spectrum Introduction SARS_CoV_2 E484K;N501Y 91;27 96;32 S 20 21 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. The P.1 lineage-defining mutations in the Spike protein, especially in the receptor-binding domains (RBD) such as K417T, E484K and N501Y, are of concern because they may enhance ACE2 affinity and contribute to antibody evasion. 2022 Microbiology spectrum Introduction SARS_CoV_2 E484K;K417T;N501Y 121;114;131 126;119;136 S;RBD 42;101 47;104 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. The first mutation of this kind, G29140T, was described by Vanaerschot, Mann in samples from California, USA. 2022 PloS one Introduction SARS_CoV_2 G29140T 33 40 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. The fourth, and most recent mutation identified is C29197T. 2022 PloS one Introduction SARS_CoV_2 C29197T 51 58 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. Two of these point mutations occur at the same nucleotide position, C29200T first described by Ziegler, Steininger, and C29200A described by Hasan, Sundararaju. 2022 PloS one Introduction SARS_CoV_2 C29200A;C29200T 120;68 127;75 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. We describe a period prevalence rate of the C29197T mutation over 3-fold higher than the statewide prevalence rate for this mutation and that exceeded the 5% rate recommended by the FDA as a trigger for additional caution and assessment of assay performance. 2022 PloS one Introduction SARS_CoV_2 C29197T 44 51 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. In a mouse model of SARS-CoV-2, the N501Y mutation emerged and conferred increased affinity towards mouse ACE2 receptor. 2022 Scientific reports Introduction SARS_CoV_2 N501Y 36 41 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. It had a mutation N501Y in the RBD region that is directly involved in contacting ACE2. 2022 Scientific reports Introduction SARS_CoV_2 N501Y 18 23 RBD 31 34 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. Mutational scanning studies of SARS-CoV-2 RBD domain in yeast showed the N501F mutation resulted in several fold increased affinity to ACE2. 2022 Scientific reports Introduction SARS_CoV_2 N501F 73 78 RBD 42 45 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. N501Y and two other mutations in the RBD domain, K417N/T and E484K, were subsequently founds in SARS-CoV-2 variants from South Africa (B.1.351) and Brazil (P.1). 2022 Scientific reports Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 61;49;49;0 66;56;56;5 RBD 37 40 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. The first of such variants with a D614G mutation at the spike protein was shown to increase viral titer and infectivity, yet it was effectively neutralized by antisera. 2022 Scientific reports Introduction SARS_CoV_2 D614G 34 39 S 56 61 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. The N501Y was of particular interest due to its presence in all three variants and its unique role in mediating a direct contact with ACE2 receptor. 2022 Scientific reports Introduction SARS_CoV_2 N501Y 4 9 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. Thus, we chose the original and N501Y RBD that appeared in B.1.1.7 and other SARS-CoV-2 variants for the investigation. 2022 Scientific reports Introduction SARS_CoV_2 N501Y 32 37 RBD 38 41 35176330 Evolutionary shift from purifying selection towards divergent selection of SARS-CoV2 favors its invasion into multiple human organs. Evolution of a key entry-point residue Y493Q indicates that Y must be mutated twice to give rise to Q as Y>H>Q but such an intermediate CoV virus is never identified in known twenty-nine bat CoV virus. 2022 Virus research Introduction SARS_CoV_2 Y493Q 39 44 35178586 Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. Also, D614G is combined with T859N in the IHU variant. 2022 Archives of virology Introduction SARS_CoV_2 D614G;T859N 6;29 11;34 35178586 Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. Although the D614G substitution already allows the trimer conformation to be unlocked, this is predicted to be facilitated even more in the presence of the additional substitution T859N. 2022 Archives of virology Introduction SARS_CoV_2 D614G;T859N 13;180 18;185 35178586 Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. In particular, P681H is located in the cleavage site of the S1-S2 subunits of the spike and is observed in other variants, including the recently emerging Omicron variant. 2022 Archives of virology Introduction SARS_CoV_2 P681H 15 20 S 82 87 35178586 Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. In the receptor binding domain (RBD), in addition to the well-known substitutions N501Y and E484K, several changes were predicted to significantly affect the neutralizing epitopes. 2022 Archives of virology Introduction SARS_CoV_2 E484K;N501Y 92;82 97;87 RBD;RBD 7;32 30;35 35178586 Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. Subsequent detection of three mutations in the spike gene in a qPCR assay to screen for variants, as performed routinely in France in cases of SARS-CoV-2 positivity, revealed an atypical combination with L452R negativity, E484K positivity, and E484Q negativity (Pentaplex assay, ID solutions, Grabels, France), which did not correspond to the pattern of the Delta variant, which was associated with almost all SARS-CoV-2 infections at that time (Table 1). 2022 Archives of virology Introduction SARS_CoV_2 E484K;E484Q;L452R 222;244;204 227;249;209 S 47 52 COVID-19 410 431 35178586 Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. These include the substitutions N501Y and E484K, which are present in the Beta, Gamma, Theta, and Omicron variants, F490S, which is present in the Lambda variant, and P681H, which is present in the Lambda and Omicron variants. 2022 Archives of virology Introduction SARS_CoV_2 E484K;F490S;N501Y;P681H 42;116;32;167 47;121;37;172 35178586 Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. Thus, the IHU variant could be distinguished in qPCR screening assays from the Delta variant (L452R positive) and the Omicron variant (L452R negative and negative for S gene detection by the TaqPath COVID-19 assay) co-circulating in southern France. 2022 Archives of virology Introduction SARS_CoV_2 L452R;L452R 94;135 99;140 S 167 168 COVID-19 199 207 35178586 Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. We analyzed a structural model of the complete spike protein of the IHU variant, generated by incorporating its specific mutational profile into the spike protein structure of the original 20B SARS-CoV-2 (Wuhan-Hu-1 isolate with the D614G substitution) and fixing all gaps in the pdb file by incorporating the missing amino acids using the Robetta protein structure prediction tool [https://robetta.bakerlab.org/], followed by energy minimization using the Polak-Ribiere algorithm as described previously. 2022 Archives of virology Introduction SARS_CoV_2 D614G 233 238 S;S 47;149 52;154 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. E484 is an immunodominant spike protein residue and the E484K substitution enables the escape from neutralizing antibody inhibition in vitro and it may be linked with reduced vaccination efficacy. 2022 Scientific reports Introduction SARS_CoV_2 E484K 56 61 S 26 31 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. In February 2021 Public Health England (PHE) published a report of Alpha (formerly B.1.1.7) genomes with acquisition of the E484K spike mutation. 2022 Scientific reports Introduction SARS_CoV_2 E484K 124 129 S 130 135 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Notably, the presence of the E484K mutation into the Alpha background led to a more-substantial loss of neutralizing activity by vaccine-elicited antibodies compared with the mutations in Alpha alone, suggesting that this variant represents a threat to the efficacy of the BNT162b2 mRNA vaccine. 2022 Scientific reports Introduction SARS_CoV_2 E484K 29 34 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. The Beta (formerly B.1.351) and Gamma (formerly P.1) variants were of particular concern because they carry the mutation E484K within the receptor binding domain (RBD). 2022 Scientific reports Introduction SARS_CoV_2 E484K 121 126 RBD;RBD 138;163 161;166 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. The data revealed a stronger immediate immune response of patients infected with the Alpha+E484K variant as compared to the parent Alpha variant. 2022 Scientific reports Introduction SARS_CoV_2 E484K 91 96 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. To address this question, we investigated the immune transcriptomes in hospitalized patients infected with the Alpha+E484K variant or the parent Alpha variant. 2022 Scientific reports Introduction SARS_CoV_2 E484K 117 122 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Using RNA-seq, a variant-agnostic approach, we identified conserved and unique host responses to E484K variants, including Beta and Gamma. 2022 Scientific reports Introduction SARS_CoV_2 E484K 97 102 35182772 Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir. Except for the mutations T21I and P132H, the mutations introduce no major changes in the chemical character of the side-chains, as indicated by low - or, in the case of T21I and P132H, moderate - values of Miyata's distances. 2022 Bioorganic & medicinal chemistry letters Introduction SARS_CoV_2 P132H;P132H;T21I;T21I 34;178;25;169 39;183;29;173 35182772 Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir. Furthermore, we chose to investigate three additional abundant Mpro mutations to cover a larger variety of lineages: T21I, which is >90% prevalent50 in B.1.1.318, a WHO variant under monitoring (VUM), L89F, which is >95% prevalent51 in the B.1.2 lineage, and L205V, which is >95% prevalent52 in the former VOI Zeta (P.2) (Figure2 b. 2022 Bioorganic & medicinal chemistry letters Introduction SARS_CoV_2 L205V;L89F;T21I 259;201;117 264;205;121 35182772 Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir. Hence, we selected the six mutations G15S, T21I, L89F, K90R, P132H and L205V for further investigations. 2022 Bioorganic & medicinal chemistry letters Introduction SARS_CoV_2 G15S;K90R;L205V;L89F;P132H;T21I 37;55;71;49;61;43 41;59;76;53;66;47 35182772 Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir. In summary, we identified the currently most prevalent Mpro variants (G15S, T21I, L89F, K90R, P132H, L205V) in different lineages of SARS-CoV-2 (C.37 Lambda, B.1.1.318, B.1.2, B.1.351 Beta, B.1.1.529 Omicron, P.2 Zeta) and found that, in a biochemical assay, they are catalytically competent to a similar degree as the wildtype. 2022 Bioorganic & medicinal chemistry letters Introduction SARS_CoV_2 K90R;L205V;L89F;P132H;T21I;G15S 88;101;82;94;76;70 92;106;86;99;80;74 35182772 Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir. Specifically the R298A mutation has become a tool to study the protease in its monomeric form, since it inactivates the protease by disrupting the Mpro dimer. 2022 Bioorganic & medicinal chemistry letters Introduction SARS_CoV_2 R298A;R298A 19;17 24;22 35182772 Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir. The mutations are G15S, which is >85% prevalent44 in the Lambda VOI (or C.37, using PANGO nomenclature), K90R, which is >95% prevalent46 in the Beta VOC (B.1.351) and P132H, which is >95% prevalent47 in the Omicron VOC (B.1.1.529). 2022 Bioorganic & medicinal chemistry letters Introduction SARS_CoV_2 G15S;K90R;P132H 18;105;167 22;109;172 35182772 Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir. The mutations G15S, T21I, L89F and K90R are located in domain I, whereas the mutations P132H and L205V are in domains II and III, respectively (Figure2 a. 2022 Bioorganic & medicinal chemistry letters Introduction SARS_CoV_2 G15S;K90R;L205V;L89F;P132H;T21I 14;35;97;26;87;20 18;39;102;30;92;24 35182772 Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir. WT SARS-CoV-2 Mpro and the mutants G15S, T21I, L89F, K90R, P132H and L205V were expressed in E. 2022 Bioorganic & medicinal chemistry letters Introduction SARS_CoV_2 G15S;K90R;L205V;L89F;P132H;T21I 35;53;69;47;59;41 39;57;74;51;64;45 E 93 94 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. 1.1.7 background were thought to be the cause of reduced vaccine efficacy; in fact, studies using a pseudo-typed virus with the E484K mutation or recombinant virus with the E484K mutation demonstrated weaker neutralizing activity of BNT162b2-vaccinated sera. 2022 Vaccine Introduction SARS_CoV_2 E484K;E484K 128;173 133;178 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. 1.1.7), which possesses the N501Y mutation, is known to be highly contagious compared to conventional strains, and was responsible for a wave of new infections globally, including in Japan. 2022 Vaccine Introduction SARS_CoV_2 N501Y 28 33 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. 1.351), which possesses both the N501Y and E484K mutations. 2022 Vaccine Introduction SARS_CoV_2 E484K;N501Y 43;33 48;38 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. E484K substitutions in the B. 2022 Vaccine Introduction SARS_CoV_2 E484K 0 5 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. However, it is unclear whether the E484K mutation affects the BNT162b2 vaccine efficacy independently of the N501Y mutation against naturally derived virus variants. 2022 Vaccine Introduction SARS_CoV_2 E484K;N501Y 35;109 40;114 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. The dominant variant in Tokyo, Japan in early 2021 was from the R.1 lineage and possessed the E484K mutation, but not the N501Y mutation. 2022 Vaccine Introduction SARS_CoV_2 E484K;N501Y 94;122 99;127 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. To determine whether the E484K mutation reduces the efficacy of the BNT162b2 vaccine independently of the N501Y mutation, we measured neutralizing antibody titers against several major SARS-CoV-2 variants, including those of the R.1 lineage, using serum samples from Japanese university staff who were immunized with two doses of BNT162b2 vaccine. 2022 Vaccine Introduction SARS_CoV_2 E484K;N501Y 25;106 30;111 35187580 Impaired detection of omicron by SARS-CoV-2 rapid antigen tests. P13L, DEL31/33, R203K and G204R, and the additional mutation S413R is present in BA.2 (Suppl. 2022 Medical microbiology and immunology Introduction SARS_CoV_2 G204R;R203K;S413R;P13L 26;16;61;0 31;21;66;4 35187580 Impaired detection of omicron by SARS-CoV-2 rapid antigen tests. Three of these mutations (P13L, DEL31/33 and S413R) are unique to VoC omicron compared to alpha, beta, gamma or delta, rendering predictions of the performance of RATs difficult. 2022 Medical microbiology and immunology Introduction SARS_CoV_2 S413R;P13L 45;26 50;30 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. B.1.427 and B.1.429 harbor L452R mutation in RBD. 2022 Process biochemistry (Barking, London, England) Introduction SARS_CoV_2 L452R 27 32 RBD 45 48 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The B.1.1.7 variant carries 17 mutations in its genome, including N501Y in the Spike Receptor-Binding Domain (RBD). 2022 Process biochemistry (Barking, London, England) Introduction SARS_CoV_2 N501Y 66 71 S;RBD 79;110 84;113 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The variant, B.1.351 and B.1.1.28 carries 9 and 11 mutations in the spike (S) protein, respectively, including three mutations in the receptor binding domain (RBD), K417N/T, E484K, and N501Y. 2022 Process biochemistry (Barking, London, England) Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 174;165;165;185 179;172;172;190 RBD;S;RBD;S 134;68;159;75 157;73;162;76 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. Very recently, a new variant of SARS-CoV-2, B.1.617 (Delta variant) discovered in India, carries two RBD mutations namely E484Q and L452R which is a double whammy. 2022 Process biochemistry (Barking, London, England) Introduction SARS_CoV_2 E484Q;L452R 122;132 127;137 RBD 101 104 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. Any other mutation combination or the absence of any mutations required the use of a second rRT-PCR mutation assay, Allplex SARS-CoV-2 Variants II Assay (Seegene, Korea), which screens for the mutations K417N, K417T, L452R, and W152C. 2022 Archives of virology Introduction SARS_CoV_2 K417N;K417T;L452R;W152C 203;210;217;228 208;215;222;233 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. At that time, samples presenting delH69/V70 and N501Y mutations were classified as "probable Alpha variant". 2022 Archives of virology Introduction SARS_CoV_2 N501Y 49 54 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. Following the scheme described above, in August 2021, we detected three strains that presented K417N, N501Y, and E484K mutations but did not present delH69/V70, W152C, K417T, L452R, or V1176F mutations. 2022 Archives of virology Introduction SARS_CoV_2 E484K;K417N;K417T;L452R;N501Y;V1176F;W152C 114;96;169;176;103;186;162 119;101;174;181;108;192;167 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. Samples containing E484K and N501Y mutations and lacking delH69/V70 mutation were also subjected to rRT-PCR melting curve analysis of K417N and V1176F (VirSNiP Assays, TIB MOLBIOL, Germany), as this assay was commercially available before the Allplex SARS-CoV-2 Variants II Assay. 2022 Archives of virology Introduction SARS_CoV_2 E484K;K417N;N501Y;V1176F 19;134;29;144 24;139;34;150 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. The first assay, Allplex SARS-CoV-2 Variants I Assay (Seegene, Korea), includes mutations delH69/V70, N501Y, and E484K. 2022 Archives of virology Introduction SARS_CoV_2 E484K;N501Y 113;102 118;107 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. SARS-CoV-2 lineages carrying the amino acid substitution N501Y spread rapidly in the United Kingdom in late autumn of 2020. 2022 Microbiology spectrum Introduction SARS_CoV_2 N501Y 57 62 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. About 14/30 substitutions including N501Y and E484K are presented in other variants as the Beta, Gamma, Theta, and Omicron. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 E484K;N501Y 46;36 51;41 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. About 20% of Brazilian isolates in May 2020 had this D614G. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 D614G 53 58 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. All Brazilian isolates in February 2021 presented the D614G mutation. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 D614G 54 59 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. B.1.1.351 has three genomic variants (K417N, E484K, and N501Y) in the RBD and is more transmissible than the parental strain; it shows an increased viral load and resistance to neutralization by antibodies generated either by natural infection or by vaccination. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 E484K;N501Y;K417N 45;56;38 50;61;43 RBD 70 73 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. Both variants (501Y.V2 and 501Y) carried another mutation: E484K. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 E484K 59 64 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. Eight genomic variants map to the spike glycoprotein, including N501Y in the receptor-binding domain, deletion 69_70, and P681H in the furin cleavage site. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 N501Y;P681H 64;122 69;127 S 34 52 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. In October 2020, a new variant (N501Y) called B.1.1.7 was detected in the UK. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 N501Y 32 37 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. In the following month, in January 2021 a new variant called P2 (E484K) was detected in Rio de Janeiro, but it is less aggressive than P1. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 E484K 65 70 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. It carries the common genomic variants D111D, G142D, D614G, and P681R in the spike protein, including the receptor-binding domain (RBD). 2022 International journal of environmental research and public health Introduction SARS_CoV_2 D111D;D614G;G142D;P681R 39;53;46;64 44;58;51;69 S;RBD 77;131 82;134 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. K417N/E484K/N501Y variants have since been isolated in Japan, the USA, France, and Italy. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 E484K;N501Y;K417N 6;12;0 11;17;5 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. Many chimeric monoclonal anti-SARS-CoV-2 antibodies have been developed based on the S protein RBD epitope, which was developed by ACRObiosystems (antibody S1N-M122) and was able to neutralize the variants identified in the United Kingdom (B.1.1.7), South Africa (B.1.351), Brazil (P.1), and California (B.1.429), and the wild-type variant carrying D614G (WT-D614G). 2022 International journal of environmental research and public health Introduction SARS_CoV_2 D614G;D614G 349;359 354;364 RBD;S 95;85 98;86 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. The E484K, K417T/N, and N501Y genomic variants are the most worrisome because they generate greater transmissibility by increasing viral contagion. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 4;11;11;24 9;18;18;29 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. The enhanced transmissibility is in part due to increased ACE2 binding and rate of S1-S2 cleavage by RBD associated with genomic variants L452R with P681R in the furin cleavage site. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 L452R;P681R 138;149 143;154 RBD 101 104 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. The first genomic variants in the SARS-CoV-2 spike glycoprotein were registered in January 2020 in China: D614G (aspartate (D) at amino acid position 614 replaced by glycine (G). 2022 International journal of environmental research and public health Introduction SARS_CoV_2 D614G;D614G 112;106 153;111 S 45 63 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. The P.2 lineage reported in Rio de Janeiro, Brazil, only carries the E484K genomic variants. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 E484K 69 74 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. These three variants contain the E484K present in all regions of Brazil. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 E484K 33 38 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. Variant B.1.429 from California, United States, shows genomic variants in L452R and can escape antibodies. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 L452R 74 79 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. Variant B.1.617, detected in India, has 13 genomic variants, including a "double mutant" in the spike protein (E484Q and L452R). 2022 International journal of environmental research and public health Introduction SARS_CoV_2 L452R;E484Q 121;111 126;116 S 96 101 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. Moreover, H655Y and N679K mutations are located near the furin cleavage site and may increase S cleavage. 2022 Life (Basel, Switzerland) Introduction SARS_CoV_2 H655Y;N679K 10;20 15;25 S 94 95 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. Some concerning S mutations are K417N, T478K, N501Y and D614G, all of which are found in the previous VOCs and responsible in the increased viral transmission and enhanced immune invasion. 2022 Life (Basel, Switzerland) Introduction SARS_CoV_2 D614G;K417N;N501Y;T478K 56;32;46;39 61;37;51;44 S 16 17 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. A study found that compared with the USAWA1/2020 strain, the variant strain containing the E484K mutation was vaccinated with two doses of SARS-CoV-2 BNT162b2 vaccine, the vaccine-induced immunity level was still lower. 2022 Micromachines Introduction SARS_CoV_2 E484K 91 96 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. Relevant data show that for strains containing E484K variants, the antibody titer induced by the vaccine should be increased. 2022 Micromachines Introduction SARS_CoV_2 E484K 47 52 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. The E484K mutation in the Beta and Gamma variants may use the receptor binding domain on the S protein to escape neutralizing antibodies caused by previous infections or vaccination. 2022 Micromachines Introduction SARS_CoV_2 E484K 4 9 RBD;S 62;93 85;94 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. The key mutation sites N501Y, E484K, L452R, etc. 2022 Micromachines Introduction SARS_CoV_2 E484K;L452R;N501Y 30;37;23 35;42;28 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. The mutation of L452R may cause the structure of the S protein to change and promote its interaction with the ACE2 receptor. 2022 Micromachines Introduction SARS_CoV_2 L452R 16 21 S 53 54 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. These evidences preliminarily indicate that these key mutation sites, such as N501Y, E484K, L452R, etc., enhance the binding affinity of the virus to the host cell ACE2 receptor, and affect the biological function of SARS-COV-2, increase the spread, severity, and vaccine or natural-induced immune escape. 2022 Micromachines Introduction SARS_CoV_2 E484K;L452R;N501Y 85;92;78 90;97;83 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. As a result of positive natural selection, it was found that D614G increases the infectivity, viral fitness, transmission rate and efficiency of cellular entry for the SARS-CoV-2 virus across a broad range of human cell types. 2022 PloS one Introduction SARS_CoV_2 D614G 61 66 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Finally, we have computationally predicted possible effects of the G1223C mutation, observed in this study, resided in the transmembrane domain of the spike protein and uniquely detected in SARS-CoV-2 from Pahang, Malaysia. 2022 PloS one Introduction SARS_CoV_2 G1223C 67 73 S 151 156 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Nevertheless, D614G mutation alone has not been shown to cause higher COVID-19 mortality or clinical severity, or alter the efficiency of the current laboratory diagnostic, therapeutics, vaccines or public health prevention strategies. 2022 PloS one Introduction SARS_CoV_2 D614G 14 19 COVID-19 70 78 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Of interest, all of the VOCs and VOIs detected in Malaysia harbour D614G mutation in their spike protein. 2022 PloS one Introduction SARS_CoV_2 D614G 67 72 S 91 96 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Since then, the highest lineage contributor during the third wave of pandemic appeared to be B.1.524, with D614G and A701V mutations in the spike protein of the virus. 2022 PloS one Introduction SARS_CoV_2 A701V;D614G 117;107 122;112 S 140 145 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Therefore, in this study, we analyzed the dominant lineages of D614G variants currently circulating in Malaysia using whole genome sequences of the Malaysian SARS-CoV-2 deposited to the Global Initiative on Sharing All Influenza Data (GISAID) database. 2022 PloS one Introduction SARS_CoV_2 D614G 63 68 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Until recently, 90.30% of all COVID-19 infection in Malaysia has been due to the D614G variant, and this mutation is present in all the new emerging variants. 2022 PloS one Introduction SARS_CoV_2 D614G 81 86 COVID-19 30 48 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. We have also investigated the divergence of the D614G variant of the Pahang SARS-CoV-2 isolates and explored its possible origin. 2022 PloS one Introduction SARS_CoV_2 D614G 48 53 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. Some cases of Q493R mutations following bamlanivimab/etesevimab administration were also reported in the literature and are associated with a reduced viral clearance and, in some patients, with fatal outcome. 2022 Viruses Introduction SARS_CoV_2 Q493R 14 19 35215823 Characterization of a Broadly Neutralizing Monoclonal Antibody against SARS-CoV-2 Variants. It has been reported that several mutations in the SARS-CoV-2 RBM, such as N439K, L452R, S477N, T478K, E484K, S494P, N501Y, and A502S, have increased the infectivity and stability of SARS-CoV-2. 2022 Viruses Introduction SARS_CoV_2 A502S;E484K;L452R;N439K;N501Y;S477N;S494P;T478K 128;103;82;75;117;89;110;96 133;108;87;80;122;94;115;101 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Since its initial emergence, SARS-CoV-2 has continued to evolve and adapt to the human population with several putatively beneficial mutations arising in Spike, such as D614G and N501Y, that affect Spike stability and binding to ACE2, and antibody-escape mutations in the amino-terminal domain (NTD). 2022 Viruses Introduction SARS_CoV_2 D614G;N501Y 169;179 174;184 S;S 154;198 159;203 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. Another mutation of note is E484K, which is found in the Beta and Gamma variants of concern and is related to a decrease in the susceptibility to monoclonal antibodies and convalescent plasma. 2022 Viruses Introduction SARS_CoV_2 E484K 28 33 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. The first mutation known to improve viral fitness was Spike D614G, which was first identified in the Alpha variant and then reached a prevalence of nearly 100% globally. 2022 Viruses Introduction SARS_CoV_2 D614G 60 65 S 54 59 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. This mutation was correlated to higher viral replication, as the mutation N501Y, which was also associated with a higher affinity for the receptor ACE2 and was identified in the Alpha, Beta, and Gamma variants. 2022 Viruses Introduction SARS_CoV_2 N501Y 74 79 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. According to this study, mutations S477N, Q498R, and N501Y increase ACE2 affinity by 37-fold, serving to anchor the RBD to ACE2, while allowing the RBD region freedom to develop further mutations, including those that reduce ACE2 affinity in order to evade the neutralizing antibody response. 2022 International journal of molecular sciences Introduction SARS_CoV_2 N501Y;Q498R;S477N 53;42;35 58;47;40 RBD;RBD 116;148 119;151 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. By providing unprecedented atomistic-level details and significant insight into molecular binding mechanisms of the SARS-CoV-2 variants, this study observed that the N501Y and E484Q mutations are particularly important for the greater stability, while the N501Y mutation is unlikely to significantly affect antibody neutralization. 2022 International journal of molecular sciences Introduction SARS_CoV_2 E484Q;N501Y;N501Y 176;166;256 181;171;261 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. Neutralization of SARS-CoV-2 by low-picomolar and mutation-tolerant VHH nanobodies that bind synergistically to the opposite sides of the RBD produced a binding avidity effect unaffected by immune-escape mutants K417N/T, E484K, N501Y, and L452R. 2022 International journal of molecular sciences Introduction SARS_CoV_2 E484K;K417N;K417T;L452R;N501Y 221;212;212;239;228 226;219;219;244;233 RBD 138 141 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. Strikingly, K417N, T478K, G496S, Y505H, and the triple S371L, S373P, S375F can reduce affinity to ACE2 while driving immune evasion and providing a final net affinity for ACE2 similar to the original virus. 2022 International journal of molecular sciences Introduction SARS_CoV_2 G496S;K417N;S371L;S373P;S375F;T478K;Y505H 26;12;55;62;69;19;33 31;17;60;67;74;24;38 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. The crystal and cryo-EM structures of Omicron RBD complexed with human ACE2 identified the role of key residues for receptor recognition showing that mutations E484A, Q493R, and Q493R are responsible for immune escape from monoclonal antibodies. 2022 International journal of molecular sciences Introduction SARS_CoV_2 E484A;Q493R;Q493R 160;167;178 165;172;183 RBD 46 49 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. The detection of common mutational changes such as D614G, E484K, N501Y, and K417N that are shared among major circulating variants B.1.1.7, B.1.351, and B.1.1.28/P.1 indicated that these positions could be particularly critical for modulation of the SARS-CoV-2 S protein responses. 2022 International journal of molecular sciences Introduction SARS_CoV_2 D614G;E484K;K417N;N501Y 51;58;76;65 56;63;81;70 S 261 262 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. The emergence of variants of concern (VOCs) with the enhanced transmissibility and infectivity profile including the D614G variant, B.1.1.7 (alpha), B.1.351 (beta), B.1.1.28/P.1 (gamma), and B.1.1.427/B.1.429 (epsilon) variants have attracted enormous attention in the scientific community and a considerable variety of the proposed mechanisms explaining functional observations from structural and biochemical perspectives. 2022 International journal of molecular sciences Introduction SARS_CoV_2 D614G 117 122 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. These studies identified a group of common resistant mutations in the dynamic RBM region (F490S, E484K, Q493K/R, F490L, F486S, F486L, and Y508H) that evade many individual nanobodies. 2022 International journal of molecular sciences Introduction SARS_CoV_2 E484K;F486L;F486S;F490L;Q493K;Q493R;Y508H;F490S 97;127;120;113;104;104;138;90 102;132;125;118;111;111;143;95 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. Using data analysis and protein structure network modeling of MD simulations, residues that exhibit long-distance coupling with the RBD opening, including sites harboring functional mutations D614G and A570D, which points to the important role of the D614G variant in modulating allosteric communications in the S protein. 2022 International journal of molecular sciences Introduction SARS_CoV_2 A570D;D614G;D614G 202;192;251 207;197;256 RBD;S 132;312 135;313 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. Omicron Spike was recognized less efficiently than D614G, Alpha, Beta, Gamma, and Delta Spikes. 2022 Cell reports Introduction SARS_CoV_2 D614G 51 56 S;S 8;88 13;94 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. Plasma from vaccinated previously infected individuals recognized more efficiently all tested Spikes (D614G, Alpha, Beta, Gamma, Delta, and Omicron) than those from naive vaccinated individuals. 2022 Cell reports Introduction SARS_CoV_2 D614G 102 107 S 94 100 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. The accumulation of E484K and K417N/T mutations along with N501Y in the receptor binding domain (RBD) led to the emergence of Beta (B.1.351) and Gamma (P.1) lineages, which rapidly spread worldwide. 2022 Cell reports Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 20;30;30;59 25;37;37;64 RBD;RBD 72;97 95;100 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. The N501Y Spike mutation increased its affinity for the ACE2 receptor, leading to increased transmissibility. 2022 Cell reports Introduction SARS_CoV_2 N501Y 4 9 S 10 15 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. In addition, it shows multiple mutations including L452R, T478K, and D950N. 2022 Pathology Introduction SARS_CoV_2 D950N;L452R;T478K 69;51;58 74;56;63 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. L452R is known to increase affinity for ACE2 receptors found on the surface of a variety of human cells such as lung cells, while the T478K has been shown to increase receptor binding activity and to enable immune escape. 2022 Pathology Introduction SARS_CoV_2 T478K;L452R 134;0 139;5 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. 4.1.2 P681R. 2022 Frontiers in immunology Introduction SARS_CoV_2 P681R 6 11 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. 4.1.3.1 N439K. 2022 Frontiers in immunology Introduction SARS_CoV_2 N439K 8 13 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. 4.1.3.2 L452R. 2022 Frontiers in immunology Introduction SARS_CoV_2 L452R 8 13 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. 4.1.3.3 Y453F. 2022 Frontiers in immunology Introduction SARS_CoV_2 Y453F 8 13 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. 4.1.3.4 E484K. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K 8 13 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. 4.1.3.5 N501Y. 2022 Frontiers in immunology Introduction SARS_CoV_2 N501Y 8 13 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. 4.1.3.6 K444R. 2022 Frontiers in immunology Introduction SARS_CoV_2 K444R 8 13 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Among these four mutations, the E484K mutation is a very significant mutation among these mutations. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K 32 37 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Another mutation in the S-glycoprotein region is D614G, which is associated with immune escape. 2022 Frontiers in immunology Introduction SARS_CoV_2 D614G 49 54 S 24 38 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Another significant mutation noted in the RBD region is L452R. 2022 Frontiers in immunology Introduction SARS_CoV_2 L452R 56 61 RBD 42 45 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. At the same time, another significant mutation is the E484D mutation among these four mutations. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484D 54 59 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. At the same time, the E484K mutation is accountable for class 2 antibody escape. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K 22 27 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. developed pseudoviruses with different RBD mutations or other parts of S-glycoprotein such as N501Y, K417N/T, and E484K, to illustrate the neutralization event. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 114;101;101;94 119;108;108;99 S;RBD 71;39 85;42 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. evaluated the mutations in the ORF3 region and found the five most frequent mutations, which are Q57H, Q57H + A99V, V13L, G252V, and G196V. 2022 Frontiers in immunology Introduction SARS_CoV_2 A99V;G196V;G252V;Q57H;Q57H;V13L 110;133;122;97;103;116 114;138;127;101;107;120 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Few mutations include K417T/N, E484K, L452R, N501Y, P681R, D614G, etc. 2022 Frontiers in immunology Introduction SARS_CoV_2 D614G;E484K;K417N;K417T;L452R;N501Y;P681R 59;31;22;22;38;45;52 64;36;29;29;43;50;57 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. first reported this novel mutation of D614G, and they concluded that this mutation might be responsible for altered antigenicity and immunogenicity. 2022 Frontiers in immunology Introduction SARS_CoV_2 D614G 38 43 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. found that the Q57H mutation (25563G>T) is located in the variants in the USA in high frequency. 2022 Frontiers in immunology Introduction SARS_CoV_2 Q57H;G25563T 15;30 19;38 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Four mutants were identified at position 484, which are E484K/E484A/E484G/E484D. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484A;E484K;E484A;E484D;E484G 56;56;62;74;68 61;61;67;79;73 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. However, they observed that some mutations (G485R and S494P) might trigger lesser antibodies escape phenomenon. 2022 Frontiers in immunology Introduction SARS_CoV_2 S494P;G485R 54;44 59;49 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. In this direction, we illustrated the mutations in the RBD region (N439K, L452R, E484K, N501Y, K444R) and other regions (D614G, P681R) of the S-glycoprotein. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K;K444R;L452R;N501Y;P681R;D614G;N439K 81;95;74;88;128;121;67 86;100;79;93;133;126;72 S;RBD 142;55 156;58 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. It has been noted that the N501Y mutation displayed a more vital interaction between binding to the receptor, ACE2. 2022 Frontiers in immunology Introduction SARS_CoV_2 N501Y 27 32 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. observed that variants with the mutations E484K, K417N, N501Y, and E484K in the S-glycoprotein might reduce the vaccine's efficiency. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K;E484K;K417N;N501Y 42;67;49;56 47;72;54;61 S 80 94 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. One of the crucial mutations was the D614G mutation in the S-glycoprotein, which was noted in the early phase of the pandemic in 2020. 2022 Frontiers in immunology Introduction SARS_CoV_2 D614G 37 42 S 59 73 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. reported this mutation as D614G variants. 2022 Frontiers in immunology Introduction SARS_CoV_2 D614G 26 31 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Researchers also noted the immune escape phenomenon during Bamlanivimab treatment of COVID-19 patients because of E484K mutation. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K 114 119 COVID-19 85 93 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Several mutations have been observed among VOI, and some common mutations are K417T/N, E484K, L452R, N501Y, P681R and D614G. 2022 Frontiers in immunology Introduction SARS_CoV_2 D614G;E484K;K417N;K417T;L452R;N501Y;P681R 118;87;78;78;94;101;108 123;92;85;85;99;106;113 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Several scientists pointed out that the coding sequence of the mutation (D614G) shows an augmented ratio of dN/dS. 2022 Frontiers in immunology Introduction SARS_CoV_2 D614G 73 78 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Similarly, another mutation was reported in the NSP6 at the nucleotide position, 11083, G>T mutation, which results in the mutation L37F. 2022 Frontiers in immunology Introduction SARS_CoV_2 L37F 132 136 Nsp6 48 52 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Similarly, L452R is accountable for class 3 antibody escape. 2022 Frontiers in immunology Introduction SARS_CoV_2 L452R 11 16 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. The D614G mutation got early attention from the researchers. 2022 Frontiers in immunology Introduction SARS_CoV_2 D614G 4 9 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. The E484K is noted in several lineages such as B.1.526 lineage, P.1 lineage, P.2 and B.1.351 lineages, etc. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K 4 9 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. The E484K mutation might trigger the immune escape phenomena in those immunocompromised patients. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K 4 9 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. The K417N/T mutation is present in two lineages, such as P.1 lineage and B.1.351 lineage. 2022 Frontiers in immunology Introduction SARS_CoV_2 K417N;K417T 4;4 11;11 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. The L452R is observed in the different lineages such as B.1.617 lineage and B.1.427/429 lineage. 2022 Frontiers in immunology Introduction SARS_CoV_2 L452R 4 9 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. The N439K mutation is also noteworthy in S-glycoprotein. 2022 Frontiers in immunology Introduction SARS_CoV_2 N439K 4 9 S 41 55 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. The N501Y mutation is considered significant in the RBD region of the S-glycoprotein. 2022 Frontiers in immunology Introduction SARS_CoV_2 N501Y 4 9 S;RBD 70;52 84;55 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. The researchers noted two immune escape mutations, which are L1637P, and L1637S. 2022 Frontiers in immunology Introduction SARS_CoV_2 L1637P;L1637S 61;73 67;79 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. The Y453F mutation is also significant in the RBD region of S-glycoprotein. 2022 Frontiers in immunology Introduction SARS_CoV_2 Y453F 4 9 S;RBD 60;46 74;49 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. These mutations are K417N/T and E484K. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K;K417N;K417T 32;20;20 37;27;27 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. They also discussed the role of escape mutation, T242N, in replication fitness and R355K mutation for early CTL escape. 2022 Frontiers in immunology Introduction SARS_CoV_2 R355K;T242N 83;49 88;54 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. They also found that the mutation always occurs mutually with mutation 1059C>T-(T85I). 2022 Frontiers in immunology Introduction SARS_CoV_2 C1059T;T85I 71;80 78;84 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. They concluded that D614G substitution might be responsible for higher COVID-19 mortality. 2022 Frontiers in immunology Introduction SARS_CoV_2 D614G 20 25 COVID-19 71 79 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. They found two significant mutations (S477N, E484K) related to the antibody escape phenomenon. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K;S477N 45;38 50;43 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. They have found that K417N/T is accountable for class 1 antibody escape. 2022 Frontiers in immunology Introduction SARS_CoV_2 K417N;K417T 21;21 28;28 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. This study has noted three significant mutations (E484K, K417N/T, L452R) responsible for different categories of antibody escape. 2022 Frontiers in immunology Introduction SARS_CoV_2 K417N;K417T;L452R;E484K 57;57;66;50 64;64;71;55 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Three mutants were identified at 444 positions in the RBD region: K444R, K444Q, and K444N. 2022 Frontiers in immunology Introduction SARS_CoV_2 K444N;K444Q;K444R 84;73;66 89;78;71 RBD 54 57 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Using pseudotyped reporter virus, they constructed the virus with mutations, E484K/K417N/N501Y. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K;K417N;N501Y 77;83;89 82;88;94 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. Furthermore, inclusion of class 2 antibodies in cell culture rVSV-SARS-CoV-2 replication assays rapidly drove the emergence of E484K mutations. 2022 Diagnostic microbiology and infectious disease Introduction SARS_CoV_2 E484K 127 132 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. In parallel, our regional SARS-CoV-2 sequencing program provided the opportunity to detect newly emerging E484K-containing lineages and ascertain the potential epidemiological association, if any, with individuals receiving monoclonal antibody therapy. 2022 Diagnostic microbiology and infectious disease Introduction SARS_CoV_2 E484K 106 111 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. Plasma from vaccinated individuals was 1-3-fold less potent in neutralization assays against E484K-pseudotyped virus which correlated with complete elimination of binding against E484K by individual class 2 antibodies. 2022 Diagnostic microbiology and infectious disease Introduction SARS_CoV_2 E484K;E484K 93;179 98;184 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. The E484K variant in the Spike protein has emerged numerous times in different lineages, including in several emerging variants of concern: B.1.1.7, B.1.351 and P.1. 2022 Diagnostic microbiology and infectious disease Introduction SARS_CoV_2 E484K 4 9 S 25 30 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. Neutralizing antibodies triggered by VOCs show varying patterns of breadth compared with the original D614G and one another, suggesting that spikes with different genotypes differentially affect the repertoire of triggered antibodies. 2022 Cell reports. Medicine Introduction SARS_CoV_2 D614G 102 107 S 141 147 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. We used convalescent sera from individuals infected with D614G to show that Beta partially evades several Fc effector functions. 2022 Cell reports. Medicine Introduction SARS_CoV_2 D614G 57 62 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. 6), where it could impact nAb binding, much like N655Y and D796Y discussed above. 2022 Research square Introduction SARS_CoV_2 D796Y;N655Y 59;49 64;54 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. A crystal structure of the post-fusion six-helix bundle formed by HR1 and HR2 segments in the spike protein trimer is available, enabling visualization of the N1192S mutation site. 2022 Research square Introduction SARS_CoV_2 N1192S 159 165 S 94 99 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. A second mutation, V94A, maps to a region located between putative transmembrane helices 1 and 2 in the nsp4 protein, and there is likewise no relevant experimental structural data for this region of nsp4. 2022 Research square Introduction SARS_CoV_2 V94A 19 23 Nsp4;Nsp4 104;200 108;204 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. A smaller set of RBD mutations (S371L, S373P, S375F, K417N) display little or no surface exposure. 2022 Research square Introduction SARS_CoV_2 K417N;S373P;S375F;S371L 53;39;46;32 58;44;51;37 RBD 17 20 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. A third mutation in ORF1ab, F694Y, occurs in the RNA-dependent RNA polymerase and is most intriguing. 2022 Research square Introduction SARS_CoV_2 F694Y 28 33 RdRp;ORF1ab 49;20 77;26 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. A third set of mutations (T547K, N764K, N856K, Q954H, N969K, L981F) occur in the interior of the receptor trimer assembly at positions that likely will alter monomer-monomer packing interactions. 2022 Research square Introduction SARS_CoV_2 L981F;N764K;N856K;N969K;Q954H;T547K 61;33;40;54;47;26 66;38;45;59;52;31 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. As a result, the R346K mutation might impact receptor and/or nAb recognition and binding. 2022 Research square Introduction SARS_CoV_2 R346K 17 22 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. Figure 4B illustrates the dramatic increase in this mutation since 8 December 2021, suggesting that F694Y may provide a notable fitness advantage for the virus. 2022 Research square Introduction SARS_CoV_2 F694Y 100 105 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. Finally, there are two mutations (N679K, P681H) in the S1/S2 cleavage segment. 2022 Research square Introduction SARS_CoV_2 P681H;N679K 41;34 46;39 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. For example, we observed the emergence of the P681R mutation in the U.S. 2022 Research square Introduction SARS_CoV_2 P681R 46 51 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. However, both A701V and I1081V are conservative mutations and may have little impact. 2022 Research square Introduction SARS_CoV_2 A701V;I1081V 14;24 19;30 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. Interestingly, the first reported haplotype was "RAINVVFGF" on October 17, 2021 in Abuja of Nigeria, Africa, indicating that mutants L106F and D343G were long in existence. 2022 Research square Introduction SARS_CoV_2 D343G;L106F 143;133 148;138 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. Most of these mutations (G339D, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H) present on the RBD surface. 2022 Research square Introduction SARS_CoV_2 E484A;G446S;G496S;N440K;N501Y;Q493R;Q498R;S477N;T478K;Y505H;G339D 60;39;74;32;88;67;81;46;53;95;25 65;44;79;37;93;72;86;51;58;100;30 RBD 117 120 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. Note that we use a polymutant nomenclature without the ending amino acid designated, e.g., D614 as opposed to D614G, because several polymutants exhibit multiple mutations. 2022 Research square Introduction SARS_CoV_2 D614G 110 115 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. One mutation, V1069I, maps to a region in the non-structural protein 3 (nsp3), just prior to the nsp3 nucleic acid binding domain, but there is no relevant structural information for this region of nsp3 to assess possible impacts. 2022 Research square Introduction SARS_CoV_2 V1069I 14 20 Nsp3;Nsp3;Nsp3 72;97;198 76;101;202 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. Similarly, A701V and I1081V are also observed in multiple countries. 2022 Research square Introduction SARS_CoV_2 A701V;I1081V 11;21 16;27 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. Similarly, there are two mutations (A67V, T95I) in the interior of the N-terminal domain. 2022 Research square Introduction SARS_CoV_2 T95I;A67V 42;36 46;40 N 71 72 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. Some, like D614G, are observed in all three variant families and the impact of this mutation has been well documented. 2022 Research square Introduction SARS_CoV_2 D614G 11 16 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. The A701V mutation is located on the exterior of the receptor trimer stalk region. 2022 Research square Introduction SARS_CoV_2 A701V 4 9 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. The final emerging mutation, D343G, is present in the nucleocapsid phosphoprotein C-terminal dimerization domain, located in a short loop connecting b-strand b2 to the a6 helix. 2022 Research square Introduction SARS_CoV_2 D343G 29 34 N 54 66 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. The fourth emerging spike protein mutation, N1192S, is less prevalent thus far but is extremely interesting and of potential concern. 2022 Research square Introduction SARS_CoV_2 N1192S 44 50 S 20 25 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. The fourth polymutant N1192S emerged only very recently and has been reported from Hong Kong (2 sequences), Israel (1) and United Kingdom (1). 2022 Research square Introduction SARS_CoV_2 N1192S 22 28 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. The I1081V mutation is in the interior of the receptor trimer assembly and might influence conformation via altered side chain packing interactions. 2022 Research square Introduction SARS_CoV_2 I1081V 4 10 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. The L106F mutation occurs in ORF3a, in a region that codes for a putative ion channel 3a. 2022 Research square Introduction SARS_CoV_2 L106F 4 9 ORF3a 29 34 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. The Omicron variants thus far display the P681H mutation observed in earlier Alpha variants, unlike the P681R mutation observed in Delta, which has been documented experimentally to contribute to increased infectivity. 2022 Research square Introduction SARS_CoV_2 P681H;P681R 42;104 47;109 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. The polymutant R346K is observed among 347 of 4296 viruses and started increasing around day 25, leveling around day 40. 2022 Research square Introduction SARS_CoV_2 R346K 15 20 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. The R346K mutation is in the RBD. 2022 Research square Introduction SARS_CoV_2 R346K 4 9 RBD 29 32 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. Two additional mutations (N655Y, D796Y) are present on the surface of the receptor trimer stalk region. 2022 Research square Introduction SARS_CoV_2 D796Y;N655Y 33;26 38;31 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. As such, it has been challenging to determine with certainty whether infection with the Delta VOC is more virulent in children than non-VOC SARS-CoV-2 or other VOCs, such as those with the N501Y mutation. 2022 Clinical infectious diseases Introduction SARS_CoV_2 N501Y 189 194 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. In the Canadian province of Ontario, the VOC carrying the N501Y mutation (including the Alpha/B.1.1.7, Beta/B.1.351, and Gamma/P.1 VOC) replaced earlier SARS-CoV-2 lineages by April 2021 but were, in turn, replaced by the Delta (B.1.617.2) variant, which has been the dominant variant in the province since July 2021. 2022 Clinical infectious diseases Introduction SARS_CoV_2 N501Y 58 63 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. Our objectives were to estimate age-specific risks of severe illness in individuals infected with the Delta or N501Y-positive VOC relative to non-VOC SARS-CoV-2 infection, determine whether there is heterogeneity in differential risk by age group, and explore the possible sources of any such heterogeneity. 2022 Clinical infectious diseases Introduction SARS_CoV_2 N501Y 111 116 COVID-19 150 170 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. 2a), similar to previous findings for BA.1 and BA.1+R346K (ref. 2022 Nature Introduction SARS_CoV_2 R346K 52 57 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. a marked and significant loss of neutralizing activity of the serum against BA.1+R346K and BA.2 relative to D614G was noted, with neutralizing titres for numerous samples dropping below the limit of detection. 2022 Nature Introduction SARS_CoV_2 D614G;R346K 108;81 113;86 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. Among these samples, the mean serum neutralizing titres against Omicron sublineages were significantly lower than the mean titre for D614G; although the mean titre was slightly lower for BA.2, the difference from that of the BA.1 sublineages did not reach statistical significance (P = 0.242). 2022 Nature Introduction SARS_CoV_2 D614G 133 138 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. As above, neutralizing titres dropped significantly against authentic BA.2 virus relative to D614G. 2022 Nature Introduction SARS_CoV_2 D614G 93 98 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. CB6 was adversely affected by the D405N alteration, probably owing to its position in the epitope of this antibody. 2022 Nature Introduction SARS_CoV_2 D405N 34 39 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. In fact, the BA.1+R346K sublineage now accounts for about 40% of Omicron sequences globally, and about 35-60% in New Zealand, the UK and the USA. 2022 Nature Introduction SARS_CoV_2 R346K 18 23 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. It is not clear how T19I and L24S alterations in the NTD subtly impaired the neutralizing activity of class 1 antibodies to the RBD. 2022 Nature Introduction SARS_CoV_2 L24S;T19I 29;20 33;24 RBD 128 131 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. Notably, S371F seems to be responsible for the loss in potency of S309, although this alteration was not observed previously as a marker for clinical resistance to sotrovimab. 2022 Nature Introduction SARS_CoV_2 S371F 9 14 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. Of course, BA.1+R346K has one alteration more than BA.1. 2022 Nature Introduction SARS_CoV_2 R346K 16 21 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. S371F broadly affected most of the RBD-directed antibodies, similar to what was observed for S371L in BA.1 (ref. 2022 Nature Introduction SARS_CoV_2 S371L;S371F 93;0 98;5 RBD 35 38 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. The loss of neutralizing activity against BA.1+R346K or BA.2 sublineages was less prominent for sera obtained from individuals who received a booster vaccination. 2022 Nature Introduction SARS_CoV_2 R346K 47 52 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. The wild-type D614G pseudovirus was included as a comparator. 2022 Nature Introduction SARS_CoV_2 D614G 14 19 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. A prominent amino acid change in the S protein of the B.1.617.2 variant is L452R that is also found in various other lineages. 2022 Nature communications Introduction SARS_CoV_2 L452R 75 80 S 37 38 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. A.27 is characterized by a mutational profile including L18F, L452R and N501Y in the S protein that combines genetic changes found in various VOCs/VOIs, while lacking the D614G substitution present in most other lineages. 2022 Nature communications Introduction SARS_CoV_2 D614G;L18F;L452R;N501Y 171;56;62;72 176;60;67;77 S 85 86 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. Early in the pandemic, SARS-CoV-2 acquired the S D614G substitution that has been associated with increased transmissibility and set the genetic foundation for the large number of B.1 derived lineages. 2022 Nature communications Introduction SARS_CoV_2 D614G 49 54 S 47 48 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. Moreover, a B.1.1.7 sub-lineage with an additional E484K substitution in the RBD has been detected in multiple countries. 2022 Nature communications Introduction SARS_CoV_2 E484K 51 56 RBD 77 80 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. The E484K amino acid change is also found in other VOCs/VOIs and has been shown to reduce antibody neutralization. 2022 Nature communications Introduction SARS_CoV_2 E484K 4 9 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. These variants are characterized by specific patterns of concerning S mutations: apart from the D614G substitution, lineage B.1.1.7 has the N501Y amino acid substitution associated with increased affinity to ACE2 and two deletions in the NTD, among other changes. 2022 Nature communications Introduction SARS_CoV_2 D614G;N501Y 96;140 101;145 S 68 69 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. The viruses responsible for the outbreak in Italy, in early 2020, with an amino acid change in the spike protein D614G were classified into lineage B.1 . 2021 Wellcome open research Introduction SARS_CoV_2 D614G 113 118 S 99 104 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. Viruses of the lineage B.1 have acquired several other amino acid replacements in the Receptor Binding Domain of the Spike protein - specifically in the lineages which have been designated as VOCs, namely -B.1.1.7 (N501Y), B.1.351 (N501Y, E484K, K417T) and P.1 from the lineage B.1.1.28 (N501Y, E484K, K417T). 2021 Wellcome open research Introduction SARS_CoV_2 E484K;E484K;K417T;K417T;N501Y;N501Y;N501Y 239;295;246;302;215;232;288 244;300;251;307;220;237;293 RBD;S 86;117 109;122 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. The D614G substitution has been shown to decrease shedding of S1 from spike on virions, consistent with increased stability of the pre-fusion conformation. 2022 Nature communications Introduction SARS_CoV_2 D614G 4 9 S 70 75 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. The virus has evolved in the human host during the pandemic and we and others have demonstrated that the predominant D614G substitution, located in a monomer-monomer interface of the spike trimer, increases its propensity to adopt the open conformation that is competent to bind receptor. 2022 Nature communications Introduction SARS_CoV_2 D614G 117 122 S 183 188 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. This enabled us to directly compare the pre-fusion spikes of the new variants with those of the original strain (first identified in Wuhan) and the D614G-only variant we described in previous studies, findings that agree with reports that used non-stabilised spikes. 2022 Nature communications Introduction SARS_CoV_2 D614G 148 153 S;S 51;259 57;265 35257681 Simultaneous detection of SARS-CoV-2 and identification of spike D614G mutation using point-of-care real-time polymerase chain reaction. For the simultaneous detection of SARS-CoV-2 and its variant (D614G mutant), FAM and ROX fluorophores were attached to each probe during probe sequence design to enable target discrimination. 2022 Journal of virological methods Introduction SARS_CoV_2 D614G 62 67 35257681 Simultaneous detection of SARS-CoV-2 and identification of spike D614G mutation using point-of-care real-time polymerase chain reaction. In the experiment, the specificity and sensitivity of RdRp and N target primer pairs and probe sets were confirmed in the L clade, chosen to represent viruses containing the target gene without the D614G mutation. 2022 Journal of virological methods Introduction SARS_CoV_2 D614G 198 203 RdRP;N 54;63 58;64 35257681 Simultaneous detection of SARS-CoV-2 and identification of spike D614G mutation using point-of-care real-time polymerase chain reaction. In this milieu, we developed a rRT-PCR detection method that simultaneously detects common SARS-CoV-2 and the SARS-CoV-2 D614 strain (a mutant with the replacement of aspartic acid with glycine at position 614 of the spike glycoprotein (S protein)), which has become a major circulating strain worldwide in a short period. 2022 Journal of virological methods Introduction SARS_CoV_2 D614G 167 209 S;S 217;237 235;238 35257681 Simultaneous detection of SARS-CoV-2 and identification of spike D614G mutation using point-of-care real-time polymerase chain reaction. In this study, we demonstrated simultaneous detection of SARS-CoV-2 and identification of the highly infectious D614G mutation using specific primer pairs and probe sets in a newly designed portable chip-based real-time PCR device. 2022 Journal of virological methods Introduction SARS_CoV_2 D614G 112 117 35257681 Simultaneous detection of SARS-CoV-2 and identification of spike D614G mutation using point-of-care real-time polymerase chain reaction. indicating that samples contained the D614G mutation. 2022 Journal of virological methods Introduction SARS_CoV_2 D614G 38 43 35257681 Simultaneous detection of SARS-CoV-2 and identification of spike D614G mutation using point-of-care real-time polymerase chain reaction. The specificity and sensitivity of S target primer pairs and probe set were confirmed in the G clade, representing viruses containing the target gene with the D614G mutation. 2022 Journal of virological methods Introduction SARS_CoV_2 D614G 159 164 S 35 36 35257681 Simultaneous detection of SARS-CoV-2 and identification of spike D614G mutation using point-of-care real-time polymerase chain reaction. We also designed a primer pair and probe set to amplify the spike (S) gene containing G23403 to detect the D614G mutation. 2022 Journal of virological methods Introduction SARS_CoV_2 D614G 107 112 S;S 60;67 65;68 35257681 Simultaneous detection of SARS-CoV-2 and identification of spike D614G mutation using point-of-care real-time polymerase chain reaction. With the new method described herein, it would be possible to identify the exact time when mutations such as D614G occur, allowing the detection methods to be rapidly adjusted to the specific mutation, which is crucial for epidemiological surveillance. 2022 Journal of virological methods Introduction SARS_CoV_2 D614G 109 114 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. Some mutations including T478K, N501Y, N655Y, N679K, and P681H overlap with those in other VOCs or VOIs such as Delta, Gamma, Alpha, and Beta. 2022 GeroScience Introduction SARS_CoV_2 N501Y;N655Y;N679K;P681H;T478K 32;39;46;57;25 37;44;51;62;30 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. V445E and K444 Q/R/N in the RBD and K150 T/Q/R/E, and N148S in NTD may be responsible for antibody escape. 2022 GeroScience Introduction SARS_CoV_2 K150E;K150Q;K150R;K150T;K444Q;K444R;N148S;V445E 36;36;36;36;10;10;54;0 48;48;48;48;20;20;59;5 RBD 28 31 35262011 Use of amplicon melt temperature to detect SARS-CoV-2 Lineage B.1.1.7 variant through the G28048T mutation in the ORF 8 gene. One of the other SNPs is in the ORF8 gene (G28048T) and this appears to be confined to this lineage. 2021 Journal of clinical virology plus Introduction SARS_CoV_2 G28048T 43 50 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. Altered closed versus open state occupancy also explains the expected S371L/F fitness cost, as a tradeoff between closed-state occupancy and infectivity was recently established via smFRET characterization of the altered conformational dynamics due to the D614G and Alpha variant mutations by Yang et al. 2022 bioRxiv Introduction SARS_CoV_2 D614G;S371F;S371L 256;70;70 261;77;77 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. Further, BA.1/BA.2 mutations S37P, S375F, T376A, and Y505H in the RBDdown-RBDdown interface may modulate the Omicron spike-closed RBD packing and opening dynamics to compensate for S371L/F. 2022 bioRxiv Introduction SARS_CoV_2 S371F;S371L;S375F;S37P;T376A;Y505H 181;181;35;29;42;53 188;188;40;33;47;58 S;RBD 117;130 122;133 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. Future work to characterize the BA.1/BA.2 mutations that compensate for the S371L/F fitness cost would be particularly valuable toward understanding the Omicron evolutionary landscape, surveilling these compensatory sites for future mutation on Omicron or novel variants, and designing therapeutic antibodies targeting the compensatory sites which may be functionally-constrained to mutate. 2022 bioRxiv Introduction SARS_CoV_2 S371F;S371L 76;76 83;83 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. In summary, we offer a plausible biological explanation for the profound escape conferred by S371L/F as measured by Liu et al and Iketani et al., and believe that further experimental and structural investigation is warranted. 2022 bioRxiv Introduction SARS_CoV_2 S371F;S371L 93;93 100;100 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. in the context of the spike trimer to toward elucidating additional mechanistic details of S371L/F escape. 2022 bioRxiv Introduction SARS_CoV_2 S371F;S371L 91;91 98;98 S 22 27 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. Investigation of class 1 to 4 antibody epitopes in the context of the open and closed states of trimeric spike suggests the S371L/F escape mechanism involves altered RBD conformational dynamics. 2022 bioRxiv Introduction SARS_CoV_2 S371F;S371L 124;124 131;131 S;RBD 105;166 110;169 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. observed a profoundly broad escape effect for S371L and S371F. 2022 bioRxiv Introduction SARS_CoV_2 S371F;S371L 56;46 61;51 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. provide a detailed analysis of loss of potency by evaluating vaccine/convalescent sera and therapeutic antibodies against pseudotyped viruses with D614G spike proteins harboring single point mutations from the variants of concern (VOCs). 2022 bioRxiv Introduction SARS_CoV_2 D614G 147 152 S 153 158 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. S371L/F may confer a predominantly "locked" spike closed state and reduced occupancy of the spike open state. 2022 bioRxiv Introduction SARS_CoV_2 S371F;S371L 0;0 7;7 S;S 44;92 49;97 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. S371L/F mediated escape is unlikely to be explained by long-range conformational changes within the protein structure of monomeric RBD. 2022 bioRxiv Introduction SARS_CoV_2 S371F;S371L 0;0 7;7 RBD 131 134 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. Significantly, both the S371L/F escape effect and fitness cost appear to be reduced in combination with other BA.1/BA.2 mutations. 2022 bioRxiv Introduction SARS_CoV_2 S371F;S371L 24;24 31;31 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. That is, in the closed spike state class 1 and class 4 antibody epitopes are not accessible while class 2 and 3 antibody epitopes are largely accessible (Figure 1A), and the relative closed-state accessibility for each antibody predicted whether a given antibody was weakly/moderately (class 2 and 3) or strongly (class 1 and 4) escaped by S371L/F (Figure 1B). 2022 bioRxiv Introduction SARS_CoV_2 S371F;S371L 340;340 347;347 S 23 28 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. That is, the S371L/F escape effect exceeds the BA.1/BA.2 escape effect for a number of antibodies, and it is apparent from Omicron's global dominance that S371L/F in combination with other mutations such as G339D, S37P, S375F, and T376A results in a fit lineage. 2022 bioRxiv Introduction SARS_CoV_2 G339D;S371F;S371F;S371L;S371L;S375F;S37P;T376A 207;13;155;13;155;220;214;231 212;20;162;20;162;225;218;236 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. The escape of S371L/F mutation across antibodies targeting all four epitope classes was observed only when assayed in the context of the spike trimer by Liu et al. 2022 bioRxiv Introduction SARS_CoV_2 S371F;S371L 14;14 21;21 S 137 142 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. To further characterize the epitope accessibility-escape trend for S371L/F and to additionally benchmark the observed trend against other BA.1 and BA.2 escape mutations, we computed the ratio of antibody epitope accessibility in the spike-closed conformation as compared to the spike-open conformation and plotted this metric against the antibody escape across BA.1 and BA.2 mutations (Figure 2). 2022 bioRxiv Introduction SARS_CoV_2 S371F;S371L 67;67 74;74 S;S 233;278 238;283 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. to open versus closed spike protein structures and found that S371L/F-mediated escape was strongly associated with epitope accessibility in the spike closed (3 RBDdown) vs spike open (1-3 RBDup) conformational states (Figure 1). 2022 bioRxiv Introduction SARS_CoV_2 S371F;S371L 62;62 69;69 S;S;S 22;144;172 27;149;177 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. Two BA.2 mutations of particular interest as potential compensatory sites are D405N and R408S, as Sztain et al. 2022 bioRxiv Introduction SARS_CoV_2 D405N;R408S 78;88 83;93 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. Unlike the allosteric disruption of RBD structure observed in the case of the E406W mutation that also lead to broad antibody escape, the S371 mutations did not impact ACE-2 binding and only slightly reduced monomeric RBD expression when assayed via yeast display. 2022 bioRxiv Introduction SARS_CoV_2 E406W 78 83 RBD;RBD 36;218 39;221 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. We found that for S371L and S371F:but not for other BA.1 or BA.1/2 escape mutations such as K417N or E484A nor for the full suite of BA.1/2 mutations:epitope inaccessibility in the RBDdown conformation was associated with greater antibody escape. 2022 bioRxiv Introduction SARS_CoV_2 E484A;K417N;S371F;S371L 101;92;28;18 106;97;33;23 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. While S371L/F mutations occur in class 4 antibody epitopes, Liu et al. 2022 bioRxiv Introduction SARS_CoV_2 S371L;S371F 6;6 13;13 35262083 A structural dynamic explanation for observed escape of SARS-CoV-2 BA.2 variant mutation S371L/F. While the degree of class 2/3 accessibility in the closed state was correlated with escape for S371L, the association was weaker for S371F suggesting that additional features contributing to escape are at play, particularly across class 3 antibodies. 2022 bioRxiv Introduction SARS_CoV_2 S371F;S371L 133;95 138;100 35262087 Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites. Additionally, L452R increases both structural stability and viral fusogenicity, and decreases cell-mediated immune response. 2022 medRxiv Introduction SARS_CoV_2 L452R 14 19 35262087 Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites. Conveniently, the currently circulating Omicron variant (B.1.1.529) harbors both L452R and SDelta69-70, so we used these assays to quickly identify its emergence at Clemson University and the surrounding Upstate South Carolina in December 2021. 2022 medRxiv Introduction SARS_CoV_2 L452R 81 86 35262087 Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites. K417T and K417N SNPs and many substitutions at E484 also reduce viral susceptibility to neutralizing antibodies. 2022 medRxiv Introduction SARS_CoV_2 K417N;K417T 10;0 15;5 35262087 Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites. We also evaluated the efficacy of TaqPath assays for K417T, E484K, E484Q, and L452R in saliva. 2022 medRxiv Introduction SARS_CoV_2 E484K;E484Q;K417T;L452R 60;67;53;78 65;72;58;83 35262087 Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites. We chose to evaluate assays for biochemically significant mutations that also provide differential strain typing for SARS-CoV-2 VOCs, namely SDelta69-70, ORF1aDelta3675-3677, K417T, E484K, E484Q, and L452R. 2022 medRxiv Introduction SARS_CoV_2 E484K;E484Q;K417T;L452R 182;189;175;200 187;194;180;205 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. We also analyzed the neutralization capacity of vaccinees' sera on two ancestral strains (Wuhan-like and D614G), three VOCs (Alpha, Beta, and Delta), and one VBM (Eta). 2022 Microbiology spectrum Introduction SARS_CoV_2 D614G 105 110 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. All three variants have the N501Y mutation, and its presence has been associated with increased transmissibility (Leung et al.; Zhao et al.). 2022 3 Biotech Introduction SARS_CoV_2 N501Y 28 33 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. Another variant, B.1.351 (Mwenda et al.) and P.1 variant (Francisco et al.) carries 9 and 11 spike protein mutations, respectively, including 3 mutations in the receptor-binding domain (RBD), K417N/T, E484K, and N501Y. 2022 3 Biotech Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 201;192;192;212 206;199;199;217 S;RBD 93;186 98;189 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. Besides these mutations, B.1.617 carries 11 additional mutations, including P681R outside of the RBD, which is located adjacent to the furin cleavage site of the spike, suggesting it might influence the way the spike is processed during infection (Cherian et al.). 2022 3 Biotech Introduction SARS_CoV_2 P681R 76 81 S;S;RBD 162;211;97 167;216;100 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. Further, molecular dynamics (MD) simulations were conducted to understand the potential consequence of the mutations L452R, E484Q and L452R-E484Q. 2022 3 Biotech Introduction SARS_CoV_2 E484Q;L452R;L452R;E484Q 124;117;134;140 129;122;139;145 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. The literature strongly supported that the L452R mutation has been reported in B.1.429 variant (Zhang et al.). 2022 3 Biotech Introduction SARS_CoV_2 L452R 43 48 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. Very recently, a "double mutant" L452R-E484Q variant of SARS-CoV-2, B.1.617, has been reported (Cherian et al.), which caused a transmission outburst with a vast number of deaths and active cases. 2022 3 Biotech Introduction SARS_CoV_2 L452R;E484Q 33;39 38;44 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. We have studied the impact of mutations such as L452R, E484Q and L452R-E484Q, which are associated with the host cell attachment and the virus entry into the host cell. 2022 3 Biotech Introduction SARS_CoV_2 E484Q;L452R;L452R;E484Q 55;48;65;71 60;53;70;76 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. While the E484Q mutation is found in B.1.1.7, B.1.351, P.1, and B.1.526 variants (Tang et al.; Bhattarai et al.; Antony and Vijayan). 2022 3 Biotech Introduction SARS_CoV_2 E484Q 10 15 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. Also, the E484Q mutation is similar to the E484K mutation found in the B.1.351 variant, which exhibited reduced neutralization by convalescent-phase sera or monoclonal antibodies. 2022 mBio Introduction SARS_CoV_2 E484K;E484Q 43;10 48;15 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. B.1.617.1 (Kappa), which carries E154K in the N-terminal domain (NTD) of spike, L452R and E484Q mutations in the RBD of spike, and P681R in proximity to the furin cleavage site, has been designated a variant of interest (VOI) by the World Health Organization (WHO) (https://www.who.int). 2022 mBio Introduction SARS_CoV_2 E154K;E484Q;L452R;P681R 33;90;80;131 38;95;85;136 S;S;RBD;N 73;120;113;46 78;125;116;47 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. B.1.617.2 (Delta), which carries L452R and T478K mutations in the RBD of spike, as well as P681R, has been designated a VOC (https://www.who.int). 2022 mBio Introduction SARS_CoV_2 L452R;P681R;T478K 33;91;43 38;96;48 S;RBD 73;66 78;69 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. B.1.618 harbors Delta145-146 (deletion of the 145th and 146th residues) and an E484K mutation in the NTD and RBD, respectively. 2022 mBio Introduction SARS_CoV_2 E484K 79 84 RBD 109 112 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. For example, the D614G mutation, identified during the earlier stage of the pandemic, promotes spike binding to ACE2, leading to enhanced virus transmission. 2022 mBio Introduction SARS_CoV_2 D614G 17 22 S 95 100 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. For example, the L452R mutation has been spotted in the B.1.427 and B.1.429 variants, which have enhanced transmissibility and reduced sensitivity to vaccine-elicited antibodies. 2022 mBio Introduction SARS_CoV_2 L452R 17 22 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. For the Kappa and Delta variants, this is the first time that L452R and E484Q (Kappa)/T478K (Delta) mutations have been found to coexist and the first time that P681R has been observed; for B.1.618, this is the first time the combination of Delta145-146 in the NTD domain and E484K has been observed. 2022 mBio Introduction SARS_CoV_2 E484K;E484Q;L452R;P681R;T478K 276;72;62;161;86 281;77;67;166;91 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. In addition, K417N and E484K, found in the B.1.351 variant, contribute to evasion of neutralization by multiple monoclonal antibodies. 2022 mBio Introduction SARS_CoV_2 E484K;K417N 23;13 28;18 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. In addition, spike with the N501Y mutation has gained the ability to utilize mouse ACE2 as the receptor to infect the mouse, expanding its host range. 2022 mBio Introduction SARS_CoV_2 N501Y 28 33 S 13 18 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. Subsequently, the N501Y mutation found in the B.1.1.7, B.1.351, and B.1.1.28.1 spike proteins has increased the binding affinity between the receptor-binding domain (RBD) and ACE2, increasing viral fitness and infectivity. 2022 mBio Introduction SARS_CoV_2 N501Y 18 23 S;RBD 79;166 84;169 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. T478K has been seen in Mexican variant B.1.1.519. 2022 mBio Introduction SARS_CoV_2 T478K 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. Currently, the WHO has identified the Gamma lineage (B.1.1.28.1, P.1 or Gamma; Nextstrain clade 20J/V3) with the following key S mutations: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F. 2022 Genetics and molecular biology Introduction SARS_CoV_2 D138Y;D614G;E484K;H655Y;K417T;L18F;N501Y;P26S;R190S;T1027I;T20N;V1176F 158;193;179;200;172;140;186;152;165;207;146;219 163;198;184;205;177;144;191;156;170;213;150;225 S 127 128 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. Key S mutations: L452R, D614G, P681R, +- (E484Q, Q107H, T19R, del157/158, T478K, D950N). 2022 Genetics and molecular biology Introduction SARS_CoV_2 D614G;D950N;L452R;P681R;Q107H;T19R;T478K;E484Q 24;81;17;31;49;56;74;42 29;86;22;36;54;60;79;47 S 4 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. Nine key mutations involving the S glycoprotein have been identified: 69/70del, 144del, N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H. 2022 Genetics and molecular biology Introduction SARS_CoV_2 144del;A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 80;95;134;102;88;109;123;116 86;100;140;107;93;114;128;121 S 33 47 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. Regarding SARS-CoV-2, the coronavirus RaTG13 of the brown bat (Rhinolophs affinis) is a potential ancestor.Their genomes have 97.41% identity ; however, at least five amino acid (aa) substitutions (F486L, Q493Y, S494R, N501D, and Y505H) at critical sites of the Spike (S) glycoprotein receptor-binding domain (RBD) of RaTG13 are crucial for the Wuhan-SARS-CoV-2 lineage to acquire high tropism with its cognate human cell receptor (cell-surface peptidase angiotensin-converting enzyme 2, ACE2). 2022 Genetics and molecular biology Introduction SARS_CoV_2 N501D;Q493Y;S494R;Y505H;F486L 219;205;212;230;198 224;210;217;235;203 S;RBD;S 262;310;269 267;313;270 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. The first strain of SARS-CoV-2 identified in Wuhan, China, in December 2019, was also characterized as having five critical amino acid differences in its RBD when compared with SARS-CoV (L455Y, F486L, Q493N, S494D, N501T; SARS-CoV-2 and SARS-CoV aa respectively; Wan et al., 2020). 2022 Genetics and molecular biology Introduction SARS_CoV_2 F486L;N501T;Q493N;S494D;L455Y 194;215;201;208;187 199;220;206;213;192 RBD 154 157 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. The WHO and other reports identified several key SARS-CoV-2 S mutations in Beta (B.1.351): D80A, D215G, 241/243del, K417N, E484K, N501Y, D614G, A701V. 2022 Genetics and molecular biology Introduction SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;N501Y 144;97;137;91;123;116;130 149;102;142;95;128;121;135 S 60 61 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. A deletion at positions 69 and 70 linked with the B.1.1.7 mutation is thought to contribute to the transmissibility of SARS CoV-2. 2022 Journal of virological methods Introduction SARS_CoV_2 del 69 2 26 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. B.1.617 variant with three sublines, including B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.617.3 which are recognized according to three amino acid mutations, L452R, T478K, and E484Q. 2022 Journal of virological methods Introduction SARS_CoV_2 E484Q;L452R;T478K 179;161;168 184;166;173 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. D614G as a common mutation identified in most variants of SARS CoV-2 is occurred in the nucleotide sequence number 23403, leading to the change of amino acid codon from aspartate to glycine codon. 2022 Journal of virological methods Introduction SARS_CoV_2 D614G 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. Delta as a variant of concern (VOC) possesses L452R and T478K mutation, while the two other subtypes of B.1.617 cited with L452R and E484Q mutation. 2022 Journal of virological methods Introduction SARS_CoV_2 E484Q;L452R;L452R;T478K 133;46;123;56 138;51;128;61 35273217 A SARS-CoV-2 Wuhan spike virosome vaccine induces superior neutralization breadth compared to one using the Beta spike. However, neutralization of the Wuhan strain was reduced when a variant vaccine was used that contained the K417N, E484K, N501Y and D614G mutations, which agrees well with our results. 2022 Scientific reports Introduction SARS_CoV_2 D614G;E484K;K417N;N501Y 131;114;107;121 136;119;112;126 35273217 A SARS-CoV-2 Wuhan spike virosome vaccine induces superior neutralization breadth compared to one using the Beta spike. To assess whether the lower heterologous neutralization activity in Beta virosome-vaccinated mice indicates a generalized lower breadth of the neutralizing response, we next determined the neutralizing activity against other variants: D614G, Alpha, Gamma, and Delta. 2022 Scientific reports Introduction SARS_CoV_2 D614G 235 240 35273217 A SARS-CoV-2 Wuhan spike virosome vaccine induces superior neutralization breadth compared to one using the Beta spike. Two weeks after the second vaccination, the neutralizing activity of Beta virosome-vaccinated mice was also significantly lower for D614G, Alpha and Delta (4.0-fold p = 0.0001, 3.6-fold p = 0.02 and 3.2-fold p = 0.007, respectively. 2022 Scientific reports Introduction SARS_CoV_2 D614G 132 137 35273335 The SARS-CoV-2 Alpha variant exhibits comparable fitness to the D614G strain in a Syrian hamster model. Experimental data from human lung epithelium and animal models revealed that the D614G substitution increased virus infectivity and transmissibility as compared to an original D614 strain. 2022 Communications biology Introduction SARS_CoV_2 D614G 81 86 35273335 The SARS-CoV-2 Alpha variant exhibits comparable fitness to the D614G strain in a Syrian hamster model. From January 2020, viruses carrying the spike D614G mutation emerged in several countries. 2022 Communications biology Introduction SARS_CoV_2 D614G 46 51 S 40 45 35273335 The SARS-CoV-2 Alpha variant exhibits comparable fitness to the D614G strain in a Syrian hamster model. In June, D614G SARS-CoV-2 lineage B.1 became the dominant form of circulating virus worldwide and replaced the initial SARS-CoV-2 strains related to the outbreak in Wuhan, China. 2022 Communications biology Introduction SARS_CoV_2 D614G 9 14 35273335 The SARS-CoV-2 Alpha variant exhibits comparable fitness to the D614G strain in a Syrian hamster model. In late 2020, three SARS-CoV-2 variants sharing the N501Y spike mutation located in the receptor-binding motif (RBM) emerged almost simultaneously in the United Kingdom (Alpha variant from lineage B.1.1.7; initially named VOC 202012/01), in South Africa (Beta variant from lineage B.1.351) and in Brazil (P.1 variant from lineage B.1.1.28.1). 2022 Communications biology Introduction SARS_CoV_2 N501Y 52 57 S 58 63 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. According to US FDA reports, the mAb cocktail retained neutralization activity against B.1.1.7 (carrying N501Y) and B.1.617.2/AY.3 (carrying L452R + T478K). 2022 Frontiers in medicine Introduction SARS_CoV_2 L452R;N501Y;T478K 141;105;149 146;110;154 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Additionally, P681R mutation at the S1-S2 cleavage site is thought to increase viral replication, leading to higher viral loads and increased transmission. 2022 Frontiers in medicine Introduction SARS_CoV_2 P681R 14 19 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Among the mutations reported, D769H has been described to reduce susceptibility to neutralizing antibodies. 2022 Frontiers in medicine Introduction SARS_CoV_2 D769H 30 35 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. And cilgavimab had lower activity against N501Y+D614G mutants, including B.1.429 (carrying L452R), B.1.617.2 (carrying L452R + T478K) and B.1.351 (carrying K417N + E484K + N501Y). 2022 Frontiers in medicine Introduction SARS_CoV_2 E484K;K417N;L452R;L452R;N501Y;N501Y;T478K;D614G 164;156;91;119;42;172;127;48 169;161;96;124;47;177;132;53 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Both P4715L and P323L was observed along with S protein D614G mutation, suggesting a co-evolutionary pattern. 2022 Frontiers in medicine Introduction SARS_CoV_2 D614G;P323L;P4715L 56;16;5 61;21;11 S 46 47 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. D614G in the RBM domain has shown to increase the S-protein density on the viral surface, thereby enhancing infectivity. 2022 Frontiers in medicine Introduction SARS_CoV_2 D614G 0 5 S 50 51 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. D950N present on the HR1 domain in Delta lineages have been mapped to the spike trimer interface, suggesting an alteration in spike dynamics for the highly virulent delta strain. 2022 Frontiers in medicine Introduction SARS_CoV_2 D950N 0 5 S;S 74;126 79;131 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. E484 substitutions have been identified in a number of VOCs, including B.1.351 (E484K), P.1 (E484K), B.1.617.2 (E484K/E484Q) and B.1.1.529 (E484A) (https://covariants.org/variants/S.E484). 2022 Frontiers in medicine Introduction SARS_CoV_2 E484A;E484K;E484K;E484K;E484Q 140;80;93;112;118 145;85;98;117;123 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Examples include the N501Y, S477N, N439K, D364Y and E484K substitutions identified in most VOCs, which correlate with higher transmissibility. 2022 Frontiers in medicine Introduction SARS_CoV_2 D364Y;E484K;N439K;N501Y;S477N 42;52;35;21;28 47;57;40;26;33 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Fitness-enhancing mutations have been reported in nsp3, namely F206F, S1197R and T1198K, that has been associated with increased severity of infection for B.1.1 lineages. 2022 Frontiers in medicine Introduction SARS_CoV_2 F206F;S1197R;T1198K 63;70;81 68;76;87 Nsp3 50 54 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. For instance, it was found that the European variant 20A.EU1 carrying N-mutation A220V and the S-mutation A222V had become dominant in summer 2020, probably an outcome of synergistic effect. 2022 Frontiers in medicine Introduction SARS_CoV_2 A220V;A222V 81;106 86;111 N;S 70;95 71;96 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. For the P.1 variant carrying K417T + E484K + N501Y, neutralization assays using pseudotyped virus-like particles showed a reduction in neutralization (FDA). 2022 Frontiers in medicine Introduction SARS_CoV_2 E484K;K417T;N501Y 37;29;45 42;34;50 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. further speculate T190I and A191V in 3CLpro can alter polarity and affect the binding of therapeutic molecules. 2022 Frontiers in medicine Introduction SARS_CoV_2 A191V;T190I 28;18 33;23 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Further, certain mutations in 3CLpro: T45I, K90R, R279C, A266V, A234Vand N151D have been found in the VOCs B.1.1.7, B.1.351, P.1 and B1.617. 2022 Frontiers in medicine Introduction SARS_CoV_2 A234A;A234N;A234V;A266V;K90R;N151D;R279C;T45I 64;64;64;57;44;73;50;38 71;71;71;62;48;78;55;42 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. However, higher amino acid variations in the C-terminal domain of the E-protein, such as S55F, V62F and R69I, may affect the binding of SARS-Cov-2 E-protein to the tight junction proteins impacting pathogenesis. 2022 Frontiers in medicine Introduction SARS_CoV_2 R69I;S55F;V62F 104;89;95 108;93;99 E;E 70;147 71;148 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. However, in-vitro neutralization assays show that casirivimab alone (without imdevimab) had reduced activity against (i) K417N+ E484K substitutions found in P.1 lineage (Brazil variant), and (ii) E484Q mutation expressed in B.1.617.1/B.1.617.3 lineages (Delta/Indian variants) (FDA). 2022 Frontiers in medicine Introduction SARS_CoV_2 E484K;E484Q;K417N 128;196;121 133;201;126 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. However, it has been warned that if P337H/L/R/T and E340A/K/G arises, the mAb can show a reduced susceptibility of more than 100-fold (FDA). 2022 Frontiers in medicine Introduction SARS_CoV_2 E340A;E340G;E340K;P337H;P337L;P337R;P337T 52;52;52;36;36;36;36 61;61;61;47;47;47;47 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. However, it showed a significant reduction in the neutralization of B.1.351 (carrying K417N + E484K +N501Y). 2022 Frontiers in medicine Introduction SARS_CoV_2 E484K;K417N;N501Y 94;86;101 99;91;106 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. In addition, some of the notable substitutions in NTD are R246I (in B.1.351), W152C (in B.1.429), L18F (in B.1.351 and P.1), T19R (in B.1.17 and B.1.617) and G142D (in B.1.617 lineages), all of which are associated with immune-escape. 2022 Frontiers in medicine Introduction SARS_CoV_2 G142D;L18F;R246I;T19R;W152C 158;98;58;125;78 163;102;63;129;83 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. In the US, Q57H mutation in the ORF3a region, and S24L and L84S in ORF8 was found to be prevalent, suggesting a positive effect on transmission or virulence. 2022 Frontiers in medicine Introduction SARS_CoV_2 L84S;Q57H;S24L 59;11;50 63;15;54 ORF3a;ORF8 32;67 37;71 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. In-vitro analysis on chimeric viruses showed slightly reduced potency of tixagevimab against B.1.351 (with K417N + E484K + N501Y) and P.1 (with K417N + E484K + N501Y). 2022 Frontiers in medicine Introduction SARS_CoV_2 E484K;E484K;K417N;K417N;N501Y;N501Y 115;152;107;144;123;160 120;157;112;149;128;165 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Nevertheless, studies have reported point mutations in ORF1a/b corresponding to RdRp, which are P4715L, P323L and T265I b. 2022 Frontiers in medicine Introduction SARS_CoV_2 P323L;P4715L;T265I 104;96;114 109;102;119 ORF1a;RdRP 55;80 60;84 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. One of the first identified and highly prevalent mutations is D614G, wherein the aspartic acid at residue 614 (D614) is replaced by glycine (G614). 2022 Frontiers in medicine Introduction SARS_CoV_2 D614G 62 67 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. report the increased prevalence of I82T and V70L mutations in several lineages, suggesting it is beneficial for the virus, probably by facilitating increased glucose uptake. 2022 Frontiers in medicine Introduction SARS_CoV_2 I82T;V70L 35;44 39;48 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. reports an SNP Q289H in N-gene impacted forward primer binding and markedly reduced RT-PCR assay sensitivity. 2022 Frontiers in medicine Introduction SARS_CoV_2 Q289H 15 20 N 24 25 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Similarly, K417N/T found in B.1.351 and P.1 was also found to evade antibody binding, though less potent than E484 substitutions (https://covariants.org/variants/S.E484). 2022 Frontiers in medicine Introduction SARS_CoV_2 K417N;K417T 11;11 18;18 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Specific mutations in the RBD of omicron, namely T478K, Q493K, Q498R, and E484A are thought to impact mAb binding efficacy. 2022 Frontiers in medicine Introduction SARS_CoV_2 E484A;Q493K;Q498R;T478K 74;56;63;49 79;61;68;54 RBD 26 29 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Studies by Ascoli propose polyclonal anti-N antibodies to be sensitive against the N501Y, H69/V70, D796H and D614G mutations. 2022 Frontiers in medicine Introduction SARS_CoV_2 D614G;D796H;N501Y 109;99;83 114;104;88 N 42 43 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. The antibody evasion of many variants has been attributed to E484K mutation on the spike protein. 2022 Frontiers in medicine Introduction SARS_CoV_2 E484K 61 66 S 83 88 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. The common mutations detected in the N-terminal domain are V5F, E8D, V5I, and Y2H, which might affect the viral efficiency. 2022 Frontiers in medicine Introduction SARS_CoV_2 E8D;V5F;V5I;Y2H 64;59;69;78 67;62;72;81 N 37 38 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. The common mutations observed in N-protein are R203K and G204R. 2022 Frontiers in medicine Introduction SARS_CoV_2 G204R;R203K 57;47 62;52 N 33 34 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. The D364Y mutation was found to enhance the spike protein's structural stability, thereby increasing its affinity for the receptor. 2022 Frontiers in medicine Introduction SARS_CoV_2 D364Y 4 9 S 44 49 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. The D614G substitution is found in most of the circulating VOCs, including Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2), Gamma (P.1) and the recent delta plus (AY lineage) and Omicron (B.1.1.529) variants (https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html). 2022 Frontiers in medicine Introduction SARS_CoV_2 D614G 4 9 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. The delta variants carry the L452R and T478K mutations in the RBD, and E156del-F157del in the N-terminus that are implicated in immune escape. 2022 Frontiers in medicine Introduction SARS_CoV_2 L452R;T478K 29;39 34;44 RBD;N 62;94 65;95 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. The E484K has also been implicated in immune-escape. 2022 Frontiers in medicine Introduction SARS_CoV_2 E484K 4 9 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. The T478K, Q493K, and Q498R mutations on the recently emerged VOC B1.1.529 (omicron) have shown to double the electrostatic potential, increasing the RBD-ACE2 binding affinity. 2022 Frontiers in medicine Introduction SARS_CoV_2 Q493K;Q498R;T478K 11;22;4 16;27;9 RBD 150 153 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. To date, there is no data available comparing the effectiveness of Remdesivir against variants, although in-silico studies show that mutations such as F480L, V557L, D722Y, V472D and L469S on RdRp may disrupt the binding capacity of Remdesivir. 2022 Frontiers in medicine Introduction SARS_CoV_2 D722Y;F480L;L469S;V472D;V557L 165;151;182;172;158 170;156;187;177;163 RdRP 191 195 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Unlike the previous VOCs, the B.1.1.529 (Omicron variant) surprisingly exhibit a number of S2 substitutions, namely D796Y, N856K, Q954H, N969K and L981F (https://covariants.org/variants/21K.Omicron). 2022 Frontiers in medicine Introduction SARS_CoV_2 D796Y;L981F;N856K;N969K;Q954H 116;147;123;137;130 121;152;128;142;135 35277343 A prospective evaluation of diagnostic performance of a combo rapid antigen test QuickNavi-Flu+COVID19 Ag. The study period coincided with the time when the variant carrying L452R spike mutation accounted for approximately 80% in the community. 2022 Journal of infection and chemotherapy Introduction SARS_CoV_2 L452R 67 72 S 73 78 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Alpha variant and Beta variant, which share the N501Y mutation, have higher transmission than other variants. 2022 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 N501Y 48 53 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. In addition, Beta variant is resistant to many monoclonal antibodies against the N-terminal domain and the RBD, mostly due to the E484K mutation. 2022 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 E484K 130 135 RBD;N 107;81 110;82 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. L452R and T478K mutations of Delta variant could result in the reduction of antibody neutralization and induce a strong immune escape ability. 2022 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 T478K;L452R 10;0 15;5 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The Alpha variant, Gamma variant, and Beta variant linages have the same N501Y mutation, which increases transmissibility through increased binding with ACE2. 2022 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 N501Y 73 78 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The E484K mutation, which decreases the in vitro efficacy of neutralizing antibodies, was found in both Beta variant and Gamma variant. 2022 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 E484K 4 9 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The N501Y, K417N, and E484K mutations in Beta variant may induce a conformational change of the spike protein and promote the infectivity of SARS-CoV-2. 2022 Biomedicine & pharmacotherapy Introduction SARS_CoV_2 E484K;K417N;N501Y 22;11;4 27;16;9 S 96 101 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. B.1.1.7, which was firstly detected in the United Kingdom, has an N501Y mutation in the receptor binding domain (RBD) of S protein. 2022 Frontiers in immunology Introduction SARS_CoV_2 N501Y 66 71 RBD;RBD;S 88;113;121 111;116;122 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. B.1.351, which was found in South Africa, has three mutations (K417N, E484K, and N501Y) in the RBD. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K;N501Y;K417N 70;81;63 75;86;68 RBD 95 98 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. B.1.617.2, which was confirmed in India, has mutations (L452R and T478K) in the RBD, leading to higher viral load in infected individuals, in addition to the P681R mutation which increases the virus transmissibility. 2022 Frontiers in immunology Introduction SARS_CoV_2 P681R;T478K;L452R 158;66;56 163;71;61 RBD 80 83 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. D614G_KR, which had D614G mutation of S protein and 203_204delinsKR mutation of nucleocapsid protein, and its lineage were predominant during the first to third waves, from March 2020 to February 2021. 2022 Frontiers in immunology Introduction SARS_CoV_2 D614G;D614G 20;0 25;5 N;S 80;38 92;39 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. Finally, B.1.1.529, which was detected in Botswana on November 11, 2021 and South Africa on November 14, 2021, has 15 mutations (G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, and Y505H) in the RBD. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484A;G446S;G496S;K417N;N440K;N501Y;Q493R;Q498R;S371L;S373P;S375F;S477N;T478K;Y505H;G339D 192;171;206;157;164;220;199;213;136;143;150;178;185;231;129 197;176;211;162;169;225;204;218;141;148;155;183;190;236;134 RBD 245 248 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. In this study, we analyzed the longevity and breadth of neutralizing activity of COVID-19 convalescent sera across the VOCs (B1.1.7, P.1, and B.1.351) and the D614G. 2022 Frontiers in immunology Introduction SARS_CoV_2 D614G 159 164 COVID-19 81 89 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. P.1, which was identified in Brazil, has three mutations (K417T, E484K, and N501Y) in the RBD. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K;N501Y;K417T 65;76;58 70;81;63 RBD 90 93 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The D614G mutation of spike protein (S protein) was found worldwide by the end of June, 2020. 2022 Frontiers in immunology Introduction SARS_CoV_2 D614G 4 9 S;S 22;37 27;38 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The E484K mutation in the RBD of B.1.351 and P1 is involved in immune escape. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K 4 9 RBD 26 29 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The K417N mutation of B.1.351 and B.1.1.529 and K417T mutation of P.1 are suggested to change the conformation of S protein, allowing escape from Nabs. 2022 Frontiers in immunology Introduction SARS_CoV_2 K417N;K417T 4;48 9;53 S 114 115 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The N501Y mutation shared among B.1.1.7, B.1.351, P1 and B.1.1.529 have influence on the affinity between the angiotensin-converting enzyme 2 (ACE2) receptor and the RBD of the S protein, which causes high transmissibility of the virus. 2022 Frontiers in immunology Introduction SARS_CoV_2 N501Y 4 9 RBD;S 166;177 169;178 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. Of note, most AY.4.2 sequences (93%) now include the T95I mutation in the NTD of the spike, a substitution that was rarely observed in the original Delta B1.617.2 lineage, but which gradually appeared and is now present in 40% of Delta sequences on GISAID. 2022 EBioMedicine Introduction SARS_CoV_2 T95I 53 57 S 85 90 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. spike: T19R, G142D or D950N) are also present at low frequencies in other sublineages. 2022 EBioMedicine Introduction SARS_CoV_2 D950N;G142D;T19R 22;13;7 27;18;11 S 0 5 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. The A222V mutation was noted in the B.1.177 (or 20A.EU1) lineage that emerged in Spain and spread throughout Europe in summer 2020. 2022 EBioMedicine Introduction SARS_CoV_2 A222V 4 9 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. The AY.4.2 sub-lineage is notably defined by the presence of Y145H and A222V mutations that lie within the N-terminal Domain (NTD) of the spike. 2022 EBioMedicine Introduction SARS_CoV_2 A222V;Y145H 71;61 76;66 S;N 138;107 143;108 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. The effect of combined Y145H and A222V mutations on the Delta spike background remains unknown. 2022 EBioMedicine Introduction SARS_CoV_2 A222V;Y145H 33;23 38;28 S 62 67 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. The increased transmissibility of VOCs may also be due to mutations in other viral proteins, such as R203N in the nucleocapsid (N). 2022 EBioMedicine Introduction SARS_CoV_2 R203N 101 106 N;N 114;128 126;129 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. The spike protein of Delta contains 9 mutations, when compared to the B.1 ancestral strain (D614G), including five changes in the NTD (T19R, G142D, Delta156, Delta157, R158G), two in the receptor binding domain (RBD) (L452R, T478K), one mutation close to the furin cleavage site (P681R) and one in the S2 region (D950N). 2022 EBioMedicine Introduction SARS_CoV_2 G142D;R158G;T478K;D614G;D950N;L452R;P681R;T19R 141;168;225;92;313;218;280;135 146;173;230;97;318;223;285;139 RBD;S;RBD 187;4;212 210;9;215 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. The T95I substitution was previously detected in the close B.1.617.1 lineage (also termed Kappa). 2022 EBioMedicine Introduction SARS_CoV_2 T95I 4 8 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. Through modelling, the Y145H substitution has been predicted to decrease spike stability, but this has not been experimentally demonstrated. 2022 EBioMedicine Introduction SARS_CoV_2 Y145H 23 28 S 73 78 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. When introduced into the D614G spike, the A222V substitution slightly but not significantly impacted neutralization of pseudoviruses by human convalescent sera. 2022 EBioMedicine Introduction SARS_CoV_2 A222V;D614G 42;25 47;30 S 31 36 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. A similar mutation, P681H, has been identified in B.1.1.7, which were reported to promote cleavage of the S protein precursor and affect O-glycosylation of the spike protein, but may not substantially impact viral entry or cell-cell spread. 2022 Emerging microbes & infections Introduction SARS_CoV_2 P681H 20 25 S;S 160;106 165;107 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Additionally, two mutations exist in the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein which are L452R and E484Q in B.1.617.1 and 3 or L452R and T478K in B.1.617.2. 2022 Emerging microbes & infections Introduction SARS_CoV_2 E484Q;L452R;L452R;T478K 123;113;151;161 128;118;156;166 S;RBD 89;66 94;69 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Among them, L452R is the representative mutation site of variants B.1.427 and B.1.429. 2022 Emerging microbes & infections Introduction SARS_CoV_2 L452R 12 17 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Finally, the P681R mutation locates upstream of the furin restriction site (PRRAR). 2022 Emerging microbes & infections Introduction SARS_CoV_2 P681R 13 18 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. L452R, E484Q, D614G, and P681R) are identical or similar to those in other globally circulating SARS-CoV-2 variants. 2022 Emerging microbes & infections Introduction SARS_CoV_2 D614G;E484Q;P681R;L452R 14;7;25;0 19;12;30;5 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Mutation sites involved in the B.1.617 sub-lineages include T19R, T95I, G142D, E154K, F157del, R158del, L452R, T478K, E484Q, D614G, P681R, D950N, Q1071H, and H1101D. 2022 Emerging microbes & infections Introduction SARS_CoV_2 D614G;D950N;E154K;E484Q;F157del;G142D;H1101D;L452R;P681R;Q1071H;R158del;T19R;T478K;T95I 125;139;79;118;86;72;158;104;132;146;95;60;111;66 130;144;84;123;93;77;164;109;137;152;102;64;116;70 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. The D614G mutation has spread fast and alters SARS-CoV-2 fitness, nearly all SARS-CoV-2 viruses thus far contain the D614G mutation. 2022 Emerging microbes & infections Introduction SARS_CoV_2 D614G;D614G 4;117 9;122 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. The E484Q mutation site in B.1.617 is similar to mutations in variants B.1.351 and P.1(E484K), which is a key site that lead to immune escape. 2022 Emerging microbes & infections Introduction SARS_CoV_2 E484Q;E484K 4;87 9;92 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Three common mutations (L452R, D614G, and P681R) are shared by all viruses of the B.1.617 lineage. 2022 Emerging microbes & infections Introduction SARS_CoV_2 D614G;P681R;L452R 31;42;24 36;47;29 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. A novel real-time fluorescent visualization RT-LAMP assay based on the R203M mutation was developed and validated, and this strategy allowed for the discrimination of Delta variants while detecting SARS-CoV-2 simultaneously. 2022 Emerging microbes & infections Introduction SARS_CoV_2 R203M 71 76 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Delta variants have a number of characteristic mutations in their spike protein, including single-nucleotide polymorphisms (SNPs) resulting in T19R, R158G, L452R, T478 K, D614G, P681R, and D950N, which are usually chosen as the detection targets of the molecular diagnostics for Delta genotyping. 2022 Emerging microbes & infections Introduction SARS_CoV_2 D614G;D950N;L452R;P681R;R158G;T19R;T478K 171;189;156;178;149;143;163 176;194;161;183;154;147;169 S 66 71 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Newly reported N mutations, such as R203M and D377Y, are highly exclusive to the Delta variant. 2022 Emerging microbes & infections Introduction SARS_CoV_2 D377Y;R203M 46;36 51;41 N 15 16 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Indeed, recent reports demonstrated diminished sensitivity of spike PVs bearing L452R and E484Q to BNT162b2 mRNA vaccine-elicited antibodies but a lack of synergy between these two mutations in conferring the resistance. 2022 Life science alliance Introduction SARS_CoV_2 E484Q;L452R 90;80 95;85 S 62 67 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. The spike protein from B.1.617 lineage harboring L452R and E484Q mutations was reported to have contributed to the pathogenicity. 2022 Life science alliance Introduction SARS_CoV_2 E484Q;L452R 59;49 64;54 S 4 9 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Here, we report a case of an immunocompromised patient with an indolent, protracted course of SARS-CoV-2 infection from whom a RDV resistance mutation, E802D, was identified during recrudescence of viral shedding following treatment with the antiviral agent. 2022 Nature communications Introduction SARS_CoV_2 E802D 152 157 COVID-19 94 114 35305699 Neutralisation sensitivity of the SARS-CoV-2 omicron (B.1.1.529) variant: a cross-sectional study. Deep mutational scanning data suggest that E484A and K417N, in addition to G446S and Q493R (which are not present in other variants of concern) are the largest contributors to the resistance profile of the omicron variant. 2022 The Lancet. Infectious diseases Introduction SARS_CoV_2 E484A;G446S;K417N;Q493R 43;75;53;85 48;80;58;90 35305699 Neutralisation sensitivity of the SARS-CoV-2 omicron (B.1.1.529) variant: a cross-sectional study. Mutations at amino acid positions 484, 417, and 501 are common to multiple variants of concern, and these three mutations alone (but E484K instead of E484A in the omicron variant) explain the majority of resistance exhibited by the beta (B.1.351) variant, which has no other receptor binding domain mutations. 2022 The Lancet. Infectious diseases Introduction SARS_CoV_2 E484A;E484K 150;133 155;138 RBD 275 298 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? Mutations that alter the characteristics of the RBD in the spike protein, such as L452R and T478K in the Delta variant, can affect antibody neutralization. 2022 Frontiers in microbiology Introduction SARS_CoV_2 L452R;T478K 82;92 87;97 S;RBD 59;48 64;51 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? One such VOC, B.1.617.2, also known as the Delta variant and first identified in India in October 2020, is characterized by mutations T19R, G142D, Delta157-158, R158G, L452, T478K, D614G, P681R, and D950N in the spike protein. 2022 Frontiers in microbiology Introduction SARS_CoV_2 D614G;D950N;G142D;P681R;R158G;T19R;T478K 181;199;140;188;161;134;174 186;204;145;193;166;138;179 S 212 217 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? The key mutations, L452R and T478K, in the receptor-binding domain (RBD) of the spike protein have been associated with higher transmission rates as they enhance the binding to the ACE2 receptor. 2022 Frontiers in microbiology Introduction SARS_CoV_2 L452R;T478K 19;29 24;34 S;RBD 80;68 85;71 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. Whole-genome sequencing (WGS) of all included cases (44 per cent of all cases successful) allowed the analysis be restricted to a single, dominant viral variant (B.1-C15324T, 60 per cent of cases). 2022 Virus evolution Introduction SARS_CoV_2 C15324T 166 173 35311662 Reduced DMPC and PMPC in lung surfactant promote SARS-CoV-2 infection in obesity. Importantly, DMPC and PMPC inhibited wild type and D614G mutant SARS-CoV-2 infection. 2022 Metabolism Introduction SARS_CoV_2 D614G 51 56 COVID-19 64 84 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. Based on docking studies with single-mutant S proteins, the Q493K, N501Y, S371L, S373P, S375F, Q498R, and T478K mutations have been reported to contribute significantly to the high binding affinity of the Omicron S protein to hACE2. 2022 Journal of chemical information and modeling Introduction SARS_CoV_2 N501Y;Q493K;Q498R;S371L;S373P;S375F;T478K 67;60;95;74;81;88;106 72;65;100;79;86;93;111 S;S 44;213 45;214 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The L452R and T478K mutations are located in the RBD, and they significantly increase the binding affinity of the S protein to hACE2. 2022 Journal of chemical information and modeling Introduction SARS_CoV_2 L452R;T478K 4;14 9;19 RBD;S 49;114 52;115 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The mutations of the S protein in the Delta variant are T19R, E156G, Delta157/158, L452R, T478K, D614G, P681R, and D950N. 2022 Journal of chemical information and modeling Introduction SARS_CoV_2 D614G;D950N;E156G;L452R;P681R;T19R;T478K 97;115;62;83;104;56;90 102;120;67;88;109;60;95 S 21 22 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The N501Y mutation being located in the RBD causes the S protein to have increased binding affinity to hACE2 and a consequent increase in the transmission ability of the virus. 2022 Journal of chemical information and modeling Introduction SARS_CoV_2 N501Y 4 9 RBD;S 40;55 43;56 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The S protein mutations in the alpha variant are DeltaH69/DeltaV70, Delta144/144, N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H. 2022 Journal of chemical information and modeling Introduction SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 89;128;96;82;103;117;110 94;134;101;87;108;122;115 S 4 5 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). A missense mutation (U1355G in the S gene) of RBD, representing L452R, has been observed in the India and California strains (B.1.617 and B.1.427 / B.1.429, respectively). 2022 PloS one Introduction SARS_CoV_2 L452R 64 69 RBD;S 46;35 49;36 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). We established a novel RT-LAMP-BART method to detect SARS-CoV-2 (SARS-RT-LAMP-BART) and an RT-LAMP-BART method to identify genotypes with the L452R spike mutation (L452R-RT-LAMP-BART). 2022 PloS one Introduction SARS_CoV_2 L452R;L452R 142;164 147;169 S 148 153 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. We compare the specificity of Delta-elicited antibodies to those elicited by earlier SARS-CoV-2 variants, including the early 2020 (i.e., Wuhan-Hu-1 and D614G) and Beta variants. 2022 bioRxiv Introduction SARS_CoV_2 D614G 153 158 35314694 Genetic alteration of human MYH6 is mimicked by SARS-CoV-2 polyprotein: mapping viral variants of cardiac interest. Among these, a human genetic variant of MYH6 (c.5410 C > A; Q1804K) is identical to a peptide of the reference SARS-CoV-2 replicase polyprotein. 2022 Cell death discovery Introduction SARS_CoV_2 Q1804K;C5410A 60;46 66;58 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Additional mutations are found in the BA.1 spike protein, including 10 substitutions (A67V, T95I, Y145D, L212I, S371L, G446S, G496S, T547K, N856K, and L981F), three deletions (H69-/V70-, G142-/V143-/Y144-, and N211-) and a three amino-acid insertion at position 214. 2022 MedComm Introduction SARS_CoV_2 G446S;G496S;L212I;L981F;N856K;S371L;T547K;T95I;ins 214;Y145D;A67V 119;126;105;151;140;112;133;92;223;98;86 124;131;110;156;145;117;138;96;265;103;90 S 43 48 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Additional mutations found in the Omicron variant (e.g., A67V, T95I, G142-/V143-/Y144-/Y145D, and N211-/L212I) are associated with infectious capacity, but their precise role remains to be elucidated. 2022 MedComm Introduction SARS_CoV_2 A67V;T95I;L212I;Y145D 57;63;104;87 61;67;109;92 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Although E484K is not known to exist in the Omicron variant, the analogous E484A can be reasonably speculated to perform a similar role. 2022 MedComm Introduction SARS_CoV_2 E484A;E484K 75;9 80;14 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Although the Omicron-specific RBD substitutions (K417N and E484A) reduced binding of the spike protein to ACE2, other mutations that increased the affinity for ACE2 could compensate for such effects. 2022 MedComm Introduction SARS_CoV_2 E484A;K417N 59;49 64;54 S;RBD 89;30 94;33 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Another example is the P681H mutation located in the furin protease cleavage site. 2022 MedComm Introduction SARS_CoV_2 P681H 23 28 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. For instance, ORF1a shows five substitutions (K856R, L2084I, A2170T, T3255I, and P3395H) and four deletions (S2083-, L3674-, S3675-, and G3676-). 2022 MedComm Introduction SARS_CoV_2 A2170T;L2084I;P3395H;T3255I;K856R 61;53;81;69;46 67;59;87;75;51 ORF1a 14 19 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. For instance, the K417N and N501Y mutations were known to confer protection against a number of mAbs. 2022 MedComm Introduction SARS_CoV_2 K417N;N501Y 18;28 23;33 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Furthermore, consistent with the observations highlighted above, the Q498R substitution may act synergistically with the existing N501Y substitution to increase the affinity of the spike protein to ACE2. 2022 MedComm Introduction SARS_CoV_2 N501Y;Q498R 130;69 135;74 S 181 186 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. However, in the presence of E484K, the protection range could be extended. 2022 MedComm Introduction SARS_CoV_2 E484K 28 33 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. In addition, SARS-CoV-2 variants (e.g., Omicron) with N440K mutation are also more likely to escape antibody neutralization activities. 2022 MedComm Introduction SARS_CoV_2 N440K 54 59 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. In another study, the antiviral activity of 19 different mAbs against eight variants (Alpha, B.1.526, B.1.429, Delta, Gamma, Beta, Omicron, B.1.1.529 + R346K) of SARS-CoV-2 was evaluated by calculating the fold changes in IC50, compared with WT virus. 2022 MedComm Introduction SARS_CoV_2 R346K 152 157 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Interestingly, S477N and E484A are found in the Omicron variant. 2022 MedComm Introduction SARS_CoV_2 E484A;S477N 25;15 30;20 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Interestingly, the presence of the K417N mutation did not affect spike-ACE2 binding affinity but produced positive cooperativity with E484K/N501Y. 2022 MedComm Introduction SARS_CoV_2 E484K;K417N;N501Y 134;35;140 139;40;145 S 65 70 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. One example is the N501Y mutation, shared by Alpha, Beta, and Gamma variants, which enhances the binding of spike to ACE2. 2022 MedComm Introduction SARS_CoV_2 N501Y 19 24 S 108 113 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. ORF1b has two substitutions (P314L and I1566V). 2022 MedComm Introduction SARS_CoV_2 I1566V;P314L 39;29 45;34 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. ORF9b has substitution (P10S) and three deletions (E27-, N28-, and A29-). 2022 MedComm Introduction SARS_CoV_2 P10S 24 28 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Other mutations that confer the ability to escape antibody neutralizing activities in the Omicron variant spike protein include Q493R and G446S, which affected the neutralizing activities of mAbs as well as polyclonal sera, while S371L affected four RBD classes of mAbs. 2022 MedComm Introduction SARS_CoV_2 G446S;Q493R;S371L 138;128;230 143;133;235 S;RBD 106;250 111;253 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Previous studies illustrated that D614G reduces the binding affinity to ACE2 but enhances the protease cleavage of S1/S2, leading to higher transmissibility. 2022 MedComm Introduction SARS_CoV_2 D614G 34 39 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. S477N and E484A showed high resistance to multiple mAbs in neutralization assays. 2022 MedComm Introduction SARS_CoV_2 E484A;S477N 10;0 15;5 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Specifically, BA.1 and BA.2 display 20 identical spike mutations, which are G339D, S373P, S375F, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K. 2022 MedComm Introduction SARS_CoV_2 D614G;D796Y;E484A;G339D;H655Y;K417N;N440K;N501Y;N679K;N764K;N969K;P681H;Q493R;Q498R;Q954H;S373P;S375F;S477N;T478K;Y505H 160;195;125;76;167;97;104;146;174;188;213;181;132;139;202;83;90;111;118;153 165;200;130;81;172;102;109;151;179;193;218;186;137;144;207;88;95;116;123;158 S 49 54 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Structural modeling and comparisons of the binding interface between the spike protein and ACE2 in Omicron and Delta variants suggest the three mutations (Q493R, G496S, and Q498R) found only in the Omicron variant formed additional interactions with ACE2. 2022 MedComm Introduction SARS_CoV_2 G496S;Q498R;Q493R 162;173;155 167;178;160 S 73 78 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. The D614G mutation, present in all VOCs, is associated with higher viral load in the upper respiratory tract of younger patients. 2022 MedComm Introduction SARS_CoV_2 D614G 4 9 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. The G496S substitution formed a new hydrogen bond not presented in the Delta variant. 2022 MedComm Introduction SARS_CoV_2 G496S 4 9 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. The H655Y substitution is also found in the furin cleavage site. 2022 MedComm Introduction SARS_CoV_2 H655Y 4 9 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. The impact of other novel substitutions in the Omicron RBD (e.g., G339D, S371L, S373P, and S375F) are suggested to have relatively milder impacts on the binding affinity to ACE2. 2022 MedComm Introduction SARS_CoV_2 G339D;S371L;S373P;S375F 66;73;80;91 71;78;85;96 RBD 55 58 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. The N440K and Y505H substitutions, found only in the Omicron variant, are associated with increased infectivity. 2022 MedComm Introduction SARS_CoV_2 N440K;Y505H 4;14 9;19 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. The Omicron variant spike protein mutations G446S, E484A, Q493A, and K417N conferred protection against neutralizing antibodies in four of these six epitope groups. 2022 MedComm Introduction SARS_CoV_2 E484A;G446S;K417N;Q493A 51;44;69;58 56;49;74;63 S 20 25 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. The results revealed an 8.4-fold decrease in the mean neutralizing activity against Omicron, compared to the D614G reference strain. 2022 MedComm Introduction SARS_CoV_2 D614G 109 114 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. The S477N substitution was also reported to enhance the binding between spike protein and ACE2, leading to a slight increase in infectivity, compared with N501Y. 2022 MedComm Introduction SARS_CoV_2 N501Y;S477N 155;4 160;9 S 72 77 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. The T478K substitution, found in Delta and Omicron variants, is located within the RBD of the spike protein. 2022 MedComm Introduction SARS_CoV_2 T478K 4 9 S;RBD 94;83 99;86 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. There are new salt bridges formed by the Q493R and Q498R substitutions. 2022 MedComm Introduction SARS_CoV_2 Q493R;Q498R 41;51 46;56 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. These include T9I in the envelope (E) protein, D3G, Q19E, and A63T in the membrane (M) protein, and a number of deletions (E31-, R32-, S33-) and substitutions (P13L, R203K, and G204R) in the nucleocapsid (N) protein. 2022 MedComm Introduction SARS_CoV_2 A63T;D3G;G204R;Q19E;R203K;T9I;P13L 62;47;177;52;166;14;160 66;50;182;56;171;17;164 N;Membrane;E;N 191;74;35;205 203;82;36;206 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Three of these mutations are in position 477 (S477N, S477G, and S477R) and four in position 484 (E484A, E484D, E484G, and E484K). 2022 MedComm Introduction SARS_CoV_2 E484D;E484G;E484K;S477G;S477R;E484A;S477N 104;111;122;53;64;97;46 109;116;127;58;69;102;51 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Thus, the presence of the three mutations N501Y/E484A/K417N may increase the binding affinity of spike protein to ACE2 and raise the possibility that this triple mutation may enhance the transmissibility of the Omicron variant. 2022 MedComm Introduction SARS_CoV_2 N501Y;E484A;K417N 42;48;54 47;53;59 S 97 102 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Using four different sera from recovered subjects, E484A allowed the Omicron variant to escape the neutralization of all four sera and S477N allowed the escape of two out of four sera. 2022 MedComm Introduction SARS_CoV_2 E484A;S477N 51;135 56;140 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. We outlined above that the S371L, N440K, G446S, and Q493R substitutions participated in the escape of antibody neutralization of the Omicron variant. 2022 MedComm Introduction SARS_CoV_2 G446S;N440K;Q493R;S371L 41;34;52;27 46;39;57;32 35317190 SARS-CoV-2 Omicron variant: Immune escape and vaccine development. Yeast surface display technology revealed that spike proteins harboring the E484K/N501Y double mutations could induce stronger affinity than the N501Y alone. 2022 MedComm Introduction SARS_CoV_2 E484K;N501Y;N501Y 76;145;82 81;150;87 S 47 52 35321260 Heat Treatment Promotes Ubiquitin-Mediated Proteolysis of SARS-CoV-2 RNA Polymerase and Decreases Viral Load. Although our study lacks adequate evidence obtained from in vivo animal model showing the inhibitory effect of mild heat treatment on the SARS-CoV-2 virulence, we do provide clear evidence that mild daily treatment is sufficient to maintain low levels of both WT and P323L mutant of NSP12. 2022 Research (Washington, D.C.) Introduction SARS_CoV_2 P323L 267 272 Nsp12 283 288 35321260 Heat Treatment Promotes Ubiquitin-Mediated Proteolysis of SARS-CoV-2 RNA Polymerase and Decreases Viral Load. Both WT and P323L mutants of NSP12 were robustly ubiquitinated upon heat treatment within 0.5 h, implying ubiquitin-dependent degradation of NSP12 by the mild heat stress (Figure 1(d)). 2022 Research (Washington, D.C.) Introduction SARS_CoV_2 P323L 12 17 Nsp12;Nsp12 29;141 34;146 35321260 Heat Treatment Promotes Ubiquitin-Mediated Proteolysis of SARS-CoV-2 RNA Polymerase and Decreases Viral Load. Hence, fever-range and clinically relevant hyperthermia-based approaches could be rapidly developed for currently prevalent and emerging SARS-CoV-2 variants harboring P323L mutation, including delta, delta plus, omicron, and IHU. 2022 Research (Washington, D.C.) Introduction SARS_CoV_2 P323L 167 172 35321260 Heat Treatment Promotes Ubiquitin-Mediated Proteolysis of SARS-CoV-2 RNA Polymerase and Decreases Viral Load. In comparison to the spike protein, NSP12 is much less mutation-prone, although one mutation, P323L, has been concurrently identified on NSP12 in several SARS-CoV-2 variants including delta, delta plus, omicron (B.1.1.529), and IHU. 2022 Research (Washington, D.C.) Introduction SARS_CoV_2 P323L 94 99 S;Nsp12;Nsp12 21;36;137 26;41;142 35321260 Heat Treatment Promotes Ubiquitin-Mediated Proteolysis of SARS-CoV-2 RNA Polymerase and Decreases Viral Load. Notably, daily mild heat treatment (40 C, 0.5 h/day) is sufficient to maintain low levels of both WT and P323L mutant of NSP12 (Figures 1(n) and 1(o), compare lanes 3, 4 to 1), suggesting clinical potential of heat treatment against both WT and P323L mutation harboring SARS-CoV-2 variants. 2022 Research (Washington, D.C.) Introduction SARS_CoV_2 P323L;P323L 105;245 110;250 Nsp12 121 126 35321260 Heat Treatment Promotes Ubiquitin-Mediated Proteolysis of SARS-CoV-2 RNA Polymerase and Decreases Viral Load. Notably, we found that P323L mutant and wild-type (WT) NSP12 display similar heat sensitivity (Figure 1(c)), suggesting that heat treatment could be a potential intervention against SARS-CoV-2 variants regardless of their RNA polymerase mutation status. 2022 Research (Washington, D.C.) Introduction SARS_CoV_2 P323L 23 28 Nsp12 55 60 35321335 Omicron Variant of SARS-CoV-2 Virus: In Silico Evaluation of the Possible Impact on People Affected by Diabetes Mellitus. Some of these mutations, such as Q498R and N501Y, have already proven to lead to an increased affinity with ACE2 in respect to WT-Spike. 2022 Frontiers in endocrinology Introduction SARS_CoV_2 N501Y;Q498R 43;33 48;38 S 130 135 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. At the same time, the enhanced exposure of the RBM in the D614G variant led to increased sensitivity to neutralizing antibodies. 2022 eLife Introduction SARS_CoV_2 D614G 58 63 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. By the summer of 2020, the SARS-CoV-2 S variant D614G (B.1 lineage) had supplanted the ancestral virus (strain Wuhan-1) worldwide, and structural analysis showed that D614G disrupts an interprotomer contact. 2022 eLife Introduction SARS_CoV_2 D614G;D614G 48;167 53;172 S 38 39 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Nonetheless, antibodies that target the S2 stalk further promoted the RBD-up conformation on the D614G spike. 2022 eLife Introduction SARS_CoV_2 D614G 97 102 S;RBD 103;70 108;73 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. The D614G spike existed in an equilibrium where the RBD favors the up conformation prior to antibody binding. 2022 eLife Introduction SARS_CoV_2 D614G 4 9 S;RBD 10;52 15;55 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The B.1.617.1 is characterized by mutations L452R, P681R, and E484Q in S, whereas the Delta variant is characterized by the presence of mutations L452R, P681R, and T478K in S. 2022 Genes Introduction SARS_CoV_2 E484Q;L452R;L452R;P681R;P681R;T478K 62;44;146;51;153;164 67;49;151;56;158;169 S;S 71;173 72;174 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The D614G mutation in spike (S) was one of the first discovered, improves viral infectivity, and shifts the spike (S) protein conformation toward binding a fusion-competent state. 2022 Genes Introduction SARS_CoV_2 D614G 4 9 S;S;S;S 22;108;29;115 27;113;30;116 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The E484K mutation, present in the receptor-binding ridge, has been detected in S protein in multiple lineages. 2022 Genes Introduction SARS_CoV_2 E484K 4 9 S 80 81 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The L452R and T478K enhance S protein's binding affinity with human angiotensin-converting enzyme 2 (ACE2) receptor. 2022 Genes Introduction SARS_CoV_2 L452R;T478K 4;14 9;19 S 28 29 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The P681H and D614G mutations have been thought to be responsible for the B.1.1.7 increased transmissibility. 2022 Genes Introduction SARS_CoV_2 D614G;P681H 14;4 19;9 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The P681H and P681R improve S protein fusion to the host cell. 2022 Genes Introduction SARS_CoV_2 P681H;P681R 4;14 9;19 S 28 29 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The P681H mutations have been found in the B.1.1.7, B.1.1.318, and P.3, whereas mutation P681R has been found in the A.23.1 lineages and all B.1.617 variants. 2022 Genes Introduction SARS_CoV_2 P681H;P681R 4;89 9;94 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. As the pandemic progressed, a number of single amino acid mutations in the Spike protein were detected, such as D614G and A222V. 2022 Frontiers in immunology Introduction SARS_CoV_2 A222V;D614G 122;112 127;117 S 75 80 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. For instance, the E484K mutation in the RBD in several VOCs has been reported to cause up to a ten-fold reduction of neutralisation, while the more recent L452R mutation found in B.1.427/B.1.429, a VOC originally detected in California, USA, resulted in a 4 fold reduction. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K;L452R 18;155 23;160 RBD 40 43 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. Referred to as Cluster 5 or B.1.1.298, several different groups of mutations were identified, with the most abundant population containing missense and deletion mutations on the Spike; 69/70del, Y453F and D614G. 2022 Frontiers in immunology Introduction SARS_CoV_2 D614G;Y453F 205;195 210;200 S 178 183 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. The D614G mutation was found to increase the density of Spike protein on virions and infectivity. 2022 Frontiers in immunology Introduction SARS_CoV_2 D614G 4 9 S 56 61 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. This new variant has the E484K mutation in the Spike protein that is believed to have a strong impact on antibody evasion. 2022 Frontiers in immunology Introduction SARS_CoV_2 E484K 25 30 S 47 52 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. We also included the B.1.617.2 K417N variant informally named as Delta Plus ( Table 1 ). 2022 Frontiers in immunology Introduction SARS_CoV_2 K417N 31 36 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. Nevertheless, mutations in SARS-CoV-2 have been detected and viruses with a D614G exchange became dominant early in the pandemic. 2022 PloS one Introduction SARS_CoV_2 D614G 76 81 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. The D614G exchange increases the percentage of S proteins present in the "open" conformation required for efficient ACE2 binding and viruses bearing this exchange show accelerated transmission kinetics in animal models. 2022 PloS one Introduction SARS_CoV_2 D614G 4 9 S 47 48 35336868 Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens. Omicron has posed a serious public health concern due to the mutations/deletions associated with increased binding affinity to ACE2 (S:Q498R and S:N501Y), increased transmissibility (S:H655Y, S:N679K, and S:P681H), increased viral load (N:R203K and N:G204R), innate immune evasion (ORF1a:L3674-, ORF1a:S3675-, and ORF1a:G3676), and S-gene target failure (S:H69-). 2022 Viruses Introduction SARS_CoV_2 G204R;H655Y;N679K;P681H;R203K 251;185;194;207;239 256;190;199;212;244 ORF1a;ORF1a;ORF1a;N;N;S;S;S;S;S 282;296;314;237;249;183;192;205;332;355 287;301;319;238;250;184;193;206;333;356 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. In addition to the P681R mutation, the Delta variant also contains a D614G mutation, which promotes the RBD of the S-protein in an "open" conformation, making its binding with the ACE2 receptor easier, as well as enhancing the protease cleavage at the S1/S2 cleavage site. 2022 Viruses Introduction SARS_CoV_2 D614G;P681R 69;19 74;24 RBD;S 104;115 107;116 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. In view of this overarching importance of the P681R and D614G mutations, it is therefore crucial to understand the role that these mutations play in the phenomenology of the Delta variant at the atomic scale, which can only be accomplished by unleashing the best that the ab initio quantum chemical methodology has to offer. 2022 Viruses Introduction SARS_CoV_2 D614G;P681R 56;46 61;51 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. Interestingly, the P681R mutation right at the furin cleavage site of the Delta variant plays an important role in enhancing the S-protein cleavage and is hypothesized as the main culprit for the Delta variant infectivity. 2022 Viruses Introduction SARS_CoV_2 P681R 19 24 S 129 130 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. Specifically, we study the atomically resolved structure and quantify the interatomic impact of P681R and D614G in the SD2 to FP (SD2-FP) domains of the S-protein, together with the effect of the double mutation, and compare the results with the unmutated case or the wild type (WT). 2022 Viruses Introduction SARS_CoV_2 D614G;P681R 106;96 111;101 S 153 154 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. The specific aim of this study is to investigate the nature of these two important mutations, P681R and D614G, in the Delta variant using ultra large-scale ab initio quantum chemical modeling, combined with an advanced analysis that allows for a quantitative assessment of the impact of mutations on the atomic resolution scale. 2022 Viruses Introduction SARS_CoV_2 D614G;P681R 104;94 109;99 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. Another mutation, which is common in the Kappa lineage but not in the Delta variant, causes the substitution of glutamic acid to glutamine at location 484 (S:E484Q) in the receptor binding domain of the spike protein. 2022 Viruses Introduction SARS_CoV_2 E484Q 158 163 RBD;S;S 172;203;156 195;208;157 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. Due to the risk of a higher transmission potential, the combination of B.1.617.2 with E484Q was added to the list of variants under monitoring (VOM) in August 2021. 2022 Viruses Introduction SARS_CoV_2 E484Q 86 91 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. Even though the E484Q mutation was found in other lineages (B.1.617.1, B.1.617.3), it was the B.1.617.2 lineage that became dominant. 2022 Viruses Introduction SARS_CoV_2 E484Q 16 21 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. However, on 23 August, the E484Q mutation was found in 509 sequences representing a 27% increase in only a week's time. 2022 Viruses Introduction SARS_CoV_2 E484Q 27 32 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. In this report, we present genomic surveillance combined with clinical contact tracing of a highly transmissible and vaccine-evading chain of infections with B.1.617.2 harbouring S:E484Q that resulted in an uncharacteristically high prevalence of spinning vertigo, a possible neurotrophic symptom. 2022 Viruses Introduction SARS_CoV_2 E484Q 181 186 S 179 180 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. Only 401 (0.13%) of them harboured the immune escape mutation E484Q, first reported on 30 January 2021 in the USA. 2022 Viruses Introduction SARS_CoV_2 E484Q 62 67 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. The combination of E484Q with the B.1.617.2 lineage has the potential to be an evolutionary gain for SARS-CoV-2. 2022 Viruses Introduction SARS_CoV_2 E484Q 19 24 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. The lineage B.1.617.2 is linked to reduced sensitivity to neutralizing antibodies due to a L452R substitution. 2022 Viruses Introduction SARS_CoV_2 L452R 91 96 35336952 Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. We also show the high prevalence of the R346K mutation as well as the emergence of different haplotypes during this period. 2022 Viruses Introduction SARS_CoV_2 R346K 40 45 35337002 Protective Immunity of the Primary SARS-CoV-2 Infection Reduces Disease Severity Post Re-Infection with Delta Variants in Syrian Hamsters. Among these sub-lineages, AY.1 and AY.2 possess the K417N substitution, which is also present in the B.1.351 variant, suggesting that it plays a role in immune evasion. 2022 Viruses Introduction SARS_CoV_2 K417N 52 57 35337002 Protective Immunity of the Primary SARS-CoV-2 Infection Reduces Disease Severity Post Re-Infection with Delta Variants in Syrian Hamsters. AY.1 has amino acid substitutions at T19R, E156G, 157/158 del, W258L, K417N, L452R, T478K, D614G, D950N and P681R. 2022 Viruses Introduction SARS_CoV_2 D614G;D950N;E156G;K417N;L452R;P681R;T19R;T478K;W258L 91;98;43;70;77;108;37;84;63 96;103;48;75;82;113;41;89;68 35337002 Protective Immunity of the Primary SARS-CoV-2 Infection Reduces Disease Severity Post Re-Infection with Delta Variants in Syrian Hamsters. The amino acid substitutions in the spike protein of the Delta variant, such as D614G, T478K, P681R and L452R, are known to affect transmissibility and neutralization. 2022 Viruses Introduction SARS_CoV_2 D614G;L452R;P681R;T478K 80;104;94;87 85;109;99;92 S 36 41 35337002 Protective Immunity of the Primary SARS-CoV-2 Infection Reduces Disease Severity Post Re-Infection with Delta Variants in Syrian Hamsters. The SARS-CoV-2 B.1 variant possessing the D614G mutation in the spike protein was found to be highly transmissible and became the predominant variant during the early phase of the pandemic. 2022 Viruses Introduction SARS_CoV_2 D614G 42 47 S 64 69 35337002 Protective Immunity of the Primary SARS-CoV-2 Infection Reduces Disease Severity Post Re-Infection with Delta Variants in Syrian Hamsters. This ancestral variant with only the D614G mutation in the spike protein has been used as a comparator virus in multiple research studies. 2022 Viruses Introduction SARS_CoV_2 D614G 37 42 S 59 64 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. More recently, the BA.2 and BA.1.1 sublines see continued expansion within Europe, the former of which lacks certain sequence variances in the Spike-Gene (notably del-HV69-70) and the latter featuring an additional one (R346K), both of which have been shown to affect antibody efficacy. 2022 Viruses Introduction SARS_CoV_2 R346K 220 225 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. Multiple methods have been developed targeting single-nucleotide polymorphisms (e.g., N501Y and E484K) or characteristic deletions (e.g., spike SDelta69/70 deletion and ORF1a Delta3675-3677) in the genome (often the spike domain) of the SARS-CoV-2 virus. 2022 Viruses Introduction SARS_CoV_2 E484K;N501Y 96;86 101;91 ORF1a;S;S 169;138;216 174;143;221 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. The emergence of a triple-mutated variant (K417T, E484K, N501Y, B.1.1.28), referred to as Gamma SARS-CoV-2, has been reported in Brazil. 2022 The Journal of biological chemistry Introduction SARS_CoV_2 E484K;N501Y;K417T 50;57;43 55;62;48 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. The N501Y mutation emerged among the Alpha variants and improves S-protein binding to cellular receptors and enhances virulence. 2022 The Journal of biological chemistry Introduction SARS_CoV_2 N501Y 4 9 S 65 66 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. The N501Y mutation located in the RBD is found in all the VOCs except Delta. 2022 The Journal of biological chemistry Introduction SARS_CoV_2 N501Y 4 9 RBD 34 37 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. This N501Y mutation is associated with the highest transmissibility and has given rise to other lineages with additional mutations in the S-protein RBD. 2022 The Journal of biological chemistry Introduction SARS_CoV_2 N501Y 5 10 RBD;S 148;138 151;139 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. As in cases of reinfection, by the non-synonymous convergent spike mutations N501Y, appearing in all of them, E484K occurring on the Gamma and in the Beta and K417T taking place in the Gamma variant. 2022 PeerJ Introduction SARS_CoV_2 E484K;K417T;N501Y 110;159;77 115;164;82 S 61 66 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. It presents the following mutations: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, and T1027I. 2022 PeerJ Introduction SARS_CoV_2 D138Y;E484K;H655Y;K417T;L18F;N501Y;P26S;R190S;T1027I;T20N 55;76;90;69;37;83;49;62;101;43 60;81;95;74;41;88;53;67;107;47 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. One of those effects revealed by Nelson and collaborators is the increased affinity between the Receptor-Binding Domain (RBD) and the Angiotensin-Converting Enzyme 2 (ACE2) protein caused by the N501Y and E484K mutations, which also have their potentiality enhanced when possessing the K417N/T modification. 2022 PeerJ Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 205;286;286;195 210;293;293;200 RBD 121 124 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. The Alpha variant fastly spread across dozens of countries and carried 17 mutations, including eight in the spike protein (HV 69-70 deletion, Y144 deletion, N501Y, A570D, P681H, T761I, S982A, and D1118H), which are the basis of three COVID-19 vaccines licensed. 2022 PeerJ Introduction SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;T761I 164;196;157;171;185;178 169;202;162;176;190;183 S 108 113 COVID-19 234 242 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. The Beta variant has non-synonymous spike mutations such as LAL 242-244 deletion, D80A, D215G, E484K, N501Y, A701V, L18F, R246I, K417N, and D614G. 2022 PeerJ Introduction SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;L18F;N501Y;R246I 109;88;140;82;95;129;116;102;122 114;93;145;86;100;134;120;107;127 S 36 41 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. We utilized the L452R, P681R, and E484Q key mutations of Delta, to model the variant's interface against both complexes. 2022 PeerJ Introduction SARS_CoV_2 E484Q;L452R;P681R 34;16;23 39;21;28 35341060 An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. Among many non-synonymous mutations, Q27STOP in the ORF8 protein contributed to the extrapolation of the branch leading to lineage B.1.1.7. 2022 PeerJ Introduction SARS_CoV_2 Q27X 37 44 ORF8 52 56 35341060 An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. The clade S, a subtype of SARS-CoV-2, was identified to possess the mutation L84S in the ORF8 protein sequence. 2022 PeerJ Introduction SARS_CoV_2 L84S 77 81 ORF8;S 89;10 93;11 35341060 An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. The present study aimed at characterizing the unique variations of truncated ORF8 proteins (T-ORF8) due to the Q27STOP mutation. 2022 PeerJ Introduction SARS_CoV_2 Q27X 111 118 ORF8;ORF8 77;94 81;98 35341060 An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. The Q27STOP mutation inactivates the ORF8 protein favoring further downstream mutations, and could be responsible for the increased transmissibility of the B.1.1.7 variant. 2022 PeerJ Introduction SARS_CoV_2 Q27X 4 11 ORF8 37 41 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. Interestingly, patients infected with a SARS-CoV-2 variant carrying the Delta382 deletion or the L84S mutation of the open reading frame 8 (ORF8) accessory protein experienced milder inflammatory responses and attenuated disease outcomes, suggesting a crucial role for ORF8 in triggering COVID-19 proinflammatory sequelae. 2022 mBio Introduction SARS_CoV_2 L84S 97 101 ORF8;ORF8 140;269 144;273 COVID-19 288 296 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. We also demonstrated that the disruption of ORF8 and hIL-17R interaction attenuated its proinflammatory responses and that a variant form of ORF8 associated with mild COVID-19 (L84S) showed decreased binding activity to hIL-17RA, resulting in an attenuated proinflammatory response. 2022 mBio Introduction SARS_CoV_2 L84S 177 181 ORF8;ORF8 44;141 48;145 COVID-19 167 175 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. Furthermore, vaccine-induced antibody neutralisation by the AstraZeneca COVID-19 vaccine was reduced against the beta variant compared to the original D614G variant. 2022 BMC medicine Introduction SARS_CoV_2 D614G 151 156 COVID-19 72 80 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. Neutralisation activity against the beta variant was reduced by 13-fold in convalescent sera from individuals infected with the original D614G variant. 2022 BMC medicine Introduction SARS_CoV_2 D614G 137 142 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. The beta variant bears genetic changes in the functional domain of the SARS-CoV-2 spike (S) protein including substitutions in the receptor-binding domain (RBD) (E484K, N501Y and K417N), four substitutions and a deletion in N-terminal domain (NTD) (L18F, D80A, D215G, L242H and R246I) and substitutions in S2 (D614G and A701V) regions. 2022 BMC medicine Introduction SARS_CoV_2 A701V;D215G;D80A;K417N;L242H;N501Y;R246I;D614G;E484K;L18F 320;261;255;179;268;169;278;310;162;249 325;266;259;184;273;174;283;315;167;253 S;RBD;N;S 82;156;224;89 87;159;225;90 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. To our knowledge, the only published adenovirus-based vaccine study done in an African population was done using the Johnson and Johnson Ad26.COV2.S single-dose vaccine in South Africa, which showed vaccination following prior infection significantly boosts spike-binding antibodies, antibody-dependent cellular cytotoxicity, and neutralising antibodies against D614G, beta, and delta VOCs. 2022 BMC medicine Introduction SARS_CoV_2 D614G 362 367 S;S 258;147 263;148 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. Here, we report a sensitive method for the detection of G339D and D796Y variations of Omicron BA.1. 2022 Biochemical and biophysical research communications Introduction SARS_CoV_2 D796Y;G339D 66;56 71;61 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. In those many mutations on the Spike protein gene, we focused on Omicron BA.1 specific G339D (Nucleotide mutation: G22578A) and D796Y (Nucleotide mutation: G23948T) variations because there is no mutation in the vicinity of those nucleotides. 2022 Biochemical and biophysical research communications Introduction SARS_CoV_2 D796Y;G22578A;G23948T;G339D 128;115;156;87 133;122;163;92 S 31 36 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. reported the detection of D614G (nucleotide mutation: A23403G) and L452R (nucleotide mutation: T22917G) variations in the SARS-CoV-2 spike protein by post-PCR HRM analysis, respectively. 2022 Biochemical and biophysical research communications Introduction SARS_CoV_2 A23403G;D614G;L452R;T22917G 54;26;67;95 61;31;72;102 S 133 138 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. As vaccine development was initiated almost immediately after the pandemic started, current major vaccines, including BNT162b2, mRNA1273 and ChAdOx1-S, are all based on the original strain without D614G. 2022 Future microbiology Introduction SARS_CoV_2 D614G 197 202 S 149 150 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. Beta+R346K and Mu+K417N share the same haplotype with R346K, K417N, E484K and N501Y mutations in the receptor-binding domain (RBD) in the spike protein, as shown in Figure 2. 2022 Future microbiology Introduction SARS_CoV_2 E484K;K417N;N501Y;R346K;K417N;R346K 68;61;78;54;18;5 73;66;83;59;23;10 S;RBD 138;126 143;129 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. In June, another variant harboring E484K and R346K was found in Angola with low neutralization titer against mRNA1273 vaccinated serum. 2022 Future microbiology Introduction SARS_CoV_2 E484K;R346K 35;45 40;50 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. In late September, the Alpha variant (B.1.1.7) harboring the N501Y mutation that conferred higher infectivity emerged in the UK and spread rapidly all over the world before vaccines became widely available in December. 2022 Future microbiology Introduction SARS_CoV_2 N501Y 61 66 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. One of the salient mutations, spike-D614G, appeared in January 2020 and soon became ubiquitously dominant by April. 2022 Future microbiology Introduction SARS_CoV_2 D614G 36 41 S 30 35 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. Similarly, the Mu variant (B.1.621) with spike-K417N mutation (Mu+K417N) has been identified not only in the South American countries, such as Columbia and Peru, but also in North America and European nations. 2022 Future microbiology Introduction SARS_CoV_2 K417N;K417N 66;47 71;52 S 41 46 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. To answer the question of whether immunity escape against existing vaccines or prior infections is prevalent, the authors have conducted a neutralizing antibody study against a fictitious strain, the Beta variant with spike-R346K mutation (Beta+R346K). 2022 Future microbiology Introduction SARS_CoV_2 R346K;R346K 245;224 250;229 S 218 223 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. This article evaluated the in vitro antiviral effect of the ATV against the D614G strain, Delta, and Mu variants of SARS-CoV-2, and identified the interaction affinity between ATV and two viral proteins, using an in silico structure-based molecular docking approach. 2022 Frontiers in microbiology Introduction SARS_CoV_2 D614G 76 81 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. Two mutations in the RBD (L452R, E484Q), the area important for viral entry, are present in this variation. 2022 Indian journal of medical microbiology Introduction SARS_CoV_2 E484Q;L452R 33;26 38;31 RBD 21 24 35370361 CRISPR-Cas13a cascade-based viral RNA assay for detecting SARS-CoV-2 and its mutations in clinical samples. The specific amplification of NASBA and the single base recognition ability of Cas13a guarantee the high specificity of the method, enabling the discrimination of highly homologous coronaviruses and allowing to discriminate single-nucleotide mutation in the SARS-Cov-2 variant, N501Y. 2022 Sensors and actuators. B, Chemical Introduction SARS_CoV_2 N501Y 278 283 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. We compared the magnitude of neutralization escape by Omicron to the D614G and Delta SARS-CoV-2 variants to help inform public health decisions and to offer further data to understand correlates of protection. 2022 Science translational medicine Introduction SARS_CoV_2 D614G 69 74 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. Additionally, the mutation S194L in N protein was reported to be associated with the symptomatic patients and is located in the flexible linker region of the protein N. 2022 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 S194L 27 32 N;N 36;166 37;167 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. reported P25L mutation in the Orf3a region to be strongly associated with higher mortality rates as a result of structural modification including the acquisition of escalated antigen diversity and B-cell epitope loss. 2022 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 P25L 9 13 ORF3a 30 35 35396165 A self-amplifying RNA vaccine protects against SARS-CoV-2 (D614G) and Alpha variant of concern (B.1.1.7) in a transmission-challenge hamster model. A point mutation in spike, D614G, emerged early in the pandemic, and the B lineage (B.1) bearing this change became predominant across the world. 2022 Vaccine Introduction SARS_CoV_2 D614G 27 32 S 20 25 35396165 A self-amplifying RNA vaccine protects against SARS-CoV-2 (D614G) and Alpha variant of concern (B.1.1.7) in a transmission-challenge hamster model. Immunization of hamsters with saRNA induced serum neutralising antibodies that cross neutralized both an historic D614G virus isolate from summer 2020 (B.1.238), or an isolate of Alpha VOC (B.1.1.7) virus. 2022 Vaccine Introduction SARS_CoV_2 D614G 114 119 35396165 A self-amplifying RNA vaccine protects against SARS-CoV-2 (D614G) and Alpha variant of concern (B.1.1.7) in a transmission-challenge hamster model. Immunization with a Wuhan-like spike encoded saRNA vaccine efficiently protected against weight loss induced by either the D614G or the Alpha VOC virus. 2022 Vaccine Introduction SARS_CoV_2 D614G 123 128 S 31 36 35396511 Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage. Upon comparison of the mutational profiles between the new and older C.1 sequences (which only contain the D614G spike mutation), it was clear that the new sequences had mutated substantially. 2022 Nature communications Introduction SARS_CoV_2 D614G 107 112 S 113 118 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Along with it other S protein mutations describing the British variant appeared: HV 69-70 deletion, Y144 deletion, A570D, P681H, T716I, S982A, and D1118H. 2022 Journal of applied genetics Introduction SARS_CoV_2 A570D;D1118H;P681H;S982A;T716I 115;147;122;136;129 120;153;127;141;134 S 20 21 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Along with the Y453F mutation, three other mutations have been identified: 69-70delHV, I692V, and M1229I (European Centre for Disease Prevention and Control). 2022 Journal of applied genetics Introduction SARS_CoV_2 I692V;M1229I;Y453F 87;98;15 92;104;20 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Also, SARS-CoV-2 can interact with Y41, K353, G354 residues of human ACE2 and Y41, K353, R354 of mink ACE2 when it has N501T substitution (Welkers et al.). 2022 Journal of applied genetics Introduction SARS_CoV_2 N501T 119 124 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Also, the P681H mutation has a significant biological function due to its presence near the furin cleavage site (Public Health England). 2022 Journal of applied genetics Introduction SARS_CoV_2 P681H 10 15 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Further, the N501T mutation was observed in minks from the Netherlands. 2022 Journal of applied genetics Introduction SARS_CoV_2 N501T 13 18 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. has described that three substitutions (Y453F, F486L, and N501T) facilitate SARS-CoV-2 interaction with different residues of human and mink ACE2, which suggest that having one of these mutations will allow SARS-CoV-2 to infect both human and mink. 2022 Journal of applied genetics Introduction SARS_CoV_2 F486L;N501T;Y453F 47;58;40 52;63;45 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. However, there is no data available that any of the mutations, which were expected to be crucial for SARS-CoV-2 infection in minks (Y453F, F486L, N501T, and D614G), alter S protein glycosylation. 2022 Journal of applied genetics Introduction SARS_CoV_2 D614G;F486L;N501T;Y453F 157;139;146;132 162;144;151;137 S 171 172 COVID-19 101 121 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. In Denmark and the Netherlands, several cases of mink with the S protein Y453F mutation have been reported, but the strains from both countries did not belong to the same genetic clades (European Centre for Disease Prevention and Control). 2022 Journal of applied genetics Introduction SARS_CoV_2 Y453F 73 78 S 63 64 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. In the case of F486L substitution, the coronavirus interrelates L79, M82, Y83, and H79, T82, Y83 residues of human and mink ACE2, respectively. 2022 Journal of applied genetics Introduction SARS_CoV_2 F486L 15 20 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. In the mouse model, the N501Y mutation has been associated with increased infectivity and virulence of SARS-CoV-2 (Gu et al.). 2022 Journal of applied genetics Introduction SARS_CoV_2 N501Y 24 29 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Nowadays, a SARS-CoV-2 amino acid change, D614G, is considered as dominant as this variant has more potential to neutralize antibodies, which may be relevant for vaccine development (Thomson et al). 2022 Journal of applied genetics Introduction SARS_CoV_2 D614G 42 47 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Nowadays, the N501Y mutation characterizes the novel SARS-CoV-2 variant from the UK named VOC202012/01 (B.1.1.7) (European Centre for Disease Prevention and Control), which was recently detected in Poland (Hryhorowicz et al.). 2022 Journal of applied genetics Introduction SARS_CoV_2 N501Y 14 19 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Some of these mutations, such as the 69-70 deletion in combination with the N501Y variant, increase the transmissibility of SARS-CoV-2. 2022 Journal of applied genetics Introduction SARS_CoV_2 N501Y 76 81 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. The D501N mutation of RaTG13 RBD was shown to cause a significant increase (almost ninefold) in the binding strength with ACE2 among other mutations with increased ACE2 binding and SARS-CoV-2 transmission efficiency. 2022 Journal of applied genetics Introduction SARS_CoV_2 D501N 4 9 RBD 29 32 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. The D501N mutation was found in the SARS-CoV-2 S protein sequence from Wuhan-Hu-1 (NC_045512), suggesting that it comes from the bat coronavirus RaTG13 (MN996532). 2022 Journal of applied genetics Introduction SARS_CoV_2 D501N 4 9 S 47 48 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. The D614G mutation promotes an open conformation of the S protein, resulting in enhanced infectivity in human cells (Mansbach et al.). 2022 Journal of applied genetics Introduction SARS_CoV_2 D614G 4 9 S 56 57 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. The L486F, Y493Q, and D501N residue changes from RaTG13 to SARS-CoV-2 may also be responsible for the transmission of SARS-CoV-2 to humans, as is the conservation of Leu455 between RaTG13 and SARS-CoV-2 (Shang et al.; Zhang et al.). 2022 Journal of applied genetics Introduction SARS_CoV_2 D501N;L486F;Y493Q 22;4;11 27;9;16 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. The RBD included 44 mutation sites, in which the S77N, V483A, A344S, and N501Y mutations were the most frequent, while the Y453, G476, F486, T500, and N501 mutations were close to the ACE2 (Guruprasad). 2022 Journal of applied genetics Introduction SARS_CoV_2 A344S;N501Y;S77N;V483A 62;73;49;55 67;78;53;60 RBD 4 7 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. The Y453F RBD mutation can be considered as an adaptation to the mink ACE2, which may increase affinity for human ACE2 (Bayarri-Olmos et al.). 2022 Journal of applied genetics Introduction SARS_CoV_2 Y453F 4 9 RBD 10 13 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Thomson et al demonstrated that the N439K mutation increases RBD affinity for the ACE2. 2022 Journal of applied genetics Introduction SARS_CoV_2 N439K 36 41 RBD 61 64 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Within the RBD, one of the very common mutations is the N439K substitution. 2022 Journal of applied genetics Introduction SARS_CoV_2 N439K 56 61 RBD 11 14 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Y453F substitution lets SARS-CoV-2 interact with the H34 residue of human ACE2 and the Y34 residue of mink ACE2. 2022 Journal of applied genetics Introduction SARS_CoV_2 Y453F 0 5 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. A variant with a single-residue substitution of aspartic acid with glycine at position 614 of the virus's spike protein (D614G) suddenly became the dominant strain all over the world in 2020. 2022 Cell reports Introduction SARS_CoV_2 D614G;D614G 48;121 90;126 S 106 111 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. All these variants contain the D614G mutation. 2022 Cell reports Introduction SARS_CoV_2 D614G 31 36 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. But, how the D614G mutation and newly evolved spike variants facilitate the spike conformational change for membrane fusion for enhanced viral infectivity is unknown. 2022 Cell reports Introduction SARS_CoV_2 D614G 13 18 Membrane;S;S 108;46;76 116;51;81 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Following D614G, several variants of concern have emerged, including B.1.1.7 lineage first reported in the United Kingdom (Alpha), the B.1.351 lineage in South Africa (Beta), and the B.1.617.2 lineage in India, also known as Delta variant. 2022 Cell reports Introduction SARS_CoV_2 D614G 10 15 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Here we focus on membrane fusion enhancement, mediated by SARS-CoV-2 D614G and newly evolved spike variants and compare their fusion efficacy. 2022 Cell reports Introduction SARS_CoV_2 D614G 69 74 Membrane;S 17;93 25;98 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Here, we design a fluorescent labeling platform for in vitro reconstitution of the SARS-CoV-2 spike protein-mediated membrane fusion between viral and liposomal membrane to probe the fusion dynamics of the WT spike and D614G spike variants and compare with B.1.1.7, B.1.351, and B.1.617.2 spike variants. 2022 Cell reports Introduction SARS_CoV_2 D614G 219 224 Membrane;Membrane;S;S;S;S 117;161;94;209;225;289 125;169;99;214;230;294 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Most importantly, the role of Ca2+ in D614G spike, B.1.1.7, B.1.351, and B.1.617.2 variants mediating membrane fusion for enhanced viral entry is also unknown. 2022 Cell reports Introduction SARS_CoV_2 D614G 38 43 Membrane;S 102;44 110;49 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Overall, our findings (1) unravel the fundamental mechanism of SARS-CoV-2 spike-mediated membrane fusion and fusion enhancement mediated by D614G and evolved spike variant of concern, (2) suggest a model in which the Ca2+ concentration and low pH is critical for ensuring the efficient spike conformational change for membrane fusion, and (3) suggest that spatiotemporal dynamics of Ca2+ are important for viral entry. 2022 Cell reports Introduction SARS_CoV_2 D614G 140 145 Membrane;Membrane;S;S;S 89;318;74;158;286 97;326;79;163;291 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Recent work has reported that the D614G variant shows increased infectivity by altering the receptor-binding conformation with receptor ACE2. 2022 Cell reports Introduction SARS_CoV_2 D614G 34 39 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. The B.1.1.7 and B.1.351 spike variants show higher membrane fusion efficacy compared to D614G, while B.1.617.2 variant shows the highest calcium-dependent membrane fusion efficiency among all the spike strains. 2022 Cell reports Introduction SARS_CoV_2 D614G 88 93 Membrane;Membrane;S;S 51;155;24;196 59;163;29;201 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. The D614G spike trimer is reported to sample the RBD up-conformation more frequently than the wild-type (WT) spike, but it binds more weakly to the recombinant ACE2 than the WT. 2022 Cell reports Introduction SARS_CoV_2 D614G 4 9 S;S;RBD 10;109;49 15;114;52 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. The putative importance of the D614G spike variant has been observed owing to its high infectivity and enhanced transmissibility in animal models. 2022 Cell reports Introduction SARS_CoV_2 D614G 31 36 S 37 42 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. The structural study of D614G trimers revealed the breaking of a salt bridge between D614 and a lysine residue (K854) in the fusion peptide proximal region (FPPR), which may help in clamping the RBD in the pre-fusion up-conformation and also prevent premature dissociation of the G614 trimer, but it does not explain the enhance fusion activity of spike fusion domain of D614G spike variants. 2022 Cell reports Introduction SARS_CoV_2 D614G;D614G 24;371 29;376 S;S;RBD 348;377;195 353;382;198 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Therefore, understanding the role of D614G mutation and newly evolved spike variants in spike protein-mediated membrane fusion for facilitating viral entry is important for developing novel intervention strategies against COVID-19. 2022 Cell reports Introduction SARS_CoV_2 D614G 37 42 Membrane;S;S 111;70;88 119;75;93 COVID-19 222 230 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. To resolve these issues, we report here the membrane fusion consequences due to D614G substitution and compare with B.1.1.7, B.1.351, and B.1.617.2 spike variants in the context of the full-length spike protein by reconstituting the fusion between pseudotyped SARS-CoV-2-S virions and proteoliposomes. 2022 Cell reports Introduction SARS_CoV_2 D614G 80 85 Membrane;S;S;S 44;148;197;271 52;153;202;272 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. We found that D614G spike variant is 150% more sensitive to the physiological Ca2+ concentration for fusion peptide binding to target membrane and 100% more fusion efficient compared to WT. 2022 Cell reports Introduction SARS_CoV_2 D614G 14 19 Membrane;S 134;20 142;25 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. We found that the high Ca2+ sensitivity of D614G spike variants facilitates pre- to post-fusion conformational change of S2 domain, leading to the enhanced membrane fusion efficiency compared to WT spike. 2022 Cell reports Introduction SARS_CoV_2 D614G 43 48 Membrane;S;S 156;49;198 164;54;203 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. We have identified cellular Ca2+ as the catalyzing chemical factor for SARS-CoV-2 spike activation for membrane fusion, and visualizing the mechanism of action is significant because these three interacting molecules, ACE2, NRP1, and TMPRSS2, individually and independently can enhance D614G spike-mediated membrane fusion by interacting directly with spike trimer in the presence of calcium at low pH condition, suggesting the lysosome as the point of entry for the virus. 2022 Cell reports Introduction SARS_CoV_2 D614G 286 291 Membrane;Membrane;S;S;S 103;307;82;292;352 111;315;87;297;357 35398519 Immune evasion and chronological decrease in titer of neutralizing antibody against SARS-CoV-2 and its variants of concerns in COVID-19 patients. Even in the early stage of the pandemic, the D614G mutation increased and replaced the previous strain within a few months; however, since this mutation was outside the RBD, it did not have a serious impact on the titers of neutralizing antibodies, and increased transmissibility is thought to be the cause of its spread. 2022 Clinical immunology (Orlando, Fla.) Introduction SARS_CoV_2 D614G 45 50 RBD 169 172 35398519 Immune evasion and chronological decrease in titer of neutralizing antibody against SARS-CoV-2 and its variants of concerns in COVID-19 patients. Even therapeutic monoclonal antibodies have been reported to have reduced or lost neutralizing ability against variants with the E484K mutation. 2022 Clinical immunology (Orlando, Fla.) Introduction SARS_CoV_2 E484K 129 134 35398519 Immune evasion and chronological decrease in titer of neutralizing antibody against SARS-CoV-2 and its variants of concerns in COVID-19 patients. In Japan, variants with the D614G mutation were initially the majority, and VOC and VOI strains were not detected until the end of 2020. 2022 Clinical immunology (Orlando, Fla.) Introduction SARS_CoV_2 D614G 28 33 35398519 Immune evasion and chronological decrease in titer of neutralizing antibody against SARS-CoV-2 and its variants of concerns in COVID-19 patients. Therefore, by the end of 2020, most infected patients were infected with variants having only the D614G mutation. 2022 Clinical immunology (Orlando, Fla.) Introduction SARS_CoV_2 D614G 98 103 35398519 Immune evasion and chronological decrease in titer of neutralizing antibody against SARS-CoV-2 and its variants of concerns in COVID-19 patients. This lineage has three main subtypes: B.1.617.1 (Kappa variant) and B.1.617.3, characterized by L452R and E484Q mutation in RBD, and B.1.617.2 (Delta variant), characterized by L452R and T478K in RBD. 2022 Clinical immunology (Orlando, Fla.) Introduction SARS_CoV_2 E484Q;L452R;L452R;T478K 106;96;177;187 111;101;182;192 RBD;RBD 124;196 127;199 35401825 Inhibitor screening using microarray identifies the high capacity of neutralizing antibodies to Spike variants in SARS-CoV-2 infection and vaccination. For example, the D614G variant, which was first identified in July 2020, has a faster infection rate and higher viral load in the upper respiratory tract than the wild-type "Wuhan-Hu-1" strain. 2022 Theranostics Introduction SARS_CoV_2 D614G 17 22 35401825 Inhibitor screening using microarray identifies the high capacity of neutralizing antibodies to Spike variants in SARS-CoV-2 infection and vaccination. Similar results were obtained when testing a B.1.1.7 variant with an additional E484K mutation. 2022 Theranostics Introduction SARS_CoV_2 E484K 80 85 35401825 Inhibitor screening using microarray identifies the high capacity of neutralizing antibodies to Spike variants in SARS-CoV-2 infection and vaccination. The B.1.1.7 variant (D614G, N501Y) is more infectious and may lead to increased mortality compared to the parental strain. 2022 Theranostics Introduction SARS_CoV_2 N501Y;D614G 28;21 33;26 35401825 Inhibitor screening using microarray identifies the high capacity of neutralizing antibodies to Spike variants in SARS-CoV-2 infection and vaccination. The B.1.351 and P.1 variants contain three RBD mutations at E484K, N501Y, and K417N or K417T, respectively. 2022 Theranostics Introduction SARS_CoV_2 E484K;K417N;K417T;N501Y 60;78;87;67 65;83;92;72 RBD 43 46 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Added value of this study: We analyzed the pathogenesis, disease severity and immune response generated in Syrian hamsters by Omicron (R346K) variant and compared the same with the Delta variant in hamsters. 2022 EBioMedicine Introduction SARS_CoV_2 R346K 135 140 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. All the published animal studies till date has used the Omicron variant of BA.1 sub lineage without the R346K mutation. 2022 EBioMedicine Introduction SARS_CoV_2 R346K 104 109 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Apart from the signature mutations of the Omicron variant, the isolate also possessed the R346K mutation. 2022 EBioMedicine Introduction SARS_CoV_2 R346K 90 95 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Apart from the unique mutations identified in the spike protein of this VOC, an additional amino acid change R346K in the variant is being monitored. 2022 EBioMedicine Introduction SARS_CoV_2 R346K 109 114 S 50 55 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Here, we report the characterization of Omicron variant of BA.1.1 sub lineage [Omicron (R346K) variant] in Syrian hamster model for its pathogenicity, virus shedding pattern and immune response. 2022 EBioMedicine Introduction SARS_CoV_2 R346K 88 93 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Implications of all the available evidence: Our findings shows that Omicron variant with R364K mutation replicates to high levels in respiratory tract and is capable of inducing lung disease in hamsters. 2022 EBioMedicine Introduction SARS_CoV_2 R364K 89 94 Lung diseases 178 190 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Neutralizing antibody response generated against the Omicron (R346K) variant was found poor in neutralizing the earlier as well as currently circulating SARS-CoV-2 VOCs. 2022 EBioMedicine Introduction SARS_CoV_2 R346K 62 67 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Of the spike gene mutations in the Omicron variant, the substitution R346K is being monitored by the World Health Organization. 2022 EBioMedicine Introduction SARS_CoV_2 R346K 69 74 S 7 12 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. The deep sequencing of the specimens revealed only 0.0066% difference in the hamster passage sequence with that of the clinical sample with an additional Q19E substitution in the M gene. 2022 EBioMedicine Introduction SARS_CoV_2 Q19E 154 158 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. This variant with R346K mutation has been now designated as BA.1.1 sublineage of Omicron and has been reported from at least 151 countries. 2022 EBioMedicine Introduction SARS_CoV_2 R346K 18 23 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. We also studied the neutralization potential of Omicron (R346K) infected hamster sera with other Variant of Concerns like Alpha, Beta and Delta. 2022 EBioMedicine Introduction SARS_CoV_2 R346K 57 62 35408761 Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor. Additionally, the mutation N501Y exhibits a compensatory effect since it favors pi-pi interaction with the residue Y41. 2022 Molecules (Basel, Switzerland) Introduction SARS_CoV_2 N501Y 27 32 35408761 Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor. The alpha variant has three mutations of interest in the spike protein: (i) the N501Y mutation that corresponds to the receptor-binding motif (RBM); (ii) a 69/70 deletion in the receptor binding domain (RBD) that triggers a notable change in the conformation of the RBM; and (iii) the P681H mutation found near the furin S1/S2 cleavage site. 2022 Molecules (Basel, Switzerland) Introduction SARS_CoV_2 N501Y;P681H 80;285 85;290 RBD;S;RBD 178;57;203 201;62;206 35408761 Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor. The beta variant, also known as 20H/501Y.V2, was identified in South Africa and is characterized by carrying the K417N, E484K and N501Y mutations in the RBM of the spike protein. 2022 Molecules (Basel, Switzerland) Introduction SARS_CoV_2 E484K;K417N;N501Y 120;113;130 125;118;135 S 164 169 35408761 Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor. The gamma variant carries the K417T, E484K and N501Y mutations previously described in RBM. 2022 Molecules (Basel, Switzerland) Introduction SARS_CoV_2 E484K;K417T;N501Y 37;30;47 42;35;52 35408761 Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor. While the K417T mutation results in the loss of a salt bridge with D30, mutation E484K increases the electrostatic complementarity of the binding partners. 2022 Molecules (Basel, Switzerland) Introduction SARS_CoV_2 E484K;K417T 81;10 86;15 35409572 Increased Secondary Attack Rate among Unvaccinated Household Contacts of Coronavirus Disease 2019 Patients with Delta Variant in Japan. SARS-CoV-2 VOCs bearing the L452R spike protein mutation demonstrate increased transmissibility, infectivity, and avoidance of antibody neutralization. 2022 International journal of environmental research and public health Introduction SARS_CoV_2 L452R 28 33 S 34 39 35421378 Efficacy of vaccination and previous infection against the Omicron BA.1 variant in Syrian hamsters. Here, in the hamster model, we addressed these issues under controlled conditions using the Omicron variant and isolates that are no longer circulating in nature (i.e., a Wuhan-like isolate and an isolate with only a D614G spike mutation). 2022 Cell reports Introduction SARS_CoV_2 D614G 217 222 S 223 228 35421842 Split T7 promoter-based isothermal transcription amplification for one-step fluorescence detection of SARS-CoV-2 and emerging variants. Additionally, variants of SARS-CoV-2 with the 23,403 A > G mutation (p. 2022 Biosensors & bioelectronics Introduction SARS_CoV_2 A403G 49 58 35421842 Split T7 promoter-based isothermal transcription amplification for one-step fluorescence detection of SARS-CoV-2 and emerging variants. D614G), conferring greater infectivity and more rapid spread, have become predominant in various regions. 2022 Biosensors & bioelectronics Introduction SARS_CoV_2 D614G 0 5 35421842 Split T7 promoter-based isothermal transcription amplification for one-step fluorescence detection of SARS-CoV-2 and emerging variants. Moreover, STAR was utilized for multiplex detection of the D614G mutation and N gene of SARS-CoV-2 in a single tube as well as for the direct detection of bacterial 16S rRNA without additional nucleic acid purification, thereby confirming the wide applicability of this method for nucleic acid biomarker detection. 2022 Biosensors & bioelectronics Introduction SARS_CoV_2 D614G 59 64 N 78 79 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. A decreased affinity was observed in B.1.1.7 variant S-glycoprotein and neutralizing mAbs (monoclonal antibodies) due to the mutation (N501Y substitution). 2022 Infection, genetics and evolution Introduction SARS_CoV_2 N501Y 135 140 S 53 67 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. Among these three mutations, L452R and E484Q are located in the RBD region. 2022 Infection, genetics and evolution Introduction SARS_CoV_2 E484Q;L452R 39;29 44;34 RBD 64 67 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. Another significant mutation, D614G, was reported by researchers and was found outside the RBD. 2022 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 30 35 RBD 91 94 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. Furthermore, the P681R mutation is located outside the RBD, near the furin cleavage site of the S-glycoprotein. 2022 Infection, genetics and evolution Introduction SARS_CoV_2 P681R 17 22 S;RBD 96;55 110;58 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. L452R is related to a reduction in therapeutic antibodies and is associated with neutralization using convalescent plasma. 2022 Infection, genetics and evolution Introduction SARS_CoV_2 L452R 0 5 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. One primary mutation is N501Y, which is located in the RBD. 2022 Infection, genetics and evolution Introduction SARS_CoV_2 N501Y 24 29 RBD 55 58 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. Ostrov also confirmed this significant mutation associated with B.1.1.7 (N501Y), which increased the binding ability between the S-glycoprotein and ACE2 (Angiotensin-Converting Enzyme 2) receptor. 2022 Infection, genetics and evolution Introduction SARS_CoV_2 N501Y 73 78 S 129 143 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. The D614G mutation, also observed in S-glycoprotein, was reported in this variant and was related to increased infectivity and virion density. 2022 Infection, genetics and evolution Introduction SARS_CoV_2 D614G 4 9 S 37 51 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. The identified three important mutations were L452R, E484Q, and P681R. 2022 Infection, genetics and evolution Introduction SARS_CoV_2 E484Q;L452R;P681R 53;46;64 58;51;69 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. The major mutations observed were L452R, E484Q, and P681R. 2022 Infection, genetics and evolution Introduction SARS_CoV_2 E484Q;L452R;P681R 41;34;52 46;39;57 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. The variant has another mutation, P681H, located outside the RBD and near the furin cleavage site (S1/S2 furin cleavage). 2022 Infection, genetics and evolution Introduction SARS_CoV_2 P681H 34 39 RBD 61 64 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. This study was aimed in three directions to comprehend the biological and epidemiological properties of two emerging variants, namely B.1.1.7 (Alpha, UK origin) and B.1.617.2 (Delta, India origin).The first aim was to comprehend the comparative genomics such as country-wise and region-wise genome sequences and their submission patterns, the mutational landscape of two variants, and the structural landscape of significant mutations such as N501Y, D614G, L452R, E484Q, and P681R of these two variants. 2022 Infection, genetics and evolution Introduction SARS_CoV_2 D614G;E484Q;L452R;N501Y;P681R 450;464;457;443;475 455;469;462;448;480 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. While, E484Q has been reported to decrease neutralization in convalescent sera. 2022 Infection, genetics and evolution Introduction SARS_CoV_2 E484Q 7 12 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. Among these, the D614G clade was the most common and was first found in late January 2020 in China, according to a study conducted by. 2022 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G 17 22 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. An initial deletion of F140 (deletion of phenylalanine at position 140) in the N-terminal domain (NTD) N3 loop of spike protein in 36% virions and subsequently an E484K substitution in the receptor-binding domain (RBD) and later an insertion in the NTD N5 loop containing a new glycan sequence were observed on simultaneous passage and RNA sequencing. 2022 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 E484K;del 140 163;29 168;70 S;RBD;N 114;214;79 119;217;80 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. Earliest samples from the USA appeared to have been derived from China and belonged to basal or L84S clades, while subsequent infected samples associated with European clades, such as D614G/Q57H. 2022 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G;L84S;Q57H 184;96;190 189;100;194 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. High-frequency co-occurring mutations (R203K and G204R) contributed to decreasing structural flexibility. 2022 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 G204R;R203K 49;39 54;44 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. It harbors the K417N mutation responsible for immune escape and affects the binding of the spike protein to the ACE2 receptor 6 . 2022 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 K417N 15 20 S 91 96 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. showed that the variant with D614G mutation in the spike protein was the most widespread variant across the globe. 2022 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G 29 34 S 51 56 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. The study reported about the V25A mutation in the transmembrane domain, which is an important factor for the homopentameric conformation of E protein and a triple cysteine motif harboring mutation L39M, A41S, A41V, C43F, C43R, C43S, C44Y, and N45R predicted to inhibit the binding of E protein with spike glycoprotein. 2022 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 A41S;A41V;C43F;C43R;C43S;C44Y;L39M;N45R;V25A 203;209;215;221;227;233;197;243;29 207;213;219;225;231;237;201;247;33 S;E;E 299;140;284 317;141;285 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. These had two co-evolving NS mutants, which differ in RdRp (P323L) and spike (S) protein (D614G). 2022 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 D614G;P323L 90;60 95;65 S;RdRP;S 71;54;78 76;58;79 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. These were the N501Y (asparagine to tyrosine substitution at position 501 in the S gene) and the 69-70del (a deletion of 6 bases coding for histidine and valine at positions 69 and 70 in the S gene) mutations. 2022 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 N501Y;N501Y 15;22 20;73 S;S 81;191 82;192 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. This variant has the same mutation N501Y like the UK variant; however, the two variants are phylogenetically not related 4 . 2022 Frontiers in cellular and infection microbiology Introduction SARS_CoV_2 N501Y 35 40 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. BA.1.1 has additional R346K mutation compared to BA.1. 2022 MedComm Introduction SARS_CoV_2 R346K 22 27 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Multiple mutation sites at RBD, especially E484K mutation superimposed other mutations, may lead to breakthrough infection. 2022 MedComm Introduction SARS_CoV_2 E484K 43 48 RBD 27 30 35434714 Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern. And compared to the original strain of SARS-CoV-2, the D614G mutation makes the S protein more stable and more flexible, which makes the virus more infectious. 2022 MedComm Introduction SARS_CoV_2 D614G 55 60 S 80 81 35434714 Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern. For example, S protein of the D614G variants has a looser and wider trimer structure of RBD. 2022 MedComm Introduction SARS_CoV_2 D614G 30 35 RBD;S 88;13 91;14 35434714 Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern. In July 2020, it was reported that the strain with the spike protein D614G mutation in Europe is more contagious and may become the main form of the virus pandemic. 2022 MedComm Introduction SARS_CoV_2 D614G 69 74 S 55 60 35436320 Occurrence of a novel cleavage site for cathepsin G adjacent to the polybasic sequence within the proteolytically sensitive activation loop of the SARS-CoV-2 Omicron variant: The amino acid substitution N679K and P681H of the spike protein. Both Alpha and Delta variants have a mutation in the polybasic sequence, precisely at P681H and P681R, respectively compared to the B.1.1.529 lineage SARS-CoV-2 (Omicron) which has two amino acid substitutions at the polybasic sequence: N679K and P681H. 2022 PloS one Introduction SARS_CoV_2 N679K;P681H;P681H;P681R 237;86;247;96 242;91;252;101 35436320 Occurrence of a novel cleavage site for cathepsin G adjacent to the polybasic sequence within the proteolytically sensitive activation loop of the SARS-CoV-2 Omicron variant: The amino acid substitution N679K and P681H of the spike protein. These substitutions have also been described for C.1.2 (N679K) and in 11% of cases of C.1.2 (N679K and P681H) (doi.org/10.1101/2021.08.20.21262342). 2022 PloS one Introduction SARS_CoV_2 P681H;N679K;N679K 103;56;93 108;61;98 35454161 Mutational Effect of Some Major COVID-19 Variants on Binding of the S Protein to ACE2. As for E484K mutation, both Beta and Gamma variants contain it, but the Alpha variant does not. 2022 Biomolecules Introduction SARS_CoV_2 E484K 7 12 35454161 Mutational Effect of Some Major COVID-19 Variants on Binding of the S Protein to ACE2. As shown in Table 1, these three variants have one point in common:that is, the N501Y mutation, which was reported to accelerate the spread of virus through stronger binding with ACE2. 2022 Biomolecules Introduction SARS_CoV_2 N501Y 80 85 35454161 Mutational Effect of Some Major COVID-19 Variants on Binding of the S Protein to ACE2. The Delta variant received a lot of attention, and the L452R and T478K mutations are considered to be one of the main reasons for the accelerating spread of the virus. 2022 Biomolecules Introduction SARS_CoV_2 L452R;T478K 55;65 60;70 35454161 Mutational Effect of Some Major COVID-19 Variants on Binding of the S Protein to ACE2. The K417N was found in the Beta variant. 2022 Biomolecules Introduction SARS_CoV_2 K417N 4 9 35454161 Mutational Effect of Some Major COVID-19 Variants on Binding of the S Protein to ACE2. We first focus on five specific mutations (N501Y, E484K, L452R, T478K and K417N) that were found in Alpha, Beta Gamma and Delta variants, and these mutations are all located on the RBDs of the SARS-CoV-2/ACE2 complex. 2022 Biomolecules Introduction SARS_CoV_2 E484K;K417N;L452R;T478K;N501Y 50;74;57;64;43 55;79;62;69;48 RBD 181 185 35455241 Durability and Cross-Reactivity of SARS-CoV-2 mRNA Vaccine in Adolescent Children. Here, we quantified relative antibody responses in adolescent children immediately following the Pfizer-BioNTech mRNA vaccination and six months post-inoculation and analyzed the efficacy of the humoral response against the D614G ("wild type") SARS-CoV-2 and latest variant of concern (VOC), Omicron. 2022 Vaccines Introduction SARS_CoV_2 D614G 224 229 35456137 Comparative Evaluation of Six SARS-CoV-2 Real-Time RT-PCR Diagnostic Approaches Shows Substantial Genomic Variant-Dependent Intra- and Inter-Test Variability, Poor Interchangeability of Cycle Threshold and Complementary Turn-Around Times. The main aim of this study was to comparatively assess the variability of Ct values generated by six previously thoroughly evaluated rtRT-PCR assays and platforms by testing serial dilutions of well-characterized SARS-CoV-2 isolates of the clinically most relevant genomic variants (Alpha, Beta, Gamma, Delta, Eta, Iota, Omicron, A.27, B.1.258.17, and B.1 with D614G mutation). 2022 Pathogens (Basel, Switzerland) Introduction SARS_CoV_2 D614G 361 366 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. According to these studies, the Omicron mutations S477N, T478K and E484A targeting the flexible region of the RBM together with K417N account for the trade-off between a moderate loss of ACE2 binding and the neutralization escape potential of the Omicron variant from the antibodies that target RBM epitopes. 2022 International journal of molecular sciences Introduction SARS_CoV_2 E484A;K417N;S477N;T478K 67;128;50;57 72;133;55;62 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. According to this study, the mutations S477N, Q498R and N501Y increase ACE2 affinity by 37-fold, serving to anchor the RBD to ACE2, while allowing the RBD region freedom to develop further mutations, including those that reduce the ACE2 affinity in order to evade the neutralizing antibody response. 2022 International journal of molecular sciences Introduction SARS_CoV_2 N501Y;Q498R;S477N 56;46;39 61;51;44 RBD;RBD 119;151 122;154 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. Another cryo-EM investigation of the S Delta variant binding noticed that L452R is not involved in direct contacts with ACE2, while a T478K substitution could induce the conformational change of the RBM loop and strengthen the interaction with the ACE2 receptor, leading to the enhanced transmissibility of the Delta variant. 2022 International journal of molecular sciences Introduction SARS_CoV_2 L452R;T478K 74;134 79;139 S 37 38 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. By examining the structural and energetic bass of Omicron binding with ACE2, this study similarly asserted that the favorable interactions formed by the mutated sites S477N, Q493R, Q496S, Q498R and N501Y to ACE2 could compensate for the loss of polar interactions caused by the mutations K417N and E484A. 2022 International journal of molecular sciences Introduction SARS_CoV_2 E484A;K417N;N501Y;Q493R;Q496S;Q498R;S477N 298;288;198;174;181;188;167 303;293;203;179;186;193;172 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. Computational mutagenesis and free energy perturbation analysis showed that Omicron RBD binds to ACE2 approximately 2-3 times stronger than the native S protein, with three mutational sites T478K, Q493K and Q498R, enhancing binding affinity through more favorable electrostatic interactions. 2022 International journal of molecular sciences Introduction SARS_CoV_2 Q493K;Q498R;T478K 197;207;190 202;212;195 RBD;S 84;151 87;152 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. MD simulations combined with the Markov state modeling of conformational states and binding free energy calculations identified four key mutations (S477N, G496S, Q498R and N501Y) for the enhanced binding of ACE2 by the Omicron RBD. 2022 International journal of molecular sciences Introduction SARS_CoV_2 G496S;N501Y;Q498R;S477N 155;172;162;148 160;177;167;153 RBD 227 230 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. Molecular dynamics (MD) simulations were combined with microscale thermophoresis to examine the binding between Omicron RBD and ACE2, showing the enhanced RBD-ACE2 interactions of the N501Y, Q493R and T478K mutational sites and revealing that the Omicron RBD exhibits a five-fold higher binding affinity to ACE2 compared to the native RBD. 2022 International journal of molecular sciences Introduction SARS_CoV_2 N501Y;Q493R;T478K 184;191;201 189;196;206 RBD;RBD;RBD;RBD 120;155;255;335 123;158;258;338 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. Mutations present in the Omicron virus (S477N, E484K and N501Y) were preferentially selected by yeast surface display affinity maturation screen of RBD against ACE2. 2022 International journal of molecular sciences Introduction SARS_CoV_2 E484K;N501Y;S477N 47;57;40 52;62;45 RBD 148 151 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. Other structural studies found that membrane fusion for the S Delta protein is substantially faster than that of other variants, whereas the Delta mutational sites L452R and T478K are not in direct contact with ACE2 and have a smaller effect on ACE2 affinity. 2022 International journal of molecular sciences Introduction SARS_CoV_2 L452R;T478K 164;174 169;179 Membrane;S 36;60 44;61 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. Several structural studies suggested that the improved electrostatic complementarity induced by the L452R and T478K substitutions accounts for a moderate increase in ACE2 affinity. 2022 International journal of molecular sciences Introduction SARS_CoV_2 L452R;T478K 100;110 105;115 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. The comparison of binding affinity changes using a randomly mutated RBD screen displayed on the yeast surface for ACE2 binding showed the higher affinity for N501Y, E484K, S477N and Q498R, where the combination of Q498R and N501Y increased the binding affinity by 26-fold and adding the S477N mutation produced a 37-fold increase in the binding affinity. 2022 International journal of molecular sciences Introduction SARS_CoV_2 E484K;N501Y;N501Y;Q498R;Q498R;S477N;S477N 165;158;224;182;214;172;287 170;163;229;187;219;177;292 RBD 68 71 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. The cryo-EM structural analysis of the Omicron variant in the unbound form and in the complex with ACE2 revealed that the interactions mediated by the mutational sites Q493R, G496S, Q498R and N501Y may restore the ACE2 binding strength that is partly compromised by other mutations. 2022 International journal of molecular sciences Introduction SARS_CoV_2 G496S;N501Y;Q493R;Q498R 175;192;168;182 180;197;173;187 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. The cryo-EM study of the full-length S protein of the Omicron variant analyzed the binding and antigenic properties of the Omicron S trimer by bio-layer interferometry (BLI), confirming the improved binding due to the N501Y, Q493R and Q498R mutations, as was similarly asserted in recent studies. 2022 International journal of molecular sciences Introduction SARS_CoV_2 N501Y;Q493R;Q498R 218;225;235 223;230;240 S;S 37;131 38;132 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. The crystal and cryo-EM structures of the Omicron RBD-ACE2 complex and the X-ray structure of the Delta RBD-ACE2 complex identified the role of key residues for receptor recognition, showing that the mutations S477N, Q493R, Q498R and N501Y can enhance the binding affinity of RBD with ACE2, while T478K may influence ACE2 binding allosterically. 2022 International journal of molecular sciences Introduction SARS_CoV_2 N501Y;Q493R;Q498R;S477N;T478K 234;217;224;210;297 239;222;229;215;302 RBD;RBD;RBD 50;104;276 53;107;279 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. The structural analysis of the key interactions at the interface with ACE2 confirmed that T478K, Q493R, G496S and Q498R could strengthen the binding of the S Omicron to ACE2, with the N501Y mutation alone improving the binding affinity by sixfold. 2022 International journal of molecular sciences Introduction SARS_CoV_2 G496S;N501Y;Q493R;Q498R;T478K 104;184;97;114;90 109;189;102;119;95 S 156 157 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. This study found that the enhanced binding affinity of the S Omicron trimer to ACE2 is comparable to that of the S Delta, but is higher than that of the S-G614, which may be due to the increased RBM-ACE2 interaction network contributed by the Q493R, and Q498R, G496S and Y505H mutant sites. 2022 International journal of molecular sciences Introduction SARS_CoV_2 G496S;Q493R;Q498R;Y505H 261;243;254;271 266;248;259;276 S;S;S 59;113;153 60;114;154 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. We show that a constellation of mutational sites (G496S, Q498R, N501Y and Y505H) correspond to key binding energy hotspots and also contribute decisively to the key interfacial communities that mediate allosteric communications between S-RBD and ACE2. 2022 International journal of molecular sciences Introduction SARS_CoV_2 N501Y;Q498R;Y505H;G496S 64;57;74;50 69;62;79;55 RBD;S 238;236 241;237 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. Furthermore, inserting the E484K mutation into the S477N spike reduces the neutralizing sensitivity of these pseudoviruses to post vaccinated sera, with no effects on viral infectivity. 2022 Viruses Introduction SARS_CoV_2 E484K;S477N 27;51 32;56 S 57 62 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. Here we used pseudoviruses to monitor the effects of FCS-spike mutations of either Alpha/Omicron (P681H), Beta (A701V), or Delta (P681R) on viral infectivity and neutralization sensitivity against sera that was drawn from fully vaccinated individuals. 2022 Viruses Introduction SARS_CoV_2 A701V;P681H;P681R 112;98;130 117;103;135 S 57 62 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. However, adding a single N501Y-RBD mutation into the wild type spike carrying FCS mutations substantially enhanced viral infectivity relative to wild-type SARS-CoV-2, with no effect on neutralization sensitivity. 2022 Viruses Introduction SARS_CoV_2 N501Y 25 30 S;RBD 63;31 68;34 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. However, combining the RBD-N501Y mutation to S477N spike, enhances pseudoviral infectivity. 2022 Viruses Introduction SARS_CoV_2 S477N;N501Y 45;27 50;32 S;RBD 51;23 56;26 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. In addition, viral infectivity of Delta SARS-CoV-2 pseudovirus is increased x2-fold, while its single RBD mutations, L452R, and T478K or double L452R/T478K has no effect on infectivity levels. 2022 Viruses Introduction SARS_CoV_2 L452R;L452R;T478K;T478K 117;144;128;150 122;149;133;155 RBD 102 105 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. Like Alpha, Omicron carries a P681H mutation within its FCS region. 2022 Viruses Introduction SARS_CoV_2 P681H 30 35 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. Lota carries S477N/E484K mutations within its RBD, as well as a A701V-FCS mutation. 2022 Viruses Introduction SARS_CoV_2 A701V;S477N;E484K 64;13;19 69;18;24 RBD 46 49 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. Our analysis shows that the single S477N-RBD mutation has no impact on viral infectivity or neutralizing sensitivity to post vaccination sera. 2022 Viruses Introduction SARS_CoV_2 S477N 35 40 RBD 41 44 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. Our analysis shows that, similarly to Delta pseudoviruses that carry L452R, T478K, and P681R, pseudoviruses with single L452R or K478T RBB mutations display a moderate reduction in neutralization sensitivity relative to wild-type SARS-CoV-2. 2022 Viruses Introduction SARS_CoV_2 K478T;L452R;L452R;P681R;T478K 129;69;120;87;76 134;74;125;92;81 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. Similarly, adding the E484K-RBD mutation to pseudoviruses that carry an FCS-mutation decreased neutralization sensitivity against our tested sera, with no effects on viral infectivity. 2022 Viruses Introduction SARS_CoV_2 E484K 22 27 RBD 28 31 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. Single mutations within the FCS region were inserted to the wild-type Wuhan spike, as we demonstrated that single, P681H, V701A, and P681R FCS mutations have no role in viral infectivity or neutralization sensitivity. 2022 Viruses Introduction SARS_CoV_2 P681H;P681R;V701A 115;133;122 120;138;127 S 76 81 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. This process is driven by both escape from neutralizing antibodies, where mutations like E484K, E484Q, S477N play key roles, and increased binding affinity of spike to the receptor, N501Y, T478K, K417N, and D614G are important. 2022 Viruses Introduction SARS_CoV_2 D614G;E484K;E484Q;K417N;N501Y;S477N;T478K 207;89;96;196;182;103;189 212;94;101;201;187;108;194 S 159 164 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. We also tested the role of single mutations within Delta RBD-L452R, T478K, and the double L452R/T478K:on pseudovirus infectivity and neutralization sensitivity. 2022 Viruses Introduction SARS_CoV_2 L452R;T478K;T478K;L452R 90;68;96;61 95;73;101;66 RBD 57 60 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. While the involvement of mutations within the Receptor Binding Domain (RBD) of spike are extensively being tested for effects on antibody-neutralization and viral infectivity, the role of 681PRRAR/SV687 FCS mutations:P681H found in Alpha or Omicron, V701A in Beta or P681R in Delta:in affecting neutralization and infectivity levels have not been explored. 2022 Viruses Introduction SARS_CoV_2 P681R;V701A;P681H 267;250;217 272;255;222 RBD;S;RBD 46;79;71 69;84;74 35461042 Increased resistance of SARS-CoV-2 Lambda variant to antibody neutralization. In this study, we prepared SARS-CoV-2 pseudoviruses carrying distinct spike proteins of the Wuhan reference strain with D614G mutation (wild-type, D614G-WT) and Lambda variant, as well as L452Q/F490S, L452Q, or F490S mutations. 2022 Journal of clinical virology Introduction SARS_CoV_2 D614G;D614G;F490S;L452Q;L452Q;F490S 120;147;211;188;201;194 125;152;216;193;206;199 S 70 75 35461042 Increased resistance of SARS-CoV-2 Lambda variant to antibody neutralization. These results showed that plasma neutralization against Lambda variant is compromised by L452Q and F490S mutations, which destroyed or weakened the binding and neutralizing activities of some antibodies from Class 2 and 3. 2022 Journal of clinical virology Introduction SARS_CoV_2 F490S;L452Q 99;89 104;94 35474907 SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants. For example, the D614G and P681R mutations in the spike protein were associated with increased viral replication in human lung epithelial cells and enhanced viral pathogenicity, respectively. 2022 Computational and structural biotechnology journal Introduction SARS_CoV_2 D614G;P681R 17;27 22;32 S 50 55 35474907 SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants. Notably, some mutations, such as N439K and E484K, are thought to be related to protective immune responses. 2022 Computational and structural biotechnology journal Introduction SARS_CoV_2 E484K;N439K 43;33 48;38 32357545 Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment. Additionally, country-based statistics of the prevalence of 23403A>G variant (p.D614G) were generated, as shown in Table 2. 2020 Pathogens (Basel, Switzerland) Method SARS_CoV_2 A23403G;D614G;D614G 60;78;80 68;85;85 32511374 An insertion unique to SARS-CoV-2 exhibits superantigenic character strengthened by recent mutations. Two mutants associated with European Covid-19 patients were constructed using CHARMM-GUI: one is the main strain mutant D614G and the other contains four mutations including Q239K, A831V, D614G and D839Y. 2020 bioRxiv Method SARS_CoV_2 A831V;D614G;D614G;D839Y;Q239K 181;120;188;198;174 186;125;193;203;179 COVID-19 37 45 32577644 Beyond Shielding: The Roles of Glycans in SARS-CoV-2 Spike Protein. In the Mutant system, N165A and N234A mutations were introduced to remove the respective N-glycans. 2020 bioRxiv Method SARS_CoV_2 N165A;N234A 22;32 27;37 N 89 90 32587973 The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. Logo plots of D614G variation were generated by WebLogo after sequence alignment. 2020 bioRxiv Method SARS_CoV_2 D614G 14 19 32587973 The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity. To track D614G variation among SARS-CoV-2 isolates, S protein sequences were downloaded from GenBank and separated by the month. 2020 bioRxiv Method SARS_CoV_2 D614G 9 14 S 52 53 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Analysis of D614G frequency in published data. 2020 bioRxiv Method SARS_CoV_2 D614G 12 17 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Single-cycle HIV-1 vectors pseudotyped with SARS-CoV-2 Spike protein, either D614 or D614G, were produced by transfection of either HIV-1 pNL4-3 Deltaenv Deltavpr luciferase reporter plasmid (pNL4-3.Luc.R-E-), or pUC57mini NL4-3 Deltaenv eGFP reporter plasmid, in combination with the indicated Spike expression plasmid, at a ratio of 4:1. 2020 bioRxiv Method SARS_CoV_2 D614G 85 90 S;S 55;295 60;300 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The frequency of D614G was calculated in the resulting data by extracting the sequence region corresponding to the gene for the S protein, spanning 21563-25384bp. 2020 bioRxiv Method SARS_CoV_2 D614G 17 22 S 128 129 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The frequency of the SARS-CoV-2 D614G S protein variant in published genomic data was examined using the full Nextstrain-curated set of sequences available from GISAID as of 25 June 2020. 2020 bioRxiv Method SARS_CoV_2 D614G 32 37 S 38 39 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The frequency was calculated as (# sequences with D614G)/(# sequences). 2020 bioRxiv Method SARS_CoV_2 D614G 50 55 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The script for analyzing and plotting D614G variant frequency is available via GitHub: https://gist.github.com/tomkinsc/c3fa656b0c833db6d3a2c579b74dcc4f. 2020 bioRxiv Method SARS_CoV_2 D614G 38 43 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. A recurrent amino acid change like L5F (Figure 7) could potentially result from a recurrent sequencing or sequence processing error, or alternatively, it may be of particular interest if it is naturally recurring homoplasy. 2020 Cell Method SARS_CoV_2 L5F 35 38 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. As somewhat expected, the D614G status is not statistically significant, even though viral load is, but the coefficient goes in the opposite direction than we would have intuited: a lower viral load is predictive of a higher probability of hospitalization. 2020 Cell Method SARS_CoV_2 D614G 26 31 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Results comparing D614G status for the two methods were also evaluated independently, and the first method showed a significant association between lower Ct values and presence of G614 (Wilcoxon p = 0.033), but the second method, with many fewer samples, did not reach significance. 2020 Cell Method SARS_CoV_2 D614G 18 23 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. The D614G amino acid change was introduced into VRC7480 by site-directed mutagenesis using the QuikChange Lightning Site-Directed Mutagenesis Kit from Agilent Technologies (Catalog # 210518). 2020 Cell Method SARS_CoV_2 D614G 4 9 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. The D614G variant was generated by site-directed mutagenesis. 2020 Cell Method SARS_CoV_2 D614G 4 9 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. The simple Fisher's exact test analysis in Figure 5 indicates that the D614G status is not predictive of hospitalization, even though it is predictive of viral load. 2020 Cell Method SARS_CoV_2 D614G 71 76 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. This revealed that only the PCR method and the D614G variant were statistically significant. 2020 Cell Method SARS_CoV_2 D614G 47 52 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. To assess the impact of available clinical parameters on viral load as measured by PCR Cts, we used a linear model, predicting Ct from PCR method, Sex, Age and D614G variant. 2020 Cell Method SARS_CoV_2 D614G 160 165 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. To explore this hypothesis, we "unmask" the aa614G by using the residuals from the regression of Ct on extraction method and D614G status to get a second predictive model for hospitalization. 2020 Cell Method SARS_CoV_2 D614G 125 130 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. We can make a first analysis to predict hospitalization from viral load, gender, age and D614G status. 2020 Cell Method SARS_CoV_2 D614G 89 94 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. We discovered a sequencing processing error that gave rise to what appeared at first to be a mutation of interest at position 943 (24389 A > C and 24390 C > G) in Spike that was evident in sequences from Belgium. 2020 Cell Method SARS_CoV_2 C24390G;A24389C 147;131 158;142 S 163 168 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. The D614G substitution was introduced with a single gBlock spanning the AspI and RsrII sites and Gibson assembly (NEB). 2020 bioRxiv Method SARS_CoV_2 D614G 4 9 32756549 SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness. Codon-optimized wild-type (D614) or D614G spike gene (Wuhan-Hu-1 strain, NCBI Reference Sequence #: NC_045512.2) was cloned into pCAGGS vector. 2020 Nature Method SARS_CoV_2 D614G 36 41 S 42 47 32756549 SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness. This virus contains two mutations (Q498T/P499Y) in the receptor binding domain (RBD) that allow binding of SARS-CoV-2 spike to the mouse angiotensin-converting enzyme 2 (ACE2) receptor and infection and replication in the upper and lower respiratory tract. 2020 Nature Method SARS_CoV_2 Q498T;P499Y 35;41 40;46 RBD;S;RBD 55;118;80 78;123;83 32779780 Atomistic simulation reveals structural mechanisms underlying D614G spike glycoprotein-enhanced fitness in SARS-COV-2. D614G mutant was generated using mutagenesis plugin in PyMol. 2020 Journal of computational chemistry Method SARS_CoV_2 D614G 0 5 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. A total of 2,803 genomes of SARS-CoV-2 (excluding non-human sequences specimens) and demographics when available were obtained from GISAID (https://gisaid.org/) (downloaded on 30 March 2020) to perform the statistical analyses of the D614G mutation (8 sequences were excluded due to ambiguous or unknown nucleotide at this position). 2020 Scientific reports Method SARS_CoV_2 D614G 234 239 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. We replaced the aspartate residue in position 614 by glycine using the "Rotamers" function in Chimera with default parameters. 2020 Scientific reports Method SARS_CoV_2 D614G 16 60 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The R408I, L455Y, F486L, Q493N, Q498Y, N501T mutations on the RBD region and A930V, D936Y mutations on the HR1 domain were mutated at respective positions (Figure 2). 2022 Journal of biomolecular structure & dynamics Method SARS_CoV_2 A930V;D936Y;F486L;L455Y;N501T;Q493N;Q498Y;R408I 77;84;18;11;39;25;32;4 82;89;23;16;44;30;37;9 RBD 62 65 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. Cumulative frequency of D614G, clades (19A, 19B, 20A, 20B, 20C), and P323L/F were calculated at each time point based on the total number of specimens up to the indicated date. 2020 medRxiv Method SARS_CoV_2 D614G;P323F;P323L 24;69;69 29;76;76 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. The original proline (P) was mutated to either leucine (L) or phenylalanine (F) as indicated, these residues along with residues containing side chains within 5 A of P323L/F are shown as sticks. 2020 medRxiv Method SARS_CoV_2 P323F;P323L 166;166 173;173 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. The P323F amino acid changes were confirmed with the NCBI deposited nucleotide sequences. 2020 medRxiv Method SARS_CoV_2 P323F 4 9 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. The rotamers for each P323L/F were assessed and those with the least rotational strain and steric hindrance were used to generate the final image. 2020 medRxiv Method SARS_CoV_2 P323F;P323L 22;22 29;29 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. To determine any NCBI deposited sequences which contain the P323F variant, standard protein BLAST from the BLASTp suite was used to find nsp12 protein sequences which contained FSTVFPFTSFGP (P323F is bold and underlined) from full length SARS-CoV-2 genomes. 2020 medRxiv Method SARS_CoV_2 P323F;P323F 60;191 65;196 Nsp12 137 142 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. Further, Boceprevir was subjected to dock within the active site of R60C mutant. 2020 PloS one Method SARS_CoV_2 R60C 68 72 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. The structure of Boceprevir in complex with Mpro (WT) and R60C mutant was subjected to energy minimization using Gromacs-5 with the CHARMM27 all atom force field. 2020 PloS one Method SARS_CoV_2 R60C 58 62 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. The structure of R60C was generated by inserting the Point mutation and modelled using modeler 9v13. 2020 PloS one Method SARS_CoV_2 R60C 17 21 32895623 Crystal structure of SARS-CoV-2 papain-like protease. C111S mutant was concentrated to 10 mg/mL before crystallization. 2021 Acta pharmaceutica Sinica. B Method SARS_CoV_2 C111S 0 5 32895623 Crystal structure of SARS-CoV-2 papain-like protease. Crystallization trials of C-terminal His-tagged C111S PLpro mutant was performed in a hanging drop vapor diffusion system at 18C. 2021 Acta pharmaceutica Sinica. B Method SARS_CoV_2 C111S 48 53 32895623 Crystal structure of SARS-CoV-2 papain-like protease. The plasmid expressing C111S mutant was constructed using site-directed mutagenesis (QuickChange). 2021 Acta pharmaceutica Sinica. B Method SARS_CoV_2 C111S 23 28 32905045 Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. Structural modeling of location of D614G was done using Mol*. 2020 Cell reports. Medicine Method SARS_CoV_2 D614G 35 40 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. For construction of D614G mNeonGreen SARS-CoV-2, seven SARS-CoV-2 genome fragments (F1 to F5, F6 containing D614G mutation, and F7-mNG containing the mNeonGreen reporter gene) were prepared and in vitro ligated as described previously. 2020 bioRxiv Method SARS_CoV_2 D614G;D614G 20;108 25;113 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Generation of SARS-CoV-2 spike D614G mutant viruses. 2020 bioRxiv Method SARS_CoV_2 D614G 31 36 S 25 30 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. The D614G mutation from the recovered viruses was confirmed by sequence analysis. 2020 bioRxiv Method SARS_CoV_2 D614G 4 9 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. The full-length infectious cDNA clone of SARS-CoV-2 D614G was assembled by in vitro ligation of seven contiguous cDNA fragments following the protocol previously described. 2020 bioRxiv Method SARS_CoV_2 D614G 52 57 32933378 Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach. Mutation (P323L) of the wild-type Nsp12 protein was created in Maestro program and mutant structure was prepared by following the same procedure as wild-type. 2022 Journal of biomolecular structure & dynamics Method SARS_CoV_2 P323L 10 15 Nsp12 34 39 32935099 SARS-CoV-2 infection severity is linked to superior humoral immunity against the spike. D614G spike protein, SARS-CoV-1 RBD, and MERS-CoV RBD were generated in-house and expressed in HEK293F cells. 2020 bioRxiv Method SARS_CoV_2 D614G 0 5 S;RBD;RBD 6;32;50 11;35;53 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. To compare the effect of 5-FU treatment on the progeny titers of wt and nsp14-E191D rMERS-CoV, confluent monolayers of HuH7 were incubated for 30 min at 37 C with solvent or a range of 5-FU concentrations. 2020 Journal of virology Method SARS_CoV_2 E191D 78 83 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. Final enzyme concentrations in the reaction mixtures were 0.15 mum for WT, S861A, S861G, and S861P mutants, and 0.45 mum for the V557L mutant. 2020 The Journal of biological chemistry Method SARS_CoV_2 S861A;S861G;S861P;V557L 75;82;93;129 80;87;98;134 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. Five independent preparations of RDV-embedded RNA templates and at least three independent preparations of SARS-CoV-2 WT and V557L mutant enzymes were used in this study. 2020 The Journal of biological chemistry Method SARS_CoV_2 V557L 125 130 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. RNA synthesis assays by SARS-CoV-2 RdRp complex on an RNA template with embedded remdesivir (5'-pUUUGUUGUURUUUUUCGCGU-3', where underlined portion is complementary to the RNA primer 5'-pACGC), or with adenosine at the equivalent position (5'-pUUUGUUGUUAUUUUUCGCGU-3'), data acquisition and quantification were done as previously reported by us with the following adjustments: reaction mixtures contained ~5 mum RNA template, and enzyme concentrations were increased to ~1 mum for the WT and ~1.5 mum for the V557L mutant RdRp complexes to favor the full template-length RNA synthesis. 2020 The Journal of biological chemistry Method SARS_CoV_2 V557L 508 513 RdRP;RdRP 35;521 39;525 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. SARS-CoV-2 RdRp WT and mutant (V557L, S861A, S861G, and S861P) were expressed and purified as we reported previously. 2020 The Journal of biological chemistry Method SARS_CoV_2 S861A;S861G;S861P;V557L 38;45;56;31 43;50;61;36 RdRP 11 15 32989130 Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation. Two mutants associated with European COVID-19 patients were constructed using CHARMM-GUI: one is the main strain mutant D614G, and the other contains four mutations including Q239K, A831V, D614G, and D839Y. 2020 Proc Natl Acad Sci U S A Method SARS_CoV_2 A831V;D614G;D614G;D839Y;Q239K 182;120;189;200;175 187;125;194;205;180 COVID-19 37 45 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. 3 muL of enriched D614G trimers, at 2.5 mg/mL, was deposited on an UltrAuFoil R1.2/1.3 300 mesh grid that had been glow discharged for 30 s in a GloQube Plus Glow Discharge System. 2020 Cell Method SARS_CoV_2 D614G 18 23 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Analysis of D614G frequency in the public database. 2020 Cell Method SARS_CoV_2 D614G 12 17 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Following the capture of the ACE2.Fc on the anti-human Fc mAb immobilized surface, 0.78 nM - 50 nM, two-fold serial dilutions, in duplicate, of soluble SARS-CoV-2 spike trimer protein, D614 or D614G, were injected for 3 min at a flow rate of 50 mL/min, with a 2 min dissociation phase in the running buffer. 2020 Cell Method SARS_CoV_2 D614G 193 198 S 163 168 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Single-cycle HIV-1 vectors pseudotyped with SARS-CoV-2 Spike protein, either D614 or D614G, were produced by transfection of either HIV-1 pNL4-3 Deltaenv Deltavpr luciferase reporter plasmid (pNL4-3.Luc.R-E-), or pUC57mini NL4-3 Deltaenv eGFP reporter plasmid, in combination with the indicated Spike expression plasmid, at a ratio of 4:1. 2020 Cell Method SARS_CoV_2 D614G 85 90 S;S 55;295 60;300 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The diversity of SNPs and their functional effects based on the same GISAID sequences and MAFFT alignment used to plot the frequency of D614G over time, with the 5' and 3' ends not masked. 2020 Cell Method SARS_CoV_2 D614G 136 141 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The frequency of D614G was calculated in the resulting data by extracting the sequence region corresponding to the gene for the S protein, spanning 21563-25384bp. 2020 Cell Method SARS_CoV_2 D614G 17 22 S 128 129 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The frequency of the SARS-CoV-2 D614G S protein variant in published genomic data was examined using the full Nextstrain-curated set of sequences available from GISAID as of 25 June 2020. 2020 Cell Method SARS_CoV_2 D614G 32 37 S 38 39 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The frequency was calculated as (# sequences with D614G)/(# sequences). 2020 Cell Method SARS_CoV_2 D614G 50 55 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The script for analyzing and plotting D614G variant frequency is available via GitHub: https://github.com/broadinstitute/sc2-variation-scripts. 2020 Cell Method SARS_CoV_2 D614G 38 43 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. Briefly, MLV-gag/pol and MLV-CMV plasmids was co-transfected into HEK293T cells along with full-length or P384A SARS-CoV-2 spike plasmids using Lipofectamine 2000 to produce pseudoviruses competent for single-round infection. 2020 bioRxiv Method SARS_CoV_2 P384A 106 111 S 123 128 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. The P986K and P987V mutations were introduced to S-2P trimer to generate wide type S trimer using FoldX. 2021 Briefings in bioinformatics Method SARS_CoV_2 P986K;P987V 4;14 9;19 S;S 49;83 50;84 33024961 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Table S3 includes one additional mutation, G24047A, from a later download, in order to represent Korber variant A829T/S. 2020 Research square Method SARS_CoV_2 A829T;A829S;G24047A 112;112;43 119;119;50 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. A 1547bp fragment containing the D614G site was amplified from each RNA samples by RT-PCR using primer set: 5'-GTAATTAGAGGTGATGAAGTCAGAC-3' and 5'-GAACATTCTGTGTAACTCCAATACC-3'. 2020 bioRxiv Method SARS_CoV_2 D614G 33 38 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Diluted antibodies or sera were mixed with 189 PFU/well WT-nLuc or D614G-nLuc virus, and the mixtures were incubated at 37 C for 1 hour. 2020 bioRxiv Method SARS_CoV_2 D614G 67 72 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Exocellular SARS-CoV-2 virions were collected from WT or D614G infected LAE culture by gently washing intact apical surface with 100uL PBS. 2020 bioRxiv Method SARS_CoV_2 D614G 57 62 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Hamsters were infected with 103 PFU of WT or D614G viruses intranasally under isoflurane anesthesia. 2020 bioRxiv Method SARS_CoV_2 D614G 45 50 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. LAE cultures from one donor were infected with MOI of 0.5 of WT and D614G mixture at 1:1 and 10:1 ratios. 2020 bioRxiv Method SARS_CoV_2 D614G 68 73 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. Mice were infected with 105 PFU of WT or D614G viruses intranasally under ketamine/xylazine anesthesia. 2020 bioRxiv Method SARS_CoV_2 D614G 41 46 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. The cells were infected with WT-nLuc or D614G-nLuc viruses at MOI of 0.1. 2020 bioRxiv Method SARS_CoV_2 D614G 40 45 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. To evaluate indirect virus transmission between hamsters, groups of hamsters (n=8 per group) were infected with 103 PFU of WT or D614G viruses intranasally under isoflurane anesthesia. 2020 bioRxiv Method SARS_CoV_2 D614G 129 134 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. To generate the D614G and D614G-nLuc variants, the amino acid substation was introduced into the S gene in the plasmid F and coupled with plasmid G with or without nLuc insertion in the ORF7a. 2020 bioRxiv Method SARS_CoV_2 D614G;D614G 16;26 21;31 ORF7a;S 186;97 191;98 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. WT and D614G competition assay and BstCI digestion. 2020 bioRxiv Method SARS_CoV_2 D614G 7 12 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. WT or D614G infected primary cell cultures were submerged in fixative (4% paraformaldehyde, 2.5% glutaraldehyde and 0.1 M sodium cacodylate) overnight. 2020 bioRxiv Method SARS_CoV_2 D614G 6 11 33024969 SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo. WT or D614G-infected LAE ALI cultures were fixed twice for 20 minutes in 4% formaldehyde in PBS and stored in PBS. 2020 bioRxiv Method SARS_CoV_2 D614G 6 11 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Protein-protein docking of WT (D614) and mutant (D614G) S protein (PDB ID 6VSB) with furin (PDB ID: 4Z2A) was done with the HDOCK server, which is based on a hybrid algorithm of template-based modeling and ab initio free docking. 2021 International journal of infectious diseases Method SARS_CoV_2 D614G 49 54 S 56 57 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. The DynaMut webserver was used to predict the effect of genetic variants on the stability and flexibility of D614G mutant S protein. 2021 International journal of infectious diseases Method SARS_CoV_2 D614G 109 114 S 122 123 33080267 Designed variants of ACE2-Fc that decouple anti-SARS-CoV-2 activities from unwanted cardiovascular effects. ACE2-Fc Arg273Ala, His378Ala and Glu402Ala, and wild-type ACE2-Fc selected for scaled production were produced from clonal stable-expressing cells. 2020 International journal of biological macromolecules Method SARS_CoV_2 R273A;R273A;E402A;E402A;H378A;H378A 9;8;34;33;20;19 17;17;42;42;29;28 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. An additional solvated model of RdRp was built to help assess the P323L mutation. 2020 NPJ vaccines Method SARS_CoV_2 P323L 66 71 RdRP 32 36 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. For construction of D614G mNeonGreen SARS-CoV-2, seven SARS-CoV-2 genome fragments (F1 to F5, F6 containing D614G mutation, and F7-mNG containing the mNeonGreen reporter gene) were prepared and in vitro ligated as described previously. 2021 Nature Method SARS_CoV_2 D614G;D614G 20;108 25;113 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. Generation of SARS-CoV-2 spike D614G mutant viruses. 2021 Nature Method SARS_CoV_2 D614G 31 36 S 25 30 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. The D614G mutation from the recovered viruses was confirmed by sequence analysis. 2021 Nature Method SARS_CoV_2 D614G 4 9 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. The full-length infectious cDNA clone of SARS-CoV-2 D614G was assembled by in vitro ligation of seven contiguous cDNA fragments following the protocol previously described. 2021 Nature Method SARS_CoV_2 D614G 52 57 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. Reaction mixtures contained 25muL of 2X GoTaq Promega Master mix (#M712C), 2.5muL primers (0.5muM), and brought to volume with nuclease-free water. 2020 Cell reports Method SARS_CoV_2 M712C 67 72 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. A mutant clone introducing the D614G change was created by site-directed mutagenesis. 2021 Journal of virology Method SARS_CoV_2 D614G 31 36 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. Finally, the first 4,242 genome sequences from Spain deposited in GISAID were used to investigate the prevalence of the D614G mutation throughout the epidemic. 2021 Journal of virology Method SARS_CoV_2 D614G 120 125 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. In order to assess the temporal variation in the proportion of D839Y mutation among sequenced samples, a binomial regression model with logarithmic link function was applied. 2020 Emerging microbes & infections Method SARS_CoV_2 D839Y 63 68 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. The genome sequences with the D839Y mutation detected abroad were downloaded from GISAD (Table S2) and subjected to clade classification and integration into "global" and Portugal phylogeny using Nextstrain (https://nextstrain.org/ncov) and Nextclade (https://clades.nextstrain.org/). 2020 Emerging microbes & infections Method SARS_CoV_2 D839Y 30 35 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. To explore the frequency of Spike D839Y variant at worldwide level, we downloaded all the amino acid sequences (and associated metadata) of SARS-CoV-2 spike protein available at GISAID (as of 23 July 2020). 2020 Emerging microbes & infections Method SARS_CoV_2 D839Y 34 39 S;S 28;151 33;156 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. Plaque forming unit (PFU) per ml of recombinant S-614D and S614-G viruses were determined by plaque assay in a 24-well format. 2020 bioRxiv Method SARS_CoV_2 S614G 59 65 S 48 49 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. Recombinant SARS-CoV-2 proteins S1-614D and S1-614G with polyhistidine-tag (Cat: 40591-V08H, 40591-V08H3) were purchased from Sino Biological. 2020 bioRxiv Method SARS_CoV_2 V08H;V08H 87;99 91;103 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. The sequence-specific primers were used to generate an amplicon of 905 bp covering the D614G region: 5'-AATCTATCAGGCCGGTAGCAC-3' and 5'-CAACAGCTATTCCAGTTAAAGCAC-3'. 2020 bioRxiv Method SARS_CoV_2 D614G 87 92 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. If the T to G mutation occurred at this position, then aspartate is replaced by glycine at position 614 of the amino acid chain, called S-G type. 2020 Infection, genetics and evolution Method SARS_CoV_2 D614G 55 103 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. It is noteworthy that we observed two nucleotides with a nonnegligible variation frequency relative to their neighboring regions: 1) C241T (5' UTR) with a variation frequency of 45.5% (and this nucleotide was in high allelic association with C3037T [nsp3, F924F], C14408T [nsp12, P4715L], and A23403G [S protein, D614G]) and 2) G29742T (3' UTR) or G29742A (3' UTR) with a variation frequency of 5.3%. 2020 Proc Natl Acad Sci U S A Method SARS_CoV_2 A23403G;C14408T;C241T;C3037T;D614G;F924F;G29742A;G29742T;P4715L 293;264;133;242;313;256;348;328;280 300;271;138;248;318;261;355;335;286 3'UTR;3'UTR;5'UTR;Nsp12;Nsp3;S 337;357;140;273;250;302 343;363;146;278;254;303 33185784 Comparison of Binding Site of Remdesivir and Its Metabolites with NSP12-NSP7-NSP8, and NSP3 of SARS CoV-2 Virus and Alternative Potential Drugs for COVID-19 Treatment. To validate these experimental data, the crystal structure of NSP12 (wild type) and V557L were generated and superimposed by SYBYL-X2.1. 2020 The protein journal Method SARS_CoV_2 V557L 84 89 Nsp12 62 67 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. and XDS, and the C145A mutant with the CrysAlis Pro software suite (Rigaku Inc.). 2020 Nature communications Method SARS_CoV_2 C145A 17 22 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Because the C145A mutant is inactive, wild-type, His-tagged Mpro was added to the eluate from the initial IMAC step at a 40:1 ratio, and the mixture was dialyzed overnight against 50 mM Tris pH 8.0, 300 mM NaCl. 2020 Nature communications Method SARS_CoV_2 C145A 12 17 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Both wild-type acyl-enzyme and C145A mutant product complex crystals belong to space group C2 with isomorphous unit cell dimensions and two molecules in the asymmetric unit (Supplementary Table 1). 2020 Nature communications Method SARS_CoV_2 C145A 31 36 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Crystals of the wild-type acyl-enzyme or C145A mutant product complexes were obtained by sitting drop vapor diffusion using 0.8 muL of protein (~10 mg/mL) and 0.8 muL reservoir containing 0.1 M MES pH 6, 10-16% PEG 3350, and 5% MPD. 2020 Nature communications Method SARS_CoV_2 C145A 41 46 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Diffraction data were collected at 100 K on beamline 23-ID-B at the Advanced Photon Source (wild-type acyl-enzyme and substrate free; 1.03317 A wavelength), or on a Rigaku MicroMax 007 HF generator equipped with Osmic VariMax optics and a Dectris Pilatus3 R 200 K detector (C145A mutant; 1.5417 A wavelength). 2020 Nature communications Method SARS_CoV_2 R200K;C145A 256;274 263;279 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. For the P9T Mpro sample, chain A of the same structure was compared to the experimental data, with rather poor fit. 2020 Nature communications Method SARS_CoV_2 P9T 8 11 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. For the wild-type and P9T mutant protein, which cleave off the N-terminal GST tag during expression to leave the native N-terminus, the eluate was concentrated by ultrafiltration (Amicon Ultra-30; Millipore Sigma) and the buffer was exchanged into 50 mM Tris pH 8, 300 mM NaCl, and 1 mM DTT to a final volume of 3 mL. 2020 Nature communications Method SARS_CoV_2 P9T 22 25 N;N 63;120 64;121 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Mutant C145A was generated using QuickChange site-directed mutagenesis (Supplementary Table 3). 2020 Nature communications Method SARS_CoV_2 C145A 7 12 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Mutant P9T was a point mutant from cloning the full-length gene. 2020 Nature communications Method SARS_CoV_2 P9T 7 10 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Scattering profiles of purified wild-type SARS-CoV-2 Mpro were collected at 9.63, 4.82, 2.41, and 1.20 mg/mL and the P9T Mpro variant at 24.49, 12.25, 6.12, 3.06, 1.53, and 0.77 mg/mL. 2020 Nature communications Method SARS_CoV_2 P9T 117 120 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. The C145A product complex has a Molprobity score of 1.74, clashscore of 2.67 and 97.04% Ramachandran favored, and 0.33% Ramachandran outliers. 2020 Nature communications Method SARS_CoV_2 C145A 4 9 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. The molar masses of wild-type Mpro and the P9T variant were determined at 22 C with a size-exclusion chromatography system equipped with a Superdex 200 HR 10/300 GL column (GE Healthcare), an Agilent 1100 series HPLC pump and UV detector (Agilent Technologies), a Dawn Heleos II 16-angle light-scattering detection module and an Optilab T-rEX differential refractometer (Wyatt Technology). 2020 Nature communications Method SARS_CoV_2 P9T 43 46 33208827 Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19. Site-directed mutagenesis was used to generate the D614G variant by changing nucleotide at position 23403 (Wuhan-Hu-1 reference strain) from A to G. 2020 Scientific reports Method SARS_CoV_2 D614G 51 56 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Logo plots of D614G variation were generated by WebLogo version 3 after sequence alignment. 2020 Nature communications Method SARS_CoV_2 D614G 14 19 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. To track the D614G variation among SARS-CoV-2 isolates, S protein sequences were downloaded from GenBank by searching for "SARS-CoV-2 spike" and by filtering the result based on sequence length "1272-1273" to retrieve full-length S protein. 2020 Nature communications Method SARS_CoV_2 D614G 13 18 S;S;S 134;56;230 139;57;231 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Five RBD mutants were considered in the study (S494P, V483A, G476S, A348T, and V367F). 2021 Biochemical and biophysical research communications Method SARS_CoV_2 A348T;G476S;V367F;V483A;S494P 68;61;79;54;47 73;66;84;59;52 RBD 5 8 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. The RBD-ACE2 complexes for wild-type, V367F, and S494P, obtained from the protein-protein docking refinement, were then studied by molecular dynamics simulation using the AMBER-ILDN force field with the aid of GROMACS 2018.1 package. 2021 Biochemical and biophysical research communications Method SARS_CoV_2 S494P;V367F 49;38 54;43 RBD 4 7 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. Briefly, MLV-gag/pol and MLV-CMV plasmids was co-transfected into HEK293T cells along with full-length or P384A SARS-CoV-2 spike plasmids using Lipofectamine 2000 to produce pseudoviruses competent for single-round infection. 2020 PLoS pathogens Method SARS_CoV_2 P384A 106 111 S 123 128 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Code to reproduce this analysis can be found at https://github.com/COG-UK/D614G_spike_mutation_analysis (https://doi.org/10.5281/zenodo.4095529). 2021 Cell Method SARS_CoV_2 D614G 74 79 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Finally, to account for correlations driven by genome similarity that are not due to the D614G mutation, we generated a variance-covariance matrix (scaled to a correlation matrix) from the phylogeny described above (after dropping all tips corresponding to genomes not in the dataset) using the ape package v. 2021 Cell Method SARS_CoV_2 D614G 89 94 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Our model included the presence of the D614G mutation and the biological sex of the patient as categorical predictors, as well as age and the time since the first case in the dataset as non-linear predictors. 2021 Cell Method SARS_CoV_2 D614G 39 44 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. To control for the effect of other mutations in the genome, we generated a time tree of the virus genomes from Scotland using an HKY + Gamma nucleotide model excluding the nucleotide position underlying the D614G mutation. 2021 Cell Method SARS_CoV_2 D614G 207 212 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. We masked the nucleotide causing the D614G mutation, as well as all mutations recommended by De Maio et al. 2021 Cell Method SARS_CoV_2 D614G 37 42 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. We used a phylogenetic generalized additive model to investigate the viral D614G polymorphism and association with severity of the infection. 2021 Cell Method SARS_CoV_2 D614G 75 80 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. SARS-CoV-2/IZSAM/46419 sequence differs from that of SARS-CoV-2/INMI1-Isolate/2020/Italy for 241C > T, 3037C > T, 14408C > T and 23403A > G. 2021 Veterinary microbiology Method SARS_CoV_2 C14408T;A23403G;C241T;C3037T 114;129;93;103 124;139;101;112 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. Therefore, SARS-CoV-2/INMI1-Isolate/2020/Italy is indicated as D614 throughout the manuscript, while SARS-CoV-2/IZSAM/46419 as D614G. 2021 Veterinary microbiology Method SARS_CoV_2 D614G 127 132 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. This latter leads to the non-synonymous mutation in the S protein encoding gene, D614G. 2021 Veterinary microbiology Method SARS_CoV_2 D614G 81 86 S 56 57 33292056 Sensing the interactions between carbohydrate-binding agents and N-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies. Also, the various plant lectins like NPA with PDB ID: 1NPL (Sauerborn et al.,), UDA with PDB ID: 1EHD (Harata & Muraki,), BanLec of wild-type (PDB ID: 3MIT) (Sharma & Vijayan,) and H84T mutant type (PDB ID: 4PIT) (Swanson et al., 2015), lectins from algal and cyanobacterial origin like GRFT (PDB ID: 2GUD) (Ziolkowska et al.,) and CV-N with PDB ID: 3GXZ (Botos et al.,), respectively, were retrieved from the PDB databank for the macromolecular docking studies with SARS CoV-2 S glycoprotein. 2020 Journal of biomolecular structure & dynamics Method SARS_CoV_2 H84T 181 185 S;N 478;335 492;336 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. Samples of S-GSAS and S-GSAS (D614G) ectodomain constructs were diluted to 100 mug/mL with room-temperature buffer containing 20 mM HEPES pH 7.4, 150 mM NaCl, 5% glycerol and 7.5 mM glutaraldehyde, and incubated 5 min; then glutaraldehyde was quenched for 5 min by addition of 1M Tris stock to a final concentration of 75 mM. 2021 Cell host & microbe Method SARS_CoV_2 D614G 30 35 S;S 11;22 12;23 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. The D614G amino acid change was introduced into VRC7480 by site-directed mutagenesis using the QuikChange Lightning Site-Directed Mutagenesis Kit from Agilent Technologies (Catalog # 210518). 2021 Cell host & microbe Method SARS_CoV_2 D614G 4 9 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. The S-GSAS template was used to include the D614G mutation (S-GSAS(D614G)). 2021 Cell host & microbe Method SARS_CoV_2 D614G;D614G 44;67 49;72 S;S 4;60 5;61 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. Variants, including the A-to-G change at nucleotide 23,403 leading to D614G, were called using nanopolish (https://github.com/jts/nanopolish) and consensus sequences compared to the reference. 2021 Cell host & microbe Method SARS_CoV_2 D614G 70 75 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. 293T cells were transfected with pcDNA3.1 plasmids expressing the wild-type or D614G SARS-CoV-2 S glycoproteins, which contain carboxy-terminal His6 tags, using Lipofectamine 3000. 2020 Journal of virology Method SARS_CoV_2 D614G 79 84 S 96 111 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Lentivirus particles containing the wild-type or D614G S gp prepared as described above were used to measure the binding of soluble ACE2 (sACE2) to the viral spike and to study the effect of sACE2 binding on the shedding of the S1 gp from the spike. 2020 Journal of virology Method SARS_CoV_2 D614G 49 54 S;S;S 158;243;55 163;248;56 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. To prepare lentivirus (HIV-1) particles containing wild-type or D614G S gp, ~7 x 106 293T cells in T75 flasks were transfected with 7.5 microg of psPAX2 and 7.5 microg of the S-expressing pcDNA3.1 plasmid using Lipofectamine 3000. 2020 Journal of virology Method SARS_CoV_2 D614G 64 69 S;S 70;175 71;176 33319124 Mutational insights into the envelope protein of SARS-CoV-2. Comparing the individual strain level mutations, we found that the S68F mutation in 250 strains (highest frequency) followed by L73F, R69I, and P71L mutations noticed in 100, 88, and 59 strains, respectively. 2021 Gene reports Method SARS_CoV_2 L73F;P71L;R69I;S68F 128;144;134;67 132;148;138;71 33319124 Mutational insights into the envelope protein of SARS-CoV-2. Highest aa mutations (n = 4) (C43R, C44Y, N45R, V47G) were found in a Moroccan strain of SARS-CoV-2 (EPI_ISL_467299) followed by two aa mutations in nine strains from England, Israel, Netherlands, Northern Ireland, Scotland, and Sierra Leone at different positions. 2021 Gene reports Method SARS_CoV_2 C44Y;N45R;V47G;C43R 36;42;48;30 40;46;52;34 33319124 Mutational insights into the envelope protein of SARS-CoV-2. Mutations (L39M, A41S, A41V, C43F, C43R, C43S, C44Y, N45R) in this interacting motif of the E protein were also evident in different strains (Supplementary Data 1). 2021 Gene reports Method SARS_CoV_2 A41S;A41V;C43F;C43R;C43S;C44Y;N45R;L39M 17;23;29;35;41;47;53;11 21;27;33;39;45;51;57;15 E 92 93 33319124 Mutational insights into the envelope protein of SARS-CoV-2. The C43F substitution was observed in six strains from England, Saudi Arabia, and the USA whereas C43R and C44Y mutations were noticed in two different strains of SARS-CoV-2 deposited to the GISAID from Morocco. 2021 Gene reports Method SARS_CoV_2 C43F;C43R;C44Y 4;98;107 8;102;111 33319124 Mutational insights into the envelope protein of SARS-CoV-2. Two aa mutations, N15A and V25F were found in the TMD which may abolish the ion channeling capability of SARS-CoV E viroporin structure, a key factor of its homopentameric conformation. 2021 Gene reports Method SARS_CoV_2 N15A;V25F 18;27 22;31 E 114 115 33319124 Mutational insights into the envelope protein of SARS-CoV-2. We also found C43S mutation in one of the Australian strains (Supplementary Data 1). 2021 Gene reports Method SARS_CoV_2 C43S 14 18 33319124 Mutational insights into the envelope protein of SARS-CoV-2. We observed the V25A mutation in six strains from Spain, Canada, and England that may hamper the oligomerization of the E protein of SARS-CoV-2, at least to some extent. 2021 Gene reports Method SARS_CoV_2 V25A 16 20 E 120 121 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. Additional spike protein expression vectors were pcCoV2.S-Delta19, pcCoV2.S-Delta19.D614G or the beta coronavirus RBD expression vectors. 2020 Cell reports Method SARS_CoV_2 D614G 84 89 S;RBD;S;S 11;114;56;74 16;117;57;75 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. The D614G mutation in S was generated by overlap extension PCR of the Delta19 S gene using internal primers overlapping the sequence encoding D614G and cloned into pcDNA6. 2020 Cell reports Method SARS_CoV_2 D614G;D614G 4;142 9;147 S;S 22;78 23;79 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. 20B emerged as a distinct clade in Europe with three consecutive mutations, e.g., G28881A, G28882A, and G28883C. 2020 Frontiers in microbiology Method SARS_CoV_2 G28881A;G28882A;G28883C 82;91;104 89;98;111 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. Further the 20C emerged as a North America-specific clade with C1059T and G25563T nucleotide changes. 2020 Frontiers in microbiology Method SARS_CoV_2 C1059T;G25563T 63;74 69;81 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. Later, 20A emerged in European outbreak from 19A parents having C3037T, C14408T, and A23403G as distinctive features. 2020 Frontiers in microbiology Method SARS_CoV_2 A23403G;C14408T;C3037T 85;72;64 92;79;70 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. The D614G mutant of the Spike protein was generated by Modeler 9.21. 2020 Frontiers in microbiology Method SARS_CoV_2 D614G 4 9 S 24 29 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. We have used Nextstrain year-letter clade nomenclature that started with 19A and 19B branched by C8782T and T28144C nucleotide changes and was initially prevalent in Asia during initial outbreak. 2020 Frontiers in microbiology Method SARS_CoV_2 C8782T;T28144C 97;108 103;115 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. SD614G encodes the same protein as SW1, with the exception of the D614G amino acid substitution. 2020 bioRxiv Method SARS_CoV_2 D614G 66 71 33335073 Cross-species recognition of SARS-CoV-2 to bat ACE2. Concentrated supernatants containing bACE2-Rm-mFc and bACE2-Rm-Y41H-mFc were individually captured by the antibody immobilized on the CM5 chip. 2021 Proc Natl Acad Sci U S A Method SARS_CoV_2 Y41H 63 67 33335073 Cross-species recognition of SARS-CoV-2 to bat ACE2. For the flow cytometry assay, bACE2-Rm, bACE2-Rm-Y41H, and hACE2 fused with eGFP were transfected into HEK293T cells. 2021 Proc Natl Acad Sci U S A Method SARS_CoV_2 Y41H 49 53 33335073 Cross-species recognition of SARS-CoV-2 to bat ACE2. The binding affinity of bACE2-Rm carrying the Y41H and/or E42Q mutations to SARS-CoV-2-RBD was also evaluated by SPR. 2021 Proc Natl Acad Sci U S A Method SARS_CoV_2 E42Q;Y41H 58;46 62;50 RBD 87 90 33335187 CoV2-ID, a MIQE-compliant sub-20-min 5-plex RT-PCR assay targeting SARS-CoV-2 for the diagnosis of COVID-19. In addition, the human SARS-CoV-2 (NC_045512.2) genomic sequence was imported to the Beacon Designer 8.2 qPCR assay design software package and an LNA-based genotyping assay for discriminating the D614G mutation (A to G) was designed. 2020 Scientific reports Method SARS_CoV_2 D614G 197 202 33335187 CoV2-ID, a MIQE-compliant sub-20-min 5-plex RT-PCR assay targeting SARS-CoV-2 for the diagnosis of COVID-19. This first was RNA isolated from cell culture infected with Sars-CoV-2 which was isolated from a clinical sample at Westmead Hospital (New South Wales, Australia); COVID19 was confirmed using N1/N2 and E gene RT-qPCR) and the second, a synthetic control RNA (Twist Biosciences), which were included as wild type controls for D614G genotyping. 2020 Scientific reports Method SARS_CoV_2 D614G 325 330 E 202 203 33377145 Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2. Atomic details at the binding interface exhibit that key residue substitutions (N501T mutation) in the SARS-CoV-2 CTD, compared to the SARS-CoV RBD, reinforce this interaction and lead to receptor binding with higher affinity. 2021 Briefings in bioinformatics Method SARS_CoV_2 N501T 80 85 RBD 144 147 33377145 Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2. In silico analysis of the 3D) structure of SARS-CoV-2 S-glycoprotein by homology modeling displayed that residue mutation Q483V in the CTD1 domain allowed RBD to bind to the ACE2 receptor with more affinity. 2021 Briefings in bioinformatics Method SARS_CoV_2 Q483V 122 127 S;RBD 54;155 68;158 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. Amino acid substitutions were introduced into the D614G pCDNA_SARS-CoV-2_Spike plasmid as previously described using the QuikChange Lightening Site-Directed Mutagenesis kit, following the manufacturer's instructions (Agilent Technologies, Inc., Santa Clara, CA). 2020 medRxiv Method SARS_CoV_2 D614G 50 55 33408342 A longitudinal study of SARS-CoV-2-infected patients reveals a high correlation between neutralizing antibodies and COVID-19 severity. A plasmid encoding the spike protein harboring the D614G mutation was generated by PCR mutagenesis. 2021 Cellular & molecular immunology Method SARS_CoV_2 D614G 51 56 S 23 28 33408342 A longitudinal study of SARS-CoV-2-infected patients reveals a high correlation between neutralizing antibodies and COVID-19 severity. For neutralization assays, a sample of ~1 x 103 pseudoparticles was incubated with a 100-fold dilution of sera or control antibodies for 1 h at 37C before infection of Vero-E6R cells. 2021 Cellular & molecular immunology Method SARS_CoV_2 E6R 173 176 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. For two high-frequency non-synonymous nucleocapsid protein mutations (R203K and G204R; co-fixed), all but three of the 30 (N173-234) flanking residues have non-synonymous variants, with 5 sites reporting an alternative allele frequency greater than 1% (A220V, S194L, S197L, M234I and P199L:S). 2021 Genome medicine Method SARS_CoV_2 G204R;M234I;P199L;S194L;S197L;A220V;R203K 80;274;284;260;267;253;70 85;279;289;265;272;258;75 N 38 50 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. In contrast, the frequency of orf3a Q57H appears to fluctuate, increasing and decreasing significantly from the time it was first observed in February 2020 (week 8) to November 2020, week 43). 2021 Genome medicine Method SARS_CoV_2 Q57H 36 40 ORF3a 30 35 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. In particular, nsp12 L314P has been used to genotype the putative S and L strains of SARS-CoV-2, which have now been clustered into further groups. 2021 Genome medicine Method SARS_CoV_2 L314P 21 26 Nsp12 15 20 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. Moreover, A222V appears to be increasing in Asia and Oceania from week 41, and S477N has increased to > 95% frequency across Oceania (N = 8321) with a peak of 9.3% in Europe (Additional file 1: Table S1, Additional file 1. 2021 Genome medicine Method SARS_CoV_2 A222V;S477N 10;79 15;84 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. Other high frequency mutations occur on the nucleocapsid gene (R203K, 38.8.0%; G204R 38.4%; across all geographical regions > 31%; Table 1), which has been the target antigen for several serological RDTs currently in use or in production. 2021 Genome medicine Method SARS_CoV_2 G204R;R203K 79;63 84;68 N 44 56 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. Specifically, the spike D614G and nsp12 N314L both appear to have a near-identical frequency with a consistent increase across all geographic regions (negating weeks with poor data collection). 2021 Genome medicine Method SARS_CoV_2 D614G;N314L 24;40 29;45 S;Nsp12 18;34 23;39 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. Spike D614G lies 73 residues downstream from the spike RBD, a region of interest as it is a primary target of protective humoral responses and bears immunodominant epitopes that play a possible role in antibody dependant enhancement. 2021 Genome medicine Method SARS_CoV_2 D614G 6 11 S;S;RBD 0;49;55 5;54;58 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. Spike mutations A222V and L18F appear to have become entrenched in Europe reaching a total frequency of 70.6% and 31.6%, respectively (Additional file 1: Table S1, Additional file 1. 2021 Genome medicine Method SARS_CoV_2 A222V;L18F 16;26 21;30 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. The 20 residues surrounding the spike mutation D614G (S604-624). 2021 Genome medicine Method SARS_CoV_2 D614G 47 52 S 32 37 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. The biological importance of spike D614G, particularly its immunological relevance and impact on transmission and disease, are still unclear. 2021 Genome medicine Method SARS_CoV_2 D614G 35 40 S 29 34 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. The most frequent mutations were the spike protein D614G (87.3%) and nsp12 L314P (87.5%), which were common across all the geographical regions (all > 86%) (Table 1), in keeping with their deep ancestral nature in the SARS-CoV-2 phylogenetic tree. 2021 Genome medicine Method SARS_CoV_2 D614G;L314P 51;75 56;80 S;Nsp12 37;69 42;74 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. The proximity of the D614G mutation to one of the functional domains of the spike protein has raised concerns, but whether it confers any gain in pathogenicity, transmissibility or immune evasion is still unclear. 2021 Genome medicine Method SARS_CoV_2 D614G 21 26 S 76 81 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. The second region (amino acids 167 to 206) contains the R203K and G204R mutations along with a cluster of high frequency variants. 2021 Genome medicine Method SARS_CoV_2 G204R;R203K 66;56 71;61 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. The spike D614G mutation does not appear to have significantly elevated HLA-I epitope prediction scores. 2021 Genome medicine Method SARS_CoV_2 D614G 10 15 S 4 9 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. Using the immuno-analytical tool, spike A222V, S477N and L18F variants were observed to have increased significantly in frequency between May and November 2020 (weeks 23-40). 2021 Genome medicine Method SARS_CoV_2 A222V;L18F;S477N 40;57;47 45;61;52 S 34 39 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. We have observed a strong correlation between the spatiotemporal accumulation of both spike D614G and nsp12 L314P. 2021 Genome medicine Method SARS_CoV_2 D614G;L314P 92;108 97;113 S;Nsp12 86;102 91;107 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. The SARS-CoV-2 spike protein ectodomain constructs used comprised the protein residues 1-1208 (GenBank: MN908947) with or without the D614G mutation, with or without the furin cleavage site RRAR (residue 682-685) mutated to GSAS or LEVLFQGP (HRV3C protease site), a C-terminal T4 fibritin trimerization motif, a C-terminal HRV3C protease cleavage site (except for the constructs where the furin site was mutated to an HRV3C site), a TwinStrepTag and an 8XHisTag. 2021 Cell reports Method SARS_CoV_2 D614G 134 139 S 15 20 33429204 PfAgo-based detection of SARS-CoV-2. Detecting D614G variant in clinical samples with SARS-CoV-2 PAND. 2021 Biosensors & bioelectronics Method SARS_CoV_2 D614G 10 15 33429204 PfAgo-based detection of SARS-CoV-2. The 23367-23430 nt fragment of the viral genome including nt23403 (D614G mutation) was amplified with primer pairs 614F and 614R (400 nM for each, Table S3). 2021 Biosensors & bioelectronics Method SARS_CoV_2 D614G 67 72 33436577 A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein. Recombinant proteins for RBD and its mutants (A435S, F342L, G476S, K458R, N354D, V367F, V483A, W436R), SARS-CoV S1, HCoV-HKU1 S1, and MERS-CoV RBD were commercial products (Sino Biological). 2021 Nature communications Method SARS_CoV_2 F342L;G476S;K458R;N354D;V367F;V483A;W436R;A435S 53;60;67;74;81;88;95;46 58;65;72;79;86;93;100;51 RBD;RBD 25;143 28;146 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. D614G frequency were conducted and verified using GraphPad Prism version 9.0.0 for Mac (GraphPad Software, San Diego, California USA, www.graphpad.com), JASP version 0.14, and RStudio version 1.3.1093. 2021 bioRxiv Method SARS_CoV_2 D614G 0 5 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. month, and P681H frequency vs. 2021 bioRxiv Method SARS_CoV_2 P681H 11 16 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. month, D614G frequency vs. 2021 bioRxiv Method SARS_CoV_2 D614G 7 12 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Pearson's correlation tests between P681H frequency vs. 2021 bioRxiv Method SARS_CoV_2 P681H 36 41 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The D614G mutation underwent assessment in the same manner for comparison. 2021 bioRxiv Method SARS_CoV_2 D614G 4 9 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Upon finding the P681H mutation among the two Hawaii strains in this study, the GISAID database was used to filter worldwide SARS-CoV-2 sequences by the P681H mutation to create a ratio of sequences containing the P681H mutation to all sequences reported in the GISAID database for a given month. 2021 bioRxiv Method SARS_CoV_2 P681H;P681H;P681H 17;153;214 22;158;219 33468695 SARS-CoV-2 Infection Severity Is Linked to Superior Humoral Immunity against the Spike. D614G spike protein, SARS-CoV-1 RBD, and MERS-CoV RBD were generated in-house and expressed in HEK293F cells. 2021 mBio Method SARS_CoV_2 D614G 0 5 S;RBD;RBD 6;32;50 11;35;53 33468702 SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia. For the PCR, 5 mul of 5x Q5 reaction buffer (NEB, M0493S), 0.5 mul of 10 mM dNTP mix (NEB, N0447S), 0.25 mul Q5 Hot Start DNA polymerase (NEB, M0493S), and either 4.0 mul of pooled primer set 1 or 3.98 mul of pooled primer set 2 were prepared for each reaction. 2021 mBio Method SARS_CoV_2 M0493S;M0493S 50;143 56;149 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. The tree was then annotated and visualized on iTOL server putting the sequences into different clades based on specific mutations proposed in GISAID, and further classified as D614G type. 2021 PloS one Method SARS_CoV_2 D614G 176 181 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. In this study, the IEDB (Dhanda et al.,) server was used to evaluate and compare the immunogenicity of the wild type and D614G mutant spike. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 D614G 121 126 S 134 139 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. The simulation was conducted for the wild and mutant (D614G) type of spike using the GROMACS package (version 2019.1) (Kutzner et al.,). 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 D614G 54 59 S 69 74 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. To get the exact details about the impact of D614G mutation on the spike, our group examined the secondary structure of the desired protein using DSSP (Zhang & Sagui,). 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 D614G 45 50 S 67 72 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. To investigate the effect of the D614G mutation on the ability of spike to bind to the hACE2 receptor, the docking process was utilized. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 D614G 33 38 S 66 71 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. Chi-squared test (chi2 test) was used to detect differences between the D614 and D614G groups in relation to gender and region (Middle East vs. 2021 Heliyon Method SARS_CoV_2 D614G 81 86 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. Linear-by-linear test for association (LBL) was used to assess the temporal changes in D614G prevalence. 2021 Heliyon Method SARS_CoV_2 D614G 87 92 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. Mann-Whitney U test (M-W) was used to assess the difference between the D614 and D614G groups in relation to age. 2021 Heliyon Method SARS_CoV_2 D614G 81 86 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. Secondary Structure Prediction of RNA-Dependent RNA Polymerase Having A97V Mutation. 2020 JMIR bioinformatics and biotechnology Method SARS_CoV_2 A97V 70 74 RdRp 34 62 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. We used the Chou and Fasman Secondary Structure Prediction (CFSSP) online server to predict the secondary structure of RNA-dependent RNA polymerase (RdRP)/NSP12 with novel A97V mutation. 2020 JMIR bioinformatics and biotechnology Method SARS_CoV_2 A97V 172 176 RdRp;Nsp12;RdRP 119;155;149 147;160;153 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. SymmDock, a geometry-based docking algorithm for the prediction of cyclically symmetric complexes, was used for symmetric docking simulations of the REF-Q57H and ALT-Q57H homotetramers. 2021 PloS one Method SARS_CoV_2 Q57H;Q57H 153;166 157;170 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. The secondary structure of the wild type and the D614G spike protein was predicted by utilizing the PSIPRED. 2021 Biochemistry and biophysics reports Method SARS_CoV_2 D614G 49 54 S 55 60 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. M0239S) and dNTP mixtures (cat. 2021 Analytical chemistry Method SARS_CoV_2 M0239S 0 6 33524589 A global analysis of replacement of genetic variants of SARS-CoV-2 in association with containment capacity and changes in disease severity. The lineage G* was further divided into three clades, including G, GH (G25563T, ORF3a aa Q57H) and GR (G28883C, N gene aa G204R). 2021 Clinical microbiology and infection Method SARS_CoV_2 G204R;Q57H;G25563T;G28883C 122;89;71;103 127;93;78;110 ORF3a;N 80;112 85;113 33524589 A global analysis of replacement of genetic variants of SARS-CoV-2 in association with containment capacity and changes in disease severity. With reference to GISAID, variants were assigned to four lineages: L (reference sequence, nucleotide T28144, ORF8 amino acid L84), S (nt T28144C, ORF8 aa L84S), V (nt G26144T, ORF3a aa G251V) and G* (nt A23403G, S gene aa D614G). 2021 Clinical microbiology and infection Method SARS_CoV_2 A23403G;D614G;G251V;G26144T;L84S;T28144C 203;222;185;167;154;137 210;227;190;174;158;144 ORF3a;ORF8;ORF8;S;S 176;109;146;131;212 181;113;150;132;213 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. coli cells harboring plasmids for SARS CoV-2 PLpro WT and C111S mutant expression were cultured in LB medium supplemented with ampicillin (150 microg/ml). 2021 Nature communications Method SARS_CoV_2 C111S 58 63 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Gene cloning, protein expression and purification of WT and C111S mutant of PLpro. 2021 Nature communications Method SARS_CoV_2 C111S 60 65 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. PLpro-WT and PLpro-C111S activities on LKGG-AMC were assayed as above with 1 microM enzyme and 40 microM LKGG-AMC substrate. 2021 Nature communications Method SARS_CoV_2 C111S 19 24 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Purification was repeated for PLpro WT and C111S mutant proteins for co-crystallization with inhibitors, following the same protocol except that 10 mM beta-mercaptoethanol was used instead of TCEP in all purification buffers, and 10 mM DTT was used instead of TCEP in the crystallization buffer. 2021 Nature communications Method SARS_CoV_2 C111S 43 48 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. The crystals of PLpro-C111S mutant protein (bipyramidal crystals up to 0.2 mm, 1-3 days of incubation at 4 C, P3221 space group) were obtained from MCSG2 screen, reagent formulation #4 (0.1 M acetate buffer pH 4.5, 0.8 M NaH2PO4/1.2 M K2HPO4). 2021 Nature communications Method SARS_CoV_2 C111S 22 27 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. The final concentrations of WT PLpro was 25 mg/ml and C111S mutant was 30 mg/ml. 2021 Nature communications Method SARS_CoV_2 C111S 54 59 33532771 Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K, and N501Y variants by BNT162b2 vaccine-elicited sera. Three recombinant SARS-CoV-2 mutants (N501Y, Delta69/70-N501Y+D614G, E484K+N501Y+D614G in spike protein) were prepared on the genetic background of an infectious cDNA clone derived from clinical strain WA1 (2019-nCoV/USA_WA1/2020) by following the PCR-based mutagenesis protocol as reported previously. 2021 bioRxiv Method SARS_CoV_2 E484K;N501Y;D614G;D614G;N501Y;N501Y 69;38;62;81;75;56 74;43;67;86;80;61 S 90 95 33545711 SARS-CoV-2 evolution during treatment of chronic infection. Amino acid substitutions were introduced into the D614G pCDNA_SARS-CoV-2_Spike plasmid as previously described using the QuikChange Lightening Site-Directed Mutagenesis kit, following the manufacturer's instructions (Agilent Technologies, Inc., Santa Clara, CA). 2021 Nature Method SARS_CoV_2 D614G 50 55 33545711 SARS-CoV-2 evolution during treatment of chronic infection. At day 66 we noted I513T in NSP2 (T2343C) and V157L (G13936T) in RdRp had emerged from undetectable at day 54 to almost 100% frequency (Figure 2, red and green dashed lines), with the polymerase being the more plausible candidate for driving this sweep. 2021 Nature Method SARS_CoV_2 I513T;V157L;G13936T;T2343C 19;46;53;34 24;51;60;40 Nsp2;RdRP 28;65 32;69 33545711 SARS-CoV-2 evolution during treatment of chronic infection. By contrast, the D796H single mutant had significantly lower infectivity as compared to wild type and double mutant had similar infectivity to wild type (Figure 4B, Extended data 7). 2021 Nature Method SARS_CoV_2 D796H 17 22 33545711 SARS-CoV-2 evolution during treatment of chronic infection. Following remdesivir at day 41 the low frequency variant analysis allowed us to observe transient amino acid changes in populations at below 50% abundance in Orf 1b, 3a and Spike, with a T39I (C27509T) mutation in ORF7a reaching 79% on day 45 (Figure 2, pink, supplementary information). 2021 Nature Method SARS_CoV_2 T39I;C27509T 187;193 191;200 ORF7a;S 214;173 219;178 33545711 SARS-CoV-2 evolution during treatment of chronic infection. In addition, patient derived serum from days 64 and 66 (one day either side of CP2 infusion) similarly showed lower potency against the D796H + DeltaH69/DeltaV70 mutants (Figure 4F, G). 2021 Nature Method SARS_CoV_2 D796H 136 141 33545711 SARS-CoV-2 evolution during treatment of chronic infection. In contrast to the early period of infection, between days 66 and 82, following the first two administrations of convalescent sera, a shift in the virus population was observed, with a variant bearing D796H in S2 and DeltaH69/DeltaV70 in the S1 N-terminal domain (NTD) becoming the dominant population at day 82. 2021 Nature Method SARS_CoV_2 D796H 201 206 N 245 246 33545711 SARS-CoV-2 evolution during treatment of chronic infection. In further support of our proposed idea of competition, noted above, frequencies of these two variants appeared to mirror changes in the NSP2 I513T mutation (Figure 2), suggesting these as markers of opposing clades in the viral population. 2021 Nature Method SARS_CoV_2 I513T 142 147 Nsp2 137 141 33545711 SARS-CoV-2 evolution during treatment of chronic infection. Notably, spike variant N501Y, which can increase the ACE2 receptor affinity, and which is present in the new UK B1.1.7 lineage, was observed on day 55 at 33% frequency, but was eliminated by the sweep of the NSP2/RdRp variant. 2021 Nature Method SARS_CoV_2 N501Y 23 28 S;Nsp2;RdRP 9;208;213 14;212;217 33545711 SARS-CoV-2 evolution during treatment of chronic infection. On Days 86 and 89, viruses obtained from upper respiratory tract samples were characterised by the Spike mutations Y200H and T240I, with the deletion/mutation pair observed on day 82 having fallen to frequencies of 10% or less (Figure 2 and 3). 2021 Nature Method SARS_CoV_2 T240I;Y200H 125;115 130;120 S 99 104 33545711 SARS-CoV-2 evolution during treatment of chronic infection. Patterns in the variant frequencies suggest competition between virus populations carrying different mutations, viruses with the D796H/DeltaH69/DeltaV70 deletion/mutation pair rising to high frequency during CP therapy, then being outcompeted by another population in the absence of therapy. 2021 Nature Method SARS_CoV_2 D796H 129 134 33545711 SARS-CoV-2 evolution during treatment of chronic infection. Sequencing of a nose and throat swab sample at day 93 identified viruses characterised by Spike mutations P330S at the edge of the RBD and W64G in S1 NTD at close to 100% abundance, with D796H along with DeltaH69/DeltaV70 at <1% abundance and the variants Y200H and T240I at frequencies of <2%. 2021 Nature Method SARS_CoV_2 D796H;P330S;T240I;W64G;Y200H 187;106;266;139;256 192;111;271;143;261 S;RBD 90;131 95;134 33545711 SARS-CoV-2 evolution during treatment of chronic infection. Specifically, these data are consistent with a lineage of viruses with the NSP2 I513T and RdRp V157L variant, dominant on day 66, being outcompeted during therapy by the mutation/deletion variant. 2021 Nature Method SARS_CoV_2 I513T;V157L 80;95 85;100 Nsp2;RdRP 75;90 79;94 33545711 SARS-CoV-2 evolution during treatment of chronic infection. The eight RBD-specific mAbs (Extended data 8) exhibited no major change in neutralisation potency and non-RBD specific COVA1-21 showing 3-5 fold reduction in potency against DeltaH69/DeltaV70+D796H and DeltaH69/DeltaV70, but not D796H alone (Extended data 8). 2021 Nature Method SARS_CoV_2 D796H;D796H 229;192 234;197 RBD;RBD 10;106 13;109 33545711 SARS-CoV-2 evolution during treatment of chronic infection. The infecting strain was assigned to lineage 20B bearing the D614G Spike variant. 2021 Nature Method SARS_CoV_2 D614G 61 66 S 67 72 33545711 SARS-CoV-2 evolution during treatment of chronic infection. The inferred linkage of D796H and DeltaH69/DeltaV70 was maintained as evidenced by the highly similar frequencies of the two variants, suggesting that the third unit of CP led to the re-emergence of this population under renewed positive selection. 2021 Nature Method SARS_CoV_2 D796H 24 29 33545711 SARS-CoV-2 evolution during treatment of chronic infection. The Spike mutations Y200H and T240I were accompanied at high frequency by two other non-synonymous variants with similar allele frequencies, coding for I513T in NSP2, V157L in RdRp and N177S in NSP15 (Figure 2A). 2021 Nature Method SARS_CoV_2 I513T;N177S;T240I;V157L;Y200H 152;185;30;167;20 157;190;35;172;25 S;Nsp2;RdRP 4;161;176 9;165;180 33545711 SARS-CoV-2 evolution during treatment of chronic infection. To establish if the mutations incurring in vivo (D796H and DeltaH69/DeltaV70) resulted in a global change in neutralization sensitivity we tested neutralising mAbs targeting the seven major epitope clusters previously described (excluding non-neutralising clusters II, V and small [n =<2] neutralising clusters IV, X). 2021 Nature Method SARS_CoV_2 D796H 49 54 33545711 SARS-CoV-2 evolution during treatment of chronic infection. To understand how the DeltaH69/DeltaV70 and D796H might confer antibody resistance, we assessed how they might affect the Spike structure (Extended data 9). 2021 Nature Method SARS_CoV_2 D796H 44 49 S 122 127 33545711 SARS-CoV-2 evolution during treatment of chronic infection. Using lentiviral pseudotyping we generated wild type, DeltaH69/DeltaV70 + D796H and single mutant Spike proteins in enveloped virions in order to measure neutralisation activity of CP against these viruses (Figure 4). 2021 Nature Method SARS_CoV_2 D796H 74 79 S 98 103 33545711 SARS-CoV-2 evolution during treatment of chronic infection. Viruses with the P330S variant were detected in two independent samples from different sampling sites, arguing against the possibility of contamination. 2021 Nature Method SARS_CoV_2 P330S 17 22 33545711 SARS-CoV-2 evolution during treatment of chronic infection. We found that D796H alone and the D796H + DeltaH69/DeltaV70 double mutant were less sensitive to neutralisation by convalescent plasma samples (Figure 4C-E, Extended data 7). 2021 Nature Method SARS_CoV_2 D796H;D796H 14;34 19;39 33545711 SARS-CoV-2 evolution during treatment of chronic infection. We observed a re-emergence of the D796H + DeltaH69/DeltaV70 viral population (Figure 2, 3). 2021 Nature Method SARS_CoV_2 D796H 34 39 33545711 SARS-CoV-2 evolution during treatment of chronic infection. With the lapse in therapy, the original strain, having acquired NSP15 N1773S and the Spike mutations Y200H and T240I, regained dominance, followed by the emergence of a separate population with the W64G and P330S mutations. 2021 Nature Method SARS_CoV_2 N1773S;P330S;T240I;W64G;Y200H 70;207;111;198;101 76;212;116;202;106 S 85 90 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. Additional SARS-CoV-2 sequences containing Spike N501Y mutation were downloaded on December 21, 2020. 2021 Antiviral research Method SARS_CoV_2 N501Y 49 54 S 43 48 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. These sequences were separated into B.1.1.7 variant if they also contained spike H69/V70 deletion, Y144 deletion, A570D, D614G, P681H, T716I, S982A, and D1118H, and separated into B.1.351 variant if they also contained spike N417N and E484K. 2021 Antiviral research Method SARS_CoV_2 A570D;D1118H;D614G;E484K;N417N;P681H;S982A;T716I 114;153;121;235;225;128;142;135 119;159;126;240;230;133;147;140 S;S 75;219 80;224 33551188 Fast and cost-effective screening for SARS-CoV-2 variants in a routine diagnostic setting. 5 mul of the extracted RNA used in a qPCR in total of 20 mul using the VirSNiP SARS-CoV-2 Spike A23063T N501Y (TIBMolbiol, Berlin, Germany) assay with the RNA Process Control Kit (Roche Diagnostics) according to manufacturers' instruction. 2021 Dental materials Method SARS_CoV_2 A23063T;N501Y 96;104 103;109 S 90 95 33551188 Fast and cost-effective screening for SARS-CoV-2 variants in a routine diagnostic setting. The N501Y specific assay delivers only an amplification signal if the Y501 variant is present. 2021 Dental materials Method SARS_CoV_2 N501Y 4 9 33556653 The G614 pandemic SARS-CoV-2 variant is not more pathogenic than the original D614 form in adult Syrian hamsters. Pseudovirions were produced by co-transfection of Lenti-X 293T cells with psPAX2, pTRIP-luc, and SARS-CoV-2 S expressing plasmid using Lipofectamine 3000. 2021 Virology Method SARS_CoV_2 X293T 56 62 S 108 109 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. ACE2-loaded biosensors were then dipped into wells containing either a His-tagged full-length furin-uncleavable/hexaproline-stabilizing ectodomain of SARS2-S-WT (Acrobiosystems, SEC-MALS verified, SPN-C52H9) or SARS2-S-D614G protein trimer (Acrobiosystems, SEC-MALS verified, SPN-C52H3) at 1.12-71.4 nM in 10X Kinetics Buffer (ForteBio). 2021 Nature communications Method SARS_CoV_2 D614G 219 224 S;S 156;217 157;218 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. C-terminally T7 epitope (T7e)-tagged S expression plasmids, pC-SARS-S-T7e, pC-SARS2-S-T7e, pC-SARS2-S-C1247A-T7e, and pC-SARS2-S-TM/CT1-T7e were generated by replacing the APOBEC3G gene of pCa-hA3G-T7e with PCR-amplified S fragments. 2021 Nature communications Method SARS_CoV_2 C1247A 102 108 S;S;S;S;S;S 37;68;84;100;127;221 38;69;85;101;128;222 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. The SARS-CoV-2 S mutants (pC-SARS2-S-H49Y, pC-SARS2-S-V367F, pC-SARS2-S-G476S, pC-SARS2-S-V483A, pC-SARS2-S-D614G, or pC-SARS2-S-C1247A), in which positions 49, 367, 476, 483, 614, or 1247 of the S protein were mutated from histidine-to-tyrosine, valine-to-phenylalanine, glycine-to-serine, valine-to-alanine, aspartic-acid-to-glycine, or cysteine-to-alanine, respectively, were created by inserting overlapping PCR fragments into Acc65I/NotI-digested pCAGGS. 2021 Nature communications Method SARS_CoV_2 C1247A;D614G;G476S;H49Y;V367F;V483A 129;108;72;37;54;90 135;113;77;41;59;95 S;S;S;S;S;S;S;S 15;35;52;70;88;106;127;196 16;36;53;71;89;107;128;197 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. The structural models of the H49Y, V367F, G476S, V483A, and D614G mutants were constructed in a similar manner. 2021 Nature communications Method SARS_CoV_2 D614G;G476S;H49Y;V367F;V483A 60;42;29;35;49 65;47;33;40;54 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. To prepare various spike protein-pseudotyped lentiviral luciferase reporter viruses, 1.1 x 105 293T cells were cotransfected with 200 ng of spike protein expression plasmids (pC-SARS-S, pC-SARS2-S (-WT, -H49Y, -V367F, -G476S, -V483A, -D614G, or -C1247A), 400 ng of psPAX2-IN/HiBiT, and 400 ng of pWPI-Luc2, using FuGENE 6 (Promega). 2021 Nature communications Method SARS_CoV_2 C1247A;D614G;G476S;H49Y;V367F;V483A 246;235;219;204;211;227 252;240;224;208;216;232 S;S;S;S 19;140;183;195 24;145;184;196 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Two-fold serially diluted sera were mixed with an equal volume of 1 ng of 24 antigen of the WT or D614G mutant SARS2-S-pseudotyped virus and incubated at 37 C for 1 h. 2021 Nature communications Method SARS_CoV_2 D614G 98 103 S 117 118 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. For accurate estimation of D614G prevalence, we only included countries with at least nine genomes in GISAID. 2021 eLife Method SARS_CoV_2 D614G 27 32 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. For temporal tracking of D614G mutations in SARS-CoV-2 genomes, we used the Nextstrain analysis tool (https://nextstrain.org/ncov) with data obtained from GISAID (https://www.gisaid.org/). 2021 eLife Method SARS_CoV_2 D614G 25 30 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. Loaded sensors were dipped into recombinant SARS-Cov-2 His-tagged Spike protein (D614 or D614G, Sino Biological, Cat # 40591-V08H and 40591-V08H3). 2021 eLife Method SARS_CoV_2 D614G 89 94 S 66 71 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. Threshold cycle data and statistical test results for University of Washington (UW) quantitative PCR data from COVID-19 patients are from (https://github.com/blab/ncov-D614G). 2021 eLife Method SARS_CoV_2 D614G 168 173 COVID-19 111 119 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. To generate pLenti-ACE2-Hygro (Addgene 161758), we amplified human ACE2 (hACE2) from pcDNA3.1-ACE2 (Addgene 1786) and cloned it into a lentiviral transfer pLEX vector carrying the hygromycin resistance gene using Gibson Assembly Master Mix (NEB E2611L). 2021 eLife Method SARS_CoV_2 E2611L 245 251 33579792 The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2. The construct coding for the D614G mutant was based on the furin-uncleavable version of the SARS-CoV-2 spike protein ectodomain with a set of stabilizing mutations (R682S, R685S, K986P, and K987P) that we described before. 2021 Proc Natl Acad Sci U S A Method SARS_CoV_2 D614G;K986P;K987P;R685S;R682S 29;179;190;172;165 34;184;195;177;170 S 103 108 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. SWISS-MODEL was used to model the full length, wild type and Q677P mutant spike glycoprotein. 2021 medRxiv Method SARS_CoV_2 Q677P 61 66 S 74 92 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. The template utilized for the model was 7BBH, which has all receptor binding domains in the down conformation.the entire furin cleavage site for the D614G ("WT") and D614G+Q677P (mutant) version of the SARS-CoV-2 Spike, based on PDB. 2021 medRxiv Method SARS_CoV_2 D614G;D614G;Q677P 149;166;172 154;171;177 RBD;S 60;213 84;218 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Five RBD mutants were considered in the study (S494P, V483A, G476S, A348T, and V367F). 2021 Biochemical and biophysical research communications Method SARS_CoV_2 A348T;G476S;V367F;V483A;S494P 68;61;79;54;47 73;66;84;59;52 RBD 5 8 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. The RBD-ACE2 complexes for wild-type, V367F, and S494P, obtained from the protein-protein docking refinement, were then studied by molecular dynamics simulation using the AMBER-ILDN force field with the aid of GROMACS 2018.1 package. 2021 Biochemical and biophysical research communications Method SARS_CoV_2 S494P;V367F 49;38 54;43 RBD 4 7 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. The amino acid exchanges S477N and S477G were modelled using the standalone CHARMM package. 2021 Scientific reports Method SARS_CoV_2 S477G;S477N 35;25 40;30 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. For S protein stability, six proline mutations (F817P, A892P, A899P, A942P, K986P, V987P) and a disulfide mutation between T883 and V705 (mutated to cysteines) were introduced. 2021 bioRxiv Method SARS_CoV_2 A892P;A899P;A942P;K986P;V987P;F817P 55;62;69;76;83;48 60;67;74;81;88;53 S 4 5 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. The IgGs were then loaded onto anti-human IgG Fc (AHC) biosensors and interacted with 30 mug/ml wild type, K417N, and E484K SARS-CoV-2 RBDs. 2021 bioRxiv Method SARS_CoV_2 E484K;K417N 118;107 123;112 RBD 135 139 33619487 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. To measure the binding kinetics of anti-SARS-CoV-2 IgGs and RBDs (wild type and K417N and E484K variants), the IgGs were diluted with kinetic buffer (1x PBS, pH 7.4, 0.01% BSA and 0.002% Tween 20) into 30 mug/ml. 2021 bioRxiv Method SARS_CoV_2 E484K;K417N 90;80 95;85 RBD 60 64 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Amino acid substitutions were introduced into the D614G pCDNA_SARS-CoV-2_S plasmid as previously described using the QuikChange Lightening Site-Directed Mutagenesis kit, following the manufacturer's instructions (Agilent Technologies, Inc., Santa Clara, CA). 2021 medRxiv Method SARS_CoV_2 D614G 50 55 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Antibody-coated biosensors were incubated for 3 min with a solution containing 5 mug/ml of WT, N501Y or E484K SARS-CoV-2 RBD in kinetic buffer, followed by a 3-min dissociation step. 2021 medRxiv Method SARS_CoV_2 E484K;N501Y 104;95 109;100 RBD 121 124 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Biotinylated RBD (WT, N501Y, or TM) were immobilized at 5 ng/uL in undiluted 10X Kinetics Buffer (Pall) to SA sensors until a load level of 1.1nm. 2021 medRxiv Method SARS_CoV_2 N501Y 22 27 RBD 13 16 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. The B.1.1.7 RBD gene was synthesized by GenScript into pCMVR with the same boundaries and construct details with a mutation at N501Y. 2021 medRxiv Method SARS_CoV_2 N501Y 127 132 RBD 12 15 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. The mutations (del-69/70, del-144, N501Y, A570D, D614G, P681H, S982A, T716I and D1118H or K417N, E484K and N501Y) were introduced by amplification with primers with similar Tm. 2021 medRxiv Method SARS_CoV_2 A570D;D1118H;D614G;E484K;K417N;N501Y;N501Y;P681H;S982A;T716I 42;80;49;97;90;35;107;56;63;70 47;86;54;102;95;40;112;61;68;75 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Additionally, we perform a new analysis using a model with the same structure to test for an effect of both the D614G mutation and the D614G/N439K mutation combination on the viral load of infected patients, as measured by cycle threshold (Ct) value. 2021 Cell Method SARS_CoV_2 D614G;D614G;N439K 112;135;141 117;140;146 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Antibody-coated biosensors were incubated for 5 min with a solution containing 5 mug /mL of SARS-CoV2 RBD WT, N439K, K417V or N439/K417V in kinetic buffer. 2021 Cell Method SARS_CoV_2 K417V;N439K;K417V 117;110;131 122;115;136 RBD 102 105 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell culture supernatant was collected three days after transfection and supplemented with 10x PBS to a final concentration of 2.5x PBS (342.5 mM NaCl, 6.75 mM KCl and 29.75 mM phosphates), or 3.2x for RBD N439R. 2021 Cell Method SARS_CoV_2 N439R 206 211 RBD 202 205 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Crystals of the SARS-CoV-2 RBD N439K-hACE2-S304-S309 complex were obtained at 20 C by sitting drop vapor diffusion. 2021 Cell Method SARS_CoV_2 N439K 31 36 RBD 27 30 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. First, mutation is a three level rather than two level factor (D614/N439, D614G/N439 and D614G/N439K) with the ancestral D614/N439 being the reference level. 2021 Cell Method SARS_CoV_2 D614G;D614G;D614N;N439K 74;89;74;95 79;94;79;100 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. In both cases we cannot estimate the marginal effect of the N439K mutation, as we only have the mutation on the 614G genetic background, so the individual effect of N439K cannot be separated from any potential epistatic interactions between the mutations. 2021 Cell Method SARS_CoV_2 N439K;N439K 60;165 65;170 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. In the Ticino region of Switzerland and during the time period of collection (February-March 2020) no N439K SARS-CoV-2 isolates were reported. 2021 Cell Method SARS_CoV_2 N439K 102 107 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Lenti-X 293T cells (Takara, 632180) were seeded in 10-cm dishes at a density of 1e5 cells/cm2 and the following day transfected with 5 mug of spike expression plasmid with TransIT-Lenti (Mirus, 6600) according to the manufacturer's instructions. 2021 Cell Method SARS_CoV_2 X293T 6 12 S 142 147 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Prior to forming the SARS-CoV-2 RBD N439K-ACE2-S304-S309 complex, recombinant hACE2 protein was digested using EndoH (New England Biolabs) and thrombin (Sigma-Aldrich). 2021 Cell Method SARS_CoV_2 N439K 36 41 RBD 32 35 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Recombinant SARS-CoV-2 RBD N439K was digested with PNGase F (New England Biolabs) and thrombin (Sigma-Aldrich). 2021 Cell Method SARS_CoV_2 N439K 27 32 RBD 23 26 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Samples from six N439K variant infected individuals were obtained from the ISARIC4C consortium (https://isaric4c.net/). 2021 Cell Method SARS_CoV_2 N439K 17 22 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Second, as we are now interested in two mutations, we estimated the phylogeny used to control for the effect of the rest of the genome excluding both the nucleotide position underlying the D614G mutation and the nucleotide position underlying the N439K mutation (in addition to the sites from De Maio et al. 2021 Cell Method SARS_CoV_2 D614G;N439K 189;247 194;252 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Spectraplate-384 plates with high protein binding treatment (custom made from Perkin Elmer) were coated overnight at 4C with 0.1 mug/mL (for mAbs) or 5 ug/mL (for sera) SARS-CoV-2 RBD WT, N439K, K417V or N439K/K417V in phosphate-buffered saline (PBS), pH 7.2. 2021 Cell Method SARS_CoV_2 K417V;N439K;N439K;K417V 195;188;204;210 200;193;209;215 RBD 180 183 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The loss or gain of neutralization potency across spike variants was calculated by dividing the variant IC50 by the parental (D614G) IC50 within each biological replicate, and then visualized as geometric mean +- geometric standard deviation. 2021 Cell Method SARS_CoV_2 D614G 126 131 S 50 55 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The N439K mutation was noted to become increasingly prevalent during April 2020. 2021 Cell Method SARS_CoV_2 N439K 4 9 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The RBD N439K-hACE2-S304-S309 complex structure was solved by molecular replacement using phaser from starting models consisting of RBD-S304-S309 (PDB: 7JX3) and hACE2 (PDB: 6m0j). 2021 Cell Method SARS_CoV_2 N439K 8 13 RBD;RBD 4;132 7;135 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The SARS-CoV-2 RBD N439K-hACE2 complex was formed together with two Fab fragments (S304 and S309) to aid in crystallization. 2021 Cell Method SARS_CoV_2 N439K 19 24 RBD 15 18 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The sequences were downsampled with weights that normalize sequence count per epiweek, maximize the number of countries and lineages represented, and enriching for sequences with the N439K mutation. 2021 Cell Method SARS_CoV_2 N439K 183 188 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. These data had previously been analyzed to test for an effect of the D614G mutation on the severity of disease; we extend that analysis here using the same methodology to test for an effect of the N439K mutation. 2021 Cell Method SARS_CoV_2 D614G;N439K 69;197 74;202 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Vero E6-hACE2 cells (Vero E6 cells induced to overexpress hACE2) either with or without TMPRSS2 overexpression (S.J.R., S.B., and A.W., unpublished data) were seeded in a 12-well plate and inoculated with an MOI of 0.01 with either the GLA1 (N439/D614G) or GLA2 (N439K/D614G) virus isolates for 1 hr before washing the cells three times in PBS and replacing with DMEM supplemented with 2% FBS. 2021 Cell Method SARS_CoV_2 N439K;D614G;D614G 263;247;269 268;252;274 33628442 Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. 3 Briefly, using the third-generation lentivirus system, pseudotyped viral particles expressing SARS-CoV-2 D614 strain or G614 variant S proteins were generated by reverse transfection of 3 x 107 of HEK293T cells with 12 mug pMDLg/PRRE (Addgene, Watertown, Massachusetts, USA), 6 mug pRSV-Rev (Addgene), 12 mug pTT5LnX-coV-SP (SARS-CoV-2 wildtype S, a kind gift from Dr Brendon John Hanson, DSO National Laboratories, Singapore) or pTT5Lnx-coV-SP-D614G (SARS-CoV-2 mutant D614G S), and 24 mug pHIV-Luc-ZsGreen (Addgen) using Lipofectamine 2000 transfection (Invitrogen, Carlsbad, California, USA). 2021 Clinical & translational immunology Method SARS_CoV_2 D614G;D614G 473;448 478;453 S;S;S;S;S 324;445;136;348;479 326;447;137;349;480 33628442 Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. Determining D614G mutation status of COVID-19 patients. 2021 Clinical & translational immunology Method SARS_CoV_2 D614G 12 17 COVID-19 37 45 33628442 Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. Sequences with nucleotide mutation A23403G were assigned as D614G. 2021 Clinical & translational immunology Method SARS_CoV_2 A23403G;D614G 35;60 42;65 33628442 Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. Serially diluted heat-inactivated plasma samples (1:10 to 1:31 250 dilutions) were incubated with equal volume of pseudovirus expressing SARS-CoV-2 S proteins of either original wildtype or D614G mutant strain (0.4 ng muL-1 of p24) at 37 C for 1 h, before being added to pre-seeded CHO-ACE2 cells. 2021 Clinical & translational immunology Method SARS_CoV_2 D614G 190 195 S 148 149 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Visualization of wild type and the H49Y, T573I, and D614G S mutants were performed on VMD. 2021 Scientific reports Method SARS_CoV_2 D614G;H49Y;T573I 52;35;41 57;39;46 S 58 59 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Focal Nextstrain build of S H655Y sequences. 2021 PLoS pathogens Method SARS_CoV_2 H655Y 28 33 S 26 27 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. The focal H655Y build (S5 Fig) was prepared as described in Hodcroft et al. 2021 PLoS pathogens Method SARS_CoV_2 H655Y 10 15 33655251 SARS-CoV-2 B.1.1.7 and B.1.351 Spike variants bind human ACE2 with increased affinity. Human ACE2 protein was purchased from Sino Biological (SinoBiological, catalog#10108-H05H) and re-suspended in PBS-T to obtain 4.54uM stock concentration. 2021 bioRxiv Method SARS_CoV_2 H05H 85 89 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Amino acid substitutions for B.1.1.7, P.1 (Brazilian lineage: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I, and V1167F), and B.1.351 variants were introduced by overlap extension PCR. 2021 Nature medicine Method SARS_CoV_2 D138Y;E484K;H655Y;K417T;L18F;N501Y;P26S;R190S;T1027I;T20N;V1167F 80;101;115;94;62;108;74;87;122;68;134 85;106;120;99;66;113;78;92;128;72;140 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Individual point mutations in the spike gene (D614G, K417N/D614G, E484K/D614G, N501Y/D614G, P681H/D614G, del69-70/N501Y/D614G, and E484K/N501Y/D614G) were introduced into an infectious cDNA clone of the 2019n-CoV/USA_WA1/2020 (WA1/2020) strain as described previously. 2021 Nature medicine Method SARS_CoV_2 E484K;E484K;K417N;N501Y;P681H;D614G;D614G;D614G;D614G;D614G;D614G;D614G;N501Y;N501Y 66;131;53;79;92;46;59;72;85;98;120;143;114;137 71;136;58;84;97;51;64;77;90;103;125;148;119;142 S 34 39 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. The full-length S gene of SARS-CoV-2 strain (SARS-CoV-2-S) isolate BetaCoV/Wuhan-Hu-1/2019 (accession number MN908947) carrying D614G was codon-optimized for expression in hamster cells and cloned into the pcDNA3 expression vector. 2021 Nature medicine Method SARS_CoV_2 D614G 128 133 S;S 16;56 17;57 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. Following expression as full-length IgG1 recombinant antibodies were quantitatively tested for their neutralization potency against both the wild type, D614G variant and the B.1.1.7 emerging variants. 2021 Cell Method SARS_CoV_2 D614G 152 157 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. SARS-CoV-2 D614G pseudotype was produced using the same procedure as described above. 2021 Cell Method SARS_CoV_2 D614G 11 16 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. Wild type SARS-CoV-2 (SARS-CoV-2/INMI1-Isolate/2020/Italy: MT066156), D614G (SARS-CoV-2/human/ITA/INMI4/2020, clade GR, D614G (S): MT527178) and B.1.1.7 (INMI-118 GISAID accession number EPI_ISL_736997) viruses were purchased from the European Virus Archive goes Global (EVAg, Spallanzani Institute, Rome)or received from the Spallanzani Institute, Rome. 2021 Cell Method SARS_CoV_2 D614G;D614G 70;120 75;125 S 127 128 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. In order to better understand the impact of the mutant genotype (hereafter referred to as MT) with 14408C>T and 23403A>G mutations on SARS-CoV-2 genome evolution and mutation rates, we used standard mathematical evolutionary biology models. 2021 Infection, genetics and evolution Method SARS_CoV_2 C14408T;A23403G 99;112 107;120 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. We further divided the remaining isolate sequences into mutant (MT) and wildtype (WT) genotypes, with isolates carrying the 14408C>T and 23403A>G mutations classified as MT, while isolates carrying neither mutation classified as WT. 2021 Infection, genetics and evolution Method SARS_CoV_2 C14408T;A23403G 124;137 132;145 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. More recently, 20D and 20I have emerged over the summer of 2020 and include two "variants of concern" (VOC) with signature spike mutation N501Y. 2021 Biochemical and biophysical research communications Method SARS_CoV_2 N501Y 138 143 S 123 128 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. Specifically, a total of 292 whole-genome sequences of SARS-CoV-2 of Malaysia uploaded to GISAID were retrieved up to January 7, 2021, for the analysis of dominance lineage and D614G frequency. 2022 Materials today. Proceedings Method SARS_CoV_2 D614G 177 182 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. The 3D structure of D614 Spike protein of YP_009724390.1 was uploaded onto the DynaMut web server to examine the effect of D614G mutation on Pahang/IIUM91 Spike protein. 2022 Materials today. Proceedings Method SARS_CoV_2 D614G 123 128 S;S 25;155 30;160 33688650 Ultrapotent miniproteins targeting the receptor-binding domain protect against SARS-CoV-2 infection and disease in mice. Binder-virus complexes were added to Vero E6 (WA1/2020) or Vero-hACE2-TMPRSS2 (B.1.1.7 and WA1/2020 E484K/N501Y/D614G) cell monolayers in 96-well plates and incubated at 37 C for 1 h. 2021 bioRxiv Method SARS_CoV_2 E484K;D614G;N501Y 100;112;106 105;117;111 33688650 Ultrapotent miniproteins targeting the receptor-binding domain protect against SARS-CoV-2 infection and disease in mice. The B.1.1.7 and WA1/2020 E484K/N501Y/D614G viruses have been described previously. 2021 bioRxiv Method SARS_CoV_2 E484K;D614G;N501Y 25;37;31 30;42;36 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. This list of mutations was merged with the list of deletion mutations that characterize the different 501Y lineages and the three cardinal 501Y lineage signature mutations, L18F, K417N/K and N501Y which, due to already high frequencies in multiple 501Y lineages could not have doubled in frequency between 15 March and 01 June 2021. 2021 medRxiv Method SARS_CoV_2 K417K;K417N;L18F;N501Y 179;179;173;191 186;186;177;196 33714462 Pyrococcus furiosus Argonaute coupled with modified ligase chain reaction for detection of SARS-CoV-2 and HPV. The spike D614G mutant was distinguished with wild type novel coronavirus using different fluorophores. 2021 Talanta Method SARS_CoV_2 D614G 10 15 S 4 9 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. Best-fit IC50 values of selected mAbs for WT and the Y453F RBD were compared with the extra-sum-of-squares F test. 2021 The Journal of biological chemistry Method SARS_CoV_2 Y453F 53 58 RBD 59 62 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. Briefly, 13 mug/ml ACE-2-Fc was loaded on anti-human Fc capture tips (500 s), base line (60 s), association to 5-point 2-fold serial dilutions starting at 100 nM for WT RBD or 60 nM for Y453F RBD (500 s), and the dissociation phase (500 s). 2021 The Journal of biological chemistry Method SARS_CoV_2 Y453F 186 191 RBD;RBD 169;192 172;195 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. Purified RBD Y453F was buffer-exchanged and biotinylated on the C-terminal AviTag with a biotin ligase kit (Avidity, CO). 2021 The Journal of biological chemistry Method SARS_CoV_2 Y453F 13 18 RBD 9 12 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. RBD WT and Y453F were subjected in triplicates to a thermal ramp of 30C/min in PBS. 2021 The Journal of biological chemistry Method SARS_CoV_2 Y453F 11 16 RBD 0 3 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. Recombinant Y453F RBD was produced by transiently transfecting Expi293 cells (Gibco, Thermo Fisher Scientific, MA) according to the manufacturer's recommendations. 2021 The Journal of biological chemistry Method SARS_CoV_2 Y453F 12 17 RBD 18 21 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. The impact of the Y453F substitution on protein stability was analyzed on a Tycho NT.6 (NanoTemper technologies GmbH, Munich, Germany). 2021 The Journal of biological chemistry Method SARS_CoV_2 Y453F 18 23 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. The next day, sera/mAbs were incubated for 1 h in low-binding round-bottom plates (Thermo Fisher Scientific) with a solution of biotinylated WT or Y453F RBD (4 ng/ml) with HS-strep-HRP (1:16,000 dilution) in PBS with 0.05% Tween-20 (PBS-T) as follows: COVID-19 convalescent sera in a 10% dilution, immunized mouse sera in an 8-point 4-fold dilution starting at 1.25% dilution, and mAbs in a 6-point 4-fold dilution starting at 20 mug/ml. 2021 The Journal of biological chemistry Method SARS_CoV_2 Y453F 147 152 RBD 153 156 COVID-19 252 260 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. The nucleotide sequence corresponding to the SARS-CoV-2 Y453F RBD variant with a C-terminal 10xHis-AviTag (SGSGHHHHHHHHHHGSGGLNDIFEAQKIEWHE) was synthesized and subcloned into a pcDNA3.4-TOPO expression vector by GeneArt (Thermo Fisher Scientific, MA). 2021 The Journal of biological chemistry Method SARS_CoV_2 Y453F 56 61 RBD 62 65 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. The relationship between the inhibition potency of sera and mAbs against the WT and Y453F RBD was estimated by the Mann-Whitney U test, linear regression analyses (reported as R2), and two-tailed Spearman rank correlation tests (reported as rho and a significance value p). 2021 The Journal of biological chemistry Method SARS_CoV_2 Y453F 84 89 RBD 90 93 33725432 Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. The pseudovirus assays for neutralization activity against the original D614G spike, an RBD triple mutant (containing only K417N, E484K, and N501Y), and the B.1.351 spike were performed at the National Institute for Communicable Diseases (South Africa). 2021 The New England journal of medicine Method SARS_CoV_2 D614G;E484K;K417N;N501Y 72;130;123;141 77;135;128;146 S;S;RBD 78;165;88 83;170;91 33725432 Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. To assess neutralization activity of vaccine-elicited antibodies against B.1.351, serum samples from group 1 participants who had negative SARS-CoV-2 serostatus at enrollment and varying pseudovirus neutralization assay titers to the original D614G spike virus at 14 days after the second injection were tested with pseudovirus and live-virus neutralization assays for activity against the B.1.351 variant. 2021 The New England journal of medicine Method SARS_CoV_2 D614G 243 248 S 249 254 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Data regarding demographics, lineage, and presence of the E484K mutation were obtained by specification in the search fields. 2021 Cureus Method SARS_CoV_2 E484K 58 63 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. We performed univariate associations between SII, viral mutations in the P.1 lineage and E484K variants, and number of COVID-19 deaths, which were estimated using the Spearman Correlation Index. 2021 Cureus Method SARS_CoV_2 E484K 89 94 COVID-19 119 127 33729394 Immunity, virus evolution, and effectiveness of SARS-CoV-2 vaccines. More interesting, it was found that SARS-CoV-2 variant carrying non-synonymous substitution D614G in the spike protein, which is localized in the TMPRSS2 cleavage site, has emerged with improved transmission across populations. 2021 Brazilian journal of medical and biological research Method SARS_CoV_2 D614G 92 97 S 105 110 33729394 Immunity, virus evolution, and effectiveness of SARS-CoV-2 vaccines. Subtypes of SARS-CoV-2 carrying D614G mutation and three other linked mutations disseminated globally. 2021 Brazilian journal of medical and biological research Method SARS_CoV_2 D614G 32 37 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. Cloning of native RBD, ACE2 and RBD K417N, E484K, N501Y. 2021 Cell Method SARS_CoV_2 E484K;K417N;N501Y 43;36;50 48;41;55 RBD;RBD 18;32 21;35 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. E.coli DH5alpha bacteria were used for transformation of plasmid pNEO-RBD K417N, E484K, N501Y. 2021 Cell Method SARS_CoV_2 E484K;K417N;N501Y 81;74;88 86;79;93 RBD 70 73 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. The B1.351 virus used in these studies contained the following mutations: D80A, D215G, L242-244 deleted, K417N, E484K, N501Y, D614G, A701V. 2021 Cell Method SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;N501Y 133;80;126;74;112;105;119 138;85;131;78;117;110;124 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. This construct encodes exactly the same protein as native RBD except the K417N, E484K and N501Y mutations, as confirmed by sequencing. 2021 Cell Method SARS_CoV_2 E484K;K417N;N501Y 80;73;90 85;78;95 RBD 58 61 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. To clone RBD K417N, E484K, N501Y, a construct of RBD with the mutation N501Y was used as the template and four primers of RBD (K417N Forward primer 5'-CAGGGCAGACCGGCAATATCGCCGACTACAATTAC-3', K417N reverse primer 5'-GTAATTGTAGTCGGCGATATTGCCGGTCTGCCCTG-3', E484K Forward primer 5'-CACCGTGTAATGGCGTGAAGGGCTTCAATTGCTAC-3' and E484K reverse primer 5'- GTAGCAATTGAAGCCCTTCACGCCATTACACGGTG-3') and two primers of pNEO vector (Forward primer 5'- CAGCTCCTGGGCAACGTGCT-3' and reverse primer 5'-CGTAAAAGGAGCAACATAG-3') were used to do PCR. 2021 Cell Method SARS_CoV_2 E484K;E484K;E484K;K417N;K417N;N501Y;N501Y;K417N 20;255;322;13;191;27;71;127 25;260;327;18;196;32;76;132 RBD;RBD;RBD 9;49;122 12;52;125 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. To express RBD, RBD K417N, E484K, N501Y and ACE2, HEK293T cells were cultured in DMEM high glucose (Sigma) supplemented with 2% FBS, 1% 100X Mem Neaa and 1% 100X L-Glutamine at 37 C for transfection. 2021 Cell Method SARS_CoV_2 E484K;K417N;N501Y 27;20;34 32;25;39 RBD;RBD 11;16 14;19 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. To measure the binding affinities of monoclonal antibodies and ACE2 with native RBD and RBD K417N, E484K, N501Y, each RBD was immobilized onto an AR2G biosensor (Fortebio). 2021 Cell Method SARS_CoV_2 E484K;K417N;N501Y 99;92;106 104;97;111 RBD;RBD;RBD 80;88;118 83;91;121 33731300 Genetic modification to design a stable yeast-expressed recombinant SARS-CoV-2 receptor binding domain as a COVID-19 vaccine candidate. The DNAs encoding RBD219-WT (residues 331-549 of the SARS-CoV-2 spike protein, GenBank: QHD43416.1), RBD219-N1 (residues 332-549), and RBD219-N1C1 (residues 332-549, C538A) were codon-optimized based on yeast codon usage preference and synthesized by GenScript (Piscataway, NJ, USA), followed by subcloning into the Pichia secretory expression vector pPICZalphaA (Invitrogen) using EcoRI/XbaI restriction sites. 2021 Biochimica et biophysica acta. General subjects Method SARS_CoV_2 C538A 166 171 S;RBD;RBD;RBD 64;18;101;135 69;21;104;138 33731300 Genetic modification to design a stable yeast-expressed recombinant SARS-CoV-2 receptor binding domain as a COVID-19 vaccine candidate. These three RBDs were also treated with PNGase-F (New England Biolabs, Ipswich, MA, USA; Cat# P0704S) following the manufacturer's instruction and loaded onto SDS-PAGE gels to evaluate the impact of size caused by glycosylation. 2021 Biochimica et biophysica acta. General subjects Method SARS_CoV_2 P0704S 94 100 RBD 12 16 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. Briefly, PCR amplification was performed using the SARS-CoV-2 Spike D614G plasmid as a template. 2021 Cell Method SARS_CoV_2 D614G 68 73 S 62 67 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. Two point mutants (V354F and V470A) were constructed by site-directed mutagenesis, and the vectors were transfected into HEK293 cells. 2021 Zoological research Method SARS_CoV_2 V470A;V354F 29;19 34;24 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. Identification of S-gene D614G mutation in Basel sequences. 2021 PLoS pathogens Method SARS_CoV_2 D614G 25 30 S 18 19 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. To identify a possible geographic origin of the synonymous C15324T mutation in ORF1ab, we performed a search on all available GISAID genomes as of August 12th 2020. 2021 PLoS pathogens Method SARS_CoV_2 C15324T 59 66 ORF1ab 79 85 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. Viral load (Ct-value) of patients that carried lineages with a mutated S-D614G gene (N = 274) were compared to patients that carried the ancestral allele (N = 12) using a Mann-Whitney U test. 2021 PLoS pathogens Method SARS_CoV_2 D614G 73 78 S 71 72 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. We used Nextclade version 0.3.5 (https://clades.nextstrain.org) to infer genomic mutations and filtered for sequences that contained C15324T. 2021 PLoS pathogens Method SARS_CoV_2 C15324T 133 140 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. Samples were analyzed at 80 kV with a Talos L120C transmission electron microscope (Thermo Fisher Scientific), and images were acquired with a CETA 16M CMOS (complementary metal-oxide semiconductor) camera. 2021 Science advances Method SARS_CoV_2 L120C 44 49 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. Splenic mononuclear cells from each group of immunized mice were cultured in the presence of DCs pulsed with or without S2PECTO, multilayered S2GDeltaHR2-presenting E2P, or I3-01v9 SApNP (1 x 10-7 muM) in complete Iscove's Modified Dulbecco's Medium (IMDM) containing IL-2 (5.0 ng/ml). 2021 Science advances Method SARS_CoV_2 E2P 165 168 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. To remove the S1/S2 cleavage site, an R667G mutation and a 682GSAGSV687 modification were introduced in the SARS-CoV-1 and SARS-CoV-2 spikes, respectively. 2021 Science advances Method SARS_CoV_2 R667G 38 43 S 134 140 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. In assays where mutated RBD harboring K417N, E484K, and N501Y mutations was used, the exact same ELISA protocol was performed after confirming that our standard (CR3022-IgG1) bound to mutant versus wild-type RBD nearly identically. 2021 Cell Method SARS_CoV_2 E484K;K417N;N501Y 45;38;56 50;43;61 RBD;RBD 24;208 27;211 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Interaction/regression analyses were performed using the lm package in R, using pNT50 estimates (normalized to wild type) for each donor sera and allowing for interaction between neutralization estimates for each wild-type RBD variant (v1/wtRBD, v2/wtRBD, or v3/wtRBD) and the variant containing only K417N+E484K+N501Y mutations to explain the composite neutralization of B.1351 v1, v2, and v3. 2021 Cell Method SARS_CoV_2 K417N;E484K;N501Y 301;307;313 306;312;318 RBD;RBD;RBD;RBD 223;241;251;264 226;244;254;267 33750399 Modelling the association between COVID-19 transmissibility and D614G substitution in SARS-CoV-2 spike protein: using the surveillance data in California as an example. During this study period, D614G appears to be the only major amino acid (AA) substitution in the S protein. 2021 Theoretical biology & medical modelling Method SARS_CoV_2 D614G 26 31 S 97 98 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The dynamic behavior of complex wild type, K417N-E484K-N501Y, K417T- E484K-N501Y, E484K, N501Y, and E484K-N501Y was checked by MD simulation performed on Amber20 (Salomon-Ferrer et al., 2013) using FF14SB force field. 2021 Journal of cellular physiology Method SARS_CoV_2 E484K;E484K;E484K;K417N;K417T;N501Y;E484K;N501Y;N501Y;N501Y 69;82;100;43;62;89;49;55;75;106 74;87;105;48;67;94;54;60;80;111 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. To estimate the real binding energy calculations of the wild type, K417N-E484K-N501Y, K417T- E484K-N501Y, E484K, N501Y, and E484K-N501Y, MMGBSA approach was used. 2021 Journal of cellular physiology Method SARS_CoV_2 E484K;E484K;E484K;K417N;K417T;N501Y;E484K;N501Y;N501Y;N501Y 93;106;124;67;86;113;73;79;99;130 98;111;129;72;91;118;78;84;104;135 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. F318W variant of the PDZ domain of PALS1 was obtained by site-directed mutagenesis using a QuickChange Lightning Site-Directed Mutagenesis kit (Agilent Technologies), accordingly to the instructions of the manufacturer. 2021 Computational and structural biotechnology journal Method SARS_CoV_2 F318W 0 5 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. In order to build the complexes between the peptides and PALS1 F318W mutant, the F318 residue of every peptide-protein complex was substituted with a Tryptophan, via Maestro tools, and the systems were minimized with Prime. 2021 Computational and structural biotechnology journal Method SARS_CoV_2 F318W 63 68 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. In silico docking of Envelope tetradecapeptides to PALS1 wild-type and preparation of the peptides-PALS1 F318W complexes. 2021 Computational and structural biotechnology journal Method SARS_CoV_2 F318W 105 110 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. The highest concentration obtained for the wild type protein was 60 muM while for the mutant F318W was 120 muM. 2021 Computational and structural biotechnology journal Method SARS_CoV_2 F318W 93 98 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. The interactions between the peptides (ligands) and the purified PALS1 PDZ domains, both wild type and F318W mutant (analytes) were measured by surface Plasmon resonance (SPR) technique using a Biacore X100 instrument (Biacore, Uppsala, Sweden). 2021 Computational and structural biotechnology journal Method SARS_CoV_2 F318W 103 108 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Modelling of the wild type and N439K variant with respect to ACE-2 binding. 2021 Heliyon Method SARS_CoV_2 N439K 31 36 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Briefly, wt or N501Y mutant RBD proteins (20mug/ml) were captured onto protein A biosensors for 300s. 2021 bioRxiv Method SARS_CoV_2 N501Y 15 20 RBD 28 31 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. For viral replication kinetics, WT, N501Y or UK-8x mutant viruses were inoculated onto the culture at a MOI of 5 in DPBS respectively. 2021 bioRxiv Method SARS_CoV_2 N501Y 36 41 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. For virus replication assays, the animals received DMEM with 2% FBS and 1% penicillin/streptomycin (Mock, n=4), wt G614 virus (n=9), N501Y mutant virus (n=9), UK-8x mutant virus (n=9) at a dose of 104 PFU/hamster. 2021 bioRxiv Method SARS_CoV_2 N501Y 133 138 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Individual point mutations in the spike gene (Delta69-70, Delta145, N501Y, A570D, P681H, T716I, S982A, D1118H and UK-8x) were introduced into an D614G infectious cDNA clone of the 2019n-CoV/USA_WA1/2020 (WA1/2020) strain as described previously. 2021 bioRxiv Method SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 75;103;145;68;82;96;89 80;109;150;73;87;101;94 S 34 39 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. One day later, one infected donor animal was co-housed with one naive animal for 8 hours (10 pairs for N501Y group, 5 pairs for the other groups) and the donors were returned to their cages. 2021 bioRxiv Method SARS_CoV_2 N501Y 103 108 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. The human ACE2 protein was purchased from Sino Biological (Beijing, China; Cat# 10108-H08H) and the human IgG1 Fc-tagged RBD proteins were made in-house using a method as previously described. 2021 bioRxiv Method SARS_CoV_2 H08H 86 90 RBD 121 124 33758837 Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice. Full-length SARS-CoV-2 Seattle, SARS-CoV-2 D614G, SARS-CoV-2 B.1.351, SARS-CoV, WIV-1, and RsSHC014 viruses were designed to express nanoluciferase (nLuc) and were recovered via reverse genetics as described previously. 2021 bioRxiv Method SARS_CoV_2 D614G 43 48 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. 7a-d, f) and potent serum neutralizing Ab titers against wild-type (D614G) SARS-CoV-2 S pseudovirus (GMT 2-3x103). 2021 bioRxiv Method SARS_CoV_2 D614G 68 73 S 86 87 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. D614G SARS-CoV-2 S (YP 009724390.1), RaTG13 S (QHR63300.2), Pangolin-Guangdong S (QLR06867.1), SARS-CoV S (YP 009825051.1), WIV1 S (AGZ48831.1), B.1.351 S and B1.1.7 S pseudotypes VSV viruses were prepared as described previously. 2021 bioRxiv Method SARS_CoV_2 D614G 0 5 S;S;S;S;S 17;104;129;153;166 18;105;130;154;167 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. MLV-based D614G SARS-CoV-2 S, SARS-CoV-2-B-1.351, SARS-CoV S, and WIV-1 S pseudotypes were prepared as previously described (Millet and Whittaker, 2016; Walls et al., 2020 a+b). 2021 bioRxiv Method SARS_CoV_2 D614G 10 15 S;S;S 27;59;72 28;60;73 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. Prepared grids were imaged in a Talos model L120C electron microscope at 57,000x (nanoparticles). 2021 bioRxiv Method SARS_CoV_2 L120C 44 49 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. The cells were harvested and lysed by microfluidization using a Microfluidics M110P at 18,000 psi in 50 mM Tris, 500 mM NaCl, 30 mM imidazole, 1 mM PMSF, 0.75% CHAPS. 2021 bioRxiv Method SARS_CoV_2 M110P 78 83 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. The SARS-CoV-2-B.1.351-RBD-Avi was synthesized by GenScript into CMVR with K417N, E484K, and N501Y mutations from the Wuhan-1 strain used in the SARS-CoV-2-RBD-Avi construct listed above. 2021 bioRxiv Method SARS_CoV_2 E484K;K417N;N501Y 82;75;93 87;80;98 RBD;RBD 23;156 26;159 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. A 250-nucleotide region around the N501Y (A23063T) position in the reference strain (GenBank accession number MN908947) was selected and used to identify the corresponding regions in the GISAID dataset using BLAST. 2021 medRxiv Method SARS_CoV_2 N501Y;A23063T 35;42 40;49 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. An 89 bp region surrounding the 23063 position was amplified using the primer set N501Y-F: 5'ggttttaattgttactttcctttacaa3' and N501Y-R: 5'gaaagtactactactctgtatggttgg3' at 1:10 ratio in an asymmetric PCR. 2021 medRxiv Method SARS_CoV_2 N501Y;N501Y 82;127 87;132 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. Each one step reaction mix was supplemented with 0.2muM of the forward primer N501Y-F and 2 muM of reverse primer N501Y-R, 0.4 muM of each of the SMB probes (SMB-501-WT and SMB-501-MT) and 1 mul of the template RNA. 2021 medRxiv Method SARS_CoV_2 N501Y;N501Y 78;114 83;119 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. CPE endpoint neutralization assays were done following the limiting dilution model and using P1 stocks of B.1.427, D614G, and USA-WA1/2020 lineages. 2021 medRxiv Method SARS_CoV_2 D614G 115 120 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. For isolation of B.1.427 and non-B.1.427/B.1.429 variant D614G viruses, 100 muL each from NP swab samples from COVID-19 patients identified as being infected by the B.1.427 or non-B.1.427/B.1.429 variant D614G lineage was diluted 1:5 in PBS supplemented with 0.75% bovine serum albumin (BSA-PBS) and added to confluent Vero-81 cells in a T25 flask. 2021 medRxiv Method SARS_CoV_2 D614G;D614G 57;204 62;209 COVID-19 111 119 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. For the B.1.429 neutralization studies, a non-B.1.427/B.1.429 variant SARS-CoV-2/human/USA/CA-UCSF-0001C/2020 clinical isolate carrying the D614G spike mutation was isolated as previously described and passaged in A549-ACE22 expressing cells. 2021 medRxiv Method SARS_CoV_2 D614G 140 145 S 146 151 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. SARS-CoV-2 spike mutants (D614G, D614G+W152C, D614G+L452R, and D614G+N501Y) were cloned using standard site-directed mutagenesis and PCR. 2021 medRxiv Method SARS_CoV_2 D614G;D614G;D614G;D614G;L452R;N501Y;W152C 33;46;63;26;52;69;39 38;51;68;31;57;74;44 S 11 16 33761008 Diverse SARS-CoV-2 variants preceded the initial COVID-19 outbreak in Croatia. In addition to the mutations described above, we also identified a unique (as of September 30, 2020, GISAID.org), high-confidence (3866x) mutation (V13I) within the Nsp5A ORF, encoding the main proteinase Mpro, in one of the samples (8U, Supplementary Table 2 and. 2021 Archives of virology Method SARS_CoV_2 V13I 148 152 33761008 Diverse SARS-CoV-2 variants preceded the initial COVID-19 outbreak in Croatia. In our analysis, we utilized the GISAID dynamic phylogenetic framework, which was developed to facilitate genomic epidemiology efforts, and we found that the majority of the fully sequenced strains belonged to clade G (6/7; D614G in the S gene). 2021 Archives of virology Method SARS_CoV_2 D614G 224 229 S 237 238 33761008 Diverse SARS-CoV-2 variants preceded the initial COVID-19 outbreak in Croatia. The analysis of structural models of the Nsp5A V13I mutation showed low mobility for the V13 position, suggesting that the mutation would have a negligible impact on protein function (e.g., conformational changes that drive catalysis) or selective advantage for the virus. 2021 Archives of virology Method SARS_CoV_2 V13I 47 51 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. Alternatively, lentivirus Lenti-GF1-SARS-CoV-2Delta19AA truncated spike envelope displaying the H49Y, S247R, V367F, R408I, V483A, H519Q, A520S, and D614G mutations was produced using the same method. 2021 JCI insight Method SARS_CoV_2 A520S;D614G;H49Y;H519Q;R408I;S247R;V367F;V483A 137;148;96;130;116;102;109;123 142;153;100;135;121;107;114;128 S 66 71 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. coli (New England Biolabs, catalog C3040I). 2021 JCI insight Method SARS_CoV_2 C3040I 35 41 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. Variants were selected based on their prevalence in the wild and evidence of high infectivity or increased fitness and chosen to target the various domains of the spike protein, including the receptor-binding domain (H519Q, A520S). 2021 JCI insight Method SARS_CoV_2 A520S;H519Q 224;217 229;222 S 163 168 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. A total of 64 SARS-CoV-2 positive nasopharyngeal swabs collected in UTM media (Copan, Italy) between December 2020-January 2021 and previously characterized by sequencing (35 of which had the N501Y mutation) were used to validate the method. 2021 Journal of virological methods Method SARS_CoV_2 N501Y 192 197 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. Next, the novel N501Y VD RT-PCR method was used on 757 nasopharyngeal swabs collected prospectively between January 20 and 27 2021, under the same conditions as previous samples. 2021 Journal of virological methods Method SARS_CoV_2 N501Y 16 21 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. Three positive controls were also tested in each run: a confirmed N501 N variant sequence, a confirmed N501Y variant sequence and a mixture of the two. 2021 Journal of virological methods Method SARS_CoV_2 N501N;N501Y 66;103 72;108 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. A two-tailed unpaired Student's t-test was used to determine the statistical significance between wild-type and D614G S-protein RMSD. 2021 Infection, genetics and evolution Method SARS_CoV_2 D614G 112 117 S 118 119 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The mutation of aspartate-614 to glycine was accomplished by the PyMol mutagenesis tool. 2021 Infection, genetics and evolution Method SARS_CoV_2 D614G 16 40 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The S-protein models used in this study were the D614G variant of the SARS-CoV-2 S-protein and the wild-type S-protein (closed-state and open-state). 2021 Infection, genetics and evolution Method SARS_CoV_2 D614G 49 54 S;S;S 4;81;109 5;82;110 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The studied molecular systems were comprised of the selected neutralizing antibodies (antigen-binding fragment, Fab) bound to the RBD or NTD of the SARS-CoV-2 S-protein (wild-type or D614G variant). 2021 Infection, genetics and evolution Method SARS_CoV_2 D614G 183 188 RBD;S 130;159 133;160 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The wild-type and D614G S-protein systems were simulated using GROMACS v2021 and CHARMM36 force field. 2021 Infection, genetics and evolution Method SARS_CoV_2 D614G 18 23 S 24 25 33778179 Mutational analysis of structural proteins of SARS-CoV-2. Similarly, the protein sequence of 6VSB was edited at 614 position to create D614G mutation. 2021 Heliyon Method SARS_CoV_2 D614G 77 82 33778179 Mutational analysis of structural proteins of SARS-CoV-2. Three separate structures of RBD with a point mutation, each namely S477N, V483A, and N501Y were created. 2021 Heliyon Method SARS_CoV_2 N501Y;S477N;V483A 86;68;75 91;73;80 RBD 29 32 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Based on the distribution of the frequent S protein mutations in SARS-CoV-2 isolates from North America and Europe, we focused on the 6 major mutational hot spots, H49Y, G476S, V483A, H519Q, A520S, and D614G. 2021 Gene reports Method SARS_CoV_2 A520S;D614G;G476S;H49Y;H519Q;V483A 191;202;170;164;184;177 196;207;175;168;189;182 S 42 43 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. These data were used to analyze the frequency of D614G mutations in the S protein of SARS-CoV-2 isolated from different geographical origins. 2021 Gene reports Method SARS_CoV_2 D614G 49 54 S 72 73 33789940 Stability of SARS-CoV-2 Spike G614 Variant Surpasses That of the D614 Variant after Cold Storage. The nonsynonymous mutations include ORF1ab-C794T(T265I), ORF1ab-C14144T(P4715L), S-A1841G(D614G), and ORF3a-G171C(Q57H). 2021 mSphere Method SARS_CoV_2 D614G;P4715L;Q57H;T265I;A1841G;C14144T;C794T;G171C 90;72;114;49;83;64;43;108 95;78;118;54;89;71;48;113 ORF1ab;ORF1ab;ORF3a;S 36;57;102;81 42;63;107;82 33789940 Stability of SARS-CoV-2 Spike G614 Variant Surpasses That of the D614 Variant after Cold Storage. There is also a mutation in the 5' untranslated region:C241T. 2021 mSphere Method SARS_CoV_2 C241T 55 60 33791702 Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2. The following sequences were generated: SARS-CoV-2 Wuhan Hu-1 (YP_009724390.1), Wuhan Hu-1 D614G, B.1.1.7 (based on Wuhan-Hu-1 coding sequence but with mutations as listed in), RaTG13 CoV (QHR63300.2), Pangolin CoV Guangdong (EPI_ISL_410721), middle eastern respiratory syndrome CoV (YP_009047204.1). 2021 bioRxiv Method SARS_CoV_2 D614G 91 96 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. A small segment (230-364 amino acids, C-terminal domain) of N protein has been experimentally crystallized (PDB: 6ZCO) recently, so we utilized that opportunity to investigate the effect of mutations P344S on the stability and dynamics of protein (Zinzula et al., 2021). 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 P344S 200 205 N 60 61 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Additionally, we also simulated the available crystal structure of N protein CTD and it's mutant P344S for 50 ns for the same. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 P344S 97 102 N 67 68 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Among seven predictors that we studied, six of them predicted that L37H mutation in E protein destabilizes the overall structure. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 L37H 67 71 E 84 85 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Another supporting evidence is the formation of new van der Waals bonds with Ala211 and Gly212 and hydrophobic contacts with Phe307, Leu339, and Asp216 in MT for the stabilization of overall structure due to R203K mutation. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 R203K 208 213 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Based on simulation data only, it is difficult to predict whether the behaviour of R203K is stabilizing or destabilizing. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 R203K 83 88 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Based on these data, it appears that R203K and G204R structures are more dynamic compared to WT and other two mutants. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 G204R;R203K 47;37 52;42 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Both the mutations, R203K and G204R have inferior outcomes according to the previously reported study (Nagy et al.,). 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 G204R;R203K 30;20 35;25 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Compaction of P13L and S197L mutant structures lead to significant increase in total number of contacts especially hydrogen bonds, polar and aromatics contacts as compared to WT and is indicated in Supplementary Table S5. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 P13L;S197L 14;23 18;28 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Contrastingly, the Rg of R203K appears to have lower values compared to WT in the entire trajectory, while the SASA of mutant appears to have a lower profile than WT. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 R203K 25 30 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. DeltaDeltaG values confirmed that P13L mutation gives stability to the MT. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 P13L 34 38 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. For the third mutation R203K, DynaMut and EnCOM based DeltaDeltaG values were significantly higher, 1.774 kcal mol-1 and 4.666 kcal mol-1 respectively and predicted stabilization compared to the other predictors. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 R203K 23 28 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Furthermore, the RMSF of all the mutants are similar except for R203K and G204R mutants which shows higher continuous fluctuations compared to WT and other two mutants suggesting that R203K and G204R mutations had an effect on the flexibility of the protein structure throughout the simulations. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 G204R;G204R;R203K;R203K 74;194;64;184 79;199;69;189 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. However, G204R appears to have similar compactions and less intramolecular contacts as of WT, but is more dynamic, therefore G204R mutations could be destabilizing the protein N structure. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 G204R;G204R 9;125 14;130 N 176 177 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. However, in nucleocapsid protein, we analysed five mutations, P13L, S197L, R302K, G204R, and P344S that were spanning the whole protein. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 G204R;P13L;P344S;R302K;S197L 82;62;93;75;68 87;66;98;80;73 N 12 24 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. However, R203K and G204R mutations bring the highest flexibility in the protein whereas residues from 225 to 315 show the rigidity in the CTD region. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 G204R;R203K 19;9 24;14 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. However, Rg and SASA of G204R appear to have similar profiles like WT. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 G204R 24 29 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. In E protein, L37H mutation is situated in the terminal part of the transmembrane domain and makes the whole transmembrane helix slightly flexible. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 L37H 14 18 E 3 4 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. In N protein, the P13L mutation site is located at the centre of protein and at the loop region. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 P13L 18 22 N 3 4 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. In P344S MT, the values of RMSF (Figure 5B) are observed significantly greater (6-19 A) than WT (6-13 A) structure. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 P344S 3 8 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. In S protein, the D614G mutation site is located at the loop region of S1 domain. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 D614G 18 23 S 3 4 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. In spike protein, D614G mutation is one of the most widely studied mutations (Fernandez,; Hou et al.,; Korber et al., 2020; Plante et al.,; Volz et al.,; Zhang et al.,). 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 D614G 18 23 S 3 8 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. In spike protein, MT (D614G) has slightly lower values of RMSF (Figure 5C) compared to the WT structure. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 D614G 22 27 S 3 8 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. In summary, mutations P13L and S197L appear to cause structural stabilization leading to an increase in compactness of structure as well as increase in polar and non-polar intramolecular interactions compared to WT and other two mutants. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 P13L;S197L 22;31 26;36 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. In the crystal structure of the C-terminal domain (CTD) of N protein, P344S mutation was found to have a destabilizing effect on mutant protein. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 P344S 70 75 N 59 60 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. In the G204R mutation, all predictors predict the destabilization of mutant N protein except for ENCoM because negative free energy change is occurring after mutation. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 G204R 7 12 N 76 77 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. It appears that Rg and SASA of WT is lower as compared to D614G mutant whereas the total number of intramolecular hydrogen bonds, calculated for the entire trajectory, are high in number in WT as compared to mutant. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 D614G 58 63 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. It can be depicted from Figure 4 that mutations, L37H of E protein, P13L and P344S of N protein and D614G in S protein give flexibility to the MT structures. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 D614G;L37H;P13L;P344S 100;49;68;77 105;53;72;82 E;N;S 57;86;109 58;87;110 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. L37H mutation is part of the terminal region in a helix of the pentameric transmembrane protein. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 L37H 0 4 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Like a P13L mutation, due to proline residue substitution in P344S mutation, MT attains flexibility but less extent at the CTD region. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 P13L;P344S 7;61 11;66 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. MD data shows the overall contacts in MT are higher compared to WT and that can be also considered supporting evidence of stabilizing effect of R203K mutation. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 R203K 144 149 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. MD results show that MT has less number of intramolecular interactions compared to WT which is a good indication of the destabilizing effect of G204R mutation on N protein. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 G204R 144 149 N 162 163 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Our data is in agreement with another study which suggests that the P13L mutation in NTD stabilizes the N protein (Singh et al.,). 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 P13L 68 72 N 104 105 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Our In silico data is further supported by the experimental evidence which suggests that the S197L mutation has mild patient outcome ranging from 76% to 1% (Nagy et al.,). 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 S197L 93 98 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. P13L mutation is located at the N-terminal IDR and substitution of proline with leucine gives the highest flexibility to the NTD as compared to the CTD with DeltaDeltaSvib 0.857 kcal mol-1 K-1. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 P13L 0 4 N 32 33 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. S197L and P13L MT structures have the lowest fluctuations which shows the gaining of rigidity compared to WT protein. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 P13L;S197L 10;0 14;5 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Similarly, R203K and G204R mutations are also positioned at the central linker IDR and the loop of proteins. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 G204R;R203K 21;11 26;16 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. The present results suggest that WT is stable and mutation D614G caused a destabilization leading to a loss of protein compactness. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 D614G 59 64 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. The results from the present work confirm that P344S mutations cause the structural destabilization of N protein leading to loss of protein compactness. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 P344S 47 52 N 103 104 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. The Rg and SASA values of mutant P13L and S197L were observed to be lower as compared to WT and other mutants which indicates that the structure of these mutants are compact compared to WT and other mutants. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 P13L;S197L 33;42 37;47 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. The second mutation, S197L is present at the central linker IDR which is the loop region of the protein. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 S197L 21 26 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. The second mutation, S197L is situated at a peripheral position of IDR in N protein. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 S197L 21 26 N 74 75 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. The total number of intramolecular contacts is also higher in mutant R203K which suggests that at 50 ns, R203K adopts a stable structure compared to WT. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 R203K;R203K 69;105 74;110 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. These results further provide supportive evidence that the structure of WT is compact compared to D614G mutant. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 D614G 98 103 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. These results suggest that P13L and S197L mutation is possibly stabilizing the structure leading to compactness of protein N structure. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 P13L;S197L 27;36 31;41 N 123 124 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. This suggests that WT and G204R mutants adopt similar compact structures during simulation. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 G204R 26 31 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. To investigate the effects of point mutation on the stability and dynamics of S protein and N protein, the wild-type (WT) and mutant structure of S protein (WT, and D614G), and modelled N protein (WT, P13L, S197L, R203K, and G204R) were subjected to 50 ns MD simulation. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 D614G;G204R;P13L;R203K;S197L 165;225;201;214;207 170;230;205;219;212 N;N;S;S 92;186;78;146 93;187;79;147 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. We observed the RMSD of WT and all the mutants are slightly different in the first half of simulation, but in the second half of simulation all the variants and WT display similar behaviour, except R203K which continuously have slightly higher values compared to all other variants. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 R203K 198 203 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. We studied single mutation, L37H, and D614G in envelope and spike proteins respectively. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 D614G;L37H 38;28 43;32 S 60 65 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. A889V (dimension points: X = 60, Y = 74, Z = 96) and V843F mutants (dimensions points: X = 64, Y = 86, Z = 102) were enclosed with 0.531 and 0.499 A spacing, respectively. 2021 Journal, genetic engineering & biotechnology Method SARS_CoV_2 V843F;A889V 53;0 58;5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. V843+A889V double mutant (dimension points: X = 92, Y = 88, Z = 112) had 0.375 A spacing (detail parameters are given in Supplementary file 1). 2021 Journal, genetic engineering & biotechnology Method SARS_CoV_2 A889V 5 10 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Genetic variations in ORF1ab: 17858 (A- > G) and ORF1ab: 17747 (C- > T) corresponded to amino acid variations in ORF1ab: p.5865Y > C and ORF1ab: p.5828P > L, or NSP13: P504L and NSP13: Y541C. 2021 Infection, genetics and evolution Method SARS_CoV_2 P504L;Y541C 168;185 173;190 ORF1ab;ORF1ab;ORF1ab;ORF1ab;Nsp13;Nsp13 22;49;113;137;161;178 28;55;119;143;166;183 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Homology modeling protein of ORF1ab and the variation of ORF1ab (P5828L and Y5865C, NSP13: P504L and NSP13: Y541C) of SARS-CoV-2 were performed by SWISS-MODEL Server (https://swissmodel.expasy.org/interactive). 2021 Infection, genetics and evolution Method SARS_CoV_2 P504L;Y541C;Y5865C;P5828L 91;108;76;65 96;113;82;71 ORF1ab;ORF1ab;Nsp13;Nsp13 29;57;84;101 35;63;89;106 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/index.shtml) and PROVEAN (v1.1) (http://provean.jcvi.org/index.php) were used to predict whether the variation in NSP13: P504L and NSP13: Y541C affected the protein function of NSP13. 2021 Infection, genetics and evolution Method SARS_CoV_2 P504L;Y541C 170;187 175;192 Nsp13;Nsp13;Nsp13 163;180;226 168;185;231 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Protein secondary structure prediction of ORF1ab (QHD43415.1) and the ORF1ab variant (p.5865Y > C and p.5828P > L, also NSP13: P504L and NSP13: Y541C) was performed based on the Chou-Fasman algorithm. 2021 Infection, genetics and evolution Method SARS_CoV_2 P504L;Y541C 127;144 132;149 ORF1ab;ORF1ab;Nsp13;Nsp13 42;70;120;137 48;76;125;142 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. In all cases but one for L18F analysis (Figure 7) the 95% credible interval obtained using the a priori method has been narrower than the 95% confidence interval calculated as 1.96x (standard error of the slope). 2021 Viruses Method SARS_CoV_2 L18F 25 29 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. In these cases we reported confidence interval, while in L18F case we reported the credible interval. 2021 Viruses Method SARS_CoV_2 L18F 57 61 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. From the beginning of January 2021, an increasing number of laboratories have joined the incentive and implemented N501Y-specific protocols. 2021 Microorganisms Method SARS_CoV_2 N501Y 115 120 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. The latest collection date of a N501Y positive whole genome dates to 11 February 2021, and the earliest to 30 November 2020 (accessed GISAID on 1 March). 2021 Microorganisms Method SARS_CoV_2 N501Y 32 37 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. The screening strategy was continuously adapted: a first step included an epidemiological case definition with a recent travel history to the UK or ZA, a second step included a microbiological case definition with an S gene dropout in the TaqPath COVID-19 Combo Kit diagnostic assay (Thermo Fisher), and a third step included the implementation of a N501Y-specific PCR. 2021 Microorganisms Method SARS_CoV_2 N501Y 351 356 S 217 218 COVID-19 248 256 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. The total dataset contained a total of 260 whole genomes from variants of concern with S:N501Y mutations from Switzerland (B.1.1.7, n = 675; B.1.351, n = 53; P.1, n = 11) (Table S4). 2021 Microorganisms Method SARS_CoV_2 N501Y 89 94 S 87 88 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. The measurement of within-lineage genetic distances was done using MEGA6, which was also used to detect the following amino acid substitutions/deletions in the spike glycoprotein sequence: D614G, E484K, N501Y, P681H, 69-70del, and K417N. 2021 Pathogens (Basel, Switzerland) Method SARS_CoV_2 D614G;E484K;K417N;N501Y;P681H 189;196;231;203;210 194;201;236;208;215 S 160 178 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. B.1.1.7 virus contained the following spike mutations: del-H69-V70, del-Y144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H. 2021 bioRxiv Method SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 85;120;92;78;99;113;106 90;126;97;83;104;118;111 S 38 43 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. B.1.351 virus contained the following spike mutations: L18F, D80A, D215G, del-L242_244, R246I, K417N, E484K, N501Y, D614G, A701V. 2021 bioRxiv Method SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;L18F;N501Y;R246I 123;67;116;61;102;95;55;109;88 128;72;121;65;107;100;59;114;93 S 38 43 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. Hamsters were infected through intranasal installation of 105 total PFU per animal of SARS-CoV-2 (USA-WA1/2020) or recombinant SARS-CoV-2 E484K in 100uL of DMEM. 2021 bioRxiv Method SARS_CoV_2 E484K 138 143 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. S-containing lentiviral pseudovirions were produced by co-transfection of packaging plasmid pCMVdR8.2, transducing plasmid pHR' CMV-Luc, S plasmid from SARS-CoV-2 (Wuhan-1, D614G, B.1.1.7, B.1.351) with TMPRSS2 into 293T cells using Fugene 6 transfection reagent (Promega, Madison, WI). 2021 bioRxiv Method SARS_CoV_2 D614G 173 178 S;S 0;137 1;138 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. The SARS-CoV RBD (residues 306-527) and ectodomain of the spike protein (residues 14-1195, with K968P/V969P mutations (GenBank: ABF65836.1) were similarly cloned. 2021 bioRxiv Method SARS_CoV_2 K968P;V969P 96;102 101;107 S;RBD 58;13 63;16 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. The SARS-CoV-2 N-terminal domain (NTD) (residues 14-305), receptor-binding domain (RBD) (residues 319-541), and ectodomain of the spike (S) protein (residues 14-1213 with R682G/R683G/R685G/K986P/V987P mutations) (GenBank: QHD43416.1), were cloned into a customized pFastBac vector. 2021 bioRxiv Method SARS_CoV_2 R682G;K986P;R683G;R685G;V987P 171;189;177;183;195 176;194;182;188;200 S;RBD;N;S 130;83;15;137 135;86;16;138 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. The D614G and B.1.1.7 variant data were taken from the Los Alamos COVID-19 Viral Genome Analysis Pipeline and GISAID, respectively. 2021 medRxiv Method SARS_CoV_2 D614G 4 9 COVID-19 66 74 33834012 Comparison of Clinical Features and Outcomes of Medically Attended COVID-19 and Influenza Patients in a Defined Population in the 2020 Respiratory Virus Season. PyMOL software (version 2.3.2) was used to map the S477N and N439K domain onto the 3D structure. 2021 Frontiers in public health Method SARS_CoV_2 N439K;S477N 61;51 66;56 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. In FEP runs for the K417N mutation, the net charge of the MD system changed from 0 to -1 e (where e is the elementary charge). 2022 Journal of medicinal chemistry Method SARS_CoV_2 K417N 20 25 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. To simulate the binding between the RBD of the South Africa variant and ACE2, we obtained the crystal structure (PDB entry 6M0J) for the RBD-ACE2 complex and introduced three mutations (N501Y, K417N, and E484K) when preparing the .psf and .pdb files for the complex. 2022 Journal of medicinal chemistry Method SARS_CoV_2 E484K;K417N;N501Y 204;193;186 209;198;191 RBD;RBD 36;137 39;140 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Moreover, to track the renowned D614G mutation frequency after July 2020, sanger sequencing of additional 67 SARS-CoV2 positive samples collected during July-October, was performed using the following primer pairs designed by ARTIC network (https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V3); 5'-CCAGCAACTGTTTGTGGACCTA-3', 5' -CAGCCCCTATTAAACAGCCTGC-3'. 2022 Transboundary and emerging diseases Method SARS_CoV_2 D614G 32 37 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. Five truncations (NNTD, NCTD, N NTD, N CTD, and NNTD-CTD) and three mutations (NR203K, NG204R, and NR203K/G204R) were generated from full-length N-mEGFP and subcloned into pET28a(+) vector. 2021 Nature communications Method SARS_CoV_2 G204R 106 111 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. mEGFP, N-mEGFP, and NR203K/G204R-mEGFP were subcloned into pCDX-Tet-On vector with an N-terminal Flag tag and fused with an mEGFP tag at C-terminus for the inducible expression in cells. 2021 Nature communications Method SARS_CoV_2 G204R 27 32 N 86 87 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. The correlation between the mortality and R203K/G204R polymorphism of N protein was calculated with a linear regression model within R 3.6.0. 2021 Nature communications Method SARS_CoV_2 R203K;G204R 42;48 47;53 N 70 71 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. The frequencies of R203K/G204R polymorphism of N protein were calculated with each country and the death ratio information of indicated countries were obtained from WHO website (https://covid19.who.int/). 2021 Nature communications Method SARS_CoV_2 R203K;G204R 19;25 24;30 N 47 48 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Cells were washed three times with 1X DPBS and then infected with 700 ul of either VSV G, SARS-CoV-2 S, SARS-Cov-2 P681H S, SARS-CoV-2 B.1.1.1.7 S, or Delta-Envelope pseudoparticles. 2021 bioRxiv Method SARS_CoV_2 P681H 115 120 S;S;S 101;121;145 102;122;146 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Mutagenesis was carried out on a pCDNA-SARs2 Wuhan-Hu 1 S plasmid to create the P681H mutation, using the Agilent QuickChange Lightning Mutagenesis kit (The original plasmid was generously provided by David Veesler, University of Washington USA). 2021 bioRxiv Method SARS_CoV_2 P681H 80 85 S 56 57 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. pCDNA-SARC-CoV-2 Wuhan-Hu1 P681H S plasmid was then extracted using the Qiagen QIAprep Spin Miniprep Kit and Sanger Sequencing was used to confirm incorporation of the mutation. 2021 bioRxiv Method SARS_CoV_2 P681H 27 32 S 33 34 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. VeroE6 and Vero-TMPRSS2 cells were transfected with a plasmid harboring the spike gene of the SARS-CoV-2 isolate Wuhan-Hu 1, SARS-CoV-2 B.1.1.7 variant, the SARS-CoV-2 isolate Wuhan-Hu 1 with a P681H mutation, or a delta-spike pCDNA3.1+ plasmid, and evaluated through an immunofluorescence assay (IFA). 2021 bioRxiv Method SARS_CoV_2 P681H 194 199 S;S 76;221 81;226 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Viral envelope plasmids included pCAGGS-VSV G as a positive control, pCDNA-SARS-CoV-2 Wuhan-Hu1 S, pCDNA- SARS-CoV-2 Wuhan-Hu1 P681H S, and pCDNA- SARS-CoV-2 B.1.1.1.7 S. 2021 bioRxiv Method SARS_CoV_2 P681H 127 132 S;S;S 96;133;168 97;134;169 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. For K417N RBD/EY6A-222, 1080of data were merged from 3 crystals. 2021 Cell Method SARS_CoV_2 K417N 4 9 RBD 10 13 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. For K417T RBD with EY6A and 222 Fabs, and the P.1 RBD in complex with ACE2, 360was collected from a single crystal. 2021 Cell Method SARS_CoV_2 K417T 4 9 RBD;RBD 10;50 13;53 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. Good crystals of EY6A Fab and 222 Fab complexed with WT, K417T, K417N, B.1.1.7, B.1.351 or P.1 RBD were all obtained from Hampton Research PEGRx 2 screen, condition 35, containing 0.15 M Lithium sulfate, 0.1 M Citric acid pH 3.5, 18% w/v PEG 6,000. 2021 Cell Method SARS_CoV_2 K417N;K417T 64;57 69;62 RBD 95 98 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. The P.1 virus used in these studies contained the following mutations: L18F, T20N, P26S, D138Y, R190S, K417T, E464K, N501Y, D614G, H655Y, T1027I, V1176F. 2021 Cell Method SARS_CoV_2 D138Y;D614G;E464K;H655Y;K417T;L18F;N501Y;P26S;R190S;T1027I;T20N;V1176F 89;124;110;131;103;71;117;83;96;138;77;146 94;129;115;136;108;75;122;87;101;144;81;152 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. To clone P.1 RBD, the construct of B.1.351 RBD was used as the template and the primers of RBD K417T and of pNEO vector mentioned above were used to do PCR. 2021 Cell Method SARS_CoV_2 K417T 95 100 RBD;RBD;RBD 13;43;91 16;46;94 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. To clone RBD K417T and RBD K417N, primers of RBD K417T (forward primer 5'-GGGCAGACCGGCACGATCGCCGACTAC-3' and reverse primer 5'-GTAGTCGGCGATCGTGCCGGTCTGCCC) and primers of RBD K417N (forward primer 5'-CAGGGCAGACCGGCAATATCGCCGACTACAATTAC-3' and reverse primer 5'-GTAATTGTAGTCGGCGATATTGCCGGTCTGCCCTG-3') were used separately, together with two primers of pNEO vector (Forward primer 5'- CAGCTCCTGGGCAACGTGCT-3' and reverse primer 5'- CGTAAAAGGAGCAACATAG-3') to do PCR, with the plasmid of WT RBD as the template. 2021 Cell Method SARS_CoV_2 K417N;K417N;K417T;K417T 27;175;13;49 32;180;18;54 RBD;RBD;RBD;RBD;RBD 9;23;45;171;489 12;26;48;174;492 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. To express RBD, RBD K417T, E484K, N501Y, RBD K417N, RBD K417T, RBD E484K and ACE2, HEK293T cells were cultured in DMEM high glucose (Sigma) supplemented with 2% FBS, 1% 100X Mem Neaa and 1% 100X L-Glutamine at 37 C for transfection. 2021 Cell Method SARS_CoV_2 E484K;E484K;K417N;K417T;K417T;N501Y 27;67;45;20;56;34 32;72;50;25;61;39 RBD;RBD;RBD;RBD;RBD 11;16;41;52;63 14;19;44;55;66 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. To measure the binding affinity of ACE2 with P.1 RBD and affinities of monoclonal antibodies and ACE2 with native RBD and, RBD K417N, RBD K417T, RBD E484K and RBD K417T E484K N501Y, eachP.1 RBD, each RBD was immobilized onto an AR2G biosensor (Fortebio). 2021 Cell Method SARS_CoV_2 E484K;E484K;K417N;K417T;K417T;N501Y 149;169;127;138;163;175 154;174;132;143;168;180 RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD 49;114;123;134;145;159;190;200 52;117;126;137;148;162;193;203 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. We identified 63 clusters for D614 all-down, 78 clusters for D614 one-up, 54 clusters for D614G all-down, and 103 clusters for D614G one-up. 2021 Science advances Method SARS_CoV_2 D614G;D614G 90;127 95;132 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. In brief, using the cryo-EM structure (RCSB: 7KMB) of the spike/ACE2 complex, after the energy-minimization, the reported mutant of the spike mutant (N501Y) or ACE2 mutant (ACE2v2 and ACE2.v2.4) in the spike/ACE2 complex was reconstructed using the PyMol mutation tool to replace each residue with the reported mutations (T27Y/L79T/N330Y/A386L for ACE2.v2 and T27Y/L79T/N330Y for ACE2.v2.4). 2021 The journal of physical chemistry. B Method SARS_CoV_2 N501Y;A386L;L79T;L79T;N330Y;N330Y 150;338;327;365;332;370 155;343;331;369;337;375 S;S;S 58;136;202 63;141;207 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. Therefore, in this study, the previously reported experimental binding affinities for the wild-type spike protein of SARS-CoV-2 with wild-type ACE2, ACE2.v2, and ACE2.v2.4 (along with the binding affinities of the N501Y variant spike protein with both wild-type ACE2 and ACE2.v2.4, which were published while this article was under review) were used to calibrate the calculated binding free energies. 2021 The journal of physical chemistry. B Method SARS_CoV_2 N501Y 214 219 S;S 100;228 105;233 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. These structures were energy-minimized using the Sander module of the Amber20 package, and their MM-PBSA binding free energies (DeltaGPB) were evaluated using the MM-PBSA.py module of Amber20, as previously reported.- Additionally, to estimate the change in binding free energy with the miniprotein inhibitors, the available crystal structures of miniproteins LCB1 (RCSB: 7JZU) and LCB3 (RCSB: 7JZM) were energy-minimized, and their binding free energies with both the wild-type spike protein and the N501Y variant were estimated using the same methodology. 2021 The journal of physical chemistry. B Method SARS_CoV_2 N501Y 501 506 S 479 484 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. For measuring affinities against SARS-CoV-2 RBD, SARS-CoV-2 RBD WT, and SARS-CoV-2 RBD N501Y, WNbFc antibodies were loaded onto sensor tips by submerging in 5 mug/mL WNbFc antibody for 200 s. 2021 Proc Natl Acad Sci U S A Method SARS_CoV_2 N501Y 87 92 RBD;RBD;RBD 44;60;83 47;63;86 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Prophylaxis Studies in Mice Using SARS-CoV-2 D614G N501Y Virus. 2021 Proc Natl Acad Sci U S A Method SARS_CoV_2 D614G;N501Y 45;51 50;56 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. WNbFc antibody affinities to SARS-CoV-2 RBD, SARS-CoV-2 spike, SARS-CoV-2 RBD WT, and SARS-CoV-2 RBD N501Y were measured using the above method with the following modifications. 2021 Proc Natl Acad Sci U S A Method SARS_CoV_2 N501Y 101 106 S;RBD;RBD;RBD 56;40;74;97 61;43;77;100 33893880 Combined RT-qPCR and pyrosequencing of a Spike glycoprotein polybasic cleavage motif can uncover pediatric SARS-CoV-2 infections associated with heterogeneous presentation. E3007E) on a Corbett Rotor-Gene 6000 instrument. 2021 Molecular and cellular pediatrics Method SARS_CoV_2 E3007E 0 6 33894500 Screening of potent phytochemical inhibitors against SARS-CoV-2 protease and its two Asian mutants. Protein mutants (R60C and I152V) were created in PyMOL and saved in.pdb format for processing. 2021 Computers in biology and medicine Method SARS_CoV_2 I152V;R60C 26;17 31;21 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. Further, the P323L mutation reported by Pachetti et al. 2021 Frontiers in molecular biosciences Method SARS_CoV_2 P323L 13 18 33900193 Introduction of ORF3a-Q57H SARS-CoV-2 Variant Causing Fourth Epidemic Wave of COVID-19, Hong Kong, China. data, https://doi.org/10.1101/2020.10.27.357558), including mutations in the RNA-dependent RNA polymerase (RdRp[L323P]), Spike(D614G), open reading frame 3a (ORF3a[Q57H]), ORF3b(E14*), and nucleocapsid (N[S194L]) proteins. 2021 Emerging infectious diseases Method SARS_CoV_2 D614G;E14X;L323P;Q57H;S194L 127;178;112;164;205 132;182;117;168;210 RdRp;N;ORF3b;S;ORF3a;RdRP;N 77;189;172;121;158;107;203 105;201;177;126;163;111;204 33900193 Introduction of ORF3a-Q57H SARS-CoV-2 Variant Causing Fourth Epidemic Wave of COVID-19, Hong Kong, China. Introduction of ORF3a-Q57H SARS-CoV-2 variant causing fourth epidemic wave of COVID-19, Hong Kong, China. 2021 Emerging infectious diseases Method SARS_CoV_2 Q57H 22 26 33900193 Introduction of ORF3a-Q57H SARS-CoV-2 Variant Causing Fourth Epidemic Wave of COVID-19, Hong Kong, China. The ORF3a(Q57H) mutation leads a major truncation of ORF3b protein, ORF3b(E14*). 2021 Emerging infectious diseases Method SARS_CoV_2 E14X;Q57H 74;10 78;14 ORF3b;ORF3b;ORF3a 53;68;4 58;73;9 33900193 Introduction of ORF3a-Q57H SARS-CoV-2 Variant Causing Fourth Epidemic Wave of COVID-19, Hong Kong, China. The wave 1 virus we studied did not have these 2 mutations; the wave 3 virus had the Spike(D614G) but not the ORF3a(Q57H) mutation (Table). 2021 Emerging infectious diseases Method SARS_CoV_2 D614G;Q57H 91;116 96;120 S;ORF3a 85;110 90;115 33900193 Introduction of ORF3a-Q57H SARS-CoV-2 Variant Causing Fourth Epidemic Wave of COVID-19, Hong Kong, China. To determine whether the ORF3a(Q57H) would affect this phenotype, we tested these viruses in human respiratory organoid cultures. 2021 Emerging infectious diseases Method SARS_CoV_2 Q57H 31 35 ORF3a 25 30 33900193 Introduction of ORF3a-Q57H SARS-CoV-2 Variant Causing Fourth Epidemic Wave of COVID-19, Hong Kong, China. To differentiate the effect of Spike(D614G) and ORF3a(Q57H) mutations in our assays, we included viruses isolated from epidemic waves 1 and 3 as controls. 2021 Emerging infectious diseases Method SARS_CoV_2 D614G;Q57H 37;54 42;58 S;ORF3a 31;48 36;53 33900193 Introduction of ORF3a-Q57H SARS-CoV-2 Variant Causing Fourth Epidemic Wave of COVID-19, Hong Kong, China. We noted that this wave 4 virus contains a Spike(D614G) mutation that is associated with enhanced virus replication and transmission (B. 2021 Emerging infectious diseases Method SARS_CoV_2 D614G 49 54 S 43 48 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. We further classified SARS-CoV-2 clades into 2 clade groups depending on the presence of the 23403A>G (D614G) spike glycoprotein variant. 2021 JAMA network open Method SARS_CoV_2 A23403G;D614G 93;103 101;108 S 110 128 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Briefly, lentiviral particles were produced by co-transfecting the gene encoding SARS-CoV-2 spike protein (D614G or B.1.526) and Env-deficient HIV backbone expressing Luciferase-IRES-ZsGreen. 2021 bioRxiv Method SARS_CoV_2 D614G 107 112 S 92 97 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Human plasma samples were assayed for neutralization activity against lentiviruses pseudotyped with SARS-CoV-2 spike containing a 21-amino acid cytoplasmic tail deletion and either D614G or mutations corresponding to lineage B.1.526 (L5F, T95I, D253G, E484K, D614G, and A701V). 2021 bioRxiv Method SARS_CoV_2 A701V;D253G;D614G;D614G;E484K;T95I;L5F 270;245;181;259;252;239;234 275;250;186;264;257;243;237 S 111 116 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Separate inference was performed for B.1.1.7 (n=354), B.1.427 (n=35), B.1.429 (n=69), B.1.526 E484 (n=569), and B.1.526 E484K (n=678). 2021 bioRxiv Method SARS_CoV_2 E484K 120 125 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. To estimate the timing and approximate linear slope of increase in B.1.526 and the E484K clade prevalence, we employed a segmented regression analysis (segmented package in R). 2021 bioRxiv Method SARS_CoV_2 E484K 83 88 33907751 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania. All 253 SARS-CoV-2 genomes that were assigned to Pango lineage B.1.1.7 and possessing the E484K spike mutation (including the study isolate CHOP_204) were downloaded from GISAID on 04/17/2021. 2021 bioRxiv Method SARS_CoV_2 E484K 90 95 S 96 101 33907767 Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. Between December 1,2020 and March 1,2021 all available specimens testing positive for SARS-CoV-2 by NAAT with RT-qPCR cycle threshold (Ct) <= 30 or transcription-mediated amplification relative light units (RLU) >= 1,100 during this period were subject to multiplex allele-specific genotyping RT-qPCR targeting three spike mutations associated with known variants of concern, including N501Y (B.1.1.7, B.1.351, P.1), E484K (B.1.351, P.1), and L452R (B.1.427/B.1.429). 2021 medRxiv Method SARS_CoV_2 E484K;L452R;N501Y 417;443;386 422;448;391 S 317 322 33907767 Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. If no L452R, N501Y, or E484K mutations were identified, the infection was designated as wild-type SARS-CoV-2. 2021 medRxiv Method SARS_CoV_2 E484K;L452R;N501Y 23;6;13 28;11;18 33907767 Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. The primary outcome was the presence of L452R mutation consistent with presumptive B.1.427/B.1.429. 2021 medRxiv Method SARS_CoV_2 L452R 40 45 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. A previous study reported that N501Y existed in a mouse-adapted strain, named MASCp6, which was isolated by serial passaging of SARS-CoV-2 in the respiratory tract of mice and led to interstitial pneumonia in this mouse challenge model. 2021 Virology journal Method SARS_CoV_2 N501Y 31 36 Pneumonia 183 205 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. Additionally, the free energy perturbation method also predicted that N501Y weaken the binding affinity of CB6 to RBD. 2021 Virology journal Method SARS_CoV_2 N501Y 70 75 RBD 114 117 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. As shown in Table 1, the neutralizing activity and binding affinity of CB6 against N501Y were decreased distinctly compared to WT (7.38- and 6.67-fold, respectively), with another two Class 1 nAbs (P2C-1F11 and REGN10933) slightly affected. 2021 Virology journal Method SARS_CoV_2 N501Y 83 88 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. Consistently, surface plasmon resonance analysis also revealed that the binding affinity of BD-23 to N501Y variant was increased 6.65-fold as compared with the wild type RBD. 2021 Virology journal Method SARS_CoV_2 N501Y 101 106 RBD 170 173 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. In addition, the K417N and E484K contribute more than a single N501Y substitution in the resistance of virus to the neutralization by nAbs in a study which measured the neutralizing potencies of eight human nAbs against two SARS-CoV-2 variants both carrying N501Y mutation (N501Y.V1 and N501Y.V2). 2021 Virology journal Method SARS_CoV_2 E484K;K417N;N501Y;N501Y;N501Y;N501Y 27;17;63;258;287;274 32;22;68;263;292;279 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. Indeed, it is reported that the neutralizing activities of four nAbs (lacking analysis of neutralizing epitope) against SARS-CoV-2_N501Y, and one nAb (03-1F9) showed a decrease of six-fold in the neutralization. 2021 Virology journal Method SARS_CoV_2 N501Y 131 136 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. Not surprisingly, the N501Y mutation did not affect the neutralizing and binding activities of S309 and EY6A. 2021 Virology journal Method SARS_CoV_2 N501Y 22 27 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. Our results were similar with that of above two studies, which indicated that the N501Y mutation may partially affect the neutralizing potencies of some nAbs. 2021 Virology journal Method SARS_CoV_2 N501Y 82 87 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. Sequence analysis revealed that another two amino acid substitutions (K417N and Q493H) appeared in RBD of SARS-CoV-2 spike besides N501Y. 2021 Virology journal Method SARS_CoV_2 N501Y;Q493H;K417N 131;80;70 136;85;75 S;RBD 117;99 122;102 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. Specifically, one flow cell of the CM5 sensor chips were covalently coated with the wild type or N501Y mutant RBDs (Sino Biological, Beijing) in 10 mM sodium acetate buffer (pH 5.0) for a final RU (response units) around 250, whereas the other flow cell was left uncoated and blocked as a control. 2021 Virology journal Method SARS_CoV_2 N501Y 97 102 RBD 110 114 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. Structural remodeling showed that the binding capacity of RBD of viral spike to mouse ACE2 protein was increased by the substitution of N501Y. 2021 Virology journal Method SARS_CoV_2 N501Y 136 141 S;RBD 71;58 76;61 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. The binding assays of monoclonal antibodies to the wild type and N501Y mutant SARS-CoV-2 RBDs were performed using the Biacore 8 K system (GE Healthcare). 2021 Virology journal Method SARS_CoV_2 N501Y 65 70 RBD 89 93 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. The mutation N501Y in the circulating strain in England is not the first time identified from SARS-CoV-2 live virus. 2021 Virology journal Method SARS_CoV_2 N501Y 13 18 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. These three nAbs of Class 2 did not contact with N501 epitope directly, so kept stable neutralizing and binding activities against N501Y mutant (Table 1, Additional file 1. 2021 Virology journal Method SARS_CoV_2 N501Y 131 136 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. To assess the effect of the N501Y substitution on the recognition with nAbs, we measured the neutralizations and binding affinities of these nAbs against the Wuhan-Hu-1 strain (WT) and N501Y mutant by pseudovirus neutralizing assay and surface plasmon resonance (SPR). 2021 Virology journal Method SARS_CoV_2 N501Y;N501Y 28;185 33;190 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. Unexpectedly, the N501Y mutant virus was more sensitive (6.58-fold) to the neutralization of BD-23, another Class 2 antibody which also contact directly with N501. 2021 Virology journal Method SARS_CoV_2 N501Y 18 23 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. The full molecular dynamics simulation of the native and the (R355D K424E) mutant structures required 2 machines with 36 CPUs each. 2021 Scientific reports Method SARS_CoV_2 K424E;R355D 68;62 73;67 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. For cryo-EM, both N501Y and unmutated SARS-CoV-2 spike ectodomain preparations were deposited on grids at a concentration of 2.25 mg/ml. 2021 PLoS biology Method SARS_CoV_2 N501Y 18 23 S 49 54 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. One hundred microliters of wild-type or N501Y SARS-CoV-2 S protein preparation was coated onto 96-well MaxiSorp plates at 2 mug/ml in PBS overnight at 4 C. 2021 PLoS biology Method SARS_CoV_2 N501Y 40 45 S 57 58 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. SARS-CoV-2 S and SARS-CoV-2 S N501Y pseudotyped retroviral particles were produced in HEK293T cells as described previously. 2021 PLoS biology Method SARS_CoV_2 N501Y 30 35 S;S 11;28 12;29 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. SARS-CoV-2 S N501Y plasmid was obtained from SARS-CoV-2 S plasmid (HDM-IDTSpike-fixK) by site-directed mutagenesis (Q5 Site-Directed Mutagenesis Kit, New England Biolabs). 2021 PLoS biology Method SARS_CoV_2 N501Y 13 18 S;S 11;56 12;57 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. The N501Y mutation was introduced by site-directed mutagenesis (Q5 Site-Directed Mutagenesis Kit, New England Biolabs). 2021 PLoS biology Method SARS_CoV_2 N501Y 4 9 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Using a Vitrobot Mark IV (Thermo Fisher Scientific), the sample was applied to either Quantifoil Holey Carbon R1.2/1.3 copper 300 mesh grids (N501Y spike alone and in complex with ACE2) or UltrAuFoil Holey Gold 300 mesh grids (N501Y spike in complex with VH ab8 or Fab ab1) at a chamber temperature of 10 C with a relative humidity level of 100%, and then vitrified in liquid ethane after blotting for 12 s with a blot force of -10. 2021 PLoS biology Method SARS_CoV_2 N501Y;N501Y 142;227 147;232 S;S;S 148;233;405 153;238;406 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Subsequently, SARS-CoV-2 Spike variants (D614G, V367F/D614G, P384L/D614G, R408I/D614G, N501Y/D614G, K417N/N501Y/D614G, E484K/N501Y/D614G) were generated using a Quikchange XL site-directed mutagenesis kit (Agilent, Santa Clara, CA, USA) according to manufacturer's instructions. 2021 Viruses Method SARS_CoV_2 E484K;K417N;N501Y;P384L;R408I;V367F;D614G;D614G;D614G;D614G;D614G;D614G;D614G;N501Y;N501Y 119;100;87;61;74;48;41;54;67;80;93;112;131;106;125 124;105;92;66;79;53;46;59;72;85;98;117;136;111;130 S 25 30 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. The 4 selected mutants (D614G, N501Y/D614G, K417N/501Y/D614G, and E484K/N501Y/D614G) in the spike protein were generated using the Build Mutant protocol in Discovery Studio 2020 (Dassault Systemes BIOVIA, San Diego, CA, USA, 2020). 2021 Viruses Method SARS_CoV_2 E484K;K417N;N501Y;D614G;D614G;D614G;D614G;N501Y 66;44;31;24;37;55;78;72 71;49;36;29;42;60;83;77 S 92 97 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. The primers used to generate SARS-CoV-2 Spike variants are described as follow: V367F forward 5'-GCTGACTACTCTTTCCTCTACAACTCT-3'; V367F reverse 5'-AGAGTTGTA GAGGAAAGAGTAGTCAGC-3'; P384L forward 5'-ATGGAGTGAGCC TAACCAAACT GAA-3'; P384L reverse 5'-TTCAGTTTGGTTAGGCTCACTCCAT-3'; R408I forward 5'-GAGATGAGGTGATACAGATTGC CCC-3'; R408I reverse 5'-GGGGCAATCTGTATCACCTCATCTC-3'; K417N forward 5'-GACAAACAGGCAACATTGCT GACTACA-3'; K417N reverse 5'-TGTAGTCAGCAATGTTGCCTGTTTGTC-3'; E484K forward 5'-ATG AATGGAGTGAAGGGCTTCAACTG-3'; E484K reverse 5'-CAGTTGAAGCCCTTCACT CCATTACAT-3'; N501Y forward 5'-CTTCCAACCAACCTATGGAGTG GGCTA-3'; N501Y reverse 5'-TAGCCCACTCCATAGGTTGGTTGGAAG-3'; D614G forward 5'-TGC TCTACCAGGGTGTGAACTGTAC-3'; D614G reverse 5'-GTACAGTTCAC ACCCTGGTAGAGCA-3'. 2021 Viruses Method SARS_CoV_2 D614G;D614G;E484K;E484K;K417N;K417N;N501Y;N501Y;P384L;P384L;R408I;R408I;V367F;V367F 667;715;469;518;370;420;568;618;179;228;275;323;80;129 672;720;474;523;375;425;573;623;184;233;280;328;85;134 S 40 45 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. Risk Ratio of Case Fatality Associated with N501Y Substitution. 2021 Viruses Method SARS_CoV_2 N501Y 44 49 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. Straightforwardly, zeta > 1 indicates that N501Y substitution is associated with an increase in case fatality risk, zeta < 1 indicates that N501Y substitution is associated with a decrease in case fatality risk, and zeta = 1 indicates that N501Y substitution is not associated with any increase or decrease in case fatality risk. 2021 Viruses Method SARS_CoV_2 N501Y;N501Y;N501Y 43;140;240 48;145;245 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. The COVID-19 outbreaks in the UK can be considered as two epidemics waves, and the N501Y substitution is observed during the second epidemic wave, which started in September 2020. 2021 Viruses Method SARS_CoV_2 N501Y 83 88 COVID-19 4 12 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. Then, the difference in the variant-specific case fatality ratios characterizing the change of mortality risk associated with N501Y substitution in SARS-CoV-2. 2021 Viruses Method SARS_CoV_2 N501Y 126 131 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. Thus, the risk ratio (RR) of N501Y substitution, denoted by zeta (>=0), can be defined as zeta = rCFRj = 1,t/rCFRj = 0,t. 2021 Viruses Method SARS_CoV_2 N501Y 29 34 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. We examined the consistency of both the sign (or comparing with 1 for RR) and the 95%CI of the effect in case fatality risk associated with N501Y substitution under the alternative settings. 2021 Viruses Method SARS_CoV_2 N501Y 140 145 33922914 Dieckol and Its Derivatives as Potential Inhibitors of SARS-CoV-2 Spike Protein (UK Strain: VUI 202012/01): A Computational Study. A model of UK SARS-CoV-2 Spike protein RBD was generated by inserting Tyr453Phe and Asn501Tyr mutations in the Spike protein RBD using PyMol. 2021 Marine drugs Method SARS_CoV_2 N501Y;Y453F 84;70 93;79 S;S;RBD;RBD 25;111;39;125 30;116;42;128 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. Five days after AdV transduction, mice were treated with 850ng of WT, 19del, or 19del + D614G PsV i.n. 2021 Journal of biomedical science Method SARS_CoV_2 19del;19del;D614G 70;80;88 75;85;93 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. To generate 19del + D614G mutation PsV plasmid (PCMV3-S614-cd19), site-directed mutagenesis was used for generating D614G mutation in the SARS-CoV-2 spike sequence. 2021 Journal of biomedical science Method SARS_CoV_2 19del;D614G;D614G 12;20;116 17;25;121 S 149 154 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. To generate the 19del pseudovirus (PsV) plasmid (PCMV3-S-cd19), 19 amino acids were deleted in the spike protein sequence of SARS-CoV-2 strain Wuhan-Hu-1. 2021 Journal of biomedical science Method SARS_CoV_2 19del 16 21 S;S 99;55 104;56 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. Plasmids expressing S proteins with D614G mutation and furin cleavage site mutation (RRAR AAAR), designated as D614G and AAAR, respectively, were generated by site-directed mutagenesis of the plasmid Str. 2021 Emerging microbes & infections Method SARS_CoV_2 D614G;D614G 36;111 41;116 S 20 21 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. Pseudovirus Str or D614G was mixed with 4-fold serial dilutions of serum at 1:1 ratio (75 microL/75 microL), incubated at 37 C for 1 h, and added to each well for spin infection. 2021 Emerging microbes & infections Method SARS_CoV_2 D614G 19 24 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. Pseudoviruses Str, D614G and AAAR were concentrated by 20% sucrose cushion ultracentrifugation at 110,000x g and 4 C for 5 h and resuspended in 1x PBS. 2021 Emerging microbes & infections Method SARS_CoV_2 D614G 19 24 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. The two-tailed Spearman correlation test was used to determine the relationship between pseudovirus NT50 titers and SARS-CoV-2 PRNT50 titers or the sampling time post symptom onset; the two-tailed Wilcoxon rank signed test the NT50 titers to pseudoviruses Str and D614G (GraphPad 6.0). 2021 Emerging microbes & infections Method SARS_CoV_2 D614G 264 269 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. To generate pseudoviruses for infection and neutralization, HEK-293T cells were seeded in 10-cm dish one day before transfection and co-transfected with 12 microg pNL4-3 R-E-miRFP and 3 microg of plasmids Str, D614G, AAAR or pVSV-G. 2021 Emerging microbes & infections Method SARS_CoV_2 D614G 210 215 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. Molecular dynamics simulations were carried out for the wild-type S protein and for the D936Y mutant in the pre-fusion and post-fusion conformations, starting from the experimental structures used for modeling the mutants (see above). 2021 Molecules (Basel, Switzerland) Method SARS_CoV_2 D936Y 88 93 S 66 67 33948590 A broadly neutralizing antibody protects against SARS-CoV, pre-emergent bat CoVs, and SARS-CoV-2 variants in mice. Full-length SARS-CoV-2 Seattle, SARS-CoV-2 D614G, SARS-CoV-2 B.1.351, SARS-CoV-2 B.1.1.7, SARS-CoV, WIV-1, and RsSHC014 viruses were designed to express nanoluciferase (nLuc) and were recovered via reverse genetics as described previously. 2021 bioRxiv Method SARS_CoV_2 D614G 43 48 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. 18 The 3D rendering of the location of S:T478K in the SARS-CoV-2 Spike/Human ACE2 complex was based on the crystal structure from, 19 deposited in the Protein Data Bank 20 entry 6VW1. 2021 Journal of medical virology Method SARS_CoV_2 T478K 42 47 S;S 66;40 71;41 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. This same trend in 1,059.C > T and 25,563.G > T in North American SARS-CoV-2 and that of the other continents was traced by the date of occurrence of the two SNPs. 2021 Transboundary and emerging diseases Method SARS_CoV_2 C059T;G563T 21;38 30;47 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. The box size was 60, 53, 80 centered between the furin cleavage domain and S247R. 2021 Computational and structural biotechnology journal Method SARS_CoV_2 S247R 75 80 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. The initial cosolvent simulations formed the rationale behind the docking and subsequent experiments to test the binding of longer HS to the PRRARS site and S247R. 2021 Computational and structural biotechnology journal Method SARS_CoV_2 S247R 157 162 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. The two systems of the S247R S protein monomer with HP and HS dodecasaccharides were prepared for MD simulations using the CHARMM glycan input generator according to the same settings outlined in 2.2. 2021 Computational and structural biotechnology journal Method SARS_CoV_2 S247R 23 28 S 29 30 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. To confirm the MD simulation results, ClusPro was used to dock heparin to an unglycosylated monomer subunit of the S protein in the "up" conformation and with the S247R mutation. 2021 Computational and structural biotechnology journal Method SARS_CoV_2 S247R 163 168 S 115 116 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. Using this same Levenshtein similarity cut-off of 0.7, sets of highly conserved basic amino acid containing sequences extracted from heparin binding proteins were used to support the validity of the proposed binding site in the SARS-CoV-2 S247R mutant S protein NTD. 2021 Computational and structural biotechnology journal Method SARS_CoV_2 S247R 239 244 S 252 253 33968806 SARS CoV-2 Nucleoprotein Enhances the Infectivity of Lentiviral Spike Particles. Site-directed mutagenesis was employed to generate a D614G mutant version of the SARS CoV-2 spike glycoprotein from the available sequence (Addgene, plasmid catalog #155297). 2021 Frontiers in cellular and infection microbiology Method SARS_CoV_2 D614G 53 58 S 92 110 33969329 Interferon antagonism by SARS-CoV-2: a functional study using reverse genetics. We constructed SARS-CoV-2 overexpression plasmids encoding wild-type protein 6 (Gln51, Gln56) as well as constructs with substitutions Gln51Glu, Gln56Glu, or both. 2021 The Lancet. Microbe Method SARS_CoV_2 Q51E;Q56E 135;145 143;153 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. The cryoEM structure of the SARS-CoV-2 (Wuhan-Hu-1) RBD/ACE2-B0AT1 complex (PDB 6M17) was used as the basis for modeling N501Y. 2021 Journal of cellular immunology Method SARS_CoV_2 N501Y 121 126 RBD 52 55 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. The prefusion SARS-CoV-2 (Wuhan-Hu-1) spike glycoprotein with a single receptor-binding domain up (PDB 6VSB) was used as the basis for modeling D570A, D614G, T716I, S982A and D1118H. 2021 Journal of cellular immunology Method SARS_CoV_2 D1118H;D570A;D614G;S982A;T716I 175;144;151;165;158 181;149;156;170;163 S 38 56 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? A preprint study published in medRxiv showed that serum of convalescent COVID-19 patients and vaccinators could neutralize the N501Y variant, suggesting that current SARS-CoV-2 vaccines will protect against the 20B/501Y.V1 strain. 2021 Journal of Korean medical science Method SARS_CoV_2 N501Y 127 132 COVID-19 72 80 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? A previous study reported that the D614G mutation increases susceptibility of the virus to neutralization, and the D614G mutation is not expected to threaten current vaccine development. 2021 Journal of Korean medical science Method SARS_CoV_2 D614G;D614G 35;115 40;120 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? Among these mutations, five (L18F, S98F, A262S, A222V, and P272L) occurred in the N-terminal domain (NTD) of the S protein, and five (N439K, Y453F, S477N, E484K, and N501Y) appeared in the S protein RBD. 2021 Journal of Korean medical science Method SARS_CoV_2 A222V;A262S;E484K;N501Y;P272L;S477N;S98F;Y453F;L18F;N439K 48;41;155;166;59;148;35;141;29;134 53;46;160;171;64;153;39;146;33;139 RBD;N;S;S 199;82;113;189 202;83;114;190 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? found that E484K reduced the neutralizing potency of convalescent sera from some donors by 10-fold. 2021 Journal of Korean medical science Method SARS_CoV_2 E484K 11 16 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? However, in another study, the D614G mutation did not alter the binding of the spike protein to ACE2 or the neutralization sensitivity of pseudoviruses. 2021 Journal of Korean medical science Method SARS_CoV_2 D614G 31 36 S 79 84 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? In addition, the D614G, S477N, and E484K mutants of the S protein are considered to pose a risk of immune escape or increased ACE2 binding by the virus, thereby affecting COVID-19 vaccine development and antibody treatment. 2021 Journal of Korean medical science Method SARS_CoV_2 D614G;E484K;S477N 17;35;24 22;40;29 S 56 57 COVID-19 171 179 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? On January 25, 2021, a preprint study in bioRxiv assessed the neutralizing capacity of sera from human subjects or non-human primates that received the mRNA-1273 vaccine and demonstrated that compared with vesicular stomatitis virus (VSV) pseudovirus, VSV pseudoviruses with S protein containing K417N-E484K-N501Y-D614G resulted in a 2.7-fold higher geometric mean titer reduction. 2021 Journal of Korean medical science Method SARS_CoV_2 K417N;D614G;E484K;N501Y 296;314;302;308 301;319;307;313 S 275 276 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? S477N, a mutation involving the RBD, has emerged independently in Australia and is responsible for much of the summer 2020 outbreak. 2021 Journal of Korean medical science Method SARS_CoV_2 S477N 0 5 RBD 32 35 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? The authors suggested that the D614G mutation might increase infectivity by assembling more functional S protein into virions. 2021 Journal of Korean medical science Method SARS_CoV_2 D614G 31 36 S 103 104 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? The E484K mutation is associated with the 501Y.V2 variant in South Africa and the 501Y.V3 variant identified in Manaus, Amazonas, and Brazil. 2021 Journal of Korean medical science Method SARS_CoV_2 E484K 4 9 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? The emergence of these variant strains is remarkable because the N501Y mutation shared by the three strains is located in the key RBD of the S protein. 2021 Journal of Korean medical science Method SARS_CoV_2 N501Y 65 70 RBD;S 130;141 133;142 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? The results showed that the neutralization activity induced by both vaccines decreased slightly, but nevertheless, significantly, against SARS-CoV-2 variants encoding E484K or N501Y, or the K417N-E484K-N501Y combination. 2021 Journal of Korean medical science Method SARS_CoV_2 E484K;K417N;N501Y;E484K;N501Y 167;190;176;196;202 172;195;181;201;207 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? There were 13 nonsynonymous mutations with a total frequency of > 1,000, and three mutations that are of interest, including D614G, A222V, L18F, S477N, N439K, S98F, L5F, A262S, P272L, P681H, D1163Y, E583D, G1167V, Y453F, E484K, and N501Y. 2021 Journal of Korean medical science Method SARS_CoV_2 A222V;A262S;D1163Y;D614G;E484K;E583D;G1167V;L18F;L5F;N439K;N501Y;P272L;P681H;S477N;S98F;Y453F 132;170;191;125;221;199;206;139;165;152;232;177;184;145;159;214 137;175;197;130;226;204;212;143;168;157;237;182;189;150;163;219 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. B.1.1.7 isolates having mutations near the ORF8-truncating mutation Q27* (C27972T) were found by downloading the GISAID database 2021-02-05_08-24.fasta.gz from https://www.gisaid.org; restricting to sequences with pangolin_lineage B.1.1.7; excluding sequences with bases other than A, C, G, or T; and finding sequences that do not contain the 15-nt context TGTACTTAACATCAA around the C27972T mutation. 2021 Nature communications Method SARS_CoV_2 C27972T;Q27X;C27972T 384;68;74 391;72;81 ORF8 43 47 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Table S3 includes one additional mutation, G24047A, from a later download, in order to represent Korber substitution A829T/S. 2021 Nature communications Method SARS_CoV_2 A829T;A829S;G24047A 117;117;43 124;124;50 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Since the variants that are most likely to influence Spike-hACE2 binding are those in the vicinity of the interaction interface, we narrowed the list to the following 16 hACE2 variants: I21T, K26R, N33D, D38E, T55A, A65V, W69C, T92V, T92I, Q102P, E329G, L351V, G377E, G377W, M383I, and P389H. 2021 Journal of molecular biology Method SARS_CoV_2 A65V;D38E;E329G;G377E;G377W;I21T;K26R;L351V;M383I;N33D;P389H;Q102P;T55A;T92I;T92V;W69C 216;204;247;261;268;186;192;254;275;198;286;240;210;234;228;222 220;208;252;266;273;190;196;259;280;202;291;245;214;238;232;226 S 53 58 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. Proteins used in the BLI experiment (hACE2, mACE2, WT-RBD, Q493K-RBD, Q498H-RBD, Q493K/Q498H-RBD) were purchased from Sino Biological. 2021 EBioMedicine Method SARS_CoV_2 Q493K;Q493K;Q498H;Q498H 59;81;70;87 64;86;75;92 RBD;RBD;RBD;RBD 54;65;76;93 57;68;79;96 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. The TM domain of E (ET), the cytoplasmic domain of E (EC), and the single-site mutants of EF, N15A and V25F, were all prepared following essentially the same protocol and resulted in similar yields. 2021 PLoS pathogens Method SARS_CoV_2 N15A;V25F 94;103 98;107 E;E 17;51 18;52 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. Two EF mutant proteins, N15A EF and V25F EF were generated using a site-directed mutagenesis kit (www.neb.com). 2021 PLoS pathogens Method SARS_CoV_2 N15A;V25F 24;36 28;40 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. Weak alignment was induced and maintained by addition of Y21M fd bacteriophage to the protein-containing micelle solutions at a final concentration of 20 mg/mL. 2021 PLoS pathogens Method SARS_CoV_2 Y21M 57 61 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. A.23.1, is notable for its lack of the D614G mutation, with a Q613H mutation instead that may be functionally similar. 2021 Clinical microbiology and infection Method SARS_CoV_2 D614G;D614G;Q613H;Q613H 40;39;63;62 45;44;68;67 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. B.1.621 has been identified in Columbia as having a similar mutation profile (E484K and N501Y) as the VOCs B.1.351 and P.1, but is from a distinct lineage. 2021 Clinical microbiology and infection Method SARS_CoV_2 N501Y;E484K 88;78 93;83 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. Data on these variants are scarce, but the presence of the E484K mutation raises concerns of immune escape. 2021 Clinical microbiology and infection Method SARS_CoV_2 E484K 59 64 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. HMN.19B - Henri Mondor 19B variant identified in France: Very little information is available about this variant, but it contains the L452R and N501Y mutations, both of which have been linked to increases in transmissibility. 2021 Clinical microbiology and infection Method SARS_CoV_2 L452R;L452R;N501Y;N501Y 135;134;145;144 140;139;150;149 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. Immune escape concerns: Both the E484Q and L452R mutations are a cause for concern of immune escape. 2021 Clinical microbiology and infection Method SARS_CoV_2 E484Q;E484Q;L452R;L452R 34;33;44;43 39;38;49;48 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. Immune escape concerns: Sera neutralization is reportedly decreased (Supplemental Table 1), and the L452R mutation has been reported to escape neutralization by bamlanivimab. 2021 Clinical microbiology and infection Method SARS_CoV_2 L452R;L452R 101;100 106;105 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. Immune escape concerns: Sub variants carrying the E484K mutation raise concerns of immune escape. 2021 Clinical microbiology and infection Method SARS_CoV_2 E484K;E484K 51;50 56;55 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. In Brazil, a new lineage, provisionally named "MG" (with a suggested designation of P.4, but the designation is still pending) has been identified with N501T and E484Q mutations in Minas Gerais. 2021 Clinical microbiology and infection Method SARS_CoV_2 E484Q;N501T 162;152 167;157 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. Initially reported as a "double mutant" for the presence of 2 prominent RBD mutations (E484Q and L452R), sequences of this lineage lacking E484Q have been found. 2021 Clinical microbiology and infection Method SARS_CoV_2 E484Q;L452R;E484Q 139;97;87 144;102;92 RBD 72 75 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. No relevant data is available for this sub-variant yet, but other E484K bearing variants have been linked to reduced vaccine efficacy and escape from some therapeutic mAbs. 2021 Clinical microbiology and infection Method SARS_CoV_2 E484K 66 71 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. Notably, it belongs to clade 19B, which had become rare since early 2020 and lacks the common D614G mutation, thus its resurgence in this variant may indicate that its mutations confer increased transmissibility. 2021 Clinical microbiology and infection Method SARS_CoV_2 D614G 94 99 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. Other remarks: This variant contains multiple mutations, notably S477N or E484K near the RBD - but not both at the same time. 2021 Clinical microbiology and infection Method SARS_CoV_2 E484K;E484K;S477N;S477N 75;74;66;65 80;79;71;70 RBD 89 92 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. P.3 is also notable for containing the N501Y mutation that is found in the 3 variants classified as VOCs by the WHO, which has been linked to increased ACEII affinity/transmissibility, ability to use rat and mouse ACEII, as well as decreased effectiveness of etesevimab. 2021 Clinical microbiology and infection Method SARS_CoV_2 N501Y;N501Y 40;39 45;44 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. Recently, the E484K mutation has been identified in multiple B.1.1.7 sequences (designated VOC202102/02). 2021 Clinical microbiology and infection Method SARS_CoV_2 E484K 14 19 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. The D253G mutation is also notable, and believed to play a role in immune escape. 2021 Clinical microbiology and infection Method SARS_CoV_2 D253G 4 9 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. The Indian SARS-CoV-2 Consortium on Genomics has reported detection of a variant with the L452R mutation and the E484Q mutations, but very little data is available at this time. 2021 Clinical microbiology and infection Method SARS_CoV_2 E484Q;L452R 113;90 118;95 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. The mutation V382L has also been reported, although its effect is unknown. 2021 Clinical microbiology and infection Method SARS_CoV_2 V382L 13 18 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. The presence of the E484K mutation by itself should be enough to qualify a variant for VOI status, and the known instances of variants with the E484K are too numerous to list here, but include: P.2, P.3, some isolates of A.23.1 and B.1.111, B.1.525, B.1.619, N.9, N.10, and A.VOI.V2. 2021 Clinical microbiology and infection Method SARS_CoV_2 E484K;E484K 20;144 25;149 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. There are now 3 recognized sub variants of B.1.617: B.1.617.1 (all with E484Q), B.1.617.2 (all with Delta157,158), and B.1.617.3, although E484Q and Delta157-158 can also be found in B.1.617 and B.1.617.3. 2021 Clinical microbiology and infection Method SARS_CoV_2 E484Q;E484Q 72;139 77;144 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. This effect is mostly due to the E484K mutation. 2021 Clinical microbiology and infection Method SARS_CoV_2 E484K 33 38 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. For HEK293F cell expression, the coding sequences of SARS-CoV-2 RBD and its three mutations (K417R, Q498H, K417R-Q498H) tagged with a C-terminal 6x His tag were cloned into the pCAGGS expression vector using the EcoRI and XhoI restriction sites. 2021 The EMBO journal Method SARS_CoV_2 K417R;Q498H;K417R;Q498H 107;100;93;113 112;105;98;118 RBD 64 67 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. For protein expression in HEK293F cells (ATCC), the pCAGGS plasmid containing the coding sequences of the SARS-CoV-2 RBD and its three mutations (K417R, Q498H, and K417R-Q498H) was transiently transfected into HEK293F cells. 2021 The EMBO journal Method SARS_CoV_2 K417R;Q498H;K417R;Q498H 164;153;146;170 169;158;151;175 RBD 117 120 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. The binding affinities of indicated mFc-fusion protein with three RBDs (SARS-CoV-2 RBD, GX/P2V/2017 RBD and GD/1/2019 RBD) or the mutations (K417R, Q498H and K417R-Q498H) of SARS-CoV-2 RBD were evaluated with SPR as previously described (Wang et al, 2020b). 2021 The EMBO journal Method SARS_CoV_2 K417R;Q498H;K417R;Q498H 158;148;141;164 163;153;146;169 RBD;RBD;RBD;RBD;RBD 66;83;100;118;185 70;86;103;121;188 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. Biotinylated SARS-CoV-2 Spike RBD-AVI & His Recombinant Protein (Sino Biological Inc., 40592-V27H-B), Biotinylated NTD-His & AVI Recombinant Protein (Sino Biological Inc., 40591-V49H-B), Biotinylated Nucleocapsid-AVI & His recombinant Protein (Sino Biological Inc., 40588-V27B-B), Biotinylated Spike S2 ECD-His Recombinant Protein (Sino Biological Inc., 40590-V08B-B), Biotinylated Spike S1-AVI & His Recombinant Protein (Sino Biological Inc., 40591-V27H-B) were used in this study. 2021 Cell research Method SARS_CoV_2 V27H;V27H;V49H 93;450;178 97;454;182 N;S;S;S;RBD 200;24;294;382;30 212;29;299;387;33 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. PCR was performed using the SARS-CoV-2 Spike D614G plasmid as a template according to the manual of PrimeSTAR (Takara) reagents. 2021 Cell research Method SARS_CoV_2 D614G 45 50 S 39 44 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. Plasma IgG responses to SARS-CoV-2 S (SARS-CoV-2 Spike S1 + S2 ECD Antibody Titer Assay Kit, Sino Biological Inc., KIT 004), RBD (SARS-CoV-2 Spike RBD Antibody Titer Assay Kit, Sino Biological Inc., KIT 002), NTD (SARS-CoV-2 Spike S1 NTD-His & AVI Recombinant Protein, Sino Biological Inc., 0591-V49H), S1-D614G (SARS-CoV-2 Spike S1(D614G)-His Recombinant Protein, Sino Biological Inc., 40591-V08H3), S1-RBD.V2 (SARS-CoV-2 Spike S1(K417N, E484K, N501Y, D614G)-His Recombinant Protein, Sino Biological Inc., 40591-V08H10), S1-501Y.V2 NTD (SARS-CoV-2 Spike S1(242-244Delta, D614G)-His, Sino Biological Inc., BD61-2) were measured by ELISA. 2021 Cell research Method SARS_CoV_2 D614G;D614G;E484K;N501Y;D614G;K417N;D614G;V49H 453;572;439;446;333;432;306;296 458;577;444;451;338;437;311;300 S;S;S;S;S;S;RBD;RBD;RBD;S 49;141;225;324;423;549;125;147;404;35 54;146;230;329;428;554;128;150;407;36 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. Models for mutant RBDs N501Y and E484K were created using Misssense3D. 2021 Journal of molecular biology Method SARS_CoV_2 E484K;N501Y 33;23 38;28 RBD 18 22 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. Protein concentrations were determined using OD280 nm measured on a Nanodrop 2000 (Thermo Scientific, Waltham USA) and extinction coefficients of epsilonm 280 nm = 101,170 M-1 cm-1 for tagged hACE2, epsilonm 280 nm = 33,850 M-1 cm-1 for wild type, E484K and K417N RBD, and epsilonm 280 nm = 35,340 M-1 cm-1 for N501Y, double and triple mutant RBD. 2021 Journal of molecular biology Method SARS_CoV_2 E484K;K417N;N501Y 248;258;311 253;263;316 RBD;RBD 264;343 267;346 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. Single amino acid changes in the RBD (N501Y, E484K, K417N) and combinations thereof were introduced using QuikChange (XL Site-Directed Mutagenesis Kit, Agilent, Santa Clara, USA). 2021 Journal of molecular biology Method SARS_CoV_2 E484K;K417N;N501Y 45;52;38 50;57;43 RBD 33 36 34039497 An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose. The target DNA was amplified from a patient sample, sequence confirmed, modified to achieve the desired design architecture as such that it harbors a suitable 5' UTR, ORF to express the S protein with G614 and double proline (2P) mutations (K986P and V987P) with a IgE-secretory signal sequence, a special 3' UTR constructed with modified alpha and beta globin in tandem, and finally a 130 residue-long poly-A tail. 2021 Vaccine Method SARS_CoV_2 V987P;K986P 251;241 256;246 3'UTR;5'UTR;S 306;159;186 312;165;187 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. Moreover, we used exact Poisson bivariate regression to explore the correlation between the D614G mutation (dependent variable) and other mutations (independent variables) due to small samples. 2021 Journal of medical virology Method SARS_CoV_2 D614G 92 97 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. To deal with a small sample size, we applied Poisson regression analysis, using a prevalence ratio (PR) as a conservative, consistent, and interpretable measure, to look for the predictors, including D614G, of a strong cycle threshold (<25) in real-time RT-PCR diagnosis of SARS-CoV-2 in the multivariate regression model. 2021 Journal of medical virology Method SARS_CoV_2 D614G 200 205 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. The dependent variables were the genetic characteristics of SARS-CoV-2 lineages (20AS, M1V, M4V and N501YV). 2021 Clinical microbiology and infection Method SARS_CoV_2 M1V;M4V 87;92 90;95 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. Those selected were sequences of 20AS obtained from respiratory samples collected before June 2020 (the predominant variant of the first epidemic in Marseille), sequences of the M1V or M4V (predominant variants during the second phase of the epidemic), and sequences harbouring N501Y substitution within the spike which is the main variant circulating during the third episode of the current epidemic in Marseille. 2021 Clinical microbiology and infection Method SARS_CoV_2 M1V;M4V;N501Y 178;185;278 181;188;283 S 308 313 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. Whole genome sequencing was performed for 20S, M1V and M4V, as previously described from 200 muL of nasopharyngeal swab fluid after viral RNA extraction with the EZ1 Virus Mini Kit v2.0, followed by reverse transcription by SuperScript IV (ThermoFisher Scientific, Waltham, MA, USA), cDNA second strand synthesis using Klenow Fragment DNA polymerase (New England Biolabs, Beverly, MA, USA), and the generation of purified DNA with Agencourt AMPure XP beads (Beckman Coulter, Villepinte, France). 2021 Clinical microbiology and infection Method SARS_CoV_2 M1V;M4V 47;55 50;58 34044153 SARS-CoV-2 N gene dropout and N gene Ct value shift as indicator for the presence of B.1.1.7 lineage in a commercial multiplex PCR assay. For validation of D3L polymorphism specific Ct shift in the N gene, each plasmid was diluted to an initial copy number of 1,25*10 8 and, subsequently diluted to 1:10, 1:100 and 1:1000 dilutions. 2021 Clinical microbiology and infection Method SARS_CoV_2 D3L 18 21 N 60 61 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. For the graphic evaluation of Brazilian lineages, all genomes available on the GISAID database until January 18th, 2021, and presenting the E484K mutation were included in the analysis. 2021 Infection, genetics and evolution Method SARS_CoV_2 E484K 140 145 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The comparative genomic analysis of the E484K mutated genomes was performed with all the 134 genomes (Table S1) presenting the E484K mutation for Brazil in GISAID until January 18th, 2021. 2021 Infection, genetics and evolution Method SARS_CoV_2 E484K;E484K 40;127 45;132 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The counting of genomes containing E484K was performed by the specification of the mutation in the search fields. 2021 Infection, genetics and evolution Method SARS_CoV_2 E484K 35 40 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The reference genome NC_045512.2 was added as an outgroup and 16 other sequences from B.1.1.28 and B.1.1.33 lineages were added to analyze the phylogeny patterns with the E484K-containing genomes. 2021 Infection, genetics and evolution Method SARS_CoV_2 E484K 171 176 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. Molecular Dynamic Simulation (MDS) on the spike RBD WT and mutated (K417 N, E484K, and N501Y) is performed using Nanoscale molecular dynamics software (NAMD) version 2.13. 2021 Biochemical and biophysical research communications Method SARS_CoV_2 E484K;N501Y;K417N 76;87;68 81;92;74 S;RBD 42;48 47;51 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. The PyMOL V2.2.2 software was utilized to prepare the corresponding RBD mutations (K417 N, E484K, and N501Y) found in SARS-CoV-2 variants 501.V2 and B.1.1.248. 2021 Biochemical and biophysical research communications Method SARS_CoV_2 E484K;N501Y;K417N 91;102;83 96;107;89 RBD 68 71 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The PDB file for the D614G SARS-CoV-2 spike protein (accession number 7BNM) was downloaded from the Protein Data Bank. 2021 mBio Method SARS_CoV_2 D614G 21 26 S 38 43 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. 1A) expressing the artificial transcription factor XVE, which activates transcription by binding with 17beta-estradiol, and pBICLBSER-ToMV-SP-His-ORF8(L84S) were introduced into tobacco BY-2 cells via Agrobacterium-mediated transformation. 2021 Biochemical and biophysical research communications Method SARS_CoV_2 L84S 151 155 ORF8;S 146;139 150;141 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. For both wild-type ORF8 and its L84S variant, 2 mg/mL of protein sample was dissolved in the NMR buffer containing 2.74 mM NaCl, 162 muM Na2HPO4, 53.6 muM KCl, 29.4 muM KH2PO4, and 10% D2O. 2021 Biochemical and biophysical research communications Method SARS_CoV_2 L84S 32 36 ORF8 19 23 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Modeling the three-dimensional structure of the L84S variant. 2021 Biochemical and biophysical research communications Method SARS_CoV_2 L84S 48 52 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. The amplified fragment was introduced into a chemically inducible ToMV vector (pBICLBSER-ToMV) to generate pBICLBSER-ToMV-SP-His-ORF8(L84S). 2021 Biochemical and biophysical research communications Method SARS_CoV_2 L84S 134 138 ORF8;S 129;122 133;124 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. The three-dimensional structure of the L84S variant was modeled on the Phyre2 web server. 2021 Biochemical and biophysical research communications Method SARS_CoV_2 L84S 39 43 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. To construct a plasmid for the producing His-tagged ORF8 L84S variant protein, His-tagged ORF8 L84S, which was fused with the Arabidopsis chitinase signal peptide at its N-terminus, was generated by PCR. 2021 Biochemical and biophysical research communications Method SARS_CoV_2 L84S;L84S 57;95 61;99 ORF8;ORF8;N 52;90;170 56;94;171 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. No S1230S, Ipswich, MA, USA) and SuperScriptIV Reverse Transcriptase (ThermoFisher, Cat. 2021 Viruses Method SARS_CoV_2 S1230S 3 9 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. Monomeric spike proteins of wt, wt+D614G and B.1.1.7 were then C3 symmetrized to generate trimeric spike protein complexes and used as starting structures for molecular dynamics (MD) simulations. 2021 Biomedicines Method SARS_CoV_2 D614G 35 40 S;S 10;99 15;104 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. These were N501Y, A570D, D614G, P681H, T716I, S982A and D1118H. 2021 Biomedicines Method SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 18;56;25;11;32;46;39 23;62;30;16;37;51;44 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. To also generate the starting structure for the MD simulations of the B.1.1.7 variant, the N501Y amino acid exchange was introduced with Swiss-PdbViewer 4.1.0. 2021 Biomedicines Method SARS_CoV_2 N501Y 91 96 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. To generate starting structures for wild type, wild type with the D614G mutation (wt+D614G), and B.1.1.7 SARS-CoV-2, we used the protein sequence annotated in UniProt (; accessed on 22 December 2020) with the identifier P0DTC2 (SARS-CoV-2; wild-type) and changed the sequence in accordance with the reported deletions (del69-70, del144) for the SARS-CoV-2 B.1.1.7 variant. 2021 Biomedicines Method SARS_CoV_2 D614G;D614G 66;85 71;90 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. Using Swiss-Model Expasy (), we generated a model for the SARS-CoV-2 wild type, wild type with the D614G mutation, and SARS-CoV-2 B.1.1.7 variant on the basis of the Cryo-EM solved structure of the triple ACE2 bound SARS-CoV-2 spike protein trimer (PDB ID: 7KMS) and used chain A as a template. 2021 Biomedicines Method SARS_CoV_2 D614G 99 104 S 227 232 34073577 Kinetics of Neutralizing Antibodies of COVID-19 Patients Tested Using Clinical D614G, B.1.1.7, and B 1.351 Isolates in Microneutralization Assays. C1P1 is a wild-type low-passage strain representing strains circulating in Finland during spring 2020 (with e.g., the D614G mutation), devoid of mutations around the furin-cleavage site. 2021 Viruses Method SARS_CoV_2 D614G 118 123 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. Two different mutant (N501Y_K417N and N501Y_E484) structures were prepared by Coot software. 2021 mAbs Method SARS_CoV_2 N501Y;N501Y;K417N 38;22;28 43;27;33 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. 3-D structural model for D614G variant of the spike protein trimer. 2021 Bioinformation Method SARS_CoV_2 D614G 25 30 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. Besides, spike protein structures with D614G substitution have been released at the time of our study and hence were included in this analysis. 2021 Bioinformation Method SARS_CoV_2 D614G 39 44 S 9 14 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. Calculation of frustration index in the local residue contacts:The effect of D614G substitution on local interaction energies was examined using Frustratometer algorithm, which follows the principle that a native protein comprises several conflicting residue contacts resulting in local frustration. 2021 Bioinformation Method SARS_CoV_2 D614G 77 82 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. To study the effect of D614G variation on the thermodynamic stability of the spike protein trimer, we calculated free energy changes upon aspartate to glycine substitution using buildmodel function in FoldX. 2021 Bioinformation Method SARS_CoV_2 D614G 23 28 S 77 82 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. Two D614G variant models were generated corresponding to closed and 1-RBD up conformations of the spike protein trimer based on the reference cryo-EM structures available in the PDB entries 6VXX and 6VYB, respectively. 2021 Bioinformation Method SARS_CoV_2 D614G 4 9 S;RBD 98;70 103;73 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. We generated an in silico model for the D614G variant of spike protein trimer using structure editing tool in UCSF chimera with default parameters. 2021 Bioinformation Method SARS_CoV_2 D614G 40 45 S 57 62 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. Similar procedures were also followed for evolutionary rate estimation of 577 SARS-CoV-2 genomes without the D614G mutation; however, analysis was restricted to isolates from California. 2021 Open forum infectious diseases Method SARS_CoV_2 D614G 109 114 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. We also used a TaqMan SARS-CoV-2 Mutation Panel for detecting spike E484K (ID: ANU7GMZ, Thermo Fisher Scientific). 2021 PLoS pathogens Method SARS_CoV_2 E484K 68 73 S 62 67 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. We designed a Custom TaqMan assay for detecting SARS-CoV-2 spike protein with the W152L and G769V mutations (Thermo Fisher Scientific). 2021 PLoS pathogens Method SARS_CoV_2 G769V;W152L 92;82 97;87 S 59 64 34098567 Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. Images were collected at a magnification of 57,000 using EPU on a Thermo Fisher Talos F200C microscope equipped with a 4k x 4k CETA 16 M camera and operated at 200 kV. 2021 Nature Method SARS_CoV_2 F200C 86 91 34098567 Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. Nanobody fragments and pMES4 phagemid were digested with PstI-HF and BstEII-HF restriction enzymes (NEB: R3140L, R3162L) and ligated (1 mug and 2 mug respectively) with T4 ligase at 16 C overnight. 2021 Nature Method SARS_CoV_2 R3140L;R3162L 105;113 111;119 34098567 Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. The IC50 of these pseudotypes were compared to a wild-type SARS-CoV-2 spike sequence carrying R683G in the subsequent analyses, as appropriate. 2021 Nature Method SARS_CoV_2 R683G 94 99 S 70 75 34098567 Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. The mutants E484K and KEN (K417N, E484K and N501Y) were constructed in the context of a pSARS-CoV-2-SDelta19 variant with a substitution in the furin cleavage site (R683G). 2021 Nature Method SARS_CoV_2 E484K;E484K;N501Y;K417N;R683G 12;34;44;27;165 17;39;49;32;170 34098567 Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. VHH(D)J and pMES4 fragments were then digested with SfiI (NEB, R0123L) and ligated (100 and 200 ng, respectively) with T4 ligase (NEB, M0202L) at 16 C overnight. 2021 Nature Method SARS_CoV_2 R0123L 63 69 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. At 4-5 days of age, Gn piglets were orally inoculated with the P1 of E191A mutant (E191A-P1) (n = 9; 100 TCID50/pig), icPC22A (n = 6; 100 TCID50/pig), or mock (n = 5; DMEM), respectively. 2021 Cell & bioscience Method SARS_CoV_2 E191A;E191A 69;83 74;88 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. One piglet in the icPC22A group (pig#1) and one showing positive viral RNA shedding (pig#8) from E191A-P1 group were euthanized at 3 dpi. 2021 Cell & bioscience Method SARS_CoV_2 E191A 97 102 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. To determine the genetic stability of E191A mutant in pig model, some fecal samples were subjected for sanger sequencing. 2021 Cell & bioscience Method SARS_CoV_2 E191A 38 43 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Vero cells infected with icPC22A or E191A-P1 at a MOI of 0.01 was harvested at 24hpi and subjected to total RNA extraction using TRIzolReagent (Invitrogen, Carlsbad, CA). 2021 Cell & bioscience Method SARS_CoV_2 E191A 36 41 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. The RNA-seq data of COVID-19 patients infected by B.1.1.7 or B.1.1.7/E484K variant will be uploaded in GEO before publishing the manuscript. 2021 medRxiv Method SARS_CoV_2 E484K 69 74 COVID-19 20 28 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Each S protein (prototype and V367F) was added as a ligand at different concentrations, ranging from 0.03 mug/ml to 10 mug/ml, and then incubated for 2 h at 37 C to allow receptor-ligand interaction. 2021 Journal of virology Method SARS_CoV_2 V367F 30 35 S 5 6 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Expression of wild-type and mutant S proteins (V367F). 2021 Journal of virology Method SARS_CoV_2 V367F 47 52 S 35 36 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. For this, the SARS-CoV-2 S-proteins, either prototype or V367F, were immobilized on the sensor chip NTA (GE, USA), according to the manufacturer's protocol. 2021 Journal of virology Method SARS_CoV_2 V367F 57 62 S 25 26 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Plasmid SARS-CoV-2 spike (G1099T), incorporating the V367F mutation in the S gene, was constructed by site-directed mutagenesis using the ClonExpress MultiS One Step cloning kit (Vazyme), as per the manufacturer's protocol. 2021 Journal of virology Method SARS_CoV_2 V367F;G1099T 53;26 58;32 S;S 19;75 24;76 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Production and titration of SARS-CoV-2 pseudoviruses bearing V367F S protein. 2021 Journal of virology Method SARS_CoV_2 V367F 61 66 S 67 68 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The genome sequences with either the V367F mutation or the V367F/D614G dual mutations in the S protein RBD were screened and analyzed in this study (see Table S1 in the supplemental material). 2021 Journal of virology Method SARS_CoV_2 V367F;V367F;D614G 37;59;65 42;64;70 RBD;S 103;93 106;94 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The wild-type and V367F constructs were transfected into HEK293 cells using polyethyleneimine. 2021 Journal of virology Method SARS_CoV_2 V367F 18 23 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. A region from the SARS-CoV-2 S gene containing N501Y/T716I/E484K mutations was reverse transcribed and amplified using a single end 5' biotin-labeled primer. 2021 eLife Method SARS_CoV_2 N501Y;E484K;T716I 47;59;53 52;64;58 S 29 30 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. For the N501Y detection using RAY, SARS-CoV-2 and control RNA samples were received from the diagnostic laboratory at CSIR-Institute of Genomics and Integrative Biology. 2021 eLife Method SARS_CoV_2 N501Y 8 13 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. M0210S). 2021 eLife Method SARS_CoV_2 M0210S 0 6 34106944 Identification and evaluation of the inhibitory effect of Prunella vulgaris extract on SARS-coronavirus 2 virus entry. Primers are following: SPDeltaC-3'primer, 5_GCAGGTACCTAGAATTTGCAGCAGGATCCAC; D614G-5', 5_GCTGTTCTTTATCAGGGTGTTAACTGCACAG; D614G-3', 5_CTGTGCAGTTAACACCCTGATAAAGAACAGC. 2021 PloS one Method SARS_CoV_2 D614G;D614G 77;122 82;127 34114829 Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study. Examples of such mutations are Asn439Lys (N439K) and Leu452Arg (L452R). 2021 The journal of physical chemistry. B Method SARS_CoV_2 N439K;L452R;L452R;N439K 31;53;64;42 40;62;69;47 34114829 Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study. For example, Asp30 was replaced by Glu to maximize contacts with Lys417 on the S protein. 2021 The journal of physical chemistry. B Method SARS_CoV_2 D30E 13 38 S 79 80 34119826 Therapeutic effect of CT-P59 against SARS-CoV-2 South African variant. All of the mutant SARS-CoV-2 RBDs (K417N, E484K, N501Y and triple mutant) were purchased from Sino Biological. 2021 Biochemical and biophysical research communications Method SARS_CoV_2 E484K;N501Y;K417N 42;49;35 47;54;40 RBD 29 33 34119951 Examining the interactions scorpion venom peptides (HP1090, Meucin-13, and Meucin-18) with the receptor binding domain of the coronavirus spike protein to design a mutated therapeutic peptide. Then, the first five suggested mutations of BeAtMuSiC server containing A9T, H4Y, A9S, H4F, K7H plus the combination of mutation one and four (A9T + H4F) (in total six mutations) were generated via SPDV Swiss-PDB viewer (https://spdbv.vital-it.ch/) in the final structure of meucin-18 peptide (that was gained from 100 ns MD simulation) distinctly. 2021 Journal of molecular graphics & modelling Method SARS_CoV_2 A9S;A9T;H4F;H4F;H4Y;K7H;A9T 82;72;87;149;77;92;143 85;75;90;152;80;95;146 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. Briefly, 96-well microtiter plates (Corning, Cat no: 9018) were coated with 100 muL of 1 mug/mL ectodomain of spike protein (ECD), S1 protein, RBD protein, RBD variants protein (RBD E484K, RBD K417N, RBD N501Y, RBD N501Y/K417N/E484K), in coating buffer (pH 9.6) overnight at 4 C, respectively. 2021 Emerging microbes & infections Method SARS_CoV_2 E484K;K417N;N501Y;N501Y;E484K;K417N 182;193;204;215;227;221 187;198;209;220;232;226 S;RBD;RBD;RBD;RBD;RBD;RBD 110;143;156;178;189;200;211 115;146;159;181;192;203;214 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. Recombinant SARS-CoV-2 ECD protein (Genscript, Cat no: Z03481) and the related RBD variants (RBD N501Y, RBD K417N, RBD E484K, RBD N501Y/K417N/E484K) were used for ELISA binding assay. 2021 Emerging microbes & infections Method SARS_CoV_2 E484K;K417N;N501Y;N501Y;E484K;K417N 119;108;97;130;142;136 124;113;102;135;147;141 RBD;RBD;RBD;RBD;RBD 79;93;104;115;126 82;96;107;118;129 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. The VSV-based SARS-CoV-2 pseudoviruses contained wild-type, D614G, B.1.351, B.1.1.7, P.1, B.1.429 and B.1.526 variants spike protein. 2021 Emerging microbes & infections Method SARS_CoV_2 D614G 60 65 S 119 124 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Although the results of assays 69/70 and E484K/N501Y and K417N were comparable with both enzymes, we had difficulties using the enzyme SuperScript III Platinum One-Step qRT-PCR System because of dimer primer formation; therefore, its use is not recommended for these assays. 2021 Frontiers in cellular and infection microbiology Method SARS_CoV_2 E484K;K417N;N501Y 41;57;47 46;62;52 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. E484K and N501Y mutations were detected in the Cal Fluor Red 610 (Probe 484K) and Quasar 670 (Probe 501Y) channels, respectively. 2021 Frontiers in cellular and infection microbiology Method SARS_CoV_2 N501Y;E484K 10;0 15;5 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. E484K/N501Y Assay. 2021 Frontiers in cellular and infection microbiology Method SARS_CoV_2 N501Y;E484K 6;0 11;5 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. For the N501Y mutation, modified bases (LNA) were used to allow better discrimination due to the low DeltaTm of hybridization between the complementary base and the mismatch. 2021 Frontiers in cellular and infection microbiology Method SARS_CoV_2 N501Y 8 13 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. K417N Mutation Assay. 2021 Frontiers in cellular and infection microbiology Method SARS_CoV_2 K417N 0 5 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. The 69/70 deletion assay was performed in 1,040 samples of COVID-19 patients, while the K417N assay and E484K/N501Y assay were performed in 378 and 517 samples, respectively. 2021 Frontiers in cellular and infection microbiology Method SARS_CoV_2 E484K;K417N;N501Y 104;88;110 109;93;115 COVID-19 59 67 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. The 69/70 deletion test is aimed at the discrimination of sequences that contain the deletion of amino acids 69 and 70, while the K417N test detects a single base substitution that causes the exchange of a Lysine (K) for an Asparagine (N), and the E484K/N501Y assay detects the single base mutations that exchange Glutamic Acid (E) for Lysine (K) at position 484, while also detects the change of an Asparagine (N) for a Tyrosine (Y) at position 501. 2021 Frontiers in cellular and infection microbiology Method SARS_CoV_2 E484K;K417N;N501Y 248;130;254 253;135;259 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. The E484K and N501Y mutations are single nucleotide variants close to each other. 2021 Frontiers in cellular and infection microbiology Method SARS_CoV_2 E484K;N501Y 4;14 9;19 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. The region corresponding to the K417N mutation presents a high complexity at designing standard probes that allow the sequence discrimination. 2021 Frontiers in cellular and infection microbiology Method SARS_CoV_2 K417N 32 37 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Thus, the detection and discrimination were carried out in a quadruplex assay, being the channels for the FAM and HEX fluorophores where the sequences without E484K and N501Y mutations will be detected through the probes "Probe 484E" and "Probe 501N", respectively. 2021 Frontiers in cellular and infection microbiology Method SARS_CoV_2 E484K;N501Y 159;169 164;174 34129831 Antibody Responses After mRNA-Based COVID-19 Vaccination in Residential Older Adults: Implications for Reopening. SARS-CoV-2 pseudovirus (PSV) was generated in 293T cells by co-transfection of pFC37K-CMV-S, an enhanced expression plasmid encoding for codon-optimized full-length SARS-CoV-2 S (Wuhan-1 sequence containing D614 G substitution or from the B.1.1.7 variant) with the N-term HiBit tag removed, and pNL4-3.luc.R-E-mCherry-luciferase, an envelope deficient HIV-1 dual reporter construct that was cloned by recombination of the pNL.luc.R-E- plasmid (NIH AIDS Reagent Program) and the fully infectious pNL4-3 mCherry luciferase plasmid (Addgene). 2021 Journal of the American Medical Directors Association Method SARS_CoV_2 D614G 207 213 N;S 265;176 266;177 34138474 High-resolution melting curve FRET-PCR rapidly identifies SARS-CoV-2 mutations. Genomic RNA of two SARS-CoV-2 viruses from american type culture collection (ATCC) served as controls and as quantitative standards: 2019-nCOV/USA-WA1/2020 which does not contain the A23403G and the C14408T mutations, and 201/501Y.V1 which contains both mutations. 2021 Journal of medical virology Method SARS_CoV_2 A23403G;C14408T 183;199 190;206 34138474 High-resolution melting curve FRET-PCR rapidly identifies SARS-CoV-2 mutations. The 6-carboxyfluorescein (6-FAM)-labeled probes were further designed to contain the unique A23403G or C14408T mutation (Table 2). 2021 Journal of medical virology Method SARS_CoV_2 A23403G;C14408T 92;103 99;110 34138474 High-resolution melting curve FRET-PCR rapidly identifies SARS-CoV-2 mutations. The A23403G and the C14408T mutations are the most common mutations from the original Wuhan strain that persists in almost all variants today. 2021 Journal of medical virology Method SARS_CoV_2 A23403G;C14408T 4;20 11;27 34138474 High-resolution melting curve FRET-PCR rapidly identifies SARS-CoV-2 mutations. We confirmed this by analyzing all available high-quality SARS-CoV-2 sequences from GISAID (https://www.gisaid.org/:accessed on April 28, 2021) which revealed the A23403G and the C14408T occurred in over 99.85% (250,568/250,945) of the five major variants recognized today (Table 1). 2021 Journal of medical virology Method SARS_CoV_2 A23403G;C14408T 163;179 170;186 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. Enzymatic activity ACE2 decoys expressing a variety of mutations:R273Q, R273K, R273L, H245A, H505L, H374N, and H378N:selected to inhibit activity in combination with the S RBD affinity-enhancing mutations T27Y and H34A were assessed in the FRET based ACE2 activity assay. 2021 Scientific reports Method SARS_CoV_2 H245A 86 91 RBD;S 172;170 175;171 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. Representative single mutants with higher mutation energy were subject to molecular dynamics (MD) simulations and the binding free energy of the antibody with RBD was confirmed to be strengthened by H:V106R, H:V104Y and L:G31L mutations of P2B-2F6. 2021 Computers in biology and medicine Method SARS_CoV_2 G31L;V104Y;V106R 222;210;201 226;215;206 RBD 159 162 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Due to a sequencing error, RBD E484K-FC used for all binding studies was determined to be RBD E484R-FC. 2021 Frontiers in immunology Method SARS_CoV_2 E484K;E484R 31;94 36;99 RBD;RBD 27;90 30;93 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Due to the similarity of the amino acid chemistry between Arginine and Lysine, the RBD E484R provides a suitable surrogate for the RBD E484K variant. 2021 Frontiers in immunology Method SARS_CoV_2 E484K;E484R 135;87 140;92 RBD;RBD 83;131 86;134 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. pMA vectors harboring a series of five wild-type DNA fragments (A23403, G25563, G26144, T28144, and G28882) and mutants (A23403G, G25563T, G26144T, T28144C, and G28882A) were obtained from Thermo Fisher Scientific (Waltham, MA, USA). 2021 Journal of infection and chemotherapy Method SARS_CoV_2 G25563T;G26144T;G28882A;T28144C;A23403G 130;139;161;148;121 137;146;168;155;128 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. E64D and camostat experiments: ACE2 or ACE2 and TMPRSS2 transfected 293T cells were either E64D (Tocris) or camostat (Sigma-Aldrich) treated for 3 hours at each drug concentration before the addition of a comparable amount of input viruses pseudotyped with WT, H69/V70 deletion or VSV-G (approx. 2021 Cell reports Method SARS_CoV_2 E64D;E64D 91;0 95;4 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Plasmids encoding the spike protein of SARS-CoV-2 D614 with a C-terminal 19 amino acid deletion with D614G, were used as a template to produce variants lacking amino acids at position H69 and V70, as well as mutations N439K and Y453F. 2021 Cell reports Method SARS_CoV_2 D614G;N439K;Y453F 101;218;228 106;223;233 S 22 27 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. The mutations (Delta69/70, Delta144, N501Y, A570D, D614G, P681H, S982A, T716I and D1118H or K417N, E484K and N501Y) were introduced by amplification with primers with similar Tm. 2021 Cell reports Method SARS_CoV_2 A570D;D1118H;D614G;E484K;K417N;N501Y;N501Y;P681H;S982A;T716I 44;82;51;99;92;37;109;58;65;72 49;88;56;104;97;42;114;63;70;77 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Absolute and fold changes between mutated and WT D614G were used to estimate the entry efficiency of SARS-CoV-2 variants. 2021 Immunity Method SARS_CoV_2 D614G 49 54 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. P2C-1F11 Fab fragments were mixed with SARS-CoV-2 RBD containing K417N-E484K-N501Y mutations at a molar ratio of 1:1.2, incubated on ice for 2 h, and further purified by gel-filtration chromatography. 2021 Immunity Method SARS_CoV_2 K417N;E484K;N501Y 65;71;77 70;76;82 RBD 50 53 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The fold change of mutant S relative to WT D614G in binding or neutralization were calculated by simple division of respective IC50 or ID50 values. 2021 Immunity Method SARS_CoV_2 D614G 43 48 S 26 27 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The overall fold change of mutant pseudovirus relative to WT D614G in neutralization of convalescent plasma was calculated by the comparison of geometric mean of the ID50 value of the 23 plasma samples. 2021 Immunity Method SARS_CoV_2 D614G 61 66 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The significance of neutralizing activities of convalescent plasma against each mutant pseudovirus relative to D614G was estimated using the unpaired Mann-Whiteny t test by Graphpad Prism 7 (n = 23). 2021 Immunity Method SARS_CoV_2 D614G 111 116 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The single mutations identified from the GISAID database were introduced into the pcDNA3.1 vector encoding WT D614G using QuickChange site-directed mutagenesis (Agilent 210519). 2021 Immunity Method SARS_CoV_2 D614G 110 115 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The variant B.1.1.7 (GISAID: EPI_ISL_601443) was constructed with total of 9 mutations including 69-70del, 144del, N501Y, A570D, D614G, P681H, T716I, S982A and D1118H. 2021 Immunity Method SARS_CoV_2 144del;A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 107;122;160;129;115;136;150;143 113;127;166;134;120;141;155;148 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The variant B.1.351 (GISAID: EPI_ISL_700450) was constructed with 10 mutations including L18F, D80A, D215G, 242-244del, S305T, K417N, E484K, N501Y, D614G and A701V. 2021 Immunity Method SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;L18F;N501Y;S305T 158;101;148;95;134;127;89;141;120 163;106;153;99;139;132;93;146;125 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The variant P.1 (GISAID: EPI_ISL_792681) was constructed with 12 mutations including L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I and V1176F. 2021 Immunity Method SARS_CoV_2 D138Y;D614G;E484K;H655Y;K417T;L18F;N501Y;P26S;R190S;T1027I;T20N;V1176F 103;138;124;145;117;85;131;97;110;152;91;163 108;143;129;150;122;89;136;101;115;158;95;169 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The wild-type pseudovirus used throughout the analysis was the prototype strain (GenBank: MN908947.3) with a D614G mutation (WT D614G). 2021 Immunity Method SARS_CoV_2 D614G;D614G 109;128 114;133 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. All four targets are within the S gene domain: a deletion at amino acid (AA) 69-70 (ACATGT), deletion at AA 145, (TTA), N501Y mutation (TAT), and S982A mutation (GCA). 2021 Journal of medical virology Method SARS_CoV_2 N501Y;S982A 120;146 125;151 S 32 33 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. C1R-A2402 cells were pulsed with or without the NF9 peptide or its derivatives [the NF9-L452R peptide (NYNYRYRLF, L5R in NF9) and the NF9-Y453F peptide (NYNYLFRLF, Y6F in NF9); synthesized by Scrum Inc.] at concentrations from 0.1 to 10 nM at 37 C for 1 h. 2021 Cell host & microbe Method SARS_CoV_2 Y6F;L452R;Y453F 164;88;138 167;93;143 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Parental virus and the L452R mutant were mixed at a 1:1 ratio based on the PFU. 2021 Cell host & microbe Method SARS_CoV_2 L452R 23 28 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Plasmids expressing the SARS-CoV-2 S protein mutants (pC-S-L452R, pC-SARS2-S-Y453F, pC-SARS2-S-N501Y, pC-SARS2-S-B.1.429 [S13I/W152C/L452R/D614G] and pC-SARS2-S-B.1.1.298 [HV69-70del/Y453F/D614G]) were generated by site-directed mutagenesis PCR using pC-SARS2-S (kindly provided by Kenzo Tokunaga) as the template and the following primers: S forward, 5'-TTG GGTACC ATG TTT GTG TTC CTG GTG CTG-3'; S reverse, 5'-GTG GCGGCCGC TCT AGA TTC AGG TGT AGT GCA GTT T-3'; S Y453F forward, 5'-GTG GGA GGC AAC TAC AAC TAC CTC TTC AGA-3'; and S L452R/Y453F reverse, 5'-GTT GTA GTT GCC TCC CAC CTT-3'; S N501Y forward, 5'-TCC TAT GGC TTC CAA CCA ACC TAT GGA-3'; S N501Y reverse, 5'-TGG TTG GAA GCC ATA GGA TTG-3'; S S13I forward, 5'-TGC CAC TGG TGT CCA TCC AGT GTG TGA ACC T-3'; S S13I reverse, 5'-AGG TTC ACA CAC TGG ATG GAC ACC AGT GGC A-3'; S W152C forward, 5'-GAA CAA CAA GTC CTG TAT GGA GTC TGA GTT C-3'; S W152C reverse, 5'-GAA CTC AGA CTC CAT ACA GGA CTT GTT GTT C-3'; S D614G forward, 5'-CTG TGC TCT ACC AGG GTG TGA ACT GTA CTG A-3'; S D614G reverse, 5'-TCA GTA CAG TTC ACA CCC TGG TAG AGC ACA G-3'; S HV69-70del forward, 5'-GGT TCC ATG CCA TCT CTG GCA CCA ATG GCA-3'; and S HV69-70del reverse, 5'-TGC CAT TGG TGC CAG AGA TGG CAT GGA ACC-3'. 2021 Cell host & microbe Method SARS_CoV_2 D614G;D614G;L452R;N501Y;N501Y;S13I;S13I;W152C;W152C;Y453F;D614G;D614G;L452R;W152C;Y453F;Y453F;S13I;L452R;N501Y;Y453F 965;1031;533;591;651;703;768;833;899;465;139;189;133;127;183;539;122;59;95;77 970;1036;538;596;656;707;772;838;904;470;144;194;138;132;188;544;126;64;100;82 S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S 35;57;75;93;111;159;260;341;398;463;531;589;649;701;766;831;897;963;1029;1095;1168 36;58;76;94;112;160;261;342;399;464;532;590;650;702;767;832;898;964;1030;1096;1169 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. SARS-CoV-2 variants containing the L452R or Y453F mutation were sorted from the verified 581,367 sequences (Tables S3, S4, and S5). 2021 Cell host & microbe Method SARS_CoV_2 L452R;Y453F 35;44 40;49 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. The L452R substitution (Figure 2G) was prepared using UCSF Chimera v1.13. 2021 Cell host & microbe Method SARS_CoV_2 L452R 4 9 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. The nucleotide variation at position 22,917 (i.e., T for parental virus, G for the L452R mutant) was quantified by using EditR. 2021 Cell host & microbe Method SARS_CoV_2 L452R 83 88 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. To generate recombinant SARS-CoV-2 mutants, mutations were inserted in fragment 8 (Table S6) using the GENEART site-directed mutagenesis system (Thermo Fisher Scientific, cat# A13312) according to the manufacturer's protocol with the following primers: Fragment 8_S L452R forward, 5'-CTA AGG TTG GTG GTA ATT ATA ATT ACC GGT ATA GAT TGT TTA GGA AGT CTA ATC-3'; Fragment 8_S L452R reverse, 5'-GAT TAG ACT TCC TAA ACA ATC TAT ACC GGT AAT TAT AAT TAC CAC CAA CCT TAG-3'; Fragment 8_S Y453F forward, 5'-GGT TGG TGG TAA TTA TAA TTA CCT GTT TAG ATT GTT TAG GAA GTC TAA TCT C-3'; Fragment 8_S Y453F reverse, 5'-GAG ATT AGA CTT CCT AAA CAA TCT AAA CAG GTA ATT ATA ATT ACC ACC AAC C-3'; Fragment 8_S N501Y forward, 5'-CAA TCA TAT GGT TTC CAA CCC ACT TAT GGT GTT GGT TAC CAA CCA TAC AG-3'; and Fragment 8_S N501Y reverse, 5'-CTG TAT GGT TGG TAA CCA ACA CCA TAA GTG GGT TGG AAA CCA TAT GAT TG-3', according to the manufacturer's protocol. 2021 Cell host & microbe Method SARS_CoV_2 L452R;L452R;N501Y;N501Y;Y453F;Y453F 266;373;690;796;480;585 271;378;695;801;485;590 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. To prepare effector cells, HEK293 cells were cotransfected with the expression plasmids for parental S or its derivatives (L452R, Y453F and N501Y) (400 ng) and pDSP1-7 (400 ng) using TransIT-LT1 (Takara, cat# MIR2300). 2021 Cell host & microbe Method SARS_CoV_2 N501Y;Y453F;L452R 140;130;123 145;135;128 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. To prepare pseudoviruses, lentivirus (HIV-1)-based, luciferase-expressing reporter viruses pseudotyped with the SARS-CoV-2 S protein and its derivatives, HEK293T cells (1 x 106 cells) were cotransfected with 1 mug of psPAX2-IN/HiBiT, 1 mug of pWPI-Luc2, and 500 ng of plasmids expressing parental S or its derivatives (L452R, Y453F, N501Y, D614G, B.1.429 and B.1.1.298) using Lipofectamine 3000 (Thermo Fisher Scientific, cat# L3000015) according to the manufacturer's protocol. 2021 Cell host & microbe Method SARS_CoV_2 D614G;N501Y;Y453F;L452R 340;333;326;319 345;338;331;324 S 123 124 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. To prepare the plasmids with the mutated RBD, megaprimers were amplified by PCR using the KAPA HiFi HotStart ReadyMix kit (Roche, cat# KK2601) with the following primers according to the manufacturer's protocol: RBD L452R forward:5'-GGA CAG CAA GGT GGG AGG CAA CTA CAA CTA CAG ATA CAG ACT GTT CAG GAA GAG CAA C-3'; RBD Y453F reverse: 5'-CTC AAA TGG TTT CAG GTT GCT CTT CCT GAA CAG TCT GAA GAG GTA GTT GTA GTT GCC TCC C-3'; RBD N501Y reverse: 5'-GTA TGG TTG GTA GCC CAC TCC ATA GGT TGG TTG GAA GCC ATA GGA TTG-3'; pCT_seq reverse: 5'-CAT GGG AAA ACA TGT TGT TTA CGG AG-3'; and pCTCON_seq forward: 5'-GCA GCC CCA TAA ACA CAC AGT AT-3'. 2021 Cell host & microbe Method SARS_CoV_2 L452R;N501Y;Y453F 216;427;319 221;432;324 RBD;RBD;RBD;RBD 41;212;315;423 44;215;318;426 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. BinaxNOW and Quidel QuickVue SARS Antigen Test results were independently evaluated by two individuals, and specimens were called negative if disagreement, inclusive of the 1:100,000 T205I BinaxNow, 1:100,000 WT QuickVue, 1:100,000 D399N QuickVue specimens. 2021 Journal of clinical virology Method SARS_CoV_2 D399N;T205I 232;183 237;188 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Lysates from 293T cells transfected with N wildtype, N T205I, N D399N, N T205I/D399N, or pcDNA4/TO vector were kept frozen at -80 C prior to use in antigen testing. 2021 Journal of clinical virology Method SARS_CoV_2 D399N;T205I;T205I;D399N 64;55;73;79 69;60;78;84 N;N;N;N 41;53;62;71 42;54;63;72 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. The N D399N construct was made following the same strategy except by combining an amplicon encoding the first half of the N wild-type gene (made by PCR using primers COVID-N-C-Strep-F and COVID N nt864R with the N wild-type plasmid) and an amplicon encoding the second half of the N gene encoding D399N (made by PCR using primers COVID N nt864R and COVID-N-C-Strep-R with the N T205I/D399N cDNA template). 2021 Journal of clinical virology Method SARS_CoV_2 D399N;D399N;T205I;D399N 6;297;378;384 11;302;383;389 N;N;N;N;N;N;N 4;122;194;212;281;336;376 5;123;195;213;282;337;377 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. The N wild-type or N T205I/D399N amplicons were then cloned into a modified pcDNA4/TO vector with a C-terminal 2x Strep-Tag II using the In-Fusion HD cloning kit (Takara Bio, Kusatsu, Shiga, Japan). 2021 Journal of clinical virology Method SARS_CoV_2 T205I;D399N 21;27 26;32 N;N 4;19 5;20 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. This resulted in a concentration of 336.2 ng/microL, 189.7 ng/microL, 403.9 ng/microL, 244.2 ng/microL for N WT, N T205I, N D399N, and N T205I/D399N, respectively. 2021 Journal of clinical virology Method SARS_CoV_2 D399N;T205I;T205I;D399N 124;115;137;143 129;120;142;148 N;N;N;N 107;113;122;135 108;114;123;136 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. To determine descriptive epidemiology of the nucleocapsid D399N mutation, SARS-CoV-2 whole genomes were downloaded from GISAID on April 18, 2021. 2021 Journal of clinical virology Method SARS_CoV_2 D399N 58 63 N 45 57 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. To estimate the concentration of N in the lysate, the estimated nanograms of N quantified by western blot was divided by 10 to account for loading volume and then multiplied by dilution factor required to bring the lysates to 0.125 mg/mL (lysates were diluted 22.4-fold, 25.6-fold, 21.6-fold, and 28-fold for N WT, N T205I, N D399N, and N T205I/D399N, respectively). 2021 Journal of clinical virology Method SARS_CoV_2 D399N;T205I;T205I;D399N 326;317;339;345 331;322;344;350 N;N;N;N;N;N 33;77;309;315;324;337 34;78;310;316;325;338 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. To obtain the construct encoding the N T205I amino acid change an amplicon encoding the first half of the N gene encoding T205I (made by PCR using primers COVID-N-C-Strep-F and COVID N nt864R with the N T205I/D399N cDNA template) and an amplicon encoding the second half of the N wild-type gene (made by PCR using primers COVID N nt864R and COVID-N-C-Strep-R with the N wild-type plasmid template), were cloned into the modified pcDNA4/TO vector with a C-terminal 2x Strep-Tag II using the In-Fusion HD cloning kit (Takara). 2021 Journal of clinical virology Method SARS_CoV_2 T205I;T205I;T205I;D399N 39;122;203;209 44;127;208;214 N;N;N;N;N;N;N 37;106;183;201;278;328;368 38;107;184;202;279;329;369 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. To obtain the ORF encoding N T205I/D399N, RNA was extracted from a previously sequenced clinical SARS-CoV-2 isolate that encodes the T205I/D399N mutations in N (WA-UW-62,718; EPI_ISL_1,366,195) and converted to cDNA using Superscript IV (ThermoFisher Scientific, Waltham, MA, USA)) with COVID-N-C-Strep-R primer followed by PCR utilizing the same primer pair that amplified N wild-type gene. 2021 Journal of clinical virology Method SARS_CoV_2 T205I;T205I;D399N;D399N 29;133;35;139 34;138;40;144 N;N;N;N 27;158;293;374 28;159;294;375 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. Binder-virus complexes were added to Vero E6 (WA1/2020) or Vero-hACE2-TMPRSS2 (B.1.1.7, WA1/2020 E484K/N501Y/D614G, and serum and tissue homogenates) cell monolayers in 96-well plates and incubated at 37 C for 1 h. 2021 Cell host & microbe Method SARS_CoV_2 E484K;D614G;N501Y 97;109;103 102;114;108 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. The B.1.1.7, WA1/2020-N501Y/D614G, and WA1/2020-E484K/N501Y/D614G viruses have been described previously. 2021 Cell host & microbe Method SARS_CoV_2 D614G;D614G;N501Y;E484K;N501Y 28;60;54;48;22 33;65;59;53;27 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. Along with V483A, other mutations were reported at the 483rd position of the RBD where Val is getting substituted to other amino acids such as phenylalanine (Phe), isoleucine (Ile), proline (Pro), aspartic acid (Asp), arginine (Arg) and lysine (Lys) in very low occurrence rate. 2021 Future virology Method SARS_CoV_2 V483A 11 16 RBD 77 80 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. Although the antibody 5A6 IgG had a high occupancy on the viral surface and had bivalent binding capacity binding to both the 'up' and 'down' positions of the RBD-ACE2 interaction surface, it showed a fourfold reduction in binding avidity to the V483A mutant strain. 2021 Future virology Method SARS_CoV_2 V483A 246 251 RBD 159 162 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. Analysis of the antigenicity of V483A mutant using monoclonal antibodies (mAbs) revealed that V483A became resistant to X593 and P2B-2F6 mAbs. 2021 Future virology Method SARS_CoV_2 V483A;V483A 32;94 37;99 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. Antibody studies conducted using the antibody 5A6 immunoglobulin-G, which has the superior neutralization capacity with many SARS-CoV-2 mutant strains, including the D614G strain, failed to neutralize the V483A mutant strain. 2021 Future virology Method SARS_CoV_2 D614G;V483A 166;205 171;210 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. Epitope analysis of the V483A mutant strain proved that 13 effective B-cell epitopes significantly advanced the mutant antigenicity compared with the wild-type strain they were 62~75, 487~492, 210~221, 181~186, 342~353, 363~377, 617~628, 405~418, 405~413, 379~389, 442~447, 458~463 and 698~709. 2021 Future virology Method SARS_CoV_2 V483A 24 29 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. For V483A, the DeltaDeltaG is found to be (DeltaDeltaG = DeltaG wild-type - DeltaG mutant) +1.1 kcal/mol. 2021 Future virology Method SARS_CoV_2 V483A 4 9 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. From the molecular dynamics simulation studies, it is observed that on average, 7.283 +- 1.568 H-bonds were formed between the ACE2 receptor and the V483A mutant strain, whereas in the tabulated H-bond data from the molecular docking study, it is reported that around 5.651 bonds were formed between the ACE2 receptor and the wild-type S protein. 2021 Future virology Method SARS_CoV_2 V483A 149 154 S 336 337 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. In the case of V483F mutation, the amino acid Val, which is hydrophobic, is substituted by bulky hydrophobic amino acid Phe, which might influence the glycosylation efficiency nearby amino acid N343 or the positioning of sugars. 2021 Future virology Method SARS_CoV_2 V483F 15 20 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. In V483A mutation, the amino acid Val, which is hydrophobic, present at the 483rd position of the spike protein at the RBD of S1 got substituted as hydrophobic Ala in some of the sequences. 2021 Future virology Method SARS_CoV_2 V483A 3 8 S;RBD 98;119 103;122 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. Investigations on the infectivity and reactivity of the V483A variants showed that they were resistant to some neutralizing antibodies. 2021 Future virology Method SARS_CoV_2 V483A 56 61 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. So it is recommended to administer the antibody 3D11 along with 5A6 IgG to compensate for this failure against the V483A strain. 2021 Future virology Method SARS_CoV_2 V483A 115 120 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. The free binding energy (DeltaG) of the wild-type S protein to the human ACE2 receptor is -14.1 kcal/mol, and for the V483A mutant, it is -15.2 kcal/mol. 2021 Future virology Method SARS_CoV_2 V483A 118 123 S 50 51 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. The Kyte-Doolittle hydropathy index value for the V483A mutant is -2.4, where the negative value indicates the loop region's hydrophilic nature. 2021 Future virology Method SARS_CoV_2 V483A 50 55 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. The number of H-bonds involved with wild-type and the V483A mutant is estimated by 20 ns simulation using molecular dynamics (MD) studies. 2021 Future virology Method SARS_CoV_2 V483A 54 59 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. The short-range Coulombic interaction energy between the RBD of wild-type and the human ACE2 receptor in a dynamic environment is -2.307 x 105 kcal/mol, and for V483A mutant is -2.320 x 105 kcal/mol. 2021 Future virology Method SARS_CoV_2 V483A 161 166 RBD 57 60 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. The V483A has not been reported as an aggressive mutation, although it is one of the most important mutations after the D614G mutation. 2021 Future virology Method SARS_CoV_2 D614G;V483A 120;4 125;9 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. The V483A mutant is exposed to solvents as they present on the RBD surface, and the loop region may stick out into the solvent. 2021 Future virology Method SARS_CoV_2 V483A 4 9 RBD 63 66 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. The V483A mutation site does not form direct contact with the ACE2 receptor, but it is on the same face of the RBD that includes the binding interface with the ACE2. 2021 Future virology Method SARS_CoV_2 V483A 4 9 RBD 111 114 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. The V483A mutation with higher frequency indicates that this mutation may favor SARS-CoV-2 by natural selection may cause this virus to be more infectious. 2021 Future virology Method SARS_CoV_2 V483A 4 9 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. Though the V483A mutation is at the RBM of the S1 protein, the amino acid is not making direct contact with the ACE2 receptor. 2021 Future virology Method SARS_CoV_2 V483A 11 16 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. Mutation calling, translation to amino acid, and identification of P681H variant sequences were carried out in R with a custom code using the Bioconductor package Seqinr. 2021 Vaccines Method SARS_CoV_2 P681H 67 72 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. One hundred TCID50 of B.1.1.50 + P681H variant, a strain commonly circulating in Israel lacking a P681H mutation (Israel WT), and B.1.1.7 variant isolates were incubated with inactivated sera from fully vaccinated individuals diluted 1:10 to 1:1280 in 96 well plates for 60 min at 33C. 2021 Vaccines Method SARS_CoV_2 P681H;P681H 33;98 38;103 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. The frequency of the P681H mutation in the spike protein was recorded for each sample. 2021 Vaccines Method SARS_CoV_2 P681H 21 26 S 43 48 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. In brief, SARS-COV-2.SctDelta19 WH1 plasmid was amplified by PCR with Phusion DNA polymerase (Thermo Fisher Scientific, Waltham, MA, USA, ref# F-549S) and the following primers: 5'-TACCAGGgCGTGAACTGTACCGAAGTGCC-3' and 5'-GTTCACGcCCTGGTACAGCACTGCCAC-3'. 2021 Viruses Method SARS_CoV_2 F549S 143 149 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. The D614G spike mutant was generated by site-directed mutagenesis as previously described. 2021 Viruses Method SARS_CoV_2 D614G 4 9 S 10 15 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. PYMOL was used to introduce the A97V and P323L mutations on the RdRp protein structure. 2021 Biomolecules Method SARS_CoV_2 A97V;P323L 32;41 36;46 RdRP 64 68 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. To understand the dynamics and interacting behaviour, both the apo WT, A97V and P323L RdRp and RdRp-RDV complexes were subjected to molecular dynamics simulations. 2021 Biomolecules Method SARS_CoV_2 A97V;P323L 71;80 75;85 RdRP;RdRP 86;95 90;99 34208912 Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. These proteins included the SARS-CoV-2 RBD (R319-F541), the UK variant RBD (R319-F541 with N501Y), the SA variant RBD (R319-F541 with K417N, E484K, and N501Y), and the BR P.1 variant RBD (R319-F541 with K417T, E484K, and N501Y). 2021 Diagnostics (Basel, Switzerland) Method SARS_CoV_2 E484K;E484K;K417N;K417T;N501Y;N501Y;N501Y 141;210;134;203;91;152;221 146;215;139;208;96;157;226 RBD;RBD;RBD;RBD 39;71;114;183 42;74;117;186 34211709 The emerging SARS-CoV-2 variants of concern. Cluster 5 or Y453F variant, which emerged in August of 2020, may potentially evade the immunity of convalescent individuals, further suggesting that this variant may challenge the vaccine strategy should it spread. 2021 Therapeutic advances in infectious disease Method SARS_CoV_2 Y453F 15 20 34211709 The emerging SARS-CoV-2 variants of concern. Another variant found to be spreading in Bengal, B.1.618, also known as "triple mutant," is suspected to have evolved from B.1.617 and has the V382L mutation in addition to E484Q and L452R. 2021 Therapeutic advances in infectious disease Method SARS_CoV_2 E484Q;L452R;V382L 173;183;143 178;188;148 34211709 The emerging SARS-CoV-2 variants of concern. D614G, a mutation of SARS-CoV-2 which emerged in early 2020, has a substitution in the gene encoding the S protein. 2021 Therapeutic advances in infectious disease Method SARS_CoV_2 D614G 0 5 S 105 106 34211709 The emerging SARS-CoV-2 variants of concern. E484K has given rise to the B.1.525/B.1.526 lineage seen spreading among New York residents, perhaps because this version is more capable of evading antibodies, as well as binding more tightly to human cells due to the co-S477N mutation. 2021 Therapeutic advances in infectious disease Method SARS_CoV_2 E484K;S477N 0;222 5;227 34211709 The emerging SARS-CoV-2 variants of concern. Furthermore, one unique lineage of interest with increased infectivity and immune escape is B.1.617, the "double mutant" that carries two prominent mutations: E484Q and L452R. 2021 Therapeutic advances in infectious disease Method SARS_CoV_2 E484Q;L452R 159;169 164;174 34211709 The emerging SARS-CoV-2 variants of concern. Mutation E484K, connected with several lineages, has been shown to avoid select antibodies; whereas K417 mutation, also seen among several lineages which include B.1.351 and the P.1 of Brazil (an offshoot of B.1.1.28, but a close relative of the B.1.351), may bind more tightly to cells. 2021 Therapeutic advances in infectious disease Method SARS_CoV_2 E484K 9 14 34211709 The emerging SARS-CoV-2 variants of concern. N439K RBM mutation has independently emerged in multiple lineages, showing increased affinity in the spike protein for ACE2, resisting several monoclonal antibodies (a therapeutic approach), and escaping some polyclonal responses. 2021 Therapeutic advances in infectious disease Method SARS_CoV_2 N439K 0 5 S 101 106 34211709 The emerging SARS-CoV-2 variants of concern. N439K was found to be less infectious than variant D614G; however, N439K still showed infectivity of COVID-19, making it a variant of interest and concern. 2021 Therapeutic advances in infectious disease Method SARS_CoV_2 D614G;N439K;N439K 51;67;0 56;72;5 COVID-19 101 109 34211709 The emerging SARS-CoV-2 variants of concern. Originating from N501Y, the last VOC, the year 2020, month 12, variant 01, referred to as SARS-CoV-2 VOC 202012/01 or B.1.1.7, emerged in the UK, containing 23 nucleotide substitutions from the initial SARS-CoV-2. 2021 Therapeutic advances in infectious disease Method SARS_CoV_2 N501Y 17 22 34211709 The emerging SARS-CoV-2 variants of concern. Receptor-binding motif (RBM) mutation is widespread among the second most commonly identified mutation in the RBD as of late 2020, N439K, which arose from lineage B.1 from the D614G mutated background. 2021 Therapeutic advances in infectious disease Method SARS_CoV_2 D614G;N439K;N439K 176;133;131 181;138;136 RBD 110 113 34211709 The emerging SARS-CoV-2 variants of concern. Surging in late 2020, mutation L452R also referred to as the CAL.20C, a variant with lineages B.1.427 and B.1.429, has not yet been shown to be more infectious, though the numbers of confirmed cases are increasing throughout the state of California. 2021 Therapeutic advances in infectious disease Method SARS_CoV_2 L452R 31 36 34211709 The emerging SARS-CoV-2 variants of concern. The D614G was the dominant form for several months worldwide, with increased infectivity and transmission. 2021 Therapeutic advances in infectious disease Method SARS_CoV_2 D614G 4 9 34211709 The emerging SARS-CoV-2 variants of concern. Therefore, priority has been placed on tracking the following mutations circulating worldwide: D614G (B.1 lineage), N501Y (several lineages), E484K (several lineages), K417 (several lineages), L452R (several lineages), Q677 (several lineages), and others. 2021 Therapeutic advances in infectious disease Method SARS_CoV_2 D614G;E484K;L452R;N501Y 95;142;193;116 100;147;198;121 34211709 The emerging SARS-CoV-2 variants of concern. They include but were not limited to COVID-19, SARS-CoV-2, Variants of Concern, genetic variations, spike mutations, N501Y, D614G, N439K, Y453F, E484K, B.1.1.7, 501Y.V1, 501Y.V2, 501.V3, and ACE2. 2021 Therapeutic advances in infectious disease Method SARS_CoV_2 D614G;E484K;N439K;N501Y;Y453F 124;145;131;117;138 129;150;136;122;143 S 100 105 COVID-19 37 45 34211709 The emerging SARS-CoV-2 variants of concern. This E484Q has a similar translocated location as E484K, which allows the virus to evade select types of antibodies. 2021 Therapeutic advances in infectious disease Method SARS_CoV_2 E484K;E484Q 50;5 55;10 34211709 The emerging SARS-CoV-2 variants of concern. Variant 501Y.V2, yet another subtype of N501Y mutation, is different from the UK 202012/01 variant. 2021 Therapeutic advances in infectious disease Method SARS_CoV_2 N501Y 40 45 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. E484D (100%) and R682W substitutions (10%-40%) were found in our virus stocks, but we did not observe selection of additional S mutations following growth in H522 cells. 2021 Cell reports Method SARS_CoV_2 R682W;E484D 17;0 22;5 S 126 127 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. E484K-R685S was an escape mutant isolated from monoclonal antibody SARS2-55 using R685S virus. 2021 Cell reports Method SARS_CoV_2 R685S;E484K;R685S 82;0;6 87;5;11 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. VSV-GFP-SARS-CoV-2-S Delta21-R685S mutant was isolated from WT stock. 2021 Cell reports Method SARS_CoV_2 R685S 29 34 S 19 20 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. The spike protein was modeled based on the Protein Data Bank coordinate set 6VXX, showing the mutation N501Y in S1 and S982A in S2. 2021 Frontiers in immunology Method SARS_CoV_2 N501Y;S982A 103;119 108;124 S 4 9 34220870 Declining Levels of Neutralizing Antibodies Against SARS-CoV-2 in Convalescent COVID-19 Patients One Year Post Symptom Onset. In order to further study the neutralizing capacity of convalescent plasma against the E484K-mutated VOC, we collected 53 samples during a 6 months period after infection to assess the neutralizing activity. 2021 Frontiers in immunology Method SARS_CoV_2 E484K 87 92 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. Briefly, 0.3 mug/ml of RBD-Fc, RBD (K417N)-His, RBD (E484K)-His, RBD (N501Y)-His or RBD (K417N, E484K, N501Y)-His (RBD-Mut) proteins was added to the 293T/ACE2 cells in the absence or presence with series of diluted mouse sera. 2021 MedComm Method SARS_CoV_2 E484K;N501Y;E484K;K417N;K417N;N501Y 96;103;53;36;89;70 101;108;58;41;94;75 RBD;RBD;RBD;RBD;RBD;RBD 23;31;48;65;84;115 26;34;51;68;87;118 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. In the neutralization assays, D614G, N501Y, or E484K represented pseudoviruses with a single mutation. 2021 MedComm Method SARS_CoV_2 D614G;E484K;N501Y 30;47;37 35;52;42 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. Luciferase-expressing pseudovirus with or without mutation (D614G, B.1.1.7, B.1.351, P.1, N501Y, E484K) was pre-incubated with serially diluted immune sera in 96-well plates for 1 h at 37 C, respectively. 2021 MedComm Method SARS_CoV_2 E484K;N501Y;D614G 97;90;60 102;95;65 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. Spike S1 recombinant protein (S1-WT, aa:16-685), spike S1 (K417N, E484K, N501Y, D614G) recombinant protein (S1-Mut, aa:16-685), RBD protein with Fc fragment (RBD-WT, aa: 319-541), RBD (K417N, aa: 319-541), RBD (E484K, aa: 319-541), RBD (N501Y, aa: 319-541), and RBD-Mut (K417N, E484K, N501Y, aa: 319-541) with His fragment, all of the recombinant proteins were purchased from Sino Biological. 2021 MedComm Method SARS_CoV_2 D614G;E484K;E484K;N501Y;N501Y;E484K;K417N;K417N;K417N;N501Y 80;66;278;73;285;211;59;185;271;237 85;71;283;78;290;216;64;190;276;242 S;S;RBD;RBD;RBD;RBD;RBD;RBD 0;49;128;158;180;206;232;262 5;54;131;161;183;209;235;265 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. The purity of recombinant protein S1-WT, S1-Mut, RBD-WT, RBD (K417N), RBD (E484K), RBD (N501Y), and RBD-Mut was more than 90%, 90%, 95 %, 87%, 90%, 95%, and 90%, respectively. 2021 MedComm Method SARS_CoV_2 E484K;K417N;N501Y 75;62;88 80;67;93 RBD;RBD;RBD;RBD;RBD 49;57;70;83;100 52;60;73;86;103 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. E484K-N501Y were escape mutants isolated from 2B04 using N501Y virus. 2021 Human vaccines & immunotherapeutics Method SARS_CoV_2 N501Y;E484K;N501Y 57;0;6 62;5;11 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. N501Y and D614G were constructed using SARS-CoV-2 Wuhan-Hu-1 spike with substitution at N501 or D614 site, respectively, and rescued by using reverse genetic system. 2021 Human vaccines & immunotherapeutics Method SARS_CoV_2 D614G;N501Y 10;0 15;5 S 61 66 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. S477N and E484K were escape mutants isolated from mAbs described as previously. 2021 Human vaccines & immunotherapeutics Method SARS_CoV_2 E484K;S477N 10;0 15;5 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. Substitutions K986P and V987P were added to stabilize the C-terminal S2 fusion machinery. 2021 Human vaccines & immunotherapeutics Method SARS_CoV_2 K986P;V987P 14;24 19;29 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. Cells were washed three times with DPBS and infected with 200 mul of either VSV G, SARS-CoV-2 S, SARS-CoV-2 P681R S, SARS-CoV-2 A.23.1 S, or Delta-envelope pseudoparticles. 2022 bioRxiv Method SARS_CoV_2 P681R 108 113 S;S;S 94;114;135 95;115;136 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. Primers (ACCTGGCTCTCCTTCGGGAGTTTGTCTGG/CCAGACAAACTCCCGAAGGAGAGCCAGGT) for mutagenesis were designed using the Agilent QuickChange Primer Design tool to create the P681R mutation (CCA->CGA). 2022 bioRxiv Method SARS_CoV_2 P681R 163 168 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. The mutated pcDNA-SARS-CoV-2 Wuhan-Hu1 P681R S plasmid was used to transform XL-10 gold ultracompetent cells, which were grown up in small culture, and then plasmid was extracted using the Qiagen QIAprep Spin Miniprep Kit. 2022 bioRxiv Method SARS_CoV_2 P681R 39 44 S 45 46 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. Viral envelope plasmids included pcDNA-SARS-CoV-2 Wuhan-Hu1 S as the WT, pcDNA-SARS-CoV-2 Wuhan-Hu1 P681R S, and pcDNA-SARS-CoV-2 A.23.1 S. 2022 bioRxiv Method SARS_CoV_2 P681R 100 105 S;S;S 60;106;137 61;107;138 34234758 A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3' Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity. We conducted molecular dynamics simulations of variants A222V (N-terminal of SARS-CoV-2 residues 1-316), S477N (RBM domain, residues 331-530) and V11766F (stalk domain trimmer, residues 1,130-1,273). 2021 Frontiers in microbiology Method SARS_CoV_2 A222V;S477N;V11766F 56;105;146 61;110;153 N 63 64 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. Specifically, protein A (Sino Biological) was firstly covalently immobilized onto a CM5 sensor chip, followed by capture of the individual antibodies and then injection of purified soluble SARS-CoV-2 WT and K417R/A/E/N/T mutant RBDs at five different concentrations. 2021 Nature communications Method SARS_CoV_2 K417A;K417E;K417N;K417R;K417T 207;207;207;207;207 220;220;220;220;220 RBD 228 232 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. To illustrate the viral subgroups with 11803G > T mutation, we rooted an unrooted tree by introducing the bat SARS-like CoV WIV16 (accession no. 2021 Bulletin of the World Health Organization Method SARS_CoV_2 G11803T 39 49 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Recombinant influenza hemagglutinin from H1N1 (A/Cali/07/2009) (11085-V08H, Sino Biological) and SARS-CoV-2 Spike S1 (40591-V08H, Sino Biological) were also coupled using identical protocols as control proteins. 2021 JCI insight Method SARS_CoV_2 V08H;V08H 70;124 74;128 S 108 113 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. SARS-CoV-2 Spike S1 (40591-V08H, Sino Biological) recombinant protein was also included as a positive control in the multiplex assay while Influenza Hemaglutinin (H1N1 A/Cal/07/2009, 11085-V08H, Sino Biological), which does not bind to ACE2, was included as a negative control. 2021 JCI insight Method SARS_CoV_2 V08H;V08H 27;189 31;193 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. All 253 SARS-CoV-2 genomes that were assigned to Pango lineage B.1.1.7 and possessing the E484K spike mutation (including the study isolate CHOP_204) were downloaded from GISAID on 04/17/2021. 2021 Open forum infectious diseases Method SARS_CoV_2 E484K 90 95 S 96 101 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. As there are hundreds of thousands of B.1.1.7 genomes available, we identified the 3 closest genomes to each of the 236 B.1.1.7+E484K genomes by sorting the GISAID genomes using the Mash distance (options: -i -p 32 -d 0.00055). 2021 Open forum infectious diseases Method SARS_CoV_2 E484K 128 133 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. This process identified 354 nonredundant B.1.1.7 and B.1.1.7+E484K genomes close to the 236 study genomes. 2021 Open forum infectious diseases Method SARS_CoV_2 E484K 61 66 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. To investigate the number of independent acquisitions of the E484K mutation, a maximum likelihood tree was constructed that has both the B.1.1.7 and B.1.1.7+E484K genomes. 2021 Open forum infectious diseases Method SARS_CoV_2 E484K;E484K 61;157 66;162 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. Cloning of SARS-CoV-2 Spike, Spike D614G, and nucleocapsid cDNA. 2021 Nature communications Method SARS_CoV_2 D614G 35 40 N;S;S 46;22;29 58;27;34 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. The coding sequence of NCP and part of Spike D614G sequence was designed according to the first SARS-CoV-2 genome. 2021 Nature communications Method SARS_CoV_2 D614G 45 50 S 39 44 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. TOP10 (for all crRNA, Spike, D614G Spike, and NCP cloning) and Stbl3 (for Cas13 cloning) bacteria were used for transformation. 2021 Nature communications Method SARS_CoV_2 D614G 29 34 S;S 22;35 27;40 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. Unpaired two-tailed Student's t-test (95% confidence interval) was used to compare the viral titer between ancestral and D614G. 2021 Nature communications Method SARS_CoV_2 D614G 121 126 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. VERO cells expressing pspCas14b-BFP and various crRNAs were then infected in a level 3 containment laboratory with 200 muL of the ancestral, D614G, or the B.1.1.7 (known as the UK variant) SARS-CoV-2 virus isolate, a kind gift from Dr. 2021 Nature communications Method SARS_CoV_2 D614G 141 146 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Frequency of spike Q677P/Q677H and FCS mutations. 2021 Archives of virology Method SARS_CoV_2 Q677P;Q677H 19;25 24;30 S 13 18 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Moreover, the spike mutations Q677H and Q677P were also analyzed in the five variants. 2021 Archives of virology Method SARS_CoV_2 Q677H;Q677P 30;40 35;45 S 14 19 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. The search for each FCS mutation in human and animal SARS-COV-2 isolates was done separately using the GISAID Initiative default search criteria, including the name of the mutation (e.g., Spike_P681H in section Variant/Subs) and the host name, e.g., Human and/or Neovison vison and Mustela lutreola for mink). 2021 Archives of virology Method SARS_CoV_2 P681H 194 199 S 188 193 34271432 Natto extract, a Japanese fermented soybean food, directly inhibits viral infections including SARS-CoV-2 in vitro. We also used UK variant N501Y RBD-His recombinant protein (Sino Biological, PA, USA). 2021 Biochemical and biophysical research communications Method SARS_CoV_2 N501Y 24 29 RBD 30 33 34273991 Estimating COVID-19 cases infected with the variant alpha (VOC 202012/01): an analysis of screening data in Tokyo, January-March 2021. confirmed s = 2 weeks earlier than screening for N501Y). 2021 Theoretical biology & medical modelling Method SARS_CoV_2 N501Y 49 54 34273991 Estimating COVID-19 cases infected with the variant alpha (VOC 202012/01): an analysis of screening data in Tokyo, January-March 2021. It should be noted that week t in our study represents the week of screening testing for N501Y mutation, not the week of PCR confirmation of cases. 2021 Theoretical biology & medical modelling Method SARS_CoV_2 N501Y 89 94 34273991 Estimating COVID-19 cases infected with the variant alpha (VOC 202012/01): an analysis of screening data in Tokyo, January-March 2021. Not only confirmed case count but also numbers of samples screened for N501Y mutation by rt-PCR and positive samples were collected (see Online Supporting Material). 2021 Theoretical biology & medical modelling Method SARS_CoV_2 N501Y 71 76 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. For SARS-CoV-1 S1 (ACRO biosystems, S1N-S52H5), HCoV-NL63 S1 (SIN-V52H3), SARS-CoV-2 S1 WT (ACRO biosystems, S1N-C52H3), and inhouse expressed SARS-CoV-2 S1 WT, D614G, B.1.1.7, and B.1.351 kinetics, test ACE2-Fc constructs and antibodies were captured to a density of 70 RU or 50 RU, respectively, on a series S protein A sensor chip (GE Healthcare, 29127555) using a Biacore T200 and Biacore 8K instruments (GE Healthcare). 2021 Journal of virology Method SARS_CoV_2 D614G 161 166 S 310 311 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. SARS-CoV-2 S1 domains (amino acids [aa] 1 to 681) from Wuhan (GenBank, QHD43416.1) or including the D614G, B.1.1.7, B.1.351, and P.1 mutations were cloned in fusion with a dual 6xHis tag using an AbVec vector. 2021 Journal of virology Method SARS_CoV_2 D614G 100 105 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. Silent Fc variants were generated with L234A/L235A and L234A/L235A/P329G mutations. 2021 Journal of virology Method SARS_CoV_2 L234A;L234A;L235A;L235A;P329G 39;55;45;61;67 44;60;50;66;72 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. A 250-nucleotide region around the N501Y (A23063T) and E484K (G23012A) positions in the reference strain (GenBank accession number MN908947) was selected and used to identify the corresponding regions in the GISAID data set using BLAST. 2021 Journal of clinical microbiology Method SARS_CoV_2 E484K;N501Y;A23063T;G23012A 55;35;42;62 60;40;49;69 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Four genome sequences (Pangolin coronavirus isolate PCoV_GX-P5L: GenBank/MT040335.1; Bat coronavirus RaTG13: GenBank/ MN996532.2; Bat SARS-like coronavirus isolate Rs4231: GenBank/KY417146.1; Bat coronavirus BtRs-BetaCoV: GenBank/MK211376.1) were used to assess the nucleotide changes among different Sarbecovirus members. 2021 Cell Method SARS_CoV_2 P5L 60 63 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Functional ELISA was performed by Sino Biological (Wayne, PA) using purified RBD from WT (Cat: 40592-V08H), A372T (Cat: 40592-V08H36), and N501Y (Cat: 40592-V08H82). 2021 Cell Method SARS_CoV_2 A372T;N501Y;V08H;V08H 108;139;101;157 113;144;105;161 RBD 77 80 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. The S protein was mutated using PyMOL to the D614G and A372T S protein variants. 2021 Cell Method SARS_CoV_2 A372T;D614G 55;45 60;50 S;S 4;61 5;62 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. To identify glycosylation propensity and predicted glycosylated residues of the WT S protein and the A372T mutant, the NetNGlyc 1.0 Server and Schrodinger-Maestro's BioLuminate (v. 2021 Cell Method SARS_CoV_2 A372T 101 106 S 83 84 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Workspace Operations was used for glycosylation of the Asn370 with N-Acetylglucosamine to identify various Asn370-glycan rotamers and to analyze the surface residue properties of the WT S Protein and A372T mutant. 2021 Cell Method SARS_CoV_2 A372T;N370G 200;107 205;117 N;S 67;186 68;187 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. D614G ARMS specific primers were designed as follows: D614 ARMS A F amplifies the wildtype A with the D614 Out R creating a 134 bp PCR product size. 2021 Meta gene Method SARS_CoV_2 D614G 0 5 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Detection of SARS CoV-2 D614G mutations. 2021 Meta gene Method SARS_CoV_2 D614G 24 29 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Forward and reverse primers (D614G IN F and D614G IN R), designed to cover both sides of the D614G mutation (A23403G), with a product size of 169 bp, from the Wuhan strain (GenBank: MN908947.3), were carefully inspected using NCBI online database for checking melting temperatures, GC contents, lengths, product sizes and locations of the primers. 2021 Meta gene Method SARS_CoV_2 D614G;D614G;A23403G;D614G 44;93;109;29 49;98;116;34 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Four primers were designed and used in a single tube multiplex reaction including D614G outer and ARMS specific primers as shown in Table 1 and. 2021 Meta gene Method SARS_CoV_2 D614G 82 87 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Outer primers, D614G Out F and D614G Out R that amplify a PCR product size of 266 bp in which both A and G variants were located. 2021 Meta gene Method SARS_CoV_2 D614G;D614G 15;31 20;36 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. RFLP method for D614G variant. 2021 Meta gene Method SARS_CoV_2 D614G 16 21 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. SARS CoV-2 RNA samples, identified by Gensig rRT PCR kit, with Cq values <30, were selected for detection of the D614G mutation by using Taqman probe-based rRT PCR, ARMS, and RFLP. 2021 Meta gene Method SARS_CoV_2 D614G 113 118 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Taqman probes including D614 D-FAM and G614 G-HEX (Macrogen, South Korea) were designed to be specific for each wildtype Adenine (A) and mutant Guanine (G), respectively, as shown in Table 1 and. 2021 Meta gene Method SARS_CoV_2 D614D;G614G 24;39 30;45 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Ten (10) mul of Addprobe rRT PCR master mix (Addbio, South Korea) was mixed with 0.5 mul (10 muM) of each primer (D614G IN F and D614G IN R) and probes (D614 D-FAM and G614 G-HEX) followed by adding 8 mul of RNA, giving 20 mul total volume with 250 nM final concentrations of primer probes. 2021 Meta gene Method SARS_CoV_2 D614G;G614G;D614D;D614G 129;168;153;114 134;174;159;119 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Therefore, PCR products, amplified by D614G Out primers, were incubated with BtsCI restriction endonuclease at 50C for 30 min in BtsCI buffer and inactivated at 80C for 20 min as recommended by the manufacturer (New England Biolabs, Ipswich, MA, USA). 2021 Meta gene Method SARS_CoV_2 D614G 38 43 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Three (3) PCR products, amplified by conventional RT PCR using D614G Out primers, were randomly sent for Sanger sequencings (Macrogen Co., Seoul, KR), to confirm D614G mutants and the sequences were submitted to NCBI using Bankit. 2021 Meta gene Method SARS_CoV_2 D614G;D614G 63;162 68;167 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. A cross-correlation matrix was used to study the effect of C241T mutation on Protein-RNA complex dynamics by analyzing how atomic displacements were coupled. 2021 Informatics in medicine unlocked Method SARS_CoV_2 C241T 59 64 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. C241T mutation is affecting SL4. 2021 Informatics in medicine unlocked Method SARS_CoV_2 C241T 0 5 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. Mutation in RNA sequence was generated by C241T in 3DNA based mut_RNA platform. 2021 Informatics in medicine unlocked Method SARS_CoV_2 C241T 42 47 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. The mutant RNA sequence was manually generated using the wild-type sequence by replacing cytosine (C) at position 241 with Uracil (U), which is mentioned as C241T in this article. 2021 Informatics in medicine unlocked Method SARS_CoV_2 C241T 157 162 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. Wild-type RNA and mutated variant with C241T, were docked with two different host factors MADP1 and hnRNP1, total four complexes were generated. 2021 Informatics in medicine unlocked Method SARS_CoV_2 C241T 39 44 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. A QuikChange II site-directed mutagenesis kit (Agilent) was used to generate the mutant D614G spike or R682A spike construct. 2021 mBio Method SARS_CoV_2 D614G;R682A 88;103 93;108 S;S 94;109 99;114 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. D614G substitution of SARS-CoV-2 spike protein increases syncytium formation and virus titer via enhanced furin-mediated spike cleavage. 2021 mBio Method SARS_CoV_2 D614G 0 5 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. The primer set for D614G spike was S-D614G-F (5'-CTCGGTACAATTCACGCCCTGATACAGCACGGC-3') and S-D614G-R (5'-GCCGTGCTGTATCAGGGCGTGAATTGTACCGAG-3'). 2021 mBio Method SARS_CoV_2 D614G;D614G;D614G 19;37;93 24;42;98 S;S;S 25;35;91 30;36;92 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. The primer set for R682A spike was 5'-ACGCTCCGGGCTCTTGCGGGAGAGTTTGTCTG-3' and 5'-CAGACAAACTCTCCCGCAAGAGCCCGGAGCGT-3'. 2021 mBio Method SARS_CoV_2 R682A 19 24 S 25 30 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. NC_045512.2) with a point mutation of D614G, resulting in B.1 lineage. 2021 Nature communications Method SARS_CoV_2 D614G 38 43 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. The B.1.1.7 Spike we used carries the mutations found in GISAID Accession Number EPI_ISL 668152: del 69-70, del145, N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H. 2021 Nature communications Method SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 123;162;130;116;137;151;144 128;168;135;121;142;156;149 S 12 17 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. The B.1.351 Spike carries the mutations D80A, D215G, del242-244, K417N, E484K, N501Y, D614G, and A701V (from EPI_ISL_745109). 2021 Nature communications Method SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;N501Y 97;46;86;40;72;65;79 102;51;91;44;77;70;84 S 12 17 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. The Spike sequences of WT, B.1.1.7, B.1.351, and E484K are available at Genbank (Accession Numbers: MW816497, MW816498, MW816499, and MW816500; please also see Supplemental Table 2). 2021 Nature communications Method SARS_CoV_2 E484K 49 54 S 4 9 34314050 SARS-CoV-2 R.1 lineage variants that prevailed in Tokyo in March 2021. RT-PCR was performed using the primers and probes provided in the VirSNiP SARS-CoV-2 Spike N501Y and VirSNiP SARS-CoV-2 Spike E484K kits (TIB Molbiol) and the LightCycler Multiplex RNA Virus Master (Roche Molecular Systems, Inc.). 2021 Journal of medical virology Method SARS_CoV_2 E484K;N501Y 126;91 131;96 S;S 85;120 90;125 34314050 SARS-CoV-2 R.1 lineage variants that prevailed in Tokyo in March 2021. To detect N501Y and E484K mutations, viral RNA was purified from the PCR-positive samples using the EZ1 Virus Mini Kit v2.0 and EZ1 advanced XL (Qiagen). 2021 Journal of medical virology Method SARS_CoV_2 E484K;N501Y 20;10 25;15 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Protein-protein complexes of WT-P681H and B.1.1.7 variant S-protein (PDB ID: 6VSB) with furin (PDB ID: 4Z2A) were modelled by employing a protein-protein docking approach using the HDOCK server, which is based on a hybrid algorithm of template-based modelling and ab initio free docking. 2021 Virus research Method SARS_CoV_2 P681H 32 37 S 58 59 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Solvated complexes of WT-P681H and B.1.1.7 neutralized by counter ions were subjected to all atoms molecular dynamics simulation using force field (ff18) in AMBER20 simulation program. 2021 Virus research Method SARS_CoV_2 P681H 25 30 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Structural-dynamics features were estimated to understand the impact of S-protein-P681H and B.1.1.7 variant on the stability, flexibility, compactness of the protein, motion using CPPTRAJ and PTRAJ. 2021 Virus research Method SARS_CoV_2 P681H 82 87 S 72 73 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. SWISS-Model was used to model the missing amino acids that were not visible in the Cryo-EM structure of the S-protein for both WT-P681H and the B.1.1.7 variant. 2021 Virus research Method SARS_CoV_2 P681H 130 135 S 108 109 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. To compute the binding differences elicited on the protein structures of S-protein-P681H and B.1.1.7, structural frames from the conformational dynamics were used to estimate binding free energy. 2021 Virus research Method SARS_CoV_2 P681H 83 88 S 73 74 34332998 The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another. Starting on week 18, all samples tested with the Variants I Assay for which no mutation was detected and those for which only the E484K mutation was found were submitted to the NovaplexSARS-CoV-2 Variants II Assay, available since early May. 2021 Journal of virological methods Method SARS_CoV_2 E484K 130 135 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. Amber20 was used to perform the dynamic behavior analysis of ORF8 WT and ORF8 with mutations of S24L, W45L, V62L, and L84S through MD simulation that uses FF14SB force field. 2021 Frontiers in microbiology Method SARS_CoV_2 L84S;S24L;V62L;W45L 118;96;108;102 122;100;112;106 ORF8;ORF8 61;73 65;77 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The Chimera software was used to simulate the structural model of SARS-CoV-2 ORF8 WT with other mutants (S24L, W45L, V62L, and L84S) based on the structure of ORF8 WT. 2021 Frontiers in microbiology Method SARS_CoV_2 L84S;V62L;W45L;S24L 127;117;111;105 131;121;115;109 ORF8;ORF8 77;159 81;163 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. SWISS-MODEL, a protein structure homology-modeling server, was used to prepare 3D structures of the three mutated viruses (501Y.V1, 501Y.V2, N439K) with the crystal structure of the complex of wild-type RBD-hACE2 (6M0J) as the target template. 2021 Computational and structural biotechnology journal Method SARS_CoV_2 N439K 141 146 RBD 203 206 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Native and mutant (N501Y & D614G) S-proteins MD simulation. 2021 Computers in biology and medicine Method SARS_CoV_2 D614G;N501Y 27;19 32;24 S 34 35 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The native and most prominent stabilizing mutants (N501Y and D614G) of the S-protein were utilized as input for the molecular dynamics simulations. 2021 Computers in biology and medicine Method SARS_CoV_2 D614G;N501Y 61;51 66;56 S 75 76 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. We analyzed the energy plot, RMSD, RMSF, the solvent-accessible surface area (SASA), Principle component analysis (PCA), and the number of hydrogen bonds (NH-bonds), and we made a comparison between native, stabilizing mutants (N501Y and D614G) to examine the structural behavior of the S-protein. 2021 Computers in biology and medicine Method SARS_CoV_2 D614G;N501Y 238;228 243;233 S 287 288 34346744 SARS-CoV-2 Quasispecies Provides an Advantage Mutation Pool for the Epidemic Variants. We used a 50-mul PCR system to conduct the PCR, and the system included 5 mul of SARS-CoV-2 cDNA, 2.5 mul of forward and reverse primers (10 mumol/liter), 25 mul of Q5 High-Fidelity 2x Master Mix (NEB, M0492S), and complement volume with nuclease-free water (Thermo Fisher). 2021 Microbiology spectrum Method SARS_CoV_2 M0492S 202 208 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. For the parameter fitting used in the calculation of occupancies, we utilized the following experimentally determined structures for which occupancy data exists as follows (acronyms described in results): S-GSAS/WT: 7KDG,7KDH; S-GSAS/D614G: 7KDI,7KDJ; S-R/x2: 6ZOX; S-R/PP/x1: 6ZOY,6ZOZ; S-R: 6ZP0; S-R/PP: 6ZP1,6ZP2. 2021 PLoS computational biology Method SARS_CoV_2 D614G 234 239 S;S;S;S;S;S 205;227;252;266;288;299 206;228;253;267;289;300 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. A total of 864131 submissions were used to establish the world frequency of each variant using specific amino acid mutations (e.g., S_D614G, etc.) by using command line search text tools. 2021 PLoS pathogens Method SARS_CoV_2 D614G 134 139 34354142 Entropy based analysis of SARS-CoV-2 spread in India using informative subtype markers. D614G mutation. 2021 Scientific reports Method SARS_CoV_2 D614G 0 5 34354142 Entropy based analysis of SARS-CoV-2 spread in India using informative subtype markers. The geographical distribution of the two major strains (S-614G and S-614D) was shown using pie charts. 2021 Scientific reports Method SARS_CoV_2 S614D;S614G 67;56 73;62 S;S 56;67 57;68 34354142 Entropy based analysis of SARS-CoV-2 spread in India using informative subtype markers. We identified the position of the D614G mutation in the multiple aligned sequences using the reference genome sequence. 2021 Scientific reports Method SARS_CoV_2 D614G 34 39 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. Determination of NtAb titers was evaluated using the following SARS-CoV-2 variants: B.1.1.1 (PMVL-1, S: D614G; hCoV-19/Russia/Moscow_PMVL-1/2020), B.1.1.7 (hCoV-19/Netherlands/NoordHolland_20432/2020, VOC 202012/01), B.1.351 (hCoV-19/Russia/SPE-RII-27029S/2021), B.1.1.141 (PMVL-31, S: M153T, T385I, D614G; hCoV-19/Russia/MOW-PMVL-31/2020), B.1.1.317 (PMVL-43, S: D138Y, S477N, A522S, D614G, Q675R, A845S; hCoV-19/Russia/MOW-PMVL-43/2021), B.1.1.28/P.1 (hCoV-19/Netherlands/NoordHolland_10915/2021), B.1.617.2 (T19R G142D E156G F157del R158del L452R T478K D614G P681R D950N) and B.1.617.3 (T19R G142D E156G F157del R158del L452R E484Q D614G P681R D950N). 2021 Vaccines Method SARS_CoV_2 A522S;A845S;D138Y;D614G;D614G;D614G;D614G;D614G;D950N;D950N;E156G;E156G;E484Q;G142D;G142D;L452R;L452R;M153T;P681R;P681R;Q675R;S477N;T385I;T478K;T19R;T19R 378;399;364;104;300;385;556;635;568;647;522;601;629;516;595;544;623;286;562;641;392;371;293;550;511;590 383;404;369;109;305;390;561;640;573;652;527;606;634;521;600;549;628;291;567;646;397;376;298;555;515;594 S;S;S 101;283;361 102;284;362 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. SARS-CoV-2 strains B.1.1.1 or PMVL-1 (GISAID EPI_ISL_421275), B.1.1.141 (T385I) or PMVL-31 (GISAID EPI_ISL_1710849) and B.1.1.317 (S477N, A522S) or PMVL-43 (GISAID EPI_ISL_1710861), B.1.617.2 (T19R G142D E156G F157del R158del L452R T478K D614G P681R D950N) and B.1.617.3 (T19R G142D E156G F157del R158del L452R E484Q D614G P681R D950N) were isolated from a nasopharyngeal swab. 2021 Vaccines Method SARS_CoV_2 A522S;D614G;D614G;D950N;D950N;E156G;E156G;E484Q;G142D;G142D;L452R;L452R;P681R;P681R;T478K;S477N;T19R;T19R;T385I 138;238;317;250;329;204;283;311;198;277;226;305;244;323;232;131;193;272;73 143;243;322;255;334;209;288;316;203;282;231;310;249;328;237;136;197;276;78 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. The absence of the different variant targets (DeltaH69/DeltaV70, N501Y, E484K) was detected by the presence of the universal target of SARS-CoV-2 only and corresponded to a wild-type strain. 2021 Diagnostics (Basel, Switzerland) Method SARS_CoV_2 E484K;N501Y 72;65 77;70 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. The Perkin Elmer RT-PCR kit had one more target for the E484K mutation, also on the S-gene. 2021 Diagnostics (Basel, Switzerland) Method SARS_CoV_2 E484K 56 61 S 84 85 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. The two screening kits presented a similar universal target of SARS-CoV-2 (N/ORF1/ab-gene), and two targets on the S-gene, the target of six nucleotides deletions (DeltaH69/DeltaV70) and the N501Y mutation. 2021 Diagnostics (Basel, Switzerland) Method SARS_CoV_2 N501Y 191 196 N;S 75;115 76;116 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Two or three positive targets that were composed by the universal target SARS-CoV-2 and the N501Y mutation +/- the E484K mutation suggested the presence of the variant 20H/501Y.V2 (B.1.351) or 20J/501Y.V3 (P.1). 2021 Diagnostics (Basel, Switzerland) Method SARS_CoV_2 E484K;N501Y 115;92 120;97 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. RT-PCR primers (Table 1 ) targeting SARS-CoV-2 D614G variant mutation were designed with Primer-BLAST tool available from the NCBI website (https://blast.ncbi.nlm.nih.gov/Blast.cgi). 2021 Virus research Method SARS_CoV_2 D614G 47 52 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. The SARS-CoV-2 D614G (A to G) mutation target sequence was 90 bp Spike fragment with location from 23421 to 23473 in SARS-COV-2's genome (GeneBank accession NC_045512.2). 2021 Virus research Method SARS_CoV_2 D614G 15 20 S 65 70 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. At one to two days post transfection, cell culture supernatants were harvested, and recombinant MHV-A59 N7-MTase mutants D330A and Y414A, as well as recombinant MHV-A59 wild type (WT), were plaque purified three times, and a single plaque was used to produce a virus stock. 2021 Emerging microbes & infections Method SARS_CoV_2 D330A;Y414A 121;131 126;136 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. CV-1, BHK-21-MHV-N, HeLa-D980R, 17CL-1, L2 and Neuro 2a cells were cultured at 37 C with 5% CO2 in Dulbecco modified Eagle's medium (DMEM, Gibco) supplemented with 10% foetal bovine serum (FBS, Gbico) and 1% penicillin/streptomycin (Gbico). 2021 Emerging microbes & infections Method SARS_CoV_2 D980R 25 30 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. For immunization, 4-week-old female C57BL/6 mice were subcutaneously vaccinated with a 100 muL volume containing either 5x105 PFU MHV-A59 WT, D330A, Y414A or DMEM mock. 2021 Emerging microbes & infections Method SARS_CoV_2 D330A;Y414A 142;149 147;154 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. GPT-positive clones were selected by three rounds of plaque purification on CV-1 cells in the presence of xanthine, hypoxanthine and mycophenolic acid, while GPT-negative clones, in which the GPT gene was replaced by the nsp14 mutant gene, were selected by three rounds of plaque purification on D980R cells in the presence of 6-thioguanine. 2021 Emerging microbes & infections Method SARS_CoV_2 D980R 296 301 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. The MHV-A59 nsp14 gene (nucleotides 17,634-17,660) was cloned from vMHV-inf-1 DNA by standard PCR, and nsp14 mutant genes containing mutations for D330A or Y414A were generated and inserted into pMD18-T to produce recombinant plasmids. 2021 Emerging microbes & infections Method SARS_CoV_2 D330A;Y414A 147;156 152;161 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. 293T cells were transfected with 3.75 mug pSFG-SARS-CoV-2 S or pSFG-SARS-CoV-2 S D614G or E484K or N501Y, 2.5 mug RDF plasmid, 3.75 mug PegPam3 and Genejuice in 1 mL Opti-MEM medium for 48 hours at 37 C under 5% CO2. 2021 Frontiers in immunology Method SARS_CoV_2 D614G;E484K;N501Y 81;90;99 86;95;104 S;S 58;79 59;80 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. Generation of Stable A549-Spike and A549-Spike Bearing D614G, E484K, or N501Y Mutation Cell Lines. 2021 Frontiers in immunology Method SARS_CoV_2 D614G;E484K;N501Y 55;62;72 60;67;77 S;S 26;41 31;46 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. pSFG-SARS-CoV-2 S D614G, E484K, or N501Y was mutagenized from pSFG-SARS-CoV-2 S plasmid using the Q5 Site-Directed Mutagenesis Kit (New England BioLabs). 2021 Frontiers in immunology Method SARS_CoV_2 D614G;E484K;N501Y 18;25;35 23;30;40 S;S 16;78 17;79 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Calibration curves for quantification were generated by performing RT-PCR assays on dilution series of a synthetic quantified gBlock gene fragment containing a partial sequence MHV-A59 N-gene (obtained from IDT, Leuven Belgium). 2021 The Science of the total environment Method SARS_CoV_2 A59N 181 186 N 185 186 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Digital droplet RT-PCR was used to quantify the N501Y and the wild-type (WIV04/2019, WT) sequence in one single tube multiplex mutation assay designed by BioRad (Assay ID: dMDS731762551). 2021 The Science of the total environment Method SARS_CoV_2 N501Y 48 53 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. For each sample, the number of negative and WT or N501Y ddPCR positive droplets were recorded and used to determine the WT or N501Y concentrations. 2021 The Science of the total environment Method SARS_CoV_2 N501Y;N501Y 50;126 55;131 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Reference genomic RNA from WT SARS-CoV-2 virus (WIV04/2019) and variants B.1.351 and B.1.1.7 containing the N501Y mutation was isolated from cell-cultured virus at passage 3 after inoculation of primary patient sample. 2021 The Science of the total environment Method SARS_CoV_2 N501Y 108 113 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. RT-ddPCR for the N501Y mutation. 2021 The Science of the total environment Method SARS_CoV_2 N501Y 17 22 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. The 95% confidence intervals in the proportion of N501Y were calculated assuming a Poisson distribution of RNA molecules in the droplets. 2021 The Science of the total environment Method SARS_CoV_2 N501Y 50 55 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. The proportion of Spike gene specific RNA fragments containing the N501Y mutation was calculated by the QuantaSoft-Analysis software as the concentration N501Y in the ddPCR reaction, divided by the sum of WT and N501Y concentrations in the ddPCR reaction. 2021 The Science of the total environment Method SARS_CoV_2 N501Y;N501Y;N501Y 67;154;212 72;159;217 S 18 23 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. This assay uses primers that amplify an 80 bp fragment of the Spike gene including the area containing an A to T point mutation that leads to the N501Y amino acid change in the Spike protein (N501Y). 2021 The Science of the total environment Method SARS_CoV_2 N501Y;N501Y 146;192 151;197 S;S 62;177 67;182 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Two dilution series were analyzed to evaluate the ability of RT-ddPCR to detect WT and the N501Y variants simultaneously in mixtures of different concentration ratios of reference genomic RNA of SARS-CoV-2 lineage B.1.351 and WT. 2021 The Science of the total environment Method SARS_CoV_2 N501Y 91 96 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Two probes are used to detect PCR-amplification in the droplets: one FAM-labeled probe which perfectly binds to the N501Y mutation and one HEX-labeled probe which perfectly binds to the wild-type SARS-CoV-2 sequence. 2021 The Science of the total environment Method SARS_CoV_2 N501Y 116 121 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Briefly, lentiviral particles were produced in HEK293T cells (ATCC CRL-11268) by co-transfecting the gene encoding SARS-CoV-2 spike protein (D614G or B.1.526) and Env-deficient HIV backbone expressing Luciferase-IRES-ZsGreen. 2021 Nature communications Method SARS_CoV_2 D614G 141 146 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Human plasma samples were assayed for neutralization activity against lentiviruses pseudotyped with SARS-CoV-2 spike containing a 21-amino acid cytoplasmic tail deletion and either D614G or mutations corresponding to lineage B.1.526 (v.1: L5F, T95I, D253G, E484K, D614G, and A701V; v.2: L5F, T95I, D253G, S477N, D614G, and Q957R; constructed using primers listed in Supplementary Table 5). 2021 Nature communications Method SARS_CoV_2 A701V;D253G;D253G;D614G;D614G;D614G;E484K;L5F;L5F;Q957R;S477N;T95I;T95I 275;250;298;181;264;312;257;239;287;323;305;244;292 280;255;303;186;269;317;262;242;290;328;310;248;296 S 111 116 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Separate inference was performed for each variant: B.1.1.7 (n = 257), B.1.427 (n = 20), B.1.429 (n = 40), B.1.526 E484 (including B.1.526.2; n = 228), B.1.526 E484K (n = 310), and B.1.526.1 (n = 143). 2021 Nature communications Method SARS_CoV_2 E484K 159 164 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The B.1.526 lineage includes B.1.526.2; B.1.526 was separated into a clade defined by E484K mutation (B.1.526 E484K), and samples without this mutation (B.1.526 E484) for some subsequent analysis. 2021 Nature communications Method SARS_CoV_2 E484K;E484K 86;110 91;115 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. A lower cycle threshold (CT) value for the N501Y mutant probe in comparison to the wild-type probe was interpreted as positive for the N501Y mutation. 2021 Microbiology spectrum Method SARS_CoV_2 N501Y;N501Y 43;135 48;140 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. As B.1.617.2 (which does not carry the H69/70 deletion nor the N501Y mutation) was not considered a VOC in Canada at the time this study was carried out and its circulation in Canada was undefined (though it was emerging in other parts of the world at the time), it was not included in the VOC assay interpretation. 2021 Microbiology spectrum Method SARS_CoV_2 N501Y 63 68 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. Each SARS-CoV-2-positive specimen was tested by both multiplex VOC assays, referred to as the DeltaH69/V70 and N501Y assays. 2021 Microbiology spectrum Method SARS_CoV_2 N501Y 111 116 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. Previous rolling 7-day averages were determined for specimens testing positive for SARS-CoV-2 and for specimens tested using the DeltaH69/V70 and N501Y variant assays. 2021 Microbiology spectrum Method SARS_CoV_2 N501Y 146 151 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. Samples testing positive for N501Y alone were initially considered presumptive VOCs (B.1.351 or P.1) and referred for genome sequencing within ProvLab to determine the lineage. 2021 Microbiology spectrum Method SARS_CoV_2 N501Y 29 34 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. Those testing positive for the H69/V70 deletion and N501Y were classified as B.1.1.7 and those negative for N501Y were classified as wild-type. 2021 Microbiology spectrum Method SARS_CoV_2 N501Y;N501Y 52;108 57;113 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. To assess the accuracy of detection for the DeltaH69/V70 and N501Y assays, a panel of B.1.1.7-positive, wild-type-positive (non-VOC), and COVID-19-negative samples were tested by both assays. 2021 Microbiology spectrum Method SARS_CoV_2 N501Y 61 66 COVID-19 138 146 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. Two in-house-designed rRT-PCR assays targeting the H69/V70 deletion and N501Y mutation in the S gene were used for the rapid screening of SARS-CoV-2 positive samples for the detection of potential variants. 2021 Microbiology spectrum Method SARS_CoV_2 N501Y 72 77 S 94 95 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. Production of HIV pseudotyped with SARS-CoV-2 spike (wildtype and mutants N501Y, W436R, R408I, N354D, V367F and N354D/D364Y were all purchased from Acro biosystems) was performed using the standard lentivirus production method. 2021 Biotechnology journal Method SARS_CoV_2 N354D;N354D;N501Y;R408I;V367F;W436R;D364Y 95;112;74;88;102;81;118 100;117;79;93;107;86;123 S 46 51 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. All L452R-containing sequences submitted in January and February 2021 for lineages B.1.232 (CAL.20A) and 50 randomly chosen B.1.427/B.1.429 (the epsilon variant) sequences were used to build phylogenetic trees based on all or only synonymous mutations by using MEGA 7 software. 2021 Journal of clinical microbiology Method SARS_CoV_2 L452R 4 9 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. The same L452R-containing genome sequences for both lineages were used to calculate the average pairwise differences based on synonymous mutations. 2021 Journal of clinical microbiology Method SARS_CoV_2 L452R 9 14 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. SARS-CoV-2/human/USA/RML-7/2020 (GenBank: MW127503.1; designated D614G throughout the manuscript) was obtained from a nasopharyngeal swab obtained on July 19, 2020. 2021 bioRxiv Method SARS_CoV_2 D614G 65 70 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Sequencing confirmed the presence of three SNPs in this stock: nsp6 D156G (present in 14% of all reads), nsp6 L257F (18%) and nsp7 V11I (13%). 2021 bioRxiv Method SARS_CoV_2 D156G;L257F;V11I 68;110;131 73;115;135 Nsp7;Nsp6;Nsp6 126;63;105 130;67;109 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Sequencing confirmed the presence of two SNPs in this stock: nsp5 P252L (17%) and nsp6 L257F (57%). 2021 bioRxiv Method SARS_CoV_2 L257F;P252L 87;66 92;71 Nsp5;Nsp6 61;82 65;86 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. The D614G, B.1.1.7 and B.1.351 stocks contained similar ratios of SARS-CoV-2 E gene copies to infectious virus. 2021 bioRxiv Method SARS_CoV_2 D614G 4 9 E 77 78 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. To compare the pathogenicity and virus shedding of VOC B.1.1.7 and B.1.351, we inoculated three groups of six rhesus macaques with three different SARS-CoV-2 isolates: SARS-CoV-2/human/USA/RML-7/2020, a contemporary clade B.1 isolate containing the D614G substitution in spike, hCOV_19/England/204820464/2020, a B.1.1.7 isolate, and hCoV-19/USA/MD-HP01542/2021, a B.1.351 isolate. 2021 bioRxiv Method SARS_CoV_2 D614G 249 254 S 271 276 34385423 Potent prophylactic and therapeutic efficacy of recombinant human ACE2-Fc against SARS-CoV-2 infection in vivo. In brief, HEK293 cells were co-transfected with reporter plasmid plenti-GFP-luc, packaging plasmid psPAX2, and coronavirus spike plasmid of interest (pcDNA3.1-SARS-CoV-S, pcDNA3.1-SARS-CoV-2-S, pcDNA3.1-SARS-CoV-2-S-D614G, pcDNA3.1-SARS-CoV-2-S-V367F, pcDNA3.1-B.1.1.7-S, pcDNA3.1-B.1.351-S, pcDNA3.1-B.1.351-S, pcDNA3.1-B.1.617.1-S, and pcDNA3.1-B.1.617.2-S) by lipofectamine 2000 (Thermo). 2021 Cell discovery Method SARS_CoV_2 D614G;V367F 216;245 221;250 S;S;S;S;S;S;S;S;S;S 123;168;191;214;243;269;289;309;331;357 128;169;192;215;244;270;290;310;332;358 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. On the basis of the WT structure, the starting structures of mutants N354D, D364Y, V367F, and Q498A were generated by the PyMOL software. 2021 Frontiers in molecular biosciences Method SARS_CoV_2 D364Y;N354D;Q498A;V367F 76;69;94;83 81;74;99;88 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The primers used are: pc3.1NheI-f ggagacccaagctggctagc; PC3.1XbaI-r gggtttaaacgggccctctaga; V367F-F gactactctttcctgtacaacagcgcctct; V367F-R tgtacaggaaagagtagtcggccacgca; Q498A-F acggcttcgcgcctacaaacggcgtgggc; Q498A-R ttgtaggcgcgaagccgtaagactggag. 2021 Frontiers in molecular biosciences Method SARS_CoV_2 Q498A;Q498A;V367F;V367F 170;209;92;132 175;214;97;137 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The V367F and Q498A mutants were constructed using overlapping PCR and cloned into a pcDNA3.1 vector. 2021 Frontiers in molecular biosciences Method SARS_CoV_2 Q498A;V367F 14;4 19;9 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Number: 210519) was used to introduce amino acid substitutions (N501Y, E484K, E417N or L452R) in pcDNA3-SARS-CoV-2-S-RBD-sfGFP plasmid by following the manufacturer's instructions. 2021 Biomedicine & pharmacotherapy Method SARS_CoV_2 E417N;E484K;L452R;N501Y 78;71;87;64 83;76;92;69 RBD;S 117;115 120;116 34389380 EGCG as an anti-SARS-CoV-2 agent: Preventive versus therapeutic potential against original and mutant virus. For in vitro binding assays, SARS-CoV-2 recombinant proteins RBD, its N501Y mutant RBDm, and S2 were labeled using the NT Protein Labeling Kit RED-NHS (Nanotemper, Germany) and mixed with increasing concentrations of EGCG in a 10 mM potassium-phosphate buffer, pH 7.4, supplemented with 0.05% Tween-20. 2021 Biochimie Method SARS_CoV_2 N501Y 70 75 RBD 61 64 34389380 EGCG as an anti-SARS-CoV-2 agent: Preventive versus therapeutic potential against original and mutant virus. The N501Y mutant of RBD (RBDm) and S2 protein were obtained analogously to RBD. 2021 Biochimie Method SARS_CoV_2 N501Y 4 9 RBD;RBD 20;75 23;78 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. S484K and S501Y rRT-PCR assays. 2021 Chinese medical journal Method SARS_CoV_2 S501Y;S484K 10;0 15;5 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. The assays were developed to target the E484K and N501Y mutations in the S gene of the B.1.351 and B.1.1.7 lineage viruses, respectively. 2021 Chinese medical journal Method SARS_CoV_2 E484K;N501Y 40;50 45;55 S 73 74 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. The primer and probe sets for the S484K and S501Y assays are listed in Table 2. 2021 Chinese medical journal Method SARS_CoV_2 S484K;S501Y 34;44 39;49 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. The S484K and S501Y rRT-PCR assays targeting S gene of SARS-CoV-2 variants, the primers and probes were (forward: 5'- CTGAAATCTATCAGGCCGGTAG -3'; reverse: 5'-CTACTCTGTATGGTTGGTAACC-3'; probe: 5'-FAM-TAATGGTGTTAAAGGTT-MGB-3') and (forward:5'- GTTACTTTCCTTTACAATCATATG-3'; reverse: 5'- TTTAGGTCCACAAACAGTTGC-3'; probe: 5'-FAM- AACCCACTTATGGTG-MGB-3'), respectively. 2021 Chinese medical journal Method SARS_CoV_2 S484K;S501Y 4;14 9;19 S 45 46 34403732 Identification of natural compounds as SARS-CoV-2 entry inhibitors by molecular docking-based virtual screening with bio-layer interferometry. For pseudovirus assay, wild-type and 4 mutants (D614G, N501Y, N439K & Y453F) SARS-CoV-2 Spike RBD pseudovirus (VectorBuilder) were added at final concentration of 4.66 x 106 TU/mL to each well containing 0, 25, 50 or 100 muM compounds and 5 mug/mL polybrene, respectively. 2021 Pharmacological research Method SARS_CoV_2 N439K;N501Y;Y453F;D614G 62;55;70;48 67;60;75;53 S;RBD 88;94 93;97 34403732 Identification of natural compounds as SARS-CoV-2 entry inhibitors by molecular docking-based virtual screening with bio-layer interferometry. Mouse Fc-tagged RBD (Catalog: 40592-V05H) and His-tagged human ACE2 (Cat: 10108-H08B) were both purchased from Sino Biological (Beijing, China). 2021 Pharmacological research Method SARS_CoV_2 V05H 36 40 RBD 16 19 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Additional models of S trimers individually harboring I68R, N74K, or S247R mutations were generated using Coot. 2021 Journal of virology Method SARS_CoV_2 I68R;N74K;S247R 54;60;69 58;64;74 S 21 22 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. The S protein of this isolate contained a single-mutation D614G, which is relatively common for SARS-CoV-2 isolates. 2021 Journal of virology Method SARS_CoV_2 D614G 58 63 S 4 5 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. Then the mutated SARS-CoV-2 RBD (N439K) structures were constructed using homology modeling by SWISS-MODEL. 2021 Frontiers in cell and developmental biology Method SARS_CoV_2 N439K 33 38 RBD 28 31 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Its mutants, including RBDN501Y, RBDK417N, RBDE484K, and RBDTriple (N501Y, K417N, E484K), were generated using the QuikChange kit. 2021 eLife Method SARS_CoV_2 E484K;K417N;N501Y 82;75;68 87;80;73 RBD;RBD;RBD 23;33;43 26;36;46 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. OaAEP1(C247A) is cysteine 247 to alanine mutant of asparaginyl endoprotease 1 from Oldenlandia affinis, abbreviated as OaAEP1 here. 2021 eLife Method SARS_CoV_2 C247A;C247A 17;7 40;12 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. Comparison of the two assays on 56 samples showed high levels of concordance (r=0 8561, p<0 0001) for Asp614Gly wild-type-mediated neutralisation between these two assays (appendix p 31). 2021 The lancet. HIV Method SARS_CoV_2 D614G 102 111 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. High levels of concordance (r=0 9165, p=0 0054) between plasma-mediated and IgG-mediated neutralisation of Asp614Gly wild-type was seen in 23 samples (appendix p 32). 2021 The lancet. HIV Method SARS_CoV_2 D614G 107 116 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. Humoral responses at baseline and after vaccination were assessed with ELISA-based antibody binding assays to recombinant SARS-CoV-2 RBD and FLS proteins from Asp614Gly wild-type and the beta variant as previously described. 2021 The lancet. HIV Method SARS_CoV_2 D614G 159 168 RBD 133 136 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. IgG was tested against both Asp614Gly wild-type and the beta variant. 2021 The lancet. HIV Method SARS_CoV_2 D614G 28 37 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. Of 51 samples, 18 (35%) showing background presumed to be mediated by antiretrovirals were excluded from further testing; acceptable samples were tested using a SARS-CoV-2-specific microneutralisation assay in the same MLV backbone expressing Asp614Gly wild-type. 2021 The lancet. HIV Method SARS_CoV_2 D614G 243 252 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. Our analysis suggests that priming by natural infection with the ancestral virus Asp614Gly wild-type before vaccination with ChAdOx1 nCoV-19 could lead to heightened neutralising antibody titres with relative preservation of activity against the beta variant compared with those who were SARS-CoV-2 seronegative when receiving the first vaccine dose. 2021 The lancet. HIV Method SARS_CoV_2 D614G 81 90 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. Samples from HIV-negative participants were tested using a SARS-CoV-2 Asp614Gly wild-type neutralisation assay at the National Institute for Communicable Diseases (South Africa) using pseudoviruses produced by cotransfection with a lentiviral backbone (HIV-1 pNL4.luc) as previously described. 2021 The lancet. HIV Method SARS_CoV_2 D614G 70 79 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. The recombinant FLS and RBD proteins from either the Asp614Gly (also known as D614G) wild-type or beta SARS-CoV-2 variant were expressed and purified as described previously and were coupled to magnetic microspheres (Bio-Rad, Philadelphia, PA, USA) using a two-step carbodiimide reaction. 2021 The lancet. HIV Method SARS_CoV_2 D614G;D614G 53;78 62;83 RBD 24 27 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. We used a subset of 40 samples, which were shown to be seropositive for Asp614Gly wild-type FLS at day 42, to evaluate neutralisation against the beta variant. 2021 The lancet. HIV Method SARS_CoV_2 D614G 72 81 34417165 Effectiveness of BNT162b2 and mRNA-1273 covid-19 vaccines against symptomatic SARS-CoV-2 infection and severe covid-19 outcomes in Ontario, Canada: test negative design study. All RT-PCR positive specimens with cycle threshold values <=35 were tested for the N501Y mutation (starting 3 February 2021) and the E484K mutation (starting 22 March 2021). 2021 BMJ (Clinical research ed.) Method SARS_CoV_2 E484K;N501Y 133;83 138;88 34417165 Effectiveness of BNT162b2 and mRNA-1273 covid-19 vaccines against symptomatic SARS-CoV-2 infection and severe covid-19 outcomes in Ontario, Canada: test negative design study. We considered samples with positive N501Y and negative E484K mutations as alpha variants, and samples with positive N501Y and E484K mutations as beta or gamma variants. 2021 BMJ (Clinical research ed.) Method SARS_CoV_2 E484K;E484K;N501Y;N501Y 55;126;36;116 60;131;41;121 34417165 Effectiveness of BNT162b2 and mRNA-1273 covid-19 vaccines against symptomatic SARS-CoV-2 infection and severe covid-19 outcomes in Ontario, Canada: test negative design study. We obtained information on variants and mutations from the Public Health Case and Contact Management system, which contains information on the clinical course of cases and the results of screening tests for N501Y and E484K mutations and whole genome sequencing results that identify specific variant of concern lineages (alpha (B.1.1.7), beta (B.1.351), gamma (P.1)). 2021 BMJ (Clinical research ed.) Method SARS_CoV_2 E484K;N501Y 217;207 222;212 34417349 SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. Grids were imaged at 92,000x magnification in a Talos F200C transmission electron microscope (TEM) equipped with a Ceta 16M detector (Thermo Fisher Scientific). 2021 Proc Natl Acad Sci U S A Method SARS_CoV_2 F200C 54 59 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. As previously described, pseudotyped lentiviral reporter viruses were produced by the co-transfection of plasmids encoding S proteins from Wuhan-1 strain (Genbank #: MN908947.3) with a D614G mutation, a luciferase reporter, lentivirus backbone, and human transmembrane protease serine 2 (TMPRSS2) genes into HEK293T/17 cells (ATCC CRL-11268). 2021 Nature immunology Method SARS_CoV_2 D614G 185 190 S 123 124 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. SARS-CoV-2/human/USA/GA-EHC-083E/2020) (referred to as the D614G variant) was derived from a residual nasopharyngeal swab collected from an Emory Healthcare patient in March 2020. 2021 Nature immunology Method SARS_CoV_2 D614G 59 64 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. To make SARS-CoV-2 pseudotyped recombinant VSV-DeltaG-firefly luciferase virus, BHK21/WI-2 cells (Kerafast, EH1011) were transfected with the Wuhan-1 strain (Genbank #: MN908947.3) S plasmid expressing full-length S with D614G mutation or S of B.1.351. 2021 Nature immunology Method SARS_CoV_2 D614G 221 226 S;S;S 181;214;239 182;215;240 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. 11906ES50, V367F Cat. 2021 Infectious diseases of poverty Method SARS_CoV_2 V367F 11 16 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. HEK293T cells (6 x 106 cells per 10-cm plate) were co-transfected with recombinant SARS-CoV-2S plasmids (wild type, V367 mutant, or N354D mutant) and the packaging vectors (pLP1, pLP2, and pLP/VSVG, Invitrogen) using liposomal transfection reagent (Yeasen, No. 2021 Infectious diseases of poverty Method SARS_CoV_2 N354D 132 137 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. HEK293T-ACE2 cells were seeded in 96-well plates at 1.5 x 104/well, and 3700 TU pseudoviruses (wild type, V367F mutant, or N354D mutant) were added to the culture medium. 2021 Infectious diseases of poverty Method SARS_CoV_2 N354D;V367F 123;106 128;111 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. Nos.18101ES50, and N354D Cat. 2021 Infectious diseases of poverty Method SARS_CoV_2 N354D 19 24 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. SARS-CoV-2 S pseudotyped virus with wild-type spike sequence and the N354D and V367F mutants were purchased from Yeasen (wild-type Cat. 2021 Infectious diseases of poverty Method SARS_CoV_2 N354D;V367F 69;79 74;84 S;S 46;11 51;12 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. The recombinant SARS-CoV-2 S plasmids containing wild type spike or the S mutants (SARS-CoV-2 S V367F and SARS-CoV-2 S N354D) were verified by DNA sequencing (Additional file 2. 2021 Infectious diseases of poverty Method SARS_CoV_2 N354D;V367F 119;96 124;101 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. V367F and N354D mutants were generated by site-directed mutagenesis. 2021 Infectious diseases of poverty Method SARS_CoV_2 N354D;V367F 10;0 15;5 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. An in-house enzyme immunoassay coated with either wild type, N501Y, or N501Y-E484K RBD was used to determine the impact of N501Y on RBD binding. 2021 EBioMedicine Method SARS_CoV_2 N501Y;N501Y;N501Y;E484K 61;71;123;77 66;76;128;82 RBD;RBD 83;132 86;135 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Anti-RBD assay for wild type, N501Y, and N501Y-E484K RBD. 2021 EBioMedicine Method SARS_CoV_2 N501Y;N501Y;E484K 30;41;47 35;46;52 RBD;RBD 5;53 8;56 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Briefly, 96-well Nunc MaxiSorpflat-bottom immunoplates (Thermo Fisher Scientific, Invitrogen, Denmark; Cat#44-2404) were coated with 100 muL/well (0.1 mug/well) of His-tagged SARS-CoV-2 spike RBD with the wild type, N501Y or N501Y-E484K-K417N RBD in 0.05 M NaHCO3 (pH 9.6) overnight at 4 C and then followed by incubation with a blocking reagent. 2021 EBioMedicine Method SARS_CoV_2 N501Y;N501Y;E484K;K417N 216;225;231;237 221;230;236;242 S;RBD;RBD 186;192;243 191;195;246 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Furthermore, we have compared the binding of WT, N501Y and N501Y-E484K RBD with a SARS-CoV-2 human antibody which was produced as previously described with modifications. 2021 EBioMedicine Method SARS_CoV_2 N501Y;N501Y;E484K 49;59;65 54;64;70 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Recombinant RBD (amino acid residues 306-543) of SARS-CoV-2 spike protein from the reference sequence Wuhan-Hu-1 (GenBank ID YP_009724390.1) (wild type) or with the mutations N501Y or N501Y-E484K-K417N were expressed and purified as we described previously with modifications. 2021 EBioMedicine Method SARS_CoV_2 N501Y;N501Y;E484K;K417N 175;184;190;196 180;189;195;201 S;RBD 60;12 65;15 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. This workflow was applied to 2,309 SARS-CoV-2 genomes with the 9-bp deletion Delta106-108 in ORF1a-nsp6 along with mutation A20262G, which demarcates the parent clade to lineage B.1.526 alongside 688 global reference viruses. 2021 Nature Method SARS_CoV_2 A20262G 124 131 ORF1a;Nsp6 93;99 98;103 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. We assayed the neutralizing activity of monoclonal antibodies, convalescent plasma and vaccinee sera against E484K, S477N and wild-type (D614G) pseudoviruses, as well as pseudovirus NYDelta5 containing all five signature mutations of B.1.526-E484K (L5F, T95I, D253G, E484K, D614G and A701V), as previously described. 2021 Nature Method SARS_CoV_2 A701V;D253G;D614G;E484K;E484K;S477N;T95I;D614G;L5F;E484K 284;260;274;109;267;116;254;137;249;242 289;265;279;114;272;121;258;142;252;247 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. Antibody preparations were evaluated by SARS-CoV-2 pseudovirus neutralization assay (PsVNA) using WA-1 strain, UK variant (B.1.1.7 with spike mutations: H69-V70del, Y144del, N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H), SA variant (B.1.351 strain with spike mutations L18F, D80A, D215G, L242-244del, R246I, K417N, E484K, N501Y, D614G, and A701V), CA variant (B.1.429 strain with spike mutations S13I, W152C, L452R, D614G) and JP variant (P.1 strain with spike mutations L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I, D614G, V1176F) (Figure S1 and Table S1). 2021 iScience Method SARS_CoV_2 A570D;A701V;D1118H;D138Y;D215G;D614G;D614G;D614G;D614G;D80A;E484K;E484K;H655Y;K417N;K417T;L18F;L18F;L452R;N501Y;N501Y;N501Y;P26S;P681H;R190S;R246I;S13I;S982A;T1027I;T20N;T716I;V1176F;W152C;Y144del 181;348;220;497;289;188;337;424;547;283;323;518;532;316;511;277;479;417;174;330;525;491;195;504;309;404;209;539;485;202;554;410;165 186;353;226;502;294;193;342;429;552;287;328;523;537;321;516;281;483;422;179;335;530;495;200;509;314;408;214;545;489;207;560;415;172 S;S;S;S 136;261;388;463 141;266;393;468 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. Biotinylated human ACE2 (AC2-H82E6) contains amino acid residues Gln 18 - Ser 740 expressed from HEK 293 cells was purchased from Acro Biosystems. 2021 iScience Method SARS_CoV_2 Q18S 65 77 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. But based on the time of collection most of the infecting viruses were D614G in the US. 2021 iScience Method SARS_CoV_2 D614G 71 76 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. Pseudovirions were produced by co-transfection Lenti-X 293T cells with psPAX2(gag/pol), pTrip-luc lentiviral vector and pcDNA 3.1 SARS-CoV-2-spike-deltaC19, using Lipofectamine 3000. 2021 iScience Method SARS_CoV_2 X293T 53 59 S 141 146 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. Recombinant SARS-CoV-2 spike receptor binding domain (RBD) and its mutants were purchased from Sino Biologicals (RBD-wt; 40592-V08H82, RBD-K417N; 40592-V08H59, RBD-N501Y; 40592-V08H82 and RBD-E484K; 40592-V08H84). 2021 iScience Method SARS_CoV_2 E484K;K417N;N501Y 192;139;164 197;144;169 RBD;S;RBD;RBD;RBD;RBD;RBD 29;23;54;113;135;160;188 52;28;57;116;138;163;191 34433426 Investigation of Interaction between the Spike Protein of SARS-CoV-2 and ACE2-Expressing Cells Using an In Vitro Cell Capturing System. 96-well ELISA plates (CIH-F8T, GSBIO) were coated with 0.5 mug/well of spike S1-his protein in PBS buffer (pH 7.0) overnight at 4 C. 2021 Biological procedures online Method SARS_CoV_2 F8T 26 29 S 71 76 34433426 Investigation of Interaction between the Spike Protein of SARS-CoV-2 and ACE2-Expressing Cells Using an In Vitro Cell Capturing System. Lysates were first incubated with S1 or S1(D614G) for 4 h at 4 C, then incubated with anti-FLAG antibody (M2, Sigma-Aldrich) or mouse IgG conjugated to Dynabeads Protein G (Thermo Fisher Scientific) overnight at 4 C. 2021 Biological procedures online Method SARS_CoV_2 D614G 43 48 34433803 ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker. B.1.1.7: H69 deletion, V70 deletion, Y144deletion, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H. 2021 Signal transduction and targeted therapy Method SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 58;93;65;51;72;86;79 63;99;70;56;77;91;84 34433803 ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker. B.1.351: D80A, D215G, A242-244 deletion, K417N, E484K, N501Y, D614G, A701V. 2021 Signal transduction and targeted therapy Method SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;N501Y 69;15;62;9;48;41;55 74;20;67;13;53;46;60 34433803 ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker. B.1.617.1: T95I, G142D, E154K, L452R, E484Q, D614G, P681R, Q1071H. 2021 Signal transduction and targeted therapy Method SARS_CoV_2 D614G;E154K;E484Q;G142D;L452R;P681R;Q1071H;T95I 45;24;38;17;31;52;59;11 50;29;43;22;36;57;65;15 34433803 ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker. P.1: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, V1176F. 2021 Signal transduction and targeted therapy Method SARS_CoV_2 D138Y;D614G;E484K;H655Y;K417T;L18F;N501Y;P26S;R190S;T1027I;T20N;V1176F 23;58;44;65;37;5;51;17;30;72;11;80 28;63;49;70;42;9;56;21;35;78;15;86 34433803 ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker. Pseudo-typed SARS-CoV-2-D614G, SARS-CoV-2, SARS-CoV, HCoV-NL63, B.1.1.7, B.1.351 and B.1.617.1 were constructed by co-transfection of two plasmids, one expressing Env-defective HIV-1 with luciferase reporter (pNL4-3.luc.RE) and the other expressing the full-length S-protein of SARS-CoV-2-D614G, SARS-CoV-2, SARS-CoV, HCoV-NL63, B.1.1.7, B.1.351, or B.1.617.1 into HEK293T cells. 2021 Signal transduction and targeted therapy Method SARS_CoV_2 D614G;D614G 24;289 29;294 S 265 266 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Single and double mutant complexes were created by mutating the amino acids Glu484 to Gln484 and Leu452 to Arg452 using Schrodinger Maestro 2019-4 (Schrodinger, LLC, New York, NY, USA). 2021 Biomolecules Method SARS_CoV_2 E484Q;L452R 76;97 92;113 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Surface potential of the wild type and L452R mutants was calculated using the Adaptive Poisson-Boltzmann Solver (APBS) in Schrodinger Maestro. 2021 Biomolecules Method SARS_CoV_2 L452R 39 44 34442817 Impact of Full Vaccination with mRNA BNT162b2 on SARS-CoV-2 Infection: Genomic and Subgenomic Viral RNAs Detection in Nasopharyngeal Swab and Saliva of Health Care Workers. Moreover, the RT-PCR method was used for the analysis of known viral mutations using the REALQUALITY SARS-CoV-2 Variants (AB ANALITICA, Padova, Italy) (targeting N501Y, K417T and K417N) and SARS-CoV-2 Nucleic Acid Mutation Diagnostic kit (Sansure Biotech Inc, Hunan, China) (targeting N501Y and HV69/70del), following the manufacturers' instructions. 2021 Microorganisms Method SARS_CoV_2 K417N;K417T;N501Y;N501Y 179;169;162;285 184;174;167;290 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. The five missense mutations, D614G (23403A>G)-S gene, Q57H (25563G>T)-ORF3a gene, P323L (14408C>T):ORF1ab/RdRP gene, R203K (28881G>A):N gene, and G204R (28883G>C):N gene (Table S2). 2021 International journal of molecular sciences Method SARS_CoV_2 D614G;G204R;P323L;Q57H;R203K;C14408T;A23403G;A23403S;G25563F;G25563R;G25563T;G28881A;G28883C 29;146;82;54;117;89;36;36;60;60;60;124;153 34;151;87;58;122;97;44;44;68;68;68;132;161 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. Overall, 18 structures (the 1-, 2-, and 3-open-complex forms for the wild type, D614G, D614A, L455F, F456L, and Q787H) were built as the inputs to the MD simulation calculation. 2021 International journal of molecular sciences Method SARS_CoV_2 D614A;D614G;F456L;L455F;Q787H 87;80;101;94;112 92;85;106;99;117 34445669 Molecular Masks for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. An amount of 0.1 microg of His-tagged recombinant SARS-CoV-2 S1 (D614G) protein (Sino Biological US Inc., Cat# 40591-V08H3, Wayne, PA, USA) was added to the column and incubated at 4C for 1 h. 2021 International journal of molecular sciences Method SARS_CoV_2 D614G 65 70 34445669 Molecular Masks for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. D614G spike coding sequence was modified with a D614G point mutation and a truncation of 19 amino acids at the end of C terminus, cloned into pCDNA 3.1 vector (Invitrogen). 2021 International journal of molecular sciences Method SARS_CoV_2 D614G;D614G 48;0 53;5 S 6 11 34445669 Molecular Masks for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. His-D614G Spike:ACE2 Protein Interaction Pull-Down Assay. 2021 International journal of molecular sciences Method SARS_CoV_2 D614G 4 9 S 10 15 34445669 Molecular Masks for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. Synthesis and Production of SARS-CoV-2 and D614G Mutant Pseudovirus . 2021 International journal of molecular sciences Method SARS_CoV_2 D614G 43 48 34445669 Molecular Masks for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. Synthesis and Production of SARS-CoV-2 and D614G Mutant Pseudovirus. 2021 International journal of molecular sciences Method SARS_CoV_2 D614G 43 48 34445669 Molecular Masks for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. To produce D614G spike pseudovirus for reporter assay, the lentivector reporter pSIN-Luc (containing luciferase as the marker gene) and lentiviral vector packaging plasmid psPAX2 (containing HIV gag and pol genes) were co-transfected with D614G spike at a ratio of 4:3:1 by lipofectamine 2000 (Thermo Fisher Scientific, Waltham, MA, USA) in 10 cm dishes of HEK293T cells (ATCC, Manassas, VA, USA). 2021 International journal of molecular sciences Method SARS_CoV_2 D614G;D614G 11;239 16;244 S;S 17;245 22;250 34445669 Molecular Masks for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. While incubating the spike protein (D614G), 0.1 microg of recombinant ACE2 protein (R&D system Inc., Cat# 933-ZN-010, Minneapolis, MN, USA) was incubated with each ACE2P1D1 and ACE2P2D1 in different concentrations (10 microM, and 100 microM) in 400 microL washing solution at cold room for 1 h by tube rotator with a gentle motion. 2021 International journal of molecular sciences Method SARS_CoV_2 D614G 36 41 S 21 26 34449757 An Autochthonous Outbreak of the SARS-CoV-2 P.1 Variant of Concern in Southern Italy, April 2021. SGTF-negative samples were screened for the presence of notable types of spike protein mutations (HV 69-70 deletion, N501Y, K417N, E484K, and K417T) using a commercial multiplex real-time PCR kit (Seegene Allplex SARS-CoV-2 Variants I Assay, Arrows Diagnostics, Genova, Italy). 2021 Tropical medicine and infectious disease Method SARS_CoV_2 E484K;K417N;K417T;N501Y 131;124;142;117 136;129;147;122 S 73 78 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Mutation calling, translation to amino acid and identification of the B.1.362+L452R variant sequences were done in R with a custom code using Bioconductor package Seqinr. 2021 Vaccines Method SARS_CoV_2 L452R 78 83 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. One hundred TCID50 (median tissue culture infectious dose) of B.1.362+L452R variant, WT strain and Alpha variant isolates were incubated with inactivated sera diluted 1:10 to 1:1280 in 96 well plates for 60 min at 33 C. 2021 Vaccines Method SARS_CoV_2 L452R 70 75 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. Screening for SARS-CoV-2 variants of concern (VOC) was performed using real-time specific RT-PCR SARS-CoV-2 Spike (i.e., deletion 69-70, E484K and N501Y mutations) (TIB Molbiol, Berlin, Germany). 2021 Viruses Method SARS_CoV_2 E484K;N501Y 137;147 142;152 S 108 113 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. The constructs for RBDWT and mutants E484K, L452R/E484Q, and N440K were all designed as single genes containing each protein of interest fused to an N-terminal micro-phosphatase signal peptide and a C-terminal hexahistidine tag. 2022 Allergy Method SARS_CoV_2 E484K;L452R;N440K;E484Q 37;44;61;50 42;49;66;55 N 149 150 34455390 Evolution of antibody responses up to 13 months after SARS-CoV-2 infection and risk of reinfection. Neutralization of infectious D614G, B.1.1.7, and B.1.351 variants grown in Vero E6 cell lines (ATCC Cat# CRL-1586, RRID: CVCL_0574) was assessed for each serum using limiting dilutions. 2021 EBioMedicine Method SARS_CoV_2 D614G 29 34 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. Neutralization assays were done essentially by the reduction of cytopathic effect (CPE) in Vero E6 cells with infectious D614G (GISAID Accession Number EPI_ISL_3509539), alpha (B.1.1.7, GISAID Accession Number EPI_ISL_1167921), and gamma (P.1, GISAID Accession Number EPI_ISL_1321471) SARS-CoV-2 variants. 2022 Journal of medical virology Method SARS_CoV_2 D614G 121 126 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. R0180C). 2022 Journal of medical virology Method SARS_CoV_2 R0180C 0 6 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Briefly, viral RNA samples from competition groups of (i) Delta versus Alpha and (ii) Delta versus Alpha-spike/Delta-backbone were used for a specific one-step RT-PCR that containing the A23063T mutation site. 2021 bioRxiv Method SARS_CoV_2 A23063T 187 194 S 105 110 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Individual point mutations for Alpha (NSP3: P153L, T183I, A890D, I1412T; NSP6: SGF106-108del; NSP12: P323L; Spike: HV69-70del, Y145del, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H; ORF8: Q27stop, R52I, Y73C, S84L; N: D3L, R203K, G204R, S235F) and individual point mutations for Delta (NSP2: P129L; NSP3: P822L; H1274Y; NSP4: A446V; NSP6: V149A; NSP12: P323L; V355A; G671S; NSP13: P77L; NSP15: H234Y; Spike: T19R, G142D, E156G, FR157-158del, L452R, T478K, D614G, P681R, D950N; ORF3a: S26L; M: I82T; ORF7a: V82A; L116F; T120I; ORF8: S84L; DF119-120del; N: D63G; R203M; D377Y; R385K) were introduced into subclones of individual fragments by overlapping fusion PCR. 2021 bioRxiv Method SARS_CoV_2 A446V;A570D;A890D;D1118H;D377Y;D3L;D614G;D614G;D63G;D950N;E156G;G142D;G204R;G671S;H1274Y;H234Y;I1412T;I82T;L116F;L452R;N501Y;P129L;P153L;P323L;P323L;P681H;P681R;P77L;P822L;Q27X;R203K;R203M;R385K;R52I;S235F;S26L;S84L;S84L;S982A;T120I;T183I;T19R;T478K;T716I;V149A;V355A;V82A;Y145del;Y73C 330;143;58;178;572;222;150;460;559;474;425;418;234;371;316;398;65;497;516;446;136;296;44;101;357;157;467;385;309;192;227;565;579;201;241;488;213;536;171;523;51;412;453;164;343;364;510;127;207 335;148;63;184;577;225;155;465;563;479;430;423;239;376;322;403;71;501;521;451;141;301;49;106;362;162;472;389;314;199;232;570;584;205;246;492;217;540;176;528;56;416;458;169;348;369;514;134;211 ORF7a;S;S;ORF3a;Nsp13;Nsp12;Nsp12;Nsp2;Nsp3;Nsp3;Nsp4;Nsp6;Nsp6;ORF8;ORF8;N;N 503;108;405;481;378;94;350;290;38;303;324;73;337;186;530;219;556 508;113;410;486;383;99;355;294;42;307;328;77;341;190;534;220;557 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. The human ACE2 protein was purchased from Sino Biological (Beijing, China; Cat# 10108-H08H) and the human IgG1 Fc-tagged RBD proteins were made in-house using a method as previously described. 2021 bioRxiv Method SARS_CoV_2 H08H 86 90 RBD 121 124 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. The reads were filtered for Q-scores of 37 at the A23063T and T14444C mutation sites and adjacent bases and counted. 2021 bioRxiv Method SARS_CoV_2 A23063T;T14444C 50;62 57;69 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Viral RNA samples from competition group of Alpha versus Alpha-spike/Delta-backbone were quantified by the T14444C mutation. 2021 bioRxiv Method SARS_CoV_2 T14444C 107 114 S 63 68 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Using the same PDB ID, the SARS-CoV-2 variants (N501Y, E484K, K417N/T, A475V, L452R, V483A, F490L, S477N, N439K) were constructed using UCSF chimera platform by editing necessary amino acids of the S protein via the swapaa command which utilizes information from a rotamer library (Shapovalov & Dunbrack,). 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 A475V;E484K;F490L;K417N;K417T;L452R;N439K;S477N;V483A;N501Y 71;55;92;62;62;78;106;99;85;48 76;60;97;69;69;83;111;104;90;53 S 198 199 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. Hamsters were anesthetized with isoflurane and were intranasally inoculated with 5 x 105 FFU of 2019n-CoV/USA_WA1/2020-D614G, Wash-B.1.351, or B.1.617.2 SARS-CoV-2 in 100 muL PBS. 2021 Immunity Method SARS_CoV_2 D614G 119 124 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. The WA1/2020 recombinant strains with substitutions D614G, B.1.351-, and B.1.1.28-variant spike genes introduced into an infectious cDNA clone of the 2019n-CoV/USA_WA1/2020 strain, were previously described. 2021 Immunity Method SARS_CoV_2 D614G 52 57 S 90 95 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. Mutation detection was performed on a Roche LightCycler 480 system (Roche Diagnostics, San Cugat, Spain), using the reagents VirSNiP SARS-CoV-2 spike N501Y and VirSNiP SARS-CoV-2 spike deletion H69-V70 (TIB MOLBIOL, Eresburgstrasse, Berlin, Germany). 2021 Diagnostic microbiology and infectious disease Method SARS_CoV_2 N501Y 150 155 S;S 144;179 149;184 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. Non-suspected cases were positive samples that did not contain either N501Y or the H69-V70 deletion. 2021 Diagnostic microbiology and infectious disease Method SARS_CoV_2 N501Y 70 75 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. Suspected cases were patients with confirmed SARS-CoV-2 infection and detection of the N501Y mutation and spike deletion H69-V70. 2021 Diagnostic microbiology and infectious disease Method SARS_CoV_2 N501Y 87 92 S 106 111 COVID-19 45 65 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. We also used COVID-3D for the structural analysis of significant mutations (E484K, K417T/N, N501Y, and D614G) in emerging variants. 2021 mBio Method SARS_CoV_2 D614G;K417N;K417T;N501Y;E484K 103;83;83;92;76 108;90;90;97;81 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. F486L, Q493N and D614G mutations were introduced by PCR-mediated mutagenesis by Phanta Master Mix (Cat. 2021 Cell research Method SARS_CoV_2 D614G;Q493N;F486L 17;7;0 22;12;5 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. The contact area between S1 (N-terminal-S680) and S2 (S686-C-terminal) was calculated to demarcate their interaction in the presence and absence of force. 2021 Cell research Method SARS_CoV_2 S686C 54 60 N 29 30 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. 3 to B.1.1.7 spike protein defining mutations - defining deletions:H69,V70,Y144/ Y145 plus defining amino acid substitutions: N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, two types of events can be observed in 21 out of 24 variants: . 2021 Meta gene Method SARS_CoV_2 A570D;D614G;N501Y;P681H;S982A;T716I 133;140;126;147;161;154 138;145;131;152;166;159 S 13 18 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. 3 to B.1.1.7 spike protein defining mutations - defining deletions:H69,V70,Y144/ Y145 plus defining amino acid substitutions: N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, two types of events can be observed in 21 out of 24 variants. 2021 Meta gene Method SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 133;168;140;126;147;161;154 138;174;145;131;152;166;159 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. According to GISAID hCoV-19 Spike Glycoprotein mutation surveillance dashboard, missense mutation C379F occurred two times worldwide in spike protein from Switzerland: hCoV-19/Switzerland/SO-ETHZ-490065/2020 and it was recently detected in spike protein from Indonesia: hCoV-19/Indonesia/JK-NIHRD-WGS07001/2021. 2021 Meta gene Method SARS_CoV_2 C379F 98 103 S;S;S 28;136;240 46;141;245 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Among them I found three extremely rare missense mutations: C379F, A93Y and V90T. 2021 Meta gene Method SARS_CoV_2 A93Y;C379F;V90T 67;60;76 71;65;80 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. As expected, most European SARS-CoV-2 spike proteins include D614G mutation. 2021 Meta gene Method SARS_CoV_2 D614G 61 66 S 38 43 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. B.1.1.7 spike protein QSQ87331.1 also contains V90T missense mutation. 2021 Meta gene Method SARS_CoV_2 V90T 47 51 S 8 13 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Crystallographic structure of neutralizing antibody 2-51 in complex with SARS-CoV-2 spike N-terminal domain (NTD) (DOI: https://doi.org/10.2210/pdb7L2C/pdb, https://www.rcsb.org/structure/7l2c) was used to predict the effect of V90T missense mutation upon protein-to-protein interaction. 2021 Meta gene Method SARS_CoV_2 V90T 228 232 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. GISAID's hCoV-19 spike mutations table (https://mendel.bii.a-star.edu.sg/METHODS/corona/current/MUTATIONS/hCoV-19_Human_2019_WuhanWIV04/hcov19_Spike_mutations_table.html) lists one worldwide occurrence of A93Y mutation, while V90T has not been reported as SARS-CoV-2 spike protein mutation so far. 2021 Meta gene Method SARS_CoV_2 A93Y;V90T 205;226 209;230 S;S 17;267 22;272 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Here I report the second worldwide occurrence of A93Y that I found in QSQ87331.1 spike protein. 2021 Meta gene Method SARS_CoV_2 A93Y 49 53 S 81 86 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Histidine deletion ( H69) and Asparagine to Tyrosine substitution (N501Y) are found to be the most stable B.1.1.7 surface glycoprotein mutations. 2021 Meta gene Method SARS_CoV_2 N501Y 67 72 S 114 134 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. I found second worldwide occurrence of A93Y among the European population and this is the first report of V90T as SARS-CoV-2 surface glycoprotein mutation. 2021 Meta gene Method SARS_CoV_2 A93Y;V90T 39;106 43;110 S 125 145 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. It contains all B.1.1.7 defining mutations plus major recurrent deletionPFNDG [85 - 89] and three missense mutations: V90T, A93Y and D138H in the N-terminal domain. 2021 Meta gene Method SARS_CoV_2 A93Y;D138H;V90T 124;133;118 128;138;122 N 146 147 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Negative change of binding affinityG =- 0.040 kcal/mol for V90T missense mutation was computed what means that newly detected V90T missense mutation in the N-terminal domain of SARS-CoV-2 spike protein, even though minimally, contributes towards escaping 2-51 neutralizing antibody. 2021 Meta gene Method SARS_CoV_2 V90T;V90T 59;126 63;130 S;N 188;156 193;157 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Novel V90T SARS-CoV-2 spike protein mutation and rare C379F and A93Y mutations. 2021 Meta gene Method SARS_CoV_2 A93Y;C379F;V90T 64;54;6 68;59;10 S 22 27 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Of all B.1.1.7 spike variants I computed and there were 25 such, this is the most polymorphic B.1.1.7 surface glycoprotein that contains two missense mutations: V90T and A93Y that were identified for the first time among the European population. 2021 Meta gene Method SARS_CoV_2 A93Y;V90T 170;161 174;165 S;S 102;15 122;20 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. On the other hand, 103 variants included D614G in addition to another mutation and 20 variants did not include D614G mutation at all. 2021 Meta gene Method SARS_CoV_2 D614G;D614G 41;111 46;116 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. On the other hand, missense mutations: A93Y and V90T were found in a highly-polymorphic B.1.1.7 surface glycoprotein variant, NCBI accession QSQ87331.1. 2021 Meta gene Method SARS_CoV_2 A93Y;V90T 39;48 43;52 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. QJT72386.1 spike protein contains only: C379F and D614G mutations (Appendix A). 2021 Meta gene Method SARS_CoV_2 C379F;D614G 40;50 45;55 S 11 16 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Since there is no V90T spike mutation listed in GISAID's spike mutations table, this is the first international report of V90T as SARS-CoV-2 surface glycoprotein mutation. 2021 Meta gene Method SARS_CoV_2 V90T;V90T 18;122 22;126 S;S;S 141;23;57 161;28;62 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. So far A93Y missense mutation is found only once worldwide in spike protein from Sri Lanka: hCoV-19/Sri Lanka/CMC11595/2020. 2021 Meta gene Method SARS_CoV_2 A93Y 7 11 S 62 67 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Uncommon alterations:I68 and V70I were found in variant V3. 2021 Meta gene Method SARS_CoV_2 V70I 29 33 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. V1 = {H69-, V70-, Y144-, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H}. 2021 Meta gene Method SARS_CoV_2 A570D;D1118H;D614G;N501Y;S982A;T716I 32;67;39;25;60;53 37;73;44;30;65;58 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. V1 V3 = {H69 - ,N501Y, A570D, D614G, P681H, T716I, S982A, D1118H}. 2021 Meta gene Method SARS_CoV_2 A570D;D1118H;D614G;S982A;T716I;N501Y 23;58;30;51;44;16 28;64;35;56;49;21 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. V1 V3 = {I68-, H69-, V70-, V70I, Y144-, Y145-, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H}. 2021 Meta gene Method SARS_CoV_2 A570D;D1118H;D614G;N501Y;S982A;T716I;V70I 54;89;61;47;82;75;27 59;95;66;52;87;80;31 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. V3 = {I68-, H69-, V70I, Y145-, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H}. 2021 Meta gene Method SARS_CoV_2 A570D;D1118H;D614G;N501Y;S982A;T716I;V70I 38;73;45;31;66;59;18 43;79;50;36;71;64;22 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. All mutations, including the "reference" D614G, are introduced using the "mutations wizard" in the PyMOL molecular modeling package (Schrodinger LLC): rotamers of non-glycine side chains are chosen from the first suggested option for S protomer A, and then, where possible, we have sought to adopt the same rotamers for protomers B and C. 2021 Journal of chemical information and modeling Method SARS_CoV_2 D614G 41 46 S 234 235 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. Mutant lysine 484 sidechains (B.1.1.28 variant; E484K variant) are left protonated. 2021 Journal of chemical information and modeling Method SARS_CoV_2 E484K 48 53 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Lenti-X 293T cells (Takara, 632180) were seeded in 10-cm2 dishes at a density of 5 x 106 cells per dish and the following day transfected with 10 microg of WT or B.1.617.2 spike expression plasmid with TransIT-Lenti (Mirus, 6600) according to the manufacturer's instructions. 2021 Nature Method SARS_CoV_2 X293T 6 12 S 172 177 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Plasmids encoding the spike protein of SARS-CoV-2 D614 with a carboxy-terminal 19-amino-acid deletion with D614G were used. 2021 Nature Method SARS_CoV_2 D614G 107 112 S 22 27 34493762 Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. For instance, if 1 week presented 30% of genomes with the mutation R203K, and the number of cases on Monday of that week was 100. 2021 Scientific reports Method SARS_CoV_2 R203K 67 72 34493762 Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. In the case of MF mutation R203K, R203, and N501, we multiply the relative frequencies of the genomes with the state of interest (R203K, R203 or N501) in a determined week by the number of cases in the day. 2021 Scientific reports Method SARS_CoV_2 R203K;R203K 27;130 32;135 34493762 Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. In the case of the HF mutation N501Y we first calculated the relative frequencies of that mutation in each week and then adjusted the relative frequencies to a logistic regression model using R software. 2021 Scientific reports Method SARS_CoV_2 N501Y 31 36 34495697 A Bifluorescent-Based Assay for the Identification of Neutralizing Antibodies against SARS-CoV-2 Variants of Concern In Vitro and In Vivo. Oligonucleotides for cloning the Venus or mCherry FP or K417N, E484K, and N501Y mutations are available upon request. 2021 Journal of virology Method SARS_CoV_2 E484K;K417N;N501Y 63;56;74 68;61;79 34495697 A Bifluorescent-Based Assay for the Identification of Neutralizing Antibodies against SARS-CoV-2 Variants of Concern In Vitro and In Vivo. The rSARS-CoV-2 strain containing mutations K417N, E484K, and N501Y present in the receptor binding domain (RBD) within the spike (S) gene of the South African (SA) B.1.351 (beta[beta]) VoC and expressing mCherry was generated using standard molecular biology techniques. 2021 Journal of virology Method SARS_CoV_2 E484K;K417N;N501Y 51;44;62 56;49;67 RBD;S;RBD;S 83;124;108;131 106;129;111;132 34495697 A Bifluorescent-Based Assay for the Identification of Neutralizing Antibodies against SARS-CoV-2 Variants of Concern In Vitro and In Vivo. Wild-type (WT, WA-1), Venus (Venus WA-1), and mCherry (mCherry WA-1) reporter-expressing rSARS-CoV-2 strains, as well as rSARS-CoV-2 strain encoding the SA B.1.351 (beta) mutations K417N, E484K, and N501Y in the S RBD expressing mCherry (mCherry SA) were rescued as previously described. 2021 Journal of virology Method SARS_CoV_2 E484K;K417N;N501Y 188;181;199 193;186;204 RBD;S 214;212 217;213 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. D614G mutants were generated by site-directed mutagenesis. 2021 Journal of virology Method SARS_CoV_2 D614G 0 5 34495709 Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. At that time, we customized the TaqMan assay to detect SARS-CoV-2 spike protein with the N501Y, E484K, K417N, and K417T mutations. 2021 Journal of clinical microbiology Method SARS_CoV_2 E484K;K417N;K417T;N501Y 96;103;114;89 101;108;119;94 S 66 71 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Following the energy minimization, the control SARS-CoV-2 RBD/ACE2 and mutant (E484K, N501Y, K417N + E484K + N501Y) SARS-CoV-2 RBD/ACE2 protein-protein dockings were performed on the HADDOCK (High Ambiguity Driven protein-protein DOCKing) 2.4 docking server (De Vries et al.,). 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 E484K;K417N;N501Y;N501Y;E484K 101;93;86;109;79 106;98;91;114;84 RBD;RBD 58;127 61;130 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). In this study, protein-protein complexes obtained from docking analysis with ACE2 of wild-type spike protein and other variants (E484K, N501Y and K417N + E484K + N501Y) were subjected to 200-ns molecular dynamics simulations to test the stability and to investigate the dynamic evolution of these systems. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 E484K;K417N;N501Y;N501Y;E484K 154;146;136;162;129 159;151;141;167;134 S 95 100 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Subsequently, using the protein editing tool of Discovery Studio Visualizer v16, the K417, E484 and N501 residues in the receptor binding motif (RBM) of the spike glycoprotein were computationally mutated into residues N417, K484 and Y501 to generate the K417N, E484K and N501Y mutants of spike glycoprotein, respectively (Figure 1). 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 E484K;K417N;N501Y 262;255;272 267;260;277 S;S 157;289 175;307 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). The PRODIGY (PROtein binDIng enerGY prediction) web server (https://bianca.science.uu.nl/prodigy/) was used to calculate the binding affinities (kcal/mol) and dissociation constants (Kd) of top-ranked protein-protein complexes (wild-type, E484K, N501Y and K417N + E484K + N501Y) obtained from the HADDOCK server. 2021 Journal of biomolecular structure & dynamics Method SARS_CoV_2 E484K;E484K;K417N;N501Y;N501Y 239;264;256;246;272 244;269;261;251;277 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. Along with wildtype, three mutants of the spike protein were created, namely, Alpha (N501Y), Kappa (L452R and E484Q) and Delta (L45R and T478K) using the Maestro Suite of Schrodinger software (2020-3, NY, USA). 2021 International journal of molecular sciences Method SARS_CoV_2 E484Q;T478K;L452R;L45R;N501Y 110;137;100;128;85 115;142;105;132;90 S 42 47 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The chosen sequences of single mutations included the following amino acid substitutions: L5F, L18F, D80A, S98F, A222V, A262S, P272L, K417 N, N439K, L452R, Y453F, S477 N, E484K, E484Q, N501T, N501Y, E583D, D614G, Q675H, Q675P, Q677H, Q677P, P681H, P681R, A701V, D1163Y, G1167V, V1176F in addition to the wild type spike protein (NCBI Reference Sequence: YP_009724390.1). 2021 Biochimie Method SARS_CoV_2 A222V;A262S;A701V;D1163Y;D614G;D80A;E484K;E484Q;E583D;G1167V;K417N;L18F;L452R;L5F;N439K;N501T;N501Y;P272L;P681H;P681R;Q675H;Q675P;Q677H;Q677P;S477N;S98F;V1176F;Y453F 113;120;255;262;206;101;171;178;199;270;134;95;149;90;142;185;192;127;241;248;213;220;227;234;163;107;278;156 118;125;260;268;211;105;176;183;204;276;140;99;154;93;147;190;197;132;246;253;218;225;232;239;169;111;284;161 S 314 319 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. Among these haplotypes, H1 contains 4 of the 9 specific sites, including C241T, C3037T, C14408T, and A23403G, and H1 has been the most prevalent haplotype all over the world since March 2020. 2021 Computational and structural biotechnology journal Method SARS_CoV_2 A23403G;C14408T;C241T;C3037T 101;88;73;80 108;95;78;86 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. And H1-4-2 has one more A17675G mutation based H1-4 (H1-4-1). 2021 Computational and structural biotechnology journal Method SARS_CoV_2 A17675G 24 31 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. In addition, we found other 6 specific mutation sites: T445C, C6286T, C22227T, G25563T, C26801G, and G29645T. 2021 Computational and structural biotechnology journal Method SARS_CoV_2 C22227T;C26801G;C6286T;G25563T;G29645T;T445C 70;88;62;79;101;55 77;95;68;86;108;60 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. In our study in the early stage of the pandemic (2019.12 - 2020.05.05), we found 9 specific mutation sites (C241T, C3037T, C8782T, C14408T, C17747T, A17858G, C18060T, A23403G, and T28144C) of SARS-CoV-2. 2021 Computational and structural biotechnology journal Method SARS_CoV_2 A17858G;A23403G;C14408T;C17747T;C18060T;C241T;C3037T;C8782T;T28144C 149;167;131;140;158;108;115;123;180 156;174;138;147;165;113;121;129;187 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. In the present study, we found another haplotype H1-3-2, which has one more mutation C1059T based on the H1-3. 2021 Computational and structural biotechnology journal Method SARS_CoV_2 C1059T 85 91 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. Thereinto, H1-1 has no other specific mutation sites based on H1; H1-2 has other 5 specific mutation sites (T445C, C6286T, C22227T, C26801G, and G29645T) based on H1; H1-3 has another 1 mutation site (G25563T) based on H1. 2021 Computational and structural biotechnology journal Method SARS_CoV_2 C22227T;C26801G;C6286T;G25563T;G29645T;T445C 123;132;115;201;145;108 130;139;121;208;152;113 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. A primer pair was designed to target the specific region containing the D614G mutation (Table 1). 2021 Heliyon Method SARS_CoV_2 D614G 72 77 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Additional, in Figure 5c, a comparison of the experimental pseudovirus infection changes and predicted BFE change of ACE2 and S protein complex induced by mutations L452R and N501Y, where the experimental data is obtained in a reference to D614G and reported in relative luciferase units. 2021 ArXiv Method SARS_CoV_2 D614G;L452R;N501Y 240;165;175 245;170;180 S 126 127 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Considering the BFE changes induced by RBD mutations for ACE2 and RBD complex, predictions on mutations L452R and N501Y have a highly similar trend with experimental data. 2021 ArXiv Method SARS_CoV_2 L452R;N501Y 104;114 109;119 RBD;RBD 39;66 42;69 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. In our predictions, L452R induces a negative BFE change (-2.39 kcal/mol), and T478K produces a positive BFE change (0.36 kcal/mol). 2021 ArXiv Method SARS_CoV_2 L452R;T478K 20;78 25;83 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Recent studies on potency of mAb CT-P59 in vitro and in vivo against Delta variants show that the neutralization of CT-P59 is reduced by L452R (13.22 ng/mL) and is retained against T478K (0.213 ng/mL). 2021 ArXiv Method SARS_CoV_2 L452R;T478K 137;181 142;186 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. SARS-CoV-2 neutralizing antibodies were quantified using lentivirus particles that incorporate SARS-CoV-2 S protein (Wuhan-Hu-1 isolate mutated to contain D614G) or the B.1.351 variant S protein (L18F-D80A-D215G- L242- A243- L244-K417N-E484K-N501Y-D614G-A701V) on their surface and express firefly luciferase reporter gene for quantitative measurements of infection by relative luminescence units (RLUs) as described. 2021 Nature medicine Method SARS_CoV_2 D614G;L18F;A701V;D215G;D614G;D80A;E484K;K417N;N501Y 155;196;254;206;248;201;236;230;242 160;200;259;211;253;205;241;235;247 S;S 106;185 107;186 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. To perform the recombinant VSV-based PsVN assay, codon-optimized full-length S protein of the D614G and variant sequences (Supplementary Table 2) were cloned into a pCAGGS vector. 2021 Nature medicine Method SARS_CoV_2 D614G 94 99 S 77 78 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. K417N: Since there are no crystallographic data nor MD trajectories available, we substituted the amino acids involved in the wild type and kept the fragments in the configurations they had in the interacting system (this is more accurate to understand the virus cell bonding interactions than re-optimizing the isolated pairs). 2022 Chembiochem Method SARS_CoV_2 K417N;K417N 0;0 6;5 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. N501Y, K417T, E484K: Professor Dong-Qing Wei from the Shanghai Jiao Tong University provided us with the required snapshots from their MD trajectories published in reference [47]. 2022 Chembiochem Method SARS_CoV_2 E484K;E484K;K417T;K417T;N501Y 15;14;8;7;0 20;19;12;12;5 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. S477N: The extended pairs were extracted from a snapshot of the MD simulations carried out by Singh and co-workers. 2022 Chembiochem Method SARS_CoV_2 S477N;S477N 0;0 6;5 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. The following proteins were purchased from Sino Biological (Beijing, China): SARS-CoV-2 recombinant Spike RBD wild type, RBD (S477N), RBD (Y453F), RBD (K458R), RBD (F342L), RBD (V367F), RBD (N354D), RBD (A435S), RBD (V483A), RBD (W436R), RBD (G476S), RBD (R408I), RBD (K417N), RBD (Y505C), RBD (N501Y), and human ACE2-histag. 2021 Scientific reports Method SARS_CoV_2 A435S;F342L;G476S;K417N;K458R;N354D;N501Y;R408I;S477N;V367F;V483A;W436R;Y453F;Y505C 204;165;243;269;152;191;295;256;126;178;217;230;139;282 209;170;248;274;157;196;300;261;131;183;222;235;144;287 S;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD 100;106;121;134;147;160;173;186;199;212;225;238;251;264;277;290 105;109;124;137;150;163;176;189;202;215;228;241;254;267;280;293 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. Briefly, specific point mutations in SARS-CoV-2 cDNAs in fragment 3 (nt11475 T to C for NSP6 I168T) and fragment 5 (nt 15845 A to C and nt 15846 G to C for NSP12 either E802A, or nt15846 G to C for NSP12 E802D) were synthesized by Biobasic and assembled into the full-length molecular clone to give pCCI-4K-SARS-CoV-2-NSP12_E802D, pCCI-4K-SARS-CoV-2-NSP12_E802A, pCCI-4K-SARS-CoV-2-NSP6_I168T, pCCI-4K-SARS-CoV-2-NSP6_I168T-NSP12_E802D-NSP6, pCCI-4K-SARS-CoV-2-NSP6_I168T-NSP12_E802D-NSP6. 2021 PLoS pathogens Method SARS_CoV_2 A15845C;E802A;E802D;I168T;E802A;E802D;E802D;E802D;I168T;I168T;I168T;G15846C 119;169;204;93;356;324;430;478;387;418;466;181 131;174;209;98;361;329;435;483;392;423;471;193 Nsp12;Nsp12;Nsp12;Nsp12;Nsp12;Nsp12;Nsp6;Nsp6;Nsp6;Nsp6;Nsp6;Nsp6 156;198;318;350;424;472;88;382;413;436;461;484 161;203;323;355;429;477;92;386;417;440;465;488 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. Data from 2 independent virus stocks with 2 replicates except we were missing one of the replicates for wild-type and a 48h pi replicated for rNSP12-E802A at 48h pi. 2021 PLoS pathogens Method SARS_CoV_2 E802A 149 154 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. Protter was used visualize the effect of the I168T mutation on organization of the transmembrane domains in NSP6. 2021 PLoS pathogens Method SARS_CoV_2 I168T 45 50 Nsp6 108 112 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. The receptor binding domain of Spike is from amino acids 319-541: B1.351 and P1 had 3 mutations in the RBD (K417N/T, E484K and N501Y) while Alpha (B.1.1.7) only had one (N501Y). 2021 PLoS pathogens Method SARS_CoV_2 E484K;N501Y;K417N;K417T;N501Y 117;127;108;108;170 122;132;115;115;175 RBD;S;RBD 4;31;103 27;36;106 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. There is phylogenetic uncertainty if V1176F was present in the ancestor preceding the formation of the Gamma (P.1) lineage, the deletion (Delta242-245; like other defining mutations) in Beta (B.1.351) is polymorphic. 2021 PLoS pathogens Method SARS_CoV_2 V1176F 37 43 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. To test for a change in sensitivity to RDV of our continually passaged SARS-CoV-2Engl2 viruses and reverse genetic derived viruses (rNSP12-E802D, rNSP12-E802A, rNSP6-I168T, rNSP6-I168T-NSP12-E802D, rNSP6-I168T-NSP12-E802A and rSARS-CoV), two different compound screen layouts were tested (S7 Fig). 2021 PLoS pathogens Method SARS_CoV_2 E802A;E802A;E802D;E802D;I168T;I168T;I168T 153;216;139;191;166;179;204 158;221;144;196;171;184;209 Nsp12;Nsp12 185;210 190;215 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. We further included the substitution observed in P1 (V1176F) and deletion in B1.351 (Delta242-245). 2021 PLoS pathogens Method SARS_CoV_2 V1176F 53 59 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. We used the following amino acids replacements and deletions in Spike for each lineage-based COG-UK defined changes for each lineage; Beta (B1.351; L18F, D80A, D215G, R246L, K417N, E484K, N501Y, A701V), Gamma (P.1; L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y H655Y, T1027I), Alpha (B.1.1.7; Delta69-70, D144, N501Y, A570D, P681H, T716I, S982A, D1118H). 2021 PLoS pathogens Method SARS_CoV_2 A570D;A701V;D1118H;D138Y;D215G;D80A;E484K;E484K;H655Y;K417N;K417T;L18F;L18F;N501Y;N501Y;N501Y;P26S;P681H;R190S;R246L;S982A;T1027I;T20N;T716I 324;195;352;233;160;154;181;254;267;174;247;148;215;188;261;317;227;331;240;167;345;274;221;338 329;200;358;238;165;158;186;259;272;179;252;152;219;193;266;322;231;336;245;172;350;280;225;343 S 64 69 34535691 Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020. In particular, we targeted three specific mutations in the spike protein (S98F, A222V, and S477N) due to their rapid expansion and dissemination across Europe during the summer months. 2021 Scientific reports Method SARS_CoV_2 A222V;S477N;S98F 80;91;74 85;96;78 S 59 64 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. 293T cells were transfected with the lentiviral vector pNL4.3 R-E- Luc (NIH AIDS Reagent Program) and a plasmid encoding for the indicated Spike glycoprotein (D614G, B.1.1.7, P.1, B.1.351, B.1.429, B.1.526, B.1.617, B.1.617.1, B.1.617.2) at a ratio of 10:1. 2021 Virology Method SARS_CoV_2 D614G 159 164 S 139 157 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Plasmids encoding B.1.429, D614G and other SARS-CoV-2 Spike single mutations were generated using the QuickChange II XL site-directed mutagenesis protocol (Stratagene) and the pCG1-SARS-CoV-2-S plasmid kindly provided by Stefan Pohlmann. 2021 Virology Method SARS_CoV_2 D614G 27 32 S;S 54;192 59;193 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. The Median Fluorescence Intensities (MFI) obtained with ACE2-Fc or plasma Abs were normalized to the MFI obtained with CV3-25 and presented as ratio of the CV3-25-normalized values obtained with the D614G Spike. 2021 Virology Method SARS_CoV_2 D614G 199 204 S 205 210 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. ObservableHQ notebook detailing N501Y lineage-specific selection results (other clades included as well): https://observablehq.com/@spond/n501y-clades@3752 . 2021 Cell Method SARS_CoV_2 N501Y 32 37 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. ObservableHQ notebook detailing N501Y lineage-specific selection results (other clades included as well): https://observablehq.com/@spond/n501y-clades@3752. 2021 Cell Method SARS_CoV_2 N501Y 32 37 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. ObservableHQ notebook for displaying a combined view of sites under selection in N501Y clades: https://observablehq.com/@spond/n501y-sites . 2021 Cell Method SARS_CoV_2 N501Y 81 86 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. ObservableHQ notebook for displaying a combined view of sites under selection in N501Y clades: https://observablehq.com/@spond/n501y-sites. 2021 Cell Method SARS_CoV_2 N501Y 81 86 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. ObservableHQ notebook for displaying a combined view of sites which may be experiencing convergence in N501Y clades: https://observablehq.com/@spond/clade-convergence . 2021 Cell Method SARS_CoV_2 N501Y 103 108 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. ObservableHQ notebook for displaying a combined view of sites which may be experiencing convergence in N501Y clades: https://observablehq.com/@spond/clade-convergence. 2021 Cell Method SARS_CoV_2 N501Y 103 108 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. This list of mutations was merged with the list of deletion mutations that characterize the different 501Y lineages and the three cardinal 501Y lineage signature mutations, L18F, K417N/K and N501Y which, due to already high frequencies in multiple 501Y lineages could not have doubled in frequency in more than a single lineage between 15 March and 01 June 2021. 2021 Cell Method SARS_CoV_2 K417K;K417N;L18F;N501Y 179;179;173;191 186;186;177;196 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. Each glycan was docked into the 3D structure of WT S-protein RBD obtained from the PDB (PDB ID: 6M0J) and the equilibrated 3D structure of N501Y S-protein RBD. 2021 The Journal of biological chemistry Method SARS_CoV_2 N501Y 139 144 RBD;RBD;S;S 61;155;51;145 64;158;52;146 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. HEK 293T cells expressing Ace2 were plated in 12 well tissue culture dishes and infected with the baculovirus pseudotyped with SARS-CoV-2 (Wuhan strain) WT S-protein containing GFP reporter (#C1110G, Montana Molecular) with serial dilutions of the stock (102 to 107). 2021 The Journal of biological chemistry Method SARS_CoV_2 C1110G 192 198 S 156 157 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. SARS-CoV-2 S-Protein RBD mutant (N501Y) was purchased from Sino Biological (Beijing, China). 2021 The Journal of biological chemistry Method SARS_CoV_2 N501Y 33 38 RBD;S 21;11 24;12 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. The tleap program was used to prepare the S-protein RBD WT-glycan and N501Y mutant-glycan complexes for MD simulation as explained before. 2021 The Journal of biological chemistry Method SARS_CoV_2 N501Y 70 75 RBD;S 52;42 55;43 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. This equilibrated structure of the N501Y mutant was used for docking. 2021 The Journal of biological chemistry Method SARS_CoV_2 N501Y 35 40 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. Using a 1-step protocol, cDNA was prepared from the RNA extracts and amplified on a LightCycler 480II (Roche Diagnostics, Rotkreuz, Switzerland) applying VirSNiP SARS-CoV-2 Spike N501Y, del H69/V70 (DeltaH69-V70), E484K, H655Y, L452R and P681R probe kits (TIB Molbiol, Berlin, Germany) followed by PCR melting curve analysis using the LightCycler 480 SW1.5.1 analysis software. 2022 Clinical microbiology and infection Method SARS_CoV_2 E484K;H655Y;L452R;N501Y;P681R 215;222;229;180;239 220;227;234;185;244 S 174 179 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. The Dot-bracket folding notations were obtained for each of the R203K/G204R sequences and used for Junction Explorer (nature.njit.edu/biosoft/Junction-Explorer/) and CHS-align (nature.njit.edu/biosoft/CHSalign/). 2021 Pathogens & immunity Method SARS_CoV_2 R203K;G204R 64;70 69;75 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. Cells for SARS-CoV-2 or SARS-CoV-2 (V367F) pseudovirus (~15,000 per well) were added to the virus-antibody mixture. 2021 MedComm Method SARS_CoV_2 V367F 36 41 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. A 901 bp fragment containing the N501Y site was amplified from each RNA sample by RT-PCR using primer set: 5'- GAAGTCAGACAAATCGCTCCAG-3' and 5'-GCAACTGAATTTTCTGCACCA-3'. 2021 Communications biology Method SARS_CoV_2 N501Y 33 38 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. Calu-3 cells in Dulbecco's Modified Eagle Medium (DMEM) (Thermo Fisher Scientific) supplemented with 5% foetal bovine serum (Thermo Fisher Scientific), and 100 IU penicillin G/ml and 100 ml streptomycin sulphate/ml (Thermo Fisher Scientific) were infected with MOI of 0.1 of B.1.1.7 and another variant of the D614G lineage, either HK-95 or HK-405 mixture at 1:1 ratio. 2021 Communications biology Method SARS_CoV_2 D614G 310 315 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. SARS-CoV-2 (2019-nCoV) spike S1 rabbit monoclonal antibody (mAb1), SARS-CoV-2 (2019-nCoV) spike neutralizing rabbit monoclonal antibody (mAb2), and recombinant proteins corresponding to the original SARS-CoV-2 spike RBD; original S1; spike S1 variant D614G; and RBD protein variants N501Y, N439K, Y453F, and E84K were purchased from Sino Biological (Wayne, PA, USA). 2022 Journal of pharmaceutical analysis Method SARS_CoV_2 D614G;E84K;N439K;N501Y;Y453F 251;308;290;283;297 256;312;295;288;302 S;S;S;S;RBD;RBD 23;90;210;234;216;262 28;95;215;239;219;265 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. Finally, a comparison of experimental CT-P59 IC50 fold change (reduction) and predicted BFE changes induced by mutations L452R and T478K showed a high correlation. 2021 ArXiv Method SARS_CoV_2 L452R;T478K 121;131 126;136 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. Further, our predicted BFE changes induced by RBD mutations L452R and N501Y for ACE2 and RBD complex have a highly similar trend with experimental data in relative luciferase units. 2021 ArXiv Method SARS_CoV_2 L452R;N501Y 60;70 65;75 RBD;RBD 46;89 49;92 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. Mutant RBDs (K417T/E484K/N501Y, L452R/T478K, and L452R) were purchased from Sino Biological. 2021 Biochemical and biophysical research communications Method SARS_CoV_2 L452R;L452R;K417T;E484K;N501Y;T478K 32;49;13;19;25;38 37;54;18;24;30;43 RBD 7 11 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. Pseudoviruses for Gamma, Delta, Epsilon, Kappa, L452R, T478K, and P681H, K417T, E484K, and N501Y were produced. 2021 Biochemical and biophysical research communications Method SARS_CoV_2 E484K;K417T;L452R;N501Y;P681H;T478K 80;73;48;91;66;55 85;78;53;96;71;60 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Codon-optimized full-length spike (S) protein of the original Wuhan-Hu-1 isolate with D614G mutation (D614G) was cloned into a pCAGGS vector. 2021 Journal of virology Method SARS_CoV_2 D614G;D614G 86;102 91;107 S;S 28;35 33;36 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Geometric mean titers, lower limit of quantification, and fold change relative to D614G were included. 2021 Journal of virology Method SARS_CoV_2 D614G 82 87 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. This codon-optimized D614G vector was used as a template for site-directed mutagenesis to incorporate the S variants, listed in Table 1. 2021 Journal of virology Method SARS_CoV_2 D614G 21 26 S 106 107 34550770 Discovery and Evaluation of Entry Inhibitors for SARS-CoV-2 and Its Emerging Variants. Mutation K417T in the P.1 variant was altered to K471N to generate the structure of the B.1.351 S-RBD variant using the Prime modeling program of Schrodinger Suite. 2021 Journal of virology Method SARS_CoV_2 K417T;K471N 9;49 14;54 RBD;S 98;96 101;97 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. About, 20 ns of production MD simulations of 25 mAb-spike complexes were run for both the WT and E484K mutant. 2022 Briefings in bioinformatics Method SARS_CoV_2 E484K 97 102 S 52 57 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. The E484K mutation was built by PyMOL based on initial wild-type (WT) structures. 2022 Briefings in bioinformatics Method SARS_CoV_2 E484K 4 9 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. Since the D614G mutation in the spike glycoprotein of SARS-CoV-2 surged in early March 2020, variant cases were selected between March to April 2020. 2021 PeerJ Method SARS_CoV_2 D614G 10 15 S 32 50 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. On day 0, 10 mice in each group were intramuscularly immunized with purified SARS-CoV-2 plasmid comprising D614G reference strain, Alpha (B.1.1.7) variant, Beta (B.1.351) variant, or Gamma (P.1) variant and an aluminum adjuvant (50 microg per mouse). 2021 Signal transduction and targeted therapy Method SARS_CoV_2 D614G 107 112 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. To obtain SARS-CoV-2 S protein-overexpressing cells, 293T cells were transfected with SARS-CoV-2-spike_pcDNA-3.1 comprising D614G reference strain, B.1.1.7 variant, B.1.351 variant, or P.1 variant using Lipofectamine 3000 (Invitrogen, USA). 2021 Signal transduction and targeted therapy Method SARS_CoV_2 D614G 124 129 S 21 22 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. According to the calculation results of the wild-type complexes and the corresponding mutants, the influences of the E484K mutation on the binding affinities of RBD with the receptor hACE2 as well as with the neutralizing antibodies/nanobodies were evaluated. 2021 Journal of molecular graphics & modelling Method SARS_CoV_2 E484K 117 122 RBD 161 164 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In order to explore the molecular mechanism for the influences of E484K mutation on the binding free energy, the MMGBSA calculation results were also decomposed into per-residue contributions. 2021 Journal of molecular graphics & modelling Method SARS_CoV_2 E484K 66 71 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In order to further validate the simulation results for RBD-hACE2 complex with notable conformational changes, another MD simulation in a much longer time scale (500 ns) was also performed both for the wild-type complex structure and the E484K mutant. 2021 Journal of molecular graphics & modelling Method SARS_CoV_2 E484K 238 243 RBD 56 59 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In this work, our study focused on the impacts of E484K mutation on the binding affinities, and thus the studied systems were selected as those where Glu484 directly involved in the interactions between RBD and the antibodies/nanobodies. 2021 Journal of molecular graphics & modelling Method SARS_CoV_2 E484K 50 55 RBD 203 206 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. To investigate the impacts of the E484K mutation on the binding affinities of these complexes, the same MMGBSA calculations were carried out both for the systems formed by the wild-type RBD and the corresponding mutated systems formed by the RBD with the E484K mutation. 2021 Journal of molecular graphics & modelling Method SARS_CoV_2 E484K;E484K 34;255 39;260 RBD;RBD 186;242 189;245 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. To investigate the impacts of the E484K mutation on the binding affinity of RBD with hACE2 and the neutralizing antibodies/nanobodies, the residue Glu484 was replaced with Lys in these complex structures by using the UCSF chimera software to construct the corresponding mutated structures, in which the sidechain conformation of the mutated residue was chose as the rotamer with the highest probability according to the Dunbrack 2010 library. 2021 Journal of molecular graphics & modelling Method SARS_CoV_2 E484K 34 39 RBD 76 79 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Al foldon trimerization domain based on phage T4 fibritin followed by a c-myc epitope and a hexa-repeat histidine tag were introduced to the C-termini of both S-D614 and S-D614G as described previously. 2021 The Journal of biological chemistry Method SARS_CoV_2 D614G 172 177 S;S 159;170 160;171 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Cryo-EM sample preparation of S-D614G and data collection. 2021 The Journal of biological chemistry Method SARS_CoV_2 D614G 32 37 S 30 31 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Expression and purification of SARS-CoV-2 S and its variant, S-D614G. 2021 The Journal of biological chemistry Method SARS_CoV_2 D614G 63 68 S;S 42;61 43;62 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Four microliters of S-D614 and S-D614G that were treated at different temperatures and durations:fresh (day 0), fresh samples incubated at 50C/60C for 30 min, and fresh samples incubated at 4C/37C for 6 days:were used to prepare negative staining EM grids at a concentration of 50 mug/ml. 2021 The Journal of biological chemistry Method SARS_CoV_2 D614G 33 38 S;S 20;31 21;32 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. The atomic coordinates were divided into individual domains and manually fit into the cryoEM maps of S-D614G by using UCSF-Chimera, UCSF-ChimeraX and Coot. 2021 The Journal of biological chemistry Method SARS_CoV_2 D614G 103 108 S 101 102 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. The D614G mutation was subsequently introduced to generate S-D614G. 2021 The Journal of biological chemistry Method SARS_CoV_2 D614G;D614G 4;61 9;66 S 59 60 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. The exact sequences of S-D614G and S-D614 are included in the Protein Data Bank (PDB) entries of the reported structures. 2021 The Journal of biological chemistry Method SARS_CoV_2 D614G 25 30 S;S 23;35 24;36 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. The plasmids of S-D614 and S-D614G were transiently transfected into HEK293 Freestyle cells with polyethylenimine (PEI, linear, 25 kDa, Polysciences). 2021 The Journal of biological chemistry Method SARS_CoV_2 D614G 29 34 S;S 16;27 17;28 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. The thermal unfolding of S-D614 and S-D614G was analyzed by DSC (Automatic MicroCal PEAQ-DSC). 2021 The Journal of biological chemistry Method SARS_CoV_2 D614G 38 43 S;S 25;36 26;37 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. This study reported five structures of S-D614G under the PDB entries 7EAZ, 7EB0, 7EB3, 7EB4, and 7EB5. 2021 The Journal of biological chemistry Method SARS_CoV_2 D614G 41 46 S 39 40 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. To identify conformational heterogeneity of S-D614G trimer, ~660k particles were initially classified by ab-initio reconstruction with a C1 symmetry, followed by heterogeneous refinement to generate five distinct classes. 2021 The Journal of biological chemistry Method SARS_CoV_2 D614G 46 51 S 44 45 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Afterward, the sequences were uploaded to Iterative Threading Assembly Refinement (I-TASSER) platform to model the starting structures for the L452R, S477N, N439K, and E484K mutants before MD simulations. 2021 Biomolecules Method SARS_CoV_2 E484K;L452R;N439K;S477N 168;143;157;150 173;148;162;155 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. For RBD structure preparation, the X-ray structures (starting structures) were downloaded from Protein Data Bank for WT RBD (PDB ID: 6M0J) and N501Y mutant (PDB ID: 7NEG). 2021 Biomolecules Method SARS_CoV_2 N501Y 143 148 RBD;RBD 4;120 7;123 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. The starting coordinates for each MD simulation system were either X-ray structures (i.e., for the WT RBD and N501Y mutants) or the modeled structures for the L452R, S477N, N439K, and E484K mutants. 2021 Biomolecules Method SARS_CoV_2 E484K;L452R;N439K;N501Y;S477N 184;159;173;110;166 189;164;178;115;171 RBD 102 105 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. A time-scaled Bayesian phylogeographic analysis was next performed to infer the geographical source and dissemination pattern of the Uruguayan B.1.1.28 + Q675H + Q677H (now P.6) samples, and to estimate the time of their most recent common ancestors (TMRCA). 2021 Viruses Method SARS_CoV_2 Q675H;Q677H 154;162 159;167 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Additionally, we downloaded four B.1.1.28 from the USA (n = 2), Spain (n = 1), and Belgium (n = 1) that also harbored both S:Q675H and S:Q677H mutations (Tables S2 and S3). 2021 Viruses Method SARS_CoV_2 Q675H;Q677H 125;137 130;142 S;S 123;135 124;136 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. As only one B.1.1.28 (not carrying Q675H + Q677H mutations) was identified in May 2021, we kept our analysis from November 2020 to April 2021. 2021 Viruses Method SARS_CoV_2 Q675H;Q677H 35;43 40;48 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Determination of Prevalence of Q675H + Q677H. 2021 Viruses Method SARS_CoV_2 Q675H;Q677H 31;39 36;44 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. To assess the prevalence of B.1.1.28 + Q675H + Q677H clade in the context of the different SARS-CoV-2 lineages circulating in Uruguay, we used the lineage assignments obtained for the 260 samples presented in this study, 335 additional samples already available at EpiCoV/GISAID, and 342 records available at the IiWG domain. 2021 Viruses Method SARS_CoV_2 Q675H;Q677H 39;47 44;52 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. To assess the prevalence of co-occurring S:Q675H and S:Q677H in worldwide SARS-CoV-2 genomes, we downloaded from EpiCoV/GISAID (accessed on 7 July 2021) 129 complete genomes, with high quality and full collection date information. 2021 Viruses Method SARS_CoV_2 Q675H;Q677H 43;55 48;60 S;S 41;53 42;54 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. The cloning and production of SARS-CoV-2 RBD (residues 319-541, GenBank: MN_908947.3), RBD mutants (RBDMACSp25: Q493H, N501Y; RBDMACSp36: K417N, Q493H, N501Y), hACE2 (residues 19-624, GenBank: NM_021804.3), and mACE2 (residues 19-739, GenBank: NM_001130513.1) were synthesized and subcloned into the mammalian expression vector pCAGGS with a C-terminal 2 x StrepTag to facilitate protein purification. 2021 Nature communications Method SARS_CoV_2 K417N;N501Y;N501Y;Q493H;Q493H 138;119;152;112;145 143;124;157;117;150 RBD;RBD 41;87 44;90 34594910 Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. A forward primer and two specific reverse probes for A and G nucleotides of A23403G polymorphism were designed using Oligo7 software. 2021 China CDC weekly Method SARS_CoV_2 A23403G 76 83 34594910 Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. The PDRA assay included two real-time RAA reactions (A and G) to detect the A and G nucleotides of the D614G mutation (A23403G polymorphism), respectively. 2021 China CDC weekly Method SARS_CoV_2 D614G;A23403G 103;119 108;126 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. In Lithuania, repeat PCR testing of SARS-CoV-2 positive samples is occasionally carried out to detect N501Y, E484K and S gene target failure (SGTF) caused by the HV69Delta deletion. 2021 Nature communications Method SARS_CoV_2 E484K;N501Y 109;102 114;107 S 119 120 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Prior to official lineage designation as B.1.620, most of its genomes could be identified by the presence of spike protein E484K and S477N mutations and the HV69/70Delta deletion. 2021 Nature communications Method SARS_CoV_2 E484K;S477N 123;133 128;138 S 109 114 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Searching GISAID for mutations E484K, S477N and HV69/70Delta, which are found in numerous VOCs individually but not in combination, identified additional genomes that contained other mutations and deletions found in B.1.620. 2021 Nature communications Method SARS_CoV_2 E484K;S477N 31;38 36;43 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. This study was initiated upon detection of SARS-CoV-2 strains in Lithuania bearing spike protein amino acid substitutions E484K, S477N and numerous B.1.1.7-like (HV69/70Delta and Y144Delta) and B.1.351-like (LLA241/243Delta) deletions, amongst others. 2021 Nature communications Method SARS_CoV_2 E484K;S477N 122;129 127;134 S 83 88 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Upon detection of E484K-positive cases, samples were redirected to sequencing. 2021 Nature communications Method SARS_CoV_2 E484K 18 23 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. We have modelled the RBD-ACE2 interface with the S477N and E484K substitutions using the final refinement step of HADDOCK 2.4. 2021 Nature communications Method SARS_CoV_2 E484K;S477N 59;49 64;54 RBD 21 24 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Other individual mutations were subsequently introduced into the D614G S by the same process. 2021 The EMBO journal Method SARS_CoV_2 D614G 65 70 S 71 72 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The D614G S plasmid was generated by introducing the mutation into the Wuhan reference strain via Q5 site-directed mutagenesis (NEB). 2021 The EMBO journal Method SARS_CoV_2 D614G 4 9 S 10 11 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The D614G viral strain was sourced through the European Virus Archive goes Global (EVAg) platform, which is funded by the European Union's Horizon 2020 research and innovation program under grant agreement 653316. 2021 The EMBO journal Method SARS_CoV_2 D614G 4 9 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The Wuhan SARS-CoV-2 strain (BetaCoV/France/IDF0372/2020) and the D614G strain (hCoV-19/France/GE1973/2020) were supplied by Dr. 2021 The EMBO journal Method SARS_CoV_2 D614G 66 71 34607456 A Combination of Receptor-Binding Domain and N-Terminal Domain Neutralizing Antibodies Limits the Generation of SARS-CoV-2 Spike Neutralization-Escape Mutants. A plaque-purified rVSV-SARS2 corresponding to the passage 9 (plaque 2 virus) described previously was used for these studies and carries W64R, G261R, A372T, H655Y, and R685 mutations in addition to the c-tail truncation (C1253*) mutation. 2021 mBio Method SARS_CoV_2 A372T;G261R;H655Y;W64R 150;143;157;137 155;148;162;141 34607456 A Combination of Receptor-Binding Domain and N-Terminal Domain Neutralizing Antibodies Limits the Generation of SARS-CoV-2 Spike Neutralization-Escape Mutants. Sequencing of the virus stock revealed a single mutation (a histidine-to-tyrosine change at amino acid position 655, H655Y) in the spike glycoprotein relative to the reference Washington state isolate. 2021 mBio Method SARS_CoV_2 H655Y;H655Y 117;60 122;115 S 131 149 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. 22, 2021, the province initiated universal screening for N501Y and E484K mutations using a multiplex real-time PCR assay on all specimens testing positive for SARS-CoV-2 with a cycle threshold value of 35 or less. 2021 CMAJ Method SARS_CoV_2 E484K;N501Y 67;57 72;62 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. 30, 2021, and all non-Delta cases testing positive for a mutation other than N501Y, regardless of date). 2021 CMAJ Method SARS_CoV_2 N501Y 77 82 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. Although cases of COVID-19 caused by VOCs were identified in Ontario beginning in December 2020, systematic screening for SARS-CoV-2 lineage was not implemented until February 2021, after which time all specimens positive for SARS-CoV-2 with a cycle threshold value of 35 or less on testing with the polymerase chain reaction (PCR) were screened for the N501Y mutation. 2021 CMAJ Method SARS_CoV_2 N501Y 354 359 COVID-19 18 26 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. As hospitalization, ICU admission and death were relatively rare among cases, we considered odds ratios to approximate relative risks under the "rare disease assumption." To compare the virulence of Delta variant directly to N501Y-positive VOCs, we also conducted restriction analyses in which we constructed models after exclusion of all non-VOC cases. 2021 CMAJ Method SARS_CoV_2 N501Y 225 230 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. By late April 2021, more than 90% of infections in Ontario were screen-positive for N501Y; subsequently, N501Y mutations became less common, and N501Y-negative specimens subjected to whole genome sequencing were shown to be predominantly Delta variant, with Delta representing more than 60% of new infections in Ontario on July 1, 2021. 2021 CMAJ Method SARS_CoV_2 N501Y;N501Y;N501Y 84;105;145 89;110;150 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. Initially, all specimens with the N501Y or E484K mutation and a cycle threshold value of 30 or less were sequenced; however, as of June 2021, routine whole genome sequencing was no longer performed on specimens without E484K, under the presumption that such specimens were of the Alpha lineage. 2021 CMAJ Method SARS_CoV_2 E484K;E484K;N501Y 43;219;34 48;224;39 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. We classified cases as N501Y-positive (screening positive for N501Y or identified as Alpha, Beta or Gamma by whole genome sequencing), probable Delta variant (as identified by whole genome sequencing at any point or screening negative for N501Y and any other mutations from May 1, 2021, onward) or not VOC (all cases negative for N501Y between Feb. 2021 CMAJ Method SARS_CoV_2 N501Y;N501Y;N501Y;N501Y 23;62;239;330 28;67;244;335 34611654 Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein. 1847 movies were collected for FnM-point spike ectodomain, 4784 movies were collected for FnM-deletion spike ectodomain and 4563 movies were collected for K417V/FnM-deletion spike ectodomain. 2021 Research square Method SARS_CoV_2 K417V 155 160 S;S;S 41;103;174 46;108;179 34611654 Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein. For K417V/FnM-deletion spike ectodomain, 1,267,763 particles were initially extracted and subjected to 2D alignment and clustering using RELION. 2021 Research square Method SARS_CoV_2 K417V 4 9 S 23 28 34611654 Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein. SARS-CoV-2 spike ectodomains (residues 1-1211) were cloned into the vector containing mutations of interest, in addition to two proline mutations in S2 (K986P, V987P), a C-terminal foldon trimerization tag, and a C-terminal His6-tag. 2021 Research square Method SARS_CoV_2 V987P;K986P 160;153 165;158 S 11 16 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. This enabled the first identification of the B.1.1.7-related mutations 69-70Del, 144Del, N501Y, S982A, and D1118H and B.1.351-related mutations D215G, 242Del K417N, N501Y, and E484K. 2021 Microbiology spectrum Method SARS_CoV_2 D1118H;D215G;E484K;K417N;N501Y;N501Y;S982A 107;144;176;158;89;165;96 113;149;181;163;94;170;101 34613786 Highly Efficient SARS-CoV-2 Infection of Human Cardiomyocytes: Spike Protein-Mediated Cell Fusion and Its Inhibition. Human iPSC-CMs were plated on 35-mm round glass-bottom dishes and transfected with SARS-CoV-2 spike protein, with or without furin inhibitor treatment, or transfected with SARS-CoV-2 R682S mutant spike protein, as previously described. 2021 Journal of virology Method SARS_CoV_2 R682S 183 188 S;S 94;196 99;201 34613786 Highly Efficient SARS-CoV-2 Infection of Human Cardiomyocytes: Spike Protein-Mediated Cell Fusion and Its Inhibition. The R682S furin cleavage mutation was introduced into the SARS-CoV-2 S expression plasmid by QuikChange site-directed mutagenesis (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions. 2021 Journal of virology Method SARS_CoV_2 R682S 4 9 S 69 70 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. An additional 40-ns simulation was performed for the D614G mutant spike for the closed and the partially open states. 2021 Proc Natl Acad Sci U S A Method SARS_CoV_2 D614G 53 58 S 66 71 34615860 Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil. Custom Gamma (P.1) and Zeta (P.2) ASP assays were designed to identify lineage-specific and highly sensitive single-nucleotide polymorphisms (SNPs) S:K417T (Gamma, P.1) and ORF1a:L3468V (Zeta, P.2). 2021 Nature communications Method SARS_CoV_2 K417T;L3468V 150;179 155;185 ORF1a;S 173;148 178;149 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. (5), we calculate the maximum likelihood estimation (MLE) of eta to determine transmission advantage of D614G substitution. 2021 BMC infectious diseases Method SARS_CoV_2 D614G 104 109 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. To demonstrate the application of the framework, we adopted the data of COVID-19 in California, USA, and estimated the transmission advantage eta of the D614G substitution. 2021 BMC infectious diseases Method SARS_CoV_2 D614G 153 158 COVID-19 72 80 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). The LOD was evaluated using synthetic DNA of the RdRP and the S gene (1-2160 nt) that harbored the HV69/70 del, E484K and N501Y (Genewiz, Seattle, USA). 2021 Journal of clinical virology Method SARS_CoV_2 E484K;N501Y 112;122 117;127 RdRP;S 49;62 53;63 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. MD simulations of the WT main protease and the P108S mutant were performed using GROMACS 2018.6 with the CHARMM36m force field. 2021 Biophysics and physicobiology Method SARS_CoV_2 P108S 47 52 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Missing residues and the mutation P108S were generated from the WT structure with Modeller. 2021 Biophysics and physicobiology Method SARS_CoV_2 P108S 34 39 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. Briefly, the neutralizing activity of each serum sample was evaluated by a neutralization assay against each living SARS-CoV-2 variant (D614G, B.1.1.7, P.1, or B.1.351) in a biosafety level 3 laboratory. 2021 Open forum infectious diseases Method SARS_CoV_2 D614G 136 141 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. We used the SARS-CoV-2 Biken-2 (B2) strain with a D614G mutation as a conventional variant (currently applying for the registration), which was provided by BIKEN Innovative Vaccine Research Alliance Laboratories. 2021 Open forum infectious diseases Method SARS_CoV_2 D614G 50 55 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. SARS-CoV-2 strain D614 was propagated in Vero E6 cells; strains D614G and B.1.351K were propagated in Vero-CCL81 cells. 2021 Antiviral research Method SARS_CoV_2 D614G 64 69 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. SARS-CoV-2 strain D614G was obtained through BEI Resources, NIAID, NIH: SARS-Related Coronavirus 2, Isolate Germany/BavPat1/2020, NR-52370. 2021 Antiviral research Method SARS_CoV_2 D614G 18 23 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. SIN-C52H3, Spike S1 (B.1.1.7 lineage mut): SARS-CoV-2 (2019-nCoV) Spike S1 (HV69-70 deletion, Y144 deletion, N501Y, A570D, D614G, P681H)-His: Sino, Cat: 40,591-V08H12, Spike S1 (B.1.351 lineage mut): SARS-CoV-2 (2019-nCoV) Spike S1 (K417N, E484K, N501Y, D614G)-His: Sino, Cat: 40,591-V08H10) and Spike S1 (B.1.617.2 lineage mut): SARS-CoV-2 (2019-nCoV) Spike S1 (T19R, G142D, E156G, 157-158 deletion, L452R, T478K, D614G, P681R)-His: Sino, Cat: 40,591-V08H23) were added to the corresponding wells for a 1h RT incubation. 2021 Antiviral research Method SARS_CoV_2 A570D;D614G;D614G;D614G;E156G;E484K;G142D;L452R;N501Y;N501Y;P681H;P681R;T478K;K417N;T19R 116;123;254;415;376;240;369;401;109;247;130;422;408;233;363 121;128;259;420;381;245;374;406;114;252;135;427;413;238;367 S;S;S;S;S;S 11;66;168;223;296;353 16;71;173;228;301;358 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. The SARS-CoV-2 Spike S1, SARS-CoV-2 (2019-nCoV) Spike S1- B.1.1.7 lineage mut (HV69-70 deletion, Y144 deletion, N501Y, A570D, D614G, P681H)-His, SARS-CoV-2 (2019-nCoV) Spike S1- B.1.351 lineage mut (K417N, E484K, N501Y, D614G)-His and Spike S1- B.1.617.2 lineage mut (T19R, G142D, E156G, 157-158 deletion, L452R, T478K, D614G, P681R)-His proteins were prepared at six different dilutions (range 1.56 nM-50 nM) in a running buffer of 0.01 M HEPES pH 7.4, 0.15 M NaCl, 3 mM EDTA, 0.05% v/v Surfactant P20 (HBS EP+). 2021 Antiviral research Method SARS_CoV_2 A570D;D614G;D614G;D614G;E156G;E484K;G142D;L452R;N501Y;N501Y;P681H;P681R;T478K;K417N;T19R 119;126;220;320;281;206;274;306;112;213;133;327;313;199;268 124;131;225;325;286;211;279;311;117;218;138;332;318;204;272 S;S;S;S 15;48;168;235 20;53;173;240 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. Three SARS-CoV-2 strains (D614, D614G, and B.1.351) were used in this study. 2021 Antiviral research Method SARS_CoV_2 D614G 32 37 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. Both constructs contained an AVI-tag and a 6xHis tag at the C-terminus separated by a single G4S linker. 2021 FASEB journal Method SARS_CoV_2 G4S 93 96 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. The ACE2 (UniProt entry: Q9BYF1) ectodomain (18-740) was synthesized with FLAG and 6xHis tags at the C-terminal end separated by a single G4S linker before cloning into the pFUSE vector. 2021 FASEB journal Method SARS_CoV_2 G4S 138 141 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. To determine the binding EC50 of VNAR clones, high binding 96-well microplates (Greiner) were coated overnight at 4 C with 100 mul of S1, S1-RBD or HSA at 5 microg/ml and S1-RBD E484K and S1-RBD N501Y at 1 microg/ml. 2021 FASEB journal Method SARS_CoV_2 E484K;N501Y 178;195 183;200 RBD;RBD;RBD 141;174;191 144;177;194 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. Additionally, mutation rate was estimated in the subset of genomes which acquired the C14408T mutation in SS4 cluster and in the subset of genomes which acquired the C14805T mutation in the SS1 and SS2B clusters. 2021 Infection, genetics and evolution Method SARS_CoV_2 C14408T;C14805T 86;166 93;173 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Of these 10 samples, 5 were from D614G reference strain-infected patients, four were from B.1.1.7-infected patients, and three were from B.1.351-infected patients. 2021 Communications biology Method SARS_CoV_2 D614G 33 38 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. One-way ANOVA and Holm-Sidak's multiple comparisons test were used to identify differences relative to the D614G reference strain. 2021 Communications biology Method SARS_CoV_2 D614G 107 112 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. In FEP runs for the E484Q mutation, the net charge of the MD system changed from -1 to 0e (where e is the elementary charge). 2021 Journal of chemical information and modeling Method SARS_CoV_2 E484Q 20 25 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Pseudovirions were produced by co-transfection of Lenti-X 293T cells with psPAX2, pTRIP-luc, and SARS-CoV-2 S expressing plasmid using Lipofectamine 3000. 2021 Journal of chemical information and modeling Method SARS_CoV_2 X293T 56 62 S 108 109 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. SARS-CoV-2 recombinant viruses containing 2019-nCoV/USA_WA1/2020 sequence or mutations (L452R/E484Q/D614G, E484Q/D614G) in the spike protein of the Kappa variant were generated using a 7-plasmid reverse genetic system, which was based on the virus strain (2019-nCoV/USA_WA1/2020) isolated from the first reported SARS-CoV-2 case in the US. 2021 Journal of chemical information and modeling Method SARS_CoV_2 E484Q;L452R;D614G;D614G;E484Q 107;88;100;113;94 112;93;105;118;99 S 127 132 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. 24-hours later, normalized amounts of WT (no 19del), WT, D614G, N501Y (no 19del), N501Y, N501Y + D614G, N501Y + L452R + D614G, or N501Y + K417N +E484K + D614G PsVs were treated intranasally in a volume of 50ul, followed by 30uL of PBS wash intranasally. 2021 Cell reports Method SARS_CoV_2 19del;19del;D614G;D614G;D614G;D614G;K417N;L452R;N501Y;N501Y;N501Y;N501Y;N501Y;E484K 45;74;57;97;120;153;138;112;64;82;89;104;130;145 50;79;62;102;125;158;143;117;69;87;94;109;135;150 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. 293TT cells were co-transfected with a packaging plasmid expressing Gag and Pol (CMVDelta8.91), a lentivirus vector expressing luciferase (pCDH1puro-LucGFP), and an expression plasmid with either pCMV3-SARS-CoV-2-S, pCMV3-SARS-CoV-2-S-N501Y, pCMV3-SARS-CoV-2-S-cd19, pCMV3-SARS-CoV-2-S-N501Y-cd19, pCMV3-SARS-CoV-2-S-cd19-D614G, or pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y. 2021 Cell reports Method SARS_CoV_2 D614G;D614G;N501Y;N501Y;N501Y 322;356;235;286;362 327;361;240;291;367 S;S;S;S;S;S 213;233;259;284;315;349 214;234;260;285;316;350 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. All plasmids were at 1.0mug/ml and used in the following ratios: pCDH1puro-Luc, 9 mul; pCMVDelta8.91, 12 mul; and pCMV3-SARS-CoV-2-S, pCMV3-SARS-CoV-2-S-N501Y, pCMV3-SARS-CoV-2-S-cd19, pCMV3-SARS-CoV-2-S-N501Y-cd19, pCMV3-SARS-CoV-2-S-cd19-D614G, or pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y, 3 mul. 2021 Cell reports Method SARS_CoV_2 D614G;D614G;N501Y;N501Y;N501Y 240;274;153;204;280 245;279;158;209;285 S;S;S;S;S;S 131;151;177;202;233;267 132;152;178;203;234;268 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. BHK-21 cells (ATCC) were transfected with pCMV3-SARS-CoV-2-S, pCMV3-SARS-CoV-2-S-N501Y, pCMV3-SARS-CoV-2-S-cd19, pCMV3-SARS-CoV-2-S-N501Y-cd19, pCMV3-SARS-CoV-2-S-cd19-D614G, pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y, pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y-K417N-E484K, pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y-K417N-L452R-E484Q, or pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y-L452R using Lipofectamine 2000 (Invitrogen). 2021 Cell reports Method SARS_CoV_2 D614G;D614G;D614G;D614G;D614G;E484K;E484Q;K417N;K417N;L452R;L452R;N501Y;N501Y;N501Y;N501Y;N501Y;N501Y 168;199;236;285;343;254;309;248;297;303;355;81;132;205;242;291;349 173;204;241;290;348;259;314;253;302;308;360;86;137;210;247;296;354 S;S;S;S;S;S;S;S;S 59;79;105;130;161;192;229;278;336 60;80;106;131;162;193;230;279;337 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Cells were then incubated with WT or N501Y-RBD-His (Sino Biological) at various dilutions at 4 C for 30 minutes and stained with anti-His secondary antibody (1:50, BioLegend) at 4 C for 15 minutes. 2021 Cell reports Method SARS_CoV_2 N501Y 37 42 RBD 43 46 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Expi293F cells were transfected with pfuse-RBD-mIgG2aFc or pfuse-RBD-N501Y-mIgG2aFc. 2021 Cell reports Method SARS_CoV_2 N501Y 69 74 RBD;RBD 43;65 46;68 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. For confirmation of infection in the airway, lungs were collected 24-hours post infection with either D614G or N501Y + D614G GFP+ VsV PsVs. 2021 Cell reports Method SARS_CoV_2 D614G;D614G;N501Y 102;119;111 107;124;116 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. PCR fragment was amplified by primers (TAATACGACTCACTATAGGG, GAAAGTAACAGTTGAAGCCCTGCACTCCATTACATGGTGTGC, GCACACCATGTAATGGAGTGCAGGGCTTCAACTGTTACTTTC, and AAATCTAGATTAACAACAGGAGCCACAGGAA) and template (pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y-K417N-L452R-E484K) and cloned into PCMV3 vector. 2021 Cell reports Method SARS_CoV_2 D614G;E484K;K417N;L452R;N501Y 224;248;236;242;230 229;253;241;247;235 S 217 218 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. PCR fragment was amplified by primers (TAATACGACTCACTATAGGG, GAAAGTAACAGTTGAAGCCCTTCACTCCATTACATGGTGTGC, GCACACCATGTAATGGAGTGAAGGGCTTCAACTGTTACTTTC, and AAATCTAGATTAACAACAGGAGCCACAGGAA) and template (pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y-K417N) and cloned into PCMV3 vector. 2021 Cell reports Method SARS_CoV_2 D614G;K417N;N501Y 224;236;230 229;241;235 S 217 218 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. PCR fragment was amplified by primers (TAATACGACTCACTATAGGG, GGCACCTCAGTACAGTTCACACCCTGGTAGAGCACAGCCACC, GGTGGCTGTGCTCTACCAGGGTGTGAACTGTACTGAGGTGCC, and AAATCTAGATTAACAACAGGAGCCACAGGAA) and template (pCMV3-SARS-CoV-2-S-N501Y-cd19) and cloned into PCMV3 vector. 2021 Cell reports Method SARS_CoV_2 N501Y 219 224 S 217 218 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. PCR fragment was amplified by primers (TAATACGACTCACTATAGGG, TGGGAGGCAACTACAACTACCGCTACAGACTGTTCAGGAAGAGC, GCTCTTCCTGAACAGTCTGTAGCGGTAGTTGTAGTTGCCTCCCA, and AAATCTAGATTAACAACAGGAGCCACAGGAA) and template (pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y-K417N-E484K) and cloned into PCMV3 vector. 2021 Cell reports Method SARS_CoV_2 D614G;E484K;K417N;N501Y 228;246;240;234 233;251;245;239 S 221 222 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. PCR fragment was amplified by primers (TAATACGACTCACTATAGGG, TGGGAGGCAACTACAACTACCGCTACAGACTGTTCAGGAAGAGC, GCTCTTCCTGAACAGTCTGTAGCGGTAGTTGTAGTTGCCTCCCA, and AAATCTAGATTAACAACAGGAGCCACAGGAA) and template (pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y) and cloned into PCMV3 vector. 2021 Cell reports Method SARS_CoV_2 D614G;N501Y 228;234 233;239 S 221 222 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. PCR fragment was amplified by primers (TAATACGACTCACTATAGGG, TTTGTAGTTGTAGTCAGCAATGTTGCCTGTTTGTCCAGGGGC, GCCCCTGGACAAACAGGCAACATTGCTGACTACAACTACAAA, and AAATCTAGATTAACAACAGGAGCCACAGGAA) and template (pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y) and cloned into PCMV3 vector. 2021 Cell reports Method SARS_CoV_2 D614G;N501Y 224;230 229;235 S 217 218 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. RBD-Fc and N501Y-RBD-Fc protein was expressed using Expi293F expression system kit (Thermo Fisher Scientific, Waltham, MA) according to the manufacturer's instructions. 2021 Cell reports Method SARS_CoV_2 N501Y 11 16 RBD;RBD 0;17 3;20 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. RBD-Fc and RBD-N501Y-Fc proteins were purified by a HiTrap protein G column (GE Healthcare Life Sciences, Marlborough, MA. 2021 Cell reports Method SARS_CoV_2 N501Y 15 20 RBD;RBD 0;11 3;14 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. To determine anti-WT or N501Y + K417N + E484K + D614G RBD IgG, IgM, and IgA antibody levels, ELISA plates were coated with either WT or N501Y + K417N + E484K + D614G RBD protein at a concentration of 2 ug/ml overnight in PBS. 2021 Cell reports Method SARS_CoV_2 D614G;D614G;E484K;E484K;K417N;K417N;N501Y;N501Y 48;160;40;152;32;144;24;136 53;165;45;157;37;149;29;141 RBD;RBD 54;166 57;169 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. To generate 19del + D614G mutation PsV plasmid (pCMV3-SARS-CoV-2-S-cd19-D614G), site-directed mutagenesis was used for generating D614G mutation in the SARS-CoV-2 spike sequence. 2021 Cell reports Method SARS_CoV_2 19del;D614G;D614G;D614G 12;20;130;72 17;25;135;77 S;S 163;65 168;66 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. To generate 19del + N501Y + D614G + K417N + E484K mutation PsV plasmid (pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y-K417N-E484K), site-directed mutagenesis was used for generating E484K mutation in the SARS-CoV-2 spike sequence. 2021 Cell reports Method SARS_CoV_2 19del;D614G;E484K;E484K;K417N;N501Y;D614G;E484K;K417N;N501Y 12;28;44;172;36;20;96;114;108;102 17;33;49;177;41;25;101;119;113;107 S;S 205;89 210;90 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. To generate 19del + N501Y + D614G + K417N + L452R +E484K mutation PsV plasmid (pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y-K417N-L452R-E484K), site-directed mutagenesis was used for generating L452R mutation in the SARS-CoV-2 spike sequence. 2021 Cell reports Method SARS_CoV_2 19del;D614G;K417N;L452R;L452R;N501Y;E484K;D614G;E484K;K417N;L452R;N501Y 12;28;36;44;185;20;51;103;127;115;121;109 17;33;41;49;190;25;56;108;132;120;126;114 S;S 218;96 223;97 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. To generate 19del + N501Y + D614G + K417N + L452R +E484Q mutation PsV plasmid (pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y- K417N-L452R-E484Q), site-directed mutagenesis was used for generating E484Q mutation in the SARS-CoV-2 spike sequence. 2021 Cell reports Method SARS_CoV_2 19del;D614G;E484Q;K417N;K417N;L452R;N501Y;E484Q;D614G;E484Q;L452R;N501Y 12;28;186;36;116;44;20;51;103;128;122;109 17;33;191;41;121;49;25;56;108;133;127;114 S;S 219;96 224;97 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. To generate 19del + N501Y + D614G + K417N mutation PsV plasmid (pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y-K417N), site-directed mutagenesis was used for generating K417N mutation in the SARS-CoV-2 spike sequence. 2021 Cell reports Method SARS_CoV_2 19del;D614G;K417N;K417N;N501Y;D614G;K417N;N501Y 12;28;36;158;20;88;100;94 17;33;41;163;25;93;105;99 S;S 191;81 196;82 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. To generate 19del + N501Y + D614G + L452R mutation PsV plasmid (pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y-L452R), site-directed mutagenesis was used for generating L452R mutation in the SARS-CoV-2 spike sequence. 2021 Cell reports Method SARS_CoV_2 19del;D614G;L452R;L452R;N501Y;D614G;L452R;N501Y 12;28;36;158;20;88;100;94 17;33;41;163;25;93;105;99 S;S 191;81 196;82 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. To generate 19del + N501Y + D614G mutation PsV plasmid (pCMV3-SARS-CoV-2-S-cd19-D614G-N501Y), site-directed mutagenesis was used for generating D614G mutation in the SARS-CoV-2 spike sequence. 2021 Cell reports Method SARS_CoV_2 19del;D614G;D614G;N501Y;D614G;N501Y 12;28;144;20;80;86 17;33;149;25;85;91 S;S 177;73 182;74 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. To generate 19del + N501Y mutation PsV plasmid (pCMV3-SARS-CoV-2-S-N501Y-cd19), site-directed mutagenesis was used for generating N501Y mutation in the SARS-CoV-2 spike sequence. 2021 Cell reports Method SARS_CoV_2 19del;N501Y;N501Y;N501Y 12;20;130;67 17;25;135;72 S;S 163;65 168;66 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. To generate pfuse-RBD-N501Y-mIgG2aFc, PCR fragment was amplified by primers (AAAGAATTCGATGAGGGTCCAACCAACAGAG and TTTAGATCTGAAGTTCACACACTTGTTCTT) and template (pCMV3-SARS-CoV-2-S-N501Y) and cloned into pFuse-mIgG2a-Fc2 vector (Invivogen, San Diego, USA). 2021 Cell reports Method SARS_CoV_2 N501Y;N501Y 22;178 27;183 RBD;S 18;176 21;177 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. To generate the 19del pseudovirus (PsV) plasmid (pCMV3-SARS-CoV-2-S-cd19), 19 amino acids were deleted in the spike protein sequence of SARS-CoV-2 variant Wuhan-Hu-1. 2021 Cell reports Method SARS_CoV_2 19del 16 21 S;S 110;66 115;67 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. To generate the N501Y mutation PsV plasmid (pCMV3-SARS-CoV-2-S-N501Y), site-directed mutagenesis was used for generating the N501Y mutation in the SARS-CoV-2 spike sequence. 2021 Cell reports Method SARS_CoV_2 N501Y;N501Y;N501Y 16;125;63 21;130;68 S;S 158;61 163;62 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Structure dynamics of the wild-type and mutants (N439K, S477 N, T478K) RBDs in complex with ACE2 were evaluated in a solvated system neutralized by counterions. 2021 Computers in biology and medicine Method SARS_CoV_2 S477N;T478K;N439K 56;64;49 62;69;54 RBD 71 75 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. The 3D structures of mutations (N439K, S477 N, T478K), predicted to induce greater stability change and increase the binding affinity by many folds, were modeled using Modeller v15.2 embedded in Chimera software. 2021 Computers in biology and medicine Method SARS_CoV_2 S477N;T478K;N439K 39;47;32 45;52;37 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. To estimate the binding free energy of wild-type and mutants (N439K, S477 N, T478K) complexes, we used the molecular mechanics generalized Born surface area (MM/GBSA) approach, which was previously used by Abbas et al., 2021 to explore the binding differences of the wild-type and SARS-CoV-2 variants. 2021 Computers in biology and medicine Method SARS_CoV_2 S477N;T478K;N439K 69;77;62 75;82;67 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. Next, in the set of genomes found, we verified all mutations, excluding those that define the B.1.1.28 lineage (C241T, F924F, P4715L, D614G, V1176F, R203K, R203R and G204R). 2021 Frontiers in public health Method SARS_CoV_2 D614G;F924F;G204R;P4715L;R203K;R203R;V1176F;C241T 134;119;166;126;149;156;141;112 139;124;171;132;154;161;147;117 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. The first is composed of complete genome sequences generated in this study along with high coverage sequences available in GISAID of B.1.1.28 lineage with L452R mutation as well as representatives from B.1.1.28, P.1, P.2, P.3, B.1.1.7, B.1.427, B.1.429, B.1.617 lineages plus the reference sequence WIV04/2019 EPI_ISL_402124. 2021 Frontiers in public health Method SARS_CoV_2 L452R 155 160 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. Using the database, we searched for all genomes that contain the T22917G (L452R) mutation. 2021 Frontiers in public health Method SARS_CoV_2 T22917G;L452R 65;74 72;79 34663909 SARS-CoV-2 promotes RIPK1 activation to facilitate viral propagation. Flag-NSP12 P323L was generated using MutExpress II mutagenesis kit (Vazyme Biotech). 2021 Cell research Method SARS_CoV_2 P323L 11 16 Nsp12 5 10 34663909 SARS-CoV-2 promotes RIPK1 activation to facilitate viral propagation. The nasopharyngeal swab from patients was used to isolate WT and C14408T variant virus with signed permission. 2021 Cell research Method SARS_CoV_2 C14408T 65 72 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Additionally, for the N501Y mutation test interpretation, various situations were obtained as summarized in Table 2. 2021 Journal of medical virology Method SARS_CoV_2 N501Y 22 27 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. After the test of a gold standard method of RT-qPCR, positive patients were examined with the mutation kit of a Bio-Speedy SARS CoV-2 N501Y Mutation Kit. 2021 Journal of medical virology Method SARS_CoV_2 N501Y 134 139 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. For the detection of N501Y mutation within 2757 (19.7%) of 13,972 patients' samples, a Bio-Speedy (SARS CoV-2 N501Y Mutation Kit) was used. 2021 Journal of medical virology Method SARS_CoV_2 N501Y;N501Y 21;110 26;115 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. N501Y mutation RT-PCR tests. 2021 Journal of medical virology Method SARS_CoV_2 N501Y 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The mutation-specific B.1.1.7 strain (carboxylic acid [Cy5]) was targeted for differentiation of VOC-202012/01 from other strains (B.1.351, P.1) containing the N501Y mutation. 2021 Journal of medical virology Method SARS_CoV_2 N501Y 160 165 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The N501Y mutation (6-carbocyl-X-Rhoddamine [ROX]) has been targeted to detect N501Y containing variants. 2021 Journal of medical virology Method SARS_CoV_2 N501Y;N501Y 4;79 9;84 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The N501Y mutation in the SARS-CoV-2 Spike (S) protein is present in all three emerging lineages. 2021 Journal of medical virology Method SARS_CoV_2 N501Y 4 9 S;S 37;44 42;45 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The samples containing the N501Y mutation are concluded as VOC-202012/01 positive, according to the kit protocol. 2021 Journal of medical virology Method SARS_CoV_2 N501Y 27 32 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. A python script (https://github.com/hridoy04/counting-mutations) was used to partition that data set into two subsets (RdRp wild-type or "C" variant: 9,815; and mutant or "T" variant: 27 364) based on the presence of RdRp: C14408T mutation and then estimate the genome-wide single nucleotide polymorphisms (SNPs) for each strain (Supplementary Material 2). 2021 Journal of medical virology Method SARS_CoV_2 C14408T 223 230 RdRP;RdRP 119;217 123;221 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. The change C26801G is at the transmembrane region 3 (TM3) of the virion membrane. 2021 Journal of medical virology Method SARS_CoV_2 C26801G 11 18 Membrane 72 80 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. The change C6286T is in between the nucleic acid-binding (NAB) domain and betacoronavirus-specific marker (betaSM) domain of the NSP3 region. 2021 Journal of medical virology Method SARS_CoV_2 C6286T 11 17 Nsp3 129 133 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. The Mfold web server was used with default parameters to check the folding pattern of RNA secondary structure in the mutated 5'-UTR, synonymous leader (T445C), and NSP3 region (C3037T). 2021 Journal of medical virology Method SARS_CoV_2 C3037T;T445C 177;152 183;157 Nsp3 164 168 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. Thus, changing in C6286T and C26801G will not affect the function significantly and was not predicted here. 2021 Journal of medical virology Method SARS_CoV_2 C26801G;C6286T 29;18 36;24 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. SARS-CoV-2/human/USA/RML-7/2020 (GenBank: MW127503.1; designated D614G throughout the manuscript) was obtained from a nasopharyngeal swab obtained on 19 July 2020. 2021 Science advances Method SARS_CoV_2 D614G 65 70 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Sequencing confirmed the presence of the following three SNPs in this stock: nsp6 D156G (present in 14% of all reads), nsp6 L257F (18%), and nsp7 V11I (13%). 2021 Science advances Method SARS_CoV_2 D156G;L257F;V11I 82;124;146 87;129;150 Nsp7;Nsp6;Nsp6 141;77;119 145;81;123 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Sequencing confirmed the presence of two SNPs in this stock: nsp5 P252L (17%) and nsp6 L257F (57%). 2021 Science advances Method SARS_CoV_2 L257F;P252L 87;66 92;71 Nsp5;Nsp6 61;82 65;86 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. The D614G, B.1.1.7, and B.1.351 stocks contained similar ratios of SARS-CoV-2 E gene copies to infectious virus, i.e., 1.3 x 104, 1.6 x 104, and 1.5 x 104 RNA copies/TCID50, respectively. 2021 Science advances Method SARS_CoV_2 D614G 4 9 E 78 79 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. To compare the pathogenicity and virus shedding of VOC B.1.1.7 and B.1.351, we inoculated three groups of six rhesus macaques with three different SARS-CoV-2 isolates: SARS-CoV-2/human/USA/RML-7/2020, a contemporary clade B.1 isolate containing the D614G substitution in spike; hCOV_19/England/204820464/2020, a B.1.1.7 isolate; and hCoV-19/USA/MD-HP01542/2021, a B.1.351 isolate. 2021 Science advances Method SARS_CoV_2 D614G 249 254 S 271 276 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. Based on previous works, for detecting del-HV69/70 and N501Y via RT-qPCR, we designed and tested further assays to be able to detect and discriminate all lineages currently holding VOC status (, accessed on 28 June 2021): del-Y144/145, E484K, E484Q, P681H, P681R, L452R, and V1176F. 2021 Diagnostics (Basel, Switzerland) Method SARS_CoV_2 E484K;E484Q;L452R;N501Y;P681H;P681R;V1176F 236;243;264;55;250;257;275 241;248;269;60;255;262;281 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. Different SARS-CoV-2 isolates, either from cell culture supernatant or clinical samples, were used to represent the respective SNPs (I) WT: Hamburg-1, (II) B.1.480: E484K + P681H + delY144/145, (III) B.1.617.1: E484Q + P681R + L452R. 2021 Diagnostics (Basel, Switzerland) Method SARS_CoV_2 E484K;E484Q;L452R;P681H;P681R 165;211;227;173;219 170;216;232;178;224 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. For assays located within the Spike-gene receptor-binding domain (E484K/ E484Q and L452R), an additional reverse primer is added ("Rev-2"/"RBD-universal rev", Table 1, Supplementary Table S1) to enhance cDNA generation and overall assay performance. 2021 Diagnostics (Basel, Switzerland) Method SARS_CoV_2 E484Q;L452R;E484K 73;83;66 78;88;71 S;RBD 30;139 35;142 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. Simultaneous detection of the L452R, E484Q, and P681R SNPs further allows differentiation between the B.1.617.1/3 and B.1.617.2 lineages in a single reaction. 2021 Diagnostics (Basel, Switzerland) Method SARS_CoV_2 E484Q;L452R;P681R 37;30;48 42;35;53 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. Spike-gene mutations L452R, P681R, E484K, and E484Q were positive in 78, 77, 17, and 7 samples, respectively. 2021 Diagnostics (Basel, Switzerland) Method SARS_CoV_2 E484K;E484Q;L452R;P681R 35;46;21;28 40;51;26;33 S 0 5 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. The lower limit of detection for all assays was determined using a clinical sample containing B.1.617.1 lineage (L452R positive, E484Q positive, P681R positive) as reference, adjusted to IU/mL according to WHO standard (NISBSC, UK; ) (accessed on 28 June 2021). 2021 Diagnostics (Basel, Switzerland) Method SARS_CoV_2 E484Q;P681R;L452R 129;145;113 134;150;118 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. Then, 500 ng/mL SARS-CoV-2 Spike S1 (Trenzyme GmbH, Konstanz, Germany), spike S1 D614G, N50Y, or a mix of K417N, E484K, and N501Y (Sino Biological Europe GmbH, Eschborn, Germany)-His recombinant protein were added into each sample, and samples were further incubated for 30-60 min. 2021 Pharmaceuticals (Basel, Switzerland) Method SARS_CoV_2 D614G;E484K;K417N;N501Y;N50Y 81;113;106;124;88 86;118;111;129;92 S;S 27;72 32;77 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. Both Lenti-CTRL and Lenti-S D614G were used at 15 multiplicity of infection (MOI). 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Method SARS_CoV_2 D614G 28 33 S 26 27 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. Construction of pLenti-CMV-SARS-CoV-2-S mutation D614G (Asp 17 614 Gly) and pLenti-CMV-MCS-hACE2-IRES-sfGFP-SV-Puro Vectors. 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Method SARS_CoV_2 D614G 49 54 S 38 39 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. Furthermore, the effect of Spike variant was evaluated and a viral vector expressing D614G Spike mutation was also used for the purpose of this study (Lenti-S D614G). 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Method SARS_CoV_2 D614G;D614G 85;159 90;164 S;S;S 27;91;157 32;96;158 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. In addition, with the purpose of reducing the thrombotic effect led by the aforementioned conditions, Lipo-ACE2 and anti-IL6 antibodies were used in combination with SARS-CoV-2, Lipo-S, and Lenti-S D614G. 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Method SARS_CoV_2 D614G 198 203 S;S 183;196 184;197 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. Previous ligase reaction the NheI and EcoRI digestion sites in SARS-CoV-2-S D614G insert were converted in the XbaI-BamHI compatible with the backbone vector. 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Method SARS_CoV_2 D614G 76 81 S 74 75 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. Similarly, pcDNA3.1 SARS-CoV-2 S D614G (Addgene-158075) was cloned into pLenti-CMV-MCS-GFP-SV-puro. 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Method SARS_CoV_2 D614G 33 38 S 31 32 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. The GFP sequence was removed by restriction enzyme digestions (XbaI-BamHI) and replaced with SARS-CoV-2 S D614G insertion sequence. 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Method SARS_CoV_2 D614G 106 111 S 104 105 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. The S protein-mediated effects were compared on thrombosis in two additional conditions: 1) Lipo-S and 2) a lentivirus with the Spike mutation D614G (Asp614 Gly substitution in S1 subunit). 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Method SARS_CoV_2 D614G;D614G 143;150 148;160 S;S;S 128;4;97 133;5;98 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. HEK293T cells were transfected with 5 mug of SARS-CoV-2 original variant spike (D614G), Beta or Delta spike plasmids using PEI-MAX 40,000 (Polysciences) and incubated for 2 days at 37 C. 2021 Cell host & microbe Method SARS_CoV_2 D614G 80 85 S;S 73;102 78;107 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. Palivizumab was used as a negative control, while CR3022 was used as a positive control, and P2B-2F6 to differentiate the Beta from the D614G variant. 2021 Cell host & microbe Method SARS_CoV_2 D614G 136 141 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. SARS-CoV-2 pseudotyped lentiviruses were prepared by co-transfecting the HEK293T cell line with either the SARS-CoV-2 ancestral variant spike (D614G), the Beta spike (L18F, D80A, D215G, K417N, E484K, N501Y, D614G, A701V, 242-244 del) or the Delta spike (T19R, R158G L452R, T478K, D614G, P681R, D950N, 156-157 del) plasmids in conjunction with a firefly luciferase encoding lentivirus backbone plasmid. 2021 Cell host & microbe Method SARS_CoV_2 A701V;D215G;D614G;D614G;D80A;D950N;E484K;K417N;L452R;N501Y;P681R;R158G;T478K;D614G;L18F;T19R 214;179;207;280;173;294;193;186;266;200;287;260;273;143;167;254 219;184;212;285;177;299;198;191;271;205;292;265;278;148;171;258 S;S;S 136;160;247 141;165;252 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. End preparation and Barcoding was performed using Blunt/TA Ligase MasterMix (New England Biolabs; M0367L), NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs; E7546L) and Native Barcoding Expansion 1-12 (PCR-free) (Oxford Nanopore Technologies; EXP-NBD104). 2022 The Science of the total environment Method SARS_CoV_2 M0367L 98 104 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. The reverse-transcribed cDNA was amplified using Q5 High-Fidelity DNA Polymerase (New England Biolabs; M0491S), 5x Q5 Reaction Buffer (New England Biolabs; M0491S), dNTPs mix (New England Biolabs; N0447S) and primer pools 40 U/ul SARS-CoV-2 primers (Pool A & B) 100uM (ARCTIC) (New England Biolabs; GTR_066_COVID25). 2022 The Science of the total environment Method SARS_CoV_2 M0491S;M0491S 103;156 109;162 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. In brief, 293T cells were transfected with SARS-CoV-2-WT-S or SARS-CoV-2-N501Y-S plasmids with Lipofectamine 3000 (Thermo Fisher Scientific). 2021 EBioMedicine Method SARS_CoV_2 N501Y 73 78 S;S 57;79 58;80 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. The complex of ACE2 and N501Y RBD was built by superimposition of N501Y RBD (code: 7NEG) with wildtype RBD. 2021 EBioMedicine Method SARS_CoV_2 N501Y;N501Y 24;66 29;71 RBD;RBD;RBD 30;72;103 33;75;106 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. The generated SARS-CoV-2-WT-S-, or SARS-CoV-2-N501Y-S-pseudoviruses were harvested at 16h post inoculation. 2021 EBioMedicine Method SARS_CoV_2 N501Y 46 51 S;S 28;52 29;53 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. The SARS-CoV-2-WT-S and SARS-CoV-2-N501Y-S pseudoviruses were generated in 293T cells according to a previously established protocol. 2021 EBioMedicine Method SARS_CoV_2 N501Y 35 40 S;S 18;41 19;42 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. Codon changes were introduced on the optimized sequence for the K417N, K417T, E484K, N501Y, and their combination K417N_E484K_N501Y (N_K_Y) or K417T_E484K_N501Y (T_K_Y). 2021 Frontiers in immunology Method SARS_CoV_2 E484K;K417N;K417N;K417T;K417T;N501Y;E484K;E484K;N501Y;N501Y 78;64;114;71;143;85;120;149;126;155 83;69;119;76;148;90;125;154;131;160 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Some adaptive mutations, namely Y453F, S477N, T478K, E484K, S494P and N501Y, were also found in long-term COVID-19 infections. 2021 Viruses Method SARS_CoV_2 E484K;N501Y;S477N;S494P;T478K;Y453F 53;70;39;60;46;32 58;75;44;65;51;37 COVID-19 106 114 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. All N501Y positive samples are further analyzed for the presence of K417N (88 bp) and V1176F (160 bp) mutations. 2021 Viruses Method SARS_CoV_2 K417N;N501Y;V1176F 68;4;86 73;9;92 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. For this purpose, RNA eluate of N501Y positive saliva samples is further analyzed by commercially available SNIP assays for K417N and V1176F presence (VirSNiP SARS-CoV-2 Spike K417N and VirSNiP SARS-CoV-2 Spike V1176F, TIB MolBio, Berlin, Germany). 2021 Viruses Method SARS_CoV_2 K417N;K417N;N501Y;V1176F;V1176F 124;176;32;134;211 129;181;37;140;217 S;S 170;205 175;210 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. Positive primary samples are screened for the mutation variant N501Y. 2021 Viruses Method SARS_CoV_2 N501Y 63 68 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. Sample is considered positive for K417N or V1176F when the melting curve analysis shows a Tm of 61 C (+-2 C) or 57.9 C (+-1 C) respectively. 2021 Viruses Method SARS_CoV_2 K417N;V1176F 34;43 39;49 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. Samples are counted as positive for N501Y when the melting curve analysis shows a melting temperature of 61.2 C (+-2 C). 2021 Viruses Method SARS_CoV_2 N501Y 36 41 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. The 160 bp long fragment is analyzed by RT-PCR melting curve analysis using a commercially available SNIP assay (VirSNiP SARS-CoV-2 Spike N501Y, TIB MolBio, Berlin, Germany). 2021 Viruses Method SARS_CoV_2 N501Y 138 143 S 132 137 34705425 Gold-Nanostar-Chitosan-Mediated Delivery of SARS-CoV-2 DNA Vaccine for Respiratory Mucosal Immunization: Development and Proof-of-Principle. QHD43416.1; with D614G mutation) as the envelope glycoproteins instead of the commonly used VSV-G. 2021 ACS nano Method SARS_CoV_2 D614G 17 22 34705425 Gold-Nanostar-Chitosan-Mediated Delivery of SARS-CoV-2 DNA Vaccine for Respiratory Mucosal Immunization: Development and Proof-of-Principle. The SC2 spike D614G pseudotyped lentivirus can be used to measure the activity of neutralizing antibody against SC2 in a Biosafety Level 2 facility. 2021 ACS nano Method SARS_CoV_2 D614G 14 19 S 8 13 34705425 Gold-Nanostar-Chitosan-Mediated Delivery of SARS-CoV-2 DNA Vaccine for Respiratory Mucosal Immunization: Development and Proof-of-Principle. The SC2 spike D614G pseudotyped lentiviruses were produced using SC2 Spike. 2021 ACS nano Method SARS_CoV_2 D614G 14 19 S;S 8;69 13;74 34705425 Gold-Nanostar-Chitosan-Mediated Delivery of SARS-CoV-2 DNA Vaccine for Respiratory Mucosal Immunization: Development and Proof-of-Principle. We characterized the particle size and morphology of the AuNS-CS loaded with SC2 plasmid using transmission electron microscopy (TEM, FEI-Tecnai G2 F20 X-TWIN) equipped with an ORIUS CCD camera through digital micrography. 2021 ACS nano Method SARS_CoV_2 F20X 148 153 34705425 Gold-Nanostar-Chitosan-Mediated Delivery of SARS-CoV-2 DNA Vaccine for Respiratory Mucosal Immunization: Development and Proof-of-Principle. We seeded 3 x 106 HEK293 cells in 10 cm well plates and transfected with 10 mug pDNA (pcDNA, SC2-Wuhan, SC2-beta mutant, and SC2-D614G mutant) using lipofectamine 3000 reagent (Thermo Fisher Scientific), and after 48 h treatment, we harvested and processed cells further for immunoblot analysis using anti-SPK antibody as outlined in our earlier work. 2021 ACS nano Method SARS_CoV_2 D614G 129 134 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Pseudovirions incorporated with S protein of SARS, SARS-CoV-2 WT, D614G, N501Y.V1 and N501Y.V2 lineages were diluted with DMEM and incubated in a 37 C or 42 C water bath. 2021 Frontiers in cellular and infection microbiology Method SARS_CoV_2 D614G;N501Y;N501Y 66;73;86 71;78;91 S 32 33 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Deep sequencing confirmed the presence of three SNPs in this stock: nsp6 D156G (present in 14% of all reads), nsp6 L257F (18%) and nsp7 V11I (13%). 2021 Emerging microbes & infections Method SARS_CoV_2 D156G;L257F;V11I 73;115;136 78;120;140 Nsp7;Nsp6;Nsp6 131;68;110 135;72;114 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Originally, 6 AGMs per group were assigned to each group but one animal in the D614G group had to be euthanized for an animal welfare concern reason prior to study start leaving the D614G group with only 5 animals. 2021 Emerging microbes & infections Method SARS_CoV_2 D614G;D614G 79;182 84;187 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. SARS-CoV-2 isolate SARS-CoV-2/human/USA/RML-7/2020 (MW127503.1), strain D614G (co-circulating progenitor), was obtained from a nasopharyngeal swab obtained on 19 July 2020. 2021 Emerging microbes & infections Method SARS_CoV_2 D614G 72 77 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Studies were performed in successive weeks and different animal study groups to avoid contamination between studies, the D416G study was run first followed by the B.1.1.7 study. 2021 Emerging microbes & infections Method SARS_CoV_2 D416G 121 126 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Twelve SARS-CoV-2 seronegative AGMs (3.8-6.7 kg) were randomly divided into 2 groups for infection with either the contemporary D614G progenitor variant (RML7) (n = 5; Table S1) or the B.1.1.7 (UK; Alpha) variant (n = 6; Table S1). 2021 Emerging microbes & infections Method SARS_CoV_2 D614G 128 133 34728625 Potent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants. Lenti-X293T cells were grown to 80% confluency before transfection with VSV-G pseudotyped DeltaG-luciferase, pWPXL and pSFAX2. 2021 Nature communications Method SARS_CoV_2 X293T 6 11 34728625 Potent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants. Serially diluted mAbs with volume of 50 muL were incubated with the same volume of the Lenti-X293T cell supernatants containing pseudovirus for 1 h at 37 C. 2021 Nature communications Method SARS_CoV_2 X293T 93 98 34728625 Potent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants. The IgG heavy and light chains of mAbs genes in these memory B cells were obtained by single cell PCR and transiently transfected into Lenti-X293T cells (TAKARA, 632180) for the identification of mAbs with capabilities of the neutralization against SARS-CoV-2 pseudovirus. 2021 Nature communications Method SARS_CoV_2 X293T 141 146 34728625 Potent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants. These pseudovirus-antibody mixtures were added to ACE2 expressing Lenti-X293 T cells (293 T/ACE2). 2021 Nature communications Method SARS_CoV_2 X293T 72 78 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. The D614G mutant was generated by site-direction mutagenesis with specific primers as described in our previous study. 2022 Glycobiology Method SARS_CoV_2 D614G 4 9 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. The HCD and EThcD MS2 data were then processed by Byonic (v 3.10.10 for S-2P/fm2P/D614G O-glycopeptide identification, and v 3.11.3 for S-Alpha O-glycopeptide and all N-glycopeptide identification) using the following general parameters: search against the SARS-CoV-2 spike protein sequence with semi specific cleavages at F, Y, W, L, K, R residues, allowing up to two missed cleavages, with the precursor ion mass tolerance set at 4 ppm and the fragment ion mass tolerance at 10 ppm. 2022 Glycobiology Method SARS_CoV_2 D614G 82 87 S;N;S;S 268;167;72;136 273;168;73;137 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. The same construct design of S-fm2P was used for the D614G and Alpha variants (hereafter designated as S-D614G and S-Alpha, respectively). 2022 Glycobiology Method SARS_CoV_2 D614G;D614G 53;105 58;110 S;S;S 29;103;115 30;104;116 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. They are: S.K417T.AAG.ACG, S.D614G.GAT.GGT, S.E484K.GAA.AAA, S.E484Q.GAA.CAA, S.K417N.AAG.AAT, S.L452R.CTG.CGG, S.N501Y.AAT.TAT, S.P681R.CCT.CGT, S.T20N.ACC.AAC, S.delH69V70, S.delL242.244L, orf8.Q27ST.CAA.TAA, S.A701V.GCA.GTA and S.T478K.ACA.AAA (Applied Biosystem, Thermo Fisher Scientific) with gene name, mutation present and reference and mutant codons. 2021 Infection and drug resistance Method SARS_CoV_2 A701V;D614G;E484K;E484Q;K417N;K417T;L452R;N501Y;P681R;Q27S;Q27T;T20N;T478K 213;29;46;63;80;12;97;114;131;196;196;148;233 218;34;51;68;85;17;102;119;136;201;201;152;238 ORF8;S;S;S;S;S;S;S;S;S;S;S;S;S 191;10;27;44;61;78;95;112;129;146;162;175;211;231 195;11;28;45;62;79;96;113;130;147;163;176;212;232 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. To assess the ability of antibodies to link to mutated S-proteins, we used the recently reported mutation of the S-protein corresponding to MT1: N501Y, MT2: E484K/N501Y, and MT3: K417N/E484K/N501Y. 2021 Scientific reports Method SARS_CoV_2 E484K;K417N;N501Y;E484K;N501Y;N501Y 157;179;145;185;163;191 162;184;150;190;168;196 S;S 55;113 56;114 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The soluble SARS-CoV-2 S2P trimer proteins of the D614G, B.1.1.7, B.1.351, P.1 and B.1.1.248 strains were generated by transfecting Expi293 cells with the trimer protein-expressing constructs using FectPRO DNA transfection reagent and purified from cell supernatants 5 days later using Strep-Tactin resin, according to the manufacturer's protocol. 2021 iScience Method SARS_CoV_2 D614G 50 55 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Live cells were incubated with the recombinant protein, S1 domain of SARS-CoV-2 spike C-terminally fused with His tag (Sino Biological #40591-V08H, 1mug/ml) at 4 C for 30 min. 2021 PLoS pathogens Method SARS_CoV_2 V08H 142 146 S 80 85 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. The coordinates and structure factor files for the SARS-CoV-2 Y453F RBD/mink ACE2 complex have been deposited in the Protein Data Bank (PDB) under accession number 7F5R. 2021 PLoS pathogens Method SARS_CoV_2 Y453F 62 67 RBD 68 71 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. The crystal of SARS-CoV-2 RBD Y453F and mink ACE2 complex was obtained in a well solution of 1.6 M sodium/potassium phosphate using the sitting drop method. 2021 PLoS pathogens Method SARS_CoV_2 Y453F 30 35 RBD 26 29 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. The gene encoding 333-527aa of SARS-CoV-2 RBD (WT or Y453F mutant) was cloned into the pFastbac-dual vector using the BamH1 and Hind3 restriction enzyme. 2021 PLoS pathogens Method SARS_CoV_2 Y453F 53 58 RBD 42 45 34756912 RT-qPCR detection of SARS-CoV-2 mutations S 69-70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples. RT-qPCR was performed in a reaction volume of 20 muL, consisting of 5 muL TaqPath 1-Step RT-qPCR Master Mix, CG (ThermoFisher Scientific), 500 nM (ND3L), 400 nM (Sdel), 250 nM (N501Y) final concentration of each primer (ThermoFisher Scientific), 500 nM (D3L, Sdel), 250 nM (N501Y) of each probe (ThermoFisher Scientific), 4 muL of template RNA and Invitrogen nuclease free H2O (ThermoFisher Scientific). 2022 The Science of the total environment Method SARS_CoV_2 D3L;N501Y;N501Y 254;177;274 257;182;279 34756912 RT-qPCR detection of SARS-CoV-2 mutations S 69-70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples. The N D3L mutation, consisting of a GAT->CTA mutation at position 28280 in B.1.1.7 was chosen due to close proximity to the N1 RT-qPCR assay currently in use for detection of SARS-CoV-2 in wastewater. 2022 The Science of the total environment Method SARS_CoV_2 D3L 6 9 N 4 5 34756912 RT-qPCR detection of SARS-CoV-2 mutations S 69-70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples. The spike protein N501Y mutation consisting of an A->T at position 23063 alters one of the key contact residues within the receptor binding domain, leading to increased binding affinity to ACE2 in humans. 2022 The Science of the total environment Method SARS_CoV_2 N501Y 18 23 RBD;S 123;4 146;9 34756912 RT-qPCR detection of SARS-CoV-2 mutations S 69-70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples. To further support the specificity of these SNPs, an investigation of 20,000 Canadian SARS-CoV-2 sequences collected prior to the detection of B.1.1.7, B.1.351, and P.1 in Canada, occurrences of S N501Y, S 69/70 del, and N D3L were found to be 0.019%, 0.028%, and 0.014% respectively, thus making them effective targets for variant detection (G. 2022 The Science of the total environment Method SARS_CoV_2 D3L;N501Y 223;197 226;202 N 221 222 34756912 RT-qPCR detection of SARS-CoV-2 mutations S 69-70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples. Two gene targets were chosen from the S gene: a deletion at 69-70 (Sdel) associated with B.1.1.7, and the N501Y mutation (SN501Y) associated with B.1.1.7, B.1.351, and P.1, along with one N gene mutation (D3L) associated with B.1.1.7. 2022 The Science of the total environment Method SARS_CoV_2 N501Y;D3L 106;205 111;208 N;S 188;38 189;39 34763050 Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation. The putative structures of SARS-CoV-2 S protein harboring mutations S:D614G and S:D614A were generated by homology modeling the Phyre2 web server. 2021 Infection, genetics and evolution Method SARS_CoV_2 D614A;D614G 82;70 87;75 S;S;S 38;68;80 39;69;81 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. (ii) The [D614G] mutation is present in alpha, beta and gamma strains, and are labeled as alpha/beta/gamma [D614G]. 2021 Scientific reports Method SARS_CoV_2 D614G;D614G 10;108 15;113 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. (iii) The [N501Y] mutation is present in alpha, beta and gamma strains, and are labeled as alpha/beta/gamma [N501Y]. 2021 Scientific reports Method SARS_CoV_2 N501Y;N501Y 11;109 16;114 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. (iv)The [E484K] mutation is present only in the beta strain and is labeled as beta [E484K]. 2021 Scientific reports Method SARS_CoV_2 E484K;E484K 9;84 14;89 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Recombinant SARS-CoV-2 (Original) RBD protein (Cat # 40592-VO8H), (Original) Spike [D614] S1 protein (Cat # 40591-V02H), (Original) [D614G] S1 protein (Cat # 40591-V08H3), Mink [Y453F] RBD protein (Cat # 40592-V08H80), (alpha/beta/gamma) [N501Y] RBD (Cat #40592-V08H82) and (beta) (E484K) RBD proteins (Cat # 40592-Vo8H84) were purchased from SinoBiologicals U.S. 2021 Scientific reports Method SARS_CoV_2 E484K;D614G;N501Y;Y453F;V02H 282;133;239;178;114 287;138;244;183;118 S;RBD;RBD;RBD;RBD 77;34;185;246;289 82;37;188;249;292 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Immunogenicity of the N501Y variant was compared with native spike using the immune epitope database (IEDB) server which is funded by the National Institute of Allergy and Infectious Diseases. 2022 Journal of cellular biochemistry Method SARS_CoV_2 N501Y 22 27 S 61 66 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Our group utilizes MD to investigate the effect of N501Y displacement on the structural characteristics of the spike. 2022 Journal of cellular biochemistry Method SARS_CoV_2 N501Y 51 56 S 111 116 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. The N501Y mutation is located in the interaction interface of spike protein with its receptor. 2022 Journal of cellular biochemistry Method SARS_CoV_2 N501Y 4 9 S 62 67 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. The sequences of native and N501Y spike variants were retrieved from UniProt in FASTA format. 2022 Journal of cellular biochemistry Method SARS_CoV_2 N501Y 28 33 S 34 39 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. To calculate the binding free energy of the native and N501Y spike-ACE2 complexes, g_mmpbsa which is equipped with the MM-PBSA algorithm was implemented. 2022 Journal of cellular biochemistry Method SARS_CoV_2 N501Y 55 60 S 61 66 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. To equilibrate systems, the Canonical ensemble (constant number, volume, temperature) was performed for temperature coupling at 310 K by V-rescale algorithm for 150 ps, as well as isothermal-isobaric ensemble (constant number, pressure, temperature) by Parrinello-Rahman algorithm for 500 ps was accomplished for pressure coupling at 1 bar. 2022 Journal of cellular biochemistry Method SARS_CoV_2 K310V 128 138 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. To rigorously investigate the impact of the N501Y mutation on the folding characteristics of spike protein, structural alignment along with three functions including the probability density function (PDF), contact map, and tunnel analysis were applied for the residues around the mutated position. 2022 Journal of cellular biochemistry Method SARS_CoV_2 N501Y 44 49 S 93 98 34783635 Identification of the SARS-CoV-2 Delta variant C22995A using a high-resolution melting curve RT-FRET-PCR. Analysis of the available whole-genome SARS-CoV-2 sequences in GISAID (www.gisaid.org) confirmed previous reports that the C22995A (T478K) mutation is one of the most common mutations present in the SARS-CoV-2 Delta variant. 2022 Emerging microbes & infections Method SARS_CoV_2 C22995A;T478K 123;132 130;137 34783635 Identification of the SARS-CoV-2 Delta variant C22995A using a high-resolution melting curve RT-FRET-PCR. Comparison of the melting temperatures between SARS-CoV-2 viruses with and without C22995A mutation was analyzed by the T test (Statistica, StatSoft, Tulsa, USA). 2022 Emerging microbes & infections Method SARS_CoV_2 C22995A 83 90 34783635 Identification of the SARS-CoV-2 Delta variant C22995A using a high-resolution melting curve RT-FRET-PCR. Seventeen of the 30 positive nasal swabs were found to be the Delta variant by whole genome sequencing, with the remainder not having the C22995A mutation. 2022 Emerging microbes & infections Method SARS_CoV_2 C22995A 138 145 34783635 Identification of the SARS-CoV-2 Delta variant C22995A using a high-resolution melting curve RT-FRET-PCR. The 6-carboxyfluorescein (6-FAM)-labeled probe was specifically designed to contain the unique C22995A mutation: upstream primer: 5'-CAGGCTGCGTTATAGCTT-3'; downstream primer: 5'-TATGGTTGGTAACCAACACC-3'; 6-Fam-probe: 5'-CCGGTAGCAAMCCTTGTAAT-6-FAM-3'; LCRed 640 probe: 5'-LCR640- GTGTTGAAKGWTTTAWTTGTTACTTT -phosphate-3'. 2022 Emerging microbes & infections Method SARS_CoV_2 C22995A 95 102 34783635 Identification of the SARS-CoV-2 Delta variant C22995A using a high-resolution melting curve RT-FRET-PCR. The C22995A mutation is present in 99.73% (320,730 / 321,061) of the Delta variant, but in only 0.006% (62 / 962,990) of classical isolates, three other variants of concern (VOC), and six variants of interest (VOI) (Table S1). 2022 Emerging microbes & infections Method SARS_CoV_2 C22995A 4 11 34784198 Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study. Further, we considered one charge-flip mutation R167E that was reported to be 20 times less efficient in hydrolyzing ISG15 by SCoV-PLpro. 2021 Journal of chemical information and modeling Method SARS_CoV_2 R167E 48 53 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. Based on the different melting profiles (Tm) of E484 and N501 molecular beacons in each sample, the E484K and N501Y mutations were determined. 2021 Microbiology spectrum Method SARS_CoV_2 E484K;N501Y 100;110 105;115 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. These samples were subjected to a molecular beacon-based real-time asymmetric PCR and melting curve analysis to identify the SARS-CoV-2 E484K/Q and N501Y mutations, as described previously. 2021 Microbiology spectrum Method SARS_CoV_2 E484K;E484Q;N501Y 136;136;148 143;143;153 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. MN908947); (iv) the L lineage fragment of ORF8 with mutation of S84L; and (v) the nucleoprotein (NP) gene fragment (nt 28,274 to 29,533; GenBank accession no. 2021 Microbiology spectrum Method SARS_CoV_2 S84L 64 68 ORF8 42 46 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. The SARS-CoV-2 target sequences include (i) the wild-type (WT) gene fragment of S protein (S; nucleotides [nt] 21,563 to 25,384; GenBank accession number MN908947); (ii) the mutant gene fragments of S protein, including mutations L5F, D80A, D215G, R246I, K417N, L452R/Q, Y453F, T478K, E484Q/K, N501Y, A570D, D614G, P681H, A701V, T716I, S982A, D1118H, and P1263L; (iii) the S lineage gene fragment of open reading frame 8 (ORF8; nt 27,894 to 28,259; GenBank accession no. 2021 Microbiology spectrum Method SARS_CoV_2 A570D;A701V;D1118H;D215G;D614G;D80A;E484K;E484Q;K417N;L452Q;L452R;L5F;N501Y;P1263L;P681H;R246I;S982A;T478K;T716I;Y453F 301;322;343;241;308;235;285;285;255;262;262;230;294;355;315;248;336;278;329;271 306;327;349;246;313;239;292;292;260;269;269;233;299;361;320;253;341;283;334;276 ORF8;S;S;S 422;80;91;199 426;81;92;200 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. The S gene mutation plasmids (plasmid 1, containing the HV69-70del, K417N, E484K, N501Y, D614G, and P681H mutations, and plasmid 2, containing the L452R, E484Q, and P681R mutations) of SARS-CoV-2 variants (Alpha, Beta, Iota, Epsilon, Gamma, and Delta) were synthesized by Sangon Biotech (Shanghai, China). 2021 Microbiology spectrum Method SARS_CoV_2 D614G;E484K;E484Q;K417N;L452R;N501Y;P681H;P681R 89;75;154;68;147;82;100;165 94;80;159;73;152;87;105;170 S 4 5 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. The S-F1/R1 amplification product contained one mutation type (HV69-70del), the S-F2/R2 amplification product contained five mutation types (K417N, E484K, E484Q, N501Y, and L452R), and the S-F3/R3 amplification product contained three mutation types (D614G, P681H, and P681R). 2021 Microbiology spectrum Method SARS_CoV_2 E484K;E484Q;L452R;N501Y;P681H;P681R;D614G;K417N 148;155;173;162;258;269;251;141 153;160;178;167;263;274;256;146 34794434 SARS-CoV-2 exposure in Malawian blood donors: an analysis of seroprevalence and variant dynamics between January 2020 and July 2021. SARS-CoV-2-pseudotyped lentiviruses were prepared by co-transfecting the HEK 293T cell line with either the SARS-CoV-2 original spike (D614G) or the SARS-CoV-2 beta spike (L18F, D80A, D215G, K417N, E484K, N501Y, D614G, A701V, 242-244 del) plasmids in conjunction with a firefly luciferase encoding pNL4 lentivirus backbone plasmid. 2021 BMC medicine Method SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;N501Y;D614G;L18F 219;184;212;178;198;191;205;135;172 224;189;217;182;203;196;210;140;176 S;S 128;165 133;170 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. A UNIQUE MUTATION SITE FOR DELTA VARIANT: T478K. 2021 Immune network Method SARS_CoV_2 T478K 42 47 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. Among them E484Q and L452R, that are present in both SARS-CoV-2 kappa, and B.1.617.3 variants of interest and alert. 2021 Immune network Method SARS_CoV_2 E484Q;L452R 11;21 16;26 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. Astonishingly, critical protein structure studies were not able to identify the unique T478K mutation site of delta variant and the common L452R mutation site of delta, epsilon, iota, kappa, and B.1.617.3 variants. 2021 Immune network Method SARS_CoV_2 L452R;T478K 139;87 144;92 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. Besides this mutation, there are two additional unique mutation sites of SARS-CoV-2 delta variant, E156del and R158G with red letters in the NTD of S1 region with no known functionality (Table 1). 2021 Immune network Method SARS_CoV_2 E156del;R158G 99;111 106;116 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. Only two mutation sites, E484K/Q and N501Y, are present in ACE2 interaction sites among 6 mutation sites in the RBM of the ten SARS-CoV-2 variants. 2021 Immune network Method SARS_CoV_2 E484K;E484Q;N501Y 25;25;37 32;32;42 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. The T478K was found within the critical receptor binding motif (RBM) of S gene suggested by Lan et al., which is indicated with a large font with a red-letter. 2021 Immune network Method SARS_CoV_2 T478K 4 9 S 72 73 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. The three unique mutation sites, E156del, R158G, and T478K in the SARS-CoV-2 delta variant must be investigated if a recent outbreak of COVID-19 depends on the mutation sites in the S gene of SARS-CoV-2 delta variant. 2021 Immune network Method SARS_CoV_2 E156del;R158G;T478K 33;42;53 40;47;58 S 182 183 COVID-19 136 144 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Investigation of E484K mutation. 2021 Infection, genetics and evolution Method SARS_CoV_2 E484K 17 22 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. A DNA insert encoding a 6xHis tag followed by a TEV protease cleavage site and SARS CoV-2 Mpro (306 amino acids) bearing an active-site C145A mutation was cloned into the pJ414 vector (ATUM) and transformed into Escherichia coli BL21(DE3) cells (Agilent). 2021 IUCrJ Method SARS_CoV_2 C145A 136 141 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. Cells were grown in Luria-Bertani medium, and the Mpro/C145A fusion protein was expressed using established protocols. 2021 IUCrJ Method SARS_CoV_2 C145A 55 60 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. Crystallization conditions for the Mpro/C145A mutant were discovered by automated high-throughput screening at the Hauptman-Woodward Medical Research Institute (Luft et al., 2003). 2021 IUCrJ Method SARS_CoV_2 C145A 40 45 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. Crystallography of the Mpro/C145A-substrate complex . 2021 IUCrJ Method SARS_CoV_2 C145A 28 33 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. Crystallography of the Mpro/C145A-substrate complex. 2021 IUCrJ Method SARS_CoV_2 C145A 28 33 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. Expression and purification of Mpro/C145A . 2021 IUCrJ Method SARS_CoV_2 C145A 36 41 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. Expression and purification of Mpro/C145A. 2021 IUCrJ Method SARS_CoV_2 C145A 36 41 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. The last residue in the TEV protease recognition sequence (ENLYFQG/S) was chosen to be a serine, such that upon cleavage the Mpro/C145A construct starts with the native N-terminal Ser1 residue. 2021 IUCrJ Method SARS_CoV_2 C145A 130 135 N 169 170 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. The Mpro/C145A-substrate structure was solved by molecular replacement using PDB entry 6wqf (Kneller, Phillips, O'Neill et al., 2020) with Phaser (McCoy et al., 2007) from CCP4. 2021 IUCrJ Method SARS_CoV_2 C145A 9 14 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. Upon completion of the cleavage and adjustment of the EDTA concentration to 0.25 mM, Mpro/C145A was collected in the flowthrough from the Ni-NTA column, concentrated and then subjected again to isocratic fractionation on Superose 12 in 25 mM Tris pH 7.6, 150 mM NaCl, 1 mM TCEP. 2021 IUCrJ Method SARS_CoV_2 C145A 90 95 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Simulations of both wild-type and D614G systems were carried out for 450 ns each. 2021 Current research in structural biology Method SARS_CoV_2 D614G 34 39 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. The D614G mutation was then introduced in all three chains of the model in UCSF Chimera. 2021 Current research in structural biology Method SARS_CoV_2 D614G 4 9 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. One-way ANOVA and Holm-Sidak's multiple comparisons test were used to analyse differences relative to the D614G reference strain. 2022 Emerging microbes & infections Method SARS_CoV_2 D614G 106 111 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. The primers used to construct the G75 V, T76I, G75V + T76I, Del246-252+D253N, L452Q, F490S, L452Q + F490S, T859N, and Lambda variant plasmids are listed in Table 1. 2022 Emerging microbes & infections Method SARS_CoV_2 F490S;F490S;G75V;G75V;L452Q;L452Q;T76I;T76I;T859N;D253N 85;100;34;47;78;92;41;54;107;71 90;105;39;51;83;97;45;58;112;76 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. For the spike N501Y general LAMP primer design, point mutation sites should be put between F2-F1, F1-B1c, or B2c-B1c sites. 2021 Analytical chemistry Method SARS_CoV_2 N501Y 14 19 S 8 13 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Both the B.1.1.7 and the B.1 strains contains the S:D614G and ORF1b:P314L mutations. 2021 eLife Method SARS_CoV_2 D614G;P314L 52;68 57;73 S 50 51 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Briefly, 13 microg/ml ACE-2-Fc was loaded on anti-human Fc capture sensors (Pall Life Sciences, California, USA) for 500 s, followed by baseline for 60 s, association to 12-point 1.5-fold serial dilutions starting at 150 nM for RBD wt, N439K, and N501Y for 500 s, and finally dissociation for another 500 s. 2021 eLife Method SARS_CoV_2 N439K;N501Y 236;247 241;252 RBD 228 231 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. The B.1.1.7 differs from the B.1 in the spike protein on positions S:N501Y, S:A570D, S:T716I, S:P681H, S:S982A, S:D1118H, S:del69/70, and S:del144/145. 2021 eLife Method SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;T716I 78;114;69;96;105;87 83;120;74;101;110;92 S;S;S;S;S;S;S;S;S 40;67;76;85;94;103;112;122;138 45;68;77;86;95;104;113;123;139 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. The Freiburg isolate FR-4286 is the Wuhan-like early European B.1 lineage containing the S:D614G, and ORF1b:P314L, as well as E:L37R. 2021 eLife Method SARS_CoV_2 D614G;L37R;P314L 91;128;108 96;132;113 E;S 126;89 127;90 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. The impact of the N439K and N501Y substitutions on the thermal stability of the RBD was analysed in triplicates on a Tycho NT.6 (NanoTemper Technologies GmbH, Munich, Germany) using a thermal ramp of 30 C/min in phosphate-buffered Saline (PBS). 2021 eLife Method SARS_CoV_2 N439K;N501Y 18;28 23;33 RBD 80 83 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. The nucleotide sequence corresponding to the SARS-CoV-2 RBD (QIC53204.1, aa R319-S593) with either an N439K or N501Y substitution and a C-terminal 10xHis-AviTag were synthesized and subcloned into pcDNA3.4-TOPO expression vectors by GeneArt (Thermo Fisher Scientific, Massachusetts, USA). 2021 eLife Method SARS_CoV_2 N439K;N501Y 102;111 107;116 RBD 56 59 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. For the generation of the R203K/G204R mutant virus, GGG AAC nucleotide substitutions were introduced into a subclone of pUC57-F7 containing the nucleocapsid gene of the SARS-CoV-2 wild-type infectious clone by overlap-extension PCR. 2021 Cell host & microbe Method SARS_CoV_2 R203K;G204R 26;32 31;37 N 144 156 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Generation of the R203K/G204R mutant virus. 2021 Cell host & microbe Method SARS_CoV_2 R203K;G204R 18;24 23;29 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. In accordance with previous findings, we also identified LG_1 (D614G), LG_2 (L84S) and LG_3 (R203K/G204R). 2021 Cell host & microbe Method SARS_CoV_2 D614G;L84S;R203K;G204R 63;77;93;99 68;81;98;104 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. In I2, R203K/G204R present an r- with LG_4, an r- with S194L, an r+ with LG_5 and an r+ with S477N ("Cor_mut.pdf" in Data S1). 2021 Cell host & microbe Method SARS_CoV_2 R203K;S194L;S477N;G204R 7;55;93;13 12;60;98;18 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. R203K/G204R show a significant positive correlation (r+) with C313T in I1, a significant negative correlation (r-) with LG_4 and an r+ with LG_6 in D. 2021 Cell host & microbe Method SARS_CoV_2 C313T;G204R;R203K 62;6;0 67;11;5 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. There is no linkage disequilibrium between D614G and R203K/G204R (rho2 = 0.043, Table S1B), suggesting the independence in evolution between R203K/G204R and D614G. 2021 Cell host & microbe Method SARS_CoV_2 D614G;D614G;R203K;R203K;G204R;G204R 43;157;53;141;147;59 48;162;58;146;152;64 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. To further understand the confounding effects of A222V (LG_4) and N501Y (LG_5) on 203K/204R, we evaluated the IF changes of the 8 combinations of these polymorphisms and identified four dominant lineages, ANR, VNR, ANK and AYK (Figure 3A). 2021 Cell host & microbe Method SARS_CoV_2 A222V;N501Y 49;66 54;71 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. We calculated CLR m/t for a 3000 bp region centered on 28881-28883 (the location of R203K/G204R). 2021 Cell host & microbe Method SARS_CoV_2 R203K;G204R 84;90 89;95 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. We first created 7-bp sequences by combining the nucleotide sequences of different strains at seven mutation sites (R203K/G204R (LG_3), N501Y (LG_5), A222V (LG_4), C313T, S477N, S194L and I120F). 2021 Cell host & microbe Method SARS_CoV_2 A222V;C313T;I120F;N501Y;S194L;S477N;R203K;G204R 150;164;188;136;178;171;116;122 155;169;193;141;183;176;121;127 34822912 Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR. Details of the primers and duel labelled probes used are previously described and used to detect the presence of the following spike protein mutations: N501Y, E484 K and L452R with K417 as reference: N501Y, E484 K, K417 and L452R. 2022 Journal of virological methods Method SARS_CoV_2 E484K;E484K;L452R;L452R;N501Y;N501Y 159;207;170;224;152;200 165;213;175;229;157;205 S 127 132 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. A B.1.617.2/Delta isolate (strain TKYTK1734; GISAID ID: EPI_ISL_2378732) and a D614G-bearing B.1.1 isolate (strain TKYE610670; GISAID ID: EPI_ISL_479681) were isolated from SARS-CoV-2-positive individuals in Japan. 2022 Nature Method SARS_CoV_2 D614G 79 84 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. A plasmid expressing the SARS-CoV-2 S D614G/P681R mutant was generated by site-directed mutagenesis PCR using pC-SARS2-S D614G as the template and the following primers: P681R Fw, 5'-CCAGACCAACAGCCGGAGGAGGGCAAGGTCT-3' and P681R Rv, 5'-AGACCTTGCCCTCCTCCGGCTGTTGGTCTGG-3'. 2022 Nature Method SARS_CoV_2 D614G;D614G;P681R;P681R;P681R 38;121;170;222;44 43;126;175;227;49 S;S 36;119 37;120 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Chemiluminescence was detected using SuperSignal West Femto Maximum Sensitivity Substrate (Thermo Fisher Scientific, 34095) or Western BLoT Ultra Sensitive HRP Substrate (Takara, T7104A) according to the manufacturer's instructions. 2022 Nature Method SARS_CoV_2 T7104A 179 185 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. DNA fragments including the inserted mutations were obtained by RT-PCR using PrimeSTAR GXL DNA polymerase (Takara, R050A) and the following primers: WK-521 23339-23364 forward, 5'-GGTGGTGTCAGTGTTATAACACCAGG-3'; and WK-521 24089-24114 reverse, 5'-CAAATGAGGTCTCTAGCAGCAATATC-3'. 2022 Nature Method SARS_CoV_2 R050A 115 120 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. For the clinical isolates (a B.1.617.2/Delta isolate (strain TKYTK1734; GISAID ID: EPI_ISL_2378732) and a D614G-bearing B.1.1 isolate (strain TKYE610670; GISAID ID: EPI_ISL_479681)), the detected variants that were present in the original sequences were excluded. 2022 Nature Method SARS_CoV_2 D614G 106 111 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. For virological examinations, four hamsters per group were intranasally infected with the D614G or the D614G/P681R viruses (104 TCID50 in 30 mul); at 3 and 7 d.p.i., the hamsters were euthanized, and nasal turbinates and lungs were collected. 2022 Nature Method SARS_CoV_2 D614G;D614G;P681R 90;103;109 95;108;114 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. four hamsters per group were intranasally inoculated with the D614G or the D614G/P681R viruses (104 TCID50 in 30 mul) under isoflurane anaesthesia. 2022 Nature Method SARS_CoV_2 D614G;D614G;P681R 62;75;81 67;80;86 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. However, the S protein of this viral sequence (GISAID ID: EPI_ISL_2220643) possesses neither L452R nor P681R mutations, both of which are features of the B.1.617 lineage. 2022 Nature Method SARS_CoV_2 L452R;P681R 93;103 98;108 S 13 14 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. In brief, nine DNA fragments encoding the partial genome of SARS-CoV-2 (strain WK-521, PANGO lineage A; GISAID ID: EPI_ISL_408667) were prepared by PCR using PrimeSTAR GXL DNA polymerase (Takara, R050A). 2022 Nature Method SARS_CoV_2 R050A 196 201 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Plasmids expressing the SARS-CoV-2 S proteins of parental D614G (pC-SARS2-S D614G), B.1.1.7/Alpha (pC-SARS2-S Alpha), B.1.351/Beta (pC-SARS2-Beta) and B.1.617.2/Delta (pC-SARS2-S Delta) were prepared in a previous study. 2022 Nature Method SARS_CoV_2 D614G;D614G 58;76 63;81 S;S;S;S 35;74;108;177 36;75;109;178 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Qualitative and semiquantitative visual image analysis of the lungs was performed in three uninfected Syrian hamsters and the hamsters infected with D614G (n = 4) or D614G/P681R (n = 4) viruses at 7 d.p.i. 2022 Nature Method SARS_CoV_2 D614G;D614G;P681R 149;166;172 154;171;177 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. The viral particles that were pseudotyped with D614G S or D614G/P681R S were incubated with serial dilutions of heat-inactivated human serum samples or three receptor-binding-domain-targeting neutralizing antibodies (8A5, Elabscience, E-AB-V1021; 4A3, Elabscience, E-AB-V1024; and CB6, Elabscience, E-AB-V1028) at 37 C for 1 h. 2022 Nature Method SARS_CoV_2 D614G;D614G;P681R 47;58;64 52;63;69 S;S 53;70 54;71 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. To generate recombinant SARS-CoV-2 mutants, mutations were inserted in fragment 8 (Supplementary Table 3) using the GENEART site-directed mutagenesis system (Thermo Fisher Scientific, A13312) according to the manufacturer's protocol with the following primers: Fragment 8_S D614G forward, 5'-CCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTG-3'; Fragment 8_S D614G reverse, 5'-CAGGGACTTCTGTGCAGTTAACACCCTGATAAAGAACAGCAACCTGG-3'; Fragment 8_S P681R forward, 5'-AGACTCAGACTAATTCTCGTCGGCGGGCACGTAGTGTA-3'; and Fragment 8_S P681R reverse, 5'-TACACTACGTGCCCGCCGACGAGAATTAGTCTGAGTCT-3', according to the manufacturer's protocol. 2022 Nature Method SARS_CoV_2 D614G;D614G;P681R;P681R 274;357;440;518 279;362;445;523 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. ACE2 E37A, ACE2 D38A, and ACE2 D37A/D38A mutations were introduced by Splice-verlap Extention PCR using the Thermo scientific Phusion High-Fidelity PCR Kit and subcloned into a pCG-expression construct. 2021 Nature communications Method SARS_CoV_2 D37A;D38A;E37A;D38A 31;16;5;36 35;20;9;40 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Cloning and reconstitution of rec-SARS-CoV-2 d6-YFP and d6-YFP-R403T. 2021 Nature communications Method SARS_CoV_2 R403T 63 68 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. For virus reconstitution, a co-culture of HEK293T cells stably expressing either ACE2 (Hoffmann, 2020; PMID: 32142651; cloned into pLV-EF1a-IRES-Blast, addgene #85133) or the viral N protein (amplified from patient material; cloned into pLV-EF1a-Blast) and T7-RNA polymerase (amplified from pCAGT7, kind gift from Marco Thomas; cloned into pLV-EF1a-IRES-Puro, addgene #85132) was transfected with pBelo-S-CoV-2-d6-YFP or d6-YFP_Spike R403T using GenJet Reagent (II) (SL100489, SignaGen Laboratories, Frederick, MD, USA) according to the manufacturer's protocol. 2021 Nature communications Method SARS_CoV_2 R403T 434 439 N 181 182 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. The SARS-CoV-2 S R403T and RaTG13 S T403R/T403A mutant plasmids were generated using Q5 Site-Directed Mutagenesis Kit (NEB). 2021 Nature communications Method SARS_CoV_2 R403T;T403R;T403A 17;36;42 22;41;47 S;S 15;34 16;35 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. The spike R403T point mutation was generated by two-step Lambda-Red Recombination using pBSCoV2_d6-YFP as template, resulting in pBSCoV2_d6-YFP_Spike R403T. 2021 Nature communications Method SARS_CoV_2 R403T;R403T 10;150 15;155 S 4 9 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. To analyze growth kinetics, Caco-2 cells were infected with either SARS-CoV-2 d6-YFP wild type, SARS-CoV-2 d6-YFP R403T, or mock at an MOI of 0.005 or 0.02. 2021 Nature communications Method SARS_CoV_2 R403T 114 119 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. Briefly, 0.1 mug/mL biotinylated SARS-CoV-2 spike S1 (Cat: 40591-V08H-B; Sino Biological) was incubated with 1 mug/mL recombinant mAb or a human ACE2-Fc fusion protein (Cat fc-hace2: Invivogen, San Diego, CA, USA) at 37 oC for one hour. 2021 Diagnostics (Basel, Switzerland) Method SARS_CoV_2 V08H 65 69 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. The following S1 antigens were obtained from Sino Biological, Chesterbrook, PA: Wuhan-Hu-1 S1 (L): SARS-CoV-2 (2019-nCoV) Spike S1-His Recombinant Protein (Cat: 40591-V08H); Wuhan-Hu-1 S1 with D614G: SARS-CoV-2 (2019-nCoV) Spike S1 (D614G)-His Recombinant Protein (Cat: 40591-V08H3); Wuhan-Hu-1 RBD (L): SARS-CoV-2 (2019-nCoV) Spike RBD-His Recombinant Protein (Cat: 40592-V08H); alpha S1 (B.1.1.7, UK): SARS-CoV-2 (2019-nCoV) Spike S1(HV69-70 deletion, Y144 deletion, N501Y, A570D, D614G, P681H)-His Recombinant Protein (Cat: 40591-V08H12); beta S1 (B.1.351, South Africa), only RBD and D614G changes: SARS-CoV-2 (2019-nCoV) Spike S1(K417N, E484K, N501Y, D614G)-His Recombinant Protein (Cat: 40591-V08H10); beta S1 (B.1.351, South Africa): SARS-CoV-2 (2019-nCoV) Spike S1 (L18F, D80A, D215G, LAL242-244 deletion, R246I, K417N, E484K, N501Y, D614G)-His Recombinant Protein (Cat# 40591-V08H15); gamma RBD (P.1, Brazil/Japan): SARS-CoV-2 (2019-nCoV) Spike RBD (K417T, E484K, N501Y) Protein (His Tag) (Cat: 40592-V08H86); gamma S1 (P.1, Brazil/Japan): SARS-CoV-2 (2019-nCoV) Spike S1 (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y) Protein (His Tag) (Cat# 40591-V08H14); epsilon S1 (B.1.429, California): SARS-CoV-2 (2019-nCoV) Spike S1 (W152C, L452R, D614G) Protein (His Tag) (Cat: 40591-V08H17); kappa RBD (B.1.617.1, India): SARS-CoV-2 (2019-nCoV) Spike RBD (L452R, E484Q) Protein (His Tag) (Cat# 40592-V08H88); delta RBD (B.1.617.2, India): SARS-CoV-2 Spike RBD (L452R, T478K) Protein (His Tag) (Cat# 40592-V08H90); N501Y (alpha) RBD: SARS-CoV-2 (2019-nCoV) Spike RBD (N501Y)-His Recombinant Protein (Cat# 40592-V08H82); E484K RBD: SARS-CoV-2 (2019-nCoV) Spike RBD(E484K)-His Recombinant Protein (Cat# 40592-V08H84); K417N RBD: SARS-CoV-2 (2019-nCoV) Spike RBD (K417N)-His Recombinant Protein (Cat# 40592-V08H59); Wuhan-Hu-1 S1 (L) biotinylated: SARS-CoV-2 (2019-nCoV) Spike S1-His Recombinant Protein, Biotinylated (Cat: 40591-V08H-B). 2021 Diagnostics (Basel, Switzerland) Method SARS_CoV_2 A570D;D138Y;D215G;D614G;D614G;D614G;D614G;D614G;D614G;D614G;D80A;E484K;E484K;E484K;E484K;E484K;E484Q;H655Y;K417N;K417N;K417T;L452R;N501Y;N501Y;N501Y;N501Y;N501Y;N501Y;P26S;P681H;R190S;R246I;T20N;T478K;D614G;E484K;K417N;K417N;K417T;L18F;L18F;L452R;L452R;N501Y;W152C;V08H;V08H;V08H;V08H;V08H 476;1100;786;193;483;588;656;842;1135;1269;780;642;828;966;1121;1642;1386;1142;821;1738;1114;1262;469;649;835;973;1128;1537;1094;490;1107;814;1088;1491;233;1686;635;1783;959;774;1082;1379;1484;1590;1255;167;373;1949;1729;1826 481;1105;791;198;488;593;661;847;1140;1274;784;647;833;971;1126;1647;1391;1147;826;1743;1119;1267;474;654;840;978;1133;1542;1098;495;1112;819;1092;1496;238;1691;640;1788;964;778;1086;1384;1489;1595;1260;171;377;1953;1733;1830 S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD 122;223;327;427;626;764;948;1072;1245;1368;1473;1579;1676;1772;1890;295;333;580;900;954;1321;1374;1438;1479;1551;1585;1648;1682;1744;1778 127;228;332;432;631;769;953;1077;1250;1373;1478;1584;1681;1777;1895;298;336;583;903;957;1324;1377;1441;1482;1554;1588;1651;1685;1747;1781 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. The S1 protein (Wuhan-Hu-1 S1 (L): SARS-CoV-2 (2019-nCoV) Spike S1-His Recombinant Protein (Cat: 40591-V08H)) was immobilized on a nitrilotriacetic acid (NTA) sensor chip following EDTA conditioning. 2021 Diagnostics (Basel, Switzerland) Method SARS_CoV_2 V08H 103 107 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. Infections were carried out with viral stocks produced from two Colombian SARS-CoV-2 isolates: D614G strain (EPI_ISL_536399) and Delta variant (EPI_ISL_5103929). 2021 Molecules (Basel, Switzerland) Method SARS_CoV_2 D614G 95 100 34834983 High Individual Heterogeneity of Neutralizing Activities against the Original Strain and Nine Different Variants of SARS-CoV-2. Eleven patients were infected by spike D614G-harbouring B lineage strains that spread during the first wave of COVID-19 infections in France, 9 were infected by the Marseille-4/B.1.160 variant, 10 were infected by the Alpha variant, and 12 were infected by the Beta/B.1.351.2 variant. 2021 Viruses Method SARS_CoV_2 D614G 39 44 S 33 38 COVID-19 111 130 34834984 Macrophages and Monocytes: "Trojan Horses" in COVID-19. SARS-CoV-2 strains, including the wild type Chinese-derived strain (D614, lineage A), Italian strain PV10734 (D614G, lineage B.1.1) and Alpha variant (lineage B.1.1.7), were isolated at 33 C from infected patients' nasal swabs in the permissive VERO E6 (VERO C1008 (Vero 76, clone E6, Vero E6; ATCC1CRL-1586TM) cell line. 2021 Viruses Method SARS_CoV_2 D614G 110 115 34835101 Impact of the Double Mutants on Spike Protein of SARS-CoV-2 B.1.617 Lineage on the Human ACE2 Receptor Binding: A Structural Insight. The L452R and T478R substitutions were performed for the delta variant. 2021 Viruses Method SARS_CoV_2 L452R;T478R 4;14 9;19 34835288 Antibody Titer Kinetics and SARS-CoV-2 Infections Six Months after Administration with the BNT162b2 Vaccine. Three clinical isolates of SARS-CoV-2 were obtained and propagated in Vero E6 cells as previously described: D614G (hCoV-19/Italy/UniSR1/2020; GISAID Accession ID: EPI_ISL_413489), B.1.1.7 (Alpha) (19/Italy/LOM-UniSR7/2021; GSAID Accession ID: EPI_ISL_1924880), B.1.351 (Beta) (hCoV-19/Italy/LOM-UniSR6/2021, GISAID Accession ID: EPI_ISL_1599180). 2021 Vaccines Method SARS_CoV_2 D614G 109 114 34840498 Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021. Besides, the mapping of D614G mutation from the isolates derived from the database was also performed in this study based of the study from Korber et al. 2021 Bulletin of the National Research Centre Method SARS_CoV_2 D614G 24 29 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Then, homology modeling of the mutated NSP2 (I120F) was carried out. 2021 Current research in microbial sciences Method SARS_CoV_2 I120F 45 50 Nsp2 39 43 34842604 Fc-Independent Protection from SARS-CoV-2 Infection by Recombinant Human Monoclonal Antibodies. 10256-H08S, Sino Biological, Beijing, China) were used to coat 96-well plates at 2 microg/mL. 2021 Antibodies (Basel, Switzerland) Method SARS_CoV_2 H08S 6 10 34842604 Fc-Independent Protection from SARS-CoV-2 Infection by Recombinant Human Monoclonal Antibodies. CT009-H08H; ranging from 75 to 300 nM) in pH 6.0, for 60 s (association phase) and transferred to buffer-containing wells for an additional 60 s (dissociation phase). 2021 Antibodies (Basel, Switzerland) Method SARS_CoV_2 H08H 6 10 34842604 Fc-Independent Protection from SARS-CoV-2 Infection by Recombinant Human Monoclonal Antibodies. For that matter, additional three mutations were inserted into the Fc sequence, aiming at disrupting the N-linked glycosylation motif Asn-X-Ser/Thr (N297G/S298G/T299A). 2021 Antibodies (Basel, Switzerland) Method SARS_CoV_2 N297G;S298G;T299A 149;155;161 154;160;166 N 105 106 34843105 SARS-CoV-2 Neutralization in Convalescent Plasma and Commercial Lots of Plasma-Derived Immunoglobulin. SARS-CoV-2 D614G (Human 2019-nCoV ex China_BavPat1/2020_Germany ex China, GISAID ID: EPI_ISL_406862) was kindly provided by Prof. 2022 BioDrugs Method SARS_CoV_2 D614G 11 16 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. cerevisiae harboring the various RBD display plasmids were grown in 1ml M19D (5 g/l casamino acids, 40 g/l dextrose, 80 mM MES free acid, 50 mM citric acid, 50 mM phosphoric acid, 6.7 g/l yeast nitrogen base, adjusted to pH7 with 9M NaOH, 1M KOH) overnight at 30 C. 2021 bioRxiv Method SARS_CoV_2 M19D 72 76 RBD 33 36 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. Expression was induced by resuspending the M19D culture to OD600=1 in M19G (5 g/l casamino acids, 40 g/l galactose, 80 mM MES free acid, 50 mM citric acid, 50 mM phosphoric acid, 6.7 g/l yeast nitrogen base, adjusted to pH7 with 9M NaOH, 1M KOH) and growing 22 h at 22 C with shaking at 300 rpm. 2021 bioRxiv Method SARS_CoV_2 M19D;M19G 43;70 47;74 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. pastoris do contain the N343 glycan that was removed from designs optimized for yeast surface display via an N343Q mutation. 2021 bioRxiv Method SARS_CoV_2 N343Q 109 114 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. pastoris plasmids by Q5 site-directed mutagenesis (NEB) using primers Q343N_SDM_WT_D1_D3_F and Q343N_SDM_R. 2021 bioRxiv Method SARS_CoV_2 Q343N;Q343N 70;95 75;100 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. pJS699 (Wuhan-Hu-1 S-RBD(333-537)-N343Q for fusion to the C-terminus of AGA2) was previously described (Banach et al. 2021 bioRxiv Method SARS_CoV_2 N343Q 34 39 RBD;S 21;19 24;20 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. To visualize the N343 glycan, samples were incubated for 1 h at 37 C with 1 mul Endo H in GlycoBuffer 3 (NEB P0702S) after denaturing in SDS sample buffer prior to running SDS-PAGE. 2021 bioRxiv Method SARS_CoV_2 P0702S 109 115 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. coli (NEB Cat#: C3040H) or DH5alpha cells and for DNA transformation. 2021 bioRxiv Method SARS_CoV_2 C3040H 16 22 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. The ORF3a mutant variants (Q57H and DeltaG188) were generated by overlapping PCR with mutant-specific primers (Table S1) and cloned onto the same pLVX-EF1alpha-IRES-Puro plasmid via Gibson assembly method. 2021 bioRxiv Method SARS_CoV_2 DeltaG188;Q57H 36;27 45;31 ORF3a 4 9 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. After washing with M199 media, groups of 30 cumulus-oocyte complexes (COCs) selected randomly were cultured in 500 muL in vitro maturation (IVM) medium (M199 medium containing 0.3% bovine serum albumin (BSA), 0.23 mM sodium pyruvate, 2 mM L-Glutamine, 100 unit/mL penicillin, 100 unit/mL streptomycin) with different concentrations of N501Y (0 mug/ml, 20 mug/ml, or 50 mug/ml) at 37 C, 5% CO2. 2021 Reproductive sciences (Thousand Oaks, Calif.) Method SARS_CoV_2 N501Y 335 340 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. In the present study, the treatment of N501Y was divided into three groups with the final concentration of 0 mug/ml (vehicle control, named control), 20 mug/ml, and 50 mug/ml in the culture medium. 2021 Reproductive sciences (Thousand Oaks, Calif.) Method SARS_CoV_2 N501Y 39 44 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. N501Y Treatment. 2021 Reproductive sciences (Thousand Oaks, Calif.) Method SARS_CoV_2 N501Y 0 5 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. One hundred mug N501Y recombinant protein (Sino Biological Inc., Cat: 40,592-V05H, Beijing, China) were dissolved in 400 mul of sterile water. 2021 Reproductive sciences (Thousand Oaks, Calif.) Method SARS_CoV_2 N501Y;V05H 16;77 21;81 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. From this, non-synonymous and functionally meaningful point-mutations present in VOI or VOC are used here to define 'mutations of concern', such as E484K. 2021 Microbial genomics Method SARS_CoV_2 E484K 148 153 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Screening for E484K and N501Y mutations was done by RT-qPCR, using module 2 of the MUT-SARS-CoV-2 kit (Genes2Life SAPI de CV) simultaneously in the same reaction using RNA previously identified as positive for SARS-CoV-2, as previously described. 2021 Microbial genomics Method SARS_CoV_2 E484K;N501Y 14;24 19;29 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Thus, detection and discrimination are carried out in a fourplex assay, the channels being for the FAM and HEX dyes dedicated to detection of wildtype background; and the Cal Fluor Red 610 and Quasar 670 dye channels used for detection of the E484K and N501Y mutations, respectively. 2021 Microbial genomics Method SARS_CoV_2 E484K;N501Y 243;253 248;258 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. We marked the important mutations S477N, T478K, E484K, D614G, P681H/R and T732A. 2021 Microbial genomics Method SARS_CoV_2 D614G;E484K;P681H;P681R;S477N;T478K;T732A 55;48;62;62;34;41;74 60;53;69;69;39;46;79 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. K417N, E484K, and N501Y). 2021 Nature communications Method SARS_CoV_2 E484K;N501Y;K417N 7;18;0 12;23;5 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. K417T, E484K, and N501Y) while the Kappa variant presents only two mutations. 2021 Nature communications Method SARS_CoV_2 E484K;N501Y;K417T 7;18;0 12;23;5 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. L452R and E484Q) in their RBD domain. 2021 Nature communications Method SARS_CoV_2 E484Q;L452R 10;0 15;5 RBD 26 29 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. N501Y) in their RBD domain, while Beta has three mutations. 2021 Nature communications Method SARS_CoV_2 N501Y 0 5 RBD 16 19 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. Designing HV69/70-Deletion-, E484K-, and N501Y-Specific RT-qPCR Assays. 2021 Analytical chemistry Method SARS_CoV_2 E484K;N501Y 29;41 34;46 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. SARS-CoV-2 HV69/70-, E484K-, and N501Y-Specific RT-qPCR Assays. 2021 Analytical chemistry Method SARS_CoV_2 E484K;N501Y 21;33 26;38 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. The HV69/70-, E484K-, and N501Y-specific assays were performed using the Bio-Rad CFX96 real-time PCR System (Bio-Rad Laboratories, California, USA). 2021 Analytical chemistry Method SARS_CoV_2 E484K;N501Y 14;26 19;31 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. The HV69/70-, E484K-, and N501Y-specific RT-qPCR assays were transferred to the peakPCR platform (Diaxxo AG, Zurich, Switzerland) on which FAM-labeled probes detected the mutated sequence variations only. 2021 Analytical chemistry Method SARS_CoV_2 E484K;N501Y 14;26 19;31 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. We developed assays targeting the HV69/70-deletion, the E484K-, and N501Y-single-nucleotide polymorphisms (SNPs). 2021 Analytical chemistry Method SARS_CoV_2 E484K;N501Y 56;68 61;73 34855904 Niclosamide shows strong antiviral activity in a human airway model of SARS-CoV-2 infection and a conserved potency against the Alpha (B.1.1.7), Beta (B.1.351) and Delta variant (B.1.617.2). Briefly, human bronchial epithelial cells were apically infected with the European D614G strain of SARS-CoV-2 (BavPat1 D614G) at a multiplicity of infection (MOI) of 0.1 and cultivated in basolateral media that contained different concentrations of niclosamide ethanolamine (in duplicates) or no drug (virus control) for up to 4 days (treatment pre-infection and once daily post-infection). 2021 PloS one Method SARS_CoV_2 D614G;D614G 83;119 88;124 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. From the WT RBD structure, each variant was modeled with the following mutations: Alpha (N501Y), Beta (K417N, E484K, N501Y), Gamma (K417T, E484K, N501Y), Epsilon (L452R), Kappa (L452R, E484Q), and Delta (L452R, T478K). 2021 Journal of chemical theory and computation Method SARS_CoV_2 E484K;E484K;E484Q;N501Y;N501Y;T478K;K417N;K417T;L452R;L452R;L452R;N501Y 110;139;185;117;146;211;103;132;163;178;204;89 115;144;190;122;151;216;108;137;168;183;209;94 RBD 12 15 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. The recombinant human ACE2 protein (GenBank accession: AF291820.1, Sino Biological 10108-H08H; Wayne, PA) was labeled with RED-NHS (second Generation) dye using the Monolith Protein Labeling Kit (NanoTemper Technologies, MO-L011, Munchen, Germany). 2021 Journal of chemical theory and computation Method SARS_CoV_2 H08H 89 93 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Furin inhibitor (Decanoyl-RVKR-CMK) was from R&D Systems (Bristol, UK, Cat#: 3501) Cathepsin inhibitor (E64D) was from Apexbio (Shanghai, China, Cat#: A1903). 2022 Emerging microbes & infections Method SARS_CoV_2 E64D 104 108 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. Then, samples were incubated for 1 h at 37 C with an equal volume of a SARS-CoV-2 33782CL-SARS-CoV-2 strain (lineage B, D614G), Alpha (B.1.1.7), Gamma (P.1) and Delta (B.1.617.2) variants. 2021 Frontiers in immunology Method SARS_CoV_2 D614G 120 125 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. Occurrence of D614G mutation over time was visualized using NextStrain platform where data is enabled from the GISAID. 2021 Frontiers in genetics Method SARS_CoV_2 D614G 14 19 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. The D614G variant carrying the spike protein amino acid change at 614D to G, SARS-CoV-2/Massachusetts/VPT1/2020 (MA/VPT1), was isolated from Vero E6 cells from a nasopharyngeal specimen collected in April 2020. 2021 Frontiers in chemistry Method SARS_CoV_2 D614G;D614G 66;4 75;9 S 31 36 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. The LC-MS/MS spectra were searched against the FASTA sequence of the spike protein of the SARS-CoV-2 original virus or the D614G variant using Byos (Version 3.10; Protein Metrics Inc.). 2021 Frontiers in chemistry Method SARS_CoV_2 D614G 123 128 S 69 74 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. The PNGase F-treated WA1 and D614G peptides were dried by speed vacuum and resuspended in 20 mul of 10 mM TEAB. 2021 Frontiers in chemistry Method SARS_CoV_2 D614G 29 34 34869681 Arterial and Venous Thrombosis Complicated in COVID-19: A Retrospective Single Center Analysis in Japan. As the proportion of SARS-CoV-2 variants carrying either N501Y, E484K, and L452R mutations was expanded, RT-PCR was performed using VirSNiP SARS-CoV-2 (TIB Molbiol, Berlin, Germany). 2021 Frontiers in cardiovascular medicine Method SARS_CoV_2 E484K;L452R;N501Y 64;75;57 69;80;62 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Single mutations Ala222Val, Tyr265Cys, and Asp614Gly were introduced to the spike glycoprotein structure via Visual Molecular Dynamics (VMD) software with a Mutator Plugin. 2021 PloS one Method SARS_CoV_2 A222V;D614G;Y265C 17;43;28 26;52;37 S 76 94 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Single mutations Ala222Val, Tyr265Cys, and Asp614Gly, were introduced to the structure using the CHARMM-GUI Solution Builder module. 2021 PloS one Method SARS_CoV_2 A222V;D614G;Y265C 17;43;28 26;52;37 34871906 Highly sensitive and specific detection of the SARS-CoV-2 Delta variant by double-mismatch allele-specific real time reverse transcription PCR. Some of these individual mutations are shared by other variants but we noted that the combination of spike mutations L452R and T478K (nucleotide positions T22917G and C22995A, respectively) within the receptor binding domain can effectively differentiate Delta from other variants. 2022 Journal of clinical virology Method SARS_CoV_2 C22995A;L452R;T22917G;T478K 167;117;155;127 174;122;162;132 RBD;S 201;101 224;106 34871906 Highly sensitive and specific detection of the SARS-CoV-2 Delta variant by double-mismatch allele-specific real time reverse transcription PCR. The following samples were obtained: IC19 (hCoV-19/England/IC19/2020 EPI_ISL_475572 2020-03-17), a B.1 lineage virus with the D614G spike mutation but otherwise the same as the original "wild-type" Wuhan virus. 2022 Journal of clinical virology Method SARS_CoV_2 D614G 126 131 S 132 137 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. The sequences of the two proteins include mutated furin cleavage site and K986P, V987P substitutions. 2021 Scientific reports Method SARS_CoV_2 K986P;V987P 74;81 79;86 34886945 Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020. The second stream was the detections of the D614G mutation, where Zd D and Zd G are the number of SARS-CoV-2 isolates among reconstructed phylogenetic clusters sampled on day d with D614 and G614, respectively (Figure 1). 2021 Euro surveillance Method SARS_CoV_2 D614G 44 49 34886945 Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020. We assumed that the mutation D614G was the only site of interest that characterised the two cocirculating strains, but their differential transmissibility (if any) might be attributable to the combination of D614G and other mutations. 2021 Euro surveillance Method SARS_CoV_2 D614G;D614G 29;208 34;213 34888394 A Multidimensional Cross-Sectional Analysis of Coronavirus Disease 2019 Seroprevalence Among a Police Officer Cohort: The PoliCOV-19 Study. The viral strain consisting of the mutation D614G in the S protein (Nextstrain clade 20A and its descendants) was the dominating circulating variant in 2020 in Switzerland. 2021 Open forum infectious diseases Method SARS_CoV_2 D614G 44 49 S 57 58 34888394 A Multidimensional Cross-Sectional Analysis of Coronavirus Disease 2019 Seroprevalence Among a Police Officer Cohort: The PoliCOV-19 Study. We used isogenic SARS-CoV-2 viruses harboring either the D614G spike, the full-length B.1.1.7 spike (Alpha variant), or the full-length B.1.351 spike (Beta variant). 2021 Open forum infectious diseases Method SARS_CoV_2 D614G 57 62 S;S;S 63;94;144 68;99;149 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. All samples with N501Y, D614G, and 69/70 deletion mutations were detected. 2022 Biosensors & bioelectronics Method SARS_CoV_2 D614G;N501Y 24;17 29;22 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. In addition, as a single-base mutation of D614G and N501Y, an additional mismatch was introduced in the seed region of their crRNA-W and crRNA-M to enhance the differentiability between the WT and MT variants (Table S2). 2022 Biosensors & bioelectronics Method SARS_CoV_2 D614G;N501Y 42;52 47;57 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. The DNA targets of WT S gene and MT SARS-CoV-2 (covering D614G, N501Y and 69/70 deletion sites) were synthesized (Table S4) and then cloned into pUC57 plasmid. 2022 Biosensors & bioelectronics Method SARS_CoV_2 D614G;N501Y 57;64 62;69 S 22 23 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. High resolution melting was used for the qualitative detection of p.N501Y and p.E484K mutations in the SARS-CoV-2 genome. 2021 PloS one Method SARS_CoV_2 E484K;N501Y;E484K;N501Y 78;66;80;68 85;73;85;73 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.E484K is associated with a shift from 52 C to 57 C while p.N501Y is associated with a shift from 60 C to 65 C. 2021 PloS one Method SARS_CoV_2 N501Y;E484K;N501Y;E484K 59;2;61;0 66;7;66;7 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. The D614G variant data were taken from the Los Alamos COVID-19 Viral Genome Analysis Pipeline on 17 June 2021. 2021 Nature communications Method SARS_CoV_2 D614G 4 9 COVID-19 54 62 34909775 Intranasal immunization with a vaccinia virus vaccine vector expressing pre-fusion stabilized SARS-CoV-2 spike fully protected mice against lethal challenge with the heavily mutated mouse-adapted SARS2-N501Y MA30 strain of SARS-CoV-2. Green, G418R plaques were picked at 48 hours post infection, following the addition of an agarose overlay. 2021 bioRxiv Method SARS_CoV_2 G418R 7 12 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. Constructs encoding N- and C-terminal flag-tagged SARS-CoV-2 spike (S) for each variant : D614G, Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2) : were synthesized and cloned into pcDNA3.1 vector using KpnI/BamHI restriction enzyme cloning by GenScript BioTech (Piscataway, NJ). 2021 bioRxiv Method SARS_CoV_2 D614G 90 95 S;N;S 61;20;68 66;21;69 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. Pseudotyped lentivirus was produced by co-transfection of HEK293T cells with pNL4-3-HIV-1-inGluc and pcDNA3.1 vector expressing the spike of interest (D614G, B.1.1.7, B.1.351, or B.1.617.2) in a 2:1 ratio using polyethylenimine (PEI) transfection. 2021 bioRxiv Method SARS_CoV_2 D614G 151 156 S 132 137 34909788 SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection. P2 stock was sequenced and confirmed Omicron with the following substitutions: E:T9I,M:D3G,M:Q19E,M:A63T,N:P13L,N:R203K,N:G204R,ORF1a:K856R,ORF1a:L2084I,ORF1a:A2710T,ORF1a:T3255I,ORF1a:P3395H,ORF1a:I3758V,ORF1b:P314L,ORF1b:I1566V,ORF9b:P10S,S:A67V,S:T95I,S:Y145D,S:L212I,S:G339D,S:R346K,S:S371L,S:S373P,S:S375F,S:K417N,S:N440K,S:G446S,S:S477N,S:T478K,S:E484A,S:Q493R,S:G496S,S:Q498R,S:N501Y,S:Y505H,S:T547K,S:D614G,S:H655Y,S:N679K,S:P681H,S:N764K,S:D796Y,S:N856K,S:Q954H,S:N969K,S:L981F. 2021 medRxiv Method SARS_CoV_2 A2710T;A63T;A63N;A67V;A67S;D3G;D3M;D614G;D796Y;D796S;E484A;E484S;G204R;G339D;G339S;G446S;G496S;H655Y;H655S;I1566V;I3758V;K417N;K417S;K856R;L2084I;L212I;L212S;L981F;N440K;N440S;N501Y;N501S;N679K;N679S;N764K;N764S;N856K;N856S;N969K;N969S;P10S;P13L;P13N;P314L;P3395H;P681H;P681S;Q19E;Q19M;Q493R;Q493S;Q498R;Q498S;Q954H;Q954S;R203K;R203N;R346K;R346S;S371L;S371S;S373P;S373S;S375F;S375S;S477N;S477S;T3255I;T478K;T478S;T547K;T547S;T95I;T95S;T9I;T9M;Y145D;Y145S;Y505H;Y505S 159;100;100;243;243;87;87;409;449;449;353;353;122;273;273;329;369;417;417;223;198;313;313;134;146;265;265;481;321;321;385;385;425;425;441;441;457;457;473;473;236;107;107;211;185;433;433;93;93;361;361;377;377;465;465;114;114;281;281;289;289;297;297;305;305;337;337;172;345;345;401;401;250;250;81;81;257;257;393;393 165;104;104;247;247;90;90;414;454;454;358;358;127;278;278;334;374;422;422;229;204;318;318;139;152;270;270;486;326;326;390;390;430;430;446;446;462;462;478;480;240;111;111;216;191;438;438;97;97;366;366;382;382;470;470;119;119;286;286;294;294;302;302;310;310;342;342;178;350;350;406;406;254;254;84;84;262;262;398;398 ORF1a;ORF1a;ORF1a;ORF1a;ORF1a;ORF1a;E;N;N;N;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S 128;140;153;166;179;192;79;105;112;120;241;248;255;263;271;279;287;295;303;311;319;327;335;343;351;359;367;375;383;391;399;407;415;423;431;439;447;455;463;471;479 133;145;158;171;184;197;80;106;113;121;242;249;256;264;272;280;288;296;304;312;320;328;336;344;352;360;368;376;384;392;400;408;416;424;432;440;448;456;464;472;480 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Lastly, we studied cases that occurred in Japan, because the initial outbreak in Japan was exclusively characterized by the Wuhan reference strain until late February 2020 and a separate outbreak occurred starting early March 2020 during which approximately 95% of cases were characterized by the D614G variant. 2021 PLoS computational biology Method SARS_CoV_2 D614G 297 302 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Specifically, approximately 100% of cases in Hong Kong from February 2 to 29, 2020 were characterized by the Wuhan reference strain, and approximately 85% of cases in Brazil from March 1 to May 31, 2020 were characterized by the D614G variant. 2021 PLoS computational biology Method SARS_CoV_2 D614G 229 234 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. The dataset collected during the subsequent outbreak in the USA, from January 22 to May 30, 2020, represents cases that occurred at a time when approximately 70% of cases were characterized by the D614G variant. 2021 PLoS computational biology Method SARS_CoV_2 D614G 197 202 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. The independent study used to confirm the order of discernible symptoms in cases of the D614G variant occurred in Brazil and included up to 67,180 individuals with COVID-19. 2021 PLoS computational biology Method SARS_CoV_2 D614G 88 93 COVID-19 164 172 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Two validation datasets were collected to determine the order of symptoms of the Wuhan reference strain and the D614G variant in Hong Kong and Brazil, respectively. 2021 PLoS computational biology Method SARS_CoV_2 D614G 112 117 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. We estimated the percentage of the D614G variant and the Wuhan reference strain in our datasets using the results of a study that observed the changes in prevalence of these strains globally. 2021 PLoS computational biology Method SARS_CoV_2 D614G 35 40 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. For models of spike protein ectodomain alone, SARS-CoV-2 HexaPro S trimer with N501Y mutation (PDB code 7MJG) were docked into cryo-EM density using UCSF Chimera v.1.15. 2021 Cell reports Method SARS_CoV_2 N501Y 79 84 S;S 14;65 19;66 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The E484K and N501Y mutant complexes were built from the wild-type SARS-CoV2 RBD-ACE2 complex by mutating the glutamate to lysine at 484th residue and asparagine to tyrosine at the 501st residue, respectively, in the spike RBD region. 2022 International immunopharmacology Method SARS_CoV_2 E484K;N501Y 4;14 9;19 S;RBD;RBD 217;77;223 222;80;226 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The E484K-B38 and N501Y-B38 complexes were prepared by carrying out the specific mutations on the wild-type SARS-CoV2 RBD-B38 complex using the mutagenesis toolkit of Visual Molecular Dynamics (VMD). 2022 International immunopharmacology Method SARS_CoV_2 E484K;N501Y 4;18 9;23 RBD 118 121 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The optimized wild-type and mutant (E484K and N501Y) SARS-CoV2 RBDs complexed with ACE2 and B38 were immersed in a triclinic box filled with TIP3P water such that the minimum distance between any protein atom and box edges was > 10 A. 2022 International immunopharmacology Method SARS_CoV_2 N501Y;E484K 46;36 51;41 RBD 63 67 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. ACE2 and RBD K417N, E484K, N501Y were constructed as previously described. 2022 Cell host & microbe Method SARS_CoV_2 E484K;K417N;N501Y 20;13;27 25;18;32 RBD 9 12 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Briefly, serially diluted Ab was mixed with SARS-CoV-2 strains Victoria, Alpha, Beta, Gamma, Alpha+E484K, Delta, or B.1.525 and incubated for 1 hr at 37C. 2022 Cell host & microbe Method SARS_CoV_2 E484K 99 104 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Cloning of ACE2 and RBD K417N, E484K, N501Y. 2022 Cell host & microbe Method SARS_CoV_2 E484K;K417N;N501Y 31;24;38 36;29;43 RBD 20 23 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. E.coli DH5alpha bacteria were used for transformation of plasmid pNEO-RBD K417N, E484K, N501Y. 2022 Cell host & microbe Method SARS_CoV_2 E484K;K417N;N501Y 81;74;88 86;79;93 RBD 70 73 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Each antibody was assigned a vector containing IC50 responses against seven virus strains (Victoria, Alpha, Beta, Gamma, Delta, B.1.525, Alpha+E484K) where the responses within each virus strain were normalised using a mean of 0 and a standard deviation of 1. 2022 Cell host & microbe Method SARS_CoV_2 E484K 143 148 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. The Beta RBD-only model from crystal structure (residues 334-515) with Beta-22 was then aligned with the N501Y-mAb-222 RBD structure and combined with the mAb 222 fab. 2022 Cell host & microbe Method SARS_CoV_2 N501Y 105 110 RBD;RBD 9;119 12;122 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. The Beta virus used in these studies contained the following mutations: D80A, D215G, L242-244 deleted, K417N, E484K, N501Y, D614G, A701V. 2022 Cell host & microbe Method SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;N501Y 131;78;124;72;110;103;117 136;83;129;76;115;108;122 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. To construct RBD K417N, E484K, N501Y, the RBD N501Y construct was used as the template and K417N primers (Forward 5'-CAGGGCAGACCGGCAATATCGCCGACTACAATTAC-3', Reverse 5'-GTAATTGTAGTCGGCGATATTGCCGGTCTGCCCTG-3'), E484K primers (Forward 5'- CACCGTGTAATGGCGTGAAGGGCTTCAATTGCTAC-3', Reverse 5'- GTAGCAATTGAAGCCCTTCACGCCATTACACGGTG-3') and primers of pNEO vector (Forward 5'- CAGCTCCTGGGCAACGTGCT-3' and Reverse 5'-CGTAAAAGGAGCAACATAG-3') were used to amplify DNA fragments. 2022 Cell host & microbe Method SARS_CoV_2 E484K;E484K;K417N;K417N;N501Y;N501Y 24;209;17;91;31;46 29;214;22;96;36;51 RBD;RBD 13;42 16;45 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. To construct the expression plasmids for the S protein of Beta, a construction of trimeric S of the Wuhan strain was used as the template and nine pairs of primers of S (L18F forward primer 5'-GAGCAGCCAGTGCGTGAATTTCACCACCAGAACCCAGCTG-3', L18F reverse primer 5'-CAGCTGGGTTCTGGTGGTGAAATTCACGCACTGGCTGCTC -3'; D80A forward primer 5'-GCACCAAGAGATTCGCCAATCCTGTGCTGCC-3' and D80A reverse primer 5'-GGCAGCACAGGATTGGCGAATCTCTTGGTGC-3'; D215G forward primer 5'-ATTAATCTGGTGAGAGGCCTGCCTCAGGGCTTC-3', D215G reverse primer 5'-GAAGCCCTGAGGCAGGCCTCTCACCAGATTAAT-3'; 242-244 deletion and R246I forward primer 5'-CCAGATTCCAGACCCTGCACATATCATATCTTACACCAG-3', 242-244 deletion and R246I reverse primer 5'-CTGGTGTAAGATATGATATGTGCAGGGTCTGGAATCTGG-3'; K417N forward primer 5'-CAGGGCAGACCGGCAATATCGCCGACTACAATTAC-3', K417N reverse primer 5'-GTAATTGTAGTCGGCGATATTGCCGGTCTGCCCTG -3'; E484K forward primer 5'-CACCGTGTAATGGCGTGAAGGGCTTCAATTGCTAC-3', E484K reverse primer 5'-GTAGCAATTGAAGCCCTTCACGCCATTACACGGTG-3'; N501Y forward primer 5'-GCTTCCAGCCTACCTATGGCGTGGGCTAC-3', N501Y reverse primer 5'-GTAGCCCACGCCATAGGTAGGCTGGAAGC-3'; D614G forward primer 5'-GCCGTGCTGTACCAGGGCGTGAATTGCACCGAG-3', D614G reverse primer 5'-CTCGGTGCAATTCACGCCCTGGTACAGCACGGC-3'; A701V forward primer 5'-CACCATGAGCCTGGGCGTCGAGAATAGCGTGGCC-3', A701V reverse primer 5'-GGCCACGCTATTCTCGACGCCCAGGCTCATGGTG-3') and two primers of pHLsec vector (pHLsec forward primer 5'-CCTCAATTTGAGAAATAATGACTCGAGACTAGTATCGCG-3', pHLsec reverse primer 5'-CGCGATACTAGTCTCGAGTCATTATTTCTCAAATTGAGG-3') were used to do PCR. 2022 Cell host & microbe Method SARS_CoV_2 A701V;A701V;D215G;D215G;D614G;D614G;D80A;D80A;E484K;E484K;K417N;K417N;L18F;N501Y;N501Y;R246I;R246I;L18F 1227;1290;428;490;1103;1165;307;369;859;923;730;794;238;987;1045;573;662;170 1232;1295;433;495;1108;1170;311;373;864;928;735;799;242;992;1050;578;667;174 S;S;S 45;91;167 46;92;168 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. To determine the binding to recombinant RBD or NTD, MAXISORP immunoplates were coated with 5 mug/ml of purified recombinant RBD-K417N, E484K, N501Y or NTD at 4C overnight. 2022 Cell host & microbe Method SARS_CoV_2 E484K;N501Y;K417N 135;142;128 140;147;133 RBD;RBD 40;124 43;127 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. To express RBD, RBD K417N, E484K, N501Y and ACE2, HEK293T cells were cultured in DMEM high glucose (Sigma) supplemented with 2% FBS, 1% 100X Mem Neaa and 1% 100X L-Glutamine at 37C for transfection. 2022 Cell host & microbe Method SARS_CoV_2 E484K;K417N;N501Y 27;20;34 32;25;39 RBD;RBD 11;16 14;19 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. To generate an initial model, the deposited cryo-EM Beta 2-RBD up spike model (PDB: 7lyk) was rigid body fitted into the locally filtered map in chimera before the crystal structure of N501Y-mAb 222 (PDB: 7nx9) was initially superimposed on the upwards RBDs before rigid body fitting into the map. 2022 Cell host & microbe Method SARS_CoV_2 N501Y 185 190 S;RBD;RBD 66;59;253 71;62;257 34923570 Heterologous prime-boost immunizations with chimpanzee adenoviral vectors elicit potent and protective immunity against SARS-CoV-2 infection. pS-B.1.1.7 and pS-B.1.351 plasmids were constructed with mutant S genes expressing the spike protein of the B.1.1.7 variant (GenBank: QQH18545.1, containing the H69, V70, and Y145 deletions and N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H mutations) and B.1.351 variant (GenBank: QRI43207.1, containing the L242, A243, and L244 deletions and L18F, D80A, D215G, S305T, K417N, E484K, N501Y, D614G, and A701V mutations) using the same method. 2021 Cell discovery Method SARS_CoV_2 A570D;A701V;D1118H;D215G;D614G;D614G;D80A;E484K;K417N;L18F;N501Y;N501Y;P681H;S305T;S982A;T716I 201;408;240;362;208;397;356;383;376;350;194;390;215;369;229;222 206;413;246;367;213;402;360;388;381;354;199;395;220;374;234;227 S;S 87;64 92;65 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Dynamic behavior analysis of NSP13 WT and its mutants, P77L, Q88H, D260Y, E341D, and M429I, through molecular dynamics (MD) simulation was determined using AMBER20 using FF14SB force field. 2021 Frontiers in microbiology Method SARS_CoV_2 D260Y;E341D;M429I;P77L;Q88H 67;74;85;55;61 72;79;90;59;65 Nsp13 29 34 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Mutations, including P77L, Q88H, D260Y, E341D, and M429I, were introduced to model the mutant structures based on the structure of NSP13 WT. 2021 Frontiers in microbiology Method SARS_CoV_2 D260Y;E341D;M429I;P77L;Q88H 33;40;51;21;27 38;45;56;25;31 Nsp13 131 136 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Groups of female BALB/c mice (6 to 8 weeks old) (n=5 per group) were immunized with Ad-S, Ad-S-F135N/N137T, Ad-S-R158N/Y160T, Ad-S-N370/A372T, or Ad-S-H519N/P521T vectors at 5 x 107 plaque-forming unit (pfu) per dose in PBS (pH 7.4) in the first set of immunization experiments, and immunized with Ad-S, Ad-S-N354/K356T, Ad-S-G413N, and Ad-S-D428N vectors at 1 x 108 pfu per dose in the second set of immunization experiments. 2021 Frontiers in immunology Method SARS_CoV_2 A372T;K356T;N137T;P521T;Y160T;D428N;F135N;G413N;H519N;R158N 136;314;101;157;119;342;95;326;151;113 141;319;106;162;124;347;100;331;156;118 S;S;S;S;S;S;S;S;S 87;93;111;129;149;301;307;324;340 88;94;112;130;150;302;308;325;341 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. HEK293A cells were infected with Ad-S, Ad-S-F135N/N137T, Ad-S-R158N/Y160T, Ad-N354/K356T, Ad-S-N370/A372T, Ad-S-G413N, Ad-S-D428N and Ad-S-H519N/P521T at an MOI = 5 for 48 h, then lysed with Glo Lysis buffer (Promega), and subjected to centrifugation at 12000 x g for 5 min at 4 C to remove the cell debris. 2021 Frontiers in immunology Method SARS_CoV_2 A372T;K356T;N137T;P521T;Y160T;D428N;F135N;G413N;H519N;R158N 100;83;50;145;68;124;44;112;139;62 105;88;55;150;73;129;49;117;144;67 S;S;S;S;S;S;S 36;42;60;93;110;122;137 37;43;61;94;111;123;138 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Site-directed mutagenesis was used to produce the glycan-masking S mutant genes, with the addition of an N-linked glycosylation motif at the S protein residues 135N/N137T, R158N/Y160T, N354/K356T, N370/A372T, G413N, D428N and H519N/P521T. 2021 Frontiers in immunology Method SARS_CoV_2 D428N;G413N;H519N;R158N;A372T;K356T;N137T;P521T;Y160T 216;209;226;172;202;190;165;232;178 221;214;231;177;207;195;170;237;183 N;S;S 105;65;141 106;66;142 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. AlphaFold and Modeller were employed to generate mutant structures for Omicron and N501Y RBD. 2022 Travel medicine and infectious disease Method SARS_CoV_2 N501Y 83 88 RBD 89 92 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. To test the hypothesis and predict the tyrosine kinases that might phosphorylate the mutated Spike RBD at N501Y, several bioinformatics tools are applied. 2022 Travel medicine and infectious disease Method SARS_CoV_2 N501Y 106 111 S;RBD 93;99 98;102 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. After 1.5 min of baseline equilibration, 5 min of association was conducted at 10-100 nM S(D614G), SAlpha or SBeta, followed by 5 min of dissociation in the same buffer, which was used for baseline equilibration. 2022 Nature Method SARS_CoV_2 D614G 91 96 S 89 90 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Because the first contact hamster (cage 6) in the competition trial wt-S614G versus Alpha, died at 2 dpc, the second contact hamster for this cage was also co-housed with the donor hamster; thus the first and second contact hamsters in this cage were labelled contact 1a and contact 1b, respectively. 2022 Nature Method SARS_CoV_2 S614G 71 76 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. For SARS-CoV-2 Alpha (L4549, SARS-CoV-2 B.1.1.7 NW-RKI-I-0026/2020 passage 3), one silent mutation in the ORF1a (sequence position 11741) was determined (C to T with 27% T, 57% strand bias). 2022 Nature Method SARS_CoV_2 C27T 154 168 ORF1a 106 111 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. For SARS-CoV-2 Beta (L4550, available under ENA study accession number MZ433432), one nucleotide exchange was detected (A12022C) resulting in the amino acid exchange D3923A in ORF1a and one SNP at sequence position 11730 (C to T with 41%, stand bias 52%). 2022 Nature Method SARS_CoV_2 D3923A;A12022C;C41T 166;120;222 172;127;236 ORF1a 176 181 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Four specific RT-qPCR assays for SARS-CoV-2 wt-S614G, Alpha and Beta were designed based on the specific genome deletions within ORF1 and the S gene (Extended Data Table 2). 2022 Nature Method SARS_CoV_2 S614G 47 52 S 142 143 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Isogenic variants with the Alpha spike (wt-SAlpha) or individual Alpha spike mutations were introduced into a wild-type SARS-COV-2 'Wuhan' backbone strain comprising the D614G amino acid change (wt-S614G), as described. 2022 Nature Method SARS_CoV_2 D614G;S614G 170;198 175;203 S;S 33;71 38;76 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Nasal washes, oropharyngeal swabs, and organ samples were tested by RT-qPCR analysis for the ratio of the two different viruses used for inoculation, by applying two different assays, each of them specific for one variant: either the wt-S614G, Alpha or Beta variant (Extended Data Tables 2, 3). 2022 Nature Method SARS_CoV_2 S614G 237 242 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Of these, six ferrets were inoculated with an equal 250 microl mixture of SARS-CoV-2 wt-S614G and Alpha. 2022 Nature Method SARS_CoV_2 S614G 88 93 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. SARS-CoV-2 S protein expression plasmids were constructed to encode the ectodomain of S protein S(D614G) or SAlpha (residues 1-1208, with a mutated furin cleavage site and K986P/V987P substitutions) followed by a T4 fold on the trimerization domain and a polyhistidine purification tag. 2022 Nature Method SARS_CoV_2 K986P;D614G;V987P 172;98;178 177;103;183 S;S;S 11;86;96 12;87;97 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. SARS-CoV-2 wt-S614G (PRJEB45736; wt-S614G ID#49 vial 2) and SARS-CoV-2 Beta (L4550) were used to inoculate hamsters in the wt-S614G versus Beta study; SARS-CoV-2 Alpha (L4549), and SARS-CoV-2 Beta (L4550) were used for inoculation in the Alpha versus Beta hamster study. 2022 Nature Method SARS_CoV_2 S614G;S614G;S614G 14;36;126 19;41;131 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. SARS-CoV-2 wt-S614G, wt-SAlpha, Alpha (L4549) and Beta (L4550) were used to inoculate hACE2 humanized mice in all single virus or mixed virus competition experiments. 2022 Nature Method SARS_CoV_2 S614G 14 19 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Serum samples from the wt-S614G versus Alpha, wt-S614G versus Beta, and Alpha versus Beta co-inoculated hamsters and ferrets were tested by ELISA for sero-reactivity against the RBD domain using a Tecan i-control 2014 1.11 plate reader and data was analysed using Microsoft Excel 16.0. 2022 Nature Method SARS_CoV_2 S614G;S614G 26;49 31;54 RBD 178 181 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Six Syrian hamsters (Mesocricetus auratus) (Janvier Labs) were inoculated intranasally under a brief inhalation anaesthesia with a 70 mul mixture of two SARS-CoV-2 VOCs (wt-S614G and Alpha mixture, wt-S614G and Beta mixture, or Alpha and Beta mixture). 2022 Nature Method SARS_CoV_2 S614G;S614G 173;201 178;206 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. The wt-S614G and Alpha mixture held a 1:1.6 ratio with TCID50 of 104.3 per hamster, the wt-S614G versus Beta mixture held a 1:3.8 ratio with TCID50 of 104.25 per hamster, and the Alpha versus Beta mixture held a 1.8:1 ratio with TCID50 of 105.06 per hamster. 2022 Nature Method SARS_CoV_2 S614G;S614G 7;91 12;96 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. The wt-S614G versus Alpha mixture held a 1:1.2 ratio with 105.875 TCID50 distributed equally into each nostril of donor ferrets. 2022 Nature Method SARS_CoV_2 S614G 7 12 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. C145A Mpro mutant protein was obtained in the same way with an additional step of intact N-terminus generation, because the non-active C145A Mpro form cannot process itself during E.coli expression. 2021 Frontiers in pharmacology Method SARS_CoV_2 C145A;C145A 135;0 140;5 N 89 90 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. For this purpose, IMAC-purified GST-C145A MproHis protein was treated by wild type Mpro (the GST-C145A Mpro-His/Mpro-ratio was 100:1), then the IMAC step was repeated to remove free Mpro. 2021 Frontiers in pharmacology Method SARS_CoV_2 C145A;C145A 36;97 41;102 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. The concentration of FRET-S in all the experiments was 2.5 muM, while concentrations of Mpro or its C145A mutant were varied from 0.1 to 3.0 muM. 2021 Frontiers in pharmacology Method SARS_CoV_2 C145A 100 105 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. The gene of the C145A Mpro mutant was generated by PCR-mediated site-directed mutagenesis using two overlapping primers and the Mpro pGEX6p vector as a template. 2021 Frontiers in pharmacology Method SARS_CoV_2 C145A 16 21 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. Then C145A MproHis protein was subjected for PreSsissionPro cleavage and further procedures as described above. 2021 Frontiers in pharmacology Method SARS_CoV_2 C145A 5 10 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. A 50 muL reaction mixture was prepared with 25 muL 2x Reaction Buffer (TwistAmpLiquid Basic), 2.25 muL dNTPs (10 mM each dNTP, NEB, N0447S), 5 muL 10x Basic E-mix (TwistAmpLiquid Basic), 2.4 muL each of the RPA primers (10 muM), 1.6 muL AMV Reverse Transcriptase (NEB: M0277L, only required for RT-RPA), 2.5 muL 20x Core Reaction Mix, 2.5 muL of 280mM MgOAc, and 5 muL RNA or DNA template, water to make up the volume to 50 muL. 2021 PloS one Method SARS_CoV_2 M0277L 269 275 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. These patients were among the first cohort identified with A105V mutation during the largest COVID-19 outbreak in Northeastern Romania and used to track the origin of virus introduction in Romania. 2021 Biology Method SARS_CoV_2 A105V 59 64 COVID-19 93 101 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. Three systems were created: one for WT ORF7a and two for mutants A105V and A106V, respectively, the latter included to act as a second control to the computational study design. 2021 Biology Method SARS_CoV_2 A105V;A106V 65;75 70;80 ORF7a 39 44 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. Using HADDOCK, the wild-type and B.1.620 complexes (S477N-E484K) were subjected to interaction modeling to explore binding differences. 2021 Biology Method SARS_CoV_2 S477N;E484K 52;58 57;63 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. In our institution, identification of the N501Y was performed by real-time RT-PCR testing using CFX96 Real-Time System (Bio-Rad, Hercules, CA, USA) from saliva samples collected during hospitalization. 2021 Journal of clinical medicine Method SARS_CoV_2 N501Y 42 47 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. In the Public Health Institute, identification of the N501Y was performed by real-time RT-PCR under the reaction conditions according to the manual of the National Institute of Infectious Diseases (Japan). 2021 Journal of clinical medicine Method SARS_CoV_2 N501Y 54 59 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. Screening of N501Y Mutation. 2021 Journal of clinical medicine Method SARS_CoV_2 N501Y 13 18 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. The point mutation was determined by using fluorescent labeling probes, primer/probe N501Y (RC344A, TaKaRa, Japan). 2021 Journal of clinical medicine Method SARS_CoV_2 N501Y 85 90 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. The sample size was calculated based on the expected prevalence of fever over 38C in patients infected with wild-type 501N (25% to 40%) in non-critical COVID-19 population, expecting an odds ratio to be 5.0 to 8.0 for patients infected with N501Y compared with wild-type 501N. 2021 Journal of clinical medicine Method SARS_CoV_2 N501Y 241 246 COVID-19 152 160 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. The samples used for PCR testing to identify N501Y mutation were taken from the saliva of the participants and no additional invasive tests were done for the study. 2021 Journal of clinical medicine Method SARS_CoV_2 N501Y 45 50 34953513 Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. The plasmids encoding the different SARS-CoV-2 S variants (D614G, B.1.1.7, B.1.351, P.1, B.1.526 and B.1.617.2) were previously described. 2022 Cell host & microbe Method SARS_CoV_2 D614G 59 64 S 47 48 34953513 Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. To produce the pseudoviruses, 293T cells were transfected with the lentiviral vector pNL4.3 R-E- Luc (NIH AIDS Reagent Program) and a plasmid encoding for the indicated S glycoprotein (D614G, B.1.1.7, P.1, B.1.351, B.1.617.2, B.1.526 and SARS-CoV) at a ratio of 10:1. 2022 Cell host & microbe Method SARS_CoV_2 D614G 185 190 S 169 183 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The interaction of ACE2 with the three mutant models of Spike (L452R, T478K and N501Y) were studied using High Ambiguity Driven protein-protein DOCKing (HADDOCK) version 2.4 program which uses an information-driven flexible protein-protein docking approach. 2022 Journal of King Saud University. Science Method SARS_CoV_2 N501Y;T478K;L452R 80;70;63 85;75;68 S 56 61 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. Three mutant models of Spike protein-L452R, T478K and N501Y were generated using the mutagenesis program of PyMOL Molecular Graphics System software version 2.3.3 Schrodinger, LLC. 2022 Journal of King Saud University. Science Method SARS_CoV_2 N501Y;T478K;L452R 54;44;37 59;49;42 S 23 28 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. An empirically pre-determined fixed amount of pseudovirus (Wuhan, E484Q, E484K, or the B.1.351 spike) was dispensed by WDII liquid dispenser on titrated serum antibodies and controls and pre-incubated for 20 minutes at 37 C. 2021 Frontiers in immunology Method SARS_CoV_2 E484K;E484Q 73;66 78;71 S 95 100 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. E484K and E484Q mutagenesis reactions were performed using the QuickChange Lightning Site-Directed Mutagenesis Kit (Agilent #210519) using a template of a spike mammalian expression vector based on the Wuhan sequence (Genbank MN908947.3) with a deletion of the C-terminal 19 amino acids. 2021 Frontiers in immunology Method SARS_CoV_2 E484Q;E484K 10;0 15;5 S 155 160 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. In the serology assay, we used the latter method to calculate the titers (cut point for full-length spike, spike-RBD, spike-NTD, and NCP was set as 3, and cut point for spike-RBD E484Q was set as 1000). 2021 Frontiers in immunology Method SARS_CoV_2 E484Q 179 184 S;S;S;S;RBD;RBD 100;107;118;169;113;175 105;112;123;174;116;178 34959053 Isolation of SARS-CoV-2 B.1.1.28.2 (P2) variant and pathogenicity comparison with D614G variant in hamster model. SARS-CoV-2 B.1 variant (D614G variant), NIV-2020-770 (GISAID identifier: EPI_ISL_420546) isolated from a patient's throat/nasal swab sample with a titre of 106.5 tissue culture infective dose 50 (TCID50)/mL was used for the pathogenicity comparison study in hamsters with the B.1.1.28.2 isolate (GISAID identifier: EPI_ISL_2013029). 2022 Journal of infection and public health Method SARS_CoV_2 D614G 24 29 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. One-way analysis of variance (ANOVA) with Dunnett's multiple comparisons tests (variants compared to WT(D614G)), Mann-Whitney test for the comparison of two groups with unmatched pairs (Pfizer BNT162b2 compared to Moderna) and geometric mean titers (GMT) with 95% confidence intervals were performed using GraphPad Prism software. 2021 Viruses Method SARS_CoV_2 D614G 104 109 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The B.1 spike containing D614G was used as wild type (WT(D614G)). 2021 Viruses Method SARS_CoV_2 D614G;D614G 25;57 30;62 S 8 13 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. WT(D614G) pseudovirus was run as a control for every assay. 2021 Viruses Method SARS_CoV_2 D614G 3 8 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Biocomputational Studies of Q675H Variants. 2021 Viruses Method SARS_CoV_2 Q675H 28 33 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. In particular, the B.1.1.7 dataset includes n = 1500 genomes plus n = 278 strains carrying the Q675H mutation; the B.1.351 dataset includes n = 1100 genomes plus n = 104 strains carrying the Q675H mutation; the P.1 dataset includes n = 1400 genomes plus n = 59 carrying the Q675H mutation; the B.1.617 + A.Y.x dataset includes n = 1776 genomes plus n = 664 carrying the Q675H mutation. 2021 Viruses Method SARS_CoV_2 Q675H;Q675H;Q675H;Q675H 95;191;274;370 100;196;279;375 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Molecular dynamics simulations were performed for the SARS-CoV-2 spike proteins to estimate the stability and dynamics features of Q675 and Q675H. 2021 Viruses Method SARS_CoV_2 Q675H 140 145 S 65 70 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Pymol mutagenesis wizard was used to model Q675H and D614G for both wild-type (wt) and mutant systems. 2021 Viruses Method SARS_CoV_2 D614G;Q675H 53;43 58;48 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. The DynaMut, webserver was used to predict the effect of genetic variants on the stability and flexibility of Q675H mutant spike protein. 2021 Viruses Method SARS_CoV_2 Q675H 110 115 S 123 128 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. The fold change of the mutant spike relative to WT D614G in binding or neutralization was calculated by simple division of the respective IC50 or MFI values. 2021 Frontiers in immunology Method SARS_CoV_2 D614G 51 56 S 30 35 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. The SARS-CoV-2 RBD, RBD-3M, carrying K417N/E484K/N501Y mutations and ACE2 peptidase domain contains a C-terminal six-histidine tag. 2021 Frontiers in immunology Method SARS_CoV_2 K417N;E484K;N501Y 37;43;49 42;48;54 RBD;RBD 15;20 18;23 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Briefly, C1R-A2402 cells were pulsed with or without the NF9 peptide or its derivatives [the NF9-L452Q peptide (NYNYQYRLF, L5Q in NF9) and the NF9-L452Q peptide (NYNYRYRLF, L5R in NF9); synthesized by Scrum, Inc.] at concentrations from 0.1 to 10 nM at 37 C for 1 h. 2022 Cell reports Method SARS_CoV_2 L5Q;L5R;L452Q;L452Q 123;173;97;147 126;176;102;152 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Megaprimers for targeted mutagenesis were amplified by PCR using the KAPA HiFi HotStart ReadyMix kit (Roche, Cat# KK2601) with the following pairs of primers according to the manufacturer's protocol: RBD_L452Q_F, 5'-GGA CAG CAA GGT GGG AGG CAA CTA CAA CTA CCA ATA CAG ACT GTT CAG GAA GAG CAA C-3'; pCT_seq reverse, 5'-CAT GGG AAA ACA TGT TGT TTA CGG AG-3'; RBD_int_F, 5'-CTA CAA ACT GCC TGA TGA CTT CAC-3'; and RBD_F490S_R, 5'-GGT TGG TTG GAA GCC ATA GGA TTG GAG TGG AGA GTA ACA GTT GAA GCC CTC CAC TCC-3'. 2022 Cell reports Method SARS_CoV_2 F490S;L452Q 415;204 420;209 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Plasmids expressing the S proteins of the Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Lambda (C.37) variants and the point mutants were generated by site-directed overlap extension PCR using pC-SARS2-S D614G as the template and the following primers listed in Table S6. 2022 Cell reports Method SARS_CoV_2 D614G 227 232 S;S 24;225 25;226 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. The double mutant L452Q/F490S was prepared using F490S megaprimers and pJYDC1-RBD L452Q as the template. 2022 Cell reports Method SARS_CoV_2 F490S;L452Q;L452Q;F490S 49;18;82;24 54;23;87;29 RBD 78 81 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. The Genotype to Phenotype Japan (G2P-Japan) Consortium: Mika Chiba, Shigeru Fujita, Hirotake Furihata, Naoko Misawa, Nanami Morizako, Akiko Oide, Seiya Ozono, Mai Suganami, Miyoko Takahashi, Mako Toyoda, and Miyabishara Yokoyama. 2022 Cell reports Method SARS_CoV_2 G2P 33 36 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. 3D structures of all mutants (V367F, R408I, G476S, V483A and N501Y) along with wildtype were energy minimized using GROMACS. 2022 Computer methods and programs in biomedicine Method SARS_CoV_2 G476S;N501Y;R408I;V483A;V367F 44;61;37;51;30 49;66;42;56;35 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Distinct missense mutations which represented different strains of SARS-CoV2 such as V367F, R408I, G476S, V483A, N501Y were prepared in PyMOL as previously described. 2022 Computer methods and programs in biomedicine Method SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 99;113;92;85;106 104;118;97;90;111 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The spike mutants include N74K, D614G, V622F, Q677H, S943T, D115G with the human receptor ACE2 using the HAWKDOCK server. 2022 Computers in biology and medicine Method SARS_CoV_2 D115G;D614G;N74K;Q677H;S943T;V622F 60;32;26;46;53;39 65;37;30;51;58;44 S 4 9 34968879 SARS-CoV-2 wastewater surveillance in Germany: Long-term RT-digital droplet PCR monitoring, suitability of primer/probe combinations and biomarker stability. Additional investigations of selected samples for the evaluation of alternative primers and probes (set 5-7) and the detection of the N501Y mutation and wildtype (sets 8 and 9) were carried out. 2022 Water research Method SARS_CoV_2 N501Y 134 139 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The 3D structures of mutations (N501I, N501T, N501V), which were predicted to tempt higher stability change and consequently increases the affinity by manifolds, were modeled using Modeller v15.2 integrated in Chimera software. 2022 Computers in biology and medicine Method SARS_CoV_2 N501T;N501V;N501I 39;46;32 44;51;37 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The AMBER20 was used to perform the dynamic behaviour of wild type complex, N501I, N501T and N501V, through MD simulation using FF19SB force field. 2022 Computers in biology and medicine Method SARS_CoV_2 N501I;N501T;N501V 76;83;93 81;88;98 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The binding variations between the wild type and the predicted hypothetical emerging mutants (N501I, N501T, N501V) were explored through HADDOCK (high ambiguity-driven protein-protein docking) algorithm. 2022 Computers in biology and medicine Method SARS_CoV_2 N501T;N501V;N501I 101;108;94 106;113;99 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The MM-GBSA and MM-PBSA approaches were used to analyze the actual binding energy of wild type complex, N501I, N501T and N501V. 2022 Computers in biology and medicine Method SARS_CoV_2 N501I;N501T;N501V 104;111;121 109;116;126 34982246 Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing. F548S, Thermo Fisher Scientific). 2022 Current microbiology Method SARS_CoV_2 F548S 0 5 34982509 Engineered small extracellular vesicles displaying ACE2 variants on the surface protect against SARS-CoV-2 infection. We generated the D614G mutant, the RBD mutations in Beta variant (K417N, E484K, and N501Y), mutations in Delta variant (L452R, E484K, and D614G) via site-directed mutagenesis as previously described (Liu & Naismith,). 2022 Journal of extracellular vesicles Method SARS_CoV_2 D614G;D614G;E484K;E484K;N501Y;K417N;L452R 17;138;73;127;84;66;120 22;143;78;132;89;71;125 RBD 35 38 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. In the second duplex assay, one primer/probe set was used to target C1709A for identifying the Alpha variant, and another set was used to target C56G for identifying the Delta variant. 2022 Microbiology spectrum Method SARS_CoV_2 C1709A;C56G 68;145 74;149 34987509 An Intranasal OMV-Based Vaccine Induces High Mucosal and Systemic Protecting Immunity Against a SARS-CoV-2 Infection. In addition to the 3xGGGS spacer and mCRAMP sequence, the aspartic acid at position 614 in the original HexaPro spike protein was replaced with a glycine (D614G). 2021 Frontiers in immunology Method SARS_CoV_2 D614G 155 160 S 112 117 34987509 An Intranasal OMV-Based Vaccine Induces High Mucosal and Systemic Protecting Immunity Against a SARS-CoV-2 Infection. Sequencing of their rpsL gene showed that they contained amino acid change K88R compared to the starting material, a mutation known to confer streptomycin resistance in other bacteria. 2021 Frontiers in immunology Method SARS_CoV_2 K88R 75 79 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Briefly, The Gv coding sequence was fused at the N-terminus of the D614G_RBD or B.1.351_RBD sequence. 2022 Cell reports Method SARS_CoV_2 D614G 67 72 N 49 50 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Briefly, the Talos L120C (ThermoFisher) was operated at an accelerating voltage 120 kV to collect data on the sample. 2022 Cell reports Method SARS_CoV_2 L120C 19 24 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. D614G and B.1.351 were used to challenge mice. 2022 Cell reports Method SARS_CoV_2 D614G 0 5 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. D614G_RBD-NP and B.1.351_RBD-NP were eluted in retention of retaining 11 mL to 14 mL. 2022 Cell reports Method SARS_CoV_2 D614G 0 5 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. DNA sequences of SP-Gv-D614G_RBD and SP-Gv-B.1.351_RBD were codon-optimized for mammalian cell expression and cloned into vector plasmid pLVX. 2022 Cell reports Method SARS_CoV_2 D614G 23 28 S;S 17;37 19;39 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Ferritin, D614G_RBD-NP, and B.1.351_RBD-NP were diluted into different concentrations and then injected (30 mL min-1). 2022 Cell reports Method SARS_CoV_2 D614G 10 15 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. For BALB/c mice vaccination, five BALB/c mice were subcutaneously immunized with 10 mug of D614G/B.1.351_RBD-NP formulated with Alum (InvivoGen) adjuvant. 2022 Cell reports Method SARS_CoV_2 D614G 91 96 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Gv-D614G_RBD and Gv-B.1.351_RBD were incubated with Sd-Ferritin in the Tris-HCl buffer. 2022 Cell reports Method SARS_CoV_2 D614G 3 8 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Lentiviruses released in the supernatant were collected 60 h after transfection and then infected anchorage-dependent CHO-K1 cells cultured in F12K medium. 2022 Cell reports Method SARS_CoV_2 F12K 143 147 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Mice in D614G_RBD-NP and B.1.351_RBD-NP groups were immunized with equal moles of D614G_RBD-NP and B.1.351_RBD-NP. 2022 Cell reports Method SARS_CoV_2 D614G 82 87 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Mice in the Ferritin group were immunized with equal moles of ferritin, which were the same as the D614G/B.1.351_RBD-NP group. 2022 Cell reports Method SARS_CoV_2 D614G 99 104 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. On Day 282, four monkeys were immunized with 50 mug of D614G/B.1.351_RBD-NP vaccine. 2022 Cell reports Method SARS_CoV_2 D614G 55 60 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Recombinant D614G_RBD and B.1.351_RBD protein was diluted to a concentration of 2 mug/mL concentration in coating buffer to coat on high-binding 96-well plates (Corning) respectively, overnight at 4C. 2022 Cell reports Method SARS_CoV_2 D614G 12 17 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. SARS-CoV-2 strains, named as hCoV-19/CHN/SYSU-IHV/2020 (D614G) (Accession ID on GISAID: EPI_ISL_444969) and 19nCoV-CDC-Tan-GDPCC (B.1.351) were propagated in Vero E6 cells as published before. 2022 Cell reports Method SARS_CoV_2 D614G 56 61 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The bivalent D614G/B.1.351_RBD-NP vaccine comprises a 1:1 mix of D614G_RBD-NP and B.1.351_RBD-NP. 2022 Cell reports Method SARS_CoV_2 D614G;D614G 13;65 18;70 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The concentrations of D614G and B.1.351 were determined by FRNT as described below. 2022 Cell reports Method SARS_CoV_2 D614G 22 27 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The concentrations of D614G_RBD and B.1.351_RBD were determined by BCA assay. 2022 Cell reports Method SARS_CoV_2 D614G 22 27 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The D614G strain was isolated from the sputum of a female COVID-19 patient who was infected by a UK traveler in April 2020 by us, and the B.1.351 strain was isolated from a South Africa traveler by the Guangdong Center for Disease Control in January 2021. 2022 Cell reports Method SARS_CoV_2 D614G 4 9 COVID-19 58 66 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The D614G_RBD and B.1.351_RBD were expressed and purified from Chinese hamster ovary K (CHO-K1) cells. 2022 Cell reports Method SARS_CoV_2 D614G 4 9 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The F12K medium was then replaced with CHO S4 medium, which was used for cell suspension and expansion to a density of 3x106 cells/mL. 2022 Cell reports Method SARS_CoV_2 F12K 4 8 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The measurements of Ferritin, D614G_RBD, B.1.351_RBD, D614G_RBD-NP, and B.1.351_RBD-NP binding to hACE2 were carried out with a BIAcore T100 instrument (GE Healthcare). 2022 Cell reports Method SARS_CoV_2 D614G;D614G 30;54 35;59 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The moles of D614G/B.1.351 RBD in the monomers group were the same as D614G_RBD-NP and B.1.351_RBD-NP in the D614G/B.1.351_RBD-NP group, respectively. 2022 Cell reports Method SARS_CoV_2 D614G;D614G;D614G 13;109;70 18;114;75 RBD 27 30 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The purified Gv-D614G_RBD and Gv-B.1.351_RBD were irreversibly covalently conjugated to the Sd-Ferritin to generate the D614G_RBD-nanoparticle (NP) and B.1.351_RBD-NP. 2022 Cell reports Method SARS_CoV_2 D614G 120 125 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The supernatant was removed 8 h later and changed with new a F12K medium for another day of culture. 2022 Cell reports Method SARS_CoV_2 F12K 61 65 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Transmission electron microscopy (TEM) Grids of SD-Ferritin, D614G_RBD-NP, and B.1.351_RBD-NP have proceeded to negative-stain electron microscopy in Shuimu BioSciences Ltd. 2022 Cell reports Method SARS_CoV_2 D614G 61 66 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. 293T, hACE2.293T, NK cells, and H84T-BanLec CAR-NK cells were coated with 50ng of recombinant protein, then stained first with His antibody (R&D Systems), followed by PE-anti-mouse F(ab)2 (R&D Systems) and analyzed using flow cytometry. 2021 Frontiers in immunology Method SARS_CoV_2 H84T 32 36 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. CAR expression on the surface of transduced NK cells was evaluated 4 and 14 days post-transduction using primary staining with H84T.BanLec Ab and secondary staining with AlexaFluor647-anti-rabbit F(ab)2 (Jackson ImmunoResearch, West Grove, PA). 2021 Frontiers in immunology Method SARS_CoV_2 H84T 127 131 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. Histidine (His)-tagged recombinant S-proteins: trimera (SPN-C52H9) and D614G trimera (SPN-C52H3) were purchased from ACROBiosystems (Newark, DE). 2021 Frontiers in immunology Method SARS_CoV_2 D614G 71 76 S 35 36 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. More specifically, the lectin is linked to a CD8alpha hinge and transmembrane domain, CD137 intracellular domain, and the intracellular domain of TCRzeta.(H84T-BanLec.4-1BB.zeta). 2021 Frontiers in immunology Method SARS_CoV_2 H84T 155 159 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. The sequence of H84T-BanLec was synthesized (GeneArt, ThermoFisher Scientific) and subcloned into a pSFG retroviral vector backbone linked to the intracellular domains of 4-1BB (CD137) and TCRzeta. 2021 Frontiers in immunology Method SARS_CoV_2 H84T 16 20 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. Western blot analysis was performed with the following antibodies: mouse anti-human CD247 (clone 1D4; BD Biosciences), mouse anti-human phosphorylated CD247 (pY142, clone K25-407.69; BD Biosciences), and rabbit anti-human H84T.BanLec Ab. 2021 Frontiers in immunology Method SARS_CoV_2 H84T 222 226 35007661 A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: Effects on proteolytic cleavage and ACE2 binding. His- and biotin-tagged peptides containing the wild type, mutant (P681R and R683Q), and triple R-deleted SARS-CoV-2-specific furin motif were added at a concentration of 10 ng/well (prepared with PBS) to the blocked (2% BSA) Ni-NTA-coated wells of the 8-well microplate strips and incubated for 1 h at RT. 2022 Immunology letters Method SARS_CoV_2 R683Q;P681R 76;66 81;71 35007661 A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: Effects on proteolytic cleavage and ACE2 binding. His-tagged SARS-CoV-2 protein containing the S1/S2 boundary furin site, His-tagged peptides containing the wild type, mutant (P681R and R683Q), and triple R-deleted SARS-CoV-2-specific furin motif (EpiGentek), and His-tagged SARS-CoV-2 S1 RBD protein lacking the S1/S2 boundary furin site (EpiGentek) were added at a concentration of 10 ng/well (prepared with PBS) to the blocked (2% BSA) Ni-NTA-coated strips and incubated for 1 h at 37 C. 2022 Immunology letters Method SARS_CoV_2 R683Q;P681R 136;126 141;131 RBD 239 242 35007661 A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: Effects on proteolytic cleavage and ACE2 binding. Peptides (EpiGentek) containing the wild type, mutant (P681R and R683Q), and triple R-deleted SARS-CoV-2-specific furin motif and tagged with His- and biotin at the N- and C-terminals, respectively, were added at a concentration of 10 ng/well (prepared with PBS) to the blocked (2% BSA) Ni-NTA-coated strips and incubated for 1 h at RT. 2022 Immunology letters Method SARS_CoV_2 R683Q;P681R 65;55 70;60 N 165 166 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Indeed, the FoldX AnalyseComplex assay was performed to determine the interaction energy between the investigated minimized protein complexes consisting of the SARS-CoV-2 spike RBD mutants (N501Y, E484K/Q, N439K, K417N/T, L452R, S477N, S494P, the double mutants L452R-E484Q, S477N-E484K, and the triple mutants N501Y-E484K-K417N, N501Y-E484K-S494P, and N501Y-E484K-K417T) and ACE2. 2022 The EPMA journal Method SARS_CoV_2 E484K;E484Q;K417N;K417T;L452R;L452R;N439K;N501Y;N501Y;N501Y;S477N;S477N;S494P;N501Y;E484K;E484K;E484K;E484K;E484Q;K417N;K417T;S494P 197;197;213;213;222;262;206;311;330;353;229;275;236;190;281;317;336;359;268;323;365;342 204;204;220;220;227;267;211;316;335;358;234;280;241;195;286;322;341;364;273;328;370;347 S;RBD 171;177 176;180 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Starting from the atomic coordinates of the SARS-CoV-2 spike RBD protein domain extracted from 6m0j.pdb (according to the YP_009724390.1 sequence), we built the 3D comparative models of the investigated RBD mutants with specific reference to the single mutants N501Y, E484K/Q, N439K, K417N/T, L452R, S477N, and S494P; the double mutants L452R-E484Q and S477N-E484K; and the triple mutants N501Y-E484K-K417N, N501Y-E484K-S494P, and N501Y-E484K-K417T by using the mutagenesis tool implemented in SwissPDBViewer. 2022 The EPMA journal Method SARS_CoV_2 E484K;E484Q;K417N;K417T;L452R;L452R;N439K;N501Y;N501Y;N501Y;N501Y;S477N;S477N;S494P;E484K;E484K;E484K;E484K;E484Q;K417N;K417T;S494P 268;268;284;284;293;337;277;261;389;408;431;300;353;311;359;395;414;437;343;401;443;420 275;275;291;291;298;342;282;266;394;413;436;305;358;316;364;400;419;442;348;406;448;425 S;RBD;RBD 55;61;203 60;64;206 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Biotinylated RBD of SARS-CoV-1 (Sino Biological, 40634-V27H-B) or SARS-CoV-2 (Sino Biological, 40592-V27H-B) were multimerized with fluorescently labelled streptavidin (SA) for 1 h at 4 C. 2022 Nature Method SARS_CoV_2 V27H;V27H 55;101 59;105 RBD 13 16 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Omicron pseudovirus contains the following mutations: A67V, H69del, V70del, T95I, G142D, V143del, Y144del, Y145del, N211del, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K and L981F. 2022 Nature Method SARS_CoV_2 A67V;D614G;D796Y;E484A;G142D;G339D;G446S;G496S;H655Y;H69del;K417N;L212I;L981F;N211del;N440K;N501Y;N679K;N764K;N856K;N969K;P681H;Q493R;Q498R;Q954H;S371L;S373P;S375F;S477N;T478K;T547K;T95I;V143del;V70del;Y144del;Y145del;Y505H 54;255;290;206;82;143;185;220;262;60;171;125;321;116;178;234;269;283;297;311;276;213;227;304;150;157;164;192;199;248;76;89;68;98;107;241 58;260;295;211;87;148;190;225;267;66;176;130;326;123;183;239;274;288;302;316;281;218;232;309;155;162;169;197;204;253;80;96;74;105;114;246 35018385 Integrin/TGF-beta1 inhibitor GLPG-0187 blocks SARS-CoV-2 Delta and Omicron pseudovirus infection of airway epithelial cells which could attenuate disease severity. Briefly, 293FT cells (Invitrogen) at 75% confluency were co-transfected with the backbone vector pHAGE-fullEF1alpha-Luciferase-IRES-ZsGreen, plasmids expressing lentiviral proteins Tat, Rev and Gag/Pol, and plasmids expressing D614 or D614G S protein (a gift from Dr. 2022 medRxiv Method SARS_CoV_2 D614G 235 240 S 241 242 35018385 Integrin/TGF-beta1 inhibitor GLPG-0187 blocks SARS-CoV-2 Delta and Omicron pseudovirus infection of airway epithelial cells which could attenuate disease severity. Hyeryun Choe, The Scripps Research Institute, Jupiter, FL), or S protein with N501Y, E484K, N501Y+E484K or N501Y+E484K+K417N mutations. 2022 medRxiv Method SARS_CoV_2 E484K;N501Y;N501Y;N501Y;E484K;E484K;K417N 85;78;92;107;98;113;119 90;83;97;112;103;118;124 S 63 64 35026305 SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021. Samples identified with S mutations and 38 non-variant samples (selected randomly) were then subjected to Allplex SARS-CoV-2 Variants I Assay (Seegene, South Korea) that detects SARS-CoV-2 RdRp gene, HV69/70 deletion, E484K and N501Y mutations. 2022 Journal of virological methods Method SARS_CoV_2 E484K;N501Y 218;228 223;233 RdRP;S 189;24 193;25 35026305 SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021. Viral RNA was tested using Allplex SARS-CoV-2 Master Assay (Seegene, South Korea) that screens for SARS-CoV-2 envelope (E), nucleoprotein (N), RNA-dependent RNA polymerase (RdRp), S gene, and S mutations (any of the HV69/70 deletion, Y144 deletion, E484K, N501Y, and P681H) following manufacturer's instructions. 2022 Journal of virological methods Method SARS_CoV_2 E484K;N501Y;P681H 249;256;267 254;261;272 RdRp;RdRP;E;N;S;S 143;173;120;139;180;192 171;177;121;140;181;193 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. High-resolution Gamma-A520S RBD/hACE2 complex crystals were grown in 0.1 M MES (pH 6.0), 15% w/v PEG 4000. 2022 Journal of medical virology Method SARS_CoV_2 A520S 22 27 RBD 28 31 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The SARS-CoV-2 variant RBD plasmids (including Alpha RBD, Beta RBD, Gamma RBD, Alpha A520S RBD, Beta A520S RBD, and Gamma A520S RBD) were completed by subcloning. 2022 Journal of medical virology Method SARS_CoV_2 A520S;A520S;A520S 85;101;122 90;106;127 RBD;RBD;RBD;RBD;RBD;RBD;RBD 23;53;63;74;91;107;128 26;56;66;77;94;110;131 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The sitting-drop method was used to obtain high-resolution Gamma-A520S RBD/hACE2 complex crystals. 2022 Journal of medical virology Method SARS_CoV_2 A520S 65 70 RBD 71 74 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The structure of the Gamma-A520S RBD/hACE2 complex was determined by the molecular replacement method using Phaser with a previously reported complex structure of the SARS-CoV-2-RBD complex with human ACE2 (PDB: 6LZG). 2022 Journal of medical virology Method SARS_CoV_2 A520S 27 32 RBD;RBD 33;179 36;182 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Two types of cells were used for fusion experiments, and 293T cells were first transfected with spike protein sequences carrying the D614G variant or a combined single mutant and the GFP1-7 RLN plasmid. 2022 Journal of medical virology Method SARS_CoV_2 D614G 133 138 S 96 101 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. G8830A). 2021 Frontiers in public health Method SARS_CoV_2 G8830A 0 6 35056592 SARS-CoV-2 Evolution and Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIV Immune Suppression. After culture, PBMCs were centrifuged, pelleted and washed with Phosphate-buffered saline (PBS) and incubated 35 min at room temperature with LIVE/DEAD Fixable Aqua Dead Cell Stain (Life Technologies), anti-CD14-BV510 (clone MphiP9), anti-CD19-BV510 (clone SJ25C1), anti-CD56-BV510 (clone NMCAM16.2), anti-CD45RA-FITC (clone L48), anti-CD8-APC (clone SK-1), anti-CD27-APCH7 (clone M-T271), anti-PD-1-BV786 (CD279, clone EH12-1), and anti-CD3-BV711 (clone SK-7) (BD Bioscience); and anti-TIGIT-PerCPCy5.5 (clone A15153G) (BioLegend). 2022 Microorganisms Method SARS_CoV_2 A15153G 511 518 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. pCAGGS-SARS-CoV-2-S-dc-D614G expressing WT spike protein with D614G was generated by overlapping-PCR based mutagenesis using pCAGGS-SARS-CoV-2-S-C9 (gifted from Dr. 2022 Emerging microbes & infections Method SARS_CoV_2 D614G;D614G 62;23 67;28 S;S;S 43;18;143 48;19;144 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. The VSV-DeltaG-based SARS-CoV-2 pseudoviruses were packaged with spike proteins from the D614G and SARS-CoV-2 variants according to a published protocol with slight modification. 2022 Emerging microbes & infections Method SARS_CoV_2 D614G 89 94 S 65 70 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. The RBD binding site for antibody C121, a neutralizing antibody known to bind RBD (PDB ID: 7K8X), and the E484K mutant known to escape C121 binding were used to determine the impact of the double mutants L452R/T478K, L452R/E484Q and E484K/N501Y on the antibody binding structure. 2021 Viruses Method SARS_CoV_2 E484K;E484K;L452R;L452R;E484Q;N501Y;T478K 106;233;204;217;223;239;210 111;238;209;222;228;244;215 RBD;RBD 4;78 7;81 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. Three RBD double mutants, L452R/T478K (delta), L452R/E484Q (Kappa) and E484K/N501Y (beta, gamma), and five RBD single mutants of L452R, T478K, E484Q, E484K, and N501Y, included in the double mutants, were used in the study. 2021 Viruses Method SARS_CoV_2 E484K;E484K;E484Q;L452R;L452R;L452R;N501Y;T478K;E484Q;N501Y;T478K 71;150;143;26;47;129;161;136;53;77;32 76;155;148;31;52;134;166;141;58;82;37 RBD;RBD 6;107 9;110 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. We compared the mutated N501Y, L452R, and T478K structures with other known SARS-CoV-2 crystal structures (PDB ID: 7MJN, 7ORB and 7ORA), and observed a 99.48%, 99.46%, and 99.46% similarity, respectively, indicating that the mutated crystal structures were comparable to the reference crystal structure. 2021 Viruses Method SARS_CoV_2 L452R;N501Y;T478K 31;24;42 36;29;47 35062211 SARS-CoV-2 Spike Expression at the Surface of Infected Primary Human Airway Epithelial Cells. Authentic SARS-CoV-2 viruses were isolated, sequenced, and amplified from clinical samples obtained from patients infected with SARS-CoV-2 D614G or B.1.1.7 (Alpha variant) by the Laboratoire de Sante Publique du Quebec (LSPQ). 2021 Viruses Method SARS_CoV_2 D614G 139 144 35062211 SARS-CoV-2 Spike Expression at the Surface of Infected Primary Human Airway Epithelial Cells. SARS-CoV-2 authentic viruses (D614G or B.1.1.7 (alpha) variant) were used to infect the pAECs at a multiplicity of infection (MOI) of 0.1. 2021 Viruses Method SARS_CoV_2 D614G 30 35 35062214 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. Since all mutants examined in this study occurred in haplotypes harboring the D614G substitution, reference structures harboring this mutation (PDB codes 6ZWV; 7KRR; 7KRS) were used as templates. 2021 Viruses Method SARS_CoV_2 D614G 78 83 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. The Median Fluorescence intensities (MFI) obtained with ACE2-Fc or plasma Abs were normalized to the MFI obtained with the conformationally and temperature independent CV3-25 anti-S2 antibody and presented as ratio of the CV3-25-normalized values obtained with the D614G Spike. 2022 Viruses Method SARS_CoV_2 D614G 265 270 S 271 276 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. The pCG1-SARS-CoV-2 S was kindly provided by Stefan Pohlmann, its D614G variant was previously described. 2022 Viruses Method SARS_CoV_2 D614G 66 71 S 20 21 35062734 Immunogenicity of a Heterologous Prime-Boost COVID-19 Vaccination with mRNA and Inactivated Virus Vaccines Compared with Homologous Vaccination Strategy against SARS-CoV-2 Variants. A live virus microneutralization (vMN) assay was performed in the Biosafety Level 3 facility at HKU to compare the effectiveness of antibody levels against different SARS-CoV-2 strains, including the HKU-001a (wild type, GenBank accession number MT230904) strain (WT), B.1.36.27 (D614G), B.1.1.7 (alpha variant), B.1.351 (beta variant), P.3. 2022 Vaccines Method SARS_CoV_2 D614G 280 285 35071665 Infection spread simulation technology in a mixed state of multi variant viruses. Currently, the virus of interest is d strain (L452R) found in India. 2022 AIMS public health Method SARS_CoV_2 L452R 46 51 35071665 Infection spread simulation technology in a mixed state of multi variant viruses. Variant virus that is prevalent in Tokyo and is seen as almost by a strain virus (N501Y). 2022 AIMS public health Method SARS_CoV_2 N501Y 82 87 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. For this purpose, the viral mutants isolated in the virus escape experiment, labelled A1 (containing the mutation Spike S477R), B11 (containing the mutation Spike T345N), and C25 (containing the insertion E 13IV->IACLV) were mixed with the parental SARS-CoV-2 strain Slovakia/SK-BMC5/2020 in order to obtain equal amounts of infectious viruses. 2022 EBioMedicine Method SARS_CoV_2 S477R;T345N 120;163 125;168 S;S 114;157 119;162 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. It is the ectodomain of SARS-CoV-2 spike protein expressed in HEK293 cells, which contains amino acids Val16 - Pro1213 of Spike (GenBank: QHD43416.1) with T4 fibritin trimerization motif, a polyhistidine tag at the C-terminus, proline substitutions (F817P, A892P, A899P, A942P, K986P, V987P) and alanine substitutions (R683A and R685A) to stabilize the trimeric pre-fusion conformation, and mutations identified in the Omicron variant (A67V, HV69-70del, T95I, G142D, VYY143-145del, N211del, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F). 2022 EBioMedicine Method SARS_CoV_2 A892P;A899P;A942P;D614G;D796Y;E484A;G142D;G339D;G446S;G496S;H655Y;K417N;K986P;L212I;L981F;N211del;N440K;N501Y;N679K;N764K;N856K;N969K;P681H;Q493R;Q498R;Q954H;R685A;S371L;S373P;S375F;S477N;T478K;T547K;T95I;V987P;Y505H;A67V;F817P;R683A 257;264;271;621;656;572;460;509;551;586;628;537;278;491;684;482;544;600;635;649;663;677;642;579;593;670;329;516;523;530;558;565;614;454;285;607;436;250;319 262;269;276;626;661;577;465;514;556;591;633;542;283;496;689;489;549;605;640;654;668;682;647;584;598;675;334;521;528;535;563;570;619;458;290;612;440;255;324 S;S 35;122 40;127 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. The ends of amplicons were treated with a NEBNext Ultra II End repair / dA-tailing Module (E7442L, New England Biolabs) and barcoded using a Native Barcoding Expansion 96 kit (EXP-NBD196, Oxford Nanopore Technologies) and a Blunt/TA Ligation Master Mix (M0367L, New England Biolabs). 2022 EBioMedicine Method SARS_CoV_2 M0367L 254 260 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. The following HPLC-purified primer pairs (synthesized by Generi Biotech, Czech Republic) were used: N501Y, GGCTTTCAGCCGACCTATGGCGTGGGCTATCAG, and CTGATAGCCCACGCCATAGGTCGGCTGAAAGCC; N439K, GATTGCGTGGAACAGC AAGAACCTGGATAGCAAAG and CTTTGCTATCCAGGTTCTTGCTGTTCCACGCAATC; E484K, CCG TGCAACGGCGTGAAAGGCTTTAACTGCT and AGC AGTTAAAGCCTTTCACGCCGTTGCACGG; 417N, CGGGCCAGACCGGCAATATTGCGGATTATAACTA and TAGTTATAATCCGCAATATTGCCGGTCTGGCC CG; T345N, CGAAGTGTTTAACGCGAACCGCTTTGCGAGCG and CGCTCGCAAAGCGGTTCGCGTTAAACACTTCG; S477R, CGAAATTTATCAGGCG GGCCGCACCCCGTGCAACG and CGTTGCAC GGGGTGCGGCCCGCCTGATAAATTTCG. 2022 EBioMedicine Method SARS_CoV_2 E484K;N439K;N501Y;S477R;T345N 266;181;100;504;426 271;186;105;509;431 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. The strain Slovakia/SK-BMC5/2020 (available at https://www.european-virus-archive.com/virus/sars-cov-2-strain-slovakiask-bmc52020) represents strains circulating in Europe in spring 2020 and carries the Spike D614G mutation (lineage B.1). 2022 EBioMedicine Method SARS_CoV_2 D614G 209 214 S 203 208 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. 3CLpro WT or P108S at a final concentration of 5 mumol/l was incubated in a buffer of 20 m mol/l Tris-HCl (pH7.5), 100 m mol/l NaCl, and 5 m mol/l DTT with the addition of the substrate at a final concentration of 3.125, 6.25, 12.5, 25, 50, 100 or 200 mumol/l at room temperature. 2022 Scientific reports Method SARS_CoV_2 P108S 13 18 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Both of the partial specific volumes of WT 3CLpro and P108S were 0.731 cm3/g, which was calculated based on the amino acid composition of each sample using the program SEDNTERP 1.09. 2022 Scientific reports Method SARS_CoV_2 P108S 54 59 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Eighty mumol/l of protein solutions (SARS CoV-2 3CLpro WT and SARS CoV-2 3CLpro P108S) were diluted 20-fold with 20 mmol/l Tris-HCl buffer solution (pH 7.3) prepared with D2O containing 150 mmol/l NaCl, and incubated at 20 C for various hydrogen/deuterium exchange time period (0.5, 1, 10, 60, or 240 min). 2022 Scientific reports Method SARS_CoV_2 P108S 80 85 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. For the inhibition assay, the SARS-CoV 3CLpro inhibitor GC376 (Selleck) at a final concentration of 1, 2, 5, 10, or 20 mumol/l was incubated with 5 mumol/l 3CLpro WT or P108S and 12.5, 25 or 50 mumol/l of substrate. 2022 Scientific reports Method SARS_CoV_2 P108S 169 174 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. The enzymatic activities of 3CLpro WT and P108S were determined using a fluorescent substrate with the cleavage site of SARS CoV-2 3CLpro (Dabcyl-KTSAVLQ SGFRKME-Edans; GL Biochem). 2022 Scientific reports Method SARS_CoV_2 P108S 42 47 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. The expression vectors for the 3CLpro Wuhan strain type (WT) or the Pro108Ser mutant (P108S) were transformed into BL21 (DE3), and the bacteria were incubated in LB with ampicillin at 37 C until OD600 was reached at 0.8. 2022 Scientific reports Method SARS_CoV_2 P108S;P108S 68;86 77;91 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. The SARS-CoV-2 3CLpro DNA fragments encoding the Wuhan strain or the strain containing Pro108Ser in non-structural polyprotein 5 (NSP5) gene were prepared using a reverse transcription kit (SuperScript III, ThermoFishher) and were amplified by PCR using primers (forward: 5'-TTTGGATCCAGTGGTTTTAGAAAAATGGCA-3', reverse: 5'-TTTGTCGACTCATTGGAAAGTAACACCTGAGCA-3'). 2022 Scientific reports Method SARS_CoV_2 P108S 87 96 Nsp5 130 134 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. The SV-AUC experiments were performed using the Optima AUC (Beckman Coulter) at 20 C with 1, 2.5, 5, 10, 20, 40, and 80 micromol/l of 3CLpro WT and P108S dissolved in 20 mmol/l Tris-HCl buffer solution (pH7.3) containing 150 mmol/l NaCl. 2022 Scientific reports Method SARS_CoV_2 P108S 149 154 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. variant B.1.1.7: 40592-V08H82; South Africa variant B.1.351: 40592-V08H84; Brazil variant P.1: 40591-V08H5) are from Sino Biological (Beijing). 2022 Analytical chemistry Method SARS_CoV_2 V08H 101 105 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. Point mutations were introduced into the WuHan-1 plasmid to construct 19 mutants: D614G, A222V+D614G, B.1.1.7, S477N+D614G, P1162R+D614G+A222V, D839Y+D614G, L176F+D614G, B.1.1.7+L216F, B.1.1.7+M740V, B.1.258, B.1.258+L1063F, B.1.258+N751Y, S477N, D839Y, L176F, L216F+D614G, M740V+D614G, L1063F+D614G, and N751Y+D614G. 2022 Archives of virology Method SARS_CoV_2 A222V;D614G;D839Y;D839Y;L1063F;L176F;L176F;L216F;M740V;N751Y;P1162R;S477N;S477N;A222V;D614G;D614G;D614G;D614G;D614G;D614G;D614G;D614G;D614G;L1063F;L216F;M740V;N751Y 89;82;144;247;287;157;254;261;274;305;124;111;240;137;95;117;131;150;163;267;280;294;311;217;178;193;233 94;87;149;252;293;162;259;266;279;310;130;116;245;142;100;122;136;155;168;272;285;299;316;223;183;198;238 35090164 Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants. In additional to the reported mutations (A67V, Delta69-70, T95I, G142D, Delta143-145, Delta211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K and L981F) on Omicron, the proline substitutions at 817, 892, 899, 942, 986 and 987, 'GSAS' substitutions at the S1/S2 furin cleavage site (residues 682-685) and a C-terminal T4 foldon trimerization domain were also introduced in the Omicron S construct to stabilize the trimeric conformation of S protein. 2022 Nature Method SARS_CoV_2 D614G;D796Y;E484A;G142D;G339D;G446S;G496S;H655Y;K417N;L212I;L981F;N440K;N501Y;N679K;N764K;N856K;N969K;P681H;Q493R;Q498R;Q954H;S371L;S373P;S375F;S477N;T478K;T547K;T95I;Y505H;A67V 226;261;177;65;114;156;191;233;142;96;292;149;205;240;254;268;282;247;184;198;275;121;128;135;163;170;219;59;212;41 231;266;182;70;119;161;196;238;147;101;297;154;210;245;259;273;287;252;189;203;280;126;133;140;168;175;224;63;217;45 S;S 530;584 531;585 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. In a post-hoc analysis, neutralising antibody and binding antibody responses against the D614G variant were measured in a panel of human convalescent-serum samples (Sanguine Biobank, Waltham, MA, USA; iSpecimen, Lexington, MA, USA; PPD, Wilmington, NC, USA; 79 samples) using the same assays that were used on the participant serum samples, in the same laboratory, and within a contemporaneous timeframe to minimise assay variability over time. 2022 The Lancet. Infectious diseases Method SARS_CoV_2 D614G 89 94 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. Neutralising antibody and binding antibody responses to D614G were measured in all participants on day 1, day 22, and day 36. 2022 The Lancet. Infectious diseases Method SARS_CoV_2 D614G 56 61 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. SARS-CoV-2 neutralising-antibody titres against the D614G variant and the beta (B.1.351) variant were measured with a pseudovirus neutralisation assay, using HIV-1 pseudovirions expressing the full-length S protein of the respective variant, at Monogram Biosciences LabCorp (South San Francisco, CA, USA). 2022 The Lancet. Infectious diseases Method SARS_CoV_2 D614G 52 57 S 205 206 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. The primary immunogenicity objective was to describe the neutralising antibody response to the D614G variant 14 days after the second vaccination (on day 36) in participants who were SARS-CoV-2 naive. 2022 The Lancet. Infectious diseases Method SARS_CoV_2 D614G 95 100 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. The D614G containing strain, SARS-CoV-2/England/IC19/2020, was used as previously described. 2022 Cell reports Method SARS_CoV_2 D614G 4 9 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Unless otherwise stated all SARS-CoV-2 spike expression plasmids were based on the Wuhan-hu-1 reference sequence, with the additional substitutions D614G and K1255*STOP (aka the Delta19 mutation or cytoplasmic tail truncation). 2022 Cell reports Method SARS_CoV_2 D614G 148 153 S 39 44 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Where appropriate the relevant synthetic cDNA fragment carried the mutation D614G or Y453F + D614G in the viral S gene. 2022 Cell reports Method SARS_CoV_2 D614G;D614G;Y453F 76;93;85 81;98;90 S 112 113 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Bioinformatic characterization of S939F and D614G variants. 2022 Computational and structural biotechnology journal Method SARS_CoV_2 D614G;S939F 44;34 49;39 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Distribution of S939F and D614G variants in the world over time was provided by COVID-19 CoV Genetics browser (https://covidcg.org). 2022 Computational and structural biotechnology journal Method SARS_CoV_2 D614G;S939F 26;16 31;21 COVID-19 80 88 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Distribution of S939F variant in Europe at the indicated time points was verified by interrogating GISAID database (https://www.gisaid.org). 2022 Computational and structural biotechnology journal Method SARS_CoV_2 S939F 16 21 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Here we scan all the peptides selected by proteasome simulation with lengths 8-11 from the spike protein of the reference virus SARS-CoV-2 and of the mutated virus, including the two mutations D614G and S939F. 2022 Computational and structural biotechnology journal Method SARS_CoV_2 D614G;S939F 193;203 198;208 S 91 96 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Information about S939F and D614G variants counts and frequency were obtained by 2019nCoVR browser (https://bigd.big.ac.cn/ncov). 2022 Computational and structural biotechnology journal Method SARS_CoV_2 D614G;S939F 28;18 33;23 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. We only estimate the binding affinities for peptides selected by proteasome using NetChop 3.1 and that differ between the reference and the mutated (D614G and S939F) SARS-CoV-2 virus. 2022 Computational and structural biotechnology journal Method SARS_CoV_2 S939F;D614G 159;149 164;154 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. We perform the scan for the spike protein of the reference virus SARS-CoV-2 and of the mutated virus which includes the two mutations D614G and S939F. 2022 Computational and structural biotechnology journal Method SARS_CoV_2 D614G;S939F 134;144 139;149 S 28 33 35104067 Neutralizing Antibodies and Cytokines in Breast Milk After Coronavirus Disease 2019 (COVID-19) mRNA Vaccination. Cytokines were measured in a multiplex assay (Mesoscale Discovery) according to the manufacturer's instructions using 10-plex human V-PLEX Proinflammatory Panel 1 plates (K15049D). 2022 Obstetrics and gynecology Method SARS_CoV_2 K15049D 171 178 35104067 Neutralizing Antibodies and Cytokines in Breast Milk After Coronavirus Disease 2019 (COVID-19) mRNA Vaccination. We are reporting results for wildtype spike (referred to as spike) and four spike variants: D614G, B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma). 2022 Obstetrics and gynecology Method SARS_CoV_2 D614G 92 97 S;S;S 38;60;76 43;65;81 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. As it was already evident that 20B and its subclades contains lineages of R203K/G204R samples, subsamples from 20B and its subclades were sufficient to obtain a total of 16,386 samples. 2022 Nature communications Method SARS_CoV_2 R203K;G204R 74;80 79;85 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Origin of R203K/G204R SNPs. 2022 Nature communications Method SARS_CoV_2 R203K;G204R 10;16 15;21 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. The three consecutive SNPs (G28881A, G28882A, G28883C), corresponding to N protein mutation sites R203K and G204R, were introduced by megaprime PCR mutagenesis using the primers listed in Supplementary Table S10. 2022 Nature communications Method SARS_CoV_2 G204R;G28882A;G28883C;R203K;G28881A 108;37;46;98;28 113;44;53;103;35 N 73 74 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. To identify if there are lineages of triplet SNPs in clades other than 20B, a phylogenetic tree was constructed by including all R203K/G204R samples found in other clades outside 20B and its subclades. 2022 Nature communications Method SARS_CoV_2 R203K;G204R 129;135 134;140 35113647 Divergent SARS-CoV-2 Omicron-reactive T and B cell responses in COVID-19 vaccine recipients. PBMCs were thawed in Gibco Roswell Park Memorial Institute 1640 medium (Gibco) supplemented with 10% human serum (Sanquin, Rotterdam), penicillin (100 IU/ml; Lonza, Belgium), streptomycin (100 mug/ml; Lonza, Belgium), and 2 mM L-glutamine (Lonza, Belgium; R10H medium) and treated with Benzonase (50 IU/ml; Merck) at 37 C for 30 min. 2022 Science immunology Method SARS_CoV_2 R10H 256 260 35113647 Divergent SARS-CoV-2 Omicron-reactive T and B cell responses in COVID-19 vaccine recipients. The beta variant (clade B.1.351) passage 3 sequence contained two mutations compared the original respiratory specimen: one synonymous mutations C13860T (Wuhan-1 position) in ORF1ab and a L71P change in the E gene (T26456C, Wuhan-1 position). 2022 Science immunology Method SARS_CoV_2 C13860T;L71P;T26456C 145;188;215 152;192;222 ORF1ab;E 175;207 181;208 35113647 Divergent SARS-CoV-2 Omicron-reactive T and B cell responses in COVID-19 vaccine recipients. The beta variant contained the following spike changes: L18F, D80A, D215G, del241-243, K417N, E484K, N501Y, D614G, and A701V. 2022 Science immunology Method SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;L18F;N501Y 119;68;108;62;94;87;56;101 124;73;113;66;99;92;60;106 S 41 46 35113647 Divergent SARS-CoV-2 Omicron-reactive T and B cell responses in COVID-19 vaccine recipients. The delta variant contained the following spike changes: T19R, G142D, del156-157, R158G, A222V, L452R, T478K, D614G, P681R and D950N. 2022 Science immunology Method SARS_CoV_2 A222V;D614G;D950N;G142D;L452R;P681R;R158G;T19R;T478K 89;110;127;63;96;117;82;57;103 94;115;132;68;101;122;87;61;108 S 42 47 35113647 Divergent SARS-CoV-2 Omicron-reactive T and B cell responses in COVID-19 vaccine recipients. The omicron variant contained the following spike mutations: A67VS, del69-70, T95I, G142-, del143-144, Y145D, del211, L212I, ins215EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F. 2022 Science immunology Method SARS_CoV_2 D614G;D796Y;E484A;G339D;G446S;G496S;H655Y;K417N;L212I;L981F;N440K;N501Y;N679K;N764K;N856K;N969K;P681H;Q493R;Q498R;Q954H;S371L;S373P;S375F;S477N;T478K;T547K;T95I;Y145D;Y505H 248;283;199;136;178;213;255;164;118;311;171;227;262;276;290;304;269;206;220;297;143;150;157;185;192;241;78;103;234 253;288;204;141;183;218;260;169;123;316;176;232;267;281;295;309;274;211;225;302;148;155;162;190;197;246;82;108;239 S 44 49 35113647 Divergent SARS-CoV-2 Omicron-reactive T and B cell responses in COVID-19 vaccine recipients. These patients were infected during the first wave in 2020, all with a D614G SARS-CoV-2. 2022 Science immunology Method SARS_CoV_2 D614G 71 76 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. Analytes used in kinetic analysis were uncleavable S trimer, RBD-SD1, RBD wild-type, RBD mutants, commercially purchased recombinant SARS-CoV-2 S2 and SARS-CoV-2 S1 (SinoBiological; Cat #s 40,590- and 40,591-V08H, respectively). 2022 Cell reports Method SARS_CoV_2 V08H 208 212 RBD;RBD;RBD 61;70;85 64;73;88 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. Twenty microliters of 0.25 mug/mL SULFO-tag, anti-Human antibody (MSD; Cat #R32A) were added to the wells and incubated for 1 h followed by six washes as before. 2022 Cell reports Method SARS_CoV_2 R32A 76 80 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. VH and VL sequences of candidate sequences were cloned into a pEAK8 based vector (Edge Bio) with dual CMV promotor harboring IgG1 heavy chain and light chain backbone using NEBuilder Hifi DNA Assembly Master Mix (NEB; Cat #E261L). 2022 Cell reports Method SARS_CoV_2 E261L 223 228 35114688 ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. and GX-Pangolin-CoV (P2V, ambiguous nucleotide in codon 515 (SARS-CoV-2 numbering) was resolved to retain amino acid Phe515, which is conserved across all other sarbecoviruses). 2022 Nature Method SARS_CoV_2 P2V 21 24 35114688 ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. BtKY72 mutant constructs T498W (BtKY72 S residue 487) and K493Y/T498W (BtKY72 S residue 482/487) were subcloned by GenScript from the BtKY72 RBD construct. 2022 Nature Method SARS_CoV_2 K493Y;T498W;T498W 58;25;64 63;30;69 RBD;S;S 141;39;78 144;40;79 35114688 ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. Mouse (Mus musculus) ACE2 (UniProt: Q8R0I0-1) was purchased from Sino Biological (50249-M03H), consisting of residues 18-740 spanning an intrinsic dimerization domain, followed by a His tag and human IgG1 Fc domain used for downstream detection. 2022 Nature Method SARS_CoV_2 M03H 88 92 35114688 ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. The BtKY72 mutant S constructs T498W (BtKY72 S residue 487) and K493Y/T498W (BtKY72 S residue 482/487) were subcloned by GenScript from the BtKY72 S construct. 2022 Nature Method SARS_CoV_2 K493Y;T498W;T498W 64;31;70 69;36;75 S;S;S;S 18;45;84;147 19;46;85;148 35115523 Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. A tertiary PCR (50 microL) was performed to add adapter sequences required for Illumina cluster generation with forward and reverse primers (0.2 microM each), dNTPs (200 microM each) (New England Biolabs, N0447L) and Phusion High-Fidelity DNA Polymerase (1U) (New England Biolabs, M0530L). 2022 Nature communications Method SARS_CoV_2 M0530L 281 287 35115523 Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. RNA isolated from wastewater was used to generate cDNA using ProtoScript II Reverse Transcriptase kit (New England Biolabs, M0368S). 2022 Nature communications Method SARS_CoV_2 M0368S 125 131 35115523 Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. rRNA Libraries were amplified using ProtoScript II Reverse Transcriptase (New England Biolabs, M0368S) and pooled and sequenced on the iSeq100 as described above. 2022 Nature communications Method SARS_CoV_2 M0368S 96 102 35115523 Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. Secondary PCR (25 microL) was performed on RBD amplifications using 5 microL of the primary PCR as template with MiSeq nested gene specific primers containing 5' adapter sequences (Supplementary Table 1) (0.5 microM each), dNTPs (100 microM each) (New England Biolabs, N0447L) and Q5 DNA polymerase (New England Biolabs, M0541S). 2022 Nature communications Method SARS_CoV_2 M0541S 321 327 RBD 43 46 35115523 Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. The RBD region was amplified using Q5 High-Fidelity DNA Polymerase (New England Biolabs, M0491S) using primers that incorporate Illumina adapters (see Supplementary Table 2). 2022 Nature communications Method SARS_CoV_2 M0491S 90 96 RBD 4 7 35115523 Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. This construct was modified to enhance transduction efficiency by truncating the last 19 amino acids and introducing the D614G amino acid change. 2022 Nature communications Method SARS_CoV_2 D614G 121 126 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. Biotinylated wildtype, B.1.1.7, or E406W RBD at a concentration of 5 ng/muL in 10X kinetics buffer was loaded at 30C onto pre-hydrated streptavidin biosensor to a 1 nm total shift. 2022 bioRxiv Method SARS_CoV_2 E406W 35 40 RBD 41 44 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. E406W and wildtype pseudotyped VSV particles were produced as previously described. 2022 bioRxiv Method SARS_CoV_2 E406W 0 5 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. E406W and wildtype pseudoviruses were diluted 1:25 in DMEM and incubated with vaccine-elicited sera for 30 minutes at room temperature. 2022 bioRxiv Method SARS_CoV_2 E406W 0 5 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. Purified SARS-CoV-2 spike ectodomain harboring the E406W mutation was added to a freshly glow discharged 2.0/2.0 UltraFoil grid (200 mesh). 2022 bioRxiv Method SARS_CoV_2 E406W 51 56 S 20 25 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. The cells were then washed 5 times with Opti-MEM (Life Technologies) and transfected with 24 mug of plasmid encoding either the wildtype or E406W SARS-CoV-2 spike protein using Lipofectamine 2000 (Life Technologies). 2022 bioRxiv Method SARS_CoV_2 E406W 140 145 S 157 162 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. The construct encoding spike ectodomain harboring the E406W mutation was obtained from the Institute for Protein Design. 2022 bioRxiv Method SARS_CoV_2 E406W 54 59 S 23 28 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. The construct encoding the E406W RBD was generated by performing around-the-horn mutagenesis using a pCMVR vector encoding the wildtype SARS-CoV-2 RBD containing an N-terminal mu-phosphatase signal peptide and a C-terminal avi tag and octa-histidine tag. 2022 bioRxiv Method SARS_CoV_2 E406W 27 32 RBD;RBD;N 33;147;165 36;150;166 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. The wildtype, B.1.1.7, and E406W RBDs were produced by transfecting 25 mL of Expi293 cells at a density of 2.5 x 106 cells per mL with 25 mug of DNA using the ExpiFectamine 293 Transfection Kit. 2022 bioRxiv Method SARS_CoV_2 E406W 27 32 RBD 33 37 35118471 Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail. To produce the SARS-CoV-2 spike ectodomain containing the E406W mutation, 125 mL of Expi293 cells were grown to density of 2.5 x 106 cells per mL and transfected with 125 mug of DNA using PEI MAX diluted in Opti-MEM. 2022 bioRxiv Method SARS_CoV_2 E406W 58 63 S 26 31 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. In each variant, the Alpha includes N501Y mutation, Delta has L452R and T478K mutations, and Omicron contains 15 mutated amino acids, i.e., G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q483K/R, G496S, Q498R, N501Y, and Y505H (see also Figures 1B and 2D). 2022 bioRxiv Method SARS_CoV_2 E484A;G339D;G446S;G496S;K417N;L452R;N440K;N501Y;N501Y;Q483K;Q483R;Q498R;S371L;S373P;S375F;S477N;T478K;T478K;Y505H 203;140;182;219;168;62;175;36;233;210;210;226;147;154;161;189;72;196;244 208;145;187;224;173;67;180;41;238;217;217;231;152;159;166;194;77;201;249 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. Recombinant human ACE2 protein (GenBank accession: AF291820.1, Sino Biological 10108-H08H, Wayne, PA) was labeled with RED-NHS (2nd Generation) dye using the Monolith Protein Labeling Kit (NanoTemper Technologies, MO-L011, Munchen, Germany). 2022 bioRxiv Method SARS_CoV_2 H08H 85 89 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. To improve statistical results, 20 independent simulation runs of two Omicron variants, Q493K and Q493R, were performed for at least 40 ns to secure that the RBD and ACE2 are entirely dissociated from each other. 2022 bioRxiv Method SARS_CoV_2 Q493K;Q493R 88;98 93;103 RBD 158 161 35118474 Breadth of SARS-CoV-2 Neutralization and Protection Induced by a Nanoparticle Vaccine. D614G spike mutation: D614G; Alpha (B.1.1.7) spike mutations: Delta69-70, Delta144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H; Beta (B.1.351) spike mutations: L18F, D80A, D215G, Delta242-244, R246I, K417N, E484K, N501Y, D614G, A701V; Delta (B.1.617 AY.3) spike mutations: T19R, G142D, Delta156-157, R158G, L452R, T478K, D614G, P681R, D950N; Epsilon (B.1.429) spike mutations: S13I, W152C, L452R, D614G; Omicron (B.1.1.529) spike mutations: A67V, Delta69-70, T95I, G142D, Delta143-145, Delta211, L212I, +214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F. 2022 bioRxiv Method SARS_CoV_2 A570D;A67V;A701V;D1118H;D215G;D614G;D614G;D614G;D614G;D614G;D614G;D796Y;D80A;D950N;E484A;E484K;G142D;G142D;G339D;G446S;G496S;H655Y;K417N;K417N;L18F;L212I;L452R;L452R;L981F;N440K;N501Y;N501Y;N501Y;N679K;N764K;N856K;N969K;P681H;P681H;P681R;Q493R;Q498R;Q954H;R158G;R246I;S13I;S371L;S373P;S375F;S477N;S982A;T19R;T478K;T478K;T547K;T716I;T95I;W152C;Y505H;D614G 91;447;234;126;178;22;98;227;327;403;630;665;172;341;581;213;285;471;518;560;595;637;206;546;166;502;313;396;693;553;84;220;609;644;658;672;686;105;651;334;588;602;679;306;199;383;525;532;539;567;119;279;320;574;623;112;465;389;616;0 96;451;239;132;183;27;103;232;332;408;635;670;176;346;586;218;290;476;523;565;600;642;211;551;170;507;318;401;698;558;89;225;614;649;663;677;691;110;656;339;593;607;684;311;204;387;530;537;544;572;124;283;325;579;628;117;469;394;621;5 S;S;S;S;S;S 6;45;149;262;366;430 11;50;154;267;371;435 35118474 Breadth of SARS-CoV-2 Neutralization and Protection Induced by a Nanoparticle Vaccine. In the second study, cynomolgus macaques (n=5) were were immunized twice with 50 mug of S-2P mRNA-LNP (encoding the transmembrane spike protein stabilized with K986P and V987P mutations) and boosted once with 100 mug of RBD-scNP, NTD-scNP and S2P-scNP adjuvanted with 5 mug of 3M-052 aqueous formulation admixed with 500 mug of alum in PBS. 2022 bioRxiv Method SARS_CoV_2 K986P;V987P 160;170 165;175 S;RBD 130;220 135;223 35118474 Breadth of SARS-CoV-2 Neutralization and Protection Induced by a Nanoparticle Vaccine. The S-2P mRNA was designed based on the SARS-CoV-2 spike (S) protein sequence (Wuhan-Hu-1) and encoded the full-length S with K986P and V987P amino acid substitutions. 2022 bioRxiv Method SARS_CoV_2 K986P;V987P 126;136 131;141 S;S;S 51;58;119 56;59;120 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. Assessment of Neutralization Titers Against D614G Wild-type and Omicron Variant. 2022 medRxiv Method SARS_CoV_2 D614G 44 49 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. No formal statistical comparisons were made between Omicron and wild-type (D614G) or age groups. 2022 medRxiv Method SARS_CoV_2 D614G 75 80 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. Omicron neutralization titers in serum samples obtained on the day 1 prior to dose 1 and one month after dose 2 in adults and adolescents who received 100 mug mRNA-1273, and children who received 50 mug mRNA-1273 were compared to corresponding neutralization titers of the same serum samples assayed against the prototypic wild-type (D614G) strain. 2022 medRxiv Method SARS_CoV_2 D614G 334 339 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. Serum samples from three ongoing clinical trials were assessed for neutralization of Omicron variant compared with the prototypic wild-type D614G strain. 2022 medRxiv Method SARS_CoV_2 D614G 140 145 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. The D614G (B.1) variant contained D614G as the only spike mutation. 2022 medRxiv Method SARS_CoV_2 D614G;D614G 4;34 9;39 S 52 57 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. The Omicron (B.1.1.529) variant contained spike mutations A67V, Delta69-70, T95I, G142D, Delta143-145, Delta211, L212I, +214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L9. 2022 medRxiv Method SARS_CoV_2 A67V;D614G;D796Y;E484A;G142D;G339D;G446S;G496S;H655Y;K417N;L212I;N440K;N501Y;N679K;N764K;N856K;N969K;P681H;Q493R;Q498R;Q954H;S371L;S373P;S375F;S477N;T478K;T547K;T95I;Y505H 58;241;276;192;82;129;171;206;248;157;113;164;220;255;269;283;297;262;199;213;290;136;143;150;178;185;234;76;227 62;246;281;197;87;134;176;211;253;162;118;169;225;260;274;288;302;267;204;218;295;141;148;155;183;190;239;80;232 S 42 47 35118475 mRNA-1273 Vaccine-elicited Neutralization of SARS-CoV-2 Omicron in Adolescents and Children. The pseudovirus neutralization assay performed at Duke has been described in detail and is a formally validated adaptation of the assay utilized by the VRC; the Duke assay is FDA approved for D614G. 2022 medRxiv Method SARS_CoV_2 D614G 192 197 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. Similarly, we have considered the average simulated structures of D155Y and S171L variants of ORF3a and used them to dock to the human caveolin-1 protein via HADDOCK webserver. 2022 Computational and structural biotechnology journal Method SARS_CoV_2 D155Y;S171L 66;76 71;81 ORF3a 94 99 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. We also calculated the substitution frequency (f) of D155Y and S171L worldwide using the formula, f = (No. 2022 Computational and structural biotechnology journal Method SARS_CoV_2 D155Y;S171L 53;63 58;68 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. We introduced the necessary mutations (D155Y and S171L) by modelling the residues in Swiss PDB Viewer. 2022 Computational and structural biotechnology journal Method SARS_CoV_2 S171L;D155Y 49;39 54;44 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. To perform PCR amplification of the viral cDNA, the following reagents were added to 2.5 mul of the previous mixture: 0.25 mul Q5 Hot Start DNA polymerase (NEB, M0493S), 5 mul of 5X Q5 Reaction Buffer (NEB, M0493S), 0.5 mul of 10 mM dNTPs Mix (NEB, N0447S), either 4.0 mul of pooled primer set 1 or 3.98 mul of pooled primer set 2, and nuclease-free water to bring to a final volume of 25 mul. 2022 mBio Method SARS_CoV_2 M0493S;M0493S 161;207 167;213 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Additionally, in Figure 5c a comparison of the experimental pseudovirus infection changes and predicted BFE change of ACE2 and S protein complex induced by mutations L452R and N501Y, where the experimental data is obtained in a reference to D614G and reported in relative luciferase units. 2022 ACS infectious diseases Method SARS_CoV_2 D614G;L452R;N501Y 241;166;176 246;171;181 S 127 128 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Considering the BFE changes induced by RBD mutations for ACE2 and RBD complex, predictions on mutations L452R and N501Y have a highly similar trend with experimental data. 2022 ACS infectious diseases Method SARS_CoV_2 L452R;N501Y 104;114 109;119 RBD;RBD 39;66 42;69 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. In our predictions, L452R induces a negative BFE change (-2.39 kcal/mol), and T478K produces a positive BFE change (0.36 kcal/mol). 2022 ACS infectious diseases Method SARS_CoV_2 L452R;T478K 20;78 25;83 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Recent studies on potency of mAb CT-P59 in vitro and in vivo against Delta variants show that the neutralization of CT-P59 is reduced by L452R (13.22 ng/mL) and is retained against T478K (0.213 ng/mL). 2022 ACS infectious diseases Method SARS_CoV_2 L452R;T478K 137;181 142;186 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. B.1.617.1 E484A HexaPro. 2022 Nature communications Method SARS_CoV_2 E484A 10 15 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. B.1.617.1 E484I HexaPro. 2022 Nature communications Method SARS_CoV_2 E484I 10 15 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. For ELISA, 100 microL of wild-type (D614G), Kappa or Delta SARS-CoV-2 S proteins were coated onto 96-well MaxiSorp plates at 2 microg/mL in PBS overnight at 4 C. 2022 Nature communications Method SARS_CoV_2 D614G 36 41 S 70 71 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. For models of spike protein ectodomain alone, the SARS-CoV-2 HexaPro S trimer with N501Y mutation (PDB code 7MJG) was docked into the cryo-EM density map using UCSF Chimera v.1.15. 2022 Nature communications Method SARS_CoV_2 N501Y 83 88 S;S 14;69 19;70 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The production of the SARS-CoV-2 wild-type (D614G) S protein was described previously. 2022 Nature communications Method SARS_CoV_2 D614G 44 49 S 51 52 35151002 Rapid biosensing SARS-CoV-2 antibodies in vaccinated healthy donors. Biotinylation of S-ECD and RBD-N501Y was conducted according to the biotinylating kit protocol, followed by a desalting protocol to remove any unbound biotin, and a BCA protein assay protocol. 2022 Biosensors & bioelectronics Method SARS_CoV_2 N501Y 31 36 RBD;S 27;17 30;18 35151002 Rapid biosensing SARS-CoV-2 antibodies in vaccinated healthy donors. The biotinylated SARS-CoV-2 spike RBD-His recombinant protein, SARS-CoV-2 spike RBD(N501Y)-His recombinant protein, SARS-CoV-2 spike ECD (S1+S2)-His recombinant protein, SARS-CoV-2 spike pseudovirus (containing 1010 virus copies/mL and 860 ng/mL of SARS-CoV-2-S1), human recombinant ACE2 protein (biotinylated), rabbit SARS-CoV-2 spike neutralizing antibody, SARS-CoV-2 spike RBD recombinant protein (HRP labeled, customized), SARS-CoV-2 (2019-nCoV) Spike RBD Antibody Titer Assay Kit, and SARS-CoV-2 (2019-nCoV) Inhibitor Screening ELISA Kit were purchased from Sino Biologicals (Beijing, China). 2022 Biosensors & bioelectronics Method SARS_CoV_2 N501Y 84 89 S;S;S;S;S;S;S;RBD;RBD;RBD;RBD 28;74;127;181;330;370;450;34;80;376;456 33;79;132;186;335;375;455;37;83;379;459 35151002 Rapid biosensing SARS-CoV-2 antibodies in vaccinated healthy donors. The process for establishing the S-ECD-specific BAbs (i.e., anti-S-ECD BAbs) and RBD-N501Y-specific BAb (i.e., anti-RBD N501Y BAbs) biosensors is the same as that described above. 2022 Biosensors & bioelectronics Method SARS_CoV_2 N501Y;N501Y 120;85 125;90 RBD;RBD;S;S 81;116;33;65 84;119;34;66 35151002 Rapid biosensing SARS-CoV-2 antibodies in vaccinated healthy donors. Three types of antigens, SARS-CoV-2 extracellular domain of spike protein (S-ECD), receptor binding domain (RBD), and RBD-N501Y mutation, were labeled with biotin for interaction. 2022 Biosensors & bioelectronics Method SARS_CoV_2 N501Y 122 127 RBD;S;RBD;RBD;S 83;60;108;118;75 106;65;111;121;76 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. All the available SARS-CoV-2 sequences with the mutation S:T1117I, up to April 30th and from all the locations worldwide, were retrieved from the GISAID database (Global Initiative on Sharing All Influenza Data, www.gisaid.org). 2022 Gene reports Method SARS_CoV_2 T1117I 59 65 S 57 58 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. All the worldwide sequences with the mutation S:T1117I were aligned using MAFFT v7.471. 2022 Gene reports Method SARS_CoV_2 T1117I 48 54 S 46 47 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. The analysis was done using the reference spike PDB model (wild type, WT) as well as with the mutated version with the mutations S:D614G and S:T1117I. 2022 Gene reports Method SARS_CoV_2 D614G;T1117I 131;143 136;149 S;S;S 42;129;141 47;130;142 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. Then, the modification to I1117 (mutated, S:T1117I) was done manually. 2022 Gene reports Method SARS_CoV_2 T1117I 44 50 S 42 43 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. To assess the effects of the mutations S:D614G and S:T1117I, the two spike mutations of the lineage B.1.1.389, on the interaction of the spike with a specific ligand, we performed a molecular docking analysis. 2022 Gene reports Method SARS_CoV_2 D614G;T1117I 41;53 46;59 S;S;S;S 69;137;39;51 74;142;40;52 35157870 Detection of SARS-CoV-2 RNA in wastewater, river water, and hospital wastewater of Nepal. A N501Y mutation-specific qPCR assay that targets nucleotide at spike receptor binding domain (adenine replaced by uracil at position 23,063 with reference to NC_045512.2) was also tested to detect N501Y mutation. 2022 The Science of the total environment Method SARS_CoV_2 N501Y;N501Y 2;198 7;203 RBD;S 70;64 93;69 35157870 Detection of SARS-CoV-2 RNA in wastewater, river water, and hospital wastewater of Nepal. The thermal conditions were as follows: 25 C for 10 min and 95 C for 30 s, followed by 45 cycles of 95 C for 5 s and 60 C for 60 s (for N_Sarbeco, NIID_2019-nCOV_N, PMMoV, TMV, and MNV), or 60 C for 30 s (for CDC-N1 and CDC-N2, N501Y, and crAssphage). 2022 The Science of the total environment Method SARS_CoV_2 N501Y 233 238 35157870 Detection of SARS-CoV-2 RNA in wastewater, river water, and hospital wastewater of Nepal. To draw a standard curve, six 10-fold serial dilutions of gBlocks gene fragments (Integrated DNA Technologies, Coralville, IA, USA) (for NIID_2019-nCOV_N, N_Sarbeco, and N501Y), 2019-nCoV_N Positive Control (Integrated DNA Technologies, cat. 2022 The Science of the total environment Method SARS_CoV_2 N501Y 170 175 35162151 Shorter Incubation Period among Unvaccinated Delta Variant Coronavirus Disease 2019 Patients in Japan. Among unvaccinated COVID-19 patients with a definite single date of exposure, we defined non-Delta strain cases as either those reported from November 2020 to 6 June or those reported after 7 June and with L452R mutation negative results for not less than two people among the patients and their contacts. 2022 International journal of environmental research and public health Method SARS_CoV_2 L452R 206 211 COVID-19 19 27 35162151 Shorter Incubation Period among Unvaccinated Delta Variant Coronavirus Disease 2019 Patients in Japan. Among unvaccinated COVID-19 patients with a definite single date of exposure, we determined the following patients with the Delta variant strain: cases reported from 8 July to September 2021 and in which the L452R variant was detected in the patients or their contacts. 2022 International journal of environmental research and public health Method SARS_CoV_2 L452R 208 213 COVID-19 19 27 35162151 Shorter Incubation Period among Unvaccinated Delta Variant Coronavirus Disease 2019 Patients in Japan. Because the result of L452R mutation was sometimes false negative, we thought that we could not classify a patient as non-Delta in case only one L452R variant was negative in the patient or among their contacts. 2022 International journal of environmental research and public health Method SARS_CoV_2 L452R;L452R 22;145 27;150 35162151 Shorter Incubation Period among Unvaccinated Delta Variant Coronavirus Disease 2019 Patients in Japan. However, almost all cases with the L452R mutation in Japan were confirmed to be the Delta variant by RNA sequencing. 2022 International journal of environmental research and public health Method SARS_CoV_2 L452R 35 40 35162151 Shorter Incubation Period among Unvaccinated Delta Variant Coronavirus Disease 2019 Patients in Japan. If a case was reported after 7 June, and, in addition, L452R mutation screening was not performed for the patient, or was all negative, or only one L452R variant was negative in the patient or among their contacts as described above, the patient was excluded from the study. 2022 International journal of environmental research and public health Method SARS_CoV_2 L452R;L452R 55;148 60;153 35162151 Shorter Incubation Period among Unvaccinated Delta Variant Coronavirus Disease 2019 Patients in Japan. In Japan, screening for the L452R mutation was implemented for approximately 40-50% of samples from July to August 2021. 2022 International journal of environmental research and public health Method SARS_CoV_2 L452R 28 33 35162151 Shorter Incubation Period among Unvaccinated Delta Variant Coronavirus Disease 2019 Patients in Japan. No L452R variant had been confirmed in COVID-19 cases reported until 7 June 2021 in these areas. 2022 International journal of environmental research and public health Method SARS_CoV_2 L452R 3 8 COVID-19 39 47 35162151 Shorter Incubation Period among Unvaccinated Delta Variant Coronavirus Disease 2019 Patients in Japan. The L452R mutation was also found in other variant strains of interest, such as the B.1.617.1 (Kappa) variant. 2022 International journal of environmental research and public health Method SARS_CoV_2 L452R 4 9 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. A systematic mutational scanning and sensitivity analysis of the functional RBD residues (K417, E484, N501), S-B.1.1.7 mutational sites (N501Y, A570D, P681H, T716I, S982A, and D1118H) and S-B.1.351 mutational sites (L18F, D80A, D215G, K417N, E484K, N501Y, D614G, and A701V). 2022 International journal of molecular sciences Method SARS_CoV_2 A570D;A701V;D1118H;D215G;D614G;D80A;E484K;K417N;N501Y;P681H;S982A;T716I;L18F;N501Y 144;267;176;228;256;222;242;235;249;151;165;158;216;137 149;272;182;233;261;226;247;240;254;156;170;163;220;142 RBD 76 79 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. The following cryo-EM structures of the SARS-CoV-2 S protein variants were used in molecular simulations: the S-D614G variant in the 3RBD-down closed state (pdb id 7KRQ), S-D614G variant in the 1 RBD-up form (pdb id 7KRR), S-B.1.1.7 variant in the 3 RBD-down closed form (pdb id 7N1U), S-B.1.1.7 variant in the 1 RBD-up open state (pdb id 7N1V), S-B.1.351 variant in the 3 RBD-down closed form (pdb id 7N1T) and S-B.1.351 variant in the 1 RBD-up open state (pdb id 7N1Q). 2022 International journal of molecular sciences Method SARS_CoV_2 D614G;D614G 112;173 117;178 RBD;RBD;RBD;RBD;RBD;S;S;S;S;S;S;S 196;250;313;373;439;51;110;171;223;286;346;412 199;253;316;376;442;52;111;172;224;287;347;413 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. The glycosylated microenvironment for atomistic models of the simulation trajectories was mimicked by using the structurally resolved glycan conformations for 22 most occupied N-glycans in each as determined in the cryo-EM structures of the SARS-CoV-2 spike S trimer in the closed state (K986P/V987P,) (pdb id 6VXX) and open state (pdb id 6VYB), and the cryo-EM structure SARS-CoV-2 spike trimer (K986P/V987P) in the open state (pdb id 6VSB). 2022 International journal of molecular sciences Method SARS_CoV_2 K986P;K986P;V987P;V987P 288;397;294;403 293;402;299;408 S;S;N;S 252;383;176;258 257;388;177;259 35164548 Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. C3040H) or DH5alpha cells and for DNA transformation. 2022 mBio Method SARS_CoV_2 C3040H 0 6 35164548 Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. The ORF3a mutant variants (Q57H and DeltaG188) were generated by overlapping PCR with mutant-specific primers (see Table S1 in the supplemental material) and cloned onto the same pLVX-EF1alpha-IRES-Puro plasmid via the Gibson assembly method. 2022 mBio Method SARS_CoV_2 Q57H 27 31 ORF3a 4 9 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. D614G point mutation was introduced into both untagged full-length pCMV3 SD614 and double-tagged SD614 Q3/A4 constructs to generate both untagged and tagged SG614 variants. 2022 mBio Method SARS_CoV_2 D614G 0 5 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. E484K and N501Y were further introduced into the untagged SG614 individually and together. 2022 mBio Method SARS_CoV_2 N501Y;E484K 10;0 15;5 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. E484K point mutation was introduced into both untagged and tagged pcDNA3.1 SAlpha by site-specific mutagenesis. 2022 mBio Method SARS_CoV_2 E484K 0 5 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. Lentivirus particles used for smFRET imaging were made in 293T cells by transfecting a 20-fold excess of plasmid encoding SD614, SG614, SAlpha, or SAlpha+E484K over their corresponding 427-Q3/556-A4 to ensure that, on average, every virus particle carried a single Q3/A4-tagged S protomer. 2022 mBio Method SARS_CoV_2 E484K 154 159 S 278 279 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. To conduct studies of S variants by smFRET, we introduced the labeling peptide tags Q3 and A4 at the same positions (427 and 556, respectively) in S1 of SG614, SAlpha, and E484K-carrying SAlpha (SAlpha+E484K) variants as in previously reported SD614. 2022 mBio Method SARS_CoV_2 E484K;E484K 172;202 177;207 S 22 23 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. 2 literally having K417N, T478K, E484A and N501Y mutation in the Sanger sequences. 2022 Scientific reports Method SARS_CoV_2 E484A;K417N;N501Y;T478K 33;19;43;26 38;24;48;31 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. If we found the mutation from Guanine (G) to Adenine (A) or Cystine (C)at nt23012, further identification was done as follows: double mutation of T22917G (referred to L452R) and C22995A (referred to T478K) for B.1.617.2 (Delta), T22917G (referred to L452R) and G23012C (referred to E484Q) for B.1.617.1 (Kappa) and T22917A (referred to L452Q) and T23031C (referred to F490S) for C.37 (Lambda). 2022 Scientific reports Method SARS_CoV_2 C22995A;E484Q;F490S;G23012C;L452Q;L452R;L452R;T22917A;T22917G;T22917G;T23031C;T478K 178;282;368;261;336;167;250;315;146;229;347;199 185;287;373;268;341;172;255;322;153;236;354;204 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. The Delta variant without mutation at nt22813 is the ordinary B.1.617.2 (Delta) but it is AY.1 or AY.2 (Delta Plus) if there is mutation from Guanine (G) to Thymine (T) at nt22813 (referred to K417N). 2022 Scientific reports Method SARS_CoV_2 K417N 193 198 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. The initial checkpoint was set at nucleotide position nt23063 and if we found mutation from adenine (A) to thymine (T) at nt23063, further identification was done as follows: double mutation of A23063T (referred to N501Y) and C23271A (referred to A570D) for B.1.1.7 (Alpha), G23013A (referred to E484K) and A23063T for B.1.351 (Beta) and triple mutation of G23012A, A23063T and C23525T (referred to H655Y) for P.1 (Gamma). 2022 Scientific reports Method SARS_CoV_2 A23063T;A23063T;A23063T;A570D;C23271A;C23525T;E484K;G23012A;G23013A;H655Y;N501Y;A23063T 194;307;366;247;226;378;296;357;275;399;215;91 201;314;373;252;233;385;301;364;282;404;220;129 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. The last checkpoint was set at nucleotide position nt22917 and if we found single mutation from Thymine (T) to Guanine (G) at nt22917 (referred to L452R) only, it is supposed to be B.1.429 (Epsilon). 2022 Scientific reports Method SARS_CoV_2 L452R 147 152 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. One primer pair targeting D614G Hotspot-FCS Region was designed for the polymerase chain reaction (PCR): F3.CoV-2.S, 5'-CTGTCCGTGATCCACAGACACT-3'; R3.CoV-2.S, 5'- GCACCAAGTGACATAGTGTAGGC-3'. 2022 International microbiology Method SARS_CoV_2 D614G 26 31 S;S 114;156 115;157 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. The D614G Hotspot-FCS Region (amino acid position = 600-700 [spike]; nucleotide position = 23,360-23,662 [Wuhan-Hu-1 NCBI Reference Sequence: NC_045512.2]) was extracted for further analysis. 2022 International microbiology Method SARS_CoV_2 D614G 4 9 S 61 66 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. Constructs encoding N- and C-terminal flag-tagged SARS-CoV-2 spike protein for each variant : D614G, Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529; also known as BA1.1 containing the R346K mutation) : were synthesized and cloned into pcDNA3.1 vector using KpnI/BamHI restriction enzyme cloning by GenScript Biotech. 2022 Science translational medicine Method SARS_CoV_2 D614G;R346K 94;212 99;217 S;N 61;20 66;21 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. Pseudotyped lentivirus was produced by co-transfection of HEK293T cells with pNL4-3-HIV-1-inGluc and pcDNA3.1 vector expressing the spike protein of interest (D614G, B.1.1.7, B.1.351, B.1.617.2, or B.1.1.529) in a 2:1 ratio using polyethylenimine (PEI) transfection. 2022 Science translational medicine Method SARS_CoV_2 D614G 159 164 S 132 137 35168024 Development of SARS-CoV-2 variant protein microarray for profiling humoral immunity in vaccinated subjects. Followed by incubation with 50 muL of Cy5-conjugated Streptavidin 2 ng/mL (Jackson Laboratory, #016-170-084), biotinylated ACE2 125 pg/mL (Sino biological, #10108-H08H-B), and anti-human IgG conjugated with Cy3 1.5 mug/mL (Jackson Laboratory, #109-165-003) for 1 hr, washed, dried, and then scanned. 2022 Biosensors & bioelectronics Method SARS_CoV_2 H08H 163 167 35168024 Development of SARS-CoV-2 variant protein microarray for profiling humoral immunity in vaccinated subjects. The CoVariant protein microarrays stored at -80 C were thawed to room temperature, washed with 1X TBST (TBS with 0.1% Tween 20) for 10 min, blocked by SuperBlock buffer (ThermoFisher, #37537) for 15 min, and incubated with 50 muL of 647-conjugated Rabbit Anti-His tag 1.1 ng/mL (Jackson Lab, #300-605-240), anti-spike antibody 31.25 ng/mL (Sino Biological, #40150-D001) with anti-human IgG conjugated with Cy3 1.5 mug/mL (Jackson Laboratory, #109-165-003), or biotinylated ACE2 125 pg/mL (Sino Biological, #10108-H08H-B) with Cy5-conjugated Streptavidin 2 ng/mL (Jackson Lab, #016-170-084) for quality control. 2022 Biosensors & bioelectronics Method SARS_CoV_2 H08H 514 518 S 313 318 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Specifically, recombinant plasmids coding Beta-RBD (the K417N, E484K, and N501Y mutations) or Delta-RBD (the L452R and T478K mutations) were made based on the plasmid pcDNA3.4-SARS-2-RBD by using the Mut ExpressTM II Fast Mutagenesis Kit V2 (Vazyme, China). 2022 Nature communications Method SARS_CoV_2 E484K;K417N;L452R;N501Y;T478K 63;56;109;74;119 68;61;114;79;124 RBD;RBD;RBD 47;100;183 50;103;186 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. To prepare the constructs of prefusion-stabilized S proteins of SARS-CoV-2 G614 and Delta (B.1.617.2) variants, D614G amino acid substitution of G614 variant and the mutations of Delta variant (T19R, E156DEL, F157DEL, R158G, L452R, T478K, D614G, P681R and D950N) were introduced by site-directed mutagenesis, using our previous prefusion-stabilized SARS-CoV-2 S-trimer expression plasmid. 2022 Nature communications Method SARS_CoV_2 D614G;D614G;D950N;delE156;delF157;L452R;P681R;R158G;T478K;T19R 112;239;256;200;209;225;246;218;232;194 117;244;261;207;216;230;251;223;237;198 S;S 50;360 51;361 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. 49.7% of all sequences included the N:G215C mutation characteristic for the dominant Delta clade, using the Wuhan-Hu-1 isolate (GenBank QHD43423) as the ancestral reference. 2022 bioRxiv Method SARS_CoV_2 G215C 38 43 N 36 37 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. For N:G215C the MW is 47027.15 Da and for N:D63G it is 46,923 Da. 2022 bioRxiv Method SARS_CoV_2 D63G;G215C 44;6 48;11 N 42 43 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. For the concentration series of N:G215C, the integrated weight-average sedimentation coefficients, sw were assembled into sw isotherms and modeled with a monomer-dimer equilibrium in the software SEDPHAT. 2022 bioRxiv Method SARS_CoV_2 G215C 34 39 N 32 33 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. SARS-CoV-2 N-protein accession # YP_009724397, the N:G215C mutant and the N:D63G mutant were acquired from EXONBIO (San Diego, CA; catalog# 19CoV-N150, 19Cov-N180, and 19Cov-N170). 2022 bioRxiv Method SARS_CoV_2 D63G;G215C 76;53 80;58 N;N;N 11;51;74 12;52;75 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. SARS-CoV-2 nucleocapsid protein # YP_009724397 with quadruple D63G, R203M, G215C, and D377Y mutations including 6His with TEV cleavage site was synthesized and cloned into the pET-29a(+) expression vector by GenScript (Pisctaway, NJ). 2022 bioRxiv Method SARS_CoV_2 D377Y;D63G;G215C;R203M 86;62;75;68 91;66;80;73 N 11 23 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. The mass distribution of N:G215C was determined using a Refeyn One instrument (Refeyn, Oxford, UK). 2022 bioRxiv Method SARS_CoV_2 G215C 27 32 N 25 26 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. The ratio of absorbance at 260 nm to 280 nm of Nref, N:D63G and N:G215C was 0.52, 0.56 and 0.56 respectively. 2022 bioRxiv Method SARS_CoV_2 D63G;G215C 55;66 59;71 N;N 53;64 54;65 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. A panel of 10 N501Y VOCs (including one with a mixed population) and 5 wild-type specimens was sent out to six different microbiology laboratories in Ontario to provide interlaboratory comparison data and to assist those laboratories to validate the assay prior to implementation. 2022 Microbiology spectrum Method SARS_CoV_2 N501Y 14 19 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. A panel of 160 SARS-CoV-2-positive clinical specimens that had been characterized by partial Sanger sequencing of the S gene were used for validation of the N501Y SNP assay. 2022 Microbiology spectrum Method SARS_CoV_2 N501Y 157 162 S 118 119 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Analytical sensitivity (95% LOD) in copies per reaction was conducted for both N501Y and N501 targets in the N501Y SNP rRT-PCR. 2022 Microbiology spectrum Method SARS_CoV_2 N501Y;N501Y 79;109 84;114 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Any results with targets not detected (or CT of >37) were reported "unable to complete," and if both N501 and N501Y were "unable to complete," they would have an attached interpretation stating, "Unable to screen for N501Y gene mutations as SARS-CoV-2 virus was not detected with the multiplex VOC SNP assay." An additional note would also be provided on the report stating, "SARS-CoV-2 VOC N501Y S gene mutation screening could not be performed as SARS-CoV-2 virus was not detected with the multiplex VOC SNP assay." This could be due to low viral load in the specimen, PCR inhibition, or other technical issues. 2022 Microbiology spectrum Method SARS_CoV_2 N501Y;N501Y;N501Y 110;217;391 115;222;396 S 397 398 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Clinical specimens that met these criteria with a CT value of <=30 underwent Sanger sequencing of a 698-bp (nucleotide positions 22516 to 23214) S gene fragment, which includes the locations of key receptor-binding domain (RBD) mutations (K417N/T, E484K, and N501Y). 2022 Microbiology spectrum Method SARS_CoV_2 E484K;N501Y;K417N;K417T 248;259;239;239 253;264;246;246 RBD;S 223;145 226;146 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. During optimization, it was determined that nonspecific signals in the N501Y target occurred above a CT of 37, as these were observed when making serial 10-fold dilutions of strongly positive (CT of <25) specimens known to be wild type based on Sanger sequencing. 2022 Microbiology spectrum Method SARS_CoV_2 N501Y 71 76 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. For the N501Y and N501 targets, we used a clinical specimen quantified using a known standard that is characterized as B.1.1.7 and wild type by WGS, respectively. 2022 Microbiology spectrum Method SARS_CoV_2 N501Y 8 13 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. If a sequence was wild type at positions 22813, 23012, and A23063T, which correspond to K417, E484, and N501Y, respectively, then it was called a probable UK variant. 2022 Microbiology spectrum Method SARS_CoV_2 A23063T;N501Y 59;104 66;109 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Intrarun repeatability was evaluated for both N501Y and N501 targets starting with 6.18 log copies/reaction and 6.40 log copies/reaction, respectively, and 10-fold serial dilutions down to 10-5 of starting material were tested. 2022 Microbiology spectrum Method SARS_CoV_2 N501Y 46 51 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. N501Y SNP rRT-PCR assay. 2022 Microbiology spectrum Method SARS_CoV_2 N501Y 0 5 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Primers and probes selected for the detection of SNP A23063T are reported in Table S1 in the supplemental material. 2022 Microbiology spectrum Method SARS_CoV_2 A23063T 53 60 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Specimens were screened using our N501Y RT-PCR assay to detect the presence of the N501Y mutation and were subsequently sequenced with WGS. 2022 Microbiology spectrum Method SARS_CoV_2 N501Y;N501Y 34;83 39;88 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The result obtained by our rRT-PCR N501Y SNP assay was compared to the known sequence results previously obtained by partial S gene sequencing and used to calculate PPA and NPA. 2022 Microbiology spectrum Method SARS_CoV_2 N501Y 35 40 S 125 126 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The same analysis done for intrarun repeatability was done to assess interrun reproducibility for both N501Y and N501 targets; however, we conducted this analysis over 3 days. 2022 Microbiology spectrum Method SARS_CoV_2 N501Y 103 108 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The same nucleic acid eluates were used for performing both N501Y SNP rRT-PCR and Sanger sequencing. 2022 Microbiology spectrum Method SARS_CoV_2 N501Y 60 65 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The study set consisted of all SARS-CoV-2-positive specimens with N501Y available at PHO Laboratory in addition to a convenience sample of specimens wild type at position 501 (N501). 2022 Microbiology spectrum Method SARS_CoV_2 N501Y 66 71 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The time interval between sequencing and running the N501Y rRT-PCR assay ranged from 1 to 14 days. 2022 Microbiology spectrum Method SARS_CoV_2 N501Y 53 58 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. It is also used to demonstrate the linear relationship in the activities of antisera in recognizing and in neutralizing both the WT and the N501Y RBD. 2022 Scientific reports Method SARS_CoV_2 N501Y 140 145 RBD 146 149 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. Recombinant SARS-CoV-2 spike receptor-binding domain (RBD) proteins contained a tissue plasminogen activator (TPA) signal peptide followed by amino acids 318-529 of spike (wild type or N501Y mutant) with a HRV-3C protease site and a C-terminal His (8)-streptavidin binding peptide tag. 2022 Scientific reports Method SARS_CoV_2 N501Y 185 190 S;S;RBD 23;165;54 28;170;57 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. ROC analysis was performed to determine the sensitivity and specificity of neutralization assays against the WT and the N501Y RBD proteins. 2022 Scientific reports Method SARS_CoV_2 N501Y 120 125 RBD 126 129 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. 1.617.2, which possesses the L452R and E484Q mutations) (Delta) strains. 2022 Vaccine Method SARS_CoV_2 E484Q;L452R 39;29 44;34 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. Different three-dimensional structures of the RBD variants namely, K417N, K417T, E484K, E484Q, L452R, N501Y, L452R-E484Q, K417N-E484K-N501Y, and K417T-E484K-N501Y were modeled using the BuildModel module of FoldX. 2022 Process biochemistry (Barking, London, England) Method SARS_CoV_2 E484K;E484Q;K417N;K417N;K417T;K417T;L452R;L452R;N501Y;E484K;E484K;E484Q;N501Y;N501Y 81;88;67;122;74;145;95;109;102;128;151;115;134;157 86;93;72;127;79;150;100;114;107;133;156;120;139;162 RBD 46 49 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Modeling the relative binding strength of N679K, P681H and P681R variants to furin. 2022 Microbiology spectrum Method SARS_CoV_2 N679K;P681H;P681R 42;49;59 47;54;64 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. The variants N679K, P681H and P681R loops were built by using Point mutant ("pmut") scan application of Rosetta onto a modeled native loop. 2022 Microbiology spectrum Method SARS_CoV_2 N679K;P681H;P681R 13;20;30 18;25;35 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. For example, positivity for mutant N501Y is when the FAM channel has a signal, and negativity for N501Y is when the HEX channel has a positive signal. 2022 Microbiology spectrum Method SARS_CoV_2 N501Y;N501Y 35;98 40;103 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. In addition, three separate assays were designed to detect spike mutations and wild type, E484K versus E484E, L452R versus L452L, and K417N versus K417K. 2022 Microbiology spectrum Method SARS_CoV_2 E484E;E484K;K417K;K417N;L452L;L452R 103;90;147;134;123;110 108;95;152;139;128;115 S 59 64 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. The assay for detection of the N501Y mutation was adapted from a multiplex RT-PCR assay for detection of spike mutants in SARS-CoV-2. 2022 Microbiology spectrum Method SARS_CoV_2 N501Y 31 36 S 105 110 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. The primer and probe overlap the sequences that contain mutant amino acids N501Y and its wild type N501N (Table 3). 2022 Microbiology spectrum Method SARS_CoV_2 N501N;N501Y 99;75 104;80 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. To verify the assay accuracy in our RT-PCR method, VOCs were also detected used VirSNiP SARS-CoV-2 mutation assays for strain surveillance (TIB Molbiol, Berlin, Germany), which used real-time RT-PCR postmelting curve analysis to detect mutations targeting specific spike protein variations (HV69/70, K417N, L452R, E484K, N501Y, P681H, and P681R). 2022 Microbiology spectrum Method SARS_CoV_2 E484K;K417N;L452R;N501Y;P681H;P681R 314;300;307;321;328;339 319;305;312;326;333;344 S 265 270 35197485 An adjuvanted subunit SARS-CoV-2 spike protein vaccine provides protection against Covid-19 infection and transmission. Determination of RBD-ACE2 blocking antibodies and virus-neutralizing antibody titers were determined against SARS-CoV-2 wild-type with D614G mutant and delta variant viruses as described above. 2022 NPJ vaccines Method SARS_CoV_2 D614G 135 140 RBD 17 20 35197485 An adjuvanted subunit SARS-CoV-2 spike protein vaccine provides protection against Covid-19 infection and transmission. For determining the virus-neutralizing antibodies 1000 TCID50 of wild-type (D614G) or delta variant of SARS-CoV-2 were used. 2022 NPJ vaccines Method SARS_CoV_2 D614G 76 81 35197485 An adjuvanted subunit SARS-CoV-2 spike protein vaccine provides protection against Covid-19 infection and transmission. Serum samples from four hamsters previously infected with the wild-type SARS-CoV-2 virus with a D614G mutation in the spike protein were used for comparison. 2022 NPJ vaccines Method SARS_CoV_2 D614G 96 101 S 118 123 35197485 An adjuvanted subunit SARS-CoV-2 spike protein vaccine provides protection against Covid-19 infection and transmission. Serum samples were complement inactivated at 56 C for 30 min then serially two-fold diluted in medium (DMEM-2% FCS-1% Antibiotic-Antimycotic; in final dilutions of 1:20 to 1:2560) and incubated in duplicates at 1:1 ratio with 1000 TCID50 of SARS-CoV-2 D614G mutant. 2022 NPJ vaccines Method SARS_CoV_2 D614G 253 258 35197485 An adjuvanted subunit SARS-CoV-2 spike protein vaccine provides protection against Covid-19 infection and transmission. The virus strain hCoV-19/Kazakhstan/KazNAU-NSCEDI481/2020 of wildtype SARS-CoV-2 with D614G mutation in spike protein was used. 2022 NPJ vaccines Method SARS_CoV_2 D614G 86 91 S 104 109 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. (Shanghai, China), containing the corresponding mutation site to be tested, and the length is 492 bp, including: non-mutation plasmid fragment, N501Y (AAT > TAT), N501H (AAT > CAT) mutant plasmid fragment, E484K (GAA > AAA), E484Q (GAA > CAA) mutant plasmid fragments, L452R (CTG > CGG), L452P (CTG > CCG) mutant plasmid fragments. 2022 Micromachines Method SARS_CoV_2 E484K;E484Q;L452P;L452R;N501H;N501Y 206;225;288;269;163;144 211;230;293;274;168;149 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. CC mutation template: 1.28 x 105 copies/muL 452 T > C mutation concentration plasmid was selected as the template for detection. 2022 Micromachines Method SARS_CoV_2 T452C 44 53 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. Download the gene sequences of four VOCs on the NCBI Genebank website, using DNAman V6 for sequence alignment, locating the mutation sites of K417N, L452R, E484K and N501Y genes, and design molecular markers. 2022 Micromachines Method SARS_CoV_2 E484K;K417N;L452R;N501Y 156;142;149;166 161;147;154;171 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. GG mutation template: select 1.28 x 105 copies/muL 452 T > G mutation concentration plasmid as template for detection. 2022 Micromachines Method SARS_CoV_2 T452G 51 60 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. Preliminary verification of PARMS technology and methodology for L452R, E484K, and N501Y sites, it is expected that TT, GG, AA type of T452G, G484A, A501T SARS-CoV-2 plasmids can be detected FAM fluorescent signals, GG, AA, TT type can be detected HEX fluorescence signal, no signal generated from other plasmids, as shown in Table 3, and the mutations of key sites are reflected by different fluorescent signals after PCR amplification. 2022 Micromachines Method SARS_CoV_2 A501T;E484K;G484A;L452R;N501Y;T452G 149;72;142;65;83;135 154;77;147;70;88;140 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. Taking the detection of T > G at the L452R locus as an example, the detection ability of PARMS PCR on related gene loci was investigated. 2022 Micromachines Method SARS_CoV_2 L452R 37 42 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. The PARMS technology methodological verification was performed on the sites including L452R, E484K, and N501Y respectively. 2022 Micromachines Method SARS_CoV_2 E484K;L452R;N501Y 93;86;104 98;91;109 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. Detection of the amplicons for each specific SARS-CoV-2 target (L452R or E484) was performed using a single fluorescence channel, usually FAM. 2022 Microorganisms Method SARS_CoV_2 L452R 64 69 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. Each assay can differentiate among some of these viral variants by identifying typical mutations: Alpha (B.1.1.7) by means of N501Y probe and, in some sequences, E484K probe; Beta (B.1.351) with N501Y, E484K and K417N probes; Gamma (P.1) with N501Y, E484K and K417T probes; Delta (B.1.617.2) through L452R probe and, in some sequences but not all, together with K417N probe; Iota (B.1.526) with E484K probe and, in some sequences, L452R probe; and Kappa (B.1.617.1) through L452R and E484Q probes. 2022 Microorganisms Method SARS_CoV_2 E484K;E484K;E484K;E484K;E484Q;K417N;K417N;K417T;L452R;L452R;L452R;N501Y;N501Y;N501Y 162;202;250;395;484;212;362;260;300;431;474;126;195;243 167;207;255;400;489;217;367;265;305;436;479;131;200;248 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. Five RUO multiplex real-time qualitative RT-PCR assays targeting some of the most widespread mutations in the spike protein (i.e., L452R, W152C, K417T, K417N, E484Q, E484K, N501Y) were used on positive specimens for a rapid and presumptive detection of the SARS-CoV-2 variants (Figure 1 and Table 1). 2022 Microorganisms Method SARS_CoV_2 E484K;E484Q;K417N;K417T;L452R;N501Y;W152C 166;159;152;145;131;173;138 171;164;157;150;136;178;143 S 110 115 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. Furthermore, these assays can be used to assume the presumptive presence of Eta (B.1.525) through E484K probe; Mu (B.1.6121) through N501Y and, occasionally, E484K; Zeta (P.1) through E484K; Theta (P.3) through E484K-N501Y; Epsilon (B.1.427/B.1.429) through L452 mutations; Lambda (C.37) through other L452 mutations; Omicron (B.1.1.529) through N501Y, K417N and E484, as well as others, that is, E484A; and B.1.640.2, which is the last discovered variant, often cited as "Cameroonian" (no WHO label has been attributed), through E484K and N501Y. 2022 Microorganisms Method SARS_CoV_2 E484A;E484K;E484K;E484K;E484K;E484K;K417N;N501Y;N501Y;N501Y;N501Y 397;98;158;184;211;530;353;133;346;540;217 402;103;163;189;216;535;358;138;351;545;222 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. L452R, E484K, E484Q and N501Y mutations are identified through this RT-PCR, usable for any type of positive SARS-CoV-2 biological samples. 2022 Microorganisms Method SARS_CoV_2 E484K;E484Q;N501Y;L452R 7;14;24;0 12;19;29;5 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. Reverse transcription and amplification were performed using the CFX96 thermal cycler to read FAM (wild-type sequences), HEX (E484K and E484Q mutations), Texas Red (N501Y mutation) and Cy5 (L452R mutation) fluorescence signals. 2022 Microorganisms Method SARS_CoV_2 E484Q;E484K;L452R;N501Y 136;126;190;165 141;131;195;170 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. Simplexa SARS-CoV-2 Variants Direct is an RT-PCR assay intended for detection of the N501Y, E484K, E484Q and L452 mutations in the spike genomic region of SARS-CoV-2 from NP or nasal swab samples from patients who are currently infected. 2022 Microorganisms Method SARS_CoV_2 E484K;E484Q;N501Y 92;99;85 97;104;90 S 131 136 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. The SARS-CoV-2 Variants II Assay is a multiplex RT-PCR assay for the detection of spike protein mutations L452R, W152C, K417T and K417N, and it is validated for lower and upper respiratory tract specimens. 2022 Microorganisms Method SARS_CoV_2 K417N;K417T;L452R;W152C 130;120;106;113 135;125;111;118 S 82 87 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. The UltraGene Assay SARS-CoV-2 452R & 484K & 484Q Mutations V1 is an RT-PCR test intended for use in the screening of SARS-CoV-2 mutations L452R, E484K and E484Q on the spike region from NP swab samples. 2022 Microorganisms Method SARS_CoV_2 E484K;E484Q;L452R 146;156;139 151;161;144 S 169 174 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. This molecular kit is a multi-target designed assay intended for use as a reflex test for the detection of the mutations L452R, E484K, E484Q and N501Y of the spike gene on NP, oropharyngeal and nasal swabs. 2022 Microorganisms Method SARS_CoV_2 E484K;E484Q;L452R;N501Y 128;135;121;145 133;140;126;150 S 158 163 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. A total of selected 986 complete whole genome sequences of Malaysian variants with D614G mutation were retrieved from GISAID database (S1 Table; S1 File). 2022 PloS one Method SARS_CoV_2 D614G 83 88 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. The first virus from each lineage with D614G mutation in spike protein was extracted using patient's status metadata downloaded from GISAID on July 19, 2021. 2022 PloS one Method SARS_CoV_2 D614G 39 44 S 57 62 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. To study the dominant lineages and D614G frequency, a total of 1356 complete genome sequences of SARS-CoV-2 of Malaysian origin, submitted to GISAID from March 1, 2020 to July 19, 2021 were retrieved (S1 Table). 2022 PloS one Method SARS_CoV_2 D614G 35 40 35215765 Versatile SARS-CoV-2 Reverse-Genetics Systems for the Study of Antiviral Resistance and Replication. Point mutations in nsp12 (L323P, A97V, N491S, F480L, and V557L) were introduced using an in-house mega primer PCR approach as previously described with minor modifications (35 min elongation time instead of 20 min). 2022 Viruses Method SARS_CoV_2 A97V;F480L;N491S;V557L;L323P 33;46;39;57;26 37;51;44;62;31 Nsp12 19 24 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. For each sample, screening of the E484K mutation was performed with a real-time PCR (TIB MOLBIOL VirSNiP Assay 484K, ref: 53-0789). 2022 Viruses Method SARS_CoV_2 E484K 34 39 35215911 Ferristatin II Efficiently Inhibits SARS-CoV-2 Replication in Vero Cells. The plates were incubated for 48 h (for Wuhan G614D virus) or 72 h (for Delta and Omicron viruses) at 37 C, 5% CO2, until a clear cytopathic effect was seen in positive control wells. 2022 Viruses Method SARS_CoV_2 G614D 46 51 35215911 Ferristatin II Efficiently Inhibits SARS-CoV-2 Replication in Vero Cells. The SARS-CoV-2 isolates hCoV-19/St_Petersburg-3524S/2020 (Wuhan D614G lineage), hCoV-19/Russia/SPE-RII-32759V/2021 (Delta lineage) and hCoV-19/Russia/SPE-RII-6086V/2021 (Omicron lineage) were obtained from Smorodintsev Research Institute of Influenza (Saint Petersburg, Russia). 2022 Viruses Method SARS_CoV_2 D614G 64 69 35215988 Influenza A(H1N1)pdm09 Virus but Not Respiratory Syncytial Virus Interferes with SARS-CoV-2 Replication during Sequential Infections in Human Nasal Epithelial Cells. SARS-CoV-2 RNA was sequenced by MinION technology (Oxford Nanopore technologies, Oxford, UK), and the D614G substitution was detected in the spike protein. 2022 Viruses Method SARS_CoV_2 D614G 102 107 S 141 146 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. The plasmids encoding the SARS-CoV-2 Spike variants; D614G, B.1.1.7, B.1.351, P.1 and B.1.617.2 were previously described. 2022 Cell reports Method SARS_CoV_2 D614G 53 58 S 37 42 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. This sequence initially contained the Q493K substitution, as previously reported. 2022 Cell reports Method SARS_CoV_2 Q493K 38 43 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. To produce SARS-CoV-2 pseudoviruses, 293T cells were transfected with the lentiviral vector pNL4.3 R-E- Luc (NIH AIDS Reagent Program) and a plasmid encoding for the indicated S glycoprotein (D614G, Alpha, Beta, Gamma, Delta or Omicron) at a ratio of 10:1. 2022 Cell reports Method SARS_CoV_2 D614G 192 197 S 176 190 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. We therefore generated and used an Omicron Spike bearing the Q493R mutation for the full manuscript (Figures 1 and 2 and Figure S1). 2022 Cell reports Method SARS_CoV_2 Q493R 61 66 S 43 48 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. Co-localization of Y380Q with B and T-cell epitopes. 2022 Diagnostic microbiology and infectious disease Method SARS_CoV_2 Y380Q 19 24 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. The search in Immune Epitope Database (IEDB) considered T-cells epitopes for SARS-CoV-2 spike protein (region of 10 residues flanking the Y380Q) with 70% similarity in BLAST. 2022 Diagnostic microbiology and infectious disease Method SARS_CoV_2 Y380Q 138 143 S 88 93 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Many other mutations have been found in the Omicron variant, such as Q493R, G496S, Q498R in RBD and throughout the S-glycoprotein. 2022 Frontiers in immunology Method SARS_CoV_2 G496S;Q493R;Q498R 76;69;83 81;74;88 S;RBD 115;92 129;95 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Simultaneously, some mutations such as R203K and G204R are too noted in the Omicron variant. 2022 Frontiers in immunology Method SARS_CoV_2 G204R;R203K 49;39 54;44 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. The D614G mutation has been reported as a positive selection. 2022 Frontiers in immunology Method SARS_CoV_2 D614G 4 9 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. The N501Y mutation is noted in the Omicron along with other variants. 2022 Frontiers in immunology Method SARS_CoV_2 N501Y 4 9 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. The Omicron variant also has a D614G mutation. 2022 Frontiers in immunology Method SARS_CoV_2 D614G 31 36 35223905 Molecular and Epidemiological Characterization of Emerging Immune-Escape Variants of SARS-CoV-2. For instance, a Delta variant spike haplotype consisting of T19R, 256_258delinsG, L452R, T478K, D614G, P681R, and D950N is also assigned to another haplotype group of T19R, L452R, T478K, D614G, P681R, and D950N, which is missing a 256_258delinsG variant. 2022 Frontiers in medicine Method SARS_CoV_2 D614G;D614G;D950N;D950N;L452R;L452R;P681R;P681R;T19R;T19R;T478K;T478K 96;187;114;205;82;173;103;194;60;167;89;180 101;192;119;210;87;178;108;199;64;171;94;185 S 30 35 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. E484K mutation rapid tests. 2022 Diagnostic microbiology and infectious disease Method SARS_CoV_2 E484K 0 5 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. PCR/Restriction Digest test: cDNA from SARS-CoV-2 specimens was amplified using primers spanning the G23012A polymorphism which encodes E484K: CTTGATTCTAAGGTTGGTGGT and GTAAAGGAAAGTAACAAGTAAAACC. 2022 Diagnostic microbiology and infectious disease Method SARS_CoV_2 E484K;G23012A 136;101 141;108 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. For ELISA, ADCP and ADCD assays, SARS-CoV-2 original and Beta variant full spike (L18F, D80A, D215G, K417N, E484K, N501Y, D614G, A701V, 242-244 del), RBD original and Beta (K417N, E484K and N501Y, D614G) and NTD original and Beta (L18F, D80A, D215G and 242-244 del) proteins were expressed in Human Embryonic Kidney (HEK) 293F suspension cells by transfecting the cells with the respective expression plasmid. 2022 Cell reports. Medicine Method SARS_CoV_2 A701V;D215G;D215G;D614G;D614G;D80A;D80A;E484K;E484K;K417N;N501Y;N501Y;K417N;L18F;L18F 129;94;243;122;197;88;237;108;180;101;115;190;173;82;231 134;99;248;127;202;92;241;113;185;106;120;195;178;86;235 S;RBD 75;150 80;153 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. For spike assays, HEK293T cells were transfected with 5mug of SARS-CoV-2 original variant spike (D614G), Beta, Gamma, Delta or SARS-1 spike plasmids using PEI-MAX 40,000 (Polysciences) and incubated for 2 days at 37C. 2022 Cell reports. Medicine Method SARS_CoV_2 D614G 97 102 S;S;S 4;90;134 9;95;139 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. Palivizumab was used as a negative control, while CR3022 was used as a positive control, and P2B-2F6 to differentiate the Beta from the D614G variant. 2022 Cell reports. Medicine Method SARS_CoV_2 D614G 136 141 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. Pseudotyped lentiviruses were prepared by co-transfecting HEK293T cell line with either the SARS-CoV-2 ancestral variant spike (D614G) or the Beta spike plasmids in conjunction with a firefly luciferase encoding lentivirus backbone plasmid as previously described. 2022 Cell reports. Medicine Method SARS_CoV_2 D614G 128 133 S;S 121;147 126;152 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. The SARS-CoV-2 Wuhan-1 spike, cloned into pCDNA3.1 was mutated using the QuikChange Lightning Site-Directed Mutagenesis kit (Agilent Technologies) and NEBuilder HiFi DNA Assembly Master Mix (NEB) to include D614G (original) or lineage defining mutations for Alpha (DEL69-70, DEL144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H), Beta (L18F, D80A, D215G, 242-244del, K417N, E484K, N501Y, D614G and A701V), Gamma (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, V1176F) or Delta (T19R, 156-157del, R158G, L452R, T478K, D614G, P681R and D950N). 2022 Cell reports. Medicine Method SARS_CoV_2 A570D;A701V;D1118H;D138Y;D215G;D614G;D614G;D614G;D614G;D614G;D80A;D950N;E484K;E484K;H655Y;K417N;K417T;L452R;N501Y;N501Y;N501Y;P26S;P681H;P681R;R158G;R190S;S982A;T1027I;T20N;T478K;T716I;V1176F;L18F;L18F;T19R 290;402;325;435;352;207;297;392;470;549;346;566;378;456;477;371;449;535;283;385;463;429;304;556;528;442;318;484;423;542;311;492;340;417;510 295;407;331;440;357;212;302;397;475;554;350;571;383;461;482;376;454;540;288;390;468;433;309;561;533;447;323;490;427;547;316;498;344;421;514 S 23 28 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. A) Clade-2 sarbecoviruses: SARS-CoV-2 Ancestral, SARS-CoV-2 VOCs (Alpha, Beta, Gamma, Delta, Omicron), SARS-CoV-2 variants of interest (Delta plus, Lambda, Mu), bat CoV RaTG13, pangolin CoV GX-P5L); B) Clade-1 sarbecoviruses: SARS-CoV-1 and bat CoVs WIV-1, Rs2018B, LYRa11 and RsSHC014. 2022 Research square Method SARS_CoV_2 P5L 193 196 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. Biotinylated RBD proteins from ancestral SARS-CoV-2, SARS-CoV-2 Alpha, Delta, Beta, Gamma, bat CoV RaTG13, Pangolin CoV GX-P5L and SARS-CoV-1 were custom-made by Genscript. 2022 Research square Method SARS_CoV_2 P5L 123 126 RBD 13 16 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. Rabbit anti-SARS-CoV-2, GX-P5L, RaTG13, RmYN02, SL-ZC45 and HKU1 RBD sera were all custom produced by Genscript. 2022 Research square Method SARS_CoV_2 P5L 27 30 RBD 65 68 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. SARS-CoV-2 Wuhan-hu-1 (ancestral), delta, Omicron and GX-P5L full-length spike pseudotyped viruses were produced and packaged as previously described. 2022 Research square Method SARS_CoV_2 P5L 57 60 S 73 78 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. As of June 2021, routine sequencing was discontinued on N501Y-positive/E484-negative specimens, which were presumed to be the Alpha lineage. 2022 Clinical infectious diseases Method SARS_CoV_2 N501Y 56 61 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. Initial screening focused on the N501Y mutation, with screening for both N501Y and E484K initiated in March 2020. 2022 Clinical infectious diseases Method SARS_CoV_2 E484K;N501Y;N501Y 83;33;73 88;38;78 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. More than 90% of infections were positive for the N501Y mutation as of April 2021, but that fraction decreased subsequently with emergence of the Delta variant, which represented more than 60% of all infections by July 2021. 2022 Clinical infectious diseases Method SARS_CoV_2 N501Y 50 55 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. The Alpha lineage (rather than Beta or Gamma) represented the overwhelming majority of Ontario's N501Y-positive isolates. 2022 Clinical infectious diseases Method SARS_CoV_2 N501Y 97 102 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. We constructed age group-specific logistic regression models for associations between N501Y-positive or Delta VOC infection and infection severity, defined as hospitalization, ICU admission, or death. 2022 Clinical infectious diseases Method SARS_CoV_2 N501Y 86 91 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. We used Ontario's Case and Contact Management (CCM) database to create a retrospective cohort of SARS-CoV-2 cases who underwent screening for VOCs and had test report dates between 7 February 2021 and 31 October 2021 (as routine screening for N501Y and E484K mutations began on 7 February 2021). 2022 Clinical infectious diseases Method SARS_CoV_2 E484K;N501Y 253;243 258;248 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. The RBD Omicron variant was ordered as GeneString from GeneArt (Thermo Fisher) according to EPI_ISL_6590608 (partial RBD Sanger sequencing from Hong Kong), EPI_ISL_6640916, EPI_ISL_6640919, and EPI_ISL_6640917 including Q493K which was corrected later to Q493R. 2022 BMC medicine Method SARS_CoV_2 Q493K;Q493R 220;255 225;260 RBD;RBD 4;117 7;120 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. SARS-CoV-2 variants D614G (GISAID: EPI_ISL_497840) and BA.2 (GISAID: EPI_ISL_9845731) were isolated from respiratory tract specimens of patients with COVID-19 in Hong Kong by J.F.-W.C., K.-Y.Y. 2022 Nature Method SARS_CoV_2 D614G 20 25 COVID-19 150 158 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. All the variant spikes were expressed in suspension-cultured Expi293F cells (Gibco) cells and purified as described before for the D614G spike. 2022 Nature communications Method SARS_CoV_2 D614G 131 136 S;S 16;137 22;142 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. Models for the unbound trimeric spikes were based on our model of D614G spike (PDB IDs 7BNM, 7BNN, 7BNO). 2022 Nature communications Method SARS_CoV_2 D614G 66 71 S;S 32;72 38;77 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. The following variant spikes were made (SA, Alpha and mink) (all mutations listed with reference to the NCBI sequence YP_009724390.1): 2P Alpha (Delta69-70, Delta144, N501Y, A570D, D614G, P681H, T716A, S982A, D1118H, and K986P, V987P), FUR2P Alpha (Delta69-70, Delta144, N501Y, A570D, D614G, T716A, S982A, D1118H, and R682S, R685S, K986P, V987P), FUR2P D614 Alpha (Delta69-70, Delta144, N501Y, A570D, T716A, S982A, D1118H, and R682S, R685S, K986P, V987P), 2P P681H-only (P681H and K986P, V987P), P681R-only (P681R and K986P, V987P), 2P Beta spike (L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G, A701V, and K986P, V987P), FUR2P Beta spike (L18F, D80A, D215G, Delta242-244, R246I, K417N, E484K, N501Y, D614G, A701V, and R682S, R685S, K986P, V987P), FUR2P mink (Delta69-70, Y453F, D614G, I692V, and R682S, R685S, K986P, V987P), FUR2P D614 mink (Delta69-70, Y453F, I692V, and R682S, R685S, K986P, V987P). 2022 Nature communications Method SARS_CoV_2 A570D;A570D;A570D;A701V;A701V;D1118H;D1118H;D1118H;D215G;D215G;D614G;D614G;D614G;D614G;D614G;D80A;D80A;E484K;E484K;I692V;I692V;K417N;K417N;K986P;K986P;K986P;K986P;K986P;K986P;K986P;K986P;K986P;N501Y;N501Y;N501Y;N501Y;N501Y;P681H;P681H;P681R;R246I;R246I;R682S;R682S;R682S;R682S;R682S;R685S;R685S;R685S;R685S;R685S;S982A;S982A;S982A;T716A;T716A;T716A;V987P;V987P;V987P;V987P;V987P;V987P;V987P;V987P;V987P;Y453F;Y453F;L18F;L18F;P681H;P681R 174;278;394;602;714;209;306;415;560;658;181;285;595;707;785;554;652;581;693;792;868;574;686;221;332;441;481;518;613;739;817;893;167;271;387;588;700;188;459;496;567;679;318;427;725;803;879;325;434;732;810;886;202;299;408;195;292;401;228;339;448;488;525;620;746;824;900;778;861;548;646;471;508 179;283;399;607;719;215;312;421;565;663;186;290;600;712;790;558;656;586;698;797;873;579;691;226;337;446;486;523;618;744;822;898;172;276;392;593;705;193;464;501;572;684;323;432;730;808;884;330;439;737;815;891;207;304;413;200;297;406;233;344;453;493;530;625;751;829;905;783;866;552;650;476;513 S;S;S 22;541;639 28;546;644 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. The variant spikes were stabilised in the pre-fusion conformation (K986P and V987P) with the furin-cleavage site ([PH]RRAR) either intact ('2P' constructs) or mutated to the uncleavable sequence PSRAS ('FUR2P' constructs). 2022 Nature communications Method SARS_CoV_2 V987P;K986P 77;67 82;72 S 12 18 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. The foundation of the hypothesis that peptides may have an effect on viral replication was that the Y96F variant displayed increased methyltransferase activity in the literature and had occurred in other virus sequences in the subfamily. 2022 Informatics in medicine unlocked Method SARS_CoV_2 Y96F 100 104 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. The new peptide variants chosen were C73I, C73V, C79A, F68Y, H80R, K93R, L92F, L92Y, Y96C, Y96W. 2022 Informatics in medicine unlocked Method SARS_CoV_2 C73I;C73V;C79A;F68Y;H80R;K93R;L92F;L92Y;Y96C;Y96W 37;43;49;55;61;67;73;79;85;91 41;47;53;59;65;71;77;83;89;95 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. These variants were G70A, G94A, G94D, H80A, K93A, K95A, R78A, R78G, S72A, Y96A, Y96F, Y96I, Y96V. 2022 Informatics in medicine unlocked Method SARS_CoV_2 G70A;G94A;G94D;H80A;K93A;K95A;R78A;R78G;S72A;Y96A;Y96F;Y96I;Y96V 20;26;32;38;44;50;56;62;68;74;80;86;92 24;30;36;42;48;54;60;66;72;78;84;90;96 35262011 Use of amplicon melt temperature to detect SARS-CoV-2 Lineage B.1.1.7 variant through the G28048T mutation in the ORF 8 gene. Thomas' Hospital were also subjected to DNA sequence analysis (Eurofins) to determine if the G28048T SNP was present. 2021 Journal of clinical virology plus Method SARS_CoV_2 G28048T 93 100 35262087 Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites. SARS-CoV-2 TaqMan Assays for S substitutions K417T, E484K, E484Q, and L452R were performed per manufacturer's instructions (Thermo Fisher) with 4 muL of template. 2022 medRxiv Method SARS_CoV_2 E484K;E484Q;K417T;L452R 52;59;45;70 57;64;50;75 S 29 30 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. However, we did not notice any significant difference between neutralization titers against Alpha isolate used in this study (one substitution, R682W, in the furin cleavage site in all the sequence reads) and Alpha isolate used in our previous study (intact furin cleavage site). 2022 Microbiology spectrum Method SARS_CoV_2 R682W 144 149 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. SARS-CoV-2 isolates: FIN1-20 (lineage B; GenBank accession number MZ934691 for passaged virus and GISAID accession number EPI_ISL_407079 for the original patient sample), FIN25-20 (B.1, D614G; MW717675.1 and EPI_ISL_412971), FIN32-21 (B.1.351, Beta variant; OK448476.1 and EPI_ISL_3471851), FIN33-21 (B.1.525, Eta variant; OK638135 and EPI_ISL_3471854), FIN35-21 (B.1.1.7, Alpha variant; OK448478.1 and EPI_ISL_2589882), and FIN37-21 (B.1.617.2, Delta variant; OK626882.1/Laboratory A, MZ945494/Laboratory B, and EPI_ISL_2557176). 2022 Microbiology spectrum Method SARS_CoV_2 D614G 186 191 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. The protein movements and the dynamic motions of WT and L452R, E484Q, double mutant L452R-E484Q throughout the trajectories in the subspace were further identified by Cartesian coordinates projecting the most important eigenvectors from the complete analysis (Ahamad et al.). 2022 3 Biotech Method SARS_CoV_2 E484Q;L452R;L452R;E484Q 63;56;84;90 68;61;89;95 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. We mapped the three mutations, namely L452R, E484Q, and L452R-E4844Q at the corresponding positions, and mutant structures were constructed using the BuildModel module of FoldX (Schymkowitz et al.). 2022 3 Biotech Method SARS_CoV_2 E484Q;L452R;L452R;E4844Q 45;38;56;62 50;43;61;68 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. The desired mutations in the spike proteins of Kappa, Delta, and B.1.618 variants in an SARS-CoV-2 isolate, Wuhan-Hu-1, with a D614G (WT) backbone and the trVLP, were generated as previously described. 2022 mBio Method SARS_CoV_2 D614G 127 132 S 29 34 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. The latter lineage has nine recognized mutations in addition to the P.1 lineage-defining ones: ORF1ab (synC1150T, synC1912T, D762G, T1820I), ORF3a (D155Y, S180F), M (synC26954T), N (synC28789T), and S glycoprotein (A262S). 2022 Genetics and molecular biology Method SARS_CoV_2 D762G;S180F;T1820I;A262S;D155Y 125;155;132;215;148 130;160;138;220;153 S;ORF1ab;ORF3a;N 199;95;141;179 213;101;146;180 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. Finally, a 598 PCR product containing L452R, E484K/Q, T478K, and D614G were synthesized, and then sequencing was done. 2022 Journal of virological methods Method SARS_CoV_2 D614G;E484K;E484Q;L452R;T478K 65;45;45;38;54 70;52;52;43;59 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. Samples with the positive result for del69-70, E484K, E484Q, D614G, and L452R assays were considered screen-positive and collected for Sanger sequencing. 2022 Journal of virological methods Method SARS_CoV_2 D614G;E484K;E484Q;L452R 61;47;54;72 66;52;59;77 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. SARS-CoV-2 positive samples were examined for D614G, L452R, and T478K mutations by High-resolution melting analysis. 2022 Journal of virological methods Method SARS_CoV_2 D614G;L452R;T478K 46;53;64 51;58;69 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. SARS-CoV-2 positive samples were screened for del69-70, E484K, E484Q, D614G, and L452R mutations by five separate RT-PCR assays. 2022 Journal of virological methods Method SARS_CoV_2 D614G;E484K;E484Q;L452R 70;56;63;81 75;61;68;86 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. We opted to utilize the existing primer for the sequencing-forward primer of L452R and the reverse primer of D614G since the mutations addressed were in close proximity to each other. 2022 Journal of virological methods Method SARS_CoV_2 D614G;L452R 109;77 114;82 35273217 A SARS-CoV-2 Wuhan spike virosome vaccine induces superior neutralization breadth compared to one using the Beta spike. Pre-fusion spike protein ectodomain DNA constructs were designed containing the following mutations compared to the Wuhan variant (Wuhan Hu-1; GenBank: MN908947.3): deletion of H69, V70 and Y144, N501Y, A570D, D614G, P681H, T716I, S982A and D1118H in Alpha; L18F, D80A, D215G, L242H, R246I, K417N, E484K, N501Y, D614G and A701V in Beta; L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y and T1027I in Gamma. 2022 Scientific reports Method SARS_CoV_2 A570D;A701V;D1118H;D138Y;D215G;D614G;D614G;D614G;D80A;E484K;E484K;H655Y;K417N;K417T;L18F;L18F;L242H;N501Y;N501Y;N501Y;P26S;P681H;R190S;R246I;S982A;T1027I;T20N;T716I 203;322;241;355;270;210;312;390;264;298;376;397;291;369;258;337;277;196;305;383;349;217;362;284;231;407;343;224 208;327;247;360;275;215;317;395;268;303;381;402;296;374;262;341;282;201;310;388;353;222;367;289;236;413;347;229 S 11 16 35273335 The SARS-CoV-2 Alpha variant exhibits comparable fitness to the D614G strain in a Syrian hamster model. To quantify D614:G614 ratios using a previously described method, 498 bp fragment that contained the spike mutation D614G was amplified from extracted RNA (QIAamp 96 DNA kit and Qiacube HT robot). 2022 Communications biology Method SARS_CoV_2 D614G 116 121 S 101 106 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The QuikChange Lightning Site-Directed Mutagenesis Kit (Agilent Technologies Inc., Santa Clara, CA) was used to introduce amino acid substitutions (N501Y, E484K, K417N, K417N-E484K-N501Y, K417T-E484K-N501Y or L452R-T478K) in pcDNA3-SARS-CoV-2-S-RBD-sfGFP plasmid by following the manufacturer's instructions. 2022 Biomedicine & pharmacotherapy Method SARS_CoV_2 E484K;K417N;K417N;K417T;L452R;N501Y;E484K;E484K;N501Y;N501Y;T478K 155;162;169;188;209;148;175;194;181;200;215 160;167;174;193;214;153;180;199;186;205;220 RBD;S 245;243 248;244 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The live virus neutralization assay against SARS-CoV-2 variants (D614G, B.1.1.7, P.1, and B.1.351) was done as previously reported according to Biosafety Level 3 regulations. 2022 Frontiers in immunology Method SARS_CoV_2 D614G 65 70 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The SARS-CoV-2 Biken-2 (B2) strain including the D614G mutation was used as the conventional virus (accession number: LC644163), and was received from BIKEN Innovative Vaccine Research Alliance Laboratories. 2022 Frontiers in immunology Method SARS_CoV_2 D614G 49 54 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. The inclusive E-sarbeco, which detects SC-2 RNA regardless of the variant (6-carboxyfluorescein [FAM] fluorophore), ND3L reaction, which detects the Alpha variant (HEX channel), S157del reaction, which detects the Delta variant (Texas Red channel), and an endogenous control reaction for the human RNase P gene (Cy5 channel). 2022 Microbiology spectrum Method SARS_CoV_2 S157del 178 185 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. The primers for the amplification of the S157del and Orf8119del reaction targets are detailed in Table 1. 2022 Microbiology spectrum Method SARS_CoV_2 S157del 41 48 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. The D614G spike plasmid was generated by introducing the mutation into the Wuhan reference strain via Q5 site-directed mutagenesis (NEB). 2022 EBioMedicine Method SARS_CoV_2 D614G 4 9 S 10 15 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. The T95I, Y145H and A222V were successively introduced into the Delta spike by the same process. 2022 EBioMedicine Method SARS_CoV_2 A222V;T95I;Y145H 20;4;10 25;8;15 S 70 75 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Horses were immunized using the SARS-CoV-2 RBD protein (original strain WH-1; RBD identical to the D614G reference strain) with Freund's incomplete adjuvant at an initial dose of 3 mg. 2022 Emerging microbes & infections Method SARS_CoV_2 D614G 99 104 RBD;RBD 43;78 46;81 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Mice were immunized with purified SARS-CoV-2 plasmid comprising the D614G reference strain, B.1.351 variant, or B.1.429 variant (50 microg per mouse) at day 0. 2022 Emerging microbes & infections Method SARS_CoV_2 D614G 68 73 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Nine samples were from patients in Beijing who had been infected with the D614G reference strain. 2022 Emerging microbes & infections Method SARS_CoV_2 D614G 74 79 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. The spike protein was modelled based on the following Protein Data Bank coordinate sets: 7chh for X593, RBD-7B8 for 7B8, RBD-Ab5 for 9G11, and 7c01 for CB6; these revealed mutations L452R, T478K, and E484Q, respectively. 2022 Emerging microbes & infections Method SARS_CoV_2 E484Q;L452R;T478K 200;182;189 205;187;194 S;RBD;RBD 4;104;121 9;107;124 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. During the RT-LAMP detection of Delta R203M, a single loop primer (LF or LB) close to the R203M-containing region was designed instead of a pair of loop primers (both LF and LB) to achieve distinct single nucleotide mutation discrimination. 2022 Emerging microbes & infections Method SARS_CoV_2 R203M;R203M 38;90 43;95 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. RNA from clinical specimens was then used as a template to calculate the Cq ratio, including the wild-type, Delta and non-Delta variants (20A, 20I (Alpha, V1), and 20H (Beta, V2)), which cover common sequence types near the R203M mutation site. 2022 Emerging microbes & infections Method SARS_CoV_2 R203M 224 229 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Similarly, R203K/G204R (GGG AAC) and T205I (C T) mutations were also prepared. 2022 Emerging microbes & infections Method SARS_CoV_2 R203K;T205I;G204R 11;37;17 16;42;22 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Site-directed mutagenesis was performed on the 608th nucleotide of the wild-type N gene plasmid, which is the R203M mutation (G T). 2022 Emerging microbes & infections Method SARS_CoV_2 R203M 110 115 N 81 82 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The Cq ratio-based RT-LAMP method was established to detect the R203M mutation. 2022 Emerging microbes & infections Method SARS_CoV_2 R203M 64 69 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The negative control used the same amount of DEPC water instead of nucleic acid as a template, and four plasmids for the N gene (wild-type, R203M, R203K/G204R and T205I mutations) at a concentration of 108 copies/mL were used as positive controls. 2022 Emerging microbes & infections Method SARS_CoV_2 R203K;R203M;T205I;G204R 147;140;163;153 152;145;168;158 N 121 122 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The wild-type and R203M N gene plasmids (from 103 to 108 copies/mL) were used as templates, the wild-type and R203M primers were used, and three replicates were performed for each concentration. 2022 Emerging microbes & infections Method SARS_CoV_2 R203M;R203M 18;110 23;115 N 24 25 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. To determine the detection limit (LOD) of RT-LAMP for Delta and non-Delta strains, samples from two types of SARS-CoV-2 RNA (wild-type and R203M-mutant) in 2-fold serial dilutions were used as the template in RT-LAMP reactions with the R203M primer set. 2022 Emerging microbes & infections Method SARS_CoV_2 R203M;R203M 139;236 144;241 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. All other plasmids expressing spike protein mutants such as pcDNA 3.1 bs(-) T19R, pcDNA 3.1 bs(-) T95I, pcDNA 3.1 bs(-) E156G/Delta157-158, pcDNA 3.1 bs(-) L452R, pcDNA 3.1 bs(-) E484Q, pcDNA 3.1 bs(-) E156G/Delta157-158/L452R, pcDNA 3.1 bs(-) E156G/Delta157-158/E484Q, pcDNA 3.1 bs(-) E156G/Delta157-158/L452R/E484Q, and pcDNA 3.1 bs(-) ICS-05 were generated using site-directed mutagenesis by PCR using the pcDNA 3.1 bs(-) spike D614G plasmid as the template. 2022 Life science alliance Method SARS_CoV_2 D614G;E156G;E156G;E156G;E156G;E484Q;L452R;T19R;T95I;E484Q;E484Q;L452R;L452R 431;120;202;244;286;179;156;76;98;263;311;221;305 436;125;207;249;291;184;161;80;102;268;316;226;310 S;S 30;425 35;430 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. The cells were co-transfected, with pScalps Zsgreen Luciferase (8 mug), psPAX2 (6 mug), pcDNA 3.1 bs(-) N protein-encoding plasmid (2 mug), and either 2 mug of the parental spike (D614G) or its derivatives plasmids, by the calcium phosphate transfection method. 2022 Life science alliance Method SARS_CoV_2 D614G 180 185 S;N 173;104 178;105 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. The following primers S: D614G forward; 5'GTGCTGTACCAGGGCGTGAATTGCACC-3' reverse; 5'GGTGCAATTCACGCCCTGGTACAGCAC-3'; S: T19R forward; 5'TCTGGTCTCGTCTCAGTGCGTGAACCTGAGAACTAGAACCCAGCTGCCTC-3' reverse; 5'CTAGCAGCAGCTGCCGCAGGA-3'; S: T95I forward; 5'GCGTGTACTTCGCCTCCATTGAGAAGAGCAACATCATC-3' reverse; 5'GATGATGTTGCTCTTCTCAATGGAGGCGAAGTACACGC-3'; S: E156G/Delta157-158 forward; 5'AAGGTGCAATTGTTGGCGGAGCTGTACACGCCGCTCTCCATCCAGGACT-3' reverse; 5'AGTCCTGGATGGAGAGCGGCGTGTACAGCTCCGCCAACAATTGCACCTT3'; S: L452R forward; 5'GCAACTACAATTACCGGTACCGCCTGTTCCG-3' reverse 5'CGGAACAGGCGGTACCGGTAATTGTAGTTGC-3'; S: E484Q forward; 5'CCATGCAATGGAGTGCAGGGCTTCAACTGCT reverse; 5'AGCAGTTGAAGCCCTGCACTCCATTGCATGG-3' were used to generate the abovementioned plasmids. 2022 Life science alliance Method SARS_CoV_2 D614G;E156G;E484Q;L452R;T19R;T95I 25;344;595;494;119;229 30;349;600;499;123;233 S;S;S;S;S;S 22;116;226;341;491;592 23;117;227;342;492;593 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. The pcDNA 3.1 bs (-) spike D614G mutant was generated by site-directed mutagenesis first. 2022 Life science alliance Method SARS_CoV_2 D614G 27 32 S 21 26 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. E802D and E802A mutations were confirmed in icSARS-CoV-2 mNG backbone by Sanger sequencing using the primer: gatgatactctctgacgatg. 2022 Nature communications Method SARS_CoV_2 E802A;E802D 10;0 15;5 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Each icSARS-CoV-2 mutant virus (E802D and E802A) was cultured in the presence of increasing concentrations of RDV, ranging from 0.39 to 40 muM. 2022 Nature communications Method SARS_CoV_2 E802A;E802D 42;32 47;37 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Genome sequences which contain the E802D mutation were identified from the GISAID database (accessed on 10/31/21; Supplementary Table 4) and were compared to sequences in the global Auspice dataset. 2022 Nature communications Method SARS_CoV_2 E802D 35 40 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Introduction of the E802D and E802A was confirmed at a minimum frequency of 0.82-0.9 in initial stocks. 2022 Nature communications Method SARS_CoV_2 E802A;E802D 30;20 35;25 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Isolates from initial stocks were expanded and used to infect Vero-E6 cells with 0.01 MOI of each E802D and E802A mutant virus to assess their replication kinetics. 2022 Nature communications Method SARS_CoV_2 E802A;E802D 108;98 113;103 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Site-directed mutagenesis and full length icSARS-CoV-2 mNG E802D and E802A production. 2022 Nature communications Method SARS_CoV_2 E802A;E802D 69;59 74;64 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. The icSARS-CoV-2 mNG (mNeonGreen) backbone previously reported was employed to construct both full-length E802D and E802A mutant viruses utilizing the following primer pairs: forward (E802D): gttggactgaTactgaccttactaaaggac, reverse (E802D): aggtcagtAtcagtccaacattttgcttc; and forward (E802A): gttggactgCgactgaccttactaaaggac, reverse (E802A): aggtcagtcGcagtccaacattttgcttc. 2022 Nature communications Method SARS_CoV_2 E802A;E802D;E802A;E802A;E802D;E802D 116;106;285;334;184;233 121;111;290;339;189;238 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. The reverse genetics system used to generate E802D and E802A SARS-CoV-2 mutants is described at length elsewhere. 2022 Nature communications Method SARS_CoV_2 E802A;E802D 55;45 60;50 35304531 In vitro evaluation of therapeutic antibodies against a SARS-CoV-2 Omicron B.1.1.529 isolate. Drosten through EVA GLOBAL (https://www.european-virus-archive.com/) and contains the D614G mutation. 2022 Scientific reports Method SARS_CoV_2 D614G 86 91 35305699 Neutralisation sensitivity of the SARS-CoV-2 omicron (B.1.1.529) variant: a cross-sectional study. Plasmids encoding the spikes from the B.1 (D614G), mu (B.1.621), and delta variants were obtained from the G2P-UK National Virology consortium. 2022 The Lancet. Infectious diseases Method SARS_CoV_2 G2P;D614G 107;43 110;48 S 22 28 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? M0210S; New England Biolabs, Ipswich, MA, United States). 2022 Frontiers in microbiology Method SARS_CoV_2 M0210S 0 6 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. For SARS-CoV-2 gRNA design, the target sequence containing both the PAM (5'-TTTN) and the D614G mutant site is selected as the protospacer. 2022 Chemical science Method SARS_CoV_2 D614G 90 95 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. SARS-CoV-2 plasmids containing the wild-type and D614G mutant spike gene (catalog numbers: GS-200519_A001 and GS-200519_A012, respectively) were ordered from GENEWIZ Biotechnology Co., Ltd (Suzhou, China). 2022 Chemical science Method SARS_CoV_2 D614G 49 54 S 62 67 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. Due to the loss of single sequencing plate, missing numbers on 29, 30 and 31 March were imputed by assuming a constant ratio of the B.1-C15324T variant amongst the sequenced samples. 2022 Virus evolution Method SARS_CoV_2 C15324T 136 143 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. Of these 247 (247/411, 60 per cent) contained the monophyletic C15324T mutation in the B.1 lineage (B.1-C15324T) characteristic to the virus variant that originated in this tri-national area. 2022 Virus evolution Method SARS_CoV_2 C15324T;C15324T 63;104 70;111 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. Of these 60 per cent would be attributed to the B.1-C15324T variant, leading to a percentage of 88 per cent of unreported/unsequenced cases to consider (calculated as , with npopulation being the population of the city, the reported case counts and fraction of the B.1-C15324T variant, and pinfected the estimated fraction of the total infected population). 2022 Virus evolution Method SARS_CoV_2 C15324T;C15324T 52;270 59;277 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. Only B.1-C15324T cases were used for further analysis. 2022 Virus evolution Method SARS_CoV_2 C15324T 9 16 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. While the computation of the temporal variations in mobility was described above, the overall time-dependent effective reproductive number is obtained by applying a Kalman filter to the daily case counts of individuals having newly contracted the B.1-C15324T variant of SARS-CoV-2 in all of Basel-City. 2022 Virus evolution Method SARS_CoV_2 C15324T 251 258 35311662 Reduced DMPC and PMPC in lung surfactant promote SARS-CoV-2 infection in obesity. Briefly, the target HEK293T cells were transfected with 2019-nCov_pcDNA3.1(+)-P2A-eGFP plasmid (from Haisheng Yu and obtained from Genscript (Piscataway, NJ, USA)), resulting in simultaneous expression of spike protein and eGFP in the same cell. 2022 Metabolism Method SARS_CoV_2 P2A 78 81 S 205 210 35311662 Reduced DMPC and PMPC in lung surfactant promote SARS-CoV-2 infection in obesity. The mutant D614G SARS-CoV-2 Spike gene was obtained from Addgene (158075). 2022 Metabolism Method SARS_CoV_2 D614G 11 16 S 28 33 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. In previous studies, viral particles of the Omicron variant were further subclassified into two types: those containing the Q493K and Q493R mutations. 2022 Journal of chemical information and modeling Method SARS_CoV_2 Q493K;Q493R 124;134 129;139 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The omicron variant has 15 mutations in the RBD domain of the S protein: G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493K/R, G496S, Q498R, N501Y, and Y505H. 2022 Journal of chemical information and modeling Method SARS_CoV_2 E484A;G339D;G446S;G496S;K417N;N440K;N501Y;Q493K;Q493R;Q498R;S371L;S373P;S375F;S477N;T478K;Y505H 136;73;115;152;101;108;166;143;143;159;80;87;94;122;129;177 141;78;120;157;106;113;171;150;150;164;85;92;99;127;134;182 RBD;S 44;62 47;63 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The structures of complexes formed by the binding of hACE2 to the RBD of the wild type (PDB ID:6M0J), Delta variant (PDB ID:7V8B), and Omicron variant containing the Q493R mutation (PDB ID:7T9L), and individually to eight different monoclonal antibodies (Table S1), were downloaded from the Protein Data Bank . 2022 Journal of chemical information and modeling Method SARS_CoV_2 Q493R 166 171 RBD 66 69 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). For the L452R-RT-LAMP-BART assay, 100 nM of PNA was added. 2022 PloS one Method SARS_CoV_2 L452R 8 13 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). In addition, a primer set targeting L452R of the spike protein (S gene; hCoV-19/Japan/IC-0604/2021; GISAID accession ID, EPI_ISL_779690; S3 Fig) plus a peptide nucleic acid (PNA) probe for L452 (Table 2) were developed. 2022 PloS one Method SARS_CoV_2 L452R 36 41 S;S 49;64 54;65 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). The following F2 primers for SARS-RT-LAMP and L452R-RT-LAMP were used to sequence the target regions: RdRp-F2, 5'-CTC AAA TGA ATC TTA AGT ATG CC-3'; and L452R-F2, 5'-AGA TGA TTT TAC AGG CTG CGT-'. 2022 PloS one Method SARS_CoV_2 L452R;L452R 46;153 51;158 RdRP 102 106 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. coli (NEB 10-beta electrocompetent cells, New England BioLabs C3020K) and plated at a target bottleneck of 100,000 variants per duplicate library, corresponding to >25 barcodes per mutant within each library. 2022 bioRxiv Method SARS_CoV_2 C3020K 62 68 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. Delta infection was corroborated by the experimental findings in this paper that all plasmas bound to Delta spike and RBD and better neutralized Delta spike-pseudotyped lentiviral particles relative to D614G particles. 2022 bioRxiv Method SARS_CoV_2 D614G 202 207 S;S;RBD 108;151;118 113;156;121 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. Duplicate single-mutant site-saturation variant libraries were designed in the background of the spike receptor binding domain (RBD) from SARS-CoV-2 Delta variant (identical to that from Wuhan-Hu-1, Genbank accession number MN908947, residues N331-T531, with the addition of the L452R and T478K amino-acid substitutions), and produced by Twist Bioscience. 2022 bioRxiv Method SARS_CoV_2 L452R;T478K 279;289 284;294 RBD;S;RBD 103;97;128 126;102;131 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. For experiments involving D614G spike, we used spike-pseudotyped lentiviral particles that were generated essentially as described in, using a codon-optimized SARS-CoV-2 spike from Wuhan-Hu-1 strain that contains a 21-amino-acid deletion at the end of the cytoplasmic tail and the D614G mutation that is now predominant in human SARS-CoV-2. 2022 bioRxiv Method SARS_CoV_2 D614G;D614G 26;281 31;286 S;S;S 32;47;170 37;52;175 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. The Genbank map of the plasmid encoding the unmutated SARS-CoV-2 Delta RBD in the yeast-display vector is available at https://github.com/jbloomlab/SARS-CoV-2-RBD_Delta/blob/main/data/plasmids/3159_pETcon-SARS-CoV-2-RBD-L452R-T478K.gb. 2022 bioRxiv Method SARS_CoV_2 L452R;T478K 220;226 225;231 RBD;RBD 71;216 74;219 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. The plasmid encoding the SARS-CoV-2 spike gene used to generate pseudotyped lentiviral particles, HDM_Spikedelta21_D614G, is available from Addgene (#158762) and BEI Resources (NR-53765). 2022 bioRxiv Method SARS_CoV_2 D614G 115 120 S 36 41 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. The plasmid encoding this spike, HDM_Spikedelta21_D614G, is available from Addgene (#158762) and BEI Resources (NR-53765), and the full sequence is at (https://www.addgene.org/158762). 2022 bioRxiv Method SARS_CoV_2 D614G 50 55 S 26 31 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. The plasmid map for the unmutated Delta RBD in the yeast-display expression vector is at https://github.com/jbloomlab/SARS-CoV-2-RBD_Delta/blob/main/data/plasmids/3159_pETcon-SARS-CoV-2-RBD-L452R-T478K.gb. 2022 bioRxiv Method SARS_CoV_2 L452R;T478K 190;196 195;201 RBD;RBD 40;186 43;189 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. The spike amino acid-sequence matches that of the Wuhan-Hu-1 spike with the following substitutions: T19R, G142D, del156-157, R158G, L452R, T478K, D614G, P681R, D950N. 2022 bioRxiv Method SARS_CoV_2 D614G;D950N;G142D;L452R;P681R;R158G;T19R;T478K 147;161;107;133;154;126;101;140 152;166;112;138;159;131;105;145 S;S 4;61 9;66 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. SDeltaTM hetero-trimers for smFRET experiments were expressed by co-transfection with both the untagged SDeltaTM (D614 or D614G) construct and the corresponding 161/345A4-tagged SDeltaTM plasmid at a 2:1 molar ratio. 2022 eLife Method SARS_CoV_2 D614G 122 127 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. The D614G amino acid change into both untagged and 161/345A4-tagged SDeltaTM constructs was done using the Q5 Site-Directed Mutagenesis Kit (NEB, Ipswich, MA) according to the manufacturer's instructions. 2022 eLife Method SARS_CoV_2 D614G 4 9 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. B.1.617.1 (pcDNA 3.1+) and B.1.617.2 (pcDNA 3.1+) Spike plasmids were kindly donated by Dalan Bailey, Pirbright Institute, G2P Consortium. 2022 Frontiers in immunology Method SARS_CoV_2 G2P 123 126 S 50 55 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. B.1.617.2 K417N was generated in house by site directed mutagenesis. 2022 Frontiers in immunology Method SARS_CoV_2 K417N 10 15 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. In total, we created four SD2-FP models, including the WT model, mutated with P681R and D614G mutations, and double mutation consisting of both D614G and P681R. 2022 Viruses Method SARS_CoV_2 D614G;D614G;P681R;P681R 88;144;78;154 93;149;83;159 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. The SD2-FP models involved in the present work are: (a) the wild type (WT), (b) the mutated model P681R, (c) the mutated model D614G, and (d) the double mutation with both D614G and P681R. 2022 Viruses Method SARS_CoV_2 D614G;D614G;P681R;P681R 127;172;98;182 132;177;103;187 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. To prepare the mutated models with a single mutation (P681R or D614G) or a double mutation (P681R and D614G), we used Dunbrack backbone-dependent rotamer library, implemented by the UCSF Chimera package. 2022 Viruses Method SARS_CoV_2 D614G;D614G;P681R;P681R 63;102;54;92 68;107;59;97 35337002 Protective Immunity of the Primary SARS-CoV-2 Infection Reduces Disease Severity Post Re-Infection with Delta Variants in Syrian Hamsters. Delta AY.1 variant had D614G, E156G, F157del, K417N, L452R, P681R, R158del, T19R, T95I and T478K substitutions; the Delta variant had A222V, D614G, D950N, G142D, L452R, P681R, T19R, T478K substitutions; and the B.1 variant had the D614G substitution in the spike protein. 2022 Viruses Method SARS_CoV_2 A222V;D614G;D614G;D614G;D950N;E156G;F157del;G142D;K417N;L452R;L452R;P681R;P681R;R158del;T19R;T19R;T478K;T478K;T95I 134;23;141;231;148;30;37;155;46;53;162;60;169;67;76;176;91;182;82 139;28;146;236;153;35;44;160;51;58;167;65;174;74;80;180;96;187;86 S 257 262 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. By using this approach, we generated two Omicron "specific" targets (A67V + DEL69/70; and P681H + N679K). 2022 Viruses Method SARS_CoV_2 N679K;P681H;A67V 98;90;69 103;95;73 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. Five interactions were analyzed further due to high binding energy (RBD-484-fwd: RBD-484-fwd (2x), P681-fwd: P681fwd, RBD-484-fwd: P681R-probe, RBD-484-fwd: P681H-probe) (Supplementary Figure S1). 2022 Viruses Method SARS_CoV_2 P681H;P681R 157;131 162;136 RBD;RBD;RBD;RBD 68;81;118;144 71;84;121;147 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. For the furin-cleavage-site, probe-4 ("P681H") also covers N679K with an LNA-base. 2022 Viruses Method SARS_CoV_2 N679K;P681H 59;39 64;44 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. For the HV69-70 deletion, the probe sequence was modified to omit the affected bases and an LNA-base positioned at the A67V SNP (probe 1, "SDEL2"). 2022 Viruses Method SARS_CoV_2 A67V 119 123 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. For the P681R target, a clinical Delta-variant sample (confirmed by NGS) was normalized to WHO standard using the same method. 2022 Viruses Method SARS_CoV_2 P681R 8 13 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. However, many of these are now accompanied by additional SNPs within potential probe regions, such as A67V or N679K. 2022 Viruses Method SARS_CoV_2 A67V;N679K 102;110 106;115 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. The multiplex assay amplifies three regions of the SARS-CoV-2 S-gene: 102bp within the N-terminal domain (NTD) (probe 1: "SDEL2"), 353/80bp within the receptor-binding-domain (RBD) (probe 3, "E484A"), and 95bp at the furin-cleavage-site (probe 2: "P681R", probe 4: "P681H") (Figure 1). 2022 Viruses Method SARS_CoV_2 E484A;P681H;P681R 192;266;248 197;271;253 RBD;N;S 176;87;62 179;88;63 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. The Omicron variant features a number of mutations (SNPs and deletions) which have previously been found in other VOCs, e.g., del-HV69-70 and P681H (, accessed 24 December 2021). 2022 Viruses Method SARS_CoV_2 P681H 142 147 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. Molecular docking of energy-minimized heparin or BoSG disaccharides to the equilibrated 3D structure of N501Y S-protein RBD was performed using AutoDock Vina. 2022 The Journal of biological chemistry Method SARS_CoV_2 N501Y 104 109 RBD;S 120;110 123;111 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. SARS-CoV-2 S-protein RBD (wt), N501Y, L452R, and triple (K417T/E484K/N501Y) mutants were a gift from John Bates (University of Mississippi). 2022 The Journal of biological chemistry Method SARS_CoV_2 L452R;N501Y;K417T;E484K;N501Y 38;31;57;63;69 43;36;62;68;74 RBD;S 21;11 24;12 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. The published equilibrated 3D structure of the mutant variant N501Y S-protein RBD was used for molecular docking. 2022 The Journal of biological chemistry Method SARS_CoV_2 N501Y 62 67 RBD;S 78;68 81;69 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. A Gamma lineage RBD (with mutations E484K, N501Y, and K417T) was modelled comparatively using SWISS-MODEL. 2022 PeerJ Method SARS_CoV_2 E484K;K417T;N501Y 36;54;43 41;59;48 RBD 16 19 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. The comparison of seropositivity of IgM, IgA, IgG, and neutralising antibodies, and the escape percentage of the D614G, beta, and delta variants from neutralising antibodies was done with the chi2 test, or Fisher's exact test when appropriate. 2022 The Lancet. Microbe Method SARS_CoV_2 D614G 113 118 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. SARS-CoV-2-pseudotyped lentiviruses were prepared by co-transfecting the HEK 293T cell line with either the SARS-CoV-2 original spike (D614G) or the SARS-CoV-2 beta or delta spike plasmids in conjunction with a firefly luciferase encoding pNL4 lentivirus backbone plasmid. 2022 BMC medicine Method SARS_CoV_2 D614G 135 140 S;S 128;174 133;179 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. The RBD proteins were derived from the original D614G strain and the four variants of concern, namely alpha, beta, gamma, and delta. 2022 BMC medicine Method SARS_CoV_2 D614G 48 53 RBD 4 7 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. The SARS-CoV-2 original (D614G) spike and RBD proteins were expressed in human embryonic kidney (HEK) 293F suspension cells by transfecting the cells with the spike plasmid. 2022 BMC medicine Method SARS_CoV_2 D614G 25 30 S;S;RBD 32;159;42 37;164;45 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. The primer pairs were designed to detect Delta (B.1.617.2)-specific L452R (T22917G mutation) and Omicron BA.1-specific G339D (G22578A mutation) and D796Y (G23948T mutation) variations. 2022 Biochemical and biophysical research communications Method SARS_CoV_2 D796Y;G339D;L452R;G22578A;G23948T;T22917G 148;119;68;126;155;75 153;124;73;133;162;82 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. Cells (2.5 x 104 cells/well) were infected with D614G strain at an MOI of 0.01 in DMEM with 2% FBS. 2022 Frontiers in microbiology Method SARS_CoV_2 D614G 48 53 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. The cells were infected with viral stocks produced from three Colombian isolates of SARS-CoV-2: D614G strain (EPI_ISL_536399), Delta (EPI_ISL_5103929), and Mu (EPI_ISL_4005445) variants. 2022 Frontiers in microbiology Method SARS_CoV_2 D614G 96 101 35370361 CRISPR-Cas13a cascade-based viral RNA assay for detecting SARS-CoV-2 and its mutations in clinical samples. SARS-CoV-2, MERS-CoV, SARS-CoV and SARS-CoV-2(N501Y) pseudovirus were procured from Jiman Biotechnology Co., Ltd. 2022 Sensors and actuators. B, Chemical Method SARS_CoV_2 N501Y 46 51 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. The significance of neutralizing activities of serum samples against each variant pseudovirus relative to D614G was estimated using the Wilcoxon matched-pairs signed-rank test. 2022 Frontiers in immunology Method SARS_CoV_2 D614G 106 111 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. ACMACS antigenic cartography software (https://acmacs-web.antigenic-cartography.org/) was used to create a geometric interpretation of neutralization titers against the D614G, Delta, and Omicron variants. 2022 Science translational medicine Method SARS_CoV_2 D614G 169 174 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. The codon-optimized D614G and Delta spike expression plasmids were purchased from Genscript. 2022 Science translational medicine Method SARS_CoV_2 D614G 20 25 S 36 41 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. The next day 4 mug of the pcDNA3.1(+) plasmid encoding Delta spike or 0.5 mug of the VRC8400 plasmid encoding the D614G or Omicron spike, 5 mug of Luciferase reporter plasmid DNA, and 5 mug HIV gag/pol were combined with FuGENE-6 transfection reagent (Promega), according to the manufacturer's instructions. 2022 Science translational medicine Method SARS_CoV_2 D614G 114 119 S;S 61;131 66;136 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. M0210S). 2022 Frontiers in cellular and infection microbiology Method SARS_CoV_2 M0210S 0 6 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. The mutation for recovered (S194*) and mortality (S194L) was incorporated using PyMOL. 2022 Frontiers in cellular and infection microbiology Method SARS_CoV_2 S194X;S194L 28;50 33;55 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. Purification of SARS-CoV-2 nsp5 (WT and S46A) and SARS-CoV nsp5 (WT and A46S) was carried out as described previously. 2022 Journal of virology Method SARS_CoV_2 A46S;S46A 72;40 76;44 Nsp5;Nsp5 27;59 31;63 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. SARS-CoV-2 nsp5 (S46A) and SARS-CoV nsp5 (A46S) mutants were generated by overlap extension PCR using SARS-CoV-2 nsp5 or SARS-CoV nsp5 as the template. 2022 Journal of virology Method SARS_CoV_2 A46S;S46A 42;17 46;21 Nsp5;Nsp5;Nsp5;Nsp5 11;36;113;130 15;40;117;134 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. The FRET assays were conducted by mixing 50 nM purified SARS-CoV-2 nsp5 (WT or S46A) or SARS-CoV nsp5 (WT or A46S) proteins with 40 muM substrate in 50 mM Tris-HCl, pH 7.3, containing 1 mM EDTA. 2022 Journal of virology Method SARS_CoV_2 A46S;S46A 109;79 113;83 Nsp5;Nsp5 67;97 71;101 35396165 A self-amplifying RNA vaccine protects against SARS-CoV-2 (D614G) and Alpha variant of concern (B.1.1.7) in a transmission-challenge hamster model. Briefly, 10 cm dishes of HEK 293Ts were transfected using lipofectamine 3000 (Thermo) with a mixture of pCSFLW, pCAGGS-GAGPOL and either D614G or B.1.1.7 spike proteins expressed in pcDNA3.1. 2022 Vaccine Method SARS_CoV_2 D614G 137 142 S 154 159 35396511 Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage. A subset of eleven of these samples were used to test neutralization activity against Delta (N = 11) and C.1.2 (N = 11) using the pseudovirus neutralization assay and ADCC (N = 9) activity against D614G and C.1.2. 2022 Nature communications Method SARS_CoV_2 D614G 197 202 35396511 Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage. ChAdOx1 nCOV-19 (AZD1222) Vaccinees: samples from donors vaccinated with the ChAdOx1 nCOV-19 (AZD1222) vaccine were previously assessed for neutralization activity against the D614G (N = 11) and Beta variants (N = 11). 2022 Nature communications Method SARS_CoV_2 D614G 176 181 35396511 Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage. HEK293T cells were transfected with 5 mug of SARS-CoV-2 wild-type variant spike (D614G), Beta, Delta or C.1.2 spike plasmids using PEI-MAX 40,000 (Polysciences) and incubated for 2 days at 37C. 2022 Nature communications Method SARS_CoV_2 D614G 81 86 S;S 74;110 79;115 35396511 Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage. Janssen/Johnson and Johnson (Ad26.COV2.S) Vaccinees: samples from healthy donors vaccinated with the Janssen/Johnson and Johnson (Ad26.COV2.S) vaccine during the Sisonke Trial were obtained 2 months after vaccination and used for the pseudovirus neutralization against D614G (N = 10), Beta (N = 10), Delta (N = 10), and C.1.2 (N = 9) and ADCC activity against D614G (N = 15) and C.1.2 (N = 15). 2022 Nature communications Method SARS_CoV_2 D614G;D614G 269;360 274;365 S;S 39;140 40;141 35396511 Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage. Neutralization activity has previously been assessed for this cohort against the D614G (N = 10) and Beta (N = 10) variants, a subset of these were used to measure wave 2 antibody responses against Delta (N = 10) and C.1.2 (N = 7) using the pseudovirus neutralization assay and ADCC (N = 10) activity against D614G and C.1.2. 2022 Nature communications Method SARS_CoV_2 D614G;D614G 81;308 86;313 35396511 Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage. Palivizumab was used as a negative control, while CR3022 was used as a positive control, and P2B-2F6 to differentiate the Beta from the D614G variant. 2022 Nature communications Method SARS_CoV_2 D614G 136 141 35396511 Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage. Pfizer/BioNTech (BNT162b2) Vaccinees: samples from donors vaccinated with BNT162b2 were used for the pseudovirus neutralization assay against D614G (N = 6), Beta (N = 6), Delta (N = 6), and C.1.2 (N = 7) and ADCC activity (N = 11) against D614G and C.1.2. 2022 Nature communications Method SARS_CoV_2 D614G;D614G 142;239 147;244 35396511 Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage. The SARS-CoV-2 Wuhan-1 spike, cloned into pCDNA3.1, was mutated using the QuikChange Lightning Site-Directed Mutagenesis kit (Agilent Technologies) and NEBuilder HiFi DNA Assembly Master Mix (NEB) to include D614G (wild-type) or lineage defining mutations for Beta (L18F, D80A, D215G, 241-243del, K417N, E484K, N501Y, D614G and A701V), Delta (T19R, 156-157del, R158G, L452R, T478K, D614G, P681R and D950N) and C.1.2 (P9L, C136F, Y144del, R190S, D215G, 242-243del, Y449H, E484K, N501Y, D614G, H655Y, N679K, T716I and T859N). 2022 Nature communications Method SARS_CoV_2 A701V;C136F;D215G;D215G;D614G;D614G;D614G;D614G;D80A;D950N;E484K;E484K;H655Y;K417N;L452R;N501Y;N501Y;N679K;P681R;R158G;R190S;T478K;T716I;T859N;Y144del;Y449H;L18F;P9L;T19R 328;422;278;445;208;318;382;485;272;399;304;471;492;297;368;311;478;499;389;361;438;375;506;516;429;464;266;417;343 333;427;283;450;213;323;387;490;276;404;309;476;497;302;373;316;483;504;394;366;443;380;511;521;436;469;270;420;347 S 23 28 35396511 Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage. These samples have previously been used to assess antibody responses to the D614G (N = 10 Wave 1; N = 9 Wave 3) and Beta (N = 5 Wave 1; N = 9 Wave 3) variants, a subset of these were used to measure wave 1 and wave 3 immune responses to Delta (N = 5 Wave 1; N = 9 Wave 3) and C.1.2 (N = 7 Waves 1 and 3) using the pseudovirus neutralization assay and ADCC activity against D614G (N = 10 Wave 1; N = 9 Wave 3) and C.1.2 (N = 10 Wave 1; N = 9 Wave 3). 2022 Nature communications Method SARS_CoV_2 D614G;D614G 76;373 81;378 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Alignment analysis indicated the presence of three main substitutions:Y453F, F486L, and N501T, which were expected to be crucial for SARS-CoV-2 infection in minks according to Welkers et al. 2022 Journal of applied genetics Method SARS_CoV_2 F486L;N501T;Y453F 77;88;70 82;93;75 COVID-19 133 153 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. The D614G mutation was present together with the Y453F mutation in 10 mink coronavirus isolates from Denmark and 2 mink coronavirus isolates from Poland. 2022 Journal of applied genetics Method SARS_CoV_2 D614G;Y453F 4;49 9;54 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. The F486L mutation was observed in only one mink coronavirus isolate from the Netherlands; however, it was not observed in mink coronavirus isolates from Denmark and Poland. 2022 Journal of applied genetics Method SARS_CoV_2 F486L 4 9 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. The N501T mutation was found in only one mink coronavirus isolate from the Netherlands; however, it was not detected in mink coronavirus isolates from Denmark and Poland. 2022 Journal of applied genetics Method SARS_CoV_2 N501T 4 9 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. The Y453F mutation was detected in 5 out of 13 mink coronavirus isolates from the Netherlands, in 8 out of 12 mink coronavirus isolates from Denmark, and in 2 out of 14 mink coronavirus isolates from Poland. 2022 Journal of applied genetics Method SARS_CoV_2 Y453F 4 9 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. The Y453F, F486L, and N501T mutations were not found in the SARS-CoV-2 variant B.1.1.7, but the D614G mutation was present. 2022 Journal of applied genetics Method SARS_CoV_2 D614G;F486L;N501T;Y453F 96;11;22;4 101;16;27;9 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Cy3-tetrazine-labelled at 836th position of WT-S* or D614G-S* virions were used to follow the fusion peptide conformational motion by anisotropy measurements to determine whether the fusion peptide of the spike is getting inserted into the liposome during membrane fusion reaction. 2022 Cell reports Method SARS_CoV_2 D614G 53 58 Membrane;S;S;S 256;205;47;59 264;210;48;60 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Cy3/Cy5 labeled D614G-S** virions were produced following similar procedure. 2022 Cell reports Method SARS_CoV_2 D614G 16 21 S 22 23 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. DiO-labelled virions with either WT spike or D614G spike were combined with proteo-liposomes coated with either hACE2-ectodomain or NRP1-b1 or hTMPRSS2-ectodomain or all the receptor together and incubated for 5 min to enable virus and liposome binding at pH 7. 2022 Cell reports Method SARS_CoV_2 D614G 45 50 S;S 36;51 41;56 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Expression of the dominant negative eRF1 E55D mutant increased amber suppression efficiency. 2022 Cell reports Method SARS_CoV_2 E55D 41 45 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. For anisotropy measurements, HEK293T/17 cells were transfected with a 1:5 ratio of plasmids encoding SARS-CoV-2S* and wild-type SARS-CoV-2S, and plasmids encoding HIV-1 Gag-Pol, NESPylRSAF/tRNAPyl, and eRF1 (E55D), and grown in the presence of 0.5 mM TCO* ncAA. 2022 Cell reports Method SARS_CoV_2 E55D 208 212 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. For FRET measurements, HEK293T/17 cells were transfected with a 1:5 ratio of plasmids encoding SARS CoV-2S** and wild-type SARS-CoV-2S, and plasmids encoding HIV-1 Gag-Pol, NESPylRSAF/tRNAPyl, and eRF1 (E55D), and grown in the presence of 0.5 mM TCO* ncAA. 2022 Cell reports Method SARS_CoV_2 E55D 203 207 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. HEK293T/17 cells were transfected with plasmids encoding HIV-1 GagPol and either wild type SARS-CoV-2 spike (Wuhan) or SARS-CoV-2 D614G/B.1.1.7/B.1.351/B.1.617.2 spike variant. 2022 Cell reports Method SARS_CoV_2 D614G 130 135 S;S 102;162 107;167 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Liposomes were incubated with dithionite for 30 min, and following dithionite reduction, virions having either WT spike or D614G spike were mixed, and inner leaflet lipid-mixing were measured exactly as described for total lipid-mixing earlier. 2022 Cell reports Method SARS_CoV_2 D614G 123 128 S;S 114;129 119;134 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Non-canonical amino acid incorporation into SARS-CoV-2 WT spike and D614G spike. 2022 Cell reports Method SARS_CoV_2 D614G 68 73 S;S 58;74 63;79 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Sequestering intracellular Ca2+ completely abrogate the viral entry for both the WT and D614G spike pseudovirions (Figure S1B). 2022 Cell reports Method SARS_CoV_2 D614G 88 93 S 94 99 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Similarly SARS-CoV-2 D614G spike pseudotyped virion was first evaluated by transfecting HEK293T cells with plasmids encoding the D614G Spike, TAG-mutated D614G-S and NESPylRSAF/tRNAPyl, eRF1 E55D, and HIV-1 Gag-Pol. 2022 Cell reports Method SARS_CoV_2 D614G;D614G;D614G;E55D 21;129;154;191 26;134;159;195 S;S;S 27;135;160 32;140;161 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Similarly, Cy3 labeled D614G-S* virions were produced. 2022 Cell reports Method SARS_CoV_2 D614G 23 28 S 29 30 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. The formation of SARS-CoV-2 spike pseudotyped virion was first evaluated by transfecting HEK293T cells with plasmids encoding the Spike, TAG-mutated S and NESPylRSAF/tRNAPyl, eRF1 E55D, and HIV-1 Gag-Pol. 2022 Cell reports Method SARS_CoV_2 E55D 180 184 S;S;S 28;130;149 33;135;150 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. The viral membrane of virions with either WT spike or D614G spike were incubated with 20uM DiO for 2 h at room temperature. 2022 Cell reports Method SARS_CoV_2 D614G 54 59 Membrane;S;S 10;45;60 18;50;65 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. The WT-S*-Cy3 and WT-S**-Cy3/Cy5 has been found to be 92% and 90% fusogenic relative to WT-S respectively and D614G-S*-Cy3 and D614G-S**-Cy3/Cy5 is 95% and 92% fusogenic relative to D614G spike respectively (Figure S6). 2022 Cell reports Method SARS_CoV_2 D614G;D614G;D614G 110;127;182 115;132;187 S;S;S;S;S;S 188;7;21;91;116;133 193;8;22;92;117;134 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. To generate S-MEN particles, plasmids encoding pCMV-S (Wuhan/D614G/B.1.1.7/B.1.351/B.1.617.2 variant), pLVX-M (SARS-CoV-2 membrane protein plasmid), an pLVX-E (SARS-CoV-2 envelope protein plasmid, and pLVX-N (SARS-CoV-2 nucleocapsid expressing plasmid) were transfected at a ratio of 5:5:5:5 into HEK293T/17 cell. 2022 Cell reports Method SARS_CoV_2 D614G;W614G 61;61 66;66 N;Membrane;S;S 220;122;12;52 232;130;13;53 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Virions having either Cy3 labeled WT-spike or D614G spike (fluorophore lebelling described above) were mixed with proteo-liposomes having all the receptors (hACE2/NRP1/hTMPRSS2) and incubated with buffer at pH4.6 for 5 min so that virus can bind the liposome, followed by anisotropy measurement was started. 2022 Cell reports Method SARS_CoV_2 D614G 46 51 S;S 37;52 42;57 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Virions having wither WT spike or D614G spike were mixed with NBD/RHO-labeled liposomes, coated with recombinant hACE2, NRP1-b1 and hTMPRSS2, maintaining equal stoichiometry (1:1:1). 2022 Cell reports Method SARS_CoV_2 D614G 34 39 S;S 25;40 30;45 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Virions with either wild-type spike or D614G spike having Q836TCO* and G1035TCO* were labeled with tetrazine-Cy3 (donor) and tetrazine-Cy5 (acceptor), as described above. 2022 Cell reports Method SARS_CoV_2 D614G 39 44 S;S 30;45 35;50 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Virus particle with D614G spike shows approximately double fusiogenicity compared to WT spike (Figure S1B). 2022 Cell reports Method SARS_CoV_2 D614G 20 25 S;S 26;88 31;93 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. We incorporated two TCO* ncAAs into the S2 domain of SARS-CoV-2 WT spike and D614G spike through amber stop codon suppression, as previously done for influenza HA and Ebola GP. 2022 Cell reports Method SARS_CoV_2 D614G 77 82 S;S 67;83 72;88 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. A commercially available SARS-CoV-2 surrogate virus neutralizaton test (sVNT) kit (Cat # L00847-A, Genscript, Piscataway, United States) for the Omicron variant based on antibody mediated blockage of the ACE-2 receptor- RBD interaction was used to assess the neutralization of the Omicron (R346K) variant infected hamster sera samples. 2022 EBioMedicine Method SARS_CoV_2 R346K 290 295 RBD 220 223 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Hundred microlitre of a virus [Omicron (R346K) variant] dose of 2 13 x 104 TCID50 was used to infect the twenty hamsters intranasally. 2022 EBioMedicine Method SARS_CoV_2 R346K 40 45 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. On deep sequencing following amino acid changes were found in the isolate.(NSP5_P132H,Spike_T95I,Spike_K417N,Spike_S373P,Spike_Q493R,Spike_N969K, Spike_H655Y,Spike_N856K,N_R203K,Spike_S371L,NSP3_A1892T,Spike_Q954H,Spike_G339D,N_P13L,Spike_N501Y,NSP14_I42V,Spike_P681H,M_Q19E,Spike_N440K,NSP4_T492I,Spike_S375F,Spike_Q498R,Spike_G446S,Spike_N679K,Spike_N764K,Spike_S477N,Spike_Y505H,NSP3_K38R,Spike_R346K,NSP6_I189V,Spike_T547K,M_D3G,Spike_D796Y,Spike_E484A,N_G204R,Spike_T478K,E_T9I,Spike_L981F,M_A63T,NSP12_P323L,Spike_D614G,Spike_G496S). 2022 EBioMedicine Method SARS_CoV_2 A1892T;A1892T,S;A63T;D3G;D614G;D614G,S;D796Y;D796S;E484A;G204R;G204R,S;G339D;G446S;G446S,S;G496S;H655Y;H655Y,S;I189V;I189V,S;I42V;I42V,S;K38R;K38R,S;K417N,S;L981F;N440K;N501Y;N679K;N679K,S;N764K;N764K,S;N856K;N969K;P132H,S;P13L;P13L,S;P323L;P323L,S;P681H;Q19E;Q19E,S;Q493R,S;Q498R;Q498R,S;Q954H;Q954H,S;R203K;R203K,S;R346K;S371L;S373P,S;S375F;S375F,S;S477N;S477N,S;T478K;T492I;T492I,S;T547K;T95I,S;T9I;Y505H 195;195;497;429;520;520;439;439;451;459;459;220;328;328;532;152;152;409;409;251;251;387;387;103;489;281;239;340;340;352;352;164;139;80;228;228;508;508;262;270;270;127;316;316;208;208;172;172;398;184;115;304;304;364;364;471;292;292;421;92;479;376 201;201;501;432;525;525;444;444;456;464;464;225;333;333;537;157;157;414;414;255;255;391;391;108;494;286;244;345;345;357;357;169;144;85;232;232;513;513;267;274;274;132;321;321;213;213;177;177;403;189;120;309;309;369;369;476;297;297;426;96;482;381 S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;S;Nsp12;Nsp3;Nsp3;Nsp4;Nsp5;Nsp6 86;97;109;121;133;146;158;178;202;214;233;256;275;298;310;322;334;346;358;370;392;415;433;445;465;483;514;526;502;190;382;287;75;404 91;102;114;126;138;151;163;183;207;219;238;261;280;303;315;327;339;351;363;375;397;420;438;450;470;488;519;531;507;194;386;291;79;408 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. SARS-CoV-2 Omicron (R346K) variant (GISAID accession no: EPI_ISL_8542938) belonging to the BA.1.1 sub lineage isolated from nasopharyngeal swab of a COVID-19 patient by inoculating into Syrian hamster was used for the study. 2022 EBioMedicine Method SARS_CoV_2 R346K 20 25 COVID-19 149 157 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. The live virus neutralization assay was performed against B.1 variant (GISAID accession no: EPI_ISL_420546), Alpha (GISAID accession no: EPI_ISL_825086), Beta (GISAID accession no: EPI_ISL_2014131), Delta (GISAID accession no: EPI_ISL_2400521) and Omicron (R346K) VOCs of SARS-CoV-2 as described earlier. 2022 EBioMedicine Method SARS_CoV_2 R346K 257 262 35409572 Increased Secondary Attack Rate among Unvaccinated Household Contacts of Coronavirus Disease 2019 Patients with Delta Variant in Japan. Almost all cases with the N501Y mutation during the study period in Japan were confirmed to be the Alpha variant by RNA sequencing. 2022 International journal of environmental research and public health Method SARS_CoV_2 N501Y 26 31 35409572 Increased Secondary Attack Rate among Unvaccinated Household Contacts of Coronavirus Disease 2019 Patients with Delta Variant in Japan. Among unvaccinated COVID-19 contacts, we defined contact of the index case with the L452R variant among the patients or their contacts as contacts of the Delta variant. 2022 International journal of environmental research and public health Method SARS_CoV_2 L452R 84 89 COVID-19 19 27 35409572 Increased Secondary Attack Rate among Unvaccinated Household Contacts of Coronavirus Disease 2019 Patients with Delta Variant in Japan. Contact with the Alpha strain was defined as contact of the index patient with positive results for N501Y mutation until 20 June 2021 or negative results for L452R mutation after 21 June 2021 among the patient, or the patient's contacts. 2022 International journal of environmental research and public health Method SARS_CoV_2 L452R;N501Y 158;100 163;105 35409572 Increased Secondary Attack Rate among Unvaccinated Household Contacts of Coronavirus Disease 2019 Patients with Delta Variant in Japan. However, almost all cases with the L452R mutation in Japan have been confirmed to be the Delta variant by RNA sequencing. 2022 International journal of environmental research and public health Method SARS_CoV_2 L452R 35 40 35409572 Increased Secondary Attack Rate among Unvaccinated Household Contacts of Coronavirus Disease 2019 Patients with Delta Variant in Japan. If the index case was reported after 22 March, and both N501Y and L452R mutation screening were not performed, or not detected for the index patient and contacts, the contact was excluded from the study. 2022 International journal of environmental research and public health Method SARS_CoV_2 L452R;N501Y 66;56 71;61 35409572 Increased Secondary Attack Rate among Unvaccinated Household Contacts of Coronavirus Disease 2019 Patients with Delta Variant in Japan. In Ibaraki prefecture, the N501Y mutation was not found in the tests until the 11th week of 2021, and thus, the wild strains were selected from the participants tested by the 11th week of 2021. 2022 International journal of environmental research and public health Method SARS_CoV_2 N501Y 27 32 35409572 Increased Secondary Attack Rate among Unvaccinated Household Contacts of Coronavirus Disease 2019 Patients with Delta Variant in Japan. In Japan, screening for the L452R mutation was implemented in approximately 40-50% of samples from July 2021. 2022 International journal of environmental research and public health Method SARS_CoV_2 L452R 28 33 35409572 Increased Secondary Attack Rate among Unvaccinated Household Contacts of Coronavirus Disease 2019 Patients with Delta Variant in Japan. The L452R mutation is also found in other variant strains of interest, such as the B.1.617.1 (Kappa) variant. 2022 International journal of environmental research and public health Method SARS_CoV_2 L452R 4 9 35409572 Increased Secondary Attack Rate among Unvaccinated Household Contacts of Coronavirus Disease 2019 Patients with Delta Variant in Japan. The proportion of N501Y mutation was 98.7% in the 23rd week (7-13 June 2021), and the first L452R mutation was detected in the 25th week (21-27 June 2021) in Ibaraki. 2022 International journal of environmental research and public health Method SARS_CoV_2 L452R;N501Y 92;18 97;23 35412379 Differences in Transmission between SARS-CoV-2 Alpha (B.1.1.7) and Delta (B.1.617.2) Variants. The detection of the L452R mutation by TaqMan assay was used as a proxy measure of the Delta variant. 2022 Microbiology spectrum Method SARS_CoV_2 L452R 21 26 35421378 Efficacy of vaccination and previous infection against the Omicron BA.1 variant in Syrian hamsters. Early contemporary S-614D and S-614G isolates (SARS-CoV-2/UT-NCGM02/Human/2020/Tokyo and SARS-CoV-2/UT-HP095-1N/Human/2020/Tokyo, respectively) were described previously. 2022 Cell reports Method SARS_CoV_2 S614D;S614G 19;30 25;36 S;S 19;30 20;31 35421378 Efficacy of vaccination and previous infection against the Omicron BA.1 variant in Syrian hamsters. The ELISA was performed using a recombinant S-614G protein with a C-terminal HIS-tag purified by using TALON metal affinity resin from Expi293F cells (Thermo Fisher Scientific). 2022 Cell reports Method SARS_CoV_2 S614G 44 50 S 44 45 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. Analysis of the structural landscape of significant mutations such as N501Y, D614G L452R, E484Q, and P681R, which are found in these two variants. 2022 Infection, genetics and evolution Method SARS_CoV_2 D614G;E484Q;L452R;N501Y;P681R 77;90;83;70;101 82;95;88;75;106 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. The COVID-3D server was used for the structural analysis of significant mutations (N501Y, D614G L452R, E484Q, and P681R) in two emerging variants. 2022 Infection, genetics and evolution Method SARS_CoV_2 D614G;E484Q;L452R;P681R;N501Y 90;103;96;114;83 95;108;101;119;88 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. Therefore, the generated RDD of the B.1.617.2 variant by introducing two significant mutations in control RBD, 452R and E484Q. 2022 Infection, genetics and evolution Method SARS_CoV_2 E484Q 120 125 RBD 106 109 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Briefly, 293T cells were first transfected with the SARS-CoV-2 spike protein expression plasmids of D614G or VOCs/VOIs (Alpha, Beta, Gamma, Delta, Lambda, Mu, and Omicron). 2022 MedComm Method SARS_CoV_2 D614G 100 105 S 63 68 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. D614G (GISAID: EPI_ISL_766872), BA.1 (GISAID: EPI_ISL_6590782.2), BA.2 (GISAID: EPI_ISL_7644798), BA.3 (GISAID: EPI_ISL_7740765), C.1.2 (GISAID: EPI_ISL_8801147), B.1.630 (GISAID: EPI_ISL_6368831), B.1.640.1 (GISAID: EPI_ISL_8013598), and B.1.640.2 (GISAID: EPI_ISL_8376567) spike protein expression plasmids are all entrusted to General Biology (Anhui) Co., Ltd. 2022 MedComm Method SARS_CoV_2 D614G 0 5 S 275 280 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Each guinea pig was subcutaneously immunized with 100 mug of purified spike proteins of different SARS-CoV-2 variants (Acro Biosystems Co.), including the D614G reference strain, current VOCs (Alpha, Beta, Gamma, Delta, Omicron) and VOIs (Lambda, Mu). 2022 MedComm Method SARS_CoV_2 D614G 155 160 S 70 75 35436320 Occurrence of a novel cleavage site for cathepsin G adjacent to the polybasic sequence within the proteolytically sensitive activation loop of the SARS-CoV-2 Omicron variant: The amino acid substitution N679K and P681H of the spike protein. FASTA format sequences of the S protein peptides spanning the S1/S2 interface of SARS-CoV-1 (UniProtKB: P0DTC2) 660YHTVSLLRSTSQKS673, SARS-CoV-2 (Wuhan, WIV04, UniProtKB: P59594) 678TNSPRRARSVASQS691, SARS-CoV-2 P681H (Alpha) 678TNSHRRARSVASQS691, SARS-CoV-2 P681R (Delta) 678TNSRRRARSVASQS691, SARS-CoV-2 (C.1.2) 674YQTQTKSPRRARSVASQS691, and SARS-CoV-2 (Omicron) 674YQTQTKSHRRARSVASQS691 were retrieved from UniProtKB (https://www.uniprot.org). 2022 PloS one Method SARS_CoV_2 P681H;P681R 212;259 217;264 S 30 31 35436320 Occurrence of a novel cleavage site for cathepsin G adjacent to the polybasic sequence within the proteolytically sensitive activation loop of the SARS-CoV-2 Omicron variant: The amino acid substitution N679K and P681H of the spike protein. SARS-CoV-1 660YHTVSLLRSTSQKS673, SARS-CoV-2 (Wuhan) 678TNSPRRARSVASQS691, SARS-CoV-2 P681H (Alpha) 678TNSHRRARSVASQS691, SARS-CoV-2 P681R (Delta) 678TNSRRRARSVASQS691, SARS-CoV-2 (Wuhan) 674YQTQTNSPRRARSVASQS691, SARS-CoV-2 (Alpha) 674YQTQTNSHRRARSVASQS691, SARS-CoV-2 (C.1.2) 674YQTQTKSPRRARSVASQS691, or SARS-CoV-2 (Omicron) 674YQTQTKSHRRARSVASQS691 peptides, spanning the polybasic sequence, were synthesized by EMC Microcollections GmbH (Tubingen, Germany) and purified by reversed-phase HPLC using a C18 250 x 8 column (Dr. 2022 PloS one Method SARS_CoV_2 P681H;P681R 85;132 90;137 35441172 Receptor binding domain of SARS-CoV-2 is a functional alphav-integrin agonist. His-tagged S1 and S1-RBD of SARS-CoV-2 were purchased from Sino Biological (40591-V08H) and R&D Systems (10523-CV;), respectively. 2022 bioRxiv Method SARS_CoV_2 V08H 82 86 RBD 21 24 35455241 Durability and Cross-Reactivity of SARS-CoV-2 mRNA Vaccine in Adolescent Children. Serological analyses were performed using an in-house enzyme-linked immunosorbent assay (ELISA) that detects IgG against the D614G ("wild type") SARS-CoV-2 Spike, the D614G ("wild type") Receptor-Binding Domain (RBD), or the Omicron SARS-CoV-2 VOC RBD by using the previously described method. 2022 Vaccines Method SARS_CoV_2 D614G;D614G 125;167 130;172 S;RBD;RBD 156;212;248 161;215;251 35456137 Comparative Evaluation of Six SARS-CoV-2 Real-Time RT-PCR Diagnostic Approaches Shows Substantial Genomic Variant-Dependent Intra- and Inter-Test Variability, Poor Interchangeability of Cycle Threshold and Complementary Turn-Around Times. The following 10 SARS-CoV-2 variants were selected for this study: Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), Eta (B.1.525), Iota (B.1.526), Omicron (B.1.1.529) A.27, B.1.258.17, and B.1 with D614G mutation, all of which are deposited in the EVA-GLOBAL Virus Archive under the following reference numbers (Ref-SKU): 005V-04053, 005V-04107, 005V-04248, 005V-04249, 005V-04109, 005V-04401, 005V-04479, 005V-04144, 005V-04394, and 005V-03961. 2022 Pathogens (Basel, Switzerland) Method SARS_CoV_2 D614G 214 219 35458530 Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice. It contains A348P, Y365W and P527L stabilising mutations. 2022 Viruses Method SARS_CoV_2 A348P;P527L;Y365W 12;29;19 17;34;24 35458530 Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice. mRBD1-3.2-beta was generated in the background of stabilised mRBD1-3.2 (A348P, Y365W and P527L), and it has three important mutations (K417N, E484K and N501Y) present in the RBD of the Beta (B.1.351) VOC. 2022 Viruses Method SARS_CoV_2 E484K;N501Y;P527L;Y365W;A348P;K417N 142;152;89;79;72;135 147;157;94;84;77;140 RBD 174 177 35458530 Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice. Three SARS-CoV-2 isolates viz., VIC31-D614G (hCoV-19/Australia/VIC31/2020, containing the D614G mutation) and the two variants of concern (VOC) Delta (hCoV-19/Australia/VIC18440/2021) and Omicron BA.1.1 (hCoV-19/Australia/VIC28585/2021), were kindly provided by Drs Caly and Druce at the Victorian Infectious Diseases Reference Laboratory (VIDRL; Melbourne, Australia). 2022 Viruses Method SARS_CoV_2 D614G;D614G 90;38 95;43 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. A QuikChange Lightening Site-Directed Mutagenesis kit was used to generate amino acid substitutions in the pCDNA wild-type spike plasmid carrying a D614G (received from S. 2022 Viruses Method SARS_CoV_2 D614G 148 153 S;S 123;169 128;170 35461811 Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. Site directed mutagenesis was performed to make each of the variants (K90R, G15S or P132H). 2022 The Journal of biological chemistry Method SARS_CoV_2 G15S;P132H;K90R 76;84;70 80;89;74 35464418 Decreased and Heterogeneous Neutralizing Antibody Responses Against RBD of SARS-CoV-2 Variants After mRNA Vaccination. Primers used for the construction of the RBD-mFc proteins for the different variants (Alpha RBD-mFc, containing mutation N501Y; Gamma RBD-mFc containing mutations K417T, E484K, and N501Y; Delta RBD-mFc containing mutations L452R and T478K); Epsilon RBD-mFc containing mutation L452R; and Kappa RBD-mFc containing mutations L452R and E484Q), were obtained from Sigma-Aldrich and are shown in Supplementary Table 2 . 2022 Frontiers in immunology Method SARS_CoV_2 E484K;E484Q;K417T;L452R;L452R;L452R;N501Y;N501Y;T478K 170;333;163;223;277;323;121;181;233 175;338;168;228;282;328;126;186;238 RBD;RBD;RBD;RBD;RBD;RBD 41;92;134;194;249;294 44;95;137;197;252;297 35480056 Safety and Immunogenicity of Inactivated COVID-19 Vaccines Among People Living with HIV in China. Briefly, all subjects' neutralizing antibody responses to the D614G variant and delta variant were tested using the SARS-CoV-2 pseudotyped virus kit (purchased from Zhongyanguobang Biological Technology Co., Ltd.). 2022 Infection and drug resistance Method SARS_CoV_2 D614G 62 67 35480056 Safety and Immunogenicity of Inactivated COVID-19 Vaccines Among People Living with HIV in China. We used a pseudovirus neutralization assay to evaluate the neutralizing antibody responses to the D614G variant and delta variant of all subjects. 2022 Infection and drug resistance Method SARS_CoV_2 D614G 98 103 32300673 Genomic characterization of a novel SARS-CoV-2. 29095C>T is found in the subset of them. 2020 Gene reports Result SARS_CoV_2 C29095T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. Both 8782C>T and 29095C>T are synonymous; however, 28144T>C causes amino acid to change L84S in ORF8. 2020 Gene reports Result SARS_CoV_2 T28144C;C29095T;C8782T;L84S 51;17;5;88 59;25;12;92 ORF8 96 100 32300673 Genomic characterization of a novel SARS-CoV-2. Notably, most of 8782C>T and 28144T>Cvariant substrains are found outside of Wuhan. 2020 Gene reports Result SARS_CoV_2 T28144C;C8782T 29;17 37;24 32300673 Genomic characterization of a novel SARS-CoV-2. The most common variants were 8782C>T(ORF1ab) in 13 samples, 28144T>C (ORF8) in 14 samples and 29095C>T (N) in 8samples. 2020 Gene reports Result SARS_CoV_2 C29095T;C8782T 95;30 103;37 ORF1ab;ORF8 38;71 44;75 32300673 Genomic characterization of a novel SARS-CoV-2. The occurrences of 8782C>T and 28144T>C coincide. 2020 Gene reports Result SARS_CoV_2 T28144C;C8782T 31;19 39;26 32357545 Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment. Among the twelve variants in the B-cell epitopes, 23403A>G variant (p.D614G) in one of the epitopes in spike protein between residue 601 and 640 stands out, with 175 samples in 615 total samples. 2020 Pathogens (Basel, Switzerland) Result SARS_CoV_2 A23403G;D614G;D614G 50;68;70 58;75;75 S 103 108 32357545 Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment. The variant is located in the middle of that epitope and the amino acid change in the 23403A>G variant (p.D614G) involves a change of large acidic residue D (aspartic acid) into small hydrophobic residue G (glycine). 2020 Pathogens (Basel, Switzerland) Result SARS_CoV_2 A23403G;D614G;D614G 86;104;106 94;111;111 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. Sequencing of the extracted viral RNA from the lung showed that the virus derived from Claude A2a with G11083T (ORF1a L3606F) mutation Table 2. 2020 American journal of clinical pathology Result SARS_CoV_2 G11083T;L3606F 103;118 110;124 ORF1a 112 117 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. The non-synonymous D614G mutation in the spike protein occurred at a high frequency. 2020 The Indian journal of medical research Result SARS_CoV_2 D614G 19 24 S 41 46 32478289 The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey. Since all three isolates have a D614G variant in spike glycoprotein, they belong to G clade based on GISAID classification. 2020 Northern clinics of Istanbul Result SARS_CoV_2 D614G 32 37 S 49 67 32511374 An insertion unique to SARS-CoV-2 exhibits superantigenic character strengthened by recent mutations. A rare mutation, D839Y/E, recently observed in a SARS2 strain from Europe contributes to stabilizing the interaction with TCR. 2020 bioRxiv Result SARS_CoV_2 D839E;D839Y 17;17 24;24 32511374 An insertion unique to SARS-CoV-2 exhibits superantigenic character strengthened by recent mutations. Interestingly, the SARS-CoV-2 spike binding region harbors three residues that have been recently reported to have mutated in new strains from Europe and USA: D614G, A831V and D839Y/N/E). 2020 bioRxiv Result SARS_CoV_2 A831V;D614G;D839E;D839N;D839Y 166;159;176;176;176 171;164;185;185;185 S 30 35 32511374 An insertion unique to SARS-CoV-2 exhibits superantigenic character strengthened by recent mutations. Its substitution by glutamate in the mutant D839E increases the strength of the intermolecular (and thereby virus-T cell) association. 2020 bioRxiv Result SARS_CoV_2 D839E 44 49 32511374 An insertion unique to SARS-CoV-2 exhibits superantigenic character strengthened by recent mutations. Thus, the D839Y/N/E mutations would be expected to strengthen/support the above described association between the superantigenic PRRA-containing segment and the TCRVbeta. 2020 bioRxiv Result SARS_CoV_2 D839E;D839N;D839Y 10;10;10 19;19;19 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. As Gly lacks a side-chain, the transient hydrogen bond as observed in the wild-type S protein would be lost in the variant with D614G mutation. 2020 Journal of biosciences Result SARS_CoV_2 D614G 128 133 S 84 85 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. In addition to these, 24933 G/T mutation in the gene coding for Spike glycoprotein (G1124V) and triple base mutations of 2881-2883 GGG/AAC in the gene coding for nucleocapsid resulting in two consecutive amino acid changes R203K and G204R were detected in S2, S3 and S2, S3, S5 respectively. 2020 Journal of biosciences Result SARS_CoV_2 G204R;R203K;G1124V 233;223;84 238;228;90 S;N 64;162 82;174 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. Possible implications of D614G mutation (in SD domain) on protein structural stability. 2020 Journal of biosciences Result SARS_CoV_2 D614G 25 30 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. Possible implications of G1124V mutation (in S2 subunit) on protein structural stability. 2020 Journal of biosciences Result SARS_CoV_2 G1124V 25 31 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. These consisted of the 14408 C/T mutation resulting in a change of P323L in the RdRp and the 23403 A/G mutation resulting in a change of D614G in the Spike glycoprotein of the virus. 2020 Journal of biosciences Result SARS_CoV_2 D614G;P323L 137;67 142;72 S;RdRP 150;80 168;84 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. Two individuals, S11 and S12, harboured viral genome sequences that shared a unique 13730 C/T (A88V) mutation which was not found in any other sequence reported from India or rest of the World. 2020 Journal of biosciences Result SARS_CoV_2 A88V 95 99 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. We analysed the 28881-3 GGG/AAC mutations in the nucleocapsid gene which results in contiguous amino acid changes of R203K and G204R for their potential role in alteration of structure of the encoded protein. 2020 Journal of biosciences Result SARS_CoV_2 G204R;R203K 127;117 132;122 N 49 61 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. We detected a total of six mutations in this gene in the nine samples, out of which four were nonsynonymous, including the A2a clade specific 14408 C/T (RdRp: P323L) mutation. 2020 Journal of biosciences Result SARS_CoV_2 P323L 159 164 RdRP 153 157 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Although the CGMH-CGU-02 strain did not carry the ORF8-L84S mutation due to the aforementioned ORF8 deletion, it shared the ORF1ab-C8517T mutation with Taiwan/2 and other strains in this clade (Figures 2B and 3B). 2020 Emerging microbes & infections Result SARS_CoV_2 C8517T;L84S 131;55 137;59 ORF1ab;ORF8;ORF8 124;50;95 130;54;99 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. CGMH-CGU-04 was found to have 3 ORF1ab nucleotide substitutions (A4788G, C10809T, and G21055A); the third position was a non-synonymous change with a G7019S amino acid substitution (Figure 3D). 2020 Emerging microbes & infections Result SARS_CoV_2 C10809T;G21055A;G7019S;A4788G 73;86;150;65 80;93;156;71 ORF1ab 32 38 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. In addition to the signature mutation ORF3a-G251V of clade II, CGMH-CGU-09 also has 3 more mutations in ORF1ab (Figure 3C). 2020 Emerging microbes & infections Result SARS_CoV_2 G251V 44 49 ORF1ab;ORF3a 104;38 110;43 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. In addition to the signature mutation S-D614G annotated by GISAID in clade III, all the Taiwanese genomes shared two ORF1ab mutations C2772T and C14144T (P4715L) (Figure 3E). 2020 Emerging microbes & infections Result SARS_CoV_2 C14144T;C2772T;P4715L;D614G 145;134;154;40 152;140;160;45 ORF1ab;S 117;38 123;39 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Locally clustered and global transmission in the new ORF1ab-V378I clade. 2020 Emerging microbes & infections Result SARS_CoV_2 V378I 60 65 ORF1ab 53 59 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Moreover, 8 Taiwanese genomes (including 5 determined from samples obtained from clustered infection cases in the first wave) exhibited the mutation ORF1ab-V378I that was not mentioned before; these strains have now been included in the new genetic clade IV (Figure 2D) along with some foreign strains identified from patients who had a travel history to Europe and the Middle East. 2020 Emerging microbes & infections Result SARS_CoV_2 V378I 156 161 ORF1ab 149 155 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. On the other hand, CGMH-CGU-07 showed only one non-synonymous substitution from the baseline at a different ORF1ab position C19547T (S6248L) (Figure 3D). 2020 Emerging microbes & infections Result SARS_CoV_2 C19547T;S6248L 124;133 131;139 ORF1ab 108 114 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. One strain hCoV-19/Singapore/14/2020 showed only one synonymous mutation ORF1ab-C8517T, which was also found in CGMH-CGU-02. 2020 Emerging microbes & infections Result SARS_CoV_2 C8517T 80 86 ORF1ab 73 79 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. The latter was a non-synonymous mutation resulting in an amino acid change at position 5526 from K to R (K5526R). 2020 Emerging microbes & infections Result SARS_CoV_2 K5526R 105 111 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. The other two (hCoV-19/Singapore/12/2020 and hCoV-19/Singapore/13/2020) each additionally showed two different non-synonymous mutations S-T2449C (F817L) and ORF3a-C176A (A59D), and ORF1ab-T17459C (V5820A) and N-C595T (P199S), respectively. 2020 Emerging microbes & infections Result SARS_CoV_2 A59D;F817L;P199S;V5820A;C176A;C595T;T17459C;T2449C 170;146;218;197;163;211;188;138 174;151;223;203;168;216;195;144 ORF1ab;ORF3a;N;S 181;157;209;136 187;162;210;137 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. The other two mutations in CGMH-CGU-02 were also non-synonymous, located in the S gene at C145T (H49Y) and C2651T (S884F). 2020 Emerging microbes & infections Result SARS_CoV_2 C145T;C2651T;H49Y;S884F 90;107;97;115 95;113;101;120 S 80 81 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. To better illustrate phylogenetic clades, we designated and numbered yellow clade as IV harbouring ORF1ab-V378I mutation in this study and three others (blue clade I of ORF8-L84S, gray clade II of ORF3a-G251V, and pink clade III of S-D614G) identified based on previous GISAID annotations of clades S, V, and G, respectively. 2020 Emerging microbes & infections Result SARS_CoV_2 D614G;G251V;L84S;V378I 234;203;174;106 239;208;178;111 ORF1ab;ORF3a;ORF8;S 99;197;169;232 105;202;173;233 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Two were located at the ORF1ab position 8517 changing from C to T (as C8517T) and position 16577 from A to G (A16577G). 2020 Emerging microbes & infections Result SARS_CoV_2 A16577G;C8517T;A16577G 91;70;110 108;76;117 ORF1ab 24 30 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Viral genomes of CGMH-CGU-03 to -07 were determined from clustered infection samples (-03 was the index patient), together with -08 (a case originating from the United Kingdom), and -10 and -11 (having travel history to Turkey) were shown in clade IV of ORF1ab-V378I (Figure 2D). 2020 Emerging microbes & infections Result SARS_CoV_2 V378I 261 266 ORF1ab 254 260 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. We further found 4 Taiwanese strains (CGMH-CGU-12, -13, -18, and -20, top four in Figure 3E) shared the same N gene mutations R203K and G204R resulting from 3 nucleotide mutations G608A, G609A, and G610C. 2020 Emerging microbes & infections Result SARS_CoV_2 G204R;G608A;G609A;G610C;R203K 136;180;187;198;126 141;185;192;203;131 N 109 110 32577641 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Among the 25 loci where at least one of these isolates differs from the reference genome, T27772A is a nonsense mutation that disrupts ORF7b but is present in 7% of the viral RNA in ZJU-11, suggesting that this ORF is not essential for replication. 2020 bioRxiv Result SARS_CoV_2 T27772A 90 97 ORF7b 135 140 32577641 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. First, we investigated Sarbecovirus conservation of 14 amino acids in the spike protein in which mutations appear to be accumulating in the SARS-CoV-2 population, namely D614G, L5F, L8V/W, H49Y, Y145H, Q239K, V367F, G476S, V483A, V615I/F, A831V, D839Y/N/E, S943P, P1263L. 2020 bioRxiv Result SARS_CoV_2 A831V;D614G;D839Y;D839E;D839N;G476S;H49Y;L5F;L8V;L8W;P1263L;Q239K;S943P;V367F;V483A;V615F;V615I;Y145H 239;170;246;246;246;216;189;177;182;182;264;202;257;209;223;230;230;195 244;175;255;255;255;221;193;180;187;187;270;207;262;214;228;237;237;200 S 74 79 32577641 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Furthermore, its start codon is lost in one strain, and most strains have a stop codon three codons before the ORF14 stop (Supplemental. 2020 bioRxiv Result SARS_CoV_2 F14X 113 121 32577641 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. In contrast, L5F, L8V/W, H49Y, Y145H, Q239K, G476S, and V483A are in amino acids that are not conserved and are in poorly-conserved regions of the protein, so they are less likely to be required for a conserved function. 2020 bioRxiv Result SARS_CoV_2 G476S;H49Y;L5F;L8V;L8W;Q239K;V483A;Y145H 45;25;13;18;18;38;56;31 50;29;16;23;23;43;61;36 32577641 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Interestingly, one of the highly disruptive mutations, G23607A, is a radical R->Q amino acid change in the polybasic cleavage site of S, which is only present in SARS-CoV-2; it is present in all viral RNA in ZJU-1, whose viral load was near the mean, suggesting that this residue might have little effect on the ability of the virus to gain access to and replicate in cells. 2020 bioRxiv Result SARS_CoV_2 G23607A 55 62 S 134 135 32577641 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Likewise, two others, V615I/F and P1263L are mutations of perfectly conserved amino acids, while A831V is in a highly-conserved region of the protein and its amino acid is conserved in all but the two most distantly-related strains. 2020 bioRxiv Result SARS_CoV_2 A831V;P1263L;V615F;V615I 97;34;22;22 102;40;29;29 32577641 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Of particular interest is D614G, which has risen in frequency in multiple geographic locations, suggesting that it increases transmissibility. 2020 bioRxiv Result SARS_CoV_2 D614G 26 31 32577641 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. The two outliers with unusually high viral load after 24 hours, ZJU-10 and ZJU-11, each have exactly one mutation that we classified as highly disruptive, namely C16114T in ZJU-10 and a trimer substitution TTG->CGA at 27775-27777 in ZJU-11, suggesting that these are the mutations most likely to be responsible for the higher viral load. 2020 bioRxiv Result SARS_CoV_2 C16114T 162 169 32577644 Beyond Shielding: The Roles of Glycans in SARS-CoV-2 Spike Protein. Analysis of the RMSD values along the trajectory shows that even a single point N234A mutation contributes to destabilize the RBD "up" conformation (Figure S2). 2020 bioRxiv Result SARS_CoV_2 N234A 80 85 RBD 126 129 32577644 Beyond Shielding: The Roles of Glycans in SARS-CoV-2 Spike Protein. Furthermore, Calpha atoms' RMSD values indicate that even a single point N234A mutation may be sufficient to destabilize the RBD "up" conformation (Figure S2 and Section 3 of SI). 2020 bioRxiv Result SARS_CoV_2 N234A 73 78 RBD 125 128 32595352 An updated analysis of variations in SARS-CoV-2 genome. A23403G variation is one of the most important variations that have been reported previously (Phan et al., 2020) caused D614G substitution on S protein. 2020 Turkish journal of biology Result SARS_CoV_2 D614G;A23403G 120;0 125;7 S 142 143 32595352 An updated analysis of variations in SARS-CoV-2 genome. Although C14805T (submitted on February 9th, 2020 England; EPI_ISL_412116) variation is rarer, it was emerged earlier than C14408T variation. 2020 Turkish journal of biology Result SARS_CoV_2 C14408T;C14805T 123;9 130;16 32595352 An updated analysis of variations in SARS-CoV-2 genome. As in the C14408T of Nsp12 variation, A23403G variation of S protein is also available in 70.46% frequency in SARS-CoV-2 genomes isolated all over the world (Figure 2). 2020 Turkish journal of biology Result SARS_CoV_2 A23403G;C14408T 38;10 45;17 Nsp12;S 21;59 26;60 32595352 An updated analysis of variations in SARS-CoV-2 genome. C1059T variation has been caused T266I amino acid exchange on Nsp2. 2020 Turkish journal of biology Result SARS_CoV_2 T266I;C1059T 33;0 38;6 32595352 An updated analysis of variations in SARS-CoV-2 genome. C14408T (first reported by Pachetti et al., 2020) and C14805T found to be present on Nsp12 gene region with a frequency of 70.42% and 10.01% of isolates, respectively. 2020 Turkish journal of biology Result SARS_CoV_2 C14805T;C14408T 54;0 61;7 Nsp12 85 90 32595352 An updated analysis of variations in SARS-CoV-2 genome. C14408T and A23403G is common all over the world but especially in Africa, then S. 2020 Turkish journal of biology Result SARS_CoV_2 A23403G;C14408T 12;0 19;7 S 80 81 32595352 An updated analysis of variations in SARS-CoV-2 genome. C14408T variation observed to be responsible from P323L exchange causing a missense mutation. 2020 Turkish journal of biology Result SARS_CoV_2 P323L;C14408T 50;0 55;7 32595352 An updated analysis of variations in SARS-CoV-2 genome. Despite C14408T variation occurred later than C14805T, the incidence of this variation has increased sharply and reach over 70%, recently (Figure 2). 2020 Turkish journal of biology Result SARS_CoV_2 C14408T;C14805T 8;46 15;53 32595352 An updated analysis of variations in SARS-CoV-2 genome. Figure 3 clearly shows that; G25563T mutation is developed by the isolates in N. 2020 Turkish journal of biology Result SARS_CoV_2 G25563T 29 36 N 78 79 32595352 An updated analysis of variations in SARS-CoV-2 genome. G11083T variation (reported previously by van Dorp et al., 2020) causing L36F exchange was present on Nsp6 gene region that is known with its role in inducing vesicles located around the microtubule regulation centre and ensuring membrane proliferation (Angelini et al., 2013). 2020 Turkish journal of biology Result SARS_CoV_2 L36F;G11083T 73;0 77;7 Membrane;Nsp6 230;102 238;106 32595352 An updated analysis of variations in SARS-CoV-2 genome. G25560T variation also causes amino acid exchange of glutamine to histidine in residue 57 (Q57H). 2020 Turkish journal of biology Result SARS_CoV_2 Q57H;Q57H;G25560T 53;91;0 89;95;7 32595352 An updated analysis of variations in SARS-CoV-2 genome. G25563T variation is on the gene region of Orf3a which is a unique membrane protein with its 3-membrane structure, the largest protein in the SARS related CoVs accessory protein family and is essential for the pathogenesis of the disease (Lu et al., 2010; Issa et al., 2020). 2020 Turkish journal of biology Result SARS_CoV_2 G25563T 0 7 Membrane;Membrane;ORF3a 67;95;43 75;103;48 32595352 An updated analysis of variations in SARS-CoV-2 genome. G28881A and G28882A exchanges cause R204K and G28883C exchange causes G205R amino acid substitutions on the N protein. 2020 Turkish journal of biology Result SARS_CoV_2 G205R;G28882A;G28883C;R204K;G28881A 70;12;46;36;0 75;19;53;41;7 N 108 109 32595352 An updated analysis of variations in SARS-CoV-2 genome. It has been observed that 8 of these 11 variations; C1059T, G11083T, C14408T, A23403G, G25563T, G28881A, G28882A, and G28883C cause amino acid substitutions. 2020 Turkish journal of biology Result SARS_CoV_2 A23403G;C1059T;C14408T;G11083T;G25563T;G28881A;G28882A;G28883C 78;52;69;60;87;96;105;118 85;58;76;67;94;103;112;125 32595352 An updated analysis of variations in SARS-CoV-2 genome. Nearly all isolates which carry G25563T, also carry C14408T and A23403G variations although their location distributions are not similar. 2020 Turkish journal of biology Result SARS_CoV_2 A23403G;C14408T;G25563T 64;52;32 71;59;39 32595352 An updated analysis of variations in SARS-CoV-2 genome. Nearly no isolates carried GGG to AAC variations and G25563T variation simultaneously (Figure 4). 2020 Turkish journal of biology Result SARS_CoV_2 G25563T 53 60 32595352 An updated analysis of variations in SARS-CoV-2 genome. Our mutation analysis revealed that most of the isolates carry C14408T and A23403 variations simultaneously (Figure 4) in all continents (Figure 3). 2020 Turkish journal of biology Result SARS_CoV_2 C14408T 63 70 32595352 An updated analysis of variations in SARS-CoV-2 genome. The first variation C3037T causes a synonymous mutation and seen in frequency of 29.3% in gene region encoding Nsp3 that is an important unit of the replication/transcription complex in CoVs (Lei et al., 2018). 2020 Turkish journal of biology Result SARS_CoV_2 C3037T 20 26 Nsp3 111 115 32595352 An updated analysis of variations in SARS-CoV-2 genome. The increasing number of isolate genome entries in EpiCoV and rate changes of the most frequent variations by isolate collection dates are also given in Figure 2 for G25563T variation on accessory protein and A23403G variation on S protein and 3 consecutive variations (G28881A, G28882A, and G28883C) named as GGG to AAC on N protein. 2020 Turkish journal of biology Result SARS_CoV_2 A23403G;G25563T;G28882A;G28883C;G28881A 209;166;279;292;270 216;173;286;299;277 N;S 324;230 325;231 32595352 An updated analysis of variations in SARS-CoV-2 genome. The isolate genome sequence harbouring C14408T variation was first submitted to the GISAID from Lombardy, Italy, on February 20th, 2020 (EPI_ISL_412973), 20 days after the first COVID-19 case confirmed in Italy. 2020 Turkish journal of biology Result SARS_CoV_2 C14408T 39 46 COVID-19 178 186 32595352 An updated analysis of variations in SARS-CoV-2 genome. The other 3 variations, C1059T, G11083T, and C14408T causing amino acid substitutions are in gene regions of Nsp2, Nsp6, and Nsp12, respectively, in ORF1ab; with the incidence of over 10%. 2020 Turkish journal of biology Result SARS_CoV_2 C1059T;C14408T;G11083T 24;45;32 30;52;39 ORF1ab;Nsp12;Nsp2;Nsp6 149;125;109;115 155;130;113;119 32595352 An updated analysis of variations in SARS-CoV-2 genome. These 3 variations (G28881A, G28882A and G28883C) were seen simultaneously in about 99% of all isolates harbouring the variations. 2020 Turkish journal of biology Result SARS_CoV_2 G28882A;G28883C;G28881A 29;41;20 36;48;27 32595352 An updated analysis of variations in SARS-CoV-2 genome. This observation may be evaluated as a remarkable data about the effect of C14408T variation on the spread of the virus. 2020 Turkish journal of biology Result SARS_CoV_2 C14408T 75 82 32595352 An updated analysis of variations in SARS-CoV-2 genome. When the 30366 SARS-CoV-2 genome sequences were aligned, the first encountered variation was observed to be C241T in the 5' untranslated region (5' UTR) being occurred nearly in 70% of SARS-CoV-2 isolates. 2020 Turkish journal of biology Result SARS_CoV_2 C241T 108 113 5'UTR 145 151 32595352 An updated analysis of variations in SARS-CoV-2 genome. When the C14408T, G25563T, A23403G, and GGG to AAC variations with over 20% frequency were analysed, dramatic observations were seen in terms of appearance of these mutations in different continents (Figure 3). 2020 Turkish journal of biology Result SARS_CoV_2 A23403G;C14408T;G25563T 27;9;18 34;16;25 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. In more than 40% of the viral isolates, one or more of nucleotide substitutions of C3037T, C14408T ,A23403G, and G25563T were observed, which are present in the coding regions for the Nsp3, RNA-dependent RNA polymerase, spike glycoprotein and ORF3a protein, respectively (Table 1). 2020 Turkish journal of biology Result SARS_CoV_2 C14408T;C3037T;G25563T;A23403G 91;83;113;100 98;89;120;107 RdRp;S;ORF3a;Nsp3 190;220;243;184 218;238;248;188 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Additionally, when HEK-293 cells or SupT1 cells had been rendered infectable by stable expression of exogenous ACE2 and TMPRSS2, D614G was 9-fold more infectious than D614 (Figure 2). 2020 bioRxiv Result SARS_CoV_2 D614G 129 134 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Although recent data for South America are sparse, available sequences suggest D614G is approaching fixation in this continent as well. 2020 bioRxiv Result SARS_CoV_2 D614G 79 84 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Although these sequences suggest that the D614G variant first emerged in China or Germany, given how few virus genomes have been sequenced from early in the outbreak, its geographic origin cannot be determined. 2020 bioRxiv Result SARS_CoV_2 D614G 42 47 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Analysis of D614G variant frequency is expected to gain resolution as sequences are released for samples banked across the duration of the pandemic. 2020 bioRxiv Result SARS_CoV_2 D614G 12 17 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. As a first step to examine whether the increased infectivity of D614G is species-specific, plasmids were generated to express ACE2 orthologues from human (Homo sapiens), Malayan pangolin (Manis javanica), pig (Sus scrofa), cat (Felis catus), dog (Canis lupis), rat (Rattus norvegicus), and mouse (Mus musculus). 2020 bioRxiv Result SARS_CoV_2 D614G 64 69 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. As all four of these monoclonal antibodies bind epitopes within the Spike protein receptor binding domain, it remains important to determine whether the D614G variants changes neutralization sensitivity to other classes of anti-Spike monoclonal antibodies. 2020 bioRxiv Result SARS_CoV_2 D614G 153 158 RBD;S;S 82;68;228 105;73;233 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. At the end of January 2020, a nonsynonymous nucleotide change from the ancestral virus, A23403G, first appeared in virus genomes reported in China (hCoV-19/Zhejiang/HZ103/2020; 24 January 2020) and in Germany (hCoV-19/Germany/BavPat1-ChVir929/2020; 28 January 2020). 2020 bioRxiv Result SARS_CoV_2 A23403G 88 95 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. D614G is sensitive to neutralization by monoclonal antibodies targeting the receptor binding domain. 2020 bioRxiv Result SARS_CoV_2 D614G 0 5 RBD 76 99 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Effect of D614G on infectivity of different ACE2 orthologues. 2020 bioRxiv Result SARS_CoV_2 D614G 10 15 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Examination of D614G infectivity using ACE2s encoded by other mammalian species may provide further insight into the structure and function of this Spike variant. 2020 bioRxiv Result SARS_CoV_2 D614G 15 20 S 148 153 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. HEK-293 were transfected separately with each of the ACE2 expression plasmids and challenged with luciferase-reporter-lentiviral pseudotypes bearing SARS-CoV-2 Spike protein, either D614 or D614G. 2020 bioRxiv Result SARS_CoV_2 D614G 190 195 S 160 165 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. If SARS-CoV-2 Spike D614G is an adaptive mutant that was selected for increased human-to-human transmission following spillover from an animal reservoir, increased infectivity might only be evident on cells bearing ACE2 orthologues similar to that of the human. 2020 bioRxiv Result SARS_CoV_2 D614G 20 25 S 14 19 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. It is predicted that the D614G variant would abrogate this interaction and destabilize the inter-protomer interface. 2020 bioRxiv Result SARS_CoV_2 D614G 25 30 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Mammalian expression plasmids were engineered to encode the ancestral S protein (D614) and the D614G variant, as described previously. 2020 bioRxiv Result SARS_CoV_2 D614G 95 100 S 70 71 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Modeling the effect of D614G on structure. 2020 bioRxiv Result SARS_CoV_2 D614G 23 28 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Over the course of the COVID-19 pandemic, the SARS-CoV-2 D614G S protein variant supplanted the ancestral virus. 2020 bioRxiv Result SARS_CoV_2 D614G 57 62 S 63 64 COVID-19 23 31 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Over the course of the whole pandemic, the D614G variant is present in approximately 74% of published sequences (Figure 1A). 2020 bioRxiv Result SARS_CoV_2 D614G 43 48 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Relative increase in infectivity due to D614G was comparable in cells expressing human, pangolin, pig, cat, or dog ACE2 orthologues (Figure 3). 2020 bioRxiv Result SARS_CoV_2 D614G 40 45 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Since its first appearance, the frequency of the D614G variant has increased steadily over time in the global SARS-CoV-2 genomic dataset released by GISAID, to the point that it is nearly fixed in the viruses sampled globally (Figure 1A) or specifically in Europe, North America, Oceania, and Asia (Figure 1B). 2020 bioRxiv Result SARS_CoV_2 D614G 49 54 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The ability of the SARS-CoV-2 D614G S protein variant to target virions for infection of ACE2-positive cells was assessed using single-cycle lentiviral vector pseudotypes in tissue culture. 2020 bioRxiv Result SARS_CoV_2 D614G 30 35 S 36 37 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The D614G variant emerged at higher frequency in Africa and South America, suggesting a founder effect where a plurality of introductions carried D614G to these regions. 2020 bioRxiv Result SARS_CoV_2 D614G;D614G 4;146 9;151 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The global spread and enhanced infectivity of the SARS-CoV-2 D614G variant raises the question of whether this change in Spike protein structure may compromise the effectiveness of antiviral therapies targeting that protein. 2020 bioRxiv Result SARS_CoV_2 D614G 61 66 S 121 126 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The relative effect of D614G on infectivity using cells bearing rat or mouse ACE2 orthologues could not be determined since in both cases the luciferase activity with D614 was not clearly above background. 2020 bioRxiv Result SARS_CoV_2 D614G 23 28 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The SARS-CoV-2 D614G S protein variant increases infectivity. 2020 bioRxiv Result SARS_CoV_2 D614G 15 20 S 21 22 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The SARS-CoV-2 Spike protein variant D614G, then, was not present in the common ancestor of the sampled isolates but has risen to high frequency across many regions. 2020 bioRxiv Result SARS_CoV_2 D614G 37 42 S 15 20 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. This nucleotide change encodes the spike (S) protein variant D614G. 2020 bioRxiv Result SARS_CoV_2 D614G 61 66 S;S 35;42 40;43 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. This raises the question whether D614G confers a selective replication advantage to SARS-CoV-2, or whether it may explain regional differences in rates of death or other clinical parameters. 2020 bioRxiv Result SARS_CoV_2 D614G 33 38 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. To date, more severe disease outcome with D614G has not been reported, but several studies suggest that it is associated with a modest increase in viral load (; Wagner et al.). 2020 bioRxiv Result SARS_CoV_2 D614G 42 47 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. When Caco-2 human colon epithelial cells were used as the target cells 4-fold higher infectivity was observed with D614G (Figure 2). 2020 bioRxiv Result SARS_CoV_2 D614G 115 120 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. When Calu-3 human lung epithelial cells were used as targets, challenge with lentivirus bearing D614G resulted in 6-fold more GFP-positive cells, or 5-fold more bulk luciferase activity, than did particles bearing D614 S protein (Figure 2). 2020 bioRxiv Result SARS_CoV_2 D614G 96 101 S 219 220 32637944 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. While understanding will improve around the historical trajectory of its ascendence to fixation, the D614G variant is now universally common on every continent except Antarctica. 2020 bioRxiv Result SARS_CoV_2 D614G 101 106 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. A comparison of D614G status and hospitalization (combining IP and ICU) was not significant (p = 0.66, Fisher's exact test), although comparing ICU admission with IP and OP did have borderline significance (p = 0.047) (Figure 5B). 2020 Cell Result SARS_CoV_2 D614G 16 21 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. A generalized linear model (GLM) used to predict the PCR Ct based on the RT-PCR method, sex, age, and D614G status showed only the RT-PCR method (p < 2e-16) and D614G status (p = 0.037) to be statistically significant (Figure 5A). 2020 Cell Result SARS_CoV_2 D614G;D614G 102;161 107;166 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. At that time, the G614 form was rare globally but gaining prominence in Europe, and GISAID was also tracking the clade carrying the D614G substitution, designating it the "G clade." The D614G change is almost always accompanied by three other mutations: a C-to-T mutation in the 5' UTR (position 241 relative to the Wuhan reference sequence), a silent C-to-T mutation at position 3,037, and a C-to-T mutation at position 14,408 that results in an amino acid change in RNA-dependent RNA polymerase (RdRp P323L). 2020 Cell Result SARS_CoV_2 C241T;D614G;D614G;P323L 256;132;186;503 300;137;191;508 RdRp;5'UTR;RdRP 468;279;498 496;285;502 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Further analysis showed that viral load was not masking a potential D614G status effect on hospitalization (STAR Methods). 2020 Cell Result SARS_CoV_2 D614G 68 73 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Here we present results for the first amino acid variant to stand out by these metrics, D614G. 2020 Cell Result SARS_CoV_2 D614G 88 93 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. One early Wuhan sequence and one early Thai sequence had the D614G change but not the other 3 mutations (Figure S5D); these may have arisen independently. 2020 Cell Result SARS_CoV_2 D614G 61 66 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Origins of the D614G 4-Base Haplotype. 2020 Cell Result SARS_CoV_2 D614G 15 20 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Structural Implications of the Spike D614G Change. 2020 Cell Result SARS_CoV_2 D614G 37 42 S 31 36 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. The cytoplasmic tail of Spike also contains a site of interest, P1263L. 2020 Cell Result SARS_CoV_2 P1263L 64 70 S 24 29 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. The D614G Variant. 2020 Cell Result SARS_CoV_2 D614G 4 9 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. The earliest examples of sequences carrying parts of the 4-mutation haplotype that characterizes the D614G GISAID G clade were found in China and Germany in late January 2020, and they carried 3 of the 4 mutations that define the clade, lacking only the RdRp P323L substitution (Figure S5D). 2020 Cell Result SARS_CoV_2 D614G;P323L 101;259 106;264 RdRP 254 258 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. The mutation resulting in the signal peptide L5F change recurs many times in the tree and is stably maintained in about 0.6% of the global GISAID data. 2020 Cell Result SARS_CoV_2 L5F 45 48 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. The Spike D614G amino acid change is caused by an A-to-G nucleotide mutation at position 23,403 in the Wuhan reference strain; it was the only site identified in our first Spike variation analysis in early March 2020 that met our threshold criterion. 2020 Cell Result SARS_CoV_2 D614G 10 15 S;S 4;172 9;177 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. We also tested whether the D614G variations would be similarly neutralized by a polyclonal antibody. 2020 Cell Result SARS_CoV_2 D614G 27 32 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. We found no significant association between D614G status and disease severity as measured by hospitalization outcomes. 2020 Cell Result SARS_CoV_2 D614G 44 49 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. Among the mutations we analyzed, the frequencies of ORF1ab 4715L-type and S 614G-type viruses showed significant positive correlations with fatality rates (Pearson's correlation coefficient (r) = 0.41, P = 0.029 and r = 0.43, P = 0.022, respectively. 2020 Journal of human genetics Result SARS_CoV_2 S614G 74 80 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. Comparing the mutations among the three clusters, the average frequency of an L variant of an ORF1ab P4715L in the countries classified as the cluster 1 was 14.7%, which is significantly lower than 81.3% and 73.2%, respectively, in the countries classified as the clusters 2 and 3 (P = 1.3 x 10-6 and P = 2.5 x 10-5, respectively; Supplementary. 2020 Journal of human genetics Result SARS_CoV_2 P4715L 101 107 ORF1ab 94 100 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. However, the significant correlations became not statistically significant after adjusted by the frequency of S 614G variant in multiple regression (P = 0.13 for HLA-A*11:01, P = 0.73 for HLA-A*02:06 and P = 0.45 for HLA-B*54:01). 2020 Journal of human genetics Result SARS_CoV_2 S614G 110 116 S 110 111 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. In addition, in the cluster 1, L and F variants of N P13L and ORF1ab L3606F were predominantly enriched. 2020 Journal of human genetics Result SARS_CoV_2 L3606F;P13L 69;53 75;57 ORF1ab;N 62;51 68;52 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. In the cluster 2, K/R variants of N protein R203K/G204R mutations were significantly enriched at 43.1%, compared with the other clusters (5.2%, P = 0.00011 for the cluster 1 and 11.8%, P = 5.6 x 10-7 for the cluster 3; Supplementary. 2020 Journal of human genetics Result SARS_CoV_2 R203K;G204R 44;50 49;55 N 34 35 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. Similarly, the frequency of a G variant of S protein D614G was significantly lower in the cluster 1 than the other two clusters (P = 1.2 x 10-6 and P = 1.7 x 10-5, respectively, for the clusters 2 and 3; Supplementary. 2020 Journal of human genetics Result SARS_CoV_2 D614G 53 58 S 43 44 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. Since the clusters 2 and 3 were separated mainly by the frequency of N 203K/204R, we also examined the correlations of this variant or S 614G-N 203R/204G haplotype with fatality rates; however, the correlations were not statistically significant (r = 0.31, P = 0.11; r = 0.27, P = 0.17, respectively; Supplementary. 2020 Journal of human genetics Result SARS_CoV_2 S614G 135 141 S 135 136 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. The F variant of ORF1ab L3606F was detected at a higher frequency of 40.1% than 10.0% and 7.9% in the clusters 2 and 3, respectively (P = 0.0035 and P = 0.00050; Supplementary. 2020 Journal of human genetics Result SARS_CoV_2 L3606F 24 30 ORF1ab 17 23 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. The L variant of N P13L was found at 17.8%, which was significantly higher than 0.2% and 1.4%, respectively, in the clusters 2 and 3 (P = 0.012 and P = 0.0079; Supplementary. 2020 Journal of human genetics Result SARS_CoV_2 P13L 19 23 N 17 18 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. We also found the frequencies of S 614G variant showed a trend of positive correlation with fatality rates (r = 0.54, P = 0.090. 2020 Journal of human genetics Result SARS_CoV_2 S614G 33 39 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. We finally searched peptide epitopes with a high binding affinity to HLA molecules, which we previously reported, involving the two SARS-CoV-2 mutations, ORF1ab P4715L and S D614G, to investigate the association with host immune responses. 2020 Journal of human genetics Result SARS_CoV_2 D614G;P4715L 174;161 179;167 ORF1ab;S 154;172 160;173 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. We found that several epitopes, which include the position of ORF1ab P4715L or S protein D614G, are possibly bind to HLA molecules, including HLA-A*02:06, HLA-A*11:01, HLA-B*07:02, and HLA-B*54:01, although the mutated epitopes from variant SARS-CoV-2 also predicted to bind to HLA molecules at similar affinities (Supplementary Table 3). 2020 Journal of human genetics Result SARS_CoV_2 D614G;P4715L 89;69 94;75 ORF1ab;S 62;79 68;80 32699850 Bivalent binding of a fully human IgG to the SARS-CoV-2 spike proteins reveals mechanisms of potent neutralization. 4c), including the D614G mutation that has spread at an alarming rate and become the dominant pandemic strain with a global frequency of 70.5% (GISAID), since its first identification in Europe in March. 2020 bioRxiv Result SARS_CoV_2 D614G 19 24 32699850 Bivalent binding of a fully human IgG to the SARS-CoV-2 spike proteins reveals mechanisms of potent neutralization. 5A6 IgG had a 4-fold reduction in binding avidity to the V483A mutation but was insensitive to the other five mutations. 2020 bioRxiv Result SARS_CoV_2 V483A 57 62 32699850 Bivalent binding of a fully human IgG to the SARS-CoV-2 spike proteins reveals mechanisms of potent neutralization. 8b), but its neutralizing potency against the D614G mutant was partially reduced. 2020 bioRxiv Result SARS_CoV_2 D614G 46 51 32699850 Bivalent binding of a fully human IgG to the SARS-CoV-2 spike proteins reveals mechanisms of potent neutralization. Consistent with the binding results, 5A6 significantly lost neutralizing capacity against the V483A mutant pseudovirus. 2020 bioRxiv Result SARS_CoV_2 V483A 94 99 32699850 Bivalent binding of a fully human IgG to the SARS-CoV-2 spike proteins reveals mechanisms of potent neutralization. Hence, 3D11 could potentially rescue the loss of 5A6 neutralization potency in a virus strain bearing the V483A mutation, if these two antibodies are used in combination. 2020 bioRxiv Result SARS_CoV_2 V483A 106 111 32699850 Bivalent binding of a fully human IgG to the SARS-CoV-2 spike proteins reveals mechanisms of potent neutralization. These include N439K in 246 samples (244 Scottish, 1 England, 1 Romania), V483A in 30 samples (26 USA/WA, 2 USA/UN, 1 USA/CT, 1 England), G476S in 18 samples (13 USA/WA, 2 USA/OR, 1 USA/ID, 1 USA/CT, 1 Belgium), S494P in 7 samples (3 USA/MI, 1 England, 1 Spain, 1 India, 1 Sweden), V483I in 2 English samples, and L455I together with F456V in one Brazilian sample. 2020 bioRxiv Result SARS_CoV_2 F456V;G476S;L455I;N439K;S494P;V483A;V483I 333;137;313;14;211;73;281 338;142;318;19;216;78;286 32699850 Bivalent binding of a fully human IgG to the SARS-CoV-2 spike proteins reveals mechanisms of potent neutralization. These interactions provide a structural framework that suggests why 5A6 is not affected by the V483I mutation while Leu 94 in the L3 loop is a potential liability in binding to the 483A mutation. 2020 bioRxiv Result SARS_CoV_2 V483I 95 100 32703419 Proteasome activator PA28gamma-dependent degradation of coronavirus disease (COVID-19) nucleocapsid protein. EV-pSG5+PA28gammaWT, EV-pSG5+PA28gamma, N151Y, and HA-nCoV + EV-FRT were transfected into cells as negative controls for comparison. 2020 Biochemical and biophysical research communications Result SARS_CoV_2 N151Y 40 45 32703419 Proteasome activator PA28gamma-dependent degradation of coronavirus disease (COVID-19) nucleocapsid protein. In addition, when the inactive mutant N151Y PA28gamma was transfected into the cells with HA-nCoV, we found that the level of nCoV N remained relatively equal to that of the control. 2020 Biochemical and biophysical research communications Result SARS_CoV_2 N151Y 38 43 N 131 132 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Although the eight single mutations (i.e., Q239K, V341I, A435S, K458R, I472V, H519P, A831V, and S943T) in both groups A and B do not exist by themselves, they were found to occur in combination with D614G. 2020 Cell Result SARS_CoV_2 A435S;A831V;D614G;H519P;I472V;K458R;Q239K;S943T;V341I 57;85;199;78;71;64;43;96;50 62;90;204;83;76;69;48;101;55 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. As shown in Figure 1 , group A represents all high-frequency variants and combined variants with D614G across the entire S gene (29 strains) excluding receptor-binding domain (RBD) region. 2020 Cell Result SARS_CoV_2 D614G 97 102 RBD;S 176;121 179;122 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. As shown in Figure 4, five mAbs (i.e., 157, 247, CB6, P2C-1F11 and B38) were unable to effectively neutralize both A475V and N234Q. 2020 Cell Result SARS_CoV_2 A475V;N234Q 115;125 120;130 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Finally, Y508H reduced the sensitivity to mAb H014, N439K to mAb H00S022, A831V to mAb B38, D614G+I472V to mAb X593, and D614G+A435S to mAb H014 by more than 4 times. 2020 Cell Result SARS_CoV_2 A831V;D614G;D614G;N439K;Y508H;A435S;I472V 74;92;121;52;9;127;98 79;97;126;57;14;132;103 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Furthermore, H00S022 was unable to neutralizing N439K and N234Q. 2020 Cell Result SARS_CoV_2 N234Q;N439K 58;48 63;53 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. However, the neutralization sensitivity of both F490L and H519P to three of ten patient sera were found to have decreased by more than 4 times, while six variants and mutants (N149H, N149Q, N165Q, N354D, N709Q, and N1173Q) became over 4-fold sensitive to one or two of the ten tested sera. 2020 Cell Result SARS_CoV_2 F490L;H519P;N1173Q;N149Q;N165Q;N354D;N709Q;N149H 48;58;215;183;190;197;204;176 53;63;221;188;195;202;209;181 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. In addition, mAb H014 was incapable of neutralizing N234Q, Y508H, and D614G+A435S, whereas mAbs H4 and 261-262 were found not to neutralize F490L. 2020 Cell Result SARS_CoV_2 D614G;F490L;N234Q;Y508H;A435S 70;140;52;59;76 75;145;57;64;81 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. In addition, some changes in the RBD region, including V367F, Q409E, Q414E, I468F, I468T, Y508H, and A522V, were observed to be more susceptible to neutralization mediated by mAbs. 2020 Cell Result SARS_CoV_2 A522V;I468F;I468T;Q409E;Q414E;V367F;Y508H 101;76;83;62;69;55;90 106;81;88;67;74;60;95 RBD 33 36 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. It is worth mentioning that some variants including F338L, V367F, I468F, I468T, and V615L (Figure 5B) were even more sensitive to the convalescent sera compared with reference strain, whereas more variants were found to be resistant to the convalescent sera. 2020 Cell Result SARS_CoV_2 F338L;I468F;I468T;V367F;V615L 52;66;73;59;84 57;71;78;64;89 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. It is worth noting that double glycosylation deletions at N331 and N343 resulted in a drastic reduction in viral infectivity (1,200-fold), whereas single deletion at each site caused modest reduction in viral infectivity, with the infectivity of N331Q reduced by only 3-fold and N343Q by 20-fold. 2020 Cell Result SARS_CoV_2 N331Q;N343Q 246;279 251;284 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Moreover, the non-natural double glycosylation mutations in RBD (N331Q and N343Q) resulted in significantly reduced infectivity, suggesting that the two glycosylation sites in the RBD region may participate in the binding of the receptor or maintain the conformation of the RBD region. 2020 Cell Result SARS_CoV_2 N343Q;N331Q 75;65 80;70 RBD;RBD;RBD 60;180;274 63;183;277 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Moreover, V483A became resistant to mAbs X593 and P2B-2F6, and L452R to mAbs X593 and P2B-2F6. 2020 Cell Result SARS_CoV_2 L452R;V483A 63;10 68;15 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Mutant N165Q actually became more sensitive to mAb P2B-2F6, whereas N234Q reduced the neutralization sensitivity to different set of mAbs including 157, 247, CB6, P2C-1F11, H00S022, B38, AB35, and H014. 2020 Cell Result SARS_CoV_2 N165Q;N234Q 7;68 12;73 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Neither X593 nor P2B-2F6 was effective in neutralizing L452R, V483A, and F490L, whereas P2B-2F6 was more effective in neutralizing N165Q. 2020 Cell Result SARS_CoV_2 F490L;L452R;N165Q;V483A 73;55;131;62 78;60;136;67 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Notably, single D614G and combined variants with D614G (D614G+L5F, D614G+V341I, D614G+K458R, D614G+I472V, D614G+D936Y, D614G+S939F, and D614G+S943T) demonstrated increased infectivity compared to the reference strain in all the four cell lines (Figures 3A-3D), whereas no difference was found between single D614G and D614G combined variants, suggesting that the enhanced infectivity was more likely ascribed to D614G itself. 2020 Cell Result SARS_CoV_2 D614G;D614G;D614G;D614G;D614G;D614G;D614G;D614G;D614G;D614G;D614G;D614G;D936Y;I472V;K458R;L5F;S939F;S943T;V341I 16;49;67;80;93;106;119;136;308;318;412;56;112;99;86;62;125;142;73 21;54;72;85;98;111;124;141;313;323;417;61;117;104;91;65;130;147;78 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Similar to natural variants, although the magnitude of some glycosylation deletions in sensitivity to the sera is less than 4-fold, the differences between mutants and the reference strain (Wuhan-1) were found to be still several-fold and statistically significant, i.e., glycosylation mutants N331Q and N709Q significantly increased the sensitivity to convalescent sera (Figure 5B). 2020 Cell Result SARS_CoV_2 N331Q;N709Q 294;304 299;309 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Specifically, A475V reduced the sensitivity to mAbs 157, 247, CB6, P2C-1F11, B38, and CA1, whereas F490L reduced the sensitivity to mAbs X593, 261-262, H4, and P2B-2F6. 2020 Cell Result SARS_CoV_2 A475V;F490L 14;99 19;104 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Therefore, the pseudotyped viruses for the eight single mutants were also constructed to compare with the double mutants with D614G. 2020 Cell Result SARS_CoV_2 D614G 126 131 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. These variants include single amino acid change such as Y145del, Q414E, N439K, G446V, K458N, I472V, A475V, T478I, V483I, F490L, and A831V, as well as the double amino acid changes including D614G+Q321L, D614G+I472V, D614G+A831V, D614G+A879S and D614G+M1237I. 2020 Cell Result SARS_CoV_2 A475V;A831V;D614G;D614G;D614G;D614G;D614G;F490L;G446V;I472V;K458N;N439K;Q414E;T478I;V483I;Y145del;A831V;A879S;I472V;M1237I;Q321L 100;132;190;203;216;229;245;121;79;93;86;72;65;107;114;56;222;235;209;251;196 105;137;195;208;221;234;250;126;84;98;91;77;70;112;119;63;227;240;214;257;201 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. This group includes both variants (N74K, N149H, and T719A) and investigational mutants that we made for the analyses of the effects of glycosylation. 2020 Cell Result SARS_CoV_2 N149H;T719A;N74K 41;52;35 46;57;39 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Variant V341I and investigational glycosylation mutant (N331Q+N343Q) were deemed as no-infectivity as demonstrated by over 100-fold decrease in RLU values compared with the reference strain. 2020 Cell Result SARS_CoV_2 V341I;N331Q;N343Q 8;56;62 13;61;67 32732280 Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. In the mutants, other amino acids were substituted at certain locations; for example, A23063T indicates that alanine at position 23063 was replaced by threonine.) Structural remodeling also suggested that the N501Y substitution in the RBD of SARS-CoV S protein increased the binding affinity of the protein to mouse ACE2. 2020 Science (New York, N.Y.) Result SARS_CoV_2 A23063T;A23063T;N501Y 86;109;209 93;160;214 RBD;S 235;251 238;252 32732280 Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. T23063 readily emerged after a single passage in one of the three mouse lung homogenates (table S2), and the proportion of A23063T mutation gradually increased during subsequent passages. 2020 Science (New York, N.Y.) Result SARS_CoV_2 A23063T 123 130 32732280 Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. The A23063T mutation resulted in a N501Y amino acid substitution in the RBD of the S protein, which is assumed to be responsible for receptor recognition and host range of SARS-CoV-2. 2020 Science (New York, N.Y.) Result SARS_CoV_2 A23063T;N501Y 4;35 11;40 RBD;S 72;83 75;84 32732280 Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. Thus, the increased virulence of SARS-CoV-2 MASCp6 in mice was likely attributed to the rapid emergence of N501Y substitution in the RBD of SARS-CoV-2 S protein. 2020 Science (New York, N.Y.) Result SARS_CoV_2 N501Y 107 112 RBD;S 133;151 136;152 32732280 Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. To further trace the adaption history of MASCp6, the emergence of N501Y substitution was further analyzed by means of deep sequencing. 2020 Science (New York, N.Y.) Result SARS_CoV_2 N501Y 66 71 32735992 Design of an engineered ACE2 as a novel therapeutics against COVID-19. The obtained results demonstrated that the threonine 27 to Arginine mutation is the only mutation which met the selection criteria. 2020 Journal of theoretical biology Result SARS_CoV_2 T27R 43 67 32735992 Design of an engineered ACE2 as a novel therapeutics against COVID-19. The Proline 451 to methionine mutation (PoPMuSiC prediction) and the glycine 448 to tryptophan mutation (HotMuSiC prediction) were predicted to increase the thermodynamic stability and thermostability of the ACE2. 2020 Journal of theoretical biology Result SARS_CoV_2 G448W;P451M 69;4 94;29 32735992 Design of an engineered ACE2 as a novel therapeutics against COVID-19. The results of mutation analyses have shown that the mutation form aspartate 427 to arginine would increase the thermal stability of the ACE2. 2020 Journal of theoretical biology Result SARS_CoV_2 D427R 67 92 32735992 Design of an engineered ACE2 as a novel therapeutics against COVID-19. Therefore, we preferred to mutate the Arginine 273 residue to Glutamine and the Threonine 445 residue to Glycine. 2020 Journal of theoretical biology Result SARS_CoV_2 T445G 80 112 32742035 Variant analysis of SARS-CoV-2 genomes. Although frameshift variants are considered deleterious, for instance, S135fs (more precisely S135Rfs*9) caused by 670_671del, ORF1ab is truncated at residue 143 before NSP2 and translation might resume from the methionine at residue 174 near the end of NSP1. 2020 Bulletin of the World Health Organization Result SARS_CoV_2 S135fs;S135Rfs 71;94 77;101 ORF1ab;Nsp2 127;169 133;173 32742035 Variant analysis of SARS-CoV-2 genomes. Among the L3606F subclades, L3606F/G251V/ forms the largest group with 419 samples. 2020 Bulletin of the World Health Organization Result SARS_CoV_2 L3606F;L3606F;G251V 10;28;35 16;34;40 32742035 Variant analysis of SARS-CoV-2 genomes. Among the variants in the receptor binding domain, V483A (26 samples), G476S (9 samples) and V367F (12 samples) are highly recurrent. 2020 Bulletin of the World Health Organization Result SARS_CoV_2 G476S;V367F;V483A 71;93;51 76;98;56 RBD 26 49 32742035 Variant analysis of SARS-CoV-2 genomes. G251V frequently appears in samples from the United Kingdom (329 samples), Australia (95 samples), the United States (80 samples) and Iceland (76 samples). 2020 Bulletin of the World Health Organization Result SARS_CoV_2 G251V 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. Most samples in the D614G clade also display the non-coding variant 241C > T, the synonymous variant 3037C > T and ORF1ab P4715L. 2020 Bulletin of the World Health Organization Result SARS_CoV_2 C241T;C3037T;D614G;P4715L 68;101;20;122 76;110;25;128 ORF1ab 115 121 32742035 Variant analysis of SARS-CoV-2 genomes. NSP10 Y126* is located only 13 residues upstream of the stop codon; therefore, a truncation may not significantly affect function of the protein. 2020 Bulletin of the World Health Organization Result SARS_CoV_2 Y126X 6 11 32742035 Variant analysis of SARS-CoV-2 genomes. Of the in-frame deletions, ORF1 D448del stands out with 250 samples. 2020 Bulletin of the World Health Organization Result SARS_CoV_2 D448del 32 39 32742035 Variant analysis of SARS-CoV-2 genomes. Of the NSP3 missense variants, A58T was the most common (159 samples) followed by P153L (101 samples; Table 2). 2020 Bulletin of the World Health Organization Result SARS_CoV_2 A58T;P153L 31;82 35;87 Nsp3 7 11 32742035 Variant analysis of SARS-CoV-2 genomes. Other variants including ORF3a Q57H (2893 samples), ORF1ab T265I (NSP3 T85I; 2442 samples), ORF8 L84S (1669 samples), N203_204delinsKR (1573 samples), ORF1ab L3606F (NSP6 L37F; 1070 samples) were the key variants for identifying clades. 2020 Bulletin of the World Health Organization Result SARS_CoV_2 L3606F;L37F;L84S;Q57H;T265I;T85I 158;171;97;31;59;71 164;175;101;35;64;75 ORF1ab;ORF1ab;ORF3a;Nsp3;Nsp6;ORF8 52;151;25;66;166;92 58;157;30;70;170;96 32742035 Variant analysis of SARS-CoV-2 genomes. The L84S/P5828L/ subclade is predominantly observed in the United States. 2020 Bulletin of the World Health Organization Result SARS_CoV_2 L84S;P5828L 4;9 8;15 32742035 Variant analysis of SARS-CoV-2 genomes. The largest clade is D614G clade with five subclades. 2020 Bulletin of the World Health Organization Result SARS_CoV_2 D614G 21 26 32742035 Variant analysis of SARS-CoV-2 genomes. The most common variants were the synonymous variant 3037C > T (6334 samples), ORF1ab P4715L (RdRp P323L; 6319 samples) and SD614G (6294 samples). 2020 Bulletin of the World Health Organization Result SARS_CoV_2 C3037T;P323L;P4715L 53;99;86 62;104;92 ORF1ab;RdRP 79;94 85;98 32742035 Variant analysis of SARS-CoV-2 genomes. The recurrent stop-gained variant Y4379* (NSP10 Y126*) is found in 51 samples in the D614G clade. 2020 Bulletin of the World Health Organization Result SARS_CoV_2 D614G;Y126X 85;48 90;53 32742035 Variant analysis of SARS-CoV-2 genomes. The remaining two clades D448del and G392D are small and they are without any significant subclades at this point. 2020 Bulletin of the World Health Organization Result SARS_CoV_2 D448del;G392D 25;37 32;42 32742035 Variant analysis of SARS-CoV-2 genomes. The second largest major clade is L84S clade, which was observed among travellers from Wuhan in the early days of the outbreak, and the clade consists of 1662 samples with 2 subclades. 2020 Bulletin of the World Health Organization Result SARS_CoV_2 L84S 34 38 32742035 Variant analysis of SARS-CoV-2 genomes. We also detected mutations in the nonstructural protein RNA-dependent RNA polymerase (RdRp), such as P323L (6319 samples). 2020 Bulletin of the World Health Organization Result SARS_CoV_2 P323L 101 106 RdRp;RdRP 56;86 84;90 32742035 Variant analysis of SARS-CoV-2 genomes. Within D614G clade, D614G/Q57H/T265I subclade forms the largest subclade with 2391 samples. 2020 Bulletin of the World Health Organization Result SARS_CoV_2 D614G;D614G;Q57H;T265I 7;20;26;31 12;25;30;36 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. 23403A>G is a nonsynonymous mutation in the surface glycoprotein, while 3037C>T is a synonymous mutation in nsp3, a replication scaffolding protein. 2020 PeerJ Result SARS_CoV_2 C3037T;A23403G 72;0 79;8 S;Nsp3 44;108 64;112 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. A recent study postulated that one of the co-mutations of 14408C>T, namely 23403A>G that causes D614G mutation in the S protein, may result in a more transmissible form of SARS-CoV-2. 2020 PeerJ Result SARS_CoV_2 C14408T;A23403G;D614G 58;75;96 66;83;101 S 118 119 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. A study by suggested that D614G mutation creates an additional protease cleavage site near the S1-S2 junction, which may increase the success of viral integration with the host cell, and linked its dominance in Europe to certain human variants that control expression of TMPRSS2. 2020 PeerJ Result SARS_CoV_2 D614G 26 31 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. Although preliminary studies suggest that 14408C>T (P323L in RdRp) could lower replication fidelity, it is less clear how the synonymous 15324C>T mutation could lead to lower mutation rates. 2020 PeerJ Result SARS_CoV_2 C14408T;C15324T;P323L 42;137;52 50;145;57 RdRP 61 65 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. Based on the lack of successful spreading of the virus in its absence and our results showing increased mutability in its presence, we speculate that 14408C>T could be cooperating with the other two mutations. 2020 PeerJ Result SARS_CoV_2 C14408T 150 158 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. Despite weeks of existence, 23403A>G became the dominant form only after the appearance of the first Italian case with all four mutations on February 20. 2020 PeerJ Result SARS_CoV_2 A23403G 28 36 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. Emergence of 14408C>T in South America, North America and Africa was 5, 7 and 8 days following the first European mutant virus, and again became the dominant form, as 81.3%, 59.4% and 80.3% of viral genomes carry the mutation, respectively. 2020 PeerJ Result SARS_CoV_2 C14408T 13 21 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. In contrast to Europe, North and South America, where 14408C>T became the dominant form together with its co-mutations (23403A>G and 3037C>T), 14408C>T and its co-mutations remained as the minor form in Asia, 14408C>T being present in only 15.9% (137/859) of viral genomes. 2020 PeerJ Result SARS_CoV_2 C14408T;C14408T;C14408T;C3037T;A23403G 54;143;209;133;120 62;151;217;140;128 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. It is possible that 15324C is part of an as-yet-unknown viral sequence that interacts with host factor(s) and 15324C>T mutation indirectly affects the 14408C>T mutation through modulation of this interaction; as there are currently only 305 genome sequences available with this mutation, this question may be better answered as more viral genome sequences accumulate and functional studies are performed. 2020 PeerJ Result SARS_CoV_2 C14408T;C15324T 151;110 159;118 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. It should be noted that 288 of 305 (94.4%) genomes worldwide with the 15324C>T mutation also have the 14408C>T mutation, and MoE rate is 1.39% (4/288) among double mutants, whereas it is 11.13% (749/6,727) for 14408C>T-only mutants. 2020 PeerJ Result SARS_CoV_2 C14408T;C14408T;C15324T 102;210;70 110;218;78 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. On the other hand, it is intriguing that between the first appearance of three co-mutations (on 14408, 23403, 3037) on January 24 in a Chinese isolate (EPI_ISL_422425) and their second co-appearance on February 20 in an Italian isolate (EPI_ISL_412973), there are at least six and possibly eight different viral genomes where three of the four co-mutations exist, with the exception of 14408C>T: on January 28 in Germany (EPI_ISL_406862), on February 5, 6, 7 and 8 in China (EPI_ISL_429080, EPI_ISL_429081, EPI_ISL_416334, EPI_ISL_412982, and EPI_ISL_429089); and two more Chinese viral sequences that failed our quality control standards and were eliminated from the overall analysis. 2020 PeerJ Result SARS_CoV_2 C14408T 386 394 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. Other than 14408C>T, two of the top 50 mutations were also in the RdRP coding sequence, although both of them are synonymous mutations that presumably do not affect the protein structure. 2020 PeerJ Result SARS_CoV_2 C14408T 11 19 RdRP 66 70 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. Out of these three, 14408C>T was previously established as a mutation of interest for the RdRp gene. 2020 PeerJ Result SARS_CoV_2 C14408T 20 28 RdRP 90 94 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. The first 14408C>T mutation dates to a patient whose sample was collected on January 24 in China, but sequenced and submitted to GISAID on April 10. 2020 PeerJ Result SARS_CoV_2 C14408T 10 18 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. This claim was based mainly on the observation that D614G mutant virus became the dominant form in more than one geographical location upon its introduction, as summarized above for its co-mutation 14408C>T. 2020 PeerJ Result SARS_CoV_2 C14408T;D614G 198;52 206;57 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. Three other mutations that co-evolved and are seen together with 14408C>T are 23403A>G (D614G in S protein) and 3037C>T (F106F in NSP3). 2020 PeerJ Result SARS_CoV_2 C14408T;A23403G;C3037T;D614G;F106F 65;78;112;88;121 73;86;119;93;126 Nsp3;S 130;97 134;98 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. Thus, our results suggest that SARS-CoV-2 genomes with the 14408C>T mutation are 1.5 times more likely to have MoE. 2020 PeerJ Result SARS_CoV_2 C14408T 59 67 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. Two days later, on February 22, the first case with 14408C>T was reported in Australia, 31 days after the first SARS-CoV-2 case in the country. 2020 PeerJ Result SARS_CoV_2 C14408T 52 60 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. Two of the top 50 sites were found in the membrane glycoprotein coding region, with 26729T>C being a synonymous mutation and 27046C>T being a nonsynonymous mutation causing a T175M mutation in the peptide sequence. 2020 PeerJ Result SARS_CoV_2 T26729C;C27046T;T175M 84;125;175 92;133;180 Membrane 42 50 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. Whereas the 14408C>T mutation predicted higher risk of MoE, the other three significant mutations in RdRp predicted a lower risk, particularly the 15324C>T mutation, which predicted about 10-fold reduced risk of MoE. 2020 PeerJ Result SARS_CoV_2 C14408T;C15324T 12;147 20;155 RdRP 101 105 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. The D614G mutation on the Spike protein is located at the C-terminus of the S1 fragment and outside of the receptor-binding domain, and thus is unlikely to directly influence ACE2 binding. 2020 bioRxiv Result SARS_CoV_2 D614G 4 9 S 26 31 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. We did not observe any significant localization differences between Spike WT and Spike D614G in transiently transfected cells. 2020 bioRxiv Result SARS_CoV_2 D614G 87 92 S;S 68;81 73;86 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. With the human ACE2 however, we observed an 11% enhancement of D614G GFP+ cell depletion compared to WT Spike, which although small in magnitude achieved statistical significance (p <0.02) (Figure 1F). 2020 bioRxiv Result SARS_CoV_2 D614G 63 68 S 104 109 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. Among the mutant systems, Y489A and N501A occupied more conformational space with high trace value (trace value of 108.07 and 104.57 nm2 respectively) as compared wild type (trace value of 60.89 nm2). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501A;Y489A 36;26 41;31 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. Among the mutants systems, N501A displayed higher RMSD of 0.33 +- 0.09 nm as compared to the other complex systems. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501A 27 32 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. Among the mutants, N501A displayed somewhat little higher Rg of ~3.37 nm (Figure 3). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501A 19 24 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. As compared to wild type (0.16 nm), the average RMSF values for the RBM site was computed to be 0.28, 0.18, 0.37, 0.40 and 0.13 nm respectively for the mutant Y449A, N487A, Y489A, N501A and Y505A systems respectively. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N487A;N501A;Y449A;Y489A;Y505A 166;180;159;173;190 171;185;164;178;195 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. Comparing to the wild type 6M0J complex (solved at 2.45 A resolution), the Calpha-RMSD of representative structure of each systems were found to be 1.87, 1.68, 1.66, 2.66, 1.77 and 2.28 A respectively for Wild type, Y449A, N487A, Y489A, N501A and Y505A systems indicates that complex systems maintained their structural integrity throughout MD simulation. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N487A;N501A;Y449A;Y489A;Y505A 223;237;216;230;247 228;242;221;235;252 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. In order to investigate the significant motions in wild type, Y449A, N487A, Y489A, N501A and Y505A ACE2-RBD complexes, PCA was carried out. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N487A;N501A;Y449A;Y489A;Y505A 69;83;62;76;93 74;88;67;81;98 RBD 104 107 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. In wild type system, the hydrogen bonds were found to be maintained during the MD simulations, while, in mutant displayed decline in the H-bonds with least number in N487A, and Y489A systems. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N487A;Y489A 166;177 171;182 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. The Wild type and Y505A system of the ACE2-RBD complex displayed lowest RMSD of 0.25 +- 0.03 nm and 0.25 +- 0.03 respectively, followed by Y449A, N487A, Y489 and N501A mutant systems. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N487A;N501A;Y449A;Y505A 146;162;139;18 151;167;144;23 RBD 43 46 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. Though Y449A system displayed a greater number of non-bonded contacts which may be attributed due to mutations, on the other hand it has lost few crucial H-bonds crucial for stability of the ACE2-RBD complex. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 Y449A 7 12 RBD 196 199 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. While, in ACE2 we also observed significant inward motions in Y449A, Y489A and Y505A systems towards the RBD (SARS-Cov-2). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 Y449A;Y489A;Y505A 62;69;79 67;74;84 RBD 105 108 32764372 Comprehensive Analyses of SARS-CoV-2 Transmission in a Public Health Virology Laboratory. All ICVL staff members exhibited the 20C clade-defining mutations G25563T and C1059T. 2020 Viruses Result SARS_CoV_2 C1059T;G25563T 78;66 84;73 32764372 Comprehensive Analyses of SARS-CoV-2 Transmission in a Public Health Virology Laboratory. All samples sequenced were associated with clade 20, harboring the clade's mutations A23403G and C14408T (Nextstrain nomenclature). 2020 Viruses Result SARS_CoV_2 A23403G;C14408T 85;97 92;104 32764372 Comprehensive Analyses of SARS-CoV-2 Transmission in a Public Health Virology Laboratory. Although they shared the 20C clade-defining mutation C1059T with ICVL members S1, S4 and S5, which produced a high-confidence split from non-ICVL members S7 and S8 (bootstrap value of 73%, Figure 1), given their additional mutations, which may have been acquired individually or from a different transmission chain, S2 and S3 cannot be placed within the ICVL transmission chain. 2020 Viruses Result SARS_CoV_2 C1059T 53 59 32764372 Comprehensive Analyses of SARS-CoV-2 Transmission in a Public Health Virology Laboratory. As specified, 7/14 mutations were associated with the 20B and 20C clades (Table 3), 4/14 mutations were detected in all sequences compared to the reference sequence (C241T, C3037T, C14408T, A23403G), and the rest of the mutations (3/14) were uniquely observed in S2, S3, S6, S7 and S8 (Table 3). 2020 Viruses Result SARS_CoV_2 A23403G;C14408T;C3037T;C241T 190;181;173;166 197;188;179;171 32764372 Comprehensive Analyses of SARS-CoV-2 Transmission in a Public Health Virology Laboratory. S1, S4 and S5 had identical sequences (Figure 1), while S6 exhibited only one difference:a uniquely observed mutation in nsp12:G15243T (Figure 1 and Table 3). 2020 Viruses Result SARS_CoV_2 G15243T 127 134 Nsp12 121 126 32764372 Comprehensive Analyses of SARS-CoV-2 Transmission in a Public Health Virology Laboratory. S8 (S3's spouse) lacked one of the 20C mutations C1059T; Interestingly, S7 (S4's spouse), exhibited three additional mutations, G28881A, G28882A and G28883C, which are associated with clade 20B. 2020 Viruses Result SARS_CoV_2 C1059T;G28881A;G28882A;G28883C 49;128;137;149 55;135;144;156 32764372 Comprehensive Analyses of SARS-CoV-2 Transmission in a Public Health Virology Laboratory. S8 was placed in the 20C clade due to a shared mutation with all ICVL members, G25563T, in addition to its own unique mutation. 2020 Viruses Result SARS_CoV_2 G25563T 79 86 32780783 Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2. 29742G>A/T and 29774C>T are the most familiar variants of 3'UTR among all the continents. 2020 PloS one Result SARS_CoV_2 C29774T 15 23 3'UTR 58 63 32780783 Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2. 5'UTR variant 187A>G fall within the SL5A stem-loop and 241C>T variant was within SL5B stem-loop. 2020 PloS one Result SARS_CoV_2 A187G;C241T 14;56 20;62 5'UTR 0 5 32780783 Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2. Another common variation in the 5'UTR is 187A>G, that is present in seven of our populations being most prevalent in Italy and Canada. 2020 PloS one Result SARS_CoV_2 A187G 41 47 5'UTR 32 37 32780783 Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2. Another important variant of 3'UTR is 29734G>C, which is mostly seen in Europe and Australia, but Italy has a quite high percentage of this variant than others (Fig 2). 2020 PloS one Result SARS_CoV_2 G29734C 38 46 3'UTR 29 34 32780783 Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2. Another study reported that this variant has co-evolved with three coding region mutations (3037C > T, 14408C > T, and 23403A > G) of nsp3, RNA primase and spike glycoprotein. 2020 PloS one Result SARS_CoV_2 C14408T;A23403G;C3037T 103;119;92 113;129;101 S;Nsp3 156;134 174;138 32780783 Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2. From our analysis, it is evident that Russia had no such frequent variation in the UTR, except the 241C>T variant which was present in 100% of the population. 2020 PloS one Result SARS_CoV_2 C241T 99 105 32780783 Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2. India had two striking variations in the 3'UTR, 29827A>T, 29830G>T, which was found nowhere in this global mutational landscape (S1 Table). 2020 PloS one Result SARS_CoV_2 A29827T;G29830T 48;58 56;66 3'UTR 41 46 32780783 Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2. Similarly, South America also had five unique mutations in the positions 29783G>T, 29786G>C, 29834T>C, 29838C>T and 29839A>G of 3'UTR. 2020 PloS one Result SARS_CoV_2 G29786C;T29834C;C29838T;A29839G 83;93;103;116 91;101;111;124 3'UTR 128 133 32780783 Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2. The most common high frequency variant is the 241C>T, which lies in the leader sequence of the SARS-CoV-2 viral genome. 2020 PloS one Result SARS_CoV_2 C241T 46 52 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Apart from the aforementioned D614G mutation observed in the Spike protein, the second most common amino acid changing mutation is P314L, affecting the Non-structural Protein 12 (NSP12), the viral RNA-dependent RNA polymerase. 2020 Frontiers in microbiology Result SARS_CoV_2 D614G;P314L 30;131 35;136 RdRp;S;Nsp12 197;61;179 225;66;184 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Clustering all genomes clearly highlights the five major phylogenetic groups G, GH, GR, S, and V and their characterizing mutations (Figure 4), as well as more nascent clades (e.g., in the GH clade, further split by a novel mutation in the NSP2 locus, C1059T), and a general distribution of non-recurring mutations for the majority of sequences. 2020 Frontiers in microbiology Result SARS_CoV_2 C1059T 252 258 Nsp2 240 244 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Currently, the vastly prevalent genome in North America is GH (mutations in Spike D614G and ORF3a Q57H), accounting for more than 50% sequences submitted. 2020 Frontiers in microbiology Result SARS_CoV_2 D614G;Q57H 82;98 87;102 S;ORF3a 76;92 81;97 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. In Asia, while the most common mutation was G11083T for samples sequenced between December 2019 and March 2020, recent sequencing efforts have highlighted a current profile similar to those of the other continents (Figure 3A). 2020 Frontiers in microbiology Result SARS_CoV_2 G11083T 44 51 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. More than 1% of sequenced viruses show a T175M mutation in the Membrane protein. 2020 Frontiers in microbiology Result SARS_CoV_2 T175M 41 46 Membrane 63 71 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Other two major clades are called "S," named after the mutation in ORF8 L84S (Ceraolo and Giorgi,), also characterized by a silent C8782T genomic mutation, and "V," from the ORF3a:G251V mutation, almost always co-occurring with the NSP6:L37F event, and identified by early phylogenetic studies (Forster et al.,). 2020 Frontiers in microbiology Result SARS_CoV_2 C8782T;L84S;G251V;L37F 131;72;180;237 137;76;185;241 ORF3a;Nsp6;ORF8 174;232;67 179;236;71 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Our prediction, based on the Vienna RNA suite (Figure 6B) shows no significant difference in the secondary structure of the wild-type (WT) genome and the C241T variant, since this nucleotide is not participating in any hydrogen bond with other nucleotides. 2020 Frontiers in microbiology Result SARS_CoV_2 C241T 154 159 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Specifically, the four mutations C241T, C3037T, C14408T, and A23403G are observed in all samples from the clade "G" (named after the Spike D614G mutation) and its two derivative GH (further characterized by the ORF3a:Q57H mutation) and GR (affected by the trinucleotide mutation in the Nucleocapsid gene, inducing a RG203KR mutation). 2020 Frontiers in microbiology Result SARS_CoV_2 A23403G;C14408T;C241T;C3037T;D614G;Q57H 61;48;33;40;139;217 68;55;38;46;144;221 N;S;ORF3a 286;133;211 298;138;216 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Specifically, the GR clade, carrying the combination of Spike D614G and Nucleocapsid RG203KR mutations, is currently the most common representative of the SARS-CoV-2 population worldwide. 2020 Frontiers in microbiology Result SARS_CoV_2 D614G 62 67 N;S 72;56 84;61 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. The G15S mutation in the viral protease NSP5 is the 16th most common event worldwide, with 1,798 samples affected (3.7%), however it seems to be too peripheric, in the protein sequence, to influence catalytic activity, and folding (Zhang et al.,). 2020 Frontiers in microbiology Result SARS_CoV_2 G15S 4 8 Nsp5 40 44 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. The most prevalent mutation in sequenced genomes worldwide is a transversion affecting the 23,403rd nucleotide adenosine (Supplementary File 6), transformed into a guanosine (A23403G), defining the so-called G-clade of SARS-CoV-2 genomes, prevalent in Europe (where overall the highest sequencing effort has been undertaken, and therefore the highest number of samples), Oceania, South America, and Africa (Figure 3A). 2020 Frontiers in microbiology Result SARS_CoV_2 A23403G 175 182 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. The Nucleocapsid protein, apart from the clade GR-defining RG203KR mutation, has several non-silent mutations above the threshold of 1% frequency in the population, specifically P13L, D103Y, S194L, and S197L (Figure 6A). 2020 Frontiers in microbiology Result SARS_CoV_2 D103Y;P13L;S194L;S197L 184;178;191;202 189;182;196;207 N 4 16 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. The Spike protein, apart from the discussed D614G mutation, has no other event present in more than 1% of the viral population; amongst the top 5, a N439K variant located in the Spike/ACE2 interaction domain is observed in 0.7% of the viruses. 2020 Frontiers in microbiology Result SARS_CoV_2 D614G;N439K 44;149 49;154 S;S 4;178 9;183 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. This mutation causes a D614G (aspartate to glycine in protein position 614) aa-change of the Spike (S) protein, which is responsible for the initial entry of the virus in the cell via the ACE2 human receptor (Guzzi et al.,). 2020 Frontiers in microbiology Result SARS_CoV_2 D614G 23 28 S;S 93;100 98;101 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Three mutations show similar frequency with A23403G: C14408T, C241T, and C3037T (Figure 3A). 2020 Frontiers in microbiology Result SARS_CoV_2 A23403G;C14408T;C241T;C3037T 44;53;62;73 51;60;67;79 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. We also analyzed the C241T mutation, located in the SARS-CoV-2 5'UTR. 2020 Frontiers in microbiology Result SARS_CoV_2 C241T 21 26 5'UTR 63 68 32818213 Characterizing SARS-CoV-2 mutations in the United States. Additionally, an interesting finding is that the mutations occurred at the same residue position such as A348S and A348T, P384L and P384S, and Q414E and Q414P always have similar binding affinity changes. 2020 Research square Result SARS_CoV_2 A348S;A348T;P384L;P384S;Q414E;Q414P 105;115;122;132;143;153 110;120;127;137;148;158 32818213 Characterizing SARS-CoV-2 mutations in the United States. Additionally, mutation 1059C>T-(T85I) always occurs together with mutation 25563G>T-(Q57H). 2020 Research square Result SARS_CoV_2 C1059T;G25563T;Q57H;T85I 23;75;85;32 30;83;89;36 32818213 Characterizing SARS-CoV-2 mutations in the United States. Although A348T and N354K have relatively low frequencies due to the limited number of genome samples, their high binding affinity changes lead to a more contagious SARS-CoV-2 substrain. 2020 Research square Result SARS_CoV_2 A348T;N354K 9;19 14;24 32818213 Characterizing SARS-CoV-2 mutations in the United States. Although away from the RBM, the relatively high frequency and positive binding affinity changes of N354K, R403K, and G467S indicate more attention should be paid to them in the future. 2020 Research square Result SARS_CoV_2 G467S;N354K;R403K 117;99;106 122;104;111 32818213 Characterizing SARS-CoV-2 mutations in the United States. Although P323L mutates the residue of proline (P) to leucine (L), these two residues are both non-polar and aliphatic, indicating P323L may not affect the functionality of NSP12 too much. 2020 Research square Result SARS_CoV_2 P323L;P323L 9;130 14;135 Nsp12 172 177 32818213 Characterizing SARS-CoV-2 mutations in the United States. Although the negative value reveals that T85I may destabilize the structure of NSP2, this small change is negligible. 2020 Research square Result SARS_CoV_2 T85I 41 45 Nsp2 79 83 32818213 Characterizing SARS-CoV-2 mutations in the United States. Although the number of single mutations with positive binding affinity changes is less than those with negative binding affinity changes, the high frequency of N354K slightly enhances the infectivity of SARS-CoV-2. 2020 Research square Result SARS_CoV_2 N354K 160 165 32818213 Characterizing SARS-CoV-2 mutations in the United States. Among 7823 complete genome sequences, 5918 are connected to P323L. 2020 Research square Result SARS_CoV_2 P323L 60 65 32818213 Characterizing SARS-CoV-2 mutations in the United States. Among them, 3 mutations are synonymous ones (i.e., 3037C>T-(F106F), 8782C>T-(S76S), and 18060C>T-(L7L)) and 8 mutations are the missense mutations (i.e., 14408C>T-(P323L), 23403A>G-(D614G), 25563G>T-(Q57H), 1059C>T-(T85I), 28144T>C-(L84S), 17858A>G-(Y541C), 17747C>T-(P504L), and 27964C>T-(S24L)). 2020 Research square Result SARS_CoV_2 C1059T;C14408T;C17747T;A17858G;C18060T;A23403G;G25563T;C27964T;T28144C;C3037T;C8782T;D614G;F106F;L7L;L84S;P323L;P504L;Q57H;S24L;S76S;T85I;Y541C 207;154;258;240;88;172;190;280;223;51;68;182;60;98;233;164;268;200;290;77;216;250 214;162;266;248;96;180;198;288;231;58;75;187;65;101;237;169;273;204;294;81;220;255 32818213 Characterizing SARS-CoV-2 mutations in the United States. Among them, 4818 variants have the [25563G>T-(Q57H), 23403A>G-(D614G)] co-mutations. 2020 Research square Result SARS_CoV_2 A23403G;D614G;Q57H;G25563T 53;63;46;36 61;68;50;44 32818213 Characterizing SARS-CoV-2 mutations in the United States. Another mutation on ORF8 is 28144T>C-(L84S), the number of sequences with the L84S mutation in the United States is 1437, which accounts for more than 50% proportion of the isolates in the world. 2020 Research square Result SARS_CoV_2 T28144C;L84S;L84S 28;78;38 36;82;42 ORF8 20 24 32818213 Characterizing SARS-CoV-2 mutations in the United States. As discussed earlier, the female patients with S24L mutation on ORF8 account for a large proportion, which indicates that the S24L is most likely to happen in the female population in the United States. 2020 Research square Result SARS_CoV_2 S24L;S24L 47;126 51;130 ORF8 64 68 32818213 Characterizing SARS-CoV-2 mutations in the United States. As illustrated in Figure 2, the ratio of the 25563G>T-(Q57H) mutation on ORF3a in each 10-day period kept increasing once it was introduced to the United States. 2020 Research square Result SARS_CoV_2 G25563T;Q57H 45;55 53;59 ORF3a 73 78 32818213 Characterizing SARS-CoV-2 mutations in the United States. As of July 14, 2020, 3865 complete genome sequences have the Q57H mutation in the United States, while 6765 isolates carry this type of single mutation in the world. 2020 Research square Result SARS_CoV_2 Q57H 61 65 32818213 Characterizing SARS-CoV-2 mutations in the United States. As of July 14, 2020, more than half of mutation1059C>T-(T85I) counts found worldwide are from the United States. 2020 Research square Result SARS_CoV_2 T85I;C1059T 56;47 60;54 32818213 Characterizing SARS-CoV-2 mutations in the United States. As stated earlier, mutations 17858A>G-(Y541C) and 17747C>T-(P504L) happen simultaneously after analyzing 24715 genome sequences, which means the folding stability changes on the NSP13 are superimposed by two simultaneously occurred mutations. 2020 Research square Result SARS_CoV_2 C17747T;A17858G;P504L;Y541C 50;29;60;39 58;37;65;44 Nsp13 178 183 32818213 Characterizing SARS-CoV-2 mutations in the United States. As we mentioned above, the S protein plays an important role in viral transmission, indicating that mutation 25563G>T-(Q57H) may also be of great importance for viral transmission. 2020 Research square Result SARS_CoV_2 G25563T;Q57H 109;119 117;123 S 27 28 32818213 Characterizing SARS-CoV-2 mutations in the United States. Based on the function of ORF8 that involved in the immune response, we deduce that L84S may disfavor SARS-CoV-2 and favor the host immune surveillance to decrease the viral load in the human cells, which provides an explanation that the ratio of L84S in Figure 2 keeps decreasing. 2020 Research square Result SARS_CoV_2 L84S;L84S 83;246 87;250 ORF8 25 29 32818213 Characterizing SARS-CoV-2 mutations in the United States. Based on the protein-specific analysis mentioned above, we can deduce that mutations Y541C and P504L prevent SARS-CoV-2 from efficiently interacting with host interferon signaling molecules and impede the NSP13 from efficacious participation in the replication/transcription process. 2020 Research square Result SARS_CoV_2 P504L;Y541C 95;85 100;90 Nsp13 205 210 32818213 Characterizing SARS-CoV-2 mutations in the United States. Based on the statistical values of co-mutations in Table 3, we can see that 14408C>T-(P323L) always shows up with 1059C>T-(T85I), 23403A>G-(D614G), 25563G>T-(Q57H), and 27964C>T-(S24L) simultaneously. 2020 Research square Result SARS_CoV_2 C1059T;C14408T;A23403G;G25563T;C27964T;D614G;P323L;Q57H;S24L;T85I 114;76;130;148;169;140;86;158;179;123 121;84;138;156;177;145;91;162;183;127 32818213 Characterizing SARS-CoV-2 mutations in the United States. Due to the small number of sequence data, we can say that the ratio of L84S has a decreasing tendency. 2020 Research square Result SARS_CoV_2 L84S 71 75 32818213 Characterizing SARS-CoV-2 mutations in the United States. Figure 14 (b) shows that the ORF8 becomes slightly less rigidity after both L84S and S24L mutations. 2020 Research square Result SARS_CoV_2 L84S;S24L 76;85 80;89 ORF8 29 33 32818213 Characterizing SARS-CoV-2 mutations in the United States. Finally, mutation 27964C>T-(S24L) has an usually behavior. 2020 Research square Result SARS_CoV_2 C27964T;S24L 18;28 26;32 32818213 Characterizing SARS-CoV-2 mutations in the United States. Finally, since the infectivity-strengthening D614G mutation is associated with all clusters and essentially all the US genome isolates, it may be quite reasonable to say all of the US SARS-CoV-2 substrains become more infectious compared with the original genome collected on December 24, 2019 in China. 2020 Research square Result SARS_CoV_2 D614G 45 50 32818213 Characterizing SARS-CoV-2 mutations in the United States. First, as shown in Table 3, mutations 14408C>T-(P323L) and 23403A>G-(D614G) appear concurrently and thus have an identical trajectory as shown in Figure 2. 2020 Research square Result SARS_CoV_2 C14408T;A23403G;D614G;P323L 38;59;69;48 46;67;74;53 32818213 Characterizing SARS-CoV-2 mutations in the United States. From Table 1, we can see that R346K, A348T, and N354K have relatively high binding affinity changes. 2020 Research square Result SARS_CoV_2 A348T;N354K;R346K 37;48;30 42;53;35 32818213 Characterizing SARS-CoV-2 mutations in the United States. From Table 2, one can see that mutation D614G was initially detected in China on January 24, 2020. 2020 Research square Result SARS_CoV_2 D614G 40 45 32818213 Characterizing SARS-CoV-2 mutations in the United States. From Table 3, we can see that 4827 SNP variants have 25563G>T-(Q57H) mutation on ORF3a. 2020 Research square Result SARS_CoV_2 G25563T;Q57H 53;63 61;67 ORF3a 81 86 32818213 Characterizing SARS-CoV-2 mutations in the United States. However, D614G was not widely spread in China, which is probably due to the strict social distancing rules and the Wuhan lockdown implemented by the Chinese government. 2020 Research square Result SARS_CoV_2 D614G 9 14 32818213 Characterizing SARS-CoV-2 mutations in the United States. However, its trajectory became identical to those of its co-mutations 17747C>T-(P504L) and 17858A>G-(Y541C) after February 20, 2020. 2020 Research square Result SARS_CoV_2 C17747T;A17858G;P504L;Y541C 70;91;80;101 78;99;85;106 32818213 Characterizing SARS-CoV-2 mutations in the United States. However, the growing trend in Figure 2 still indicates that 1059C>T-(T85I) is an infectivity-strengthening mutation, which mainly benefits from the co-mutation with other infectivity-strengthening mutations, such as 23403A>G-(DD614) and 25563G>T-(Q57H). 2020 Research square Result SARS_CoV_2 C1059T;A23403G;G25563T;Q57H;T85I 60;216;237;247;69 67;224;245;251;73 32818213 Characterizing SARS-CoV-2 mutations in the United States. However, the negative folding stability changes in Table 4 suggest that P323L destabilizes the NSP12, which may make SARS-CoV-2 less contagious. 2020 Research square Result SARS_CoV_2 P323L 72 77 Nsp12 95 100 32818213 Characterizing SARS-CoV-2 mutations in the United States. However, the overall upward trend of the S24L ratio over time reveals that S24L may enhance SARS-CoV-2's ability to spread. 2020 Research square Result SARS_CoV_2 S24L;S24L 41;75 45;79 32818213 Characterizing SARS-CoV-2 mutations in the United States. However, the Q57H mutation locates near TRAF, ion channel, and caveolin binding domain, which may affect the NLRP3 inflammasome activation. 2020 Research square Result SARS_CoV_2 Q57H 13 17 32818213 Characterizing SARS-CoV-2 mutations in the United States. In addition, R403K has the highest frequency among the nine infectivity-strengthen mutations. 2020 Research square Result SARS_CoV_2 R403K 13 18 32818213 Characterizing SARS-CoV-2 mutations in the United States. In Cluster A, B, C, and D, the co-mutations with the highest number of descendants are [8782C>T, 18060C>T, 28144T>C], [241C>T, 3037C>T, 14408C>T, 23403A>G], [11083G>T], and [3037C>T, 14408C>T], respectively. 2020 Research square Result SARS_CoV_2 C14408T;C14408T;C18060T;A23403G;T28144C;C3037T;G11083T;C241T;C3037T;C8782T 136;183;97;146;107;127;158;119;174;88 144;191;105;154;115;134;166;125;181;95 32818213 Characterizing SARS-CoV-2 mutations in the United States. In contrast, the time evolution plot shows that the ratio of mutation 28144T>C-(L84S) goes up before the beginning of March, and then the ratio goes down and approach zero after May 23, 2020. 2020 Research square Result SARS_CoV_2 T28144C;L84S 70;80 78;84 32818213 Characterizing SARS-CoV-2 mutations in the United States. In early March, the ratio of both mutations start to decrease and approach zero after May 19, 2020, suggesting that mutations 17858A>G-(Y541C) and 17747C>T-(P504L) may hinder the transmission of SARS-CoV-2. 2020 Research square Result SARS_CoV_2 C17747T;A17858G;P504L;Y541C 147;126;157;136 155;134;162;141 32818213 Characterizing SARS-CoV-2 mutations in the United States. In Figure 2, the ratio of S24L per 10 days is slightly going up before June 2, 2020. 2020 Research square Result SARS_CoV_2 S24L 26 30 32818213 Characterizing SARS-CoV-2 mutations in the United States. In the middle of February, the hot spot with the most COVID-19 cases shifted from China to Europe and the D614G variant rapidly pervades in Europe. 2020 Research square Result SARS_CoV_2 D614G 106 111 COVID-19 54 62 32818213 Characterizing SARS-CoV-2 mutations in the United States. It is interesting to address that these two high-frequency mutations S24L and L84S mutate reversibly. 2020 Research square Result SARS_CoV_2 L84S;S24L 78;69 82;73 32818213 Characterizing SARS-CoV-2 mutations in the United States. It is interesting to note that in Table 3, 17858A>G-(Y541C) and 17747C>T-(P504L) never show up with 23403A>G-(D614G) in more than a thousand SNP variant, which provides a side evidence that these two mutations may inhibit the contagiousness of SARS-CoV-2. 2020 Research square Result SARS_CoV_2 C17747T;A17858G;A23403G;D614G;P504L;Y541C 64;43;100;110;74;53 72;51;108;115;79;58 32818213 Characterizing SARS-CoV-2 mutations in the United States. Meanwhile, the positive folding stability change of 27964C>T-(S24L) lists in Table 4 reveals that this type of mutation may enhance the function of ORF8. 2020 Research square Result SARS_CoV_2 C27964T;S24L 52;62 60;66 ORF8 148 152 32818213 Characterizing SARS-CoV-2 mutations in the United States. Moreover, the D614G mutation ratio in Figure 2 keeps climbing, and the ratio is approaching the unity after June 16, 2020, which also proves that SARS-CoV-2 becomes more contagious as time goes on. 2020 Research square Result SARS_CoV_2 D614G 14 19 32818213 Characterizing SARS-CoV-2 mutations in the United States. Moreover, the first confirmed case with 27964C>T-(S24L) was discovered on February 20, 2020, in the United States, suggesting that S24L initially happened in the US. 2020 Research square Result SARS_CoV_2 C27964T;S24L;S24L 40;131;50 48;135;54 32818213 Characterizing SARS-CoV-2 mutations in the United States. Mutation 1059C>T-(T85I) was first detected in Singapore on February 16, 2020. 2020 Research square Result SARS_CoV_2 T85I 18 22 32818213 Characterizing SARS-CoV-2 mutations in the United States. Mutation 14408C>T-(P323L) on the NSP12 (also called RNA-dependent RNA polymerase, abbreviation RdRp) was first found in the United Kingdom on February 03, 2020. 2020 Research square Result SARS_CoV_2 C14408T;P323L 9;19 17;24 RdRp;Nsp12;RdRP 52;33;95 80;38;99 32818213 Characterizing SARS-CoV-2 mutations in the United States. Mutation 23403A>G-(D614G) located on the spike protein has the second-highest frequency in the United States, which has been recently considered as the key mutation that makes SARS-CoV-2 more infectious worldwide. 2020 Research square Result SARS_CoV_2 A23403G;D614G 9;19 17;24 S 41 46 32818213 Characterizing SARS-CoV-2 mutations in the United States. Mutation 25563G>T-(Q57H) is on the ORF3a protein. 2020 Research square Result SARS_CoV_2 G25563T;Q57H 9;19 17;23 ORF3a 35 40 32818213 Characterizing SARS-CoV-2 mutations in the United States. Mutation 28144T>C-(L84S), the first known mutation globally, has had a very unsteady trajectory. 2020 Research square Result SARS_CoV_2 T28144C;L84S 9;19 17;23 32818213 Characterizing SARS-CoV-2 mutations in the United States. Mutation P323L locates on this interface domain, which, however, is still poorly characterized. 2020 Research square Result SARS_CoV_2 P323L 9 14 32818213 Characterizing SARS-CoV-2 mutations in the United States. Mutation Y541C changes the amino acid tyrosine (Y) to cysteine (C). 2020 Research square Result SARS_CoV_2 Y541C 9 14 32818213 Characterizing SARS-CoV-2 mutations in the United States. Notably, after analyzing 28726 complete genome sequences, none of them have mutations 28144T>C-(L84S) and 27964C>T-(S24L) happened simultaneously. 2020 Research square Result SARS_CoV_2 C27964T;T28144C;L84S;S24L 106;86;96;116 114;94;100;120 32818213 Characterizing SARS-CoV-2 mutations in the United States. Notably, although 27964C>T-(S24L) has the lowest frequency in the top 8 missense mutations, more than 94.1% mutation 27964C>T-(S24L) worldwide were found in the United States. 2020 Research square Result SARS_CoV_2 C27964T;C27964T;S24L;S24L 18;117;28;127 26;125;32;131 32818213 Characterizing SARS-CoV-2 mutations in the United States. Notably, the mutation 23010T>C-(V483A) has the highest frequency (30) localized on the RBM has the positive binding affinity change, which indicates that V483A is prevalent in COVID-19 patients' in the United States has a potential capacity to enhance the infectivity of SARS-CoV-2. 2020 Research square Result SARS_CoV_2 T23010C;V483A;V483A 22;154;32 30;159;37 COVID-19 176 184 32818213 Characterizing SARS-CoV-2 mutations in the United States. Note that three of the top 8 missense mutations, i.e., 17858A>G-(Y541C), 17747C>T-(P504L), and 27964C>T-(S24L), first appeared in the United States. 2020 Research square Result SARS_CoV_2 C17747T;A17858G;C27964T;P504L;S24L;Y541C 73;55;95;83;105;65 81;63;103;88;109;70 32818213 Characterizing SARS-CoV-2 mutations in the United States. On February 29, 2020, the first SNP variants with mutation 1059C>T-(T85I) appeared in the United States. 2020 Research square Result SARS_CoV_2 C1059T;T85I 59;68 66;72 32818213 Characterizing SARS-CoV-2 mutations in the United States. Once mutations 17858A>G-(Y541C) and 17747C>T-(P504L) were first found in the United States, they had a rapid increase in the first two weeks. 2020 Research square Result SARS_CoV_2 C17747T;P504L;Y541C 36;46;25 44;51;30 32818213 Characterizing SARS-CoV-2 mutations in the United States. One can see that amino acids near position 614 are very conservative, indicating that D614G mutation will play an important role in the functions of the S protein of SARS-CoV-2. 2020 Research square Result SARS_CoV_2 D614G 86 91 S 153 154 32818213 Characterizing SARS-CoV-2 mutations in the United States. One mutation (17747C>T-(P504L)) does not affect the rigidity much whereas the other mutation (17858A>G-(Y541C)) leads to a significant decrease in the NSP12 rigidity, which may make NSP13 not as robust as before to involve in the viral infection and replication process. 2020 Research square Result SARS_CoV_2 C17747T;A17858G;P504L;Y541C 14;94;24;104 22;102;29;109 Nsp13;Nsp12 182;151 187;156 32818213 Characterizing SARS-CoV-2 mutations in the United States. Similar to 27964C>T-(S24L), although 17858A>G-(Y541C), 17747C>T-(P504L) are in the final list in Table 2, more than 87% of them were detected in the United States. 2020 Research square Result SARS_CoV_2 C17747T;A17858G;C27964T;P504L;S24L;Y541C 55;37;11;65;21;47 63;45;19;70;25;52 32818213 Characterizing SARS-CoV-2 mutations in the United States. Since then, the D614G mutation has become a majority variant, and 68.7% of patients carry D614G in the United States as of July 14, 2020. 2020 Research square Result SARS_CoV_2 D614G;D614G 16;90 21;95 32818213 Characterizing SARS-CoV-2 mutations in the United States. Spatiotemporally, mutation Q57H locates at the intramolecular interface and in touch with the membrane, which indicates the special functionality changes that Q57H can induce., and Figure 8 (b) is the visualization of ORF3a, which is generated by an online server Protter. 2020 Research square Result SARS_CoV_2 Q57H;Q57H 27;159 31;163 Membrane;ORF3a 94;218 102;223 32818213 Characterizing SARS-CoV-2 mutations in the United States. Table 4 shows that both high-frequency mutations Y541C and P504L have negative folding stability changes, which will destabilize the structure of NSP13. 2020 Research square Result SARS_CoV_2 P504L;Y541C 59;49 64;54 Nsp13 146 151 32818213 Characterizing SARS-CoV-2 mutations in the United States. Table 4 shows that the folding stability change of 28144T>C-(L84S) is -0.99 kcal/mol, indicating that ORF8 becomes unstable. 2020 Research square Result SARS_CoV_2 T28144C;L84S 51;61 59;65 ORF8 102 106 32818213 Characterizing SARS-CoV-2 mutations in the United States. Table 4 shows that the folding stability change of T85I is -0.05 kcal/mol. 2020 Research square Result SARS_CoV_2 T85I 51 55 32818213 Characterizing SARS-CoV-2 mutations in the United States. The D614G mutation is one of the most popular mutations of SARS-CoV-2, which changes the amino acid aspartate (D) with the polar negative charged side changes to the amino acid glycine (G) with a non-polar side chain. 2020 Research square Result SARS_CoV_2 D614G 4 9 32818213 Characterizing SARS-CoV-2 mutations in the United States. The first case with the D614G mutation in the United States was reported on February 28, 2020. 2020 Research square Result SARS_CoV_2 D614G 24 29 32818213 Characterizing SARS-CoV-2 mutations in the United States. The first group involves 5 mutations 1059C>T-(T85I), 14408C>T-(P323L), 23403A>G-(D614G), 25563G>T-(Q57H), and 27964C>T-(S24L) that are strongly correlated, though have a wide range of frequencies. 2020 Research square Result SARS_CoV_2 C1059T;C14408T;A23403G;G25563T;C27964T;D614G;P323L;Q57H;S24L;T85I 37;53;71;89;110;81;63;99;120;46 44;61;79;97;118;86;68;103;124;50 32818213 Characterizing SARS-CoV-2 mutations in the United States. The first missense mutation, 23403A>G-(D614G), occurred in China on January 24, 2020. 2020 Research square Result SARS_CoV_2 A23403G;D614G 29;39 37;44 32818213 Characterizing SARS-CoV-2 mutations in the United States. The first top mutation recorded in the US was 28144T>C-(L84S), on January 19. 2020 Research square Result SARS_CoV_2 T28144C;L84S 46;56 54;60 32818213 Characterizing SARS-CoV-2 mutations in the United States. The FRI rigidity change is also minor, as is shown in Figure 4 (c), indicating the mutation of T85I on the NSP2 does not change the flexibility of NSP2 too much. 2020 Research square Result SARS_CoV_2 T85I 95 99 Nsp2;Nsp2 107;147 111;151 32818213 Characterizing SARS-CoV-2 mutations in the United States. The increasing ratio of P323L in Figure 2 indicates that this type of mutations may favor SARS-CoV-2 and enhance the transmission capacity of SARS-CoV-2. 2020 Research square Result SARS_CoV_2 P323L 24 29 32818213 Characterizing SARS-CoV-2 mutations in the United States. The missense mutation with the highest frequency, 14408C>T-(P323L), occurred in the United Kingdom on February 3, 2020. 2020 Research square Result SARS_CoV_2 C14408T;P323L 50;60 58;65 32818213 Characterizing SARS-CoV-2 mutations in the United States. The mutation that has the highest frequency is D614G, which was reported to enhance SARS-CoV-2 infectivity. 2020 Research square Result SARS_CoV_2 D614G 47 52 32818213 Characterizing SARS-CoV-2 mutations in the United States. The negative folding stability changes of mutation Q57H in Table 4 reveals that ORF3a becomes unstable following the Q57H mutation, which may harm the function of ORF3a in apoptosis and increase the viral load in the host cell. 2020 Research square Result SARS_CoV_2 Q57H;Q57H 51;117 55;121 ORF3a;ORF3a 80;163 85;168 32818213 Characterizing SARS-CoV-2 mutations in the United States. The ORF8 protein also has two high-frequency mutations, 28144T>C-(L84S) and 27964C>T-(S24L). 2020 Research square Result SARS_CoV_2 C27964T;T28144C;L84S;S24L 76;56;66;86 84;64;70;90 ORF8 4 8 32818213 Characterizing SARS-CoV-2 mutations in the United States. The other three mutations, 17747C>T-(P504L), 17858A>G-(Y541C), and 28144T>C-(L84S), occur mostly together and have similar numbers of frequencies. 2020 Research square Result SARS_CoV_2 C17747T;A17858G;T28144C;L84S;P504L;Y541C 27;45;67;77;37;55 35;53;75;81;42;60 32818213 Characterizing SARS-CoV-2 mutations in the United States. The Q57H mutation changes the amino acid glutamine (Q) with a non-charged polar side chain to the positively charged polar side chain of amino acid histidine (H). 2020 Research square Result SARS_CoV_2 Q57H 4 8 32818213 Characterizing SARS-CoV-2 mutations in the United States. The red rectangle marks the Q57H mutations with its two neighborhoods. 2020 Research square Result SARS_CoV_2 Q57H 28 32 32818213 Characterizing SARS-CoV-2 mutations in the United States. The third pair of mutations, 17747C>T-(P504L) and 17858A>G-(Y541C), first detected and occurred mostly in the US, have an identical evolution trajectory. 2020 Research square Result SARS_CoV_2 C17747T;A17858G;P504L;Y541C 29;50;39;60 37;58;44;65 32818213 Characterizing SARS-CoV-2 mutations in the United States. The trajectories of the other two high frequency S protein mutations (Q675R and E583D) indicate that they are co-mutations with infectivity-enhancing S protein mutations, such as D614G. 2020 Research square Result SARS_CoV_2 D614G;E583D;Q675R 179;80;70 184;85;75 S;S 49;150 50;151 32818213 Characterizing SARS-CoV-2 mutations in the United States. The United States found its first case related to 14408C>T-(P323L) on February 28, 2020. 2020 Research square Result SARS_CoV_2 C14408T;P323L 50;60 58;65 32818213 Characterizing SARS-CoV-2 mutations in the United States. The V483A mutation is localized on the RBM with the highest frequency, indicating that V483A may favor SARS-CoV-2 by natural selection and cause SARS-CoV-2 more infectious. 2020 Research square Result SARS_CoV_2 V483A;V483A 4;87 9;92 32818213 Characterizing SARS-CoV-2 mutations in the United States. There is an apparent gender difference in mutation 27964C>T-(S24L) on the ORF8 protein. 2020 Research square Result SARS_CoV_2 C27964T;S24L 51;61 59;65 ORF8 74 78 32818213 Characterizing SARS-CoV-2 mutations in the United States. Therefore, its time evolution trajectory is extremely similar to that of 25563G>T-(Q57H). 2020 Research square Result SARS_CoV_2 G25563T;Q57H 73;83 81;87 32818213 Characterizing SARS-CoV-2 mutations in the United States. Therefore, we can deduce that the increasing tendency of P323L ratios per 10-days is due to its co-mutation with other infectivity-strengthening mutations, such as 23403A>G-(D614G). 2020 Research square Result SARS_CoV_2 A23403G;P323L;D614G 164;57;174 172;62;179 32818213 Characterizing SARS-CoV-2 mutations in the United States. This explains the increasing trend in the ratio of S24L. 2020 Research square Result SARS_CoV_2 S24L 51 55 32818213 Characterizing SARS-CoV-2 mutations in the United States. This tendency indicates that mutation Q57H becomes popular in the viral patients of the United States, which may make the SARS-CoV-2 more infectious. 2020 Research square Result SARS_CoV_2 Q57H 38 42 32818213 Characterizing SARS-CoV-2 mutations in the United States. To be noted, A475V on the RBM has a negative binding affinity change with a relatively high frequency compared to the other 3 mutations in Cluster C. 2020 Research square Result SARS_CoV_2 A475V 13 18 32818213 Characterizing SARS-CoV-2 mutations in the United States. To be noted, the rigidity changes induced by S24L is less than the L84S. 2020 Research square Result SARS_CoV_2 L84S;S24L 67;45 71;49 32818213 Characterizing SARS-CoV-2 mutations in the United States. We found that the other high frequency S protein mutation L5F is independent of mutation D614G. 2020 Research square Result SARS_CoV_2 D614G;L5F 89;58 94;61 S 39 40 32818213 Characterizing SARS-CoV-2 mutations in the United States. We use the red rectangle to mark the position of D614G and its neighborhoods. 2020 Research square Result SARS_CoV_2 D614G 49 54 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. All of the sequences belonging to the Suceava cluster (Figure 1 purple highlight) presented a particular synonymous mutation, A20268G that is related to subtype B.1.5 assignment. 2020 Life (Basel, Switzerland) Result SARS_CoV_2 A20268G 126 133 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. Furthermore, all of the sequences belonging to Bucharest cluster 2 (Figure 1 blue highlight) presented a particular non-synonymous mutation, C16049T (T870I in Nsp12). 2020 Life (Basel, Switzerland) Result SARS_CoV_2 C16049T;T870I 141;150 148;155 Nsp12 159 164 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. Interestingly, in the sequences from Bucharest cluster 1 (Figure 1 pink highlight), we observed a genetic signature, a synonymous mutation (T19839C). 2020 Life (Basel, Switzerland) Result SARS_CoV_2 T19839C 140 147 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. Of particular interest is the K489E mutation, found in one of the Romanian sequences SARS-CoV-2 sequence from Bucharest cluster 2 (EPI_ISL468150) and tagged with a black star on top of the mutation marker in Figure 3. 2020 Life (Basel, Switzerland) Result SARS_CoV_2 K489E 30 35 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. One of these sequences had additional mutations: A9744G (Y397C in Nsp4), A22803C and C28603T. 2020 Life (Basel, Switzerland) Result SARS_CoV_2 A22803C;A9744G;C28603T;Y397C 73;49;85;57 80;55;92;62 Nsp4 66 70 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. The frequency of R203K and G204R variants in the GISAID database mutational statistics is 23.6% (n = 12,784). 2020 Life (Basel, Switzerland) Result SARS_CoV_2 G204R;R203K 27;17 32;22 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. The sequences from the BMA presented specific mutations: G28881A, G28882A (R203K in N gene) and G28883C (G204R in N gene). 2020 Life (Basel, Switzerland) Result SARS_CoV_2 G28881A;G28882A;G28883C;G204R;R203K 57;66;96;105;75 64;73;103;110;80 N;N 84;114 85;115 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. These mutations, C3037T, C14408T (P323L in Nsp12) and A23403G (D614G in S), were present in all Romanian sequences. 2020 Life (Basel, Switzerland) Result SARS_CoV_2 A23403G;C14408T;C3037T;D614G;P323L 54;25;17;63;34 61;32;23;68;39 Nsp12;S 43;72 48;73 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. When looking into the GISAID database mutational statistics, which uses hCoV-19/Wuhan/WIV04/2019 EPI_ISL_402124 as a reference strain (COVsurver tool), both P323L and D614G mutations are present in a high percentage (61.7%/61.8%, n = 33480 and n = 33537). 2020 Life (Basel, Switzerland) Result SARS_CoV_2 D614G;P323L 167;157 172;162 32839745 miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East. The interesting finding here that the 1841A > G, and D614G showed a change in the predicted miRNA and an increase in the target score from 91 to 92 (hsa-miR-4793-5p to hsa-miR-3620-3p). 2020 Non-coding RNA research Result SARS_CoV_2 A1841G;D614G 38;53 47;58 32839745 miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East. The original sequence of the del 432TTA, and the del Y144 have the same miRNA with a target score of 91. 2020 Non-coding RNA research Result SARS_CoV_2 del 432TTA 29 39 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. A lower number of hydrogen bonds were observed on HR1 mutations A930V, D936Y with 55.98 and 59.12, in contrast, WT-HR1 formed 60.70 hydrogen bonds during the run time (Figure 8B). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y 64;71 69;76 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. Consequently, HR1 mutants A930V and D936Y revealed high alterations between the residues ~910-920 and ~930-940 explored loss of contacts between HR1 domain residues on spike crude structure (Supplemental Figure S6B(i-iii)). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y 26;36 31;41 S 168 173 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. Interestingly the mutations on the RBD region like L455Y, F486L, Q493N, and N501T that forms binding with ACE2 receptor were observed to be with the highest deviations. 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 F486L;L455Y;N501T;Q493N 58;51;76;65 63;56;81;70 RBD 35 38 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. Interestingly, the maximum drift of fluctuation was noticed in R408I, F486L with an RMSD range of ~1.0 nm (Figure 4A). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 F486L;R408I 70;63 75;68 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. It was noticed that the RBD mapped mutations R408I, L455Y, F486L, Q493N, Q498Y, and N501T showed the average highest Rg value of ~2.6 nm and WT was with 2.5 nm (Figure 7A). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 F486L;L455Y;N501T;Q493N;Q498Y;R408I 59;52;84;66;73;45 64;57;89;71;78;50 RBD 24 27 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. RBD mutant R408I revealed Q414, Y421, F543, N544, G545 residues to have high negative fluctuations, L455Y mutant demonstrated higher fluctuations at position D398, Y453, F456, F543, N544, G545, F486L mutant revealed maximum fluctuations on residues D398, G413, Q414, D420, Y421, F543, N544, G545, and Q493N revealed high fluctuations at positions D398, R403-Q409, G413, and Q414 respectively (Figure 5A(i-iv)). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 F486L;L455Y;Q493N;R408I 194;100;301;11 199;105;306;16 RBD 0 3 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. Remarkably, it was also observed that the RBD residue N501 involved in hydrogen bond formation with ACE2 has shown alterations in forming the intra-molecular bond number in the presence of mutation N501T revealing the damaging effect on the RBD loop lying from 319-591 on spike glycoprotein (Supplemental Table S4). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501T 198 203 S;RBD;RBD 272;42;241 290;45;244 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. Spotting HR1 domain, mutant A930V was marked with projected higher fluctuations on residues I907-I931, K933, I934, Q935, L938, S939, Q957, A958, N960, T961, L962, K964, Q965, L966, N969-A972, and S974-S982 followed by, mutant D936Y showed higher relative alterations at positions I907-G910, A930, K933, I934, Q935-A944, K947-D970, V976-N978, I980-S982, respectively (Figure 5B(i, ii)). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y 28;226 33;231 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. Subsequently, the SASA of mutants A930V and D936Y of HR1 domain projected maximum fluctuations with 49nm2 range and WT was with 48nm2, respectively (Figure 6C). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y 34;44 39;49 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The analysis of SASA and Rg data suggested the compactness, area of stability was consistent for both WT structures and R408I, L455Y, F486L, Q493N, Q498Y, N501T mutations on RBD region and A930V, D936Y mutations of HR1 altered maximally towards the end of simulations leading to structural destabilization, loss of shape and folding on spike glycoprotein native structure. 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y;F486L;L455Y;N501T;Q493N;Q498Y;R408I 189;196;134;127;155;141;148;120 194;201;139;132;160;146;153;125 S;RBD 336;174 354;177 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The analysis of the RMSDs of the HR1 domain mutants revealed a minimum constant range of ~1.3 nm for WT, whereas the highest fluctuations were observed for the structures with mutations A930V, D936Y with RMSD in the range of ~2.0 nm (Figure 4C). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y 186;193 191;198 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The analysis revealed that the probability distribution of WT was within the threshold of 0.6 nm whereas the R408I, L455Y, F486L, Q493N, Q498Y, N501T mutant structures revealed maximum alterations of 1.0 nm, 0.9 nm, 1.1 nm, 0.7 nm, 0.7 nm, 0.7 nm, respectively (Figure 4B). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 F486L;L455Y;N501T;Q493N;Q498Y;R408I 123;116;144;130;137;109 128;121;149;135;142;114 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The comparative analysis of HR1 WT and the mutants showed A930V and D936Y presented the least compactness with the highest deviation score of ~1.0 nm noticed, whereas ~2.0 nm of Rg was marked on WT in all the time scales of generated trajectories, respectively (Figure 7C). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y 58;68 63;73 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The decrease in SASA was noticed on mutation D936Y with a PDF-SASA average of 47nm2 and sharp alteration peaks were spotted for A930V with 49nm2 range,in contrast, 48nm2 range was noticed on WT for HR1 mutations (Figure 6D) and (Supplemental Table S3). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y 128;45 133;50 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The density area of each atom within the structure of mutant proteins of the HR1 domain was WT (0.7nm-3) and found to be 0.9-3 for A930V, 0.7nm-3 for D936Y (Figure 10B(i-iii)). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y 131;150 136;155 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The employed dynamic programs revealed the deleterious impact of R408I, L455Y, F486L, Q493N, Q498Y, N501T mutations in the RBD and A930V, D936Y mutations in the HR1 domain on the stability of the SARS-CoV-2 spike glycoprotein native structure (Table 1). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y;F486L;L455Y;N501T;Q493N;Q498Y;R408I 131;138;79;72;100;86;93;65 136;143;84;77;105;91;98;70 S;RBD 207;123 225;126 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The functional effects of R408I, L455Y, F486L, Q493N, Q498Y, N501T mutations in the RBD domain, and A930V, D936Y mutations in the HR1 domain were predicted using SIFT, PolyPhen, I-mutant 2.0, PROVEAN, PhD SNP online servers. 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y;F486L;L455Y;N501T;Q493N;Q498Y;R408I 100;107;40;33;61;47;54;26 105;112;45;38;66;52;59;31 RBD 84 87 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The global free energy minima (marked with KJ/mol) that are confined in the case of RBD and HR1 WT revealing the steady states, in contrast, the observations marked differences in the folding behavior on R408I, L455Y, F486L, Q493N, Q498Y, N501T mutations on RBD region (Supplemental Figure S5A(i-vii)) and A930V, D936Y mutations of HR1 domain (Supplemental Figure S5B(i-iii)). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y;F486L;L455Y;N501T;Q493N;Q498Y;R408I 306;313;218;211;239;225;232;204 311;318;223;216;244;230;237;209 RBD;RBD 84;258 87;261 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The intramolecular hydrogen bonds found low numbering on mutation structures like F486L and Q498Y with 142.50 and 146.87, whereas, the average number of hydrogen bonds were noticed on RBD mutants R408I, L455Y, Q493N, and N501T with 166.55, 166.71, 167.01, 167.28, respectively (Figure 8A). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 F486L;L455Y;N501T;Q493N;Q498Y;R408I 82;203;221;210;92;196 87;208;226;215;97;201 RBD 184 187 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The MD simulation of the WT of the RBD region noticeably displays a steady RMSD of ~0.5 nm, throughout the simulation, whereas L455Y shows a fluctuation of ~0.8 nm, followed by Q493N, Q498Y, N501T structures with a range of ~0.7 nm, respectively. 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 L455Y;N501T;Q493N;Q498Y 127;191;177;184 132;196;182;189 RBD 35 38 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The mutants R408I, L455Y, F486L, Q493N, Q498Y, N501T mutations on RBD region and A930V, D936Y mutations of HR1 covered large region along the PC1 and PC2 lanes particularly compared to WT. 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y;F486L;L455Y;N501T;Q493N;Q498Y;R408I 81;88;26;19;47;33;40;12 86;93;31;24;52;38;45;17 RBD 66 69 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The mutation Q498Y revealed highest fluctuations on the maximum number of residues positioned at D398, R403-Q409, K417-Y421, Y449, Y453, L455, L492, Q493, G496, Q498, P499, T500, G502-Y505, K528, K529, F543, N544, followed by N501T with fluctuations at D398, Y453, L455, and F543 respectively (Figure 5A(v-vi)). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501T;Q498Y 226;13 231;18 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The overall degradation of residue displacement was noticed due to the presence of R408I, L455Y, F486L, Q493N, Q498Y, N501T mutations on the RBD region and A930V, D936Y mutations on HR1 domains in turn de-stabilizing the SARS-CoV-2 spike glycoprotein crude structure. 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y;F486L;L455Y;N501T;Q493N;Q498Y;R408I 156;163;97;90;118;104;111;83 161;168;102;95;123;109;116;88 S;RBD 232;141 250;144 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The overall flexibility of the RBD-WT and R408I, L455Y, F486L, Q493N, Q498Y, N501T mutant structures, as well as HR1-WT and A930V, D936Y structures were analyzed with Calpha-RMSF relative fluctuations (Supplemental Figure S2A-B). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y;F486L;L455Y;N501T;Q493N;Q498Y;R408I 124;131;56;49;77;63;70;42 129;136;61;54;82;68;75;47 RBD 31 34 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The overall results suggested that R408I, L455Y, F486L, Q493N, Q498Y, N501T mutations on RBD region showed the highest fluctuation of ~0.2 nm to ~1.0 nm, whereas WT revealed highest drift of ~0 to 0.2 nm throughout the MD simulations (Supplemental Figure S3A-B) and the A930V, D936Y mutations of HR1 domain showed unstable fluctuation of ~0.2 nm to ~1.5 nm, distinguished with WT range of ~0.2 nm, respectively (Supplemental Figure S3C-D). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y;F486L;L455Y;N501T;Q493N;Q498Y;R408I 270;277;49;42;70;56;63;35 275;282;54;47;75;61;68;40 RBD 89 92 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The PDF analysis of A930V and D936Y mutations further confirmed the loss of gyration between the atoms in the presence of A930V with an Rg average of 1.67 nm, D936Y with 1.65 nm revealing decreased peaks when compared to WT with 2.27 nm of Rg average (Figure 7D) and (Supplemental Table S3). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;A930V;D936Y;D936Y 20;122;30;159 25;127;35;164 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The PDF investigations revealed WT with 1.5 nm and mutants exhibited a high drift of fluctuations for A930V, D936Y with 2.7 and 2.5 nm of average PDF-RMSD ranges (Figure 4D) and (Supplemental Table S3). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y 102;109 107;114 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The PDF of the obtained results revealed maximum drifts for the mutants R408I, L455Y, F486L, Q493N, Q498Y, N501T with a range of 169.24nm2, 168.23nm2, 168.42nm2, 169.65nm2, 169.61nm2, 169.62nm2, where are WT was shown with 169.10nm2 respectively (Figure 6B). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 F486L;L455Y;N501T;Q493N;Q498Y;R408I 86;79;107;93;100;72 91;84;112;98;105;77 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The results indicate that the protein becomes less stable and displays multiple minimum energy wells in certain cases like L455Y in RBD and all the HR1 mutants. 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 L455Y 123 128 RBD 132 135 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The results revealed that a stable partial density area was observed for WT within 3.5 nm-3 for RBD whereas decreased density was noticed for R408I, L455Y, F486L, Q493N, Q498Y, N501T ranging from 2.4 to 3.0 nm-3 (Figure 10A(i-vii)). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 F486L;L455Y;N501T;Q493N;Q498Y;R408I 156;149;177;163;170;142 161;154;182;168;175;147 RBD 96 99 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The SASA analysis revealed that the R408I, Q493N, Q498Y, and N501T had a higher range of SASA values with a range of 169nm2, followed by L455Y, F486L with 168nm2, whereas WT showed a minimum range of SASA (Figure 6A). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 F486L;L455Y;N501T;Q493N;Q498Y;R408I 144;137;61;43;50;36 149;142;66;48;55;41 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The study was further investigated to note the PDF between the WT and mutants revealed there was an unsteady drift in the graph with average Rg of noticed on R408I with 2.68 nm, L455Y with 2.77 nm, F486L with 2.47 nm, Q493N with 2.63 nm, Q498Y with 2.68 nm and N501T with 2.68 nm, whereas the difference in value was noticed on WT with 2.5 nm (Figure 7B). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 F486L;L455Y;N501T;Q493N;Q498Y;R408I 198;178;261;218;238;158 203;183;266;223;243;163 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. Thereby, it was correlated that the R408I, L455Y, F486L, Q493N, Q498Y, N501T mutations on the RBD region and A930V, D936Y mutations are in turn responsible for the de-stabilizing the native spike glycoprotein further probably halting the process of forming a 6HB on the virus to host entry. 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 A930V;D936Y;F486L;L455Y;N501T;Q493N;Q498Y;R408I 109;116;50;43;71;57;64;36 114;121;55;48;76;62;69;41 S;RBD 190;94 208;97 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). A7V occurs on the N-finger, which is a critical region for Mpro dimer stability. 2020 Journal of chemical information and modeling Result SARS_CoV_2 A7V 0 3 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). A7V significantly increased the number of proximal interactions to neighboring residues when compared to the reference protein (Figure 2) and gained in hydrophobic interactions, although a clash in the van der Waals radius is additionally present. 2020 Journal of chemical information and modeling Result SARS_CoV_2 A7V 0 3 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). Another cluster of mutations is distributed in domain II and includes 3 subgroups: a group of fully immobilized positions (A116V, A129V, P132L, T135I, and I136V), a group of bridging (hinge-like) sites that connect rigid and flexible regions (Y101C, R105H, P108S, N151D, V157I/L, C160S, A173V, and P184L/S), and a group of mostly mobile residues (T190I, A191V, and A193V) (Figure 18, panel B). 2020 Journal of chemical information and modeling Result SARS_CoV_2 A129V;A173V;A191V;A193V;C160S;I136V;N151D;P108S;P132L;P184L;P184S;R105H;T135I;V157I;V157L;A116V;T190I;Y101C 130;287;354;365;280;155;264;257;137;298;298;250;144;271;271;123;347;243 135;292;359;370;285;160;269;262;142;305;305;255;149;278;278;128;352;248 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). As seen in Figure 1, most residue mutations have occurred in solvent-accessible surfaces, with the exception of A7V, V20L, L89F, A116V, A129V, T135I, I136V, V157I/L, C160S, A173V, T201A, A234V, and A266V, which were predicted to be buried by the PyMOL script findSurfaceResidues, using a default cutoff of 2.5 A2. 2020 Journal of chemical information and modeling Result SARS_CoV_2 A116V;A129V;A173V;A234V;A266V;A7V;C160S;I136V;L89F;T135I;T201A;V157I;V157L;V20L 129;136;173;187;198;112;166;150;123;143;180;157;157;117 134;141;178;192;203;115;171;155;127;148;185;164;164;121 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). Both EPI_ISL_415503 and EPI_ISL_416720 have been described in section 3.5 as having higher RMSF values at positions 46-54 due to the mutations V157I and Y237H. 2020 Journal of chemical information and modeling Result SARS_CoV_2 V157I;Y237H 143;153 148;158 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). By replacing alanine with valine at position 116, an increased amount of proximal interactions is gained at V116 in sample EPI_ISL_425284, with a higher amount of hydrophobic contacts to the residue. 2020 Journal of chemical information and modeling Result SARS_CoV_2 A116V 13 48 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). EPI_ISL_423772, which contains the M17I mutation displayed a relatively high backbone mobility, more particularly along one of the alpha-helices of domain III. 2020 Journal of chemical information and modeling Result SARS_CoV_2 M17I 35 39 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). G15D is found to increase the number of proximal contacts by the largest extent while also modestly increasing the number of hydrophobic interactions. 2020 Journal of chemical information and modeling Result SARS_CoV_2 G15D 0 4 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). However, the M17I mutation does not significantly change the non-bonded interaction in EPI_ISL_423772 but occurs on a beta strand in domain I. 2020 Journal of chemical information and modeling Result SARS_CoV_2 M17I 13 17 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). In all, these samples involve mutations A7V, M17I, A70T, A116V, K236R, Y237H, D248E, A266V, and N274D, in which the last five are exclusive to domain III. 2020 Journal of chemical information and modeling Result SARS_CoV_2 A116V;A266V;A70T;A7V;D248E;K236R;M17I;N274D;Y237H 57;85;51;40;78;64;45;96;71 62;90;55;43;83;69;49;101;76 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). In EPI_ISL_420610 (N274D), however, we observed a yet undescribed relatively stable pose for PHE140. 2020 Journal of chemical information and modeling Result SARS_CoV_2 N274D 19 24 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). In sample EPI_ISL_420241, the P184L mutation occurs in a solvent-exposed loop, and no major non-bonded interactions were detected from the side chains or backbone atoms. 2020 Journal of chemical information and modeling Result SARS_CoV_2 P184L 30 35 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). In the case of the D248E mutation in EPI_ISL_425886, the D248 side chain is H-bonded to Q244 in the reference structure, possibly stabilizing the helical structure. 2020 Journal of chemical information and modeling Result SARS_CoV_2 D248E 19 24 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). In the same domain, the A116V mutation occurs on a beta strand, which is supported by a rich network of hydrogen bonds. 2020 Journal of chemical information and modeling Result SARS_CoV_2 A116V 24 29 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). Independent simulations performed in duplicate (not shown) of dimeric Mpro containing the mutants G11A, E14A, and R298A and even of the triple mutant (G11A/R298A/Q299A) did not dissociate over a period of 100 ns, even though these were experimentally shown to be inactive monomers in SARS-CoV, suggesting that particular equilibrium states may need to be traversed before observing such events. 2020 Journal of chemical information and modeling Result SARS_CoV_2 E14A;G11A;R298A;G11A;Q299A;R298A 104;98;114;151;162;156 108;102;119;155;167;161 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). Isolate EPI_ISL_415610 (bearing mutation A193V) displayed the highest median interprotomer COM distance. 2020 Journal of chemical information and modeling Result SARS_CoV_2 A193V 41 46 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). It is possible that such an increase in interaction may improve the stability around this region in domain III for the Y237H mutation. 2020 Journal of chemical information and modeling Result SARS_CoV_2 Y237H 119 124 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). M17I occurs on an internal loop that connects a beta strand to a helix in domain I, while A70T occurs on a solvent-exposed loop in the same domain. 2020 Journal of chemical information and modeling Result SARS_CoV_2 A70T;M17I 90;0 94;4 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). Mutation A116V occurs in a buried beta strand within domain II. 2020 Journal of chemical information and modeling Result SARS_CoV_2 A116V 9 14 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). Mutation R105H (occurring on a loop region) in EPI_ISL_419984 leads to the loss of an H-bond with F181 but forms a pi-pi stacking interaction with Y182. 2020 Journal of chemical information and modeling Result SARS_CoV_2 R105H 9 14 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). Mutations V157I/L both reduced the number of local hydrophobic contacts and resulted in a reduced van der Waals clash compared to the reference. 2020 Journal of chemical information and modeling Result SARS_CoV_2 V157I;V157L 10;10 17;17 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). N-finger poses corresponding to the RMSD KDE peaks for EPI_ISL_423772 (M17I mutant) and the reference protease are shown in Figure 6. 2020 Journal of chemical information and modeling Result SARS_CoV_2 M17I 71 75 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). One cluster of mutations is located in highly mobile regions of domain III (T198I, T201A, L220F, L232F, A234V, K236R, Y237H, D248E, A255V, T259I, A260V, V261A, A266V, N274D, R279C, and S301L). 2020 Journal of chemical information and modeling Result SARS_CoV_2 A234V;A255V;A260V;A266V;D248E;K236R;L220F;L232F;N274D;R279C;S301L;T201A;T259I;V261A;Y237H;T198I 104;132;146;160;125;111;90;97;167;174;185;83;139;153;118;76 109;137;151;165;130;116;95;102;172;179;190;88;144;158;123;81 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). One such mutation has already happened at position 7 (A7V) in the N-finger. 2020 Journal of chemical information and modeling Result SARS_CoV_2 A7V 54 57 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). P184L had a reduced number of proximal contacts compared to the reference, while P184S was very similar to its equivalent position in the reference. 2020 Journal of chemical information and modeling Result SARS_CoV_2 P184S;P184L 81;0 86;5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). Protonated aspartic acid (ASH) was found in both protomers of sample EPI_ISL_420510, which was the only isolate to contain the N151D mutation. 2020 Journal of chemical information and modeling Result SARS_CoV_2 N151D 127 132 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). Similarly, the Y237H mutation, present only in sample EPI_ISL_416720, occurs as an HID in both of its protomers. 2020 Journal of chemical information and modeling Result SARS_CoV_2 Y237H 15 20 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). T201A in EPI_ISL_423642 abolishes the H-bond that is otherwise present between T201 and the backbone oxygen atom of E240, very likely weakening their interaction. 2020 Journal of chemical information and modeling Result SARS_CoV_2 T201A 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). The group of potential hinge sites may be important for controlling regulatory motions, and mutations in these regions (such as V157I/L and P184L/S) may affect global movements in the protease and its enzymatic activity. 2020 Journal of chemical information and modeling Result SARS_CoV_2 P184L;P184S;V157I;V157L 140;140;128;128 147;147;135;135 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). The local impacts of the A116V mutation are discussed further in section 3.2. 2020 Journal of chemical information and modeling Result SARS_CoV_2 A116V 25 30 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). The local impacts of the A7V mutation are discussed in section 3.2. 2020 Journal of chemical information and modeling Result SARS_CoV_2 A7V 25 28 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). The main physicochemical difference in A193V is the higher molecular weight and volume of the valine side chain; however, the mutation occurs in the solvent-exposed linker that connects domains II and III. 2020 Journal of chemical information and modeling Result SARS_CoV_2 A193V 39 44 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). The mutability of hinge sites (Y101C, R105H, P108S, V157I/L, C160S, A173V, and P184L/S) and nearby sites (T190I, A191V, and A193V) may be related with their structural and dynamic signatures to reside in the exposed protein regions rather than in the more conserved protein core. 2020 Journal of chemical information and modeling Result SARS_CoV_2 A173V;A191V;A193V;C160S;P108S;P184L;P184S;R105H;V157I;V157L;T190I;Y101C 68;113;124;61;45;79;79;38;52;52;106;31 73;118;129;66;50;86;86;43;59;59;111;36 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). The R105H mutation (present only in sample EPI_ISL_419984) occurs as an HID in each protomer. 2020 Journal of chemical information and modeling Result SARS_CoV_2 R105H 4 9 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). The V157I mutation in EPI_ISL_415503 does not significantly alter the non-bonded interactions but occurs on a beta strand on domain II. 2020 Journal of chemical information and modeling Result SARS_CoV_2 V157I 4 9 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). The Y237H mutation in EPI_ISL_416720 introduces two carbon H-bonds (one with L272 and another with V233), in addition to the pi-alkyl interaction that is present in both the reference and this mutant, which seem to hold the solvent-exposed helices together in domain III. 2020 Journal of chemical information and modeling Result SARS_CoV_2 Y237H 4 9 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). These mutations comprised residues that underwent a higher number of mutations (G15D/S, V157I/L, and P184L/S) in addition to mutations that occurred at or close to the dimer interface (A7V and A116V). 2020 Journal of chemical information and modeling Result SARS_CoV_2 A116V;P184L;P184S;V157I;V157L;A7V;G15D;G15S 193;101;101;88;88;185;80;80 198;108;108;95;95;188;86;86 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). This being said, in the case of the Mpro enzyme, a relatively higher rate of non-synonymous mutations has occurred at residue position 15 (G15D/S) in domain I, residue position 157 (V157I/L) in domain II, and at position 184 (P184L/S) within the interdomain linker region. 2020 Journal of chemical information and modeling Result SARS_CoV_2 G15D;G15S;P184L;P184S;V157I;V157L 139;139;226;226;182;182 145;145;233;233;189;189 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). This is very likely an artifact linked to the absence of the two C-terminal residues, as the residue is a solvent-exposed protein and displays very similar residue interactions at position 255 in both the reference and the mutant, even though A255V occurs on a helix. 2020 Journal of chemical information and modeling Result SARS_CoV_2 A255V 243 248 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). This may be attributable to the S301L mutation, which reduces H-bonding at the end of the C-terminal helical structure. 2020 Journal of chemical information and modeling Result SARS_CoV_2 S301L 32 37 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. 5D illustrates that mutations found across circulating S sequences were rare: Besides D614G (found in 69.4% of sequences), the next most frequent substitution is found in 1.96% of sequences (synonymous), with sequences sampled from infected individuals, on average, 0.55 mutations away from the consensus sequence (consisting of 0.12 synonymous and 0.43 nonsynonymous mutations). 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 86 91 S 55 56 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Across the genome, there were, on average, 4.05 nucleotide mutations per individual genome when compared to the consensus, with only P4715L and D614G found in >50% of sequences. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G;P4715L 144;133 149;139 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Because diversifying selection is often associated with the host adaptive response, we considered whether the D614G mutation coincided with targets of antibody and T cell responses. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 110 115 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Comparing these sequences to the consensus sequence derived from all of the sequences sampled to date, there was only one mutation: D614G. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 132 137 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Given the importance of S for virus entry and as a target of the host neutralizing response, the biologic implications of the D614G mutation are under intense scrutiny. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 126 131 S 24 25 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. In contrast, the D614G mutation was introduced in Europe at the end of January (first sequence identified in Germany, dated January 28), and it rapidly became dominant on that continent and at every location where the virus subsequently spread. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 17 22 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. One S Mutation (D614G) Has Become Dominant. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 16 21 S 4 5 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Since the beginning of the pandemic, two mutations across the genome have become consensus: P4715L in ORF1ab (nucleotide 14,143, C to T) and D614G in S (nucleotide 23,403, A to G). 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G;P4715L 141;92 146;98 ORF1ab;S 102;150 108;151 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. The others were nonsynonymous: G476S (n = 10 sequences, 0.05%), Y453F (n = 5, 0.02%), G446V (n = 3, 0.02%), and A475V (n = 2, 0.01%). 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 A475V;G446V;G476S;Y453F 112;86;31;64 117;91;36;69 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. The rapid spread of sequences carrying the D614G mutation implies that the growing viral population should become more homogeneous, that is, the frequency of sequences with shared polymorphisms will increase. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 43 48 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Then, the D614G mutation was not observed in China until March 13. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 10 15 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Therefore, we predict that antibodies to the native S protein would cross-react with S containing the D614G mutation, in agreement with recent reports. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 102 107 S;S 52;85 53;86 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Yet, genomes with the D614G mutation showed a median of five substitutions, whereas those with D at position 614 differed by eight substitutions. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 22 27 32869023 SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution. Additionally, SNV signatures of previously characterized Brazilian genomes were found in most samples, such as G28881A and G28882A (98.6%; resulting in R203K change in N), G28883C (98.6%; resulting in G204R change in N), T27299C (91.6%; resulting in I33T change in ORF6), and T29148C (90.1%; resulting in I292T change in N). 2020 bioRxiv Result SARS_CoV_2 G204R;G28881A;G28882A;G28883C;I292T;I33T;R203K;T27299C;T29148C 201;111;123;172;305;250;152;221;276 206;118;130;179;310;254;157;228;283 ORF6;N;N;N 265;168;217;321 269;169;218;322 32869023 SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution. Another 85 SNVs were observed in our sequences in a lower frequency (1.4-19.7%; S2 Table), including nine non-synonymous mutations in S protein (V16F, V367L, K558N, Q675H, A879V, S939F, V1176F, K1191N and G1219V). 2020 bioRxiv Result SARS_CoV_2 A879V;G1219V;K1191N;K558N;Q675H;S939F;V1176F;V367L;V16F 172;205;194;158;165;179;186;151;145 177;211;200;163;170;184;192;156;149 S 134 135 32869023 SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution. Four genetically linked mutations previously described as the globally dominant haplotype in April 2020 were found in the majority of our consensus sequences: C241T (100%; 5'UTR region), C3037T (98.6%; silent mutation), C14408T (100%; resulting in P4715L/P323L amino acid change in ORF1ab) and A23403G (100%; resulting in D614G amino acid change in S). 2020 bioRxiv Result SARS_CoV_2 A23403G;C14408T;C241T;C3037T;D614G;P4715L;P323L 294;220;159;187;322;248;255 301;227;164;193;327;254;260 ORF1ab;5'UTR;S 282;172;349 288;177;350 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. 20A is a derivative of 19A and contains mutations C3037T, C14408T and A23403G (resulting in D614G). 2020 medRxiv Result SARS_CoV_2 A23403G;C14408T;C3037T;D614G 70;58;50;92 77;65;56;97 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. 20B is defined by mutations G28881A, G28882A and G28883C, and 20C contains C1059T and G25563T. 2020 medRxiv Result SARS_CoV_2 C1059T;G25563T;G28881A;G28882A;G28883C 75;86;28;37;49 81;93;35;44;56 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. A total of 173 cases were analyzed to determine the number and relative proportion of the specimens which carried the D614G spike protein variant in Nevada. 2020 medRxiv Result SARS_CoV_2 D614G 118 123 S 124 129 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. Clade 19A and 19B are defined by C8782T and T28144C, respectively. 2020 medRxiv Result SARS_CoV_2 C8782T;T28144C 33;44 39;51 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. Earlier studies have revealed the emergence, spread and potential importance of an alteration, D614G (genomic change at 23403A>G), of the spike protein. 2020 medRxiv Result SARS_CoV_2 A23403G;D614G 120;95 128;100 S 138 143 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. For the Wuhan isolate at 14,407 and 14,408 there is CC for proline (P), the variants have CT for leucine (P323L) and TT for phenylalanine (P323F). 2020 medRxiv Result SARS_CoV_2 P323F;P323L 139;106 144;111 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. Prevalence of amino acid variant D614G of SARS-CoV-2 spike protein in specimens collected in Nevada. 2020 medRxiv Result SARS_CoV_2 D614G 33 38 S 53 58 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. Prevalence of amino acid variant P323L/F of SARS-CoV-2 nsp12 (RdRp) in Nevada. 2020 medRxiv Result SARS_CoV_2 P323F;P323L 33;33 40;40 Nsp12;RdRP 55;62 60;66 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. The combined nucleotide diversity across the entire SARS-CoV-2 genome for the Nevada specimens is shown in figure 1D, along with the genomic areas that were assessed for change in frequency corresponding to amino acids D614G, P323L/F and nucleotide 379. 2020 medRxiv Result SARS_CoV_2 D614G;P323F;P323L 219;226;226 224;233;233 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. The global trend by continent of D614G is also similar, with G614 at a higher frequency, the one noted exception is in Asia, where D614 and G614 continue to exist in equal proportions. 2020 medRxiv Result SARS_CoV_2 D614G 33 38 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. To assess the introduction and spread of P323L/F in Nevada, the cumulative frequency of P323, L323 and F323 were plotted from March 6 to June 5. 2020 medRxiv Result SARS_CoV_2 P323F;P323L 41;41 48;48 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. We performed phylogenetic reconstruction of the Nevada specimens and noted the P323L/F variants on the circular dendrogram with the indicated colors. 2020 medRxiv Result SARS_CoV_2 P323F;P323L 79;79 86;86 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. We used a subsampling of Nextstrain.org data to assess the frequency of P323L/F in the United States and globally during the same time period (March 6 to June 5). 2020 medRxiv Result SARS_CoV_2 P323L;P323F 72;72 79;79 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. We used a subsampling of sequence data from Nextstrain.org to assess the frequency of D614G in the United States and globally during the same time period (March 6 to June 5). 2020 medRxiv Result SARS_CoV_2 D614G 86 91 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. 14408 C>T and 23403 A>G mutations are associated with mutation density increase over time. 2020 PeerJ Result SARS_CoV_2 A23403G;C14408T 14;0 23;9 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. Although it is unclear whether the 14805 C>T synonymous mutation has any stabilizing effect on the WT MDe, as the mutation is found in only 1,698 samples out of all isolates that passed our quality filters, including non-UK and non-US isolates, and 1,106 of those isolates are UK-WT and US-WT isolates, its high frequency in WT isolates is more likely to be the result of a founder effect, rather than any selection. 2020 PeerJ Result SARS_CoV_2 C14805T 35 44 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. Furthermore, we focused only on isolates that were sequenced after the first genome with both 14408 C>T and 23403 A>G mutations were identified in the respective geographic regions (26 February 2020 for UK, 28 February 2020 for US). 2020 PeerJ Result SARS_CoV_2 C14408T;A23403G 94;108 103;117 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. In order to determine whether the SARS-CoV-2 strain with 14408 C>T / 23403 A>G mutations was different from those that carried neither mutation, with respect to time-dependent changes in mutation density, we first determined the number of synonymous and non-synonymous mutations. 2020 PeerJ Result SARS_CoV_2 C14408T;A23403G 57;69 66;78 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. Isolates with 14408 C>T & 23403 A>G mutations (MT genotype) show steady increase in mutations in both S and RdRp over time. 2020 PeerJ Result SARS_CoV_2 C14408T;A23403G 14;26 23;35 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. S4-S5), with MT genome mutations more visible in most bins in the 121-140 day period, with the major exception of the 14805 C>T mutation being preserved in WT isolates. 2020 PeerJ Result SARS_CoV_2 C14805T 118 127 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. To eliminate the bias that would be caused by the 14408 C>T and 23403 A>G mutations on the nonsynonymous mutation density of isolates they were present in, which would be substantial considering their high frequency, these two nucleotides were also masked during calculations of non-synonymous mutation density. 2020 PeerJ Result SARS_CoV_2 C14408T;A23403G 50;64 59;73 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. We can see that in the 60-80 day period, the distribution of mutations across the regions were largely comparable between WT and MT genomes, with the exception of the synonymous 14805 C>T mutation in the RdRp, which is exclusive to WT isolates. 2020 PeerJ Result SARS_CoV_2 C14805T 178 187 RdRP 204 208 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. We identified a strong positive correlation between non-synonymous MDe and time in both UK and US in MT samples (rho = 0.70, p-value < 0.001), however, a much weaker correlation was observed in WT samples rho = 0.27, p-value (= 0.002), indicating a potential relationship between non-synonymous mutations and 14408 C>T / 23403A>G genotype. 2020 PeerJ Result SARS_CoV_2 C14408T;A23403G 309;321 318;329 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. A large fluctuation was noticed in the hydrogen bond network of Mpro and its R60C mutant (Fig 5A). 2020 PloS one Result SARS_CoV_2 R60C 77 81 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. Brazil and Vietnam isolate showed only one change at 3606 (Leucine to Phenylalanine) and 3323 (Arginine to Cystine), respectively (Table 1). 2020 PloS one Result SARS_CoV_2 L3606F 53 84 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. Fig 4B illustrates the Rg of Calpha atoms plot of the complexed Mpro from SARS-CoV-2 and the Vietnam mutant Mpro (R60C). 2020 PloS one Result SARS_CoV_2 R60C 114 118 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. Fig 4C shows the change of SASA of native and R60C mutant with time. 2020 PloS one Result SARS_CoV_2 R60C 46 50 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. For instance, India, Finland, Australia, South Korea and Sweden SARS-CoV-2 isolates showed one amino acid change at 408 (Arginine to Isoleucine), 49 (Histidine to Tyrosine), 247 (Serine to Arginine), 221 (Serine to Tryptophan) and 797 (Phenylalanine to Cysteine), respectively (Table 2 and Fig 3C). 2020 PloS one Result SARS_CoV_2 S221W;S247R;R408I;H49Y;F797C 200;174;116;146;231 226;198;144;172;262 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. Here, we also noted two amino acid mutations (in ORF1ab) in each SARS-CoV-2 sequences isolated from China (2708: Asparagine to Serine; 2908: Phenylalanine to Isoleucine), South Korea (902: Methionine to Isoleucine; 6891: Threonine to Methionine) and Sweden (818: Glycine to Serine; 4321: Phenylalanine to Leucine). 2020 PloS one Result SARS_CoV_2 F2908I;F4321L;N2708S;G818S;M902I 135;282;107;258;184 168;312;133;280;213 ORF1ab 49 55 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. In the present study, we performed the MD simulations for the Boceprevir bound complexes of SARS-CoV-2 Mpro and its R60C mutant to study the effect of mutation on the protein dynamics. 2020 PloS one Result SARS_CoV_2 R60C 116 120 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. Indian SARS-CoV-2 sequence showed three changes at 671 (Isoleucine to Threonine), 2144 (Proline to Serine) and 2798 (Alanine to Valine) compared to all other 12 isolates. 2020 PloS one Result SARS_CoV_2 P2144S;A2798V;I671T 82;111;51 106;135;80 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. It was found that R60C mutation results in the changes in local environment that cascade further to the short helix and loop of the catalytic active site of Mpro. 2020 PloS one Result SARS_CoV_2 R60C 18 22 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. It was found that the binding of inhibitor within the active site of Mpro (WT) was stronger as compared to the R60C mutant. 2020 PloS one Result SARS_CoV_2 R60C 111 115 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. One amino acid change occurred in each envelope protein of South Korea SARS-CoV-2 isolate at 37 (Leucine to Histidine) and nucleocapsid protein of Japan SARS-CoV-2 isolate at 344 (Proline to Serine) when compared among 13 SARS-CoV-2 isolates (Tables 4 and 5, Fig 3D and 3E), while, 5 and 45 changes has been reported in envelop and nucleocapsid proteins, respectively as compared to SARS-CoV. 2020 PloS one Result SARS_CoV_2 P344S;L37H 175;93 198;118 N;N 123;332 135;344 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. Only one mutation (A406V) was observed in the RdRp of Indian SARS-CoV-2 isolate (Fig 3B). 2020 PloS one Result SARS_CoV_2 A406V 19 24 RdRP 46 50 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. RMSF plot clearly indicates the fluctuation in residues and showed the existence of higher degree of flexibility in R60C mutant Mpro. 2020 PloS one Result SARS_CoV_2 R60C 116 120 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. RMSF values of native as well as R60C mutant Mpro were calculated to determine the impact of mutation on dynamic behavior of protein at residue level. 2020 PloS one Result SARS_CoV_2 R60C 33 37 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. The analysis of hydrogen bond network revealed that the R60C mutation also cause disturbance in the interactions with inhibitor as well as other surrounding active site residues of Mpro. 2020 PloS one Result SARS_CoV_2 R60C 56 60 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. The analysis of Mpro reveals that there was only one point mutation (R60C) in the Vietnam strain of SARS-CoV-2 (Fig 3A). 2020 PloS one Result SARS_CoV_2 R60C 69 73 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. The analysis of ORF3a showed 3 mutations within different SARS-CoV-2 strains: W128L (South Korea), L140V (Japan), G251V (Australia, South Korea, Brazil, Italy, Sweden) (Table 3). 2020 PloS one Result SARS_CoV_2 G251V;L140V;W128L 114;99;78 119;104;83 ORF3a 16 21 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. The greater value of SASA for R60C mutant (in complexed form) was supported by Rg plot. 2020 PloS one Result SARS_CoV_2 R60C 30 34 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. The R60C mutant shows slightly lower value for Rg as compared to its WT. 2020 PloS one Result SARS_CoV_2 R60C 4 8 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. The root mean square deviations of the backbone were calculated to analyze the trajectories of Mpro from SARS-CoV-2 and its R60C mutant. 2020 PloS one Result SARS_CoV_2 R60C 124 128 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. The value of DeltaDeltaG show that the mutant R408I (0.49732107 kcal/mol) mutation was having stabilization effect on spike protein. 2020 PloS one Result SARS_CoV_2 R408I 46 51 S 118 123 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. This suggests that R60C mutation affects the stability of Mpro. 2020 PloS one Result SARS_CoV_2 R60C 19 23 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. Furthermore, the evaluation of the antigenicity of spike protein predicted 14 highest scoring antigenic epitopes (antigenic scores >= 1.0) due to variations in each (at positions L54F, L54W, F55I, S71F, D111N, F157L, L293M, L293V, D294E, D294I, A419S, V367F, A348V, and A653V). 2020 Journal of laboratory physicians Result SARS_CoV_2 A348V;A348V;A419S;A419S;A653V;A653V;D111N;D111N;D294E;D294E;D294I;D294I;F157L;F157L;F55I;F55I;L293M;L293M;L293V;L293V;L54F;L54F;L54W;L54W;S71F;S71F;V367F;V367F 260;259;246;245;271;270;204;203;232;231;239;238;211;210;192;191;218;217;225;224;180;179;186;185;198;197;253;252 264;264;250;250;275;275;208;208;236;236;243;243;215;215;195;195;222;222;229;229;183;183;189;189;201;201;257;257 S 51 56 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. In addition to several single mutations in the S gene of all available genomes, we also predicted double mutations such as 22436G>T, 22439C>G, 22444C>A, 22445C>T (corresponding to four amino acid antigenic drift ALDP -> SVES at position 292-295) and 21723T>G (L54W); 21726T>A (F55I) in two different genomes from the United States. 2020 Journal of laboratory physicians Result SARS_CoV_2 T21723G;T21726A;G22436T;C22439G;C22444A;C22445T;F55I;L54W 250;267;123;133;143;153;277;260 258;275;131;141;151;161;281;264 S 47 48 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. Other speculated mutations in the putative epitopes lying within RBD showing less antigenicity were T323I, A344S, R408I, G476S, V483A, H519Q, A520S, A522S, and K529E out of which T323I, A344S, A522S, and K529E are also novel. 2020 Journal of laboratory physicians Result SARS_CoV_2 A344S;A344S;A520S;A522S;A522S;G476S;H519Q;K529E;K529E;R408I;T323I;T323I;V483A 107;186;142;149;193;121;135;160;204;114;100;179;128 112;191;147;154;198;126;140;165;209;119;105;184;133 RBD 65 68 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. Out of these, amino acid changes were noted at positions A348V, V367F and A419S in the RBD with V367F and A419S being novel. 2020 Journal of laboratory physicians Result SARS_CoV_2 A348V;A419S;A419S;V367F;V367F 57;74;106;64;96 62;79;111;69;101 RBD 87 90 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. The most predominant SNP predicted in the gene encoding S protein was 23402A>G in 48.2% of overall genomes under study. 2020 Journal of laboratory physicians Result SARS_CoV_2 A23402G 70 81 S 56 57 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. Two mutations A930V and D936Y were observed in the heptad repeat domain 1 (HR1) and one mutation D1168H in heptad repeat domain 2 (HR2). 2020 Journal of laboratory physicians Result SARS_CoV_2 A930V;D1168H;D936Y 14;97;24 19;103;29 32895623 Crystal structure of SARS-CoV-2 papain-like protease. For example, several crystal structures of SARS-CoV-2 PLpro C111S mutant complexed by various non-covalent inhibitors have been recently deposited in Protein Data Bank (PDB ID: 7JIT, 7JIR and 7JIV), which support our assertion. 2021 Acta pharmaceutica Sinica. B Result SARS_CoV_2 C111S 60 65 32895623 Crystal structure of SARS-CoV-2 papain-like protease. In the absence of ligand, only the C-terminal His-tagged PLpro C111S mutant yielded measurable crystals. 2021 Acta pharmaceutica Sinica. B Result SARS_CoV_2 C111S 63 68 32895623 Crystal structure of SARS-CoV-2 papain-like protease. The catalytically null mutant C111S served as the negative control. 2021 Acta pharmaceutica Sinica. B Result SARS_CoV_2 C111S 30 35 32895623 Crystal structure of SARS-CoV-2 papain-like protease. The unique packing interaction, large solvent space and reasonable resolution (2.5 A) of the current crystal form offer several advantages for fragment-based screening using crystallographic approach: (1) Although the active site cysteine mutation C111S of this crystal form prevents the screening of cysteine reactive inhibitor/fragment, it is still useful for identifying non-covalent inhibitor targeting substrate binding pockets S1-S4 and allosteric sites. 2021 Acta pharmaceutica Sinica. B Result SARS_CoV_2 C111S 248 253 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. 8 ), and there were 5 variable sites with non-synonymous substitutions frequency over 20, including a trinucleotide substitution which led to two consecutive aa substitutions of R203K and G204R (Table 2). 2020 Sustainable cities and society Result SARS_CoV_2 G204R;R203K 188;178 193;183 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. Since the 541th aa is one of the known key sites of NSP13 for binding to nucleic acids in SARS-CoV, the non-synonymous substitution hotspot of ORF1ab-Y5865C (NSP13-Y541C) in NSP13 probably affects the function of NSP13. 2020 Sustainable cities and society Result SARS_CoV_2 Y541C;Y5865C 164;150 169;156 ORF1ab;Nsp13;Nsp13;Nsp13;Nsp13 143;52;158;174;213 149;57;163;179;218 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. The 675th aa on S protein was the seventh amino acid upstream of RRAR, and we found S-Q675H and S-Q675R made original polar amino acids from no-charged to positively charged. 2020 Sustainable cities and society Result SARS_CoV_2 Q675H;Q675R 86;98 91;103 S;S;S 16;84;96 17;85;97 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. The two main types were the reference type (2561 strains) and the mutant type of N-R203K_G204R (494 strains). 2020 Sustainable cities and society Result SARS_CoV_2 G204R;R203K 89;83 94;88 N 81 82 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. There were 7 mutant strains with S-G2025C (S-Q675H) and one with S-A2024G (S-Q675R) among 3,239 sequenced strains. 2020 Sustainable cities and society Result SARS_CoV_2 A2024G;G2025C;Q675H;Q675R 67;35;45;77 73;41;50;82 S;S;S;S 33;43;65;75 34;44;66;76 32905045 Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. A total of 14/24 (58.3%) patients deemed to be COVID-19+ by the reference composite standard were positive by both rapid NAAT and antibody testing, and 14/14 were infected with strains bearing D614G, indicating that POC serological tests were able to detect infections with this variant. 2020 Cell reports. Medicine Result SARS_CoV_2 D614G 193 198 COVID-19 47 55 32905045 Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. Those with positive NAAT and sequence available were predominantly infected with strains containing the D614G mutation in Spike, downstream of the receptor-binding domain and located on the Spike surface (Figures 3A and 3B). 2020 Cell reports. Medicine Result SARS_CoV_2 D614G 104 109 S;S 122;190 127;195 32905045 Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. To understand the relationship between POC band intensity and neutralization activity further, we identified 3 participants (all infected with D614G Spike mutant) with stored samples at multiple time points in their illness (Figure 4). 2020 Cell reports. Medicine Result SARS_CoV_2 D614G 143 148 S 149 154 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. 1e), indicating that the D614G mutation does not affect viral replication or virion infectivity on Vero E6 cells. 2020 bioRxiv Result SARS_CoV_2 D614G 25 30 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. 1f), indicating that D614G enhances viral replication. 2020 bioRxiv Result SARS_CoV_2 D614G 21 26 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. 1h), indicating that the D614G mutation increases the infectivity of SARS-CoV-2 produced from the human lung cell line. 2020 bioRxiv Result SARS_CoV_2 D614G 25 30 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. 5), suggesting that mutation D614G may confer higher susceptibility to serum neutralization. 2020 bioRxiv Result SARS_CoV_2 D614G 29 34 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. An important question is whether substitution D614G could reduce vaccine efficacy, assuming G614 virus continues to circulate. 2020 bioRxiv Result SARS_CoV_2 D614G 46 51 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Collectively, the results demonstrate that substitution D614G enhances viral replication through increased virion infectivity when SARS-CoV-2 replicates on primary human upper airway tissues. 2020 bioRxiv Result SARS_CoV_2 D614G 56 61 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Dramatic enhancement of viral replication by spike mutation D614G in a primary human airway tissue model. 2020 bioRxiv Result SARS_CoV_2 D614G 60 65 S 45 50 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Effect of spike mutation D614G on neutralization susceptibility. 2020 bioRxiv Result SARS_CoV_2 D614G 25 30 S 10 15 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Enhancement of viral replication and infectivity by the spike D614G substitution in human lung epithelial cells. 2020 bioRxiv Result SARS_CoV_2 D614G 62 67 S 56 61 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Increased fitness in the hamster upper airway of SARS-CoV-2 with the D614G substitution. 2020 bioRxiv Result SARS_CoV_2 D614G 69 74 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Nevertheless, the results suggest that mutation D614G may enhance the infectivity of SARS-CoV-2 in the respiratory tract, particularly in the upper airway of infected animals. 2020 bioRxiv Result SARS_CoV_2 D614G 48 53 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Overall, the results demonstrate that the D614G mutation leads to a higher infectious virus production and shedding in the upper airway of infected hamsters. 2020 bioRxiv Result SARS_CoV_2 D614G 42 47 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. The in vivo relevance of the S-D614G mutation was evaluated in the golden Syrian hamster model (Extended Data. 2020 bioRxiv Result SARS_CoV_2 D614G 31 36 S 29 30 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. The results suggest that mutation D614G may modulate spike protein conformation to affect mAb neutralization in an epitope-specific manner. 2020 bioRxiv Result SARS_CoV_2 D614G 34 39 S 53 58 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. These results suggest that (i) more spike protein is cleaved to S1/S2 within virions produced from Calu-3 cells than those produced from Vero E6 cells and (ii) the D614G substitution does not significantly affect the spike cleavage ratio. 2020 bioRxiv Result SARS_CoV_2 D614G 164 169 S;S 36;217 41;222 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. To further define the function of D614G mutation in human respiratory tract, we characterized the replication of D614 and G614 viruses in a primary human airway tissue model. 2020 bioRxiv Result SARS_CoV_2 D614G 34 39 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. To further examine the role of D614G mutation in antibody recognition and neutralization, we evaluated a panel of eleven human receptor-binding domain (RBD) mAbs against the D614 and G614 mNeonGreen SARS-CoV-2 viruses. 2020 bioRxiv Result SARS_CoV_2 D614G 31 36 RBD 152 155 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. We first examined the effect of the spike D614G substitution on viral replication in cell culture. 2020 bioRxiv Result SARS_CoV_2 D614G 42 47 S 36 41 32933378 Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach. For these reasons, studies should be addressed in order to reveal the impact of P323L mutation on Nsp12-drug interactions and Nsp12/Nsp8 complex formation. 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 P323L 80 85 Nsp12;Nsp12;Nsp8 98;126;132 103;131;136 32933378 Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach. Mutation of P323L on Nsp12 was found near to the interaction interface where Nsp8 protein binds and residues between 100 and 124 of Nsp8 forms an alpha-helix-loop-alpha-helix structure in the interaction site (Figure 2). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 P323L 12 17 Nsp12;Nsp8;Nsp8 21;77;132 26;81;136 32933378 Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach. Only C14408T variations caused amino acid exchange (P323L) on Nsp12 of SARS-CoV-2, shown in Figure 1. 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 C14408T;P323L 5;52 12;57 Nsp12 62 67 32933378 Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach. Previous studies on SARS-CoV Nsp12/Nsp8 complexes showed that mutations of D99A, P116A, P183A, R190A in Nsp8 caused a decrease in primer extension and de novo polymerase activities (Subissi et al.,). 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 D99A;P116A;P183A;R190A 75;81;88;95 79;86;93;100 Nsp12;Nsp8;Nsp8 29;35;104 34;39;108 32933378 Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach. The mutation in the Nsp12 protein converted Proline-323 to Leucine, and this mutation was located inside the hydrophobic cavity in the ligand-binding region. 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 P323L 44 66 Nsp12 20 25 32933378 Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach. Therefore, the Nsp12-Nsp8 interaction cleft where the P323L mutation was found is a significant region for docking of drugs which aim to dissect the Nsp12-Nsp8 interaction. 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 P323L 54 59 Nsp12;Nsp12;Nsp8;Nsp8 15;149;21;155 20;154;25;159 32933378 Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach. Three variations were found on the gene sequence encoding Nsp12: C14408T (first reported by Pachetti et al.,), C14805T and C15324T. 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 C14408T;C14805T;C15324T 65;111;123 72;118;130 Nsp12 58 63 32933378 Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach. Two ligands which have the lowest binding energy in both proteins were selected from the library and docked to wild and mutant (P323L) forms of Nsp12 protein. 2022 Journal of biomolecular structure & dynamics Result SARS_CoV_2 P323L 128 133 Nsp12 144 149 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. Mutation D614G in Spain. 2020 Zoological research Result SARS_CoV_2 D614G 9 14 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. Of note, the two French cases were identical and were one-step mutation derivatives of the basal B3a lineage (transition C25553T on top of B3a sequence motif; Figure 4), whereas the first Spanish genomes matched the root of this haplogroup (see below). 2020 Zoological research Result SARS_CoV_2 C25553T 121 128 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. Recent reports have discussed a potential link between amino-acid mutation D614G and SARS-CoV-2 infectivity, pointing to a higher advantage of mutation carriers in viral dispersion. 2020 Zoological research Result SARS_CoV_2 D614G 75 80 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. The A2a5c root haplotype (i.e., with substitution G29734C on top of A2a5 sequence motif; #H3: C241T-C3037T-C14408T-A20268G-A23403G-G29734C; Table 2) reached its highest incidence in Spain (n=44), and appeared only sporadically in other countries (e.g., Colombia, Chile, Portugal, UK). 2020 Zoological research Result SARS_CoV_2 C241T;G29734C;A20268G;A23403G;C14408T;C3037T;G29734C 94;50;115;123;107;100;131 99;57;122;130;114;106;138 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. The ancestral haplotype of B3a (#H1: C8782T-T9477A-C14805T-G25979T-T28144C-C28657T-C28863T; Table 2) occurred 113 times in Spain (first introduction on 27 March), 75 of which occurred in the Basque Country. 2020 Zoological research Result SARS_CoV_2 C8782T;C14805T;C28657T;C28863T;G25979T;T28144C;T9477A 37;51;75;83;59;67;44 43;58;82;90;66;74;50 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. The core haplotype of A2a10 (#H4: C241T-C3037T-C14408T-A23403G-C29144T; Table 2) was observed 16 times in Spain, eight times in Portugal, and one time in Chile. 2020 Zoological research Result SARS_CoV_2 C241T;A23403G;C14408T;C29144T;C3037T 34;55;47;63;40 39;62;54;70;46 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. The first Italian A2a5 genome corresponding to the root haplotype (#H2: C241T-C3037T-C14408T-A20268G-A23403G; Table 2) appeared on 26 February. 2020 Zoological research Result SARS_CoV_2 C241T;A20268G;A23403G;C14408T;C3037T 72;93;101;85;78 77;100;108;92;84 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. The most frequent haplogroups in Spain were A2a5 (n=354; 38.4% of Spanish haplotypes; diagnostic variants: C241T-C3037T-C14408T-A20268G-A23403G), A2a4 (n=72; 7.8%; diagnostic variants: C241T-C3037T-C14408T-A23403G plus characteristic MNP: GGG28881AAC), A2a10 (n=26; 2.8%; diagnostic variants: C241T-C3037T-C14408T-A23403G-C29144T), B3a (n=278; 30.2%; diagnostic variants: C8782T-T9477A-C14805T-G25979T-T28144C-C28657T-C28863T), and B9 (n=80; 8.7%; diagnostic variants: C8782T-C26088T-T28144C); together, these haplogroups made up 87.9% of the whole database (n=810). 2020 Zoological research Result SARS_CoV_2 C241T;C241T;C241T;C8782T;C8782T;G28881A;G28881C;A20268G;A23403G;A23403G;A23403G;C14408T;C14408T;C14408T;C14805T;C26088T;C28657T;C28863T;C29144T;C3037T;C3037T;C3037T;G25979T;T28144C;T28144C;T9477A 107;185;293;372;469;239;239;128;136;206;314;120;198;306;386;476;410;418;322;113;191;299;394;402;484;379 112;190;298;378;475;250;250;135;143;213;321;127;205;313;393;483;417;425;329;119;197;305;401;409;491;385 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. The nucleotide change leading to the amino-acid mutation D614G is a diagnostic variant of haplogroup A2, namely, A23403T. 2020 Zoological research Result SARS_CoV_2 A23403T;D614G 113;57 120;62 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. The root haplotype of B9 (#H5: C8782T-C26088T-T28144C; Table 2) appeared in the Spanish database 14 times (first in Madrid) and nine times in other locations abroad (e.g., 23 February in Australia, and 10 and 13 March in Mexico). 2020 Zoological research Result SARS_CoV_2 C8782T;C26088T;T28144C 31;38;46 37;45;53 32937868 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. However, the FUBAR test showed that four sites (L3606F and G392D on ORF1ab, D936Y on S protein, T205I on N protein) were under episodic positive/diversifying selection with posterior probability >= 0.95 and log BF >= 25. 2020 Viruses Result SARS_CoV_2 D936Y;G392D;T205I;L3606F 76;59;96;48 81;64;101;54 ORF1ab;N;S 68;105;85 74;106;86 32937868 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. Mutations C241T, C3037T, C14408T, and A23403G (MP4) provided the basis for the other MPs patterns; meanwhile, mutations G28881A, G28882A, and G28883C appeared together. 2020 Viruses Result SARS_CoV_2 A23403G;C14408T;C241T;C3037T;G28881A;G28882A;G28883C 38;25;10;17;120;129;142 45;32;15;23;127;136;149 32937868 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. The basis, together with mutations C1059T, G24368T, and G25563T, constituted MP6. 2020 Viruses Result SARS_CoV_2 C1059T;G24368T;G25563T 35;43;56 41;50;63 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. 5D), although the E191D mutant appeared to be somewhat more sensitive to the mutagenic agent, yielding ~1-log-lower progeny titers than wt virus upon treatment with 5-FU concentrations between 100 and 400 muM. 2020 Journal of virology Result SARS_CoV_2 E191D 18 23 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. 8), which was much more viable than the H229C mutant in the context of our reverse genetics studies. 2020 Journal of virology Result SARS_CoV_2 H229C 40 45 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. A clearly different result was again obtained with the E191D mutant, which displayed an activity level comparable to that of wt nsp14, corresponding to the properties of the corresponding virus mutant. 2020 Journal of virology Result SARS_CoV_2 E191D 55 60 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Again, MERS-CoV-specific genomic and subgenomic RNA synthesis was detected only for the E191D mutant and the wt virus control (data not shown). 2020 Journal of virology Result SARS_CoV_2 E191D 88 93 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Among our MERS-CoV ExoN active-site mutants, only the E191D mutant yielded viable progeny. 2020 Journal of virology Result SARS_CoV_2 E191D 54 59 Exon 19 23 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Analyzing the substrate degradation pattern of the H229C mutant. 2020 Journal of virology Result SARS_CoV_2 H229C 51 56 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Characterization of rMERS-CoV-nsp14-E191D replication kinetics and 5-FU sensitivity. 2020 Journal of virology Result SARS_CoV_2 E191D 36 41 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. ExoN activity of MERS-CoV active-site and H229C mutants. 2020 Journal of virology Result SARS_CoV_2 H229C 42 47 Exon 0 4 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Four independently engineered and fully sequenced SARS-CoV-2 BAC clones were used to transcribe full-length RNA carrying the D90A/E92A double mutation in ExoN motif I, which has been used in many studies with MHV and SARS-CoV ExoN knockout mutants. 2020 Journal of virology Result SARS_CoV_2 D90A;E92A 125;130 129;134 Exon;Exon 154;226 158;230 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Full-length genome sequencing of passage 2 of the E191D mutant virus revealed that it had acquired two additional mutations compared with the recombinant wt control: a synonymous mutation in the nsp2-coding region (U to C at nucleotide [nt] position 2315) and a nonsynonymous mutation (C to A at position 6541), corresponding to an A1235D substitution in the betacoronavirus-specific marker (betaSM) domain of nsp3, which has been predicted to be a nonenzymatic domain and is absent in alpha- and deltacoronaviruses. 2020 Journal of virology Result SARS_CoV_2 A1235D;E191D;C6541A 332;50;286 338;55;309 Nsp2;Nsp3 195;410 199;414 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. However, a similar reduction of ExoN activity was observed for the E191D mutant. 2020 Journal of virology Result SARS_CoV_2 E191D 67 72 Exon 32 36 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. However, it did not result in the recovery of infectious progeny for any of six nonviable mutants tested (D90E, E191A, D273A, H268A, DM, and C210H mutants), unless (as was occasionally observed) reversion had first occurred, as confirmed by reverse transcription-PCR (RT-PCR) amplification and sequencing of the nsp14-coding region. 2020 Journal of virology Result SARS_CoV_2 C210H;D273A;E191A;H268A;D90E 141;119;112;126;106 146;124;117;131;110 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. In combination with the fact that the other ZF mutations (C210H in ZF1 and C261A and H264R in ZF2) abolished MERS-CoV replication, our study establishes the importance of both ExoN ZF motifs for MERS-CoV viability. 2020 Journal of virology Result SARS_CoV_2 C261A;H264R;C210H 75;85;58 80;90;63 Exon 176 180 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. In conclusion, with the exception of E191D (see below), all our engineered ExoN active-site mutations abrogated detectable viral RNA synthesis, suggesting that in the case of MERS-CoV:and likely also SARS-CoV-2:the enzyme is indispensable for basic productive replication in cell culture. 2020 Journal of virology Result SARS_CoV_2 E191D 37 42 Exon 75 79 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. including the D90A/E92A motif I double mutant (DM), which was frequently used as a prototypic viable ExoN knockout mutant in MHV and SARS-CoV studies. 2020 Journal of virology Result SARS_CoV_2 D90A;E92A 14;19 18;23 Exon 101 105 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Interestingly, the E191D mutation transforms the DEEDh catalytic motif into the DEDDh motif, which is characteristic of members of the exonuclease family to which the CoV ExoN belongs. 2020 Journal of virology Result SARS_CoV_2 E191D 19 24 Exonuclease;Exon 135;171 146;175 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Introduction of the D90A/E92A motif I double substitution resulted in a major reduction of ExoN activity, although a certain level of residual activity was observed, in particular when large amounts of nsp14. 2020 Journal of virology Result SARS_CoV_2 D90A;E92A 20;25 24;29 Exon 91 95 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Moreover, nsp14 R310A and D331A mutants were used as negative controls in view of their predicted involvement in the binding of the triphosphate moiety of the RNA chain and the methyl donor (S-adenosylmethionine [SAM]), respectively. 2020 Journal of virology Result SARS_CoV_2 D331A;R310A 26;16 31;21 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. replacement with Ala of each of the five active-site residues resulted in a nearly complete loss of ExoN activity, with the D90A, E92A, and H268A substitutions appearing to be slightly less detrimental than E191A and D273A. 2020 Journal of virology Result SARS_CoV_2 D273A;D90A;E191A;E92A;H268A 217;124;207;130;140 222;128;212;134;145 Exon 100 104 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. RNA accumulation was evaluated at 1 and 2 dpt for seven selected ExoN active-site mutants (D90A, D90E, E191A, E191D, D273A, and H268A mutants and DM) using samples from two independent experiments both comprising duplicate transfections for each mutant. 2020 Journal of virology Result SARS_CoV_2 D273A;D90E;E191A;E191D;H268A;D90A 117;97;103;110;128;91 122;101;108;115;133;95 Exon 65 69 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Similar dose-dependent reductions of plaque size were observed for E191D and wt virus, with E191D virus plaques being barely visible upon treatment with 200 muM 5-FU. 2020 Journal of virology Result SARS_CoV_2 E191D;E191D 67;92 72;97 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Still, the E191D mutant was found to be somewhat crippled, yielding smaller plaques and somewhat lower progeny titers in HuH7 cells. 2020 Journal of virology Result SARS_CoV_2 E191D 11 16 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Taken together, our observations indicate that the H229C mutant is viable but severely crippled. 2020 Journal of virology Result SARS_CoV_2 H229C 51 56 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Taken together, these experiments demonstrated that overall replication of the E191D mutant is only mildly affected and that it is somewhat more sensitive to 5-FU treatment than wt MERS-CoV. 2020 Journal of virology Result SARS_CoV_2 E191D 79 84 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. The four ZF virus mutants were launched as described above, after which a low level of replication could be observed only for the H229C ZF1 mutant. 2020 Journal of virology Result SARS_CoV_2 H229C 130 135 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. The H229C mutation clearly reduced ExoN activity in vitro, potentially by affecting the structure of the ExoN domain, as ZF1 is in close proximity to the nsp10 interaction surface. 2020 Journal of virology Result SARS_CoV_2 H229C 4 9 Exon;Exon 35;105 39;109 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. The single exception was the mutant carrying the conservative E191D replacement in ExoN motif II. 2020 Journal of virology Result SARS_CoV_2 E191D 62 67 Exon 83 87 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. This suggests that the H229C replacement may affect additional functions or interactions of the ExoN domain that are important for viral RNA synthesis and viability. 2020 Journal of virology Result SARS_CoV_2 H229C 23 28 Exon 96 100 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Thus, we assumed that any changes in viral replication were likely caused by the E191D mutation in nsp14 ExoN. 2020 Journal of virology Result SARS_CoV_2 E191D 81 86 Exon 105 109 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. To characterize the E191D mutant in more detail, its replication and fitness in cell culture were analyzed. 2020 Journal of virology Result SARS_CoV_2 E191D 20 25 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Two residues of the nonclassical ZF2 motif were also substituted (C261A and H264R) to evaluate the ZF2 mutations previously analyzed by Ma et al., leading to disruption of ExoN activity in vitro. 2020 Journal of virology Result SARS_CoV_2 H264R;C261A 76;66 81;71 Exon 172 176 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Upon direct in-gel hybridization analysis using a 32P-labeled probe recognizing the 3' end of all viral mRNAs, the characteristic nested set of MERS-CoV transcripts could be detected only for the E191D mutant and the wt control. 2020 Journal of virology Result SARS_CoV_2 E191D 196 201 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. We also evaluated the impact of the H229C ZF1 mutation, which:despite its conservative nature:yielded a crippled mutant virus. 2020 Journal of virology Result SARS_CoV_2 H229C 36 41 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. We employed the same assay to assess the phenotype of the E191D mutant in more detail, by performing plaque assays in HuH7 cells in the presence of increasing 5-FU concentrations. 2020 Journal of virology Result SARS_CoV_2 E191D 58 63 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. We next examined the sensitivity of E191D and wt virus to the mutagenic agent 5-FU, which is converted intracellularly into a nucleoside analogue that is incorporated into viral RNA. 2020 Journal of virology Result SARS_CoV_2 E191D 36 41 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. When cell cultures (BHK-21 mixed with Vero or HuH7 cells) were analyzed by immunofluorescence microscopy at 2 days posttransfection (dpt), using antibodies recognizing dsRNA and nsp4, abundant signal and virus spread were always observed for wild-type MERS-CoV and the E191D mutant. 2020 Journal of virology Result SARS_CoV_2 E191D 269 274 Nsp4 178 182 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. While the R310A and D331A control mutations fully inactivated the N7-MTase activity of MERS-CoV nsp14, none of the ExoN active-site mutations tested was found to alter the enzyme's activity. 2020 Journal of virology Result SARS_CoV_2 D331A;R310A 20;10 25;15 Exon 115 119 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Wild-type SARS-CoV and its corresponding (viable) ExoN knockout mutant (D90A/E92A; DM) were used as positive controls in these experiments. 2020 Journal of virology Result SARS_CoV_2 D90A;E92A 72;77 76;81 Exon 50 54 32941419 Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization. Both subtypes, CCCGCCAGGGA and TCCGCCAGTGG, have an A23403G mutation (corresponding to position 14 in the ISM) which has been discussed in recent studies. 2020 PLoS computational biology Result SARS_CoV_2 A23403G 52 59 32941419 Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization. Indeed, Fig 10 illustrates how, in late February, A23403G started to take off in abundance and has quickly overwhelmed the initially more prevalent subtype. 2020 PLoS computational biology Result SARS_CoV_2 A23403G 50 57 32941419 Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization. Lastly, the studies also reported a SNV of G26144T, which corresponds to ISM site 16 and has been observed in the predominant subtypes found in Europe and New York. 2020 PLoS computational biology Result SARS_CoV_2 G26144T 43 50 32941419 Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization. Some studies suggest that this D614G variant of the S spike protein provides greater survival and transmission ability to the virus, however there need to be additional studies conducted to confirm these claims. 2020 PLoS computational biology Result SARS_CoV_2 D614G 31 36 S;S 54;52 59;53 32941419 Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization. Subtypes including the A23403G/D614G spike protein variant. 2020 PLoS computational biology Result SARS_CoV_2 A23403G;D614G 23;31 30;36 S 37 42 32941419 Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization. The SNV A23403G (resulting in D614G variant in spike protein) is a major viral mutation that has been observed in the major European countries of Italy, Spain, France, as well as Middle Eastern regions of Turkey and Israel. 2020 PLoS computational biology Result SARS_CoV_2 A23403G;D614G 8;30 15;35 S 47 52 32941419 Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization. These SNVs include C8782T and T28144C and correspond to hotspot sites 6 and 17 respectively. 2020 PLoS computational biology Result SARS_CoV_2 C8782T;T28144C 19;30 25;37 32941419 Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization. These studies also identified a SNV of A23403G in the S spike protein to be heavily associated with the dominant subtype of both Europe and New York, correlating to ISM hotspot site 14 from our analysis. 2020 PLoS computational biology Result SARS_CoV_2 A23403G 39 46 S;S 56;54 61;55 32941419 Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization. Various studies have demonstrated the SNV C14408T in ORF1b to be associated with a virus subtype found abundantly in New York as well as multiple European countries, which is designated as an ISM hotspot site 8 in Table 1. 2020 PLoS computational biology Result SARS_CoV_2 C14408T 42 49 32941419 Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization. WA1 lineage is noted to have three characteristic SNVs, namely, C17747T, A17858G, and C18060T which correspond matches with our ISM positions of 10, 11 and 12 respectively. 2020 PLoS computational biology Result SARS_CoV_2 A17858G;C17747T;C18060T 74;65;87 80;71;93 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. Amino acid substitutions, R191C, R209I and G238C were found in 4.65% (2/43), 4.65% (2/43) and 6.97% (3/43) of the Colombian sequences, respectively (Table 1). 2020 Infection, genetics and evolution Result SARS_CoV_2 G238C;R191C;R209I 43;26;33 48;31;38 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. Furthermore, substitutions G181V and D936Y were found at low frequencies of 2.3% (1/43) and 2.3% (1/43) respectively (Table 1). 2020 Infection, genetics and evolution Result SARS_CoV_2 D936Y;G181V 37;27 42;32 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. In the N protein, five amino acid substitutions were found; the most frequent being R203K and G204R in 13.95% (6/43) of the sequences. 2020 Infection, genetics and evolution Result SARS_CoV_2 G204R;R203K 94;84 99;89 N 7 8 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. Non-synonymous substitutions R203K and G204R, which are the hallmarks of the B.1.1 lineage, were the most frequent in the N protein of South American sequences. 2020 Infection, genetics and evolution Result SARS_CoV_2 G204R;R203K 39;29 44;34 N 122 123 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. The analysis of substitution frequencies by country shows that D614G substitution in the S protein was frequent in Argentina, Brazil, Chile, Colombia and Peru, with 80-100% of the reported sequences. 2020 Infection, genetics and evolution Result SARS_CoV_2 D614G 63 68 S 89 90 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. The most frequent in S were D614G (83%) V1176F (2.2%) and P1263L (1.5%), while the most frequent in N were R203K (34.5%), G204R (34.3%), I292T (15.8%) and S197L (3.3%). 2020 Infection, genetics and evolution Result SARS_CoV_2 D614G;G204R;I292T;P1263L;R203K;S197L;V1176F 28;122;137;58;107;155;40 33;127;142;64;112;160;46 N;S 100;21 101;22 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. The spatiotemporal distribution pattern of this substitution was similar to that of R203K and G204R, increasing from March to April in Chile, Argentina and Brazil in contrast to Colombia and Uruguay where this substitution was almost absent in genomes registered on April. 2020 Infection, genetics and evolution Result SARS_CoV_2 G204R;R203K 94;84 99;89 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. The substitution I292T in the N protein was rare in Argentina (10.7%), Chile (4.6%) and Uruguay (2.2%); and absent in Colombia, Peru and Ecuador. 2020 Infection, genetics and evolution Result SARS_CoV_2 I292T 17 22 N 30 31 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. These included G181V and D936Y in S, and R191C and G238C in N, as observed in the Colombian genomes. 2020 Infection, genetics and evolution Result SARS_CoV_2 D936Y;G181V;G238C;R191C 25;15;51;41 30;20;56;46 N;S 60;34 61;35 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. Three amino acid substitutions were observed in the S protein, D614G was present in 81% (35/43) of the sequences. 2020 Infection, genetics and evolution Result SARS_CoV_2 D614G 63 68 S 52 53 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. (2020) reported two non-synonymous mutations (R203K and L3606F) that were shared across ORFs of the SARS-CoV-2 genomes of six continents, and recurrent mutations were also common in different countries along with unique mutations. 2021 Transboundary and emerging diseases Result SARS_CoV_2 L3606F;R203K 56;46 62;51 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A strain from Bosnia_and_Herzegovina (EPI_ISL_463893) had the highest number of aa changes/substitutions (n = 6) at six positions (R246I, L276I, T430A, D614G, S750N, L922V) of S protein. 2021 Transboundary and emerging diseases Result SARS_CoV_2 D614G;L276I;L922V;S750N;T430A;R246I 152;138;166;159;145;131 157;143;171;164;150;136 S 176 177 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. All these mutations were found between March and April at a lower frequency (N439K with maximum frequency in 41 Scottish strains and one Romanian strain), except Q493L found in two USA strains reported in May. 2021 Transboundary and emerging diseases Result SARS_CoV_2 Q493L;N439K 162;77 167;82 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Among these replacements, aa residues at position 5 (L5F) and 614 (D614G) were found to be the common in Asia, Europe, North America, South America, Africa and Australia (Figure 5b). 2021 Transboundary and emerging diseases Result SARS_CoV_2 D614G;L5F 67;53 72;56 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Furthermore, a total of 50 aa substitutions within the S protein were observed that incorporated asparagine (N) in S protein of SARS-CoV-2 including seven within the RBD region (S359N, K378N, K417N, K458N, S477N, T523N and K529N) (Data S2). 2021 Transboundary and emerging diseases Result SARS_CoV_2 K378N;K417N;K458N;K529N;S477N;T523N;S359N 185;192;199;223;206;213;178 190;197;204;228;211;218;183 RBD;S;S 166;55;115 169;56;116 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Moreover, eight glycosylated sites of S protein underwent aa conversions including three substitutions in the NTD region (N17K, N74K and N149H), five substitutions at four sites in the S1 region (N17K, N74K, N149H, N603S and N603K) and four mutations in the S2 region (N717T, N1074D, N1158S and N1194S) (Watanabe et al., 2020). 2021 Transboundary and emerging diseases Result SARS_CoV_2 N1074D;N1158S;N1194S;N149H;N149H;N603K;N603S;N74K;N74K;N17K;N17K;N717T 276;284;295;137;208;225;215;128;202;122;196;269 282;290;301;142;213;230;220;132;206;126;200;274 S 38 39 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Moreover, in the furin cleavage site (R685 and S686), we also observed a non-synonymous mutation (S686G) in a single strain (Russia/Krasnodar-63401/2020 EPI_ISL_428867 2020-03-11) (Data S2). 2021 Transboundary and emerging diseases Result SARS_CoV_2 S686G 98 103 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Notably, position 614 showed two variants, substitution D614G (Aspartic acid Glycine) found in 74.82% (n = 26,749) of the cleaned sequences ( 96.22% of the mutated sequences), and another variant D614N (Aspartic acid Asparagine) was observed only in four strains from England and Wales (EPI_ISL_439400, EPI_ISL_443658 and EPI_ISL_445498, EPI_ISL_472913). 2021 Transboundary and emerging diseases Result SARS_CoV_2 D614G;D614N 56;199 61;204 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Our analysis showed that only two core aa substitutions at positions 614 (D614G) and 936 (D936Y) were shared across all the climatic zones (Figure 5c). 2021 Transboundary and emerging diseases Result SARS_CoV_2 D614G;D936Y 74;90 79;95 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q493R position showed variation in an English strain (EPI_ISL_470150) found in April. 2021 Transboundary and emerging diseases Result SARS_CoV_2 Q493R 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. The variant D614G in the S protein has overcome the wild-type variant from China since its first appearance in Germany on 28 January 2020 (Comandatore et al., 2020; Eaaswarkhanth et al., 2020; Kim et al., 2020; Korber et al., 2020; Trucchi et al., 2020). 2021 Transboundary and emerging diseases Result SARS_CoV_2 D614G 12 17 S 25 26 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. We also found aa substitutions at six positions within the RBD region that are directly involved in binding with ACE-2 receptor (Wang et al., 2020; Yuan et al., 2020) including N439K (Scotland, Romania), L455F (England), A475V (USA, Australia), and F456L, Q493L and N501Y (USA) (Data S2). 2021 Transboundary and emerging diseases Result SARS_CoV_2 A475V;F456L;L455F;N439K;N501Y;Q493L 221;249;204;177;266;256 226;254;209;182;271;261 RBD 59 62 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. We found mutations in the variable regions between SARS-CoV-2 and RaTG13, and these recurrent mutations (S50L, T76I, A372T, N439K) are supposed to be converted to RaTG13 from SARS-CoV-2 (Table S1). 2021 Transboundary and emerging diseases Result SARS_CoV_2 A372T;N439K;T76I;S50L 117;124;111;105 122;129;115;109 32967693 A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual. Alignment analyses showed that, with respect to the Wuhan-Hu-1 Reference Genome NC_045512.2, SARS-CoV-UNIBS-2 AP66 consensus sequence displayed 6 nucleotide substitutions (C241T; C3037T; C14408T; T21784G; C21846T; A23403G) leading to 4 non-synonymous changes (ORF1ab polypeptide: P4715L; S protein: N74K, T95I, D614G). 2020 Journal of translational medicine Result SARS_CoV_2 A23403G;C14408T;C21846T;C3037T;D614G;N74K;P4715L;T21784G;T95I;C241T 214;187;205;179;311;299;280;196;305;172 221;194;212;185;316;303;286;203;309;177 ORF1ab;S 260;288 266;289 32967693 A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual. Interestingly, SARS-CoV2-UNIBS-GZ69 consensus differed from the early SARS-CoV-2-UNIBS-AP66 variant in 9 positions (C2939T; C3828T; G21784T; T21846C; T24631C; G28881A; G28882A; G28883C; G29810T) and these genetic variations have led to 4 non-synonymous substitutions in the ORF1ab (P892S, S1188L), in the S protein (K74N, I95T) and in the N protein (R203K, G204R). 2020 Journal of translational medicine Result SARS_CoV_2 C3828T;G204R;G21784T;G28881A;G28882A;G28883C;G29810T;I95T;S1188L;T21846C;T24631C;C2939T;K74N;P892S;R203K 124;357;132;159;168;177;186;322;289;141;150;116;316;282;350 130;362;139;166;175;184;193;326;295;148;157;122;320;287;355 ORF1ab;N;S 274;339;305 280;340;306 32967693 A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual. Less pathogenic GZ69 consensus sequence differed from Wuhan-Hu-1 isolate in 11 nucleotide positions (C241T; C2939T; C3037T; C3828T; C14408T; A23403G; T24631C; G28881A; G28882A; G28883C; G29810T) and 6 of them were non-synonymous (ORF1ab polypeptide: P892S, S1188L, P4715L; S protein D614G; N Protein: R203K, G204R). 2020 Journal of translational medicine Result SARS_CoV_2 A23403G;C14408T;C2939T;C3037T;C3828T;D614G;G204R;G28881A;G28882A;G28883C;G29810T;P4715L;P892S;R203K;S1188L;T24631C;C241T 141;132;108;116;124;283;308;159;168;177;186;265;250;301;257;150;101 148;139;114;122;130;288;313;166;175;184;193;271;255;306;263;157;106 ORF1ab;N;S 230;290;273 236;291;274 32967693 A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual. This mutation (P4715L), together with the D614G in the S protein, are recurrent mutations that have emerged in Europe starting from February 2020 as recently clearly described by Pachetti et al. 2020 Journal of translational medicine Result SARS_CoV_2 D614G;P4715L 42;15 47;21 S 55 56 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. Delayed chain termination is not observed with the S861G mutant. 2020 The Journal of biological chemistry Result SARS_CoV_2 S861G 51 56 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. However, it is important to note that the selectivity (Vmax/Km (ATP)/Vmax/Km (RDV-TP)) is almost identical for V557L and the WT enzyme. 2020 The Journal of biological chemistry Result SARS_CoV_2 V557L 111 116 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. However, the increase in efficiency of UTP usage with the V557L mutant does not translate in increases in the amount of the full-length product. 2020 The Journal of biological chemistry Result SARS_CoV_2 V557L 58 63 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. However, the structural reasons for V557L resistance remain elusive and a fuller dynamic examination or structural data may be required. 2020 The Journal of biological chemistry Result SARS_CoV_2 V557L 36 41 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. Incorporation of the next nucleotide (ATP) is not significantly affected by the V557L mutant enzyme. 2020 The Journal of biological chemistry Result SARS_CoV_2 V557L 80 85 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. Moreover, the S861G mutant specifically reduces delayed chain termination and does not affect template-dependent inhibition of RNA synthesis. 2020 The Journal of biological chemistry Result SARS_CoV_2 S861G 14 19 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. Moreover, V557L is also not significantly different from the WT in assays monitoring delayed chain termination with either single or multiple sites of incorporation for RDV-TP. 2020 The Journal of biological chemistry Result SARS_CoV_2 V557L 10 15 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. The collective data provide evidence to show that the effect of V557L is specific to RDV embedded in the template, which in turn suggests that this type of inhibition is biologically relevant. 2020 The Journal of biological chemistry Result SARS_CoV_2 V557L 64 69 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. The effect of F480L is subtle and structural data do not suggest a direct effect on RNA synthesis. 2020 The Journal of biological chemistry Result SARS_CoV_2 F480L 14 19 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. The effect of V557L is specific to incorporation of UTP opposite RDV. 2020 The Journal of biological chemistry Result SARS_CoV_2 V557L 14 19 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. The primary observation is that the UTP concentration required to overcome inhibition at position 10 and to generate the product at position 11 is lower with the Val-557 mutant (0.7 versus 4 mum for 50% incorporation and 10 versus 50 mum for 90% incorporation of UTP by V557L and WT, respectively). 2020 The Journal of biological chemistry Result SARS_CoV_2 V557L 270 275 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. The S861A mutation shows only subtle reductions in delayed chain termination. 2020 The Journal of biological chemistry Result SARS_CoV_2 S861A 4 9 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. The V557L mutation in nsp12 counteracts the inhibitory effects of RDV in the template. 2020 The Journal of biological chemistry Result SARS_CoV_2 V557L 4 9 Nsp12 22 27 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. Thus, V557L does not show a resistance phenotype at the level of incorporation of RDV-TP. 2020 The Journal of biological chemistry Result SARS_CoV_2 V557L 6 11 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. We compared RNA synthesis of the WT SARS-CoV-2 RdRp complex with S861G, S861A, and S861P mutants. 2020 The Journal of biological chemistry Result SARS_CoV_2 S861A;S861G;S861P 72;65;83 77;70;88 RdRP 47 51 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. We compared WT RdRp with the V557L mutant. 2020 The Journal of biological chemistry Result SARS_CoV_2 V557L 29 34 RdRP 15 19 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. We further show that the bulkier side chain of S861P shows subtle increases in UTP concentrations required to overcome delayed chain termination. 2020 The Journal of biological chemistry Result SARS_CoV_2 S861P 47 52 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. We therefore expressed and purified the V557L mutant and studied its potential effect on the concentration of UTP required to overcome the obstacle imposed by the complementary RDV. 2020 The Journal of biological chemistry Result SARS_CoV_2 V557L 40 45 32980406 Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13). According to the genome sequence data by 7 April 2020; there is no isolate harboring C17747T and A17858G mutations simultaneously in Asia, Africa and continental Europe yet (Supplement. 2020 International journal of biological macromolecules Result SARS_CoV_2 A17858G;C17747T 97;85 104;92 32980406 Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13). Accordingly, we have selected two mutations C17747T and A17858G on the gene sequences encoding helicase being present simultaneously in 11,6% of 3458 isolates (Supplement. 2020 International journal of biological macromolecules Result SARS_CoV_2 A17858G;C17747T 56;44 63;51 Helicase 95 103 32980406 Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13). Both P504L and Y541C mutations were in the 2A domain and caused a more hydrophobic 2A domain. 2020 International journal of biological macromolecules Result SARS_CoV_2 P504L;Y541C 5;15 10;20 32980406 Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13). Especially, Y541C mutation was very close to the ATP hydrolysis site and previous in silico study on SARS-CoV-2 helicase showed that the compounds interacted with nearby residues including D534, S535 and S539. 2020 International journal of biological macromolecules Result SARS_CoV_2 Y541C 12 17 Helicase 112 120 32980406 Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13). In this way, the difference in sites P504L and Y541C, where there are amino acid changes, can be analyzed with reference to the wild type. 2020 International journal of biological macromolecules Result SARS_CoV_2 P504L;Y541C 37;47 42;52 32980406 Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13). It was found that the sapropterin interacted within the ATP-binding site with Gln404 and the residues adjacent to the mutation site of Y541C (Gln537, Gly538, Glu540) (Supplement File 1. 2020 International journal of biological macromolecules Result SARS_CoV_2 Y541C 135 140 32980406 Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13). Residue 504 was substituted from proline (wild type) to leucine (mutant) in the mentioned mutation P504L and both residues are non-polar and aliphatic residues. 2020 International journal of biological macromolecules Result SARS_CoV_2 P504L 99 104 32980406 Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13). Two substitutions causing missense mutations (P504L and Y541C) in the region encoding Nsp13 in the SARS-CoV-2 genome is shown in. 2020 International journal of biological macromolecules Result SARS_CoV_2 Y541C;P504L 56;46 61;51 Nsp13 86 91 32989130 Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation. A Rare Mutation, D839Y/E, Recently Observed in a SARS2 Strain from Europe May Contribute to Stabilizing the Interaction with TCR. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 D839E;D839Y 17;17 24;24 32989130 Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation. Interestingly, the SARS-CoV-2 S binding region harbors three residues that have been recently reported to have mutated in new strains from Europe and the United States: D614G, A831V, and D839Y/N/E. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 A831V;D614G;D839E;D839N;D839Y 176;169;187;187;187 181;174;196;196;196 S 30 31 32989130 Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation. The interfacial interactions in the D839Y mutant are stabilized by a hydrogen bond between Y839 and D32, an aromatic (polar-pi) interaction between Y839 and N30, and possible electrostatic interactions with K73 and S97. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 D839Y 36 41 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. A23403G was first reported at the end of January 2020 in virus genomes from China and Germany. 2020 Cell Result SARS_CoV_2 A23403G 0 7 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Additionally, when HEK293 cells or SupT1 cells had been rendered infectable by stable expression of exogenous ACE2 and TMPRSS2, D614G was 9-fold more infectious than was D614 (Figure 2A). 2020 Cell Result SARS_CoV_2 D614G 128 133 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Although D614G is located outside of the receptor-binding domain, this non-conservative amino acid change might alter ACE2-binding properties via allosteric effects. 2020 Cell Result SARS_CoV_2 D614G 9 14 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. At 25 C, the rate of association with ACE2 was little different between D614G and D614, but D614G dissociated from ACE2 at a rate 4-fold faster than D614, resulting in a 5.7-fold reduction in binding affinity (Figure 4 ). 2020 Cell Result SARS_CoV_2 D614G;D614G 72;92 77;97 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. At 37 C, the association rate between D614G and ACE2 was slower than that between D614 and ACE2, and the dissociation rate of D614G was faster, again resulting in 5-fold reduction in binding affinity (Figure 4). 2020 Cell Result SARS_CoV_2 D614G;D614G 38;126 43;131 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Based on the resolved ensemble cryo-EM density map (Figure 6A) and the primary sequence (Figure 6C), an atomic model of D614G without the RBD was built (Figure 6D; PDB: 6XS6) and validated (Figure S1G, model-to-map FSC; Figure S1H, local resolution). 2020 Cell Result SARS_CoV_2 D614G 120 125 RBD 138 141 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Because the increased infectivity of D614G was not explained by increased affinity for ACE2 (Figure 4), cryo-electron microscopy (cryo-EM) was used to illuminate potential structural features that distinguish D614G from D614 (Table 1 ). 2020 Cell Result SARS_CoV_2 D614G;D614G 37;209 42;214 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Both S protein variants, D614 and D614G, were expressed in mammalian cells as soluble trimers. 2020 Cell Result SARS_CoV_2 D614G 34 39 S 5 6 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Comparing the map of D614G with that of D614, the N-terminal domain (NTD), the intermediary domain (INT), and the C-terminal domain (CTD) of the S1 subunit were clearly identified (Figure 6A and 6B). 2020 Cell Result SARS_CoV_2 D614G 21 26 N 50 51 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. D614G and the Ancestral S Protein Are Equally Sensitive to Neutralization by Monoclonal Antibodies Targeting the Receptor-Binding Domain. 2020 Cell Result SARS_CoV_2 D614G 0 5 S 24 25 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. D614G Changes the Conformation of the S1 Domain in the SARS-CoV-2 S Protein. 2020 Cell Result SARS_CoV_2 D614G 0 5 S 66 67 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. D614G Decreases the Affinity for ACE2 by Increasing the Rate of Dissociation. 2020 Cell Result SARS_CoV_2 D614G 0 5 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. D614G Does Not Alter S Protein Synthesis, Processing, and Incorporation into SARS-CoV-2 Particles. 2020 Cell Result SARS_CoV_2 D614G 0 5 S 21 22 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. D614G Increases Infectivity on Target Cells Bearing ACE2 Orthologs from Multiple Species. 2020 Cell Result SARS_CoV_2 D614G 0 5 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. D614G Shifts the Probability that SARS-CoV-2 S Protein Trimers Occupy Open Conformations. 2020 Cell Result SARS_CoV_2 D614G 0 5 S 45 46 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Each ACE2 transfectant was then challenged with luciferase reporter viruses bearing SARS-CoV-2 Spike protein, either D614 or D614G. 2020 Cell Result SARS_CoV_2 D614G 125 130 S 95 100 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Each of these monoclonal antibodies, whether tested individually or in various combinations, demonstrated similar neutralization potency against D614G as they did against D614 (Figure 5 ). 2020 Cell Result SARS_CoV_2 D614G 145 150 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. First, D614G disrupts the inter-protomer hydrogen bond with Thr859 (Figures 6H and 6I), weakening the stability of the trimer. 2020 Cell Result SARS_CoV_2 D614G 7 12 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Further classification of D614G homotrimers to determine the distribution of RBD conformations revealed four categories (Figure 7D). 2020 Cell Result SARS_CoV_2 D614G 26 31 RBD 77 80 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Given how few SARS-CoV-2 genomes have been sequenced from early in the outbreak, the geographic origin of A23403G cannot be determined. 2020 Cell Result SARS_CoV_2 A23403G 106 113 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. However, the density corresponding to the RBD, which was well resolved in D614 (arrows, Figure 6B), was scattered in the D614G map (Figure 6A), suggesting that its RBD is flexible and adopts multiple conformations (see section below). 2020 Cell Result SARS_CoV_2 D614G 121 126 RBD;RBD 42;164 45;167 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Human ACE2 was immobilized, and the binding of soluble, trimeric SARS-CoV-2 S protein, either D614 or D614G, was detected. 2020 Cell Result SARS_CoV_2 D614G 102 107 S 76 77 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. In effect, D614 acts as a "latch" that secures two protomers together, and D614G loosens this latch (Figures 6H and 6I). 2020 Cell Result SARS_CoV_2 D614G 75 80 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. In the structural model, the S2 subunit of D614G overlapped well with the published structures for D614 (root-mean-square deviation [RMSD] = 0.77 A). 2020 Cell Result SARS_CoV_2 D614G 43 48 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Mammalian expression plasmids were engineered to encode the ancestral S protein D614 or the D614G variant. 2020 Cell Result SARS_CoV_2 D614G 92 97 S 70 71 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Relative increase in infectivity due to D614G was comparable in cells expressing all of these ACE2 orthologs (Figure 2B), demonstrating that increased infectivity due to D614G is not specific for human ACE2. 2020 Cell Result SARS_CoV_2 D614G;D614G 40;170 45;175 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Sequences available over recent weeks, though, indicate that A23403G has nearly reached fixation globally (Figures 1A and 1B). 2020 Cell Result SARS_CoV_2 A23403G 61 68 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Surface plasmon resonance (SPR) was used to determine whether the kinetics of SARS-CoV-2 S protein binding to human ACE2 is changed by D614G. 2020 Cell Result SARS_CoV_2 D614G 135 140 S 89 90 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The ability of the D614G S protein variant to target virions for infection of ACE2-positive cells was assessed by using single-cycle lentiviral vector pseudotypes in tissue culture. 2020 Cell Result SARS_CoV_2 D614G 19 24 S 25 26 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The atomic model showed that D614G has two consequences. 2020 Cell Result SARS_CoV_2 D614G 29 34 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The closed conformation of D614G overlapped well with the closed conformation of D614, whereas the open conformation of D614G showed significant deviation of all S1 domains away from the S2 subunit when compared with the open conformation of D614 (Figure 7C). 2020 Cell Result SARS_CoV_2 D614G;D614G 27;120 32;125 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The effect of D614G on S protein synthesis, processing, and incorporation into virion particles produced by SARS-CoV-2 structural proteins was assessed next (Figure 3 A). 2020 Cell Result SARS_CoV_2 D614G 14 19 S 23 24 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The effect of D614G on this interaction could be assessed since local resolution in the map generated here reached 3.2 A. 2020 Cell Result SARS_CoV_2 D614G 14 19 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The frequency of A23403G has increased steadily over time and is now present in approximately 74% of all published sequences (Figure 1 A). 2020 Cell Result SARS_CoV_2 A23403G 17 24 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The global spread and enhanced infectivity of the SARS-CoV-2 D614G variant raises the question of whether this structural change would compromise the effectiveness of antiviral therapies targeting the S protein, especially if they were designed to target D614. 2020 Cell Result SARS_CoV_2 D614G 61 66 S 201 202 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The likely zoonotic origin of SARS-CoV-2 raises the question of whether D614G was selected during the pandemic as a result of human-to-human transmission. 2020 Cell Result SARS_CoV_2 D614G 72 77 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The S proteins D614 and D614G were produced to comparable levels, processed to S1 and S2 with comparable efficiency, and incorporated into SARS-CoV-2 virus-like particles at similar levels (Figure 3B). 2020 Cell Result SARS_CoV_2 D614G 24 29 S 4 5 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The SARS-CoV-2 D614G S Protein Variant Increases Infectivity of Pseudotyped Lentiviruses in Cell Culture. 2020 Cell Result SARS_CoV_2 D614G 15 20 S 21 22 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The SARS-CoV-2 D614G S Protein Variant Supplanted the Ancestral Virus in Humans. 2020 Cell Result SARS_CoV_2 D614G 15 20 S 21 22 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. These data demonstrate that the increased infectivity of D614G is not explained by greater ACE2 binding strength. 2020 Cell Result SARS_CoV_2 D614G 57 62 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. These data further emphasize the contrast between D614G conformational space and that of D614. 2020 Cell Result SARS_CoV_2 D614G 50 55 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. These four SNPs include C241U in the 5'UTR, a silent mutation C3037U, C14408U encoding the RNA-dependent RNA polymerase variant P323L, and A23403G encoding the spike protein variant D614G. 2020 Cell Result SARS_CoV_2 A23403G;D614G;P323L 139;182;128 146;187;133 RdRp;S;5'UTR 91;160;37 119;165;42 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. These results suggest that increased infectivity due to D614G is primarily manifested after virion assembly, during entry into target cells. 2020 Cell Result SARS_CoV_2 D614G 56 61 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Three-dimensional clustering and refinement generated the final density map for D614G (Figure 6 A, EMDB: EMD-22301), which showed a similar overall architecture to the published map of D614 (Figure 6B). 2020 Cell Result SARS_CoV_2 D614G 80 85 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. To determine whether the increased infectivity of D614G is specific for certain ACE2 orthologs, HEK293 cells were transfected separately with plasmids encoding ACE2 orthologs from human (Homo sapiens), Chinese rufous horseshoe bat (Rhinolophus sinicus), Malayan pangolin (Manis javanica), cat (Felis catus), and dog (Canis lupis). 2020 Cell Result SARS_CoV_2 D614G 50 55 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Unmasked Fourier shell correlation (FSC) analysis indicated that the D614G map had a mean resolution of 3.7 A (gold-standard criteria, Figure S1E; half-map FSC, Figure S1F) which is sufficient to reveal fine differences from D614. 2020 Cell Result SARS_CoV_2 D614G 69 74 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. When Caco-2 human colon epithelial cells were used as target cells, 4-fold higher infectivity was observed with D614G (Figure 2A). 2020 Cell Result SARS_CoV_2 D614G 112 117 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. When Calu-3 human lung epithelial cells were used as targets, challenge with virus bearing D614G resulted in 6-fold more GFP-positive cells, or 5-fold more bulk luciferase activity, than did particles bearing D614 S protein (Figure 2 A). 2020 Cell Result SARS_CoV_2 D614G 91 96 S 214 215 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. When the S1 subunit of D614G was superimposed on D614 in the open conformation, the S1-NTD was shifted outward by 3 A, whereas the S1-INT overlapped well with that of D614 (Figure 6F). 2020 Cell Result SARS_CoV_2 D614G 23 28 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. When the S1 subunit of D614G was superimposed on the closed conformation of D614, the S1-NTD and S1-INT shifted away from each other by 6 A and 4 A, respectively (Figures 6E, S2 B, and S2C), revealing a wider space between these two domains. 2020 Cell Result SARS_CoV_2 D614G 23 28 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. CR3022 neutralizes SARS-CoV-2 P384A but not WT. 2020 bioRxiv Result SARS_CoV_2 P384A 30 35 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. Crystal structure reveals the impact of P384A in CR3022 binding. 2020 bioRxiv Result SARS_CoV_2 P384A 40 45 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. Four SARS-CoV-2 RBD mutants, namely A372T, P384A, T430M, and H519N (SARS-CoV-2 numbering), were recombinantly expressed and examined (Figure 1A). 2020 bioRxiv Result SARS_CoV_2 A372T;H519N;P384A;T430M 36;61;43;50 41;66;48;55 RBD 16 19 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. However, CR3022 is now able to neutralize the SARS-CoV-2 P384A mutant at an IC50 of 3.2 mug/ml, which is comparable to its neutralizing activity to SARS-CoV (IC50 of 5.2 mug/ml). 2020 bioRxiv Result SARS_CoV_2 P384A 57 62 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. However, it is unclear whether the emergence of P384A is due to neutral drift or positive selection in bats or other species. 2020 bioRxiv Result SARS_CoV_2 P384A 48 53 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. In addition, given that residue 384 is proximal to the S2 domain when the RBD is in the "down" conformation (Figure 3B), whether P384A can modulate the conformational dynamics of the "up and down" configurations of the RBD in the S trimer and influence the viral replication fitness will require additional studies. 2020 bioRxiv Result SARS_CoV_2 P384A 129 134 RBD;RBD;S 74;219;230 77;222;231 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. Interestingly, the CR3022 Fab neutralized SARS-CoV-2 P384A mutant with an IC50 of 4.4 mug/ml, which is similar to that of CR3022 IgG (3.2 mug/ml) (Figure 2). 2020 bioRxiv Result SARS_CoV_2 P384A 53 58 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. P384A increases binding affinity of SARS-CoV-2 RBD to CR3022. 2020 bioRxiv Result SARS_CoV_2 P384A 0 5 RBD 47 50 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. Phylogenetic analysis implies that P384A emerged during the evolution of SARSr-CoV in bats (Figure 3A), which is the natural reservoir of SARSr-CoV. 2020 bioRxiv Result SARS_CoV_2 P384A 35 40 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. To test this hypothesis, we compared neutralization of SARS-CoV-2 WT and the P384A mutant by CR3022. 2020 bioRxiv Result SARS_CoV_2 P384A 77 82 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. While binding of CR3022 mutants A372T (KD = 66 nM), T430M (KD = 64 nM), and H519N (KD = 60 nM) was comparable to wild type (WT) SARS-CoV-2 RBD (KD = 68 nM), binding of CR3022 to the P384A mutant (KD = 1.4 nM) was greatly increased (Figure 1B), akin now to that with the SARS-CoV RBD (KD = 1.0 nM). 2020 bioRxiv Result SARS_CoV_2 A372T;H519N;P384A;T430M 32;76;182;52 37;81;187;57 RBD;RBD 139;279 142;282 32995830 Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report. At day 14 and 42, nAb titers (IC50) were 1:260 and 1:382 against D614 (Wuhan) pseudovirus, and were 1:449 and 1:1168 against a mutated D614G pseudovirus, showing differential increase of nAb to D614G pseudovirus compared to the Wuhan strain (Figures 3D and S5). 2020 medRxiv Result SARS_CoV_2 D614G;D614G 135;194 140;199 32995830 Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report. Conspicuously, the July sequence (InCoV139-July) harbors none of the canonical mutations defining clade 19B and instead shares the canonical mutations defining clade 20A (C3037T, C14408T and A23403G), 1 canonical mutation of clade 20C (G25563T), as well as 1 other 20A mutation. 2020 medRxiv Result SARS_CoV_2 A23403G;C14408T;C3037T;G25563T 191;179;171;236 198;186;177;243 32995830 Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report. Importantly, present in InCoV139-July (but not in InCoV139-March) is the A23403G mutation, which confers the D614G amino acid change in spike protein, and defines the SARS-CoV-2 strain with greater replicative fitness, introduced separately to the US East Coast via Europe. 2020 medRxiv Result SARS_CoV_2 A23403G;D614G 73;109 80;114 S 136 141 32995830 Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report. InCoV139-March additionally shares C18060T with the first US case WA1 (Genbank: MN985325), which was circulating in Asia and introduced via a traveler returning from Wuhan, China to the Puget Sound area north of Seattle in mid-January. 2020 medRxiv Result SARS_CoV_2 C18060T 35 42 32995830 Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report. The InCoV139-March sequence (Genbank: MT252824) shares the canonical mutations (C8782T and T28144C) which define clade 19B and distinguish it from the original clade 19A, Wuhan-Hu-1 reference strain (Genbank: NC_045512.2). 2020 medRxiv Result SARS_CoV_2 T28144C;C8782T 91;80 98;86 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Among all mutations destabilizing full-length S protein, G431W has introduced the largest positive DeltaDeltaG for trimer (189.93 kcal/mol) and monomer (59.92 kcal/mol). 2021 Briefings in bioinformatics Result SARS_CoV_2 G431W 57 62 S 46 47 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Consistently, S438F has the maximum DeltaDeltaG at 10.980 kcal/mol for RBD stability. 2021 Briefings in bioinformatics Result SARS_CoV_2 S438F 14 19 RBD 71 74 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G496W and G496Y induced the largest binding energy change at 17.418 kcal/mol in all RBD mutations (Table 2). 2021 Briefings in bioinformatics Result SARS_CoV_2 G496Y;G496W 10;0 15;5 RBD 84 87 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. However, G1124V (DeltaDeltaG = 3.595 kcal/mol) in 24 strains and S943I (DeltaDeltaG = 0.299 kcal/mol) in 26 strains reduce the stability of S protein. 2021 Briefings in bioinformatics Result SARS_CoV_2 G1124V;S943I 9;65 15;70 S 140 141 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. However, G476S in eight strains, A520S in seven strains and Q414E in six strains can destabilize the RBD region. 2021 Briefings in bioinformatics Result SARS_CoV_2 A520S;G476S;Q414E 33;9;60 38;14;65 RBD 101 104 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. In all RBD mutations, G431W introduced the highest positive DeltaDeltaG at 55.323 kcal/mol, and all mutations in G431 could highly reduce the protein stabilities of RBD and full-length S (Figure 2). 2021 Briefings in bioinformatics Result SARS_CoV_2 G431W 22 27 RBD;RBD;S 7;165;185 10;168;186 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. In contrast, G502 has the second largest positive DeltaDeltaDeltaG mean at 2.922 kcal/mol and G502P (DeltaDeltaDeltaG = 11.767 kcal/mol) has the highest destabilizing effect on RBD-ACE2 complex. 2021 Briefings in bioinformatics Result SARS_CoV_2 G502P 94 99 RBD 177 180 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. In contrast, V341I has the minimum folding free energy change at -1.256 kcal/mol and can increase RBD stability. 2021 Briefings in bioinformatics Result SARS_CoV_2 V341I 13 18 RBD 98 101 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. In RBD region, the largest folding energy change takes place in S438F (DeltaDeltaG = 18.399 kcal/mol) for S stability. 2021 Briefings in bioinformatics Result SARS_CoV_2 S438F 64 69 RBD;S 3;106 6;107 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Interestingly, G431A has the maximum DeltaDeltaG value among all substitutions to alanine in both full-length S and RBD, and S514A has the minimum DeltaDeltaG value among all substitutions to alanine in RBD. 2021 Briefings in bioinformatics Result SARS_CoV_2 G431A;S514A 15;125 20;130 RBD;RBD;S 116;203;110 119;206;111 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. K353F has the smallest DeltaDeltaDeltaG at -1.937 kcal/mol. 2021 Briefings in bioinformatics Result SARS_CoV_2 K353F 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Mutations of S50L (DeltaDeltaG = -2.614 kcal/mol), T724I (DeltaDeltaG = -2.590 kcal/mol) and T240I (DeltaDeltaG = -2.476 kcal mol) have strong stabilizing effects on SARS-Cov-2 full-length S protein. 2021 Briefings in bioinformatics Result SARS_CoV_2 S50L;T240I;T724I 13;93;51 17;98;56 S 189 190 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Residue D355 (DeltaDeltaDeltaG mean = 2.031 kcal/mol) and mutation D355Y (DeltaDeltaDeltaG = 7.284 kcal/mol) in this position have maximum effects on destabilizing the RBD-ACE2 complex. 2021 Briefings in bioinformatics Result SARS_CoV_2 D355Y 67 72 RBD 168 171 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Residue Y41 (DeltaDeltaDeltaG mean = -0.742 kcal/mol) and mutation D355Y (DeltaDeltaDeltaG = -1.808 kcal/mol) can increase the RBD-ACE2 interaction. 2021 Briefings in bioinformatics Result SARS_CoV_2 D355Y 67 72 RBD 127 130 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Similarly, D936Y (DeltaDeltaG = -0.304 kcal/mol) in 37 strains and H49Y (DeltaDeltaG = -1.902 kcal/mol) in 25 strains can make S protein more stable. 2021 Briefings in bioinformatics Result SARS_CoV_2 D936Y;H49Y 11;67 16;71 S 127 128 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. The DeltaDeltaDeltaG of common variants V483A and V367F are close to 0, meaning that these mutations have no effects on binding affinity. 2021 Briefings in bioinformatics Result SARS_CoV_2 V367F;V483A 50;40 55;45 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. The largest negative binding free energy change is introduced by N501E at -2.490 kcal/mol. 2021 Briefings in bioinformatics Result SARS_CoV_2 N501E 65 70 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. The most common variation, D614G in 5703 virus strains, has stabilizing effects on the S protein (DeltaDeltaG = -0.784 kcal/mol). 2021 Briefings in bioinformatics Result SARS_CoV_2 D614G 27 32 S 87 88 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V483A in 24 strains have small effects (DeltaDeltaG = -0.196 kcal/mol) and V367F in 13 strains has moderate stabilizing effects (DeltaDeltaG = -0.597 kcal/mol) on RBD. 2021 Briefings in bioinformatics Result SARS_CoV_2 V367F;V483A 75;0 80;5 RBD 163 166 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. We observed that G476S can decrease RBD-ACE2 binding affinity (DeltaDeltaDeltaG = 0.751 kcal/mol), but L452R has small stabilizing effect (DeltaDeltaDeltaG = -0.395 kcal/mol) on RBD-ACE2 complex. 2021 Briefings in bioinformatics Result SARS_CoV_2 G476S;L452R 17;103 22;108 RBD;RBD 36;178 39;181 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. All contained two the more frequency variations, a total of 18 types, except for one triple variations (T29I, D614G, and G1124V). 2020 Frontiers in immunology Result SARS_CoV_2 D614G;G1124V;T29I 110;121;104 115;127;108 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. Among the 18 amino acid variation sites, the highest frequency substitution was D614G. 2020 Frontiers in immunology Result SARS_CoV_2 D614G 80 85 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. Among them, amino acid substitutions T29I, G476S, D936Y, S943P, and P1263L changed the length of the linear B cell epitopes, whereas V483A, Q675H, and A706V had no influence on the length of linear epitopes, and the others had no effect on linear B cell epitopes (Table 1). 2020 Frontiers in immunology Result SARS_CoV_2 A706V;D936Y;G476S;P1263L;Q675H;S943P;T29I;V483A 151;50;43;68;140;57;37;133 156;55;48;74;145;62;41;138 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. Binding level results of T29I, V367F, A706V, and A831V demonstrated that these substitutions had low binding affinity in HLA-A01:01, HLA-B07:02, and HLA-B35:01 compared to the wild type, while H49Y, Q239K, V483A, D839Y, S943P, A1078S, and P1263L substitutions still had strong binding affinity with HLA molecules. 2020 Frontiers in immunology Result SARS_CoV_2 A1078S;A706V;A831V;D839Y;H49Y;P1263L;Q239K;S943P;T29I;V367F;V483A 227;38;49;213;193;239;199;220;25;31;206 233;43;54;218;197;245;204;225;29;36;211 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. By construction of the 3D structures of S protein with the amino acid substitutions, we found that G476S substitution rendered the peptide as a non-epitope and A706V had no effect on epitope prediction. 2020 Frontiers in immunology Result SARS_CoV_2 A706V;G476S 160;99 165;104 S 40 41 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. D936Y nearly abolished the original epitope (DSLSST, 936-941), whereas S943P induced the formation of a novel 9 amino acid epitope (DSLSSTAPAL, 936-945). 2020 Frontiers in immunology Result SARS_CoV_2 S943P;D936Y 71;0 76;5 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. For variant S proteins, T29I, H49Y, Q239K, V367F, V483A, A706V, A831V, D839Y, S943P, A1078S, and P1263L were located in the predicted CTL epitopes according to the HLA class I allele (Table 3). 2020 Frontiers in immunology Result SARS_CoV_2 A1078S;A706V;A831V;D839Y;H49Y;P1263L;Q239K;S943P;T29I;V367F;V483A 85;57;64;71;30;97;36;78;24;43;50 91;62;69;76;34;103;41;83;28;48;55 S 12 13 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. G476S shortened epitope length from 13 to 11 amino acids (YQAGSTPCNGAEG to YQASSTPCNGV), whereas V483A remained the same. 2020 Frontiers in immunology Result SARS_CoV_2 V483A;G476S 97;0 102;5 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. In contrast, G476S, D614G, Q675H, A879S, D936Y, and G1124V were outside of the CTL epitopes. 2020 Frontiers in immunology Result SARS_CoV_2 A879S;D614G;D936Y;G1124V;G476S;Q675H 34;20;41;52;13;27 39;25;46;58;18;32 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. Of note, G476S shortened a linear B cell epitope length and even abolished the discontinuous B cell epitope. 2020 Frontiers in immunology Result SARS_CoV_2 G476S 9 14 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. Remarkably, most of them harbored with D614G mutation (226 of 228). 2020 Frontiers in immunology Result SARS_CoV_2 D614G 39 44 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. V367F decreased the peptide binding affinity for the HLA-B35:01 allele, whereas V483A had no effect on either cell epitope. 2020 Frontiers in immunology Result SARS_CoV_2 V483A;V367F 80;0 85;5 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. We observed that most remaining sites had their special temporal and regional propensities, such as Q239K, A831V, D839Y, A879S, D936Y, S943P, and P1263L, which were mainly concentrated in Europe in March, 2020. 2020 Frontiers in immunology Result SARS_CoV_2 A831V;A879S;D839Y;D936Y;P1263L;Q239K;S943P 107;121;114;128;146;100;135 112;126;119;133;152;105;140 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. We observed that three amino acid substitutions within the RBD (V367F, G476S, and V483A) were identified, whose impacts in predicted cell epitope were different. 2020 Frontiers in immunology Result SARS_CoV_2 G476S;V483A;V367F 71;82;64 76;87;69 RBD 59 62 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. For markers located in ORF3a (G251V) and ORF8 (L84S), all genomes were observed as identical and belonged in G and L clades. 2020 Heliyon Result SARS_CoV_2 G251V;L84S 30;47 35;51 ORF3a;ORF8 23;41 28;45 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. However, the spike protein marker (D614G) varied significantly among viruses, where 28 (43.8%) of the genomes revealed the original aspartic acid residue, which was replaced by glycine in 36 (56.2%) (Table 2). 2020 Heliyon Result SARS_CoV_2 D614G 35 40 S 13 18 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. In the S protein, the regions encompassing the ACE2 receptor-binding domain located in the S1 subunit (positions 451-510) were conserved, except for the I468V substitution detected in 3 (4.7%) genomes. 2020 Heliyon Result SARS_CoV_2 I468V 153 158 S 7 8 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. Likewise, the polybasic cleavage site (RRAR) and neighboring amino acids (positions 667-694) were retained, except for the single N679K substitution. 2020 Heliyon Result SARS_CoV_2 N679K 130 135 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. On the nucleotide level, the genomes were highly similar, with nucleotide identities of 99.9%, displaying variations in 7 positions (T17432C, T18870C, T25556G, T26728C, G28874A, G28875A, G28876C). 2020 Heliyon Result SARS_CoV_2 G28874A;G28875A;G28876C;T18870C;T25556G;T26728C;T17432C 169;178;187;142;151;160;133 176;185;194;149;158;167;140 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. Only two amino acid substitutions, occurring in ORF3a (Q57H) and nucleocapsid (N) protein (RG203KR) were noted. 2020 Heliyon Result SARS_CoV_2 Q57H 55 59 N;ORF3a;N 65;48;79 77;53;80 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. The mutation (A23403G) resulting in this substitution is significant, as it is not only the most frequently-detected mutation worldwide, but likely to impact one of the B cell epitopes located on the S protein of SARS-CoV-2 as well. 2020 Heliyon Result SARS_CoV_2 A23403G 14 21 S 200 201 33024144 Molecular epidemiology of the first wave of severe acute respiratory syndrome coronavirus 2 infection in Thailand in 2020. This branch was defined as type T based on a nucleotide substitution in the S gene (G24047A) and an amino acid change in the Spike protein (A829T). 2020 Scientific reports Result SARS_CoV_2 A829T;G24047A 140;84 145;91 S;S 125;76 130;77 33024144 Molecular epidemiology of the first wave of severe acute respiratory syndrome coronavirus 2 infection in Thailand in 2020. Type G has single nucleotide changes in ORF1b (C14408T) and S (A23403G). 2020 Scientific reports Result SARS_CoV_2 A23403G;C14408T 63;47 70;54 S 60 61 33024144 Molecular epidemiology of the first wave of severe acute respiratory syndrome coronavirus 2 infection in Thailand in 2020. Type O had nucleotide substitutions in ORF1b (C13730T), S (C23929T) and ORF9b (C28311T). 2020 Scientific reports Result SARS_CoV_2 C13730T;C23929T;C28311T 46;59;79 53;66;86 S 56 57 33024144 Molecular epidemiology of the first wave of severe acute respiratory syndrome coronavirus 2 infection in Thailand in 2020. Type S was detected during the early period of the outbreak, and it has nucleotide substitutions at position 8,782 in ORF1ab (C8782T) and 28,144 (T28144C) in ORF8. 2020 Scientific reports Result SARS_CoV_2 C8782T;T28144C 126;146 132;153 ORF1ab;ORF8;S 118;158;5 124;162;6 33024144 Molecular epidemiology of the first wave of severe acute respiratory syndrome coronavirus 2 infection in Thailand in 2020. Type V differed from type L at positions in ORF1b (C14805T) and ORF3a (G26144T). 2020 Scientific reports Result SARS_CoV_2 C14805T;G26144T 51;71 58;78 ORF3a 64 69 33024961 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Among them, radical-amino-acid-change D614G, which rose in frequency across multiple cities and increases infectivity in vitro, disrupts a perfectly-conserved residue (across Sarbecoviruses), and lies in a stretch of 11 perfectly-conserved amino acids. 2020 Research square Result SARS_CoV_2 D614G 38 43 33024961 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Another three are in moderately-conserved contexts (V367F, D839Y/N/E, D936Y/H) less likely to be functional, and eight lie in repeatedly-altered amino acids in poorly-conserved regions and likely-neutral. 2020 Research square Result SARS_CoV_2 D839E;D839N;D839Y;D936H;D936Y;V367F 59;59;59;70;70;52 68;68;68;77;77;57 33024961 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Of the other 15 Spike variants, two are in perfectly-conserved residues (V615I/F, P1263L) and two in mostly-conserved residues in highly-conserved regions (A831V, A829T/S), indicating likely-functional changes. 2020 Research square Result SARS_CoV_2 A829T;A829S;P1263L;A831V;V615F;V615I 163;163;82;156;73;73 170;170;88;161;80;80 S 16 21 33024961 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Spike D614G was nearly always co-inherited with Pol P4715L (also radical and altering a perfectly-conserved residue in a highly-conserved context, but potentially-deleterious given Pol's slow evolution and less-likely-to-be-adaptive function), nsp3 nucleotide change C3037T (repeatedly-observed synonymous change, outside synonymously-constrained elements, likely-neutral), and nucleotide change C241T (perfectly-conserved, non-coding, in a loop of six unpaired bases in the conserved 5'UTR SL5B secondary structure 25 nucleotides upstream of ORF1ab). 2020 Research square Result SARS_CoV_2 C241T;C3037T;D614G;P4715L 396;267;6;52 401;273;11;58 ORF1ab;S;5'UTR;Nsp3 543;0;485;244 549;5;490;248 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. 13 different mutations of spike protein are observed of which D614G is most notable and exist among 37 samples, especially among isolates from the European countries. 2020 Microbes and infection Result SARS_CoV_2 D614G 62 67 S 26 31 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. An incident of the concurrence of R203K and G204R is found in Belgium, Brazil, Peru, Mexico, Nigeria, Switzerland, and Vietnam from the present analysis. 2020 Microbes and infection Result SARS_CoV_2 G204R;R203K 44;34 49;39 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. Coexistence of P4715L in RdRp and D614G in Spike protein among European and American samples. 2020 Microbes and infection Result SARS_CoV_2 D614G;P4715L 34;15 39;21 S;RdRP 43;25 48;29 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. D614G mutation of spike protein does not effect human Ace2 binding. 2020 Microbes and infection Result SARS_CoV_2 D614G 0 5 S 18 23 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. In spike glycoprotein, D614G is favored by the attainment of molecular stability (DeltaDeltaG = 1.128 kcal/mol) and vibrational entropy changes (DeltaDeltaSVib ENCoM = -4.531 kcal.mol-1.K-1) leading to decrease in molecular flexibility. 2020 Microbes and infection Result SARS_CoV_2 D614G 23 28 S 3 21 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. It can be called that V74F variation in ORF7b is primarily restricted to the Asian continent. 2020 Microbes and infection Result SARS_CoV_2 V74F 22 26 ORF7b 40 45 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. It is interesting to find that L4715 RdRp and D614G spike variants show co-occurrence. 2020 Microbes and infection Result SARS_CoV_2 D614G 46 51 S;RdRP 52;37 57;41 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. P4715L in RdRp accounts for stable conformation change confirmed by binding conformational enthalpy change (DeltaDeltaG = 1.540 kcal/mol). 2020 Microbes and infection Result SARS_CoV_2 P4715L 0 6 RdRP 10 14 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. P4715L RdRp and D614G spike is the primary determining factor to cluster the different SARS-CoV-2 isolates into different clades. 2020 Microbes and infection Result SARS_CoV_2 D614G;P4715L 16;0 21;6 S;RdRP 22;7 27;11 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. P4715L substitution in RdRp protein from the ORF1ab region is linked with 'FPPTSFG' epitope loss from the site. 2020 Microbes and infection Result SARS_CoV_2 P4715L 0 6 ORF1ab;RdRP 45;23 51;27 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. P4715L variant of ORF1ab is remarkable to occur among 37 samples in the RNA dependent RNA polymerase (RdRp) site. 2020 Microbes and infection Result SARS_CoV_2 P4715L 0 6 RdRp;ORF1ab;RdRP 72;18;102 100;24;106 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. S1498F is the most frequent mutation at the multi-domain essential replication/transcription complex- Nsp3 of ORF1a and reflected among multiple Indian isolates with travel history to Italy. 2020 Microbes and infection Result SARS_CoV_2 S1498F 0 6 ORF1a;Nsp3 110;102 115;106 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. S1498F mutation of Nsp3 is responsible for the loss of linear-epitope consisting of five residues 'YKDWS'from the region. 2020 Microbes and infection Result SARS_CoV_2 S1498F 0 6 Nsp3 19 23 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. Structural impact due to P4715L in RdRp and D614G in Spike protein. 2020 Microbes and infection Result SARS_CoV_2 D614G;P4715L 44;25 49;31 S;RdRP 53;35 58;39 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. The change of amino acid L84S in ORF8 has been observed among the viral samples of more than 12 countries. 2020 Microbes and infection Result SARS_CoV_2 L84S 25 29 ORF8 33 37 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. The incidence of occurrence of G251V is high among various samples irrespective of geographical locations. 2020 Microbes and infection Result SARS_CoV_2 G251V 31 36 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. The inter-atomic interactions with the neighboring residues remain the same after D614G mutation. 2020 Microbes and infection Result SARS_CoV_2 D614G 82 87 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. The mutation P4715L led to the formation of an intramolecular hydrogen bonding between Leu4715 and Phe4718. 2020 Microbes and infection Result SARS_CoV_2 P4715L 13 19 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. The P4715L mutation of RdRp and D614G mutation in spike protein, predominant in viral strains of Europe and America, has a major role in outrageous infection evident from the high fatality rate. 2020 Microbes and infection Result SARS_CoV_2 D614G;P4715L 32;4 37;10 S;RdRP 50;23 55;27 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. The second epitope loss is associated with G251V in ORF3a. 2020 Microbes and infection Result SARS_CoV_2 G251V 43 48 ORF3a 52 57 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. The third loss of epitope S1498F is found in non-structural protein Nsp3 of ORF1a among Indian isolates. 2020 Microbes and infection Result SARS_CoV_2 S1498F 26 32 ORF1a;Nsp3 76;68 81;72 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. V74F is the deleterious mutation found in ORF7b among an isolate from Kuwait and five Indian isolates sampled at Iran in March 2020. 2020 Microbes and infection Result SARS_CoV_2 V74F 0 4 ORF7b 42 47 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Although the D614G substitution did not affect the overall thermal stability of the S protein, the loop region of the D614G mutant showed a more dynamic structure compared with WT D614 S protein. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G;D614G 13;118 18;123 S;S 84;185 85;186 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. As a result of thermodynamic analysis indicating that the S protein D614G substitution is less stable, we modeled the binding of furin (PDB ID 4Z2A) to the RRAR cleavage site of D614 S protein and G614 S protein (Figure 2C). 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 68 73 S;S;S 58;183;202 59;184;203 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. As a result, the D614G substitution may enhance viral entry to the host cell, causing higher infectivity. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 17 22 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Genome sequences of SARS-CoV2 deposited in the GISAID database showed a D614G substitution on the S protein, which is the point of entry of the virus to the host cell, to be the most common in Europe and the world. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 72 77 S 98 99 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Interatomic interactions in D614G mutant S protein. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 28 33 S 41 42 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Moreover, MD simulations of WT D614 S protein showed a profile similar to that for the D614G mutant, showing high convergence in the initial stages, which can be attributed to the substitution in the loop region. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 87 92 S 36 37 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Our analysis showed that the D614G substitution disturbed the structural stability of the SARS-Cov-2 S protein, which consequently increased the binding affinity of furin for the S protein. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 29 34 S;S 101;179 102;180 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. S protein D614G substitution. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 10 15 S 0 1 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. S protein stability analysis using the DynaMut webserver showed that the D614G substitution in the loop region resulted in a slightly more dynamic structure with DeltaDeltaG of -0.086 kcal mol-1 and vibrational entropy (DeltaDeltaS Vib) of 0.137 kcal mol-1 K-1 (Figure 1B). 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 73 78 S 0 1 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Since the D614G substitution correlates with higher infectivity, we calculated the binding affinities (K d) of the furin bound to D614 S protein and G614 S protein structures at different temperatures using the PRODIGY server (Figure 2D). 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 10 15 S;S 135;154 136;155 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Such structural dynamics resulted in furin showing a higher binding affinity for the D614G mutant, which implies that increased infectivity may result from the D614G substitution. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G;D614G 85;160 90;165 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. The D614G substitution can affect the internal dynamics of the protein, resulting in higher fluctuation than in the WT D614 S protein. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 4 9 S 124 125 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. The D614G substitution is a change from a negatively charged aspartate (D) to glycine (G) in the S1 domain loop region of the S protein. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 4 9 S 126 127 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. The dynamic structure was probably due to the D614G substitution in the loop region, causing changes in conformational dynamics and ultimately affecting the interaction with furin. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 46 51 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. The greater mobility observed close to the loop region between residues 600 and 620 could be the result of higher binding affinity of furin for the D614G mutant. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 148 153 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Therefore, the D614G mutant may result in more efficient cleavage of the S protein and subsequent interaction with ACE2, which may result in a more virulent strain. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 15 20 S 73 74 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Therefore, the higher RMSF demonstrated by the D614G mutant caused greater conformational mobility, which may expose the RARR cleavage site and result in a more favorable S protein-furin binding interaction through conformational selection or an induced-fit mechanism. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 47 52 S 171 172 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Therefore, the loss of the hydrogen bond in the D614G mutant may have two consequences: (1) loss of hinging of the S2 subunit, which increases its flexibility in the transition state when interacting with the host cell receptor; and (2) increased flexibility, resulting in a more accessible furin cleavage site concomitant with increased infectivity of the D614G mutant. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G;D614G 48;357 53;362 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Thermodynamic analysis of the D614G substitution. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 30 35 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. This high convergence at the start of the simulation may have been the result of instability in the structure caused by the D614G substitution, resulting in a more flexible loop region. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 124 129 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. This hydrogen bond is lost in the D614G mutant since glycine lacks a hydrogen-bond donor or acceptor side chain (Figure 2B). 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 34 39 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. This, in turn, increased the surface accessibility of the RARR cleavage site, inducing stronger binding affinity of the S protein variant at hyperthermic temperatures, which may explain the infectivity of the D614G mutant. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 209 214 S 120 121 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. To further confirm the impact of the D614G substitution on the binding of furin, the total binding free energy was determined by the MMGBSA method (molecular mechanics, generalized Born model and solvent accessibility model). 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 37 42 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. We used MD simulations to elucidate the effect of the substitution on the structure and stability of the S protein to formulate a hypothesis about potential factors involved in effects of the D614G mutant of the S protein. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 192 197 S;S 105;212 106;213 33080267 Designed variants of ACE2-Fc that decouple anti-SARS-CoV-2 activities from unwanted cardiovascular effects. ACE2-Fc Arg273Ala, His378Ale and Glu402Ala, and wild-type ACE2-Fc proteins were further tested for their antiviral potency. 2020 International journal of biological macromolecules Result SARS_CoV_2 R273A;R273A;E402A;E402A;H378A;H378A;H378E;H378E;H378L;H378L 9;8;34;33;20;19;20;19;20;19 17;17;42;42;29;28;29;28;29;28 33080267 Designed variants of ACE2-Fc that decouple anti-SARS-CoV-2 activities from unwanted cardiovascular effects. Competitive inhibition of pseudotyped viral transduction by R273A, H378A and E402A mutants ofACE2-Fc. 2020 International journal of biological macromolecules Result SARS_CoV_2 E402A;H378A;R273A 77;67;60 82;72;65 33080267 Designed variants of ACE2-Fc that decouple anti-SARS-CoV-2 activities from unwanted cardiovascular effects. For instance, while Mca-APK(Dnp) showed no activity of 7 ACE2-Fc mutants, including 4 substrate-binding residues of Arg273Ala, His345Ala, Pro346Ala and His505Ala. 2020 International journal of biological macromolecules Result SARS_CoV_2 R273A;H505A;P346A 116;152;138 125;161;147 33080267 Designed variants of ACE2-Fc that decouple anti-SARS-CoV-2 activities from unwanted cardiovascular effects. His345Ala, Pro346Ala and His505Ala remained active toward AngII and apelin-13. 2020 International journal of biological macromolecules Result SARS_CoV_2 H505A;P346A 25;11 34;20 33080267 Designed variants of ACE2-Fc that decouple anti-SARS-CoV-2 activities from unwanted cardiovascular effects. In addition, His374Ala, one of the Zn2+-binding residues, retained a low level of activity against Apelin-13. 2020 International journal of biological macromolecules Result SARS_CoV_2 H374A 13 22 33080267 Designed variants of ACE2-Fc that decouple anti-SARS-CoV-2 activities from unwanted cardiovascular effects. In contrast, Arg273Ala mutant of the substrate-binding pocket, which showed complete loss-of-activity toward all three substrates, is situated on the distal lobe and is less likely to affect desired viral binding. 2020 International journal of biological macromolecules Result SARS_CoV_2 R273A 13 22 33080267 Designed variants of ACE2-Fc that decouple anti-SARS-CoV-2 activities from unwanted cardiovascular effects. Overall, the wild-type protein showed the highest binding affinity, whereas all three Zn2+-binding site mutants, His374Ala, His378Ala and Glu402Ala, had the lowest affinities to RBD. 2020 International journal of biological macromolecules Result SARS_CoV_2 E402A;H374A;H378A 138;113;124 147;122;133 RBD 178 181 33080267 Designed variants of ACE2-Fc that decouple anti-SARS-CoV-2 activities from unwanted cardiovascular effects. When all three substrates are considered, Arg273Ala, His378Ala and Glu402Ala were completely lack of peptidase activity. 2020 International journal of biological macromolecules Result SARS_CoV_2 R273A;E402A;H378A 42;67;53 51;76;62 33080267 Designed variants of ACE2-Fc that decouple anti-SARS-CoV-2 activities from unwanted cardiovascular effects. with wild-type ACE2-Fc had a leading IC50 of 0.13 mug/mL, followed by His378Ala, Arg273Ala and Glu402Ala with their IC50s of 0.16 mug/mL, 0.19 mug/mL and 0.25 mug/mL, respectively. 2020 International journal of biological macromolecules Result SARS_CoV_2 R273A;E402A;H378A 81;95;70 90;104;79 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. Comparison of the titres by virus isolate (SA01, VIC01, and VIC31) revealed that the D614G mutation had little effect on neutralisation efficiency following vaccination. 2020 NPJ vaccines Result SARS_CoV_2 D614G 85 90 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. It is not immediately clear what effect the P323L mutation has on virulence. 2020 NPJ vaccines Result SARS_CoV_2 P323L 44 49 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. Recent findings suggested the superior infectivity of G614 is through the D614G mutation stabilising the interaction between the S1 and S2 domains. 2020 NPJ vaccines Result SARS_CoV_2 D614G 74 79 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. Secondly, a parallel C-to-U substitution at position 14,408 in the genome, resulting in a P323L (P314L in orf1b) mutation in the RNA-dependent polymerase (RdRp/nsp12), has been associated with D614G (including in VIC31) and should therefore be considered for potential contribution to infectivity. 2020 NPJ vaccines Result SARS_CoV_2 D614G;P323L;P314L 193;90;97 198;95;102 Nsp12;RdRP 160;155 165;159 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. The aspartate-to-glycine change at 614 removes the inter-chain D614-K854 and might actually destabilise the interaction between S1 and S2 domains. 2020 NPJ vaccines Result SARS_CoV_2 D614G 4 38 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. The P323L mutation appears to partially obstruct R349 in the cleft. 2020 NPJ vaccines Result SARS_CoV_2 P323L 4 9 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. The Pro323 to Leu mutation may relieve some backbone constraints and contribute local conformational stability. 2020 NPJ vaccines Result SARS_CoV_2 P323L 4 17 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. We used Australian isolates which either possess or lack the D614G mutation but are otherwise comparable in S protein sequence and also devoid of significant mutations of consequence within viral proteins responsible for cell binding and entry (as discerned with Geneious Prime 2020.1 software; c.f. 2020 NPJ vaccines Result SARS_CoV_2 D614G 61 66 S 108 109 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. We used molecular models of the spike protein (both our molecular dynamics simulations and another spike model) to examine the structural context of the D614G mutation to address possible concerns of adverse vaccine efficacy and the plausibility of recently-proposed selection advantages. 2020 NPJ vaccines Result SARS_CoV_2 D614G 153 158 S;S 32;99 37;104 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. Whilst we agree with studies suggesting that the D614G mutation introduces an elastase cleavage site, our molecular dynamics simulations do not support their inference of increased replication efficiency by promoting elastase-mediated S1/S2 cleavage. 2020 NPJ vaccines Result SARS_CoV_2 D614G 49 54 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. 11 After structural alignment, we found that four mutants exhibited a significant difference in protein structural morphology from their control ones (RMSD >= 5.0 A), which were Q57H Orf3a, G251V Orf3a, S194L N, and R203K/G204R N (Figure 1 and Table S1). 2021 Journal of medical virology Result SARS_CoV_2 G251V;Q57H;R203K;S194L;G204R 191;179;217;204;223 196;183;222;209;228 ORF3a;ORF3a;N;N 184;197;210;229 189;202;211;230 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. Among them, we noticed that the incidence of R203K/G204R in N was as high as 86.97% in Bangladesh; meanwhile, it was also over 50% in the other four countries, with a trend of escalation (Figure 4D). 2021 Journal of medical virology Result SARS_CoV_2 R203K;G204R 45;51 50;56 N 60 61 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. Analogously, the frequency of Q57H in Orf3a in Finland, Egypt, South Korea, and Denmark had shown high incidences, which were 69.4%, 67.26%, 59.72%, and 58.03%, respectively (Figure 4A). 2021 Journal of medical virology Result SARS_CoV_2 Q57H 30 34 ORF3a 38 43 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. Hence, to link SARS-CoV-2 mutations and COVID-19 prevalence, we analyzed the occurrence of these four types of mutations (Q57H and G251V in Orf3a, S194L and R203K/G204R in N) based on CNCB 2019nCoVR. 2021 Journal of medical virology Result SARS_CoV_2 G251V;R203K;S194L;Q57H;G204R 131;157;147;122;163 136;162;152;126;168 ORF3a;N 140;172 145;173 COVID-19 40 48 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. In particular, Q57 residue in control Orf3a was not involved in the protein-binding interfaces, but amino acid substitution Q57H became a hot spot in both Orf3a-S and Orf3a-Orf8 complexes (Figure 3). 2021 Journal of medical virology Result SARS_CoV_2 Q57H 124 128 ORF3a;ORF3a;ORF3a;ORF8;S 38;155;167;173;161 43;160;172;177;162 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. In particular, there were also some mutation combinations, such as P504L/Y541C in nsp13 and R203K/G204R in N (Table S1). 2021 Journal of medical virology Result SARS_CoV_2 P504L;R203K;G204R;Y541C 67;92;98;73 72;97;103;78 Nsp13;N 82;107 87;108 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. Meanwhile, two single substitutions were observed in nsp2, nsp12, nsp13, S, Orf3a, or Orf8, among which mutation D614G in S had the highest incidence (43.27%), and five single ones were found in N. 2021 Journal of medical virology Result SARS_CoV_2 D614G 113 118 ORF3a;Nsp13;Nsp12;Nsp2;ORF8;N;S;S 76;66;59;53;86;195;73;122 81;71;64;57;90;196;74;123 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. Moreover, in the process of Orf3a interacting with M or S, Q57H mutant pairs showed enhanced binding affinity, while G251V mutant pairs had attenuated ones as just mentioned (Figure 2A), suggesting that diverse amino acid replacements in the same protein have given different consequences on binding affinity. 2021 Journal of medical virology Result SARS_CoV_2 G251V;Q57H 117;59 122;63 ORF3a;S 28;56 33;57 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. Strikingly, the binding affinity of Q57H Orf3a-S complex showed the greatest increase (DeltaDeltaG = 4.2 kcal/mol), while the most dramatic decrease was observed in the binding affinity of G251V Orf3a-M complex (DeltaDeltaG = -2.3 kcal/mol; Figure 2A). 2021 Journal of medical virology Result SARS_CoV_2 G251V;Q57H 189;36 194;40 ORF3a;ORF3a;S 41;195;47 46;200;48 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. 12 novel mutations were identified in travelling patients: one stop codon (6887A T) in NSP3(Table 2), eight mutations in ORF1ab: NSP3(7766A > C), NSP4 (8897A > T), NSP5(10,595 T > C), NSP12 (14369G > T, 14993C > T) NSP13 (16301G > T) and NSP14(18670G > T, 19499A > C), two missense mutations in spike S2 (22093G > T, 22425C > T) and one mutation in E gene (26428A > T). 2021 Genomics Result SARS_CoV_2 C14993T;A19499C;C22425T;T10595C;G14369T;G16301T;G18670 T;G18670T;G22093T;A26428T;A7766 C;A8897T 203;256;317;169;191;222;244;244;305;357;134;152 213;266;327;181;201;232;254;254;315;367;143;161 ORF1ab;S;Nsp13;Nsp12;Nsp3;Nsp3;Nsp4;Nsp5;E 121;295;215;184;87;129;146;164;349 127;300;220;189;91;133;150;168;350 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. Among these mutations, four novel mutations were found only in the local patients (NSP3: 6198C > A; NSP8: 12297A > T; NSP4: 8651A > fs; ORF3a: 26103-5TGA > del), two were found in local patients and in patient travelling from France (NSP3: 6281A > G/T; 6285C > A). 2021 Genomics Result SARS_CoV_2 A12297T;C6198A;C6285A 106;89;253 116;98;262 ORF3a;Nsp3;Nsp3;Nsp4;Nsp8 136;83;234;118;100 141;87;238;122;104 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. The most common variants were 23403A > G in the spike protein S2 and 14408C > T in ORF1ab, both in eight samples, and 25563G > T in ORF3a in six samples (Table 1). 2021 Genomics Result SARS_CoV_2 C14408T;A23403G;G25563T 69;30;118 79;40;128 ORF1ab;S;ORF3a 83;48;132 89;53;137 33097660 SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling. Interestingly, when we compared the relative position of Flag-Orf6 and Flag-Orf6M58R to NPCs detected using Nup358 antibodies, we found that the majority of Orf6 signal was <160 nm from NPCs consistent with its association with the NPCs, while the Flag-Orf6M58R foci were broadly distributed across the nuclear envelope. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 M58R;M58R 80;257 84;261 ORF6;ORF6;ORF6;ORF6 62;76;157;253 66;80;161;257 33097660 SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling. Prompted by this observation, we investigated whether a methionine-to-arginine substitution at residue 58 (M58R) was able to affect Orf6 binding to the Nup98-Rae1 complex. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 M58R;M58R 56;107 105;111 ORF6 132 136 33097660 SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling. S7, both KPNA1 and KPNA2 localized to the nucleus in Orf6M58R-expressing cells, indicating that the SARS-CoV-2-dependent cytoplasmic accumulation of the KPNAs is likely a result of the impaired nucleocytoplasmic trafficking due to the Orf6-Nup98 interaction. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 M58R 57 61 ORF6;ORF6 53;235 57;239 33097660 SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling. Strikingly, the M58R mutation dramatically decreased the ability of SARS-CoV-2 Orf6 to interact with overexpressed (SI Appendix. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 M58R 16 20 33097660 SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling. While wild-type SARS-CoV and SARS-CoV-2 Orf6 strongly inhibited the ISRE promoter as expected, the M58R mutation completely abolished the Orf6 IFN antagonistic function. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 M58R 99 103 ORF6;ORF6 40;138 44;142 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. 1e), indicating that the D614G mutation does not affect viral replication or virion infectivity in Vero E6 cells. 2021 Nature Result SARS_CoV_2 D614G 25 30 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. 1f), indicating that D614G enhances viral replication. 2021 Nature Result SARS_CoV_2 D614G 21 26 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. 1h), indicating that the D614G mutation increases the infectivity of SARS-CoV-2 produced from a human lung cell line. 2021 Nature Result SARS_CoV_2 D614G 25 30 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. 7), suggesting that mutation D614G may confer higher susceptibility to serum neutralization. 2021 Nature Result SARS_CoV_2 D614G 29 34 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. An important question is whether the D614G substitution could reduce vaccine efficacy, assuming G614 virus continues to circulate. 2021 Nature Result SARS_CoV_2 D614G 37 42 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. Dramatic enhancement of viral replication by spike mutation D614Gin a primary human airway tissue model. 2021 Nature Result SARS_CoV_2 D614G 60 67 S 45 50 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. Effect of spike mutation D614G on neutralization susceptibility. 2021 Nature Result SARS_CoV_2 D614G 25 30 S 10 15 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. Enhancement of viral replication and infectivity by the spike D614G substitution in human lung epithelial cells. 2021 Nature Result SARS_CoV_2 D614G 62 67 S 56 61 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. However, the G614 virus retained higher infectivity than the D614 virus at all temperatures, suggesting that the D614G mutation may increase the stability of SARS-CoV-2. 2021 Nature Result SARS_CoV_2 D614G 113 118 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. The in vivo relevance of the D614G mutation was evaluated in the golden Syrian hamster model (Extended Data. 2021 Nature Result SARS_CoV_2 D614G 29 34 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. The results suggest that mutation D614G may modulate spike protein conformation to affect mAb neutralization in an epitope-specific manner. 2021 Nature Result SARS_CoV_2 D614G 34 39 S 53 58 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. These results suggest that (i) more spike protein is cleaved to S1/S2 within virions produced from Calu-3 cells compared to Vero E6 cells and (ii) the D614G substitution does not significantly affect the spike cleavage ratio. 2021 Nature Result SARS_CoV_2 D614G 151 156 S;S 36;204 41;209 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. To examine the effect of D614G on virus stability, we measured the decay of infectivity of D614 and G614 viruses over time at 33 C, 37 C, and 42 C (Extended Data. 2021 Nature Result SARS_CoV_2 D614G 25 30 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. To further define the function of D614G mutation inhuman respiratory tract, we characterized the replication of D614 and G614 viruses in a primary human airway tissue model. 2021 Nature Result SARS_CoV_2 D614G 34 39 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. We first examined the effect of the spike D614G substitution on viral replication in cell culture. 2021 Nature Result SARS_CoV_2 D614G 42 47 S 36 41 33106822 COVID-19 neutralizing antibodies predict disease severity and survival. Given the importance of humoral immunity in preventing most viral infections, the recent emergence of a mutation in the SARS-CoV-2 spike protein (D614G) has raised concerns for the potential for convalescent patients to become re-infected. 2020 medRxiv Result SARS_CoV_2 D614G 146 151 S 131 136 33106822 COVID-19 neutralizing antibodies predict disease severity and survival. To determine the impact of this variant on the neutralization potency of sera from patients previously infected with SARS-CoV-2, we introduced the D614G mutation into the SARS-CoV-2 Delta18 spike (Figure 5A). 2020 medRxiv Result SARS_CoV_2 D614G 147 152 S 190 195 33108902 ACE2 and TMPRSS2 Potential Involvement in Genetic Susceptibility to SARS-COV-2 in Cancer Patients. In Finnish male, the E37 K variant was found with a frequency of 0.05%. 2020 Cell transplantation Result SARS_CoV_2 E37K 21 26 33108902 ACE2 and TMPRSS2 Potential Involvement in Genetic Susceptibility to SARS-COV-2 in Cancer Patients. Interestingly, among those with the highest frequency, the variant S19P belongs to the SARS-CoV-2 spike protein binding site and it was exclusively present in Africans with a frequency of 0.2%. 2020 Cell transplantation Result SARS_CoV_2 S19P 67 71 S 98 103 33109270 Molecular detection of drug resistant polymorphisms in Plasmodium falciparum isolates from Southwest, Nigeria. For Pfk13 C580Y locus, mixed alleles (both 580C and 580Y) were suspected in 2 isolates but the mutant type variant was not confirmed by Sanger sequencing of amplicons against the reference strain P. 2020 BMC research notes Result SARS_CoV_2 C580Y 10 15 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. Of these, n = 79 (57%) carried the S protein D614G SNV, a mutation implicated in higher pathogenicity of the virus. 2020 Cell reports Result SARS_CoV_2 D614G 45 50 S 35 36 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. Samples carrying the D614G SNV had higher SARS-CoV-2 genome loads as measured by CDC N3-primer directed real-time qRT-PCR for SARS-CoV-2 (p <= 0.002 by Wilcoxon signed rank test). 2020 Cell reports Result SARS_CoV_2 D614G 21 26 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. A total of 154 (53.1%) harbored the D614G substitution in the S protein and were distributed in clades 20A (n = 126; 43.4%), 20B (n = 23; 7.9%), and 20C (n = 5; 1.7%). 2021 Journal of virology Result SARS_CoV_2 D614G 36 41 S 62 63 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. Among these genomes, 30 (17.1%) carried the D614G substitution and were obtained from samples from nine different regions of Spain (Madrid, Andalusia, Canary Islands, Castilla y Leon, Extremadura, Catalonia, Balearic Islands, Basque Country, and Valencia). 2021 Journal of virology Result SARS_CoV_2 D614G 44 49 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. Approximately 40% of all genome sequences from Spain harbored the L84S substitution in ORF8, which is, by far, the highest frequency found in Europe. 2021 Journal of virology Result SARS_CoV_2 L84S 66 70 ORF8 87 91 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. On the other hand, 114 (39.3%) branched in clade 19B, characterized by the presence of the L84S substitution in ORF8. 2021 Journal of virology Result SARS_CoV_2 L84S 91 95 ORF8 112 116 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. Several sequences from Spain were distributed throughout clade 19A, which includes 13 Spanish sequences harboring the G251V substitution in ORF3 (GISAID clade V), 7 genomes included in GISAID group O, and 3 other sequences in GISAID group L. 2021 Journal of virology Result SARS_CoV_2 G251V 118 123 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. The remaining 23 genome sequences branched within clade 19A (7.9%), including 13 sequences presenting the G251V substitution in ORF3 (4.5%) and 10 without this genetic marker (3.4%) (Table S1). 2021 Journal of virology Result SARS_CoV_2 G251V 106 111 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. This phylogenetic cluster included sequences with the G251V substitution in ORF3 protein along with other sequences without any of the major clade-defining residues. 2021 Journal of virology Result SARS_CoV_2 G251V 54 59 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. Variants with the D614G substitution became dominant in Spain in week 12 (15 to 21 March 2020). 2021 Journal of virology Result SARS_CoV_2 D614G 18 23 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. After the first Spike Y839 variant was detected in Italy (Lombardy) on 21 February, the mutation D839Y has been reported in 12 other countries from four continents (Europe, Oceania, Asia and America) (Figure 5). 2020 Emerging microbes & infections Result SARS_CoV_2 D839Y 97 102 S 16 21 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Concordantly, the first D839Y genome sequence reported worldwide was collected in Italy (Lombardy) on 21 February (Italy/PV-5314-N/2020; GISAID accession number EPI_ISL_451307) (Table S2), being identical (i.e, Nextstrain clade 20A background plus the G24077 T SNP) to the "founder" Spike Y839 variant genome sequences detected in Portugal (https://insaflu.insa.pt/covid19). 2020 Emerging microbes & infections Result SARS_CoV_2 D839Y;G24077T 24;252 29;260 S 283 288 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. In this particular case, we cannot exclude the hypothesis that the G24077 T nucleotide change might have been introduced in a clade "20C" SARS-CoV-2 by recombination, as "20C" and "20A harbouring Y839" viruses co-circulated in Wales during the collection period (13 out of the 51 Spike 839Y genomes from UK were collected in Wales between 10 April and 25 May). 2020 Emerging microbes & infections Result SARS_CoV_2 G24077T 67 75 S 280 285 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Most viruses (89.8%) integrate the phylogenetic branch enrolling clades 20A (40.8%), 20B (46.1%) and 20C (2.9%), carrying, among other genetic markers, the D614G amino acid replacement in the Spike protein. 2020 Emerging microbes & infections Result SARS_CoV_2 D614G 156 161 S 192 197 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Notwithstanding, fine-tune integration of the 92 Spike Y839 genomes detected abroad in the "global" phylogeny (using Nextstrain https://nextstrain.org/ncov and Nextclade https://clades.nextstrain.org/) pointed out that the D839Y amino acid change likely emerged independently in two other instances. 2020 Emerging microbes & infections Result SARS_CoV_2 D839Y 223 228 S 49 54 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Of those, 92 genomes revealed the same G24077T nucleotide substitution (leading to the D839Y amino acid replacement) in a SARS-CoV-2 with Spike G614 background. 2020 Emerging microbes & infections Result SARS_CoV_2 D839Y;G24077T 87;39 92;46 S 138 143 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. proportion of confirmed cases with SARS-CoV-2 genome data) between the different countries, it is noteworthy that, apart from Portugal, D839Y genomes represent ~5% of all sequences made available at GISAID (as of 23 July 2020) by three countries (Estonia, Georgia and New Zealand) (Figure 5). 2020 Emerging microbes & infections Result SARS_CoV_2 D839Y 136 141 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. The potential third independent emergence of a Spike Y839 variant is supported by the four genomes collected in India, as they cluster apart from other G614+Y839 genomes, forming a sub-branch (supported by 6 SNPs, including G24077T) within a large cluster mostly enrolling genomes from India. 2020 Emerging microbes & infections Result SARS_CoV_2 G24077T 224 231 S 47 52 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. This observation is supported by one genome sequence collected in the United Kingdom (Wales) on 24 April (Wales/PHWC-35B01/2020; GISAID accession EPI_ISL_474528), which presents all clade-defining SNPs of Nextstrain Clade 20C plus four additional SNPs (including G24077 T). 2020 Emerging microbes & infections Result SARS_CoV_2 G24077T 263 271 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. To explore the frequency of SARS-CoV-2 D839Y mutation (and other mutations in 839 protein position) at worldwide level, we downloaded 66548 amino acid sequences (and associated metadata) of SARS-CoV-2 Spike protein available at GISAID (as of 23 July 2020). 2020 Emerging microbes & infections Result SARS_CoV_2 D839Y 39 44 S 201 206 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Within clade 20A, a SARS-CoV-2 variant carrying the Spike amino acid change D839Y (due to a G24077 T SNP) was detected early (7 March 2020) during the COVID-19 epidemic in Portugal. 2020 Emerging microbes & infections Result SARS_CoV_2 D839Y;G24077T 76;92 81;100 S 52 57 COVID-19 151 159 33140034 Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein. As a result, ablation of these N-linked sites reduces the binding responses for N165A and N234A mutants to ~90% and ~60% (p = 0.0051 and p = 0.0002, Student's t test) as high as the parent S-2P variant, respectively (Figure 4). 2020 ACS central science Result SARS_CoV_2 N165A;N234A 80;90 85;95 N;S 31;189 32;190 33140034 Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein. Here, through biolayer interferometry experiments, we show that binding to ACE2 is remarkably reduced for the N234A mutant and slightly impaired for the N165A variant, whereas it is completely abolished in the case of an engineered S protein with all three RBDs locked in the "down" state. 2020 ACS central science Result SARS_CoV_2 N165A;N234A 153;110 158;115 RBD;S 257;232 261;233 33140034 Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein. Importantly, a negative control spike (HexaPro), engineered with S383C/D985C mutations to lock all three RBDs in the closed state through a disulfide bond, shows no binding to ACE2. 2020 ACS central science Result SARS_CoV_2 S383C;D985C 65;71 70;76 S;RBD 32;105 37;109 33140034 Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein. In light of these observations, an additional third system, "Mutant", was generated from Open by introducing N165A and N234A mutations, which led to glycan deletions at the respective sites. 2020 ACS central science Result SARS_CoV_2 N165A;N234A 109;119 114;124 33140034 Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein. In this context, our findings pinpoint the possibility of controlling the RBD conformational plasticity by introducing N165A and N234A mutations. 2020 ACS central science Result SARS_CoV_2 N165A;N234A 119;129 124;134 RBD 74 77 33140034 Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein. This behavior is confirmed even in the case of a single point mutation (N234A), as revealed by the additional independent simulations of the spike head described in Section 2 of SI. 2020 ACS central science Result SARS_CoV_2 N234A 72 77 S 141 146 33140034 Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein. To quantify RBD accessibility in solution, we used biolayer interferometry to measure ACE2 binding to the S protein containing either N165A or N234A substitutions. 2020 ACS central science Result SARS_CoV_2 N165A;N234A 134;143 139;148 RBD;S 12;106 15;107 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. Because the S1 component of the S is the domain that interacts with receptor, a reductionist approach was used to determine if the D614G played a role in hACE2 binding by monomeric S1 proteins. 2020 bioRxiv Result SARS_CoV_2 D614G 131 136 S 32 33 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. Collectively, these results show that the D614G change in the S protein is associated with enhanced hACE2 binding and increased replication in primary human airway epithelial models of SARS-CoV-2 infection. 2020 bioRxiv Result SARS_CoV_2 D614G 42 47 S 62 63 COVID-19 185 205 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. Recombinant S1 constructs that express two S1 molecules attached to an IgG carboxyl-terminus were generated to further evaluate the impact the S-D614G substitution. 2020 bioRxiv Result SARS_CoV_2 D614G 145 150 S 143 144 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. The enhanced binding to hACE2 protein rendered by the S-D614G substitution also resulted in enhanced S1 binding to Baby Hamster Kidney (BHK) cells expressing exogenous hACE2 (BHK-hACE2) in a different binding assay (Figure 1B, Extended Data Figure 1B). 2020 bioRxiv Result SARS_CoV_2 D614G 56 61 S 54 55 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. These observations confirm that in the case of SARS-CoV-2S-614D or SARS-CoV-2S-614G infections, the S-D614G substitution does not seem crucial for clinical outcomes, which again underscores the hamster as a highly sensitive disease model. 2020 bioRxiv Result SARS_CoV_2 D614G 102 107 S 100 101 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. To assess the impact of S-614G in the context of virus infection we generated an isogenic D614G virus pair based on our reverse genetics system for SARS-CoV-2. 2020 bioRxiv Result SARS_CoV_2 D614G 90 95 S 24 25 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. To determine whether the S-D614G substitution directly affects the binding between the S and hACE2, we first used the biolayer interferometry (BLI) technology to quantify their biding affinity. 2020 bioRxiv Result SARS_CoV_2 D614G 27 32 S;S 25;87 26;88 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. For Illumina sequencing, G22017T was found in 5.0% (356/7082) of the reads in the first specimen, while this mutation was found in 60.4% (4578/7574) in the second specimen. 2021 Clinical microbiology and infection Result SARS_CoV_2 G22017T 25 32 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. For nanopore sequencing, the G22017T (guanine to thymine) was found in 3.8% (158/4116) of the reads in the sputum specimen collected on day 7 (first specimen) after symptom onset, while it accounts for 67.8% (12060/17795) of reads in the saliva specimen collected on day 9 after symptom onset (second specimen). 2021 Clinical microbiology and infection Result SARS_CoV_2 G22017T 29 36 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. G22017T resulted in the non-synonymous mutation of W152L (tryptophan to leucine) in the N-terminal domain of the S1 subunit. 2021 Clinical microbiology and infection Result SARS_CoV_2 W152L;G22017T 51;0 56;7 N 88 89 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. Next, we determined the prevalence of W152L mutation among SARS-CoV-2 isolates deposited in GISAID up to 15 September 2020 (Table S5). 2021 Clinical microbiology and infection Result SARS_CoV_2 W152L 38 43 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. Of 92942 sequences available, 21 (0.023%) had W152L mutation. 2021 Clinical microbiology and infection Result SARS_CoV_2 W152L 46 51 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. As expected, the genomes harboring the S-protein variant were more numerous than those that preserved the original mutation, which is consistent with the rapid expansion of the D614G mutation and its associated haplotype. 2020 Evolutionary bioinformatics online Result SARS_CoV_2 D614G 177 182 S 39 40 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. It is important to note that unlike D614G and L323P, the amino acid present in the reference sequence remains dominant in these cases. 2020 Evolutionary bioinformatics online Result SARS_CoV_2 D614G;L323P 36;46 41;51 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. Similarly, a P323L mutation in NSP12, the viral RNA-dependent RNA polymerase encoded in ORF1b also showed a reversal in entropy of -0.22 bits, as the leucine (L) variant increased in prevalence 18.6% (from 63.8% to 82.4%) over the proline (P) reference, which also decreased 18.6% in incidence. 2020 Evolutionary bioinformatics online Result SARS_CoV_2 P323L 13 18 RdRp;Nsp12 48;31 76;36 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. The P153S mutation of NSP3 was a second variant that originated in April in Asia. 2020 Evolutionary bioinformatics online Result SARS_CoV_2 P153S 4 9 Nsp3 22 26 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. The spread of the D614G mutation in the S-protein tightly followed that of the P323L mutation of NSP12, confirming their haplotypic relationship. 2020 Evolutionary bioinformatics online Result SARS_CoV_2 D614G;P323L 18;79 23;84 Nsp12;S 97;40 102;41 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. This observation agrees with previously reported evidence (assessed April 6) of a D614G mutation of S-protein that increases case fatality rate. 2020 Evolutionary bioinformatics online Result SARS_CoV_2 D614G 82 87 S 100 101 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. With the exception of the P13L mutation of the N-protein, all variants of structural proteins originated preponderantly in Europe during the months of January and February but expanded globally to other continents in subsequent months. 2020 Evolutionary bioinformatics online Result SARS_CoV_2 P13L 26 30 N 47 48 33157300 SARS-CoV-2 spread across the Colombian-Venezuelan border. Additionally, we identified three substitutions in the nucleocapsid (N) gene of VEN-89312 changing GGG-to-AAC at positions 28,616-28,618 resulting R203K/G204R substitutions according to the whole-genome position after removing the 5'UTR. 2020 Infection, genetics and evolution Result SARS_CoV_2 R203K;G204R 147;153 152;158 N;5'UTR;N 55;231;69 67;236;70 33157300 SARS-CoV-2 spread across the Colombian-Venezuelan border. The three Venezuelan genomes carried a G-to-A point mutation at position 23,403 resulting in a D614G substitution in the spike (S) protein. 2020 Infection, genetics and evolution Result SARS_CoV_2 D614G 95 100 S;S 121;128 126;129 33157300 SARS-CoV-2 spread across the Colombian-Venezuelan border. These R203K/G204R substitutions, which have been reported previously in other South American genomes, were absent from the two other Venezuelan genomes we sequenced. 2020 Infection, genetics and evolution Result SARS_CoV_2 R203K;G204R 6;12 11;17 33159417 Humanized COVID-19 decoy antibody effectively blocks viral entry and prevents SARS-CoV-2 infection. Notably, NTU3, NTU14, and NTU25 strains harbor the D614G mutation, which has been reported to increase the viral infectivity (Korber et al, 2020; Yurkovetskiy et al, 2020). 2021 EMBO molecular medicine Result SARS_CoV_2 D614G 51 56 33159417 Humanized COVID-19 decoy antibody effectively blocks viral entry and prevents SARS-CoV-2 infection. We design a humanized decoy antibody (ACE2-FC fusion protein) that specifically binds to the SARS-CoV-2 Spike protein and blocks entry of six clinical isolates including the D614G variant strains with high infectivity, thus inhibiting SARS-CoV-2 infection of host cells. 2021 EMBO molecular medicine Result SARS_CoV_2 D614G 174 179 S 104 109 COVID-19 235 255 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. aspartic acid 614 codon "GAT" (reference sequence) was substituted by glycine 614 codon "GGT" (D614G) by chromatographic DNA sequencing result. 2020 Immune network Result SARS_CoV_2 D614G 95 100 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. Chromatographic DNA sequencing data of the four patients exhibited valine 524 codon "GTT" (reference sequence) that was substituted by aspartic acid 524 codon "GAT" (V524D). 2020 Immune network Result SARS_CoV_2 V524D 166 171 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. DNA sequencing of the S gene cDNA revealed three mutations in addition to the known D614G mutation. 2020 Immune network Result SARS_CoV_2 D614G 84 89 S 22 23 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. Interestingly, the known mutation site D614G residue including three novel mutation sites are conserved between severe acute respiratory syndrome (SARS) and SARS-CoV2 in. 2020 Immune network Result SARS_CoV_2 D614G 39 44 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. The alignment of four SARS-CoV2 spike amino acid sequences compared to the wild type sequence revealed that there are two additional mutations in the critical RBD and another mutation in subdomain (SD) 2, which is very close to the known mutation residue D614G. 2020 Immune network Result SARS_CoV_2 D614G 255 260 S;RBD 32;159 37;162 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. The chromatographic DNA sequencing result of the four patients showed glycine 504 codon "GGT" (reference sequence) was substituted by aspartic acid 504 codon "GAT" (G504D). 2020 Immune network Result SARS_CoV_2 G504D 165 170 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. The known mutation (D614G) residue highlighted by light blue with red amino acid residue. 2020 Immune network Result SARS_CoV_2 D614G 20 25 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. The known single point mutation at D614G in SD2 of spike has been reported by different groups. 2020 Immune network Result SARS_CoV_2 D614G 35 40 S 51 56 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. The last mutation site was due to proline 579 codon "CCA" (reference sequence) being replaced by leucine 579 codon "CTA" (P579L) in all four patients. 2020 Immune network Result SARS_CoV_2 P579L 122 127 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. Therefore, we focused on the specific mutation region of S gene in which aspartic acid 614 was mutated into glycine (D614G). 2020 Immune network Result SARS_CoV_2 D614G;D614G 73;117 115;122 S 57 58 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. This known D614G mutation was present in all four patients. 2020 Immune network Result SARS_CoV_2 D614G 11 16 33163695 Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh. We have observed two types of aa (H125Y, A2V) changes in the membrane (M) protein followed by no changes in the envelope (E) protein. 2020 Gene reports Result SARS_CoV_2 A2V;H125Y 41;34 44;39 Membrane;E 61;122 69;123 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. Among them, the ORF1ab polyprotein harbored 22 non-synonymous mutations: seven in nsp2 (T265I, V378I, G392D, H417R, I739V, P765S, and D448Del) three in nsp12-RdRp (M4555T, T4847I and T5020I), three in nsp13-nsp13 (V5661A, P5703L, and M5865V), two in nsp3-multi-domains (A876T and T1246I), two in nsp5-main proteinase (G3278S and K3353R), two in nsp15-EndoRNAse (I6525T, Ter6668W), and one in each of three proteins; nsp6-transmembrane domain (L3606F), nsp4-transmembrane domain-2 (F3071Y), and nsp14-exonuclease (S5932F). 2020 PloS one Result SARS_CoV_2 G392D;H417R;I739V;K3353R;M5865V;P5703L;P765S;T1246I;T4847I;T5020I;V378I;A876T;F3071Y;G3278S;I6525T;L3606F;M4555T;S5932F;T265I;V5661A 102;109;116;329;234;222;123;280;172;183;95;270;481;318;362;443;164;513;88;214 107;114;121;335;240;228;128;286;178;189;100;275;487;324;368;449;170;519;93;220 Exonuclease;EndoRNAse;ORF1ab;Nsp13;Nsp13;Nsp12;Nsp2;Nsp3;Nsp4;Nsp5;Nsp6;RdRP 500;351;16;201;207;152;82;250;452;296;416;158 511;360;22;206;212;157;86;254;456;300;420;162 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. C1 is also composed of two subclades, SCB 1 sharig the mutation G251V (ORF3a) first identified in strains from china and further emerged in European strains, such as England and Iceland. 2020 PloS one Result SARS_CoV_2 G251V 64 69 ORF3a 71 76 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. Following the first appearance it started emerging in other European countries mainly in Spain, this clade has also emerged in the USA in mid-Jan and gives birth to a new cluster containing 444 strains all sharing a C17747T mutation (Leu5828Leu, ORF1ab) starting from mid-Feb. 2020 PloS one Result SARS_CoV_2 C17747T;L5828L 216;234 223;244 ORF1ab 246 252 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. For the four other hotspot mutations were distributed in ORF3a (Q57H and G251V) and nucleocapsid phosphoprotein (R203K and G204R). 2020 PloS one Result SARS_CoV_2 G204R;G251V;Q57H;R203K 123;73;64;113 128;78;68;118 N;ORF3a 84;57 96;62 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. However, among the recurrent non-synonymous, synonymous, deletion and intergenic mutations, we found G251V (in ORF3a), and S5932F (in ORF1ab) present on all continents except Africa (Fig 3). 2020 PloS one Result SARS_CoV_2 G251V;S5932F 101;123 106;129 ORF1ab;ORF3a 134;111 140;116 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. However, cluster harboring D614G (in spike), F924F (in orf1ab), and L4715L (in orf1ab) mutations, showed no correlation and were scatted through all countries especially those from Europe. 2020 PloS one Result SARS_CoV_2 D614G;F924F;L4715L 27;45;68 32;50;74 ORF1ab;ORF1ab;S 55;79;37 61;85;42 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. In Algeria, the genomes harbored mutations very similar to those in Europe, including two recurrent mutations T265I and Q57H of the ORF3a. 2020 PloS one Result SARS_CoV_2 Q57H;T265I 120;110 124;115 ORF3a 132 137 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. Likewise, the spike protein harbored three non-synonymous mutations, including V483A in the receptor-binding domain (RBD). 2020 PloS one Result SARS_CoV_2 V483A 79 84 S;RBD 14;117 19;120 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. On the other hand, mutations as V378I and L3606F (in orfab1), 29742 C>T (intergenic), L139L in (in nucleocapside) were mainly correlated with Pakistan, Norway, Georgia, Taiwan, Kuwait, Australia, and Turkey while (S2839S, F3071Y and T4847I), D128D and G196V mutations in orf1ab, nucleocapsid, ORF3a, respectively, were mainly present in Spain, Chile, and Greece. 2020 PloS one Result SARS_CoV_2 C29742T;D128D;F3071Y;G196V;L139L;L3606F;T4847I;V378I;S2839S 62;242;222;252;86;42;233;32;214 71;247;228;257;91;48;239;37;220 N;ORF1ab;ORF3a 279;271;293 291;277;298 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. SARS-CoV-2 genomes also harbored three co-occurrent mutations R203K, R203R and G204R in the N protein and were present in all continents except Africa and Asia (besides Taiwan). 2020 PloS one Result SARS_CoV_2 G204R;R203K;R203R 79;62;69 84;67;74 N 92 93 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. Strains from the second clad C2 shared the spike mutation D614G (S) and harbored three subclades, this clade started in shanghai end of Jan. 2020 PloS one Result SARS_CoV_2 D614G 58 63 S;S 43;65 48;66 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. The first subcluster SCB3 harbored strain sharing two mutation R203K (N) and G204R (N) harboring largely strains from Europe and some strains from North Africa (France and USA). 2020 PloS one Result SARS_CoV_2 G204R;R203K 77;63 82;68 N;N 70;84 71;85 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. The most represented was D614G mutation at spike protein with 43.46% (n = 1.333) of the genomes, the second was L84S (at ORF8) found in 23.21% (n = 712). 2020 PloS one Result SARS_CoV_2 D614G;L84S 25;112 30;116 S;ORF8 43;121 48;125 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. The phylogenetic analysis revealed two main clades C1 and C2; the original clade C1 harboring the mutation F3606L and starting since the beginning of the pandemic contains mainly Chinese strains from Dec to mid-Feb. 2020 PloS one Result SARS_CoV_2 F3606L 107 113 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. The remainder was found in the core phosphoprotein (S193I, S194L, S197L, S202N, R203K, and G204R), membrane glycoprotein (D3G, T175M), ORF3a (Q57H, H93Y, G196V, and G251S V62) and ORF62884). 2020 PloS one Result SARS_CoV_2 G196V;G204R;G251S;H93Y;R203K;S194L;S197L;S202N;T175M;D3G;Q57H;S193I 154;91;165;148;80;59;66;73;127;122;142;52 159;96;170;152;85;64;71;78;132;125;146;57 Membrane;ORF3a 99;135 107;140 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. The second subclade SCB2 also stared in China at the beginning of Jan and harbored the mutation L84S (ORF8). 2020 PloS one Result SARS_CoV_2 L84S 96 100 ORF8 102 106 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. The second subcluster SCB4 harbored strain from Europe with the Q57H (ORF3a) mutation, these clusters started in France and Netherland during mid-Feb. 2020 PloS one Result SARS_CoV_2 Q57H 64 68 ORF3a 70 75 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. The T265I, D614G and L84S hotspot mutations located in orf1ab and Spike proteins respectively were introduced into the virus for the first time in late February (Fig 4B). 2020 PloS one Result SARS_CoV_2 D614G;L84S;T265I 11;21;4 16;25;9 ORF1ab;S 55;66 61;71 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. Thus, the gene coding for orf1ab had four mutations hotspots, including S5932F of nsp14-exonuclease, M5865V of nsp13 helicase L3606F of nsp6 transmembrane domain and T265I of nsp2 found with 17.02%, 16.56%, 14.38% and 10.66% of the total genomes, respectively. 2020 PloS one Result SARS_CoV_2 L3606F;M5865V;S5932F;T265I 126;101;72;166 132;107;78;171 Exonuclease;Helicase;ORF1ab;Nsp13;Nsp2;Nsp6 88;117;26;111;175;136 99;125;32;116;179;140 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. We observed that most recurrent mutations clusters could be divided into four groups; the bigger cluster compromised nine mutations from the ten hotspots, while the first cluster harbored only the orf1ab mutation L3606F. 2020 PloS one Result SARS_CoV_2 L3606F 213 219 ORF1ab 197 203 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. While F924F, L4715L (in orf1ab), D614G (in spike) appeared in all strains except those from Asia. 2020 PloS one Result SARS_CoV_2 D614G;F924F;L4715L 33;6;13 38;11;19 ORF1ab;S 24;43 30;48 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. 3B) G28881A, G28882A, and G28883C. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 G28881A;G28882A;G28883C 4;13;26 11;20;33 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. Among the TTG signature SNVs, C14408T (nsp12, P4715L) is located in the RdRp gene that plays a role in replication, and A23403G (S protein, D614G) impacts the S protein that plays a role in receptor binding, membrane fusion, and virus entry. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 A23403G;C14408T;D614G;P4715L 120;30;140;46 127;37;145;52 Membrane;Nsp12;RdRP;S;S 208;39;72;129;159 216;44;76;130;160 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. and they exhibited relatively low pairwise allelic associations:R2(G11083T, C14805T) = 0.469, R2(G11083T, G26144T) = 0.553, and R2(C14805T, G26144T) = 0.723. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 C14805T;G26144T;G26144T;C14805T;G11083T;G11083T 76;106;140;131;67;97 83;113;147;138;74;104 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. For example, in type II signature SNVs C8782T and T28144C that were also used to define the S and L type of SARS-CoV-2, these two SNVs (i.e., S type) first coappeared in strain MT291826 on December 30, 2019, and the coefficient of allelic association is R2 = 0.987. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 C8782T;T28144C 39;50 45;57 S 92 93 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. However, the TTG signature SNVs persisted, but C23575T was lost immediately in the samples. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 C23575T 47 54 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. If C3730T contributes to the fitness gain, it must be at the RNA level. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 C3730T 3 9 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. In addition to the three type VI signature SNVs, five additional subtype SNVs with variation frequencies of >0.1 included C1059T (nsp2, T265I), G25563T (ORF3a, Q57H), G28881A (N, R203K), G28882A (N, R203K), and G28883C (N, G204R). 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 C1059T;G204R;G25563T;G28881A;G28882A;G28883C;Q57H;R203K;R203K;T265I 122;223;144;167;187;211;160;179;199;136 128;228;151;174;194;218;164;184;204;141 ORF3a;Nsp2;N;N;N 153;130;176;196;220 158;134;177;197;221 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. In addition to the three type VI signature SNVs, VIa carries signature SNVs C1059T and G25563T and was first coobserved in France (EPI_ISL_418218) on February 21, 2020, and the coefficient of allelic association R2 = 0.735. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 C1059T;G25563T 76;87 82;94 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. In addition, the signature SNVs with high allelic association are typically located in distant regions, except for type IV signature SNVs C17747T and A17858G and the sub-VI SNVs (refer to the next section and. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 A17858G;C17747T 150;138 157;145 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. In contrast, type III signature SNVs G11083T, C14805T, and G26144T first occurred sequentially in different strains on different dates. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 C14805T;G11083T;G26144T 46;37;59 53;44;66 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. Interestingly, C3730T (nsp3, F924F) is a synonymous mutation in nsp3. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 C3730T;F924F 15;29 21;34 Nsp3;Nsp3 23;64 27;68 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. Nevertheless, the significance of C241T SNV deserves further investigation. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 C241T 34 39 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. S6), with another SNV C23575T (S protein, C671C) in the same strain EPI_ISL_422425 in China. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 C23575T;C671C 22;42 29;47 S 31 32 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. Since the SNV C241T in the 5' untranslated region (UTR) has uncertain significance, and the association properties can be represented by the other three strongly associated signature SNVs. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 C241T 14 19 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. The proportion of VIb signature SNVs G28881A, G28882A, and G28883C in type VI (38.56%) has exceeded the proportion of VIa signature SNVs C1059T and G25563T (34.20%). 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 C1059T;G25563T;G28881A;G28882A;G28883C 137;148;37;46;59 143;155;44;53;66 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. The SNV (C241T) in the 5' UTR in type VI is also in strong allelic association with the three signature SNVs. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 C241T 9 14 5'UTR 23 29 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. There is another SNV in type VI (C241T in the 5' UTR) that is in strong allelic association with the three signature SNVs. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 C241T 33 38 5'UTR 46 52 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. This additional C23575T SNV reappeared in different strains occasionally in later samples. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 C23575T 16 23 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. Two type IV signature SNVs, C17747T and A17858G, first coappeared in strain EPI_ISL_413456 in the United States on February 20, 2020, and the coefficient of allelic association is R2(C17747T, A17858G) = 0.973. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 A17858G;A17858G;C17747T;C17747T 40;192;28;183 47;199;35;190 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. Two type V signature SNVs, G1397A and T28688C, first coappeared in strain EPI_ISL_412981 from China on January 18, 2020, and the coefficient of allelic association is R2 = 0.962. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 G1397A;T28688C 27;38 33;45 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. Type VI signature SNVs C3037T, C14408T, and A23403G (abbreviated as CCA for the reference genome and TTG for type VI) first coappeared in strain EPI_ISL_422425 from China on January 24, 2020, and the pairwise coefficient of allelic association is R2(C3037T, C14408T) = 0.977, R2(C3037T, A23403G) = 0.992, and R2(C14408T, A23403G) = 0.977. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 A23403G;A23403G;A23403G;C14408T;C14408T;C3037T;C14408T;C3037T;C3037T 44;287;321;31;258;23;312;250;279 51;294;328;38;265;29;319;256;285 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. VIb carries signature SNVs G28881A, G28882A, and G28883C in strong allelic association and was first coobserved in Germany (EPI_ISL_412912) on the same date, February 25, 2020, and the coefficient of pairwise allelic association is R2(G28881A, G28882A) = 0.997, R2(G28881A, G28883C) = 0.997, and R2(G28882A, G28883C) = 1. 2020 Proc Natl Acad Sci U S A Result SARS_CoV_2 G28881A;G28882A;G28882A;G28883C;G28883C;G28883C;G28881A;G28881A;G28882A 27;36;244;49;274;308;235;265;299 34;43;251;56;281;315;242;272;306 33185784 Comparison of Binding Site of Remdesivir and Its Metabolites with NSP12-NSP7-NSP8, and NSP3 of SARS CoV-2 Virus and Alternative Potential Drugs for COVID-19 Treatment. The crystal structure of NSP12 (wild type) and its mutation of V557L were generated and superimposed in. 2020 The protein journal Result SARS_CoV_2 V557L 63 68 Nsp12 25 30 33185784 Comparison of Binding Site of Remdesivir and Its Metabolites with NSP12-NSP7-NSP8, and NSP3 of SARS CoV-2 Virus and Alternative Potential Drugs for COVID-19 Treatment. VAL557 is located in between ARG555 and U10 (Uridine phosphate); the metabolite of remdesivir has H-bonds with ARG555 (NSP12) and U10 (UTP), explaining the counteractive nature of the V557L mutation, in regard to the inhibitory effects of remdesivir; the threefold reduction in the efficiency of ATP incorporation with the mutant enzyme. 2020 The protein journal Result SARS_CoV_2 V557L 184 189 Nsp12 119 124 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. The most ubiquitous modifications were C3037T, C14408T (P323L) and A23403G (D614G) occurring in 40/44 samples. 2020 PloS one Result SARS_CoV_2 A23403G;C14408T;C3037T;D614G;P323L 67;47;39;76;56 74;54;45;81;61 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. These variants are key markers to define lineages B.1 (C241T, C3037T, A23403G) and B.1.1 (C241T, C3037T, A23403G, GGG28881..28883AAC), the major lineages in our study. 2020 PloS one Result SARS_CoV_2 A23403G;A23403G;C3037T;C3037T;C241T;C241T 70;105;62;97;55;90 77;112;68;103;60;95 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. Two novel mutations were associated with frameshifts as mentioned previously, the others were non-synonymous changes, namely C4733T (L672F) and A29122C (Q283H). 2020 PloS one Result SARS_CoV_2 A29122C;C4733T;L672F;Q283H 144;125;133;153 151;131;138;158 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. Two other variants C241T and GGG to AAC at 28881-3 were detected in 39 and 33 sequences, respectively. 2020 PloS one Result SARS_CoV_2 C241T 19 24 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. All H57 strains clustered within the clades with spike G614, indicating that this mutation has co-evolved with the D614G mutation (blue box in Figure 1A and coloured as blue in Figure 1C). 2020 Emerging microbes & infections Result SARS_CoV_2 D614G 115 120 S 49 54 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. Also, the Delta3b viruses contain both the orf3a Q57H substitution and D614G mutation. 2020 Emerging microbes & infections Result SARS_CoV_2 D614G;Q57H 71;49 76;53 ORF3a 43 48 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. Based on such drastic change in encoded protein length and structure, we therefore hypothesized that the premature stop codon imposed by Q57H substitution of orf3a would contribute to a loss of function of orf3b in these circulating strains. 2020 Emerging microbes & infections Result SARS_CoV_2 Q57H 137 141 ORF3b;ORF3a 206;158 211;163 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. Consistent with published findings, we identified a distinct clade that represents the G25563T nucleotide mutation, which results in Q57H amino acid substitution in orf3a (red box in Figure 1A, and red lines in Figure 1B). 2020 Emerging microbes & infections Result SARS_CoV_2 G25563T;Q57H 87;133 94;137 ORF3a 165 170 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. For instance, viruses with D614G mutation in Spike protein have acquired enhanced transmissibility and infectivity and become the dominant circulating strain. 2020 Emerging microbes & infections Result SARS_CoV_2 D614G 27 32 S 45 50 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. In our analysis, spike D614G substitution was also included as a reference since it signifies the evolutionary phases of SARS-CoV-2 (blue box in Figure 1A, and blue lines in Figure 1C). 2020 Emerging microbes & infections Result SARS_CoV_2 D614G 23 28 S 17 22 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. Notably, almost all (99.69%) genome sequences with Delta3b genotype contain spike D614G substitution. 2020 Emerging microbes & infections Result SARS_CoV_2 D614G 82 87 S 76 81 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. Q57H substitution in SARS-CoV-2 orf3a contributes to orf3b truncation. 2020 Emerging microbes & infections Result SARS_CoV_2 Q57H 0 4 ORF3b;ORF3a 53;32 58;37 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. Recent emergence of SARS-CoV-2 orf3a Q57H and spike D614G genotype. 2020 Emerging microbes & infections Result SARS_CoV_2 D614G;Q57H 52;37 57;41 S;ORF3a 46;31 51;36 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. The G25563T mutation gives rise to orf3a Q57H substitution and also introduces an early stop codon to orf3b after amino acid 13 (Delta3b), causing a large truncation of 44 amino acids to the protein (Figure 2B). 2020 Emerging microbes & infections Result SARS_CoV_2 G25563T;Q57H 4;41 11;45 ORF3b;ORF3a 102;35 107;40 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. These data reflect that the Q57H substitution resulted in a loss of function of orf3b by introducing an early stop codon. 2020 Emerging microbes & infections Result SARS_CoV_2 Q57H 28 32 ORF3b 80 85 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. This is consistent with our phylogenetic analysis (Figure 1) and further suggests the co-evolution of Delta3b genotype and spike D614G substitution. 2020 Emerging microbes & infections Result SARS_CoV_2 D614G 129 134 S 123 128 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. While some spike G614 strains contain the orf3a Q57H mutation, all orf3a H57 strains contain the spike D614G mutation. 2020 Emerging microbes & infections Result SARS_CoV_2 D614G;Q57H 103;48 108;52 S;S;ORF3a;ORF3a 11;97;42;67 16;102;47;72 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. A structure of a SARS-CoV-1 Mpro C145A mutant in complex with its C-terminal prosequence at 2.2 A resolution has been published previously, representing an enzyme-substrate (ES) Michaelis-like complex. 2020 Nature communications Result SARS_CoV_2 C145A 33 38 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Although the P1'-P3' positions in the SARS-CoV-2 C-terminal processing site are distinct compared to SARS-CoV-1 (SAV vs GKF, respectively), the structure of the S3' subsite region is near identical (RMSD = 0.363 A on 50 common atoms) with the only differences compared to SARS-CoV-1 an A46S substitution on one edge of the cavity that could provide, along with the Ser307 (P1'), van der Waals interactions with the smaller P3' valine. 2020 Nature communications Result SARS_CoV_2 A46S 286 290 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Biological small-angle X-ray scattering (bioSAXS) and SEC-MALS demonstrate the wild-type protein is exclusively a dimer across a range of protein and salt concentrations, while the P9T mutant is predominantly monomeric (Supplementary Figs. 2020 Nature communications Result SARS_CoV_2 P9T 181 184 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Capture of a well-ordered product complex in the catalytically impaired SARS-CoV-2 Mpro C145A mutant is clearly defined in the electron density maps. 2020 Nature communications Result SARS_CoV_2 C145A 88 93 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Crystallographic structure of the SARS-CoV-2 Mpro C145A product complex with physiological substrate. 2020 Nature communications Result SARS_CoV_2 C145A 50 55 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. First, an acyl-enzyme intermediate with the C-terminal residues bound in the active site of a neighboring dimer and Gln306 covalently bound to catalytic Cys145 in the wild-type protein and, second, a product-like form with the same C-terminal autocleavage sequence observed bound non-covalently in the active site of a catalytically inactive C145A mutant. 2020 Nature communications Result SARS_CoV_2 C145A 342 347 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. For the C145A mutant product-like complex, the C-terminus binds in the same extended manner, forming analogous main chain and side chain interactions. 2020 Nature communications Result SARS_CoV_2 C145A 8 13 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. In particular, the S2 subsite is significantly altered when bound to the N-terminal autoprocessing sequence with Leu (P2), as observed in complex with a SARS-CoV-1 Mpro H41A mutant (referred to as Leu-S2 like) compared to that captured here in complex with the wild-type SARS-CoV-2 C-terminal autoprocessing sequence (referred to as Phe-S2 like). 2020 Nature communications Result SARS_CoV_2 H41A 169 173 N 73 74 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. In that context, the active site of the empty protomer in the C145A structure reveals electron density for five water molecules, including one not observed in the wild-type substrate-free protomer active site and lying completely coincident with the proposed deacylating water position in the acyl-enzyme intermediate above, only observed at even greater occupancy. 2020 Nature communications Result SARS_CoV_2 C145A 62 67 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Mutation of the catalytic cysteine to alanine (C145A) abolishes activity, while the dimerization defective P9T (with native active site) lowers the catalytic efficiency by >50 fold. 2020 Nature communications Result SARS_CoV_2 P9T;C145A 107;47 110;52 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. The ordered water (B-factor = 30 A2), is again positioned orthogonally with respect to the other atoms in the trigonal planar thioester group and with a near identical Burgi-Dunitz angle as verified by superposition of the substrate-free active site of the C145A and native acyl-enzyme structures. 2020 Nature communications Result SARS_CoV_2 C145A 257 262 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. This region is critical to dimerization and enzymatic activity, and many mutations affecting both map to this site (for review of these see), including mutation of Pro9 to threonine (P9T) identified and characterized here, which shows significantly diminished dimerization and activity (Supplementary Figs. 2020 Nature communications Result SARS_CoV_2 P9T;P9T 164;183 181;186 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. we also describe a putative deacylating water observed in both the acyl-enzyme intermediate and the empty active site protomer of the C145A mutant product complex. 2020 Nature communications Result SARS_CoV_2 C145A 134 139 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. We also produced the catalytic mutant C145A and a mutant that impacts dimerization, P9T, with similar protocols, see "Methods". 2020 Nature communications Result SARS_CoV_2 C145A;P9T 38;84 43;87 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. We note a structure of SARS-CoV-1 Mpro C145A in a product complex with its C-terminal autocleavage site at 2.8 A resolution has been published previously; however, potentially due to the lower resolution a catalytic water was not observed in that case. 2020 Nature communications Result SARS_CoV_2 C145A 39 44 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. We note the only substitution between SARS-CoV-1 and -2 Mpro in the S3' site:A46S:is in close proximity to the phenyl biaryl and the Ser46 hydroxyl could be a unique site to engage for further development. 2020 Nature communications Result SARS_CoV_2 A46S 77 81 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. Wild-type and C145A Mpro were crystallized at pH 6 in space group C2 with isomorphous unit cell dimensions (Supplementary Table 1). 2020 Nature communications Result SARS_CoV_2 C145A 14 19 33208827 Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19. Pseudovirus carrying the current dominant D614G variant spike was also generated and neutralizing antibodies from mice immunized with S-2P with CpG 1018 and alum were effective against both pseudoviruses carrying the wild-type D614 and mutant D614G versions of spike proteins. 2020 Scientific reports Result SARS_CoV_2 D614G;D614G 42;243 47;248 S;S;S 56;261;134 61;266;135 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. Four additional substitutions (VAF, 79.4%-92.1%) that are almost always accompanied by S D614G (5'UTR 241C>T [VAF, 79.4%], nsp3 F106F [VAF, 88.7%], P323L [VAF, 92.1%], and ORF3a Q57H [VAF, 80.0%]) were also detected in the viral genome from the second infection, which suggests the majority of viral genome in the second infection was clade "G." We also found that 9 variants (ie, nsp1 R124C, nsp2 T85I, nsp3 L744F, nsp3 L1035F, nsp4 V407fs, nsp4 S481L, nsp9 L42P, nsp13 T115I, N T165=) emerged in the second infection with low VAF (20.5%-66.0 %). 2021 Clinical infectious diseases Result SARS_CoV_2 C241T;D614G;F106F;L1035F;L42P;L744F;P323L;Q57H;R124C;S481L;T115I;T85I 102;89;128;421;459;409;148;178;386;447;471;398 108;94;133;427;463;414;153;182;391;452;476;402 ORF3a;Nsp13;5'UTR;Nsp2;Nsp3;Nsp3;Nsp3;Nsp4;Nsp4;N;S 172;465;96;393;123;404;416;429;442;478;87 177;470;101;397;127;408;420;433;446;479;88 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. Notably, the substitution D614G in S protein (VAF, 84.8%) was detected, which implies that this viral genome corresponds with another clade ("G"). 2021 Clinical infectious diseases Result SARS_CoV_2 D614G 26 31 S 35 36 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. Of these, nsp6 L37F and ORF3a G251V were the key substitutions that characterized clade "V". 2021 Clinical infectious diseases Result SARS_CoV_2 G251V;L37F 30;15 35;19 ORF3a;Nsp6 24;10 29;14 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. The substitutions (ie, nsp1 Q87D, nsp3 M951I, nsp3 N1181=, nsp3 T1334A, nsp6 L37F, nsp12 Y455=, ORF3a T223I, and ORF3a G251V) that constituted the majority of viral genomes from the primary infection were still detected but with lowered VAF (8%-59.4%) in the viral RNA from the second infection. 2021 Clinical infectious diseases Result SARS_CoV_2 G251V;L37F;M951I;Q87D;T1334A;T223I 119;77;39;28;64;102 124;81;44;32;70;107 ORF3a;ORF3a;Nsp12;Nsp3;Nsp3;Nsp3;Nsp6 96;113;83;34;46;59;72 101;118;88;38;50;63;76 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. We found that the variant nsp1 Q87D detected in the initial infection was still observed in a few mappable sequence reads, while the variants that emerged in reinfection (ie, second hospitalization) were not detected (Supplementary Table 6). 2021 Clinical infectious diseases Result SARS_CoV_2 Q87D 31 35 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. For synonymous mutations, 15324C > T was the most common and present in 553 genomes. 2020 Virology journal Result SARS_CoV_2 C15324T 26 36 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. The 71 missense mutations affected rear part of RdRP (amino acid 627-752), with 9 SNVs found on 4 conserved domains, leading to amino acid changes at polymerase motif A (P627S), zinc binding site (H642N), non-structural protein 8 (nsp8) interaction site (M666I) and polymerase motif B (G683V, D684G, A699S, V700I, V700A and N705D). 2020 Virology journal Result SARS_CoV_2 A699S;D684G;N705D;V700A;V700I;G683V;H642N;M666I;P627S 300;293;324;314;307;286;197;255;170 305;298;329;319;312;291;202;260;175 Nsp8;RdRP 231;48 235;52 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. The frequency of M666I (15438G > T) was the highest (n = 34). 2020 Virology journal Result SARS_CoV_2 M666I;G15438T 17;24 22;34 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. In cat 5, however, two different variants in ORF1ab, G1756G and L3606F, became fixed after transmission. 2021 bioRxiv Result SARS_CoV_2 G1756G;L3606F 53;64 59;70 ORF1ab 45 51 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Interestingly, S H655Y and E S67S became fixed together following transmission in two transmission pairs (contact cats 4 and 6) and were lost together during transmission to contact animal 5. 2021 bioRxiv Result SARS_CoV_2 H655Y;S67S 17;29 22;33 E;S 27;15 28;16 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Neither of these iSNVs were detected above 3% frequency in the inoculum, but when we mined all sequencing reads, S H655Y and E S67S can be detected at 0.85% and 0.34% in the inoculum, respectively. 2021 bioRxiv Result SARS_CoV_2 H655Y;S67S 115;127 120;131 E;S 125;113 126;114 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. ORF1ab G1756G was not detected above 3% and L3606F was found at 17.2% in the day 5 sample from the index cat 2 (the cat transmitting to cat 5), and interestingly was not found in the inoculum at any detectable frequency. 2021 bioRxiv Result SARS_CoV_2 G1756G;L3606F 7;44 13;50 ORF1ab 0 6 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. S H655Y and E S67S) were detectable at all timepoints in cat 3 on days that SARS-CoV-2 was detectable >= 104 copies/mL and day 8 but stayed below consensus level. 2021 bioRxiv Result SARS_CoV_2 H655Y;S67S 2;14 7;18 E;S 12;0 13;1 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. S H655Y was the consensus sequence on days 2-5 and days 7-8 in index cat 1 as well as on days 4 and 8 in index cat 2 and remained detectable above our 3% variant threshold throughout infection (Fig 3). 2021 bioRxiv Result SARS_CoV_2 H655Y 2 7 S 0 1 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Similarly, envelope S67S (E S67S) was the consensus sequence on day 8 in index cat 1 and day 1 in index cat 2. 2021 bioRxiv Result SARS_CoV_2 S67S;S67S 20;28 24;32 E 26 27 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. This consensus sequence remained largely unchanged throughout infection in all index cats with the notable exception of two variants: H655Y in Spike (nucleotide site 23,525) and a synonymous change at amino acid position 67 in envelope (nucleotide site 26,445; S67S) arose rapidly in all 3 index cats and rose to consensus levels (>=50% frequency) at various timepoints throughout infection in all index cats. 2021 bioRxiv Result SARS_CoV_2 H655Y;S67S 134;261 139;265 S 143 148 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. 4d shows that PVD614, PVG614, and PVFKO are similarly susceptible to neutralizing plasma derived from convalescent patients, indicating that antibody-mediated control of viruses carrying SD614 and SG614 would be similar, and that the vaccines based on the D614 genotype will still be effective against the virus carrying the D614G mutation. 2020 Nature communications Result SARS_CoV_2 D614G 325 330 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. It has previously been speculated that D614G mutation promotes an open configuration of the S protein that is more favorable to ACE2 association. 2020 Nature communications Result SARS_CoV_2 D614G 39 44 S 92 93 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. The D614G mutation is associated with enhanced infectivity. 2020 Nature communications Result SARS_CoV_2 D614G 4 9 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. The D614G mutation neither increases S protein affinity for ACE2 nor makes PV more resistant to neutralization. 2020 Nature communications Result SARS_CoV_2 D614G 4 9 S 37 38 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Thus, enhanced entry of PV containing the D614G mutation correlates with reduced shedding of the S1 domain and greater incorporation of functional spikes into the virion. 2020 Nature communications Result SARS_CoV_2 D614G 42 47 S 147 153 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. To confirm that the monomeric interaction between hACE2 and S protein is not affected by the D614G mutation, we performed surface plasmon resonance assays. 2020 Nature communications Result SARS_CoV_2 D614G 93 98 S 60 61 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. To determine if the D614G mutation alters the properties of the S protein in a way that could impact transmission or infection, we assessed its role in viral entry. 2020 Nature communications Result SARS_CoV_2 D614G 20 25 S 64 65 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. We next investigated the mechanism with which the D614G mutation increased entry of PVG614. 2020 Nature communications Result SARS_CoV_2 D614G 50 55 33252670 SARS-CoV-2 Among Military and Civilian Patients, Metro Manila, Philippines. Four amino acid substitutions (ORF1b-P314L, S-D614G, N-R203K, and N-G204R), unique to clade GR (both lineages B.1.1 and B.1.1.28), were seen in all sequences in this clade. 2021 Military medicine Result SARS_CoV_2 D614G;G204R;P314L;R203K 46;68;37;55 51;73;42;60 N;N;S 53;66;44 54;67;45 33252670 SARS-CoV-2 Among Military and Civilian Patients, Metro Manila, Philippines. Twenty-two of the 23 sequences collected after June 25, 2020, contained the D614G mutation. 2021 Military medicine Result SARS_CoV_2 D614G 76 81 33253226 SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia. A secondary cluster within this healthcare-associated cluster contained six sequences with an additional mutation C21627T (T22I) in the spike protein. 2020 PLoS neglected tropical diseases Result SARS_CoV_2 C21627T;T22I 114;123 121;127 S 136 141 33253226 SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia. Eight Malaysian sequences, including 6 from this study, had the additional substitution C6310A, resulting in the amino acid change S1197R in nsp3. 2020 PLoS neglected tropical diseases Result SARS_CoV_2 C6310A;S1197R 88;131 94;137 Nsp3 141 145 33253226 SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia. None of the 41 rare receptor binding variants described in GISAID-including the two most common, S477N and N439K -were observed in the Malaysian sequences. 2020 PLoS neglected tropical diseases Result SARS_CoV_2 N439K;S477N 107;97 112;102 33253226 SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia. Some mutations were unique to Malaysian B.6 genomes, such as C2508A, A3223G, C9438T, C9803T, C13329T, C20823T, C26607T, A29086T and C29218T; others, including C6310A, T7621C and C19524T, were also observed in B.6 sequences from other countries including Singapore, Australia and India (Fig 3). 2020 PLoS neglected tropical diseases Result SARS_CoV_2 A29086T;A3223G;C13329T;C19524T;C20823T;C2508A;C26607T;C29218T;C6310A;C9438T;C9803T;T7621C 120;69;93;178;102;61;111;132;159;77;85;167 127;75;100;185;109;67;118;139;165;83;91;173 33253226 SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia. The 17 sequences in the healthcare-associated cluster had a non-synonymous mutation C25549T (P53F) in ORF3a (Fig 1). 2020 PLoS neglected tropical diseases Result SARS_CoV_2 C25549T;P53F 84;93 91;97 ORF3a 102 107 33253226 SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia. The mutation D614G in the spike protein, which may increase infectivity of SARS-CoV-2 and has become prevalent in many countries, was only observed in 13 (11.3%) Malaysian sequences from lineages B.1, B.1.1, B.1.1.1 and B.1.36 (S3 Table), but was not present in lineage B.6. 2020 PLoS neglected tropical diseases Result SARS_CoV_2 D614G 13 18 S 26 31 33253226 SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia. This C6310A mutation led to reduced sensitivity by 1,000-10,000 viral copies (> 10 cycles) with one of the commercial real-time PCR assays used in our laboratory when compared to the well-established Charite assay and updated primers/probes issued by the assay manufacturer in response to this likely sequence mismatch (S2 Table). 2020 PLoS neglected tropical diseases Result SARS_CoV_2 C6310A 5 11 33259879 Evolution and genetic diversity of SARS-CoV-2 in Africa using whole genome sequences. Although more evidence is still required to determine the extent of the effect of the D614G mutation on the virulence factors of the virus, current evidence from in vitro studies seem to support the hypothesis of increased transmissibility of this variant of the virus. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 86 91 33259879 Evolution and genetic diversity of SARS-CoV-2 in Africa using whole genome sequences. Our results revealed high prevalence of D614G mutation among Afr-SARS-CoV-2 at 59/69 (82.61%). 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 40 45 33259879 Evolution and genetic diversity of SARS-CoV-2 in Africa using whole genome sequences. Prior to this report the D614G spike mutation was found predominantly in Europe accompanied by high number of cases and significant mortality rate. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 25 30 S 31 36 33259879 Evolution and genetic diversity of SARS-CoV-2 in Africa using whole genome sequences. The Afr-SARS-CoV-2 sequences were analyzed for the D614G mutation within the S1 subunit of the spike protein, which has been reported to contribute to increased transmissibility of SARS-CoV-2. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 51 56 S 95 100 33259879 Evolution and genetic diversity of SARS-CoV-2 in Africa using whole genome sequences. We identified a relatively high prevalence of the D614G spike protein variant of the virus capable of rapid transmission in all countries sampled. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 50 55 S 56 61 33262895 Genomic characterization of SARS-CoV-2 in Egypt. Asn1673Asn) detected in 6/61 samples, followed by c.2772delC (p. 2021 Journal of advanced research Result SARS_CoV_2 2772delC 50 60 33262895 Genomic characterization of SARS-CoV-2 in Egypt. Asp614Gly). 2021 Journal of advanced research Result SARS_CoV_2 D614G 0 9 33262895 Genomic characterization of SARS-CoV-2 in Egypt. His125Arg) and one in ORF8 c.251 T > C (p.Leu84Ser). 2021 Journal of advanced research Result SARS_CoV_2 T251C;L84S;L84S;H125R 27;40;42;0 38;50;50;9 ORF8 22 26 33262895 Genomic characterization of SARS-CoV-2 in Egypt. In this study, one (0.8%) missense mutation was detected in the M gene c.374A > G (p. 2021 Journal of advanced research Result SARS_CoV_2 A374G 71 81 33262895 Genomic characterization of SARS-CoV-2 in Egypt. In this study, three frameshift mutations were detected, one of which was detected in ORF1ab, c.10818delG (p. 2021 Journal of advanced research Result SARS_CoV_2 10818delG 94 105 ORF1ab 86 92 33262895 Genomic characterization of SARS-CoV-2 in Egypt. Leu3606fs) in 3c like proteinase, and one frameshift mutation was detected in S gene c.13delC (p.Val6fs). 2021 Journal of advanced research Result SARS_CoV_2 13delC 85 93 S 78 79 33262895 Genomic characterization of SARS-CoV-2 in Egypt. Leu74Leu) and c.213C > T (p.Tyr71Tyr) respectively (supplementary S2) https://github.com/mabouelhoda/nCovEgypt. 2021 Journal of advanced research Result SARS_CoV_2 C213T;Y71Y;Y71Y;L74L 14;26;28;0 24;36;36;8 33262895 Genomic characterization of SARS-CoV-2 in Egypt. p.Ser171Leu) in 2/61, and c.251 T > C (p.Leu84Ser) in 2/61. 2021 Journal of advanced research Result SARS_CoV_2 T251C;L84S;L84S;S171L 26;39;41;2 37;49;49;11 33262895 Genomic characterization of SARS-CoV-2 in Egypt. Phe924Phe) was detected in 57 of the 61 samples followed by c.5019C > T (p. 2021 Journal of advanced research Result SARS_CoV_2 C5019T;F924F 60;0 71;9 33262895 Genomic characterization of SARS-CoV-2 in Egypt. Ser5398Leu) and c.13794A > G (p.Thr4598Thr) in 2/61 samples. 2021 Journal of advanced research Result SARS_CoV_2 A13794G 16 28 33262895 Genomic characterization of SARS-CoV-2 in Egypt. The most common variation of the S gene is the missense mutation c.1841A > G (p. 2021 Journal of advanced research Result SARS_CoV_2 A1841G 65 76 S 33 34 33262895 Genomic characterization of SARS-CoV-2 in Egypt. The most frequent ones within these 11 variations are c.171G > T (p.Gln57His) in 30/61, c.512C > T (p. 2021 Journal of advanced research Result SARS_CoV_2 G171T;C512T;Q57H;Q57H 54;88;66;68 64;98;76;76 33262895 Genomic characterization of SARS-CoV-2 in Egypt. There are 72 synonymous mutations, two of them are in E and M regions {c.222G > C (p. 2021 Journal of advanced research Result SARS_CoV_2 G222C 71 81 E 54 55 33262895 Genomic characterization of SARS-CoV-2 in Egypt. Three variations were found in the RNA dependent RNA polymerase area: c.14144C > T (p.Pro4715Leu) in 56/61 samples followed by c.16193C > T in 3/61 samples (p. 2021 Journal of advanced research Result SARS_CoV_2 C14144T;C16193T;P4715L 70;127;84 82;139;96 RdRp 35 63 33262895 Genomic characterization of SARS-CoV-2 in Egypt. We annotated our variations with this list and found that only 15 of our variations (15/204 = 7.35%) are in regions under positive pressure and there is no site in this dataset under negative pressure The variations under positive pressure are N:c.623C > T; ORF1ab:c.10818delG; N:c.605G > A; N:c.15560C > T; N:c.974C > G; ORF1ab:c.17765C > T; ORF1ab:c.17414C > T; ORF1ab:c.16193C > T; ORF1ab:c.926C > T; S:c.293C > T; ORF1ab:c.2675C > T; ORF1ab:c.10058A > G; ORF1ab:c.3737C > T; ORF1ab:c.14144C > T; S:c.1841A > G. 2021 Journal of advanced research Result SARS_CoV_2 A10058G;10818delG;C14144T;C15560T;C16193T;C17414T;C17765T;A1841G;C2675T;C293T;C3737T;G605A;C623T;C926T;C974G 447;266;486;294;371;350;329;503;425;406;466;280;246;392;310 457;276;498;306;383;362;341;513;436;416;477;290;256;402;320 ORF1ab;ORF1ab;ORF1ab;ORF1ab;ORF1ab;ORF1ab;ORF1ab;ORF1ab;ORF1ab;N;N;N;N;S;S 258;322;343;364;385;418;438;459;479;244;278;292;308;404;500 264;328;349;370;391;424;444;465;485;245;279;293;309;405;501 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. 4E), while the interaction between the RBD and ACE2 is driven by electrostatic interactions for the V367F variant. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 V367F 100 105 RBD 39 42 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. A348T RBD variant shows the least binding affinity to ACE2 among all the population variants. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 A348T 0 5 RBD 6 9 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Another variant, S494P, is observed in several SARS-CoV2 strains from Michigan, USA. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 S494P 17 22 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Comparison of selection sites and alignment reveals three RBM population variants under selection bias, G476S, V483A, and S494P that are in close contact with the ACE2 binding surface. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 G476S;S494P;V483A 104;122;111 109;127;116 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. For the G476S variant, the overall interfacial contacts between the RBD and ACE2 reduces significantly, evident from a reduction of RBD and ACE2 interfacial area by ~50 A2 in comparison to the Wuhan RBD-ACE2 complex. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 G476S 8 13 RBD;RBD;RBD 68;132;199 71;135;202 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. G476S variants are widespread and found in seven viral strains reported from the Washington State, USA. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 G476S 0 5 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. However, the number of hydrogen bonds between ACE2 and RBD decreases significantly for the S494P variants. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 S494P 91 96 RBD 55 58 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. In V367F, the enhanced binding energy is primarily contributed by an altered orientation of Lys31 which enhances its contribution to the binding free energy (-4.59 kcal/mol). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 V367F 3 8 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Interaction energy decomposition also shows that the van der Waals energy increases between the RBD and ACE2 for the S494P variant during the later simulation timescale. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 S494P 117 122 RBD 96 99 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. On the other hand, the V367F variant forms a higher number of hydrogen bonds with the ACE2 in comparison to the wild-type. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 V367F 23 28 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Root mean square deviation analysis over the entire trajectory reveals that the V367F and S494P RBD variants remain stable throughout the simulation when complexed with ACE2. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 S494P;V367F 90;80 95;85 RBD 96 99 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. S494P RBD variant almost very similarly binds with ACE2 like the Wuhan SARS-CoV2 RBD. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 S494P 0 5 RBD;RBD 6;81 9;84 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Sequence alignment reveals the population variants for those sites are A348T and V367F. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 A348T;V367F 71;81 76;86 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. The A348T, G476S, and V483A variants display reduced affinity to ACE2 in comparison to the Wuhan SARS-CoV2 spike protein (Wild-type). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 A348T;G476S;V483A 4;11;22 9;16;27 S 107 112 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. The A520S variant was reported in two viral strains from Washington, USA. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 A520S 4 9 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. The binding ability of five spike population variants, A348T, V367F, G476S, V483A, and S494P with ACE2 has been explored using the protein-protein docking and binding free energy calculations. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 A348T;G476S;S494P;V367F;V483A 55;69;87;62;76 60;74;92;67;81 S 28 33 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. The buried RBM-ACE2 interfacial surface area increases by 2 nm2 for the S494P variant in comparison to the wild-type and V367F variant during the simulation. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 S494P;V367F 72;121 77;126 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. The most common RBD variant is V483A which was reported in different states in the USA. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 V483A 31 36 RBD 16 19 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. The reduction of binding affinity of the V483A mutant in comparison to Wuhan SARS-CoV2 is primarily due to the altered orientation of Tyr505 which weakens the hydrogen bonding interaction with Arg393 by more than 1 kcal/mol. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 V483A 41 46 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. This indicates the enhanced binding affinity of S494P is attributed to strong interfacial complementarity during ACE2 recognition, while the V367F variant interacts with the ACE2 mediated by a higher number of hydrogen bonds. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 S494P;V367F 48;141 53;146 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. V367F variation is observed in two viral strains obtained from Hong Kong and the USA. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 V367F 0 5 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. While the V367F and S494P population variants display a higher binding affinity towards human ACE2, compared to the Wild-type spike protein. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 S494P;V367F 20;10 25;15 S 126 131 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. CR3022 neutralizes SARS-CoV-2 P384A but not WT. 2020 PLoS pathogens Result SARS_CoV_2 P384A 30 35 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. Crystal structure reveals the impact of P384A in CR3022 binding. 2020 PLoS pathogens Result SARS_CoV_2 P384A 40 45 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. Four SARS-CoV-2 RBD mutants, namely A372T, P384A, T430M, and H519N (SARS-CoV-2 numbering), were recombinantly expressed and examined (Fig 1A). 2020 PLoS pathogens Result SARS_CoV_2 A372T;H519N;P384A;T430M 36;61;43;50 41;66;48;55 RBD 16 19 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. However, CR3022 is now able to neutralize the SARS-CoV-2 P384A mutant at an IC50 of 3.2 mug/ml, which is comparable to its neutralizing activity to SARS-CoV (IC50 of 5.2 mug/ml). 2020 PLoS pathogens Result SARS_CoV_2 P384A 57 62 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. However, it is unclear whether the emergence of P384A is due to neutral drift or positive selection in bats or other species. 2020 PLoS pathogens Result SARS_CoV_2 P384A 48 53 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. In addition, given that residue 384 is proximal to the S2 domain when the RBD is in the "down" conformation (Fig 3B), whether P384A can modulate the conformational dynamics of the "up and down" configurations of the RBD in the S trimer and influence the viral replication fitness will require additional studies. 2020 PLoS pathogens Result SARS_CoV_2 P384A 126 131 RBD;RBD;S 74;216;227 77;219;228 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. Interestingly, the CR3022 Fab neutralized SARS-CoV-2 P384A mutant with an IC50 of 4.4 mug/ml, which is similar to that of CR3022 IgG (3.2 mug/ml) (Fig 2). 2020 PLoS pathogens Result SARS_CoV_2 P384A 53 58 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. P384A increases binding affinity of SARS-CoV-2 RBD to CR3022. 2020 PLoS pathogens Result SARS_CoV_2 P384A 0 5 RBD 47 50 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. Phylogenetic analysis implies that P384A emerged during the evolution of SARSr-CoV in bats (Figs 3A and S1), which is the natural reservoir of SARSr-CoV. 2020 PLoS pathogens Result SARS_CoV_2 P384A 35 40 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. To test this hypothesis, we compared neutralization of SARS-CoV-2 WT and the P384A mutant by CR3022. 2020 PLoS pathogens Result SARS_CoV_2 P384A 77 82 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. While binding of CR3022 mutants A372T (KD = 66 nM), T430M (KD = 64 nM), and H519N (KD = 60 nM) was comparable to wild type (WT) SARS-CoV-2 RBD (KD = 68 nM), binding of CR3022 to the P384A mutant (KD = 1.4 nM) was greatly increased (Fig 1B), akin now to that with the SARS-CoV RBD (KD = 1.0 nM). 2020 PLoS pathogens Result SARS_CoV_2 A372T;H519N;P384A;T430M 32;76;182;52 37;81;187;57 RBD;RBD 139;276 142;279 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. The association between the D614G polymorphism and severity of disease was estimated with high uncertainty, but the posterior was centered close to zero indicating that a biologically relevant effect is unlikely (mean: 0.03; 95% CI: -0.80-0.84). 2021 Cell Result SARS_CoV_2 D614G 28 33 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. V615I occurs on the background of 614D, while V615F co-occurs with 614G (Table 3). 2021 Cell Result SARS_CoV_2 V615F;V615I 46;0 51;5 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. We investigated associations between the D614G polymorphism and virulence by linking virus genome sequence data with clinical data on patient outcomes. 2021 Cell Result SARS_CoV_2 D614G 41 46 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Within the United Kingdom and global SARS-CoV-2 phylogenies, there are multiple instances of the D614G mutation as well as reversions back to 614D. 2021 Cell Result SARS_CoV_2 D614G 97 102 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. An analysis of viral titers revealed that D614G replicated in bovine tissues at higher magnitude than D614 at 48 hpi (p < 0.05) in tracheal EVOCs; at 48 hpi (p< 0.01) and 72 hpi (p < 0.05) in lung EVOCs. 2021 Veterinary microbiology Result SARS_CoV_2 D614G 42 47 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. Differences between the two SARS-CoV-2 isolates were observed only at 24 hpi in tracheal EVOCs as D614G virus showed a slight, but statistically significant, higher number of RNA copies. 2021 Veterinary microbiology Result SARS_CoV_2 D614G 98 103 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. Quantification of RNA copies in EVOCs supernatants revealed more apparent differences between D614 and D614G. 2021 Veterinary microbiology Result SARS_CoV_2 D614G 103 108 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. SARS-CoV-2 with D614G exhibits greater replication. 2021 Veterinary microbiology Result SARS_CoV_2 D614G 16 21 33292056 Sensing the interactions between carbohydrate-binding agents and N-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies. In the molecular docking, the mutant (H84T) and the wild-type BanLec lectin showed variable interactions with the S glycoprotein glycans of SARS-CoV-2 (Table 3). 2020 Journal of biomolecular structure & dynamics Result SARS_CoV_2 H84T 38 42 S 114 128 33292056 Sensing the interactions between carbohydrate-binding agents and N-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies. The single amino acid substitution in mutant BanLec (H84T), the amino acid Thr84 was seen to interact only in the initial 30 ns of the 100 ns MD simulation as compared to the His84 which was seen to interact with amino acids of S glycoprotein at various time points throughout the 100 ns MD simulation. 2020 Journal of biomolecular structure & dynamics Result SARS_CoV_2 H84T 53 57 S 228 242 33292056 Sensing the interactions between carbohydrate-binding agents and N-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies. Therefore, we decided to perform the macromolecular docking of BanLec with SARS-CoV-2 S glycoprotein by using wild-type (PDB ID: 3MIT) as well as a mutant (H84T, in which the mitogenic activity of BanLec is separated from the antiviral activity) (PDB ID: 4PIT) of BanLec. 2020 Journal of biomolecular structure & dynamics Result SARS_CoV_2 H84T 156 160 S 86 100 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. 5d) is unaffected by the mutation in the solvated RBD; on the other hand, residues 502-505 are more solvent exposed after the G502P mutation in the ACE2-RBD complex. 2020 bioRxiv Result SARS_CoV_2 G502P 126 131 RBD;RBD 50;153 53;156 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. We also computed the relative binding strength (DeltaDeltaG) between the wild-type (WT) F486 SARS-CoV-2 and the mutant F486L. 2020 bioRxiv Result SARS_CoV_2 F486L 119 124 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. We found a negative DeltaDeltaG (see Table 1), implying that the mutant has a larger affinity for the human receptor, and we compared unbiased MD simulations of the WT and N501T mutant to determine the reasons of this change. 2020 bioRxiv Result SARS_CoV_2 N501T 172 177 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. We mutated glycine 502 to proline, which has a dual effect: (i) it is incapable of interacting with K353, although it could in principle maintain the helical shape of the tetrad 502PVGY505, and (ii) it might introduce steric clashes with ACE2. 2020 bioRxiv Result SARS_CoV_2 G502P 11 33 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. We tested the difference between asparagine and glutamine by running MD simulations of the ACE2-RBD WT and Q493N mutant of SARS-CoV-2. 2020 bioRxiv Result SARS_CoV_2 Q493N 107 112 RBD 96 99 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. We tested the impact of this replacement by alchemically substituting N501 with a threonine, and we computed the relative binding free energy of ACE2 and RBD between the WT SARS-CoV-2 and the N501T mutant following the same thermodynamic cycle as for the F486L mutation. 2020 bioRxiv Result SARS_CoV_2 F486L;N501T 255;192 260;197 RBD 154 157 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. Although we identified major mutations on CD8 T cell epitopes including L5F, D614G and G1124V for the SARS-CoV-2 S protein, the detailed mechanisms driving these mutations are not known. 2020 PloS one Result SARS_CoV_2 D614G;G1124V;L5F 77;87;72 82;93;75 S 113 114 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. Effect of D614G mutation on CD8 T cell epitope generation. 2020 PloS one Result SARS_CoV_2 D614G 10 15 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. Effect of G1124V mutation on CD8 T cell epitope generation. 2020 PloS one Result SARS_CoV_2 G1124V 10 16 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. Effect of L5F mutation on CD8 T cell epitope generation. 2020 PloS one Result SARS_CoV_2 L5F 10 13 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. In addition, these mutations are exclusively L to F at position 5, D to G at position 614 and G to V at position 1124. 2020 PloS one Result SARS_CoV_2 D614G;G1124V;L5F 67;94;45 89;117;65 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. Similarly, we reanalyzed the 9-mer CD8 T cell epitope for the reference S protein with a single D614G mutation. 2020 PloS one Result SARS_CoV_2 D614G 96 101 S 72 73 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. The comparison data in Table 2 showed that L5F mutation increased the epitope binding affinity for 37 different HLA alleles, meanwhile only 10 other alleles had decreased binding affinity for the mutated epitope FVFFVLLPL. 2020 PloS one Result SARS_CoV_2 L5F 43 46 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. These results illustrated differential effects of D614G mutation on the capability to present S protein specific CD8 T cell epitopes by different HLA alleles. 2020 PloS one Result SARS_CoV_2 D614G 50 55 S 94 95 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. To examine whether a single mutation of L to F at position 5 on the SARS-CoV-2 S protein would affect FVFLVLLPL epitope presentation by different HLA alleles, we replaced the L with F at position 5 on the reference S protein sequence and re-analyzed the 9-mer CD8 epitopes for all the 80 HLA-A, B and C alleles using NetMHC 4.0 as described. 2020 PloS one Result SARS_CoV_2 L5F;L5F 40;175 60;197 S;S 79;215 80;216 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. 57% of our cohort's sequences contain the D614G mutation co-occurring with SNPs C241 T, C3037 T, and C14408 T, the latter causing the AA replacement P323L in the RNA-dependent RNA polymerase (RdRP) gene of nsp12 (Figure 2A, C, Figures S2 and S4). 2021 Emerging microbes & infections Result SARS_CoV_2 C14408T;C241T;C3037T;D614G;P323L 101;80;88;42;149 109;86;95;47;154 RdRp;Nsp12;RdRP 162;206;192 190;211;196 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. Accordingly, the spike D614G mutation and clade G-related viruses, in consequence, are not associated with any clinical parameters, severity, or lethality. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 23 28 S 17 22 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. Consistent with the mutational analysis of our internal data set (Figure 2), the phylogenetic analysis of the publicly available Uruguayan sequences reveals a predominance of clades S and G (G, GH, and GR), the former occupying most of the upper half of the maximum-likelihood tree (Figure S5A) and the right half of the haplotype network (Figure S5B), the latter the respective opposite halves, highlighted by green and red arrows for spike D614G and ORF8 L84S key mutations, respectively. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G;L84S 442;457 447;461 S;ORF8;S 436;452;182 441;456;183 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. D614G only correlates with co-occurring/inversely occurring mutations, treating healthcare institutions, and time since sampling started (Figure 6C, Figure S11). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 0 5 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. Diverse SARS-CoV-2 mutation profiles with increased prevalence of spike D614G variants and associated mutations in the evolving epidemic. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 72 77 S 66 71 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. In addition, we found three more SNPs to be significantly associated, namely C17470 T, C25521 T, and C26088 T, which collectively build a strongly significant, positive correlation cluster composed of five mutations (Figure S4). 2021 Emerging microbes & infections Result SARS_CoV_2 C17470T;C25521T;C26088T 77;87;101 85;95;109 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. In March and early April, ORF8 mutation L84S and the associated C8782 T SNP were most abundant (>1/3 of sequences) (Figure 2A, C, Figures S2 and S3). 2021 Emerging microbes & infections Result SARS_CoV_2 C8782T;L84S 64;40 71;44 ORF8 26 30 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. Interestingly, after April, most sequences belonged to clade G (sublineage B.1), defined by the spike protein's D614G mutation. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 112 117 S 96 101 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. Sera from macaques and humans immunized with RBD-only immunogens more potently neutralized G614 pseudovirus even though the D614G mutation was not in the RBD, and this observation suggested that the mutation induced a structural change in the expressed spike that increased the exposure of neutralizing epitopes on the RBD. 2021 Cell host & microbe Result SARS_CoV_2 D614G 124 129 S;RBD;RBD;RBD 253;45;154;319 258;48;157;322 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. The observation that the G variant was more sensitive to antibodies induced by both a D614-containing cell surface spike trimer and an RBD-secreted monomer suggests that the G614 mutation increases RBD-mediated neutralization despite the fact that D614G lies in S1 outside the RBD. 2021 Cell host & microbe Result SARS_CoV_2 D614G 248 253 S;RBD;RBD;RBD 115;135;198;277 120;138;201;280 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. This shift toward the 1-up state demonstrates an allosteric effect of the D614G mutation on RBD dynamics and suggests a mechanism for the enhanced neutralization susceptibility of the G614 variant. 2021 Cell host & microbe Result SARS_CoV_2 D614G 74 79 RBD 92 95 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Although all three mutants with altered endodomain cysteine residues were expressed on the cell surface and incorporated into lentivirus particles, only the 2nd 5C-to-A mutant supported cell-cell fusion and virus infection at wild-type S levels. 2020 Journal of virology Result SARS_CoV_2 C5A 161 168 S 236 237 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Both lentivirus and VSV vectors pseudotyped with the D614G S gp infected cells 4- to 16-fold more efficiently than viruses with the wild-type S gp. 2020 Journal of virology Result SARS_CoV_2 D614G 53 58 S;S 59;142 60;143 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Compared to the wild-type S gp, the F888R mutant exhibited a lower ratio of the S1 gp in cell lysates relative to the S1 gp in cell supernatants, suggesting a decrease in the association of S1 with the S trimer. 2020 Journal of virology Result SARS_CoV_2 F888R 36 41 S;S 26;202 27;203 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. F888R was severely compromised in the ability to mediate cell-cell fusion; however, this ability was recovered when TMPRSS2 was coexpressed with ACE2 in the target cells. 2020 Journal of virology Result SARS_CoV_2 F888R 0 5 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Importantly, the viruses with D614G S gp were ~7-fold more sensitive to soluble ACE2 and 2- to 5-fold more sensitive to neutralizing antisera than viruses with wild-type S gp. 2020 Journal of virology Result SARS_CoV_2 D614G 30 35 S;S 36;170 37;171 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. In three additional mutants, the N-terminal five cysteine residues (1st 5C-to-A), the C-terminal five cysteine residues (2nd 5C-to-A), or all 10 cysteine residues (10 C-to-A) were altered to alanine residues. 2020 Journal of virology Result SARS_CoV_2 C5A;C5A 72;125 79;132 N 33 34 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. L821A and F823A retained the ability to mediate cell-cell fusion, although the syncytia formed were smaller than those induced by the wild-type S gp. 2020 Journal of virology Result SARS_CoV_2 F823A;L821A 10;0 15;5 S 144 145 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Of note, the infectivity of lentiviruses pseudotyped with the 1st 5C-to-A and 10 C-to-A mutants was near the background of the assay. 2020 Journal of virology Result SARS_CoV_2 C5A 66 73 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Proteolytic processing of the 2nd 5C-to-A and 10 C-to-A mutants was more efficient than that of the wild-type S gp. 2020 Journal of virology Result SARS_CoV_2 C5A 34 41 S 110 111 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. S1 association with detergent-solubilized S gp trimers was greater for D614G than for wild-type S over a range of temperatures from 4 to 37 C. 2020 Journal of virology Result SARS_CoV_2 D614G 71 76 S;S 42;96 43;97 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Soluble ACE2 bound and induced the shedding of S1 from D614G lentivirus particles more efficiently than from particles with the wild-type S gp. 2020 Journal of virology Result SARS_CoV_2 D614G 55 60 S 138 139 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. The change in Asp614 to a glycine residue (D614G) is found in the predominant emerging SARS-CoV-2 strains worldwide. 2020 Journal of virology Result SARS_CoV_2 D614G;D614G 14;43 33;48 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. The D614G change in the predominant SARS-CoV-2 strain increases S1-trimer association, virus infectivity, and sensitivity to soluble ACE2 and neutralizing antisera. 2020 Journal of virology Result SARS_CoV_2 D614G 4 9 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. The D614G S gp was cleaved slightly more efficiently than the wild-type S gp but shed less S1 into the medium of expressing cells. 2020 Journal of virology Result SARS_CoV_2 D614G 4 9 S;S 10;72 11;73 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. The DeltaCT, 1st 5C-to-A, and 2nd 5C-to-A mutants consisted of two species, one without palmitoylation and the other with a single palmitoylated cysteine. 2020 Journal of virology Result SARS_CoV_2 C5A;C5A 17;34 24;41 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. The efficiencies of cell-cell fusion mediated by the D614G and wild-type S glycoproteins were comparable. 2020 Journal of virology Result SARS_CoV_2 D614G 53 58 S 73 88 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. The L821A and F823A mutants were processed slightly less efficiently than the wild-type S gp. 2020 Journal of virology Result SARS_CoV_2 F823A;L821A 14;4 19;9 S 88 89 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. The lentivirus particles with D614G S gp exhibited a significantly greater association of the S1 subunit with the trimer (half-life of >5 days at 37 C) compared with viruses with wild-type S gp (half-life of 2 to 3 days at 37 C). 2020 Journal of virology Result SARS_CoV_2 D614G 30 35 S;S 36;189 37;190 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. The ratio of palmitoylated to unmodified S2 glycoprotein was significantly greater for the 2nd 5C-to-A mutant than for the DeltaCT and 1st 5C-to-A mutants. 2020 Journal of virology Result SARS_CoV_2 C5A;C5A 95;139 102;146 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. The stabilities of the viruses pseudotyped with D614G and wild-type S glycoproteins on ice were comparable. 2020 Journal of virology Result SARS_CoV_2 D614G 48 53 S 68 83 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Thus, the D614G change enhances virus infectivity, responsiveness to ACE2, and S1 association with the trimeric spike. 2020 Journal of virology Result SARS_CoV_2 D614G 10 15 S 112 117 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. We introduced analogous changes into the putative fusion peptide of the SARS-CoV-2 S gp (L821A and F823A) and also made a change (F888R) in the downstream region implicated in SARS-CoV-1 S gp function. 2020 Journal of virology Result SARS_CoV_2 F823A;F888R;L821A 99;130;89 104;135;94 S;S 83;187 84;188 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. A variant SARS-CoV-2 containing a D614G point mutation in the spike protein has been found to be circulating in the human population with increasing prevalence. 2020 Cell reports Result SARS_CoV_2 D614G 34 39 S 62 67 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. ACE2 Microbody Blocks Entry of Virus with D614G Spike. 2020 Cell reports Result SARS_CoV_2 D614G 42 47 S 48 53 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. Analysis of the infectivity of the D614G and wild-type pseudotyped viruses on the panel of cell lines showed that the mutation increased the infectivity of virus 2- to 4-fold on 293T, ACE2.293T, Vero, and VeroE6 cells, consistent with previous reports. 2020 Cell reports Result SARS_CoV_2 D614G 35 40 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. Different amounts of wild-type or D614G pseudotyped virions were then incubated with the beads, and the amount of virions bound was quantified by immunoblot analysis. 2020 Cell reports Result SARS_CoV_2 D614G 34 39 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. The D614G mutation was found to decrease shedding of the spike protein from the virus and to assume a fusion-ready conformation, resulting in increased infectivity and most likely contributing to its increasing prevalence. 2020 Cell reports Result SARS_CoV_2 D614G 4 9 S 57 62 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. The results showed that the wild-type and H345A microbody proteins bound more efficiently than soluble ACE2 to the spike protein, and that they bound well to both the wild-type and D614G spike protein pseudotyped virions. 2020 Cell reports Result SARS_CoV_2 D614G 181 186 S;S 115;187 120;192 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. To determine the ability of the soluble ACE2 proteins to block entry of virus with the D614G spike protein, we introduced the mutation into the Delta19 spike protein expression vector and generated pseudotyped reporter viruses (Figure 6 A). 2020 Cell reports Result SARS_CoV_2 D614G 87 92 S;S 93;152 98;157 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. To determine the ability of the soluble ACE2 proteins to neutralize the virus with the variant spike protein, we tested serial dilutions of the soluble ACE2 proteins for their ability to block wild-type and D614G S pseudotyped virus. 2020 Cell reports Result SARS_CoV_2 D614G 207 212 S;S 95;213 100;214 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. To test the relative binding affinities of the soluble ACE2 proteins for the wild-type and D614G spike proteins, we used an ACE2/virion binding assay in which the soluble ACE2 proteins were bound to nickel beads via their His-tag (Figure 6D). 2020 Cell reports Result SARS_CoV_2 D614G 91 96 S 97 102 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. Among the common variants, the most frequent mutations are 23403 A > G (D614G, S gene), 241 C > T (5' UTR), 14408 C > T (P4715L, RdRP gene), 3037 C > T (F942F, NSP3), 28881 G > A (R203K, N gene), 28882 G > A (R203R, N gene), 28883 G > C (G204R, N gene), and 28144 T > C (L84S, ORF8) with presence in more than 15% of all of our sequenced genomes (Supplementary Table 1). 2020 Frontiers in microbiology Result SARS_CoV_2 C14408T;A23403G;C241T;T28144C;G28881A;G28882A;G28883C;C3037T;D614G;F942F;G204R;L84S;P4715L;R203K;R203R 108;59;88;258;167;196;225;141;72;153;238;271;121;180;209 119;70;97;269;178;207;236;151;77;158;243;275;127;185;214 5'UTR;Nsp3;ORF8;RdRP;N;N;N;S 99;160;277;129;187;216;245;79 105;164;281;133;188;217;246;80 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. Among the ORF1ab mutations, 4,715 P > L change in nsp12, also known as RdRP (the viral RNA dependent RNA polymerase), was the most common one followed by a synonymous change (F924F) in nsp3 protein (Figure 2B). 2020 Frontiers in microbiology Result SARS_CoV_2 F924F;P715L 175;30 180;39 RdRp;ORF1ab;Nsp12;Nsp3;RdRP 87;10;50;185;71 115;16;55;189;75 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. As reported in earlier publications, we also noticed D614G as a highly prevalent mutation in highly transmitted and evolved strains belonging to clades 20A and 20B in the Indian scenario; therefore, we carried out molecular modeling analysis. 2020 Frontiers in microbiology Result SARS_CoV_2 D614G 53 58 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. Both 20A and 20B clades predominantly contain a mutation in protein coding sequence 23403A > G, and the mutation is traced back to the West European region in late January. 2020 Frontiers in microbiology Result SARS_CoV_2 A23403G 84 94 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. Clades 20A and 20B have almost similar mutation profile with major mutated positions 241 C > T mutation in leader sequence, ORF1ab 3037 C > T, ORF1ab 14408 C > T (RdRP), and S gene 23403 A > G mutations. 2020 Frontiers in microbiology Result SARS_CoV_2 C14408T;A23403G;C241T;C3037T 150;181;85;131 161;192;94;141 ORF1ab;ORF1ab;RdRP;S 124;143;163;174 130;149;167;175 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. Effect of D614G on Viral Load. 2020 Frontiers in microbiology Result SARS_CoV_2 D614G 10 15 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. In clade 19B samples, we observed a very distinct ORF8 T > C mutation at 28144 position, two N gene mutations at positions 28326 and 28878 with some ORF1ab mutation in lower frequency (Figure 2C). 2020 Frontiers in microbiology Result SARS_CoV_2 T28144C 55 78 ORF1ab;ORF8;N 149;50;93 155;54;94 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. In clade 20A, we observed two mutations at ORF3a and M protein coding gene at position 25,563 G > T, 26,735 C > T but in less frequencies in comparison with other mutated sites (Figure 2C). 2020 Frontiers in microbiology Result SARS_CoV_2 G563T;C735T 90;104 99;113 ORF3a 43 48 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. Molecular Modeling Depicted Enhanced Interaction of D614G-Mutated Spike Protein With TMPRSS2 Protease. 2020 Frontiers in microbiology Result SARS_CoV_2 D614G 52 57 S 66 71 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. The isolates that were grouped in 19A clade depicted prevalence of mostly ORF1ab mutations with one distinct N gene C > T mutation at 28311 position (Figure 2C). 2020 Frontiers in microbiology Result SARS_CoV_2 C28311T 116 139 ORF1ab;N 74;109 80;110 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. The missense mutation in Spike protein coding gene causes a change in 614 D > G position of Spike protein and reported to increase the shedding of S1 subunit of the protein, which leads to the increased infectivity. 2020 Frontiers in microbiology Result SARS_CoV_2 D614G 70 79 S;S 25;92 30;97 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. We also assessed the frequency of D614G mutation from Covid19 Beacon database (CSIRO and CSIR-IGIB, access date: February 8, 2020) in global and all the SARS-CoV-2 sequence published from India, and the occurrence of G614 in Indian genomes is 76.31% where the global frequency is 43.8% (Supplementary Figure 2C). 2020 Frontiers in microbiology Result SARS_CoV_2 D614G 34 39 33330626 Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM. It shows that DeltaDeltaGbind for mutants, I40A, V104A, and R86A are comparatively high, suggesting that primarily these residues play a significant role in the heterodimer formation, which is in accordance with the decomposition of energy. 2020 Frontiers in molecular biosciences Result SARS_CoV_2 I40A;R86A;V104A 43;60;49 47;64;54 33330626 Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM. The binding free energy components calculated from the CAS mutagenesis for residues I40A, V104A, R86A, V78A, V44A, M247A, and Q87A of nsp16 are listed in Table 5 and compared with the WT. 2020 Frontiers in molecular biosciences Result SARS_CoV_2 I40A;M247A;Q87A;R86A;V104A;V44A;V78A 84;115;126;97;90;109;103 88;120;130;101;95;113;107 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. Although both forms of spike displayed significant co-localization with the lysosomal marker Lamp2, the D614G mutation appeared to induce a shift in spike protein sorting towards the lysosome. 2020 bioRxiv Result SARS_CoV_2 D614G 104 109 S;S 23;149 28;154 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. Although the relative amounts of lysosome-localized spike varied significantly from one cell to another in both cell populations, digital image analysis quantified the effect of the D614G mutation as 54% increase in its lysosomal staining (p = 0.00000024; Student's t-test; 2-tailed; two-sample, unequal variance), from an average of 817 +/- 44 (standard error of the mean (s.e.m.)) in Htet1/SW1 cells (n = 34 images) to an average of 1265 +/- 64 (s.e.m) in Htet1/SD614G cells (n = 37 images). 2020 bioRxiv Result SARS_CoV_2 D614G;D614G 182;465 187;470 S;S;S 52;374;448 57;375;449 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. Although this form of spike differs from SW1 by just a single amino acid, all four plasmas revealed enhanced staining of spike in these large, non-Golgi intracellular compartments, raising the possibility that the D614G mutation either enhances the trafficking of spike to these compartments or enhances a conformational shift that allows its detection by the antibodies in these plasmas. 2020 bioRxiv Result SARS_CoV_2 D614G 214 219 S;S;S 22;121;264 27;126;269 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. Given that the D614G mutation has a significant impact on SARS-CoV-2 infectivity and transmission, we asked whether this mutation might impact the lysosomal sorting of spike. 2020 bioRxiv Result SARS_CoV_2 D614G 15 20 S 168 173 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. Given the central role of spike in SARS-CoV-2 biology, the pronounced impact of the D614G mutation on the COVID-19 pandemic, and the fact that all leading vaccine candidates are based solely on spike, we sought to determine the identity of these large, spike-containing structures. 2020 bioRxiv Result SARS_CoV_2 D614G 84 89 S;S;S 26;194;253 31;199;258 COVID-19 106 114 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. Given the recent report that the biogenesis of newly-synthesized MHV particles occurs via lysosomes and that MHV-infected cells accumulate MHV particles in lysosomes, we tested whether the D614G mutation might promote the lysosomal accumulation of spike and spike-containing vesicles in SARS-CoV-2-infected cells. 2020 bioRxiv Result SARS_CoV_2 D614G 189 194 S;S 248;258 253;263 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. However, the D614G mutation did induce a slight shift in the relative extent of processing at the S1/S2 boundary, shown here by somewhat less full-length spike in Htet1/SD614G cells relative to Htet1/SW1 cells. 2020 bioRxiv Result SARS_CoV_2 D614G;D614G 13;170 18;175 S 154 159 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. In light of these findings, we tested whether plasma antibodies might shed light on the effects of the spike D614G mutation, which is known to enhance viral fitness through an increase in SARS-CoV-2 infectivity and transmission. 2020 bioRxiv Result SARS_CoV_2 D614G 109 114 S 103 108 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. The D614G mutation enhances the lysosomal sorting of spike. 2020 bioRxiv Result SARS_CoV_2 D614G 4 9 S 53 58 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. These results suggest a model of SARS-CoV-2 biogenesis in which the D614G mutation enhances spike protein trafficking to the lysosome. 2020 bioRxiv Result SARS_CoV_2 D614G 68 73 S 92 97 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. This was done by inducing Htet1/SD614G cells to express spike and then processing the cells for immunofluorescence microscopy using plasma G4 and antibodies directed against marker proteins of various subcellular compartments. 2020 bioRxiv Result SARS_CoV_2 D614G 33 38 S 56 61 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. To determine the subcellular distribution of the D614 and G614 forms of spike, doxycycline-induced Htet1/SW1 and Htet1/SD614G cells were processed for immunofluorescence microscopy using an antibody that binds the C-terminal 14 amino acids of spike (-DSEPVLKGVKLHYTCOOH), a region of the protein that is shielded by a lipid bilayer from the D614G mutation and the conformational changes it might induce. 2020 bioRxiv Result SARS_CoV_2 D614G 341 346 S;S 72;243 77;248 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. Towards this end, we generated the Htet1/SD614G cell line and interrogated S D614G-expressing cells using the same four plasmas. 2020 bioRxiv Result SARS_CoV_2 D614G;D614G 77;42 82;47 S 75 76 33335073 Cross-species recognition of SARS-CoV-2 to bat ACE2. In contrast, introducing Q42 to the bACE2-Rm (H41-E42) mutant, which results in bACE2-Rm (H41-Q42), rescued its binding capacity to SARS-CoV-2 RBD (KD = 2.22 muM), whereas mutation of E42Q in the wild-type bACE2-Rm resulted in a slightly higher binding affinity to SARS-CoV-2 RBD (KD = 0.25 muM). 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 E42Q 184 188 RBD;RBD 143;276 146;279 33335073 Cross-species recognition of SARS-CoV-2 to bat ACE2. Mutational analysis was further conducted by transiently expressing bACE2-Rm carrying the Y41H and/or E42Q mutations in HEK293T cells. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 E42Q;Y41H 102;90 106;94 33335073 Cross-species recognition of SARS-CoV-2 to bat ACE2. The results showed that the binding capacity of SARS-CoV-2 RBD to bACE2-Rm is attenuated with the introduction of the Y41H mutation. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 Y41H 118 122 RBD 59 62 33335187 CoV2-ID, a MIQE-compliant sub-20-min 5-plex RT-PCR assay targeting SARS-CoV-2 for the diagnosis of COVID-19. An analysis of all clinical samples using the D614G genotyping assay revealed that all isolates harboured the A to G transition, characteristic of the more infectious phenotype, whereas the control clinical sample and Twist BioScience control 1 were both wild type, A, at this location (supplementary data file, Table 7). 2020 Scientific reports Result SARS_CoV_2 D614G 46 51 33350913 Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China. Finally, the third subgroup included the cases from cluster 6, an SSE originating from a Buddhist worship hall, in which Orf1ab-G295V were identified. 2021 Emerging infectious diseases Result SARS_CoV_2 G295V 128 133 ORF1ab 121 127 33350913 Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China. Orf3a-G251V was the most frequent amino acid substitution; 44/50 (88.0%) of the samples harbored this mutation, after which Orf1ab-H3233Y (30/50, 60.0%) and S-L8V (27/50, 54.0%) were most common. 2021 Emerging infectious diseases Result SARS_CoV_2 G251V;H3233Y;L8V 6;131;159 11;137;162 ORF1ab;ORF3a;S 124;0;157 130;5;158 33350913 Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China. The second group originated with a single robust node with bootstrap value of 94% and a common mutation Orf3a-G251V. 2021 Emerging infectious diseases Result SARS_CoV_2 G251V 110 115 ORF3a 104 109 33350913 Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China. These samples shared the same missense mutations at S-L8V and Orf1ab-H3233Y. 2021 Emerging infectious diseases Result SARS_CoV_2 H3233Y;L8V 69;54 75;57 ORF1ab;S 62;52 68;53 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. (2) An alternative, contrasting, hypothesis is that the Asp614Gly mutation allowed for more efficient host cell entry, but decreased production of virus by the cell and it was only the addition of Pro323Leu nsp12 that enhanced the replication efficiency, resulting in increased production of virus. 2020 Genome biology Result SARS_CoV_2 D614G;P323L 56;197 65;206 Nsp12 207 212 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. (3) It is possible that the Pro323Leu nsp12 led to enhanced transmission simply from increased genome diversity by generating a higher number of mutations, which is supported by our analysis above. 2020 Genome biology Result SARS_CoV_2 P323L 28 37 Nsp12 38 43 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. 2) consists of the mutation Thr85Ile at the same loop of nsp2, followed by Gln57His in ORF3a; site 57 is predicted to be part of a helix break at the first transmembrane segment. 2020 Genome biology Result SARS_CoV_2 Q57H;T85I 75;28 83;36 ORF3a;Nsp2 87;57 92;61 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. 2) involves two haplotypes found in the state of Washington in the USA that correspond to nearly adjacent mutations in the nsp13 protein (Pro504Leu and Tyr541Cys). 2020 Genome biology Result SARS_CoV_2 Y541C;P504L 152;138 161;147 Nsp13 123 128 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. 2) is a Pro323Leu mutation in the RNA-dependent RNA polymerase protein nsp12. 2020 Genome biology Result SARS_CoV_2 P323L 8 17 RdRp;Nsp12 34;71 62;76 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. A recent paper, suggested that the Asp614Gly mutation in S allowed the virus to spread to nearly half the global population. 2020 Genome biology Result SARS_CoV_2 D614G 35 44 S 57 58 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. A single Ser25Leu mutation is found in nsp7 (250 individuals, mainly in New York and the northeast of the USA) and may also affect replication. 2020 Genome biology Result SARS_CoV_2 S25L 9 17 Nsp7 39 43 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. also show that the Asp614Gly S variant significantly increases the infectivity of pseudotyped lentiviruses in human cell cultures and on cells bearing ACE2 orthologs from other mammals. 2020 Genome biology Result SARS_CoV_2 D614G 19 28 S 29 30 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. As discussed above, within the SARS-CoV-2 GISAID sequences, there is a very frequent (72% of the sampled sequences) Asp to Gly substitution at position 614 at the terminus of the S1 subunit of the spike protein. 2020 Genome biology Result SARS_CoV_2 D614G 116 155 S 197 202 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Closer inspection reveals that the nsp12 and S signals reflect single mutations found at high frequency within the sampled population (Pro323Leu and Asp614Gly, respectively), which is also the case with the synonymous mutation at nsp3106. 2020 Genome biology Result SARS_CoV_2 D614G;P323L 149;135 158;144 Nsp12;S 35;45 40;46 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. corresponds to a mutation in nsp3 at site 106 that is completely linked to Asp614Gly in S (i.e., every individual with Asp614Gly also carries nsp3106). 2020 Genome biology Result SARS_CoV_2 D614G;D614G 75;119 84;128 Nsp3;S 29;88 33;89 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Finally, among the other non-conservative mutations registered for SARS-CoV-2 S, the multiple mutations at site 483, Val483Gly (Ala, Asp), may require special attention. 2020 Genome biology Result SARS_CoV_2 V483G 117 126 S 78 79 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Finally, the mutation Asp103Tyr is within the peak identified in the wavelet analysis. 2020 Genome biology Result SARS_CoV_2 D103Y 22 31 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Further experiments are needed to reconcile the reported higher infectivity, abundance of open states of S, lower affinity to ACE2, and the decreased S1 shedding caused by the Asp614Gly S variant. 2020 Genome biology Result SARS_CoV_2 D614G 176 185 S;S 105;186 106;187 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Further work on specific strains of the virus (comprising solely Asp614Gly S or Pro323Leu nsp12, and the combination of both) is needed to clarify which, if any, of these hypotheses are correct. 2020 Genome biology Result SARS_CoV_2 D614G;P323L 65;80 74;89 Nsp12;S 90;75 95;76 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. However, as we indicated in our mutational analysis above, viruses that harbored only the Asp614Gly S mutation were unsuccessful and it was only the addition of the Pro323Leu nsp12 mutation that provided for rapid transmission of the virus throughout the globe (branch 1-2. 2020 Genome biology Result SARS_CoV_2 D614G;P323L 90;165 99;174 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. However, the subsequent addition of the mutation in nsp12 may have allowed it to spread as a compensatory adaptive change, or possibly Asp614Gly is neutral and the nsp12 mutation alone is responsible for the majority of the enhanced viral fitness. 2020 Genome biology Result SARS_CoV_2 D614G 135 144 Nsp12;Nsp12 52;164 57;169 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. However, these results cannot determine which mutation is responsible for this observation because the intermediate haplotype with only the Asp614Gly S was not tested. 2020 Genome biology Result SARS_CoV_2 D614G 140 149 S 150 151 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. However, we find 11 individuals from nearby British Columbia, Canada, that are infected with a SARS-CoV-2 harboring only the Tyr541Cys variant and not the Pro504Leu. 2020 Genome biology Result SARS_CoV_2 P504L;Y541C 155;125 164;134 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. In a recent study from the Scripps Research Institute (https://www.scripps.edu/), not yet peer-reviewed, pseudoviruses containing the variant Asp614Gly of SARS-CoV-2 S were able to infect HEK293T cells with significantly higher efficiency than those containing the native S protein. 2020 Genome biology Result SARS_CoV_2 D614G 142 151 S;S 166;272 167;273 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. in contrast with the Ser202Asn, for example. 2020 Genome biology Result SARS_CoV_2 S202N 21 30 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. In fact, by obtaining the first cryo-EM derived map of the Asp614Gly S variant, Yurkovetskiy et al. 2020 Genome biology Result SARS_CoV_2 D614G 59 68 S 69 70 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. In support of this, a previous in vitro study of SARS-CoV nsp13 showed that the double substitution Ser539Ala/Tyr541Ala decreased helicase unwinding activity. 2020 Genome biology Result SARS_CoV_2 S539A;S539Y;Y541A 100;100;110 109;109;119 Helicase;Nsp13 130;58 138;63 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Notably, despite the higher probability of exposure of the RBDs, the dissociation rate of the Asp614Gly S variant from ACE2 is 4-fold faster than the wildtype, showing that the basis of the increased infectivity of Asp614Gly S does not rely on a stronger interaction with ACE2. 2020 Genome biology Result SARS_CoV_2 D614G;D614G 94;215 103;224 RBD;S;S 59;104;225 63;105;226 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Notably, many of these mutations correspond to a loss of potential phosphorylation sites (serines and threonines), namely, Ser188Leu, Ser193Ile, Ser194Leu, Ser197Leu, Ser202Asn(Ile), and Thr205Ile. 2020 Genome biology Result SARS_CoV_2 S188L;S193I;S194L;S197L;S202N;T205I 123;134;145;156;167;187 132;143;154;165;176;196 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. One of the potentially adaptive branches consists of the sequential mutations Val198Ile and Pro91Ser in nsp2 (branch 3-4. 2020 Genome biology Result SARS_CoV_2 P91S;V198I 92;78 100;87 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Particularly, the Val483Gly substitution may increase conformational flexibility of the loop. 2020 Genome biology Result SARS_CoV_2 V483G 18 27 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Several non-synonymous mutations were identified in nsp12, including the Pro323Leu, which is one of the mutations in a potentially adaptive lineage in our network (2. 2020 Genome biology Result SARS_CoV_2 P323L 73 82 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. The addition of the Pro323Leu in nsp12 may impair not only proofreading capability but also its replicase activity, decreasing the severity of disease which allowed for further transmission in asymptomatic or mildly symptomatic individuals. 2020 Genome biology Result SARS_CoV_2 P323L 20 29 Nsp12 33 38 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. The double substitution, Pro504Leu and Tyr541Cys, defines a large clade that is mostly present in North America (92% of individuals with the mutations). 2020 Genome biology Result SARS_CoV_2 P504L;Y541C 25;39 34;48 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. The fifth branch (12-13) is defined by the Thr85Ile mutation in nsp2 followed by Gln57His in ORF3a. 2020 Genome biology Result SARS_CoV_2 Q57H;T85I 81;43 89;51 ORF3a;Nsp2 93;64 98;68 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. The haplotype network shows that this mutation is immediately followed by Pro504Leu substitution, which is located at a superficial region of the 2A domain. 2020 Genome biology Result SARS_CoV_2 P504L 74 83 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. The hypermutable site at 21575 corresponds to Leu5Phe and the heteroplasmy at 21570 to a Val3Gly; both are located in the signal peptide (SP) in the N-terminal domain of the S protein. 2020 Genome biology Result SARS_CoV_2 L5F;V3G 46;89 53;96 S;N;S 138;149;174 140;150;175 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. The impact of this variation, corresponding to a double mutation at the protein level (Arg203Lys and Gly204Arg), results in an additional positively charged site, and possibly, it increases local rigidity with the subtraction of Gly204. 2020 Genome biology Result SARS_CoV_2 G204R;R203K 101;87 110;96 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. The second highest scored site has three alleles (Asp936Tyr, Asp936His in S) which may explain its significant iRF score, i.e., it is predictive of or predicted by more sites than expected because there are more than two alleles. 2020 Genome biology Result SARS_CoV_2 D936H;D936Y 61;50 70;59 S 74 75 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. The short half-life of this haplotype could indicate that the initial Tyr541Cys mutation was not sustainable by itself, requiring Pro504Leu to persist and expand. 2020 Genome biology Result SARS_CoV_2 P504L;Y541C 130;70 139;79 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. the substitution Asp614Gly likely dramatically perturbs the network of salt bridge and hydrogen bond interactions involving residues of the FPPR (Lys835, Asp848, Arg847, and Asp843), Asn556, at the CTD1, and Glu281, at the N-terminal domain (NTD). 2020 Genome biology Result SARS_CoV_2 D614G 17 26 N 223 224 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. The wavelet analysis simultaneously displays the location, frequency, and mutational density at different scales and identified a cluster of moderately frequent mutations involving 14 amino acids in a serine/arginine-rich motif of N (Ser180Ile, Ser183Tyr, Ser188Leu, Ser190Asn, Ser193Ile, Ser194Leu, Arg195Lys, Ser197Leu, Ser202Asn, Arg203Lys, Gly204Arg, Thr205Ile, Ala208Val, and Arg209Thr) and the C-terminal end of the nsp13 protein. 2020 Genome biology Result SARS_CoV_2 A208V;R195K;R203K;R209T;G204R;S183Y;S188L;S190N;S193I;S194L;S197L;S202N;T205I;S180I 366;300;333;381;344;245;256;267;278;289;311;322;355;234 375;309;342;390;353;254;265;276;287;298;320;331;364;243 Nsp13;N 422;231 427;232 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. There are three potential explanations for this observation: (1) the Asp614Gly S mutation conferred greater capacity for the virus to enter cells which resulted in more severe medical outcomes in those individuals (or the infected cells), and therefore, the virus was not able to transmit further. 2020 Genome biology Result SARS_CoV_2 D614G 69 78 S 79 80 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. This data suggests that Pro504Leu may be compensating the putative loss of performance of Tyr541Cys nsp13. 2020 Genome biology Result SARS_CoV_2 P504L;Y541C 24;90 33;99 Nsp13 100 105 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. This haplotype is defined by the Asp614Gly mutation in the S protein (numeral 1. 2020 Genome biology Result SARS_CoV_2 D614G 33 42 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. This is supported by Korber et al., who showed that plasma samples from individuals carrying the virus with Asp614Gly S and Pro323Leu nsp12 have higher counts of viruses than those that carry neither. 2020 Genome biology Result SARS_CoV_2 D614G;P323L 108;124 117;133 Nsp12;S 134;118 139;119 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. This result suggests that the mutation to alanine will likely not impact the interaction with ACE2, while the mutation to a negatively charged residue (Val483Asp) may alter the interfacial contacts. 2020 Genome biology Result SARS_CoV_2 V483D 152 161 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. We identified three different substitutions at site 1198, namely, Thr1198Lys, Thr1198Ile, and Thr1198Arg. 2020 Genome biology Result SARS_CoV_2 T1198R;T1198I;T1198K 94;78;66 104;88;76 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. We suggest that future studies should test the hypothesis that Pro504Leu directly or indirectly improves nsp12-nsp13 binding and, thus, reestablishes viral replication capacity. 2020 Genome biology Result SARS_CoV_2 P504L 63 72 Nsp13;Nsp12 111;105 116;110 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. While the Asp614Gly S variant may be increasing infectivity, a higher propensity to exhibit more extreme symptoms in individuals carrying this variant was not clearly verified. 2020 Genome biology Result SARS_CoV_2 D614G 10 19 S 20 21 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. Another mutation (G71S) in the nonstructural protein 5 region was present at a frequency of 70% in the study sample (Supplementary Figure S1). 2021 International journal of infectious diseases Result SARS_CoV_2 G71S 18 22 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. Interestingly, the common G71S mutation was not seen in the family cluster I, which belonged to B.1.1 (GR). 2021 International journal of infectious diseases Result SARS_CoV_2 G71S 26 30 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. Some of the identified mutations were defining a specific clade such as G204R and D614G in the Spike protein that constitutes the B.1.1.27 and the B.1.1 (GR). 2021 International journal of infectious diseases Result SARS_CoV_2 D614G;G204R 82;72 87;77 S 95 100 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. The most prevalent mutation was P323L (94.7%) found in the non-structural protein 12 followed by the D614G (92.6%) in the Spike glycoprotein (Supplementary Figure S1). 2021 International journal of infectious diseases Result SARS_CoV_2 D614G;P323L 101;32 106;37 S 122 140 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. The mutation I280V belonged to lineage B.1.113 (GH), it was detected in cluster V in Al Batinah South and Muscat. 2021 International journal of infectious diseases Result SARS_CoV_2 I280V 13 18 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. Two unique missense mutations were detected in this study; I280V in the NSP15 and R502C in the NSP13, which existed at low frequencies of 6 (5.3%) and 2 (2.1%), respectively (Supplementary Figure S1). 2021 International journal of infectious diseases Result SARS_CoV_2 I280V;R502C 59;82 64;87 Nsp13 95 100 33359807 SARS-Cov-2 ORF3a: Mutability and function. A54S, at the inter-subunit interface TM1-TM3' (prime denotes the other subunit), is relatively rare and it has been observed in the top five frequencies only in April and May isolates mostly in UK. 2021 International journal of biological macromolecules Result SARS_CoV_2 A54S 0 4 33359807 SARS-Cov-2 ORF3a: Mutability and function. Among these mutations, the variant G251V is consistently highly frequent and has been isolated all over the world. 2021 International journal of biological macromolecules Result SARS_CoV_2 G251V 35 40 33359807 SARS-Cov-2 ORF3a: Mutability and function. Among these, five mutant sites in the transmembrane portion lay in a position lining the central pore or the tunnels connecting it to the cytosolic compartment: L46F, A54S, Q57H, K75N and R126S (Table 3 and. 2021 International journal of biological macromolecules Result SARS_CoV_2 A54S;K75N;L46F;Q57H;R126S 167;179;161;173;188 171;183;165;177;193 33359807 SARS-Cov-2 ORF3a: Mutability and function. By analogy with G172V, it may be speculated that this mutation stabilizes the beta-barrel by adding hydrophobic interaction. 2021 International journal of biological macromolecules Result SARS_CoV_2 G172V 16 21 33359807 SARS-Cov-2 ORF3a: Mutability and function. Considering the order of temporal appearance of mutations during the pandemic, the double mutant Q57H + A99V has been isolated mainly in European countries at the beginning of the pandemic and overall, it is one of the five top variants observed over the entire period. 2021 International journal of biological macromolecules Result SARS_CoV_2 A99V;Q57H 104;97 108;101 33359807 SARS-Cov-2 ORF3a: Mutability and function. F207L replace an aromatic residue with Leu at the interface with the lipid bilayer. 2021 International journal of biological macromolecules Result SARS_CoV_2 F207L 0 5 33359807 SARS-Cov-2 ORF3a: Mutability and function. For example, Q57H is ubiquitous and is consistently the most frequent ORF3a substitution described in the literature. 2021 International journal of biological macromolecules Result SARS_CoV_2 Q57H 13 17 ORF3a 70 75 33359807 SARS-Cov-2 ORF3a: Mutability and function. Four of these variants contain the mutation Q57H paired with another amino acidic change (A99V, S58N, Y264C, G172V). 2021 International journal of biological macromolecules Result SARS_CoV_2 G172V;Q57H;S58N;Y264C;A99V 109;44;96;102;90 114;48;100;107;94 33359807 SARS-Cov-2 ORF3a: Mutability and function. In two cases, the associated mutations are in the extracellular domain (G172V and Y264C). 2021 International journal of biological macromolecules Result SARS_CoV_2 Y264C;G172V 82;72 87;77 33359807 SARS-Cov-2 ORF3a: Mutability and function. Mutation L108F was detected in July in UK with a relatively high frequency. 2021 International journal of biological macromolecules Result SARS_CoV_2 L108F 9 14 33359807 SARS-Cov-2 ORF3a: Mutability and function. Only the variant Q57H has a frequency constantly high in all the collection periods whereas the frequency of the other mutations fluctuates. 2021 International journal of biological macromolecules Result SARS_CoV_2 Q57H 17 21 33359807 SARS-Cov-2 ORF3a: Mutability and function. S58N at the inter-subunit interface TM1-TM3' is present in a double mutant Q57H + S58N relatively frequent in August, isolated primarily in Netherlands. 2021 International journal of biological macromolecules Result SARS_CoV_2 Q57H;S58N;S58N 75;82;0 79;86;4 33359807 SARS-Cov-2 ORF3a: Mutability and function. Similarly, L46F is a relatively rare change isolated mainly in India in June 2020 that creates an aromatic interaction at the end of the transmembrane helix 1 (TM1), already described as deleterious by other authors. 2021 International journal of biological macromolecules Result SARS_CoV_2 L46F 11 15 33359807 SARS-Cov-2 ORF3a: Mutability and function. T223I emerged in the top five relative frequencies in the isolates collected in August from UK. 2021 International journal of biological macromolecules Result SARS_CoV_2 T223I 0 5 33359807 SARS-Cov-2 ORF3a: Mutability and function. The A99V mutation is predicted to be only marginally destabilizing (Table 4). 2021 International journal of biological macromolecules Result SARS_CoV_2 A99V 4 8 33359807 SARS-Cov-2 ORF3a: Mutability and function. The analyses conducted by DynaMut and DUET servers predicted that S58N substitution reduces ORF3a stability (Table 4). 2021 International journal of biological macromolecules Result SARS_CoV_2 S58N 66 70 ORF3a 92 97 33359807 SARS-Cov-2 ORF3a: Mutability and function. The mutation T223I occurs in the loop connecting beta7 to beta8 and it is predicted to be destabilizing (Table 4). 2021 International journal of biological macromolecules Result SARS_CoV_2 T223I 13 18 33359807 SARS-Cov-2 ORF3a: Mutability and function. The substitution G172V may contribute the stabilization of the beta-barrel by increasing the hydrophobic interactions while decreasing local flexibility. 2021 International journal of biological macromolecules Result SARS_CoV_2 G172V 17 22 33359807 SARS-Cov-2 ORF3a: Mutability and function. The substitution G196V showed a peak frequency in March but, overall, it is among the top five more frequent variants. 2021 International journal of biological macromolecules Result SARS_CoV_2 G196V 17 22 33359807 SARS-Cov-2 ORF3a: Mutability and function. The substitution K75N appears relatively frequent in August and was isolated exclusively in UK. 2021 International journal of biological macromolecules Result SARS_CoV_2 K75N 17 21 33359807 SARS-Cov-2 ORF3a: Mutability and function. The variant Q57H + G172V emerged in the top five relative frequencies in the isolates collected exclusively in the USA in August. 2021 International journal of biological macromolecules Result SARS_CoV_2 G172V;Q57H 19;12 24;16 33359807 SARS-Cov-2 ORF3a: Mutability and function. The variant R126S emerged mainly in June and July isolates from South Africa. 2021 International journal of biological macromolecules Result SARS_CoV_2 R126S 12 17 33359807 SARS-Cov-2 ORF3a: Mutability and function. This substitution is predicted to be destabilizing although not at the level of R126S. 2021 International journal of biological macromolecules Result SARS_CoV_2 R126S 80 85 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. Dynamic Tracking of SARS-CoV-2 S Glycoprotein D614G Mutation. 2020 Genes Result SARS_CoV_2 D614G 46 51 S 31 45 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. In addition, the SARS-CoV-2 variant containing the D614G mutation is predominantly transmitted outside of China. 2020 Genes Result SARS_CoV_2 D614G 51 56 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. Taken together, we speculate that the lower ACE2 expression in European and North American populations is a result of this genetic variation, and provides the driving force for the positive selection of SARS-CoV-2 S glycoprotein D614G mutation. 2020 Genes Result SARS_CoV_2 D614G 229 234 S 214 228 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. The SARS-CoV-2 S glycoprotein D614G mutation may be selected as a result of enhanced transmission ability in populations with lower ACE2 expression (Figure 2). 2020 Genes Result SARS_CoV_2 D614G 30 35 S 15 29 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. Therefore, the evolutionary adaptation of the D614G mutation may have occurred in Europe or North America. 2020 Genes Result SARS_CoV_2 D614G 46 51 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. This indicated that differences in ACE2 expression across geographic regions is a driving force for the positive selection of the SARS-CoV-2 S glycoprotein D614G mutation. 2020 Genes Result SARS_CoV_2 D614G 156 161 S 141 155 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. To understand the global dynamic of SARS-CoV-2 D614G mutation frequencies, we analyzed 121,895 SARS-CoV-2 sequences from 1 January to 12 October 2020 from the Los Alamos National Laboratory website (COVID-19 Viral Genome Analysis Pipeline, ; Figure 1A). 2020 Genes Result SARS_CoV_2 D614G 47 52 COVID-19 199 207 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. Considering the total number of sequences, the most frequent Spike protein variation is confirmed to be D614G. 2020 Journal of translational medicine Result SARS_CoV_2 D614G 104 109 S 61 66 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. Next, there are a few variants with a frequency of 2-7% that are slowly rising in the viral populations, namely S477N, Q613H and A222V. 2020 Journal of translational medicine Result SARS_CoV_2 A222V;Q613H;S477N 129;119;112 134;124;117 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. On the other hand, the N439K is dominating the isolates landscape in Ireland and England from August 2020. 2020 Journal of translational medicine Result SARS_CoV_2 N439K 23 28 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. The geographical distribution shows how the S477N variant is strongly rooted in Australia, and the N439K is associated with clusters starting from the United Kingdom (Scotland). 2020 Journal of translational medicine Result SARS_CoV_2 N439K;S477N 99;44 104;49 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. The overall Epitope score, that takes into account a variable amino acid window surrounding the mutation, is slightly increased, from 0.535/0.516 in the WT sequence to 0.561 and 0.548 for S477N and N439K, respectively (Additional file 1: Table S5). 2020 Journal of translational medicine Result SARS_CoV_2 N439K;S477N 198;188 203;193 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. The S477N has been firstly identified in Colombia and is harbored in more than 60% of the isolates sequenced in Australia from June 2020. 2020 Journal of translational medicine Result SARS_CoV_2 S477N 4 9 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. The S477N mutation lies in the RBD locus, while all the other RBD variants are below the 1% penetrance threshold. 2020 Journal of translational medicine Result SARS_CoV_2 S477N 4 9 RBD;RBD 31;62 34;65 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. When focusing on the predicted class 1 binders for the same epitope/HLA combination in mutated peptides, IYQAGNTPC (S477N) shows increased immunogenicity for all considered HLAs. 2020 Journal of translational medicine Result SARS_CoV_2 S477N 116 121 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. When focusing to all the mutated epitopes caused by S477N and N439K, none cause a shift of the amino acid exposition, as they are both predicted to be in the exposed status. 2020 Journal of translational medicine Result SARS_CoV_2 N439K;S477N 62;52 67;57 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. All mutations reported for spike protein in Table 2 are unique for animal isolates except the mutation in the SP for the dog (L8V). 2020 PeerJ Result SARS_CoV_2 L8V 126 129 S;S 27;110 32;112 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. Also, two unique substitutions (R20S and K23S) in the ORF6 protein of the mink isolates had a frequency of more than 2% (Table 3). 2020 PeerJ Result SARS_CoV_2 K23S;R20S 41;32 45;36 ORF6 54 58 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. Fifteen unique mutations were identified in mink isolates (Table S2), four of which (L452M, Y453F, F486L, N501T) were located within the RBM of S protein. 2020 PeerJ Result SARS_CoV_2 F486L;N501T;Y453F;L452M 99;106;92;85 104;111;97;90 S 144 145 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. Four unique amino acid substitution positions (H182L or H182Y, L219V, G224C, T229I) within the ORF3a protein of mink isolates had a frequency of more than 2%. 2020 PeerJ Result SARS_CoV_2 G224C;H182Y;L219V;T229I;H182L 70;56;63;77;47 75;61;68;82;52 ORF3a 95 100 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. In addition, nsp10 of SARS-CoV-2 isolated from the cat displayed one unique amino acid substitution (K4377E), while nsp12 (RNA-dependent RNA polymerase, RdRp) exhibited three unique amino acid substitutions, one for the cat (T4418I) and two for the mink (M4588I and T5195I). 2020 PeerJ Result SARS_CoV_2 T5195I;K4377E;M4588I;T4418I 266;101;255;225 272;107;261;231 RdRp;Nsp12;RdRP 123;116;153 151;121;157 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. In the mouse isolate, two unique amino acid substitutions (Q498H and N969S) were identified, with one of them (Q498H) located within the RBM. 2020 PeerJ Result SARS_CoV_2 N969S;Q498H;Q498H 69;59;111 74;64;116 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. Moreover, nsp9 (RNA/DNA binding activity) and nsp15 (Poly(U) specific endoribonuclease) of SARS-CoV-2 isolated from the mink exhibited one unique amino acid substitution at (G4177E or R) and (A6544T), respectively. 2020 PeerJ Result SARS_CoV_2 A6544T;G4177E 192;174 198;180 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. SARS-CoV-2 isolated from the mink exhibited three unique amino acid substitutions (R41L, P80L, and P199Q) with a frequency of 2.7%, while SARS-CoV-2 isolated from the cat had one unique amino acid substitution (T247I) with a frequency of 16.7% (Table 2). 2020 PeerJ Result SARS_CoV_2 P199Q;P80L;R41L;T247I 99;89;83;211 104;93;87;216 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. The frequency of the non-synonymous mutations was below the 2% threshold, therefore not reported in Table 2 except the T175M substitution in the cat isolate (16.7%). 2020 PeerJ Result SARS_CoV_2 T175M 119 124 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. The non-synonymous mutations reported for spike protein in Table 2 were distributed as follows: one in the signal peptide (SP), two in the N-terminal domain (NTD), six in the receptor-binding domain (RBD), one downstream of the RBD (D614G), and one in the heptad repeat 1 (HR1) (Refer to. 2020 PeerJ Result SARS_CoV_2 D614G 233 238 S;RBD;RBD;S;N 42;200;228;123;139 47;203;231;125;140 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. The nsp2 exhibited six unique amino acid substitutions, one in cat isolate (H388Y) and five in mink isolates (E352Q, A372V, R398C, A405T, and E743V), while nsp3 (Papain-like proteinase domain) revealed three (D953Y, V1052I, and K1202N), one (D2101G), and four (P1096L, H1113Y, I1508V, and M1588K) unique amino acid substitutions in SARS-CoV-2 isolates from the cat, dog, and mink, respectively. 2020 PeerJ Result SARS_CoV_2 A372V;A405T;E743V;H1113Y;I1508V;K1202N;M1588K;R398C;V1052I;D2101G;D953Y;E352Q;H388Y;P1096L 117;131;142;269;277;228;289;124;216;242;209;110;76;261 122;136;147;275;283;234;295;129;222;248;214;115;81;267 Nsp2;Nsp3 4;156 8;160 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. The nsp5 (3C-like proteinase domain) had two unique amino acid substitutions, one in cat isolate (I3512T) and the other in mink isolate (I3522V). 2020 PeerJ Result SARS_CoV_2 I3512T;I3522V 98;137 104;143 Nsp5 4 8 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. Two unique amino acid substitutions (I5582V and A5770D) were recorded in mink isolate for nsp13 (helicase). 2020 PeerJ Result SARS_CoV_2 A5770D;I5582V 48;37 54;43 Helicase;Nsp13 97;90 105;95 33385461 Development of new vaccine target against SARS-CoV2 using envelope (E) protein: An evolutionary, molecular modeling and docking based study. From the pair-wise alignment, three point mutations (T55S, V56F and E69R) and one amino acid deletion (G70del) were observed to occur in E-protein of SARS-CoV-2. 2021 International journal of biological macromolecules Result SARS_CoV_2 E69R;V56F;G70del;T55S 68;59;103;53 72;63;109;57 E 137 138 33385461 Development of new vaccine target against SARS-CoV2 using envelope (E) protein: An evolutionary, molecular modeling and docking based study. Two point mutations (T55S, V56F) caused coil helix transformation and mutation E69R and G70del causes turn helix transformation in that particular location. 2021 International journal of biological macromolecules Result SARS_CoV_2 E69R;G70del;V56F;T55S 79;88;27;21 83;94;31;25 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. Based on the collection data, most (39/60, 65%) virus genomes contained the D614G mutation representing clade G (2), GR (7) and GH (30). 2020 PeerJ Result SARS_CoV_2 D614G 76 81 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. Moreover, WGS of virus from patient-1, patient-2 and patient 3 showed nine amino acid mutations in six proteins, including NSP3 (P679S), NSP12 (P323L, A656S), NSP13 (M576I), spike (D614G), NS3 (A54V, Q57H, A99S), and NP (Q160R); four amino acid mutations in four proteins: NSP3 (P822L), NSP12 (P323L), Spike (D614G) and NS3 (Q57H); and five amino acid mutations in five proteins: NSP3 (P822L), NSP12 (P323L), Spike (D614G), NS3 (Q57H) and NS7a (H73Y), respectively; whereas those from patient-4 consisted of only one mutation in the NSP5 protein (M49I) (Table 1). 2020 PeerJ Result SARS_CoV_2 A656S;A99S;Q57H;A54V;D614G;D614G;D614G;H73Y;M49I;M576I;P323L;P323L;P323L;P679S;P822L;P822L;Q160R;Q57H;Q57H 151;206;200;194;181;309;416;445;547;166;144;294;401;129;279;386;221;325;429 156;210;204;198;186;314;421;449;551;171;149;299;406;134;284;391;226;329;433 S;S;S;Nsp13;Nsp12;Nsp12;Nsp12;Nsp3;Nsp3;Nsp3;Nsp5;NS3;NS3;NS3 174;302;409;159;137;287;394;123;273;380;533;189;320;424 179;307;414;164;142;292;399;127;277;384;537;192;323;427 33398275 An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. After titrating the concentrations of 8his-tagged sACE22(WT) and sACE22.v2.4 and measuring bound protein to S-expressing cells by flow cytometry, it was found S-N501W and S-N501Y do show enhanced specificity for wild type sACE22, but the effect is small and sACE22.v2.4 remains the stronger binder (Figure 5C). 2020 bioRxiv Result SARS_CoV_2 N501W;N501Y 161;173 166;178 S;S;S 108;159;171 109;160;172 33398275 An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. BLI kinetics between immobilized sACE22-IgG1 and monomeric RBD as the analyte showed reduced affinity of a representative mutant, RBD-Y449K, to both wild type and engineered sACE22 (Table 1). 2020 bioRxiv Result SARS_CoV_2 Y449K 134 139 RBD;RBD 59;130 62;133 33398275 An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. Both N501W and N501Y mutants of SARS-CoV-2 RBD displayed increased affinity for wild type ACE2 and engineered ACE2.v2.4, with larger affinity gains in favor of the wild type receptor (Table 1). 2020 bioRxiv Result SARS_CoV_2 N501W;N501Y 5;15 10;20 RBD 43 46 33398275 An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. However, affinity changes in the picomolar range for sACE22.v2.4 are hidden during avid binding to full-length S-Y449K at the cell surface, whereas avid binding of wild type sACE22 to S-Y449K (with affinity measured by BLI in the moderate nanomolar range) is substantially reduced. 2020 bioRxiv Result SARS_CoV_2 Y449K;Y449K 113;186 118;191 S;S 111;184 112;185 33398275 An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. N501 of S is located in the 498-506 loop and its substitution to large aromatic side chains might alter the loop conformation to cause steric strain with nearby ACE2 mutation N330Y in sACE22.v2.4. 2020 bioRxiv Result SARS_CoV_2 N330Y 175 180 S 8 9 33398275 An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. Soluble ACE22.v2.4 has three mutations from wild type ACE2: T27Y buried within the RBD interface, and L79T and N330Y at the interface periphery (Figure 5A). 2020 bioRxiv Result SARS_CoV_2 L79T;N330Y 102;111 106;116 RBD 83 86 33398275 An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. These S mutations were Y449K/Q/S, L455G/R/Y, and G504K. 2020 bioRxiv Result SARS_CoV_2 G504K;L455G;L455R;L455Y;Y449K;Y449Q;Y449S 49;34;34;34;23;23;23 54;43;43;43;32;32;32 S 6 7 33398275 An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. Two S mutants were investigated further in sACE22 titration experiments, N501W and N501Y, which both retained high receptor binding and displayed small shifts towards wild type sACE22 in the competition experiment. 2020 bioRxiv Result SARS_CoV_2 N501W;N501Y 73;83 78;88 S 4 5 33398275 An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. We found all cysteine-to-alanine mutations severely diminish S surface expression in Expi293F cells, including C391A and C525A on the RBD 'backside' that were neutral in the yeast display scan. 2020 bioRxiv Result SARS_CoV_2 C391A;C525A 111;121 116;126 RBD;S 134;61 137;62 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. At day 66 we noted I513T in NSP2 and V157L in RdRp had emerged from undetectable at day 54 to 100% frequency (Figure 4 orange line), with the polymerase being the more plausible candidate for driving this sweep. 2020 medRxiv Result SARS_CoV_2 I513T;V157L 19;37 24;42 Nsp2;RdRP 28;46 32;50 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. By contrast, the D796H single mutant had significantly lower infectivity as compared to wild type and the double mutant had similar infectivity to wild type (Figure 6B, supplementary figure 7). 2020 medRxiv Result SARS_CoV_2 D796H 17 22 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. D796H is in an exposed loop in S2 (Figure 8) and appears to be in a region frequently targeted by antibodies, despite mutations at position 796 being rare (Supplementary table 7). 2020 medRxiv Result SARS_CoV_2 D796H 0 5 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. Following the third course of remdesivir (day 93) and third CP (day 95), we observed a re-emergence of the D796H + DeltaH69/DeltaV70 viral population. 2020 medRxiv Result SARS_CoV_2 D796H 107 112 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. In addition, patient derived serum from days 64 and 66 (one day either side of CP2 infusion) similarly showed lower potency against the D796H + DeltaH69/DeltaV70 mutants (Figure 6F, G). 2020 medRxiv Result SARS_CoV_2 D796H 136 141 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. In contrast to the early period of infection, between days 66 and 82, following the first two administrations of convalescent sera, a dramatic shift in the virus population was observed, with a variant bearing D796H in S2 and DeltaH69/DeltaV70 in the S1 N-terminal domain (NTD) becoming the dominant population at day 82. 2020 medRxiv Result SARS_CoV_2 D796H 210 215 N 254 255 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. In further support of our proposed idea of competition, noted above, frequencies of these two variants appeared to mirror changes in the NSP2 I513T mutation (Figure 4), suggesting these as markers of opposing clades in the viral population. 2020 medRxiv Result SARS_CoV_2 I513T 142 147 Nsp2 137 141 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. Notably, spike variant N501Y, which can increase the ACE2 receptor affinity, and which is present in the new UK B1.1.7 lineage, was observed on day 55 at 33% frequency, but was eliminated by the sweep of the NSP2/RdRp variant. 2020 medRxiv Result SARS_CoV_2 N501Y 23 28 S;Nsp2;RdRP 9;208;213 14;212;217 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. On Days 86 and 89, viruses obtained from upper respiratory tract samples were characterised by the Spike mutations Y200H and T240I, with the deletion/mutation pair observed on day 82 having fallen to frequencies of 10% or less (Figure 4 and 5). 2020 medRxiv Result SARS_CoV_2 T240I;Y200H 125;115 130;120 S 99 104 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. Patterns in the variant frequencies suggest competition between virus populations carrying different mutations, viruses with the D796H/ DeltaH69/DeltaV70 deletion/mutation pair rising to high frequency during CP therapy, then being outcompeted by another population in the absence of therapy. 2020 medRxiv Result SARS_CoV_2 D796H 129 134 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. Sequencing of a nose and throat swab sample at day 93 identified viruses characterised by Spike mutations P330S at the edge of the RBD and W64G in S1 NTD at close to 100% abundance, with D796H along with DeltaH69/DeltaV70 at <1% abundance and the variants Y200H and T240I at frequencies of <2%. 2020 medRxiv Result SARS_CoV_2 D796H;P330S;T240I;W64G;Y200H 187;106;266;139;256 192;111;271;143;261 S;RBD 90;131 95;134 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. Specifically, these data are consistent with a lineage of viruses with the NSP2 I513T and RdRp V157L variant, dominant on day 66, being outcompeted during therapy by the mutation/deletion variant. 2020 medRxiv Result SARS_CoV_2 I513T;V157L 80;95 85;100 Nsp2;RdRP 75;90 79;94 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. The infecting strain was assigned to lineage 20B bearing the D614G Spike variant. 2020 medRxiv Result SARS_CoV_2 D614G 61 66 S 67 72 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. The inferred linkage of D796H and DeltaH69/DeltaV70 was maintained as evidenced by the highly similar frequencies of the two variants, suggesting that the third unit of CP led to the re-emergence of this population under renewed positive selection. 2020 medRxiv Result SARS_CoV_2 D796H 24 29 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. The inferred linkage of D796H and DeltaH69/DeltaV70 was maintained as evidenced by the highly similar frequencies of the two variants. 2020 medRxiv Result SARS_CoV_2 D796H 24 29 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. The seven RBD-specific mAbs (Supplementary table 6) exhibited no major change in neutralisation potency and non-RBD specific COVA1-21 showing 3-5 fold reduction in potency against DeltaH69/DeltaV70+D796H and DeltaH69/DeltaV70, but not D796H alone (Figure 7). 2020 medRxiv Result SARS_CoV_2 D796H;D796H 235;198 240;203 RBD;RBD 10;112 13;115 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. The Spike mutations Y200H and T240I were accompanied at high frequency by two other non-synonymous variants with similar allele frequencies, coding for I513T in NSP2, V157L in RdRp and N177S in NSP15 (Figure 4). 2020 medRxiv Result SARS_CoV_2 I513T;N177S;T240I;V157L;Y200H 152;185;30;167;20 157;190;35;172;25 S;Nsp2;RdRP 4;161;176 9;165;180 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. To establish if the mutations incurring in vivo (D796H and DeltaH69/DeltaV70) resulted in a global change in neutralization sensitivity we tested neutralising mAbs targeting the seven major epitope clusters previously described (excluding non-neutralising clusters II, V and small [n =<2] neutralising clusters IV, X). 2020 medRxiv Result SARS_CoV_2 D796H 49 54 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. Using lentiviral pseudotyping we generated wild type, DeltaH69/DeltaV70 + D796H and single mutant Spike proteins in enveloped virions in order to measure neutralisation activity of CP against these viruses (Figure 6). 2020 medRxiv Result SARS_CoV_2 D796H 74 79 S 98 103 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. Viruses with the P330S variant were detected in two independent samples from different sampling sites, arguing against the possibility of contamination. 2020 medRxiv Result SARS_CoV_2 P330S 17 22 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. We found that D796H alone and the D796H + DeltaH69/DeltaV70 double mutant were less sensitive to neutralisation by convalescent plasma samples (Figure 6C-E). 2020 medRxiv Result SARS_CoV_2 D796H;D796H 14;34 19;39 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. We observed a re-emergence of the D796H + DeltaH69/DeltaV70 viral population. 2020 medRxiv Result SARS_CoV_2 D796H 34 39 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. With the lapse in therapy, the original strain, having acquired NSP15, N1773S and the Spike mutations, regained dominance, followed by the emergence of a separate population with the W64G and P330S mutations. 2020 medRxiv Result SARS_CoV_2 N1773S;P330S;W64G 71;192;183 77;197;187 S 86 91 33407987 Impact of population density and weather on COVID-19 pandemic and SARS-CoV-2 mutation frequency in Bangladesh. About 82% of the isolates from Bangladesh had D614G at S protein. 2021 Epidemiology and infection Result SARS_CoV_2 D614G 46 51 S 55 56 33407987 Impact of population density and weather on COVID-19 pandemic and SARS-CoV-2 mutation frequency in Bangladesh. Another two mutations, R203K and G204R at N protein were most common (73%) in the Bangladeshi novel coronaviruses. 2021 Epidemiology and infection Result SARS_CoV_2 G204R;R203K 33;23 38;28 N 42 43 33407987 Impact of population density and weather on COVID-19 pandemic and SARS-CoV-2 mutation frequency in Bangladesh. Fourth, amount of rainfall was also strongly correlated with frequency of D614G. 2021 Epidemiology and infection Result SARS_CoV_2 D614G 74 79 33407987 Impact of population density and weather on COVID-19 pandemic and SARS-CoV-2 mutation frequency in Bangladesh. Frequency of D614G had the highest correlation (rs = 0.611) with average temperature but frequency of rare mutation at spike protein had the highest correlation (rs = 0.658) with maximum temperature. 2021 Epidemiology and infection Result SARS_CoV_2 D614G 13 18 S 119 124 33407987 Impact of population density and weather on COVID-19 pandemic and SARS-CoV-2 mutation frequency in Bangladesh. Important mutational events, namely, common mutation at ORF1ab, rare mutation at ORF1ab, S (D614G), rare mutation at spike protein (S), first time mutation at S, common mutation at other structural proteins and rare mutations at other structural proteins were detected and included in this study. 2021 Epidemiology and infection Result SARS_CoV_2 D614G 92 97 ORF1ab;ORF1ab;S;S;S;S 56;81;117;89;132;159 62;87;122;90;133;160 33407987 Impact of population density and weather on COVID-19 pandemic and SARS-CoV-2 mutation frequency in Bangladesh. The most common mutation at ORF1ab region were P323L (NSP12) (88%) and I120F (NSP2) (72%). 2021 Epidemiology and infection Result SARS_CoV_2 I120F;P323L 71;47 76;52 ORF1ab;Nsp12;Nsp2 28;54;78 34;59;82 33407987 Impact of population density and weather on COVID-19 pandemic and SARS-CoV-2 mutation frequency in Bangladesh. Third, relative humidity had highest correlation (rs = 0.389) with frequency of D614G. 2021 Epidemiology and infection Result SARS_CoV_2 D614G 80 85 33408342 A longitudinal study of SARS-CoV-2-infected patients reveals a high correlation between neutralizing antibodies and COVID-19 severity. D614G substitution is not associated with resistance to SARS-CoV-2 neutralization. 2021 Cellular & molecular immunology Result SARS_CoV_2 D614G 0 5 33408342 A longitudinal study of SARS-CoV-2-infected patients reveals a high correlation between neutralizing antibodies and COVID-19 severity. However, we found that the D614G mutation did not affect the nAb activity of the serum samples from our cohort, as shown by similar neutralization profiles. 2021 Cellular & molecular immunology Result SARS_CoV_2 D614G 27 32 33408342 A longitudinal study of SARS-CoV-2-infected patients reveals a high correlation between neutralizing antibodies and COVID-19 severity. To address the possibility of a neutralization escape phenotype potentially conferred by the D614G mutation, we used the SARS-CoV-2pp assay, which is particularly suitable for comparing the nAb activity of serum specimens against pseudoparticles harboring this mutation. 2021 Cellular & molecular immunology Result SARS_CoV_2 D614G 93 98 33412089 COVID-19-neutralizing antibodies predict disease severity and survival. It has also been suggested that D614G spike may exist in a more open conformation that does not impact antibody neutralization. 2021 Cell Result SARS_CoV_2 D614G 32 37 S 38 43 33412089 COVID-19-neutralizing antibodies predict disease severity and survival. Recent studies have demonstrated that infection with live SARS-CoV-2 harboring the D614G spike variant yielded higher virus titers in respiratory cultures and increased transmissibility in hamster models. 2021 Cell Result SARS_CoV_2 D614G 83 88 S 89 94 33412089 COVID-19-neutralizing antibodies predict disease severity and survival. The recent emergence of a mutation in the SARS-CoV-2 spike protein (D614G) has raised concerns for the potential for convalescent patients to become reinfected. 2021 Cell Result SARS_CoV_2 D614G 68 73 S 53 58 33412089 COVID-19-neutralizing antibodies predict disease severity and survival. To determine the impact of this variant on the neutralization potency of patients previously infected with SARS-CoV-2, we introduced the D614G mutation into the SARS-CoV-2 Delta18 spike (Figure 6 A). 2021 Cell Result SARS_CoV_2 D614G 137 142 S 180 185 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. Although the percentage of D614G mutation gradually increased from February towards May in both groups, there was more D614G mutation in severely affected group compared with mildly affected group in March (68.2% vs. 2020 Genomics & informatics Result SARS_CoV_2 D614G;D614G 27;119 32;124 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. Among all the mutations in the non-coding region of SARS-CoV-2 genome, the 241C>T mutation in the 5 UTR appeared most predominantly in severely affected group (85.7%) compared with mildly affected group (45.7%, p < 0.001) (Table 1). 2020 Genomics & informatics Result SARS_CoV_2 C241T 75 81 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. Among the silent mutations present in ORF1ab, 3037C>T mutation was found more commonly in severely affected group (64.3%) compared with mildly affected group (45.7%, p = 0.06). 2020 Genomics & informatics Result SARS_CoV_2 C3037T 46 53 ORF1ab 38 44 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. Another mutation 5700C>A in ORF1ab caused missense mutation A1812D at the amino acid level. 2020 Genomics & informatics Result SARS_CoV_2 C5700A;A1812D 17;60 24;66 ORF1ab 28 34 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. In ORF1ab, 11083G>T mutation at the nucleotide level caused L3606F mutation at the amino acid level and involved non-structural protein (nsp) 6. 2020 Genomics & informatics Result SARS_CoV_2 G11083T;L3606F 11;60 19;66 ORF1ab 3 9 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. In ORF3a, 25563G>T mutation at the nucleotide level resulted in Q57H mutation at the amino acid level, and this mutation was more prevalent in severely affected group (26.8%) compared with mildly affected group (10.9%, p = 0.08). 2020 Genomics & informatics Result SARS_CoV_2 G25563T;Q57H 10;64 18;68 ORF3a 3 8 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. In ORF8, 28144T>C mutation at the nucleotide level resulted in L84S mutation at the amino acid level. 2020 Genomics & informatics Result SARS_CoV_2 T28144C;L84S 9;63 17;67 ORF8 3 7 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. In Table 2, we showed collection period of viral isolates in month and frequency of D614G mutation in mildly affected and severely affected groups. 2020 Genomics & informatics Result SARS_CoV_2 D614G 84 89 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. In the open reading frame (ORF) 1ab of the SARS-CoV-2 genome, the most frequent mutation identified was 14,408C>T at the nucleotide level. 2020 Genomics & informatics Result SARS_CoV_2 C408T 107 113 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. In the severely affected group, however, 241C>T, and 23403A>G coincided, and 3037C>T and 14408C>T occurred in subsets of them. 2020 Genomics & informatics Result SARS_CoV_2 C14408T;A23403G;C241T;C3037T 89;53;41;77 97;61;47;84 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. In the spike protein, 23403A>G mutation at the nucleotide level resulted in D614G mutation at the amino acid level, and it was predominantly found in severely affected group (85.7%) compared with mildly affected group (45.7%, p < 0.001) (Table 1. 2020 Genomics & informatics Result SARS_CoV_2 A23403G;D614G 22;76 30;81 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. Of note, in the mildly affected group, four most common mutations (241C>T, 3037C>T, 14408C>T, and 23403A>G) coincided. 2020 Genomics & informatics Result SARS_CoV_2 C14408T;A23403G;C3037T;C241T 84;98;75;67 92;106;82;73 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. Of note, the percentage of D614G mutation was found higher in severely affected group compared with mildly affected group for both India and Belgium (Table 3). 2020 Genomics & informatics Result SARS_CoV_2 D614G 27 32 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. The 29742G>A, 29827A>T and 29830G>T mutations in the 3' UTR appeared at a frequency of 17.4%, 34.8%, and 43.5%, respectively, in mildly affected group; but none of these mutations was found in the severely affected group (Table 1). 2020 Genomics & informatics Result SARS_CoV_2 G29742A;A29827T;G29830T 4;14;27 12;22;35 3'UTR 53 59 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. There was temporal and geographical variation in the distribution of 23403A>G mutation that cause D614G mutation in the spike protein of SARS-CoV-2. 2020 Genomics & informatics Result SARS_CoV_2 A23403G;D614G 69;98 77;103 S 120 125 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. This finding suggests that increased spike protein D614G mutation in severely affected group was unlikely to be due to temporal variation in the distribution of the mutation. 2020 Genomics & informatics Result SARS_CoV_2 D614G 51 56 S 37 42 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. This mutation results in a missense mutation P4715L at the amino acid level of ORF1ab polyprotein that ultimately appears as P323L mutation in the RdRp enzyme. 2020 Genomics & informatics Result SARS_CoV_2 P323L;P4715L 125;45 130;51 ORF1ab;RdRP 79;147 85;151 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. To explore whether this fact contributed to the increased spike protein D614G mutation in severely affected group, we showed frequency of D614G mutation in mildly affected and severely affected groups for India and Belgium in Table 3. 2020 Genomics & informatics Result SARS_CoV_2 D614G;D614G 72;138 77;143 S 58 63 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. As observed for S-GSAS/D614G, the SD2 domain showed little conformational change and formed a stable motif anchoring the mobile NTD and RBD domains. 2021 Cell reports Result SARS_CoV_2 D614G 23 28 RBD;S 136;16 139;17 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Because our expression system (i.e., 293Freestyle cells) endogenously expresses furin, in order to obtain uncleaved S that we could then test for protease cleavage in vitro, we engineered a HRV3C site (eight amino acids long) to replace the furin cleavage site (four amino acids long) at the S1/S2 junction, resulting in the S-HRV3C and S-HRV3C/D614G S ectodomain constructs (Figure 1A). 2021 Cell reports Result SARS_CoV_2 D614G 345 350 S;S;S;S 116;325;337;351 117;326;338;352 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Both proteins expressed in 293F cells but at lower yields compared with the S-GSAS constructs (36 and 410 mug/L for the S-HRV3C and S-HRV3C/D614G proteins, respectively). 2021 Cell reports Result SARS_CoV_2 D614G 140 145 S;S;S 76;120;132 77;121;133 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Comparing with the S-GSAS dataset, we observed an increased proportion of the 1-RBD-up form versus the 3-RBD-down form in the S-GSAS/D614G cryo-EM dataset. 2021 Cell reports Result SARS_CoV_2 D614G 133 138 RBD;RBD;S;S 80;105;19;126 83;108;20;127 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Consistent with the enhanced cleavage observed for the S-HRV3C/D614G S relative to the S-HRV3C S, in the furin-site-restored Ss, we observed a higher proportion of cleaved S in S-RRAR/D614G relative to S-RRAR, suggesting that the D614G mutation makes the S more susceptible to furin cleavage. 2021 Cell reports Result SARS_CoV_2 D614G;D614G;D614G 230;63;184 235;68;189 S;S;S;S;S;S;S;S 55;69;87;95;172;177;202;255 56;70;88;96;173;178;203;256 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Effect of the D614G Substitution on Furin Cleavage Efficiency at the S1/S2 Junction. 2021 Cell reports Result SARS_CoV_2 D614G 14 19 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. In addition to the D614G mutation, the SD2 subdomain also harbors a multibasic furin cleavage site (residues 682-685) that separates the S1 and S2 subunits (Figure 1). 2021 Cell reports Result SARS_CoV_2 D614G 19 24 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. In summary, the SEC and SDS-PAGE profiles showed that, although both the S-RRAR and S-RRAR/D614G constructs were cleaved by endogenous furin (Figure 6B) during protein expression, the S1 and S2 subunits remained together in solution (Figure 6A). 2021 Cell reports Result SARS_CoV_2 D614G 91 96 S;S 73;84 74;85 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. In summary, these results show that acquisition of the D614G mutation in the S protein SD2 domain resulted in increased furin cleavage of the S ectodomain. 2021 Cell reports Result SARS_CoV_2 D614G 55 60 S;S 77;142 78;143 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Indeed, the SD2' super subdomain that harbors the D614G mutation appears to form a conformationally invariant anchor with the highly mobile RBD and NTD domains at either end (Figure 4D). 2021 Cell reports Result SARS_CoV_2 D614G 50 55 RBD 140 143 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. NSEM of the purified S-RRAR (Figure 6C; Data S5) and S-RRAR/D614G (Figure 6D; Data S5) confirmed that both of these furin-site-restored S- proteins formed well-folded S ectodomains. 2021 Cell reports Result SARS_CoV_2 D614G 60 65 S;S;S;S 21;53;136;167 22;54;137;168 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. NSEM of the S-GSAS/D614G S ectodomain revealed typical and well-dispersed pre-fusion S particles (Figure 3B; Data S2). 2021 Cell reports Result SARS_CoV_2 D614G 19 24 S;S;S 12;25;85 13;26;86 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. NSEM showed fully folded ectodomains for the furin-digested and SEC-purified S-RRAR/D614G protein (Figure 6H). 2021 Cell reports Result SARS_CoV_2 D614G 84 89 S 77 78 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. On SDS-PAGE (Figure 6B), the peak corresponding to the S ectodomain showed the S-RRAR construct as having one major band at the molecular weight corresponding to the S monomer and some fainter bands corresponding to the S1 and S2 subunits, while the S-RRAR/D614G protein showed a band corresponding to the S monomer and the two bands corresponding to the molecular weights of the S1 and S2 subunits. 2021 Cell reports Result SARS_CoV_2 D614G 257 262 S;S;S;S;S 55;79;166;250;306 56;80;167;251;307 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Our results confirm that the D614G mutation in the SD2 domain, even though distal from the RBD region, has an allosteric effect leading to alteration of up/down RBD dispositions. 2021 Cell reports Result SARS_CoV_2 D614G 29 34 RBD;RBD 91;161 94;164 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Overall, our data show that for the SARS-CoV-2 S ectodomain, the S-GSAS construct shows similar structural, antigenic, and stability behavior as the S-GSAS/PP construct that included the K986P and V987P mutations at the junction of the CH and HR1 regions. 2021 Cell reports Result SARS_CoV_2 K986P;V987P 187;197 192;202 S;S;S 47;65;149 48;66;150 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Overall, these analyses show that the D614G mutation is acquired within a key structural region, encompassing the SD2 domain and an additional beta strand contributed by residues 311-319 of the N2R linker, that forms a region of relative structural stillness separating the mobile NTD and RBD, as well as isolating the motions in S1 from the S2 subunit. 2021 Cell reports Result SARS_CoV_2 D614G 38 43 RBD 289 292 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. SEC and SDS-PAGE profiles were similar to the S-GSAS and S-GSAS/D614G proteins, confirming well-folded and homogeneous S preparations (Figures 5A and 5B). 2021 Cell reports Result SARS_CoV_2 D614G 64 69 S;S;S 46;57;119 47;58;120 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. SEC purification of the fully digested S-RRAR/D614G ectodomain revealed a peak corresponding to the ectodomain (Figure 6F). 2021 Cell reports Result SARS_CoV_2 D614G 46 51 S 39 40 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Similar to observations made with the S-GSAS/D614G S ectodomain structure, the RBD up/down motion in the furin-cleaved G614 S ectodomain was associated with a movement in the SD1 domain and in the region of the RBD-to-NTD linker that joined the SD1 beta sheet. 2021 Cell reports Result SARS_CoV_2 D614G 45 50 RBD;RBD;S;S;S 79;211;38;51;124 82;214;39;52;125 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Structure and Antigenicity of the Furin-Cleaved D614G S Ectodomain. 2021 Cell reports Result SARS_CoV_2 D614G 48 53 S 54 55 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. The D614G mutated S-GSAS construct (S-GSAS/D614G) yielded an average of ~2 mg of purified protein per liter of culture (n = 4). 2021 Cell reports Result SARS_CoV_2 D614G;D614G 4;43 9;48 S;S 18;36 19;37 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. The proximity of the D614G mutation to the furin cleavage site and the increased conformational diversity observed in the cryo-EM dataset of the S-GSAS/D614G ectodomain (Figures 3C-3E) prompted us to examine the effect of the D614G substitution on furin cleavage. 2021 Cell reports Result SARS_CoV_2 D614G;D614G;D614G 21;226;152 26;231;157 S 145 146 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. The SARS-CoV-2 S Glycoprotein D614G Mutation. 2021 Cell reports Result SARS_CoV_2 D614G 30 35 S 15 29 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. The SDS-PAGE, SEC, and DSF profiles of the S-GSAS/D614G (Figure 3 A) were similar to that of the S-GSAS S ectodomain (Figures 2A, 2B, and 2E). 2021 Cell reports Result SARS_CoV_2 D614G 50 55 S;S;S 43;97;104 44;98;105 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. The SEC profile of the S-RRAR S preparation showed small populations of lower-molecular-weight peaks that were not observed for the S-RRAR/D614G protein (Figure 6A). 2021 Cell reports Result SARS_CoV_2 D614G 139 144 S;S;S 23;30;132 24;31;133 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. The smaller molecular weight bands corresponding to the S1 and S2 subunits were in higher proportions in the S-RRAR/D614G S preparation compared with the S-RRAR preparation. 2021 Cell reports Result SARS_CoV_2 D614G 116 121 S;S;S 109;122;154 110;123;155 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. These results suggested that the D614G mutation increased the susceptibility of protease cleavage at the S1/S2 junction. 2021 Cell reports Result SARS_CoV_2 D614G 33 38 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. This is consistent with our previous observations made with NSEM data that showed an increase in the RBD-up population for the S-GSAS/D614G S ectodomain. 2021 Cell reports Result SARS_CoV_2 D614G 134 139 RBD;S;S 101;127;140 104;128;141 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. This is in contrast with cryo-EM results of the D614G mutation published in the context of a S-GSAS/PP S that show S populations with 2- or 3-RBDs in the "up" state, suggesting that the PP mutations (K986P, V987P) may have a role in increasing the propensity of the RBD "up" forms. 2021 Cell reports Result SARS_CoV_2 D614G;V987P;K986P 48;207;200 53;212;205 RBD;RBD;S;S;S 142;266;93;103;115 146;269;94;104;116 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. To study the effect of the D614G substitution on protease cleavage at the S1/S2 junction with the native furin site, we generated S ectodomains constructs where the furin site was restored to the native sequence, resulting in two constructs named S-RRAR and S-RRAR/D614G (Figure 1A). 2021 Cell reports Result SARS_CoV_2 D614G;D614G 27;265 32;270 S;S;S 130;247;258 131;248;259 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. To test the protease cleavage susceptibility of the HRV3C site engineered at the junction of the S1 and S2 subunits, we incubated the purified S-HRV3C and S-HRV3C/D614G S with the HRV3C enzyme and followed the digestion by analyzing aliquots taken at different time points by SDS-PAGE (Figures 5E-5G). 2021 Cell reports Result SARS_CoV_2 D614G 163 168 S;S;S 143;155;169 144;156;170 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. To understand the molecular details of the S D614G mutation that arose and quickly dominated circulating SARS-CoV-2 isolates globally, we sought to assess the impact of the D614G mutation on the structure and antigenicity of the SARS-CoV-2 S ectodomain. 2021 Cell reports Result SARS_CoV_2 D614G;D614G 45;173 50;178 S;S 43;240 44;241 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. To visualize structural details at higher resolution, we determined the cryo-EM structures of S-GSAS/D614G construct (Figures 3C-3E; Table S1; Data S2). 2021 Cell reports Result SARS_CoV_2 D614G 101 106 S 94 95 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. We found that the digestion of the S-HRV3C/D614G S (Figures 5F and 5G) proceeded at a faster rate than that of the S-HRV3C S (Figures 5E-5G), with the S-HRV3C/D614G S almost 100% digested within the first 10 min of incubation, whereas the S-HRV3C constructs achieved only 50% of cleavage after 24 h, and a substantial portion remained uncleaved even upon addition of more enzyme followed by 4 additional hours of incubation. 2021 Cell reports Result SARS_CoV_2 D614G;D614G 43;159 48;164 S;S;S;S;S;S;S 35;49;115;123;151;165;239 36;50;116;124;152;166;240 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. We next digested the SEC-purified fractions of the S-RRAR and S-RRAR/D614G ectodomains (Figures 6A-6D) in vitro by adding furin (Figure 6E). 2021 Cell reports Result SARS_CoV_2 D614G 69 74 S;S 51;62 52;63 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. We observed an increased proportion of the 3-RBD-down population in the furin-cleaved S-RRAR/D614G dataset compared with the uncleaved S-GSAS/D614G ectodomain dataset. 2021 Cell reports Result SARS_CoV_2 D614G;D614G 93;142 98;147 RBD;S;S 45;86;135 48;87;136 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. While the shifts were modest (with a maximal displacement of ~2.2 A), interestingly, identical trends were observed in the 1-RBD-up structures of the S-GSAS, S-GSAS/D614G, and furin-cleaved S-GSAS/D614G S ectodomains, suggesting that this region of the SD2 domain responds to NTD motion and adopts a different conformation depending on the NTD environment (Figure 7D). 2021 Cell reports Result SARS_CoV_2 D614G;D614G 165;197 170;202 RBD;S;S;S;S 125;150;158;190;203 128;151;159;191;204 33429204 PfAgo-based detection of SARS-CoV-2. S11) and applied to identify D614G point mutation of SARS-CoV-2 in clinical samples which were identified as positive in the last session. 2021 Biosensors & bioelectronics Result SARS_CoV_2 D614G 29 34 33429204 PfAgo-based detection of SARS-CoV-2. The D614G point mutation in spike (S) protein caused by a single-based mutation at nt23403 was chosen as the target. 2021 Biosensors & bioelectronics Result SARS_CoV_2 D614G 4 9 S;S 28;35 33;36 33433004 Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure. As the M129I mutation in nsp8 is associated with native RdRp, the RdRp-nsp7-nsp8 M129I supercomplex was modeled. 2021 Journal of medical virology Result SARS_CoV_2 M129I;M129I 7;81 12;86 Nsp7;Nsp8;Nsp8;RdRP;RdRP 71;25;76;56;66 75;29;80;60;70 33433004 Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure. Due to the nsp7 S25L mutation, surface complementarity increased by 10%, indicating that this mutation may play a beneficial role in supercomplex stability (Table S6). 2021 Journal of medical virology Result SARS_CoV_2 S25L 16 20 Nsp7 11 15 33433004 Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure. Interestingly, only one instance of the same viral genome carrying mutations in both nsp7 (S25L) and nsp8 (A21V) was observed (Genbank accession number MT370871.1). 2021 Journal of medical virology Result SARS_CoV_2 A21V;S25L 107;91 111;95 Nsp7;Nsp8 85;101 89;105 33433004 Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure. It was observed that genomes carrying both frequently occurring mutations in nsp7 (S25L and S26F) also had the P323L mutation in RdRp (Table S2), while genomes carrying both frequently occurring mutations in nsp8 (M129I and I156V) had native RdRp sequences (Table S4). 2021 Journal of medical virology Result SARS_CoV_2 I156V;P323L;S26F;M129I;S25L 224;111;92;214;83 229;116;96;219;87 Nsp7;Nsp8;RdRP;RdRP 77;208;129;242 81;212;133;246 33433004 Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure. It was observed that the M129I mutation abolishes the steric clash between M129 of nsp8 and N386 of RdRp (Figure 2B). 2021 Journal of medical virology Result SARS_CoV_2 M129I 25 30 Nsp8;RdRP 83;100 87;104 33433004 Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure. nsp7 S25L and S26F mutations are significantly associated with the P323L mutation in RdRp in the 218 genomes carrying mutations in nsp7 (chi 2 test, p < .001); nsp8 M129I and I156V mutations are significantly associated with native RdRp in the 130 genomes carrying mutations in nsp8 (chi 2 test, p < .001). 2021 Journal of medical virology Result SARS_CoV_2 I156V;M129I;P323L;S25L;S26F 175;165;67;5;14 180;170;72;9;18 Nsp7;Nsp7;Nsp8;Nsp8;RdRP;RdRP 0;131;160;278;85;232 4;135;164;282;89;236 33433004 Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure. The M129I mutation therefore appears to stabilize the interaction between nsp8 and RdRp in the supercomplex. 2021 Journal of medical virology Result SARS_CoV_2 M129I 4 9 Nsp8;RdRP 74;83 78;87 33433004 Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure. The most commonly occurring mutations in nsp7 protein were S25L (n = 165) and S26F (n = 28), and the most common mutations in nsp8 were M129I (n = 34) and I156V (n = 32). 2021 Journal of medical virology Result SARS_CoV_2 I156V;M129I;S25L;S26F 155;136;59;78 160;141;63;82 Nsp7;Nsp8 41;126 45;130 33433004 Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure. The P323L mutation in RdRp also increased surface complementarity by 10% due to better interaction with N118 of nsp8 (Figure 2A). 2021 Journal of medical virology Result SARS_CoV_2 P323L 4 9 Nsp8;RdRP 112;22 116;26 33433004 Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure. The P323L mutation is commonly observed in RdRp sequences and is speculated to have an effect on RdRp function. 2021 Journal of medical virology Result SARS_CoV_2 P323L 4 9 RdRP;RdRP 43;97 47;101 33433004 Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure. Three residues in nsp8 were mutated to two different amino acids: A14 to S and V, A27 to T and V, and I156 to V and L. 2021 Journal of medical virology Result SARS_CoV_2 A14S;A14V;A27T;A27V;I156T;I156V 66;66;82;82;102;102 80;80;96;96;117;117 Nsp8 18 22 33436577 A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein. A monoclonal antibody reformatted to fully human immunoglobulin (IgG), termed CT-P59, was assessed for its neutralization potency by in vitro plaque reduction neutralization test (PRNT) against authentic SARS-CoV-2 and SARS-CoV-2 D614G variant. 2021 Nature communications Result SARS_CoV_2 D614G 230 235 33436577 A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein. We found that CT-P59 reduced the replication of the D614G variant with the value of IC50 (5.7 ng/ml) to a similar extent as the wild-type virus. 2021 Nature communications Result SARS_CoV_2 D614G 52 57 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. All the remaining sequences have the D614G mutation. 2021 bioRxiv Result SARS_CoV_2 D614G 37 42 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Branching from the New York strains cluster is the Washington, USA, strain (MT994395), exclusively having the I584V mutation. 2021 bioRxiv Result SARS_CoV_2 I584V 110 115 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Clustering near the Hawaii Strain MW066483 are the two strains from New York, USA (MW035565 and MW035511), both containing the E780Q mutation and MW035565 also containing the A522S mutation and a synonymous phenylalanine mutation at amino acid 541. 2021 bioRxiv Result SARS_CoV_2 A522S;E780Q 175;127 180;132 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Eleven of the thirteen mutations resulted in non-synonymous mutations (A522S, F543L, R577C, I584V, D614G, S680C, P681H, I726F, A771S, E780Q, and F797C) (Table 1 and Figure 1). 2021 bioRxiv Result SARS_CoV_2 A771S;D614G;E780Q;F543L;F797C;I584V;I726F;P681H;R577C;S680C;A522S 127;99;134;78;145;92;120;113;85;106;71 132;104;139;83;150;97;125;118;90;111;76 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Further, from March 01, 2020 through December 31, 2020 GISAID reports a total of 5,955 strains that have the P681H mutation. 2021 bioRxiv Result SARS_CoV_2 P681H 109 114 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Further, Pearson's correlation indicates positive correlation (r = 0.71, P = 0.03) between the worldwide prevalence of P681H and D614G (Figure 2C). 2021 bioRxiv Result SARS_CoV_2 D614G;P681H 129;119 134;124 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. GISAID reported the first P681H mutation on March 12, 2020 (EPI_ISL_430887). 2021 bioRxiv Result SARS_CoV_2 P681H 26 31 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. MT627421 strain from Hawaii and MT407659 strain from China are identical and are the only sequences to contain the D614G mutation exclusively. 2021 bioRxiv Result SARS_CoV_2 D614G 115 120 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. P681H mutations were not reported in May 2020. 2021 bioRxiv Result SARS_CoV_2 P681H 0 5 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Pearson's correlation between time in months versus prevalence of P681H (Figure 2A) and D614G (Figure 2B) of logarithmically transformed data indicates an increase in the number of strains having the P681H mutation (r = 0.96, P < 0.0001) (Figure 2A) and plateauing of the D614G mutation (r = 0.78, P = 0.008) (Figure 2B). 2021 bioRxiv Result SARS_CoV_2 D614G;D614G;P681H;P681H 88;272;66;200 93;277;71;205 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The Hawaii strain MW064483 is the next closest cluster to the D614G defining node and additionally contains the synonymous tyrosine mutation at amino acid 790. 2021 bioRxiv Result SARS_CoV_2 D614G 62 67 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The P681H mutation is unique to the Hawaii strains from this study (MW237663 and MW237664). 2021 bioRxiv Result SARS_CoV_2 P681H 4 9 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The Sweden strain (MT093571) has a F797C mutation. 2021 bioRxiv Result SARS_CoV_2 F797C 35 40 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The three sequences lacking the D614G mutation (NC_045512, MT344949, and MT093571) are separated from sequences with the D614G mutation with a bootstrap value of 100, except for the MW066483 Hawaii sequence, which also does not have the D614G mutation. 2021 bioRxiv Result SARS_CoV_2 D614G;D614G;D614G 32;121;237 37;126;242 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The two Hawaii strains from this study (MW237663 and MW237664) have the emerging P681H mutation and cluster closely with previously published SARS-CoV-2 sequences from Hawaii (MT627421) and China (MT407659). 2021 bioRxiv Result SARS_CoV_2 P681H 81 86 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Within the SARS-CoV-2 branch of beta coronavirus lineage B, the D614G mutation was the defining node for branch separation. 2021 bioRxiv Result SARS_CoV_2 D614G 64 69 33447831 Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces shedding of SARS-CoV-2 D614G in rhesus macaques. Finally, levels of binding antibodies at 0 DPI against wildtype RBD and N501Y RBD were compared. 2021 bioRxiv Result SARS_CoV_2 N501Y 72 77 RBD;RBD 64;78 67;81 33447831 Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces shedding of SARS-CoV-2 D614G in rhesus macaques. For IN inoculation of Syrian hamsters 28 days post vaccination, we used isolate SARS-CoV-2/human/USA/RML-7/2020 which contains the D614G mutation in the S protein. 2021 bioRxiv Result SARS_CoV_2 D614G 131 136 S 153 154 33447831 Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces shedding of SARS-CoV-2 D614G in rhesus macaques. N501Y is found in the RBD of two new variants of SARS-CoV-2: VOC2020-12/01 (B.1.1.7) and 501Y.V2 (B.1.351). 2021 bioRxiv Result SARS_CoV_2 N501Y 0 5 RBD 22 25 33447831 Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces shedding of SARS-CoV-2 D614G in rhesus macaques. Two SNPs encoded a non-synonymous mutation; Asp839Glu and Lys1255Gln. 2021 bioRxiv Result SARS_CoV_2 D839E;K1255Q 44;58 53;68 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. Further, it seems the evolution of mutation at site D614G in the spike protein may have occurred independently in both L-type and S-type strains. 2021 Indian journal of medical microbiology Result SARS_CoV_2 D614G 52 57 S;S 65;130 70;131 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. It was observed that D614G mutation was seen in S-type strains collected in February 2020 from Wuhan, China, but it still formed a single clade with the rest of the S-type strains. 2021 Indian journal of medical microbiology Result SARS_CoV_2 D614G 21 26 S;S 48;165 49;166 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. Moreover, the complete genome phylogenetic analysis of 33 sequences (32 complete genome and one partial) reveals the type-S strains forming a distinct clade (S-clade/19B), while the D614G (clade-G) forming another distinct clade. 2021 Indian journal of medical microbiology Result SARS_CoV_2 D614G 182 187 S;S 122;158 123;159 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. The D614G (G clade) showed an average 0.00025 (0.02%) p-distance, while the later L-type that had formed a separate clade (B6/L-type) has an average of 0.00023 or (0.02%) pairwise distance from the L-type 19A clade. 2021 Indian journal of medical microbiology Result SARS_CoV_2 D614G 4 9 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. The inter group or inter clade p-distance of S type, D614G (clade G or A2a clade) and rest L type with reference to the 19A clade L-type strains are as follows: S clade type-S has a p-distance of 0.00018 or 0.018% dissimilarity with the 19A clade. 2021 Indian journal of medical microbiology Result SARS_CoV_2 D614G 53 58 S;S;S 45;161;174 46;162;175 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. While the D614G that evolved from the original L-type strains has formed a distinct clade G as seen in the phylogenetic analysis of 32 whole genome sequencing data (see figure-2). 2021 Indian journal of medical microbiology Result SARS_CoV_2 D614G 10 15 33467732 Intranasal Infection of Ferrets with SARS-CoV-2 as a Model for Asymptomatic Human Infection. A single polymorphism, Y453F, was identified in the spike protein in samples from all three animals. 2021 Viruses Result SARS_CoV_2 Y453F 23 28 S 52 57 33467732 Intranasal Infection of Ferrets with SARS-CoV-2 as a Model for Asymptomatic Human Infection. The amino acid changes in the ORF1ab-encoded protein, A1670E and F1925C, were both found in samples from two of three animals, whilst the L3606F polymorphism was identified in all three animals. 2021 Viruses Result SARS_CoV_2 A1670E;F1925C;L3606F 54;65;138 60;71;144 ORF1ab 30 36 33468695 SARS-CoV-2 Infection Severity Is Linked to Superior Humoral Immunity against the Spike. 5a), suggesting the D614G epitope was not a major antigenic site. 2021 mBio Result SARS_CoV_2 D614G 20 25 33468695 SARS-CoV-2 Infection Severity Is Linked to Superior Humoral Immunity against the Spike. SARS-CoV-2 has acquired a D614G mutation within the spike protein, and viruses carrying this mutation have since become the dominant circulating strain globally as of early April 2020. 2021 mBio Result SARS_CoV_2 D614G 26 31 S 52 57 33468695 SARS-CoV-2 Infection Severity Is Linked to Superior Humoral Immunity against the Spike. Spike antibodies cross-react with the D614G mutant and SARS-CoV-1. 2021 mBio Result SARS_CoV_2 D614G 38 43 S 0 5 33468695 SARS-CoV-2 Infection Severity Is Linked to Superior Humoral Immunity against the Spike. These data indicate that the region that encompasses the D614G mutation is not immunodominant or does not affect the antigenicity of epitopes at or near this site. 2021 mBio Result SARS_CoV_2 D614G 57 62 33468695 SARS-CoV-2 Infection Severity Is Linked to Superior Humoral Immunity against the Spike. We did not observe a difference in antibody titers against the wild-type (WT) and D614G spike antigens within our acute cohort. 2021 mBio Result SARS_CoV_2 D614G 82 87 S 88 93 33468702 SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia. All genomes from Philadelphia were found to encode the D614G spike polymorphism suggested to promote efficient spread in humans. 2021 mBio Result SARS_CoV_2 D614G 55 60 S 61 66 33468702 SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia. Philadelphia sequences also all encoded P314L in the virus-encoded RdRp (ORF1b), marking them as lineage B.1, Nextstrain clade 20A or 20C, GISAID clade G or GH, and clade A2a. 2021 mBio Result SARS_CoV_2 P314L 40 45 RdRP 67 71 33468702 SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia. The closest to significance were a set of 4 single nucleotide polymorphisms (SNPs) (C18998T, C23230T, G29540A, and T1918C) that are shared between two patients (211 and 222) who both died (Fisher's P value = 0.074; prior to correction for multiple comparison). 2021 mBio Result SARS_CoV_2 C23230T;G29540A;T1918C;C18998T 93;102;115;84 100;109;121;91 33468702 SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia. Three of the polymorphisms are synonymous, while one caused A1844V in ORF1b. 2021 mBio Result SARS_CoV_2 A1844V 60 66 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. Among SARS-CoV-2 sequences reported from Bangladesh, 241C>T and 3037C>T changes were the two most abundant mutations found in 58 out of 64 isolates, and were always found simultaneously (Table 2). 2021 PloS one Result SARS_CoV_2 C241T;C3037T 53;64 59;71 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. D614G mutations in spike protein. 2021 PloS one Result SARS_CoV_2 D614G 0 5 S 19 24 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. Finally, a missense mutation at 1163A>T changing the amino acid isoleucine to phenylalanine in Nsp2 protein was found uniquely among 44 isolates in Bangladesh but absent among all the selected sequences from other countries. 2021 PloS one Result SARS_CoV_2 A1163T 32 39 Nsp2 95 99 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. In addition, other co-evolving mutations found were (241C>T, 3037C>T, 14408C>T, 23403A>G), (28881G>A, 28882G>A, 28883G>C), (8782C>T, 28144T>C), (4444G>T, 8371G>T, 29403A>G). 2021 PloS one Result SARS_CoV_2 C14408T;A23403G;T28144C;G28882A;G28883C;A29403G;C3037T;G8371T;C241T;G28881A;G4444T;C8782T 70;80;133;102;112;163;61;154;53;92;145;124 78;88;141;110;120;171;68;161;59;100;152;131 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. On the other hand, 57 sequences were found to harbor 14408C>T and 23403A>G mutations which altered amino acid Pro>Leu and Asp>Gly respectively, and these two mutations were found to be present simultaneously as well. 2021 PloS one Result SARS_CoV_2 C14408T;A23403G 53;66 61;74 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. The D614G mutation generates an additional serine protease (Elastase) cleavage site near the S1-S2 junction of the Spike protein. 2021 PloS one Result SARS_CoV_2 D614G 4 9 S 115 120 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. The SARS-CoV-2 sequences were also categorized according to D614G type mutation (Fig 1). 2021 PloS one Result SARS_CoV_2 D614G 60 65 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. According to the results of the CAVER Web (v1.0), following of the D614G mutation, remarkable changes occurred in the cavities and tunnels surrounding the target residue (Figure 3). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 D614G 67 72 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. Analysis of DSSP results shows that in the structure containing the D614G there is a great tendency to form helix structures around this position. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 D614G 68 73 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. As expected, the D614G mutation causes major alterations in the secondary structure of the residues around the mutation position. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 D614G 17 22 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. Based on the observation of FoldX and ROSETTA outputs, our group found out that the D614G mutation increases the stability of spike protein conformation. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 D614G 84 89 S 126 131 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. Due to the importance of the subject, the binding pattern of the spike carrying the D614G mutation to its receptor was investigated. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 D614G 84 89 S 65 70 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. Due to the proximity of the mutation position to the cleavage site-1 (CS1), it can be expected that the D614D mutation will affect the spike biological modifications. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 D614D 104 109 S 135 140 33477951 Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. All genomes had the D614G substitution, whereas the remaining variations were identified each in a single genome. 2021 Viruses Result SARS_CoV_2 D614G 20 25 33477951 Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. All of our study sequences had both P323L (nsp12) and D614G (Spike) substitutions. 2021 Viruses Result SARS_CoV_2 D614G;P323L 54;36 59;41 S;Nsp12 61;43 66;48 33477951 Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. Comparison of the SARS-CoV-2 genomes from our study identified two of the previously reported D614G, V622F and one novel M731I substitutions in the spike protein (Supplementary Materials Table S1, Figure 4a). 2021 Viruses Result SARS_CoV_2 D614G;M731I;V622F 94;121;101 99;126;106 S 148 153 33477951 Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. Most of the study viruses (n = 14) showed close relationship among each other and clustered in the GH clade, which is characterized by two amino acid changes in spike gene (D614G) and NS3 (Q57H) (Figure 3b). 2021 Viruses Result SARS_CoV_2 D614G;Q57H 173;189 178;193 S;NS3 161;184 166;187 33477951 Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. The most prevalent substitution found in orf3a (NS3) was Q57H followed by A51S and S216P (Figure 4c). 2021 Viruses Result SARS_CoV_2 A51S;Q57H;S216P 74;57;83 78;61;88 ORF3a;NS3 41;48 46;51 33477951 Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. Therefore, we constructed the structural homology models to further analyze the coevolution of P323L and D614G (Figure 4a,b). 2021 Viruses Result SARS_CoV_2 D614G;P323L 105;95 110;100 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. 74 different double co-mutations were also observed, with L84S, V62L being the most frequent, and were found in 330 sequences, followed by L84S,A65S and L84S,E19D that were found in 28 and 27 different sequences respectively, and finally S24L, S69L that were found in 17 different sequences. 2021 Gene reports Result SARS_CoV_2 L84S;L84S;L84S;S24L;S69L;V62L;A65S;E19D 58;139;153;238;244;64;144;158 62;143;157;242;248;68;148;162 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. A deletion of 6 bases (Refseq: 28090-28095del (GTTCTA)) was reported in 16 different sequences, mostly from England, from the GR, GH, G and O clades leading to G66-S67del and K68E substitution in ORF8 protein. 2021 Gene reports Result SARS_CoV_2 K68E 175 179 ORF8 196 200 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. A phylogenetic tree with Bat CoV RaTG13, Bat-SL-CoVZC45, and Pangolin Coronavirus reveals that L84S is closer to them than to the SARS-COV-2 Wuhan-Hu-1 reference sequence (indicated as SARS COV2 ORF8). 2021 Gene reports Result SARS_CoV_2 L84S;L84S 96;95 100;99 ORF8 195 199 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. A65S in 83 sequences, A51V in 44 sequences, S67F in 38 sequences, Q18* in 29 sequences, and E19D and T26I were each found in 27 different sequences (Table S2). 2021 Gene reports Result SARS_CoV_2 A51V;A65S;E19D;Q18X;S67F;T26I 22;0;92;66;44;101 26;4;96;70;48;105 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. Besides the L84S which is the largest clade, others, such as S24L, V62L, Q72H, R52, and I121L were also observed. 2021 Gene reports Result SARS_CoV_2 I121L;L84S;Q72H;S24L;V62L 88;12;73;61;67 93;16;77;65;71 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. Concerning nonsynonymous mutations, the number of sequences with L84S worldwide is 3233, followed by S24L in 879 sequences mostly from United States of America (USA), V62L in 172. 2021 Gene reports Result SARS_CoV_2 L84S;S24L;V62L 65;101;167 69;105;171 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. However, V62F was found in our analysis (EPI_ISL_456596) but not documented by COV-GLUE. 2021 Gene reports Result SARS_CoV_2 V62F 9 13 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. L84S and V62L associated with other nonsynonymous mutations constituted a subclade inside the L84S clade in the DNA tree. 2021 Gene reports Result SARS_CoV_2 L84S;V62L;L84S 94;9;0 98;13;4 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. Others such as P70S (EPI_ISL_425132), I39V,P38V (EPI_ISL_434511), E64V (EPI_ISL_455774), H112R (EPI_ISL_465538), I74L (EPI_ISL_455577), Q29R (EPI_ISL_440153), Q91H (EPI_ISL_428962), A14S (EPI_ISL_462306) and S24L,D34E,D35E, N89S (EPI_ISL_427171), were not included in the protein and in the DNA phylogenetic trees construction due to the presence of N stretches in ORF8 sequence. 2021 Gene reports Result SARS_CoV_2 A14S;E64V;H112R;I39V;I74L;N89S;P70S;Q29R;Q91H;S24L;D34E;D35E;P38V 182;66;89;38;113;224;15;136;159;208;213;218;43 186;70;94;42;117;228;19;140;163;212;217;222;47 ORF8;N 365;350 369;351 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. P85T and F86S were not found after sequence verification. 2021 Gene reports Result SARS_CoV_2 F86S;P85T 9;0 13;4 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. The other deletion is of 344 nts from 27,910 to 28,254 causing a deletion of amino acids from Leucine at position 7 to Isoleucine at position 121 (L7-I121del), was found in two sequences (Table 2). 2021 Gene reports Result SARS_CoV_2 L7I 94 129 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. Twelve triple co-mutations were also observed, where for example, L84S,V62L,P36S was found in 4 sequences, whilst each of L84S,V62L,I88V and V62A,R48G,V49L co-mutation was observed in 2 different sequences. 2021 Gene reports Result SARS_CoV_2 L84S;L84S;V62A;I88V;P36S;R48G;V49L;V62L;V62L 66;122;141;132;76;146;151;127;71 70;126;145;136;80;150;155;131;75 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. Variants, such as V62L,R115S (EPI_ISL_469002), V62L,K53N (EPI_ISL_459067), L84S,V62L,C102Y (EPI_ISL_436434), I121L,F120V,L118* (EPI_ISL_454578), C102F,L60F (EPI_ISL_451832), A65S,V62F,Q72H (EPI_ISL_456596), and A65T,C83Y (EPI_ISL_430806) were excluded from protein and DNA phylogenetic trees construction because of the uncertainty of their associations (presence of letters, like K, R, Y, M, S, W reflecting the presence of virus quasi-species). 2021 Gene reports Result SARS_CoV_2 A65S;A65T;A65T;C102F;I121L;L84S;V62L;V62L;C102Y;C83Y;F120V;K53N;L118*;L118X;L60F;Q72H;R115S;V62F;V62L 174;211;211;145;109;75;18;47;85;216;115;52;121;121;151;184;23;179;80 178;215;217;150;114;79;22;51;90;220;120;56;126;126;155;188;28;183;84 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. Analysis of temporal trend of spread of the D614G mutant of SARS-CoV-2 in the whole MENA region as a single unit revealed an increasing prevalence of D614G from 63.0% in January 2020 to reach 98.5% in June 2020 (p < 0.001; LBL, Figure 2 ). 2021 Heliyon Result SARS_CoV_2 D614G;D614G 44;150 49;155 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. Analysis of the D614G mutant per country showed its presence in all MENA countries included in the study with exception of Iran and Qatar (Figure 1 ). 2021 Heliyon Result SARS_CoV_2 D614G 16 21 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. D614G) showed a higher prevalence of D614G in North Africa compared to the Middle East (95.0% vs. 2021 Heliyon Result SARS_CoV_2 D614G;D614G 37;0 42;5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. In addition, a higher prevalence of D614G variant was noticed in the second half of the study period (April, May and June vs. 2021 Heliyon Result SARS_CoV_2 D614G 36 41 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. Temporal trend of D614G mutant spread in the MENA. 2021 Heliyon Result SARS_CoV_2 D614G 18 23 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. The highest number of unique S gene mutations (including D614G) was noticed in Oman (n = 16), followed by Egypt (n = 15), Bahrain (n = 9), and KSA (n = 6, Table 2). 2021 Heliyon Result SARS_CoV_2 D614G 57 62 S 29 30 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. The median estimate for tMRCA for this cluster having the D614G mutation was February 8, 2020 (95% highest posterior density interval [HPD]: October 19, 2019-February 13, 2020, Figure 4 ). 2021 Heliyon Result SARS_CoV_2 D614G 58 63 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. The most frequent mutation detected in the whole S region was D614G (n = 435), followed by Q677H (n = 8), and V6F (n = 5). 2021 Heliyon Result SARS_CoV_2 D614G;Q677H;V6F 62;91;110 67;96;113 S 49 50 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. Variables associated with a higher prevalence of D614G mutation. 2021 Heliyon Result SARS_CoV_2 D614G 49 54 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. Effect of Missense Mutation A97V on the Secondary Structure of NSP12/RdRP. 2020 JMIR bioinformatics and biotechnology Result SARS_CoV_2 A97V 28 32 Nsp12;RdRP 63;69 68;73 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. In addition to 23403A>G (D614G), 3 uncommon mutations, 23374A>G (Q271R), 24933G>T (G1124V), and 22444C>T (D294D), were also observed in the S gene of the "major group" (Table 1). 2020 JMIR bioinformatics and biotechnology Result SARS_CoV_2 C22444T;A23374G;A23403G;G24933T;D294D;D614G;G1124V;Q271R 96;55;15;73;106;25;83;65 104;63;23;81;111;30;89;70 S 140 141 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. Intriguingly, 28854C>T (S194L) in the N gene was found to coevolve with the 22444C>T (D294D) mutation in the S gene of 11 samples in the major group (Table 1). 2020 JMIR bioinformatics and biotechnology Result SARS_CoV_2 C22444T;C28854T;D294D;S194L 76;14;86;24 84;22;91;29 N;S 38;109 39;110 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. Out of the 67 isolates of the major group, 28 revealed 4 novel mutations: 28854C>T (S194L; n=13), 28881-28883GGG>AAC (R203K and G204R; n=13), and coevolving mutation 29451C>T (T393I) and 28395G>A (R41R; n=2) in the N gene (Table 1). 2020 JMIR bioinformatics and biotechnology Result SARS_CoV_2 G28395A;C28854T;C29451T;G204R;R203K;R41R;S194L;T393I 187;74;166;128;118;197;84;176 195;82;174;133;123;201;89;181 N 215 216 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. The "major group," which, of 95 isolates, was comprised of 66 (69.4%), revealed 4 coexisting SNPs: 241C>T in the five prime untranslated region (5' UTR), 3037C>T (F106F) in the NSP3 gene, 14408C>T (P323L) in the NSP12 gene, and 23403A>G (D614G) in the S gene (Table 1). 2020 JMIR bioinformatics and biotechnology Result SARS_CoV_2 C14408T;A23403G;C241T;C3037T;D614G;F106F;P323L 188;228;99;154;238;163;198 196;236;105;161;243;168;203 5'UTR;Nsp12;Nsp3;S 145;212;177;252 151;217;181;253 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. The A97V mutation resulted in substitution of alpha-helixes at positions 94, 95, and 96 within the beta-sheets in the RdRP secondary structure, which may alter its tertiary conformation and affect functionality (Multimedia Appendix 10). 2020 JMIR bioinformatics and biotechnology Result SARS_CoV_2 A97V 4 8 RdRP 118 122 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. The effect of P323L on the secondary structure of RdRP has already been described. 2020 JMIR bioinformatics and biotechnology Result SARS_CoV_2 P323L 14 19 RdRP 50 54 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. The other 21 (22.1%) samples, which represent the "minor group," harbored 5 coexisting mutations: 23929C>T (Y789Y) in the S gene, 28311C>T (P13L) in the N gene, 6312C>A (T1198K) in the NSP3 gene, 11083G>T (L37F) in the NSP6 gene, and 13730C>T (A97V) in the NSP12/RdRP gene (Table 2). 2020 JMIR bioinformatics and biotechnology Result SARS_CoV_2 G11083T;C13730T;C23929T;C28311T;C6312A;A97V;L37F;P13L;T1198K;Y789Y 196;234;98;130;161;244;206;140;170;108 204;242;106;138;168;248;210;144;176;113 Nsp12;Nsp3;Nsp6;RdRP;N;S 257;185;219;263;153;122 262;189;223;267;154;123 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. Therefore, we analyzed the effect of novel mutation A97V on the secondary structure of RdRP by using the CFSSP server. 2020 JMIR bioinformatics and biotechnology Result SARS_CoV_2 A97V 52 56 RdRP 87 91 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. We also observed 1059T>A (T85I) change within the NSP2 gene (n=2) and 6466A>G (K1249K) change in the NSP3 gene (n=2). 2020 JMIR bioinformatics and biotechnology Result SARS_CoV_2 T1059A;A6466G;K1249K;T85I 17;70;79;26 24;77;85;30 Nsp2;Nsp3 50;101 54;105 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. We have identified 2 missense mutations in the RdRP protein: P323L associated with the "major group" isolates and A97V associated with the "minor group" isolates. 2020 JMIR bioinformatics and biotechnology Result SARS_CoV_2 A97V;P323L 114;61 118;66 RdRP 47 51 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. With the 3 samples of the minor group, 6310C>A (S1197R) was found to be associated. 2020 JMIR bioinformatics and biotechnology Result SARS_CoV_2 C6310A;S1197R 39;48 46;54 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. 2) Mutation at position 25563 on codon 57 of the ORF3a protein characterised by a Q to H (Q57H) amino acid change. 2021 PloS one Result SARS_CoV_2 Q57H 90 94 ORF3a 49 54 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Although previously studied, the Q57H mutation has not been associated with virulence and the precise mechanism for its selective advantage and increased frequency across populations has not been investigated. 2021 PloS one Result SARS_CoV_2 Q57H 33 37 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. As previously mentioned, the choice for highlighting this mutation is: 1) a consequence of the significant scores obtained by Q57H by both our model types (see Tables 1 and 2) its unique pattern of correlation with respect to death and transmission rates. 2021 PloS one Result SARS_CoV_2 Q57H 126 130 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Australia follows a similar transition pattern, from REF-P13L to ALT-P13L, as described above, however the introduction of the mutation in the Australian population appears to have preceded that of USA and Canada. 2021 PloS one Result SARS_CoV_2 P13L;P13L 57;69 61;73 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Comparison of the structures obtained using the REF-Q57H mutation and the ALT-Q57H (see Fig 8A and 8B) show significant differences both in structural conformation as well as stability. 2021 PloS one Result SARS_CoV_2 Q57H;Q57H 52;78 56;82 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. For comparison reasons we also perform the analysis on the D614G mutation. 2021 PloS one Result SARS_CoV_2 D614G 59 64 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. For comparison, mutation tracking of the well-studied D614G mutation is also performed (S3 Fig). 2021 PloS one Result SARS_CoV_2 D614G 54 59 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Further, in depth molecular analysis reveals disruption of hydrogen bonds and hampering and shifts in other inter-molecular interactions in the ALT-Q57H compared to the REF-Q57H structure of the protein (see Fig 8C and 8D). 2021 PloS one Result SARS_CoV_2 Q57H;Q57H 148;173 152;177 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. However, statistical analysis of the deaths for populations with and without the Q57H mutations shows evidence that the two distributions are marginally not different (Wilcoxon test-p-value 0.069:see Fig 6A). 2021 PloS one Result SARS_CoV_2 Q57H 81 85 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. In fact the earliest ALT-P13L mutation outside of Asia was identified in Australia (NSW25.2020.EPI_ISL_417388.2020.03.05.Oceania). 2021 PloS one Result SARS_CoV_2 P13L 25 29 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. In North America, initial infected samples across the continent showed an establishment of the original REF-P13L form, as the pandemic progressed, the ALT-P13L appeared in both USA and Canada, becoming a well-documented form in both nations by the end of March. 2021 PloS one Result SARS_CoV_2 P13L;P13L 108;155 112;159 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. In order to provide an explanation for the reasons why the P13L mutation appears to be associated with decreased transmission and death rates, we turn to structural prediction and docking tools. 2021 PloS one Result SARS_CoV_2 P13L 59 63 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. In summary, our analysis of the data shows that the REF-P13L form may be under selective advantage as shown by persistent, recurring transitions to the ALT-P13L form in multiple regional geographical location throughout the pandemic. 2021 PloS one Result SARS_CoV_2 P13L;P13L 56;156 60;160 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. In the case of P13L, this mutations attained high significance (p-values: 0.002 and 0.005) according to our models. 2021 PloS one Result SARS_CoV_2 P13L 15 19 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. In the case of Q57H, this mutation showed high significance according to type a models (p-value: 0.007) however, it was not deemed significant according to type b models. 2021 PloS one Result SARS_CoV_2 Q57H 15 19 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. In the UK, the ALT-P13L form began circulating later in the pandemic (April). 2021 PloS one Result SARS_CoV_2 P13L 19 23 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. It is difficult to track the P13L mutation in China due to the lack of available Chinese sequences in GISAID after March 1st. 2021 PloS one Result SARS_CoV_2 P13L 29 33 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. It is evident that these countries also had a higher occurrence of the ALT-Q57H mutation. 2021 PloS one Result SARS_CoV_2 Q57H 75 79 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Korea, Australia, UK, USA), the reference P13L (REF-P13L) form appeared to be dominate in this early period of the pandemic (Fig 4A). 2021 PloS one Result SARS_CoV_2 P13L;P13L 42;52 46;56 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Most Asian samples showed a dominance of the original Wuhan REF-P13L form in early in the pandemic (February), however for Asian countries outside of China, the ALT-P13L form was well-documented and becoming established by March (Fig 4A). 2021 PloS one Result SARS_CoV_2 P13L;P13L 64;165 68;169 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Our highlighted mutations were also compared to the well-studied D614G mutation in our consecutive detailed analyses (see S1 Fig). 2021 PloS one Result SARS_CoV_2 D614G 65 70 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. P13L and potential mechanisms for enhanced fitness. 2021 PloS one Result SARS_CoV_2 P13L 0 4 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. P13L and viral transmission and virulence. 2021 PloS one Result SARS_CoV_2 P13L 0 4 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. P13L is being tracked by the GISAID, we refer to the clade of sequences that constitute this mutation as the "P13L" clade (see S2 Fig for the P13L phylogenetic clade position on our ML tree). 2021 PloS one Result SARS_CoV_2 P13L;P13L;P13L 142;110;0 146;114;4 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. P13L is located on the surface of the Nucleocapsid (N) protein known to form helical ribonucleocapsids (RNPs) with the positive-sense, single-stranded RNA genome of the SARS-CoV-2 virus. 2021 PloS one Result SARS_CoV_2 P13L 0 4 N;N 38;52 50;53 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Q57H and potential mechanisms for enhanced fitness. 2021 PloS one Result SARS_CoV_2 Q57H 0 4 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Q57H and viral transmission and virulence. 2021 PloS one Result SARS_CoV_2 Q57H 0 4 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Q57H has an elevated frequency level across countries and in the overall population (see Fig 1). 2021 PloS one Result SARS_CoV_2 Q57H 0 4 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Statistical analysis of the populations with and without the P13L mutations shows substantial evidence that the two distributions are significantly different (Wilcoxon test-p-value 2.2e-16) (see Fig 5A). 2021 PloS one Result SARS_CoV_2 P13L 61 65 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Structural prediction analysis for the Q57H mutation provides evidence to support its association with decreased death rates and increased transmission. 2021 PloS one Result SARS_CoV_2 Q57H 39 43 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Structures of the REF-P13L and ALT-P13L mutations, exhibited significant differences in protein stability, with the later presenting a decrease in stability, compared to the REF-P13L compound (DeltaDeltaG = 0.629+-0.012kcal/mol). 2021 PloS one Result SARS_CoV_2 P13L;P13L;P13L 22;35;178 26;39;182 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. The ALT-Q57H is defined by a substitution to a positively-charged and polar Histidine (His). 2021 PloS one Result SARS_CoV_2 Q57H 8 12 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. The introduction of alternate P13L (ALT- P13L) in the population, was followed by a rise in its frequency, and in some cases ALT-P13L constituted ~50% of the population (Fig 4A). 2021 PloS one Result SARS_CoV_2 P13L;P13L;P13L 30;41;129 34;45;133 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. The overall analysis for the Q57H mutation showed both death and transmission rates increased with response times, however there was significant drop in deaths per million for populations with the ALT-Q57H compared to cases per million (see Fig 6C and 6D). 2021 PloS one Result SARS_CoV_2 Q57H;Q57H 29;201 33;205 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. The P13L mutation is characterized by a change from C-to-T,Y (C or T), G base change at position 28311 in the Wuhan reference strain. 2021 PloS one Result SARS_CoV_2 P13L 4 8 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. The P13L mutation tracking analysis. 2021 PloS one Result SARS_CoV_2 P13L 4 8 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. The Q57H mutation has previously been studied in detail so we do not perform a detailed mutation tracking for this mutation. 2021 PloS one Result SARS_CoV_2 Q57H 4 8 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. The Q57H mutation is located on the outer surface of the protein and specifically in the binding domain that is directly involved in the tetramerization process. 2021 PloS one Result SARS_CoV_2 Q57H 4 8 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. The Q57H mutation tracking analysis. 2021 PloS one Result SARS_CoV_2 Q57H 4 8 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. The REF-P13L -M protein complex exhibited an increase of the binding affinity (DeltaG -13.050+-0.495kcal/mol and Kd 2.95E-10+-2.192E-10M) compared to the ALT-P13L -M protein complex (DeltaG -12.750+-0.212kcal/mol and Kd 4.600E-10+-1.270E-10M). 2021 PloS one Result SARS_CoV_2 P13L;P13L 8;158 12;162 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. The transmissibility and death rates patterns of Q57H mutation are consistent with the high contamination and low lethality of SARS-CoV-2. 2021 PloS one Result SARS_CoV_2 Q57H 49 53 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. This can account for the much higher frequencies (~10 times) of the ALT-P13L form observed in Australia compared to the former two countries. 2021 PloS one Result SARS_CoV_2 P13L 72 76 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Through March, ALT-P13L became documented in South America, and it constituted a substantial percent of contemporary sampling (Fig 4A). 2021 PloS one Result SARS_CoV_2 P13L 19 23 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. We highlight two mutations of relatively low global frequencies (see Fig 1): 1) Mutation at position 28311 characterized by a P to L change on codon 13 (P13L) in the N protein. 2021 PloS one Result SARS_CoV_2 P13L 153 157 N 166 167 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. We hypothesize that if the P13L mutation can affect transmissibility and death rates, it might also impact severity of disease. 2021 PloS one Result SARS_CoV_2 P13L 27 31 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. Interestingly, the same N501Y mutation has recently been reported in newly emerging SARS-CoV-2 variants (20B/501Y.V1 strain) with potentially enhanced human transmission potential. 2021 medRxiv Result SARS_CoV_2 N501Y 24 29 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. N501Y mutation does not affect SARS-CoV-2 neutralization by human convalescent and post vaccination serum. 2021 medRxiv Result SARS_CoV_2 N501Y 0 5 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. N501Y mutation does not affect SARS-CoV-2 neutralization by mouse convalescent and post vaccination serum. 2021 medRxiv Result SARS_CoV_2 N501Y 0 5 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. One of the amino-acid changes in the RBD of spike protein in the virus, N501Y, has previously been reported to be associated with mouse-adaptation of SARS-CoV-2 and is predicted to increase binding to mACE-2. 2021 medRxiv Result SARS_CoV_2 N501Y 72 77 S;RBD 44;37 49;40 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. Overall, our study shows that the N501Y mutation in the RBD domain of the SARS-CoV-2 spike protein does not compromise the neutralization potential of this virus by convalescent and post-vaccination human sera. 2021 medRxiv Result SARS_CoV_2 N501Y 34 39 S;RBD 85;56 90;59 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. The adjuvanted-spike vaccination sera were found to be neutralizing to the same extent against both strains of the virus, irrespective of the N501Y mutation. 2021 medRxiv Result SARS_CoV_2 N501Y 142 147 S 15 20 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. The comparison of post-vaccination and post-challenge sera from mice showed that both WT- and MA-SARS-CoV-2 strains were neutralized to the same extent indicating that the N501Y substitution in the receptor binding domain of Spike does not mediate antibody escape. 2021 medRxiv Result SARS_CoV_2 N501Y 172 177 RBD;S 198;225 221;230 33502471 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Replication and Tropism in the Lungs, Airways, and Vascular Endothelium of Patients With Fatal Coronavirus Disease 2019: An Autopsy Case Series. In contrast, all 15 case patients without the D614G variant (with full genome sequences obtained) died between 24 February and 22 March 2020. 2021 The Journal of infectious diseases Result SARS_CoV_2 D614G 46 51 33502471 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Replication and Tropism in the Lungs, Airways, and Vascular Endothelium of Patients With Fatal Coronavirus Disease 2019: An Autopsy Case Series. Spike amino acid variant D614G was identified in 9 of 26 (35%) case patients; all 9 of them died between 19 March and 1 July 2020. 2021 The Journal of infectious diseases Result SARS_CoV_2 D614G 25 30 S 0 5 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. 4 (a) shows the locations of two single amino acid variants, del Y144 & D614G, on spike protein. 2021 Biochemistry and biophysics reports Result SARS_CoV_2 D614G;del Y144 72;61 77;69 S 82 87 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. Table 3 shows that D614G has the highest mutation frequency. 2021 Biochemistry and biophysics reports Result SARS_CoV_2 D614G 19 24 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. The D614G substitution was previously reported as a dominant mutation in interconnected Europe and later worldwide. 2021 Biochemistry and biophysics reports Result SARS_CoV_2 D614G 4 9 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. The del Y144 & D614G have relatively the highest mutation sensitivity scores and (b) shows the mutation sensitivity histograms for all four single amino acid variants on spike protein; Y 144, D 614, D 1139, and G 1167 calculated according to Ref. 2021 Biochemistry and biophysics reports Result SARS_CoV_2 D614G;del Y144 15;4 20;12 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. The deletion of Y144, D1139, and G1167, in addition to D614G has a low to neutral mutational sensitivity scores indicating a most likely neutral effect on the function of the spike protein. 2021 Biochemistry and biophysics reports Result SARS_CoV_2 D614G 55 60 S 175 180 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. The prediction output of the secondary structure of the wild type spike glycoprotein versus the D614G variant showed that the substitution from D (aspartate) to G (glycine). 2021 Biochemistry and biophysics reports Result SARS_CoV_2 D614G 96 101 S 66 84 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. The second variant represented by 62% showed aspartate substitution to glycine at D614G located in the SARS-CoV-2_Spike_S1_RBD (spike recognition binding site). 2021 Biochemistry and biophysics reports Result SARS_CoV_2 D614G 82 87 S 128 133 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. The third variant represented by 5% showed aspartate substitution to tyrosine at D1139Y and forth variant represented by 5% glycine substitution to serine at G1167S the last two located in the Corona_S2 domain. 2021 Biochemistry and biophysics reports Result SARS_CoV_2 D1139Y;G1167S 81;158 87;164 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. With a neutral mutation sensitivity, the D614G mutation showed the substitution of aspartate, a bulky amino acid, to glycine, the simplest amino acid. 2021 Biochemistry and biophysics reports Result SARS_CoV_2 D614G 41 46 33506644 Genotype-phenotype correlation identified a novel SARS-CoV-2 variant possibly linked to severe disease. No statistically significant enrichments were identified (two tailed t-test), though missense (Q271R) and synonymous (R41R) mutations in the S and N proteins, respectively, were identified in 2/27 patients with severe COVID-19 but not in patients with mild or moderate disease (0/86; p = .05, Fisher's Exact Test). 2022 Transboundary and emerging diseases Result SARS_CoV_2 Q271R;R41R 95;118 100;122 N;S 147;141 148;142 COVID-19 218 226 33506644 Genotype-phenotype correlation identified a novel SARS-CoV-2 variant possibly linked to severe disease. Some mutations were more frequent than others; for example, the 241C>T, 3037C>T, 14408C>T, and the 23403A>G (also known as the D614G mutation in the S protein), were each seen in 58 of the genomes (Table S3). 2022 Transboundary and emerging diseases Result SARS_CoV_2 C14408T;A23403G;C241T;C3037T;D614G 81;99;64;72;127 89;107;70;79;132 S 149 150 33506644 Genotype-phenotype correlation identified a novel SARS-CoV-2 variant possibly linked to severe disease. The majority (11/20) were coding missense mutations including two (N657S and Q1036L) in the S protein (Table S3). 2022 Transboundary and emerging diseases Result SARS_CoV_2 Q1036L;N657S 77;67 83;72 S 92 93 33506644 Genotype-phenotype correlation identified a novel SARS-CoV-2 variant possibly linked to severe disease. The predominance of European cluster is consistent with the higher infectivity rates associated with the D614G mutation carried by most strains in this cluster (Figure S1). 2022 Transboundary and emerging diseases Result SARS_CoV_2 D614G 105 110 33508515 Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. Given that the RNA dependent RNA Polymerase (RdRp) holds the key to viral genome conservation, hence, we focused on understanding if there existed a non-random association between the known clade-G A23403G (S: D614G) variant and the high frequency RdRp variant C14408U (NSP12:P323L) among the clade-G viruses. 2021 Infection, genetics and evolution Result SARS_CoV_2 A23403G;D614G;P323L 198;210;276 205;215;281 RdRp;Nsp12;RdRP;RdRP;S 15;270;45;248;207 43;275;49;252;208 33508515 Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. Linkage disequilibrium between the A23403G (S: D614G) and the C14408U (NSP12:P323L) variants. 2021 Infection, genetics and evolution Result SARS_CoV_2 A23403G;D614G;P323L 35;47;77 42;52;82 Nsp12;S 71;44 76;45 33508515 Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. The first clade G viruses to be sequenced from India were isolated on the 3rd of March from Italian tourists (Accession IDs: EPI_ISL_420543, EPI_ISL_420545, EPI_ISL_420547, EPI_ISL_420549, EPI_ISL_420551 and EPI_ISL_420553) and were clade G variants harboring an additional amino acid change in the NSP3 protein [C4,809U (S697F)] followed by an Indian from Iran and two contacts of Indians with travel history to Italy (EPI_ISL_424362, EPI_ISL_424364, EPI_ISL_424365). 2021 Infection, genetics and evolution Result SARS_CoV_2 S697F 322 327 Nsp3 299 303 33508515 Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. The second cluster was formed by the clade G viruses (n = 173) which differed at three loci resulting in one amino acid change each in the RdRp, S protein [C3037U, C14,408 U (RdRp: P323L), A23,403G (S:D614G)] known to be in LD across the world. 2021 Infection, genetics and evolution Result SARS_CoV_2 P323L;D614G 181;201 186;206 RdRP;RdRP;S;S 139;175;145;199 143;179;146;200 33508515 Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. There were 17 variants [C1707U, C6310A, U8022G, G11083U, A8026U, G11083U, G12685U, A15435G, C19524U, A21550C, A21551U, A24389U, G24390C, U24622C, C28311U, G29742U, A29827U, A29830U] that could not be included in the network analysis because of the presence of unresolved bases at multiple viral genome sequences and the G26144U (ORF3a:G251V) variant that segregates clade V was excluded because of allele frequency cutoff of 1%. 2021 Infection, genetics and evolution Result SARS_CoV_2 A15435G;A21550C;C6310A;G24390C;G251V 83;101;32;128;335 90;108;38;135;340 ORF3a 329 334 33508515 Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. There were two major clusters of haplotypes that were found to have emerged from the ancestral Wuhan-Hu-1 virus (clade L); the first identified to be belonging to a variant of the clade L which has been annotated here as Lv (n = 208) and harbored the RNA dependent RNA polymerase (RdRp) protein [C13,730 U,(A97V)] from which a sub-cluster (n = 126) was formed harboring an additional non-synonymous change in the NSP3 protein [C6312A (T1198K)]. 2021 Infection, genetics and evolution Result SARS_CoV_2 A97V;T1198K;C6312A 307;435;427 311;441;433 RdRp;Nsp3;RdRP 251;413;281 279;417;285 33508515 Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. Two sub-clusters were observed evolving from clade G; GH variant mentioned here as GHv with the variants C18877U, G25563U (ORF3a:Q57H), C26735U having multiple evolving branches and GR with the tri-nucleotide GGG-AAC substitution at positions 28,881-28,883 resulting in two amino acid changes R203K, G204R in the N protein. 2021 Infection, genetics and evolution Result SARS_CoV_2 G204R;R203K;Q57H 300;293;129 305;298;133 ORF3a;N 123;313 128;314 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. An amino acid change in the virus' spike protein, D614G, emerged early during the pandemic, and viruses containing G614 are now dominant in many places around the world. 2021 Analytical chemistry Result SARS_CoV_2 D614G 50 55 S 35 40 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. D614G mutation anchored in either presubstrate A probe or presubstrate B probe would be dramatically discriminated by the RNA assay (Figures 4B and S5, in the Supporting Information). 2021 Analytical chemistry Result SARS_CoV_2 D614G 0 5 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. Even the amount of wild viral RNAs was 50 times that of D614G mutated viral RNAs, and the fluorescent variation was much smaller than that in the presence of D614G mutated viral RNAs. 2021 Analytical chemistry Result SARS_CoV_2 D614G;D614G 56;158 61;163 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. The fluorescent response of the assay toward 1, 5, 10, and 50 amounts of wild viral RNAs compared to D614G mutated viral RNAs was tested (Figure 4D). 2021 Analytical chemistry Result SARS_CoV_2 D614G 101 106 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. The involvement of Cas13a-gRNA recognition would significantly improve the ability to discriminate the D614G mutation, especially, the D614G mutation which was located on the crRNA binding sites (Figures 4C and S7, in the Supporting Information). 2021 Analytical chemistry Result SARS_CoV_2 D614G;D614G 103;135 108;140 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. To estimate the ability of the assay to profile D614G mutation of SARS-CoV-2, lentiviruses containing partial S genes (wild or with D614G mutation), N genes, E genes, and ORF1 a/b genes of SARS-CoV-2 were constructed (Figure S1 in the Supporting Information). 2021 Analytical chemistry Result SARS_CoV_2 D614G;D614G 48;132 53;137 E;N;S 158;149;110 159;150;111 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. We designed a series of Presubstrate probes (1-6) to target the D614G mutation. 2021 Analytical chemistry Result SARS_CoV_2 D614G 64 69 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. We estimated the ability of the assay to discriminate D614G mutations in the presence of wild viral RNAs. 2021 Analytical chemistry Result SARS_CoV_2 D614G 54 59 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. We further proceed to estimate the dual recognition effect on the specificity of D614G discrimination. 2021 Analytical chemistry Result SARS_CoV_2 D614G 81 86 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. Wild and mutated SARS-CoV-2 pseudoviruses were sequenced, and the presence of the D614G mutation was confirmed (Figure 4A). 2021 Analytical chemistry Result SARS_CoV_2 D614G 82 87 33513449 Different SARS-CoV-2 haplotypes associate with geographic origin and case fatality rates of COVID-19 patients. By grouping the haplotypes into "D" and "G" types, a Mann-Whitney test revealed a significant association between the D614G genotypes and case severity (p = 0.031085). 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 118 123 33513449 Different SARS-CoV-2 haplotypes associate with geographic origin and case fatality rates of COVID-19 patients. However, there was an apparent trend with regard to the D614G mutation. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 56 61 33524589 A global analysis of replacement of genetic variants of SARS-CoV-2 in association with containment capacity and changes in disease severity. with S-D614G consistently detected from clades G, GR and GH of lineage G*. 2021 Clinical microbiology and infection Result SARS_CoV_2 D614G 7 12 S 5 6 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. 2C) mutation while D210Y mutation leads to replacement of turn structure by beta-sheet. 2021 Biochemistry and biophysics reports Result SARS_CoV_2 D210Y 19 24 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. 2F) decreased the protein disorder while S171L. 2021 Biochemistry and biophysics reports Result SARS_CoV_2 S171L 41 46 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Our analysis revealed that Y160H. 2021 Biochemistry and biophysics reports Result SARS_CoV_2 Y160H 27 32 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Similarly, R126S mutation caused maximum negative DeltaDeltaG (-2.02 kcal/mol), leading to decrease in the stability of Orf3a. 2021 Biochemistry and biophysics reports Result SARS_CoV_2 R126S 11 16 ORF3a 120 125 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. The detailed analysis revealed that Y160H mutation has led to shift of beta-sheet to coiled-coil structure. 2021 Biochemistry and biophysics reports Result SARS_CoV_2 Y160H 36 41 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. The maximum positive DeltaDeltaG (1.7 kcal/mol) was obtained for G49V mutation, leading to increase in stability. 2021 Biochemistry and biophysics reports Result SARS_CoV_2 G49V 65 69 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. The turn structure is replaced by coiled coil at S171L. 2021 Biochemistry and biophysics reports Result SARS_CoV_2 S171L 49 54 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. Mutation at position 6312 C>T{T2016K} is on NSP3 in sample GMCKN443/2020, GMCRR1191/2020, and OUMRK1090/2020. 2021 PloS one Result SARS_CoV_2 C6312K;C6312T;T2016K 21;21;30 29;29;36 Nsp3 44 48 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. One synonymous (23929C>T in the S gene) and four nonsynonymous mutations (6312 C>A{T2016N}, 11083G>T{L3606F}, 13730C>T{A4489V} in ORF1ab; 28311C>T{P13L} in the N gene) were observed in the sample (OUMRK1090/2020) collected from patient with travel history to UAE. 2021 PloS one Result SARS_CoV_2 G11083F;G11083L;G11083T;C13730A;C13730T;C13730V;C28311L;C28311P;C28311T;C23929T;C6312A;C6312N;C6312T;A4489V;L3606F;P13L;T2016N 92;92;92;110;110;110;138;138;138;16;74;74;74;119;101;147;83 100;100;100;118;118;118;146;146;146;24;82;82;82;125;107;151;89 ORF1ab;N;S 130;160;32 136;161;33 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. One synonymous (23929C>T in the S gene) and four nonsynonymous mutations (6312 C>T{T2016K}, 11083G>T{L3606F}, 13730C>T{A4489V} in ORF1ab; 28311C>T{P13L} in the N gene) were observed in the sample (GMCRR1191/2020) collected from patient with cluster infection and no travel history, and who succumbed to the disease. 2021 PloS one Result SARS_CoV_2 G11083F;G11083L;G11083T;C13730A;C13730T;C13730V;C28311L;C28311P;C28311T;C23929T;C6312K;C6312T;A4489V;L3606F;P13L;T2016K 92;92;92;110;110;110;138;138;138;16;74;74;119;101;147;83 100;100;100;118;118;118;146;146;146;24;82;82;125;107;151;89 ORF1ab;N;S 130;160;32 136;161;33 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. One synonymous (23929C>T in the S gene) and four nonsynonymous mutations (6312C>A{T2016K}, 11083G>T{L3606F}, 13730C>T{A4489V} in ORF1ab; 28311C>T{P13L} in the N gene) were observed in the sample (GMCKN443/2020) collected from patient with travel history to Indonesia. 2021 PloS one Result SARS_CoV_2 G11083F;G11083L;G11083T;C13730A;C13730T;C13730V;C28311L;C28311P;C28311T;C23929T;C6312A;C6312K;C6312T;A4489V;L3606F;P13L;T2016K 91;91;91;109;109;109;137;137;137;16;74;74;74;118;100;146;82 99;99;99;117;117;117;145;145;145;24;81;81;81;124;106;150;88 ORF1ab;N;S 129;159;32 135;160;33 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. One synonymous (3037C>T in ORF1ab) and four nonsynonymous mutations (14408C>T{P4714L} in ORF1ab; 23403A>G{D614G} in the S gene; 28881G>A{R203L}, 28883G>C{G204R} in the N gene) were observed in the sample (GMCTC469/2020) collected from patient with travel history to UK. 2021 PloS one Result SARS_CoV_2 A23403D;A23403G;G28881A;G28881L;G28881R;G28883C;G28883G;G28883R;C14408L;C14408P;C14408T;C3037T;D614G;G204R;P4714L;R203L 97;97;128;128;128;145;145;145;69;69;69;16;106;154;78;137 105;105;136;136;136;153;153;153;77;77;77;23;111;159;84;142 ORF1ab;ORF1ab;N;S 27;89;168;120 33;95;169;121 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. One synonymous (3037C>T in ORF1ab) and two nonsynonymous mutations (14408C>T{P4714L} in ORF1ab; 23403A>G{D614G} in the S gene) were observed in the sample (GMCKN318/2020) collected from patient with travel history to Italy. 2021 PloS one Result SARS_CoV_2 A23403D;A23403G;C14408L;C14408P;C14408T;C3037T;D614G;P4714L 96;96;68;68;68;16;105;77 104;104;76;76;76;23;110;83 ORF1ab;ORF1ab;S 27;88;119 33;94;120 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. RK100 showed Y28H mutation, while sample nos KN318, TC469, and KP1125 showed D614G mutation, and samples KN443, RK1090 and RR1191 spike protein are similar to Wuhan reference. 2021 PloS one Result SARS_CoV_2 D614G;Y28H 77;13 82;17 S 130 135 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. The mutation 11083G>T{L3606F} was observed in NSP6 in sample GMCKN443/2020, GMCRR1191/2020, and OUMRK1090/2020. 2021 PloS one Result SARS_CoV_2 G11083F;G11083L;G11083T;L3606F 13;13;13;22 21;21;21;28 Nsp6 46 50 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. The mutation 28311C>T{P13L}, was found in three samples GMCKN443/2020, OUMRK1090/2020, GMCRR1191/2020, while one mutation in each was observed in other three samples. 2021 PloS one Result SARS_CoV_2 C28311L;C28311P;C28311T;P13L 13;13;13;22 21;21;21;26 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. The mutation 6312 C>T{T2016K} falls on relative position of 1198 on NSP3 protein sequence. 2021 PloS one Result SARS_CoV_2 C6312K;C6312T;T2016K 13;13;22 21;21;28 Nsp3 68 72 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. The two mutations out of four in N-protein reported from our analysis (28311C>T{P13L} and 28883G>C{G204R}) are present in IDRs suggesting there may be variation for RNA binding activity among the N-protein of different variants of SARS-CoV-2. 2021 PloS one Result SARS_CoV_2 G28883C;G28883G;G28883R;C28311L;C28311P;C28311T;G204R;P13L 90;90;90;71;71;71;99;80 98;98;98;79;79;79;104;84 N;N 33;196 34;197 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. These mutations were distinctly different with varied affinities as assessed by theoretical analysis, wherein the affinity of Wuhan was higher followed by Y28H and D614G (Table 4). 2021 PloS one Result SARS_CoV_2 D614G;Y28H 164;155 169;159 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. Two mutations were observed in NSP11, in which the first mutation 13730:C>T{A4489V} was present in samples GMCKN443/2020 GMCRR1191/2020 and OUMRK1090/2020; and the second 14408:C>A{P4714L} was observed in samples GMCKN318/2020, GMCTC469/2020, and GMCKP1125/2020. 2021 PloS one Result SARS_CoV_2 C14408A;C14408L;C14408P;A4489V;P4714L 171;171;171;76;181 180;180;180;82;187 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. Two synonymous (15324C>T in ORF1ab; 24130C>T in S) and two nonsynonymous mutations (21644T>C{Y28H} in the S gene; 29303C>T{P344S} in the N gene) were observed in the sample (OUMRK100/2020) collected from patient with travel history to Dubai. 2021 PloS one Result SARS_CoV_2 C24130T;C29303P;C29303S;C29303T;C15324T;T21644C;T21644H;T21644Y;P344S;Y28H 36;114;114;114;16;84;84;84;123;93 44;122;122;122;24;92;92;92;128;97 ORF1ab;N;S;S 28;137;48;106 34;138;49;107 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. Two synonymous (3037C>T, 18877C>T in ORF1ab) and three nonsynonymous mutations (14408C>T{P4714L} in ORF1ab; 23403 A>G{D614G} in the S gene; 25563G>T{Q57H} in the N gene) were observed in the sample (GMCKP1125/2020) collected from patient with travel history to USA. 2021 PloS one Result SARS_CoV_2 C18877T;A23403D;A23403G;G25563H;G25563Q;G25563T;C14408L;C14408P;C14408T;C3037T;D614G;P4714L;Q57H 25;108;108;140;140;140;80;80;80;16;118;89;149 33;117;117;148;148;148;88;88;88;23;123;95;153 ORF1ab;ORF1ab;N;S 37;100;162;132 43;106;163;133 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. We observed 3 distinct variants Y28H (RK100), D614G (KN318, TC469, KP1125), and similar to Wuhan reference NC_045512.2 (KN443, RK1090 and RR1191). 2021 PloS one Result SARS_CoV_2 D614G;Y28H 46;32 51;36 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? A similar distribution pattern was found for the A220V mutation of the Nucleocapsid. 2021 Biology Result SARS_CoV_2 A220V 49 54 N 71 83 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? A222V and L18F in the Spike were also mutations detected in our analysis (MRs = 0.58 and 0.28 respectively) (Figure 1B). 2021 Biology Result SARS_CoV_2 L18F;A222V 10;0 14;5 S 22 27 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? According to our data, the A222V (Spike) mutation was already detected in March in Tunisia and Iran, in April in Turkey, and in May in Mexico and Canada, among others, although the MR of the A222 residue was still low ( 0.03). 2021 Biology Result SARS_CoV_2 A222V 27 32 S 34 39 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? Alanine substitution by the bulkier valine in A222V can change inter-residue contacts and the 3D structure of the region. 2021 Biology Result SARS_CoV_2 A222V 46 51 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? Another mutation in the Nucleocapsid, the A220V, has gained importance recently (MR = 0.57). 2021 Biology Result SARS_CoV_2 A220V 42 47 N 24 36 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? As a hypothesis, viral variants with additional mutations but with the original R203/G204 residues could have increased their frequency and expansion around the globe due to higher infectivity and so diminish the percentage of the viruses containing the R203K/G204R mutations. 2021 Biology Result SARS_CoV_2 R203K;G204R 254;260 259;265 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? As described in Figure 2, the high increase in the incidence of the D614G mutation happened in March, where there are many countries in different areas of the globe with MR higher than 0.90, such as Estonia (MR = 1), Morocco (MR = 1), Argentina (MR = 1), Romania (MR = 1), Faroe Islands (MR = 1), Mongolia (MR = 1), Italy (MR = 0.99), Hungary (MR = 0.98), Bosnia and Herzegovina (MR = 0.96), Russia (MR = 0.96), Switzerland (MR = 0.95), France (MR = 0.94), Croatia (MR = 0.94), Brazil (MR = 0.94), Denmark (MR = 0.93), Luxembourg (MR = 0.93), Czech Republic (MR = 0.93), Costa Rica (MR = 0.92), Sweden (MR = 0.92), and the Democratic Republic of the Congo (MR = 0.91). 2021 Biology Result SARS_CoV_2 D614G 68 73 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? As RdRp catalyzes the replication of RNA, the P323L mutation could affect the speed of the viral replication. 2021 Biology Result SARS_CoV_2 P323L 46 51 RdRP 3 7 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? Both mutations D614G and A222V are located within areas defined as possible B-cell epitopes. 2021 Biology Result SARS_CoV_2 A222V;D614G 25;15 30;20 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? Conversely, we only found significant results in one out of 12 thresholds when we looked for an association between higher MRs or the presence of the D614G mutation and increased mortality. 2021 Biology Result SARS_CoV_2 D614G 150 155 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? However, computational studies have shown that P323L and A185V mutations could have an effect in the preservation of the secondary structure of the protein that could affect protein function and drug binding. 2021 Biology Result SARS_CoV_2 A185V;P323L 57;47 62;52 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? However, in February, other countries showed a remarkable increase in the presence of the D614G mutation, such as Saudi Arabia (MR = 1), Switzerland (MR = 0.97), Italy (MR = 0.96), France (MR = 0.78), Austria (MR = 0.75), the Netherlands (MR = 0.63), and Brazil (MR = 0.6 but only five analyzed sequences). 2021 Biology Result SARS_CoV_2 D614G 90 95 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? However, mutations such as E484K or K417N from the variant 501Y.V2 are marginally present in our data (MRs 0.004). 2021 Biology Result SARS_CoV_2 E484K;K417N 27;36 32;41 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? However, the P323L mutation is situated far away from the catalytic site. 2021 Biology Result SARS_CoV_2 P323L 13 18 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? In fact, the mutation P323L is near the binding region between NSP12 and NSP8 and could have an impact in the polymerase complex stability (Figure 4C). 2021 Biology Result SARS_CoV_2 P323L 22 27 Nsp12;Nsp8 63;73 68;77 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? In February 2020, different European countries already displayed the R203K mutation. 2021 Biology Result SARS_CoV_2 R203K 69 74 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? In March 2020, the R203K mutation had already extended to other countries, such as Brazil, Greece, the Czech Republic, Estonia, Ireland, Russia, and Vietnam, among others, with an MR higher than 0.5. 2021 Biology Result SARS_CoV_2 R203K 19 24 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? L18F is a mutation also included in the variant 501Y.V2. 2021 Biology Result SARS_CoV_2 L18F 0 4 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? L18F is not represented in the 3D structure, since the crystallized protein is missing residues M1-P26. 2021 Biology Result SARS_CoV_2 L18F 0 4 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? More recent viral mutations, such as A222V (S), L18F (S), A220V (N), and L67F (NS9c) were mostly detected in Europe and should be further monitored to estimate their impact in viral evolution. 2021 Biology Result SARS_CoV_2 A220V;A222V;L18F;L67F 58;37;48;73 63;42;52;77 N;S;S 65;44;54 66;45;55 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? Mutations R203K (N), G204R (N), and G50N (NS9c) spread over the world but are less stable than the mutation D614G (S), and those residue positions were subjected to back-mutation toward the original state in multiple areas. 2021 Biology Result SARS_CoV_2 D614G;G204R;G50N;R203K 108;21;36;10 113;26;40;15 N;N;S 17;28;115 18;29;116 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? Mutations such as G50N (MR = 0.23) and L67F (MR = 0.64) in the NS9c are highly correlated with residues R203/G204 and A220 from the Nucleocapsid due to possible overlapping in the reading frame. 2021 Biology Result SARS_CoV_2 G50N;L67F 18;39 22;43 N 132 144 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? Nevertheless, it was in Japan, Brazil, and Vietnam in April and in Lithuania, Russia, Oman, and Zimbabwe in May, where the R203K mutation reached the threshold of 90%. 2021 Biology Result SARS_CoV_2 R203K 123 128 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? Our data showed that D614G (S) and P323L (NSP12) mutations overtook the entire globe. 2021 Biology Result SARS_CoV_2 D614G;P323L 21;35 26;40 Nsp12;S 42;28 47;29 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? Previous studies already confirmed a cluster variant with both A222V and A220V that emerged during the summer, presumably in Spain, and posteriorly spread in Europe. 2021 Biology Result SARS_CoV_2 A220V;A222V 73;63 78;68 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? Previous studies have shown significant correlations between the presence of D614G mutation and increased case fatality rates. 2021 Biology Result SARS_CoV_2 D614G 77 82 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? The D614G mutation has already been studied in different publications. 2021 Biology Result SARS_CoV_2 D614G 4 9 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? The D614G mutation has been associated with an increase of infectivity but not with an augment of the disease severity. 2021 Biology Result SARS_CoV_2 D614G 4 9 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? The D614G mutation was already present in January 2020 in the sequences analyzed from Germany (MR = 1, sequences = 9). 2021 Biology Result SARS_CoV_2 D614G 4 9 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? The mutation D614G could interrupt the mentioned hydrogen bond between both protomers, provide higher protein flexibility, or even modify glycosylation at close residues, such as N616. 2021 Biology Result SARS_CoV_2 D614G 13 18 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? The mutation L18F in the Spike was marginally present in the United Kingdom in February and in different countries in March (MRs 0.005). 2021 Biology Result SARS_CoV_2 L18F 13 17 S 25 30 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? The mutation L18F was also recently detected as part of the variant 501Y.V2 described in South Africa. 2021 Biology Result SARS_CoV_2 L18F 13 17 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? The mutations A222V and L18F are far from the main D614G mutation and are located in the N-terminal domain of the S1 subunit. 2021 Biology Result SARS_CoV_2 A222V;D614G;L18F 14;51;24 19;56;28 N 89 90 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? The mutations in the Nucleocapsid, which are located mainly in residues R203 and G204, showed different evolution patterns compared to D614G (Figure 3B). 2021 Biology Result SARS_CoV_2 D614G 135 140 N 21 33 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? The Nucleocapsid also presented two consecutive residues with high mutation rates, which were equivalent to the mutations R203K and G204R (MRs = 0.22) (Figure 1B). 2021 Biology Result SARS_CoV_2 G204R;R203K 132;122 137;127 N 4 16 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? The P323L mutation in the NSP12 (RNA-dependent RNA polymerase, RdRp) protein accompanies the D614G (S) mutation in most of the analyzed sequences (MR = 0.996). 2021 Biology Result SARS_CoV_2 D614G;P323L 93;4 98;9 RdRp;Nsp12;RdRP;S 33;26;63;100 61;31;67;101 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? The sequences in October-December yielded an increase of the A222V mutation in multiple countries in Europe, in New Zealand (MR = 0.32 in December), and Tunisia (MR = 0.11 in November). 2021 Biology Result SARS_CoV_2 A222V 61 66 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? The variant with A222V completely overtook Spain in August (MR = 0.84) and continued its expansion to Norway (MR = 0.39), Latvia (MR = 0.24), Switzerland (MR = 0.22), the United Kingdom (MR = 0.17), Denmark (MR = 0.17), Italy (MR = 0.11), and other European countries (France, the Netherlands, Ireland, Sweden, Germany, and Belgium). 2021 Biology Result SARS_CoV_2 A222V 17 22 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? The viral variant with D614G contains also the P323L mutation in the NSP12. 2021 Biology Result SARS_CoV_2 D614G;P323L 23;47 28;52 Nsp12 69 74 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? This mutation along with A222V (Spike) have been already included in a viral variant spread in Europe during the summer 2020 (variant 20A.EU1). 2021 Biology Result SARS_CoV_2 A222V 25 30 S 32 37 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? We detected in that period the D614G mutation in Australia and China, but the original residue was still highly conserved (MRs = 0.05 and 0.01 respectively). 2021 Biology Result SARS_CoV_2 D614G 31 36 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? We divided the GISAID global sequence data over several months and performed a temporal residue mutation analysis for the whole proteome and the main mutations D614G (S), A222V (S), L18F (S), P323L (NSP12), R203K (N), G204R (N), A220V (N), G50N (NS9c), and L67F (NS9c) (see Figure 2). 2021 Biology Result SARS_CoV_2 A220V;A222V;D614G;G204R;G50N;L18F;L67F;P323L;R203K 229;171;160;218;240;182;257;192;207 234;176;165;223;244;186;261;197;212 Nsp12;N;N;N;S;S;S 199;214;225;236;167;178;188 204;215;226;237;168;179;189 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? When we investigated the residue mutations occurred during the first period, such as the D614G and P323L mutations, the ascend in the residue mutation rate is steeper in March with an abrupt rise in the mutation rate from 0.20 to 0.69 until a current value of 1 (Figure 2B). 2021 Biology Result SARS_CoV_2 D614G;P323L 89;99 94;104 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. A comparison of MERS PLpro high resolution structure (PDB id: 4RNA) with SARS-CoV-2 PLpro C111S mutant shows much bigger differences (RMSD 1.82 A), with the largest structural shifts occurring again in the structural zinc-binding region and in the N-terminal Ubl domain, but also in the palm subdomain. 2021 Nature communications Result SARS_CoV_2 C111S 90 95 N 248 249 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. CV-2 generates fluorescent signal in response to the protease activity of PLpro, and critically, is unresponsive in the C111S variant. 2021 Nature communications Result SARS_CoV_2 C111S 120 125 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. In the high resolution structure of PLpro C111S mutant, there is a phosphate ion bound to the active site at the N-terminus of helix alpha4 (contributing Cys111) that is coordinated by Trp106, Asn109, and His272. 2021 Nature communications Result SARS_CoV_2 C111S 42 47 N 113 114 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Supplementary Methods, and Supplementary Data 1) three using C111S mutant and one wild-type enzyme (PDB ids: 7JIR, 7JIT, 7JIV, and 7JIW). 2021 Nature communications Result SARS_CoV_2 C111S 61 66 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. The SARS PLpro Cys112Ser mutant in complex with ubiquitin (PDB id: 4M0W) shows RMSD 0.53 A with our highest resolution structure of SARS-CoV-2 PLpro C111S mutant (PDB id: 6WRH). 2021 Nature communications Result SARS_CoV_2 C111S;C112S 149;15 154;24 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. The structure of 2 bound to the PLpro C111S mutant was determined at 1.95 A (PDB id: 7JIT), the highest resolution for all complexes to date, and this structure will be used here as a reference. 2021 Nature communications Result SARS_CoV_2 C111S 38 43 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. The structures of inhibitor 3 were determined in both forms: wild-type at 2.30 A (PDB id: 7JIW) and C111S mutant at 2.05 A (PDB id: 7JIV). 2021 Nature communications Result SARS_CoV_2 C111S 100 105 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. These structures are virtually identical with the high resolution wild-type and C111S mutant structures showing RMSD 0.10 A, while 293 and 100 K mutant structures show RMSD 0.27 A. 2021 Nature communications Result SARS_CoV_2 C111S 80 85 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. We have determined apo-structures of wild-type enzyme and inactive mutant in which single sulfur atom was replaced by oxygen (C111S). 2021 Nature communications Result SARS_CoV_2 C111S 126 131 33531496 Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. We report here seven structures of PLpro from SARS-CoV-2, including wild-type apo-protein structure determined at 100 K and refined to 1.79 A (PDB id: 6WZU), the apo-PLpro active site C111S mutant under cryogenic conditions 100 K at 1.60 A (PDB id: 6WRH) and at 293 K at 2.50 A (PDB id: 6XG3). 2021 Nature communications Result SARS_CoV_2 C111S 184 189 33532796 The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. In the case of convalescent donor sera with low or moderate IgG against SARS-CoV-2 S protein, the drop in neutralization efficiency could result in neutralization ID50 values similar to negative control samples, resulting in low or even absence of neutralization of the E484K recombinant virus by those sera. 2021 medRxiv Result SARS_CoV_2 E484K 270 275 S 83 84 33532796 The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. Serum neutralization efficiency was lower against the E484K rSARS-CoV-2 (vaccination samples: 3.4 fold; convalescent low IgG: 2.4 fold, moderate IgG: 4.2 fold and high IgG: 2.6 fold based on geometric means) which was significantly different for the convalescent sera (see Figure 1), suggesting that the single E484K mutation in the RBD affects binding by serum polyclonal neutralizing antibodies from both convalescent and vaccinated donors. 2021 medRxiv Result SARS_CoV_2 E484K;E484K 54;311 59;316 RBD 333 336 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Additional amino acid substitutions that conferred resistance to serum 13 include T345S and G446D. 2021 Cell host & microbe Result SARS_CoV_2 G446D;T345S 92;82 97;87 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Again, the specific substitution of a given residue impacted the effect, as T345A and T345N required higher concentrations of hACE2 to inhibit infection, whereas T345S was similar to wild type. 2021 Cell host & microbe Result SARS_CoV_2 T345A;T345N;T345S 76;86;162 81;91;167 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. All four sera neutralized the single substitution S477N as well as wild-type virus (Figures 4A and 4B). 2021 Cell host & microbe Result SARS_CoV_2 S477N 50 55 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. As the L517R or S514F substitutions were not identified in isolation, it remains unclear whether they cause resistance to 2H04 or SARS2-19, respectively. 2021 Cell host & microbe Result SARS_CoV_2 L517R;S514F 7;16 12;21 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. E484A exhibited a high degree of resistance to 2B04, 1B07, SARS2-01, SARS2-07, SARS2-19, SARS2-32, and SARS2-38; E484G exhibited resistance to 2B04, 1B07, SARS2-01, SARS2-32, and SARS2-38; E484K was resistant to 2B04, 1B07, SARS2-01, SARS2-02, SARS2-16, and SARS2-32; and E484D was resistant only to 1B07 (Figures 3A and S3). 2021 Cell host & microbe Result SARS_CoV_2 E484D;E484G;E484K;E484A 272;113;189;0 277;118;194;5 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Finally, substitution P499L was resistant to SARS2-07, SARS2-16, and SARS2-19. 2021 Cell host & microbe Result SARS_CoV_2 P499L 22 27 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. For 2H04, substitution T345A likely arose first, as we isolated this mutation alone, and acquisition of the L517R substitution appeared to enhance infectivity as judged by plaque morphology (Figure S2). 2021 Cell host & microbe Result SARS_CoV_2 L517R;T345A 108;23 113;28 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. For example, K444E was resistant to SARS2-38 and 2H04 with some resistance to SARS2-1, SARS2-2, and SARS2-7, whereas K444N conferred complete resistance to SARS2-38, partial resistance to 2H04, and only weak resistance to SARS2-1 and SARS2-2. 2021 Cell host & microbe Result SARS_CoV_2 K444E;K444N 13;117 18;122 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. For SARS2-19, S477N was isolated as a single variant, suggesting that this substitution arose first; however, acquisition of the S514F did not alter plaque morphology (Figure S2). 2021 Cell host & microbe Result SARS_CoV_2 S477N;S514F 14;129 19;134 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. For the 2B04-resistant mutant E484A, we selected T345A, R346G, and K444E; for mutant E484K, we isolated R346K, A372T, and K444E; and for mutant F486S, we selected T345S. 2021 Cell host & microbe Result SARS_CoV_2 A372T;E484A;E484K;F486S;K444E;K444E;R346G;R346K;T345A;T345S 111;30;85;144;67;122;56;104;49;163 116;35;90;149;72;127;61;109;54;168 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Four other substitutions (K444E, G446V, L452R, and F490S) resulted in resistance to neutralization of sera 13, 35, and 37 (Figures 4A and S5A). 2021 Cell host & microbe Result SARS_CoV_2 F490S;G446V;L452R;K444E 51;33;40;26 56;38;45;31 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. G446D was resistant to SARS2-2, SARS2-32, and SARS2-38, but G446V acquired resistance to SARS2-01. 2021 Cell host & microbe Result SARS_CoV_2 G446V;G446D 60;0 65;5 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. However, using the 2B04 resistant viruses E484A, E484K, and F486S, we selected additional mutations by growth in the presence of 2H04 (Figure 7 ; Table S1). 2021 Cell host & microbe Result SARS_CoV_2 E484A;E484K;F486S 42;49;60 47;54;65 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Of the four substitutions observed at position E484, only E484D was less sensitive (4.6-fold, p < 0.0001) to hACE2 inhibition. 2021 Cell host & microbe Result SARS_CoV_2 E484D 58 63 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Sequence analysis identified the mutations E484A, E484K, and F486S (Figure 1B), each of which falls within the RBD and maps to residues involved in ACE2 binding (Figure 2 ). 2021 Cell host & microbe Result SARS_CoV_2 E484A;E484K;F486S 43;50;61 48;55;66 RBD 111 114 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Sera 13 and 35 also did not efficiently neutralize S477G, L441R, and T478I. 2021 Cell host & microbe Result SARS_CoV_2 L441R;S477G;T478I 58;51;69 63;56;74 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Several mutants required higher (3-5-fold) concentrations of hACE2 to block infection, including substitutions at T345A, T345N, G446D, G446V, E484D, and F486Y. 2021 Cell host & microbe Result SARS_CoV_2 E484D;F486Y;G446D;G446V;T345A;T345N 142;153;128;135;114;121 147;158;133;140;119;126 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Substitution F486S was resistant to 2B04, 1B07, SARS2-07, SARS2-16, and SARS2-19, whereas F486Y exhibited resistance only to 1B07 and SARS2-16. 2021 Cell host & microbe Result SARS_CoV_2 F486S;F486Y 13;90 18;95 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Substitution F486S, which altered sensitivity to soluble ACE2, escaped neutralization by serum 35 but not 13, 29, or 37. 2021 Cell host & microbe Result SARS_CoV_2 F486S 13 18 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Substitution L452R conferred resistance to SARS2-01, SARS2-02, and SARS2-32; S477N, S477G, and S477R were each highly resistant to SARS2-07, SARS2-16, and SARS2-19, and S477N and S477G result in a degree of resistance across the entire panel of antibodies; and T478I yielded resistance to SARS2-16 and SARS2-19. 2021 Cell host & microbe Result SARS_CoV_2 L452R;S477G;S477G;S477N;S477N;S477R;T478I 13;84;179;77;169;95;261 18;89;184;82;174;100;266 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Substitution S477N was sensitive to neutralization by sera 13 and 35 except in the presence of a second S514F substitution (Figures 4A and S5A). 2021 Cell host & microbe Result SARS_CoV_2 S477N;S514F 13;104 18;109 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Substitutions N450D and N450Y, but not N450K, were resistant to sera 13 and 35. 2021 Cell host & microbe Result SARS_CoV_2 N450D;N450K;N450Y 14;39;24 19;44;29 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Substitutions N450K and N450Y were resistant to SARS2-01 and SARS2-32, whereas N450D facilitated resistance to SARS2-07. 2021 Cell host & microbe Result SARS_CoV_2 N450D;N450K;N450Y 79;14;24 84;19;29 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. The fourth most frequent substitution is S477N, which is present in 4.6% of sequenced isolates and the dominant virus in Oceana. 2021 Cell host & microbe Result SARS_CoV_2 S477N 41 46 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. The most frequent S sequence variant seen in clinical isolates is D614G, which is present in 69% of sequenced isolates. 2021 Cell host & microbe Result SARS_CoV_2 D614G 66 71 S 18 19 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. The most striking effect was observed for F486S, where we achieved only 38% inhibition at the highest concentration (20 mug/mL) of hACE2-Fc tested (Figures 3B and 3C). 2021 Cell host & microbe Result SARS_CoV_2 F486S 42 47 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. The penetrance of the remaining substitutions among clinical isolates is relatively low, with G446V, T478I, E484K, S477I, and S494P ranking 79, 102, 123, 135, and 146 of the top 150 variants in S or roughly 0.05% of sequenced variants. 2021 Cell host & microbe Result SARS_CoV_2 E484K;G446V;S477I;S494P;T478I 108;94;115;126;101 113;99;120;131;106 S 194 195 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. This effect was substitution dependent, as N450K was 6-fold more sensitive to hACE2 than N450Y (p < 0.001). 2021 Cell host & microbe Result SARS_CoV_2 N450K;N450Y 43;89 48;94 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. To extend these findings, we employed a higher throughput screening assay to test 16 additional human sera (11, 15, 16, 18, 21, 23, 27, 28, 30, 31, 32, 34, 35, 37, 38, and 39) for their ability to neutralize the VSV-SARS-CoV-2 mutants N450Y, S477N, E484A, E484D, and E484K (Figure 4D). 2021 Cell host & microbe Result SARS_CoV_2 E484A;E484D;E484K;N450Y;S477N 249;256;267;235;242 254;261;272;240;247 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Two mAbs gave rise to variants containing linked amino acid substitutions: 2H04 (T345A and L517R) and SARS2-19 (S477N and S514F). 2021 Cell host & microbe Result SARS_CoV_2 L517R;S514F;S477N;T345A 91;122;112;81 96;127;117;86 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Two of the mutants (R346K and A372T) were not seen in our prior selection campaigns with 2H04 alone, although both variants exist in human isolates (Figure 6). 2021 Cell host & microbe Result SARS_CoV_2 A372T;R346K 30;20 35;25 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. We consistently noticed that some sera also led to an increase in infectivity of specific escape mutants (e.g., E484A) at some concentrations (Figure 4B). 2021 Cell host & microbe Result SARS_CoV_2 E484A 112 117 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. Additionally, another similar pattern of mutations was shared among these strains at six different sites: three (T4346C, C9286T, C10376T), one (C14708T), one (C28725T), and one (G29692T) in ORF1a, ORF1b, N, and non-coding regions, respectively; four of them were nonsynonymous. 2021 PloS one Result SARS_CoV_2 C10376T;C9286T;C14708T;C28725T;G29692T;T4346C 129;121;144;159;178;113 136;127;151;166;185;119 ORF1a;N 190;204 195;205 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. Additionally, the D614G variant of S65 had the T22020C mutation in the same region, and S66 had the C21789T mutation in the spike region; both of these mutations resulted in amino acid changes (153: Methionine to Threonine and 76: Threonine to Isoleucine) (Fig 4). 2021 PloS one Result SARS_CoV_2 T76I;C21789T;D614G;T22020C;M153T 227;100;18;47;194 254;107;23;54;222 S 124 129 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. All European type GR strains in the first wave had similar mutations at eight different sites: one in a non-coding region (C241T), two in ORF1a (C313T, C3037T), one in ORF1b (C14408T), one in S (A23403G), and three in N (G28881A, G28882A, G28883C); half were nonsynonymous. 2021 PloS one Result SARS_CoV_2 C3037T;G28882A;G28883C;A23403G;C14408T;C241T;C313T;G28881A 152;230;239;195;175;123;145;221 158;237;246;202;182;128;150;228 ORF1a;N;S 138;218;192 143;219;193 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. Four amino acid substitutions were found in Asian strain O: three (218: Arginine to Glycine, 2016: Threonine to Lysine, 3606: Leucine to Phenylalanine) were in ORF1a and one (13: Proline to Leucine) was in N. 2021 PloS one Result SARS_CoV_2 T2016K;L3606F;P13L;R218G 93;120;175;67 118;150;197;91 ORF1a;N 160;206 165;207 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. Four similar patterns of amino acid substitutions were found in all European strains from both the first and second waves: ORF1b had one (214: Proline to Leucine), spike had one (614: Aspartic acid to Glycine), and nucleocapsid had two (2020: Arginine to Lysine and 203: Glycine to Arginine). 2021 PloS one Result SARS_CoV_2 G203R;R2020K;P214L;D614G 266;237;138;179 290;261;161;208 N;S 215;164 227;169 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. Notably, all four European strains from the second wave shared four similar patterns of amino acid substitutions (1361: Serine to Proline and 3371: Proline to Serine in ORF1a, 314: Alanine to Valine in ORF1b, and 151: Proline to Lysine in nucleocapsid). 2021 PloS one Result SARS_CoV_2 P151K;A314V;P3371S;S1361P 213;176;142;114 235;198;165;137 N;ORF1a 239;169 251;174 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. Notably, all seven European strains shared a triple mutation at G28881A, G28882A, and G28883C in the N gene. 2021 PloS one Result SARS_CoV_2 G28881A;G28882A;G28883C 64;73;86 71;80;93 N 101 102 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. The D614G amino acid change was found in the spike region of European strain GR, and this amino acid change was accompanied by the silent mutation of C241T in a non-coding region, C313T and C3037T in ORF1a, the nonsynonymous mutation at C14408T (P214L) in ORF1b, and triple mutation of G28881A, G28882A, and G28883C resulting in amino acid changes (R202K and G203R) in N. 2021 PloS one Result SARS_CoV_2 C14408T;C241T;C3037T;C313T;D614G;G203R;G28881A;G28882A;G28883C;P214L;R202K 237;150;190;180;4;359;286;295;308;246;349 244;155;196;185;9;364;293;302;315;251;354 ORF1a;S;N 200;45;369 205;50;370 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. The D614G variants of European strain GR. 2021 PloS one Result SARS_CoV_2 D614G 4 9 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. A similar indirect effect on RDV susceptibility was recently identified for Ebola virus, where an F548S mutation, also in the fingers domain, was seen to confer low level resistance. 2021 Antiviral research Result SARS_CoV_2 F548S 98 103 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. A449V, with an occurrence of 0.57%, is in the fingers domain and could have an indirect impact on residues in the F-motif, including V557 and A558. 2021 Antiviral research Result SARS_CoV_2 A449V 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. Among the whole set of >90,000 analyzed SARS-CoV-2 human clinical isolates, nsp12 amino acid substitution F480L was detected in a single isolate sequence and V557A in a single independent isolate sequence. 2021 Antiviral research Result SARS_CoV_2 F480L;V557A 106;158 111;163 Nsp12 76 81 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. Both SARS-Cov-2 variants also each contained one prevalent substitution in Nsp13; K460R was observed in 51% of B.1.1.7 isolates and T588I was observed in 14% of B.1.351 isolates. 2021 Antiviral research Result SARS_CoV_2 K460R;T588I 82;132 87;137 Nsp13 75 80 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. Each of these substitutions except for Nsp12 P323L was observed in <0.5% of human clinical isolates (Table 3 ). 2021 Antiviral research Result SARS_CoV_2 P323L 45 50 Nsp12 39 44 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. Excluding P323L, no other substitutions were observed in 87% of SARS-CoV-2 clinical isolates in nsp12. 2021 Antiviral research Result SARS_CoV_2 P323L 10 15 Nsp12 96 101 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. In order to obtain reliable and interpretable data, we included only months with >=1000 clinical isolate sequences available and focused on amino acid substitutions with total frequency >=0.5% In the genes of the RNA replication complex, only the Nsp12 P323L substitution consistently increased in frequency in human clinical isolates over time. 2021 Antiviral research Result SARS_CoV_2 P323L 253 258 Nsp12 247 252 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. Nsp12 T739I was observed in 26.1%, Nsp13 I285V in 27.9%, and Nsp13 R392C in 10.5% of mink isolates. 2021 Antiviral research Result SARS_CoV_2 I285V;R392C;T739I 41;67;6 46;72;11 Nsp13;Nsp13;Nsp12 35;61;0 40;66;5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. Nsp13 substitutions P504L and Y541C decreased in frequency over time. 2021 Antiviral research Result SARS_CoV_2 P504L;Y541C 20;30 25;35 Nsp13 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. P323L, A97V and T141I are all solvent exposed residues which are > 25 A from the polymerase active site. 2021 Antiviral research Result SARS_CoV_2 A97V;T141I;P323L 7;16;0 11;21;5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. S861F was observed in another single independent isolate sequence. 2021 Antiviral research Result SARS_CoV_2 S861F 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. Similar to human clinical isolates, the most prevalent substitution was nsp12 P323L, which was observed in 89.5% of mink isolates. 2021 Antiviral research Result SARS_CoV_2 P323L 78 83 Nsp12 72 77 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. The most prevalent substitution in RNA replication complex was nsp12 P323L, which was observed in 100% of the B.1.1.7 isolates and the B.1.351 isolates analyzed. 2021 Antiviral research Result SARS_CoV_2 P323L 69 74 Nsp12 63 68 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. The most prevalent substitution in RNA replication complex was nsp12 P323L, which was observed in 75,892/92,334 (82%) clinical isolates from 103 of 109 countries. 2021 Antiviral research Result SARS_CoV_2 P323L 69 74 Nsp12 63 68 33551188 Fast and cost-effective screening for SARS-CoV-2 variants in a routine diagnostic setting. Using the N501Y assay, no signal could be detected during qPCR for 435 samples, indicative for wildtype N501. 2021 Dental materials Result SARS_CoV_2 N501Y 10 15 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. Among these sites, a subset of 11 early high-frequency sites (of which 8 were coding [ORF8 -L84S, ORF1a - V378I, ORF1a - L3606F, ORF1a - A3220V, ORF3a - G251V, ORF1a - L3606F, S - D614G, ORF1b - P314L]) enabled defining the phylogenetic clade structure of the viral sequences. 2021 Infection, genetics and evolution Result SARS_CoV_2 A3220V;D614G;G251V;L3606F;L3606F;P314L;V378I;L84S 137;180;153;121;168;195;106;92 143;185;158;127;174;200;111;96 ORF1a;ORF1a;ORF1a;ORF1a;ORF3a;ORF8;S 98;113;129;160;145;86;176 103;118;134;165;150;90;177 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. D614G mutation generates a novel neutrophil elastase cleavage site. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 0 5 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. The A2a clade with the highest frequency is defined by nucleotide changes at two sites that are in complete non-random association (linkage disequilibrium): D614G in the Spike glycoprotein and P314L in Orf1b polyprotein (also known as, RdRp:P323L). 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;P314L;P323L 157;193;241 162;198;246 S;RdRP 170;236 188;240 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. The non-synonymous D614G mutation is located between S1-RBD and S1/S2 junctions of the SARS-CoV-2 spike (S) protein. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;D614G 20;19 25;24 S;RBD;S 98;56;105 103;59;106 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Aa change L17I increased from 0.5% in epiweek 30 to 2.8% in epiweek 32, dropping its frequency in the last epiweeks. 2021 Viruses Result SARS_CoV_2 L17I 10 14 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Although the available N sequences differed across European countries and epiweeks, this same increase-decrease tendency was observed in Italy, Denmark, and Switzerland, whereas in other countries the R203K and G204R combination frequency increased over time (as in Netherlands, Spain, and Sweden), or only in the last available epiweeks with 10 sequences (as in Germany). 2021 Viruses Result SARS_CoV_2 G204R;R203K 211;201 216;206 N 23 24 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. As 92% of the North American N sequences belonged to the USA (Table S3), this regional curve probably describes what happened only in this country, where the R203K and G204R combination frequency reached 50% in epiweek 23, and then dropped to 20% in the following epiweeks, except for an isolated increase to 38% in epiweek 36. 2021 Viruses Result SARS_CoV_2 G204R;R203K 168;158 173;163 N 29 30 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Brazil showed the highest frequency of this combination (88.7%, Table S4), and in epiweeks 10-19 (those that met our criteria), the R203K and G204R combination raised >90% since epiweek 15, observing a drop in the next epiweeks with <10 sequences, with the absence of that combination in the nine N sequences available in epiweek 30. 2021 Viruses Result SARS_CoV_2 G204R;R203K 142;132 147;137 N 297 298 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Change A2S increased from 0.2% in epiweek 24 to 1.4% in epiweek 30, mainly due to Australian sequences, but no further increase was observed after this epiweek. 2021 Viruses Result SARS_CoV_2 A2S 7 10 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Change D209Y showed a localized increase in frequency (from 0.2% to 1.1%) in epiweek 26. 2021 Viruses Result SARS_CoV_2 D209Y 7 12 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. D3G first appeared in European sequences (Lithuania) in epiweek 5 and was not detected in other regions until epiweek 10 (North and South America) and 11 (Asia, Africa, and Oceania). 2021 Viruses Result SARS_CoV_2 D3G 0 3 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. D3G was the most frequent change in Africa (3.4%) and South America (2.8%) and T175M in Europe (1.6%). 2021 Viruses Result SARS_CoV_2 T175M;D3G 79;0 84;3 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. D614G was also the most frequent aa substitution in all regions as follows: Africa (94.7%), Asia (57.7%), Europe (82.9%), North America (84.3%), South America (93%), and Oceania (82%). 2021 Viruses Result SARS_CoV_2 D614G 0 5 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. D614G was found for the first time in epiweek 4 in Asia in two (1%) Chinese sequences, and in Oceania in one (11%) Australian sequence. 2021 Viruses Result SARS_CoV_2 D614G 0 5 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Finally, in South America, although some epiweeks did not meet our criteria for the time analysis, the R203K and G204R combination in N increased until epiweek 22, with great variations in frequency in the last epiweeks. 2021 Viruses Result SARS_CoV_2 G204R;R203K 113;103 118;108 N 134 135 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. G204R and R203K, both located in the SR-linker (Figure 1D), tended to appear simultaneously in N protein and were the most frequent aa changes in the following six geographic regions: Africa (55.7%), Asia, (26.8%), Europe (44.1%), North America (12%), South America (60.4%), and Oceania (65.9%). 2021 Viruses Result SARS_CoV_2 R203K;G204R 10;0 15;5 N 95 96 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Globally, we observed a significant change over time in the following six aa substitutions in the M protein: A2S, L17I, D209Y, H125Y, V23L, and V60L. 2021 Viruses Result SARS_CoV_2 A2S;D209Y;H125Y;L17I;V23L;V60L 109;120;127;114;134;144 112;125;132;118;138;148 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. H125Y increased during the last epiweeks available, from 0.4 in epiweek 31 to 1.3% in epiweek 34, mainly due to UK sequences, specifically English and Scottish. 2021 Viruses Result SARS_CoV_2 H125Y 0 5 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. However, when comparing data from the available epiweeks with more than 10 sequences, we also observed an increase in the frequency of the R203K and G204R combination in N sequences from Costa Rica (from 7.4% in epiweek 12 to 69.2% in epiweek 27) and Mexico (from 9.5% in epiweek 21 to 63.6% in epiweek 32); the global frequency of that combination in both countries was 28.1% and 19.3%, respectively (Table S4). 2021 Viruses Result SARS_CoV_2 G204R;R203K 149;139 154;144 N 170 171 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. In China, although the R203K and G204R combination total frequency was low, most sequences grouped up in the first epiweeks, where these changes were absent or extremely infrequent. 2021 Viruses Result SARS_CoV_2 G204R;R203K 33;23 38;28 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. In Europe, D614G appeared in epiweek 5 for the first time, mainly in Germany (41%), and in North America (31%), in three Canadian sequences. 2021 Viruses Result SARS_CoV_2 D614G 11 16 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. In Europe, the R203K and G204R combination steadily increased until 85% around epiweek 30, decreasing to 3.2% in epiweek 37, where most of the sequences belonged to Wales. 2021 Viruses Result SARS_CoV_2 G204R;R203K 25;15 30;20 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. In Oceania, the R203K and G204R combination frequency steadily increased from epiweek 20-31. 2021 Viruses Result SARS_CoV_2 G204R;R203K 26;16 31;21 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. In Singapore, the R203K and G204R combination was absent until epiweek 28, when it increased from 4% to 47% in epiweek 36. 2021 Viruses Result SARS_CoV_2 G204R;R203K 28;18 33;23 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. In the analysis by geographic region, the mutation rate was less than 1% in all regions except in Africa, where V5F (1.5%) was present in 36 sequences (35 from Egypt), 92% of them belonging to the last epiweeks with African sequences available (33 and 34). 2021 Viruses Result SARS_CoV_2 V5F 112 115 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. In the regional analysis, the most frequent N mutations were the already mentioned D103Y, S194L, and S197L in Europe (3.2%, 2.8%, and 2.3%, respectively), S194L in North America (4.3%); P13L and S194L in Asia (15% and 6.4%), and P13L and S197L in Oceania (5.7% and 4.8%, respectively). 2021 Viruses Result SARS_CoV_2 D103Y;P13L;P13L;S194L;S194L;S194L;S197L;S197L 83;186;229;90;155;195;101;238 88;190;233;95;160;200;106;243 N 44 45 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. In the regional analysis, V1176F aa change stood out in South America (18.2%, 286 sequences), with all sequences but one belonging to Brazil. 2021 Viruses Result SARS_CoV_2 V1176F 26 32 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. It was the case for S197L (1.7%, 1686 sequences, 56% from Spain), P13L (1.8%, 1782 sequences, 62% from India and Singapore and 21% from Australia), D103Y (1.9%, 1863 sequences, 89% from England), S194L (3.2%, 3194 sequences, 39% from England and Scotland, 29% from the USA, and 11% from India), and G204R (37%, 36,598 sequences) and R203K (37.3%, 36,876 sequences) with the highest global frequency. 2021 Viruses Result SARS_CoV_2 D103Y;G204R;P13L;R203K;S194L;S197L 148;299;66;333;196;20 153;304;70;338;201;25 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Lastly, V60L frequency increased around epiweeks 27 and 28 (1.6 and 1.2%) due to European sequences, specifically from England and Switzerland, decreasing later and rising again in epiweek 34 (1.4%), mainly due to sequences from Scotland and Switzerland. 2021 Viruses Result SARS_CoV_2 V60L 8 12 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Most Asian sequences in these epiweeks (>50% in epiweek 26 and 100% in epiweeks 27 and 31) were from Singapore and South Korea, where the R203K and G204R combination was infrequent, explaining the frequency drop in these epiweeks. 2021 Viruses Result SARS_CoV_2 G204R;R203K 148;138 153;143 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Most changes had a very low frequency (<=0.2%), except for D3G (0.7%, 724 sequences), and T175M (1%, 1026 sequences) (Figure 1C). 2021 Viruses Result SARS_CoV_2 D3G;T175M 59;90 62;95 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Most sequences with T9I, R69I, P71L, and L73F belonged to Europe. 2021 Viruses Result SARS_CoV_2 L73F;P71L;R69I;T9I 41;31;25;20 45;35;29;23 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Other frequent mutations not mentioned before were S202N in Asia and Africa (2.5% and 3.8%, respectively), I292T in South America (25%), Q384H in Africa (7%), and L230F in Oceania (2.7%). 2021 Viruses Result SARS_CoV_2 I292T;L230F;Q384H;S202N 107;163;137;51 112;168;142;56 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. S477N in the S protein was present in all the geographic regions, but mainly in Oceania (56.8%, 3851 Australian sequences), where its frequency rose from 6% (epiweek 20) to 100% (epiweek 31). 2021 Viruses Result SARS_CoV_2 S477N 0 5 S 13 14 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. S68F was present in all regions except in South America, and mainly in Europe (86%, 177 sequences), specifically England (68.9%) where its frequency raised from epiweek 12 (0.6%) to epiweek 19 (3%), decreasing to 0.2% in the last epiweek available. 2021 Viruses Result SARS_CoV_2 S68F 0 4 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. South Africa showed a steady increase in the R203K and G204R combination frequency ( 90% frequency in epiweeks 30-35), in the DRC the frequency varied largely between epiweeks, and in Egypt it was very infrequent, only present in 4% of the total sequences, explaining the drop of the regional rate (Table S4). 2021 Viruses Result SARS_CoV_2 G204R;R203K 55;45 60;50 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. T175M was detected for the first time in epiweek 9 in Europe (England and Netherlands), and later in Asia and South America (epiweek 10), North America and Oceania (epiweek 11) and, lastly, in Africa (epiweek 12). 2021 Viruses Result SARS_CoV_2 T175M 0 5 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. The G204R and R203K combination was first detected in epiweek 5 in three German sequences, then in epiweek 8 in Nigeria, epiweek 9 in Mexico and the USA, and epiweek 10 in Asia, Oceania, and South America. 2021 Viruses Result SARS_CoV_2 G204R;R203K 4;14 9;19 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. The global rate of the G204R and R203K combination rose from 23% in epiweek 10 to 81% in epiweek 30, dropping to 16% in epiweek 37. 2021 Viruses Result SARS_CoV_2 G204R;R203K 23;33 28;38 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. The most frequent aa change was D614G (81.5%, 82,183 sequences), located in S1 (Figure 1A), followed by S477N (4.1%), located in the receptor binding motif of the receptor binding domain (Figure 1A). 2021 Viruses Result SARS_CoV_2 D614G;S477N 32;104 37;109 RBD 163 186 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. The most prevalent aa change found in E was S68F, present in 221 (0.2%) global sequences, followed by L73F (122 sequences), R69I (92), P71L (68), T9I (56), and V62F (52), all with a frequency of 0.1%. 2021 Viruses Result SARS_CoV_2 L73F;P71L;R69I;S68F;T9I;V62F 102;135;124;44;146;160 106;139;128;48;149;164 E 38 39 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. The number and frequency of sequences carrying the R203K and G204R combination in N protein by epiweek in each geographic region and country are described in Table S4, the aa combinations for positions 203 and 204 in each region and epiweek used for the scatter plots are available in Table S5. 2021 Viruses Result SARS_CoV_2 G204R;R203K 61;51 66;56 N 82 83 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. The regional presence of the R203K and G204R combination changes in N varied greatly between countries (Table S4). 2021 Viruses Result SARS_CoV_2 G204R;R203K 39;29 44;34 N 68 69 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. To analyze if these regional fluctuations were related to the country of origin of the sequences or the uneven distribution of the sequences from each country along the epiweeks, the statistical average of the R203K and G204R combination was analyzed between epiweeks and countries. 2021 Viruses Result SARS_CoV_2 G204R;R203K 220;210 225;215 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. V23L increased from 0.4% (epiweek 19) to 1.4% (epiweek 22). 2021 Viruses Result SARS_CoV_2 V23L 0 4 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. V62F was present in 70% of sequences from the USA in North America, where frequency increased in epiweeks 22 and 23 but dropped later. 2021 Viruses Result SARS_CoV_2 V62F 0 4 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Because a large body of literature has shown that lentiviral compatibility of a variety of viral envelopes is determined by their cytoplasmic tail (CT) domains, we compared the sequences of this domain (as well as the transmembrane (TM) domain) in S proteins and found that SARS2-S has one (alanine-to-cysteine at position 1247) and two (valine-to-isoleucine at position 1216 and leucine-to-methionine at position 1233) amino acid differences in the CT and TM domains, respectively. 2021 Nature communications Result SARS_CoV_2 L1233M;A1247C;V1216I 380;291;338 418;327;375 S;S 248;280 249;281 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. D614G mutation confers structural flexibility to S protein. 2021 Nature communications Result SARS_CoV_2 D614G 0 5 S 49 50 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. D614G protein binds ACE2 more efficiently than WT protein. 2021 Nature communications Result SARS_CoV_2 D614G 0 5 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. D614G variant remains susceptible to neutralization by patient sera against prototypic viruses. 2021 Nature communications Result SARS_CoV_2 D614G 0 5 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Given that the D614G S protein is biologically and structurally different from the WT protein, we hypothesized that this mutation might affect the antigenicity of the S protein. 2021 Nature communications Result SARS_CoV_2 D614G 15 20 S 167 168 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. However, our preliminary data did not clearly show the difference in ACE2-binding between WT and D614G in an immunoprecipitation-Western blot assay, probably due to practical limitations of its assay sensitivity. 2021 Nature communications Result SARS_CoV_2 D614G 97 102 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Regardless of serum concentration, the anti-SARS-CoV-2 patient sera but not the control serum efficiently neutralized both viruses pseudotyped with the SARS2-S WT and D614G mutant proteins. 2021 Nature communications Result SARS_CoV_2 D614G 167 172 S 158 159 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Remarkably, the D614G mutant displayed the highest level of entry activity among naturally mutated S proteins tested here (~3.5-fold higher than that of the WT protein). 2021 Nature communications Result SARS_CoV_2 D614G 16 21 S 99 100 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. SARS2-S D614G variant displays highest entry efficiency among natural S variants. 2021 Nature communications Result SARS_CoV_2 D614G 8 13 S;S 6;70 7;71 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Similar difference in cell entry between WT and D614G S-pseudoviruses was clearly observed in human small airway epithelial cells. 2021 Nature communications Result SARS_CoV_2 D614G 48 53 S 54 55 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. The D614G S protein trimer bound to the ACE2 dimer with comparable association kinetics compared with the WT S trimer at all temperatures tested. 2021 Nature communications Result SARS_CoV_2 D614G 4 9 S;S 10;109 11;110 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. The Fc-tagged ACE2 dimer was immobilized to anti-Fc biosensors, which were dipped into wells containing different concentrations of a soluble ectodomain of either WT or D614G S protein trimer, and their ACE2-binding affinity was evaluated. 2021 Nature communications Result SARS_CoV_2 D614G 169 174 S 175 176 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. These naturally occurring S mutations resulted in reduced (G476S), equal (V483A), or enhanced (D614G, V367F, and H49Y) cell entry. 2021 Nature communications Result SARS_CoV_2 H49Y;V367F;D614G;G476S;V483A 113;102;95;59;74 117;107;100;64;79 S 26 27 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. These results are particularly important because the D614G mutation defines the clade A2a (also called G) that is rapidly spreading worldwide, accounting for the great majority of isolates. 2021 Nature communications Result SARS_CoV_2 D614G 53 58 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. These results indicate that the D614G mutation in the SARS2-S protein maintains neutralization sensitivity to the anti-SARS2-S antibodies, i.e., its antigenicity per se. 2021 Nature communications Result SARS_CoV_2 D614G 32 37 S;S 60;125 61;126 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Thus, we created a SARS2-S C1247A mutant and a chimeric SARS2-S harboring the TM/CT domains of SARS-S. 2021 Nature communications Result SARS_CoV_2 C1247A 27 33 S;S;S 25;62;100 26;63;101 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. To examine this possibility, we performed neutralization assays to compare the neutralizing sensitivity of the WT and D614G S proteins to anti-SARS-CoV-2 sera. 2021 Nature communications Result SARS_CoV_2 D614G 118 123 S 124 125 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. To test whether D614G mutation could alter binding affinity for ACE2, we first performed in vitro binding assays using cell lysates expressing ACE2 and SARS2-S proteins. 2021 Nature communications Result SARS_CoV_2 D614G 16 21 S 158 159 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. We created plasmids expressing five different S variants that were initially identified in China (H49Y), Europe (V367F and D614G), and the United States (G476S and V483A). 2021 Nature communications Result SARS_CoV_2 D614G;V483A;G476S;H49Y;V367F 123;164;154;98;113 128;169;159;102;118 S 46 47 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. We therefore conclude that the D614G mutation of SARS2-S protein increases binding affinity for the ACE2 receptor, probably resulting from a mutation-induced structural flexibility. 2021 Nature communications Result SARS_CoV_2 D614G 31 36 S 55 56 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. Among these, Spike_D614G and NSP12_P323L were present in all the 22 analyzed sequences, followed by N_G204R and N_R203K occurring in 9 of the 22 sequences (Table 1 ). 2021 Biosafety and health Result SARS_CoV_2 D614G;G204R;P323L;R203K 19;102;35;114 24;107;40;119 S;Nsp12 13;29 18;34 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. Further, the mutations N R203K and N G204R have occurred, till now, 8,744 and 8,715 times respectively in 65 countries (https://www.gisaid.org/). 2021 Biosafety and health Result SARS_CoV_2 G204R;R203K 37;25 42;30 N;N 23;35 24;36 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. The mutation Spike M1237I, found just once in our sequences, had occurred earlier, 11 times worldwide in six countries. 2021 Biosafety and health Result SARS_CoV_2 M1237I 19 25 S 13 18 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. The mutations NSP10_R134S, NSP15_D335N, NSP16_I169L, NSP3_L431H, NSP3_P1292L and Spike_V6F were highlighted once in Moroccan sequences, with no record in other sequences around the world. 2021 Biosafety and health Result SARS_CoV_2 D335N;I169L;L431H;P1292L;R134S 33;46;58;70;20 38;51;63;76;25 S;Nsp3;Nsp3 81;53;65 86;57;69 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. The mutations NSP12_M196I, NSP3_A1819V, M_L13F, NSP14_D324A, NSP14_T75I and NSP5_V125I were found once in our sequences and were reported in only one sequence in the GISAID database. 2021 Biosafety and health Result SARS_CoV_2 A1819V;D324A;L13F;M196I;T75I;V125I 32;54;42;20;67;81 38;59;46;25;71;86 Nsp12;Nsp3;Nsp5 14;27;76 19;31;80 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. Therefore, NSP12_M196I, NSP3_A1819V, M_L13F, NSP14_D324A, NSP14_T75I and NSP5_V125I occurred once in India (hCoV-19/India/GBRC46/2020), Poland (hCoV-19/Poland/PL_P15/2020), Switzerland/100144/2020; United Kingdom / England EPI_ISL_423899, Australia, EPI_ISL_426742 and South America EPI_ISL_445334. 2021 Biosafety and health Result SARS_CoV_2 A1819V;D324A;L13F;M196I;T75I;V125I 29;51;39;17;64;78 35;56;43;22;68;83 Nsp12;Nsp3;Nsp5 11;24;73 16;28;77 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. Until June 7, 2020, the mutations Spike_D614G and NSP12_P323L had occurred 23,612 and 23,543 times respectively throughout 75 countries (https://www.gisaid.org/). 2021 Biosafety and health Result SARS_CoV_2 D614G;P323L 40;56 45;61 S;Nsp12 34;50 39;55 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. From these computations, it seems that the N501Y does not induce a large conformational change. 2021 International journal of molecular sciences Result SARS_CoV_2 N501Y 43 48 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. If we then consider the three residue replacements of interest here (N501Y, K417N, E484K), we observe that N501 (UK and South African strains) is solvent exposed on the free Spike protein and becomes essentially buried upon ACE2 binding. 2021 International journal of molecular sciences Result SARS_CoV_2 E484K;K417N;N501Y 83;76;69 88;81;74 S 174 179 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. It was found to be more favorable for the UK strain (N501Y) as compared to the initial structure (i.e., when N is at position 501). 2021 International journal of molecular sciences Result SARS_CoV_2 N501Y 53 58 N 109 110 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. The coarse-grained simulations were performed on the initial RBD input structure, on the N501Y variant (UK strain) and on the K417N, E484K, N501Y variants (South African strain). 2021 International journal of molecular sciences Result SARS_CoV_2 E484K;K417N;N501Y;N501Y 133;126;89;140 138;131;94;145 RBD 61 64 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. The combined K417N, E484K, N501Y substitutions also do not seem to destabilize the RBD domain of the Spike protein as for all the ten simulated structures; we obtained G values around -0.5 or -0.6 kcal/mol. 2021 International journal of molecular sciences Result SARS_CoV_2 E484K;K417N;N501Y 20;13;27 25;18;32 S;RBD 101;83 106;86 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. The N501Y (UK) was found to be slightly destabilizing (depending the input simulated structures and methods, around -0.2 to -0.3 kcal/mol). 2021 International journal of molecular sciences Result SARS_CoV_2 N501Y 4 9 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. These structural data further suggest that the N501Y variant can still be neutralized efficiently by an antibody, indicating that most likely, vaccines should be efficient against this variant. 2021 International journal of molecular sciences Result SARS_CoV_2 N501Y 47 52 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. This is somewhat supported by a recent cryo-EM structure of the N501Y mutant co-crystalized with a potent neutralizing antibody. 2021 International journal of molecular sciences Result SARS_CoV_2 N501Y 64 69 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. Yet, the predicted global interaction score between the Spike and ACE2 proteins seems less favorable for the South African strain (K417N, E484K, N501Y) than for the original input structure or for the UK strain. 2021 International journal of molecular sciences Result SARS_CoV_2 E484K;N501Y;K417N 138;145;131 143;150;136 S 56 61 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. Using the trans-complementation assay, we have shown that introduction of just the Spike D614G point mutation increases infection using intact (replication-competent) SARS-CoV-2 virus. 2021 eLife Result SARS_CoV_2 D614G 89 94 S 83 88 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. A second cluster carrying the S477N substitution that included genomes from EU (France, Netherlands, Norway, Belgium and Denmark; n = 15, 78.95%), AF (Tunisia; n = 2, 10.52), AS (Hong Kong; n = 1, 5.26%) and OC (New Zealand; n = 1, 5.26%) (Figure 6A) was detected during September 2020 and November 2020. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 S477N 30 35 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. An I120F substitution was also present in high frequency in OC (43.2%, n = 155) (Table 1). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 I120F 3 8 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. Meanwhile, R203K presented a dN/dS negative value, but again, this was not significant (Table 1). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 R203K 11 16 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. Positive selection was seen in T85S (dN/dS = 5.89; p < 0.01) and P323L (dN/dS = 7.49; p < 0.01), while I120F, D614G, Q57H and G204R had positive values of dN/dS, but these were not significant. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D614G;G204R;I120F;P323L;Q57H;T85S 110;126;103;65;117;31 115;131;108;70;121;35 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. These seven frequencies varied by region: T85I and Q57H (nsp2) were the most frequent in US; I120F (nsp2) in OC; and R203K and G204R (N protein) in LA, AF and OC; P323L (nsp12) and D614G (S protein) were highly frequent in all regions. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D614G;G204R;I120F;P323L;Q57H;R203K;T85I 181;127;93;163;51;117;42 186;132;98;168;55;122;46 Nsp12;Nsp2;Nsp2;N;S 170;57;100;134;188 175;61;104;135;189 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. We focused on the dN substitutions located in the S protein (D614G), nsp12 (P323L) and N protein (R203K and G204R) to analyze associations between viral variants and disease severity. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 G204R;D614G;P323L;R203K 108;61;76;98 113;66;81;103 Nsp12;N;S 69;87;50 74;88;51 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. We found a dN substitution in the S gene (G22992A > S477N) with a dN/dS value of 1.92 (p = 0.485) and a frequency of 42.6% (n = 153) in the virus population from the OC region. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 S477N;G22992A 52;42 57;49 S 34 35 33579701 Insights into neutralizing antibody responses in individuals exposed to SARS-CoV-2 in Chile. Although it was not possible to determine which variant of the virus infected these patients, our data indicate that the D614G mutation not only confers increased infectivity to the pseudotype but also is able to affect the susceptibility to NAbs present in plasma samples from individuals exposed to SARS-CoV-2. 2021 Science advances Result SARS_CoV_2 D614G 121 126 33579701 Insights into neutralizing antibody responses in individuals exposed to SARS-CoV-2 in Chile. Considering that 83% of SARS-CoV-2 sequences obtained from Chile until 24 November 2020 correspond to the D614G variant. 2021 Science advances Result SARS_CoV_2 D614G 106 111 33579701 Insights into neutralizing antibody responses in individuals exposed to SARS-CoV-2 in Chile. Impact of the D614G variant of the spike protein on the susceptibility to NAbs. 2021 Science advances Result SARS_CoV_2 D614G 14 19 S 35 40 33579701 Insights into neutralizing antibody responses in individuals exposed to SARS-CoV-2 in Chile. It has been widely reported that the D614G variant of S protein confers increased infectivity when assessed in different pseudotyped viruses. 2021 Science advances Result SARS_CoV_2 D614G 37 42 S 54 55 33579701 Insights into neutralizing antibody responses in individuals exposed to SARS-CoV-2 in Chile. This negative effect of M and E proteins on infectivity was not exclusive for the SDelta19 version of the spike protein as it was also observed with full-length S carrying the reference sequence or the D614G mutation. 2021 Science advances Result SARS_CoV_2 D614G 202 207 S;E;S 106;30;161 111;31;162 33579701 Insights into neutralizing antibody responses in individuals exposed to SARS-CoV-2 in Chile. We identified that 31.6% of the samples (12 of 38) presented a significant decrease in their ability to neutralize the pseudotype carrying the D614G variant and 5.3% (2 of 38) of the samples contained NAbs targeting more potently the pseudovirus containing this highly prevalent spike variant. 2021 Science advances Result SARS_CoV_2 D614G 143 148 S 279 284 33580132 Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada. One heterozygous variant in the orf1ab gene of S11 (C9994A) was confirmed on both sequencing platforms, with no consistent evidence of heterozygous sequences in any of the other samples (Supplementary Table 2). 2021 Scientific reports Result SARS_CoV_2 C9994A 52 58 ORF1ab 32 38 33580132 Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada. There are two missense variants (A23403G and G25217T) and three synonymous variants (C24382T, T24982C, C25357T) in the gene encoding the S protein. 2021 Scientific reports Result SARS_CoV_2 C25357T;G25217T;T24982C;A23403G;C24382T 103;45;94;33;85 110;52;101;40;92 S 137 138 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. Besides, there are two important nonsynonymous mutations C1059T (ORF1a), G25563T (ORF3a). 2021 Briefings in bioinformatics Result SARS_CoV_2 C1059T;G25563T 57;73 63;80 ORF1a;ORF3a 65;82 70;87 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. By comparison, C28144T could reduce virus virulence a little, since the DeltaDeltaG values for the mutation is near zero. 2021 Briefings in bioinformatics Result SARS_CoV_2 C28144T 15 22 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. Here we got DeltaDeltaG values with -0.67, -0.83, -0.93, -0.9 for C1059T, C14408T, A23403G and G25563T, respectively. 2021 Briefings in bioinformatics Result SARS_CoV_2 A23403G;C1059T;C14408T;G25563T 83;66;74;95 90;72;81;102 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. In Table 4, DeltaG and Kd in SARS-CoV-2 spike is decreased by the A23403G, which means that the mutation in SARS-CoV-2 increases the spike-ACE2 interaction, and finally leads to the enhancement of its infectivity. 2021 Briefings in bioinformatics Result SARS_CoV_2 A23403G 66 73 S;S 40;133 45;138 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. In total, we detected five dominant mutations T8782C, C28144T, C3037T, C14408T and A23403G, the origin nucleotides of which were almost substituted by the mutation in the latest virus strains. 2021 Briefings in bioinformatics Result SARS_CoV_2 A23403G;C14408T;C28144T;C3037T 83;71;54;63 90;78;61;69 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. Since spike-ACE2 interaction can affect virus infectivity, we analyzed the alteration of the interaction caused by spike-ACE2 binding affinity due to A23403G using PPA-Pred. 2021 Briefings in bioinformatics Result SARS_CoV_2 A23403G 150 157 S;S 6;115 11;120 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. Three dominant nonsynonymous mutations C28144T, C14408T and A23403G and two potential dominant mutations C1059T and G25563T were evaluated by bioinformatics tools for investigating the functional alterations caused by these mutations. 2021 Briefings in bioinformatics Result SARS_CoV_2 A23403G;C1059T;C14408T;C28144T;G25563T 60;105;48;39;116 67;111;55;46;123 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. Thus, C1059T and G25563T could be potential dominant mutations. 2021 Briefings in bioinformatics Result SARS_CoV_2 C1059T;G25563T 6;17 12;24 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. Other than that EPI_ISL_514753, isolated from Iran, also have goof nuber of unique mutations like NSP1_W161L, NSP2_E309A, NSP2_C136S, NSP3_R1341L, NSP3_K232T, NSP3_N1778S, NSP3_E229A, NSP3_C296R, NSP6_H64 N, Spike_D808G, Spike_H146R, Spike_N1192S. 2021 Microbial pathogenesis Result SARS_CoV_2 C136S;C296R;D808G;E229A;E309A;H146R;K232T;N1192S;N1778S;R1341L;W161L 127;189;214;177;115;227;152;240;164;139;103 132;194;219;182;120;232;157;246;170;145;108 S;S;S;Nsp2;Nsp2;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp6;N 208;221;234;110;122;134;147;159;172;184;196;205 213;226;239;114;126;138;151;163;176;188;200;206 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. The most common, high impact variants were 10818delTinsG, 2772delCinsC, 14159delCinsC and 2789delAinsA. 2021 Microbial pathogenesis Result SARS_CoV_2 10818delTinsG;2789delAinsA 43;90 56;102 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. These mutations include NSP1_W161L, NSP1_V116A, NSP1_V106G, NSP1_V54A, NSP2_I393T, NSP2_N92S, NSP2_T153L, NSP2_L506S, NSP2_E309A, NSP2_A159D, NSP2_C136S, NSP3_K1838R, NSP3_R1341L, NSP3_K1596R, NSP3_R1345L, NSP3_A886D, NSP3_M1865T, NSP3_I468T, NSP3_K140Q, NSP3_A1279D, NSP3_A1105G, NSP3_G1389D, NSP3_N1778S, NSP3_L781S, NSP3_G1944V, NSP3_L1523H, NSP3_K1715R, NSP3_C296R, NSP3_R558P, NSP3_V1673D, NSP3_E378V, NSP3_S674Y, NSP3_S721 N, NSP4_P274L, NSP4_L321P, NSP4_A48D, NSP4_L243P, NSP4_L329H, NSP4_L176Q, NSP4_Q488L, NSP4_P168Q, NSP5_G174V, NSP5_E166V, NSP5_N84S, NSP5_S62Y, NSP5_P9L, NSP5_T111 N, NSP5_P52L, NSP6_C221Y, NSP6_A119G, NSP6_W140L, NSP6_S53Y, NSP6_C68Y, NSP6_F70Y, NSP6_F184S, NSP6_H64 N, NSP6_G188D, NSP6_V101G, NSP6_G48D, NSP6_F220S, NSP6_P87L, NSP7_L13S, NSP8_D134E, NSP9_P57H, NSP10_V119A, NSP10_E135A, NSP10_R134H, NSP11_Q5P, NSP12_E144D, NSP13_D160E, Spike_G1246A, Spike_R1185H, Spike_L368P, Spike_S974P, Spike_G268D, Spike_R190S, Spike_A411D, Spike_G798A, Spike_A672D, Spike_V1230E, Spike_Q774R, Spike_H146R, Spike_P337R, Spike_Q607L, E_I33T, M_P59T, M_K14E, NS7a_F114I, NS8_V62 M, N_Q390L, N_P20H, N_R10Q, N_R149L. 2021 Microbial pathogenesis Result SARS_CoV_2 A1105G;A119G;A1279D;A159D;A411D;A48D;A672D;A886D;C136S;C221Y;C296R;C68Y;D134E;D160E;E135A;E144D;E166V;E309A;E378V;F114I;F184S;F220S;F70Y;G1246A;G1389D;G174V;G188D;G1944V;G268D;G48D;G798A;H146R;I33T;I393T;I468T;K140Q;K14E;K1596R;K1715R;K1838R;L13S;L1523H;L176Q;L243P;L321P;L329H;L368P;L506S;L781S;M1865T;N1778S;N84S;N92S;P168Q;P20H;P274L;P337R;P52L;P57H;P59T;P87L;Q390L;Q488L;Q607L;Q774R;R10Q;R1185H;R1341L;R1345L;R134H;R149L;R190S;R558P;S53Y;S62Y;S674Y;S974P;T153L;V101G;V106G;V116A;V119A;V1230E;V1673D;V54A;W140L;W161L 273;624;260;135;954;461;980;211;147;612;363;659;774;861;811;848;544;123;400;1082;681;740;670;874;286;532;705;324;928;729;967;1020;1055;76;236;248;1071;185;350;159;763;337;496;472;449;484;902;111;312;223;299;556;88;520;1111;437;1033;601;786;1063;752;1102;508;1046;1007;1119;888;172;198;824;1127;941;375;648;567;412;915;99;717;53;41;798;993;387;65;636;29 279;629;266;140;959;465;985;216;152;617;368;663;779;866;816;853;549;128;405;1087;686;745;674;880;292;537;710;330;933;733;972;1025;1059;81;241;253;1075;191;356;165;767;343;501;477;454;489;907;116;317;229;305;560;92;525;1115;442;1038;605;790;1067;756;1107;513;1051;1012;1123;894;178;204;829;1132;946;380;652;571;417;920;104;722;58;46;803;999;393;69;641;34 S;S;S;S;S;S;S;S;S;S;S;S;S;S;Nsp13;Nsp12;Nsp2;Nsp2;Nsp2;Nsp2;Nsp2;Nsp2;Nsp2;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp3;Nsp4;Nsp4;Nsp4;Nsp4;Nsp4;Nsp4;Nsp4;Nsp4;Nsp7;Nsp8;Nsp5;Nsp5;Nsp5;Nsp5;Nsp5;Nsp5;Nsp5;Nsp6;Nsp6;Nsp6;Nsp6;Nsp6;Nsp6;Nsp6;Nsp6;Nsp6;Nsp6;Nsp6;Nsp6;Nsp6;N;N;N 868;882;896;909;922;935;948;961;974;987;1001;1014;1027;1040;855;842;71;83;94;106;118;130;142;154;167;180;193;206;218;231;243;255;268;281;294;307;319;332;345;358;370;382;395;407;419;432;444;456;467;479;491;503;515;758;769;527;539;551;562;573;583;596;607;619;631;643;654;665;676;688;700;712;724;735;747;429;593;697 873;887;901;914;927;940;953;966;979;992;1006;1019;1032;1045;860;847;75;87;98;110;122;134;146;158;171;184;197;210;222;235;247;259;272;285;298;311;323;336;349;362;374;386;399;411;423;436;448;460;471;483;495;507;519;762;773;531;543;555;566;577;587;600;611;623;635;647;658;669;680;692;704;716;728;739;751;430;594;698 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. 2 still indicates that 1059C>T-(T85I) is an infectivity-strengthening mutation, which may mainly benefit from the co-mutation with other infectivity-strengthening mutations, such as 23403A>G-(D614G) and 25563G>T-(Q57H). 2021 Communications biology Result SARS_CoV_2 C1059T;A23403G;G25563T;D614G;Q57H;T85I 23;182;203;192;213;32 30;190;211;197;217;36 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. 3c, indicating the mutation of T85I on the NSP2 does not change the flexibility of NSP2 too much. 2021 Communications biology Result SARS_CoV_2 T85I 31 35 Nsp2;Nsp2 43;83 47;87 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. A higher prevalence of D614G in the east coast of the US was reported. 2021 Communications biology Result SARS_CoV_2 D614G 23 28 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Additionally, an interesting finding is that the mutations occurred at the same residue position such as A348S and A348T, P384L and P384S have similar binding free energy changes. 2021 Communications biology Result SARS_CoV_2 A348S;A348T;P384L;P384S 105;115;122;132 110;120;127;137 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Additionally, mutation 1059C>T-(T85I) always occurs together with mutation 25563G>T-(Q57H). 2021 Communications biology Result SARS_CoV_2 C1059T;G25563T;Q57H;T85I 23;75;85;32 30;83;89;36 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Additionally, these two high-frequency mutations S24L and L84S mutate reversibly. 2021 Communications biology Result SARS_CoV_2 L84S;S24L 58;49 62;53 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Although 28881G>A-(R203K), 28882G>A-(R203K), and 28883G>C-(G204R) have their frequencies being higher than 1000 in the United States, no more than 12% of these three mutations are prevalent in the US. 2021 Communications biology Result SARS_CoV_2 G28881A;G28882A;G28883C;G204R;R203K;R203K 9;27;49;59;19;37 17;35;57;64;24;42 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Although A348T has relatively low frequencies due to the limited number of genome samples, their high binding free energy changes may lead to a more contagious SARS-CoV-2 substrain. 2021 Communications biology Result SARS_CoV_2 A348T 9 14 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Although away from the RBM, the relatively high-frequency and positive binding free energy changes of V367F, R403K, and A411S indicate that more attention should be paid to them in the future. 2021 Communications biology Result SARS_CoV_2 A411S;R403K;V367F 120;109;102 125;114;107 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Although mutatin A475V on the RBM has a negative binding free energy change with a relatively high frequency (5) on the RBM, the much higher frequencies of two mutations G476S (7) and V483A (31) with positive binding free energy change suggests that the mutations in Cluster C may strengthen the infectivity of SARS-CoV-2 in general. 2021 Communications biology Result SARS_CoV_2 A475V;G476S;V483A 17;170;184 22;175;189 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Although N354K has relatively high binding free energy change, the frequency is low. 2021 Communications biology Result SARS_CoV_2 N354K 9 14 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Although P323L mutates the residue of proline (P) to leucine (L), these two residues are both non-polar and aliphatic, indicating P323L may not affect the functionality of NSP12. 2021 Communications biology Result SARS_CoV_2 P323L;P323L 9;130 14;135 Nsp12 172 177 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Although the negative value reveals that T85I may destabilize the structure of NSP2, this small change is negligible. 2021 Communications biology Result SARS_CoV_2 T85I 41 45 Nsp2 79 83 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Although the number of single mutations with positive binding free energy changes is less than that with negative binding free energy changes, the high frequency of K444N on RBM enhances the infectivity of SARS-CoV-2. 2021 Communications biology Result SARS_CoV_2 K444N 165 170 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Amino acids near position 614 are very conservative, indicating that D614G mutation will play an important role in the functions of the S protein of SARS-CoV-2. 2021 Communications biology Result SARS_CoV_2 D614G 69 74 S 136 137 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Among 1176 samples having 27964C>T-(S24L) mutation, 251 isolates have gender labels (female: 147, male: 104). 2021 Communications biology Result SARS_CoV_2 C27964T;S24L 26;36 34;40 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Among 12,754 complete genome sequences, 5918 are connected to P323L. 2021 Communications biology Result SARS_CoV_2 P323L 62 67 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Among them, 3 mutations are synonymous ones (i.e., 3037C>T-(F106F), 8782C>T-(S76S), and 18060C>T-(L7L)) and 11 mutations are the missense mutations (i.e., 1059C>T-(T85I), 14408C>T-(P323L), 23403A>G-(D614G), 25563G>T-(Q57H), 28144T>C-(L84S), 17858A>G-(Y541C), 17747C>T-(P504L), 27964C>T-(S24L), 28881G>A-(R203K), 28882G>A-(R203K), and 28883G>C-(G204R)). 2021 Communications biology Result SARS_CoV_2 C1059T;C14408T;C17747T;A17858G;C18060T;A23403G;G25563T;C27964T;T28144C;G28881A;G28882A;G28883C;C3037T;C8782T;D614G;F106F;G204R;L7L;L84S;P323L;P504L;Q57H;R203K;R203K;S24L;S76S;T85I;Y541C 155;171;259;241;88;189;207;277;224;294;312;334;51;68;199;60;344;98;234;181;269;217;304;322;287;77;164;251 162;179;267;249;96;197;215;285;232;302;320;342;58;75;204;65;349;101;238;186;274;221;309;327;291;81;168;256 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Among them, 7079 variants have the [25563G>T-(Q57H), 23403A>G-(D614G)] co-mutations. 2021 Communications biology Result SARS_CoV_2 A23403G;D614G;Q57H;G25563T 53;63;46;36 61;68;50;44 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. And 2481 samples do not have the 27964C>T-(S24L) mutation (female: 1201, male: 1280). 2021 Communications biology Result SARS_CoV_2 C27964T;S24L 33;43 41;47 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. As of 11 September 2020, more than half of mutation 1059C>T-(T85I) counts found worldwide are from the United States. 2021 Communications biology Result SARS_CoV_2 C1059T;T85I 52;61 59;65 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. As reported in Deng et al., 17858A>G-(Y541C) and 17747C>T-(P504L) occurred among Grand princess strains and some WA state strains (aka WA1 lineage). 2021 Communications biology Result SARS_CoV_2 C17747T;A17858G;P504L;Y541C 49;28;59;38 57;36;64;43 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Based on the function of ORF8 that involved in the immune response, we deduce that L84S may be one of the factors that disfavor SARS-CoV-2 and favor the host immune surveillance to decrease the viral load in the human cells, which provides an explanation that the ratio of L84S in. 2021 Communications biology Result SARS_CoV_2 L84S;L84S 83;273 87;277 ORF8 25 29 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Based on the protein-specific analysis mentioned above, we deduce that mutations Y541C and P504L prevent SARS-CoV-2 from efficiently interacting with host interferon signaling molecules and impede the NSP13 from efficacious participation in the replication/transcription process. 2021 Communications biology Result SARS_CoV_2 P504L;Y541C 91;81 96;86 Nsp13 201 206 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Due to the small number of sequence data, we can say that the ratio of L84S has a decreasing tendency. 2021 Communications biology Result SARS_CoV_2 L84S 71 75 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Figure S10b in the Supplementary Information shows that the ORF8 becomes slightly less rigidity after both L84S and S24L mutations. 2021 Communications biology Result SARS_CoV_2 L84S;S24L 107;116 111;120 ORF8 60 64 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Finally, mutation 27964C>T-(S24L) has an unusual behavior. 2021 Communications biology Result SARS_CoV_2 C27964T;S24L 18;28 26;32 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. First, as shown in Table 2, mutations 14408C>T-(P323L) and 23403A>G-(D614G) appear concurrently and thus have an identical trajectory as shown in. 2021 Communications biology Result SARS_CoV_2 C14408T;A23403G;D614G;P323L 38;59;69;48 46;67;74;53 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. From Table 1, one can see that mutation D614G was initially detected in China on 24 January 2020. 2021 Communications biology Result SARS_CoV_2 D614G 40 45 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. From Table 2, we can see that 14408C>T-(P323L) always shows up with 1059C>T-(T85I), 23403A>G-(D614G), 25563G>T-(Q57H), and 27964C>T-(S24L) simultaneously. 2021 Communications biology Result SARS_CoV_2 C1059T;C14408T;A23403G;G25563T;C27964T;D614G;P323L;Q57H;S24L;T85I 68;30;84;102;123;94;40;112;133;77 75;38;92;110;131;99;45;116;137;81 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. From Table 2, we can see that 7106 sequences have 25563G>T-(Q57H) mutation on ORF3a. 2021 Communications biology Result SARS_CoV_2 G25563T;Q57H 50;60 58;64 ORF3a 78 83 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Here, the Fisher's exact test is applied to verify our deduction that 27964C>T-(S24L) is a female-dominated mutation. 2021 Communications biology Result SARS_CoV_2 C27964T;S24L 70;80 78;84 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. However, a more likely reason is that P323L is a co-mutation of D614G, suggesting that mutation P323L may be enhanced by mutation D614G. 2021 Communications biology Result SARS_CoV_2 D614G;D614G;P323L;P323L 64;130;38;96 69;135;43;101 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. However, its trajectory became identical to those of its co-mutations 17747C>T-(P504L) and 17858A>G-(Y541C) after 20 February 2020. 2021 Communications biology Result SARS_CoV_2 C17747T;A17858G;P504L;Y541C 70;91;80;101 78;99;85;106 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. However, since the infectivity-strengthening D614G mutation is associated with all clusters and essentially all the US genome isolates, it may be reasonable to say all of the US SARS-CoV-2 substrains become more infectious compared with the original genome collected on 24 December 2019 in China. 2021 Communications biology Result SARS_CoV_2 D614G 45 50 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. However, the Q57H mutation locates near TNF receptor-associated factors (TRAFs), ion channel, and caveolin binding domain, which may affect the NLRP3 inflammasome activation. 2021 Communications biology Result SARS_CoV_2 Q57H 13 17 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. In addition, mutation A344S has the highest frequency among the 13 infectivity-weaken mutations. 2021 Communications biology Result SARS_CoV_2 A344S 22 27 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. In Cluster A, B, C, and D, the co-mutations with the highest number of descendants are [241C>T, 3037C>T, 14408C>T, 23403A>G], [3037C>T, 14408C>T], [8782C>T, 18060C>T, 28144T>C], and [3037C>T, 14408C>T, 23403A>G] respectively. 2021 Communications biology Result SARS_CoV_2 C14408T;C14408T;C14408T;C18060T;A23403G;A23403G;T28144C;C3037T;C241T;C3037T;C3037T;C8782T 105;136;192;157;115;202;167;96;88;127;183;148 113;144;200;165;123;210;175;103;94;134;190;155 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. In contrast, the time evolution plot shows that the ratio of mutation 28144T>C-(L84S) goes up before the beginning of March, and then the ratio goes down and approach zero after 23 May 2020. 2021 Communications biology Result SARS_CoV_2 T28144C;L84S 70;80 78;84 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. In early March, the ratio of both mutations start to decrease and approach zero after 19 May 2020, suggesting that mutations 17858A>G-(Y541C) and 17747C>T-(P504L) may hinder the transmission of SARS-CoV-2. 2021 Communications biology Result SARS_CoV_2 C17747T;A17858G;P504L;Y541C 146;125;156;135 154;133;161;140 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. In Table 2, 17858A>G-(Y541C) and 17747C>T-(P504L) do not show up with 23403A>G-(D614G) in more than a thousand SNP profiles. 2021 Communications biology Result SARS_CoV_2 C17747T;A17858G;A23403G;D614G;P504L;Y541C 33;12;70;80;43;22 41;20;78;85;48;27 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. In the US, there is an apparent gender difference in mutation 27964C>T-(S24L) on the ORF8 protein. 2021 Communications biology Result SARS_CoV_2 C27964T;S24L 62;72 70;76 ORF8 85 89 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Meanwhile, the positive folding stability change of 27964C>T-(S24L) lists in Table 3 reveals that this type of mutation may enhance the function of ORF8. 2021 Communications biology Result SARS_CoV_2 C27964T;S24L 52;62 60;66 ORF8 148 152 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. More than 94.2% mutation 27964C>T-(S24L) worldwide were found in the United States. 2021 Communications biology Result SARS_CoV_2 C27964T;S24L 25;35 33;39 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Moreover, another possible reason is that mutations 17858A>G-(Y541C) and 17747C>T-(P504L) may weaken the transmission capacity of SARS-CoV-2. 2021 Communications biology Result SARS_CoV_2 C17747T;A17858G;P504L;Y541C 73;52;83;62 81;60;88;67 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Moreover, on the RBM, we can see that mutation Q493L has a relatively high binding free energy change and frequency. 2021 Communications biology Result SARS_CoV_2 Q493L 47 52 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Moreover, the D614G mutation ratio in. 2021 Communications biology Result SARS_CoV_2 D614G 14 19 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Mutation 14408C>T-(P323L) on the NSP12 (aka RNA-dependent RNA polymerase (RdRp)) is one of dominant mutations in the United States. 2021 Communications biology Result SARS_CoV_2 C14408T;P323L 9;19 17;24 RdRp;Nsp12;RdRP 44;33;74 72;38;78 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Mutation 187A>G has the second-highest frequencies in the US and the World, which are 36 and 207, respectively. 2021 Communications biology Result SARS_CoV_2 A187G 9 15 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Mutation 23010T>C-(V483A) has the highest frequency (31) localized on the RBM has the positive binding free energy change, which indicates that V483A is prevalent in COVID-19 patients' in the United States has a potential capacity to enhance the infectivity of SARS-CoV-2. 2021 Communications biology Result SARS_CoV_2 T23010C;V483A;V483A 9;144;19 17;149;24 COVID-19 166 174 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Mutation 23403A>G-(D614G) located on the spike protein has the second-highest frequency in the United States, which has been considered as the key mutation that makes SARS-CoV-2 more infectious worldwide. 2021 Communications biology Result SARS_CoV_2 A23403G;D614G 9;19 17;24 S 41 46 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Mutation 241C>T is the most common mutation that has 9628 and 36,786 frequencies respectively in the US and the World, indicating the 241C>T mutation is important for the genomic replication process. 2021 Communications biology Result SARS_CoV_2 C241T;C241T 9;134 15;140 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Mutation 25563G>T-(Q57H) is on the ORF3a protein. 2021 Communications biology Result SARS_CoV_2 G25563T;Q57H 9;19 17;23 ORF3a 35 40 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Mutation 28144T>C-(L84S), the first known mutation globally, has had a very unsteady trajectory. 2021 Communications biology Result SARS_CoV_2 T28144C;L84S 9;19 17;23 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Mutation 28883G>C-(G204R) may affect the hydrophilicity of N protein, which is in consistent with the predicted negative folding stability changes of R203K and G204 shown in Table 3. 2021 Communications biology Result SARS_CoV_2 G28883C;R203K;G204R 9;150;19 17;155;24 N 59 60 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Mutation Q57H locates at the intramolecular interface and in touch with the membrane, which indicates the special functionality changes that Q57H can induce. 2021 Communications biology Result SARS_CoV_2 Q57H;Q57H 9;141 13;145 Membrane 76 84 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Mutation Y541C changes the amino acid tyrosine (Y) to cysteine (C). 2021 Communications biology Result SARS_CoV_2 Y541C 9 14 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Mutations 17858A>G-(Y541C) and 17747C>T-(P504L) happen simultaneously after analyzing 45,494 genome sequences, indicating the folding stability changes on the NSP13 are superimposed by two simultaneously occurred mutations. 2021 Communications biology Result SARS_CoV_2 C17747T;A17858G;P504L;Y541C 31;10;41;20 39;18;46;25 Nsp13 159 164 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Mutations P384S and Q414E have negative binding free energy changes, with the total frequency equals to 4. 2021 Communications biology Result SARS_CoV_2 P384S;Q414E 10;20 15;25 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Notably, after analyzing 28,726 complete genome sequences, none of them have mutations 28144T>C-(L84S) and 27964C>T-(S24L) happened simultaneously. 2021 Communications biology Result SARS_CoV_2 C27964T;T28144C;L84S;S24L 107;87;97;117 115;95;101;121 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Notably, the V483A mutation is localized on the RBM with the highest frequency, indicating that V483A may favor SARS-CoV-2 by natural selection and cause SARS-CoV-2 more infectious. 2021 Communications biology Result SARS_CoV_2 V483A;V483A 13;96 18;101 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. On the protein level, mutation 28883G>C leads to G204R. 2021 Communications biology Result SARS_CoV_2 G28883C;G204R 31;49 39;54 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Once mutations 17858A>G-(Y541C) and 17747C>T-(P504L) were first found in the United States, they had a rapid increase in the first 2 weeks. 2021 Communications biology Result SARS_CoV_2 C17747T;A17858G;P504L;Y541C 36;15;46;25 44;23;51;30 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. One mutation (17747C>T-(P504L)) does not affect the rigidity much, whereas the other mutation (17858A>G-(Y541C)) leads to a decrease in the NSP12 rigidity, which may make NSP13 not as robust as before to involve in the viral infection and replication process. 2021 Communications biology Result SARS_CoV_2 C17747T;A17858G;P504L;Y541C 14;95;24;105 22;103;29;110 Nsp13;Nsp12 171;140 176;145 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. One possible reason for the declined ratios for 17858A>G-(Y541C) and 17747C>T-(P504L) may be due to the efficient lockdown measures enforced in WA and CA at the early stage of the outbreak in the US. 2021 Communications biology Result SARS_CoV_2 C17747T;A17858G;P504L;Y541C 69;48;79;58 77;56;84;63 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Only 14.3% sequences in the US have mutations 28881G>A, 28881G>A, and 28883G>C. 2021 Communications biology Result SARS_CoV_2 G28881A;G28881A;G28883C 46;56;70 54;64;78 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. R203K is caused by both 28881G>A and 28882G>A. 2021 Communications biology Result SARS_CoV_2 G28881A;G28882A;R203K 24;37;0 32;45;5 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Similar to 27964C>T-(S24L), although 17858A>G-(Y541C), 17747C>T-(P504L) are in the final list in Table 1, more than 87% of them were detected in the United States. 2021 Communications biology Result SARS_CoV_2 C17747T;A17858G;C27964T;P504L;S24L;Y541C 55;37;11;65;21;47 63;45;19;70;25;52 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Since then, SARS-CoV-2 with the mutation D614G has become a major variant, and 82.3% of patients carry D614G in the United States as of 11 September 2020. 2021 Communications biology Result SARS_CoV_2 D614G;D614G 41;103 46;108 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Table 3 shows that both high-frequency mutations Y541C and P504L have negative folding stability changes, which will destabilize the structure of NSP13. 2021 Communications biology Result SARS_CoV_2 P504L;Y541C 59;49 64;54 Nsp13 146 151 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Table 3 shows that the folding stability change of 28144T>C-(L84S) is -0.99 kcal/mol, indicating that ORF8 becomes unstable. 2021 Communications biology Result SARS_CoV_2 T28144C;L84S 51;61 59;65 ORF8 102 106 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Table 3 shows that the folding stability change of T85I is -0.05 kcal/mol. 2021 Communications biology Result SARS_CoV_2 T85I 51 55 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The co-mutations of the second groups have eight unique single mutations: 1059C>T-(T85I), 14408C>T-(P323L), 23403A>G-(D614G), 25563G>T-(Q57H), and 27964C>T-(S24L), 28881G>A-(R203K), 28882G>A-(R203K), and 28883G>C-(G204R). 2021 Communications biology Result SARS_CoV_2 C1059T;C14408T;A23403G;G25563T;C27964T;G28881A;G28882A;G28883C;D614G;G204R;P323L;Q57H;R203K;R203K;S24L;T85I 74;90;108;126;147;164;182;204;118;214;100;136;174;192;157;83 81;98;116;134;155;172;190;212;123;219;105;140;179;197;161;87 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The D614G mutation is one of the most prevalent mutations of SARS-CoV-2, which changes the amino acid aspartate (D) with the polar negative charged side changes to the amino acid glycine (G) with a non-polar side chain. 2021 Communications biology Result SARS_CoV_2 D614G 4 9 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The female patients with S24L mutation on ORF8 account for a large proportion, which indicates that the S24L is most likely to happen in the female population in the United States. 2021 Communications biology Result SARS_CoV_2 S24L;S24L 25;104 29;108 ORF8 42 46 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The first case with the D614G mutation in the United States was reported on 28 February 2020 in Florida (2 sequences) and Rhode Island (1 sequence). 2021 Communications biology Result SARS_CoV_2 D614G 24 29 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The first confirmed case with 27964C>T-(S24L) was discovered on 9 March 2020, in the United States, suggesting that S24L initially happened in the US. 2021 Communications biology Result SARS_CoV_2 C27964T;S24L;S24L 30;116;40 38;120;44 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The first group involves 5 mutations together: 1059C>T-(T85I), 14408C>T-(P323L), 23403A>G-(D614G), 25563G>T-(Q57H), and 27964C>T-(S24L) that are strongly correlated, though have a wide range of frequencies. 2021 Communications biology Result SARS_CoV_2 C1059T;C14408T;A23403G;G25563T;C27964T;D614G;P323L;Q57H;S24L;T85I 47;63;81;99;120;91;73;109;130;56 54;71;89;107;128;96;78;113;134;60 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The first missense mutation with the highest frequency, 23403A>G-(D614G), occurred in China on 24 January 2020. 2021 Communications biology Result SARS_CoV_2 A23403G;D614G 56;66 64;71 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The first top mutation recorded in the US was 28144T>C-(L84S), on 19 January. 2021 Communications biology Result SARS_CoV_2 T28144C;L84S 46;56 54;60 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The frequencies other six mutations (i.e., 199G>T, 222C>T, 208G>T, 218C>T, 242G>T, and 169A>G) are <50. 2021 Communications biology Result SARS_CoV_2 A169G;G199T;G208T;C218T;C222T;G242T 87;43;59;67;51;75 93;49;65;73;57;81 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The high-frequency mutations that detected on the Nucleocapsid (N) protein are 28881G>A, 28881G>A, and 28883G>C. 2021 Communications biology Result SARS_CoV_2 G28881A;G28881A;G28883C 79;89;103 87;97;111 N;N 50;64 62;65 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The increasing ratio of P323L in. 2021 Communications biology Result SARS_CoV_2 P323L 24 29 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The L455F mutation localized on the RBM has low frequency but the highest absolute binding free energy changes, while the A411S localized outside the RBM with low positive binding free energy change has the highest frequency. 2021 Communications biology Result SARS_CoV_2 A411S;L455F 122;4 127;9 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The missense mutation with the second-highest frequency, 14408C>T-(P323L), occurred in Spain on 25 January 2020. 2021 Communications biology Result SARS_CoV_2 C14408T;P323L 57;67 65;72 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The mutation that has the highest frequency is D614G, which was reported to enhance SARS-CoV-2 infectivity. 2021 Communications biology Result SARS_CoV_2 D614G 47 52 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The negative folding stability changes in Table 3 suggest that P323L destabilizes the NSP12. 2021 Communications biology Result SARS_CoV_2 P323L 63 68 Nsp12 86 91 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The negative folding stability changes of mutation Q57H in Table 3 reveals that ORF3a becomes unstable following the Q57H mutation, which may harm the function of ORF3a in apoptosis and increase the viral load in the host cell. 2021 Communications biology Result SARS_CoV_2 Q57H;Q57H 51;117 55;121 ORF3a;ORF3a 80;163 85;168 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The ORF8 protein has two high-frequency mutations, 28144T>C-(L84S) and 27964C>T-(S24L). 2021 Communications biology Result SARS_CoV_2 C27964T;T28144C;L84S;S24L 71;51;61;81 79;59;65;85 ORF8 4 8 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The other three mutations, 17747C>T-(P504L), 17858A>G-(Y541C), and 28144T>C-(L84S), occur mostly together and have similar numbers of frequencies. 2021 Communications biology Result SARS_CoV_2 C17747T;A17858G;T28144C;L84S;P504L;Y541C 27;45;67;77;37;55 35;53;75;81;42;60 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The overall upward trend of the S24L ratio over time reveals that S24L may enhance SARS-CoV-2's ability to spread. 2021 Communications biology Result SARS_CoV_2 S24L;S24L 32;66 36;70 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The Q57H mutation changes the amino acid glutamine (Q) with a non-charged polar side chain to the positively charged polar side chain of amino acid histidine (H). 2021 Communications biology Result SARS_CoV_2 Q57H 4 8 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. the ratio of the 25563G>T-(Q57H) mutation on ORF3a in each 7-day period kept increasing once it was introduced to the United States. 2021 Communications biology Result SARS_CoV_2 G25563T;Q57H 17;27 25;31 ORF3a 45 50 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The rest of 88% of 28881G>A-(R203K), 28882G>A(R203K), and 28883G>C-(G204R) are dominated in the European countries. 2021 Communications biology Result SARS_CoV_2 G28881A;G28882A;G28883C;G204R;R203K;R203K 19;37;58;68;29;46 27;45;66;73;34;51 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The rigidity changes induced by S24L is less than the L84S. 2021 Communications biology Result SARS_CoV_2 L84S;S24L 54;32 58;36 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The third pair of mutations, 17747C>T-(P504L) and 17858A>G-(Y541C), first detected and occurred mostly in the US, have an identical evolution trajectory. 2021 Communications biology Result SARS_CoV_2 C17747T;A17858G;P504L;Y541C 29;50;39;60 37;58;44;65 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The trajectories of the other two high-frequency S protein mutations (Q675R and E583D) indicate that they are co-mutations with infectivity-enhancing S protein mutations, such as D614G. 2021 Communications biology Result SARS_CoV_2 D614G;E583D;Q675R 179;80;70 184;85;75 S;S 49;150 50;151 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Therefore, its time evolution trajectory is extremely similar to that of 25563G>T-(Q57H). 2021 Communications biology Result SARS_CoV_2 G25563T;Q57H 73;83 81;87 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Therefore, the mutation R203K may not affect N protein function. 2021 Communications biology Result SARS_CoV_2 R203K 24 29 N 45 46 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Therefore, we can deduce that the increasing tendency of P323L ratios per 7-days is due to its co-mutation with other infectivity-strengthening mutations, such as 23403A>G-(D614G). 2021 Communications biology Result SARS_CoV_2 A23403G;P323L;D614G 163;57;173 171;62;178 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Therefore, we can say that mutation 27964C>T-(S24L) has a female-dominance pattern. 2021 Communications biology Result SARS_CoV_2 C27964T;S24L 36;46 44;50 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. This could be one possible reason why the ratio of S24L is on the rise. 2021 Communications biology Result SARS_CoV_2 S24L 51 55 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. This tendency indicates that mutation Q57H becomes prevalent in the viral patients of the United States, which may make the SARS-CoV-2 more infectious. 2021 Communications biology Result SARS_CoV_2 Q57H 38 42 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Three of the top 11 missense mutations, i.e., 17858A>G-(Y541C), 17747C>T-(P504L), and 27964C>T-(S24L), appeared in the United States first. 2021 Communications biology Result SARS_CoV_2 C17747T;A17858G;C27964T;P504L;S24L;Y541C 64;46;86;74;96;56 72;54;94;79;100;61 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. We found that the other high-frequency S protein mutation L5F is independent of mutation D614G. 2021 Communications biology Result SARS_CoV_2 D614G;L5F 89;58 94;61 S 39 40 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. A schematic summarizing the key lineage-specific and shared protein polymorphisms of the US S: Q677P and S:Q677H variants is shown in FIG 4. 2021 medRxiv Result SARS_CoV_2 Q677P;Q677H 95;107 100;112 S;S 92;105 93;106 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. A second Q677H clade, distinguished from Robin 1 by an N2361K substitution in orf1a, first appeared from a Oct 6, 2020 sample from Alabama and is named "Robin 2" owing to its similarity to the parental Robin 1 sub-lineage. 2021 medRxiv Result SARS_CoV_2 N2361K;Q677H 55;9 61;14 ORF1a 78 83 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. According to the most recent LSUHS data, which covers collection dates up to Jan 19, 2021, the Q677H polymorphism occurs in 5.7% of total SARS-CoV-2 genome data. 2021 medRxiv Result SARS_CoV_2 Q677H 95 100 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. All mutations leading to Q677H or Q677P involve transversions. 2021 medRxiv Result SARS_CoV_2 Q677H;Q677P 25;34 30;39 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Although the Q677P position is outside the furin binding pocket, we speculate that the presence of a proline at this site may introduce a favorable kink that promotes the dynamic conformational changes necessary for cleavage at the S1/S2 junction, which is governed not only by furin-like activities, but also by trypsin-like proteases (e.g., TMPRSS2) and cathepsins. 2021 medRxiv Result SARS_CoV_2 Q677P 13 18 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. An S:Q677H variant was first detected from Louisiana in the summer of 2021 in LSUHS samples collected on July 21, 2020 and Aug 11, 2020. 2021 medRxiv Result SARS_CoV_2 Q677H 5 10 S 3 4 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Broad-scale genomic surveillance efforts conducted by the New Mexico Department of Health (NM DOH) and the UNM HSC in December and January, 2021 revealed that 83 of 733 SARS-CoV-2 genomes sequenced in New Mexico between December 1st and January 19th contained the S:Q677P variant at a general frequency of 11.3% in the SARS-CoV-2 positive individuals. 2021 medRxiv Result SARS_CoV_2 Q677P 266 271 S 264 265 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. However, this Q677P variant also amounted to 14% of all LSUHS samples collected in Jan 2021, and 11.4% of all Louisiana samples collected between Jan 01 - Jan 19, 2021. 2021 medRxiv Result SARS_CoV_2 Q677P 14 19 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. In addition to the Q677P sub-lineage, our analyses indicated that SARS-CoV-2 variants carrying non-synonymous mutations affecting S codon 677 have arisen at least six other times in the United States. 2021 medRxiv Result SARS_CoV_2 Q677P 19 24 S 130 131 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. In contrast, the S:Q677P variant occurs by virtue of an A to C change at position 23592. 2021 medRxiv Result SARS_CoV_2 A23592C;Q677P 56;19 87;24 S 17 18 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. In December 2020, our New Mexico-based surveillance effort detected 23 genomes harboring the Q677P mutation, with an additional 59 detected in January 2021. 2021 medRxiv Result SARS_CoV_2 Q677P 93 98 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. In late January of 2021, our two independent SARS-CoV-2 genomic surveillance programs, based at the University of New Mexico Health Sciences (UNM HSC) in Albuquerque, New Mexico and the Louisiana State University Health Sciences Center (LSUHS) in Shreveport, Louisiana, each noticed increasing numbers of PANGO lineage B.1.2 / Nextstrain clade 20G viruses carrying an S:Q677P mutation, and that this variant had increased in frequency in samples collected in late 2020 to mid January. 2021 medRxiv Result SARS_CoV_2 Q677P 370 375 S 368 369 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. In New Mexico, the S:Q677P substitution was first observed from a December 12, 2020 sample, and its frequency among sequenced viruses increased through January. 2021 medRxiv Result SARS_CoV_2 Q677P 21 26 S 19 20 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. In part due to deep sampling of the large outbreak, the Q677P virus amounted to 37.2% of all viral genomes sequenced from Dec 2020 samples collected in Louisiana (LSUHS submissions account for 481 of the 503, or 95.6% of Dec 2020 viral genome sequences available on GISAID for the state). 2021 medRxiv Result SARS_CoV_2 Q677P 56 61 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. In the case of the S: Q677H substitution, histidine protonation could similarly act as a conformational switch affecting accessibility to proteases. 2021 medRxiv Result SARS_CoV_2 Q677H 22 27 S 19 20 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Only 2 additional S:Q667H sequences were collected from the entire state of Louisiana in Nov, both on the 27th. 2021 medRxiv Result SARS_CoV_2 Q667H 20 25 S 18 19 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Similarly, genomic surveillance efforts conducted by LSUHS together with the Louisiana Department of Health detected a first occurrence of the S:Q677P variant on Dec 1, 2020, which over the month rose to 187 complete genomes, many from a single, large congregate facility outbreak. 2021 medRxiv Result SARS_CoV_2 Q677P 145 150 S 143 144 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. The largest of the 677 variant sub-lineages ("Robin 1") is a B.1.2 / 20G clade virus carrying Q677H that first appears in GISAID data from a sample with a August 17, 2020 collection date. 2021 medRxiv Result SARS_CoV_2 Q677H 94 99 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. The next largest cluster is the Q677P variant of 20G (B.1.2) ("Pelican"), which was first detected in Oregon from a sample with collection date of Oct 23, 2020 and as of Feb 3, 2021 contains 504 sequences. 2021 medRxiv Result SARS_CoV_2 Q677P 32 37 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. The Q677P variant has been detected in LA, NM, NC, WY, MA, ID, MI AZ, CA, TX, WI, and MD, and five international sequences (Australia (2), Denmark, Switzerland, India). 2021 medRxiv Result SARS_CoV_2 Q677P 4 9 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. The remaining Q677H sub-lineages each contain around 100 or fewer sequences, and are named: Yellowhammer, detected mostly in the southeast US; Bluebird, mostly in the northeast United States; Quail, mainly in the Southwest and Northeast; and Mockingbird, mainly in the South-central and East coast states (Table 1. 2021 medRxiv Result SARS_CoV_2 Q677H 14 19 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Thus, the observation of a sudden and contemporaneous increase in the abundance of S: Q677H and Q677P variants by surveillance programs in two different states along the southeast / southwest corridor is remarkable. 2021 medRxiv Result SARS_CoV_2 Q677H;Q677P 86;96 91;101 S 83 84 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. We used SWISS MODEL to model this inherently flexible region and spotlight the Q677P residue. 2021 medRxiv Result SARS_CoV_2 Q677P 79 84 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. When considered in unison, S: Q677P and S: Q677H samples together comprise 47.5% of all Dec 2020 viral genomes collected from Louisiana, and 17.1% of the genome sequences collected in the state from Jan 01 - 19, 2021. 2021 medRxiv Result SARS_CoV_2 Q677H;Q677P 43;30 48;35 S;S 27;40 28;41 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. 4E), while the interaction between the RBD and ACE2 is driven by electrostatic interactions for the V367F variant. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 V367F 100 105 RBD 39 42 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. A348T RBD variant shows the least binding affinity to ACE2 among all the population variants. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 A348T 0 5 RBD 6 9 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Another variant, S494P, is observed in several SARS-CoV2 strains from Michigan, USA. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 S494P 17 22 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Comparison of selection sites and alignment reveals three RBM population variants under selection bias, G476S, V483A, and S494P that are in close contact with the ACE2 binding surface. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 G476S;S494P;V483A 104;122;111 109;127;116 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. For the G476S variant, the overall interfacial contacts between the RBD and ACE2 reduces significantly, evident from a reduction of RBD and ACE2 interfacial area by ~50 A2 in comparison to the Wuhan RBD-ACE2 complex. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 G476S 8 13 RBD;RBD;RBD 68;132;199 71;135;202 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. G476S variants are widespread and found in seven viral strains reported from the Washington State, USA. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 G476S 0 5 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. However, the number of hydrogen bonds between ACE2 and RBD decreases significantly for the S494P variants. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 S494P 91 96 RBD 55 58 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. In V367F, the enhanced binding energy is primarily contributed by an altered orientation of Lys31 which enhances its contribution to the binding free energy (-4.59 kcal/mol). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 V367F 3 8 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Interaction energy decomposition also shows that the van der Waals energy increases between the RBD and ACE2 for the S494P variant during the later simulation timescale. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 S494P 117 122 RBD 96 99 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. On the other hand, the V367F variant forms a higher number of hydrogen bonds with the ACE2 in comparison to the wild-type. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 V367F 23 28 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Root mean square deviation analysis over the entire trajectory reveals that the V367F and S494P RBD variants remain stable throughout the simulation when complexed with ACE2. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 S494P;V367F 90;80 95;85 RBD 96 99 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. S494P RBD variant almost very similarly binds with ACE2 like the Wuhan SARS-CoV2 RBD. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 S494P 0 5 RBD;RBD 6;81 9;84 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Sequence alignment reveals the population variants for those sites are A348T and V367F. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 A348T;V367F 71;81 76;86 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. The A348T, G476S, and V483A variants display reduced affinity to ACE2 in comparison to the Wuhan SARS-CoV2 spike protein (Wild-type). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 A348T;G476S;V483A 4;11;22 9;16;27 S 107 112 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. The A520S variant was reported in two viral strains from Washington, USA. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 A520S 4 9 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. The binding ability of five spike population variants, A348T, V367F, G476S, V483A, and S494P with ACE2 has been explored using the protein-protein docking and binding free energy calculations. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 A348T;G476S;S494P;V367F;V483A 55;69;87;62;76 60;74;92;67;81 S 28 33 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. The buried RBM-ACE2 interfacial surface area increases by 2 nm2 for the S494P variant in comparison to the wild-type and V367F variant during the simulation. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 S494P;V367F 72;121 77;126 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. The most common RBD variant is V483A which was reported in different states in the USA. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 V483A 31 36 RBD 16 19 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. The reduction of binding affinity of the V483A mutant in comparison to Wuhan SARS-CoV2 is primarily due to the altered orientation of Tyr505 which weakens the hydrogen bonding interaction with Arg393 by more than 1 kcal/mol. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 V483A 41 46 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. This indicates the enhanced binding affinity of S494P is attributed to strong interfacial complementarity during ACE2 recognition, while the V367F variant interacts with the ACE2 mediated by a higher number of hydrogen bonds. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 S494P;V367F 48;141 53;146 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. V367F variation is observed in two viral strains obtained from Hong Kong and the USA. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 V367F 0 5 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. While the V367F and S494P population variants display a higher binding affinity towards human ACE2, compared to the Wild-type spike protein. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 S494P;V367F 20;10 25;15 S 126 131 33606828 SARS-CoV-2 genetic diversity in Venezuela: Predominance of D614G variants and analysis of one outbreak. In addition to the D614G mutation in the spike protein characteristic of lineage B (A23403G), all the Venezuelan sequences belonging to lineage B bore the mutation C241T in the UTR, C14408T in the RdRP, and the synonymous mutation C3037T (Fig 4). 2021 PloS one Result SARS_CoV_2 C14408T;C241T;C3037T;D614G;A23403G 182;164;231;19;84 189;169;237;24;91 S;RdRP 41;197 46;201 33606828 SARS-CoV-2 genetic diversity in Venezuela: Predominance of D614G variants and analysis of one outbreak. Other 4 isolates from Maracaibo city (Zulia State), for which a 1000 nt sequence surrounding position 23403 was available, also bear the mutation D614G (Accession numbers MW040500-MW040503), for a total of 10/11 D614G isolates. 2021 PloS one Result SARS_CoV_2 D614G;D614G 146;212 151;217 33606828 SARS-CoV-2 genetic diversity in Venezuela: Predominance of D614G variants and analysis of one outbreak. The other 6 isolates belonged to lineage B: two B.1, two B1.1, one B.1.117 and one B.1.5, all with the mutation D614G (Figs 2 and 3). 2021 PloS one Result SARS_CoV_2 D614G 112 117 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. A mutation in the S gene, G1167V (Glycine to Valine) was identified in Oklahoma-ADDL-4. 2020 Frontiers in genetics Result SARS_CoV_2 G1167V 26 32 S 18 19 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. A previously reported deleterious variation in the protein expressed from ORF3a, Q57H, was recorded in Oklahoma-ADDL-1, the genome isolated at the beginning of the pandemic in Oklahoma. 2020 Frontiers in genetics Result SARS_CoV_2 Q57H 81 85 ORF3a 74 79 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. A previously reported mutation in S gene - D614G (Aspartate to Glycine), was identified in all the genomes sequenced. 2020 Frontiers in genetics Result SARS_CoV_2 D614G 43 48 S 34 35 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. A previously reported mutation in the ORF1ab gene P4715L) (Proline to Leucine) was recorded alongside novel mutations at various amino acid locations. 2020 Frontiers in genetics Result SARS_CoV_2 P4715L 50 56 ORF1ab 38 44 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. D614G mutation in S gene, which corresponds to changes in the spike protein, has already been reported widely in the literature. 2020 Frontiers in genetics Result SARS_CoV_2 D614G 0 5 S;S 62;18 67;19 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. N gene mutations idenfied in this study (S194L, R203K, and G204R) are located in the region 180-247, which is suggested to be a flexible linker region that lacks organized structure. 2020 Frontiers in genetics Result SARS_CoV_2 G204R;R203K;S194L 59;48;41 64;53;46 N 0 1 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. Oklahoma-ADDL-4 carried mutation T4412A (Threonine to Alanine) in ORF1ab, while Oklahoma-ADDL-2 and 3 carried mutation A6269S (Alanine to Serine). 2020 Frontiers in genetics Result SARS_CoV_2 A6269S;T4412A 119;33 125;39 ORF1ab 66 72 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. Oklahoma-ADDL-4, carried a non-synonymous mutation S194L while Oklahoma-ADDL 2,3,5 carried R203K and G204R. 2020 Frontiers in genetics Result SARS_CoV_2 G204R;R203K;S194L 101;91;51 106;96;56 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. P3371S (Proline to Serine) mutation in ORF1ab and ORF1a was detected in Oklahoma-ADDL-5. 2020 Frontiers in genetics Result SARS_CoV_2 P3371S 0 6 ORF1ab;ORF1a 39;50 45;55 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. P4715L mutation has been implicated to play a major role in interaction with other proteins that regulate RNA Dependent RNA polymerase activity. 2020 Frontiers in genetics Result SARS_CoV_2 P4715L 0 6 RdRp 106 134 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. T28I in ORF7b gene, a non-synonymous mutation (Threonine to Isoleucine) in the genome Oklahoma-ADDL-5 and in ORF8, G96R non-synonymous mutations resulting in Glycine to Arginine were noted in Oklahoma-ADDL-2 and Oklahoma-ADDL-3. 2020 Frontiers in genetics Result SARS_CoV_2 G96R;T28I 115;0 119;4 ORF7b;ORF8 8;109 13;113 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. The D614G mutation has been reported to cause a decrease in PCR cycle thresholds, suggestive of higher upper respiratory tract viral load in the host. 2020 Frontiers in genetics Result SARS_CoV_2 D614G 4 9 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. The mutation G1167V in S gene is proposed to be located in the stalk region of spike protein. 2020 Frontiers in genetics Result SARS_CoV_2 G1167V 13 19 S;S 79;23 84;24 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. 3, reveal notable differences: There is a pronounced interaction hotspot on hACE2 opposite to residue S477 of the RBD in the native system as well as in the S477N variant, while it is missing in the S477G variant. 2021 Scientific reports Result SARS_CoV_2 S477G;S477N 199;157 204;162 RBD 114 117 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. 6), S477N and hACE2 started dissociating at 390 ps, whereas the S477G variant delayed the disassociation process with hACE2 for around 100 ps. 2021 Scientific reports Result SARS_CoV_2 S477G;S477N 64;4 69;9 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. 8) show that the S477N variant features the highest binding affinity with hACE2 compared to its native RBD and S477G (Table 1). 2021 Scientific reports Result SARS_CoV_2 S477G;S477N 111;17 116;22 RBD 103 106 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. A mutation corresponding to S477G results in two consecutive Gly residues at position 476 and 477, with the resulting arrangement A475-G476-S477G (AGG), This AGG motif might favour easier structural arrangements of side chains which are otherwise restricted. 2021 Scientific reports Result SARS_CoV_2 S477G;S477G 28;140 33;145 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. Although we expected an increased local flexibility of the loop in the S477G variant, this hypothesis surprisingly turned out not to be true. 2021 Scientific reports Result SARS_CoV_2 S477G 71 76 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. In line with that, the average total numbers of interface hydrogen bonds per trajectory frame of the 100 ns simulations are 5.7, 6.0, 6.7, for the native, S477G and S477N variants, respectively. 2021 Scientific reports Result SARS_CoV_2 S477G;S477N 155;165 160;170 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. Interestingly, there is a significant difference in the rupture force between the RBD and its variants S477G and S477N throughout different force constants. 2021 Scientific reports Result SARS_CoV_2 S477G;S477N 103;113 108;118 RBD 82 85 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. Our detailed NMA suggested that there is a flexible domain of highly correlated dynamical residues on RBM, and local amino acid exchanges S477G and S477N have a very high potential to affect local conformation significantly upon binding. 2021 Scientific reports Result SARS_CoV_2 S477G;S477N 138;148 143;153 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. Our results are in line with experimentally reported changes in the binding affinity of S477G and S477N variants. 2021 Scientific reports Result SARS_CoV_2 S477G;S477N 88;98 93;103 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. S477G delayed the detachment of RBD from hACE2. 2021 Scientific reports Result SARS_CoV_2 S477G 0 5 RBD 32 35 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. time, indicating that the S477G RBD variant is significantly delaying the disengagement process. 2021 Scientific reports Result SARS_CoV_2 S477G 26 31 RBD 32 35 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. To verify the impact of the mutation S477G in affecting the binding with hACE2, molecular dynamics simulations (MD) have been carried out to obtain volumetric maps to visualize the captured signature of inter atomic contacts. 2021 Scientific reports Result SARS_CoV_2 S477G 37 42 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. We performed 100 ns MDs with the native hACE2:RBD complex and the hACE2:RBD S477G and S477N variant complexes. 2021 Scientific reports Result SARS_CoV_2 S477G;S477N 76;86 81;91 RBD;RBD 46;72 49;75 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. A pseudovirus bearing only the three RBD mutations (K417N, E484K, and N501Y), largely, but not entirely, recapitulated the escape phenotype (Figure 4C). 2021 medRxiv Result SARS_CoV_2 E484K;N501Y;K417N 59;70;52 64;75;57 RBD 37 40 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. However, neutralization of the Brazilian/Japanese P.2 variant, whose RBD contains a E484K mutation, was significantly decreased (13.4-fold, p < 0.001) (Figure 3C and S2). 2021 medRxiv Result SARS_CoV_2 E484K 84 89 RBD 69 72 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Interestingly, neutralization of D614G was slightly decreased in individuals who received two doses of vaccine (~2-fold decrease for 2-dose BNT162b2) (Figure 3A-C and S2), which was in contrast to previous studies in convalescent sera that we and others conducted demonstrating slightly increased neutralization of D614G variant versus wild type following natural infection. 2021 medRxiv Result SARS_CoV_2 D614G;D614G 33;315 38;320 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Remarkably, neutralization assays conducted with sera from 22 individuals that received the 2-dose BNT162b2 vaccine revealed that neutralization of B.1.351 v1 and v2 in the absence of RBD mutations was comparable to that of D614G (Figure 4B-C). 2021 medRxiv Result SARS_CoV_2 D614G 224 229 RBD 184 187 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Separately, the B.1.1.298 variant found in Danish minks contained a Y453F mutation in RBD, and the California variant B.1.429 contained an L452R. 2021 medRxiv Result SARS_CoV_2 L452R;Y453F 139;68 144;73 RBD 86 89 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Similarly, neutralizing antibody responses were also significantly decreased for the Brazilian/Japanese P.1 strain (15.1-fold, p < 0.0001), which harbors three mutations in RBD (K417T, E484K, and N501Y) and has also been found in cases of re-infection. 2021 medRxiv Result SARS_CoV_2 E484K;N501Y;K417T 185;196;178 190;201;183 RBD 173 176 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. The effect was even more pronounced in individuals who received one vaccine (p < 0.05 for 1-dose mRNA-1273), some of which had undetectable neutralization of D614G despite detectable neutralization of wild-type SARS-CoV-2 (Figure 3B). 2021 medRxiv Result SARS_CoV_2 D614G 158 163 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. The three main RBD mutations of concern are: (i) N501Y, present in B.1.1.7, P.1, and B.1.351 variants; (ii) E484K, present in the P.2, P.1, and B.1.351 variants; and (iii) K417T for the P.1 variant and K417N for the B.1.351 variants. 2021 medRxiv Result SARS_CoV_2 E484K;K417N;K417T;N501Y 108;202;172;49 113;207;177;54 RBD 15 18 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. These strains contain the same three RBD mutations as P.1 except for an asparagine versus threonine substitution at K417 (K417N) (Figure 3C and S2) and several additional mutations in non-RBD regions. 2021 medRxiv Result SARS_CoV_2 K417N 122 127 RBD;RBD 37;188 40;191 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. This difference may be a consequence of the vaccine encoding the wild-type spike sequence, while many convalescent individuals in previous studies were likely infected with D614G variant SARS-CoV-2, given it had already become the globally dominant strain by the summer of 2020. 2021 medRxiv Result SARS_CoV_2 D614G 173 178 S 75 80 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. This is in line with previous studies suggesting that the E484K mutation can evade polyclonal antibody responses and has been found in cases of SARS-CoV-2 re-infection. 2021 medRxiv Result SARS_CoV_2 E484K 58 63 COVID-19 144 167 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. When assessing variants containing one RBD mutation as part of their mutational landscape, the UK variant B.1.1.7 (N501Y), Danish mink variant B.1.1.298 (Y453F), and California variant B.1.429 (L452R) exhibited neutralization that was similar to that of wild-type and the parental D614G variant. 2021 medRxiv Result SARS_CoV_2 D614G;L452R;N501Y;Y453F 281;194;115;154 286;199;120;159 RBD 39 42 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. 1f-g), we observed additional loss of activity against the mutant B.1.1.7 spike with E484K, with fold change of 11.4 relative to WT. 2021 medRxiv Result SARS_CoV_2 E484K 85 90 S 74 79 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. 4d) showed a complete loss of binding to N501Y RBD mutant. 2021 medRxiv Result SARS_CoV_2 N501Y 41 46 RBD 47 50 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. 4d), 16 showed a complete or partial loss of binding to E484K RBD mutant. 2021 medRxiv Result SARS_CoV_2 E484K 56 61 RBD 62 65 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. 4g-h), consistent with findings that E484K is an important viral escape mutation. 2021 medRxiv Result SARS_CoV_2 E484K 37 42 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. All constructs also contained D614G. 2021 medRxiv Result SARS_CoV_2 D614G 30 35 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. As above, we addressed the role of E484K mutation in escape from RBM-specific antibodies, by testing the binding of 50 RBD-specific mAbs to WT and E484K mutant RBD by biolayer interferometry. 2021 medRxiv Result SARS_CoV_2 E484K;E484K 35;147 40;152 RBD;RBD 119;160 122;163 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. As of 10th Feb 2021, twenty three English and two Welsh B.1.1.7 sequences from viral isolates contained the E484K substitution. 2021 medRxiv Result SARS_CoV_2 E484K 108 113 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. B.1.1.7 with spike E484K mutation and neutralization by vaccine and convalescent sera. 2021 medRxiv Result SARS_CoV_2 E484K 19 24 S 13 18 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Based on our previous deep-mutational scanning measurements using dimeric ACE2, we propose that the K417N mutation is slightly detrimental to ACE2 binding explaining the intermediate affinity determined for the TM RBD compared to the B.1.17 and WT RBDs, likely as a result of disrupting the salt bridge formed with ACE2 residue D30. 2021 medRxiv Result SARS_CoV_2 K417N 100 105 RBD;RBD 214;248 217;252 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. DeltaH69/V70, Delta144, N501Y and A570D in the S1 subunit and P681H, T716I, S982A and D1118H in the S2 subunit. 2021 medRxiv Result SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;T716I 34;86;24;62;76;69 39;92;29;67;81;74 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. E484K is also known to be present in the B.1.351 (501Y.V2) and P.1 (501Y.V3) lineages in combination with amino acid replacements at N501 and K417. 2021 medRxiv Result SARS_CoV_2 E484K 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Enhanced binding of the B.1.1.7 RBD to human ACE2 resulting from the N501Y mutation might participate in the efficient ongoing transmission of this newly emergent SARS-CoV-2 lineage, and possibly reduced opportunity for antibody binding. 2021 medRxiv Result SARS_CoV_2 N501Y 69 74 RBD 32 35 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Following second dose, we observed a significant loss of neutralising activity for the pseudovirus with B.1.1.7 spike mutations and E484K (Fig 3d-e). 2021 medRxiv Result SARS_CoV_2 E484K 132 137 S 112 117 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. RBD antibodies against N501Y could play a role in decreased neutralisation by sera, with the overall impact possibly modulated by other mutations present in B.1.1.7, as well as the relative dominance of NTD versus RBM antibodies in polyclonal sera. 2021 medRxiv Result SARS_CoV_2 N501Y 23 28 RBD 0 3 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Similarly, 3 of the 19 mAbs that lost neutralization of TM mutant (S2D8, S2H7 and S2X128) were previously shown to lose binding and neutralization to the K417V mutant, and here shown to be sensitive to either N501Y or E484K mutations. 2021 medRxiv Result SARS_CoV_2 E484K;K417V;N501Y 218;154;209 223;159;214 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. The E484K substitution. 2021 medRxiv Result SARS_CoV_2 E484K 4 9 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. The fold change in ID50 for neutralisation of B.1.1.7 versus wild type (D614G) was 4.5. 2021 medRxiv Result SARS_CoV_2 D614G 72 77 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. The inclusion of the K417N substitution was prompted by the observation that substitutions at this position have been found in 5 sequences from recent viral isolates within the B.1.1.7 lineage (K417 to N, E or R). 2021 medRxiv Result SARS_CoV_2 K417N 21 26 N 202 203 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. The mean fold change for the E484K B.1.1.7 Spike was 6.7 compared to 1.9 for B.1.1.7, relative to WT. 2021 medRxiv Result SARS_CoV_2 E484K 29 34 S 43 48 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. This is in keeping with convergent evolution of the virus towards an RBD with N501Y, E484K and K417N/T as evidenced by B.1.351 and P.1 lineages (K417N or K417T, respectively) causing great concern globally. 2021 medRxiv Result SARS_CoV_2 E484K;K417N;K417T;K417T;N501Y;K417N 85;95;95;154;78;145 90;102;102;159;83;150 RBD 69 72 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Three of these 16 mAbs also lost binding to an RBD carrying N501Y, indicating that a fraction of RBM antibodies are sensitive to both N501Y and E484K mutations. 2021 medRxiv Result SARS_CoV_2 E484K;N501Y;N501Y 144;60;134 149;65;139 RBD 47 50 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. To address the role of B.1.1.7 N501Y mutation in the neutralization escape from RBM-specific antibodies, we tested the binding of 50 RBD-specific mAbs to WT and N501Y mutant RBD by biolayer interferometry. 2021 medRxiv Result SARS_CoV_2 N501Y;N501Y 31;161 36;166 RBD;RBD 133;174 136;177 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. To assess the effect of E484K on this panel of mAbs we generated a SARS-CoV-2 pseudotype carrying the K417N, E484K and N501Y mutations (TM). 2021 medRxiv Result SARS_CoV_2 E484K;E484K;K417N;N501Y 24;109;102;119 29;114;107;124 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. To understand the impact of TM mutations (K417N, E484K and N501Y), we evaluated binding of ACE2 to the immobilized TM RBD using biolayer interferometry. 2021 medRxiv Result SARS_CoV_2 E484K;N501Y;K417N 49;59;42 54;64;47 RBD 118 121 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. To understand the potential contribution of receptor interaction to infectivity, we set out to evaluate the influence of the B.1.1.7 RBD substitution N501Y on receptor engagement. 2021 medRxiv Result SARS_CoV_2 N501Y 150 155 RBD 133 136 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Using lentiviral pseudotyping we studied WT (wild type bearing D614G) and mutant B.1.1.7 S proteins. 2021 medRxiv Result SARS_CoV_2 D614G 63 68 S 89 90 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. We then generated mutated pseudoviruses carrying S protein with mutations N501Y, A570D and the H69/V70 deletion. 2021 medRxiv Result SARS_CoV_2 A570D;N501Y 81;74 86;79 S 49 50 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. We therefore generated pseudoviruses bearing B.1.1.7 spike mutations with or without additional E484K and tested these against sera obtained after first and second dose mRNA vaccine as well as against convalescent sera. 2021 medRxiv Result SARS_CoV_2 E484K 96 101 S 53 58 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. A recent preprint alerted us to the finding that a common G29140T SNV, found in 22.3% of the study's samples from Madera County, California, was adversely affecting SARS-CoV-2 detection by the NIID_2019-nCoV_N_F2 diagnostic primer used at their sequencing center; the single SNV caused a ~ 30-fold drop in the quantity of amplicon produced by the NIID_2019-nCov_N_F2/R2 primer pair. 2021 eLife Result SARS_CoV_2 G29140T 58 65 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. Another rare RBD S477N mutation, which was found in only 1% of the Australian SARS-CoV-2 sequences before June, has constituted 84% of the sequenced June through December genomes (Figure 2C). 2021 eLife Result SARS_CoV_2 S477N 17 22 RBD 13 16 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. Figure 4 shows a variety of different D614G population dynamics in different areas. 2021 eLife Result SARS_CoV_2 D614G 38 43 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. For example, users can track D614G distributions across any region of interest over time. 2021 eLife Result SARS_CoV_2 D614G 29 34 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. For instance, as of December 2020, an S477N mutation in the receptor binding domain (RBD) has become dominant in Australia (69% of Australian SARS-CoV-2 genotypes, all time) although it constitutes less than 6% of SARS-CoV-2 genotypes globally (Figure 2A). 2021 eLife Result SARS_CoV_2 S477N 38 43 RBD;RBD 60;85 83;88 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. Globally, the S477N mutation was first detected in a single sample of lineage B.1.1.25 that was collected on March 19, 2020, in Victoria, Australia, and became the dominant SARS-CoV-2 variant in the region between June and September (Figure 5B). 2021 eLife Result SARS_CoV_2 S477N 14 19 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. In particular, the set of SNVs that co-occur with the S477N mutation in Australia (all time, as well as prior to May 2020 before the most recent outbreak) are different from the set of co-occurring SNVs in the United Kingdom (Figure 5C) : suggesting that the S477N mutation occurred separately in the Australian and the UK lineages. 2021 eLife Result SARS_CoV_2 S477N;S477N 54;259 59;264 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. In September 2020, we observed that the SARS-CoV-2 spike S477N mutation had become more prevalent in Australia (Figure 5A). 2021 eLife Result SARS_CoV_2 S477N 57 62 S 51 56 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. In the case of the S477N variant that is now dominating in Australia, the sequencing data alone indicate that the local transmission of this variant in Australia since March 2020 or earlier cannot be ruled out. 2021 eLife Result SARS_CoV_2 S477N 19 24 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. SNV frequency in a given region can also shift over time, for example, an RBD N439K mutation not found in Ireland prior to July was present in 42% of the genomes collected mid-July through September, peaking in August and gradually fading after (Figure 2B). 2021 eLife Result SARS_CoV_2 N439K 78 83 RBD 74 77 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. We used COVID-19 CG to detect other SNVs that could impact the use of this primer pair, discovering that there are SARS-CoV-2 variants in several countries with a different C29144T mutation at the very 3' end of the same NIID_2019-nCoV_N_F2 primer (Figure 3A). 2021 eLife Result SARS_CoV_2 C29144T 173 180 COVID-19 8 16 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. 16.7% of these mAbs demonstrated a >2-fold reduction of RBD binding in response to the N439K mutation (Figures 6C, 6D, and S5; Data S1). 2021 Cell Result SARS_CoV_2 N439K 87 92 RBD 56 59 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. 6.8% of the tested sera showed a >2-fold reduction in binding to N439K RBD as compared to WT (Figures 6A, 6B, and S4; Data S1). 2021 Cell Result SARS_CoV_2 N439K 65 70 RBD 71 74 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. A similar percentage, 9.7% for K417V and 14.6% for N439K/K417V, lost >2-fold binding to these variants (Figures 6C, 6D, and S5; Data S1). 2021 Cell Result SARS_CoV_2 K417V;N439K;K417V 31;51;57 36;56;62 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Across multiple assay formats, we found that the N439K and N439R variants exhibited an ~2-fold enhanced binding affinity for hACE2 as compared to the original N439 variant (termed herein WT) (Figure 4D). 2021 Cell Result SARS_CoV_2 N439K;N439R 49;59 54;64 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. All other results from the severity analysis were qualitatively similar to a previous analysis of the D614G mutation. 2021 Cell Result SARS_CoV_2 D614G 102 107 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Assuming the PCR was 95% efficient, then a mean Ct difference of 0.65 would represent an RNA copy number increase of 1.54-fold in N439K/D614G relative to N439/D614G. 2021 Cell Result SARS_CoV_2 N439K;D614G;D614G 130;136;159 135;141;164 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. At a minimum, we found no evidence for any decreased success of N439K lineage i relative to other lineages present in Scotland at the same time (Figure S3A). 2021 Cell Result SARS_CoV_2 N439K 64 69 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. At the nucleotide level, all N439K variants to date have arisen from the same mutation: a C-to-A transversion in the third codon position. 2021 Cell Result SARS_CoV_2 N439K 29 34 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Because salt bridges can be strong non-covalent bonds, and therefore the N439K mutation plausibly adds a strong interaction at the binding interface, we hypothesized that the N439K variant has enhanced binding for hACE2. 2021 Cell Result SARS_CoV_2 N439K;N439K 73;175 78;180 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Because Scotland has a high sampling frequency for its population size (Table S2), it is possible to calculate a growth rate for N439K lineage i based on a comparison with other Scottish lineages (see STAR methods and http://sars2.cvr.gla.ac.uk/RiseFallScotCOVID/). 2021 Cell Result SARS_CoV_2 N439K 129 134 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Because there is concern that mutations with high prevalence may have increased virus transmissibility, we next evaluated whether any difference could be detected in the rate of spread of the N439K lineages as compared to other lineages. 2021 Cell Result SARS_CoV_2 N439K 192 197 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Collectively, these results indicate that the N439K mutation results in viral fitness that is similar or possibly slightly improved relative to the WT N439 virus. 2021 Cell Result SARS_CoV_2 N439K 46 51 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Consistent with this prediction, VHH-72 showed enhanced potency against N439K SARS-CoV-2 pseudovirus compared to WT N439 (Figures 7A and 7C), highlighting the possibility that a single mutation can impact antibody efficacy positively as well as negatively. 2021 Cell Result SARS_CoV_2 N439K 72 77 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. D614G has previously been associated with higher viral loads/lower Ct values; although our data suggest a similar trend in a naive analysis, when controlling for confounders (given above), we could not detect this effect (Table S4). 2021 Cell Result SARS_CoV_2 D614G 0 5 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. For comparison, we also evaluated the K417V and N439K/K417V mutations. 2021 Cell Result SARS_CoV_2 K417V;N439K;K417V 38;48;54 43;53;59 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Having established that the N439K mutation has no detectable effect on virus replication, we sought to test whether it promotes evasion of antibody-mediated immunity by evaluating recognition of N439K RBD by mAbs and by polyclonal immune serum from 442 recovered individuals, including six donors who were infected by the SARS-CoV-2 N439K variant. 2021 Cell Result SARS_CoV_2 N439K;N439K;N439K 28;195;333 33;200;338 RBD 201 204 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. However, the N439K mutation appears in >6,000 additional sequences in the GISAID database as of January 6, 2021. 2021 Cell Result SARS_CoV_2 N439K 13 18 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. If detected cases represent 5%-33% of true infections, as has been estimated for the United States, then a very rough approximation of the actual cumulative number of N439K-associated infections would be in the range of 2-15 million. 2021 Cell Result SARS_CoV_2 N439K 167 172 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. If the proportion of N439K sequences in each country predicts what proportion of its confirmed infections are associated with N439K variants, then N439K variants correspond to ~764,000 of the confirmed SARS-CoV-2 infections as of January 6, 2021 (Table S2). 2021 Cell Result SARS_CoV_2 N439K;N439K;N439K 21;126;147 26;131;152 COVID-19 202 223 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. In addition to its frequency and repeated emergence, the N439K mutation stood out from other circulating RBM mutations as having a plausible mechanism for maintenance of viral fitness. 2021 Cell Result SARS_CoV_2 N439K 57 62 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Interestingly, 4,209 of sequences in lineage ii/B.1.258 also carry the S 69-70 deletion that has occurred independently multiple times in the pandemic and most notably with the Y453F amino acid replacement associated with mink infections. 2021 Cell Result SARS_CoV_2 Y453F 177 182 S 71 72 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. N439K demonstrated similar fitness as the WT N439 variant, with a slight fitness advantage for N439K in cells expressing TMPRSS2. 2021 Cell Result SARS_CoV_2 N439K;N439K 95;0 100;5 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. N439K is a prevalent RBM mutation (the second most common mutation in the RBD through the end of 2020) which was first sampled in March 2020 in Scotland from lineage B.1 on the background of D614G. 2021 Cell Result SARS_CoV_2 D614G;N439K 191;0 196;5 RBD 74 77 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. N439K lineages i and ii have recently received the lineage designations B.1.141 and B.1.258, respectively. 2021 Cell Result SARS_CoV_2 N439K 0 5 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. N439K RBD forms a new interaction with hACE2 and has enhanced hACE2 affinity. 2021 Cell Result SARS_CoV_2 N439K 0 5 RBD 6 9 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. N439K SARS-CoV-2 maintains fitness and virulence. 2021 Cell Result SARS_CoV_2 N439K 0 5 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Nevertheless, when comparing the percentage of N439K sequences over time in countries with sufficient data, the proportion can be significant: ~10% in Scotland from March to June 2020 and ~10% in Denmark from August to December 2020, both countries with high sequencing rates, and ~13% in Ireland from July to December 2020, where regional coverage is reasonable, but the sequencing rate is lower (Figure 3C). 2021 Cell Result SARS_CoV_2 N439K 47 52 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Our analysis found strong evidence that the N439K/D614G genotype was associated with marginally lower Ct than the N439/D614G genotype, even after controlling for confounders: age, sex, viral co-ancestry, and epidemic stage (mean Ct value difference between N439K/D614G and N439/D614G: -0.65, 95% confidence interval [CI]: -1.22, -0.07) (Figure 5B; Table S4). 2021 Cell Result SARS_CoV_2 N439K;N439K;D614G;D614G;D614G;D614G 44;257;50;263;119;278 49;262;55;268;124;283 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Our data are in line with the DMS results, which show a 2-fold loss of binding for K417V and no change for N439K/R, as the two assays are inherently different and the DMS data are much higher-throughput but lower sensitivity. 2021 Cell Result SARS_CoV_2 K417V;N439K;N439R 83;107;107 88;114;114 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Our ordinal regression indicated that the N439K/D614G viral genotype was associated with similar clinical outcomes compared to D614G or ancestral genotypes (posterior mean of N439K/D614G genotype effect: 0.06, 95% CI: -1.21, 1.33) (Table S5). 2021 Cell Result SARS_CoV_2 D614G;N439K;N439K;D614G;D614G 127;42;175;48;181 132;47;180;53;186 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Overall, the spread of N439K to at least 34 countries is concerning, as is its repeated independent emergence. 2021 Cell Result SARS_CoV_2 N439K 23 28 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Overall, these data indicate that acquisition of the N439K mutation enhances hACE2 binding, which could have implications in vivo in the context of infection and transmission. 2021 Cell Result SARS_CoV_2 N439K 53 58 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Phylogenetic analysis of the prevalent SARS-CoV-2 RBM mutation N439K. 2021 Cell Result SARS_CoV_2 N439K 63 68 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Sequence counts are heavily influenced by sampling frequency, which varies widely between countries, and N439K as a percentage of total sequences appears low: as of January 6, 2021, there have been 6,868 N439K observations in GISAID, 2% out of ~290,000 SARS-CoV-2 genome sequences for the 34 countries where this mutation has been detected (Table S2). 2021 Cell Result SARS_CoV_2 N439K;N439K 105;204 110;209 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Subsequently, numbers of N439K and all other variants decreased in Scotland concurrent with control of the pandemic after initiation of stringent public health measures, with this specific N439K lineage (designated here as lineage i) not being detected since June 2020 (Figures 3B and 3C). 2021 Cell Result SARS_CoV_2 N439K;N439K 25;189 30;194 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The enhanced affinity could compensate for other mutations that would otherwise decrease binding (e.g., K417V), further highlighting the plasticity of the RBM and the need for surveillance. 2021 Cell Result SARS_CoV_2 K417V 104 109 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The enhanced hACE2 affinity conferred by the N439K mutation, its geographical emergence as independent lineages, as well as its prevalence among circulating viral isolates is consistent with no effect on viral fitness. 2021 Cell Result SARS_CoV_2 N439K 45 50 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The equivalent position to N439K in the SARS-CoV RBM is also a positively charged amino acid (R426), which forms a salt bridge with hACE2 (Figure 4A). 2021 Cell Result SARS_CoV_2 N439K 27 32 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The low percent for E484 is also consistent with the non-conservative amino acid replacements observed for circulating variants (e.g., the most common E484 substitution is currently E484K), with a positively charged lysine substituting for the negatively charged glutamate. 2021 Cell Result SARS_CoV_2 E484K 182 187 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The magnitude of this enhancement was paralleled by an ~2-fold loss of binding affinity for the K417V variant relative to WT. 2021 Cell Result SARS_CoV_2 K417V 96 101 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The majority of the panel were site I, hACE2-blocking mAbs; the mAbs with sensitivity to N439K were enriched for site I mAbs with moderate or weak/no hACE2 blockade, consistent with the positioning of N439K at the edge of the RBM (Figures 1A and 6F; Data S1). 2021 Cell Result SARS_CoV_2 N439K;N439K 89;201 94;206 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The N439K mutation promotes evasion of antibody-mediated immunity. 2021 Cell Result SARS_CoV_2 N439K 4 9 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The N439K variant replicated slightly faster initially after inoculation (Figure 5D). 2021 Cell Result SARS_CoV_2 N439K 4 9 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The sera from the six individuals known to have recovered from infection with SARS-CoV-2 N439K virus all showed <2-fold change in binding levels to WT RBD as compared to N439K RBD (Figures 6A, 6B, and S4). 2021 Cell Result SARS_CoV_2 N439K;N439K 89;170 94;175 RBD;RBD 151;176 154;179 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. These clinical outcome data indicate that the N439K virus is neither linked to an attenuated phenotype nor linked to increased severity. 2021 Cell Result SARS_CoV_2 N439K 46 51 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. These experimental data indicate that the N439K mutation does not exhibit positive or negative effects on viral growth. 2021 Cell Result SARS_CoV_2 N439K 42 47 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. These results may relate to the improved hACE2 affinity measured for the N439K RBD in the SPR binding assays, or could relate to additional mechanisms, such as changes to S density on the viral particle surface or changes to the conformational dynamics of the S protein. 2021 Cell Result SARS_CoV_2 N439K 73 78 RBD;S;S 79;171;260 82;172;261 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Thus, the response to the RBD can be significantly influenced by the N439K mutation in a number of individuals infected by WT SARS-CoV-2. 2021 Cell Result SARS_CoV_2 N439K 69 74 RBD 26 29 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. To define the potential biological importance of these mutations for evasion of antibody-mediated neutralization, we tested mAbs against pseudoviruses expressing S variants N439K, K417V, and N439K/K417V (Figures 7A-7C and S7; Data S1). 2021 Cell Result SARS_CoV_2 K417V;N439K;N439K;K417V 180;173;191;197 185;178;196;202 S 162 163 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. To further assess fitness for replication in cultured cells, we carried out a cross-competition assay using inoculation of cells at a matched MOI followed by quantitation of N439 and N439K by metagenomic sequencing over time (Figure 5E). 2021 Cell Result SARS_CoV_2 N439K 183 188 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. To test this hypothesis, we used surface plasmon resonance (SPR) to evaluate binding of recombinant N439K S or RBD protein to recombinant hACE2. 2021 Cell Result SARS_CoV_2 N439K 100 105 RBD;S 111;106 114;107 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Using phylogenetic analysis, we determined that the earliest reported N439K sequences represented a single SARS-CoV-2 lineage (Figure 3A) that increased in frequency to 542 sequences in Scotland by June 20, 2020 (~10% of the available Scottish viral genome sequences for this time period). 2021 Cell Result SARS_CoV_2 N439K 70 75 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Variant counts for the clinical outcome analysis were double mutant (N439K/D614G, n = 399), D614G mutants (with N439 WT, n = 735), or ancestral genotype (N439/D614, n = 457). 2021 Cell Result SARS_CoV_2 D614G;N439K;D614G 92;69;75 97;74;80 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Variants were either N439K/D614G (n = 406), N439/D614G (n = 978), or ancestral (N439/D614) (n = 534). 2021 Cell Result SARS_CoV_2 N439K;D614G;D614G 21;27;49 26;32;54 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Very recently, this deletion has also been observed to co-occur with another RBM mutation, N501Y. 2021 Cell Result SARS_CoV_2 N501Y 91 96 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. We also evaluated the N439R and K417V variants, each of which are found in SARS-CoV at these positions, and the latter of which would remove a salt bridge at the RBD:hACE2 interface. 2021 Cell Result SARS_CoV_2 K417V;N439R 32;22 37;27 RBD 162 165 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. We also observe at least seven instances of the N439K mutation that have arisen independently of these two large lineages, including again in the United States in at least four linked infections, and in Brazil and Nigeria where no lineage ii/B.1.258 has been observed, resulting in a total of 34 countries where N439K has been detected to date (Figures 3A and 3B). 2021 Cell Result SARS_CoV_2 N439K;N439K 48;312 53;317 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. We also tested the effect of the N439K/R and K417V mutations in combination. 2021 Cell Result SARS_CoV_2 K417V;N439K;N439R 45;33;33 50;40;40 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. We determined the X-ray structure of the N439K RBD in complex with hACE2 at 2.8 A resolution and observed that this new interaction does indeed form (Figure 4C; Table S3). 2021 Cell Result SARS_CoV_2 N439K 41 46 RBD 47 50 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. We find that while the N439K/D614G lineage is one of the largest to emerge in Scotland, its growth rate is similar to the median N439/D614 or N439/D614G WT growth rates, with no evidence for a faster growth conferred by the N439K mutation (Figure S3A). 2021 Cell Result SARS_CoV_2 N439K;N439K;D614G;D614G 23;224;29;147 28;229;34;152 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. We next experimentally tested growth of two representative SARS-CoV-2 isolates, GLA1 (N439) and GLA2 (N439K), both with the D614G background (Table S6). 2021 Cell Result SARS_CoV_2 D614G;N439K 124;102 129;107 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. We set out to directly examine N439K impact on viral fitness by evaluating clinical data and outcomes associated with virus carrying the N439K mutation versus WT N439, as well as by direct in vitro viral growth and competition. 2021 Cell Result SARS_CoV_2 N439K;N439K 31;137 36;142 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. We therefore hypothesized that the N439K SARS-CoV-2 variant may form a similar salt bridge at the RBD-hACE2 interface (RBD N439K:hACE2 E329) (Figure 4B). 2021 Cell Result SARS_CoV_2 N439K;N439K 35;123 40;128 RBD;RBD 98;119 101;122 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. A D614G mutation in the S-protein could disturb the rigidity of the protein, and due to glycine, hydrophobicity will affect the intra-hydrogen bond formation with G594. 2021 mSystems Result SARS_CoV_2 D614G 2 7 S 24 25 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. Clade c descended from clade a had a different set of co-mutations with Nsp3-ORF8 proteins, while clade d descended further from clade c had two mutations in Nsp13 (P409L/Y446C) in addition to Nsp3/ORF8 proteins. 2021 mSystems Result SARS_CoV_2 P409L;Y446C 165;171 170;176 Nsp13;Nsp3;Nsp3;ORF8;ORF8 158;72;193;77;198 163;76;197;81;202 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. In the remaining eight genomes, five genomes (MT246474.1 [G-to-A substitution at position 354 with respect to the reference genome], MT276329.1, MT276330.1, and MT276598.1 [C-to-T substitution at position 313], and MT246455.1 [G-to-T substitution at position 332]) showed point mutations in the 5' CpG island, whereas three genomes (MT159718.1 [C-to-T substitution at position 2840] and MT159717.1 and MT184911.1 [G-to-T substitution at position 28378]) showed point mutations in the 3' CpG end. 2021 mSystems Result SARS_CoV_2 G354A;C2840T;C313T;G354A;G28378T 60;345;173;58;414 93;381;208;93;451 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. Interestingly, the mutation of L37F caused stiffness in the secondary structure of Nsp6 and leads to low stability of the protein structure as observed in most recent strains isolated from Asia, America, Oceania, and Europe. 2021 mSystems Result SARS_CoV_2 L37F 31 35 Nsp6 83 87 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. Mutation in ORF8 sequence (L84S) was found conserved; therefore, to predict its effect, it was critical to examine its biological function in SARS-CoV-2 interaction with human proteins. 2021 mSystems Result SARS_CoV_2 L84S 27 31 ORF8 12 16 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. Mutation L37F (Nsp6) and T85I (Nsp2) were also highly conserved and thus could profoundly damage the function of the respective protein. 2021 mSystems Result SARS_CoV_2 L37F;T85I 9;25 13;29 Nsp2;Nsp6 31;15 35;19 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. Out of 14 high-frequency SNPs, only 9 mutations (Nsp2 [T85I], Nsp3 [S1103P], Nsp6 [L37F], Nsp12 [P324L], Nsp13 [P409L and Y446C], S [D614G], Orf3a [Q577H], and Orf8 [L84S]) were found to be reflected at the protein level with the highest frequency of 238 in Nsp3 (Table 1). 2021 mSystems Result SARS_CoV_2 Y446C;D614G;L37F;L84S;P324L;P409L;Q577H;S1103P;T85I 122;133;83;166;97;112;148;68;55 127;138;87;170;102;117;153;74;59 ORF3a;Nsp13;Nsp12;Nsp2;Nsp3;Nsp3;Nsp6;ORF8;S 141;105;90;49;62;258;77;160;130 146;110;95;53;66;262;81;164;131 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. Overall, the results of structural and interactome analyses suggest that the identified mutations (Nsp2 [T85I], Nsp3 [S1103P], Nsp6 [L37F], Nsp12 [P324L], Nsp13 [P409L and Y446C], and S [D614G]) in SARS-CoV-2 might play an important role in modifying the efficacy of viral entry and its pathogenesis. 2021 mSystems Result SARS_CoV_2 Y446C;D614G;L37F;P324L;P409L;S1103P;T85I 172;187;133;147;162;118;105 177;192;137;152;167;124;109 Nsp13;Nsp12;Nsp2;Nsp3;Nsp6;S 155;140;99;112;127;184 160;145;103;116;131;185 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. Similarly, mutations present in the Nsp12, Nsp13, Nsp2, Nsp3, and Nsp6 of SARS-CoV-2 could inhibit the interaction with RPS6, but these mutations promote the binding with ATP6V1G1 except Nsp6 (L37F). 2021 mSystems Result SARS_CoV_2 L37F 193 197 Nsp13;Nsp12;Nsp2;Nsp3;Nsp6;Nsp6 43;36;50;56;66;187 48;41;54;60;70;191 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. The mutation (P409L) in Nsp13 was present in the RNA virus helicase C-terminal domain. 2021 mSystems Result SARS_CoV_2 P409L 14 19 Helicase;Nsp13 59;24 67;29 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. The mutation in spike protein (D614G) has been reported to outcompete other preexisting subtypes, including the ancestral one. 2021 mSystems Result SARS_CoV_2 D614G 31 36 S 16 21 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. The ORF3a mutation (Q57H) is located near tumor necrosis factor (TNF) receptor-associated factor 3 (TRAF-3) regions and has been reported as molecular difference marker in many genomes, including Indian SARS-CoV-2 genomes for their delineation. 2021 mSystems Result SARS_CoV_2 Q57H 20 24 ORF3a 4 9 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. The P324L (Nsp12) mutation was in the RNA binding domain located on the surface of the protein; modification of this residue could disturb interactions with other molecules or other parts of the protein. 2021 mSystems Result SARS_CoV_2 P324L 4 9 Nsp12 11 16 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. The P409L mutation leads to increased affinity of helicase RNA interaction, whereas Y446C is a destabilizing mutation increasing the molecular flexibility and leading to decreased affinity of helicase binding with RNA. 2021 mSystems Result SARS_CoV_2 P409L;Y446C 4;84 9;89 Helicase;Helicase 50;192 58;200 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. The presence of the Nsp3 mutation (S1103P) in 238 strains underlined the origin of mutation from the reference strain highlighting the first mutation- induced divergence in SARS-CoV-2 strains. 2021 mSystems Result SARS_CoV_2 S1103P 35 41 Nsp3 20 24 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. The protein stability analysis showed that all the identified mutations decreased the stability of seven proteins (Nsp2, Nsp6, Nsp12, Nsp13, S, Orf3a, and Orf8) except Nsp3 (T1103P) which was predicted to increase protein stability. 2021 mSystems Result SARS_CoV_2 T1103P 174 180 ORF3a;Nsp13;Nsp12;Nsp2;Nsp3;Nsp6;ORF8;S 144;134;127;115;168;121;155;141 149;139;132;119;172;125;159;142 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. This result suggests that the D614G mutation in S-protein could affect viral entry into the host. 2021 mSystems Result SARS_CoV_2 D614G 30 35 S 48 49 33628442 Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. According to Singapore's SARS-CoV-2 clade pattern from December 2019 till July 2020 based on n = 736 cases with genome availability, the D614G mutation, indicated as G clade following the GISAID clade nomenclature, only appeared in March 2020 (Figure 1c). 2021 Clinical & translational immunology Result SARS_CoV_2 D614G 138 143 33628442 Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. Hence, with knowledge on the D614G status of a subset of COVID-19 patients (n = 44 infected with D614, n = 6 infected with G614, n = 7 containing all other clades: O, S, L, V, G, GH or GR; Table 1, Figure 1c), the neutralising capacity of these anti-SARS-CoV-2 antibodies was assessed using pseudotyped lentiviruses expressing the SARS-CoV-2 S protein tagged with a luciferase reporter as a surrogate of live virus. 2021 Clinical & translational immunology Result SARS_CoV_2 D614G 29 34 S;S 167;342 168;343 COVID-19 57 65 33628442 Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. Of clinical importance, all the patients infected with either the D614 or G614 clade elicited a similar degree of neutralisation against both D614 and G614 pseudoviruses (Figure 1f), suggesting that the D614G mutation does not impact the neutralisation capacity of the elicited antibodies. 2021 Clinical & translational immunology Result SARS_CoV_2 D614G 204 209 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Based on discriminant mutation profiling in C3, the missense substitution C28311U (P13 L) in protein N might represent an important variation since it replaces a Proline by a Leucine at codon 13 in a structural protein. 2021 Virus research Result SARS_CoV_2 P13L;P13L 162;83 194;88 N 101 102 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Besides the five SNVs (C100U, G23012A, C28253U, G28628U, and G28975U) reported, we were able to detect two novel mutations in orf1ab, namely U10667G (L3468V) and C11824U (I3853I) both in orf1ab. 2021 Virus research Result SARS_CoV_2 G23012A;I3853I;L3468V 30;171;150 37;177;156 ORF1ab;ORF1ab 126;187 132;193 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Different from the first report, the missense variant G23012A (E484K) in S protein, associated with escape from neutralizing antibodies against SARS-CoV-2, occurred in all samples from this group suggesting mutation fixation. 2021 Virus research Result SARS_CoV_2 G23012A;E484K 54;63 61;68 S 73 74 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Given the emergence of this cluster as a potential novel lineage, we assigned the name VUI-NP13L until Pangolin provides a lineage classification. 2021 Virus research Result SARS_CoV_2 P13L 92 96 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. No alterations in amplification from target primers were observed in sequences with the P13L mutation. 2021 Virus research Result SARS_CoV_2 P13L 88 92 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Samples from C4 harbored a novel missense A23889G (K776R) in Spike, which was not observed in GISAID. 2021 Virus research Result SARS_CoV_2 A23889G;K776R 42;51 49;56 S 61 66 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. The synonymous variant U8514C (F2838F) detected in this group was not previously reported in GISAID, and is first described in this study. 2021 Virus research Result SARS_CoV_2 F2838F 31 37 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Thus, SARS-CoV-2 co-infection was characterized by the presence of the E484 K mutation in S protein supporting the hypothesis of co-infection by two distinct lineages of SARS-CoV-2 in both samples. 2021 Virus research Result SARS_CoV_2 E484K 71 77 S 90 91 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. 4B), H49Y (RMSD = 9.347 A. 2021 Scientific reports Result SARS_CoV_2 H49Y 5 9 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. 70% of the most populated conformations were grouped into the first 17, 15, 24, and 17 clusters for WT, D614G, H49Y, and T573I, respectively (Table S2); this clustering dispersion indicates that proteins possess a complex structural behavior. 2021 Scientific reports Result SARS_CoV_2 D614G;H49Y;T573I 104;111;121 109;115;126 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. According to PCA analysis, the first 15 eigenvectors captured 91-97% of the total protein motions (95.43, 91.22, 96.88, and 96.59% for WT, D614G, H49Y, and T573I, respectively). 2021 Scientific reports Result SARS_CoV_2 D614G;H49Y;T573I 139;146;156 144;150;161 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Also, hydrophobic interactions with Y449, N450, Y451, L452, E484, F490, L492, Q493 and S496 residues of the RBD domain of the D614G mutant were observed with cepharanthine. 2021 Scientific reports Result SARS_CoV_2 D614G 126 131 RBD 108 111 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. and T573I (RMSD = 9.368 A. 2021 Scientific reports Result SARS_CoV_2 T573I 4 9 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Aside, it was found that the H49Y mutant virus has increased cell entry compared to WT S protein. 2021 Scientific reports Result SARS_CoV_2 H49Y 29 33 S 87 88 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Cepharanthine bound to WT spike protein with the highest binding free energy (- 6.57 kcal/mol), followed by H49Y mutant (6.42 kcal/mol) that also interacts with residues of the RBD (Y449, N450, Y451, L452, F490, L492, S494, and Q493) only by hydrophobic interactions. 2021 Scientific reports Result SARS_CoV_2 H49Y 108 112 S;RBD 26;177 31;180 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Cepharanthine from H49Y-cepharanthine complex was a little bit displaced compared to the WT-cepharanthine complex, which might be responsible for the binding energy reduction. 2021 Scientific reports Result SARS_CoV_2 H49Y 19 23 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Comparing among mutants, it can be seen that nelfinavir-T573I complex was energetically more favorable than the corresponding with WT-nelfinavir complex (- 39.34 vs - 19.52 kcal/mol), followed by nelfinavir-H49Y complex, in whose case the binding free energy becomes more positive, indicating a lesser favored complex (- 13.96 vs - 19.52 kcal/mol). 2021 Scientific reports Result SARS_CoV_2 H49Y;T573I 207;56 211;61 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Contrarily, its complex with D614G was not energetically favorable (Table 1). 2021 Scientific reports Result SARS_CoV_2 D614G 29 34 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. D614G change is caused by an A/G nucleotide mutation at position 23,403 in the WT strain, this mutant is being associated with higher viral loads and enhances viral infection effectivity in patients. 2021 Scientific reports Result SARS_CoV_2 D614G 0 5 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. D614G shows compactness from 35 to 50 ns with values from 46 to 45 A, from 50 to 100 ns the Rg values are 45 A (+- 1), while T573I show compactness since the 25 to 40 ns of the trajectory with values from 47 to 43 A, from 50 to 100 ns the Rg values are 43 A (+- 1), respectively. 2021 Scientific reports Result SARS_CoV_2 T573I;D614G 125;0 130;5 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Finally, in T573I, the flexible regions were located at amino acids V62-Y204, P225-Y266, A363-N536, V736-A766, D830-L858, L962-T1009, and S1121-D1146 of the protein. 2021 Scientific reports Result SARS_CoV_2 T573I 12 17 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Finally, in the Cepharanthine-T573I complex, cepharanthine was slightly moved away from the initial binding site. 2021 Scientific reports Result SARS_CoV_2 T573I 30 35 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Finally, T573I mutant has no information available until now, but the change of T/I implies a modification from polar residue to non-polar hydrophobic residue changing the chemical environment to a more hydrophobic site. 2021 Scientific reports Result SARS_CoV_2 T573I 9 14 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Finally, the T573I mutation increases the magnitude of the protein's movements at the S1 subunit; regarding the S2 subunit, it was observed that the direction of the movements is opposite to the WT. 2021 Scientific reports Result SARS_CoV_2 T573I 13 18 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. followed by D614G (RMSD = 9.391 A. 2021 Scientific reports Result SARS_CoV_2 D614G 12 17 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. For Hydroxychloroquine complexes, those formed with WT and D614G were diffused, indicating that a favorable complex was not formed. 2021 Scientific reports Result SARS_CoV_2 D614G 59 64 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. From the trajectories of hydroxychloroquine with WT and the mutated proteins, it was observed that D614G complex form the most stable complex with values around 5 A (+- 1). 2021 Scientific reports Result SARS_CoV_2 D614G 99 104 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. H49Y mutant is produced by C/T change at position 21,707 in the WT from S protein sequence, producing a residue change from a positive histidine to an aromatic and polar tyrosine (H/Y). 2021 Scientific reports Result SARS_CoV_2 H49Y 0 4 S 72 73 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. H49Y present compactness from 30 to 50 ns with values from 48 to 43 A, in the last 30 ns remains around 45 A (+- 1). 2021 Scientific reports Result SARS_CoV_2 H49Y 0 4 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. H49Y showed slightly higher conformational mobility in comparison to T573I system. 2021 Scientific reports Result SARS_CoV_2 T573I;H49Y 69;0 74;4 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. However, for D614G the direction of the movement changes in comparison to WT, the magnitude of the movement was higher for RBD region and S2 subunit, contrastingly for the NTD segment, a significantly minor detriment in the magnitude of the movements was observed. 2021 Scientific reports Result SARS_CoV_2 D614G 13 18 RBD 123 126 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. However, it is interesting how T573I and H49Y mutant produce more energetically favorable complex, so further experimental studies regarding these other spike inhibitors deserve to be experimentally studied. 2021 Scientific reports Result SARS_CoV_2 H49Y;T573I 41;31 45;36 S 153 158 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. However, the highest values on this zone belong to H49Y and followed by T573I. 2021 Scientific reports Result SARS_CoV_2 H49Y;T573I 51;72 55;77 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. In D614G mutant, the fluctuations were located between amino acids T63-D88, T95-Y200, P209-Y265, T323-P589, S735-K776, G832-L864, T961-T1017, and W1046-P1069. 2021 Scientific reports Result SARS_CoV_2 D614G 3 8 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. In H49Y, the most flexible residues were A67-D80, T108-S116, K129-Y170, V320-P589, I693-S721, D830-F855, and A1070-D1146. 2021 Scientific reports Result SARS_CoV_2 H49Y 3 7 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. In its complex with H49Y, cepharanthine is still bound to the same place as at the beginning of the MD simulation. 2021 Scientific reports Result SARS_CoV_2 H49Y 20 24 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. In RMSF values for the trajectory with hydroxychloroquine, the T573I shows the higher values at RBD domain followed by the D614G, while the WT and H49Y have the lowest values. 2021 Scientific reports Result SARS_CoV_2 D614G;H49Y;T573I 123;147;63 128;151;68 RBD 96 99 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. In T573I mutant, reduced fluctuations from amino acids I587-I720 were observed, which correspond to the central portion of the protein, this lead to a more compacted form of the protein, which is in line with the Rg observations; therefore, T573I mutation seems to induce structural stability compared to the WT protein as well as in the region around where the mutation is found. 2021 Scientific reports Result SARS_CoV_2 T573I;T573I 3;241 8;246 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. In the case of cepharanthine complexes, the WT-cepharanthine complex (- 15.53 kcal/mol) was the least favorable in comparison to the corresponding complex with mutant proteins, where the most favorable complex was formed with H49Y (- 19.43 kcal/mol), followed by T573I (- 18.83 kcal/mol) and D614G (- 16.36 kcal/mol). 2021 Scientific reports Result SARS_CoV_2 D614G;H49Y;T573I 292;226;263 297;230;268 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. In the case of H49Y mutant, the whole mobility decreased, which was reflected in the magnitude of the porcupine representation in. 2021 Scientific reports Result SARS_CoV_2 H49Y 15 19 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. In the case of nelfinavir-T573I mutant complex, interacted mainly with residues of the HR1 region by the formation of hydrogen bonds with amino acids S943, D950 and D954, and by hydrophobic interactions with K947, V951, R1014, it also formed a hydrogen bond with K310 and hydrophobic interaction with P665. 2021 Scientific reports Result SARS_CoV_2 T573I 26 31 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. In the case of WT and the D614G mutant, the ligand diffuses from the proteins. 2021 Scientific reports Result SARS_CoV_2 D614G 26 31 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. In WT S protein and both D614 and H49Y mutants, hydroxychloroquine interacted with residues of the RBD that participate in ACE-RBD recognition. 2021 Scientific reports Result SARS_CoV_2 H49Y 34 38 RBD;RBD;S 99;127;6 102;130;7 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Interaction of the chemical compound hydroxychloroquine and H49Y mutant is mediated by the formation of hydrogen bonds with amino acids S349, Y449, N450, and S494 and by hydrophobic interactions with R346, F347, A348, Y351, A352, Y451 and L452. 2021 Scientific reports Result SARS_CoV_2 H49Y 60 64 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Interestingly, the Nelfinavir-H49Y complex also shows nine van der Waals contacts but no localized interaction. 2021 Scientific reports Result SARS_CoV_2 H49Y 30 34 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. It seems that T573I mutation might affect the binding affinity of this protein with cepharanthine and maybe the reason for the biological effect of cepharanthine as anti-SARS-CoV-2 agent. 2021 Scientific reports Result SARS_CoV_2 T573I 14 19 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Multiple sequence alignments of reported SARS-CoV-2 S proteins sequence show three mutants present in Mexican population (H49Y, T573I, and D614G). 2021 Scientific reports Result SARS_CoV_2 D614G;T573I;H49Y 139;128;122 144;133;126 S 52 53 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Nelfinavir was bound to WT S protein with the highest binding free energy (- 7.88 kcal/mol), followed by H49Y (- 7.52 kcal/mol), D614G (- 6.10 kcal/mol), and finally, T573I mutant (- 5.38 kcal/mol). 2021 Scientific reports Result SARS_CoV_2 D614G;H49Y;T573I 129;105;167 134;109;172 S 27 28 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. On the other hand, D614G mutant substitutions change from negative charge and high hindrance effects to none-radical group (H), which showed a stabilizing structure, suggesting a prevalent role in S protein evolution. 2021 Scientific reports Result SARS_CoV_2 D614G 19 24 S 197 198 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. On the other hand, D614G showed a more compact cluster distribution than the other systems, suggesting a reduction in conformational mobility due to single residue mutation; additionally, it showed a dissimilar conformer distribution along the subspace in comparison to the others systems, this behavior suggests that the trajectory sampled different regions of the phase space with different minima and small energy barrier, in this sense, D614G mutant affects the structural behavior of the protein, which is also reflected in the conformations observed during MD simulation. 2021 Scientific reports Result SARS_CoV_2 D614G;D614G 19;441 24;446 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. On the other hand, hydroxychloroquine and T573I mutant interacting residues were F342, W436, and R509, with which the compound formed hydrogen bonds and hydrophobic interactions were observed with amino acids S438, L441, N343, A344, S373, F374, N437, S438, which are not involved in ACE2-RBD interaction. 2021 Scientific reports Result SARS_CoV_2 T573I 42 47 RBD 288 291 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Only energetically favorable complexes were formed with T573I (- 15.53 kcal/mol) and H49Y (- 14.05 kcal/mol), in which case is found among the least favorable complexes, this points out that hydroxychloroquine did not form stable complexes with WT spike protein and D614G- Pandey et al., found by molecular docking that hydroxychloroquine has lower affinity by WT S protein, which could be due to the labile and bulkier carbon chain, which disturb hydroxychloroquine binding reducing in this way the binding site. 2021 Scientific reports Result SARS_CoV_2 D614G;H49Y;T573I 266;85;56 271;89;61 S;S 248;364 253;365 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. RMSF values with nelfinavir ligand present similar values for all the protein-ligand trajectories at the RBD, but shows an increase in fluctuation on the residues located at S1 for H49Y, WT, and D614G. 2021 Scientific reports Result SARS_CoV_2 D614G;H49Y 195;181 200;185 RBD 105 108 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. S1C), but this complex at the last 10 ns of the trajectory loses the equilibrium, whereas the trajectory with H49Y reach the equilibrium at 20 ns and remain for the rest of the trajectory with values at 8 A (+- 1). 2021 Scientific reports Result SARS_CoV_2 H49Y 110 114 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Similar behavior as with cepharanthine was observed, hydroxychloroquine reaches its binding site on the RBD of the WT spike protein as well as on the D614G and H49Y mutants, while in T573I mutant hydroxychloroquine was moved away from this site, and it was reflected on the detriment of the binding free energy (Table S3. 2021 Scientific reports Result SARS_CoV_2 D614G;H49Y;T573I 150;160;183 155;164;188 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Similar cluster distribution was observed for H49Y and T573I mutants. 2021 Scientific reports Result SARS_CoV_2 H49Y;T573I 46;55 50;60 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Specifically, WT structural differences were observed in most of the structure, it is RBD region, HR1 (T912-L984) region, central helix (CH, D985-G1035) region, and small differences were observed from amino acids D287-F318 that are part of the N-terminal domain (NTD), and G550-T696 that include fusion peptide domain (FPD) belonging to the S1 subunit, in previous reports higher fluctuations on RBD region in monomeric and trimeric form were found; contrastingly, D614G mutant showed differences in regions spanning from D287-Q321 to T530-T696 which indicates that a single residue mutation affected the stability of the central portion of the S protein structure compared to the WT S protein. 2021 Scientific reports Result SARS_CoV_2 D614G 466 471 RBD;RBD;N;S;S 86;397;245;646;685 89;400;246;647;686 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. The hydroxychloroquine complexes were only stable with the H49Y and T573I mutants, where they migrate from different pockets of the RBD regions. 2021 Scientific reports Result SARS_CoV_2 H49Y;T573I 59;68 63;73 RBD 132 135 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. The hydroxychloroquine-T573I complex shows one H H weak hydrogen bond with A522 and act as an acceptor for a C-H pi interaction formed with I332. 2021 Scientific reports Result SARS_CoV_2 T573I 23 28 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. The interaction of this compound with D614G is mediated by the formation of hydrogens bonds between the compound and amino acids E484, F490, L492 and Q493 and hydrophobic interactions with S494, Y449, L452, L455 and P491. 2021 Scientific reports Result SARS_CoV_2 D614G 38 43 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. The nelfinavir trajectories show the most stables trajectories with D614G; however, it was dissociated at the last five ns of the trajectory. 2021 Scientific reports Result SARS_CoV_2 D614G 68 73 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. The nelfinavir-T573I has a greater number of localized interactions. 2021 Scientific reports Result SARS_CoV_2 T573I 15 20 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. The pi-interactions govern the complexation of hydroxychloroquine with H49Y. 2021 Scientific reports Result SARS_CoV_2 H49Y 71 75 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. The RMSF values of the trajectories with cepharanthine show that D614G exhibited the highest fluctuations on the RBD zone, follows by the WT, while T573I possesses the lowest fluctuations at this region. 2021 Scientific reports Result SARS_CoV_2 D614G;T573I 65;148 70;153 RBD 113 116 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. The T573I complexes reach equilibrium at 25 ns with values at 9 A (+ 1). 2021 Scientific reports Result SARS_CoV_2 T573I 4 9 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. The trajectories with cepharanthine show that the most stable trajectory at 50 ns corresponds to H49Y with values at 7 A (+- 1), while the trajectory of the WT is still unstable. 2021 Scientific reports Result SARS_CoV_2 H49Y 97 101 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Therefore, the ligand-protein interaction depicted a similar energy behavior than the observed with cepharanthine and hydroxychloroquine, where WT protein-ligand complex has the highest binding energy, while T573I-ligand complex has the lowest binding energy, which could indicate that the mutation on T573I position could be relevant for drug-spike protein interaction affecting not only the binding mode but also the binding free energy. 2021 Scientific reports Result SARS_CoV_2 T573I;T573I 208;302 213;307 S 344 349 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. These results are consistent with the in silico predictions of energetic stability induced mainly by H49Y mutation and, to a lesser extent, by D614G mutant. 2021 Scientific reports Result SARS_CoV_2 D614G;H49Y 143;101 148;105 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. This analysis explains why the Nelfinavir-T573I system has such great free energy of binding compared to the rest of the complexes, which is also predicted by the NCI integrals. 2021 Scientific reports Result SARS_CoV_2 T573I 42 47 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. To test the stability of the ligand-S protein complexes (WT, H49Y, D614G and T573I) obtained by molecular docking, 50 ns of MD simulation studies were carried out. 2021 Scientific reports Result SARS_CoV_2 D614G;H49Y;T573I 67;61;77 72;65;82 S 36 37 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Whereas nelfinavir docking with H49Y mutant was through a couple of residues of the HR1 region and by hydrophobic interactions with amino acids (A942 and S943), in addition, nelfinavir also interacted with residues of the N-terminal domain of the S protein (S13-L303) and with amino acids (T302, L303, K304) by hydrogens bonds, and with residues (V47, L48, Y49, S305) by hydrophobic interactions, in this case, nelfinavir was displaced out from the HR domain more evidently than with the D614G mutant. 2021 Scientific reports Result SARS_CoV_2 D614G;H49Y 488;32 493;36 N;S 222;247 223;248 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Whereas, the projections of the first two principal components (PC1 vs PC2) contributed to 54-72% of the collective motions (72.13, 54.02, 73.16, and 71.95% for WT, D614G, H49Y, and T573I, respectively). 2021 Scientific reports Result SARS_CoV_2 D614G;H49Y;T573I 165;172;182 170;176;187 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. While in the H49Y mutant, structural changes were observed in RBD and NTD domain compared to WT; H49Y induces fewer structural changes on the HR1 region, which correspond to what we observed in the above RMSD and RMSF. 2021 Scientific reports Result SARS_CoV_2 H49Y;H49Y 13;97 17;101 RBD 62 65 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. While the nelfinavir-D614G complex was not energetically favorable (Table 1). 2021 Scientific reports Result SARS_CoV_2 D614G 21 26 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. While within the T573I mutant, cepharanthine moved away from the typical interaction site and formed hydrogen bond with R509 and hydrophobic interactions with F342, N343, A344, W436, N437, S438, N439 and N440 none of these residues belong to ACE2-RBD interacting residues. 2021 Scientific reports Result SARS_CoV_2 T573I 17 22 RBD 247 250 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. While, D614G and T573I showed a decrease in binding free energy (- 5.95 and - 5.39, respectively). 2021 Scientific reports Result SARS_CoV_2 D614G;T573I 7;17 12;22 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. With D614G, it is slightly displaced with respect to the initial site. 2021 Scientific reports Result SARS_CoV_2 D614G 5 10 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. WT and D614G proteins exhibited differences in their secondary structure and displacements in loops, alpha-helices, and beta-sheets structures, leading to a more compacted structure than WT S in agreement with our Rg findings. 2021 Scientific reports Result SARS_CoV_2 D614G 7 12 S 190 191 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. WT S protein showed similar clustering dispersion with D614G and T573I, while H49Y mutant showed higher clustering dispersion, which suggests it has complex structural behavior. 2021 Scientific reports Result SARS_CoV_2 D614G;H49Y;T573I 55;78;65 60;82;70 S 3 4 33634309 A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. Although an effect is clearly predicted for A570D, due to the differences in interactions around A570 shown in Figure 5, whether it is as large as that reported for D614G, and whether it would tend towards further opening (beyond the D614G level) or revert to more closed (towards the D614 level), is unknown. 2021 Briefings in bioinformatics Result SARS_CoV_2 A570D;D614G;D614G 44;165;234 49;170;239 33634309 A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. Comparison of LA bound and unbound closed trimer structures reveals that interactions around R355 and D614 both vary, coupling an important SARS-CoV-2 variant (D614G) to the charge pair examined currently (D398-R355). 2021 Briefings in bioinformatics Result SARS_CoV_2 D614G 160 165 33634309 A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. Environments around D398 - R355 and D614 are summarized in Figure 5A, for 6zp2 (closed S trimer with LA bound), 6zp1 (closed S trimer without LA), 7kdk (closed D614G S trimer) and 7a98 (open S trimer). 2021 Briefings in bioinformatics Result SARS_CoV_2 D614G 160 165 S;S;S;S 87;125;166;191 88;126;167;192 33634309 A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. From the current work, since there is a concerted change in structural environments, it is suggested that A570D could alter the balance of closed to open conformation through a similar mechanism to D614G. 2021 Briefings in bioinformatics Result SARS_CoV_2 A570D;D614G 106;198 111;203 33634309 A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. Further, the effects of LA binding extend also to the region around D614, where close packing leads to the hypothesis that D614 interactions act as a latch for the closed state which is lost with D614G mutation. 2021 Briefings in bioinformatics Result SARS_CoV_2 D614G 196 201 33634309 A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. In the absence of a structure for A570D, this uncertainty is shown schematically in Figure 5B. 2021 Briefings in bioinformatics Result SARS_CoV_2 A570D 34 39 33634309 A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. It has been reported that evolution of the furin cleavage site at the S1/S2 junction and the D614G mutation act to balance infectivity and stability of SARS-CoV-2. 2021 Briefings in bioinformatics Result SARS_CoV_2 D614G 93 98 33634309 A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. The D614G structure is more open around G614, and intermediate (between closed trimers with and without LA) around R355. 2021 Briefings in bioinformatics Result SARS_CoV_2 D614G 4 9 33634309 A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. This is an intriguing hypothesis in the context of the establishment of the D614G mutation in SARS-CoV-2 genomes over the first year of the pandemic, and reports that the mutation may bias towards the (ACE2 binding) open form, altering barriers to conformational change between open and closed. 2021 Briefings in bioinformatics Result SARS_CoV_2 D614G 76 81 33634309 A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. This is of interest since A570D is one of a set of S protein mutations that contribute to the B.1.1.7 lineage of SARS-CoV-2 reported towards the end of 2020. 2021 Briefings in bioinformatics Result SARS_CoV_2 A570D 26 31 S 51 52 33634309 A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. Thus far A570D has not been included in those discussions. 2021 Briefings in bioinformatics Result SARS_CoV_2 A570D 9 14 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. In cat 5, however, two different variants in ORF1ab, G1756G and L3606F, became fixed after transmission. 2021 PLoS pathogens Result SARS_CoV_2 G1756G;L3606F 53;64 59;70 ORF1ab 45 51 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Interestingly, S H655Y and E S67S became fixed together following transmission in two transmission pairs (contact cats 4 and 6) and were lost together during transmission to contact animal 5. 2021 PLoS pathogens Result SARS_CoV_2 H655Y;S67S 17;29 22;33 E;S 27;15 28;16 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Neither of these iSNVs were detected above 3% frequency in the inoculum, but when we mined all sequencing reads, S H655Y and E S67S could be detected at 0.85% and 0.34%, respectively. 2021 PLoS pathogens Result SARS_CoV_2 H655Y;S67S 115;127 120;131 E;S 125;113 126;114 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. ORF1ab G1756G was not detected above 3% and L3606F was found at 17.2% in the day 5 sample from the index cat 2 (the cat transmitting to cat 5); it was not found in the inoculum at any detectable frequency. 2021 PLoS pathogens Result SARS_CoV_2 G1756G;L3606F 7;44 13;50 ORF1ab 0 6 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. S H655Y and E S67S were detectable on days 1-7 in cat 3 but stayed below consensus level. 2021 PLoS pathogens Result SARS_CoV_2 H655Y;S67S 2;14 7;18 E;S 12;0 13;1 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. S H655Y was the consensus sequence on days 2-5 and days 7-8 in index cat 1, as well as on days 4 and 8 in index cat 2, and remained detectable above our 3% variant threshold throughout infection (Fig 3). 2021 PLoS pathogens Result SARS_CoV_2 H655Y 2 7 S 0 1 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Similarly, envelope S67S (E S67S) was the consensus sequence on day 8 in index cat 1 and day 1 in index cat 2. 2021 PLoS pathogens Result SARS_CoV_2 S67S;S67S 20;28 24;32 E 26 27 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. This consensus sequence remained largely unchanged throughout infection in all index cats with the notable exception of two variants: H655Y in Spike (nucleotide site 23,525) and a synonymous change at amino acid position 67 in envelope (nucleotide site 26,445; S67S), which arose rapidly in all 3 index cats and rose to consensus levels (>=50% frequency) at various timepoints throughout infection in all index cats. 2021 PLoS pathogens Result SARS_CoV_2 H655Y;S67S 134;261 139;265 S 143 148 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. A slight fluctuation (~0.5 A) was noticed in the A191V. 2021 Saudi journal of biological sciences Result SARS_CoV_2 A191V 49 54 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. A191V has been reported so far in 34 countries. 2021 Saudi journal of biological sciences Result SARS_CoV_2 A191V 0 5 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. A191V, another active site mutation with occurrence rate of 0.30% of the total sampled sequence was also considered in this study. 2021 Saudi journal of biological sciences Result SARS_CoV_2 A191V 0 5 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. MD studies for the top-scoring molecule from each category in complex with their respective target (Imiglitazar-WT, PF-03715455-Y54C, Salvianolic-A-N142S, Salvianolic-A-T190I and Montelukast-A191V) were performed. 2021 Saudi journal of biological sciences Result SARS_CoV_2 A191V;N142S;T190I;Y54C 191;148;169;128 196;153;174;132 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. miltiorrhiza was found to be most effective against the N142S and T190I. 2021 Saudi journal of biological sciences Result SARS_CoV_2 N142S;T190I 56;66 61;71 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. Montelukast, was found to be the most active compound against A191V. 2021 Saudi journal of biological sciences Result SARS_CoV_2 A191V 62 67 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. N142S was another mutation considered in this study, has been reported 17 times from 5 different countries. 2021 Saudi journal of biological sciences Result SARS_CoV_2 N142S 0 5 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. PF-03715455, a p38 inhibitor administrated for the treatment of chronic obstructive pulmonary disease was found to be most effective against Y54C Mpro. 2021 Saudi journal of biological sciences Result SARS_CoV_2 Y54C 141 145 Chronic obstructive pulmonary disease 64 101 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. Salvianolic-A was found to be highly stable with T190I mutant, and a deviation of less than 2 A was observed, while this compound was found to be unstable with the N142S mutant. 2021 Saudi journal of biological sciences Result SARS_CoV_2 N142S;T190I 164;49 169;54 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. T190I, a mutation occurring 110 times (0.03% of the sequenced NSP5) has been reported from 15 different countries (https://www.gisaid.org/). 2021 Saudi journal of biological sciences Result SARS_CoV_2 T190I 0 5 Nsp5 62 66 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. This compound also demonstrated high binding affinity against N142S, T190I and A191V, where it was binding with the PLP fitness score of 94.66, 88.58 and 92.62, respectively (Table 2 ). 2021 Saudi journal of biological sciences Result SARS_CoV_2 A191V;N142S;T190I 79;62;69 84;67;74 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. This compound known for its chemo preventative and cardioprotective properties was found to bind with the PLP fitness score of 97.85 and 94.2 against N142S and T190I, respectively (Table 1, Table 2). 2021 Saudi journal of biological sciences Result SARS_CoV_2 N142S;T190I 150;160 155;165 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. This selective cysteinyl leukotriene receptor antagonist was found to be very effective against T190I and N142S as well (Table 2). 2021 Saudi journal of biological sciences Result SARS_CoV_2 N142S;T190I 106;96 111;101 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. While Salvianolic-A was not forming the constant hydrogen bonds with the N142S mutant, while for the T190I mutant the hydrogen bonds were mostly constant throughout the simulation. 2021 Saudi journal of biological sciences Result SARS_CoV_2 N142S;T190I 73;101 78;106 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. Y54C, an Mpro mutant reported in March 2020 in Malaysia was considered in this study. 2021 Saudi journal of biological sciences Result SARS_CoV_2 Y54C 0 4 33655250 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. 20C/CAL.20C) that has risen to high frequency in southern California contains L452R, which escapes LY-CoV555. 2021 bioRxiv Result SARS_CoV_2 L452R 78 83 33655250 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. 20J/501Y.V3) lineages contain combinations of mutations (E484K and K417N/T) that individually escape each antibody. 2021 bioRxiv Result SARS_CoV_2 K417N;K417T;E484K 67;67;57 74;74;62 33655250 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. have reported that E484K and K417N dramatically and specifically reduce neutralization by LY-CoV555 and LY-CoV016, respectively, while N501Y has no impact on neutralization by either antibody. 2021 bioRxiv Result SARS_CoV_2 E484K;K417N;N501Y 19;29;135 24;34;140 33655250 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. However, there are some sites where single mutations escape binding by both LY-CoV555 and LY-CoV016, and as a result a 1:1 cocktail of the two antibodies is escaped by several single mutations including I472D, G485P, and Q493R/K. 2021 bioRxiv Result SARS_CoV_2 G485P;I472D;Q493K;Q493R 210;203;221;221 215;208;228;228 33655250 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. Mutations at position Q493 are notably well tolerated with respect to ACE2 binding and RBD expression (Fig 1A, S2):indeed, Q493K has been observed in a persistently infected immunocompromised patient. 2021 bioRxiv Result SARS_CoV_2 Q493K 123 128 RBD 87 90 33655250 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. The escape mutations present at the highest frequency among sequenced isolates are E484K, L452R, and S494P for LY-CoV555, and K417N/T for LY-CoV016. 2021 bioRxiv Result SARS_CoV_2 E484K;K417N;K417T;L452R;S494P 83;126;126;90;101 88;133;133;95;106 33655250 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. We also note that single mutations that escape both antibodies (Q493R and Q493K) have been observed in a handful of sequenced isolates. 2021 bioRxiv Result SARS_CoV_2 Q493K;Q493R 74;64 79;69 33662015 Genomic characterization and evolution of SARS-CoV-2 of a Canadian population. Among all the nonsynonymous mutations, only S1841 (D614G) is located in Spike, but not in RBD region. 2021 PloS one Result SARS_CoV_2 D614G 51 56 S;RBD 72;90 77;93 33662015 Genomic characterization and evolution of SARS-CoV-2 of a Canadian population. Three variants T8502C (ORFla), T10506C (ORF1a), and C6017T (ORF1b) found in this Canadian population were rare among other populations (frequencies < 1%) (Table 2). 2021 PloS one Result SARS_CoV_2 C6017T;T10506C;T8502C 52;31;15 58;38;21 ORF1a 40 45 33662015 Genomic characterization and evolution of SARS-CoV-2 of a Canadian population. We found that 3 out of 11 non-synonymous substitutions affected functions (deleterious) of SARS-CoV-2, including P1427L (ORF1b), Y1464C (ORF1b), and Q57H (ORF3a), implying potential changes of fitness of the strains harbouring these mutations (Table 3). 2021 PloS one Result SARS_CoV_2 P1427L;Q57H;Y1464C 113;149;129 119;153;135 ORF3a 155 160 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. A B.1.1.7 isolate had signature changes in the spike gene including the 69-70 and 144-145 deletions, and N501Y, A570D, D614G, and P681H substitutions. 2021 Nature medicine Result SARS_CoV_2 A570D;D614G;N501Y;P681H 112;119;105;130 117;124;110;135 S 47 52 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. A heatmap analysis showed that most individuals lost neutralizing activity against all three viruses containing the E484K and N501Y mutations (Fig 2f). 2021 Nature medicine Result SARS_CoV_2 E484K;N501Y 116;126 121;131 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Although the S309 + S2E12 combination showed reduced (~10-fold) potency against the E484K/N501Y/D614G strain, it performed effectively against the Wash SA-B.1.351 virus, again suggesting that additional mutations in natural variants (e.g., K417N) enable some antibodies to function better against viruses containing E484K and N501Y mutations. 2021 Nature medicine Result SARS_CoV_2 E484K;E484K;K417N;N501Y;D614G;N501Y 84;316;240;326;96;90 89;321;245;331;101;95 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Based on experiments with the mAbs, we used Vero-hACE2-TMPRSS2 cells and focused our testing on WA1/2020 D614G, B.1.1.7, Wash SA-B.1.351, and WA1/2020 D614G with mutations at K417N, E484K/N501Y, or K417N/E484K/N501Y (Fig 2 and Extended Data Fig 4). 2021 Nature medicine Result SARS_CoV_2 D614G;D614G;E484K;K417N;K417N;E484K;N501Y;N501Y 105;151;182;175;198;204;188;210 110;156;187;180;203;209;193;215 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Compared to the D614G virus, mAbs COV2-2196, COV2-3025, COV2-2381 and S2E12 showed 4- to 5-fold reduced activity against the E484K virus, and COV2-2050, 1B07, COVOX-384, and S2H58 lost virtually all neutralizing potential; (e) The combination of E484K and N501Y mutations, which is present in the circulating South African B.1.351 and Brazilian B.1.1.248 strains, showed even greater effects (6- to 13-fold reductions) on the activity of class 1 mAbs COV2-2196, COV2-3025, COV2-2381, and S2E12 mAbs; (f) When we tested class 1 mAbs for inhibition of the Wash SA-B.1.351 virus containing the full South African spike sequence, as expected, several mAbs (COV2-2050, 1B07, COVOX-384, and S2H58) lost activity in both Vero-hACE2-TMPRSS2 and Vero-TMPRSS2 cells. 2021 Nature medicine Result SARS_CoV_2 D614G;E484K;E484K;N501Y 16;125;246;256 21;130;251;261 S 610 615 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Compared to the WA1/2020 D614G variant, we observed moderate reductions in neutralizing activity (GMTs) of B.1.1.7 (2-fold, P < 0.01; Fig 4a) and E484K/N501Y (4-fold, P < 0.0001; Fig 4c) and larger decreases in activity against Wash SA-B.1.351 (10-fold, P < 0.0001; Fig 4d), with all subjects showing substantially reduced potency (Fig 4f), results that agree with pseudovirus studies. 2021 Nature medicine Result SARS_CoV_2 D614G;E484K;N501Y 25;146;152 30;151;157 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. For serum samples from mice, when comparing the GMTs of neutralization to the WA1/2020 D614G strain, we observed a slight increase (1.9-fold, P < 0.05) with K417N (Fig 3b), decreases with E484K/N501Y (9-fold, P < 0.001; Fig 3c), K417N/E484K/N501Y (5-fold, P < 0.01; Fig 3d), and Wash SA-B.1.351 (5-fold, P < 0.01; Fig 3e), yet no significant differences with B.1.1.7. 2021 Nature medicine Result SARS_CoV_2 D614G;E484K;K417N;K417N;E484K;N501Y;N501Y 87;188;157;229;235;194;241 92;193;162;234;240;199;246 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Given the limited remaining serum quantities, we performed neutralization experiments on Vero-TMPRSS2 cells with WA1/2020 D614G, B.1.1.7, and Wash SA-B.1.351, and Wash BR-B.1.1.248 viruses. 2021 Nature medicine Result SARS_CoV_2 D614G 122 127 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Given these results with viruses encoding E484K mutations, we performed separate studies with human convalescent serum (n =10) and a chimeric SARS-CoV-2 WA1/2020 strain encoding a Brazilian variant spike gene (Wash BR-B.1.1.248; L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F [Extended Data Fig 5a]). 2021 Nature medicine Result SARS_CoV_2 D138Y;D614G;E484K;E484K;H655Y;K417T;L18F;N501Y;P26S;R190S;T1027I;T20N;V1176F 247;282;42;268;289;261;229;275;241;254;296;235;308 252;287;47;273;294;266;233;280;245;259;302;239;314 S 198 203 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. However, the reductions in neutralizing potential by other class 1 mAbs (COV2-2196, COV2-3025, COV2-2381, and S2E12) seen against the E484K/N501Y virus were absent with Wash SA-B.1.351, which contains additional mutations. 2021 Nature medicine Result SARS_CoV_2 E484K;N501Y 134;140 139;145 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. If anything, several class 1 mAbs and also SARS2-44 showed slightly improved inhibitory activity (P = 0.002, two-tailed Wilcoxon matched-pairs signed rank test) with this mutation; (c) Mutation at N501Y reduced the neutralizing activity of COVOX-40, SARS2-31, and SARS2-10 slightly but did not alter the potency of other mAbs substantively; this result is consistent with data showing that human convalescent sera efficiently neutralize viruses with N501Y substitutions; (d) The E484K mutation negatively impacted the potency of several class 1 antibodies. 2021 Nature medicine Result SARS_CoV_2 E484K;N501Y;N501Y 479;197;450 484;202;455 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. In a heatmap plot (Fig 3p), 9 of the 10 mouse sera show a loss of neutralizing activity against multiple viruses containing the E484K mutation. 2021 Nature medicine Result SARS_CoV_2 E484K 128 133 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. In comparison, with B.1.1.7 (Fig 3k) or K417N (Fig 3l) viruses, we detected no or small (1.5-fold increase, P < 0.05) significant differences in neutralization, respectively. 2021 Nature medicine Result SARS_CoV_2 K417N 40 45 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. In NHPs, we also observed a substantial decrease (9- to 11-fold, P < 0.05) in serum neutralization of E484K/N501Y, K417N/E484K/N501Y, and Wash SA-B.1.351 (Fig 3m-o). 2021 Nature medicine Result SARS_CoV_2 E484K;K417N;E484K;N501Y;N501Y 102;115;121;108;127 107;120;126;113;132 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Initially, we performed neutralization tests with WA1/2020 D614G and the two Vero cell types (Fig 1d-i and Extended Data Fig 2). 2021 Nature medicine Result SARS_CoV_2 D614G 59 64 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. It was difficult to assess the impact of the P681H and other mutations on the NTD mAbs, since these mAbs neutralized the D614G virus poorly at baseline in Vero-hACE2-TMPRSS2 cells; (b) The K417N mutation resulted in ~27-fold reduction in neutralization by mAb COVOX-40 but did not negatively affect other mAbs in our panel. 2021 Nature medicine Result SARS_CoV_2 D614G;K417N;P681H 121;189;45 126;194;50 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Significant differences in neutralizing activity were not detected with K417N/D614G (Fig 4b). 2021 Nature medicine Result SARS_CoV_2 K417N;D614G 72;78 77;83 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Statistically significant differences in neutralization were not observed with K417N and B.1.1.7 viruses (Fig 3f, g). 2021 Nature medicine Result SARS_CoV_2 K417N 79 84 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. The heatmap analysis showed that all NHP sera consistently exhibited reduced neutralizing activity against viruses containing the E484K mutation (Fig 3r). 2021 Nature medicine Result SARS_CoV_2 E484K 130 135 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. The K417N substitution, which is located at the edge of the RBM (Fig 1b) and enhances neutralization by some class 1 mAbs, may compensate for the negative effects on inhibition of the E484K/N501Y mutations. 2021 Nature medicine Result SARS_CoV_2 E484K;K417N;N501Y 184;4;190 189;9;195 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. These experiments (Extended Data Fig 9) revealed the following: (a) Convalescent and vaccine sera showed small yet significant reductions (1.7- to 2.5- fold, P < 0.01) in neutralizing activity of B.1.1.7 compared to the WA1/2020 D614G virus (Fig 5a, e). 2021 Nature medicine Result SARS_CoV_2 D614G 229 234 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Using Vero-hACE2-TMPRSS2 cells, we assessed serum neutralization of WA1/2020 D614G, B.1.1.7, Wash SA-B.1.351, and recombinant WA1/2020 D614G viruses with mutations at K417N, E484K/N501Y, or K417N/E484K/N501Y (Extended Data Fig 6). 2021 Nature medicine Result SARS_CoV_2 D614G;D614G;E484K;K417N;K417N;E484K;N501Y;N501Y 77;135;174;167;190;196;180;202 82;140;179;172;195;201;185;207 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. We created a chimeric, fully-infectious SARS-CoV-2 with a South African spike gene (Wash SA-B.1.351; D80A, 242-244 deletion, R246I, K417N, E484K, N501Y, D614G, and A701V) and a panel of isogenic spike mutants (D614G, K417N/D614G, E484K/D614G, N501Y/D614G, P681H/D614G, del69-70/N501Y/D614G, E484K/N501Y/D614G, and K417N/E484K/N501Y/D614G) in the Washington strain background (2019n-CoV/USA_WA1/2020 [WA1/2020]). 2021 Nature medicine Result SARS_CoV_2 A701V;D614G;D80A;E484K;E484K;E484K;K417N;K417N;K417N;N501Y;N501Y;P681H;R246I;D614G;D614G;D614G;D614G;D614G;D614G;D614G;D614G;E484K;N501Y;N501Y;N501Y 164;153;101;139;230;291;132;217;314;146;243;256;125;210;223;236;249;262;284;303;332;320;278;297;326 169;158;105;144;235;296;137;222;319;151;248;261;130;215;228;241;254;267;289;308;337;325;283;302;331 S;S 72;195 77;200 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. We observed a marked decrease (10- to 12-fold, P < 0.01) in serum neutralization of E484K/N501Y, K417N/E484K/N501Y, and Wash SA-B.1.351 (Fig 3h-j). 2021 Nature medicine Result SARS_CoV_2 E484K;K417N;E484K;N501Y;N501Y 84;97;103;90;109 89;102;108;95;114 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. We observed the following patterns with the variant viruses: (a) The P681H mutation (in the C-terminal region of S1) and the 69-70 deletion (in the NTD) had marginal effects on neutralization potency of the RBM and RBD mAbs we evaluated. 2021 Nature medicine Result SARS_CoV_2 P681H 69 74 RBD 215 218 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. When compared to the WA1/2020 D614G virus, we observed the following: (a) differences in neutralization were not observed with the B.1.1.7 strain (Fig 2a); (b) a small increase (1.5-fold, P < 0.05) in neutralization was detected with the K417N virus (Fig 2b), similar to that seen with some mAbs (Fig 1h); (c) serum neutralization titers were lower against E484K/N501Y (5-fold, P < 0.0001), K417N/E484K/N501Y (3.5-fold, P < 0.0001), and Wash SA-B.1.351 (4.6-fold, P < 0.0001) viruses (Fig 2c-e), all of which contain the E484K mutation. 2021 Nature medicine Result SARS_CoV_2 D614G;E484K;E484K;K417N;K417N;E484K;N501Y;N501Y 30;357;521;238;391;397;363;403 35;362;526;243;396;402;368;408 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. With the D614G strain, neutralization by the majority of class 1 and class 2 mAbs was similar in Vero-hACE2-TMPRSS2 and Vero-TMPRSS2 cells. 2021 Nature medicine Result SARS_CoV_2 D614G 9 14 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. Antibodies belonging to this group showed lower affinity to the S protein trimer (KD 64.0 E-10M-757.0 E-10M) compared to Group I nAbs and medium neutralization potencies ranging from 155.0 to 492.2 ng/mL against the authentic WT and D614G (Figures 3D-3I; Figure S4; Table S5). 2021 Cell Result SARS_CoV_2 D614G 233 238 S 64 65 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. In addition to the D614G and the B.1.1.7 variants, the S1 RBD-specific nAb J08 showed also to neutralize SARS-CoV-2 variants containing the E484K mutation. 2021 Cell Result SARS_CoV_2 D614G;E484K 19;140 24;145 RBD 58 61 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. nAbs were tested against lentiviral pseudotypes expressing the SARS-CoV-2, SARS-CoV-2 D614G, SARS-CoV, and Middle East respiratory syndrome (MERS)-CoV S protein on their viral membrane surface. 2021 Cell Result SARS_CoV_2 D614G 86 91 Membrane;S 176;151 184;152 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. Neutralization activity was shown against SARS-CoV-2 and D614G pseudotypes, therefore confirming previous data. 2021 Cell Result SARS_CoV_2 D614G 57 62 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. The antibody J08-MUT also showed extreme neutralization potency against emerging variants as it was able to neutralize the B.1.1.7 with an identical IC100 compared to the WT virus (Figure S6K; Table S5) and has also showed to neutralize variants that include the E484K mutation. 2021 Cell Result SARS_CoV_2 E484K 263 268 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. The first group (Group I) is composed of S1 RBD-specific nAbs (J08, I14, F05, G12, C14, and B07), which showed neutralization potency against the authentic wild type (WT), the D614G variant, and the emerging variant recently isolated in the UK B.1.1.7. 2021 Cell Result SARS_CoV_2 D614G 176 181 RBD 44 47 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. The first two point mutations (M428L and N434S) were introduced to enhance antibody half-life and to increase tissue distribution and persistence. 2021 Cell Result SARS_CoV_2 N434S;M428L 41;31 46;36 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. The Group IV nAb L19 shows the lowest neutralization potency with 19.8 mug/mL for the authentic WT, 12.5 mug/mL against the D614G, and 9.9 mug/mL against the B.1.1.7 variant (Figures 3D-3I; Table S5). 2021 Cell Result SARS_CoV_2 D614G 124 129 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. The remaining three point mutations (L234A, L235A, and P329G) were introduced to reduce antibody dependent functions such as binding to FcgammaRs and cell-based activities. 2021 Cell Result SARS_CoV_2 L235A;P329G;L234A 44;55;37 49;60;42 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. The three engineered antibodies were tested to confirm their binding specificity and neutralization potency against both the WT, the widespread SARS-CoV-2 D614G mutant and the emerging variant B.1.1.7 to evaluate their cross-neutralization ability. 2021 Cell Result SARS_CoV_2 D614G 155 160 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. The three engineered nAbs maintained their S1 domain binding specificity and extremely high neutralization potency with J08-MUT and F05-MUT being able to neutralize both the WT and the D614G variant with an IC100 lower than 10 ng/mL (both at 3.9 ng/mL for the WT and the D614G strains) (Figure S6F - K; Table S5). 2021 Cell Result SARS_CoV_2 D614G;D614G 185;271 190;276 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. In particular, as our previous findings pointed to differences in mutation profiles between the two groups, we compared isolates that carried the 14408C>T and the 23403A>G mutations to isolates that did not. 2021 Infection, genetics and evolution Result SARS_CoV_2 C14408T;A23403G 146;163 154;171 33671631 Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants. One third of the 20A samples (52 out of 146) belonged to a variant characterized by the G29734C mutation in the 3'UTR region. 2021 Microorganisms Result SARS_CoV_2 G29734C 88 95 3'UTR 112 117 33671631 Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants. The D614G mutation in the Spike protein (A23403G) was detected in 16.7% of the samples from the first week (year-week 10), quickly increased in frequency up to 90% in the next two weeks and stayed over 80% until the end of the study period (Figure 1). 2021 Microorganisms Result SARS_CoV_2 D614G;A23403G 4;41 9;48 S 26 31 33671631 Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants. There were 17 mutations found in more than ten genomes, many of them are among the most frequently found globally, including a cluster of five mutations associated to clades 20A and 20B (lineage B and its sublineages): C241T (5'UTR, 78.1% of the samples), C3037T (nsp3 F924F, 79.5%), C14408T (nsp12 P4715L, 76.3%), A20268G (nsp15 L216L, 68.8%) and A23403G (Spike D614G, 79.5%). 2021 Microorganisms Result SARS_CoV_2 A20268G;A23403G;C14408T;C241T;C3037T;D614G;F924F;L216L;P4715L 315;348;284;219;256;363;269;330;299 322;355;291;224;262;368;274;335;305 S;5'UTR;Nsp12;Nsp3 357;226;293;264 362;231;298;268 33672021 Molecular Epidemiological Investigation of a Nosocomial Cluster of C. auris: Evidence of Recent Emergence in Italy and Ease of Transmission during the COVID-19 Pandemic. A genetic alteration recently associated with a high-level resistance to fluconazole, due to a transcriptional upregulation of ABC-type efflux pumps, was additionally identified in all sequenced isolates in TAC1B(A640V). 2021 Journal of fungi (Basel, Switzerland) Result SARS_CoV_2 A640V 213 218 33672021 Molecular Epidemiological Investigation of a Nosocomial Cluster of C. auris: Evidence of Recent Emergence in Italy and Ease of Transmission during the COVID-19 Pandemic. auris isolates belonging to the South Asian clade, a strong association with the ERG11(K143R) variant was observed at a global level (Figure 2B), corroborating a significant contribution of both alterations to clinical fluconazole resistance. 2021 Journal of fungi (Basel, Switzerland) Result SARS_CoV_2 K143R 87 92 33672021 Molecular Epidemiological Investigation of a Nosocomial Cluster of C. auris: Evidence of Recent Emergence in Italy and Ease of Transmission during the COVID-19 Pandemic. Conversely, the presence of the same amino acid substitution ERG11(K143R), being previously shown to reduce azole susceptibility, has been detected in all isolates. 2021 Journal of fungi (Basel, Switzerland) Result SARS_CoV_2 K143R 67 72 33672021 Molecular Epidemiological Investigation of a Nosocomial Cluster of C. auris: Evidence of Recent Emergence in Italy and Ease of Transmission during the COVID-19 Pandemic. Interestingly, following a large-scale analysis of WGS data aimed at evaluating the distribution and frequency of the TAC1B(A640V) substitution over 400 C. 2021 Journal of fungi (Basel, Switzerland) Result SARS_CoV_2 A640V 124 129 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. A single Q18stop/E110stop ORF8 sequence was classified in clade 20A. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 Q18X;E110X 9;17 16;25 ORF8 26 30 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. Although with much lower numbers, the mutation K68stop (n = 16) was found in the background of five spike mutations. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 K68X 47 54 S 100 105 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. Apart from D614G, the most frequent mutations were the two spike deletions, HV69-70del (n = 62) and Y145H/del (n = 48). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 D614G;Y145del;Y145H 11;100;100 16;109;109 S 59 64 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. D614G was the only spike mutation associated with all ORF8 mutations, being found in 1704 genomes. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 D614G 0 5 S;ORF8 19;54 24;58 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. Despite having a lower number of sequence (n = 158), Q27stop stands out for being associated with seven different spike mutations, explained by the inclusion of the VOC-202012/01. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 Q27X 53 60 S 114 119 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. Eleven spike mutations were not found associated with ORF8 variants: L8V/W, N234Q, Q239K, L452R, A475V, G476S, V483A, F490L, V615I/F, A831V and D839Y/N/E. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 A475V;A831V;D839E;D839N;D839Y;F490L;G476S;L452R;L8V;L8W;N234Q;Q239K;V483A;V615F;V615I 97;134;144;144;144;118;104;90;69;69;76;83;111;125;125 102;139;153;153;153;123;109;95;74;74;81;88;116;132;132 S;ORF8 7;54 12;58 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. For example, a variant with five spike mutation, three of relevance (L5F, HV69-70del and D614G), was found associated with E59stop in a sample from Poland (EPI_ISL_732828). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 D614G;E59X;L5F 89;123;69 94;130;72 S 33 38 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. I found one sequence (EPI_ISL_700264) with three (G8stop, E106stop and E110stop) and 247 sequences with two ORF8 premature stop codons. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E106X;E110X;G8X 58;71;50 66;79;56 ORF8 108 112 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. I found that 95.3% of ORF8-deficient variants had the spike D614G mutation. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 D614G 60 65 S;ORF8 54;22 59;26 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. If E106stop and E110stop occurred first in those lineages, there may not be any selective relaxation for the occurrence of the second premature stop codon. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E106X;E110X 3;16 11;24 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. Interestingly, 98% (243 out of 248) of the cases with more than one nonsense mutation included the two most ORF8 C-terminal premature stop codons (E106stop and E110stop). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E110X;E106X 160;147 168;155 ORF8 108 112 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. Interestingly, this cluster did not include the VOC-202012/01 variant (defined by having Q27stop), but had some spike mutations of interest. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 Q27X 89 96 S 112 117 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. Nevertheless, E106stop and E110stop were the most prevalent mutations in variants with more than one premature stop. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E106X;E110X 14;27 22;35 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. Q27stop and E106stop stand out by being present in more than 20 countries, despite being represented here by less than 200 sequences each. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E106X;Q27X 12;0 20;7 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. SARS-CoV-2 variants with ORF8 Q27stop and E106stop are found in more than 20 countries, despite not being the most frequent ones. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E106X;Q27X 42;30 50;37 ORF8 25 29 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. Ten sequences with five spike mutations were found associated with Q18stop, in three different combinations and branches of the SARS-CoV-2 phylogeny. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 Q18X 67 74 S 24 29 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The 11 spike mutations found in both Q27stop and K68stop (I68del, HV69-70del, Y144del, Y145H/del, N501Y, A570D, D614G, P681H, T716I, S982A and D1118H) were found in eight sequences from England and two from the Netherlands (Table 1). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 A570D;D1118H;D614G;K68X;N501Y;P681H;Q27X;S982A;T716I;Y144del;Y145H;Y145del;I68del 105;143;112;49;98;119;37;133;126;78;87;87;58 110;149;117;56;103;124;44;138;131;85;96;96;64 S 7 12 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The 20B clade includes 265 (76.1%) of the 348 E64stop sequences. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E64X 46 53 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The highest mean number of spike mutations per genome was observed in ORF8 variants K68stop (mean = 4; SD = 4.43), K53stop (mean = 3; SD = 0), Q27stop (mean = 2.51; SD = 2.75) and G50stop (mean = 2.40; SD = 1.30), as shown in Supplementary. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 G50X;K53X;K68X;Q27X 180;115;84;143 187;122;91;150 S;ORF8 27;70 32;74 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The HV69-70del mutation was found in six different ORF8 nonsense mutations, including the Q27stop observed in the VOC-202012/01 variant. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 Q27X 90 97 ORF8 51 55 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The list includes two deletions (HV69-70del and Y145H/del) that remove amino acids from the spike protein. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 Y145H;Y145del 48;48 53;57 S 92 97 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The maximum number of spike mutations in a genome was found associated with Q27stop and K68stop (11 mutations), explained by including the VOC-202012/01. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 K68X;Q27X 88;76 95;83 S 22 27 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The most divergent sequences within the Q18stop/E110stop cluster had five spike mutations and were detected in England. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 Q18X;E110X 40;48 47;56 S 74 79 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The most frequent combination of ORF8 mutations included Q18stop and E110stop, found in 241 sequences. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E110X;Q18X 69;57 77;64 ORF8 33 37 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The next ORF8-deficient variant (E64stop) had six spike mutations (I68del, HV69-70del, L189F, N439K, D614G and V772I), two of them of putative biological relevance (HV69-70del and D614G). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 D614G;D614G;L189F;N439K;V772I;E64X 101;180;87;94;111;33 106;185;92;99;116;40 S;ORF8 50;9 55;13 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The only exception were the five sequences from the VOC-202012/01 variant that had both Q27stop and K68stop mutations. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 K68X;Q27X 100;88 107;95 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The ORF8 Q18stop mutation was the most frequent in our dataset (n = 534) and was associated with the largest number of different spike mutations (n = 8. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 Q18X 9 16 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The ORF8-deficient variants detected in more countries were E64stop (25 countries), E106stop (24 countries), Q18stop (23 countries) and Q27stop (20 countries), as shown in. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E106X;E64X;Q18X;Q27X 84;60;109;136 92;67;116;143 ORF8 4 8 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The phylogenetic inference also revealed a large cluster of related ORF8-deficient variants with E64stop in clade 20B. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E64X 97 104 ORF8 68 72 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The Q18stop/E110stop cluster of variants explained near half of the Q18stop cases and more than two thirds of the E110stop cases. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E110X;Q18X;Q18X;E110X 114;4;68;12 122;11;75;20 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The Q18stop/E110stop ORF8 variants formed a large cluster in clade 20B. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 Q18X;E110X 4;12 11;20 ORF8 21 25 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The Q27stop is present in the VOC-202012/01 variant, which lacks the widespread D614G mutation. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 D614G;Q27X 80;4 85;11 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The same pattern was observed even for rare mutations, including the five mutations observed in less than 10 sequences each (L7stop, Q29stop, K44stop, L60stop and C61stop). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 C61X;K44X;L60X;Q29X;L7X 163;142;151;133;125 170;149;158;140;131 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The spike L5F mutation was also observed in the background of six different ORF8 nonsense mutations. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L5F 10 13 S;ORF8 4;76 9;80 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. This pattern may indicate that both regions (Latvia and Northern Ireland/England) shared an early variant with an E64stop, which then spread locally in both areas. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E64X 114 121 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. Variants with Q27stop and E106stop did not form any clear cluster, despite being frequent in our dataset. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E106X;Q27X 26;14 34;21 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. When considered independently, the most frequent ORF8 nonsense mutations were Q18stop (n = 534), E64stop (n = 348), E110stop (n = 306), Q27stop (n = 158) and E106stop (n = 123) (Table 1). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E106X;E110X;E64X;Q18X;Q27X 158;116;97;78;136 166;124;104;85;143 ORF8 49 53 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. When excluding variants with D614G, the top countries were England (n = 106), Denmark (n = 40), Netherlands (n = 16), Scotland (n = 12) and USA (n = 8), as shown in Supplementary. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 D614G 29 34 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. When not considering D614G, all variants with ORF8 nonsense mutations were found in at least two countries. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 D614G 21 26 ORF8 46 50 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Among sub-haplogroups in clade 2, subclade 2A with the amino acid changes in Spike D614G and Nucleocapsid R203K and G204R was highly prevalent in Asia (18.82%) and Europe (29.72%), respectively (Supplemental. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;G204R;R203K 83;116;106 88;121;111 N;S 93;77 105;82 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Analysis of the daily new SARS-CoV-2 genome sequences indicated that the first clade 1 variant containing the amino acid change at ORF8 L84S was sequenced from the isolate (2019-nCoV_HKU-SZ-002a_2020, GenBank: MN938384) collected in January 10, 2020 in China, and then clade 1 variants were spread in all continents with approximately 85% (n = 909) in America, just around 7% in Asia (n = 70), and Oceania (n = 82), respectively. 2021 Infection, genetics and evolution Result SARS_CoV_2 L84S 136 140 ORF8 131 135 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. In addition, the sequence of haplotype clade 2 was first reported in the variant with the change at Spike D614G on January 28, 2020 in Germany (GenBank: MT270101). 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 106 111 S 100 105 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Interestingly, clade 2 with the mutation Spike D614G was the most predominant and prevalent haplotype among global variants. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 47 52 S 41 46 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Interestingly, sub-haplogroup 1A variants with the amino acid changes at nsp15 V172L and ORF8 L84S were observed only in Thailand (Supplemental. 2021 Infection, genetics and evolution Result SARS_CoV_2 L84S;V172L 94;79 98;84 ORF8 89 93 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Moreover, subclade 2C variant with the changes at Spike D614G, ORF3a Q57H, and nucleocapsid S194L (GenBank: MT630421) was first reported in Saudi Arabia on March 15. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;Q57H;S194L 56;69;92 61;73;97 N;S;ORF3a 79;50;63 91;55;68 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Most subclade 2C variants (92.86%) with the amino acid changes at Spike D614G, ORF3a Q57H, and Nucleocapsid S194L was prevalent in Asia counties, including India (61/70), Bangladesh (3/70), and Saudi Aribia (1/65) (Supplemental. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;Q57H;S194L 72;85;108 77;89;113 N;S;ORF3a 95;66;79 107;71;84 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Recently, only 2 variants with the changes at Spike D614G (haplotype 1) and ORF8 L84S (haplotype 2) were detected in USA on March 24. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;L84S 52;81 57;85 S;ORF8 46;76 51;80 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Remarkably, among the subclades in clade 2, sub-haplogroup 2B variants (Spike D614G, ORF3a Q57H, and nsp2 T85I) distributed quickly, and then dominated in this continent. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;Q57H;T85I 78;91;106 83;95;110 S;ORF3a;Nsp2 72;85;101 77;90;105 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Sub-clade 1B with the amino acid changes at nsp1 D75E, nsp3 P153L, and ORF8 V62L and L84S was reported in USA (57/73) and Australia (16/73). 2021 Infection, genetics and evolution Result SARS_CoV_2 D75E;L84S;P153L;V62L 49;85;60;76 53;89;65;80 Nsp3;ORF8 55;71 59;75 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Sub-clade 1C with the amino acid changes at nsp13 P504L and ORF8 L84S was the largest sub-haplogroup in clade 1 among all genome sequences from global (19.91%), America (26.29%) and Oceania (6.52%), respectively. 2021 Infection, genetics and evolution Result SARS_CoV_2 L84S;P504L 65;50 69;55 Nsp13;ORF8 44;60 49;64 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Sub-clade 2A with the amino acid changes at Spike D614G and Nucleocapsid R203K and G204R was the second most frequent sub-clade among haplotype 2, and appeared in all continents. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;G204R;R203K 50;83;73 55;88;78 N;S 60;44 72;49 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Subclade 2A variant with the changes at Spike D614G and nucleocapsid R203K and G204R (GenBank: MT358640) was firstly sequenced and reported on February 15 in Germany. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;G204R;R203K 46;79;69 51;84;74 N;S 56;40 68;45 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Subclade 2B with the amino acid changes at nsp2 T85I, Spike D614G, and ORF3a Q57H was firstly reported on March 4, 2020 in USA, becoming the most frequent sub-clade in the world (36.21%) and America (45.81%), respectively. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;Q57H;T85I 60;77;48 65;81;52 S;ORF3a;Nsp2 54;71;43 59;76;47 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. The first subclade 2B variant with the changes at Spike D614G, ORF3a Q57H, and nsp2 T85I (GenBank: MT325596) was documented in USA on March 4. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;Q57H;T85I 56;69;84 61;73;88 S;ORF3a;Nsp2 50;63;79 55;68;83 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. The phylogenetic analysis of genome sequences from 4230 SARS-CoV-2 variants by the NJ method indicated four haplotypes with the unique nucleotide variation and amino acid changes: T27879C (ORF8 L84S) in clade 1 (1072 variants, 25.34%), A23138G (spike D614G) in clade 2 (2688 variants, 63.54%), G10818T (nsp6 L37F), C14540T (nsp12 T442I), and G25879T (ORF3a V251F) in clade 3 (109 variants, 2.58%), and miscellaneous changes in clade 4 (361 variants, 8.54%). 2021 Infection, genetics and evolution Result SARS_CoV_2 A23138G;C14540T;D614G;G10818T;G25879T;L37F;L84S;T27879C;T442I;V251F 236;315;251;294;342;308;194;180;330;357 243;322;256;301;349;312;198;187;335;362 S;ORF3a;Nsp12;Nsp6;ORF8 245;351;324;303;189 250;356;329;307;193 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. Altogether, these results suggest the SARS-CoV-2 Malaysia isolate was subjected to intense positive selection pressure and a persistent D614G mutation identified may be responsible for the quick spread of SARS-CoV-2 in Malaysia. 2022 Materials today. Proceedings Result SARS_CoV_2 D614G 136 141 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. An earlier study showed that the substitution of Asp614 with glycine changes hydrogen bonding around residue 614, as the Asp614-Thr859 hydrogen bond was eliminated while interaction with intradomain Ala647 was strengthened. 2022 Materials today. Proceedings Result SARS_CoV_2 D614G 49 68 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. Gained in molecule flexibility due to D614G mutation in Pahang/IIUM91 may increase protein thermostability, enabling the mutated virus to absorb more heat for the same increase in temperature than wild-type virus. 2022 Materials today. Proceedings Result SARS_CoV_2 D614G 38 43 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. In this study, we reported that the D614G mutated SARS-CoV-2 of Pahang isolate-Pahang/IIUM91earlier collected from an asymptomatic patient on April 2, 2020 (highlighted in grey (Table 2)) has been deposited in GenBank and GISAID database with the accession number MW079428 and the GISAID EpiCoV EPI_ISL_455313, respectively. 2022 Materials today. Proceedings Result SARS_CoV_2 D614G 36 41 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. Insight into the mechanism by which D614G increases infectivity, D614G mutation had increased both the stability (Table 5 ) and molecule flexibility (Table 6 ) of Pahang/IIUM91 Spike protein. 2022 Materials today. Proceedings Result SARS_CoV_2 D614G;D614G 36;65 41;70 S 177 182 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. On top of that, disruption of the interprotomer latch between D614 in S1 and T859 in S2 due to D614G mutation results in increased distance between the promoters and a dramatic flip in the ratio of open to closed Spike protein particle, thus more open confirmation of its RBD. 2022 Materials today. Proceedings Result SARS_CoV_2 D614G 95 100 S;RBD 213;272 218;275 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. These conformational changes in G614 trimmer, rendered virus with D614G mutating to be more immunogenic than wild-type D614 virus. 2022 Materials today. Proceedings Result SARS_CoV_2 D614G 66 71 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. This study also reported that of 250 high coverage complete genome hCoV-19/Malaysia strains deposited in the GISAID database, 114 of the virus strains harboured D614G mutations in Spike protein (Table 3 ). 2022 Materials today. Proceedings Result SARS_CoV_2 D614G 161 166 S 180 185 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. While MOH announced D614G mutation was first identified in Malaysia on July 13, 2020, which belongs to Sivagangga cluster in Kedah, our analysis revealed 31 strains of hCoV-19/Malaysia harbouring D614G mutation were detected as early as in March to May 2020 (Table 2 ). 2022 Materials today. Proceedings Result SARS_CoV_2 D614G;D614G 20;196 25;201 33683658 Isolation and genetic characterization of SARS-CoV-2 from Indian patients in a single family without H/O travel abroad. A1812D mutation was in the protease domain of nsp3 region of orf1ab protein. 2021 Virus genes Result SARS_CoV_2 A1812D 0 6 ORF1ab;Nsp3 61;46 67;50 33683658 Isolation and genetic characterization of SARS-CoV-2 from Indian patients in a single family without H/O travel abroad. A1812D, P1821S and Q677H mutations, respectively, in nsp3, exoN of ORF1ab and spike protein were unique to IRSHA isolates. 2021 Virus genes Result SARS_CoV_2 P1821S;Q677H;A1812D 8;19;0 14;24;6 ORF1ab;S;Nsp3;Exon 67;78;53;59 73;83;57;63 33683658 Isolation and genetic characterization of SARS-CoV-2 from Indian patients in a single family without H/O travel abroad. Eight mutations resulted in amino acid changes at positions 5700 (nsp3, A1812D), 14,408 (RdRp, P314L), 18,928 (3' to 5' exonuclease, exoN, P1821S), 23,403 (spike protein, D614G), and 23,593 (spike protein, Q677H). 2021 Virus genes Result SARS_CoV_2 A1812D;D614G;P1821S;P314L;Q677H 72;171;139;95;206 78;176;145;100;211 Exonuclease;S;S;Nsp3;Exon;RdRP 120;156;191;66;133;89 131;161;196;70;137;93 33683658 Isolation and genetic characterization of SARS-CoV-2 from Indian patients in a single family without H/O travel abroad. In our isolates, a unique mutation Q677H located near the S1-S2 junction region (681-684) might affect the SARS-CoV-2 fusion with cell membrane. 2021 Virus genes Result SARS_CoV_2 Q677H 35 40 Membrane 135 143 33683658 Isolation and genetic characterization of SARS-CoV-2 from Indian patients in a single family without H/O travel abroad. IRSHA sequences clustered together with sequences derived from Italy and other European countries are classified as clade G due to the presence of D614G mutation in the spike protein. 2021 Virus genes Result SARS_CoV_2 D614G 147 152 S 169 174 33683658 Isolation and genetic characterization of SARS-CoV-2 from Indian patients in a single family without H/O travel abroad. Mutation in exoN, P1821S might increase the fidelity of RNA synthesis by correcting nucleotide incorporation errors made by RdRp. 2021 Virus genes Result SARS_CoV_2 P1821S 18 24 Exon;RdRP 12;124 16;128 33683658 Isolation and genetic characterization of SARS-CoV-2 from Indian patients in a single family without H/O travel abroad. On several introductions / transmissions of SARS-CoV-2 in Europe, D614G mutation was identified in Italian patients with no travel history. 2021 Virus genes Result SARS_CoV_2 D614G 66 71 33683658 Isolation and genetic characterization of SARS-CoV-2 from Indian patients in a single family without H/O travel abroad. Origin of D614G variant, located in the S1 domain of spike protein, was associated with accelerating the spread of infections in Europe and North America. 2021 Virus genes Result SARS_CoV_2 D614G 10 15 S 53 58 33683658 Isolation and genetic characterization of SARS-CoV-2 from Indian patients in a single family without H/O travel abroad. The distribution of the 11 mutations recorded was C241T (5'UTR), C313T, C3037T, C5700A, C14408T, C18928T (ORF1ab), A23403G, G23593C (spike protein) and G28881A, G28882A, G28883C (nucleocapsid phosphoprotein) (Table 1). 2021 Virus genes Result SARS_CoV_2 A23403G;C14408T;C18928T;C241T;C3037T;C313T;C5700A;G23593C;G28881A;G28882A;G28883C 115;88;97;50;72;65;80;124;152;161;170 122;95;104;55;78;70;86;131;159;168;177 N;ORF1ab;S;5'UTR 179;106;133;57 191;112;138;62 33683658 Isolation and genetic characterization of SARS-CoV-2 from Indian patients in a single family without H/O travel abroad. The mutations at G28881A, G28882A and G28883C resulted in amino acid changes, R9455K and G9456R in nucleocapsid (203 and 204) region. 2021 Virus genes Result SARS_CoV_2 G28881A;G28882A;G28883C;G9456R;R9455K 17;26;38;89;78 24;33;45;95;84 N 99 111 33683658 Isolation and genetic characterization of SARS-CoV-2 from Indian patients in a single family without H/O travel abroad. The sequence (GenBank accession No MT066156) was similar to Wuhan, China, except for a unique G251V mutation forming a separate clade V. 2021 Virus genes Result SARS_CoV_2 G251V 94 99 33683658 Isolation and genetic characterization of SARS-CoV-2 from Indian patients in a single family without H/O travel abroad. They formed separate cluster with four common nucleotide mutations at G1437A, G11083T (Orf1a), T28688C (Nucleocapsid) and G29742T (3'UTR). 2021 Virus genes Result SARS_CoV_2 G11083T;G1437A;G29742T;T28688C 78;70;122;95 85;76;129;102 N;ORF1a;3'UTR 104;87;131 116;92;136 33683658 Isolation and genetic characterization of SARS-CoV-2 from Indian patients in a single family without H/O travel abroad. Two mutations at positions, C313T and C3037T, were synonymous mutations with no change in amino acids, leucine (L) and phenylalanine (F). 2021 Virus genes Result SARS_CoV_2 C3037T;C313T 38;28 44;33 33688650 Ultrapotent miniproteins targeting the receptor-binding domain protect against SARS-CoV-2 infection and disease in mice. 50 mug dose of LCB1v1.3 or control binder one day prior to inoculation with 103 PFU of B.1.1.7 or E484K/N501/D614G SARS-CoV-2. 2021 bioRxiv Result SARS_CoV_2 E484K;D614G 98;109 103;114 33688650 Ultrapotent miniproteins targeting the receptor-binding domain protect against SARS-CoV-2 infection and disease in mice. Accordingly, we evaluated the activity of LCB1v1.3 against a B.1.1.7 isolate containing deletions at 69-70 and 144-145, and substitutions at N501Y, A570D, D614G, and P681H, and against a recombinant WA1/2020 strain containing key substitutions present in the B.1.351 and B.1.248 variant strains at residues E484K, N501Y, and D614G. 2021 bioRxiv Result SARS_CoV_2 A570D;D614G;D614G;E484K;N501Y;N501Y;P681H 148;155;325;307;141;314;166 153;160;330;312;146;319;171 33688650 Ultrapotent miniproteins targeting the receptor-binding domain protect against SARS-CoV-2 infection and disease in mice. Although the neutralizing activity of LCB1v1.3 against the B.1.1.7 and E484K/N501Y/D614G strains was approximately 45 to 50-fold lower than for the WA1/2020 strain, the EC50 values still were ~800 pM and 667 pM, respectively (Fig 6A). 2021 bioRxiv Result SARS_CoV_2 E484K;D614G;N501Y 71;83;77 76;88;82 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. Additionally, whereas a convergent A701V mutation is also found in the B.1.526 and S/E484K carrying lineage that was first identified in New York, P681H is found in the S/E484K and S/N501Y carrying P.3 lineage first identified in the Philippines, and both S/H655Y and S/P681H are found in the highly mutated S/E484K carrying A.VOI.V2 lineage first identified in Tanzanian travellers. 2021 medRxiv Result SARS_CoV_2 A701V;P681H;H655Y;N501Y;P681H;E484K;E484K;E484K 35;147;256;181;268;83;169;308 40;152;263;188;275;90;176;315 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. An F at residue S/18 is also observed in 10% of other known Sarbecoviruses and the L18F mutation was the 28th most common in sampled SARS-CoV-2 genomes on 04 June 2021. 2021 medRxiv Result SARS_CoV_2 L18F 83 87 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. Any of H655Y, P681H, A701V or T716I might directly impact the efficiency of viral entry into host cells. 2021 medRxiv Result SARS_CoV_2 A701V;H655Y;P681H;T716I 21;7;14;30 26;12;19;35 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. Based on the observed degree of frequency increases, mutations such as ORF1a/1708D (corresponding to nsp3/890D with 15.8 and >12.0 fold increases in V2 and V3 respectively), S/26S (>13 fold increase in V2), S/716I (3.7 and >13.5 fold increases in V2 and V3 respectively), S/1027I (>44 fold increase in V2), S/1118H (4.0 and >20 fold increases in V2 and V3 respectively), S/1176F (19.5 fold increase in V2) and ORF3/171L (11.9 fold increase in V3) are the signature mutations that, in addition to the ORF1a/3675-3677Del, S/18F, S/417N/T E484K and S/501Y mutations, are likely to have the greatest positive impact on the fitness of the 501Y lineage viruses within which they occur. 2021 medRxiv Result SARS_CoV_2 E484K 536 541 ORF1a;ORF1a;Nsp3;S;S;S;S;S;S;S;S 71;500;101;174;207;272;307;371;520;527;546 76;505;105;175;208;273;308;372;521;528;547 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. In addition to the 28 convergent mutations that displayed frequency increases between 15 March and 01 June 2021, the meta-signature includes deletion mutations at ORF1a/3675-3677, S/69-70, S/144, and S/241-243 (which, while displaying convergence between the different 501Y lineages, were not amenable to selection analyses) and the convergent signature substitutions L18F, K417N/K and N501Y (which were already at high frequencies in multiple 501Y lineages by 15 March 2021). 2021 medRxiv Result SARS_CoV_2 K417K;K417N;L18F;N501Y 374;374;368;386 381;381;372;391 ORF1a 163 168 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. In this regard, while mutations at S/20, S/80, S/138, S/215 and S/570 in different lineages do not predominantly converge on the same encoded amino acid states, they could nevertheless still be convergent on similar fitness objectives (immune escape or compensation for the fitness costs of other mutations): such as is likely the case with the also not-strictly-convergent V2 K417N and V3 K417T signature mutations. 2021 medRxiv Result SARS_CoV_2 K417N;K417T 377;390 382;395 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. S/18 falls within multiple different predicted CTL epitopes and the L18F mutation is known to reduce viral sensitivity to some neutralizing monoclonal antibodies. 2021 medRxiv Result SARS_CoV_2 L18F 68 72 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. SARS-CoV-2 variants with deletions of the furin cleavage site have reduced pathogenicity and the P681H mutation - which falls within this site - likely increases the efficiency of furin cleavage by replacing a less favourable uncharged amino acid with a more favourable positively charged basic one. 2021 medRxiv Result SARS_CoV_2 P681H 97 102 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. Similarly, among the nine positively selected sites where non-signature mutations both converge between viruses in two or more of the 501Y lineages, and then more than double in frequency between 15 March and 01 June 2021, ORF1b/1522I (corresponding to Helicase/590I with 1.9, 12.7 and 4.8 fold increases in V1, V2 and V3 respectively), S/98F (2.5, 5.3 and >6.0 fold increases in V1, V2 and V3 respectively), and E71T/R (respectively 5.8 and >10 fold increases in V1) are likely the most fitness-enhancing mutations. 2021 medRxiv Result SARS_CoV_2 E71R;E71T 413;413 419;419 Helicase;S 253;337 261;338 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. Whereas sites S/655, and S/681 are also detectably evolving under positive selection in at least one of the lineage specific datasets, S/655, S/681, A/701 and S/716 are all detectably evolving under positive selection in the March and April 2021 global SARS-CoV-2 datasets; important additional indicators that are consistent with the H655Y, P681H, A701V and T716I mutations being adaptive. 2021 medRxiv Result SARS_CoV_2 A701V;H655Y;P681H;T716I 349;335;342;359 354;340;347;364 S;S;S;S;S 14;25;135;142;159 15;26;136;143;160 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. Whereas some V2 and V3 sequences had, by March 2021, independently acquired the signature V1 mutations, P681H and T716I, some V1 and V2 sequences had independently acquired the V3 signature mutation, H655Y, and some V1 sequences had independently acquired the V2 signature mutation, A701V. 2021 medRxiv Result SARS_CoV_2 A701V;H655Y;P681H;T716I 283;200;104;114 288;205;109;119 33688681 The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. Whereas the L18F mutation is almost fixed in all currently sampled V3 lineage sequences, it occurred (and persisted in descendent variants) at least twice in the V1 lineage and at least four times in the V2 lineage. 2021 medRxiv Result SARS_CoV_2 L18F 12 16 33688689 Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. A single individual was found to have been infected with the P.2 strain, which carries the spike E484K mutation and was described in Brazil from a re-infection case. 2021 medRxiv Result SARS_CoV_2 E484K 97 102 S 91 96 33688689 Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. Moderately prevalent mutations were observed at spike position 681 (P681H, n=29 and P681R, n=1), which is within the furin recognition site, and at spike position 677, where two different amino acid substitutions were observed in this cohort (Q677H, n=21 and Q677P, n=10). 2021 medRxiv Result SARS_CoV_2 P681R;Q677P;P681H;Q677H 84;259;68;243 89;264;73;248 S;S 48;148 53;153 33688689 Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. Notably, mutations at spike position 501 were not observed, and thus no instances of the B.1.1.7 strain or any other strain bearing the N501Y mutation were detected in any sample during this period. 2021 medRxiv Result SARS_CoV_2 N501Y 136 141 S 22 27 33688689 Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. These lineages are separated by differing mutations ORF1a and ORF1b, including ORF1b:P976L and ORF1a:I4205V, respectively. 2021 medRxiv Result SARS_CoV_2 I4205V;P976L 101;85 107;90 ORF1a;ORF1a 52;95 57;100 33688689 Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. We observed SARS-CoV-2 genome sequences that belonged to PANGO lineages B.1.427 and B.1.429, both of which share a trio of recent mutations in the spike protein (S13I, W152C, and L452R) (Figure 2). 2021 medRxiv Result SARS_CoV_2 L452R;W152C;S13I 179;168;162 184;173;166 S 147 152 33692211 SARS-CoV-2 rapidly adapts in aged BALB/c mice and induces typical pneumonia. Applying the whole-genome sequencing method to the LG strain isolated from the lungs of aged mice, we found that the mutation in the S gene occurred at the RBD region, leading to the changes of residue 498 of S protein from glutamine to histidine (Q498H). 2021 Journal of virology Result SARS_CoV_2 Q498H 248 253 RBD;S;S 156;133;209 159;134;210 33692211 SARS-CoV-2 rapidly adapts in aged BALB/c mice and induces typical pneumonia. Importantly, SARS-CoV-2 effectively replicated in the respiratory tracts of all aged BALB/c mice, which might be attributed to the enhanced binding affinity between its Q498H mutant RBD and the mouse ACE2 receptor. 2021 Journal of virology Result SARS_CoV_2 Q498H 169 174 RBD 182 185 33692211 SARS-CoV-2 rapidly adapts in aged BALB/c mice and induces typical pneumonia. Protein structure and affinity prediction analysis indicated the Q498H mutation could increase the binding affinity between mouse ACE2 (mACE2) and the RBD of the SARS-CoV-2 S protein. 2021 Journal of virology Result SARS_CoV_2 Q498H 65 70 RBD;S 151;173 154;174 33692211 SARS-CoV-2 rapidly adapts in aged BALB/c mice and induces typical pneumonia. the LG had the following nucleotide mutations: (i) one synonymous variant, A8203G (nsp3, V-V); and (ii) the remaining mutations that were nonsynonymous, including T17825C (EndoRNAse, I-T) and A23056C (spike, RBD, Q498H). 2021 Journal of virology Result SARS_CoV_2 A23056C;A8203G;Q498H;T17825C 192;75;213;163 199;81;218;170 EndoRNAse;S;Nsp3;RBD 172;201;83;208 181;206;87;211 33692211 SARS-CoV-2 rapidly adapts in aged BALB/c mice and induces typical pneumonia. the LG strain isolated from the lungs of aged mice had the following nucleotide mutations: (i) one synonymous variant, A8203G (nsp3, V-V); and (ii) the remaining mutations that were nonsynonymous, including T21784A (spike, NTD, N74K), A23056C (spike, RBD, Q498H), C23525T (spike, S1, H655Y), and G29573A (ORF10, I6V). 2021 Journal of virology Result SARS_CoV_2 A23056C;A8203G;C23525T;G29573A;H655Y;I6V;N74K;Q498H;T21784A 235;119;264;296;284;312;228;256;207 242;125;271;303;289;315;232;261;214 S;S;S;Nsp3;RBD 216;244;273;127;251 221;249;278;131;254 33692211 SARS-CoV-2 rapidly adapts in aged BALB/c mice and induces typical pneumonia. The mutation in the S gene occurred at the RBD region, thereby changing residue 498 of the S protein from glutamine to histidine (Q498H). 2021 Journal of virology Result SARS_CoV_2 Q498H 130 135 RBD;S;S 43;20;91 46;21;92 33692211 SARS-CoV-2 rapidly adapts in aged BALB/c mice and induces typical pneumonia. the passaged virus WH-DC had the following nonsynonymous mutations: C17825T (EndoRNAse, T-I), T21784A (spike, NTD, N74K), C23525T (spike, S1, H655Y), and G29573A (ORF10, I6V). 2021 Journal of virology Result SARS_CoV_2 C17825T;C23525T;G29573A;H655Y;I6V;N74K;T21784A 68;122;154;142;170;115;94 75;129;161;147;173;119;101 EndoRNAse;S;S 77;103;131 86;108;136 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. A new vaccine therapeutic intervention is thus needed for Surat isolate as it harbors a potential mutation (P1089V) in its spike protein. 2021 Computers in biology and medicine Result SARS_CoV_2 P1089V 108 114 S 123 128 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. A total of 171 D614G mutations are identified from 460 Indian isolates in which 59 mutations in Surat isolates. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G 15 20 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Besides, a rare mutation (P1089V) is identified in the spike protein of Surat isolate (GBRC275b). 2021 Computers in biology and medicine Result SARS_CoV_2 P1089V 26 32 S 55 60 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. D614G is a frequent mutation identified from Telangana, Himachal Pradesh (GBRC97b), and Surat (GBRC275b) isolates. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G 0 5 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Emodin is a proficient antiviral targeting spike protein, which shows more binding specificity to Indian isolates except for the D614G variant. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G 129 134 S 43 48 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Genomic variations C199T, A2250C, C833T, C2794T, C2995T, G4258T, C11041T, C14366T, C14529T, C18526T, C18835T, C19112T, G21682T, C22402T, A23361G, G25521T, C26693T, C28812T and C29708T identified from Indian isolates introducing mutations in corresponding proteins. 2021 Computers in biology and medicine Result SARS_CoV_2 A2250C;A23361G;C11041T;C14366T;C14529T;C18526T;C18835T;C19112T;C199T;C22402T;C26693T;C2794T;C28812T;C29708T;C2995T;C833T;G21682T;G25521T;G4258T 26;137;65;74;83;92;101;110;19;128;155;41;164;176;49;34;119;146;57 32;144;72;81;90;99;108;117;24;135;162;47;171;183;55;39;126;153;63 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. However, there is no radical change in the drug specificity of a new mutation (N5928H) in Gandhinagar isolate (GBRC239) except ribavirin. 2021 Computers in biology and medicine Result SARS_CoV_2 N5928H 79 85 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Interestingly, we found a new functional shift from virulence to metabolic process upon T5538I mutation in helicase of Kerala (IND/166) isolate, suggested that its survivability and adaptability in host systems. 2021 Computers in biology and medicine Result SARS_CoV_2 T5538I 88 94 Helicase 107 115 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. The study found two new protein mutations W6152R and N5928H in exonuclease of Surat isolate (GBRC275b) and Gandhinagar isolate (GBRC239), respectively. 2021 Computers in biology and medicine Result SARS_CoV_2 N5928H;W6152R 53;42 59;48 Exonuclease 63 74 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. There is a drastic change in the folding rate of exonuclease of Indian isolates as the results of W6152R and N5928H mutations. 2021 Computers in biology and medicine Result SARS_CoV_2 N5928H;W6152R 109;98 115;104 Exonuclease 49 60 33714462 Pyrococcus furiosus Argonaute coupled with modified ligase chain reaction for detection of SARS-CoV-2 and HPV. Experimental results proved that PLCR can distinguish mock wild type novel coronavirus and its spike D614G mutant samples. 2021 Talanta Result SARS_CoV_2 D614G 101 106 S 95 100 33714462 Pyrococcus furiosus Argonaute coupled with modified ligase chain reaction for detection of SARS-CoV-2 and HPV. The spike D614G which is more infectious has a single base difference from the wild-type novel coronavirus in genome sequence. 2021 Talanta Result SARS_CoV_2 D614G 10 15 S 4 9 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. Determination of the inhibition capacity of COVID-19 convalescent patients against the Y453F variant. 2021 The Journal of biological chemistry Result SARS_CoV_2 Y453F 87 92 COVID-19 44 52 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. Linear regression and Spearman rank correlation analyses of the IC50 values against WT and Y453F RBD revealed that the inhibition potencies against both variants correlated strongly (R2 = 0.9613, rho = 0.8919, p < 0.0001). 2021 The Journal of biological chemistry Result SARS_CoV_2 Y453F 91 96 RBD 97 100 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. Sera from RBD immunized mice inhibited the WT and Y453F RBD binding to ACE-2 with an IC50 of 28,369 and 26,579, respectively, several fold more effectively than sera from spike immunized mice (IC50 of 7,075 and 6,363, respectively). 2021 The Journal of biological chemistry Result SARS_CoV_2 Y453F 50 55 S;RBD;RBD 171;10;56 176;13;59 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. The Y453F variant bound with a 4-fold higher affinity than the WT (3.85 nM vs 15.5 nM) and analyses of the Ka and Kdis revealed that it bound faster to ACE-2 (Ka 1.5 x 105 Ms vs 4 x 105 Ms) and remained bound for longer (7 x 10-4 s-1 vs 6 x 10-3 s-1). 2021 The Journal of biological chemistry Result SARS_CoV_2 Y453F 4 9 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. To determine the biological significance of the Y453F mutation, we studied the impact on protein stability and function by thermal denaturation and binding kinetics experiments. 2021 The Journal of biological chemistry Result SARS_CoV_2 Y453F 48 53 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. Using the ratio of the intrinsic fluorescence at 350 and 330 nm over a temperature gradient from 35 to 95C, we observed no significant differences in the inflection temperatures (53.43 and 53.37C for the WT RBD and Y453F, respectively), suggesting that the variant has no critical effect on protein stability. 2021 The Journal of biological chemistry Result SARS_CoV_2 Y453F 215 220 RBD 207 210 33725432 Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. Of note, the D215G mutation found in the B.1.351 variant is within a region that had prevalent T-cell antigen responses. 2021 The New England journal of medicine Result SARS_CoV_2 D215G 13 18 33725432 Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. Six of 13 vaccine recipients (46%) without evidence of previous SARS-CoV-2 infection showed no neutralization activity against an RBD triple-mutant pseudovirus (containing K417N, E484K, and N501Y variants), and 11 of the 13 (85%) had no neutralization activity against B.1.351 pseudovirus (Figure 2B). 2021 The New England journal of medicine Result SARS_CoV_2 E484K;K417N;N501Y 179;172;190 184;177;195 RBD 130 133 COVID-19 64 84 33725432 Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. There were 25 participants in group 1 (the group of 70 participants who also had laboratory measures evaluated as part of their safety analysis) who were SARS-CoV-2 seronegative at enrollment and had neutralizing antibody activity against the original D614G virus on the pseudovirus neutralization assay at 14 days after the second dose. 2021 The New England journal of medicine Result SARS_CoV_2 D614G 252 257 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. A sort of "twisted" patterns were detected for both P.1 lineage and E484K variants change substantially according to the level of SII in the previous week, in which the nadir seems to be when SII value is approximately 40%. 2021 Cureus Result SARS_CoV_2 E484K 68 73 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Between October 2020 and January 2021, the state of Amazonas experienced an overwhelming rise in the prevalence of E484K compared to Brazil overall. 2021 Cureus Result SARS_CoV_2 E484K 115 120 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Conversely, for whole Brazil, there were no statistically significant associations between the prevalence of P.1 and further COVID-19 deaths, whereas there were statistically significant negative correlations in the four weeks following the detection of E484K variants (Spearman Rho=-0.61; R2=37.5%; p<0.01; n=32). 2021 Cureus Result SARS_CoV_2 E484K 254 259 COVID-19 125 133 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Figures 4, 5 show the association between SII and prevalence of the P.1 lineage and E484K variants in the following week in the state of Amazonas (Brazil), respectively. 2021 Cureus Result SARS_CoV_2 E484K 84 89 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Figures 6, 7 illustrate temporal progression of the prevalence of P.1 lineage and E484K variant, respectively, according to the level of SII in the previous week, through 3D surfaces. 2021 Cureus Result SARS_CoV_2 E484K 82 87 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. For both correlations with P.1 lineage and E484K variants, figures were shown for SII below 40% and above 40%. 2021 Cureus Result SARS_CoV_2 E484K 43 48 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. In Brazil, the proportion of all E484K samples was nearly negligible between June 2020 and September 2020, emerging in October and hovering at slightly above 40% until January 2021. 2021 Cureus Result SARS_CoV_2 E484K 33 38 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. In the state of Amazonas, the correlations between the prevalence of both P.1 lineage and E484K variants, and the number of COVID-19 deaths in the following weeks were positive, statistically significant and strongest in the two weeks following the detection of the mutations (Spearman Rho=0.71; R2=51.1%; p<0.01; n=14). 2021 Cureus Result SARS_CoV_2 E484K 90 95 COVID-19 124 132 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. In the State of Amazonas, the E484K mutation was not detected until October 2020, with a steep and relatively linear rise from November 2020 onward, reaching 100% in January 2021. 2021 Cureus Result SARS_CoV_2 E484K 30 35 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. In the State of Amazonas, the SII in a given week was positively, moderate-to-intense, and significantly associated with the prevalence of E484K variants within the six weeks following the SII of a given week. 2021 Cureus Result SARS_CoV_2 E484K 139 144 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Paradoxically, in overall Brazil, correlations between the E484K variants and the SII were significantly negative between four to eight weeks after the SII of a given week. 2021 Cureus Result SARS_CoV_2 E484K 59 64 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Social isolation and the subsequent prevalence of P.1 and E484K in Amazonas and Brazil. 2021 Cureus Result SARS_CoV_2 E484K 58 63 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Table 3 shows the correlation between the SII on a given week and the prevalence of E484K variations in the following weeks. 2021 Cureus Result SARS_CoV_2 E484K 84 89 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Tables 4, 5 show the correlation between the prevalence of all P.1 lineage and E484K variants, respectively, and the number of COVID-19 deaths in the following weeks in the state of Amazonas and in whole Brazil. 2021 Cureus Result SARS_CoV_2 E484K 79 84 COVID-19 127 135 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. The growth in P.1 and E484K in the state of Amazonas and Brazil according to the level of social isolation. 2021 Cureus Result SARS_CoV_2 E484K 22 27 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. The prevalence of P.1 and E484K SARS-CoV-2 in the state of Amazonas and Brazil. 2021 Cureus Result SARS_CoV_2 E484K 26 31 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. When SII was above 40%, apparently exponential positive correlations between SII and prevalence of both P.1 lineage and E484K variants were observed. 2021 Cureus Result SARS_CoV_2 E484K 120 125 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. When SII was found to be below 40%, P.1 lineage or E484K variants were not detected. 2021 Cureus Result SARS_CoV_2 E484K 51 56 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. 2A,B), the N501Y mutation resulted in an increase in free energies. 2021 FEBS letters Result SARS_CoV_2 N501Y 11 16 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. After obtaining protein structures for both bound and free states in respective MD simulations, we employed the FEP method to calculate the binding free energy difference for the N501Y mutation on the sRBD, using the thermodynamic cycle shown in. 2021 FEBS letters Result SARS_CoV_2 N501Y 179 184 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. As a biologics drug, CB6 can be modified accordingly to accommodate the N501Y mutation in sRBD. 2021 FEBS letters Result SARS_CoV_2 N501Y 72 77 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. Below, we focus on how the N501Y mutation can affect the binding between sRBD and the mAb CB6. 2021 FEBS letters Result SARS_CoV_2 N501Y 27 32 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. CR3022 [29], S309 [30] and REGN10987 [31]) bind different epitopes and thus the N501Y mutation has little effect on such binding. 2021 FEBS letters Result SARS_CoV_2 N501Y 80 85 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. for the N501Y mutation in bound/free states, the original sRBD with N501 is present in the initial stage and, in the final stage, the same residue becomes Y501 through the alchemical process in the FEP calculation. 2021 FEBS letters Result SARS_CoV_2 N501Y 8 13 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. From FEP calculations, we found that DeltaG A = 68.62 kcal mol-1 for the N501Y mutation in the bound state. 2021 FEBS letters Result SARS_CoV_2 N501Y 73 78 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. In the emergent SARS-CoV-2 variant, the presence of the N501Y mutation in sRBD indeed caused the disease to become more contagious, a consequence of the enhanced binding between the hACE2 and sRBD. 2021 FEBS letters Result SARS_CoV_2 N501Y 56 61 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. In the final stage of FEP calculations for the N501Y mutation. 2021 FEBS letters Result SARS_CoV_2 N501Y 47 52 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. It is still unknown how the N501Y mutation affects the binding between the S-protein of SARS-CoV-2 and neutralizing antibodies. 2021 FEBS letters Result SARS_CoV_2 N501Y 28 33 S 75 76 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. It is worth noting that, as a result of multiple epitopes on the spike protein targeted by various mAbs, the single N501Y mutation might not allow the virus to evade the human immune system. 2021 FEBS letters Result SARS_CoV_2 N501Y 116 121 S 65 70 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. Overall, the value of DeltaDeltaG is -0.81 kcal mol-1 (with an error of 0.67 kcal mol-1), suggesting that the N501Y mutation increases the binding affinity between hACE2 and sRBD (consistent with previous experimental results [13, 14]). 2021 FEBS letters Result SARS_CoV_2 N501Y 110 115 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. The above results suggest that the N501Y mutation is favorable in the bound state. 2021 FEBS letters Result SARS_CoV_2 N501Y 35 40 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. The changes in sRBD's binding free energies induced by the N501Y mutation can be calculated as DeltaDeltaG = DeltaG 2 - DeltaG 1 = DeltaG A - DeltaG B. 2021 FEBS letters Result SARS_CoV_2 N501Y 59 64 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. The positive value of DeltaDeltaG indicates that the N501Y mutation can weaken the binding between sRBD and the CB6 Fab. 2021 FEBS letters Result SARS_CoV_2 N501Y 53 58 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. Therefore, the N501Y mutation is likely to affect the binding of these mAbs to sRBD. 2021 FEBS letters Result SARS_CoV_2 N501Y 15 20 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. Thus, the N501Y mutation in the free state is unfavorable. 2021 FEBS letters Result SARS_CoV_2 N501Y 10 15 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. To unveil the underlying molecular mechanism of the N501Y mutation, we performed FEP calculations [18]. 2021 FEBS letters Result SARS_CoV_2 N501Y 52 57 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. We further explored the molecular mechanism of the N501Y mutation by analyzing the interfacial atomic structures in the simulation trajectory. 2021 FEBS letters Result SARS_CoV_2 N501Y 51 56 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. With respect to the value of DeltaG B for the N501Y mutation in the free state (Table 1), DeltaDeltaG = 0.62 kcal mol-1 (with an error of 0.47 kcal mol-1). 2021 FEBS letters Result SARS_CoV_2 N501Y 46 51 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. A number of isolates of B.1.351 have been described, all of which have the key mutations K417N, E484K, and N501Y in the RBD. 2021 Cell Result SARS_CoV_2 E484K;K417N;N501Y 96;89;107 101;94;112 RBD 120 123 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. Although P.1 does not harbor NTD deletions, the changes L18F, T20N, and P26S would be expected to impact markedly on binding at the NTD epitope. 2021 Cell Result SARS_CoV_2 L18F;P26S;T20N 56;72;62 60;76;66 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. Antibodies resistant to K417N, E484K, and N501Y. 2021 Cell Result SARS_CoV_2 E484K;K417N;N501Y 31;24;42 36;29;47 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. In the evolution of both the B.1.1.7 variant in the UK and the B.1.351 variant in South Africa, a substantial population of N-terminal domain (NTD)-deletion-only mutants (Delta69-70 in B.1.1.7 and Delta242-244 in B.1.153), and N501Y-only mutants were observed in both countries preceding the rising dominance of strains harboring both deletions and 501Y (Figures 1A and 1B). 2021 Cell Result SARS_CoV_2 N501Y 227 232 N 124 125 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. N501Y is on the right shoulder, K417N at the back of the neck, and E484R on the left shoulder. 2021 Cell Result SARS_CoV_2 E484R;K417N;N501Y 67;32;0 72;37;5 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. reported an isolate containing 10 changes relative to the Wuhan sequence: L18F, D80A, D215G, L242-244 deleted, R246I, K417N, E484K, N501Y, D614G, and A701V. 2021 Cell Result SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;L18F;N501Y;R246I 150;86;139;80;125;118;74;132;111 155;91;144;84;130;123;78;137;116 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. Sequencing of the strain used in this report, from a case in the UK, shows only 8 changes and lacks L18F and R246I compared with the isolate. 2021 Cell Result SARS_CoV_2 L18F;R246I 100;109 104;114 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. The effect of N501Y and K417N on mAb binding. 2021 Cell Result SARS_CoV_2 K417N;N501Y 24;14 29;19 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. The effects of the E484K mutation. 2021 Cell Result SARS_CoV_2 E484K 19 24 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. The FRNT50 titers for mAbs 55, 165, 253, and 318 were also relatively equal between Victoria and B.1.351, indicating that their epitopes are not perturbed by the K417N, E484K, and N501Y mutations. 2021 Cell Result SARS_CoV_2 E484K;K417N;N501Y 169;162;180 174;167;185 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. The triple mutation K417N, E484R, and N501Y is characteristic of the B.1.351 RBD. 2021 Cell Result SARS_CoV_2 E484R;K417N;N501Y 27;20;38 32;25;43 RBD 77 80 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. These results broadly follow the neutralization results (compare panels C and D of Figure 6; see Table S3), suggesting that the observed pattern of effects on neutralization is largely due to the amino acid substitutions in the RBD, that is, K417N, E484K, and N501Y. 2021 Cell Result SARS_CoV_2 E484K;K417N;N501Y 249;242;260 254;247;265 RBD 228 231 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. This mAb approaches the binding site from the front of the left shoulder, burying 82% of the solvent-accessible area of E484 by hydrogen bonding with Y50, T57, and Y59 as well as making a salt bridge with R52 of the LC CDR2 (Figure 5D), thereby explaining the catastrophic impact of the E484K mutation on binding (Table S3). 2021 Cell Result SARS_CoV_2 E484K 287 292 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. We would therefore expect that the combined effects of the K417N and N501Y mutations would severely compromise the binding of most IGHV3-53 and IGHV3-66 class mAbs. 2021 Cell Result SARS_CoV_2 K417N;N501Y 59;69 64;74 33731300 Genetic modification to design a stable yeast-expressed recombinant SARS-CoV-2 receptor binding domain as a COVID-19 vaccine candidate. The new C538A-mutated construct based on the RBD219-N1 backbone was able to express the protein (RBD219-N1C1) with low yeast-derived hyperglycosylation, without the presence of extensive non-RBD specific proteins or HCPs. 2021 Biochimica et biophysica acta. General subjects Result SARS_CoV_2 C538A 8 13 RBD;RBD;RBD 45;97;191 48;100;194 33731300 Genetic modification to design a stable yeast-expressed recombinant SARS-CoV-2 receptor binding domain as a COVID-19 vaccine candidate. This suggested the potential formation of an intermolecular disulfide bond between a potential free cysteine found in the molecule, and therefore, a C538A-mutated form of RBD219-N1, RBD219-N1C1, was constructed. 2021 Biochimica et biophysica acta. General subjects Result SARS_CoV_2 C538A 149 154 RBD;RBD 171;182 174;185 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. Accordingly, mutating Y489 into alanine and isoleucine quantified the strength of this network as DeltaDeltaGCoV-2(Y489A) = -2.96 +- 0.33 kcal/mol and DeltaDeltaGCoV-2(Y489I) = -2.01 +- 0.17 kcal/mol (Table S2), respectively. 2021 ACS nano Result SARS_CoV_2 Y489A;Y489I 115;168 120;173 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. As such, the total free energy change for mutating N501 in alanine in our CAS study was reported to be small, and equal to DeltaDeltaGCoV-2(N501A) = -2.40 +- 0.28 kcal/mol. 2021 ACS nano Result SARS_CoV_2 N501A 140 145 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. Based on these data, the predicted relevant variation of the binding affinity of the T501 variant for ACE2 is equal to DeltaDeltaGCoV-2(N501T) = +0.28 +- 0.11 kcal/mol (Figure 21A, Table S2). 2021 ACS nano Result SARS_CoV_2 N501T 136 141 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. Both in silico and experimental data presently suggest mostly neutral-to-disrupting protein/protein binding effects, with an exception made for the T501 mutant, for which computational mutagenesis predicts a weak interface-stabilizing outcome, in agreement with experiment (Figure 21A, Table S2, Figure S30, and Table S32; for a discussion on N501W data, see Supporting Information). 2021 ACS nano Result SARS_CoV_2 N501W 343 348 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. Consistent with these data, the current in silico mutagenesis data and the relative experimental evidence agree on the interface-disrupting role for all mutants considered, with the interesting exception of the Q498W substitution for which the experiment reports a weak positive effect, while the present MD simulations report a substantial decrease in receptor affinity for this mutant (DeltaDeltaGCoV-2(Q498W) = -4.18 +- 0.11 kcal/mol, Figure 20B, Table S2, Figure S29, and Table S31; for a discussion on Q498W data, see Supporting Information). 2021 ACS nano Result SARS_CoV_2 Q498W;Q498W;Q498W 211;507;405 216;512;410 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. Consistent with this, the absence of these two HBs in the N487A or N487I S-RBDCoV-2 mutants reflects in a non-negligible interface destabilization, quantified by the corresponding variation of the binding free energies (DeltaDeltaGCoV-2(N487A) = -2.25 +- 0.35 kcal/mol, and DeltaDeltaGCoV-2(N487I) = -2.39 +- 0.11 kcal/mol, respectively, Table S2), in agreement with experiment (Figure 17A). 2021 ACS nano Result SARS_CoV_2 N487A;N487I;N487A;N487I 58;67;237;291 63;72;242;296 S 73 74 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. Eventually, this translates into a stabilization of the relevant protein/protein complex (DeltaDeltaGACE2(L79W) = +1.05 +- 0.15 kcal/mol, Table S1), in agreement with experiment (Figure 7C). 2021 ACS nano Result SARS_CoV_2 L79W 106 110 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. For the proximal Y453 S-protein residue, the original CAS study predicted only a small change in affinity of the Y453A S-RBDCoV-2 mutant for ACE2 (DeltaDeltaGCoV-2(Y453A) = -0.79 +- 0.30 kcal/mol), in line with the limited role played by this residue in the wild-type complex (a polar intermolecular interaction with ACE2 H34 and one intramolecular CI with Q493, Figure 4A). 2021 ACS nano Result SARS_CoV_2 Y453S;Y453A;Y453A 17;113;164 23;118;169 S;S 22;119 23;120 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. In addition, the negatively charged side chain of D455 is able to form a stable intramolecular salt bridge with K417 (3.74 +- 0.29 A), so that the overall affinity of the D455 isoform of the S-RBDCoV-2 for the human receptor is higher than that of the wild-type S-protein (DeltaDeltaGCoV-2(L455D) = +1.69 +- 0.06 kcal/mol, Figure 18A, and Table S2). 2021 ACS nano Result SARS_CoV_2 L455D 290 295 S;S 191;262 192;263 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. In addition, the related network of interactions seen in the wild-type complex is practically unchanged (see Figure 4A, Figure 16D, and Table S22), ultimately resulting in slightly positive predicted variation of the corresponding protein/protein binding free energy (DeltaDeltaGCoV-2(Y453K) = +0.19 +- 0.07 kcal/mol, Figure 16B and Table S2). 2021 ACS nano Result SARS_CoV_2 Y453K 285 290 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. In agreement with this, all considered Y505 mutants (including the previously investigated Y505A, for which DeltaDeltaGCoV-2(Y505A) = -3.27 +- 0.31 kcal/mol) considerably reduce the binding affinity of S-RBDCoV-2 for ACE2 with the exception of the Y505K variant, for which an interface-stabilizing effect is both predicted and observed (Figure 17C and Table S2). 2021 ACS nano Result SARS_CoV_2 Y505A;Y505K;Y505A 91;248;125 96;253;130 S 202 203 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. In energetic terms, this translates to a slightly more favorable DeltaDeltaG value for the W505 mutant with respect to the wild-type S-RBDCoV-2 Y505 (DeltaDeltaGCoV-2(Y505W) = +0.64 +- 0.19 kcal/mol, Figure 17C, and Table S2). 2021 ACS nano Result SARS_CoV_2 Y505W 167 172 S 133 134 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. In keeping with this, the abrogation of these CIs within the ACE2 L79A mutant/S-RBDCoV-2 complex was predicted to marginally reduce the affinity of the A79 receptor for the viral S-protein (DeltaDeltaGACE2(L79A) = -1.04 +- 0.16 kcal/mol). 2021 ACS nano Result SARS_CoV_2 L79A;L79A 66;206 70;210 S 179 180 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. In line with the value predicted for the Y449A mutant (DeltaDeltaGCoV-2(Y449A) = -3.21 +- 0.31 kcal/mol), the actual computational and experimental results both report interface destabilizing effects in all ACE2/mutant S-RBDCoV-2 complexes considered (Figure 16A, Table S2, Figure S19, and Table S21). 2021 ACS nano Result SARS_CoV_2 Y449A;Y449A 41;72 46;77 S 219 220 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. In line, an increase in affinity of the W455 viral mutant RBD for ACE2 is predicted (DeltaDeltaGCoV-2(L455W) = +0.95 +- 0.19 kcal/mol, Figure 18, Table S2). 2021 ACS nano Result SARS_CoV_2 L455W 102 107 RBD 58 61 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. In particular, both techniques mostly report interface neutral-to-disrupting effects for all residues except for the Q493K variant, for which an interface stabilizing effect is jointly determined (Figure 20A, Table S2, Figure S28, and Table S30; for a discussion on Q493I, Q493T, and Q493W data, see Supporting Information). 2021 ACS nano Result SARS_CoV_2 Q493I;Q493K;Q493T;Q493W 266;117;273;284 271;122;278;289 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. In particular, in the ACE2/(L455D)S-RBDCoV-2 complex, besides all wild-type inter- and intramolecular interaction, MD simulations reveal the formation of three further stabilizing contacts (Figure 19A, Table S27). 2021 ACS nano Result SARS_CoV_2 L455D 28 33 S 34 35 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. In the same context, our previous CAS results revealed that ACE2M82 affords only weakly stabilizing intra/intermolecular CIs with L79 and F486, respectively (Figure 6A), supported by the corresponding DeltaDeltaG value predicted for the M82A mutant receptor/S-RBDCoV-2 complex (DeltaDeltaGACE2(M82A) = -0.76 +- 0.12 kcal/mol). 2021 ACS nano Result SARS_CoV_2 M82A;M82A 237;294 241;298 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. Interestingly, when L is replaced by I at the same position, the different geometry of I79 allows this amino acid to establish the same CIs of its wild-type isomer along with a slight compaction of the corresponding binding interface region (Figure 6A,B, Table S9); consequently, the predicted variation of binding free energy is slightly positive (DeltaDeltaGACE2(L79I) = +0.35 +- 0.10 kcal/mol, Figure 7C, and Table S1). 2021 ACS nano Result SARS_CoV_2 L79I 365 369 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. Removing all these interactions by replacing the side chain of Y83 with alanine yielded a predicted loss of binding free energy equal to DeltaDeltaGACE2(Y83A) = -3.18 +- 0.20 kcal/mol. 2021 ACS nano Result SARS_CoV_2 Y83A 153 157 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. The actual in silico/experimental data also commonly describe neutral-to-mildly destabilizing effects for the W453, I453, S453, and T453 mutants, respectively, a stronger negative influence on the protein/protein complex stability in the presence of Y453D substitution and, quite interestingly, a small increase in affinity of the Y453K mutant S-RBDCoV-2 for the human receptor (Figure 16 panels B and D, Table S2, Figure S20, and Table S22). 2021 ACS nano Result SARS_CoV_2 Y453D;Y453K 250;331 255;336 S 344 345 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. The CAS study also reported that the substitution of Q498 with alanine was accompanied by a substantial loss in binding free energy (DeltaDeltaGCoV-2(Q498A) = -5.36 +- 0.37 kcal/mol). 2021 ACS nano Result SARS_CoV_2 Q498A 150 155 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. The effects of mutating the ACE2 wild-type residue L79 into I, S, T, D, K, and W are more surprising, in that experimental/computational mutagenesis results both predict receptor/S-RBDCoV-2 interface stabilization for the two substitution L79I and L79W, whereas replacement with polar (S, T) or charged residues (D, K) reflects into neutral/mildly protein/protein destabilizing effects (Figures 6B-C, S7 and 7C, Table S1, and Table S9) (for a discussion on L79T data, see Supporting Information). 2021 ACS nano Result SARS_CoV_2 L79I;L79T;L79W 239;457;248 243;461;252 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. The effects produced by the L79W mutation are utterly similar to those just discussed for the L79I ACE2 variant, with the further engagement by W79 of F486 in a pi/pi interaction and enhanced dispersive interactions with the side chains of all residues shaping this hydrophobic patch of the ACE2/S-RBDCoV-2 binding interface (Figure 6C, Table S9). 2021 ACS nano Result SARS_CoV_2 L79I;L79W 94;28 98;32 S 296 297 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. The Y453K variant of the S-protein RBD indeed engages the same CIs of its wild-type isomer yet in a somewhat more efficient manner, resulting in a slight compaction of the corresponding binding interface region (Figure 16D, Table S22). 2021 ACS nano Result SARS_CoV_2 Y453K 4 9 RBD;S 35;25 38;26 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. Thus, the variation in binding free energy is slight favorable to the mutant isoform (DeltaDeltaGCoV-2(Q493K) = +0.76 +- 0.11 kcal/mol, Figure 20A, and Table S2), in agreement with the experimental evidence. 2021 ACS nano Result SARS_CoV_2 Q493K 103 108 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. While both experimental and the present computational mutagenesis data report neutral-to-mild interface destabilizing effects for the L455I/S/T/K mutants, in vitro/in silico data diverge when the two remaining mutations (i.e., L455D and L455W) are concerned (Figure 18A and Table S2; for a discussion on L455S data, see Supporting Information). 2021 ACS nano Result SARS_CoV_2 L455D;L455I;L455K;L455S;L455T;L455S;L455W 227;134;134;134;134;304;237 232;145;145;145;145;309;242 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. Y41 on ACE2 alpha-helix 1 is another predicted hot spot at the binding interface between the human receptor and the viral S-protein RBD, since mutating this tyrosine into alanine yielded a substantial loss in the relevant binding free energy (DeltaDeltaGACE2(Y41A) = -4.43 +- 0.33 kcal/mol). 2021 ACS nano Result SARS_CoV_2 Y41A 259 263 RBD;S 132;122 135;123 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. 501Y.V2-1 was a relatively early variant in the second wave of this epidemic; it carries the E484K and N501Y mutations but not the K417N mutation. 2021 Cell Result SARS_CoV_2 E484K;K417N;N501Y 93;131;103 98;136;108 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. Briefly, escape from the 157, 2H10, and 1F9 antibodies was caused by the K417N mutation; escape from 261-262, 9G11, P2B-2F6, and LKLH was caused by the E484K mutation; escape from H00S022 and 10F9 was caused by the N501Y mutation; and escape from 10D12, 11D12, and 247 was caused by both K417N and N501Y (Figure 3). 2021 Cell Result SARS_CoV_2 E484K;K417N;K417N;N501Y;N501Y 152;73;288;215;298 157;78;293;220;303 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. Further, it was again conspicuous that the K417N mutation increased viral susceptibility to neutralization. 2021 Cell Result SARS_CoV_2 K417N 43 48 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. However, and recalling that the 501Y.V2-2 pseudotyped virus carries two additional mutations (L18F and K417N), it is consistent that 501Y.V2-2's escape spectrum is wider than 501Y.V2-1's spectrum for this panel of neutralizing antibodies (Figure 3). 2021 Cell Result SARS_CoV_2 K417N;L18F 103;94 108;98 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. Moreover, the pseudotyped viruses carrying double (K417N+N501Y) and triple (K417N+E484K+N501Y) mutations exhibited yet-higher increases in infectivity compared to the single mutants (Figure 2B). 2021 Cell Result SARS_CoV_2 K417N;K417N;E484K;N501Y;N501Y 51;76;82;57;88 56;81;87;62;93 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. Neutralization assays with the pseudotyped viruses showed that mutations at a single site did not lead to significant alteration of the neutralization activity of polyclonal antibodies; only the simultaneous presence of the E484K and N501Y mutations resulted in a significant decrease in neutralization (p < 0.05) (Figure 4B). 2021 Cell Result SARS_CoV_2 E484K;N501Y 224;234 229;239 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. Note that 501Y.V2-1 lacks the K417N mutation, so it appears that for 501Y.V2-2 and for 501Y.V2-3, the presence of K417N apparently increases susceptibility to neutralization by polyclonal antibodies. 2021 Cell Result SARS_CoV_2 K417N;K417N 30;114 35;119 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. The 501Y.V2 variants, derived from B.1, have the D614G S protein mutation. 2021 Cell Result SARS_CoV_2 D614G 49 54 S 55 56 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. Three single-residue variants, K417N, E484K, and N501Y:all located at the RBD region:respectively displayed 7-fold, 3-fold, and 5-fold increases in infectivity compared to the reference 614G variant (Figure 2B). 2021 Cell Result SARS_CoV_2 E484K;K417N;N501Y 38;31;49 43;36;54 RBD 74 77 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. We found that the antibody escape spectrum of our pseudotyped virus 501Y.V2-1 was essentially the same as for the 614G+E484K+N501Y triple RBD mutation variants. 2021 Cell Result SARS_CoV_2 E484K;N501Y 119;125 124;130 RBD 138 141 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. We found that the E484K and N501Y mutations led to a decrease in neutralization, and the combination of these two mutations resulted in an apparently superimposed resistance to neutralization (Figure 5B). 2021 Cell Result SARS_CoV_2 E484K;N501Y 18;28 23;33 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. In addition, 10 of the 11 SARS-CoV-2 isolates carried the NSP2 (Y537Y), NSP3 (F106F), and ORF3a (Q57H) substitutions (Table 1). 2021 International journal of infectious diseases Result SARS_CoV_2 F106F;Q57H;Y537Y 78;97;64 83;101;69 ORF3a;Nsp2;Nsp3 90;58;72 95;62;76 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. The amino acid substitutions S (D614G) in the spike protein and NSP12b in the non-structural protein (NSP) occurred in all SARS-CoV-2 isolates. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 32 37 S;S 46;29 51;30 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. Among the identified mutations, 28,881 G > A & 28,882 G > A (R203K; N protein), 23,403 A > G (D614G; S glycoprotein), 28,883 G > C (G204R; N protein), 14,408 C > T (P4715 L; nsp12), and 1163 A > T (I300 F; nsp2) are the most frequently occurring common mutations found in Bangladesh with a frequency of 650, 365, 325, 304 and 243, respectively. 2021 Virus research Result SARS_CoV_2 A1163T;D614G;G204R;I300F;P4715L;R203K;A403G;C408T;G881A;G882A;G883C 186;94;132;198;165;61;83;154;35;50;121 196;99;137;204;172;66;92;163;44;59;130 S;Nsp12;Nsp2;N;N 101;174;206;68;139 115;179;210;69;140 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. Firstly, the UMs (A889V and V843F) were found in the main domain of nsp3 that is important for processing endopeptidases from coronaviruses. 2021 Virus research Result SARS_CoV_2 V843F;A889V 28;18 33;23 Nsp3 68 72 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. Meanwhile, R203K and G204R mutations in N protein were previously reported in Indian, Spanish, Italian, and French samples. 2021 Virus research Result SARS_CoV_2 G204R;R203K 21;11 26;16 N 40 41 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. Nucleotide mutations of 28,881 G > A and 28,882 G > A resulted in R203K due to codon degeneracy. 2021 Virus research Result SARS_CoV_2 R203K;G881A;G882A 66;27;44 71;36;53 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. Other variations 28,881 G > A and 28,882 G > A together convert polar to non-polar amino acid (R203K) and 28,883 G > C variation converts nonpolar to polar amino acid (G204R). 2021 Virus research Result SARS_CoV_2 G204R;R203K;G881A;G882A;G883C 168;95;20;37;109 173;100;29;46;118 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. Secondly, some UMs (e.g., G1691C, A602S and L373M) are found in the topological (cytoplasmic) domain. 2021 Virus research Result SARS_CoV_2 A602S;G1691C;L373M 34;26;44 39;32;49 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. The observed mutation P4715L in nsp12 was also found in most of the US states (28 out of 31 states from where the sequences were deposited). 2021 Virus research Result SARS_CoV_2 P4715L 22 28 Nsp12 32 37 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. Thirdly, we observed one UM (L373M) in the ADP-ribose-1'-phosphatase (ADRP) or (Macro) domain of nsp3. 2021 Virus research Result SARS_CoV_2 L373M 29 34 Nsp3 97 101 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. This correlation indicates that the genomes containing D614G mutation also bear more mutations which is aligned with the various reports on the link between the transmission and pathogenesis of SARS-CoV-2, and this mutation increases cell entry and transduction due to resistance to proteolytic cleavage. 2021 Virus research Result SARS_CoV_2 D614G 55 60 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. We noticed that 98 % of genomes from Bangladesh have D614G mutation, which is also dominant in the world. 2021 Virus research Result SARS_CoV_2 D614G 53 58 33738124 SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity. Additionally, SNV signatures of previously characterized Brazilian genomes were found in most samples, such as G28881A and G28882A (98.6%; resulting in R203K change in N), G28883C (98.6%; resulting in G204R change in N), T27299C (91.6%; resulting in I33T change in ORF6), and T29148C (90.1%; resulting in I292T change in N). 2021 Virus evolution Result SARS_CoV_2 G204R;G28881A;G28882A;G28883C;I292T;I33T;R203K;T27299C;T29148C 201;111;123;172;305;250;152;221;276 206;118;130;179;310;254;157;228;283 ORF6;N;N;N 265;168;217;321 269;169;218;322 33738124 SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity. Another 85 SNVs were observed in our consensus sequences at lower frequency (1.4%-19.7%; Supplementary Table S2), including nine non-synonymous mutations in S protein (V16F, V367L, K558N, Q675H, A879V, S939F, V1176F, K1191N, and G1219V). 2021 Virus evolution Result SARS_CoV_2 A879V;G1219V;K1191N;K558N;Q675H;S939F;V1176F;V367L;V16F 195;229;217;181;188;202;209;174;168 200;235;223;186;193;207;215;179;172 S 157 158 33738124 SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity. Four genetically linked mutations previously described as the globally dominant haplotype in April 2020 were found in the majority of our consensus sequences: C241T (100%; 5'UTR region), C3037T (98.6%; silent mutation), C14408T (100%; resulting in P4715L/P323L amino acid change in ORF1ab) and A23403G (100%; resulting in D614G amino acid change in S). 2021 Virus evolution Result SARS_CoV_2 A23403G;C14408T;C241T;C3037T;D614G;P4715L;P323L 294;220;159;187;322;248;255 301;227;164;193;327;254;260 ORF1ab;5'UTR;S 282;172;349 288;177;350 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. According to interaction energy analysis, SARS-CoV-2 strains with the spike-S1 V354F or V470A substitutions were likely novel strains with increased infectivity (Figures 4D, 5A). 2021 Zoological research Result SARS_CoV_2 V354F;V470A 79;88 84;93 S 70 75 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. Although variant site Y449N belonged to the interaction sites for ACE2-spike-S1, the frequency of the spike-S1 variant was 9.10E-05. 2021 Zoological research Result SARS_CoV_2 Y449N 22 27 S;S 71;102 76;107 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. As shown in Figure 3F, we found that the SARS-CoV-2 mutant with L84S in ORF8 had a closer phylogenetic relationship to its ancestors compared to that of SARS-CoV-2-Wuhan01 (Figure 3F). 2021 Zoological research Result SARS_CoV_2 L84S 64 68 ORF8 72 76 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. As shown in Figure 4C, the three amino acid substitutions affected the physical and chemical parameters of the spike-S1 protein, with the V354F mutant having the smallest impact among the three mutants. 2021 Zoological research Result SARS_CoV_2 V354F 138 143 S 111 116 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. As shown in Figure 4D, V354F had the lowest energy and interaction score in the ACE2-spike-S1 complexes based on structural comparison and protein-protein interaction analysis (Figure 4D, Supplementary Table S6). 2021 Zoological research Result SARS_CoV_2 V354F 23 28 S 85 90 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. As shown in Figure 5A and B, an increasing number of amino acid substitutions were seen in the RBD of spike-S1 with the spread of SARS-CoV-2, but most amino acid substitutions were random events, except for V354F, G463S, and V470A. 2021 Zoological research Result SARS_CoV_2 G463S;V354F;V470A 214;207;225 219;212;230 S;RBD 102;95 107;98 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. As shown in Figure 5D, both the V354F and V470A mutants had significantly lower EC50 (concentration for 50% of maximal effect) values (EC50=1.32 mug/mL for V354F and EC50=1.24 mug/mL for V470A) than the wild-type (EC50=1.86 mug/mL), demonstrating that the V354F and V470A mutants had higher binding affinity and potentially increased infectivity. 2021 Zoological research Result SARS_CoV_2 V354F;V354F;V354F;V470A;V470A;V470A 32;156;256;42;187;266 37;161;261;47;192;271 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. Both the V354F and V470A variants exhibited increased binding to the human ACE2 receptor compared to the wild-type, consistent with our computer simulation (Figures 4D, 5A). 2021 Zoological research Result SARS_CoV_2 V354F;V470A 9;19 14;24 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. By 10 April 2020, based on 16 491 complete genomes of SARS-CoV-2, the number of mutant viruses with V354F, G463S, and V470A of spike-S1 reached 20, 19, and 30, respectively (Figure 5C). 2021 Zoological research Result SARS_CoV_2 G463S;V354F;V470A 107;100;118 112;105;123 S 127 132 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. For example, the V354F and V470A mutants have potentially increased infectivity. 2021 Zoological research Result SARS_CoV_2 V354F;V470A 17;27 22;32 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. Furthermore, the detected number of patients with these three mutants, i.e., V354F, G463S, and V470A, increased. 2021 Zoological research Result SARS_CoV_2 G463S;V354F;V470A 84;77;95 89;82;100 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. Hence, the SARS-CoV-2 mutant L84S was more likely be an ancestral variant than a virus with increased infectivity. 2021 Zoological research Result SARS_CoV_2 L84S 29 33 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. However, the 10 amino acid substitutions recurred in SARS-CoV-2, i.e., I789V of papain-like protease, H36Y and V354F of spike-S1, G251V of ORF3a, D209H of membrane glycoprotein, V62L, L84S, and P85S of ORF8, and S194L, S202N, and P344S of nucleocapsid phosphoprotein (Figure 3E). 2021 Zoological research Result SARS_CoV_2 D209H;G251V;H36Y;I789V;L84S;P344S;P85S;S194L;S202N;V354F;V62L 146;130;102;71;184;230;194;212;219;111;178 151;135;106;76;188;235;198;217;224;116;182 N;Membrane;S;ORF3a;ORF8 239;155;120;139;202 251;163;125;144;206 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. In addition, epidemiological and evolutionary data for H36Y, N341D, D351Y, and V354F of spike-S1, G251V of ORF3a, V62L and L84S of ORF8, and S194L and S202N of nucleocapsid phosphoprotein were analyzed. 2021 Zoological research Result SARS_CoV_2 D351Y;G251V;H36Y;L84S;N341D;S194L;S202N;V354F;V62L 68;98;55;123;61;141;151;79;114 73;103;59;127;66;146;156;84;118 N;S;ORF3a;ORF8 160;88;107;131 172;93;112;135 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. In addition, the SARS-CoV-2 mutant-V354F had no L84S mutant in ORF8. 2021 Zoological research Result SARS_CoV_2 L84S;V354F 48;35 52;40 ORF8 63 67 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. Interestingly, five patients from France with 100% identical protein sequences (Supplementary Table S6) shared the same V354F mutation, and this amino acid substitution was in the RBD region of spike-S1 (V354F). 2021 Zoological research Result SARS_CoV_2 V354F;V354F 120;204 125;209 S;RBD 194;180 199;183 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. Only one amino acid variant, K26R (rs ID (identity document): rs4646116), was distributed in the spike-binding regions of ACE2, but the variant site did not belong to the interaction sites for ACE2-spike-S1 (Figure 2A, C). 2021 Zoological research Result SARS_CoV_2 K26R 29 33 S;S 97;198 102;203 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. Previous research has indicated that the SARS-CoV-2 mutant L84S has reduced infectivity. 2021 Zoological research Result SARS_CoV_2 L84S 59 63 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. The amino acid substitution of ORF3a, i.e., G251V, had the second highest substitution rate (value=17) among the 10 mutant residues (Figure 3E). 2021 Zoological research Result SARS_CoV_2 G251V 44 49 ORF3a 31 36 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. The amino acid substitution of ORF8, i.e., L84S, had the highest substitution rate (value=36) among the 10 mutant residues (Figure 3E). 2021 Zoological research Result SARS_CoV_2 L84S 43 47 ORF8 31 35 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. The dN/dS (omega) value for SARS-CoV-2 mutant-V354F was 7.0E-4/0.00 (NA) compared to the wild-type spike-S1. 2021 Zoological research Result SARS_CoV_2 V354F 46 51 S 99 104 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. The dN/dS (omega) value for the SARS-CoV-2 mutant-L84S was 3.6E-3/0.00 (NA) compared to the wild-type ORF8. 2021 Zoological research Result SARS_CoV_2 L84S 50 54 ORF8 102 106 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. Therefore, given its potential increase in infectivity, SARS-CoV-2 mutant-V354F deserves close epidemic surveillance. 2021 Zoological research Result SARS_CoV_2 V354F 74 79 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. Therefore, the SARS-CoV-2 mutants (V354F and V470A) with potentially increased infectivity should be under close epidemic surveillance to avoid potential additional waves of SARS-CoV-2 infection worldwide. 2021 Zoological research Result SARS_CoV_2 V470A;V354F 45;35 50;40 COVID-19 174 194 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. Therefore, three mutants found in spike-S1 (N341D, D351Y, and V354F) were utilized to investigate the docking of spike-S1 to ACE2. 2021 Zoological research Result SARS_CoV_2 D351Y;V354F;N341D 51;62;44 56;67;49 S;S 34;113 39;118 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. Therefore, we focused on SARS-CoV-2 without L84S in ORF8. 2021 Zoological research Result SARS_CoV_2 L84S 44 48 ORF8 52 56 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. These results further suggest that spike-S1 with the V354F amino acid substitution had a higher affinity for ACE2 than wild-type spike-S1, which potentially led to increased infectivity. 2021 Zoological research Result SARS_CoV_2 V354F 53 58 S;S 35;129 40;134 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. These results suggest that the SARS-CoV-2 mutant with the V354F-spike-S1 mutation potentially exhibits increased infectivity. 2021 Zoological research Result SARS_CoV_2 V354F 58 63 S 64 69 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. To examine the binding capacity of spike-S1 mutants to ACE2, we constructed expression plasmids for two mutants, V354F and V470A (additional variant subsequently reported in the USA in Figure 5A-C) and purified sufficient protein for receptor-ligand binding assay. 2021 Zoological research Result SARS_CoV_2 V354F;V470A 113;123 118;128 S 35 40 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. To further explore the epidemic impact of the V354F mutant, spike-S1 sequences were downloaded from the GISAID EpiFluTM and CNCB/BIG databases at three different time points (22 February, 25 March, and 10 April 2020). 2021 Zoological research Result SARS_CoV_2 V354F 46 51 S 60 65 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. Among our samples, we found no significant difference in viral loads between patients with and without the S-D614G mutation (z = -0.881, p = 0.38). 2021 PLoS pathogens Result SARS_CoV_2 D614G 109 114 S 107 108 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. By searching all genomes available on GISAID (N = 80,189; as of August 12th 2020), filtering for genomes belonging nextstrain emerging clade 20A/15324 and sampled until March 23rd (N = 2,856), we find that the C15324T mutation has subsequently been observed in other countries but remains most prevalent in Switzerland (NGISAID = 57/213, 26.8%; NGISAID+this study = 386/675, 57.2%; first genome 42173111 from March 2nd) (Fig 4D and S3 Table). 2021 PLoS pathogens Result SARS_CoV_2 C15324T 210 217 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. Potential ski-holiday related cluster (C1059T) 2021 PLoS pathogens Result SARS_CoV_2 C1059T 39 45 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. Potential ski-holiday related cluster (C1059T). 2021 PLoS pathogens Result SARS_CoV_2 C1059T 39 45 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. Previous reports have identified viruses in lineage B.1 carrying SNP C1059T (amino acid change ORF1a-T265I) in travel returners from ski holidays in Ischgl, Austria. 2021 PLoS pathogens Result SARS_CoV_2 C1059T;T265I 69;101 75;106 ORF1a 95 100 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. The clade B.1-C15324T, within which 68.2% (N = 319) of our Basel area cohort sequences fall, henceforth referred to as the "Basel cluster", is characterized by synonymous SNP C15324T in ORF1ab. 2021 PLoS pathogens Result SARS_CoV_2 C15324T;C15324T 175;14 182;21 ORF1ab 186 192 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. The clade defining SNP C15324T (GISAID emerging clades label 20A/15324T) was identified for the first time on March 2nd simultaneously in the Basel area sample 42173111 and GISAID sample Germany/FrankfurtFFM7/2020, suggesting unsampled circulation of this variant in Europe from mid-February. 2021 PLoS pathogens Result SARS_CoV_2 C15324T 23 30 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. The spike protein S-D614G mutation is associated with the B.1 lineage and all those derived from this (Fig 4). 2021 PLoS pathogens Result SARS_CoV_2 D614G 20 25 S;S 4;18 9;19 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. The virus genome of Patient 1 carries a synonymous mutation at C313T in ORF1ab, which is found in samples from Israel, Hungary, Japan, USA, Argentina, Greece, India, Brazil, Morocco, and Netherlands among others (nextstrain.org), all sharing an unsampled hypothetical common ancestor that emerged around February 25th (CI February 23-26th). 2021 PLoS pathogens Result SARS_CoV_2 C313T 63 68 ORF1ab 72 78 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. The virus genome of Patient 2 carries a synonymous mutation at T19839C in ORF1ab and not C313T, and clusters together with eight identical virus genomes sampled between February 26th and March 23rd. 2021 PLoS pathogens Result SARS_CoV_2 C313T;T19839C 89;63 94;70 ORF1ab 74 80 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. Two additional samples forming a family cluster (Family 1, Fig 4B) diagnosed on March 3rd, carry the T19839C plus non-synonymous mutation G28179A leading to amino acid change ORF8-G96S. 2021 PLoS pathogens Result SARS_CoV_2 G28179A;T19839C;G96S 138;101;180 145;108;184 ORF8 175 179 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. We identified a major clade, within lineage B.1, B.1-C15324T, comprising 68.2% of our samples (319/468 samples with 264 (82.8%) from patients from cantons Basel-City and Basel-Landschaft; Fig 4A). 2021 PLoS pathogens Result SARS_CoV_2 C15324T 53 60 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. A similar 2P mutation (K986P/V987P) was introduced into the SARS-CoV-2 spike (termed S2P), which has been used to isolate and characterize NAbs and is the antigen in almost all vaccine candidates in clinical development. 2021 Science advances Result SARS_CoV_2 K986P;V987P 23;29 28;34 S 71 76 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. After CR3022 and SEC purification, we obtained 0.3 to 0.4, 0.5 to 1.0, and 0.8 to 1.2 mg of protein for S2GDeltaHR2-5GS-FR, S2GDeltaHR2-5GS-E2p-L4P, and S2GDeltaHR2-10GS-I3-01v9-L7P, respectively. 2021 Science advances Result SARS_CoV_2 L4P;L7P 144;178 147;181 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. Following the strategy established for FR, SARS-CoV-1/2 RBDs were attached to the I3-01v9-L7P SApNP using the SPY system. 2021 Science advances Result SARS_CoV_2 L7P 90 93 RBD 56 60 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. Here, SpyTag was fused to the C terminus of RBD, while SpyCatcher was fused to the N terminus of an SApNP subunit, both with a 5-amino acid G4S linker. 2021 Science advances Result SARS_CoV_2 G4S 140 143 RBD;N 44;83 47;84 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. Here, two of the best designs, E2p-LD4-PADRE (or E2p-L4P) and I3-01v9-LD7-PADRE (or I3-01v9-L7P), were tested for their ability to display SARS-CoV-1/2 RBDs. 2021 Science advances Result SARS_CoV_2 L4P;L7P 53;92 56;95 RBD 152 156 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. However, some impurities were noted for the RBD-presenting E2p-L4P SApNPs. 2021 Science advances Result SARS_CoV_2 L4P 63 66 RBD 44 47 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. On the basis of this consideration, we displayed the S2GDeltaHR2 spike on FR with a 5-amino acid G4S linker, on E2p with a 5-amino acid G4S linker, and on I3-01v9 with a 10-amino acid (G4S)2 linker, resulting in SApNPs with diameters of 47.9, 55.9, and 59.3 nm, respectively. 2021 Science advances Result SARS_CoV_2 G4S;G4S;G4S 97;136;185 100;139;188 S 65 70 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. The multilayered E2p-L4P and I3-01v9-L7P, which were validated for presenting RBDs. 2021 Science advances Result SARS_CoV_2 L4P;L7P 21;37 24;40 RBD 78 82 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. Three production runs for each of the three constructs generated highly consistent SEC profiles, despite the variation of low-molecular-weight impurities observed for FR and E2p-L4P. 2021 Science advances Result SARS_CoV_2 L4P 178 181 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. To test this possibility, we designed a fusion construct containing SARS-CoV-1/2 RBD, a short 5-amino acid G4S linker (with a 2-amino acid restriction site), and a trimeric viral capsid protein, SHP [Protein Data Bank (PDB): 1TD0]. 2021 Science advances Result SARS_CoV_2 G4S 107 110 RBD 81 84 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. We first created uncleaved spike ectodomain (SECTO) constructs for SARS-CoV-1/2, both containing the 2P mutation (K968P/V969P and K986P/V987P, respectively), a 5-amino acid G4S linker, a trimerization motif (PDB: 1TD0), and a C-terminal His6 tag. 2021 Science advances Result SARS_CoV_2 G4S;K986P;K968P;V969P;V987P 173;130;114;120;136 176;135;119;125;141 S 27 32 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. We then compared a pair of SECTO constructs for SARS-CoV-1/2, both containing a double glycine (2G) mutation, K968G/V969G and K986G/V987G, respectively. 2021 Science advances Result SARS_CoV_2 K968G;K986G;V969G;V987G 110;126;116;132 115;131;121;137 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. A pseudovirus bearing only the three RBD mutations (K417N, E484K, and N501Y) largely, but not entirely, recapitulated the escape phenotype (Figures 5B and 5D). 2021 Cell Result SARS_CoV_2 E484K;N501Y;K417N 59;70;52 64;75;57 RBD 37 40 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Despite this escape, antibodiesexhibited reduced, but detectable, binding to mutant RBD protein harboring B.1.351 mutations (K417N, E484K, and N501Y) by ELISA, which correlated with K417N+E484K+N501Y pseudovirus neutralization (R2 = 0.67, p < 0.0001) (Figure 5E). 2021 Cell Result SARS_CoV_2 E484K;K417N;N501Y;K417N;E484K;N501Y 132;182;143;125;188;194 137;187;148;130;193;199 RBD 84 87 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. However, neutralization of the Brazilian/Japanese P.2 variant, whose RBD contains an E484K mutation, was significantly decreased (5.8-fold for BNT162b2, p < 0.001; 2.9-fold for mRNA-1273, p < 0.01) (Figures 4C-4D and S4A). 2021 Cell Result SARS_CoV_2 E484K 85 90 RBD 69 72 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Neutralization of D614G pseudovirus was similar to that of wild type in individuals who received two doses of vaccine (1.2-fold decrease for both two-dose vaccines) (Figures 4A-4D and S4A), which was in contrast to previous studies in convalescent sera that we and others conducted demonstrating slightly increased neutralization of D614G variant versus wild type following natural infection. 2021 Cell Result SARS_CoV_2 D614G;D614G 18;333 23;338 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Remarkably, neutralization assays conducted with sera from 24 individuals that received the two-dose BNT162b2 vaccine revealed that neutralization of B.1.351 v1, v2, and v3 in the absence of RBD mutations was comparable to that of D614G (Figures 5B and 5C). 2021 Cell Result SARS_CoV_2 D614G 231 236 RBD 191 194 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Separately, the B.1.1.298 variant found in Danish minks contained a Y453F mutation in RBD, and the California variant B.1.429 contained an L452R mutation. 2021 Cell Result SARS_CoV_2 L452R;Y453F 139;68 144;73 RBD 86 89 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Similarly, neutralizing antibody responses were also significantly decreased for the Brazilian/Japanese P.1 strain (6.7-fold for BNT162b2, p < 0.0001; 4.5-fold for mRNA-1273, p < 0.001), which harbors three mutations in RBD (K417T, E484K, and N501Y) and has also been found in cases of reinfection. 2021 Cell Result SARS_CoV_2 E484K;N501Y;K417T 232;243;225 237;248;230 RBD 220 223 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. The effect was more pronounced in individuals who received one dose of vaccine, some of which had undetectable neutralization of D614G despite detectable neutralization of wild-type SARS-CoV-2 (Figures 4A and 4B). 2021 Cell Result SARS_CoV_2 D614G 129 134 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. The three main RBD mutations of concern are (1) N501Y, present in B.1.1.7, P.1, and B.1.351 variants; (2) E484K, present in the P.2, P.1, and B.1.351 variants; and (3) K417T for the P.1 variant and K417N for the B.1.351 variants. 2021 Cell Result SARS_CoV_2 E484K;K417N;K417T;N501Y 106;198;168;48 111;203;173;53 RBD 15 18 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. These strains contain the same three RBD mutations as P.1 except for an asparagine versus threonine substitution at K417 (K417N) and several additional mutations in non-RBD regions. 2021 Cell Result SARS_CoV_2 K417N 122 127 RBD;RBD 37;169 40;172 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. This difference may be a consequence of the vaccine encoding the wild-type spike sequence, while many convalescent individuals in previous studies were likely infected with D614G variant SARS-CoV-2, given it had already become the globally dominant strain by the summer of 2020. 2021 Cell Result SARS_CoV_2 D614G 173 178 S 75 80 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. This is in line with previous studies suggesting that the E484K mutation can evade polyclonal antibody responses and has been found in cases of SARS-CoV-2 reinfection. 2021 Cell Result SARS_CoV_2 E484K 58 63 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. When assessing variants containing one RBD mutation as part of their mutational landscape, the UK variant B.1.1.7 (N501Y), Danish mink variant B.1.1.298 (Y453F), and California variant B.1.429 (L452R) exhibited neutralization that was generally similar to that of wild-type and the parental D614G variant. 2021 Cell Result SARS_CoV_2 D614G;L452R;N501Y;Y453F 291;194;115;154 296;199;120;159 RBD 39 42 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. A23403G. 2021 Frontiers in microbiology Result SARS_CoV_2 A23403G 0 7 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. analyzed the entropy of variation of these two mutations (D614G and P323L) until May. 2021 Frontiers in microbiology Result SARS_CoV_2 P323L;D614G 68;58 73;63 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. C1059T. 2021 Frontiers in microbiology Result SARS_CoV_2 C1059T 0 6 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. C14408T. 2021 Frontiers in microbiology Result SARS_CoV_2 C14408T 0 7 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. C241T. 2021 Frontiers in microbiology Result SARS_CoV_2 C241T 0 5 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. C3037T causes a codon change from TTC to TTT. 2021 Frontiers in microbiology Result SARS_CoV_2 C3037T 0 6 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. C3037T. 2021 Frontiers in microbiology Result SARS_CoV_2 C3037T 0 6 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. Finally, OTU_5 presents all the mutations of OTU_4 plus one nsp2 mutation (C1059T). 2021 Frontiers in microbiology Result SARS_CoV_2 C1059T 75 81 Nsp2 60 64 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. For example, the four mutations that define OTU_2 (C241T, C30307T, C14408T, and A23403G) rarely had been described separately and similarly with mutations that characterize OTU_3 (G28881A, G28882A, and G28883C; Supplementary Figure S4). 2021 Frontiers in microbiology Result SARS_CoV_2 A23403G;C14408T;C30307T;G28882A;G28883C;C241T;G28881A 80;67;58;189;202;51;180 87;74;65;196;209;56;187 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. G25563T. 2021 Frontiers in microbiology Result SARS_CoV_2 G25563T 0 7 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. G28881A, G28882A, and G28883C. 2021 Frontiers in microbiology Result SARS_CoV_2 G28882A;G28883C;G28881A 9;22;0 16;29;7 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. How these effects occur at the structural level remains unclear, although some hypotheses have been put forward: (1) We think that there is no evidence for hydrogen-bond between D614 and T859 mentioned by, and distances between D614 and T859 are too long for a hydrogen bond (Supplementary Figure S13B), (2) distances between Q613 and T859 (Supplementary Figure S13C) could be reduced by increased flexibility due to D614G substitution, forming a stabilizing hydrogen bond, and (3) currently available structures do not show salt-bridges between D614 and R646 as proposed by; Supplementary Figure S13D). 2021 Frontiers in microbiology Result SARS_CoV_2 D614G 417 422 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. In concordance with this, protein dynamics simulations showed a stability increase of the Nsp12 P323L variant. 2021 Frontiers in microbiology Result SARS_CoV_2 P323L 96 101 Nsp12 90 95 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. In the absence of P322, the mutation P323L would probably be disfavored due to the flexibilization of the turn at the end of helix 10. 2021 Frontiers in microbiology Result SARS_CoV_2 P323L 37 42 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. It has been suggested that the D614G change in the S1 domain that results from the A23403G mutation generates a more infectious virus, less spike shedding, greater incorporation in pseudovirions, and higher viral load. 2021 Frontiers in microbiology Result SARS_CoV_2 A23403G;D614G 83;31 90;36 S 140 145 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. Mutation C1059T lies on Nsp2. 2021 Frontiers in microbiology Result SARS_CoV_2 C1059T 9 15 Nsp2 24 28 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. Mutation C3037T is a synonymous mutation in Nsp3; therefore, it is more difficult to associate this change with an evolutionary advantage for the virus. 2021 Frontiers in microbiology Result SARS_CoV_2 C3037T 9 15 Nsp3 44 48 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. Mutation G25563T produces the Q57H variant of Orf3a (Supplementary Figure S14C). 2021 Frontiers in microbiology Result SARS_CoV_2 G25563T;Q57H 9;30 16;34 ORF3a 46 51 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. Mutation G28883C that changes a glycine for arginine at position 204 contributes one more positive charge to each N protein. 2021 Frontiers in microbiology Result SARS_CoV_2 G28883C;R204G 9;32 16;68 N 114 115 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. Mutations G28881A and G28882A produce a change from arginine to lysine. 2021 Frontiers in microbiology Result SARS_CoV_2 G28881A;G28882A 10;22 17;29 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. On February 16th in the United Kingdom, a SARS-CoV-2 with three adjacent mutations (G28881A, G28882A, and G28883C; Supplementary Figure S3) in N protein was isolated. 2021 Frontiers in microbiology Result SARS_CoV_2 G28882A;G28883C;G28881A 93;106;84 100;113;91 N 143 144 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. OTU_4 does not present mutations in N protein; instead, it presents a variation in Orf3a (G25563T). 2021 Frontiers in microbiology Result SARS_CoV_2 G25563T 90 97 ORF3a;N 83;36 88;37 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. Showing simultaneously four mutations different to OTU_1 (C241T, C3037T, C14408T, and A23403G), OTU_2 is the first group containing the D614G and the P323L mutations in the spike and nsp12 protein, respectively. 2021 Frontiers in microbiology Result SARS_CoV_2 A23403G;C14408T;C3037T;D614G;P323L;C241T 86;73;65;136;150;58 93;80;71;141;155;63 S;Nsp12 173;183 178;188 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. The C14408T mutation changes P323 to leucine in Nsp12, the RNA-dependent RNA polymerase of SARS-CoV2 (Supplementary Figures S12A,B). 2021 Frontiers in microbiology Result SARS_CoV_2 C14408T;P323L 4;29 11;44 RdRp;Nsp12 59;48 87;53 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. The C241T mutation is present in the 5'-UTR region. 2021 Frontiers in microbiology Result SARS_CoV_2 C241T 4 9 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. The three consecutive mutations G28881A, G28882A, and G28883C falls at the 5' ends of the forward primer of "China-CDC-N" (Supplementary Table S1). 2021 Frontiers in microbiology Result SARS_CoV_2 G28881A;G28882A;G28883C 32;41;54 39;48;61 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. This observation correlates well with studies focused in South America that detect the establishment of D614G mutation at the end of March (mutation presents in OTU_2, OTU_3, OTU_4 and OTU_5) and a high frequency of pangolin lineage B1.1 in Chile and in general in South America that contains the same characteristics mutations that our OTU_3. 2021 Frontiers in microbiology Result SARS_CoV_2 D614G 104 109 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. We modeled Q57H mutation and we did not observe differences in the radius of constriction (Supplementary Figure S14C) formed by residue 57 but we observed slight differences in the electrostatic surface due to the ionizability of the histidine side chain (Supplementary Figure S14D). 2021 Frontiers in microbiology Result SARS_CoV_2 Q57H 11 15 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. A single novel mutation (N228K) was detected in the hCoV-19/Pakistan/NIH-45143 isolate, in a 55-year-old female patient (Table 1). 2021 ACS omega Result SARS_CoV_2 N228K 25 30 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. A substitution of aliphatic Leu with an aromatic Phe amino acid might have functional implications, where the Phe residue performs cation-pi interactions, affecting protein interactions in the L37F MT. 2021 ACS omega Result SARS_CoV_2 L37F 193 197 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. A total of 128 genomes from Indian patients were analyzed, among which all the SARS-CoV2 genomes had mutations at Q57H of the protein ORF3a, except a single genome (accession no. 2021 ACS omega Result SARS_CoV_2 Q57H 114 118 ORF3a 134 139 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. About 35% of the variants, including V30A, contain high and low binding affinity epitopes. 2021 ACS omega Result SARS_CoV_2 V30A 37 41 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. All the GH clades harbor Q57H mutation in NS3 proteins. 2021 ACS omega Result SARS_CoV_2 Q57H 25 29 NS3 42 45 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Although mutation N228K is present far from the catalytic site in domain III residues, it may affect dimerization, required for catalytic activity depending on the dimerization of the enzyme. 2021 ACS omega Result SARS_CoV_2 N228K 18 23 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Among the three mutations (NS8_L84S, NS8_E92K, and NS8_W45L) in NS8 (ORF8) of SARS-CoV-2, the appearance of E92K has not been reported in earlier studies. 2021 ACS omega Result SARS_CoV_2 E92K;E92K;L84S;W45L 108;41;31;55 112;45;35;59 ORF8 69 73 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. In all novel mutations where the crystal structure is not available, the MTs' [NSP2(D268del), NS3 (F105S), and orf1ab (Q2702H)] function implication is difficult to be predicted and need further validation. 2021 ACS omega Result SARS_CoV_2 F105S;Q2702H 99;119 104;125 ORF1ab;Nsp2;NS3 111;79;94 117;83;97 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. In CoV-2, residue T285 is substituted by A285 and I286 is substituted by L286 F. 2021 ACS omega Result SARS_CoV_2 L286F 73 79 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. In the current study, a single substitution A237T was detected in the NSP13, which shows a more stabilizing effect on the helicase structure activity (Figure 7). 2021 ACS omega Result SARS_CoV_2 A237T 44 49 Helicase;Nsp13 122;70 130;75 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. In the current study, NSP6 harbors two mutations:L37F (5 isolates) and M86I (2 isolates). 2021 ACS omega Result SARS_CoV_2 M86I;L37F 71;49 75;53 Nsp6 22 26 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. In the current study, two mutations, N_S202N and N_S327L, were detected (Figures 1, 6 and Table 3). 2021 ACS omega Result SARS_CoV_2 S202N;S327L 39;51 44;56 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. L84S destabilizes the folding, which may cause upregulation of the host-immune activity (Figure 5). 2021 ACS omega Result SARS_CoV_2 L84S 0 4 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. LC528232), while 2702Q > H and 5561A > T seem novel in Pakistani isolates. 2021 ACS omega Result SARS_CoV_2 Q2702H;A5561T 17;31 26;40 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Mutant P323L shifts the structure integrity and might have functional consequences. 2021 ACS omega Result SARS_CoV_2 P323L 7 12 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Mutation (N228K) in NSP5. 2021 ACS omega Result SARS_CoV_2 N228K 10 15 Nsp5 20 24 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Mutation L37F in NSP6 leads to a weak SARS-CoV-2 subtype which may help in SARS-CoV-2 transmission and evolution across various regions over time during the pandemic. 2021 ACS omega Result SARS_CoV_2 L37F 9 13 Nsp6 17 21 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Mutation L37F is present outside the trans-membrane and as a part coil segment. 2021 ACS omega Result SARS_CoV_2 L37F 9 13 Membrane 43 51 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Mutation L84S in ORF8 has been associated with decreased stability of ORF8. 2021 ACS omega Result SARS_CoV_2 L84S 9 13 ORF8;ORF8 17;70 21;74 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Mutation L84S in the current study has been detected in two isolates, which is a strain determining mutation of clade S (Table 3). 2021 ACS omega Result SARS_CoV_2 L84S 9 13 S 118 119 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Mutation N_S202N was detected in N2a; however, its impacts on the interaction with Nsp3 need to be evaluated. 2021 ACS omega Result SARS_CoV_2 S202N 11 16 Nsp3 83 87 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Mutation P323L in NSP12 (RdRp) in Pakistani isolates is the second-most common variant (Table 2). 2021 ACS omega Result SARS_CoV_2 P323L 9 14 Nsp12;RdRP 18;25 23;29 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Mutation P323L lies in residue A250-R365, which is known as the interface domain of the RdRp. 2021 ACS omega Result SARS_CoV_2 P323L 9 14 RdRP 88 92 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Mutation Q57H in our genome (Table 4) seems very common in Indian isolates. 2021 ACS omega Result SARS_CoV_2 Q57H 9 13 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Mutation S327L has been detected in the C-terminal domain (247-364) (Figure 1), and its impact on the N-CTD dynamics is shown in Figure 6. 2021 ACS omega Result SARS_CoV_2 S327L 9 14 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Mutations (L3606F) (Table 2), which link with the position L37F of NSP6 (Table 3), are present in isolates from the USA, China, Hong Kong, France, Singapore, and Italy. 2021 ACS omega Result SARS_CoV_2 L37F;L3606F 59;11 63;17 Nsp6 67 71 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. NS3_Q57H mutation is a clade determinant (GH) mutation. 2021 ACS omega Result SARS_CoV_2 Q57H 4 8 NS3 0 3 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Pro4715Leu has been detected in NSP12/RdRP (orf1ab). 2021 ACS omega Result SARS_CoV_2 P4715L 0 10 ORF1ab;Nsp12;RdRP 44;32;38 50;37;42 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Recently, it was observed that 327S > L may increase the stability in N proteins but decrease the molecular flexibility. 2021 ACS omega Result SARS_CoV_2 S327L 31 39 N 70 71 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. S202N is present in the serine-arginine-rich region (residues 184-2024), close to the N-terminal domain (N-NTD). 2021 ACS omega Result SARS_CoV_2 S202N 0 5 N 86 87 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. The 20A/G clades are characterized by D614G mutation in spike protein, suggesting increased transmissibility but not pathogenicity. 2021 ACS omega Result SARS_CoV_2 D614G 38 43 S 56 61 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. The effect of mutation NSP3_Q1884H could not be evaluated due to the unavailability of the complete crystal structure and suitable temple for the homology model. 2021 ACS omega Result SARS_CoV_2 Q1884H 28 34 Nsp3 23 27 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. The most common mutations detected in the Pakistani isolates were NSP6_L37F (5), spike_D614G, NSP12_P323L (4), and NS3_Q57H (4). 2021 ACS omega Result SARS_CoV_2 D614G;L37F;P323L;Q57H 87;71;100;119 92;75;105;123 S;Nsp12;Nsp6;NS3 81;94;66;115 86;99;70;118 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. The mutation 327S > L is present in the C-terminal domain of N proteins. 2021 ACS omega Result SARS_CoV_2 S327L 13 21 N 61 62 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. The mutation L3606F in orf1ab was also reported in Japanese isolate (accession no. 2021 ACS omega Result SARS_CoV_2 L3606F 13 19 ORF1ab 23 29 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. The N protein primarily promotes the binding and packing of the RNA ribonucleoprotein complex (nucleocapsid).- A single mutation 241C > T in the 5' UTR region was detected in the current study, which was also reported recently in a whole genome sequence from Gilgit (accession no. 2021 ACS omega Result SARS_CoV_2 C241T 129 137 N;5'UTR;N 95;145;4 107;151;5 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. The variant D614G in S protein detected in the current study is more commonly present in European isolates, such as those from Spain, Belgium, France, Italy, Switzerland, and the Netherlands, and appears more severe and fatal, accounting for a huge death toll (); Germany, Kuwait, and Pakistan have the wild-type 614D at S in a majority of strains, with a lower death toll. 2021 ACS omega Result SARS_CoV_2 D614G 12 17 S;S 21;321 22;322 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. We detected a novel mutation, V30L in ORF10 (Table 2); however, its effect needs to be elucidated for a better understanding of immunogenicity. 2021 ACS omega Result SARS_CoV_2 V30L 30 34 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. We predicted the stability effect of MTs NS8_E92K and NS8_W45L through DynaMut online server. 2021 ACS omega Result SARS_CoV_2 E92K;W45L 45;58 49;62 33750399 Modelling the association between COVID-19 transmissibility and D614G substitution in SARS-CoV-2 spike protein: using the surveillance data in California as an example. Hence, the changing dynamics of Rt are likely associated with the key mutations that are solely contributed to by the D614G substitution. 2021 Theoretical biology & medical modelling Result SARS_CoV_2 D614G 118 123 33750399 Modelling the association between COVID-19 transmissibility and D614G substitution in SARS-CoV-2 spike protein: using the surveillance data in California as an example. However, we noticed that since (roughly) April 15, 2020, the prevalence of the D614G substitution increased, but Rt remained constant. 2021 Theoretical biology & medical modelling Result SARS_CoV_2 D614G 79 84 33750399 Modelling the association between COVID-19 transmissibility and D614G substitution in SARS-CoV-2 spike protein: using the surveillance data in California as an example. In other words, the D614G substitution is considered a key mutation and is likely dominant in accounting for the changes in COVID-19 transmissibility due to a mutation at the molecular level. 2021 Theoretical biology & medical modelling Result SARS_CoV_2 D614G 20 25 COVID-19 124 132 33750399 Modelling the association between COVID-19 transmissibility and D614G substitution in SARS-CoV-2 spike protein: using the surveillance data in California as an example. Previous analysis implied that the D614G substitution may alter the conformation of the S protein and thus may theoretically functionally enhance receptor binding capacity, leading to an increase in SARS-CoV-2 transmissibility and pathogenicity. 2021 Theoretical biology & medical modelling Result SARS_CoV_2 D614G 35 40 S 88 89 33750399 Modelling the association between COVID-19 transmissibility and D614G substitution in SARS-CoV-2 spike protein: using the surveillance data in California as an example. Sensitivity analysis with alternative model structures in Eqns (3)-(5) indicates that the positive association between the D614G substitution and Rt holds robustly and significantly (data not shown). 2021 Theoretical biology & medical modelling Result SARS_CoV_2 D614G 123 128 33750399 Modelling the association between COVID-19 transmissibility and D614G substitution in SARS-CoV-2 spike protein: using the surveillance data in California as an example. The significant positive association between the D614G substitution and Rt is biologically reasonable and consistent with findings in previous studies. 2021 Theoretical biology & medical modelling Result SARS_CoV_2 D614G 49 54 33750399 Modelling the association between COVID-19 transmissibility and D614G substitution in SARS-CoV-2 spike protein: using the surveillance data in California as an example. we found that the prevalence of the D614G substitution matches the trends of Rt in March 2020. 2021 Theoretical biology & medical modelling Result SARS_CoV_2 D614G 36 41 33750399 Modelling the association between COVID-19 transmissibility and D614G substitution in SARS-CoV-2 spike protein: using the surveillance data in California as an example. When theta = 0.8, we found that the g-measure of the S protein appeared to be solely contributed to by the D614G substitution. 2021 Theoretical biology & medical modelling Result SARS_CoV_2 D614G 107 112 S 53 54 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Additionally, as reported that the salt-bridges and other interactions are increased in the mutant complexes than the wild type, which is possible due to the increase in the electrostatic energy, specifically in the E484K complex. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K 216 221 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. At some intervals, the N501Y (ACE2-spike RBD) possesses similar behavior as the wild type over the course of the simulation. 2021 Journal of cellular physiology Result SARS_CoV_2 N501Y 23 28 S;RBD 35;41 40;44 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Binding comparison discovered that there is a noticeable divergence in spike RBD binding between wild type, E484K, N501Y, E484K-N501Y, K417N-E484K-N501Y, and K417T-E484K-N501Y complexes. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;E484K;K417N;K417T;N501Y;E484K;E484K;N501Y;N501Y;N501Y 108;122;135;158;115;141;164;128;147;170 113;127;140;163;120;146;169;133;152;175 S;RBD 71;77 76;80 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Comparative genomics inspection of genomes obtained from the UK, South Africa, Brazil, and other parts of the world revealed that the spike protein had acquired multiple crucial mutations including (K417N, K417T, E484K, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H) and deletions (69-70, 144). 2021 Journal of cellular physiology Result SARS_CoV_2 A570D;D1118H;D614G;E484K;K417T;N501Y;P681H;S982A;T716I;K417N 227;262;234;213;206;220;241;255;248;199 232;268;239;218;211;225;246;260;253;204 S 134 139 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Figure 6a shows that the region between 40 and 50 in N501Y displayed considerably higher fluctuation than the others. 2021 Journal of cellular physiology Result SARS_CoV_2 N501Y 53 58 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Finally, we calculated the stability of the E484K-N501Y (ACE2-spike RBD) complex, which shows that the system RMSD increased continuously during the 100 ns simulation. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;N501Y 44;50 49;55 S;RBD 62;68 67;71 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. For the Brazilian variant (K417T- E484K-N501Y) the total binding energy was reported to be -90.99 kcal/mol. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;K417T;N501Y 34;27;40 39;32;45 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. For the K417N- E484K-N501Y variant the KD was reported to be 4.2E-10 which reflects the tighter binding of the new variant than wild type. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;K417N;N501Y 15;8;21 20;13;26 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. For the wild type and the mutants, the Van der Waals energy was reported to be -59.6 +- 2.3 (wild complex), -53.6 +- 5.3 (E484K), -55.2 +-1.9 (N501Y), and -59.2 +- 7.5 for the double mutants. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;N501Y 122;143 127;148 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. From this data, it is evident that the N501Y possess similar behavior to the wild type; hence it can be inferred that the already developed vaccines might work against the new N501Y variant. 2021 Journal of cellular physiology Result SARS_CoV_2 N501Y;N501Y 39;176 44;181 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Furthermore, the novel mutation N501Y reported in the UK variant is also reported to increases the spread and thus responsible for increased coronavirus cases (Leung et al., 2021). 2021 Journal of cellular physiology Result SARS_CoV_2 N501Y 32 37 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Furthermore, the total binding energy for the E484K-N501Y (ACE2-spike RBD) was observed to be -77.53 kcal/mol. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;N501Y 46;52 51;57 S;RBD 64;70 69;73 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Herein the wild type the binding affinity DeltaG was predicted to be -13.2 and the KD value for the wild complex was reported to be 5.2E-10, for the E484K the DeltaG was predicted to be -13.2 while the KD was 3.0E-10, for the N501Y the DeltaG was predicted to be -13.1 while the KD was 6.6E-10. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;N501Y 149;226 154;231 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Herein to understand the impact of double substitution on the binding of ACE2-spike RBD, we also generated the E484K-N501Y mutant. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;N501Y 111;117 116;122 S;RBD 78;84 83;87 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. In addition, the mutants with the hypothetical mutant (E484K-N501Y) were observed to be radical, thus implying the biological significance of the designed mutant, which may result in relatively higher infectivity than the wild type. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;N501Y 55;61 60;66 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. In case of the double mutant (E484K-N501Y), the predicted DeltaG value was -12.8 kcal/mol while the KD 9.4E-10 was reported. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;N501Y 30;36 35;41 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. In comparison, in the case of N501Y, the regions 500-505 have higher fluctuation but not others (Figure 6C). 2021 Journal of cellular physiology Result SARS_CoV_2 N501Y 30 35 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. In E484K, the region where the mutated residue (E484K) reside possesses higher fluctuation. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;E484K 3;48 8;53 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. In the case of the K417N-E484K-N501Y mutant, the Rg value remained higher comparatively. 2021 Journal of cellular physiology Result SARS_CoV_2 K417N;E484K;N501Y 19;25;31 24;30;36 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. In the case of the K417T-E484K-N501Y variant, a more radical behavior was observed during the simulation. 2021 Journal of cellular physiology Result SARS_CoV_2 K417T;E484K;N501Y 19;25;31 24;30;36 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Interestingly the electrostatic energy significantly increased in the ACE2-spike RBD (E484K) and E484K-N501Y (ACE2-spike RBD) complexes. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;E484K;N501Y 97;86;103 102;91;108 S;S;RBD;RBD 75;115;81;121 80;120;84;124 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Intriguingly, the total binding energy of the wild type (-73.11 kcal/mol) and N501Y (-73.00 kcal/mol) was comparable. 2021 Journal of cellular physiology Result SARS_CoV_2 N501Y 78 83 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. It can be seen from Figure 4 that N501Y gained stability at 2.0 A. 2021 Journal of cellular physiology Result SARS_CoV_2 N501Y 34 39 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. It can be seen that the mutated residues, such as K417N, E484K, and N501Y, are involved primarily in interactions. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;K417N;N501Y 57;50;68 62;55;73 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Looking into the significant role of these substitutions in the RBD domain of the spike glycoprotein, we generated K417N-E484K-N501Y, K417T- E484K-N501Y, E484K, N501Y, and E484K-N501Y double mutant to perform comparative structural and binding analysis. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;E484K;E484K;K417N;K417T;N501Y;E484K;N501Y;N501Y;N501Y 141;154;172;115;134;161;121;127;147;178 146;159;177;120;139;166;126;132;152;183 S;RBD 82;64 100;67 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Next, we calculated the stability index for the N501Y (ACE2-spike RBD) complex to reveal the dynamic behavior. 2021 Journal of cellular physiology Result SARS_CoV_2 N501Y 48 53 S;RBD 60;66 65;69 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Scientists have speculated that the available vaccines against COVID-19 might not be effective against it the E484K variant and hence, therefore, E484K along with other interface residues are key hotspots for the drug discovery against the SARS-CoV-2 variants. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;E484K 110;146 115;151 COVID-19 63 71 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Similarly, the Rg value for K417T-E484K-N501Y increased during the simulation. 2021 Journal of cellular physiology Result SARS_CoV_2 K417T;E484K;N501Y 28;34;40 33;39;45 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Since only two variants E484K and N501Y are reported alone but not simultaneously. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;N501Y 24;34 29;39 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Since these mutations, K417N, K417T, E484K, and N501Y modulates the binding pattern of the spike protein and supports their adaptive significance. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;K417N;K417T;N501Y 37;23;30;48 42;28;35;53 S 91 96 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Structural-dynamics features of the K417N-E484K-N501Y variant were further characterized. 2021 Journal of cellular physiology Result SARS_CoV_2 K417N;E484K;N501Y 36;42;48 41;47;53 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The average Rg value for the K417T-E484K-N501Y variant was observed to the same as K417N-E484K-N501Y which shows a similar behavior of the two variants. 2021 Journal of cellular physiology Result SARS_CoV_2 K417N;K417T;E484K;E484K;N501Y;N501Y 83;29;35;89;41;95 88;34;40;94;46;100 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The average Rg value for the wild type was observed to be (31.2 A), for E484K (31.6 A), for N501Y (31.8 A) while for the E484K-N501Y the average Rg value was observed to be 31.6 A. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;E484K;N501Y;N501Y 72;121;92;127 77;126;97;132 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The average Rg value was observed to be 32.0 A which is similar to that of the K417N-E484K-N501Y variant. 2021 Journal of cellular physiology Result SARS_CoV_2 K417N;E484K;N501Y 79;85;91 84;90;96 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The binding of spike RBD with the E484K to the ACE2 was more efficient than any other. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K 34 39 S;RBD 15;21 20;24 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The docking score for the Brazilian variant carrying K417T mutation with the E484K and N501Y was reported to be -127.0 +- 1.4 kcal/mol. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;K417T;N501Y 77;53;87 82;58;92 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The E484K (ACE2-spike RBD) complex initially converged largely between 0 and 18 ns reaching at 5.0 A. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K 4 9 S;RBD 16;22 21;25 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The E484K (ACE2-spike RBD) complex possesses a higher docking score than the wild type. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K 4 9 S;RBD 16;22 21;25 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The E484K substitution as mentioned earlier is responsible for the fast spread and high infectivity of the SARS-CoV-2 variant is actively involved in both salt bridges and hydrogen bonding interaction and consequently enhanced the binding affinity and infectivity. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K 4 9 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The E484K-N501Y mutant complex formed 1 salt bridge, 11 hydrogen bonds, and 121 nonbonded interactions. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;N501Y 4;10 9;15 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The electrostatic energy for the wild type reported here to be -181.4 +- 15.5, for the E484K complex it was reported to be -274.1 +- 10.0, for the N501Y it was reported to be -205.8 +- 10.3 for E484K-N501Y complex the electrostatic energy was found to be -182.4 +- 24.3, for K417N-E484K-N501Y the electrostatic contribution was -212.2 +- 39.0 while for K417T-E484K-N501Y it was -207.7 +- 15.2 kcal/mol. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;E484K;K417N;K417T;N501Y;E484K;E484K;N501Y;N501Y;N501Y 87;194;275;353;147;281;359;200;287;365 92;199;280;358;152;286;364;205;292;370 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The HADDOCK docking score for E484K (ACE2-spike RBD) was reported to be -128.8 +- 2.6 kcal/mol. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K 30 35 S;RBD 42;48 47;51 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The mutants were generated by using Chimera and are given in Figure 1c (wild type), Figure 1d (E484K), Figure 1e (N501Y), Figure 1f (E484K-N501Y), Figure 1g (K417N-E484K-N501Y), Figure 1h (K417T- E484K-N501Y). 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;E484K;E484K;K417N;K417T;N501Y;E484K;N501Y;N501Y;N501Y 196;95;133;158;189;114;164;139;170;202 201;100;138;163;194;119;169;144;175;207 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The RMSD results show that the K417N-E484K-N501Y system initially converged until 30 ns but afterward the complex attained stability and did not face substantial perturbation. 2021 Journal of cellular physiology Result SARS_CoV_2 K417N;E484K;N501Y 31;37;43 36;42;48 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The scientist also speculated the available vaccine developed recently against the Wuhan strain may work against the UK (N501Y; VOC 202012/01) variant but not against the South African variant (K417N-E484K-N501Y; 501Y.V2 Variant) and the Brazil variant (K417T-E484K-N501Y) formally known as P.1 (or B.1.1.248). 2021 Journal of cellular physiology Result SARS_CoV_2 K417N;K417T;N501Y;E484K;E484K;N501Y;N501Y 194;254;121;200;260;206;266 199;259;126;205;265;211;271 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The systematic investigation revealed that the South African and Brazilian variants are more lethal than the others due to interprotein contacts specifically the electrostatic while the N501Y is comparable with the wild type. 2021 Journal of cellular physiology Result SARS_CoV_2 N501Y 186 191 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The total binding energy of the ACE2-spike RBD (E484K) complex was reported to be the highest (-79.19 kcal/mol). 2021 Journal of cellular physiology Result SARS_CoV_2 E484K 48 53 S;RBD 37;43 42;46 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The triple variants exhibiting K417N-E484K-N501Y (reported in South Africa) and K417T-E484K-N501Y (reported in Brazil) mutations were also subjected to molecular docking investigation. 2021 Journal of cellular physiology Result SARS_CoV_2 K417N;K417T;E484K;E484K;N501Y;N501Y 31;80;37;86;43;92 36;85;42;91;48;97 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. The vdW and electrostatic energies for the wild type and N501Y are comparable thus justify this notion that the already developed vaccine may work against the UK mutant but not against the variants that emerged in South Africa and Brazil. 2021 Journal of cellular physiology Result SARS_CoV_2 N501Y 57 62 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Therefore, we used HADDOCK to perform the protein-protein docking of ACE2 with the wild spike-RBD, E484K spike-RBD, N501Y spike-RBD, double mutant (E484K-N501Y) spike-RBD, K417N-E484K-N501Y spike-RBD, and K417T-E484K-N501Y spike-RBD domain to explore the structural mechanism behind the higher infectivity of the SARS-CoV-2 variants. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;K417N;K417T;N501Y;E484K;E484K;E484K;N501Y;N501Y;N501Y 99;172;205;116;148;178;211;154;184;217 104;177;210;121;153;183;216;159;189;222 S;S;S;S;S;S;RBD;RBD;RBD;RBD;RBD;RBD 88;105;122;161;190;223;94;111;128;167;196;229 93;110;127;166;195;228;97;114;131;170;199;232 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. This shows a more rigid binding of the ACE2 and E484K-spike RBD. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K 48 53 S;RBD 54;60 59;63 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. This shows that the binding of K417N-E484K-N501Y (reported in South Africa) is due to the substitutions which formed essential extra interactions and thus signifies the higher infectivity. 2021 Journal of cellular physiology Result SARS_CoV_2 K417N;E484K;N501Y 31;37;43 36;42;48 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. This shows that the fixed amino acid substitution (E484K) has helped the viral protein to evolve stably and thus binds to the host receptor with stronger affinity. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K 51 56 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. This shows that the naturally reported K417N, K417T, E484K, and N501Y mutations have stably evolved than the hypothetical E484K-N501Y mutations. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;E484K;K417N;K417T;N501Y;N501Y 53;122;39;46;64;128 58;127;44;51;69;133 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. To characterize the binding of the South African variant (K417N- E484K-N501Y) the total binding energy remained higher than any other variant. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K;K417N;N501Y 65;58;71 70;63;76 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. To determine how the N501Y impacts the binding of the ACE2-spike RBD domain, herein structural insight was provided. 2021 Journal of cellular physiology Result SARS_CoV_2 N501Y 21 26 S;RBD 59;65 64;68 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. While for the K417T-E484K-N501Y the KD value was reported to be 4.2E-08. 2021 Journal of cellular physiology Result SARS_CoV_2 K417T;E484K;N501Y 14;20;26 19;25;31 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. With an extra salt bridge and an additional hydrogen bond formed by the substituted residue Lys484 increased the binding ACE2-E484K mutant complex. 2021 Journal of cellular physiology Result SARS_CoV_2 E484K 126 131 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. According to GISAID clade nomenclature (https://www.gisaid.org/references/statements-clarifications/clade-and-lineage-nomenclature-aids-in-genomic-epidemiology-of-active-hcov-19-viruses/), Pakistani strains NIH-44905 and NIH-HAS001 belong to S clade having characteristic genetic markers C8782T, T28144C, and NS8-L84S whereas strains NIH-45090, NIH-45143, and NIH-45579 belong to GH clade having marker variations C241T, C3037T, A23403G, G25563T, S-D614G, and NS3-Q57H. 2021 PloS one Result SARS_CoV_2 A23403G;C241T;C3037T;C8782T;G25563T;T28144C;D614G;L84S;Q57H 429;414;421;288;438;296;449;313;464 436;419;427;294;445;303;454;317;468 NS3;S;S 460;242;447 463;243;448 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. Five missense mutations were common in all the strains, three in ORF1ab polyprotein (a.a Q2702H, L3606F, P4715L), one in surface glycoprotein (a.a D614G), and one in ORF3a protein (a.a Q57H). 2021 PloS one Result SARS_CoV_2 D614G;L3606F;P4715L;Q2702H;Q57H 147;97;105;89;185 152;103;111;95;189 S;ORF1ab;ORF3a 121;65;166 141;71;171 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. Furthermore, Gilgit1/2020 (EPI_ISL_417444) strain had similar variations at 241C>T and 11083G>T in ORF1ab while KP-RMI-01/2020 (EPI_ISL_632908) showed a single change (11083G>T in ORF1ab) (Fig 3A). 2021 PloS one Result SARS_CoV_2 G11083T;C241T;G11083T 87;76;168 95;82;176 ORF1ab;ORF1ab 99;180 105;186 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. Furthermore, strain NIH-45090 showed a missense mutation in ORF8 protein (a.a W45L), strain NIH-45143 revealed novel amino acid substitutions in ORF1ab polyprotein (a.a N3491K) and in ORF3a protein (a.a F105S). 2021 PloS one Result SARS_CoV_2 F105S;N3491K;W45L 203;169;78 208;175;82 ORF1ab;ORF3a;ORF8 145;184;60 151;189;64 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. In addition, strain NIH-45090 showed 28027G>T & 29696C>T, NIH-45143 displayed 10738T>A, 25706T>C & 29868G>A and NIH-45579 had 1613C>T, 3613T>C, 18603T>C, 18788C>T, 28378G>C & 28878G>A nucleotide changes. 2021 PloS one Result SARS_CoV_2 T10738A;C1613T;T18603C;C18788T;T25706C;G28027T;G28378C;G28878A;C29696T;G29868A;T3613C 78;126;144;154;88;37;164;175;48;99;135 86;133;152;162;96;45;172;183;56;107;142 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. Pakistani strains UN-UVAS-Sialkot/2020 (EPI_ISL_548946) and UN-UVAS-Lahore-I/2020 (EPI_ISL_548942) contained one amino acid change each in ORF1ab (a.a P4715L) and surface glycoprotein (a.a D614G), respectively. 2021 PloS one Result SARS_CoV_2 D614G;P4715L 189;151 194;157 S;ORF1ab 163;139 183;145 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. Strain NIH-45579 showed two amino acid changes in ORF1ab polyprotein (novel mutation a.a L450F and T6175I), and one in nucleocapsid protein (a.a S202N). 2021 PloS one Result SARS_CoV_2 L450F;S202N;T6175I 89;145;99 94;150;105 N;ORF1ab 119;50 131;56 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. The KP-RMI-01/2020 (EPI_ISL_632908) and Gilgit1/2020 (EPI_ISL_417444) strains showed a similar amino acid change (L3606F in ORF1ab) with our GH clade strains. 2021 PloS one Result SARS_CoV_2 L3606F 114 120 ORF1ab 124 130 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. The KPK-KUST-SJTU/2020 contained nucleotide changes in ORF1ab (2416C>T, 8371G>T, 11083G>T), S-gene (22477C>T) and ORF3a (25563G>T). 2021 PloS one Result SARS_CoV_2 G11083T;G8371T;C22477T;C2416T;G25563T 81;72;100;63;121 89;79;108;70;129 ORF1ab;ORF3a;S 55;114;92 61;119;93 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. The Pakistani S clade strains contained nine common SNPs (2461T>C, 8782C>T, 11230G>T, 24051A>C, 26313C>T, 28144T>C, 28167G>A, 28878G>A, and 29742G>A). 2021 PloS one Result SARS_CoV_2 G11230T;A24051C;C26313T;T28144C;G28167A;G28878A;G29742A;C8782T;T2461C 76;86;96;106;116;126;140;67;58 84;94;104;114;124;134;148;74;65 S 14 15 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. The strain NIH-44905 also had a nucleotide change at position 355C>T (Table 3). 2021 PloS one Result SARS_CoV_2 C355T 62 68 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. The two Pakistani strains of clade S contained five missense mutations: one in ORF1ab polyprotein (a.a M3655I), a novel mutation in surface glycoprotein (a.a D830A), two missense mutations in ORF8 protein (a.a L84S and E92K), and one in nucleocapsid phosphoprotein (a.a S202N) (Table 3). 2021 PloS one Result SARS_CoV_2 D830A;E92K;L84S;M3655I;S202N 158;219;210;103;270 163;223;214;109;275 S;N;ORF1ab;ORF8;S 132;237;79;192;35 152;249;85;196;36 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. three in ORF1ab (a.a Q2702H, L3606F & P4715L), one each in surface glycoprotein (a.a D614G) and OFR3a (a.a Q57H) (Fig 3B). 2021 PloS one Result SARS_CoV_2 D614G;L3606F;P4715L;Q2702H;Q57H 85;29;38;21;107 90;35;44;27;111 S;ORF1ab 59;9 79;15 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. We have analyzed the genome-wide single-nucleotide polymorphisms (SNPs) and found nine common nucleotide variations (241C>T, 2416C>T, 3037C>T, 8371G>T, 11083G>T, 14408C>T, 22477C>T, 23403A>G, and 25563G>T) among Pakistani viruses of clade GH compared with the reference Wuhan strain (NC_045512). 2021 PloS one Result SARS_CoV_2 G11083T;C14408T;C22477T;A23403G;C2416T;G25563T;C3037T;G8371T;C241T 152;162;172;182;125;196;134;143;117 160;170;180;190;132;204;141;150;123 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. When compared with SARS-CoV-2 isolates submitted in GISAID from Pakistan at the same nucleotide positions, three strains UN-UVAS-Sialkot/2020 (EPI_ISL_548946), UN-UVAS-Lahore-I/2020 (EPI_ISL_548942) and KPK-KUST-SJTU/2020 (EPI_ISL_513925) showed same nucleotide variations at position 241C>T, 3037C>T, 14408C>T (ORF1ab) and 23403A>G (S-gene) compared to current study strains of GH clade (NIH-45090, NIH-45143, & NIH-45579). 2021 PloS one Result SARS_CoV_2 C14408T;A23403G;C241T;C3037T 302;324;285;293 310;332;291;300 ORF1ab;S 312;334 318;335 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. According to SPR measurements, the affinities for PALS1 F318W mutant of the longer viral tetradecapeptides used in this assay, are in good agreement with what previously reported for the shorter ones with a different experimental technique. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 F318W 56 61 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. As analytes, PDZ domains of PALS1, both wild-type and F318W variant, were used. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 F318W 54 59 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. At first, two 500 ns long molecular dynamic simulations of both PALS1 wild-type and F318W mutant alone were performed. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 F318W 84 89 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. Moreover, the experimental evidence that the mutant F318W has a higher affinity for both the viral peptides (but not for the endogenous peptide CRB1) with respect to wild type PALS1 protein, suggests a direct involvement of this residue into the binding mechanism of the viral peptides. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 F318W 52 57 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. Noticeably, the complex PALS1 F318W - SARS-CoV-1 E-SLiM was run three times, as the peptide was not stable along the entire simulation in at least two over three cases. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 F318W 30 35 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. Starting from the reported 3D structure of the complex wild-type PALS1 and CRB1 peptide, three different computational models were prepared (see Materials and Methods section for detailed information on the molecular docking procedures): a) PALS1 F318W in complex with SARS-CoV-2 E-SLiM, b) PALS1 F318W in complex with SARS-CoV-1 E-SLiM and c) PALS1 F318W in complex with CRB1 SLiM. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 F318W;F318W;F318W 247;297;350 252;302;355 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. This model suggests a lower affinity of PALS1 F318W for peptides binding in the internal groove, if the affinity change is simply driven by a reduction in the on-rate of formation of the active complex, and could explain the three-fold higher value of CRB1 Kd for PALS1 F318W compared to the wild type protein. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 F318W;F318W 46;270 51;275 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. A23403G and C14408T were observed at higher frequencies (>50%) in all the genomes, while G25563T, C13730T, G11083T C6312A, C241T, C3037T, G11083T, C13730T, C28311T, C6312A and C23929T mutations were predominated (>24% frequency) in Indian genomes (Additional File1). 2021 Heliyon Result SARS_CoV_2 C13730T;C13730T;C14408T;C23929T;C241T;C28311T;C3037T;C6312A;C6312A;G11083T;G11083T;G25563T;A23403G 98;147;12;176;123;156;130;115;165;107;138;89;0 105;154;19;183;128;163;136;121;171;114;145;96;7 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Among all the variations, twelve (L5F, L8V, L18F, R21I, L54F, N439K, D614G, A829T, A879S, D936Y, G1124V, P1263L) were dominant (greater than 1000 genomes) (Figure 6). 2021 Heliyon Result SARS_CoV_2 A829T;A879S;D614G;D936Y;G1124V;L18F;L54F;L8V;N439K;P1263L;R21I;L5F 76;83;69;90;97;44;56;39;62;105;50;34 81;88;74;95;103;48;60;42;67;111;54;37 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Clade G and GH identified by the signature marker D614G variant in spike protein which is increasing its frequency across globe and specially developed countries. 2021 Heliyon Result SARS_CoV_2 D614G 50 55 S 67 72 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Clades are characterized as S (C8782T, T28144C, NS8-L84S), L (C241, C3037, A23403, C8782, G11083, G25563, G26144, T28144, G228882), V (NSP6-L37F, NS3-G251V), G (S-D614S), GH (S-D614S, NS3-Q57H), S (S-D614S, NG204R). 2021 Heliyon Result SARS_CoV_2 T28144C;C8782T;G251V;L37F;L84S;Q57H 39;31;150;140;52;188 46;37;155;144;56;192 Nsp6;NS3;NS3;S;S;S;S;S 135;146;184;28;161;175;195;198 139;149;187;29;162;176;196;199 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. D614G mutation in spike protein, which is considered as a prevalent global mutation, was present in 2062 of the 2525 (81.66%) sequenced genomes. 2021 Heliyon Result SARS_CoV_2 D614G 0 5 S 18 23 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Even a single mutation introduced in these contacts, for example, K353A could abrogate the interactions between the two proteins, highlighting the importance of the polar contacts. 2021 Heliyon Result SARS_CoV_2 K353A 66 71 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Examining the variants from the O clade isolates observed the most frequent variant as G11083T (46.7%), C28311T (22.7%), and C13730T (20.4%). 2021 Heliyon Result SARS_CoV_2 C13730T;C28311T;G11083T 125;104;87 132;111;94 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Global characterization of the SARS-CoV-2 variants from all ~50,500 viral genomes sequences, suggested three major variants groups as 1,771 isolate Group 1 "C241T, C3037T, C14408T, A23403G, G28881A, G28882A, G28883C", the 1,458-isolate Group 2 "C241T, C1059T, C3037T, C14408T, A23403G, G25563T", and the 727-isolate Group 3 "C241T, C3037T, -C14408T, A23403G". 2021 Heliyon Result SARS_CoV_2 A23403G;A23403G;A23403G;C1059T;C14408T;C14408T;C3037T;C3037T;C3037T;G25563T;G28881A;G28882A;G28883C;C241T;C241T;C241T;C14408T 181;277;350;252;172;268;164;260;332;286;190;199;208;157;245;325;341 188;284;357;258;179;275;170;266;338;293;197;206;215;162;250;330;348 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Gujrat and Madhya Pradesh showed similar trends in prevalent mutations in spike (D614G) and NSP12 (P323L), where West Bengal showed NSP12 (A97V), N (S202N), NSP2(G339S) mutations predominately (Figure 3). 2021 Heliyon Result SARS_CoV_2 A97V;D614G;G339S;P323L;S202N 139;81;162;99;149 143;86;167;104;154 S;Nsp12;Nsp12;Nsp2;N 74;92;132;157;146 79;97;137;161;147 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. However, co-evolving mutations observed in developed countries associated with clades G,GH and GR such as G25563T (ORF3a), C26735T (NSP14) and C18877T (M protein) were observed less frequently (<15%) in Indian genomes. 2021 Heliyon Result SARS_CoV_2 C18877T;C26735T;G25563T 143;123;106 150;130;113 ORF3a 115 120 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Interpreting mutation effect of N439K in RBM region. 2021 Heliyon Result SARS_CoV_2 N439K 32 37 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Interpreting N439K in RBM region in the context of antibody epitopes. 2021 Heliyon Result SARS_CoV_2 N439K 13 18 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Mutations C241T, C3037T, A23403G and C14408T were observed at higher frequencies (>50%) in Indian genomes consistent with global trends. 2021 Heliyon Result SARS_CoV_2 A23403G;C14408T;C241T;C3037T 25;37;10;17 32;44;15;23 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Of these proteins, NSP12 has the largest number of variants including, P323L as dominant (n = 1998) followed by A97V (n = 328). 2021 Heliyon Result SARS_CoV_2 A97V;P323L 112;71 116;76 Nsp12 19 24 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Only 2 (R21I, L54F) were located at N-terminal domain (NTD), 3 variations were found in signal peptide (L5F, L8V, L18F). 2021 Heliyon Result SARS_CoV_2 L18F;L54F;L8V;L5F;R21I 114;14;109;104;8 118;18;112;107;12 N 36 37 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Only a single variant D614G reported in 85.34% of the genome sequenced globally in 87 countries (Figure 7). 2021 Heliyon Result SARS_CoV_2 D614G 22 27 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Other key variants including ORF3a: Q57H, ORF1ab: T265I (NSP3: T85I), ORF8: L84S, N203 (204del-insKR), ORF1ab: L3606F (NSP6, L37F) were also observed in genomes retrieved from India. 2021 Heliyon Result SARS_CoV_2 L3606F;L37F;L84S;Q57H;T265I;T85I 111;125;76;36;50;63 117;129;80;40;55;67 ORF1ab;ORF1ab;ORF3a;Nsp3;Nsp6;ORF8 42;103;29;57;119;70 48;109;34;61;123;74 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Overall, within genome sequences from high fatality rates of COVID-19 regions, we observed a mutation D614G as prevalent with its resembling clades G, GH and GR. 2021 Heliyon Result SARS_CoV_2 D614G 102 107 COVID-19 61 69 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Prevalence of D614G observed in Tamil Nadu and Delhi was less as compared to Maharashtra. 2021 Heliyon Result SARS_CoV_2 D614G 14 19 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Prevalent mutation observed in Maharashtra was in spike protein D614G (75%), followed by non-structural protein NSP12 (P323L) and in nucleoprotein (G204R, R203K). 2021 Heliyon Result SARS_CoV_2 D614G;R203K;G204R;P323L 64;155;148;119 69;160;153;124 S;Nsp12 50;112 55;117 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. RBM mutant types (N439K) exhibited significantly lowered DeltaG, suggesting a slight increased affinity to human ACE2; compared to the prototype. 2021 Heliyon Result SARS_CoV_2 N439K 18 23 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Recently reported as per Korber et al, D614G mutation increased infectivity of the virus. 2021 Heliyon Result SARS_CoV_2 D614G 39 44 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Simulations predict that N439K variant binds tighter to human ACE2. 2021 Heliyon Result SARS_CoV_2 N439K 25 30 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Single variations (N439K) were found at the receptor-binding domain (RBD) while three variations (A 829T, A879SV, and D936Y) were found at heptad repeat 1 (HR1) domain. 2021 Heliyon Result SARS_CoV_2 D936Y;A829T;N439K 118;98;19 123;104;24 RBD 69 72 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Single variations were found in signal sub-domain-2 (D614G), sub-domain-3 and heptad repeat 2 domain (G1124V) (D1168H), and cytoplasmic tail domain (P1263L) each. 2021 Heliyon Result SARS_CoV_2 D1168H;D614G;G1124V;P1263L 111;53;102;149 117;58;108;155 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Statewise mutation analysis suggests predominance of mutation in spike D614G with increased transmission and infectivity. 2021 Heliyon Result SARS_CoV_2 D614G 71 76 S 65 70 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Structural binding predictions suggests that prevalent mutation in spike RBD region, N439K did not overlap with currently characterized epitopes of neutralizing antibodies recovered from human convalescent patient. 2021 Heliyon Result SARS_CoV_2 N439K 85 90 S;RBD 67;73 72;76 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. The dominant mutation observed in Maharashtra, Tamil Nadu and Delhi was D614G, NSP12 (P323L) and NSP12 (A97V) respectively. 2021 Heliyon Result SARS_CoV_2 D614G;A97V;P323L 72;104;86 77;108;91 Nsp12;Nsp12 79;97 84;102 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. The four most common mutations were (C241T/5UTR in orf1ab, C3037T in orf1ab (F924F, C14408T P4715L), and D614G in spike protein. 2021 Heliyon Result SARS_CoV_2 C14408T;C3037T;D614G;P4715L;C241T;F924F 84;59;105;92;37;77 91;65;110;98;42;82 ORF1ab;ORF1ab;S 51;69;114 57;75;119 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. The most common variant observed globally, 3037C > T, ORF1ab: P4715L, RdRp: P323L; and D614G mostly reported from Europe and the USA were also observed in Indian population. 2021 Heliyon Result SARS_CoV_2 C3037T;D614G;P323L;P4715L 43;87;76;62 52;92;81;68 ORF1ab;RdRP 54;70 60;74 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Thus, simulations coupled with binding free energy calculations suggest that the N439K variant binds ACE2 tighter than the wildtype. 2021 Heliyon Result SARS_CoV_2 N439K 81 86 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Thus, to understand the effect of the N439K variation, the mutant structure was built using Chimera software. 2021 Heliyon Result SARS_CoV_2 N439K 38 43 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. To better define the RBM's mutations N439K for antibody escape, we examined structural and binding constraint in the epitopes of antibodies with prototype structures of SARS-CoV-2 RBD. 2021 Heliyon Result SARS_CoV_2 N439K 37 42 RBD 180 183 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. We screened and evaluated interaction analysis of mutant N349K as it was most prevalent mutation observed in RBD-RBM region. 2021 Heliyon Result SARS_CoV_2 N349K 57 62 RBD 109 112 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. 3a), the N501Y and UK-8x mutants replicated significantly faster in early stages of infection, as measured in PFU. 2021 bioRxiv Result SARS_CoV_2 N501Y 9 14 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Altogether, these results demonstrate a clear fitness advantage conferred by N501Y for shedding in the upper airway, including after transmission. 2021 bioRxiv Result SARS_CoV_2 N501Y 77 82 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. As the SARS-CoV-2 pandemic has progressed, several mutations have been convergently selected in variant lineages; of the 8 spike substitutions seen in the UK variant, only Delta69-70 and N501Y have evolved convergently in other variants, consistent with our fitness results. 2021 bioRxiv Result SARS_CoV_2 N501Y 187 192 S 123 128 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Because it conferred the major phenotype among the 8 spike gene mutations, we next examined N501Y in tracheal necropsies sampled on days 2 and 4 days in both donors and recipients. 2021 bioRxiv Result SARS_CoV_2 N501Y 92 97 S 53 58 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Coupled with our in vivo and in vitro competition results, these data indicate that the N501Y substitution provides a major fitness advantage to variants that maintain it. 2021 bioRxiv Result SARS_CoV_2 N501Y 88 93 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Evaluating nasal washes on days 1-4, N501Y conferred a significant fitness advantage beginning on day 3 in the donors, and this advantage was maintained in day 1-4 recipient washes. 2021 bioRxiv Result SARS_CoV_2 N501Y 37 42 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. except that Delta69-70 no longer impacted fitness, while A570D increased and two other mutations (S982A and D1118H) decreased fitness. 2021 bioRxiv Result SARS_CoV_2 A570D;D1118H;S982A 57;108;98 62;114;103 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. In HAE cells, both N501Y. 2021 bioRxiv Result SARS_CoV_2 N501Y 19 24 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. In mixed competition infections, N501Y showed significantly higher fitness at nearly all time points in Vero and Calu-3 cells. 2021 bioRxiv Result SARS_CoV_2 N501Y 33 38 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. In the subsequent study, we found that N501Y also conferred an advantage across both early and late times of nasal shedding. 2021 bioRxiv Result SARS_CoV_2 N501Y 39 44 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. In Vero cells sampled 12-48 hr post-infection, UK-8x and N501Y consistently replicated to higher titers than the wt as measured using infectious plaque assays (Extended Data. 2021 bioRxiv Result SARS_CoV_2 N501Y 57 62 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Nasal washes of these infected animals showed consistently higher titers on days 1-3 and 5 for both N501Y and UK-8x, but only when measured in PFU. 2021 bioRxiv Result SARS_CoV_2 N501Y 100 105 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Overall, our in vivo experiments revealed a consistent fitness advantage of N501Y and UK-8x, and to a lesser extent Delta69-70, for replication in the upper hamster airway. 2021 bioRxiv Result SARS_CoV_2 N501Y 76 81 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Overall, these experiments demonstrated that only the N501Y substitution conferred a consistent, significant, major fitness benefit in the upper airway, comparable to UK-8x. 2021 bioRxiv Result SARS_CoV_2 N501Y 54 59 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Similar to nasal washes, the tracheal samples showed a consistent fitness advantage of N501Y at both timepoints. 2021 bioRxiv Result SARS_CoV_2 N501Y 87 92 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. The competition results assessed from nasal washes indicated that, of the 8 mutations examined, only the deletion of codons 69-70 (Delta69-70), N501Y, S982A, and the combined UK-8x conferred significant fitness advantages, with other substitutions showing slightly but inconsistently reduced fitness or no difference from wt. 2021 bioRxiv Result SARS_CoV_2 N501Y;S982A 144;151 149;156 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. The frequency of the N501Y mutation worldwide has increased dramatically since October, 2020. 2021 bioRxiv Result SARS_CoV_2 N501Y 21 26 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. The N501Y substitution increased the RBD/ACE2 binding, as indicated by the >350-fold and >819-fold improved KD and Koff, respectively. 2021 bioRxiv Result SARS_CoV_2 N501Y 4 9 RBD 37 40 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. The RNA:PFU ratios were significantly lower for N501Y and UK-8x compared to wt on days 1-3, suggesting greater specific infectivity of these mutants. 2021 bioRxiv Result SARS_CoV_2 N501Y 48 53 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. There were no major differences among the 3 strains in Calu-3 cells, although N501Y and UK-8x had a trend of faster replication that was not statistically significant (Extended Data. 2021 bioRxiv Result SARS_CoV_2 N501Y 78 83 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. These mutations were engineered into the USA-WA1/2020 strain containing the D614G spike substitution that has become dominant worldwide due to its increased transmission efficiency; the resulting SARS-CoV-2 strain [USA-WA1/2020-G614, hereafter called wild-type (wt)], was generated using site-directed mutagenesis of a cDNA clone. 2021 bioRxiv Result SARS_CoV_2 D614G 76 81 S 82 87 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. These results suggest that the N501Y substitution improves viral fitness for replication in the upper airway, resulting in enhanced transmission, via an enhanced spike/receptor interaction. 2021 bioRxiv Result SARS_CoV_2 N501Y 31 36 S 162 167 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. To assess potential effects on virulence, individual mutant infections of hamsters were examined for weight loss, with no significant differences observed between wt, N501Y and the UK-8x mutant (Extended Data. 2021 bioRxiv Result SARS_CoV_2 N501Y 167 172 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Together, these results again suggest a fitness benefit for N501Y replication and transmission from the upper airways in the hamster model of COVID-19. 2021 bioRxiv Result SARS_CoV_2 N501Y 60 65 COVID-19 142 150 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. We next examined the mechanism for this fitness advantage, focusing on the impact of N501Y on receptor binding. 2021 bioRxiv Result SARS_CoV_2 N501Y 85 90 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Yet, significant fitness gains were observed in recipients for N501Y and A570D as well as UK-8x, suggesting more efficient transmission of these variants, and significant losses were maintained only for S982A. 2021 bioRxiv Result SARS_CoV_2 A570D;N501Y;S982A 73;63;203 78;68;208 33758837 Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice. 2C) and SARS-CoV-2 NTD (Fig 2D), mice immunized with chimeras 1-4 in the prime and boost generated similar magnitude binding antibodies to SARS-CoV-2 D614G compared to mice immunized with the SARS-CoV-2 furin KO spike mRNA-LNP (Fig 2B). 2021 bioRxiv Result SARS_CoV_2 D614G 150 155 S 212 217 33758837 Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice. Mice immunized with the chimeric spikes 1-4 all together or separately in the prime and boost generated similar magnitude binding antibody responses against SARS-CoV-2 D614G, Pangolin GXP4L, and RaTG13 spikes. 2021 bioRxiv Result SARS_CoV_2 D614G 168 173 S;S 33;202 39;208 33758837 Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice. the monovalent SARS-CoV-2 vaccine against two variants of concern (VOC): the predominant D614G variant and the B.1.351 South African variant. 2021 bioRxiv Result SARS_CoV_2 D614G 89 94 33758837 Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice. The serum of aged mice immunized with the multiplexed chimeras and the monovalent SARS-CoV-2 vaccine neutralized the dominant D614G variant with similar potency as the wild type D614 non-predominant variant. 2021 bioRxiv Result SARS_CoV_2 D614G 126 131 33758853 Recombinant SARS-CoV-2 genomes are currently circulating at low levels. Among these positions is the nucleotide substitution of A to C at site 23403, which is responsible for the D614G mutation in the spike protein that has been associated with increased transmissibility. 2021 bioRxiv Result SARS_CoV_2 A23403C;D614G 56;107 76;112 S 129 134 33758853 Recombinant SARS-CoV-2 genomes are currently circulating at low levels. Both recombinant genotypes have D614G substitutions, but no other substitutions in the spike protein or in other proteins that are currently suspected of altering transmission characteristics. 2021 bioRxiv Result SARS_CoV_2 D614G 32 37 S 87 92 33758853 Recombinant SARS-CoV-2 genomes are currently circulating at low levels. Further, a recombination event that unlinks the nucleotides at positions 25563 and 28881-3 could be parsimoniously explained as a de novo T to G mutation at position 25563 in a clade 20A-2 genome or a de novo G to T mutation at this position in a clade 20B-2 genome. 2021 bioRxiv Result SARS_CoV_2 T25563G 138 171 33758853 Recombinant SARS-CoV-2 genomes are currently circulating at low levels. Notably, two N501Y recombinant genotypes appear to be spreading, having been sampled multiple times in South Africa and in multiple provinces in Belgium. 2021 bioRxiv Result SARS_CoV_2 N501Y 13 18 33758853 Recombinant SARS-CoV-2 genomes are currently circulating at low levels. The remaining site, C29095T is not one of the cdSNPs we identified, but is a low frequency allele that is found in multiple clades and is thus very likely a homoplasy. 2021 bioRxiv Result SARS_CoV_2 C29095T 20 27 33758853 Recombinant SARS-CoV-2 genomes are currently circulating at low levels. These putative recombinants include 847 genomes that harbor the D614G substitution, 8 with N501Y, and 5 with E484K. 2021 bioRxiv Result SARS_CoV_2 D614G;E484K;N501Y 64;109;91 69;114;96 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. Escape of an NTD and E484K mutant virus from polyclonal post-vaccination serum is negligible but NTD mutations significantly impact the neutralizing activity of NTD binding mAbs. 2021 medRxiv Result SARS_CoV_2 E484K 21 26 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. For sera from the six vaccinated individuals, however, the highest reduction seen was only two-fold for E406Q, N440K, E484K and F490K (Figure 5B). 2021 medRxiv Result SARS_CoV_2 E406Q;E484K;F490K;N440K 104;118;128;111 109;123;133;116 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. In contrast, E484K on its own decreased affinity by 4-fold. 2021 medRxiv Result SARS_CoV_2 E484K 13 18 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. In fact, for most mAbs, no impact on binding was observed (Figure 5C) with the exception of PVI.V3-9, which lost binding to the RBD carrying F486A. 2021 medRxiv Result SARS_CoV_2 F486A 141 146 RBD 128 131 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. In general, single mutants E406Q, E484K and F490K exerted the biggest impact on binding. 2021 medRxiv Result SARS_CoV_2 E406Q;E484K;F490K 27;34;44 32;39;49 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. Interestingly, almost all sera bound better to N501Y RBD (B.1.1.7) than to wild type (average 129% compared to wild type). 2021 medRxiv Result SARS_CoV_2 N501Y 47 52 RBD 53 56 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. Specifically, N501Y and Y453F combined with N439K increased affinity for human ACE2 by 5-fold (Figure 4, Suppl. 2021 medRxiv Result SARS_CoV_2 N439K;N501Y;Y453F 44;14;24 49;19;29 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. The highest reduction observed for E484K, F484A, B.1.351 and P.1 were also approximately two-fold but this did not apply to all six vaccinees. 2021 medRxiv Result SARS_CoV_2 E484K;F484A 35;42 40;47 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. Through the Mount Sinai Hospital's Pathogen Surveillance Program, we had access to the SARS-CoV-2 isolate PV14252 (Clade 20C, Pango lineage B.1) that featured two mutations (W64R, L141Y) and one deletion (Delta142-145) in the NTD as well as the E484K mutation in the RBD (strain, Figure 5D). 2021 medRxiv Result SARS_CoV_2 E484K;L141Y;W64R 245;180;174 250;185;178 RBD 267 270 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. Using biolayer interferometry (BLI), we measured rates of association and dissociation of the N501Y RBD mutant (B.1.1.7 carries that mutation as its sole RBD mutation), Y453F as found in mink isolates, N439K which is found in some European clades, a combination of Y453F and N439K, E484K (part of B.1.351 and P.1) as well as for the B.1.351 RBDs for a recombinant version of human ACE2. 2021 medRxiv Result SARS_CoV_2 E484K;N439K;N439K;N501Y;Y453F;Y453F 282;202;275;94;169;265 287;207;280;99;174;270 RBD;RBD;RBD 100;154;341 103;157;345 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. A total of 50 patient samples, 20 confirmed COVID-19 positives and 30 confirmed COVID-19 negatives were tested using the SMB N501Y assay. 2021 medRxiv Result SARS_CoV_2 N501Y 125 130 COVID-19;COVID-19 44;80 52;88 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. However, Tm peak heights produced by both SMB 501-WT and SMB 501-MT) could still be reproducibly detected at the lowest concentration tested (4 GE/reaction) when tested against both WT and N501Y mutant strains, defining the assay limit of detection as <4 GE per reaction. 2021 medRxiv Result SARS_CoV_2 N501Y 189 194 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. In all cases, the WT or mutant sequences identified by the SMB N501Y assay were confirmed by the sequencing result. 2021 medRxiv Result SARS_CoV_2 N501Y 63 68 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. It should also be noted that of the 6 mutants samples tested by Sanger sequencing, the sequencing study showed that one of the samples (Pt12) also had mutation at 484th amino acid position along with N501Y. 2021 medRxiv Result SARS_CoV_2 N501Y 200 205 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. Similarly, when RNA was tested with the SMB 501-MT probe, WT-RNA produced a Tm of 58.2 C+-1, and MT N501Y RNA produced a Tm of 62.25 C+-0.6. 2021 medRxiv Result SARS_CoV_2 N501Y 100 105 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. These results clearly indicate that the combination of both SMB 501-WT and SMB 501-MT probes can specifically detect and differentiate the N501Y variants from the wild type strains with high confidence. 2021 medRxiv Result SARS_CoV_2 N501Y 139 144 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. Using the confirmed sequencing results as a gold standard, 4/4 of the wild type clinical samples were detected as WT by the SMB N501Y assay, and 6/6 N501Y mutant results were detected as mutant by the assay, demonstrating a clinical sensitivity and specificity of 100%. 2021 medRxiv Result SARS_CoV_2 N501Y;N501Y 128;149 133;154 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. Using these reference RNA samples, when RNA was tested with the SMB 501-WT probe, WT-RNA produced a Tm of 59.8 C+-0.4 and MT N501Y RNA produced a Tm of 55.2 C+-0.4. 2021 medRxiv Result SARS_CoV_2 N501Y 125 130 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. A novel variant, subsequently named 20C/L452R according to the NextStrain nomenclature system or B.1.427/B.1.429 according to the Pango system (henceforth referred to using the Pango designation to distinguish between the B.1.427 and B.1.429 lineages), was identified in 21.1% (459 of 2,172) of the genomes (Supplementary Table 1). 2021 medRxiv Result SARS_CoV_2 L452R 40 45 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Both lineages share a triad of coding mutations in the spike protein (S13I, W152C, and L452R), one coding mutation in the orf1b protein (D1183Y), and an additional 2 non-coding mutations (Figure 2A). 2021 medRxiv Result SARS_CoV_2 L452R;W152C;D1183Y;S13I 87;76;137;70 92;81;143;74 S 55 60 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Four additional mutations, one of them a coding mutation orf1a:I4205V, were specific to B.1.429, while 3 additional non-coding mutations were specific to B.1.427. 2021 medRxiv Result SARS_CoV_2 I4205V 63 69 ORF1a 57 62 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Nine of 10 (90%) convalescent patients showed reduced TCID50 titers to a B.1.427 lineage virus, with 5.3 (p=0.0039) and 4.0-fold (p=0.0039) median reductions for USA-WA1/2020) and D614G isolates, respectively. 2021 medRxiv Result SARS_CoV_2 D614G 180 185 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Pseudoviruses carrying the W152C mutation demonstrated small increases in infection of 293T cells and HAO relative to the D614 control, although these increases were not as pronounced as those observed for the L452R and N501Y pseudoviruses. 2021 medRxiv Result SARS_CoV_2 L452R;N501Y;W152C 210;220;27 215;225;32 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. There were no differences in neutralization between WA1 or D614G isolates by convalescent or post-vaccination plasma (Figure 5A, right). 2021 medRxiv Result SARS_CoV_2 D614G 59 64 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. This increase in infection with L452R mutation is slightly lower than the increase observed with the N501Y mutation (11.4 to 30.9-fold increase in 293T cells and 23.5 to 37.8-fold increase in HAO relative to D614G alone), which has previously been reported to increase pseudovirus entry. 2021 medRxiv Result SARS_CoV_2 D614G;L452R;N501Y 208;32;101 213;37;106 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. To examine the effect of the L452R mutation on antibody binding, we performed neutralizing antibody assays. 2021 medRxiv Result SARS_CoV_2 L452R 29 34 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. To understand the effects of L452R RBD mutation on viral entry, pseudoviruses carrying D614G with L452R or W152C, or D614G alone were generated and used for infection of 293T cells stably expressing the ACE2 cell entry receptor and TMPRSS2 cofactor for SARS-CoV-2 and human airway lung organoids (HAO) stably expressing ACE2. 2021 medRxiv Result SARS_CoV_2 D614G;D614G;L452R;L452R;W152C 87;117;29;98;107 92;122;34;103;112 RBD 35 38 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. We observed increased entry by pseudoviruses carrying the L452R mutation compared to D614G alone, with a 6.7 to 22.5-fold increase in 293T cells and a 5.8 to 14.7-fold increase in HAOs (Figure 4B and 4C). 2021 medRxiv Result SARS_CoV_2 D614G;L452R 85;58 90;63 33760807 SARS-CoV-2 variants reveal features critical for replication in primary human cells. Orf3a (Q57H) and nsp2 (T85I) variants were found in 20% of our patient samples, a similar prevalence to that found worldwide for the individual variants (Fig 3B). 2021 PLoS biology Result SARS_CoV_2 Q57H;T85I 7;23 11;27 ORF3a;Nsp2 0;17 5;21 33760807 SARS-CoV-2 variants reveal features critical for replication in primary human cells. These 3 isolates were unique in this phenotype, and each harbored combined amino acid substitutions in Orf3a (Q57H) and nsp2 (T85I) that were not identified in any other isolate (S3 Table), suggestive of an association between these specific changes and the observed cell-specific replication. 2021 PLoS biology Result SARS_CoV_2 Q57H;T85I 110;126 114;130 ORF3a;Nsp2 103;120 108;124 33760807 SARS-CoV-2 variants reveal features critical for replication in primary human cells. These data indicate that, unlike the Orf3a (Q57H) and nsp2 (T85I) variants that exhibit biased replication to BEpCs, the E (V5G/A, S6W) and S furin cleavage site deletion variants that exhibit biased replication to Vero-CCL81 cells are positively selected for during passaging in Vero-CCL81 cells. 2021 PLoS biology Result SARS_CoV_2 Q57H;T85I 44;60 48;64 ORF3a;Nsp2;S 37;54;140 42;58;141 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. According to the result, altering each of these residues lead to reduce the binding affinity in SARS-CoV-2 and the lowest binding affinity was observed for Phe456Ala substitution. 2021 Scientific reports Result SARS_CoV_2 F456A 156 165 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Comparative analysis of the RBD between SARS-CoV-2 and SARS-CoV showed the presence of several mutations in this area including Tyr442Leu, Leu443Phe, Leu472Phe, Asn479Gln, Tyr484Gln, and Thr487Asn. 2021 Scientific reports Result SARS_CoV_2 N479Q;L443F;L472F;T487N;Y442L;Y484Q 161;139;150;187;128;172 170;148;159;196;137;181 RBD 28 31 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. For instance, mutation Tyr442Leu leads to change in interaction pattern between spike-ACE2 from SARS-CoV to SARS-CoV-2. 2021 Scientific reports Result SARS_CoV_2 Y442L 23 32 S 80 85 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. For instance, substitution of Leu443 alanine decreased the number of interaction between two proteins in which the lowest binding affinity was also observed in this substitution. 2021 Scientific reports Result SARS_CoV_2 L443A 30 44 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. In contrast to the selected SARS-CoV-2 alanine scanning results, except for Leu443Ala, the rest of substitution for SARS-CoV have increased the binding affinity to ACE2. 2021 Scientific reports Result SARS_CoV_2 L443A 76 85 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Mutation Asn479Gln also altered the binding free energy of these from - 2 kcal mol-1 in SARS-CoV to - 4 kcal mol-1 in SARS-CoV-2. 2021 Scientific reports Result SARS_CoV_2 N479Q 9 18 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Mutations Pro462Ala and Leu472Phe in SARS-CoV-2 altered the binding free energy from - 2 kcal mol-1 in SARS-CoV to - 6 kcal mol-1. 2021 Scientific reports Result SARS_CoV_2 L472F;P462A 24;10 33;19 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. The Pro462Ala mutation makes the region flexible as a hinge, and therefore, facilitates the binding of the virus to its receptor. 2021 Scientific reports Result SARS_CoV_2 P462A 4 13 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. There are three mutations in this region, including Tyr442Lue, Leu443Phe, and Asn479Gln. 2021 Scientific reports Result SARS_CoV_2 N479Q;L443F 78;63 87;72 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. These results revealed that two mutation including Tyr442Leu and Leu443Phe in SARS-CoV-2 have changed binding free energies from - 1.6539 +- 0.4785 kcal mol-1 and - 0.5149 +- 0.0363 kcal mol-1 in SARS-CoV to - 2.7769 +- 0.17222 kcal mol-1 and - 1.6744 +- 0.2814 kcal mol-1 in SARS-CoV-2. 2021 Scientific reports Result SARS_CoV_2 L443F;Y442L 65;51 74;60 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. However, mAb 20 neutralized Wuhan Hu-1 at IC50 of 5.3 x 10-10 M but neutralized D614G mutants with higher potency at IC50 of 3.5 x 10-10 M (Figure 5). 2021 JCI insight Result SARS_CoV_2 D614G 80 85 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. In another notable result plasma from subject 4 neutralized H519Q spike-pseudotyped viruses 100-fold more potently than any other spike-pseudotyped viruses (Supplemental Figure 4, A and B). 2021 JCI insight Result SARS_CoV_2 H519Q 60 65 S;S 66;130 71;135 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. Interestingly, germline mAbs 13, 15, and 20 neutralized H49Y spike mutants as well their mutated counterparts (Figure 6), indicating that the H49Y mutation does not perturb the binding epitope responsible for neutralization. 2021 JCI insight Result SARS_CoV_2 H49Y;H49Y 56;142 60;146 S 61 66 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. Neutralization of A520S spike mutants by mAbs 5, 13, and 15 but not by mAb 20 depended on somatic mutations (Figure 6). 2021 JCI insight Result SARS_CoV_2 A520S 18 23 S 24 29 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. Neutralization of D614G mutants by mAb 20 (and also by mAbs 5, 13, and 15) depended on somatic mutations, as the germline-encoded Ab was at least 100-fold less efficacious (Figure 6). 2021 JCI insight Result SARS_CoV_2 D614G 18 23 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. Of these variants, A520S and D614G have notably greater infectivity than WT Wuhan Hu-1. 2021 JCI insight Result SARS_CoV_2 A520S;D614G 19;29 24;34 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. To determine if natural infection induced broadly neutralizing Abs, we tested neutralization of pseudotyped viruses with spike protein variants in the S1 N-terminal domain (H49Y, V247R, V367F, R408I), in the receptor-binding domain (V483A, H519Q, A520S), and in the S1-C-terminal domain (D614G). 2021 JCI insight Result SARS_CoV_2 A520S;H519Q;R408I;V247R;V367F;D614G;H49Y;V483A 247;240;193;179;186;288;173;233 252;245;198;184;191;293;177;238 S;N 121;154 126;155 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. While plasma 3 exhibited broad neutralization, plasma from subject 102 did not neutralize at all viruses pseudotyped with the Wuhan-1, D614G, S247R, or H49Y spikes but neutralized moderately H519Q, and A520S spike-pseudotyped viruses, suggesting that the plasma contains Abs with narrow specificity for the mutant RBD (Supplemental Figure 4, A and B). 2021 JCI insight Result SARS_CoV_2 A520S;D614G;H49Y;H519Q;S247R 202;135;152;191;142 207;140;156;196;147 S;S;RBD 157;208;314 163;213;317 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. Mean age of patients with N501Y was 47.8 +- 25.8 years (range 0-96) compared to 51.7 +- 25.9 years (range 0-104) for patients without this mutation (p = 0.06). 2021 Journal of virological methods Result SARS_CoV_2 N501Y 26 31 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. NGS was performed on 11 of these 63 strain N501Y variants to ascertain the specific genotypes and linages. 2021 Journal of virological methods Result SARS_CoV_2 N501Y 43 48 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. The N501Y mutation was present in 12 samples (5.8 %) with Ct of over 30 and wild type in 34 (6.25 %) such samples (p = 0.9). 2021 Journal of virological methods Result SARS_CoV_2 N501Y 4 9 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. The N501Y mutation was present in 206 samples (27.4 %). 2021 Journal of virological methods Result SARS_CoV_2 N501Y 4 9 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. According to the estimated binding energies, the D614G S-protein interacted better with the CB6 than the wild wild-type S-protein. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 49 54 S;S 55;120 56;121 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Among the domains, the NTD is expected to be the least affected by the D614G mutation since the site of variation is within the CTD. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 71 76 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Analysis of the molecular dynamics simulation trajectories and structures have shown that the D614G S-protein has distinct structural conformation and residue-specific variations in residue flexibility compared to the wild-type S-protein. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 94 99 S;S 100;228 101;229 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Analysis of the simulation trajectories has demonstrated that indeed the D614G S-protein has a distinct structural conformation and residue-specific flexibility variations compared to the wild-type S-protein. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 73 78 S;S 79;198 80;199 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Collectively, the backbone-RMSD and domain-specific RMSD show that the D614G S-protein adopts a distinct conformation, but seems to be skewed towards the open-state conformation more than the wild-type conformation. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 71 76 S 77 78 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Comparing the RBD of the wild-type and D614G S-proteins shows the mutation affects the structural dynamics of the RBD. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 39 44 RBD;RBD;S 14;114;45 17;117;46 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Concerning the interactions with CB6, energy contributions for some residues varied for the wild-type and D614G S-proteins. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 106 111 S 112 113 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Estimating the MM-PBSA binding energy has shown that the D614G S-protein has better interactions with the CB6 than the wild-type S-protein, but comparable interactions with 4A8 and P2B:2F6. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 57 62 S;S 63;129 64;130 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Evaluating the residue movement and flexibility would contribute to understanding the structural similarities or differences between the wild-type and D614G S-proteins as well as help in the study of the S-protein interactions with neutralizing antibodies. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 151 156 S;S 157;204 158;205 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. higher energies to the D614G-CB6 interaction than the wild-CB6 interaction. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 23 28 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. However, the interactions between the S-protein and 4A8 or P2B-2F6 were relatively similar for the wild-type and D614G variant. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 113 118 S 38 39 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. In general, the open-state NTD has a distinct residue flexibility pattern compared to the wild-type and D614G S-proteins. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 104 109 S 110 111 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Moreover, there was a large difference in polar solvation energy for the wild-CB6 (1095.091 kJ/mol) and D614G-CB6 (1434.865 kJ/mol) complexes. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 104 109 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Nonetheless, the observed variations in residue flexibility for the D614G RBD may affect the interactions underlying the neutralization of the variant. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 68 73 RBD 74 77 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Several studies have suggested that the D614G S-protein adopts a conformation similar to the open-state. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 40 45 S 46 47 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Structural superposition of the proteins structures (middle structures of the top cluster groups) also shows that the D614G RBD adopts a conformation similar to the open-state RBD. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 118 123 RBD;RBD 124;176 127;179 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The average RMSD values for the wild-type and D614G RBD were 0.38 +- 0.03 nm and 0.34 +- 0.05 nm, respectively. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 46 51 RBD 52 55 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The average RMSD values of the wild-type and D614G S-proteins were 1.09 +- 0.04 nm and 1.26 +- 0.1 nm, respectively. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 45 50 S 51 52 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The binding energy of the wild-CB6 complex and D614G-CB6 complex were - 35.1 kJ/mol and - 101.7 kJ/mol, respectively. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 47 52 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The binding energy of the wild-P2B-2F6 complex and D614G-P2B-2F6 complex were - 35.1 kJ/mol and - 101.7 kJ/mol, respectively. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 51 56 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The contributions from wild-type S-protein residues ranged from -54.6 to 58.2 kJ/mol and - 39.5 to 36.0 kJ/mol from the D614G S-protein residues. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 120 125 S;S 33;126 34;127 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The electrostatic energy contribution towards the complexation of CB6 was -443.078 kJ/mol for the wild-type S-protein and - 815.532 kJ/mol for the D614G S-protein. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 147 152 S;S 108;153 109;154 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The flexibility pattern of the RBD residues were also similar in some regions (residue 330-391) of the D614G and open-state S-proteins. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 103 108 RBD;S 31;124 34;125 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The molecular systems were composed of the selected neutralizing antibody (Fab domain) bound to the RBD or NTD of the wild-type and D614G S-proteins. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 132 137 RBD;S 100;138 103;139 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The NTDs of the wild-type and D614G S-proteins have similar RMSD evolution profile. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 30 35 S 36 37 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The open-state NTD showed higher RMSD (0.42 +- 0.16 nm) than the NTD of both the wild-type (0.32 +- 0.02 nm) and the D614G variant (0.34 +- 0.02 nm). 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 117 122 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. the RBD for the wild-type and D614G S-proteins have lower conformational stability than the open-state RBD. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 30 35 RBD;RBD;S 4;103;36 7;106;37 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The RMSD evolution of the NTD, RBD and S2-domain were computed for the wild-type, D614G and open-state S-proteins. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 82 87 RBD;S 31;103 34;104 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The S2-domain of the D614G S-protein showed the highest RMSD compared to the wild-type and open-state. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 21 26 S 27 28 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The wild-4A8 complex and D614G-4A8 complex showed binding energy of -1314.3 kJ/mol and - 1297.7 kJ/mol, respectively. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 25 30 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. There was a significant difference (p < 0.05) in the structural similarity and conformational stability of the wild-type and D614G S-proteins. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 125 130 S 131 132 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. There were large variations in the RBD residue flexibility for the wild-type and D614G S-protein. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 81 86 RBD;S 35;87 38;88 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. These differences may affect the interactions between the D614G S-protein and neutralizing antibody (nAb). 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 58 63 S 64 65 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. To further understand the structural similarities of the D614G S-protein and the wild-type conformations, we studied the domain-specific conformational stability by computing the RMSD evolution of each S-protein domain. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 57 62 S;S 63;202 64;203 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Unlike CB6, the contributions from key residues to the interactions with P2B-2F6 and 4A8 were comparable for the wild-type and D614G S-proteins. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 127 132 S 133 134 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. We have also used the RMSD parameter to decide the similarities or differences between the wild-type, D614G and open-state S-proteins. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 102 107 S 123 124 33777333 Specific epitopes form extensive hydrogen-bonding networks to ensure efficient antibody binding of SARS-CoV-2: Implications for advanced antibody design. CC12.1 with VL G68D mutation was also docked on SARS-CoV-2 RBD. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 G68D 15 19 RBD 59 62 33777333 Specific epitopes form extensive hydrogen-bonding networks to ensure efficient antibody binding of SARS-CoV-2: Implications for advanced antibody design. Heavy chain mutation VH V98E for advanced antibody design and specific epitopes identified for antibody binding. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 V98E 24 28 33777333 Specific epitopes form extensive hydrogen-bonding networks to ensure efficient antibody binding of SARS-CoV-2: Implications for advanced antibody design. Light chain mutation VL G68D for advanced antibody design and specific epitopes identified for antibody binding. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 G68D 24 28 33777333 Specific epitopes form extensive hydrogen-bonding networks to ensure efficient antibody binding of SARS-CoV-2: Implications for advanced antibody design. The binding mode of CC12.1 with VH V98E mutation on SARS-CoV-2 RBD was predicted by docking to further validate our results. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 V98E 35 39 RBD 63 66 33777333 Specific epitopes form extensive hydrogen-bonding networks to ensure efficient antibody binding of SARS-CoV-2: Implications for advanced antibody design. The OG1 atom of T500 forms a hydrogen bond with OD1/OD2 atom of VL D68 (mutated) alternatively during the whole 5 ns simulation, which means the VL G68 D mutation is helpful in forming efficient interaction with T500 of RBD. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 G68D 148 153 RBD 220 223 33778179 Mutational analysis of structural proteins of SARS-CoV-2. 84% of the mutated S protein sequences possessed D614G mutation. 2021 Heliyon Result SARS_CoV_2 D614G 49 54 S 19 20 33778179 Mutational analysis of structural proteins of SARS-CoV-2. A significant mutation observed in nine sequences of E protein was P71L. 2021 Heliyon Result SARS_CoV_2 P71L 67 71 E 53 54 33778179 Mutational analysis of structural proteins of SARS-CoV-2. Additionally, mutations that resulted in similar kinds of amino acids were V70F (nonpolar to nonpolar) and H125Y (polar to polar) obtained in more than ten isolates. 2021 Heliyon Result SARS_CoV_2 H125Y;V70F 107;75 112;79 33778179 Mutational analysis of structural proteins of SARS-CoV-2. Also, P132S mutation caused the occurrence of a casein kinase II phosphorylation site (Figure 3f). 2021 Heliyon Result SARS_CoV_2 P132S 6 11 33778179 Mutational analysis of structural proteins of SARS-CoV-2. Another was in the case of the docked structure of N501Y-RBD: ACE-2 interaction, T500 of S protein failed to form H bond with Y41 of ACE-2 and showed only hydrophobic interaction. 2021 Heliyon Result SARS_CoV_2 N501Y 51 56 RBD;S 57;89 60;90 33778179 Mutational analysis of structural proteins of SARS-CoV-2. Further, a polar to nonpolar amino acid mutation S68F was observed in five isolates of E protein. 2021 Heliyon Result SARS_CoV_2 S68F 49 53 E 87 88 33778179 Mutational analysis of structural proteins of SARS-CoV-2. Further, Q498 (S) generated an additional hydrophobic interaction with L45 (ACE-2) in the docked structure of N501Y-RBD: ACE-2. 2021 Heliyon Result SARS_CoV_2 N501Y 110 115 RBD;S 116;15 119;16 33778179 Mutational analysis of structural proteins of SARS-CoV-2. However, these interactions were not seen in the mutated structure (D614G mutation) of the S protein (Figure 4b). 2021 Heliyon Result SARS_CoV_2 D614G 68 73 S 91 92 33778179 Mutational analysis of structural proteins of SARS-CoV-2. Impact of D614G mutation on its intramolecular interaction. 2021 Heliyon Result SARS_CoV_2 D614G 10 15 33778179 Mutational analysis of structural proteins of SARS-CoV-2. In addition, a single amino acid substitution V10A in isolate QLF97810.1 at the 10th position of the M protein sequence resulted in N-myristoylation site (Figure 3e). 2021 Heliyon Result SARS_CoV_2 V10A 46 50 N 132 133 33778179 Mutational analysis of structural proteins of SARS-CoV-2. In M protein, D209Y, T175M, and K15R mutations with all polar to polar amino acid substitution were seen in 20, 19, and 18 isolates respectively. 2021 Heliyon Result SARS_CoV_2 D209Y;K15R;T175M 14;32;21 19;36;26 33778179 Mutational analysis of structural proteins of SARS-CoV-2. In S477A and V483A RBD structure docked with ACE-2, additional hydrophobic interaction between L455 (S) with K31 (ACE-2) was observed. 2021 Heliyon Result SARS_CoV_2 S477A;V483A 3;13 8;18 RBD;S 19;101 22;102 33778179 Mutational analysis of structural proteins of SARS-CoV-2. L73F mutation, a nonpolar to nonpolar amino acid substitution occurred in four isolates. 2021 Heliyon Result SARS_CoV_2 L73F 0 4 33778179 Mutational analysis of structural proteins of SARS-CoV-2. Nonetheless, mutation with a change in polar to nonpolar amino acid was also observed, D3G, in various isolates. 2021 Heliyon Result SARS_CoV_2 D3G 87 90 33778179 Mutational analysis of structural proteins of SARS-CoV-2. Presence of RGD sequence in S protein and D614G mutation resulted in an additional N-myristoylation site in S protein of SARS-CoV-2. 2021 Heliyon Result SARS_CoV_2 D614G 42 47 N;S;S 83;28;108 84;29;109 33778179 Mutational analysis of structural proteins of SARS-CoV-2. The D3G mutation was observed in 12 isolates of M protein resulting in N-myristoylation site at 3-8 position (Figure 3d). 2021 Heliyon Result SARS_CoV_2 D3G 4 7 N 71 72 33778179 Mutational analysis of structural proteins of SARS-CoV-2. The most prominent mutation D614G was observed in 4555 isolates, out of 6476 total isolates. 2021 Heliyon Result SARS_CoV_2 D614G 28 33 33778179 Mutational analysis of structural proteins of SARS-CoV-2. The S477N (polar to polar) and V483A (nonpolar to nonpolar) mutation was observed in 39 and 22 isolates. 2021 Heliyon Result SARS_CoV_2 S477N;V483A 4;31 9;36 33778179 Mutational analysis of structural proteins of SARS-CoV-2. The second and third prominent mutation was nonpolar aliphatic to an aromatic amino acid, L5F and L54F, each observed in 68 isolates. 2021 Heliyon Result SARS_CoV_2 L54F;L5F 98;90 102;93 33778179 Mutational analysis of structural proteins of SARS-CoV-2. We identified a single mutation, E8K, in an isolate QKO24093.1 from the USA in E protein of SARS-CoV-2 (Figure 3a). 2021 Heliyon Result SARS_CoV_2 E8K 33 36 E 79 80 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Here, we identified that only the D614G mutation was present in the tested samples, where the D614G was identified in 1 of 16 Korean isolates (6.25%), 10 of 12 Finnish isolates (83.33%), and 8 of 8 North American isolates (100%). 2021 Gene reports Result SARS_CoV_2 D614G;D614G 34;94 39;99 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. In North America (n = 29,198), the D614G mutation was first reported at the end of February 2020. 2021 Gene reports Result SARS_CoV_2 D614G 35 40 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. No other mutations were detected except the D614G. 2021 Gene reports Result SARS_CoV_2 D614G 44 49 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. The frequencies of the D614G mutation between March and April 2020, when we collected SARS-CoV-2 clinical isolates for this study showed different patterns with geographic origins. 2021 Gene reports Result SARS_CoV_2 D614G 23 28 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. The PCR-based sequencing method using the primer sets was first applied to rapidly detect the H49Y, G476S, V483A, H519Q, A520S, and D614G mutations in the S protein of the SARS-CoV-2 isolates from Korean, Finnish, and North American. 2021 Gene reports Result SARS_CoV_2 A520S;D614G;G476S;H49Y;H519Q;V483A 121;132;100;94;114;107 126;137;105;98;119;112 S 155 156 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. As a consequence, there are two changes in amino acid as well, P323L and P323H. 2021 Virus research Result SARS_CoV_2 P323H;P323L 73;63 78;68 33785459 Emergence and outcomes of the SARS-CoV-2 'Marseille-4' variant. Among these mutations, 13 are hallmarks of this variant (C4543T, G5629T, G9526T, C11497T, G13993T, G15766T, A16889G, G17019T, G22992A, C25710T, T26876C, G28975C, and G29399A) (Supplementary material Figure S2). 2021 International journal of infectious diseases Result SARS_CoV_2 A16889G;C11497T;C25710T;G13993T;G15766T;G17019T;G22992A;G28975C;G29399A;G5629T;G9526T;T26876C;C4543T 108;81;135;90;99;117;126;153;166;65;73;144;57 115;88;142;97;106;124;133;160;173;71;79;151;63 33785459 Emergence and outcomes of the SARS-CoV-2 'Marseille-4' variant. Fifteen additional mutations were observed in >=5 viral genomes obtained in the study institute (C222U, C503U, G2600U, A2647G, C8937U, G18105U, C23191U, G25534U, U26442C, G26720U, G27877U, C27942U, G28086U, G29701A, and G29511U). 2021 International journal of infectious diseases Result SARS_CoV_2 A2647G;G29701A 119;207 125;214 33785459 Emergence and outcomes of the SARS-CoV-2 'Marseille-4' variant. It adds to the D614G substitution that was reported to increase the stability of spike trimers and to confer greater affinity for ACE2. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G 15 20 S 81 86 33785459 Emergence and outcomes of the SARS-CoV-2 'Marseille-4' variant. It is worth noting that the first genome available in the GISAID database (EPI_ISL_7079562020-03-24), originating from Germany on March 24, 2020, does not harbour this S477N substitution, which may explain why it did not apparently spread further. 2021 International journal of infectious diseases Result SARS_CoV_2 S477N 168 173 33785459 Emergence and outcomes of the SARS-CoV-2 'Marseille-4' variant. Other critical mutations may be substitution Q57H in ORF3a, a viroporin that forms ion channels and was reported as required for viral replication, virulence, and release, and is also predicted to be a pro-apoptotic protein, and substitutions A176S in the RdRP and K1141R and E1184D in the NTPase/helicase. 2021 International journal of infectious diseases Result SARS_CoV_2 A176S;E1184D;K1141R;Q57H 243;276;265;45 248;282;271;49 Helicase;ORF3a;RdRP 297;53;256 305;58;260 33785459 Emergence and outcomes of the SARS-CoV-2 'Marseille-4' variant. Seven (46%) are non-synonymous mutations, including two located in the RNA-dependent RNA polymerase (RdRP) (nsp12; A176S and V767L), two in the NTPase/helicase (nsp13; K1141R and E1184D), two in the nucleocapsid (N; M234I and A376T), and one in the spike glycoprotein (S; S477N). 2021 International journal of infectious diseases Result SARS_CoV_2 A176S;A376T;E1184D;K1141R;M234I;S477N;V767L 115;226;179;168;216;272;125 120;231;185;174;221;277;130 RdRp;S;N;Helicase;Nsp13;Nsp12;RdRP;N;S 71;249;199;151;161;108;101;213;269 99;267;211;159;166;113;105;214;270 33785459 Emergence and outcomes of the SARS-CoV-2 'Marseille-4' variant. The genome obtained from a German patient sampled on March 24, 2020 (EPI_ISL_7079562020-03-24) is atypical as it is devoid of the S477N substitution, one of the Marseille-4 hallmark mutations, but harbours more mutations (n = 31) than the other Marseille-4 strains, including in the Nsp2, Nsp3, S, and N proteins, and in ORF1b, particularly the Nsp14 exonuclease, which has proofreading activity. 2021 International journal of infectious diseases Result SARS_CoV_2 S477N 130 135 Exonuclease;Nsp2;Nsp3;N;S 351;283;289;302;295 362;287;293;303;296 33785459 Emergence and outcomes of the SARS-CoV-2 'Marseille-4' variant. The Marseille-4 variant harbours the S477N substitution within the receptor binding domain (RBD) of the spike glycoprotein. 2021 International journal of infectious diseases Result SARS_CoV_2 S477N 37 42 RBD;S;RBD 67;104;92 90;122;95 33785459 Emergence and outcomes of the SARS-CoV-2 'Marseille-4' variant. The S477N substitution has been reported to be associated with broad resistance to monoclonal neutralizing antibodies. 2021 International journal of infectious diseases Result SARS_CoV_2 S477N 4 9 33785459 Emergence and outcomes of the SARS-CoV-2 'Marseille-4' variant. This may be related to the S477N mutation, which could change the affinity of RBD for ACE2 and decrease the sensitivity of the variant virus to anti-RBD-specific neutralizing antibodies. 2021 International journal of infectious diseases Result SARS_CoV_2 S477N 27 32 RBD;RBD 78;149 81;152 33785459 Emergence and outcomes of the SARS-CoV-2 'Marseille-4' variant. This node pointed to the common mutation Q57H in ORF3a described above. 2021 International journal of infectious diseases Result SARS_CoV_2 Q57H 41 45 ORF3a 49 54 33791702 Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2. Again, when compared to Wu-Hu-1 and Wu-Hu-1 D614G, spike incorporation was modestly reduced in B.1.1.7 PV. 2021 bioRxiv Result SARS_CoV_2 D614G 44 49 S 51 56 33791702 Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2. D614G is associated with increased viral fitness, likely through reduced shedding of the S1 subunit and/or greater occupancy of the RBD 'up' conformation of spike, which may promote ACE2 interaction, but with modest effects on neutralisation sensitivity. 2021 bioRxiv Result SARS_CoV_2 D614G 0 5 S;RBD 157;132 162;135 33791702 Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2. However, B.1.1.7, and all current variants of concern, arose from the previously dominant variant which, unlike Wu-Hu-1, contains a D614G spike mutation. 2021 bioRxiv Result SARS_CoV_2 D614G 132 137 S 138 143 33791702 Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2. virus bearing the D614G mutation), the spike mutations found in B.1.1.7 have a negative effect on virus entry into some cell types. 2021 bioRxiv Result SARS_CoV_2 D614G 18 23 S 39 44 33791702 Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2. We therefore compared Wu-Hu-1, B.1.1.7 and Wu-Hu-1 bearing the D614G mutation. 2021 bioRxiv Result SARS_CoV_2 D614G 63 68 33791702 Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2. Wu-Hu-1 D614G permitted greater infection of HeLa ACE2 cells than both Wu-Hu-1 and B.1.1.7 spike, whereas in HEK 293T cells Wu-Hu-1 D614G and B.1.1.7 spike exhibited equivalent activity. 2021 bioRxiv Result SARS_CoV_2 D614G;D614G 8;132 13;137 S;S 91;150 96;155 33791722 SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis. All sequences showed mutations at the S gene, being the most prevalent A23403G (95.79% sequences) conferring the D614G aminoacid change. 2021 medRxiv Result SARS_CoV_2 A23403G;D614G 71;113 78;118 S 38 39 33791722 SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis. Three of the analyzed sequences showed the aminoacid changes T183I, A890D, I1412T, P323L, L493F, N501Y, T553I, A570D, D614G, P681H, T716I, S982A, D1118H, Q27, R52I, Y73C, D3L, R203K, G204R and S235F placing them in the B.1.1.7 lineage. 2021 medRxiv Result SARS_CoV_2 A570D;A890D;D1118H;D3L;D614G;G204R;I1412T;L493F;N501Y;P323L;P681H;R203K;R52I;S235F;S982A;T183I;T553I;T716I;Y73C 111;68;146;171;118;183;75;90;97;83;125;176;159;193;139;61;104;132;165 116;73;152;174;123;188;81;95;102;88;130;181;163;198;144;66;109;137;169 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. In N protein, it has been reported that the mutations, P13L and R203K are among the top ten high-frequency SNPs (Wang et al.,). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 P13L;R203K 55;64 59;69 N 3 4 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Moreover, P13L is present in the first disordered region, R203K and G204R are in the second disordered region, while P344S is in the CTD domain (Dasgupta,). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 G204R;P13L;P344S;R203K 68;10;117;58 73;14;122;63 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. S1 and S2 domains have multiple regions like N-terminal domain (NTD), NTD to residue binding domain (RBD) linker N2R, and subdomains SD1 and SD2 in S1 while, fusion peptide (FP), heptad repeat 1 (HR1), central helix (CH), connector domain (CD), heptad repeat 2 (HR2), transmembrane domain (TM), and cytoplasmic tail (CT) in S2 (Gobeil et al.,; Saputri et al.,) . 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N2R 113 116 RBD;N 101;45 104;46 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. The single mutation, D614G in S protein was predicted neutral. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 D614G 21 26 S 30 31 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Three mutations in N protein (P13L, S197L, and G204R) were found to have a deleterious effect on protein functions whereas, the remaining two mutations, R203K and P344S were predicted to be neutral in nature. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 G204R;P344S;R203K;S197L;P13L 47;163;153;36;30 52;168;158;41;34 N 19 20 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. We started with the L37H mutation that is located in the transmembrane domain (TMD) of the envelope protein. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 L37H 20 24 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. A889V showed a notably altered radius of gyration (Rg) (Supplementary file 5). 2021 Journal, genetic engineering & biotechnology Result SARS_CoV_2 A889V 0 5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. According to the MUpro, V121D, V843F, and G1691C can destabilize the proteins (Table 2). 2021 Journal, genetic engineering & biotechnology Result SARS_CoV_2 G1691C;V121D;V843F 42;24;31 48;29;36 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. Among them, only A889V substitution occurred due to C T (Pyrimidine Pyrimidine) transition. 2021 Journal, genetic engineering & biotechnology Result SARS_CoV_2 A889V 17 22 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. However, V843F + A889V double mutant exhibited a slightly higher value at the end. 2021 Journal, genetic engineering & biotechnology Result SARS_CoV_2 A889V;V843F 17;9 22;14 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. However, V843F + A889V PLPro showed slightly less affinity (- 6.2 kcal/mol) than others. 2021 Journal, genetic engineering & biotechnology Result SARS_CoV_2 A889V;V843F 17;9 22;14 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. However, V843F mutant exhibited a significantly lower docking score and binding affinity (- 11.1 kcal/mol) with higher dissociation constant (Table 4). 2021 Journal, genetic engineering & biotechnology Result SARS_CoV_2 V843F 9 14 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. In contrast, only A889V mutant PLPro can increase protein stability (Table 2). 2021 Journal, genetic engineering & biotechnology Result SARS_CoV_2 A889V 18 23 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. Moreover, PROVEAN determined that the V121D and G1691C substitutions are deleterious for the biological functions of the proteins. 2021 Journal, genetic engineering & biotechnology Result SARS_CoV_2 G1691C;V121D 48;38 54;43 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. The Sanger sequencing reads for both wild type and V843F are given in Supplementary file 4. 2021 Journal, genetic engineering & biotechnology Result SARS_CoV_2 V843F 51 56 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. The wild type, A889V and V843F + A889V double mutants showed nearly the same binding affinity (- 15.4 to - 15.5 kcal/mol) toward the C-terminal domain of ISG-15. 2021 Journal, genetic engineering & biotechnology Result SARS_CoV_2 A889V;A889V;V843F 15;33;25 20;38;30 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. These V843F-positive patients had mild to moderate symptoms and did not require any intensive care from hospitals. 2021 Journal, genetic engineering & biotechnology Result SARS_CoV_2 V843F 6 11 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. V843F and A889V single mutants have the same interacting residue CYS155 which interacted with the inhibitor through hydrogen bonding. 2021 Journal, genetic engineering & biotechnology Result SARS_CoV_2 A889V;V843F 10;0 15;5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. V843F PLPro (- 6.7 kcal/mol) and A889V PLPro (- 6.9 kcal/mol) showed more binding affinity scores than the wild type one (- 6.6 kcal/mol) against GRL0617 (Table 3). 2021 Journal, genetic engineering & biotechnology Result SARS_CoV_2 A889V;V843F 33;0 38;5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. V843F PLPro was the most common mutant that significantly reduced the affinity toward ISG-15. 2021 Journal, genetic engineering & biotechnology Result SARS_CoV_2 V843F 0 5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. When these mutations were screened in 27 clinical samples, 8 samples (~ 29%) showed V843F mutation in PLPro. 2021 Journal, genetic engineering & biotechnology Result SARS_CoV_2 V843F 84 89 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Also, we used prediction tools based on computational methods to predict whether variation (P504L and Y541C) influenced the NSP13 function. 2021 Infection, genetics and evolution Result SARS_CoV_2 Y541C;P504L 102;92 107;97 Nsp13 124 129 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Among them, 5'UTR was the untranslated region, and the variations in ORF1ab: 3037 (NSP3:F106F), ORF1ab: 8782 (NSP4:S76S), and ORF1ab: 18060 (NSP14:L7L) were synonymous. 2021 Infection, genetics and evolution Result SARS_CoV_2 F106F;L7L;S76S 88;147;115 93;150;119 ORF1ab;ORF1ab;ORF1ab;5'UTR;Nsp3;Nsp4 69;96;126;12;83;110 75;102;132;17;87;114 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. COVID-19 outcomes in states with different proportions of strains containing variation in NSP13: P504L and NSP13: Y541C. 2021 Infection, genetics and evolution Result SARS_CoV_2 P504L;Y541C 97;114 102;119 Nsp13;Nsp13 90;107 95;112 COVID-19 0 8 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Effects of NSP13: P504L and NSP13: Y541C on NSP13 function. 2021 Infection, genetics and evolution Result SARS_CoV_2 P504L;Y541C 18;35 23;40 Nsp13;Nsp13;Nsp13 11;28;44 16;33;49 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. From previous analysis, genetic variations in ORF1ab: 17858 (A- > G, 286 strains) and ORF1ab: 17747 (C- > T, 285 strains) corresponded to amino acid variations in ORF1ab: p.5865Y > C (NSP13: Y541C) and ORF1ab: p.5828P > L (NSP13: P504L). 2021 Infection, genetics and evolution Result SARS_CoV_2 P504L;Y541C 230;191 235;196 ORF1ab;ORF1ab;ORF1ab;ORF1ab;Nsp13;Nsp13 46;86;163;202;184;223 52;92;169;208;189;228 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Furthermore, 69.05% of strains from Washington State showed variation in ORF1ab (p.5828P > L and p.5865Y > C, NSP13: P504L and NSP13: Y541C), with some regions showing a 100% variation rate, e.g., Umatilla County, Snohomish County, Clark County, and Tacoma. 2021 Infection, genetics and evolution Result SARS_CoV_2 P504L;Y541C 117;134 122;139 ORF1ab;Nsp13;Nsp13 73;110;127 79;115;132 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Furthermore, when comparing COVID-19 infections and deaths between Washington State and Minnesota, Utah, Wisconsin, and California, which contained a small percentage of strains with the ORF1ab variations (p.5828P > L and p.5865Y > C, NSP13: P504L and NSP13: Y541C), significant differences were found (P = 3.64E-29), including in the death and recovery rates (P = 4.12E-21. 2021 Infection, genetics and evolution Result SARS_CoV_2 P504L;Y541C 242;259 247;264 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. In addition, King County, Snohomish County, Pierce County, Clark County, and Grant County, with more than half of strains containing ORF1ab variation (p.5828P > L and p.5865Y > C, NSP13: P504L and NSP13: Y541C), showed high infection and fatality rates. 2021 Infection, genetics and evolution Result SARS_CoV_2 P504L;Y541C 187;204 192;209 ORF1ab;Nsp13;Nsp13 133;180;197 139;185;202 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. ORF1ab variations (NSP13: P504L and NSP13: Y541C) in SARS-CoV-2. 2021 Infection, genetics and evolution Result SARS_CoV_2 P504L;Y541C 26;43 31;48 ORF1ab;Nsp13;Nsp13 0;19;36 6;24;41 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Results showed that amino acid variation in ORF1ab (p.5828P > L and p.5865Y > C, NSP13: P504L and NSP13: Y541C) was an important characteristic of the clade. 2021 Infection, genetics and evolution Result SARS_CoV_2 P504L;Y541C 88;105 93;110 ORF1ab;Nsp13;Nsp13 44;81;98 50;86;103 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. The PolyPhen-2 tool showed high scores of the variants (NSP13: P504L and NSP13: Y541C) in HumDiv and HumVar, with the tendency that the closer the score is to 1.0, the greater effect on protein function. 2021 Infection, genetics and evolution Result SARS_CoV_2 P504L;Y541C 63;80 68;85 Nsp13;Nsp13 56;73 61;78 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. The top variation sites were S: 23403 (S:D614G, 597 strains), ORF1ab: 3037 (NSP3:F106F, 595 strains), ORF1ab: 14408 (NSP12b:P314L, 594 strains), 5'UTR: 241 (592 strains), ORF1ab: 8782 (NSP4:S76S, 423 strains), ORF8: 28144 (ORF8:L84S, 423 strains), ORF1ab: 18060 (NSP14:L7L, 292 strains), ORF1ab: 17858 (NSP13:Y541C, 286 strains), and ORF1ab: 17747 (NSP13:P504L, 285 strains). 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;F106F;L7L;L84S;P314L;P504L;S76S;Y541C 41;81;269;228;124;355;190;309 46;86;272;232;129;360;194;314 ORF1ab;ORF1ab;ORF1ab;ORF1ab;ORF1ab;ORF1ab;Nsp13;Nsp13;5'UTR;Nsp3;Nsp4;ORF8;ORF8;S;S 62;102;171;248;288;334;303;349;145;76;185;210;223;29;39 68;108;177;254;294;340;308;354;150;80;189;214;227;30;40 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. These results demonstrated that the variations (NSP13: P504L and NSP13: Y541C) tended to change the function of the NSP13. 2021 Infection, genetics and evolution Result SARS_CoV_2 P504L;Y541C 55;72 60;77 Nsp13;Nsp13;Nsp13 48;65;116 53;70;121 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. To better understand the consequences of amino acid variation in NSP13: P504L and NSP13: Y541C in NSP13 of SARS-CoV-2, we performed sequence alignment of the variant against other coronaviruses. 2021 Infection, genetics and evolution Result SARS_CoV_2 P504L;Y541C 72;89 77;94 Nsp13;Nsp13;Nsp13 65;82;98 70;87;103 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. To further analyze the variation in ORF1ab (p.5828P > L and p.5865Y > C, NSP13: P504L and NSP13: Y541C) in SARS-CoV-2, we explored variation frequency over time. 2021 Infection, genetics and evolution Result SARS_CoV_2 P504L;Y541C 80;97 85;102 ORF1ab;Nsp13;Nsp13 36;73;90 42;78;95 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Variation heatmap of countries demonstrated the composition of several significant genetic variation sites, including variation in ORF1ab (8782C- > T, NSP4:S76S, synonymous), S (23403 A- > G, S:D614G, missense), ORF1ab (17858 A- > G, NSP13:Y541C, missense), and ORF1ab (17747C- > T, NSP13:P504L, missense). 2021 Infection, genetics and evolution Result SARS_CoV_2 C17747T;A17858G;A23403G;C8782T;D614G;P504L;S76S;Y541C 270;220;178;139;194;289;156;240 281;232;190;149;199;294;160;245 ORF1ab;ORF1ab;ORF1ab;Nsp13;Nsp13;Nsp4;S;S 131;212;262;234;283;151;175;192 137;218;268;239;288;155;176;193 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. We also found that 271 variants (NSP13: P504L and NSP13: Y541C) from the United States, accounting for 51.13% of all strains from this country, contained the ORF1ab variants. 2021 Infection, genetics and evolution Result SARS_CoV_2 P504L;Y541C 40;57 45;62 ORF1ab;Nsp13;Nsp13 158;33;50 164;38;55 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. Apart from deletions in the NTD and mutations in the RBD region, the 501Y.V1 harbors P681H mutation in the vicinity of the polybasic 'furin (PRRAR)' cleavage site. 2021 Viruses Result SARS_CoV_2 P681H 85 90 RBD 53 56 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. Besides NTD deletions, the most concerning mutation common to 501Y.V1, 501Y.V2 and P.1 lineages is N501Y, located in the RBD region (Figure 1D). 2021 Viruses Result SARS_CoV_2 N501Y 99 104 RBD 121 124 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. Finally, in terms of binding energy, the highest affinity of C135 was found with N440K (-45.03 +- 12.14 kcal/mol) followed by N501Y (-28.63 +- 16.20 kcal/mol) and wildtype (-25.86 +- 13.10 kcal/mol). 2021 Viruses Result SARS_CoV_2 N440K;N501Y 81;126 86;131 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. Finally, in the case of N440K, the total number of hydrogen bond interactive residues was found to be 12. 2021 Viruses Result SARS_CoV_2 N440K 24 29 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. Finally, when MM/GBSA free binding energy was calculated between the protomers, it found that wildtype (-43.92 +- 12.07 kcal/mol) had slightly better binding than R52I (-39.90 +- 12.29 kcal/mol) (Figure 5D). 2021 Viruses Result SARS_CoV_2 R52I 163 167 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. However, in India, the N440K high frequency variant was observed to be located at the C135-RBD interaction interface, where the mutation led to a weaker interaction network (Figure S3C,D). 2021 Viruses Result SARS_CoV_2 N440K 23 28 RBD 91 94 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. However, mutation analysis predicted highest stabilization effect conferred by S235F to the N protein (Table S1). 2021 Viruses Result SARS_CoV_2 S235F 79 84 N 92 93 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. However, the mutants (N440K and N501Y) had the highest number of hydrogen bond contacts in most of the frames (Figure 3A). 2021 Viruses Result SARS_CoV_2 N501Y;N440K 32;22 37;27 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. In case of the N501Y mutant, the residues K378, G381 and K386 were the major interacting ones, having interaction for more than 50% of the simulation time. 2021 Viruses Result SARS_CoV_2 N501Y 15 20 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. In line with hydrogen bond counts, the MM/GBSA binding free energy showed that the binding affinity of N501Y mutant (-90.03 +- 10.08 kcal/mol) decreased in comparison to the wildtype (-103.01 +- 23.39 kcal/mol) and N440K mutant (-100.53 +- 8.76 kcal/mol) towards the CR3022 antibody. 2021 Viruses Result SARS_CoV_2 N440K;N501Y 215;103 220;108 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. In the case of N501Y and N440K, the interactions were identical to the wildtype, however two crucial interactions, T500 and G502 were lost in N501Y variant (Figure S6). 2021 Viruses Result SARS_CoV_2 N440K;N501Y;N501Y 25;15;142 30;20;147 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. In the case of N501Y, total number of interactive residues increased to 20, and among these, N440 and N442 were best and they were interacting with F52 and S95 for 0.11 and 0.17 fraction of time, respectively. 2021 Viruses Result SARS_CoV_2 N501Y 15 20 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. In the case of RBD-CR3022 interactions analysed during MD simulations, the number of hydrogen bond counts suggested that the average hydrogen bond interaction between N501Y mutant (3.32 +- 1.2) and CR3022 significantly reduced in comparison to wildtype (5.63 +- 2.32) and N440K (5.90 +- 2.14) (Figure 4A). 2021 Viruses Result SARS_CoV_2 N440K;N501Y 272;167 277;172 RBD 15 18 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. Interestingly, the N440K mutation was the only mutation to show 100% co-occurrence with C64F in the membrane glycoprotein of SARS-CoV-2 (Figure S4), along with the globally frequent D614G (S protein) and P323L (ORF1ab) variants. 2021 Viruses Result SARS_CoV_2 C64F;D614G;N440K;P323L 88;182;19;204 92;187;24;209 Membrane;ORF1ab;S 100;211;189 108;217;190 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. MD simulation outcomes of S protein-ACE2 complexes showed better H-bond networks of N440K (3.89 +- 1.64) compared to wildtype spike (3.83 +- 1.64) and N501Y (3.30 +- 1.31) throughout the simulation period (Figure 2A). 2021 Viruses Result SARS_CoV_2 N440K;N501Y 84;151 89;156 S;S 126;26 131;27 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. Protein stability predictions assessed from the impact of mutations showed mild stabilization of the S protein RBD by N501Y and destabilization by the E484K mutation. 2021 Viruses Result SARS_CoV_2 E484K;N501Y 151;118 156;123 RBD;S 111;101 114;102 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. Protein-protein interaction analysis showed that the P681H mutation can putatively promote association of cleavage sites with TMPRSS2 (Figure S5). 2021 Viruses Result SARS_CoV_2 P681H 53 58 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. Similarly, in case of the N440K mutant, the residues K381, G386 and R403 were the major interactive residues. 2021 Viruses Result SARS_CoV_2 N440K 26 31 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. Simulations of R52I variant showed slight lowering of interaction affinity between ORF8 monomers compared to wildtype strain. 2021 Viruses Result SARS_CoV_2 R52I 15 19 ORF8 83 87 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. The 501Y.V2 and P.1 variants show a different set of mutations besides N501Y:E484K in both and K417N (in 501Y.V2) and K417T (in P.1). 2021 Viruses Result SARS_CoV_2 K417N;K417T;N501Y;E484K 95;118;71;77 100;123;76;82 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. The D3L and T205I, S235F mutations in the N protein occur outside the dimer and RNA interaction interfaces, in the unstructured regions in its NTD and linker regions, respectively (Figure S10). 2021 Viruses Result SARS_CoV_2 D3L;S235F;T205I 4;19;12 7;24;17 N 42 43 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. The highly frequent S477N mutation in the Australian population was located outside the RBD-C135/CR3022 interaction interface (Figure S3B). 2021 Viruses Result SARS_CoV_2 S477N 20 25 RBD 88 91 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. The N501Y mutation can promote S protein affinity with host ACE2 receptors. 2021 Viruses Result SARS_CoV_2 N501Y 4 9 S 31 32 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. The N501Y mutation was, however, distantly located from the CR3022/C135 (SARS-CoV-2 neutralizing monoclonal antibodies)-RBD interaction interface (Figures S2 and S3A). 2021 Viruses Result SARS_CoV_2 N501Y 4 9 RBD 120 123 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. The N501Y was also observed to have highest co-occurrence (>90%) with R203K, G204R mutations in the N protein, widely accumulated in North American and European populations (Table 1). 2021 Viruses Result SARS_CoV_2 G204R;N501Y;R203K 77;4;70 82;9;75 N 100 101 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. The N501Y, E484K, K417N/T mutations are localized near the ACE2 interaction interface but distant from C135/CR3022 binding sites (Figure S3A,B). 2021 Viruses Result SARS_CoV_2 E484K;K417N;K417T;N501Y 11;18;18;4 16;25;25;9 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. The P.1 specific E92K in ORF8 showed >90% co-occurrence with its L84S mutation and S202N, M86I in N and nsp6 (ORF1ab) proteins, respectively. 2021 Viruses Result SARS_CoV_2 E92K;L84S;M86I;S202N 17;65;90;83 21;69;94;88 ORF1ab;Nsp6;ORF8;N 110;104;25;98 116;108;29;99 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. The P71L mutation in the E protein (501Y.V2 variant) is located in the vicinity of the putative host MPP5-interacting C-terminal domain but was not observed to perturb local interaction network (Figure S9). 2021 Viruses Result SARS_CoV_2 P71L 4 8 E 25 26 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. The R52I and Y73C mutations in ORF8 of 501Y.V1 variant are localized at its dimerization interface. 2021 Viruses Result SARS_CoV_2 R52I;Y73C 4;13 8;17 ORF8 31 35 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. The R52I localized at the dimer interface could affect dimer assembly process of ORF8. 2021 Viruses Result SARS_CoV_2 R52I 4 8 ORF8 81 85 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. The S protein was observed to have the highest binding affinity towards ACE-2, followed by the N440K mutant (-93.14 +- 16.68 kcal/mol) and N501Y (-89.80 +- 7.30 kcal/mol) (Figure 2D). 2021 Viruses Result SARS_CoV_2 N440K;N501Y 95;139 100;144 S 4 5 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. When the average structure from the simulated trajectories was analysed, it was found that the 501st residue of the spike protein was involved in hydrophobic interactions only in the wildtype and N501Y mutant (Figure 2B,C). 2021 Viruses Result SARS_CoV_2 N501Y 196 201 S 116 121 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. When the simulated ORF8 proteins were investigated for the number of hydrogen bonds, it was found that both wildtype ORF8 (6.16 +- 1.77) and R52I (6.20 +- 1.81) had a similar number of hydrogen bonds with another protomer throughout the simulations (Figure 5A). 2021 Viruses Result SARS_CoV_2 R52I 141 145 ORF8;ORF8 19;117 23;121 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. Among these residues, until 12 February 2021, substitution F490S (first collected on 13 December 2020, GISAID accession ID: EPI_ISL_736026) was reported in the highest number of genomes (28 genomes in England). 2021 Viruses Result SARS_CoV_2 F490S 59 64 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. As may be expected,> , which reflects the fact that the A20.EU1 strain has a replicative advantage over previously dominant non-VOC D614G strains. 2021 Viruses Result SARS_CoV_2 D614G 132 137 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. As of 12 February 2021, as much as 1186 spike L18F VOC genomes have been reported in England. 2021 Viruses Result SARS_CoV_2 L18F 46 50 S 40 45 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. Concluding, we showed that the D614G strain that spread worldwide towards fixation had replicative advantage of 1.42 in relation to D614 strains in England. 2021 Viruses Result SARS_CoV_2 D614G 31 36 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. E484K. 2021 Viruses Result SARS_CoV_2 E484K 0 5 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. Growth of the L18F Substrain. 2021 Viruses Result SARS_CoV_2 L18F 14 18 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. In addition to 69-70HV, mutation N501Y in the RBD of spike is considered as the most important recent mutation. 2021 Viruses Result SARS_CoV_2 N501Y 33 38 S;RBD 53;46 58;49 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. In England, the D614G strain appeared during the spring wave of epidemic in 2020, and in summer it exceeded 98% of all sequenced genomes (Figure 1). 2021 Viruses Result SARS_CoV_2 D614G 16 21 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. In Figure 7 we show the exponential growth of the L18F VOC substrain in England in the five-week period of 7 December 2020-17 January 2021, in relation to the VOC genomes non-mutated at residue 18, denoted L18. 2021 Viruses Result SARS_CoV_2 L18F 50 54 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. In the considered period, the ratio of the L18F to the L18 genomes increased with the fitted weekly growth rate of 1.75, which gives == 1.72 [95% CrI: 1.57-2.02]. 2021 Viruses Result SARS_CoV_2 L18F 43 47 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. In the USA, where we have not found a dominating D614G substrain, we compare the VOC with all non-VOC genomes. 2021 Viruses Result SARS_CoV_2 D614G 49 54 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. In this period, the ratio of the A20.EU1 to other non-VOC D614G strains grows at a rate of 1.25 [95% CI: 1.23-1.28] per week, which gives== 1.24 [95% CI: 1.22-1.27]. 2021 Viruses Result SARS_CoV_2 D614G 58 63 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. It was suggested that E484K may compromise binding of class 2 neutralizing antibodies, while the A501V mutation interferes with binding of class 1 antibodies. 2021 Viruses Result SARS_CoV_2 A501V;E484K 97;22 102;27 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. Its substrain A20.EU1 had replicative advantage of 1.24 over bulk D614G, and reached the proportion of 68% of genomes in England. 2021 Viruses Result SARS_CoV_2 D614G 66 71 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. Mutations at residue Q677 (either Q677H or Q677P) were found in several independent lineages spreading over the autumn of 2020 and into the winter of 2021 in the USA. 2021 Viruses Result SARS_CoV_2 Q677H;Q677P 34;43 39;48 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. Of note, in Autumn 2020, that is, before the VOC lineage has become the dominant strain, the L18F substitution was a ubiquitous mutation in England. 2021 Viruses Result SARS_CoV_2 L18F 93 97 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. S494P. 2021 Viruses Result SARS_CoV_2 S494P 0 5 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The advantage of L18F substrain is supported by data from Wales, UK, where the L18F VOC genomes constituted 17% (390 out of 2301) of all VOC genomes reported in January, substantially more than in the same period in England, 3.0% (1333 out of 43,700). 2021 Viruses Result SARS_CoV_2 L18F;L18F 17;79 21;83 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The first occurrence of the spike L18F substitution has been reported in a VOC strain genome collected on 4 December 2020 (GISAID ID: EPI_ISL_720875). 2021 Viruses Result SARS_CoV_2 L18F 34 38 S 28 33 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The first prevailing mutation of SARS-CoV-2 was D614G substitution in spike protein (the first GISAID reported genome, EPI_ISL_913915, was collected on 2 January 2020, in Mexico). 2021 Viruses Result SARS_CoV_2 D614G 48 53 S 70 75 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The fraction of spike L18F mutation in the expanding 20A.EU1 strain was slowly increasing from 35% (1332 out of 3799) in September, 43% (5658 out of 13,046) in October, till 52% (8917 out of 17,470) in November 2020, which may suggest that this mutation was beneficial for the 20A.EU1 strain. 2021 Viruses Result SARS_CoV_2 L18F 22 26 S 16 21 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The most prevalent mutation, defining a fast growing variant is the L18F substitution (1186 genomes) in the N-terminal domain (NTD) of spike protein. 2021 Viruses Result SARS_CoV_2 L18F 68 72 S;N 135;108 140;109 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The other two fast growing "sibling" mutations in VOC:Q677H (256 genomes) and Q675H (86 genomes):are present in the the proximity of the polybasic cleavage site (residues 682-685) at the S1/S2 boundary influencing RBD:ACE2 binding. 2021 Viruses Result SARS_CoV_2 Q675H;Q677H 78;54 83;59 RBD 214 217 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The same mutation has occurred in the fast expanding South African and Brazilian (Manaus) strains that share with the VOC substitution N501Y and additionally have a mutation of residue 417: either K417N (South African strain 501Y.V2) or K417T (Manaus strain P.1). 2021 Viruses Result SARS_CoV_2 K417N;K417T;N501Y 197;237;135 202;242;140 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The second most prevalent is L5F (658 genomes) localized in the signal peptide of spike. 2021 Viruses Result SARS_CoV_2 L5F 29 32 S 82 87 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The third most prevalent mutation, that is also by far the most prevalent RBM as well as in whole RBD mutation, is S494P (441 genomes). 2021 Viruses Result SARS_CoV_2 S494P 115 120 RBD 98 101 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The VOC strain is also a substrain of the D614G lineage, independent of 20A.EU1, which started expanding in week 43 (before week 43, less than 5 VOC genomes were collected per week), and in week 51 reached 57% of all sequenced genomes. 2021 Viruses Result SARS_CoV_2 D614G 42 47 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The VOC-202012/01 strain spike RBM mutations of special concern are substitutions E484K and S494P. 2021 Viruses Result SARS_CoV_2 E484K;S494P 82;92 87;97 S 25 30 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. This analysis suggests an advantage of the L18F VOC substrain in relation to the remaining VOC genomes, but since it is based on short period, it must be taken with caution. 2021 Viruses Result SARS_CoV_2 L18F 43 47 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. This credible interval is calculated assuming a binomial distribution of the number of the L18F and L18 VOC genomes in each week (see Methods). 2021 Viruses Result SARS_CoV_2 L18F 91 95 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. This mutation occurred independently in the South African strain 501Y.V2, where it is accompanied by two other mutations in spike RBD: K417N and E484K. 2021 Viruses Result SARS_CoV_2 E484K;K417N 145;135 150;140 S;RBD 124;130 129;133 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. Till 12 February 2021, most of the L18F non-VOC genomes in England (97.6%, 25,655 out of 26,280) were found within the 20A.EU1 strain. 2021 Viruses Result SARS_CoV_2 L18F 35 39 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. We estimated this advantage by fitting a trend line to data points from weeks 34-45 of 2020, because for this period the exponential growth of the ratio of the A20.EU1 strain to other non-VOC D614G strains is observed (Figure 2C). 2021 Viruses Result SARS_CoV_2 D614G 192 197 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. 41 years (IQR 25-57; N501Y negative). 2021 Microorganisms Result SARS_CoV_2 N501Y 21 26 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. 44 years (IQR 29-60; N501Y negative); at Bioanalytica the median age was 43 years (IQR 29-53; N501Y positive) vs. 2021 Microorganisms Result SARS_CoV_2 N501Y;N501Y 21;94 26;99 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. 48 years (IQR 32-67; N501Y negative); and at Viollier AG the median age was 41 years (IQR 26-54; N501Y positive) vs. 2021 Microorganisms Result SARS_CoV_2 N501Y;N501Y 21;97 26;102 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. A total of 739 S:N501Y-carrying (B.1.1.7 n = 675, and B.1.351 n = 53; P.1 n = 11) Swiss high quality genomes were available for phylogenetic analysis. 2021 Microorganisms Result SARS_CoV_2 N501Y 17 22 S 15 16 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. At the University Hospital Basel the median age of patients with N501Y positive was 34 years (IQR 12-47) whereas the median age of patients with N501Y negative was 38 years (27-54); at the University of Bern the media age was 33 years (IQR 20-51; N501Y positive) vs. 2021 Microorganisms Result SARS_CoV_2 N501Y;N501Y;N501Y 65;145;247 70;150;252 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. However, at this stage our data does not allow the reliable determination of a Swiss-wide prevalence, as not all PCR positive cases are fully re-analyzed with the N501Y-specific PCR. 2021 Microorganisms Result SARS_CoV_2 N501Y 163 168 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. However, some laboratories re-analyze every SARS-CoV-2 positive case and thereby individual prevalence rates for VoCs could be determined for the last five weeks, clearly demonstrating the rapid increase and displacement of non-N501Y lineage strains (Table 2). 2021 Microorganisms Result SARS_CoV_2 N501Y 228 233 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Since the second week of January 2021, increasing numbers of SARS-CoV-2 positive samples were analysed using an N501Y-specific PCR. 2021 Microorganisms Result SARS_CoV_2 N501Y 112 117 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Some laboratories have reported the median age (with interquartile ranges) in years between patients with and without the N501Y variants. 2021 Microorganisms Result SARS_CoV_2 N501Y 122 127 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. The amino acid substitution D614G was detected in the vast majority of sequences (n = 566, 97.8%), and the wild type (D614) was last identified in June 2020. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D614G 28 33 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. The amino acid substitutions N501Y and P681H besides the deletion Delta69/70 were consistently found among the lineage B.1.1.7 sequences, while N501I was detected in a single sequence from the first Jordan lineage B.1.1.312. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 N501I;N501Y;P681H 144;29;39 149;34;44 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. The following amino acid substitutions were totally absent from the sequences that were analyzed in this study: K417N and E484K. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 E484K;K417N 122;112 127;117 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. The molecular signature found consistently in the Spike gene region of the first Jordan lineage B.1.1.312 was the replacement of adenine by thymine at position 24,432 (A24432T) of the reference genome NC_045512 (thymine instead of uracil since the results were those of DNA sequencing). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 A24432T 168 175 S 50 55 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. The molecular signature in the Spike gene region for the second Jordan lineage B.1.36.10 was C22444T (a synonymous mutation). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 C22444T 93 100 S 31 36 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. This mutation was non-synonymous resulting in the replacement of glutamine (Q) by leucine (L) at position 957 of the spike glycoprotein (Q957L). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 Q957L 137 142 S 117 135 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. Using the Protein Variation Effect Analyzer (PROVEAN) tool, two amino acid substitutions were predicted to be deleterious for the spike glycoprotein: T716I detected among B.1.1.7 sequences and Q957L found in the first Jordan lineage B.1.1.312 (Table 2). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 Q957L;T716I 193;150 198;155 S 130 148 33810168 Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa. A closer look at this cluster suggests an introduction from the Netherlands, with the 24862A>G mutation being inherited from the Netherlands lineage and 5209A>G emerging within the Cape Town cluster (Figure 3D). 2021 Viruses Result SARS_CoV_2 A24862G;A5209G 86;153 94;160 33810168 Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa. Our sequences averaged between 0 and 12 mutations (Supplementary Table S4), with seven mutation sites occurring at a high frequency, including two mutations (5209A>G and 24862A>G) occurring at a higher frequency in the Cape Town sequences than globally (Figure 3C). 2021 Viruses Result SARS_CoV_2 A24862G;A5209G 170;158 178;165 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. Mutations (C241T, C3037T, A23403G, and C14408T) were dominant with frequency (>60%) in all the genomes (Gujarat, India, and global), whereas mutations (G11083T, C13730T, C28311T, C6312A, C313T, C5700A, G29868A, and C23929T) dominated (>19%) in the Indian genomes compared with the Gujarat and global genomes. 2021 Frontiers in genetics Result SARS_CoV_2 A23403G;C13730T;C14408T;C23929T;C28311T;C3037T;C313T;C5700A;C6312A;G29868A;C241T;G11083T 26;161;39;215;170;18;187;194;179;202;11;152 33;168;46;222;177;24;192;200;185;209;16;159 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. Mutations G11083T and C6312A lie in the region of Orf1a encoding Nsp6, whereas mutation GGG28881AAC is present in the N gene. 2021 Frontiers in genetics Result SARS_CoV_2 C6312A;G11083T 22;10 28;17 ORF1a;Nsp6;N 50;65;118 55;69;119 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. The mutations G25563T, C26735T, and C18877T (>55%), followed by C2836T, C22444T, and C28854T (>40%), followed by G21724T, C29750T, C18568T, G4300T, and A2292C (>13%) in viral genomes were sequenced from Gujarat. 2021 Frontiers in genetics Result SARS_CoV_2 A2292C;C18568T;C18877T;C22444T;C26735T;C2836T;C28854T;C29750T;G21724T;G25563T;G4300T 152;131;36;72;23;64;85;122;113;14;140 158;138;43;79;30;70;92;129;120;21;146 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. With reference to viral isolates from India, GGG28881AAC, G11083T, C28311T, C6312A, C23929T, and C13730T were found to be occurring at greater than 19% frequencies (p-value <0.001). 2021 Frontiers in genetics Result SARS_CoV_2 C13730T;C23929T;C28311T;C6312A;G11083T 97;84;67;76;58 104;91;74;82;65 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. Apparently, the Cys 15-Cys 136 disulfide bond is not absolutely essential for S glycoprotein function, but may contribute to the stability of the functional spike. 2021 bioRxiv Result SARS_CoV_2 C15C 16 26 S;S 78;157 92;162 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. As the S1170F change does not alter a potential N-linked glycosylation site, it apparently affects other post-translational modifications; as discussed above, resistance of the 63-kD PNGase F product to O-glycosidase appears to rule out modification by Core 1 or Core 3 O-glycans (Figure 11C). 2021 bioRxiv Result SARS_CoV_2 S1170F 7 13 N 48 49 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. Both the S1 and S2 glycoproteins of the wild-type and D614G SARS-CoV-2 strains migrated faster when expressed in the GALE/GALK2 293T cells compared with the migration of these glycoproteins expressed in 293T cells (Figure 10A). 2021 bioRxiv Result SARS_CoV_2 D614G 54 59 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. Both the wild-type SARS-CoV-2 S glycoprotein and the prevalent D614G variant S glycoprotein were expressed in 293T cells and in the GALE/GALK2 293T cells. 2021 bioRxiv Result SARS_CoV_2 D614G 63 68 S;S 30;77 44;91 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. By contrast, the C301F and C379F changes, which eliminate the Cys 291-Cys 301 and Cys 379-Cys 432 disulfide bonds respectively located in the S1 N-terminal domain and receptor-binding domain, resulted in S glycoproteins that were not processed into S1 and S2 glycoproteins (Figure 11 and Table 2). 2021 bioRxiv Result SARS_CoV_2 C301F;C379F;C291C;C379C 17;27;62;82 22;32;73;93 S;N 204;145 219;146 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. Despite this alteration, the C15F S glycoprotein was proteolytically processed nearly as efficiently as the wild-type S glycoprotein and exhibited wild-type association of the S1 and S2 subunits (Figure 11 and Table 2). 2021 bioRxiv Result SARS_CoV_2 C15F 29 33 S;S 34;118 48;132 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. However, after freeze-thawing, the relative infectivity of the C15F mutant virus decreased dramatically (data not shown). 2021 bioRxiv Result SARS_CoV_2 C15F 63 67 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. The 63-kD S2 glycoprotein band seen in PNGase F-treated lysates from 293T cells expressing the wild-type S glycoproteins was not evident in lysates from cells expressing the S1170F mutant (Figure 11B and C). 2021 bioRxiv Result SARS_CoV_2 S1170F 174 180 S 105 120 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. The C15F change eliminates the Cys 15-Cys 136 disulfide bond in the S1 N-terminal domain. 2021 bioRxiv Result SARS_CoV_2 C15F;C15C 4;31 8;41 N 71 72 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. The infectivity of VSV vectors pseudotyped with the C15F S glycoproteins was approximately 31% of that of virus pseudotyped with the wild-type S glycoproteins. 2021 bioRxiv Result SARS_CoV_2 C15F 52 56 S;S 57;143 72;158 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. The S673I mutant was processed inefficiently and only supported the infection of pseudotyped VSV vectors at a very low level. 2021 bioRxiv Result SARS_CoV_2 S673I 4 9 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. The S676I and S1170F mutants supported the entry of VSV pseudotypes as efficiently as the wild-type S glycoprotein (Table 2). 2021 bioRxiv Result SARS_CoV_2 S1170F;S676I 14;4 20;9 S 100 114 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. The T323I-pseudotyped viruses infected cells with approximately 41% of the efficiency of viruses pseudotyped with the wild-type S glycoproteins, but the infectivity of these viruses decreased further upon freeze-thawing. 2021 bioRxiv Result SARS_CoV_2 T323I 4 9 S 128 143 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. The T323I, S676I and S1170F mutants were processed nearly as efficiently as the wild-type S glycoprotein, and exhibited good subunit association (Figure 11A and Table 2). 2021 bioRxiv Result SARS_CoV_2 S1170F;S676I;T323I 21;11;4 27;16;9 S 90 104 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. Thus, of these rare cysteine variants of the SARS-CoV-2 S glycoprotein, only one (C15F) allows partial, but unstable, infectivity. 2021 bioRxiv Result SARS_CoV_2 C15F 82 86 S 56 70 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. Viruses pseudotyped with the C301F and C379F S glycoproteins exhibited very low levels of infectivity. 2021 bioRxiv Result SARS_CoV_2 C301F;C379F 29;39 34;44 S 45 60 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. We examined the sensitivity of the two most replication-competent S glycoprotein mutants, T676I and S1170F, to neutralization by soluble ACE2 (sACE2) and sera from convalescing SARS-CoV-2-infected individuals. 2021 bioRxiv Result SARS_CoV_2 S1170F;T676I 100;90 106;95 S 66 80 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. Because B.1.1.7 emerged after D614G became globally common, the absolute fitness of B.1.1.7 is likely greater. 2021 medRxiv Result SARS_CoV_2 D614G 30 35 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. D614G shows a very similar pattern in the UK and Netherlands where the mutant was spreading in a way that is nearly indistinguishable from the wild-type strains for a period of several weeks in the early epidemic period. 2021 medRxiv Result SARS_CoV_2 D614G 0 5 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. In both cases the mutant strain is much slower to rise, occurring over a period of months rather than weeks as was the case with D614G. 2021 medRxiv Result SARS_CoV_2 D614G 129 134 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. S5 and S6 for D614G and B.1.1.7, respectively. 2021 medRxiv Result SARS_CoV_2 D614G 14 19 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. The dynamics of B.1.1.7 in the UK and Netherlands are substantially different from both D614G and each other. 2021 medRxiv Result SARS_CoV_2 D614G 88 93 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. The isotonic regression method rejected this null hypothesis in 33 of 38 countries with sufficient data for D614G and all 24 of the countries with sufficient data for B.1.1.7 at the 5% significance level. 2021 medRxiv Result SARS_CoV_2 D614G 108 113 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. The mean of that global distribution for s is 0.25 (90% credible interval (CrI): [0.14, 0.35]) for D614G and 0.26 (90% CrI: [0.14, 0.36]) for B.1.1.7, both confidently greater than zero. 2021 medRxiv Result SARS_CoV_2 D614G 99 104 S 41 42 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. the overall global distribution of s is substantially wider, both for D614G (90% CrI: [-0.16, 0.68]. 2021 medRxiv Result SARS_CoV_2 D614G 70 75 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. The overall stochastic model fits to D614G and B.1.1.7 for the UK and Netherlands are shown in. 2021 medRxiv Result SARS_CoV_2 D614G 37 42 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. The profile likelihoods of s, the increase in contagiousness for the mutant variant, for the D614G and B.1.1.7 are shown in. 2021 medRxiv Result SARS_CoV_2 D614G 93 98 S 27 28 33834012 Comparison of Clinical Features and Outcomes of Medically Attended COVID-19 and Influenza Patients in a Defined Population in the 2020 Respiratory Virus Season. N439K, S477N and N501Y which located in the receptor-binding domain may affect the immunogenicity or vaccination. 2021 Frontiers in public health Result SARS_CoV_2 N501Y;S477N;N439K 17;7;0 22;12;5 33834012 Comparison of Clinical Features and Outcomes of Medically Attended COVID-19 and Influenza Patients in a Defined Population in the 2020 Respiratory Virus Season. Our result showed S477N and N439K mutations have the capability to enhance the affinity with receptor (Figures 2D,E). 2021 Frontiers in public health Result SARS_CoV_2 N439K;S477N 28;18 33;23 33834012 Comparison of Clinical Features and Outcomes of Medically Attended COVID-19 and Influenza Patients in a Defined Population in the 2020 Respiratory Virus Season. There were 18,539 nonsynonymous mutations on the spike protein, the D614G mutation was unusually enriched and present in more than 8,000 strains. 2021 Frontiers in public health Result SARS_CoV_2 D614G 68 73 S 49 54 33834012 Comparison of Clinical Features and Outcomes of Medically Attended COVID-19 and Influenza Patients in a Defined Population in the 2020 Respiratory Virus Season. Up to February 1st 2021, nearly 300,000 strains containing D614G variation, A222V and L18F were the second and third mutations (Figure 2C). 2021 Frontiers in public health Result SARS_CoV_2 A222V;D614G;L18F 76;59;86 81;64;90 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. Altogether, the obtained value of DeltaDeltaG is 9.59 kcal/mol, suggesting that the K417N mutation significantly reduced the binding affinity between the RBD and CB6. 2022 Journal of medicinal chemistry Result SARS_CoV_2 K417N 84 89 RBD 154 157 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. By definition, binding free energy changes for the RBD with either ACE2 or CB6 (due to the K417N mutation) can be obtained as DeltaDeltaG = DeltaG2 - DeltaG1 (see Figure 3). 2022 Journal of medicinal chemistry Result SARS_CoV_2 K417N 91 96 RBD 51 54 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. In the free state (Figure 3d,e), the K417N mutation yielded a free energy change DeltaGB of -32.08 kcal/mol. 2022 Journal of medicinal chemistry Result SARS_CoV_2 K417N 37 42 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. More importantly, the phenomenon of weakening the binding affinity of the RBD-CB6 complex observed in the K417N mutation is not unique. 2022 Journal of medicinal chemistry Result SARS_CoV_2 K417N 106 111 RBD 74 77 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. Previously, it was demonstrated in an experiment that the K417N mutation weakened the binding affinity between the RBD and ACE2, which is consistent with our simulation results. 2022 Journal of medicinal chemistry Result SARS_CoV_2 K417N 58 63 RBD 115 118 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. The calculations of the binding free energy change induced by the K417N mutation were accomplished using the free energy perturbation (FEP) method. 2022 Journal of medicinal chemistry Result SARS_CoV_2 K417N 66 71 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. The free energy loss due to the K417N mutation is mainly caused by the change in electrostatic energy. 2022 Journal of medicinal chemistry Result SARS_CoV_2 K417N 32 37 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. Therefore, the K417N mutation could be evidence of viral adaptation to the human immune system or natural selection under the "pressure" of human neutralizing mAbs. 2022 Journal of medicinal chemistry Result SARS_CoV_2 K417N 15 20 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. Thus, the K417N mutation also reduced the binding affinity between the RBD and ACE2, but the reduction is ~6.5 times less than that between the RBD and CB6. 2022 Journal of medicinal chemistry Result SARS_CoV_2 K417N 10 15 RBD;RBD 71;144 74;147 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. With protein structures for both bound (or complex) and free states in respective MD simulations, we employed the FEP alchemy method to calculate the binding free energy difference for the K417N mutation on the RBD, using the thermodynamic cycle shown in panels b-e of Figure 3. 2022 Journal of medicinal chemistry Result SARS_CoV_2 K417N 189 194 RBD 211 214 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Both groups also carried B.4 [G1397A-T28688C-G29742T] variants. 2022 Transboundary and emerging diseases Result SARS_CoV_2 G1397A;G29742T;T28688C 30;45;37 36;52;44 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. D614G, the most prevalent mutation globally, was also the most prevalent spike mutation in viral isolates from Iran, while showing an increasing trend from mid-May, observed mostly within the [B.1.*/20A] cluster. 2022 Transboundary and emerging diseases Result SARS_CoV_2 D614G 0 5 S 73 78 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. G11083T is one of the most frequent mutations observed in Asia from December 2019 to March 2020 (Koyama et al., 2020; Mercatelli and Giorgi, 2020) and, not surprisingly, is observed mostly along with B.4 substitutions. 2022 Transboundary and emerging diseases Result SARS_CoV_2 G11083T 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Moreover, Sanger sequencing of additional 67 SARS-CoV2 positive samples confirmed the increase in D614G frequency till October, becoming the dominant mutation in the Iranian outbreak (Figure 5). 2022 Transboundary and emerging diseases Result SARS_CoV_2 D614G 98 103 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Notably, just four variants, namely G1397A, T28688C, G29742T and G11083T, contributed to >70% of samples; comprising the common co-occurrence of variants, [G1397A-T28688C-G29742T] in B.4 lineage. 2022 Transboundary and emerging diseases Result SARS_CoV_2 G11083T;G1397A;G29742T;T28688C;G1397A;G29742T;T28688C 65;36;53;44;156;171;163 72;42;60;51;162;178;170 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Other less frequent variants were observed in ~19% of samples constituting the known co-occurrence of variants; [C241T-C3037T-C14408T-A23403G] and [C241T-C3037T-C14408T-A23403G-G25563T], occurring in clade G (B.1), which is prevalent in Europe, Oceania, South America and Africa and clade GH (B.1.*), prevalent in North America (Mercatelli and Giorgi, 2020). 2022 Transboundary and emerging diseases Result SARS_CoV_2 C241T;C241T;A23403G;A23403G;C14408T;C14408T;C3037T;C3037T;G25563T 113;148;134;169;126;161;119;154;177 118;153;141;176;133;168;125;160;184 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Remarkably, co-occurrence of D614G mutation with B.4 [G1397A-T28688C-G29742T] and G11083T variants was also observed in three samples. 2022 Transboundary and emerging diseases Result SARS_CoV_2 D614G;G11083T;G1397A;G29742T;T28688C 29;82;54;69;61 34;89;60;76;68 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Remarkably, we observed two specific haplotypes; the co-occurrence of [G20887A-C28830T-C21627T] and [G8653T-C884T] variants in 17% and 11% of samples, respectively. 2022 Transboundary and emerging diseases Result SARS_CoV_2 G20887A;G8653T;C21627T;C28830T;C884T 71;101;87;79;108 78;107;94;86;113 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. T22I mutation was only observed in the [B.4/19A] cluster. 2022 Transboundary and emerging diseases Result SARS_CoV_2 T22I 0 4 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. The [B.1.*/20A] samples did not show [G1397A-T28688C-G29742T] substitutions but instead harboured [C241T-C3037T-C14408T-A23403G] or [C241T-C3037T-C14408T-A23403G-G25563T], which are the common patterns of variant co-occurrence of B.1 and B.1.* lineages in Europe and North America (Mercatelli & Giorgi, 2020). 2022 Transboundary and emerging diseases Result SARS_CoV_2 C241T;C241T;G1397A;A23403G;A23403G;C14408T;C14408T;C3037T;C3037T;G25563T;G29742T;T28688C 99;133;38;120;154;112;146;105;139;162;53;45 104;138;44;127;161;119;153;111;145;169;60;52 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. The [B/19A] samples also carry the G1397A and G29742T substitutions but not T28688C. 2022 Transboundary and emerging diseases Result SARS_CoV_2 G1397A;G29742T;T28688C 35;46;76 41;53;83 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. The older green cluster is comprised of 36 genomes almost all of the B.4 lineage [B.4/19A], carrying [G1397A-T28688C-G29742T] substitutions (Eden et al., 2020). 2022 Transboundary and emerging diseases Result SARS_CoV_2 G1397A;G29742T;T28688C 102;117;109 108;124;116 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. This suggests that the three [G1397A-T28688C-G29742T] substitutions might have occurred before their introduction to Iran, subsequently becoming the major lineage and driving the epidemic in the country. 2022 Transboundary and emerging diseases Result SARS_CoV_2 G1397A;G29742T;T28688C 30;45;37 36;52;44 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. We thus focussed on variants located in spike protein of viral isolates from Iran and identified spike variants in 28 samples (53%), in which D614G and T22I were occurring at higher frequencies of 24.5% and 17%, respectively (Table 2). 2022 Transboundary and emerging diseases Result SARS_CoV_2 D614G;T22I 142;152 147;156 S;S 40;97 45;102 33836314 Implementation of an in-house real-time reverse transcription-PCR assay for the rapid detection of the SARS-CoV-2 Marseille-4 variant. Thirdly, we tested 26 samples identified by next-generation genome sequencing as containing SARS-CoV-2 strains that were not Marseille-4 variants (including 17 N501Y variants, 5 Marseille-2 variants, 3 clade 20A strains and 1 clade 20C strain): none of them were positive using our Marseille-4 specific qPCR. 2021 Journal of clinical virology Result SARS_CoV_2 N501Y 160 165 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. In the future, analysis of patient clinical outcomes and the coupled SARS-CoV-2 genome sequences will provide important evidences regarding the effect of NR203K/G204R polymorphism on the biology of SARS-CoV-2. 2021 Nature communications Result SARS_CoV_2 G204R;R203K 161;155 166;160 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. NR203K/G204R gained greater ability to undergo RNA-induced LLPS. 2021 Nature communications Result SARS_CoV_2 G204R 7 12 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. This GGG-to-AAC variation resulted in the amino acid substitutions, R203K/G204R, in N protein. 2021 Nature communications Result SARS_CoV_2 R203K;G204R 68;74 73;79 N 84 85 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. To examine the effect of this high-frequency variation on the LLPS of N, we prepared the recombinant proteins of these variants, NR203/G204, NR203K, NG204R, and NR203K/G204R. 2021 Nature communications Result SARS_CoV_2 G204R 168 173 N 70 71 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. We also analyzed the correlation between the mortality and R203K/G204R polymorphism of N. 2021 Nature communications Result SARS_CoV_2 R203K;G204R 59;65 64;70 N 87 88 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. We found that the polymorphism of NR203K/G204R, which exhibited a higher propensity to undergo LLPS in the presence of RNAs, showed a greater effect on the inhibition of IFN expression. 2021 Nature communications Result SARS_CoV_2 G204R 41 46 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. We next examined the inhibitory effect of N proteins (both NR203K/G204R and NR203/G204) on the RNA-induced expression of IFN. 2021 Nature communications Result SARS_CoV_2 G204R 66 71 N 42 43 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. When incubated with viral RNA, we found that, interestingly, NR203K/G204R gained greater ability to undergo LLPS. 2021 Nature communications Result SARS_CoV_2 G204R 68 73 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. Among the 23 sites, we found that 6 mutation sites (T445C, C6286T, C22227T, G25563T, C26801G and G29645T) with a frequency greater than 20% might be highly linked (Table 2. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 C22227T;C26801G;C6286T;G25563T;G29645T;T445C 67;85;59;76;97;52 74;92;65;83;104;57 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. Among the prevalent haplotype subgroups, H5, H7, H9 and H11 all had A23403G mutations, which indicated that the single A23403G mutation was related to infectivity, pathogenicity or host adaptability of SARS-CoV-2, while H10 had the other three specific mutations, including C241T, C3037T and C14408T, indicating that the combined mutations of these 3 sites also had a certain impact on infectivity, pathogenicity or host adaptability of SARS-CoV-2. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 A23403G;A23403G;C14408T;C241T;C3037T 68;119;292;274;281 75;126;299;279;287 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. Among these 23 sites, except for the 4 specific sites (C241T C3037T C14408T and A23403G) of the previous H1 haplotype with mutation frequency greater than 0.8, only the above 6 mutation sites of highly linked had higher frequencies, which indicated that the mutations of these 10 sites were more significant at the present stage. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 A23403G;C14408T;C3037T;C241T 80;68;61;55 87;75;67;60 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. Besides, the G25563T mutation was also found in several other haplotypes H9-2, H5-2 and H7-2 (Table 3). 2021 Computational and structural biotechnology journal Result SARS_CoV_2 G25563T 13 20 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. Haplotype H1-2 with 5 new mutations (T445C, C6286T, C22227T, C26801G and G29645T) accounted for 19.36% of the population and appeared in the later stage (July 21, 2020), which showed a trend of increasing gradually (Table 3. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 C22227T;C26801G;C6286T;G29645T;T445C 52;61;44;73;37 59;68;50;80;42 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. The above haplotype subgroup epidemic trends showed that the mutation of 5 sites (T445C, C6286T, C22227T, C26801G and G29645T) or the single G25563T mutation may have some influence on infectivity, pathogenicity or host adaptability of SARS-CoV-2. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 C22227T;C26801G;C6286T;G25563T;G29645T;T445C 97;106;89;141;118;82 104;113;95;148;125;87 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. we still find that the 4 specific sites (C241T C3037T C14408T and A23403G) in Europe have an important influence on the viral infectivity, pathogenicity or host adaptability. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 A23403G;C14408T;C3037T;C241T 66;54;47;41 73;61;53;46 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. While haplotype H1-3 with only one new mutation (G25563T) accounted for 15.46% of the population and appeared in the early stage (February 7, 2020) (Table 3. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 G25563T 49 56 33842902 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. have reported that E484K and K417N dramatically and specifically reduce neutralization by LY-CoV555 and LY-CoV016, respectively, while N501Y has no impact on neutralization by either antibody. 2021 Cell reports. Medicine Result SARS_CoV_2 E484K;K417N;N501Y 19;29;135 24;34;140 33842902 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. However, there are some sites where single mutations escape binding by both LY-CoV555 and LY-CoV016, and as a result a 1:1 cocktail of the 2 antibodies is escaped by several single mutations, including I472D, G485P, and Q493R/K (Figures 1A and S2; see the magnifiable interactive maps at https://jbloomlab.github.io/SARS-CoV-2-RBD_MAP_LY-CoV555/ to examine these mutations at higher resolution). 2021 Cell reports. Medicine Result SARS_CoV_2 G485P;I472D;Q493K;Q493R 209;202;220;220 214;207;227;227 33842902 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. In addition, the B.1.429 lineage (also known as 20C/CAL.20C) that has risen to high frequency in southern California contains L452R, which escapes LY-CoV555 (Figure 2B). 2021 Cell reports. Medicine Result SARS_CoV_2 L452R 126 131 33842902 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. Mutations at position Q493 are notably well tolerated with respect to ACE2 binding and RBD expression (Figures 1A and S2):Q493K has been observed in a persistently infected immunocompromised patient. 2021 Cell reports. Medicine Result SARS_CoV_2 Q493K 122 127 RBD 87 90 33842902 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. Of particular note, the B.1.351 (also known as 20H/501Y.V2) and P.1 (also known as 20J/501Y.V3) lineages contain combinations of mutations (E484K and K417N/T) that individually escape each antibody (Figure 2B), suggesting that the LY-CoV555+LY-CoV016 cocktail may be ineffective against these lineages. 2021 Cell reports. Medicine Result SARS_CoV_2 K417N;K417T;E484K 150;150;140 157;157;145 33842902 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. Subsequent to the release of our original preprint version of this article, the US Food and Drug Administration's (FDA's) fact sheet for bamlanivimab EUA was updated, confirming our findings by noting that L452R reduces bamlanivimab neutralization >1,000-fold. 2021 Cell reports. Medicine Result SARS_CoV_2 L452R 206 211 33842902 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. The escape mutations present at the highest frequency among the sequenced isolates are E484K, L452R, and S494P for LY-CoV555 and K417N/T for LY-CoV016. 2021 Cell reports. Medicine Result SARS_CoV_2 E484K;K417N;K417T;L452R;S494P 87;129;129;94;105 92;136;136;99;110 33842902 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. This observation coincides with recommendations to reduce the use of bamlanivimab monotherapy in locations where L452R is prominent. 2021 Cell reports. Medicine Result SARS_CoV_2 L452R 113 118 33842902 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. We also note that single mutations that escape both antibodies (Q493R and Q493K) have been observed in a handful of sequenced isolates (Figure 2A). 2021 Cell reports. Medicine Result SARS_CoV_2 Q493K;Q493R 74;64 79;69 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. For both B.1.1.7 and Wuhan-Hu1 P681H particles, we detected increased cleavage of the spike protein compared to Wuhan-Hu1 (WT); see Table 1. 2021 bioRxiv Result SARS_CoV_2 P681H 31 36 S 86 91 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. In this study, MLV pseudoparticles containing the B.1.1.7, Wuhan-Hu1 SARS-CoV-2 S protein (WT), and a P681H point mutant of Wuhan-Hu1 were also generated alongside positive control particles containing the vesicular stomatitis virus (VSV) G protein, along with negative control particles (Deltaenvpp) lacking envelope proteins (not shown), using the HEK293T cell line for particle production. 2021 bioRxiv Result SARS_CoV_2 P681H 102 107 S 80 81 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. These data show that the P681H mutation had no effect on membrane fusion activity of the SARS-CoV-2 spike protein under the conditions tested. 2021 bioRxiv Result SARS_CoV_2 P681H 25 30 Membrane;S 57;100 65;105 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Vero-TMPRSS2 and VeroE6 cells were transfected with the B.1.1.7, Wuhan-Hu1 (WT) and Wuhan-Hu1 P681H spike gene and we then evaluated syncytia formation as a read-out of membrane fusion. 2021 bioRxiv Result SARS_CoV_2 P681H 94 99 Membrane;S 169;100 177;105 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. While Vero-TMPRSS2 cells formed more extensive syncytia than VeroE6 cells, we observed no difference in the syncytia formation following spike protein expression for either B.1.1.7, Wuhan-Hu1 (WT) or Wuhan-Hu1 P681H. 2021 bioRxiv Result SARS_CoV_2 P681H 210 215 S 137 142 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. While Vero-TMPRSS2 cells gave overall higher luciferase signal indicative of more efficient entry, we observed little difference in infection between pseudoparticles displaying spike protein from either B.1.1.7, Wuhan-Hu1 (WT) or Wuhan-Hu1 P681H. 2021 bioRxiv Result SARS_CoV_2 P681H 240 245 S 177 182 33851162 A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. D614G became globally dominant in 2020 possibly due to higher viral loads. 2021 bioRxiv Result SARS_CoV_2 D614G 0 5 33851162 A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. In addition to the Spike mutations, B.1.x includes N:M234I (G28975A), which also appears in Variants of Interest B.1.526 and P.2 (G28975T). 2021 bioRxiv Result SARS_CoV_2 G28975A;G28975T;M234I 60;130;53 67;137;58 S;N 19;51 24;52 33851162 A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. N:M234I has been predicted to be stabilizing for the protein structure. 2021 bioRxiv Result SARS_CoV_2 M234I 2 7 N 0 1 33851162 A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. S494P is also located within the ACE2 receptor binding domain and experimental evidence suggests that mutations at this position decrease antibody binding affinity. 2021 bioRxiv Result SARS_CoV_2 S494P 0 5 RBD 38 61 33851162 A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. Similarly, P681H is located within the spike protein furin cleavage site which is thought to be a hotspot of viral adaptive evolution (e.g., ). 2021 bioRxiv Result SARS_CoV_2 P681H 11 16 S 39 44 33851162 A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. Specifically, each sample contains Spike mutations S494P, N501Y, D614G, P681H, K854N, and E1111K. 2021 bioRxiv Result SARS_CoV_2 D614G;E1111K;K854N;N501Y;P681H;S494P 65;90;79;58;72;51 70;96;84;63;77;56 S 35 40 33851162 A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. Specifically, N501Y is thought to be important for viral replication because it enables the virus to bind ACE2 and enter host cells more efficiently. 2021 bioRxiv Result SARS_CoV_2 N501Y 14 19 33851162 A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. The three nucleotide mutations that cause N:M234I (G28975A, G28975C, G28975T) have all been observed at the roots of several Pango lineages (Table S2) and the frequency of N:M234I in 480,704 samples available from GISAID as of 2 April 2021 with collection dates 2021-01-01 to 2021-03-31 is 7.0%. 2021 bioRxiv Result SARS_CoV_2 G28975C;G28975T;G28975A;M234I;M234I 60;69;51;44;174 67;76;58;49;179 N;N 42;172 43;173 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. A small number of sequences, including the K417T mutation, inclusive of the P.1 lineage, have been observed in sequencing from Japan, France, Belgium, Italy, the Netherlands, and Colombia (Figure S1). 2021 Cell Result SARS_CoV_2 K417T 43 48 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. Although P.1 does not harbor deletions in the NTD like B.1.1.7 (Delta69-70,Delta144) or B.1.351 (Delta242-244), it is clear that the NTD mutations in P.1 (L18F, T20N, P26S, D138Y, and R190S) disrupt the epitope for mAb159 (Figure 4A). 2021 Cell Result SARS_CoV_2 D138Y;P26S;R190S;T20N;L18F 173;167;184;161;155 178;171;189;165;159 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. Compared to the Wuhan sequence, P.1 contains the following mutations: L18F, T20N, P26S, D138Y, and R190S in the NTD; K417T, E484K, and N501Y in the RBD; D614G and H655Y at the C terminus of S1; and T1027I and V1176F in S2. 2021 Cell Result SARS_CoV_2 D138Y;D614G;E484K;H655Y;K417T;L18F;N501Y;P26S;R190S;T1027I;T20N;V1176F 88;153;124;163;117;70;135;82;99;198;76;209 93;158;129;168;122;74;140;86;104;204;80;215 RBD 148 151 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. Here, we have expressed P.1 RBD (K417T, E484K, and N501Y). 2021 Cell Result SARS_CoV_2 E484K;N501Y;K417T 40;51;33 45;56;38 RBD 28 31 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. However, with RBDs bearing K417N/T mutations, a buffer molecule/ion (most likely a sulfate in some cases and a glycerol in others) moves to form bridging interactions, which may mitigate the loss of the salt bridge. 2021 Cell Result SARS_CoV_2 K417N;K417T 27;27 34;34 RBD 14 18 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. Mutations K417T, E484K, and N501Y in the ACE2 interacting surface are of the greatest concern because of their potential to promote escape from the neutralizing antibody response, which predominately targets this region (Figure 1D). 2021 Cell Result SARS_CoV_2 E484K;K417T;N501Y 17;10;28 22;15;33 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. N501Y increased affinity 7-fold, and the combination of 417, 484, and 501 mutations further increased affinity (19-fold compared to Wuhan). 2021 Cell Result SARS_CoV_2 N501Y 0 5 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. Of note, two of the NTD changes in P.1 introduce N-linked glycosylation sequons T20N (residues TRT to NRT) and R190S (residues NLR to NLS; Figure 1E). 2021 Cell Result SARS_CoV_2 R190S;T20N 111;80 116;84 N 49 50 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. Residue 501 makes contact with CDR-L1 of mAb 222 (Figures 4D and 4F); however, the interaction with P30 is probably slightly strengthened by the N501Y mutation, which provides a stacking interaction with the proline, conferring resilience. 2021 Cell Result SARS_CoV_2 N501Y 145 150 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. The escape from REGN10933 and LY-CoV555 mirrors that of other potent antibodies (including 316 and 384 in our set), which make strong interactions with residues 484-486 and are severely compromised by the marked change E484K, whereas LY-CoV16, an IGHV3-53 mAb, is affected by changes at 417 and 501. 2021 Cell Result SARS_CoV_2 E484K 219 224 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. The results with P.1 showed an impact greater compared to B.1.1.7 but similar to B.1.351; this is expected, since both contain mutation of the same three residues in the RBD, only differing at position 417, K417N in B.1.351 and K417T in P.1. 2021 Cell Result SARS_CoV_2 K417N;K417T 207;228 212;233 RBD 170 173 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. To understand how 222 is still able to neutralize P.1, we solved the crystal structures of six ternary complexes of 222 Fab with the RBDs for (1) the original virus and bearing mutations: (2) K417N; (3) K417T; (4) N501Y; the 417, 484, and 501 changes characteristic of B.1.351 (5) and P.1 (6). 2021 Cell Result SARS_CoV_2 K417N;K417T;N501Y 192;203;214 197;208;219 RBD 133 137 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. We have previously measured the affinity of RBD-ACE2 interaction for Wuhan, B.1.1.7 (N501Y), and B.1.351 (K417N, E484K, and N501Y) RBDs. 2021 Cell Result SARS_CoV_2 E484K;N501Y;K417N;N501Y 113;124;106;85 118;129;111;90 RBD;RBD 44;131 47;135 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. We have previously solved the structures of mAbs 150, 158, and 269 (Figure 4B), which show that while there are no contacts with residue 484, there are interactions of CDR-H3 with K417 and CDR-L1 with N501, meaning that binding and neutralization by VH3-53 antibodies would be predicted to be compromised by the N501Y change in variant viruses B.1.1.7, B.1.351, and P.1, while the additional change at 417 in P.1 (K417T) and B.1.351 (K417N) might be expected to have an additive effect. 2021 Cell Result SARS_CoV_2 N501Y;K417N;K417T 312;434;414 317;439;419 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. We used biolayer interferometry (BLI) to measure the affinity of the RBD-binding antibodies and found that compared to Victoria (SARS-CoV-2/human/AUS/VIC01/2020), an early isolate of SARS-CoV-2, which has a single change S247R in S compared to the Wuhan strain, mAb binding was significantly impacted, with a number showing complete knockout of activity (Figure 2I). 2021 Cell Result SARS_CoV_2 S247R 221 226 RBD;S 69;230 72;231 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Combination of D614G with the mink-specific mutation Y453F (mutant D614G+Y453F) or Y453F in conjunction with H69Delta, H70Delta (mutant D614G+H69Delta/H70Delta/Y453F) did not modulate entry efficiency when compared to D614G alone (Figure 2B). 2021 Cell reports Result SARS_CoV_2 D614G;D614G;D614G;D614G;Y453F;Y453F;Y453F;Y453F 15;67;136;218;53;83;160;73 20;72;141;223;58;88;165;78 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Finally, mutation D614G+cluster 5 reduced entry into several cell lines but was compatible with robust entry into the human intestinal cell line Caco-2 and the lung cell line Calu-3 (Figure 2B). 2021 Cell reports Result SARS_CoV_2 D614G 18 23 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Finally, the interference of Y453F with entry inhibition by casirivimab/REGN10933 was in keeping with position 453 being located at the interface of the S protein and the antibody (Figure S3) and with results reported by a previous study. 2021 Cell reports Result SARS_CoV_2 Y453F 29 34 S 153 154 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Further, an S protein of identical amino acid sequence but harboring a glycine at position 614 (D614G) was used as a reference for S protein variants containing the dominant D614G mutation (Figure 1D). 2021 Cell reports Result SARS_CoV_2 D614G;D614G 174;96 179;101 S;S 12;131 13;132 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Importantly, mutation Y453F reduced inhibition by most serum/plasma samples tested, albeit with variable efficiency (median increase of serum/plasma titer required for 50% neutralization [NT50] = 1.62x, range = 1.02x to 3.43x), indicating that this RBD mutation may compromise SARS-CoV-2 control by preexisting neutralizing antibody responses (Figures 3A and S2). 2021 Cell reports Result SARS_CoV_2 Y453F 22 27 RBD 249 252 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Preincubation of particles bearing S protein with soluble ACE2 and preincubation of Calu-3 lung cells with camostat efficiently blocked entry driven by all S proteins analyzed (Figures 2C and 2D), with mutant D614G+cluster 5 being particularly sensitive to inhibition by soluble ACE2 (Figure 2C). 2021 Cell reports Result SARS_CoV_2 D614G 209 214 S;S 35;156 36;157 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Similarly, the mutation Y453F reduced inhibition by one (casirivimab/REGN10933) out of a cocktail of two antibodies with EUA for COVID-19 therapy (REGN-COV2), while an unrelated, non-neutralizing antibody was inactive (immunoglobulin G1 [IgG1]) (Figures 3B and S3). 2021 Cell reports Result SARS_CoV_2 Y453F 24 29 COVID-19 129 137 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Substitution D614G, which is dominant in SARS-CoV-2 from humans and was also found in viruses from mink, increased the efficiency of S-protein-driven entry, as expected. 2021 Cell reports Result SARS_CoV_2 D614G 13 18 S 133 134 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Thus, mutation Y453F that arose in infected mink can compromise viral inhibition by human antibodies induced upon SARS-CoV-2 infection or under development for COVID-19 treatment. 2021 Cell reports Result SARS_CoV_2 Y453F 15 20 COVID-19;COVID-19 160;114 168;134 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. We focused our analysis on mutation Y453F, since this mutation is located in the RBD, which constitutes the primary target for neutralizing antibodies. 2021 Cell reports Result SARS_CoV_2 Y453F 36 41 RBD 81 84 33860605 Polysulfates Block SARS-CoV-2 Uptake through Electrostatic Interactions*. From the total number of contacts (Figure 5 f, inset) and interaction energies (Figure 5 e), we found that LPGS binds to N501Y RBD as effectively as to wild-type RBD, but more tightly to E484K RBD, which is consistent with the presence of an extra cationic residue on this mutant surface. 2021 Angewandte Chemie (International ed. in English) Result SARS_CoV_2 E484K;N501Y 187;121 192;126 RBD;RBD;RBD 127;162;193 130;165;196 33860605 Polysulfates Block SARS-CoV-2 Uptake through Electrostatic Interactions*. The successful comparison between experimental and simulated results for wild-type RBD-LPGS interactions encouraged us to indirectly test the effectiveness of LPGS in inhibiting SARS-CoV-2 mutants via simulations, specifically those exhibiting the E484K and N501Y mutations in the RBD. 2021 Angewandte Chemie (International ed. in English) Result SARS_CoV_2 E484K;N501Y 248;258 253;263 RBD;RBD 83;281 86;284 33860605 Polysulfates Block SARS-CoV-2 Uptake through Electrostatic Interactions*. These amino acids form a positively charged patch located at the exterior of the RBD (shown blue in Figure 2 b), which is reported to improve the virus binding affinity to the ACE2 receptor.[ 26 , 27 ] For the new E484K variant, the K484 adds another positive charge to the RBD and is therefore expected to further strengthen viral binding to HS. 2021 Angewandte Chemie (International ed. in English) Result SARS_CoV_2 E484K 215 220 RBD;RBD 81;275 84;278 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. In contrast, the inter-protomer S1-S2 interactions are strongly affected by the D614G substitution in the open conformation. 2021 Science advances Result SARS_CoV_2 D614G 80 85 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. In summary, we find three contributions to symmetrizations associated with the D614G substitution: (i) symmetrization in the inter-protomer contacts, (ii) symmetrization in the correlations between the RBDs, and (iii) symmetrization of a specific inter-protomer hydrogen bond. 2021 Science advances Result SARS_CoV_2 D614G 79 84 RBD 202 206 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. Inspired by this rationale, we use an Ising model, an established and straightforward method that has been applied to many different applications in physics, to predict how the D614G substitution can affect the relative stability of the open and closed Spike conformations. 2021 Science advances Result SARS_CoV_2 D614G 177 182 S 253 258 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. The average number of persistent intra-protomer contacts between S1 and S2 was not affected by the D614G substitution in either the open or closed Spike conformation. 2021 Science advances Result SARS_CoV_2 D614G 99 104 S 147 152 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. The distinct contact signatures associated with the D614G substitution may be associated with alterations in the relative population of the all-down and one-up ensembles of the Spike protein. 2021 Science advances Result SARS_CoV_2 D614G 52 57 S 177 182 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. To capture the specific regions where the inter-protomer S1-S2 contacts are most affected by the D614G substitution, we carried out a global differential contact analysis, in which we identified persistent contacts that existed in one form but not the other in the all-down or one-up states. 2021 Science advances Result SARS_CoV_2 D614G 97 102 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. To elucidate how specific interactions are altered by the D614G substitution, we calculated residue-residue contacts that are formed between subunits of all three protomers. 2021 Science advances Result SARS_CoV_2 D614G 58 63 33875719 Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology. Viral clades carrying D614G mutation also emerged. 2021 Scientific reports Result SARS_CoV_2 D614G 22 27 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. Future versions of these engineered ACE2 proteins may wish to focus on residue changes that directly implicate new hydrogen bonds with either the wild-type or N501Y spike protein. 2021 The journal of physical chemistry. B Result SARS_CoV_2 N501Y 159 164 S 165 170 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. Interestingly, in eq 1 (which was updated using the newly reported experimental data for the N501Y mutant of SARS-CoV-2 spike, published while our article was under review), the correction coefficient of the DeltaGPB value is 0.265 (see Figure 2 for the correlation between the directly calculated DeltaGPB values and the experimental binding free energies), which is very close to our previously reported correction coefficient (0.3057) obtained for the cannabinoid 2 (CB2) receptor binding with its ligands using the methodology.Equation 1 was then used to correct all the DeltaGPB values obtained, creating an estimated binding affinity (Kd) for the N501Y mutant spike protein at 0.44 nM (which is very close to the experimentally determined binding affinity of 0.8 nM, reported while our article was under review). 2021 The journal of physical chemistry. B Result SARS_CoV_2 N501Y;N501Y 93;653 98;658 S;S 120;666 125;671 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. The A386L mutation introduces a sterically bulkier residue next to E37, pressing it closer to R403. 2021 The journal of physical chemistry. B Result SARS_CoV_2 A386L 4 9 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. The cause behind the increase in binding affinity from the wild-type spike protein to the N501Y mutant is clear when looking at interactions between the ACE2 and the spike protein when the N501Y mutation is introduced. 2021 The journal of physical chemistry. B Result SARS_CoV_2 N501Y;N501Y 90;189 95;194 S;S 69;166 74;171 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. The N330Y mutation has an effect similar to the A386L mutation, a sterically bulkier residue presses upon G496 in the spike protein, pressing it closer Y41 and strengthening its hydrogen bond (Figure 3D,H). 2021 The journal of physical chemistry. B Result SARS_CoV_2 A386L;N330Y 48;4 53;9 S 118 123 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. The obtained binding structures for the wild-type ACE2 binding with the wild-type and N501Y spike proteins are depicted in Figure 1. 2021 The journal of physical chemistry. B Result SARS_CoV_2 N501Y 86 91 S 92 97 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. This additional intermolecular hydrogen bond accounts for the increased binding affinity for the N501Y mutant with ACE2. 2021 The journal of physical chemistry. B Result SARS_CoV_2 N501Y 97 102 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. This change to Y501 removes a strong hydrogen bond with E22 and D3 in LCB1 and LCB3, respectively, leading to a large DeltaDeltaG change between the wild-type and N501Y spike proteins (Table 2). 2021 The journal of physical chemistry. B Result SARS_CoV_2 N501Y 163 168 S 169 174 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. This effect is lost between ACE2.v2 and ACE2.v2.4 due to the lack of the A386L residue change (Figure 3B,F). 2021 The journal of physical chemistry. B Result SARS_CoV_2 A386L 73 78 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. Whereas N501 in the wild-type spike protein hydrogen-bonds with no ACE2 residues (Figure 1C), the hydroxyl group on the Y501 side chain in the N501Y mutant can hydrogen-bond with both the amine group on the K353 side chain of ACE2 and intramolecularly with the amine group on the Q498 side chain (Figure 1D). 2021 The journal of physical chemistry. B Result SARS_CoV_2 N501Y 143 148 S 30 35 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. While the N501Y mutation appears to increase the binding affinity against the wild-type and engineered ACE2 proteins, the same cannot be said of the miniprotein designs. 2021 The journal of physical chemistry. B Result SARS_CoV_2 N501Y 10 15 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. With these approximations in place, a more quantitative estimation of the effects of the N501Y spike mutation can be performed, allowing for an estimation of the N501Y spike Kd with these miniproteins. 2021 The journal of physical chemistry. B Result SARS_CoV_2 N501Y;N501Y 89;162 94;167 S;S 95;168 100;173 33882219 Vaccine Breakthrough Infections with SARS-CoV-2 Variants. In Patient 1, these mutations included E484K (which confers resistance to a commonly elicited class of neutralizing antibodies) and D614G, and in Patient 2, these mutations included D614G and S477N (Table 1). 2021 The New England journal of medicine Result SARS_CoV_2 D614G;D614G;E484K;S477N 132;182;39;192 137;187;44;197 33882219 Vaccine Breakthrough Infections with SARS-CoV-2 Variants. We therefore further tested the serum sample obtained from Patient 1 to measure its effectiveness against the wild-type virus, the E484K mutant, and the B.1.526 variant, and we found that the serum was equally effective against each (Figure 4). 2021 The New England journal of medicine Result SARS_CoV_2 E484K 131 136 33883059 Severe Acute Respiratory Syndrome Coronavirus 2 P.2 Lineage Associated with Reinfection Case, Brazil, June-October 2020. Of note, sequences recovered from the reinfection case and from 2 additional cases in the state of Paraiba harbor the substitution S-E484K (G23012A) and were classified as lineage P.2, which was initially detected in the state of Rio de Janeiro. 2021 Emerging infectious diseases Result SARS_CoV_2 G23012A;E484K 140;133 147;138 S 131 132 33883059 Severe Acute Respiratory Syndrome Coronavirus 2 P.2 Lineage Associated with Reinfection Case, Brazil, June-October 2020. We identified 5 lineage-defining single-nucleotide polymorphisms: C100U (5' untranslated region), T10667G (NSP5_L205V), C11824T (NSP6), G23012A (S_E484K), and G28628T (N_A119S) that distinguish P.2 sequences from all other B.1.1.28 sequences available in Brazil. 2021 Emerging infectious diseases Result SARS_CoV_2 C11824T;G23012A;G28628T;T10667G;A119S;E484K;L205V 120;136;159;98;170;147;112 127;143;166;105;175;152;117 Nsp5;Nsp6 107;129 111;133 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. As we found, for the N501Y mutant, and variant B.1.1.7, which also contains the N501Y substitution, the Tyr residues produced 9 and 7 interactions with the ACE2 receptor, respectively in comparison to the Asp residue present in the WT spike protein that produced only 4 interactions. 2021 EXCLI journal Result SARS_CoV_2 N501Y;N501Y 21;80 26;85 S 235 240 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. For the VegaZZ software, the average RMSDs were 2.33+-0.55 A for WT, 2.45+-0.54 A for the N501Y mutant, and 2.37+-0.32 A for the B.1.1.7 mutant. 2021 EXCLI journal Result SARS_CoV_2 N501Y 90 95 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. In our analysis the highest Miyata values, indicating the largest differences between the WT and spike protein mutants were found for the following residue substitutions: N501Y, F490S, Q493L, G446V, and Y508H. 2021 EXCLI journal Result SARS_CoV_2 F490S;G446V;N501Y;Q493L;Y508H 178;192;171;185;203 183;197;176;190;208 S 97 102 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. In the case of the Y505W mutant, exhibiting the lowest binding free energy, the number of direct interactions between the Trp residue and ACE2 increased to 8 as compared to the Tyr residue in the WT spike protein that produced 5 interactions. 2021 EXCLI journal Result SARS_CoV_2 Y505W 19 24 S 199 204 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. Interestingly, the Y505W mutant showed the lowest binding free energy among the analyzed mutants. 2021 EXCLI journal Result SARS_CoV_2 Y505W 19 24 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. Our molecular docking analysis revealed the binding free energy for the N501Y mutant to be -13.8 kcal/mol. 2021 EXCLI journal Result SARS_CoV_2 N501Y 72 77 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. Several mutants, including A475V, V455E, V445L, and V445I interacted with the higher binding free energy of -10.7 kcal/mol, -11.2 kcal/mol, -11.4 kcal/mol, and -10.8 kcal/mol, respectively, resulting in less stable interaction with ACE2 than the WT spike protein. 2021 EXCLI journal Result SARS_CoV_2 A475V;V445I;V445L;V455E 27;52;41;34 32;57;46;39 S 249 254 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. Similar structural effects were observed for the L455P and K493R mutants, which also produced changes in the number and type of interactions. 2021 EXCLI journal Result SARS_CoV_2 K493R;L455P 59;49 64;54 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. Similarly, to the WT spike protein, the K444R mutant did not show any direct interactions with ACE2. 2021 EXCLI journal Result SARS_CoV_2 K444R 40 45 S 21 26 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. The median average RMSDs obtained with the CASB-flex software were 1.05+-0.77 A for WT, 0.99+-0.65 A for the N501Y mutant, and 0.91+- 0.58 A for the B.1.1.7 mutant. 2021 EXCLI journal Result SARS_CoV_2 N501Y 109 114 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. The N501Y spike protein mutant was described as a highly transmissible variant in the current SARS-CoV-2 pandemic (Leung et al., 2021). 2021 EXCLI journal Result SARS_CoV_2 N501Y 4 9 S 10 15 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. The other investigated mutants, including the B.1.1.7 (-13.4 kcal/mol), K444R (-13.8 kcal/mol), L455F (-13.7 kcal/mol), Q493R (-13.5 kcal/mol) and Y505W (-14.4 kcal/mol) had the binding free energy lower than the WT spike protein, which indicated their higher affinity for the human ACE2 receptor. 2021 EXCLI journal Result SARS_CoV_2 K444R;L455F;Q493R;Y505W 72;96;120;147 77;101;125;152 S 216 221 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. The stabilization effect of the G476A and Q493K mutations was confirmed by the DeepDDG software. 2021 EXCLI journal Result SARS_CoV_2 G476A;Q493K 32;42 37;47 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. The substitutions G476A, K444N, N440K, Q493K, Q493L, and Q493R were identified as stabilizing by the DUET software. 2021 EXCLI journal Result SARS_CoV_2 G476A;K444N;N440K;Q493K;Q493L;Q493R 18;25;32;39;46;57 23;30;37;44;51;62 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. Thus, our further analysis was focused on the mutants that exhibited similar or lower binding free energy than that found for the N501Y mutant, including the B.1.1.7, K444R, L455F, Q493R, and Y505W variants (see Table 3(Tab. 2021 EXCLI journal Result SARS_CoV_2 K444R;L455F;N501Y;Q493R;Y505W 167;174;130;181;192 172;179;135;186;197 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. To validate further the results obtained by the molecular docking, the selected spike protein mutants (N501Y and B.1.1.7) were analyzed by the MD simulations and compared to the WT spike protein. 2021 EXCLI journal Result SARS_CoV_2 N501Y 103 108 S;S 80;181 85;186 33886690 The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways. Also mutation D614G rendered SARS-2-S pseudovirus significantly less dependent on TTSP activation to enter HEK293T cells (Fig 8C). 2021 PLoS pathogens Result SARS_CoV_2 D614G 14 19 S 36 37 33886690 The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways. Also substitution D614G generated a stabilizing effect, which was most pronounced at 39 C (P = 0.044). 2021 PLoS pathogens Result SARS_CoV_2 D614G 18 23 33886690 The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways. As mentioned above, the enhancing effect of SARS-2-S mutation D614G was higher in Vero E6 cells than in Calu-3 cells, suggesting that variation SG614 might boost in particular the cathepsin-dependent entry route. 2021 PLoS pathogens Result SARS_CoV_2 D614G 62 67 S 51 52 33886690 The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways. Combined with the above data from pseudovirus assays, this virus experiment provides evidence that mutation D614G increases entry of SARS-CoV-2 via the cathepsin route. 2021 PLoS pathogens Result SARS_CoV_2 D614G 108 113 33886690 The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways. For comparison, we created a mutant form of SARS-S, bearing the SARS-2-S multibasic cleavage site and preceding residues, and we generated a mutant of MERS-S, in which the furin motif was destroyed (R748C) (Fig 1C). 2021 PLoS pathogens Result SARS_CoV_2 R748C 199 204 S;S;S 49;71;156 50;72;157 33886690 The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways. Next, we investigated the impact of mutation D614G and of different alterations at the S1/S2 cleavage site (Fig 1C), on S priming and pseudovirus entry. 2021 PLoS pathogens Result SARS_CoV_2 D614G 45 50 S 120 121 33886690 The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways. Regarding mutation D614G in SARS-2-S, the SG614 form showed 4.7-fold higher entry into Vero E6 cells than the SD614 variant, while the difference in Calu-3 cells was only 1.5-fold and not significant (Fig 5C). 2021 PLoS pathogens Result SARS_CoV_2 D614G 19 24 S 35 36 33886690 The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways. To assess the effect of temperature on authentic SARS-CoV-2 virus replication and a possible effect of the D614G mutation, we used two SARS-CoV-2 virus strains (achieved as clinical isolates) bearing SD614 or SG614. 2021 PLoS pathogens Result SARS_CoV_2 D614G 107 112 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. 2 B, Top) and the N501Y variant. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N501Y 18 23 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. All of the WNbFc fusions were able to block ACE2 interaction with the E484K variant with better potencies compared to WT RBD, with relative IC50s of 0.09, 0.10, 0.19, and 0.04 nM for WNbFc 2, 7, 15, and 36, respectively. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 E484K 70 75 RBD 121 124 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Bivalent Nanobody-Fc Fusions Bind to RBD Natural Variants and Neutralize the SARS-CoV-2 D614G N501Y Virus. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G;N501Y 88;94 93;99 RBD 37 40 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Furthermore, while WNbFc 2 and 36 showed lower binding to F490S compared to WT RBD, they were still able to inhibit RBD-ACE2 interaction at less than 0.7 nM, suggesting that binding affinities may not fully correlate with the ability to inhibit complex formation. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 F490S 58 63 RBD;RBD 79;116 82;119 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. It has also been previously shown that N501Y significantly increases virus adaptation in a mouse model. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N501Y 39 44 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. N501 on the RBD is important for ACE2 interaction, and the N501Y variant increases binding affinity of the RBD for ACE2. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N501Y 59 64 RBD;RBD 12;107 15;110 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Notably, all WNbFc fusions exhibited higher relative IC50s with the N501Y variant RBD in comparison to WT but were still able to inhibit ACE2 binding when administered at 10- to 20-fold higher concentrations. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N501Y 68 73 RBD 82 85 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. The higher IC50 values are most likely a reflection of the higher affinity of human ACE2 to the N501Y variant due to the competitive format of the assay where all binding components (RBD, ACE2, and nanobody) were added simultaneously. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N501Y 96 101 RBD 183 186 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. The K417N variant would disallow the formation of a salt bridge. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 K417N 4 9 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. The mixture combination WNbFc 2 + 7, WNbFc 2 + 15, WNbFc 36 + 7, and WNbFc 36 + 15 showed PRNT IC50 values ranging between 0.12 to 0.46 nM against WT SARS-CoV-2, with similar neutralization potencies between WT and SARS-CoV-2 N501Y D614G variant. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G;N501Y 232;226 237;231 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. These results show that the WNbFc fusions bound to the N501Y RBD variant at similar antibody affinities compared to WT RBD and neutralized SARS-CoV-2 N501Y D614G virus at comparable potencies to WT SARS-CoV-2, with concentrations between 0.1 to 5.1 nM. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G;N501Y;N501Y 156;55;150 161;60;155 RBD;RBD 61;119 64;122 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. These WNbFc 2, WNbFc 7, WNbFc 15, and WNbFc 36 lead candidates bound to most RBD variants with relative half maximal effective concentration (EC50) values ranging from 0.7 to 14 nM, with the exception of WNbFc 2 and 36, which had weaker binding to F490S with EC50 of 42 and 20 nM, respectively. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 F490S 248 253 RBD 77 80 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. This is consistent with our results showing that WNb 2 and WNb 36 have similar binding affinities to N501Y compared to WT RBD. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N501Y 101 106 RBD 122 125 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. To test the prophylactic efficacy of the WNbFc fusions, we administered the antibodies by intraperitoneal injection 24 h prior to challenge of C57BL/6J mice with human clinical isolate of SARS-CoV-2 (hCoV-19/Australia/VIC2089/2020), which has the N501Y D614G mutations. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G;N501Y 253;247 258;252 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Using SARS-CoV-2 N501Y D614G, WNbFc 2, 7, 15, and 36 showed PRNT IC50 values of 0.30, 5.04, 4.91, and 0.11 nM, respectively, with most showing comparable neutralization potencies to WT virus with less than a twofold difference. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G;N501Y 23;17 28;22 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. We used a plaque reduction neutralization test (PRNT) to determine if the WNbFc fusions were able to neutralize both the WT (hCoV-19/Australia/VIC01/2020) and SARS-CoV-2 (hCoV-19/Australia/VIC2089/2020) with the D614G N501Y mutations. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G;N501Y 212;218 217;223 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. While the E484K variant lacks the ability to form a salt bridge with K59, our results show that WNb 2 bound to E484A or E484K with relative EC50 values of 2 and 5 nM, respectively, and competitively inhibited E484K interaction with ACE2 at higher potency compared to WT RBD. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 E484A;E484K;E484K;E484K 111;10;120;209 116;15;125;214 RBD 270 273 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. WNbFc 2, 7, 15, and 36 bound to WT RBD with relative EC50 of 2.65, 1.80, 2.48, and 0.97 nM, respectively, and showed less than 2.5-fold reduction in binding to either E484K or N501Y variant RBDs. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 E484K;N501Y 167;176 172;181 RBD;RBD 35;190 38;194 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. WNbFc 36 was the most potent inhibitor of complex formation with most relative IC50s to the RBD variant array within 0.4 nM (with the exception of the N501Y variant RBD). 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N501Y 151 156 RBD;RBD 92;165 95;168 33893880 Combined RT-qPCR and pyrosequencing of a Spike glycoprotein polybasic cleavage motif can uncover pediatric SARS-CoV-2 infections associated with heterogeneous presentation. Also, not E484K could be detected. 2021 Molecular and cellular pediatrics Result SARS_CoV_2 E484K 10 15 33893880 Combined RT-qPCR and pyrosequencing of a Spike glycoprotein polybasic cleavage motif can uncover pediatric SARS-CoV-2 infections associated with heterogeneous presentation. Due to the incremental transmission of SARS-CoV-2 variants-of-concern, we note that the used strategy can uncover (Spike) P681H allowing the pre-selection of SARS-CoV-2 B.1.1.7 candidate specimens for deep sequencing. 2021 Molecular and cellular pediatrics Result SARS_CoV_2 P681H 122 127 S 115 120 33893880 Combined RT-qPCR and pyrosequencing of a Spike glycoprotein polybasic cleavage motif can uncover pediatric SARS-CoV-2 infections associated with heterogeneous presentation. Remarkably, N501Y was seen in 2 other adult samples (Figure S7), but neither E484K nor P681H (data not shown). 2021 Molecular and cellular pediatrics Result SARS_CoV_2 E484K;N501Y;P681H 77;12;87 82;17;92 33893880 Combined RT-qPCR and pyrosequencing of a Spike glycoprotein polybasic cleavage motif can uncover pediatric SARS-CoV-2 infections associated with heterogeneous presentation. Using different sequencing primers (Table S1), we could not detect N501Y in the P681H sample, which is a key substitution for 3 variants-of-concern. 2021 Molecular and cellular pediatrics Result SARS_CoV_2 N501Y;P681H 67;80 72;85 33893880 Combined RT-qPCR and pyrosequencing of a Spike glycoprotein polybasic cleavage motif can uncover pediatric SARS-CoV-2 infections associated with heterogeneous presentation. Whereas we did not see the P681H substitution in any of the analyzed pediatric specimens, we could detect it in 1 adult (Figure S5). 2021 Molecular and cellular pediatrics Result SARS_CoV_2 P681H 27 32 33894500 Screening of potent phytochemical inhibitors against SARS-CoV-2 protease and its two Asian mutants. 3a), while R60C made 9 common and four new interactions (Thr25, Thr26, Cys44, Thr45). 2021 Computers in biology and medicine Result SARS_CoV_2 R60C 11 15 33894500 Screening of potent phytochemical inhibitors against SARS-CoV-2 protease and its two Asian mutants. However, the mutant I152V protease-kazinol T was not a stable complex from 0 to 25 ns, but formed a stable complex from 25 to 100 ns. 2021 Computers in biology and medicine Result SARS_CoV_2 I152V 20 25 33894500 Screening of potent phytochemical inhibitors against SARS-CoV-2 protease and its two Asian mutants. I152V revealed 8 common and six new interactions (Phe140, Leu141, Tyr54, Glu166, Val186, Arg188) compared to the native protease. 2021 Computers in biology and medicine Result SARS_CoV_2 I152V 0 5 33894500 Screening of potent phytochemical inhibitors against SARS-CoV-2 protease and its two Asian mutants. MD simulation was run to monitor the atomic level interaction and stability of the best pose complexes of the main protease and its two mutants (R60C and I152V) with NPC474104 (kazinzol T). 2021 Computers in biology and medicine Result SARS_CoV_2 I152V;R60C 154;145 159;149 33894500 Screening of potent phytochemical inhibitors against SARS-CoV-2 protease and its two Asian mutants. The comparative protein backbone RMSD plot showed the stability of the protein backbone of the wild-type protease and its two mutants (R60C and I152V). 2021 Computers in biology and medicine Result SARS_CoV_2 I152V;R60C 144;135 149;139 33894500 Screening of potent phytochemical inhibitors against SARS-CoV-2 protease and its two Asian mutants. The inhibition analysis showed various binding affinities for the mutants R60C and I152V, with decreased S-values of -5.9 and -7.09, respectively. 2021 Computers in biology and medicine Result SARS_CoV_2 I152V;R60C 83;74 88;78 S 105 106 33894500 Screening of potent phytochemical inhibitors against SARS-CoV-2 protease and its two Asian mutants. The real-time simulation of 100 ns (ns) showed that the kazinol T-protease (wild-type and R60C and I152V mutants) complexes were stable in a dynamic environment at 300 K temperature and 1.01325 bar pressure. 2021 Computers in biology and medicine Result SARS_CoV_2 I152V;R60C 99;90 104;94 33894500 Screening of potent phytochemical inhibitors against SARS-CoV-2 protease and its two Asian mutants. The RMSD pattern averaged around 1.8 A for the wild-type protease-kazinol T and mutant R60C-kazinol T complexes and 1.5 A for the mutant I152V-kazinol T complex. 2021 Computers in biology and medicine Result SARS_CoV_2 I152V;R60C 137;87 142;91 33894500 Screening of potent phytochemical inhibitors against SARS-CoV-2 protease and its two Asian mutants. The wild-type protease and mutant R60C showed the same RMSD pattern. 2021 Computers in biology and medicine Result SARS_CoV_2 R60C 34 38 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. F28L - 0.001; "Other" vs. 2021 Emerging microbes & infections Result SARS_CoV_2 F28L 0 5 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. I82T - 0.00035; "Other" vs. 2021 Emerging microbes & infections Result SARS_CoV_2 I82T 0 5 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. V70L - 6.24E-08). 2021 Emerging microbes & infections Result SARS_CoV_2 V70L 0 5 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. After peaking in December, the M:I48V missense mutation appear to be diminishing with a current 0.13% frequency in the USA (Table 1, Table S1, Figure 2). 2021 Emerging microbes & infections Result SARS_CoV_2 I48V 33 37 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. Another mutation carried by most isolates in this clade (98%) that is worth noting is N:T205I, because it is present in multiple VOCs including CAL.20C (B.1.429 and B.1.427) and B.1.351, and that M and N proteins are both important for viral assembly. 2021 Emerging microbes & infections Result SARS_CoV_2 T205I 88 93 N;N 86;202 87;203 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. Another mutation in the same codon, M:V70F, has persisted at low frequencies across multiple countries since March 2020. 2021 Emerging microbes & infections Result SARS_CoV_2 V70F 38 42 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. Between November to February, about 87% (1537/1760) of the M:A2S - carrying virus isolates belong to the B.1.1.7 lineage. 2021 Emerging microbes & infections Result SARS_CoV_2 A2S 61 64 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. Cross checking the country of origin and Pangolin lineage assignment, we observed that many of the isolates belong to the B.1.1.7 lineage, while most I48V mutation isolates belonged to lineage B.1.375. 2021 Emerging microbes & infections Result SARS_CoV_2 I48V 150 154 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. Currently, 99.7% of the B.1.525 lineage isolates carry the M:I82T mutation. 2021 Emerging microbes & infections Result SARS_CoV_2 I82T 61 65 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. During the same period of October 2021 to February 2021, M:M84T increased from 0.1% to 0.23% in the USA. 2021 Emerging microbes & infections Result SARS_CoV_2 M84T 59 63 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. However, the surge in other M mutations, and the emergence of a potentially new sub-B1 M:I82T carrying clade exceed what would be expected by a hijacking effect alone. 2021 Emerging microbes & infections Result SARS_CoV_2 I82T 89 93 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. In contrast, the M:I82T mutation increased in frequency 116 fold from 0.014% in October 2020 to 1.62% in February 2021 in the USA and continues to grow. 2021 Emerging microbes & infections Result SARS_CoV_2 I82T 19 23 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. In the UK, M:V70L first appeared in September 2020 and the frequency increased 382 fold from 0.004% in October to 1.5% in February 2021, when it was also present in Switzerland at 3.6% and in Belgium at 3.0%. 2021 Emerging microbes & infections Result SARS_CoV_2 V70L 13 17 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. Indeed, some Spike missense mutations, like D614G and E484K, are advantageous, leading to rapid spread and increased frequency in the overall population and the emergence of a number of VOCs that uniformly include mutations like the D614G, which is now found in nearly every isolate worldwide but was unreported a year ago. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G;D614G;E484K 44;233;54 49;238;59 S 13 18 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. It presents mainly within the R.1 (34.2%) and B.1.1.7 (48.9%) lineages, with 98% of the R.1 lineage isolates carry the M:F28L as a signature mutation. 2021 Emerging microbes & infections Result SARS_CoV_2 F28L 121 125 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. M:A2S has existed widely across the world since last March, peaked to 0.9% in July globally, and has re-emerged globally at 1.0%, with levels of up to 3.22% in Spain and 1.76% in UK. 2021 Emerging microbes & infections Result SARS_CoV_2 A2S 2 5 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. M:F28L first appeared in November 2020 and is highest in Austria (02/2021, 39.3%), Ghana (01/2021, 6.4%) and Japan (01/2021, 2.3%) but also observed in Spain (2.1%), Belgium (0.4%), and the Netherlands (0.8%), by February 2021. 2021 Emerging microbes & infections Result SARS_CoV_2 F28L 2 6 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. Over the last three months, 129 of the 293 viral sequences from Rhode Island had the same M:I48V missense mutation, an approximately 9.5 fold higher frequency than in other USA locations. 2021 Emerging microbes & infections Result SARS_CoV_2 I48V 92 96 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. The four mutations are M:A2S, M:F28L, M:I82T, and M:V70L. 2021 Emerging microbes & infections Result SARS_CoV_2 A2S;F28L;I82T;V70L 25;32;40;52 28;36;44;56 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. The largest M:I82T carrying clade is part of a young M:I82T sub-B.1 lineage that has surged over the past 3 months to account for 14.4% of B.1 lineage isolates in February, and now constitutes 0.7% of all B.1 lineages. 2021 Emerging microbes & infections Result SARS_CoV_2 I82T;I82T 14;55 18;59 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. The M gene is relatively silent, with only 4 missense mutations that each account for 0.4% or more of the global viral genomes in the month of February 2021 (M:A2S at 1.01%, M:V70L at 1.004%, M:I82T at 0.68%, and M:F28L at 0.41%). 2021 Emerging microbes & infections Result SARS_CoV_2 A2S;F28L;I82T;V70L 160;215;194;176 163;219;198;180 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. The M:I48V mutation is highly specific to the USA at 1.18% in January 2021 (Table 1, Table S1), 87 times that observed in samples from outside the USA (0.014%). 2021 Emerging microbes & infections Result SARS_CoV_2 I48V 6 10 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. The M:V70L and M:A2S mutations both stayed within a narrow range of 1.1% to 1.5% within the B.1.1.7 lineage between December 2020 and February 2021, suggesting that a hijacking effect may account for these observed changes. 2021 Emerging microbes & infections Result SARS_CoV_2 A2S;V70L 17;6 20;10 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. The M:V70L-carrying virus isolates are part of the minor lineages under the B.1.1.7 lineage. 2021 Emerging microbes & infections Result SARS_CoV_2 V70L 6 10 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. The novel combination of M:I82T, the three signature Spike mutations (S:S494P, the S:P681H and S:T716I) from B.1.1.7, and the N:T205I mutation is therefore of particular concern. 2021 Emerging microbes & infections Result SARS_CoV_2 I82T;P681H;S494P;T205I;T716I 27;85;72;128;97 31;90;77;133;102 S;N;S;S;S 53;126;70;83;95 58;127;71;84;96 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. The p-values ranged from 0.9999884 or non-significant to 1.33E-40 or very significant for the six mutations of interest (A2S: 0.9999884; F28L: 1.31E-09; I48V: 1.33E-40; I82T: 2.08E-39; M84T: 1.28E-08; V70L: 1.02E-09). 2021 Emerging microbes & infections Result SARS_CoV_2 F28L;I48V;I82T;M84T;V70L;A2S 137;153;169;185;201;121 141;157;173;189;205;124 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. The second largest M:I82T carrying clade arose only recently in December 2020 and is mainly circulating in Europe and Africa, where it was co-segregating with the S:E484K Spike protein mutation, forming lineage B.1.525 (Table S2, https://cov-lineages.org/global_report_B.1.525.html). 2021 Emerging microbes & infections Result SARS_CoV_2 E484K;I82T 165;21 170;25 S;S 171;163 176;164 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. There were 10 other missense mutations present in at least 90% of the isolates in this clade and 8 of them were enriched by 73 to 146 fold compared to the general B.1 lineage including the 3 signature mutations in the spike protein (S:S494P, the S:P681H and S:T716I) found in the B.1.1.7 lineage (Table 2). 2021 Emerging microbes & infections Result SARS_CoV_2 P681H;S494P;T716I 248;235;260 253;240;265 S;S;S;S 218;233;246;258 223;234;247;259 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. This clade is smaller than the M:I82T clade in the USA, as described above, which lacks the S:E484K mutation. 2021 Emerging microbes & infections Result SARS_CoV_2 E484K;I82T 94;33 99;37 S 92 93 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. This suggests that M:I82T may confer a biologically selective advantage independent of the S:E484K, a known predictor of more severe viral infection. 2021 Emerging microbes & infections Result SARS_CoV_2 E484K;I82T 93;21 98;25 S 91 92 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. Thus, the M:I82T clade is significantly phylogenetically separated from other B.1 lineage clades, and may deserve consideration for a separate lineage designation (Figures 3 and 4). 2021 Emerging microbes & infections Result SARS_CoV_2 I82T 12 16 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. While it predominately circulated in New York and New Jersey, over the past 2 months M:I82T has surged outside the USA including Aruba (5.2%) and Nigeria (33.1%) (Table 1, Table S1). 2021 Emerging microbes & infections Result SARS_CoV_2 I82T 87 91 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. As a result, the residues from 5 to 120 (alpha1, alpha2, alpha3, beta1, beta2, and beta-hairpin) and 830-933 (alpha40-45, beta22, and beta23) were obtained with large cross-correlation networks from RdRp-Remdesivir and SCHEMBL20144212 complexes (Figures 3A,C), whereas the P323L-Remdesivir obtained less cross-correlation networks especially at the region from 5 to 120 residues (Figure 3E). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 P323L 273 278 RdRP 199 203 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. For RdRp protein carrying the P323L mutation, we observed that the compounds 134502628, 70649275, 137648734, and 145074552 possessed higher binding affinity than Remdesivir. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 P323L 30 35 RdRP 4 8 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. Here, we observed the differences in the residues from 5 to 120 from the P323L-Remdesivir complex (Figure 3F) compared to the other three docked complexes. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 P323L 73 78 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. However, the differences can be seen with the P323L-Remdesivir and P323L-SCHEMBL20144212 complexes, especially at the region from 5 to 120 residues. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 P323L;P323L 46;67 51;72 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. Our results exhibited similar network cross-correlation for P323L-SCHEMBL20144212 (Figure 3G) when compared to the RdRp-SCHEMBL20144212 complex. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 P323L 60 65 RdRP 115 119 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. The P323L-Remdesivir complex exhibited the least residue cross-correlation; the possible reason for this could be mutation at 323rd position in RdRp. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 P323L 4 9 RdRP 144 148 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. The RdRp-SCHEMBL20144212 and P323L-SCHEMBL20144212 complexes (Figures 4B,C) illustrate the strongly correlated motions and less anticorrelation as compared to that of RdRp-Remdesivir and P323L-Remdesivir complexes (Figures 4A,C). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 P323L;P323L 29;187 34;192 RdRP;RdRP 4;167 8;171 33900165 Susceptibility to SARS-CoV-2 of Cell Lines and Substrates Commonly Used to Diagnose and Isolate Influenza and Other Viruses. During this study, we noticed that the proportion of naturally circulating virus containing a D614G substitution in the spike protein was rapidly increasing. 2021 Emerging infectious diseases Result SARS_CoV_2 D614G 94 99 S 120 125 33900165 Susceptibility to SARS-CoV-2 of Cell Lines and Substrates Commonly Used to Diagnose and Isolate Influenza and Other Viruses. Replication of SARS-CoV-2 with Spike D614G Substitution. 2021 Emerging infectious diseases Result SARS_CoV_2 D614G 37 42 S 31 36 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. Infection by strains lacking the 23403A>G variant showed higher mortality in multivariable analysis (OR, 22.4; 95% CI, 0.6 to 5.6; P = .01). 2021 JAMA network open Result SARS_CoV_2 A23403G 33 41 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. Several variants were associated with lower hospitalization rate, including 12809C>T (L4182F ORF1ab, 3 of 91 hospitalizations [3.3%] vs 22 of 211 hospitalizations [10.4%]; chi21 = 4.215; P = .04) and 27964C>T (S24L ORF8, 0 of 91 hospitalizations [0%] vs 13 of 211 hospitalizations [6.2%]; chi21 = 5.878; P = .01). 2021 JAMA network open Result SARS_CoV_2 C12809T;C27964T;L4182F;S24L 76;200;86;210 84;208;92;214 ORF1ab;ORF8 93;215 99;219 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. The most common nonsynonymous variants identified were 23403A>G (D614G spike) and 14408C>T (P323L ORF1ab). 2021 JAMA network open Result SARS_CoV_2 C14408T;A23403G;D614G;P323L 82;55;65;92 90;63;70;97 ORF1ab;S 98;71 104;76 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. These 2 variants along with intergenic 241C>T (intergenic) and silent 3037C>T (F924 ORF1ab) variants had a coincident rate of 100% (eFigure 2 in the Supplement). 2021 JAMA network open Result SARS_CoV_2 C241T;C3037T 39;70 45;77 ORF1ab 84 90 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. Variants associated with clade group 2 (241C>T, 3037C>T, 14408C>T, and 23403A>G) were associated with increased patient survival when hospitalized (64 of 74 patients [86.5%] vs 10 of 17 patients [58.8%]; chi21 = 6.907; P = .009). 2021 JAMA network open Result SARS_CoV_2 C14408T;A23403G;C3037T;C241T 57;71;48;40 65;79;55;46 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. Of those, E484D was present in over 95% of the viral population. 2021 Antimicrobial agents and chemotherapy Result SARS_CoV_2 E484D 10 15 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. Outside S, the only other positions in which we found a clear indication of significant evolution at the amino acid level (that is, a sustained increase in the frequency of a residue over the three analyzed Huh7.5 passages) were T11522G (F184V in nsp6), C19895T (A92V in nsp15), C26333T (T30I in E), and C28331T (P20S in N) (Table 2). 2021 Antimicrobial agents and chemotherapy Result SARS_CoV_2 C19895T;C26333T;C28331T;T11522G;A92V;F184V;P20S;T30I 254;279;304;229;263;238;313;288 261;286;311;236;267;243;317;292 Nsp6;E;N;S 247;296;321;8 251;297;322;9 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. SARS-CoV-2_DK-AHH1 harbors the high-frequency polymorphisms D614G in S, which is now dominant throughout the world and has been linked to increased infectivity in cell culture and in animal models, and P323L in nsp12, which has not yet been clearly linked to any phenotype. 2021 Antimicrobial agents and chemotherapy Result SARS_CoV_2 D614G;P323L 60;202 65;207 Nsp12;S 211;69 216;70 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. The deletion and the E484D substitution were already dominant (frequency of >90%) after the first passage in Huh7.5 cells (P1Huh7.5) (Table 2). 2021 Antimicrobial agents and chemotherapy Result SARS_CoV_2 E484D 21 26 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. The region coding for the spike protein accumulated a significant number of high-frequency (>90% of the viral population) changes, including a deletion leading to the removal of 9 amino acids in the N-terminal domain (from nt 21762 to nt 21788) and 3 nonsynonymous mutations: A23014C (E484D amino acid change according to S-protein-specific numbering), C23997G (P812R), and A24424C (Q954H). 2021 Antimicrobial agents and chemotherapy Result SARS_CoV_2 A23014C;A24424C;C23997G;E484D;P812R;Q954H 276;374;353;285;362;383 283;381;360;290;367;388 S;N;S 26;199;322 31;200;323 33905891 Spike protein mutational landscape in India during the complete lockdown phase: Could Muller's ratchet be a future game-changer for COVID-19? In this ancestor 2 clade, several variants (L5F, T22I, L54F, G261S, T572I, E583D, Q677H, A706S, H1083Q) indicated their stability in the population via mutating further, giving rise to additional variants. 2021 Infection, genetics and evolution Result SARS_CoV_2 A706S;E583D;G261S;H1083Q;L54F;Q677H;T22I;T572I;L5F 89;75;61;96;55;82;49;68;44 94;80;66;102;59;87;53;73;47 33905891 Spike protein mutational landscape in India during the complete lockdown phase: Could Muller's ratchet be a future game-changer for COVID-19? Of these, the variant K77M evolved further to yield three more variants isolated from three different states (Bihar, Tamil Nadu and Telengana), suggesting the emergence of K77M as another stable variant. 2021 Infection, genetics and evolution Result SARS_CoV_2 K77M;K77M 22;172 26;176 33905891 Spike protein mutational landscape in India during the complete lockdown phase: Could Muller's ratchet be a future game-changer for COVID-19? Phylogenetic analysis showed the Wuhan-Hu-1/2019 variant of the spike protein as the most ancestral one, as expected, while the D614G variant emerged from the Wuhan-Hu-1/2019 variant appeared to be another stable variant circulating in the Indian population. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 128 133 S 64 69 33905891 Spike protein mutational landscape in India during the complete lockdown phase: Could Muller's ratchet be a future game-changer for COVID-19? Since both these variants have established themselves in the worldwide population as two major ancestors of SARS CoV-2 spike protein variants, we here onwards will refer the Wuhan-Hu-1/2019 and D614G variants as ancestor 1 and ancestor 2 respectively. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 194 199 S 119 124 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. In addition, no structural variants in the receptor-binding domain (RBD) of the Spike protein (N439K, T481I, V483A, E484E, N501Y nor G476S) were identified. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484E;G476S;N501Y;T481I;V483A;N439K 116;133;123;102;109;95 121;138;128;107;114;100 S;RBD 80;68 85;71 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Interestingly, the second most detected variant in the Spike gene in our analyses was the T1117I, present in 29.2% of the Costa Rican genomes. 2021 Infection, genetics and evolution Result SARS_CoV_2 T1117I 90 96 S 55 60 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. On the other hand, the L84S variant in the ORF8 was only found in two genomes (the same without the D614G in the Spike). 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;L84S 100;23 105;27 S;ORF8 113;43 118;47 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. The clades and lineages are separated in the tree, including a clear cluster for all the 54 sequences carrying the Spike-T1117I variant (as part of the clade GR). 2021 Infection, genetics and evolution Result SARS_CoV_2 T1117I 121 127 S 115 120 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. The most frequent substitutions were D614G in the Spike and P4715L in the ORF1ab-RdRp both in 98.9% (183) of the genomes. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;P4715L 37;60 42;66 ORF1ab;S;RdRP 74;50;81 80;55;85 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. The T1117I and D614G are located in different domains. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;T1117I 15;4 20;10 33907518 SARS-CoV-2 main protease suppresses type I interferon production by preventing nuclear translocation of phosphorylated IRF3. G15S and K90R are two common polymorphic variants of SARS-CoV-2 NSP5 in circulating strains of SARS-CoV-2. 2021 International journal of biological sciences Result SARS_CoV_2 K90R;G15S 9;0 13;4 Nsp5 64 68 33907518 SARS-CoV-2 main protease suppresses type I interferon production by preventing nuclear translocation of phosphorylated IRF3. Notably, G15S is a novel substitution only seen in SARS-CoV-2, whereas K90R has also been observed in SARS-CoV. 2021 International journal of biological sciences Result SARS_CoV_2 G15S;K90R 9;71 13;75 33907518 SARS-CoV-2 main protease suppresses type I interferon production by preventing nuclear translocation of phosphorylated IRF3. To determine whether the non-synonymous substitutions might affect type I IFN antagonism of SARS-CoV-2 NSP5, we created its G15S and K90R variants. 2021 International journal of biological sciences Result SARS_CoV_2 G15S;K90R 124;133 128;137 Nsp5 103 107 33907518 SARS-CoV-2 main protease suppresses type I interferon production by preventing nuclear translocation of phosphorylated IRF3. Whereas the G15S variant is common in European strains, the K90R variant is more frequently found in Chinese and Icelandic strains. 2021 International journal of biological sciences Result SARS_CoV_2 G15S;K90R 12;60 16;64 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Among the nucleotide mutations in lineage B.1.526, the most characteristic include A16500C (NSP13 Q88H), A22320G (spike D253G), and T9867C (NSP4_L438P). 2021 bioRxiv Result SARS_CoV_2 A16500C;A22320G;D253G;Q88H;T9867C;L438P 83;105;120;98;132;145 90;112;125;102;138;150 S;Nsp13;Nsp4 114;92;140 119;97;144 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Around 54% (n=678) of the B.1.526 genomes contain the E484K mutation, which has also been rising in frequency since early 2021. 2021 bioRxiv Result SARS_CoV_2 E484K 54 59 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. As part of the phylodynamic analysis, we inferred the time of most recent common ancestor (TMRCA) for the B.1.526 E484K clade to be 08 November 2020 (95% HPD: 22 October - 24 November). 2021 bioRxiv Result SARS_CoV_2 E484K 114 119 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Regarding four of the spike mutations prevalent in this lineage: (1) E484K is known to attenuate neutralization of multiple anti-SARS-CoV-2 antibodies, particularly those found in class 2 anti-RBD neutralizing antibodies, and is also present in variants B.1.351 and P.1/B.1.1.248, (2) D253G has been reported as an escape mutation from antibodies against the N-terminal domain, (3) S477N has been identified in several earlier lineages, is near the epitopes of multiple antibodies, and has been implicated to increase viral infectivity through enhanced interactions with ACE2, and (4) A701V sits adjacent to the S2' cleavage site of the neighboring protomer and is shared with variant B.1.351. 2021 bioRxiv Result SARS_CoV_2 A701V;D253G;E484K;S477N 585;285;69;382 590;290;74;387 S;RBD;N 22;193;359 27;196;360 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Specifically, we estimated the growth rate for the B.1.1.7, B.1.427, and B.1.429 variants and for two subsets of the B.1.526 clade sequences (with and without the E484K mutation). 2021 bioRxiv Result SARS_CoV_2 E484K 163 168 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The B.1.526 E484K clade experienced more rapid exponential growth compared with other lineages: 23.2 (95% highest posterior density [HPD]: 19.6-27.1). 2021 bioRxiv Result SARS_CoV_2 E484K 12 17 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The E484K-containing B.1.526 pseudovirus had a statistically significant reduced neutralization titer compared to the D614G control: for vaccinee plasma, 4.5-fold reduced (p = 0.00005); for 1.3-month convalescent plasma, 6.0-fold reduced (p = 0.03); and for 6.2-month convalescent plasma, 4.8-fold reduced (p = 0.02) (Figure 5a and Supplementary Table 2). 2021 bioRxiv Result SARS_CoV_2 D614G;E484K 118;4 123;9 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The geographic distribution of over 600 B.1.526 E484K cases is similar (Figure 4B). 2021 bioRxiv Result SARS_CoV_2 E484K 48 53 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The S477N/Q957R-containing B.1.526 pseudovirus demonstrated a smaller effect on plasma neutralization (Figure 5b). 2021 bioRxiv Result SARS_CoV_2 S477N;Q957R 4;10 9;15 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The weekly average of B.1.526 genomes with E484K has been above 10% since 01 February 2021 and has been increasing around 0.4% per day (Figure 3B). 2021 bioRxiv Result SARS_CoV_2 E484K 43 48 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. This variant is found within the 20.C clade and is distinguished by 3 defining spike mutations: L5F, T95I, and D253G. 2021 bioRxiv Result SARS_CoV_2 D253G;L5F;T95I 111;96;101 116;99;105 S 79 84 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. We generated HIV-based pseudoviruses expressing SARS-CoV-2 spike protein containing either the most common B.1.526 mutation pattern (v.1: L5F, T95I, D253G, E484K, D614G, and A701V), the 2nd most common pattern (v.2: L5F, T95I, D253G, S477N, D614G, and Q957R), or only D614G. 2021 bioRxiv Result SARS_CoV_2 A701V;D253G;D253G;D614G;D614G;D614G;E484K;L5F;L5F;Q957R;S477N;T95I;T95I 174;149;227;163;241;268;156;138;216;252;234;143;221 179;154;232;168;246;273;161;141;219;257;239;147;225 S 59 64 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. We note that the evolutionary history at spike position 701 varies depending on whether the tree is rooted using a molecular clock (Figure 1) versus its sister clade (characterized by an L452R mutation; Supplementary Figure 2), the latter of which posits a substitution A701V followed by a reversion V701A. 2021 bioRxiv Result SARS_CoV_2 A701V;L452R;V701A 270;187;300 275;192;305 S 41 46 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Within B.1.526, the largest sub-clade is defined by E484K and two distinct sub-clades are each defined by S477N; both of these mutations located within the receptor-binding domain (RBD) of spike (Figure 2 and Supplementary Table 1). 2021 bioRxiv Result SARS_CoV_2 E484K;S477N 52;106 57;111 S;RBD 189;181 194;184 33907767 Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. Forty-two (36.5%) samples were positive for isolated L452R mutation, and were presumptive B.1.427/B.1.429 variant. 2021 medRxiv Result SARS_CoV_2 L452R 53 58 33907767 Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. In multivariate analysis, when controlling for community prevalence of L452R mutation the week prior to positive test (when exposure likely occurred), vaccination status at time of positive test was not significantly associated with presumptive B.1.427/B.1.429 (Table 3). 2021 medRxiv Result SARS_CoV_2 L452R 71 76 33907767 Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. In unadjusted analysis, PVSCs infected with L452R-containing viruses were more likely than those with no identified mutations to have tested positive after the second vaccine dose, or to be partially- or fully-vaccinated at time of positive test (Table 1); this variant was not associated with age, gender, job role, brand of vaccine received, immunocompromised status, or symptomatic infection. 2021 medRxiv Result SARS_CoV_2 L452R 44 49 33907767 Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. No E484K mutations were found by RT-PCR. 2021 medRxiv Result SARS_CoV_2 E484K 3 8 33907767 Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. Three PVSCs were found to have N501Y mutation; all were symptomatic, two tested positive while partially vaccinated (>14 days after first vaccine dose but prior to the second dose) and one was fully vaccinated (>14 days after second dose). 2021 medRxiv Result SARS_CoV_2 N501Y 31 36 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. Although substitution mutations, R203K, G204R at nucleocapsid and P323L at NSP12 were detected in ~90% of the isolates in Japan, the frequency reduced during January to February 2021. 2021 Epidemiology and infection Result SARS_CoV_2 G204R;P323L;R203K 40;66;33 45;71;38 N;Nsp12 49;75 61;80 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. Among 22 point mutations at N and other eight non-structural proteins, eight namely, N_S194L, N_R203K, N_G204R, NS3_Q57H, NSP2_T85I, NSP5_G15S, NSP6_L37F and NSP12_P323L were persistent throughout the COVID-19 pandemic in Japan. 2021 Epidemiology and infection Result SARS_CoV_2 G15S;G204R;L37F;P323L;Q57H;R203K;S194L;T85I 138;105;149;164;116;96;87;127 142;110;153;169;120;101;92;131 Nsp12;Nsp2;Nsp5;Nsp6;NS3;N 158;122;133;144;112;28 163;126;137;148;115;29 COVID-19 201 209 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. At spike protein, D614G was detected in about 100% isolates. 2021 Epidemiology and infection Result SARS_CoV_2 D614G 18 23 S 3 8 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. However, during the second wave starting from October 2020 substitution point mutations E780Q, K417N, T478I, N501Y, E484K, N439K, V1176F, S477N and A222V became common at spike protein in the isolates in Japan. 2021 Epidemiology and infection Result SARS_CoV_2 A222V;E484K;E780Q;K417N;N439K;N501Y;S477N;T478I;V1176F 148;116;88;95;123;109;138;102;130 153;121;93;100;128;114;143;107;136 S 171 176 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. Point mutation at RBDs namely, Y145del had strong correlation with maximum temperature (rs = 0.61), snow fall (rs = 0.41), N501Y with maximum temperature (rs = 0.46) and sun hours (rs = 0.49), N439K with minimum temperature (rs = 0.43), A222V with sun hours (rs = 0.51), E484K with sun hours (rs = 0.53), T478I with RH (rs = 0.49) and E780Q with RH (rs = 0.43). 2021 Epidemiology and infection Result SARS_CoV_2 A222V;E484K;E780Q;N439K;N501Y;T478I;Y145del 237;271;335;193;123;305;31 242;276;340;198;128;310;38 RBD 18 22 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. Significant correlation was detected between NSP5_G15S and UV (rs = 0.91), followed by NS8_S24L and maximum temperature (rs = 0.51), NSP3_T1198K and RH (rs = 0.45), respectively (Table 5). 2021 Epidemiology and infection Result SARS_CoV_2 G15S;S24L;T1198K 50;91;138 54;95;144 Nsp3;Nsp5 133;45 137;49 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. Substitution mutation, T478I (55%) at spike protein were predominant during April 2020 to September 2020. 2021 Epidemiology and infection Result SARS_CoV_2 T478I 23 28 S 38 43 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. The highest correlation between mutations of nucleocapsid protein and weather was detected for N_I292T and UV (rs = 0.68), followed by snowfall (rs = 0.67) and rainfall (rs = 0.61). 2021 Epidemiology and infection Result SARS_CoV_2 I292T 97 102 N 45 57 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. For these reasons, the (R355D K424E) should be tested against potential vaccine candidates. 2021 Scientific reports Result SARS_CoV_2 K424E;R355D 30;24 35;29 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. Mutation V367F was reported in 12 countries and appeared in 51 sequences. 2021 Scientific reports Result SARS_CoV_2 V367F 9 14 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. No other sequence reported a G413V mutation. 2021 Scientific reports Result SARS_CoV_2 G413V 29 34 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. The 2-point mutation (V367F G413V) that was reported in Spain appears to have evolved from the widely spread mutated sequence (V367F) reported in 12 countries. 2021 Scientific reports Result SARS_CoV_2 G413V;V367F;V367F 28;22;127 33;27;132 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. The PROVEAN tool predicted that the top 2-point mutation (R355D K424E) might have an impact on the biological structure and function of the spike protein. 2021 Scientific reports Result SARS_CoV_2 K424E;R355D 64;58 69;63 S 140 145 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. The sequence with the 3-point mutation (Q506H P507S Y508N) could have undergone its first destabilizing mutation (Q506H ) and then experienced two stabilizing single point mutations (P507S ) and (Y508N ). 2021 Scientific reports Result SARS_CoV_2 P507S;Y508N;P507S;Q506H;Q506H;Y508N 46;52;183;40;114;196 51;57;188;45;119;201 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. The spike trimer contains an arginine (R) at position 355. 2021 Scientific reports Result SARS_CoV_2 R355R 28 58 S 4 9 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. This method predicted that the 2-point mutation (R355D K424E) contributes strong structural stability to the spike protein and should be tested against potential vaccines and inhibitors. 2021 Scientific reports Result SARS_CoV_2 K424E;R355D 55;49 60;54 S 109 114 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. To further explore the effect of the (R355D K424E) mutation on the spike's structure and stability compared to the non-mutant native type, we ran molecular dynamics simulation of 50 nanoseconds on both the full non-mutant native type and mutant structures. 2021 Scientific reports Result SARS_CoV_2 K424E;R355D 44;38 49;43 S 67 72 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. A cryo-EM structure of the spike protein ectodomain with the N501Y mutation was obtained at an average resolution of approximately 2.8 A (Table 1; S2 Fig). 2021 PLoS biology Result SARS_CoV_2 N501Y 61 66 S 27 32 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Consistent with these measurements, neutralization experiments carried out with VH Fc ab8 show that it can neutralize the N501Y mutant with a potency similar to that of the unmutated form, while IgG ab1 exhibits a slightly diminished neutralization potency for the N501Y mutant relative to pseudoviruses expressing the unmutated form (Fig 2B; S1 Table). 2021 PLoS biology Result SARS_CoV_2 N501Y;N501Y 122;265 127;270 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Cryo-EM density maps unambiguously show the location of residue 501 in the N501Y mutant spike protein ectodomains (Fig 3C). 2021 PLoS biology Result SARS_CoV_2 N501Y 75 80 S 88 93 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Cryo-EM structural analysis of the complex formed between the N501Y spike protein ectodomain and the ACE2 receptor ectodomain provides a detailed glimpse of both the overall structure of the receptor and the binding interface between the RBD and ACE2 (Fig 1; S4 Fig). 2021 PLoS biology Result SARS_CoV_2 N501Y 62 67 S;RBD 68;238 73;241 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Cryo-EM structural analysis of the complex formed between VH ab8 and the N501Y spike protein ectodomain shows a single dominant conformation with 2 VH ab8 fragments bound to RBDs in the down conformation and weak density for the other RBD, which is flexible and primarily in the up position (Fig 3A; S7 Fig). 2021 PLoS biology Result SARS_CoV_2 N501Y 73 78 S;RBD;RBD 79;174;235 84;178;238 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. ELISA analysis of IgG ab1 and VH Fc ab8 interactions with unmutated or N501Y spike ectodomains demonstrates that the N501Y mutation has no significant effect on VH Fc ab8 binding but results in a slightly higher EC50 for IgG ab1 (Fig 2A; S1 Table). 2021 PLoS biology Result SARS_CoV_2 N501Y;N501Y 71;117 76;122 S 77 82 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. N501Y has minimal effects on the binding and potency of 2 neutralizing antibodies with RBD epitopes. 2021 PLoS biology Result SARS_CoV_2 N501Y 0 5 RBD 87 90 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Neutralizing antibodies bind N501Y spikes in different conformational states. 2021 PLoS biology Result SARS_CoV_2 N501Y 29 34 S 35 41 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Next, we tested the effect of the N501Y mutation on the relative strengths of binding and neutralization potency of VH Fc ab8 and IgG ab1 (Fig 2). 2021 PLoS biology Result SARS_CoV_2 N501Y 34 39 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Notably, several studies have demonstrated that the N501Y mutation confers much larger increases (3- to 16-fold) in ACE2 binding affinity when using minimal RBD constructs. 2021 PLoS biology Result SARS_CoV_2 N501Y 52 57 RBD 157 160 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Overall, binding and neutralization analyses show that the N501Y mutation results in enhanced ACE2 binding, minimal effects on the binding and potency of VH Fc ab8, and a small reduction in the binding and potency of IgG ab1. 2021 PLoS biology Result SARS_CoV_2 N501Y 59 64 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Second, competition experiments establish that IgG ab1 more efficiently prevents ACE2 binding of the unmutated ectodomain compared to the N501Y mutant (Fig 2C), while VH Fc ab8 prevents ACE2 binding of unmutated and N501Y mutant spike proteins to similar extents (Fig 2D). 2021 PLoS biology Result SARS_CoV_2 N501Y;N501Y 138;216 143;221 S 229 234 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Taken together with recent reports, these 3 results are consistent with the hypothesis that the greater infectivity of the N501Y mutant stems from improved binding to ACE2. 2021 PLoS biology Result SARS_CoV_2 N501Y 123 128 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. The comparison of neutralization profiles shows that the IC50 for neutralization of the N501Y mutant is lower, suggesting that full-length spikes bearing the N501Y mutation bind ACE2-mFc to a higher extent. 2021 PLoS biology Result SARS_CoV_2 N501Y;N501Y 88;158 93;163 S 139 145 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. The higher relative luminescence unit (RLU) intensity from cells infected by the N501Y mutant (6,000 +- 2,000 RLU, mean +- standard deviation) compared to control viruses expressing the unmutated form (3,000 +- 800 RLU) suggests that the N501Y mutation may result in increased infectivity, assuming equal incorporation of spike proteins within the pseudotyped particles utilized. 2021 PLoS biology Result SARS_CoV_2 N501Y;N501Y 81;238 86;243 S 322 327 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. The N501Y mutation confers increased ACE2 binding affinity. 2021 PLoS biology Result SARS_CoV_2 N501Y 4 9 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. The N501Y mutation would thus be expected to have a small effect on the antibody binding epitope. 2021 PLoS biology Result SARS_CoV_2 N501Y 4 9 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. This finding is in agreement with a recent report demonstrating increased cell entry of pseudoviral particles incorporating the N501Y and D614G mutations relative to D614G alone. 2021 PLoS biology Result SARS_CoV_2 D614G;D614G;N501Y 138;166;128 143;171;133 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. This is further confirmed by negative stain experiments, where VH ab8 interferes with ACE2 binding in both the unmutated and N501Y spikes (S6 Fig). 2021 PLoS biology Result SARS_CoV_2 N501Y 125 130 S 131 137 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. This revealed that the N501Y mutation confers a modest increase in affinity for ACE2, mainly driven by a reduction in the dissociation rate constant (koff) (S5C and S5D Fig; S1 Table). 2021 PLoS biology Result SARS_CoV_2 N501Y 23 28 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. To investigate whether the N501Y mutation increases the binding strength of the SARS-CoV-2 spike to ACE2, we measured the binding parameters between ACE2 and either unmutated or N501Y spike protein ectodomain trimers via biolayer interferometry (BLI). 2021 PLoS biology Result SARS_CoV_2 N501Y;N501Y 27;178 32;183 S;S 91;184 96;189 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. To test the influence of the N501Y mutation on ACE2 binding, we used a luciferase reporter to measure the infectivity of pseudotyped viruses presenting N501Y or unmutated spike proteins for cells overexpressing ACE2 (S5 Fig). 2021 PLoS biology Result SARS_CoV_2 N501Y;N501Y 29;152 34;157 S 171 176 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. To understand the effects of these antibodies at a structural level, we next determined cryo-EM structures of the complexes formed by VH ab8 (variable domain of the bivalent fusion construct VH FC Ab8) and Fab ab1 (the antigen binding fragment of IgG ab1) with the N501Y mutant spike protein ectodomain. 2021 PLoS biology Result SARS_CoV_2 N501Y 265 270 S 278 283 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. To understand the structural effects of the N501Y mutation on ACE2 binding, we expressed and purified spike (S) protein ectodomains with and without the N501Y mutation in Expi293F cells (S1 Fig), and conducted microscopy studies on the ACE2-spike complexes. 2021 PLoS biology Result SARS_CoV_2 N501Y;N501Y 44;153 49;158 S;S;S 102;241;109 107;246;110 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Together, the cryo-EM structures are fully consistent with the studies presented in Fig 2 that show a small but significant effect of the N501Y mutation on Fab ab1 binding and neutralization, but with no measurable effects on VH ab8 binding or neutralization. 2021 PLoS biology Result SARS_CoV_2 N501Y 138 143 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. We also determined the relative efficiency of neutralization of pseudoviruses expressing either the N501Y mutant or unmutated form of the spike protein. 2021 PLoS biology Result SARS_CoV_2 N501Y 100 105 S 138 143 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. We also measured the efficiency of exogenously added soluble ACE2-mFc proteins to neutralize unmutated and N501Y pseudoviruses via preincubation prior to cell infection (S5B Fig). 2021 PLoS biology Result SARS_CoV_2 N501Y 107 112 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. We compared the efficiencies of these 2 antibodies, as well as the ACE2 receptor ectodomain, to bind spike proteins with and without the N501Y mutation. 2021 PLoS biology Result SARS_CoV_2 N501Y 137 142 S 101 106 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Consistent with previous reports, we also observed that the D614G variant has more cleavage efficiency than WT as shown in Figure 3 bottom lane. 2021 Viruses Result SARS_CoV_2 D614G 60 65 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Furthermore, both K417N and E484K substitution promote the cleavage of spike protein and cell-to-cell fusion, leading to enhanced SARS-CoV-2 infectivity (Figure 1, Figure 3 and Figure 4). 2021 Viruses Result SARS_CoV_2 E484K;K417N 28;18 33;23 S 71 76 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Given that the D614G has been shown to enhance cleavage efficiency due to substitution on spike conformational diversity, we next investigated the effect of RBD mutant of the spike on cleavage state of both Wuhan variant and SA variant. 2021 Viruses Result SARS_CoV_2 D614G 15 20 S;S;RBD 90;175;157 95;180;160 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Herein, we show that K417N and E484K spike mutations derived from SARS-CoV-2 B.1.351 variant has a greater affinity for ACE2 as compared to the D614G derived from SARS-CoV-2 Wuhan variant via MD simulation-based predictions (Table 1 and Figure 2). 2021 Viruses Result SARS_CoV_2 D614G;E484K;K417N 144;31;21 149;36;26 S 37 42 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. However, the molecular mechanism by which spike mutant harboring either K417N/N501Y/D614G or E484K/N501Y/ D614G mutation promotes the cleavage efficacy of S1/S2 to facilitate membrane fusion activity needs to be further studied. 2021 Viruses Result SARS_CoV_2 D614G;E484K;K417N;D614G;N501Y;N501Y 106;93;72;84;78;99 111;98;77;89;83;104 Membrane;S 175;42 183;47 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. However, the spike variants (N501Y, K417N, E484K) harboring SARS-CoV-2 B.1.351 lineage was partially resistant against Casirivimab. 2021 Viruses Result SARS_CoV_2 E484K;K417N;N501Y 43;36;29 48;41;34 S 13 18 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Importantly, even with this reduced activity, Imdevimab that was tested was still capable to fully neutralize the pseudoviruses harboring K417N/N501Y/D614G and E484K/N501Y/D614G mutations (Figure 5). 2021 Viruses Result SARS_CoV_2 E484K;K417N;D614G;D614G;N501Y;N501Y 160;138;150;172;144;166 165;143;155;177;149;171 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. In addition, the D614G combined with other residues show similar activity with D614G. 2021 Viruses Result SARS_CoV_2 D614G;D614G 17;79 22;84 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. In order to ascertain whether cleavage capability of both K417N/N501Y/D614G and E484K/N501Y/D641G variants is required for cell-to-cell fusion, we tested the formation of syncytia. 2021 Viruses Result SARS_CoV_2 E484K;K417N;D614G;D641G;N501Y;N501Y 80;58;70;92;64;86 85;63;75;97;69;91 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. In particular, three mutations:K417N, E484K, and N501Y:appeared as particular mutation sites of B.1.351. 2021 Viruses Result SARS_CoV_2 E484K;N501Y;K417N 38;49;31 43;54;36 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Indeed, D614G was found in all the variants, followed by the chosen additional six noteworthy amino acid changes (i.e., V367F, P384L, R408I, N501Y, K417N, E484K) in the spike RBD of both SARS-CoV-2 lineages. 2021 Viruses Result SARS_CoV_2 D614G;E484K;K417N;N501Y;P384L;R408I;V367F 8;155;148;141;127;134;120 13;160;153;146;132;139;125 S;RBD 169;175 174;178 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Interestingly, expression of spike either K417N/N501Y/D614G or E484K/N501Y/D614G variant significantly facilitated cell-to-cell fusion (syncytia formation) as compared to WT spike protein. 2021 Viruses Result SARS_CoV_2 E484K;K417N;D614G;D614G;N501Y;N501Y 63;42;54;75;48;69 68;47;59;80;53;74 S;S 29;174 34;179 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Interestingly, the full length:S2 ratio is markedly greater in both K417N/N501Y/D614G and E484K/N501Y/ D614G compared to the other mutants including N501Y/D614G (Figure 3). 2021 Viruses Result SARS_CoV_2 D614G;E484K;K417N;N501Y;D614G;D614G;N501Y;N501Y 103;90;68;149;80;155;96;74 108;95;73;154;85;160;101;79 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Moreover, the total amount of the spike protein in pseudoviruses harboring both K417N/N501Y/D614G and E484K/N501Y/ D614G is also much higher than others, although the same titer of pseudovirus was transduced (Figure 3). 2021 Viruses Result SARS_CoV_2 D614G;E484K;K417N;D614G;N501Y;N501Y 115;102;80;92;86;108 120;107;85;97;91;113 S 34 39 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Moreover, this study demonstrates that K417N and E484K mutations are crucial in the enhancement of SARS-CoV-2 B.1.351 lineage infectivity and transmissibility. 2021 Viruses Result SARS_CoV_2 E484K;K417N 49;39 54;44 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Notably, the E484K/N501Y/D614G mutant robustly increased binding affinity to ACE2 compared to either K417N/N501Y/D614G or N501Y/D614G. 2021 Viruses Result SARS_CoV_2 E484K;K417N;N501Y;D614G;D614G;D614G;N501Y;N501Y 13;101;122;25;113;128;19;107 18;106;127;30;118;133;24;112 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Our results found that neutralizing activity of Casirivimab, was significantly reduced against K417N/N501Y/D614G and E484K/N501Y/D614G mutations (Figure 5). 2021 Viruses Result SARS_CoV_2 E484K;K417N;D614G;D614G;N501Y;N501Y 117;95;107;129;101;123 122;100;112;134;106;128 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. These data further confirmed that the efficiency of B.1.351 SARS-CoV-2 lineage (particularly K417N/N501Y/D614G and E484K/N501Y/D614G) entry into target cells were greater than other variants. 2021 Viruses Result SARS_CoV_2 E484K;K417N;D614G;D614G;N501Y;N501Y 115;93;105;127;121;99 120;98;110;132;126;104 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. This suggests that E484K mutant may have an impact on the stability of ACE2's binding interface. 2021 Viruses Result SARS_CoV_2 E484K 19 24 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Three RBM mutants (K417N, E484K, and N501Y) together with D614G of spike protein showed higher binding affinity than WT. 2021 Viruses Result SARS_CoV_2 D614G;E484K;N501Y;K417N 58;26;37;19 63;31;42;24 S 67 72 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. To examine the potential conformational changes due to the amino acid changes in the RBM in the spike protein of B.1.351 variant compared with WT and D614G variant of spike protein, we conducted 100 ns in silico Molecular Dynamic (MD) simulations for refinement of each monomeric mutant structure of SARS-CoV-2 spike protein complex with ACE2 residues 21-615, and trajectories obtained from MD simulations were used to calculate their binding affinities. 2021 Viruses Result SARS_CoV_2 D614G 150 155 S;S;S 96;167;311 101;172;316 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. Using site-directed mutagenesis and a full-length codon-optimized authentic SARS-CoV-2 spike (wild-type, WT) coding sequence, we constructed luciferase-expressing Maloney murine leukemia virus (MLV)-based pseudotyped virus bearing VSV glycoprotein (VSV-G) and several mutant spike proteins which represented Wuhan lineage (D614G, V367F/D614G, P384L/D614G, R408I/D614G) and SA lineage (N501Y/D615G, K417N/N501Y/D614G and E484K/N501Y/ D614G). 2021 Viruses Result SARS_CoV_2 D614G;E484K;K417N;P384L;R408I;V367F;D614G;N501Y;D614G;D614G;D614G;D614G;D615G;N501Y;N501Y 433;420;398;343;356;330;323;385;336;349;362;410;391;404;426 438;425;403;348;361;335;328;390;341;354;367;415;396;409;431 S;S 87;275 92;280 33917138 The Impact on Infectivity and Neutralization Efficiency of SARS-CoV-2 Lineage B.1.351 Pseudovirus. We observed that three mutants regarded as B.1.351 (N501Y/D614G, K417N/N501Y/D614G, E484K/N501Y/D614G) infected these cells with approximately 2.5-fold higher than did D614G alone or in combination with the other variants (V367F/D614G, P384L/D614G, R408I/D614G) (Figure 1B). 2021 Viruses Result SARS_CoV_2 D614G;E484K;K417N;P384L;R408I;N501Y;V367F;D614G;D614G;D614G;D614G;D614G;D614G;N501Y;N501Y 168;84;65;236;249;52;223;58;77;96;229;242;255;71;90 173;89;70;241;254;57;228;63;82;101;234;247;260;76;95 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. A similar phenomenon was also reported regarding the previous D614G substitution. 2021 Viruses Result SARS_CoV_2 D614G 62 67 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. As an example of the influenza virus, on one hand, the R384G substitution in H3N2 enhances the ability of in-host immune-escape, which indicates an increase in infectivity, but this substitution appears detrimental. 2021 Viruses Result SARS_CoV_2 R384G 55 60 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. By rapidly screening recent peer-reviewed literature, we identified 4 relevant studies that investigated the risk of clinical severity associated with N501Y, or alternatively, B.1.1.7, variants, and they detected either no statistically significant evidence (3 out of 4) or weakly positive association (1 out of 4). 2021 Viruses Result SARS_CoV_2 N501Y 151 156 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. Fifth, this study focuses on exploring the effects on changing the case fatality risk associated with a single mutation, that is, N501Y, but the intrinsic biological mechanisms are commonly more complex and remain uncovered. 2021 Viruses Result SARS_CoV_2 N501Y 130 135 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. However, by screening the literature of COVID-19, we find no evidence that h(s) or delta(q) is varied associated with the N501Y substitution, and thus we adopted fixed distributions to govern the process. 2021 Viruses Result SARS_CoV_2 N501Y 122 127 COVID-19 40 48 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. On the other hand, the co-mutations of R384G in nucleoprotein (NP) could improve and compensate the viral fitness or functionality of, such that the mutated strains reached fixation rapidly in the 1993-1994 flu season. 2021 Viruses Result SARS_CoV_2 R384G 39 44 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. Sixth, there are co-mutations of N501Y, for example, Delta69/Delta70 deletion and E484K, and we remark that the independent effects of each co-mutation cannot be disentangled in this study, where the interaction among these co-mutations is unassessed. 2021 Viruses Result SARS_CoV_2 E484K;N501Y 82;33 87;38 33918060 Inferring the Association between the Risk of COVID-19 Case Fatality and N501Y Substitution in SARS-CoV-2. The D614G substitution is believed to increase the intensity of the COVID-19 pandemic during the same period, which includes increasing COVID-19 deaths globally. 2021 Viruses Result SARS_CoV_2 D614G 4 9 COVID-19;COVID-19 68;136 76;144 33918332 Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. The sequences in the latter lineage also have the N439K substitution in S. 2021 Microorganisms Result SARS_CoV_2 N439K 50 55 S 72 73 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. Mutation profile analysis revealed a total of 34 B.1.1.33 sequences harboring the S:E484K mutation. 2021 Viruses Result SARS_CoV_2 E484K 84 89 S 82 83 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. One subclade, that mostly contains sequences from Sao Paulo state, probably arose on 16th October (95% HPD: 22th September-5th November) and was defined by additional mutations NSP3:S1285F and NSP15:K12N. 2021 Viruses Result SARS_CoV_2 K12N;S1285F 199;182 203;188 Nsp3 177 181 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. The B.1.1.33 (S:E484K) dyad comprises two sequences from the Maranhao state and were characterized by a different set of non-synonymous mutations (Supplementary Table S2). 2021 Viruses Result SARS_CoV_2 E484K 16 21 S 14 15 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. The other subclade that mostly comprises sequences from the North region probably arose on 29th October (95% HPD: 5th October-17th November) and was defined by additional mutations NSP1:T170I and S:A344S (Figure 1d). 2021 Viruses Result SARS_CoV_2 A344S;T170I 198;186 203;191 S 196 197 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. The other two sequences harboring the S:E484K mutation branched separately in a highly supported (SH-aLRT = 100%) dyad (Figure 1a). 2021 Viruses Result SARS_CoV_2 E484K 40 45 S 38 39 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. The VOI N.9 is characterized by four non-synonymous lineage-defining mutations (NSP3:A1711V, NSP6:F36L, S:E484K, and NSP7b:E33A) and also contains a group of three B.1.1.33 sequences from the Amazonas state that has no sequencing coverage in the position 484 of the S protein, but share the remaining N.9 lineage-defining mutations (Table 1), thus forming a cluster of 35 sequences. 2021 Viruses Result SARS_CoV_2 A1711V;E33A;E484K;F36L 85;123;106;98 91;127;111;102 NSP7b;Nsp3;Nsp6;S;S 117;80;93;104;266 122;84;97;105;267 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. (i) Since the emergence of the spike variant D614G (Figure 5A) in January 2020 and the NSP12 variant P323L (Figure 5B) in January 2020, they have become the dominant variants across all continents, with an increasing prevalence over time (Figure 4B). 2021 Biomedicines Result SARS_CoV_2 D614G;P323L 45;101 50;106 S;Nsp12 31;87 36;92 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. (ii) During the pandemic, from July to December 2020, the prevalence of A222V in spike, A220V in nucleocapsid (Figure 5C), and V30L in ORF10 increased continuously in Europe and Africa, while their emergence in other continents was less common. 2021 Biomedicines Result SARS_CoV_2 A220V;A222V;V30L 88;72;127 93;77;131 N;S 97;81 109;86 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. (iii) Two neighboring variants in nucleocapsid, R203K and G204R (Figure 5C), showed roughly similar frequencies over time in the same geographic areas. 2021 Biomedicines Result SARS_CoV_2 G204R;R203K 58;48 63;53 N 34 46 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. (iv) Temporal trends of the NSP2 variant T85I (Figure 5D) and the ORF3a variant Q57H were distinct on different continents. 2021 Biomedicines Result SARS_CoV_2 Q57H;T85I 80;41 84;45 ORF3a;Nsp2 66;28 71;32 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. Among all frequent variants, D614G in spike and P323L in NSP12, with a high frequency, were common on the six continents (Figure 4A). 2021 Biomedicines Result SARS_CoV_2 D614G;P323L 29;48 34;53 S;Nsp12 38;57 43;62 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. D614G (97.26%) and P323L (97.29%) (Table 2) in South America exhibited the highest variant prevalence. 2021 Biomedicines Result SARS_CoV_2 P323L;D614G 19;0 24;5 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. Fifteen variants with the prevalence >5% were identified, including (i) four variants in nucleocapsid: S194L (6.29%), R203K (28.45%), G204R (28.13%), and A220V (25.96%); (ii) four variants in spike: L18F (12.08%), A222V (26.14%), S477N (6.62%), and D614G (93.88%); (iii) two variants in NSP2: T85I (15.38%) and I120F (5.23%); (iv) five variants in each of the 5 proteins: L37F (6.52%) in NSP6, P323L (93.74%) in NSP12, Q57H (23.60%) in ORF3a, S24L (5.24%) in ORF8, and V30L (26.01%) in ORF10. 2021 Biomedicines Result SARS_CoV_2 A220V;A222V;D614G;G204R;I120F;L18F;L37F;P323L;Q57H;R203K;S194L;S24L;S477N;T85I;V30L 154;214;249;134;311;199;372;394;419;118;103;443;230;293;469 159;219;254;139;316;203;376;399;423;123;108;447;235;297;473 N;S;ORF3a;Nsp12;Nsp2;Nsp6;ORF8 89;192;436;412;287;388;459 101;197;441;417;291;392;463 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. Figure 4A shows that these variants were found mainly in nucleocapsid (P67S, S194L, P199L, R203K, G204R, A220V, M234I, and A376T), spike (L18F, A222V, N439K, S477N, and D614G), NSP12 (A185S, P323L, and V776L), NSP13 (K218R, E261D, and H290Y), NSP2 (T85I and I120F), and ORF3a (Q57H and G172V), respectively. 2021 Biomedicines Result SARS_CoV_2 A220V;A222V;A376T;D614G;E261D;G172V;G204R;H290Y;I120F;M234I;N439K;P199L;P323L;R203K;S194L;S477N;V776L;A185S;K218R;L18F;P67S;Q57H;T85I 105;144;123;169;224;286;98;235;258;112;151;84;191;91;77;158;202;184;217;138;71;277;249 110;149;128;174;229;291;103;240;263;117;156;89;196;96;82;163;207;189;222;142;75;281;253 N;S;ORF3a;Nsp13;Nsp12;Nsp2 57;131;270;210;177;243 69;136;275;215;182;247 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. For example, the 20A clade is featured with the variants D614G (spike) and P323L (NSP12), while the 20A.EU2 clade is defined by three variants of P323L (NSP12), S477N (spike), and D614G (spike). 2021 Biomedicines Result SARS_CoV_2 D614G;D614G;P323L;P323L;S477N 57;180;75;146;161 62;185;80;151;166 S;S;S;Nsp12;Nsp12 64;168;187;82;153 69;173;192;87;158 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. From March to December 2020, the prevalence of T85I and Q57H was higher in North America than on other continents. 2021 Biomedicines Result SARS_CoV_2 Q57H;T85I 56;47 60;51 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. Furthermore, T85I (NSP2) and Q57H (ORF3a) were circulating with a high frequency in North America (Figure 4B). 2021 Biomedicines Result SARS_CoV_2 Q57H;T85I 29;13 33;17 ORF3a;Nsp2 35;19 40;23 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. In addition, there was one variant in each of the seven proteins NSP4 (M324I), NSP5 (L89F), NSP6 (L37F), NSP14 (N129D), NSP16 (R216C), ORF8 (S24L), and ORF10 (V30L). 2021 Biomedicines Result SARS_CoV_2 L37F;L89F;M324I;N129D;R216C;S24L;V30L 98;85;71;112;127;141;159 102;89;76;117;132;145;163 Nsp4;Nsp5;Nsp6;ORF8 65;79;92;135 69;83;96;139 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. Moreover, the 20E (EU1) clade, with P323L (NSP12), A222V (spike), D614G (spike), A220V (nucleocapsid), and V30L (ORF10), gradually gained their predominance in Europe over time. 2021 Biomedicines Result SARS_CoV_2 A220V;A222V;D614G;P323L;V30L 81;51;66;36;107 86;56;71;41;111 N;S;S;Nsp12 88;58;73;43 100;63;78;48 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. R203K and G204R in nucleocapsid showed different prevalence on the six continents. 2021 Biomedicines Result SARS_CoV_2 G204R;R203K 10;0 15;5 N 19 31 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. Seven common variants were mainly prevalent on a single continent, including the NSP2 variant T85I in North America, the NSP2 variant I120F in Oceania, the spike variant A222V in Europe, the spike variant S477N in Oceania, the ORF3a variant Q57H in North America, the nucleocapsid variant A220V in Europe, and the ORF10 variant V30L in Europe. 2021 Biomedicines Result SARS_CoV_2 A220V;A222V;I120F;Q57H;S477N;T85I;V30L 289;170;134;241;205;94;328 294;175;139;245;210;98;332 N;S;S;ORF3a;Nsp2;Nsp2 268;156;191;227;81;121 280;161;196;232;85;125 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. These two variants, plus P323L (NSP12) and D614G (spike), define the 20C clade. 2021 Biomedicines Result SARS_CoV_2 D614G;P323L 43;25 48;30 S;Nsp12 50;32 55;37 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. We next explored the temporal and geographic dynamics of the variants with a frequency >15%, including: D614G (93.88%) and A222V (26.14%) in spike; A220V (25.96%), R203K (28.45%), and G204R (28.13%) in nucleocapsid; T85I (15.38%) in NSP2; Q57H (23.60%) in ORF3a; P323L (93.74%) in NSP12; V30L (26.01%) in ORF10 (Table 2). 2021 Biomedicines Result SARS_CoV_2 A220V;A222V;D614G;G204R;P323L;Q57H;R203K;T85I;V30L 148;123;104;184;263;239;164;216;288 153;128;109;189;268;243;169;220;292 N;S;ORF3a;Nsp12;Nsp2 202;141;256;281;233 214;146;261;286;237 33922914 Dieckol and Its Derivatives as Potential Inhibitors of SARS-CoV-2 Spike Protein (UK Strain: VUI 202012/01): A Computational Study. The relative positions of Tyr453Phe and Asn501Tyr mutations are also depicted. 2021 Marine drugs Result SARS_CoV_2 N501Y;Y453F 40;26 49;35 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. However, E484K mutation decreases the FEB to -0.59 kcal/mol for SA-VOC. 2021 Microorganisms Result SARS_CoV_2 E484K 9 14 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. However, the mutation N501Y increases molecular interactions in all VOC, while the residue Y501 (Tyr501) forms a H-bond with K353 (Lys353) on hACE2 (H-bond lengths ranging from 2.82 to 2.94 A). 2021 Microorganisms Result SARS_CoV_2 N501Y 22 27 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. In addition, several aa substitutions can be seen in the NSP3 (S370L, K977Q), NSP12 (P323L), and NSP13 (E341D), NS3 (S253P), NS8 (E92K), N-protein (P80R, R203K, G204R). 2021 Microorganisms Result SARS_CoV_2 G204R;K977Q;R203K;E341D;E92K;P323L;P80R;S253P;S370L 161;70;154;104;130;85;148;117;63 166;75;159;109;134;90;152;122;68 Nsp13;Nsp12;Nsp3;NS3;N 97;78;57;112;137 102;83;61;115;138 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. In addition, the SA-VOC has several aa substitutions in NSP2 (R4C), NSP3 (K837N), NSP12 (P323L), NSP13 (E168D), NSP14 (S28C), and NSP15 (P205L), NS3 (Q57H, S171L), E (P71L), N-protein (T205I) (Table 1). 2021 Microorganisms Result SARS_CoV_2 S171L;E168D;K837N;P205L;P323L;P71L;Q57H;R4C;S28C;T205I 156;104;74;137;89;167;150;62;119;185 161;109;79;142;94;171;154;65;123;190 Nsp13;Nsp12;Nsp2;Nsp3;NS3;E;N 97;82;56;68;145;164;174 102;87;60;72;148;165;175 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. In addition, the UK-VOC contains several nonsynonymous mutations that cause seven aa substitutions at positions N501Y, A570D, D614G, P681H, T716I, S982A, D1118H in S-protein, in which N501Y mutation occurs in the key residue of RBD. 2021 Microorganisms Result SARS_CoV_2 A570D;D1118H;D614G;N501Y;N501Y;P681H;S982A;T716I 119;154;126;112;184;133;147;140 124;160;131;117;189;138;152;145 RBD;S 228;164 231;165 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Interestingly, E484K mutation in BR-VOC shows a favorable contribution to the total binding energy by -2.17 kcal/mol. 2021 Microorganisms Result SARS_CoV_2 E484K 15 20 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Moreover, the UK-VOC contains several aa substitutions in other genomic regions, including NSP3: T183I, A890D, I1412T, NSP12: P323L, NS8: R52I, Y73C, and N-protein; D3L, R203K, G204R, S235F. 2021 Microorganisms Result SARS_CoV_2 A890D;D3L;G204R;I1412T;P323L;R203K;R52I;S235F;T183I;Y73C 104;165;177;111;126;170;138;184;97;144 109;168;182;117;131;175;142;189;102;148 Nsp12;Nsp3;N 119;91;154 124;95;155 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Several mutations can be seen in the RBD of VOC, including K417N/T, E484K and N501Y, while two later mutations are located in contact residue responsible to directly bind to hACE2 (Figure 2). 2021 Microorganisms Result SARS_CoV_2 E484K;K417N;K417T;N501Y 68;59;59;78 73;66;66;83 RBD 37 40 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. The BR-VOC is highly mutated in the S-gene resulting in 12 aa substitutions in the S-protein including L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F. 2021 Microorganisms Result SARS_CoV_2 D138Y;D614G;E484K;H655Y;K417T;L18F;N501Y;P26S;R190S;T1027I;T20N;V1176F 121;156;142;163;135;103;149;115;128;170;109;182 126;161;147;168;140;107;154;119;133;176;113;188 S;S 36;83 37;84 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. The COH-VOC has two mutations at positions N501Y and D614G in the S-protein, while harboring several mutations in the NSP2 (T85I), NSP3 (T181I, A256V), NSP5 (L89F, P108S), NSP6 (G258E), NSP12 (P323L), NSP14 (N129D), and NSP16 (R216C), NS3 (Q57H, G172V), NS7a (T120I), NS8 (S24L), and N-protein (P67S, P199L) (Table 1). 2021 Microorganisms Result SARS_CoV_2 A256V;D614G;G172V;N501Y;P108S;P199L;G258E;L89F;N129D;P323L;P67S;Q57H;R216C;S24L;T120I;T181I;T85I 144;53;246;43;164;301;178;158;208;193;295;240;227;273;260;137;124 149;58;251;48;169;306;183;162;213;198;299;244;232;277;265;142;128 Nsp12;Nsp2;Nsp3;Nsp5;Nsp6;NS3;N;S 186;118;131;152;172;235;284;66 191;122;135;156;176;238;285;67 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. The mutation E484K in SA-VOC and BR-VOC shows different molecular interactions with hACE2. 2021 Microorganisms Result SARS_CoV_2 E484K 13 18 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. The N501Y mutation is common in all VOC. 2021 Microorganisms Result SARS_CoV_2 N501Y 4 9 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. The SA-VOC has seven aa substitutions in the S-protein, including D80A, D215G, K417N, E484K, N501Y, D614G, and A701V, and three aa 'LLA' are deleted between positions 241-243. 2021 Microorganisms Result SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;N501Y 111;72;100;66;86;79;93 116;77;105;70;91;84;98 S 45 46 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Therefore, considering FEB, it seems that the E484K mutation is in favor of complex formation between RBD and residue E75 on hACE2 (Figure 3). 2021 Microorganisms Result SARS_CoV_2 E484K 46 51 RBD 102 105 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. 293TT cells expressing hACE2 were infected with WT, 19del, or 19del + D614G PsVs (normalized for 25ng Gag protein). 2021 Journal of biomedical science Result SARS_CoV_2 D614G 70 75 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. 293TT cells expressing hACE2 were pretreated with RBD protein one hour prior to WT, 19del, or 19del + D614G PsV infection. 2021 Journal of biomedical science Result SARS_CoV_2 19del;19del;D614G 84;94;102 89;99;107 RBD 50 53 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. Comparatively, both the 19del and 19del + D614G variant PsVs yielded a significantly higher degree of infection, 830- and 2325-fold increase over uninfected, respectively. 2021 Journal of biomedical science Result SARS_CoV_2 19del;19del;D614G 24;34;42 29;39;47 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. Consistent with our in vitro findings, infection was detected in both 19del and 19del + D614G PsV infected mice. 2021 Journal of biomedical science Result SARS_CoV_2 D614G 88 93 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. Following this, mice were administered equal amounts of either 19del or 19del + D614G PsVs i.n. 2021 Journal of biomedical science Result SARS_CoV_2 D614G 80 85 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. Given the substantial infectivity of 19del and 19del + D614G SARS-CoV-2 PsVs we observed in vitro and in vivo, we sought to explore the model's potential to test SARS-CoV-2 interventions. 2021 Journal of biomedical science Result SARS_CoV_2 19del;D614G 47;55 52;60 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. Given this, we further pursued the infection potential of 19del and 19del + D614G PsVs in vivo. 2021 Journal of biomedical science Result SARS_CoV_2 19del;19del;D614G 58;68;76 63;73;81 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. Prior to 19del or 19del + D614G SARS-CoV-2 PsV infection, mice were treated intranasally with RBD. 2021 Journal of biomedical science Result SARS_CoV_2 D614G 26 31 RBD 94 97 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. RBD treatment successfully lowered the infection level of WT, 19del, and 19del + D614G PsVs in vitro, as significantly lower luciferase activity occurred upon RBD addition. 2021 Journal of biomedical science Result SARS_CoV_2 19del;19del;D614G 62;73;81 67;78;86 RBD;RBD 0;159 3;162 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. S1a), with significantly higher levels of infection observed in 19del + D614G PsV infected mice. 2021 Journal of biomedical science Result SARS_CoV_2 19del;D614G 64;72 69;77 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. We aimed to test this approach's potential to limit WT, 19del, and 19del + D614G PsV infection in our model. 2021 Journal of biomedical science Result SARS_CoV_2 19del;19del;D614G 56;67;75 61;72;80 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. with significantly higher levels of infection observed following 19del + D614G PsV infection. 2021 Journal of biomedical science Result SARS_CoV_2 19del;D614G 65;73 70;78 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. A similar trend of correlations between NT50 titers to pseudovirus D614G and IgG binding to RBD and S1 but not to N protein was also observed (Figures S5(D)-S5(F)), though not as strong as those between NT50 titers to pseudovirus Str and IgG binding. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 67 72 RBD;N 92;114 95;115 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. Analysis of 15 samples revealed that NT50 titers to Str were higher than those to D614G (Figures 4(C) and S4, Table S1) and NT50 titers decreased as sampling days increased (Figure 4(D)). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 82 87 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. Based on the miRFP signals at 72 h, a neutralization curve was generated with NT50 titers of 361 (to Str) and 186 (to D614G) for one case (Figure 4(A)). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 118 123 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. Compared with D614G, Str had comparable amounts of S2 protein, slightly increased S protein and greatly reduced S1 protein. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 14 19 S 82 83 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. Consistent with this, Str and D614G had a similar ratio of the intensity of S2 to p24 intensity but greatly reduced ratio of S1 to p24, suggesting lower S1 density on Str pseudovirus particles compared with D614G particles (Figure 3(E)). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G;D614G 30;207 35;212 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. In addition to pCAGGS, designated as plasmid S, which expresses the S protein of SARS-CoV-2 Wuhan-Hu-1 strain (containing D614), we generated 3 plasmids to facilitate the incorporation of S protein into pseudovirus: plasmid Str expressing S protein with truncation of C-terminal 19 amino acids, an ER-Golgi retention signal, plasmid D614G containing the D614G substitution and plasmid AAAR containing the AAAR mutation at the multibasic cleavage site, both in the Str backbone (Figure 1(A)). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G;D614G 333;354 338;359 S;S;S;S 45;68;188;239 46;69;189;240 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. Interestingly, a linear relationship was also observed when comparing the NT50 titers to pseudovirus D614G and PRNT50, PRNT80 or PRNT90 titers to USA-WA-1 strain, though not as strong as those to pseudovirus Str (Figure 4(H,J)). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 101 106 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. The infectivity of pseudovirus AAAR was higher than that of D614G, which in turn was higher than that of Str (Figures 2(A)-2(C)); the peak signals were between 72 and 96 h post-infection for Str and D614G and >120 h for AAAR probably due to its ability of syncytial formation (Figure 2(B)). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G;D614G 60;199 65;204 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. Using the ratio of the intensity of S2 or S1 protein to that of total S protein to calculate the % cleavage, we found Str and D614G had comparable % cleavage based on S2 but greatly reduced % cleavage based on S1 (11% vs. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 126 131 S 70 71 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. We next employed pseudoviruses Str and D614G to perform neutralization test for confirmed COVID-19 cases. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 39 44 COVID-19 90 98 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. We next examined the infection kinetics of 3 pseudoviruses (Str, D614G and AAAR) in different target cells. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 65 70 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. With the AAAR cleavage site mutation only S protein was found in AAAR, whereas S, S1 and S2 proteins were detected in Str and D614G. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 126 131 S;S 42;79 43;80 33930563 Assessment of basic reproduction number (R0), spatial and temporal epidemiological determinants, and genetic characterization of SARS-CoV-2 in Bangladesh. Besides all other essential protein, another most abundant changes were observed in the N protein (R203K, G204R), which is mainly targeted in the diagnostics purposes. 2021 Infection, genetics and evolution Result SARS_CoV_2 G204R;R203K 106;99 111;104 N 88 89 33930563 Assessment of basic reproduction number (R0), spatial and temporal epidemiological determinants, and genetic characterization of SARS-CoV-2 in Bangladesh. In case of S protein, we found 20 predominant mutation sites, among which 13 were in N-terminal domain (NTD) fragment (T95I, Q14H, S13I, T75I, H49Y, N211Y, D138H, V127F, P26, G75V, S255, Y248H, and S95F). 2021 Infection, genetics and evolution Result SARS_CoV_2 D138H;G75V;H49Y;N211Y;Q14H;S13I;S95F;T75I;V127F;Y248H;T95I 156;175;143;149;125;131;198;137;163;187;119 161;179;147;154;129;135;202;141;168;192;123 N;S 85;11 86;12 33930563 Assessment of basic reproduction number (R0), spatial and temporal epidemiological determinants, and genetic characterization of SARS-CoV-2 in Bangladesh. On the other hand, we found the unique aa substitutions at position 518 (L> > I) and some unusual mutations like L5F, D138, G594S, and S98F in the S protein. 2021 Infection, genetics and evolution Result SARS_CoV_2 G594S;L5F;S98F 124;113;135 129;116;139 S 147 148 33930563 Assessment of basic reproduction number (R0), spatial and temporal epidemiological determinants, and genetic characterization of SARS-CoV-2 in Bangladesh. The fusion peptide region, S' including heptad repeats HR1 and HR2 regions contains 3 (G769V, T791I, A783S), 2(S939Y D936Y), 1(K1191N) mutated regions, respectively. 2021 Infection, genetics and evolution Result SARS_CoV_2 A783S;D936Y;T791I;G769V;K1191N;S939Y 101;117;94;87;127;111 106;122;99;92;133;116 S 27 28 33930563 Assessment of basic reproduction number (R0), spatial and temporal epidemiological determinants, and genetic characterization of SARS-CoV-2 in Bangladesh. The remaining other sites were located in different regions within the protein, including L5F, D614G, G769V, E516Q, T791I, L518I. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;E516Q;G769V;L518I;L5F;T791I 95;109;102;123;90;116 100;114;107;128;93;121 33930563 Assessment of basic reproduction number (R0), spatial and temporal epidemiological determinants, and genetic characterization of SARS-CoV-2 in Bangladesh. We detected only two mutations sites (E516Q, L518I) in RdRp conserved peptide region. 2021 Infection, genetics and evolution Result SARS_CoV_2 L518I;E516Q 45;38 50;43 RdRP 55 59 33930563 Assessment of basic reproduction number (R0), spatial and temporal epidemiological determinants, and genetic characterization of SARS-CoV-2 in Bangladesh. We observed the most common amino acid substitutions D614G in S protein and I120F in NSP2. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;I120F 53;76 58;81 Nsp2;S 85;62 89;63 33930563 Assessment of basic reproduction number (R0), spatial and temporal epidemiological determinants, and genetic characterization of SARS-CoV-2 in Bangladesh. We observed three types of aa (S4F, H125Y, A2V) changes in the membrane (M) protein followed by three changes (A99V, L21F, F20L) in the E protein. 2021 Infection, genetics and evolution Result SARS_CoV_2 A2V;F20L;H125Y;L21F;A99V 43;123;36;117;111 46;127;41;121;115 Membrane;E 63;136 71;137 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. A missense mutation at 16457 (S5398L) was associated with an increased risk of progressive fever [RR: 23.5, 95% CI: 6.06-30.0, p.adjust < 0.001]. 2021 Biochimica et biophysica acta. Molecular basis of disease Result SARS_CoV_2 S5398L 30 36 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. Additionally, 21 missense mutations in ORF3a were identified, resulting in APA-viroporin Q57H variants. 2021 Biochimica et biophysica acta. Molecular basis of disease Result SARS_CoV_2 Q57H 89 93 ORF3a 39 44 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. Additionally, patients with a synonymous mutation in the 28,846 gene encoding the R191* N protein had a significantly increased risk of developing sore throat [RR: 9.00, 95% CI: 3.94-20.57, p.adjust < 0.001] and fatigue [RR: 6.0, 95% CI: 2.53-14.2, p.adjust < 0.001] compared to patients without the mutation by 800% and 500%, respectively. 2021 Biochimica et biophysica acta. Molecular basis of disease Result SARS_CoV_2 R191X 82 87 N 88 89 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. Furthermore, ORF1a has accumulated numerous other mutations at various positions, including 3 synonymous at 313 (L16*) and 3 missense at 677 (A138T) encoding for nsp1, 4 synonymous at 934 (D223*) and 5 missense at 2706 (T814I) encoding for nsp2, 6 missense at 9483 (E3073A) and 9968 (A323S) encoding for nsp4, 6 missense at 10,097 (G3728S) encoding for 3C-like proteinase, 5 frameshifts at 11,082 encoding nsp6 (L3606fs), 5 missenses at 11,991 encoding nsp7-replicase (E3909G), 9 missenses at 12,534 encoding nsp8-replicase (T4040I), 3 synonymous at 13,348 encoding nsp10 (V4361*), 3 missense at 16,457 (S5398L), 7 synonymous at 16,647 (T5461*) and 4 synonymous at 16,915 (L5551*) encoding for nsp13-helicase, and 13 synonymous at 18877 encoding for nsp-11 3'exonuclease (L6205*). 2021 Biochimica et biophysica acta. Molecular basis of disease Result SARS_CoV_2 A138T;A323S;D223X;E3073A;E3909G;G3728S;L16X;S5398L;T4040I;T814I 142;284;189;266;469;332;113;604;525;220 147;289;194;272;475;338;117;610;531;225 Exonuclease;Helicase;ORF1a;Nsp13;Nsp2;Nsp4;Nsp7;Nsp8;Nsp6 759;700;13;694;240;304;453;509;406 770;708;18;699;244;308;457;513;410 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. In the S gene encoding the spike glycoprotein, we observed missense mutations at 23,403 (D614G, n = 47), 23,480 (S640A, n = 6), and 23,593 (Q677H, n = 6), 8 frameshift deletions at 21,574 (V6fs), and 7 synonymous mutations at 23,731 (T723*). 2021 Biochimica et biophysica acta. Molecular basis of disease Result SARS_CoV_2 D614G;Q677H;S640A;T723X 89;140;113;234 94;145;118;239 S;S 27;7 45;8 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. Out of the 25 mutations accumulating in ORF9/N gene encoding the nucleocapsid protein, we observed synonymous mutations at 28,846 (R191*, n = 5), 28,849 (N192*, n = 9) and 291,719 (P312*, n = 4) while, 7 missense at 28,908 (G212V). 2021 Biochimica et biophysica acta. Molecular basis of disease Result SARS_CoV_2 G212V;N192X;P312X;R191X 224;154;181;131 229;159;186;136 N;ORF9 65;40 77;44 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. Patients harboring a synonymous mutation at position 934 encoding nsp2 (D233*) had an 820% increased risk of developing myalgia/arthralgia [RR: 9.20, 95% CI: 4.02-21.05, p.adjust < 0.001]. 2021 Biochimica et biophysica acta. Molecular basis of disease Result SARS_CoV_2 D233X 72 77 Nsp2 66 70 Ayalgia/arthralgia 120 138 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. Significant co-occurring variations were observed in 11,991 encoding E3909G-nsp7/replicase and 16,915 encoding L5551*-nsp-13/helicase (r = 0.9, p < 0.001), 18,877 encoding L6205*-nsp-11/3'exonuclease (r = 0.6, p < 0.001) and 29,744-3'UTR (r = 0.4, p = 0.009). 2021 Biochimica et biophysica acta. Molecular basis of disease Result SARS_CoV_2 E3909G 69 75 Exonuclease;Helicase;3'UTR;Nsp7 188;125;232;76 199;133;237;80 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. The mutation at 21,574 encoding V6fs-spike glycoprotein was moderately correlated with the mutations at 2706 encoding T814I-nsp2, 3373 encoding D1036E-nsp3, and 16,647 encoding T5461*-nsp13 helicase (r = 0.5, p < 0.001), but was only weakly correlated with the mutations at 677 encoding A138T-nsp1 (r = 0.3, p = 0.01) and 9968 encoding for A323S-nsp4 (r = 0.3, p = 0.01). 2021 Biochimica et biophysica acta. Molecular basis of disease Result SARS_CoV_2 A138T;A323S;D1036E;T814I 287;340;144;118 292;345;150;123 S;Helicase;Nsp13;Nsp2;Nsp3;Nsp4 37;190;184;124;151;346 55;198;189;128;155;350 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. The recurrent mutations in ORF1a encoding RdRp were 6 synonymous at 13,536 (Y4424*) and 44 missense at 14,408 (P4715L), whereas those encoding nsp3 were synonymous mutations in 3011 (L916*, n = 9), 3037 (F924*, n = 45), 5020 (D1585*, n = 8), and 5284 (N1673*, n = 8). 2021 Biochimica et biophysica acta. Molecular basis of disease Result SARS_CoV_2 F924X;L916X;P4715L 204;183;111 209;188;117 ORF1a;Nsp3;RdRP 27;143;42 32;147;46 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. There was a strong positive correlation between mutations in ORF1a, including 9483 encoding E3073A-nsp4, and nsp3 mutations at 4345 (E1363) (r = 0.7, p < 0.0001) and 3011 (L916*) (r = 0.6, p < 0.001). 2021 Biochimica et biophysica acta. Molecular basis of disease Result SARS_CoV_2 E3073A;L916X 92;172 98;177 ORF1a;Nsp3;Nsp4 61;109;99 66;113;103 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. D614G leads to higher viral load, without apparent effects on virulence. 2021 Science translational medicine Result SARS_CoV_2 D614G 0 5 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. However, we tested this hypothesis in a GLM with week of sample collection and D614G variant as potential predictors of age. 2021 Science translational medicine Result SARS_CoV_2 D614G 79 84 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. The local transmission clusters obtained are shown at https://nextstrain.org/groups/blab/ncov/wa-phylodynamics?c=cluster_size, and their size distribution and D614G makeup are shown in. 2021 Science translational medicine Result SARS_CoV_2 D614G 159 164 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. To test whether amino acid substitutions beyond D614G affected the chance of SARS-CoV-2 of spreading locally, we next tested whether introductions of lineages with more amino acid substitutions were more successful in spreading locally. 2021 Science translational medicine Result SARS_CoV_2 D614G 48 53 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. We again found the D614G variant to be significantly associated with Ct values (N1 and N2 primers, n = 184, P = 0.03). 2021 Science translational medicine Result SARS_CoV_2 D614G 19 24 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. We did not find any evidence that D614G variant affected clinical outcome. 2021 Science translational medicine Result SARS_CoV_2 D614G 34 39 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. We found that the D614G variant and days since symptom onset were significant (P = 1.9 x 10-7) predictors of Ct values. 2021 Science translational medicine Result SARS_CoV_2 D614G 18 23 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. We next tested whether factors other than the D614G variant predicted Ct values. 2021 Science translational medicine Result SARS_CoV_2 D614G 46 51 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. We next tested whether substitutions other than spike D614G contributed to observed Ct differences. 2021 Science translational medicine Result SARS_CoV_2 D614G 54 59 S 48 53 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. With ORF1ab primers, D61G variant was not a significant predictor; however, the residuals were not normally distributed, suggesting the model fit poorly with ORF1ab primers. 2021 Science translational medicine Result SARS_CoV_2 D61G 21 25 ORF1ab;ORF1ab 5;158 11;164 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. With ORF1ab primers, the D614G variant was not significantly associated with Ct values nor were residuals normally distributed (n = 63) (table S2). 2021 Science translational medicine Result SARS_CoV_2 D614G 25 30 ORF1ab 5 11 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. Finally, we followed the buried surface area over the simulation time within the MDcons approach finding the post-fusion assembly to be, overall, more compact (i.e., featuring a moderately higher buried surface area upon complex formation) for the wild-type system, as compared to the D936Y mutant (see Figure S13). 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 D936Y 285 290 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. In addition, the GH clade presents the NS3-Q57H mutation, the GR clade presents the N-G204R mutations, and GV clade presents the S-A222V mutation. 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 A222V;G204R;Q57H 131;86;43 136;91;47 NS3;N;S 39;84;129 42;85;130 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. In particular, S929T is mainly associated with the GV clade and D936Y is mainly associated with the GH clade, while S939F is roughly equally associated with the GR, GH, GV, and G clades. 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 D936Y;S929T;S939F 64;15;116 69;20;121 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. Notably, the total number of occurrences of the D936Y mutation amounted to 17% of all the 1089 sequences available from Finland and to 12% of all the 1768 sequences available from Sweden. 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 D936Y 48 53 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. Of the remaining most frequent mutations, S939F is completely exposed to the solvent and, therefore, like in the pre-fusion conformation, expected to act unfavorably on the protein solvation energy. 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 S939F 42 47 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. The difference in the rmsd values between the wild-type protein and the D936Y mutant (Figure 5a) is negligible for the pre-fusion conformation, 0.05 (+-0.1) A. 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 D936Y 72 77 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. The first occurrence of the D936Y mutation was, instead, deposited in GISAID on 8 March 2020, which was sequenced in Sweden. 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 D936Y 28 33 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. The first occurrence of the S929T mutation was deposited in GISAID on 18 April 2020, which is sequenced in Canada. 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 S929T 28 33 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. The first occurrence of the S939F mutation was deposited in GISAID on 25 February 2020 from the United Arab Emirates. 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 S939F 28 33 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. The G clade carries the D614G mutation, now globally dominant, accompanied by other mutations upstream the S protein gene (C241T, C3037T). 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 C3037T;D614G;C241T 130;24;123 136;29;128 S 107 108 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. When comparing the effect of the mutations on the pre-fusion and post-fusion structures, it emerges that the D936Y mutation is the one expected to have the greatest structural impact. 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 D936Y 109 114 33948590 A broadly neutralizing antibody protects against SARS-CoV, pre-emergent bat CoVs, and SARS-CoV-2 variants in mice. Importantly, live virus neutralization also demonstrated the broadly neutralizing activity of DH1047 with IC50 values against D614G, B.1.1.7, and B1.351 were 0.059, 0.081, and 0.111mug/ml, respectively. 2021 bioRxiv Result SARS_CoV_2 D614G 126 131 33948590 A broadly neutralizing antibody protects against SARS-CoV, pre-emergent bat CoVs, and SARS-CoV-2 variants in mice. We therefore evaluated if DH1047 could neutralize the prevalent variants of concern (VOCs): SARS-CoV-2 D614G, SARS-CoV-2 UK B.1.1.7., SARS-CoV-2 California B1.429, and SARS-CoV South Africa B1.351 using both pseudovirus and live virus neutralization assays. 2021 bioRxiv Result SARS_CoV_2 D614G 103 108 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. As a comparison, we show the growth observed for Spike mutations S:N501Y, which rose in November 2020 (Figure 2C), and S:D614G, which exponentially grew in frequency starting from February 2020 (Figure 2D). 2021 Journal of medical virology Result SARS_CoV_2 D614G;N501Y 121;67 126;72 S;S;S 49;65;119 54;66;120 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. In particular, the position of S:T478K is on the interface with ACE2, as shown by crystal structures of the complex (Figure 3A). 2021 Journal of medical virology Result SARS_CoV_2 T478K 33 38 S 31 32 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. In total, we could detect the Spike:T478K (S:T478K) mutation in 11,435 distinct patients as of April 27, 2021, more than twice the number observed one month before, on March 26, 2021 (4214). 2021 Journal of medical virology Result SARS_CoV_2 T478K;T478K 36;45 41;50 S;S 30;43 35;44 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. One is D614G (99.83% co-occurrence), one of the founding events of SARS-CoV-2 lineage B, currently the most diffused Worldwide (Table 1). 2021 Journal of medical virology Result SARS_CoV_2 D614G 7 12 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. One of the reasons of concern about S:T478K is that it is rapidly growing over time, both in the number of detected samples (Figure 2A) and in prevalence, calculated as the number of cases over the total number of sequenced genomes (Figure 2B). 2021 Journal of medical virology Result SARS_CoV_2 T478K 38 43 S 36 37 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. S:T478K does not seem to be significantly associated with patient age (one-way analysis of variance test p > .1, Figure 1B and Figure S2), nor with patient sex (Figure 1C). 2021 Journal of medical virology Result SARS_CoV_2 T478K 2 7 S 0 1 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. S:T478K is also present in 68 out of 85 (80%) reported samples from the B.1.214.3; however, the low total number of cases for this lineage do not make it a variant of concern yet. 2021 Journal of medical virology Result SARS_CoV_2 T478K 2 7 S 0 1 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. S:T478K is frequently co-occurring with three other Spike mutations located outside the canonical ACE2 interaction region. 2021 Journal of medical virology Result SARS_CoV_2 T478K 2 7 S;S 52;0 57;1 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. The geographic distribution of S:T478K (Figure 1D and Figure S3) shows a noticeable prevalence in Mexico, where it constitutes 52.8% (3202 distinct cases) of all sequenced SARS-CoV-2 genomes. 2021 Journal of medical virology Result SARS_CoV_2 T478K 33 38 S 31 32 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. The location of S:T478K is within the interaction domain with the human receptor ACE2, roughly encompassing amino acids 350 to 550 of the SARS-CoV-2 Spike protein. 2021 Journal of medical virology Result SARS_CoV_2 T478K 18 23 S;S 149;16 154;17 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. The majority of these mutations (20,205 samples, Figure 1A and Figure S1) are associated with PANGOLIN lineage B.1.1.519; S:T478K is present in 97.0% of B.1.1.519 cases. 2021 Journal of medical virology Result SARS_CoV_2 T478K 124 129 S 122 123 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. The other two are P681H and T732A, with 93.8% and 88.7% co-occurrence with S:T478K, respectively (Table 1). 2021 Journal of medical virology Result SARS_CoV_2 P681H;T732A;T478K 18;28;77 23;33;82 S 75 76 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. The remaining S:T478K events are distributed in small numbers (N < 250) in other lineages phylogenetically not derived from B.1.1.519, supporting the hypothesis that this mutation has arisen more than once in distinct events. 2021 Journal of medical virology Result SARS_CoV_2 T478K 16 21 S 14 15 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. The S:T478K is therefore primarily present in North America, constituting more than 50% of all the sequences generated in Mexico (Figure 1D and Figure S4). 2021 Journal of medical virology Result SARS_CoV_2 T478K 6 11 S 4 5 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. The Spike S:T478K mutation is frequently co-existing also with mutations in other proteins, such as the diffused two-aa Nucleocapsid mutation N:RG203KR, and mutations in nonstructural proteins (NSPs) derived from the polyprotein encoded ORF1, which include for example the viral RNA-dependent RNA polymerase NSP12 (Table 2). 2021 Journal of medical virology Result SARS_CoV_2 T478K 12 17 RdRp;N;S;Nsp12;N;S 279;120;4;308;142;10 307;132;9;313;143;11 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. We could detect S:T478K in copresence with other Spike mutations as well, but currently all at much lower frequencies (<4%). 2021 Journal of medical virology Result SARS_CoV_2 T478K 18 23 S;S 49;16 54;17 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. We could detect S:T478K mutations in 7133 samples from the United States of America, totaling 2.7% of all genomes generated in the country. 2021 Journal of medical virology Result SARS_CoV_2 T478K 18 23 S 16 17 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. We detected this growth starting at the beginning of 2021, and S:T478K is, at the time of writing (April 27, 2021) characterizing more than 2.0% of all sequenced SARS-CoV-2. 2021 Journal of medical virology Result SARS_CoV_2 T478K 65 70 S 63 64 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 1,059.C > T and 25,563.G > T) were present in approximately half of North American SARS-CoV-2 isolates (479/1063 = 45% and 574/1063 = 54%), particularly North American lineage B.1 (479/691 = 69% and 573/691 = 83%) (Table 1). 2021 Transboundary and emerging diseases Result SARS_CoV_2 C059T;G563T 2;19 11;28 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. Among these 21 SNPs, we also identified two previously reported SNPs, 8,782.C > T and 28,144.T > C (p-value = 4.03 x 10-28 and 9.73 x 10-33), resulting in a synonymous mutation and a missense mutation (Leu 84 Ser) (Tang et al., 2020) (Table 1). 2021 Transboundary and emerging diseases Result SARS_CoV_2 L84S;T144C;C782T 202;89;72 212;98;81 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. Interestingly, three sequential SNP sites (28881-3.GGG>ACA) were fixed in 22% (207/951) of the European SARS-CoV-2 isolates, resulting in a synonymous mutation and two missense mutations (Arg 203 Lys and Gly 204 Arg) (Table 1). 2021 Transboundary and emerging diseases Result SARS_CoV_2 G204R;R203K 204;188 215;199 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. Thr265 Ile and Gln57 His) in ORF1ab and ORF3a, respectively. 2021 Transboundary and emerging diseases Result SARS_CoV_2 Q57H;T265I 15;0 24;10 ORF1ab;ORF3a 29;40 35;45 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. As predicted, the positive region near the H245-R246 is made more basic by the S247R mutation, and this facilitated HS binding. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 S247R 79 84 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. Compare this to the sulfates of the HS molecule, which were primarily located at either end of the chain, giving rise to a binding mode involving both the furin site and binding to the distal 245H-S247R site. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 S247R 197 202 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. Given our data, it would be interesting to model the interactions of specific HS structures known to be present in the lung with the S protein to examine whether these structures bind in the way suggested in our model, and so link the furin cleavage site with the region around S247R or H245-R246. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 S247R 278 283 S 133 134 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. HP molecules bound to R246-S247R and the furin cleavage site. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 S247R 27 32 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. In light of this, we were able to identify a gap in the glycan shield at 245H-S247R that may imply an increased viral infectivity of the S247R mutant. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 S247R;S247R 137;78 142;83 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. It is this flexibility that allows the bridging of the two regions (furin cleavage site and the 245H-S247R region), in a manner similar to what was observed in the studies by Perkins and Rashid. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 S247R 101 106 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. Of particular interest was the S247R mutation, which is physically located close to the PRRARS furin cleavage site and close to some of the deletions in the UK mutant strain (B.1.1.7) (Table S5). 2021 Computational and structural biotechnology journal Result SARS_CoV_2 S247R 31 36 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. Only HS bridges the gap between the furin site and S247R, while HP sits in the pocket between the PRRARS loop and the loop containing R634. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 S247R 51 56 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. The putative binding site at 245H-S247R did not appear with a Levenshtein cut-off of 0.7, but did at 0.65 (Table 1). 2021 Computational and structural biotechnology journal Result SARS_CoV_2 S247R 34 39 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. The S247R mutation is adjacent to two charged amino acids (H245-R246) that have been targeted by neutralizing antibodies. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 S247R 4 9 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. They otherwise differently bind to the S protein: HS bridges the gap between the PRRARS domain and S247R and does not have any strong interactions with the glycan shield, whereas the N-glycans near the furin cleavage site exert a shielding effect on the short HP dodecasaccharide examined here. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 S247R 99 104 N;S 183;39 184;40 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. This is because the sequence 241-246 (LLALHR) extended by the S247R mutation (LLALHRR) is quite rare and not conserved in the library of heparin-binding proteins used for the analysis. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 S247R 62 67 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. Using GROMACS, we ran MD simulations with the HS and HP dodecasaccharides to conduct an in depth analysis of the binding to the mutated site, S247R, and the PRRARS furin cleavage site. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 S247R 142 147 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. We docked heparin to the unglycosylated S247R monomer in the "up" conformation. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 S247R 40 45 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. We hypothesized that the S247R mutation would augment the basic nature of this region containing H245-R246 and favor bridging of GAG molecules between this region and the furin cleavage site. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 S247R 25 30 33968806 SARS CoV-2 Nucleoprotein Enhances the Infectivity of Lentiviral Spike Particles. Additional experiments using D614G mutant also indicated that the N-inclusive particles would require a higher amount of the neutralizing agent in comparison to N-exclusive counterpart ( Supplementary Figure 1F ). 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G 29 34 N;N 66;161 67;162 33968806 SARS CoV-2 Nucleoprotein Enhances the Infectivity of Lentiviral Spike Particles. Further, based on recent reports of a relatively more infectious D614G spike glycoprotein variant, we decided to screen the same to assess the effect of N protein. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G 65 70 N 153 154 33969329 Interferon antagonism by SARS-CoV-2: a functional study using reverse genetics. However, we note that the charge with both Gln51Glu and Gln56Glu, as in SARS-CoV, is negative. 2021 The Lancet. Microbe Result SARS_CoV_2 Q51E;Q56E 43;56 51;64 33969329 Interferon antagonism by SARS-CoV-2: a functional study using reverse genetics. SARS-CoV-2 ORF6 overexpression constructs expressing CTD charged residues, as found in SARS-CoV ORF6 (Gln51Glu, Gln56Glu, or both; appendix 1 p 11) showed reduced ISRE promotor activation compared with wild-type SARS-CoV-2 ORF6 (figure 4J). 2021 The Lancet. Microbe Result SARS_CoV_2 Q56E;Q51E 112;102 120;110 ORF6;ORF6;ORF6 11;96;223 15;100;227 33969329 Interferon antagonism by SARS-CoV-2: a functional study using reverse genetics. We identified two SARS-CoV-2 sequences uploaded to GISAID (as of Aug 12, 2020) that encode substitutions from non-charged to positively charged residues at positions 51 and 56 (Gln51Lys EPI_ISL_487291 [South Africa] and Gln56Arg EPI_ISL_433754 [UK]; appendix 1 pp 12-13). 2021 The Lancet. Microbe Result SARS_CoV_2 Q56R;Q51K 220;177 228;185 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. 1,207 FDA approved drugs were docked to the interface site formed between position D614G and T859 of neighboring chains in the spike protein trimer. 2021 Journal of cellular immunology Result SARS_CoV_2 D614G 83 88 S 127 132 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. Although N501Y has the potential to influence neutralizing antibody binding, this semiconservative difference is located at the edge of the ACE2/spike protein interface, therefore not expected to dramatically alter neutralizing antibody responses. 2021 Journal of cellular immunology Result SARS_CoV_2 N501Y 9 14 S 145 150 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. Collectively, these data suggest that: 1) the UK variant B.1.1.7 exhibits a change that enhances affinity for the coronavirus receptor ACE2 (N501Y), and 2) mutations may enhance dynamic virus fusion mechanisms by reducing intermolecular stability of spike protein subunits (A570D, D614G, S982A). 2021 Journal of cellular immunology Result SARS_CoV_2 D614G;S982A;A570D;N501Y 281;288;274;141 286;293;279;146 S 250 255 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. Drugs were estimated to bind the UK variant B.1.1.7 at the D614G site, such as the anti-leprosy drug sulfoxone, DeltaG -24.4 kcal/mol (Figure 4). 2021 Journal of cellular immunology Result SARS_CoV_2 D614G 59 64 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. Emerging mutations such as D614G can serve as the basis for drug discovery efforts to target specific highly transmissible variants such as UK variant B.1.1.7. 2021 Journal of cellular immunology Result SARS_CoV_2 D614G 27 32 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. N501Y was modeled based on the cryoEM structure of the Wuhan-Hu-1 spike protein/ACE2 complex (Figure 2A, PDB 6M17), indicating that the gain in affinity likely results from aromatic interactions (pi stacking) between Tyr501 and Tyr41 of ACE2 (Figure 2B). 2021 Journal of cellular immunology Result SARS_CoV_2 N501Y 0 5 S 66 71 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. One mutation (N501Y) enhanced the affinity of the spike protein with ACE2. 2021 Journal of cellular immunology Result SARS_CoV_2 N501Y 14 19 S 50 55 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. P681H represents a potentially important difference between Wuhan-Hu-1 sequence and UK variant B.1.1.7. 2021 Journal of cellular immunology Result SARS_CoV_2 P681H 0 5 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. Since SARS-CoV-2 variants with D614G, such as UK variant B.1.1.7, currently predominate globally, we asked if the interface between individual chains of the spike protein trimer at position 614 may be druggable. 2021 Journal of cellular immunology Result SARS_CoV_2 D614G 31 36 S 157 162 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. The A570D substitution in the UK variant B.1.1.7 variant introduces steric clash with the backbone amide of K964 (Figure 3D). 2021 Journal of cellular immunology Result SARS_CoV_2 A570D 4 9 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. The D614G substitution results in the formation of a distinctive cavity at the interface of spike protein subunits in the UK variant B.1.1.7 trimer (Figure 3E). 2021 Journal of cellular immunology Result SARS_CoV_2 D614G 4 9 S 92 97 33969357 Structural Consequences of Variation in SARS-CoV-2 B.1.1.7. The S982A in UK variant B.1.1.7 lacks intermolecular hydrogen (H) bonding potential between spike protein subunits at this site (Figure 3F). 2021 Journal of cellular immunology Result SARS_CoV_2 S982A 4 9 S 92 97 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. A third possible explanation is that the D614G mutation biases the spike protein towards its ACE2-binding-competent state, making cell fusion more likely but possibly making the protein more susceptible to antibodies; in that case, the mutation might offer a fitness advantage through increased transmission in an immunologically naive host population, but then shift to a disadvantage once most potential hosts have been previously exposed. 2021 Nature communications Result SARS_CoV_2 D614G 41 46 S 67 72 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Among them, radical-amino-acid-change D614G, which rose in frequency across multiple cities and increases infectivity in vitro, disrupts a residue that is perfectly conserved among our 44 sarbecoviruses, and lies in a stretch of 11 otherwise perfectly conserved amino acids. 2021 Nature communications Result SARS_CoV_2 D614G 38 43 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Another three are in moderately conserved contexts (V367F, D839Y/N/E, D936Y/H) less likely to be functional, and eight lie in repeatedly-altered amino acids in poorly conserved regions and are more likely to be neutral. 2021 Nature communications Result SARS_CoV_2 D839E;D839N;D839Y;D936H;D936Y;V367F 59;59;59;70;70;52 68;68;68;77;77;57 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. E484K arose independently in another lineage, P.2, also found in Brazil. 2021 Nature communications Result SARS_CoV_2 E484K 0 5 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. For example, the B.1.1.7 lineage includes mutations C5388A (orf1ab:A1708D) in a string of 7 perfectly conserved amino acids in a well-conserved region of nsp3, C14676T, a synonymous change in a large SCE in RdRp (situated between two conserved structures predicted by RNAz so possibly part of a containing structure too large for the prediction algorithm), T24506G (spike:S982A) in an extremely well-conserved region of S2, a three-nucleotide mutation at position 28280 (nucleocapsid:D3L) which weakens the initiation context of ORF9b, and C27972T (ORF8:Q27*) which truncates and presumably inactivates ORF8, which we discuss in more detail below; B.1.351 includes A10323G (orf1ab:K3353R) in a moderately conserved region of 3CLpro, G25563T (ORF3a:Q57H) which introduces radical amino changes in both ORF3a and ORF3c, and G13843T (orf1ab:D4527Y, present in about half of B.1.351 isolates) in a string of 33 perfectly conserved amino acids in RdRp; and finally, P1 includes G17259T (orf1ab:E5665D) in an extremely well-conserved region of Hel and C24642T (spike:T1027I) in string of 13 perfectly conserved amino acids in S2. 2021 Nature communications Result SARS_CoV_2 A10323G;C14676T;C24642T;C27972T;C5388A;G13843T;G17259T;G25563T;T24506G;A1708D;D3L;D4527Y;E5665D;K3353R;Q27X;Q57H;S982A;T1027I 665;160;1046;540;52;822;973;733;357;67;484;838;989;681;554;748;372;1061 672;167;1053;547;58;829;980;740;364;73;487;844;995;687;558;752;377;1067 N;ORF1ab;ORF1ab;ORF1ab;ORF1ab;S;S;ORF3a;ORF3a;Nsp3;ORF8;ORF8;RdRP;RdRP 471;60;674;831;982;366;1055;742;801;154;549;603;207;942 483;66;680;837;988;371;1060;747;806;158;553;607;211;946 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. However, as noted above, ORF8 shows strong evolutionary evidence of protein-coding function across this coronavirus species and experimental evidence of expression in SARS-CoV-2, together indicating that ORF8 loss would be expected to have a fitness cost, which is only tolerated due to hitchhiking with the highly advantageous N501Y spike protein substitution and possibly additional selected variants in the haplotype. 2021 Nature communications Result SARS_CoV_2 N501Y 328 333 S;ORF8;ORF8 334;25;204 339;29;208 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. However, the D614G substitution also increases SARS-CoV-2 infectivity in Chinese rufous horseshoe bats and Malayan pangolin cells, suggesting that host differences alone are not sufficient to explain the discrepancy. 2021 Nature communications Result SARS_CoV_2 D614G 13 18 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. N501Y arose, apparently independently, in the B.1.153 lineage, which rapidly rose in frequency in South Africa and also includes spike-protein substitutions E484K and K417N, which are thought to decrease binding of antibodies from monoclonal antibody cocktails or from immune response to vaccines or previous infection with the wild-type virus. 2021 Nature communications Result SARS_CoV_2 E484K;K417N;N501Y 157;167;0 162;172;5 S 129 134 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Of the other 15 spike-gene mutations, two are in perfectly conserved residues (V615I/F, P1263L) and two in mostly conserved residues in highly conserved regions (A831V, A829T/S), indicating likely functional changes. 2021 Nature communications Result SARS_CoV_2 A829T;A829S;P1263L;A831V;V615F;V615I 169;169;88;162;79;79 176;176;94;167;86;86 S 16 21 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Spike-protein D614G was nearly always co-inherited with RdRp P4715L (also radical and altering a perfectly conserved residue in a highly conserved context, but potentially deleterious given RdRp's slow evolution and less-likely-to-be-adaptive function), nsp3 nucleotide change C3037T (repeatedly observed synonymous change, outside synonymously constrained elements, likely neutral), and nucleotide change C241T (perfectly conserved, non-coding, in a loop of six unpaired bases in the conserved 5'-UTR SL5B secondary structure 25 nucleotides upstream of ORF1a). 2021 Nature communications Result SARS_CoV_2 C241T;C3037T;D614G;P4715L 406;277;14;61 411;283;19;67 ORF1a;S;Nsp3;RdRP;RdRP 554;0;254;56;190 559;5;258;60;194 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. The B.1.1.7 lineage, which rapidly rose in frequency in the United Kingdom, includes spike-protein substitution N501Y, which was found to increase ACE2-binding affinity and is thought to be responsible for the increased infectivity. 2021 Nature communications Result SARS_CoV_2 N501Y 112 117 S 85 90 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. The regions around E484K and N501Y are highly variable among sarbecoviruses, containing many non-synonymous amino acid substitutions and, in the case of E484K, indels, consistent with the observed positive selection in SARS-CoV-2. 2021 Nature communications Result SARS_CoV_2 E484K;E484K;N501Y 19;153;29 24;158;34 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. These likely represent positive selection, as only 6 other isolates show mutations affecting the 15-base neighborhood surrounding Q27* (2 deletions and 4 SNVs of 3 distinct nucleotides), indicating that 7 distinct *27Q reversions are unlikely by chance. 2021 Nature communications Result SARS_CoV_2 Q27X 130 134 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Two of these three substitutions, E484K and N501Y, affect contact residues within the receptor-binding motif, the main functional motif that forms the interface with the human ACE2 receptor, and show evidence of positive selection in the SARS-CoV-2 population based on excess of non-synonymous substitutions and increasing frequency. 2021 Nature communications Result SARS_CoV_2 E484K;N501Y 34;44 39;49 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. We next examined the Sarbecovirus evolutionary context for each of the mutations co-inherited with any of D614G, N501Y, E484K, and K417N/T to determine those most likely to have some functional effect. 2021 Nature communications Result SARS_CoV_2 D614G;E484K;K417N;K417T;N501Y 106;120;131;131;113 111;125;138;138;118 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. We next investigated the truncation of ORF8 by the mutation ORF8:Q27* (C27972T), which changes a CAA sense codon to a UAA stop codon in the rapidly spreading B.1.1.7 SARS-CoV-2 lineage. 2021 Nature communications Result SARS_CoV_2 C27972T;Q27X 71;65 78;69 ORF8;ORF8 39;60 43;64 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. We reasoned that nonsense-to-sense reversion of ORF8:Q27* may provide a further fitness benefit for B.1.1.7, and searched for isolates containing such events. 2021 Nature communications Result SARS_CoV_2 Q27X 53 57 ORF8 48 52 33991677 Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage. In addition, sequences that span codons 1-618 of the spike gene and allow the identification of this variant by covering 4 of its hallmark mutations (C21614T (substitution L18F), G22468T, T22917G (L452R), A23063T (N501Y)) and by being devoid of the Nextstrain clade 20 A23403G mutation, were obtained for 43 other patients (deposited at: https://doi.org/10.35081/43r6-sz33). 2021 Clinical microbiology and infection Result SARS_CoV_2 A23063T;A23403G;G22468T;L18F;T22917G;C21614T;L452R;N501Y 205;269;179;172;188;150;197;214 212;276;186;176;195;157;202;219 S 53 58 33991677 Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage. Moreover, 21 genomes, one from our institute, the 8 ones from Mayotte, and 12 other genomes from France or Turkey were clustered and all harbored the spike Q677H substitution. 2021 Clinical microbiology and infection Result SARS_CoV_2 Q677H 156 161 S 150 155 33991677 Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage. These mutations include aa substitution N501Y, associated with aa substitutions L18F, L452R, A653V, H655Y, D796Y, and G1219V, and a synonymous mutation at nucleotide position 22,468 [in reference to NC_045512.2); Figures 1 a, 1b]; an eighth spike aa susbtitution, Q677H, was identified in one of these genomes. 2021 Clinical microbiology and infection Result SARS_CoV_2 A653V;D796Y;G1219V;H655Y;L18F;L452R;N501Y;Q677H 93;107;118;100;80;86;40;264 98;112;124;105;84;91;45;269 S 241 246 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Although the E484K mutation does not interact directly with hACE2, it modifies the conformation of Spike RBD's loop, resulting in a significant gain of average solvation energy (-11 kcal/mol). 2021 Journal of molecular biology Result SARS_CoV_2 E484K 13 18 S;RBD 99;105 104;108 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Among the antibody escape mutants identified using a cell-based infectivity assay, N440K is resistant to C135 and E484K to C121. 2021 Journal of molecular biology Result SARS_CoV_2 E484K;N440K 114;83 119;88 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Among the unfavorable Spike mutations, L452F and P491T occur at or near the antiparallel beta strands located in the middle of S-RBM's concave interaction surface, supporting our observation about the rarity of high-affinity mutations in this region. 2021 Journal of molecular biology Result SARS_CoV_2 L452F;P491T 39;49 44;54 S 22 27 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. An exception to this rule is the high-affinity mutant S494T, which occurs near the short beta strand in the center of S interaction surface. 2021 Journal of molecular biology Result SARS_CoV_2 S494T 54 59 S 118 119 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Averaged affinities predicted by structural modeling indicate that the mutations fall into three groups (Figure 6 (a)): very high-affinity (80 to 90% better that WT; S477N/E484K/N501Y, S477N/E484K and E484K/N501Y), high-affinity (40 to 50% better than WT; S477N, E484K, N501Y), WT-like (S477N/N501Y, K417T/E484K/N501Y, N439K, Y453F), and low-affinity (<70% of WT; K417T/E484K, K417T, K417T/N501Y). 2021 Journal of molecular biology Result SARS_CoV_2 E484K;E484K;K417T;K417T;K417T;K417T;N439K;N501Y;S477N;S477N;S477N;Y453F;S477N;E484K;E484K;E484K;E484K;N501Y;N501Y;N501Y;N501Y;N501Y 201;263;300;364;377;384;319;270;166;185;256;326;287;191;172;306;370;207;293;312;178;390 206;268;305;369;382;389;324;275;171;190;261;331;292;196;177;311;375;212;298;317;183;395 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. By our affinity measures N440K is predicted both to be capable of escaping antibody C135 and to bind hACE2 with high affinity, attributes that make it a prime candidate for viral surveillance. 2021 Journal of molecular biology Result SARS_CoV_2 N440K 25 30 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Compared with the WT complex, N440K gains 6 kcal/mol in solvation energy and 18 kcal/mol in van der Waals energy, whereas G476S gains 8 kcal/mol in van der Waals energy and 27 kcal/mol in electrostatic energy. 2021 Journal of molecular biology Result SARS_CoV_2 G476S;N440K 122;30 127;35 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Consistent with this result, experimental analyses of L452R using deep mutagenesis and in vitro evolution do not suggest it produces an enhanced affinity relative to WT. 2021 Journal of molecular biology Result SARS_CoV_2 L452R 54 59 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Examining specific examples, the point mutations Y442F and L472F, which are adapted to hACE2, produced better affinities relative to the WT complex (-26.0 kcal/mol and -27.8 kcal/mol versus -22.0 kcal/mol). 2021 Journal of molecular biology Result SARS_CoV_2 L472F;Y442F 59;49 64;54 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Figure 3), most have improved contact van der Waals energies (gain of 10-20 kcal/mol), and complexes S-G502P/hACE2-T92V and S-T470S/hACE2-W69C also have enhanced electrostatic energies (gain of ~30 kcal/mol). 2021 Journal of molecular biology Result SARS_CoV_2 G502P;T470S;T92V;W69C 103;126;115;138 108;131;119;142 S;S 101;124 102;125 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Given the infectivity potential and resistance of N440K and E484K/R variants, there is a need to monitor their spread. 2021 Journal of molecular biology Result SARS_CoV_2 E484K;E484R;N440K 60;60;50 67;67;55 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. High-affinity Spike mutations N440K and E484K/R coincide with antibody escape mutants. 2021 Journal of molecular biology Result SARS_CoV_2 E484K;E484R;N440K 40;40;30 47;47;35 S 14 19 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. If electrostatic energy is the deciding factor in C121 antibody resistance, then the E484K variant can be regarded as chemically similar to our top affinity candidate E484R; indeed, recent deep mutagenesis analysis showed that E484R is resistant to three neutralizing antibodies (COV2-2050, COV2-2096, COV2-2479; Figure 5 (b)). 2021 Journal of molecular biology Result SARS_CoV_2 E484K;E484R;E484R 85;167;227 90;172;232 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. In contrast to E484K and N501Y, K417T alone appears not favored for receptor recognition, and this is reflected in reduced affinities for K417T/N501Y and K417T/E484K combinations, which are not observed together in sequenced viral genomes; K417N has similar characteristics (not shown). 2021 Journal of molecular biology Result SARS_CoV_2 E484K;K417N;K417T;K417T;K417T;N501Y;E484K;N501Y 15;240;32;138;154;25;160;144 20;245;37;143;159;30;165;149 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. In contrast, the mutant N501Y residue is closely packed in proximity of the K353 hotspot of hACE2 and its sidechain shows only minimal conformational changes. 2021 Journal of molecular biology Result SARS_CoV_2 N501Y 24 29 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. In contrast, three hACE2 variants (A65V, A102P and G377W) interact unfavorably with most S mutations examined. 2021 Journal of molecular biology Result SARS_CoV_2 A102P;G377W;A65V 41;51;35 46;56;39 S 89 90 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. In particular, at position 443, the corresponding residue in SARS-CoV strains is a conserved A, so the S443A mutation in SARS-CoV-2 could account for its enhanced binding to hACE2. 2021 Journal of molecular biology Result SARS_CoV_2 S443A 103 108 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. In vitro evolution of optimized Spike RBD repeatedly recovered S477N, E484K and N501Y mutations but not K417N/T. 2021 Journal of molecular biology Result SARS_CoV_2 E484K;K417N;K417T;N501Y;S477N 70;104;104;80;63 75;111;111;85;68 S;RBD 32;38 37;41 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Indeed, the hACE2 variants N33D, D38E, T92V, E329G and M383I interact favorably with many S mutations (Figure 3(a)). 2021 Journal of molecular biology Result SARS_CoV_2 D38E;E329G;M383I;N33D;T92V 33;45;55;27;39 37;50;60;31;43 S 90 91 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Interestingly, the optimized Y442F/472F double mutant generated a very high affinity complex (-42.6 kcal/mol), consistent with association (1/KD value over 3 times greater than that for L472F) and infectivity data. 2021 Journal of molecular biology Result SARS_CoV_2 L472F;Y442F 186;29 191;34 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Lastly, the mutation T487S, which is judged to be less adapted to human ACE2 based on frequencies of occurrence of these mutants in civet and human SARS-CoV, yielded a poorer affinity (-16.5 kcal/mol), in agreement with expectation. 2021 Journal of molecular biology Result SARS_CoV_2 T487S 21 26 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Mutants E484K/R exhibit high levels of antibody resistance (C121, COV2-2050, COV2-2096) and K417N/T have some degree of resistance (STE90-C11, COV2-2082), but some other mutations display negligible antibody resistance (Figure 5(a) and (b)). 2021 Journal of molecular biology Result SARS_CoV_2 E484K;E484R;K417N;K417T 8;8;92;92 15;15;99;99 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. On the hACE2 interface, variants T92V/I cause the alpha1 helix and a loop (residues 87-92) to move closer to the S interface, reflecting improved van der Waals energies. 2021 Journal of molecular biology Result SARS_CoV_2 T92V;T92I 33;33 39;39 S 113 114 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. On the S interface, four mutations (N440K, S443A, Q498N, G502P) generated significant conformational changes in two loops (437-452, 494-507). 2021 Journal of molecular biology Result SARS_CoV_2 G502P;Q498N;S443A;N440K 57;50;43;36 62;55;48;41 S 7 8 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Relative to the WT complex (Spike, wheat; hACE2, yellow), the single Spike G476S mutation generated a large conformational switch in a local RBM loop (residues 475-AGST-478) causing it to orient toward the N-terminal of hACE2 alpha1 helix, a region found to have more contacts with the S-protein of SARS-CoV-2 than with SARS-CoV (Figure 4(a)). 2021 Journal of molecular biology Result SARS_CoV_2 G476S 75 80 S;S;N;S 28;69;206;286 33;74;207;287 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Similar to E484K/R, E484Q is predicted to have a strong average affinity for hACE2 (Figure 6(a)). 2021 Journal of molecular biology Result SARS_CoV_2 E484K;E484R;E484Q 11;11;20 18;18;25 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Since both L452R and E484Q have significant antibody escape propensity (Figure 5(b)), our affinity analysis suggests the rapid spread of the L452R/E484Q variant likely stems from antibody resistance. 2021 Journal of molecular biology Result SARS_CoV_2 E484Q;L452R;L452R;E484Q 21;11;141;147 26;16;146;152 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Structural mapping of N440K and E484R variants confirms that they overlap, respectively, with the independent binding sites of C135 and C121 on the S protein (Figure 5(a) and (b)). 2021 Journal of molecular biology Result SARS_CoV_2 E484R;N440K 32;22 37;27 S 148 149 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The affinity ranking of G476S is dominated by its binding to WT hACE2, whereas the other three S mutants interact favorably with multiple hACE2 variants (Figure 3(a)). 2021 Journal of molecular biology Result SARS_CoV_2 G476S 24 29 S 95 96 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The double mutant L452R/E484Q has a strong favorable solvation energy but this is overcompensated by the entropic penalty of complex formation, resulting in a lower overall affinity relative to WT but similar to that for the L452R mutation. 2021 Journal of molecular biology Result SARS_CoV_2 L452R;L452R;E484Q 18;225;24 23;230;29 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The favorable affinity for N501Y is produced by gains in entropic (6 kcal/mol) and van der Waals (7 kcal/mol) energies. 2021 Journal of molecular biology Result SARS_CoV_2 N501Y 27 32 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The G502P mutation, which is adjacent to the key N501 residue, alters the local interface conformation, providing structural support for increased S-hACE2 binding (Figure 4(a)). 2021 Journal of molecular biology Result SARS_CoV_2 G502P 4 9 S 147 148 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The high affinity group consists of single mutants S477N, E484K and N501Y, indicating that the fast-spreading variants combine these mutations to achieve higher binding affinities; recent molecular dynamics simulations also predicted that S477N has a higher affinity than WT. 2021 Journal of molecular biology Result SARS_CoV_2 E484K;N501Y;S477N;S477N 58;68;51;239 63;73;56;244 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The high-affinity of the double mutant E484K/N501Y is produced by gains in solvation (11 kcal/mol), van der Waals (2 kcal/mol) and entropic (5 kcal/mol) energies, indicating the approximate additive effect of its energy components. 2021 Journal of molecular biology Result SARS_CoV_2 E484K;N501Y 39;45 44;50 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The highest affinity group includes fast-spreading double mutants S477N/E484K and E484K/N501Y in Brazil, South Africa, US and UK (cdc.gov/coronavirus/2019-ncov); the triple mutant S477N/E484K/N501Y with the best affinity has not been reported. 2021 Journal of molecular biology Result SARS_CoV_2 E484K;S477N;S477N;E484K;E484K;N501Y;N501Y 82;66;180;72;186;88;192 87;71;185;77;191;93;197 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The L452R mutation, also identified in patient samples from California, does not directly interact with the hACE2 interface, in contrast to the adjacent residue Y453. 2021 Journal of molecular biology Result SARS_CoV_2 L452R 4 9 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The N440K mutation involves a charge change and an extended conformation alteration in the RBM loop (Figure 4(b)). 2021 Journal of molecular biology Result SARS_CoV_2 N440K 4 9 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The newly identified S interface variants now in wide circulation across the globe include K417N/T, N439K, Y453F, S477N, E484K, N501Y and their combinations. 2021 Journal of molecular biology Result SARS_CoV_2 E484K;K417N;K417T;N439K;N501Y;S477N;Y453F 121;91;91;100;128;114;107 126;98;98;105;133;119;112 S 21 22 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The SARS-CoV-2 S mutations fulfilling this stringent criterion are N440K, S443A, G476S, E484R and G502P. 2021 Journal of molecular biology Result SARS_CoV_2 E484R;G476S;G502P;N440K;S443A 88;81;98;67;74 93;86;103;72;79 S 15 16 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The single Spike N440K mutation occurs near the anti-parallel beta-sheet core of RBD but produced an extended perturbation in the RBM loop region facing the hACE2 K353 hotspot (Figure 4(b)). 2021 Journal of molecular biology Result SARS_CoV_2 N440K 17 22 S;RBD 11;81 16;84 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The top 7 high-affinity double mutation cases, in decreasing affinity, are S-S443A/hACE-E329G, S-G502P/hACE2-T92V, S-T470S/hACE2-W69C, S-N440K/hACE2-T92I, S-S443A/hACE2-D38E, S-Q498N/hACE2-E329G, and S-G502P/hACE2-M383I (superimposed and individual complexes in Figures 4(c) and Suppl. 2021 Journal of molecular biology Result SARS_CoV_2 D38E;E329G;E329G;G502P;G502P;M383I;N440K;Q498N;S443A;S443A;T470S;T92I;T92V;W69C 169;88;189;97;202;214;137;177;77;157;117;149;109;129 173;93;194;102;207;219;142;182;82;162;122;153;113;133 S;S;S;S;S;S;S 75;95;115;135;155;175;200 76;96;116;136;156;176;201 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The urgency of characterizing fast-spreading variants is illustrated by the recent emergence of the L452R/E484Q variant in India and other countries. 2021 Journal of molecular biology Result SARS_CoV_2 L452R;E484Q 100;106 105;111 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The WT-like group includes K417T/E484K/N501Y (spreading in South Africa, Brazil), N439K (Denmark) and Y453F (UK). 2021 Journal of molecular biology Result SARS_CoV_2 K417T;N439K;Y453F;E484K;N501Y 27;82;102;33;39 32;87;107;38;44 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. This indicates that K417N/T is not a major contributor to affinity, in agreement with our predicted binding affinities. 2021 Journal of molecular biology Result SARS_CoV_2 K417N;K417T 20;20 27;27 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Thus, the selective advantage of K417N/T is likely their ability to confer antibody resistance. 2021 Journal of molecular biology Result SARS_CoV_2 K417N;K417T 33;33 40;40 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Thus, variants S477N/E484K, E484K/N501Y and K417T/E484K/N501Y indicate that they combine high or WT-like affinity and antibody resistant mutations, which may account for their spread in multiple countries. 2021 Journal of molecular biology Result SARS_CoV_2 E484K;K417T;S477N;E484K;E484K;N501Y;N501Y 28;44;15;21;50;34;56 33;49;20;26;55;39;61 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Two Spike variants (N440K and G476S), both in solvent-exposed residues at opposite ends of the binding interface, form high-affinity complexes in combination with WT hACE2 (Figure 4 (a) and (b)). 2021 Journal of molecular biology Result SARS_CoV_2 G476S;N440K 30;20 35;25 S 4 9 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. We consider seven cases representing distinct animal-human adaptive mutations in the SARS-CoV S-protein (Figure 2 (a)): adaptations from civet, an intermediate animal host, to human ACE2 (Y442F, L472F); mutations obtained by reversing civet to human adaptations (L472P, N479K, D480G); unfavorable mutation (T487S); and a previously designed double mutant (Y442F/L472F) optimized for hACE2 binding. 2021 Journal of molecular biology Result SARS_CoV_2 D480G;L472F;N479K;L472P;T487S;Y442F;Y442F;L472F 277;195;270;263;307;188;356;362 282;200;275;268;312;193;361;367 S 94 95 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. We found no high-affinity hACE2 variants (20% above WT affinity) and, with the exception of D38E and E329G, most hACE2 variants in fact lead to lower binding affinities (Figure 3(a)). 2021 Journal of molecular biology Result SARS_CoV_2 D38E;E329G 92;101 96;106 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. When two of the hACE2-adapted mutations in SARS-CoV are reversed to those found in civet (L472P, N479K), the predicted affinities decreased dramatically (-4.9 kcal/mol and -14.8 kcal/mol, respectively). 2021 Journal of molecular biology Result SARS_CoV_2 N479K;L472P 97;90 102;95 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. 4e), Q498H-RBD. 2021 EBioMedicine Result SARS_CoV_2 Q498H 5 10 RBD 11 14 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. 4f), Q493K/Q498H-RBD. 2021 EBioMedicine Result SARS_CoV_2 Q493K;Q498H 5;11 10;16 RBD 17 20 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. 4g) with an equilibrium dissociation constant (KD) of 2.68 x 10-9, 1.23 x 10-9 and 1.04 x 10-9, respectively, with the double mutant Q493K/Q498H-RBD being the strongest binder. 2021 EBioMedicine Result SARS_CoV_2 Q493K;Q498H 133;139 138;144 RBD 145 148 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. Although Q493K and Q498H were able to increase RBD binding affinities with mACE2, they were substantially lower than that with hACE2. 2021 EBioMedicine Result SARS_CoV_2 Q493K;Q498H 9;19 14;24 RBD 47 50 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. Another key position in RBD, the C23039A (Q493K) mutation which probably mediates the virus binding affinity with mACE2, began to appear in the P5 viral gene pool. 2021 EBioMedicine Result SARS_CoV_2 C23039A;Q493K 33;42 40;47 RBD 24 27 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. Consistent with our hypothesis, mACE2 interacted with Q493K-RBD. 2021 EBioMedicine Result SARS_CoV_2 Q493K 54 59 RBD 60 63 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. In particular, three of the thirteen P11 variations (C1912T, C12915T, C23039A) increased frequency going from P8 to P11; two of those three changes C12915T (T77I in NSP9) and C23039A (Q493K in RBD) are nonsynonymous and likely contribute to the high pathogenicity of WBP-1 in mice. 2021 EBioMedicine Result SARS_CoV_2 C12915T;C12915T;C23039A;C23039A;C1912T;Q493K;T77I 61;148;70;175;53;184;157 68;155;77;182;59;189;161 RBD 193 196 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. Most notably, two of the mutations, C23039A (Q493K) and A23056C (Q498H), were mapped to the RBD of the S protein which is key host determining factor, suggesting that these two mutations is likely responsible for efficient WBP-1 replication in mice. 2021 EBioMedicine Result SARS_CoV_2 A23056C;C23039A;Q493K;Q498H 56;36;45;65 63;43;50;70 RBD;S 92;103 95;104 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. P5 viruses showed 21 mutations, including three stable mutations (A8203G, 0.889; T17825C, 0.986; and A23056C, 1.000) and 19 low frequency mutations with rates varying from 0.044118 to 0.272727. 2021 EBioMedicine Result SARS_CoV_2 A23056C;T17825C;A8203G 101;81;66 108;88;72 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. Q498H interacting with Y41 was found to form a solid pi-bond interaction. 2021 EBioMedicine Result SARS_CoV_2 Q498H 0 5 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. Structure remodeling suggested the binding affinity of Q493K/Q498H-RBD to hACE2 were almost unchanged compared to that of WT RBD. 2021 EBioMedicine Result SARS_CoV_2 Q493K;Q498H 55;61 60;66 RBD;RBD 67;125 70;128 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. The result showed that neither Q493K nor Q498H had a substantial effect on the RBD binding affinity with hACE2. 2021 EBioMedicine Result SARS_CoV_2 Q493K;Q498H 31;41 36;46 RBD 79 82 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. The substitution of residue Q493K interact with N71 of mouse ACE2 via H-bond. 2021 EBioMedicine Result SARS_CoV_2 Q493K 28 33 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. To investigate whether the mouse-adapted WBP-1 viral strain, which acquired Q493K and Q498H mutations in RBD, use mouse ACE2 (mACE2) to enter the cell, Hela cells were infected with Wuhan-Hu-1 or WBP-1 viruses after transfection of hACE2 or mACE2 expressing plasmids. 2021 EBioMedicine Result SARS_CoV_2 Q493K;Q498H 76;86 81;91 RBD 105 108 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. To our surprise, in the retrospective analysis, the stable mutation A23056C (Q498H in RBD) dominated after only one passage in aged mice (Figure S2). 2021 EBioMedicine Result SARS_CoV_2 A23056C;Q498H 68;77 75;82 RBD 86 89 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. By contrast, HMA binding was not affected by the V25F mutation, since the chemical shifts of signals from residues near the HMA binding site were unchanged and their CSPs were identical to those observed for wild-type E protein (Fig 11B-11D). 2021 PLoS pathogens Result SARS_CoV_2 V25F 49 53 E 218 219 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. Effects of N15A and V25F mutations on structure and HMA binding of E protein. 2021 PLoS pathogens Result SARS_CoV_2 N15A;V25F 11;20 15;24 E 67 68 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. In contrast, only minor perturbations were observed for signals from residues adjacent to the mutation site in the V25F mutant E protein (Fig 10B-10D). 2021 PLoS pathogens Result SARS_CoV_2 V25F 115 119 E 127 128 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. N15A and V25F mutations of E protein affect VLP production. 2021 PLoS pathogens Result SARS_CoV_2 V25F;N15A 9;0 13;4 E 27 28 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. Previous mutational studies of polypeptides containing the transmembrane helix of SARS-CoV E protein have shown that a single mutation, e.g., N15A or V25F, can disrupt ion channel activity in lipid bilayers. 2021 PLoS pathogens Result SARS_CoV_2 N15A;V25F 142;150 146;154 E 91 92 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. Similar to the T16A mutation in IBV E protein, the N15A mutation in SARS-CoV-2 E protein increased VLP production by approximately 40% compared to the wild-type E protein, while the V25F mutation decreased VLP production by 60% compared to wild-type E protein, similar to the effect of the A26F mutation on the IBV E protein (Fig 9B and 9C). 2021 PLoS pathogens Result SARS_CoV_2 A26F;N15A;T16A;V25F 290;51;15;182 294;55;19;186 E;E;E;E;E 36;79;161;250;315 37;80;162;251;316 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. Since no significant differences were observed among the circular dichroism spectra from wild-type E protein and these two mutant proteins, the relatively large and wide spread chemical shift perturbations by the N15A mutation may result from changes in intermolecular hydrogen bonding involving Asn15 side chains. 2021 PLoS pathogens Result SARS_CoV_2 N15A 213 217 E 99 100 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. The mutations T16A and A26F in the IBV E protein have been shown to affect its oligomeric state. 2021 PLoS pathogens Result SARS_CoV_2 A26F;T16A 23;14 27;18 E 39 40 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. The N15A and V25F mutations in SARS-CoV-2 E protein increased their expression compared to the wild-type protein in HEK293T cell lysates (Fig 9A). 2021 PLoS pathogens Result SARS_CoV_2 N15A;V25F 4;13 8;17 E 42 43 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. The N15A mutation results in significant chemical shift perturbations of resonances from residues throughout the N-terminal region of E protein, especially for the signals from Ser6, Glu7, Leu12, and Ser16 (Fig 10A-10C). 2021 PLoS pathogens Result SARS_CoV_2 N15A 4 8 E;N 134;113 135;114 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. To determine the impact of similar mutations in SARS-CoV-2 E protein, two mutants were generated, N15A and V25F, which are analogous to IBV E protein residues Thr16 and Ala26, respectively (S1 Fig). 2021 PLoS pathogens Result SARS_CoV_2 N15A;V25F 98;107 102;111 E;E 59;140 60;141 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. We found that the N15A mutation of SARS-CoV-2 E protein decreased HMA binding, since no significant chemical shift changes are observed in the presence of HMA, with the exception of Ser6 (Fig 11A-11C). 2021 PLoS pathogens Result SARS_CoV_2 N15A 18 22 E 46 47 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. , four ACE2 binding-strengthening mutations have a rapid growth since late December 2020: N501Y, K417N, E484K, and P479S. 2021 Genomics Result SARS_CoV_2 E484K;K417N;N501Y;P479S 104;97;90;115 109;102;95;120 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. 13 , shows that, in addition to well-known mutations E484K, K417N, and N501Y, mutations N439K, L452R, S477N, S477R, and N501T are also ACE2 binding-strengthening mutations that have a high growth rate recently with high frequency. 2021 Genomics Result SARS_CoV_2 E484K;K417N;L452R;N439K;N501T;N501Y;S477N;S477R 53;60;95;88;120;71;102;109 58;65;100;93;125;76;107;114 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. 2 shows that T478K leads to the highest increase in ACE2-S protein RBD BFE change, indicating that fast-growing mutation T478K may potentially make the SARS-CoV-2 more transmissible and infectious. 2021 Genomics Result SARS_CoV_2 T478K;T478K 13;121 18;126 RBD;S 67;57 70;58 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. 5, vaccine escape mutation E484K has dramatically disruptive effects on antibodies such as H11-H4, LY-CoV555, and DH1041. 2021 Genomics Result SARS_CoV_2 E484K 27 32 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. 5, we can see that mutation E484K will disruptively weaken the binding of S protein with antibodies such as LY-CoV555 and DH1041, which are marked in dark red. 2021 Genomics Result SARS_CoV_2 E484K 28 33 S 74 75 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. ACE2 binding-strengthening mutation L452R has a fast-growing tendency since December 8, 2020. 2021 Genomics Result SARS_CoV_2 L452R 36 41 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. ACE2 binding-strengthening mutations in India include N440K, L452R, E484Q, N501Y, and E484K. 2021 Genomics Result SARS_CoV_2 E484K;E484Q;L452R;N440K;N501Y 86;68;61;54;75 91;73;66;59;80 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Additionally, ACE2 binding-strengthening mutations T385I, N439K, S477R, and L452R also have a high log growth rate since late 2020. 2021 Genomics Result SARS_CoV_2 L452R;N439K;S477R;T385I 76;58;65;51 81;63;70;56 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Among 651 mutations that are detected on RBD, mutations N501Y, S477N, L452R, N439K, and E484K have the highest frequency up to April 18, 2021. 2021 Genomics Result SARS_CoV_2 E484K;L452R;N439K;N501Y;S477N 88;70;77;56;63 93;75;82;61;68 RBD 41 44 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Among them, K417N and E484K are both VE mutations with relatively high BFE changes, suggesting that researchers should keep tracking these mutations in the following months in Denmark. 2021 Genomics Result SARS_CoV_2 E484K;K417N 22;12 27;17 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Among them, T478K is part of the Mexico variant B.1.1.222 and has the highest growth rate since late October 2020. 2021 Genomics Result SARS_CoV_2 T478K 12 17 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Among them, the N501Y and L452R mutations have relatively high BFE changes of 0.55 kcal/mol and 0.58 kcal/mol, respectively. 2021 Genomics Result SARS_CoV_2 L452R;N501Y 26;16 31;21 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. As first reported in the United Kingdom, the N501Y mutation also has a fast-growing tendency since early December 2020, making the SARS-CoV-2 more infectious. 2021 Genomics Result SARS_CoV_2 N501Y 45 50 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Based on our study of mutation impacts on 106 antibodies, we found that the E484K mutation may cause a dramatically disruptive effect on antibodies such as H11-D4, P2B:2F6, Fab 2-4, H11-H4, COVA2-39, BD368-2, VH binder, S2M11, S2H13, CV07-270, P2C-1A3, P17, etc, which is consistent with the finding that E484K may affect neutralization by some polyclonal and monoclonal antibodies. 2021 Genomics Result SARS_CoV_2 E484K;E484K 76;305 81;310 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Binding-strengthening mutation S477N has a high growth rate from late July to early December. 2021 Genomics Result SARS_CoV_2 S477N 31 36 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. By checking the results reported early, we note that mutation L452R may make antibodies such as H11-D4, P2B:2F6, SR4, MR17, MR17-K99Y, H11-H4, BD-368-2, CV07-270, Fabs 298 52, CT-P59, etc., ineffective. 2021 Genomics Result SARS_CoV_2 L452R;K99Y 62;129 67;133 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Considering the recent emergence of 'double mutation' L452R and E484Q in India, Singapore needs to pay more attention to tracking new variant B.1.617. 2021 Genomics Result SARS_CoV_2 E484Q;L452R 64;54 69;59 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Finally, mutation E484Q may weaken the binding of many antibodies (such as LY-CoV555, DH1047, H11-H4, H11-D4, and CV07-270) in complex with S protein. 2021 Genomics Result SARS_CoV_2 E484Q 18 23 S 140 141 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. From analyzing the SNP profiles in Mexico, we notice that 6 ACE2 binding-strengthening mutations, L452R, S477N, T478K, S494P, E484K, and A552V, have a rapid growth since late October 2020. 2021 Genomics Result SARS_CoV_2 A552V;E484K;L452R;S477N;S494P;T478K 137;126;98;105;119;112 142;131;103;110;124;117 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. From Table 4, mutation L452R may disrupt the binding of 28 existing antibodies with S protein. 2021 Genomics Result SARS_CoV_2 L452R 23 28 S 84 85 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Furthermore, the B.1.351 lineage (also known as 20H/501Y.V2) was first identified in Nelson Mandela Bay, South Africa, which can be traced back to the beginning of October 2020, carries K417N, E484K, and N501Y on S protein RBD. 2021 Genomics Result SARS_CoV_2 E484K;K417N;N501Y 193;186;204 198;191;209 RBD;S 223;213 226;214 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. However, mutation N439K is not as disruptive as E484K, K417N, N501Y, and N501T. 2021 Genomics Result SARS_CoV_2 E484K;K417N;N439K;N501T;N501Y 48;55;18;73;62 53;60;23;78;67 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. However, T478K does not pose a problem to antibodies. 2021 Genomics Result SARS_CoV_2 T478K 9 14 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. However, the increasing rate of the N439K mutation slows down recently. 2021 Genomics Result SARS_CoV_2 N439K 36 41 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. It can be seen that mutations N501Y, L452R, T478K, N501T, N550K, F490S, V483F, L452M, and A348S have relatively high BFE changes of the binding of S protein and ACE2, suggesting that they may lead to more infectious variants. 2021 Genomics Result SARS_CoV_2 A348S;F490S;L452M;L452R;N501T;N501Y;N550K;T478K;V483F 90;65;79;37;51;30;58;44;72 95;70;84;42;56;35;63;49;77 S 147 148 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. It is interesting to understand whether newly identified fast-growing mutations N439K, L452R, S477R, and E484K are also disruptive to vaccines and antibodies. 2021 Genomics Result SARS_CoV_2 E484K;L452R;N439K;S477R 105;87;80;94 110;92;85;99 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. It is worth to mention that except for N440K, all the ACE2 binding-strengthen mutations in India are either VE or VW mutations and have rapidly grown since February 06, 2021. 2021 Genomics Result SARS_CoV_2 N440K 39 44 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Moreover, India variant B.1.617 has a 'double mutation' L452R and E484Q that are more infectious and vaccine evading, indicating that India's dire COVID-19 situation. 2021 Genomics Result SARS_CoV_2 E484Q;L452R 66;56 71;61 COVID-19 147 155 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Moreover, L452R, N501Y, and N501T are also HF mutations, which should receive high attention. 2021 Genomics Result SARS_CoV_2 L452R;N501T;N501Y 10;28;17 15;33;22 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Moreover, mutation N501Y will moderately weaken the binding of S protein with antibodies such as CC12.1/CR3022, COVOX-88/-45, COVOX-88, etc. 2021 Genomics Result SARS_CoV_2 N501Y 19 24 S 63 64 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Moreover, mutations V367F, E484K, N354D, and S373L with positive BFE changes also have a relatively higher mutation rate since early 2021, indicating that these four mutations may strengthen the binding of ACE2 and the S protein RBD, and potentially increase the infectivity of SARS-CoV-2. 2021 Genomics Result SARS_CoV_2 E484K;N354D;S373L;V367F 27;34;45;20 32;39;50;25 RBD;S 229;219 232;220 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Moreover, one ACE2 binding-strengthening mutation N440K with a high frequency has a relatively high growth rate since 2021. 2021 Genomics Result SARS_CoV_2 N440K 50 55 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Moreover, the frequency and predicted BFE changes are both at a high level for mutations N501T, Y508H. 2021 Genomics Result SARS_CoV_2 N501T;Y508H 89;96 94;101 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Mutation K417N will disruptively weaken the binding of S protein with a large number of antibodies. 2021 Genomics Result SARS_CoV_2 K417N 9 14 S 55 56 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Mutation N501T could weaken antibodies B38, CC12.1, S309 S2H12 S304, etc. 2021 Genomics Result SARS_CoV_2 N501T 9 14 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Mutation N501Y could weaken antibodies B38, A fab, CC12.1, VH binder, S309 S2H12 S304, C1A:B12, 910 30, STE90-C11, COVOX-150, COVOX-40, COVOX-88, and COVOX-269. 2021 Genomics Result SARS_CoV_2 N501Y 9 14 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Mutation S477R may even enhance the binding of most antibodies to the RBD. 2021 Genomics Result SARS_CoV_2 S477R 9 14 RBD 70 73 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Mutation S477R that induce the positive BFE changes has a very rapid growth between November 28, 2020, to December 08, 2020, while the number of S447R mutations has recently not increased rapidly. 2021 Genomics Result SARS_CoV_2 S447R;S477R 145;9 150;14 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Mutation S494P will disruptively weaken the binding of S protein with antibodies such as H11-D4, H11-H4, and LY-CoV555. 2021 Genomics Result SARS_CoV_2 S494P 9 14 S 55 56 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Mutation T478K has the largest BFE change which is nearly 1 kcal/mol. 2021 Genomics Result SARS_CoV_2 T478K 9 14 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Notably, the growth rate of mutation E484Q increases at the middle March of 2021. 2021 Genomics Result SARS_CoV_2 E484Q 37 42 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. S477N can slightly weaken antibodies BD23 and CV07-250. 2021 Genomics Result SARS_CoV_2 S477N 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Similar to the United Kingdom, the VW mutation N501Y and VE mutation E484K recently have a high log growth rate. 2021 Genomics Result SARS_CoV_2 E484K;N501Y 69;47 74;52 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Similarly, mutation K417N, which is a helix-residue of the RBD, could weaken antibodies B38, CB6, CV30, CC12.1, COVA2-04, BD-604, BD-236, A fab, P2C:1F11, C1A:B12, C1A:B3, C1A:F10, C1A:C2, etc. 2021 Genomics Result SARS_CoV_2 K417N 20 25 RBD 59 62 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Singapore also has ACE2 binding-strengthening mutations K417N, E484K, N501Y, S477N, and L452R, as those found in other countries. 2021 Genomics Result SARS_CoV_2 E484K;K417N;L452R;N501Y;S477N 63;56;88;70;77 68;61;93;75;82 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. The N501Y, S477N, L452R, N439K, and E484K mutations are the top mutations with significant frequencies. 2021 Genomics Result SARS_CoV_2 E484K;L452R;N439K;N501Y;S477N 36;18;25;4;11 41;23;30;9;16 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. The number of ACE2 binding-strengthening mutation N439K has kept a high growth rate since early August. 2021 Genomics Result SARS_CoV_2 N439K 50 55 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. This variant contains three mutations in the S protein RBD: VE mutation K417T, VE mutation E484K, and VW mutation N501Y. 2021 Genomics Result SARS_CoV_2 E484K;K417T;N501Y 91;72;114 96;77;119 RBD;S 55;45 58;46 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. To be noted, L452R is a VE mutation and HF mutation that had been reported as the key mutation that linked to COVID-19 outbreaks in California on January 17, 2021. 2021 Genomics Result SARS_CoV_2 L452R 13 18 COVID-19 110 118 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. To be noted, neither S477R nor S477N has much negative effect on the existing antibodies. 2021 Genomics Result SARS_CoV_2 S477N;S477R 31;21 36;26 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. we can see that the N501Y mutation with a positive BFE change have a relatively high growth rate since early September 2020, which consist with the news that a new strain B.1.1.7 (also known as 20I/501Y.V1) in the United Kingdom has the potential to increase the pandemic trajectory. 2021 Genomics Result SARS_CoV_2 N501Y 20 25 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. We can see that VE mutations F490S, L452R, VW mutations F490L, N501Y, V483A, and N501T have relatively high BFE changes of the binding of S protein and ACE2, suggesting that they are high-risk mutations. 2021 Genomics Result SARS_CoV_2 F490L;F490S;L452R;N501T;N501Y;V483A 56;29;36;81;63;70 61;34;41;86;68;75 S 138 139 34011679 Shedding of Viable Virus in Asymptomatic SARS-CoV-2 Carriers. All SARS-CoV-2 strains belonged to clade 19A identified by Nextstrain, and they harbored a single nucleotide mutation at position 11083 (G11083T transversion), leading to a nonsynonymous amino acid substitution (Leu37Phe) in nonstructural protein 6 (nsp6), as previously described from the Diamond Princess outbreak event. 2021 mSphere Result SARS_CoV_2 G11083T;L37F 137;212 144;220 Nsp6 250 254 34011679 Shedding of Viable Virus in Asymptomatic SARS-CoV-2 Carriers. The consensus sequence obtained from Carrier_1 on 21 and 24 February shared the same intrahost single nucleotide variation (iSNV) at position 5218 with a frequency of 29 to 62% (T5218C transition). 2021 mSphere Result SARS_CoV_2 T5218C 178 184 34011679 Shedding of Viable Virus in Asymptomatic SARS-CoV-2 Carriers. The former mutation in the nsp4 gene is synonymous, whereas the latter leads to a nonsynonymous amino acid substitution (Ala138Val) in nsp14, which possesses a 3'-to-5' exonuclease activity. 2021 mSphere Result SARS_CoV_2 A138V 121 130 Exonuclease;Nsp4 169;27 180;31 34011679 Shedding of Viable Virus in Asymptomatic SARS-CoV-2 Carriers. While iSNV at position 5218 was not found after 28 February, two novel SNVs emerged in the sample collected on March 1 at positions 8626 (C8626T transition) and 18452 (C18452T transition). 2021 mSphere Result SARS_CoV_2 C18452T;C8626T 168;138 175;144 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. As shown in the Figure 1B and Figure S3A, all the mutation sites stay far away from the protein-protein interface except for GLY476 (giving G476S mutant), ARG408 (giving R408I mutant) and VAL484 (giving V483A mutant). 2021 Briefings in bioinformatics Result SARS_CoV_2 G476S;R408I;V483A 140;170;203 145;175;208 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. Compared to -16.04 kcal/mol binding free energy of the prototype SARS-CoV-2 RBD system, three mutant types, N354D/D364Y, D364Y and V367F, showed significant lower values indicating the significant higher binding affinities with hACE2. 2021 Briefings in bioinformatics Result SARS_CoV_2 D364Y;N354D;V367F;D364Y 121;108;131;114 126;113;136;119 RBD 76 79 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. For cases of F342L, N354D, N354D/D364Y, D364Y, V367F and R408I, old interaction disappeared or new strong interaction formed, thus drastic binding affinity changes were observed (Figure 2). 2021 Briefings in bioinformatics Result SARS_CoV_2 D364Y;F342L;N354D;N354D;R408I;V367F;D364Y 40;13;20;27;57;47;33 45;18;25;32;62;52;38 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. For each of the mutant types, which include V341I, F342L, N354D, N354D/D364Y, D364Y, V367F, R408I, A435S, W436R, G476S and V483A, two independent MD runs were carried out. 2021 Briefings in bioinformatics Result SARS_CoV_2 A435S;D364Y;F342L;G476S;N354D;N354D;R408I;V341I;V367F;V483A;W436R;D364Y 99;78;51;113;58;65;92;44;85;123;106;71 104;83;56;118;63;70;97;49;90;128;111;76 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. For the R408I case, in the prototype ARG408 forming a salt-bridge with the ASP405, moreover, it can also interact with GLN414 by forming a side chain-side chai hydrogen-bond (Figure S3G). 2021 Briefings in bioinformatics Result SARS_CoV_2 R408I 8 13 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. For this reason, the W436R mutant achieves the lowest RBD free energy than the other RBDs, suggesting its high RBD stability. 2021 Briefings in bioinformatics Result SARS_CoV_2 W436R 21 26 RBD;RBD;RBD 54;85;111 57;89;114 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. For V483A case, no polar contact with nearby residues has been observed before or after the mutation. 2021 Briefings in bioinformatics Result SARS_CoV_2 V483A 4 9 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. Four mutant types showed comparable binding affinity with the wild type, which are V341I, A435S, W436R and V483A. 2021 Briefings in bioinformatics Result SARS_CoV_2 A435S;V341I;V483A;W436R 90;83;107;97 95;88;112;102 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. Four mutant types showed lower binding affinity than the prototype system, which are F342L, N354D, R408I and G476S. 2021 Briefings in bioinformatics Result SARS_CoV_2 F342L;G476S;N354D;R408I 85;109;92;99 90;114;97;104 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. From other publication, R408I was once reported to have a lower binding affinity, which is consistent with our study. 2021 Briefings in bioinformatics Result SARS_CoV_2 R408I 24 29 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. In the case of N354D/D364Y, D364Y mutation significantly enhanced the binding affinity, while N354D lowered the binding affinity, indicating the mutation on Asp364 contributed more to the increment of the mutant N354D/D364Y binding affinity. 2021 Briefings in bioinformatics Result SARS_CoV_2 D364Y;N354D;N354D;N354D;D364Y;D364Y 28;15;94;212;21;218 33;20;99;217;26;223 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. It is pointed out that the single D364Y mutant has not been observed in any country. 2021 Briefings in bioinformatics Result SARS_CoV_2 D364Y 34 39 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. On the other hand, as for W436R, the TRP436 formed two hydrogen bonds with ARG509 in the wild type (Figure S3I); after it was mutated into ARG, four hydrogen bonds formed between ARG436 and ARG509/SER373 (Figure S4H). 2021 Briefings in bioinformatics Result SARS_CoV_2 W436R 26 31 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. Overall, most of the RBDs had comparable free energies with that of the prototype RBD except for R408I and W436R. 2021 Briefings in bioinformatics Result SARS_CoV_2 R408I;W436R 97;107 102;112 RBD;RBD 21;82 25;85 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. R408I exhibited a significantly higher RBD free energy than the prototype, while W436R RBD had a significantly lower free energy than the prototype. 2021 Briefings in bioinformatics Result SARS_CoV_2 W436R;R408I 81;0 86;5 RBD;RBD 39;87 42;90 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. The predicted binding affinities in our study were about 0.5-fold higher than the experimental values, with binding affinity of W436R was slightly higher than that of the prototype, and other two types, V367F and N354D/D364Y, exhibiting more higher binding affinities (Table 1 and Table S1). 2021 Briefings in bioinformatics Result SARS_CoV_2 N354D;V367F;W436R;D364Y 213;203;128;219 218;208;133;224 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. The simulation results suggested that all the three mutants (N354D/D364Y, V367F and W436R) can enhance the binding between spike RBD and hACE2, which agrees with the experiment. 2021 Briefings in bioinformatics Result SARS_CoV_2 V367F;W436R;N354D;D364Y 74;84;61;67 79;89;66;72 S;RBD 123;129 128;132 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. The unfavorable RBD energy and less binding affinity make R408I less risk compared to other mutants. 2021 Briefings in bioinformatics Result SARS_CoV_2 R408I 58 63 RBD 16 19 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. To be specific, V341I, A435S, W436R, G476S and V483I, part of or all of interaction formed before mutation remained after the mutation, and only slight binding affinity change was observed for these types. 2021 Briefings in bioinformatics Result SARS_CoV_2 A435S;G476S;V341I;V483I;W436R 23;37;16;47;30 28;42;21;52;35 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. Two of these three mutants, N354D/D364Y and V367F, have drawn extensive attention as they showed up in multiple countries, indicating its enhanced binding affinity in the real world. 2021 Briefings in bioinformatics Result SARS_CoV_2 N354D;V367F;D364Y 28;44;34 33;49;39 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. Unlike GLY476, the DeltaDeltaGinter of ARG408 is neglectable (~ -0.2 kcal/mol) and the DeltaDeltaGinter of VAL483 is only significant for a few mutants including A435S and G476S. 2021 Briefings in bioinformatics Result SARS_CoV_2 A435S;G476S 162;172 167;177 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. A new mutation in the Receptor Binding Domain (RBD) of the spike protein (G23012A: E484) was found in two genomes (9.5%) (GISAID IDs: EPI_ISL_832010 and EPI_ISL_832013) from mid-October 2020. 2021 BMC genomics Result SARS_CoV_2 G23012A 74 81 RBD;S;RBD 22;59;47 45;64;50 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. All B.1.1.248 sequences shared C241T (5 UTR), C3037T (ORF1ab nsp3:F924), C12053T (ORF1ab nsp7:L3930F), C14408T (ORF1ab RdRp:L4715), A23403G (S:D614G), G25088T (S:V1176F), and GGG28881-28883AAC (N:RG203-204KR) replacements. 2021 BMC genomics Result SARS_CoV_2 A23403G;C12053T;C14408T;C241T;C3037T;G25088T;D614G;L3930F;V1176F 132;73;103;31;46;151;143;94;162 139;80;110;36;52;158;148;100;168 ORF1ab;ORF1ab;ORF1ab;Nsp3;Nsp7;RdRP;N;S;S 54;82;112;61;89;119;194;141;160 60;88;118;65;93;123;195;142;161 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. All B.1.1.33 sequences shared T27299C (ORF6:I33T), GGG28881-28883AAC (N:RG203-204KR), and T29148C (N:I292T) mutations. 2021 BMC genomics Result SARS_CoV_2 T27299C;T29148C;I292T;I33T 30;90;101;44 37;97;106;48 ORF6;N;N 39;70;99 43;71;100 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. High frequency (>5 genomes) missense mutations were observed in the following positions (absolute nucleotide position: amino acid inside the gene): ORF1ab (C12053T: L3930F), Surface (S) glycoprotein (A23403G: D614G; G25088T: V1176F), ORF6 (T27299C: I33T), and Nucleocapsid (N) protein (GGG28881-28883ACC: RG203-204KR; T29148C: I292T). 2021 BMC genomics Result SARS_CoV_2 D614G;G25088T;I292T;I33T;L3930F;T29148C;V1176F;A23403G;C12053T;T27299C 209;216;327;249;165;318;225;200;156;240 214;223;332;253;171;325;231;207;163;247 N;ORF1ab;ORF6;N;S 260;148;234;274;183 272;154;238;275;184 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. Most importantly, the introduction of the P.2 lineage that harbors the E484K mutation was dated on September 09, 2020 (95% HPD: September 09October 05, 2020) probably introduced from the Rio de Janeiro state. 2021 BMC genomics Result SARS_CoV_2 E484K 71 76 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. We also identified another cluster of four patients characterized by three unique mutations: 25429 (ORF3a: V13L), 25,509 (ORF3a), and 27,976 (ORF8: H28R). 2021 BMC genomics Result SARS_CoV_2 H28R;V13L 148;107 152;111 ORF3a;ORF3a;ORF8 100;122;142 105;127;146 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. Flow cytometry and SPR data showed that both the SARS-CoV-2 RBD and the K417R mutant have no detectable interaction with mouse, rat, or European hedgehog ACE2, but the Q498H and K417R-Q498H mutants acquired high-binding affinity with the ACE2s from mouse (287.7 +- 23.7 nM and 248.0 +- 21.9 nM), rat (338.7 +- 74.9 nM and 319.8 +- 70.0 nM), and European hedgehog (258.3 +- 9.5 nM and 484.0 +- 42.9 nM) (Fig 6A-C). 2021 The EMBO journal Result SARS_CoV_2 K417R;K417R;Q498H;Q498H 72;178;168;184 77;183;173;189 RBD 60 63 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. In addition, the Q498H mutant displayed 5-fold stronger binding affinity with hACE2 than the wild-type SARS-CoV-2 RBD (Fig 6C). 2021 The EMBO journal Result SARS_CoV_2 Q498H 17 22 RBD 114 117 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. In agreement with observation above, while the N38 residue on European hedgehog ACE2 is neutral as D38, the Q42E mutation introduced negative charges which further attract the Q498H mutant (Fig EV5A and B). 2021 The EMBO journal Result SARS_CoV_2 Q42E;Q498H 108;176 112;181 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. In particular, the Q498H mutation found in both pangolin CoV RBDs may strengthen the interaction with the helix alpha1 of hACE2 by enhancing positive charge (Fig EV5B), and the K417R mutation from GD/1/2019 RBD may also enhance the contacts with hACE2 by forming one extra H-bond. 2021 The EMBO journal Result SARS_CoV_2 K417R;Q498H 177;19 182;24 RBD;RBD 61;207 65;210 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. The mutation from glutamine (Q) to histidine (H) leads to a drastic increase in positive charges, which enhanced the affinity between Q498H mutants with human, mouse, or rat ACE2. 2021 The EMBO journal Result SARS_CoV_2 Q498H 134 139 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. Therefore, we introduced the K417R, Q498H, or K417R-Q498H mutation to the SARS-CoV-2 RBD to mimic the key variant residues of GD/1/2019 RBD. 2021 The EMBO journal Result SARS_CoV_2 K417R;K417R;Q498H;Q498H 29;46;36;52 34;51;41;57 RBD;RBD 85;136 88;139 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. To explore the mechanism of the changes in binding affinity caused by Q498H mutation, we identified 4 conserved residues (D38, Y41, Q42, and S45) on the surface of human, mouse, and rat ACE2s that interact with Q498H mutation, and a Q42E mutation on European hedgehog ACE2 interacting with Q498H. 2021 The EMBO journal Result SARS_CoV_2 Q42E;Q498H;Q498H;Q498H 233;70;211;290 237;75;216;295 34019466 Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. Blastn search of the N gene from a sequence enclosing both 28932C > T and 28948C > T revealed the presence of five additional sequences with this very same mutation pair, all of which were from Switzerland. 2021 Emerging microbes & infections Result SARS_CoV_2 C28932T;C28948T 59;74 69;84 N 21 22 34019466 Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. In addition, a non-synonymous mutation was present at position 28932C > T (N gene A220 V) which was shared by all B.1.177.75 sequences (Figure 1A). 2021 Emerging microbes & infections Result SARS_CoV_2 C28932T;A220V 63;82 73;88 N 75 76 34019466 Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. Interestingly, a unique mutation, synonymous 28948C > T, was found in the N-negative B.1.177.75 strains. 2021 Emerging microbes & infections Result SARS_CoV_2 C28948T 45 55 N 74 75 34019466 Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. Thus, B.1.177.75 virus variants containing the 28932C > T mutation were diagnosed as positive for SARS-CoV-2 RNA with the canonical diagnostic +/+/+ pattern, while B.1.177.75 virus variants containing both the 28932C > T and 28948C > T mutation resulted in +/+/- for ORF1ab, S and N genes, respectively. 2021 Emerging microbes & infections Result SARS_CoV_2 C28932T;C28932T;C28948T 47;210;225 57;220;235 ORF1ab;N;S 267;281;275 273;282;276 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. and tested the antibodies against D614G and RBD.V2 pseudovirus. 2021 Cell research Result SARS_CoV_2 D614G 34 39 RBD 44 47 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. As this interaction is mediated by the main chain group, the E484K substitution only has a limited impact on the neutralizing power of BD-623. 2021 Cell research Result SARS_CoV_2 E484K 61 66 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. BD-604 is also slightly affected by the K417N mutation. 2021 Cell research Result SARS_CoV_2 K417N 40 45 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. N501Y also accounted for NT50 reduction but less than E484K, while K417N did not reduce neutralization by plasma. 2021 Cell research Result SARS_CoV_2 E484K;K417N;N501Y 54;67;0 59;72;5 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. N501Y and K417N mutations also contributed to neutralization reduction, but to a much lower degree than E484K, resulting in a 1.5-fold and a 1.9-fold increase in IC50, respectively. 2021 Cell research Result SARS_CoV_2 E484K;K417N;N501Y 104;10;0 109;15;5 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. Plasma's efficacy against SARS-CoV-2 is first validated by VSV-pseudovirus (D614G) neutralization assay. 2021 Cell research Result SARS_CoV_2 D614G 76 81 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. Similar to NAb results, E484K largely contributed to the loss of plasma neutralizing activity caused by RBD mutations. 2021 Cell research Result SARS_CoV_2 E484K 24 29 RBD 104 107 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. Strikingly, 50 out of 80 anti-RBD NAbs showed a > 3-fold reduction of neutralization toward pseudovirus carrying K417N/E484K/N501Y mutations (RBD.V2), among which 43 anti-RBD NAbs display a > 10-fold increase in half-maximal inhibitory concentration (IC50). 2021 Cell research Result SARS_CoV_2 K417N;E484K;N501Y 113;119;125 118;124;130 RBD;RBD;RBD 30;142;171 33;145;174 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. The majority of neutralization reduction was caused by E484K, which could completely abolish antibodies' neutralization activity, resulting in a > 10-fold increase on average in IC50 values. 2021 Cell research Result SARS_CoV_2 E484K 55 60 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. Thus, K417N, or E484K, or N501Y found in the 501Y.V2 variant would all greatly reduce the interaction between RBD and BD-508. 2021 Cell research Result SARS_CoV_2 E484K;K417N;N501Y 16;6;26 21;11;31 RBD 110 113 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. Together, 501Y.V2 would cause a major reduction in neutralization by convalescent plasma and CoronaVac vaccinee plasma through E484K and 242-244Delta, with the effects being additive. 2021 Cell research Result SARS_CoV_2 E484K 127 132 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. A similar mutation (K417V) was experimentally shown to reduce affinity 2-fold. 2021 Journal of molecular biology Result SARS_CoV_2 K417V 20 25 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. According to deep mutational scanning analysis, the polar rearrangements upon mutation of glutamate to lysine at position 484 slightly increase affinity for the receptor. 2021 Journal of molecular biology Result SARS_CoV_2 E484K 90 125 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. As the K417T mutation in strain P.1 (first identified in Brazil) will likewise disrupt the intramolecular salt bridge, we expect a similar intermediate affinity for this variant. 2021 Journal of molecular biology Result SARS_CoV_2 K417T 7 12 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. Compared to the effect of N501Y, the effect of the single E484K mutation on binding affinity is minor (1.4-fold; Figure 1(F), table 1). 2021 Journal of molecular biology Result SARS_CoV_2 E484K;N501Y 58;26 63;31 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. Double mutant E484K/N501Y forms a slightly more stable complex with hACE2 than the N501Y single mutant (1.4 nM instead of 2.4 nM, Table 1, Figure 1(F)). 2021 Journal of molecular biology Result SARS_CoV_2 E484K;N501Y;N501Y 14;83;20 19;88;25 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. E484K is a charge reversal mutation, resulting in the loss of an ion-pair across the interface with hACE2 lysine 31 (Figure 1(B)). 2021 Journal of molecular biology Result SARS_CoV_2 E484K 0 5 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. Interestingly, while the increase in affinity for N501Y is due to decreased dissociation, increased affinity for E484K is accomplished through faster association. 2021 Journal of molecular biology Result SARS_CoV_2 E484K;N501Y 113;50 118;55 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. The change in affinity is predominantly caused by a reduction in the dissociation rate constant, indicating the N501Y spike protein remains bound to the receptor for a longer time period than wild type RBD, increasing the chance to undergo the proper conformational change and induce membrane fusion and cell entry. 2021 Journal of molecular biology Result SARS_CoV_2 N501Y 112 117 Membrane;S;RBD 284;118;202 292;123;205 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. The combination of all three mutations, as present in strain B.1.351 (first identified in South Africa), is predominantly additive and results in a 2.4-fold less stable complex than for N501Y alone due to the effect of K417N, but still 3-fold more stable than with wild type RBD (Figure 1(F), table 1). 2021 Journal of molecular biology Result SARS_CoV_2 K417N;N501Y 219;186 224;191 RBD 275 278 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. The increase in affinity for the N501Y variant is 7.1-fold (K D = 2.4 nM instead of 17 nM; Figure 1(F), table 1). 2021 Journal of molecular biology Result SARS_CoV_2 N501Y 33 38 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. The K417N mutation is expected to reduce affinity as replacement of the lysine with a shorter asparagine (in B.1.351, or threonine in P.1) will disrupt the salt-bridge across the interface (Figure S1(E) and (F)). 2021 Journal of molecular biology Result SARS_CoV_2 K417N 4 9 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. The single K417N mutation destabilizes the interaction with hACE2 4-fold through a combination of slower binding and faster dissociation (Figure 1(F), table 1). 2021 Journal of molecular biology Result SARS_CoV_2 K417N 11 16 34029587 Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication. Cells transfected with Flag-N or Flag-N harboring R95K, R177K, R95K/R177K and p5'-UTR:CoV-2 were labeled with 4-thiouridine and UV cross-linked. 2021 The Journal of biological chemistry Result SARS_CoV_2 R177K;R95K;R95K;R177K 56;50;63;68 61;54;67;73 N;N 28;38 29;39 34029587 Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication. Cells with N protein with R95K or R95K/R177K substitution showed increased SG formation in comparison to those transfected with Flag-N or Flag-N R177K (Figure 4 A, R95K 35.82+-3.03%, R177K 26.74+-2.52%, R95K/R177K 36.62+-2.78% versus wild type N 25.30+-2.62%). 2021 The Journal of biological chemistry Result SARS_CoV_2 R177K;R177K;R95K;R95K;R95K;R95K;R177K;R177K 145;183;26;34;164;203;39;208 150;188;30;38;168;207;44;213 N;N;N;N 11;133;143;244 12;134;144;245 34029587 Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication. Importantly, both the single R95K and R177K or the double R95K/R177K substitution of N protein abolished RNA binding activity (Figure 5B). 2021 The Journal of biological chemistry Result SARS_CoV_2 R177K;R95K;R95K;R177K 38;29;58;63 43;33;62;68 N 85 86 34029587 Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication. Mutation of arginine 68 (R68K) in the N-terminal fragment had no significant effect on arginine methylation, while mutation of arginine 95 (R95K) completely abolished PRMT1 methylation (Figure 1E), suggesting that R95 was the methylated residue in the GST-N 1-150 fragment. 2021 The Journal of biological chemistry Result SARS_CoV_2 R68K;R95K 25;140 29;144 N 38 39 34029937 Corilagin prevents SARS-CoV-2 infection by targeting RBD-ACE2 binding. the preferential binding pocket for corilagin involved residues Cys 336 to Phe 374. 2021 Phytomedicine Result SARS_CoV_2 C336F 64 78 34033650 SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. A thermodynamic analysis showed that D614G mutation resulted in slightly destabilizing the protein with a DeltaDeltaG: -0.086 kcal/mol and increasing the vibrational entropy to DeltaDeltaSVib 0.137 kcal.mol-1.K-1 as seen in Fig 8A where the red parts indicate more flexibility. 2021 PloS one Result SARS_CoV_2 D614G 37 42 34033650 SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. D614G mutation. 2021 PloS one Result SARS_CoV_2 D614G 0 5 34033650 SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. P314L mutation (or Position P323 on the protein structure PDB ID:6M71 because of a frame shift and written as P323L hereafter) is positioned on the interface domain of the RdRp (or nsp12) between A250-R365 residues. 2021 PloS one Result SARS_CoV_2 P323L;P314L 110;0 115;5 Nsp12;RdRP 181;172 186;176 34033650 SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. P314L/P323L mutation. 2021 PloS one Result SARS_CoV_2 P323L;P314L 6;0 11;5 34033650 SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. Such flexibility will render the furin cleavage site more accessible which is concomitant with the virulence of the D614G mutation. 2021 PloS one Result SARS_CoV_2 D614G 116 121 34033650 SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. Therefore, the D614G mutation is believed to increase SARS-CoV-2 virulence. 2021 PloS one Result SARS_CoV_2 D614G 15 20 34039497 An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose. In march 2020, we found a total of 15 D614G sequences out of 170 reference sequences of SARS-CoV-2. 2021 Vaccine Result SARS_CoV_2 D614G 38 43 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. A multivariate generalized Poisson regression model with the E gene (C t < 25) as the dependent variable showed that the presence of the D614G mutation in the SARS-CoV-2 spike protein was more likely to have a lower C t (C t < 25) in real-time RT-PCR than the original (D614) (prevalence ratio = 2.75; 95% confidence interval, 1.19-6.38) (Table S5). 2021 Journal of medical virology Result SARS_CoV_2 D614G 137 142 S;E 170;61 175;62 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. All of the eight isolates had the D614G mutation and were classified as 20C clade (lineage B.1 according to Pangolin). 2021 Journal of medical virology Result SARS_CoV_2 D614G 34 39 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. Association between D614G and lower C t of real-time PCR of SARS-CoV-2 E gene. 2021 Journal of medical virology Result SARS_CoV_2 D614G 20 25 E 71 72 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. In particular, the A to G mutation at nucleotide position 23,403 caused Spike D614G amino acid change (Table S3). 2021 Journal of medical virology Result SARS_CoV_2 D614G 78 83 S 72 77 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. ORF8 had one missense mutation at position T28144C that led to an amino acid change from Leucine to Serine (L84S). 2021 Journal of medical virology Result SARS_CoV_2 T28144C;L84S 43;108 50;112 ORF8 0 4 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. Particularly, G8388A in NSP3 and A8987T in NSP4 which lead to amino acid change including S2708D and I2907F were the most common (27/27 samples). 2021 Journal of medical virology Result SARS_CoV_2 A8987T;G8388A;I2907F;S2708D 33;14;101;90 39;20;107;96 Nsp3;Nsp4 24;43 28;47 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. Sequences of these two SARS-CoV-2 strains were identical (>99%) and originated from the United States, classified as in 19B clade, but did not have D614G mutation (Figure 1). 2021 Journal of medical virology Result SARS_CoV_2 D614G 148 153 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. We also found an alteration in the nonstructural protein RNA-dependent RNA polymerase (RdRp) that resulted in amino acid changes, including P314L (18/27 samples) (Table S3). 2021 Journal of medical virology Result SARS_CoV_2 P314L 140 145 RdRp;RdRP 57;87 85;91 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. We also found that the appearance of the ORF1ab-14408 mutation was inversely correlated with D614G (Table S4). 2021 Journal of medical virology Result SARS_CoV_2 D614G 93 98 ORF1ab 41 47 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. Compared to those infected with 20AS or the M1V, patients infected with the M4V were older and more likely to present with fever. 2021 Clinical microbiology and infection Result SARS_CoV_2 M1V;M4V 44;76 47;79 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. Finally, a lower rate of hospitalisation associated with N501YV infection as compared to 20AS and M4V. 2021 Clinical microbiology and infection Result SARS_CoV_2 M4V 98 101 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. In addition, lower rate of rhinitis was observed in M4V infection as compared to 20AS and a higher hospitalisation rate was associated with M4V infection as compared to M1V. 2021 Clinical microbiology and infection Result SARS_CoV_2 M1V;M4V;M4V 169;52;140 172;55;143 Rhinitis 27 35 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. It should be noted that no patient infected with the M1V was transferred to an ICU or died. 2021 Clinical microbiology and infection Result SARS_CoV_2 M1V 53 56 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. Notably, lower rates of dyspnoea, rhinitis and hospitalisation were seen in patients infected with the M1V as compared to those infected with 20AS. 2021 Clinical microbiology and infection Result SARS_CoV_2 M1V 103 106 Rhinitis 34 42 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. Older age and fever associated with N501YV infection as compared to M1V. 2021 Clinical microbiology and infection Result SARS_CoV_2 M1V 68 71 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. The M1V reached a very weak peak but represented up to 100% of infections during part of the month of July, then disappeared after a month-and-a-half. 2021 Clinical microbiology and infection Result SARS_CoV_2 M1V 4 7 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. The M4V which appeared in July presented an atypical wave form and continued to represent a significant proportion of the cases in February, indicating a duration of seven months which is not comparable to that of the other two epidemics. 2021 Clinical microbiology and infection Result SARS_CoV_2 M4V 4 7 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. We identified 1,080 patients infected with four principal lineages: 20AS (N=339), M1V (N=98), M4V (N=420) and N501YV (N=223). 2021 Clinical microbiology and infection Result SARS_CoV_2 M1V;M4V 82;94 85;97 34044153 SARS-CoV-2 N gene dropout and N gene Ct value shift as indicator for the presence of B.1.1.7 lineage in a commercial multiplex PCR assay. These analyses revealed that all of the samples which had previously yielded N gene-specific Ct shifts or dropouts (DeltaCt N/RdRp or N/S score > 6) belonged to the B.1.1.7 lineage, whereas the remaining 58 SARS-CoV-2 positive samples with DeltaCt N/RdRp or DeltaCt N/S < 6 were all classified as non-B.1.1.7 variants (B.1.1.317 (n=2), B.1.351 (n=1), N501Y+, E484K+ (n=1), N501Y-, E484K+ (n=1) and N501Y-, Del. 2021 Clinical microbiology and infection Result SARS_CoV_2 E484K;E484K;N501Y;N501Y;N501Y 359;381;351;373;398 364;386;356;378;403 RdRP;RdRP;N 126;250;77 130;254;78 34044153 SARS-CoV-2 N gene dropout and N gene Ct value shift as indicator for the presence of B.1.1.7 lineage in a commercial multiplex PCR assay. This confirmed that the D3L mutation can be identified by the Allplex SARS-CoV-2/FluA/FluB/RSV assay, but not by the Allplex 2019-nCoV test (Figure 2). 2021 Clinical microbiology and infection Result SARS_CoV_2 D3L 24 27 34044153 SARS-CoV-2 N gene dropout and N gene Ct value shift as indicator for the presence of B.1.1.7 lineage in a commercial multiplex PCR assay. To elucidate the underlying molecular mechanism resulting in the observed N gene dropout or Ct value shift, we cloned the N gene coding sequence with and without D3L mutation into pCR -TOPO vectors which were then used for PCR analysis. 2021 Clinical microbiology and infection Result SARS_CoV_2 D3L 162 165 N;N 74;122 75;123 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. A similar trend was observed in Brazil, as E484K was observed in sequences obtained from October (n = 31), November (n = 87), and December (n = 40). 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 43 48 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. As B.1.1.28 is the ancestral lineage of P.1 and P.2, sequences from these three lineages harbor the G25088T (S:V1176F) mutation. 2021 Infection, genetics and evolution Result SARS_CoV_2 G25088T;V1176F 100;111 107;117 S 109 110 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. clades are part of a larger monophyletic group with B.1.1.28, which is separated from the B.1.1.33 and N.9 (B.1.1.33 with E484K) clades and the reference genome. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 122 127 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Firstly detected in the South African B.1.351 lineage, the S1 protein mutation E484K is now present in new emerging variants from Brazil. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 79 84 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. For these residues under adaptive pressure, six are included in known mutation sites of spike protein, including E484K (L5F, S12F, P26S, D138Y, A688V). 2021 Infection, genetics and evolution Result SARS_CoV_2 A688V;D138Y;E484K;P26S;S12F;L5F 144;137;113;131;125;120 149;142;118;135;129;123 S 88 93 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Four sequences classified as N.9 carry B.1.1.33 lineage-defining mutations (T27299C (NS6:I33T) and T29148C (N:I292T)), but have also five missense mutations in ORF1ab and one in ORF7b (E33A). 2021 Infection, genetics and evolution Result SARS_CoV_2 T29148C;E33A;T27299C;I292T;I33T 99;185;76;110;89 106;189;83;115;93 ORF1ab;ORF7b;N 160;178;108 166;183;109 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. In this way, the spike protein of P.1 lineages in these Brazilian E484K mutated genomes is characterized by the presence of a variable number of modified sites, without the fixation of all known mutations. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 66 71 S 17 22 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Interestingly, the B.1.1.28 genomes grouped in the clades of P.1 and P.2 lineages according to the presence of the Nsp7:L71F mutation. 2021 Infection, genetics and evolution Result SARS_CoV_2 L71F 120 124 Nsp7 115 119 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Lineage-defining mutations as S:K471T, S:N501Y, S:T1027I, N:P80R, Nsp6:S106-107del, Nsp6:F108del, and NS8:E92K were found only in the P.1 group and reported for all 19 P.1 sequences. 2021 Infection, genetics and evolution Result SARS_CoV_2 E92K;F108del;K471T;N501Y;P80R;T1027I 106;89;32;41;60;50 110;96;37;46;64;56 Nsp6;Nsp6;N;S;S;S 66;84;58;30;39;48 70;88;59;31;40;49 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. New specific single substitutions (S:A27V, N:T16M, N:P151L, N:A267V, Nsp13:T216N, and Nsp14:P443S) were also evaluated. 2021 Infection, genetics and evolution Result SARS_CoV_2 A267V;A27V;P151L;P443S;T16M;T216N 62;37;53;92;45;75 67;41;58;97;49;80 Nsp13;N;N;N;S 69;43;51;60;35 74;44;52;61;36 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Of these, only site 222 is not related to the E484K-presenting lineages (A626S and P1263L/S are known). 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K;P1263L;P1263S;A626S 46;83;83;73 51;91;91;78 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Other mutations such as S:V1176F were not found only in N.9 (B.1.1.33.9) lineage. 2021 Infection, genetics and evolution Result SARS_CoV_2 V1176F 26 32 S 24 25 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Regarding the lineage-defining mutations from P.1 lineages, 14 of a total of 19 genomes from the Amazonas monophyletic group present the spike mutations L18F, T20N, P26S, D138Y, and R190S. 2021 Infection, genetics and evolution Result SARS_CoV_2 D138Y;L18F;P26S;R190S;T20N 171;153;165;182;159 176;157;169;187;163 S 137 142 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. S:D614G, N:R203K, N:G204R, 5'UTR:C241T, and synonymous substitutions in nucleotide positions C3037T and C14408T). 2021 Infection, genetics and evolution Result SARS_CoV_2 C14408T;C3037T;C241T;D614G;G204R;R203K 104;93;33;2;20;11 111;99;38;7;25;16 5'UTR;N;N;S 27;9;18;0 32;10;19;1 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Specifically, S:A27V is located in the N-terminal domain. 2021 Infection, genetics and evolution Result SARS_CoV_2 A27V 16 20 N;S 39;14 40;15 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The analysis of genomes containing E484K, downloaded from the GISAID database, showed a distribution of 169 amino acid residues corresponding to nonsynonymous mutations and four amino acid residue deletions in 134 Brazilian samples (Table S1) collected between October and December 2020. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 35 40 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The analysis of the E484K mutated sequence EPI_ISL_832010, early detected in the municipality of Esteio, Rio Grande do Sul, shows a simpler set of nonsynonymous mutations (n = 10) when compared to others. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 20 25 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The arising of E484K mutated genomes with at least four different associated mutation patterns for lineages P.1, P.2, and N.9 (B.1.1.33.9) can be seen over time in the aligned genomes. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 15 20 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The N.9 (B.1.1.33.9) lineage carrying the E484K mutation was found in Sao Paulo (n = 3) and Amazonas (n = 1), while P.1 sequences were found only in the Amazonas state (n = 19). 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 42 47 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The number of genetic changes associated with each E484K Brazilian lineage is highly diverse. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 51 56 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The presence of spike S:D614G, N:R203K, N:G204R, and Nsp12:P323L in all sequenced E484-containing genomes was observed. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;G204R;P323L;R203K 24;42;59;33 29;47;64;38 S;Nsp12;N;N;S 16;53;31;40;22 21;58;32;41;23 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The worldwide emergence of E484K began in March 2020, with three sequences firstly represented. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 27 32 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. There are also those mutations that are not known as lineage markers but were found in all lineages (n = 19) as Nsp3:K977Q, Nsp13:E341D, and NS3:S253P. 2021 Infection, genetics and evolution Result SARS_CoV_2 E341D;K977Q;S253P 130;117;145 135;122;150 Nsp13;Nsp3;NS3 124;112;141 129;116;144 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. This genome combines all the prevalent substitutions D614G from spike protein, N:R203K, N:G204R, and Nsp12:P323L, allied to other very frequent mutations (S:V1176F, N:A119S, N:M234I, Nsp5:L205V, and Nsp7:L71F). 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;A119S;G204R;L205V;L71F;M234I;P323L;R203K;V1176F 53;167;90;188;204;176;107;81;157 58;172;95;193;208;181;112;86;163 S;Nsp12;Nsp7;Nsp5;N;N;N;N;S 64;101;199;183;79;88;165;174;155 69;106;203;187;80;89;166;175;156 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. This pattern indicates a new lineage derived from B.1.1.33 (posteriorly defined as B.1.1.33.9 or N.9 lineage), which also possesses the E484K replacement, as P.1 and P.2 sequences. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 136 141 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Three of them (189, 191, and 564) are near residues presenting known nonsynonymous mutations in the E484K mutated genomes, as S:R190S and S:F565L. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K;F565L;R190S 100;140;128 105;145;133 S;S 126;138 127;139 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. Additionally, K417 N mutation is responsible for the loss of one H-bond in the Mut ACE2-spike RBD variant. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 K417N 14 20 S;RBD 88;94 93;97 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. As shown in the table, the salt bridge formed in the WT ACE2-spike RBD complex is not present in the mutated variant due to the E484K mutation. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E484K 128 133 S;RBD 61;67 66;70 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. In the mutant RBD isoform, the N501Y may be responsible for better binding of the RBD to the host cell receptors, as we reported previously in the UK variant of SARS-CoV-2 (VOC-202012/01). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 N501Y 31 36 RBD;RBD 14;82 17;85 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. On the other hand, the N501Y mutation is responsible for forming one H-bond and one hydrophobic contact in the mutated variants of SARS-CoV-2. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 N501Y 23 28 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. Surprisingly, the WT has a salt bridge between E484 (RBD) and K31 (ACE2); this bridge is broken in the E484K isoform. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E484K 103 108 RBD 53 56 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. Table 2 shows the docking scores and the interactions established upon docking of the ACE2 into SARS-CoV-2 spike RBD in WT and the 501.V2 variant (K417 N, E484K, and N501Y) without GRP78. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E484K;E484K;N501Y;N501Y;K417N 156;155;167;166;147 160;160;171;171;153 S;RBD 107;113 112;116 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. The essential E484K mutant in the SARS-CoV-2 spike RBD is responsible for three H-bonds to GRP78 residue, T458. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E484K 14 19 S;RBD 45;51 50;54 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. The RMSF values for this region that bear E484K of the Mut RBD is twice that of WT RBD, which is in good agreement with the docking study. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E484K 42 47 RBD;RBD 59;83 62;86 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. The three mutations (K417 N, E484K, and N501Y) are labeled with asterisks on the RMSF graph and colored sticks in the structures. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E484K;N501Y;K417N 29;40;21 34;45;27 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. There is a net 5% increase in the HADDOCK score in the E484K isoform (-120.0 +- 4.1) compared to the WT (-126.1 +- 3.3). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E484K 55 60 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. This increase in the score is also reported in the UK, N501Y RBD, variant (HADDOCK score -120.8 +- 1.7) and the triple mutant (K417 N, E484K, and N501Y) RBD variant (HADDOCK score -121.0 +- 3.2). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E484K;N501Y;N501Y;K417N 135;55;146;127 140;60;151;133 RBD;RBD 61;153 64;156 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. To check the effect of spike RBD mutation E484K alone on the ACE2 binding, we perform another mutated spike RBD isoform with only E484K mutant. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E484K;E484K 42;130 47;135 S;S;RBD;RBD 23;102;29;108 28;107;32;111 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. 3 indicating the interaction of E484K with IgG antibody. 2021 Microbial pathogenesis Result SARS_CoV_2 E484K 32 37 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. Among these mutations, E484K and D614G are recently noted as significant mutations due to their effect on SARS-CoV 2 virulence. 2021 Microbial pathogenesis Result SARS_CoV_2 D614G;E484K 33;23 38;28 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. D614G mutation situated exactly at the receptor-binding domain of the spike protein. 2021 Microbial pathogenesis Result SARS_CoV_2 D614G 0 5 S 70 75 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. E484K mutation on the spike protein causes SARS-CoV 2 to escape from the neutralizing effect of the human immune systems mediated by antibodies. 2021 Microbial pathogenesis Result SARS_CoV_2 E484K 0 5 S 22 27 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. H49Y[blue], W64L, A67S, G75S(77), T76I(77)[magenta], R78 M, R102I[blue], V127F, L141del[sky], G142del[sky], V143del[sky], Y144del(143)[sky], E154G, E156D, M177I, S255F(257)[blue], I358V[yellow], L452 M[yellow], S459F[yellow], E484Q[yellow], E484K[yellow], L513F, D614G[blue], V622I, Q675H(674)[blue], S689I(692), A871S, I909V, L1063F, E1092A and H1101Y. 2021 Microbial pathogenesis Result SARS_CoV_2 A67S;A871S;D614G;E1092A;E154G;E156D;E484K;E484Q;G142del;G75S;H1101Y;I358V;I909V;L1063F;L141del;L452M;L513F;M177I;Q675H;R102I;R78M;S255F;S459F;S689I;T76I;V127F;V143del;V622I;W64L;Y144del;H49Y 18;313;263;335;141;148;241;226;94;24;346;180;320;327;80;195;256;155;283;60;53;162;211;301;34;73;108;276;12;122;0 22;318;268;341;146;153;246;231;101;28;352;185;325;333;87;201;261;160;288;65;58;167;216;306;38;78;115;281;16;129;4 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. Now to understand the actual effect of the D614G and E484K mutations in these six Bahraini isolates, we have performed in silico docking assay of wild type SARS CoV-2 Spike protein (PDB id: 6ZB4) with human IgG antibody heavy chain (PDB id: 7CM4_2 and 6ZER_3). 2021 Microbial pathogenesis Result SARS_CoV_2 D614G;E484K 43;53 48;58 S 167 172 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. Now when we have inserted both the mutations (E484k and D614G), the binding affinity has been significantly altered. 2021 Microbial pathogenesis Result SARS_CoV_2 D614G 56 61 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. On the other hand, D614G mutation on the spike protein has high infectivity in human cells having ACE2 receptors. 2021 Microbial pathogenesis Result SARS_CoV_2 D614G 19 24 S 41 46 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. Such alteration of affinity is also experimentally observed in other SARS-COV2 stains with E484K mutation which could help SARS-COV2 to evade the neutralizing antibody. 2021 Microbial pathogenesis Result SARS_CoV_2 E484K 91 96 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. These six isolates also possess D614G mutations. 2021 Microbial pathogenesis Result SARS_CoV_2 D614G 32 37 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. Total 6 isolates from the Kingdom of Bahrain possess E484K mutation at 23012 positions of their genome as represented by the multiple sequence alignment and Single Nucleotide Polymorphisms analysis in. 2021 Microbial pathogenesis Result SARS_CoV_2 E484K 53 58 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. We have also performed the background check of the six isolates that possess both the E484K and D614G mutation. 2021 Microbial pathogenesis Result SARS_CoV_2 D614G;E484K 96;86 101;91 34059617 A core-shell structured COVID-19 mRNA vaccine with favorable biodistribution pattern and promising immunity. However, the capacity to neutralize the E484K variant was dramatically decreased in C57BL/6 mice, but was not found in BALB/c mice. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 E484K 40 45 34059617 A core-shell structured COVID-19 mRNA vaccine with favorable biodistribution pattern and promising immunity. We also compared neutralizing ability of Abs against the wild-type SARS-CoV-2 and the live D614G mutant using the PRNT assay, and found equal levels of neutralization. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G 91 96 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. 3A and B), while B.1.351, B.1.1.248, and E484K were neutralized with 3.1-, 2.7-, and 4.3-fold decreases in titers. 2021 mBio Result SARS_CoV_2 E484K 41 46 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. A detailed analysis of two donor sera chosen at random showed that the sera neutralized B.1.1.7 and its constitutive point mutations similarly, with the exception of T716I, which was more easily neutralized than D614G. 2021 mBio Result SARS_CoV_2 D614G;T716I 212;166 217;171 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. A direct comparison of neutralizing titers of B.1.1.7 (Delta69-70, N501Y, and Delta69-70/N501Y/P681H) with those of D614G showed a close correlation of neutralizing titers for each donor. 2021 mBio Result SARS_CoV_2 D614G;N501Y;N501Y;P681H 116;67;89;95 121;72;94;100 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Analysis of B.1.351 and its constituent E484K point mutation showed that both viruses were neutralized by convalescent-phase sera with titers similar to that of D614G. 2021 mBio Result SARS_CoV_2 D614G;E484K 161;40 166;45 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Analysis of the B.1.1.7 variant and its component mutations showed that the single point mutations had little effect on infectivity (Delta69-70, Y144Del, N501Y, A570D, P681H, and D1118H), except for T716I, which had 5.8-fold decreased infectivity, and S982A, which had significantly increased (1.6-fold) infectivity. 2021 mBio Result SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;T716I 161;179;154;168;252;199 166;185;159;173;257;204 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Analysis of the single mutations of B.1.351 showed that the escape from REGN10933 was due to K417N and E484K, each of which on its own was sufficient. 2021 mBio Result SARS_CoV_2 E484K;K417N 103;93 108;98 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Analysis of the single point mutations showed that the decrease in neutralizing titers was caused by E484K, K417N, and Y453F mutations. 2021 mBio Result SARS_CoV_2 E484K;K417N;Y453F 101;108;119 106;113;124 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Analysis of the variant spike proteins in an ACE2 binding assay in which virions were incubated with matrix-bound sACE2 confirmed the finding that spike proteins that contained N501Y had an increased affinity for ACE2 (N501Y, Delta69-70/N501Y, COH.20G/677H, and B.1.351). 2021 mBio Result SARS_CoV_2 N501Y;N501Y;N501Y 177;219;237 182;224;242 S;S 24;147 29;152 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Analysis of the variants containing the full complement of mutations showed that the B.1.351, B.1.1.248, 20A.EU2, and COH.20G/677H spike proteins were stable and processed like the parental D614G, while B.1.1.7 was poorly expressed and present at a low copy number on virions. 2021 mBio Result SARS_CoV_2 D614G 190 195 S 131 136 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. B.1.351 also showed increased ACE2 binding, and this was due to N501Y, as none of the other point mutations had an effect. 2021 mBio Result SARS_CoV_2 N501Y 64 69 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. B.1.351, B.1.1.248, 20A.EU2, B.1.1.248, and COH.20G/677H were all processed to an extent similar to that of D614G. 2021 mBio Result SARS_CoV_2 D614G 108 113 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Because the B.1.1.7 spike protein with the full complement of mutations was poorly expressed, we used a triple mutant containing the critical Delta69-70/N501Y/P681H B.1.1.7 mutations. 2021 mBio Result SARS_CoV_2 N501Y;P681H 153;159 158;164 S 20 25 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. COH.20G/677H and B.1.1.248 pseudotyped viruses, which also contain N501Y, also displayed increased ACE2 binding. 2021 mBio Result SARS_CoV_2 N501Y 67 72 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Immunoblot analysis showed that each spike protein was expressed in cells and incorporated into virions at levels comparable to those of the wild-type D614G spike protein, with the exception of T716I and the fully mutated B.1.1.7 spike proteins, which were expressed at lower levels. 2021 mBio Result SARS_CoV_2 D614G;T716I 151;194 156;199 S;S;S 37;157;230 42;162;235 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. In contrast, pseudotyped virus containing the single N501Y mutation, as well as those that included N501Y (Delta69-70/N501Y and Delta69-70/N501Y/P681H), showed increased ACE2 binding. 2021 mBio Result SARS_CoV_2 N501Y;N501Y;N501Y;N501Y;P681H 53;100;118;139;145 58;105;123;144;150 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. In this analysis, the B.1.1.7 pseudotyped virus did not show increased ACE2 affinity compared to D614G. 2021 mBio Result SARS_CoV_2 D614G 97 102 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. In this study, the D614G spike protein is considered the "wild type," and the variants tested contain G614. 2021 mBio Result SARS_CoV_2 D614G 19 24 S 25 30 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Incubation of the viruses for 1 h at 50 C caused a 40-fold decrease in the infectivity of the D614G virus. 2021 mBio Result SARS_CoV_2 D614G 94 99 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Measurement of spike protein proteolytic processing, as determined by the ratio of processed (S2) to full-length (S) proteins, showed that some of the mutations in the B.1.1.7 spike protein increased the extent of processing (N501Y, A570D, P681H, T716I, Delta69-70/N501Y, and Delta69-70/N501Y/P681H). 2021 mBio Result SARS_CoV_2 A570D;P681H;T716I;N501Y;N501Y;N501Y;P681H 233;240;247;226;265;287;293 238;245;252;231;270;292;298 S;S;S 15;176;114 20;181;115 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Neutralization titers against N501Y, S982A, B.1.1.7 (Delta69-70/N501Y/P681H), COH.20G/677H, and 20A.EU2 were similar to that against D614G. 2021 mBio Result SARS_CoV_2 D614G;N501Y;S982A;N501Y;P681H 133;30;37;64;70 138;35;42;69;75 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. On day 28, all donors had high titers of neutralizing antibodies against virus with the D614G spike protein, with an average neutralizing titer of 1:1,800, 7-fold higher than that of convalescent-phase serum samples. 2021 mBio Result SARS_CoV_2 D614G 88 93 S 94 99 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Overall, the reduction in the 50% inhibitory concentrations (IC50s) of B.1.351, B.1.1.248, and E484K pseudotypes was about 1.7-fold. 2021 mBio Result SARS_CoV_2 E484K 95 100 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. P681H was present at a high copy number but was processed more efficiently than the wild type, as demonstrated by a higher ratio of S2 to full-length protein levels. 2021 mBio Result SARS_CoV_2 P681H 0 5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Pseudotyped viruses with N501Y, S982A, and Delta69-70/N501Y/P681H spikes and B.1.351 decreased their infectivity <20-fold, suggesting that the mutations increase spike protein stability. 2021 mBio Result SARS_CoV_2 N501Y;S982A;N501Y;P681H 25;32;54;60 30;37;59;65 S;S 66;162 72;167 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Pseudotyped viruses with the mink-associated mutations were fully infectious except for the spike protein containing all 4 mutations (Delta69-70/Y453F/I692V/M1229F), which was 2-fold reduced in infectivity. 2021 mBio Result SARS_CoV_2 I692V;M1229F;Y453F 151;157;145 156;163;150 S 92 97 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Pseudotypes with spike proteins bearing the single mutations (Delta69-70 and N501Y) were neutralized as efficiently as the parental D614G. 2021 mBio Result SARS_CoV_2 D614G;N501Y 132;77 137;82 S 17 22 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Pseudotypes with the 20A.EU2 spike and the COH.20G/677H spike were neutralized with titers similar (0.9- and 1.1-fold, respectively) to that of D614G. 2021 mBio Result SARS_CoV_2 D614G 144 149 S;S 29;56 34;61 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. REGN10933 was highly active against D614G, B.1.1.7, and COH.20G/677H, with IC50s of 7.4, 8.4, and 6.0 ng/ml, respectively, but had weak activity against B.1.351, B.1.1.248, and mink cluster 5, with IC50s 76.3-, >260-, and 214.9-fold higher, respectively, than that of D614G. 2021 mBio Result SARS_CoV_2 D614G;D614G 36;268 41;273 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Spike proteins containing each of the other individual B.1.351 mutations were neutralized as well as D614G. 2021 mBio Result SARS_CoV_2 D614G 101 106 S 0 5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. T716I was expressed at a significantly lower level, accounting for the decreased infectivity of this spike protein. 2021 mBio Result SARS_CoV_2 T716I 0 5 S 101 106 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The addition of the P681H mutation in the triple mutant increased processing to a level similar to that of the P681H single point mutation. 2021 mBio Result SARS_CoV_2 P681H;P681H 20;111 25;116 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The combination of REGN10933 and REGN10987 was highly potent against virus with the D614G spike, with an IC50 of 1.69 ng/ml, but against B.1.351, B.1.1.248, and mink cluster 5, neutralizing titers were decreased 9.14-, 15.7-, and 16.2-fold, respectively, compared to D614G. 2021 mBio Result SARS_CoV_2 D614G;D614G 84;267 89;272 S 90 95 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The D614G mutation caused significant increases in viral infectivity and binding to ACE2. 2021 mBio Result SARS_CoV_2 D614G 4 9 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The decrease in the neutralization of B.1.351 and B.1.1.248 appears largely due to the E484K mutation. 2021 mBio Result SARS_CoV_2 E484K 87 92 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The double mutant Delta69-70/N501Y and the triple mutant Delta69-70/N501Y/P681H also had increased infectivity (1.3- and 1.5-fold), suggesting that the two mutations coordinate to increase infectivity. 2021 mBio Result SARS_CoV_2 N501Y;N501Y;P681H 29;68;74 34;73;79 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The escape from the mink cluster 5 variant was caused by Y453F. 2021 mBio Result SARS_CoV_2 Y453F 57 62 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The IC50 for each donor for the E484K single mutant was similar to that of B.1.351, suggesting that the E484K single amino acid change was responsible for the decrease in neutralizing titer. 2021 mBio Result SARS_CoV_2 E484K;E484K 32;104 37;109 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The N501Y and A570D mutations resulted in a small decrease in the copy number on virions. 2021 mBio Result SARS_CoV_2 A570D;N501Y 14;4 19;9 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. This was also the case for COH.20G/677H, 20A.EU2, and mink cluster 5 spike variants, which were more easily neutralized (1.9-fold) than the D614G pseudotype. 2021 mBio Result SARS_CoV_2 D614G 140 145 S 69 74 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Virus pseudotyped by the B.1.1.7 spike protein was neutralized slightly (1.3-fold) less well than the parental D614G, an effect that was noticeable in the lack of donors with high neutralizing titers. 2021 mBio Result SARS_CoV_2 D614G 111 116 S 33 38 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. We found that REGN10987 neutralized D614G with an IC50 of 19.4 ng/ml. 2021 mBio Result SARS_CoV_2 D614G 36 41 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. While this is a significant drop in titers, it remains higher than the titer found for convalescent-phase sera against D614G pseudotyped virus. 2021 mBio Result SARS_CoV_2 D614G 119 124 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. 1D presents 1H NMR spectra for wild-type ORF8 and its L84S variant at 30C. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 54 58 ORF8 41 45 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. 3, the peak intensity of the L84S variant at pH 6.2 was much greater than that of wild-type ORF8 at pH 6.1. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 29 33 ORF8 92 96 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. After 7 days, the production of wild-type ORF8 and its L84S variant was confirmed in the culture medium. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 55 59 ORF8 42 46 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Conformation of the L84S variant. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 20 24 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Following purification, wild-type ORF8 and its L84S variant in the culture medium were obtained as single proteins and both existed as dimeric forms. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 47 51 ORF8 34 38 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. It was found that the denaturing temperature of L84S variant is slightly higher than that of wild type. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 48 52 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. The L84S variant had an identical structure to that of ORF8 excluding the orientation of the ORF-specific flexible loop. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 4 8 ORF8 55 59 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. the L84S variant was also heat-stable. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 4 8 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. The mutation from Leu to Ser at residue 84 is expected to reduce the hydrophobicity of the molecular surface, because L84 is located at a loop exposed to solvent. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 18 42 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. The NMR spectrum of the redissolved sample at pH 8.4 was identical to that of the L84S variant at pH 7.8. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 82 86 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. The results clearly indicated that both wild-type ORF8 and its L84S variant maintained their dimeric nature, indicating that stability of conformation and retention were achieved even in the redissolved state after precipitation. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 63 67 ORF8 50 54 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. The solution of the L84S variant also became cloudy at lower pH. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 20 24 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Therefore, the L84S variant had greater solubility at reduced pH (6.1-6.2) than wild-type ORF8. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 15 19 ORF8 90 94 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Thus, the L84S variant exhibited conformational reversibility following pH fluctuation similar to wild-type ORF8. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 10 14 ORF8 108 112 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Thus, the L84S variant exhibited the same ability to regain its original conformation following temperature fluctuation as wild-type ORF8. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 10 14 ORF8 133 137 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. To compare the physicochemical properties of wild-type ORF8 and its L84S variant, we attempted to mass-produce L84S. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S;L84S 68;111 72;115 ORF8 55 59 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. To obtain supporting information, we also attempted to model the three-dimensional structure of the L84S variant. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 100 104 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Unlike wild-type ORF8, the L84S variant had a clear 1H NMR spectrum at 70C, but not at 75C. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 27 31 ORF8 17 21 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. When the sample was cooled to room temperature, the L84S variant displayed a spectrum identical to that observed for the initial sample at 30C. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L84S 52 56 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. During phase 1, three Nextstrain clade 20A variants (C3037T, C14408T, and A23403G) were identified, which accounted for 43.3% of cases. 2021 Viruses Result SARS_CoV_2 A23403G;C14408T;C3037T 74;61;53 81;68;59 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. During phase 2, variants of clade 20B (G28881A, G28882A, and G28883C) emerged, accounting for 45.5% of cases in this phase and 100% in phase 3. 2021 Viruses Result SARS_CoV_2 G28882A;G28883C;G28881A 48;61;39 55;68;46 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Four mutations were located within nonstructural proteins (Nsp3: T1246I, Nsp3: T1250I, Nsp5: G3278S, Nsp12: P4715L), three in the nucleocapsid (S2F, R203K, G204R), and two affecting the spike protein (D614G, T307I) (Figure 3). 2021 Viruses Result SARS_CoV_2 G204R;G3278S;P4715L;R203K;T1246I;T1250I;T307I;D614G 156;93;108;149;65;79;208;201 161;99;114;154;71;85;213;206 N;S;Nsp12;Nsp3;Nsp3;Nsp5 130;186;101;59;73;87 142;191;106;63;77;91 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Here, we performed coarse-grained molecular dynamics simulations of the spike trimer's soluble domain for the WT, D614G, and the double mutant T307I-D614G. 2021 Viruses Result SARS_CoV_2 D614G;T307I;D614G 114;143;149 119;148;154 S 72 77 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. However, two variants of Nextstrain clade 20C (C1059T and G25563T) emerged during this initial phase (56.7%). 2021 Viruses Result SARS_CoV_2 G25563T;C1059T 58;47 65;53 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Molecular dynamic simulations revealed a close attractive interaction between F306 and the hydrophobic cluster in the WT and D614G mutant (Figure 4c left image). 2021 Viruses Result SARS_CoV_2 D614G 125 130 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. One of the haplotype-defining mutations was the spike T307I amino acid change caused by a C-to-T transition at position 22,482 (Figure 3b). 2021 Viruses Result SARS_CoV_2 T307I 54 59 S 48 53 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Qualitatively, the spike WT, the D614G, and the D614G-T307I variants showed the same behavior, although with different amplitudes. 2021 Viruses Result SARS_CoV_2 D614G;D614G;T307I 33;48;54 38;53;59 S 19 24 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Recent evidence suggests that the D614G mutation alters the equilibrium between RBD-closed and RBD-open conformations of the spike protein. 2021 Viruses Result SARS_CoV_2 D614G 34 39 S;RBD;RBD 125;80;95 130;83;98 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Structural and Molecular Dynamic Analysis of T307I. 2021 Viruses Result SARS_CoV_2 T307I 45 50 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. The T307I mutation was firstly detected on June 11 and subsequently co-existed with the unmutated T307 variant (Figure 2c). 2021 Viruses Result SARS_CoV_2 T307I 4 9 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. The trace of the covariance matrixes (which provide a quantitative gauge of the movement's variance) calculated on the S1 segment resulted in 135 nm, 130 nm, and 118 nm for the WT and the D614G and T307I-D614G mutants, respectively. 2021 Viruses Result SARS_CoV_2 D614G;T307I;D614G 188;198;204 193;203;209 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. This may agree with the reported structural similarity between WT and D614G. 2021 Viruses Result SARS_CoV_2 D614G 70 75 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. This non-covalent bond was deranged in the double D614G-T307I mutant through the change from a polar to a hydrophobic amino acid at position 307, resulting in a permanent removal of F306 from its hydrophobic cluster and in a new attractive interaction with the mutated isoleucine in position 307 (Figure 4c right image and Supplementary Video S4). 2021 Viruses Result SARS_CoV_2 D614G;T307I 50;56 55;61 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. To analyze the structural effect of the genetic variations within the GLD, we compared the WT and D614G to the avian infectious bronchitis virus, which contains a glycine at the homologous position of F306. 2021 Viruses Result SARS_CoV_2 D614G 98 103 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. Among SARS-CoV-2 sequences reported from Bangladesh, 241C > T, 3037C > T, 14408C > T, 23403A > G, 28881G > A, and 28883G > C mutations were the six most abundant nucleotide mutations that occurred in 98% sequences. 2021 Microorganisms Result SARS_CoV_2 C14408T;A23403G;C241T;G28881A;G28883C;C3037T 74;86;53;98;114;63 84;96;61;108;124;72 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. Furthermore, other potential mutations (L5F, N354S, A520K, Q675H/R, P681H/R, D936Y, and M1229Y) were detected in the current study (Figure 5c) and have been described for increased infectivity of the virus in vivo. 2021 Microorganisms Result SARS_CoV_2 A520K;D936Y;M1229Y;N354S;P681H;P681R;Q675H;Q675R;L5F 52;77;88;45;68;68;59;59;40 57;82;94;50;75;75;66;66;43 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. In Bangladesh, the globally recognized mutation D614G (the most common form of SARS-CoV2) in the S protein was found in 767 out of 791 sequences (96%) belonging to lineage B (mainly B1.1.25). 2021 Microorganisms Result SARS_CoV_2 D614G 48 53 S 97 98 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. In summary, the spike E484K mutation and the UK variant strain (B.1.1.7) were introduced in Bangladesh in late December 2020 and already emerged as the next dominant SARS-CoV-2 variant in the country. 2021 Microorganisms Result SARS_CoV_2 E484K 22 27 S 16 21 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. Notably, two potential mutations, E484K (B.1.1.25) and N501Y (B.1.1.7-UK Variant/GRY clade), at the receptor-binding domain (RBD) were determined in this analysis: E484K occurred in two strains sampled on 19 December 2020 from the capital city Dhaka (EPI_ISL_890188 and EPI_ISL_774976), whereas N501Y was found in three strains collected on 31 December 2020 (EPI_ISL_906091), 4 January 2021 (EPI_ISL_906098), and 6 January 2021 (EPI_ISL_890237), respectively, from another big city, Sylhet. 2021 Microorganisms Result SARS_CoV_2 E484K;E484K;N501Y;N501Y 34;164;55;295 39;169;60;300 RBD 125 128 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. The other significant S protein mutations observed at the N-terminal domain (NTD) were L18F (n = 1), His69del (n = 5), V70del (n = 5), and Y144del/Y145 del (n = 7), depicted in Figure 4c. 2021 Microorganisms Result SARS_CoV_2 L18F 87 91 N;S 58;22 59;23 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. As aspartate 614 is missing (D614G), lysine 854 is unmatched in this variant. 2021 Biomedicines Result SARS_CoV_2 D614G 29 34 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. D614G Induces Flexibility around the Fusion Peptide via Salt Bridge Rearrangement. 2021 Biomedicines Result SARS_CoV_2 D614G 0 5 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. For all three variants, wt, wt+D614G and B.1.1.7, partial interaction between arginine 646 and aspartate 867 or glutamate 868 was found (Figure 2a, Figure S3b). 2021 Biomedicines Result SARS_CoV_2 D614G 31 36 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. N501Y Replacement Displaces Glutamine 498 from the SARS-CoV-2 ACE2 Interface. 2021 Biomedicines Result SARS_CoV_2 N501Y 0 5 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. Taken together, we identified how the D614 mutation (in combination with the A570D mutation) induces a loss of conformational stability that increases flexibility in a pre- and postcleavage state. 2021 Biomedicines Result SARS_CoV_2 A570D 77 82 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. The N501Y Mutation Decreses Electrostatic Binding in B.1.1.7. 2021 Biomedicines Result SARS_CoV_2 N501Y 4 9 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. The only amino acid exchange localized in the RBD is N501Y, which resides at the RBD-ACE2 interface (Figure S1a). 2021 Biomedicines Result SARS_CoV_2 N501Y 53 58 RBD;RBD 46;81 49;84 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. The RMSD values were low and very similar for the variants analyzed (wt, wt+D614G and B.1.1.7). 2021 Biomedicines Result SARS_CoV_2 D614G 76 81 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. This additional destabilization in B.1.1.7 could be explained by the A570D mutation (Figure 2a, orange box). 2021 Biomedicines Result SARS_CoV_2 A570D 69 74 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. Thus, we hypothesized that changes in RBD behavior are a direct effect of the N501Y mutation and further analyzed it. 2021 Biomedicines Result SARS_CoV_2 N501Y 78 83 RBD 38 41 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. To analyze the direct effect of the D614G mutation in this matter, we also calculated MD simulations of a wt variant with an inserted glycine for aspartate at position 614 (wt+D614G). 2021 Biomedicines Result SARS_CoV_2 D614G;D614G;D614G 36;134;176 41;171;181 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. We also identified a markedly increased number of contacts for the newly inserted tyrosine at position 501 to lysine 353 in B.1.1.7 when compared to the wt asparagine residue (Figure S5a, individual runs shown in Figures S7 and S8). 2021 Biomedicines Result SARS_CoV_2 Y501K 82 116 34067745 An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. Figure 3 is the NJ tree of the 406 unclassified sequences with the L3606F mutation, along with the representative clade sequences, which show two different clusters. 2021 Viruses Result SARS_CoV_2 L3606F 67 73 34067745 An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. Finally, the G-S variant, defined by the presence of the D614G and L84S mutations in the S and ORF8 proteins, respectively, was observed in four sequences of SARS-CoV-2 reported from Gujarat in June 2020. 2021 Viruses Result SARS_CoV_2 D614G;L84S 57;67 62;71 ORF8;S;S 95;15;89 99;16;90 34067745 An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. Firstly, the GR-GH variants defined by the presence of the D614G, G204R, and Q57H mutations in the S, N, and ORF3a proteins, respectively, were observed in 14 sequences from different parts of India, starting from May 2020 (Figure 2). 2021 Viruses Result SARS_CoV_2 D614G;G204R;Q57H 59;66;77 64;71;81 ORF3a;N;S 109;102;99 114;103;100 34067745 An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. Guanine (G) was found in 59% of B.4 (CI2 sequences) at position 8 in ORF8, resulting in the G8stop codon mutation in the ORF8 protein along with the ORF1ab (D6270G) amino acid change. 2021 Viruses Result SARS_CoV_2 G8X 92 98 ORF1ab;ORF8;ORF8 149;69;121 155;73;125 34067745 An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. Interestingly, another conserved pattern was also observed in 61/406 sequences in the ORF1ab (R207C, V378I, and M2790I) and classified within the B.4 variant in the PangoLIN classification (Figure 3, green). 2021 Viruses Result SARS_CoV_2 M2790I;V378I;R207C 112;101;94 118;106;99 ORF1ab 86 92 34067745 An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. It was noted that 331/406 sequences had a conserved pattern in the ORF1ab (T2016K, A4489V) and N: P13L, Figure 3 (blue and its shades). 2021 Viruses Result SARS_CoV_2 A4489V;P13L;T2016K 83;98;75 89;102;81 ORF1ab;N 67;95 73;96 34067745 An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. Secondly, the GV-GR variant defined by the presence of A222V in the S and G204R mutations in the N protein, along with the common D614G mutation of the G clade, were observed starting from August 2020 in Maharashtra (n = 1) and Telangana (n = 2). 2021 Viruses Result SARS_CoV_2 A222V;D614G;G204R 55;130;74 60;135;79 N;S 97;68 98;69 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Below, we demonstrate how our contact data may be applied to evaluate potential consequences of specific mutations, such as N501Y in the recently prevalent B.1.1.7 lineage that was originally detected in the UK. 2021 Viruses Result SARS_CoV_2 N501Y 124 129 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. For this, we note that N501Y would enable the formation of stabilizing cation- interaction with K353 of ACE2. 2021 Viruses Result SARS_CoV_2 N501Y 23 28 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. For this, we performed in-silico mutagenesis of N501Y in the RBD-ACE2 complex, using the FoldX software. 2021 Viruses Result SARS_CoV_2 N501Y 48 53 RBD 61 64 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Hence, a tyrosine (N501Y) side chain that allows for more favorable hydrogen bonds between molecules would further facilitate binding. 2021 Viruses Result SARS_CoV_2 N501Y 19 24 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. In addition, the longer side chain of N501Y (relative to N501) may facilitate the intermolecular hydrogen-bonding between the OH group of N501Y (tyrosine) and ACE2 residues, including K353 (Figure 3b). 2021 Viruses Result SARS_CoV_2 N501Y;N501Y 38;138 43;143 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. In fact, of these seven RBD residues, two are sites where the common mutations Y453F and N501Y occur, and the remaining five are highly conserved among pandemic variants. 2021 Viruses Result SARS_CoV_2 N501Y;Y453F 89;79 94;84 RBD 24 27 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. In recent months, the new B.1.1.7 variant of SARS-CoV-2, carrying the mutation N501Y in the RBD (Figure 3), reportedly accounts for overof new COVID-19 cases in South East England. 2021 Viruses Result SARS_CoV_2 N501Y 79 84 RBD 92 95 COVID-19 143 151 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. In the next section further below, we apply our contact statistics, as shown in Figure 2a, to assess how the N501Y mutation in B.1.1.7 may facilitate virus-receptor binding. 2021 Viruses Result SARS_CoV_2 N501Y 109 114 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Moreover, the N501Y mutation introduces additional stabilizing contributions: i.e., the aromatic-aromatic interaction between N501Y and Y41 (i.e., -stacking; Figure 3b). 2021 Viruses Result SARS_CoV_2 N501Y;N501Y 14;126 19;131 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Notably, N501Y would lead to enhanced hydrophobic effects in the inside of the binding surface. 2021 Viruses Result SARS_CoV_2 N501Y 9 14 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Simulated Interactions Help Assess the Effects of Mutations, Such As N501Y in RBD. 2021 Viruses Result SARS_CoV_2 N501Y 69 74 RBD 78 81 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Since the N501Y mutation site is at the RBD-ACE2 binding interface (Figure 3a), we will examine how this mutation may modulate the virus-host interaction, a factor that can determine infectivity. 2021 Viruses Result SARS_CoV_2 N501Y 10 15 RBD 40 43 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Specifically, Y453F is a mutation that originates from minks in Denmark and has been found in over 1400 out of ~314,000 sequences recorded globally (i.e.,global frequency), as of 16 January 2021. 2021 Viruses Result SARS_CoV_2 Y453F 14 19 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. that have demonstrated enhanced RBD-ACE2 affinity through N501Y. 2021 Viruses Result SARS_CoV_2 N501Y 58 63 RBD 32 35 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. The N501Y RBD mutation, which first became prominent in the B.1.1.7 lineage, has been found in over 18,000 out of ~314,000 sequences (i.e.,global frequency). 2021 Viruses Result SARS_CoV_2 N501Y 4 9 RBD 10 13 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. The significant interactions provide reason to specifically focus on these two host residues and assess how their contact formation with the N501Y mutation may alter stability (Figure 3b). 2021 Viruses Result SARS_CoV_2 N501Y 141 146 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. This N501Y variant is associated with increased affinity to host receptor, but the molecular factors responsible for this is unclear. 2021 Viruses Result SARS_CoV_2 N501Y 5 10 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. To describe the consequences of N501Y, we first identify all ACE2 residues that frequently interact with N501, the mutation site in RBD. 2021 Viruses Result SARS_CoV_2 N501Y 32 37 RBD 132 135 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Together, our analysis demonstrates how N501Y implicates numerous energetic factors whose combined effect likely facilitates the binding of the mutated virus to host cells. 2021 Viruses Result SARS_CoV_2 N501Y 40 45 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Utilizing the interaction statistics from Figure 2a as basis, together with a structural and chemical-physical analysis, we argue below how N501Y facilitates the binding of RBD to ACE2, which may contribute to enhanced infectivity. 2021 Viruses Result SARS_CoV_2 N501Y 140 145 RBD 173 176 34073577 Kinetics of Neutralizing Antibodies of COVID-19 Patients Tested Using Clinical D614G, B.1.1.7, and B 1.351 Isolates in Microneutralization Assays. Hence, we compared neutralizing antibody titers against FIN-1, a Wuhan-like strain from January 2020 using VE6 cells both with and without TMPRSS2 expression to a D614G isolate C1P1 using VE6 cells expressing TMPRSS2 (VE6T). 2021 Viruses Result SARS_CoV_2 D614G 163 168 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. As before, a double mutation version with K417N and N501Y protein (N417/Y501-RBD) was produced and binding to ACE2 was assessed by SPR. 2021 mAbs Result SARS_CoV_2 K417N;N501Y 42;52 47;57 RBD 77 80 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. As this E484K mutation incorporates the positively charged residue lysine in the place of the negatively charged residue glutamic acid, we expected a drastic drop of binding affinity between 484 K/501Y-RBD and ACE2. 2021 mAbs Result SARS_CoV_2 E484K 8 13 RBD 202 205 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. First, we introduced only the E484K mutation into the existing N501Y-RBD to generate a double mutation of RBD (484 K/501Y-RBD), which exist in both the South African and Brazilian variants, and expressed it in 293 F cells. 2021 mAbs Result SARS_CoV_2 E484K;N501Y 30;63 35;68 RBD;RBD;RBD 69;106;122 72;109;125 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. Furthermore, when the E484K mutation is introduced, the binding between K484/Y501-RBD and the antibody is completely abolished (Figure 2(a) and (c)). 2021 mAbs Result SARS_CoV_2 E484K 22 27 RBD 82 85 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. In February 2021, we reported that N501Y-RBD (N501 mutated to Y501) derived from the United Kingdom variant has an ~10-fold increased binding affinity (0.566 nM) toward ACE2 compared to the wildtype (5.768 nM). 2021 mAbs Result SARS_CoV_2 N501Y 35 40 RBD 41 44 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. On the basis of Y501-RBD, two additional mutations, K417N and E484K existing in the South African variant, were introduced and expressed in 293 F cells as previously reported. 2021 mAbs Result SARS_CoV_2 E484K;K417N 62;52 67;57 RBD 21 24 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. We then proceeded to introduce another mutation, K417N within the South African variant, on the basis of 501Y-RBD. 2021 mAbs Result SARS_CoV_2 K417N 49 54 RBD 110 113 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. We used the available complex structure to analyze how this critical E484K mutation causes a loss of binding. 2021 mAbs Result SARS_CoV_2 E484K 69 74 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. A matrix of nucleic acid difference showed that YO-UGM-10001|EPI_ISL_576113 and YO-UGM-10003|EPI_ISL_576115 were identical on their ORF (nucleic acid and protein levels) and both virus strains had differences of 2 nucleic acids and 1 amino acid in the NSP2 protein which correspond with V247A substitution in YO-UGM-10001|EPI_ISL_576113 and YO-UGM-10003|EPI_ISL_576115 and T256I substitution in YO-UGM-10002|EPI_ISL_576114, respectively (Table 4). 2021 BMC medical genomics Result SARS_CoV_2 T256I;V247A 373;287 378;292 Nsp2 252 256 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. A range of Ct values was found amongst different stages of severity, nevertheless all the virus samples with D614G mutations, except one (YO-UGM-10004/2020|EPI_ISL_576116), showed lower Ct values (clade GH, GR, and O, Ct range 16.9-24.7) than those with no mutation in this position (clade L, Ct 27.9). 2021 BMC medical genomics Result SARS_CoV_2 D614G 109 114 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Dual mutations of V213A and D614G on spike protein were detected in four patients, and two of these eventually died after a period of hospitalization. 2021 BMC medical genomics Result SARS_CoV_2 D614G;V213A 28;18 33;23 S 37 42 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Furthermore, various amino acid mutations were also found in the other proteins of virus samples, including on NSP2 (A205V, V247A, T256I, Q321K), NSP3 (P679S, T1022I, A1179V, T1198K, F1354C, P1665L), NSP4 (A231V), NSP5 (K12R, M49I, P184S), NSP6 (L37F), NSP8 (A21T), NSP9 (L42F), NSP12/RdRp (A97V, P227L, T248I, A656S, H892Y, M906V), NSP13 (T127I, T153I, V169F, M576I, P203L), NSP15 (H337Y), NSP16 (Y222C), NS3 (A54V, A99S, T151I, D222Y), NS7a (H73Y), and N (P13L, A119S, Q160R, S193I, R195S, P199S, R203K, G204R, M234I). 2021 BMC medical genomics Result SARS_CoV_2 A1179V;A119S;A656S;A99S;D222Y;F1354C;G204R;H892Y;M234I;M49I;M576I;M906V;P1665L;P184S;P199S;P203L;P227L;Q160R;Q321K;R195S;R203K;S193I;T1022I;T1198K;T151I;T153I;T248I;T256I;V169F;V247A;A205V;A21T;A231V;A54V;A97V;H337Y;H73Y;K12R;L37F;L42F;P13L;P679S;T127I;Y222C 167;464;311;417;430;183;506;318;513;226;361;325;191;232;492;368;297;471;138;485;499;478;159;175;423;347;304;131;354;124;117;259;206;411;291;383;444;220;246;272;458;152;340;398 173;469;316;421;435;189;511;323;518;230;366;330;197;237;497;373;302;476;143;490;504;483;165;181;428;352;309;136;359;129;122;263;211;415;295;388;448;224;250;276;462;157;345;403 Nsp13;Nsp12;Nsp2;Nsp3;Nsp4;Nsp8;Nsp5;Nsp6;RdRP;NS3;N 333;279;111;146;200;253;214;240;285;406;455 338;284;115;150;204;257;218;244;289;409;456 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Other unique mutations in the other viral proteins were detected in these three virus strains which were not shown in the other study viruses, including V213A (Spike), K12R (NSP5), T248I (NSP12/RdRp), A119S and S193I (N). 2021 BMC medical genomics Result SARS_CoV_2 A119S;K12R;S193I;T248I;V213A 201;168;211;181;153 206;172;216;186;158 S;Nsp12;Nsp5;RdRP;N 160;188;174;194;218 165;193;178;198;219 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Second amino acid mutations that were frequently detected were P232L substitution on NSP12 (RdRp) protein (15x), followed by Q57H substitution on NS3 (14x) and P822L substitution on NSP3 protein (13x). 2021 BMC medical genomics Result SARS_CoV_2 P232L;P822L;Q57H 63;160;125 68;165;129 Nsp12;Nsp3;RdRP;NS3 85;182;92;146 90;186;96;149 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. The majority of the virus samples (16/17) possessed D614G substitution on spike protein and 56% of these (9/16) showed other amino acid substitutions on this protein, including L5F, V83L, V213A, W258R, Q677H, and N811I. 2021 BMC medical genomics Result SARS_CoV_2 D614G;L5F;N811I;Q677H;V213A;V83L;W258R 52;177;213;202;188;182;195 57;180;218;207;193;186;200 S 74 79 34081630 Epitope-specific antibody responses differentiate COVID-19 outcomes and variants of concern. The introduction of the P681H mutation, which has been found in multiple VOCs, into the S-671 peptide, completely abolished antibody binding. 2021 JCI insight Result SARS_CoV_2 P681H 24 29 S 88 89 34081630 Epitope-specific antibody responses differentiate COVID-19 outcomes and variants of concern. These data indicate that the P681H mutation altered the specificity of the corresponding epitope (S-671) and rendered it unrecognizable by antibodies against the original coronavirus (as the plasma sample was collected prior to the emergence of the B.1.1.7 variant, although the genotype of the virus was not determined). 2021 JCI insight Result SARS_CoV_2 P681H 29 34 S 98 99 34081630 Epitope-specific antibody responses differentiate COVID-19 outcomes and variants of concern. To confirm this finding, we synthesized another version of the S-671 epitope in which the P681 residue and the P681H mutation were placed in the center of the corresponding peptides and printed both versions of the original and mutant peptides in incremental concentrations in an array. 2021 JCI insight Result SARS_CoV_2 P681H 111 116 S 63 64 34081630 Epitope-specific antibody responses differentiate COVID-19 outcomes and variants of concern. While the original epitopes exhibited increased IgG binding with time, the P681H-mutant epitope did not show detectable antibody binding signal for the same plasma samples. 2021 JCI insight Result SARS_CoV_2 P681H 75 80 34087220 Synthetic proteins for COVID-19 diagnostics. The bold residues in peptide 3 show two residues that when changed in SARS-CoV-1 affect ACE2 binding (N479K, T487S). 2021 Peptides Result SARS_CoV_2 T487S;N479K 109;102 114;107 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. Further, our calculations of the free energy changes upon D614G substitution show that the total free energy differences (DeltaDeltaG) between two variants of spike protein trimer are - 2.6 kcal/mol and -2.0 kcal/mol for closed and 1-RBD up conformations, respectively. 2021 Bioinformation Result SARS_CoV_2 D614G 58 63 S;RBD 159;234 164;237 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. The D614G substitution is present in the CTD3 domain and is highlighted in the sequence alignment between ancestral and dominant variants (Figure 1A). 2021 Bioinformation Result SARS_CoV_2 D614G 4 9 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. We analyzed the effect of D614G substitution on the interaction energies by computing the frustration index of residues in the SD614 and SG614. 2021 Bioinformation Result SARS_CoV_2 D614G 26 31 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. Notably, the recently described D614G mutation in the spike protein, caused by nucleotide G-to-A substitution at position 23 403 in the Wuhan reference strain NC_045512.2 (Figure 3B; Supplementary Table 3), was present in all but 1 of our isolates (140/141, 99.3%). 2021 Open forum infectious diseases Result SARS_CoV_2 D614G;G23403A 32;90 37;128 S 54 59 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. Only 1 isolate without the D614G variation in the spike protein belonging to phylogenetic clade 19B was identified, and none of the isolates belonging to phylogenetic clade 19A, which consists of the very first isolates from Asia (Figure 1). 2021 Open forum infectious diseases Result SARS_CoV_2 D614G 27 32 S 50 55 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. The only other frameshift mutation found in the cohort was the c.361delA mutation in ORF8, which was also found in only 1 isolate in our cohort but reported 25 times previously according to CHLA CARD. 2021 Open forum infectious diseases Result SARS_CoV_2 361delA 63 72 ORF8 85 89 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. There were 2 other mutations that coexist with the D614G mutation in all isolates located in ORF1ab: F924F (c.2772C > T) is a synonymous mutation, while P4715L (c.14144C > T) is a nonsynonymous mutation (Figure 3B). 2021 Open forum infectious diseases Result SARS_CoV_2 D614G;F924F;P4715L;C14144T;C2772T 51;101;153;161;108 56;106;159;173;119 ORF1ab 93 99 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. To further investigate the association between viral isolates with the D614G mutation and the rate of viral evolution, we analyzed 577 viral genomes from California at different time points without the D614G mutation. 2021 Open forum infectious diseases Result SARS_CoV_2 D614G;D614G 71;202 76;207 34097003 Detecting SARS-CoV-2 and its variant strains with a full genome tiling array. Our analysis identified two mutated positions in the coding region of the spike protein: position 23 403 was mutated in four samples, coincident with the infamous D614G mutation; position 24 694 was mutated in two samples, without changing the amino acid outcome (Figure 4B). 2021 Briefings in bioinformatics Result SARS_CoV_2 D614G 163 168 S 74 79 34097003 Detecting SARS-CoV-2 and its variant strains with a full genome tiling array. The first nonsynonymous mutation appeared in sample S6 at position number 28 311, changing Pro to Leu (P13L). 2021 Briefings in bioinformatics Result SARS_CoV_2 P13L 103 107 34097003 Detecting SARS-CoV-2 and its variant strains with a full genome tiling array. The second nonsynonymous mutation also appeared in sample S6 but was located at position number 28 863, changing Ser to Leu (S197L). 2021 Briefings in bioinformatics Result SARS_CoV_2 S197L 125 130 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. A consecutive analysis detected the W152L/E484K/G769V mutations in three patients who provided samples on January 14, 2021. 2021 PLoS pathogens Result SARS_CoV_2 W152L;E484K;G769V 36;42;48 41;47;53 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. A parental lineage without the ORF1b G814C mutation has been prevalent mainly in Japan and the United States (Fig 3A). 2021 PLoS pathogens Result SARS_CoV_2 G814C 37 42 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. Among the missense mutations, four were in the spike protein (W152L, E484K, D614G, and G769V), four were in ORF1ab (T4692I, N6301S, L6337M, and I6525T), one was in the membrane protein (F28L), and four were in the nucleocapsid protein (S187L, R203K, G204R, and Q418H). 2021 PLoS pathogens Result SARS_CoV_2 D614G;E484K;G204R;G769V;I6525T;L6337M;N6301S;Q418H;R203K;F28L;S187L;T4692I;W152L 76;69;250;87;144;132;124;261;243;186;236;116;62 81;74;255;92;150;138;130;266;248;190;241;122;67 N;Membrane;ORF1ab;S 214;168;108;47 226;176;114;52 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. For the rapid detection of SARS-CoV-2 R.1 lineage isolates, we designed a TaqMan assay that detects the hallmark spike protein mutations (W152L, E484K, and G769V) (Table 1). 2021 PLoS pathogens Result SARS_CoV_2 E484K;G769V;W152L 145;156;138 150;161;143 S 113 118 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. Household transmission of SARS-CoV-2 harboring a spike protein with the E484K mutation. 2021 PLoS pathogens Result SARS_CoV_2 E484K 72 77 S 49 54 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. Subsequently, a sublineage, which has been observed in Austria and the United States, diverged after acquiring the ORF1b G814C mutation around October 19, 2020 (Fig 3A). 2021 PLoS pathogens Result SARS_CoV_2 G814C 121 126 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. The parental lineage harboring the E484K mutation later acquired spike protein W152L and G769V mutations, and the SARS-CoV-2 R.1 lineage was predicted to have emerged around September 9, 2020 (Fig 3A). 2021 PLoS pathogens Result SARS_CoV_2 E484K;G769V;W152L 35;89;79 40;94;84 S 65 70 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. To determine the timing of the emergence of the SARS-CoV-2 R.1 lineage and its acquisition of characteristic mutations, we analyzed a phylogeny of SARS-CoV-2 carrying the E484K mutation, generated from global data. 2021 PLoS pathogens Result SARS_CoV_2 E484K 171 176 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. We previously identified P.1 lineage SARS-CoV-2, which harbors the K417T/E484K/N501Y mutations, in one patient. 2021 PLoS pathogens Result SARS_CoV_2 K417T;E484K;N501Y 67;73;79 72;78;84 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. All E191A-P1-inoculated pigs had moderate-severe diarrhea and the accumulated days for diarrhea was 2.33 +- 0.58 days. 2021 Cell & bioscience Result SARS_CoV_2 E191A 4 9 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Among the four pigs inoculated with E191A-P1, the viruses from two pigs (pig#10 and #11) retained the E191A mutation and had no additional mutations within nsp14, but the virus from pig#8 had reverted to wildtype nsp14 by 2 dpi. 2021 Cell & bioscience Result SARS_CoV_2 E191A;E191A 36;102 41;107 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Among those mutants, only the recombinant PEDV carrying E191A mutation was viable. 2021 Cell & bioscience Result SARS_CoV_2 E191A 56 61 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. At 22 dpi, pigs in the E191A-P1 and mock groups were challenged with the highly virulent icPC22A at a high dose (106 PFU/pig). 2021 Cell & bioscience Result SARS_CoV_2 E191A 23 28 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Collectively, these data suggest that recombinant PEDV E191A quickly reverted to wildtype either in vivo or in vitro, indicating the low genetic stability of ExoN mutant. 2021 Cell & bioscience Result SARS_CoV_2 E191A 55 60 Exon 158 162 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. E191A mutant induced partial protection against virulent icPC22A challenge in pigs. 2021 Cell & bioscience Result SARS_CoV_2 E191A 0 5 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. E191A-P1 was attenuated in neonatal piglets. 2021 Cell & bioscience Result SARS_CoV_2 E191A 0 5 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Histopathological analysis indicated that severe villous atrophy was caused by virulent icPC22A infection as reported previously, minor microlesion was observed in E191A-P1-inoculated pigs, but not in the mock pigs. 2021 Cell & bioscience Result SARS_CoV_2 E191A 164 169 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. However, no lesions were observed from the E191A-P1-inoculated pigs. 2021 Cell & bioscience Result SARS_CoV_2 E191A 43 48 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. However, only sporadic N protein staining was observed in ileum of pigs infected with E191A-P1. 2021 Cell & bioscience Result SARS_CoV_2 E191A 86 91 N 23 24 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. In addition to Vero cells, porcine intestinal epithelial cells, IPEC-DQ, was also used for the propagation of E191A mutant. 2021 Cell & bioscience Result SARS_CoV_2 E191A 110 115 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. In comparison, significantly diminished and delayed PEDV fecal RNA shedding (5.06 +- 0.16 log10 copies/mL) was detected in three E191A-P1-inoculated pigs. 2021 Cell & bioscience Result SARS_CoV_2 E191A 129 134 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. In contrast, only two pigs showed moderate diarrhea at 6 dpi and no mortality was observed in E191A-P1 group. 2021 Cell & bioscience Result SARS_CoV_2 E191A 94 99 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. In summary, E191A-P1 inoculation provided pigs with partial protection, with reduced viral shedding and severity of diarrhea against challenge with the highly virulent icPC22A. 2021 Cell & bioscience Result SARS_CoV_2 E191A 12 17 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Low passage (P1-P3) of E191A mutant replicated to much lower infectious titers (1.80 +- 0.12 log10 TCID50/mL) than icPC22A (5.14 +- 0.23 log10 TCID50/mL) in Vero cells, which is an efficacious PEDV propagation system. 2021 Cell & bioscience Result SARS_CoV_2 E191A 23 28 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Low passages of E191A mutant showed poor replication in vitro. 2021 Cell & bioscience Result SARS_CoV_2 E191A 16 21 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Neonatal Gn pigs were used to investigate pathogenesis and immunogenicity of the E191A mutant. 2021 Cell & bioscience Result SARS_CoV_2 E191A 81 86 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Pigs in E191A-P1 group exhibited peak PEDV RNA shedding (9.03 +- 0.44 log10 copies/mL) at 3 dpc. 2021 Cell & bioscience Result SARS_CoV_2 E191A 8 13 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Significantly higher serum VN antibody titers were detected in mock-challenged pigs than the E191A-P1-inoculated pigs at 31 dpi/9 dpc (p = 0.2000). 2021 Cell & bioscience Result SARS_CoV_2 E191A 93 98 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Similar levels of sgmRNA-3 and sgmRNA-N were observed in E191A mutant and icPC22A, but the mutant showed significantly lower genomic RNA titers at 24 hpi than icPC22A. 2021 Cell & bioscience Result SARS_CoV_2 E191A 57 62 N 38 39 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Supernatants containing rescued viruses were harvested, designated as the P0 of E191A mutant. 2021 Cell & bioscience Result SARS_CoV_2 E191A 80 85 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. The complete genome of E191A-P1 was verified by Sanger sequencing. 2021 Cell & bioscience Result SARS_CoV_2 E191A 23 28 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. The E191A-P1 showed much smaller plaques (0.2268 +- 0.0790 mm in diameter) than the P4 virus (0.5236 +- 0.1537 mm in diameter), which was similar to icPC22A (0.4412 +- 0.1510 mm in diameter). 2021 Cell & bioscience Result SARS_CoV_2 E191A 4 9 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. The E191A-P4 exhibited dramatically high infectious titer (5.55 +- 0.35 log10 TCID50/mL), which was not significantly different from icPC22A (p = 0.3002) in Vero cells. 2021 Cell & bioscience Result SARS_CoV_2 E191A 4 9 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. The Recombinant E191A mutant was genetically unstable. 2021 Cell & bioscience Result SARS_CoV_2 E191A 16 21 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. These results suggest dramatically reduced replication efficiency of E191A mutant. 2021 Cell & bioscience Result SARS_CoV_2 E191A 69 74 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. To analyze the effect of E191A mutation on PEDV subgenomic mRNAs (sgmRNAs) and genomic RNA synthesis, we analyzed sgmRNA-3 and sgmRNA-N. 2021 Cell & bioscience Result SARS_CoV_2 E191A 25 30 N 134 135 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. To evaluate genetic stability, E191A-P4 as well as the viruses shed in fecal samples of E191A-P1 inoculated pigs were subjected to Sanger sequencing. 2021 Cell & bioscience Result SARS_CoV_2 E191A;E191A 31;88 36;93 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Two of five pigs in the mock group died at 6- or 7- days post-challenge (dpc), while no mortality was observed in the E191A-P1 group. 2021 Cell & bioscience Result SARS_CoV_2 E191A 118 123 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Vero cells inoculated with either E191A-P1 or icPC22A were harvest at 24 hpi and subjected to qRT-PCR detection. 2021 Cell & bioscience Result SARS_CoV_2 E191A 34 39 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Viral RNA copy numbers in the samples from fecal and intestinal contents of E191A-P1-inoculated pigs were too low to get the whole genome sequence. 2021 Cell & bioscience Result SARS_CoV_2 E191A 76 81 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. VN antibodies were elicited at 15 dpi upon E191A-P1 mutant inoculation. 2021 Cell & bioscience Result SARS_CoV_2 E191A 43 48 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. We calculated the sgmRNAs/TCID50 and genomic RNA/TCID50 ratios and found that E191A had significantly higher ratios than icPC22A. 2021 Cell & bioscience Result SARS_CoV_2 E191A 78 83 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. We found that E191A-P4 has lost the E191A mutation and reverted to wildtype. 2021 Cell & bioscience Result SARS_CoV_2 E191A;E191A 14;36 19;41 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. 3d) and the significantly higher expressed genes in B.1.1.7+E484K are enriched in cytokine responsive signaling and viral, including SARS-CoV-2, infection pathway. 2021 medRxiv Result SARS_CoV_2 E484K 60 65 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. 3f), the top 50 induced gene in the B.1.1.7+E484K variant compared to B.1.1.7 at the second time point are related to interferon and JAK/STAT signaling. 2021 medRxiv Result SARS_CoV_2 E484K 44 49 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. A direct comparison of the transcriptomes from three B1.1.7 and three B.1.1.7+E484K patients that had received at least one dose highlighted the different responses. 2021 medRxiv Result SARS_CoV_2 E484K 78 83 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. A higher number of differentially expressed genes (DEGs) were identified between patients infected with the B.1.1.7+E484K variant compared to controls (4399) than found in the comparison between patients infected with the B.1.1.7 variant and controls (3071). 2021 medRxiv Result SARS_CoV_2 E484K 116 121 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. At days 1-5, 294 genes were preferentially expressed in B.1.1.7+E484K patients compared to B.1.1.7 with genes mapping to interferon and JAK/STAT pathways. 2021 medRxiv Result SARS_CoV_2 E484K 64 69 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Comparison of early response immune transcriptomes of patients infected with B.1.1.7+E484K to those of patients infected with B.1.1.7. 2021 medRxiv Result SARS_CoV_2 E484K 85 90 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Differences in temporal progression of the immune response in patients following B.1.1.7+E484K as compared to B.1.1.7 infection. 2021 medRxiv Result SARS_CoV_2 E484K 89 94 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. For this, we compared the immune transcriptomes of patients infected with either the B.1.1.7+E484K or the B.1.1.7 parent variant within the first five days after the onset of COVID-19 symptomology. 2021 medRxiv Result SARS_CoV_2 E484K 93 98 COVID-19 175 183 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Genes preferentially activated in the B.1.1.7+E484K variant are part of the interferon and JAK/STAT pathways. 2021 medRxiv Result SARS_CoV_2 E484K 46 51 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Immune transcriptomes in vaccinated patients infected with B.1.1.7 and B.1.1.7+E484K. 2021 medRxiv Result SARS_CoV_2 E484K 79 84 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Key components of ISGs are expressed highest in patients infected with B.1.1.7+E484K and B.1.1.7 compared to the other variants. 2021 medRxiv Result SARS_CoV_2 E484K 79 84 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. left panel), the transcriptomes from B.1.1.7+E484K patients diverged only on PC2. 2021 medRxiv Result SARS_CoV_2 E484K 45 50 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Next, we investigated whether the E484K escape mutant in the backbone of B.1.1.7 (B.1.1.7+E484K) leads to an altered immune response. 2021 medRxiv Result SARS_CoV_2 E484K;E484K 34;90 39;95 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Next, we utilized temporally matched samples from patients infected with B.1.1.7 (n=5) and B.1.1.7+E484K (n=4) to compare temporal progression of the immune transcriptome at days 1-5 versus 10-14 following symptomology (Supplementary Data 7-9). 2021 medRxiv Result SARS_CoV_2 E484K 99 104 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Notably, the decrease was more pronounced in the B.1.1.7 variant with a more sustained immune response in the B.1.1.7+E484K variant. 2021 medRxiv Result SARS_CoV_2 E484K 118 123 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. RNA-seq was conducted on seven B.1.1.7+E484K patients and 14 B.1.1.7 patients. 2021 medRxiv Result SARS_CoV_2 E484K 39 44 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Since B.1.1.7+E484K induced a more expansive immune transcriptome than the B.1.1.7 parent variant, we directly compared their transcriptomes between days 10-14 after symptomology. 2021 medRxiv Result SARS_CoV_2 E484K 14 19 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. The transcriptomes from the three B.1.1.7+E484K patients who received their first dose between 8 and 22 days prior to developing symptoms were compared with six unvaccinated B.1.1.7+E484K patients. 2021 medRxiv Result SARS_CoV_2 E484K;E484K 42;182 47;187 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. These experiments demonstrate that the acquisition of the E484K escape mutation in the B.1.1.7 background elicits a significantly different immune response than the parent variant itself. 2021 medRxiv Result SARS_CoV_2 E484K 58 63 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Transcriptomes from 28 patients infected with the B.1.1.7 variant and 12 patients infected with the B.1.1.7+E484K variant were compared (Table 1). 2021 medRxiv Result SARS_CoV_2 E484K 108 113 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. From missense mutations found from Gujarat SARS-CoV-2 genomes, C28854T, deleterious mutation in the nucleocapsid (N) gene was significantly associated with patients' mortality. 2021 European journal of medical research Result SARS_CoV_2 C28854T 63 70 N;N 100;114 112;115 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. Studies have demonstrated that the C14408T and A23403G alterations in the Nsp12 and S proteins are the most prominent alterations in the world, leading to miserable mutations.The spike D614G amino acid change has become the most common variant since December 2019. 2021 European journal of medical research Result SARS_CoV_2 A23403G;C14408T;D614G 47;35;185 54;42;190 S;Nsp12;S 179;74;84 184;79;85 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. The other significant deleterious variant (G25563T) is found in patients located in Orf3a and has a potential role in viral pathogenesis. 2021 European journal of medical research Result SARS_CoV_2 G25563T 43 50 ORF3a 84 89 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Higher-affinity mutant V367F showed a considerable decrease of the root mean square of fluctuation (RMSF) at this region, demonstrating a more rigid structure; this was not observed for other mutants. 2021 Journal of virology Result SARS_CoV_2 V367F 25 30 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Afterwards, the V367F mutants emerged mainly in Europe, including the United Kingdom, the Netherlands, Austria, and Iceland as well as in the United States, Australia, and China. 2021 Journal of virology Result SARS_CoV_2 V367F 16 21 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. All the mutants were clustered into 96 mutant types, six of which were dominant mutant types that were found in more than ten isolates (Table 1): V483A (35x), V367F (34x), V341I (23x), N439K (16x), A344S (15x), and G476S (12x). 2021 Journal of virology Result SARS_CoV_2 A344S;G476S;N439K;V341I;V367F;V483A 198;215;185;172;159;146 203;220;190;177;164;151 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. At 24 h postinfection (h p.i.), the V367F pseudoviruses showed 6.08x higher copy numbers than the prototype in Caco-2 cells (P < 0.01). 2021 Journal of virology Result SARS_CoV_2 V367F 36 41 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. At 48 h p.i., the V367F pseudoviruses showed 6.61x and 9.16x higher copy numbers than the prototype in Vero (P < 0.0001) and Caco-2 cells (P < 0.0001), respectively. 2021 Journal of virology Result SARS_CoV_2 V367F 18 23 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Coincidentally, the substitutions that account for the affinity increase of V367F are all located near this fragment. 2021 Journal of virology Result SARS_CoV_2 V367F 76 81 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Compared to the KD (14.7 nM) of the prototype RBD, the KD of the V367F mutant was calculated as 0.11 nM. 2021 Journal of virology Result SARS_CoV_2 V367F 65 70 RBD 46 49 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Compared with all the single-mutation (V367F) variants, dual-mutation (V367F+D614G) variants were emergent in both GH and GR clades. 2021 Journal of virology Result SARS_CoV_2 V367F;V367F;D614G 39;71;77 44;76;82 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Convergence of SARS-CoV-2 RBD and D614G mutations in dominant mutation isolates. 2021 Journal of virology Result SARS_CoV_2 D614G 34 39 RBD 26 29 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Experimental validation of the enhanced affinity and infectivity of the V367F mutant. 2021 Journal of virology Result SARS_CoV_2 V367F 72 77 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Indeed, residues 475 to 485, which is a random coil near the binding site, showed a remarkably higher RMSF for the "similar-affinity" mutants than the higher-affinity V367F mutant. 2021 Journal of virology Result SARS_CoV_2 V367F 167 172 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Intriguingly, all of the dual-mutation variants (V367F+D614G) emerging later formed a distinct subcluster in GH, GR, and G clades, separate from the L and S clades. 2021 Journal of virology Result SARS_CoV_2 V367F;D614G 49;55 54;60 S 155 156 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. It has been confirmed that the D614G mutants, which have spread widely, increase virus infectivity by elevating its sensitivity to protease. 2021 Journal of virology Result SARS_CoV_2 D614G 31 36 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Moreover, the higher-affinity mutant V367F exhibited a generally decreased DeltaG in the binding site region in contrast to that of the similar-affinity mutants. 2021 Journal of virology Result SARS_CoV_2 V367F 37 42 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Multiple dual-mutation (V367F+D614G) variants located in different clades had mutations undetected in early V367F mutants. 2021 Journal of virology Result SARS_CoV_2 V367F;V367F;D614G 108;24;30 113;29;35 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Second, we performed surface plasmon resonance (SPR) experiments, which yielded the same conclusion: the prototype had a KD of 5.08 nM compared to the V367F mutant with a KD of 2.70 nM. 2021 Journal of virology Result SARS_CoV_2 V367F 151 156 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The D614G mutation in the S1 subunit accounted for most of the polymorphism and divergence. 2021 Journal of virology Result SARS_CoV_2 D614G 4 9 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The D614G mutation is located in the S1 region and is outside the RBD of the SARS-CoV-2 spike protein. 2021 Journal of virology Result SARS_CoV_2 D614G 4 9 S;RBD 88;66 93;69 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The D614G+V367F dual mutant initially emerged in March 2020 in the Netherlands (see Table S1). 2021 Journal of virology Result SARS_CoV_2 D614G;V367F 4;10 9;15 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The DeltaG of the V367F mutant was significantly low (~60 kJ/mol) (P = 0.0151), approximately 25% lower than for the prototype strain (-46.5 kJ/mol, calculated from the experimentally measured equilibrium dissociation constant [KD]). 2021 Journal of virology Result SARS_CoV_2 V367F 18 23 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The phylogenetic analysis of the V367F mutant genomes during the early transmission phase showed that V367F mutants clustered more closely with the SARS-CoV-2 prototype strain in the L clade. 2021 Journal of virology Result SARS_CoV_2 V367F;V367F 33;102 38;107 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The result showed that the V367F mutation lowered the 50% effective dose (ED50) concentration (ED50 = 0.8 +- 0.04 mug/ml) compared to that of the prototype (ED50 = 1.7 +- 0.14 mug/ml). 2021 Journal of virology Result SARS_CoV_2 V367F 27 32 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The S1 gene exhibited a high dN/dS (2.05) due to the widely spreading nonsynonymous mutation D614G in the S1 gene. 2021 Journal of virology Result SARS_CoV_2 D614G 93 98 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The V367F mutants were initially discovered in January 2020 in Hong Kong. 2021 Journal of virology Result SARS_CoV_2 V367F 4 9 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Therefore, the binding affinity and the infectivity of the V367F mutant were further validated experimentally. 2021 Journal of virology Result SARS_CoV_2 V367F 59 64 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Therefore, the computation and protein and cell validations were consistent with each other: the V367F mutant had enhanced affinity and infectivity. 2021 Journal of virology Result SARS_CoV_2 V367F 97 102 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. This demonstrates that the V367F mutant has a higher affinity to human ACE2 than the prototype. 2021 Journal of virology Result SARS_CoV_2 V367F 27 32 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. To elucidate the structural basis of the increased affinity of the V367F mutant, we investigated the dynamics of the residues in these structures in greater detail. 2021 Journal of virology Result SARS_CoV_2 V367F 67 72 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. V367F is the only mutant with a higher binding affinity, as calculated by MD simulation. 2021 Journal of virology Result SARS_CoV_2 V367F 0 5 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. V367F mutant emergent during the early transmission phase binds human ACE2 receptor with higher affinity. 2021 Journal of virology Result SARS_CoV_2 V367F 0 5 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. V367F mutants occurred on 22 January 2020, which was the earliest dominant mutant type. 2021 Journal of virology Result SARS_CoV_2 V367F 0 5 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. V367F mutants were found on all four continents. 2021 Journal of virology Result SARS_CoV_2 V367F 0 5 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. V483A and V367F accounted for 11.59% and 11.26% of 302 mutants, respectively. 2021 Journal of virology Result SARS_CoV_2 V367F;V483A 10;0 15;5 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Among the four amplicon sizes that we investigated, an amplicon of 580 bp gave a clear discernible signal distinguishing the N501Y mutation over the WT sample (Figure 3A, Materials and methods). 2021 eLife Result SARS_CoV_2 N501Y 125 130 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Among these SNVs, N501Y is present across 3/5 of the VOCs (B.1.1.7, P.1, and B.1.351). 2021 eLife Result SARS_CoV_2 N501Y 18 23 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Among these, the E484K mutation has been associated with high transmissibility and the possibility of reinfection. 2021 eLife Result SARS_CoV_2 E484K 17 22 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Importantly, amplicons containing the E484K mutation do not show cross-reactivity with the N501Y sgRNA, highlighting the specificity of the assay between variants (Figure 4H). 2021 eLife Result SARS_CoV_2 E484K;N501Y 38;91 43;96 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Importantly, RAY correctly classified all eight WT samples where neither the N501Y mutation nor any other lineage variants were present as seen by either an absence of a distinct band or an extremely faint band in the test line (Figure 3C). 2021 eLife Result SARS_CoV_2 N501Y 77 82 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Next, we investigated the sensitivity of the assay on serial dilutions of a WT and a N501Y mutant patient sample with moderately high viral load (Ct <25). 2021 eLife Result SARS_CoV_2 N501Y 85 90 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Next, we tested RAY on RNA extracted from samples of eight qRT-PCR-positive SARS-CoV-2-infected individuals who harbored the N501Y mutation (along with other mutations). 2021 eLife Result SARS_CoV_2 N501Y 125 130 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Notably, we were able to successfully validate RAY for two more mutations E484K and T716I in patient samples using corresponding sgRNAs suggesting that the assay can be optimized and adapted for other VOCs in addition to N501Y (Figure 4G). 2021 eLife Result SARS_CoV_2 E484K;N501Y;T716I 74;221;84 79;226;89 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. RAY can successfully discriminate N501Y and WT nCoV2 substrates. 2021 eLife Result SARS_CoV_2 N501Y 34 39 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Since the 149 bp amplicon did not contain the SWT sgRNA-binding site, we modified the assay to perform two simultaneous PCR reactions from the same sample, one generating the N501Y specific amplicon (149 bp), and another corresponding to the SWT sgRNA from the original FELUDA assay (287 bp) (Figure 4C). 2021 eLife Result SARS_CoV_2 N501Y 175 180 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Single Amplicon RAY can discriminate N501Y and WT nCoV-2 substrates from patient samples with high viral load. 2021 eLife Result SARS_CoV_2 N501Y 37 42 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Taken together, RAY is sufficiently sensitive in detecting the N501Y VOC in a sample with only a few copies of the virus and is comparable to other sequencing platforms. 2021 eLife Result SARS_CoV_2 N501Y 63 68 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. The electrophoresis based identification of the N501Y(A23063T) mutation can be adapted for COVID-19 detection under laboratory conditions. 2021 eLife Result SARS_CoV_2 N501Y;A23063T 48;54 53;61 COVID-19 91 99 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. The samples were sequenced in parallel to detect the presence of N501Y mutation. 2021 eLife Result SARS_CoV_2 N501Y 65 70 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Thus, RAY can identify the N501Y SNV with high accuracy in patient samples underscoring its impact as a rapid screening methodology for SARS-CoV-2 VOCs. 2021 eLife Result SARS_CoV_2 N501Y 27 32 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. To generate a visually distinctive signal between WT and mutant sample, we performed a single-step reverse transcription PCR to generate a biotin-labeled amplified product that can be detected by a single sgRNA (called SWT) if the sample is WT and by both sgRNAs (SWT and SN501Y) if the sample contains the N501Y variant (Figure 2B,C). 2021 eLife Result SARS_CoV_2 N501Y 307 312 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. To increase the band intensity further, we reduced the length of the PCR amplicon containing the N501Y mutation and found that within the same sample, amplicons with shorter lengths had higher band intensities (Figure 4B). 2021 eLife Result SARS_CoV_2 N501Y 97 102 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. We designed primer pairs surrounding the N501Y mutation after analyzing the mutational spectrum in SARS-CoV-2 strains obtained from the publicly available sequencing database, GISAID. 2021 eLife Result SARS_CoV_2 N501Y 41 46 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. We found that catalytically active FnCas9 was able to successfully cleave the dsDNA substrate containing the N501Y mutation while leaving the WT sequence intact (Figure 2A). 2021 eLife Result SARS_CoV_2 N501Y 109 114 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. We reasoned that in order to enable RAY to distinguish two samples different by a single mismatch on a paper strip, the intensity of the one mismatched sgRNA (as the other mismatch corresponds to N501Y SNV) should be several folds higher than wild-type samples (having two mismatches with the sgRNA, one at the SNV position and another synthetic mismatch). 2021 eLife Result SARS_CoV_2 N501Y 196 201 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. We reasoned that including the S-gene sgRNA which lies in the vicinity of the N501Y variant would serve as an internal positive control both for the presence of the SARS-CoV-2 virus in the sample as well as quality control for the amplicons generated in the RT PCR step of the assay. 2021 eLife Result SARS_CoV_2 N501Y 78 83 S 31 32 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. We tested the N501Y sgRNA containing the variant mismatch at PAM proximal 2nd position to selectively bind and cleave the mutant substrate, while not affecting the WT substrate due to mismatch at PAM proximal 2nd and 6th positions. 2021 eLife Result SARS_CoV_2 N501Y 14 19 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. We then proceeded to test RAY on a set of patient samples containing either the WT (n = 37) or the N501Y variants (n = 22) identified by sequencing. 2021 eLife Result SARS_CoV_2 N501Y 99 104 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. With a single run of the assay, SN501Y was able to detect 36/37 WT samples and 19/22 N501Y samples corresponding to a sensitivity of 86% and a specificity of 97% across all ranges of Ct values (Figure 4F, Supplementary file 2). 2021 eLife Result SARS_CoV_2 N501Y 85 90 34107326 SARS-CoV-2 reinfection with a virus harboring mutation in the Spike and the Nucleocapsid proteins in Panama. Additionally, we detected a nucleotide deletion (21984-21993del) inducing a loss of 3 amino acids (L141del, G142del, V143del) and a nucleotide insertion (22005-22013 in.) associated with the insertion of 3 amino acids (A215, G216, Y217), balancing the reading frame of the translated S protein. 2021 International journal of infectious diseases Result SARS_CoV_2 G142del;V143del;L141del 108;117;99 115;124;106 S 284 285 34107326 SARS-CoV-2 reinfection with a virus harboring mutation in the Spike and the Nucleocapsid proteins in Panama. In contrast, the L452R mutation is located in the region binding domain (RBD) for ACE2 receptor, D614G being between the RBD and the amino acid bridge between the S1 and S2 subunits. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G;L452R 97;17 102;22 RBD;RBD 73;121 76;124 34107326 SARS-CoV-2 reinfection with a virus harboring mutation in the Spike and the Nucleocapsid proteins in Panama. Of these nucleotide substitutions, 15 induced amino acid changes: 3 in the S protein (D215A, L452R, D614G), 5 in ORF1a (1 in NSP1, 2 in NSP3, 1 in NSP4, 1 in NSP6), 4 in the Nucleocapsid (N), 2 in helicase and 1 in ORF3a. 2021 International journal of infectious diseases Result SARS_CoV_2 D614G;L452R;D215A 100;93;86 105;98;91 N;Helicase;ORF1a;ORF3a;Nsp3;Nsp4;Nsp6;N;S 174;197;113;215;136;147;158;188;75 186;205;118;220;140;151;162;189;76 34107326 SARS-CoV-2 reinfection with a virus harboring mutation in the Spike and the Nucleocapsid proteins in Panama. The deletion of amino acid LGV (Leucine, Glycine, Valine) at positions 141-143 and the insertion of AGY (Alanine, Glycine, Tyrosine) inducing the substitution D215A are in the N-terminal domain (NTD). 2021 International journal of infectious diseases Result SARS_CoV_2 D215A 159 164 N 176 177 34107326 SARS-CoV-2 reinfection with a virus harboring mutation in the Spike and the Nucleocapsid proteins in Panama. The mutations S197L, M234I are located in the link region between the RNA-binding domain and the dimerization domain, whereas the P383L is in the C-terminal domain of the N protein (Supplementary Table S1, Supplementary Figure S2B,). 2021 International journal of infectious diseases Result SARS_CoV_2 M234I;P383L;S197L 21;130;14 26;135;19 N 171 172 34114829 Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study. According to the CDC, laboratory studies suggest that specific monoclonal antibody treatments may be less effective for treating cases of COVID-19 caused by variants with the E484K substitution in the spike protein.- Additionally, there are three circulating variants of concern, which present such mutation: B.1.351 lineage (also known as (a.k.a.) 20H/501Y.V2) first described in South Africa; P.1 lineage (a.k.a. 2021 The journal of physical chemistry. B Result SARS_CoV_2 E484K 175 180 S 201 206 COVID-19 138 146 34114829 Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study. Additionally, the substitution of Asp30 by a Glu seems to favor the affinity between the systems since the top 2 ranked solutions present this designed replacement (Figure 2A). 2021 The journal of physical chemistry. B Result SARS_CoV_2 D30E 34 48 34114829 Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study. As for the ZDOCK top predictions, the Asp30 substitution by Glu also seems to play an important role in the predicted binding affinity since modifications 3 and 13 show this feature (Figure S1, SI). 2021 The journal of physical chemistry. B Result SARS_CoV_2 D30E 38 63 34114829 Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study. However, in the E484K-mutated RBD and modification 15 complex, the interactions of this specific type have reduced persistence (Figure 7B). 2021 The journal of physical chemistry. B Result SARS_CoV_2 E484K 16 21 RBD 30 33 34114829 Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study. Stability and Profile Interaction in the Presence of E484K RBD Mutation. 2021 The journal of physical chemistry. B Result SARS_CoV_2 E484K 53 58 RBD 59 62 34114829 Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study. The ligand RMSD values calculated from the MD trajectory of E484K-mutated RBD/modification 15 and 11 reveal stable profiles of the peptides with respect to the protein and to their internal fluctuations (Figure S5). 2021 The journal of physical chemistry. B Result SARS_CoV_2 E484K 60 65 RBD 74 77 34114829 Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study. Therefore, we decided to analyze the interaction profile and stability of modification 15 in the presence of the spike protein RBD presenting the E484K mutation. 2021 The journal of physical chemistry. B Result SARS_CoV_2 E484K 146 151 S;RBD 113;127 118;130 34114829 Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study. This increase in the H-bond interactions must contribute to the good stability of modification 15/E484K-mutated RBD complex, as demonstrated by the stable profile seen in the RMSD parameters. 2021 The journal of physical chemistry. B Result SARS_CoV_2 E484K 98 103 RBD 112 115 34114829 Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study. Together these results lead us to hypothesize that the E484K mutation present in different SARS-CoV-2 lineages will not hamper the ability of modification 15 or modification 11 to bind the viral RBD. 2021 The journal of physical chemistry. B Result SARS_CoV_2 E484K 55 60 RBD 195 198 34119826 Therapeutic effect of CT-P59 against SARS-CoV-2 South African variant. CT-P59 inhibited SARS-CoV-2 D614G pseudovirus with IC50 value of 10 ng/mL, but showed 33-fold reduced neutralization of B.1.351 pseudotyped viruses, with an IC50 value of 330 ng/mL. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 D614G 28 33 34119826 Therapeutic effect of CT-P59 against SARS-CoV-2 South African variant. KD values of CT-P59 were reduced by approximately 2-, 2-, and 10-fold in E484K, N501Y, and triple mutant (K417N/E484K/N501Y), respectively (Table 1 ). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E484K;N501Y;K417N;E484K;N501Y 73;80;106;112;118 78;85;111;117;123 34119826 Therapeutic effect of CT-P59 against SARS-CoV-2 South African variant. The equilibrium dissociation constant (KD) of CT-P59 against K417N was equivalent to that against wild type. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 K417N 61 66 34119826 Therapeutic effect of CT-P59 against SARS-CoV-2 South African variant. To assess the efficacy of CT-P59 against SA variant, we determined the binding affinity of CT-P59 against individual and triple mutant RBDs (K417N, E484K, N501Y, and K417N/E484K/N501Y), which define the SA variant, by using BLI. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 E484K;K417N;N501Y;K417N;E484K;N501Y 148;166;155;141;172;178 153;171;160;146;177;183 RBD 135 139 34119951 Examining the interactions scorpion venom peptides (HP1090, Meucin-13, and Meucin-18) with the receptor binding domain of the coronavirus spike protein to design a mutated therapeutic peptide. According to docking results, mutation 2 (H4Y) of the meucin-18 had a better HADDOCK score with the RBD domain; nevertheless, according to MM/GBSA results, the mutation 1 (A9T) of the meucin-18 had better interaction with the RBD domain. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 A9T;H4Y 172;42 175;45 RBD;RBD 100;226 103;229 34119951 Examining the interactions scorpion venom peptides (HP1090, Meucin-13, and Meucin-18) with the receptor binding domain of the coronavirus spike protein to design a mutated therapeutic peptide. Because MM/GBSA results were obtained from 50 ns MD simulation and were more accurate, we chose mutation 1 or A9T mutation as the most suitable peptide for binding to the RBD domain of the spike protein. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 A9T 110 113 S;RBD 189;171 194;174 34119951 Examining the interactions scorpion venom peptides (HP1090, Meucin-13, and Meucin-18) with the receptor binding domain of the coronavirus spike protein to design a mutated therapeutic peptide. In mut1 electrostatics energy is major factor in binding to RBD domain and mutation A9T in meucin-18 lead to enhancement of electrostatic interaction. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 A9T 84 87 RBD 60 63 34119951 Examining the interactions scorpion venom peptides (HP1090, Meucin-13, and Meucin-18) with the receptor binding domain of the coronavirus spike protein to design a mutated therapeutic peptide. These results demonstrated that mutation 1 (A9T) causes the greatest decrease in binding free energy and therefore it is the most appropriate mutation for the meucin-18 peptide. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 A9T 44 47 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. 1H1 and 5E1 recognize RBD WT and RBD variants in a similar manner, but relatively weaker to RBD E484K, RBD K417N, and RBD N501Y/K417N/E484K. 2021 Emerging microbes & infections Result SARS_CoV_2 E484K;K417N;N501Y;E484K;K417N 96;107;122;134;128 101;112;127;139;133 RBD;RBD;RBD;RBD;RBD 22;33;92;103;118 25;36;95;106;121 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. 7G5 binds strongly to RBD WT and RBD E484K, weakly to RBD K417N, and fails to recognize RBD N501Y and RBD N501Y/K417N/E484K (Figure 3(B)). 2021 Emerging microbes & infections Result SARS_CoV_2 E484K;K417N;N501Y;N501Y;E484K;K417N 37;58;92;106;118;112 42;63;97;111;123;117 RBD;RBD;RBD;RBD;RBD 22;33;54;88;102 25;36;57;91;105 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. 9H1 and 7G5 could neutralize D614G, B.1.429 and B.1.526 variants, but not the other three variants tested. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 29 34 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. 9H1 binds well to RBD WT and most RBD variants except no detectable binding to RBD N501Y. 2021 Emerging microbes & infections Result SARS_CoV_2 N501Y 83 88 RBD;RBD;RBD 18;34;79 21;37;82 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. Another SARS-CoV-2 lineage, B.1.351, in South Africa (501.V2) had three altered residues in the ACE2 binding site of RBD, including K417N, E484K and N501Y. 2021 Emerging microbes & infections Result SARS_CoV_2 E484K;K417N;N501Y 139;132;149 144;137;154 RBD 117 120 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. Consistent with ELISA data of 1H1 and 5E1 binding with RBD N501Y, the neutralization potency of 1H1 and 5E1 is similar to that of the wild type and D614G strain, while 9H1 and 7G5 which failed to bind to RBD 501Y also presented neutralization resistance of the B.1.1.7 variant. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G;N501Y 148;59 153;64 RBD;RBD 55;204 58;207 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. Despite the neutralization potency against in the B.1.526 strain with D614G and E484K mutation has been slightly reduced by four RmAbs, all four RmAbs isolated from our study were still capable to neutralize B.1.526 variant in presence of E484K mutation. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G;E484K;E484K 70;80;239 75;85;244 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. For Brazil P.1 with three RBD mutations (K417T/E484K/N501Y), only 1H1 was found to mediate neutralization in our study. 2021 Emerging microbes & infections Result SARS_CoV_2 K417T;E484K;N501Y 41;47;53 46;52;58 RBD 26 29 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. N501Y mutation leads to enhanced binding to ACE2, whereas K417N/E484K/N501Y in variant 501.V2 increases their infectivity. 2021 Emerging microbes & infections Result SARS_CoV_2 K417N;E484K;N501Y;N501Y 58;64;70;0 63;69;75;5 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. Notably, 1H1 was able to neutralize all emerging SARS-CoV-2 variants tested at microgram or sub microgram level, 5E1 could neutralize against D614G, B.1.1.7, B.1.429, and B.1.526, B.1.351 except to P.1. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 142 147 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. On the contrary, RBD E484K and K417N had little impact on 9H1 recognition with RBD. 2021 Emerging microbes & infections Result SARS_CoV_2 E484K;K417N 21;31 26;36 RBD;RBD 17;79 20;82 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. RBD L452R mutation from B.1.429 variant leads to a slightly increased neutralization resistance of these RmAbs. 2021 Emerging microbes & infections Result SARS_CoV_2 L452R 4 9 RBD 0 3 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. Since the attenuated neutralizing activity of convalescent sera against emergent variants was largely attributed to the E484K substitution, we then tested the other three E484K harboring variants, including P.1, B.1.526, and B.1.351. 2021 Emerging microbes & infections Result SARS_CoV_2 E484K;E484K 120;171 125;176 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. Specifically, we found that neutralization of D614G variant was comparable with wild-type strain by four RmAbs, in line with previous reports. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 46 51 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. Subsequently, to determine whether these mutations impact RmAb recognition of RBD, we first compared the antibody binding to wild-type RBD (RBD WT) with that to variants RBD N501Y, RBD K417N, RBD E484K, and RBD N501Y/K417N/E484K. 2021 Emerging microbes & infections Result SARS_CoV_2 E484K;K417N;N501Y;N501Y;E484K;K417N 196;185;174;211;223;217 201;190;179;216;228;222 RBD;RBD;RBD;RBD;RBD;RBD;RBD 78;135;140;170;181;192;207 81;138;143;173;184;195;210 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. To determine whether these RmAbs could neutralize currently circulating SARS-CoV-2 variants, we then tested the neutralization potency of RmAbs against six emerging SARS-CoV-2 variants including the D614G variant, the B.1.1.7 variant, the B.1.429 variant, the P.1 variant, the B.1.526 variant, and the B.1.351 variant (Figure 5(A, B)). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 199 204 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. Variant B.1.1.7 has a key mutation N501Y in its spike RBD region and deletion of H69-V70 (S1 del (69-70)) on the spike. 2021 Emerging microbes & infections Result SARS_CoV_2 N501Y 35 40 S;S;RBD 48;113;54 53;118;57 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Although F486L and N501T is not predicted that does not damage the structure of the spike protein (Table 2), it has been stated that the N501T and F486L mutations affect the stability of the spike protein. 2021 Bioinformatics and biology insights Result SARS_CoV_2 F486L;F486L;N501T;N501T 9;147;19;137 14;152;24;142 S;S 84;191 89;196 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Another example where 3 mutations occurred at the same isolated sequence is QKY60177, which has Q506H, Y508N, and P507S mutations. 2021 Bioinformatics and biology insights Result SARS_CoV_2 P507S;Q506H;Y508N 114;96;103 119;101;108 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. As in Europe and Africa, there are similar mutations that occurred at different positions, such as T29I, T76I, and T791I. 2021 Bioinformatics and biology insights Result SARS_CoV_2 T29I;T76I;T791I 99;105;115 103;109;120 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. As in Table 5, Threonine (T) changes to Isoleucine (I) at different positions such as T22I, T76I, T95I, T572I, T791I, and T827I; whereas Glutamine (Q) changed to Histidine (H) (QLA10116 and QKW92184). 2021 Bioinformatics and biology insights Result SARS_CoV_2 T22I;T572I;T76I;T791I;T827I;T95I 86;104;92;111;122;98 90;109;96;116;127;102 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. As seen in all regions, D614G was the most variant for all regions (Tables 1 to 5); 240 isolated samples had this variant in Asia (Table 5). 2021 Bioinformatics and biology insights Result SARS_CoV_2 D614G 24 29 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. As seen in sequences from all regions, the D614G mutation predicted structure damage for this region. 2021 Bioinformatics and biology insights Result SARS_CoV_2 D614G 43 48 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Based on 760 whole sequences from Oceania and South America, the most common mutations are found to be G1124V (25 mutations) and D614G (20 mutations), while other different mutations tend to increase, such as S50L (10 mutations), A262T (11 mutations), L5F (5 mutations), D138H (3 mutations), S221L (3 mutations), G485R (3 mutations) (Table 3). 2021 Bioinformatics and biology insights Result SARS_CoV_2 A262T;D138H;D614G;G1124V;G485R;L5F;S221L;S50L 230;271;129;103;313;252;292;209 235;276;134;109;318;255;297;213 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Based on results (some are shown on Table 4), more than 255 mutations for D614G was determined. 2021 Bioinformatics and biology insights Result SARS_CoV_2 D614G 74 79 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Because, even D614G mutation predicted a damaged structure (Table 1), no significant link between the D614G alteration and disease severity was found. 2021 Bioinformatics and biology insights Result SARS_CoV_2 D614G;D614G 14;102 19;107 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Besides, QKV37632 sample has 2 mutations which are T29I and S704 (Table 3). 2021 Bioinformatics and biology insights Result SARS_CoV_2 T29I 51 55 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. But it is known that compared with the D614 variant, higher viral loads were found in patients infected with the G614 variant, but clinical data suggested no significant link between the D614G alteration and disease severity, and also suggesting the alteration may have increased the infectivity of SARS-CoV-2. 2021 Bioinformatics and biology insights Result SARS_CoV_2 D614G 187 192 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Eighty four whole spike protein sequences isolated from Africa are used, and the most common mutations are found to be Q667H (5 mutations), D614G (3 mutations), R408I (2 mutations), and others (1 mutations), which was found containing 8 different mutations (Table 1). 2021 Bioinformatics and biology insights Result SARS_CoV_2 D614G;Q667H;R408I 140;119;161 145;124;166 S 18 23 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Even the D936Y mutation did not predict the damage to the spike protein structure, however, this mutation is predicted to reduce the stability of spike proteins. 2021 Bioinformatics and biology insights Result SARS_CoV_2 D936Y 9 14 S;S 58;146 63;151 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. For example, a distinct rise in the prevalence of SARS-CoV-2 bearing a D614G mutation has been noted over time. 2021 Bioinformatics and biology insights Result SARS_CoV_2 D614G 71 76 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. For instance, Alanine can change to Serine at 2 different positions such as A845S and A892S (Table 2). 2021 Bioinformatics and biology insights Result SARS_CoV_2 A845S;A892S 76;86 81;91 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. For instance, QKG89654 (A845D) and QKV35819 (A845V) have different mutations at the same position. 2021 Bioinformatics and biology insights Result SARS_CoV_2 A845D;A845V 24;45 29;50 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. In addition, mutations more than 3 were found, such as L54F (40 mutations), R78M (15 mutations), V367F (5 mutations), A829T (10 mutations), H1083Q (4 mutations), T791I (12 mutations), Q677H (4 mutations), E583D (15 mutations), T572I (10 mutations), and L8V (4 mutations). 2021 Bioinformatics and biology insights Result SARS_CoV_2 A829T;E583D;H1083Q;L54F;L8V;Q677H;R78M;T572I;T791I;V367F 118;205;140;55;253;184;76;227;162;97 123;210;146;59;256;189;80;232;167;102 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. In addition, Threonine (T) can change to Isoleucine at 3 different positions T22I, T240I, and T676I. 2021 Bioinformatics and biology insights Result SARS_CoV_2 T22I;T240I;T676I 77;83;94 81;88;99 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. In the sample sequences isolated for this study, some other mutations were found, such as L5F (19 mutations), D138H (18 mutations), E554D (13 mutations), and P631L (10 mutations). 2021 Bioinformatics and biology insights Result SARS_CoV_2 D138H;E554D;L5F;P631L 110;132;90;158 115;137;93;163 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. In this area, only D614G mutation predicted a damaged structure. 2021 Bioinformatics and biology insights Result SARS_CoV_2 D614G 19 24 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. In this region, some mutations found include C1243F, Q1201K, K1191N, D1153Y, P507S, among others. 2021 Bioinformatics and biology insights Result SARS_CoV_2 C1243F;D1153Y;K1191N;P507S;Q1201K 45;69;61;77;53 51;75;67;82;59 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Korber et al suggested that the alteration (D614G) may have increased the infectivity of SARS-CoV-2, and higher viral loads were found in patients infected with the G614 variant, and Toyoshima et al said that this variant has also higher fatality rate., Like this suggestion, when T393P occurs at the spike protein, it may affect on both infectivity of SARS-CoV-2 and higher viral loads. 2021 Bioinformatics and biology insights Result SARS_CoV_2 T393P;D614G 281;44 286;49 S 301 306 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Like QLA46612 isolated from South Korea, QJD23249 isolated from Wilayah Persekutuan Malaysia has 4 mutations which includes L293M, D294I, P295H, and H519Q. 2021 Bioinformatics and biology insights Result SARS_CoV_2 D294I;H519Q;L293M;P295H 131;149;124;138 136;154;129;143 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. One of these sequences, QJX45344, which was isolated from Tunisia, has 2 mutations which are A288T and Q314R (Table 1). 2021 Bioinformatics and biology insights Result SARS_CoV_2 A288T;Q314R 93;103 98;108 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Only 2 (T393P and D614G) of these mutant sequence predicted a structure damage (Table 2). 2021 Bioinformatics and biology insights Result SARS_CoV_2 D614G;T393P 18;8 23;13 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Other examples are QKG91034 (Q836P) and QKG81751 (Q836L) (Table 4). 2021 Bioinformatics and biology insights Result SARS_CoV_2 Q836L;Q836P 50;29 55;34 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Predicted structure damage for D614G mutation (found in all regions) is due to substitution, which replaces glycine originally located in a bend curvature in this area (Figure 1A). 2021 Bioinformatics and biology insights Result SARS_CoV_2 D614G 31 36 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. QLA46612 isolated from South Korea has 4 different mutations L54F, F86S, T95I, and QKY60177, whereas India has 4 mutations Q506H, P507S, Y508N, and K786N, respectively (Table 5). 2021 Bioinformatics and biology insights Result SARS_CoV_2 F86S;K786N;L54F;P507S;Q506H;T95I;Y508N 67;148;61;130;123;73;137 71;153;65;135;128;77;142 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. T393P isolated from Europe substitutes and introduces a buried proline which triggers disallowed phi/psi alert. 2021 Bioinformatics and biology insights Result SARS_CoV_2 T393P 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. T393P mutation, which the other predicted a structure damage, is found only in Europe (Table 2). 2021 Bioinformatics and biology insights Result SARS_CoV_2 T393P 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. The maximum D614G mutation rates are found in North America in 2,700 complete sequences of only spike proteins. 2021 Bioinformatics and biology insights Result SARS_CoV_2 D614G 12 17 S 96 101 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. The most common mutations were found to be D614G (39 mutations), H49Y (3 mutations), Y453 F (8 mutations), G261D (6 mutations), A845S (4 mutations), T676I (2 mutations), S254F (2 mutations), and I197V (2 mutations), respectively, while the others that have only one mutation are shown on Table 2. 2021 Bioinformatics and biology insights Result SARS_CoV_2 A845S;D614G;G261D;H49Y;I197V;S254F;T676I;Y453F 128;43;107;65;195;170;149;85 133;48;112;69;200;175;154;91 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. The predicted reason for M177I isolated from Asia is that substitution results in a change between the buried and exposed state of the target variant residue. 2021 Bioinformatics and biology insights Result SARS_CoV_2 M177I 25 30 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. The substitution in T95I mutant sequence isolated from Asia and North America disrupts all side-chain/side-chain H-bond(s) and/or side-chain/main-chain H-bond(s) formed by a buried Threonine residue (RSA 0.0%) (Figure 1I). 2021 Bioinformatics and biology insights Result SARS_CoV_2 T95I 20 24 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. The substitution in the G75V mutant sequence isolated from North America replaces a buried GLY residue (RSA 3.5%) with a buried Valine residue (RSA 0.0%) (Figure 1G). 2021 Bioinformatics and biology insights Result SARS_CoV_2 G75V 24 28 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. The substitution in the L293M mutant sequence resulted in a change between buried and exposed state of the target variant residue. 2021 Bioinformatics and biology insights Result SARS_CoV_2 L293M 24 29 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. The substitution in the P295H mutant sequence isolated from Asia replaces a buried uncharged residue (Proline, RSA 0.7%) with a charged residue Histidine and leads to the expansion of cavity volume by 142.128 A^3 (Figure 1E). 2021 Bioinformatics and biology insights Result SARS_CoV_2 P295H 24 29 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. The substitution in the P507S mutant sequence isolated from Asia replaces a buried uncharged residue (Proline, RSA 0.0%) with a charged residue Histidine (Figure 1D). 2021 Bioinformatics and biology insights Result SARS_CoV_2 P507S 24 29 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. This (G143V) substitution triggers a disallowed phi/psi alert. 2021 Bioinformatics and biology insights Result SARS_CoV_2 G143V 6 11 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. All 9 samples detected as E484K mutants had similar RT-qPCR curves. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 E484K 26 31 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. E484K/N501Y Assay. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 N501Y;E484K 6;0 11;5 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. For example, using the synthetic control C + without-Mut484-501-417 (without the K417N mutation) or RNA from clinical samples, the reaction that contains the primer that is 100% complementary to the sequences that do not present the K417N mutation showed a lower Cq value. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 K417N;K417N 81;233 86;238 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. In contrast, in the presence of the synthetic control "C+ Mut484-501-417" (that presents the N501Y mutation), only amplification by the "Probe 501Y" probe was observed, which is specific for detection of the mutation ( Figure 4D ). 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 N501Y 93 98 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. K417N Assay. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 K417N 0 5 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. On the other hand, in the presence of the synthetic control C+ Mut484-501-417 (with the E484K mutation) only the amplification by the 484K probe was observed, specific for detecting the mutation ( Figure 4B ). 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 E484K 88 93 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Regarding the N501Y mutation, in the presence of the sequence without this mutation ( Figure 4C ), we only observed amplification by part of the sequence designed for its detection (Probe 501N HEX) either by adding the RNA from a clinical sample or the synthetic control C + without-Mut484-501-417. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 N501Y 14 19 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. The assay aimed to detect the K417N mutation, discriminating between the sequences containing or not the mutation. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 K417N 30 35 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. The assays performed in the presence of the sequence without the E484K mutation ( Figure 4A ) only showed amplification in the sequence designed for its detection (Probe 484E) either by adding the COVID-19 patient sample or the synthetic control (C + without-Mut484-501-417). 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 E484K 65 70 COVID-19 197 205 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. The clinical characteristics of those patients with samples containing the E484K mutation are described inTable 4 . 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 E484K 75 80 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. The following 4 electropherograms show the sequencing results of four representative samples of samples with the E484K mutation. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 E484K 113 118 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Through the analysis of 517 samples, we detected 9 positive samples for the E484K mutation, indicating a prevalence of 1.74% in Mexican patients from this study, diagnosed from January 11 to February 12, 2021. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 E484K 76 81 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. We could not detect the other three mutations (69-70del, K417N, and N501Y) in any patient.Figure 5shows four representative RT-qPCR curves from four cases with the E484K mutation. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 E484K;K417N;N501Y 164;57;68 169;62;73 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. (Table 2), and findings, when examined globally, were not as striking, going in the same 4 months from 0% (0/69514) to 0.01% (20/107841) to 0.2% (403/195853) and to 0.56% (469/82392) in B.1.1.7 lineage and 0% (0/932) to 0.6% (11/1816) to 15.4% (400/2592) and to 37% (464/1253) in B.1.1.7-M:V70L sub-lineage, respectively (Figure 2(A) and Table 2). 2021 Emerging microbes & infections Result SARS_CoV_2 V70L 290 294 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. By April, the prevalence of SARS-CoV-2 isolates carrying the S:D178H mutation increased to 1.05% nationally and as high as 14.77% in Washington. 2021 Emerging microbes & infections Result SARS_CoV_2 D178H 63 68 S 61 62 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. California and Washington showed the greatest increases in terms of the percentage of B.1.1.7 isolates carrying the S:D178H mutation. 2021 Emerging microbes & infections Result SARS_CoV_2 D178H 118 123 S 116 117 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. In California, S:D178H was first seen in December 2020, but it was not seen within the B.1.1.7 lineage until 4 February 2021 (Table 3). 2021 Emerging microbes & infections Result SARS_CoV_2 D178H 17 22 S 15 16 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. In the vast majority of cases, the M:V70L mutation occurred on the B.1.1.7 lineage. 2021 Emerging microbes & infections Result SARS_CoV_2 V70L 37 41 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. In Washington, the S:D178H mutation was absent until February 2021, where it quickly increased to account for 9.6% (296/3077) of all viral isolates in March and 14.8% (364/2464) in April (Table 3). 2021 Emerging microbes & infections Result SARS_CoV_2 D178H 21 26 S 19 20 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Origin and transmission of the B.1.1.7-M:V70L-S:D178H sub-lineage. 2021 Emerging microbes & infections Result SARS_CoV_2 D178H;V70L 48;41 53;45 S 46 47 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Overall the percentage of isolates that carried the M:V70L mutation had been relatively stable in the US and globally with a gradual month to month increase (Table 1). 2021 Emerging microbes & infections Result SARS_CoV_2 V70L 54 58 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Overall, 98.93% of the S:D178H carrying viral isolates belonged to this new B.1.1.7 sub-lineage. 2021 Emerging microbes & infections Result SARS_CoV_2 D178H 25 30 S 23 24 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Signature mutations of the B.1.1.7-M:V70L-S:D178H sub-lineage. 2021 Emerging microbes & infections Result SARS_CoV_2 D178H;V70L 44;37 49;41 S 42 43 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. The B.1.1.7-M:V70L-S:D178H sub-lineage was exclusive to the U.S. 2021 Emerging microbes & infections Result SARS_CoV_2 D178H;V70L 21;14 26;18 S 19 20 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. The D178H branch divergence date was estimated to be 23 January 2021, with a date confidence interval of 17 January 2021 to February 3, 2021. 2021 Emerging microbes & infections Result SARS_CoV_2 D178H 4 9 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. The S:D178H mutation was also seen in other lineages including B.1.234 and B.1. 2021 Emerging microbes & infections Result SARS_CoV_2 D178H 6 11 S 4 5 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. To understand the origin and evolution of this B.1.1.7-M:V70L-S:D178H sub-lineage, we used (a) all 1125 S:D178H carrying viral sequences reported across the globe, (b) 1600 subsampled M:V70L carrying viral sequences across the world, and (c) the NC_045512 reference genome. 2021 Emerging microbes & infections Result SARS_CoV_2 D178H;D178H;V70L;V70L 64;106;57;186 69;111;61;190 S;S 62;104 63;105 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Using these results we were able to show that the S:D178H mutation is close structurally to two signature deletions of B.1.1.7, HV69_70del and Y144del (Figure 4). 2021 Emerging microbes & infections Result SARS_CoV_2 Y144del;D178H 143;52 150;57 S 50 51 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. We focused initially on the M mutations that we previously identified, including V70L, that was spiking near the end of 2020. 2021 Emerging microbes & infections Result SARS_CoV_2 V70L 81 85 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. We identified the acquisition of another S mutation, D178H, in this B.1.1.7 sub-lineage (Figure 1 and Table 2), which was estimated to have occurred on 23 January 2021. 2021 Emerging microbes & infections Result SARS_CoV_2 D178H 53 58 S 41 42 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. When we examined the prevalence of S:D178H in the context of the B.1.1.7 lineage and the B.1.1.7-M:V70L sub-lineage, the numbers were even more striking (Figure 2). 2021 Emerging microbes & infections Result SARS_CoV_2 D178H;V70L 37;99 42;103 S 35 36 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. While the percentage of all B.1.1.7 isolates that carried the S:178H mutation increased from 0% (0/1365) in January 2021 to 0.15% (18/6859) in February 2021, to 1.11% (402/36034) in March 2021, and to 1.8% (469/25837) in April 2021, there was a significant increase from 0% (0/150) to 3.48% (10/287) to 41.8% (399/953) and 64.8% (464/716) in B.1.1.7-M:V70L sub-lineage isolates that carried the S:D178H mutation observed in the same 4-month time period. 2021 Emerging microbes & infections Result SARS_CoV_2 D178H;V70L 397;352 402;356 S;S 62;395 63;396 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. While the percentage of B.1.1.7 isolates with the V70L mutation remained relatively stable across the world, the percentage fluctuated significantly in the US, attributable largely to the initial small number of B.1.1.7 cases in the U.S. 2021 Emerging microbes & infections Result SARS_CoV_2 V70L 50 54 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Within this sub-lineage, the most common signature mutations were the same as B.1.1.7 signature mutations, with the additional M:V70L and S:D178H mutations. 2021 Emerging microbes & infections Result SARS_CoV_2 D178H;V70L 140;129 145;133 S 138 139 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. 5): mutation S98F is located next to amino acid 69, which is deleted in variant B.1.1.7; substitution D574Y maps next to amino acid 570, which changes from alanine (A) to aspartic acid (D) in B.1.1.7 viruses; and mutations T478A, F490S, and S494P locate in the RBD, near amino acid 501, which changes from asparagine (N) to tyrosine (Y) in B.1.1.7. 2021 mSystems Result SARS_CoV_2 D574Y;F490S;S494P;S98F;T478A 102;230;241;13;223 107;235;246;17;228 RBD 261 264 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. Most of these mutations have been found in clinical isolates from England, some of them in relatively large numbers, such as S98F and S494P (Table 3). 2021 mSystems Result SARS_CoV_2 S494P;S98F 134;125 139;129 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. nPCR product B contains codon GAT at nucleotide position 28280, which changes to CTA in B.1.1.7 lineage viruses, resulting in the amino acid substitution aspartic acid to leucine at residue 3 of the nucleocapsid (N) protein. 2021 mSystems Result SARS_CoV_2 D3L 154 191 N;N 199;213 211;214 34129831 Antibody Responses After mRNA-Based COVID-19 Vaccination in Residential Older Adults: Implications for Reopening. SARS-CoV-2 pseudovirus NT50 levels ranged from 2 to 8218 (mdn = 135) against the D614 G and B.1.1.7 variants and were strongly correlated (P < .001) with Beckman Coulter antibody levels (D614 G NT50, rs = 0.91; B.1.1.7 [UK] NT50, rs = 0.91) (Figure 2 ). 2021 Journal of the American Medical Directors Association Result SARS_CoV_2 D614G;D614G 81;187 87;193 34134034 Rapid and simultaneous identification of three mutations by the Novaplex SARS-CoV-2 variants I assay kit. Among them, four samples collected between February and March were determined to be variants; two (cases 1 and 2) were positive for both H69/V70 deletion and N501Y substitution mutations (UK variant), while the other two (cases 3 and 4) were positive for E484K substitution mutation alone (Table 1 ). 2021 Journal of clinical virology Result SARS_CoV_2 E484K;N501Y 255;158 260;163 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. Based on the partial sequencing of spike gene of SGTF samples, 93.5% (n = 29/31) showed the characteristic N501Y, A570D, P681H, and T716I mutations found in the B.1.1.7 variant. 2021 Frontiers in public health Result SARS_CoV_2 A570D;N501Y;P681H;T716I 114;107;121;132 119;112;126;137 S 35 40 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. Sample NIH-4474AE had unique mutations (K444R and V445L) and NIH-5818BB showed a novel mutation H655P in the S protein (Table 1). 2021 Frontiers in public health Result SARS_CoV_2 H655P;V445L;K444R 96;50;40 101;55;45 S 109 110 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. The age of patients infected with the N501Y variant ranged from 12 to 90 years with a median age of 32.5 years. 2021 Frontiers in public health Result SARS_CoV_2 N501Y 38 43 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. The distribution of N501Y positive cases according to a geographic area is shown in Figure 2B. 2021 Frontiers in public health Result SARS_CoV_2 N501Y 20 25 34138474 High-resolution melting curve FRET-PCR rapidly identifies SARS-CoV-2 mutations. Similarly, there was a marked difference in the T m of the control 2019-nCOV/USA-WA1/2020 with no C14408T mutation (54.3 C) and that of the T m obtained with the control 201/501Y.V1 that had the C14408T mutation (57.7 C). 2021 Journal of medical virology Result SARS_CoV_2 C14408T;C14408T 98;195 105;202 34138474 High-resolution melting curve FRET-PCR rapidly identifies SARS-CoV-2 mutations. The control 2019-nCOV/USA-WA1/2020 without the A23403G mutation had a T m of 63.1 C in the RT FRET-PCRs for the A23403G mutation (Figure 1). 2021 Journal of medical virology Result SARS_CoV_2 A23403G;A23403G 47;112 54;119 34138474 High-resolution melting curve FRET-PCR rapidly identifies SARS-CoV-2 mutations. This T m of 63.1 C was clearly distinguished from the T m of 58.2 C obtained with the control 201/501Y.V1 that had the A23403G mutation. 2021 Journal of medical virology Result SARS_CoV_2 A23403G 119 126 34140350 Characterization of a new SARS-CoV-2 variant that emerged in Brazil. Deep sequencing analysis of these virus stocks revealed that TY7-501 contained one addition mutation (G181V) at amino acid position 181 of the S protein (SI Appendix, Table S1). 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 G181V 102 107 S 143 144 34140350 Characterization of a new SARS-CoV-2 variant that emerged in Brazil. However, studies have shown that the N501Y mutation in the RBD renders mice susceptible to SARS-CoV-2 infection. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N501Y 37 42 RBD 59 62 COVID-19 91 111 34140350 Characterization of a new SARS-CoV-2 variant that emerged in Brazil. NCGM02 encodes aspartic acid (D) at amino acid position 614 of the S protein, whereas HP095 possesses a nonsynonymous mutation that encodes a D614G variant at this position. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G;D614D 142;14 147;60 S 67 68 34140350 Characterization of a new SARS-CoV-2 variant that emerged in Brazil. Previous studies have shown that the E484K substitution in the RBD of the SARS-CoV-2 S protein confers resistance to monoclonal and polyclonal neutralizing antibodies in COVID-19 convalescent and postvaccination sera, suggesting that P.1 variants with this mutation may be antigenically different from contemporary SARS-CoV-2. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 E484K 37 42 RBD;S 63;85 66;86 COVID-19 170 178 34140350 Characterization of a new SARS-CoV-2 variant that emerged in Brazil. Taken together, these observations suggest that mutations in the RBD of TY7-501, such as E484K and N501Y, may alter the binding affinity or specificity of the S protein for mouse cell surface molecules (including ACE2), thereby allowing the variant to replicate efficiently in mice. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 E484K;N501Y 89;99 94;104 RBD;S 65;159 68;160 34140350 Characterization of a new SARS-CoV-2 variant that emerged in Brazil. The G181V substitution, which is located in the N-terminal domain of the S protein, probably does not have a pivotal role in antigenic change, since amino acid substitutions at position 181 have never conferred resistance to neutralizing human monoclonal antibodies. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 G181V 4 9 N;S 48;73 49;74 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. 3s, inhibition in the surrogate virus neutralization assay modified to assess competition by the ACE2 Triple Decoy for ACE2 (WT) binding to S RBD was similar for S RBD WT, E484K, N501Y, L452R, and K417N/E484K/N501Y. 2021 Scientific reports Result SARS_CoV_2 E484K;K417N;L452R;N501Y;E484K;N501Y 172;197;186;179;203;209 177;202;191;184;208;214 RBD;RBD;S;S 142;164;140;162 145;167;141;163 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. All but the construct expressing L452R/K417N showed higher affinity for ACE(WT) (Table S7 in the "Supplementary Information S1"), which aligns with what might be predicted from the results in Table S5:K417N decreases affinity and N501Y increases affinity. 2021 Scientific reports Result SARS_CoV_2 L452R;N501Y;K417N;K417N 33;230;39;201 38;235;44;206 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. As compared to the ACE2 Triple Decoy binding affinity for S RBD WT, affinities for S RBD E484K/N501Y, N501Y alone and L452R were higher; affinities for S RBD E484K, K417N/N501Y, N417N/E484K/N501Y, K417K/E484K, and K417N were lower. 2021 Scientific reports Result SARS_CoV_2 E484K;E484K;K417K;K417N;K417N;L452R;N417N;N501Y;E484K;E484K;N501Y;N501Y;N501Y 89;158;197;165;214;118;178;102;184;203;95;171;190 94;163;202;170;219;123;183;107;189;208;100;176;195 RBD;RBD;RBD;S;S;S 60;85;154;58;83;152 63;88;157;59;84;153 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. E484K alone did not affect binding affinity to ACE2. 2021 Scientific reports Result SARS_CoV_2 E484K 0 5 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. Findings were similar with the wild type ACE2 decoy, with the highest affinity seen for E484K/N501Y and N501Y alone, and the lowest affinities for variants expressing K417N. 2021 Scientific reports Result SARS_CoV_2 E484K;K417N;N501Y;N501Y 88;167;104;94 93;172;109;99 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. For these simulations, the B.1.351 variant comprising the E484K, K417N, and N501Y mutations was used because these mutations occur together naturally and thus this combination has high physiological relevance. 2021 Scientific reports Result SARS_CoV_2 E484K;K417N;N501Y 58;65;76 63;70;81 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. Given the rapidly evolving landscape of variants and the risk of recombination events, to extend our analysis to 'theoretical' variants, in this instance combination of L452R with other mutations, we produced and tested S RBD L452R/K417N, L452R/E484K, L452R/N501Y, and L452R/K417N/E484K/N501Y. 2021 Scientific reports Result SARS_CoV_2 L452R;L452R;L452R;L452R;L452R;E484K;E484K;K417N;K417N;N501Y;N501Y 269;169;226;239;252;245;281;232;275;258;287 274;174;231;244;257;250;286;237;280;263;292 RBD;S 222;220 225;221 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. Interestingly, affinity in combination appears to be additive, with the KD being 8.77 for E484K alone (as compared to 9.33 for RBD WT) and 5.58 for L452R alone; together the KD for binding to ACE2 (WT) is 4.10. 2021 Scientific reports Result SARS_CoV_2 E484K;L452R 90;148 95;153 RBD 127 130 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. K417N weakened binding affinity for ACE2(WT) and the Triple Decoy, but affinity was restored when combined with N501Y. 2021 Scientific reports Result SARS_CoV_2 N501Y;K417N 112;0 117;5 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. N501Y and L452R showed ~ 2-3-fold increase in binding affinity for both wild type ACE2 decoy and ACE2 Triple Decoy. 2021 Scientific reports Result SARS_CoV_2 L452R;N501Y 10;0 15;5 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. The ACE2 Triple Decoy shows enhanced binding to S RBD N501Y and L452R variants, with the highest affinity for S RBD with both N501Y and E484K. 2021 Scientific reports Result SARS_CoV_2 E484K;L452R;N501Y;N501Y 136;64;54;126 141;69;59;131 RBD;RBD;S;S 50;112;48;110 53;115;49;111 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. The BLI analysis of both the ACE2(WT)-IgG1FC and the ACE2 Triple Decoy to S RBD WT or a S RBD with a series of mutations found in the B.1.351 (E484K/K417N/N501Y), B.1.1.7 (N501Y), and B.1.427/B.1.429 (L452R) variants is shown in. 2021 Scientific reports Result SARS_CoV_2 E484K;L452R;N501Y;K417N;N501Y 143;201;172;149;155 148;206;177;154;160 RBD;RBD;S;S 76;90;74;88 79;93;75;89 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. The E484K, K417N and N501Y mutations occur together in the B.1.351 strain, whereas L452R alone is found in B.1.427/B.1.429, therefore assessment of ACE2 WT binding to these variants as they occur in nature may be considered the most physiologically relevant. 2021 Scientific reports Result SARS_CoV_2 E484K;K417N;L452R;N501Y 4;11;83;21 9;16;88;26 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. The percent inhibition with the ACE2 Triple Decoy and S RBD K417N was significantly lower than the other mutants, but still very high. 2021 Scientific reports Result SARS_CoV_2 K417N 60 65 RBD;S 56;54 59;55 34141447 Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2. C3037U, C8782U, G16647U, C18060U, G23401A, and U28144C, are found differentially occurred in the two clusters. 2021 Virus evolution Result SARS_CoV_2 G23401A 34 41 34141447 Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2. Curiously, deletion of the RGTSPA sequence in N protein is exclusively found in Cluster B (Table 2), and the R203K-G204R variations are highly constrained in Cluster B (Table 2) and E (Supplementary Table S3). 2021 Virus evolution Result SARS_CoV_2 R203K;G204R 109;115 114;120 N 46 47 34141447 Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2. Likewise, the D614G variation in S proteins is highly constraint in cluster B, which has been recently suggested to increase infectivity of SARS-CoV-2. 2021 Virus evolution Result SARS_CoV_2 D614G 14 19 S 33 34 34141447 Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2. Several non-synonymous variations are found differential between cluster A and B, for example, C14408U, A23403G, and G28881A-G28882A-G28883C resulting in Nsp12 P323L, S protein D614G, and N protein R203K-G204R, were found differ, respectively (Table 2). 2021 Virus evolution Result SARS_CoV_2 A23403G;D614G;G28881A;P323L;R203K;G204R;G28882A;G28883C 104;177;117;160;198;204;125;133 111;182;124;165;203;209;132;140 Nsp12;N;S 154;188;167 159;189;168 34141447 Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2. The R203K-G204R variations are located in the Ser/Arg (S/R)-rich region in N protein, which is part of the disordered central linker region (CLR) in between the N-terminal RNA binding domain and the C-terminal dimerization domain. 2021 Virus evolution Result SARS_CoV_2 R203K;G204R 4;10 9;15 N;N 75;161 76;162 34141447 Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2. Thus, why variant SL5b is highly concurrent with S-protein D614G mutations and whether such concurrency contributes to the infectivity should be studied further in the future. 2021 Virus evolution Result SARS_CoV_2 D614G 59 64 S 49 50 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. 3 of the clades are due to the high recurrent mutations [Nsp6:L37F (Clade 1), Spike:D614G (Clade 3) and Nsp12:P323L (Clade 4)] and one of the clade is due to the moderately recurring mutation [ORF8:L84S (Clade 2)]. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;L37F;L84S;P323L 84;62;198;110 89;66;202;115 S;Nsp12;Nsp6;ORF8 78;104;57;193 83;109;61;197 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. 3).V13L of ORF3a is a moderately recurring mutation (PF = 2.6%) with England holding the top position followed by Wales and Scotland. 2021 Infection, genetics and evolution Result SARS_CoV_2 V13L 3 7 ORF3a 11 16 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Additionally, H93Y and G196V in ORF3a (PF = 0.76%) are found to be low recurring mutations (Table S2). 2021 Infection, genetics and evolution Result SARS_CoV_2 G196V;H93Y 23;14 28;18 ORF3a 32 37 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Additionally, S24L (PF = 2.2%) and V62L (PF = 1.2%) are the moderately recurring mutations in ORF8. 2021 Infection, genetics and evolution Result SARS_CoV_2 S24L;V62L 14;35 18;39 ORF8 94 98 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Although the catalytic site and N-terminal finger of Nsp5 are conserved, G15S located in the chymotrypsin-like domain is recurring at a moderate PF of 1.6%. 2021 Infection, genetics and evolution Result SARS_CoV_2 G15S 73 77 Nsp5;N 53;32 57;33 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Among the moderately recurring mutations, following mutations are found in the hospitalized patients in the following order of frequency: ORF8:L84S > ORF3a:G251V > ORF8:S24L > N protein: S197L > Nsp4:F308Y. 2021 Infection, genetics and evolution Result SARS_CoV_2 S197L;F308Y;G251V;L84S;S24L 187;200;156;143;169 192;205;161;147;173 ORF3a;Nsp4;ORF8;ORF8 150;195;138;164 155;199;142;168 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Among these, S193I, S194L and S197L recur with the percentage frequency in the range of 1 to 1.6% (moderate recurrence). 2021 Infection, genetics and evolution Result SARS_CoV_2 S193I;S194L;S197L 13;20;30 18;25;35 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Apart from these, P13L (N-terminal disordered region, the highest in Australia) (PF = 1.03%) and D103Y (PF = 1.05%) also occur at a moderate percentage frequency. 2021 Infection, genetics and evolution Result SARS_CoV_2 D103Y;P13L 97;18 102;22 N 24 25 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. F233L (~1.26%) and A320V of Nsp14 (~1.26%) are moderately recurring mutation. 2021 Infection, genetics and evolution Result SARS_CoV_2 A320V;F233L 19;0 24;5 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Followed by these, ORF3a:Q57H is found in the hospitalized patients. 2021 Infection, genetics and evolution Result SARS_CoV_2 Q57H 25 29 ORF3a 19 24 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. For instance, additional mutations in Spike:D614G (Clade 3a) have led to: Clade 3b (Nsp12:P323L), Clade 3c (Nsp12:P323L and ORF3a:Q57H), Clade 3d (Nsp12:P323L, ORF3a:Q57H & Nsp2:T85I) and Clade 3e (Nsp12:P323L & N protein:R203K & G204R). 2021 Infection, genetics and evolution Result SARS_CoV_2 G204R;D614G;P323L;P323L;P323L;P323L;Q57H;Q57H;R203K;T85I 230;44;90;114;153;204;130;166;222;178 235;49;95;119;158;209;134;170;227;182 S;ORF3a;ORF3a;Nsp12;Nsp12;Nsp12;Nsp12;Nsp2;N 38;124;160;84;108;147;198;173;212 43;129;165;89;113;152;203;177;213 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Further, 4 major sub-clades of Clade 3 (Spike:D614G) have also emerged during the pre-lockdown. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 46 51 S 40 45 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Further, P323L in Nsp12 that is located in the proximity of the Nsp8-Nsp12 binding site. 2021 Infection, genetics and evolution Result SARS_CoV_2 P323L 9 14 Nsp12;Nsp12;Nsp8 18;69;64 23;74;68 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. G251V of ORF3a protein is the moderately recurring mutation with the second highest percentage frequency (~9%) among the moderately recurring mutations and is highly occurring in England (PF = 5.18%). 2021 Infection, genetics and evolution Result SARS_CoV_2 G251V 0 5 ORF3a 9 14 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. In addition to above, Q57H in ORF3a is found to be the highly recurring mutation with the percentage frequency of 24.43% in 51 countries. 2021 Infection, genetics and evolution Result SARS_CoV_2 Q57H 22 26 ORF3a 30 35 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. In M protein, T175M is a moderately recurring mutation with the percentage frequency of ~1.6%. 2021 Infection, genetics and evolution Result SARS_CoV_2 T175M 14 19 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. In Nsp13, the exchange between the aliphatic A18 and V18 (PF = 1.1%), P504L (PF = 5.6%) and Y541C (PF = 5.8%) are found with the moderate recurrence. 2021 Infection, genetics and evolution Result SARS_CoV_2 P504L;Y541C 70;92 75;97 Nsp13 3 8 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. In Nsp2, T85I mutation recurs at the percentage frequency of 20.43% in 47 countries. 2021 Infection, genetics and evolution Result SARS_CoV_2 T85I 9 13 Nsp2 3 7 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. In spike protein, D614G (present in the S1 subunit flanked by the receptor binding site). 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 18 23 S 3 8 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Indeed, certain countries have percentage frequency more than 1.5% for these mutations: S193I (the highest in Wales followed by England), S194I (the highest in Scotland followed by England, India and Wales) and S197L (the highest Australia followed by Scotland, England and Spain). 2021 Infection, genetics and evolution Result SARS_CoV_2 S193I;S194I;S197L 88;138;211 93;143;216 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. L84S in ORF8 is the moderately recurring mutation with the upmost percentage frequency (~9.8%) among the moderately recurring mutations and is highly recurring in USA (PF = 5.93%). 2021 Infection, genetics and evolution Result SARS_CoV_2 L84S 0 4 ORF8 8 12 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. N protein co-mutations (dependent), R203K and G204R are also found to occur with a high percentage frequency (~23.6%). 2021 Infection, genetics and evolution Result SARS_CoV_2 G204R;R203K 46;36 51;41 N 0 1 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Next, A97V of Nsp12 is a moderately recurring mutation (1.2%). 2021 Infection, genetics and evolution Result SARS_CoV_2 A97V 6 10 Nsp12 14 19 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Not surprisingly, the available patient condition data for 1040 sequences (as on May 17, 2020) indicates that Spike:D614G and Nsp12:P323L are dominantly found in the hospitalized patients due to their surge after January 2020. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;P323L 116;132 121;137 S;Nsp12 110;126 115;131 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Notably, 11 recurring mutations (including R203K and G204R co-mutations) occur in the S180-R209 stretch of SR rich linker region, for which, the structural information is unknown. 2021 Infection, genetics and evolution Result SARS_CoV_2 G204R;R203K 53;43 58;48 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Nsp3 mutations that are found with a moderate percentage frequency are: A58T which is present in the UBL1 domain of Nsp3 is the moderately recurring mutation with the percentage frequency of 1.8%, P153L (occurs at the percentage frequency in the range of 0.7% and 0.26% respectively in USA and Australia) and T428I (England possesses the highest PF of 0.86%). 2021 Infection, genetics and evolution Result SARS_CoV_2 A58T;P153L;T428I 72;197;309 76;202;314 Nsp3;Nsp3 0;116 4;120 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. S25L is the only recurring mutation in Nsp7. 2021 Infection, genetics and evolution Result SARS_CoV_2 S25L 0 4 Nsp7 39 43 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. S25L of Nsp7 occurs at a moderate percentage frequency of 1.33%. 2021 Infection, genetics and evolution Result SARS_CoV_2 S25L 0 4 Nsp7 8 12 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Similarly, L37F in Nsp6 has a percentage frequency > 11.98%. 2021 Infection, genetics and evolution Result SARS_CoV_2 L37F 11 15 Nsp6 19 23 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Similarly, P585S (~4.1%), I559V (~3.8%), deletion of D268 (~2.87%) and G212D (~2.64%) in Nsp2 are found at a moderate percentage frequency. 2021 Infection, genetics and evolution Result SARS_CoV_2 G212D;I559V;P585S 71;26;11 76;31;16 Nsp2 89 93 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Simultaneous occurrence of Nsp6:L37F and ORF3a:G251V has led to Clade 1b. 2021 Infection, genetics and evolution Result SARS_CoV_2 G251V;L37F 47;32 52;36 ORF3a;Nsp6 41;27 46;31 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Some notable substitutions, co-occurring mutations, deletions and insertions which occur with a low to moderate recurrence and may have a significant influence on the viral pathogenic mechanism are: co-deletion (dependent) of K141, S142 and F143, co-deletion (dependent) of G82 and H83, D75E, co-occurring (dependent) S135N, Y136 deletion and M85 deletion in Nsp1, D268 deletion, G212D, co-occurring (dependent) I559V and P585S, F10L, V198I, P91S, T166I, H237R, T371I, S211F and G339S in Nsp2, A58T, P153L and T428I in Nsp3, F308Y, T295I (0.3%) and M33I in Nsp4, G15S and K90R in Nsp5, S25L and S26F in Nsp7, A97V and A449V in Nsp12, A18V and co-mutation P504L & Y541C in Nsp13, F233L and A320V in Nsp14, V13L in ORF3a, S24L and A62L in ORF8, D936Y in spike and P13L, D103Y, S193I, S194L and S197L with a percentage frequency above 1% in nucleoprotein. 2021 Infection, genetics and evolution Result SARS_CoV_2 A18V;A320V;A449V;A58T;A62L;A97V;D103Y;D75E;D936Y;F10L;F233L;F308Y;G15S;G212D;G339S;H237R;I559V;K90R;M33I;P13L;P153L;P504L;P585S;P91S;S135N;S193I;S194L;S197L;S211F;S24L;S25L;S26F;T166I;T295I;T371I;T428I;V13L;V198I;Y541C 634;689;618;494;729;609;768;287;743;429;679;525;563;380;479;455;412;572;549;762;500;655;422;442;318;775;782;792;469;720;586;595;448;532;462;510;705;435;663 638;694;623;498;733;613;773;291;748;433;684;530;567;385;484;460;417;576;553;766;505;660;427;446;323;780;787;797;474;724;590;599;453;537;467;515;709;440;668 S;ORF3a;Nsp13;Nsp12;Nsp2;Nsp3;Nsp4;Nsp7;Nsp5;ORF8 752;713;672;627;488;519;557;603;580;737 757;718;677;632;492;523;561;607;584;741 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Spike:D614G and Nsp12:P323L mutations are highly found in the hospitalized patients. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;P323L 6;22 11;27 S;Nsp12 0;16 5;21 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. The Clade 5 (that lacks high recurrent mutations) followed by Clade 2 (which are deficient of Spike:D614G mutation) are found to be prevalent in China which is the epicenter of the pandemic. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 100 105 S 94 99 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Thus, Nsp2:T85I, Nsp6:L37F, Nsp12:P323L, Spike:D614G, ORF3a:Q57H, N protein:R203K and G204R have occurred at a high recurrence during the early stage of the pandemic. 2021 Infection, genetics and evolution Result SARS_CoV_2 G204R;D614G;L37F;P323L;Q57H;R203K;T85I 86;47;22;34;60;76;11 91;52;26;39;64;81;15 S;ORF3a;Nsp12;Nsp2;Nsp6;N 41;54;28;6;17;66 46;59;33;10;21;67 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. whereas, S188L and S190I occur with the percentage frequency of 0.45% and 0.23% respectively (TableSD27.xlsx). 2021 Infection, genetics and evolution Result SARS_CoV_2 S188L;S190I 9;19 14;24 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. Among them, the binding energy of H:R106 increases most significantly in H:V106 R/H:P107Y double mutant. 2021 Computers in biology and medicine Result SARS_CoV_2 P107Y;V106H;V106R 84;75;75 89;83;83 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. Among them, the mutation energies of H:V106R/H:P107Y and H:V104Y/H:V106W are higher than others, with the values < -3.0 kcal/mol. 2021 Computers in biology and medicine Result SARS_CoV_2 P107Y;V104H;V104Y;V106H;V106R;V106W 47;59;59;39;39;67 52;66;66;46;46;72 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. Comparatively, the mutation energies of E484K, E484K/N501Y and K417N/E484K/N501Y binding with H:V106R/H:P107Y are smaller than WT P2B-2F6. 2021 Computers in biology and medicine Result SARS_CoV_2 E484K;E484K;K417N;E484K;N501Y;N501Y;P107Y;V106R;V106H 40;47;63;69;53;75;104;96;96 45;52;68;74;58;80;109;103;103 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. For the H:V106R/H:P107Y double mutant, the phenolic hydroxyl group of H:Y107 donates a hydrogen bond to the amide oxygen of T470 on RBD with a high occupancy of 88.12% (Table 1). 2021 Computers in biology and medicine Result SARS_CoV_2 P107Y;V106R;V106H 18;10;10 23;17;17 RBD 132 135 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. From computational scanning mutageneses and MD simulations, we found the single mutation H:V106R and the double mutations H:V106R/H:P107Y of P2B-2F6 resulted in higher binding affinities with the RBD domain of SARS-CoV-2 than others. 2021 Computers in biology and medicine Result SARS_CoV_2 P107Y;V106R;V106R;V106H 132;91;124;124 137;96;131;131 RBD 196 199 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. However, the E484K spike protein mutation decreased its binding affinity with both the WT and optimized P2B-2F6 antibodies. 2021 Computers in biology and medicine Result SARS_CoV_2 E484K 13 18 S 19 24 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. It is found that the MM/GBSA binding free energies of H:V106R, H:V104Y, and L:G31L mutants of P2B-2F6 with RBD are strengthened by 11.07, 6.40, and 1.84 kcal/mol, respectively, relative to that of WT P2B-2F6. 2021 Computers in biology and medicine Result SARS_CoV_2 G31L;V104Y;V106R 78;65;56 82;70;61 RBD 107 110 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. L:G31F and L:G31L mutations caused large fluctuations near the mutation site. 2021 Computers in biology and medicine Result SARS_CoV_2 G31F;G31L 2;13 6;17 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. Mutations of H:V106R and H:V106R/H:P107Y produce an obvious impact on the hydrogen-bonding network formed by the antibody and RBD of SARS-CoV-2. 2021 Computers in biology and medicine Result SARS_CoV_2 P107Y;V106R;V106H;V106R 35;15;27;27 40;20;34;34 RBD 126 129 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. N501Y mutation has been reported to accelerate the spread of SARS-CoV-2 recently. 2021 Computers in biology and medicine Result SARS_CoV_2 N501Y 0 5 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. On the other hand, the optimized antibodies of H:V106R and H:V106R/H:P107Y have increased binding affinities with most single spike protein mutants including the highest frequency mutant of N501Y. 2021 Computers in biology and medicine Result SARS_CoV_2 N501Y;P107Y;V106R;V106H;V106R 190;69;49;61;61 195;74;54;68;68 S 126 131 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. Some SARS-CoV-2 variants possess combination mutations such as E484K/N501Y and K417N/E484K/N501Y. 2021 Computers in biology and medicine Result SARS_CoV_2 E484K;K417N;E484K;N501Y;N501Y 63;79;85;69;91 68;84;90;74;96 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. The calculated mutation energy of N501Y of RBD binding with P2B-2F6 is 0.01 kcal/mol, confirming that N501Y mutation does not affect their interaction. 2021 Computers in biology and medicine Result SARS_CoV_2 N501Y;N501Y 34;102 39;107 RBD 43 46 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. The free energy decomposition demonstrates that the enhanced binding ability of the mutant antibody to RBD is mainly induced by the increase of polar interactions (DeltaG ele + egb) for H:V106 R/H:P107Y and H:V104Y/H:V106R mutants, and van der Waals interactions for H:V104Y/H:V106W mutant. 2021 Computers in biology and medicine Result SARS_CoV_2 P107Y;V104H;V104H;V104Y;V104Y;V106H;V106R;V106R;V106W 197;209;269;209;269;188;188;217;277 202;216;276;216;276;196;196;222;282 RBD 103 106 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. The H:V106R mutation leads to additional hydrogen bonds formation between the side chains of H:R106 and E484 of RBD (Table 1). 2021 Computers in biology and medicine Result SARS_CoV_2 V106R 6 11 RBD 112 115 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. The increase of van der Waals interactions induced by H:V104Y and polar interactions (DeltaG ele + egb) induced by H:V106R are the main contributors to the enhanced binding of the mutated P2B-2F6 with RBD. 2021 Computers in biology and medicine Result SARS_CoV_2 V104Y;V106R 56;117 61;122 RBD 201 204 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. The MM/GBSA binding free energies of H:V106R/H:P107Y, H:V104Y/H:V106W, and H:V104Y/H:V106R mutants with RBD are 13.59, 4.80, and 4.59 kcal/mol, respectively, higher than WT P2B-2F6. 2021 Computers in biology and medicine Result SARS_CoV_2 P107Y;V104H;V104H;V104Y;V104Y;V106R;V106H;V106R;V106W 47;56;77;56;77;85;39;39;64 52;63;84;63;84;90;46;46;69 RBD 104 107 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. The mutation energies of H:V104Y and H:V106R were greater than -1.5 kcal/mol, while those of H:S31F, H:S31E, H:V104W, H:V104F, H:V105W, H:V106F and H:V106Y were greater than -1.0 kcal/mol, indicating that these mutations might strengthen the binding of the antibody with RBD domain of SARS-CoV-2. 2021 Computers in biology and medicine Result SARS_CoV_2 S31E;S31F;V104F;V104W;V104Y;V105W;V106F;V106R;V106Y 103;95;120;111;27;129;138;39;150 107;99;125;116;32;134;143;44;155 RBD 271 274 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. The paratope consists 12 heavy chain residues (Y27, S28, S30, S31, and Y33 of HCDR1 [IMGT number: Y28, S29, S31, S35, Y37]; H54 of HCDR2 [IMGT number: H58]; I103-P107 and R112 of HCDR3 [IMGT number: I111, V111A, V111B, V111C, P112D, and R113]) and 4 light chain residues (G31-Y34 of LCDR1 [IMGT number: G35-Y38]) interacting with R346, K444-L452 and V483-S494 of RBD. 2021 Computers in biology and medicine Result SARS_CoV_2 P112D;V111A;V111C 226;205;219 231;210;224 RBD 363 366 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. The results indicate that H:V106R mutation of P2B-2F6 might reduce aggregation but H:V106R/H:P107Y double mutations might increase aggregation. 2021 Computers in biology and medicine Result SARS_CoV_2 P107Y;V106R;V106H;V106R 93;28;85;85 98;33;92;92 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. The results indicate the binding affinity of WT P2B-2F6 remains almost unchanged with most single spike protein mutants except for E484K and L452R. 2021 Computers in biology and medicine Result SARS_CoV_2 E484K;L452R 131;141 136;146 S 98 103 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. The Zeta values of H:V106R and H:V106R/H:P107Y mutants are greater than WT P2B-2F6, suggesting that the optimized antibodies are more stable than WT P2B-2F6. 2021 Computers in biology and medicine Result SARS_CoV_2 P107Y;V106R;V106R;V106H 41;21;33;33 46;26;40;40 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. Thereby, H:V106R/H:P107Y, H:V104Y/H:V106W, and H:V104Y/H:V106R (considering the mutation effect of H:V104Y and H:V106R. 2021 Computers in biology and medicine Result SARS_CoV_2 P107Y;V104Y;V104H;V104H;V104Y;V104Y;V106R;V106R;V106H;V106R;V106W 19;101;28;49;28;49;57;113;11;11;36 24;106;35;56;35;56;62;118;18;18;41 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. Therefore, we predicted the aggregation propensity of WT P2B-2F6 and the optimized mutants of H:V106R and H:V106R/H:P107Y by identifying hydrophobic surface patches in the CDR regions. 2021 Computers in biology and medicine Result SARS_CoV_2 P107Y;V106R;V106H;V106R 116;96;108;108 121;101;115;115 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. This indicates that the N501Y variant of SARS-CoV-2 would not escape the immune effect of P2B-2F6. 2021 Computers in biology and medicine Result SARS_CoV_2 N501Y 24 29 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. = 0.0003%) and Y505W (freq. 2021 Frontiers in immunology Result SARS_CoV_2 Y505W 15 20 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. A second group of RBD variants, L452R (15%), G446V (10%), and N440Y (5%) disrupted fewer NAb interactions, while all NAbs bound efficiently (>50%, relative to WT reference) to RBD variants T345I, A475V, and Y505W. 2021 Frontiers in immunology Result SARS_CoV_2 A475V;G446V;L452R;N440Y;T345I;Y505W 196;45;32;62;189;207 201;50;37;67;194;212 RBD;RBD 18;176 21;179 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Additional conserved RBD contacts within the C2 NAb epitope suggests RBD variants G446V, L452R, and S494P can also impact C2 interactions. 2021 Frontiers in immunology Result SARS_CoV_2 G446V;L452R;S494P 82;89;100 87;94;105 RBD;RBD 21;69 24;72 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Based on the in silico NAb epitope analysis, nine RBD variants that localize to the C1 (K417T, A475V, N501Y, Y505W), C1D/C2 (G446V, L452R and E484K) and C3 epitopes (T345I, N440Y, and G446V) were produced for binding studies with the unknown NAbs. 2021 Frontiers in immunology Result SARS_CoV_2 A475V;E484K;G446V;L452R;N440Y;N501Y;Y505W;G446V;K417T;T345I 95;142;184;132;173;102;109;125;88;166 100;147;189;137;178;107;114;130;93;171 RBD 50 53 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Based on this definition, C1 RBD variants K417T (25%) and N501Y (25%), and C2 variant E484K (30%), most frequently disrupted NAb binding ( Figure 5 ). 2021 Frontiers in immunology Result SARS_CoV_2 E484K;K417T;N501Y 86;42;58 91;47;63 RBD 29 32 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Efficient binding of all NAbs to T345I (freq. 2021 Frontiers in immunology Result SARS_CoV_2 T345I 33 38 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Finally, there are several common contact residues in the C4 NAb epitope, suggesting that N370S, T376I, V382L, P384L, T385I, and R408I could disrupt C4 NAbs. 2021 Frontiers in immunology Result SARS_CoV_2 N370S;P384L;R408I;T376I;T385I;V382L 90;111;129;97;118;104 95;116;134;102;123;109 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Furthermore, for those NAbs exhibiting >50% reduction in binding levels, relative to WT RBD, E484K and N501Y exclusively disrupted NAbs classified as C2 and C1, respectively ( Figure 5C ). 2021 Frontiers in immunology Result SARS_CoV_2 E484K;N501Y 93;103 98;108 RBD 88 91 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. In contrast to the invariant residues, 9 ACE2 binding residues (K417, G446, L455, A475, G476, E484, F486, and N501) have undergone significant sequence variation ( Figure 2 ) with the largest frequencies occurring at four positions: N501Y (0.208%), E484K (0.079%), Y453F (0.062%), and F486L (0.059%). 2021 Frontiers in immunology Result SARS_CoV_2 E484K;F486L;N501Y;Y453F 249;285;233;265 254;290;238;270 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. In contrast, K417T, which disrupts a salt bridge with ACE2 ( Figure 2B ), exhibited two-fold lower binding affinity for ACE2, relative to WT RBD ( Figure 6B ). 2021 Frontiers in immunology Result SARS_CoV_2 K417T 13 18 RBD 141 144 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. T345I and N440Y also exhibited WT RBD-ACE2 binding affinity, while G446V and A475V exhibited disrupted ACE2 binding affinities, like K417T. 2021 Frontiers in immunology Result SARS_CoV_2 A475V;G446V;K417T;N440Y;T345I 77;67;133;10;0 82;72;138;15;5 RBD 34 37 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. The N501Y variant, which occurs at the highest frequency, is the only residue located within the RBD knob, while Y453F is located in the RBD base and E484K and F486L are localized in the tip ( Figure 2A ). 2021 Frontiers in immunology Result SARS_CoV_2 E484K;F486L;N501Y;Y453F 150;160;4;113 155;165;9;118 RBD;RBD 97;137 100;140 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. The two RBD variants that disrupted the largest number of NAb interactions (E484K, and N501Y) bound to ACE2 within 15% (e.g. 2021 Frontiers in immunology Result SARS_CoV_2 N501Y;E484K 87;76 92;81 RBD 8 11 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. This is consistent with many C2 NAbs being sensitive to the E484K variant [ andFigure 5 ]. 2021 Frontiers in immunology Result SARS_CoV_2 E484K 60 65 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Thus, C1 NAb epitopes are predicted to be sensitive to K417N/T, Y453F, L455F, A475V, F486L, and N501Y variants. 2021 Frontiers in immunology Result SARS_CoV_2 A475V;F486L;K417N;K417T;L455F;N501Y;Y453F 78;85;55;55;71;96;64 83;90;62;62;76;101;69 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Thus, L452R disrupts several NAbs, but also binds to ACE2 with higher affinity. 2021 Frontiers in immunology Result SARS_CoV_2 L452R 6 11 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Thus, RBD variants that could disrupt C1D NAbs include L455F, A475V, F486L, as well as E484K, and G485R. 2021 Frontiers in immunology Result SARS_CoV_2 A475V;E484K;F486L;G485R;L455F 62;87;69;98;55 67;92;74;103;60 RBD 6 9 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Thus, the L452R mutant, associated with a recently identified California VoC (B.1.427/B.1.429-California) has evolved to enhance ACE2 binding while simultaneously disrupting a significant number of NAbs in the C2 classification. 2021 Frontiers in immunology Result SARS_CoV_2 L452R 10 15 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Two RBD mutations (L452R and Y505W) exhibited higher affinity for ACE2 than WT RBD. 2021 Frontiers in immunology Result SARS_CoV_2 Y505W;L452R 29;19 34;24 RBD;RBD 4;79 7;82 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Y505W also enhances RBD-ACE2 interactions but was not disruptive to any of the NAbs tested ( Figure 5A ). 2021 Frontiers in immunology Result SARS_CoV_2 Y505W 0 5 RBD 20 23 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. DNA templates were amplified from pre-prepared pMA vectors harboring five mutational sites (A23403G, G25563T, G26144T, T28144C, and G28882A; Table 1), before proceeding to HRM analysis. 2021 Journal of infection and chemotherapy Result SARS_CoV_2 G25563T;G26144T;G28882A;T28144C;A23403G 101;110;132;119;92 108;117;139;126;99 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. Interestingly, the viral strains from Saudi Arabia, South Africa, USA, Russia and New Zealand have 3 genetic variations: P333L (RNA -dependant RNA polymerase), D614G (spike), and P4715L (ORF1ab). 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;P333L;P4715L 160;121;179 165;126;185 ORF1ab;S 187;167 193;172 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. The G251V variation was shared by both Italian and Sri Lankan strains (Table S1, Table S2). 2021 Computers in biology and medicine Result SARS_CoV_2 G251V 4 9 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. We have also noticed few other shared variations like R203K and G204R in nucleocapsid protein among the viral strains from Saudi Arabia and Russia, and the S166A variation in the viral strains from Saudi and India. 2021 Computers in biology and medicine Result SARS_CoV_2 G204R;R203K;S166A 64;54;156 69;59;161 N 73 85 34158771 Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study. Amino acid changes: Analysis showed that spike protein was a highly conserved protein, and only one high frequent mutation (D614G) was detected in comparison with the reference sequence. 2021 Ethiopian journal of health sciences Result SARS_CoV_2 D614G 124 129 S 41 46 34159336 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. Cryo-electron microscopy structures have been reported recently that reveal the structural consequences of this mutation and provide a plausible mechanistic explanation for the increased infectivity of D614G-carrying variants. 2021 bioRxiv Result SARS_CoV_2 D614G 202 207 34159336 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. It is natural to name the haplotype T478K-D614G-P681H-T732A as a B.1.1.222. 2021 bioRxiv Result SARS_CoV_2 T478K;D614G;P681H;T732A 36;42;48;54 41;47;53;59 34159336 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. N501Y has also been shown to reduce susceptibility to some nAbs, although the B.1.1.7 variant appears to remain susceptible to some extent to natural infection-acquired and vaccine-induced nAbs. 2021 bioRxiv Result SARS_CoV_2 N501Y 0 5 34159336 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. Of the five remaining VRVs in the W1 haplotype, A570, T716, and S982 seem relatively benign in that mutations at these positions are already decreasing in certain states/territories (this trend is also true to some extent for N501Y). 2021 bioRxiv Result SARS_CoV_2 N501Y 226 231 34159336 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. The D614G mutation observed in the W1 haplotype has been associated with increased infectivity/transmissibility. 2021 bioRxiv Result SARS_CoV_2 D614G 4 9 34159336 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. The L452R mutation is situated in the RBD; homology modelling of the RBD-ACE2 complex shows that while R452 does not directly contact ACE2, the guanidinium side chain of R452 is surface-exposed and thus could potentially impact nAb binding. 2021 bioRxiv Result SARS_CoV_2 L452R 4 9 RBD;RBD 38;69 41;72 34159336 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. The L452R mutation was recently shown to reduce binding affinity to some RBD-targeting monoclonal antibodies, as well as to reduce susceptibility to nAbs. 2021 bioRxiv Result SARS_CoV_2 L452R 4 9 RBD 73 76 34159336 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. The N501Y mutation (present in the B.1.1.7 variant) is located in the receptor-binding domain (RBD) and has been reported to enhance binding affinity to the angiotensin-converting enzyme-2. 2021 bioRxiv Result SARS_CoV_2 N501Y 4 9 RBD 95 98 34159336 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. The P681H mutation occurs in the S1/S2 cleavage segment of the Spike protein, which is typically not resolved in cryo-electron microscopy or x-ray diffraction experiments. 2021 bioRxiv Result SARS_CoV_2 P681H 4 9 S 63 68 34159336 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. The S13I and W152C mutations, which are situated in the N-terminal domain (NTD) of the Spike protein, have been implicated in escape from NTD-targeting monoclonal antibodies. 2021 bioRxiv Result SARS_CoV_2 S13I;W152C 4;13 8;18 S;N 87;56 92;57 34159336 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. The US variants also carry the D614G mutation. 2021 bioRxiv Result SARS_CoV_2 D614G 31 36 34159336 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. The VRV-haplotype S13I-W152C-L452R (ICR-3) appeared in Fall 2020 and is rapidly becoming dominant in states on the West Coast, as well as appearing in selected Southwestern and Southeastern states. 2021 bioRxiv Result SARS_CoV_2 S13I;L452R;W152C 18;29;23 22;34;28 34159336 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy. We are not aware of any reports that D1118H impacts transmissibility or morbidity, but the location of this mutation in the Spike protein trimer assembly. 2021 bioRxiv Result SARS_CoV_2 D1118H 37 43 S 124 129 34159627 Genome-wide association analysis of COVID-19 mortality risk in SARS-CoV-2 genomes identifies mutation in the SARS-CoV-2 spike protein that colocalizes with P.1 of the Brazilian strain. It is important to note that locus at 25,088 bp colocalizes with the P.1 variant that has become part of the CDC definition (precisely, substitution V1176F) of the Brazilian strain in April 2021 (UCSC Genome Browser on SARS-CoV-2, ). 2021 Genetic epidemiology Result SARS_CoV_2 V1176F 149 155 34160124 Preliminary Structural Data Revealed That the SARS-CoV-2 B.1.617 Variant's RBD Binds to ACE2 Receptor Stronger Than the Wild Type to Enhance the Infectivity. The RBD-specific mutations (L452R-E484 K) reported in India requires careful examination in the search for new therapeutic alternatives. 2021 Chembiochem Result SARS_CoV_2 L452R 28 33 RBD 4 7 34160124 Preliminary Structural Data Revealed That the SARS-CoV-2 B.1.617 Variant's RBD Binds to ACE2 Receptor Stronger Than the Wild Type to Enhance the Infectivity. This study was conducted to explore the binding differences of the spike RBD of the wild and B.1.617 variant (L452R-E484Q) with the host ACE2 by using combined structural modelling and biophysical approaches. 2021 Chembiochem Result SARS_CoV_2 L452R;E484Q 110;116 115;121 S;RBD 67;73 72;76 34160124 Preliminary Structural Data Revealed That the SARS-CoV-2 B.1.617 Variant's RBD Binds to ACE2 Receptor Stronger Than the Wild Type to Enhance the Infectivity. We concluded that L452R-E484Q mutations and other factors such as genetic variability in the other proteins might help the virus enforce infection and its severity. 2021 Chembiochem Result SARS_CoV_2 L452R;E484Q 18;24 23;29 34161337 SARS-CoV-2 uses major endothelial integrin alphavbeta3 to cause vascular dysregulation in-vitro during COVID-19. A point mutation at K403R introduces a widely recognised integrin recognition motif, Arginine-Glycine-Aspartic acid (RGD), into the spike protein. 2021 PloS one Result SARS_CoV_2 K403R 20 25 S 132 137 34162440 Deletion of ER-retention motif on SARS-CoV-2 spike protein reduces cell hybrid during cell-cell fusion. Further studies would have to look more into the expression level and trafficking of the S-Delta19 protein, as it compares to the original S-WT protein. 2021 Cell & bioscience Result SARS_CoV_2 Delta19 93 98 S;S 89;139 90;140 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. A lineage containing DeltaH69/V70 was first detected in the United Kingdom with the RBD mutation N501Y along with multiple other spike and other mutations (Figure 1; Figure S2). 2021 Cell reports Result SARS_CoV_2 N501Y 97 102 S;RBD 129;84 134;87 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. A second lineage with N439K, B.1.258, emerged later and subsequently acquired DeltaH69/V70, leading to the initial rapid increase in the frequency of viruses possessing this deletion, spreading into Europe (Figure 1A). 2021 Cell reports Result SARS_CoV_2 N439K 22 27 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. As expected, the VSV-G pseudotyped particles were not affected by addition of E64D or camostat. 2021 Cell reports Result SARS_CoV_2 E64D 78 82 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. D614G bearing Wuhan-1 spike-expressing DNA plasmid (WT) was co-transfected in HEK293T producer cells along with plasmids encoding a lentiviral capsid and genome for luciferase. 2021 Cell reports Result SARS_CoV_2 D614G 0 5 S 22 27 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. DeltaH69/V70 was first detected in the Y453F background on August 24, 2020 and so far appears to be limited to Danish sequences (Figures 1 and 5B), although an independent acquisition was recently reported along with DeltaH69/V70 in an immune-compromised Russian individual with chronic infection. 2021 Cell reports Result SARS_CoV_2 Y453F 39 44 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. For example, N439K, an amino acid replacement reported to define variants increasing in numbers in Europe and other regions (; Figures 1 and 5A) now mostly co-occurs with DeltaH69/V70. 2021 Cell reports Result SARS_CoV_2 N439K 13 18 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. In addition to RBD N501Y and NTD DeltaH69/V70, B.1.1.7 is defined by further S mutations across S2 (T716I, S982A, and D1118H) and S1 (DeltaY144, A570D, and P681H) (Figure 6A). 2021 Cell reports Result SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;DeltaY144;T716I 145;118;19;156;107;134;100 150;124;24;161;112;143;105 RBD;S 15;77 18;78 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. N439K appears to have reduced susceptibility to some convalescent sera as well as mAbs targeting the RBD while increasing affinity for ACE2 in vitro. 2021 Cell reports Result SARS_CoV_2 N439K 0 5 RBD 101 104 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. The available sequence data did not enable determination of whether the Alpha variant B.1.1.7 mutations N501Y and DeltaH69/V70 arose as a result of an N501Y virus acquiring DeltaH69/V70 or vice versa, although a United Kingdom Alpha variant B.1.1.7 sequence was identified with N501Y, A570D, DeltaH69/V70, and D1118H (Figure S2). 2021 Cell reports Result SARS_CoV_2 A570D;D1118H;N501Y;N501Y;N501Y 285;310;104;151;278 290;316;109;156;283 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. The earliest DeltaH69/V70 detected on a D614G background occurred in Sweden in April 2020. 2021 Cell reports Result SARS_CoV_2 D614G 40 45 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. The first lineage possessing N439K (and not DeltaH69/V70), B.1.141, is now extinct. 2021 Cell reports Result SARS_CoV_2 N439K 29 34 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. The second significant cluster with DeltaH69/V70 and RBD mutants involves Y453F, another spike RBD mutation that increases binding affinity to ACE2, and has been found to be associated with mink-human infection. 2021 Cell reports Result SARS_CoV_2 Y453F 74 79 S;RBD;RBD 89;53;95 94;56;98 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. To explore whether D614G was required for this enhanced spike cleavage and infectivity, we generated PVs bearing D614 spike with and without DeltaH69/V70, followed by infection of HEK293T cells. 2021 Cell reports Result SARS_CoV_2 D614G 19 24 S;S 56;118 61;123 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. To probe this, spike pseudotyped lentiviruses bearing WT spike, DeltaH69/V70 spike, or vesicular stomatitis virus G protein (VSV-G) were used to transduce HEK293T-ACE2 or HEK293T-ACE2/TMPRSS2 cells in the presence of E64D or camostat at different drug concentrations (Figure 4E). 2021 Cell reports Result SARS_CoV_2 E64D 217 221 S;S;S 15;57;77 20;62;82 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. We conclude that B.1.1.7 spike mediates faster fusion kinetics than the WT bearing D614G Wuhan-1 spike that is dependent on DeltaH69/V70. 2021 Cell reports Result SARS_CoV_2 D614G 83 88 S;S 25;97 30;102 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. We hypothesized that DeltaH69/V70 might have arisen after Y453F and N439K to compensate for potential loss of infectivity, which has been reported previously for these RBD mutants. 2021 Cell reports Result SARS_CoV_2 N439K;Y453F 68;58 73;63 RBD 168 171 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. We observed a similar 2-fold enhancement of infection and a proportional increase in spike incorporation as we did for D614G spike PVs (Figures S1A and S1B). 2021 Cell reports Result SARS_CoV_2 D614G 119 124 S;S 85;125 90;130 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. We therefore generated mutant spike plasmids bearing RBD mutations Y453F and N439K (Figure 5C) with and without DeltaH69/V70 and performed infectivity assays in the lentiviral pseudotyping system. 2021 Cell reports Result SARS_CoV_2 N439K;Y453F 77;67 82;72 S;RBD 30;53 35;56 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Y453F has also been described as an escape mutation for mAb REGN10933, shows reduced susceptibility to convalescent sera, and is possibly a T cell escape mutation. 2021 Cell reports Result SARS_CoV_2 Y453F 0 5 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. A similar trend was also seen for pseudoviruses carrying only the K417T mutant (Figure 3C; Figure S4). 2021 Immunity Result SARS_CoV_2 K417T 66 71 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. As shown in Figure 4 , the three variants B.1.1.7, B.1.351, and P.1 gained substantial ability to infect HeLa mouse ACE2, which correlated with pseudoviruses bearing single (K417N, K417T, E484K, and N501Y) and triple (K417N-E484K-N501Y) mutations. 2021 Immunity Result SARS_CoV_2 E484K;K417T;N501Y;K417N;K417N;E484K;N501Y 188;181;199;174;218;224;230 193;186;204;179;223;229;235 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Consistent with the findings for mAbs, the B.1.351 and P.1 pseudoviruses demonstrated more resistance than B.1.1.7 in absolute ID50 (Figures 3A and 3B) and fold changes (Figure 3C) relative to WT D614G. 2021 Immunity Result SARS_CoV_2 D614G 196 201 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Examination of the resistance patterns across the single- and triple-mutant pseudoviruses showed that the K417N and K417T mutations correlated with resistance to class I mAbs, whereas the E484K mutation correlated with resistance to class II mAbs (Figure 1C). 2021 Immunity Result SARS_CoV_2 E484K;K417N;K417T 188;106;116 193;111;121 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. For each plasma sample, eight serial dilutions were made, starting from 1:60 or 1:200, and neutralization activity was estimated based on half-maximal inhibitory dilution (ID50) and fold changes relative to that against the WT D614G pseudovirus (Figure 3 ; Figure S4). 2021 Immunity Result SARS_CoV_2 D614G 227 232 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Furthermore, two single-mutant pseudoviruses, Y453F and F486L, also substantially improved entry efficiency. 2021 Immunity Result SARS_CoV_2 F486L;Y453F 56;46 61;51 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. However, the E484K mutation resulted in complete loss of BD368-2 and P5A-1B9 neutralization (Figure 1C; Figure S1). 2021 Immunity Result SARS_CoV_2 E484K 13 18 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. In contrast, for pseudoviruses carrying only the K417N mutant, neutralization efficacy invariably increased for all plasma sample studied, with an average 2.0-fold improvement. 2021 Immunity Result SARS_CoV_2 K417N 49 54 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Last, soluble human ACE2 showed improved binding to all three variants as well as pseudoviruses bearing single N501Y and triple K417N-E484K-N501Y mutations (Figure 1D; Figure S2). 2021 Immunity Result SARS_CoV_2 K417N;N501Y;E484K;N501Y 128;111;134;140 133;116;139;145 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. N439K, located in the REGN10987 epitope, showed a 26.6-fold reduction in IC50. 2021 Immunity Result SARS_CoV_2 N439K 0 5 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. On the other hand, the single-mutant E484K and triple-mutant K417N-E484K-N501Y pseudoviruses substantially reduced the neutralization activity for 8 of 23 samples (C-Plasma6, C-Plasma10, C-Plasma15, C-Plasma16, C-Plasma17, C-PlasmaP#2, C-PlasmaP#5, and C-PlasmaP#22), which corresponded to their diminished or loss of neutralization against the B.1.351 and P.1 pseudoviruses. 2021 Immunity Result SARS_CoV_2 E484K;K417N;E484K;N501Y 37;61;67;73 42;66;72;78 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Several mutations within the REGN10933 epitope, such as Y453F and F486L, were also associated with a substantial reduction in neutralization. 2021 Immunity Result SARS_CoV_2 F486L;Y453F 66;56 71;61 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Similar to the WT RBD, P2C-1F11 did not directly bind to E484K in RBD-3M (Figure 2B; Table S2). 2021 Immunity Result SARS_CoV_2 E484K 57 62 RBD;RBD 18;66 21;69 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Single N501Y mutations found in B.1.1.7 and two of three (K417N and N501Y) found in B.1.351 and P.1 therefore likely enhanced binding to mouse ACE2, improving entry efficiency into HeLa mouse ACE2. 2021 Immunity Result SARS_CoV_2 N501Y;N501Y;K417N 7;68;58 12;73;63 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Such enhancement occurred only with the E484K-bearing variant B.1.351 and P.1 but not with the E484K-missing variant B.1.1.7, suggesting that the added and/or synergistic effect of E484K with other mutant residues facilitates entry into these two cell lines. 2021 Immunity Result SARS_CoV_2 E484K;E484K;E484K 40;95;181 45;100;186 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The entry efficiency was measured and presented as fold change relative to WT D614G. 2021 Immunity Result SARS_CoV_2 D614G 78 83 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The extra interactions between RBD-3M and P2C-1F11 around Y501 may also contribute to the retained binding and neutralization of P2C-1F11 against SARS-CoV-2 variants carrying the triple K417N-E484K-N501Y mutation. 2021 Immunity Result SARS_CoV_2 K417N;E484K;N501Y 186;192;198 191;197;203 RBD 31 34 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The half-maximal inhibitory concentration (IC50) of REGN10933 dropped 13.0- and 8.2-fold against B.1.351 and P.1, respectively, largely because of the K417N/T and E484K mutations (Figure 1C). 2021 Immunity Result SARS_CoV_2 E484K;K417N;K417T 163;151;151 168;158;158 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The K417N mutation would therefore be less disruptive to P2C-1F11 than to those in class I or RBS-A, such as P5A-1D2, P22A-1D1, and CB6, studied here, and CC12.1, CC12.3, COVA2-04, and COVA2-07, characterized elsewhere. 2021 Immunity Result SARS_CoV_2 K417N 4 9 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The loss of plasma neutralizing activities is attributed, to varying degrees, to the 242-244del in the NTD, E484K, and triple K417N-E484K-N501Y mutations in the RBD, depending on individual plasma. 2021 Immunity Result SARS_CoV_2 E484K;K417N;E484K;N501Y 108;126;132;138 113;131;137;143 RBD 161 164 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The reduction and loss of neutralization were largely attributed to K417N/T (Figure 1C). 2021 Immunity Result SARS_CoV_2 K417N;K417T 68;68 75;75 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The single K417N mutation, however, decreased ACE2 binding by about 6.4-fold. 2021 Immunity Result SARS_CoV_2 K417N 11 16 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The single mutant N501Y pseudovirus, reported previously to enhance ACE2 binding, had limited effects on the neutralizing activity of convalescent plasma. 2021 Immunity Result SARS_CoV_2 N501Y 18 23 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The single-mutant E484K pseudovirus also enhanced entry into HeLa mouse ACE2 and HeLa mink ACE2. 2021 Immunity Result SARS_CoV_2 E484K 18 23 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The triple-mutant K417N-E484K-N501Y pseudovirus, like B.1.351 and P.1, was resistant to class I and II mAbs, suggesting that combination of the three RBD mutations is key for conferring complete resistance. 2021 Immunity Result SARS_CoV_2 K417N;E484K;N501Y 18;24;30 23;29;35 RBD 150 153 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The wild-type (WT) pseudovirus used throughout the analysis was the prototype strain with a D614G mutation (WT D614G). 2021 Immunity Result SARS_CoV_2 D614G;D614G 92;111 97;116 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Therefore, the E484K mutation would diminish such interaction and render this class of antibodies ineffective against B.1.351 and P.1. 2021 Immunity Result SARS_CoV_2 E484K 15 20 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. These interactions were diminished by the K417N mutation but replaced by one hydrogen bond between Y52 and mutant N417 (Figure 2B; Table S2). 2021 Immunity Result SARS_CoV_2 K417N 42 47 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. These results indicate that the NTD mutations Y144del and 242-244del and the RBD mutations K417N/T, E484K, and N501Y confer substantial mAb resistance. 2021 Immunity Result SARS_CoV_2 E484K;K417N;K417T;N501Y 100;91;91;111 105;98;98;116 RBD 77 80 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. This agreed well with recent reports where single N501Y or triple K417N-Q493H-N501Y mutations were found in the mouse-adapted SARS-CoV-2 strains, although the triple mutant causes more severe acute respiratory symptoms and mortality in standard laboratory mice. 2021 Immunity Result SARS_CoV_2 K417N;N501Y;N501Y;Q493H 66;50;78;72 71;55;83;77 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. This explains why E484K had no detectable effect on the binding and neutralizing activity of P2C-1F11. 2021 Immunity Result SARS_CoV_2 E484K 18 23 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. This finding indicates that N501Y plays a role in enhanced binding, which is consistent with earlier reports of human and mouse ACE2. 2021 Immunity Result SARS_CoV_2 N501Y 28 33 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. We determined the crystal structure of the SARS-CoV-2 RBD carrying K417N-E484K-N501Y mutations (RBD-3M) bound by P2C-1F11 at a resolution of 2.10 A (PDB: 7E8M; Table S1). 2021 Immunity Result SARS_CoV_2 K417N;E484K;N501Y 67;73;79 72;78;84 RBD;RBD 54;96 57;99 34168138 The architecture of the SARS-CoV-2 RNA genome inside virion. D614G and accompanying mutations on structure remodeling. 2021 Nature communications Result SARS_CoV_2 D614G 0 5 34168138 The architecture of the SARS-CoV-2 RNA genome inside virion. However, the C14408U mutation in RdRP (P323L) might introduce a novel structure with a smaller apical loop (14,380-14,441 nt). 2021 Nature communications Result SARS_CoV_2 P323L 39 44 RdRP 33 37 34168138 The architecture of the SARS-CoV-2 RNA genome inside virion. In addition, the D614G accompanying mutations at 241, 3037, and 14,408 nt all resided in the single-stranded internal or apical loops. 2021 Nature communications Result SARS_CoV_2 D614G 17 22 34168138 The architecture of the SARS-CoV-2 RNA genome inside virion. Interestingly, we found that the A23403G mutation fine-tuned the two local bulge structures into a thermodynamically more favorable six-nucleotide bulge structure (-10.3 kcal/mol vs. 2021 Nature communications Result SARS_CoV_2 A23403G 33 40 34168138 The architecture of the SARS-CoV-2 RNA genome inside virion. Some mutations are beneficial to SARS-CoV-2 and emerge as dominant strains in the global pandemic, such as D614G and three accompanying mutations. 2021 Nature communications Result SARS_CoV_2 D614G 107 112 34168138 The architecture of the SARS-CoV-2 RNA genome inside virion. The D614G mutation had been demonstrated to increase the infectivity and stability of virions. 2021 Nature communications Result SARS_CoV_2 D614G 4 9 34168138 The architecture of the SARS-CoV-2 RNA genome inside virion. The most prevalent D614G mutant caused by an A-to-G nucleotide transition at position 23,403, was located in the single-nucleotide bulge of a stem-loop. 2021 Nature communications Result SARS_CoV_2 D614G 19 24 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. For each sample, a total of nine mutations were found in the spike protein: H69-70-, Y144-, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H. 2021 Journal of medical virology Result SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 99;134;106;92;113;127;120 104;140;111;97;118;132;125 S 61 66 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. Thus, even an A to T single-nucleotide polymorphism (SNP), such as that present in the N501Y mutation (S1B) is easily distinguishable by RT-ddPCR by screening for droplets with S1B probe amplitude above a fluorescent threshold of 5700. 2021 Journal of medical virology Result SARS_CoV_2 N501Y 87 92 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Additionally, the three sequences that contain the Y453F mutation were isolated from cats in Denmark: two identical sequences (GISAID ID: EPI_ISL_683164 and EPI_ISL_683166) and another sequence (GISAID ID: EPI_ISL_683165) of a distinct origin (Figure S2). 2021 Cell host & microbe Result SARS_CoV_2 Y453F 51 56 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Although the L452 residue is not directly located at the binding interface (Figure 2A), structural analysis and in silico mutagenesis suggest that the L452R substitution promotes electrostatic complementarity (Figure 2G). 2021 Cell host & microbe Result SARS_CoV_2 L452R 151 156 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Although the L452R mutant was first detected in the B.1.39 lineage in Denmark on March 17, 2020 (GISAID ID: EPI_ISL_429311) (Table 1), this variant did not spread. 2021 Cell host & microbe Result SARS_CoV_2 L452R 13 18 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Altogether, these findings suggest that the L452R substitution increases the binding affinity of the SARS-CoV-2 RBD toward human ACE2, protein stability, and viral infectivity. 2021 Cell host & microbe Result SARS_CoV_2 L452R 44 49 RBD 112 115 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Altogether, these results suggest that the NF9 peptide, which is derived from the SARS-CoV-2 S protein RBM, is an immunodominant epitope of HLA-A24 and that two naturally occurring mutants, L452R and Y453F, are able to evade HLA-A24-restricted cellular immunity. 2021 Cell host & microbe Result SARS_CoV_2 L452R;Y453F 190;200 195;205 S 93 94 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. As shown in Figure 2E, although the N501Y mutation slightly affected viral infectivity in this assay, the L452R mutation significantly increased it compared to the parental S protein. 2021 Cell host & microbe Result SARS_CoV_2 L452R;N501Y 106;36 111;41 S 173 174 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. As shown in Figure 2I, the cytotoxicity of the L452R mutant was higher than that of the other mutants and the parental virus. 2021 Cell host & microbe Result SARS_CoV_2 L452R 47 52 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Because residue 452 is located in close proximity to a negatively charged patch of ACE2 residues (E35, E37, and D38), the increase in viral infectivity caused by the L452R substitution can be attributed to an increase in electrostatic interaction with ACE2. 2021 Cell host & microbe Result SARS_CoV_2 L452R 166 171 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Consistent with recent studies, including ours, the N501Y mutation, which is a common mutation in B1.1.7, B1.351, and P.1 variants (reviewed in), as well as the Y453F mutation, significantly increased binding affinity for human ACE2 (Figures 2B and 2C; RBD parental K D = 2.05 +- 0.26 nM, RBD N501Y K D = 0.59 +- 0.03 nM, and RBD Y453F K D = 0.51 +- 0.06 nM). 2021 Cell host & microbe Result SARS_CoV_2 N501Y;N501Y;Y453F;Y453F 52;293;161;330 57;298;166;335 RBD;RBD;RBD 253;289;326 256;292;329 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. In contrast to the yeast display assay (Figures 2B and 2C), the infectivity of the Y453F mutant was significantly lower than that of the parental S protein (Figure 2E). 2021 Cell host & microbe Result SARS_CoV_2 Y453F 83 88 S 146 147 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. In contrast, the level of IFN-gamma expression induction by the NF9-Y453F derivative was significantly lower than that by parental NF9, and intriguingly, the NF9-L452R derivative did not induce IFN-gamma expression, even at the highest concentration tested (10 nM) (Figure S1C). 2021 Cell host & microbe Result SARS_CoV_2 L452R;Y453F 162;68 167;73 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. In contrast, the NF9-L452R derivative did not activate all CD8+ T cells tested, and seven out of the eight HLA-A24-positive COVID-19 convalescent samples failed to be activated by the NF9-Y453F derivative (Figures 1H and 1I). 2021 Cell host & microbe Result SARS_CoV_2 L452R;Y453F 21;188 26;193 COVID-19 124 132 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. In silico analyses using five tools predicted that the L452R mutation decreases the binding affinity of NF9 to HLA-A24, and four out of the five tools predicted that the Y453F mutation decreases the binding affinity (Figure S1A). 2021 Cell host & microbe Result SARS_CoV_2 L452R;Y453F 55;170 60;175 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Increase in pseudovirus infectivity by the L452R mutation. 2021 Cell host & microbe Result SARS_CoV_2 L452R 43 48 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Increase in viral fusogenicity by the L452R mutation. 2021 Cell host & microbe Result SARS_CoV_2 L452R 38 43 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Intriguingly, the L452R mutations increased surface expression, which reflects protein stability, but the Y453F and N501Y mutations decreased it (Figure 2D). 2021 Cell host & microbe Result SARS_CoV_2 L452R;N501Y;Y453F 18;116;106 23;121;111 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Moreover, a competition assay using the parental virus and the L452R mutant showed that the L452R mutant expanded more predominantly than the parental virus (Figure 2M). 2021 Cell host & microbe Result SARS_CoV_2 L452R;L452R 63;92 68;97 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Moreover, we demonstrated that the infectivity of the reporter virus pseudotyped with the S protein of the B.1.429 variant, which harbors the L452R mutation, was significantly higher than those of parental S as well as the D614G-harboring S, while that of the B.1.1.298 variant, which harbors the Y453F mutation, was not (Figure 2F). 2021 Cell host & microbe Result SARS_CoV_2 D614G;L452R;Y453F 223;142;297 228;147;302 S;S;S 90;206;239 91;207;240 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Nevertheless, the epidemic of a fraction of the B.1.1.298 lineage containing the Y453F mutation in Denmark peaked from October to November 2020 and then gradually declined (Figure 3D). 2021 Cell host & microbe Result SARS_CoV_2 Y453F 81 86 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Notably, lineages B.1.427/429 and B.1.1.298 of the PANGO lineages (https://cov-lineages.org/index.html) mainly harbor the L452R and Y453F mutations, respectively (Figure 1G; Table S3). 2021 Cell host & microbe Result SARS_CoV_2 L452R;Y453F 122;132 127;137 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Our data suggest that the L452R mutation promotes viral replication by increasing viral fusogenicity. 2021 Cell host & microbe Result SARS_CoV_2 L452R 26 31 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Regarding the Y453F mutation, 1,274 of the 1,380 mutated sequences belong to the B.1.1.298 lineage, which has been exclusively detected in Denmark (Table S4). 2021 Cell host & microbe Result SARS_CoV_2 Y453F 14 19 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Similar to the observations using human ACE2 (Figure 2E), the L452R mutant, but not the other mutants including the Y453F mutant, significantly increased infection efficacy using mink ACE2 as the receptor (Figure S1D). 2021 Cell host & microbe Result SARS_CoV_2 L452R;Y453F 62;116 67;121 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. The B.1.427/B.1.429 lineage harboring the L452R mutation started expanding in California at the beginning of November 2020 (Figure 3B, top). 2021 Cell host & microbe Result SARS_CoV_2 L452R 42 47 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. The L452R mutants were mainly found (3,967 sequences) in the B.1.427/B.1.429 lineage, which forms a single clade (Figure 3 A; Table S4). 2021 Cell host & microbe Result SARS_CoV_2 L452R 4 9 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. The L452R substitution was most frequent among the sequences analyzed (5,677 sequence), and 1,380 of the sequences reported contain the Y453F substitution (Table 1 ). 2021 Cell host & microbe Result SARS_CoV_2 L452R;Y453F 4;136 9;141 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. The oldest sequence in the B.1.1.298 lineage that contains the Y453F mutation was isolated from a human in Denmark on April 20, 2020 (GISAID ID: EPI_ISL_714253) (Figure 3C). 2021 Cell host & microbe Result SARS_CoV_2 Y453F 63 68 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. The oldest sequence that contains the L452R mutation in the B.1.427/B.1.429 lineage was isolated in Quintana Roo state, Mexico, on July 6, 2020 (GISAID ID: EPI_ISL_942929) (Table 1), and L452R-harboring mutants were first collected in California, USA, on September 28, 2020 (GISAID ID: EPI_ISL_730092 and EPI_ISL_730345) (Figure 3B). 2021 Cell host & microbe Result SARS_CoV_2 L452R;L452R 38;187 43;192 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. The predominance of the L452R mutant was observed at different doses (Figure S1E). 2021 Cell host & microbe Result SARS_CoV_2 L452R 24 29 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. The variant containing the Y453F mutation was last collected in Denmark on January 18, 2021 (GISAID ID: EPI_ISL_925998), and it has not been reported worldwide since (Figure 3D). 2021 Cell host & microbe Result SARS_CoV_2 Y453F 27 32 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. To directly assess the effect of these RBM mutations on binding to ACE2, we prepared yeasts expressing the parental SARS-CoV-2 receptor-binding domain (RBD) (residues 336-528) and derivatives (L452R, Y453F, and N501Y) and performed an in vitro binding assay using the yeast surface display of the RBD and soluble ACE2 protein. 2021 Cell host & microbe Result SARS_CoV_2 N501Y;Y453F;L452R 211;200;193 216;205;198 RBD;RBD 152;297 155;300 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. To experimentally address the possibility that these naturally occurring mutations, L452R and Y453F in the NF9 region, confer evasion ability from NF9-specific CD8+ T cells in HLA-A24-positive COVID-19 convalescents, two NF9 derivatives containing either substitution (NF9-L452R and NF9-Y453F) were prepared and used for stimulation experiments. 2021 Cell host & microbe Result SARS_CoV_2 L452R;Y453F;L452R;Y453F 84;94;273;287 89;99;278;292 COVID-19 193 201 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Together with the results of the binding assay (Figures 2B-2D) and the assay using pseudoviruses (Figures 2E, 2F, and S1E), our results suggest that the L452R mutation promotes viral replication. 2021 Cell host & microbe Result SARS_CoV_2 L452R 153 158 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Using the SARS-CoV-2 S-based fusion assay, we demonstrated that the L452R mutation significantly increased fusion efficacy compared to the parental S, as well as the other mutants (Figure 2N). 2021 Cell host & microbe Result SARS_CoV_2 L452R 68 73 S;S 21;148 22;149 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. We also found that the growth rates of the L452R mutant in VeroE6/TMPRSS2 cells (Figure 2J), HEK293 cells stably expressing human ACE2 (HEK293-ACE2; Figure 2K), and A549 cells stably expressing human ACE2 (A549-ACE2; Figure 2L) were significantly higher than those of the parental virus. 2021 Cell host & microbe Result SARS_CoV_2 L452R 43 48 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. We also found that the L452R mutant significantly increased the binding affinity to human ACE2 (Figures 2B and 2C; RBD L452R K D = 1.20 +- 0.06 nM). 2021 Cell host & microbe Result SARS_CoV_2 L452R;L452R 23;119 28;124 RBD 115 118 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. We next tested how the L452R mutation increases viral infectivity and cytotoxicity by performing a SARS-CoV-2 S-based fusion assay. 2021 Cell host & microbe Result SARS_CoV_2 L452R 23 28 S 110 111 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Based on the western blot quantification, the expected pg of N per swab from the 1:10 dilution is 5.6 x 105 pg, 9.5 x 105 pg, 6.7 x 105 pg, 12.2 x 105 pg for N WT, N T205I, N D399N, and N T205I/D399N, respectively. 2021 Journal of clinical virology Result SARS_CoV_2 D399N;T205I;T205I;D399N 175;166;188;194 180;171;193;199 N;N;N;N;N 61;158;164;173;186 62;159;165;174;187 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Both mutations are located in areas of the 419 aa protein without an available structure, with the T205I in the serine-arginine rich region and the D399N in the far C-terminus. 2021 Journal of clinical virology Result SARS_CoV_2 D399N;T205I 148;99 153;104 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Clinical specimens with nucleocapsid T205I/D399N mutation repeatedly test negative on quidel sofia 2 antigen test. 2021 Journal of clinical virology Result SARS_CoV_2 T205I;D399N 37;43 42;48 N 24 36 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. D399N rarely emerges alone as a single variant in the N gene (n = 11, 5.0%), and most frequently appears with only T205I (n = 78, 35.1%). 2021 Journal of clinical virology Result SARS_CoV_2 T205I;D399N 115;0 120;5 N 54 55 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Ectopically expressed nucleocapsid protein containing the D399N mutation results in a ~1000-fold reduction in analytical sensitivity specifically on the quidel sofia sars antigen fia test. 2021 Journal of clinical virology Result SARS_CoV_2 D399N 58 63 N 22 34 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Furthermore, the Abbott BinaxNOW test detected lysates that contain N with just the single mutation D399N or N WT with sensitivity equivalent to the other N variants. 2021 Journal of clinical virology Result SARS_CoV_2 D399N 100 105 N;N;N 68;109;155 69;110;156 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Given that the N D399N mutation rarely emerges alone, no clinical specimens were available for antigen testing to directly address whether D399N mutation is solely responsible for the reduced sensitivity of the Quidel Sofia 2 antigen test. 2021 Journal of clinical virology Result SARS_CoV_2 D399N;D399N 17;139 22;144 N 15 16 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. In contrast to lysates containing N T205I alone or N WT, the sensitivity of the Quidel Sofia 2 antigen test for lysates containing N D399N mutation alone was reduced by 1000-fold (comparing the last dilution where all tests were positive), similar to lysates containing the N T205I/D399N double mutant. 2021 Journal of clinical virology Result SARS_CoV_2 D399N;T205I;T205I;D399N 133;36;276;282 138;41;281;287 N;N;N;N 34;51;131;274 35;52;132;275 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. In contrast to our findings on the Quidel Sofia 2 antigen tests, no significant difference was observed in sensitivity between any of the N variants, indicating that the Quidel QuickVue test is not affected by the D399N mutation (Table 4). 2021 Journal of clinical virology Result SARS_CoV_2 D399N 214 219 N 138 139 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. In contrast to the Abbott BinaxNOW kit, the Quidel Sofia 2 antigen test exhibited significantly lower sensitivity for clinical specimens associated with N T205I/D399N compared to clinical specimens associated with N T205I. 2021 Journal of clinical virology Result SARS_CoV_2 T205I;T205I;D399N 155;216;161 160;221;166 N;N 153;214 154;215 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. In contrast, Quidel Sofia 2 antigen test has approximately equivalent sensitivity between lysates containing N WT and N T205I since both were 100% detected (3/3) at 1:104 dilution or approximately 560 pg of N WT protein and 948 pg of N T205I protein. 2021 Journal of clinical virology Result SARS_CoV_2 T205I;T205I 120;236 125;241 N;N;N;N 109;118;207;234 110;119;208;235 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. In testing of clinical specimens, as described above, the Abbott BinaxNOW test detected specimens associated with both N T205I and N T205I/D399N variants with similar sensitivity. 2021 Journal of clinical virology Result SARS_CoV_2 T205I;T205I;D399N 121;133;139 126;138;144 N;N 119;131 120;132 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Likewise, the Abbott BinaxNOW kit detected each of these N variants in 293T lysates with equivalent sensitivity down to the 1:105 dilution (3/3 or 2/3 positive tests), corresponding to approximately 95 pg of N205I and 122 pg of N T205I/D399N (Table 4). 2021 Journal of clinical virology Result SARS_CoV_2 N205I;T205I;D399N 208;230;236 213;235;241 N;N 57;228 58;229 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Of the 1144,036 GISAID consensus sequences available as of April 18, 2021, we found 222 sequences with the D399N mutation, for a global prevalence of only 0.019%. 2021 Journal of clinical virology Result SARS_CoV_2 D399N 107 112 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. T205I is a common N gene mutation in global consensus sequences, at 42.9% prevalence, making the co-occurrence of D399N and T205I a relatively rare event at only 0.16% of total T205I mutations. 2021 Journal of clinical virology Result SARS_CoV_2 D399N;T205I;T205I;T205I 114;124;177;0 119;129;182;5 N 18 19 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Testing of 293T lysates containing N T205I or N T205I/D399N on the Quidel Sofia 2 antigen test confirmed this finding with the antigen test exhibiting an approximately 1000-fold reduced sensitivity between lysates containing variants N T205I versus N T205I/D399N, based on comparing the final dilution where all tests were positive. 2021 Journal of clinical virology Result SARS_CoV_2 T205I;T205I;T205I;T205I;D399N;D399N 37;48;236;251;54;257 42;53;241;256;59;262 N;N;N;N 35;46;234;249 36;47;235;250 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Testing of available clinical samples showed that the Quidel Sofia 2 antigen test has reduced sensitivity for specimens associated with the N T205I/D399N variant, but not for specimens associated with the N T205I variant. 2021 Journal of clinical virology Result SARS_CoV_2 T205I;T205I;D399N 142;207;148 147;212;153 N;N 140;205 141;206 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. The N wildtype gene from Wuhan-Hu-1 (N WT) and N gene variants N T205I, N D399N, and N T205I/D399N were each cloned into a CMV expression vector with a C-terminal 2XStrep-Tag II. 2021 Journal of clinical virology Result SARS_CoV_2 D399N;T205I;T205I;D399N 74;65;87;93 79;70;92;98 N;N;N;N;N;N 4;37;47;63;72;85 5;38;48;64;73;86 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. These findings demonstrate that the N D399N mutation alone was sufficient to reduce the sensitivity of the Quidel Sofia 2 antigen test significantly by 1000-fold. 2021 Journal of clinical virology Result SARS_CoV_2 D399N 38 43 N 36 37 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. This corresponded to a difference of approximately 948 pg N T205I and 1.22 x 106 pg of N T205I/D399N (Table 4). 2021 Journal of clinical virology Result SARS_CoV_2 T205I;T205I;D399N 60;89;95 65;94;100 N;N 58;87 59;88 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. This mutation is found mostly in the United States (n = 125, 56.3% of total D399N variants), and most commonly in the background of the B.1.429 / 20C clade (n = 63). 2021 Journal of clinical virology Result SARS_CoV_2 D399N 76 81 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Thus, the Abbott BinaxNOW test appears unaffected by the N variants T205I, D399N, or T205/D399N. 2021 Journal of clinical virology Result SARS_CoV_2 D399N;T205I;D399N 75;68;90 80;73;95 N 57 58 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. To determine if D399N alone is sufficient for the reduced sensitivity of the Quidel Sofia 2 antigen test, we next tested lysates that contain N D399N mutation alone. 2021 Journal of clinical virology Result SARS_CoV_2 D399N;D399N 16;144 21;149 N 142 143 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. To evaluate the role of the D399N mutation alone or in combination with T205I, we transiently expressed N variants in 293T cells and subjected lysates from these 293T cells to antigen testing. 2021 Journal of clinical virology Result SARS_CoV_2 D399N;T205I 28;72 33;77 N 104 105 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. We further analyzed D399N in the context of other N gene mutations. 2021 Journal of clinical virology Result SARS_CoV_2 D399N 20 25 N 50 51 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. We next tested the 293T lysates containing N variants on another point-of-care, rapid, FDA authorized COVID-19 antigen test manufactured by Quidel Corporation, Quidel QuickVue, to determine if the Quidel QuickVue kit sensitivity is affected by the N D399N mutation. 2021 Journal of clinical virology Result SARS_CoV_2 D399N 250 255 N;N 43;248 44;249 COVID-19 102 110 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Whole genome sequencing revealed two coding mutations in the N gene, T205I and D399N. 2021 Journal of clinical virology Result SARS_CoV_2 D399N;T205I 79;69 84;74 N 61 62 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. A significant increase in the conformational mobility of the S-D614 and S-D614G open states was seen for the RBD-up protomer (Figure 2B). 2021 ACS omega Result SARS_CoV_2 D614G 74 79 RBD;S;S 109;61;72 112;62;73 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. A similar pattern was seen in the mutational profile of the open state where D614G and D614N mutations displayed favorable and comparable stabilization changes (Figure 6B). 2021 ACS omega Result SARS_CoV_2 D614G;D614N 77;87 82;92 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Accordingly, the D614G mutation may exert its effect through allosteric stabilization of the S1-S2 interfaces limiting shedding of the S1 domain and by reducing flexibility and enhancing thermodynamic preferences of the open state. 2021 ACS omega Result SARS_CoV_2 D614G 17 22 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Although D614G eliminates favorable interactions with T859 and K854, the tight packing is maintained between residues of the interprotomer hinge cluster (Figure 5C). 2021 ACS omega Result SARS_CoV_2 D614G 9 14 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Although our results showed no substantial alteration of the dynamic signatures caused by the D614G mutation, simulations pointed to a marginally greater stabilization of the open form for the S-G614 mutant, which is consistent with previous assertions. 2021 ACS omega Result SARS_CoV_2 D614G 94 99 S 193 194 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Although recent studies indicated that the D614G variant did not itself drive to escape from antibody binding, it was found that D614G can remarkably potentiate escape mutations at some positions in certain patients, supporting an allosteric mechanism of action triggered by this mutation on dynamics and function in remote regions exposed to interactions with antibodies. 2021 ACS omega Result SARS_CoV_2 D614G;D614G 43;129 48;134 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Conformational dynamics profiles were similar for the closed forms, and no radical changes were detected in the dynamics profile of the D614G mutant (Figure 2A). 2021 ACS omega Result SARS_CoV_2 D614G 136 141 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Consistent with this experimental study, we found that D614G/N mutations can moderate the repulsive charge interactions at the interface between S1 and S2 domains and allow for the tighter interdomain packing. 2021 ACS omega Result SARS_CoV_2 D614G;D614N 55;55 62;62 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Hence, dynamic network modeling and community analysis of the S-D614 and S-G614 proteins revealed that the D614G mutation can induce a partial rearrangement of the residue interaction networks and promote the larger number of stable communities in both the closed and open forms by enhancing the S1-S2 interdomain interactions. 2021 ACS omega Result SARS_CoV_2 D614G 107 112 S;S 62;73 63;74 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Hence, the D614G mutation may also exert allosteric effect by partly immobilizing the distal NTD and RBD regions. 2021 ACS omega Result SARS_CoV_2 D614G 11 16 RBD 101 104 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. However, the D614G mutation can incur a more significant stabilization in the site of mutation and in the neighboring regions, particularly enhancing stability of the hinge site cluster formed by F318, F592, G593, G614, K854, F855, N856, and T859 residues (Figure 7C,D). 2021 ACS omega Result SARS_CoV_2 D614G 13 18 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. In light of these newly emerging experimental data, our results argue that the D614G mutation may exert its global impact on other sites by acting as an important mediating center governing regulation of the SARS-CoV-2 machine. 2021 ACS omega Result SARS_CoV_2 D614G 79 84 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. In the closed form of the S-D614 trimer, most of D614 mutations can result in the improved stability, highlighting, in particular, an appreciable stabilization of the D614C, D614G, and D614N mutants (Figure 6A). 2021 ACS omega Result SARS_CoV_2 D614C;D614G;D614N 167;174;185 172;179;190 S 26 27 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. In the locked closed form of S-G614 the largest destabilization changes were induced by the G614K, G614D, and G614E mutations (Supporting Information, Figure S4B), highlighting the fact that the reverse G614D mutation could significantly destabilize the S-G614 trimer. 2021 ACS omega Result SARS_CoV_2 G614D;G614D;G614E;G614K 99;203;110;92 104;208;115;97 S;S 29;254 30;255 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Mutational Sensitivity Cartography in the SARS-CoV-2 Spike Trimers Reveals D614G-Induced Stabilization of the Closed and Open States. 2021 ACS omega Result SARS_CoV_2 D614G 75 80 S 53 58 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Network Modeling and Community Analysis Suggest D614G-Induced Reorganization of the Residue Interaction Networks and Improved Allosteric Signaling in the Open States. 2021 ACS omega Result SARS_CoV_2 D614G 48 53 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Notably, the D614G mutation caused the largest energetic change as compared to other substitutions. 2021 ACS omega Result SARS_CoV_2 D614G 13 18 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Our findings of the network analysis support the latest experimental data by showing that the D614G mutation may strengthen the stability of the local community Q314-S596-Q613 and promote hydrogen-bonding interactions between Q613 and T859 of adjacent protomer afforded by the local backbone flexibility at the mutational site. 2021 ACS omega Result SARS_CoV_2 D614G 94 99 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Our findings support the notion that the D614G mutation in the SD2 domain could strengthen stability of the distal NTD and RBD regions in the open state and potentially promote exposure to the host receptor. 2021 ACS omega Result SARS_CoV_2 D614G 41 46 RBD 123 126 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. The destabilization changes caused by mutations of G614 were greater in the open form, thereby indicating that the D614G mutation may have a stronger stabilization effect on the open state. 2021 ACS omega Result SARS_CoV_2 D614G 115 120 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. The key community near mutational site Q314-S596-Q613 is uniquely present only in the open form of the S-G614 mutant, likely pointing to state-specific rearrangements of stable interactions induced by the D614G mutation (Table 5). 2021 ACS omega Result SARS_CoV_2 D614G 205 210 S 103 104 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. The mutational sensitivity profile of the SARS-CoV-2 S-D614 in the locked closed form also showed moderate destabilization changes, whereas D614G, D614C, D614H, and D614N modifications resulted in the improved stability of the closed form (Supporting Information, Figure S4A). 2021 ACS omega Result SARS_CoV_2 D614C;D614G;D614H;D614N 147;140;154;165 152;145;159;170 S 53 54 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. The presented results also partly reconciled several scenarios offered to explain functional effects of the D614G mutation. 2021 ACS omega Result SARS_CoV_2 D614G 108 113 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. The stabilizing communities in the S1-S2 interfaces appeared to strengthen the stability of both closed and open S-G614 forms, which is consistent with the experimentally observed increase in protein stability of the D614G mutant. 2021 ACS omega Result SARS_CoV_2 D614G 217 222 S 113 114 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. These findings are consistent with the latest differential scanning fluorimetry studies showing that the D614G- and D614N-induced changes have a very similar effect, leading to a considerable improvement of thermal stability, which may be explained by a decrease in premature shedding of the S1 domain. 2021 ACS omega Result SARS_CoV_2 D614G;D614N 105;116 110;121 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. These findings support the previously suggested notion that the D614G mutation in the SD2 domain could allosterically strengthen the stability of the distal NTD and RBD regions in the open state and therefore potentially promote exposure to the host receptor and greater infectivity. 2021 ACS omega Result SARS_CoV_2 D614G 64 69 RBD 165 168 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. These observations are in line with experimental studies, indicating that the D614G mutational site may be located in the immobilized structural region of the SD2 domain where the local environment of D614 combined with the beta strand formed by residues 311-319 may correspond to a hinge center governing motions of NTD and RBD, as well as isolating the motions in S1 from the S2 subunit. 2021 ACS omega Result SARS_CoV_2 D614G 78 83 RBD 325 328 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. These results are consistent with the latest experimental data that demonstrated the improved stability of the D614G mutant as compared to that of the S-D614 protein, allowing for reduction in a premature shedding of the S1 domain. 2021 ACS omega Result SARS_CoV_2 D614G 111 116 S 151 152 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. These results may reconcile the experimental studies showing that the D614G mutation confers the increased structural flexibility in the closed state, which may promote the exchange between the open and closed forms and the increased exposure of the RBDs for interactions with ACE2. 2021 ACS omega Result SARS_CoV_2 D614G 70 75 RBD 250 254 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. These results offer support to the experimental observations that the enhanced stability of the S-D614G mutant may be linked with the mechanism of the reduced S1 shedding. 2021 ACS omega Result SARS_CoV_2 D614G 98 103 S 96 97 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. These results revealed small and largely synchronous dynamic changes in the closed and open forms of the D614G mutant, showing no indication of a dramatic alteration of the dynamic signatures to suggest a clear mechanistic trigger for the dynamic preferences of the D614G mutant toward the open form, as was proposed in a computational study. 2021 ACS omega Result SARS_CoV_2 D614G;D614G 105;266 110;271 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. To provide further analysis of molecular drivers underlying functional effects of the D614G variant, we conducted the ensemble-based profiling and mutational scanning of protein stability in different functional forms of the S-G614 trimer. 2021 ACS omega Result SARS_CoV_2 D614G 86 91 S 225 226 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. We argue that by enhancing the interdomain communications in the open state, the D614G mutation could potentially improve stability of the S-G614 trimer and limit shedding of the S1 subunit. 2021 ACS omega Result SARS_CoV_2 D614G 81 86 S 139 140 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. Otherwise, all spike protein sequences obtained from the virus propagations were identical to the sequences obtained from the respective original patient sample, all also contained the D614G substitution linked to increased fitness and transmissibility. 2021 Nature communications Result SARS_CoV_2 D614G 185 190 S 15 20 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. The amino acid changes in the spike protein, especially the aforementioned E484K, K417N, and N501Y have recently been reported to affect the neutralizing efficacy of the antibodies. 2021 Nature communications Result SARS_CoV_2 E484K;K417N;N501Y 75;82;93 80;87;98 S 30 35 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. The MNT titres for two D614G-containing isolates, FIN-25 and SR121, correlated very well, as also did FIN-25 and 85HEL (B.1.1.7) (r > 0.8, p < 0.0001). 2021 Nature communications Result SARS_CoV_2 D614G 23 28 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. The neutralizing titres with two D614G isolates FIN-25 and SR121 were almost identical both 3 weeks (p = 0.02) and 6 weeks after the first dose (p = 0.11). 2021 Nature communications Result SARS_CoV_2 D614G 33 38 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. The sequence of FIN-25 that was passaged initially in VeroE6 cells had close to the furin cleavage site a deletion of amino acids 674-678 in 45% and R682W mutation at the furin cleavage site in 41% of the virus population, indicating some heterogeneity of the FIN-25 virus stock, which did, however, not affect the growth properties of the virus. 2021 Nature communications Result SARS_CoV_2 R682W 149 154 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. The three B.1.351 variant substitutions E484K, K417N, and N501Y are in the groove of the RBD-ACE2 interaction domain. 2021 Nature communications Result SARS_CoV_2 E484K;K417N;N501Y 40;47;58 45;52;63 RBD 89 92 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. To analyze the neutralization capacity of the vaccinees' sera, we isolated for microneutralization tests four virus variants circulating in Finland: D614G variants FIN-25 (spring 2020) representing B.1 lineage and SR121 (autumn 2020) representing B.1.463 lineage, a variant of concern 85HEL representing B.1.1.7 lineage and a variant of concern HEL12-102 representing B.1.351 lineage. 2021 Nature communications Result SARS_CoV_2 D614G 149 154 34184982 Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. Examination of the D614G mutation in the spike protein. 2021 Microbial genomics Result SARS_CoV_2 D614G 19 24 S 41 46 34184982 Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. In April the proportion of genomes that were wild type had reduced to 10.7 % (n=47) while those with the D614G mutation were dominant at 89.3 % (n=392). 2021 Microbial genomics Result SARS_CoV_2 D614G 105 110 34184982 Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. In March, 66.6 % (n=24) of samples contained the wild type and 33.3 % (n=12) contained the D614G mutation. 2021 Microbial genomics Result SARS_CoV_2 D614G 91 96 34184982 Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. In May the proportion of genomes that were wild type had reduced to 5.5 % (n=22) compared with 94.4 % (n=374) of genomes having the D614G mutation. 2021 Microbial genomics Result SARS_CoV_2 D614G 132 137 34184982 Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. Overall, in the Norfolk dataset, 89.4 % (n=819) of samples had the D614G mutation while only 10.6 % (n=97) had the wild type. 2021 Microbial genomics Result SARS_CoV_2 D614G 67 72 34184982 Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. There is evidence that a mutation in the spike protein of SARS-CoV-2 (an amino acid change from D to G at position 614; D614G) increases infectivity of a pseudotype virus in vitro in cells; this is associated with an observed increase in viral loads in patients. 2021 Microbial genomics Result SARS_CoV_2 D614G;D614G 96;120 118;125 S 41 46 34188167 Activation of NF-kappaB and induction of proinflammatory cytokine expressions mediated by ORF7a protein of SARS-CoV-2. 6A), it was of interest to see if a single amino acid change from G to V at position 251 of ORF3a would affect the NF-kappaB activation. 2021 Scientific reports Result SARS_CoV_2 G251V 66 88 ORF3a 92 97 34188167 Activation of NF-kappaB and induction of proinflammatory cytokine expressions mediated by ORF7a protein of SARS-CoV-2. ORF3a sequences from the affected lions belonged to clade V as defined by the G251V substitution. 2021 Scientific reports Result SARS_CoV_2 G251V 78 83 ORF3a 0 5 34188167 Activation of NF-kappaB and induction of proinflammatory cytokine expressions mediated by ORF7a protein of SARS-CoV-2. We concluded that G251V mutation in ORF3a did not change the property for NF-kappaB activation. 2021 Scientific reports Result SARS_CoV_2 G251V 18 23 ORF3a 36 41 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. 50-mug dose of LCB1v1.3 or control binder 1 day prior to inoculation with 103 PFU of B.1.1.7 or a recombinant WA1/2020 strain with E484K/N501/D614G mutations. 2021 Cell host & microbe Result SARS_CoV_2 E484K;D614G 131;142 136;147 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. Accordingly, we evaluated the activity of LCB1v1.3 against a B.1.1.7 isolate containing deletions at 69-70 and 144-145 and substitutions at N501Y, A570D, D614G, and P681H, and against a recombinant WA1/2020 strain containing key substitutions present in the B.1.351 and B.1.1.28 variant strains at residues E484K, N501Y, and D614G. 2021 Cell host & microbe Result SARS_CoV_2 A570D;D614G;D614G;E484K;N501Y;N501Y;P681H 147;154;325;307;140;314;165 152;159;330;312;145;319;170 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. Although the neutralizing activity of LCB1v1.3 against the B.1.1.7 and WA1/2020-E484K/N501Y/D614G strains was approximately 45- to 50-fold lower than for the WA1/2020 strain, the EC50 values still were ~800 pM and 667 pM, respectively (Figure S6). 2021 Cell host & microbe Result SARS_CoV_2 D614G;N501Y;E484K 92;86;80 97;91;85 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. Animals receiving LCB1v1.3 at D-5 or D-3 prior to inoculation with WA1/2020-E484K/N501Y/D614G gained weight (Figure 6M) and had reduced viral RNA levels in the lungs (Figure 6N) compared to control binder-treated animals. 2021 Cell host & microbe Result SARS_CoV_2 D614G;N501Y;E484K 88;82;76 93;87;81 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. To corroborate our findings, we tested the efficacy of LCB1-Fc in a non-transgenic 129S2 mouse model of SARS-CoV-2 infection with two strains containing the mouse-adapting N501Y substitution: a recombinant WA1/2020 strain containing N501Y and D614G substitutions and a B.1.1.7 natural isolate. 2021 Cell host & microbe Result SARS_CoV_2 D614G;N501Y;N501Y 243;172;233 248;177;238 COVID-19 104 124 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. We also tested the durability of LCB1v1.3 prophylaxis against the WA1/2020-E484K/N501Y/D614G strain when administered by i.n. 2021 Cell host & microbe Result SARS_CoV_2 D614G;N501Y;E484K 87;81;75 92;86;80 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. Escape of an NTD and E484K mutant virus from polyclonal post-vaccination serum is negligible but NTD mutations significantly impact the neutralizing activity of NTD binding mAbs. 2021 Cell Result SARS_CoV_2 E484K 21 26 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. For sera from the six vaccinated individuals, however, the highest reduction seen was only 2-fold for E406Q, N440K, E484K, and F490K (Figure 5B). 2021 Cell Result SARS_CoV_2 E406Q;E484K;F490K;N440K 102;116;127;109 107;121;132;114 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. In addition, B.1.1.7 carries the N501Y RBD mutation and B.1.351 carries N417K, E484K, and N501Y mutations in the RBD (Figures 4A and 4B). 2021 Cell Result SARS_CoV_2 E484K;N417K;N501Y;N501Y 79;72;33;90 84;77;38;95 RBD;RBD 39;113 42;116 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. In contrast, E484K on its own decreased affinity by 4-fold. 2021 Cell Result SARS_CoV_2 E484K 13 18 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. In fact, for most mAbs, no impact on binding was observed (Figure 5C) with the exception of PVI.V3-9, which lost binding to the RBD carrying F486A. 2021 Cell Result SARS_CoV_2 F486A 141 146 RBD 128 131 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. In general, single mutants E406Q, E484K, and F490K exerted the biggest impact on binding. 2021 Cell Result SARS_CoV_2 E406Q;E484K;F490K 27;34;45 32;39;50 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. Interestingly, almost all sera bound better to N501Y RBD (B.1.1.7) than to wild-type RBD (average 129% compared to wild-type). 2021 Cell Result SARS_CoV_2 N501Y 47 52 RBD;RBD 53;85 56;88 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. Specifically, N501Y and Y453F combined with N439K increased affinity for human ACE2 by 5-fold (Figures 4D and S3 ). 2021 Cell Result SARS_CoV_2 N439K;N501Y;Y453F 44;14;24 49;19;29 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. The highest reduction observed for E484K, F484A, B.1.351, and P.1 were also approximately 2-fold but this did not apply to all six vaccinees. 2021 Cell Result SARS_CoV_2 E484K;F484A 35;42 40;47 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. Through the Mount Sinai Hospital's Pathogen Surveillance Program, we had access to the SARS-CoV-2 isolate PV14252 (Clade 20C, Pango lineage B.1) that featured two mutations (W64R, L141Y) and one deletion (Delta142-145) in the NTD as well as the E484K mutation in the RBD (Figure 5D). 2021 Cell Result SARS_CoV_2 E484K;L141Y;W64R 245;180;174 250;185;178 RBD 267 270 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. Using biolayer interferometry (BLI), we measured association and dissociation rates of the N501Y RBD mutant (B.1.1.7 carries that mutation as its sole RBD mutation), Y453F, as found in mink isolates, N439K, which is found in some European clades, a combination of Y453F and N439K, E484K (part of B.1.351 and P.1) as well as for the B.1.351 and the P.1 RBDs for a recombinant version of human ACE2 (Figures 4A, 4B, and 4D). 2021 Cell Result SARS_CoV_2 E484K;N439K;N439K;N501Y;Y453F;Y453F 281;200;274;91;166;264 286;205;279;96;171;269 RBD;RBD;RBD 97;151;352 100;154;356 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. A sub-lineage of the variant contains an additional non-synonymous mutation in the S protein at position A27S (G21641T) (Figure 1B). 2021 Vaccines Result SARS_CoV_2 A27S;G21641T 105;111 109;118 S 83 84 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. As the P681H mutation is also found in the B.1.1.7 variant, its frequency has increased in some locations since late December 2020, following the first introduction of B.1.1.7 into Israel. 2021 Vaccines Result SARS_CoV_2 P681H 7 12 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. Characterization of the B.1.1.50 + P681H Variant. 2021 Vaccines Result SARS_CoV_2 P681H 35 40 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. Effective Neutralization of the B.1.1.50 + P681H Variant. 2021 Vaccines Result SARS_CoV_2 P681H 43 48 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. Identification of the P681H Mutation in Sewage. 2021 Vaccines Result SARS_CoV_2 P681H 22 27 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. The B.1.1.50 + P681H variant is characterized by the non-synonymous S protein mutation P681H (C23604A) and four additional synonymous mutations: Nsp3:C7765T, Nsp12b:C13821T, Nsp16:T21111C, and C29545A. 2021 Vaccines Result SARS_CoV_2 C29545A;P681H;P681H;C23604A;C13821T;C7765T;T21111C 193;15;87;94;165;150;180 200;20;92;101;172;156;187 Nsp3;S 145;68 149;69 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. The B.1.1.50 + P681H variant is unique to Israel, aside from 2 sequences originating in the Palestinian authorities, sharing a border with Israel. 2021 Vaccines Result SARS_CoV_2 P681H 15 20 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. The neutralization potency of antibodies against the B.1.1.50 + P681H variant was compared to the neutralization of other strains commonly circulating in Israel. 2021 Vaccines Result SARS_CoV_2 P681H 64 69 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. The P681H mutation was also frequently identified by SARS-CoV-2 whole genome sequencing of samples from waste-water treatment plants in nine locations across Israel, which were collected once a month from August 2020 to January 2021 (Figure 1). 2021 Vaccines Result SARS_CoV_2 P681H 4 9 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. The results demonstrate comparable neutralizations of the sera against the B.1.1.50 + P681H variant, the B.1.1.7 variant, and an Israel WT strain (Figure 3). 2021 Vaccines Result SARS_CoV_2 P681H 86 91 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. Two distinct clusters, each with the P681H mutation, were observed; a large cluster, representing the B.1.1.7 variant and a separate smaller cluster emerging from the B.1.1.50 lineage with the P681H mutation (Figure 1A). 2021 Vaccines Result SARS_CoV_2 P681H;P681H 37;193 42;198 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. Up to January 2021, a total of 181 individuals were detected with the B.1.1.50 + P681H variant. 2021 Vaccines Result SARS_CoV_2 P681H 81 86 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. VERO-E6 cells were infected with (a) the B.1.1.50 + P681H variant (isolate hCoV-19/Israel/CVL-45176-P681H-ngs/2020), (b) an Israel WT strain (isolate hCoV-19/Israel/CVL-45526-ngs/2020), and (c) the B.1.1.7 variant (isolate hCoV-19/Israel/CVL-46879-ngs/2020). 2021 Vaccines Result SARS_CoV_2 P681H;P681H 52;100 57;105 34203844 SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence. conducted in China showed no significant differences between two variants (clade I (ORF3a: p.251G > V, or S: p.614D > G (subclade G)); clade II (ORF8: p.84L > S (28,144U > C) and ORF1ab: p.2839S (8782C > U)) regarding disease severity and blood parameters indicative of severity. 2021 Journal of clinical medicine Result SARS_CoV_2 U28144C;C8782U;G251V;D614G;L84S 162;196;93;111;154 173;205;101;119;160 ORF1ab;ORF3a;ORF8;S 179;84;145;106 185;89;149;107 34203844 SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence. In a study conducted among 44 Vietnamese patients, 85 mutations covering 67 variant types were reported, of which P323L and D614G variants were the most frequent (present in 40/44 patients), followed by C241U (39/44) and GGG to AAC at 28881-3 variants (33/44). 2021 Journal of clinical medicine Result SARS_CoV_2 D614G;P323L 124;114 129;119 34203844 SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence. In this in vitro study, the authors showed a non-significant increase in infectivity in cell lines for any of pseudotyped viruses with the B.1.351 variant compared to the D614G variant. 2021 Journal of clinical medicine Result SARS_CoV_2 D614G 171 176 34203844 SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence. showed that infection with SARS-CoV-2 variants harboring the D614G substitution was not associated with disease severity, overall mortality, transfer to ICU, mechanical ventilation and length of stay at hospital. 2021 Journal of clinical medicine Result SARS_CoV_2 D614G 61 66 34203844 SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence. The new variant N501Y has been described as being more transmissible but is not associated with severity of COVID-19 infection. 2021 Journal of clinical medicine Result SARS_CoV_2 N501Y 16 21 COVID-19 108 126 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. Altogether, these data indicate that, relative to WH1 and D614G, cross-neutralization of B.1.1.7 was worse in vaccinated individuals in comparison to infected ones. 2021 Viruses Result SARS_CoV_2 D614G 58 63 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. B.1.1.7 neutralization was still reduced when compared to D614G (fold change of 1.55, p = 0.0027) but, overall, the response in the vaccinated previously infected group was improved in comparison to vaccinated only individuals (Figure 4A,B). 2021 Viruses Result SARS_CoV_2 D614G 58 63 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. However, in comparison to vaccinated only individuals, the cross-neutralizing response against both D614G and B.1.1.7 was superior to WH1 and the response against B.1.1.7 was only marginally reduced compared to D614G (fold change of 1.28, p = 0.034). 2021 Viruses Result SARS_CoV_2 D614G;D614G 100;211 105;216 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. Importantly, individuals infected by the B.1.1.7 variant were still able to cross-neutralize the original WH1 spike and the D614G mutant. 2021 Viruses Result SARS_CoV_2 D614G 124 129 S 110 115 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. In contrast, vaccinated individuals showed significantly higher potency to neutralize the intermediate D614G mutant (p < 0.0001) (Figure 2A). 2021 Viruses Result SARS_CoV_2 D614G 103 108 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. In fact, we observed a general trend of improving cross-neutralization capacities against both D614G and the B.1.1.7 variant when compared with WH1, although it was only significant for the latter (fold change evolving from 1.2 to 0.6, p = 0.024, M-W, Figure 3B). 2021 Viruses Result SARS_CoV_2 D614G 95 100 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. Individuals sampled 48 days after infection showed a small but significant decrease in neutralization capacity against the B.1.1.7 variant when compared with the D614G mutant (median fold change of 1.53, p = 0.031, Friedman test, Figure 3A,B). 2021 Viruses Result SARS_CoV_2 D614G 162 167 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. Interestingly though, in these limited cohorts, decay of the neutralization response was only significant when measured against WH1 (p = 0.0374, K-W, Figure 3A) and not against D614G or B.1.1.7. 2021 Viruses Result SARS_CoV_2 D614G 177 182 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. Similarly, the fold change between B.1.1.7 and D614G was significantly different between the all vaccinated and the all infected groups (median values 1.9 vs 1.17, respectively; p < 0.0001, M-W test, Figure 2D). 2021 Viruses Result SARS_CoV_2 D614G 47 52 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. The highest neutralization (p < 0.0001) was noticed for the D614G mutant, while no significant differences were observed between WH1 and B.1.1.7. 2021 Viruses Result SARS_CoV_2 D614G 60 65 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. This was significant in comparison to both WH1 (fold change of 2.04, p = 0.0021) and D614G (fold change of 2.65, p = <0.0001). 2021 Viruses Result SARS_CoV_2 D614G 85 90 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. We tested all the plasma samples (n = 98) against pseudoviruses expressing three different spike glycoproteins: a spike corresponding to the original SARS-CoV-2 virus, isolated in Wuhan, and named here WH1; a D614G mutant based on the WH1 spike and a spike including the defining mutations of the B.1.1.7 variant and named B.1.1.7. 2021 Viruses Result SARS_CoV_2 D614G 209 214 S;S;S;S 91;114;239;251 110;119;244;256 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. When comparing ratios with first wave participants, B.1.1.7 infected individuals showed a significant increase in the neutralization of B.1.1.7 vs D614G (fold change going from 1.53 to 1, p = 0.0006) (Figure 3D). 2021 Viruses Result SARS_CoV_2 D614G 147 152 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. All these analyses showed that the mutant A97V-RdRp does not have a large effect on RDV binding, in contrast, P323L-RdRp structure has a stabilising effect on RDV binding. 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 42;110 46;115 RdRP;RdRP 47;116 51;120 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. As for the A97V-RdRp mutant, the H-bonds formed with residues in the same vicinity as WT-RDV complex (K545, S549, K551, T556, and S682). 2021 Biomolecules Result SARS_CoV_2 A97V 11 15 RdRP 16 20 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. As for the P323L-apo (pink) structure, the RMSD showed a similar profile to the WT until 175 ns, where the structure decreased instability and the RMSD increased to 3.5 A. 2021 Biomolecules Result SARS_CoV_2 P323L 11 16 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. As such, the eigenvectors showed that the P323L-RdRp that bound to RDV contributed to a 13% variance in comparison to WT-RdRp and A97V-Rdrp (Figure 6C). 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 130;42 134;47 RdRP;RdRP;RdRP 48;121;135 52;125;139 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. As such, these results suggested that P323L induced a conformational change, which favours RDV binding. 2021 Biomolecules Result SARS_CoV_2 P323L 38 43 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Based on the change in DeltaG of 1.4 kcal mol-1 equal to a 10-fold change in the equilibrium constant, RDV showed a DeltaG -14.4 kcal/mol binding affinity to A97V RdRp, which presented a 20-fold weaker binding in comparison to WT-RdRp. 2021 Biomolecules Result SARS_CoV_2 A97V 158 162 RdRP;RdRP 163;230 167;234 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Concurrent with RMSD and MMGBSA analyses, the strong binding between RDV and P323L-RdRp mutant stabilised the protein structure. 2021 Biomolecules Result SARS_CoV_2 P323L 77 82 RdRP 83 87 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. From the FEL, the lowest energy conformations are shown in the H-bond network between RDV in complex with WT, A97V, and P323L (Figure 2). 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 110;120 114;125 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Furthermore, PCA was used to detect the high amplitude of motion of -WT-RdRp, A97V and P323L-RdRp mutant systems in apo and in complex with RDV. 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 78;87 82;92 RdRP;RdRP 72;93 76;97 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. However, in the P323L-Remdesivir complex, the H-bonds were closer to the active site (T556, S759, T680, S682, N691). 2021 Biomolecules Result SARS_CoV_2 P323L 16 21 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. In the apo form, WT, A97V, and P323L all showed similar fluctuation behaviours. 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 21;31 25;36 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. In the case of the apo WT, A97V and P323L-RdRp structures (Figure 6A), the first three eigenvectors show significant dominant motions, indicating significant fluctuations, while the remaining eigenvectors showed a localised fluctuation in each complex. 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 27;36 31;41 RdRP 42 46 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. In the case of the P323L-RDV complex, no motion was detected, indicating only localised fluctuation in the system. 2021 Biomolecules Result SARS_CoV_2 P323L 19 24 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. In WT and P323L-RdRp apo structures, the first three eigenvectors contributed a 70% variation, while in A97V-RdRp, the first three eigenvectors showed a 60% variation. 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 104;10 108;15 RdRP;RdRP 16;109 20;113 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Interaction analysis using a two-step energy minimisation method showed that the A97V-RdRp structure formed five hydrogen bonds (H-bonds) with residues K545, S549, K551, T556, and S682; whereas, in the P323L-RdRp structure, RDV formed H-bonds with T556, S759, T680, S682, and N691 (Figure 2). 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 81;202 85;207 RdRP;RdRP 86;208 90;212 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. It is clear from the RMSF graph that P323L-RdRp active sites experienced higher fluctuations as they adjusted to bind to RDV. 2021 Biomolecules Result SARS_CoV_2 P323L 37 42 RdRP 43 47 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. On the other hand, in the WT-apo system, the lowest conformational state was attained at 21 ns, while the A97V-apo attained three, and P323L attained the two lowest conformation states at 45 ns, 42 ns, 186 ns, 6 ns, and 20 ns, respectively. 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 106;135 110;140 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. P323L-RdRp RDV complex (Figure 3D) structure demonstrated less motion as the RMSD did not change during the 200 ns simulation, implicating that RDV binding to the P323L mutant resulted in a more stable structure. 2021 Biomolecules Result SARS_CoV_2 P323L;P323L 163;0 168;5 RdRP 6 10 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Structural Modeling of the A97V and P323L RdRp. 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 27;36 31;41 RdRP 42 46 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. The A97V-RdRp apo structure (red) (Figure 3A) showed a higher stability at the start of the simulation with a lower RMSD of 1.5 A. 2021 Biomolecules Result SARS_CoV_2 A97V 4 8 RdRP 9 13 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. The alanine to valine (A97V) and the proline to leucine (P323L) mutations were introduced into the RdRp structure using the protein structural analysis software PyMOL (Figure 1). 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 23;57 27;62 RdRP 99 103 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. The P323L-RdRp structure showed higher van der Waals interactions compared to WT and A97V-RdRp structures. 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 85;4 89;9 RdRP;RdRP 10;90 14;94 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. The projections of motions in the phase space from PCA of WT, A97V, and P323L-RdRp in the apo and RDV complex state were plotted (Figure 5). 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 62;72 66;77 RdRP 78 82 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. The root mean square fluctuations (RMSF) of the Calpha were calculated from the MD simulations to find the local fluctuations in RdRp WT and mutations A97V and P323L in the apo form and bound to RDV (Figure 4). 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 151;160 155;165 RdRP 129 133 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. The same fluctuation behaviours were observed for WT and A97V mutations when bound to RDV. 2021 Biomolecules Result SARS_CoV_2 A97V 57 61 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. The two most frequent mutations found in the RdRp protein are A97V and P323L; however, the structures of both RdRp mutations have not been solved. 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 62;71 66;76 RdRP;RdRP 45;110 49;114 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. The wild type (apo) lowest conformational states were achieved at 43 ns, A97V-apo at 77 ns, and P323L-apo at 111 ns. 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 73;96 77;101 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Therefore, the overall interaction of P332L-RdRp with RDV may have only perturbed the internal motions of the structure, with such energy subspaces affecting the behaviour of the binding. 2021 Biomolecules Result SARS_CoV_2 P332L 38 43 RdRP 44 48 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. This graph clearly showed that, in the case of P323L-RdRp structure, the system covered a more localised subspace showing stability in the system. 2021 Biomolecules Result SARS_CoV_2 P323L 47 52 RdRP 53 57 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. To gain insight into the effects that A97V and P323L mutations exhibited on the RdRp structures in apo and in complex with RDV they were subjected to 200 ns MD simulations (Figure 3). 2021 Biomolecules Result SARS_CoV_2 A97V;P323L 38;47 42;52 RdRP 80 84 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. When in complex with RDV, the WT and A97V-RdRp structures showed the same pattern, whereby the first three eigenvectors contributed to 70% of the variation. 2021 Biomolecules Result SARS_CoV_2 A97V 37 41 RdRP 42 46 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Whereas, with the P323L mutation, an increase in internal fluctuation was observed when in complex with RDV; particularly, the region between N380 and K675 showed the highest flexibility. 2021 Biomolecules Result SARS_CoV_2 P323L 18 23 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. While, the DeltaG for RDV bound to P323L-RdRp was -24.1 kcal/mol, which demonstrated a 40-fold higher binding affinity of RDV to P323L-RdRp mutant in comparison to WT-RdRp. 2021 Biomolecules Result SARS_CoV_2 P323L;P323L 35;129 40;134 RdRP;RdRP;RdRP 41;135;167 45;139;171 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. In lineage B.1.1.29, F338X, F342X, A344P, V367L, G446V, P507L and V510L were each represented in a different sequence, and in lineage B.1.177, only the S477G mutation was found in the RBD in only one sequence. 2021 Viruses Result SARS_CoV_2 A344P;F338X;F342X;G446V;P507L;S477G;V367L;V510L 35;21;28;49;56;152;42;66 40;26;33;54;61;157;47;71 RBD 184 187 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. In the B.1.258 lineage, three mutations, F374I, K417N and K528E, were detected in the RBD and were found in different sequences. 2021 Viruses Result SARS_CoV_2 F374I;K417N;K528E 41;48;58 46;53;63 RBD 86 89 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. Interestingly, the K417N mutation was reported to be one of the lineage-defining mutations of South African lineage B.1.351. 2021 Viruses Result SARS_CoV_2 K417N 19 24 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. Most mutations found in all six lineages were concentrated on the S1 subunit of the S protein; however, in the B.1.1.7 lineage, mutations such as S982A and D1118H were identified on the S2 subunit. 2021 Viruses Result SARS_CoV_2 D1118H;S982A 156;146 162;151 S 84 85 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. The D614G mutation was present in essentially all the sequences of all six lineages, and it was the only common mutation found in lineages B.1, B.1.1.29 and B.1.2. 2021 Viruses Result SARS_CoV_2 D614G 4 9 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. The sequences of lineage B.1.177 contained L18F, A222V and D614G mutations, and those of lineage B.1.258 contained DeltaH69/V70, N439K and D614G mutations/deletions. 2021 Viruses Result SARS_CoV_2 A222V;D614G;D614G;L18F;N439K 49;59;139;43;129 54;64;144;47;134 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. These mutations/deletions were DeltaH69/V70, S98F, DeltaY144, S162G, N501Y, A570D, D614G, P681H, T716I, S982A and D1118H. 2021 Viruses Result SARS_CoV_2 A570D;D1118H;D614G;DeltaY144;N501Y;P681H;S162G;S982A;S98F;T716I 76;114;83;51;69;90;62;104;45;97 81;120;88;60;74;95;67;109;49;102 34208912 Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. The E484K or K417N/T mutations contained in the SA and BR P.1 RBDs very likely influenced Ab7 to lose its neutralizing activity. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 E484K;K417N;K417T 4;13;13 9;20;20 RBD 62 66 34208912 Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. The reduced neutralizing activity of Ab5 against the UK RBD was likely caused by the N501Y mutation, the only reported mutation contained in the UK variant RBD. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 N501Y 85 90 RBD;RBD 56;156 59;159 34208912 Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. This indicates that the Ab7 epitope was not affected by the shared N501Y mutation but was very likely affected by the E484K or K417N/T mutations. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 E484K;K417N;K417T;N501Y 118;127;127;67 123;134;134;72 34208912 Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. This suggests that the Ab5 epitope was in the proximity of the N501Y mutation, which is the only mutation shared among the UK, SA, and BR P.1 RBDs. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 N501Y 63 68 RBD 142 146 34208912 Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. Thus, the weak binding activity of the Ab7-Ab4 pair (and Ab7-Ab1 pair) to the SA and BR P.1 RBDs compared with the SARS-CoV-2 and UK RBDs indicates that the E484K and K417N/T mutations contained in the SA and BR P.1 RBDs most likely induced conformational changes near or within the epitopes of where these antibodies bind. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 E484K;K417N;K417T 157;167;167 162;174;174 RBD;RBD;RBD 92;133;216 96;137;220 34208912 Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. With regard to the UK, SA, and BR P.1 variant RBDs, two antibodies, Ab1 and Ab4 of bin A, maintained strong neutralizing activity against all three variant RBDs, with NC50 values between 0.69 and 1.08 mug/mL, suggesting that these two antibodies targeted an epitope that was not affected by the mutations (N501Y, E484K, and K417N/T) contained in these three variant RBDs. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 E484K;K417N;K417T;N501Y 313;324;324;306 318;331;331;311 RBD;RBD;RBD 46;156;366 50;160;370 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. A recent article points in the same direction where negative stain electron microscopy reconstructions of the D614G form of the S-protein shows that the mutation favours the 'up' conformation, 82% population compared to 42% in the wild type. 2021 Scientific reports Result SARS_CoV_2 D614G 110 115 S 128 129 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. A similar striking increase in the frequency of both the D614G and P323L mutations should be noted. 2021 Scientific reports Result SARS_CoV_2 D614G;P323L 57;67 62;72 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Although similar experiments have to be carried out for the case of SARS-CoV-2, R190 and P116 are very close in space to the point of the P323L mutation, and P116 interacts directly with S325 of the 321FPPTS325 stretch. 2021 Scientific reports Result SARS_CoV_2 P323L 138 143 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Another molecular dynamics study published during the revision of the present manuscript also concludes that the D614G mutation favors the open conformation of the RDB. 2021 Scientific reports Result SARS_CoV_2 D614G 113 118 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Co-emergence and concurrence of the D614G and the P323L mutations. 2021 Scientific reports Result SARS_CoV_2 D614G;P323L 36;50 41;55 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. D614G mutation alters the interactions around the point of the mutation. 2021 Scientific reports Result SARS_CoV_2 D614G 0 5 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. P323L mutation of the SARS-CoV-2 RdRp polymerase. 2021 Scientific reports Result SARS_CoV_2 P323L 0 5 RdRP 33 37 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. S-protein D614G increases cell transduction of pseudotyped lentivectors. 2021 Scientific reports Result SARS_CoV_2 D614G 10 15 S 0 1 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Similar kinetics in the appearance of D614G and P323L led us to further analyse the relationship between the two mutations. 2021 Scientific reports Result SARS_CoV_2 D614G;P323L 38;48 43;53 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. The conformational freedom of the proline-rich 321FPPTS325 stretch, where the P323L mutation lies, is expected to be limited due to the pyrrolidine ring of the two Pro residues, which provide a degree of local structural rigidity. 2021 Scientific reports Result SARS_CoV_2 P323L 78 83 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. The D614G mutation stabilizes the open conformation of the S-protein as the pairwise RMSD correlation matrix is very stable (Supplementary Figure 2) even for the RDB (A) domain exposed to the solvent. 2021 Scientific reports Result SARS_CoV_2 D614G 4 9 S 59 60 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. The D614G mutation will disrupt the formation of the D614(A)-K835(C) salt bridge in the closed conformation, but very little will change in the open conformation. 2021 Scientific reports Result SARS_CoV_2 D614G 4 9 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. The level of association of nsp8 has been shown to be an important factor for obtaining a high RNA polymerase activity in SARS-CoV-1, and therefore enhanced interaction between the nsp12 and nsp8 upon the P323L mutation may give an evolutionary advantage to the virus. 2021 Scientific reports Result SARS_CoV_2 P323L 205 210 Nsp12;Nsp8;Nsp8 181;28;191 186;32;195 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. The P323L mutation is located on the interface domain of nsp12, and specifically on the loop that connects the three helices of the interface domain to the three beta-strands of the same domain. 2021 Scientific reports Result SARS_CoV_2 P323L 4 9 Nsp12 57 62 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Therefore, we anticipate the P323L mutation to have an impact on the nsp8 association. 2021 Scientific reports Result SARS_CoV_2 P323L 29 34 Nsp8 69 73 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. To understand the impact of the S-protein D614G mutation on infectivity, we produced S-protein pseudotyped lentivectors. 2021 Scientific reports Result SARS_CoV_2 D614G 42 47 S;S 32;85 33;86 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Two abundant amino acid changes in SARS-CoV-2: S protein D614G and RNA-dependent RNA polymerase (RdRp) P323L. 2021 Scientific reports Result SARS_CoV_2 D614G;P323L 57;103 62;108 RdRp;RdRP;S 67;97;47 95;101;48 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Using the original D614/P323 variant (NC_045512.2) as a reference, we identified two highly abundant SARS-CoV-2 mutations leading to amino acid changes: the D614G mutation in the S-protein, and the P323L mutation in the RNA-dependent RNA polymerase (RdRp). 2021 Scientific reports Result SARS_CoV_2 D614G;P323L 157;198 162;203 RdRp;RdRP;S 220;250;179 248;254;180 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. 2a) had three nucleotide substitutions from the reference sequence, Wuhan-Hu-1, and two amino acid changes, P323L in the RNA-dependent RNA polymerase (RdRP, NSP12) and D614G in the S protein. 2021 Scientific reports Result SARS_CoV_2 D614G;P323L 168;108 173;113 RdRp;Nsp12;RdRP;S 121;157;151;181 149;162;155;182 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. Additionally, S194L mutation in the N protein was much more prevalent in California, compared to other regions. 2021 Scientific reports Result SARS_CoV_2 S194L 14 19 N 36 37 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. Eight other sequences had mutations of T85I in the NSP2 protein and Q57H in the ORF3a protein (red circle in. 2021 Scientific reports Result SARS_CoV_2 Q57H;T85I 68;39 72;43 ORF3a;Nsp2 80;51 85;55 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. Five other sequences shared the mutation S194L in the N protein (purple circle in. 2021 Scientific reports Result SARS_CoV_2 S194L 41 46 N 54 55 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. In USA and California, the prevalence of T85I in NSP2 and Q57H in ORF3a were observed to be above 40%, as shown in. 2021 Scientific reports Result SARS_CoV_2 Q57H;T85I 58;41 62;45 ORF3a;Nsp2 66;49 71;53 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. Mass circulation of G clade strains were confirmed by around 80% prevalence of P323L in RdRP and D614G in the S protein globally. 2021 Scientific reports Result SARS_CoV_2 D614G;P323L 97;79 102;84 RdRP;S 88;110 92;111 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. Ten of the 25 sequences shared additional mutations of R203K and G204R in the N (nucleocapsid) protein (skyblue circle in. 2021 Scientific reports Result SARS_CoV_2 G204R;R203K 65;55 70;60 N;N 81;78 93;79 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. The prevalence of P1263L mutation in the S protein was sixfold greater in California than the global prevalence. 2021 Scientific reports Result SARS_CoV_2 P1263L 18 24 S 41 42 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. These include M755I in RdRP (NSP12) and V117F in the ORF8 protein (Table 1). 2021 Scientific reports Result SARS_CoV_2 M755I;V117F 14;40 19;45 Nsp12;ORF8;RdRP 29;53;23 34;57;27 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Chimeric VSV-GFP-SARS-CoV-2-SDelta21 bearing the E484D substitution specifically enhanced viral entry in H522 cells but did not affect the infection of 293T-ACE2 cells (Figures 2F-2H). 2021 Cell reports Result SARS_CoV_2 E484D 49 54 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Combination of the E484D and R682W substitutions did not further promote viral entry (Figure 2I). 2021 Cell reports Result SARS_CoV_2 E484D;R682W 19;29 24;34 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Consistent with these findings, we found that lentivirus pseudoparticles bearing the E484D substitution allowed low but reproducibly detectable levels of infection, whereas pseudoparticles bearing WT or R682W S were unable to infect H522s (Figure 2I). 2021 Cell reports Result SARS_CoV_2 E484D;R682W 85;203 90;208 S 209 210 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Despite the enhanced viral entry, we observed no viral spread with VSV-GFP-SARS-CoV-2-SDelta21 E484D in H522s (Figure 2H), suggesting that additional viral factors may be needed to facilitate viral egress and spread. 2021 Cell reports Result SARS_CoV_2 E484D 95 100 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. E64D, bafilomycin A, SGC-AAK1-1, and apilimod reduced cell-associated viral RNAs in a dose-dependent manner, whereas camostat mesylate increased viral RNA levels (Figure 4 A). 2021 Cell reports Result SARS_CoV_2 E64D 0 4 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Given the requirement for S E484D in H522 but not in ACE2-expressing cells, we screened a panel of eight S monoclonal antibodies (mAbs) in H522 and Vero E6 cells (Figures 2K and 2L). 2021 Cell reports Result SARS_CoV_2 E484D 28 33 S;S 26;105 27;106 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. In contrast, E484K/R685S substitutions did not enable VSV-GFP entry into H522 cells (Figures 2F and 2H). 2021 Cell reports Result SARS_CoV_2 E484K;R685S 13;19 18;24 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. In contrast, WT and E484D lentivirus pseudoparticles efficiently infected 293T-ACE2 cells, and the R682W substitution further enhanced entry (Figure 2J). 2021 Cell reports Result SARS_CoV_2 E484D;R682W 20;99 25;104 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Infection of H522 cells depends on SARS-CoV-2 S and requires the E484D substitution. 2021 Cell reports Result SARS_CoV_2 E484D 65 70 S 46 47 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Moreover, the E484D mutation within the RBD of S is required in H522 cells, but not ACE2-expressing cells. 2021 Cell reports Result SARS_CoV_2 E484D 14 19 RBD;S 40;47 43;48 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. The E484D S variant has been found to circulate within the human population, and given the alternative mechanism of entry and the requirement for the E484D substitution, we evaluated the ability of sera from vaccinated and convalescent individuals to block the infection of H522 cells. 2021 Cell reports Result SARS_CoV_2 E484D;E484D 4;150 9;155 S 10 11 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. This revealed the presence of the E484D substitution within the RBD and the less prevalent R682W substitution within the furin cleavage site. 2021 Cell reports Result SARS_CoV_2 E484D;R682W 34;91 39;96 RBD 64 67 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. To begin to decipher the mechanism(s) of SARS-CoV-2 entry into H522 cells, we performed infections in the presence of compounds that interfere with SARS-CoV-2 entry, including camostat mesylate (TMPRSS2 inhibitor), E64D (broad spectrum inhibitor of proteases, including endosomal cathepsins), bafilomycin A (inhibitor of vATPase), and apilimod (inhibitor of PIKfyve). 2021 Cell reports Result SARS_CoV_2 E64D 215 219 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Additionally, the mutation G446D compared to G446S and G446V shows a noteworthy effect on the binding affinity between RBD and ACE2. 2021 Virology Result SARS_CoV_2 G446D;G446S;G446V 27;45;55 32;50;60 RBD 119 122 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. All other 11 mutations (N501I, N501S, N501T, N501Y, Q493L, Q493H, A475V, L455F, G446S and K417R) were predicted to have a neutral effect on the protein function. 2021 Virology Result SARS_CoV_2 A475V;G446S;K417R;L455F;N501S;N501T;N501Y;Q493H;Q493L;N501I 66;80;90;73;31;38;45;59;52;24 71;85;95;78;36;43;50;64;57;29 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. All the 12 systems, RBD WT, RBD with single amino acid substitutions viz, K417R, Q493L, Q493H, N501I, and N501Y, RBD + ACE2 WT, RBD K417R + ACE2, RBD Q493L + ACE2, RBD Q493H + ACE2, RBD N501I + ACE2, RBD N501Y + ACE2, were simulated separately for 100 ns. 2021 Virology Result SARS_CoV_2 K417R;K417R;N501I;N501I;N501Y;N501Y;Q493H;Q493H;Q493L;Q493L 74;132;95;186;106;204;88;168;81;150 79;137;100;191;111;209;93;173;86;155 RBD;RBD;RBD;RBD;RBD;RBD;RBD;RBD 20;28;113;128;146;164;182;200 23;31;116;131;149;167;185;203 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Consistently, the variant K417N has the highest binding free energy (-51.25 kcal/mol) with a difference of -8.41 kcal/mol from the WT (-59.66 kcal/mol), resulting in the lowest binding affinity between the ACE2 and RBD complex. 2021 Virology Result SARS_CoV_2 K417N 26 31 RBD 215 218 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Contrarily, the variants N501T and Q493K do not have significant effect on the protein structure but change the binding free energy of the complex, with N501T increasing the binding affinity and Q493K decreasing the affinity of the complex. 2021 Virology Result SARS_CoV_2 N501T;N501T;Q493K;Q493K 25;153;35;195 30;158;40;200 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. For N501Y, the backbone RMSD fluctuated within a small range between 20 and 60 ns. 2021 Virology Result SARS_CoV_2 N501Y 4 9 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. For the K417R mutant system, the motion was observed in the core domain of RBD and the upper helical region of the ACE2 not involved in the RBD interaction. 2021 Virology Result SARS_CoV_2 K417R 8 13 RBD;RBD 75;140 78;143 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Hence, the binding free energy of the WT RBD-ACE2 complex increases from -59.66 kcal/mol to -55.95 kcal/mol for the mutant G446D RBD-ACE2 complex. 2021 Virology Result SARS_CoV_2 G446D 123 128 RBD;RBD 41;129 44;132 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. However, a slight fluctuation was observed in the RBD Q493L during the last 30ns of the simulation period. 2021 Virology Result SARS_CoV_2 Q493L 54 59 RBD 50 53 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. However, for N501Y, the directions were identical to the WT complex, but the RBM possessed large movements towards ACE2, indicating increased binding affinity. 2021 Virology Result SARS_CoV_2 N501Y 13 18 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. However, T when replaced with S at position 500 reduces the binding affinity between RBD and ACE2, whereas the variants L455F and A475V increase their binding affinity. 2021 Virology Result SARS_CoV_2 A475V;L455F 130;120 135;125 RBD;S 85;30 88;31 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. However, the maximum number of hydrogen bonds were observed in the case of the K417R mutant complex. 2021 Virology Result SARS_CoV_2 K417R 79 84 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. However, the other mutations N501T, N501I and N501S have the binding free energy -62.15, -61.69 and -61.04 kcal/mol, respectively. 2021 Virology Result SARS_CoV_2 N501I;N501S;N501T 36;46;29 41;51;34 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. However, there is a slight increase in the conformational space of the N501I and N501Y mutant complexes along PC1 suggesting that these mutations in the RBD may increase some flexibility in the ACE2-RBD complex. 2021 Virology Result SARS_CoV_2 N501I;N501Y 71;81 76;86 RBD;RBD 153;199 156;202 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. In the Q493H complex, the direction of RBM motion was towards ACE2, suggesting a higher binding affinity between them. 2021 Virology Result SARS_CoV_2 Q493H 7 12 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. On the other hand, N501I and N501Y complexes show higher magnitude of motion in both RBD and ACE2. 2021 Virology Result SARS_CoV_2 N501I;N501Y 19;29 24;34 RBD 85 88 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Only two point mutations, Y495F and G446V, were predicted to be deleterious by the consensus classifier. 2021 Virology Result SARS_CoV_2 G446V;Y495F 36;26 41;31 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Our simulation results confirmed the stability of the RBD structure as well as the ACE2 and RBD complexes for the mutations K417R, Q493H, Q493L, N501I and N501Y occurring in the SARS-CoV-2 S protein variants. 2021 Virology Result SARS_CoV_2 K417R;N501I;N501Y;Q493H;Q493L 124;145;155;131;138 129;150;160;136;143 RBD;RBD;S 54;92;189 57;95;190 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Similarly, the point mutations Q493L has DeltaDeltaG 0.66 kcal/mol and Q493H has the value 0.29 kcal/mol resulting in an increase in structural stability of the RBD. 2021 Virology Result SARS_CoV_2 Q493H;Q493L 71;31 76;36 RBD 161 164 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The K417R mutant of RBD has a much lower binding free energy for ACE2 interaction (-62.04 kcal/mol), and an increased number of contacts between the complex result in high binding affinity between the two proteins. 2021 Virology Result SARS_CoV_2 K417R 4 9 RBD 20 23 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The magnitude of motion in both Q493H and Q493L complexes was observed to be lower than the WT. 2021 Virology Result SARS_CoV_2 Q493H;Q493L 32;42 37;47 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The motion of WT ACE2-RBD complex and mutant complexes K417R, Q493H and Q493L shows a small conformational space in comparison to N501I and N501Y mutant complexes. 2021 Virology Result SARS_CoV_2 K417R;N501I;N501Y;Q493H;Q493L 55;130;140;62;72 60;135;145;67;77 RBD 22 25 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The mutant K417N has the next minimum DeltaDeltaG value. 2021 Virology Result SARS_CoV_2 K417N 11 16 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The mutant Q493L does not make any considerable change at the interface; rather, it interacts with H34 of ACE2 instead of E35. 2021 Virology Result SARS_CoV_2 Q493L 11 16 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The mutation at position G446 to G446D, G446S and G446V shows the maximum destabilizing effect on the RBD with DeltaDeltaG values, -4.12, -4.11 and -2.64 kcal/mol, respectively. 2021 Virology Result SARS_CoV_2 G446D;G446S;G446V 33;40;50 38;45;55 RBD 102 105 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The mutation N501Y has been found in several VOC strains of SARS-CoV-2 such as B.1.1.7, B.1.351 and P.1. 2021 Virology Result SARS_CoV_2 N501Y 13 18 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The mutation Y495F and G446V also reduced the RBD stability according to their DeltaDeltaG values predicted in the previous section. 2021 Virology Result SARS_CoV_2 G446V;Y495F 23;13 28;18 RBD 46 49 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The naturally occurring variants with change at residue position N501 to N501Y, N501S, N501I and N501T show neutral to stabilizing effect on the RBD structure. 2021 Virology Result SARS_CoV_2 N501I;N501S;N501T;N501Y 87;80;97;73 92;85;102;78 RBD 145 148 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The number of interface residues is 20 and 17 for ACE2 and RBD, respectively, which remains unchanged upon individually occurring point mutations N501I, N501Y, Q493L, Q493H, K417R in the RBM (Table S1). 2021 Virology Result SARS_CoV_2 K417R;N501I;N501Y;Q493H;Q493L 174;146;153;167;160 179;151;158;172;165 RBD 59 62 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The point mutation N501Y has a stabilizing effect on the RBD with DeltaDeltaG value 0.53 kcal/mol and result in the highest binding affinity between RBD and ACE2 (-67.86 kcal/mol). 2021 Virology Result SARS_CoV_2 N501Y 19 24 RBD;RBD 57;149 60;152 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The point mutations L455F, A475V and T500S have negligible destabilizing effect on the RBD structure with the DeltaDeltaG values -0.09, -0.17 and -0.15 kcal/mol, respectively. 2021 Virology Result SARS_CoV_2 A475V;L455F;T500S 27;20;37 32;25;42 RBD 87 90 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The RMSD for the WT complex and mutant complexes K417R, Q493H, Q493L and N501I was stable throughout the 100 ns simulation. 2021 Virology Result SARS_CoV_2 K417R;N501I;Q493H;Q493L 49;73;56;63 54;78;61;68 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The RMSD of WT RBD and the mutants K417R, Q493H, N501I, N501Y lies relatively in the same range and converges at the end with no significant deviations during the simulation. 2021 Virology Result SARS_CoV_2 K417R;N501I;N501Y;Q493H 35;49;56;42 40;54;61;47 RBD 15 18 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The S protein with RBD variants N501I, N501S, N501Y, Q493L, Q493H and K417R are predicted to increase RBD stability, ACE2 binding affinity and have no effect on its function. 2021 Virology Result SARS_CoV_2 K417R;N501I;N501S;N501Y;Q493H;Q493L 70;32;39;46;60;53 75;37;44;51;65;58 RBD;RBD;S 19;102;4 22;105;5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The single amino acid variation N501I and N501Y leads to an increased number of contacts at the hotspot-353. 2021 Virology Result SARS_CoV_2 N501I;N501Y 32;42 37;47 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The variant B.1.617 with RBD mutations E484Q and L452R in complex with ACE2 has the total binding free energy of -64.89 kcal/mol. 2021 Virology Result SARS_CoV_2 E484Q;L452R 39;49 44;54 RBD 25 28 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The variants with more negative binding free energy (high binding affinity) than the WT complex are N501Y, N501T, K417R, N501I, L455F, A475V, N501S, Y453F, Q493H, G446S, G446V, Q493L and Y495F. 2021 Virology Result SARS_CoV_2 A475V;G446S;G446V;K417R;L455F;N501I;N501S;N501T;N501Y;Q493H;Q493L;Y453F;Y495F 135;163;170;114;128;121;142;107;100;156;177;149;187 140;168;175;119;133;126;147;112;105;161;182;154;192 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The variation N501I also has the maximum DeltaDeltaG value 0.8 kcal/mol with highest stabilizing effect on the RBD. 2021 Virology Result SARS_CoV_2 N501I 14 19 RBD 111 114 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Thus, the mutations K417R, Q493H, Q493L, N501I and N501Y in the RBM increase the RBD stability and the ACE2 binding affinity. 2021 Virology Result SARS_CoV_2 K417R;N501I;N501Y;Q493H;Q493L 20;41;51;27;34 25;46;56;32;39 RBD 81 84 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. To understand the change in interface statistics between the WT RBD-ACE2 complex and the reported mutants (N501I, N501Y, Q493L, Q493H and K417R) we analyzed detailed molecular interactions of these complexes. 2021 Virology Result SARS_CoV_2 K417R;N501Y;Q493H;Q493L;N501I 138;114;128;121;107 143;119;133;126;112 RBD 64 67 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Whereas, the variant B.1.1.7 (N501Y and E484K) RBD-ACE2 complex has the binding free energy of -67.76 kcal/mol. 2021 Virology Result SARS_CoV_2 E484K;N501Y 40;30 45;35 RBD 47 50 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. As shown inFigure 3A , the neutralization ability of most of the convalescent sera against VOC-202012/01, D614G+69-70del+N439K and D614G+A222V was not changed (0.9, 1.3 and 1.3-fold compared to D614G, respectively). 2021 Frontiers in immunology Result SARS_CoV_2 D614G;D614G;D614G;A222V;N439K 106;131;194;137;121 111;136;199;142;126 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Furthermore, mAbs H00S022 and 2F7 lost most of their neutralizing activity against the D614G+69-70del+N439K and N439K+D614G variants. 2021 Frontiers in immunology Result SARS_CoV_2 D614G;N439K;D614G;N439K 87;112;118;102 92;117;123;107 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. In our assay, the mutations did not impact neutralization significantly ( Figure 3F ), whereas VOC-202012/01 showed a slight decrease (0.8-fold compared to D614G), which was similar to the RBD-elicited horse sera. 2021 Frontiers in immunology Result SARS_CoV_2 D614G 156 161 RBD 189 192 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Moreover, neutralization activity towards D614G+S477N did not decrease. 2021 Frontiers in immunology Result SARS_CoV_2 D614G;S477N 42;48 47;53 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Six of the 18 mAbs, including H00S022, 1F9, 10D12, 10F9, A247, and 11D12, displayed significantly reduced neutralizing activity against the VOC-202012/01 variant and variants carrying a single N501Y mutation ( Figure 2A ). 2021 Frontiers in immunology Result SARS_CoV_2 N501Y 193 198 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Structure modeling of the mutation N501Y in S1 and S982A in S2 was showed asFigure 2B . 2021 Frontiers in immunology Result SARS_CoV_2 N501Y;S982A 35;51 40;56 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. The convalescent sera showed somewhat increased neutralization activity against D614G+L18F+A222V (2.6-fold) and decreased neutralization activity against D614G+S477N (0.5-fold). 2021 Frontiers in immunology Result SARS_CoV_2 D614G;D614G;A222V;L18F;S477N 80;154;91;86;160 85;159;96;90;165 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. The results indicated that the N439K, S477N, and N501Y mutations in the RBD could affect the susceptibility of SARS-CoV-2 variants to neutralization. 2021 Frontiers in immunology Result SARS_CoV_2 N439K;N501Y;S477N 31;49;38 36;54;43 RBD 72 75 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. The S477N variant showed decreased susceptibility to mAb 7B8, but most of the other antibodies were still effective ( Figure 2AandSupplementary Figure 1 ). 2021 Frontiers in immunology Result SARS_CoV_2 S477N 4 9 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. The sera showed a slightly increased reaction to D614G+L18F+A222V and D614G+A222V, which was similar to the convalescent sera. 2021 Frontiers in immunology Result SARS_CoV_2 D614G;D614G;A222V;A222V;L18F 49;70;60;76;55 54;75;65;81;59 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. VOC-202012/01 showed slightly decreased neutralization by sera from both RBD protein-immunized mice and horses, whereas D614G+L18F+A222V and D614G+A222V did not show an increase of neutralization sensitivity. 2021 Frontiers in immunology Result SARS_CoV_2 D614G;D614G;A222V;A222V;L18F 120;141;131;147;126 125;146;136;152;130 RBD 73 76 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. Amongst all S protein mutations, D614G had the highest mutation frequency (94%). 2021 Virologica Sinica Result SARS_CoV_2 D614G 33 38 S 12 13 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. F61, F163, C25, H184 and B110 showed low sensitivity against single-residue variants with A475V and S477I. 2021 Virologica Sinica Result SARS_CoV_2 A475V;S477I 90;100 95;105 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. H121, C25, A8 were evaluated to have low potencies against Q414E. 2021 Virologica Sinica Result SARS_CoV_2 Q414E 59 64 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. In contrast, mutations in B.1.351 (D80A, D215G, 242-244del, R246I, K417N, E484K, N501Y, D614G, and A701V) had a much lower mutation frequency (0.2%). 2021 Virologica Sinica Result SARS_CoV_2 A701V;D215G;D614G;E484K;K417N;N501Y;R246I;D80A 99;41;88;74;67;81;60;35 104;46;93;79;72;86;65;39 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. Moreover, A199 exhibited a low sensitivity towards R246A and P384L. 2021 Virologica Sinica Result SARS_CoV_2 P384L;R246A 61;51 66;56 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. Mutation L452R in India epidemic strain B.1.617 showed no resistance to F61 and H121, but reduced the neutralization sensitivity of C25, A8, H184, and B110. 2021 Virologica Sinica Result SARS_CoV_2 L452R 9 14 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. Mutations in B.1.1.7 (including 69-70del, Y144del, N501Y, A570D, T716I, S982A, D1118H, and D614G) had a mutation frequency of around 5%. 2021 Virologica Sinica Result SARS_CoV_2 A570D;D1118H;D614G;N501Y;S982A;T716I;Y144del 58;79;91;51;72;65;42 63;85;96;56;77;70;49 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. Remarkably, F61 and F163 efficiently neutralized multiple mutations within RBD, including A475V and S477I which reduced the binding sensitivity of F61 and F163. 2021 Virologica Sinica Result SARS_CoV_2 A475V;S477I 90;100 95;105 RBD 75 78 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. While, antibodies H121, C25, H184 and B110 exhibited a low sensitivity towards N354K, A348T, and A435S. 2021 Virologica Sinica Result SARS_CoV_2 A348T;A435S;N354K 86;97;79 91;102;84 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. Based on D614G, other mutations existing in RBD are K417N/K417T, E484K, and N501Y which might affect the recognition and binding of SARS-CoV-2 to ACE2. 2021 MedComm Result SARS_CoV_2 D614G;E484K;K417N;K417T;N501Y;K417T 9;65;52;52;76;58 14;70;57;57;81;63 RBD 44 47 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. Consistent with other studies, the protective effect of serum from S1-WT-immunized mice against wild-type, D614G, B.1.1.7 pseudoviruses did not obviously change (Figures 5A, 5D, 5E and 5H), but the protective effect against B.1.351 and P.1 significantly decreased (Figures 5B and 5C). 2021 MedComm Result SARS_CoV_2 D614G 107 112 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. However, the neutralizing effect of serum from S1-WT group was impaired for pseudovirus with E484K mutation. 2021 MedComm Result SARS_CoV_2 E484K 93 98 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. Interestingly, the serum of S1-Mut group showed a better ability to inhibit RBD (E484K) than S1-WT group (Figure 3E). 2021 MedComm Result SARS_CoV_2 E484K 81 86 RBD 76 79 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. Nevertheless, S1-Mut protein showed a stronger neutralizing effect for E484K pseudovirus (Figure 5G). 2021 MedComm Result SARS_CoV_2 E484K 71 76 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. RBD-WT and RBD-Mut (K417N, E484K, N501Y) proteins were used for binding cell surface receptor ACE2. 2021 MedComm Result SARS_CoV_2 E484K;N501Y;K417N 27;34;20 32;39;25 RBD;RBD 0;11 3;14 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. RBD-WT, RBD-Mut (K417N, E484Kand N501Y), S1-WT, and S1-Mut (K417N, E484K, N501Y, and D614G) proteins were used as coated antigens for antibodies assay. 2021 MedComm Result SARS_CoV_2 D614G;E484K;N501Y;N501Y;K417N;K417N 85;67;33;74;17;60 90;72;38;79;22;65 RBD;RBD 0;8 3;11 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. The protective effect was not significantly different between sera from mice immunized with S1-WT or S1-Mut proteins against pseudovirus with N501Y (Figure 5F). 2021 MedComm Result SARS_CoV_2 N501Y 142 147 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. There was no significant difference in the ability to block RBD (K417N) and RBD (N501Y) between the two groups (Figures 3D and 3F). 2021 MedComm Result SARS_CoV_2 K417N;N501Y 65;81 70;86 RBD;RBD 60;76 63;79 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. Therefore, we chose S1-Mut which contains K417N, E484K, N501Y, and D614G to formulate the recombinant protein vaccine. 2021 MedComm Result SARS_CoV_2 D614G;E484K;K417N;N501Y 67;49;42;56 72;54;47;61 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. These findings demonstrated that immunization with S1-WT and S1-Mut proteins has a stronger blockade on RBD-WT and RBD-Mut, respectively, and suggested that the E484K mutation might play an essential role in the resistance of S1-WT. 2021 MedComm Result SARS_CoV_2 E484K 161 166 RBD;RBD 104;115 107;118 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. These findings suggest that S1-Mut protein could induce stronger protective immunity to block mutant viruses containing E484K mutation, such as B.1.351 and P.1. 2021 MedComm Result SARS_CoV_2 E484K 120 125 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. To figure out which single mutation could cause the phenomenon, we used three mutant RBD proteins, including RBD (K417N), RBD (E484K), and RBD (N501Y). 2021 MedComm Result SARS_CoV_2 E484K;K417N;N501Y 127;114;144 132;119;149 RBD;RBD;RBD;RBD 85;109;122;139 88;112;125;142 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. To further investigate the neutralizing effect of two spike proteins against other mutant pseudoviruses, wild-type, D614G, B.1.1.7, B.1.351, and P.1 pseudoviruses with luciferase-expressing were used. 2021 MedComm Result SARS_CoV_2 D614G 116 121 S 54 59 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. Among those mutants were S477N and E484K which exhibit resistance to multiple mAbs and are present in emerging variants of concern. 2021 Human vaccines & immunotherapeutics Result SARS_CoV_2 E484K;S477N 35;25 40;30 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. To examine whether this purified polyclonal human IgG could neutralize SARS-CoV-2, we performed a plaque reduction neutralization test assay using SARS-CoV-2 with the D614G (Munich strain) S substitution. 2021 Human vaccines & immunotherapeutics Result SARS_CoV_2 D614G 167 172 S 189 190 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. We also generated the dominant D614G, and the mouse adapted N501Y and E484K-N501Y variants. 2021 Human vaccines & immunotherapeutics Result SARS_CoV_2 D614G;E484K;N501Y;N501Y 31;70;60;76 36;75;65;81 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. We therefore tested whether the Tc-hIgG-SARS-CoV-2 also retains potency against a combination of substitutions E484K-N501Y in S. 2021 Human vaccines & immunotherapeutics Result SARS_CoV_2 E484K;N501Y 111;117 116;122 S 126 127 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. For both A.23.1 and Wuhan-Hu1 P681R particles, we detected increased cleavage of the spike protein compared to Wuhan-Hu1 (WT); see Figure 4. 2022 bioRxiv Result SARS_CoV_2 P681R 30 35 S 85 90 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. In this study, MLV pseudoparticles containing the A.23.1, Wuhan-Hu1 SARS-CoV-2 S protein (WT), and a P681R point mutant of Wuhan-Hu1 were also generated alongside positive control particles containing the vesicular stomatitis virus (VSV) G protein, along with negative control particles (Deltaenvpp) lacking envelope proteins (not shown), using the HEK293T cell line for particle production. 2022 bioRxiv Result SARS_CoV_2 P681R 101 106 S 79 80 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. We observed no difference in infection between pseudoparticles displaying spike protein from our P681R point mutant in Calu-3 cells and lowered infection on Vero E6 and Vero-TMPRSS2 cells. 2022 bioRxiv Result SARS_CoV_2 P681R 97 102 S 74 79 34234758 A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3' Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity. Previously, it has been shown that S477N slightly improves the folding of the Spike protein and the fitness of RBD-ACE2 binding and more flexibility in the NTD could help to bind ACE2 receptor. 2021 Frontiers in microbiology Result SARS_CoV_2 S477N 35 40 S;RBD 78;111 83;114 34234758 A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3' Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity. Regardless the fact that all genomes from B.1.1.7 lineage contain the Q27* variant, around 14% of these genomes contain another downstream stop codon, Q68* (Figure 3E), confirming that ORF8 is prone to accumulate non-sense variants and B.1.1.7 lineage transmits successfully without expression of ORF8. 2021 Frontiers in microbiology Result SARS_CoV_2 Q27X;Q68X 70;151 74;155 ORF8;ORF8 185;297 189;301 34234758 A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3' Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity. Taken together, non-neutral amino acid changes in SARS-CoV-2 can change viral protein motility and might confer improved fitness to the virus, as appears to be the case of the S477N variant. 2021 Frontiers in microbiology Result SARS_CoV_2 S477N 176 181 34234758 A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3' Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity. The A222V change is predicted to decrease the motility of the N-terminal of Spike protein (NTD), while the S477N and V1176F variants are predicted to increase the motility of the Receptor Binding Domain (RBD) and Stalk domain of the Spike protein, respectively (Figure 2E). 2021 Frontiers in microbiology Result SARS_CoV_2 A222V;S477N;V1176F 4;107;117 9;112;123 RBD;S;S;RBD;N 179;76;233;204;62 202;81;238;207;63 34234758 A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3' Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity. The emergent SARS-CoV-2 B.1.1.7 lineage in United Kingdom contained at least 21 non-synonymous substitutions including a stop codon in the ORF8 gene (Q27*, Figure 3E) and is constantly increasing its worldwide viral frequency in GISAID database since the beginning of November 30, 2020 until the time of writing of this manuscript. 2021 Frontiers in microbiology Result SARS_CoV_2 Q27X 150 154 ORF8 139 143 34234758 A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3' Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity. Two spike protein substitutions from European outbreaks containing Ala > Val (A222V, viral frequency = 17%) and Ser > Asn (S477N, viral frequency = 6.2%) including one Val > Phe substitution from a Brazilian outbreak (V1176F, viral frequency = 0.22%) readily changed Spike protein's free energy-based motility to varying extents. 2021 Frontiers in microbiology Result SARS_CoV_2 A222V;S477N;V1176F 78;123;218 83;128;224 S;S 4;267 9;272 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. However, since K417N is not present in the RBM, we did not further investigate this effect. 2022 Allergy Result SARS_CoV_2 K417N 15 20 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. In contrast, the introduction of a single E484K mutation in the RBD (RBDE484K) did not affect receptor affinity (shown in Figure 2D,F). 2022 Allergy Result SARS_CoV_2 E484K 42 47 RBD;RBD 64;69 67;72 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. In parallel, we have produced RBD of the isolate P.1 exhibiting RBD with three-point mutations (RBDTRIP) namely K417N, a lysine (K) to asparagine (N) at position 417, E484K, a glutamate (E) to lysine at position 484 and N501Y, an asparagine (N) to tyrosine (Y) at position 501, two of which are located in the RBM (E484K, N501Y; shown in Figure 1A). 2022 Allergy Result SARS_CoV_2 E484K;K417N;N501Y;N501Y;E484K 167;112;220;322;315 172;117;225;327;320 RBD;RBD 30;64 33;67 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. Interestingly, K417N mutation in the single RBD mutant (RBDK417N) resulted in completely altered binding properties (shown in Figure 2E). 2022 Allergy Result SARS_CoV_2 K417N 15 20 RBD;RBD 44;56 47;59 34241897 Genomic monitoring unveil the early detection of the SARS-CoV-2 B.1.351 (beta) variant (20H/501Y.V2) in Brazil. Finally, we characterize the P.2 VOI that was distinguished by five mutations: ORF1ab: C100U; Orf8: C28253U; nucleocapsid: G28628U, G28975U, and C29754U; and spike: G23012A (E484K). 2021 Journal of medical virology Result SARS_CoV_2 G23012A;E484K 165;174 172;179 N;ORF1ab;S;ORF8 109;79;158;94 121;85;163;98 34241897 Genomic monitoring unveil the early detection of the SARS-CoV-2 B.1.351 (beta) variant (20H/501Y.V2) in Brazil. However, a fact that draws attention is the rise of the A23403G (D614G) mutation being present in all samples. 2021 Journal of medical virology Result SARS_CoV_2 A23403G;D614G 56;65 63;70 34241897 Genomic monitoring unveil the early detection of the SARS-CoV-2 B.1.351 (beta) variant (20H/501Y.V2) in Brazil. P.1 defining mutations related to each genomic region were the following: ORF1ab: S1188L, K1795Q, E5665D; spike: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I; Orf8: E92K; and nucleocapsid: P80. 2021 Journal of medical virology Result SARS_CoV_2 D138Y;E484K;E5665D;E92K;H655Y;K1795Q;K417T;L18F;N501Y;P26S;R190S;S1188L;T1027I;T20N 131;152;98;187;166;90;145;113;159;125;138;82;173;119 136;157;104;191;171;96;150;117;164;129;143;88;179;123 N;ORF1ab;S;ORF8 197;74;106;181 209;80;111;185 34241897 Genomic monitoring unveil the early detection of the SARS-CoV-2 B.1.351 (beta) variant (20H/501Y.V2) in Brazil. The B.1.351 VOC was characterized by K417N, E484K, N501Y in the spike region and 19 mutations and 2 deletions as follows: ORF1ab: T265I, R724K, S1612L, K1655N, K3353R, SGF 3675_F3677del, P4715L, E5585D; spike: D80A, D215G, L242_L244del, A262D, D614G, C1247F; ORF3a: Q57H, S171L, E: P71L, ORF7b: Y10F, N: T205I, ORF14: L52F (Figure 1D). 2021 Journal of medical virology Result SARS_CoV_2 A262D;C1247F;D215G;D614G;D80A;E484K;E5585D;K1655N;K3353R;K417N;L52F;N501Y;P4715L;P71L;Q57H;R724K;S1612L;S171L;T205I;T265I;Y10F 237;251;216;244;210;44;195;152;160;37;318;51;187;282;266;137;144;272;304;130;295 242;257;221;249;214;49;201;158;166;42;322;56;193;286;270;142;150;277;309;135;299 ORF1ab;ORF7b;S;S;ORF3a;E;N 122;288;64;203;259;279;301 128;293;69;208;264;280;302 34241897 Genomic monitoring unveil the early detection of the SARS-CoV-2 B.1.351 (beta) variant (20H/501Y.V2) in Brazil. V1), was characterized by 14 mutations that define this isolate, 6 of which in spike (ORF1ab: C3267T, C5388A, T6954C; spike: A23063T, C23271A, C23604A, C23709T, T24506G, G24914C; Orf8: C27972T, G28048T, A28111G; nucleocapsid: C28977T). 2021 Journal of medical virology Result SARS_CoV_2 A23063T;A28111G;C23271A;C23604A;C23709T;C27972T;C28977T;C3267T;C5388A;G24914C;G28048T;T24506G;T6954C 125;203;134;143;152;185;226;94;102;170;194;161;110 132;210;141;150;159;192;233;100;108;177;201;168;116 N;ORF1ab;S;S;ORF8 212;86;79;118;179 224;92;84;123;183 34241897 Genomic monitoring unveil the early detection of the SARS-CoV-2 B.1.351 (beta) variant (20H/501Y.V2) in Brazil. We additionally observed the D614G mutation in the spike, as well as the mutation G25088T (V1176F). 2021 Journal of medical virology Result SARS_CoV_2 D614G;G25088T;V1176F 29;82;91 34;89;97 S 51 56 34241897 Genomic monitoring unveil the early detection of the SARS-CoV-2 B.1.351 (beta) variant (20H/501Y.V2) in Brazil. We also highlight the presence of the two mutations:D614G and V1176F:in the spike gene in all analyzed P.1 and P.2 variants of this study. 2021 Journal of medical virology Result SARS_CoV_2 V1176F;D614G 62;52 68;57 S 76 81 34242876 Energetic and structural basis for the differences in infectivity between the wild-type and mutant spike proteins of SARS-CoV-2 in the Mexican population. Analysis of the key residues for the three systems pointed out a higher degree of similarity between S-proteinWT-ACE2 and S-proteinH49Y-ACE2 complexes with respect to S-proteinD614G-ACE2, indicating a more significant impact of D614G substitution in the stabilization of the protein-protein interface. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 D614G 228 233 S;S;S 101;122;167 102;123;168 34242876 Energetic and structural basis for the differences in infectivity between the wild-type and mutant spike proteins of SARS-CoV-2 in the Mexican population. Analysis of the map of interactions among the three systems shows that primarily D614G impacted the map of interactions at the protein-protein interface compared with S-proteinWT-ACE2 and S-proteinH49Y-ACE2 complexes. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 D614G 81 86 S;S 167;188 168;189 34242876 Energetic and structural basis for the differences in infectivity between the wild-type and mutant spike proteins of SARS-CoV-2 in the Mexican population. Comparison among the number of interactions for the three systems suggests a higher affinity for the S-proteinWT-ACE2 and S-proteinH49Y-ACE2 complexes compared with the S-proteinD614G-ACE2 complex. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 D614G 178 183 S;S;S 101;122;169 102;123;170 34242876 Energetic and structural basis for the differences in infectivity between the wild-type and mutant spike proteins of SARS-CoV-2 in the Mexican population. Henceforth, altered SARS-CoV-2 spike conformation and enhanced protease cleavage at the S1/S2 Junction was found due to D614G mutation that results in increased fitness and transmissibility of D614G isolates. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 D614G;D614G 120;193 125;198 S 31 36 34242876 Energetic and structural basis for the differences in infectivity between the wild-type and mutant spike proteins of SARS-CoV-2 in the Mexican population. However, considering the standard deviations of DeltaGbind values of S-proteinD614G-ACE2 and S-proteinWT-ACE2 indicates an overlap of both binding free energy values, indicating that D614G mutation does not impact importantly the binding free energy with respect to S-proteinWT-ACE2 system. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 D614G 183 188 S;S;S 69;93;266 70;94;267 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. Consistent with binding analysis, P22A-1D1, P5A-3C8 and P2C-1F11 remain sensitive to K417R pseudovirus, except P5A-1D2 had neutralizing activity below the detection limit (BDL) even when tested at the highest concentration (1 mug/mL). 2021 Nature communications Result SARS_CoV_2 K417R 85 90 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. Except that of P2C-1F11 where 4.4-fold increase was found, binding to mutant K417R RBD among the rest public antibodies was similar to that of WT, likely due to the similar positive-charged side chains between residue K and R. 2021 Nature communications Result SARS_CoV_2 K417R 77 82 RBD 83 86 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. For example, Y421A and F456A have broad impact on all four public antibodies, whereas T415A, Y473A, and N487A on three of the four. 2021 Nature communications Result SARS_CoV_2 F456A;N487A;T415A;Y421A;Y473A 23;104;86;13;93 28;109;91;18;98 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. In contrast, K417A/E/N/T mutants substantially reduced binding by P22A-1D1 and P5A-1D2, while impact on P5A-3C8 and P2C-1F11 was relatively moderate. 2021 Nature communications Result SARS_CoV_2 K417A;K417E;K417N;K417T 13;13;13;13 24;24;24;24 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. K417A/E/N/T mutants resulted in complete resistance to P5A-3C8, P22A-1D1, and P5A-1D2 while remaining sensitive to P2C-1F11. 2021 Nature communications Result SARS_CoV_2 K417A;K417E;K417N;K417T 0;0;0;0 11;11;11;11 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. K417A/E/N/T mutations disrupted these salt bridges, leading to loss of neutralizing activity. 2021 Nature communications Result SARS_CoV_2 K417A;K417E;K417N;K417T 0;0;0;0 11;11;11;11 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. Of note, K417N/T mutation has been recently identified in the SA501Y.V2 (B.1.351) variant from South Africa and in BR501Y.V3 (P.1) from Brazil and found capable of substantially reducing antibody and vaccine efficacy including those already approved for emergence use. 2021 Nature communications Result SARS_CoV_2 K417N;K417T 9;9 16;16 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. On the other hand, K417A, D420A, L455A, R457A, N460A, and Y489A only reduced binding for two of the four antibodies. 2021 Nature communications Result SARS_CoV_2 D420A;K417A;L455A;N460A;R457A;Y489A 26;19;33;47;40;58 31;24;38;52;45;63 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. Sequence analysis of the resistant strains from the highest antibody concentration identified K417N and K417T mutations in P22A-1D1-treated wells and K417T mutation in P5A-3C8-treated wells, all of which were present in 20 out of the 20 clones analyzed. 2021 Nature communications Result SARS_CoV_2 K417N;K417T;K417T 94;104;150 99;109;155 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. These residues are highlighted in orange boxes including T415A, Y421A, L455A, F456A, R457A, Y473A, N487A, Y489A, and Y505A. 2021 Nature communications Result SARS_CoV_2 F456A;L455A;N487A;R457A;T415A;Y421A;Y473A;Y489A;Y505A 78;71;99;85;57;64;92;106;117 83;76;104;90;62;69;97;111;122 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. Through analysis of a total of 1,234,882 unique genome sequences in GISAID database (by May 17th, 2021), we found that 5,992 sequences bearing the K417N mutation, 11,734 sequences containing K417T mutation, 20 sequences with K417R mutation, and 3 sequences with K417E mutation (https://cov.lanl.gov/content/index, ), indicating residue at 417 is highly variable and likely under strong immune selection. 2021 Nature communications Result SARS_CoV_2 K417E;K417N;K417R;K417T 262;147;225;191 267;152;230;196 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. We then constructed pseudovirus bearing each of the K417R, K417A, K417E, K417N, or K417T mutation and analyzed their neutralizing sensitivity to the public antibodies. 2021 Nature communications Result SARS_CoV_2 K417A;K417E;K417N;K417R;K417T 59;66;73;52;83 64;71;78;57;88 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. We then produced mutant RBDs containing each of the K417R/A/E/N/T and tested their binding affinities to public antibodies and ACE2. 2021 Nature communications Result SARS_CoV_2 K417A;K417E;K417N;K417R;K417T 52;52;52;52;52 65;65;65;65;65 RBD 24 28 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. Y505A appears to have more profound impact on P22A-1D1 than the rest three antibodies. 2021 Nature communications Result SARS_CoV_2 Y505A 0 5 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. After nonsignificantly correlated features (p > 0.001) were filtered out, the logit of the death event can be predicted based on the following features: three SNVs enriched in death group, including G25088T(S:V1176F), T27484C (ORF7a:L31L), and T25A (upstream of ORF1ab), three age groups above 40 years old, as well as the gender male in the way that where stands for the ith feature (either 1 or 0). 2021 Journal of medical virology Result SARS_CoV_2 G25088T;T25A;T27484C;L31L;V1176F 199;244;218;233;209 206;248;225;237;215 ORF1ab;ORF7a;S 262;227;207 268;232;208 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. All of them were enriched in the male and nondeath groups but in different age groups, for example, C5700A (nsp3:A994D) and G21724T (S:L54F) were over-represented in the group under 20 and 40-59, respectively, while the other five SNVs tended to be in the group of 20-39 years old. 2021 Journal of medical virology Result SARS_CoV_2 C5700A;G21724T;A994D;L54F 100;124;113;135 106;131;118;139 Nsp3;S 108;133 112;134 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Although C27944T on ORF8 is a synonymous mutation, it falls in a stem-loop structure of ORF8 messenger RNA which may influence ORF8 translation. 2021 Journal of medical virology Result SARS_CoV_2 C27944T 9 16 ORF8;ORF8;ORF8 20;88;127 24;92;131 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Another mutation C21614T (S:L18F) in the emerging group A.E3 SNV is located in N-linked glycan sites, which likely play a role in protein folding and immune evasion and may have implications in viral virulence and vaccine design. 2021 Journal of medical virology Result SARS_CoV_2 C21614T;L18F 17;28 24;32 N;S 79;26 80;27 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. For example, group A.E1 included four other synonymous mutations (G21255C, T445C, C6286T, and C26801G), and three nonsynonymous mutations, C22227T (S:A222V), G29645T (ORF10:V30L), C28932T (N:A220V), on proteins S, N, and ORF10, respectively. 2021 Journal of medical virology Result SARS_CoV_2 C22227T;C26801G;C28932T;C6286T;G29645T;T445C;G21255C;A220V;A222V;V30L 139;94;180;82;158;75;66;191;150;173 146;101;187;88;165;80;73;196;155;177 N;N;S;S 189;214;148;211 190;215;149;212 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. For example, N: A220V was located at the bottom of a pocket. 2021 Journal of medical virology Result SARS_CoV_2 A220V 16 21 N 13 14 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. For example, the mutation on nsp7:L71F (C12053T) might clash with D66 (Figure 4E), in addition to nsp14:A320V (C18998T) with V381 (Figure 4F), ORF3a:S253P (T26149C) with I249, nsp12:V354A (T14501C) with V299 and L351, and nsp7:S25L (C11916T) with L28. 2021 Journal of medical virology Result SARS_CoV_2 C11916T;C12053T;C18998T;T14501C;T26149C;A320V;L71F;S253P;S25L;V354A 233;40;111;189;156;104;34;149;227;182 240;47;118;196;163;109;38;154;231;187 ORF3a;Nsp12;Nsp7;Nsp7 143;176;29;222 148;181;33;226 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Four SNVs in groups A.E1-A.E3 are nonsynonymous variants, including ORF10:V30L (G29645T), N:A220V (C28923T), and two on S protein, A222V (C22227T) and L18F (C21614T) (Figure 1A). 2021 Journal of medical virology Result SARS_CoV_2 A222V;L18F;C21614T;C22227T;C28923T;G29645T;A220V;V30L 131;151;157;138;99;80;92;74 136;155;164;145;106;87;97;78 N;S 90;120 91;121 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. In group A.E2, synonymous SNV C27944T (ORF8:H17H) was detected in China in January 2020 for the first time, whereas the other one G204T located upstream of ORF1ab was identified in the United States in March 2020. 2021 Journal of medical virology Result SARS_CoV_2 C27944T;G204T;H17H 30;130;44 37;135;48 ORF1ab;ORF8 156;39 162;43 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. In other words, at least two or more major features together are expected to remarkably increase the death probability, for example, aged people with mutation T27484C may have a 91% probability of death given such a linear combination of the predictors. 2021 Journal of medical virology Result SARS_CoV_2 T27484C 159 166 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Interestingly, mutation S:V1176F (G25088T) was in the loop structure of two alpha-helix in the C-terminal of S (Figure 4G), causing increased mass. 2021 Journal of medical virology Result SARS_CoV_2 G25088T;V1176F 34;26 41;32 S;S 24;109 25;110 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. It has been reported that G22992A (S:S477N) was in the S protein receptor-binding domain (RBD), which is a flexible and disordered loop in the unbound state but later becomes ordered in all the available ACE2-bound SARS-CoV-2 S structures. 2021 Journal of medical virology Result SARS_CoV_2 G22992A;S477N 26;37 33;42 RBD;S;S;S 90;35;55;226 93;36;56;227 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. It is not surprising to see that group A of SNVs has prevailed since June 2020, represented by A23403G (S:D614G) and C14408T (OFR1ab:P4715L). 2021 Journal of medical virology Result SARS_CoV_2 A23403G;C14408T;D614G;P4715L 95;117;106;133 102;124;111;139 S 104 105 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Meanwhile, Group B (T28144C, n = 199) and Group D (G1440A/G2891 A, n = 7) nearly diminished in newly collected SARS-CoV-2 genomes. 2021 Journal of medical virology Result SARS_CoV_2 G1440A;T28144C 51;20 57;27 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Only 4 SNVs, including G21724T (S:L54F), C27046T (M:T175M), C2836T (nsp3:C39C), and C22444T (S:D294D), were notably enriched in the age between 40 and 59, even though this group had second largest population. 2021 Journal of medical virology Result SARS_CoV_2 C22444T;C27046T;C2836T;G21724T;C39C;D294D;L54F;T175M 84;41;60;23;73;95;34;52 91;48;66;30;77;100;38;57 Nsp3;S;S 68;32;93 72;33;94 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Other mutations in IDRs of S, for example, C21575T (L5F), G25049T (D1163Y), G25062T (G1167V), are located nearby N-linked glycan sites (11, 1, and 5 residues, respectively). 2021 Journal of medical virology Result SARS_CoV_2 C21575T;G25049T;G25062T;D1163Y;G1167V;L5F 43;58;76;67;85;52 50;65;83;73;91;55 N;S 113;27 114;28 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. S:L18F was found lurking in humans since February 2020 in England. 2021 Journal of medical virology Result SARS_CoV_2 L18F 2 6 S 0 1 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Seven SNVs were identified in all three groups, C5700A (nsp3:A994D), C6312A (nsp3:T1198K), C13730T (nsp12:A97V), C23929T (S:Y789Y), C28311T (ORF9:P13L), C19524T (nsp14:L495L), and G21724T (S:L54F). 2021 Journal of medical virology Result SARS_CoV_2 C13730T;C19524T;C23929T;C28311T;C5700A;C6312A;G21724T;A97V;A994D;L495L;L54F;P13L;T1198K;Y789Y 91;153;113;132;48;69;180;106;61;168;191;146;82;124 98;160;120;139;54;75;187;110;66;173;195;150;88;129 Nsp12;Nsp3;Nsp3;ORF9;S;S 100;56;77;141;122;189 105;60;81;145;123;190 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Ten SNVs were specific to the age and mortality but independent of the gender, including G25088T (S:V1176F), C12053T (nsp7:L71F), C11916T (nsp7:S25L), C18998T (nsp14:A320V), and G29540A which were enriched in the death group as well as in aged groups from 60 to 79 and at least 80-year-old. 2021 Journal of medical virology Result SARS_CoV_2 C11916T;C12053T;C18998T;G25088T;G29540A;A320V;L71F;S25L;V1176F 130;109;151;89;178;166;123;144;100 137;116;158;96;185;171;127;148;106 Nsp7;Nsp7;S 118;139;98 122;143;99 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. The group C featured by SNVs G11083T and G26144T disappeared, being detected in only 53 genomes after June 2020. 2021 Journal of medical virology Result SARS_CoV_2 G11083T;G26144T 29;41 36;48 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. The origin of S:A924A can be traced back to Japan in March 2020. 2021 Journal of medical virology Result SARS_CoV_2 A924A 16 21 S 14 15 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. There were another three SNVs specific to males with a strong connection to the mortality, G11083T (nsp6:L37F), G28878A (ORF9:S202N), and G22468T (S:T302T), which all were enriched in the nondeath group. 2021 Journal of medical virology Result SARS_CoV_2 G11083T;G22468T;G28878A;L37F;S202N;T302T 91;138;112;105;126;149 98;145;119;109;131;154 Nsp6;ORF9;S 100;121;147 104;125;148 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. This SNV group encompassed over 99% of genomes that harbored at least one of 52 SNVs, confirming continuity of variant D614G on S protein. 2021 Journal of medical virology Result SARS_CoV_2 D614G 119 124 S 128 129 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Twenty-seven SNVs were enriched across two groups of different ages (Figure 2B), for instance, three consecutive SNVs at 28881-28883 were enriched in the population younger than 40 years old, while C12053T (ORF1ab:L3930F) and several other SNVs preferred in the group older than 60. 2021 Journal of medical virology Result SARS_CoV_2 C12053T;L3930F 198;214 205;220 ORF1ab 207 213 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Two more SNVs on S, C21614T (S:L18F) and C24334T (S:A924A), were identified in group A.E3. 2021 Journal of medical virology Result SARS_CoV_2 C21614T;C24334T;A924A;L18F 20;41;52;31 27;48;57;35 S;S;S 17;29;50 18;30;51 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. Due to 11083G > T mutation, the clustering of taxa on viral phylogenies was obvious with spatially structured host population between all these subgroups (50%; 14/28. 2021 Bulletin of the World Health Organization Result SARS_CoV_2 G11083T 7 17 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. For the nucleocapsid phosphoprotein, we found mutations in the RNA binding domain (P46S) and the arginine-serine domain (G215S). 2021 Bulletin of the World Health Organization Result SARS_CoV_2 G215S;P46S 121;83 126;87 N 8 20 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. For the spike protein, two mutations, F157L and G181V, were identified. 2021 Bulletin of the World Health Organization Result SARS_CoV_2 F157L;G181V 38;48 43;53 S 8 13 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. In the other NSPs, we detected two mutations: A3070V in NSP4 and L3829F in NSP6. 2021 Bulletin of the World Health Organization Result SARS_CoV_2 A3070V;L3829F 46;65 52;71 Nsp4;Nsp6 56;75 60;79 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. In three samples, we found two mutations, 29736G > T and 29751G > T in the stem loop-II motif. 2021 Bulletin of the World Health Organization Result SARS_CoV_2 G29736T;G29751T 42;57 52;67 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. One hypothesis is that RNA recombination occurred in these cases to gain the 11083G > T mutation. 2021 Bulletin of the World Health Organization Result SARS_CoV_2 G11083T 77 87 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. Only variant /USA/CruiseA-14/ had two mutations, T2124I and L3829F in NSP3 and NSP6, respectively (Table 1). 2021 Bulletin of the World Health Organization Result SARS_CoV_2 L3829F;T2124I 60;49 66;55 Nsp3;Nsp6 70;79 74;83 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. Second, the nonsynonymous mutation 11083G > T was found in USA-AZ1 (EPI_ISL_406223) on 22 January. 2021 Bulletin of the World Health Organization Result SARS_CoV_2 G11083T 35 45 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. Seven samples contain the 11083G > T mutation although they belong to different subgroups. 2021 Bulletin of the World Health Organization Result SARS_CoV_2 G11083T 26 36 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. The analysis revealed two possibilities of the viral origin: either the virus (except hCoV-19/USA/CruiseA-18/2020) originated from a single primary case with the WIV04 sequence and all substitution mutations occurred during the quarantine; or there were two simultaneously primary cases, one identical to the WIV04 sequence and one containing the 11083G > T substitution. 2021 Bulletin of the World Health Organization Result SARS_CoV_2 G11083T 347 357 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. This result supports the hypothesis that 11083G > T mutation had been gained via RNA recombination in these four variants. 2021 Bulletin of the World Health Organization Result SARS_CoV_2 G11083T 41 51 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. To determine whether four variants from different subgroups (samples /USA/CruiseA-23/, /USA/CruiseA-24/, /Japan/TK/20-31-3/2020 and /Japan/Hu_DP_Kng_19-027/2020) obtained the G11083 > T mutation via RNA recombination, we analysed the patterns of linkage disequilibrium between variants with minor alleles of two SARS-CoV-2 variants (available in the data repository). 2021 Bulletin of the World Health Organization Result SARS_CoV_2 G11083T 175 185 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. We detected the mutations 11083G > T and 26326 C > T, present in the UPHL-01 sequence, in the two variants: /USA/CruiseA-6/ and /USA/CruiseA-7. 2021 Bulletin of the World Health Organization Result SARS_CoV_2 G11083T;C26326T 26;41 36;52 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. We found five missense variants in NSP3: T945I; Q998H; P1158S in the macro domain; K1860N in papain-like protease; and T2124I in the group 2 marker domain. 2021 Bulletin of the World Health Organization Result SARS_CoV_2 K1860N;P1158S;Q998H;T2124I;T945I 83;55;48;119;41 89;61;53;125;46 Nsp3 35 39 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. We identified five subgroups after rooting the phylogenetic tree with an outgroup virus sequence of SARS-WIV16: (i) 3099C > T and 28378G > T (two samples); (ii) 11083G > T (three samples); (iii) 11410G > A and 26326C > T (two samples); (iv) 29635C > T (four samples); and (v) 29736G > T (three samples. 2021 Bulletin of the World Health Organization Result SARS_CoV_2 G11083T;G11410A;C26326T;G28378T;C29635T;G29736T;C3099T 161;195;210;130;241;276;116 171;205;220;140;251;286;125 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. Whether the single 11083G > T substitution spontaneously occurred during the quarantine or the patients had been infected with a viral variant containing this mutation before boarding the ship is unclear. 2021 Bulletin of the World Health Organization Result SARS_CoV_2 G11083T 19 29 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. A new variant, termed Cluster 5, with two additional amino acid substitutions, i.e., I692V downstream of the transmembrane protease serine 2 (TMPRSS2)/furin cleavage site and M1229I within the transmembrane domain, was identified in September 2020 on 5 mink farms and in 12 human cases (age: 7-79 years; symptoms: asymptomatic to mild). 2021 Frontiers in microbiology Result SARS_CoV_2 I692V;M1229I 85;175 90;181 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. A two-amino acid residue deletion (DeltaH69/V70) in the N-terminal domain appeared together with the Y453F in August 2020 and occurred in the subsequent Clusters 2, 3, and 4 (Figure 1). 2021 Frontiers in microbiology Result SARS_CoV_2 Y453F 101 106 N 56 57 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. Of these, three amino acid substitutions (Y453F, I692V, and M1229I) and a two amino acid deletion (DeltaH69/V70) occur in the spike protein (Figure 1C and Supplementary Figure 1 relative to circulating variants of concern). 2021 Frontiers in microbiology Result SARS_CoV_2 I692V;M1229I;Y453F 49;60;42 54;66;47 S 126 131 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. The receptor binding domain (RBD) substitution Y453F, also observed among Dutch farmed mink, appeared in the first transmission Cluster in June (Cluster 1; Figure 1). 2021 Frontiers in microbiology Result SARS_CoV_2 Y453F 47 52 RBD;RBD 4;29 27;32 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. By contrast, DeltaH cal for the H41D and H41E variants increased to 162 +- 21 and 222 +- 9 kJ/mol, respectively. 2021 Frontiers in chemistry Result SARS_CoV_2 H41D;H41E 32;41 36;45 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. For the H41A variant, the thermographic peak shifted to a lower T m value and the calorimetric enthalpy (DeltaH cal) of unfolding decreased 3-fold, from 104 +- 4 kJ/mol for the WT enzyme to 32 +- 1 kJ/mol for the H41A variant (Figure 5C). 2021 Frontiers in chemistry Result SARS_CoV_2 H41A;H41A 8;213 12;217 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. Further, Cys145 was substituted with serine, as in the catalytic triad of serine proteases in which serine acts as a nucleophile during catalysis. 2021 Frontiers in chemistry Result SARS_CoV_2 C145S 9 43 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. However, serine substitution of Cys145 did not allow for the catalytic activity of 3CLpro (Figure 2B). 2021 Frontiers in chemistry Result SARS_CoV_2 C145S 9 38 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. However, smaller decrease in the T m of Cys145 mutants was observed upon increasing the enzyme concentration with a drop of 2.6 and 4.3 C in the T m of C145A and C145S mutants, respectively. 2021 Frontiers in chemistry Result SARS_CoV_2 C145A;C145S 152;162 157;167 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. However, the H41D and H41E variants did not exhibit any activity even at high enzyme concentration tested (5.0 muM; Figure 2B), and neither variant complemented the role of His41 in the catalytic mechanism. 2021 Frontiers in chemistry Result SARS_CoV_2 H41D;H41E 13;22 17;26 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. However, the largest drop, of 5.3 C, in T m was observed for the C145S variant (T m of 42.7 +- 0.3 C). 2021 Frontiers in chemistry Result SARS_CoV_2 C145S 65 70 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. Overall, with the exception of the C145A variant, the late peak corresponding to the monomeric state of 3CLpro disappeared in the gel filtration profiles of all His41 and Cys145 variants, which exhibited the same dimeric peak. 2021 Frontiers in chemistry Result SARS_CoV_2 C145A 35 40 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. Similarly, the thermal ability decreased for variants at His41 with a decrease of 6.4 C was observed with H41A mutant and ~9.0 C for H41D and H41E mutants (Figure 6). 2021 Frontiers in chemistry Result SARS_CoV_2 H41A;H41D;H41E 106;133;142 110;137;146 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. T m decreased from 46.8 +- 0.1 C (WT) to 44.7 +- 0.6, 44.0 +- 0.1, and 42.2 +- 0.5 C, for the H41A, H41D, and C145S variants, respectively (Figure 5B). 2021 Frontiers in chemistry Result SARS_CoV_2 C145S;H41A;H41D 110;94;100 115;98;104 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. T m of the H41E variant was not affected. 2021 Frontiers in chemistry Result SARS_CoV_2 H41E 11 15 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. T m of the H41E variant was unchanged relative to the WT and increased to 48.2 +- 0.1 C for the C145A variant, in close agreement with what was observed using DSF. 2021 Frontiers in chemistry Result SARS_CoV_2 C145A;H41E 96;11 101;15 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. The C145S variant had the most interesting DSC profile, with the highest drop in the T m value (4.6 C) and the highest increase in the DeltaH cal value (119 +- 1 kJ/mol) among all variants tested (Figures 5B,C). 2021 Frontiers in chemistry Result SARS_CoV_2 C145S 4 9 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. The DeltaH cal values decreased 2-fold for the C145A variant, to 56 +- 4 kJ/mol; however, DeltaH cal increased 2-fold for the C145S variant, to 223 +- 1 kJ/mol (Figure 5C). 2021 Frontiers in chemistry Result SARS_CoV_2 C145A;C145S 47;126 52;131 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. The gel filtration profile of the C145S variant was similar to that of the His41 variants and the WT, with a single dimeric peak; however, the size of the single peak of the C145A variant was greater than that of the dimeric peak of the WT. 2021 Frontiers in chemistry Result SARS_CoV_2 C145A;C145S 174;34 179;39 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. The highest increase in the DeltaH cal value was observed for the H41E and C145S variants even though T m of the former was not changed relative to the WT. 2021 Frontiers in chemistry Result SARS_CoV_2 C145S;H41E 75;66 80;70 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. The introduction of alternative side chains at His41 decreased T m from 48 +- 0.1 C, for the WT enzyme, to 45.2 +- 0.2 and 43.9 +- 0.1 C for the H41A and H41D variants, respectively (Figure 4B). 2021 Frontiers in chemistry Result SARS_CoV_2 H41A;H41D 145;154 149;158 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. The only small increase in the 3CLpro stability was observed for the C145A variant (T m of 48.8 +- 0.2 C). 2021 Frontiers in chemistry Result SARS_CoV_2 C145A 69 74 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Although similarities in the overall trend of neutralization compared to the WT emerged (Supplemental Figure 4A), the much lower relative IC50 values obtained in comparison with the competitive assay performed in parallel (Figure 4D) appreciably reduced the resolution of the differences in the neutralizing response between variants, in particular to N501Y, to which all mAbs demonstrated an attenuated neutralizing response in the competitive assay (Figure 4B). 2021 JCI insight Result SARS_CoV_2 N501Y 352 357 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. As shown in Figure 5A, most subjects demonstrated a reduction in the inhibition of most RBD variants, with the neutralizing response to variant N501Y being the most significantly attenuated, with many subjects demonstrating a ratio of less than 0.5 to that observed with the WT (Figure 5B), equating to over a 2-fold decrease in percentage inhibition to variant N501Y compared with the WT. 2021 JCI insight Result SARS_CoV_2 N501Y;N501Y 144;362 149;367 RBD 88 91 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Based on the relative EC50 values observed in our multiplex assay, we selected these high -affinity variants, and the emerging N439K variant present in currently circulating lineage B.1.258, as well as E484K, which is a mutation shared by B.1.351, B.1.525, and P.1 lineages, to be profiled and compared for their binding kinetics to ACE2 using bio-layer interferometry (BLI). 2021 JCI insight Result SARS_CoV_2 E484K;N439K 202;127 207;132 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. BLI profiles of the RBD variants binding to ACE2 (Figure 3E) showed that indeed variant N501Y demonstrated an enhanced affinity for the ACE2 receptor, with an almost 5-fold increase in affinity (KD 6.4 nM vs. 2021 JCI insight Result SARS_CoV_2 N501Y 88 93 RBD 20 23 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. C002 demonstrated escape from variants E484A, E484K, E484Q, and Q493L. 2021 JCI insight Result SARS_CoV_2 E484A;E484K;E484Q;Q493L 39;46;53;64 44;51;58;69 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Confirming multiplex ACE2 EC50 assay observations, variants E484K and E484D demonstrated reduced affinity to ACE2 (KD 37.2 nM and KD 110.8 nM, respectively). 2021 JCI insight Result SARS_CoV_2 E484D;E484K 70;60 75;65 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. COVA2-15 and C135 demonstrated escape to G446V, while COVA2-15 demonstrated a loss of binding and inhibition to S494P. 2021 JCI insight Result SARS_CoV_2 G446V;S494P 41;112 46;117 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Figure 3A illustrates the position of these variants on the RBD, and Figure 3B displays the more recently observed frequency of these variants according to the GISAID repository, with variant N501Y, currently the most frequent RBD variant worldwide (a key mutation present in the newly emergent B.1.1.7, B.1.351, B.1.1.70, and P.1 strains). 2021 JCI insight Result SARS_CoV_2 N501Y 192 197 RBD;RBD 60;227 63;230 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Figure 5C illustrates the percentage of patients who had a neutralizing response (i.e., >20%) to each RBD variant, with the lowest proportion of responders observed to occur to high-affinity variants N501Y (30%) and Q493L (35%). 2021 JCI insight Result SARS_CoV_2 N501Y;Q493L 200;216 205;221 RBD 102 105 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Furthermore, N501Y demonstrated an overall reduction in its ability to be inhibited across all mAbs as demonstrated by significantly weaker relative IC50 values, compared with the WT (Figure 4C), despite all mAbs having the capacity to bind RBD variant N501Y with relatively high affinity (Figure 4A). 2021 JCI insight Result SARS_CoV_2 N501Y;N501Y 13;253 18;258 RBD 241 244 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. However, likely due to the enhanced affinity of N501Y to ACE2, polyclonal convalescent plasma demonstrated a reduced ability to inhibit the ACE2-RBD interaction (Figure 5, A and B) to this variant. 2021 JCI insight Result SARS_CoV_2 N501Y 48 53 RBD 145 148 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. In addition, 1 variant that showed a reduced affinity for ACE2 (E484D) was selected to be profiled for comparison. 2021 JCI insight Result SARS_CoV_2 E484D 64 69 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. N439K and S494P had weakly enhanced overall affinity for ACE2, KD 25.2 nM and 26.1 nM, respectively, compared to the WT RBD (29.4 nM). 2021 JCI insight Result SARS_CoV_2 S494P;N439K 10;0 15;5 RBD 120 123 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Similar to the findings observed with the panel of mAbs, many convalescent plasma samples were able to bind the N501Y mutant with similar affinity to WT (Supplemental Figure 6). 2021 JCI insight Result SARS_CoV_2 N501Y 112 117 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. The enhanced affinity of N439K was the result of the almost 1.5-fold slower off rate, t1/2 111.3 s (kdis 0.00620 1/s) versus t1/2 83.7 s (kdis 0.00825 1/s) of the WT. 2021 JCI insight Result SARS_CoV_2 N439K 25 30 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. The sequence of reagent addition was also tested in a cell-based live virus microneutralization assay (Figure 4E), with preincubation of WT (VIC/01) or B.1.1.7 (RBD N501Y variant) virus and antibody compared to a competitive (combined) approach where virus and mAb were added together into the plate with ACE2-expressing cells. 2021 JCI insight Result SARS_CoV_2 N501Y 165 170 RBD 161 164 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. These samples were collected early in the pandemic (March-April 2020), before the detection of the N501Y variant in Australia. 2021 JCI insight Result SARS_CoV_2 N501Y 99 104 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. These were N501Y, Q493L, S494P, and S477N, which demonstrated the lowest overall relative EC50 values (0.2, 3.6, 6.3, and 8.3 mug/mL, respectively) as determined by our ACE2-RBD multiplex assay (Figure 3C). 2021 JCI insight Result SARS_CoV_2 N501Y;Q493L;S477N;S494P 11;18;36;25 16;23;41;30 RBD 174 177 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. This included the RBD variant S477N, which emerged and rose to be the second most frequent variant in the following months. 2021 JCI insight Result SARS_CoV_2 S477N 30 35 RBD 18 21 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. This was followed by N439K (60%), N477N (65%), and E484K (65%). 2021 JCI insight Result SARS_CoV_2 E484K;N439K;N477N 51;21;34 56;26;39 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Though it is now well-known that N501Y, which is the shared mutation in the B.1.1.7, B.1.351, B.1.1.70, and P.1 lineages, is predicted to have a higher affinity for ACE2, here we sought to characterize the binding kinetics of N501Y to WT RBD and other potential high-affinity variants. 2021 JCI insight Result SARS_CoV_2 N501Y;N501Y 33;226 38;231 RBD 238 241 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Variant S477N also demonstrated enhanced (KD 10 nM) affinity for ACE2, although variant Q483L (KD 21 nM) demonstrated a slower off rate, t1/2 211.5 seconds versus t1/2 160.6 seconds by comparison. 2021 JCI insight Result SARS_CoV_2 Q483L;S477N 88;8 93;13 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Variants with mutations at positions 446 and 484 (with the exception of E484D) of the RBD prominently demonstrated antibody escape and consequently poor inhibition. 2021 JCI insight Result SARS_CoV_2 E484D 72 77 RBD 86 89 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. In our analysis, more than 20 nonsynonymous mutation sites were identified in the S protein, in which 13 (S13I, Q14H, P26L, H49Y, G75V, T75I, S95F, T95I, V127F, D138H, N211Y, Y248H, and S255F) were observed in the N-terminal domain (NTD). 2021 Virus genes Result SARS_CoV_2 D138H;G75V;H49Y;N211Y;P26L;Q14H;S255F;S95F;T75I;T95I;V127F;Y248H;S13I 161;130;124;168;118;112;186;142;136;148;154;175;106 166;134;128;173;122;116;191;146;140;152;159;180;110 N;S 214;82 215;83 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Moreover, several mutations were found that persisted, (I120F, T412I, L37F, P323L, G204R, R203K, and D614G) for more than 6 weeks (Table 1 and. 2021 Virus genes Result SARS_CoV_2 D614G;G204R;L37F;P323L;R203K;T412I;I120F 101;83;70;76;90;63;56 106;88;74;81;95;68;61 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. The fusion peptide region, S' including heptad repeats HR1 and HR2 regions contains 3 mutated regions (G769V, A783S, T791I), 2 (D936Y, S939Y), 1 (K1191N), respectively. 2021 Virus genes Result SARS_CoV_2 A783S;S939Y;T791I;D936Y;G769V;K1191N 110;135;117;128;103;146 115;140;122;133;108;152 S 27 28 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. 48 h post-infection, VERO cells expressing pspCas13-BFP and various crRNAs were infected with either the ancestral or D614G mutant SARS-CoV-2, and the viral loads in supernatants were quantified by RT-PCR 1 h (to determine the initial viral input of both strains), 24 h and 48 h post-infection. 2021 Nature communications Result SARS_CoV_2 D614G 118 123 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. 6 provide strong evidence that optimized single crRNAs are likely to retain efficacy against spontaneous point-mutations that arise during viral replication and can efficiently silence ancestral and emerging SARS-CoV-2 strains, including the D614G. 2021 Nature communications Result SARS_CoV_2 D614G 242 247 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. A single nucleotide substitution in the receptor binding domain (RBD) of the Spike protein led to the global emergence of the SARS-CoV-2 D614G variant with increased ACE-2 affinity and infective potential. 2021 Nature communications Result SARS_CoV_2 D614G 137 142 RBD;S;RBD 40;77;65 63;82;68 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. Again, the moderate reduction in suppression of the D614G strain with these three crRNAs was likely attributed to the initial higher viral titer of this D614G strain. 2021 Nature communications Result SARS_CoV_2 D614G;D614G 52;153 57;158 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. Among the four tiled crRNAs targeting the ancestral D614 position in the Spike RNA, three of them (15, 20, and 30) showed efficient viral suppression reaching 78-84% and 44-60% in cells infected with the ancestral and D614G strains respectively, at both 24 and 48 h timepoints. 2021 Nature communications Result SARS_CoV_2 D614G 218 223 S 73 78 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. As anticipated, all SARS-CoV-2 targeting crRNAs tested showed no significant viral suppression against the ancestral nor the D614G strains 1-hour post-infection. 2021 Nature communications Result SARS_CoV_2 D614G 125 130 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. b), we hypothesized that crRNAs designed against ancestral Spike D614 genomic sequence should remain effective against the D614G mutant RNAs despite a single-nucleotide mismatch at the spacer-target interface. 2021 Nature communications Result SARS_CoV_2 D614G 123 128 S 59 64 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. By contrast, crRNAs with a mismatch at position 5 or 10 showed reduced silencing efficiency estimated at approximatively 65-88% removal of the D614G mutant transcript. 2021 Nature communications Result SARS_CoV_2 D614G 143 148 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. G-U mismatch created by these crRNAs targeting the D614G region can still base-pair through a G-U RNA wobble, which may stabilize the RNA-RNA duplex and mask the impact of single-nucleotide mismatch on pspCas13b silencing. 2021 Nature communications Result SARS_CoV_2 D614G 51 56 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. Importantly, the ability of pspCas13b to tolerate up to 3-nt mismatches revealed here, especially in internal regions (14-16), indicates its potential to remain effective against the majority of variants with single-nucleotide polymorphisms in the target sequence, conferring protection against potential viral escape mutants such as the D614G mutation in the SARS-CoV-2 Spike protein, and mutations that compromise the efficacy of therapeutic antibodies against SARS-CoV-2. 2021 Nature communications Result SARS_CoV_2 D614G 338 343 S 371 376 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. In the positive control, NCP-1 crRNA was used to target a fully matching sequence within the Nucleocapsid RNA that is conserved in both the ancestral and D614G strains. 2021 Nature communications Result SARS_CoV_2 D614G 154 159 N 93 105 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. In the virus-free reporter model, we demonstrated that pspCas13b crRNAs targeting the D614 genomic region remained effective against the spike transcript of D614G variant despite a G-U mismatch at various positions. 2021 Nature communications Result SARS_CoV_2 D614G 157 162 S 137 142 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. Interestingly, crRNAs with a single-nucleotide mismatch at spacer position 15, 20, 25, or 30 were highly effective and exhibited >95% silencing efficiency against the D614G mutant transcript. 2021 Nature communications Result SARS_CoV_2 D614G 167 172 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. Last, the fourth crRNA we tested (harbouring a mismatch with the D614G mutation at spacer position 10) showed the lowest affinity and viral suppression potential with 62-71% suppression of the ancestral strain, and only 3-7% suppression of the D614G, which was not statistically significant at 24 nor at 48 h. 2021 Nature communications Result SARS_CoV_2 D614G;D614G 65;244 70;249 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. The comparison of viral loads in the supernatant of cells infected with either the ancestral or D614G in the control groups (NT) showed 7.7, 4.2, and 2.3-fold higher viral loads in the D614G samples at timepoints 1 h, 24 h, and 48 h, respectively. 2021 Nature communications Result SARS_CoV_2 D614G;D614G 96;185 101;190 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. The moderate loss of viral suppression in cells infected with the D614G mutant was likely attributable to the 7-fold higher initial viral titer. 2021 Nature communications Result SARS_CoV_2 D614G 66 71 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. the NCP-1 crRNA again showed a very high silencing efficiency, and suppressed 84-88% and 73-74% of replication-competent ancestral and D614G viruses, respectively, at both the 24 and 48 h timepoints. 2021 Nature communications Result SARS_CoV_2 D614G 135 140 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. The spacer sequences of all six tiled crRNAs tested were designed to fully match the ancestral Spike sequence (D614) and harbour one nucleotide mismatch (G-U mismatch) with the Spike transcript of D614G mutant at spacer positions 5, 10, 15, 20, 25, and 30. 2021 Nature communications Result SARS_CoV_2 D614G 197 202 S;S 95;177 100;182 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. These data showed that the initial D614G viral load used here was more than 7 times higher than the ancestral strain. 2021 Nature communications Result SARS_CoV_2 D614G 35 40 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. To test the mismatch tolerance of pspCas13b system against various replication-competent SARS-CoV-2 viral strains, we transfected VERO cells with NT crRNA, NCP-1 targeting crRNA (positive control), or 4 tiled crRNAs (10, 15, 20, 30) fully matching the ancestral Spike sequence D614 but therefore containing a single-nucleotide mismatch (G-U) with the D614G variant (see the schematic illustration in. 2021 Nature communications Result SARS_CoV_2 D614G 351 356 S 262 267 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. To test this possibility, we tested an additional six crRNAs harbouring a G-G mismatch with the targeted D614G sequence, and six crRNAs with a full match with the target through G-C match that served as a control. 2021 Nature communications Result SARS_CoV_2 D614G 105 110 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. To test this, we cloned part of the D614G Spike coding sequence (1221 bp; D614G SARS-CoV-2 genomic region between 22,760:23,980) that hasn't been codon-optimized into the mCherry reporter system, and assessed the silencing efficiency of six tiled crRNAs targeting this frequently mutated hotspot. 2021 Nature communications Result SARS_CoV_2 D614G;D614G 36;74 41;79 S 42 47 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. Together, these data suggest that pspCas13 and the D614G targeting crRNAs with a single-nucleotide mismatch are likely to remain effective against both ancestral and D614G mutant in infected cells. 2021 Nature communications Result SARS_CoV_2 D614G;D614G 51;166 56;171 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. We found that all six crRNAs significantly degraded the D614G mutant transcript (P < 0.0001). 2021 Nature communications Result SARS_CoV_2 D614G 56 61 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. We observed a moderate reduction in silencing efficiency when a G was introduced at position 15 and 30 that led to the removal of 74% and 81% of D614G transcript, respectively. 2021 Nature communications Result SARS_CoV_2 D614G 145 150 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. where the crRNA harbouring a single-nucleotide mismatch with D614G at spacer position 10 exhibited the lowest silencing efficiency among the 4 crRNAs tested. 2021 Nature communications Result SARS_CoV_2 D614G 61 66 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. A688V was the second-most prevalent FCS mutation among human isolates (n = 3273), with wide geographic distribution. 2021 Archives of virology Result SARS_CoV_2 A688V 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Frequency and tracing of spike FCS mutations and Q677P/Q677H. 2021 Archives of virology Result SARS_CoV_2 Q677P;Q677H 49;55 54;60 S 25 30 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Furthermore, P681H was detected in isolates from different animal species, including dog (n = 3), cat (n = 2) monkey (n = 2), lion (n = 1), tiger (n = 1), and leopard (n = 1), and was found in environmental samples (n = 167) (Table 1). 2021 Archives of virology Result SARS_CoV_2 P681H 13 18 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Interestingly, Q677P and Q677H have not been detected in animal isolates, whereas Q677H has been detected twice in environmental samples (USA and Europe). 2021 Archives of virology Result SARS_CoV_2 Q677H;Q677H;Q677P 25;82;15 30;87;20 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Interestingly, the recently detected P681H substitution was the most prevalent FCS mutation, detected in 395,711 human isolates worldwide. 2021 Archives of virology Result SARS_CoV_2 P681H 37 42 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Major FCS mutations in animal isolates were mainly detected in pangolins and bats, whereas very few mutations were detected in other animal species, such as A684S, which was detected once in a Danish mink isolate. 2021 Archives of virology Result SARS_CoV_2 A684S 157 162 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. On the other hand, 13 FCS mutations, namely, S680P, S680F, P681H, P681R, P681S, P681L, R682W, A684T, A684V, V687I, A688S, A688V, and S689I, among over 1,144,793 human isolates had a high frequency, with wide geographic distribution. 2021 Archives of virology Result SARS_CoV_2 A684T;A684V;A688S;A688V;P681H;P681L;P681R;P681S;R682W;S680F;S680P;S689I;V687I 94;101;115;122;59;80;66;73;87;52;45;133;108 99;106;120;127;64;85;71;78;92;57;50;138;113 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Other genetic polymorphisms, S680F, S680P, P681L, P681R, P681S, A684V, A684T, V687I, A688S, and S689I, were found in isolates 298, 14, 443, 3,023, 71, 684, 112, 265, 308, and 619, respectively, from humans, with wide geographic distribution. 2021 Archives of virology Result SARS_CoV_2 A684T;A684V;A688S;P681L;P681R;P681S;S680F;S680P;S689I;V687I 71;64;85;43;50;57;29;36;96;78 76;69;90;48;55;62;34;41;101;83 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Q677P was detected once in an isolate of variant B.1.1.7, whereas mutation Q677H was detected in all variants: B.1.1.7 (n = 1938), B.1.351 (n = 28), P.1 (n = 9), B.1.429 + B.1.427 (n = 132), and B.1.525 (n = 1584). 2021 Archives of virology Result SARS_CoV_2 Q677H;Q677P 75;0 80;5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Structural models were made to examine the effects of a few selected F1 FCS mutations and nearby polymorphisms (Q677P/H) in human and animal strains. 2021 Archives of virology Result SARS_CoV_2 Q677H;Q677P 112;112 119;119 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? Both mutants E484K and E484Q would likely increase local molecular flexibility. 2021 Journal of medical virology Result SARS_CoV_2 E484K;E484Q 13;23 18;28 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? E484Q exerts a destabilizing effect, again with no strong consensus from the two methods. 2021 Journal of medical virology Result SARS_CoV_2 E484Q 0 5 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? However, in this case, our results predict that both mutants (K417N and K417T) could destabilize the protein and increase local flexibility. 2021 Journal of medical virology Result SARS_CoV_2 K417T;K417N 72;62 77;67 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? In particular, the Tyr replacing Asn501 may form an aromatic interaction with ACE2 Tyr41, a hydrogen bond with ACE2 D38, and a potential cation-pi interaction with ACE2 Lys353. 2021 Journal of medical virology Result SARS_CoV_2 Y501N 19 39 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? Mutation L452R is predicted to be destabilizing with increased local flexibility. 2021 Journal of medical virology Result SARS_CoV_2 L452R 9 14 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? Mutation T478K is stabilizing and is predicted to decrease local protein flexibility. 2021 Journal of medical virology Result SARS_CoV_2 T478K 9 14 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? Our data predict that mutation E484K is stabilizing, although data from DynaMut and DUET do not match. 2021 Journal of medical virology Result SARS_CoV_2 E484K 31 36 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? Starting with position 501 within a loop in the RDB interacting with the ACE2 receptor, we note that the mutation N501Y does not show any clear structural effect as the negative DeltaDeltaG values are very close to 0.0 kcal/mol in DynaMut. 2021 Journal of medical virology Result SARS_CoV_2 N501Y 114 119 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. Four sequences from samples collected in Colombia between December 26, 2020 and January 14, 2021 presented a characteristic mutation pattern, including two amino acid changes in the Spike protein (L249S and E484K). 2021 Frontiers in medicine Result SARS_CoV_2 E484K;L249S 207;197 212;202 S 182 187 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. The B.1+L249S+E484K intra-lineage (0.000208 substitutions per site between each pair of sequences) and between-lineages p-distances (0.000733-0.001918 substitutions per site between each pair of sequences) suggest a drastic divergence of the new lineage from the most closely related lineages (Supplementary Table 2). 2021 Frontiers in medicine Result SARS_CoV_2 E484K;L249S 14;8 19;13 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. The inclusion of SARS-CoV-2 sequences representative from the different lineages circulating in Colombia, as well as sequences representative of the major lineages and VOC circulating worldwide allowed to demonstrate the emergence of a novel and phylogenetically distant lineage of SARS-CoV-2 (provisionally named: B.1+L249S+E484K). 2021 Frontiers in medicine Result SARS_CoV_2 E484K;L249S 325;319 330;324 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. The phylogenetic analysis allowed to identify a highly distant lineage clustering the sequences containing the+L249S and E484K amino acid changes (Figure 1). 2021 Frontiers in medicine Result SARS_CoV_2 E484K;L249S 121;111 126;116 34268528 SARS-CoV-2 Infections in mRNA Vaccinated Individuals are Biased for Viruses Encoding Spike E484K and Associated with Reduced Infectious Virus Loads that Correlate with Respiratory Antiviral IgG levels. Spike substitution analysis showed that the S: E484K is associated with genomes of the vaccinated group (p = 0.0032, Figure 1F and Supplementary tables 3, 4, and 5). 2021 medRxiv Result SARS_CoV_2 E484K 47 52 S;S 0;44 5;45 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. 8] show that in March 2020, all regions have had cases of the A1841G nucleotide mutation in the spike protein of the SARS-CoV-2 virus. 2021 Biomedical journal Result SARS_CoV_2 A1841G 62 68 S 96 101 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. A month after the first cases appeared in Europe, in February 2020, the A1841G mutation appeared in Asia (n = 3). 2021 Biomedical journal Result SARS_CoV_2 A1841G 72 78 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Additionally, in Africa there were three types of mutation, which are D614G (n = 16), T29I (n = 2) and Y279N (n = 1). 2021 Biomedical journal Result SARS_CoV_2 D614G;T29I;Y279N 70;86;103 75;90;108 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. After that, cases of the D614G mutation spread in February 2020 to Asia. 2021 Biomedical journal Result SARS_CoV_2 D614G 25 30 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Among the various forms of mutation, the most common occurrence of amino acid mutations was in D614G. 2021 Biomedical journal Result SARS_CoV_2 D614G 95 100 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. As of March, all five regions reported cases of D614G amino acid mutation with the most cases in Europe (n = 24). 2021 Biomedical journal Result SARS_CoV_2 D614G 48 53 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Based on this graph, the most common occurrence of the A1841G mutation was in Europe (n = 49) from December 2019 to July 2020. 2021 Biomedical journal Result SARS_CoV_2 A1841G 55 61 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Even though it started in Europe, in June 2020, Europe no longer had cases of the D614G amino acid mutation. 2021 Biomedical journal Result SARS_CoV_2 D614G 82 87 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. For example, in April 2020 in America, the mutation of the amino acid D614G was always followed by a mutation of A1841G in the nucleotide base. 2021 Biomedical journal Result SARS_CoV_2 A1841G;D614G 113;70 119;75 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Here we describe how the distribution of the A1841G mutation in each area is presented in each month [Fig. 2021 Biomedical journal Result SARS_CoV_2 A1841G 45 51 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. However, there was one time when the mutation in D614G amino acid in spike protein of SARS-CoV-2 had two types of mutated nucleotide bases (A1841G and C1560T). 2021 Biomedical journal Result SARS_CoV_2 C1560T;D614G;A1841G 151;49;140 157;54;146 S 69 74 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. In addition, based on our analysis, Europe was also the first region where the A1841G mutation occurred, precisely in January 2020 (n = 3). 2021 Biomedical journal Result SARS_CoV_2 A1841G 79 85 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. In addition, in Asia there are several types of mutations with varying frequencies such as C882T (n = 6), C2367T (n = 5), G2485A (n = 3) and other types of mutations consisting of only one or two frequencies. 2021 Biomedical journal Result SARS_CoV_2 C2367T;C882T;G2485A 106;91;122 112;96;128 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. In addition, the mutation types with the second most common frequencies in other areas were as follows: in Europe with C145T (n = 2), in America with C2472T (n = 3) and in Australia with C96T (n = 2) and the other mutation types had just one frequency in all areas. 2021 Biomedical journal Result SARS_CoV_2 C145T;C2472T;C96T 119;150;187 124;156;191 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. In addition, there were mutation types that have more than one case such as in Asia, the mutations A829T (n = 3), P25L (n = 2), V367F (n = 2), R682Q (n = 2), S13I (n = 2), and T22I (n = 2) while the other types have just one case. 2021 Biomedical journal Result SARS_CoV_2 A829T;P25L;R682Q;S13I;T22I;V367F 99;114;143;158;176;128 104;118;148;162;180;133 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. In America, there is only one type of mutation that has occurred and it is located in D614G. 2021 Biomedical journal Result SARS_CoV_2 D614G 86 91 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. In amino acid mutations, we found that the mutation located at position D614G has the highest number compared with other amino acid mutations. 2021 Biomedical journal Result SARS_CoV_2 D614G 72 77 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. In Europe we found that most of the mutation types that have occurred in Europe have been just one type, namely H49Y (n = 2). 2021 Biomedical journal Result SARS_CoV_2 H49Y 112 116 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. In May 2020 data in America, it is known that mutations occurred in two types of nucleotides (T2115C and C2472T) but there were no mutations in their amino acids. 2021 Biomedical journal Result SARS_CoV_2 C2472T;T2115C 105;94 111;100 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. In the last 2 months (June-July 2020), the lone region that still had D614G mutation cases was Asia (light blue bar) [Fig. 2021 Biomedical journal Result SARS_CoV_2 D614G 70 75 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. In this month, the case of the D614G mutation jumped very rapidly (n = 49). 2021 Biomedical journal Result SARS_CoV_2 D614G 31 36 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. In this month, there were mutations of nucleotides A2763G, C210T, G906T, and C2367T but there was no mutation (NA) in amino acids. 2021 Biomedical journal Result SARS_CoV_2 A2763G;C210T;C2367T;G906T 51;59;77;66 57;64;83;71 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. In this study, we also found association of Adenine 1841 Guanine (A1841G) mutation pattern with amino acid D614G mutation. 2021 Biomedical journal Result SARS_CoV_2 A1841G;D614G;A1841G 72;107;64 64;112;72 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. In this study, we also found that the A1841G mutation was identified in most cases in all areas (Asia, Europe, America, Australia and Africa). 2021 Biomedical journal Result SARS_CoV_2 A1841G 38 44 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Interestingly, the additional mutation located at G2485A was only found in Asia (Thailand). 2021 Biomedical journal Result SARS_CoV_2 G2485A 50 56 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. it is known that there were no cases of mutation of the amino acid D614G in December 2019, at the beginning of the emergence of COVID-19. 2021 Biomedical journal Result SARS_CoV_2 D614G 67 72 COVID-19 128 136 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. It shows that G2485A (Guanine 2485 Adenine) that encodes Alanine (GCA) can have substitution with threonine (ACA). 2021 Biomedical journal Result SARS_CoV_2 G2485A;G2485A 22;14 42;20 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Since appearing in January 2020 in Europe, cases of the A181G mutation have begun to spread to various regions. 2021 Biomedical journal Result SARS_CoV_2 A181G 56 61 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Since its appearance, cases of the A1841G mutations in Asia (blue bar) have always appeared every month. 2021 Biomedical journal Result SARS_CoV_2 A1841G 35 41 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Substitution of Adenine to Guanine in nucleotide base 1841 leads to the change of base that encodes aspartate (GAT to GGT) which encodes glycine. 2021 Biomedical journal Result SARS_CoV_2 A1841G 16 58 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. The A1841G mutation which in this study is the dominant mutation and causes changes in the amino acid D614G. 2021 Biomedical journal Result SARS_CoV_2 A1841G;D614G 4;102 10;107 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. The cases of the A1841G mutation in Europe increased in March 2020 (n = 24) and April 2020 (n = 13) as seen in. 2021 Biomedical journal Result SARS_CoV_2 A1841G 17 23 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. The graph shows that Australia has three types of mutations and D614G mutation occurred more than other mutations. 2021 Biomedical journal Result SARS_CoV_2 D614G 64 69 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. The sequence location with the highest mutations is located at position A1841G. 2021 Biomedical journal Result SARS_CoV_2 A1841G 72 78 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. This also is the same pattern in nucleotide mutation located at G2485A indicating an association with amino acid mutation located at A829T. 2021 Biomedical journal Result SARS_CoV_2 A829T;G2485A 133;64 138;70 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Total amino acids mutations at D614G reported occurred mostly in Europe, Asia, America, Africa and Australia with 49, 33, 17, 16 and 4, respectively. 2021 Biomedical journal Result SARS_CoV_2 D614G 31 36 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Total nucleotide mutations at A1841G were reported to occur the most in Europe, Asia, America, Africa and Australia with the number of mutations of 49, 37, 17, 16 and 4, respectively. 2021 Biomedical journal Result SARS_CoV_2 A1841G 30 36 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Until July 2020, cases of the A1841G mutation still appeared in Asia with four cases of mutations. 2021 Biomedical journal Result SARS_CoV_2 A1841G 30 36 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. We identified that A1841G is located in the coding region of the genome that encodes aspartate (D) (GAT). 2021 Biomedical journal Result SARS_CoV_2 A1841G 19 25 34271432 Natto extract, a Japanese fermented soybean food, directly inhibits viral infections including SARS-CoV-2 in vitro. 4C indicated that RBD protein carrying a point mutation, N501Y, was degraded. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 N501Y 57 62 RBD 18 21 34271432 Natto extract, a Japanese fermented soybean food, directly inhibits viral infections including SARS-CoV-2 in vitro. In addition, evolutionary analysis of the SARS-CoV-2 RBD protein indicated that V367F is one of important mutations for higher binding affinity toward ACE2 receptor. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 V367F 80 85 RBD 53 56 34271432 Natto extract, a Japanese fermented soybean food, directly inhibits viral infections including SARS-CoV-2 in vitro. The N501Y mutant in RBD has become predominant in England. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 N501Y 4 9 RBD 20 23 34271432 Natto extract, a Japanese fermented soybean food, directly inhibits viral infections including SARS-CoV-2 in vitro. The RBD protein carrying V367Y is also degraded by treatment with the natto-extract (data not shown). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 V367Y 25 30 RBD 4 7 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. Amino acid changes in hospitalized patients compared with all patients with >=10% prevalence and a 5% change between the 2 groups showed that 4 mutations (S: P681H, NSP6: 106-108del, N: S194L, and N: T205I) were present to a higher degree, but not significantly higher or didn't reach statistical significance. 2022 Clinical infectious diseases Result SARS_CoV_2 P681H;S194L;T205I 158;186;200 163;191;205 Nsp6;N;N;S 165;183;197;155 169;184;198;156 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. Filtering for more common substitutions (Supplementary Figure 1B) showed a major increase in February in changes associated with B.1.1.7 (eg, S:N501Y, S:A570D, S:T716I, S:S982A, and S:D1118H) while substitutions associated with B.1.2 declined. 2022 Clinical infectious diseases Result SARS_CoV_2 A570D;D1118H;N501Y;S982A;T716I 153;184;144;171;162 158;190;149;176;167 S;S;S;S;S 142;151;160;169;182 143;152;161;170;183 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. Of the 93 substitutions that were present in 2020, 61 were no longer present during March 2021 (Figure 5C), and only 8 were present in >5% of samples during March 2021 (NSP2:T85I, NSP12:P323L, S:L5F, S:D614G, NS3aQ57H, NS8:S24L, N:R203K, and N:G204R). 2022 Clinical infectious diseases Result SARS_CoV_2 D614G;G204R;L5F;P323L;R203K;S24L;T85I 202;244;195;186;231;223;174 207;249;198;191;236;227;178 Nsp12;Nsp2;N;N;S;S 180;169;229;242;193;200 185;173;230;243;194;201 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. Only a subset of B.1.1.207 carried S:E484K, and this lineage has dropped off in frequency. 2022 Clinical infectious diseases Result SARS_CoV_2 E484K 37 42 S 35 36 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. Other lineages with L452R included A.2.5, B.1.526.1, and B.1.1.487 (Supplementary Figure 2). 2022 Clinical infectious diseases Result SARS_CoV_2 L452R 20 25 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. Others, such as S:P681H, S:L452R, N:R203K, and S:E484K, were present in multiple lineages and showed an undulating pattern (Supplementary Table 2). 2022 Clinical infectious diseases Result SARS_CoV_2 E484K;L452R;P681H;R203K 49;27;18;36 54;32;23;41 N;S;S;S 34;16;25;47 35;17;26;48 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. The most common amino acid substitutions across lineages were S:D614G, NSP12:P323L, NSP2:T85I, and NS3:Q57H. 2022 Clinical infectious diseases Result SARS_CoV_2 D614G;P323L;Q57H;T85I 64;77;103;89 69;82;107;93 Nsp12;Nsp2;NS3;S 71;84;99;62 76;88;102;63 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. The most common lineage to carry S:E484K was a subset of B.1.1.207 (46 samples), which also carried the S:P681H mutation, followed by lineage R.1 (40 samples). 2022 Clinical infectious diseases Result SARS_CoV_2 E484K;P681H 35;106 40;111 S;S 33;104 34;105 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. The other lineage, B.1.1.318 within our population with both S:E484K and S:P681H, was present in 6 samples between mid-February and mid-March. 2022 Clinical infectious diseases Result SARS_CoV_2 E484K;P681H 63;75 68;80 S;S 61;73 62;74 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. The presence of 2 lineages with S:P681H and S:E484K (B.1.1.207 and B.1.1.318) within this region was initially concerning, as these changes were found in VOCs but almost never reported together (Supplementary Figure 2). 2022 Clinical infectious diseases Result SARS_CoV_2 E484K;P681H 46;34 51;39 S;S 32;44 33;45 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. This lineage, similar to B.1.429, harbors the S: L452R. 2022 Clinical infectious diseases Result SARS_CoV_2 L452R 49 54 S 46 47 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. Variants carrying S: P681H but not the S: E484K belonged to diverse lineages (Supplementary Figure 2). 2022 Clinical infectious diseases Result SARS_CoV_2 E484K;P681H 42;21 47;26 S;S 18;39 19;40 34278277 SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high risk variants into the United Kingdom. In addition, a number of other VOCs including B.1.617.2 (n = 28; 1.7%), P.1 (n = 6; 0.4%), B.1.1.7 with E484K (n = 3; 0.2%) and VUIs B.1.617.1 (n = 49; 2.9%), B.1.617 (n = 9; 0.6%), B.1.617.3 (n = 3; 0.2%), B.1.525 (n = 31; 2.0%) and B.1.1.318 (n = 7; 0.4%) were identified. 2021 EClinicalMedicine Result SARS_CoV_2 E484K 104 109 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. 1E) was a caucasian male in his late sixties with B-cell chronic leukemia (CLL) stage Binet C who had persistent positive SARS-CoV-2 RT-qPCR (3 12 x 107copies/mL, strain B.1.258, harbouring E484E) 44 days after the first positive SARS-CoV-2 RT-qPCR in December 2020 before scheduled initiation of CLL treatment with ibrutinib. 2021 The Lancet regional health. Europe Result SARS_CoV_2 E484E 190 195 B cell chronic leukemia;B cell chronic leukemia;B cell chronic leukemia 50;75;297 73;78;300 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. A subsequent increase of the viral load to 4 82 x 106 copies/mL prompted us to perform whole-genome sequencing on day 52 (day 8 after bamlanivimab administration), which identified the E484K mutant. 2021 The Lancet regional health. Europe Result SARS_CoV_2 E484K 185 190 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. Admission screening (d1) revealed a SARS-CoV-2 infection with 2 22 x 107 copies/ml (strain B.1.1, harbouring E484E). 2021 The Lancet regional health. Europe Result SARS_CoV_2 E484E 109 114 COVID-19 36 56 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. At admission, her SARS-CoV-2 viral load was 9 36 x 106 (strain B.1.160, harbouring E484E). 2021 The Lancet regional health. Europe Result SARS_CoV_2 E484E 83 88 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. At this point, whole genome sequencing revealed the E484K mutant. 2021 The Lancet regional health. Europe Result SARS_CoV_2 E484K 52 57 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. In the further course a high SARS-CoV-2 viral load persisted (2 26 x 106copies/mL, still harbouring E484K) so that we decided to administer imdevimab/casirivimab, which was well tolerated by the patient. 2021 The Lancet regional health. Europe Result SARS_CoV_2 E484K 100 105 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. Interestingly, at day 15 we observed continuous evolution to E484Q, reverting back to E484K on day 16 after administration of three units of convalescent plasma (CP). 2021 The Lancet regional health. Europe Result SARS_CoV_2 E484K;E484Q 86;61 91;66 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. On day 74, SARS-CoV-2 RT-qPCR was positive again on a nasopharyngeal swab with 2 0 x 105 copies/mL (strain B.1.177, harbouring E484E). 2021 The Lancet regional health. Europe Result SARS_CoV_2 E484E 127 132 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. SARS-CoV-2-RNA levels remained high for about one week and then further increased up to 2 9 x 109 copies/mL with simultaneous detection of the E484K substitution. 2021 The Lancet regional health. Europe Result SARS_CoV_2 E484K 143 148 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. This prompted us to perform whole genome sequence analysis, which revealed the presence of the E484K immune escape mutation in strain B.1. 2021 The Lancet regional health. Europe Result SARS_CoV_2 E484K 95 100 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. Viral load was initially low with 5 27 x 104 copies/mL (strain B.1.177, harbouring E484E), increased on the day of bamlanivimab administration, then dropped and became negative over the next few days. 2021 The Lancet regional health. Europe Result SARS_CoV_2 E484E 83 88 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. Whole genome sequencing revealed the E484K mutant on day 87. 2021 The Lancet regional health. Europe Result SARS_CoV_2 E484K 37 42 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. Amino acid substitutions such as T428I and G15S in ORF1a were reported in sublineages C.1 and C.2, and the S477N substitution in the spike (S) protein along with I120F in nsp2 specifically established the sublineage D.2. 2021 mBio Result SARS_CoV_2 G15S;I120F;S477N;T428I 43;162;107;33 47;167;112;38 ORF1a;S;Nsp2;S 51;133;171;140 56;138;175;141 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. Dominance of the D614G variant. 2021 mBio Result SARS_CoV_2 D614G 17 22 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. Genomes with D614G mutations were assigned as B.1 by PANGOLIN or GH/GR by GISAID. 2021 mBio Result SARS_CoV_2 D614G 13 18 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. Notably, founder lineage B.1 and its sublineages B.1.X, B.1.1.X, D.X, and C.X that carry both D614G and P323L mutations have become the dominant variants across the world (87% of global collection per CoV-GLUE as of 30 November 2020). 2021 mBio Result SARS_CoV_2 D614G;P323L 94;104 99;109 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. Other major mutations noted are Q57H (26.5%), R203K/G204R (33%), G15S (12%), I120F (11.5%), and T85I (14%). 2021 mBio Result SARS_CoV_2 G15S;I120F;Q57H;R203K;T85I;G204R 65;77;32;46;96;52 69;82;36;51;100;57 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. Structural analysis of double (D614G + S477N; D614G + A222V) and triple (D614G + S477N + A222V) mutation patterns in the S protein indicated DeltaDeltaG values of 0.228, 0.195 and 0.129, respectively (Table 3). 2021 mBio Result SARS_CoV_2 A222V;A222V;D614G;S477N;S477N;D614G;D614G 54;89;46;39;81;31;73 59;94;51;44;86;36;78 S 121 122 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. The amino acid changes in M (T175M) indicated a stabilizing effect, while E does not account for any stabilizing variant. 2021 mBio Result SARS_CoV_2 T175M 29 34 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. The combination of G251V and L37F, which was initially considered a defining mutation pattern for the B.2 to B.6 lineage (clade V in GISAID classification), has shown under more detailed analysis that isolates carrying the G251V mutation are distributed in other lineages too. 2021 mBio Result SARS_CoV_2 G251V;G251V;L37F 19;223;29 24;228;33 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. The first major mutation to appear was L84S in ORF8 (present in 8.6% of the genomes) that has defined the A lineage (i.e., clade S in the GISAID classification). 2021 mBio Result SARS_CoV_2 L84S 39 43 ORF8;S 47;129 51;130 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. The major mutations D614G and S477N were located at potential epitope regions (codons 469 to 882), with S477N particularly positioned in the receptor-binding domain (RBD) of the S protein (319 to 541). 2021 mBio Result SARS_CoV_2 D614G;S477N;S477N 20;30;104 25;35;109 RBD;S 166;178 169;179 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. The most frequent amino acid substitutions were observed in the nucleocapsid (N) protein, in which the variants S194L, D103Y, P13L, S197L, M234I, and S188L were predicted to be stabilizing according to both the analytical servers (Table 2). 2021 mBio Result SARS_CoV_2 D103Y;M234I;P13L;S188L;S194L;S197L 119;139;126;150;112;132 124;144;130;155;117;137 N;N 64;78 76;79 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. The predominant lineage-defining mutations in the whole data set were D614G (85.5%) and P323L (85.5%), after originally appearing in late January 2020. 2021 mBio Result SARS_CoV_2 D614G;P323L 70;88 75;93 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. The subsequent amino acid substitutions L37F in ORF3a and G251V in nsp6 were found to be present in 13.3% and 1.4% of genomes, respectively. 2021 mBio Result SARS_CoV_2 G251V;L37F 58;40 63;44 ORF3a;Nsp6 48;67 53;71 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. The widely discussed D614G variant is speculated to have been introduced in Europe at the end of January (EPI_ISl_422424) before becoming globally dominant. 2021 mBio Result SARS_CoV_2 D614G 21 26 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. These are Q57H (nucleotide 25,563, G to T) in ORF3a, the R203K + G204R combination (nucleotide 28,881, GGG to AAC) in nucleocapsid, and T85I (nucleotide 1,059, C to T) in ORF1a. 2021 mBio Result SARS_CoV_2 G204R;Q57H;R203K;T85I 65;10;57;136 70;14;62;140 N;ORF1a;ORF3a 118;171;46 130;176;51 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. This signifies that accumulation of spike mutation in D614G-bearing lineages could potentially be affecting the stability of the spike and therefore may influence the binding affinity toward the ACE2 receptor. 2021 mBio Result SARS_CoV_2 D614G 54 59 S;S 36;129 41;134 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. Two mutations have become consensus: D614G in S (nucleotide 23,403, A to G) and P323L (also known as P4715L) in nsp12 (nucleotide 14,143, C to T). 2021 mBio Result SARS_CoV_2 D614G;P323L;P4715L 37;80;101 42;85;107 Nsp12;S 112;46 117;47 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. As this receptor decoy has the potential to bind S glycoproteins of viruses that utilize ACE2 as host cell receptor, binding kinetics were generated for the S1 spike domain of SARS-CoV-1, SARS-CoV-2 Wuhan, D614G, B.1.1.7, B.1.351, and P.1 variants, and HCoV-NL63, comparing to the leading anti-SARS-CoV-2 antibodies LY-CoV555, REGN10933, and REGN10987. 2021 Journal of virology Result SARS_CoV_2 D614G 206 211 S;S 49;160 64;165 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. Inhouse purified recombinant S1 domains from Wuhan, D614G, B.1.1.7, B.1.351, and P.1 variants demonstrated similar properties to commercially sourced S1 wild-type (WT) protein. 2021 Journal of virology Result SARS_CoV_2 D614G 52 57 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. Interestingly, the Wuhan and D614G variants displayed a similar thermal unfolding profile, with the first transition event (melting temperature; Tm) at 42.9 and 42.2 C, respectively, while the P.1, B.1.1.7, and B.1.351 resulted in a 4.1, 6.9, and 11.5 C increase in temperature compared to that of S1 Wuhan, respectively. 2021 Journal of virology Result SARS_CoV_2 D614G 29 34 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. Next, to investigate the degree of neutralization efficiency against the SARS-CoV-2 variants of interest, the receptor decoy was tested against the engineered replication-deficient lentiviral vectors pseudotyped with the glycoproteins of SARS-CoV-2 Wuhan, D614G mutation, B.1.1.7, and B.1.351 variants and SARS-CoV-1. 2021 Journal of virology Result SARS_CoV_2 D614G 256 261 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. The monoclonal antibody LY-CoV555 showed a marked reduction in neutralization capacity for the D614G and B.1.1.7 variants, 3- and 8-fold, respectively, significantly affecting the antibody efficacy, with an almost complete abrogation of neutralization against the B.1.351 variant. 2021 Journal of virology Result SARS_CoV_2 D614G 95 100 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. The SARS-CoV-2 D614G variant was instead the most efficient, with viral titer 2.6-fold higher than that of Wuhan. 2021 Journal of virology Result SARS_CoV_2 D614G 15 20 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. The SARS-CoV-2 S1 WT, D614G, and B.1.351 displayed overall similar kinetic affinities, although the latter showed an off-rate (kd) 1.5-fold lower than that of WT S1, which was compensated by a slightly lower on-rate (ka). 2021 Journal of virology Result SARS_CoV_2 D614G 22 27 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. The well-established L234A/L235A (LALA) mutations of the CH2 domain and the LALA combination with P329G (LALA-PG) were introduced in the human IgG1 Fc portion of the ACE2-Fc fusion protein. 2021 Journal of virology Result SARS_CoV_2 L234A;P329G;L235A 21;98;27 26;103;32 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. To assess the infectivity conferred by the SARS-CoV-2 spike variants, we engineered replication-deficient lentiviral vectors pseudotyped with the WT glycoprotein or carrying the D614G, B.1.1.7, and B.1.351 mutations, alongside SARS-CoV-1. 2021 Journal of virology Result SARS_CoV_2 D614G 178 183 S 54 59 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. When the two antibodies constituting the cocktail were analyzed individually, the REGN10933 showed a 3-fold decrease in neutralization capacity for the D614G and B.1.1.7 variants, with a staggering >1,000-fold reduction for the B.1.351 variant, while the REGN10987 showed a 4-fold neutralization reduction for the B.1.1.7 variant and a 10-fold shift for the D614G variant. 2021 Journal of virology Result SARS_CoV_2 D614G;D614G 152;358 157;363 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. Considering that the major three VOCs contain either N501Y alone (B.1.1.7) or both N501Y and E484K mutations (B.1.351 and P.1), the presence of this single 484K mutant indicates that this sample contains the variant of interest, B.1.525/B.1.526, which originated in New York City. 2021 Journal of clinical microbiology Result SARS_CoV_2 E484K;N501Y;N501Y 93;53;83 98;58;88 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. However, Tm peak heights produced by both SMB 501-WT/SMB 484-WT and SMB 501-MT/SMB 484-MT could still be reproducibly detected at concentrations down to 10 GE/reaction when tested against both WT and N501Y mutant strains, defining the assay limit of detection as <=10 GE per reaction for both the SMB-501 and SMB-484 assays. 2021 Journal of clinical microbiology Result SARS_CoV_2 N501Y 200 205 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. In all cases, the WT or mutant sequences identified by the SMB N501Y assay were confirmed by the sequencing result. 2021 Journal of clinical microbiology Result SARS_CoV_2 N501Y 63 68 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. It should be noted that one of the specimens (SMBP-27) contained an E484K mutation but was found to have a WT sequence at codon 501. 2021 Journal of clinical microbiology Result SARS_CoV_2 E484K 68 73 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. Similarly, when RNA was tested with the SMB 501-MT probe, WT-RNA produced a Tm of 58.2 +- 1 C, while MT N501Y RNA from B.1.1.7/B.1.351/P.1 variants produced Tm values of 62.2 +- 0.6 C/63.1 +- 0.01 C/63 +- 0.16 C, respectively. 2021 Journal of clinical microbiology Result SARS_CoV_2 N501Y 104 109 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. These results clearly indicate that the combination of both SMB 501-WT and SMB 501-MT probes can specifically detect and differentiate the N501Y variants from the wild-type strains with high confidence. 2021 Journal of clinical microbiology Result SARS_CoV_2 N501Y 139 144 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. Using the confirmed sequencing results as a gold standard, 4/4 of the wild-type clinical samples were detected as WT by the SMB N501Y assay, and 8/8 N501Y mutant results were detected as mutant by the assay, demonstrating a clinical sensitivity and specificity of 100%. 2021 Journal of clinical microbiology Result SARS_CoV_2 N501Y;N501Y 128;149 133;154 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. We also observed that the frequency of N501Y and E484K variants increased substantially between the clinical samples obtained in October 2020 and the samples obtained in February and March 2021. 2021 Journal of clinical microbiology Result SARS_CoV_2 E484K;N501Y 49;39 54;44 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. When reference RNA (1,000 GE/reaction) was tested with the SMB 501-WT probe, WT-RNA produced a Tm of 59.8 +- 0.4 C, while MT N501Y RNA from B.1.1.7/B.1.351/P.1 variants produced Tm values of 55.2 +- 0.4 C, 56.2 +- 0.01 C, and 56.3 +- 0.07 C, respectively. 2021 Journal of clinical microbiology Result SARS_CoV_2 N501Y 125 130 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. A schematic of the A372T mutant is presented in Figure 4 A; although not depicted, the D614G mutant was made by replacing the WT codon (GAT) with the glycine-encoding codon (GGC). 2021 Cell Result SARS_CoV_2 A372T;D614G 19;87 24;92 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. A total of six such sites were identified (Table S1); notably, only a single site (A1114G, genomic position 22,676; Figure 1B) was centrally located in one of the sweep regions; this is within the codon position 372 of the S protein. 2021 Cell Result SARS_CoV_2 A1114G 83 89 S 223 224 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. A372T titers did not differ significantly from the WT at any time point for temperature (Figures 4E and 4F). 2021 Cell Result SARS_CoV_2 A372T 0 5 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Additionally, molecular mechanics generalized born surface area (MM/GBSA) free energy of binding of ACE2 to S protein was calculated for WT, T372, and N370-glycosylated T372 S protein. 2021 Cell Result SARS_CoV_2 T372S 169 175 S;S 108;174 109;175 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. As expected, 50% effective dose (EC50) values were lower for the N510Y mutant (5.83 +- 0.94 ng/mL; Figure 3 A) than the WT (12.48 +- 1.26 ng/mL), indicating a stronger binding affinity for hACE2. 2021 Cell Result SARS_CoV_2 N510Y 65 70 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Comparative molecular modeling of wild-type (WT) (A372, SARS-CoV-2), T372, and G614 S protein was performed to connect the selective sweep G1114A mutation to structural data (Figure 2 ). 2021 Cell Result SARS_CoV_2 G1114A 139 145 S 84 85 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Compared with the WT, D614G had modest differences of 2.9-, 2.9-, 1.3-, and 0.8-fold in viral titers 1, 2, 3, and 4 dpi, respectively; in contrast, compared with the WT, A372T titers were 1.8-, 5.5-, 31.1-, and 64.1-fold lower 1, 2, 3, and 4 dpi, respectively (Figure 4D). 2021 Cell Result SARS_CoV_2 A372T;D614G 170;22 175;27 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Concurrently, we generated the S D614G mutant, which increases replication in human cells. 2021 Cell Result SARS_CoV_2 D614G 33 38 S 31 32 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. EC50 values compared directly showed robust differences between the WT and A372T or N501Y (Figure 3B; both p < 0.0001 by one-way ANOVA with Dunnett's multiple comparisons test). 2021 Cell Result SARS_CoV_2 A372T;N501Y 75;84 80;89 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Following 48-h incubation at room temperature, the titer of D614G was higher than that of WT SARS-CoV-2 (p = 0.0303), which is consistent with a previous report. 2021 Cell Result SARS_CoV_2 D614G 60 65 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Following virus rescue, viral plaque morphology on Vero E6 cells was similar for all three viruses, although the A372T mutant plaques appear slightly smaller (Figure 4B). 2021 Cell Result SARS_CoV_2 A372T 113 118 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. For clarity, we will refer to the mutant as A372T because we reverted WT SARS-CoV-2 (A372) to its ancestral form (T372). 2021 Cell Result SARS_CoV_2 A372T 44 49 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Here we sought to define the effect of the S T372A mutation on viral replication in human cells. 2021 Cell Result SARS_CoV_2 T372A 45 50 S 43 44 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. In Calu-3 cells, the D614G mutant produced significantly higher titers than WT 1 day post-infection (dpi), but levels were similar for the remaining time points (Figure 4D; p = 0.0066 by 2-way ANOVA with Dunnett's correction at 1 dpi). 2021 Cell Result SARS_CoV_2 D614G 21 26 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. In contrast, EC50 values were markedly higher for the A372T mutant (26.29 +- 0.08 ng/mL), consistent with our molecular modeling data suggesting a weaker interaction with hACE2 compared with the WT. 2021 Cell Result SARS_CoV_2 A372T 54 59 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. N370 glycosylation of T372 S protein occurs in close structural proximity to the essential glycosylation site of N343, further providing additional N-glycan shielding of the RBD (Figure 2A). 2021 Cell Result SARS_CoV_2 T372S 22 28 RBD;N;S 174;148;27 177;149;28 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. No differences were observed 24 h after infection between the WT and A372T mutant, but later time points showed a marked reduction in replication for the A372T mutant (p = 0.0033, p < 0.0001, and p < 0.0001 for 2, 3, and 4 dpi, respectively). 2021 Cell Result SARS_CoV_2 A372T;A372T 69;154 74;159 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. SARS-CoV-2 S A372T reduces binding to human ACE2. 2021 Cell Result SARS_CoV_2 A372T 13 18 S 11 12 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Surface maps also reveal an additional space-filling and polar surface that is now occupied by the N370 N-glycan (Figures 2B and 2C). 2021 Cell Result SARS_CoV_2 N370N 99 105 N 104 105 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. The amino acid threonine in this position of the four Sarbecovirus members was substituted with alanine (Thr372Ala) in human SARS-CoV-2. 2021 Cell Result SARS_CoV_2 T372A 105 114 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. The N501Y mutation is present in several variants of concern and has been shown previously to increase binding to hACE2. 2021 Cell Result SARS_CoV_2 N501Y 4 9 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. The S D614G mutant was included because it now predominates worldwide and has been associated with higher titers in nasopharyngeal swabs in humans and increased replication in human cells and hamsters. 2021 Cell Result SARS_CoV_2 D614G 6 11 S 4 5 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. These results suggest that the S T372A mutation that occurred in the SARS-CoV-2 ancestral virus enhanced affinity to hACE2. 2021 Cell Result SARS_CoV_2 T372A 33 38 S 31 32 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. To determine whether A372T altered SARS-CoV-2 thermal stability, we incubated 105 plaque-forming units (PFUs) of WT SARS-CoV-2, D614G, or A372T at room temperature (~25 C) or 37 C to mimic environmental and human body temperature, respectively. 2021 Cell Result SARS_CoV_2 A372T;A372T;D614G 21;138;128 26;143;133 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. To further probe, in a simple model, the effect of the predicted glycosylation site at N370 as a result of the presence of a threonine at position 372 of S protein, N370 was glycosylated with an N-acetylglucosamine (GlcNAc) glycan and energy minimized on the T372 S protein model to observe any minor, local side chain readjustment as a result of a simple N-glycan presence. 2021 Cell Result SARS_CoV_2 T372S 259 265 N;N;S;S 195;356;154;264 196;357;155;265 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. We next evaluated the replication kinetics of each virus:WT, S A372T, and S D614G:in Vero E6 and Calu-3 cell lines, monkey kidney and human lung epithelial cell lines, respectively. 2021 Cell Result SARS_CoV_2 A372T;D614G 63;76 68;81 S;S 61;74 62;75 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. We probed hACE2 with RBDs from WT (A372), A372T, and N501Y as a positive control; D614G could not be used because it is not within the RBD. 2021 Cell Result SARS_CoV_2 A372T;D614G;N501Y 42;82;53 47;87;58 RBD;RBD 21;135 25;138 34292870 Inhalable nanocatchers for SARS-CoV-2 inhibition. Considering that the SARS-CoV-2 D614G variant exhibits a stronger infectious ability than the wild type and has become globally prevalent, the neutralization ability of NCs against the pseudotyped SARS-CoV-2 D614G variant was investigated. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G;D614G 32;208 37;213 34292870 Inhalable nanocatchers for SARS-CoV-2 inhibition. Notably, 293T cell-derived NVs without the overexpression of hACE2 showed rather weak neutralization ability against either wild-type SARS-CoV-2 or the D614G variant. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 152 157 34292870 Inhalable nanocatchers for SARS-CoV-2 inhibition. the NCs bound to the D614G variant exhibited a half maximal inhibitory concentration (IC50) at 16.3 mug/mL, comparable with that against the wild-type pseudovirus (9.5 mug/mL), demonstrating that our hACE2-containing NCs could act as a potent competitor with host cells for virus binding to protect cells from SARS-CoV-2 infection regardless of viral mutations. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 21 26 COVID-19 310 330 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. 3D and SI Appendix, Table S3; see Brief Methods), in which the central hubs are D614G in the spike (S) protein and two adjacent substitutions in the nucleocapsid (N) protein, R203K and G204R, the three most common positively selected mutations. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G;G204R;R203K 80;185;175 85;190;180 N;S;N;S 149;93;163;100 161;98;164;101 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. Additionally, apart from the selective advantage of a single replacement, it should be emphasized that D614G (but not G614D) is a central hub of the epistatic network. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G;G614D 103;118 108;123 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. Additionally, S 501T (in the same site) began to rise to prominence in Oceania in November. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 S501T 14 20 S 14 15 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. Additionally, S N439K, a signature mutation for variant B.1.258_DELTA that has been demonstrated to enable immune escape, is observed in a large portion of the tree. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N439K 16 21 S 14 15 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. Also, notably, although S 477N initially appeared in February/March 2020 in Europe, Oceania, and North America, it dramatically rose to prominence in Oceania in April, about 3 mo before this mutation became prominent elsewhere. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 S477N 24 30 S 24 25 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. Although not considered a candidate for positive selection in our analysis due to its NCN context, ORF8 S84L is a hub in the larger epistatic network including all strongly associated residues. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 S84L 104 108 ORF8 99 103 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. As a result, the reverse replacement G614D appears often enough to pass our statistical criteria for positive selection. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 G614D 37 42 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. As discussed above, these early mutations (including S G614D) might provide only a modest selective advantage in isolation but exert a much greater effect through multiple epistatic interactions. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 G614D 55 60 S 53 54 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. As we suggest for S D614G, these variant signature mutations are likely to exert a greater influence through multiple epistatic interactions than in isolation, and each signature mutation can be a member of multiple epistatic ensembles beyond the group of signature mutations within which it was originally identified. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 20 25 S 18 19 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. By increasing the receptor affinity, D614G apparently opens up new adaptive routes for later steps in the viral lifecycle. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 37 42 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. Four more substitutions in the RBD, among others, N234Q, L452R, A475V, and V483A, have been demonstrated to confer antibody resistance. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 A475V;L452R;N234Q;V483A 64;57;50;75 69;62;55;80 RBD 31 34 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. In addition to 614G, 31 spike mutations, most within the RBD, are signature mutations for divergent clades v1 to v3; emergent variants vAfrica or vOceania (see below); or established variants B.1.1.7, B.1.1.7_E484K, B.1.258_delta, B.1.351, B.1.429, P.1, or P.2 (SI Appendix, Table S4, List 1). 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 E484K 209 214 S;RBD 24;57 29;60 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. In addition to the many mutations of interest in the N and S proteins, Orf3a Q57H is a signature mutation for partitions 6, 7, and v1. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 Q57H 77 81 ORF3a;N;S 71;53;59 76;54;60 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. In fact, the most statistically significant signature mutation (based on the Kullback-Leibler divergence) for vAfrica (consistent with variant B.1.351; see below) is N T205I. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 T205I 168 173 N 166 167 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. In particular, S N501Y and N S235F are both signature mutations for variants B.1.1.7 and B.1.1.7_E484K (SI Appendix, Table S4, List 2), and this pair is in the top 25% of cooccurring pairs in our network, ranked by lowest probability of random cooccurrence. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N501Y;S235F;E484K 17;29;97 22;34;102 N;S 27;15 28;16 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. N234Q, A475V, and V483A were never or rarely found in our alignment, but L452R is a signature of variant B.1.429. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 A475V;L452R;V483A;N234Q 7;73;18;0 12;78;23;5 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. N501T in the same site is of additional concern and has also been observed in mink populations. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N501T 0 5 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. N501Y is among the 22 strongest candidates for positive selection and has been demonstrated to escape neutralizing antibodies. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N501Y 0 5 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. Of greatest concern is perhaps N501Y. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N501Y 31 36 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. Of particular interest seems to be ORF8 Q27*, which is a signature for variants B.1.1.7 and B.1.1.7_E484K and could be epistatically linked to positively selected residues including N R203K and S D614G. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G;Q27X;R203K;E484K 196;40;184;100 201;44;189;105 ORF8;N;S 35;182;194 39;183;195 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. Partition 8, the only partition where N 203K and 204R were fixed, became dominant in every region outside of North America in the period that followed (SI Appendix. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N203K 38 44 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. Q57H is the fourth most common positively selected mutation. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 Q57H 0 4 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. S 477N is a signature mutation for v1 stemming from partition 3; however, the sequences from Oceania bearing this mutation from summer 2020 are in partition 8. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 S477N 0 6 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. S 484K first rose to prominence in South America in September 2020, while appearing in sequences from Europe and North America as early as July. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 S484K 0 6 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. Spike D614G appears to boost the infectivity of the virus, possibly by increasing the binding affinity between the spike protein and the cell surface receptor of SARS-CoV-2, ACE2. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 6 11 S;S 0;115 5;120 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. The extinction of the earliest partitions, 1 and 2, corresponds to the advent of S D614G, which became fixed in all other partitions and was globally ubiquitous by June 2020. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 83 88 S 81 82 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. This amino acid replacement is a signature of variants B.1.1.7, B.1.1.7_E484K, and B.1.351, P.1; divergent clade v2; and emergent variant vAfrica. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 E484K 72 77 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. Three of these signature mutations pass the strict criteria for positive selection:S N501Y, S S477N, and S V1176F:and S N501Y makes the shortlist of the 22 strongest candidates. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N501Y;N501Y;S477N;V1176F 85;120;94;107 90;125;99;113 S;S;S;S 83;92;105;118 84;93;106;119 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. Thus, the key mutation S 501Y first emerged in May 2020 in Oceania, months before rising to global prominence in November. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 S501Y 23 29 S 23 24 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. To resolve this trend, at least two principal variants, N 203K/204R in partition 8 and N 220V in partition 5, have to be considered, and we identified six key amino acid replacements of interest for this period (N 203K/204R, N 220V, N 199L, N 194L, N205I, and N206F). 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N194L;N199L;N220V;N220V;N205I;N206F 241;233;87;225;249;260 247;239;93;231;254;265 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. E484K replacement alters the immunologic profile of SARS-CoV-2, and Greaney et al reported that E484Q reduced viral neutralization for some plasma samples. 2021 The American journal of pathology Result SARS_CoV_2 E484Q;E484K 96;0 101;5 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. Early in the pandemic, it was reported that nasopharyngeal samples from patients infected with strains having the spike protein D614G variant have, on average, significantly lower CT values (considered to be a proxy for higher virus loads) on initial diagnosis. 2021 The American journal of pathology Result SARS_CoV_2 D614G 128 133 S 114 119 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. Eighteen patients with this N440K replacement were identified, and 10 patients had the identical combination of spike amino acid replacements: L18R, T95I, R158S, N440K, D614G, P681H, A688V, S735A, and T1027I. 2021 The American journal of pathology Result SARS_CoV_2 A688V;D614G;L18R;N440K;N440K;P681H;R158S;S735A;T1027I;T95I 183;169;143;28;162;176;155;190;201;149 188;174;147;33;167;181;160;195;207;153 S 112 117 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. For example, E484K polymorphism was found in samples from 69 patients infected with VOI P.2 and 43 patients infected with the newly described variant R.1. 2021 The American journal of pathology Result SARS_CoV_2 E484K 13 18 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. N440K Spike Protein Replacement. 2021 The American journal of pathology Result SARS_CoV_2 N440K 0 5 S 6 11 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. Of note, 11 patients infected with B.1.1.7 plus the E484K amino acid change, and one patient each infected with B.1.1.7 sample plus either an E484Q or an E484D amino acid change were identified. 2021 The American journal of pathology Result SARS_CoV_2 E484D;E484K;E484Q 154;52;142 159;57;147 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. R.1 has the following core spike protein amino acid changes: W152L, E484K, D614G, and G769V (Outbreak.info, https://outbreak.info/situation-reports?pango=r.1, last accessed May 17, 2021). 2021 The American journal of pathology Result SARS_CoV_2 D614G;E484K;G769V;W152L 75;68;86;61 80;73;91;66 S 27 32 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. Some R.1 variants also contain R21T, L54F, S254P, or P1162L changes. 2021 The American journal of pathology Result SARS_CoV_2 L54F;P1162L;R21T;S254P 37;53;31;43 41;59;35;48 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. The N440K amino acid change in spike protein has recently gained interest because samples with this polymorphism have been reported to cause widespread COVID-19 in some states in India, increase viral titer in vitro, and have been associated with resistance to some candidate monoclonal antibody therapies. 2021 The American journal of pathology Result SARS_CoV_2 N440K 4 9 S 31 36 COVID-19 152 160 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. These two variants are characterized by a core group of amino acid replacements in spike protein: L452R, T478K or E484Q, D614G, and P681R (Figure 6). 2021 The American journal of pathology Result SARS_CoV_2 D614G;E484Q;L452R;P681R;T478K 121;114;98;132;105 126;119;103;137;110 S 83 88 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. Three hundred and sixty-three samples were identified with changes at E484 (E484K, n = 353; E484Q, n = 9; and E484D, n = 1) that occurred in many genetically diverse SARS-CoV-2 lineages were identified, some of which have not shared a recent common ancestor. 2021 The American journal of pathology Result SARS_CoV_2 E484D;E484Q;E484K 110;92;76 115;97;81 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. Two additional patients had SARS-CoV-2 of this same spike protein genotype with an additional T376I amino acid replacement. 2021 The American journal of pathology Result SARS_CoV_2 T376I 94 99 S 52 57 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. A notable feature was the mutation at nucleotide position 27707, leading to a change from alanine to valine in ORF7a sequence, at aminoacid 105 (A105V) and present in 17 out of the 62 analyzed samples. 2021 Frontiers in microbiology Result SARS_CoV_2 A105V 145 150 ORF7a 111 116 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Another recurring mutation is represented by a change from cytosine to adenine at position 3225, leading to a substitution of threonine by asparagine at position 987 (T987N) of the ORF1ab region. 2021 Frontiers in microbiology Result SARS_CoV_2 T987N;T987N 126;167 165;172 ORF1ab 181 187 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Moreover, one cluster from Suceava is formed based on the mutation at position 27707 (A105V), in the ORF7a region. 2021 Frontiers in microbiology Result SARS_CoV_2 A105V 86 91 ORF7a 101 106 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Mutation at position 27707 (C > T) altered the ORF7a protein, 121 aminoacid residues long, changing the alanine in position 105 to a valine. 2021 Frontiers in microbiology Result SARS_CoV_2 C27707T;A105V 21;104 34;139 ORF7a 47 52 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Patients infected with the virus carrying the A105V mutation had a significant increase in C-Reactive Protein (9.66 +- 2.7 mg/dL) compared to the wild type (5.45 +- 1.14 mg/dL), P = 0.039. 2021 Frontiers in microbiology Result SARS_CoV_2 A105V 46 51 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. The same recurring mutations were identified in the deceased patients, with 42.8% presenting the A105V mutation, 42.8% the T987N mutations and 28.5%, the nucleotide deletion at position 29725 (Figure 5). 2021 Frontiers in microbiology Result SARS_CoV_2 A105V;T987N 97;123 102;128 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. The second mutation considered for modeling was T987N in ORF1ab. 2021 Frontiers in microbiology Result SARS_CoV_2 T987N 48 53 ORF1ab 57 63 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. The well-known S-protein mutation, 614 D > G that gives rise to GISAID "G" clade, was present in all 62 samples. 2021 Frontiers in microbiology Result SARS_CoV_2 D614G 35 44 S 15 16 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. We found that 30% of the mild/severe cases had the A105V mutation in the ORF7a region and 8.9% presented a T987N mutation in NSP3 domain, ORF1ab region. 2021 Frontiers in microbiology Result SARS_CoV_2 A105V;T987N 51;107 56;112 ORF1ab;ORF7a;Nsp3 138;73;125 144;78;129 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. In the primer-probe rRT PCR method, two primers (D614G IN forward and reverse) with two probes (D-FAM and G-HEX) were designed for detecting D614 and G614 variants of SARS CoV-2, respectively. 2021 Meta gene Result SARS_CoV_2 D614G 49 54 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Incubations of PCR products, amplified by D614G Out primers, with BtsCI enzyme, produced no cleavages indicated that only G614 mutants of SARS CoV-2 are prevalent in the region. 2021 Meta gene Result SARS_CoV_2 D614G 42 47 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A879S mutation was present in the USA, Scotland, Japan, India, Finland, UK. 2021 Virusdisease Result SARS_CoV_2 A879S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. And A1020S and A1078S mutations are present in the USA and South Africa and Spain. 2021 Virusdisease Result SARS_CoV_2 A1020S;A1078S 4;15 10;21 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. H1101Y mutations are present in the USA, Scotland, and India. 2021 Virusdisease Result SARS_CoV_2 H1101Y 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. H655Y mutation was observed in the USA, Scotland, China, South Africa while P809S mutation was present in the USA, Scotland, South Africa, Germany. 2021 Virusdisease Result SARS_CoV_2 P809S;H655Y 76;0 81;5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. However, D614G mutations are high in worldwide isolates. 2021 Virusdisease Result SARS_CoV_2 D614G 9 14 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. In the USA, the total sequences that we have analyzed are 2,583 and the number of D614G mutations are 2025 (82%). 2021 Virusdisease Result SARS_CoV_2 D614G 82 87 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Moreover, our study found common mutations and the data was presented in Table 4; L5F mutation was identified in the USA, Scotland, Japan, South Africa, France, India, Italy, Norway, and Peru. 2021 Virusdisease Result SARS_CoV_2 L5F 82 85 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Out of total 734, 625, 592, 556, 542, 462, 339, sequences from China, Japan, South Africa, France, India, Spain and Germany, D614G mutations are 43 (6%), 331 (53%), 579 (98%), 517(93%), 179 (33%), 276 (60%) and 292 (86%) respectively. 2021 Virusdisease Result SARS_CoV_2 D614G 125 130 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Out of total Finland sequences 263, D614G are 253 (96%); Russia sequences 240, D614G are 211 (88%); Brazil sequences 220, D614G are 187 (85%); UK sequences 141, D614G 84 (60%); Italy sequences 128, D614G are 120 (95%); Norway sequences 53, D614G are 43 (81%); Australia sequences 48, D614G are 13 (27%); Peru sequences 34, D614G are 29 (85%); Mexico sequences 20 of D614G are 9 (45%). 2021 Virusdisease Result SARS_CoV_2 D614G;D614G;D614G;D614G;D614G;D614G;D614G;D614G;D614G 36;79;122;161;198;240;284;323;366 41;84;127;166;203;245;289;328;371 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Similarly in Scotland out of 1134 sequences, the number of D614G mutations are 847 (75%). 2021 Virusdisease Result SARS_CoV_2 D614G 59 64 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T22I mutation was observed in the USA, India, Germany, and Iran. 2021 Virusdisease Result SARS_CoV_2 T22I 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. The frequent mutations in different isolates are L5F, T22I, T29I, H49Y, L54F, V90F, S98F, S221L, S254F, V367F, A520S, T572I, D614G, H655Y, P809S, A879S, D936Y, A1020S, A1078S, and H1101Y. 2021 Virusdisease Result SARS_CoV_2 A1020S;A1078S;A520S;A879S;D614G;D936Y;H1101Y;H49Y;H655Y;L54F;L5F;P809S;S221L;S254F;S98F;T22I;T29I;T572I;V367F;V90F 160;168;111;146;125;153;180;66;132;72;49;139;90;97;84;54;60;118;104;78 166;174;116;151;130;158;186;70;137;76;52;144;95;102;88;58;64;123;109;82 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. The L54F mutation was present in the USA, China, South Africa, France, and India. 2021 Virusdisease Result SARS_CoV_2 L54F 4 8 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. The other major mutation at D614G at the position 614 with glycine instead of aspartic acid in the spike protein. 2021 Virusdisease Result SARS_CoV_2 D614G 28 33 S 99 104 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. The other mutations, S98F mutation (USA, China, and Spain), S221L mutation (USA and South Africa), S254F and V367F mutations (USA and France), A520S mutations (USA and India), T572I mutation (USA, India and along with France) were observed in various countries. 2021 Virusdisease Result SARS_CoV_2 A520S;S221L;S254F;S98F;T572I;V367F 143;60;99;21;176;109 148;65;104;25;181;114 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. The T29I mutation variant is present in Spain and Germany, whereas H49Y is the most common mutation in the USA, India, China, and Mexico. 2021 Virusdisease Result SARS_CoV_2 H49Y;T29I 67;4 71;8 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. These spike protein mutations are present at both upstream and downstream of the receptor-binding domain (RBD) and the mutation Q271R has been found to affect the secondary structure of the S1 domain. 2021 Virusdisease Result SARS_CoV_2 Q271R 128 133 S;RBD 6;106 11;109 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V90F mutation was observed in the USA and Scotland. 2021 Virusdisease Result SARS_CoV_2 V90F 0 4 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. 4A, explains the MADP1 residual fluctuation in both complexes, where amino acid residues from 1 to 60 show less fluctuation in wild type complex compared to the mutant (C241T) complex. 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 169 174 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. 6 , Dynamics cross-correlation matrix was calculated between inter and intra protein motions in both wild-type and mutant (C241T) complexes. 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 123 128 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. Based on the docking score, wild-type RNA showed to have a better binding profile with a high binding constant value (more negative) of -143.0+-3.5 compared to mutant complex -138.4+-1.6, as well as the RMSD value for MADP1 was 0.9+-0.6 compared to the mutated (C241T) sequence was 1.1+-0.7 (see Table 2 for details). 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 262 267 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. C241T mutation leads to structural changes in the folding of RNA (Supplementary Figure S2) which in turn affects the binding of MADP1 with SL1 sequence of 5'UTR and hnRNP1 with TLR sequence within SL3. 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 0 5 5'UTR 155 160 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. Dynamics of SL4, where the mutation C241T was observed is important to create this enhance cavity around wild-type complex which is further elaborated from RMSF studies. 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 36 41 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. For MADP1, a total of 117 structures in 8 cluster(s) were clustered in HADDOCK for wild type complex representing 58.5% of the water-refined models, while 119 structures in 8 cluster(s), were generated for the mutant sequence (C241T) which represented 59.5% of the water-refined models. 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 227 232 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. From both forcefields C241T mutation affects the change in 5'UTR which leads decreased stability of 5'UTR with host transcription factors. 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 22 27 5'UTR;5'UTR 59;100 64;105 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. In the present study, molecular dynamics and interaction of two human transcription factors MADP1 and hnRNP1 were studied with a most common 5' UTR mutation C241T in the viral genome. 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 157 162 5'UTR 141 147 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. Lys42, showed more positive correlation with wild-type RNA compared to Mutant RNA (C241T). 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 83 88 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. Major aim was to justify the effect of C241T mutation in two different forcefields. 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 39 44 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. MD simulations of four complexes were performed for 100ns because early dissociation of MADP1 with Mutant (C241T) was observed at 98-99 ns (ns) (Supplementary Videos S1 and S2). 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 107 112 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. Molecular dynamics (MD) simulations were performed on two variants (C241T) of 5' UTR with two different host transcription factors MADP1 and hnRNP1 after performing molecular docking in HADDOCK. 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 68 73 5'UTR 78 84 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. Nucleotide sequences of the wild type and mutant (C241T) viral 5' UTR sequences were taken from GenBank accession id MN908947.3 and secondary structures were generated (Supplementary Table S1). 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 50 55 5'UTR 63 69 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. Our major aim was to study the effect the mutation C241T with respect to host replication factor MADP1, docking and molecular simulation studies shows the effect of mutation in favour of host. 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 51 56 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. Overall wild-type complex seems to be more stable compared to mutant (C241T) complex with respect to both proteins. 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 70 75 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. RNA secondary structure was predicted using X3-DNA-DSSR in dot-bracket format and the data were visualized in Varna-GUI and structural differences due to C241T were interpreted. 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 154 159 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. The 5' UTR variant C241T has emerged in March 2020 and its one of the most observed variants in genomes sequenced in 2020, with a frequency of 0.505. 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 19 24 5'UTR 4 10 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. To correlate these variations in RNA structure with the favourable or non-favourable binding of host transcription factors, protein-RNA docking and the resulting binding energy was calculated to identify the effects of binding between both sequences wild-type and mutant (C241T) RNA. 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T 272 277 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. All together, these results suggest that the putative function of the D614G mutation in the S protein of SARS-CoV-2 is dependent on enhanced cleavage at the furin substrate motif at the S1/S2 boundary, which contributes to an increased membrane fusion activity. 2021 mBio Result SARS_CoV_2 D614G 70 75 Membrane;S 236;92 244;93 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. Consistently with this finding, the difference in the effects of S-D614 and S-G614 on reporter activity was abolished when the furin substrate site was mutated by introduction of the R682A substitution. 2021 mBio Result SARS_CoV_2 R682A 183 188 S;S 65;76 66;77 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. Genetic heterogeneity beyond the D614G substitution among different SARS-CoV-2 isolates might cause confusion regarding our observation. 2021 mBio Result SARS_CoV_2 D614G 33 38 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. The results obtained with the virus isolates suggest a possible functional effect of the D614G substitution in increasing virus production. 2021 mBio Result SARS_CoV_2 D614G 89 94 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. Therefore, these results suggested a putative effect of the D614G substitution in enhancing the cleavage of the S protein. 2021 mBio Result SARS_CoV_2 D614G 60 65 S 112 113 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. To confirm the effect of the D614G substitution on S and ACE2 binding-mediated cell syncytium formation, we established a luciferase-based reporter assay to quantitatively compare levels of syncytium induction by the S-G614 and S-D614 proteins (schematically illustrated in. 2021 mBio Result SARS_CoV_2 D614G 29 34 S;S;S 51;217;228 52;218;229 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. To examine if the D614G substitution might contribute to increased accessibility of the S protein for cleavage by furin, we compared the patterns of S protein cleavage at this site for viruses containing either the S-G614 or the S-D614 protein. 2021 mBio Result SARS_CoV_2 D614G 18 23 S;S;S;S 88;149;215;229 89;150;216;230 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. To investigate the effect of the D614G mutation on SARS-CoV-2 replication, we first compared the virus titers of 18 clinical SARS-CoV-2 isolates (NTU01 to NTU18) (see Tables S1 and S2 in the supplemental material) containing either S-D614 or S-G614 from infected Calu-3 and Vero E6 cells. 2021 mBio Result SARS_CoV_2 D614G 33 38 S;S 232;242 233;243 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. At one month post-completion of the two-dose regimen, the Sputnik V vaccine generated respectable virus neutralizing titers (VNT) against rcVSV-CoV2-S bearing the WT (D614G) and B.1.1.7 spike proteins. 2021 Nature communications Result SARS_CoV_2 D614G 167 172 S;S 186;149 191;150 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Conversely, the steep Hill slope for the E484K curves resulted in maximal neutralization potencies that were not significantly different from WT or B.1.1.7 despite significantly lower reciprocal IC50 values (compare. 2021 Nature communications Result SARS_CoV_2 E484K 41 46 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Experimental measurements of both RBD and trimeric spike binding to ACE2 have revealed that the E484K mutation alone does not confer increase binding affinity for ACE2 unlike N501Y. 2021 Nature communications Result SARS_CoV_2 E484K;N501Y 96;175 101;180 S;RBD 51;34 56;37 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Furthermore, the E484K mutant was more sensitive to RBD-Fc inhibition than B.1.1.7. 2021 Nature communications Result SARS_CoV_2 E484K 17 22 RBD 52 55 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Group (C) sera generally exhibited effective neutralization of WT, B.1.1.7, and even E484K at high serum concentrations, but not B.1.351. 2021 Nature communications Result SARS_CoV_2 E484K 85 90 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. However, GMT against B.1.351 and E484K was reduced by a median 6.8- and 2.8-fold, respectively, compared to WT. 2021 Nature communications Result SARS_CoV_2 E484K 33 38 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. In contrast, Group (B) sera neutralized E484K and B.351 with similar potencies to WT and B.1.1.7, especially at high serum concentrations. 2021 Nature communications Result SARS_CoV_2 E484K 40 45 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Indeed, the now concerning E484K mutation, present in many variants of concern (VOC), was identified as an antibody escape mutation using rcVSV-CoV-2-S. 2021 Nature communications Result SARS_CoV_2 E484K 27 32 S 150 151 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Next, we generated isogenic rcVSV-CoV2-S expressing the B.1.1.7, B.1.351, or E484K S to evaluate the neutralizing activity of Sputnik V vaccine sera from Argentina. 2021 Nature communications Result SARS_CoV_2 E484K 77 82 S;S 39;83 40;84 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. One serum sample (SP012) exhibited little to no neutralizing activity against WT, E484K and B.1.351, yet it neutralized B.1.1.7 as well as Group A-C sera. 2021 Nature communications Result SARS_CoV_2 E484K 82 87 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Our data reinforces the notion that the mechanism underlying the increased neutralization resistance of E484K containing variants and mutants do not involve ACE2 binding affinity per se, but rather affects a key immunodominant epitope targeted by a significant class of human neutralizing antibodies, variably termed as RBM class II, RBS-B, or Cluster 2 antibodies. 2021 Nature communications Result SARS_CoV_2 E484K 104 109 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. The Hill Slope of the neutralization curves against B.1.351 was significantly different from WT, B.1.1.7 and E484K. 2021 Nature communications Result SARS_CoV_2 E484K 109 114 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. This is not surprising as both harbor the N501Y mutation known to enhance affinity of RBD for ACE2. 2021 Nature communications Result SARS_CoV_2 N501Y 42 47 RBD 86 89 34314050 SARS-CoV-2 R.1 lineage variants that prevailed in Tokyo in March 2021. WGS analysis of the selected samples revealed that the 501N + 484K type is an R.1 lineage (W152L, E484K, D614G, G769V) variant, which is the sublineage of B.1.1.316. 2021 Journal of medical virology Result SARS_CoV_2 D614G;E484K;G769V;W152L 105;98;112;91 110;103;117;96 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. 3B) exhibited a more stable system, where the complex converged to 2 A at 5 ns, compared to P681H.Subsequentlythe complex stabilised at 2 A from 5 to 30 ns. 2021 Virus research Result SARS_CoV_2 P681H 92 97 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. After which, the complex converged to 2.5 A from 30 to 35 ns, where the B.1.1.7-furin complex fluctuated between 2.5 to 3 A, for the remainder of the simulation (100 ns) indicating a more stable complex than P681H-furin complex. 2021 Virus research Result SARS_CoV_2 P681H 208 213 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Binding energies of furin to P681H and B.1.1.7. 2021 Virus research Result SARS_CoV_2 P681H 29 34 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Furin docking to P681H and B.1.1.7. 2021 Virus research Result SARS_CoV_2 P681H 17 22 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Furin-S-protein docking was conducted with HDOCK to elucidate how the conformational changes of P681H and B.1.1.7 S-protein structures affect the binding to furin. 2021 Virus research Result SARS_CoV_2 P681H 96 101 S;S 6;114 7;115 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Genome sequencing of the new B.1.1.7 SARS-CoV-2 strain presented missense mutations (N501Y, A570D, P681H, D614G, T716I, S982A, D1118H) and three deletions in residues H69, V70, Y144. 2021 Virus research Result SARS_CoV_2 A570D;D1118H;D614G;P681H;S982A;T716I;N501Y 92;127;106;99;120;113;85 97;133;111;104;125;118;90 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Here, we compared the S-protein-P681H structure with the S-protein-B.1.1.7 variant structure. 2021 Virus research Result SARS_CoV_2 P681H 32 37 S;S 22;57 23;58 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Molecular dynamic simulations of P681H and B.1.1.7 S-protein bound to furin. 2021 Virus research Result SARS_CoV_2 P681H 33 38 S 51 52 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Moreover, surface accessible surface area (SASA) analysis showed that the B.1.1.7 (P681H) HRRAR, in the furin cleavage site residues, demonstrated a SASA at the H (163.075), A (176.744), A (216.679), A (100.593), A (84.162), in contrast, the WT PRRAR furin site showed a SASA of P (137.106), A (119.285), A (115.560), A (7.003), A (71.406). 2021 Virus research Result SARS_CoV_2 P681H 83 88 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. One of the notable mutations in the B.1.1.7 variant is the P681H, which is a substitution of proline (P) to histidine (H) on the S-protein "PRRAR" furin cleavage site. 2021 Virus research Result SARS_CoV_2 P681H 59 64 S 129 130 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. S-protein P681H and B.1.1.7 mutations. 2021 Virus research Result SARS_CoV_2 P681H 10 15 S 0 1 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Since the substitution of P681H on the furin cleavage site may affect S-protein structure, enhancing the infectivity of the new SARS-CoV-2 variant. 2021 Virus research Result SARS_CoV_2 P681H 26 31 S 70 71 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Subsequently, from 40 to 100 ns, the S-protein-P681H-furin complex displayed high dynamic fluctuations presenting high structural perturbation, with the RMSD decreasing to 2 A between 40-60 ns and then increased back to 3 A at the end of the simulation. 2021 Virus research Result SARS_CoV_2 P681H 47 52 S 37 38 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. The binding affinity of furin to B.1.1.7 S-protein presented binding free energy of -57.08+-0.73 (kcal/mol) compared with -12.4+-0.45 kcal/mol for furin bound to P681H S-protein, indicating that the mutations and deletions present in the B.1.1.7 variant S-protein structure resulted in a tighter binding to furin than the S-protein-P681H mutation. 2021 Virus research Result SARS_CoV_2 P681H;P681H 162;332 167;337 S;S;S;S 41;168;254;322 42;169;255;323 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. The impact of S-protein-B.1.1.7 and P681H on the interaction with furin was examined by calculating the Calpha-atoms root mean square deviation (RMSD) and root-mean-square fluctuation (RMSF) trajectories. 2021 Virus research Result SARS_CoV_2 P681H 36 41 S 14 15 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. The P681H and B.1.1.7-furin complexes demonstrated a similar RMSF profile with the P681H-complex demonstrating higher residual fluctuations neat the loop region between residues 800 and 1000 where furin binds to S-protein. 2021 Virus research Result SARS_CoV_2 P681H;P681H 4;83 9;88 S 212 213 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. The P681H-furin complex demonstrated a deviation from 0 to 3 A in the initial 20 ns. 2021 Virus research Result SARS_CoV_2 P681H 4 9 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. The RMSF values from the 100 ns simulations of S-protein-P681H and B.1.1.7 bound to furin are depicted in. 2021 Virus research Result SARS_CoV_2 P681H 57 62 S 47 48 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. The S-protein-furin binding interaction occurs through conformational selection or an induced-fit mechanism (Tsai et al., 2001,), resulting in a more stable structure between B.1.1.7 and furin than the P681H-furin complex. 2021 Virus research Result SARS_CoV_2 P681H 202 207 S 4 5 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. The S-protein-P681H and S-protein-B.1.1.7 variant were modeled with the Swiss Model server using the 3.5-A-resolution cryo-EM structure of the SARS-CoV-2 S-protein (PDB ID: 6VSB) as a scaffold. 2021 Virus research Result SARS_CoV_2 P681H 14 19 S;S;S 4;24;154 5;25;155 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. The S-protein-P681H. 2021 Virus research Result SARS_CoV_2 P681H 14 19 S 4 5 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. The stability and dynamics of P681H-furin and B.1.1.7-furin S-protein complexes are presented by RMSD values. 2021 Virus research Result SARS_CoV_2 P681H 30 35 S 60 61 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. To characterize the structural stability and dynamic features at the atomic and spatial resolution, S-protein P681H-Furin and B.1.1.7-furin complexes, we ran 100 ns MD simulations using AMBER 20 package. 2021 Virus research Result SARS_CoV_2 P681H 110 115 S 100 101 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Whereby, a recent structural study involving B.1.17 variant suggested the N501Y variant in the RBD domain enhanced the binding to ACE2, resulting in a more infective virus strain. 2021 Virus research Result SARS_CoV_2 N501Y 74 79 RBD 95 98 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. In total, four amino acid changes (V3G, S50L, N87S, and A222V) and two deletions (18-30del and 141-144del) occurred in the virus spike protein. 2021 mSphere Result SARS_CoV_2 A222V;N87S;S50L;V3G 56;46;40;35 61;50;44;38 S 129 134 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. Of note, two SNPs (T21570G and C21771T, leading to spike amino acid changes V3G and S50L) detected in this sample displayed intrahost intermediate frequency (52% and 93%), suggesting that they might be recent emerging mutations. 2021 mSphere Result SARS_CoV_2 C21771T;S50L;V3G;T21570G 31;84;76;19 38;88;79;26 S 51 56 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. The outbreak-causing SARS-CoV-2 belongs to COG-UK lineage B.1.1.401 and Nextstrain clade 20B, carrying the spike amino acid change D614G (Table 1). 2021 mSphere Result SARS_CoV_2 D614G 131 136 S 107 112 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. As given in Table 1, it can be seen that the substitution at position (AWLQAIAS) T2W increased the binding affinity from - 9.4 kcal/mol to - 11.70 kcal/mol. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 T2W 81 84 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. For T2W, the total binding energy was observed to be -70.04, while the vdW was reported to be - 81.01 kcal/mol. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 T2W 4 7 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. For the decoy peptide T2Y, the total binding energy was reported to be - 66.47 kcal/mol. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 T2Y 22 25 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. Furthermore, the total binding energy for L3R was reported to be - 67.47 kcal/mol with - 80.73 kcal/mol vdW, - 225.82 kcal/mol electrostatic, and -9.52 kcal/mol SASA. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 L3R 42 45 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. In addition, the Rg value for the A5W was reported to be 22.1A. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 A5W 34 37 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. In addition, the T2Y complex remained more stable when compared to the wild and T2W. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 T2W;T2Y 80;17 83;20 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. In case of the L3R peptide the energy paradigm changed by at different residues. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 L3R 15 18 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. In the case of (AYLQAIAS) T2Y substitution, the binding affinity was observed to be - 11.56 kcal/mol, while the dAffinity was reported to be -1.00 kcal/mol. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 T2Y 26 29 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. In the case of A5W (ATLQWIAS) substitution, extra interactions with the key residue His41 were observed. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 A5W 15 18 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. In the case of A5W, both the vdW and electrostatic energies increased when compared to the wild type. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 A5W 15 18 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. In the case of L3R, the average RMSD remained ~ 2.0A, with an acceptable convergence between 55 and 60 ns. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 L3R 15 18 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. In the case of L3R, the systems remained compact, but convergence between 80 and 100 ns was observed, which is in comparison with the RMSD, which shows a little unstable behavior. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 L3R 15 18 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. In the case of T2Y, the system was comparatively more compact than the wild type and T2W. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 T2W;T2Y 85;15 88;18 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. In the case of the T2W and T2Y, the flexibility increased at the substitution point, while the L3R and A5W flexibility decreased. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 A5W;L3R;T2W;T2Y 103;95;19;27 106;98;22;30 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. In the case of wild-type peptide complex, the first three eigenvectors contributed 72% variance to the total observed motion, while in T2W 72%, in T2Y 42%, in L2R and A5W accounted for 33% variance in motion. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 A5W;L2R;T2W;T2Y 167;159;135;147 170;162;138;150 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. In the wild-type and T2Y peptide complexes, more periodic jumps and continuous overlapping can be observed, while in the case of T2W, L3R and A5W showed localized fluctuations. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 A5W;L3R;T2W;T2Y 142;134;129;21 145;137;132;24 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. On the other hand, the A5W system also remained stable, with a convergence between 87-88 ns. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 A5W 23 26 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. On the other hand, the Rg of the T2W remained stable, and the system showed more compactness. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 T2W 33 36 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. On the other hand, the T2W system relatively showed higher RMSD, but no major convergence was observed like the wild type. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 T2W 23 26 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. On the other hand, the total binding energy for A5W was reported to be - 65.55 kcal/mol. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 A5W 48 51 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. The affinity for L3R was reported to be - 11.64 kcal/mol. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 L3R 17 20 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. The average Rg for L3R was observed to 22.2A. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 L3R 19 22 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. The average Rg value for T2Y was 22.2A. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 T2Y 25 28 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. The average RMSD for A5W was also reported to be ~ 2.0A. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 A5W 21 24 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. The average RMSD for the T2W was ~ 2.0A. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 T2W 25 28 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. The electrostatic energy for T2W was reported to be - 111.12 kcal/mol, while SASA was observed to be - 9.6 kcal/mol. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 T2W 29 32 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. The replacement of (ATRQAIAS) L3R shifts the interaction paradigm and favors significant interactions through the binding energy is relatively lower than the first two peptides. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 L3R 30 33 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. The Rg value for T2Y decreased after 50 ns, which shows the tight binding of the peptide to the receptor. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 T2Y 17 20 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. The SASA for T2Y was reported to be - 9.55 kcal/mol. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 T2Y 13 16 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. The vdW and electrostatic energies for T2Y were observed to be - 79.08 kcal/mol and - 106.72 kcal/mol, respectively. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 T2Y 39 42 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. The vdW for A5W was reported to be - 76.45 kcal/mol, while electrostatic for A5W was observed to be - 124.13 kcal/mol. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 A5W;A5W 12;77 15;80 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. This substitution of Tyrosine, an aromatic amino acid, favors an extra interaction with Thr190 along with those reported in T2W. 2021 Interdisciplinary sciences, computational life sciences Result SARS_CoV_2 T2W 124 127 34326308 Structural and functional basis for pan-CoV fusion inhibitors against SARS-CoV-2 and its variants with preclinical evaluation. Moreover, variants with combinational mutations in S protein, including K417N/E484K, N501Y/K417N, N501Y/E484K and N501Y/K417N/E484K, were still sensitive to EK1 and EK1C4. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 K417N;N501Y;N501Y;N501Y;E484K;E484K;E484K;K417N;K417N 72;85;98;114;78;104;126;91;120 77;90;103;119;83;109;131;96;125 S 51 52 34326308 Structural and functional basis for pan-CoV fusion inhibitors against SARS-CoV-2 and its variants with preclinical evaluation. Most recently, the newly emerged variants carrying crucial mutations in their S proteins, e.g., K417N, E484K, N501Y or D614G, quickly became the locally dominant variants. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G;E484K;K417N;N501Y 119;103;96;110 124;108;101;115 S 78 79 34326308 Structural and functional basis for pan-CoV fusion inhibitors against SARS-CoV-2 and its variants with preclinical evaluation. Recently, some variants with mutation in HR1 region were also identified (https://www.gisaid.org/), including A924V, I931F/V, I934M/T/V, K947I/R/T, D950H/N/Y, V951L, V952A and L959V. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 A924V;D950H;D950N;D950Y;I931F;I931V;I934M;I934T;I934V;K947I;K947R;K947T;L959V;V951L;V952A 110;148;148;148;117;117;126;126;126;137;137;137;176;159;166 115;157;157;157;124;124;135;135;135;146;146;146;181;164;171 34326308 Structural and functional basis for pan-CoV fusion inhibitors against SARS-CoV-2 and its variants with preclinical evaluation. To explore whether EK1 peptides are antivirally active against infection mediated by spike protein carrying these mutations, we assessed their antiviral efficacy on infection by pseudoviruses (PsVs) with K417N, E484K, N501Y or D614G single mutation in their S proteins. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G;E484K;K417N;N501Y 227;211;204;218 232;216;209;223 S;S 85;258 90;259 34332998 The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another. Of these 47 had the L452R mutation. 2021 Journal of virological methods Result SARS_CoV_2 L452R 20 25 34332998 The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another. This shows an increase in the number of variants carrying the L452R mutation between weeks 22 and 25. 2021 Journal of virological methods Result SARS_CoV_2 L452R 62 67 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. Comparatively, the S24L structure remained more stable than the WT. 2021 Frontiers in microbiology Result SARS_CoV_2 S24L 19 23 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. HADDOCK was used to perform the protein-protein docking of IRF3 with the ORF8 WT and ORF8 mutants including S24L, W45L, V62L, L84S, and V62L and L84S double mutants to unwind the structural mechanisms behind the higher infectivity of different variants of SARS-CoV-2. 2021 Frontiers in microbiology Result SARS_CoV_2 L84S;L84S;S24L;V62L;V62L;W45L 126;145;108;120;136;114 130;149;112;124;140;118 ORF8;ORF8 73;85 77;89 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. However, further experiments are needed to determine whether S24L binds to IRF3 more efficiently compared to ORF8 WT and antagonize IFNss more efficiently. 2021 Frontiers in microbiology Result SARS_CoV_2 S24L 61 65 ORF8 109 113 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. However, there was no significant difference in the nuclear translocation of IRF3 after overexpressing ORF8 WT or ORF8 L84S in HEK-293T cells. 2021 Frontiers in microbiology Result SARS_CoV_2 L84S 119 123 ORF8;ORF8 103;114 107;118 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. It was observed that the number of H-bonds in the ORF8 WT complex is 152 and is less than in the mutant complexes in which the average H-bonds are 157, 161, 159, 165, and 154 for the mutants S24L, W45L, V62L, L84S, and V62L-L84S, respectively. 2021 Frontiers in microbiology Result SARS_CoV_2 L84S;S24L;V62L;V62L;W45L;L84S 209;191;203;219;197;224 213;195;207;223;201;228 ORF8 50 54 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. It was reported that V62L mutation was accompanied with L84S mutation in ORF8. 2021 Frontiers in microbiology Result SARS_CoV_2 L84S;V62L 56;21 60;25 ORF8 73 77 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. On the other hand, the S24L mutant structure abruptly converged after reaching 10 ns, and the RMSD increased from 0.2 to 0.4 A. 2021 Frontiers in microbiology Result SARS_CoV_2 S24L 23 27 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. Ser339-Glu92 was responsible for forming the hydrogen bonds by IRF3-V62L-ORF8, whereas the salt bridges included Glu92-Arg338 and Glu59-Arg373 residues (Figure 3B). 2021 Frontiers in microbiology Result SARS_CoV_2 V62L 68 72 ORF8 73 77 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. Similarly, the V62L also exhibits a rigid structure, and the RMSD continues to increase over time. 2021 Frontiers in microbiology Result SARS_CoV_2 V62L 15 19 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. Similarly, the W45L complex followed a similar pattern as the WT, and the RMSD observed was about 0.6 A; however, the system remained more stable, though the RMSD remained higher and increased continuously. 2021 Frontiers in microbiology Result SARS_CoV_2 W45L 15 19 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The average Rg values for each mutant S24L, W45L, V62L, L84S, and V62L-L84S were 22.40, 23.20, 22.00, 23.20, and 23.40 A, respectively. 2021 Frontiers in microbiology Result SARS_CoV_2 L84S;S24L;V62L;V62L;W45L;L84S 56;38;50;66;44;71 60;42;54;70;48;75 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The behavior of L84S exhibits some convergence from the mean position during the first 50 ns. 2021 Frontiers in microbiology Result SARS_CoV_2 L84S 16 20 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The binding energies for ORF8 WT, mutant S24L, W45L, V62L, L84S, and V62L-L84S are -28.47, -45.18, -55.77, -55.66, -35.61, and -41.47 kcal/mol, respectively (Table 1), and are dominated by the van der Waals forces, while the electrostatic energies did not significantly influence the binding. 2021 Frontiers in microbiology Result SARS_CoV_2 L84S;S24L;V62L;V62L;W45L;L84S 59;41;53;69;47;74 63;45;57;73;51;78 ORF8 25 29 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The docking results indicated a strong interaction of ORF8 protein with W45L mutation, suggesting that this mutation may further increase the function of the ORF8 protein in the evasion of the host immune system. 2021 Frontiers in microbiology Result SARS_CoV_2 W45L 72 76 ORF8;ORF8 54;158 58;162 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The HADDOCK docking score for L84S (IRF3-L84S) was reported to be -301.28 kcal/mol. 2021 Frontiers in microbiology Result SARS_CoV_2 L84S;L84S 30;41 34;45 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The HADDOCK docking score for S24L (IRF3-ORF8) is -321.26 kcal/mol. 2021 Frontiers in microbiology Result SARS_CoV_2 S24L 30 34 ORF8 41 45 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The HADDOCK docking score for W45L (IRF3-ORF8) was -351.49 kcal/mol. 2021 Frontiers in microbiology Result SARS_CoV_2 W45L 30 34 ORF8 41 45 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The hydrogen bonds formed by the IRF3-V62L, L84S ORF8 included Arg213-Asp63 and Ser339-Glu92, while the salt-bridge included Glu92-Arg338 and Asp63-Arg213 residues (Figure 3C). 2021 Frontiers in microbiology Result SARS_CoV_2 L84S;V62L 44;38 48;42 ORF8 49 53 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The molecular interaction of this complex revealed an interaction interface with three salt bridges, two hydrogen bonds, and 157 non-bonded contacts formed by L84S. 2021 Frontiers in microbiology Result SARS_CoV_2 L84S 159 163 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The molecular interaction of this complex revealed an interaction interface with two salt bridges, while six hydrogen bonds and 134 non-bonded contacts formed by the substituted residue W45L. 2021 Frontiers in microbiology Result SARS_CoV_2 W45L 186 190 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The mutation W45L in ORF8 was first reported in Saudi Arabia to cause more severe disease and may affect the function of this protein. 2021 Frontiers in microbiology Result SARS_CoV_2 W45L 13 17 ORF8 21 25 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The overall results showed that all the complexes exhibit rigid structures except the double mutant (V62L-L84S). 2021 Frontiers in microbiology Result SARS_CoV_2 V62L;L84S 101;106 105;110 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The predicted score of HADDOCK for the double-mutant V62L and L84S (IRF3-V62L-L84S double mutants) complex was -325.79 kcal/mol, which was comparable to that for the ORF8 WT complex. 2021 Frontiers in microbiology Result SARS_CoV_2 L84S;V62L;L84S;V62L 62;53;78;73 66;57;82;77 ORF8 166 170 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The predicted score of HADDOCK for V62L (IRF3-V62L) was -345.84 kcal/mol. 2021 Frontiers in microbiology Result SARS_CoV_2 V62L;V62L 35;46 39;50 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The S24L mutation was found to enhance the function of the ORF8 protein; therefore, it could be speculated that S24L will antagonize IFNss more strongly and hinder the eradication of SARS-CoV-2. 2021 Frontiers in microbiology Result SARS_CoV_2 S24L;S24L 4;112 8;116 ORF8 59 63 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The second most frequent mutation in SARS-CoV-2 ORF8 is S24L and accounts for 94.2% of the mutant sequences recorded in the United States of America. 2021 Frontiers in microbiology Result SARS_CoV_2 S24L 56 60 ORF8 48 52 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The V62L mutation was predicted to be neutral. 2021 Frontiers in microbiology Result SARS_CoV_2 V62L 4 8 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. Therefore, it was speculated that W45L mutation may increase its binding to IRF3. 2021 Frontiers in microbiology Result SARS_CoV_2 W45L 34 38 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. This observation revealed that ORF8 containing the double mutations of V62L and L84S may not affect the function of the ORF8 protein. 2021 Frontiers in microbiology Result SARS_CoV_2 L84S;V62L 80;71 84;75 ORF8;ORF8 31;120 35;124 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. To investigate whether ORF8 WT or ORF8 mutants could affect their interaction with IRF3, we generated S24L, W45L, V62L, L84S, and V62L-L84S double mutants by using Chimera (Figures 1A-F). 2021 Frontiers in microbiology Result SARS_CoV_2 L84S;S24L;V62L;V62L;W45L;L84S 120;102;114;130;108;135 124;106;118;134;112;139 ORF8;ORF8 23;34 27;38 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. 3 (b)-(d) show the interfaces and residues between the SARS-CoV-2 RBD and hACE2 for the wild-type 501Y.V1 variant, 501Y.V2 variant and N439K variant, respectively. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 N439K 135 140 RBD 66 69 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. 3 (d) shows the composite structure of the N439K variant, which formed new but weak hydrogen bonds between residues LYS439 and GLU329, thus slightly enhancing the binding affinity of the SARS-CoV-2 RBD. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 N439K 43 48 RBD 198 201 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. 3 explains why 501Y.V1 had the highest binding affinity to humans among the three variants, followed by N439K and 501Y.V2. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 N439K 104 109 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. As Tables S3-S4 shown, the 501Y.V1 variant is commonly considered to significantly increase the binding affinity of RBD to ACE2, while 501Y.V2 and N439K show small increasement in binding affinity. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 N439K 147 152 RBD 116 119 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. Both the 501Y.V1 and N439K variants have single mutated residues in the RBD, while the 501Y.V2 variant is comprised of three mutated residues (K417N, E484K, and N501Y). 2021 Computational and structural biotechnology journal Result SARS_CoV_2 E484K;N439K;N501Y;K417N 150;21;161;143 155;26;166;148 RBD 72 75 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. For the three variants, the 501Y.V1 variant exhibited the strongest binding energy of the RBD-hACE2 complex at -17.741 kcal/mol, followed by the N439K variant (-16.794 kcal/mol) and the 501Y.V2 variant (-15.501 kcal/mol). 2021 Computational and structural biotechnology journal Result SARS_CoV_2 N439K 145 150 RBD 90 93 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. From Table 1, the 501Y.V1, 501Y.V2 and N439K variants had a binding free energy increased by 36.8%, 19.6% and 29.5%, with binding energy changes () of -4.775, -2.536, and -3.829 kcal/mol, respectively. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 N439K 39 44 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. However, compared with the single N501Y mutation, the additional K417N and E484K mutations resulted in a decreased affinity between 501Y.V2 and hACE2 (as shown in Table 1). 2021 Computational and structural biotechnology journal Result SARS_CoV_2 E484K;K417N;N501Y 75;65;34 80;70;39 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. In addition, the N439K variant showed only slightly lower binding free energy than the wild-type SARS-CoV-2. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 N439K 17 22 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. In the 501Y.V1 and 501Y.V2 variants, the mutation from ASN501 to TYR501 formed strong hydrogen bonds and salt bridges between residues TYR501-TYR41 and THR500-ASP355, as shown in. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 N501Y 55 71 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. Overall, our results show that the mutations (N501Y, K417N, E484K, and N439K) in the three variants were all capable of enhancing the binding affinity and thus probably increasing the infectivity of the virus, and this result agrees well with previously published experimental results. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 E484K;K417N;N439K;N501Y 60;53;71;46 65;58;76;51 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. The mutations in the RBD of the three studied variants (501Y.V1, 501Y.V2 and N439K) are also shown in. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 N439K 77 82 RBD 21 24 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. The N501Y mutation significantly increased the binding affinity of the variant, while N439K showed little effect on binding affinity. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 N439K;N501Y 86;4 91;9 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. The results show that the RMSDs of variants 501Y.V1, 501Y.V2 and N439K were approximately 2.0-2.1 A, which were slightly greater than that of the wild-type RBD-hACE2 complex. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 N439K 65 70 RBD 156 159 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. The SASA value of wild-type RBD-hACE2 was 34996.9 A2, which was slightly smaller than those of the 501Y.V1 (35165.5 A2), 501Y.V2 (35496.9 A2) and N439K (35783.6 A2) variants. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 N439K 146 151 RBD 28 31 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. To evaluate the impact of the mutations in the SARS-CoV-2 RBD on binding affinity, the three variants (501Y.V1, 501Y.V2 and N439K) with different mutations in the RBD were selected for further molecular dynamics (MD) simulations. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 N439K 124 129 RBD;RBD 58;163 61;166 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. We also presented the experimental relative equilibrium dissociation constant (KD) of the four RBD-hACE2 complexes (wild-type, 501Y.V1, 501Y.V2, N439K) compared with the wild-type SARS-CoV-2 complex and the comparison of binding free energies changes () of the three variants between theoretical calculations and experimental results in Supporting Information (Table S3 and S4). 2021 Computational and structural biotechnology journal Result SARS_CoV_2 N439K 145 150 RBD 95 98 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. A total of 31 non-synonymous mutations were detected in the NTD (Supplementary File S1), among which V5F (n = 39), E8D (n = 35), V5I (n = 17), and Y2H (n = 14) were common. 2021 Informatics in medicine unlocked Result SARS_CoV_2 E8D;V5F;V5I;Y2H 115;101;129;147 118;104;132;150 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. However, both the MTs (P71S and P73F) demonstrated more HB than the WT. 2021 Informatics in medicine unlocked Result SARS_CoV_2 P73F;P71S 32;23 36;27 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. However, T9I (DeltaDeltaG: 0.190 kcal/mol), P71L (DeltaDeltaG: 0.012 kcal/mol), and S68F (DeltaDeltaG: 0.362 kcal/mol) shows a stabilizing effect (Supplementary File S1). 2021 Informatics in medicine unlocked Result SARS_CoV_2 P71L;S68F;T9I 44;84;9 48;88;12 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. In MT P71S, the proline has been substituted into serine, present in the active site of many enzymes. 2021 Informatics in medicine unlocked Result SARS_CoV_2 P71S 6 10 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. MT S68F exhibited fewer HB than P71S and P73F. 2021 Informatics in medicine unlocked Result SARS_CoV_2 P71S;P73F;S68F 32;41;3 36;45;7 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. Mutations in the CTD, namely, S55F (128), V62F (129), and R69I (159) may affect the virus pathogenesis, altering the binding of the E protein to a tight junction. 2021 Informatics in medicine unlocked Result SARS_CoV_2 R69I;S55F;V62F 58;30;42 62;34;46 E 132 133 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. P71S exhibited maximum HB (295) during the first 25ns simulations. 2021 Informatics in medicine unlocked Result SARS_CoV_2 P71S 0 4 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. Similar to S68F, the MT L73F also demonstrated low-level fluctuation when compared with the WT. 2021 Informatics in medicine unlocked Result SARS_CoV_2 L73F;S68F 24;11 28;15 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. Similar to the S68F, the L73F exhibited more interactions. 2021 Informatics in medicine unlocked Result SARS_CoV_2 L73F;S68F 25;15 29;19 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. Similarly, P71S also exhibited very low RMSF at CTD (5.7 A) when compared to the WT. 2021 Informatics in medicine unlocked Result SARS_CoV_2 P71S 11 15 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. Some of them were T91, S55F, V62F, S68F, R691, P71L, P71S, and L73F. 2021 Informatics in medicine unlocked Result SARS_CoV_2 L73F;P71L;P71S;S55F;S68F;V62F 63;47;53;23;35;29 67;51;57;27;39;33 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. The DynaMut prediction outcome of L73F (DeltaDeltaG: -0.417 kcal/mol), P71S (DeltaDeltaG: -0.255 kcal/mol) exert a destabilizing effect. 2021 Informatics in medicine unlocked Result SARS_CoV_2 L73F;P71S 34;71 38;75 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. The green areas in P71S, L73F are more prevalent that WT which shows stability next to blue regions. 2021 Informatics in medicine unlocked Result SARS_CoV_2 L73F;P71S 25;19 29;23 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. The most common mutations were detected at the C-terminal (Ser68Phe, Pro71Ser, and Leu73Phe) were also assessed through MD simulations, exerting a stabilizing effect on the E protein of CoV-2. 2021 Informatics in medicine unlocked Result SARS_CoV_2 L73F;P71S;S68F 83;69;59 91;77;67 E 173 174 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. The MT S68F exhibited more stable folding than the WT, whereas P71S and L73F also presented stable folding for the 18.9-50ns period. 2021 Informatics in medicine unlocked Result SARS_CoV_2 L73F;P71S;S68F 72;63;7 76;67;11 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. The MTs S68F and P71S seem more stable from 55ns to 100 ns, exhibiting 9 A and 10.5 A RMSDs, respectively. 2021 Informatics in medicine unlocked Result SARS_CoV_2 P71S;S68F 17;8 21;12 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. The RMSD of the WT still exhibiting fluctuations at 100 ns? Similar to the other MTs, L73F is also exhibiting stable deviations through the simulation period, with 13.7 A to 14.5 A RMSD. 2021 Informatics in medicine unlocked Result SARS_CoV_2 L73F 86 90 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. The S68F exhibited a different geometry due to the aromatic nature of phenylalanine substitutions. 2021 Informatics in medicine unlocked Result SARS_CoV_2 S68F 4 8 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. The S68F MT shows the lowest fluctuations from 21ns to 100 ns (1.3 nm). 2021 Informatics in medicine unlocked Result SARS_CoV_2 S68F 4 8 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. The WTs at this position exhibited 6.89 A (55 aa), 9.88 A (71 aa), and 9.5 A (75 aa); S68F demonstrated very low RMSF, below 4 A, for the majority of the residues and 5.1 A at 75 aa, which was significantly low as compared to the WT. 2021 Informatics in medicine unlocked Result SARS_CoV_2 S68F 86 90 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. Transmembrane variants such T9I (n = 168), F20L (n = 90), L21F (n = 84), V24 M (n = 76), and T30I (n = 72) may affect the homo pentameric configuration of the E protein. 2021 Informatics in medicine unlocked Result SARS_CoV_2 F20L;L21F;T30I;T9I;V24M 43;58;93;28;73 47;62;97;31;78 E 159 160 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. We analyzed the thermodynamic properties of most common variants (Ser68Phe, Pro71Ser, and Leu73Phe) present in the CTD in relation to the E structure stability in comparison with the wild type (WT). 2021 Informatics in medicine unlocked Result SARS_CoV_2 L73F;P71S;S68F 90;76;66 98;84;74 E 138 139 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. WT E protein showed more stable state that two MTs (P71S, L73F) whereas the MT S68F seems more stable than WT. 2021 Informatics in medicine unlocked Result SARS_CoV_2 L73F;S68F;P71S 58;79;52 62;83;56 E 3 4 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. Actually, the other predicted largely-increased rigidity of L452K mutation also corresponds to the observed high expression (Figure S1). 2021 ACS omega Result SARS_CoV_2 L452K 60 65 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. Although the sequence flexibility/rigidity map cannot predict the high binding affinity of the mutation site such as N501Y, which was measured by the quantitative deep mutational scanning, it can rationalize the neutralization escape ability well. 2021 ACS omega Result SARS_CoV_2 N501Y 117 122 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. As shown above, the D614G variant is now the dominant form worldwide. 2021 ACS omega Result SARS_CoV_2 D614G 20 25 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. As shown in Figure 4, the SSSCPreds data of the expanded S477N variant before B.1.1.7 and B.1.351 indicate that the S477N mutation increases the rigidity of the protein foundation GVEGFNCYFPLQ. 2021 ACS omega Result SARS_CoV_2 S477N;S477N 57;116 62;121 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. B.1.1.7 and B.1.617.2 strains have the P681H/R mutation sites at the furin cleavage site of SARS-CoV-2. 2021 ACS omega Result SARS_CoV_2 P681H;P681R 39;39 46;46 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. D614G Mutation. 2021 ACS omega Result SARS_CoV_2 D614G 0 5 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. It corresponds to the reports that the escape ability of P.1 with K417T is weaker than that of B.1.351 with K417N. 2021 ACS omega Result SARS_CoV_2 K417N;K417T 108;66 113;71 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. K417N with the more flexible SSSC sequence can escape neutralization more effectively than K417T with the less flexible one. 2021 ACS omega Result SARS_CoV_2 K417T;K417N 91;0 96;5 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The binding affinity of the mutation site such as N501Y cannot be predicted by SSSCPreds because it is decided by the interaction between two proteins. 2021 ACS omega Result SARS_CoV_2 N501Y 50 55 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The high ACE2-binding affinity of the single N501Y mutation has been reported. 2021 ACS omega Result SARS_CoV_2 N501Y 45 50 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The increased rigidity from the SSSCPreds data of L452R mutation seems to rationalize well the 2-fold increased B.1.427/B.1.429 viral shedding in vivo and the 18.6-24% increase in transmissibility relative to wild-type circulating strains in a similar manner to D614G. 2021 ACS omega Result SARS_CoV_2 D614G;L452R 262;50 267;55 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The L452R mutation increases the rigidity of the amino acid sequence YRYRLFR. 2021 ACS omega Result SARS_CoV_2 L452R 4 9 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The N501Y mutation site is also located on the opposite edge of flexible regions. 2021 ACS omega Result SARS_CoV_2 N501Y 4 9 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The ratio of frequencies of the S477N mutation has gradually increased, but the mutation has not contributed to the pandemic. 2021 ACS omega Result SARS_CoV_2 S477N 32 37 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The sequence flexibility/rigidity map patterns of the P681H/R mutation sites are more flexible than that of the wild-type strain. 2021 ACS omega Result SARS_CoV_2 P681H;P681R 54;54 61;61 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The sequence flexibility/rigidity maps of all of the single amino acid mutations at the D614G mutation site using SSSCPreds indicate that only the mutation to glycine makes the other-type conformation ("T" conformation) rigid and reproduces the observed "T" conformations of Cryo-EM structures (Figure 2). 2021 ACS omega Result SARS_CoV_2 D614G 88 93 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The SSSCPreds data of B.1.427/429 and B.1.617.2 near the L452R mutation site are largely different from those of B.1.1.7, B.1.351, P.1, and the wild-type strain (Figure 4). 2021 ACS omega Result SARS_CoV_2 L452R 57 62 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The SSSCPreds data of K417T (P.1) and K417N (B.1.351) indicated the large difference of rigidity between K417N and K417T (Figure 5). 2021 ACS omega Result SARS_CoV_2 K417N;K417N;K417T;K417T 38;105;22;115 43;110;27;120 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The SSSCPreds data of the N501Y mutation for B.1.1.7 show a similar increased stability of the foundation, but the sequence flexibility/rigidity map patterns of B.1.1.7 and the wild-type strain closely resemble one another. 2021 ACS omega Result SARS_CoV_2 N501Y 26 31 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. As a meta result, i-stable predicted, out of 62 nonsynonymous mutations, 40 nonsynonymous mutations (L5F, L8V, L8W, L18F, L54F, T76I, V120I, D138Y, Y145H, M153T, F157S, L176F, G181V, D215H, A262T, V367F, G476S, V483A, L611F, Q675H, A706V, T791I, P809S, A845S, A846V, A879S, V1040F, P1162L, D936H, S939F, T941A, D1163G, I1216T, M1229I, M1237L, M1237I, C1247F, C1254F, D1260 N, and P1263L) with decreased the stability and 22 nonsynonymous mutations (H49Y, S50L, S71F, S221L, S221W, Q239K, S247R, S254F, W258L, S438F, N501Y, D614G, Q675R, A831V, D839Y, A845V, A852V, P1143L, D936Y, S940F, S940T, and S943P) with increased stability (Table 1). 2021 Computers in biology and medicine Result SARS_CoV_2 A262T;A706V;A831V;A845S;A845V;A846V;A852V;A879S;C1247F;C1254F;D1163G;D1260N;D138Y;D215H;D614G;D839Y;D936H;D936Y;F157S;G181V;G476S;I1216T;L176F;L18F;L54F;L611F;L8V;L8W;M1229I;M1237I;M1237L;M153T;N501Y;P1143L;P1162L;P1263L;P809S;Q239K;Q675H;Q675R;S221L;S221W;S247R;S254F;S438F;S50L;S71F;S939F;S940F;S940T;S943P;T76I;T791I;T941A;V1040F;V120I;V367F;V483A;W258L;Y145H;H49Y;L5F 190;232;537;253;551;260;558;267;351;359;311;367;141;183;523;544;290;573;162;176;204;319;169;116;122;218;106;111;327;343;335;155;516;565;282;380;246;481;225;530;467;474;488;495;509;455;461;297;580;587;598;128;239;304;274;134;197;211;502;148;449;101 195;237;542;258;556;265;563;272;357;365;317;374;146;188;528;549;295;578;167;181;209;325;174;120;126;223;109;114;333;349;341;160;521;571;288;386;251;486;230;535;472;479;493;500;514;459;465;302;585;592;603;132;244;309;280;139;202;216;507;153;453;104 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. By analyzing the solvent-accessible surface area (SASA) Plots, we determined the geometry and surface of native and mutant (N501Y and D614G) S- proteins. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;N501Y 134;124 139;129 S 141 142 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. from the beginning to the end of the simulation, the N501Y and D614G mutants have higher fluctuation in the SASA values compared to native structure. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;N501Y 63;53 68;58 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Furthermore, the RMSF value analysis revealed a significant difference in the fluctuation of residues between the native and mutant (N501Y and D614G) S-proteins. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;N501Y 143;133 148;138 S 150 151 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Hence, we implemented the MD simulation approach to investigate how the structural transition in the mutant (N501Y and d614G) S- proteins influencing the interaction with ACE2. 2021 Computers in biology and medicine Result SARS_CoV_2 N501Y 109 114 S 126 127 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. In combination, structure-based online servers predicted 17 nonsynonymous mutations (L8V, L8W, L18F, S71F, Y145H, M153T, F157S, S221L, S221W, S247R, G476S, L611F, A831V, A852V, A879S, C1247F, and C1254F) with decreased stability, and 7 nonsynonymous mutations (H49Y, S50L, D215H, N501Y, D614G, A845V, and P1143L) with increased stability in the S-protein (Table 2). 2021 Computers in biology and medicine Result SARS_CoV_2 A831V;A845V;A852V;A879S;C1247F;C1254F;D215H;D614G;F157S;G476S;L18F;L611F;L8W;M153T;N501Y;P1143L;S221L;S221W;S247R;S50L;S71F;Y145H;H49Y;L8V 163;294;170;177;184;196;273;287;121;149;95;156;90;114;280;305;128;135;142;267;101;107;261;85 168;299;175;182;190;202;278;292;126;154;99;161;93;119;285;311;133;140;147;271;105;112;265;88 S 345 346 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. MD simulation of native and mutants (N501Y and D614G) S-proteins. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;N501Y 47;37 52;42 S 54 55 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Our analysis confirmed that both the nonsynonymous mutations (N501Y and d614G) stabilized and showed better interaction with ACE2. 2021 Computers in biology and medicine Result SARS_CoV_2 N501Y 62 67 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Overall, the mutant structures (N501Y and D614G) exhibited more motion and flexibility than the native S-protein. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;N501Y 42;32 47;37 S 103 104 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The average RMSD, RMSF, SASA, and H-bond values of the native and mutant (N501Y and D614G) structures are listed in Table 5 . 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;N501Y 84;74 89;79 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The changes of SASA of native and mutant (N501Y and D614G) S-protein over time are depicted in. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;N501Y 52;42 57;47 S 59 60 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The destabilizing nonsynonymous mutations (L8V, L8W, L18F, Y145H, M153T, F157S, G476S, L611F, A879S, C1247F, and C1254F) of S-protein and ACE2 complexes exhibits a lesser number of H-bonds compared to the native S-protein _ACE2 complex. 2021 Computers in biology and medicine Result SARS_CoV_2 A879S;C1247F;C1254F;F157S;G476S;L18F;L611F;L8W;M153T;Y145H;L8V 94;101;113;73;80;53;87;48;66;59;43 99;107;119;78;85;57;92;51;71;64;46 S;S 124;212 125;213 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The four stabilizing nonsynonymous mutations (H49Y, S50L, D614G, and P1143L) of S-protein_ACE2 complexes show a greater number of h-bonds and other nonsynonymous mutations (N501Y andA845V) shows the same number of h-bonds compared to the native complex. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;P1143L;S50L;H49Y;N501Y 58;69;52;46;173 63;75;56;50;178 S 80 81 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The Haddock scores of the native S-protein-ACE2 complex, and destabilizing S-proteins of S-protein-ACE2 (L8V-ACE2, L8W-ACE2, L18F-ACE2, Y145H-ACE2, M153T-ACE2, F157S-ACE2, G476S-ACE2, L611F-ACE2, A879S-ACE2, C1247F-ACE2, and C1254F-ACE2) complexes were -123.5 +- 13.2, -118.8 +- 6.1, -120.8 +- 16.0, -116.0 +- 3.2, -119.0 +- 9.9, -115.5 +- 1.2, -118.4 +- 2.8, -119.2 +- 6.5, -117.0 +- 14.4, -116.8 +- 12.7, -117.1 +- 4.0, and -113.4 +- 8.0, respectively, shown in Table 3 a. 2021 Computers in biology and medicine Result SARS_CoV_2 A879S;C1247F;C1254F;F157S;G476S;L18F;L611F;L8W;M153T;Y145H;L8V 196;208;225;160;172;125;184;115;148;136;105 201;214;231;165;177;129;189;118;153;141;108 S;S;S 33;75;89 34;76;90 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The HADDOCK tool and HawkDock Server was used to examine the binding energy between the native and mutant S-proteins [destabilizing (L8V, L8W, L18F, Y145H, M153T, F157S, G476S, L611F, A879S, C1247F, and C1254F) and stabilizing (H49Y, S50L, N501Y, D614G, A845V, and P1143L)] with the ACE2 receptor. 2021 Computers in biology and medicine Result SARS_CoV_2 A845V;A879S;C1247F;C1254F;D614G;F157S;G476S;L18F;L611F;L8W;M153T;N501Y;P1143L;S50L;Y145H;H49Y;L8V 254;184;191;203;247;163;170;143;177;138;156;240;265;234;149;228;133 259;189;197;209;252;168;175;147;182;141;161;245;271;238;154;232;136 S 106 107 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The hydrogen bond interactions between the stabilizing nonsynonymous mutations (H49Y, S50L, N501Y, and D614G) of the S-protein with the ACE2 receptor are depicted in. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;N501Y;S50L;H49Y 103;92;86;80 108;97;90;84 S 117 118 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The Mutants N501Y and D614G structures have a greater degree of fluctuation in the residue of 501 and 614 along with neighboring residues than native S-protein throughout the simulation and shown in. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;N501Y 22;12 27;17 S 150 151 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The native and mutant (N501Y and D614G) S-protein systems show the convergence from the beginning to the end of the simulation. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;N501Y 33;23 38;28 S 40 41 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The recent studies reported that N501Y and d614G stabilized nonsynonymous mutations are the most promising in S-protein. 2021 Computers in biology and medicine Result SARS_CoV_2 N501Y 33 38 S 110 111 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. the RMSD value of the native and mutant structures (N501Y and D614G) is 2.73 nm, 2.88 nm, and 3.01 nm, respectively (Table 5). 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;N501Y 62;52 67;57 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. These results motivated us to observe the structural changes of native and these two advantageous nonsynonymous mutations (N501Y and d614G) at the atomic level. 2021 Computers in biology and medicine Result SARS_CoV_2 N501Y 123 128 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. This further confirms the overall increased flexibility of the mutants (N501Y and D614G) compared to the native S-protein at 300 K. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;N501Y 82;72 87;77 S 112 113 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. To better understand the stability of native and mutant (N501Y and D614G) S-proteins, we measured the intramolecular H-bond concerning time. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;N501Y 67;57 72;62 S 74 75 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. To investigate the convergence of the native and mutant (N501Y and D614G) protein systems, the total energy was measured and displayed in. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;N501Y 67;57 72;62 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. To investigate the stability of the native and mutant (N501Y and D614G) protein system, the RMSD matrix for all Calpha-atoms from the initial structure was measured. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;N501Y 65;55 70;60 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Together, both sequence and structure-based online servers predicted 11 nonsynonymous mutations (L8V, L8W, L18F, Y145H, M153T, F157S, G476S, L611F, A879S, C1247F, and C1254F) exhibiting decreased stability and 6 nonsynonymous mutations (H49Y, S50L, N501Y, D614G, A845V, and P1143L) exhibiting increased stability in the S-protein upon mutations (Table 1, Table 2). 2021 Computers in biology and medicine Result SARS_CoV_2 A845V;A879S;C1247F;C1254F;D614G;F157S;G476S;L18F;L611F;L8W;M153T;N501Y;P1143L;S50L;Y145H;H49Y;L8V 263;148;155;167;256;127;134;107;141;102;120;249;274;243;113;237;97 268;153;161;173;261;132;139;111;146;105;125;254;280;247;118;241;100 S 320 321 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. We analyzed the total energy, Root mean square deviation (RMSD), Root mean square fluctuation (RMSF), Solvent accessible surface area (SASA), and Hydrogen bond (H-bonds) analysis to investigate the differences in structural variations between the native and mutant (N501Y and D614G) S-proteins. 2021 Computers in biology and medicine Result SARS_CoV_2 D614G;N501Y 276;266 281;271 S 283 284 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Whereas the HADDOCK score of stabilizing nonsynonymous mutations of S-protein -ACE2 complexes (H49Y-ACE2, S50L-ACE2, N501Y-ACE2, D614G-ACE2, A845V-ACE2, and P1143L-ACE2) were -136.5 +- 6.7, -131.3 +- 10.3, -136.3 +- 6.3, -128.2 +- 12.0, -127.7 +- 4.7, and -125.9 +- 17.1, respectively, are shown in Table 3 b. 2021 Computers in biology and medicine Result SARS_CoV_2 A845V;D614G;N501Y;P1143L;S50L;H49Y 141;129;117;157;106;95 146;134;122;163;110;99 S 68 69 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Whereas the MM_GBSA score of stabilizing nonsynonymous mutations of S-protein (H49Y, S50L, N501Y, D614G, A845V, and P1143L) and ACE2 receptor complexes were -73.06, -80.89, -66.53, -79.81, -63.05, and -68.62, respectively (Table 4 b). 2021 Computers in biology and medicine Result SARS_CoV_2 A845V;D614G;N501Y;P1143L;S50L;H49Y 105;98;91;116;85;79 110;103;96;122;89;83 S 68 69 34346744 SARS-CoV-2 Quasispecies Provides an Advantage Mutation Pool for the Epidemic Variants. However, the origins of the 3118G T was different in that MFG had likely evolved from the Wuhan-Hu-1 strain, but the variants from North America had evolved from strains with the dominant SNV of 1841A G (D614G). 2021 Microbiology spectrum Result SARS_CoV_2 D614G 204 209 34346744 SARS-CoV-2 Quasispecies Provides an Advantage Mutation Pool for the Epidemic Variants. In particular, the predominant amino acid variation, D614G, was found in 19 minor mutants from SG2-0131-SP, FG1-0126-SP, FG4-0127-NS, and FG5-0205-ST. 2021 Microbiology spectrum Result SARS_CoV_2 D614G 53 58 S;S 104;117 106;119 34346744 SARS-CoV-2 Quasispecies Provides an Advantage Mutation Pool for the Epidemic Variants. Strains of H0001 (with D614G) disseminated rapidly and further evolved into several epidemic variants, such as B.1.1.7, B.1.248, B.1.351, B.1.526, B.1.525, and B.1.429+427. 2021 Microbiology spectrum Result SARS_CoV_2 D614G 23 28 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. As can be seen, only A570D and D614G involve glue point partners within the Spike protein. 2021 Microbiology spectrum Result SARS_CoV_2 A570D;D614G 21;31 26;36 S 76 81 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. Here, we examine the triple alanine mutant ARG357ALA, ASN394ALA, and HIS519ALA across the entire SARS-CoV-2 Spike protein (mutating 6VSB, see Materials and Methods) in order to determine if these key glue points alone could cause a conformational change in the absence of any latch mutations. 2021 Microbiology spectrum Result SARS_CoV_2 R357A;N394A;H519A 43;54;69 52;63;78 S 108 113 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. Note that both D614G and N501Y are also present in the South African variant (B.1.351). 2021 Microbiology spectrum Result SARS_CoV_2 D614G;N501Y 15;25 20;30 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. The N501Y mutation may demonstrate a significant increase in binding to hACE2 due to the highly favorable Y-Y hydrophobic interaction pair in the new mutant state (Table S3); however, this remains to be concretely verified. 2021 Microbiology spectrum Result SARS_CoV_2 N501Y 4 9 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. 501.V2 includes the mutations L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G, A701V. 2021 PLoS computational biology Result SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;L18F;N501Y;R246I 84;42;77;36;63;56;30;70;49 89;47;82;40;68;61;34;75;54 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. A newer variation of the Delta strain, AY.1 (or Delta+) does however contain the K417N mutation (that we predict to increase open state occupancy) similar to the South African strain 501.V2. 2021 PLoS computational biology Result SARS_CoV_2 K417N 81 86 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. A number of other glycine residues could also accept mutations that we predict to increase the occupancy of the open state: G72W; G404W; G413M; G416E,W; and G404I. 2021 PLoS computational biology Result SARS_CoV_2 G404I;G404W;G413M;G416E;G416W;G72W 157;130;137;144;144;124 162;135;142;149;149;128 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. According to our calculations, the N501Y mutant shows DeltaSvib (open) = -1.60x10-2 J.K-1 and DeltaSvib (closed) = 2.37x10-1 J.K-1, with VDS = 2.53x10-1 J.K-1. 2021 PLoS computational biology Result SARS_CoV_2 N501Y 35 40 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Additionally, D467P,W and I468T are also positions that are adjacent to others that can accommodate mutations that may lead to a conformational shift favouring the open state. 2021 PLoS computational biology Result SARS_CoV_2 D467P;D467W;I468T 14;14;26 19;19;31 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. An important event in the progression of the COVID-19 pandemic was the appearance of the D614G variant in mid-February 2020 in Europe. 2021 PLoS computational biology Result SARS_CoV_2 D614G 89 94 COVID-19 45 53 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Analysis of the effect of mutations on the Dynamical Signature shows that the D614G mutation produces similar dynamical patterns largely independent of the other mutations accumulated, and dynamical patterns that are distinct from that of the wild type and other mutants on both the open and closed states, as highlighted in the sections of the dendrogram marked in red. 2021 PLoS computational biology Result SARS_CoV_2 D614G 78 83 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. As shown for D614G, infection does not rely on binding affinity alone, and even a strain with higher dissociation rates from ACE2 can bring about fitness advantages. 2021 PLoS computational biology Result SARS_CoV_2 D614G 13 18 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. COG-UK recently detected a strain containing the mutation N501Y that has been observed to be spreading rapidly at the time of writing. 2021 PLoS computational biology Result SARS_CoV_2 N501Y 58 63 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. D614G shows that changes in the occupancy of conformational states can impact infectivity despite no changes or even weaker binding affinities. 2021 PLoS computational biology Result SARS_CoV_2 D614G 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. For example, the Indian variant B.1.617.2 (also known as Delta), contains a core number of mutations in Spike (G142D, E154K, L452R, E484Q, D614G, P681R, Q1071H) but also additional sub-strain variations (T95I, H1101D or V382L). 2021 PLoS computational biology Result SARS_CoV_2 D614G;E154K;E484Q;H1101D;L452R;P681R;Q1071H;V382L;G142D;T95I 139;118;132;210;125;146;153;220;111;204 144;123;137;216;130;151;159;225;116;208 S 104 109 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Furthermore, N501W appears to have increased expression relative to the wild type with a Deltalog(MFI) of 0.1 compared to decrease in relative expression of -0.14 for N501Y. 2021 PLoS computational biology Result SARS_CoV_2 N501W;N501Y 13;167 18;172 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. However, even with a Deltalog(MFI) of -0.14, N501Y is viable and spreading. 2021 PLoS computational biology Result SARS_CoV_2 N501Y 45 50 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. However, mutations like K417N and K417T were not observed to cause favourable changes on expression (a proxy measurement for stability) or binding as well as immune recognition, but in our high throughput evaluation they were, as well as several substitutions in this position, predicted to increase the occupancy of the open state. 2021 PLoS computational biology Result SARS_CoV_2 K417N;K417T 24;34 29;39 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. However, the double mutant representing the N501Y mutation in the context of G614 also shows an increase in the occupancy of the open state to 35.06%. 2021 PLoS computational biology Result SARS_CoV_2 N501Y 44 49 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. In the case of the mutation D614G, we obtain DeltaSvib (open) = 5.26x10-2 J.K-1 and DeltaSvib (closed) = -9.27x10-2 J.K-1 with a VDS (calculated as DeltaSvib (open)- DeltaSvib (closed)) of 1.45x10-1 J.K-1. 2021 PLoS computational biology Result SARS_CoV_2 D614G 28 33 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Namely, B.1.1.7 contains N501Y, A570D, D614G, P681H, T716I, S982A, D1118H and deletions on positions 69, 70 and 144. 2021 PLoS computational biology Result SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 32;67;39;25;46;60;53 37;73;44;30;51;65;58 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Namely, R403S and K417D,E,G,P. 2021 PLoS computational biology Result SARS_CoV_2 K417D;K417E;R403S 18;18;8 23;23;13 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Notice that N501Y has a VDS value of 2.53x10-1 J.K-1 that is slightly below the 3.00x10-1 J.K-1 threshold, suggesting that there may be many other mutations with VDS values below our set threshold that turn out to have augmented occupancies for the open state relative to the wild type. 2021 PLoS computational biology Result SARS_CoV_2 N501Y 12 17 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. P.1 variant includes the mutations L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I. 2021 PLoS computational biology Result SARS_CoV_2 D138Y;D614G;E484K;H655Y;K417T;L18F;N501Y;P26S;R190S;T1027I;T20N 53;88;74;95;67;35;81;47;60;102;41 58;93;79;100;72;39;86;51;65;108;45 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. The dynamical characteristics of D614G are very specific and cannot be obtained with random mutations (S1 Fig and S2 Table). 2021 PLoS computational biology Result SARS_CoV_2 D614G 33 38 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. The E484K mutation does not increase the occupancy of the open state in our predictions and also does not increase ACE2 binding affinity, but was observed to facilitate immune escape in a study with human serum antibodies from subjects that recovered from COVID-19. 2021 PLoS computational biology Result SARS_CoV_2 E484K 4 9 COVID-19 256 264 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. The mutation N501W is predicted to have the largest effect in augmenting the occupancy of the open state relative to the wild type. 2021 PLoS computational biology Result SARS_CoV_2 N501W 13 18 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. The mutation N501Y above appears in the B.1.1.7 variant first observed in the UK as well as the 501.V2 variant first observed in South Africa and the P.1 variant from Brazil that are rapidly spreading around the globe. 2021 PLoS computational biology Result SARS_CoV_2 N501Y 13 18 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. The mutation that favours the open state the most in our calculations is N501W with DeltaSvib (open) = 6.02x10-1 J.K-1 and DeltaSvib (closed) = 2.30x10-1 J.K-1 and a resulting VDS value of 3.72x10-1 J.K-1 leading to occupancies compared to those of the wild type (in parenthesis) of 62.7% (25.8%) and 37.3% (74.2%) for the open and closed states respectively. 2021 PLoS computational biology Result SARS_CoV_2 N501W 73 78 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. The N501Y substitution, as mentioned, is among the candidates we pointed as enabling occupancy shifts towards the open conformation, but was also shown to have higher binding affinity to the receptor ACE2. 2021 PLoS computational biology Result SARS_CoV_2 N501Y 4 9 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. The predicted occupancies for the N501Y mutant compared to those of the wild type (in parenthesis) are 54.3% (25.8%) and 45.7% (74.2%) for the open and closed states, respectively. 2021 PLoS computational biology Result SARS_CoV_2 N501Y 34 39 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. The recently observed A222V mutation on the other hand, does not show in our analysis any propensity of altering the occupancy of states with a negative VDS of -1.64x10-2 J.K-1. 2021 PLoS computational biology Result SARS_CoV_2 A222V 22 27 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Therefore, N501W might be even more stable and infective. 2021 PLoS computational biology Result SARS_CoV_2 N501W 11 16 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Therefore, the N501Y mutant shows a marked increase of the occupancy of the open state relative to other mutations. 2021 PLoS computational biology Result SARS_CoV_2 N501Y 15 20 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Therefore, we predict that N501Y has a strong potential to contribute to increased transmission. 2021 PLoS computational biology Result SARS_CoV_2 N501Y 27 32 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. These variants were: S-GSAS/D614, an engineered Spike with the sequence GSAS in the Furin cleavage site and no 614 mutation; S-GSAS/G614, with the same Furin site modifications and the D614G mutation; S-R, the Spike protein with original Furin site RRAR; S-R/x2, with added S383C, D985C mutations inducing a disulfide bond; S-R/PP, engineered with two prolines in positions 986 and 987; S-R/PP/x1, in which from the double prolines sequence the mutations G413C, V987C were performed to induce a disulfide bond. 2021 PLoS computational biology Result SARS_CoV_2 D614G;D985C;G413C;S383C;V987C 185;281;455;274;462 190;286;460;279;467 S;S;S;S;S;S;S;S 48;210;21;125;201;255;324;387 53;215;22;126;202;256;325;388 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. This mutation is associated with stronger binding to ACE2 (Deltalog10(KD,app) = 0.11) relative to the wild type Spike (but lower than N501Y). 2021 PLoS computational biology Result SARS_CoV_2 N501Y 134 139 S 112 117 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Thus, considering the lesser infectivity of SARS-CoV relative to SARS-CoV-2 and our aforementioned results for the D614G mutation, we expected the SARS-CoV Spike to be more rigid in the closed state and more flexible in the open state relative to Spike from SARS-CoV-2. 2021 PLoS computational biology Result SARS_CoV_2 D614G 115 120 S;S 156;247 161;252 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. However, we observed a reduction in neutralization in some sera against N439K mutant (0.53+-0.45) as reported in, which was not observed when Delta69-70 was added (Figs 2H and S5), and also against L452R mutant (0.48+-0.23) that is associated with the most recent variants of concern B.1.427/9, as reported in. 2021 PLoS pathogens Result SARS_CoV_2 L452R;N439K 198;72 203;77 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. Importantly, S494P mutation appeared independently on several occasions and is under positive selection, and is now a variant in monitoring, especially when combined with E484K or N501Y. 2021 PLoS pathogens Result SARS_CoV_2 E484K;N501Y;S494P 171;180;13 176;185;18 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. In fact, S494P alone did not significantly reduce neutralization, becoming significant when N501Y (0.70+-0.4), or E484K (0.5+-0.3) mutations were introduced. 2021 PLoS pathogens Result SARS_CoV_2 E484K;N501Y;S494P 114;92;9 119;97;14 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. Interestingly, N501Y, L452R and S417N have been associated with increased viral transmission and, when combined with E484K, augmented resistance to neutralizing antibodies. 2021 PLoS pathogens Result SARS_CoV_2 E484K;L452R;N501Y;S417N 117;22;15;32 122;27;20;37 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. Interestingly, the E484K/S494P/N501Y triple mutant reduced neutralization over the 4-fold criteria applied (0.17+-0.34, Fig 4F and 4G). 2021 PLoS pathogens Result SARS_CoV_2 E484K;N501Y;S494P 19;31;25 24;36;30 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. Mutations in S494 have been found in circulating strains, and the S494P mutation was shown to reduce the binding by polyclonal plasma antibodies whilst having no or modest effect in RBD-ACE2 binding. 2021 PLoS pathogens Result SARS_CoV_2 S494P 66 71 RBD 182 185 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. Our results indicate that the S494P mutation can facilitate the escape of the virus from antibodies, maintaining the ability to bind to the receptor and enter host cells, and should be surveilled worldwide. 2021 PLoS pathogens Result SARS_CoV_2 S494P 30 35 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. The mutation E484K alone reduced sera neutralization capacity by 3.6-fold [ratio NT50 mutant/NT50 WT of 0.028+-0.37 (geometric mean +- SD)], and inclusion of additional mutations (K417N and N501Y) further decreased the neutralization (0.08+-0.05), emphasizing the role of synergic mutations on immune evasion and underscoring the need for evaluating single and combined mutations on variants. 2021 PLoS pathogens Result SARS_CoV_2 E484K;N501Y;K417N 13;190;180 18;195;185 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. This value was further reduced when this mutation was combined with N501Y (0.28+-0.21, Fig 4F and 4G), or when combined with E484K (0.25+-0.32, Fig 4F and 4G). 2021 PLoS pathogens Result SARS_CoV_2 E484K;N501Y 125;68 130;73 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. To elucidate the role of this mutation in antibody neutralization, we used our neutralization assay and found that mutation S494P alone leads to a reduction in neutralization by convalescence sera that is significant (Figs 4F and S9, and S5 Table) despite not reaching our 4-fold criteria (ratio NT50 of mutant in relation to WT of 0.39+-0.28, Fig 4G). 2021 PLoS pathogens Result SARS_CoV_2 S494P 124 129 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. We constructed these spike mutants because we aimed at understanding if mutations that increased the ability to bind ACE2, such as N501Y, could synergize with mutations escaping antibody neutralization. 2021 PLoS pathogens Result SARS_CoV_2 N501Y 131 136 S 21 26 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. We found that the mutations N501Y, Delta69-70/N501 and Delta69-70/N501+P681H, associated with B.1.1.7 variant, behave as WT spike. 2021 PLoS pathogens Result SARS_CoV_2 N501Y;P681H 28;71 33;76 S 124 129 34352360 A discernable increase in the severe acute respiratory syndrome coronavirus 2 R.1 lineage carrying an E484K spike protein mutation in Japan. However, there is a greater concern about other immune evasion mutations, such as the E484K (Glu484 Lys) mutation in the spike (S) protein found in B.1.351 (501Y V2) variant that emerged in South Africa, and P.1 (501Y V3) variant in Brazil. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K;E484K 86;93 91;103 S;S 121;128 126;129 34352360 A discernable increase in the severe acute respiratory syndrome coronavirus 2 R.1 lineage carrying an E484K spike protein mutation in Japan. Indeed, E484K could be a pivotal amino acid substitution with the potential to mediate immune escape. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 8 13 34352360 A discernable increase in the severe acute respiratory syndrome coronavirus 2 R.1 lineage carrying an E484K spike protein mutation in Japan. Recently, a new R.1 lineage carrying the spike protein mutation E484K has been detected in 5-37.6% of all COVID-19-positive cases within a span of six weeks (mid-January to early March 2021), and there has been a sharp increase in the number of cases. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 64 69 S 41 46 COVID-19 106 114 34352360 A discernable increase in the severe acute respiratory syndrome coronavirus 2 R.1 lineage carrying an E484K spike protein mutation in Japan. Thus far, B.1.1.318, B.1.525, R.1, R.2, and P.2 have been reported as variants carrying the E484K single mutation in the receptor-binding domain. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 92 97 34354142 Entropy based analysis of SARS-CoV-2 spread in India using informative subtype markers. D614G mutation analysis. 2021 Scientific reports Result SARS_CoV_2 D614G 0 5 34354142 Entropy based analysis of SARS-CoV-2 spread in India using informative subtype markers. This indicates SARS-CoV-2 underwent an important D614G mutation to infect the population in other regions with different climatic conditions and diet pattern. 2021 Scientific reports Result SARS_CoV_2 D614G 49 54 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. Among the identified mutations, NSP2_T153M, NSP14_I42V and Spike_L18F mutations showed a positive correlation to CFR (Figure 2A-C). 2021 Genes Result SARS_CoV_2 I42V;L18F;T153M 50;65;37 54;69;42 S;Nsp2 59;32 64;36 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. However, NS8_L84S and NSP12_A97V mutations showed a negative correlation to the number of Cases per million (Figure 5C,D). 2021 Genes Result SARS_CoV_2 A97V;L84S 28;13 32;17 Nsp12 22 27 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. However, NSP3_T73I and NSP3_Q180H, NSP13_Y541C showed a negative correlation to CFR (Figure 3A-C). 2021 Genes Result SARS_CoV_2 Q180H;T73I;Y541C 28;14;41 33;18;46 Nsp13;Nsp3;Nsp3 35;9;23 40;13;27 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. NSP12_P323L and Spike_D614G mutations showed a positive correlation to number of cases per million (Figure 5A,B). 2021 Genes Result SARS_CoV_2 D614G;P323L 22;6 27;11 S;Nsp12 16;0 21;5 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. Spike_D614G and NSP12_P323L mutations displayed a positive correlation to deaths per million (Figure 4A,B). 2021 Genes Result SARS_CoV_2 D614G;P323L 6;22 11;27 S;Nsp12 0;16 5;21 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The N_G204R mutation was reported at 22.31%, 75.69%, 46.59%, 52.36% and 76.01% in SARS-CoV-2 genome sequences isolated from Africa, Asia, Australia, Europe and South America, respectively. 2021 Genes Result SARS_CoV_2 G204R 6 11 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The N_I292T mutation was reported at 20.50% in SARS-CoV-2 genome sequences isolated from South America. 2021 Genes Result SARS_CoV_2 I292T 6 11 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The N_R203K mutation was reported at 24.24%, 75.88%, 47.90%, 53.51%, 15.08% and 76.41% in SARS-CoV-2 genome sequences isolated from Africa, Asia, Australia, Europe, North America and South America, respectively. 2021 Genes Result SARS_CoV_2 R203K 6 11 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NS3_Q57H mutation was reported at 46.10%, 32.99% and 63.30% in SARS-CoV-2 genome sequences isolated from Africa, Australia and North America, respectively. 2021 Genes Result SARS_CoV_2 Q57H 8 12 NS3 4 7 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NS3_S171L mutation was reported at 30.37% in SARS-CoV-2 genome sequences isolated from Africa. 2021 Genes Result SARS_CoV_2 S171L 8 13 NS3 4 7 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NS8_L84S mutation was reported at 4.09%, 1.39%, 3.29%, 0.25%, 0.51% and 0.25% in SARS-CoV-2 genome sequences isolated from Africa, Asia, Australia, Europe, North America and South America, respectively (Figure 4I and Figure 5G). 2021 Genes Result SARS_CoV_2 L84S 8 12 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NS8_Q27stop mutation was reported at 46.36% in SARS-CoV-2 genome sequences isolated from Europe. 2021 Genes Result SARS_CoV_2 Q27X 8 15 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NS8_S24L mutation was reported at 33.88% in SARS-CoV-2 genome sequences isolated from North America. 2021 Genes Result SARS_CoV_2 S24L 8 12 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NSP12_A97V mutation was reported at 0.28%, 0.52%, 1.98%, 0.05%, 0.23% and 0.09% % in SARS-CoV-2 genome sequences isolated from Africa, Asia, Australia, Europe, North America and South America, respectively (Figure 4J and Figure 5H). 2021 Genes Result SARS_CoV_2 A97V 10 14 Nsp12 4 9 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NSP12_P323L mutation was reported at 88.66%, 95.52%, 91.08%, 98.35%, 94.79% and 96.43% in the SARS-CoV-2 genome sequences isolated from Africa, Asia, Australia, Europe, North America and South America, respectively (Figure 4G and Figure 5E). 2021 Genes Result SARS_CoV_2 P323L 10 15 Nsp12 4 9 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NSP13_Y541C mutation was reported at 0.01%, 0.84%, 0.01%, 0.15% and 0.04% in SARS-CoV-2 genome sequences isolated from Asia, Australia, Europe, North America and South America, respectively (Figure 3F). 2021 Genes Result SARS_CoV_2 Y541C 10 15 Nsp13 4 9 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NSP14_I42V mutation was reported at 0.017 and 0.003 in SARS-CoV-2 genome sequences isolated from Africa and Europe, respectively (Figure 2E). 2021 Genes Result SARS_CoV_2 I42V 10 14 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NSP2_T153M mutation was reported at 1.18%, 0.02%, 0.04%, 0.07% and 0.07% in SARS-CoV-2 genome sequences isolated from Africa, Asia, Europe, North America and South America, respectively (Figure 2D). 2021 Genes Result SARS_CoV_2 T153M 9 14 Nsp2 4 8 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NSP2_T85I mutation was reported at 40.20% and 59.59% in SARS-CoV-2 genome sequences isolated from Africa and South America, respectively. 2021 Genes Result SARS_CoV_2 T85I 9 13 Nsp2 4 8 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NSP3_Q180H mutation was reported at 0.05%, 0.15%, 0.18%, 0.08%, 1.18% and 0.10% in SARS-CoV-2 genome sequences isolated from Africa, Asia, Australia, Europe, North America and South America, respectively (Figure 3E). 2021 Genes Result SARS_CoV_2 Q180H 9 14 Nsp3 4 8 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NSP3_T1198K mutation was reported at 0.21%, 1.56%, 0.18%, 0.01%, 0.02% and 0.07% in SARS-CoV-2 genome sequences isolated from Africa, Asia, Australia, Europe, North America and South America, respectively (Figure 4H). 2021 Genes Result SARS_CoV_2 T1198K 9 15 Nsp3 4 8 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NSP3_T1198K, NS8_L84S and NSP12_A97V mutations showed a significant negative correlation to deaths per million (Figure 4C-E). 2021 Genes Result SARS_CoV_2 A97V;L84S;T1198K 36;21;9 40;25;15 Nsp12;Nsp3 30;4 35;8 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NSP3_T73I mutation was reported at 0.02%, 0.05%, 0.18%, 0.05%, 0.10% and 0.03% in SARS-CoV-2 genome sequences isolated from Africa, Asia, Australia, Europe, North America and South America, respectively (Figure 3D). 2021 Genes Result SARS_CoV_2 T73I 9 13 Nsp3 4 8 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The Spike_A222V mutation was reported at 26.59% in SARS-CoV-2 genome sequences isolated from Europe. 2021 Genes Result SARS_CoV_2 A222V 10 15 S 4 9 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The Spike_D614G mutation was reported at 91.97%, 96.46%, 91.02%, 98.99%, 97.91% and 97.02% in SARS-CoV-2 genome sequences isolated from Africa, Asia, Australia, Europe, North America and South America, respectively (Figure 4F and Figure 5F). 2021 Genes Result SARS_CoV_2 D614G 10 15 S 4 9 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The Spike_E484K mutation was reported at 35.63% in SARS-CoV-2 genome sequences isolated from Africa. 2021 Genes Result SARS_CoV_2 E484K 10 15 S 4 9 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The Spike_H69del mutation was reported at 48.93% in SARS-CoV-2 genome sequences isolated from Europe. 2021 Genes Result SARS_CoV_2 H69del 10 16 S 4 9 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The Spike_K417N mutation was reported at 34.36% in SARS-CoV-2 genome sequences isolated from Africa. 2021 Genes Result SARS_CoV_2 K417N 10 15 S 4 9 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The Spike_L18F mutation was reported at 16.02%, 0.72%, 1.86%, 10.90%, 1.25% and 5.94% in SARS-CoV-2 genome sequences isolated from Africa, Asia, Australia, Europe, North America and South America, respectively (Figure 2F). 2021 Genes Result SARS_CoV_2 L18F 10 14 S 4 9 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The Spike_N501Y mutation was reported at 36.55% and 47.23% in SARS-CoV-2 genome sequences isolated from Africa and Europe, respectively. 2021 Genes Result SARS_CoV_2 N501Y 10 15 S 4 9 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The Spike_V1176F mutation was reported at 29.30% in SARS-CoV-2 genome sequences isolated from South America. 2021 Genes Result SARS_CoV_2 V1176F 10 16 S 4 9 34358019 Antibodies Targeting Two Epitopes in SARS-CoV-2 Neutralize Pseudoviruses with the Spike Proteins from Different Variants. different from the basal and D614G variants, and five a.a. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D614G 29 34 34358019 Antibodies Targeting Two Epitopes in SARS-CoV-2 Neutralize Pseudoviruses with the Spike Proteins from Different Variants. It was noted that the Alpha and Beta variants, unlike the D614G strain, have one a.a. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D614G 58 63 34358019 Antibodies Targeting Two Epitopes in SARS-CoV-2 Neutralize Pseudoviruses with the Spike Proteins from Different Variants. Pseudoviruses with the spike proteins from different SARS-CoV-2 variants:including the basal strain, single point mutation D614G strain, and two other different variants prevalent around the world (the Alpha and Beta variants):were used as the challenging viruses. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D614G 123 128 S 23 28 34358019 Antibodies Targeting Two Epitopes in SARS-CoV-2 Neutralize Pseudoviruses with the Spike Proteins from Different Variants. Sequences of these two linear epitopes from the original strain (SARS-CoV-2 Wuhan-hu-1; basal; wild-type), three other different variants (D614G; Alpha variant; Beta variant) prevalent around the world ( accessed on 28 June 2021), and SARS-CoV were compared (Figure 1). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D614G 139 144 34358019 Antibodies Targeting Two Epitopes in SARS-CoV-2 Neutralize Pseudoviruses with the Spike Proteins from Different Variants. The half-maximal inhibition concentration (IC50) of Ab 14745 for the wild-type, D614G, Alpha, and Beta variants was 1.7, 1.8, 1.1, and 2.3 ug/mL, respectively. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D614G 80 85 34358019 Antibodies Targeting Two Epitopes in SARS-CoV-2 Neutralize Pseudoviruses with the Spike Proteins from Different Variants. The IC50 of Ab 14902 for the wild-type, D614G, Alpha, and Beta variants was 1.5, 1.3, 1.1, and 2.1 ug/mL, respectively. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D614G 40 45 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. The RBD variability data obtained for SARS-CoV-2 variants from Moscow patients (Figure 2, dashed lines) are generally consistent with the variability data for Russian sequences available in GISAID (Figure 2, solid lines and Figure S1) showing increasing prevalence of S477N, A522S, E484K, N501Y, T385I, S494P, N439K, K417N, T487K, N501T, and Y508H mutations. 2021 Vaccines Result SARS_CoV_2 A522S;E484K;K417N;N439K;N501T;N501Y;S477N;S494P;T385I;T487K;Y508H 275;282;317;310;331;289;268;303;296;324;342 280;287;322;315;336;294;273;308;301;329;347 RBD 4 7 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. The study of the neutralizing activity of Sputnik V induced sera against SARS-CoV-2 variants showed no significant differences in the levels of VNT for B.1.1.1, B.1.1.141 (T385I), B.1.1.317 (S477N, A522S), B.1.1.7, and B.1.617.3. 2021 Vaccines Result SARS_CoV_2 A522S;S477N;T385I 198;191;172 203;196;177 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. Then, we examined B.1.1.7, B.1.351, and B.1.617, already present in Russia, as well as combinations of variants including B.1.1.317 (S477N, A522S) and B.1.1.141 (T385I) that we were able to isolate using cell culture. 2021 Vaccines Result SARS_CoV_2 A522S;S477N;T385I 140;133;162 145;138;167 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. All of these 13 UK variants presented with one mutation in the S-gene, near the DeltaH69/DeltaV70 deletion: either S71F in position 21,774, or A67S in position 21,761 on the reference genome. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 A67S;S71F 143;115 147;119 S 63 64 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Among the 15 remaining samples, surprisingly, 13 were UK variants (B.1.1.7) and 2 belonged to lineage A.27 (19B/501Y) with a N501Y mutation. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 N501Y 125 130 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. For samples with the S71F mutation, the fluorescence intensity of the DeltaH69/DeltaV70 target was lower (Figure 1E, red curve) than in B.1.1.7, without this mutation (Figure 1D). 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 S71F 21 25 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. In the case of A67S mutations, we did not observe any impact on the detection of the UK variant (Figure 1D). 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 A67S 15 19 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. In total, the PerkinElmer kit allowed for the identification of the UK variant, although the fluorescence was not equivalent to the positive control or the UK variant without the mutation S71F. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 S71F 188 192 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. The 530 remaining samples (24.1%) were other variants, without mutation N501Y nor deletion DeltaH69/DeltaV70 (e.g., lineages B1.177 or B1.160). 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 N501Y 72 77 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Using the ID Solution kit screening, 71.8% of the samples (1585/2207) belonged to UK variant (B.1.1.7) (detection of the three targets SARS-CoV-2, N501Y and DeltaH69/DeltaV70, Figure 1A), and 4.1% (92 samples/2207) to variants B.1.351 or P.1 (detection of two targets SARS-CoV and 501Y, Figure 1C). 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 N501Y 147 152 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Using the ID Solution kit, the S71F and A67S mutations impacted the detection of DeltaH69/DeltaV70 deletion (Figure 1B). 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 A67S;S71F 40;31 44;35 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. A synonymous mutation D111D was observed to be co-occurring with the RBD mutations L452R and E484Q in lineage B.1.617.1. 2021 Microorganisms Result SARS_CoV_2 D111D;E484Q;L452R 22;93;83 27;98;88 RBD 69 72 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Estimation of the minimized energies of the wildtype and L452R occurring with the E484Q mutant structure of the RBD complexed with ACE2 showed energy values of -93732.305 kcal/mol and -94543.180 kcal/mol, respectively. 2021 Microorganisms Result SARS_CoV_2 E484Q;L452R 82;57 87;62 RBD 112 115 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. In the case of the mutant RBD possessing L452R with T478K (Figure 5B), though no additional intermolecular contact was affected, three additional hydrogen bonds (H-bonds) were formed by K478 with F486. 2021 Microorganisms Result SARS_CoV_2 L452R;T478K 41;52 46;57 RBD 26 29 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Induction of a P681R point mutation in the modeled structure further revealed that the side chain of R681 could facilitate additional interactions with furin. 2021 Microorganisms Result SARS_CoV_2 P681R 15 20 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Mutation G142D and P681R, within the spike but outside the RBD region, were common to all the three new lineages (Figure 3). 2021 Microorganisms Result SARS_CoV_2 G142D;P681R 9;19 14;24 S;RBD 37;59 42;62 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. P681R is noted in the S1-S2 furin cleavage site. 2021 Microorganisms Result SARS_CoV_2 P681R 0 5 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. PangoLIN lineage classification of 1791 whole genomes revealed the presence of 40 lineages, with the majority within GISAID clades G/GH/GR/GRY/GV, evident from the D614G mutation in the S protein. 2021 Microorganisms Result SARS_CoV_2 D614G 164 169 S 186 187 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Similarly, mutations K77T and A222V were found in a proportion of B.1.617.2. 2021 Microorganisms Result SARS_CoV_2 A222V;K77T 30;21 35;25 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Similarly, the implications of RBD mutations, L452R and T478K, as in lineage B.1.617.2, were studied. 2021 Microorganisms Result SARS_CoV_2 L452R;T478K 46;56 51;61 RBD 31 34 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Specific mutations such as T95I, H1101D and D1153Y were found in a proportion of B.1.617.1. 2021 Microorganisms Result SARS_CoV_2 D1153Y;H1101D;T95I 44;33;27 50;39;31 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The effect of the E484Q mutation is noted in terms of disruption in an electrostatic bond of the spike RBD residue E484 with K31 in the ACE2 interaction interface (Figure 5A, Supplementary Table S1). 2021 Microorganisms Result SARS_CoV_2 E484Q 18 23 S;RBD 97;103 102;106 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The intramolecular interaction L452-L492 associated with the L452R mutation was disrupted before. 2021 Microorganisms Result SARS_CoV_2 L452R 61 66 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The L452R mutation abolishes the hydrophobic interaction with L492 of the RBD. 2021 Microorganisms Result SARS_CoV_2 L452R 4 9 RBD 74 77 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The L452R mutation breaks the hydrophobic interactions with both residues I103 and V105 and also disrupts the H-bond and electrostatic interaction with R112. 2021 Microorganisms Result SARS_CoV_2 L452R 4 9 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The lineage B.1.617.3 was characterized by mutations T19R and E484Q. 2021 Microorganisms Result SARS_CoV_2 E484Q;T19R 62;53 67;57 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The mutations L452R and E484Q are seen to disrupt the interfacial interactions of the spike RBD with specific neutralizing antibodies (Figure 5C,D; Supplementary Table S2), The heavy chain of monoclonal antibody REGN10933 interacts with the RBD by making two H-bonds between E484 of the RBD and Y53 and S56 of the antibody. 2021 Microorganisms Result SARS_CoV_2 E484Q;L452R 24;14 29;19 S;RBD;RBD;RBD 86;92;241;287 91;95;244;290 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The mutations L452R and E484Q within the RBD were specific to lineage B.1.617.1 and B.1.617.3 while L452R and T478K were specific to lineage B.1.617.2. 2021 Microorganisms Result SARS_CoV_2 E484Q;L452R;L452R;T478K 24;14;100;110 29;19;105;115 RBD 41 44 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The RBD mutation E484Q disrupts the two H-bonds with S56 and Y53 (Figure 5C). 2021 Microorganisms Result SARS_CoV_2 E484Q 17 22 RBD 4 7 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The structural implications of the RBD mutations, L452R and E484Q, as in lineages B.1.617.1 and B.1.617.3, were analyzed in terms of interaction with the ACE2 receptor and neutralizing antibodies that are known to have interactions with these residues (Figure S3). 2021 Microorganisms Result SARS_CoV_2 E484Q;L452R 60;50 65;55 RBD 35 38 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Design specific crRNA for SARS-CoV-2 D614G mutation. 2021 Virus research Result SARS_CoV_2 D614G 37 42 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Detection of the synthetic SARS-CoV-2 D614G RNA. 2021 Virus research Result SARS_CoV_2 D614G 38 43 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Furthermore, when the synthetic DNA templates of SARS-CoV-2 D614G mutation were 10-fold diluted from 6 x 104 to 6 x 100 copies/muL, the dsmCRISPR system successfully distinguished G614 from D614 even when the templates were as low as 6 x 100 copies. 2021 Virus research Result SARS_CoV_2 D614G 60 65 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Hence, when combined with RT-PCR, the dsmCRISPR system can detect the nucleic acids with template number as low as few copies, thus providing a highly sensitive and specific method to detect the SARS-CoV-2 D614G mutation. 2021 Virus research Result SARS_CoV_2 D614G 206 211 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Optimization of Cas12a-based detection of SARS-CoV-2 D614G mutation. 2021 Virus research Result SARS_CoV_2 D614G 53 58 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Sensitivity evaluation Cas12a-based detection of SARS-CoV-2 D614G mutation. 2021 Virus research Result SARS_CoV_2 D614G 60 65 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. There was only one single nucleotide difference of crRNA-0 at 23403 (A>G) in SARS-CoV-2's genome (GeneBank accession NC_045512.2) between SARS-CoV-2 D614 and SARS-CoV-2 G614. 2021 Virus research Result SARS_CoV_2 A23403G 62 73 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. To further improve the sensitivity and specificity of the method, the 3' end of the forward primer was designed at the SNP (A23403G) site of the D614G mutation. 2021 Virus research Result SARS_CoV_2 D614G;A23403G 145;124 150;131 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. To get a better distinction, we introduced additional mismatches of the crRNAs from -3 to +3 around the D614G mutation site with high target efficiency calculated by the CRISPR-DT tool. 2021 Virus research Result SARS_CoV_2 D614G 104 109 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. To obtain a high sensitivity of detection, we optimized the crRNA and designed a SARS-CoV-2 D614G mutation specific crRNA targeting the S gene (crRNA-0). 2021 Virus research Result SARS_CoV_2 D614G 92 97 S 136 137 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. To verify the specificity of the synthetic mismatched primers for the G614 RNA template, we performed reverse transcription polymerase chain reaction (RT-PCR) to amplify the synthetic RNA sequence of SARS-CoV-2 D614G mutation. 2021 Virus research Result SARS_CoV_2 D614G 211 216 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. After the importation of B.1.1 lineages characterized by N:R203K and N:G204R mutations, community transmission massively occurred and gave rise to B.1.1.28 (S:V1176F) and B.1.1.33 lineages (ORF6:I33T and N:I292T), widely distributed in Brazilian regions along the first year of the pandemic. 2021 Virus research Result SARS_CoV_2 G204R;I292T;I33T;R203K;V1176F 71;206;195;59;159 76;211;199;64;165 ORF6;N;N;N;S 190;57;69;204;157 194;58;70;205;158 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. Almost all sequences from Brazil harbor the S:D614G and ORF1b:P314L, which were imported from other continents to Brazil (mainly to Southeastern states) in the early epidemic wave of COVID-19. 2021 Virus research Result SARS_CoV_2 D614G;P314L 46;62 51;67 S 44 45 COVID-19 183 191 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. The adjacent replacement GGG28881AAC (N:RG203-204KR) was found in 85.17%, representing a clear signature of B.1.1 lineage. 2021 Virus research Result SARS_CoV_2 G28881A;G28881C 25;25 36;36 N 38 39 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. The G23012A (S:E484K) mutation in the Receptor Binding Domain (RBD) of spike that recently emerged independently in three Brazilian lineages (B.1.1.33, P.1 and P.2) is already among the most frequent detected up to February, 2021 (11.42%). 2021 Virus research Result SARS_CoV_2 G23012A;E484K 4;15 11;20 RBD;S;RBD;S 38;71;63;13 61;76;66;14 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. The G25088T (S:V1176F) replacement from B.1.1.28 occurred in 47.56% of all sequences, while T29148C (N:I292T) and T27299C (ORF6:I33T) from B.1.1.33 in 32.5%. 2021 Virus research Result SARS_CoV_2 G25088T;T27299C;T29148C;I292T;I33T;V1176F 4;114;92;103;128;15 11;121;99;108;132;21 ORF6;N;S 123;101;13 127;102;14 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. The viruses containing the E484K mutation have been spreading mostly between mid-2020 up to early-2021. 2021 Virus research Result SARS_CoV_2 E484K 27 32 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. Three mutations were found in > 95% of the genomes: A23403G (S:D614G), C14408T (ORF1ab:L4715), and C3037T (ORF1ab:F924), which are signatures of the B.1 and derived lineages that spread early in the pandemic. 2021 Virus research Result SARS_CoV_2 A23403G;C14408T;C3037T;D614G 52;71;99;63 59;78;105;68 ORF1ab;ORF1ab;S 80;107;61 86;113;62 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. As expected, while the N7-MTase activity of the WT nsp14 was set as 100%, the N7-MTase activity of mutant nsp14 D330A and Y414A was very low, reaching 14% and 17%, respectively, but was significantly higher than the background value (Figure 1(B)), suggesting that the single amino acid substitution D330A and Y414A can partially abolish N7-MTase activity of MHV nsp14. 2021 Emerging microbes & infections Result SARS_CoV_2 D330A;D330A;Y414A;Y414A 112;299;122;309 117;304;127;314 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. As Figure 2(G) shows, IFN-beta levels in the sera of D330A-infected and Y414A-infected mice accumulated from 8 hpi and peaked at 12 hpi, while the IFN-beta levels of WT-infected mice were significantly lower than N7-MTase mutants. 2021 Emerging microbes & infections Result SARS_CoV_2 D330A;Y414A 53;72 58;77 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. At the early stage of infection (<=24 h), mice infected with mutant D330A, Y414A or WT suffered a short-term body weight plateau with minor symptoms of illness. 2021 Emerging microbes & infections Result SARS_CoV_2 D330A;Y414A 68;75 73;80 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. Both liver histopathological analysis and alanine aminotransferase (ALT) measurement showed that only minimal signs of disease occurred in mice after infection with the D330A and Y414A mutants at 1 dpi (Figure 2(E,F)). 2021 Emerging microbes & infections Result SARS_CoV_2 D330A;Y414A 169;179 174;184 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. Considering the genetic stability of the mutants during viral replication, we continuously passaged the mutant viruses P0 on Neuro 2a cells for 10 rounds and found that D330A and Y414A mutations still remained, while no extra mutation was introduced within the nsp14 gene segment according to the sequencing results of P10 mutants (Figure 1(D)). 2021 Emerging microbes & infections Result SARS_CoV_2 D330A;Y414A 169;179 174;184 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. For vaccination, groups of 4-week-old male C57BL/6 mice were subcutaneously (s.c.) inoculated with a dose of 5x105 PFU mutant D330A, Y414A and WT MHV-A59, while DMEM was used as a mock control (Figure 3(A)). 2021 Emerging microbes & infections Result SARS_CoV_2 D330A;Y414A 126;133 131;138 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. Further structure-function analysis suggested that the single amino acid substitution D331A, which is in the DxG S-adenosyl-L-methionine (SAM)-binding motif, and Y420A, which is in the supporting structure of the SAM-binding pocket, can affect the SAM-binding affinity of SARS-CoV N7-MTase and abolish its N7-methylation activity in vitro. 2021 Emerging microbes & infections Result SARS_CoV_2 D331A;Y420A 86;162 91;167 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. Furthermore, mice infected with the WT virus presented significantly higher levels of viral titres in the liver at 1, 2, 5 dpi, whereas the viral load of mice infected with D330A and Y414A could only be detected at 1 dpi and manifested as 68-fold and 350-fold decrease compared to WT virus-infected mice, respectively (Figure 2(D)). 2021 Emerging microbes & infections Result SARS_CoV_2 D330A;Y414A 173;183 178;188 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. However, as the infection progressed, both D330A- and Y414A-infected mice started to gain weight slowly and their survival rate increased compared to WT-infected mice, which lost massive weight until death (Figure 2(B,C)). 2021 Emerging microbes & infections Result SARS_CoV_2 D330A;Y414A 43;54 48;59 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. Meanwhile, the Y414A mutant showed a slightly reduced replication capacity in Neuro 2a cells but possessed similar replication kinetics to WT viruses in L2 cells (Figure 1(E)). 2021 Emerging microbes & infections Result SARS_CoV_2 Y414A 15 20 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. Notably, the strength of the T cell response was similar in the D330A, Y414A, and WT groups. 2021 Emerging microbes & infections Result SARS_CoV_2 D330A;Y414A 64;71 69;76 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. Similarly, higher Ifnb mRNA levels were induced in mouse bone marrow-derived dendritic cells (BMDCs) at 8 h after infection with mutant D330A (2.13-fold increase) and mutant Y414A (4.96-fold increase) compared to WT virus-infected mice (Figure 2(H)). 2021 Emerging microbes & infections Result SARS_CoV_2 D330A;Y414A 136;174 141;179 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. Taken together, these results suggest that N7-MTase mutant coronaviruses harbouring a single amino acid substitution of D330A or Y414A are stable and slightly attenuated in vitro. 2021 Emerging microbes & infections Result SARS_CoV_2 D330A;Y414A 120;129 125;134 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. The one-step growth curves of mutants in mammalian cell line Neuro 2a and L2 showed that the D330A mutant replicated slightly slower than the WT virus during the early stages (4-12 h), but peaked at similar levels to the WT virus. 2021 Emerging microbes & infections Result SARS_CoV_2 D330A 93 98 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. The rescued mutant viruses P0 were sequenced and it was confirmed that the designed mutation D330A and Y414A were introduced (data not shown). 2021 Emerging microbes & infections Result SARS_CoV_2 D330A;Y414A 93;103 98;108 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. The splenocytes of mice immunized with Y414A produced higher levels of cytokines than cells immunized with the WT virus (IFN-gamma, P = 0.0399; IL-2, P = 0.0388; IL-10, P = 0.0010). 2021 Emerging microbes & infections Result SARS_CoV_2 Y414A 39 44 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. These results indicate that the mutant D330A and Y414A were sharply replication-limited and were quickly cleared by host animals. 2021 Emerging microbes & infections Result SARS_CoV_2 D330A;Y414A 39;49 44;54 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. To compare the virulence and pathogenicity of the mutant and WT viruses in vivo, groups of 4-week-old male C57BL/6 mice were intrahepatically inoculated (i.h.) with 2x106 PFU of mutant D330A, Y414A or WT MHV-A59. 2021 Emerging microbes & infections Result SARS_CoV_2 D330A;Y414A 185;192 190;197 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. To further explore the details of these two mutations in terms of coronavirus replication and pathogenicity, we engineered and rescued two MHV N7-MTase mutant viruses, D330A and Y414A, and wild-type (WT) MHV using a vaccinia virus-based reverse genetic system. 2021 Emerging microbes & infections Result SARS_CoV_2 D330A;Y414A 168;178 173;183 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. To verify the effects of these conserved key residues on MHV N7-MTase enzymatic activity, we introduced the two mutations into MHV-A59 nsp14 and expressed MHV nsp14 mutant protein D330A as well as Y414A in E. 2021 Emerging microbes & infections Result SARS_CoV_2 D330A;Y414A 180;197 185;202 E 206 207 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. Consistently, S309-CAR-NKprimary cells can also specifically kill A549-Spike D614G cells, indicating that S309-CAR-NKprimary cells are unaffected to the G614 variant (Figure 6C). 2021 Frontiers in immunology Result SARS_CoV_2 D614G 77 82 S 71 76 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. Furthermore, we also showed that S309-CAR-NKprimary can bind to other variants of pseudotyped SARS-CoV-2 viral particles, including the E484K and N501Y mutations ( Figure S5A ). 2021 Frontiers in immunology Result SARS_CoV_2 E484K;N501Y 136;146 141;151 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. In addition to using expanded PBNK, CD19-CAR-NK cells (specific for the treatment of B-acute lymphoblastic leukemia) were also included to show the specificity of S309-CAR-NKprimary against target cells expressing wild-type S protein or the D614G variant. 2021 Frontiers in immunology Result SARS_CoV_2 D614G 241 246 S 224 225 B acute lymphoblastic leukemia 85 115 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. More importantly, the intracellular cytokine productions of S309-CAR-NKprimary cells when cocultured with A549-Spike D614G target cells were similar to that of A549-Spike, indicating S309-CAR-NKprimary cells can also target and kill cells infected by the SARS-CoV-2 D614G variant. 2021 Frontiers in immunology Result SARS_CoV_2 D614G;D614G 117;266 122;271 S;S 111;165 116;170 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. Next, we evaluated the ability by which S309-CAR-NKprimary cells bind to pseudotyped SARS-CoV-2 D614G variant by flow cytometry. 2021 Frontiers in immunology Result SARS_CoV_2 D614G 96 101 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. Next, we used the Cr51 release assay to further determine the killing activities of S309-CAR-NKprimary cells against A549-Spike D614G target cells. 2021 Frontiers in immunology Result SARS_CoV_2 D614G 128 133 S 122 127 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. S309-CAR-NKprimary Cells Can Also Target SARS-CoV-2 D614G, K484, and Y501 Variants. 2021 Frontiers in immunology Result SARS_CoV_2 D614G 52 57 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. Subsequently, we generated A549-Spike D614G cell line using the retrovirus system, which 293T cells were transduced with a combination of RDF, Pegpam3, and SARS-CoV-2 S D614G in SFG backbone. 2021 Frontiers in immunology Result SARS_CoV_2 D614G;D614G 38;169 43;174 S;S 32;167 37;168 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. To ensure the functions of S309-CAR-NKprimary are not altered by the G614 mutation, we also generated A549-Spike D614G cell line. 2021 Frontiers in immunology Result SARS_CoV_2 D614G 113 118 S 107 112 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. 3B) shows the high linear correlation between the expected proportion and detected proportion of N501Y and WT respectively. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 97 102 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. After the emergence of variants containing the N501Y mutation, the increase in the proportion of this marker in wastewater follows a trend that is comparable with the increase of N501Y containing variants in patients. 2021 The Science of the total environment Result SARS_CoV_2 N501Y;N501Y 47;179 52;184 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Detection of N501Y was possible in a sample dilution containing a theoretical concentration of only 2.7 copies of B.1.351 or WT detection in a sample containing 2.3 copies of WT suggests the feasibility for specific detection of low concentrations of WT and N501Y. 2021 The Science of the total environment Result SARS_CoV_2 N501Y;N501Y 13;258 18;263 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Emergence of the SARS-CoV-2 N501Y mutation in sewage. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 28 33 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. For the period of Nov 9, 2020 to Mar 1, 2021 concentrations of SARS-CoV-2 RNA was measured in sewage from WWTP Amsterdam and Utrecht with RT-qPCR directed to the N2 amplicon of the N-gene and with RT-ddPCR as the sum of WT and N501Y sequences of the Spike gene. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 227 232 S;N 250;181 255;182 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. For this, we isolated RNA from wild type virus and a B.1.351 strain containing the N501Y mutation. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 83 88 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. It also shows that low concentrations of N501Y mutation can be detected in the presence of WT virus RNA and vice versa. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 41 46 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. It is expected that the assay can be used to detect low concentrations of WT and N501Y and to obtain reliable insight in the proportion of N501Y in mixtures of viruses, and therefore has the potency to collect information about the spread of variants. 2021 The Science of the total environment Result SARS_CoV_2 N501Y;N501Y 81;139 86;144 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. The concentration SARS-CoV-2 in these samples was first determined using RT-qPCR and compared to COVID-19 incidence and the emergence of N501Y was subsequently studied on the same set of samples. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 137 142 COVID-19 97 105 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. The earliest detection of N501Y was in the wastewater sample of December 8 2020 in Amsterdam and in the wastewater sample of December 21 2020 in Utrecht. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 26 31 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. The first detection of N501Y in wastewater from Utrecht was two weeks later. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 23 28 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. The introduction and emergence of SARS-CoV-2 variants containing the N501Y mutation in Utrecht wastewater aligns more in time with the national 'average' emergence as obtained through the genomic pathogen surveillance data. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 69 74 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. The percentage of N501Y containing variants appears to be higher in Amsterdam wastewater in the complete period suggesting earlier introduction in Amsterdam than in Utrecht. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 18 23 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. The proportion of N501Y gradually increased to 85% on February 22 2021 in Amsterdam and 81% on February 22 2021 in Utrecht. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 18 23 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. The proportion of N501Y to WT sequences in wastewater is determined and compared with publicly available data from the Dutch National Institute for Public Health and the Environment (RIVM). 2021 The Science of the total environment Result SARS_CoV_2 N501Y 18 23 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. The specificity of the assay to detect the N501Y mutation was confirmed on RNA from SARS-CoV-2 lineage B.1.1.7, the specificity of the N501Y assay for RNA from B.1.1.7 and B.1.351 VOC's is demonstrated in Supplemental. 2021 The Science of the total environment Result SARS_CoV_2 N501Y;N501Y 43;135 48;140 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. The total SARS-CoV-2 RNA concentrations were higher in wastewater from Amsterdam compared to Utrecht (Tables S1 and S2), yielding a more accurate assessment of the N501Y proportion, as indicated by the error-bars. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 164 169 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. These results demonstrate that the assay can be used to discriminate between WT SARS-CoV-2 RNA and variants containing the N501Y mutation and simultaneous detection and quantification of these sequences. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 123 128 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. These results demonstrate the ability of the method to simultaneously detect and discriminate between the sequences of WT and the N501Y mutation in lineage B.1.351 from a mixed sample. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 130 135 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. This corresponds to the first detection of N501Y in wastewater from Amsterdam. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 43 48 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. To study the ability of RT-ddPCR to differentiate between 501Y and 501N sequences and to detect low concentrations of SARS-CoV-2 N501Y mutant in the background of WT RNA two dilutions series were analyzed. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 129 134 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. Additionally, for the T716I and S982A variants, substitution frequencies increased over time (respectively, from 0.88% in December to 51.61% in February (OR: 10.59, 95% CI: 7.13-16.11, p < 0.0001) and from 0.88% in December to 50.97% in February (OR: 10.53, 95% CI: 6.97-15.72, p < 0.0001). 2021 Viruses Result SARS_CoV_2 S982A;T716I 32;22 37;27 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. Co-existence of DeltaH69V70, DeltaY144, P681H, T716I, S982A, A570D, N501Y, and D1118H was the signature for the B.1.1.7 (20H/501Y.V1) variant. 2021 Viruses Result SARS_CoV_2 A570D;D1118H;DeltaY144;N501Y;P681H;S982A;T716I 61;79;29;68;40;54;47 66;85;38;73;45;59;52 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. D614G substitution was fixed (97.47%) in the circulating viruses in Poland. 2021 Viruses Result SARS_CoV_2 D614G 0 5 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. Genetic variability of the SARS-CoV-2 and number of spike mutation containing variants increased rapidly since September 2020, with additional accumulation of P681H, N439K, S98F, during the second wave of SARS CoV-2 epidemics in Poland (Figure 5, Tables S1 and S2). 2021 Viruses Result SARS_CoV_2 N439K;P681H;S98F 166;159;173 171;164;177 S 52 57 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. Interestingly, only the frequency of N439K dropped, from 26.31 to 10.97% (OR: 0.68, 95% CI 0.57-0.82, p < 0.0001) in the analyzed months. 2021 Viruses Result SARS_CoV_2 N439K 37 42 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. Notably, DeltaH69V70 frequency rose from 26.31% in November to 60.65% in February (OR: 1.54, 95% CI: 1.30-1.83, p < 0.0001); for the DeltaY144 mutation this increase was from 1.23% in December to 51.32% in February; and for the P681H mutation from 0.88% in November to 60% in February (OR: 9.52, 95% CI: 6.46-14.35, p < 0.0001 and OR: 4.30, 95% CI: 3.32-5.67, p < 0.0001, respectively). 2021 Viruses Result SARS_CoV_2 DeltaY144;P681H 133;228 142;233 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. Of note, when excluding the B.1.1.7 variant from temporal trends analysis, only four mutations (delH69V70, P681H, S98F, A222V) had a significantly different frequency from November 2020 until February 2021 (see Figure S5 and Table S4). 2021 Viruses Result SARS_CoV_2 A222V;P681H;S98F 120;107;114 125;112;118 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. The first one was DeltaH69V70 and N439 in lineage B.1.258 (20A), then D138Y with S477N observed for B.1.1.317 (20B), and finally A222V and L18F in the B.1.177 (20E EU1) strains. 2021 Viruses Result SARS_CoV_2 A222V;D138Y;L18F;S477N 129;70;139;81 134;75;143;86 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. The last notable increasing trend was detected for D1118H, from 0.88% in December to 49.68% in February (OR: 9.90, 95% CI 6.83-15.01, p < 0.0001). 2021 Viruses Result SARS_CoV_2 D1118H 51 57 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. Two mutations, A570D and N501Y, were in perfect linkage; therefore, the increase in incidence from 0.88% in December to 51.32% in February (OR: 10.12, 95% CI 6.83-15.37, p < 0.0001) was the same. 2021 Viruses Result SARS_CoV_2 A570D;N501Y 15;25 20;30 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. 4a) is similar to the distribution of approximately 2400 cases of B.1.526 without the E484K mutation. 2021 Nature communications Result SARS_CoV_2 E484K 86 91 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. A closely related lineage, B.1.526.1, is defined by spike mutations D80G, Delta144, F157S, L452R, T859N, and D950H. 2021 Nature communications Result SARS_CoV_2 D80G;D950H;F157S;L452R;T859N 68;109;84;91;98 72;114;89;96;103 S 52 57 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Among the nucleotide mutations in lineage B.1.526, the most characteristic include A16500C (NSP13 Q88H), A22320G (spike D253G), and T9867C (NSP4 L438P). 2021 Nature communications Result SARS_CoV_2 A16500C;A22320G;D253G;L438P;Q88H;T9867C 83;105;120;145;98;132 90;112;125;150;102;138 S;Nsp13;Nsp4 114;92;140 119;97;144 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Around 58% (n = 2864) of the B.1.526 genomes contain the E484K mutation, which has also been rising in frequency since early 2021. 2021 Nature communications Result SARS_CoV_2 E484K 57 62 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. One of these sub-lineages defined by spike mutations S477N, V701A, and Q957R, has been designated B.1.526.2, but for the purposes of characterizing epidemic and phylodynamic growth of this variant, we combine B.1.526 and B.1.526.2. 2021 Nature communications Result SARS_CoV_2 Q957R;S477N;V701A 71;53;60 76;58;65 S 37 42 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Regarding four of the spike mutations prevalent in this lineage: (1) E484K is known to attenuate neutralization of multiple anti-SARS-CoV-2 antibodies, particularly those found in class 2 anti-RBD neutralizing antibodies, and is also present in variants B.1.351 and P.1/B.1.1.248, (2) D253G has been reported as an escape mutation from antibodies against the N-terminal domain, (3) S477N has been identified in several earlier lineages, is near the epitopes of multiple antibodies, and has been implicated to increase viral infectivity through enhanced interactions with ACE2, and (4) A701V sits adjacent to the S2' cleavage site of the neighboring protomer and is shared with variant B.1.351. 2021 Nature communications Result SARS_CoV_2 A701V;D253G;E484K;S477N 585;285;69;382 590;290;74;387 S;RBD;N 22;193;359 27;196;360 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Specifically, we estimated the exponential growth rate for the B.1.1.7, B.1.427, and B.1.429 variants, for two subsets of the B.1.526 clade sequences (with and without the E484K mutation), and the B.1.526.1 lineage. 2021 Nature communications Result SARS_CoV_2 E484K 172 177 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The 4.5-fold reduced titer of vaccinee plasma against E484K-containing B.1.526 can be compared to an 8.4-fold reduction found against variant B.1.351. 2021 Nature communications Result SARS_CoV_2 E484K 54 59 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The B.1.526 E484K clade experienced the most rapid exponential growth compared with other lineages circulating at the same time: 11.82 (95% highest posterior density [HPD]: 9.19-14.54). 2021 Nature communications Result SARS_CoV_2 E484K 12 17 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The E484K-containing B.1.526 pseudovirus had a statistically significant reduced neutralization titer compared to the D614G control: for vaccinee plasma, 4.5-fold reduced (p = 0.00005); for 1.3-month convalescent plasma, 6.0-fold reduced (p = 0.03); and for 6.2-month convalescent plasma, 4.8-fold reduced (p = 0.02). 2021 Nature communications Result SARS_CoV_2 D614G;E484K 118;4 123;9 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The geographic distribution of over 3300 cases associated with B.1.526 E484K. 2021 Nature communications Result SARS_CoV_2 E484K 71 76 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The latter rooting posits a substitution A701V followed by a reversion V701A. 2021 Nature communications Result SARS_CoV_2 A701V;V701A 41;71 46;76 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The S477N/Q957R-containing B.1.526 pseudovirus demonstrated a smaller effect on plasma neutralization. 2021 Nature communications Result SARS_CoV_2 S477N;Q957R 4;10 9;15 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The weekly mean of B.1.526 genomes with E484K has been above 10% since 01 February 2021, and its maximum increase in daily prevalence inferred with the logistic model was 0.4% per day. 2021 Nature communications Result SARS_CoV_2 E484K 40 45 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. These changes are consistent with the effects expected for E484K-containing viruses. 2021 Nature communications Result SARS_CoV_2 E484K 59 64 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. This behavior is consistent for both B.1.526 E484 and B.1.526 E484K, as well as B.1.1.7. 2021 Nature communications Result SARS_CoV_2 E484K 62 67 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. This uncertainty is not unexpected, as recurrent mutations in spike are common in this part of the phylogeny: both S477N and T95I are homoplastic. 2021 Nature communications Result SARS_CoV_2 S477N;T95I 115;125 120;129 S 62 67 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. This variant is found within the 20.C clade and is distinguished by 3 defining spike mutations: L5F, T95I, and D253G. 2021 Nature communications Result SARS_CoV_2 D253G;L5F;T95I 111;96;101 116;99;105 S 79 84 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. We estimate the TMRCA of B.1.526 with E484K to be 21 November 2020 (95% HPD: 20 October-13 December), B.1.526 with E484 (including B.1.526.2) to be 7 July 2020 (95% HPD 10 May-30 August), and the B.1.526.1 clades to be 8 November 2020 (95% HPD: 2 October-14 December). 2021 Nature communications Result SARS_CoV_2 E484K 38 43 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. We generated HIV-based pseudoviruses expressing SARS-CoV-2 spike protein containing either the most common B.1.526 mutation pattern (v.1: L5F, T95I, D253G, E484K, D614G, and A701V), the 2nd most common pattern (v.2: L5F, T95I, D253G, S477N, D614G, and Q957R), or only D614G. 2021 Nature communications Result SARS_CoV_2 A701V;D253G;D253G;D614G;D614G;D614G;E484K;L5F;L5F;Q957R;S477N;T95I;T95I 174;149;227;163;241;268;156;138;216;252;234;143;221 179;154;232;168;246;273;161;141;219;257;239;147;225 S 59 64 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Within B.1.526, the largest sub-clade is defined by E484K, and two distinct sub-clades are each defined by S477N; both of these mutations located within the receptor-binding domain (RBD) of spike. 2021 Nature communications Result SARS_CoV_2 E484K;S477N 52;107 57;112 S;RBD 190;182 195;185 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. Accuracies for the VOC assays using a limited panel of 114 samples, including B.1.1.7 positive (n = 10), wild-type positive (n = 99), and SARS-CoV-2 negative (n = 5) samples demonstrated values of 98.25% (95% confidence interval [CI] 93.8 to 99.8%) for the DeltaH69/V70 assay and 100% (95% CI 96.8 to 100%) for the N501Y assay. 2021 Microbiology spectrum Result SARS_CoV_2 N501Y 315 320 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. Also during this prospective comparison, a total of 152 samples tested positive for N501Y alone (without the H69/70 deletion); these belonged to the B.1 (n = 27), B.1.351 (n = 17), B.1.438 (n = 2), and P.1 (n = 106) lineages. 2021 Microbiology spectrum Result SARS_CoV_2 N501Y 84 89 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. During this time, 585 samples with the H69/V70 deletion alone (without the N501Y mutation) were detected, which were found to be lineages B.1.525 (n = 574), B.1 (n = 5), B.1.160 (n = 3), B.1.258 (n = 2), and B.1.280 (n = 1). 2021 Microbiology spectrum Result SARS_CoV_2 N501Y 75 80 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. For the N051Y assay, the analytical sensitivities were 3 and 3 copies/reaction (corresponding to 257 and 294 copies/ml of sample) for the wild-type and N501Y templates, respectively. 2021 Microbiology spectrum Result SARS_CoV_2 N501Y 152 157 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. For the N501Y assay, inter- and intra-assay variabilities were all less than 3% for both mutant and wild-type probes. 2021 Microbiology spectrum Result SARS_CoV_2 N501Y 8 13 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. In this analysis, samples positive for both the DeltaH69/V70 and N501Y assays were interpreted as positive for B.1.1.7; samples negative for the DeltaH69/V70 assay and positive for the N501Y assay were considered presumptively positive for P.1/B.1.351 (essentially non-B.1.1.7 VOCs); and samples negative for both VOC assays were considered wild-type (non-VOCs), since B.1.617.2 was not considered a VOC during this time period. 2021 Microbiology spectrum Result SARS_CoV_2 N501Y;N501Y 65;185 70;190 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. Performance of the DeltaH69/V70 and N501Y assays. 2021 Microbiology spectrum Result SARS_CoV_2 N501Y 36 41 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. Samples that yielded discordant results included eight samples that were misclassified as P.1/B.1.351 rather than B.1.1.7 (all of which were negative on the DeltaH69/V70 assay and showed the presence of the C21774T mutation adjacent to the H69/V70 deletion region), two samples that were misclassified as wild-type rather than B.1.1.7 (both of which had the N501Y mutation undetected by the N501Y assay), and 29 samples that were misclassified as P.1/B.1.351 rather than wild-type (all of which showed the presence of the A23063T mutation corresponding to N501Y in the B.1 [n = 27] or B.1.438 [n = 2] lineages). 2021 Microbiology spectrum Result SARS_CoV_2 A23063T;C21774T;N501Y;N501Y;N501Y 522;207;358;391;556 529;214;363;396;561 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. This is reflected in the eventual rise in the 7-day rolling average and proportion of samples screened by the DeltaH69/V70 and N501Y assays, from 2.2% of samples on 12 January 2021 to ~100% of samples by 9 February 2021, with consistently high proportions of samples tested for VOCs thereafter. 2021 Microbiology spectrum Result SARS_CoV_2 N501Y 127 132 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. Accordingly, only HTS0483 inhibits the binding between ACE2 and all RBD mutants including W436R and R408I. 2021 Biotechnology journal Result SARS_CoV_2 R408I;W436R 100;90 105;95 RBD 68 71 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. As shown in Figure 4a, HTS0422, HTS0433 and HTS0446 bind with both wildtype and mutant (N501Y, W463R, N354D, V367F, both N354D and D364Y) RBD significantly. 2021 Biotechnology journal Result SARS_CoV_2 D364Y;N354D;N354D;V367F;W463R;N501Y 131;102;121;109;95;88 136;107;126;114;100;93 RBD 138 141 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. As shown in Figure 6a, the infection of mutants N354D, V367F and N354D/D364Y could be inhibited by all 4 antibodies. 2021 Biotechnology journal Result SARS_CoV_2 N354D;N354D;V367F;D364Y 48;65;55;71 53;70;60;76 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. Consistent with the binding assay data, the neutralization of HTS0433 to N501Y mutant strain was also reduced obviously, suggesting that the point mutation in CDR3 of VL is important to block the infection of host cells. 2021 Biotechnology journal Result SARS_CoV_2 N501Y 73 78 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. In addition, only HTS0483 binds with R408I, suggesting that R408I is essential for the binding of HTS0422, HTS0433 and HTS0446, and mutations at R408I abolished the binding of antibodies to the virus RBD, and HTS0483 may have broader cross-neutralization effect against SARS-CoV-2 RBD mutations. 2021 Biotechnology journal Result SARS_CoV_2 R408I;R408I;R408I 37;60;145 42;65;150 RBD;RBD 200;281 203;284 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. In this study, six different SARS-CoV-2 RBD mutants (N501Y, R408I, W463R, N354D, V367F and N354D/D364Y) which were found in different regions all around the world were obtained from ACRO BIOSYSTEMS. 2021 Biotechnology journal Result SARS_CoV_2 N354D;N354D;R408I;V367F;W463R;N501Y;D364Y 74;91;60;81;67;53;97 79;96;65;86;72;58;102 RBD 40 43 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. Meanwhile, it can also be found that even though all antibodies bind to N501Y significantly, the affinity of HTS0433 is much lower than the others as well as the inhibition of the binding between ACE2 and N501Y. 2021 Biotechnology journal Result SARS_CoV_2 N501Y;N501Y 72;205 77;210 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. This information will aid the affinity maturation of antibody to the more transmissible SARS-CoV-2 lineages with N501Y mutation. 2021 Biotechnology journal Result SARS_CoV_2 N501Y 113 118 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. To further substantiate that the antibody has cross-neutralization activity, a neutralization assay against different mutant strains (N501Y, W436R, R408I, N354D, V367F and N354D/D364Y) by these antibodies was performed. 2021 Biotechnology journal Result SARS_CoV_2 N354D;N354D;R408I;V367F;W436R;N501Y;D364Y 155;172;148;162;141;134;178 160;177;153;167;146;139;183 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. What's more, although the CDR region is same between HTS0433 and HTS0446, there are three amino acids in the frame region of VL are different (DIV AIR), suggesting that the frame region is also important in binding to N501Y mutation. 2021 Biotechnology journal Result SARS_CoV_2 N501Y 218 223 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. While the mutants W436R and R408I could only be inhibited by HTS0483, suggesting great potential of HTS0483 in opposing mutant SARS-CoV-2 (Figure 6b). 2021 Biotechnology journal Result SARS_CoV_2 R408I;W436R 28;18 33;23 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. While the other antibodies (HTS0422, HTS0433 and HTS0446) can only restrict the interaction between ACE2 and wildtype, N501Y, N354D, V367F or N354D/D364Y (Figure 4b), implying that the mutations at W436R and R408I in RBD may cause the virus to escape from antibody blocking and, as a result, make the developing of broad vaccine become a considerable challenge. 2021 Biotechnology journal Result SARS_CoV_2 N354D;N354D;N501Y;R408I;V367F;W436R;D364Y 126;142;119;208;133;198;148 131;147;124;213;138;203;153 RBD 217 220 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. A Nextstrain-generated phylogenetic tree of a subset of the lineages in which L452R occurs, based on genomes randomly sampled from GISAID by Nextstrain on the same day (i.e., 12 June 2021), is depicted in. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 78 83 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. According to genomic analysis, the epsilon variant has also been defined by 4 additional amino acid mutations, including two spike protein mutations, S13I and W152C, located in the signal peptide and N-terminal domain, respectively. 2021 Journal of clinical microbiology Result SARS_CoV_2 S13I;W152C 150;159 154;164 S;N 125;200 130;201 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. According to the GISAID database, while only 6 nCoV genomes with L452R were deposited in September and October 2020 (all from California), 142 additional genomes with the mutation were deposited in November 2020 (95.7% from California), 488 were deposited in December 2020 (79.1% from California), and 619 were deposited in January 2021 (69.2% from California). 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 65 70 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. According to the GISAID genome depositions, in May 2021, L452R mutations were found in 15.9% of all nCoV isolates. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 57 62 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. All of the amino acid mutations had been reported previously and were identified in nCoV sequences deposited to GISAID, with five samples containing the common E484K mutation found, among other lineages, in the Brazil variant B.1.1.28 (VOI zeta). 2021 Journal of clinical microbiology Result SARS_CoV_2 E484K 160 165 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Among the September-October samples, four samples (4.7%) had a single mutation each: two different synonymous mutations (c1497t in two samples and t1695c in one sample) and one missense (nonsynonymous) mutation that resulted in the amino acid change E484K. 2021 Journal of clinical microbiology Result SARS_CoV_2 E484K 250 255 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Analysis of the GISAID-deposited genomes revealed that, on 12 June 2021, the CAL.20A-including lineage B.1.232 contained a total of 1,494 deposited genomes, but only 453 of them (30.3%) contained the L452R mutation. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 200 205 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. At the same time, some of those strains carry either S13I alone (GISAID number 977963) or S13I together with W152 (GISAID number 847642 and number 977918). 2021 Journal of clinical microbiology Result SARS_CoV_2 S13I;S13I 53;90 57;94 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Based on the genome-wide analysis, all nCoV variants with L452R and S13I/W152C mutations were in the same clade as the reference epsilon variant strain (GISAID number 730092; isolated in September 2020). 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R;S13I;W152C 58;68;73 63;72;78 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Both S13I and W152C mutations were found in 10 nonduplicative samples, suggesting their identity with the epsilon variant. 2021 Journal of clinical microbiology Result SARS_CoV_2 S13I;W152C 5;14 9;19 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. By far, however, the most frequent mutation found in region 414 to 583 was L452R, occurring in 14 of 39 (35.9%) nonduplicative samples and isolated from 9 of 18 separate collection sites. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 75 80 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Examination of the GISAID database on 12 June 2021 revealed a total of 60,273 nCoV genomes with L452R. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 96 101 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Genomes with two other mutations at position L452:L452M and L452E:were also found, though they did not form as extensive lineages. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452E;L452M 60;50 65;55 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. However, we found genomes in the B.1.427/B.1.429 lineage that are very closely related to the epsilon variant but are without L452R. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 126 131 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. In addition, we included in the analysis some genomes that we have identified as the most closely related to the L452R variants but without this mutation. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 113 118 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. In contrast, the missense mutations were distributed nonrandomly and, except for one mutation (P463S), were clustered either within the main epitope regions of RBD or in the 570-to-572 loop of CTD1. 2021 Journal of clinical microbiology Result SARS_CoV_2 P463S 95 100 RBD 160 163 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. In fact, L452R was the only missense mutation in the entire genome that separated CAL.20A from the closest non-L452R strain within the B.1.232 lineage (GISAID number 636127). 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R;L452R 9;111 14;116 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. In sharp contrast, the variants without S13I/W152C mutations formed a distinct phylogenetic clade that is distant from the epsilon variants and shared none of the epsilon variant-specific mutations. 2021 Journal of clinical microbiology Result SARS_CoV_2 S13I;W152C 40;45 44;50 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Indeed, the L452R mutation has received significant attention due to the report of the California Department of Public Health released 17 January 2021 and a follow-up publication stating a sharp rise in isolation of nCoV variants with L452R across multiple outbreaks in California. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R;L452R 12;235 17;240 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Interestingly, a different missense mutation at position L452:L452Q:was found in one more epidemiologically important lineage (C.37; VOI lambda) that has been expanding in Peru and Chile and has an additional mutation in the 414-to-583 regio:F490S. 2021 Journal of clinical microbiology Result SARS_CoV_2 F490S;L452Q 242;62 247;67 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. It was originally reported that, besides L452R, all epsilon variant strains carry 4 more missense mutations in the genome, including S13I and W152C in the spike protein. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R;S13I;W152C 41;133;142 46;137;147 S 155 160 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. L452R was found mostly but not exclusively in samples and sites from California. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 0 5 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Notably, the notorious "Indian" lineage B.1.617.2 (VOC the delta) contained L452R, as did its close cousin B.1.617.1 (VOI kappa). 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 76 81 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Relative to the Wuhan-Hu-1 reference strain and in contrast to the epsilon variant, L452R was the only omnipresent amino acid mutation in the spike protein of CAL.20A. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 84 89 S 142 147 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Surprisingly, in 4 samples with L452R, no additional mutations in the N-terminal domain were found. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 32 37 N 70 71 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. The delta and kappa variants differed from each other by the presence of additional mutations located in the 414-to-583 region of the RBD targeted for amplification in our study, i.e., T478K and E484Q, respectfully. 2021 Journal of clinical microbiology Result SARS_CoV_2 E484Q;T478K 195;185 200;190 RBD 134 137 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. There is a clear temporal trend in the number of isolated strains carrying the L452R mutations, with only 47 strains identified before November 2020, 2,594 identified in November and December 2020, 21,068 identified in January and February 2021, and 80,293 identified since March 2021 (Table S4). 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 79 84 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. This suggests that, similar to that for CAL.20A, L452R was a trigger event for the massive clonal expansion of the epsilon variant. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 49 54 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Those samples originated from two separate sites (two samples in each) in California, with one of the sample pairs carrying the T572I mutation in the 414-to-583 region (see above). 2021 Journal of clinical microbiology Result SARS_CoV_2 T572I 128 133 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Thus, acquisition of L452R appears to be the primary evolutionary event that triggered emergence of CAL.20A. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 21 26 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Thus, the spike mutations in the epsilon variant-containing lineage were acquired sequentially, and the L452R mutation was acquired last. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 104 109 S 10 15 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. To determine how closely the L452R variants without S13I and W152C mutations were related to the epsilon variant, full-genome sequencing was performed on three of those samples and on four L452R samples with S13I and W152C. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R;L452R;S13I;S13I;W152C;W152C 29;189;52;208;61;217 34;194;56;212;66;222 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Using an approach similar to our sequencing of region 414 to 583, we amplified and sequenced the aa 1 to 250 coding region in all samples with the L452R mutation. 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 147 152 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. We designated this novel L452R-carrying variant 20A/S:452R/B.1.232 (CAL.20A for brevity). 2021 Journal of clinical microbiology Result SARS_CoV_2 L452R 25 30 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Additionally, a clear nasal discharge was observed on 6 dpi in a single animal inoculated with D614G. 2021 bioRxiv Result SARS_CoV_2 D614G 95 100 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Although B.1.1.7 appears to be detected in the various tissue samples more frequently than D614G and B.1.351, these differences were not statistically significant in individual tissues. 2021 bioRxiv Result SARS_CoV_2 D614G 91 96 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Analysis of the abundance of antigen presence in each lung lobe of all animals again indicated a gradient of viral antigen abundance from D614G to B.1.1.7 and B.1.351. 2021 bioRxiv Result SARS_CoV_2 D614G 138 143 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Analysis of the histology scores assigned to each lung lobe of all animals indicated that lesions in D614G, B.1.1.7 and B.1.351-inoculated animals occurred on a gradient from more to less severe, respectively; these differences were statistically significantly more severe in D614G and B.1.1.7-inoculated animals than in B.1.351-inoculated animals. 2021 bioRxiv Result SARS_CoV_2 D614G;D614G 101;276 106;281 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Clinical scores were significantly lower in the animals inoculated with B.1.351 than B.1.1.7 and D614G on several days after inoculation. 2021 bioRxiv Result SARS_CoV_2 D614G 97 102 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Fewer nasal turbinate samples had detectable infectious virus in the group of B.1.351-inoculated animals than in those inoculated with D614G or B.1.1.7, but this difference was not statistically significant. 2021 bioRxiv Result SARS_CoV_2 D614G 135 140 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. In nasal samples, we observed a striking difference in the immune response in B.1.1.7-inoculated animals compared to those inoculated with D614G and B.1.351. 2021 bioRxiv Result SARS_CoV_2 D614G 139 144 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. No SNPs were detected in the D614G inoculum at an allelic fraction >0.1, and only one SNP was detected in the BAL sample of one animal; this was a synonymous mutation in nsp6 (Table S1). 2021 bioRxiv Result SARS_CoV_2 D614G 29 34 Nsp6 170 174 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Notably, this response was absent in B.1.351-inoculated animals as indicated by these samples clustering separately from D614G- and B.1.1.7-inoculated animals. 2021 bioRxiv Result SARS_CoV_2 D614G 121 126 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. On observation, lung lesions in animals inoculated with D614G were generally more severe than B.1.1.7 and B.1.351 while there were minimal differences between animals inoculated with B.1.1.7 and B.1.351. 2021 bioRxiv Result SARS_CoV_2 D614G 56 61 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. On observation, the animals inoculated with D614G generally had more viral antigen than those inoculated with B.1.1.7 or B.1.351. 2021 bioRxiv Result SARS_CoV_2 D614G 44 49 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Significantly lower virus titers were detected in the lungs of B.1.351-inoculated animals than in those inoculated with D614G. 2021 bioRxiv Result SARS_CoV_2 D614G 120 125 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. The B.1.1.7 inoculum contained 3 SNPs at >0.1 allelic fraction compared to the reference sequence; the D156G in nsp6 was detected in all animals, but at an allelic fraction <0.1 in 5 out of 6 animals. 2021 bioRxiv Result SARS_CoV_2 D156G 103 108 Nsp6 112 116 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. The B.1.351 inoculum contained 2 amino acid substitutions compared to the reference sequence; of these, the P252L substitution in nsp5 was maintained in 5 of 6 animals at slightly higher percentages than in the inoculum, whereas the L257F substitution in nsp6 was maintained at levels similar to the virus inoculum in all animals (Table S1). 2021 bioRxiv Result SARS_CoV_2 L257F;P252L 233;108 238;113 Nsp5;Nsp6 130;255 134;259 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. The B.1.351-inoculated animals had fewer days with a reduced appetite and only 3 out of 6 animals inoculated with B.1.351 showed respiratory signs of disease at any time after inoculation, compared to 5 out of 6 for D614G and 4 out of 6 for B.1.1.7. 2021 bioRxiv Result SARS_CoV_2 D614G 216 221 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. The L257F substitution in nsp6 was maintained in all animals, and the V11I substitution increased in frequency in 5 out of 6 animals (Table S1). 2021 bioRxiv Result SARS_CoV_2 L257F;V11I 4;70 9;74 Nsp6 26 30 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. The pathogenicity of two VOC isolates, B.1.1.7 and B.1.351, was compared to the pathogenicity of a recent clade B.1 isolate containing the D614G substitution in the spike protein. 2021 bioRxiv Result SARS_CoV_2 D614G 139 144 S 165 170 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. There was statistically significantly more antigen present in the lungs of D614G-inoculated animals than in those inoculated with B.1.351. 2021 bioRxiv Result SARS_CoV_2 D614G 75 80 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Three groups of six rhesus macaques were inoculated intranasally and intratracheally with a total dose of 2x106 TCID50 of one of the following SARS-CoV-2 isolates: SARS-CoV-2/human/USA/RML-7/2020, containing the D614G substitution in spike, hCOV_19/England/204820464/2020, a B.1.1.7 isolate, and hCoV-19/USA/MD-HP01542/2021, a B.1.351 isolate. 2021 bioRxiv Result SARS_CoV_2 D614G 212 217 S 234 239 34385423 Potent prophylactic and therapeutic efficacy of recombinant human ACE2-Fc against SARS-CoV-2 infection in vivo. Considering that multiple variations of SARS-CoV-2 are prevalent around the world, six emerging SARS-CoV-2 pp were generated bearing the D614G mutation, V367F mutation and the mutations present in B.1.1.7 (Alpha strain), B.1.351 (Beta strain), B.1.617.2 (Delta strain), and B.1.617.1 (Kappa strain). 2021 Cell discovery Result SARS_CoV_2 D614G;V367F 137;153 142;158 34385423 Potent prophylactic and therapeutic efficacy of recombinant human ACE2-Fc against SARS-CoV-2 infection in vivo. hACE2-Fc WT and hACE2-Fc mutant showed comparable neutralizing activity against SARS-CoV-2 mutants bearing D614G, and was similar to the neutralizing activity found using WT SARS-CoV-2 pp. 2021 Cell discovery Result SARS_CoV_2 D614G 107 112 34385423 Potent prophylactic and therapeutic efficacy of recombinant human ACE2-Fc against SARS-CoV-2 infection in vivo. Similar inhibitory activity using WT and mutant hACE2-Fc was detected against SARS-CoV-2 mutant bearing V367F. 2021 Cell discovery Result SARS_CoV_2 V367F 104 109 34385423 Potent prophylactic and therapeutic efficacy of recombinant human ACE2-Fc against SARS-CoV-2 infection in vivo. Spike protein with the D614G mutation was considered as a key mutation to increase virus transmission and infectivity, and the V367F mutant exhibited significantly increased affinity to hACE2, while VOCs may increase virulence and reduce sensitivity to some neutralizing antibodies and convalescent sera at different extent. 2021 Cell discovery Result SARS_CoV_2 D614G;V367F 23;127 28;132 S 0 5 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. A new 493GLN (E21)-34HIS (O) hydrogen bond was generated in both the N354D and V367F systems after excluding the hydrogen bond contained in the WT system. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N354D;V367F 69;79 74;84 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. According to the analysis of the results in Table 1, the binding energy of N354D and D364Y were reduced, and the entire PPI networks were destroyed. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y;N354D 85;75 90;80 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. All the coils in the non-RBM group became turn (Figure 5A), while the Q498A and WT systems showed a similar trend, they were converted from coil to turn in less than half of the simulation frames (Figure 5D). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 Q498A 70 75 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. All the mutant systems had fewer hydrogen bonds than had the WT system; in particular, the V367F system only produced 14 hydrogen bonds. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 V367F 91 96 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. Although mutations in the Q498A system resulted in the disappearance of all associated hydrogen bonds, the formation of new hydrogen bonds near position 498 kept the entire RBM region stable. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 Q498A 26 31 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. Although no hydrogen bond was formed at site 498 in the binding interface of both the V367F (Supplementary Figure S2B) and Q498A (Supplementary Figure S2C) systems, the hydrophobic interaction at this site was found to increase. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 Q498A;V367F 123;86 128;91 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. As a result, the electrostatic interaction was the main factor leading to the change in the binding free energy of the N354D and D364Y systems. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y;N354D 129;119 134;124 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. As the simulation progressed, the secondary structure of the D364Y system changed from beta-sheet to coil after 47 ns(Figure 4B). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y 61 66 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. At the same time, the mutation of the Q498A system caused the loss of glutamine hydrogen donor, which also led to the loss of hydrogen bonds. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 Q498A 38 43 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. Because the mutated alanine in the Q498A system is a hydrophobic amino acid, the original strong polar solvation energy of this site is weakened. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 Q498A 35 40 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. Compared with the WT system, both the non-RBM group and the Q498A system lacked six sets of hydrogen bonds [34HIS (HE2)-494SER (O), 487ASN (D21)-24GLN (O), 498GLN (E21)-38ASP (OD1), 500THR (HG1)-355ASP (OD1), 478THR (HG1)-24GLN (OE1), and 24GLN (E21)-487ASN (OD1)]. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 Q498A 60 65 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. Consistent with the result of our cell-cell fusion assay, recently, a study also found the enhanced affinity and infectivity of the V367F Spike mutant based on ELISA, SPR and the pseudovirus entry assay, implying the important role of V367F mutant in this epidemic strain. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 V367F;V367F 132;235 137;240 S 138 143 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. For the N354D system, the polarity of the mutation point did not change, but an uncharged amino acid changed to a charged amino acid. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N354D 8 13 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. For the V367F and Q498A systems, although the electrostatic interaction and polar solvation energy were reduced, the polar solvation energy decreased more dramatically and the binding free energy of these two systems (V367F and Q498A) was higher than that of the WT system. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 Q498A;Q498A;V367F;V367F 18;228;8;218 23;233;13;223 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. In addition, comparison with the WT system revealed that the secondary conformation of both the D364Y and Q498A systems did not change significantly in this region (Supplementary Figures S1A,B). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y;Q498A 96;106 101;111 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. In addition, the random coil (Asn134-Glu140) between alpha1 and alpha2 in the ACE2 domain of the D364Y system fluctuated greatly, and the RMSF value was 0.5 nm, compared to 0.4 nm for the WT system. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y 97 102 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. In contrast, the V367F system was almost entirely 3-helix during the whole simulation (Figure 4E), which indicated that the conformation of the random coil Pro384-Asp389 of the V367F system was very stable. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 V367F;V367F 17;177 22;182 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. In sharp contrast, the interface of ACE2 and RBD in the D364Y system has the same motion trend (Figure 7C), which makes the binding state between them very stable. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y 56 61 RBD 45 48 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. In the D364Y system, the hydrogen bond between Lys353 and the binding loop of Tyr505 was disrupted, significantly increasing the distance of their hydrophobic interaction (Supplementary Figure S2A). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y 7 12 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. In the RBM region of the Q498A system (Figure 7E), the movement trend of most residues is similar to that of the WT system, but the movement trend of residues near the alanine mutation point is chaotic, which may be related to the rearrangement of water molecules around the mutation point. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 Q498A 25 30 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. On the contrary, the binding energy of the Q498A mutation located in the RBM region was also reduced, but the PPI network was not destroyed. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 Q498A 43 48 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The binding free energy of the D364Y, V367F and Q498A was higher than that of the WT system, which was -298.563, -200.852, and -222.705 kJ/mol, respectively (Table 2). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y;Q498A;V367F 31;48;38 36;53;43 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The binding loop of the N354D system (Figure 6B) of the RBM group generates the most hydrogen bonds and hydrophobic interactions, which is related to the changes in the adjacent random coil (Ala475-Gly485). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N354D 24 29 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The contributions of the polar solvation energy of the WT, N354D, D364Y, V367F, and Q498A systems are 1,086.042, 861.460, 920.047, 871.004, and 795.021 kJ/mol, respectively. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y;N354D;Q498A;V367F 66;59;84;73 71;64;89;78 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The D364Y and Q498A systems lost the 353LYS (HZ1)-496GLY (O) hydrogen bond, but formed three new hydrogen bonds: 500THR (HG1)-355ASP (OD2), 353LYS (HZ1)-495TYR (O), and 83TYR (HH)-487ASN (ND2). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y;Q498A 4;14 9;19 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The electrostatic interaction of the D364Y system is 62 kJ/mol, which is higher than that of the WT system, whereas the electrostatic interaction of the N354D system is much smaller than that of the other four systems. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y;N354D 37;153 42;158 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The free energies of the binding loop in WT, N354D, D364Y, V367F and Q498A were of 8.30, 5.30, 13.51, 6.38, and 8.11 kJ/mol, respectively. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y;N354D;Q498A;V367F 52;45;69;59 57;50;74;64 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The movement trend of the RBM region in the V367F system deviated from some angles (Figure 7D), which may be related to the overall decrease of the polar solvation energy in the RBM region. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 V367F 44 49 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The mutation of charged Asp to uncharged Tyr in the D364Y system modified the electrostatic interaction at site 364 from 71.99 to 0.01 kJ/mol. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y 52 57 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The N354D system displayed the highest flexibility in this segment, whereas the V367F system, also from the non-RBM group, had the lowest flexibility. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N354D;V367F 4;80 9;85 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The polar solvation energy of all mutation systems were decreased, and the Q498A system changed the most, which may be related to the hydrophobicity of alanine. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 Q498A 75 80 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The polarity and electrification of the V367F system residue did not change, but the binding free energy was greater than that of the WT system. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 V367F 40 45 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The Q498A mutation also increased luciferase activity (RLU Ratio = 8.36 +- 0.61), but it was slightly lower than the V367F mutation. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 Q498A;V367F 4;117 9;122 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The random coil Pro384-Asp389 in the WT system is a mixture of 3-helix, bend, and turn (Figure 4C), but the 3-helix in the N354D system is almost entirely replaced by coil (Figure 4D). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N354D 123 128 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The RBM region (marked blue) in the N354D system has much less motion amplitude than has the WT system (Figures 7A,B), and the motion direction is disordered. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N354D 36 41 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The results showed that the binding free energy of the N354D system was -52.085 kJ/mol, lower than that of the WT system -85.611 kJ/mol. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N354D 55 60 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The RMSD value of Q498A in the RBM group was 0.23 nm, which was higher than for the other four systems (Figure 2D). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 Q498A 18 23 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The RMSD values of N354D, D364Y, and V367F in the non-RBM group all approximated 0.22 nm, which is slightly higher than the 0.19 nm value observed in the WT system (Figures 2A-C). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y;N354D;V367F 26;19;37 31;24;42 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The Spike protein mutants N354D, D364Y, and especially V367F, which has been detected at high density, were detected in the early breakout area. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y;N354D;V367F 33;26;55 38;31;60 S 4 9 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. Therefore, we speculate that D364Y not only changes the conformation of the RBD domain but also affects the binding state of the complex. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y 29 34 RBD 76 79 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. This indicates that the affinity between Spike protein and human ACE2 is enhanced after V367F mutation. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 V367F 88 93 S 41 46 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. This indicates that the N354D mutation increases the flexibility of this region and thus affects the spatial position of adjacent secondary structures. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N354D 24 29 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. This indicates that the stability of mutant systems is lower than that of the WT system and that the Q498A system located in the RBM region is the most unstable. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 Q498A 101 106 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. This result showed that compared with the WT (RLU Ratio = 4.27 +- 0.54), the V367F mutation enhanced luciferase activity (RLU Ratio = 8.97 +- 0.91). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 V367F 77 82 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. This should be the main reason for the significant reduction of electrostatic interaction in the N354D system. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N354D 97 102 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. We compared the fluctuations of random coils (Asn134-Glu140) in the ACE2 domain of the D364Y and WT systems. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D364Y 87 92 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. We conducted cytological experiments to confirm the functional outcomes of V367F mutation on the binding of Spike protein with ACE2. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 V367F 75 80 S 108 113 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. WT and Q498A mutant were used as controls (Figure 8). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 Q498A 7 12 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Although no significant frequency change has been observed for the N439K mutant, there has been a more than 70-fold increase in the presence of the S477N mutation, suggesting that selection may be playing a role in the propagation of this RBD mutant. 2021 Antibody therapeutics Result SARS_CoV_2 N439K;S477N 67;148 72;153 RBD 239 242 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Although seemingly contrasting, these data are complementary in suggesting a high C->U transition frequency when excluding the high number of G1430A mutations in this dataset, as it represents a potentially selected mutation. 2021 Antibody therapeutics Result SARS_CoV_2 G1430A 142 148 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Analysis of mutational frequency showed that approximately 75.2% of all nucleotide mutations were G1430A, 6.8% were C1317A, 0.9% were G1144T, and 42 additional mutants ranged between 0.1 and 0.9% frequency. 2021 Antibody therapeutics Result SARS_CoV_2 C1317A;G1144T;G1430A 116;134;98 122;140;104 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Approximately 69% of all SARS-CoV-2 sequences in Australia contained the S477N mutation in the RBD. 2021 Antibody therapeutics Result SARS_CoV_2 S477N 73 78 RBD 95 98 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. As expected, all S proteins carrying the S477N mutation also carried the D614G mutation providing evidence for this co-occurrence (Supplementary Table 4). 2021 Antibody therapeutics Result SARS_CoV_2 D614G;S477N 73;41 78;46 S 17 18 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. C1317A at 5% and G1558T at 0.9% lead to N439K and A520S mutations, respectively. 2021 Antibody therapeutics Result SARS_CoV_2 A520S;G1558T;N439K;C1317A 50;17;40;0 55;23;45;6 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Collectively, 13 mutations found in our GISAID analysis coded for an RBD that improved binding affinity to the ACE2 receptor, these included S477N, N439K, V367F, and N510Y among others (Table 2; Supplementary Table 1). 2021 Antibody therapeutics Result SARS_CoV_2 N439K;N510Y;S477N;V367F 148;166;141;155 153;171;146;160 RBD 69 72 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Here we report that these mutations now represent 6.7% (S477N) and 0.6% (N439K) of the total GISAID population. 2021 Antibody therapeutics Result SARS_CoV_2 N439K;S477N 73;56 78;61 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Importantly, at the time, mutations at residues S477N and N439K represented 0.09 and 0.4% of the total GISAID sequences (31 570 total sequences). 2021 Antibody therapeutics Result SARS_CoV_2 N439K;S477N 58;48 63;53 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. In both cases, all SARS-CoV-2 sequences containing either the S477N mutation or N439K mutation also contained the D614G mutation. 2021 Antibody therapeutics Result SARS_CoV_2 D614G;N439K;S477N 114;80;62 119;85;67 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Moreover, these data showed that the S477N and the N439K mutant RBDs had a higher affinity for the ACE2 receptor than their WT counterparts, with only S477N showing improved expression in yeast cells. 2021 Antibody therapeutics Result SARS_CoV_2 N439K;S477N;S477N 51;37;151 56;42;156 RBD 64 68 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Overall, the S477N mutation was present in 14 countries with N439K present in 10 (Supplementary Table 4). 2021 Antibody therapeutics Result SARS_CoV_2 N439K;S477N 61;13 66;18 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. The G1430A mutation led to the S477N mutant which represented 76.5% of all 9 121 amino acid mutations. 2021 Antibody therapeutics Result SARS_CoV_2 G1430A;S477N 4;31 10;36 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. The highest incidence of N439K mutants was found in England (4.1%) followed by Scotland, Ireland, and Wales. 2021 Antibody therapeutics Result SARS_CoV_2 N439K 25 30 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. The N439K/D614G double mutant was found in 10 countries with a high prevalence in England (Supplementary Table 5). 2021 Antibody therapeutics Result SARS_CoV_2 N439K;D614G 4;10 9;15 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. The potential negative impact of improved ACE2 binding during SARS-CoV-2 infection led us to analyze whether the high frequency S477N mutant co-occurred with the D614G spike mutation (a high frequency mutation producing more infectious SARS-CoV-2 particles). 2021 Antibody therapeutics Result SARS_CoV_2 D614G;S477N 162;128 167;133 S 168 173 COVID-19 62 82 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. The S477N/D614G double mutant was found in 14 countries with a high prevalence in Australia (Supplementary Table 4). 2021 Antibody therapeutics Result SARS_CoV_2 S477N;D614G 4;10 9;15 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. There was no incidence of a sequenced N439K/S477N double mutant. 2021 Antibody therapeutics Result SARS_CoV_2 N439K;S477N 38;44 43;49 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. To look at the association of D614G with S477N or N439K, we reanalyzed the dataset by increasing the length of our RBD nucleotide sequence to include the D614G codon (see Analyses overview). 2021 Antibody therapeutics Result SARS_CoV_2 D614G;D614G;N439K;S477N 30;154;50;41 35;159;55;46 RBD 115 118 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. After treatment of the cells with 300 mug/mL GB-2, the number of 293 T cells with low binding to the RBD with L452R mutation was significantly increased in both ACE2-positive cells and the top population in a dose-dependent manner. 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 L452R 110 115 RBD 101 104 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. After treatment of the cells with the indicated concentration of GB-2, the number of 293 T cells with low binding to RBD with a triple mutation (K417N-E484K-N501Y) was significantly increased in both ACE2-positive cells and the top population in a dose-dependent manner . 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 145;151;157 150;156;162 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. After treatment of the cells with the indicated concentration of GB-2, the number of 293 T cells with low binding to the RBD with a single mutation (N501Y or K417N) was significantly increased in both ACE2-positive cells and the top population in a dose-dependent manner . 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;N501Y 158;149 163;154 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Effect of GB-2 on the interaction between ACE2 and RBD of the spike protein with triple mutation (K417N-E484K-N501Y) 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 98;104;110 103;109;115 S;RBD 62;51 67;54 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Effect of GB-2 on the interaction between ACE2 and RBD of the spike protein with triple mutation (K417N-E484K-N501Y). 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 98;104;110 103;109;115 S;RBD 62;51 67;54 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Effect of GB-2 on the interaction between ACE2 and the RBD of the spike protein with a single mutation (K417N, E484K, N501Y, L452R) 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 E484K;L452R;N501Y;K417N 111;125;118;104 116;130;123;109 S;RBD 66;55 71;58 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Effect of GB-2 on the interaction between ACE2 and the RBD of the spike protein with a single mutation (K417N, E484K, N501Y, L452R). 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 E484K;L452R;N501Y;K417N 111;125;118;104 116;130;123;109 S;RBD 66;55 71;58 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. However, the number of 293 T cells with high binding to the RBD with a single mutation (E484K) was slightly increased in both ACE2-positive cells and the top population. 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 E484K 88 93 RBD 60 63 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. In our previous results, GB-2 could inhibit the binding between ACE2 and the RBD of the spike protein with a triple mutation (K417N-E484K-N501Y). 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 126;132;138 131;137;143 S;RBD 88;77 93;80 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Moreover, the K417N and E484K mutations dramatically enhanced cell-cell fusion and may be more transmissible than the N501Y mutation-containing SARS-CoV-2 variant. 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 E484K;K417N;N501Y 24;14;118 29;19;123 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. N501Y in the RBD was discovered in both alpha variant (B.1.1.7 lineage) and beta variant. 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 N501Y 0 5 RBD 13 16 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Next, through dual-color flow cytometric analysis, we investigated the effect of GB-2 on the binding between ACE2 and the RBD of the spike protein with the triple mutation (K417N-E484K-N501Y). 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 173;179;185 178;184;190 S;RBD 133;122 138;125 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Next, we also investigated the effect of 300 mug/mL GB-2 on the interaction between ACE2 and L452R mutation of the RBD through dual-color flow cytometric analysis. 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 L452R 93 98 RBD 115 118 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Previous study reported that triple mutations (N501Y, K417N, and E484K) in the RBD of beta variant may increase the infectivity and resistance to neutralization of monoclonal antibodies. 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 E484K;K417N;N501Y 65;54;47 70;59;52 RBD 79 82 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. The mutation of N501Y was discovered to increase the ACE2 binding and infectivity of SARS-CoV-2. 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 N501Y 16 21 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. The number of 293 T cells with high binding to the RBD with a single mutation (N501Y or K417N) was also decreased in both ACE2-positive cells and the top population in a dose-dependent manner. 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;N501Y 88;79 93;84 RBD 51 54 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. The number of 293 T cells with high binding to the RBD with a triple mutation (K417N-E484K-N501Y) was also decreased in ACE2-positive cells and the top population in a dose-dependent manner. 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 79;85;91 84;90;96 RBD 51 54 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. The number of 293 T cells with high binding to the RBD with L452R mutation was also decreased in both ACE2-positive cells and the top population in a dose-dependent manner. 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 L452R 60 65 RBD 51 54 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. The previous studies reported that L452R mutation could increase transmissibility, infectivity, and resist to antibody neutralization. 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 L452R 35 40 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. These results suggested that 200-300 mug/mL GB-2 inhibited the binding between ACE2 and RBD with a triple mutation (K417N-E484K-N501Y). 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 116;122;128 121;127;133 RBD 88 91 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. These results suggested that 200-300 mug/mL GB-2 inhibited the binding between ACE2 and the RBD with a single mutation (K417N or N501Y) except the E484K mutation. 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 E484K;N501Y;K417N 147;129;120 152;134;125 RBD 92 95 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. These results suggested that 300 mug/mL GB-2 could inhibit the interaction between ACE2 and the RBD with L452R mutation. 2021 Biomedicine & pharmacotherapy Result SARS_CoV_2 L452R 105 110 RBD 96 99 34389380 EGCG as an anti-SARS-CoV-2 agent: Preventive versus therapeutic potential against original and mutant virus. We considered two variants of the receptor binding domain: the consensus one (RBD) and its analog harboring the N501Y mutation in the ACE2-binding site (RBDm). 2021 Biochimie Result SARS_CoV_2 N501Y 112 117 RBD;RBD 34;78 57;81 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. Our preliminary results suggested that the S501Y assay is as sensitive as the ORF1ab assay and the S484K assay is slightly less sensitive than the ORF1ab assay in detecting viral RNA (data not shown). 2021 Chinese medical journal Result SARS_CoV_2 S484K;S501Y 99;43 104;48 ORF1ab;ORF1ab 78;147 84;153 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. Similar results were obtained using the S501Y and ORF1ab duplex rRT-PCR assays for detecting B and B.1.1.7 lineage viruses, respectively [Figure 3]. 2021 Chinese medical journal Result SARS_CoV_2 S501Y 40 45 ORF1ab 50 56 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. The S484K and ORF1ab duplex rRT-PCR assays were used to detect B (original strain [HCoV-19/Wuhan/IVDC-HB-04/2020]) and B.1.351 lineage viruses, respectively. 2021 Chinese medical journal Result SARS_CoV_2 S484K 4 9 ORF1ab 14 20 34403732 Identification of natural compounds as SARS-CoV-2 entry inhibitors by molecular docking-based virtual screening with bio-layer interferometry. Notably, the most effective compound EGCG is predicted to bind at P2, which does not harbour any of the mutations D614G, N439K, Y453F, N501Y. 2021 Pharmacological research Result SARS_CoV_2 D614G;N439K;N501Y;Y453F 114;121;135;128 119;126;140;133 34403732 Identification of natural compounds as SARS-CoV-2 entry inhibitors by molecular docking-based virtual screening with bio-layer interferometry. Of note, three mutations on the RBD (N439K, Y453F, N501Y) and one in the S1 region (D614G) of SARS-CoV-2 confers SARS-CoV-2 pseudovirus with greater infectivity on HEK293 cells . 2021 Pharmacological research Result SARS_CoV_2 N501Y;Y453F;D614G;N439K 51;44;84;37 56;49;89;42 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. However, a distinctive profile of synonymous and non-synonymous substitutions was found in the Spike protein of B.1.621, including T95I, Y144T, Y145S in the N-terminal domain in addition to substitutions R346K, E484K and N501Y in the RBD, P681H in the S1/S2 furin cleavage site (Table 1 ) and the insertion 146N in the N-terminal domain (NTD) (supplementary table 1). 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K;N501Y;P681H;R346K;T95I;Y144T;Y145S 211;221;239;204;131;137;144 216;226;244;209;135;142;149 S;RBD;N;N 95;234;157;319 100;237;158;320 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. The genetic background of the B.1.621 lineage includes some convergent amino acid changes in the RBD of the Spike protein which have appeared independently in several VOI and VOC: N501Y, present in B.1.1.7, B.1.351, and P.1 lineages; and E484K present in B.1.351 and P.1 (Harvey et al., 2021) as well as P681H in the S1/S2 furin cleavage site in B.1.1.7 and B.1.1.50 + P681H Variant. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K;N501Y;P681H;P681H 238;180;304;369 243;185;309;374 S;RBD 108;97 113;100 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. 4C demonstrated that the insertion in the NTD and H655Y mutation identified in high-passage-number WA1/2020 did not abrogate furin-mediated processing of S protein. 2021 Journal of virology Result SARS_CoV_2 H655Y 50 55 S 154 155 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. A second dominant mutation, H655Y, was in the CTD2 domain. 2021 Journal of virology Result SARS_CoV_2 H655Y 28 33 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Another mutation in the FCS (R685H) was detectable at early passages and likely inactivated the furin-mediated cleavage. 2021 Journal of virology Result SARS_CoV_2 R685H 29 34 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. CoV-2/GFP/ins P2 sample did not acquire additional mutations in NTD but had S686G mutation in the FSC in 4% of the genomes. 2021 Journal of virology Result SARS_CoV_2 S686G 76 81 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. However, additional contributions of other mutations in the NTD of the spike protein, such as S68R or N74K, which may additionally increase its affinity to HS, are also possible. 2021 Journal of virology Result SARS_CoV_2 N74K;S68R 102;94 106;98 S 71 76 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. However, it was eliminated by passage 7, suggesting that the latter mutation was less advantageous than S686G for viral spread. 2021 Journal of virology Result SARS_CoV_2 S686G 104 109 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. However, the possible benefit of S247R for viral infectivity and spread cannot be completely ruled out. 2021 Journal of virology Result SARS_CoV_2 S247R 33 38 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. However, the S686G mutation, which is located in the P1' position of the FCS, strongly affected the efficiency of cleavage, and most of the S protein in the released virions remained unprocessed. 2021 Journal of virology Result SARS_CoV_2 S686G 13 18 S 140 141 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. In addition, we have also detected an S247R substitution in all the samples of passaged WA1/2020. 2021 Journal of virology Result SARS_CoV_2 S247R 38 43 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. In addition, we have also sequenced genomes in the virions pooled from three independent electroporations of the in vitro-synthesized CoV-2/GFP RNAs and found that rescued viruses also contained mutations in FCS site (S686G at 59% and R683P at 30%). 2021 Journal of virology Result SARS_CoV_2 R683P;S686G 235;218 240;223 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Interestingly, the double-mutant CoV-2/GFP/ins/G, which contained both the insertion in the NTD and S686G mutation, was also eluted by 0.35 M NaCl. 2021 Journal of virology Result SARS_CoV_2 S686G 100 105 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. It was less abundant than the above insertion and H655Y mutation and present in a smaller fraction of viral genomes, and its frequency was not increasing. 2021 Journal of virology Result SARS_CoV_2 H655Y 50 55 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Next, we experimentally evaluated the effect of the S686G mutation on processing of the S protein in released viral particles. 2021 Journal of virology Result SARS_CoV_2 S686G 52 57 S 88 89 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. One of the variants encoded the above-described insertion in its NTD (CoV-2/GFP/ins), the second one had an S686G mutation downstream in P1' position of FCS (CoV-2/GFP/G), and the third mutant (CoV-2/GFP/ins/G) contained both modifications in the S protein. 2021 Journal of virology Result SARS_CoV_2 S686G 108 113 S 247 248 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Preliminary Sanger sequencing of the S gene in the high-passage-number viral pool identified a single nucleotide mutation resulting in S686G substitution, which was the first aa downstream of the FCS. 2021 Journal of virology Result SARS_CoV_2 S686G 135 140 S 37 38 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. The H655Y mutation was already abundant in P5 virus and thus could not directly increase viral infectivity, at least while being alone. 2021 Journal of virology Result SARS_CoV_2 H655Y 4 9 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. The recombinant virus with S686G substitution demonstrated intermediate sensitivity. 2021 Journal of virology Result SARS_CoV_2 S686G 27 32 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. The S686G mutation did not increase the positive charge of the S protein surface, but it likely transformed the unprocessed furin cleavage site into the heparin-binding site. 2021 Journal of virology Result SARS_CoV_2 S686G 4 9 S 63 64 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Therefore, it was difficult to make definitive conclusions about the effects of GLTSKRN insertion and S686G mutation on virions' affinity to heparin. 2021 Journal of virology Result SARS_CoV_2 S686G 102 107 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. This suggested that the S686G substitution had a stimulatory effect on viral spread in Vero cells. 2021 Journal of virology Result SARS_CoV_2 S686G 24 29 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Thus, both the insertion and S686G mutation increased affinities of the viruses to heparin Sepharose. 2021 Journal of virology Result SARS_CoV_2 S686G 29 34 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Two of them, S68R and N74K, increased the positive charge of the surface of this domain. 2021 Journal of virology Result SARS_CoV_2 N74K;S68R 22;13 26;17 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Variants containing the S686G mutation (the late-passage CoV-2/GFP, CoV-2/GFP/G, and CoV-2/GFP/ins/G) demonstrated less efficient processing of the S protein. 2021 Journal of virology Result SARS_CoV_2 S686G 24 29 S 148 149 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Variants having the S686G mutation exhibited one more interesting characteristic. 2021 Journal of virology Result SARS_CoV_2 S686G 20 25 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. We found that CoV-2/GFP/G has accumulated several low-frequency mutations in the NTD (N74K, 6%; S274R, 8%; and T259K, 6%). 2021 Journal of virology Result SARS_CoV_2 S274R;T259K;N74K 96;111;86 101;116;90 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. Although, K417N site does not combine with ACE2, it is an epitope of neutralizing antibody-like E484K, and so it may be selected to evade humoral immune reaction. 2021 Frontiers in public health Result SARS_CoV_2 E484K;K417N 96;10 101;15 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. B.1.351, P.1, and B.1.525 have mutation E484K. 2021 Frontiers in public health Result SARS_CoV_2 E484K 40 45 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. Cluster 5 (also known as "DeltaFVI-spike"): Some researchers found that mutation Y453F in the RBD of S protein of this variant did not reduce existing humoral immunity or affect the neutralization response, but it increased transmissibility due to its enhanced affinity with ACE2. 2021 Frontiers in public health Result SARS_CoV_2 Y453F 81 86 S;RBD;S 35;94;101 40;97;102 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. E484K is located in RBM and directly contacts specific ACE2 residues. 2021 Frontiers in public health Result SARS_CoV_2 E484K 0 5 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. In addition, Y453F is a high mutation frequency of 1,075, but its role is unclear. 2021 Frontiers in public health Result SARS_CoV_2 Y453F 13 18 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. It has 17 unique amino acid changes, 3 deletions, 4 synonymous mutations, and one 4nt insertion, including three mutations in the RBD of S protein: K417T, E484K, N501Y. 2021 Frontiers in public health Result SARS_CoV_2 E484K;K417T;N501Y 155;148;162 160;153;167 RBD;S 130;137 133;138 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. It shares mutation P681H with B.1.1.7, which may represent an independent homogeneity of the UK strain. 2021 Frontiers in public health Result SARS_CoV_2 P681H 19 24 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. L452R, located in RBM, may increase infectivity by enhancing the binding of S protein to ACE2 receptor and evading neutralizing antibodies and has evolved independently in multiple lineages. 2021 Frontiers in public health Result SARS_CoV_2 L452R 0 5 S 76 77 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. So N501Y, E484K, and K417N/T may have become the main genotypes for the spread of SARS-CoV-2 and may change the structure, properties, and other characteristics of S protein. 2021 Frontiers in public health Result SARS_CoV_2 E484K;K417N;K417T;N501Y 10;21;21;3 15;28;28;8 S 164 165 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. The frequencies of N501Y, E484K, K417N, and K417T are respectively, 65,636, 2,102, 1,208, and 107, high on the list. 2021 Frontiers in public health Result SARS_CoV_2 E484K;K417N;K417T;N501Y 26;33;44;19 31;38;49;24 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. The lineages B.1.1.7, B.1.351, P.1, and COH.20G all have mutation N501Y. 2021 Frontiers in public health Result SARS_CoV_2 N501Y 66 71 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. The mutation Q677H and N501Y in S protein have been proved to have higher affinity binding to ACE2. 2021 Frontiers in public health Result SARS_CoV_2 N501Y;Q677H 23;13 28;18 S 32 33 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. The mutations of S protein include S13I, W152C, and L452R. 2021 Frontiers in public health Result SARS_CoV_2 L452R;S13I;W152C 52;35;41 57;39;46 S 17 18 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. The mutations Q52R, E484K, Q677H, and F888 are in S protein. 2021 Frontiers in public health Result SARS_CoV_2 E484K;Q52R;Q677H 20;14;27 25;18;32 S 50 51 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. The physiological function of K417T is similar to K417N. 2021 Frontiers in public health Result SARS_CoV_2 K417N;K417T 50;30 55;35 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. There are three mutations, N501Y, K417N, and E484K, in the RBD of S protein. 2021 Frontiers in public health Result SARS_CoV_2 E484K;K417N;N501Y 45;34;27 50;39;32 RBD;S 59;66 62;67 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. There is evidence that mutation E484K may affect the neutralization of therapeutic antibodies. 2021 Frontiers in public health Result SARS_CoV_2 E484K 32 37 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. Third, mutation P681H is located near the insertion sites of four amino acids, connecting S1 and S2 subunits in S protein, in other words, adjacent to the furin cleavage site, which may cause S protein to be more easily cleaved by the protease, thereby, enhancing its affinity with the ACE2 receptor and promoting the virus to enter respiratory epithelial cells. 2021 Frontiers in public health Result SARS_CoV_2 P681H 16 21 S;S 112;192 113;193 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. Three mutations in S gene of these mutations have potential biological effects: First, mutation N501Y is located in the receptor-binding motif (RBM), one of the six key contact residues within the receptor-binding domain (RBD), and has been identified to enhance the affinity of the virus to ACE2. 2021 Frontiers in public health Result SARS_CoV_2 N501Y 96 101 RBD;S 222;19 225;20 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. Among these seven mutations, only four were found neutral (T148I, V880I, Q822H and D893Y) and rest were deleterious for the RdRp protein at -2.5 cut-off values of PROVEAN score (Table 2). 2021 Archives of microbiology Result SARS_CoV_2 D893Y;Q822H;V880I;T148I 83;73;66;59 88;78;71;64 RdRP 124 128 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. Our analysis also showed a point mutation at position 148 where threonine is substituted by isoleucine and is favored by helix formation. 2021 Archives of microbiology Result SARS_CoV_2 T148I 54 102 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. Out of 384 mutations only R118C, T148I, Y149C, E802A, Q822H, V880I and D893Y were used in this study (Table 1). 2021 Archives of microbiology Result SARS_CoV_2 D893Y;E802A;Q822H;R118C;T148I;V880I;Y149C 71;47;54;26;33;61;40 76;52;59;31;38;66;45 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. Point mutation was further observed at position 822 where glutamine is replaced by histidine. 2021 Archives of microbiology Result SARS_CoV_2 Q822H 48 92 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. Similarly, in D893Y mutant there is a loss of turn structure at 893 position. 2021 Archives of microbiology Result SARS_CoV_2 D893Y 14 19 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. The detailed analysis further explained substitution of glutamic acid by alanine at position 802 of the RdRp protein. 2021 Archives of microbiology Result SARS_CoV_2 E802A 56 96 RdRP 104 108 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. The free energy change was recorded highest in E802A (1.725 kcal/mol) followed by T148I, Y149C and V880I as shown in Table 4. 2021 Archives of microbiology Result SARS_CoV_2 E802A;T148I;V880I;Y149C 47;82;99;89 52;87;104;94 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. The most rigid structure was that of Q822H (- 5.021 kcal/mol/K) mutant, followed by D893Y, R118C and V880I, however, the mutant Y149C (- 3.621 kcal/mol/K) showed less rigidity and this mutant protein had nearly flexible structure as indicated in the. 2021 Archives of microbiology Result SARS_CoV_2 D893Y;Q822H;R118C;V880I;Y149C 84;37;91;101;128 89;42;96;106;133 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. The visual representation of the flexibility analysis by Dynamut showed all RdRp mutants exhibiting a rigid structure except for Y149C mutant which gained flexibility upon mutation (shown as red region in. 2021 Archives of microbiology Result SARS_CoV_2 Y149C 129 134 RdRP 76 80 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. Two mutations, Y149C and V880I in this study did not show any changes in the secondary structure however, rest of the five mutations showed significant changes. 2021 Archives of microbiology Result SARS_CoV_2 V880I;Y149C 25;15 30;20 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. All the N439K are included in the D614G interestingly, which is mainly concentrated in Europe since March 2020. 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 D614G;N439K 34;8 39;13 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. Although the flexibility patterns of residues in the N439K-mutated RBD-hACE2 complex display similar fluctuations with wild-type complex (Figure 2C), certain regions of the two complexes show differences in flexibility. 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K 53 58 RBD 67 70 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. And more notably, N439K is the highest frequency of variant in the RBD region, which accounts for 0.72% of all SARS-CoV-2. 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K 18 23 RBD 67 70 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. From results of RMSD, the wild and mutant systems had reached a stable state from their respective MD trajectories, CB6 systems had lower average RMSD values than the REGN10987 complexes, and a higher RMSD was calculated in N439K-REGN10987 than wild-type (Figure 4D). 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K 224 229 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. Furthermore, there are only 16 mutations on S protein with a mutation rate of more than 0.16% (Supplementary Table 1), and those mutants occur frequently together with the variant D614G (Figure 1D). 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 D614G 180 185 S 44 45 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. It revealed that the estimated binding free energy of wild-type CB6-RBD complexes (-129.73 kj/mol) is higher than N439K-mutated CB6-RBD complexes (-51.28 kj/mol) in the heavy chain, the unfavorable contribution from DeltaGpol (491.56 kj/mol) was relatively lower compared to mutant type (703.82 kj/mol) (Table 2). 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K 114 119 RBD;RBD 68;132 71;135 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. It was observed that the N439K-mutated RBD-hACE2 complex (9.68 +- 3.24) can form more hydrogen bonds than the wild-type (7.26 +- 2.59) during the MD trajectory (P = 2.43 x 10-138) (Figure 2D and Supplementary Table 4). 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K 25 30 RBD 39 42 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. N439K Became Resistant to SARS-CoV-2 Neutralizing Antibody REGN10987. 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K 0 5 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. Overall, our research suggested that the N439K reduced the sensitivity to the CB6 mAb. 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K 41 46 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. Subsequently, we have investigated the binding free energy of REGN10987-RBD complexes, the DeltaGbind of N439K-mutated REGN10987-RBD complexes (24.10 kj/mol) was found to be lower (P = 2.22e-16) than wild-type (-85.65 kj/mol) in the heavy chain (Figure 4F and Table 2). 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K 105 110 RBD;RBD 72;129 75;132 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. Taken together, comparing the interaction interfaces of the N439K-mutated and wild RBD-hACE2 complexes reveals the change from ASN439 to LYS439 might result in a tighter association because of the new salt bridge formation and higher affinity. 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K;N439K 127;60 143;65 RBD 83 86 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. The binding energy DeltaGbind (-1526.17 +- 133.13 kj/mol) of the N439K-hACE2 was higher in magnitude as compared to the wild-type RBD-hACE2 (-1084.06 +- 80.23kj/mol) (Figure 3A), in which the electrostatic energy between wild and mutant types had a significant difference, which the average DeltaEelec (-1876.25 +- 45.23 kj/mol) of the N439K-hACE2 also higher than that of wild-type (-1301 +- 23.14 kj/mol) (Figure 2B). 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K;N439K 65;336 70;341 RBD 130 133 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. The mutation of N439K in the RBD formed a new salt bridge with Glu329 of hACE2 (3.6 A), and a weak salt bridge between Lys439 and Asp442 of SARS-CoV-2 RBD (Figure 2D). 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K 16 21 RBD;RBD 29;151 32;154 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. The N439K-Mutated RBD Binds hACE2 With Higher Affinity Than Wild Type. 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K 4 9 RBD 18 21 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. The PROCHECK analysis show both wild-type and N439K S protein model are in good quality, the detail information can be found in Supplementary File 2. 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K 46 51 S 52 53 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. The total binding free energy change between wild-type and RBD-hACE2 (N439K) complexes is 462.88 kj/mol (Figure 3C), mostly concentrated in the electrostatic energy (Figure 3B). 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K 70 75 RBD 59 62 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. The variant D614G accounts for 75.92% of 64039 SARS-CoV-2, following by D936Y accounts for 1.11%. 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 D614G;D936Y 12;72 17;77 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. To conclude, the amino acid changes seem to have been accumulated progressively over time, among which N439K is the most dominant variant in the RBD region and should be preferentially employed to characterize the influence of mutations on pathogen evolution. 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K 103 108 RBD 145 148 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. To further verify the convergence of MD simulations equilibrium, we estimated the root mean square deviations (RMSD) of backbone atoms relative to the corresponding crystal structure, and the wild complex had a relatively smaller average RMSD than the N439K-mutated complex (2.2 vs. 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K 252 257 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. To investigate the antigenicity of the N439K mutant, we exploited 100 ns MD simulations of the binary complexes of hACE2 with neutralizing monoclonal antibodies REGN10987 and CB6 complexes. 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K 39 44 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. To test the reliability of our simulation, we increase the MD simulation time to 200 ns, the binding energy of 200 ns MD simulation show a similar result, the DeltaGbind (-1597.25 +- 179.57 kj/mol) of the N439K-hACE2 also higher than that of wild-type (-959.29 +- 130.36 kj/mol) (Supplementary Table 5). 2021 Frontiers in cell and developmental biology Result SARS_CoV_2 N439K 205 210 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. AFM showed a higher binding probability and binding strength for the two variants containing N501Y. 2021 eLife Result SARS_CoV_2 N501Y 93 98 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Because previous ensemble measurements showed that the N501Y mutation contributes most to the higher binding affinity of the RBD, we mainly focus on RBDN501Y, RBDTriple, and wild-type RBD for AFM-SMFS studies and comparisons. 2021 eLife Result SARS_CoV_2 N501Y 55 60 RBD;RBD;RBD 125;149;184 128;152;187 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Consequently, the SMD simulations further demonstrate that the RBDN501Y-ACE2 and RBDTriple-ACE2 complexes have a higher unbinding force than wild-type RBD-ACE2 complexes, and that the additional pi-pi and cation-pi interactions that result from the N501Y mutation may provide the molecular mechanism that underlies this result. 2021 eLife Result SARS_CoV_2 N501Y 249 254 RBD;RBD 63;151 66;154 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. N501Y mutation slowed the dissociation of the RBD from the ACE2 receptor. 2021 eLife Result SARS_CoV_2 N501Y 0 5 RBD 46 49 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. SMD simulations revealed a higher unbinding force for the complexes due to additional pi-pi and cation-pi interactions resulting from the N501Y mutation. 2021 eLife Result SARS_CoV_2 N501Y 138 143 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. The mutation resulted in a slightly weaker or similar affinity to cell-surface ACE2, whereas the N501Y, K417N, E484K triple mutation resulted in an affinity similar to that of the wild type RBD. 2021 eLife Result SARS_CoV_2 E484K;K417N;N501Y 111;104;97 116;109;102 RBD 190 193 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. The N501Y mutation from the B.1.1.7 variant showed a fourfold greater affinity than wild-type RBD for the cell surface. 2021 eLife Result SARS_CoV_2 N501Y 4 9 RBD 94 97 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. These results demonstrated that N501Y is the key residue change that increases binding affinity. 2021 eLife Result SARS_CoV_2 N501Y 32 37 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. This result again emphasized the role of N501Y, rather than the other two mutations, in increasing binding affinity by slowing the rate of dissociation from the ACE2 receptor. 2021 eLife Result SARS_CoV_2 N501Y 41 46 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Two other amino acid mutations (K417N and E484K) had less impact on ACE2 binding, as verified by two single-point mutants (Figure 2:figure supplement 1). 2021 eLife Result SARS_CoV_2 E484K;K417N 42;32 47;37 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. Among 13 HIV-negative vaccinees with neutralisation activity against Asp614Gly wild-type, only two participants retained activity against the beta variant. 2021 The lancet. HIV Result SARS_CoV_2 D614G 69 78 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. By contrast, among 20 people with HIV with neutralisation activity against Asp614Gly wild-type, ten vaccinees retained activity against the beta variant, eight of whom were seropositive for SARS-CoV-2 at baseline (appendix p 36). 2021 The lancet. HIV Result SARS_CoV_2 D614G 75 84 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. In the 26 HIV-negative participants vaccinated with ChAdOx1 nCoV-19 who were assessed for neutralisation activity against Asp614Gly wild-type, the GMT of SARS-CoV-2 neutralising antibodies strongly correlated with Asp614Gly wild-type antigen-specific IgG GMCs on days 28 and 42. 2021 The lancet. HIV Result SARS_CoV_2 D614G;D614G 122;214 131;223 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. Using an MLV-based neutralisation assay, we also assessed neutralising antibody activity against Asp614Gly wild-type in all samples from people with HIV who were RBD seropositive at day 42. 2021 The lancet. HIV Result SARS_CoV_2 D614G 97 106 RBD 162 165 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. When assessing cross-reactivity of binding antibodies to the FLS from the beta variant, vaccinated people with HIV and HIV-negative participants showed strong correlations in their ability to bind FLS from Asp614Gly wild-type and the beta variant, regardless of baseline SARS-CoV-2 serostatus (figure 4). 2021 The lancet. HIV Result SARS_CoV_2 D614G 206 215 34417165 Effectiveness of BNT162b2 and mRNA-1273 covid-19 vaccines against symptomatic SARS-CoV-2 infection and severe covid-19 outcomes in Ontario, Canada: test negative design study. Vaccine effectiveness estimates observed >=7 days after two doses were, however, high (all >=88%) and comparable across all subgroups, including against variants with the E484K mutation. 2021 BMJ (Clinical research ed.) Result SARS_CoV_2 E484K 171 176 34417349 SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. All plasmas were collected between March and May 2020 where only the original Wuhan virus and D614G variants were circulating. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 94 99 34417349 SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. Four plasma samples did not show neutralization activity against the SARS-CoV-2 WT and SARS-CoV-2 D614G variant. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 98 103 34417349 SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. In contrast, the single mutation in the RBD (E484K) swaps the charge of the sidechain, which would significantly alter the electrostatic complementarity of antibody binding to this region. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 E484K 45 50 RBD 40 43 34417349 SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. Neutralization activity tested against the SARS-CoV-2 WT and D614G variant also showed variable titers. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 61 66 34417349 SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. Sequence analyses revealed a deletion of the phenylalanine in position 140 (F140) on the S-protein NTD N3 loop in 36% of the virions. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 del 140F 29 74 S 89 90 34417349 SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. The E484K substitution was rapidly followed by a third and final change comprising an 11-amino acid insertion between Y248 and L249 in the NTD N5 loop (248aKTRNKSTSRRE248k). 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 E484K 4 9 34417349 SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. These antibodies also showed a variable neutralization potency against the SARS-CoV-2 WT and D614G viruses ranging from 3.9 ng/mL to 500.0 ng/mL. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 93 98 34417349 SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. This time, the glutamic acid in position 484 of the RBD was substituted with a lysine (E484K). 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 E484K 87 92 RBD 52 55 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. By contrast, only 6/8 NHP that received a single dose of 30 mug had detectable neutralizing responses against D614G at that same timepoint, and none (0/8) had detectable neutralizing antibodies against B.1.351 (Extended Data Figs. 2021 Nature immunology Result SARS_CoV_2 D614G 110 115 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. Consistent with a prior study, there was a ~100-fold increase in D614G-specific lentiviral pseudovirus neutralizing antibodies following a boost with 30 or 100 mug of mRNA-1273 (Extended Data. 2021 Nature immunology Result SARS_CoV_2 D614G 65 70 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. Last, there was an average 3-fold reduction in GMT (EC-50) in serum neutralizing activity against B.1.617.2 compared to D614G in animals that received two doses of 30 or 100 mug of mRNA-1273 and undetectable responses in the 30 mug single dose group. 2021 Nature immunology Result SARS_CoV_2 D614G 120 125 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. Neutralizing titers against B.1.351 were compared to D614G, the benchmark strain. 2021 Nature immunology Result SARS_CoV_2 D614G 53 58 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. Notably, in NHP that received a single 30 mug dose of mRNA, the reciprocal ID50 GMT against D614G was ~130, but there were no detectable neutralizing antibodies against B.1.351. 2021 Nature immunology Result SARS_CoV_2 D614G 92 97 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. To extend the analysis, there was little change in neutralization in any vaccine group comparing D614G to B.1.1.7. 2021 Nature immunology Result SARS_CoV_2 D614G 97 102 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. Using a D614G lentiviral-based pseudovirus neutralization assay, the reciprocal ID50 geometric mean titer (GMT) was ~3,600 following two doses of 100 mug. 2021 Nature immunology Result SARS_CoV_2 D614G 8 13 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. We observed similar outcomes comparing D614G to B.1.351 using VSV-based pseudovirus. 2021 Nature immunology Result SARS_CoV_2 D614G 39 44 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. Of all 60 types of mutants, the number of E484K was the largest with 86 585 sequences, followed by S477N with 55 442 sequences (Table 2). 2021 Infectious diseases of poverty Result SARS_CoV_2 E484K;S477N 42;99 47;104 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. The N354D mutant and wild-type counterpart showed a similar sensitivity to neutralizing antibody, while the V367F mutant was more sensitive to neutralizing antibody than wild-type counterpart (P < 0.001). 2021 Infectious diseases of poverty Result SARS_CoV_2 N354D;V367F 4;108 9;113 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. The V367F mutant (5.132 x 106 RLU) and the N354D mutant (5.408 x 106 RLU) were more highly infectious than the wild-type counterpart (2.243 x 106 RLU). 2021 Infectious diseases of poverty Result SARS_CoV_2 N354D;V367F 43;4 48;9 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. Up to 30 May, 2021, E484K strains in Brazil and S477N in Australia accounted for more than 50%, while S477N strains accounted for more than 10% in Switzerland, France, and Luxembourg. 2021 Infectious diseases of poverty Result SARS_CoV_2 E484K;S477N;S477N 20;48;102 25;53;107 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. We infected HEK293T cells with SARS-CoV-2 pseudoviruses (wild-type, V367F mutant, and N354D mutant), and then tested the infectivity and immune reactivity. 2021 Infectious diseases of poverty Result SARS_CoV_2 N354D;V367F 86;68 91;73 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. As controls, we have randomly tested 99 anti-N IgG positive serum specimens from patients infected with non-N501Y viruses, that were collected between 9 and 14 days after symptom onset. 2021 EBioMedicine Result SARS_CoV_2 N501Y 108 113 N 45 46 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Comparison of anti-RBD IgG against wild type, N501Y, and N501Y-E484K RBD. 2021 EBioMedicine Result SARS_CoV_2 N501Y;N501Y;E484K 46;57;63 51;62;68 RBD;RBD 19;69 22;72 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. For the 6 viruses, 3 were isolated from patients returning from England, including 2 viruses in the B.1.1.7 lineage and 1 virus in the B.1.160 lineage (a non-N501Y lineage); 3 other viruses were isolated from patients who acquired the infection in Hong Kong, including 2 viruses in the B.1.1.63 lineage collected in July 2020, and 1 virus in the B.1.36.27 lineage collected in December 2020. 2021 EBioMedicine Result SARS_CoV_2 N501Y 158 163 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Furthermore, the normalized OD values for N501Y-E484K-K417N RBD was significantly lower than that of N501Y RBD (mean difference, 0.4497; SE of difference, 0.02648). 2021 EBioMedicine Result SARS_CoV_2 N501Y;N501Y;E484K;K417N 42;101;48;54 47;106;53;59 RBD;RBD 60;107 63;110 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. However, for B117-2 virus, there was a statistically significant decrease in MN titer when compared with all non-N501Y lineages. 2021 EBioMedicine Result SARS_CoV_2 N501Y 113 118 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Identification of patients with N501Y variants at RBD. 2021 EBioMedicine Result SARS_CoV_2 N501Y 32 37 RBD 50 53 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. In the GISAID database (as of 25th May 2021), nsp13 K460R was present in 23.7% (156257 of 658890) of sequences within the B.1.1.7 lineage (Supplementary Table S3), while spike A1056V and nsp2 S512Y mutation was present in 0.0127% (84/660147) and 0.0006% (4/657159) of sequences, respectively. 2021 EBioMedicine Result SARS_CoV_2 A1056V;K460R;S512Y 176;52;192 182;57;197 S;Nsp13;Nsp2 170;46;187 175;51;191 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Performance of commercially-available antibody assays for patients infected with N501Y variants. 2021 EBioMedicine Result SARS_CoV_2 N501Y 81 86 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. The MN titer of B117-1 (geometric mean titer [GMT], 80; 95% confidence interval [CI], 47-136) were similar to those of non-N501Y viruses, while the MN titer of B117-2 (GMT, 20; 95% CI, 11-36) was statistically significantly reduced when compared with non-N501Y viruses (P < 0.01; repeated measures one-way ANOVA with Dunnett's multiple comparisons test). 2021 EBioMedicine Result SARS_CoV_2 N501Y;N501Y 123;255 128;260 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. The normalized OD values for N501Y RBD (mean difference from wild type RBD, 0.1116; standard error [SE] of difference, 0.01405) and N501Y-E484K-K417N RBD (mean difference from wild type RBD, 0.5613, SE of difference, 0.02773) were statistically significantly lower than those from wild type RBD (P < 0.0001, repeated measures one-way ANOVA with Tukey's multiple comparisons test). 2021 EBioMedicine Result SARS_CoV_2 N501Y;N501Y;E484K;K417N 29;132;138;144 34;137;143;149 RBD;RBD;RBD;RBD;RBD 35;71;150;186;291 38;74;153;189;294 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. There was no statistically significant difference in MN titer between B117-1 virus and viruses in non-N501Y lineages. 2021 EBioMedicine Result SARS_CoV_2 N501Y 102 107 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. To eliminate the effect from other mutations, we compared the levels of anti-RBD antibodies using recombinant RBD with or without N501Y mutation for 272 recovered COVID-19 patients' sera. 2021 EBioMedicine Result SARS_CoV_2 N501Y 130 135 RBD;RBD 77;110 80;113 COVID-19 163 171 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. We assessed the anti-N and anti-spike S1 subunit (containing the RBD) for 7 patients infected with N501Y variant, including 5 patients with B.1.1.7 lineage and 2 patients with B.1.351 lineage. 2021 EBioMedicine Result SARS_CoV_2 N501Y 99 104 S;RBD;N 32;65;21 37;68;22 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. We have also tested a human anti-RBD monoclonal IgG, but there was no significant difference in the OD between the wild type, N501Y and N501Y-E484K-K417N RBD. 2021 EBioMedicine Result SARS_CoV_2 N501Y;N501Y;E484K;K417N 126;136;142;148 131;141;147;153 RBD;RBD 33;154 36;157 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. We have identified 14 patients infected with B.1.1.7 lineage with N501Y alone, 4 patients infected with B.1.351 lineage with N501Y, E484K and K417N, and 1 patient infected with P.3 lineage with N501Y and E484K. 2021 EBioMedicine Result SARS_CoV_2 E484K;E484K;K417N;N501Y;N501Y;N501Y 132;204;142;66;125;194 137;209;147;71;130;199 34423327 Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing. Interestingly, the majority of the B.1.1.7 variant that appeared in January in Nice had an additional A522S (G23126T) mutation in the spike protein. 2021 The Lancet regional health. Europe Result SARS_CoV_2 A522S;G23126T 102;109 107;116 S 134 139 34423327 Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing. The decline of the A522S mutation in March also suggests that this additional spike mutation does not provide improved fitness when compared to the original B.1.1.7 lineage. 2021 The Lancet regional health. Europe Result SARS_CoV_2 A522S 19 24 S 78 83 34423327 Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing. This A522S spike protein mutation had been reported in only 226 out of 27,268 (0.8%) and 207 out of 385,840 (0.05%) GISAID submitted B.1.1.7 sequences for France and the UK, respectively. 2021 The Lancet regional health. Europe Result SARS_CoV_2 A522S 5 10 S 11 16 34423327 Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing. This is in line with a recent SARS-CoV-2 / ACE2 interaction modelling study that only found a slight increase of SARS-CoV-2 receptor affinity for the A522S mutation. 2021 The Lancet regional health. Europe Result SARS_CoV_2 A522S 150 155 34423327 Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing. This variant then became gradually diluted by B.1.1.7 lacking the A522S mutation which is predominant in France. 2021 The Lancet regional health. Europe Result SARS_CoV_2 A522S 66 71 34423763 Severe Acute Respiratory Syndrome Coronavirus 2 in Farmed Mink (Neovison vison), Poland. The G75V mutation is present in 199 isolates published in GISAID (https://www.gisaid.org), and the C1257F mutation in 83 isolates. 2021 Emerging infectious diseases Result SARS_CoV_2 C1257F;G75V 99;4 105;8 34423763 Severe Acute Respiratory Syndrome Coronavirus 2 in Farmed Mink (Neovison vison), Poland. Two specific mutations present in all samples were found in the spike protein: G75V and C1247F. 2021 Emerging infectious diseases Result SARS_CoV_2 C1247F;G75V 88;79 94;83 S 64 69 34424256 Emergence of the First Strains of SARS-CoV-2 Lineage B.1.1.7 in Romania: Genomic Analysis. Another noteworthy mutation is N844S within nonstructural protein 3 (Nsp3) present in the Suceava sample, which is recorded in only 8 other samples sequenced so far, most of them also from England. 2021 JMIRx med Result SARS_CoV_2 N844S 31 36 Nsp3 69 73 34424256 Emergence of the First Strains of SARS-CoV-2 Lineage B.1.1.7 in Romania: Genomic Analysis. Furthermore, the P681H mutation of the S protein might influence the cleavage of the S protein due to its proximity to the S1/S2 furin cleavage site. 2021 JMIRx med Result SARS_CoV_2 P681H 17 22 S;S 39;85 40;86 34424256 Emergence of the First Strains of SARS-CoV-2 Lineage B.1.1.7 in Romania: Genomic Analysis. Namely, the N50Y mutation of the S gene significantly increases its interaction force and number of interactions with the human receptor ACE2. 2021 JMIRx med Result SARS_CoV_2 N50Y 12 16 S 33 34 34424256 Emergence of the First Strains of SARS-CoV-2 Lineage B.1.1.7 in Romania: Genomic Analysis. The Prahova sample is again distinct from others in Romania through the appearance of L15F in ORF3a, a mutation recorded in 5 samples from Nagasaki, Japan, sampled in April 2020, among 243 samples collected worldwide, mostly from the United Kingdom. 2021 JMIRx med Result SARS_CoV_2 L15F 86 90 ORF3a 94 99 34424256 Emergence of the First Strains of SARS-CoV-2 Lineage B.1.1.7 in Romania: Genomic Analysis. The sample from Prahova also has a mutation in Nsp3 (D455N), which has been recorded in only one other sample, collected in Japan in April 2020, belonging to clade B1.1. 2021 JMIRx med Result SARS_CoV_2 D455N 53 58 Nsp3 47 51 34424256 Emergence of the First Strains of SARS-CoV-2 Lineage B.1.1.7 in Romania: Genomic Analysis. This idea is supported by the fact that, although the first sequenced samples carrying the new strain originated in Kent and Greater London, on September 20 and 21, 2020, respectively, the hallmark N501Y mutation first appeared in Italy in August 2020. 2021 JMIRx med Result SARS_CoV_2 N501Y 198 203 34428371 Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation. In addition, the N501Y mutation promotes the binding of some RBD AAs, such as T500, Y489, F486, and L475, but it interrupts the binding of others, such as Q498, Y495, and Y449. 2021 Journal of chemical information and modeling Result SARS_CoV_2 N501Y 17 22 RBD 61 64 34428371 Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation. The K417N mutation in Beta reduces the binding due to loss of the salt-bridge between K417 (SARS2) and D30 of ACE2, while the E484K mutation (i.e., Group C) provides a slight increase in the binding via forming an ion pair with E75 of ACE2. 2021 Journal of chemical information and modeling Result SARS_CoV_2 E484K;K417N 126;4 131;9 34428371 Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation. The N501Y facilitates Y505 to create three pairings with A386, A387, and E393 in Alpha that were not seen in SARS2. 2021 Journal of chemical information and modeling Result SARS_CoV_2 N501Y 4 9 34428371 Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation. The pair Y505:E37 in SARS2 has a strong binding, which is disrupted due to N501Y mutation in Alpha. 2021 Journal of chemical information and modeling Result SARS_CoV_2 N501Y 75 80 34428371 Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation. These implications caused by the N501Y mutation are also present in the Beta model. 2021 Journal of chemical information and modeling Result SARS_CoV_2 N501Y 33 38 34428371 Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation. These observations of N501Y are also true when comparing the Beta vs SARS2 model (Figure 2C). 2021 Journal of chemical information and modeling Result SARS_CoV_2 N501Y 22 27 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. Antibody binding of hCoV-2IG batches to RBD and RBD mutants: K417N, N501Y, and E484K. 2021 iScience Result SARS_CoV_2 E484K;K417N;N501Y 79;61;68 84;66;73 RBD;RBD 40;48 43;51 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. E484K is shared between the JP and SA variants, and K417 is mutated to T in the JP variant, and to N in the SA variant. 2021 iScience Result SARS_CoV_2 E484K 0 5 N 99 100 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. However, binding to RBD-E484K resulted in an average 19-fold reduction in hCoV-2IG binding compared with the WA-1 RBD (Figure 3B). 2021 iScience Result SARS_CoV_2 E484K 24 29 RBD;RBD 20;114 23;117 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. N501Y is shared among the UK, JP, and SA variants. 2021 iScience Result SARS_CoV_2 N501Y 0 5 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. The hCoV-2IG binding to RBD-N501Y was reduced by ~2-fold compared with WA-1 RBD. 2021 iScience Result SARS_CoV_2 N501Y 28 33 RBD;RBD 24;76 27;79 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. The K417N had minimal to no impact on hCoV-2IG binding. 2021 iScience Result SARS_CoV_2 K417N 4 9 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. To further explore the possible contribution of the key mutations in binding of hCoV-2IG batches, purified RBD proteins with individual mutations (K417N, N501Y, and E484K) were analyzed in SPR based antibody binding assays (Figure 3A). 2021 iScience Result SARS_CoV_2 E484K;N501Y;K417N 165;154;147 170;159;152 RBD 107 110 34431691 Emergence of Multiple SARS-CoV-2 Antibody Escape Variants in an Immunocompromised Host Undergoing Convalescent Plasma Treatment. However, the third tracheal aspirate sample collected 1 week later (day 27) was predominated by the haplotype ORF1a:A138T, S:141-144LGVY deletion, and S:E484K (>95% mutation frequency). 2021 mSphere Result SARS_CoV_2 A138T;E484K 116;153 121;158 ORF1a;S;S 110;123;151 115;124;152 34431691 Emergence of Multiple SARS-CoV-2 Antibody Escape Variants in an Immunocompromised Host Undergoing Convalescent Plasma Treatment. If this was due to superinfection, the patient would have had to acquire three different viral genotypes, i.e., S:Q493R and 243-244LA, ORF1a:A138T, S:141-144del, and E484K, and ORF1a:A138T, S:141-144del, and S:E493K, circulating in the ICU at the same time. 2021 mSphere Result SARS_CoV_2 E484K;A138T;A138T;E493K;Q493R 166;141;183;210;114 171;146;188;215;119 ORF1a;ORF1a;S;S;S;S 135;177;112;148;190;208 140;182;113;149;191;209 34431691 Emergence of Multiple SARS-CoV-2 Antibody Escape Variants in an Immunocompromised Host Undergoing Convalescent Plasma Treatment. In particular, the E484K mutation has been linked to the rapid spread of B.1.351 and B.1.1.28 variants in South Africa and Brazil, respectively. 2021 mSphere Result SARS_CoV_2 E484K 19 24 34431691 Emergence of Multiple SARS-CoV-2 Antibody Escape Variants in an Immunocompromised Host Undergoing Convalescent Plasma Treatment. Intriguingly, the cooccurrence of 141-144LGVY and E484K in the third tracheal aspirate specimen completely replaced other mutants, suggesting this haplotype may have compensated for a fitness cost or have a higher antibody resistance level. 2021 mSphere Result SARS_CoV_2 E484K 50 55 34431691 Emergence of Multiple SARS-CoV-2 Antibody Escape Variants in an Immunocompromised Host Undergoing Convalescent Plasma Treatment. The day 3 sample, which likely reflects the antibody titers from the convalescent plasma donor, demonstrated robust neutralization titers against all pseudoviruses, with the highest titers against Wuhan-Hu-1 with D614G PVs (>1:3,000) and medium levels against the B.1.1.7 (UK variant) and the B.1.427 (California variant) (1:1,400 to 1:1,800), but the lowest levels against variants harboring E484K mutations (B.1.1.7 with E484K, B.1.351, and P1; 1:250 to 1:350). 2021 mSphere Result SARS_CoV_2 D614G;E484K;E484K 213;393;423 218;398;428 34431691 Emergence of Multiple SARS-CoV-2 Antibody Escape Variants in an Immunocompromised Host Undergoing Convalescent Plasma Treatment. The Q493K/R and E484K substitutions are located in the RBD region of the spike protein and are associated with resistance to monoclonal antibodies or convalescent plasma. 2021 mSphere Result SARS_CoV_2 E484K;Q493K;Q493R 16;4;4 21;11;11 S;RBD 73;55 78;58 34431691 Emergence of Multiple SARS-CoV-2 Antibody Escape Variants in an Immunocompromised Host Undergoing Convalescent Plasma Treatment. The S protein Q493R substitution and 243 to 244 LA (243-244LA) deletion had ~70% frequency, while open reading frame 1a (ORF1a) A138T, S protein 141 to 144 LGVY (141-144LGVY) deletion, and E484K and Q493K substitutions demonstrated ~30%, ~30%, ~20%, and ~10% mutation frequencies, respectively. 2021 mSphere Result SARS_CoV_2 A138T;E484K;Q493K;Q493R 128;189;199;14 133;194;204;19 ORF1a;S;S 121;4;135 126;5;136 34432488 Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern. Notably, two samples from one patient had signal for E484K (2/2) and N501Y (1/2), which were not identified in the consensus. 2021 Journal of clinical microbiology Result SARS_CoV_2 E484K;N501Y 53;69 58;74 34432488 Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern. Probes using locked nucleic acids (LNAs) centered on specific mutations to selectively detect sequences encoding K417 (reference), E484K (GAA AAA), and N501Y (AAU UAU). 2021 Journal of clinical microbiology Result SARS_CoV_2 E484K;N501Y 131;152 136;157 34433426 Investigation of Interaction between the Spike Protein of SARS-CoV-2 and ACE2-Expressing Cells Using an In Vitro Cell Capturing System. 5B, incubated with S1 / S1(D614G) proteins and ACE2-expresing cell lysate, then pull down the ACE2-S1 protein complex with antibodies. 2021 Biological procedures online Result SARS_CoV_2 D614G 27 32 34433426 Investigation of Interaction between the Spike Protein of SARS-CoV-2 and ACE2-Expressing Cells Using an In Vitro Cell Capturing System. the S1 protein with D614G mutation showed a significantly higher cell capturing ability than wild type S protein. 2021 Biological procedures online Result SARS_CoV_2 D614G 20 25 S 103 104 34433426 Investigation of Interaction between the Spike Protein of SARS-CoV-2 and ACE2-Expressing Cells Using an In Vitro Cell Capturing System. This data prove that higher cell capturing ability of S1(D614G) is due to its stronger affinity to ACE2. 2021 Biological procedures online Result SARS_CoV_2 D614G 57 62 34433426 Investigation of Interaction between the Spike Protein of SARS-CoV-2 and ACE2-Expressing Cells Using an In Vitro Cell Capturing System. To access this possibility, we compared the cell capturing ability of wild type S1 protein and S1 protein with the amino acid change from aspartate to a glycine residue at position 614(D614G) which is associated with enhanced infectivity and increased spike-ACE2-binding affinity. 2021 Biological procedures online Result SARS_CoV_2 D614G;D614G 138;185 184;190 S 252 257 34433426 Investigation of Interaction between the Spike Protein of SARS-CoV-2 and ACE2-Expressing Cells Using an In Vitro Cell Capturing System. We found that S1(D614G) bind more ACE2 proteins. 2021 Biological procedures online Result SARS_CoV_2 D614G 17 22 34433426 Investigation of Interaction between the Spike Protein of SARS-CoV-2 and ACE2-Expressing Cells Using an In Vitro Cell Capturing System. We further determined whether the binding affinity between S1(D614G) and ACE2 is more stronger by a Co-IP experiment. 2021 Biological procedures online Result SARS_CoV_2 D614G 62 67 34433803 ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker. All pseudoviruses could infect HEK293F cells that ectopically express human ACE2, while SARS-CoV-2-D614G showed significantly enhanced infectivity when compared to the original SARS-CoV-2. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G 99 104 34433803 ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker. In comparison, B38, a SARS-CoV-2 RBD-targeting antibody currently under clinical development, could only suppress the infectivity of SARS-CoV-2, SARS-CoV-2-D614G, B.1.1.7, and B.1.617.1, but not B.1.351, SARS-CoV, or HCoV-NL63. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G 156 161 RBD 33 36 34433803 ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker. We investigated the abilities of 3E8 to block the ACE2 binding of S1-subunits or RBD from SARS-CoV-2, SARS-CoV-2-D614G, B.1.1.7, B.1.351, B.1.617.1, P.1, SARS-CoV, and HCoV-NL63. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G 113 118 RBD 81 84 34433803 ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker. We next constructed pseudo-typed coronaviruses with full-length S-proteins from SARS-CoV-2, SARS-CoV-2-D614G, B.1.1.7, B.1.351, B.1.617.1, SARS-CoV, and HCoV-NL63. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G 103 108 S 64 65 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. An important consequence of this is that the S477N mutation increased the affinity of RBD for ACE2 WT but decreased its affinity for ACE2 S19P. 2021 eLife Result SARS_CoV_2 S477N 45 50 RBD 86 89 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Both S19P and K26R increased the affinity of WT RBD binding by ~3.7- and ~ 2.4-fold (Figure 4A). 2021 eLife Result SARS_CoV_2 K26R 14 18 RBD 48 51 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Changes in electrostatic interactions can dramatically affect the kon and are a plausible explanation for the effects of the mutations K417T, K417N, and E484K on kon. 2021 eLife Result SARS_CoV_2 E484K;K417N;K417T 153;142;135 158;147;140 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. E484K has also appeared in VOC-202102-02, a subset of the Alpha variant identified in the UK. 2021 eLife Result SARS_CoV_2 E484K 0 5 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Example sensorgrams are shown of mutations that increased (N501Y, Figure 3A) or decreased (K417N, Figure 3B) the binding affinity, while the key results from all mutants are summarised in Figure 3C. 2021 eLife Result SARS_CoV_2 K417N;N501Y 91;59 96;64 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. In the case of VOC-202102-02, the addition of the E484K mutation to N501Y further increased the affinity, to ~15-fold higher than WT RBD (KD ~5 nM), by further increasing the kon. 2021 eLife Result SARS_CoV_2 E484K;N501Y 50;68 55;73 RBD 133 136 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Interestingly, N501Y, E484K, and S477N were the main mutations that appeared following random RBD mutagenesis and in vitro selection of mutants with enhanced ACE2 binding. 2021 eLife Result SARS_CoV_2 E484K;N501Y;S477N 22;15;33 27;20;38 RBD 94 97 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. K26R is observed in all the major gnomAD populations but is most common in Ashkenazi Jews (1%) and (non-Finnish) north-western Europeans (0.6%). 2021 eLife Result SARS_CoV_2 K26R 0 4 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. The affinity of the Beta (K417N/ E484K/N501Y) and Gamma (K417T/E484K/N501Y) RBD variants for ACE2 increased by 3.7- and 5.3-fold, respectively, relative to wild-type RBD, by both increasing the kon and decreasing the koff rate constants. 2021 eLife Result SARS_CoV_2 E484K;K417N;K417T;E484K;N501Y;N501Y 33;26;57;63;39;69 38;31;62;68;44;74 RBD;RBD 76;166 79;169 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. The E484K mutation is present in the Beta and Gamma variants and has appeared independently in many other lineages, including Zeta (P.2; 20B/S.484K), B.1.1.318, Eta (B.1.525; 20A/S:484 K), and Iota (B.1.526; 20 C/S.484K). 2021 eLife Result SARS_CoV_2 E484K 4 9 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. The K417T and K417N mutations decreased the affinity ~2- and ~ 4-fold, respectively, mainly by decreasing the kon but also by increasing the koff. 2021 eLife Result SARS_CoV_2 K417N;K417T 14;4 19;9 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. The N501Y mutation had the biggest effect, increasing the affinity ~10 fold to KD ~7 nM, by increasing the kon ~1.8-fold and decreasing the koff by ~7-fold. 2021 eLife Result SARS_CoV_2 N501Y 4 9 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. The N501Y mutation has appeared in the Alpha (B.1.1.7; 20I/501Y.V1), Beta (B.1.351; 20 H/501Y.V2), and Gamma (P.1; 20 J/501Y.V3) variants, which were first identified in the UK, South Africa, and Brazil, respectively. 2021 eLife Result SARS_CoV_2 N501Y 4 9 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. The one exception was the combination of ACE2 S19P and RBD S477N variants, where the measured value was significantly lower than the predicted value (Figure 4B), indicating that these mutations were not independent. 2021 eLife Result SARS_CoV_2 S477N 59 64 RBD 55 58 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. The S477N and E484K mutations increased the affinity more modestly (~1.5-fold), by decreasing the koff (S477N) or increasing the kon (E484K). 2021 eLife Result SARS_CoV_2 E484K;S477N;E484K;S477N 14;4;134;104 19;9;139;109 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. The S477N mutation became dominant for periods in Australia (clade 20 F) and parts of Europe (20A.EU2) and then appeared in New York in the Iota or B.1.526 lineage. 2021 eLife Result SARS_CoV_2 S477N 4 9 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. The single mutations S477N, E484K, and N501Y all enhanced binding. 2021 eLife Result SARS_CoV_2 E484K;N501Y;S477N 28;39;21 33;44;26 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Thus, the mutations K417N/T and E484K would decrease and increase, respectively, long-range electrostatic forces that may accelerate association. 2021 eLife Result SARS_CoV_2 E484K;K417N;K417T 32;20;20 37;27;27 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. We also examined the effect on ACE2 binding of combinations of RBD mutations, including combinations present in VOC-202102-02, a subset of the Alpha lineage (N501Y) with the E484K mutation ("SARS-CoV-2 Variants of concern and variants under investigation - GOV.UK," 2021), and the Beta and Gamma variants (Figure 3C, Table 1). 2021 eLife Result SARS_CoV_2 E484K;N501Y 174;158 179;163 RBD 63 66 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. We next examined the effects of mutations of ACE2 (S19P and K26R) on binding to both wild-type and common variants of RBD (Figure 4, Figure 4:figure supplement 1, and Table 1). 2021 eLife Result SARS_CoV_2 K26R 60 64 RBD 118 121 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. We selected for analysis the two most common mutations of ACE2 within the RBD binding site, K26R and S19P (Figure 1C). 2021 eLife Result SARS_CoV_2 K26R 92 96 RBD 74 77 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. A consensus adenine to guanine substitution in spike gene nucleotide position 23,403, corresponding to D614G was detected on January 10 and 18 in the Columbia WWTP influent. 2021 The Science of the total environment Result SARS_CoV_2 D614G 103 108 S 47 52 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. A notable exception is the D614G mutation in the spike protein observed in both the January 10 and 18 samples, where 100% of the reads aligned to the D614G variant, which is consistent with the global trend and evidence that the D614G mutation increases infectivity. 2021 The Science of the total environment Result SARS_CoV_2 D614G;D614G;D614G 27;150;229 32;155;234 S 49 54 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. Consistent with this study, we identified R203K, G204R, S194L, and M234I in the nucleocapsid protein as shared mutations between Columbia and Rock Hill WWTP influents in January 2021 (Supplementary Table S3). 2021 The Science of the total environment Result SARS_CoV_2 G204R;M234I;R203K;S194L 49;67;42;56 54;72;47;61 N 80 92 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. Four mutations in the spike gene were detected that are present in one or more variants of interest (VOI) or variants of concern (VOC), which are listed in parenthesis: S477N (B.1.526, Iota), T478K (B.1.617.2, Delta), D614G (present in all VOC as of May 2021), H655Y (P.1, Gamma). 2021 The Science of the total environment Result SARS_CoV_2 D614G;H655Y;S477N;T478K 218;261;169;192 223;266;174;197 S 22 27 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. Globally, 34 sequences collected from June 28 to July 31, 2020, were deposited into both NCBI Virus and GISAID with the N501Y mutation. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 120 125 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. However, no sequences with the N501Y mutation were found from South Carolina in GISAID during this time frame, although there was an earlier reported observation of this mutation in May 2020. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 31 36 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. In July 2020, the N501Y mutation of the spike gene was observed at 215x coverage. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 18 23 S 40 45 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. In particular, R203K and G204R both had a mutation rate of 0.22, indicating that they were present in 22% of all sequences as of December 2020. 2021 The Science of the total environment Result SARS_CoV_2 G204R;R203K 25;15 30;20 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. The H49Y mutation has been associated with enhanced cell entry, although at present it is not considered a variant of interest or concern. 2021 The Science of the total environment Result SARS_CoV_2 H49Y 4 8 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. The mutation H49Y was detected in the January 18 Columbia sample at 50% frequency. 2021 The Science of the total environment Result SARS_CoV_2 H49Y 13 17 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. The N501Y mutation was not detected in the negative control for the July 2020 sequencing run. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 4 9 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. The N501Y observation in wastewater in South Carolina during July 2020 suggests a possible transmission event of a variant with the N501Y mutation between these two states, although it is also possible that there were already variants with the N501Y mutation present in South Carolina that were not captured in GISAID. 2021 The Science of the total environment Result SARS_CoV_2 N501Y;N501Y;N501Y 4;132;244 9;137;249 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. Twenty-six of the sequences with the N501Y mutation in the July time frame were from the USA (Table 2 ), and all except one were collected from patients in Texas. 2021 The Science of the total environment Result SARS_CoV_2 N501Y 37 42 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. A change from a hydrophobic leucine on the protein surface to arginine (L452R) also increases its interactions with water molecules that could further stabilize the protein. 2021 Biomolecules Result SARS_CoV_2 L452R 72 77 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. After Glu484 was mutated to Gln484, this salt bridge was disrupted in the E484Q and double mutant complexes. 2021 Biomolecules Result SARS_CoV_2 E484Q 74 79 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Apart from these conserved interactions, in the E484Q mutant complex, the backbone and sidechain of Lys353 in hACE2 interacted with Gly502 and Gly496 of S RBD (Figure 4B). 2021 Biomolecules Result SARS_CoV_2 E484Q 48 53 RBD;S 155;153 158;154 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Besides these interactions, residues of single mutant L452R, Tyr489 and Gly496 of S protein, interacted with Gln24 and Lys353 of hACE2, respectively (Figure 4A). 2021 Biomolecules Result SARS_CoV_2 L452R 54 59 S 82 83 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Hence, the simulation data suggests that the E484Q mutation could play a role in disrupting the interfacial interaction. 2021 Biomolecules Result SARS_CoV_2 E484Q 45 50 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. However, as expected, this salt bridge was observed in the L452R single mutant complex (Figure 4A). 2021 Biomolecules Result SARS_CoV_2 L452R 59 64 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. However, studies indicate an increased fitness of the E484Q mutant when compared to the wild type. 2021 Biomolecules Result SARS_CoV_2 E484Q 54 59 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. In support of our results, Cherian and colleagues reported that the L452R mutation, and E484Q, could reduce intramolecular and intermolecular interactions and disrupts an electrostatic bond with Lys31 of hACE2. 2021 Biomolecules Result SARS_CoV_2 E484Q;L452R 88;68 93;73 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. In the single mutant complex involving the E484Q mutant, DeltaGbind values computed were -131.25 +- 20.95 kcal/mol, -143.47 +- 14.96 kcal/mol, and -149.14 +- 20.98 kcal/mol, and for the L452R mutant the values were -146.58 +- 19.70 kcal/mol, -148.60 +- 17.67 kcal/mol, and -117.22 +- 22.15 kcal/mol. 2021 Biomolecules Result SARS_CoV_2 E484Q;L452R 43;186 48;191 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Molecular dynamics simulations trajectories of three systems:single mutants E484Q and L452R, and double mutant E484Q + L452R:in triplicate were analyzed. 2021 Biomolecules Result SARS_CoV_2 E484Q;E484Q;L452R;L452R 76;111;86;119 81;116;91;124 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. reported that the E484K mutation causes conformational changes in the RBD that favors the up state and reduces antibody binding. 2021 Biomolecules Result SARS_CoV_2 E484K 18 23 RBD 70 73 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Similar to the E484Q, in the double mutant complex, the sidechain of Lys31 of hACE2 consistently interacted with Gln493 of the S protein in all simulations (Figure 4C). 2021 Biomolecules Result SARS_CoV_2 E484Q 15 20 S 127 128 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Since this interaction is weaker in the E484Q mutant complex, it could favor the up conformation of the RBD and result in higher hACE2 binding affinity and immune escape. 2021 Biomolecules Result SARS_CoV_2 E484Q 40 45 RBD 104 107 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Studies have also demonstrated that the E484Q mutation could reduce the neutralization by plasma and antibodies by 10-fold. 2021 Biomolecules Result SARS_CoV_2 E484Q 40 45 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. The changes induced by L452R mutation prevents the binding of neutralizing antibodies and promotes high infectivity. 2021 Biomolecules Result SARS_CoV_2 L452R 23 28 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. The number of intermolecular hydrogen bonds is also higher in the mutant complexes (mean +- SD for E484Q+L452R simulations: 10.8 +- 2.1, 10.4 +- 1.9, 10.3 +- 2.0; E484Q simulations: 11.4 +- 2.2, 11.6 +- 1.9, 14.4 +- 2.1; L452R simulations: 11.9 +- 2.0, 13 +- 1.9, 8.9 +- 2.2). 2021 Biomolecules Result SARS_CoV_2 E484Q;E484Q;L452R;L452R 99;163;221;105 104;168;226;110 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Thus, conformational changes in the RBD, induced by the E484Q mutation, could impact the stability of the hACE2 binding surface. 2021 Biomolecules Result SARS_CoV_2 E484Q 56 61 RBD 36 39 34442775 Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally. Another important key mutation is E484K for the South African variant which was found as 0.5% in studied genomes of the S protein. 2021 Microorganisms Result SARS_CoV_2 E484K 34 39 S 120 121 34442775 Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally. In the N protein, the highest mutation was R203K (61.3%). 2021 Microorganisms Result SARS_CoV_2 R203K 43 48 N 7 8 34442775 Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally. In the ORF8 protein, mutations were found at Q27stop (49.7%) and Y73C (50.2%) (Figure 7 and Figure 8, and Supplementary File S1). 2021 Microorganisms Result SARS_CoV_2 Q27X;Y73C 45;65 52;69 ORF8 7 11 34442775 Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally. N501Y and P681H are key mutations in the alpha variant. 2021 Microorganisms Result SARS_CoV_2 P681H;N501Y 10;0 15;5 34442775 Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally. On the other hand, the NS3 and NS8 protein of environmental strains showed frequent mutations at Q57H and Q27stop, respectively. 2021 Microorganisms Result SARS_CoV_2 Q27X;Q57H 106;97 113;101 NS3 23 26 34442775 Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally. The most common amino acid substitutions were D614G (83.4%) followed by N501Y (44.6%), S982A (44.4%), A570D (43.3%), T716I (40.4%), and P681H (40.1%) in Spike (S) protein. 2021 Microorganisms Result SARS_CoV_2 A570D;D614G;N501Y;P681H;S982A;T716I 102;46;72;136;87;117 107;51;77;141;92;122 S;S 153;160 158;161 34442817 Impact of Full Vaccination with mRNA BNT162b2 on SARS-CoV-2 Infection: Genomic and Subgenomic Viral RNAs Detection in Nasopharyngeal Swab and Saliva of Health Care Workers. The analysis was performed using two commercial kits (REALQUALITY SARS-CoV-2 Variants -AB ANALITICA, Padova, Italy- targeting N501Y, K417T and K417N and SARS-CoV-2 Nucleic Acid Mutation Diagnostic kit-Sansure Biotech Inc., Hunan, China- targeting N501Y and 69/70del) in order to combine the targeted mutations. 2021 Microorganisms Result SARS_CoV_2 K417N;K417T;N501Y;N501Y 143;133;126;247 148;138;131;252 34442817 Impact of Full Vaccination with mRNA BNT162b2 on SARS-CoV-2 Infection: Genomic and Subgenomic Viral RNAs Detection in Nasopharyngeal Swab and Saliva of Health Care Workers. The majority of individuals 6/8 (75%) were found to have both the N501Y and 69/70del mutations (associated with the B.1.1.7 variant), while 2/8 (25%) tested positive for the K417T mutation (associated with the the P.1-type variants). 2021 Microorganisms Result SARS_CoV_2 K417T;N501Y 174;66 179;71 34442817 Impact of Full Vaccination with mRNA BNT162b2 on SARS-CoV-2 Infection: Genomic and Subgenomic Viral RNAs Detection in Nasopharyngeal Swab and Saliva of Health Care Workers. Viral mutations (N501Y, 69/70del, K417T and K417N) were further investigated in both saliva and NPS using RT-PCR. 2021 Microorganisms Result SARS_CoV_2 K417N;K417T;N501Y 44;34;17 49;39;22 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. According to the % frequencies of the genetic markers A570D (23271C>A), D614G (23403A>G), P681H (23604C>A), T716I (23709C>T), S982A (24506T>G), and D1118H (24914GG>C), the Beta.1.1.7/alpha lineage VOC was detected in 80.6% +- 8.3 (mean +- SE), (median of 80.8%) of the total sequencing reads. 2021 International journal of molecular sciences Result SARS_CoV_2 A570D;D1118H;D614G;P681H;S982A;T716I;C23271A;A23403G;C23604A;C23709T;T24506G;G24914C 54;148;72;90;126;108;61;79;97;115;133;156 59;154;77;95;131;113;69;87;105;123;141;165 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Although these mutations are located on the linker region (LKR) of the nucleocapsid phosphoprotein, which spans from position 175-254aa, only R203K belongs to the LKR's crucial Ser/Arg (SR)-rich motif that contains putative phosphorylation sites. 2021 International journal of molecular sciences Result SARS_CoV_2 R203K 142 147 N 71 83 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. As a result, the H625R-mutant spike protein may exhibit differential biochemical properties, which should be further investigated, since they may have a severe impact on the functionality of the protein, making the virus more transmissible and/or infectious. 2021 International journal of molecular sciences Result SARS_CoV_2 H625R 17 22 S 30 35 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Consequently, the absence of R203 residue is expected to have an immediate impact on the N protein folding and functionality, while any of the variations in position 204 of the protein (G204R, G204L, or G204H) lead only to subtle modifications (Figure 5). 2021 International journal of molecular sciences Result SARS_CoV_2 G204H;G204L;G204R 203;193;186 208;198;191 N 89 90 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Even though two similar amino acids are substituted, based on the in silico protein structure analysis, H625R leads to subtle alterations in the spike protein folding (Figure 5). 2021 International journal of molecular sciences Result SARS_CoV_2 H625R 104 109 S 145 150 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Finally, a significant growing trend from 7% in September to 27% in October/November samples was revealed for the missense mutation S194L (28854C>T), in line with a similar trend observed worldwide (09/2020, 13% and 11/2020, 21%). 2021 International journal of molecular sciences Result SARS_CoV_2 S194L;C28854T 132;139 137;147 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Five well-characterized missense mutations, D614G (23403A>G)-S gene, Q57H (25563G>T)-ORF3a gene, P323L (14408C>T):ORF1ab/RdRP gene, R203K (28881G>A):N gene, and G204R (28883G>C):N gene, were initially targeted as proof-of-principle of our methodology to perform the analysis and quantification of SARS-CoV-2 mutations/strains in wastewater samples. 2021 International journal of molecular sciences Result SARS_CoV_2 D614G;G204R;P323L;Q57H;R203K;C14408T;A23403G;A23403S;G25563F;G25563R;G25563T;G28881A;G28883C 44;161;97;69;132;104;51;51;75;75;75;139;168 49;166;102;73;137;112;59;59;83;83;83;147;176 ORF1ab;ORF3a;RdRP;N;N;S 114;85;121;149;178;61 120;90;125;150;179;62 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Focusing on the N gene, a declining trend was observed for the missense point mutations 28881G>A (R203K) and 28883G>C (G204R), as well as the synonymous substitution 28882G>A, from ~90% in September to ~70% in October/November samples. 2021 International journal of molecular sciences Result SARS_CoV_2 G28881A;G28882A;G28883C;G204R;R203K 88;166;109;119;98 96;174;117;124;103 N 16 17 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. In addition to the characterized D614G mutation, a previously unknown point mutation within S gene, H625R (23436A>G), was found at a frequency of 5.7% in September samples. 2021 International journal of molecular sciences Result SARS_CoV_2 D614G;H625R;A23436G 33;100;107 38;105;115 S 92 93 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Interestingly, a point substitution 28884G>T, which has been observed in ~1% worldwide, was overrepresented in our datasets, 09/2020, ~70% and 10-11/2020, ~35%. 2021 International journal of molecular sciences Result SARS_CoV_2 G28884T 36 44 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Interestingly, the A570D (23271C>A) substitution was observed in a significantly lower percentage, i.e., 44.41%. 2021 International journal of molecular sciences Result SARS_CoV_2 A570D;C23271A 19;26 24;34 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Interestingly, the Q57H (25563G>T) mutation in the ORF3a gene was solely found observed in October/November samples at a percentage of ~47%, which is in accordance with the growing trend observed worldwide during the last months (11/2020, ~43%). 2021 International journal of molecular sciences Result SARS_CoV_2 Q57H;G25563T 19;25 23;33 ORF3a 51 56 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. More importantly, our analysis highlighted the significant correlation of 28884G>T and 28883G>C point mutations, resulting in a novel amino acid substitution from glycine to leucine in position 204 (G204L) as compared with the single 28883G>C (G204R) or 28884G>T (G204V) substitutions. 2021 International journal of molecular sciences Result SARS_CoV_2 G28883C;G28883C;G28884T;G28884T;G204L;G204L;G204R;G204V 87;234;74;254;163;199;244;264 95;242;82;262;197;204;249;269 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Moreover, a novel point substitution, A54V (25553C>T), was also detected at a percentage rate of ~9% of September samples, resulting in the change of alanine to valine at position 54 of the ORF3a polypeptide. 2021 International journal of molecular sciences Result SARS_CoV_2 A54V;A54V;C25553T 38;150;44 42;182;52 ORF3a 190 195 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Similar to R203K, the S194L mutation is also located on the SR-rich motif of the N protein and involves substitution of the hydroxylic neutral serine with the aliphatic neutral leucine. 2021 International journal of molecular sciences Result SARS_CoV_2 R203K;S194L 11;22 16;27 N 81 82 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Similarly, the P323L (14408C>T) substitution in the ORF1ab/RdPR gene was also prevalent, ~99.9%, in both time periods of sampling, also in agreement with the genomic epidemiology data (~99% worldwide and in Europe). 2021 International journal of molecular sciences Result SARS_CoV_2 P323L;C14408T 15;22 20;30 ORF1ab 52 58 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Since this region regulates the N protein oligomerization upon phosphorylation, the S194L could have a significant impact on protein function; this notion is in accordance with the dramatic changes in the predicted protein structure, and therefore merits further study. 2021 International journal of molecular sciences Result SARS_CoV_2 S194L 84 89 N 32 33 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. The 23436A>G substitution results in the change of histidine to arginine at position 625 of the spike protein. 2021 International journal of molecular sciences Result SARS_CoV_2 A23436G;H625R 4;51 12;88 S 96 101 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. The analysis highlighted that the G614 strain of SARS-CoV-2, originating from the D614G (23403A>G) point mutation in S gene, was exclusively detected (>99.9%) over the D614 strain. 2021 International journal of molecular sciences Result SARS_CoV_2 D614G;A23403G 82;89 87;97 S 117 118 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. The findings obviously indicate that R203K co-exists with G204R, G204L, or G204H variations. 2021 International journal of molecular sciences Result SARS_CoV_2 G204H;G204L;G204R;R203K 75;65;58;37 80;70;63;42 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. These two simultaneous indels lead to the R203K and G204H missense mutations of the nucleocapsid protein. 2021 International journal of molecular sciences Result SARS_CoV_2 G204H;R203K 52;42 57;47 N 84 96 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. D614G had lower energy than the wild type in all steps. 2021 International journal of molecular sciences Result SARS_CoV_2 D614G 0 5 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. D614G was also a stable mutant (Figure 7 and Table 4). 2021 International journal of molecular sciences Result SARS_CoV_2 D614G 0 5 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. From the results for each open-complex form, the D614G mutant appeared to be more stable than the other mutant types in all open-complex forms. 2021 International journal of molecular sciences Result SARS_CoV_2 D614G 49 54 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. In the 1-open-complex form, the D614G and Q787H mutants had lower MM/PBSA values (Figure 5 and Table 2). 2021 International journal of molecular sciences Result SARS_CoV_2 D614G;Q787H 32;42 37;47 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. In the 1-open-complex form, the Q787H mutant in the S2 region had lower energy values but not in the 2-open-complex form. 2021 International journal of molecular sciences Result SARS_CoV_2 Q787H 32 37 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. In the 2-open-complex form, all mutant types:D614G, D614A, L455F, F456L, and Q787H:showed lower distance and SD values than wild type (Figure 3 and Table 1). 2021 International journal of molecular sciences Result SARS_CoV_2 D614A;F456L;L455F;Q787H;D614G 52;66;59;77;45 57;71;64;82;50 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. In the 2-open-complex form, the RBD mutants L455F and F456L were more unstable than the wild type. 2021 International journal of molecular sciences Result SARS_CoV_2 F456L;L455F 54;44 59;49 RBD 32 35 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. In the 2-open-complex form, the SD values among chains was about 4.5 nm in the wild type and about 4 nm in the mutant types D614G, D614A, L455F, and F456L. 2021 International journal of molecular sciences Result SARS_CoV_2 D614A;D614G;F456L;L455F 131;124;149;138 136;129;154;143 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. In the 3-open-complex form, D614G had the lowest SD value of 0.27 nm, similar to the values for the V503 residue. 2021 International journal of molecular sciences Result SARS_CoV_2 D614G 28 33 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. In the 3-open-complex form, mutant types D614A and Q787H had lower SD values than the wild type, and D614G had the lowest SD value among the chains (Figure 4 and Table 1). 2021 International journal of molecular sciences Result SARS_CoV_2 D614A;D614G;Q787H 41;101;51 46;106;56 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. Mutants D614A, L455F, F456L, and Q787H had energy values no lower than the wild type. 2021 International journal of molecular sciences Result SARS_CoV_2 D614A;F456L;L455F;Q787H 8;22;15;33 13;27;20;38 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. The D614G and D614A mutations of the S protein were identified at the same location as amino acids classified G, GH, GR, and GV clade. 2021 International journal of molecular sciences Result SARS_CoV_2 D614A;D614G 14;4 19;9 S 37 38 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. The D614G mutant had a lower SD value of distance than the wild type in each complex form. 2021 International journal of molecular sciences Result SARS_CoV_2 D614G 4 9 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. The D614G mutant had the lowest stable energy (Figure 6 and Table 3). 2021 International journal of molecular sciences Result SARS_CoV_2 D614G 4 9 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. The D614G mutant remained stable in both steps. 2021 International journal of molecular sciences Result SARS_CoV_2 D614G 4 9 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. The L455F and F456L mutation of the S protein were located in receptor-binding domain associated with ACE2 interaction of host cell. 2021 International journal of molecular sciences Result SARS_CoV_2 F456L;L455F 14;4 19;9 S 36 37 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. The Q787H mutation of the S protein was located at cleavage site of the S2 subunit protein. 2021 International journal of molecular sciences Result SARS_CoV_2 Q787H 4 9 S 26 27 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. We identified five non-synonymous mutations (L455F, F456L, D614G, D614A, and Q787H) that could affect the structure of the SARS-CoV-2 S protein, based on analysis of whole-genome sequence from COVID-19 patients in South Korea. 2021 International journal of molecular sciences Result SARS_CoV_2 D614A;D614G;F456L;Q787H;L455F 66;59;52;77;45 71;64;57;82;50 S 134 135 COVID-19 193 201 34445669 Molecular Masks for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. ACE2P1D1 was more effective than ACE2P2D1 in blocking the SARS-CoV-2 pseudovirus containing the D614G mutant spike protein. 2021 International journal of molecular sciences Result SARS_CoV_2 D614G 96 101 S 109 114 34445669 Molecular Masks for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. Furthermore, ACE2P1D1 and ACE2P2D1 effectively blocked the infection of SARS-CoV-2 pseudovirus containing the D614G mutant spike protein (Figure 3c,d). 2021 International journal of molecular sciences Result SARS_CoV_2 D614G 110 115 S 123 128 34445669 Molecular Masks for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. Of the two peptoids, ACE2P1D1 seems more effective than ACE2P2D1 in blocking the interaction of D614G spike protein and ACE2. 2021 International journal of molecular sciences Result SARS_CoV_2 D614G 96 101 S 102 107 34445669 Molecular Masks for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. The D614G mutation in the spike protein makes the virus more contagious. 2021 International journal of molecular sciences Result SARS_CoV_2 D614G 4 9 S 26 31 34445669 Molecular Masks for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. We also found that both ACE2P1D1 of ACE2P2D1 blocked the interaction of D614G spike protein and ACE2, although the effect seems lesser than on the unmutated version of the spike protein (Figure 2d). 2021 International journal of molecular sciences Result SARS_CoV_2 D614G 72 77 S;S 78;172 83;177 34449757 An Autochthonous Outbreak of the SARS-CoV-2 P.1 Variant of Concern in Southern Italy, April 2021. Therefore, samples were subjected to molecular screening for variants and designated the P.1 variant because of the presence of the K417T, E484K, and N501Y spike mutations. 2021 Tropical medicine and infectious disease Result SARS_CoV_2 E484K;K417T;N501Y 139;132;150 144;137;155 S 156 161 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. Additionally, two of these genomes (18.2%) carry T11296G (ORF1ab nsp6: F3677L) and eight (72.7%) harbor G25641T (ORF3a: L83F) substitutions. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 F3677L;G25641T;L83F;T11296G 71;104;120;49 77;111;124;56 ORF1ab;ORF3a;Nsp6 58;113;65 64;118;69 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. Among all identified clusters, the most diverse was Cluster 5, which contains three samples from this study and has five defining mutations: four in ORF1ab (synT4705C, synC11095T, syn11518, and T5541I (helicase)) and one in ORF7a: E16D. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 E16D;T5541I 231;194 235;200 Helicase;ORF1ab;ORF7a 202;149;224 210;155;229 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. Clade 2 sequences harbored two mutations in ORF1ab:V2862L (nsp4) and synC10507T and one in ORF3a:M260K, and it comprised 81 genomes. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 M260K;V2862L 97;51 102;57 ORF1ab;ORF3a;Nsp4 44;91;59 50;96;63 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. Clade 3 is represented by three ORF1ab mutations (synC1420T, D1600N [nsp3], and synT8392A) in three of the seven local genomes. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D1600N 61 67 ORF1ab;Nsp3 32;69 38;73 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. Clade 4 is characterized by two ORF1ab substitutions (G400S (nsp2) and S6822I (2'-O-ribose methyltransferase)), one N:synT26861C in three genomes, and carries other additional mutations (ORF1ab: synG10096A, G3676S (nsp6), F3677L (nsp6)) and M:synT26861C. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 F3677L;G3676S;S6822I;G400S 222;207;71;54 228;213;77;59 ORF1ab;ORF1ab;Nsp2;Nsp6;Nsp6;N 32;187;61;215;230;116 38;193;65;219;234;117 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. Clusters 1 and 3 have, respectively, one (ORF1ab: G3676S (nsp6)) and two (ORF1ab: synC1471T and A1049V (nsp3)) shared mutations. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 A1049V;G3676S 96;50 102;56 ORF1ab;ORF1ab;Nsp3;Nsp6 42;74;104;58 48;80;108;62 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. Fifteen substitutions (10 in the spike protein: L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, and T1027I) are P.1 lineage-defining mutations (Figure 1B and Table 2). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D138Y;E484K;H655Y;K417T;L18F;N501Y;P26S;R190S;T1027I;T20N 66;87;101;80;48;94;60;73;112;54 71;92;106;85;52;99;64;78;118;58 S 33 38 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. Moreover, this local sequence accrued seven specific mutations: ORF1ab:synA7201G, S2926F (nsp4), V6871A (2'-O-ribose methyltransferase), S:G1251V, ORF7a:G38V, N:synC28333T, and intergenic:G29688T. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 S2926F;V6871A;G1251V;G29688T;G38V 82;97;139;188;153 88;103;145;195;157 ORF1ab;ORF7a;Nsp4;N;S 64;147;90;159;137 70;152;94;160;138 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. Moreover, two sequences share one distinct mutation (ORF1ab: F3677L (nsp6)). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 F3677L 61 67 ORF1ab;Nsp6 53;69 59;73 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. Most importantly, this local genome harbors seven other mutations: ORF1ab:T2087I (nsp3), D3022N (nsp4), N3970S (nsp8), V4436A (RNA-dependent RNA polymerase), synC13724T, synG18973A, and intergenic:G29736T. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D3022N;N3970S;V4436A;G29736T;T2087I 89;104;119;197;74 95;110;125;204;80 RdRp;ORF1ab;Nsp3;Nsp4;Nsp8 127;67;82;97;112 155;73;86;101;116 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. This clade is supported by the ORF1ab:synC15810T mutation and includes a subclade characterized by the ORF1ab:L4182F mutation, where the local sequence is placed together with four samples from Sao Paulo (SP), one from Portugal, and one from Chile (Figure S4). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 L4182F 110 116 ORF1ab;ORF1ab;S 31;103;205 37;109;207 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. This clade possesses three defining mutations (ORF1ab nsp4: V2862L, synC10507T, and ORF3a: M260K), but it does not fall into a lineage designation at this moment but deserves further monitoring (Figure S1). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 M260K;V2862L 91;60 96;66 ORF1ab;ORF3a;Nsp4 47;84;54 53;89;58 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. This combination was previously described and gave rise to the P.1.2 lineage, which harbors three ORF1ab replacements (synC1912T, D762G, and T1820I), one in ORF3a (D155Y), and one in N protein (synC28789T) (Table 2). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D762G;T1820I;D155Y 130;141;164 135;147;169 ORF1ab;ORF3a;N 98;157;183 104;162;184 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Although the B.1.362 background lineage is detected in numerous countries, only sequences of this lineage originating in Israel formed a cluster representing the B.1.362+L452R variant. 2021 Vaccines Result SARS_CoV_2 L452R 170 175 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. An additional characterizing mutation in the ORF3a gene:W131C (G25785T):was acquired at a later time-point and exists in most of the variant sequences (Figure 1B). 2021 Vaccines Result SARS_CoV_2 G25785T;W131C 63;56 70;61 ORF3a 45 50 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Characterization and Epidemiology of the B.1.362+L452R Variant. 2021 Vaccines Result SARS_CoV_2 L452R 49 54 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Neutralizing Capacity against the B.1.362+L452R Variant Following BNT162b2 Vaccination. 2021 Vaccines Result SARS_CoV_2 L452R 42 47 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Results show that the B.1.362+L452R variant had X2.3 and X4 folds reduced neutralization capacity compared to the Alpha variant and the Israeli WT strain, respectively (Figure 3). 2021 Vaccines Result SARS_CoV_2 L452R 30 35 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. The neutralization potency of sera from vaccinated individuals against the B.1.362+L452R variant was compared to the neutralization capacity against two other strains:the Alpha variant (isolate hCoV-19/Israel/CVL-46879-ngs/2020) and a local WT strain from Israel (isolate hCoV-19/Israel/CVL-45526-ngs/2020). 2021 Vaccines Result SARS_CoV_2 L452R 83 88 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. The novel B.1.362+L452R variant forms a distinct cluster in a phylogenetic tree representing randomly chosen sequenced samples from Israel (Figure 1A), constructed as part of the national program for SARS-CoV-2 whole genome sequencing and variant surveillance. 2021 Vaccines Result SARS_CoV_2 L452R 18 23 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. The variant is characterized by two non-synonymous mutations in the S protein, L452R (T22917G), which lies within the receptor binding domain (RBD), and L1063F (G24751T), in addition to a non-synonymous mutation in the NSP16 gene in D2179Y (G20002T) and a synonymous mutation in the M protein in G26840A. 2021 Vaccines Result SARS_CoV_2 D2179Y;G26840A;L1063F;L452R;G20002T;G24751T;T22917G 233;296;153;79;241;161;86 239;303;159;84;248;168;93 RBD;RBD;S 118;143;68 141;146;69 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Until April 2021, a total of 270 individuals were infected with the B.1.362+L452R variant. 2021 Vaccines Result SARS_CoV_2 L452R 76 81 34452356 Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. Among those, three alterations are of particular concern as they are located in the NTD or RBD epitope regions, respectively, and are suspected to result in immune escape (L18F, L452R and N501Y) and/or higher infectivity and transmissibility (L452R and N501Y). 2021 Viruses Result SARS_CoV_2 L452R;N501Y;N501Y;L18F;L452R 178;188;253;172;243 183;193;258;176;248 RBD 91 94 34452356 Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. Antibody escape data for the RBD, integrating multiple experimental studies (, accessed on 3 May 2021), assign maximum mutation escape scores of 0.97 (L452R) and 0.90 (N501Y) over multiple antibodies/sera or antibody/serum types. 2021 Viruses Result SARS_CoV_2 L452R;N501Y 151;168 156;173 RBD 29 32 34452356 Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. D614G is associated with increased receptor binding and infectivity. 2021 Viruses Result SARS_CoV_2 D614G 0 5 34452356 Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. Importantly, A.27 does not possess the D614G change, which emerged early in the pandemic and rapidly became dominant. 2021 Viruses Result SARS_CoV_2 D614G 39 44 34452356 Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. In total, A.27 harbors 17 lineage-defining mutations (Figure 3A and Figure 4A), seven of which result in non-synonymous nucleotide substitutions in the spike protein: L18F, L452R, N501Y, A653V, H655Y, D796Y, G1219V. 2021 Viruses Result SARS_CoV_2 A653V;D796Y;G1219V;H655Y;L18F;L452R;N501Y 187;201;208;194;167;173;180 192;206;214;199;171;178;185 S 152 157 34452356 Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. Intriguingly, one of the genomes (EPI_ISL_1567985) encoded S-L452R, S-N501Y, and S-G1219V associated with six other amino acid changes in the spike (A570D, D614G, P681H, T716I, S982A, I1221V), most interestingly comprising D614G and also P681H (Figure 4B). 2021 Viruses Result SARS_CoV_2 D614G;D614G;I1221V;P681H;P681H;S982A;T716I;A570D;G1219V;L452R;N501Y 156;223;184;163;238;177;170;149;83;61;70 161;228;190;168;243;182;175;154;89;66;75 S;S;S;S 142;59;68;81 147;60;69;82 34452356 Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. Neither does A.27 contain the likely functionally equivalent Q613H that is present in A.23.1 (Figure 3C). 2021 Viruses Result SARS_CoV_2 Q613H 61 66 34452356 Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. Recently, the L452R change in the RBD also known from B.1.427/429 and B.1.617.2 and its novel sublineages AY.1 and AY.2 (Figure 3C) was suggested to contribute to escaping human leukocyte antigen-restricted cellular immunity while also increasing the binding affinity to ACE2, thus increasing viral infectivity and potentially enhancing virus replication. 2021 Viruses Result SARS_CoV_2 L452R 14 19 RBD 34 37 34452356 Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. S-N501Y also appears in VOCs B.1.1.7, P.1 and B.1.351, and may increase infectivity in vitro and appears to confer resistance against some RBD targeting antibodies (class 1). 2021 Viruses Result SARS_CoV_2 N501Y 2 7 RBD;S 139;0 142;1 34452356 Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. The H655Y substitution adjacent to the S1/S2 cleavage site and also known from P.1 was recently detected in a potential new VOI within the A lineage (temporarily designated A.VOI.V2) identified from three cases of incoming travelers from Tanzania to Angola. 2021 Viruses Result SARS_CoV_2 H655Y 4 9 34452356 Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. The L18F replacement is part of an antigenic supersite in the N-terminal domain of the spike protein. 2021 Viruses Result SARS_CoV_2 L18F 4 8 S;N 87;62 92;63 34452356 Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. The polymorphic positions are labeled on the S protein structure (Figure 3B), indicating the localization of L452R (reduced antibody neutralization) and N501Y (related to increased transmissibility) in the RBD, A653V/H655Y in proximity to the S1/S2 furin cleavage site at position 681 that promotes infection and cell-cell fusion, and D795Y, closely located to the essential TMPRSS2-cleavage site at position 815. 2021 Viruses Result SARS_CoV_2 A653V;D795Y;L452R;N501Y;H655Y 211;335;109;153;217 216;340;114;158;222 RBD;S 206;45 209;46 34452356 Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. The S-L18F alteration also appears in VOCs that are associated with immune escape and reinfection, such as B.1.351 and P.1. 2021 Viruses Result SARS_CoV_2 L18F 6 10 S 4 5 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. At day 7, E484K was not detected by any of these tests, but a S494P, also described in several VOC, particularly under selection by immunoglobulins, was detected on the S gene. 2021 Viruses Result SARS_CoV_2 E484K;S494P 10;62 15;67 S 169 170 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. E484A was detected again at day 9. 2021 Viruses Result SARS_CoV_2 E484A 0 5 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. No selection of the E484K was observed, neither by specific PCR screening nor by whole genome sequencing. 2021 Viruses Result SARS_CoV_2 E484K 20 25 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. Of note, a Q493R mutation, which may impact ACE-2 affinity, was observed in the S gene at day 23. 2021 Viruses Result SARS_CoV_2 Q493R 11 16 S 80 81 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. Such transient appearance of E484K has been observed in previous case reports. 2021 Viruses Result SARS_CoV_2 E484K 29 34 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. The viral evolution demonstrated a E484K selection 12 days after bamlanivimab infusion, quickly followed by viral load decrease, before becoming negative at day 18. 2021 Viruses Result SARS_CoV_2 E484K 35 40 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. The viral evolution presented an early selection of E484K mutation at day 6 after bamlanivimab infusion, detected by both specific RT-PCR screening and whole genome sequencing. 2021 Viruses Result SARS_CoV_2 E484K 52 57 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. The viral load first decreased, from 15 to 27 Ct, before a new increase to 14 Ct on day 26 (day 15 after symptom onset), associated with the E484K detection at day 26 and 38. 2021 Viruses Result SARS_CoV_2 E484K 141 146 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. Viral evolution showed the emergence of the E484A mutation at day 6 post-infusion and E484K at day 7. 2021 Viruses Result SARS_CoV_2 E484A;E484K 44;86 49;91 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. Viral follow-up demonstrated a E484K selection on day 14, associated with a viral load increase. 2021 Viruses Result SARS_CoV_2 E484K 31 36 34452511 Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. As an example of this processing, the sequence '1212G(G404G) 1501T(N501Y) 1709A(A570D)' with 100 counts would have the covariants of '1212G(G404G)', '1501T(N501Y)', '1709A(A570D)', '1212G(G404G) 1501T(N501Y)', '1212G(G404G) 1709A(A570D)', '1501T(N501Y) 1709A(A570D)' and '1212G(G404G) 1501T(N501Y) 1709A(A570D)', and contribute 100 counts to each. 2021 Viruses Result SARS_CoV_2 A570D;A570D;A570D;A570D;A570D;G404G;G404G;G404G;G404G;G404G;N501Y;N501Y;N501Y;N501Y;N501Y 80;172;230;259;304;54;140;188;217;278;67;156;201;246;291 85;177;235;264;309;59;145;193;222;283;72;161;206;251;296 34452511 Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. As that is the only sample where those covariant sequences were observed and the polymorphisms are not frequently reported in GISAID (outside of P.1 for A688V), we did not feel we could validate this sequence as a novel lineage and instead tentatively assigned it to the reference category. 2021 Viruses Result SARS_CoV_2 A688V 153 158 34452511 Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. For example, using the previously mentioned SARS-CoV-2 spike ORF as the reference sequence, a sequence read that matches the reference except for having a T at position 1501 instead of the reference A would be reported simply as '1501A(N501Y)'. 2021 Viruses Result SARS_CoV_2 N501Y 236 241 S 55 60 34452511 Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. For instance, in a sample where '1501T(N501Y)' has an abundance of 0.32 and '1709A(A570D)' has an abundance of 0.35, the expected abundance of the covariant '1501T(N501Y) 1709A(A570D)' would be 0.112 [0.32 x 0.35]. 2021 Viruses Result SARS_CoV_2 A570D;A570D;N501Y;N501Y 83;177;39;164 88;182;44;169 34452511 Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. From these results, we can conclude that the SARS-CoV-2 population of this sewershed changed in March 2021 from almost exclusively the D614G B.1 lineage to mainly the B.1.1.7 lineage, with the introduction of P.1 early in April 2021. 2021 Viruses Result SARS_CoV_2 D614G 135 140 34452511 Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. Sequences from the RBD amplicon matched reference sequence, lineages B.1.1.7 with '1501T(N501Y) 1709A(A570D)', P.1 with '1250C(K417T) 1450A(E484K) 1501T(N501Y)', or had the single variations of T478K or L452R (Supplementary 11). 2021 Viruses Result SARS_CoV_2 L452R;T478K;A570D;E484K;K417T;N501Y;N501Y 203;194;102;140;127;89;153 208;199;107;145;132;94;158 RBD 19 22 34452511 Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. Sequences from the S1S2 amplicon matched lineage B.1.1.7 with '1841G(D614G) 2042A(P681H) 2147T(T716I)', lineage P.1 with '1841G(D614G) 1963T(H655Y) 2063T(A688V)' or the B.1 lineage with only the now ubiquitous D614G variation (Supplementary 12). 2021 Viruses Result SARS_CoV_2 D614G;A688V;D614G;D614G;H655Y;P681H;T716I 210;154;69;128;141;82;95 215;159;74;133;146;87;100 34452511 Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. T478K and L452R each have lineage associations. 2021 Viruses Result SARS_CoV_2 L452R;T478K 10;0 15;5 34452511 Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. The 03-23 S1S2 sample had a sequence '1841G(D614G) 2037G(N679K) 2063T(A688V)'. 2021 Viruses Result SARS_CoV_2 A688V;D614G;N679K 70;44;57 75;49;62 34452511 Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. then '1216-1216Del 1501T(N501Y) 1709A(A570D)', '1212G(G404G) 1501T(N501Y) 1709A(A570D)' and '1217-1217Del 1501T(N501Y) 1709A(A570D)' would not be reported. 2021 Viruses Result SARS_CoV_2 A570D;A570D;A570D;G404G;N501Y;N501Y;N501Y 38;80;125;54;25;67;112 43;85;130;59;30;72;117 34452511 Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. These differences were more pronounced with covariants with relatively low abundance, such as is seen with 3-30 RBD samples, where one detects T478K and the other does not (Figure 5). 2021 Viruses Result SARS_CoV_2 T478K 143 148 RBD 112 115 34452511 Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. We classified the sequences found from the NTD amplicon as matching reference sequence, lineage B.1.1.7 (Alpha) with '203-208Del 429-431Del' or lineage P.1 (Gamma) with '412T(D138Y) 570T(R190S)' (Supplementary 10). 2021 Viruses Result SARS_CoV_2 D138Y;R190S 175;187 180;192 34452511 Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. While A688V is associated with P.1, it does not appear in that context here. 2021 Viruses Result SARS_CoV_2 A688V 6 11 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. Anti-RBD IgG ELISA shows that antibodies induced by infection with wild-type Wuhan SARS-CoV-2 fail to recognize the RBD mutants L452R/E484Q (variant B.1.617) and E484K (variants P.1 and B.1.351), while recognition of RBDN440K is unaltered. 2022 Allergy Result SARS_CoV_2 E484K;L452R;E484Q 162;128;134 167;133;139 RBD;RBD;RBD 5;116;217 8;119;220 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. As shown previously, vaccination induces antibodies with broader specificity than viral infection, resulting in antibodies that showed reduced binding to RBD carrying mutation E484K while all other RBDs, including the Indian variants of concern were recognized well by the vaccine-induced immune sera (Figure 3C). 2022 Allergy Result SARS_CoV_2 E484K 176 181 RBD;RBD 154;198 157;202 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. Binding kinetics of RBD mutants to ACE2 show increased affinity due L452R/E484Q and E484K mutations. 2022 Allergy Result SARS_CoV_2 E484K;L452R;E484Q 84;68;74 89;73;79 RBD 20 23 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. In contrast to direct binding of immune sera to RBD, inhibition of the RBD-ACE2 interaction was more severely affected and reduced for all mutations, most notably E484K and L452R/E484Q (Figure 3D). 2022 Allergy Result SARS_CoV_2 E484K;L452R;E484Q 163;173;179 168;178;184 RBD;RBD 48;71 51;74 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. RBD mutants L452R/E484Q and E484K evade recognition and neutralization by convalescent sera while neutralization by BNT162b2 immune sera is impaired only. 2022 Allergy Result SARS_CoV_2 E484K;L452R;E484Q 28;12;18 33;17;23 RBD 0 3 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. The results show that the affinity of ACE2 for RBDL452R/E484Q (KD = 4.6 nM, Figure 2C) is fivefold higher than that measured for RBDWT (KD = 21.3 nM, Figure 2A). 2022 Allergy Result SARS_CoV_2 E484Q 56 61 RBD 47 50 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. This observation is reproduced in the RBD-ACE2 binding inhibition assays (Figure 3B), where the neutralizing activity of the convalescent sera is significantly affected by mutations E484K and L452R/E484Q and not by N440K. 2022 Allergy Result SARS_CoV_2 E484K;L452R;N440K;E484Q 182;192;215;198 187;197;220;203 RBD 38 41 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. To address the questions of antibody binding strength and competition mechanistically, we have expressed recombinant versions of the RBD containing mutations E484K (shared between the Brazilian isolate P.1 and the South African isolate B.1.351), L452R/E484Q (Indian variant B.1.617), and N440K (variant B.1.36, also emerged in India). 2022 Allergy Result SARS_CoV_2 E484K;L452R;N440K;E484Q 158;246;288;252 163;251;293;257 RBD 133 136 34454120 The low contagiousness and new A958D mutation of SARS-CoV-2 in children: An observational cohort study. A19945G and C24435A are missense variants; the others are synonymous variants. 2021 International journal of infectious diseases Result SARS_CoV_2 C24435A;A19945G 12;0 19;7 34454120 The low contagiousness and new A958D mutation of SARS-CoV-2 in children: An observational cohort study. Among these mutations, the new A958D mutation of the spike protein (24435C>A mutation in the virus genome) is of special interest because it is the only one for which the 3D structure of the protein has been solved. 2021 International journal of infectious diseases Result SARS_CoV_2 A958D;C24435A 31;68 36;76 S 53 58 34454120 The low contagiousness and new A958D mutation of SARS-CoV-2 in children: An observational cohort study. The new A958D mutation improves theoretically viral thermostability. 2021 International journal of infectious diseases Result SARS_CoV_2 A958D 8 13 34454120 The low contagiousness and new A958D mutation of SARS-CoV-2 in children: An observational cohort study. The structure suggests that the A958D mutation will lead to strong salt bridge formation between D958 and R1014 (Figure 2. 2021 International journal of infectious diseases Result SARS_CoV_2 A958D 32 37 34455390 Evolution of antibody responses up to 13 months after SARS-CoV-2 infection and risk of reinfection. Anti-RBD IgG titers >2.0 log BAU/mL neutralized D614G, B.1.1.7 at > 2.5 log IC50, and B.1.351 at >= 2.0 log IC50. 2021 EBioMedicine Result SARS_CoV_2 D614G 48 53 RBD 5 8 34455390 Evolution of antibody responses up to 13 months after SARS-CoV-2 infection and risk of reinfection. Anti-RBD titers around 1.4 log BAU/mL neutralized D614G, B.1.1.7 but not B.1.351 variants at more than 2.0 log IC50. 2021 EBioMedicine Result SARS_CoV_2 D614G 50 55 RBD 5 8 34455390 Evolution of antibody responses up to 13 months after SARS-CoV-2 infection and risk of reinfection. Sera collected from unvaccinated participants showed median neutralizing antibody titers of 2.31 log IC50 (IQR: 2.03-2.76), 2.10 log IC50 (IQR: 1.76-2.45) and 1.51 log IC50 (IQR: 1.48-1.87) against D614G, B.1.1.7 and B.1.351 live-strains, respectively. 2021 EBioMedicine Result SARS_CoV_2 D614G 198 203 34455390 Evolution of antibody responses up to 13 months after SARS-CoV-2 infection and risk of reinfection. Strong correlation was observed at M11-13 between neutralizing antibody titers assessed by S-Fuse neutralization assay and anti-RBD IgG titers measured by CMIA with Spearman correlation coefficients of 0.967, 0.968 and 0.944 for variants D614G, B.1.1.7, and B.1.351, respectively (p values<0.0001). 2021 EBioMedicine Result SARS_CoV_2 D614G 238 243 RBD;S 128;91 131;92 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. About 88% of the sequences clustered in GR clade the distinctive feature of which is G204R mutation in the nucleocapsid protein (Figure 4 and Table 3). 2021 Heliyon Result SARS_CoV_2 G204R 85 90 N 107 119 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. Beside these, two of the high frequency (86%) SNVs (R203K and G204R) occurred in COVID-19 diagnostic RT-PCR target and B-Cell predicted epitope regions, of which the later was predicted to cause altered function of the nucleocapsid protein (Figure 1). 2021 Heliyon Result SARS_CoV_2 G204R;R203K 62;52 67;57 N 219 231 COVID-19 81 89 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. Further analysis revealed two SNVs (L3606F, H125Y) were predicted to cause altered ordered interface and altered transmembrane protein for ORF1ab polyprotein (NSP6) and Membrane (M) protein respectively where L3606F was predicted to cause gain of sulfation at Y360 position of NSP3 protein (Table 2). 2021 Heliyon Result SARS_CoV_2 H125Y;L3606F;L3606F 44;209;36 49;215;42 Membrane;ORF1ab;Nsp3;Nsp6 169;139;277;159 177;145;281;163 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. The common distinctive feature of these three clades is D614G mutation. 2021 Heliyon Result SARS_CoV_2 D614G 56 61 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. The latter caused D614G amino acid change in the spike protein of the virus. 2021 Heliyon Result SARS_CoV_2 D614G 18 23 S 49 54 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. The most common mutation in non-coding region was 241C>T, observed in 96% (312) of the isolates. 2021 Heliyon Result SARS_CoV_2 C241T 50 56 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. The mutation with highest frequency (~98%) in coding region was 3037C>T (synonymous) and 14408C>T (missense) in ORF1ab gene, and 23403A>G (missense) in S gene. 2021 Heliyon Result SARS_CoV_2 C14408T;A23403G;C3037T 89;129;64 97;137;71 ORF1ab;S 112;152 118;153 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. The P4715L, one of the highest frequent SNVs, occurred in the RNA dependent RNA polymerase (RdRp) region of ORF1ab polyprotein. 2021 Heliyon Result SARS_CoV_2 P4715L 4 10 RdRp;ORF1ab;RdRP 62;108;92 90;114;96 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. The T592I mutation in ORF1ab polyprotein (NSP2) was strongly predicted for CD8+ T-Cell epitope that was also predicted for altered protein function. 2021 Heliyon Result SARS_CoV_2 T592I 4 9 ORF1ab;Nsp2 22;42 28;46 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. These mutation events comprised of 56 SNVs and 2 deletions where D614G was the mutation of highest frequency that occurred in 97.2% (315) isolates. 2021 Heliyon Result SARS_CoV_2 D614G 65 70 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. A significant decrease in neutralization antibody titer was detected with the alpha and gamma variants relative to D614G variant among the three age ranges (Figure 1B). 2022 Journal of medical virology Result SARS_CoV_2 D614G 115 120 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. Although no significant decrease was detected, the GMT of the neutralization antibody titer of D614G variant suggested a reduced neutralization ability for older people (Figure 1B). 2022 Journal of medical virology Result SARS_CoV_2 D614G 95 100 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. Finally, two samples showed a higher neutralization ability against the Gamma variant than the D614G and Alpha variants (pattern 4). 2022 Journal of medical virology Result SARS_CoV_2 D614G 95 100 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. Nine plasma samples showed a lower potency of neutralization against the Alpha variant than D614G and Gamma variants, and with a higher neutralization antibody titer against the D614G variant than the Gamma variant (pattern 3). 2022 Journal of medical virology Result SARS_CoV_2 D614G;D614G 92;178 97;183 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. Plasma samples obtained from vaccinated individuals exhibited good neutralization of D614G variant, with a geometric mean titer (GMT) of 75.1 (Figure 1). 2022 Journal of medical virology Result SARS_CoV_2 D614G 85 90 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. The mean fold decrease in neutralization relative to D614G variant was 4.1-fold for alpha (p < 0.0001), and 7.5-fold for gamma (p < 0.0001) (Figure 1A). 2022 Journal of medical virology Result SARS_CoV_2 D614G 53 58 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. Thirty samples showed a decrease of neutralization antibody titer with alpha and gamma variants compared to D614G variant (pattern 1). 2022 Journal of medical virology Result SARS_CoV_2 D614G 108 113 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. This is the first study to our knowledge that evaluates the neutralizing antibody response against the alpha, gamma, and D614G variants in vaccinated people with two doses of CoronaVac. 2022 Journal of medical virology Result SARS_CoV_2 D614G 121 126 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. Three samples showed a higher neutralization antibody titer against the Alpha variant than the D614G and Gamma variants (pattern 2). 2022 Journal of medical virology Result SARS_CoV_2 D614G 95 100 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. We report that the potency of the neutralizing response against Alpha and Gamma variants was significantly lower than for D614G variant in CoronaVac-immunized people at 2 months p.i. 2022 Journal of medical virology Result SARS_CoV_2 D614G 122 127 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. When assessing the alpha (GMT = 18.5) and gamma (GMT = 10.0) variants, exhibited neutralization that was significantly decreased to the parental D614G variant (GMT = 75.1). 2022 Journal of medical virology Result SARS_CoV_2 D614G 145 150 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Delta spike has accumulated mutations T19R, G142D, E156G, F157-R158 deletion, L452R, T478K, D614G, P681R, and D950N, among which P681R is located at a furin cleavage site (PRRAR S with P681 underlined and " " indicating furin cleavage) that is absent in other group 2B coronaviruses. 2021 bioRxiv Result SARS_CoV_2 D614G;D950N;E156G;G142D;L452R;P681R;P681R;T19R;T478K 92;110;51;44;78;99;129;38;85 97;115;56;49;83;104;134;42;90 S;S 6;178 11;179 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. It should be noted that the Alpha variant also has a spike mutation at amino acid position 681 (P681H), which may contribute to the increase in spike cleavage when compared with the wild-type USA/WA1-2020 virus; however, a recent study showed that mutation P681H alone did not enhance viral fitness or transmission. 2021 bioRxiv Result SARS_CoV_2 P681H;P681H 257;96 262;101 S;S 53;144 58;149 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Since the furin cleavage site was shown to be important for SARS-CoV-2 replication and pathogenesis, we hypothesized that mutation P681R may improve the furin cleavage efficiency of full-length spike to S1 and S2, leading to a more efficient virus entry into respiratory epithelial cells. 2021 bioRxiv Result SARS_CoV_2 P681R 131 136 S 194 199 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. These results demonstrate that mutation P681R at the furin cleavage site plays a critical role in enhancing the replication of the Delta variant on primary human airway cultures. 2021 bioRxiv Result SARS_CoV_2 P681R 40 45 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. To test this hypothesis, we reverted the Delta P681R mutation to wild-type P681 in the Delta SARS-CoV-2 (Extended data. 2021 bioRxiv Result SARS_CoV_2 P681R 47 52 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Within the RBD, the Alpha RBD has a N501Y mutation, whereas Delta RBD has L452R and T478K mutations. 2021 bioRxiv Result SARS_CoV_2 L452R;N501Y;T478K 74;36;84 79;41;89 RBD;RBD;RBD 11;26;66 14;29;69 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Across all variants, the binding affinity of Chondramide C3 (1) remained constant (Tables S1-S3) except towards N501Y (-6.6 kcal/mol) and E484K (-7.2 kcal/mol) (Table 1). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y 138;112 143;117 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. After determining the binding affinities of the chondramides towards point-mutated SARS-CoV-2 spike variants, the selected compounds were subjected to molecular docking against recently known strains with more than one amino acid substitutions in the spike RBD sequence namely, the South African variant (Wibmer et al.,) (N501Y-E484K-K417N) and the Brazilian variant (Nonaka et al., 2021) (N501Y-E484K-K417T). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501Y;N501Y;E484K;E484K;K417N;K417T 322;390;328;396;334;402 327;395;333;401;339;407 S;S;RBD 94;251;257 99;256;260 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Among the derivatives, chondramide C (2) showed strong affinities against N501Y (-9.1 kcal/mol) and E484K (-8.7 kcal/mol) SARS-CoV-2 variants. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y 100;74 105;79 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Based on computational analysis performed on chondramide C (2) against the single-substituted spike variants (N501Y and E484K), it is expected that this compound would exhibit similar strong affinities against the South African and Brazilian variants (Table 2). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y 120;110 125;115 S 94 99 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Based on post-docking analysis of 1 against the N501Y variant, we observed that the new residue (Tyr501) is responsible for an observable decrease of the binding affinity since it did not exhibit significant interactions with the ligand. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501Y 48 53 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Furthermore, E484K has been linked with some cases of reinfection in Brazil (Nonaka et al., 2021). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K 13 18 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. In particular, V483A is prevalent among patients with COVID-19 in the United States which has the highest mutation frequency within the receptor-binding motif of the spike indicating that the mutation makes SARS-CoV-2 more infectious (Wang et al.,). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 V483A 15 20 S 166 171 COVID-19 54 62 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Li and co-workers identified single amino acid substitutions in the viral spike RBD (A475V, I472V, L452R, V483A, and F490L) which were found to affect binding of neutralizing antibodies (Li et al.,) and were identified to occur in higher frequencies during the time evolution of SARS-CoV-2 spike protein RBD indicating stronger transmission capacity (Chen et al.,). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 F490L;I472V;L452R;V483A;A475V 117;92;99;106;85 122;97;104;111;90 S;S;RBD;RBD 74;290;80;304 79;295;83;307 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. On the other hand, the mutation E484K found in the RBD is responsible for a 10-fold decrease in neutralization by convalescent serum antibodies (Greaney et al.,). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K 32 37 RBD 51 54 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. On the other hand, the mutation to a lysine residue as observed in the E484K variant provided structural accommodation for hydrogen bonding with free hydroxyl moieties. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K 71 76 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Other metabolites that exhibited an increase in binding affinity towards N501Y variant, compared to the wild-type are chondramides D (4), E2 (5), and A9 (8). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501Y 73 78 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Post-docking analysis of 2 against N501Y variant revealed the presence of a conventional hydrogen bonding between the phenol residue and Gly496 and, a pi-pi stacking between the indole moiety and Tyr501 and Tyr505. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501Y 35 40 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Regarding the E484K variant, the outcome of the docking calculation of 2 showed that this derivative is able to form a strong H-bonds network involving the phenol moiety (against Asn501 and Tyr505) and the ester group (against 453). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K 14 19 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Remarkably, among the mutations in the UK variant, the mutation N501Y within the RBD showed increased binding affinity to human and murine ACE2. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501Y 64 69 RBD 81 84 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Sharing similar E484K mutation with the South African variant, the Brazilian variant may be also associated with antibody escape. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K 16 21 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Similarly, the South African variant is characterized by two additional mutations in the RBD namely N501Y and K417N (Wibmer et al.,). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 K417N;N501Y 110;100 115;105 RBD 89 92 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Similarly, to represent the variants, chondramide C (2) showed selectivity towards spike protein variants (N501Y, -9.1 kcal/mol and E484K, -8.7 kcal/mol) than ACE2. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y 132;107 137;112 S 83 88 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. The same was observed for depsipeptide 1 considering the E484K variant. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K 57 62 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. The swap to a tyrosine residue as in the case of the N501Y variant promoted hydrogen bonding with phenolic moieties and pi-pi stacked interactions with the indole feature of chondramides due to the presence of phenol moiety in tyrosine but absent in asparagine. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501Y 53 58 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. These data support our observation that having a free (no ortho substituent) phenol and/or further oxygenation in the chondramide core may increase binding to certain RBD variants, particularly those with non-conservative mutations like N501Y and E484K where their binding receptor environment is particularly polar. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y 247;237 252;242 RBD 167 170 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. A GH clade strain from May had L lineage associated mutation (Orf1ab L3606F and P323L) in addition to those typical of its clade. 2021 PloS one Result SARS_CoV_2 L3606F;P323L 69;80 75;85 ORF1ab 62 68 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. G clade strains displayed the greatest number of variations with lineage associated variants including nsp3 924F, RdRp P4715L and S D614G. 2021 PloS one Result SARS_CoV_2 D614G;P4715L 132;119 137;125 Nsp3;RdRP;S 103;114;130 107;118;131 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. In N gene, the most frequent ns-SNV were R209I and S194L where in the S-gene the most frequent ns-SNV was D614G (S2 Table). 2021 PloS one Result SARS_CoV_2 D614G;R209I;S194L 106;41;51 111;46;56 N;S 3;70 4;71 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. N gene R209I (20%), Orf1ab; nsp6 L3606F (15%), N geneS194L (15%), Orf1ab; Nsp3 Q2702H (13%), Fig 4. 2021 PloS one Result SARS_CoV_2 L3606F;Q2702H;R209I 33;79;7 39;85;12 ORF1ab;ORF1ab;Nsp3;Nsp6;N;N 20;66;74;28;0;47 26;72;78;32;1;48 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. Of the mutations in Orf1ab, six were associated with evolutionary changes; 8782 (nsp4 2839S), 14408 (RdRp P4715L), 1397 (nsp2 V378I), 3037 (nsp3 924F) and 1059 (nsp3 T265I). 2021 PloS one Result SARS_CoV_2 P4715L;T265I;V378I 106;166;126 112;171;131 ORF1ab;Nsp2;Nsp3;Nsp3;Nsp4;RdRP 20;121;140;161;81;101 26;125;144;165;85;105 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. The most frequent variants were observed at positions 5' UTR; 241C>T (78.8%), S gene D614G (76%) Orf1ab; Nsp3 924F (74%), Orf1ab; RdRp P4715L (72%), Orf3a Q57H (70%), exonuclease 1ab 6205L (51%), M gene 71Y (51%). 2021 PloS one Result SARS_CoV_2 C241T;D614G;P4715L;Q57H 62;85;135;155 68;90;141;159 Exonuclease;5'UTR;ORF1ab;ORF1ab;ORF3a;Nsp3;RdRP;S 167;54;97;122;149;105;130;78 178;60;103;128;154;109;134;79 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. Consistent with the weight loss data, 2C08 treatment reduced viral RNA by more than 10,000-fold in the lungs of the D614G- and B.1.617.2-challenged hamsters (p < 0.001 and p = 0.008, respectively) and by approximately 1,000-fold in those challenged with Wash-B.1.351 (p = 0.008) 4 dpi compared with the isotype control mAb groups (Figure 2B). 2021 Immunity Result SARS_CoV_2 D614G 116 121 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. From a pool of S-binding germinal center B cell-derived mAbs, we selected 13 human anti-RBD mAbs that bound avidly to the historically circulating WA1/2020 D614G SARS-CoV-2 strain referred to hereafter as the D614G strain. 2021 Immunity Result SARS_CoV_2 D614G;D614G 156;209 161;214 RBD;S 88;15 91;16 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. In comparison, the D614G substitution was present in 49% of sequenced isolates (Figure S2C). 2021 Immunity Result SARS_CoV_2 D614G 19 24 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. mAb 2C08 protects hamsters from D614G and variant SARS-CoV-2 challenge. 2021 Immunity Result SARS_CoV_2 D614G 32 37 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. Only five mAbs (2C08, 1H09, 1B12, 2B06, and 3A11) showed high neutralization potency against D614G with 80% neutralization values of less than 100 ng/mL. 2021 Immunity Result SARS_CoV_2 D614G 93 98 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. Prophylactic treatment also significantly reduced infectious virus titers for all strains detected in the lungs 4 dpi (p < 0.001 for D614G, p = 0.008 for both variants) (Figure 2C). 2021 Immunity Result SARS_CoV_2 D614G 133 138 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. Sequence analysis identified the S escape mutations G476D, G476S, G485D, F486P, F486V, and N487D:all of which were within the RBD and mapped to residues involved in hACE2 binding (Figure 3 A). 2021 Immunity Result SARS_CoV_2 F486P;F486V;G476D;G476S;G485D;N487D 73;80;52;59;66;91 78;85;57;64;71;96 RBD;S 126;33 129;34 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. The average weights between the isotype- and 2C08-treated animals differed by 7.1% 3 dpi (p < 0.001) and 10.4% 4 dpi (p < 0.001) for the D614G challenge, by 6.8% 3 dpi (p = 0.095) and 9.1% 4 dpi (p = 0.056) for the Wash-B.1.351 challenge, and by 8.5% 3 dpi (p = 0.008) and 9.7% 4 dpi (p = 0.008) for the B.1.617.2 challenge (Figure 2 A). 2021 Immunity Result SARS_CoV_2 D614G 137 142 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. To define the RBD residues targeted by 2C08, we used VSV-SARS-CoV-2-S chimeric viruses (S from D614G strain) to select for variants that escape 2C08 neutralization as previously described. 2021 Immunity Result SARS_CoV_2 D614G 95 100 RBD;S;S 14;68;88 17;69;89 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. We assessed mAbs binding to recombinant RBDs derived from the D614G strain and four SARS-CoV-2 variants:B.1.1.7 (alpha), B.1.351 (beta), B.1.1.28 (gamma), and B.1.617.2 (delta):by enzyme-linked immunosorbent assay (ELISA). 2021 Immunity Result SARS_CoV_2 D614G 62 67 RBD 40 44 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. We evaluated the prophylactic efficacy of 2C08 against the D614G strain, a fully infectious recombinant chimeric SARS-CoV-2 with the B.1.351 S gene in the WA1/2020 backbone (Wash-B.1.351; D80A, 242-244 deletion, R246I, K417N, E484K, N501Y, D614G and A701V), and the B.1.617.2 strain in 5-to-6-week-old male Syrian hamsters. 2021 Immunity Result SARS_CoV_2 A701V;D614G;D614G;D80A;E484K;K417N;N501Y;R246I 250;59;240;188;226;219;233;212 255;64;245;192;231;224;238;217 S 141 142 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. We next examined the in vitro neutralization capacity of the 13 mAbs against the D614G SARS-CoV-2 strain using a high-throughput focus reduction neutralization test (FRNT) with authentic virus. 2021 Immunity Result SARS_CoV_2 D614G 81 86 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. Mutations detected in the N protein of all samples analyzed were M1X, D3L, R203K, G204R and S235F. 2021 Diagnostic microbiology and infectious disease Result SARS_CoV_2 D3L;G204R;M1X;R203K;S235F 70;82;65;75;92 73;87;68;80;97 N 26 27 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. The N501Y mutation and the H69-V70 deletion were detected in all samples sequenced. 2021 Diagnostic microbiology and infectious disease Result SARS_CoV_2 N501Y 4 9 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. The P151L mutation was detected in only one sample. 2021 Diagnostic microbiology and infectious disease Result SARS_CoV_2 P151L 4 9 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. To analyze agreement between the Allplex and VirSNiP assays, we selected cases with Ct values >35 in the RdRP and S-gene targets and N-gene target failure with the Allplex assay (n = 12); four were negative for N501Y and H69-V70 deletion and 2 were positive only for N501Y. 2021 Diagnostic microbiology and infectious disease Result SARS_CoV_2 N501Y;N501Y 211;267 216;272 RdRP;N;S 105;133;114 109;134;115 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. To confirm the suspected cases of VOC B.1.1.7, the WGS study of 5 randomly selected cases with N501Y and the H69-V70 deletion confirmed that all the sequenced variants were VOC B.1.1.7. 2021 Diagnostic microbiology and infectious disease Result SARS_CoV_2 N501Y 95 100 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Another mutation (nonsynonymous mutation P681H) was observed in the S protein of the B.1.1.7 lineage. 2021 mBio Result SARS_CoV_2 P681H 41 46 S 68 69 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Finally, the D614G mutation was analyzed. 2021 mBio Result SARS_CoV_2 D614G 13 18 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Furthermore, we analyzed the K417N mutation. 2021 mBio Result SARS_CoV_2 K417N 29 34 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Here, the structure of D614G was changed due to the replacement of Asp614 Gly. 2021 mBio Result SARS_CoV_2 D614G;D614G 67;23 77;28 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Here, the structure of E484K changes due to the replacement Glu484 Lys. 2021 mBio Result SARS_CoV_2 E484K;E484K 23;60 28;70 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Here, the structure of K417N is changed due to the replacement Lys417 Asn. 2021 mBio Result SARS_CoV_2 K417N;K417N 23;63 28;73 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Here, the structure of N501Y was altered due to the replacement Asn501 Tyr. 2021 mBio Result SARS_CoV_2 N501Y;N501Y 64;23 74;28 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Simultaneously, it was reported that the mutation D614G can augment the capability to spread compared to the wild type. 2021 mBio Result SARS_CoV_2 D614G 50 55 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Simultaneously, we also analyzed the N501Y mutation. 2021 mBio Result SARS_CoV_2 N501Y 37 42 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Some significant mutations (E484K, K417T/N, N501Y, and D614G) found in emerging variants and their structural landscapes. 2021 mBio Result SARS_CoV_2 D614G;K417N;K417T;N501Y;E484K 55;35;35;44;28 60;42;42;49;33 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. The structural analysis of D614G is shown in different forms, such as interaction abilities of the wild-type residues. 2021 mBio Result SARS_CoV_2 D614G 27 32 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. The structural analysis of E484K is shown in different forms, such as the interaction abilities of the wild-type residues. 2021 mBio Result SARS_CoV_2 E484K 27 32 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. The structural analysis of K417N is shown in different forms, such as interaction abilities of the wild-type residues. 2021 mBio Result SARS_CoV_2 K417N 27 32 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. The structural analysis of K417T is shown in different forms, such as interaction abilities of the wild-type residues. 2021 mBio Result SARS_CoV_2 K417T 27 32 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. The structural analysis of N501Y is shown in different forms, such as interaction abilities of the wild-type residues. 2021 mBio Result SARS_CoV_2 N501Y 27 32 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. These are present in spike receptor binding domain (RBD) (E484K, K417T/N, and N501Y). 2021 mBio Result SARS_CoV_2 K417N;K417T;N501Y;E484K 65;65;78;58 72;72;83;63 RBD;S;RBD 27;21;52 50;26;55 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. We have analyzed the E484K mutation. 2021 mBio Result SARS_CoV_2 E484K 21 26 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. We next analyzed the K417T mutation, and the structure of K417T is altered due to the replacement Lys417 Thr. 2021 mBio Result SARS_CoV_2 K417T;K417T;K417T 21;58;98 26;63;108 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. We performed structural landscape analysis of some significant mutations, such as E484K, K417T/N, N501Y, and D614G, which are frequently reported in emerging variants. 2021 mBio Result SARS_CoV_2 D614G;E484K;K417N;K417T;N501Y 109;82;89;89;98 114;87;96;96;103 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Compared with 11.3 pN force to detach S1/S2 in SARS2-SWT, a much smaller tensile force (~8.2 pN) is required to detach S1 and S2 in SARS2-SD614G. 2021 Cell research Result SARS_CoV_2 D614G 139 144 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Considering that D614G variation makes RBD more flexible and more readily to adopt an up conformation, we hypothesized that D614G mutation might affect force-dependent regulation of the SARS2-S/ACE2 bond lifetime. 2021 Cell research Result SARS_CoV_2 D614G;D614G 17;124 22;129 RBD;S 39;192 42;193 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. D614G mutation was reported to decrease S1/S2 cleavage and increase incorporation of the spike into the pseudo-virion. 2021 Cell research Result SARS_CoV_2 D614G 0 5 S 89 94 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. D614G variation accelerates force-induced S1/S2 detachment. 2021 Cell research Result SARS_CoV_2 D614G 0 5 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. e), suggesting that the D614G variation partially impairs S1/S2 assembly. 2021 Cell research Result SARS_CoV_2 D614G 24 29 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Functionally, the D614G variant exhibits higher pseudovirus (the HIV-based lentivirus pseudotyped with SARS2-S) infectivity to ACE2-expressing cells than WT. 2021 Cell research Result SARS_CoV_2 D614G 18 23 S 109 110 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. However, the authentic virion does not demonstrate these phenotypes, suggesting that the changed level of S1/S2 cleavage or spike incorporation into the virion is not a convincing explanation for the higher infectivity of the D614G mutant. 2021 Cell research Result SARS_CoV_2 D614G 226 231 S 124 129 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. In contrast, SARS2-SWT, SARS2-S1WT, SARS2-S1D614G, and SARS2-RBDWT bind ACE2 with almost the same force-dependent bond lifetimes. 2021 Cell research Result SARS_CoV_2 D614G 44 49 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Indeed, we found that SARS2-SD614G bound ACE2 much more strongly than SARS2-SWT under force with an almost four-time longer optimal lifetime (11.2 s for SARS2-SD614G vs 3.2 s for SARS2-SWT) under the 10 pN optimal force. 2021 Cell research Result SARS_CoV_2 D614G;D614G 29;160 34;165 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Integrating force-dependent spike/ACE2 disassociation and S1/S2 detachment kinetics, we built up a kinetic model and revealed that the D614G variant with stronger force-dependent ACE2 binding not only accelerated S1/S2 detachment but also had an 8-time higher probability than WT to make this detachment occur (0.92 for D614G vs 0.1 for WT at 8.4 pN). 2021 Cell research Result SARS_CoV_2 D614G;D614G 135;320 140;325 S 28 33 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Interestingly, a shorter S1/S2 detaching distance on average (~19.1 nm) was observed for a single SARS2-SD614G. 2021 Cell research Result SARS_CoV_2 D614G 105 110 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Moreover, both SARS2-RBD Q493N and F486L mutations reduce the force-dependent bond lifetime of SARS2-RBD/ACE2 interaction, shortening the maximum bond lifetime almost by two to three folds. 2021 Cell research Result SARS_CoV_2 F486L;Q493N 35;25 40;30 RBD;RBD 21;101 24;104 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Moreover, SARS2-SWT and SARS2-SD614G have comparable binding affinities to ACE2 as both slightly increased and decreased affinities of the mutant to ACE2 were reported. 2021 Cell research Result SARS_CoV_2 D614G 31 36 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. providing an unprecedented quantitative kinetic evidence and molecular mechanism to explain higher infectivity of the D614G variant. 2021 Cell research Result SARS_CoV_2 D614G 118 123 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. SARS2 with spike D614G variation was more epidemic with enhanced replication and transmission than that without this variation. 2021 Cell research Result SARS_CoV_2 D614G 17 22 S 11 16 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Similarly, SARS2-RBD Q493N and F486L mutants, which show similar binding affinities but shorter force-dependent bond lifetimes than WT in the interaction with ACE2. 2021 Cell research Result SARS_CoV_2 F486L;Q493N 31;21 36;26 RBD 17 20 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Simulations on F486L mutant (SARS2-RBDF486L) further reveal unstable SARS2-RBDF486L/ACE2 associations (Supplementary information. 2021 Cell research Result SARS_CoV_2 F486L;F486L 15;78 20;83 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. The D614G variation reduces the number of interdomain hydrogen bonds. 2021 Cell research Result SARS_CoV_2 D614G 4 9 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. These results demonstrate that D614G variation enhances force-dependent SARS2-S recognition of ACE2. 2021 Cell research Result SARS_CoV_2 D614G 31 36 S 78 79 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. These results suggest that S1/S2 subunits in SARS2-SD614G are less mechanically stable than those in SARS2-SWT. 2021 Cell research Result SARS_CoV_2 D614G 52 57 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. This increased infectivity of the D614G variant can be explained by a longer force-dependent bond lifetime of SARS2-SD614G than WT in binding with ACE2, despite their similar in-solution or in-situ binding affinities to ACE2. 2021 Cell research Result SARS_CoV_2 D614G;D614G 34;117 39;122 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. This led us to hypothesize that D614G variation might weaken S1/S2 association. 2021 Cell research Result SARS_CoV_2 D614G 32 37 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. To further test this model, we next focused on examining how a spike mutant with higher viral infectivity (SARS2 spike D614G variant, SARS2-SD614G) is impacted by mechano-regulation. 2021 Cell research Result SARS_CoV_2 D614G 119 124 S;S 63;113 68;118 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. We next performed single-molecule pulling experiments with MT to characterize S1/S2 mechanical stability in the presence of the D614G variation. 2021 Cell research Result SARS_CoV_2 D614G 128 133 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. 3) and also two edit events (non-defining amino acid substitutions): L18F and P812L are required to transform variant V1 into V18. 2021 Meta gene Result SARS_CoV_2 L18F;P812L 69;78 73;83 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Having linked variants V18 and V22 together, as Ward's algorithm applied on Jaccard and Sorensen-Dice did, minimum edit distance equals three, as P812L non-defining substitution and deletion of defining substitutions: P681H, S982A mutually differ V18/V22. 2021 Meta gene Result SARS_CoV_2 P681H;P812L;S982A 218;146;225 223;151;230 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Two edit events: L18F non-defining substitution and deletion of defining S982A substitution are required to transform variant V9 into V22. 2021 Meta gene Result SARS_CoV_2 L18F;S982A 17;73 21;78 34466655 Furin and the adaptive mutation of SARS-COV2: a computational framework. Considering both the D614G mutation and the facilitated action of furin in this process, we assume parameters inclusive of these characteristics. 2021 Modeling earth systems and environment Result SARS_CoV_2 D614G 21 26 34467913 An innovative approach for the non-invasive surveillance of communities and early detection of SARS-CoV-2 via solid waste analysis. Compared to the Wuhan prototype strain, the two isolated strains featured the amino acid substitutions A222V and P521S. 2021 The Science of the total environment Result SARS_CoV_2 A222V;P521S 103;113 108;118 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. Analysis of B.1.1.7 (U.K.) and 501Y.V2.noDelta South Africa; (late November 2020) immediately shows that a large portion of predicted epitopes in the RBD are conserved compared to the reference D614G. 2021 Journal of chemical information and modeling Result SARS_CoV_2 D614G 194 199 RBD 150 153 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. Importantly, mutants N439K, is correctly predicted as an escape variant from all Abs for which experimental data proved lower efficacy. 2021 Journal of chemical information and modeling Result SARS_CoV_2 N439K 21 26 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. In Table 2 and Figure 3 we report such conservation ratios for each D614G S epitope on each simulated variant, and confront them with available experimental data (at the time of writing) on the variant's reactivity towards the Ab that would be expected to bind to that particular epitope. 2021 Journal of chemical information and modeling Result SARS_CoV_2 D614G 68 73 S 74 75 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. On the other hand, the overwhelming majority of cases for which Abs retain activity against a variant (yellow cells) are also confirmed by our prediction to retain their respective epitopes (conservation ratio > 0.5) with respect to D614G S. 2021 Journal of chemical information and modeling Result SARS_CoV_2 D614G 233 238 S 239 240 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. The reference S structure we use here is the dominant D614G variant. 2021 Journal of chemical information and modeling Result SARS_CoV_2 D614G 54 59 S 14 15 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. This is an important validation of our prediction: whenever a variant's predicted epitope residues:that is according to MLCE, contiguous residues uncoupled from the S protein core:shrink in number compared to D614G S, it is very likely that experimental data will also confirm that variant evades Abs binding to the shrunk or lost epitopes. 2021 Journal of chemical information and modeling Result SARS_CoV_2 D614G 209 214 S;S 165;215 166;216 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. Chronic lung disease and the SNV N E253A were significantly associated with symptom duration (multiple regression analysis, P < 0.05, respectively). 2021 GeroScience Result SARS_CoV_2 E253A 35 40 N 33 34 Chronic lung disease 0 20 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. For higher anti-S2 IgG levels, the presence of NSP3 D218E was revealed as the only independent predictor, which is in strong contrast to anti-S1 IgG. 2021 GeroScience Result SARS_CoV_2 D218E 52 57 Nsp3 47 51 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. The absence of the genetic SARS-CoV-2 variant NSP3 D218E was an additional independent predictor for higher anti-S1 IgG levels whereas the absence of chronic liver disease was one for higher anti-S/N IgG levels. 2021 GeroScience Result SARS_CoV_2 D218E 51 56 Nsp3 46 50 Chronic liver disease 150 171 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. The blood group A + was identified as an independent predictor for bronchial secretions and cough whereas the latter demonstrated the SNV ORF3a S177I as an additional independent predictor (P < 0.05, respectively). 2021 GeroScience Result SARS_CoV_2 S177I 144 149 ORF3a 138 143 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. The only other SNV identified as independent was NSP12 Q444H for taste and smell disorders (OR 5.444, P = 0.0426). 2021 GeroScience Result SARS_CoV_2 Q444H 55 60 Nsp12 49 54 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. The variants c.C2772T (ORF1ab F924F), c.C14144T (ORF1ab P4715L), c.A1841G (S D614G), and a transition from C to T in the 5' UTR at position 241 were identified in all 55 samples. 2021 GeroScience Result SARS_CoV_2 D614G;F924F;P4715L;A1841G;C14144T;C2772T 77;30;56;67;40;15 82;35;62;73;47;21 5'UTR;ORF1ab;ORF1ab;S 121;23;49;75 127;29;55;76 34471122 Targeting SARS-CoV-2 receptor-binding domain to cells expressing CD40 improves protection to infection in convalescent macaques. In an in vitro assay using authentic viruses, we confirmed that antibodies raised by the vaccine not only neutralizes the variant containing the D614G present in the alphaCD40.RBD. 2021 Nature communications Result SARS_CoV_2 D614G 145 150 RBD 176 179 34472141 Pseudoephedrine and its derivatives antagonize wild and mutated severe acute respiratory syndrome-CoV-2 viruses through blocking virus invasion and antiinflammatory effect. As shown in Figure 4, sequence alignment revealed that these sequences are highly homologous, and mutations N501Y, E484Q, and L452R were highlighted in red. 2021 Phytotherapy research Result SARS_CoV_2 E484Q;L452R;N501Y 115;126;108 120;131;113 34472141 Pseudoephedrine and its derivatives antagonize wild and mutated severe acute respiratory syndrome-CoV-2 viruses through blocking virus invasion and antiinflammatory effect. Importantly, the highlighted mutated residues N501Y of B.1.1.7, and E484Q and L452R of B.1.617 were also in green, indicating that the built models are reliable. 2021 Phytotherapy research Result SARS_CoV_2 E484Q;L452R;N501Y 68;78;46 73;83;51 34472141 Pseudoephedrine and its derivatives antagonize wild and mutated severe acute respiratory syndrome-CoV-2 viruses through blocking virus invasion and antiinflammatory effect. In addition, mutated amino acid residues such as N501Y, E484Q, L452R, K417N, and E484K seldom perform interactions with the two active compounds (only mutated amino acid Tyr501 of variety B.1.351 has interactions with MHJ-11 and MHJ-17, Figure 7e,f). 2021 Phytotherapy research Result SARS_CoV_2 E484K;E484Q;K417N;L452R;N501Y 81;56;70;63;49 86;61;75;68;54 34472141 Pseudoephedrine and its derivatives antagonize wild and mutated severe acute respiratory syndrome-CoV-2 viruses through blocking virus invasion and antiinflammatory effect. SARS-CoV-2 lineage B.1.1.7 has a mutation called N501Y, and lineage B.1.617 is used to refer to two mutations in S protein at the positions E484Q and L452R. 2021 Phytotherapy research Result SARS_CoV_2 E484Q;L452R;N501Y 140;150;49 145;155;54 S 113 114 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. 1E), a similar enhancement was observed with both the N501Y mutant and the B.1.1.7 variant at low temperatures. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 54 59 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. Altogether, this indicates that low temperatures or the N501Y mutation confers analogous affinity changes that are favorable for Spike RBD-ACE2 interaction. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 56 61 S;RBD 129;135 134;138 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. Compared with ACE2 binding to RBD WT, the increase in binding affinity upon a drop in temperature is larger for the N501Y mutant with the KD changing from 6.9 nM at 35C to 1 nM at 15C. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 116 121 RBD 30 33 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. Compared with its WT counterpart, introduction of the N501Y mutation significantly decreased the off rate resulting in a 4.6-fold increase in KD when performed at 25C. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 54 59 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. Furthermore, as expected, the binding affinity of sACE2 to RBD N501Y was at least 6-fold higher than to RBD WT. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 63 68 RBD;RBD 59;104 62;107 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. Importantly, ACE2 bound to the B.1.1.7 Spike about two times more than to the D614G Spike at 37C. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 78 83 S;S 39;84 44;89 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. In 2021 sequences, most residues were still found to be >99% conserved except for variations found at residues 417 (K417N, 1.5%; K417T, 2.6%) and 501 (N501Y, 65.2%), with the latter becoming predominant among all the deposited sequences in 2021. 2021 The Journal of biological chemistry Result SARS_CoV_2 K417T;K417N;N501Y 129;116;151 134;121;156 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. In agreement with a better affinity for ACE2 at lower temperatures, more SARS-CoV-2 D614G pseudoviral particles were captured at 4C compared with 37C. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 84 89 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. In agreement with results from transfected cells, the binding of ACE2 to cell surface Spike was higher at cold temperature (4C) compared with 37C for both D614G- and B.1.1.7-infected cells. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 155 160 S 86 91 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. In line with these results, we also observed enhanced infectivity and cell-to-cell fusion mediated by SARS-CoV-2 Spike D614G at 4C compared with 37C, while a marginal increase was seen with an unrelated viral glycoprotein (VSV-G). 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 119 124 S 113 118 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. Over the 2019 to 2020 period, no major sequence variations were observed except for the N501Y mutation (4.4%), which started to arise at the end of the year in at least three independent lineages of interest (B.1.1.7, B.1.351, P.1). 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 88 93 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. Remarkably, RBD WT reached a similar affinity for sACE2 at 10C than the one achieved by RBD N501Y at 25C. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 92 97 RBD;RBD 12;88 15;91 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. S1), notably mutations L452R (8.8%), E484K (7.7%), T478K (5.9%), S477N (2.2%), and N439K (1.2%), which are also found in other various VOCs and were shown to either increase infectivity or promote the evasion of antibody responses. 2021 The Journal of biological chemistry Result SARS_CoV_2 E484K;L452R;N439K;S477N;T478K 37;23;83;65;51 42;28;88;70;56 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. Similar effects of temperature on Spike-mediated attachment and fusion and on sensitivity to sACE2 neutralization were observed when using the Spike N501Y mutant or B.1.1.7 variant. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 149 154 S;S 34;143 39;148 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. Similar level of binding could only be achieved for the D614G Spike by decreasing the temperature to 4C. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 56 61 S 62 67 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. Similarly, the capacity of soluble ACE2 (sACE2) to neutralize pseudovirions bearing SARS-CoV-2 Spike D614G was significantly improved when preincubating the virus with sACE2 at 4C when compared with 37C prior infection of 293T-ACE2 target cells. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 101 106 S 95 100 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. Since temperature was suggested to also affect Spike stability, which in turn could explain its decreased receptor binding at 37C, we introduced the D614G change, known to increase trimer stability in combination or not with furin cleavage site mutations (FKO), known to prevent Spike proteolytic cleavage. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 149 154 S;S 47;279 52;284 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. The KD value for the N501Y mutant is 2.9 nM at 25C and the respective values for the enthalpy and entropy contributions are -16.6 and 4.9 kcal/mol. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 21 26 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. The N501Y mutation is located at the RBD-ACE2 interface and has been previously shown to strengthen the interaction with ACE2 by inserting an aromatic ring into a cavity at the binding interface. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 4 9 RBD 37 40 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. These mutations are found in emergent variants of concern (VOCs), including the B.1.1.7 (N501Y), B.1.351 (K417N/N501Y), and P.1 lineages (K417T/N501Y). 2021 The Journal of biological chemistry Result SARS_CoV_2 K417N;K417T;N501Y;N501Y;N501Y 106;138;89;112;144 111;143;94;117;149 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. This lineage spread rapidly and is the major circulating strain in early 2021 worldwide, replacing the D614G strain, which was predominant in 2019 to 2020. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 103 108 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. To analyze the impact of temperature on viral replication in a more physiological model, we used authentic SARS-CoV-2 D614G viruses to infect reconstituted primary human airway epithelia (MucilAir). 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 118 123 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. To confirm our observations in a more physiological model, we infected a highly permissive cell line (Vero E6) and primary airway epithelial cells (AECs) from two different healthy donors using authentic SARS-CoV-2 virus isolated from patients infected with SARS-CoV-2 D614G or B.1.1.7. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 269 274 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. To extend these results to the Spike of emergent circulating strains, we evaluated ACE2-Fc binding to the Spike N501Y mutant and the Spike from the B.1.1.7 lineage. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 112 117 S;S;S 31;106;133 36;111;138 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. We observed that the binding cooperativity of ACE2 to Spike D614G was slightly negative at 37C (h = 0.816), while being neutral at 4C (h = 1.004). 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 60 65 S 54 59 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. A475V, p = 0.0625; Wuhan reference vs. 2021 Frontiers in immunology Result SARS_CoV_2 A475V 0 5 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. D614G, p = 0.0625). 2021 Frontiers in immunology Result SARS_CoV_2 D614G 0 5 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. E484Q, p = 0.1250; and Wuhan reference vs. 2021 Frontiers in immunology Result SARS_CoV_2 E484Q 0 5 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. It is notable that antibody B38 was unable to effectively neutralize A475V variant pseudovirus (Figure 6D) while the neutralizing activity of antibody 2-4 against E484Q variant pseudovirus was also decreased nearly 1,000-fold (Figure 6E). 2021 Frontiers in immunology Result SARS_CoV_2 A475V;E484Q 69;163 74;168 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. Neutralization Analysis of RBD-Specific mAbs Against A475V and E484Q Variant Pseudoviruses. 2021 Frontiers in immunology Result SARS_CoV_2 A475V;E484Q 53;63 58;68 RBD 27 30 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. The neutralization curves of three RBD-specific mAbs (CC12.1, 2-4, and B38) against the Wuhan reference pseudovirus, A475V and E484Q variant pseudoviruses are respectively shown in Figures 6A-C, respectively. 2021 Frontiers in immunology Result SARS_CoV_2 A475V;E484Q 117;127 122;132 RBD 35 38 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. The results of the relative neutralizing activity analysis suggested that A475V and E484Q might decrease the sensitivity of the variant to the polyclonal antibodies from the convalescent plasma. 2021 Frontiers in immunology Result SARS_CoV_2 A475V;E484Q 74;84 79;89 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. Three variant pseudoviruses with a single amino acid mutation including A475V, E484Q, and D614G consistently altered the neutralization sensitivity to the five convalescent plasma samples. 2021 Frontiers in immunology Result SARS_CoV_2 A475V;D614G;E484Q 72;90;79 77;95;84 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. We found that CC12.1 was effective in neutralizing both A475V and E484Q variant pseudoviruses. 2021 Frontiers in immunology Result SARS_CoV_2 A475V;E484Q 56;66 61;71 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. When compared with the Wuhan reference pseudovirus (GMT = 579.4), paired neutralization analysis showed that the convalescent plasma reduced the neutralizing activity against A475V (GMT = 341.5, Figure 5B) and E484Q (GMT = 405.6, Figure 5C) variants but increased the neutralizing activity against the D614G variant (GMT = 2,017.0, Figure 5D). 2021 Frontiers in immunology Result SARS_CoV_2 A475V;D614G;E484Q 175;302;210 180;307;215 34492088 Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination. One more amino-acid substitution, the S-A879S was present only in the strains of Farm A, whereas S-V227L and S-P812L, were present in farm B (Table 1). 2021 PLoS pathogens Result SARS_CoV_2 A879S;P812L;V227L 40;111;99 45;116;104 S;S;S 38;97;109 39;98;110 34492088 Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination. The mink specific S protein amino-acid substitution (Y453F) was present in all the sequenced genomes (S1A Fig), as well as the ubiquitous European S-D614G substitution (Table 1). 2021 PLoS pathogens Result SARS_CoV_2 Y453F;D614G 53;149 58;154 S;S 18;147 19;148 34493762 Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. 2b (I33T), c (A222V), and d (P67S)). 2021 Scientific reports Result SARS_CoV_2 A222V;I33T;P67S 14;4;29 19;8;33 34493762 Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. D614G in the first group. 2021 Scientific reports Result SARS_CoV_2 D614G 0 5 34493762 Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. Delta69-70, N501Y, and E484K, all present in the second group. 2021 Scientific reports Result SARS_CoV_2 E484K;N501Y 23;12 28;17 34493762 Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. In our previous work, we observed that the mutation T85I in nsp2 has a higher frequency in North America than in other continents. 2021 Scientific reports Result SARS_CoV_2 T85I 52 56 Nsp2 60 64 34493762 Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. K997Q on nsp3 and S202C on N protein). 2021 Scientific reports Result SARS_CoV_2 S202C;K997Q 18;0 23;5 Nsp3;N 9;27 13;28 34493762 Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. This explains why this mutation did not increases its frequency steadily and can be an evidence of constant competition between MFR203K and not-MFR203K. 2021 Scientific reports Result SARS_CoV_2 R203K 146 151 34493762 Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. To test these hypotheses, we analyzed whether different degree of control measures could affect differently to SARS-CoV-2 genomes bearing the HF mutation N501Y (HFN501Y) or not bearing the HF mutation N501Y (not-HFN501Y) in nine countries that have more than 15 sequenced genomes per week during March 2020 to April 2021. 2021 Scientific reports Result SARS_CoV_2 N501Y;N501Y;N501Y 154;201;214 159;206;219 34495697 A Bifluorescent-Based Assay for the Identification of Neutralizing Antibodies against SARS-CoV-2 Variants of Concern In Vitro and In Vivo. Towards this objective, we generated an rSARS-CoV-2 containing the K417N, E484K, and N501Y mutations found in the S RBD of the SA strain of SARS-CoV-2 and expressing also mCherry, referred to as rSARS-CoV-2 mCherry SA. 2021 Journal of virology Result SARS_CoV_2 E484K;K417N;N501Y 74;67;85 79;72;90 RBD;S 116;114 119;115 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. D614G mutation or cytoplasmic tail truncation does not alter Spike protein sensitivity to convalescent serum. 2021 Journal of virology Result SARS_CoV_2 D614G 0 5 S 61 66 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. Effects were also observed using Spike protein pseudoviruses, where the D614G mutation increased Spike incorporation into vector particles, despite minimal or no effect on Spike expression in vector-producing cells, and increased transduction rates on various cell lines. 2021 Journal of virology Result SARS_CoV_2 D614G 72 77 S;S;S 33;97;172 38;102;177 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. Furthermore, it is likely that an upper limit for these effects reduces the impact of the D614G mutation when combined with a tail truncation. 2021 Journal of virology Result SARS_CoV_2 D614G 90 95 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. In parallel, in vitro studies have shown that D614G enhances replication of the virus on human lung epithelial cells and primary airway tissue and increases replication or transmissibility in human ACE2 transgenic mice and hamster models. 2021 Journal of virology Result SARS_CoV_2 D614G 46 51 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. In sum, these observations suggest that a primary effect of both the tail truncation and the D614G mutation is on Spike protein incorporation, which in turn leads to enhanced titers, at least on cells with high enough levels of ACE2. 2021 Journal of virology Result SARS_CoV_2 D614G 93 98 S 114 119 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. Instead, in agreement with previous studies using full-length Spike-pseudotyped RV and LV vectors, we found that the D614G mutation enhanced Spike incorporation, albeit with a much larger effect for the full-length Spike versus the truncated protein (~9-fold versus ~2-fold effect). 2021 Journal of virology Result SARS_CoV_2 D614G 117 122 S;S;S 62;141;215 67;146;220 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. Since we had noted that cytoplasmic tail truncation of Spike protein had effects similar to those of the D614G mutation and increased incorporation rates and transduction efficiencies. 2021 Journal of virology Result SARS_CoV_2 D614G 105 110 S 55 60 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. This suggests that neither the D614G mutation nor the cytoplasmic tail truncation alters the sensitivity of the Spike protein to neutralization. 2021 Journal of virology Result SARS_CoV_2 D614G 31 36 S 112 117 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. We examined whether the D614G mutation or the cytoplasmic tail truncation altered sensitivity to neutralization by a panel of convalescent sera. 2021 Journal of virology Result SARS_CoV_2 D614G 24 29 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. we next examined the impact of the D614G mutation in the context of both full-length and truncated Spike proteins. 2021 Journal of virology Result SARS_CoV_2 D614G 35 40 S 99 104 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. We used the VSV pseudovirus system to examine the impact of the D614G mutation of Spike protein. 2021 Journal of virology Result SARS_CoV_2 D614G 64 69 S 82 87 34495709 Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. Among the common substitutions present in these lineages, four occurred in the spike protein (S494P, D614G, P681H, and T716I). 2021 Journal of clinical microbiology Result SARS_CoV_2 D614G;P681H;T716I;S494P 101;108;119;94 106;113;124;99 S 79 84 34495709 Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. Between week 20 and week 26 of 2021, we identified 194 cases with lineage B.1.575, which had acquired another S mutation, E484K, classified in the GISAID EpiCoV and Pangolin databases as representing sublineage B.1.575.2. 2021 Journal of clinical microbiology Result SARS_CoV_2 E484K 122 127 S 110 111 34495709 Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. In contrast, we did not identify any genomes of the B.1.575 or B.1.575.1 lineage carrying the E484K mutation. 2021 Journal of clinical microbiology Result SARS_CoV_2 E484K 94 99 34495709 Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. In the TaqMan assay, all samples identified by sequencing as B.1.575.2 showed the E484K mutation. 2021 Journal of clinical microbiology Result SARS_CoV_2 E484K 82 87 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). A surface plasmon resonance study showed that the N501Y mutation had a faster association rate and slower dissociation constant (Kd) upon binding to ACE2 (Tian et al.,). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501Y 50 55 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Another remarkable point is that in our analysis, the N501Y, E484K, and spike triple mutants have been found to have significantly larger numbers of amino acid residues in the spike RBD/ACE2 binding interface: 66, 57 and 62, respectively (Table 2). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y 61;54 66;59 S;S;RBD 72;176;182 77;181;185 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). As can be seen in Figures 2c and 5c and Figure S2c (supplementary file) and supported by MM-PBSA results (Table 4), we also found that the triple mutated spike protein is strongly bent (although in a different way compared to the E484K mutant, as seen in supplementary file Figure S2c) yielding significant conformational changes relative to the wild-type. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K 230 235 S 154 159 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). As can be seen in our study, the spike protein carrying the E484K mutation binds to ACE2 in a slightly different conformation compared to the wild-type (Figure 2a). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K 60 65 S 33 38 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Based on the interface analysis we performed using EMBL-EBI PDBePISA web server (Krissinel & Henrick,) and DS Visualizer v16, the interface areas of the spike (N501Y)-ACE2, spike (E484K)-ACE2, and spike (K417N + E484K + N501Y)-ACE2 complexes were found to be 1027.3 A2, 968.8 A2 and 1026 A2, respectively, whereas this value was 901.6 A2 for the wild-type spike-ACE2 complex (Table 2). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y;E484K;K417N;N501Y 212;220;180;204;160 217;225;185;209;165 S;S;S;S 153;173;197;356 158;178;202;361 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Besides, a slight enhanced mobility relative to the native spike was found in the spike residues 448, 460-470 and 481 in the case of N501Y mutation, in the residue 477 in the E484K mutation and in the residues 480 and 385-390 in the case of the triple mutation. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y 175;133 180;138 S;S 59;82 64;87 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Consistent with our results, it has been reported that the N501Y mutation increases the hydrophobic interactions between RBD and ACE2, while decreasing the hydrophilic repulsion, thereby increasing the transmissibility of the infection (Li et al.,). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501Y 59 64 RBD 121 124 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Despite the apparently weaker hydrogen bond network, the system with the N501Y mutation showed a more negative free energy of binding than the wild-type system. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501Y 73 78 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). However, the overall interaction pattern of N501Y with ACE2 did not differ greatly from that of the wild-type spike/ACE2 complex (Figure 5b and supplementary file Figure S2a), and it was suggested that this mutation would not pose a significant disadvantage to the vaccine efficacy (Zhang et al.,). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501Y 44 49 S 110 115 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). In addition, two novel electrostatic interactions occurred between Lys458 and Glu484 residues of the N501Y mutant and Glu23 and Lys31 of ACE2, two of which were absent in the wild-type mutant (supplementary file Tables S1 and S2). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501Y 101 106 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). In line with our views on the induced conformational change in the spike RBD, it has been reported that the E484K mutation reduces or completely abolishes the neutralizing antibody response in convalescent serums, and also weakens the binding of serum polyclonal antibodies to the receptor binding domain (RBD) of the spike glycoprotein (Ferrareze et al.,; Jangra et al.,; Wang et al.,; Wise,; Xie et al.,). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K 108 113 RBD;S;S;RBD;RBD 281;318;67;73;306 304;336;72;76;309 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). In our protein-protein docking analysis, the spike N501Y showed a significantly higher binding capacity to the ACE2 receptor compared to the wild-type (Table 1). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501Y 51 56 S 45 50 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). In our study, the spike triple variant (K417N + E484K + N501Y) also showed a significantly more favorable binding affinity to the ACE2 than the wild-type (Table 1) and caused some conformational changes in the spike protein (Figure 2c). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y;K417N 48;56;40 53;61;45 S;S 18;210 23;215 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). In particular, novel electrostatic interactions (Glu23-Lys458, and Lys31-Glu484 for N501Y; Glu35-Lys484 for E484K) were observed in docking simulations of spike mutants N501Y and E484K (supplementary file Table S1). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;E484K;N501Y;N501Y 108;179;84;169 113;184;89;174 S 155 160 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). In Spike South Africa triple mutant (K417N + E484K + N501Y), Asn417 and Lys484 did not appear to undergo any bond formation reaction with ACE2, while Tyr501 formed a hydrogen bond contact with Lys353 of ACE2. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y;K417N 45;53;37 50;58;42 S 3 8 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). In the E484K mutant, Lys484 interacted with Glu35 of ACE2 via a salt bridge interaction, whereas in wild-type spike, Glu484 interacted with Lys31 of ACE2 via a carbon-hydrogen bond. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K 7 12 S 110 115 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Indeed, by following the distances between chosen pairs of residues we could show that the pattern of neighboring residues along the simulation of the N501Y mutated system does not differ substantially from the wild spike one (supplementary file Figures S3-S9). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501Y 151 156 S 216 221 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). It has also been reported in other MD simulations that this mutant combination, compared with E484K or N501Y, maximally induces conformational changes when bound to ACE2, resulting in novel contacts between RBD and ACE2, and leading to a viral 'escape' conformation (Franceschi, Ferrareze et al.,; Nelson et al.,). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y 94;103 99;108 RBD 207 210 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). It is clear from the heatmap that mutations N501Y and E484K (except the South Africa triple mutant) resulted in an increase in the frequency of novel contacts between spike protein and ACE2 compared to the wild-type spike. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y 54;44 59;49 S;S 167;216 172;221 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). It is clear that the interface area of the multiple mutant is higher than of the other complexes, but the interface area of the E484K mutant is also somewhat higher than the wild-type, whereas the interface area of the N501Y mutant is almost the same as the wild-type complex. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y 128;219 133;224 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Lys417 of E484K also formed a novel electrostatic interaction with Asp30 of the ACE2 receptor (supplementary file Tables S1 and S2). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K 10 15 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). The binding affinity (kcal/mol) and dissociation constant (Kd, in molar) values obtained from the PRODIGY web server were found as -10.7 and 1.4 x 10-8 for wild-type (control) spike-ACE2, -13.3 and 1.7 x 10 -10 for spike (N501Y)-ACE2, -12.9 and 3.4 x 10 -10 for spike (E484K)-ACE2, and -12.4 and 7.6 x 10-10 for spike South Africa triple mutant (K417N + E484K + N501Y)- ACE2 complex. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y;E484K;K417N;N501Y 354;362;269;346;222 359;367;274;351;227 S;S;S;S 176;215;262;312 181;220;267;317 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). The comparison of the conformations of the wild-type spike-ACE2 complex with the E484K mutated spike-ACE2 complex (Figure 5a) shows clearly a conformational transition, where the spike protein is bent toward one of the ACE2 helices (residues 549-560). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K 81 86 S;S;S 53;95;179 58;100;184 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). The conversion of negatively charged Glu484 to positively charged Lys484 in the E484K mutant, which we found to be the most stable complex according to the results of MM-PBSA analysis, has also been shown in another study to have profound effects on a highly flexible loop in the RBD (Franceschi, Caldana et al.,; Nelson et al.,). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K 80 85 RBD 280 283 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). The increase on the magnitude of the total interface area (A2) and in the number of amino acids at the interface and the increase of non-covalent salt bridges and H-bond interactions indicate that the variants of E484K, N501Y and South Africa triple strains induce conformational changes in the spike RBD (Figure 2) and may explain why these 'variants of concern' have increased infectious ability. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y 213;220 218;225 S;RBD 295;301 300;304 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). The increased number of chemical contacts (supplementary file Figure S1) shows that the N501Y and E484K mutations cause conformational changes in the spike glycoprotein's receptor binding domain (RBD) which interacts with ACE2, resulting in an increased interface surface area. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y 98;88 103;93 RBD;S;RBD 171;150;196 194;168;199 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). The mutation in the residue 501 (Asn to Tyr, both polar non-charged residues) also contributes to the stabilization of the complex, but much less than the E484K mutation. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501Y;E484K 28;155 42;160 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). The spike triple mutant (K417N + E484K + N501Y) we analyzed in our study showed significantly higher binding free energy than wild-type in molecular dynamics simulations and MM-PBSA analysis (Table 4). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y;K417N 33;41;25 38;46;30 S 4 9 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). The strongest interaction, however, was found for the system with the mutation E484K, where the binding free energy was remarkably stronger than in the wild-type. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K 79 84 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). The system with three mutations (K417N + E484K + N501Y) showed roughly the same number of hydrogen bonds: 7.87 +- 2.82, whereas the N501Y mutation system displayed a smaller number of hydrogen bonds (6.05 +- 2.00) and the E484K mutation system displayed the largest number of hydrogen bonds: 9.81 +- 2.64 (Table 3). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;E484K;N501Y;N501Y;K417N 41;222;49;132;33 46;227;54;137;38 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Therefore, considering the Kd, the N501Y mutant binds ACE2 82-fold stronger, the spike E484K mutant binds ACE2 41-fold stronger, and the South African triple mutant (K417N + E484K + N501Y) binds ACE2 18-fold stronger than the wild-type spike protein. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;E484K;N501Y;N501Y;K417N 87;174;35;182;166 92;179;40;187;171 S;S 81;236 86;241 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Therefore, the most stable mutant complexes in our study can be ranked as: E484K > South Africa triple (K417N + E484K + N501Y) > N501Y. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;E484K;N501Y;N501Y;K417N 75;112;120;129;104 80;117;125;134;109 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). These were 20, 18 and 11 for the N501Y, E484K and South Africa triple mutant, respectively (Table 2). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y 40;33 45;38 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Thus, the mutations N501Y, E484K and South Africa triple (K417N + E484K + N501Y) greatly increase the strength of spike/ACE2 intermolecular interactions. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;E484K;N501Y;N501Y;K417N 27;66;20;74;58 32;71;25;79;63 S 114 119 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). When the residues interacting with ACE2 are compared, it was revealed that only 38% of the contacting residues in the N501Y mutant, 45% in the E484K mutant and 30% in the triple mutant resemble the contacting residues of the wild-type spike (supplementary file Table S2). 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 E484K;N501Y 143;118 148;123 S 235 240 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). While Tyr501 in N501Y mutant forms one hydrogen bond with Thr324 and Lys353 of ACE2, Asn501 does not appear to interact with ACE2 in the wild-type spike protein. 2021 Journal of biomolecular structure & dynamics Result SARS_CoV_2 N501Y 16 21 S 147 152 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. In addition, the fluctuation in the mutant residues was not high in the case of Kappa, although, it was found that residue Val445 had more fluctuations than the WT and N501Y mutants (Figure 2B). 2021 International journal of molecular sciences Result SARS_CoV_2 N501Y 168 173 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. It was observed that there was an increase in intra-chain interaction Spike protein due to mutation of E484Q. 2021 International journal of molecular sciences Result SARS_CoV_2 E484Q 103 108 S 70 75 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. While the Delta and Kappa mutations were found to be stabilizing the spike protein, but not N501Y of Alpha, increase/change in the intrachain interaction in the spike protein was observed in all the studied variants. 2021 International journal of molecular sciences Result SARS_CoV_2 N501Y 92 97 S;S 69;161 74;166 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. 3b, the clades 19A and 20A/S.Q675H were clustering (cluster A) far in terms of linkage from clades 20A and its subclades clusters (cluster B, C and D). 2021 Biochimie Result SARS_CoV_2 Q675H 29 34 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. 4 and Tables 4 and 5 The summary of our superimposition results includes that the following we-named first group of variants; 20A/S.A262S, 20A/S.L452R, 20A/S.N501T, 20A/S.N501Y, 20A/S.P681H, 20A/S.P681R, 20A/S.V1176F, 20A/S.N439K, 20A/S.S98F, 20A/S.L5F, 20A/S.P272L, 20A/S.D1163Y, 20A/S.N439K, 20A/S.S98F, 20A/S.L5F, 20A/S.P272L, 20A/S.D1163Y and 20A/S.G1167V have no structural superimposition changes at all, which means red structures were only apparent; this is in agreement with DynaMut results for variants stabilizing the spike protein structure. 2021 Biochimie Result SARS_CoV_2 A262S;D1163Y;D1163Y;G1167V;L452R;L5F;L5F;N439K;N439K;N501T;N501Y;P272L;P272L;P681H;P681R;S98F;S98F;V1176F 132;273;336;353;145;249;312;224;287;158;171;260;323;184;197;237;300;210 137;279;342;359;150;252;315;229;292;163;176;265;328;189;202;241;304;216 S 529 534 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. Discussing E484K has led us to compare it with E484Q, which has lost interatomic interactions with Y489 and F490 without gaining interatomic interactions with F486, which might explain the higher negative (destabilizing) value of DynaMut DeltaDeltaG equal to -0.187 kcal/mol and -0.488 kcal/mol respectively. 2021 Biochimie Result SARS_CoV_2 E484K;E484Q 11;47 16;52 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. For example, E484K has lost interatomic interactions with Y489 and F490 but gained interatomic interactions with F486, as shown in Table 2. 2021 Biochimie Result SARS_CoV_2 E484K 13 18 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. For example, E484K or E484Q is situated in the amino sequence C480-NGVEGFN-C488. 2021 Biochimie Result SARS_CoV_2 E484K;E484Q 13;22 18;27 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. However, some other variants have destabilized the protein with increased flexibility (e.g., E484K, K417 N, E484Q, Q675P, G1167V, E583D and Q675H). 2021 Biochimie Result SARS_CoV_2 E484K;E484Q;E583D;G1167V;K417N;Q675H;Q675P 93;108;130;122;100;140;115 98;113;135;128;106;145;120 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. Interestingly, the results of the NMA analysis revealed that some variants are stabilizing but with increased protein flexibility (e.g., D080A, A701V and D614G). 2021 Biochimie Result SARS_CoV_2 A701V;D614G 144;154 149;159 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. It is important that Q675H had the highest negative (destabilizing) value of DynaMut DeltaDeltaG with -0.621 kcal/mol, and Q677H had the highest (stabilizing) value of DynaMut DeltaDeltaG with 2.661 kcal/mol. 2021 Biochimie Result SARS_CoV_2 Q675H;Q677H 21;123 26;128 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. On the other hand, only 10 variants have destabilized the spike protein (e.g., E484K, K417 N, V1176F, E484Q, Q675P, G1167V, E553D, L5F, Y453F and Q675H) meanwhile, 18 variants (e.g., A262S, D080A, Q677P, N501T, A701V, Q677H, L452R, N501Y, D614G, P681R, L18F, S98F, A222V, P272L, N439K, S477 N, D1163Y and P681H) showed stabilizing tendency. 2021 Biochimie Result SARS_CoV_2 A222V;A262S;A701V;D1163Y;D614G;E484K;E484Q;E553D;G1167V;K417N;L18F;L452R;L5F;N439K;N501T;N501Y;P272L;P681H;P681R;Q675H;Q675P;Q677H;Q677P;S477N;S98F;V1176F;Y453F 265;183;211;294;239;79;102;124;116;86;253;225;131;279;204;232;272;305;246;146;109;218;197;286;259;94;136 270;188;216;300;244;84;107;129;122;92;257;230;134;284;209;237;277;310;251;151;114;223;202;292;263;100;141 S 58 63 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. Other examples include the sites of N439K, Y453F, S477 N, N501Y or N501T, and L452R; the variants located in the amino sequence between C391with C525 the disulphide partners with Sss score of -2.653 where the amino acid substitution in these two locations are expected to decrease the spike protein thermodynamic flexibility as shown in the DynaMut results in Table 2. 2021 Biochimie Result SARS_CoV_2 L452R;N439K;N501T;N501Y;S477N;Y453F 78;36;67;58;50;43 83;41;72;63;56;48 S;N 285;55 290;56 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The A20/S.Q677P has changed a Furin region to a small Beta sheet. 2021 Biochimie Result SARS_CoV_2 Q677P 10 15 S 8 9 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The comparison among the clade 20A and its derived subclades variants and the following 10 clades variants; B.1.1.7 (20I/501Y.V1) or Alpha, B.1.351 (20H/501Y.V2) or Beta, P.1 (20J/501Y.V3) or Gamma, B.1.617.2 (21A/478K.V1) or Delta, B.1.429 (21C/452R) or Epsilon, B.1.526 (21F/253G.V1) or Iota, in the presence of D614G in all of them, in addition to clade 19A, showed high structural similarity neighbourhood's near each other except for clade 19A and 20A/S.Q675H . 2021 Biochimie Result SARS_CoV_2 D614G;Q675H 314;459 319;464 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The DynaMut results showed that D614G and the Q675P had decreased the spike protein stability. 2021 Biochimie Result SARS_CoV_2 D614G;Q675P 32;46 37;51 S 70 75 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The fifth group of variants with located superimposition change, up to 5 A in the RBD, included the following variants: the 20A/S.D80A, 20A/S.A222V, 20A/S.K417 N, 20A/S.477 N, A20/S E484K, A20/S E484Q, 20A/S.Y453F and 20A/S.E583D have changed a Furin region to an Alpha helix structure. 2021 Biochimie Result SARS_CoV_2 E484K;E484Q;A222V;D80A;E583D;Y453F 182;195;142;130;224;208 187;200;147;134;229;213 RBD 82 85 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The outcome of SuperPose v 1.0 with 3D visualization for the spike protein D614G variant of the clade 20A versus the clade 19A is shown in. 2021 Biochimie Result SARS_CoV_2 D614G 75 80 S 61 66 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The results of normal mode analysis (NMA) by DynaMut shown in Table 2 for the predicted thermodynamic effect of studied variants on the stability and flexibility of the spike protein of SARS-CoV-2 has revealed that out of 28 studied variants, 10 variants increased the protein flexibility (e.g., E484K, D080A, K417 N, A701V, E484Q, D614G, Q675P, E583D, G1167V and Q675H) meanwhile 18 variants decreased the protein flexibility (e.g., A262S, Q677P, N501T, Q677H, L452R, V1176F, N501Y, P681R, L5F, L18F, S98F, A222V, P272L, N439K, Y483F, S477 N, D1163Y and P681H). 2021 Biochimie Result SARS_CoV_2 A222V;A262S;A701V;D1163Y;D614G;E484K;E484Q;E583D;G1167V;K417N;L18F;L452R;L5F;N439K;N501T;N501Y;P272L;P681H;P681R;Q675H;Q675P;Q677H;Q677P;S477N;S98F;V1176F;Y483F 508;434;318;544;332;296;325;346;353;310;496;462;491;522;448;477;515;555;484;364;339;455;441;536;502;469;529 513;439;323;550;337;301;330;351;359;316;500;467;494;527;453;482;520;560;489;369;344;460;446;542;506;475;534 S 169 174 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The second group of variants with enormous superimposition changes with more than 12 A for amino acids along the spike protein sequence included 20A versus 19A on the one hand and the 20A/S.Q675H versus 20A on the other hand. 2021 Biochimie Result SARS_CoV_2 Q675H 190 195 S 113 118 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The third group of variants with located superimposition change up to 12 A for many structural regions included the following variants; 20A/S.L18F and B.1.429 (21C/452R at the Furin cleavage, which both hidden a Furin region. 2021 Biochimie Result SARS_CoV_2 L18F 142 146 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. This had led us to consider the clade 20A with D614G to be as a new reference structure instead of the clade 19A when we carried out superimposition structure analysis with Template Modeling score (TM-score) since the global percentage of the D614G is 98% as shown in Table 2 (data on 08-08-2021). 2021 Biochimie Result SARS_CoV_2 D614G;D614G 47;243 52;248 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. Among the 17 sites, 11 caused amino acid changes, of which 5 mutation sites were located on the S protein (including N501Y, P681H, T716I, S982A, and D1118H) (Table 3). 2021 Computational and structural biotechnology journal Result SARS_CoV_2 D1118H;N501Y;P681H;S982A;T716I 149;117;124;138;131 155;122;129;143;136 S 96 97 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. Among them, 8 specific mutations were missense mutation, including 83L>V (T350G) on the E6 gene, 219P>S (C3409T) on the E2 gene, 39I>L (A3977C) and 60I>V (A4040G) on the E5 gene, 43E>D (A4363T) and 330L>F (A5224C) on the L2 gene, 228H>D (C6240G) and 292 T>A (A6432G) on the L1 gene. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 E43D;H228D;I39L;L330F;P219S;T292A 179;230;129;198;97;250 184;236;134;204;103;257 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. For the UK, the 5 of 6 haplotypes (including H1-1-1, H1-2-1, H1-4-1, H1-4-2, and H1-4-3), which derived from H1 with previous 4 specific mutation sites (C241T, C3037T, C14408T, and A23403G), accounted for 91.95% of the population (Table 4). 2021 Computational and structural biotechnology journal Result SARS_CoV_2 A23403G;C14408T;C241T;C3037T 181;168;153;160 188;175;158;166 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. H1-2-1 with previous 4 specific mutation sites and the other 5 specific mutation sites (T445C, C6286T, C22227T, C26801G, and G29645T) appeared around July 21, 2020, became one of the major haplotypes circulating in the UK in early December 2020, and gradually decreased, and there was only a very small population still circulating by late Feb 2021. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 C22227T;C26801G;C6286T;G29645T;T445C 103;112;95;125;88 110;119;101;132;93 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. H1-3-2 and H1-3-3 were derived from H1-3 directly, and H1-3 derived from H1 directly with one more mutation site (G25563T) compared with H1. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 G25563T 114 121 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. H1-3-2 had previous 5 specific sites (C241T, C3037T, C14408T, A23403G, and G25563T) and C1059T (Table 5, Table 6), which had a stable prevalent trend between December 01, 2020 and February 02, 2021 in the USA. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 A23403G;C1059T;C14408T;C241T;C3037T;G25563T 62;88;53;38;45;75 69;94;60;43;51;82 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. H1-3-3 had previous 5 specific sites and 8 new missense mutation sites (C1059T, C10319T, A18424G, C21304T, G25907T, C27964T, C28472T, and C28869T) (Table 5, Table 6), which increased gradually between December 01, 2020 and February 02, 2021 in the USA. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 A18424G;C10319T;C1059T;C21304T;C27964T;C28472T;C28869T;G25907T 89;80;72;98;116;125;138;107 96;87;78;105;123;132;145;114 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. Notably, the H1-4-1 and H1-4-2 haplotypes both had A23063T mutation causing the N501Y mutation on the S protein, and the N501Y mutation was almost completely linked with the other 16 mutation sites (C913T, C3267T, C5388A, C5986T, T6954C, C14676T, C15279T, T16176C, C23604A, C23709T, T24506G, G24914C, C27972T, G28048T, A28111G, and C28977T). 2021 Computational and structural biotechnology journal Result SARS_CoV_2 A23063T;A28111G;C14676T;C15279T;C23604A;C23709T;C27972T;C28977T;C3267T;C5388A;C5986T;C913T;G24914C;G28048T;N501Y;N501Y;T16176C;T24506G;T6954C 51;319;238;247;265;274;301;332;206;214;222;199;292;310;80;121;256;283;230 58;326;245;254;272;281;308;339;212;220;228;204;299;317;85;126;263;290;236 S 102 103 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. While H1-4-1 with previous 4 specific mutation sites and another 17 specific mutation sites (C913T, C3267T, C5388A, C5986T, T6954C, C14676T, C15279T, T16176C, A23063T, C23604A, C23709T, T24506G, G24914C, C27972T, G28048T, A28111G, and C28977T) with mutation frequencies around 0.78, and H1-4-2 with one more mutation site (A17615G) compared with H1-4-1 showed a trend of increasing gradually since early December 2020. 2021 Computational and structural biotechnology journal Result SARS_CoV_2 A17615G;A23063T;A28111G;C14676T;C15279T;C23604A;C23709T;C27972T;C28977T;C3267T;C5388A;C5986T;C913T;G24914C;G28048T;T16176C;T24506G;T6954C 323;159;222;132;141;168;177;204;235;100;108;116;93;195;213;150;186;124 330;166;229;139;148;175;184;211;242;106;114;122;98;202;220;157;193;130 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. Figure 1 shows the leucine-to-arginine mutation at position 452. 2021 Cureus Result SARS_CoV_2 L452R 19 63 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. Figure 3 presents the glutamate-to-glutamine mutation at position 484. 2021 Cureus Result SARS_CoV_2 E484Q 22 69 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. Figure 4 exhibits the threonine-to-lysine mutation at position 478. 2021 Cureus Result SARS_CoV_2 T478K 22 66 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. The sequencing results showed and confirmed the HRM analysis that all samples were identified as G614 variant by the presence of missense mutation A to G at position 23403 (NCBI Reference Sequence Wuhan-Hu-1/NC_045512.2 = 23403A > G) which causes changes in the amino acid, Aspartic Acid (D) into Glycine (G) at the Spike residue 614 (D614G) (Figure 3). 2021 Heliyon Result SARS_CoV_2 A23403G;A23403G;D614G 222;147;335 232;171;340 S 316 321 34515998 The first Italian outbreak of SARS-CoV-2 B.1.1.7 lineage in Corzano, Lombardy. Based on the phylogenetic and epidemiological history, we can exclude any correlation between the V551F mutation and multiple introductions events and assume that the newly identified mutation represents the result of selective pressure and virus-host adaptation. 2022 Journal of medical virology Result SARS_CoV_2 V551F 98 103 34515998 The first Italian outbreak of SARS-CoV-2 B.1.1.7 lineage in Corzano, Lombardy. Indeed, the V551F mutation was not found in any other area in Italy, thus its presence in Corzano represents the first evidence on the territory without any history of travel abroad. 2022 Journal of medical virology Result SARS_CoV_2 V551F 12 17 34515998 The first Italian outbreak of SARS-CoV-2 B.1.1.7 lineage in Corzano, Lombardy. Interestingly, 5 out of the 21 Corzano sequences were found to carry an additional Spike mutation in the receptor-binding domain at position 551 (V551F), which was not reported elsewhere at the time of sampling. 2022 Journal of medical virology Result SARS_CoV_2 V551F 146 151 S 83 88 34515998 The first Italian outbreak of SARS-CoV-2 B.1.1.7 lineage in Corzano, Lombardy. Of note, 3 out of the 5 sequences carrying the V551F mutation belonged to pupils (range, 4-10 years) and 2 out of 5 sequences belonged to close contacts (34 and 44 years) of the infected pupils. 2022 Journal of medical virology Result SARS_CoV_2 V551F 47 52 34515998 The first Italian outbreak of SARS-CoV-2 B.1.1.7 lineage in Corzano, Lombardy. Up to the end of March 2021, only 7 additional SARS-CoV-2 sequences belonging to B.1.1.7 lineage and carrying the V551F mutation (pink circles) were documented in the GISAID database and they were retrieved in Poland, Germany, Belgium, Denmark, Japan, and the United States. 2022 Journal of medical virology Result SARS_CoV_2 V551F 114 119 34518554 Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. Amino acid substitutions D614G was also observed in one of the fatal case, sequenced in this study. 2021 Scientific reports Result SARS_CoV_2 D614G 25 30 34518554 Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. Another spike protein based phylogenetic tree was also constructed with 125 Indian circulating strains from different parts of India since lock down period which revealed continuous presence of D614G substitution in India. 2021 Scientific reports Result SARS_CoV_2 D614G 194 199 S 8 13 34518554 Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. Five amino acid substitutions were observed in spike protein viz., E583D in a strain from Datia, D614G observed in 17 strains from Morena, Datia, Gwalior, Ashoknagar, S884F in one strain from Morena, S929T in one strain from Ashoknagar and S943P observed in one strain of introductory index case from Gwalior district. 2021 Scientific reports Result SARS_CoV_2 D614G;E583D;S884F;S929T;S943P 97;67;167;200;240 102;72;172;205;245 S 47 52 34518554 Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. Important non-synonymous variants includes RdRp: A97V observed in 7 strains including virus introductory index cases from three different districts, N: P13L observed in 4 strains, NSP3: T2016K observed in 7 strains including introductory index cases from three different districts. 2021 Scientific reports Result SARS_CoV_2 A97V;P13L;T2016K 49;152;186 53;156;192 Nsp3;RdRP;N 180;43;149 184;47;150 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Among them, F490S and L452Q are the key RBD mutations in Lambda, making Lambda a more dangerous emerging variant than Delta. 2021 ArXiv Result SARS_CoV_2 F490S;L452Q 12;22 17;27 RBD 40 43 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Considering the BFE change and antibody disruptive count of co-mutation set [N501Y, A520S] is 0.699 and 27, we suggest monitoring this variant in IN and BE. 2021 ArXiv Result SARS_CoV_2 A520S;N501Y 84;77 89;82 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. First, the 10 most observed or fast-growing RBD mutations are N501Y, L452R, T478K, E484K, K417T, S477N, N439K, K417N, F490S, and S494P, as shown in Table 1. 2021 ArXiv Result SARS_CoV_2 E484K;F490S;K417N;K417T;L452R;N439K;N501Y;S477N;S494P;T478K 83;118;111;90;69;104;62;97;129;76 88;123;116;95;74;109;67;102;134;81 RBD 44 47 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. For 4 co-mutations in Figure 2 c, [P384L, K417N, E484K, N501Y] (Beta plus) could penetrate all vaccines due to its highest antibody disruption count of 101. 2021 ArXiv Result SARS_CoV_2 E484K;K417N;N501Y;P384L 49;42;56;35 54;47;61;40 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Four RBD mutations, N501Y, L452R, F490S, and L452Q, appear in both lists and are key mutations in WHO's VOC and VOI lists. 2021 ArXiv Result SARS_CoV_2 F490S;L452Q;L452R;N501Y 34;45;27;20 39;50;32;25 RBD 5 8 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. From Figure 2, RBD 2 co-mutation set [L452R, T478K] (Delta variant) has the highest frequency (219,362) and the highest BFE change (1.575 kcal/mol). 2021 ArXiv Result SARS_CoV_2 T478K;L452R 45;38 50;43 RBD 15 18 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. From Figure 2, three 3 co-mutation sets [R345K, E484K, N501Y] (Mu), [K417T, E484K, N501Y] (Gamma), and [K417N, E484K, N501Y] (Beta) draw our attention. 2021 ArXiv Result SARS_CoV_2 E484K;E484K;E484K;N501Y;N501Y;N501Y;K417N;K417T;R345K 48;76;111;55;83;118;104;69;41 53;81;116;60;88;123;109;74;46 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Further, [R346K, E484K, N501Y] (Mu variant) has a BFE change of 0.768 kcal/mol and high antibody disruption count (60). 2021 ArXiv Result SARS_CoV_2 E484K;N501Y;R346K 17;24;10 22;29;15 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Furthermore, high-frequency 2 co-mutation sets [E484K, N501Y], [F490S, N501Y], and [S494P, N501Y] are all considered to be the emerging variants that have the potential to escape vaccines. 2021 ArXiv Result SARS_CoV_2 N501Y;N501Y;N501Y;E484K;F490S;S494P 55;71;91;48;64;84 60;76;96;53;69;89 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Furthermore, the co-mutation set [K417N, T470N, E484K, N501T] that was first found in BR on April 06, 2020, has a BFE change of 0.625 kcal/mol and antibody disruption count 84, is an emerging vaccine breakthrough co-mutation in Brazil. 2021 ArXiv Result SARS_CoV_2 E484K;N501T;T470N;K417N 48;55;41;34 53;60;46;39 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. In addition, co-mutation set [L452Q, F490S] (cyan lines) on Lambda variant was recently drawing much attention due to its potential ability to resist vaccines and enhance the infectivity, which is consistent with our predictions that co-mutation set [L452Q, F490S] has a relatively significant BFE change of S protein and ACE2 (1.421kcal/mol) and would reduce the RBD binding with 59 antibodies. 2021 ArXiv Result SARS_CoV_2 F490S;F490S;L452Q;L452Q 37;258;30;251 42;263;35;256 RBD;S 364;308 367;309 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. It can be seen that mutations L452R, E484K, K417T, K417N, F490S, and S494P disrupt more than 30% of antibody-RBD complexes, while mutations E484K and K417T may disrupt nearly 30% antibody-RBD complexes, indicating their disruptive ability to the efficacy and reliability of antibody therapies and vaccines. 2021 ArXiv Result SARS_CoV_2 E484K;E484K;F490S;K417N;K417T;K417T;L452R;S494P 37;140;58;51;44;150;30;69 42;145;63;56;49;155;35;74 RBD;RBD 109;188 112;191 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Later on, in early March 2021, the UK, US, DK, DE, NL, SE, IT, FR, BE reported the appearance of [L452R, T478K] in early March 2021, and eventually [L452R, T478K] became a dominated co-mutation, which is consistent to the finding that Delta variant remains largely susceptible to infection. 2021 ArXiv Result SARS_CoV_2 T478K;T478K;L452R;L452R 105;156;98;149 110;161;103;154 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Moreover, [L452Q, F490S] (Lambda) is another co-mutation with high frequency, high BFE changes (1.421 kcal/mol), and high antibody disruption count (59). 2021 ArXiv Result SARS_CoV_2 F490S;L452Q 18;11 23;16 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Moreover, co-mutation set [N501Y, A520S] has quickly increased IN and BE since April 16, 2021. 2021 ArXiv Result SARS_CoV_2 A520S;N501Y 34;27 39;32 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Notably, co-mutaion set [G446V, L452R, T478K] in the UK with BFE change of 1.733 kcal/mol and 46 antibody disruption counts appears to be a dangerous set of co-mutations that may affect the infectivity and vaccine/antibodies efficacy shortly. 2021 ArXiv Result SARS_CoV_2 L452R;T478K;G446V 32;39;25 37;44;30 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Note that high-frequency mutation S477N does not significantly weaken any antibody and RBD binding, and thus does not appear in any prevailing variants. 2021 ArXiv Result SARS_CoV_2 S477N 34 39 RBD 87 90 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Second, among the top 25 most observed RBD mutations, T478K, L452Q N440K, L452R, N501Y, N501T, F490S, A475V, and P384L are the 8 most infectious ones judged by their ability to strengthen the binding with ACE2, as shown in Figure 1c. 2021 ArXiv Result SARS_CoV_2 A475V;F490S;L452Q;L452R;N440K;N501T;N501Y;P384L;T478K 102;95;61;74;67;88;81;113;54 107;100;66;79;72;93;86;118;59 RBD 39 42 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. The BFE changes of S protein and ACE2 for mutation T478K is nearly 1.00 kcal/mol, which strongly enhances the binding of the RBD-ACE2 complex. 2021 ArXiv Result SARS_CoV_2 T478K 51 56 RBD;S 125;19 128;20 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. The co-mutation set [K417T, E484K, N501Y] (Gamma) with BFE change of 0.656 kcal/mol was first found in Brazil in early January 2021, and then it became the most dominated co-mutation in Brazil and Canada, and the second dominated co-mutation in the US, NL, SE, IT, FR, IN, and BE. 2021 ArXiv Result SARS_CoV_2 E484K;N501Y;K417T 28;35;21 33;40;26 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. The cyan line is for the RBD co-mutation set [L452Q, F490S] on the Lambda variant, which is more penetrative to vaccines than the Delta. 2021 ArXiv Result SARS_CoV_2 F490S;L452Q 53;46 58;51 RBD 25 28 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. The RBD co-mutation set [L452R, T478K] (Delta) with 1.575 kcal/mol BFE change was first found in IN in early January 2021, and the number of this variant increases rapidly around the world in a short period. 2021 ArXiv Result SARS_CoV_2 T478K;L452R 32;25 37;30 RBD 4 7 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Third, among the top 25 most observed RBD mutations, Y449S, S494P, K417N, F490S, L452R, E484K, K417T, E484Q, L452Q, and N501Y are the 10 most antibody disruptive ones, judged by their interactions with 130 antibodies shown in Figure 1c. 2021 ArXiv Result SARS_CoV_2 E484K;E484Q;F490S;K417N;K417T;L452Q;L452R;N501Y;S494P;Y449S 88;102;74;67;95;109;81;120;60;53 93;107;79;72;100;114;86;125;65;58 RBD 38 41 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. Together with L452R (BFE change: 0.58kcal/mol), T478K makes Delta the most infectious variant in VOCs. 2021 ArXiv Result SARS_CoV_2 L452R;T478K 14;48 19;53 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. We anticipate that although co-mutation sets [V401L, L452R, T478K], [L452R, T478K, N501Y], [A411S, L452R, T478K], and [L452R, T478K, E484K, N501Y] have relatively low frequencies at this point, they may become dangerous variants soon due to their large BFE changes and antibody disruption counts. 2021 ArXiv Result SARS_CoV_2 E484K;L452R;L452R;N501Y;N501Y;T478K;T478K;T478K;T478K;A411S;L452R;L452R;V401L 133;53;99;83;140;60;76;106;126;92;69;119;46 138;58;104;88;145;65;81;111;131;97;74;124;51 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. We would like to address that all of the co-mutations sets, except for [Y449S, N501Y] in Figure 2 have positive BFE changes, following the natural selection. 2021 ArXiv Result SARS_CoV_2 N501Y;Y449S 79;72 84;77 34518803 Emerging vaccine-breakthrough SARS-CoV-2 variants. With a BFE change of 1.4 kcal/mol and antibody disruption count of 82, co-mutation set [K417N, L452R, T478K] (Delta plus) appears to be more dangerous than all of the current VOCs and VOIs. 2021 ArXiv Result SARS_CoV_2 L452R;T478K;K417N 95;102;88 100;107;93 34519222 Improved SARS-CoV-2 PCR detection and genotyping with double-bubble primers. The N501Y mutation has been detected in three variants of concern (VOC) - alpha, beta and gamma - that have been associated with increased transmissibility or detrimental change in COVID-19 epidemiology, possible increased virulence and decreased effectiveness of public health measures. 2021 BioTechniques Result SARS_CoV_2 N501Y 4 9 COVID-19 181 189 34519222 Improved SARS-CoV-2 PCR detection and genotyping with double-bubble primers. To confirm the D-B primer's utility with authentic patient samples, we ran a one-tube end point RT-PCR with RNA from N501Y-mutated VOC3 RNA extracted from nasopharyngeal swabs of patients with a confirmed mutation (Figure 8, lanes 2-4) or wild-type (Supplementary Figure 1, lanes 5-7). 2021 BioTechniques Result SARS_CoV_2 N501Y 117 122 34519222 Improved SARS-CoV-2 PCR detection and genotyping with double-bubble primers. To determine whether a D-B primer might be able to detect the N501Y mutation, we designed it with the point mutation a t at the 3' end, as described previously. 2021 BioTechniques Result SARS_CoV_2 N501Y 62 67 34519222 Improved SARS-CoV-2 PCR detection and genotyping with double-bubble primers. Using D-B primers to detect the N501Y mutation. 2021 BioTechniques Result SARS_CoV_2 N501Y 32 37 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. All three boosters, including mRNA-1273, increased neutralization against VOCs or VOIs to levels that were statistically equivalent to the wild-type D614G benchmarks, with superior titers measured versus some VOIs. 2021 Nature medicine Result SARS_CoV_2 D614G 149 154 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. B.1.351 and P.1 neutralizing antibody GMTs were 13- to 14-fold lower and 5- to 6-fold lower, respectively, compared to wild-type D614G at the same time point in the 50-microg groups. 2021 Nature medicine Result SARS_CoV_2 D614G 129 134 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Compared to the wild-type D614G benchmarks for each group, the booster vaccines yielded superior (mRNA-1273 and mRNA-1273.211) or equivalent (mRNA-1273.351) GMTs against the wild-type D614G virus. 2021 Nature medicine Result SARS_CoV_2 D614G;D614G 26;184 31;189 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. D614G and B.1.351 neutralization before and after booster. 2021 Nature medicine Result SARS_CoV_2 D614G 0 5 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. D614G and VOCs neutralization 1 and 6 months after primary series. 2021 Nature medicine Result SARS_CoV_2 D614G 0 5 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. D614G and VOCs neutralization after booster. 2021 Nature medicine Result SARS_CoV_2 D614G 0 5 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Importantly, neutralizing antibody titers against wild-type D614G and B.1.351 measured using the clinically validated lentivirus and research grade VSV-based PsVN assays were highly correlated (r = 0.9161 against wild-type D614G and r = 0.9435 against B.1.351; Supplementary. 2021 Nature medicine Result SARS_CoV_2 D614G;D614G 60;223 65;228 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Neutralization titers against B.1.351, P.1, B.1.427/B.1.429, B.1.526, B.1.617.1 and B.1.617.2 were 1.1-fold (P value NS), 1.4-fold (P value NS), 2.7-fold (P < 0.0001), 2.2-fold (P < 0.0001), 1.2-fold (P value NS) and 1.2-fold (P value NS) higher, respectively, 2 weeks after the mRNA-1273.211 booster compared to peak titers against the wild-type D614G measured 1 month after the primary series. 2021 Nature medicine Result SARS_CoV_2 D614G 347 352 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Neutralizing antibody titers against the wild-type D614G and B.1.351 viruses increased after each booster dose compared to day 1 titers (P < 0.0001 for all booster groups). 2021 Nature medicine Result SARS_CoV_2 D614G 51 56 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Neutralizing antibody titers against the wild-type D614G virus were measured with the VSV-based PsVN assay using samples collected 2 weeks after the booster dose and were compared against wild-type D614G GMT benchmarks from samples collected 1 month after the primary series vaccination in each group. 2021 Nature medicine Result SARS_CoV_2 D614G;D614G 51;198 56;203 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. One month after the primary series, wild-type D614G neutralizing antibody GMT ranged from 1,210 to 2,213 across participants in the 50-microg booster groups. 2021 Nature medicine Result SARS_CoV_2 D614G 46 51 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Sera from a random subset of the 20 participants in the mRNA-1273 booster group was used to assess neutralization of B.1.617.1 and B.1.617.2 (n = 11 for both) 6 months after the primary series and showed a 33- to 40-fold reduction in neutralizing antibody titers against B.1.617.1 and B.1.617.2 in comparison to peak titers measured against wild-type D614G 1 month after the primary series (full mRNA-1273 interim analysis cohort; n = 20). 2021 Nature medicine Result SARS_CoV_2 D614G 351 356 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Simultaneous analysis of samples using the VSV PsVN assay showed that, approximately 6 months after the mRNA-1273 primary vaccination series, neutralizing antibody levels decreased (P < 0.0001) compared to peak titers against wild-type D614G measured 1 month after the primary series (GMTs against wild-type D614G were 6- to 7-fold lower, and GMTs against B.1.351 and P.1 were 24- to 69-fold lower). 2021 Nature medicine Result SARS_CoV_2 D614G;D614G 236;308 241;313 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Specifically, on day 29, geometric mean titers (GMTs) against the wild-type D614G virus were 16.7-, 11.3-, 46.4- and 9.2-fold higher than day 1 (pre-booster) titers in the mRNA-1273 (50 microg), mRNA-1273.351 (50 microg), mRNA-1273.211 (50 microg) and mRNA-1273.351 (20 microg) booster recipients, respectively. 2021 Nature medicine Result SARS_CoV_2 D614G 76 81 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. The wild-type D614G virus was neutralized by most samples collected before the booster dose across all groups assessed. 2021 Nature medicine Result SARS_CoV_2 D614G 14 19 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. These benchmarks were used to determine whether the boosters reached the same neutralization level shown in the pivotal study where efficacy was demonstrated (that is, levels seen for wild-type D614G where 94% efficacy was measured). 2021 Nature medicine Result SARS_CoV_2 D614G 194 199 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. These observations included participants who did not have measurable neutralizing antibodies against the wild-type D614G or B.1.351 virus before the booster dose but showed increases in their neutralizing antibody titers after the booster dose. 2021 Nature medicine Result SARS_CoV_2 D614G 115 120 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Wild-type D614G and B.1.351 neutralization were measured in samples collected immediately before the booster dose (day 1 (~6 months after the mRNA-1273 primary series)) and after the booster dose (day 29 in mRNA-1273 booster recipients and days 15 and 29 in mRNA-1273.351 and mRNA-1273.211 booster recipients) in a validated lentivirus PsVN assay. 2021 Nature medicine Result SARS_CoV_2 D614G 10 15 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Wild-type D614G neutralization was 3.8-fold (P < 0.0001), 1.7-fold (P value not significant (NS)) and 4.4-fold (P < 0.0001) higher 2 weeks after 50-microg booster doses of mRNA-1273, mRNA-1273.351 and mRNA-1273.211, respectively, compared to peak titers against wild-type D614G measured 1 month after the primary series. 2021 Nature medicine Result SARS_CoV_2 D614G;D614G 10;272 15;277 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. 4h), whereas RBD-Fc N501Y showed no inhibitory activity by antibody 4. 2021 Scientific reports Result SARS_CoV_2 N501Y 20 25 RBD 13 16 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. Antibody 5 displayed reduced binding to RBD-Fc E484K, while antibody 14 showed intermediate binding toward all RBD-Fc tested. 2021 Scientific reports Result SARS_CoV_2 E484K 47 52 RBD;RBD 40;111 43;114 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. For instance, while antibodies 1 and 2 showed strong inhibition against all RBD-Fc forms, antibody 4 showed reduced inhibition against RBD-Fc N501Y. 2021 Scientific reports Result SARS_CoV_2 N501Y 142 147 RBD;RBD 76;135 79;138 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. However, RBD mutants S477N, Y453F and N501Y showed higher apparent affinity toward hACE2 as evidenced by fourfold, eightfold, and tenfold reductions in their respective IC50 values compared to wild type RBD. 2021 Scientific reports Result SARS_CoV_2 N501Y;S477N;Y453F 38;21;28 43;26;33 RBD;RBD 9;203 12;206 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. It is noteworthy that the N501Y mutation has been linked to increased viral infectivity in BALB/c mice, and it has been identified in SARS-CoV-2 variants isolated in UK, South Africa and Brazil. 2021 Scientific reports Result SARS_CoV_2 N501Y 26 31 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. The E484K mutation impaired inhibition by antibody 5. 2021 Scientific reports Result SARS_CoV_2 E484K 4 9 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. The E484K mutation that is common in many of the virus variants showed a twofold decrease in affinity to hACE2. 2021 Scientific reports Result SARS_CoV_2 E484K 4 9 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. These results prompted us to investigate the effect of mutations E484K, Y453F and N501Y on the binding of neutralizing antibodies described in. 2021 Scientific reports Result SARS_CoV_2 E484K;N501Y;Y453F 65;82;72 70;87;77 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. All of the in vitro non-synonymous substitutions appeared within multiple lineages the circulating viruses (GISAID data accessed March 2021, S3 Data) with the exception of I68R, N709H and D985G. 2021 PLoS pathogens Result SARS_CoV_2 D985G;I68R;N709H 188;172;178 193;176;183 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. All rescued viruses with specific point mutations replicated similarly to the rescued wild-type virus (rSARS-CoV-2) in human lung cells, Calu-3, with comparable replication kinetics and achieving similar peak virus titers (Fig 3A; rSARS-CoV-2 vs rNSP12-E802D, p.adj = 0.44; rSARS-CoV-2 vs rNSP12-E802A, p.adj = 0.41; rSARS-CoV-2 vs rNSP6-I168T, p.adj = 0.51; rSARS-CoV-2 vs rNSP6-I168T+NSP12-E802A, p.adj = 0.50, rSARS-CoV-2 vs rNSP6-I168T+NSP12-E802D, p.adj = 0.50; RM One-Way Anova with Dunnett's Test). 2021 PLoS pathogens Result SARS_CoV_2 E802A;E802A;E802D;E802D;I168T;I168T;I168T 296;392;253;446;338;380;434 301;397;258;451;343;385;439 Nsp12;Nsp12 386;440 391;445 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. Except for synonymous P681P, these substitutions were not present in SARS-CoV-2Engl2 (S1 Data and S1 Text). 2021 PLoS pathogens Result SARS_CoV_2 P681P 22 27 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. Importantly, in our in vitro passaged viruses we observed both synonymous and non-synonymous substitutions occurring at the same sites within spike (H69R, E484D, N501T, H655Y, P681P) as those identified in the emerging SARS-CoV-2 variants of concern (Alpha (B.1.1.7): Delta69/70, N501Y, P681H; Gamma (P.1): E484K, N501Y, H655Y; Beta (B.1.351): E484K, N501Y) (Fig 4). 2021 PLoS pathogens Result SARS_CoV_2 E484D;E484K;E484K;H655Y;H655Y;N501T;N501Y;N501Y;N501Y;P681H;P681P;H69R 155;307;344;169;321;162;280;314;351;287;176;149 160;312;349;174;326;167;285;319;356;292;181;153 S 142 147 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. In our drug screen assays, both the E802D and E802A mutations in NSP12 recapitulated partial resistance observed in the virus populations continually passaged in RDV (Fig 3B). 2021 PLoS pathogens Result SARS_CoV_2 E802A;E802D 46;36 51;41 Nsp12 65 70 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. Indeed, viruses bearing both the NSP12 and NSP6 mutations were more sensitive to RDV in comparison to NSP12 single mutant viruses (rNSP6-I168T+NSP12-E802D, EC50 3.21muM; rNSP6-I168T+NSP12-E802A, EC50 3.89muM). 2021 PLoS pathogens Result SARS_CoV_2 E802A;E802D;I168T;I168T 188;149;137;176 193;154;142;181 Nsp12;Nsp12;Nsp12;Nsp12;Nsp6 33;102;143;182;43 38;107;148;187;47 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. Interestingly, at 24h pi, a slight shift in an increase rNSP6-I168T infectious titer was observed in comparison with wild type, though this effect disappeared by 48h. 2021 PLoS pathogens Result SARS_CoV_2 I168T 62 67 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. It is important to stress these emerging variants of concern, collectively, share a combination of three amino acid mutations in spike receptor binding domain (RBD): N501Y common to all and K417N and E484K in the Brazil and South African variants. 2021 PLoS pathogens Result SARS_CoV_2 E484K;K417N;N501Y 200;190;166 205;195;171 RBD;S;RBD 135;129;160 158;134;163 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. NSP6 I168T substitution did not confer decreased sensitivity to RDV (Fig 3B), with comparable EC50 values to rSARS-CoV-2 (S1 Table). 2021 PLoS pathogens Result SARS_CoV_2 I168T 5 10 Nsp6 0 4 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. Of note are the four spike substitutions which occurred within the receptor binding domain (RBD) at either consensus (E484D, & N501T) or sub-consensus (G413R & Q498H) frequency. 2021 PLoS pathogens Result SARS_CoV_2 N501T;Q498H;E484D;G413R 127;160;118;152 132;165;123;157 RBD;S;RBD 67;21;92 90;26;95 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. Regardless of input ratio, rSARS-CoV-2 out competed viruses containing the rNSP12-E802D mutation (Fig 3E). 2021 PLoS pathogens Result SARS_CoV_2 E802D 82 87 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. The 4 sequences with E802A substitution from May 2020 from the same geographic region (United Arab Emirates) but there is no evidence of further transmission. 2021 PLoS pathogens Result SARS_CoV_2 E802A 21 26 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. The first mutation was identified as glutamine to aspartate at amino acid 802 (E802D) in the RNA-dependent RNA polymerase (RdRp) NSP12 (Fig 2A). 2021 PLoS pathogens Result SARS_CoV_2 Q802D;E802D 37;79 77;84 RdRp;Nsp12;RdRP 93;129;123 121;134;127 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. The second mutation was an isoleucine to threonine substitution (I168T) in NSP6, a highly conserved protein involved in restricting autophagosome expansion. 2021 PLoS pathogens Result SARS_CoV_2 I168T 65 70 Nsp6 75 79 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. The sequences containing these mutations were mostly geographically and temporally dispersed suggesting they did not share homology, though there was a small cluster of sequences (E802D, n = 9) from Germany within the same time frame. 2021 PLoS pathogens Result SARS_CoV_2 E802D 180 185 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. There was a cluster of sequences containing the V557I substitution observed in the Netherlands within a week but there was no information on whether it was the same patient or whether they were treated with RDV. 2021 PLoS pathogens Result SARS_CoV_2 V557I 48 53 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. This would indicate the E802D mutation incurs a fitness cost in the absence of RDV and is unlikely to be sustained in the circulating population. 2021 PLoS pathogens Result SARS_CoV_2 E802D 24 29 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. To ascertain whether a mutation of NSP12 E802 was sufficient to mediate partial RDV resistance, we introduced either an E802D or E802A mutation at this site into SARS-CoV-2Wu1 by reverse genetics and recovered infectious virus. 2021 PLoS pathogens Result SARS_CoV_2 E802A;E802D 129;120 134;125 Nsp12 35 40 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. To examine whether the viruses containing the NSP12 E802D mutation would persist and outcompete the WT in the absence of RDV, an in vitro co-infection competition assay over multiple passages was undertaken. 2021 PLoS pathogens Result SARS_CoV_2 E802D 52 57 Nsp12 46 51 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. VeroE6-ACE2-TMPRSS2 were infected with two different MOI ratios of rSARS-CoV-2 to rNSP12-E802D (1:9 and 9:1), samples were harvested every 24 h and used to infect fresh monolayers of cells. 2021 PLoS pathogens Result SARS_CoV_2 E802D 89 94 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. We next examined the change in the ratio of wild type to E802D in the viral populations at each passage using the GridION (Oxford Nanopore Technologies). 2021 PLoS pathogens Result SARS_CoV_2 E802D 57 62 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. We noted that some in vitro substitutions in spike were changes to amino acids associated with SARS-CoV-1 spike (Q498H & N501T) adaption. 2021 PLoS pathogens Result SARS_CoV_2 N501T;Q498H 121;113 126;118 S;S 45;106 50;111 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. We observed a 2.14- to 2.54-fold change in RDV EC50; from 2.61muM for rSARS-CoV-2 to 5.58muM and 6.62muM for the E802A and E802D mutants, respectively (Fig 3B and S1 Table). 2021 PLoS pathogens Result SARS_CoV_2 E802A;E802D 113;123 118;128 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. We only identified 36 (0.004%) viral sequences with a mutation at E802; E802D was the predominant replacement (n = 24), with the remaining sequence either E802A (n = 4), E802G (n = 3), E802Q (n = 1) or E802X (n = 1). 2021 PLoS pathogens Result SARS_CoV_2 E802A;E802D;E802G;E802Q;E802X 155;72;170;185;202 160;77;175;190;207 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. We propose that the E802D mutation changes the steric interactions between amino acid side chains within this region resulting in minor structural changes, (Fig 2A), thereby influencing binding of nt+3 during synthesis of template RNA and allowing elongation when the active form of RDV is incorporated into the RNA. 2021 PLoS pathogens Result SARS_CoV_2 E802D 20 25 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. While a RDV dose-dependent reduction in titer for all viruses was observed, rNSP12-E802D and rNSP12-E802A titers were consistently higher than wild-type and rNSP6-I168T at 24h and 48h pi (Fig 3C) over a range of concentrations. 2021 PLoS pathogens Result SARS_CoV_2 E802A;E802D;I168T 100;83;163 105;88;168 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. While both stocks had high infectious titres (rSARS-CoV-2, ~2.5 x 107 pfu/ml and rNSP12-E802D, ~8.13 x 107 pfu/ml), there was a difference in the equivalent genome copies (GE)/ml, with rNSP12-E802D a ~0.5 log10 higher (rSARS-CoV-2, 7.16 x 108 GE/ml and rNSP12-E802D, 2.90 x 109 GE/ml). 2021 PLoS pathogens Result SARS_CoV_2 E802D;E802D;E802D 88;192;260 93;197;265 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. Whilst we thought it was unlikely to play a role, we also recovered virus with I168T mutation in NSP6 either alone or in combination with the NSP12 mutations (E802D or E802A). 2021 PLoS pathogens Result SARS_CoV_2 E802A;I168T;E802D 168;79;159 173;84;164 Nsp12;Nsp6 142;97 147;101 34535691 Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020. Among the three target mutations, S98F has been detected with the highest frequency (in 25.7% of our samples). 2021 Scientific reports Result SARS_CoV_2 S98F 34 38 34535691 Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020. Finally, the S477N spike mutation was first detected at the end of the summer and displays moderate regional circulation and detection frequency (13.5%). 2021 Scientific reports Result SARS_CoV_2 S477N 13 18 S 19 24 34535691 Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020. In contrast, the A222V mutation has been detected far less in the study area (in only 4.4% of our samples), despite notably higher frequencies of detection at the end of the summer in surrounding countries. 2021 Scientific reports Result SARS_CoV_2 A222V 17 22 34535691 Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020. It has recently been reported that S477N might strengthen the binding of the SARS-COV-2 spike with the human ACE2 receptor, which could potentially be associated with enhanced viral transmissibility. 2021 Scientific reports Result SARS_CoV_2 S477N 35 40 S 88 93 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Again, N501Y is the only mutation that increased plasma recognition, indicating its major role amongst all the mutations of this variant. 2021 Virology Result SARS_CoV_2 N501Y 7 12 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. also showed that the Spike from B.1.1.7 or harboring the N501Y mutation present better ACE2 binding at higher temperatures compared to the D614G strain. 2021 Virology Result SARS_CoV_2 D614G;N501Y 139;57 144;62 S 21 26 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. also significantly impacted plasma recognition by ~1.75-fold compared to D614G. 2021 Virology Result SARS_CoV_2 D614G 73 78 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Although both K417N and K417T presented a modest increase in the on-rate kinetic by ~1.56 and ~1.11 folds, the accelerated off-rate kinetics dictated the overall decrease affinity of these mutants. 2021 Virology Result SARS_CoV_2 K417N;K417T 14;24 19;29 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Among all tested emerging variants, the Spikes from B.1.617.1 and B.1.617.2 presented the most important decrease in recognition by ~1.8 and ~1.64 folds compared to D614G. 2021 Virology Result SARS_CoV_2 D614G 165 170 S 40 46 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Both its NTD mutations, S13I and W152C, were less efficiently recognized by plasma compared to D614G. 2021 Virology Result SARS_CoV_2 D614G;S13I;W152C 95;24;33 100;28;38 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Examining each variant and their single mutations more closely, though full B.1.1.7 Spike did not significantly reduce plasma binding in previously-infected vaccinated individuals, three of its single mutations, DeltaY144, P681H, and S982A significantly affected plasma recognition. 2021 Virology Result SARS_CoV_2 DeltaY144;P681H;S982A 212;223;234 221;228;239 S 84 89 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Few NTD mutations, namely T20N, P26S, D138Y, and R190S, likely contributed to the increase in ACE2 binding, with ~2, ~1.6, ~1.3 and ~1.8- fold increase compared to D614G, respectively. 2021 Virology Result SARS_CoV_2 D138Y;D614G;P26S;R190S;T20N 38;164;32;49;26 43;169;36;54;30 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Furthermore, H655Y also contributed to the immuno-evasive phenotype of the full Spike. 2021 Virology Result SARS_CoV_2 H655Y 13 18 S 80 85 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. However, combined together, the B.1.1.7 was recognized similarly to its D614G counterpart by these plasmas. 2021 Virology Result SARS_CoV_2 D614G 72 77 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. In agreement with previous reports, the N501Y mutation present in B.1.1.7, B.1.351, and P.1 significantly decreased the off-rate (Kdis) (from 6.88 x 10-3 to 1.49 x 10-3 1/s), presenting a 3.88-fold increase in KD compared to its wild-type counterpart. 2021 Virology Result SARS_CoV_2 N501Y 40 45 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. In the P.1 Spike we observed mutations in the NTD that decreased recognition (P26S, D138Y, and R190S). 2021 Virology Result SARS_CoV_2 D138Y;R190S;P26S 84;95;78 89;100;82 S 11 16 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Interestingly, the L452R mutant did not have a major impact in ACE2 affinity when tested in the context of recombinant monomeric RBD. 2021 Virology Result SARS_CoV_2 L452R 19 24 RBD 129 132 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Interestingly, the RBD mutation K417T and the S2 mutation T1027I decreased the ACE2-Fc by ~1.3 and ~1.7 folds respectively. 2021 Virology Result SARS_CoV_2 K417T;T1027I 32;58 37;64 RBD 19 22 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Interestingly, three mutations/deletion in this VOC decreased the interaction with ACE2-Fc, namely R246I and Delta242-244 in the NTD, as well as K417N in the RBD. 2021 Virology Result SARS_CoV_2 K417N;R246I 145;99 150;104 RBD 158 161 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Interestingly, variants harboring the N501Y mutation (B.1.1.7, B.1.351 and P.1) exhibited an increase in ACE2 binding compared to D614G Spike at both 4 C and 37 C, while this phenotype was only observed at 4 C with Spike from the other variants. 2021 Virology Result SARS_CoV_2 D614G;N501Y 130;38 135;43 S;S 136;215 141;220 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Inversely, the deletion DeltaH69-V70 and the substitution D1118H slightly enhanced the recognition of this Spike by plasma from previously-infected vaccinated individuals. 2021 Virology Result SARS_CoV_2 D1118H 58 64 S 107 112 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Lastly, the Spike from B.1.526 showed a ~1.8-fold increase over D614G. 2021 Virology Result SARS_CoV_2 D614G 64 69 S 12 17 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Like the above-mentioned VOCs, N501Y also likely played a role in enhanced ACE2-Fc interaction. 2021 Virology Result SARS_CoV_2 N501Y 31 36 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Mutations apparently contributing to the reduction of plasma recognition of the B.1.1.7 Spike are the DeltaY144 deletion in the NTD, P681H and T716I near the S1/S2 cleavage site. 2021 Virology Result SARS_CoV_2 P681H;T716I 133;143 138;148 S 88 93 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. No major changes were observed for the E484K mutation. 2021 Virology Result SARS_CoV_2 E484K 39 44 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Of note, the E484K mutation, also found in the RBD of other emerging variants (P.1 and B.1.526) did not significantly impact the ACE2-Fc interaction. 2021 Virology Result SARS_CoV_2 E484K 13 18 RBD 47 50 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Of note, the K417N mutation that reduced ACE2 binding. 2021 Virology Result SARS_CoV_2 K417N 13 18 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. On the other hand, its RBD mutation, L452R, increased ACE2-Fc binding by ~2.7 folds, suggesting its major contribution to the phenotype of this variant. 2021 Virology Result SARS_CoV_2 L452R 37 42 RBD 23 26 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Only the A701V substitution present in the B.1.526 reduced plasma binding. 2021 Virology Result SARS_CoV_2 A701V 9 14 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Our results show that all the NTD mutations, namely L18F, T20N, P26S, D138Y and R190S, attenuated the binding of naive-vaccinated plasma Abs. 2021 Virology Result SARS_CoV_2 D138Y;L18F;P26S;R190S;T20N 70;52;64;80;58 75;56;68;85;62 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Previously-infected vaccinated individuals developed Abs that were able to robustly recognize and bind to the emerging variants B.1.1.7, B.1.351, B.1.429 and B.1.526 at a similar level than D614G. 2021 Virology Result SARS_CoV_2 D614G 190 195 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Similarly to B.1.1.7, the N501Y mutation likely plays an important role in this phenotype. 2021 Virology Result SARS_CoV_2 N501Y 26 31 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Substitution S982A in the S2 showed the most important reduction, by ~2 folds compared to D614G. 2021 Virology Result SARS_CoV_2 D614G;S982A 90;13 95;18 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. The B.1.1.7 Spike presented the highest ACE2-Fc interaction amongst all tested Spikes, which is a 5.43-fold increase in ACE2-Fc binding compared to D614G. 2021 Virology Result SARS_CoV_2 D614G 148 153 S;S 12;79 17;85 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. The B.1.351 Spike was efficiently recognized by plasma from previously-infected vaccinated individuals with a single mutation presenting lower detection (A701V). 2021 Virology Result SARS_CoV_2 A701V 154 159 S 12 17 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. The H655Y mutation, near the S1/S2 cleavage site, also slightly increased ACE2 interaction by ~1.2 folds. 2021 Virology Result SARS_CoV_2 H655Y 4 9 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. The impact of cold temperature on ACE2 binding was more pronounced for the D614G Spike (3.62-fold increase) comparatively to Spikes from emerging variants (1.57-3.08-fold increase). 2021 Virology Result SARS_CoV_2 D614G 75 80 S;S 81;125 86;131 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. The mutations that likely contribute to this phenotype are DeltaH69-V70 in the N terminal domain (NTD) and N501Y in the RBD that enhanced binding by ~1.51 and ~2.52 folds, respectively. 2021 Virology Result SARS_CoV_2 N501Y 107 112 RBD;N 120;79 123;80 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. The N501Y substitution, also present in other emerging variants (B1.351 and P.1), is the only mutation that increased plasma recognition. 2021 Virology Result SARS_CoV_2 N501Y 4 9 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. The NTD substitution R246I decreased ACE2-Fc binding by ~1.52 folds, the Delta242-244 deletion by ~1.35 folds, whereas K417N had a greater impact with a decreased binding of ~7.7 folds relative to D614G. 2021 Virology Result SARS_CoV_2 D614G;K417N;R246I 197;119;21 202;124;26 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. The RBD mutation L452R also presented a minor ~1.16-fold decrease in recognition by plasma from vaccinated individuals. 2021 Virology Result SARS_CoV_2 L452R 17 22 RBD 4 7 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. The same phenotype is applicable to most of its mutations, with the exception of D253G substitution in the NTD, which showed a modest ~1.2-fold decrease in binding. 2021 Virology Result SARS_CoV_2 D253G 81 86 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. The Spike from B.1.351 also presented significantly higher ACE2-Fc binding compared to D614G. 2021 Virology Result SARS_CoV_2 D614G 87 92 S 4 9 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. The Spike from P.1 presented a ~4.24-fold increase in binding compared to D614G. 2021 Virology Result SARS_CoV_2 D614G 74 79 S 4 9 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. This indicate that the cold temperature and the N501Y mutation significantly impact Spike-ACE2 interaction. 2021 Virology Result SARS_CoV_2 N501Y 48 53 S 84 89 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. This VOI has two NTD mutations, S13I and W152C, both of which did not significantly impact this interaction. 2021 Virology Result SARS_CoV_2 S13I;W152C 32;41 36;46 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. When compared to D614G, Spike from B.1.1.7, P.1 and the recently emerged B.1.617.1 and B.1.617.2 variants were significantly less recognized by the plasma from vaccinated SARS-CoV-2 naive individuals. 2021 Virology Result SARS_CoV_2 D614G 17 22 S 24 29 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. When compared to the D614G Spike, all tested Spike variants, with the exception of B.1.617.1, presented significantly higher ACE2 binding. 2021 Virology Result SARS_CoV_2 D614G 21 26 S;S 27;45 32;50 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. While ACE2 displayed higher binding for the different emerging variants Spikes at 37 C, similar level of binding could only be achieved for the D614G Spike when decreasing the temperature to 4 C. 2021 Virology Result SARS_CoV_2 D614G 144 149 S;S 72;150 78;155 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. While our results identified some key mutations enhancing ACE2 interaction (i.e., N501Y, L452R and mutation/deletion in the NTD), the overall increased ACE2 affinity from any given variant appears to result from more than the sum of the effect of individual mutations composing this variant. 2021 Virology Result SARS_CoV_2 L452R;N501Y 89;82 94;87 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. While we did not observe a significant decrease in plasma recognition of the B.1.351 Spike, most single mutants of this VOC (L18F, D80A, D215G, Delta242-244, R246I in the NTD, and K417N in the RBD) exhibit decreased binding. 2021 Virology Result SARS_CoV_2 D215G;D80A;K417N;R246I;L18F 137;131;180;158;125 142;135;185;163;129 S;RBD 85;193 90;196 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Additionally, whereas a convergent A701V mutation is also found in the B.1.526 and S/E484K carrying lineage that was first identified in New York, P681H is found in the S/E484K and S/N501Y carrying P.3 lineage first identified in the Philippines, and both S/H655Y and S/P681H are found in the highly mutated S/E484K carrying A.VOI.V2 lineage first identified in Tanzanian travelers. 2021 Cell Result SARS_CoV_2 A701V;P681H;N501Y;P681H;E484K;E484K;E484K;H655Y 35;147;181;268;83;169;308;256 40;152;188;275;90;176;315;263 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. An F at residue S/18 is also observed in 10% of other known Sarbecoviruses and the L18F mutation was the 28th most common in sampled SARS-CoV-2 genomes on June 4, 2021. 2021 Cell Result SARS_CoV_2 L18F 83 87 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Any of H655Y, P681H, A701V, or T716I might directly impact the efficiency of viral entry into host cells. 2021 Cell Result SARS_CoV_2 A701V;H655Y;P681H;T716I 21;7;14;31 26;12;19;36 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Based on the observed degree of frequency increases, mutations such as ORF1a/1708D (corresponding to nsp3/890D with 15.8 and >12.0-fold increases in V2 and V3, respectively), S/26S (>13-fold increase in V2), S/716I (3.7 and >13.5-fold increases in V2 and V3, respectively), S/1027I (>44-fold increase in V2), S/1118H (4.0 and >20-fold increases in V2 and V3, respectively), S/1176F (19.5-fold increase in V2), and ORF3/171L (11.9-fold increase in V3) are the signature mutations that, in addition to the ORF1a/3675-3677Del, S/18F, S/417N/T E484K, and S/501Y mutations, are likely to have the greatest positive impact on the fitness of the 501Y lineage viruses within which they occur. 2021 Cell Result SARS_CoV_2 E484K 540 545 ORF1a;ORF1a;Nsp3;S;S;S;S;S;S;S;S 71;504;101;175;208;274;309;374;524;531;551 76;509;105;176;209;275;310;375;525;532;552 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. In addition to the 29 convergent mutations that displayed frequency increases between March 15 and June 1, 2021, the meta-signature includes deletion mutations at ORF1a/3675-3677, S/69-70, S/144, and S/241-243 (which, while displaying convergence between the different 501Y lineages, were not amenable to selection analyses) and the convergent signature substitutions L18F, K417N/K, and N501Y (which were already at high frequencies in multiple 501Y lineages by March 15, 2021). 2021 Cell Result SARS_CoV_2 K417K;K417N;L18F;N501Y 374;374;368;387 381;381;372;392 ORF1a 163 168 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. In this regard, while mutations at S/20, S/80, S/138, S/215, and S/570 in different lineages do not predominantly converge on the same encoded amino acid states, they could nevertheless still be convergent on similar fitness objectives (immune escape or compensation for the fitness costs of other mutations): such as is likely the case with the also not strictly convergent V2 K417N and V3 K417T signature mutations. 2021 Cell Result SARS_CoV_2 K417N;K417T 378;391 383;396 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. S/18 falls within multiple different predicted CTL epitopes and the L18F mutation is known to reduce viral sensitivity to some neutralizing monoclonal antibodies. 2021 Cell Result SARS_CoV_2 L18F 68 72 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. SARS-CoV-2 variants with deletions of the furin cleavage site have reduced pathogenicity and the P681H mutation:which falls within this site:likely increases the efficiency of furin cleavage by replacing a less favorable uncharged amino acid with a more favorable positively charged basic one. 2021 Cell Result SARS_CoV_2 P681H 97 102 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Similarly, among the nine positively selected sites where non-signature mutations both converge between viruses in two or more of the 501Y lineages and then more than double in frequency between March 15 and June 1, 2021, ORF1b/1522I (corresponding to Heicase/590I with 1.9-, 12.7-, and 4.8-fold increases in V1, V2, and V3, respectively), S/98F (2.5-, 5.3-, and >6.0-fold increases in V1, V2, and V3, respectively), and E71T/R (respectively 5.8- and >10-fold increases in V1) are likely the most fitness-enhancing mutations. 2021 Cell Result SARS_CoV_2 E71R;E71T 421;421 427;427 S 340 341 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Whereas sites S/655 and S/681 are also detectably evolving under positive selection in at least one of the lineage specific datasets, S/655, S/681, A/701, and S/716 are all detectably evolving under positive selection in the March and April 2021 global SARS-CoV-2 datasets; important additional indicators that are consistent with the H655Y, P681H, A701V, and T716I mutations being adaptive. 2021 Cell Result SARS_CoV_2 A701V;H655Y;P681H;T716I 349;335;342;360 354;340;347;365 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Whereas some V2 and V3 sequences had, by March 2021, independently acquired the signature V1 mutations, P681H and T716I, some V1 and V2 sequences had independently acquired the V3 signature mutation, H655Y, and some V1 sequences had independently acquired the V2 signature mutation, A701V. 2021 Cell Result SARS_CoV_2 A701V;H655Y;P681H;T716I 283;200;104;114 288;205;109;119 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Whereas the L18F mutation is effectively fixed in all currently sampled V3 lineage sequences, it occurred (and persisted in descendent variants) at least twice in the V1 lineage and at least four times in the V2 lineage. 2021 Cell Result SARS_CoV_2 L18F 12 16 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. 2 B), three differently sulfated GalNAc units were identified: non-sulfated (N0S), 6-sulfated (N6S) and 4-sulfated (N4S) units of anomeric 1H's with delta H at 4.71, 4.65 and 4.53 ppm, respectively (Table 1). 2021 The Journal of biological chemistry Result SARS_CoV_2 N4S;N6S 116;95 119;98 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. 5 A) and N501Y mutant RBD. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 9 14 RBD 22 25 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. E) predicts that heparin binds to a site close to the N501Y mutation site. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 54 59 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. F and Table S3) indicate that the marine sulfated oligosaccharides bind stronger to the WT RBD than to the N501Y mutant (though for IbSF the difference in docking scores is smaller than the standard deviations in the docking scores obtained from multiple runs with different fixed seeds). 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 107 112 RBD 91 94 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. GalNAc, which has a 4-sulfation, is seen to interact with Q498, both in the WT and N501Y mutant. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 83 88 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. Heparin binding to the N501Y mutant lacks key GlcNS(6S)-arginine interactions, which leads to a reduction in binding affinity for the mutant. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 23 28 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. However, in the N501Y mutant, IdoA binding differs from WT and is oriented towards R408, where the O3 and O4 hydroxyl groups interact with D405 and R408, respectively. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 16 21 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. Inhibition of binding of N501Y mutant RBD to a heparin surface by all three holothurian sulfated glycans was stronger than by UFH. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 25 30 RBD 38 41 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. Instead, polar interactions with E484, Q493, and Q498 are observed in the IbSF-N501Y complex. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 79 84 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. Molecular docking of the PpFucCS/IbFucCS and IbSF constructs in the binding site shows that all the molecules bind to the S-protein RBD WT and N501Y mutant in a similar binding mode. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 143 148 RBD;S 132;122 135;123 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. Peak integration of their NMR anomeric 1H's shows a ratio of 1:1:8 for N0S:N6S:N4S, indicating 80% and 10% sulfation substitution, respectively, at C4 and C6 positions of the GalNAc units. 2021 The Journal of biological chemistry Result SARS_CoV_2 N4S;N6S 79;75 82;78 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. Results have indicated that S-protein and N501Y mutant RBD's bind to heparin with KD values of 94 and 1,800 nM, respectively. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 42 47 RBD;S 55;28 58;29 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. S4A) and N501Y mutant. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 9 14 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. Similarly, the intramolecular hydrogen bond between the 2S sulfate of Fuc and the O2 hydroxyl of the neighboring GlcA was maintained ~29% of the simulation time in N501Y. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 164 169 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. The dihedral angles of the docked trisaccharides seen in the PpFucCS series show different distributions in the WT compared to the N501Y mutant. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 131 136 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. The four marine oligosaccharide building blocks were also docked into the WT S-protein RBD and its N501Y mutant using the same docking protocol. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 99 104 RBD;S 87;77 90;78 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. The top-scoring docking poses of the marine oligosaccharide constructs in the WT and N501Y mutant were then subjected to 200 ns all-atom MD simulations with explicit solvent, in order to obtain an optimal dynamic picture of the binding mode found from docking of ligand to protein. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 85 90 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. This loss of hydrogen bond interaction with the RBD is a plausible cause for the weaker binding observed experimentally in the N501Y mutant. 2021 The Journal of biological chemistry Result SARS_CoV_2 N501Y 127 132 RBD 48 51 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. Combined detection of the N501Y and DeltaH69-V70 mutations had a 100.0% concordance with WGS for detection of the B.1.1.7 lineage in 144 samples and all were SGTF. 2022 Clinical microbiology and infection Result SARS_CoV_2 N501Y 26 31 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. E484K-, H655Y-, L452R- and P681R-specific PCRs were applied according to the testing algorithm presented in Figure 1 . 2022 Clinical microbiology and infection Result SARS_CoV_2 H655Y;L452R;P681R;E484K 8;16;27;0 13;21;32;5 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. E484K, H655Y, L452R and P681R. 2022 Clinical microbiology and infection Result SARS_CoV_2 H655Y;L452R;P681R;E484K 7;14;24;0 12;19;29;5 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. Four RNA extracts failed to amplify in the N501Y assay and were not interpretable, sequencing revealed none of these were VOC/VOI, resulting in an OPA of 98.5%. 2022 Clinical microbiology and infection Result SARS_CoV_2 N501Y 43 48 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. In all samples of the Beta variant (N=65), the N501Y and E484K mutations were observed in the absence of H655Y and in all strains of the Gamma variant (N=86), the N501Y, E484K and H655Y mutations were detected. 2022 Clinical microbiology and infection Result SARS_CoV_2 E484K;E484K;H655Y;H655Y;N501Y;N501Y 57;170;105;180;47;163 62;175;110;185;52;168 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. In six samples, the E484K-specific assay displayed an aberrant Tm at 53.1+-0.5 C (vs. 2022 Clinical microbiology and infection Result SARS_CoV_2 E484K 20 25 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. N501Y. 2022 Clinical microbiology and infection Result SARS_CoV_2 N501Y 0 5 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. Six samples had an aberrant Tm in the E484K-specific assay and were identified as Kappa. 2022 Clinical microbiology and infection Result SARS_CoV_2 E484K 38 43 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. The allocation of the B.1.351 lineage (Beta) and P.1 lineage (Gamma) based on the combination of N501Y, E484K and H655Y-specific assays resulted in a 100.0% concordance with WGS. 2022 Clinical microbiology and infection Result SARS_CoV_2 E484K;H655Y;N501Y 104;114;97 109;119;102 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. The B.1.1.7 lineage (Alpha) was assigned based on two key mutations: N501Y and DeltaH69-V70, the latter causing SGTF. 2022 Clinical microbiology and infection Result SARS_CoV_2 N501Y 69 74 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. The concordance of SARS-CoV-2 strains harboring L452R and P681R in the absence of N501Y, E484K or H655Y with the B.1.617 lineage (N=54) was 98.1%. 2022 Clinical microbiology and infection Result SARS_CoV_2 E484K;H655Y;L452R;N501Y;P681R 89;98;48;82;58 94;103;53;87;63 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. The H655Y mutation is only evaluated when both N501Y and E484K are present and had a 100% concordance with the presence/absence of H655Y in WGS analysis. 2022 Clinical microbiology and infection Result SARS_CoV_2 E484K;H655Y;H655Y;N501Y 57;4;131;47 62;9;136;52 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. The identification of the B.1.427/1.429 (Epsilon), B.1.617.1 (Kappa) and B.1.617.2 (Delta) lineages was based upon the assessment of the L452R, P681R and E484Q mutations in the absence of other mutations assessed. 2022 Clinical microbiology and infection Result SARS_CoV_2 E484Q;L452R;P681R 154;137;144 159;142;149 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. The N501Y-specific PCR was performed on 567 RNA-extracts and the N501Y mutation was detected in 302 strains assigned to 4 SARS-CoV-2 lineages: B.1.1.7 (N=149), B.1.351 (N=65), P.1 (N=86) and B.1.214.2 (N=2). 2022 Clinical microbiology and infection Result SARS_CoV_2 N501Y;N501Y 4;65 9;70 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. The OPA of the E484K-specific assay was 99.7%. 2022 Clinical microbiology and infection Result SARS_CoV_2 E484K 15 20 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. We identified the B.1.427/1.429 lineage in one sample which harbored only the L452R mutation in the absence of the other mutations assessed by PCR. 2022 Clinical microbiology and infection Result SARS_CoV_2 L452R 78 83 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. When both N501Y and E484K are absent in samples without SGTF, L452R and P681R are assessed. 2022 Clinical microbiology and infection Result SARS_CoV_2 E484K;L452R;N501Y;P681R 20;62;10;72 25;67;15;77 34537363 Influence of treatment with neutralizing monoclonal antibodies on the SARS-CoV-2 nasopharyngeal load and quasispecies. A variant with the Q493R spike mutation was first detected in Patient#1 and Patient#2 on day 7 and in Patient#3 on day 14. 2022 Clinical microbiology and infection Result SARS_CoV_2 Q493R 19 24 S 25 30 34537363 Influence of treatment with neutralizing monoclonal antibodies on the SARS-CoV-2 nasopharyngeal load and quasispecies. The Q493K spike mutation was detected in Patient#4 on day 7 and a variant with the E484K spike mutation was detected in Patient#5 on day 21. 2022 Clinical microbiology and infection Result SARS_CoV_2 E484K;Q493K 83;4 88;9 S;S 10;89 15;94 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. As shown in Figure 5F, the Log10 IC50 values of the 10 antibodies against Wuhan pseudotyped virus were higher than that of D614G and E484Q pseudoviruses, but lower than A475V, suggesting that G614G and E484Q were more susceptible to neutralization while A475V showed a somewhat escape from neutralization. 2021 Frontiers in immunology Result SARS_CoV_2 A475V;A475V;D614G;E484Q;E484Q;G614G 169;254;123;133;202;192 174;259;128;138;207;197 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. As we mentioned above, the dominated variant D614G could increase infectivity while E484Q and A475V exhibited resistance to some nAbs. 2021 Frontiers in immunology Result SARS_CoV_2 A475V;D614G;E484Q 94;45;84 99;50;89 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. Interestingly, some rAbs antibodies such as CB6H-XG83L and S309H-CV30L were granted a significantly higher neutralizing ability to mutant pseudoviruses when compared with the original mAbs (ratio < 1, Table 2). 2021 Frontiers in immunology Result SARS_CoV_2 S309H 59 64 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. Our study showed that all the original mAbs and rAbs could effectively neutralize the three pseudovirus variants with a mutated S protein containing D614G, E484Q, or A475V mutation (Figures 5B-D and Table 1). 2021 Frontiers in immunology Result SARS_CoV_2 A475V;D614G;E484Q 166;149;156 171;154;161 S 128 129 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. The antibodies that targeted E484Q or A475V residue of RBD all showed increased IC50 values on mutant pseudovirus (ratio > 1, Table 2). 2021 Frontiers in immunology Result SARS_CoV_2 A475V;E484Q 38;29 43;34 RBD 55 58 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. Through the initial screening of live SARS-CoV-2 virus neutralization test, we selected nine antibodies with a relatively better neutralizing ability, including XG81, XG83, 3 SARS-CoV-2 nAbs (S309, P2B-2F6, and CB6), and four rAbs (S309H-CV30L, S309H-XG81L, CC12.1H-XG83L, and CB6H-XG83L) to determine the binding affinity using surface plasmon resonance (SPR). 2021 Frontiers in immunology Result SARS_CoV_2 S309H;S309H 245;232 250;237 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. 6), while M49I and L50F in 3CLpro. 2021 Iranian journal of microbiology Result SARS_CoV_2 L50F;M49I 19;10 23;14 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. All samples represent from other continents, randomly taken from GISAID, were also recorded harbouring D614G. 2021 Iranian journal of microbiology Result SARS_CoV_2 D614G 103 108 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Beside the A352S mutation, we also recorded the S477I mutation, which located in spike protein S1 domain. 2021 Iranian journal of microbiology Result SARS_CoV_2 A352S;S477I 11;48 16;53 S 81 86 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. From phylogenetic tree analysis of spike protein using Genious Prime, we found the similar result as nucleotide alignment, that the G clade marked as D614G mutation, dominated the result with percentage about 59% (26/44). 2021 Iranian journal of microbiology Result SARS_CoV_2 D614G 150 155 S 35 40 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. In the ORF1a region of SARS-Cov-2, we detected four different mutations: P77L and V205I which found in PLpro. 2021 Iranian journal of microbiology Result SARS_CoV_2 P77L;V205I 73;82 77;87 ORF1a 7 12 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Interestingly, we recorded a mutation in active binding site of 3CLpro, M49I, which found in one sample from Yogyakarta (EPI_ISL_516806). 2021 Iranian journal of microbiology Result SARS_CoV_2 M49I 72 76 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Meanwhile, we recorded three unique mutations at A352S, S477I, and Q677H. 2021 Iranian journal of microbiology Result SARS_CoV_2 A352S;Q677H;S477I 49;67;56 54;72;61 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Mutation Q677H was found firstly in Surabaya on April 2020 (EPI_ISL_437188), then three months later it was found in Jawa Barat, in two different samples (EPI_ISL_518751 and EPI_ ISL_518759) in July 2020. 2021 Iranian journal of microbiology Result SARS_CoV_2 Q677H 9 14 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. One different mutation form GR and GH clade which found in alignment was G28882A. 2021 Iranian journal of microbiology Result SARS_CoV_2 G28882A 73 80 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Recently, D614G mutation was spread massively and increased rapidly in late samples submitted. 2021 Iranian journal of microbiology Result SARS_CoV_2 D614G 10 15 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Surprisingly, substitution P77L was found in three samples from different regions, Yogyakarta, Jawa Tengah and Jawa Barat (EPI_ ISL_516800; EPI_ISL_525492; EPI_ISL_528752, respectively). 2021 Iranian journal of microbiology Result SARS_CoV_2 P77L 27 31 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The alignment of Q677H is showed in. 2021 Iranian journal of microbiology Result SARS_CoV_2 Q677H 17 22 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The alignment of S477I mutation is shown in. 2021 Iranian journal of microbiology Result SARS_CoV_2 S477I 17 22 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The alignment performed by MAFFT version 7 and visualized by MSAViewer showed a predominance of D614G mutation. 2021 Iranian journal of microbiology Result SARS_CoV_2 D614G 96 101 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The D614G mutation was also found in Yogyakarta, Tangerang, Jakarta, Jawa Tengah, and Sidoarjo. 2021 Iranian journal of microbiology Result SARS_CoV_2 D614G 4 9 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The last mutation was detected L50F from Bandung (EPI_ISL_511878). 2021 Iranian journal of microbiology Result SARS_CoV_2 L50F 31 35 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The mutation A352S was found in two samples EPI_ISL_458081 and EPI_ ISL_529964. 2021 Iranian journal of microbiology Result SARS_CoV_2 A352S 13 18 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The mutation of V205I was observed in Bandung (EPI_ISL_511879). 2021 Iranian journal of microbiology Result SARS_CoV_2 V205I 16 21 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The position of A352S is in the spike protein S1 domain. 2021 Iranian journal of microbiology Result SARS_CoV_2 A352S 16 21 S 32 37 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The position of Q677H is the S1 domain, relatively close to S1/S2 junction. 2021 Iranian journal of microbiology Result SARS_CoV_2 Q677H 16 21 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. This sample was also recorded harboring D614G mutation. 2021 Iranian journal of microbiology Result SARS_CoV_2 D614G 40 45 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. According to the mini-spike sequences, all SARS-CoV-2 circulating during the first epidemic wave derive from the 20A clade that evolves into two groups: one being clade 20B that comprises the ancestor viruses at the origin of the group 1 mutant virus carrying the non-synonymous mutation C18495T (leading to P1675L substitution in the ORF1b) and the synonymous mutation C19836T, and the other group comprising viruses carrying either the non-synonymous C21365T mutation compared to the 20A consensus sequence (cluster 6) or both mutations C21365T and C21789T (cluster 4). 2021 Frontiers in medicine Result SARS_CoV_2 C18495T;C19836T;C21365T;C21365T;C21789T;P1675L 288;370;453;539;551;308 295;377;460;546;558;314 S 22 27 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. Additional non-synonymous mutations were found in the mini-spike of some viruses, including G21624C (leading to a substitution R21T), C21789T (leading to a substitution T76I), and G22093C (leading to a substitution M177I), all located in the spike N-terminal domain. 2021 Frontiers in medicine Result SARS_CoV_2 C21789T;G21624C;G22093C;M177I;R21T;T76I 134;92;180;215;127;169 141;99;187;220;131;173 S;S;N 59;242;248 64;247;249 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. Regarding the viruses circulating during the inter-wave period, they belong to clade 20A with one virus which carried the non-synonymous mutation C21365T in the ORF1b. 2021 Frontiers in medicine Result SARS_CoV_2 C21365T 146 153 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. Six viruses showed only this mutation in the mini-spike region, while most other viruses (16 strains) carried an additional non-synoymous mutation C21365T in the ORF1b, leading to a P2633L substitution in the pp1ab precursor of nsp16 methyltransferase. 2021 Frontiers in medicine Result SARS_CoV_2 C21365T;P2633L 147;182 154;188 S 50 55 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. We found (Table 1) that during the first epidemic wave, all viruses derived from the Wuhan-Hu-1 reference strain but carried the non-synonymous A23403G mutation, leading to the substitution D614G in the spike. 2021 Frontiers in medicine Result SARS_CoV_2 A23403G;D614G 144;190 151;195 S 203 208 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. A closer examination of the deposited sequences in the United Kingdom shows the K203/R204 variant increasing in prevalence early in 2020, but the second wave later in the year shows a shift in the proportion of deposited sequences with the R203/G204 subset of the D614G variant (B.1.177 lineage) until the more recent appearance of the B.1.1.7 'Alpha or UK variant' that harbors the K203/R204 polymorphisms (Supplemental Figure 1 and Supplemental Table 4); supporting a likely increased infectivity of this variant. 2021 Pathogens & immunity Result SARS_CoV_2 D614G 264 269 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. Adjacent nucleocapsid polymorphisms emerged from the existing spike protein D614G variant. 2021 Pathogens & immunity Result SARS_CoV_2 D614G 76 81 N;S 9;62 21;67 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. Although the D614G change rapidly increased in prevalence in almost all regions, the prevalence rates of the K203/R204 subset of the D614G variant are variable in different geographic areas and over time (Figure 2). 2021 Pathogens & immunity Result SARS_CoV_2 D614G;D614G 13;133 18;138 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. As discussed above, the K203/R204 variants appear to have emerged within the subset of SARS-CoV-2 sequences with a D614G variant in the spike protein, which has been associated with infections with a higher viral load in the upper respiratory tract. 2021 Pathogens & immunity Result SARS_CoV_2 D614G 115 120 S 136 141 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. As of the end of January 2021, the K203/R204 variant comprises 37.4% of globally reported SARS-CoV-2 sequences (Figure 1) and almost exclusively occurs on the D614G genetic background (Supplemental Table 4). 2021 Pathogens & immunity Result SARS_CoV_2 D614G 159 164 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. Consistent with recent findings, presence of a spike D614G variant was significantly associated with lower CT values (higher viral loads) in the same subset of individuals, even when day of illness at sampling is included in the model (Supplemental Table 8A, D614/R203/G204 vs G614/R203/G204, P=0.00011, Figures 5A and B). 2021 Pathogens & immunity Result SARS_CoV_2 D614G 53 58 S 47 52 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. Interestingly, the increased levels of ORF9b may be due to the D3L mutation in the nucleocapsid that we have proposed to have arisen similarly to the R203G/G204R mutations and is associated with increased levels of B.1.1.7 sgRNA encoding ORF9b in clinical samples. 2021 Pathogens & immunity Result SARS_CoV_2 D3L;R203G;G204R 63;150;156 66;155;161 N 83 95 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. Notably, SARS-CoV-2 R203K/G204R polymorphisms modify the predicted binding of putative HLA-restricted T-cell epitopes containing these residues (Supplemental Table 2). 2021 Pathogens & immunity Result SARS_CoV_2 R203K;G204R 20;26 25;31 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. Of the 455,774 circulating variants there were 29 amino acid polymorphisms present in >5% of the deposited sequences (of a total of 9413 sites; Supplemental Table 1) including the spike D614G variant (B.1 lineage) that emerged early in the pandemic and the adjacent R203K/G204R variants (B.1.1 lineage) in the nucleocapsid protein that formed one of the main variants emerging from Europe in early 2020. 2021 Pathogens & immunity Result SARS_CoV_2 D614G;R203K;G204R 186;266;272 191;271;277 N;S 310;180 322;185 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. The adaptive potential of differential expression of sgRNAs is supported by a recent study by Thorne and colleagues that demonstrates that the B.1.1.7 ('Alpha' or UK variant) isolate containing the R203K/G204R substitutions is associated with enhanced antagonism of the innate immune response. 2021 Pathogens & immunity Result SARS_CoV_2 R203K;G204R 198;204 203;209 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. Their study also provides experimental confirmation of our findings that N* sgRNA levels are high and unique to isolates with the R203K/G204R mutations. 2021 Pathogens & immunity Result SARS_CoV_2 R203K;G204R 130;136 135;141 N 73 74 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. These findings argue against stepwise change of the nucleotides for the R203K/G204R variant. 2021 Pathogens & immunity Result SARS_CoV_2 R203K;G204R 72;78 77;83 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. This effect was independent of the reduced sensitivity to type I and III IFNs described for isolates carrying the D614G spike mutation. 2021 Pathogens & immunity Result SARS_CoV_2 D614G 114 119 S 120 125 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. This variant has acquired an R203M substitution as a result of a single nucleotide change while retaining glycine (G) at position 204. 2021 Pathogens & immunity Result SARS_CoV_2 R203M 29 34 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. A similar neutralizing potency of most mAbs against the SARS-CoV-2(V367F) pseudovirus particle was observed. 2021 MedComm Result SARS_CoV_2 V367F 67 72 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. As shown in Figures 3E and 3F, the triple-mAb cocktail containing MA1 and MA5 combined with either MA2 or MA4 exhibited a higher neutralization potency than the pair-mAb cocktails or single usage of mAb against SARS-CoV-2(V367F) pseudovirus. 2021 MedComm Result SARS_CoV_2 V367F 222 227 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. Based on the binding data, MA5 strongly interacted with the SARS-CoV-2 RBD and inhibited binding of the RBD to ACE2; however, it was less potent to neutralize the SARS-CoV-2 pseudovirus, live virus, and SARS-CoV-2(V367F) pseudovirus compared with other mAbs, indicating that it might have recognized a distinct epitope on the RBD, limiting its neutralizing activity. 2021 MedComm Result SARS_CoV_2 V367F 214 219 RBD;RBD;RBD 71;104;326 74;107;329 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. However, MA1 was less potent to neutralize the SARS-CoV-2(V367F) pseudovirus than the wild-type SARS-CoV-2 and live virus, indicating that a conformational change of RBDV367F might have occurred within these antigenic sites. 2021 MedComm Result SARS_CoV_2 V367F 58 63 RBD 166 169 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. In line with the isolation of a three-mAb RBD complex, these findings confirmed that mAbs recognizing sites I, III, and IV could bind to RBDV367F simultaneously, leading to an increase in neutralization activity against SARS-CoV-2(V367F). 2021 MedComm Result SARS_CoV_2 V367F 231 236 RBD;RBD 42;137 45;140 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. RBD-specific mAb cocktails have potent neutralizing activity against SARS-CoV-2(V367F) pseudovirus. 2021 MedComm Result SARS_CoV_2 V367F 80 85 RBD 0 3 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. Whether high-affinity RBD-targeted mAbs could efficiently neutralize SARS-CoV-2 live and pseudovirus and SARS-CoV-2(V367F) pseudovirus particles was determined. 2021 MedComm Result SARS_CoV_2 V367F 116 121 RBD 22 25 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Among 9 single site mutants, 2 mutants (N439K and S477I) did not express very well and appreciable amount of protein needed for binding studies could not be obtained for these mutants. 2021 The Journal of biological chemistry Result SARS_CoV_2 S477I;N439K 50;40 55;45 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Another interesting observation is the decrease in DeltaH value for K417N and Y453F mutants, indicating decreased strength of interactions between the mutants and CC12.1. 2021 The Journal of biological chemistry Result SARS_CoV_2 K417N;Y453F 68;78 73;83 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Apart from the single site mutations, clone carrying double mutations E484K/N501Y did not express. 2021 The Journal of biological chemistry Result SARS_CoV_2 E484K;N501Y 70;76 75;81 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Because of protein expression constraints, further studies on the mutant proteins were carried out on 7 single site mutants (K417N, Y453F, S477N, T478I, E484K, S494P and N501Y) and the triple mutant K417T/E484K/N501Y, which were purified to homogeneity along with ACE2 and CC12.1 single chain variable fragment (ScFv). 2021 The Journal of biological chemistry Result SARS_CoV_2 E484K;K417T;N501Y;S477N;S494P;T478I;Y453F;K417N;E484K;N501Y 153;199;170;139;160;146;132;125;205;211 158;204;175;144;165;151;137;130;210;216 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Compared to other mutants, T478I and E484K showed slightly lesser thermal stability. 2021 The Journal of biological chemistry Result SARS_CoV_2 E484K;T478I 37;27 42;32 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. E484K and T478I mutants however showed increased affinity towards CC12.1 ScFv with a Kd value of 1.7 +- 4.6 and 5.8 +- 3.4 nM respectively (Table 4), which suggests that CC12.1 may be able to neutralize E484K and T478I mutants. 2021 The Journal of biological chemistry Result SARS_CoV_2 E484K;T478I;T478I;E484K 203;10;213;0 208;15;218;5 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Expression levels comparable to or higher than the wild type was obtained for 5 single site mutants K417N, Y453F, S477N, S494P and N501Y. 2021 The Journal of biological chemistry Result SARS_CoV_2 K417N;N501Y;S477N;S494P;Y453F 100;131;114;121;107 105;136;119;126;112 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. For S477N mutant, Kd value was similar to that of the wild-type, but an increased DeltaH value of 16.4 +- 0.2 kcal/mol was obtained, which may indicate increased interactions between RBD and ACE2 upon mutation. 2021 The Journal of biological chemistry Result SARS_CoV_2 S477N 4 9 RBD 183 186 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. For two other mutants K417N and E484K, the Kd value obtained was higher than the wild-type protein (Table 3), indicating weaker affinity for ACE2. 2021 The Journal of biological chemistry Result SARS_CoV_2 E484K;K417N 32;22 37;27 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Other 4 variants, single site mutants K417N, Y453F, N501Y (Alpha variant) and the triple mutant K417T/E484K/N501Y (Gamma variant), showed decreased affinity towards CC12.1 binding, with Kd values of 119 +- 50 nM, 827 +- 146 nM, 63 +- 22 and 433 +- 95 nM respectively, representing escape from CC12.1. 2021 The Journal of biological chemistry Result SARS_CoV_2 K417N;K417T;N501Y;Y453F;E484K;N501Y 38;96;52;45;102;108 43;101;57;50;107;113 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Out of the 8 mutants studied, 2 single site mutations (S477N and S494P) did not impact the binding affinity of RBD towards CC12.1 ScFv. 2021 The Journal of biological chemistry Result SARS_CoV_2 S494P;S477N 65;55 70;60 RBD 111 114 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Since software used for deconvoluting CD spectra in general accounts only for regular secondary structures, minor differences in the CD spectra of the triple mutant K417T/E484K/N501Y could be due to changes in short, irregular and non-repeating secondary structures most probably in the RBM region. 2021 The Journal of biological chemistry Result SARS_CoV_2 K417T;E484K;N501Y 165;171;177 170;176;182 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. The clone carrying triple mutations (K417N/E484K/N501Y) corresponding to the Beta variant also could not be expressed, but the other clone carrying triple mutations (K417T/E484K/N501Y) corresponding to the Gamma variant showed high expression. 2021 The Journal of biological chemistry Result SARS_CoV_2 K417N;K417T;E484K;E484K;N501Y;N501Y 37;166;43;172;49;178 42;171;48;177;54;183 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. The corresponding DeltaH values did not show any significant difference for K417N mutant but showed a decreased value of 9.5 +- 0.2 kcal/mol for E484K mutant. 2021 The Journal of biological chemistry Result SARS_CoV_2 E484K;K417N 145;76 150;81 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. The levels of expression were also low for 2 other single site mutants T478I and E484K. 2021 The Journal of biological chemistry Result SARS_CoV_2 E484K;T478I 81;71 86;76 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. The other single site mutant N501Y corresponding to the Alpha variant and the triple mutant K417T/E484K/N501Y corresponding to the Gamma variant showed increased affinity for ACE2 binding with Kd values of 3.0 +- 2.1 nM and 1.6 +- 1.5 nM respectively when compared to the wild-type (Table 3). 2021 The Journal of biological chemistry Result SARS_CoV_2 K417T;N501Y;E484K;N501Y 92;29;98;104 97;34;103;109 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. There was no difference in DeltaH values for N501Y mutant and the triple mutant K417T/E484K/N501Y. 2021 The Journal of biological chemistry Result SARS_CoV_2 K417T;N501Y;E484K;N501Y 80;45;86;92 85;50;91;97 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Three of the 8 mutants, Y453F, T478I and S494P, did not show significant difference in their binding interaction with ACE2, with Kd and DeltaH values similar to the wild-type protein (Table 3). 2021 The Journal of biological chemistry Result SARS_CoV_2 S494P;T478I;Y453F 41;31;24 46;36;29 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. 4c & d) was observed between HK-405 and the Alpha variants, indicating that the pathogenicity of the Alpha variants is comparable to the pre-existing D614G variants. 2021 Communications biology Result SARS_CoV_2 D614G 150 155 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. A recent study indicated that the SARS-CoV-2 variant of concern (VOC) carrying the 501Y (B.1.1.7 or the Alpha variant) mutation showed no higher infectivity in Huh-7, Vero, and LLC-MK2 cells than ancestral D614G variants. 2021 Communications biology Result SARS_CoV_2 D614G 206 211 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. Consistently, we demonstrated that the immune stimulatory activity of conditioned media in the Alpha variant infected Calu-3 cells was much attenuated than that of the earlier D614G variants. 2021 Communications biology Result SARS_CoV_2 D614G 176 181 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. Likewise, we did not observe replication of the Alpha variant to be significantly enhanced over that of the pre-existing D614G variants (HK-95, collection date: 2020-05-15 and HK-405, collection date: 2020-12-08). 2021 Communications biology Result SARS_CoV_2 D614G 121 126 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. SARS-CoV-2 Alpha variant replicated more efficiently in the nasal cavity of hamsters than earlier D614G lineage with enhanced transmission in hamsters. 2021 Communications biology Result SARS_CoV_2 D614G 98 103 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. SARS-CoV-2 Alpha variant showed enhance replication fitness compared with earlier D614G variants. 2021 Communications biology Result SARS_CoV_2 D614G 82 87 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. These comparisons of replication fitness between the Alpha variant and earlier circulating strains were performed in Calu-3 cells and in hamsters through simultaneous co-infection at a 1:1 ratio with the Alpha variant and early variants of the D614G lineage (HK-405 or HK-95). 2021 Communications biology Result SARS_CoV_2 D614G 244 249 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. A correlation was found between mAb2-RBD affinity and the extent of inhibition of the ACE2-RBD interactions; this is because the kon, koff, and KD values of the mAb2-E484K interaction were significantly lower than those of the original RBD (which had higher KD and EC50 values, indicating lower binding affinity). 2022 Journal of pharmaceutical analysis Result SARS_CoV_2 E484K 166 171 RBD;RBD;RBD 37;91;236 40;94;239 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. Aligning with recently reported data, the RBD proteins containing the Y453F and N501Y mutations were found to exhibit significantly enhanced binding to ACE2 relative to the original sequence RBD, which might be attributable to the slower koff for these mutant RBDs. 2022 Journal of pharmaceutical analysis Result SARS_CoV_2 N501Y;Y453F 80;70 85;75 RBD;RBD;RBD 42;191;260 45;194;264 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. Based on the results for the interactions between the original RBD and mutants with mAb1, all RBD/S1 mutants, except E484K, displayed a decrease in affinity (Table S5). 2022 Journal of pharmaceutical analysis Result SARS_CoV_2 E484K 117 122 RBD;RBD 63;94 66;97 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. Hence, a higher concentration of mAb2 would be required to block the interaction between ACE2 and E484K. 2022 Journal of pharmaceutical analysis Result SARS_CoV_2 E484K 98 103 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. Preincubation of mAb2 resulted in the complete blocking of ACE2-RBD mutant binding interactions for all mutants, except for E484K, where only partial inhibition of the interaction was observed using 100 nM of mAb2. 2022 Journal of pharmaceutical analysis Result SARS_CoV_2 E484K 124 129 RBD 64 67 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. Such finding is consistent with that of recent studies where the increased infectivity of viruses with the D614G mutation was not found to be explained by a greater ACE2 binding activity. 2022 Journal of pharmaceutical analysis Result SARS_CoV_2 D614G 107 112 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. The D614G and N501Y mutant RBD/S1 proteins displayed distinct kinetic profiles. 2022 Journal of pharmaceutical analysis Result SARS_CoV_2 D614G;N501Y 4;14 9;19 RBD 27 30 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. The kon and koff of N439K were found to be approximately 0.8-fold faster, resulting in a slightly higher affinity than that of the original RBD. 2022 Journal of pharmaceutical analysis Result SARS_CoV_2 N439K 20 25 RBD 140 143 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. The kon of mutant D614G to ACE2 was 4.8-fold slower than that of the original RBD, whereas the koff was 0.5-fold faster, resulting in a 10-fold decrease in the binding affinity. 2022 Journal of pharmaceutical analysis Result SARS_CoV_2 D614G 18 23 RBD 78 81 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. The kon of N501Y and Y453F RBD mutants was comparable to that of the original RBD, whereas koff was 3.4-fold slower for N501Y and 7.8-fold slower for Y453F, resulting in an overall 3.4-fold increase in the affinity for N501Y and a 6.7-fold increase for Y453F. 2022 Journal of pharmaceutical analysis Result SARS_CoV_2 N501Y;N501Y;N501Y;Y453F;Y453F;Y453F 11;120;219;21;150;253 16;125;224;26;155;258 RBD;RBD 27;78 30;81 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. The kon of the E484K mutant was 1.5-fold faster than the ACE2-original RBD interaction, whereas the koff was 0.7-fold faster than the original RBD, resulting in a 0.7-fold decrease in the affinity. 2022 Journal of pharmaceutical analysis Result SARS_CoV_2 E484K 15 20 RBD;RBD 71;143 74;146 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. The low similarity score (21.1%) of D614G relative to the original RBD, compared to the other mutants, also highlighted the impact of the mutation relative to the binding interaction. 2022 Journal of pharmaceutical analysis Result SARS_CoV_2 D614G 36 41 RBD 67 70 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. The relative kinetic parameters for the mAb1-RBD/S1 interaction indicated that all mutant proteins had a reduced relative KD to the original RBD, except for E484K, where the affinity had increased by 11.9% (Table S6). 2022 Journal of pharmaceutical analysis Result SARS_CoV_2 E484K 157 162 RBD;RBD 45;141 48;144 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. The sensorgrams overlaid with a fitted 1:1 binding model for mAb1-original RBD and mAb1-mutant interactions revealed a significant difference in the kinetic profiles between D614G and the other RBD interactions. 2022 Journal of pharmaceutical analysis Result SARS_CoV_2 D614G 174 179 RBD;RBD 75;194 78;197 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. The Y453F and N501Y mutant RBD proteins displayed a significant increase in ACE2-RBD binding affinity relative to the original RBD, and D614G had a substantial reduction in binding affinity. 2022 Journal of pharmaceutical analysis Result SARS_CoV_2 D614G;N501Y;Y453F 136;14;4 141;19;9 RBD;RBD;RBD 27;81;127 30;84;130 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. These findings suggest a potential reduction in the neutralization capability of mAb1 for each mutant (especially D614G) and a potential increase in the likelihood of the mutated virus escaping the immune response. 2022 Journal of pharmaceutical analysis Result SARS_CoV_2 D614G 114 119 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. CT-P59 was less susceptible to L452R, but retained its own neutralizing effect against T478K, and P681H (Table 2 and Supplementary. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L452R;P681H;T478K 31;98;87 36;103;92 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. E484K (8.66-fold) and N501Y (5.49-fold) was less than 10-fold susceptible to CT-P59, but CT-P59 showed lower IC50 value (0.7-fold) against K417T. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 K417T;N501Y;E484K 139;22;0 144;27;5 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. To investigate the therapeutic efficacy of CT-P59 against Gamma, Delta and Epsilon variants, we first evaluated the binding affinity of CT-P59 against mutant RBDs (K417T/E484K/N501Y, L452R/T478K and L452R) by using Bio-Layer interferometry. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 L452R;L452R;K417T;E484K;N501Y;T478K 183;199;164;170;176;189 188;204;169;175;181;194 RBD 158 162 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. A249V exhibited a similar RMSF value for this loop of ~ 0.3 nm in free and complex systems. 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V 0 5 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. A249V mutation, where alanine (A) is replaced with valine (V) residue at the position 249 distorts a helix backbone, hence, beta-sheet is formed at the same position as compared to the Wuhan type sequence. 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V 0 5 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. Consistent with the above free energy (DeltaDeltaG) calculation, D108G displayed a greater Rg, indicating lower compactness of protein, while A249V did not show a significant change in protein compactness. 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V;D108G 142;65 147;70 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. D108G mutation shows that the substitution of aspartate (D), a bulky amino acid to glycine (G), the simplest amino acid, at position 108 resulted in a distortion of a helical structure at position 107 of the PLPro. 2022 Saudi journal of biological sciences Result SARS_CoV_2 D108G 0 5 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. However, A249V increased rigidity, while D108G confers structural flexibility at the site of the mutations in the PLPro structure. 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V;D108G 9;41 14;46 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. However, hydrogen bonds between GRL0617 and with A249V and D108G mutants were not stable and reduced to 2 bonds during the last 15 ns. 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V;D108G 49;59 54;64 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. Notably, the amino acid mutated from A to V increases the volume of the amino acid at this position in A249V. 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V 103 108 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. On the other hand, the change in the structural stability of PLPro induced by the A249V mutation indicates that the alanine to valine substitution leads to stabilization of protein structure, DeltaDeltaG of 0.594 kcal mol-1. 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V 82 87 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. One sequence was found to harbor a mutation Asp108 Gly of PLPro (D108G), while the other mutation was found at position 249 Ala249 Val (A249V). 2022 Saudi journal of biological sciences Result SARS_CoV_2 D108G;A249V;D108G 44;140;67 56;145;72 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. PLPro stability analysis showed that the D108G substitution resulted in a slightly more dynamic structure with DeltaDeltaG of -0.418 kcal mol-1 (a destabilizing mutation). 2022 Saudi journal of biological sciences Result SARS_CoV_2 D108G 41 46 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. The average Rg values of WT, D108G, and A249V mutations were found to be 2.32 +- 0.02, 2.35 +- 0.02, and 2.31 +- 0.01 nm, respectively (Table 2). 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V;D108G 40;29 45;34 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. The BL2 loop region (residues 266-271) shows significantly higher RMSF upon inhibitor binding to WT (+0.23 nm) and D108G (+0.18 nm). 2022 Saudi journal of biological sciences Result SARS_CoV_2 D108G 115 120 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. The D108G PLPro-GRL0617 complex was less stable than WT PLPro-GRL0617 and A249V PLPro-GRL0617 with average Rg values of 1.66 +- 0.02, 1.69 +- 0.02 and 1.62 +- 0.01 nm for WT, A249V and D108G, respectively. 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V;A249V;D108G;D108G 74;175;4;185 79;180;9;190 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. The exchange of the hydrophobic residue alanine with hydrophobic valine residue (A249V) also results in changes in intramolecular interactions. 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V 81 86 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. The GRL0617 interacts by up to 2 hydrogen bonds with WT and by up to 3 hydrogen bonds with A249V and D108G mutants (Table 3 ). 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V;D108G 91;101 96;106 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. The MD analysis for the WT, D108G, and A249V showing the RMSD values of the PLPro backbone for the simulated structures is presented in. 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V;D108G 39;28 44;33 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. The mean RMSF values calculated from 0 to 20 ns for the WT, D108G, and A249Vsystems are 0.10 +- 0.05, 0.10 +- 0.05, and 0.09 +- 0.04 nm, respectively (Table 2). 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V;D108G 71;60 76;65 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. The RMSD for D108G and A249V mutants were slightly higher than WT with average values of 0.17 +- 0.04, 0.18 +- 0.02, 0.19 +- 0.02 nm for WT, D108G and A249V, respectively (Table 2 ). 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V;A249V;D108G;D108G 23;151;13;141 28;156;18;146 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. The RMSD values for both D108G PLPro-GRL0617 and A249V PLPro-GRL0617 complexes exhibited roughly steady values (average ~ 0.2 nm) through the 20 ns run with some negligible fluctuations. 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V;D108G 49;25 54;30 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. The vibrational entropy energy between the WT and the mutants (D108G and A249V) yielded DeltaDeltaSVib ENCoM values of 0.495 and 0.053 kcal mol-1 K-1 respectively, which suggests an increase in overall molecular flexibility in the mutated PLPro protein (Table 1). 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V;D108G 73;63 78;68 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. These results indicating that the binding of GRL0617 might be altered by D108G more than A249V mutation. 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V;D108G 89;73 94;78 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. This indicates that D108G is less compact and more flexible, whereas A249V maintains a proper folding. 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V;D108G 69;20 74;25 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. While the D108G mutant exhibits a higher SASA of 167 nm2, A249V demonstrated a lower SASA value of 162 nm2 compared to the WT protein (Table 2). 2022 Saudi journal of biological sciences Result SARS_CoV_2 A249V;D108G 58;10 63;15 34549097 Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran. One of them (23525C > T) leads to a missense and the rest (22042T > C, 22708 G > T, 25318C > A) result in synonymous changes. 2021 Heliyon Result SARS_CoV_2 G22708T;C25318A;T22042C;C23525T 71;84;59;13 82;94;69;23 34549097 Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran. One SNV (22042T > C) was the same as one in AK-SARS-48 and two of them (22350A > V and 23997C > G) corresponded to missense changes. 2021 Heliyon Result SARS_CoV_2 C23997G;T22042C;A22350V 87;9;72 97;19;82 34549097 Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran. The remaining two SNVs, (13129A > G) and (20446A > T) in ORFab result in a synonymous change and a stop codon with very low frequency, respectively. 2021 Heliyon Result SARS_CoV_2 A13129G;A20446T 25;42 35;52 34549097 Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran. The sample AK-SARS-27 had only one SNV (23403A > G) which corresponded to the missense change D614G. 2021 Heliyon Result SARS_CoV_2 D614G;A23403G 94;40 99;50 34549097 Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran. There was only one SNV (28688T > C) in the N gene which corresponded to a synonymous change in amino acid with 100% frequency. 2021 Heliyon Result SARS_CoV_2 T28688C 24 34 N 43 44 34549097 Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran. Two SNVs (1397 G > A and 11083 G > T) of four in ORFab corresponded to a missense change with high frequency. 2021 Heliyon Result SARS_CoV_2 G11083T;G1397A 25;10 36;20 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Across the 3 versions of the B.1.351 variant tested, 6.9-fold to 8.4-fold reductions in neutralization were observed compared with that for D614G. 2021 Journal of virology Result SARS_CoV_2 D614G 140 145 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Among all variants tested, the greatest effect on neutralization was observed for A.VOI.V2 and B.1.351-v3 (8.1-fold and 8.4-fold reductions compared with activity against D614G, respectively). 2021 Journal of virology Result SARS_CoV_2 D614G 171 176 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. In contrast, all other variants examined showed significantly decreased neutralization titers compared with D614G (P < 0.01). 2021 Journal of virology Result SARS_CoV_2 D614G 108 113 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. mRNA-1273-elicited neutralization titers against B.1.1.7, B.1.1.7+E484K, B.1.427/B.1.429, P.1, and B.1.351-v1 observed herein corroborated previous findings. 2021 Journal of virology Result SARS_CoV_2 E484K 66 71 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Reductions in neutralization titers for these variants ranged from a factor of 2.1 to 8.4 compared with that for D614G. 2021 Journal of virology Result SARS_CoV_2 D614G 113 118 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Results showed minimal, statistically nonsignificant effects on neutralization titers against B.1.1.7 and A.23.1-v1 compared to D614G (P = 0.64 and 0.46, respectively). 2021 Journal of virology Result SARS_CoV_2 D614G 128 133 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. We assessed neutralization activity of sera against D614G pseudovirus (predominant variant in 2020), B.1.1.7, B.1.1.7+E484K, B.1.351-v1, B.1.351-v2, B.1.351-v3, P.1, B.1.617.2-v1, B.1.617.2-v2, B.1.525, B.1.526, B.1.617.1-v1, B.1.617.1-v2, C.37-v1, C.37-v2, B.1.427/B.1.429, B.1.621, A.23.1-v1, A.23.1-v2, and A.VOI.V2 (Table 1). 2021 Journal of virology Result SARS_CoV_2 D614G;E484K 52;118 57;123 34550770 Discovery and Evaluation of Entry Inhibitors for SARS-CoV-2 and Its Emerging Variants. Increased exposure of MU-UNMC-2 to the solvent in B.1.351 appears is due to mutation N501Y, which reduced the size of the binding pocket. 2021 Journal of virology Result SARS_CoV_2 N501Y 85 90 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Additionally, we compared seven pairs of mAb-spike (trimer) and mAb-RBD (Table 2), the same effect tendency of E484K mutation on binding free energy was observed by using trimer structure or RBD only. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 111 116 S;RBD;RBD 45;68;191 50;71;194 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. By analyzing the crystal structure, e.g., 6XE1, we found that the position of E484 is 7.7 A away from the mAb-RBD interface (Figure 4C and D); therefore, the E484K mutation should have little effect on the overall binding free energy. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 158 163 RBD 110 113 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. By structural analysis, we found 26 mAbs bind to RBM and even near the position of E484, indicating that most of the current mAbs are likely influenced by the E484K mutation. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 159 164 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. For the RBD-down state (7K43), the sum of N-glycan contribution to the overall binding free energy is -1.06 +- 0.16 kcal/mol (WT) and 2.20 +- 0.06 kcal/mol (E484K), respectively. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 157 162 RBD;N 8;42 11;43 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. For the RBD-up state (7K4N), similar results were observed, the sum of N-glycan contribution in the predicted binding free energy is also very small, which is 0.06 +- 0.00 kcal/mol (WT) and 0.97 +- 0.04 kcal/mol (E484K), respectively. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 213 218 RBD;N 8;71 11;72 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. found that a lysine mutation at residue 486 (F486K) of the RBD helps SARS-CoV-2 escape neutralization by REGN10933 with slightly decreased binding affinity to ACE2. 2022 Briefings in bioinformatics Result SARS_CoV_2 F486K 45 50 RBD 59 62 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. found that the neutralization IC50 of REGN10933 on the E484K mutant and SA 9 (B.1.351) variant was 10.5 and 58.8 times lower than that of the WT, respectively. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 55 60 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Furthermore, by structural analyses, we found that the E484K mutation causes the four residues closer to the mAb, enhancing their interactions with the mAb. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 55 60 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. However, the binding site for E484 in 7K9Z is negatively charged (Figure 4E); therefore, the E484K mutation should enhance the binding of RBD to mAbs (Table S2). 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 93 98 RBD 138 141 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. However, the F486K was not accessible via a single-nucleotide change. 2022 Briefings in bioinformatics Result SARS_CoV_2 F486K 13 18 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Impressively, one mAb combination system (PDB ID: 7K9Z) with two mAbs (52 & 298) has stronger binding affinity to E484K mutant than to WT (DeltaDeltaG = -15.87 +- 1.13 kcal/mol), which may work well to fight against the mutated virus. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 114 119 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. In summary, the E484K mutation might cause an obviously weakened binding affinity of about 85% mAbs to the spike protein of SARS-CoV-2. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 16 21 S 107 112 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. showed that S2M11 (PDB ID: 7K43) possessed lower neutralization ability in the E484K mutant, and Chen R. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 79 84 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. showed that the neutralization ability of S2E12 (PDB ID: 7K4N) was reduced about 5 folds against the E484K virus. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 101 106 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. The DeltaDeltaG between the WT and E484K mutant are 22.51 +- 1.03, 17.53 +- 0.78 and 16.34 +- 0.55 kcal/mol for glycosylated spike trimer, the spike trimer and the RBD, respectively (Table 1). 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 35 40 S;S;RBD 125;143;164 130;148;167 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. The difference of binding free energy between WT and E484K mutant RBDs to the mAb REGN10933. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 53 58 RBD 66 70 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. The diverse impacts of E484K mutation on its binding affinities to 26 mAbs. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 23 28 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. The results showed that the glycosylation of spike protein may change the specific values of the calculated free energy, but does not alter the variation tendency of the E484K mutation effect. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 170 175 S 45 50 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. The significantly reduced G of the SARS-CoV-2 harboring E484K mutation to REGN10933 suggests its weakened neutralization efficacy, which is consistent with the experimentally determined neutralization IC50 values (resistance 10.5-fold). 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 57 62 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. The slightly increased binding free energies demonstrated that E484K mutation has a little beneficial effect on the binding strength of ACE2 to the RBD, which is consistent with biophysical studies. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 63 68 RBD 148 151 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Therefore, the special role of E484K mutation in immune evasion could be attributed to its significantly reduced binding affinity to mAbs. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 31 36 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. To evaluate whether the E484K mutation affects the ACE2 binding affinity, we calculated the G of ACE2 to the WT and the E484K mutant, which are -36.43 +- 0.77 ( GWT) and - 41.52 +- 0.69 kcal/mol ( GE484K), respectively. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K;E484K 24;121 29;126 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. To explore the potential effect of the E484K mutation on its binding to those mAbs, we constructed 25 complex structures of the E484K mutant RBD and the 26 mAbs. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K;E484K 39;128 44;133 RBD 141 144 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. To further explore the impact of simulation time on binding free energy, two REGN10933-RBD complexes for WT and E484K mutant, respectively, were run for 500 ns. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 112 117 RBD 87 90 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. To further explore the mechanism of the E484K mutation affecting the neutralization ability of mAbs, we compared energy contributions of E484 and K484 to the overall binding free energy (Figure 3, Table S2). 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 40 45 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. To further look into different binding modes, 3 mAb-RBD complexes are taken as representative examples, whose neutralization ability is decreased (PDB ID: 7CWO), unchanged (PDB ID: 6XE1) and enhanced (PDB ID: 7K9Z) after the E484K mutation, respectively. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 225 230 RBD 52 55 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Two systems, viz., 6XE1 (CV30) and 7CDJ (P2C-1A3), have similar binding free energies between WT and E484K mutant (DeltaDeltaG < 2.00 kcal/mol, Table S2), indicating that the neutralization of these mAbs is insensitive to the E484K mutation. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K;E484K;P2C 101;226;41 106;231;44 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. We calculated the binding free energy ( G) of REGN10933 to the WT and E484K mutant, respectively. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 70 75 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. With 2.00 kcal/mol as criteria, 22 systems show weaker binding affinity of mAb-RBDE484K than mAb-RBDWT (Table S2), indicating that 85% of the RBD-targeting mAbs might exhibit weaker neutralization ability to the E484K mutated virus. 2022 Briefings in bioinformatics Result SARS_CoV_2 E484K 212 217 RBD;RBD 79;142 82;145 34553696 Molecular docking studies of Indian variants of pathophysiological proteins of SARS-CoV-2 with selected drug candidates. Of these, the most significant were the D614G, E583D, L54F, Q613 and T572I mutations in the spike protein (Korber et al. 2021 Journal of genetics Result SARS_CoV_2 D614G 40 45 S 92 97 34553696 Molecular docking studies of Indian variants of pathophysiological proteins of SARS-CoV-2 with selected drug candidates. Previous studies have shown that the D614G mutation may confer a competitive advantage at furin binding sites (Tang et al. 2021 Journal of genetics Result SARS_CoV_2 D614G 37 42 34553696 Molecular docking studies of Indian variants of pathophysiological proteins of SARS-CoV-2 with selected drug candidates. The L54F mutation is seen to occur coupled with the D614G mutation. 2021 Journal of genetics Result SARS_CoV_2 D614G 52 57 34553696 Molecular docking studies of Indian variants of pathophysiological proteins of SARS-CoV-2 with selected drug candidates. The most significant stable interaction is that of Spike variant 1 (D614G) with ACE2 variant 1 (rs4646116) this is closely followed by Spike variant 1 (D614G) with ACE2 variant 2 (rs756905974). 2021 Journal of genetics Result SARS_CoV_2 D614G;D614G 68;152 73;157 S;S 51;135 56;140 34553696 Molecular docking studies of Indian variants of pathophysiological proteins of SARS-CoV-2 with selected drug candidates. This once again shows the exceptional stability of the D614G mutation. 2021 Journal of genetics Result SARS_CoV_2 D614G 55 60 34553696 Molecular docking studies of Indian variants of pathophysiological proteins of SARS-CoV-2 with selected drug candidates. This seems to hint at a stability conferred by the coupling of the L54F and D614G mutations. 2021 Journal of genetics Result SARS_CoV_2 D614G 76 81 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. In addition to the S-protein D614G mutation, other missense mutations were identified in NSP12 (RNA dependent RNA polymerase; RdRp) with a P323L mutation, a T85I mutation in NSP2, and a Q57H mutation in ORF3a protein. 2021 PeerJ Result SARS_CoV_2 D614G;P323L;Q57H;T85I 29;139;186;157 34;144;190;161 RdRp;ORF3a;Nsp12;Nsp2;RdRP;S 96;203;89;174;126;19 124;208;94;178;130;20 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. The mutations occurred in the S-protein, non-structural protein, and open reading frames (ORFs) (Table 2), including the D614G variant in the S-protein in Cases 1-4; the wild-type form was identified in Case 5. 2021 PeerJ Result SARS_CoV_2 D614G 121 126 S;S 30;142 31;143 34560289 SARS-CoV-2 B.1.1.7 lineage rapidly spreads and replaces R.1 lineage in Japan: Serial and stationary observation in a community. During the first wave (March to May 2020) in Japan, the B.1 and B.1.1 lineages with spike D614G mutation were predominant (Table 1). 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G 90 95 S 84 89 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. Compared with D614G reference strain immunized mice, a comparable ADCC response was found in B.1.1.7 variant and B.1.351 variant-immunized mice (B.1.1.7 vs. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G 14 19 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. D614G, P = 0.359. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G 0 5 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. D614G, P = 0.454; B.1.351 vs. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G 0 5 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. D614G, P = 0.861. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G 0 5 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. In contrast, slightly higher ADCC activities were measured in P.1-immunized mice than the B.1.1.7 variant- and B.1.351 variant-immunized mice and with a comparable level with those in D614G-immunized mice, however, with the difference attaining no significance (P.1 vs. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G 184 189 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. Similar ADCC activity was elicited against the three SARS-CoV-2 variants, all comparable with that of the D614G strain, which was observed in mice that received any type of the vaccination. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G 106 111 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. To compare differences among the D614G reference strain and three SARS-CoV-2 VOCs (B.1.1.7 variant, B.1.351 variant, and P.1 variant) in term of their ability to trigger the ADCC response, we tested sera collected from patients and mice inoculated with SARS-CoV-2 pseudotyped viruses. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G 33 38 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. We next assessed serum from mice vaccinated with inactivated vaccine, adenovirus vector vaccine, mRNA vaccine, and recombinant protein subunit vaccine in terms of their difference in ADCC activity against VOCs (B.1.1.7, B.1.351, and P.1 variants) compared with the D614G reference strain. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G 265 270 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. After the E484K mutation, the distances between them decrease to 19.8 A, 10.9 A, 13.8 A and 11.3 A, respectively, indicating tighter RBD-hACE2 binding interface caused by the E484K mutation, as shown in. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K;E484K 10;175 15;180 RBD 133 136 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Based on these simulation trajectories, the binding free energies of the wild-type RBD and the E484K mutant, respectively, complexed with these antibodies were calculated by using the MMGBSA method, and then the changes in the binding free energies between the wild-type and the mutant systems were computed to explore the influence of the E484K mutation on the binding affinities of RBD with these various neutralizing antibodies and nanobodies. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K;E484K 95;340 100;345 RBD;RBD 83;384 86;387 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Besides that, E484K mutation also leads to the decrease of the van der Waals and the nonpolar desolvation energies as shown in Table 1, where the value of is reduce from -103.64 kcal/mol to -106.52 kcal/mol. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 14 19 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Besides the mutated residue E484K itself, the contributions to the binding free energy by the residues Tyr489, Gln493, Leu492, Phe490, Phe486 and Asn487 on RBD were also distinctly promoted, as shown in. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 28 33 RBD 156 159 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. But the impact of Asp106 is relatively small owing to its large distance to the mutated residue E484K. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 96 101 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. E484K mutation distinctly reduces the binding affinity between RBD and most of the studied neutralizing antibodies and nanobodies. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 0 5 RBD 63 66 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. E484K mutation enhances the binding affinity between RBD and the receptor hACE2. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 0 5 RBD 53 56 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. For all the above neutralizing antibodies, a similar physical mechanism is observed to be responsible for the reduced RBD-antibody binding affinity caused by the mutation E484K, where the attractive electrostatic interactions are converted to be repulsive resulted by the residue mutation with reverse charge. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 171 176 RBD 118 121 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. For most of the residues on the binding interface, the E484K mutation results in favorable electrostatic forces as well as tighter binding mode, which distinctly improves the binding affinity. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 55 60 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. For nanobody MR17-K99Y complexed with RBD, the positively charged residues Arg59, Arg33 and Lys65 on MR17-K99Y are electrostatically attractive with Glu484 on RBD in the wild-type complex, as shown in. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 K99Y;K99Y 18;106 22;110 RBD;RBD 38;159 41;162 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. For nanobody MR17-K99Y, the E484K mutation has small effects on the binding affinity between this nanobody and RBD, where the binding free energy is changed from -70.71 kcal/mol to -71.22 kcal/mol. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K;K99Y 28;18 33;22 RBD 111 114 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. From the different components of the binding free energy as displayed in Table 3, it can be observed that for all these studied systems, the electrostatic energies increase upon the mutation of E484K, which significantly penalize the binding of the antibodies/nanobodies to the mutated RBD. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 194 199 RBD 286 289 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. However, the E484K mutation significantly enhances the gas-phase electrostatic interactions and alleviates the unfavorable energies for the burial of the charged and polar groups upon the binding of RBD with hACE2 as shown in Table 1. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 13 18 RBD 199 202 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. However, these unfavorable effects caused by the E484K mutation are minor. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 49 54 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. However, upon the mutation of Glu484 by Lys, the attractive electrostatic interactions with Arg107 are changed to be repulsive, which also leads to the sidechains of Lys484 and Arg107 moving apart, as shown in. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 30 43 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In addition to the changes in the electrostatic interactions, we also investigated the mechanism for the decrease of the van der Waals and the polar desolvation energies caused by the E484K mutation. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 184 189 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In order to explore the physical mechanism and the related key residues responsible for the rising of the electrostatic energies caused by the E484K mutation, the changes of the electrostatic energy contributed by each residue. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 143 148 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In order to quantitatively monitor the conformation changes, several pairwise residues across the binding interface were selected, including Glu484(RBD)-Lys68(hACE2), Gln474(RBD)-Phe28(hACE2), Cys480(RBD)-Gln24(hACE2) and Cys488(RBD)-Leu79(hACE2), and the average Calpha-Calpha distance for each residue pair was calculated both in the wild-type complex structure and in the E484K mutant. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 375 380 RBD;RBD;RBD;RBD 148;174;200;229 151;177;203;232 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In order to validate the simulation results, another MD simulation in a much longer time scale (500 ns) was also performed to investigate the impact of E484K mutation on the conformational changes of RBD in complex with hACE2. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 152 157 RBD 200 203 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In summary, for most of the studied neutralizing antibodies/nanobodies, the E484K mutation significantly reduces the binding affinities between them with RBD, and the decrease of the binding affinities is mainly due to the repulsive electrostatic interactions caused by the mutation. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 76 81 RBD 154 157 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In the complex of nanobody Nb20 with RBD, upon the mutation of E484 by Lys, the attractive electrostatic interactions formed by Glu484 on RBD with Arg31 and Arg97 on Nb20 are changed to be repulsive, which leads to the sidechain of Lys484 swing to the opposite direction, as shown in. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 63 74 RBD;RBD 37;138 40;141 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In the present study, a total of six neutralizing antibodies and nanobodies complexed with RBD were investigated to reveal the impacts of the E484K mutation on the binding affinities between them. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 142 147 RBD 91 94 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In total, the E484K mutation has little effect on the binding affinity between the nanobody MR17-K99Y and RBD due to the compensation of the impacts on the electrostatic interactions and van der Waals interactions. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K;K99Y 14;97 19;101 RBD 106 109 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. It is found that in these six studied neutralizing antibodies/nanobodies, five antibodies including BD23, nanobody H11-D4, BD368-2, nanobody Nb20 and S2M11, exhibit significantly decreased binding affinities with the E484K mutant compared with the wild-type RBD. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 217 222 RBD 258 261 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. It is found that the residue Glu484 is located on a flexible loop of RBD, and the substitution of Glu484 by Lys leads to obvious conformational movements of the flexible loop towards the receptor hACE2, which results in the tighter binding between RBD and hACE2. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 98 111 RBD;RBD 69;248 72;251 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. It should be noted that the E484K mutation may also cause decreased binding interactions for some residues. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 28 33 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Our calculation results are consistent with the observed bioactivity changes, where the 501Y.V2 and 501Y.V3 SARS-CoV-2 strains with the E484K mutation display more transmissibility than the prototype strain. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 136 141 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Our results indicate that for most of the studied neutralizing antibodies and nanobodies, the E484K mutation significantly reduces the binding affinities between these various antibodies/nanobodies and RBD, which may lessen the neutralization activity and even immune escape of RBD from these neutralizing antibodies. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 94 99 RBD;RBD 202;278 205;281 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Our results indicate that the E484K mutation may have disadvantageous effects on the neutralization activities and even may cause the immune escape of RBD from the neutralization of these antibodies/nanobodies. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 30 35 RBD 151 154 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Our results indicate that the E484K mutation results in tighter binding between RBD and hACE2, which also contributes to the enhancements of the binding affinity for the mutant complex system. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 30 35 RBD 80 83 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Taken together, the E484K mutation obviously reduces the binding affinity between the neutralizing antibody S2M11 and RBD. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 20 25 RBD 118 121 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The 500ns MD simulation results showed that the E484K mutation leads to an obvious conformational movement of the flexible loop containing the mutation towards the receptor hACE2 (Supporting Information. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 48 53 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The 500ns MD simulation was carried out both for the wild-type complex structure and the E484K mutant, in which the snapshots in the last 300ns were sampled and the average conformation was calculated. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 89 94 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The average binding free energies for the wild-type and the mutated RBD-hACE2 complexes were -59.10 kcal/mol and -70.53 kcal/mol, respectively, which indicates that the E484K mutation significantly improves the binding affinity between RBD with its receptor hACE2. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 169 174 RBD;RBD 68;236 71;239 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The binding free energies of the wild-type RBD and the E484K mutant complexed with the receptor hACE2 were calculated, respectively, by using MD simulations combined with MMGBSA method. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 55 60 RBD 43 46 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The E484K mutation results in the conversion of these electrostatic interactions from attraction to repulsion, which also leads to the sidechain of Lys484 swing towards the concave of the antibody, as displayed in the right sub-figure in. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 4 9 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The improvements of the binding affinity contributed by these residues are mainly attributed to the tighter binding interface caused by the E484K mutation. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 140 145 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The replacement of Glu484 by Lys increases the positive electrostatic potential interface of RBD. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 19 32 RBD 93 96 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Then the difference in the binding free energy between the wild-type and the mutant systems was computed to investigate the impacts of the E484K mutation on the binding affinity of RBD with the receptor. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 139 144 RBD 181 184 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Then, the average conformations for the wild type and the mutant were superposed to detect the conformational changes caused by the E484K mutation. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 132 137 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. These results may indicate that 6ns simulation can capture the main conformational and interaction changes caused by the E484K mutation. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 121 126 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Thus, the gas-phase electrostatic binding energy are significantly decreased due to the E484K mutation, as shown in Table 1, where the electrostatic energy is reduced from -654.74 kcal/mol to -1113.71 kcal/mol. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 88 93 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Whereas, upon the substitution of Glu484 with Lys, the unfavorable electrostatic interactions were changed to be favorable and the binding free energy contributed by Glu484 became a negative value, as shown in. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 34 49 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Whereas, when Glu484 is mutated to Lys with positive charge, the attractive electrostatic interactions are changed to be repulsive as shown in Table 3, which are predominantly responsible for the decreased binding affinities of these antibodies/nanobodies with the E484K-mutated RBD. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K;E484K 265;14 270;38 RBD 279 282 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Whereas, when the negatively charged residue Glu484 is substituted by Lys with positive charge, the electrostatic repulsions exerted by Arg100 and Arg102 lead to the swing away of the sidechain of Lys484. 2021 Journal of molecular graphics & modelling Result SARS_CoV_2 E484K 45 73 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. A common feature of reported S-D614G structures, however, is the increased propensity to populate the RBD-up conformations, and the two RBD-up conformations have not been reported for S-D614 (Table S2). 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 31 36 RBD;RBD;S;S 102;136;29;184 105;139;30;185 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Both S-D614 and S-D614G exhibited two transition peaks and shared a similar melting temperature (Tm) for the first transition at ca. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 18 23 S;S 5;16 6;17 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Collectively, 62% of the total population of S-D614G had one RBD in an up conformation (one RBD-up), including three distinct substates that separated the RBD conformations, and 38% of the population had two RBDs in an up conformation (two RBD-up) with two different substates. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 47 52 RBD;RBD;RBD;RBD;RBD;S 61;92;155;208;240;45 64;95;158;212;243;46 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Contrary to S-D614, we did not observe any all RBD-down conformation in S-D614G, in line with the previous study of a similar construct without the transmembrane domain, but differs from the full-length S-D614G that exhibits significant amount of closed, all RBD-down conformation. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G;D614G 74;205 79;210 RBD;RBD;S;S;S 47;259;12;72;203 50;262;13;73;204 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. For pH 7.0 and above, only the transition between 70 and 75C showed a clear difference between the two variants, suggesting that the stabilizing effect of D614G is likely contributing to the integrity of the S protein before being endocytosed into the host cell. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 155 160 S 208 209 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Having established that the structure of S-D614G is not significantly perturbed by the D614G mutation under native conditions, we sought to investigate the impact of the D614G mutation on the thermal stability over a range of experimental conditions. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G;D614G;D614G 87;170;43 92;175;48 S 41 42 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. However, our cryo-EM structure of S-D614G showed no appreciable structural difference in the proximity of the mutation site with respect to some of the extremities of the reported S-D614 structures, including the first reported structures of S-D614 (, ), the acid-stabilized form of S-D614, the disulfide- and proline-stabilized HexPro-S variant, and the furin-cleaved S-D614 that adopts a more open conformation. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 36 41 S;S;S;S;S;S 34;180;242;283;336;369 35;181;243;284;337;370 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. However, S-D614G exhibited a higher Tm for the second transition (Tm = 68.8C) compared with that of S-D614 (Tm = 66.9C). 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 11 16 S;S 9;100 10;101 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. In contrast, S-D614G was not sensitive to cold denaturation and is more robust during transient heat shock (Table 1). 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 15 20 S 13 14 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. In contrast, the same heat shock treatment resulted in 17 +- 5% (50C) and 58 +- 6% (60C) loss of native particles for S-D614G. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 120 125 S 118 119 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Indeed, further analysis with more incubation temperatures for S-D614G yielded a two-state-like melting curve with an apparent Tm of 59C. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 65 70 S 63 64 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Indeed, the second transition peak was lost for S-D614 after incubation at 4C for 6 days, while that of S-D614G remained largely unaffected; in line with NSEM results, long-term incubation at 37C did not significantly affect both variants. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 106 111 S;S 48;104 49;105 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Knowing that the S protein is susceptible to cold denaturation, all experiments were carried out using freshly prepared S-D614 and S-D614G, which were secreted into the culture media at 37C, and purified at room temperature. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 133 138 S;S;S 17;120;131 18;121;132 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Moreover, the total enthalpy of unfolding DeltaH of S-D614G was approximately 40% higher than that for S-D614. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 54 59 S;S 52;103 53;104 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Nevertheless, the molecular basis of how the D614G mutation could allosterically change the conformation and dynamics of the RBDs remains to be established. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 45 50 RBD 125 129 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Nonetheless, pairwise comparison of the unfolding curves of S-D614 and S-D614G showed that their profiles were indistinguishable at pH 6 and below. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 73 78 S;S 60;71 61;72 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Note, however, that despite the significant reduction in the number of native-like particles after cold and/or heat treatments, the resulting 3D EM maps of S-D614 and S-D614G were very similar at the resolution of approximately 10 A (insets in. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 169 174 S;S 156;167 157;168 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. proposed that the D614G mutation may disrupt the interprotomer hydrogen bond between D614 of one protomer and T859 of the other protomer, thereby leading to increase dynamics of the S protein and the shift of equilibrium between the RBD-up and RBD-down. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 18 23 RBD;RBD;S 233;244;182 236;247;183 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. proposed that the loss of a key salt bridge formed by D614 of one protomer and K584 or the other protomer due to the D614G mutation leads to local disorder, thereby increasing the dynamics of S-D614G and more populated RBD-up conformations, a finding that could be confirmed by our cryo-EM structures. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G;D614G 117;194 122;199 RBD;S 219;192 222;193 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Remarkably, after 2 months of incubation at 37C, S-D614G remained mostly intact according to NSEM analysis. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 51 56 S 49 50 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. reported an all RBD-up conformation of S-D614G, the EM density of the RBDs is poorly defined. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 41 46 RBD;RBD;S 16;70;39 19;74;40 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. S-D614G exhibits abundant conformational heterogeneity with increased propensity of RBD-up conformation. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 2 7 RBD;S 84;0 87;1 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Since the upward conformation of the RBD is the prerequisite of host receptor ACE2 binding, the increased population of the RBD-up conformations with more conformational plasticity may explain why S-D614G is found to exhibit enhanced binding to the receptor ACE2. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 199 204 RBD;RBD;S 37;124;197 40;127;198 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. The bimodal distribution of the DSC profile of S-D614G has been reported previously, and that the second transition was missing in some cases; this may be attributed to prolonged sample storage at lower temperatures. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 49 54 S 47 48 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. The complex melting curves indicated the presence of multiple transition events sensed by the large number of tryptophans and tyrosines within S-D614 and S-D614G, but it is not trivial to assign a specific transition point to a given tryptophan or tyrosine residue. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 156 161 S;S 143;154 144;155 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. The D614G mutation enhances the thermal stability of S protein at wide range of temperature. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 4 9 S 53 54 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. The stabilization effect of the D614G mutation was most pronounced under neutral to slightly alkaline conditions as demonstrated by label-free DSF analyses of S-D614 and S-D614G over a range of pH values. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G;D614G 32;172 37;177 S;S 159;170 160;171 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Two recent studies reported several cryo-EM structures of S-D614G with or without the furin cleavage site mutations (fm) and/or the tandem proline stabilization mutation (2P, see Experimental procedures), which showed either one RBD-up or all RBD-down conformations. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 60 65 RBD;RBD;S 229;243;58 232;246;59 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Unexpectedly, S-D614G did not show significant unfolding after the same cold treatment: the 6-day incubation at 37C and 4C resulted in 1 +- 3% and 12 +- 3% loss of native particles, respectively. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 16 21 S 14 15 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Using cryo-EM single particle reconstruction aided by 3DVA analysis, we identified five distinct but equally populated clusters of conformations of S-D614G with varying degrees of RBD-up populations. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 150 155 RBD;S 180;148 183;149 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. We carried out negative stain electron microscopy (NSEM) analyses on S-D614 and S-D614G on day 0 and on day 6 after continuous incubation at 37C and 4C. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 82 87 S;S 69;80 70;81 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. We further analyzed the thermal unfolding of S-D614 and S-D614G at pH 7.6 by DSC. 2021 The Journal of biological chemistry Result SARS_CoV_2 D614G 58 63 S;S 45;56 46;57 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Additionally, all RBDs showed local minima, except for N501Y, with apparently two minima that in a confined space suggested a lower energy barrier between two conformations. 2021 Biomolecules Result SARS_CoV_2 N501Y 55 60 RBD 18 22 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Additionally, S477N and L452R showed different loop conformers at loop 457-467 (a flexible loop) of RBM, while N501Y, E484K, and N439K showed similar conformers in the same region during the simulations (Figure 3b). 2021 Biomolecules Result SARS_CoV_2 E484K;L452R;N439K;N501Y;S477N 118;24;129;111;14 123;29;134;116;19 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. As anticipated, the mutation of S477N and E484K would not form hydrogen bonds since their mutation sites are located in the binding interacting loop (Figure 2b). 2021 Biomolecules Result SARS_CoV_2 E484K;S477N 42;32 47;37 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. C-alpha root mean square deviation (C-alpha RMSD) was assessed during the 100-ns MD simulation runs for WT RBD and N501Y, L452R, S477N, N439K, and E484K RBDs systems (Figure 1). 2021 Biomolecules Result SARS_CoV_2 E484K;L452R;N439K;N501Y;S477N 147;122;136;115;129 152;127;141;120;134 RBD;RBD 107;153 110;157 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Clearly, N501Y was the only mutant RBD that featured RBM conformers that varied significantly at loop 498-502 (slightly flexible) during the 100-ns MD simulations (Figure 3b). 2021 Biomolecules Result SARS_CoV_2 N501Y 9 14 RBD 35 38 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Finally, the loop Y473-C489 of N501Y RBD showed similar flexibility to WT RBD, while the other mutant RBDs showed a significant increase in the same domain flexibility (Figure 2). 2021 Biomolecules Result SARS_CoV_2 N501Y 31 36 RBD;RBD;RBD 37;74;102 40;77;106 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Finally, the prominent motion was observed at loop Y473-C489 in L452R, S477N, N439K, and E484K RBDs, which showed high flexibility over the 100-ns MD simulations (Figure 6). 2021 Biomolecules Result SARS_CoV_2 E484K;L452R;N439K;S477N 89;64;78;71 94;69;83;76 RBD 95 99 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. For each RBD system, the Rg of N501Y, L452R, N439K, and E484K RBDs showed similar conformational compactness over the 100-ns MD simulations, while S477N RBD showed a significantly looser conformation in comparison to WT RBD (Figure 4a). 2021 Biomolecules Result SARS_CoV_2 E484K;L452R;N439K;N501Y;S477N 56;38;45;31;147 61;43;50;36;152 RBD;RBD;RBD;RBD 9;62;153;220 12;66;156;223 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. For L452R, S477N, and E484K RBDs, a similar flexibility was observed in the loop P412-D428 compared to WT RBD, while N501Y and N439K showed more rigid structures in the same domain (Figure 2). 2021 Biomolecules Result SARS_CoV_2 E484K;L452R;N439K;N501Y;S477N 22;4;127;117;11 27;9;132;122;16 RBD;RBD 28;106 32;109 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Furthermore, the alpha-helix structure of WT RBD became a turn structure in both the N439K and E484K RBDs (Figure S3D). 2021 Biomolecules Result SARS_CoV_2 E484K;N439K 95;85 100;90 RBD;RBD 45;101 48;105 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. However, the SASA of S477N RBD increased significantly in comparison to the WT RBD (Figure S1). 2021 Biomolecules Result SARS_CoV_2 S477N 21 26 RBD;RBD 27;79 30;82 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. In N439K and L452R, there was a clear area where both could sample conformational subspace differently from WT (Figure 5b,d). 2021 Biomolecules Result SARS_CoV_2 L452R;N439K 13;3 18;8 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. In the loop P384-D389, the flexibility was increased only in N501Y RBD among other mutants (Figure 2a). 2021 Biomolecules Result SARS_CoV_2 N501Y 61 66 RBD 67 70 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Moreover, an alpha-helix structure was observed in the residue range 417-422 of the N501Y, L452R, and S477N RBDs (Figure S3A-C). 2021 Biomolecules Result SARS_CoV_2 L452R;N501Y;S477N 91;84;102 96;89;107 RBD 108 112 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Only residues around Glu484 site (i.e., in E484K RBD) were changed from alpha-helix to turn structure. 2021 Biomolecules Result SARS_CoV_2 E484K 43 48 RBD 49 52 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Other RBDs (i.e., N501Y, L452R, and N439K) showed similar H-bond numbers to WT RBD, at least after 80 ns of MD simulations. 2021 Biomolecules Result SARS_CoV_2 L452R;N439K;N501Y 25;36;18 30;41;23 RBD;RBD 6;79 10;82 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Our results showed that only the mutation of N501Y and L452R formed strong hydrogen bonds (3.0 A), and a weak hydrogen bond was observed in N439K with neighboring residues (Figure 3c). 2021 Biomolecules Result SARS_CoV_2 L452R;N439K;N501Y 55;140;45 60;145;50 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Particularly, WT, N501Y, and E484K RBDs were found to sample from almost the same conformational subspace (Figure 5a,e). 2021 Biomolecules Result SARS_CoV_2 E484K;N501Y 29;18 34;23 RBD 35 39 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Rg assessment was done for a residue range of 334-516 because the starting (X-ray) structure of N501Y RBD was missing six residues of C-terminus and one residue of N-terminus compared to the original WT (i.e., the total WT residues is 333-522). 2021 Biomolecules Result SARS_CoV_2 N501Y 96 101 RBD;N 102;164 105;165 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Rg for WT and its mutants N501Y, L452R, S477N, N439K, and E484K were assessed during the 100-ns MD simulations (Figure 4). 2021 Biomolecules Result SARS_CoV_2 E484K;L452R;N439K;N501Y;S477N 58;33;47;26;40 63;38;52;31;45 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. The E484K RBD showed significant increase in alpha-helix structure in comparison to both the N501Y and S477N RBDs (Figure S3A,C). 2021 Biomolecules Result SARS_CoV_2 E484K;N501Y;S477N 4;93;103 9;98;108 RBD;RBD 10;109 13;113 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. The residue range 382-392 tended to form alpha-helix structure in N501Y and S477N RBDs in comparison to a turn structure in WT. 2021 Biomolecules Result SARS_CoV_2 N501Y;S477N 66;76 71;81 RBD 82 86 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. The results showed that the prominent motions of WT RBD were located in S366-S371 and P412-D428 domains, while these motions were well distributed in S366-S371 and P384-D389 domains, as well as in loop Y495-Y508, in N501Y (which showed different conformations, as mentioned above) (Figure 6b). 2021 Biomolecules Result SARS_CoV_2 N501Y 216 221 RBD 52 55 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. The results showed that the S366-S371 has similar flexibility to L452R and S477N compared to WT RBDs, and that this domain was significantly rigid in N439K and E484K RBDs and slightly rigid in N501Y RBD compared to WT RBD (Figure 2). 2021 Biomolecules Result SARS_CoV_2 E484K;L452R;N439K;N501Y;S477N 160;65;150;193;75 165;70;155;198;80 RBD;RBD;RBD;RBD 96;166;199;218 100;170;202;221 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. The SASA of WT, N501Y, and N439K RBDs showed similar profiles, and both L452R and E484K showed slight increases in their SASA. 2021 Biomolecules Result SARS_CoV_2 E484K;L452R;N439K;N501Y 82;72;27;16 87;77;32;21 RBD 33 37 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. The turn structure of WT RBD was changed to a bend structure in the residue range 482-487 of the S477N, N439K, and E484K RBDs (Figure S3C,E,F). 2021 Biomolecules Result SARS_CoV_2 E484K;N439K;S477N 115;104;97 120;109;102 RBD;RBD 25;121 28;125 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Therefore, trajectories from each 100-ns MD simulation system were analyzed to evaluate the RBM loops conformation of WT, N501Y, L452R, S477N, N439K, and E484K RBDs. 2021 Biomolecules Result SARS_CoV_2 E484K;L452R;N439K;N501Y;S477N 154;129;143;122;136 159;134;148;127;141 RBD 160 164 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. This loop of RBM did not vary in the other mutant RBDs (especially in E484K RBD) (Figure 3b). 2021 Biomolecules Result SARS_CoV_2 E484K 70 75 RBD;RBD 50;76 54;79 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. This was consistent with the low H-bond number observed in both the S477N and E484K RBDs during the 100-ns MD simulations (Figure S4). 2021 Biomolecules Result SARS_CoV_2 E484K;S477N 78;68 83;73 RBD 84 88 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. This was consistent with the radius of gyration analysis, as the loose conformation was observed in S477N RBD. 2021 Biomolecules Result SARS_CoV_2 S477N 100 105 RBD 106 109 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Although C145 is a residue that constitutes the catalytic dyad and plays an important role in enzyme activity, the experimental 3D structure of C145A is not significantly different from that of the wild type. 2021 International journal of molecular sciences Result SARS_CoV_2 C145A 144 149 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Although E166 of A and B chains formed hydrogen bonds between S1 of B and A chains in wild type, respectively, these hydrogen bonds were not observed in the E166A mutant. 2021 International journal of molecular sciences Result SARS_CoV_2 E166A 157 162 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Although the catalytic dyad is in a loop structure and there is a residue with a high RMSF nearby, the catalytic dyad structure is conserved with the wild type in H163A. 2021 International journal of molecular sciences Result SARS_CoV_2 H163A 163 168 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Although the final RMSD of H164A was small, the catalytic dyad of the B chain fluctuated to a large degree in the middle of the simulation, indicating a temporary change in the dynamic structure. 2021 International journal of molecular sciences Result SARS_CoV_2 H164A 27 32 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Although the ligand RMSDs of N142A, H163A, E166A, and R188A were large, the structures of the main chain and the catalytic dyad were not significantly affected. 2021 International journal of molecular sciences Result SARS_CoV_2 E166A;H163A;N142A;R188A 43;36;29;54 48;41;34;59 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Although the mutant H164A did not show significant changes in ligand recognition and the final RMSD, as well as the dynamic structure, (RMSF) did not differ much from the wild type, and the fluctuation of the catalytic dyad may affect enzymatic activity. 2021 International journal of molecular sciences Result SARS_CoV_2 H164A 20 25 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Among the mutants studied, the 3D structure of C145A has been experimentally determined. 2021 International journal of molecular sciences Result SARS_CoV_2 C145A 47 52 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. As shown in Figure S1, the structures of N142A, H163A, and E166A not only deviated from the initial structure in the final frame, but also fluctuated greatly in the middle of the simulation. 2021 International journal of molecular sciences Result SARS_CoV_2 E166A;H163A;N142A 59;48;41 64;53;46 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Because E166 forms a hydrogen bond with NCL-00024905, H172 is involved in both dimer formation and ligand recognition, perhaps causing the structure of the catalytic dyad to change significantly in H172A. 2021 International journal of molecular sciences Result SARS_CoV_2 H172A 198 203 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Because H172A and D187A are mutations that weaken the function of the enzyme itself and affect the recognition of inhibitors, they may not be as important for drug resistance, same as S144A and M165A mentioned above. 2021 International journal of molecular sciences Result SARS_CoV_2 D187A;H172A;M165A;S144A 18;8;194;184 23;13;199;189 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Both the B chain, in which conformational change of the ligand was observed, and the A chain, in which hydrogen bond cleavage was observed, showed a tendency for the ligand to detach from the protein, indicating that the mutation H163A affected inhibitor recognition. 2021 International journal of molecular sciences Result SARS_CoV_2 H163A 230 235 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Especially for H163A and E166A, final RMSDs of the ligands shown in Table 2 exceeded 2.0 A, and the ligand RMSD values fluctuated during MD trajectories as shown in Figure S1. 2021 International journal of molecular sciences Result SARS_CoV_2 E166A;H163A 25;15 30;20 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Figure 6 illustrates the residues around the ligand in the B chain of H163A and in the B chain of E166A. 2021 International journal of molecular sciences Result SARS_CoV_2 E166A;H163A 98;70 103;75 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. For H163A, the structure of the catalytic dyad was almost unchanged from the wild type, and the protein structure around the catalytic dyad was similar to that of the wild type. 2021 International journal of molecular sciences Result SARS_CoV_2 H163A 4 9 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. For the catalytic dyad RMSDs, as with the ligand RMSDs, there was a case (H172A) where the catalytic dyad of only one chain underwent a significant conformational change, as shown in Figure 4. 2021 International journal of molecular sciences Result SARS_CoV_2 H172A 74 79 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. However, for some mutants, such as S144A, RMSDs increased throughout the simulation, suggesting a trend towards a conformational change. 2021 International journal of molecular sciences Result SARS_CoV_2 S144A 35 40 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. However, the E166A mutation did not significantly affect the dimeric structure. 2021 International journal of molecular sciences Result SARS_CoV_2 E166A 13 18 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. However, the structures of H172A and D187A differed from the wild type. 2021 International journal of molecular sciences Result SARS_CoV_2 D187A;H172A 37;27 42;32 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. In addition, E166A mutant is enzymatically active (the enzymatic activity of E166A mutant is about one-third that of the wild type). 2021 International journal of molecular sciences Result SARS_CoV_2 E166A;E166A 13;77 18;82 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. In addition, the ligand substantially fluctuated thorough the simulations, however 3D structure of the catalytic dyad in E166A mutant was similar to that in wild type. 2021 International journal of molecular sciences Result SARS_CoV_2 E166A 121 126 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. In addition, the structure of the ligand docked with the B chain also changed in D187A. 2021 International journal of molecular sciences Result SARS_CoV_2 D187A 81 86 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. In addition, there was a decrease in the frequency of hydrogen bonding in the A chain of the E166A mutant, where the ligand RMSD was not so large. 2021 International journal of molecular sciences Result SARS_CoV_2 E166A 93 98 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. In contrast, the ligands in A and B chains in H163A both form three hydrogen bonds with the surrounding residues, and the ligands in A and B chains in Q189A formed three and two hydrogen bonds, respectively. 2021 International journal of molecular sciences Result SARS_CoV_2 H163A;Q189A 46;151 51;156 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. In fact, the RMSF of the ligand was larger than those of wild type by more than 0.1 A, indicating that the ligand fluctuates in the pocket of the H163A mutant. 2021 International journal of molecular sciences Result SARS_CoV_2 H163A 146 151 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. In L141A, N142A, H163A, H164A, and P168A, the number of pairs of heavy atoms in "contact" were reduced by 10 or more compared to that in wild type. 2021 International journal of molecular sciences Result SARS_CoV_2 H163A;H164A;L141A;N142A;P168A 17;24;3;10;35 22;29;8;15;40 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. In N142A and S144A, the ligand bound to the A chain moved significantly, while in H163A and E166A, the ligand bound to the B chain moved significantly. 2021 International journal of molecular sciences Result SARS_CoV_2 E166A;H163A;N142A;S144A 92;82;3;13 97;87;8;18 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. In particular, main-chain RMSDs in S144A did not converge, and the structure may be further disrupted in longer simulations. 2021 International journal of molecular sciences Result SARS_CoV_2 S144A 35 40 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. In particular, the structure of the catalytic dyad in D187A changed in both the A and B chains as shown in Figure 5, and the complex structure did not converge in the 100-ns simulation as shown in Figure S2. 2021 International journal of molecular sciences Result SARS_CoV_2 D187A 54 59 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Indeed, S144A was one of two mutants with RMSDs of the main chain exceeding 1.5 A. 2021 International journal of molecular sciences Result SARS_CoV_2 S144A 8 13 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. On the other hand, E166A (B chain) affected the positions of two neighboring residues, the N-terminal residue S1 (A chain) and H172 (B chain), which altered the shape of the pocket. 2021 International journal of molecular sciences Result SARS_CoV_2 E166A 19 24 N 91 92 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. On the other hand, S144A and M165A showed relatively large values of the main-chain RMSDs, as well as the ligand RMSDs, suggesting that both the ligand structure and structure of the entire system has changed. 2021 International journal of molecular sciences Result SARS_CoV_2 M165A;S144A 29;19 34;24 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Our current results show that the RMSDs of the main chain, ligand, and catalytic dyad were all small in C145A, consistent with the experimental results that the mutation of C145A has little effect on the protein structure. 2021 International journal of molecular sciences Result SARS_CoV_2 C145A;C145A 104;173 109;178 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Our results show that both E166A mutants of SARS-CoV and SARS-CoV-2 have similar structural features. 2021 International journal of molecular sciences Result SARS_CoV_2 E166A 27 32 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Previous study using SARS-CoV have reported that the E166A mutant form a dimer, and that the hydrogen bond between E166 and S1 is not essential for dimer-structure formation. 2021 International journal of molecular sciences Result SARS_CoV_2 E166A 53 58 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. Similar changes were also observed in the H163A A chain, in which the ligand RMSD was not as large, and a decrease in hydrogen-bonding frequency was observed in the A chain. 2021 International journal of molecular sciences Result SARS_CoV_2 H163A 42 47 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. The structure of the catalytic dyad in E166A was not significantly different from the wild type, and the protein structure around the catalytic dyad was also similar to that of the wild type. 2021 International journal of molecular sciences Result SARS_CoV_2 E166A 39 44 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. These results indicate that the structure of entire active site, including both catalytic dyad and ligand, changed in D187A. 2021 International journal of molecular sciences Result SARS_CoV_2 D187A 118 123 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. This data also indicates that the mutation E166A affects inhibitor recognition, similar to mutant H163A. 2021 International journal of molecular sciences Result SARS_CoV_2 E166A;H163A 43;98 48;103 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. This structural change was caused by entry of the Y161 side chain into the space vacated by the replacement of H163 with Ala. 2021 International journal of molecular sciences Result SARS_CoV_2 H163A 111 124 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. C22444T, another spike mutation, was seen in 39.3% of the viral sequences. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 C22444T 0 7 S 17 22 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. Clade 20A defined by C14408T (Nsp12/RdRp) and A23403G (S: D614G) was seen in 58% of the samples, clade 19A defined by positions 8782C (Nsp3) and 14408C (Nsp12/RdRp) was seen in 38% and 20B denoted by positions C3037T (Nsp3: 106F); A23403G (S: D614G); C14408T (Nsp12/RdRp: P4715L) and G28881A and G28882A (N: R203K) was seen in only 4% of the population (Figure 2A). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 A23403G;A23403G;C14408T;C14408T;C3037T;D614G;D614G;G28881A;G28882A;P4715L;R203K 46;231;21;251;210;58;243;284;296;272;308 53;238;28;258;216;63;248;291;303;278;313 Nsp12;Nsp12;Nsp12;Nsp3;Nsp3;RdRP;RdRP;RdRP;N;S;S 30;153;260;135;218;36;159;266;305;55;240 35;158;265;139;222;40;163;270;306;56;241 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. During the protein structure analysis, we observed a minor change in polarity due to the T268S (Figure S1) and S194L (Figure S2) with no significant change in the physicochemical properties. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 S194L;T268S 111;89 116;94 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. For patients without co-morbidities, mutation TG11082T in Orf1a was found to positively correlate with both severity and mortality (Tables S5 and S6). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 G11082T;T11082T 46;46 54;54 ORF1a 58 63 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. For S194L mutation, coils were turned into sheets (Figure 5). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 S194L 4 9 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. Mutation P314L was seen in 75% of the patient samples, followed by D614G in 63.8% samples. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D614G;P314L 67;9 72;14 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. Mutation S194L was found to be located in the serine-arginine (SR)-rich motif of N protein. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 S194L 9 14 N 81 82 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. non-synonymous), we selected the mutations A26194T, C28854T, C25611A for further structural analysis (Figure 3). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 A26194T;C25611A;C28854T 43;61;52 50;68;59 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. Our analysis revealed that T268S increased the protein disorder from segment (244-267)to segment (244-272) in the Orf3a region, whereas S194L mutation did not have any effect on protein disorder. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 S194L;T268S 136;27 141;32 ORF3a 114 119 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. The analysis showed that mutation A26194T was found to be positively correlated with both severity and mortality (Tables S3 and S4). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 A26194T 34 41 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. The mutation T268S was located on the C-tail end of the protein (Figure 7A). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 T268S 13 18 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. The mutations A26194T (p = 0.0023) and C25611A (p = 0.0158) were selected as they have a statistically significant correlation with disease severity. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 A26194T;C25611A 14;39 21;46 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. The mutations A26194T (p = 0.0027) and C28854T (p = 0.0366) were selected as they have a statistically significant correlation with disease mortality. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 A26194T;C28854T 14;39 21;46 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. The Q57H mutation of ORF3a was seen in more than 50% of the isolates (Table 2). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 Q57H 4 8 ORF3a 21 26 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. We focused on three mutations: A26194T (T268S) in the Orf3a region, C25611A (synonymous mutation) in the Orf3a region, and C28854T (S194L) in the N protein. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 A26194T;C25611A;C28854T;S194L;T268S 31;68;123;132;40 38;75;130;137;45 ORF3a;ORF3a;N 54;105;146 59;110;147 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. We found that 38% and 20% of the cases with the mutations A26194T and C28854T were fatal, compared to an average mortality rate of 10.5%, which shows that the mutations are positively correlated with mortality. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 A26194T;C28854T 58;70 65;77 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. We found that 92% and 72% of the cases with the mutations A26194T and C25611A, respectively, were severe compared to an average of ~50%, which shows that the mutations are positively correlated with disease severity. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 A26194T;C25611A 58;70 65;77 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. We further analyzed the secondary structure of the Orf3a protein, wherein we observed a conversion from sheets to coils at the site of mutation for T268S mutation (Figure 4). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 T268S 148 153 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. When we analyzed for C28854U (CDS Start: 28274 and CDSEnd: 29533) and C25611A (CDS Start:25393 and CDS End: 26220), the mutations led to a complete change of the secondary RNA structures and werenot limited to the site of mutation only (Figures S3 and S4). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 C25611A 70 77 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. 5-fold (4.88x) higher compared to D614G (cf. 2021 Viruses Result SARS_CoV_2 D614G 34 39 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. As evaluated in A549-AT cells, authentic SARS-CoV-2 variants harboring L452R were resistant against bamlanivimab (Figure 2). 2021 Viruses Result SARS_CoV_2 L452R 71 76 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Even at high concentrations, imdevimab was not effective against Delta indicating high resistance, but only a moderate reduction in the neutralization of all L452R variants was observed for the treatment with the clinically approved combination of casirivimab/imdevimab. 2021 Viruses Result SARS_CoV_2 L452R 158 163 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. For the Epsilon lineages, B.1.427 and B.1.429 harboring D614G and L452R, the reduction in neutralization efficiency by convalescent sera of both variants was less severe with only 2.05 and 2.96, respectively. 2021 Viruses Result SARS_CoV_2 D614G;L452R 56;66 61;71 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. In conclusion, all SARS-CoV-2 variants carrying L452R were resistant to bamlanivimab. 2021 Viruses Result SARS_CoV_2 L452R 48 53 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. In presence of L452R, limited neutralization efficacy to BNT2b2- or mRNA-1273 vaccine-elicited sera was detected (Figure 1B). 2021 Viruses Result SARS_CoV_2 L452R 15 20 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Kappa additionally harboring E484Q revealed strongly reduced susceptibility against casirivimab. 2021 Viruses Result SARS_CoV_2 E484Q 29 34 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Neutralization of Kappa by imdevimab or combination therapy with casirivimab/imdevimab together was highly effective and only slightly reduced relative to non E484Q harboring variants. 2021 Viruses Result SARS_CoV_2 E484Q 159 164 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Next, we sought to find out whether the efficacy of mAbs bamlanivimab, casirivimab, imdevimab, and the combination of casirivimab/imdevimab was reduced towards authentic SARS-CoV-2 variants harboring L452R and other substitutions in S. 2021 Viruses Result SARS_CoV_2 L452R 200 205 S 233 234 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. We found that the tested sera were less effective against authentic SARS-CoV-2 variants harboring L452R. 2021 Viruses Result SARS_CoV_2 L452R 98 103 34578363 Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India. Common in B.1.617.2 lineage: ORF1ab P4715L; spikeT19R, L452R, T478K, D614G, and P681R; ORF3a S26L; M I82T; ORF7a V82A and T120I; and N D63G, R203M, and D377Y. 2021 Viruses Result SARS_CoV_2 D377Y;D614G;D63G;I82T;L452R;P4715L;P681R;R203M;S26L;T120I;T478K;V82A 152;69;135;101;55;36;80;141;93;122;62;113 157;74;139;105;60;42;85;146;97;127;67;117 ORF1ab;ORF7a;S;ORF3a;N 29;107;44;87;133 35;112;49;92;134 34578363 Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India. Sub-lineage I (red color): mutations in ORF1ab A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, and A6319V and in N G215C; Sub-lineage II (green color): ORF1ab P309L, A3209V, V3718A, G5063S, and P5401L and ORF7a L116F; Sub-lineage III (pink color): ORF1ab A3209V, V3718A, T3750I, G5063S, and P5401L and spike A222V; Sub-lineage IV (Orange color): ORF1ab P309L, D2980N, and F3138S and spike K77T. 2021 Viruses Result SARS_CoV_2 A1306S;A222V;A3209V;A3209V;A6319V;D2980N;F3138S;G215C;G5063S;G5063S;G5063S;K77T;L116F;P2046L;P2287S;P309L;P309L;P5401L;P5401L;P5401L;T3255I;T3446A;T3750I;V2930L;V3718A;V3718A 47;324;182;271;115;376;388;131;95;198;295;405;227;55;63;175;369;103;210;307;79;87;287;71;190;279 53;329;188;277;121;382;394;136;101;204;301;409;232;61;69;180;374;109;216;313;85;93;293;77;196;285 ORF1ab;ORF1ab;ORF1ab;ORF1ab;ORF7a;S;S;N 40;168;264;362;221;318;399;129 46;174;270;368;226;323;404;130 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. A search in the EpiCoV database (accessed on 7 July 2021) for high-quality SARS-CoV-2 genomes carrying both mutations S:Q675H and S:Q677H recovered 85 non-Uruguayan sequences. 2021 Viruses Result SARS_CoV_2 Q675H;Q677H 120;132 125;137 S;S 118;130 119;131 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Of note, eight out of 10 lineage P.6-defining mutations (including S:Q675H) were also identified in a basal B.1.1.28 sequence sampled in Rio de Janeiro in January 2021, and were thus probably present in the ancestral virus that arrived from Brazil; while the remaining two mutations (ORF1ab: C8980T and S:Q677H) were fixed during the early local transmission in Uruguay. 2021 Viruses Result SARS_CoV_2 C8980T;Q675H;Q677H 292;69;305 298;74;310 ORF1ab;S;S 284;67;303 290;68;304 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Of note, the B.1.1.28 + Q675H + Q677H collected in Belgium did not belong to clade P.6, indicating an independent and recurrent appearance of both mutations (see below; Figure 1C). 2021 Viruses Result SARS_CoV_2 Q675H;Q677H 24;32 29;37 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. One B.1.1.28 introduction, however, was successfully established and originated the lineage P.6 (SH-aLRT = 98) that comprised all Uruguayan sequences (n = 314), as well as three sequences collected in the USA and Spain carrying mutations S:Q675H + Q677H. 2021 Viruses Result SARS_CoV_2 Q677H;Q675H 248;240 253;245 S 238 239 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Overall, the pair S:Q675H + Q677H appeared to be distributed in 12 different countries (in decreasing frequency order: Uruguay, England, USA, Belgium, India, Australia, Switzerland, Spain, Netherlands, Japan, Germany, and France) and in 13 different Pango lineages (in decreasing frequency order: P.6, B.1.36, B.1.2, C.36, B.1.538, B.1.1.316, B.1.526 (VOI Iota), B.1.525 (VOI Eta), B.1.243, B.1.1.70, B.1.1.7 (VOC Alpha), B.1.1.63, and B.1) (Figure S5). 2021 Viruses Result SARS_CoV_2 Q677H;Q675H 28;20 33;25 S 18 19 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Structural analysis of the SARS-CoV-2 Spike glycoprotein showed that residues Q675H and Q677H were within the subdomain SD2 of each protomer constituting the homotrimer (Figure 2C). 2021 Viruses Result SARS_CoV_2 Q675H;Q677H 78;88 83;93 S 38 56 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Substitution S:Q677H has been reported as a recurrent mutation arising independently in many SARS-CoV-2 lineages, including several VOIs, circulating worldwide by the end of 2020. 2021 Viruses Result SARS_CoV_2 Q677H 15 20 S 13 14 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. The lineage P.6 was characterized by eight lineage-defining genetic changes in addition to S:Q675H and S:Q677H, including a total of five nonsynonymous mutations (Figure 2B). 2021 Viruses Result SARS_CoV_2 Q675H;Q677H 93;105 98;110 S;S 91;103 92;104 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. The mutational profile of B.1.1.28 sequences identified 174 (26%) genomes carrying amino acid changes S:Q675H and S:Q677H that compose a new Pango lineage designated as P.6. 2021 Viruses Result SARS_CoV_2 Q675H;Q677H 104;116 109;121 S;S 102;114 103;115 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. These mutations were close to two experimentally observed O-glycosylation sites at T676 and T678, and at the same domain of the D614G mutation (Figure 2C, inset). 2021 Viruses Result SARS_CoV_2 D614G 128 133 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. To identify the probable geographic source of B.1.1.28, P.6, and P.7 lineages detected in Uruguay, all Uruguayan sequences here obtained (n = 212, Table S1) were combined with complete genome sequences of those lineages available at the EpiCoV database in GISAID sampled in Uruguay (n = 143) and Brazil (n = 1428), and with all B.1.1.28 sequences sampled worldwide that carried mutations Q675H and Q677H (USA = 2, Spain = 1 and Belgium = 1; Table S2). 2021 Viruses Result SARS_CoV_2 Q675H;Q677H 388;398 393;403 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. We also identified one additional mutation (ORF3a:M260I) that was fixed at a later step during evolution of P.6 in Uruguay (Figure 2B). 2021 Viruses Result SARS_CoV_2 M260I 50 55 ORF3a 44 49 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. Besides the four mutations (L37F, P84S, N501Y, and D128Y) identified in MASCp6, MASCp36 acquires additional eight amino acid substitutions, including I1258V, H470Y, S301L, A128V, S8F, K417N, Q493H, and R32C in the NSP3, NSP4, NSP5, NSP6, NSP7, S, and N. 2021 Nature communications Result SARS_CoV_2 A128V;D128Y;H470Y;I1258V;K417N;N501Y;P84S;Q493H;R32C;S301L;L37F 172;51;158;150;184;40;34;191;202;165;28 177;56;163;156;189;45;38;196;206;170;32 Nsp3;Nsp4;Nsp7;Nsp5;Nsp6;N;S 214;220;238;226;232;251;244 218;224;242;230;236;252;245 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. Coincidentally, a number of amino acid substitutions, such as Q493K, Q498Y, and P499T, in the RBM identified in other reported mouse-adapted SARS-CoV-2 isolates were included either in the Clus2 or Clus3, underlining the putative determinants for cross-transmission. 2021 Nature communications Result SARS_CoV_2 P499T;Q493K;Q498Y 80;62;69 85;67;74 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. However, in PI, the substitution of K with N at residue 417 in RBDMACSp36 loses the salt bridge interaction, which would be formed by K417 in the RBDWT and D30 in the hACE2, structurally explaining the reduced binding affinity of RBDMACSp36 to hACE2. 2021 Nature communications Result SARS_CoV_2 K417N 36 59 N 43 44 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. However, the third substitution of K417N significantly reduced binding activity of RBDMACSp36 to hACE2, rendering a lower affinity than that of RBDWT. 2021 Nature communications Result SARS_CoV_2 K417N 35 40 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. Interestingly, compared to RBDMACSp6 with a mutation of N501Y, RBDMACSp25, which contains an extra Q493H substitution, showed an enhanced binding affinity to hACE2. 2021 Nature communications Result SARS_CoV_2 N501Y;Q493H 56;99 61;104 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. Specially, single (N501Y), double (Q493H, N501Y), and triple (K417N, Q493H, N501Y) mutations in the RBD were identified in MASCp6, MASCp25, and MASCp36, respectively. 2021 Nature communications Result SARS_CoV_2 N501Y;N501Y;Q493H;K417N;N501Y;Q493H 42;76;69;62;19;35 47;81;74;67;24;40 RBD 100 103 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. The interaction area on the mACE2 could be primarily divided into three patches (PI, PII, and PIII), involving extensive hydrophilic and hydrophobic interactions with three regions separately clustered by three adaptation-mediated mutated residues (K417N, corresponding to Clus1; Q493H, corresponding to Clus2; and N501Y, corresponding Clus3) in the RBM. 2021 Nature communications Result SARS_CoV_2 N501Y;Q493H;K417N 315;280;249 320;285;254 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. The same as RBDMACSp36-mACE2 complex, the interaction region could be divided into three patches, the three adaption-mutated residues (K417N, located at PI; Q493H, located at PII; and N501Y, located at PIII) were located at the three patches, respectively. 2021 Nature communications Result SARS_CoV_2 N501Y;Q493H;K417N 184;157;135 189;162;140 34591922 Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example. As an example, it is shown that the recently observed N501Y substitution in the spike protein can provide an example of an inflection point bifurcation. 2021 PloS one Result SARS_CoV_2 N501Y 54 59 S 80 85 34591922 Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example. Example: The D614G mutation of spike protein. 2021 PloS one Result SARS_CoV_2 D614G 13 18 S 31 36 34591922 Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example. For this, the local topology of the recently observed new mutation at site 501N with N Y substitution is now analyzed, for its bifurcation potential. 2021 PloS one Result SARS_CoV_2 N501N 75 86 N 85 86 34591922 Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example. Since G is the only amino acid that consistently appears in all three clusters and since there is no obvious steric hindrance for a D G substitution, the prediction of the present analysis is that a D G substitution is probable at the site 614 of spike protein; this is the notorious D614G mutation that has already been observed. 2021 PloS one Result SARS_CoV_2 D614G 284 289 S 247 252 34591922 Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example. Since the N501Y substitution is not necessarily in contrast with stereochemical considerations, the energetic cost of a substitution can be minor. 2021 PloS one Result SARS_CoV_2 N501Y 10 15 34591922 Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example. The local topology of the N501Y mutation site. 2021 PloS one Result SARS_CoV_2 N501Y 26 31 34591922 Local topology and bifurcation hot-spots in proteins with SARS-CoV-2 spike protein as an example. Thus a bifurcation that relates to a flattening point, similar to that in the case of the D614G, appears unlikely. 2021 PloS one Result SARS_CoV_2 D614G 90 95 34592572 SARS-CoV-2 spike protein receptor-binding domain N-glycans facilitate viral internalization in respiratory epithelial cells. AS35 neutralization showed similar effects as of VHH72, infectivity of N331Q + N343Q decreased by ~92-fold (in HNEpc) and 64-fold (in HPAEpic) compared with the one without neutralization. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 N331Q;N343Q 71;79 76;84 34592572 SARS-CoV-2 spike protein receptor-binding domain N-glycans facilitate viral internalization in respiratory epithelial cells. Interestingly, the internalization efficiency of N331Q + N343Q was dramatically lower than the S-WT, similar to that of pseudo-VSV-G (control). 2021 Biochemical and biophysical research communications Result SARS_CoV_2 N331Q;N343Q 49;57 54;62 S 95 96 34592572 SARS-CoV-2 spike protein receptor-binding domain N-glycans facilitate viral internalization in respiratory epithelial cells. Notably, the binding between WT S1 and recombinant ACE2 was highly stable; however, the double de-glycosylation (N331Q + N343Q) drastically reduced the binding(Fig. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 N343Q;N331Q 121;113 126;118 34592572 SARS-CoV-2 spike protein receptor-binding domain N-glycans facilitate viral internalization in respiratory epithelial cells. The internalization of the single mutant N331Q or N343Q was also lower, about 23 and 56% of the S-WT, respectively. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 N331Q;N343Q 41;50 46;55 S 96 97 34592572 SARS-CoV-2 spike protein receptor-binding domain N-glycans facilitate viral internalization in respiratory epithelial cells. The N331 and N343 N-glycans were sorted by their relative abundances and the top 10 are shown with structures in Figs. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 N343N 13 19 N 18 19 34592572 SARS-CoV-2 spike protein receptor-binding domain N-glycans facilitate viral internalization in respiratory epithelial cells. The qPCR results indicated that internalization of N331Q, N343Q, and the double mutant decreased by ~37, 57, and 89%, respectively, compared with S-WT. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 N331Q;N343Q 51;58 56;63 S 146 147 34592572 SARS-CoV-2 spike protein receptor-binding domain N-glycans facilitate viral internalization in respiratory epithelial cells. The respective single deletions also reduced the binding, albeit mildly, compared to the N331Q + N343Q. 2021 Biochemical and biophysical research communications Result SARS_CoV_2 N331Q;N343Q 89;97 94;102 34595399 Genomic epidemiological analysis of SARS-CoV-2 household transmission. However, given that an identical viral genome with the same S:N30S amino acid substitution was also recovered from her cousin, who had SARS-CoV-2 RNA detected 1 week later and no further contact with case 1, supported the hypothesis that case 1 transmitted to case 7 at the family event. 2021 Access microbiology Result SARS_CoV_2 N30S 62 66 S 60 61 34595399 Genomic epidemiological analysis of SARS-CoV-2 household transmission. However, the family sequences diverged by a unique combination of two synonymous mutations from others sampled in that region (C-to-U at nucleotide 10 030 and A-to-G at nucleotide 21 625, relative to the reference). 2021 Access microbiology Result SARS_CoV_2 A21625G 159 186 34595399 Genomic epidemiological analysis of SARS-CoV-2 household transmission. Interestingly, the virus sequences recovered from the infants at the family gathering (cases 1 and 7) were found to have diverged from the rest of the family by the acquisition of an additional nonsynonymous A-to-G mutation (nucleotide 21 651 in the reference) changing residue 30 of the spike protein (S:N30S). 2021 Access microbiology Result SARS_CoV_2 N30S 305 309 S;S 288;303 293;304 34595399 Genomic epidemiological analysis of SARS-CoV-2 household transmission. Interrogation of the GISAID database revealed an identical A-to-G mutation at the same nucleotide position resulting in S:N30S in just one other sequenced genome submitted to the platform to date (hCoV-19/Panama/335944/2020, GISAID accession: EPI_ISL_496830); however, this sequence belongs to the A.2 lineage implying independent acquisition of the N30S mutation in both lineages. 2021 Access microbiology Result SARS_CoV_2 N30S;N30S 350;122 354;126 S 120 121 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Both S477N and E484K occur on the same flexible loop at the periphery of the RDB-ACE2 interface. 2021 Nature communications Result SARS_CoV_2 E484K;S477N 15;5 20;10 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Despite sharing multiple mutations and deletions with known VOCs (most prominently HV69/70Delta, LLA241/243Delta, S477N, E484K and P681H), lineage B.1.620 does not appear to be of recombinant origin. 2021 Nature communications Result SARS_CoV_2 E484K;P681H;S477N 121;131;114 126;136;119 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Furthermore, B.1.620 contains P26S, HV69/70Delta, V126A, Y144Delta, LLA241/243Delta and H245Y in the N-terminal domain (NTD) of the spike protein. 2021 Nature communications Result SARS_CoV_2 H245Y;P26S;V126A 88;30;50 93;34;55 S;N 132;101 137;102 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. In contrast, T1027I and D1118H are both buried in the trimerisation interface of the S2 subunit. 2021 Nature communications Result SARS_CoV_2 D1118H;T1027I 24;13 30;19 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Like most currently circulating variants, B.1.620 carries the D614G mutation, which enhances infectivity of SARS-CoV-2, likely through enhanced interactions with the ACE2 receptor by promoting the up-conformation of the receptor-binding domain (RDB). 2021 Nature communications Result SARS_CoV_2 D614G 62 67 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Like the mutations in the NTD, S477N and E484K individually enable broad escape from antibody-mediated immunity. 2021 Nature communications Result SARS_CoV_2 E484K;S477N 41;31 46;36 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Local transmission of B.1.620 in Lithuania has been established as a result of monitoring the outbreak in Anyksciai municipality (Utena county, Lithuania) via sequencing and repeat PCR testing of SARS-CoV-2 positive samples for the presence of E484K and N501Y mutations, as well as looking for S gene target failure (SGTF) caused by the HV69Delta deletion. 2021 Nature communications Result SARS_CoV_2 E484K;N501Y 244;254 249;259 S 294 295 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Of these, P681H is also located on the outer surface of the spike protein, directly preceding the multibasic S1/S2 furin cleavage site. 2021 Nature communications Result SARS_CoV_2 P681H 10 15 S 60 65 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Synonymous mutations at site 15324 and S:T1027I appear to be some of the earliest mutations that occurred in the evolution of lineage B.1.620, both of which are found in at least one other lineage associated with Cameroon (B.1.619), followed by S:E484K which also appears in genomes closest to lineage B.1.620. 2021 Nature communications Result SARS_CoV_2 E484K;T1027I 247;41 252;47 S;S 39;245 40;246 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. The individual V126A and H245Y substitutions are still largely uncharacterised to the best of our knowledge, but might be counterparts to the R246I substitution in B.1.351, and the latter may interfere with a putative glycan binding pocket in the NTD. 2021 Nature communications Result SARS_CoV_2 H245Y;R246I;V126A 25;142;15 30;147;20 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. The remaining mutations in the spike protein:P681H, T1027I and D1118H:are uncharacterised to the best of our knowledge. 2021 Nature communications Result SARS_CoV_2 D1118H;T1027I;P681H 63;52;45 69;58;50 S 31 36 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. The spike protein of B.1.620 also carries both S477N and E484K mutations in the RBD, but in contrast to other VOCs not the N501Y or K417 mutations. 2021 Nature communications Result SARS_CoV_2 E484K;N501Y;S477N 57;123;47 62;128;52 S;RBD 4;80 9;83 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. We have modelled the RBD-ACE2 interface with the S477N and E484K substitutions using refinement in HADDOCK 2.4. 2021 Nature communications Result SARS_CoV_2 E484K;S477N 59;49 64;54 RBD 21 24 34599175 Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Whereas S477N may modulate the loop conformation, E484K may introduce new salt bridges with E35/E75 of ACE2. 2021 Nature communications Result SARS_CoV_2 E484K;S477N 50;8 55;13 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. After 48 h of infection with the same MOI, we again found that Alpha and Beta variants produced significantly more syncytia than D614G (Fig 2C and Appendix Fig S2B) despite similar infection levels (Fig 1C). 2021 The EMBO journal Result SARS_CoV_2 D614G 129 134 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Alpha and Beta S proteins were twofold and 1.7-fold more fusogenic than D614G S, respectively (Fig 3B). 2021 The EMBO journal Result SARS_CoV_2 D614G 72 77 S;S 15;78 16;79 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Alpha and Beta variants produced slightly more extracellular viral RNA than D614G at later time points but not significantly higher levels of infectious particles (Fig 1D). 2021 The EMBO journal Result SARS_CoV_2 D614G 76 81 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Alpha produced moderately more virus than D614G in all cell lines at later time points (Fig 1A-C). 2021 The EMBO journal Result SARS_CoV_2 D614G 42 47 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Alpha S contains the 69/70 and Y144 deletions in the N-terminal domain (NTD), P681H and T716I mutations in the S1/S2 cleavage site, the S982A mutation in the heptad repeat 1 (HR1) site and the D1118H mutation in between HR1 and HR2. 2021 The EMBO journal Result SARS_CoV_2 D1118H;P681H;S982A;T716I 195;80;138;90 201;85;143;95 N 55 56 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Alpha was sequentially followed by Beta, D614G, and Wuhan S (Figs 5B and EV5A). 2021 The EMBO journal Result SARS_CoV_2 D614G 41 46 S 58 59 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Altogether, our data indicate that the S proteins of Alpha and Beta variants form more syncytia than the D614G or Wuhan strains. 2021 The EMBO journal Result SARS_CoV_2 D614G 105 110 S 39 40 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Among the mutations associated with Beta, the 242-244 deletion, as well as the K417N and E484K mutations in the RBD significantly decreased syncytia formation (Figs 4A and EV4F). 2021 The EMBO journal Result SARS_CoV_2 E484K;K417N 90;80 95;85 RBD 113 116 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. As previously mentioned, the introduction of the D614G mutation in the S1/S2 border of the Wuhan S protein also relatively increased fusion, stressing the importance of this cleavage site in fusogenicity (Fig 3B). 2021 The EMBO journal Result SARS_CoV_2 D614G 49 54 S 97 98 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Beta also induced significantly faster fusion than D614G, whereas the Wuhan S was the slowest of all the compared proteins (Fig 3C and Movie EV1). 2021 The EMBO journal Result SARS_CoV_2 D614G 51 56 S 76 77 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Beta produced more virus than D614G in Caco-2 but less in Calu-3 cells at later time points (Fig 1A and B). 2021 The EMBO journal Result SARS_CoV_2 D614G 30 35 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Both Alpha and Beta S proteins contain the N501Y mutation in the RBD and the D614G mutation in the S1/S2 cleavage site (Fig 4A). 2021 The EMBO journal Result SARS_CoV_2 D614G;N501Y 77;43 82;48 RBD;S 65;20 68;21 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Following reports of the emergence of the E484K mutation within the Alpha variant (Collier et al,), we also generated a mutant Alpha S protein with the E484K mutation. 2021 The EMBO journal Result SARS_CoV_2 E484K;E484K 42;152 47;157 S 133 134 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. For instance, Beta replicated slightly more than D614G in Caco-2 cells whereas Alpha replicated slight less than D614G in Vero cells (Fig 1A and C). 2021 The EMBO journal Result SARS_CoV_2 D614G;D614G 49;113 54;118 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. For instance, neutralizing monoclonal antibody 48 (mAb48) restricts D614G virus but not Alpha or Beta variants (Planas et al,). 2021 The EMBO journal Result SARS_CoV_2 D614G 68 73 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. IFN-beta1 was equally effective at reducing viral replication of D614G, Alpha, and Beta variants in Vero cells (Fig EV3A). 2021 The EMBO journal Result SARS_CoV_2 D614G 65 70 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. In line with our results in Vero cells which lack endogenous TMPRSS2 (Fig 3B), we found that the Alpha, Beta, and Delta variants fused more than the D614G, and the Wuhan S protein fused the least (Fig 6D). 2021 The EMBO journal Result SARS_CoV_2 D614G 149 154 S 170 171 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. In the acceptor/donor co-culture, we found that the 293T donor cells expressing the novel variant S proteins formed more syncytia with the Vero acceptor cells than either the D614G or Wuhan (Fig EV2E). 2021 The EMBO journal Result SARS_CoV_2 D614G 175 180 S 98 99 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. mAb48 did not recognize the Beta variant and more specifically did not bind to the K417N mutant (Fig 5C). 2021 The EMBO journal Result SARS_CoV_2 K417N 83 88 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. N501Y found in both Alpha and Beta drastically increased ACE2 binding, in line with previous reports indicating that this mutation enhances affinity of the viral protein to its receptor (Ali et al,; Luan et al,; Tian et al,). 2021 The EMBO journal Result SARS_CoV_2 N501Y 0 5 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Of note, D614G produced similar levels of syncytia as the Wuhan strain in both Vero and S-Fuse cells (Fig 2 and Appendix Fig S2). 2021 The EMBO journal Result SARS_CoV_2 D614G 9 14 S 88 89 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Of the mutations that are associated with Alpha, we found that the 69/70 deletion in the NTD decreased cell-cell fusion whereas P681H and D1118H substitutions both increase fusion (Figs 4A and EV4E). 2021 The EMBO journal Result SARS_CoV_2 D1118H;P681H 139;129 145;134 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Only the D251G mutation in the NTD modestly increased syncytia formation relative to D614G (Figs 4A and EV4F). 2021 The EMBO journal Result SARS_CoV_2 D251G;D614G 9;85 14;90 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. P681H displayed the greatest fusogenicity of all investigated mutations, being almost 2.5-fold higher than D614G S (Figs 4A and EV4E). 2021 The EMBO journal Result SARS_CoV_2 D614G;P681H 107;0 112;5 S 113 114 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. P681H, D1118H, and D215G substitutions facilitate fusion, whereas mutations 69/70, 242-244, K417N, and E484K antagonize cell-cell fusion. 2021 The EMBO journal Result SARS_CoV_2 D1118H;D215G;E484K;K417N;P681H 7;19;105;94;0 13;24;110;99;5 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Relative to D614G, Alpha and Beta variants produced significantly more syncytia, approximately 4.5-fold and threefold respectively, after 20 h of infection with the same MOI (Fig 2B and Appendix Fig S2A). 2021 The EMBO journal Result SARS_CoV_2 D614G 12 17 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Taken together our data show that Alpha and Beta variants replicate similarly to the ancestral D614G strain in a panel of human cell lines and in primary cells, with some slight differences. 2021 The EMBO journal Result SARS_CoV_2 D614G 95 100 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The Beta S is comprised of the L18F, D80A, D215G, and 242-244 mutations in the NTD, K417N and E484K mutations in the receptor-binding domain (RBD), and A701V in the S1/S2 cleavage site. 2021 The EMBO journal Result SARS_CoV_2 A701V;D215G;D80A;E484K;K417N;L18F 153;43;37;95;85;31 158;48;41;100;90;35 RBD 143 146 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The Delta S protein has a higher binding capacity to ACE2 than the D614G S protein, but the binding was lower than the Alpha S protein (Fig 6C). 2021 The EMBO journal Result SARS_CoV_2 D614G 67 72 S;S;S 10;73;125 11;74;126 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The Delta S protein triggered more cell-cell fusion than the D614G variant but was similar to the Alpha S protein (Fig 6A). 2021 The EMBO journal Result SARS_CoV_2 D614G 61 66 S;S 10;104 11;105 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The E484K mutant had a slightly, but not significantly, higher binding to ACE2 (Fig EV5C). 2021 The EMBO journal Result SARS_CoV_2 E484K 4 9 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The fusion kinetic of the Delta S was also similar to Alpha but more rapid than D614G (Fig 6B). 2021 The EMBO journal Result SARS_CoV_2 D614G 80 85 S 32 33 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The introduction of the E484K RBD mutation into the Alpha S protein significantly decreased its potential to form syncytia, despite not changing cell surface expression, further supporting the mutation's restrictive effect on cell-cell fusion (Figs 4B and EV2B). 2021 The EMBO journal Result SARS_CoV_2 E484K 24 29 RBD;S 30;58 33;59 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The K417N and 242-244 mutations were also responsible for decreasing S-mediated fusion, suggesting a tradeoff between antibody escape and fusion (Fig 5C). 2021 The EMBO journal Result SARS_CoV_2 K417N 4 9 S 70 71 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The K417N substitution present in the Beta S decreased ACE2 binding (Figs 5B and EV5C). 2021 The EMBO journal Result SARS_CoV_2 K417N 4 9 S 43 44 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The K417N, 242-244, and E484K mutations restrict fusogenicity but differently affect ACE2 binding, with the former two decreasing affinity and the latter slightly increasing. 2021 The EMBO journal Result SARS_CoV_2 E484K;K417N 25;4 30;9 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The Wuhan S was slightly less fusogenic that the D614G S (Fig 3B). 2021 The EMBO journal Result SARS_CoV_2 D614G 49 54 S;S 10;55 11;56 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Therefore, Alpha and Beta variants appear more fusogenic than D614G in S-Fuse and Vero cells. 2021 The EMBO journal Result SARS_CoV_2 D614G 62 67 S 71 72 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Therefore, IFN-beta1 similarly inhibited viral replication and reduced syncytia formation by D614G, Alpha, and Beta variants. 2021 The EMBO journal Result SARS_CoV_2 D614G 93 98 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Therefore, the N501Y mutation is the most significant contributor to increased ACE2 binding of the variants, though it does not affect cell-cell fusion on its own. 2021 The EMBO journal Result SARS_CoV_2 N501Y 15 20 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. This was corroborated by the observation that addition of the E484K mutation to Alpha S protein also slightly increased ACE2 binding (Figs 5B and EV5A). 2021 The EMBO journal Result SARS_CoV_2 E484K 62 67 S 86 87 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Upon infection of S-Fuse cells, we noticed that the Alpha and Beta variants formed larger and more numerous infected syncytia than either D614G or the ancestral Wuhan strain (Fig EV1A). 2021 The EMBO journal Result SARS_CoV_2 D614G 138 143 S 18 19 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. We expressed each mutant S into Vero GFP split cells and measured their potential to induce cell-cell fusion in comparison to the D614G S protein. 2021 The EMBO journal Result SARS_CoV_2 D614G 130 135 S;S 25;136 26;137 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. We first infected Caco-2, Calu-3, and Vero cells with Alpha, Beta, and D614G variants and generated multistep growth curves (Fig 1). 2021 The EMBO journal Result SARS_CoV_2 D614G 71 76 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. We had previously found that certain neutralizing antibodies differentially affect SARS-CoV-2 D614G, Alpha, and Beta variants (Planas et al,). 2021 The EMBO journal Result SARS_CoV_2 D614G 94 99 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. We introduced individual mutations into the D614G background. 2021 The EMBO journal Result SARS_CoV_2 D614G 44 49 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. We introduced the D614G mutation into the Wuhan protein and designed plasmids to express Alpha and Beta S proteins. 2021 The EMBO journal Result SARS_CoV_2 D614G 18 23 S 104 105 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. We thus characterized the impact of IFITMs on syncytia formed upon expression of D614G, Alpha, and Beta S proteins in 293T cells. 2021 The EMBO journal Result SARS_CoV_2 D614G 81 86 S 104 105 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. We thus compared the fusogenicity of the Delta S protein to that of D614G and Alpha. 2021 The EMBO journal Result SARS_CoV_2 D614G 68 73 S 47 48 34603303 A Combination Adjuvant for the Induction of Potent Antiviral Immune Responses for a Recombinant SARS-CoV-2 Protein Vaccine. Importantly, the N501Y mutation is shared by most of the recently identified variants of concern, B1.1.7, B.135.1, and P.1, among others, and plays an important role in the increased human to human transmissibility observed for these variants by increasing the affinity of the S protein for the hACE2 receptor. 2021 Frontiers in immunology Result SARS_CoV_2 N501Y 17 22 S 277 278 34603303 A Combination Adjuvant for the Induction of Potent Antiviral Immune Responses for a Recombinant SARS-CoV-2 Protein Vaccine. In addition to the changes in the S protein, the MA-virus also contains three other mutations relative to the Wuhan-Hu-1 isolate: S194T in the nucleoprotein, T7I in the M protein, and L84S in ORF8. 2021 Frontiers in immunology Result SARS_CoV_2 L84S;S194T;T7I 184;130;158 188;135;161 ORF8;S 192;34 196;35 34603303 A Combination Adjuvant for the Induction of Potent Antiviral Immune Responses for a Recombinant SARS-CoV-2 Protein Vaccine. The L84S mutation is however present in the USA-WA1/2020 strain and is most likely not due to mouse adaptation. 2021 Frontiers in immunology Result SARS_CoV_2 L84S 4 8 34603303 A Combination Adjuvant for the Induction of Potent Antiviral Immune Responses for a Recombinant SARS-CoV-2 Protein Vaccine. The MA-SARS-CoV-2 S protein contains two amino acid (aa) mutations compared to the WT virus from which it was derived, including N501Y and H655Y, and a four aa insertion within the S1 subunit. 2021 Frontiers in immunology Result SARS_CoV_2 H655Y;N501Y 139;129 144;134 S 18 19 34603303 A Combination Adjuvant for the Induction of Potent Antiviral Immune Responses for a Recombinant SARS-CoV-2 Protein Vaccine. The N501Y substitution has previously been reported by other groups in an independent mouse adaptation of SARS-CoV-2, and is thus likely to be important for increasing affinity to the mACE2 receptor. 2021 Frontiers in immunology Result SARS_CoV_2 N501Y 4 9 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. In addition, very high rate recurrent mutations exist at the following locations: spike protein; D614G, nucleocapsid phosphoprotein; S194L, R203K and G204R, ORF3a; Q57H and G251V, and ORF8; L84S. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;G204R;G251V;L84S;Q57H;R203K;S194L 97;150;173;190;164;140;133 102;155;178;194;168;145;138 N;S;ORF3a;ORF8 104;82;157;184 116;87;162;188 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. It is worth noting that the D614G mutation in the S protein coincides with P4715L variants in the ORF1ab RdRp region. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;P4715L 28;75 33;81 ORF1ab;RdRP;S 98;105;50 104;109;51 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. More so, the N protein variants having I292T mutation are prevalent in viral samples from South America. 2021 Infection, genetics and evolution Result SARS_CoV_2 I292T 39 44 N 13 14 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. Mutational analysis of the 7213 SARS-CoV-2 genome sequences revealed the following high rate recurrent mutations in the ORF1ab polyprotein sequence: T265I and D448del (nsp2 coding region), T2016K (nsp3), G3278S (nsp5), L3606F (nsp6), A4489V and P4715L (RNA dependent RNA polymerase), and P5828L, Y5865C (RNA helicase region). 2021 Infection, genetics and evolution Result SARS_CoV_2 A4489V;D448del;G3278S;L3606F;P4715L;P5828L;T2016K;T265I;Y5865C 234;159;204;219;245;288;189;149;296 240;166;210;225;251;294;195;154;302 RdRp;Helicase;ORF1ab;Nsp2;Nsp3;Nsp5;Nsp6 253;308;120;168;197;212;227 281;316;126;172;201;216;231 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. Mutations P5828L and Y5865C in nsp13 are prevalent in Oceania samples and they are concurrent in same viral sequences. 2021 Infection, genetics and evolution Result SARS_CoV_2 P5828L;Y5865C 10;21 16;27 Nsp13 31 36 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. ORF8 variants having S24L mutations are only observed in viral samples from the USA. 2021 Infection, genetics and evolution Result SARS_CoV_2 S24L 21 25 ORF8 0 4 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. The 78% viral samples bearing the D614G and P4715L mutations also bears either the concurrent N protein R203K and G204R or the ORF3a Q57H mutations (Table 2 ). 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;G204R;P4715L;Q57H;R203K 34;114;44;133;104 39;119;50;137;109 ORF3a;N 127;94 132;95 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. The following mutations: N protein (P13L and S194L), ORF8 (L84S), nsp3 (T2016K), and nsp6 (L3606F) are prevalent in Asian population. 2021 Infection, genetics and evolution Result SARS_CoV_2 S194L;L3606F;L84S;P13L;T2016K 45;91;59;36;72 50;97;63;40;78 Nsp3;Nsp6;ORF8;N 66;85;53;25 70;89;57;26 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. The R203K and G204R variants ran concurrently almost in same viral sequences. 2021 Infection, genetics and evolution Result SARS_CoV_2 G204R;R203K 14;4 19;9 34607456 A Combination of Receptor-Binding Domain and N-Terminal Domain Neutralizing Antibodies Limits the Generation of SARS-CoV-2 Spike Neutralization-Escape Mutants. For the best RBD MAb (ADI-56443), a change at amino acid position 490 in the S protein (F490S) made rVSV-SARS2 highly resistant (>2,700-fold increase in neutralization IC50 value) to this MAb. 2021 mBio Result SARS_CoV_2 F490S 88 93 RBD;S 13;77 16;78 34607456 A Combination of Receptor-Binding Domain and N-Terminal Domain Neutralizing Antibodies Limits the Generation of SARS-CoV-2 Spike Neutralization-Escape Mutants. For the NTD MAb (ADI-56479), rVSV-SARS2 neutralization-escape mutations mapped to residues 145 (Y145D), 150 (K150E), and 152 (W152R) in the NTD, and each one of these mutations individually afforded an ~1,000-fold increase in the neutralization IC50 values. 2021 mBio Result SARS_CoV_2 K150E;W152R;Y145D 109;126;96 114;131;101 34607456 A Combination of Receptor-Binding Domain and N-Terminal Domain Neutralizing Antibodies Limits the Generation of SARS-CoV-2 Spike Neutralization-Escape Mutants. In addition to F490S, binding of ADI-56443 was completely abolished by C480S/R, E484K/G/D, C488Y/S, and F490L/I/C RBD mutations. 2021 mBio Result SARS_CoV_2 C480R;C480S;C488S;C488Y;E484D;E484G;E484K;F490C;F490I;F490L;F490S 71;71;91;91;80;80;80;104;104;104;15 78;78;98;98;89;89;89;113;113;113;20 RBD 114 117 34607456 A Combination of Receptor-Binding Domain and N-Terminal Domain Neutralizing Antibodies Limits the Generation of SARS-CoV-2 Spike Neutralization-Escape Mutants. Mutations at other residues, including S494F in the RBD, also significantly reduced this MAb's binding. 2021 mBio Result SARS_CoV_2 S494F 39 44 RBD 52 55 34607456 A Combination of Receptor-Binding Domain and N-Terminal Domain Neutralizing Antibodies Limits the Generation of SARS-CoV-2 Spike Neutralization-Escape Mutants. Specifically, the sera showed a drop of 3.5-fold (Y145D) to 16-fold (K150E and W152R) in their neutralization IC50 titers compared to the parental virus. 2021 mBio Result SARS_CoV_2 W152R;K150E;Y145D 79;69;50 84;74;55 34607456 A Combination of Receptor-Binding Domain and N-Terminal Domain Neutralizing Antibodies Limits the Generation of SARS-CoV-2 Spike Neutralization-Escape Mutants. The E484K mutation is also present in multiple variants including P.1, P.2, B.1.525, and B.1.351, and viruses carrying this mutation are resistant to the currently used MAb therapy. 2021 mBio Result SARS_CoV_2 E484K 4 9 34607791 BNT162b2 vaccine-induced humoral and cellular responses against SARS-CoV-2 variants in systemic lupus erythematosus. Among patients with neutralising antibody activity against D614G strain, 100% (37/37) of patients also efficiently neutralised B.1.1.7 strain, 89% (33/37) B.1.617.1 variant, 92% (34/37) B.1.617.2 variant, 87% (32/37) B.1.1.28 variant, 89% (33/37) B.1.1.28 variant and 60% of patients (27/37) had detectable neutralising activity against B.1.351. 2022 Annals of the rheumatic diseases Result SARS_CoV_2 D614G 59 64 34607791 BNT162b2 vaccine-induced humoral and cellular responses against SARS-CoV-2 variants in systemic lupus erythematosus. As expected, we confirm a strong correlation between anti-RBD antibody levels and neutralisation titres (SARS-CoV-2 D614G r=0.82, p<0.0001; figure 3A). 2022 Annals of the rheumatic diseases Result SARS_CoV_2 D614G 116 121 RBD 58 61 34607791 BNT162b2 vaccine-induced humoral and cellular responses against SARS-CoV-2 variants in systemic lupus erythematosus. Consistent with previous studies, we found that vaccine-induced IgG antibodies efficiently cross-neutralise variants B.1.1.7 (ID50 median (min-max); D614G 1453 (30-18 910) and B.1.1.7 514.5 (30-12 625), ns; figure 3E). 2022 Annals of the rheumatic diseases Result SARS_CoV_2 D614G 149 154 34607791 BNT162b2 vaccine-induced humoral and cellular responses against SARS-CoV-2 variants in systemic lupus erythematosus. Interestingly, SARS-CoV-2-specific T cell responses were nevertheless detected in two out of six patients with very low levels of neutralising activity in their serum (ID50 below 100 for D614G strain). 2022 Annals of the rheumatic diseases Result SARS_CoV_2 D614G 187 192 34607791 BNT162b2 vaccine-induced humoral and cellular responses against SARS-CoV-2 variants in systemic lupus erythematosus. It is noteworthy that serum neutralisation activity decreased with lineages bearing the E484K mutation in the RBD (ID50 B1.617.1 341.1 (30-3996), p<0.001; B.1.617.2 379.3 (30-4982), p<0.001; B.1.617.3 317.9 (30-3604), p<0.01; B.1.1.28 302.3 (30-5757) and B.1.351 88.1 (30-2389); p<0.0001; figure 3E), but remained detectable in a majority of patients (82% for B.1.1.7; 73% for B.1.617.1; 76% for B.1.617.2; 71% for B.1.617.3; 73% for B.1.1.28; 60% for B.1.351; figure 3F). 2022 Annals of the rheumatic diseases Result SARS_CoV_2 E484K 88 93 RBD 110 113 34607791 BNT162b2 vaccine-induced humoral and cellular responses against SARS-CoV-2 variants in systemic lupus erythematosus. We confirm that naive B cell counts are positively associated with vaccine-induced neutralising antibody responses (ID50 D614G 93.4 (30-246.5) vs 340.1 (30-1632) in quartiles 1 and 2, respectively; p<0.05 vs 315.2 (30-721.1) in quartile 3; p<0.05; vs 679.9 (60.4-2510) in quartile 4; p<0.001; figure 3D). 2022 Annals of the rheumatic diseases Result SARS_CoV_2 D614G 121 126 34607791 BNT162b2 vaccine-induced humoral and cellular responses against SARS-CoV-2 variants in systemic lupus erythematosus. While a majority of MMF/MTX-treated patients still harboured detectable neutralising activity (65% (15/23) MMF-treated patients, 68% (13/19) MTX-treated patients vs 96% (81/84) patients without MMF or MTX), their serum neutralising activity drastically dropped compared with patients receiving other treatments (inhibitory dilution 50 (ID50) D614G median(min-max); 111.2 (30-18 910) in MMF-treated patients vs 90.4 (30-5527) in MTX-treated patients and 684.6 (30-12061) in other patients; p<0.05; figure 3B). 2022 Annals of the rheumatic diseases Result SARS_CoV_2 D614G 342 347 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. Adjusted risks of hospitalization, ICU admission and death were 52% (95% confidence interval [CI] 42%-63%), 89% (95% CI 67%-117%) and 51% (95% CI 30%-78%) higher, respectively, with N501Y-positive VOC than with non-VOC infections; respective differences between non-VOC and Delta infections were 108% (95% CI 78%-140%), 235% (95% CI 160%-331%) and 133% (95% CI 54%-231%). 2021 CMAJ Result SARS_CoV_2 N501Y 182 187 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. After adjustment for age, sex, vaccination status, comorbidities, health unit and temporal trend, we observed large and significant increases in the risk of hospitalization, ICU admission and death with both N501Y-positive VOC and probable Delta infections, relative to non-VOC infections (Table 2). 2021 CMAJ Result SARS_CoV_2 N501Y 208 213 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. Among all reported cases, 22.4% were infections with non-VOC, 76.7% were infections with N501Y-positive VOCs, and 2.8% were classified as probable Delta infections. 2021 CMAJ Result SARS_CoV_2 N501Y 89 94 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. In our study, VOCs with the N501Y mutation were associated with a markedly increased risk of hospitalization, ICU admission and death among infected individuals in Ontario. 2021 CMAJ Result SARS_CoV_2 N501Y 28 33 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. In restriction analyses that excluded non-VOC cases from models, we found a significant increase in risk with Delta infections relative to N501Y-positive VOC infections for hospitalization (adjusted odds ratio [OR] 1.45, 95% CI 1.27-1.64), ICU admission (adjusted OR 2.01, 95% CI 1.60-2.47) and death (adjusted OR 1.69, 95% CI 1.16-2.35). 2021 CMAJ Result SARS_CoV_2 N501Y 139 144 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. Infections by N501Y-positive variants were significantly more common in the Greater Toronto and Hamilton Area (the province's largest metropolitan area); Delta variant infections were significantly less common in Ottawa (the province's second largest metropolitan area). 2021 CMAJ Result SARS_CoV_2 N501Y 14 19 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. Our study adds to this by showing that Delta variant infection is associated with an increased risk of ICU admission and death, relative to non-VOC and N501Y-positive VOCs. 2021 CMAJ Result SARS_CoV_2 N501Y 152 157 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. People with N501Y-positive variants and probable Delta infection were significantly younger and less likely to have comorbidities than those with non-VOC infections. 2021 CMAJ Result SARS_CoV_2 N501Y 12 17 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. The Delta variant is more virulent than previously dominant N501Y-positive VOCs. 2021 CMAJ Result SARS_CoV_2 N501Y 60 65 34611654 Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein. Both the protein pull-down and pseudovirus entry assays demonstrated that compared to the wild type spike, the K417V mutation allowed more spike molecules to open up for binding ACE2 and mediating viral entry. 2021 Research square Result SARS_CoV_2 K417V 111 116 S;S 100;139 105;144 34611654 Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein. Cryo-EM analysis at 4.6 A revealed that 91% of the K417V/FnM-deletion spike molecules were open and 9% were closed. 2021 Research square Result SARS_CoV_2 K417V 51 56 S 70 75 34611654 Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein. Instead, we prepared recombinant SARS-CoV-2 spike ectodomain containing the K417V mutation and FnM deletion (in addition to proline mutations) (K417V/FnM-deletion). 2021 Research square Result SARS_CoV_2 K417V;K417V 76;144 81;149 S 44 49 34611654 Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein. The result showed that K417V/FnM-deletion spike and FnM-point spike induced significantly more neutralizing antibodies than FnM-deletion spike. 2021 Research square Result SARS_CoV_2 K417V 23 28 S;S;S 42;62;137 47;67;142 34611654 Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein. The result showed that K417V/FnM-deletion spike and FnM-point spike induced significantly more RBD-specific antibodies than FnM-deletion spike. 2021 Research square Result SARS_CoV_2 K417V 23 28 S;S;S;RBD 42;62;137;95 47;67;142;98 34611654 Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein. These data confirm that more molecules of K417V/FnM-deletion spike and of FnM-point spike are in the open conformations than FnM-deletion spike. 2021 Research square Result SARS_CoV_2 K417V 42 47 S;S;S 61;84;138 66;89;143 34611654 Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein. To understand how the RBD conformations of SARS-CoV-2 spike affect host immune responses targeting the RBD, we immunized mice with one of the following three recombinant SARS-CoV-2 spike ectodomains: FnM-deletion spike, FnM-point spike, and K417V/FnM-deletion spike (in addition to the proline mutations in all of them). 2021 Research square Result SARS_CoV_2 K417V 241 246 S;S;S;S;S;RBD;RBD 54;181;213;230;260;22;103 59;186;218;235;265;25;106 34611654 Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein. We could not obtain recombinant SARS-CoV-2 K417V spike ectodomain that was stable enough for cryo-EM analysis. 2021 Research square Result SARS_CoV_2 K417V 43 48 S 49 54 34611654 Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein. We introduced the K417V mutation into SARS-CoV-2 spike, and examined its impact on the conformation of SARS-CoV-2 spike. 2021 Research square Result SARS_CoV_2 K417V 18 23 S;S 49;114 54;119 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. Analysis of mutations characteristic of variants B.1.1.7 and B.1.351 showed that some of them were present in both, such as the SGF deletion in nsp6 (positions 11285 to 11294 in sequence NC_045512) or the N501Y substitution in the spike protein gene (nucleotide position 23094 in sequence NC_045512). 2021 Microbiology spectrum Result SARS_CoV_2 N501Y 205 210 S;Nsp6 231;144 236;148 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. Focused Sanger sequencing of the S gene region of samples 5824 and 6021 showed the presence of the 69 to 70 deletion, but the B.1.1.7 variant-associated mutation 144del and N501Y substitution were absent. 2021 Microbiology spectrum Result SARS_CoV_2 144del;N501Y 162;173 168;178 S 33 34 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. Likewise, the D215G mutation and the S gene 242 to 244 deletion are strongly associated with variant B.1.351 and have not been identified in other variants thus far. 2021 Microbiology spectrum Result SARS_CoV_2 D215G 14 19 S 37 38 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. On the other hand, the N gene D3L mutation is strongly associated with variant B.1.1.7 and is not associated with other currently dominant variants. 2021 Microbiology spectrum Result SARS_CoV_2 D3L 30 33 N 23 24 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. Others, such as the 69 to 70 deletion and N501Y substitution, developed independently and were detected in samples not classified as variant B.1.1.7. 2021 Microbiology spectrum Result SARS_CoV_2 N501Y 42 47 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. Out of 20 suspected samples, four contained the following mutations in the spike gene: D215G, the 242 to 244 deletion, K417N, E484K, and N501Y, all associated with the B.1.351 variant. 2021 Microbiology spectrum Result SARS_CoV_2 D215G;E484K;K417N;N501Y 87;126;119;137 92;131;124;142 S 75 80 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. Sanger sequencing of the spike gene region from sample 7075 contained the following mutations, all of which are characteristic of the B.1.1.7 variant: 69 to 70 deletion, 144 deletion, N501Y, S982A, and D1118H. 2021 Microbiology spectrum Result SARS_CoV_2 D1118H;N501Y;S982A 202;184;191 208;189;196 S 25 30 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. The 5'p region of the variant B.1.1.7 SC-2 N gene contains a complete codon substitution, translated into D3L amino acid substitution. 2021 Microbiology spectrum Result SARS_CoV_2 D3L 106 109 N 43 44 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. They both contained, however, a unique substitution, N439K, which is not associated with the B.1.1.7 variant. 2021 Microbiology spectrum Result SARS_CoV_2 N439K 53 58 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. This reaction was termed N gene D3L reaction:ND3L. 2021 Microbiology spectrum Result SARS_CoV_2 D3L 32 35 N 25 26 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. This variant contains two unique mutations in the spike gene, D215G and a deletion at amino acid position 242 (nucleotide positions 22281 and 22289 in sequence NC_045512). 2021 Microbiology spectrum Result SARS_CoV_2 D215G;del 242 62;74 67;109 S 50 55 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. Using this assay, 64 samples were identified as variant B.1.351 and were confirmed by sequencing to contain the D215G and S242 mutations (Table S2). 2021 Microbiology spectrum Result SARS_CoV_2 D215G 112 117 34613786 Highly Efficient SARS-CoV-2 Infection of Human Cardiomyocytes: Spike Protein-Mediated Cell Fusion and Its Inhibition. For genetic interference, we generated an expression vector differing from CoV-2 S through the single amino acid change R682S in order to disrupt the mutibasic furin cleavage site. 2021 Journal of virology Result SARS_CoV_2 R682S 120 125 S 81 82 34613786 Highly Efficient SARS-CoV-2 Infection of Human Cardiomyocytes: Spike Protein-Mediated Cell Fusion and Its Inhibition. The last panel shows that the R682S mutant of CoV-2 S is fusion-inactive. 2021 Journal of virology Result SARS_CoV_2 R682S 30 35 S 52 53 34613786 Highly Efficient SARS-CoV-2 Infection of Human Cardiomyocytes: Spike Protein-Mediated Cell Fusion and Its Inhibition. The left panel documents strong inhibition of spike protein processing by a high concentration of FI and complete lack of processing of the R682S mutant. 2021 Journal of virology Result SARS_CoV_2 R682S 140 145 S 46 51 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. (See Data Availability for access to the raw correlation coefficient data for all residues.) Yet, care should be taken with assigning the predominant role in infection to a single, non-RBD domain residue in the UK variant; several other mutations are present that could modulate the binding affinity to the ACE2 receptor (particularly N501Y in the RBD-ACE2 binding interface). 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 N501Y 335 340 RBD;RBD 185;348 188;351 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. A relatively rare mutation, A570V, resulted in a decrease of the overall stability of the spike protein in all three states, based on the FoldX empirical force field. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 A570V 28 33 S 90 95 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. As evidence, we highlight the example of the D614G mutation, which is already observed in numerous strains of the SARS-CoV-2 all over the world. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 45 50 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. As it likely did not increase the evolutionary advantage of the virus by increasing infectivity, this mutation, only occurring in one strain so far, did not become as prevalent as D614G. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 180 185 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. But such loss of hydrogen bonding is not observed in the case of the D614G mutant (SI Appendix). 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 69 74 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. Cryo-EM studies have indicated that the D614G mutation is, by itself, capable of altering the conformational dynamics of spike protein by stabilizing an RBD up state over the down conformation. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 40 45 S;RBD 121;153 126;156 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. In the D614G mutant, from our analysis, this stabilization is significantly lower in comparison to the WT (SI Appendix. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 7 12 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. Indeed, our simulations of the D614G mutant spike indicate that, unlike the wild-type (WT) system for which a significantly different dihedral angle distribution exists, there is no difference between the closed and the partially open configurations in terms of the torsion angle space explored by residue G614 (SI Appendix. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 31 36 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. On the contrary, an A570D mutation is observed in the same residue in the newly emerged and highly infectious B.1.1.7 strain in the United Kingdom. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 A570D 20 25 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. Particularly, the loss of hydrogen bond with T859 has been attributed to the higher stability of the RBD up structure in D614G mutant, by Mansbach et al. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 121 126 RBD 101 104 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. The B.1.1.7 also shows a P681H mutation close to the highly correlated N679 residue predicted from our model (SI Appendix. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 P681H 25 30 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. These hydrogen bonds will be absent in D614G mutant and likely reduce the energy cost of the conformational transition. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 39 44 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. To this end, we performed additional simulations of the open and closed states of the D614G mutant. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D614G 86 91 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. For the real-time estimating potentials, we find that the real-time estimates of eta appear unstable in February and early March, when the D614G substitution emerge, and gradually converge and stabilize since March 12, see. 2021 BMC infectious diseases Result SARS_CoV_2 D614G 139 144 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. We infer the transmission advantage eta at 1.54 (95%CI: 1.36, 1.72), which means the D614G substitution increases 54% of the transmissibility. 2021 BMC infectious diseases Result SARS_CoV_2 D614G 85 90 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. We report the estimated proportion of D614G substitution E[pt] fits the observed sequencing data well, see. 2021 BMC infectious diseases Result SARS_CoV_2 D614G 38 43 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. when the proportion of D614G substitution (pt) reaches 35% (< 0.5), the eta estimate is 2.12 (95%CI: 1.24, 3.78), which is significantly larger than 1. 2021 BMC infectious diseases Result SARS_CoV_2 D614G 23 28 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. Spike gene analysis of three isolates from three patients found that only the D614G mutation was detected among the isolates, although in #35 isolates D215Y and E484D mutations were also present. 2021 F1000Research Result SARS_CoV_2 D215Y;D614G;E484D 151;78;161 156;83;166 S 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). In contrast, the E484K and RdRp Ct values were within 2 cycles for the P.1 and B.1.351 VOCs. 2021 Journal of clinical virology Result SARS_CoV_2 E484K 17 22 RdRP 27 31 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). LOD was calculated at 698 cp/mL for NP swabs and 968 cp/mL for SG specimens using synthetic DNA of the RdRP gene and the S gene (nt 1-2160) that harbor HV69/70 del, E484K and N501Y substitution. 2021 Journal of clinical virology Result SARS_CoV_2 E484K;N501Y 165;175 170;180 RdRP;S 103;121 107;122 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). No B.1.1.7 or B.1.526 strain harboured the E484K mutation in this data set. 2021 Journal of clinical virology Result SARS_CoV_2 E484K 43 48 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). The analytical sensitivity of 100% (95% CI 99.27%-100%) and specificity of 100% (95% CI 98.99%-100%) for HV69/70 del, sensitivity of 100% (95% CI 99.55%-100%) and specificity of 100% (95% CI 93.73% - 100%) for N501Y, and sensitivity of 100% (95% CI 98.94% - 100%) and specificity of 98.10% (95% CI 96.53% - 99.08%) for E484K mutation (Table 2 ). 2021 Journal of clinical virology Result SARS_CoV_2 E484K;N501Y 319;210 324;215 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). The cycle threshold (Ct) values of the E484K positive target in the E484Q positive specimens increased by 6.15 cycles on average when compared to the Ct value for the RdRP gene (Table 3 ). 2021 Journal of clinical virology Result SARS_CoV_2 E484K;E484Q 39;68 44;73 RdRP 167 171 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). The decreased specificity observed for the E484K target was due to the cross-reactivity with the E484Q mutation found in ten B.1.627.1 variants tested. 2021 Journal of clinical virology Result SARS_CoV_2 E484K;E484Q 43;97 48;102 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). The occasional mutation E484K reported in multiple lineages was only detected in the B.1.438.1 lineage where 8 out of 15 specimens had that specific mutation. 2021 Journal of clinical virology Result SARS_CoV_2 E484K 24 29 34630410 A Barcoded Flow Cytometric Assay to Explore the Antibody Responses Against SARS-CoV-2 Spike and Its Variants. For this, we introduced in the RBD-CD8 construct the N501Y and the E484K point mutations characteristic for the alpha and beta variant, respectively ( Figure 6A ). 2021 Frontiers in immunology Result SARS_CoV_2 E484K;N501Y 67;53 72;58 RBD 31 34 34630410 A Barcoded Flow Cytometric Assay to Explore the Antibody Responses Against SARS-CoV-2 Spike and Its Variants. In addition, we introduced a glycine to isoleucine (G496I) amino acid exchange predicted to increase the interaction surface between the RBD and the ACE2 receptor. 2021 Frontiers in immunology Result SARS_CoV_2 G496I 52 57 RBD 137 140 34630410 A Barcoded Flow Cytometric Assay to Explore the Antibody Responses Against SARS-CoV-2 Spike and Its Variants. Interestingly, we found that, despite its lower expression, the N501Y mutant RBD-CD8 is bound better by ACE2-Ig than the WT RBD-CD8 construct, whereas Ramos cells expressing the G496I and E484K mutant RBD-CD8 constructs are less well bound by ACE2-Ig. 2021 Frontiers in immunology Result SARS_CoV_2 E484K;G496I;N501Y 188;178;64 193;183;69 RBD;RBD;RBD 77;124;201 80;127;204 34630410 A Barcoded Flow Cytometric Assay to Explore the Antibody Responses Against SARS-CoV-2 Spike and Its Variants. RBD-specific IgG produced during the secondary response of the 12 vaccinated persons binds to a similar extent to Ramos cells carrying the WT, N501Y or G496I RBD-CD8 but to a lesser extent to those expressing the E484K mutant RBD-CD8 constructs. 2021 Frontiers in immunology Result SARS_CoV_2 E484K;G496I;N501Y 213;152;143 218;157;148 RBD;RBD;RBD 0;158;226 3;161;229 34630410 A Barcoded Flow Cytometric Assay to Explore the Antibody Responses Against SARS-CoV-2 Spike and Its Variants. The three RBD-specific mAb (TRES224, TRES6 and R10987) bind to a similar extent to Ramos cells expressing the WT, N501Y, or G496I mutant RBD-CD8 proteins, whereas those cells expressing the E484K mutant RBD-CD8 constructs are poorly bound by these antibodies ( Figure 6D ). 2021 Frontiers in immunology Result SARS_CoV_2 E484K;G496I;N501Y 190;124;114 195;129;119 RBD;RBD;RBD 10;137;203 13;140;206 34630410 A Barcoded Flow Cytometric Assay to Explore the Antibody Responses Against SARS-CoV-2 Spike and Its Variants. These are an asparagine to tyrosine exchange (N501Y) in the alpha variant and the same mutation in combination with a glutamate to lysine (E484K) exchange mutation in the beta variant. 2021 Frontiers in immunology Result SARS_CoV_2 E484K;N501Y 139;46 144;51 34630410 A Barcoded Flow Cytometric Assay to Explore the Antibody Responses Against SARS-CoV-2 Spike and Its Variants. This experiment showed that the N501Y and E484K mutant RBD-CD8 constructs are less expressed on Ramos cells than the WT or G496I mutated construct. 2021 Frontiers in immunology Result SARS_CoV_2 E484K;G496I;N501Y 42;123;32 47;128;37 RBD 55 58 34630410 A Barcoded Flow Cytometric Assay to Explore the Antibody Responses Against SARS-CoV-2 Spike and Its Variants. This study suggests that E484K is an immune escape mutation of the S protein. 2021 Frontiers in immunology Result SARS_CoV_2 E484K 25 30 S 67 68 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. The distance fluctuated along the simulation time with clear distinctions between the WT and the P108S mutant. 2021 Biophysics and physicobiology Result SARS_CoV_2 P108S 97 102 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. The P108S mutation suppresses plasticity of catalytic dyad. 2021 Biophysics and physicobiology Result SARS_CoV_2 P108S 4 9 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Therefore, it is tempting to speculate that the mutation P108S in the main protease, frequently observed in patients with mild symptoms in Tokyo, affects dynamics of the catalytic residues, thereby causing milder symptoms. 2021 Biophysics and physicobiology Result SARS_CoV_2 P108S 57 62 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. To further quantify the difference in dynamics between the WT and P108S mutant, we computed the distances between center of gravity of the catalytic residues. 2021 Biophysics and physicobiology Result SARS_CoV_2 P108S 66 71 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. To further quantify the effect of the P108S mutation on the catalytic dyad, we performed PCA of the MD trajectories based on Calpha atom of the protein ensembles. 2021 Biophysics and physicobiology Result SARS_CoV_2 P108S 38 43 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. To more directly examine correlations of motions between the P108S mutation and other residues, we also evaluated cross-correlation of residues in the MD trajectories. 2021 Biophysics and physicobiology Result SARS_CoV_2 P108S 61 66 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Together with the fact that domain III contributes to the self-association of the two chains in the main protease and the major PCs of the mutant simulations correspond to motions in domain III, lower residue correlations in domain III of the mutant relative to the WT protease may be one of the reasons that COVID-19 patients infected by virus with the mutation P108S have milder symptoms. 2021 Biophysics and physicobiology Result SARS_CoV_2 P108S 363 368 COVID-19 309 317 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. When we superposed Calpha-atoms of the domains I and II and computed Calpha-RMSDs of the catalytic residues, we observed larger variation after 1.0 mus in the P108S catalytic residues than in those of the WT protease. 2021 Biophysics and physicobiology Result SARS_CoV_2 P108S 159 164 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. A significantly lower neutralizing titer against D614G, B.1.1.7, P.1, or B.1.351 was observed in the serum of the asymptomatic/mild COVID-19 patients compared with the critical patients (4- to 9-fold lower, P < .0001) (Figure 3A-D). 2021 Open forum infectious diseases Result SARS_CoV_2 D614G 49 54 COVID-19 132 140 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. From the first wave to the third wave, the neutralizing activity against the B.1.1.7 variant was similar to or slightly lower than that against D614G, whereas it was higher in the fourth wave (increased 4x, P = .0009). 2021 Open forum infectious diseases Result SARS_CoV_2 D614G 144 149 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. In contrast, the mean neutralizing antibody titer against P.1 was 44, and that against B.1.351 was 21; each of these values was lower than that for D614G, especially in the case of B.1.351 (3.8x, P < .0001). 2021 Open forum infectious diseases Result SARS_CoV_2 D614G 148 153 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. Interestingly, some sera of individuals showed similar or high neutralizing activity for P.1 compared with D614G (Figure 1). 2021 Open forum infectious diseases Result SARS_CoV_2 D614G 107 112 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. The mean neutralizing antibody titer for the D614G variant was 80, and that for the B.1.1.7 variant was 111. 2021 Open forum infectious diseases Result SARS_CoV_2 D614G 45 50 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. The neutralizing titer of B.1.1.7 seemed to be higher than that of D614G, but the difference was not significant. 2021 Open forum infectious diseases Result SARS_CoV_2 D614G 67 72 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. The sera of all the COVID-19 patients showed neutralizing activity against the D614G and B.1.1.7 variants regardless of the severity of the patients' symptoms. 2021 Open forum infectious diseases Result SARS_CoV_2 D614G 79 84 COVID-19 20 28 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. Three asymptomatic/mild cases and 1 case in the severe infection group with low neutralizing activity against D614G (titer 8 or 16) did not show any neutralizing activity against P.1 or B.1.351 (Figure 3C, D). 2021 Open forum infectious diseases Result SARS_CoV_2 D614G 110 115 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. We examined a total of 81 sera of patients with different disease severities who were already confirmed to have neutralizing activity against the B2 strain, which is a D614G variant. 2021 Open forum infectious diseases Result SARS_CoV_2 D614G 168 173 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. For strain D614G the PRNT50 concentrations of S1D2-hIgG1 and STI-1499-LALA were also comparable at 694.3 ng/mL and 733.2 ng/mL, respectively. 2021 Antiviral research Result SARS_CoV_2 D614G 11 16 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. MAb 11741-LALA also neutralized SARS-CoV-2 D614 and D614G at 1434.7 and 111.4 ng/mL, respectively. 2021 Antiviral research Result SARS_CoV_2 D614G 52 57 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. MAbs S1D2-hIgG1 and STI-1499-LALA neutralized SARS-CoV-2 strains D614 and D614G but not B.1.351. 2021 Antiviral research Result SARS_CoV_2 D614G 74 79 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. To determine the neutralizing abilities of mAbs 1741-LALA, S1D2-hIgG1, and STI-1499-LALA, we used the 50% plaque reduction neutralization test (PRNT50) to assess the capacities of these mAbs to neutralize SARS-CoV-2 strains B.1.351, D614, and D614G. 2021 Antiviral research Result SARS_CoV_2 D614G 243 248 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. All 10 clones retained blocking ability for S1-RBD N501Y and 4 of these showed similar blocking IC50 values when compared to S1-RBD. 2021 FASEB journal Result SARS_CoV_2 N501Y 51 56 RBD;RBD 47;128 50;131 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. Binding of these 10 VNAR-hFc antibodies was assessed against two key mutations in S1-RBD region, N501Y and E484K found in the newly emerged SARS-CoV-2 variants. 2021 FASEB journal Result SARS_CoV_2 E484K;N501Y 107;97 112;102 RBD 85 88 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. Binding of VNAR-hFc antibodies to S1-RBD N501Y remained comparable to S1-RBD from the original Wuhan variant except for 3ID10_40, which decreased EC50 affinity by approximately 13-fold (Figure 3B,C, and Table 1), whereas binding to S1-RBD E484K was reduced for all of the tested clones in comparison to S1-RBD (Figure 3D and Table 1). 2021 FASEB journal Result SARS_CoV_2 E484K;N501Y 239;41 244;46 RBD;RBD;RBD;RBD 37;73;235;306 40;76;238;309 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. S1-RBD E484K showed lower EC50 affinity by approximately fivefold, whereas S1-RBD N501Y was unchanged when compared to S1-RBD (Figure 5 and Table 1). 2021 FASEB journal Result SARS_CoV_2 E484K;N501Y 7;82 12;87 RBD;RBD;RBD 3;78;122 6;81;125 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. The binding EC50 affinities of S1-RBD Wuhan variant and the N501Y and E484K mutants to ACE2 were measured to set up a comparative in vitro inhibitory assay. 2021 FASEB journal Result SARS_CoV_2 E484K;N501Y 70;60 75;65 RBD 34 37 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. Three antibodies 3ID10_16, 6ID10_75, and 3ID10_99 blocked S1-RBD E484K with similar IC50 when compared to S1-RBD (Figure 6D and Table 2). 2021 FASEB journal Result SARS_CoV_2 E484K 65 70 RBD;RBD 61;109 64;112 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. Another associated mutation was the G12832A, detected exclusively in genomes from Austria. 2021 Infection, genetics and evolution Result SARS_CoV_2 G12832A 36 43 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. Genomes from Belgium (EPI_ISL_417025) and from Iceland (EPI_ISL_417672) carried the C14805T mutation associated with T17247C mutation. 2021 Infection, genetics and evolution Result SARS_CoV_2 C14805T;T17247C 84;117 91;124 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. In Denmark and in Sweden the two latter mutations were found fully associated with the missense mutation C7011T (A > V, nsp3 protein). 2021 Infection, genetics and evolution Result SARS_CoV_2 C7011T 105 111 Nsp3 120 124 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. In France, the G24095T resulting in the AA substitution A > S in the spike protein, was found associated with the C14805T. 2021 Infection, genetics and evolution Result SARS_CoV_2 C14805T;G24095T 114;15 121;22 S 69 74 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. In this sub-cluster two mutations resulted in AA changes, the C28863T transition resulting in S > L substitution in the nucleocapsid protein, and the G25979T transversion resulting in G > V substitution in the ORF3a protein. 2021 Infection, genetics and evolution Result SARS_CoV_2 C28863T;G25979T 62;150 69;157 N;ORF3a 120;210 132;215 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. Overall, the mutation C14408T was found in 2405 genomes out of 2425 of the SS4 profile. 2021 Infection, genetics and evolution Result SARS_CoV_2 C14408T 22 29 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. Relating to the appearance of C14408T mutation in SS4 cluster (February 20th, 2020), the average mutation rate was 1.2 x 10-3 (SE 2.7 x 10-4) sub/site/year. 2021 Infection, genetics and evolution Result SARS_CoV_2 C14408T 30 37 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. Relating to the appearance of C14805T in SS1 (February 25th, 2020) and SS2B clusters (February 27th, 2020) the average mutation rates were 1.5 x 10-3 (SE 6 x 10-4) and 1.2 x 10-3 (SE 3.4 x 10-4) sub/site/year, respectively. 2021 Infection, genetics and evolution Result SARS_CoV_2 C14805T 30 37 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. SS1 carried the signature mutations C8782T and T28144C, the last resulting in the amino acid (AA) change L > S in the ORF8 protein. 2021 Infection, genetics and evolution Result SARS_CoV_2 C8782T;T28144C 36;47 42;54 ORF8 118 122 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. SS1 genomes from Iceland showed a different profile carrying mainly the C17747T, A17858G, T17531C, C18060T and A24694T mutations. 2021 Infection, genetics and evolution Result SARS_CoV_2 A17858G;A24694T;C17747T;C18060T;T17531C 81;111;72;99;90 88;118;79;106;97 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. SS4A included 905 genomes and comprised at least five groups, each one characterized by the following mutations: the silent C15324T, mainly harbored in western Europe; the silent A20268G, relevant in Spain and Iceland, (it is noteworthy that this mutation, with the exception of two genomes, was partially associated with the A10323G which resulted in the AA change K > R in the nsp5 protein, and exclusively detected in Iceland); the A26530G (AA change D > G, membrane protein) detected mainly in Belgium, Iceland, Sweden and Italy; the A24077G (AA change D > Y, spike protein) mostly identified in Portugal; the A187G (5'UTR) mostly identified in Luxembourg. 2021 Infection, genetics and evolution Result SARS_CoV_2 A10323G;A187G;A20268G;A24077G;A26530G;C15324T 326;614;179;538;435;124 333;619;186;545;442;131 Membrane;S;5'UTR;Nsp5 461;564;621;379 469;569;626;383 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. SS4C consisted of 814 genomes, of which 801 harbored the three variations A28881G, A28882G and G28883C. 2021 Infection, genetics and evolution Result SARS_CoV_2 A28881G;A28882G;G28883C 74;83;95 81;90;102 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The C14805T mutation, a silent transition detected also in SS1 and SS2 clusters, was found in 253 genomes out of 276. 2021 Infection, genetics and evolution Result SARS_CoV_2 C14805T 4 11 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The C2558T and A2480G mutations were found in 85 and 77 genomes respectively, mainly from UK and central Europe. 2021 Infection, genetics and evolution Result SARS_CoV_2 A2480G;C2558T 15;4 21;10 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The C2558T/A2480G and the T17247C mutations were mutually exclusive in all SS2B clusters. 2021 Infection, genetics and evolution Result SARS_CoV_2 C2558T;T17247C;A2480G 4;26;11 10;33;17 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The first included 16 genomes and carried the C26088T mutation and the second comprised 88 genomes which carried five mutations (T9477A, C14805T, C28657T, C28863T and G25979T). 2021 Infection, genetics and evolution Result SARS_CoV_2 C14805T;C26088T;C28657T;C28863T;G25979T;T9477A 137;46;146;155;167;129 144;53;153;162;174;135 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The first sub-group included 83 genomes (SS4B1) of which 77 harbored the missense mutation G25563T (AA change Q > H, ORF3a protein). 2021 Infection, genetics and evolution Result SARS_CoV_2 G25563T 91 98 ORF3a 117 122 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The G26144T (SS2) and G11083T (SS3) mutations were found associated in 276 genomes throughout 18 European countries. 2021 Infection, genetics and evolution Result SARS_CoV_2 G11083T;G26144T 22;4 29;11 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The missense mutation C27046 T (AA change T > M, membrane protein), with the exception of one genome, was fully associated with the triplet. 2021 Infection, genetics and evolution Result SARS_CoV_2 C27046T 22 30 Membrane 49 57 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The missense mutations G1440A (AA change G > D, nsp2 protein) and G2891A (AA change A > T, nsp3 protein) were found fully associated with the exception of five genomes. 2021 Infection, genetics and evolution Result SARS_CoV_2 G1440A;G2891A 23;66 29;72 Nsp2;Nsp3 48;91 52;95 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The ML analysis revealed that these German clusters arose from an inferred node from which the virus evolved mainly in a different direction through the acquisition of the missense mutation C14408T (AA change P > L, nsp12 protein). 2021 Infection, genetics and evolution Result SARS_CoV_2 C14408T 190 197 Nsp12 216 221 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The mutation C5142T resulting in the AA change T > I in the nsp3 protein was detected exclusively in Iceland in more than 50% of the SS2B genomes. 2021 Infection, genetics and evolution Result SARS_CoV_2 C5142T 13 19 Nsp3 60 64 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The mutation rate was also estimated in the subset of genomes which acquired the C14408T mutation in the SS4 cluster and in the subset of genomes which acquired the C14805T mutation in SS1 and SS2B clusters. 2021 Infection, genetics and evolution Result SARS_CoV_2 C14408T;C14805T 81;165 88;172 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The mutation T17247C was found in 151 out of 276 genomes, always linked to the C14805T. 2021 Infection, genetics and evolution Result SARS_CoV_2 C14805T;T17247C 79;13 86;20 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The phylogenetic analysis suggested that the SS2 cluster evolved in the SS2B cluster through the acquisition of G11083T mutation. 2021 Infection, genetics and evolution Result SARS_CoV_2 G11083T 112 119 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The second sub-group (SS4B2) included 537 genomes and, with the exception of 6, evolved from the first by the acquisition of C1059T mutation, which resulted in the AA change T > I in the nsp2 protein. 2021 Infection, genetics and evolution Result SARS_CoV_2 C1059T 125 131 Nsp2 187 191 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The silent C2416T mutation was found associated with this subgroup. 2021 Infection, genetics and evolution Result SARS_CoV_2 C2416T 11 17 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The silent T514C mutation was mostly represented in genomes from the Netherlands (20%) and found partially associated with the missense mutation C17410T (AA change R > C, nsp13 protein). 2021 Infection, genetics and evolution Result SARS_CoV_2 C17410T;T514C 145;11 152;16 Nsp13 171 176 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The SS2 cluster was characterized by the signature mutation G26144T which resulted in the AA change G > V in the ORF3a protein. 2021 Infection, genetics and evolution Result SARS_CoV_2 G26144T 60 67 ORF3a 113 118 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The SS3 cluster carried the signature mutation G11083T resulting in the AA substitution L > F in the nsp4 protein. 2021 Infection, genetics and evolution Result SARS_CoV_2 G11083T 47 54 Nsp4 101 105 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The SS4 cluster carried the signature mutation C241T, C3037T and A23403G. 2021 Infection, genetics and evolution Result SARS_CoV_2 A23403G;C241T;C3037T 65;47;54 72;52;60 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The SS4 cluster with the acquired C14408T mutation only was found in 81 genomes gathered in a central node of the phylogenetic tree. 2021 Infection, genetics and evolution Result SARS_CoV_2 C14408T 34 41 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The two associated mutations A12790G and C13568T, the latter resulting in the AA change A > V (nsp12 protein), were detected only in Sweden. 2021 Infection, genetics and evolution Result SARS_CoV_2 A12790G;C13568T 29;41 36;48 Nsp12 95 100 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The two mutations, which resulted in the AA change P > S and I > V in the nsp2 protein respectively, were associated with the C14805T. 2021 Infection, genetics and evolution Result SARS_CoV_2 C14805T 126 133 Nsp2 74 78 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. This genome was found in a small cluster from which arose a further sub-cluster that harbored the missense mutation G6446A (AA change V > I, nsp3 protein). 2021 Infection, genetics and evolution Result SARS_CoV_2 G6446A 116 122 Nsp3 141 145 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. With the exception of some genomes, the SS3 cluster in EU/EAA has been found always associated with the mutation G1397A, which resulted in the AA change V > I in the nsp2 protein, and with the silent mutations T28688C and G29742T. 2021 Infection, genetics and evolution Result SARS_CoV_2 G1397A;G29742T;T28688C 113;222;210 119;229;217 Nsp2 166 170 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. 3A and Table S4) support the prominent contribution played by this residue in anchoring the viral protein/LY-CoV555 mAb binding interface and the LY-CoV555 escaping potential of the E484A, E484G, E484K, E484R, and E484V SARS-CoV-2 circulating mutants. 2021 Scientific reports Result SARS_CoV_2 E484A;E484G;E484K;E484R;E484V 182;189;196;203;214 187;194;201;208;219 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. 5C, Table S17) and the side chain of N487 (2.86 +- 0.15 A, DeltaDeltaGCoV-2(N487A) = - 2.03 +- 0.16 kcal/mol) and the hydroxyl group of Y489 (3.38 +- 0.13 A, DeltaDeltaGCoV-2(Y489A) = - 1.84 +- 0.09 kcal/mol), respectively. 2021 Scientific reports Result SARS_CoV_2 N487A;Y489A 76;175 81;180 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. 5D, Table S15): Y421 (DeltaDeltaGCoV-2(Y421A) = - 2.47 +- 0.18 kcal/mol) and Q493 (DeltaDeltaGCoV-2(Q493A) = - 1.59 +- 0.14 kcal/mol). 2021 Scientific reports Result SARS_CoV_2 Q493A;Y421A 100;39 105;44 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. 5D):the DeltaDeltaG values currently predicted for replacement of both these spike positions with all reported variants (T415A/I/N/S and Q493H/K/L/R) indicate only moderate interface perturbation outcomes, with the notable deviation of the T415P mutant, for which a robust loss in affinity of this viral variant for the mAb is anticipated. 2021 Scientific reports Result SARS_CoV_2 Q493H;Q493K;Q493L;Q493R;T415P;T415A;T415I;T415N;T415S 137;137;137;137;240;121;121;121;121 148;148;148;148;245;132;132;132;132 S 77 82 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. 5E) detected in the MD trajectories of all variants has only minor effects on all other important intermolecular interactions populating same region, while the phenylalanine-to-histidine mutation is virtually conservative (DeltaDeltaGCoV-2(Y473F) = - 1.67 +- 0.08 kcal/mol and DeltaDeltaGCoV-2(Y473H) = - 0.19 +- 0.16 kcal/mol, respectively, Table S18, Figure S16, Table S24). 2021 Scientific reports Result SARS_CoV_2 Y473F;Y473H 240;294 245;299 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. 7A for the K417N mutant as a paradigm, the current MD simulations show that both the double SB with the side chain of LY-CoV016 DH104 and the HB between the charged amine group of K417 and the hydroxyl moiety of YH52 cannot longer be detected in the MD trajectory of the mutant complex. 2021 Scientific reports Result SARS_CoV_2 K417N 11 16 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Accordingly, the predicted affinity of this mutant viral protein for the LY-CoV55 mAb is markedly lower than that of the native counterpart (DeltaDeltaGCoV-2(Q493R) = - 4.57 +- 0.11 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 Q493R 158 163 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Accordingly, the S-RBDCoV-2 T415P mutation reported so far in circulating viral populations is predicted to be potentially destabilizing for the S-RBDCoV-2/LY-CoV016 interface (DeltaDeltaGCoV-2(T415P) = - 2.83 +- 0.07 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 T415P;T415P 28;194 33;199 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Accordingly, the three circulating mutants S494A, S494P, and S494R are all predicted to be potential LY-CoV555 escaping variants. 2021 Scientific reports Result SARS_CoV_2 S494A;S494P;S494R 43;50;61 48;55;66 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Analogous effects are predicted for the other two mutants Q493K and Q493L, reflecting in a comparable decrease of protein/protein binding strength (DeltaDeltaGCoV-2(Q493K) = - 4.83 +- 0.12 kcal/mol and DeltaDeltaGCoV-2(Q493L) = - 4.26 +- 0.18 kcal/mol, respectively. 2021 Scientific reports Result SARS_CoV_2 Q493K;Q493L;Q493K;Q493L 58;68;165;219 63;73;170;224 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. As it could be anticipated from the relevant CAS data discussed above, the in silico mutagenesis results for these further four viral protein residues into the reported variants (Y449D/F/H/N/S, L452M/Q/R, T470A/I/K/N and F490L/S/V/Y) also confirm a remarkable degree of tolerability to substitution at each of these spike positions in binding the LY-CoV555 Ab, with the remarkable exceptions of the L452R and:albeit to a lower extent:the F490S mutations. 2021 Scientific reports Result SARS_CoV_2 F490L;F490S;F490V;F490Y;F490S;L452M;L452Q;L452R;L452R;T470A;T470K;T470I;T470N;Y449D;Y449F;Y449H;Y449N;Y449S 221;221;221;221;438;194;194;194;399;205;205;205;205;179;179;179;179;179 232;232;232;232;443;203;203;203;404;216;216;216;216;192;192;192;192;192 S 316 321 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. As such, it is not surprising that replacing K417 on the viral protein with each of the alternative circulating mutants (K417E/N/R/T) reflects into a very strong interface disrupting behavior, with the exception of the substitution K417R, for which our in silico mutagenesis data anticipate a neutral effect. 2021 Scientific reports Result SARS_CoV_2 K417R;K417E;K417N;K417R;K417T 232;121;121;121;121 237;132;132;132;132 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. As such, the variation in binding free energy between the wild-type and a mutant spike protein carrying either E or T at position 417 in complex with the LY-CoV016 mAb is predicted to be quite significant (DeltaDeltaGCoV-2(K417E) = - 7.56 +- 0.18 kcal/mol and DeltaDeltaGCoV-2(K417T) = - 7.14 +- 0.09 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 K417E;K417T 223;277 228;282 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Briefly, in the case of the Y473F mutation the loss of the HB between the wild-type tyrosine and the side chain of SH31 on the LY-CoV016 mAb HC. 2021 Scientific reports Result SARS_CoV_2 Y473F 28 33 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Figure 4A shows the results for the E484K as a representative example. 2021 Scientific reports Result SARS_CoV_2 E484K 36 41 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Finally, similarly to E484 the mutated D484 can establish SB interactions with the side chains of LY-CoV555 RH50 (2.94 +- 0.13 A) and RL96 (2.81 +- 0.19 A and 3.26 +- 0.22 A), along with the full network of CIs seen in the wild-type complex, overall resulting in a predicted neutral effect on the related protein/protein interface (DeltaDeltaGCoV-2(E484D) = - 0.61 +- 0.13 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 E484D 349 354 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. In agreement with this interaction pattern, the K417A mutation in CAS reduces the binding affinity of the corresponding S-RBDCoV-2 for the LY-CoV016 mAb by 6 kcal/mol (DeltaDeltaGCoV-2(K417A) = - 6.01 +- 0.10 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 K417A;K417A 48;185 53;190 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. In detail, SH56 is also involved in two stable HBs with the hydroxyl group of T415 (3.13 +- 0.10 A, DeltaDeltaGCoV-2(T415A) = - 1.16 +- 0.14 kcal/mol) and the side chain of D420 (3.07 +- 0.15 A, DeltaDeltaGCoV-2(D420A) = - 2.01 +- 0.11 kcal/mol), respectively. 2021 Scientific reports Result SARS_CoV_2 D420A;T415A 212;117 217;122 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. In detail, while the conservative mutation T415S ensues the preservation of the wild-type interaction network, in the case of the T415A/I/N variants the analysis of the present simulations shows that the two spike-mAb anchoring intermolecular HBs in which the wild-type residue is involved (i.e., T415-SH56 and K417-YH52. 2021 Scientific reports Result SARS_CoV_2 T415A;T415I;T415N;T415S 130;130;130;43 139;139;139;48 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. In line with this, the calculated DeltaDeltaG values numerically support moderate interface destabilizing effects upon substitution of the wild-type tyrosine with these two residues (DeltaDeltaGCoV-2(Y489C) = - 2.15 +- 0.10 kcal/mol, and DeltaDeltaGCoV-2(Y489S) = - 2.41 +- 0.07 kcal/mol, respectively. 2021 Scientific reports Result SARS_CoV_2 Y489C;Y489S 200;255 205;260 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. In line with this, the predicted changes in binding free energy for the replacement of the wild-type E484 with A/G/K/R/V in the S-RBDCoV-2/LY-CoV555 relevant complexes (DeltaDeltaGCoV-2(E484A) = - 6.18 +- 0.10 kcal/mol, DeltaDeltaGCoV-2(E484G) = - 7.58 +- 0.18 kcal/mol, DeltaDeltaGCoV-2(E484K) = - 7.83 +- 0.11 kcal/mol, DeltaDeltaGCoV-2(E484R) = - 7.99 +- 0.12 kcal/mol, DeltaDeltaGCoV-2(E484V) = - 6.02 +- 0.14 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 E484A;E484G;E484K;E484R;E484V 186;237;288;340;391 191;242;293;345;396 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. In line with this, the related value of DeltaDeltaGCoV-2(S494T) is slightly unfavorable and equal to -0.70 +- 0.15 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 S494T 57 62 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. In particular, Q493H is still able to preserve one HB with the side chain of the LY-CoV555 RH104 (3.39 +- 0.15 A) while the second HB interaction with the same mAb residue is replaced by a pi/cation interaction (Figure S2, Table S6). 2021 Scientific reports Result SARS_CoV_2 Q493H 15 20 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. In the case of the T415P variant, the remarkably negative effect on spike/mAb affinity predicted by our in silico mutagenesis is sensibly linked:aside for the same perturbating effects just discussed for the other mutations at the same viral protein location:to the absence of the additional interface HB and CIs between the side chains of Q493 on the spike and of YH102 on the mAb HC. 2021 Scientific reports Result SARS_CoV_2 T415P 19 24 S;S 68;352 73;357 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Indeed, this region involves only the LY-CoV016 mAb LC residues YL32 (DeltaDeltaGLY-CoV016(YL32A) = - 1.12 +- 0.10 kcal/mol), YL92 (DeltaDeltaGLY-CoV016(YL92A) = - 0.99 +- 0.16 kcal/mol), and TL94 (DeltaDeltaGLY-CoV016(TL94A) = - 1.15 +- 0.12 kcal/mol) in a set of stable HBs with the viral spike residues E406 (2.84 +- 0.27 A, DeltaDeltaGCoV-2(E406A) = - 1.29 +- 0.13 kcal/mol), the hydroxyl group of Y505 (3.01 +- 0.19 A, DeltaDeltaGCoV-2(Y505A) = - 1.87 +- 0.12 kcal/mol), and the nitrogen backbone atom of the same tyrosine (3.14 +- 0.13 A). 2021 Scientific reports Result SARS_CoV_2 E406A;Y505A 345;441 350;446 S 291 296 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Interesting, replacing the viral spike E484 with each of the alternative residues considered (i.e., E484A/D/G/K/Q/R/V) reflects into a robust interface disrupting behavior, with the mild exception of the E484D substitution. 2021 Scientific reports Result SARS_CoV_2 E484A;E484D;E484G;E484K;E484Q;E484R;E484V;E484D 100;100;100;100;100;100;100;204 117;117;117;117;117;117;117;209 S 33 38 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. led to the following list of naturally occurring mutations at the SARS-CoV-2 spike protein residues contacting the LY-CoV555 mAb: E484A/D/G/K/Q/R/V, Q493H/K/L/R, S494A/P/R/T, L452M/Q/R, Y449D/F/H/N/S, T470A/I/K/N, V483A/F/G/I/L, F486I/L/S, Y489C/F/H/S, and F490L/S/V/Y. 2021 Scientific reports Result SARS_CoV_2 E484A;E484D;E484G;E484K;E484Q;E484R;E484V;F486I;F486L;F486S;F490V;F490L;F490S;F490Y;L452M;L452Q;L452R;Q493H;Q493K;Q493L;Q493R;S494A;S494P;S494R;S494T;T470A;T470I;T470K;T470N;V483A;V483F;V483G;V483I;V483L;Y449D;Y449F;Y449H;Y449N;Y449S;Y489C;Y489F;Y489H;Y489S 130;130;130;130;130;130;130;229;229;229;257;257;257;257;175;175;175;149;149;149;149;162;162;162;162;201;201;201;201;214;214;214;214;214;186;186;186;186;186;240;240;240;240 147;147;147;147;147;147;147;238;238;238;268;268;268;268;184;184;184;160;160;160;160;173;173;173;173;212;212;212;212;227;227;227;227;227;199;199;199;199;199;251;251;251;251 S 77 82 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Located in between the two protein/protein interface regions just described, the third binding zone is identified by a network of van der Waals and hydrophobic interactions mainly involving the S-RBDCoV-2 residues L455 (DeltaDeltaGCoV-2(L455A) = - 1.20 +- 0.16 kcal/mol) and F456 (DeltaDeltaGCoV-2(F456A) = - 2.49 +- 0.13 kcal/mol). 2021 Scientific reports Result SARS_CoV_2 F456A;L455A 298;237 303;242 S 194 195 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Moreover, the HB involving Y473 and SH31 is also missing along the entire MD trajectories of the Y489C and Y489S S-RBDCoV-2 mutant proteins, as shown in. 2021 Scientific reports Result SARS_CoV_2 Y489C;Y489S 97;107 102;112 S 113 114 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Moreover, the S-RBDCoV-2 Y473 (DeltaDeltaGCoV-2(Y473A) = - 2.08 +- 0.12 kcal/mol) is stably engaged in an HB with the side chain of SH31 (2.83 +- 0.21 A, DeltaDeltaGLY-CoV016(SH31A) = - 0.98 +- 0.17 kcal/mol) and in a polar interaction with SH53. 2021 Scientific reports Result SARS_CoV_2 Y473A 48 53 S 14 15 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Mutagenesis of this residue into A, P, R, and T reflects into strong interface destabilizing effects, exception made for the S494T substitution for which only a mild effect is observed. 2021 Scientific reports Result SARS_CoV_2 S494T 125 130 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Nevertheless, the present computational mutagenesis data report only neutral-to-mild interface destabilizing effects for the circulating SARS-CoV-2 RBD variants of Y473 (Y473F/H) and N487 (N487D) (see Table S18, Figures S16, S17, and Tables S24, S25 for details). 2021 Scientific reports Result SARS_CoV_2 N487D;Y473F;Y473H 189;170;170 194;177;177 RBD 148 151 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. On the other hand, only minor interface perturbations are observed in the presence of the R417 mutation (Figure S11, Table S19), in line with the predicted small change in protein/protein affinity (DeltaDeltaGCoV-2(K417R) = - 0.99 +- 0.15 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 K417R 215 220 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. On the other hand, the S-RBDCoV-2 N460 residue is involved in two permanent HBs with the side chain of SH56 (3.04 +- 0.09 A) and with the oxygen atom of the backbone of GH54 (3.12 +- 0.17 A), and the relevant value of DeltaDeltaG obtained by CAS for the N460A mutation (DeltaDeltaGCoV-2(N460A) = - 2.75 +- 0.11 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 N460A;N460A 254;287 259;292 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Surprisingly, however, the computational mutagenesis data for all circulating viral mutations at these two spike positions (D420A/G/N and N460I/K/S/T) reveal strong interface-destabilizing effects in all cases, with difference in free energy of binding with respect to the wild-type protein ranging from ~ - 5 to ~ - 3 kcal/mol (i.e., DeltaDeltaGCoV-2(D420A) = - 4.36 +- 0.17 kcal/mol, DeltaDeltaGCoV-2(D420G) = - 4.39 +- 0.10 kcal/mol, DeltaDeltaGCoV-2(D420N) = - 4.23 +- 0.10 kcal/mol, DeltaDeltaGCoV-2(N460I) = - 5.01 +- 0.14 kcal/mol, DeltaDeltaGCoV-2(N460K) = - 3.28 +- 0.18 kcal/mol, DeltaDeltaGCoV-2(N460S) = - 4.06 +- 0.09 kcal/mol, and DeltaDeltaGCoV-2 N460T) = - 4.12 +- 0.14 kcal/mol) (see also Table S18). 2021 Scientific reports Result SARS_CoV_2 N460I;N460K;N460S;N460T;N460T;D420A;D420A;D420G;D420N;D420G;D420N;N460I;N460K;N460S 138;138;138;138;662;352;124;124;124;403;454;505;556;607 149;149;149;149;667;357;133;133;133;408;459;510;561;612 S 107 112 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Table S2), that is, DeltaDeltaGCoV-2(V483A) = - 1.70 +- 0.18 kcal/mol, DeltaDeltaGCoV-2(F486A) = - 1.44 +- 0.15 kcal/mol, and DeltaDeltaGGCoV-2(Y489A) = - 1.12 +- 0.09 kcal/mol, respectively. 2021 Scientific reports Result SARS_CoV_2 F486A;V483A;Y489A 88;37;145 93;42;150 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Table S4), that is, DeltaDeltaGCoV-2(Q493H) = - 1.95 +- 0.11 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 Q493H 37 42 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. The actual computational data for mutating these four viral protein residues into the SARS-CoV-2 circulating variants (E406D/Q, L455F/S/V, F456L/Y and Y505F/H/W) account for neutral-to-mildly negative effects on the stability of the corresponding S-RBDCoV-2/LY-CoV016 mAb binding interface, with estimated DeltaDeltaG values all below 1 kcal/mol for all alternative amino acids considered. 2021 Scientific reports Result SARS_CoV_2 F456L;F456Y;L455F;L455S;L455V;Y505F;Y505H;Y505W;E406D;E406Q 139;139;128;128;128;151;151;151;119;119 146;146;137;137;137;160;160;160;126;126 S 247 248 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. The analysis of the MD trajectories of all considered mutants (Q493H/K/L/R) reveals that, with respect to the wild-type Q493, all residues except H493 induce a strong destabilizing effect at the interface with the LY-CoV555 mAb. 2021 Scientific reports Result SARS_CoV_2 Q493H;Q493K;Q493L;Q493R 63;63;63;63 74;74;74;74 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. The charged-to-neutral isosteric replacement E484Q has a moderately destabilizing effect (DeltaDeltaGCoV-2(E484Q) = - 2.53 +- 0.16 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 E484Q;E484Q 45;107 50;112 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. The confirmation of the E484 as a crucial residue was an expected result as a glutamic acid (E) to lysine (K) substitution at this position (E484K) in the S-RBDCoV-2 is present in the rapidly spreading variants of concern belonging to the B.1.351 (aka South African and now Beta, according to the new WHO labeling system) and P.1 (Brazilian or Gamma) lineages, while the E484Q/L452R double mutation is a component of the B.1.617 (Delta/Kappa) lineage that is currently dramatically spreading in India (vide infra). 2021 Scientific reports Result SARS_CoV_2 E484Q;E484K;L452R 371;141;377 376;146;382 S 155 156 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. The mutagenesis results obtained by mutating these three viral spike amino acids into the reported variants (V483A/F/G/I/L, F486I/L/S, and Y489C/F/H/S, respectively) ultimately confirm the minor role played by these residues at the SARS-CoV-2 RBD/LY-CoV555 mAb binding interface. 2021 Scientific reports Result SARS_CoV_2 F486L;F486S;F486I;Y489C;Y489F;Y489H;Y489S;V483A;V483F;V483G;V483I;V483L 124;124;124;139;139;139;139;109;109;109;109;109 133;133;133;150;150;150;150;122;122;122;122;122 S;RBD 63;243 68;246 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. The predicted minor loss in binding affinity of the D487 spike variant for the LY-CoV016 mAb (DeltaDeltaGCoV-2(N487D) = - 0.70 +- 0.09 kcal/mol, Table S18 on the other hand, is the result of a compensatory effect as the mutant aspartic acid provides a permanent intermolecular SB with the guanidine group of the mAb RH97 that makes up for the loss of the two HBs between Y473 and SH31 and Y489 and RH97, respectively. 2021 Scientific reports Result SARS_CoV_2 N487D 111 116 S 57 62 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. The same data survey reported by Starr and coworkers led us to identify the following naturally occurring mutations at the SARS-CoV-2 spike protein residues contacting the LY-CoV016 Ab: E406D/Q, T415A/I/N/P/S, K417E/N/R/T, D420A/G/N, L455F/S/V, F456L/Y, N460I/K/S/T, Y473F/H, N487D, Y489C/F/H/S, Q493H/K/L/R and Y505F/H/W. 2021 Scientific reports Result SARS_CoV_2 D420A;D420G;D420N;E406D;E406Q;F456L;F456Y;K417E;K417N;K417R;K417T;L455F;L455S;L455V;N460I;N460K;N460S;N460T;N487D;Q493H;Q493K;Q493L;Q493R;T415A;T415I;T415N;T415P;T415S;Y473F;Y473H;Y489C;Y489F;Y489H;Y489S;Y505F;Y505H;Y505W 223;223;223;186;186;245;245;210;210;210;210;234;234;234;254;254;254;254;276;296;296;296;296;195;195;195;195;195;267;267;283;283;283;283;312;312;312 232;232;232;193;193;252;252;221;221;221;221;243;243;243;265;265;265;265;281;307;307;307;307;208;208;208;208;208;274;274;294;294;294;294;321;321;321 S 134 139 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. These data therefore suggest that the Q493K/L/R mutants could all be LY-CoV555 escaping mutants. 2021 Scientific reports Result SARS_CoV_2 Q493K;Q493L;Q493R 38;38;38 47;47;47 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. These evidences ultimately translate into a drastically lower affinity of the N417 mutant spike protein for the LY-CoV016 mAb (DeltaDeltaGCoV-2(K417N) = - 7.27 +- 0.07 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 K417N 144 149 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. These evidences, along with several missing stabilizing CIs at the protein/protein interface (see Table S7 for details), concur to lower the predicted affinity of the R494 mutant S-RBDCoV-2 for the LY-CoV555 mAb (DeltaDeltaGCoV-2(S494R) = - 5.81 +- 0.17 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 S494R 230 235 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. This is supported by the calculated DeltaDeltaG value obtained by changing these amino acids into alanine in the S-RBDCoV-2/LY-CoV555 Ab complex, that is, DeltaDeltaG CoV-2(Y449A) = - 1.93 +- 0.16, DeltaDeltaGCoV-2(L452A) = - 0.76 +- 0.11 kcal/mol, DeltaDeltaGCoV-2(T470A) = - 0.64 +- 0.15, and DeltaDeltaGCoV-2(F490A) = - 2.38 +- 0.22. 2021 Scientific reports Result SARS_CoV_2 F490A;L452A;T470A;Y449A 312;215;266;173 317;220;271;178 S 113 114 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. This, in turn, properly reflects in the substantial variation of the corresponding binding free energy value, so that DeltaDeltaGCoV-2(L452R) = - 5.29 +- 0.15 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 L452R 135 140 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Thus, abrogation of these intermolecular contacts by replacing the wild-type glutamine with alanine is accompanied by a ~ 4.2 kcal/mol loss in binding free energy (DeltaDeltaGCoV-2(Q493A) = - 4.18 +- 0.14 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 Q493A 181 186 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Thus, the S494A mutation actually shows a considerable variation in the corresponding DeltaDeltaG value (DeltaDeltaGCoV-2(S494A) = - 4.02 +- 0.12 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 S494A;S494A 10;122 15;127 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. When E484 is replaced with alanine in CAS, these interface-stabilizing interactions:along with the slightly beneficial contribution from the intramolecular van der Waals contacts with the two Ab HC tyrosines:are no longer made, reflecting a loss of the corresponding binding free energy of DeltaDeltaGCoV-2(E484A) = - 5.92 +- 0.12 kcal/mol. 2021 Scientific reports Result SARS_CoV_2 E484A 307 312 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. When S-RBDCoV-2 S494 is mutated into threonine (S494T), the MD-predicted interaction network at the corresponding Ab binding interface is only moderately perturbed with respect to that described above for the wild-type complex; in particular, only the HBs between T494 on the SARS-CoV-2 RBD and EH102 on the HC of LY-CoV555, and between the viral Q493 and the same glutamic acid on the mAb HC are replaced by two polar CIs (Figure S3, Table S7). 2021 Scientific reports Result SARS_CoV_2 S494T 48 53 RBD;S 287;5 290;6 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. After April 2021, Y449S has been quickly spread out to other ten countries. 2021 ArXiv Result SARS_CoV_2 Y449S 18 23 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. All of the Y449S-related cases are found in Europe and America, where the vaccination rates in those areas are relatively high. 2021 ArXiv Result SARS_CoV_2 Y449S 11 16 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Although a few vaccine-resistant mutations S438F, I434K, Y505C, and Q506K were detected before November 2020, they had relatively low frequencies. 2021 ArXiv Result SARS_CoV_2 I434K;Q506K;S438F;Y505C 50;68;43;57 55;73;48;62 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Although DK has the smallest positive cases among 12 countries, the frequency of Y449S is the highest. 2021 ArXiv Result SARS_CoV_2 Y449S 81 86 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Among all of the vaccine-resistant mutations, Y449S has the highest frequency (1189). 2021 ArXiv Result SARS_CoV_2 Y449S 46 51 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Among the 25 most observed RBD co-mutations, [Y449S, N501Y] is the only co-mutation with a significantly negative BFE change and extremely high antibody disruption count (94). 2021 ArXiv Result SARS_CoV_2 N501Y;Y449S 53;46 58;51 RBD 27 30 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Among them, the total number of cases related to Y449S has a rapid increment tendency, especially in DK, the UK, and FR. 2021 ArXiv Result SARS_CoV_2 Y449S 49 54 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Apparently, there are no vaccine-resistant 3 and 4 co-mutations at present, which indicates vaccine-resistant co-mutation [Y449S, N501Y] is quite unique. 2021 ArXiv Result SARS_CoV_2 N501Y;Y449S 130;123 135;128 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. As the most observed vaccine-resistant RBD mutation, Y449S has been detected in 12 countries, including Denmark (DK), the United Kingdom (UK), France (FR), Bulgaria (BG), the United States (US), Brazil (BR), Sweden(SE), Canada (CA), Germany (DE), Switzerland (CH), Spain (ES), and Belgium (BE), as illustrated in Figure 4 a. 2021 ArXiv Result SARS_CoV_2 Y449S 53 58 RBD 39 42 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. At the end of March 2021, vaccine-resistant mutation Y449D showed up with mutation N501Y in some genome isolates, resulting in a negative BFE change (-0.473kcal/mol) and a high antibody disruption count (98) for RBD 2 co-mutation [Y449D, N501Y]. 2021 ArXiv Result SARS_CoV_2 N501Y;N501Y;Y449D;Y449D 83;238;53;231 88;243;58;236 RBD 212 215 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Figure 4 b shows the time evolution of vaccination ratio and the frequency of Y449S in the 12 countries as mentioned above in 30-day periods. 2021 ArXiv Result SARS_CoV_2 Y449S 78 83 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Here, 12 countries that Y449S was found in are in blue. 2021 ArXiv Result SARS_CoV_2 Y449S 24 29 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Howbeit, 2 RBD mutations D427N and Y449S, have negative BFE changes. 2021 ArXiv Result SARS_CoV_2 D427N;Y449S 25;35 30;40 RBD 11 14 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. However, the frequency of Y449S in BG and the US is quite low before April 2021. 2021 ArXiv Result SARS_CoV_2 Y449S 26 31 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. In addition, at residue 449, mutations Y449H, Y449N, Y449D are all vaccine-resistant mutations that have been observed in more than 20 SARS-CoV-2 genome isolates. 2021 ArXiv Result SARS_CoV_2 Y449D;Y449H;Y449N 53;39;46 58;44;51 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. In addition, Y449S has a relatively high frequency. 2021 ArXiv Result SARS_CoV_2 Y449S 13 18 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. It can be seen that Y449S was first found in BG and the US in December 2020. 2021 ArXiv Result SARS_CoV_2 Y449S 20 25 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. It is worthy to mention that the frequency of Y449S is low in DE, CH, ES, and BE, etc., which is mainly due to the first Y449-related case in these countries was detected after June 2021. 2021 ArXiv Result SARS_CoV_2 Y449S 46 51 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. More than 800 patients carry vaccine-resistant mutation Y449S in DK. 2021 ArXiv Result SARS_CoV_2 Y449S 56 61 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Moreover, from Figure 4, it can be seen that the frequency of Y449S has a similar growing tendency as the fully vaccinated ratio, suggesting that the vaccine-resistant mutations will gradually become one of the main evolution driven forces of SARS-CoV-2, especially in those areas with high vaccination rates. 2021 ArXiv Result SARS_CoV_2 Y449S 62 67 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Notably, in May 2021, two vaccine-resistant mutations Y449S and Y449H, came back to the top 100 most observed RBD mutation list. 2021 ArXiv Result SARS_CoV_2 Y449H;Y449S 64;54 69;59 RBD 110 113 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Notably, mutation Y449S has a significantly negative BFE change (-0.8112 kcal/mol) and a pretty large antibody disruption count (89), revealing a non-typical mechanism of mutagenesis. 2021 ArXiv Result SARS_CoV_2 Y449S 18 23 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Observing the evolution trajectory of [Y449S, N501Y] shows that the infectivity transmission pathway regulated by natural selection in the population level is the major evolution-driven force of SARS-CoV-2 mutagenesis before March 2021. 2021 ArXiv Result SARS_CoV_2 N501Y;Y449S 46;39 51;44 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Since late April 2021, vaccine-resistant mutation Y449S showed up with N501Y, making RBD co-mutation [Y449S, N501Y] one of the most prevailing vaccine-resistant co-mutations. 2021 ArXiv Result SARS_CoV_2 N501Y;N501Y;Y449S;Y449S 71;109;50;102 76;114;55;107 RBD 85 88 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. Since then, Delta variants dominated in the prevailing variants, which gave Y449S a limited chance to spread out rapidly. 2021 ArXiv Result SARS_CoV_2 Y449S 76 81 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. The darker the blue is, the higher frequency of Y449S will be. 2021 ArXiv Result SARS_CoV_2 Y449S 48 53 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. The left-hand side y-axis shows the frequency of Y499S (red lines), and the right-hand side y-axis shows the vaccination ratio. 2021 ArXiv Result SARS_CoV_2 Y499S 49 54 34644287 Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. Also noteworthy, one of the newly-sequenced samples from Bahia of to this clade is the single B.1.1.306 reported in this work and additionally harbors a previously undescribed N501Y mutation in this lineage. 2021 PLoS neglected tropical diseases Result SARS_CoV_2 N501Y 176 181 34644287 Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. Finally, we report the occurrence of a single sample from the state of Rio Grande do Norte classified as B.1.1.29 that contains both E484K and N429K, uncharacteristic mutations in the lineage. 2021 PLoS neglected tropical diseases Result SARS_CoV_2 E484K;N429K 133;143 138;148 34644287 Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. To confirm its monophyly, we have reconstructed this clade's phylogeny while further increasing the sampling of N.9 sequences to contain all genomes with the E484K available at GISAID (Fig 1). 2021 PLoS neglected tropical diseases Result SARS_CoV_2 E484K 158 163 34644287 Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. We did not observe two mutations (T20N, E92K) characteristic of P.1 clade. 2021 PLoS neglected tropical diseases Result SARS_CoV_2 E92K;T20N 40;34 44;38 34644287 Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. We found 16 SNVs targeting the receptor-binding domain (RBD) in S1, of which eight were missense variants, including K417T, N439K, L452R, S477R, E484K, N501Y, L518I, A522V. 2021 PLoS neglected tropical diseases Result SARS_CoV_2 A522V;E484K;K417T;L452R;L518I;N439K;N501Y;S477R 166;145;117;131;159;124;152;138 171;150;122;136;164;129;157;143 RBD 56 59 34644287 Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. We have identified a monophyletic clade of 15 sequences containing the characteristic mutations of lineage N.9, including the E484K mutation. 2021 PLoS neglected tropical diseases Result SARS_CoV_2 E484K 126 131 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Additionally, the K417N/T mutation caused reduced neutralization activity involving five mAbs (1F9, 2H10, 10D12, CB6, and A247), whereas it increased the neutralization sensitivity of one mAb (A261-262) for more than ten times. 2021 Communications biology Result SARS_CoV_2 K417N;K417T 18;18 25;25 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. B.1.1.7 variant-infected sera also showed the highest neutralization activity against the variant itself; it was comparatively resistant to B.1.351 and other E484K-carrying sera. 2021 Communications biology Result SARS_CoV_2 E484K 158 163 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Convalescent sera from D614G infected patients showed a neutralization pattern similar to the pattern exhibited by SARS-CoV-2 immunized animal sera. 2021 Communications biology Result SARS_CoV_2 D614G 23 28 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Furthermore, N501Y causes minor changes in the local structure of the CB6-RBD complex, which also weakens the affinity between CDRL and the RBD. 2021 Communications biology Result SARS_CoV_2 N501Y 13 18 RBD;RBD 74;140 77;143 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Furthermore, the neutralization activity against the K417T/N single-mutation strain was increased among all serum samples. 2021 Communications biology Result SARS_CoV_2 K417N;K417T 53;53 60;60 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Furthermore, the variant B.1.429 and L452R single-mutation strain showed reduced susceptibility to mAbs 9G11 and X593; the variant B.1.526-1(S477N) and S477N single-mutation strain showed reduced susceptibility to mAb 7B8, and variant B.1.1.298 and Y453F single-mutation strain showed reduced sensitivity to mAb 1F9. 2021 Communications biology Result SARS_CoV_2 L452R;S477N;Y453F;S477N 37;152;249;141 42;157;254;146 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. However, an obvious decrease in neutralization sensitivity of E484K-containing SARS-CoV-2 variants was apparent in the vaccine group, especially the inactivated vaccine group. 2021 Communications biology Result SARS_CoV_2 E484K 62 67 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. However, the B.1.351 variant-infected sera showed better neutralization activity against P.1, the variant itself and E484K-carrying variants, relative to the D614G reference strain. 2021 Communications biology Result SARS_CoV_2 D614G;E484K 158;117 163;122 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. However, the immune escape of 9G11 caused by L452R and E484K cannot be directly explained by salt bridge destruction or hydrogen bond changes. 2021 Communications biology Result SARS_CoV_2 E484K;L452R 55;45 60;50 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. K417N/T and N501Y also cause minor changes in local structure, which further weakens the affinity between CDRL and RBD, especially Y503 on RBD. 2021 Communications biology Result SARS_CoV_2 N501Y;K417N;K417T 12;0;0 17;7;7 RBD;RBD 115;139 118;142 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. K417N/T destroys the salt bridge, thus reducing the affinity significantly. 2021 Communications biology Result SARS_CoV_2 K417N;K417T 0;0 7;7 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Moreover, although P.2 only has one additional mutation (V1176F) in the S2 domain, its neutralization activity was less reduced in the pseudovirus- and RBD protein-induced sera compared with the E484K single-mutation strain. 2021 Communications biology Result SARS_CoV_2 E484K;V1176F 195;57 200;63 RBD 152 155 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Moreover, the variants B.1.351 B.1.525 and B.1.526-2(E484K) showed significantly increased infectivity for Calu-3 cells. 2021 Communications biology Result SARS_CoV_2 E484K 53 58 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Notably, although most of the examined SARS-CoV-2 variants showed slightly increased infectivity, none of them had more than fourfold increased infectivity, compared with the D614G reference strain. 2021 Communications biology Result SARS_CoV_2 D614G 175 180 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Notably, the infectivities of the B.1.1.7, B.1.351, P.1, B.1.525, and B.1.1.318 were significantly increased (by more than fourfold), compared with the D614G reference strain. 2021 Communications biology Result SARS_CoV_2 D614G 152 157 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Notably, these variants all harbor the E484K mutation. 2021 Communications biology Result SARS_CoV_2 E484K 39 44 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Regarding the E484K-carrying variants, neutralization sensitivity of the RBD immunized sera reduced 2.6 to 6.2 folds, which is much obvious than other immunogens. 2021 Communications biology Result SARS_CoV_2 E484K 14 19 RBD 73 76 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Similarly, the variants B.1.525, P.2, B.1.526-2 (E484K), B.1.1.318, as well as the E484K single-mutation strain, displayed similar patterns of neutralization sensitivity involving significantly reduced neutralization activity among three mAbs (9G11, X593and A261-262). 2021 Communications biology Result SARS_CoV_2 E484K;E484K 83;49 88;54 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Single mutation analyses showed that K417T, K417N, E484K, and N501Y led to increased infectivity in mouse ACE2-overexpressed cell lines, thus explaining the dramatically increased infectivity of variants carrying these mutations. 2021 Communications biology Result SARS_CoV_2 E484K;K417N;K417T;N501Y 51;44;37;62 56;49;42;67 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Single-mutation analysis indicated that immune escape of the B.1.1.7 variant was mainly caused by the N501Y mutation. 2021 Communications biology Result SARS_CoV_2 N501Y 102 107 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. The contribution of L452 to the affinity between the two proteins is not as significant as that of E484K, causing only minor changes in local structures. 2021 Communications biology Result SARS_CoV_2 E484K 99 104 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. The decrease in neutralization against P.1 was also less pronounced compared with B.1.351; however, the increase in neutralization against the K417T/N single-mutation strain was less than that of the immunized animal sera or convalescence sera group. 2021 Communications biology Result SARS_CoV_2 K417N;K417T 143;143 150;150 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. The K417N/T mutation destroys the salt bridge, reducing affinity significantly. 2021 Communications biology Result SARS_CoV_2 K417N;K417T 4;4 11;11 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. The L452R single mutation and B.1.526-2 led to increased infectivity, whereas the B.1.1.298 variant exhibited significantly decreased infectivity in all the four cell lines. 2021 Communications biology Result SARS_CoV_2 L452R 4 9 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. The mean neutralizing antibody levels (i.e., ID50 values) were comparable between D614G and B.1.1.7, whereas B.1.351 induced much lower neutralizing antibody production. 2021 Communications biology Result SARS_CoV_2 D614G 82 87 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. The neutralization ID50 of the various immunogens against the D614G reference strain was shown in. 2021 Communications biology Result SARS_CoV_2 D614G 62 67 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. The results showed that the increased infectivity to the 293T-ACE2 cells in the presence of furin, TMPRSS2, or cathepsin L was further increased among most of the tested variants, excluding B.1.1.298 and B.1.1.318 in the TMPRSS2 group, as compared to the D614G reference strain. 2021 Communications biology Result SARS_CoV_2 D614G 255 260 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. The results were similar to those observed in the immunized animal sera and D614G convalescent patient sera experiments. 2021 Communications biology Result SARS_CoV_2 D614G 76 81 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. The S477N mutation weakens this interaction and causes escape. 2021 Communications biology Result SARS_CoV_2 S477N 4 9 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. The single mutations M1229I may be the key mutation that caused the decreased infectivity of B.1.1.298. 2021 Communications biology Result SARS_CoV_2 M1229I 21 27 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. These results were consistent with single-mutation findings involving K417T/N (1F9, 2H10, 10D12, CB6 and A247) and N501Y (1F9, 10D12, 10F9, CB6, A247 and H00S022) and E484K (9G11, X593and A261-262). 2021 Communications biology Result SARS_CoV_2 E484K;K417N;K417T;N501Y 167;70;70;115 172;77;77;120 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. This interaction is greatly weakened when the E484K mutation occurs. 2021 Communications biology Result SARS_CoV_2 E484K 46 51 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. To evaluate the impacts of infection with the B.1.1.7 and B.1.351 variants on neutralization activities, convalescent sera from patients with the two variants and the D614G reference strain were analyzed. 2021 Communications biology Result SARS_CoV_2 D614G 167 172 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. We found that the ability of the D614G reference strain to infect 293T-ACE2 cells was significantly increased when furin, TMPRSS2, or cathepsin L was overexpressed. 2021 Communications biology Result SARS_CoV_2 D614G 33 38 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. while the expression level of B.1.1.298 spike protein was significantly decreased compared to D614G mutation, which may be responsible for the observed reduced infection. 2021 Communications biology Result SARS_CoV_2 D614G 94 99 S 40 45 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Additionally, the Lambda variant has an uncommon mutation F490S in the RBD, which we show below is highly beneficial for the Lambda variant. 2021 Journal of chemical information and modeling Result SARS_CoV_2 F490S 58 63 RBD 71 74 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. After the L452Q mutation, Q452 is hydrophilic and orients itself toward water, which weakens the local interfacial binding affinity. 2021 Journal of chemical information and modeling Result SARS_CoV_2 L452Q 10 15 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. After the L452R mutation, Figure 3a shows R452 being in contact with the hydrophobic I54 and L55 residues (low dielectric media) in LY-CoV555. 2021 Journal of chemical information and modeling Result SARS_CoV_2 L452R 10 15 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. All three recombinant viruses, including the wild type SARS-CoV-2-WA1/2020 (the first isolate reported in the U.S.) and mutants with L452R/E484Q/D614G or E484Q/D614G within the WA1 backbone, propagated similarly in Vero E6 cells. 2021 Journal of chemical information and modeling Result SARS_CoV_2 E484Q;L452R;D614G;D614G;E484Q 154;133;145;160;139 159;138;150;165;144 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. As shown in Figure 4a, the half maximal inhibitory concentration (IC50) of LY-CoV555 was around 170 ng/mL against pseudovirions bearing the Wuhan-Hu-1 spike protein but became unmeasurable against the Kappa variant, indicating that L452R/E484Q mutations completely rendered the variant nonsensitive to LY-CoV555. 2021 Journal of chemical information and modeling Result SARS_CoV_2 L452R;E484Q 232;238 237;243 S 151 156 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Before the F490S mutation, F490 coordinates four nearby hydrophobic residues, namely, Y101, I52, I57, and L55, in LY-CoV555 (the VH domain) and this favorable interfacial interaction is abolished after the mutation. 2021 Journal of chemical information and modeling Result SARS_CoV_2 F490S 11 16 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. By contrast, LY-CoV555 displayed no neutralization against recombinant viruses carrying E484Q or L452R/E484Q even at the highest concentration tested (4 mug/mL). 2021 Journal of chemical information and modeling Result SARS_CoV_2 E484Q;L452R;E484Q 88;97;103 93;102;108 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Compared with the free energy change for the T478K mutation in the free state (i.e., the RBD alone), in the bound state (i.e., the complex of RBD and LY-CoV555), the free energy change for the same mutation is larger only by 0.70 kcal/mol, which suggests that the T478K mutation moderately weakens the binding between the RBD and LY-CoV555. 2021 Journal of chemical information and modeling Result SARS_CoV_2 T478K;T478K 45;264 50;269 RBD;RBD;RBD 89;142;322 92;145;325 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Compared with the local coordinations before the E484Q mutation (Figure 2b), the local interfacial interaction was significantly weakened after the removal of two salt bridges that were buried inside the complex and stabilized the entire complex (see Figure S2 in Supporting Information). 2021 Journal of chemical information and modeling Result SARS_CoV_2 E484Q 49 54 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. E484Q and L452R/E484Q Confer Escape from LY-CoV555 in Experiment. 2021 Journal of chemical information and modeling Result SARS_CoV_2 L452R;E484Q;E484Q 10;16;0 15;21;5 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. FEP Calculations for L452Q and F490S Mutations in the Lambda Variant. 2021 Journal of chemical information and modeling Result SARS_CoV_2 F490S;L452Q 31;21 36;26 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. FEP Calculations for L452R and E484Q Mutations in the Kappa Variant. 2021 Journal of chemical information and modeling Result SARS_CoV_2 E484Q;L452R 31;21 36;26 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. FEP Calculations for L452R and T478K Mutations in the Delta Variant. 2021 Journal of chemical information and modeling Result SARS_CoV_2 L452R;T478K 21;31 26;36 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Figure 3b shows that after the E484Q mutation, Q484 was away from R96 and formed a hydrogen bond with R50. 2021 Journal of chemical information and modeling Result SARS_CoV_2 E484Q 31 36 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Figure 3c shows that K478 in the RBD-v is not inside the binding interface between RBD-v and LY-CoV555, and therefore, the T478K mutation does not directly affect the RBD's binding affinity with LY-CoV555. 2021 Journal of chemical information and modeling Result SARS_CoV_2 T478K 123 128 RBD;RBD;RBD 33;83;167 36;86;170 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. For the same reason stated above, the L452R mutation can cause the Delta variant to evade LY-CoV555 as well. 2021 Journal of chemical information and modeling Result SARS_CoV_2 L452R 38 43 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Here, we performed free energy perturbation (FEP) calculations to obtain the binding free energy change (DeltaDeltaG) induced by the L452R and E484Q mutations. 2021 Journal of chemical information and modeling Result SARS_CoV_2 E484Q;L452R 143;133 148;138 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. However, the Kappa variant also contains the P681R mutation and it is intriguing to know why the Delta variant can dominate the Kappa variant. 2021 Journal of chemical information and modeling Result SARS_CoV_2 P681R 45 50 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. In addition, the Delta variant carries the T478K mutation in the RBD. 2021 Journal of chemical information and modeling Result SARS_CoV_2 T478K 43 48 RBD 65 68 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Instead of the L452R mutation in the Kappa and Delta variants, the similar mutation is L452Q. 2021 Journal of chemical information and modeling Result SARS_CoV_2 L452Q;L452R 87;15 92;20 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Meanwhile, in the experiment, it was found that the P681R mutation in the spike protein (not in the RBD-v) plays a key role in the Alpha-to-Delta variant replacement, by allowing for a more efficient cleavage by furin and thus enhancing the viral reproduction. 2021 Journal of chemical information and modeling Result SARS_CoV_2 P681R 52 57 S;RBD 74;100 79;103 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. More importantly, the experiment confirms that E484Q is more important for the variant to escape LY-CoV555. 2021 Journal of chemical information and modeling Result SARS_CoV_2 E484Q 47 52 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Overall, the E484Q mutation yields an extra charge (+e, where e is the elementary charge) buried inside the low dielectric protein media, which is highly unfavorable from the free energy point of view. 2021 Journal of chemical information and modeling Result SARS_CoV_2 E484Q 13 18 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Similar to the Kappa variant, the Delta variant also contains the L452R mutations. 2021 Journal of chemical information and modeling Result SARS_CoV_2 L452R 66 71 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. The result from FEP calculations (Table 1) shows that the DeltaDeltaG for the F490S mutation is 2.68 kcal/mol, indicating that this mutation is also very evasive to LY-CoV555. 2021 Journal of chemical information and modeling Result SARS_CoV_2 F490S 78 83 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. The rigorous FEP calculation yielded DeltaDeltaG of 3.04 kcal/mol, corroborating that the L452R mutation is energetically unfavorable. 2021 Journal of chemical information and modeling Result SARS_CoV_2 L452R 90 95 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Thus, the simultaneous mutations of L452R and F490S might be synergistic by further destabilizing the interfacial contact. 2021 Journal of chemical information and modeling Result SARS_CoV_2 F490S;L452R 46;36 51;41 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. To date, it is still not clear whether the T478K mutation could lead to an increased binding affinity between RBD-v and hACE2. 2021 Journal of chemical information and modeling Result SARS_CoV_2 T478K 43 48 RBD 110 113 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. To evaluate whether LY-CoV555 is still effective for the Kappa variant carrying the L452R and E484Q mutations, we further investigate the interfacial coordinations around L452 and E484. 2021 Journal of chemical information and modeling Result SARS_CoV_2 E484Q;L452R 94;84 99;89 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. To experimentally test the possible antibody escape conferred by mutations within the Kappa variant spike protein, we performed neutralization assays using lentiviral pseudovirions that bear the spike protein of the Wuhan-Hu-1 isolate or that of the Kappa variant (L452R/E484Q/D614G). 2021 Journal of chemical information and modeling Result SARS_CoV_2 L452R;D614G;E484Q 265;277;271 270;282;276 S;S 100;195 105;200 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Unfortunately, the importance of L452 and E484 in stabilizing the LY-CoV555's binding with the RBD as shown above also indicates that the L452R and E484Q mutations can result in strong resistance to LY-CoV555. 2021 Journal of chemical information and modeling Result SARS_CoV_2 E484Q;L452R 148;138 153;143 RBD 95 98 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Using the same FEP method, we evaluate effects of the T478K mutation on the binding between the RBD and LY-CoV555. 2021 Journal of chemical information and modeling Result SARS_CoV_2 T478K 54 59 RBD 96 99 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. With protein structures for both bound and free states in respective MD simulations, we applied the FEP alchemy method to obtain the binding free energy difference for L452R and E484Q mutations on the RBD. 2021 Journal of chemical information and modeling Result SARS_CoV_2 E484Q;L452R 178;168 183;173 RBD 201 204 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. A baseline RLU for primary infection with N501Y + D614G or N501Y + K417N + E484K + D614G PsV was set as the average RLU of 10 mice infected with the respective PsV. 2021 Cell reports Result SARS_CoV_2 D614G;D614G;E484K;K417N;N501Y;N501Y 50;83;75;67;42;59 55;88;80;72;47;64 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Accordingly, we utilized PsVs carrying the 19del in the remainder of our studies. 2021 Cell reports Result SARS_CoV_2 19del 43 48 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. All groups were then challenged with N501Y + D614G VSV PsV. 2021 Cell reports Result SARS_CoV_2 D614G;N501Y 45;37 50;42 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Although molecular visualization of SARS-CoV-2 RBD binding to hACE2 shows differences between the wild-type (WT) or N501Y RBD variant that could explain higher infectivity (Figure 1 A), the interaction between mACE2 and the N501Y RBD variant reveals major differences (Figure 1B). 2021 Cell reports Result SARS_CoV_2 N501Y;N501Y 116;224 121;229 RBD;RBD;RBD 47;122;230 50;125;233 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Although the same titer trends remained for WT IgG RBD-directed responses compared with anti-spike, significant ablation of binding was observed for IgGs against the N501Y + K417N + E484K + D614G RBD (Figure 4L; Figure S5A). 2021 Cell reports Result SARS_CoV_2 D614G;E484K;K417N;N501Y 190;182;174;166 195;187;179;171 S;RBD;RBD 93;51;196 98;54;199 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Finally, given the severe outbreak of COVID-19 in India and the presence of a variant possessing a unique combination of mutations, including N501Y + L452R + K417N + E484Q + D614G (kappa variant), we sought to explore this variant in our system. 2021 Cell reports Result SARS_CoV_2 D614G;E484Q;K417N;L452R;N501Y 174;166;158;150;142 179;171;163;155;147 COVID-19 38 46 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. First we explored the ability of plasma samples from each cohort to neutralize infection of N501Y + D614G, Los Angeles N501Y + L452R + D614G, and South Africa N501Y + K417N+ E484K + D614G PsVs on hACE2+ 293 cells. 2021 Cell reports Result SARS_CoV_2 D614G;D614G;D614G;E484K;K417N;L452R;N501Y;N501Y;N501Y 100;135;182;174;167;127;92;119;159 105;140;187;179;172;132;97;124;164 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. First we measured IgG antibody levels that specifically bind the WT RBD versus the N501Y + K417N + E484K + D614G variant RBD. 2021 Cell reports Result SARS_CoV_2 D614G;E484K;K417N;N501Y 107;99;91;83 112;104;96;88 RBD;RBD 68;121 71;124 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Following establishment of our N501Y SARS-CoV-2 VSV system, we sought to test its applicability and manipulability using convalescent plasma transfer, a classic method for infection neutralization. 2021 Cell reports Result SARS_CoV_2 N501Y 31 36 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Given the heightened infectivity and public health threat of the United Kingdom B.1.1.7 SARS-CoV-2 variant, we sought to examine the potential for murine tropism and characterize the utility of B.1.1.7 spike mutations, notably N501Y, in mouse modeling. 2021 Cell reports Result SARS_CoV_2 N501Y 227 232 S 202 207 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Given the notable enhancement N501Y provides to RBD binding and PsV infection on mACE2+ cells, we investigated whether this mutation would allow a species switch to occur in vivo. 2021 Cell reports Result SARS_CoV_2 N501Y 30 35 RBD 48 51 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Hence, we pursued the modeling potential of N501Y SARS-CoV-2 VSV PsVs in vivo. 2021 Cell reports Result SARS_CoV_2 N501Y 44 49 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. High-tier COVID-19+ and vaccinated individual plasma samples still suffered from a decrease in N501Y + K417N + E484K + D614G RBD IgG levels, but it was not as pronounced. 2021 Cell reports Result SARS_CoV_2 D614G;E484K;K417N;N501Y 119;111;103;95 124;116;108;100 RBD 125 128 COVID-19 10 18 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. However, primary infection with N501Y + D614G and secondary infection with South Africa N501Y + K417N + E484K + D614G PsVs yielded no significant reduction in RLUs (Figures 3F-3H), suggesting that N501Y + K417N + E484K + D614G may have escaped antibodies generated during the primary infection. 2021 Cell reports Result SARS_CoV_2 D614G;D614G;D614G;E484K;E484K;K417N;K417N;N501Y;N501Y;N501Y 40;112;221;104;213;96;205;32;88;197 45;117;226;109;218;101;210;37;93;202 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Importantly, the presence of the N501Y mutation in PsVs resulted in higher luciferase activity in hACE2-transduced mice. 2021 Cell reports Result SARS_CoV_2 N501Y 33 38 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. In contrast, mACE2+ cells could only be infected productively with PsVs carrying the N501Y mutation, with N501Y + D614G VSV PsV performing the best (Figure 1F). 2021 Cell reports Result SARS_CoV_2 D614G;N501Y;N501Y 114;85;106 119;90;111 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. In vitro infection assays of hACE2+ cells revealed that PsVs carrying these mutations were significantly infectious but not quite to the levels observed for the N501Y + K417N + E484K + D614G variant (Figure 6 A). 2021 Cell reports Result SARS_CoV_2 D614G;E484K;K417N;N501Y 185;177;169;161 190;182;174;166 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. In vitro infection assays reveal that PsVs carrying Los Angeles N501Y + L452R + D614G and South Africa N501Y + K417N + E484K + D614G spike mutations are infective through hACE2 (Figure 3 A) and mACE2 (Figure 3B). 2021 Cell reports Result SARS_CoV_2 D614G;D614G;E484K;K417N;L452R;N501Y;N501Y 80;127;119;111;72;64;103 85;132;124;116;77;69;108 S 133 138 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Interestingly, a clear trend was not present between WT or N501Y + K417N + E484K + D614G RBD IgM or IgA levels compared with IgG levels, where a clear decrease was observed. 2021 Cell reports Result SARS_CoV_2 D614G;E484K;K417N;N501Y 83;75;67;59 88;80;72;64 RBD 89 92 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Moreover, we compared the binding qualities of RBD-Fc and N501Y RBD-Fc with bat ACE2 (Rhinolophus sinicus, XM_019746337.1), dog ACE2, pangolin ACE2, mACE2, and hACE2, revealing that the mouse was the mammalian host most affected by the N501Y mutation (Figures S1F and S1G). 2021 Cell reports Result SARS_CoV_2 N501Y;N501Y 58;236 63;241 RBD;RBD 47;64 50;67 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. No murine infection was noted in the absence of N501Y (Figures 1G-1I), supporting its indispensable role. 2021 Cell reports Result SARS_CoV_2 N501Y 48 53 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Primary and secondary infection with N501Y + D614G PsVs yielded significantly lower RLUs upon rechallenge (Figures 3F-3H). 2021 Cell reports Result SARS_CoV_2 D614G;N501Y 45;37 50;42 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. PsVs with the K417N + E484K mutations appeared to have heightened infection, as determined by RLUs. 2021 Cell reports Result SARS_CoV_2 E484K;K417N 22;14 27;19 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Setting the baseline using this method allowed us to make fair comparisons and control for the heightened primary infection levels seen with N501Y + K417N + E484K + D614G compared with N501Y + D614G PsVs (Figures 3C-3E). 2021 Cell reports Result SARS_CoV_2 D614G;D614G;E484K;K417N;N501Y;N501Y 165;193;157;149;141;185 170;198;162;154;146;190 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Similar to in vitro, partial immune escape was observed for the South Africa N501Y + K417N + E484K + D614G variant (Figures 5E and 5F) compared with N501Y + D614G (Figures 5A and 5B). 2021 Cell reports Result SARS_CoV_2 D614G;D614G;E484K;K417N;N501Y;N501Y 101;157;93;85;77;149 106;162;98;90;82;154 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Strikingly, N501Y + D614G PsV challenge led to significant infection in the nasopharynx and lungs (Figures 1G-1I), whereas N501Y PsV displayed lower-level infection, presumably because of the lack of D614G-mediated infection enhancement. 2021 Cell reports Result SARS_CoV_2 D614G;D614G;N501Y;N501Y 20;200;12;123 25;205;17;128 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Strikingly, South Africa N501Y + K417N + E484K + D614G PsVs demonstrated significantly higher infection in the nasopharynx and lungs (Figures 3C-3E) compared with Los Angeles N501Y + L452R + D614G and N501Y + D614G PsVs. 2021 Cell reports Result SARS_CoV_2 D614G;D614G;D614G;E484K;K417N;L452R;N501Y;N501Y;N501Y 49;191;209;41;33;183;25;175;201 54;196;214;46;38;188;30;180;206 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Strikingly, when comparing WT or N501Y RBD binding with mACE2, the WT RBD did not bind, but the N501Y RBD bound strongly with a Kd of 47.6 nM (Figure 1D). 2021 Cell reports Result SARS_CoV_2 N501Y;N501Y 33;96 38;101 RBD;RBD;RBD 39;70;102 42;73;105 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. The activity of non-19del WT and N501Y PsVs was also determined (Figures S2C, S2D, and S3A-S3E). 2021 Cell reports Result SARS_CoV_2 N501Y;non-19del 33;20 38;25 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. The heightened infectivity and rechallenge susceptibility mediated by K417N + E484K mutations prompted us to explore their effects on antibody-mediated neutralization, which is of the utmost importance for formulating effective public health strategies to combat the spread of SARS-CoV-2 variants. 2021 Cell reports Result SARS_CoV_2 E484K;K417N 78;70 83;75 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. The N501Y-RBD displayed heightened binding and a lower Kd with hACE2 compared with the WT RBD in both binding assays (Figure 1C; Figures S1D and S1E). 2021 Cell reports Result SARS_CoV_2 N501Y 4 9 RBD;RBD 10;90 13;93 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. These data support the hypothesis that N501Y variant SARS-CoV-2 PsVs can be used to model infection and spike antibody-mediated prophylactic immunity. 2021 Cell reports Result SARS_CoV_2 N501Y 39 44 S 104 109 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. These findings suggest that the N501Y + K417N + E484K + D614G variant may have immune escape capabilities to natural and vaccine-induced anti-COVID-19 immunity, with differential effects exerted by WT versus variant-binding IgGs but not IgMs or IgAs. 2021 Cell reports Result SARS_CoV_2 D614G;E484K;K417N;N501Y 56;48;40;32 61;53;45;37 COVID-19 142 150 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. These results confirm that the N501Y mutation allows SARS-CoV-2 PsVs to species switch to the mouse and that it can permit rapid in vivo infection as a research tool. 2021 Cell reports Result SARS_CoV_2 N501Y 31 36 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. This binding pattern was confirmed using RBD-Fc and N501Y RBD Fc protein (Figures S1B and S1C). 2021 Cell reports Result SARS_CoV_2 N501Y 52 57 RBD;RBD 41;58 44;61 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. This decrease in neutralization ability was not observed for the Los Angeles N501Y + L452R + D614G variant (Figure 4H). 2021 Cell reports Result SARS_CoV_2 D614G;L452R;N501Y 93;85;77 98;90;82 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. This is especially striking when examining the ability of high-tier COVID-19+ and vaccinated plasma samples to control the South Africa N501Y + K417N + E484K + D614G variant. 2021 Cell reports Result SARS_CoV_2 D614G;E484K;K417N;N501Y 160;152;144;136 165;157;149;141 COVID-19 68 76 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. This supports the theories that N501Y leads to higher hACE2- and mACE2-dependent infection potential in vivo and that SARS-CoV-2 VSV PsVs serve as an easy-to-use Animal Biosafety Level 2 (ABSL-2) system to robustly study infectivity through hACE2 or mACE2. 2021 Cell reports Result SARS_CoV_2 N501Y 32 37 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. To explore this, we infected mice with N501Y + D614G PsVs. 2021 Cell reports Result SARS_CoV_2 D614G;N501Y 47;39 52;44 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. To query its feasibility in our system, N501Y + D614G PsV was preincubated with plasma from individuals infected previously with COVID-19, mice vaccinated with RBD-Fc, or control humans or mice. 2021 Cell reports Result SARS_CoV_2 D614G;N501Y 48;40 53;45 RBD 160 163 COVID-19 129 137 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. To query these interactions' biological significance, we performed surface plasmon resonance and cytometric binding assays between hACE2-expressing 293 cells and the WT or N501Y RBD. 2021 Cell reports Result SARS_CoV_2 N501Y 172 177 RBD 178 181 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Two weeks later, mice were rechallenged with N501Y + D614G or N501Y + K417N + E484K + D614G PsV, given that the E484K mutation has been linked to antibody-mediated immune escape and virulence of the South Africa variant. 2021 Cell reports Result SARS_CoV_2 D614G;D614G;E484K;E484K;K417N;N501Y;N501Y 53;86;78;112;70;45;62 58;91;83;117;75;50;67 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. We also aimed to characterize the in vivo infection potential of N501Y-bearing PsVs on hACE2+ tissues. 2021 Cell reports Result SARS_CoV_2 N501Y 65 70 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. We also explored the ability of COVID-19+ plasma to neutralize the N501Y + L452R + K417N + E484Q + D614G variant. 2021 Cell reports Result SARS_CoV_2 D614G;E484Q;K417N;L452R;N501Y 99;91;83;75;67 104;96;88;80;72 COVID-19 32 40 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. We generated VSV PsVs carrying L452R (Los Angeles variant) or K417N + E484K (South Africa, beta variant) alongside N501Y + D614G (Figure S2B). 2021 Cell reports Result SARS_CoV_2 D614G;E484K;K417N;L452R;N501Y 123;70;62;31;115 128;75;67;36;120 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. We wanted to explore factors beyond titer that could be contributing mechanistically to the immune escape seen with South Africa N501Y + K417N + E484K + D614G PsV in the presence of COVID-19+ and vaccinated individual plasma samples. 2021 Cell reports Result SARS_CoV_2 D614G;E484K;K417N;N501Y 153;145;137;129 158;150;142;134 COVID-19 182 190 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. When applying these variants in vivo, a similar phenomenon was observed; the N501Y + L452R + K417N + E484Q + D614G variant PsVs were highly infective, but significantly higher infection was observed in the nasopharynx, but not lungs, of mice infected with the N501Y + K417N + E484K + D614G variant (Figures 6B-6D). 2021 Cell reports Result SARS_CoV_2 D614G;D614G;E484K;E484Q;K417N;K417N;L452R;N501Y;N501Y 109;284;276;101;93;268;85;77;260 114;289;281;106;98;273;90;82;265 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. When examining Lenti (Figure 1E) or VSV (Figure 1F) PsV infection on hACE2+ cells, D614G and N501Y + D614G (alpha variant) displayed high-level infectivity, with N501Y + D614G VSV PsVs displaying slightly superior infection (Figure 1F). 2021 Cell reports Result SARS_CoV_2 D614G;D614G;D614G;N501Y;N501Y 83;101;170;93;162 88;106;175;98;167 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. When examining the ability of COVID-19+ and vaccinated individuals to neutralize South Africa N501Y + K417N + E484K + D614G VSV PsVs compared with N501Y + D614G VSV PsVs, markedly lower reciprocal log10IC50 values were noted for the South Africa N501Y + K417N + E484K + D614G variant, suggesting that it was not neutralized as efficiently as the N501Y + D614G variant (Figure 4G). 2021 Cell reports Result SARS_CoV_2 D614G;D614G;D614G;D614G;E484K;E484K;K417N;K417N;N501Y;N501Y;N501Y;N501Y 118;155;270;354;110;262;102;254;94;147;246;346 123;160;275;359;115;267;107;259;99;152;251;351 COVID-19 30 38 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. With this impetus, we generated Lentivirus (Lenti) and vesicular stomatitis virus (VSV) pseudoviruses (PsVs) incorporating spike variants, including WT and D614G with or without the N501Y mutation, to determine how N501Y would change the infection potential on hACE2- or mACE2-expressing cells (Figure S2A; Table S1). 2021 Cell reports Result SARS_CoV_2 D614G;N501Y;N501Y 156;182;215 161;187;220 S 123 128 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. As expected, the single E484Q substitution had a milder impact than E484K. 2021 Genome medicine Result SARS_CoV_2 E484K;E484Q 68;24 73;29 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Due to the stronger binding to ACE2 caused by the substitution N501Y and L452R, the binding affinity of B.1.351 triple mutant or B.1.617.1 double mutant RBD with ACE2 is nearly 3-fold higher than the wildtype RBD. 2021 Genome medicine Result SARS_CoV_2 L452R;N501Y 73;63 78;68 RBD;RBD 153;209 156;212 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. E484A and E484K resulted in resistance to 26-34L, 24-12K, and 25-F8 while E484Q showed a mild impact and E484D had no impact. 2021 Genome medicine Result SARS_CoV_2 E484D;E484K;E484Q;E484A 105;10;74;0 110;15;79;5 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Expectedly, the B.1.351 variant (RBD-K417N/E484K/N501Y) facilitated resistance to a somewhat wider range of NAbs than single mutations, which conferred complete resistance to five highly potent NAbs targeting major antigenic sites (site 1 and site 2) in terms of binding and neutralizing activity. 2021 Genome medicine Result SARS_CoV_2 E484K;N501Y;K417N 43;49;37 48;54;42 RBD 33 36 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. F490V, F490S, and F490L each resulted in strong resistance to 26-34L, 25-F8, and 24-12K. 2021 Genome medicine Result SARS_CoV_2 F490L;F490S;F490V 18;7;0 23;12;5 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Finally, we demonstrated that compared with the wildtype residues, the N501Y, K417N, and E484K mutations in the B.1.351-variant pseudovirus dramatically reduced the neutralizing ability of all the plasma samples, with 2.1- to 7.4-fold reductions, which was also observed in previous studies. 2021 Genome medicine Result SARS_CoV_2 E484K;K417N;N501Y 89;78;71 94;83;76 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. For example, alanine scanning revealed that the F456A mutation caused loss of binding of VH3-53/3-66 NAbs, but the natural F456L variation did not result in resistance to VH3-53/3-66 NAbs. 2021 Genome medicine Result SARS_CoV_2 F456A;F456L 48;123 53;128 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. For example, the replacement of K417 with Asn (N) greatly weakened CB6 binding affinity by disrupting a strong salt bridge between K417 in the SARS-CoV-2 RBD and the CB6 CDRH3. 2021 Genome medicine Result SARS_CoV_2 K417N 32 45 RBD 154 157 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. However, E340K and K378N disrupted the key hydrogen bonds with S309 and CR3022, respectively. 2021 Genome medicine Result SARS_CoV_2 E340K;K378N 9;19 14;24 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. In addition, the combination of mutations resulted in more resistance than single mutations due to an additive effect caused by K417N and E484K. 2021 Genome medicine Result SARS_CoV_2 E484K;K417N 138;128 143;133 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. In contrast, the double L452R and E484Q mutations appeared a moderate decrease in neutralizing activity and failed to show an obvious additive effect compared to single mutation. 2021 Genome medicine Result SARS_CoV_2 E484Q;L452R 34;24 39;29 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Markedly, K417N, F486L, L452R, E484K, and R346S resulted in resistance to at least six plasma samples, as the NAb titers were approximately 2-4 times lower than those for the wildtype, indicating that NAbs targeting these key residues were enriched in human convalescent plasma. 2021 Genome medicine Result SARS_CoV_2 E484K;F486L;K417N;L452R;R346S 31;17;10;24;42 36;22;15;29;47 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. N501Y, L452R, and S477N mutants exhibited high affinity for ACE2 and exhibited 9.24- to 14.66-fold higher binding affinity than wildtype RBD. 2021 Genome medicine Result SARS_CoV_2 L452R;S477N;N501Y 7;18;0 12;23;5 RBD 137 140 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Notably, the key antibody escape mutations K417N, N450K, E484K, E484Q, F490S, and R346S had limited effects on ACE2 binding affinity with fold changes between 0.4 and 2.5, suggesting that they were not accompanied by loss of fitness. 2021 Genome medicine Result SARS_CoV_2 E484K;E484Q;F490S;K417N;N450K;R346S 57;64;71;43;50;82 62;69;76;48;55;87 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Notably, the most frequent RBD variants seen in clinical isolates, N501Y and S477N, remained similarly sensitive to the majority of the selected NAbs; only 24-1L failed to neutralize N501Y. 2021 Genome medicine Result SARS_CoV_2 N501Y;N501Y;S477N 67;183;77 72;188;82 RBD 27 30 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. On the contrary, the RBD double mutants E484Q and L452R within antigenic 2 which featured by B.1.617.1 do not cause substantial antibody evasion. 2021 Genome medicine Result SARS_CoV_2 E484Q;L452R 40;50 45;55 RBD 21 24 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. On the other hand, both F490S and N450K resulted in resistance to neutralization by plasma samples 6 and 24; in particular, the NAb titer of plasma sample 24 against F490S was reduced by 4.6 times. 2021 Genome medicine Result SARS_CoV_2 F490S;F490S;N450K 24;166;34 29;171;39 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. P337R instead of P337S conferred resistance to S309, and R346S instead of R346T caused a significant loss of binding of 24-12K, 28-15L, and 25-C9. 2021 Genome medicine Result SARS_CoV_2 P337S;R346S;R346T;P337R 17;57;74;0 22;62;79;5 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Since the dominant S sequence variant seen in clinical isolates is D614G, all the SARS-CoV-2 pseudovirus variants we constructed were coupled with the D614G variant. 2021 Genome medicine Result SARS_CoV_2 D614G;D614G 67;151 72;156 S 19 20 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Substitutions responsible for major antigenic escape were in antigenic site 1 (K417N, F486L), antigenic site 2 (N450K, E484K, E484Q, L452R, F490S), and antigenic site 3 (R346S). 2021 Genome medicine Result SARS_CoV_2 E484K;E484Q;F486L;F490S;L452R;K417N;N450K;R346S 119;126;86;140;133;79;112;170 124;131;91;145;138;84;117;175 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Two core region mutations distant from the ACE2 binding surface, N343A and W436A, also resulted in the loss of ACE2 binding. 2021 Genome medicine Result SARS_CoV_2 N343A;W436A 65;75 70;80 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Unlike N501Y, which induced tighter binding with ACE2, S477N and L452R occurred at sites that were likely not in the ACE2 contact region. 2021 Genome medicine Result SARS_CoV_2 L452R;N501Y;S477N 65;7;55 70;12;60 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Using our immune escape mapping strategy, we identified a natural mutant, E340K, in the circulating virus that conferred resistance to a broadly reactive NAb, S309, and five mutants that resulted in resistance to CB6. 2021 Genome medicine Result SARS_CoV_2 E340K 74 79 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. V382E rather than V382L reduced the binding activity of 28-26K and CR3022 in group 5. 2021 Genome medicine Result SARS_CoV_2 V382L;V382E 18;0 23;5 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. We also observed that L452R rather than L452M led to substantial loss of binding to 24-34L, 25-F8, 24-12K, and 28-15L. 2021 Genome medicine Result SARS_CoV_2 L452M;L452R 40;22 45;27 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. We demonstrated that some mutations, namely, K417A, F456A, N460A, A475V, F486A, and N487A, led to less binding for multiple group 1 antibodies. 2021 Genome medicine Result SARS_CoV_2 A475V;F456A;F486A;K417A;N460A;N487A 66;52;73;45;59;84 71;57;78;50;64;89 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. We observed that the substitution N501Y and S477N was neutralized in the same level as the wildtype by the majority of the plasma samples, in agreement with the previous studies. 2021 Genome medicine Result SARS_CoV_2 N501Y;S477N 34;44 39;49 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. Both the trader and the nurse harboured identical B.1.617.2 sequences, additionally harbouring S71F, T250I, T572I, and K854N. 2021 Emerging microbes & infections Result SARS_CoV_2 K854N;S71F;T250I;T572I 119;95;101;108 124;99;106;113 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. The sequence confirmed Delta variant additionally harbouring A352S. 2021 Emerging microbes & infections Result SARS_CoV_2 A352S 61 66 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. The sequence confirmed Delta variant additionally harbouring R158G and C1248F. 2021 Emerging microbes & infections Result SARS_CoV_2 C1248F;R158G 71;61 77;66 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. The Spike sequence harboured G769 V and C1248F as additional mutations. 2021 Emerging microbes & infections Result SARS_CoV_2 C1248F;G769V 40;29 46;35 S 4 9 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. According to the MM/GBSA analysis, the reported mutations (N439K, S477 N, and T478K) enhanced the binding affinity toward the ACE2 receptor compared with the wild-type RBD complex. 2021 Computers in biology and medicine Result SARS_CoV_2 S477N;T478K;N439K 66;78;59 72;83;64 RBD 168 171 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Another important mutation N439K in the spike RBD reported in a recent study revealed that this mutation is reported autonomously in multiple lineages and enhances the binding of spike RBD to the ACE2 receptor. 2021 Computers in biology and medicine Result SARS_CoV_2 N439K 27 32 S;S;RBD;RBD 40;179;46;185 45;184;49;188 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Consequently, the binding network analysis revealed that the substituted T478K residue enhanced the binding of ACE2 to the spike RBD compared with the wild type by making one salt bridge, 14 hydrogen bonds, and 166 non-bonded contacts. 2021 Computers in biology and medicine Result SARS_CoV_2 T478K 73 78 S;RBD 123;129 128;132 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Conversely, the N439K complex (spike-ACE2) was equilibrated at 5 ns and gained stability at 2.0 A. 2021 Computers in biology and medicine Result SARS_CoV_2 N439K 16 21 S 31 36 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Conversely, the RMSD remained slightly higher for the S477 N than for the wild type, but the system exhibited a dynamically stable behavior, thus achieving stable binding of the mutant RBD. 2021 Computers in biology and medicine Result SARS_CoV_2 S477N 54 60 RBD 185 188 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Due to the high credibility of this method, we analyzed the effect of the reported mutations in the RBD domain (N439K, S477 N, and T478K) on the interaction network with the human receptor ACE2. 2021 Computers in biology and medicine Result SARS_CoV_2 S477N;T478K;N439K 119;131;112 125;136;117 RBD 100 103 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. During the entire simulation, the Rg values for the mutants N439K and T478K remained higher than those for the wild type, but the average value for the mutant S477 N was comparable with that for the wild type. 2021 Computers in biology and medicine Result SARS_CoV_2 N439K;S477N;T478K 60;159;70 65;165;75 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. For example, other findings have reported that a destabilizing mutation C432D in the RBD lessens ACE2-assisted entry into the cell using a spike trimer. 2021 Computers in biology and medicine Result SARS_CoV_2 C432D 72 77 S;RBD 139;85 144;88 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. In the case of the T478K variants, a higher fluctuation was observed in the 140-160 residues, which was not experienced by other systems. 2021 Computers in biology and medicine Result SARS_CoV_2 T478K 19 24 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Moreover, the dynamics behavior of S477 N and T478K were comparable, as the RMSD of both systems increased after 100 ns, and the mean RMSD for the last 400 ns increased up to 4.0 A. 2021 Computers in biology and medicine Result SARS_CoV_2 S477N;T478K 35;46 41;51 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Moreover, the N439K system remained dynamically more stable, and no notable deviation was observed until 230 ns. 2021 Computers in biology and medicine Result SARS_CoV_2 N439K 14 19 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Surprisingly, the T478K mutant showed a higher fluctuation in the 180-200 amino acids. 2021 Computers in biology and medicine Result SARS_CoV_2 T478K 18 23 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. The average hydrogen bonds were 382 in the wild type, 387 in N439K, 385 in S477 N, and 386 in T478K. 2021 Computers in biology and medicine Result SARS_CoV_2 N439K;S477N;T478K 61;75;94 66;81;99 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. The average Rg value was 31.0 A for the wild type, 31.5 A for N439K, 31.0 A for S477 N, and 32.0 A for T478K. 2021 Computers in biology and medicine Result SARS_CoV_2 N439K;S477N;T478K 62;80;103 67;86;108 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. The dynamic behavior of the wild type and N439K in terms of stability is comparable. 2021 Computers in biology and medicine Result SARS_CoV_2 N439K 42 47 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. The evolution of the variant (S477 N) was stable, increasing the binding affinity. 2021 Computers in biology and medicine Result SARS_CoV_2 S477N 30 36 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. The hydrogen bonds involved in the ACE2-N439K complex include Glu32-Lys439, Ser19-Ala475, Tyr83-Asn487, Glu35-Gln493, Asn330-Thr500, Tyr41-Thr500, Gln42-Gly446, Gln42-Tyr449, Glu38-Tyr449, Lys353-Gln498, Lys353-Gly496, and Lys353-Gly502. 2021 Computers in biology and medicine Result SARS_CoV_2 N439K 40 45 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. The recently reported spike RBD mutations, which occur in higher frequency and are associated with higher infectivity, are N439K, S477 N, and T478K. 2021 Computers in biology and medicine Result SARS_CoV_2 N439K;S477N;T478K 123;130;142 128;136;147 S;RBD 22;28 27;31 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. The RMSD differences in each superimposed structure were significant, with 1.7 A for N439K, 1.8 A for S477 N, and 0.6 A for T478K, indicating structural deviation, secondary structural element perturbation, and protein conformational variations in the mutant structures. 2021 Computers in biology and medicine Result SARS_CoV_2 N439K;S477N;T478K 85;102;124 90;108;129 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. The RMSD of the N439K system also remained stable and experienced a slight deviation at 80-160 ns, 220-300 ns, and 360 ns time intervals. 2021 Computers in biology and medicine Result SARS_CoV_2 N439K 16 21 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. the RMSD value for the S477 N complex gained stability at 2.0 A and remained steady until 100 ns. 2021 Computers in biology and medicine Result SARS_CoV_2 S477N 23 29 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. The S477 N also remained stable. 2021 Computers in biology and medicine Result SARS_CoV_2 S477N 4 10 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. The S477 N complex also showed an unusual fluctuation at 280-320, and no noticeable differences were observed in the other regions. 2021 Computers in biology and medicine Result SARS_CoV_2 S477N 4 10 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. The stability of the S477 N (ACE2-spike RBD) complex was also evaluated to demonstrate its dynamic behavior. 2021 Computers in biology and medicine Result SARS_CoV_2 S477N 21 27 S;RBD 34;40 39;43 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Therefore, our results are similar to the experimental data in terms of the higher binding affinity and infectivity of the N439K mutant. 2021 Computers in biology and medicine Result SARS_CoV_2 N439K 123 128 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. This verifies that N439K establishes additional interactions and increases the binding affinity and infectivity compared with wild-type. 2021 Computers in biology and medicine Result SARS_CoV_2 N439K 19 24 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Thus, our findings show that N439K, S477 N, and T478K have stable dynamics and have evolved stably, further increasing their unusual virulence. 2021 Computers in biology and medicine Result SARS_CoV_2 N439K;S477N;T478K 29;36;48 34;42;53 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. To compare the binding of T478K with the wild type and highlight the effect of this mutation on binding efficiency, we analyzed the binding network using the HDOCK server. 2021 Computers in biology and medicine Result SARS_CoV_2 T478K 26 31 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. To explore the interaction mechanism of the wild-type RBD and the mutants mentioned above with human ACE2, we used Chimera software to structurally model the N439K, S477 N, and T478K mutants. 2021 Computers in biology and medicine Result SARS_CoV_2 N439K;S477N;T478K 158;165;177 163;171;182 RBD 54 57 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. We also computed the stability of T478K (ACE2-spike RBD), which revealed that the system reached stability at 2.3 A and remained steady until 100 ns. 2021 Computers in biology and medicine Result SARS_CoV_2 T478K 34 39 S;RBD 46;52 51;55 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. We used the HDOCK online server to check the binding affinity of the N439K mutant to the ACE2 receptor. 2021 Computers in biology and medicine Result SARS_CoV_2 N439K 69 74 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. Also, 96 sequences presented only the mutation L452R in the analyzed fragment. 2021 Frontiers in public health Result SARS_CoV_2 L452R 47 52 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. Figure 5 illustrates the position of the mutation present on the Spike protein: G142V, N164K, Q173K, L452R, S704L, and I720V. 2021 Frontiers in public health Result SARS_CoV_2 G142V;I720V;L452R;N164K;Q173K;S704L 80;119;101;87;94;108 85;124;106;92;99;113 S 65 70 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. Following, we sequenced the complete genome of 251 samples from Porto Ferreira from those that were previously screened by Sanger, being 92 samples that presented the L452R mutation, initially classified by pangolin as B.1.1.28, 142 classified as Gamma (P.1), and 14 classified as Alpha (B.1.1.7). 2021 Frontiers in public health Result SARS_CoV_2 L452R 167 172 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. Six of those mutations occur in the Spike protein, but only L452R is in the RBD region. 2021 Frontiers in public health Result SARS_CoV_2 L452R 60 65 S;RBD 36;76 41;79 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. The analysis revealed that sequences from Porto Ferreira, with L452R mutation, grouped into a monophyletic branch, with strong branch support (aLRT 1) along with other Brazilian sequences deposited on GISAID carrying the same mutation (Figure 1; Supplementary Figure 2). 2021 Frontiers in public health Result SARS_CoV_2 L452R 63 68 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. The dataset included sequences harboring the L452R mutation from this study together with representatives of B.1.1.28, P.1, P.2, P.3, B.1.1.7, B.1.427, B.1.429, B.1.617 lineages and the reference sequence WIV04/2019 EPI_ISL_402124 available on GISAID (see Supplementary File 2 for sequence information). 2021 Frontiers in public health Result SARS_CoV_2 L452R 45 50 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. The L452R mutation had not been reported in any endogenous lineage circulating in Brazil at the time of the study (variant Delta was only introduced in the country later), so it required further investigation, through complete genome analysis, to understand which lineage we were detecting. 2021 Frontiers in public health Result SARS_CoV_2 L452R 4 9 34663909 SARS-CoV-2 promotes RIPK1 activation to facilitate viral propagation. To determine the functional significance of the differential interaction mediated by the original variant NSP12 323P and NSP12 323L encoded by the C14408T variant with RIPK1, we isolated a virus strain carrying the C14408T (NSP12 P323L) mutation from a patient nasopharyngeal swab. 2021 Cell research Result SARS_CoV_2 C14408T;C14408T;P323L 147;215;230 154;222;235 Nsp12;Nsp12;Nsp12 106;121;224 111;126;229 34671769 A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. And when we went back to sequence the viruses from earlier passages, only H655Y, which has also been found in other circulating variants such as P.1, and V1128A were found. 2021 bioRxiv Result SARS_CoV_2 H655Y;V1128A 74;154 79;160 34671769 A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Here we assessed 2-36 activity on more variants, including pseudoviruses representing the combination of key spike mutations of B.1.427/B.1.429, R.1, B.1.1.1, B.1.525, B.1.617.1, B.1.617.2 and B.1.1.7 with E484K, as well as many pseudoviruses with single spike mutations which are naturally circulating in COVID-19 patients with high frequency and located in the N-terminal domain, RBD, or S2. 2021 bioRxiv Result SARS_CoV_2 E484K 206 211 S;S;RBD;N 109;255;382;363 114;260;385;364 COVID-19 306 314 34671769 A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Indeed, when these mutations were introduced into pseudoviruses and tested for their sensitivity to 2-36, only K378T alone or in combination with the other mutations was found to be resistant to 2-36, whereas viruses with T284I, H655Y, or V1128A alone remained sensitive (Figure 4D). 2021 bioRxiv Result SARS_CoV_2 H655Y;K378T;T284I;V1128A 229;111;222;239 234;116;227;245 34671769 A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Interestingly, although the K378 position in SARS-CoV-2 spike can be mutated to other residues at very low frequency, we could not find any K378T mutation circulating in patient viruses to date (Figure 4E), further demonstrating the conserved nature of the region recognized by 2-36. 2021 bioRxiv Result SARS_CoV_2 K378T 140 145 S 56 61 34671769 A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Sequence analyses of the passage 12 virus revealed four single point spike mutations (T284I, K378T, H655Y, V1128A), all of which were found at 100% frequency. 2021 bioRxiv Result SARS_CoV_2 H655Y;K378T;V1128A;T284I 100;93;107;86 105;98;113;91 S 69 74 34671769 A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. The T284I and K378T mutations appeared only in the 2-36-resistant virus (Figure 4B). 2021 bioRxiv Result SARS_CoV_2 K378T;T284I 14;4 19;9 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. Interestingly, the mobilities of the alpha variant bands were decreased compared to the KR mt indicating an even higher level of phosphorylation, potentially due to the additional nucleocapsid mutations at D3L and S235F that alpha carries. 2022 bioRxiv Result SARS_CoV_2 D3L;S235F 206;214 209;219 N 180 192 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. Interestingly, while the R203M mutation was first detected in March of 2020, it persisted as a rare (<1%) variant until April of 2021 when it began expanding rapidly, reaching 91% of all reported sequences in July 2021. 2022 bioRxiv Result SARS_CoV_2 R203M 25 30 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. The first is the R203K/G204R double substitution (KR mt), present in the alpha, gamma, and lambda variants. 2022 bioRxiv Result SARS_CoV_2 R203K;G204R 17;23 22;28 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. The second prominent mutation, T205I, is present in the beta, eta, and mu lineages. 2022 bioRxiv Result SARS_CoV_2 T205I 31 36 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. The third prominent variant mutation is R203M, currently present in the delta and kappa variants. 2022 bioRxiv Result SARS_CoV_2 R203M 40 45 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. To do so, we made an R203A/G204A double alanine substitution mutant (AA mt) in the WA-1 mNG background. 2022 bioRxiv Result SARS_CoV_2 R203A;G204A 21;27 26;32 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. While also emerging early in the pandemic, T205I is a minority variant which peaked at 9% in February 2021. 2022 bioRxiv Result SARS_CoV_2 T205I 43 48 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. While both the beta (T205I) and kappa (R203M) variants also displayed slower electrophoretic mobility compared to WA-1, the beta variant displayed a two-band pattern reminiscent of WA-1 while kappa displayed a laddered pattern similar to the KR mt. 2022 bioRxiv Result SARS_CoV_2 R203M;T205I 39;21 44;26 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. A total of 2757 of 13 972 cases were found to be suspicious for mutation and were tested with the Bio-Speedy SARS CoV-2 N501Y Mutation Kit while a mutation was detected in 159 cases. 2021 Journal of medical virology Result SARS_CoV_2 N501Y 120 125 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. According to the results, while the mean age of positive female patients was 20.87 +- 3.23, the mean age of the female with N501Y mutation was calculated as 30.92 +- 5.61. 2021 Journal of medical virology Result SARS_CoV_2 N501Y 124 129 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. In the study, NGS technology was preferred in addition to RT-PCR studies for the identification of the N501Y mutation. 2021 Journal of medical virology Result SARS_CoV_2 N501Y 103 108 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. List of variations displayed in structure (nearest residue if in loop/termini region): H69del V70del(69) Y144del(143) N501Y A570D D614G P681H(674) T716I S982A D1118H as seen in Table 3. 2021 Journal of medical virology Result SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 124;159;130;118;136;153;147 129;165;135;123;141;158;152 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Moreover, the N501Y mutation patient's genome are analyzed in next generation sequencing (NGS) and the bioinformatic analysis was utilized in NCBI and GISAID. 2021 Journal of medical virology Result SARS_CoV_2 N501Y 14 19 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Moreover, when the N501 variant type Cq results are examined in N501Y mutation results, it is seen that it varies between 0 and 39.86 average is 30.97 +- 4.71. 2021 Journal of medical virology Result SARS_CoV_2 N501Y 64 69 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Sequence alignment of RBD from SARS-CoV-2, B.1.1.7, and B.1.351 variants spike proteins are (the N501Y, K417N, and E484K mutations) shown in red with circle. 2021 Journal of medical virology Result SARS_CoV_2 E484K;K417N;N501Y 115;104;97 120;109;102 S;RBD 73;22 78;25 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The variant of N501Y mutation (N501 and Y501) was also determined with the kit protocol. 2021 Journal of medical virology Result SARS_CoV_2 N501Y 15 20 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. Conversely, we have not found any literature for even other coronaviruses that showed ORF3a: p.Q57H correlating with the rest of the co-occurring mutations. 2021 Journal of medical virology Result SARS_CoV_2 Q57H;Q57H 93;95 99;99 ORF3a 86 91 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. Finally, a change in T445C in leader protein may not cause any change in expression or others since the structure (data not shown) and energy is the same -172.34 kcal/mol. 2021 Journal of medical virology Result SARS_CoV_2 T445C 21 26 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. However, C241T is present just upstream to the ORF1a start codon (266-268 position) and may be involved in differential RNA binding affinity to the ribosome and translational factors. 2021 Journal of medical virology Result SARS_CoV_2 C241T 9 14 ORF1a 47 52 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. In contrast, we could not predict any possible association of the 5'-UTR:C241T mutation with the S, RdRp, and NSP3 mutated proteins, as shown by sequence analysis in Zeng et al. 2021 Journal of medical virology Result SARS_CoV_2 C241T 73 78 Nsp3;RdRP;S 110;100;97 114;104;98 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. In the case of multi-domain NSP3 (papain-like protease), we have observed superior stability of the RNA after gaining the synonymous mutation 3037C0.1, and only one SNP was detected in the BAL sample of one animal; this was a synonymous mutation in nsp6 (table S1). 2021 Science advances Result SARS_CoV_2 D614G 29 34 Nsp6 170 174 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Notably, this response was absent in B.1.351-inoculated animals, as indicated by these samples clustering separately from D614G- and B.1.1.7-inoculated animals. 2021 Science advances Result SARS_CoV_2 D614G 122 127 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. On observation, lung lesions in animals inoculated with D614G were generally more severe than B.1.1.7 and B.1.351, while there were minimal differences between animals inoculated with B.1.1.7 and B.1.351. 2021 Science advances Result SARS_CoV_2 D614G 56 61 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. On observation, the animals inoculated with D614G generally had more viral antigen than those inoculated with B.1.1.7 or B.1.351. 2021 Science advances Result SARS_CoV_2 D614G 44 49 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Significantly lower virus titers were detected in the lungs of B.1.351-inoculated animals than in those inoculated with D614G. 2021 Science advances Result SARS_CoV_2 D614G 120 125 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. The B.1.1.7 inoculum contained three SNPs at >0.1 allelic fraction compared with the reference sequence; the D156G in nsp6 was detected in all animals, but at an allelic fraction <0.1 in five of six animals. 2021 Science advances Result SARS_CoV_2 D156G 109 114 Nsp6 118 122 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. The B.1.351 inoculum contained two amino acid substitutions compared with the reference sequence; of these, the P252L substitution in nsp5 was maintained in five of six animals at slightly higher percentages than in the inoculum, whereas the L257F substitution in nsp6 was maintained at levels similar to the virus inoculum in all animals (table S1). 2021 Science advances Result SARS_CoV_2 L257F;P252L 242;112 247;117 Nsp5;Nsp6 134;264 138;268 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. The B.1.351-inoculated animals had fewer days with a reduced appetite, and only three of six animals inoculated with B.1.351 showed respiratory signs of disease at any time after inoculation compared with five of six for D614G and four of six for B.1.1.7. 2021 Science advances Result SARS_CoV_2 D614G 221 226 Respiratory Disease 132 160 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. The L257F substitution in nsp6 was maintained in all animals, and the V11I substitution increased in frequency in five of six animals (table S1). 2021 Science advances Result SARS_CoV_2 L257F;V11I 4;70 9;74 Nsp6 26 30 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. The pathogenicity of two VOC isolates, B.1.1.7 and B.1.351, was compared to the pathogenicity of a recent clade B.1 isolate containing the D614G substitution in the spike protein. 2021 Science advances Result SARS_CoV_2 D614G 139 144 S 165 170 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. There was statistically significantly more antigen present in the lungs of D614G-inoculated animals than in those inoculated with B.1.351. 2021 Science advances Result SARS_CoV_2 D614G 75 80 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Three groups of six rhesus macaques were inoculated intranasally and intratracheally with a total dose of 2 x 106 median tissue culture infective dose (TCID50) of one of the following SARS-CoV-2 isolates: SARS-CoV-2/human/USA/RML-7/2020, containing the D614G substitution in spike; hCOV_19/England/204820464/2020, a B.1.1.7 isolate; and hCoV-19/USA/MD-HP01542/2021, a B.1.351 isolate. 2021 Science advances Result SARS_CoV_2 D614G 253 258 S 275 280 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. We determined the binding efficiency of D614G, B.1.1.7, and B.1.351 spikes to human and rhesus macaque ACE2 using a vesicular stomatitis virus (VSV) pseudotype entry assay and compared it to binding of the clade A prototype WA1 (nCOV-WA1-2020) spike. 2021 Science advances Result SARS_CoV_2 D614G 40 45 S;S 68;244 74;249 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. As part of this study, the following RT-PCR assays were evaluated for technical viability: E484K/Q, P681H/R, L452R, V1176F, del-Y144/145. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 E484K;E484Q;L452R;P681H;P681R;V1176F 91;91;109;100;100;116 98;98;114;107;107;122 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. L452R was the only assay to show a severe delay in CT and would require further optimization. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 L452R 0 5 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. The LoDs for individual targets were determined as follows: 182 IU/mL for L452R (95%CI: 1472-120 IU/mL), 144 IU/mL for P681R (95%CI: 197-91 IU/mL), and 79 IU/mL for E484Q (95%CI: 18.9-139 IU/mL) (Table 3). 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 E484Q;L452R;P681R 165;74;119 170;79;124 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. The only assay showing significant off-target activity was E484-WT with the E484K sequence, which was eliminated by setting an end-point fluorescence cut-off. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 E484K 76 81 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. After 30 s, this was 58.2 +- 28.7% for D614, 88.2 +- 4.6% for D614G, and 88 +- 1.3% for N501Y binding inhibition by T. 2021 Pharmaceuticals (Basel, Switzerland) Result SARS_CoV_2 D614G;N501Y 62;88 67;93 S 9 10 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. Also, in this setting, a mixture of spike mutants N501Y, K417N, and E484K was tested, and here again, T. 2021 Pharmaceuticals (Basel, Switzerland) Result SARS_CoV_2 E484K;K417N;N501Y 68;57;50 73;62;55 S 36 41 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. Cell treatment with equal amounts of spike D614 and its variants D614G and N501Y confirmed a stronger binding affinity of D614G (about 1.5-fold) and N501Y (about 3- to 4-fold) than D614 spike protein to the ACE2 surface receptor of HEK293 cells (Figure 4A). 2021 Pharmaceuticals (Basel, Switzerland) Result SARS_CoV_2 D614G;D614G;N501Y;N501Y 65;122;75;149 70;127;80;154 S;S 37;186 42;191 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. Extracts, incubated in human saliva for 30 min at 37 C before cell treatment had comparable effects on spike D614G inhibition (Figure 4H) indicating a good stability of the bioactive compounds in saliva. 2021 Pharmaceuticals (Basel, Switzerland) Result SARS_CoV_2 D614G 110 115 S 104 109 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. For this, we first incubated the cells with D614, D614G, or N501Y spike protein and subsequently with the extracts. 2021 Pharmaceuticals (Basel, Switzerland) Result SARS_CoV_2 D614G;N501Y 50;60 55;65 S 66 71 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. officinale extract and 56.1% +- 5.28 (D614) to 63.07% +- 14.55 (N501Y) for C. 2021 Pharmaceuticals (Basel, Switzerland) Result SARS_CoV_2 N501Y 64 69 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. officinale extract for D614 and D614G but somewhat lower for N501Y (Figure 4C,D). 2021 Pharmaceuticals (Basel, Switzerland) Result SARS_CoV_2 D614G;N501Y 32;61 37;66 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. officinale significantly blocked binding to D614G spike protein by about 40% (IC50 = 1.73 mg/mL). 2021 Pharmaceuticals (Basel, Switzerland) Result SARS_CoV_2 D614G 44 49 S 50 55 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. Upon extract pre-treatment, spike-binding inhibition to the cells was between 73.5% +- 5.2 (D614) to 86.3% +- 3.23 (N501Y) for T. 2021 Pharmaceuticals (Basel, Switzerland) Result SARS_CoV_2 N501Y 116 121 S 28 33 34683466 SARS-CoV-2 Evolution among Oncological Population: In-Depth Virological Analysis of a Clinical Cohort. All samples had the D614G mutation in the spike region, corresponding to the variant circulating in Europe during the first period of the pandemic. 2021 Microorganisms Result SARS_CoV_2 D614G 20 25 S 42 47 34683466 SARS-CoV-2 Evolution among Oncological Population: In-Depth Virological Analysis of a Clinical Cohort. Furthermore, only three minority variants were identified: none in patient #3, two in patient #4 at the nucleotide positions 15324 (ORF1ab region) and 29685 (untranslated region) in both the upper and lower respiratory samples (i.e., 4a and 4b, respectively) and one in patient #5 at the nucleotide position 26333 (T30I in the E gene) in both the upper and lower respiratory samples. 2021 Microorganisms Result SARS_CoV_2 T30I 315 319 ORF1ab;E 132;327 138;328 34683466 SARS-CoV-2 Evolution among Oncological Population: In-Depth Virological Analysis of a Clinical Cohort. Similarly, compared to the reference sequence MN908947, all samples had nucleotide mutations at positions 241 (untranslated region) and 3037 (ORF1ab region) and the amino acid change P4715L in the ORF1ab region (nucleotide position 14408). 2021 Microorganisms Result SARS_CoV_2 P4715L 183 189 ORF1ab;ORF1ab 142;197 148;203 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. A decrease in molecular flexibility was detected in MTs D75E Nsp1 and H110Y (Figure 3), where the blue regions indicate a rigidification and red represents a gain in flexibility. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D75E;H110Y 56;70 60;75 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. For the R24C mutant Nsp1, flexibility was altered in the region containing aa residues E65, L64, Q63, P62, C24, D16, and V14. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 R24C 8 12 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. Most of these MTs seem to exert a destabilizing effect, except V121I, V121W, and L122I, present at very low frequencies. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 L122I;V121I;V121W 81;63;70 86;68;75 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. Similarly, in MT D48G Nsp1, a gain in molecular flexibility was detected at aa residues S40, R43, Q44, K47, and G48. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D48G 17 21 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. The most common mutation (R24C), present at the N-terminal end, exhibited a destabilizing effect. 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 R24C 26 30 N 48 49 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. The most common mutation was R24C (n = 1122), followed by D75E (n = 890), D48G (n = 881), H110Y (n = 860), and D144A (n = 648) (Table 1). 2021 Pathogens (Basel, Switzerland) Result SARS_CoV_2 D144A;D48G;D75E;H110Y;R24C 111;74;58;90;29 116;78;62;95;33 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. c) Immunocytochemical analysis showed Lenti-S D614G increasing protein level of IL-6 (in red). 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result SARS_CoV_2 D614G 46 51 S 44 45 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. Fibrin surface coverage for Lipo-S was 9.53% +- 1.46% (**p < 0.01 vs control, n = 4), similarly to the Lenti-S variant D614G which also promoted significant fibrin deposition surface coverage at 9.56% +- 3.23% (**p < 0.01 vs control, n = 4) (Figure 2a,b). 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result SARS_CoV_2 D614G 119 124 S;S 33;109 34;110 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. Furthermore, anti-IL-6 staining was prominent in Lenti-S D614G transduced HAECs (Figure 3c). 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result SARS_CoV_2 D614G 57 62 S 55 56 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. Lenti-S D614G exposure upregulated cytokines (e.g., TNF-alpha, IL-6, and IL-15) and chemokines (e.g., MCP1), together with aberrantly elevated level of endothelial markers, such as vWF (*p < 0.05 vs control, n = 3) potentially through overexpression of Toll-like receptors (Figure 3b). 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result SARS_CoV_2 D614G 8 13 S 6 7 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. We further quantified cytokine gene expression in response to Lenti-S D614G. 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Result SARS_CoV_2 D614G 70 75 S 68 69 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. In addition, we included a viral isolate representing Alpha+E484K, Beta, Delta as well as a subvariant of Lambda in our experiments. 2021 EBioMedicine Result SARS_CoV_2 E484K 60 65 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. Sera from participants who were naive prior to vaccination (N=20, 8 viruses) neutralized WT WA1/USA (GMT: 356) and Iota (parental, GMT: 289, P: not significant) to comparable levels followed by - in decreasing order - Iota+E484K (GMT: 233, P: 0.0019), Gamma (GMT: 120, P: 0.0004), Iota+S477N (GMT: 197, P: 0.0009), Alpha+484K (GMT: 99, P: 0.0001), Beta (GMT: 91, P: < 0.0001) and Lambda subvariant (GMT: 84, P: < 0.0001). 2021 EBioMedicine Result SARS_CoV_2 E484K;S477N 223;286 228;291 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. The Alpha+E484K (GMT: 169, 3.4-fold, P < 0.01), the Beta variant (GMT: 160, 3.6-fold, P < 0.01) and the Lambda subvariant (GMT: 145, 4.0-fold, P < 0.01. 2021 EBioMedicine Result SARS_CoV_2 E484K 10 15 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. The Lambda subvariant (PV29369) contained additional changes compared to the consensus Lambda sequence including a 13 amino acid deletion eliminating the NTD substitutions G75V and T76I and an additional E471Q substitution in the RBD. 2021 EBioMedicine Result SARS_CoV_2 E471Q;G75V;T76I 204;172;181 209;176;185 RBD 230 233 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. There was no statistically significant difference in neutralization activity between the WA1/USA wild type isolate (GMT: 576), the ancestral Iota variant (no mutation in RBD, GMT: 478, 1.2-fold reduction) and the Iota variant with the E484K substitution (GMT: 375, 1.5-fold reduction). 2021 EBioMedicine Result SARS_CoV_2 E484K 235 240 RBD 170 173 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. There was, however, a small but statistically significant reduction in neutralization activity against the Iota variant with the S477N substitution (GMT: 298, 1.9-fold reduction; P < 0.5) and the Delta (GMT: 218, 2.6-fold, P < 0.01). 2021 EBioMedicine Result SARS_CoV_2 S477N 129 134 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. These isolates represent the three sublineages found in the NYC variants of interest: Iota (no change in RBD), Iota+E484K, Iota+S477N. 2021 EBioMedicine Result SARS_CoV_2 E484K;S477N 116;128 121;133 RBD 105 108 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. ADCC assays performed with the Beta and Delta variants showed no significant loss in activity when compared to D614G in the vaccine-only group (Figure 3B) or in individuals with prior infection (Figures 3B and 3C), demonstrating cross-reactive ADCC responses to VOCs. 2021 Cell host & microbe Result SARS_CoV_2 D614G 111 116 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. By using a SARS-CoV-2 pseudovirus assay with the D614G spike, we tested neutralizing antibodies elicited by vaccination alone. 2021 Cell host & microbe Result SARS_CoV_2 D614G 49 54 S 55 60 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. For HCWs infected in the first wave, although neutralization of Beta and Delta was maintained, titers were significantly lower for both VOCs (a reduction in GMT from 2,798 to 606 and 443, respectively, compared to those for D614G). 2021 Cell host & microbe Result SARS_CoV_2 D614G 224 229 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. However, responses to D614G elicited by vaccination alone (GMT: 39) were similar to those elicited by infection (GMT: 86 for first wave and 54 for second wave) (Figure 3A; Figure S2B). 2021 Cell host & microbe Result SARS_CoV_2 D614G 22 27 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. In all HCWs, regardless of prior infection, spike-specific binding antibodies were cross-reactive, with no significant difference in binding between the D614G and Beta spike (Figure 1C). 2021 Cell host & microbe Result SARS_CoV_2 D614G 153 158 S;S 44;168 49;173 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. In both groups with prior infection, we observed a significant boost in neutralization after vaccination against D614G and Beta (Figure 2 A; Figure S2A). 2021 Cell host & microbe Result SARS_CoV_2 D614G 113 118 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. In contrast, plasma from those infected in the second wave with Beta showed no significant difference in neutralization of D614G (GMT: 1157) but 6-fold lower neutralization of Delta (GMT: 200, p < 0.001) (Figures 2B and 2C). 2021 Cell host & microbe Result SARS_CoV_2 D614G 123 128 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. In previously infected individuals, post-vaccination responses after both waves were significantly higher against D614G, Beta, and Delta (Figure 3 A; Figure S2B), closely mirroring the fold increases of spike binding titers (Figure 1B). 2021 Cell host & microbe Result SARS_CoV_2 D614G 114 119 S 203 208 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. South Africa experienced a first wave of infections in mid-2020, dominated by the ancestral SARS-CoV-2 D614G variant. 2021 Cell host & microbe Result SARS_CoV_2 D614G 103 108 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. To determine cross-reactivity of neutralizing antibodies, we compared neutralization of D614G with Beta and Delta. 2021 Cell host & microbe Result SARS_CoV_2 D614G 88 93 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. We measured the ability of plasma antibodies to cross-link FcgammaRIIIa (CD16)-expressing cells and cell surface D614G, Beta, or Delta spikes on target cells, as a surrogate for ADCC. 2021 Cell host & microbe Result SARS_CoV_2 D614G 113 118 S 135 141 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. We tested pre- and post-vaccination plasma for immunoglobulin (Ig)G binding antibodies to the ancestral D614G spike. 2021 Cell host & microbe Result SARS_CoV_2 D614G 104 109 S 110 115 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. Notably, nine mutations in the Spike region (S: L452R, S:C480R, S: E484Q, S: D614G, S: P681R, S: N801, S: D950N, S: Q1071H, S: P1140) were observed in this study (Table 1, Supplementary Table 2). 2022 The Science of the total environment Result SARS_CoV_2 D614G;D950N;E484Q;L452R;P681R;Q1071H;C480R 77;106;67;48;87;116;57 82;111;72;53;92;122;62 S;S;S;S;S;S;S;S;S;S 31;45;55;64;74;84;94;103;113;124 36;46;56;65;75;85;95;104;114;125 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. The March-2021 samples showed L452R and E484Q mutations, while these mutations were absent in the sample collected from December-2020 to February-2021 (WWP). 2022 The Science of the total environment Result SARS_CoV_2 E484Q;L452R 40;30 45;35 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. These mutations are as follows: 23964 AT>A (S: N801del), 4369 TG > T (NSP3:L550), 18,875C > T (NSP14:C279F), 16,852/16853 GG > TT (NSP15:C206F), 23,000 T > C (S:C480R). 2022 The Science of the total environment Result SARS_CoV_2 T23000C;A23964A;T23964A;N801del;C875T;C206F;C279F;C480R 145;32;32;47;85;137;101;161 157;42;42;54;93;142;106;166 Nsp3;S;S 70;44;159 74;45;160 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. 1e-g), suggesting the K417N/T and E484K mutation in the RBD of these variants might further facilitate mouse adaptation in addition to the N501Y substitution. 2021 EBioMedicine Result SARS_CoV_2 E484K;K417N;K417T;N501Y 34;22;22;139 39;29;29;144 RBD 56 59 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. In parallel with the surge of B.1.1.7, the N501Y mutation in spike, which is one of the B.1.1.7-defining mutations, has emerged as the most predominant spike mutation since late 2020. 2021 EBioMedicine Result SARS_CoV_2 N501Y 43 48 S;S 61;152 66;157 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. In stark contrast, B.1.1.7, B.1.351, and P.3, which carry N501Y, efficiently infected and replicated in mACE2- or rACE2-expressing BHK21 cells. 2021 EBioMedicine Result SARS_CoV_2 N501Y 58 63 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Next, we evaluated the capacity of SARS-CoV-2 N501Y variants. 2021 EBioMedicine Result SARS_CoV_2 N501Y 46 51 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Our current findings reveal that B.1.1.7 and other N501Y-carrying variants can naturally infect mice, which may serve as a new animal model for SARS-CoV-2 infection that does not require prior virus adaptation or introduction of human ACE2 to the mice. 2021 EBioMedicine Result SARS_CoV_2 N501Y 51 56 COVID-19 144 164 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Our results demonstrated that BHK21 cells with mACE2 or rACE2 overexpression were permissive to the entry of SARS-CoV-2-N501Y-spike pseudoviruses, but not SARS-CoV-2-WT-spike pseudoviruses. 2021 EBioMedicine Result SARS_CoV_2 N501Y 120 125 S;S 126;169 131;174 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Our results showed that permissibility to mouse cells was not due to the D614G mutation as B.1 did not replicate in the nasal turbinate and lung of the inoculated mice. 2021 EBioMedicine Result SARS_CoV_2 D614G 73 78 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Overall, pseudovirus entry to both mACE2 and rACE2 was enabled by full-length spike of Alpha, Beta, and Gamma variants that carried the N501Y mutation. 2021 EBioMedicine Result SARS_CoV_2 N501Y 136 141 S 78 83 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. SARS-CoV-2 N501Y-carrying variants efficiently infect mice. 2021 EBioMedicine Result SARS_CoV_2 N501Y 11 16 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Since B.1.1.7, B.1.351, and P.3 all shares both the D614G and N501Y mutation in spike, we included B.1 as a control virus, which carries the D614G but not the N501Y mutation, to exclude the possibility that D614G conferred infectivity to mice. 2021 EBioMedicine Result SARS_CoV_2 D614G;D614G;D614G;N501Y;N501Y 52;141;207;62;159 57;146;212;67;164 S 80 85 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. The SARS-CoV-2 N501Y-carrying variants gained the capability to utilize mouse and rat ACE2 in mediating virus entry. 2021 EBioMedicine Result SARS_CoV_2 N501Y 15 20 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. This is associated with critical public health importance since N501Y has been implicated in an increased recognition of mouse ACE2, hinting that the naturally-emerging N501Y-carrying SARS-CoV-2 variants, including B.1.1.7, B.1.351, P.1, and P.3, may have evolved to infect rodents. 2021 EBioMedicine Result SARS_CoV_2 N501Y;N501Y 64;169 69;174 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. To directly address the question of whether these emerging SARS-CoV-2 variants have evolved to gain the capacity to cross species barrier to murine species, we intranasally challenged 6- to 8-week-old C57B6 mice (Mus musculus) with WT SARS-CoV-2, B.1.1.7, or other N501Y-carrying variants and collected tissues for virological and histological assessment. 2021 EBioMedicine Result SARS_CoV_2 N501Y 265 270 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. To further confirm the N501Y mutation was sufficient to mediate virus entry to murine cells, we generated pseudovirus expressing spike with the single N501Y amino acid substitution. 2021 EBioMedicine Result SARS_CoV_2 N501Y;N501Y 23;151 28;156 S 129 134 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Together, these findings indicate that the SARS-CoV-2 variant B.1.1.7 and other N501Y-carrying variants can infect mice with robust virus shedding from the nasal turbinate. 2021 EBioMedicine Result SARS_CoV_2 N501Y 80 85 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Together, these findings suggest that the recently emerged N501Y-carrying SARS-CoV-2 variants, including B.1.1.7, B.1.351, P.1, and P.3, can utilize murine ACE2 as entry receptor and may infect murine species without the need of further adaptation. 2021 EBioMedicine Result SARS_CoV_2 N501Y 59 64 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Wildtype SARS-CoV-2 HKU001a from lineage A (SARS-CoV-2 WT) and two other lineage B variants, B.1 and B.1.617.2, which do not carry the N501Y mutation, were included as controls. 2021 EBioMedicine Result SARS_CoV_2 N501Y 135 140 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. Additionally, six of these 22 sites were led by C-to-U transition (R134N in nsp10, A394V in nsp14, A222V and H1101D/Y in S, and P13T and T135I in N). 2021 Frontiers in microbiology Result SARS_CoV_2 A222V;A394V;H1101D;H1101Y;P13T;T135I;R134N 99;83;109;109;128;137;67 104;88;117;117;132;142;72 N;S 146;121 147;122 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. Besides the five aa substitutions (T26I, K478N, T643I, G671S, and V675) described above with occurrence frequencies >1% in the RdRp, there were other two sites (G228S and I244V) with frequencies <1% but detected in more than four sequences. 2021 Frontiers in microbiology Result SARS_CoV_2 G671S;I244V;K478N;T643I;G228S;T26I 55;171;41;48;161;35 60;176;46;53;166;39 RdRP 127 131 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. Eighteen nt sites with mutation frequency >60% were identified, of which 11 were located in the structural protein-coding regions and eight within the S gene (C56G, T284C, C333T, G425A, A460G, C1433A, C1450G, and G2848A). 2021 Frontiers in microbiology Result SARS_CoV_2 A460G;C1433A;C1450G;C333T;G2848A;G425A;T284C;C56G 186;193;201;172;213;179;165;159 191;199;207;177;219;184;170;163 S 151 152 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. Of these eight mutated sites, seven were non-synonymous mutations (T19R, I95T, G142D, K154E, T478K, Q484E, and D950N), and one was a synonymous mutation (D333). 2021 Frontiers in microbiology Result SARS_CoV_2 D950N;G142D;I95T;K154E;Q484E;T478K;T19R 111;79;73;86;100;93;67 116;84;77;91;105;98;71 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. The aa substitutions with occurrence frequencies >1% were V382L, T478K, and E484Q in the RBD of the S protein (S-RBD). 2021 Frontiers in microbiology Result SARS_CoV_2 E484Q;T478K;V382L 76;65;58 81;70;63 RBD;RBD;S;S 89;113;100;111 92;116;101;112 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. The RNA-dependent RNA polymerase (RdRp), nsp12, contained 5 aa substitutions with an occurrence frequency of over 1%: T26I, K478N, T643I, G671S, and V675I, of which G671S had the highest frequency (67.8%) (Figure 2B). 2021 Frontiers in microbiology Result SARS_CoV_2 G671S;G671S;K478N;T26I;T643I;V675I 138;165;124;118;131;149 143;170;129;122;136;154 RdRp;Nsp12;RdRP 4;41;34 32;46;38 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. Three large individual nodes (I, II, and III) were evolved from H10, of which nodes I and II differed from H10 via the U333C (synonymous mutation), C3301G/T (H1101D) and U284C (I95T), and T333C mutations; while node III differed from H10 via the C56G (T19R), C1433A (T478K), and C1450G (Q484E) mutations. 2021 Frontiers in microbiology Result SARS_CoV_2 C1433A;C1450G;C3301G;C3301T;C56G;T333C;H1101D;I95T;Q484E;T19R;T478K 259;279;148;148;246;188;158;177;287;252;267 265;285;156;156;250;193;164;181;292;256;272 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. We found that the B.1.617 viruses and H1 were distinguished by four non-synonymous mutations: U1355G (L452R), G1450C (E484Q), A1841G (D614G), and C2042G (P681R). 2021 Frontiers in microbiology Result SARS_CoV_2 A1841G;C2042G;G1450C;D614G;E484Q;L452R;P681R 126;146;110;134;118;102;154 132;152;116;139;123;107;159 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. At the same time, the E484K and N501Y RBD still caused a significant decrease in the median inhibitory potency of fully vaccinated sera (1.7-fold and 1.3-fold decrease respectively) (p < 0.0001 for both). 2021 Frontiers in immunology Result SARS_CoV_2 E484K;N501Y 22;32 27;37 RBD 38 41 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. Both the E484K and N501Y alone and as part of the N_K_Y and T_K_Y significantly impaired the antibody-mediated inhibition (p < 0.0001 for all), ranging from a 1.5-fold decrease for the N501Y alone, to a 2.39-fold for the combined T_K_Y (medians 51.33 wt, 32.26 E484K, 34.2 N501Y, 23.71 N_K_Y, 21.45 T_K_Y). 2021 Frontiers in immunology Result SARS_CoV_2 E484K;E484K;N501Y;N501Y;N501Y 9;261;19;185;273 14;266;24;190;278 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. The E484K and N501Y Mutations Enhance the Evasion Capacity of B.1.351 and P.1 Against Natural-Induced Antibody-Mediated Immunity. 2021 Frontiers in immunology Result SARS_CoV_2 E484K;N501Y 4;14 9;19 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. The E484K Is the Major Determinant of the Evasion Capacity of the RBD Variants Against Vaccine-Induced Antibodies. 2021 Frontiers in immunology Result SARS_CoV_2 E484K 4 9 RBD 66 69 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. The E484K mutant had moderate effects on a mAb from cluster 1 (1.79-fold inhibition reduction) and N501Y on mAbs from clusters 3 and 3 (reductions ranging from 1.64- to 2.23-fold) ( Figures 4C, D ). 2021 Frontiers in immunology Result SARS_CoV_2 E484K;N501Y 4;99 9;104 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. The E484K variant provides a slight gain in affinity (KD = 15.6 vs 23.9 nM), association rates (4.33x105 vs 3.15x105 M-1s-1), and dissociation rates (6.77x10-3 vs 7.55x10-3 s-1) compared to the wt ( Figure 2D ), whereas the N501Y variant results in a ten-fold affinity increase (KD = 2.26 nM, ka = 5.58x105 M-1s-1, kdis = 1.26x10-3 s-1). 2021 Frontiers in immunology Result SARS_CoV_2 E484K;N501Y 4;224 9;229 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. The effect of the N_K_Y and T_K_Y ranged from 1.6- to 1.8-fold inhibition potency decrease (p < 0.0001 for both), comparable to that of E484K alone. 2021 Frontiers in immunology Result SARS_CoV_2 E484K 136 141 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. The K417N ( Figure 4A ) and K417T mutants ( Figure 4B ) had no noticeable effect. 2021 Frontiers in immunology Result SARS_CoV_2 K417N;K417T 4;28 9;33 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. The K417N:but not the K417T:appeared to be inhibited better than the wt. 2021 Frontiers in immunology Result SARS_CoV_2 K417N;K417T 4;22 9;27 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. The N501Y had a very minor effect:if at all:on the Ti (-0.1 C). 2021 Frontiers in immunology Result SARS_CoV_2 N501Y 4 9 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. These combined and opposed effects are evidenced when analyzing the response curves of the B.1.351 RBD (N_K_Y) and P.1 RBD (T_K_Y) ( Figures 2F, G ), with binding parameters found between the ones of the RBD wt and N501Y: KDN_K_Y = 7.81 nM, KDT_K_Y = 5.64 nM, respectively. 2021 Frontiers in immunology Result SARS_CoV_2 N501Y 215 220 RBD;RBD;RBD 99;119;204 102;122;207 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. We observed a 1.9- and 1.5-fold reduction in the median inhibition of the E484K and N501Y RBD compared to the wt, while the substitutions in the 417 position had puzzlingly opposite effects with apparent 1.4- and 1.2-fold inhibition gain for K417N and K417T, respectively (Friedman test p < 0.0001 for all). 2021 Frontiers in immunology Result SARS_CoV_2 E484K;K417N;K417T;N501Y 74;242;252;84 79;247;257;89 RBD 90 93 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. When comparing the inflection temperatures (Ti) of the single RBD mutations with their wt counterpart, we observed a destabilizing effect for the E484K, and K417N mutations (-1.9 and -0.6 C respectively), and a stabilizing effect for the K417T (+2.9 C). 2021 Frontiers in immunology Result SARS_CoV_2 E484K;K417N;K417T 146;157;238 151;162;243 RBD 62 65 34695371 Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data. 151 (97%) of 156 samples contained the Asp614Gly mutation. 2021 The Lancet. Global health Result SARS_CoV_2 D614G 39 48 34695371 Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data. The branch leading to this cluster was estimated to contain five SNPs, including the replacements Phe35Ser in open reading frame (ORF)10, Lys1895Asn in ORF1A, and Lys2557Arg in ORF1B. 2021 The Lancet. Global health Result SARS_CoV_2 K1895N;K2557R;F35S 138;163;98 148;173;106 ORF1a 152 157 34695371 Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data. We established the distribution and frequency of the Asp614Gly variant in SARS-CoV-2 genomes from Zimbabwe. 2021 The Lancet. Global health Result SARS_CoV_2 D614G 53 62 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. Aside from this synonymous mutation, all C2 sequences carried other five mutations: C3037T, C14408T, C18877T, A23403G, and C25563T. 2021 Genomics, proteomics & bioinformatics Result SARS_CoV_2 A23403G;C14408T;C18877T;C25563T;C3037T 110;92;101;123;84 117;99;108;130;90 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. C3 is characterized by two nucleotide substitutions (C4002T and C13536T) in the ORF1ab gene, and the former causes an amino acid change T1246I. 2021 Genomics, proteomics & bioinformatics Result SARS_CoV_2 C13536T;T1246I;C4002T 64;136;53 71;142;59 ORF1ab 80 86 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. Cluster 2 (C2), assigned as the B.1 and B.1.36 lineages, has 24 sequences which are characterized by a synonymous nucleotide substitution (C26735T) in the M gene. 2021 Genomics, proteomics & bioinformatics Result SARS_CoV_2 C26735T 139 146 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. Consistent with the global trend, a high frequency of the viruses (140, 93.33%) harbored the D614G amino acid change (conferred by a SNP at nucleotide 23403) in the spike protein. 2021 Genomics, proteomics & bioinformatics Result SARS_CoV_2 D614G 93 98 S 165 170 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. Fourthly, nearly all C1 sequences carried the common signature nucleotide mutations (C2416T, C3037T, G8371T, C14408T, A23403G, and G25563T), which form a specific haplotype, and these descendent sequences are mainly Pakistan-specific, forming at least 2-5 transmission chains, indicating that viruses in C1 were mutated and widely transmitted in Pakistan. 2021 Genomics, proteomics & bioinformatics Result SARS_CoV_2 A23403G;C14408T;C3037T;G25563T;G8371T;C2416T 118;109;93;131;101;85 125;116;99;138;107;91 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. The descendant sequences were spread in more than 10 countries by adding two additional mutation sites (G11083T and C23929T), including 2 Pakistani samples (E108 and E118) collected in the middle of April, 2020. 2021 Genomics, proteomics & bioinformatics Result SARS_CoV_2 C23929T;G11083T 116;104 123;111 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. The largest cluster (C1) includes 74 genomes sampled from March 16 to June 2, 2020, and is characterized by a nucleotide substitution G8371T in ORF1ab, causing an amino acid change of Q2702H in ORF1ab (Table 1 ). 2021 Genomics, proteomics & bioinformatics Result SARS_CoV_2 G8371T;Q2702H 134;184 140;190 ORF1ab;ORF1ab 144;194 150;200 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Additionally, mutations K417N, K417T, T470N, T478R, E484A, F490S and Q493K were observed. 2021 Viruses Result SARS_CoV_2 E484A;F490S;K417N;K417T;Q493K;T470N;T478R 52;59;24;31;69;38;45 57;64;29;36;74;43;50 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. All these mutations were observed only in sequences from the USA except for the K417T mutation, which was also found in a sequence from Italy. 2021 Viruses Result SARS_CoV_2 K417T 80 85 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. As mentioned before, E484K is one of the prime RBM mutations found in several SARS-CoV-2 variants, and mutations at E484 reduce the binding and neutralization by RBD targeting polyclonal plasma antibodies significantly (>10-fold). 2021 Viruses Result SARS_CoV_2 E484K 21 26 RBD 162 165 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. As mentioned before, the Q493R mutation alone confers significant resistance towards bamlanivimab, etesevimab, casirivimab and C144. 2021 Viruses Result SARS_CoV_2 Q493R 25 30 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. As mentioned earlier, L452R and T478K are signature mutations in the delta variant. 2021 Viruses Result SARS_CoV_2 L452R;T478K 22;32 27;37 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Comparing the two timelines, the prevalence of L452R increased by roughly 56.07, 49.01 and 11.78% points in Asia, the UK and USA, respectively. 2021 Viruses Result SARS_CoV_2 L452R 47 52 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Country-wise, V483A mutation was found only in the USA (63/300280 sequences) and the UK (11/178878 sequences). 2021 Viruses Result SARS_CoV_2 V483A 14 19 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. During the same period, on the other hand, the T415A mutation was confined within the USA (Table 5), and the prevalence almost doubled. 2021 Viruses Result SARS_CoV_2 T415A 47 52 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. During this period, N501Y, L452R and T478K mutations increased by 15.39, 23.06 and 26.75% points, respectively, while E484K, S477N, K417T and S494P mutations decreased by 1.35, 3.09, 0.37 and 0.88% points, respectively. 2021 Viruses Result SARS_CoV_2 E484K;K417T;L452R;N501Y;S477N;S494P;T478K 118;132;27;20;125;142;37 123;137;32;25;130;147;42 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. During this period, the prevalence of Q493R, Q493K, E484A and T470N increased by 0.004, 0.001, 0.003 and 0.001% points, respectively, while the prevalence of V483A and T415A decreased by 0.01 and 0.005% points, respectively. 2021 Viruses Result SARS_CoV_2 E484A;Q493K;Q493R;T415A;T470N;V483A 52;45;38;168;62;158 57;50;43;173;67;163 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. E484K is one of the prime RBM mutations found in many SARS-CoV-2 variants, namely alpha (UK), beta (South Africa), gamma (Brazil), theta (Philippines) and iota (New York, USA). 2021 Viruses Result SARS_CoV_2 E484K 0 5 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Finally, mutations T415A and Q493R were observed in T6 apart from the other mutations discussed above. 2021 Viruses Result SARS_CoV_2 Q493R;T415A 29;19 34;24 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Finally, N501Y is another prime RBM mutation found in many SARS-CoV-2 variants, namely alpha, beta, gamma and theta. 2021 Viruses Result SARS_CoV_2 N501Y 9 14 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Finally, until 29 May 2021, the F486I mutation was not identified in any of the sequences. 2021 Viruses Result SARS_CoV_2 F486I 32 37 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Further, we observed a considerable prevalence of other adaptive mutations in the RBD, namely L452R, T478K, E484K, S477N, K417T, N439K and S494P. 2021 Viruses Result SARS_CoV_2 E484K;K417T;L452R;N439K;S477N;S494P;T478K 108;122;94;129;115;139;101 113;127;99;134;120;144;106 RBD 82 85 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Globally, these mutations were less prevalent in the studied sequences with the V483A mutation having the highest prevalence (0.014%) (Figure 1D). 2021 Viruses Result SARS_CoV_2 V483A 80 85 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. However, in our study, the T478R mutation was identified only in two countries, namely the USA (119/300280 sequences) and the UK (12/178878 sequences). 2021 Viruses Result SARS_CoV_2 T478R 27 32 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. However, unlike the previous timeline, during this period, Q493R (0.011%) was found to be the dominant mutation followed by Q493K (0.007%), E484A (0.005%), V483A (0.004%), T470N (0.002%), T415A and F486I (Figure 2C). 2021 Viruses Result SARS_CoV_2 E484A;F486I;Q493K;Q493R;T415A;T470N;V483A 140;198;124;59;188;172;156 145;203;129;64;193;177;161 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. In conclusion, globally, we found a high prevalence of N501Y mutation in the RBD of the SARS-CoV-2 S protein using the available sequence data from the NCBI database up to 28 July 2021. 2021 Viruses Result SARS_CoV_2 N501Y 55 60 RBD;S 77;99 80;100 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. In our study, the highest prevalence of L452R was found in Nepal (8/11 sequences), followed by Romania (1/2 sequences). 2021 Viruses Result SARS_CoV_2 L452R 40 45 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. In our study, the highest prevalence of the K417N mutation was found in Finland (2/13 sequences), followed by the Philippines (8/71 sequences). 2021 Viruses Result SARS_CoV_2 K417N 44 49 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. In our study, the highest prevalence of the T478K mutation was in sequences from Nepal (7/11 sequences) followed by Morocco (1/14 sequences). 2021 Viruses Result SARS_CoV_2 T478K 44 49 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. In T2, nearly 0.76% of sequences from the USA carried the V483A mutation. 2021 Viruses Result SARS_CoV_2 V483A 58 63 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. In T3, mutations N439K, Y453F, S477N, V483A, E484K, E484Q, S494P and N501Y were observed. 2021 Viruses Result SARS_CoV_2 E484K;E484Q;N439K;N501Y;S477N;S494P;V483A;Y453F 45;52;17;69;31;59;38;24 50;57;22;74;36;64;43;29 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. In T4, apart from the mutations identified in T3, mutations R346K, L452Q, L452R and T478K were observed. 2021 Viruses Result SARS_CoV_2 L452Q;L452R;R346K;T478K 67;74;60;84 72;79;65;89 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. In T5, except for the L452Q mutation, all other mutations discussed above were observed. 2021 Viruses Result SARS_CoV_2 L452Q 22 27 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. In the case of the N439K mutation, studies have shown enhanced binding to the ACE2 receptor. 2021 Viruses Result SARS_CoV_2 N439K 19 24 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Irrespective of continents/countries, the prevalence of these adaptive mutations between 30 May 2021 and 28 July 2021 were found to have the following order in the global population: N501Y (56.61%) > L452R (29.8%) > T478K (28.54%) > E484K (3.97%) > S477N (1.65%) > K417T (1.45%). 2021 Viruses Result SARS_CoV_2 E484K;K417T;L452R;N501Y;S477N;T478K 233;265;200;183;249;216 238;270;205;188;254;221 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Irrespective of continents/countries, the prevalence of these adaptive mutations until 29 May 2021 was found to have the following order in the global population; N501Y (41.24%) > L452R (6.75%) > E484K (5.32%) > S477N (4.74%) > K417T (1.82%) > T478K (1.8%) > S494P (1.11%), while the rest of the mutations were found in less than 0.7% of the sequences, with Y453F being the least found (0.01%) (Figure 1C). 2021 Viruses Result SARS_CoV_2 E484K;K417T;L452R;N501Y;S477N;S494P;T478K;Y453F 196;228;180;163;212;259;244;358 201;233;185;168;217;264;249;363 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Like the N439K mutation, the S477N mutation has been shown to exhibit enhanced ACE2 receptor binding. 2021 Viruses Result SARS_CoV_2 N439K;S477N 9;29 14;34 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. On the continent/country-level, the highest prevalence of the L452R mutation was observed in Asia (57.90%), followed by the UK (49.1%) and the USA (23.34%) (Table 4), and the highest prevalence of the T478K mutation was again observed in Asia (50.59%) followed by the UK (48.63%) and the USA (18.64%) (Table 4). 2021 Viruses Result SARS_CoV_2 L452R;T478K 62;201 67;206 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. On the other hand, the highest prevalence of the K417T mutation was found in Uruguay (1/10 sequences) followed by Brazil (2/27 sequences). 2021 Viruses Result SARS_CoV_2 K417T 49 54 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Q493K and E484A mutations were found in only sequences from Switzerland, the UK, USA and Germany. 2021 Viruses Result SARS_CoV_2 E484A;Q493K 10;0 15;5 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Q493K/R mutations, although rare, were found to confer a very high resistance towards bamlanivimab, etesevimab, casirivimab, C121 and C144. 2021 Viruses Result SARS_CoV_2 Q493K;Q493R 0;0 7;7 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Similar to the V483A mutation, the T470N mutation was also found only in sequences from the USA (4/300280 sequences) and the UK (2/178878 sequences). 2021 Viruses Result SARS_CoV_2 T470N;V483A 35;15 40;20 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Similarly, the highest prevalence of the T478K mutation was observed in Uzbekistan (76%), followed by Bahrain (73.03%), India (61.36%) and Bangladesh (44.33%) (Supplementary Material). 2021 Viruses Result SARS_CoV_2 T478K 41 46 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Similarly, the prevalence of T478K increased roughly by 49.54, 48.62 and 15.57% points in Asia, the UK and USA, respectively. 2021 Viruses Result SARS_CoV_2 T478K 29 34 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. The E484A mutation was identified only in sequences from Hong Kong (1/339 sequences), the UK (3/178878 sequences) and the USA (4/300280 sequences). 2021 Viruses Result SARS_CoV_2 E484A 4 9 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. The E484K mutation was highly prevalent in Libya (28/34 sequences), followed by South Africa (2/3 sequences), while the E484Q mutation was highly prevalent in Nepal (1/11 sequences) followed by Bahrain (12/269 sequences). 2021 Viruses Result SARS_CoV_2 E484K;E484Q 4;120 9;125 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. The E484Q mutation, on the other hand, was identified along with the L452R mutation in the kappa variant. 2021 Viruses Result SARS_CoV_2 E484Q;L452R 4;69 9;74 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. The F486I mutation was not found in any of the studied sequences. 2021 Viruses Result SARS_CoV_2 F486I 4 9 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. The F490S mutation was earlier identified in a few sequences isolated in Peru and Chile. 2021 Viruses Result SARS_CoV_2 F490S 4 9 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. The K417N mutation was first identified in South Africa (beta variant), while the K417T mutation was first identified in Brazil (gamma variant). 2021 Viruses Result SARS_CoV_2 K417N;K417T 4;82 9;87 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. The K417N/T mutation has been shown to have impaired ACE2 binding. 2021 Viruses Result SARS_CoV_2 K417N;K417T 4;4 11;11 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. The L452R mutation was first identified in California, USA (epsilon variant), and as a double mutant with the E484Q mutation in sequences isolated from Maharashtra, India (kappa variant) (BBC News published on 25 March 2021), and also as a double mutant with the T478K mutation in sequences isolated from India (delta variant). 2021 Viruses Result SARS_CoV_2 E484Q;L452R;T478K 110;4;263 115;9;268 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. The Q493K mutation was identified in sequences from four countries, with the highest prevalence in Spain (1/1173 sequences) followed by the UK (13/178878 sequences), Switzerland (1/18234 sequences) and the USA (14/300280 sequences), while the Q493R mutation was identified in sequences from three countries with the highest prevalence in Italy (1/258 sequences) followed by the USA (25/300280 sequences) and the UK (11/178878 sequences). 2021 Viruses Result SARS_CoV_2 Q493K;Q493R 4;243 9;248 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. The rest of the mutations were found in less than 0.8% of the sequences with Y453F being the least found (0.004%) (Figure 2B). 2021 Viruses Result SARS_CoV_2 Y453F 77 82 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. The S494P mutation was earlier identified in sequences isolated from Santa Cruz County, USA. 2021 Viruses Result SARS_CoV_2 S494P 4 9 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. The T415A mutation was found only in sequences from three countries, namely Italy (2/258 sequences), the USA (21/300280 sequences) and the UK (2/178878 sequences). 2021 Viruses Result SARS_CoV_2 T415A 4 9 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. The T478K mutation, which is one of the signature mutations in the Indian variant (delta variant), was first identified in sequences isolated from Mexico and California, USA (B.1.1.519 lineage). 2021 Viruses Result SARS_CoV_2 T478K 4 9 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. The T478R mutation was originally isolated from travelers who travelled within countries in southern Africa. 2021 Viruses Result SARS_CoV_2 T478R 4 9 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. The V483A mutation was shown to resist bamlanivimab roughly 48-fold, while the E484A mutation was shown to resist C144 mAb greater than 100-fold. 2021 Viruses Result SARS_CoV_2 E484A;V483A 79;4 84;9 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. The Y453F mutation was originally identified in SARS-CoV-2 isolated from minks in Denmark. 2021 Viruses Result SARS_CoV_2 Y453F 4 9 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Though a reduction in the prevalence of E484K was observed globally, the prevalence of this mutation has increased by 2.09, 1.06, 0.45 and 5.13% points in Germany, Switzerland, the UK and USA, respectively, in the last 2 months (Figure 1 and Figure 2). 2021 Viruses Result SARS_CoV_2 E484K 40 45 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Unlike the previous timeline, V483A was additionally identified in sequences from Egypt and Germany. 2021 Viruses Result SARS_CoV_2 V483A 30 35 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Until 29 May 2021, the T470N mutation was identified only in sequences from the UK and USA. 2021 Viruses Result SARS_CoV_2 T470N 23 28 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. While N439K, Y453F, V483A, E484K, S494P and N501Y mutations were only observed in sequences from the USA (0.015%), Netherlands (33.33%), USA (0.21%), USA (0.01%), USA (0.04%) and Australia (0.99%), respectively, S477N and E484Q were identified in more than one country with the highest prevalence in Lebanon (25%) and India (0.44%), respectively. 2021 Viruses Result SARS_CoV_2 E484K;E484Q;N439K;N501Y;S477N;S494P;V483A;Y453F 27;222;6;44;212;34;20;13 32;227;11;49;217;39;25;18 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. While R346K and L452R mutations were observed only in sequences from Iraq with a prevalence of 7.41% and 1.85%, respectively, the other two mutations were observed only in sequences from the USA, with each having a prevalence of approximately 0.009%. 2021 Viruses Result SARS_CoV_2 L452R;R346K 16;6 21;11 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Within Asia, the highest prevalence of the L452R mutation was observed in Uzbekistan (92%) followed by India (75.65%), Bahrain (73.03%) and Myanmar (71.43%) (Supplementary Material). 2021 Viruses Result SARS_CoV_2 L452R 43 48 34696404 Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Worldwide, except for the V483A mutation, other mutations were found in <0.008% of the sequences: Q493R (0.007%) > Q493K (0.006%) > T415A (0.005%) > E484A (0.002%) > T470N (0.001%) (Figure 1D). 2021 Viruses Result SARS_CoV_2 E484A;Q493K;Q493R;T415A;T470N;V483A 149;115;98;132;166;26 154;120;103;137;171;31 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. Detection of N501Y+/K417N+ cases were rather occasional events on two separate days, accounting for 1.7% and 0.4% of weekly cases. 2021 Viruses Result SARS_CoV_2 N501Y;K417N 13;20 18;25 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. For all N501Y+ samples, we additionally analyzed the presence of the K417N (K417N+) and V1176F (V1176F+) mutations. 2021 Viruses Result SARS_CoV_2 K417N;N501Y;V1176F;K417N;V1176F 69;8;88;76;96 74;13;94;81;102 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. Mutation V1176F was not detected in any of the positive samples. 2021 Viruses Result SARS_CoV_2 V1176F 9 15 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. Of all viral strains detected, 787 (45.9%) carried the N501Y mutation (N501Y+), 615 samples (35.9%) tested negative for the N501Y (N501Y-) mutation and the N501Y melting curve analysis remained inconclusive for 312 samples (18.2%). 2021 Viruses Result SARS_CoV_2 N501Y;N501Y;N501Y;N501Y;N501Y 55;124;156;71;131 60;129;161;76;136 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. The relative weekly fraction of N501Y+ cases increased over the observed time period from minimum 24% to maximum 68% of samples that gave conclusive results in melting curve analysis (Figure 3). 2021 Viruses Result SARS_CoV_2 N501Y 32 37 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. We identified three samples that were positive for the K417N and the N501Y mutation (N501Y+/K417N+). 2021 Viruses Result SARS_CoV_2 K417N;N501Y;N501Y;K417N 55;69;85;92 60;74;90;97 34696495 High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses. Through our Nextstrain thread, it was observed that the clade for pangolin lineage B contains certain distant variants, including P4715L in ORF1ab, Q57H in ORF 3a, and S84L in ORF8 covarying with the D614G spike protein mutation, which were found to be the most prevalent in the early phase of the pandemic in the state of Georgia. 2021 Viruses Result SARS_CoV_2 D614G;P4715L;Q57H;S84L 200;130;148;168 205;136;152;172 ORF1ab;S;ORF8 140;206;176 146;211;180 34698407 SARS-CoV-2 variant with mutations in N gene affecting detection by widely used PCR primers. hCoV-19/Finland/FinD796H/2021 had a very uncommon combination of the S protein mutations, as only 0,04% (535/1204022) of complete genome sequences deposited to Gisaid at 23.4.2021 had a similar combination (S:T95I, S: 144del, S:E484K, S:D614G, S:P681H, and S:D796D&H). 2021 Journal of medical virology Result SARS_CoV_2 144del;D614G;D796D;E484K;P681H;T95I 218;237;259;228;246;209 224;242;264;233;251;213 S;S;S;S;S;S;S 69;207;215;226;235;244;257 70;208;216;227;236;245;258 34698407 SARS-CoV-2 variant with mutations in N gene affecting detection by widely used PCR primers. In the N gene a cluster of three successive mutations (G28881A, G28882A, and G28883C) and a 3 bp deletion (CTA28896-28898---) causing deletion of one amino acid, were found (Figure 2). 2021 Journal of medical virology Result SARS_CoV_2 G28882A;G28883C;G28881A 64;77;55 71;84;62 N 7 8 34698407 SARS-CoV-2 variant with mutations in N gene affecting detection by widely used PCR primers. One nonsense mutation (GAA>TAA) was found later in ORF8 (G28209T). 2021 Journal of medical virology Result SARS_CoV_2 G28209T 57 64 ORF8 51 55 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. A proportion of 99% of those novel variants contained the S-D614G mutation together with another 7 +- 5 amino acid variations within the S protein. 2021 mBio Result SARS_CoV_2 D614G 60 65 S;S 58;137 59;138 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. A total of 139 unique S protein variants of beta (B.1.351) were clustered, with the majority carrying 7 consensus amino acid variations (D80A, D215G, K417N, E484K, N501Y, D614G, and A701V) and 1 deletion (amino acid 242). 2021 mBio Result SARS_CoV_2 A701V;D215G;D614G;E484K;K417N;N501Y;D80A 182;143;171;157;150;164;137 187;148;176;162;155;169;141 S 22 23 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. A total of 74 delta (B.1.617) S protein variants revealed from the 1,818 complete genomes were clustered into three sublineages, designated B.1.617.1 (represented by E154K), B.1.617.2 (T19R, T478K), and B.1.617.3 (T19R, T478). 2021 mBio Result SARS_CoV_2 E154K;T478K;T19R;T19R 166;191;185;214 171;196;189;218 S 30 31 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Among the amino acid mutations found in circulating SARS-CoV-2 variants, E484Q/K, P681H/R/L/S, P936Y/N/H, D950H/A/N, and D1118H/Y had a lower T cell immunogenicity than the prototype and S-D614G mutant (Table S1). 2021 mBio Result SARS_CoV_2 D1118H;D1118Y;D950A;D950H;D950N;E484K;E484Q;P681H;P681L;P681R;P681S;P936Y;P936H;P936N;D614G 121;121;106;106;106;73;73;82;82;82;82;95;95;95;189 129;129;115;115;115;80;80;93;93;93;93;104;104;104;194 S 187 188 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Among the artificial mutations, A222P/S, N439S, L452P, T478P/S/N, E484L/A/G/V/D, N501S/K, Q677K, P681A/T, T716S/P/K, P936Q, D950Y/Q, and D1118Q resulted in S protein variants with a lower T cell immunogenicity than the prototype and D614G mutant (Table 2). 2021 mBio Result SARS_CoV_2 A222P;A222S;D1118Q;D614G;D950Q;D950Y;E484V;E484A;E484D;E484G;E484L;L452P;N439S;N501K;N501S;P681A;P681T;P936Q;Q677K;T478N;T478P;T478S;T716K;T716P;T716S 32;32;137;233;124;124;66;66;66;66;66;48;41;81;81;97;97;117;90;55;55;55;106;106;106 39;39;143;238;131;131;79;79;79;79;79;53;46;88;88;104;104;122;95;64;64;64;115;115;115 S 156 157 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Among them, 4 S-D614G variants of concern (VOCs), namely, alpha (B.1.1.7), beta (B.1.351), gamma (P.1), and delta (B.1.617), emerging with multiple additional amino acid changes in the S1-RBD, have caused community outbreaks since the end of 2020 in different countries. 2021 mBio Result SARS_CoV_2 D614G 16 21 RBD;S 188;14 191;15 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. As D614G mutation achieved a stable mutation, we incorporated the artificial and D614G mutations and analyzed the impact of these amino acid changes to (i) S protein structure and (ii) T and B cell antigenicity. 2021 mBio Result SARS_CoV_2 D614G;D614G 3;81 8;86 S 156 157 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. As mentioned, an exception was observed with T478R/K + D614G or E484Q + D614G, in which these mutants resembled the prototype. 2021 mBio Result SARS_CoV_2 D614G;D614G;E484Q;T478K;T478R 55;72;64;45;45 60;77;69;52;52 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. At least 3,776 S protein variants belonging to alpha (B.1.1.7) variant lineage were identified, in which all contain 2 deletion events (amino acids 69 to 70 and 144) and 7 mutations (N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H). 2021 mBio Result SARS_CoV_2 A570D;D1118H;D614G;P681H;S982A;T716I;N501Y 190;229;197;204;218;211;183 195;235;202;209;223;216;188 S 15 16 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Between March and September 2020, a mean of 430 +- 152 S protein variants emerged per month, with 92% (2,766/3,008) of them containing an S-D614G mutation (614G). 2021 mBio Result SARS_CoV_2 D614G 140 145 S;S 55;138 56;139 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Collectively, our prediction models indicate that three yet-to-be-identified hypothetical mutations (N439S, T478S, and N501K) alter S protein structure coupled with increased binding affinity to hACE2 and lower immunogenicity. 2021 mBio Result SARS_CoV_2 N501K;T478S;N439S 119;108;101 124;113;106 S 132 133 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Compared to the prototype (NC_045512, 614D), numerous nonsynonymous mutations accumulated across the viral genome, with 97.3% of SARS-CoV-2 sequences containing S-D614G in the S protein. 2021 mBio Result SARS_CoV_2 D614G 163 168 S;S 161;176 162;177 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Dual mutants containing D614G and other amino acid changes, including those under positive selection or observed in VOCs (L5F, L18F, S98F, W152L/C, E154K, L222V, and A262S in S1-NTD; N439K, L452Q/R, S477N, L478R/K, E484K/Q, N501Y, and A570D within S1-RBD; Q677H/P and P681H/R in S1-CTD; T716I, S982A, and D1118H in S2) as well as commonly deleted residues (aa 69 to 70, 144, and 241 to 243) were further simulated for structure prediction. 2021 mBio Result SARS_CoV_2 A262S;A570D;D1118H;D614G;E154K;E484K;E484Q;L18F;L222V;L452Q;L452R;L478K;L478R;N439K;N501Y;P681H;P681R;Q677H;Q677P;S477N;S982A;S98F;T716I;W152C;W152L;L5F 166;235;305;24;148;215;215;127;155;190;190;206;206;183;224;268;268;256;256;199;294;133;287;139;139;122 171;240;311;29;153;222;222;131;160;197;197;213;213;188;229;275;275;263;263;204;299;137;292;146;146;125 RBD 251 254 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Fifty-four percent of sequenced beta (B.1.351) S genes also contained an L18F mutation. 2021 mBio Result SARS_CoV_2 L18F 73 77 S 47 48 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. For B cell epitope probability, S proteins featured in groups 1, 2, and 3 scored higher, except for the B.1 variant lineage (EPI_ISL_984896, group 2), which scored similar or higher than the prototype and D614G mutant. 2021 mBio Result SARS_CoV_2 D614G 205 210 S 32 33 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. For example, insertion of N439S, L452P, T478S, E484D, or N501K mutations into the existing alpha (B.1.1.7) S protein conferred a higher binding affinity to hACE2. 2021 mBio Result SARS_CoV_2 E484D;L452P;N439S;N501K;T478S 47;33;26;57;40 52;38;31;62;45 S 107 108 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. However, the S-D614G mutation reduced protein structure identity to the prototype by half (51%), altering its S1-RBD conformation primarily. 2021 mBio Result SARS_CoV_2 D614G 15 20 RBD;S 113;13 116;14 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. In addition, L5F, L18F, S98F, and K1191N were found in 2.6%, 1.2%, 1.3%, and 2.6% of alpha (B.1.1.7) S variant sequences, respectively. 2021 mBio Result SARS_CoV_2 K1191N;L18F;L5F;S98F 34;18;13;24 40;22;16;28 S 101 102 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. In addition, our results showed that beta (B.1.351) and alpha (B.1.1.7) variants bound stronger than S-D614G to hACE2, which is consistent with previous reports based on both in silico and in vitro studies. 2021 mBio Result SARS_CoV_2 D614G 103 108 S 101 102 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. In contrast, a number of amino acid changes were sublineage specific, such as ORF1a-T1567I in B.1.617.1, S-T478K in B.1.617.2, and ORF1a-A2344V in B.1.617.3, suggesting that independent transmissions of delta (B.1.617) ancestors in multiple communities have occurred in the early stage of the outbreak. 2021 mBio Result SARS_CoV_2 A2344V;T1567I;T478K 137;84;107 143;90;112 ORF1a;ORF1a;S 78;131;105 83;136;106 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Interestingly, delta (B.1.617) variant lineage was highly diversified across the viral genomes; only a couple of consensus amino acid variations were shared by all variants (e.g., P214L in ORF1b; L452R, D614G, and P681R in S protein; V82A in ORF7a; R203M and D377Y in N protein). 2021 mBio Result SARS_CoV_2 D377Y;D614G;L452R;P214L;P681R;R203M;V82A 259;203;196;180;214;249;234 264;208;201;185;219;254;238 ORF7a;N;S 242;268;223 247;269;224 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Interestingly, E484K was commonly observed in beta (B.1.351), gamma (P.1), P.2, and R.1, and E484Q in delta (B.1.617.1/3). 2021 mBio Result SARS_CoV_2 E484K;E484Q 15;93 20;98 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. L452R was highly specific to delta (B.1.617) but also found in other variant lineages (e.g., B.1.429). 2021 mBio Result SARS_CoV_2 L452R 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Meanwhile, incorporation of N439S artificial mutation into the existing mutations of gamma (P.1) and delta (B.1.617) also resulted in increased binding affinity to hACE2 than their respective natural mutants. 2021 mBio Result SARS_CoV_2 N439S 28 33 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Notably, we predicted that the presence of N493S, T478S, E484D, N501K, T716K, and D950Q mutations in SARS-CoV-2 variants could confer lower immunogenicity than the native variants. 2021 mBio Result SARS_CoV_2 D950Q;E484D;N493S;N501K;T478S;T716K 82;57;43;64;50;71 87;62;48;69;55;76 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. On the contrary, adding N439S and L452P or mutations into the existing EPI_ISL_712079 S protein led to a switch of structure featured in group 4 to group 3 (Table S2). 2021 mBio Result SARS_CoV_2 L452P;N439S 34;24 39;29 S 86 87 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. On the other hand, the presence of S477G in alpha (B.1.1.7), N439S, T478S, and N501K in beta (B.1.351), T478S, E484D, and N501K in gamma (P.1), and E484D in delta (B.1.617) resulted in S protein variants with a lower B cell epitope probability. 2021 mBio Result SARS_CoV_2 E484D;E484D;N439S;N501K;N501K;S477G;T478S;T478S 111;148;61;79;122;35;68;104 116;153;66;84;127;40;73;109 S 185 186 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Other than the S protein, the majority of beta (B.1.351) genomes had amino acid changes within ORF1a (T265I, K1655N, K3353R), ORF1b (P214L), ORF3a (Q57H, S171L), E (P71L), and N (T205I). 2021 mBio Result SARS_CoV_2 K1655N;K3353R;S171L;P214L;P71L;Q57H;T205I;T265I 109;117;154;133;165;148;179;102 115;123;159;138;169;152;184;107 ORF1a;ORF3a;E;N;S 95;141;162;176;15 100;146;163;177;16 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Our results showed that the binding energy of hACE2 with the prototype (NC_045512) and S-D614G mutant was -45.88 kcal/mol and -47.06 kcal/mol, respectively, while all the variants in groups 1 to 4 bound stronger to hACE2 than the prototype. 2021 mBio Result SARS_CoV_2 D614G 89 94 S 87 88 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Our S protein structure models revealed that all artificial D614G dual mutations containing amino acid changes in S1-NTD, S1-RBD, S1-CTD, or S2 shared a structure that resembled the S-D614G mutant. 2021 mBio Result SARS_CoV_2 D614G;D614G 60;184 65;189 RBD;S;S 125;4;182 128;5;183 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Overall, A222V had the highest ratio of nonsynonymous and synonymous site (dN/dS ratio) substitutions (FUBAR [fast, unconstrained Bayesian approximation] test, omega=37.06), with a GCT (A) to GTT (V) change at the second codon position commonly observed in B.1.177, followed by residues 5 (omega=28.91), 477 (omega=28.22), and 98 (omega=28.05). 2021 mBio Result SARS_CoV_2 A222V 9 14 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. S protein that did not carry D614G mutation was categorized into group 1, while the beta (B.1.351) variant that carried additional L18F mutation showed both its S1-NTD and S1-RBD unaligned to the prototype (group 3). 2021 mBio Result SARS_CoV_2 D614G;L18F 29;131 34;135 RBD;S 175;0 178;1 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. S proteins featured in group 4 had a lower B cell epitope probability than the prototype and D614G mutant. 2021 mBio Result SARS_CoV_2 D614G 93 98 S 0 1 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. S1 that contained L5V/H/P/R, L18V/I/H/R/P, S98/A/P/Y/C, A222P/T/S/G/D, K417E/Q/R/G/M, N439Y/I/S/T, T478A/S, E484G/V/D, N501I/E/D/K, T716S/P/A/R/K, D936R/A/Q, and D950R/Y/V/G/Q, S982T/P/L, and D1118R/G/A/Q artificial mutations resulted in S proteins with a lower B cell recognition ability than the respective native amino acids (Table 2, Table S1). 2021 mBio Result SARS_CoV_2 A222D;A222G;A222P;A222S;A222T;D1118A;D1118G;D1118Q;D1118R;D936A;D936Q;D936R;D950G;D950Q;D950R;D950V;D950Y;E484D;E484G;E484V;K417E;K417G;K417M;K417Q;K417R;L18V;L18H;L18I;L18P;L18R;L5H;L5P;L5R;L5V;N439I;N439S;N439T;N439Y;N501D;N501E;N501I;N501K;S982L;S982P;S982T;T478A;T478S;T716A;T716K;T716P;T716R;T716S 56;56;56;56;56;192;192;192;192;147;147;147;162;162;162;162;162;108;108;108;71;71;71;71;71;29;29;29;29;29;18;18;18;18;86;86;86;86;119;119;119;119;177;177;177;99;99;132;132;132;132;132 69;69;69;69;69;204;204;204;204;156;156;156;175;175;175;175;175;117;117;117;84;84;84;84;84;41;41;41;41;41;27;27;27;27;97;97;97;97;130;130;130;130;186;186;186;106;106;145;145;145;145;145 S 238 239 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Similarly, changes at residues 501 (N501Y in alpha, beta, and gamma; N501T in C.9) and 681 (P681H in alpha, B.1.1.519; P681R in delta; P618L in B.1.494) under positive selection were also found in several distantly related lineages, suggesting that these mutations have an adaptive benefit in host-virus interaction, probably driven by convergent evolution. 2021 mBio Result SARS_CoV_2 N501T;P618L;P681R;N501Y;P681H 69;135;119;36;92 74;140;124;41;97 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Similarly, S proteins of beta (B.1.351) variants with N439S or T478S insertion, or alteration of N501K to N501Y, resulted in a higher binding affinity to hACE2. 2021 mBio Result SARS_CoV_2 N439S;N501K;N501Y;T478S 54;97;106;63 59;102;111;68 S 11 12 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Strikingly, when N439S or T478S was simulated, or E484K mutation was replaced with E484D in the amino acid sequence of EPI_ISL_700450, its S protein structure featured in group 3 switched to group 4 (Table 3). 2021 mBio Result SARS_CoV_2 E484D;E484K;N439S;T478S 83;50;17;26 88;55;22;31 S 139 140 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. The presence of N439S, T478S, and N501K artificial mutations in all four VOCs led to a lower T cell immunogenicity than the respective natural variants. 2021 mBio Result SARS_CoV_2 N439S;N501K;T478S 16;34;23 21;39;28 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. The prototype had an overall T cell immunogenicity and B cell epitope probability score of 0.436 and 0.470, respectively, while the overall T and B cell immunogenicity scores of the D614G mutant were 0.387 and 0.470, respectively. 2021 mBio Result SARS_CoV_2 D614G 182 187 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. This lineage was characterized with a signature mutation, L452R, within S1-RBD. 2021 mBio Result SARS_CoV_2 L452R 58 63 RBD 75 78 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Twelve signature amino acid mutations (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F) were observed in the S protein as well as other consensus changes, including ORF1a (S1188L and K1795Q), ORF1b (P214L and E1164D), ORF3a (S253P), ORF8 (E92K), and N (P80R, R203K, and G204R), across the whole genome. 2021 mBio Result SARS_CoV_2 D138Y;D614G;E1164D;E484K;G204R;H655Y;K1795Q;K417T;N501Y;P26S;R190S;R203K;T1027I;T20N;V1176F;E92K;L18F;P214L;P80R;S1188L;S253P 57;92;247;78;308;99;221;71;85;51;64;297;106;45;118;277;39;237;291;210;263 62;97;253;83;313;104;227;76;90;55;69;302;112;49;124;281;43;242;295;216;268 ORF1a;ORF3a;ORF8;N;S 203;256;271;288;147 208;261;275;289;148 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. We focused on artificial mutations in S1-RBD (N439S, L452P, S477G, T478S, E484D, and N501K) that resulted in S protein conferring a lower antigenicity (Table 2) and predicted their protein conformation, hACE2 binding affinity, and antigenicity. 2021 mBio Result SARS_CoV_2 E484D;L452P;N501K;S477G;T478S;N439S 74;53;85;60;67;46 79;58;90;65;72;51 RBD;S 41;109 44;110 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. We superposed S protein models of alpha (B.1.1.7), beta (B.1.351), gamma (P.1), and delta (B.1.617) containing artificial amino acid mutations against the prototype and S-D614G mutant. 2021 mBio Result SARS_CoV_2 D614G 171 176 S;S 14;169 15;170 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. We then superposed the predicted S protein structure of a monomutant containing a D614G mutation. 2021 mBio Result SARS_CoV_2 D614G 82 87 S 33 34 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. When aligning the alpha (B.1.1.7) whole genomes against the prototype, at least 10 conserved amino acid variations within ORF1a (T1001I, A1708D, I2230T), ORF1b (P214L), ORF8 (R52I, Y73C), and N gene (D3L, R203K, G204R, S235F) were observed. 2021 mBio Result SARS_CoV_2 A1708D;G204R;I2230T;R203K;S235F;Y73C;D3L;P214L;R52I;T1001I 137;212;145;205;219;181;200;161;175;129 143;217;151;210;224;185;203;166;179;135 ORF1a;ORF8;N 122;169;192 127;173;193 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. When incorporating D614G in monomutants, we were intrigued to find that mutation of T478I + D614G or E484K + D614G resulted in mutants with protein structure like the S-D614G mutant, while other amino acid changes at the same residues, such as T478R/K + D614G or E484Q + D614G, were similar to the prototype. 2021 mBio Result SARS_CoV_2 D614G;D614G;D614G;D614G;D614G;E484K;E484Q;T478I;T478K;T478R;D614G 19;92;109;254;271;101;263;84;244;244;169 24;97;114;259;276;106;268;89;251;251;174 S 167 168 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. Ghanaian samples predominate in the branch associated with the C24370T mutation. 2021 Scientific reports Result SARS_CoV_2 C24370T 63 70 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. The branch at the bottom is directly associated with the first recorded sequences from Wuhan, China and does not carry the D614G amino acid substitution. 2021 Scientific reports Result SARS_CoV_2 D614G 123 128 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. The branch determined by the mutation G22486T (Supplementary Figure 1) may reflect migration routes because in the nextstrain analysis of the entire Africa there are also samples from Mali and Tunisia in this branch (https://nextstrain.org/ncov/africa?f_region=Africa, accessed August 14 2020). 2021 Scientific reports Result SARS_CoV_2 G22486T 38 45 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. The G-clades harbor the putatively more infective D614G amino acid substitution. 2021 Scientific reports Result SARS_CoV_2 D614G 50 55 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. The split of the tree by the A23403G (D614G) substitution into two major branches corresponds to the highest diversity found at that location. 2021 Scientific reports Result SARS_CoV_2 A23403G;D614G 29;38 36;43 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. The tree can be divided into two major branches resulting from the A23403G (D614G) substitution. 2021 Scientific reports Result SARS_CoV_2 A23403G;D614G 67;76 74;81 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. Two of the non-French-related Senegalese samples emanate from the C24370T and G22468T branches whilst the other (Senegal/136) has strong similarity with Spanish end-February samples from the early clade S (Supplementary Figure 2) pointing at multiple introductions to Senegal from France, Spain and African countries. 2021 Scientific reports Result SARS_CoV_2 C24370T;G22468T 66;78 73;85 S 203 204 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. Within the clade S, there are putatively specific West-African amino acid substitutions at the branches at C24370T and G22468T. 2021 Scientific reports Result SARS_CoV_2 C24370T;G22468T 107;119 114;126 S 17 18 34705425 Gold-Nanostar-Chitosan-Mediated Delivery of SARS-CoV-2 DNA Vaccine for Respiratory Mucosal Immunization: Development and Proof-of-Principle. At 1:10 serum dilution, the infectivity of both SC2-Wuhan pseudovirus and SC2 D614G mutant variant diminished to 38% +- 22% and 38% +- 5%, respectively, whereas for SC2-beta mutant variant, the infectivity dropped to only 67% +- 7%. 2021 ACS nano Result SARS_CoV_2 D614G 78 83 34705425 Gold-Nanostar-Chitosan-Mediated Delivery of SARS-CoV-2 DNA Vaccine for Respiratory Mucosal Immunization: Development and Proof-of-Principle. The IC50 infectivity inhibition concentrations were determined to be 1:83.8, 1:47.5, and 1:150 serum dilutions for SC2-Wuhan, SC2-beta mutant, and SC2-D614G mutant variants, respectively (Figure S1). 2021 ACS nano Result SARS_CoV_2 D614G 151 156 34705425 Gold-Nanostar-Chitosan-Mediated Delivery of SARS-CoV-2 DNA Vaccine for Respiratory Mucosal Immunization: Development and Proof-of-Principle. These trends were consistent across all three strains of pseudoviruses engineered for different variants of SC2 S proteins (i.e., SC2-Wuhan, SC2-beta mutant, and SC2-D614G mutant) with observable difference in inhibition at higher serum dilutions. 2021 ACS nano Result SARS_CoV_2 D614G 166 171 S 112 113 34705425 Gold-Nanostar-Chitosan-Mediated Delivery of SARS-CoV-2 DNA Vaccine for Respiratory Mucosal Immunization: Development and Proof-of-Principle. To evaluate S protein expression using pcDNA-SC2 plasmid (the DNA vaccine), we transfected HEK293T cells with different variants of SC2 plasmid (Wuhan, beta, and D614G) using AuNS with the optimal ratio, and the cell lysates were probed for expression of S protein using rabbit anti-SC2-spike antibody. 2021 ACS nano Result SARS_CoV_2 D614G 162 167 S;S;S 287;12;255 292;13;256 34705425 Gold-Nanostar-Chitosan-Mediated Delivery of SARS-CoV-2 DNA Vaccine for Respiratory Mucosal Immunization: Development and Proof-of-Principle. To investigate the efficacy of neutralizing antibodies generated in vaccinated mice against new emerging mutant variants of SC2, we evaluated the infectivity inhibition of vaccinated mice serum against the SC2 pseudovirus with the S protein of Wuhan strain, D614G mutant, and the South African variant (SC2-beta mutant). 2021 ACS nano Result SARS_CoV_2 D614G 258 263 S 231 232 34705425 Gold-Nanostar-Chitosan-Mediated Delivery of SARS-CoV-2 DNA Vaccine for Respiratory Mucosal Immunization: Development and Proof-of-Principle. With the consideration of such differences, it is possible that mutations in the RBD domain of Wuhan, beta, and D614G variants would be expected to induce minimal differences in antibodies, whereas this might not be the case in humans; this difference might account for some variations in immunity induced in humans against the mutant strains. 2021 ACS nano Result SARS_CoV_2 D614G 112 117 RBD 81 84 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. For the mutant R193T, there was no change in binding interactions but showed slightly lower binding affinity (-13.0 kcal/mol) compared with the wild-type complex. 2021 Bioinformatics and biology insights Result SARS_CoV_2 R193T 15 20 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. In addition, for the mutant R185W, the protein complex was found with the 37 charged-polar, 29 charged-apolar, 34 polar-apolar, and 17 apolar-apolar ICs, whereas the wild-type complex showed 40 charged-polar, 31 charged-apolar, 32 polar-apolar, and 15 apolar-apolar ICs. 2021 Bioinformatics and biology insights Result SARS_CoV_2 R185W 28 33 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. In case of mutants P681R and R683W, slight higher binding affinity (-13.5 kcl/mol) was observed along with the formation of new two hydrogen bonds between P681-D177 and P681-D228. 2021 Bioinformatics and biology insights Result SARS_CoV_2 P681R;R683W 19;29 24;34 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. Interestingly, the mutant R185W showed a slightly more binding affinity (-13.5 kcal/mol). 2021 Bioinformatics and biology insights Result SARS_CoV_2 R185W 26 31 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. Moreover, for the mutant R193T, the protein complex was found to have 39 charged-polar and 20 polar-polar ICs, whereas the wild-type complex showed 40 charged-polar and 19 polar-polar ICs. 2021 Bioinformatics and biology insights Result SARS_CoV_2 R193T 25 30 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. Moreover, the mutant G476S showed 7 polar-polar and 21 polar-apolar ICs, whereas the wild-type complex showed 5 polar-polar and 23 polar-apolar ICs. 2021 Bioinformatics and biology insights Result SARS_CoV_2 G476S 21 26 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. Moreover, the mutant Q493L showed 7 charged-polar and 24 charged-apolar ICs, whereas the wild-type complex showed 10 charged-polar and 20 charged-apolar ICs. 2021 Bioinformatics and biology insights Result SARS_CoV_2 Q493L 21 26 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. No significant change was found in binding energy as well as in interactions for the spike protein mutants P681L, P681H, P681S, P681T, R682W, R682Q, R682L, R683Q, R683P, R683L, A684E, A684P, A684T, A684S, A684V, R685C, R685G, and R685S. 2021 Bioinformatics and biology insights Result SARS_CoV_2 A684E;A684P;A684S;A684T;A684V;P681H;P681L;P681S;P681T;R682L;R682Q;R682W;R683L;R683P;R683Q;R685C;R685G;R685S 177;184;198;191;205;114;107;121;128;149;142;135;170;163;156;212;219;230 182;189;203;196;210;119;112;126;133;154;147;140;175;168;161;217;224;235 S 85 90 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. On the contrary, relatively higher binding energy (-12.9 kcal/mol) and absence of hydrogen bond between Q493 and E35 were observed for Q493L when compared with wild-type complex (Supplemental Figure S5). 2021 Bioinformatics and biology insights Result SARS_CoV_2 Q493L 135 140 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. Out of P812L, P812S, S813I, S813G, K814R, K814T, K814Q, K814E, K814M, K814N, K815S, K815M, K815K, and K815G mutants, only the P812S mutant of the spike protein revealed a significant change in binding affinity (-10.8 kcal/mol). 2021 Bioinformatics and biology insights Result SARS_CoV_2 K814E;K814M;K814N;K814Q;K814R;K814T;K815G;K815K;K815M;K815S;P812L;S813G;S813I 56;63;70;49;35;42;102;91;84;77;7;28;21 61;68;75;54;40;47;107;96;89;82;12;33;26 S 146 151 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. S19P variant of ACE2 showed relatively less binding affinity (-12.1 kcal/mol) compared with wild-type complex. 2021 Bioinformatics and biology insights Result SARS_CoV_2 S19P 0 4 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. The highest prominent change in binding energy was noticed for mutant S477I and that is -13.3 kcal/mol along with no alteration in intermolecular interactions (Figure 6). 2021 Bioinformatics and biology insights Result SARS_CoV_2 S477I 70 75 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. The most prominent alteration in binding energy was found for the mutant G476S with the binding energy of -11.7 kcal/mol. 2021 Bioinformatics and biology insights Result SARS_CoV_2 G476S 73 78 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. The R298W mutant of FURIN showed the same binding affinity and interaction as the wild type. 2021 Bioinformatics and biology insights Result SARS_CoV_2 R298W 4 9 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. We also analyzed the effect of 27 missense variants of SARS-CoV-2 spike protein (RBD) on the binding interaction of spike protein with ACE2 and observed that L452Q, T478K, L455F, F456L, S459F, A475V, N439K, L452R, T470N, E484D, E484A, E484K, E484Q, F486L, S494P, S494L, N501T, N501Y, F490L, F490S, S477N, S477T, E471D, and E471Q variants of the SARS-CoV-2 spike protein (RBD) showed almost similar interactions when compared with the wild-type complex along with having almost similar binding affinity (-12.5 kcal/mol). 2021 Bioinformatics and biology insights Result SARS_CoV_2 A475V;E471D;E471Q;E484A;E484D;E484K;E484Q;F456L;F486L;F490L;F490S;L452Q;L452R;L455F;N439K;N501T;N501Y;S459F;S477N;S477T;S494L;S494P;T470N;T478K 193;312;323;228;221;235;242;179;249;284;291;158;207;172;200;270;277;186;298;305;263;256;214;165 198;317;328;233;226;240;247;184;254;289;296;163;212;177;205;275;282;191;303;310;268;261;219;170 S;S;S;RBD;RBD 66;116;356;81;371 71;121;361;84;374 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. We analyzed the effect of seven missense variants of ACE2 on the binding interaction of ACE2 with SARS-CoV-2 spike protein (RBD) and observed that E35K, E37K, M82I, E329G, and D355N variants of ACE2 have no significant alteration in binding interaction. 2021 Bioinformatics and biology insights Result SARS_CoV_2 D355N;E329G;E35K;E37K;M82I 176;165;147;153;159 181;170;151;157;163 S;RBD 109;124 114;127 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. Whereas the mutant E230K also showed the same binding affinity, but hydrogen bond between R682-E230 and K933-E230 was missing when compared with the wild-type complex. 2021 Bioinformatics and biology insights Result SARS_CoV_2 E230K 19 24 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Cathepsins inhibitor E64d treatment absolutely inhibited the infection of WT, D614G, N501Y.V1 and N501Y.V2 RBD pseudoviruses into 293T-hACE2 cells ( Figure 5A and Supplementary Figures S4A, B ), indicating that CatB/L is the dominant proteases required for priming of SARS-CoV-2 S protein in TMPRSS2- cells. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G;N501Y;N501Y 78;85;98 83;90;103 RBD;S 107;281 110;282 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Compared with D614G, N501Y.V2 pseudovirus had significant difference in the infection efficiency of 293T-hACE2-TMPRSS2, Caco2 and Caco2-hACE2 cells. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G;N501Y 14;21 19;26 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Compared with WT pseudovirus, the viral infectivities of D614G and HV69-70 deletion were increased in all three cells. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G 57 62 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Compared with WT, pseudovirirus bearing S protein with D614G mutation (including D614G, N501Y.V1 and N501Y.V2 RBD) were significantly more infectious in several susceptible cells. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G;D614G;N501Y;N501Y 55;81;88;101 60;86;93;106 RBD;S 110;40 113;41 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Consistent with the previous study, all three inhibitors decreased the infection of WT, D614G N501Y.V1 and N501Y.V2 RBD pseudovirions in a dose-dependent manner ( Figures 5D-F and Supplementary Figures S4C, D ). 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G;N501Y;N501Y 88;94;107 93;99;112 RBD 116 119 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. For this, we first constructed S genes expression vectors of N501Y.V1 variant (with all nine mutations) and N501Y.V2 RBD mutations (K417N, E484K, N501Y and D614G) ( Figure 1A ). 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G;E484K;N501Y;N501Y;N501Y;K417N 156;139;61;108;146;132 161;144;66;113;151;137 RBD;S 117;31 120;32 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. However, compared with WT and D614G, the inhibition efficiency of these inhibitors on N501Y.V1 and N501Y.V2 RBD lineages has no significant difference ( Supplementary Figures S4C, D ). 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G;N501Y;N501Y 30;86;99 35;91;104 RBD 108 111 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. However, the infection efficiency of N501Y.V2 RBD pesudovirus is higher than N501Y.V2 in some susceptible cells. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 N501Y;N501Y 37;77 42;82 RBD 46 49 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. In addition, we detected the infection efficiency of SARS-CoV-2 WT, D614G, N501Y.V1 and N501Y.V2 RBD in target cells at 10 h, 14 h, 18 h, 24 h, and 36 h. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G;N501Y;N501Y 68;75;88 73;80;93 RBD 97 100 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. In addition, we detected the thermal stability of N501Y.V2 pseudovirus at 37 C and 42 C ( Supplementary Figures S3A - D ). 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 N501Y 50 55 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. In contrast, T716I, A570D, D118H and A701V mutations caused a modest reduction in viral infectivity. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 A570D;A701V;D118H;T716I 20;37;27;13 25;42;32;18 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. In order to study the effect of S mutations of N501Y.V1 and N501Y.V2 lineages on the stability of the virus, we measured the infectivity decay of pseudoviruses incorporated S protein of SARS, SARS-CoV-2 WT, D614G N501Y.V1 and N501Y.V2 RBD overtime at 37 C (normal body temperature) and 42 C (possible body temperature in fever). 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G;N501Y;N501Y;N501Y;N501Y 207;47;60;213;226 212;52;65;218;231 RBD;S;S 235;32;173 238;33;174 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Infectivity of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Lineages. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 N501Y;N501Y 35;48 40;53 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. It is worth noting that pseudovirions bearing S protein of N501Y.V1 and N501Y.V2 RBD variants retained higher infectivity than WT and D614G at any temperature ( Figures 4A, B ). 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G;N501Y;N501Y 134;59;72 139;64;77 RBD;S 81;46 84;47 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. It is worth noting that the N501Y mutation does not result in a significant change in the infectivity of the pseudovirus. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 N501Y 28 33 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. More importantly, Camostat had a more significant inhibitory effect on N501Y.V1 and N501Y.V2-RBD pseudoviruses than D614G ( Supplementary Figure S4B ), indicating that the priming of N501Y.V1 and N501Y.V2-RBD S protein maybe more dependent on TMPRSS2 activities. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G;N501Y;N501Y;N501Y;N501Y 116;71;84;183;196 121;76;89;188;201 RBD;RBD;S 93;205;209 96;208;210 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. More importantly, N501Y.V2 RBD pseudovirus has higher infection efficiency than D614G in all susceptible cells, while N501Y.V1 has no obviously difference. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G;N501Y;N501Y 80;18;118 85;23;123 RBD 27 30 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Next, we detected the infectivity of N501Y.V2 pseudovirus to different cells ( Supplementary Figures S2A-E ). 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 N501Y 37 42 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Next, we evaluated whether N501Y.V1 and N501Y.V2 lineages enter into host cells through endocytosis. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 N501Y;N501Y 27;40 32;45 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Our findings show that, the S protein mutations of N501Y.V1 and N501Y.V2 variants may increase the conformational stability of spike to promote the infectivity of SARS-CoV-2 virion. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 N501Y;N501Y 51;64 56;69 S;S 127;28 132;29 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Similar to N501Y.V2 RBD mutation, the stability of N501Y.V2 pseudovirus was significantly higher than that of WT and D614G. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G;N501Y;N501Y 117;11;51 122;16;56 RBD 20 23 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. The infection rate of N501Y.V2 at different time point was also higher than that of D614G ( Figures 3A-D ). 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G;N501Y 84;22 89;27 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. The purpose of this study was to gain insights into the differences of N501Y.V1 and N501Y.V2 lineages with previous WT and D614G. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G;N501Y;N501Y 123;71;84 128;76;89 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. The results indicated that all four S proteins successfully incorporate into pseudovirions, and the cleaved S protein (S2 subunit) is at the similar level, except for a slightly weakened band in N501Y.V1 ( Figure 1B ). 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 N501Y 195 200 S;S 36;108 37;109 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. The results indicated that pseudovirions bearing HV69-70 deletion, 144 deletion, E484K, D614G, P681H, S982A or D1118H single-site mutations were more stable than SARS-CoV-2 WT, whereas A570D and T716I mutations decrease the stability of SARS-CoV-2 pseudovirion. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 A570D;D1118H;D614G;E484K;P681H;S982A;T716I 185;111;88;81;95;102;195 190;117;93;86;100;107;200 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Thermal Stability Analysis of N501Y.V1 and N501Y.V2 Pseudovirions. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 N501Y;N501Y 30;43 35;48 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. These results indicated that entry of N501Y.V1 and N501Y.V2-RBD pseudovirions into host cells mainly depend on the endocytosis in 293T-hACE2 cells, but presence of TMPRSS2 attenuate this dependence. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 N501Y;N501Y 38;51 43;56 RBD 60 63 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. To determine the infectivity of N501Y.V1 and N501Y.V2 variants, a panel cell lines originated from human and animals were infected with VSV pseudoviruses of SARS-CoV-2 WT, D614G, N501Y.V1 and N501Y.V2 RBD ( Figure 2A ). 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G;N501Y;N501Y;N501Y;N501Y 172;32;45;179;192 177;37;50;184;197 RBD 201 204 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. We also detected the S protein expression of single-site mutation in N501Y.V1 and N501Y.V2 RBD. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 N501Y;N501Y 69;82 74;87 RBD;S 91;21 94;22 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. We also examined the effect of single-site mutations of N501Y.V1 and N501Y.V2 lineages on the thermal stability of SARS-CoV-2. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 N501Y;N501Y 56;69 61;74 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. We next investigated the effect of S protein mutations in N501Y.V1 and N501Y.V2 on protease dependent entry in 293T-hACE2 (TMPRSS2-) and 293T-hACE2-TMPRSS2. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 N501Y;N501Y 58;71 63;76 S 35 36 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Although vRNA and sgRNA were detectable throughout the study, infectious virus was only isolated from oropharyngeal swabs at 1 dpi with significantly higher titers for the D614G infected animals (Figure 1E). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 172 177 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. B.1.1.7 (Alpha) variant replication in the respiratory tract was increased compared to D614G. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 87 92 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. B.1.1.7 (Alpha) variant replication/shedding from the upper respiratory tract was increased compared to D614G. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 104 109 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. B.1.1.7 infected AGMs scored minimally higher earlier and peaked at 1 dpi, whereas D614G infected animals scored higher later and peaked at 3 dpi. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 83 88 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. By 7 dpi these animals were all shedding significantly more vRNA and sgRNA than those infected with D614G (Figure 1F, G). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 100 105 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Consistent with higher levels of shedding in the nasal swabs, 5 out of the 6 animals (83%) infected with B.1.1.7 variant had SARS-CoV-2 immunoreactivity in the nasal epithelium compared to only 1 of 5 (20%) infected with the D614G (Fig S2). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 225 230 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. D614G variant replication in the gastrointestinal tract was increased compared to B.1.1.7. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 0 5 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Following intranasal infection with 1 x 106 infectious particles of either the SARS-CoV-2 D614G (n = 5) or the B.1.1.7 variant (n = 6) (5 x 105 per naris) using a nasal atomization device, animals were monitored and scored daily for clinical signs of disease including changes in general appearance, respiration, food intake and fecal output and locomotion. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 90 95 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. In contrast, scores for the D614G animals increased slowly peaking at 4 dpi and remained stable until euthanasia (Figure 1A, Table S1). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 28 33 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. In D614G infected animals, only one AGM (20%) presented with inflammation and a small amount of associated viral antigen in the cecum. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 3 8 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Lesions were found in 8 of 10 bronchi (80%) from B.1.1.7 infected AGMs compared to only 2 of 8 (25%) of D614G animals, with lesions corresponding to SARS-CoV-2 immunoreactivity by immunohistochemistry (IHC) (Figure 2I,J,M,N). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 104 109 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Levels of T cell chemo-attractants IP-10 (CXCL 10) (Fig S5B) and I-Tac (CXCL 11) (Fig S5C) were also increased at 1 dpi in the D614G group but were not sustained throughout the study. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 127 132 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Levels of vRNA and sgRNA corresponded to infectious virus with only D614G animals having detectable infectious SARS-CoV-2 in these two gastrointestinal tract (GIT)-derived tissues (Figure 4C). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 68 73 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. No differences were found in the hematology (Fig S3A-L), blood chemistry (Fig S3M-T) or coagulation assays (Fig S4) between the D614G and B.1.1.7 infected AGMs. 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 128 133 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Notably and in marked contrast to respiratory tissues, AGMs infected with D614G had significantly more vRNA and sgRNA in the ileum and cecum than B.1.1.7 infected AGMs (Figure 4A, B). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 74 79 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. S5), IL6 was the only pro-inflammatory cytokine that was significantly different between the groups, with IL6 being elevated in the D614G group at 3 and 5 dpi compared to B.1.1.7 infected animals (Fig S5A). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 132 137 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. sgRNA was recovered intermittently across the study (Figure 4E), but infectious virus was recovered from rectal swabs of only one (20%) D614G animal (Figure 4F). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 136 141 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Similarly, in the trachea 5 out 6 animals (83%) infected with B.1.1.7 developed both inflammation and immunoreactivity with again only 1 of 5 animals (20%) infected with the D614G variant having any similar observable lesions or immunoreactivity (Figure 2G,H,K,L). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 174 179 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Similarly, vRNA in rectal swabs peaked and was significantly higher at 7 dpi in D614G infected animals (Figure 4D). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 80 85 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Viral replication in the ileum was associated with inflammation in all D614G infected AGMs and corresponded with detectable viral antigen by IHC (Figure 4G,H,K,L), while AGMs infected with the B.1.1.7 had no observable inflammation or viral antigen (Figure 4I,J,L,M). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 71 76 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. vRNA and sgRNA were significantly higher in the lungs of B.1.1.7 - compared to D614G-infected animals (Figure 3A, B); however, elevated levels of infectious virus in B.1.1.7 animals remained just below statistical significance (Figure 3C). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 79 84 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. vRNA in oropharyngeal swabs were significantly higher at 5 dpi in B.1.1.7 compared to D614G infected animals; this difference between variants was maintained but dropped below significance by 7 dpi (Figure 1C). 2021 Emerging microbes & infections Result SARS_CoV_2 D614G 86 91 34725366 Association between prognostic factors and the outcomes of patients infected with SARS-CoV-2 harboring multiple spike protein mutations. All viruses contained the D614G variant, except one isolate. 2021 Scientific reports Result SARS_CoV_2 D614G 26 31 34725366 Association between prognostic factors and the outcomes of patients infected with SARS-CoV-2 harboring multiple spike protein mutations. Besides the D614G mutation, the most common mutation in the S protein was L5F (18.8%), V213A (18.8%), and S689R (8.3%) (Table 3). 2021 Scientific reports Result SARS_CoV_2 D614G;L5F;S689R;V213A 12;74;106;87 17;77;111;92 S 60 61 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A highly significant less prevalent spike mutation, E484Q (23012 G>C), having a role in the immune escape was found in one 52-year-old male patient having a travel history of Bahrain (GISAID ID: EPI_ISL_2894982). 2021 Journal of medical virology Result SARS_CoV_2 E484Q;G23012C 52;59 57;68 S 36 41 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Another distinct and rare spike mutation (L5F [21575 C>T]) was also reported in one 40-year female patient (GISAID ID: EPI_ISL_2894977). 2021 Journal of medical virology Result SARS_CoV_2 L5F;C21575T 42;47 45;56 S 26 31 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Corresponding to the person who traveled back to Pakistan from UAE reported several rare missense mutations in the spike region, A27S (21641 G>T), G181V (22104 G>T), ORF1b region, L820F (NSP12b: L820F) (15925 C>T), ORF3a region, T271I (26204 C>T) and N region, K387N (29434 G>T) (GISAID ID: EPI_ISL_2438683). 2021 Journal of medical virology Result SARS_CoV_2 A27S;G181V;K387N;L820F;L820F;T271I;C15925T;G21641T;G22104T;C26204T;G29434T 129;147;261;180;195;229;203;135;154;236;268 133;152;266;185;200;234;212;144;163;245;277 S;ORF3a;N 115;215;251 120;220;252 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Furthermore, rare spike mutations, A879S (24197 G>T) and D1163Y (25049 G>T), were found in two patients (GISAID IDS: EPI_ISL_2894979 and EPI_ISL_2313084) and a unique mutation, K444R (22893 A>G), in a 26 years old male patient (GISAID ID: EPI_ISL_2757749). 2021 Journal of medical virology Result SARS_CoV_2 A879S;D1163Y;K444R;A22893G;G24197T;G25049T 35;57;177;184;42;65 40;63;182;193;51;74 S 18 23 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. The delta variant isolates reported following significant mutations: S:L452R (22917 T>G), S:T478K (22995 C>A), S:P681R (23604 C>G), S:D950N (24410 G>A), ORF3a:S26L (25469 C>T), M:I82T (26767 T>C), ORF7a:V82A (27638 T>C), ORF7a:T120I (27752 C>T), N:D63G (28461 A>G), N:R203M (28881 G>T) and N:D377Y (29402 G>T). 2021 Journal of medical virology Result SARS_CoV_2 T22917G;C22995A;C23604G;G24410A;C25469T;T26767C;T27638C;C27752T;A28461G;G28881T;G29402T;D377Y;D63G;D950N;I82T;L452R;P681R;R203M;S26L;T120I;T478K;V82A 78;99;120;141;165;185;209;234;254;275;299;292;248;134;179;71;113;268;159;227;92;203 87;108;129;150;174;194;218;243;263;284;308;297;252;139;183;76;118;273;163;232;97;207 ORF7a;ORF7a;ORF3a;N;N;N;S;S;S;S 197;221;153;246;266;290;69;90;111;132 202;226;158;247;267;291;70;91;112;133 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. The gamma variants harbors non-synonymous lineage defining mutations, ORF1a: K1795Q (NSP3: K977Q) (A5648C), ORF1a: del:11288:9 (NSP6: S106), S:T20N (C21621A), S:R19S (G22132T), S:K417T (A22812C), S:E484K (G23012A), S:N501Y (A23063T), S:H655Y (C23525T), S:T1027I (C24642T), ORF8:E92K (G28167A) and N:P80R (C28512G). 2021 Journal of medical virology Result SARS_CoV_2 K1795Q;K977Q;A22812C;A23063T;A5648C;C21621A;C23525T;C24642T;C28512G;G22132T;G23012A;G28167A;E484K;E92K;H655Y;K417T;N501Y;P80R;R19S;T1027I;T20N 77;91;186;224;99;149;243;263;305;167;205;284;198;278;236;179;217;299;161;255;143 83;96;193;231;105;156;250;270;312;174;212;291;203;282;241;184;222;303;165;261;147 ORF1a;ORF1a;Nsp3;Nsp6;ORF8;N;S;S;S;S;S;S;S 70;108;85;128;273;297;141;159;177;196;215;234;253 75;113;89;132;277;298;142;160;178;197;216;235;254 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. The mutational analysis revealed that all the beta variant isolates reported significant and lineage defining mutations as: ORF1a:K1655N (NSP3: K837N) (5230 G>T), S:D80A (21801 A>C), S:D215G (22206 A>G), S:K417N (22813 G>T), S:E484K (23012 G>A), S:N501Y (23063 A>T), S:A701V (23664 C>T), E:P71L (26456 C>T) and N:T205I (28887 C>T). 2021 Journal of medical virology Result SARS_CoV_2 K837N;A21801C;A22206G;G22813T;G23012A;A23063T;C23664T;C26456T;C28887T;G5230T;A701V;D215G;D80A;E484K;K1655N;K417N;N501Y;P71L;T205I 144;171;192;213;234;255;276;296;320;152;269;185;165;227;130;206;248;290;313 149;180;201;222;243;264;285;305;329;160;274;190;169;232;136;211;253;294;318 ORF1a;Nsp3;E;N;S;S;S;S;S;S 124;138;288;311;163;183;204;225;246;267 129;142;289;312;164;184;205;226;247;268 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Three rare mutations in the ORF1a region, T183I (NSP2: T3I) (813 C>T), S3099L (NSP4: S336L) (9561 C>T), and L3915F (NSP7: L56F) (12008 C>T) were observed in one of the virus isolates (GISAID ID: EPI_ISL_2313081). 2021 Journal of medical virology Result SARS_CoV_2 L3915F;L56F;S3099L;S336L;T183I;T3I;C12008T;C813T;C9561T 108;122;71;85;42;55;129;61;93 114;126;77;90;47;58;138;68;101 ORF1a;Nsp2;Nsp4;Nsp7 28;49;79;116 33;53;83;120 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. Between February and April, we observed the substitution C>T 241 in 73.6 % of the sequences, an increase of 35.9 % compared to the previous period. 2021 Microbial genomics Result SARS_CoV_2 C241T 57 64 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. From those, only the substitutions D614G and V1176F in the spike, and I292T in the N protein, presented positive selection pressure, according to the FUBAR analysis, with a Bayes factor (BF) of 82.4, 390.1, and 801.7, respectively. 2021 Microbial genomics Result SARS_CoV_2 D614G;I292T;V1176F 35;70;45 40;75;51 S;N 59;83 64;84 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. In comparison with the sequences of the period from May to September 2020, D614G had a decrease of 1.5 % in the frequency, V1176F increased 119.2 % and I292T, although its high BF, decreased 20.7 %. 2021 Microbial genomics Result SARS_CoV_2 D614G;I292T;V1176F 75;152;123 80;157;129 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. Interestingly, only three of the amino acid substitutions with positive selective pressure identified here were present at the previous period, from February to April 2020: D614G (100 % of frequency) and V1176F (18.7 %) in the spike; and I292T (49.2 %) in the N. 2021 Microbial genomics Result SARS_CoV_2 D614G;I292T;V1176F 173;238;204 178;243;210 S;N 227;260 232;261 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. The most frequent substitutions among sequences were L71F (22.6 %) in the NSP7; P303L (99 %) in the RNA-dependent RNA polymerase (RdRp); D614G (98.5 %) and V1176F (41%) in the spike; I33T (37.4 %) in the ORF6; R203K (93.5 %), G204R (93.8 %), and I292T (39 %) in the N protein (Table S1). 2021 Microbial genomics Result SARS_CoV_2 D614G;G204R;I292T;I33T;L71F;P303L;R203K;V1176F 137;226;246;183;53;80;210;156 142;231;251;187;57;85;215;162 RdRp;S;ORF6;Nsp7;RdRP;N 100;176;204;74;130;266 128;181;208;78;134;267 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. The nucleotide substitution C>T at the position 241 of the 5' UTR region was identified in 100 % of the sequences related to the period from May to September. 2021 Microbial genomics Result SARS_CoV_2 C241T 28 51 5'UTR 59 65 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. A previous research indicated that the mutation N165Q became more sensitive to mAb P2B-2F6, highlighting the removal of glycan modification in NTD for better recognition by the antibodies and the shielding by the glycan as self-defense of virus against the immune system. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 N165Q 48 53 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. Although n3113.1-Fc showed impaired binding (10-fold less than WT S) to the spike protein, the apparent binding affinity of n3113.1-Fc to F490S/L452Q double mutation containing RBD was determined at higher than 0.5 nM. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 F490S;L452Q 138;144 143;149 S;RBD;S 76;177;66 81;180;67 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. Based on these findings, we tried mutations of Y52, Y58, and W49 on n3113.1 to shorten the side chains and found a single Y58L mutation could recover the binding ability of n3113.1-Fc to Delta S. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 Y58L 122 126 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. During the circulation of SARS-CoV-2, the notable mutation D614G became the first dominant variant and replaced the ancestral spike. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G 59 64 S 126 131 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. However, the binding affinity of n3113 decreased by 20-50% for A348S and over 90% for L452R. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 A348S;L452R 63;86 68;91 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. In align with this, the binding affinity of n3113.1-Fc with D614G spike showed no difference with the wild-type spike (WT S) (5.5 nM for WT S and 5.3 nM for D614G S. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G;D614G 60;157 65;162 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. In alignment with this, the Y58L mutant on n3113.1-Fc reverted susceptivity to virus pseudotyped with Delta S. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 Y58L 28 32 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. Interestingly, the glutamine substitution of leucine (L452Q) has increased the binding affinity of RBD to n3113.1. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 L452Q 54 59 RBD 99 102 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. N3113.1 binds to most of the mutations including the N501Y and E484K/Q which were reported to have increased binding potency of spike with ACE2 and appeared in several VOCs and VOIs, with similar affinity as WT RBD. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 E484K;E484Q;N501Y 63;63;53 70;70;58 S;RBD 128;211 133;214 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. N3113.1-Fc bound to the spike variants of Alpha, Beta, and Gamma with a comparable affinity of 4.8 nM, 10.1 nM, and 8.4 nM, respectively, but lost the binding ability to Delta spike that contained L452R mutation. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 L452R 197 202 S;S 24;176 29;181 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. N3113.1-Fc neutralized pseudoviruses loaded with a spike of WT-D614G and Alpha variant in indiscriminate potent (IC50 of 0.07 mug/ml and 0.12 mug/ml for WT-D614G and Alpha, respectively. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G;D614G 63;156 68;161 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. The noticeable VOI - C.37 (Lambda) contained both F490S and L452Q mutations in its RBD region. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 F490S;L452Q 50;60 55;65 RBD 83 86 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. The unperturbed binding potency of n3113-Fc (especially with Y58L mutation) to variant spikes and the robust in vivo protection of n3113-Fc in SARS-CoV-2-infected mice indicate that n3113.1-Fc (Y58L) is potentially effective in conferring the antigenic drift of present emerging variants. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 Y58L;Y58L 61;194 65;198 S 87 93 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. We generated a D614G mutation into the prefusion-stabilized spike for cryo-EM structure determination. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 D614G 15 20 S 60 65 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. We investigated several RBD variants within publicly available SARS-CoV-2 sequences in the Global Initiative on Sharing All Influenza Data (GISAID) and all of the individual RBD mutants (N501Y, E484K, E484Q, K417N, K417T, L452R, L452Q, T478K) found in dominant VOCs (B.1.1.7, Alpha; B.1.352, Beta; P.1, Gamma; B.1.617.2, Delta; B.1.427/B.1.429, Epsilon) for n3113.1 binding. 2021 Signal transduction and targeted therapy Result SARS_CoV_2 E484K;E484Q;K417N;K417T;L452Q;L452R;T478K;N501Y 194;201;208;215;229;222;236;187 199;206;213;220;234;227;241;192 RBD;RBD 24;174 27;177 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. D614G increased from 74.6% to 99.9%; T265I, Q57H, R203K, and G204R started to increase in March and gradually decreased in July (Figure 3D). 2021 Frontiers in microbiology Result SARS_CoV_2 G204R;Q57H;R203K;T265I;D614G 61;44;50;37;0 66;48;55;42;5 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. R6997P and V30L co-occurred and rapidly increased starting in July 2020; M3087I, X5167Y, K4576N, N5542D, A376T, and S5585I co-occurred and gradually increased; and S477N started to rise in June but decreased again in July (Figure 3B). 2021 Frontiers in microbiology Result SARS_CoV_2 A376T;K4576N;M3087I;N5542D;S477N;S5585I;V30L;X5167Y;R6997P 105;89;73;97;164;116;11;81;0 110;95;79;103;169;122;15;87;6 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. Among other O-glycosylation sites, we only detected a low level of O-glycosylation at T678 located within the loop that harbors the furin cleavage site for the GSAS-stabilized S-fm2P but not S-D614G or S-Alpha (Supplementary Table SIV). 2022 Glycobiology Result SARS_CoV_2 D614G 193 198 S;S;S 176;191;202 177;192;203 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. In our hands, N343 does have a few oligomannose structures (~15%) but, importantly, both sites carry mostly complex type structures and are not appreciably affected by mutations in the D614G and Alpha variants. 2022 Glycobiology Result SARS_CoV_2 D614G 185 190 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. Interestingly, although single mutation at D614G retains much of the same glycosylation pattern, a significant shift is noted in the Alpha variant more than in any other sites. 2022 Glycobiology Result SARS_CoV_2 D614G 43 48 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. Like the Harvard and Swiss samples, our own S-fm2P sample yielded a small % of complex type glycan at this site, whereas samples from other sources, as well as our D614G and Alpha variants, are approaching 100% oligomannose, which may reflect a slight difference in the spatial accessibility afforded by the different trimeric assembly. 2022 Glycobiology Result SARS_CoV_2 D614G 164 169 S 44 45 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. More importantly, we consistently detected substantial increases in the relative amount of oligomannose structures at N603, N616 and N1074 in the D614G and Alpha variants. 2022 Glycobiology Result SARS_CoV_2 D614G 146 151 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. Nonetheless, the overall site-specific glycosylation characteristics of S-2P largely recapitulate the overall picture concluded from analyzing the GSAS-mutated S-fm2P, S-D614G and S-Alpha, namely with N-glycans at N234 being almost all retained as oligomannose, N74 and N282 being highly processed into complex types, and N61, N122 and N165 somewhere in between (Figure 2A). 2022 Glycobiology Result SARS_CoV_2 D614G 170 175 N;S;S;S;S 201;72;160;168;180 202;73;161;169;181 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. On average, the heterogenous glycans at N122 would thus be expected to occupy a bulkier spatial volume in the Alpha variant relative to D614G or the original non-mutated strain. 2022 Glycobiology Result SARS_CoV_2 D614G 136 141 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. On the other hand, N-glycosylation at the very N-terminal sites N17, N61, N74 and N122, are less affected by the D614G mutation alone but register more pronounced shifts in the S-Alpha variant that carries multiple mutations, including the two deletions in the NTD. 2022 Glycobiology Result SARS_CoV_2 D614G 113 118 N;N;S 19;47;177 20;48;178 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. The changes may be related to the increase propensity of the RBD to be in an open, upward conformation in S-D614G and S-Alpha. 2022 Glycobiology Result SARS_CoV_2 D614G 108 113 RBD;S;S 61;106;118 64;107;119 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. The few critical mutations in the RBD of the S-Alpha appear not to have significantly impact its glycosylation pattern any more than the single D614G mutation does. 2022 Glycobiology Result SARS_CoV_2 D614G 144 149 RBD;S 34;45 37;46 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. The overall picture gleaned from these analyses suggests that S-D614G and S-Alpha are more similar in their N-glycosylation pattern at a majority of sites and, relative to S-fm2P, generally show a shift towards less processed states for sites that originally carry a variable mixture of oligomannose and complex type structures. 2022 Glycobiology Result SARS_CoV_2 D614G 64 69 N;S;S;S 108;62;74;172 109;63;75;173 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. This feature is largely maintained by the D614G and Alpha variants although there is a significant decrease in the degree of fucosylation at N282 going from the wild type (both our own and the ref average at 73-80%) to the variants (45-48%). 2022 Glycobiology Result SARS_CoV_2 D614G 42 47 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. Three biological replicates were prepared for each of the S-2P, S-fm2P, S-D614G and S-Alpha variants (S-2P and S-fm2P refer to the trimeric spike proteins from the original strain with and without the furin cleavage site, respectively, whereas both S-D614G and S-Alpha carry the same furin site mutations as in S-fm2P, see Figure 1A), yielding a total of twelve S protein samples subjected to an analytical workflow (Figure 1B) optimized for rapid and standardized quantitative assessment of potential variations in site-specific glycosylation. 2022 Glycobiology Result SARS_CoV_2 D614G;D614G 74;251 79;256 S;S;S;S;S;S;S;S;S;S;S 140;58;64;72;84;102;111;249;261;311;362 145;59;65;73;85;103;112;250;262;312;363 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. We observed only a slight increase in oligomannose structures in the overall similar glycosylation pattern of N165 upon D614G and further mutations in the Alpha variant, albeit not without some variations in the actual complex type structural heterogeneity. 2022 Glycobiology Result SARS_CoV_2 D614G 120 125 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Cluster #1 contained 0.69% of all records, had the mutations mentioned above (from the "British variant") and the following variants: A28095T (frequency in the cluster - 49.98%), G28881A, G28882A, G28883C, A23403G (100% each), and G25437T (31.58%). 2021 Computers in biology and medicine Result SARS_CoV_2 A23403G;A28095T;G25437T;G28881A;G28882A;G28883C 206;134;231;179;188;197 213;141;238;186;195;204 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Cluster #13 was featured by 54.8% of males and 3 mutations: A23403G (100%), G25563T (100%), C26735T (5%); cluster #39 was characterized by 46.31% of males and 8 mutations: A23403G (99%), G22992A (99%), G23401A (99%), G28881A (99%), G28882A (99%), G28883C (99%), C27059T (7%), C22480T (6%). 2021 Computers in biology and medicine Result SARS_CoV_2 A23403G;A23403G;C22480T;C26735T;C27059T;G22992A;G23401A;G25563T;G28881A;G28882A;G28883C 60;172;276;92;262;187;202;76;217;232;247 67;179;283;99;269;194;209;83;224;239;254 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Cluster #25 was featured by the increased mean age (53) and could be described by 5 mutations occurring with different frequencies: A23403G (99%), G25563T (87%), C27964T (87%), C28977T (10%), and C23731T (2%). 2021 Computers in biology and medicine Result SARS_CoV_2 A23403G;C23731T;C27964T;C28977T;G25563T 132;196;162;177;147 139;203;169;184;154 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Cluster #34 demonstrated a decreased mean age of 43 and was represented by 9 mutations: C28869T (100%), C27964T (100%), A23403G (100%), G25563T (100%), G25907T (100%), C28472T (99%), G29402T (23%), A22255T (17%), G23593T (4%). 2021 Computers in biology and medicine Result SARS_CoV_2 A22255T;A23403G;C27964T;C28472T;C28869T;G23593T;G25563T;G25907T;G29402T 198;120;104;168;88;213;136;152;183 205;127;111;175;95;220;143;159;190 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Four mutations were present in the cluster with 100% frequency - G28881A, G28882A, G28883C, and A23403G. 2021 Computers in biology and medicine Result SARS_CoV_2 A23403G;G28881A;G28882A;G28883C 96;65;74;83 103;72;81;90 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Mutations found in samples uploaded mainly by Denmark and Australia formed two clusters, each containing 8 mutations (sizes regarding all studied genomes - 1.48% and 2.51%, respectively): C26735T (100%), T26876C (100%), G25563T (100%), C25710T (100%), G29399A (100%), A23403G (99%), G22992A (99%), C27434T (13%) and A23403G (99%), G22992A (99%), G23401A (99%), G28881A (99%), G28882A (99%), G28883C (99%), C27059T (7%), C22480T (6%), respectively. 2021 Computers in biology and medicine Result SARS_CoV_2 A23403G;A23403G;C22480T;C25710T;C26735T;C27059T;C27434T;G22992A;G22992A;G23401A;G25563T;G28881A;G28882A;G28883C;G29399A;T26876C 268;316;420;236;188;406;298;283;331;346;220;361;376;391;252;204 275;323;427;243;195;413;305;290;338;353;227;368;383;398;259;211 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. The cluster included one mutation in ORF3a (G26144T) and was characterized by a mean age of 57 and a gender ratio of 50.46 males per 49.54 females. 2021 Computers in biology and medicine Result SARS_CoV_2 G26144T 44 51 ORF3a 37 42 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. From March SARS-CoV-2 positive samples, 48% of them have only D614G mutation, which did not find in other months. 2021 Infection and drug resistance Result SARS_CoV_2 D614G 62 67 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. Out of 150 SARS-CoV-2 positive specimens, 69 (46%) were B.1.617.2 (Delta), 49 (32.7%) were B.1.1.7, 4 (2.7%) were P.1, 4 (2.7%) were P.2, 3 (2%) were B.1.526, 2 (1.3%) were B.1.351, 2 (1.3%) were B.1.427, and 17 (11.3%) had mutation only in D614G (Figure 1). 2021 Infection and drug resistance Result SARS_CoV_2 D614G 241 246 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. Out of nine samples, five were B.1.617.2 (Delta) and concordant with sequencing showing mutation in D614G, L452R, P681R, and T478K, two samples were B.1.1.7 (Alpha) showing mutation in D614G, N501Y, delH69V70, Q27stop, and two were B.1.526 (Iota) showing mutation in L452R and D614G (Supplementary Material S5). 2021 Infection and drug resistance Result SARS_CoV_2 D614G;D614G;D614G;L452R;L452R;N501Y;P681R;Q27X;T478K 100;185;277;107;267;192;114;210;125 105;190;282;112;272;197;119;217;130 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. The B.1.351 control showed mutation in E484K, D614G, A701V, K417N, N501Y, and L242_244L, B.1.1.7 showed mutations in D614G, delH69V70, N501Y, and Q27stop, the control B.1.617.1 showed mutation in E484Q, P681R, L452R, D614G, and P.1 showed mutations in E484K, D614G, K417T, N501Y, and T20N. 2021 Infection and drug resistance Result SARS_CoV_2 A701V;D614G;D614G;D614G;D614G;E484K;E484K;E484Q;K417N;K417T;L452R;N501Y;N501Y;N501Y;P681R;Q27X;T20N 53;46;117;217;259;39;252;196;60;266;210;67;135;273;203;146;284 58;51;122;222;264;44;257;201;65;271;215;72;140;278;208;153;288 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. Gene NSP4 (S184N) and membrane protein (A2V) from the isolate BRA/1236/2021 (G15), envelop protein (V5A) from BRA/RJ-DCVN5/2020 (G9), 2'O-mutase (R216N) from BRA/MASP2C844R2/2020 (G11) had the single mutation. 2022 Virus research Result SARS_CoV_2 A2V;R216N;S184N;V5A 40;146;11;100 43;151;16;103 Membrane;Nsp4 22;5 30;9 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. The mutant (P323L) identified in RdRp of BRA/CD1739-P4/2020 (G14) transmits its biological function from cellular process to virulence mechanism (Table 2 ). 2022 Virus research Result SARS_CoV_2 P323L 12 17 RdRP 33 37 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. Mutations MT2-3, involving a change in E484K, explain this mutation's deleterious effect in the binding between RBD and P2B-2F6 and C144. 2021 Scientific reports Result SARS_CoV_2 E484K 39 44 RBD 112 115 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. On the other hand, we observed that MT2:which includes mutation E484K:had a deleterious effect on the binding energy for P2B-2F6, reducing it to kJ mol. 2021 Scientific reports Result SARS_CoV_2 E484K 64 69 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. The introduction of E484K generated another one between K484 and E35 in ACE2. 2021 Scientific reports Result SARS_CoV_2 E484K 20 25 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. We observed the introduction of K417N eliminates the salt bridge between RBD (K417) and ACE2 (D30). 2021 Scientific reports Result SARS_CoV_2 K417N 32 37 RBD 73 76 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. All four variants exhibited modest (1.7-8.2-fold) increases in the estimated binding affinity for sACE2-Fc, relative to that of D614G. 2021 iScience Result SARS_CoV_2 D614G 128 133 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. As was seen for the VSV pseudotypes, the authentic P.1 SARS-CoV-2 variant exhibited more S1 shedding over time at 4 C than the D614G and B.1.1.7 variants (Figure 5G). 2021 iScience Result SARS_CoV_2 D614G 127 132 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. At 37 C, sACE2 induced S1 shedding from all the VSV pseudotypes, with D614G, B.1.351, P.1, and B.1.1.248 shedding S1 slightly more efficiently than D614 and B.1.1.7. 2021 iScience Result SARS_CoV_2 D614G 70 75 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. At low ACE2 expression levels, the relative infectivity of the variants exhibited the rank order: P.1, B.1.1.248 > B.1.351 > B.1.1.7 > D614G > D614. 2021 iScience Result SARS_CoV_2 D614G 135 140 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. B.1.1.7 S1, which has a deletion of three amino acids relative to D614G, as well as the S2 glycoprotein of P.1 and B.1.1.248, also migrated slower after Endo Hf but not PNGase F treatment, highlighting their additional modification by complex carbohydrates compared with that of D614G. 2021 iScience Result SARS_CoV_2 D614G;D614G 66;279 71;284 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. Consistent with other studies, the sera neutralized the B.1.1.7 variant as efficiently as D614 and D614G. 2021 iScience Result SARS_CoV_2 D614G 99 104 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. Consistent with previous reports, D614G exhibited increased infectivity for both Vero-E6 and 293T-ACE2 cells compared with that of D614 (Figure 3B). 2021 iScience Result SARS_CoV_2 D614G 34 39 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. D614, D614G, and B.1.351 were inactivated similarly on ice and at 4 C, but exhibited different levels of S1 shedding, suggesting that cold inactivation involves additional factors besides S1 shedding. 2021 iScience Result SARS_CoV_2 D614G 6 11 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. In this study, we compare the functional phenotypes of the S glycoproteins of the newly emergent SARS-CoV-2 variants B.1.1.7, B.1.351, P.1, and B.1.1.248 with those of the early/founder virus (D614) and the globally prevalent D614G variant. 2021 iScience Result SARS_CoV_2 D614G 226 231 S 59 74 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. Interestingly, the pattern of sACE2-induced S1 shedding differed on ice, with D614, D614G, and B.1.351 exhibiting more efficient S1 shedding than B.1.1.7, P.1, and B.1.1.248. 2021 iScience Result SARS_CoV_2 D614G 84 89 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. Most of the variant S glycoproteins were processed and incorporated into viral particles comparably; the proteolytic processing of D614G was slightly more efficient than that of D614 (Figure 1C), as has been previously seen. 2021 iScience Result SARS_CoV_2 D614G 131 136 S 20 35 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. Nonetheless, D614G infected the cells expressing higher ACE2 levels better than D614, and P.1 and B.1.1.248 exhibited slightly higher infectivity than the other variants. 2021 iScience Result SARS_CoV_2 D614G 13 18 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. Spontaneous S1 shedding at 0 and 4 C for D614, P.1, and B.1.1.248 was significantly greater than that of D614G, B.1.1.7, and B.1.351. 2021 iScience Result SARS_CoV_2 D614G 105 110 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The B.1.1.7 SARS-CoV-2 variant retained infectivity at 4 C better than the D614G and P.1 variants (Figure 5F). 2021 iScience Result SARS_CoV_2 D614G 75 80 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The B.1.1.7 variant, first identified in Southeast England in September 2020 and now the dominant strain in the United Kingdom, has 8 additional S glycoprotein changes, including 2 deletions in the NTD and an N501Y change in the RBD. 2021 iScience Result SARS_CoV_2 N501Y 209 214 S;RBD 145;229 159;232 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The B.1.351 variant emerged in South Africa in October 2020 and has 9 S glycoprotein changes in addition to D614G, including three in the RBD and several in the NTD. 2021 iScience Result SARS_CoV_2 D614G 108 113 S;RBD 70;138 84;141 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The D614, D614G, and B.1.351 exhibited intermediate levels of stability on ice and at 4 C. 2021 iScience Result SARS_CoV_2 D614G 10 15 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The more recently emerged B.1.1.7, B.1.351, P.1, and B.1.1.248 variants are the offspring of the D614G strain and therefore all contain the D614G change. 2021 iScience Result SARS_CoV_2 D614G;D614G 97;140 102;145 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The neutralization titers of the sera against the P.1 and B.1.1.248 variants were lower than those against D614G. 2021 iScience Result SARS_CoV_2 D614G 107 112 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The P.1 and B.1.1.248 variants exhibited ~4-fold higher infectivity for Vero-E6 cells relative to that of D614G; the B.1.1.7 and B.1.351 variants entered these cells with an efficiency similar to that of D614G. 2021 iScience Result SARS_CoV_2 D614G;D614G 106;204 111;209 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The P.1 variant is prevalent in Brazil; in addition to D614G, P.1 has 10 changes, three of which are similar to those in the RBD of B.1.351. 2021 iScience Result SARS_CoV_2 D614G 55 60 RBD 125 128 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The two additional potential N-linked glycosylation sites created by the T20N and R190S changes in the NTDs of P.1 and B.1.1.248 S1 glycoproteins likely account for the observed higher molecular weight. 2021 iScience Result SARS_CoV_2 R190S;T20N 82;73 87;77 N 29 30 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The untreated and the Endo Hf-treated S1 from P.1 and B.1.1.248 migrated slightly slower than that of D614G. 2021 iScience Result SARS_CoV_2 D614G 102 107 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The VSV pseudotypes with D614 and D614G exhibited similar sensitivities to sACE2.v2.4 on Vero-E6 cells (Figure 4C, left) and 293T-ACE2 target cells (Figure 4C, right). 2021 iScience Result SARS_CoV_2 D614G 34 39 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. We also compared the neutralizing activity of a dimeric soluble ACE2 (sACE2.v2.4) against B.1.1.7, B.1.351, P.1, and B.1.1.248 pseudotypes with that against the D614 and D614G pseudotypes. 2021 iScience Result SARS_CoV_2 D614G 170 175 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. We, therefore, evaluated the binding of soluble S glycoprotein trimers corresponding to D614G and four variants to the sACE2-Fc protein by ELISA (Figures 4A and 4B). 2021 iScience Result SARS_CoV_2 D614G 88 93 S 48 62 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. With the exception of D614G, S1 shedding for each S glycoprotein variant was less at RT and 37 C than on ice. 2021 iScience Result SARS_CoV_2 D614G 22 27 S 50 64 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. One of the viruses had the D614G mutation. 2021 PloS one Result SARS_CoV_2 D614G 27 32 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. A surface of 1668 A2 is buried at the binding interface of Y453F RBD/mink ACE2 and is comprised of 18 residues from Y453 RBD and 18 residues from mink ACE2. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 59 64 RBD;RBD 65;121 68;124 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. As expected, the binding of S1-Fc or S1 (Y453F)-Fc to HeLa cells expressing mouse ACE2 was very low and comparable to that of the empty vector control while S1-Fc efficiently bound to HeLa cells expressing human ACE2, which is consistent with previous reports. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 41 46 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. As miSARS-CoV-2 also harbored other mutations outside of RBD in the spike (Fig 1A), we purified the spike protein (1aa-1208aa) without transmembrance domain and intracellular domain with different mutations (WT, Y453F, del69-70/I692V or del69-70/Y453F/I692V) to test their binding with human or mink ACE2 respectively (S3A and S3B Fig). 2021 PLoS pathogens Result SARS_CoV_2 Y453F;I692V;I692V;Y453F 212;228;252;246 217;233;257;251 S;S;RBD 68;100;57 73;105;60 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Based on this analysis, we hypothesized that the Y453F substitution evolved in the miSARS-CoV-2 spike RBD as it enhances interaction with mink ACE2, conferring a fitness advantage in the new host and leading to circulation of the adapted virus in the mink population. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 49 54 S;RBD 96;102 101;105 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. By contrast, SARS-CoV-2 (Y453F) trVLP replicated and spread well in both cell lines (Fig 6B and 6C), consistent with our binding experiments and pseudotyped virons assays (Figs 2B, 2E, 4A and 5B). 2021 PLoS pathogens Result SARS_CoV_2 Y453F 25 30 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Consistent with the results of mink ACE2, ferret and stoat ACE2 exhibited limited binding capability with WT S1-Fc but increased binding ability with S1 (Y453F)-Fc (Figs 4A and S6A and S6B). 2021 PLoS pathogens Result SARS_CoV_2 Y453F 154 159 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Due to the high similarity of ACE2 proteins in the Mustela genus (S5A Fig), we performed the binding experiments of the S1 variants (WT or Y453F) with ferret and stoat ACE2. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 139 144 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Finally, it is also predicted that the Y453F mutation would not bring steric clashes with human ACE2 H34 and thus would not significantly change the surrounding interactions, which may explain the retained binding of Y453F RBD to human ACE2. 2021 PLoS pathogens Result SARS_CoV_2 Y453F;Y453F 39;217 44;222 RBD 223 226 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. However, the Y453F mutation dramatically increased the binding affinity with mink ACE2 without compromising binding to human ACE2, which suggests that Y453F is an adaptive mutation to improve its fitness in a new host:mink. 2021 PLoS pathogens Result SARS_CoV_2 Y453F;Y453F 13;151 18;156 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Human ACE2 bound SARS-CoV-2 RBD with a KD of 6.5nM, and Y453F RBD with a KD of 0.98nM. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 56 61 RBD;RBD 28;62 31;65 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. In addition, utilizing the recently developed SARS-CoV-2 transcription and replication-competent virus-like particles (trVLP) cell culture system, in which the SARS-CoV-2 complete life cycle is recapitulated in cells expressing SARS-CoV-2 N gene in trans, we produced SARS-CoV-2 GFP/DeltaN trVLPs (WT or Y453F) (Fig 6A). 2021 PLoS pathogens Result SARS_CoV_2 Y453F 304 309 N 239 240 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. In line with our cell-based binding assay, SPR analysis did not detect the binding of WT RBD with ferret or stoat ACE2, but Y453F RBD could bind ferret or stoat ACE2 with a KD of 31.17nM and 48.06 nM, respectively (Fig 4C). 2021 PLoS pathogens Result SARS_CoV_2 Y453F 124 129 RBD;RBD 89;130 92;133 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. In mink ACE2-transduced cells infected with SARS-CoV-2pp or SARS-CoV-2pp mink W/O Y453F, the Luc activity increased by 5.2 or 4.5 fold relative to that of mouse ACE2, respectively. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 82 87 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. In sum, these results confirm that Y453F is an adaptive mutation in the SARS-CoV-2 spike protein that dramatically enhances utilization of mink ACE2 for entry and replication, conferring a fitness advantage in the mink host. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 35 40 S 83 88 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Mink ACE2 bound Y453F SARS-CoV-2 with a KD of 78.22nM but binding to WT RBD was not detectable. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 16 21 RBD 72 75 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Moreover, after replacing the amino acid residue at position 34 of human ACE2 with its mink counterpart to generate human ACE2 (H34Y), binding to S1-Fc was reduced (86.5% [WT] vs 42.0%) but increased to S1 (Y453F)-Fc (99.1% [WT] and 98.5%). 2021 PLoS pathogens Result SARS_CoV_2 H34Y;Y453F 128;207 132;212 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Next, we inoculated the Caco-2 ACE2KO-N-hACE2 and Caco-2 ACE2KO-N-miACE2 cells with the same amount of SARS-CoV-2 GFP/DeltaN trVLP or SARS-CoV-2 GFP/DeltaN (Y453F) trVLP to achieve similar levels of initial infection. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 157 162 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Next, WT or Y453F S1-Fc (a purified fusion protein consisting of the S1 domain of SARS-CoV-2 S protein and an Fc domain of human lgG) was incubated with HeLa cells transduced with the ACE2 variants. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 12 17 S 93 94 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Notably, WT S1-Fc bound mink ACE2 with limited efficiency, in contrast, S1 (Y453F)-Fc bound mink ACE2 with 77% efficiency, demonstrating that the miSARS-CoV-2 mutation enhances binding to mink ACE2. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 76 81 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Performing the reverse by substituting the amino acid residue at position 34 of mink ACE2 with its human counterpart to generate mink ACE2 (Y34H) only slightly increased binding to S1-Fc (1.2% vs 2.2%) and binding to S1(Y453F)-Fc (77.0% vs 80.0%) (Figs 2B and S1B). 2021 PLoS pathogens Result SARS_CoV_2 Y34H;Y453F 140;220 144;225 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Potential impact of the Y453F substitution on the binding of SARS-CoV-2 spike to mink ACE2. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 24 29 S 72 77 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. S (Y453F) and S (del69-70/Y453F/I692V) could exclusively bind with mink ACE2; in contrast, other S mutants without Y453F mutation could not (S3C Fig). 2021 PLoS pathogens Result SARS_CoV_2 Y453F;Y453F;I692V;Y453F 115;3;32;26 120;8;37;31 S;S;S 0;14;97 1;15;98 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. S1 (Y453F)-Fc bound human ACE2 more efficiently than WT S1-Fc (99.1% vs 86.5%). 2021 PLoS pathogens Result SARS_CoV_2 Y453F 4 9 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Sequence analysis of the miSARS-CoV-2 "Cluster 5" variant isolated from patients identified four mutations in the spike protein: del 69-70 (a deletion of the His69 and Val70), Y453F (located in the RBD), I692V, and M1229I (Fig 1A). 2021 PLoS pathogens Result SARS_CoV_2 I692V;M1229I;Y453F 204;215;176 209;221;181 S;RBD 114;198 119;201 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Structural analysis indicated that the Y453F substitution in the spike RBD is a species-specific adaptive mutation increasing the binding to mink ACE2 (Fig 3B and S1 Table). 2021 PLoS pathogens Result SARS_CoV_2 Y453F 39 44 S;RBD 65;71 70;74 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Structural basis for the enhanced binding of mink ACE2 with Y453F RBD. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 60 65 RBD 66 69 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Taken together, all of these results suggest that the Y453F mutation increases SARS-CoV-2 RBD binding affinity with Mustela ACE2 orthologs. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 54 59 RBD 90 93 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. The enhanced capability of Y453F mutation in utilization of mink ACE2 for cell entry is not due to the high ectopic expression level of mink ACE2 in the A549 cells, as we sorted the A549 cells expressing high, medium or low level of mink ACE2 (S7A Fig), and the SARS-CoV-2pp Y453F or SARS-CoV-2pp mink could entry the cells with equivalent efficiencies, regardless of mink ACE2 expression level (S7B Fig). 2021 PLoS pathogens Result SARS_CoV_2 Y453F;Y453F 27;275 32;280 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. The overall binding mode of Y453F RBD to mink ACE2 was very similar to that of WT RBD to human ACE2 (Fig 3A and S1 Table) as evidenced by the low root mean square deviation (RMSD) value of 0.9 A for the aligned 597 Calpha atoms. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 28 33 RBD;RBD 34;82 37;85 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. The results showed that neutralization of particles bearing the Y453F S protein was almost 3.5-fold less efficient than those bearing the WT protein. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 64 69 S 70 71 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. The signal was further enhanced in A549-mink ACE2 cells inoculated with SARS-CoV-2pp Y453F or SARS-CoV-2pp mink (35- or 42-fold, respectively, compared to A549-mouse ACE2) (Fig 5B). 2021 PLoS pathogens Result SARS_CoV_2 Y453F 85 90 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. The Y453F mutation in miSARS-CoV-2 spike increases interaction with mink ACE2. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 4 9 S 35 40 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. The Y453F mutation in miSARS-CoV-2 spike increases its interaction with other Mustela ACE2 orthologs. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 4 9 S 35 40 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. These differing interactions may account for the enhanced binding of Y453F RBD to mink ACE2. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 69 74 RBD 75 78 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. These results demonstrated that Y453F mutation is essential and sufficient for enhanced binding with mink ACE2. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 32 37 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. These results suggest that the adaptive Y453F mutation can enhance interaction with mink ACE2 and consequently promote virus entry. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 40 45 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. To elucidate at the atomic level the molecular basis for the enhanced binding, we determined the crystal structure of SARS-CoV-2 Y453F RBD bound to mink ACE2 at 3.01 A resolution (Table 1). 2021 PLoS pathogens Result SARS_CoV_2 Y453F 129 134 RBD 135 138 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. To further demonstrate the biological consequences of the enhanced binding affinity of S1 (Y453F) with mink ACE2, we generated MLV retroviral particles (Fluc as the reporter) pseduotyped with SARS-CoV-2 WT spike (SARS-CoV-2pp), Y453F spike (SARS-CoV-2pp Y453F), del69-70/I692V/M1229I spike (SARS-CoV-2pp mink W/O Y453F), or del69-70/Y453F/I692V/M1229I spike (SARS-CoV-2pp mink). 2021 PLoS pathogens Result SARS_CoV_2 Y453F;Y453F;Y453F;Y453F;I692V;I692V;M1229I;M1229I;Y453F 228;254;313;91;271;339;277;345;333 233;259;318;96;276;344;283;351;338 S;S;S;S 206;234;284;352 211;239;289;357 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. To further quantify the binding of ACE2 variants with the spike protein variants, we expressed and purified recombinant WT and Y453F SARS-CoV-2 RBD as well as ACE2 variants to assay binding in vitro by surface plasmon resonance (SPR) analysis (Figs 2E and S4). 2021 PLoS pathogens Result SARS_CoV_2 Y453F 127 132 S;RBD 58;144 63;147 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. We produced MLV virons pseudotyped with WT or Y453F spike and then measured the neutralization activity of convalescent sera against these viruses (Fig 7A). 2021 PLoS pathogens Result SARS_CoV_2 Y453F 46 51 S 52 57 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Y453F spike utilized mink ACE2 with enhanced efficiency for cell entry. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 0 5 S 6 11 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. Both N501Yand A522V were the most frequent mutations that occurred at the RBS of the Iraqi strains with 37% and 53%, respectively (Figure 4). 2022 Gene reports Result SARS_CoV_2 A522V 14 19 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. D614G mutation was also reported to be the dominant (84.20%) among 2634 genome sequence data of SARS-COV2 from Qatar. 2022 Gene reports Result SARS_CoV_2 D614G 0 5 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. D614G was found to be the most predominant mutation as 96% (87 strains) of the sequenced strains were carrying the mutation (Figure 4 ). 2022 Gene reports Result SARS_CoV_2 D614G 0 5 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. However, mutations V198I in NSP2, L37F in SNP6, and T113I in NSP14 were recorded. 2022 Gene reports Result SARS_CoV_2 L37F;T113I;V198I 34;52;19 38;57;24 Nsp2 28 32 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. However, N501T reduces the binding affinity of spike protein to the human ACE2. 2022 Gene reports Result SARS_CoV_2 N501T 9 14 S 47 52 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. However, P681H, which can be found in Alpha (20I, V1), Kappa, and Delta variants, and the residue is located near to the furin cleavage; mutation of P618 to H can increase the transmissibility of the virus. 2022 Gene reports Result SARS_CoV_2 P681H 9 14 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. In terms of genome diversity, B.1.428.1 lineage is characterized by possessing several mutations in the genome including two mutations in the spike protein region which are A522V, D614G (https://www.gisaid.org/). 2022 Gene reports Result SARS_CoV_2 A522V;D614G 173;180 178;185 S 142 147 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. Mutation of T478K in the RBD can be found in both Delta and Kappa (B.1.617.2/1) variants of the virus, but not in Alpha (B.1.1.7), beta (B.1.351), or Gamma (P.1). 2022 Gene reports Result SARS_CoV_2 T478K 12 17 RBD 25 28 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. N501Y mutation can be found in Alpha, Beta, or Gamma, but not in Delta and Kappa variants. 2022 Gene reports Result SARS_CoV_2 N501Y 0 5 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. Other predominant mutations which appeared frequently among Iraq isolates were S982A (55%), A570D (53%), P681H (52%), D1118H (51%). 2022 Gene reports Result SARS_CoV_2 A570D;D1118H;P681H;S982A 92;118;105;79 97;124;110;84 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. Previously, the L452R variant was shown to become resistant to monoclonal antibodies (mAbs) X593 and P2B-2F6, however, mutating leucine (L) to glutamine (Q) or methionine (M) among the Iraqi strains could affect differently on the sensitivity of the strain towards the host and/or vaccine-induced immunity. 2022 Gene reports Result SARS_CoV_2 L452R 16 21 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. Residue 452 in the RBD of the spike protein had two variants (L452Q in accession number: EPI_ISL_1524379) and (L452M in accession number: EPI_ISL_1524347). 2022 Gene reports Result SARS_CoV_2 L452M;L452Q 111;62 116;67 S;RBD 30;19 35;22 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. SARS-COV2 variant carrying D614G mutation has been shown to alter the virus fitness and increased transmissibility of the virus compared to the wild type. 2022 Gene reports Result SARS_CoV_2 D614G 27 32 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. Similarly, D1118H, which is found in Alpha (20I, V1, B.1.1.7) lineage, can increase the transmissibility of the virus. 2022 Gene reports Result SARS_CoV_2 D1118H 11 17 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. Such mutation, same as T478K, increases the transmissibility of the virus. 2022 Gene reports Result SARS_CoV_2 T478K 23 28 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. The B.1.36 lineage was first reported in Saudi Arabia in February 2020 and it was characterized by possessing D614G and L452M mutations, whereas, sublineage B.1.36.1 has an additional mutation of N679K in the spike protein region. 2022 Gene reports Result SARS_CoV_2 D614G;L452M;N679K 110;120;196 115;125;201 S 209 214 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. The variant possesses several mutations including A222V, D614G, and L18F mutations in the spike proteins. 2022 Gene reports Result SARS_CoV_2 A222V;D614G;L18F 50;57;68 55;62;72 S 90 95 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. These mutations were L452 (Q, M), T478K, N501Y, A520S, A522V. 2022 Gene reports Result SARS_CoV_2 A520S;A522V;N501Y;T478K 48;55;41;34 53;60;46;39 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. This lineage is characterized by having a mutation in NPS and D614G mutation in the spike protein region. 2022 Gene reports Result SARS_CoV_2 D614G 62 67 S 84 89 34754982 Analysis of SARS-COV2 spike protein variants among Iraqi isolates. To our knowledge, there is no information about transmissibility and severity of the disease caused by this variant; however, it is expected to spread faster than the wild type since it is having D614G mutation. 2022 Gene reports Result SARS_CoV_2 D614G 196 201 34755818 SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil. Both lineages have the same unique beneficial mutation (E484K) and are very similar genotypically. 2021 Memorias do Instituto Oswaldo Cruz Result SARS_CoV_2 E484K 56 61 34755818 SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil. In this sense, the detection of N.9 and "N.9-like / B.1.1.33 + E484K" reinforces the importance of continuous real-time genomic surveillance to monitor the emergence and behavior of the SARS-CoV-2 variants in the population. 2021 Memorias do Instituto Oswaldo Cruz Result SARS_CoV_2 E484K 63 68 34755818 SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil. The other one (EPI_ISL_2557401), assigned by PANGO Lineage as N.9 lineage, only has one of the six synapomorphic mutations: the G23012A, S: E484K. 2021 Memorias do Instituto Oswaldo Cruz Result SARS_CoV_2 E484K;G23012A 140;128 145;135 S 137 138 34755818 SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil. They seem to be another example of convergent evolution of the E484K mutation in different lineages, and we call them "N.9-like / B.1.1.33 + E484K". 2021 Memorias do Instituto Oswaldo Cruz Result SARS_CoV_2 E484K;E484K 63;141 68;146 34755818 SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil. This convergent evolution of E484K can be evidenced by its appearance multiple times independently around the world in four variants: VOC Beta, VOC Gamma, VOC Kappa and VOI Zeta. 2021 Memorias do Instituto Oswaldo Cruz Result SARS_CoV_2 E484K 29 34 34755818 SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil. We also described an apparently B.1.1.33-derived sublineage that we called as "N.9-like / B.1.1.33 + E484K". 2021 Memorias do Instituto Oswaldo Cruz Result SARS_CoV_2 E484K 101 106 34756912 RT-qPCR detection of SARS-CoV-2 mutations S 69-70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples. In addition, there was no appreciable difference between percentage of N501Y signal detected compared with Sdel or ND3L in any sites, indicating that B.1.1.7 was the predominant variant in Canada throughout the study period. 2022 The Science of the total environment Result SARS_CoV_2 N501Y 71 76 34756912 RT-qPCR detection of SARS-CoV-2 mutations S 69-70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples. N501Y was present at 12.5% at the V3 site on 2021-02-16, followed by two weeks without detection. 2022 The Science of the total environment Result SARS_CoV_2 N501Y 0 5 34757638 Changing predominant SARS-CoV-2 lineages drives successive COVID-19 waves in Malaysia, February 2020 to March 2021. Nonsynonymous mutations seen in the B.1.524 lineage sequences were nsp3-T1198I, nsp4-T28I, nsp5-T24A, nsp12-P323L, nsp13-L428F, spike-D614G, spike-A701V, and N-S194L. 2021 Journal of medical virology Result SARS_CoV_2 A701V;D614G;L428F;P323L;S194L;T1198I;T24A;T28I 147;134;121;108;160;72;96;85 152;139;126;113;165;78;100;89 S;S;Nsp13;Nsp12;Nsp3;Nsp4;Nsp5;N 128;141;115;102;67;80;91;158 133;146;120;107;71;84;95;159 34758391 SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance. Another novel amino acid substitution was observed in the T135I mutation in Case 5 (Figure 1 ). 2022 International journal of infectious diseases Result SARS_CoV_2 T135I 58 63 34758391 SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance. These mutations occurred in the N protein (Table 1), including D3L, R203K, G204R, and S235F mutations in Cases 1-5. 2022 International journal of infectious diseases Result SARS_CoV_2 D3L;G204R;R203K;S235F 63;75;68;86 66;80;73;91 N 32 33 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. African and Brazilian super spreaders, although the E: P71L and S: A701V mutations defining the S. 2021 PeerJ Result SARS_CoV_2 A701V;P71L 67;55 72;59 E;S;S 52;64;96 53;65;97 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. As shown in Table 1 above, the D614G amino acid substitution in the S spike protein was observed in 159 of 277 (57.4%) genomes. 2021 PeerJ Result SARS_CoV_2 D614G 31 36 S;S 70;68 75;69 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. At the 6312 position there were two mutations, one with a T2016I (C- > T) change that was shared by >100 genomes and a second with a T2016K (C- > A) change that was shared by only 85 genomes. 2021 PeerJ Result SARS_CoV_2 T2016I;T2016K 58;133 64;139 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. At the genomic position of 6312, one mutation was observed in March to August (C6312A) and another appeared from September to December (C6312T). 2021 PeerJ Result SARS_CoV_2 C6312A;C6312T 79;136 85;142 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. Based on the isolation dates in GISAID, this mutation was present in the viruses isolated in March 2020, suggesting that D614G was present in Malaysia before it was first reported in the Sivaganga cluster in July-August 2020. 2021 PeerJ Result SARS_CoV_2 D614G 121 126 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. C20823T and A29086T caused non-synonymous mutations in the ORF1ab and N genes respectively, in viruses isolated in May and June. 2021 PeerJ Result SARS_CoV_2 A29086T;C20823T 12;0 19;7 ORF1ab;N 59;70 65;71 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. Except for C21516T, C21622A and A28133T, all were non-synonymous mutations, spanning ORF1ab, S protein, ORF8 and N protein in viruses isolated from September to December 2020. 2021 PeerJ Result SARS_CoV_2 A28133T;C21516T;C21622A 32;11;20 39;18;27 ORF1ab;ORF8;N;S 85;104;113;93 91;108;114;94 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. Excluding the substitution at position 241 in the 5' UTR, the top three most frequent mutations were the C3037T (59.9%), C14408T (59.9%) and A23403G (D614G) (57.4%). 2021 PeerJ Result SARS_CoV_2 A23403G;C14408T;C3037T;D614G 141;121;105;150 148;128;111;155 5'UTR 50 56 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. From March to December, substitutions appeared consistently at the genomic positions C241T, C3037T, C14408T and A23403G. 2021 PeerJ Result SARS_CoV_2 A23403G;C14408T;C241T;C3037T 112;100;85;92 119;107;90;98 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. In the sixth LD set, C18877T, C26735T and G25563T were observed, the former two as synonymous mutations in ORF1ab and M protein, respectively, and the third as a non-synonymous mutation in ORF3a. 2021 PeerJ Result SARS_CoV_2 C18877T;C26735T;G25563T 21;30;42 28;37;49 ORF1ab;ORF3a 107;189 113;194 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. Lastly, LD was observed in C24382T and G28307T causing a synonymous mutation in the S protein, and a non-synonymous mutation in the N protein, respectively. 2021 PeerJ Result SARS_CoV_2 C24382T;G28307T 27;39 34;46 N;S 132;84 133;85 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. Less frequent mutations (Table S2) included a unique 2 bp-deletion in ORF8 (genomic position 28066-28067) that was found in only one genome, and the mutations (C6310A, T7621C and C19524T) reported by neighbouring countries such as Singapore, Australia, and India. 2021 PeerJ Result SARS_CoV_2 C19524T;T7621C;C6310A 179;168;160 186;174;166 ORF8 70 74 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. None of our D614G mutations were accompanied by the S477N substitution noted to be frequently alongside D614G in the S protein. 2021 PeerJ Result SARS_CoV_2 D614G;D614G;S477N 12;104;52 17;109;57 S 117 118 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. The fifth LD set involved genomic positions C13329T, C20823T, C26607T and A29086T. 2021 PeerJ Result SARS_CoV_2 A29086T;C13329T;C20823T;C26607T 74;44;53;62 81;51;60;69 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. The first LD set was observed in the viruses isolated in October 2020, at the genomic positions of A1904G, C12488T and G23236T. 2021 PeerJ Result SARS_CoV_2 A1904G;C12488T;G23236T 99;107;119 105;114;126 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. The fourth LD set involved four mutations across three different proteins, at the genomic positions of G11083T, C13730T, C23929T and C28311T. 2021 PeerJ Result SARS_CoV_2 C13730T;C23929T;C28311T;G11083T 112;121;133;103 119;128;140;110 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. The non-synonymous mutations were in the ORF1ab (T2016K, L3606F, A4489V) and N (P13L). 2021 PeerJ Result SARS_CoV_2 A4489V;L3606F;P13L;T2016K 65;57;80;49 71;63;84;55 ORF1ab;N 41;77 47;78 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. The second LD set comprised C3037T, C14408T and A23403G mutations in viruses isolated from March to December and involving a single synonymous and non-synonymous mutation in ORF1ab, together with a single non-synonymous mutation in the S protein. 2021 PeerJ Result SARS_CoV_2 A23403G;C14408T;C3037T 48;36;28 55;43;34 ORF1ab;S 174;236 180;237 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. The third LD set was found in eight genomic positions, namely C8637T, A10124G, C17518T, C21516T, C21622A, C23664T, A28133T and C28854T. 2021 PeerJ Result SARS_CoV_2 A10124G;A28133T;C17518T;C21516T;C21622A;C23664T;C28854T;C8637T 70;115;79;88;97;106;127;62 77;122;86;95;104;113;134;68 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. There was only one genome each with the T8782C and C28144T mutations that have been used to distinguish the type B variant predominant in East Asia from the type A variant predominant in North America and Europe . 2021 PeerJ Result SARS_CoV_2 C28144T;T8782C 51;40 58;46 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. There was only one genome each with the T8782C and C28144T mutations that have been used to distinguish the type B variant predominant in East Asia from the type A variant predominant in North America and Europe. 2021 PeerJ Result SARS_CoV_2 C28144T;T8782C 51;40 58;46 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. These mutations were C5869T, C8637T, A10124G, C17518T, C21365T, C21516T, C21622A, C23664T, A28133T and C28854T. 2021 PeerJ Result SARS_CoV_2 A10124G;A28133T;C17518T;C21365T;C21516T;C21622A;C23664T;C28854T;C5869T;C8637T 37;91;46;55;64;73;82;103;21;29 44;98;53;62;71;80;89;110;27;35 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. Those shared by at least 100 genomes were at 13 genome positions (241, 3037, 6312, 8637, 10124, 14408, 17518, 21516, 21622, 23403, 23664, 28133, and 28854) with eight non-synonymous mutations in the ORF1ab (T2016I, T2791I, T3287A, P4715L, L5752F), S gene (D614G, A701V) and the N gene (S194L) respectively. 2021 PeerJ Result SARS_CoV_2 A701V;L5752F;P4715L;T2791I;T3287A;D614G;S194L;T2016I 263;239;231;215;223;256;286;207 268;245;237;221;229;261;291;213 ORF1ab;N;S 199;278;248 205;279;249 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. Two mutations, C13730T and C23929T were noted to be present in viruses isolated in March to August. 2021 PeerJ Result SARS_CoV_2 C13730T;C23929T 15;27 22;34 34763050 Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation. P.2 sequences presented E484K, D614G e V1176F and the B.1.1.28 sequences, D614G and V1176F spike mutations. 2021 Infection, genetics and evolution Result SARS_CoV_2 D614G;D614G;E484K;V1176F;V1176F 31;74;24;39;84 36;79;29;45;90 S 91 96 34763050 Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation. The Gamma sequences generated herein presented the classical mutational signatures in spike glycoprotein L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I and V1176F, with some exceptions, as in the sample hCoV-19/Brazil/LMM53965 and hCoV-19/Brazil/LMM54004 that change a guanine for an adenine in 614 position (D614G D614A) and the hCoV-19/Brazil/LMM54029 that change a histidine for a glutamic acid in 655 position (H655Y H655E). 2021 Infection, genetics and evolution Result SARS_CoV_2 D138Y;D614A;D614G;E484K;H655E;H655Y;E655H;K417T;L18F;N501Y;P26S;R190S;T1027I;T20N;V1176F;D614G;H655Y 123;344;158;144;452;165;397;137;105;151;117;130;172;111;183;336;444 128;349;163;149;457;170;433;142;109;156;121;135;178;115;189;341;449 S 86 104 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. All B.6 strains within this group contained four additional genetic variations; C6312A, C13730T, C23929T, and C28311T in addition to G11083T mutation. 2021 Scientific reports Result SARS_CoV_2 C13730T;C23929T;C28311T;C6312A;G11083T 88;97;110;80;133 95;104;117;86;140 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. All samples obtained on 21 April 2020 carried two nucleotide changes C241T and G11803T, while sample obtained on 2 May 2020 (2May20-132-Hu/2020) only possessed G11803T. 2021 Scientific reports Result SARS_CoV_2 C241T;G11803T;G11803T 69;79;160 74;86;167 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. All strains clustered under this group, including those sequenced in the current study, possessed the three GISAID clade G genetic variants, C241T, C3037T, and A23403G with an additional mutation C14408T. 2021 Scientific reports Result SARS_CoV_2 A23403G;C14408T;C241T;C3037T 160;196;141;148 167;203;146;154 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. All strains within this B.2/B.6 lineage shared genetic variation G11083T, encoded for amino acid changes from leucine to phenylalanine at position 37 of nsp6 in ORF1ab. 2021 Scientific reports Result SARS_CoV_2 G11083T;L37F 65;110 72;149 ORF1ab;Nsp6 161;153 167;157 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. Among the nine variations, six (C6312T, C8637T, A10124G, C17518T, C23664T, and C28854T) caused amino acid substitutions (nsp3-T1198I, nsp4-T28I, nsp5-T24A, nsp13-L428F, S-A701V, and N-S194L). 2021 Scientific reports Result SARS_CoV_2 A10124G;C17518T;C23664T;C28854T;C8637T;C6312T;A701V;L428F;S194L;T1198I;T24A;T28I 48;57;66;79;40;32;171;162;184;126;150;139 55;64;73;86;46;38;176;167;189;132;154;143 Nsp13;Nsp3;Nsp4;Nsp5;N;S 156;121;134;145;182;169 161;125;138;149;183;170 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. An additional shared genetic variation, G25429T encoded for an amino acid substitution of valine to leucine at position 13 of the ORF3a (ORF3a-V13L), was observed. 2021 Scientific reports Result SARS_CoV_2 G25429T;V13L;V13L 40;90;143 47;122;147 ORF3a;ORF3a 130;137 135;142 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. Based on the GISAID clade assignment, the samples detected during early April 2020 (4Apr20-3-Hu/2020 and 5Apr20-64-Hu/2020), and all samples detected in October 2020 (third epidemic wave) denoted clade G (Table 1), possessed genetic variations at C241T, C3037T, and A23403G. 2021 Scientific reports Result SARS_CoV_2 A23403G;C241T;C3037T 266;247;254 273;252;260 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. Besides the GISAID clade S-specific genetic markers, C8782T and T28144C, there were no other shared mutations between these two samples. 2021 Scientific reports Result SARS_CoV_2 C8782T;T28144C 53;64 59;71 S 25 26 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. Both strains shared an additional genetic variation, C18877T, a synonymous mutation. 2021 Scientific reports Result SARS_CoV_2 C18877T 53 60 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. For example, the B.6.1(O) subgroup was also characterized by a mutation, T7621C. 2021 Scientific reports Result SARS_CoV_2 T7621C 73 79 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. In addition to the T11803, both strains possessed additional two nucleotide variations, C14805T and G26144T. 2021 Scientific reports Result SARS_CoV_2 C14805T;G26144T 88;100 95;107 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. Our samples obtained in mid-Apr 2020 clustered within the C7621-C2554T-groups, with additional mutations detected in some of the samples. 2021 Scientific reports Result SARS_CoV_2 C2554T 64 70 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. Out of the five genetic variations, one was identified in the 5'UTR regions (G114T), three located within ORF1ab (C5869T, C11941T, and C21365T), and one in the N gene (A29426G). 2021 Scientific reports Result SARS_CoV_2 C11941T;C21365T;A29426G;C5869T;G114T 122;135;168;114;77 129;142;175;120;82 ORF1ab;5'UTR;N 106;62;160 112;67;161 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. Sequence analysis showed a common ancestor of B.1.524 lineage (T241-T3037-T14408-G23403), with the acquisition of nine mutations (C6312T, C8637T, A10124G, C17518T, C21516T, C21622A, C23664T, A28133T, and C28854T) that could have seeded transmission clusters of the two closely related groups in Sabah and Selangor (Tables 2 and 3). 2021 Scientific reports Result SARS_CoV_2 A10124G;A28133T;C17518T;C21516T;C21622A;C23664T;C28854T;C8637T;C6312T 146;191;155;164;173;182;204;138;130 153;198;162;171;180;189;211;144;136 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. So far, only strains that fell within this B.1-associated lineage carried this S-D614G amino acid substitution. 2021 Scientific reports Result SARS_CoV_2 D614G 81 86 S 79 80 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. Strains that possessed additional three genetic markers G28881A, G28882A, and G28883C, clustered under clade GH, strains which possessed G25563T was assigned as clade GR, and the strains that presented without these additional genetic variations remained as Clade G. 2021 Scientific reports Result SARS_CoV_2 G25563T;G28881A;G28882A;G28883C 137;56;65;78 144;63;72;85 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. The A23403G was encoded for substitution of aspartic acid with glycine in the S-614 (S-D614G). 2021 Scientific reports Result SARS_CoV_2 A23403G;D614G 4;87 11;92 S;S 78;85 79;86 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. The C14408T and A23403G were missense mutations (Table 2). 2021 Scientific reports Result SARS_CoV_2 A23403G;C14408T 16;4 23;11 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. The C14408T is a common mutation used to define B.1 in the Pangolin system, and it is also used to define a haplogroup A2a4 (another SARS-CoV-2 clustering system). 2021 Scientific reports Result SARS_CoV_2 C14408T 4 11 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. The C14408T was encoded for substitution of proline with leucine at position 323 in nsp12 of ORF1ab (nsp12-P323L). 2021 Scientific reports Result SARS_CoV_2 C14408T;P323L;P323L 4;44;107 11;80;112 ORF1ab;Nsp12;Nsp12 93;84;101 99;89;106 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. The C14805T was a synonymous mutation that was not originally present in China during the early spread of the virus, suggesting this mutation could have accumulated in the SARS-CoV-2 gene pool outside of China. 2021 Scientific reports Result SARS_CoV_2 C14805T 4 11 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. The C21365T caused an amino acid substitution of Proline for Leucine at position 236 in nsp16 of the ORF1ab (nsp16-P236L), while A29426G caused the substitution of arginine for glycine at position 385 in N (N-R385G). 2021 Scientific reports Result SARS_CoV_2 A29426G;G385R;C21365T;L236P;P236L;R385G 129;164;4;49;115;209 136;200;11;84;120;214 ORF1ab;N;N 101;204;207 107;205;208 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. The G11083T and G26144T were genetic markers for the assignment of GISAID Clade V. 2021 Scientific reports Result SARS_CoV_2 G11083T;G26144T 4;16 11;23 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. The G114T mutation at 5UTR detected in Selangor strains, was a novel mutation reported for the first time in our study. 2021 Scientific reports Result SARS_CoV_2 G114T 4 9 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. The G970T variation that caused an amino acid substitution at E55D in nsp2 (nsp2-E55D) was a unique genetic variation present in all Sabah strains except for hCoV-19/Malaysia/7Oct20-83-Hu/2020. 2021 Scientific reports Result SARS_CoV_2 E55D;G970T;E55D 62;4;81 66;9;85 Nsp2;Nsp2 70;76 74;80 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. The MY.14OCT20-219-Hu/2020 lacked G114T, C11941T, and A29426G but possessed different mutations (C4423T and C16376T; Table 3), likely pointing to the presence of another transmission chain. 2021 Scientific reports Result SARS_CoV_2 A29426G;C11941T;C16376T;G114T;C4423T 54;41;108;34;97 61;48;115;39;103 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. The resulting amino acid substitution, nsp2-E55D was a rare mutation currently only detected in one strain globally (https://bigd.big.ac.cn/ncov/variation/annotation/variant/970). 2021 Scientific reports Result SARS_CoV_2 E55D 44 48 Nsp2 39 43 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. The strains that possessed all four mutations (C241T-C3037T-C14408T-A23403T) were actively circulating, especially in Europe (https://bigd.big.ac.cn/ncov/) before its first documented detection in Malaysia in late March, 2020. 2021 Scientific reports Result SARS_CoV_2 C241T;A23403T;C14408T;C3037T 47;68;60;53 52;75;67;59 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. The T19524 and T19524T-A6210 strains were also detected in neighboring countries including Singapore, Thailand, and Australia (https://bigd.big.ac.cn/ncov/) but not the T19524-A6210-A2508 strains, suggesting the C2508A could be a mutation that accumulated in the SARS-CoV-2 gene pool during the second COVID-19 epidemic wave in Malaysia. 2021 Scientific reports Result SARS_CoV_2 C2508A;T19524T 212;15 218;22 COVID-19 302 310 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. These A6312A-T11083-T13730-T23929-T28311-bearing strains were segregated into multiple distinct subgroups with the presence of several unique genetic traits. 2021 Scientific reports Result SARS_CoV_2 A6312A 6 12 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. These B.12(L) strains contained two genetic variations, C11752T and C19170A. 2021 Scientific reports Result SARS_CoV_2 C11752T;C19170A 56;68 63;75 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. These C7621-bearing strains were further delineated into two groups differentiated by an additional mutation, C25549T. 2021 Scientific reports Result SARS_CoV_2 C25549T 110 117 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. These strains shared two missense mutations, the C1758T which encoded for amino acid substitution of alanine to valine at position 318 of nsp2, and the C10604T encoded for amino acid substitution proline with serine at position 184 of nsp5 (Table 2). 2021 Scientific reports Result SARS_CoV_2 A318V;C10604T;C1758T;P184S 101;152;49;196 134;159;55;231 Nsp2;Nsp5 138;235 142;239 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. This T7621C mutation was a synonymous mutation detected in 29 strains, mainly from Malaysia and Brunei (https://bigd.big.ac.cn/ncov/variation/annotation/variant/7612), suggesting that this is a unique mutation that occurred in this region and could have originated from a single origin. 2021 Scientific reports Result SARS_CoV_2 T7621C 5 11 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. We looked into the time of emergence of these mutations (https://bigd.big.ac.cn/ncov/); the first strain which carried the C1064T (nsp5-P184S) was reported in hCoV-19/Beijing/BJ53/2020 detected on 24 January 2020 from Beijing, while the first strain that carried both C1758T/C10064T was hCoV-19/Malaysia/MKAK-CL-2020-7554/2020 detected in Malaysia on 6 February 2020. 2021 Scientific reports Result SARS_CoV_2 C1064T;C1758T;C10064T;P184S 123;268;275;136 129;274;282;141 Nsp5 131 135 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. While the C14805T was an additional genetic trait present in this group. 2021 Scientific reports Result SARS_CoV_2 C14805T 10 17 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. Within B.6(O), another group with the additional mutation, C19524T, was observed; subsequently, an additional C6210A and then C2508A was detected in a subset of this group (B.6.6(O)). 2021 Scientific reports Result SARS_CoV_2 C19524T;C2508A;C6210A 59;126;110 66;132;116 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. 69.1% had mutation H182Y. 2021 PLoS pathogens Result SARS_CoV_2 H182Y 19 24 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. A query of all GISAID sequences from Neovison vison viruses revealed that 95.4% had mutations D614G and N501T. 2021 PLoS pathogens Result SARS_CoV_2 D614G;N501T 94;104 99;109 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. included S1206L-NSP3, V1871I-NSP13, T91M-NSP16, K113T-spike, A38S-M, T2051-N, and Q289H-N. 2021 PLoS pathogens Result SARS_CoV_2 A38S;K113T;Q289H;T91M 61;48;82;36 65;53;87;40 S;Nsp13;Nsp3;N;N 54;29;16;75;88 59;34;20;76;89 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. One of the two mink from farm A had mutations at T85I-NSP2, S1205L-NSP3, G37E-NSP9, P323L-NSP12, T91M-NSP15, D614G-spike, N501T-spike, Q57H-NS3, H182Y-NS3, and T205I-N as compared to hCoV-19/Wuhan/WIV04/2019. 2021 PLoS pathogens Result SARS_CoV_2 D614G;G37E;H182Y;N501T;P323L;Q57H;S1205L;T205I;T85I;T91M 109;73;145;122;84;135;60;160;49;97 114;77;150;127;89;139;66;165;53;101 S;S;Nsp12;Nsp2;Nsp3;NS3;NS3;N 115;128;90;54;67;140;151;166 120;133;95;58;71;143;154;167 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. Sequences were identical between animals from the same farm, with the exception of some ambiguous base calls and one sequence from farm A had an A38S-M mutation. 2021 PLoS pathogens Result SARS_CoV_2 A38S 145 149 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. Synonymous SNPs from this Farm A isolate included C1059T, C3037T, C6336T, G12795A, C14408T, C20930T, A23064C, A23403G, G25563T, C25936T, C28887T, were also identical to those of MW474212 from a human in Washington State. 2021 PLoS pathogens Result SARS_CoV_2 A23064C;A23403G;C1059T;C14408T;C20930T;C25936T;C28887T;C3037T;C6336T;G12795A;G25563T 101;110;50;83;92;128;137;58;66;74;119 108;117;56;90;99;135;144;64;72;81;126 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. The second farm A virus and all four farm B viruses had the same mutations as farm A, with additional mutation A38S-M, and additional mutation Q289H-N in Farm B viruses only. 2021 PLoS pathogens Result SARS_CoV_2 A38S;Q289H 111;143 115;148 N 149 150 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. The two farm C viruses had the same mutations as the initial farm A, with additional mutations K113T-spike and V187I-NSP13. 2021 PLoS pathogens Result SARS_CoV_2 K113T;V187I 95;111 100;116 S;Nsp13 101;117 106;122 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. These unique mutations included S1206L-NSP3, V1871I-NSP13, T91M-NSP16, K113T-spike, A38S-M, T2051-N, and Q289H-N. 2021 PLoS pathogens Result SARS_CoV_2 A38S;K113T;Q289H;S1206L;T2051N;T91M;V1871I 84;71;105;32;92;59;45 88;76;110;38;99;63;51 S;Nsp13;Nsp3;N;N 77;52;39;98;111 82;57;43;99;112 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. 5) and for the alpha/beta/gamma mutant [D614G] S1 protein. 2021 Scientific reports Result SARS_CoV_2 D614G 40 45 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. As for the other RBD variants the beta [E484K] RBD protein has a profound "concave-down" structure for the lower values of ACE2 binding. 2021 Scientific reports Result SARS_CoV_2 E484K 40 45 RBD;RBD 17;47 20;50 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. As summarized in Table 1, KD values for the Mink [Y453F] RBD and alpha/beta/gamma [N501Y] RBD variants are significantly reduced from 72 to 30 and 25 ng/ml ACE2, respectively. 2021 Scientific reports Result SARS_CoV_2 N501Y;Y453F 83;50 88;55 RBD;RBD 57;90 60;93 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Compared to the other RBD variants the beta [E484K] RBD has a slightly more evident lag than the original Wuhan RBD. 2021 Scientific reports Result SARS_CoV_2 E484K 45 50 RBD;RBD;RBD 22;52;112 25;55;115 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Digoxigenin has a slightly lower Ki value for Mink [Y453F] and alpha/beta/gamma [N501Y]. 2021 Scientific reports Result SARS_CoV_2 N501Y;Y453F 81;52 86;57 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Equivalent results for the Mink [Y453F] RBD protein and the alpha/beta/gamma [N501Y] RBD protein are shown in Supplementary Figs. 2021 Scientific reports Result SARS_CoV_2 N501Y;Y453F 78;33 83;38 RBD;RBD 40;85 43;88 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Figure 1c, d show the same descriptive positive cooperativity behavior in Eadie-Hofstee plots for both the alpha/beta/gamma [D614G] S1 protein and the Original [D614] RBD protein, respectively. 2021 Scientific reports Result SARS_CoV_2 D614G 125 130 RBD 167 170 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Figure 2a shows the substrate-binding isotherms for the Mink [Y453F] RBD and the alpha/beta/gamma [N501Y] RBD proteins, and compares them with the Original [D614] S1, and the Original RBD proteins. 2021 Scientific reports Result SARS_CoV_2 N501Y;Y453F 99;62 104;67 RBD;RBD;RBD 69;106;184 72;109;187 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Figure 2c, d show the same type of data for the Mink [Y453F] RBD protein and the alpha/beta/gamma [N501Y] RBD protein, respectively. 2021 Scientific reports Result SARS_CoV_2 N501Y;Y453F 99;54 104;59 RBD;RBD 61;106 64;109 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Figure 3a shows the substrate-binding plots for the recombinant beta [E484K] RBD protein. 2021 Scientific reports Result SARS_CoV_2 E484K 70 75 RBD 77 80 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Figure 7a shows the Substrate-Binding plots for ACE2 binding to the beta [E484K] RBD protein. 2021 Scientific reports Result SARS_CoV_2 E484K 74 79 RBD 81 84 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Finally, we tested the ability of cardiac glycoside drugs to inhibit ACE2 binding to the beta [E484K] RBD protein, the alpha/beta/gamma [N501Y] protein and the Mink [Y453F] RBD protein. 2021 Scientific reports Result SARS_CoV_2 E484K;N501Y;Y453F 95;137;166 100;142;171 RBD;RBD 102;173 105;176 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. However, the binding isotherm for the mutant alpha/beta/gamma [D614G] S1 differs quantitatively from that of the Original S1 and Original RBD. 2021 Scientific reports Result SARS_CoV_2 D614G 63 68 RBD 138 141 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. The highest values are for beta [E484K], regardless of which drug or drug-derivative is present in the analysis. 2021 Scientific reports Result SARS_CoV_2 E484K 33 38 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. The Hill plot for the beta [E484K] RBD protein is shown in. 2021 Scientific reports Result SARS_CoV_2 E484K 28 33 RBD 35 38 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. The mutant with the highest significance, independent of the treatment, is the beta [E484K]. 2021 Scientific reports Result SARS_CoV_2 E484K 85 90 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. The slope for the beta [E484K] RBD variant, (nH), is 1.25 +- 0.05, and is significantly higher than for the other RBD proteins. 2021 Scientific reports Result SARS_CoV_2 E484K 24 29 RBD;RBD 31;114 34;117 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. To further test for the ACE2 positive cooperativity mechanism we analyzed the beta [E484K] RBD data using an Eadie-Hoffstee plot. 2021 Scientific reports Result SARS_CoV_2 E484K 84 89 RBD 91 94 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. We also found similar results for inhibition of ACE2 binding to the alpha,beta,gamma mutant [D614G] S1 (Supplemental. 2021 Scientific reports Result SARS_CoV_2 D614G 93 98 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. If there are any, then the Ser46Ala and/or Asn65Ser sequence differences could alter the functional life-time of the SARS-CoV-2 3CLpro without changing its activity. 2021 International journal of biological macromolecules Result SARS_CoV_2 N65S;S46A 43;27 51;35 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. In rat trypsin, Lys61 (Lys60 in bovine trypsin) and Arg117 are both replaced by Asn. 2021 International journal of biological macromolecules Result SARS_CoV_2 R117N 52 83 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. In spite of this, mutation of Asn28 to alanine disrupts dimerization (active form of enzyme) and completely inactivates the 3CLpro SARS-CoV. 2021 International journal of biological macromolecules Result SARS_CoV_2 N28A 30 46 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. It was also suggested that the mutation Ser46Ala may increase the contribution of other hydrophilic amino acids to the structure of the active site. 2021 International journal of biological macromolecules Result SARS_CoV_2 S46A 40 48 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. Mutant Phe114Ile has the same enzymatic activity and molecular stability as the wild-type enzyme, but exhibites significantly slower autolytic inactivation. 2021 International journal of biological macromolecules Result SARS_CoV_2 F114I 7 16 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. Positions 65 and 66 are adjacent in the amino acid sequence, therefore, it can be reasonably assumed that Asn65Ser sequence difference would affect the contact between the Val42-Leu67 loop and the Cys85-Zone through the amino acid Phe66. 2021 International journal of biological macromolecules Result SARS_CoV_2 N65S 106 114 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. Ser46Ala and Asn65Ser, and probable autolysis regulation in the SARS-CoV-2 3CLpro. 2021 International journal of biological macromolecules Result SARS_CoV_2 N65S;S46A 13;0 21;8 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. The mutation Asn65Ser of the SARS-CoV-2 3CLpro is located near the C-terminal end of the Val42-Leu67 loop. 2021 International journal of biological macromolecules Result SARS_CoV_2 N65S 13 21 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. There is another possibility related to the functional consequences of the Ser46Ala and Asn65Ser sequence differences between the SARS-COV-2 and SARS-COV 3CLpro proteins. 2021 International journal of biological macromolecules Result SARS_CoV_2 N65S;S46A 88;75 96;83 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. Therefore, the Ser46Ala sequence difference between the SARS-CoV-2 and SARS-COV 3CLpros, located near position 58T, can affect the catalytic activity of the SARS-CoV-2 3CLpro not only by itself, but also indirectly through the IDL C-terminal extension. 2021 International journal of biological macromolecules Result SARS_CoV_2 S46A 15 23 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. As indicated above, the November viruses (following re-infection) from Farm 4 had the A22920T mutation and the deletions in the S and ORF1a coding sequences. 2021 PLoS pathogens Result SARS_CoV_2 A22920T 86 93 ORF1a;S 134;128 139;129 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. Furthermore, the viruses on Farm 4 in November also all shared changes at nt 3792 (resulting in A1176V), 5167, 10887 (resulting in G3541E), 21727 and 23815 (these latter two silent changes are in the S gene) that were not present in any of the Farm 4 sequences in August (Table 2). 2021 PLoS pathogens Result SARS_CoV_2 A1176V;G3541E 96;131 102;137 S 200 201 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. In particular, they each had the mutation A22920T in the spike protein coding sequence, resulting in the amino acid substitution Y453F. 2021 PLoS pathogens Result SARS_CoV_2 A22920T;Y453F 42;129 49;134 S 57 62 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. It is noteworthy that the Farm 4 sequences in November had changes at nt 10448 (encoding the substitution P3395S in ORF1a) and 20756 (encoding S2430I in ORF1b) that had only been seen in a subset of the August sequences from Farm 4 (samples Farm4_18_13-08-2020 and Farm4_19_13-08-2020, see Fig 3B). 2021 PLoS pathogens Result SARS_CoV_2 P3395S;S2430I 106;143 112;149 ORF1a 116 121 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. This deletion had not been identified previously in mink or in humans in combination with the Y453F substitution (see Table 2) but the deletion of these residues is shared with the SARS CoV-2 variant of concern (VOC) 202012/01. 2021 PLoS pathogens Result SARS_CoV_2 Y453F 94 99 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. Two other deletions in the ORF1a coding sequence (Delta517-519 and Delta6510-6512) and two other amino acid substitutions (P3395S in ORF1a and S2430I in ORF1b) were also observed in some of the viruses present in the mink during this initial infection in August. 2021 PLoS pathogens Result SARS_CoV_2 S2430I;P3395S 143;123 149;129 ORF1a;ORF1a 27;133 32;138 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Finally, no significant differences between neutralizing antibody titers were observed between A1 and B lineages without E484K mutation (Figure 2B). 2022 Virus research Result SARS_CoV_2 E484K 121 126 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Furthermore, in line with the previous report, the B.1+L249S+E484K sample genome is grouped in a sublineage of the B.1.111 lineage. 2022 Virus research Result SARS_CoV_2 E484K;L249S 61;55 66;60 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Molecular epidemiological data support a decrease of B.1+L249S+E484K cases between March-2020 and July-2021. 2022 Virus research Result SARS_CoV_2 E484K;L249S 63;57 68;62 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Reduced neutralization antibody titers against B1+L249S+E484K in convalescent sera. 2022 Virus research Result SARS_CoV_2 E484K;L249S 56;50 61;55 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Regarding B.1.111 isolates, although both share the mutation pattern characteristic of the B.1.111 lineage (Spike D614G, NS3 Q57H and NSP12 P323L), several divergent genome wide mutations were observed between those isolates, for example, EPI_ISL_794659 have two additional mutations at the S protein (Spike T859I and W152R) (Table 1). 2022 Virus research Result SARS_CoV_2 D614G;P323L;Q57H;T859I;W152R 114;140;125;308;318 119;145;129;313;323 S;S;Nsp12;NS3;S 108;302;134;121;291 113;307;139;124;292 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Remarkably, B.1+L249S+E484K was exclusively distributed in the Caribbean region between March-2020 and July-2021, and the decline of cases by the end of this period suggests a limited community transmission. 2022 Virus research Result SARS_CoV_2 E484K;L249S 22;16 27;21 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Remarkably, the isolate EPI_ISL_1092007 currently assigned to the B.1 lineage (PANGO v.3.1.7 2021-07-09) was proposed for lineage reassignment (B.1+L249S+E484K) and laboratory evaluation of neutralizing antibodies in convalescent sera. 2022 Virus research Result SARS_CoV_2 E484K;L249S 154;148 159;153 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Specifically, the neutralizing titers against B.1+L249S+E484K were 1.5, 1.9, 2.1 and 1.3-fold lower than against A.1, B.1.420, B.1.111-I and B.1.111-II, respectively. 2022 Virus research Result SARS_CoV_2 E484K;L249S 56;50 61;55 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Successful isolation of SARS-CoV-2 lineages with and without the Spike E484K mutation. 2022 Virus research Result SARS_CoV_2 E484K 71 76 S 65 70 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. The isolate B.1.111-I is located close to the node defining the B.1.111 lineage, while B.1.111-II is placed in a monophyletic group along with more B.1.111 sequences containing the Spike mutation W152R, which is not as divergent as B.1+L249S+E484K. 2022 Virus research Result SARS_CoV_2 W152R;E484K;L249S 196;242;236 201;247;241 S 181 186 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. The remaining isolates represented SARS-CoV-2 lineages without the E484K mutation as follows; EPI_ISL_49816 representing the A1 lineage, it was the only isolate without the characteristic D614G mutation in the S protein obtained in this study. 2022 Virus research Result SARS_CoV_2 D614G;E484K 188;67 193;72 S 210 211 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Then, the neutralizing capacity of these sera was evaluated using eight 2-fold serially diluted sera (1:20 to 1:12560) against A.1, B.1.420, B.1.111, and B.1+L249S+E484K lineages to determine the MN50 titer of each serum sample. 2022 Virus research Result SARS_CoV_2 E484K;L249S 164;158 169;163 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Thus, the E484K mutation in B.1+L249S+E484K appears not to affect the viral titer in Vero E6 cells (Table 2 ) or the virus ability to induce a cytopathic effect. 2022 Virus research Result SARS_CoV_2 E484K;E484K;L249S 10;38;32 15;43;37 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Examination of the results of FoldX, Rosetta, and OSPREY showed that the N501Y mutation increases the stability of the spike protein (Table 5). 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 73 78 S 119 124 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Furthermore, Thr500 interacts with residue Asp355 with two hydrogen bonds (2.61 and 3.06 A) versus in the N501Y variant, Tyr at position 501 is able to form one hydrogen bond with Lys353 (2.93 A), while its aromatic ring forms two hydrophobic bonds with Tyr41 (5.13 A) and Lys353 (3.94 A) ACE2. 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 106 111 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. In addition to the distance and number of interactions between the residues in the spike interface with its receptor, another factor that increases the binding potency in the N501Y is the shape of the Tyr side chain. 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 175 180 S 83 88 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. In addition to the higher binding affinity, the number of epitope regions in the native spike was higher than the N501Y variant (Figure 1). 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 114 119 S 88 93 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. In previous studies, confirmation of lineages carrying the N501Y have higher viral load and resistance to antibody neutralization, the observed decrease in immunogenicity can be attributed to the occurrence of this phenomenon. 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 59 64 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. In the final step, MD trajectory files were examined to track the effect of N501Y mutation on the affinity of spike for its receptor using functions such as a number of hydrogen bonds, the distance between interface residues, and the number of contacts at distance less than 0.6 nm for the spike-ACE2 complexes. 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 76 81 S;S 110;290 115;295 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. In the next step, FEL and PCA functions were extracted to track the effect of the N501Y mutation on the folding and the conformational energy patterns of the target structures (Figure 6). 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 82 87 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Indeed, following the N501Y mutation affinity of spike protein increases for its receptor (Table 2). 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 22 27 S 49 54 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Insight into immunological characteristics of native and N501Y variants of spike comprehensively was obtained in two steps. 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 57 62 S 75 80 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. It was observed that the N501Y spike has the less binding ability for MHC-1 compared to the native type. 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 25 30 S 31 36 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Regarding the results observed during MD simulation, it can be claimed that the N501Y mutation has a significant effect on the RBD domain of SARS-CoV-2 spike protein and can increase the spike stability and its affinity to ACE2. 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 80 85 S;S;RBD 152;187;127 157;192;130 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Residue scanning calculations of DynaMut also confirm the docking results and show that the stability of the spike-ACE2 complex improves following the N501Y mutation (-0.522 kcal/mol). 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 151 156 S 109 114 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Rosetta energies for native and N501Y variants were -1945.63 and -1948.516, respectively. 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 32 37 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. The effect of the N501Y mutation on spike folding was tracked by evaluating the Rg and SASA functions. 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 18 23 S 36 41 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. The outputs of the structural energy investigation agreed with the results of other analysis steps and indicate the positive effect of the N501Y on the stability and affinity of the spike to its receptor. 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 139 144 S 182 187 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. The pattern of residues interactions for spike-ACE2 complex in both native and N501Y variants was tracked using Rosetta docking protocol as a state-of-the-art, free, and open-source suite. 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 79 84 S 41 46 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. These results confirm the RMSD, RMSF, and Rg outputs and indicate that the flexibility and structural variation decrease following N501Y mutation. 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 131 136 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. This characteristic leads to the better formation of the binding pocket of the N501Y SARS-CoV-2 lineage. 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 79 84 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. We found that the pattern of dihedral angles and triangles area changes following the N501Y displacement. 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 86 91 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. We found that, with the exception of polar solvent energy, the other constituent functions of the binding energy were more optimal for the complex containing the N501Y mutation (Table 4). 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 162 167 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. We observed that the N501Y displacement could affect the composition of the secondary structural components of its adjacent amino acids. 2022 Journal of cellular biochemistry Result SARS_CoV_2 N501Y 21 26 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. A kinetic characterization also showed a greater rate of fluorescence increase with time in the case of a sequence with the E484K mutation and that the CRISPR-Cas12a-based detection can be done in just 15 min (Figure 1E). 2021 ACS synthetic biology Result SARS_CoV_2 E484K 124 129 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. Alternatively, the promiscuity of Cas12a in the PAM recognition can be exploited (e.g., the noncanonical PAM sequence CTTA is formed upon the N501Y mutation). 2021 ACS synthetic biology Result SARS_CoV_2 N501Y 142 147 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. At the nucleotide level, the E484K mutation is implemented as a substitution of a guanine by an adenine. 2021 ACS synthetic biology Result SARS_CoV_2 E484K 29 34 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. Consequently, the designed crRNA has two potential uses, one to detect the presence of SARS-CoV-2 in the sample and another to inform about if it harbors the E484K mutation. 2021 ACS synthetic biology Result SARS_CoV_2 E484K 158 163 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. For example, in the case of the N501Y mutation, also present in the variants Beta, Gamma, and evolved Alpha in combination with the E484K mutation, the Cas12a RVR variant might be exploited to recognize the resulting PAM sequence TATG (in the sense strand of the dsDNA amplicon). 2021 ACS synthetic biology Result SARS_CoV_2 E484K;N501Y 132;32 137;37 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. Hence, these results demonstrated that CRISPR-Cas12a reactions are useful to disclose SARS-CoV-2 infections whose genomes harbor the E484K mutation in a rapid and inexpensive way. 2021 ACS synthetic biology Result SARS_CoV_2 E484K 133 138 COVID-19 86 107 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. In a sample from patient P4, an adenine was revealed at the corresponding position (leading to the E484K mutation), while a guanine was always found in the case of all other samples (Figure 1H), in agreement with the fluorescent results. 2021 ACS synthetic biology Result SARS_CoV_2 E484K 99 104 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. Interestingly, this crRNA allowed discriminating sequences with the E484K mutation, as the fluorescence readout significantly increased as a result of the presence of the canonical PAM sequence (Figure 1C). 2021 ACS synthetic biology Result SARS_CoV_2 E484K 68 73 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. Interestingly, we found that the fluorescence readout for patient P4 was significantly higher than for the rest of patients (Figure 1G), which indicated that patient P4 was likely infected by a SARS-CoV-2 variant with the E484K mutation. 2021 ACS synthetic biology Result SARS_CoV_2 E484K 222 227 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. Therefore, if a viral genome amplification process is performed, from RNA to double stranded DNA (dsDNA), a canonical protospacer adjacent motif (PAM) sequence for Cas12a recognition is generated in the resulting amplicon if the virus harbors the E484K mutation (i.e., TTCA originally and TTTA upon mutation, in the antisense strand). 2021 ACS synthetic biology Result SARS_CoV_2 E484K 247 252 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. These methods were used to detect the D614G mutation, which arose in the first months of the pandemic and has become dominant worldwide as a consequence of providing higher infectivity to the virus. 2021 ACS synthetic biology Result SARS_CoV_2 D614G 38 43 34783635 Identification of the SARS-CoV-2 Delta variant C22995A using a high-resolution melting curve RT-FRET-PCR. DNA sequencing of the Delta RT-FRET-PCR products verified the presence and absence of the C22995A mutation as indicated by melting curve analysis. 2022 Emerging microbes & infections Result SARS_CoV_2 C22995A 90 97 34783635 Identification of the SARS-CoV-2 Delta variant C22995A using a high-resolution melting curve RT-FRET-PCR. However, the distinctive melting curves remain sharp for SARS-CoV-2 with and without C22995A mutations (Figure 1). 2022 Emerging microbes & infections Result SARS_CoV_2 C22995A 85 92 34783635 Identification of the SARS-CoV-2 Delta variant C22995A using a high-resolution melting curve RT-FRET-PCR. The clear difference in the Tm between the Delta variant and non-Delta strains enabled the convenient differentiation of strains with and without the C22995A mutation. 2022 Emerging microbes & infections Result SARS_CoV_2 C22995A 150 157 34783635 Identification of the SARS-CoV-2 Delta variant C22995A using a high-resolution melting curve RT-FRET-PCR. The delta variant with C22995A mutation demonstrated significant higher melting temperatures than those of non-Delta strains (56.13 +- 0.27 SD vs. 2022 Emerging microbes & infections Result SARS_CoV_2 C22995A 23 30 34784198 Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study. A relatively higher RMSF value was observed in the neighboring region of the mutation site (R166E), especially in the case of SCoV2(MT) (Figure 3A). 2021 Journal of chemical information and modeling Result SARS_CoV_2 R166E 92 97 34784198 Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study. Also, as reported by Daczkowski et al., the charge-flip mutation of R167E in SCoV-PLpro showed 20 times less efficiency than WT in hydrolyzing ISG15. 2021 Journal of chemical information and modeling Result SARS_CoV_2 R167E 68 73 34784198 Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study. Figure 2A reveals that the charge-flip mutation (R167E) systems exhibited many distinct conformations at varying RMSD values than their respective WT, like for the SCoV2(MT) (at ~5 and ~9 A) and MCoV(MT) (at ~7.3 and ~8.2 A) complexes. 2021 Journal of chemical information and modeling Result SARS_CoV_2 R167E 49 54 34784198 Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study. In contrast, WT-SCoV exhibited mainly hydrophobic contact nodes, while upon R167E mutation in SCoV-PLpro, it showed more hydrophilic and charged interaction networks (see Table S4 and Figures S10 and S11). 2021 Journal of chemical information and modeling Result SARS_CoV_2 R167E 76 81 34784198 Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study. Moreover, the value of their binding free energy of WT was compared with their respective mutants (R167E). 2021 Journal of chemical information and modeling Result SARS_CoV_2 R167E 99 104 34784198 Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study. Together, it reveals that the nitrogen atom of Arg57 from hISG15 forms hydrogen bonding with the oxygen of glutamine (Q174) of PLpro in SCoV2, which upon the charge-flip mutation (R166E), switch to form with the negatively charged glutamate (E166). 2021 Journal of chemical information and modeling Result SARS_CoV_2 R166E 180 185 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. For instance, four additional SNVs (T7247G, C7279T, and A8387G in ORF1a, and A27574T in ORF7a) were present at frequencies above 80% in the kidneys. 2021 Nature communications Result SARS_CoV_2 A27574T;A8387G;C7279T;T7247G 77;56;44;36 84;62;50;42 ORF1a;ORF7a 66;88 71;93 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. For instance, we identified mutations in ORF1ab (C12513T [T4083M amino acid substitution in NSP8] and C14937T [no amino acid substitution in RNA-dependent RNA polymerase]), E (C26351T [A36V amino acid substitution in E protein]), and 3' UTR (G29744A) with frequencies ranging between 33.61 and 64.31 % (Table 1 and S3). 2021 Nature communications Result SARS_CoV_2 C14937T;C12513T;C26351T;G29744A;A36V;T4083M 102;49;176;242;185;58 109;56;183;249;189;64 RdRp;3'UTR;ORF1ab;Nsp8;E;E 141;234;41;92;173;217 169;240;47;96;174;218 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. In addition, a high SNV variability was detected in viral S genes derived from the lungs, which included mutation A22920T at a frequency of 52.52% leading to Y453F amino acid substitution in RBD of S protein. 2021 Nature communications Result SARS_CoV_2 A22920T;Y453F 114;158 121;163 RBD;S;S 191;58;198 194;59;199 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. In addition, six SNVs distributed across ORF1ab (A13433G, C16092T, T18024C, T18750C, and C18979T) and ORF10 (C29592T) were almost uniquely retrieved from kidneys. 2021 Nature communications Result SARS_CoV_2 C16092T;C18979T;T18024C;T18750C;A13433G;C29592T 58;89;67;76;49;109 65;96;74;83;56;116 ORF1ab 41 47 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. Interestingly, in the kidney and liver, up to 40% of the viral genomes displayed the A23063T (N501Y amino acid substitution in S protein) alteration, a key mutation found in Alpha, Beta, and Gamma variants of concern (VOCs; Alpha 202012/01 [B.1.1.7], Beta GH/501Y.V2 [B.1.351], and Gamma GH/501Y.V3 [P1] lineages) that promotes viral binding, infectivity, and virulence. 2021 Nature communications Result SARS_CoV_2 A23063T;N501Y 85;94 92;99 S 127 128 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. Similar to the N501Y mutation, we identified the C24642T (T1027I amino acid substitution) mutation in S, present in current strains of the Gamma GH/501Y.V3 [P1] lineage, at peaking concentrations of 50% in lungs and plasma, as well as in their viral offspring in Vero E6 cells. 2021 Nature communications Result SARS_CoV_2 C24642T;N501Y;T1027I 49;15;58 56;20;64 S 102 103 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. Still, this mutation remained present in viruses propagated in Vero E6 cells from all tissues, highlighting the infection and transmission capacity of mutant N501Y viruses. 2021 Nature communications Result SARS_CoV_2 N501Y 158 163 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. Among 16 fully vaccinated HCPs, we found 1 (6.3%) and 6 (38%) samples with E484K and N501Y mutations, respectively. 2021 Microbiology spectrum Result SARS_CoV_2 E484K;N501Y 75;85 80;90 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. Importantly, among the 9 individuals fully vaccinated (i.e., >=14 days post-second dose), with available molecular data we note 1 and 2 samples harboring E484K and N501Y polymorphisms, respectfully. 2021 Microbiology spectrum Result SARS_CoV_2 E484K;N501Y 154;164 159;169 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. L452R, T478K/I, E484K/Q, and S494P mutations were identified in 32, 8, 40, and 29 genomes, respectively. 2021 Microbiology spectrum Result SARS_CoV_2 E484K;E484Q;S494P;T478I;T478K;L452R 16;16;29;7;7;0 23;23;34;14;14;5 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. Mutations associated with antibody evasion:L452R, T478K, E484K, and S494P:were found in 3, 1, 3, and 2 genomes, respectively. 2021 Microbiology spectrum Result SARS_CoV_2 E484K;S494P;T478K;L452R 57;68;50;43 62;73;55;48 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. Overall, we detected 284 E484K/Q (284/1,392, 20.4%; 12 samples failed in the E484 detection in comparison with N501Y) and 523 N501Y (523/1,404, 37.3%) mutants. 2021 Microbiology spectrum Result SARS_CoV_2 E484K;E484Q;N501Y;N501Y 25;25;111;126 32;32;116;131 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. Screening of postvaccinated SARS-CoV-2 infections indicates the rise in E484K and N501Y variants. 2021 Microbiology spectrum Result SARS_CoV_2 E484K;N501Y 72;82 77;87 COVID-19 28 49 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. The N501Y mutation was found in 4% (3/68) of the genomes, and all belonged to the VOC B.1.1.7 lineage. 2021 Microbiology spectrum Result SARS_CoV_2 N501Y 4 9 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. The prevalence of E484K/Q and N501Y from January to April was 3.2% to 25.7% and 1.0% to 49.3%, respectively. 2021 Microbiology spectrum Result SARS_CoV_2 E484K;E484Q;N501Y 18;18;30 25;25;35 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. There were 3 and 6 viral samples with E484K and N501Y polymorphisms, respectively. 2021 Microbiology spectrum Result SARS_CoV_2 E484K;N501Y 38;48 43;53 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. There were no samples from fully vaccinated HCPs with both E484K and N501Y. 2021 Microbiology spectrum Result SARS_CoV_2 E484K;N501Y 59;69 64;74 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. To contextualize the prevalence of E484K and N501Y mutations among the nonvaccinated population, we sampled 1,404 from a total of 3,000 SARS-CoV-2-positive swabs (47%), representing every other positive COVID-19 swab, from January 2021 to April 2021 within our hospital network. 2021 Microbiology spectrum Result SARS_CoV_2 E484K;N501Y 35;45 40;50 COVID-19 203 211 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. To further characterize the SARS-CoV-2 genotypes recovered from the postvaccinated individuals, we examined the spread of key mutations underlying VOCs (i.e., B.1.1.7) in New Jersey using a high-throughput molecular beacon assay designed to screen for polymorphisms N501Y/T and E484K/Q in the receptor-binding domain (RBD) region. 2021 Microbiology spectrum Result SARS_CoV_2 E484K;E484Q;N501T;N501Y 278;278;266;266 285;285;273;273 RBD 318 321 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. We recorded 3 viral samples harboring the E484K mutation, two belonging to the B.1.526 lineage first identified in New York and one from the R.1 lineage. 2021 Microbiology spectrum Result SARS_CoV_2 E484K 42 47 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. A GISAID search for sequences with the C29197T mutation returned 21,212 sequences, 144 of which did not have an assigned lineage. 2021 Microbiology spectrum Result SARS_CoV_2 C29197T 39 46 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. A retrospective analysis of our collection of SARS-CoV-2 WGS sequences revealed a set of eight B.1 lineage-related strains (from late March to mid-April 2020) with a C29200T mutation within the probe binding region similar to that previously reported by Ziegler et al. 2021 Microbiology spectrum Result SARS_CoV_2 C29200T 166 173 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. Marking the 77 lineages on a phylogenetic tree of SARS-CoV-2 indicated that the C29197T mutation was spontaneously occurring independent of evolution. 2021 Microbiology spectrum Result SARS_CoV_2 C29197T 80 87 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. The C29197T change represents a synonymous mutation of the encoded amino acid, alanine. 2021 Microbiology spectrum Result SARS_CoV_2 C29197T 4 11 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. Whole-genome sequencing (WGS) of the five B.1.1.519 lineage samples from a cluster of related cases with negative N2 results on the Xpert assay identified a C29197T single nucleotide polymorphism (SNP) mutation within the probe binding region of the U.S. 2021 Microbiology spectrum Result SARS_CoV_2 C29197T 157 164 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. 100 copies of the wild-type (417K) strain could be distinguished from 109 copies of the K417N mutation. 2021 Microbiology spectrum Result SARS_CoV_2 K417N 88 93 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. 6B), while 10 copies of the mutant strains (K417N, L452R/Q, or E484Q) could be readily distinguished from 109 copies of the wild-type (417K, 452L, or 484E) strain. 2021 Microbiology spectrum Result SARS_CoV_2 E484Q;L452Q;L452R;K417N 63;51;51;44 68;58;58;49 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. 8D) and the N501Y mutation for both the wild type and delta variant. 2021 Microbiology spectrum Result SARS_CoV_2 N501Y 12 17 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. Finally, crRNA-S-614D was used to distinguish the D614G mutation. 2021 Microbiology spectrum Result SARS_CoV_2 D614G 50 55 S 15 16 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. Furthermore, by using crRNA-S-417N specific for 417N, different results were observed between the beta variant or mutant S (K417N) control and the wild-type strain and alpha and delta variants, although moderate fluorescence signal was detected in the WT S plasmid DNA control. 2021 Microbiology spectrum Result SARS_CoV_2 K417N 124 129 S;S;S 28;121;255 29;122;256 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. Furthermore, crRNA-S-484K could readily detect the beta variant with the E484K mutation. 2021 Microbiology spectrum Result SARS_CoV_2 E484K 73 78 S 19 20 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. In this study, we used the proposed strategy to add PAM motif upstream of the three mutations K417N, L452R/Q, and E484Q that are characteristic mutations present in the S gene of beta, delta, and lambda variants of SARS-CoV-2. 2021 Microbiology spectrum Result SARS_CoV_2 E484Q;K417N;L452Q;L452R 114;94;101;101 119;99;108;108 S 169 170 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. No fluorescence signal was observed for the beta variant and mutant S (K417N) control. 2021 Microbiology spectrum Result SARS_CoV_2 K417N 71 76 S 68 69 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. Similar results were observed for the L452R mutation for the delta variant only. 2021 Microbiology spectrum Result SARS_CoV_2 L452R 38 43 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. Since the K417N mutation of the S protein only appears in the beta variant, the 417K-specific crRNA (crRNA-S-417K) could not recognize the beta variant and the negative control of the mutant S gene with the K417N mutation. 2021 Microbiology spectrum Result SARS_CoV_2 K417N;K417N 10;207 15;212 S;S;S 32;107;191 33;108;192 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. Since the kappa variant (B.1.617.1) carries E484Q mutations, we designed crRNA-S-484Q and found that it could clearly detect the mutant S plasmid DNA with the E484Q mutation. 2021 Microbiology spectrum Result SARS_CoV_2 E484Q;E484Q 44;159 49;164 S;S 79;136 80;137 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. The two viral strains of L and S lineage are characterized with a single nucleotide mutation of C/T at nt28144 in the SARS-CoV-2 ORF8. 2021 Microbiology spectrum Result SARS_CoV_2 C28144T 96 110 ORF8 129 133 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. We designed 19 crRNAs to detect the corresponding 19 mutations in the SARS-CoV-2 S gene and chose 4 crRNAs to evaluate our assay because (i) all of these 4 mutations are located in the receptor binding domain (RBD) and may affect the fusion and internalization of the virus with host cells and detection of these mutations has clear clinical implication; (ii) the crRNAs cover both wild-type S gene (crRNA-S-417K and crRNA-S-501N) and mutant S gene (crRNA-S-452R and crRNA-S-453F) (Table S4); and (iii) the PAM sequence is naturally available upstream of two mutations (Y453F, N501Y) and has to be artificially introduced in another two mutations (K417N, L452R) by using PCR primers. 2021 Microbiology spectrum Result SARS_CoV_2 L452R;N501Y;K417N;Y453F 655;577;648;570 660;582;653;575 RBD;RBD;S;S;S;S;S;S;S 185;210;81;392;406;423;442;456;473 208;213;82;393;407;424;443;457;474 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. After optimization, the final concentrations of 7 MPEs were 7.0 muM (HV69-70del), 8.09 muM (K417N), 9.09 muM (E484K/Q), 6.87 muM (N501Y), 8.12 muM (D614G), 8.48 muM (P681H/R), and 7.91 muM (L452R). 2021 Microbiology spectrum Result SARS_CoV_2 D614G;E484K;E484Q;K417N;L452R;N501Y;P681H;P681R 148;110;110;92;190;130;166;166 153;117;117;97;195;135;173;173 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. The detection limits for HV69-70del, K417N, E484K, N501Y, D614G, P681H, L452R, E484Q, and P681R were 400, 1,560, 400, 400, 400, 1,560, 400, 400, and 1,560 copies, respectively, and the total detection limit for all sites of the mPCR-MS minisequencing was 1,560 copies when using the diluted concentration of the nucleic acids of the SARS-CoV-2 nonvariants. 2021 Microbiology spectrum Result SARS_CoV_2 D614G;E484K;E484Q;K417N;L452R;N501Y;P681H;P681R 58;44;79;37;72;51;65;90 63;49;84;42;77;56;70;95 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. The extended signals of mass probe pairs 5,483 +- 3/5,512 +- 3 (HV69-70del), 5,402 +- 3/5,447 +- 3 (N501Y), 6,067 +- 3/6,091 +- 3 (K417N), 6,309 +- 3/6,333 +- 3 (P681H), 6,309 +- 3/6,349 +- 3 (P681R), 6,113 +- 3/6,129 +- 3 (D614G), 6,749 +- 3/67,33 +- 3 (E484K), 6,749 +- 3/6,709 +- 3 (E484Q), and 5,988 +- 3/5,964 +- 3 (L452R) were not detected in 21 other respiratory pathogen and non-COVID-19 patient nucleic acids, which showed that the specificity of this method was 100%. 2021 Microbiology spectrum Result SARS_CoV_2 D614G;E484K;E484Q;K417N;L452R;N501Y;P681H;P681R 224;255;286;131;321;100;162;193 229;260;291;136;326;105;167;198 COVID-19 387 395 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. The m/z of mass probe extension (MPE) original peaks at 9 mutation types (HV69-70del, N501Y, K417N, P681H, D614G, E484K, L452R, E484Q, and P681R) were 5,170 +- 3, 5,105 +- 3, 5,794 +- 3, 6,036 +- 3, 5,816 +- 3, 6,436 +- 3, 5,691 +- 3, 6,436 +- 3, and 6,036 +- 3, respectively (mass error less than 500 ppm; the same below). 2021 Microbiology spectrum Result SARS_CoV_2 D614G;E484K;E484Q;K417N;L452R;N501Y;P681H;P681R 107;114;128;93;121;86;100;139 112;119;133;98;126;91;105;144 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. A glutamic acid residue is changed to an aspartic acid residue (S:E661D). 2021 Virology journal Result SARS_CoV_2 E661D 66 71 S 64 65 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. A more detailed analysis of the mutations that occurred in the N.10-PR variant revealed one ad ditional mutation in the S protein, S:W152C, which is absent in the N.10-MA variant. 2021 Virology journal Result SARS_CoV_2 W152C 133 138 S;S 120;131 121;132 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. Among the 8 cases identified in April 2021 carrying the Gamma variant with the E661D mutation, one death was reported, 6 patients were hospitalized for more than a month, and only one patient was cured. 2021 Virology journal Result SARS_CoV_2 E661D 79 84 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. Related to the S:E661D mutation, we found, in addition to those genomes from Parana, 25 genomes whose S protein contained the mutation, S:E661D, all from 2021. 2021 Virology journal Result SARS_CoV_2 E661D;E661D 17;138 22;143 S;S;S 15;102;136 16;103;137 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. The N.10-MA variant (a term used in this article to differentiate it from the variant found in Parana, N.10-PR) was described as a variant of interest (VOI), was derived from the B.1.1.33 variant, and carried important mutations in the S protein, including the S:V445A and S:E484K mutations. 2021 Virology journal Result SARS_CoV_2 E484K;V445A 275;263 280;268 S;S;S 236;261;273 237;262;274 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. The S:W152C mutation occurs in the N-terminal domain (NTD) of the S protein and was previously described in another VOI, named B.1.429 (CAL.20C) (Additional file 6: Table S1). 2021 Virology journal Result SARS_CoV_2 W152C 6 11 N;S;S 35;4;66 36;5;67 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. This result suggests that the S:E661D mutation increases in frequency over time. 2021 Virology journal Result SARS_CoV_2 E661D 32 37 S 30 31 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. To determine the frequencies of the Gamma-like-II lineage and the S:E661D mutation in other Brazilian states, we constructed a phylogenetic tree with all Gamma genomes sequenced in Brazil (n=3,648). 2021 Virology journal Result SARS_CoV_2 E661D 68 73 S 66 67 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. When we considered the frequency in relation to the total number of Gamma variants identified, the E661D mutation appeared in 10.24% of the genomes from Parana, followed by Minas Gerais (2.94%), Bahia (1.92%), Sao Paulo (0.90%) and Rio de Janeiro (0.86%). 2021 Virology journal Result SARS_CoV_2 E661D 99 104 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. When we exclusively considered the cohort of patients analyzed in April 2021, this mutation occurred in 8 of the 75 (10.8%) Gamma genomes from Parana, with particular prevalence in the east ern and northern macroregions: approximately 25% of the VOC Gamma samples from Curitiba (5/20) and 3/12 samples from Londrina and Apucarana harbored the S:E661D mutation. 2021 Virology journal Result SARS_CoV_2 E661D 345 350 S 343 344 34790342 On the association between SARS-COV-2 variants and COVID-19 mortality during the second wave of the pandemic in Europe. A significant negative correlation between the average proportion of 20A (S:D614G) variant and second-wave deaths peak height was observed for the period from start of the second wave up to the peak (-0.47, p = 0.002), whereas its correlation with cumulative number of deaths during that period was close to reaching the significance (-0.32, p = 0. 2021 Journal of market access & health policy Result SARS_CoV_2 D614G 76 81 S 74 75 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Alanine scanning of residues four and five showed no improvement in thermostability, with Leu4Ala lowering the Tm value from 74.5 C to 64.7 C and Gly5Ala leaving the melting temperature unaltered at 74.3 C. 2022 The Journal of biological chemistry Result SARS_CoV_2 G5A;L4A 148;90 155;97 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. All amino acid substitutions tested (excluding e.g., Cys, Trp, and Gly, that would not make sense from the point of protein engineering) resulted in a Tm increase, with the highest Tm increases being measured for the Asp17Val, Asp17Ile, and Asp17Leu variants (i.e., from 74.5 C to 85.1 C, 84.8 C, and 84.6 C, respectively). 2022 The Journal of biological chemistry Result SARS_CoV_2 D17I;D17L;D17V 227;241;217 235;249;225 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. As WO'655 already demonstrated that a Met24Leu mutation strongly improves the thermostability of DARPins, we focused our analysis on Leu4, Gly5, and Asp17 on an N1C background comprising the N02 N-Cap to find out if it is possible to further improve the most stable N-Cap known to date. 2022 The Journal of biological chemistry Result SARS_CoV_2 M24L 38 46 N;N 195;266 196;267 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. First, the substitution of Asp at position 17 with Leu leads in all instances to improved interaction energies with the surrounding (Table 5). 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 27 54 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. However, the Asp17Ala mutation showed a strong improvement of the Tm value from 74.5 C to 82.4 C. 2022 The Journal of biological chemistry Result SARS_CoV_2 D17A 13 21 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. In all the three transfers, the Asp17Leu mutation increased the thermostability of the DARPin domains and added up to about 15 C in 2 M GdmCl Tm measurements (Table 6). 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 32 40 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. In the N02-background (N1C_v01 versus N1C_v05) and the mut5 C-Cap (N1C_v22 versus N1C_v23), reduced fluctuations through the Asp17Leu mutation are more pronounced in the direct vicinity of position 17. 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 125 133 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. MD simulations suggest reduced flexibility of N1C through the Asp17Leu N-Cap mutation. 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 62 70 N 71 72 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Of these alternative residues, Asp17Leu provided one of the largest improvements, which we investigated further. 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 31 39 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Overall, the Asp17Leu mutation adds about 9 C to 14 C to the Tm value of N1C independent of its concrete N- and/or C-Cap, indicating that this is a general improvement for DARPin domains. 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 13 21 N 107 108 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Overall, the described significant gain in thermostability of the Asp17Leu mutation proved to be generic and is transferable to different N- and C-Cap backgrounds and different library members selected for high affinity, including clinically validated DARPin domains. 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 66 74 N 138 139 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. The Asp17Leu mutation improved the thermostability of N1C also in the N01 and N03 backgrounds by more than 13 C (Table 3). 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 4 12 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. The Asp17Leu N-Cap mutation improves the stability of clinically validated DARPins. 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 4 12 N 13 14 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. The effects of the Asp17Leu mutation are more pronounced on the 150-ns timescale. 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 19 27 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. The increased thermostability of the Asp17Leu N-Cap mutation is independent of the N- and C-Cap background. 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 37 45 N;N 46;83 47;84 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. The localized stability may be related to the stabilizing Met24Leu mutation of N02. 2022 The Journal of biological chemistry Result SARS_CoV_2 M24L 58 66 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. The reduced flexibility of the Leu17 mutants as compared with Asp17 is in line with the increased thermostability of Asp17Leu DARPins observed in CD. 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 117 125 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. The selected DARPin domains are denoted aHER2, aVEGF (which carries a Gly5Asp framework mutation in its N-Cap; denoted as N04 in. 2022 The Journal of biological chemistry Result SARS_CoV_2 G5D 70 77 N 104 105 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Third, on the longer timescale, the Asp17Leu mutation reduces fluctuations in the N01-background (N1C_v16 versus N1C_v17) across the entire N-Cap and in one of the most flexible parts of a DARPin domain spanning from the end of the N-Cap (GADVNA motif, residues 27-32. 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 36 44 N;N 140;232 141;233 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Thus, the already very thermostable N1C_v22, comprising N02 and the mut5 C-Cap, could be further stabilized by adding the Asp17Leu mutation to its N-Cap resulting in a Tm gain of about 12 C in 2 M GdmCl. 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 122 130 N 147 148 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. To test if the improvements derived from mutating the N-Cap Asp17 are generic and independent of the N02 background, we transferred the Asp17Leu mutation onto the original N01 N-Cap and the N03 N-Cap that differs in nine amino acids from N02. 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 136 144 N;N;N 54;176;194 55;177;195 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. To test whether the observed thermostability gain derived from the N-Cap Asp17Leu is independent on the composition of randomized positions in the DARPin paratope (as mainly present in the IRs) and thus transferable to any (nonconsensus) DARPin, we tested this mutation on binders selected against human epidermal growth factor receptor 2 (HER2), vascular endothelial growth factor A (VEGF-A), and HSA (Table 6). 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 73 81 N 67 68 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. With the additional substitution of Asp17Leu in N1C_v23 (N02, mut5 background), we did not observe any unfolding transition up to 95 C when we measured the thermal unfolding of this molecule in PBS. 2022 The Journal of biological chemistry Result SARS_CoV_2 D17L 36 44 34794434 SARS-CoV-2 exposure in Malawian blood donors: an analysis of seroprevalence and variant dynamics between January 2020 and July 2021. Following previous observations that antibodies elicited by the original variant (D614G WT) are less potent against the beta variant, we reasoned that differential neutralisation potency by SARS-CoV-2 antibodies could be used to estimate the predominance of specific variants driving seroprevalence. 2021 BMC medicine Result SARS_CoV_2 D614G 82 87 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. An unexpected increasing frequency of sequences carrying the E484K mutation was found also among non-VOCs isolates. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 61 66 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. E484K mutation without the N501Y one was found in a total of 8 cases out of the 1736 samples analyzed in this study (0.5%). 2021 Infection, genetics and evolution Result SARS_CoV_2 N501Y;E484K 27;0 32;5 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. In all of them, the infecting virus carried the mutation E484K, either from a Gamma VOC or, in one sample, E3344, the E484K mutation alone (Table 3). 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K;E484K 57;118 62;123 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. In order to assess the contribution of E484K mutation to the incidence of reinfections, a review of reinfection cases was conducted until June 1st, 2021, as described in Materials and Methods. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 39 44 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Reinfection with SARS-CoV-2 genomes harboring E484K occurred only across geographically diverse regions from Brazil and among patients spanning a broad distribution of ages and baseline health status, whose initial and second infections were respectively asymptomatic or mild and mild/severe. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 46 51 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. The presence of E484K mutation in the virus (from a Gamma VOC or another lineage) infecting some cases of suspected reinfection in our study, prompted us to analyze the presence of this mutation in the sequences available worldwide in the GISAID database over time, to evaluate if the frequency of this mutation could be related to reinfection. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K 16 21 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. With this first strategy, from these first 245 isolates for which sequence was obtained, 29 carried both mutations E484K and N501Y, and one carried only the mutation E484K. 2021 Infection, genetics and evolution Result SARS_CoV_2 E484K;E484K;N501Y 115;166;125 120;171;130 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. 4), and S477N was observed in more than 90% sequences from Oceania between the week of July 15th and the week of August 16th. 2022 Infection, genetics and evolution Result SARS_CoV_2 S477N 8 13 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. 5C) variants, and N501K is observed in the Alpha, Beta, and Gamma variants. 2022 Infection, genetics and evolution Result SARS_CoV_2 N501K 18 23 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. 5D) share the same set of mutations on the spike protein (S13I, W152C, L452R), and have similar effect on transmissibility and antibody evasion. 2022 Infection, genetics and evolution Result SARS_CoV_2 L452R;W152C;S13I 71;64;58 76;69;62 S 43 48 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. 6B) match global trends, except for the Nsp12 mutation A424V, which is seen in the global data but not in Europe. 2022 Infection, genetics and evolution Result SARS_CoV_2 A424V 55 60 Nsp12 40 45 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. 6E), the Nsp8 mutation Y138H appears consistently in 5-30% of weekly sequences between late May 2020 and early November. 2022 Infection, genetics and evolution Result SARS_CoV_2 Y138H 23 28 Nsp8 9 13 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. 6F), there are no stable mutations in the RdRP complex besides the Nsp12 mutation P323L. 2022 Infection, genetics and evolution Result SARS_CoV_2 P323L 82 87 Nsp12;RdRP 67;42 72;46 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. 6G), the Nsp7 mutation L71F was observed in 78.7% of sequences from the week of November 22nd, 2020, and in 15-25% of samples from the following weeks. 2022 Infection, genetics and evolution Result SARS_CoV_2 L71F 23 27 Nsp7 9 13 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. A comparison of the secondary structure of A222V to that of D614G shows that both variants occur in a loop region. 2022 Infection, genetics and evolution Result SARS_CoV_2 A222V;D614G 43;60 48;65 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. A ribbon diagram of A222V. 2022 Infection, genetics and evolution Result SARS_CoV_2 A222V 20 25 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. A656S peaked in prevalence in mid-September and was observed in a decreasing proportion of sequences afterward, while A656T and A656V do not appear to become more prevalent with time. 2022 Infection, genetics and evolution Result SARS_CoV_2 A656T;A656V;A656S 118;128;0 123;133;5 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. All of these mutations except for Q675R and P681L appear to be increasing in prevalence with time, with the greatest increase observed for P681H. 2022 Infection, genetics and evolution Result SARS_CoV_2 P681H;P681L;Q675R 139;44;34 144;49;39 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. As of January 10th, 2021, mutations in the polymerase complex besides the Nsp12 mutation P323L were rare but their presence is stable. 2022 Infection, genetics and evolution Result SARS_CoV_2 P323L 89 94 Nsp12 74 79 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. but the rate of establishment was lower in Asia than in other continents, as with spike: D614G. 2022 Infection, genetics and evolution Result SARS_CoV_2 D614G 89 94 S 82 87 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. D614G has been shown to alter the conformational state of the receptor binding domain through a hinge mechanism involving its loop structure, and it is possible that A222V may have a similar effect on the conformational state. 2022 Infection, genetics and evolution Result SARS_CoV_2 A222V;D614G 166;0 171;5 RBD 62 85 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. D614G quickly became the dominant variant on all continents, though its rate of establishment was much lower in Asia. 2022 Infection, genetics and evolution Result SARS_CoV_2 D614G 0 5 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. D614G reached 90% prevalence in Asia during the week of June 14th. 2022 Infection, genetics and evolution Result SARS_CoV_2 D614G 0 5 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. first detected in New York (L5F, T95I, D253G; E484K or S477N; D614G, and A701V), appear together consistently after the week of October 4th, 2020, though the fact that many of these mutations are shared with other phylogenetic lineages makes it difficult to conclude that the variant originated at this time point. 2022 Infection, genetics and evolution Result SARS_CoV_2 A701V;D253G;D614G;E484K;S477N;T95I;L5F 73;39;62;46;55;33;28 78;44;67;51;60;37;31 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. found that L452R is associated with a small increase in S protein expression. 2022 Infection, genetics and evolution Result SARS_CoV_2 L452R 11 16 S 56 57 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. In addition to the mutations previously mentioned and the quickly increasing prevalence of mutations associated with the Alpha variant in the last few months of the analysis, the heatmap reveals four additional mutations that appear to be increasing in prevalence with time (L5F, S98F, A262S, and P272L). 2022 Infection, genetics and evolution Result SARS_CoV_2 A262S;P272L;S98F;L5F 286;297;280;275 291;302;284;278 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. L452R, which is observed in the variant of concern B.1.429 discovered in California, is observed in 3.49% of the sequences from North America collected during the week of January 10th and 878 sequences total. 2022 Infection, genetics and evolution Result SARS_CoV_2 L452R 0 5 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Mutations associated with the Alpha variant (H69_V70del, Y144del, N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H), have quickly increased in prevalence worldwide since November. 2022 Infection, genetics and evolution Result SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I;Y144del 73;112;80;66;87;101;94;57 78;118;85;71;92;106;99;64 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Mutations observed in more than 10% of weekly samples include the Nsp8 mutations A47V, T148I, and I156V; and the Nsp12 mutations Y521C and G823S; but these mutations are not consistently observed above this threshold. 2022 Infection, genetics and evolution Result SARS_CoV_2 A47V;G823S;I156V;T148I;Y521C 81;139;98;87;129 85;144;103;92;134 Nsp12;Nsp8 113;66 118;70 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Out of the 910 sequences containing either D1163Y, G1167V, or both, 802 contain both mutations (Supplementary Table S2). 2022 Infection, genetics and evolution Result SARS_CoV_2 D1163Y;G1167V 43;51 49;57 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. P681 was found to be highly variable: P681H was observed in 36,151 sequences total (10.47%). 2022 Infection, genetics and evolution Result SARS_CoV_2 P681H 38 43 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. P681H was the second most common mutation in North America, detected in 12.9% of samples from the week of January 10th 2021. 2022 Infection, genetics and evolution Result SARS_CoV_2 P681H 0 5 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Q677H has been observed in the United States in October 2020 by Hodcroft et al. 2022 Infection, genetics and evolution Result SARS_CoV_2 Q677H 0 5 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Q677H, observed in 2146 sequences (0.62% of total sequences), occurs outside of the furin cleavage site but may affect a QTQN consensus sequence near the site. 2022 Infection, genetics and evolution Result SARS_CoV_2 Q677H 0 5 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. S13I and L452R were detected separately in previous sequences, but W152C was not. 2022 Infection, genetics and evolution Result SARS_CoV_2 L452R;W152C;S13I 9;67;0 14;72;4 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. S17) reveals 14 mutations out of 64 total that appear to be consistently present (P681H, Q677H, Q675H, Q677P, S673T, N679K, P681R, Q675R, P681L, T676I, T678I, A684V, Q677R, and A672V). 2022 Infection, genetics and evolution Result SARS_CoV_2 A672V;A684V;N679K;P681L;P681R;Q675H;Q675R;Q677H;Q677P;Q677R;S673T;T676I;T678I;P681H 177;159;117;138;124;96;131;89;103;166;110;145;152;82 182;164;122;143;129;101;136;94;108;171;115;150;157;87 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. S19A. 2022 Infection, genetics and evolution Result SARS_CoV_2 S19A 0 4 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. S28A-C. 2022 Infection, genetics and evolution Result SARS_CoV_2 S28A 0 4 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. S29A-C) show that all the analyzed variants of concern have a median of zero polymorphisms in Nsp7 and Nsp8, and a median of one polymorphism in Nsp12. 2022 Infection, genetics and evolution Result SARS_CoV_2 S29A 0 4 Nsp12;Nsp7;Nsp8 145;94;103 150;98;107 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. S3A), and L18F has been observed on all continents. 2022 Infection, genetics and evolution Result SARS_CoV_2 L18F 10 14 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. S477N has also been observed in Europe with increasing frequency, and since August it has been observed in increasing prevalence in Europe, Africa, Asia, and North America. 2022 Infection, genetics and evolution Result SARS_CoV_2 S477N 0 5 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. S477N was observed in 18,219 sequences, and N439K was observed in 6743 sequences. 2022 Infection, genetics and evolution Result SARS_CoV_2 N439K;S477N 44;0 49;5 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Several mutations, such as the Nsp12 mutations A97V, N215S, K718N, and N911S; and the Nsp8 mutation L9F, emerged, peaked in prevalence between 5 and 25%, and later decreased to less than 4% prevalence. 2022 Infection, genetics and evolution Result SARS_CoV_2 A97V;K718N;L9F;N215S;N911S 47;60;100;53;71 51;65;103;58;76 Nsp12;Nsp8 31;86 36;90 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Similar trends are observed for the Nsp12 mutations A97V and M666I and the Nsp7 mutation S25L. 2022 Infection, genetics and evolution Result SARS_CoV_2 A97V;M666I;S25L 52;61;89 56;66;93 Nsp12;Nsp7 36;75 41;79 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The most common mutation worldwide was the substitution D614G, which quickly became prevalent after its appearance in mid-January 2020. 2022 Infection, genetics and evolution Result SARS_CoV_2 D614G 56 61 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The mutations P918S/L/H (161, 85, and 3 sequences, respectively), E919D (126 sequences), and E922D/Q/V (201, 2, and 2 sequences, respectively) are observed in the alpha helix containing the RNA binding residues F920 and M924. 2022 Infection, genetics and evolution Result SARS_CoV_2 E919D;E922D;E922Q;E922V;P918H;P918L;P918S 66;93;93;93;14;14;14 71;102;102;102;23;23;23 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The N-terminal domain (NTD) substitution A222V and the signal peptide substitution L18F gained in prevalence globally since their appearance in late July and early August, respectively, before peaking in late October and declining in prevalence. 2022 Infection, genetics and evolution Result SARS_CoV_2 A222V;L18F 41;83 46;87 N 4 5 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The Nsp12 mutation A97V peaked at 17.7% prevalence during the week of April 12th, 2020, the Nsp7 mutation S25L peaked during the week of October 25th, 2020 at 29.9%, and the Nsp12 mutation M666I peaked at 34.4% prevalence during the week of December 27th, 2020. 2022 Infection, genetics and evolution Result SARS_CoV_2 A97V;M666I;S25L 19;189;106 23;194;110 Nsp12;Nsp12;Nsp7 4;174;92 9;179;96 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The Nsp12 substitutions A185S and V776L appear to increase in prevalence together, suggesting a correlation between these variants. 2022 Infection, genetics and evolution Result SARS_CoV_2 A185S;V776L 24;34 29;39 Nsp12 4 9 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The Nsp12 substitutions P323L, V776L, A185S, and V720I appear to be stable or increasing in prevalence, while other mutations have peaked in prevalence and later disappeared. 2022 Infection, genetics and evolution Result SARS_CoV_2 A185S;P323L;V720I;V776L 38;24;49;31 43;29;54;36 Nsp12 4 9 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The Nsp12 thumb subdomain mutation P918L was observed in 22.8% of samples collected during the week of June 21st and 24.2% of sequences collected during the week of July 12th. 2022 Infection, genetics and evolution Result SARS_CoV_2 P918L 35 40 Nsp12 4 9 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The Nsp12: P323L mutation appeared in late January 2020 and was present in 50% of the sequences by early March, and 90% of the sequences by late April. 2022 Infection, genetics and evolution Result SARS_CoV_2 P323L 11 16 Nsp12 4 9 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The Nsp7 mutation S25L was also observed in North America. 2022 Infection, genetics and evolution Result SARS_CoV_2 S25L 18 22 Nsp7 4 8 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The Nsp7 mutation S25L was also observed in the region, peaking at 34.7% prevalence during the week of May 17th, 2020, and peaking again at 21.2% during the week of October 18th, 2020. 2022 Infection, genetics and evolution Result SARS_CoV_2 S25L 18 22 Nsp7 4 8 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The Nsp8 mutations T145I and Q24R along with the Nsp12 mutation V776L were present in 2.0-2.5% of sequences during the week of January 10th, 2021, and the Nsp12 mutations P227L, V354L, and V605 were present in 1.0-2.0% of sequences. 2022 Infection, genetics and evolution Result SARS_CoV_2 P227L;Q24R;T145I;V354L;V776L 171;29;19;178;64 176;33;24;183;69 Nsp12;Nsp12;Nsp8 49;155;4 54;160;8 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The RBD mutation N484K is observed in the Beta. 2022 Infection, genetics and evolution Result SARS_CoV_2 N484K 17 22 RBD 4 7 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The RBD substitution E484K was observed in South America. 2022 Infection, genetics and evolution Result SARS_CoV_2 E484K 21 26 RBD 4 7 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The RBD substitution N439K has slowly increased in prevalence since August 2020 and has been consistently observed in 2.0-4.5% of samples worldwide since the week of August 16th. 2022 Infection, genetics and evolution Result SARS_CoV_2 N439K 21 26 RBD 4 7 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The receptor binding domain (RBD) substitution S477N appeared in June and reached peak prevalence during week of July 19th, appearing in 32.1% of sequences worldwide before decreasing in prevalence to 0.5% by the week of December 6th, 2020. 2022 Infection, genetics and evolution Result SARS_CoV_2 S477N 47 52 RBD;RBD 4;29 27;32 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The same trend is observed for the N-terminal domain residues A262S and P272L, and these mutations occur together in 687 out of 1084 sequences containing either A262S, P272L, or both. 2022 Infection, genetics and evolution Result SARS_CoV_2 A262S;A262S;P272L;P272L 62;161;72;168 67;166;77;173 N 35 36 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The spike in A424V in the global data can be attributed to the high prevalence of the mutation in Asia during July 2020. 2022 Infection, genetics and evolution Result SARS_CoV_2 A424V 13 18 S 4 9 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The trend of predominance for Nsp12: P323L was observed on all continents. 2022 Infection, genetics and evolution Result SARS_CoV_2 P323L 37 42 Nsp12 30 35 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. These mutations include the Nsp12 mutations E254D, A423V, A656S, V720I, and V776L; the Nsp7 mutations S25L and M75I; and the Nsp8 mutation T145I. 2022 Infection, genetics and evolution Result SARS_CoV_2 A423V;A656S;E254D;M75I;S25L;T145I;V720I;V776L 51;58;44;111;102;139;65;76 56;63;49;115;106;144;70;81 Nsp12;Nsp7;Nsp8 28;87;125 33;91;129 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. This is supported by a stability analysis by Jacobs et al., which finds that both D614G and A222V cause rigidification in similar residues of the spike protein structure. 2022 Infection, genetics and evolution Result SARS_CoV_2 A222V;D614G 92;82 97;87 S 146 151 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. This is supported by the table of variant combinations for each cluster (Supplementary Table S4, Supplementary Table S5, Supplementary Table S6), which shows V776L occurring together with A185 in 10,273 sequences, and V776L and A185S occurring separately in 84 and 379 sequences, respectively. 2022 Infection, genetics and evolution Result SARS_CoV_2 A185S;V776L;V776L 228;158;218 233;163;223 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. This prevalence value is greater than H69_V70del and N501Y (8.0% and 5.7%, respectively), suggesting that some viral species are carrying P681H, but not other mutations associated with the Alpha variant. 2022 Infection, genetics and evolution Result SARS_CoV_2 N501Y;P681H 53;138 58;143 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. though A222V has been observed to an increasing extent in Asia, Oceania, and Africa, and North America. 2022 Infection, genetics and evolution Result SARS_CoV_2 A222V 7 12 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Two heptad repeat 2 residues, D1163Y and G1167V appear to increase in prevalence at the same time, near the end of August. 2022 Infection, genetics and evolution Result SARS_CoV_2 D1163Y;G1167V 30;41 36;47 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. which quickly became more prevalent in Europe between mid-July and October 31st, shows that the variant occurs in a loop region, like D614G. 2022 Infection, genetics and evolution Result SARS_CoV_2 D614G 134 139 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. Comparison with SARS-CoV Mpro/H41A . 2021 IUCrJ Result SARS_CoV_2 H41A 30 34 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. Comparison with SARS-CoV Mpro/H41A. 2021 IUCrJ Result SARS_CoV_2 H41A 30 34 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. In Mpro/C145A-substrate, a substrate occupies each of the two active-site grooves in the Mpro homodimer structure. 2021 IUCrJ Result SARS_CoV_2 C145A 8 13 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. In the SARS-CoV Mpro/H41A-substrate complex, the substrate pushes the catalytic Cys145 side chain away from the scissile bond towards the vacated space left by the H41A mutation to a position where the S atom is 4.5 A from the scissile carbonyl C atom. 2021 IUCrJ Result SARS_CoV_2 H41A;H41A 164;21 168;25 S 202 203 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. In this context, it is noteworthy that electron density for the C-terminal residues up to the very last Gln306 amine is clearly observed in Mpro/C145A-substrate. 2021 IUCrJ Result SARS_CoV_2 C145A 145 150 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. It is instructive to compare our room-temperature Mpro/C145A-substrate structure from SARS-CoV-2 with a low-temperature structure of the SARS-CoV main protease H41A mutant, Mpro/H41A, soaked with an 11-amino-acid peptide substrate spanning the same nsp4/nsp5 autocleavage site (Xue et al., 2008. 2021 IUCrJ Result SARS_CoV_2 H41A;C145A;H41A 160;55;178 164;60;182 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. Superposition of Mpro/C145A-substrate and our recently determined substrate-free neutron crystallographic structure of wild-type SARS-CoV-2 Mpro (PDB entry 7jun; Kneller, Phillips, Weiss et al., 2020) offers unique insights into catalysis because the Cys145-His41 dyad was observed as a zwitterionic species with the Cys145 thiolate Sgamma atom 3.8 A away from His41 Ne2, already primed for proteolysis [Fig. 2021 IUCrJ Result SARS_CoV_2 C145A 22 27 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. The Mpro/C145A-substrate structure therefore underscores the suggestion that the zwitterionic catalytic dyad is present prior to substrate binding (Kneller, Phillips, Weiss et al., 2020) instead of requiring reorganization of the catalytic site to facilitate proton transfer from Cys145 to His41 in the catalytically resting (nonreactive) state. 2021 IUCrJ Result SARS_CoV_2 C145A 9 14 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. The nearest mutation to the active site in SARS-CoV-2 Mpro, A46S, does not introduce appreciable differences despite minor differences in the S2 subsite helix. 2021 IUCrJ Result SARS_CoV_2 A46S 60 64 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. When the C-terminal residues of Mpro/C145A-substrate and the product complex reported by Lee et al. 2021 IUCrJ Result SARS_CoV_2 C145A 37 42 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. Along with the VOC-/VOI-specific mutations, we further examined the effects of different flexible RBD orientations (i.e., clockwise and anticlockwise movements of RBD) that can be caused by several mutations at hinge residues located close to the S1/S2 junction (e.g., D614G). 2021 ACS omega Result SARS_CoV_2 D614G 269 274 RBD;RBD 98;163 101;166 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. Among all of the considered mutations, it was seen that K417N has the highest effect on DeltaG and Kd (-17.2 kcal/mol, 2.50 x 10-13 M). 2021 ACS omega Result SARS_CoV_2 K417N 56 61 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. Besides the H-bond, T417N, L452Q, L452R, N501Y, and T478K caused the formation of several salt bridges at the interface. 2021 ACS omega Result SARS_CoV_2 L452Q;L452R;N501Y;T417N;T478K 27;34;41;20;52 32;39;46;25;57 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. Deletion of these glycan residues through N165A and N234A mutations significantly reduced binding of the S-protein to ACE2 as a result of a conformational shift of the RBD toward the "down" state, weakening accessibility to ACE2. 2021 ACS omega Result SARS_CoV_2 N165A;N234A 42;52 47;57 RBD;S 168;105 171;106 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. For example, a recent study showed that N439K compensated for an RBM mutation K417V that otherwise decreases the receptor-binding affinity and that several mAbs were more sensitive to these mutations in combination versus individually. 2021 ACS omega Result SARS_CoV_2 K417V;N439K 78;40 83;45 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. For example, spike K417N and the nonmutated states involve 33.33 and 44.44% residues of the C2 cluster, respectively (Table 2), which allosterically coupled with the RBD site 417 with the absolute correlation being greater than 0.7. 2021 ACS omega Result SARS_CoV_2 K417N 19 24 S;RBD 13;166 18;169 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. However, S E484K involves 44.44% residues of the C2 cluster, which is 10% less than its nonmutated form, having allosteric coupling with the RBD mutation site 484. 2021 ACS omega Result SARS_CoV_2 E484K 11 16 RBD;S 141;9 144;10 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. In particular, delta-specific RBD mutation K417N, T478K, and Lamda-specific L452Q showed a much higher SAA relative to the ACE2-bound active S-protein. 2021 ACS omega Result SARS_CoV_2 K417N;L452Q;T478K 43;76;50 48;81;55 RBD;S 30;141 33;142 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. In particular, S K417N has ACI values of 0.35, 0.31, and 0.28, respectively, when C3, C2, and C1 are considered as the active sites, which is >40% when compared with its native RBD-up conformational form, indicating strong allosteric connections for the K417N S conformation (Figure 5). 2021 ACS omega Result SARS_CoV_2 K417N;K417N 17;254 22;259 RBD;S;S 177;15;260 180;16;261 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. Interestingly, we observed a significant increase in DeltaG and Kd under the flexible RBD orientations in contrast to their lowest values for the K417N S-protein (Figure 7B). 2021 ACS omega Result SARS_CoV_2 K417N 146 151 RBD;S 86;152 89;153 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. It further shows that ACE2-bound K417N S holds 7.7 and 3.3% solvent-accessible area at the interface of ACE2 and spike, respectively, and 182 interface contact residues, which is the largest among all of the mutations. 2021 ACS omega Result SARS_CoV_2 K417N 33 38 S;S 113;39 118;40 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. Notably, the K417N S-protein holds five H-bonds with the distance cutoff of 3.00 A and four salt bridges to hold tight interactions with ACE2. 2021 ACS omega Result SARS_CoV_2 K417N 13 18 S 19 20 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. When compared among the different RBD-mutated states (i.e., E484K, K417N, L452Q, L452R, N501Y, and T478K), it showed strong allosteric signals activated by a suite of residues in C1, C2, and C3 with overall correlation >= 0.7 (Figure 4a) that allosterically coupled with the RBD mutation differentially, indicating potential long-range allosteric communication between compensatory mutation sites in NTD and the RBD mutation site (Figure 4b). 2021 ACS omega Result SARS_CoV_2 E484K;K417N;L452Q;L452R;N501Y;T478K 60;67;74;81;88;99 65;72;79;86;93;104 RBD;RBD;RBD 34;275;412 37;278;415 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. While all of the mutations have significant effects, K417N showed many more residues with very high positive X values. 2021 ACS omega Result SARS_CoV_2 K417N 53 58 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. A single amino acid substitution L452R is present in multiple lineages, including B.1.526, B.1.427, B.1.429, B.1.617.1, B.1.617.3, and lineages designated as Delta (B.1.617.2, AY.1, AY.2, and AY.3). 2021 Current research in structural biology Result SARS_CoV_2 L452R 33 38 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Although B.1.1.7 intra-NTD network is supported by 233 residues with higher degree contacts, three deletions in the N2 loop of the NTD (H69del, V70del & Y144del) greatly perturb the local interaction network which was observed to mediate around 10, 9, 15 local contacts each in the WT spike, respectively. 2021 Current research in structural biology Result SARS_CoV_2 H69del 136 142 S 285 290 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Another consecutive substitution, R158G also perturbed the formation of 5 hydrogen bonds in the variant. 2021 Current research in structural biology Result SARS_CoV_2 R158G 34 39 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. D253G and A262S are present in the supersite loop epitope of NTD. 2021 Current research in structural biology Result SARS_CoV_2 A262S;D253G 10;0 15;5 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Eight prominent mutations were present in the first group with more than 50% frequency; N501Y, P681H, T716I, D1118H, A570D, S982A, HV69/70del, and Y144del. 2021 Current research in structural biology Result SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;T716I;Y144del 117;109;88;95;124;102;147 122;115;93;100;129;107;154 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Followed by the RBD, the SD1 (542-591 a.a.) and SD2 (592-681 a.a.) regions showed a similar trend in both the WT and D614G systems with an average RMSD of 0.61 +- 0.003 nm. 2021 Current research in structural biology Result SARS_CoV_2 D614G 117 122 RBD 16 19 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. For instance, in B.1.617.2 (Delta variant) four hydrogen bonds upon T19R mutation were found, whereas only one hydrogen bond was observed at this site in the WT protein structure. 2021 Current research in structural biology Result SARS_CoV_2 T19R 68 72 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. For instance, L18F, T20N, P26S, D138Y, and R190S are present in P.1 lineage. 2021 Current research in structural biology Result SARS_CoV_2 D138Y;L18F;P26S;R190S;T20N 32;14;26;43;20 37;18;30;48;24 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. For instance, the deletions present within NTD in multiple lineages (HV69/70del, Y144del, E156-F157del) are predicted to vary the conformation of an exposed NTD loop. 2021 Current research in structural biology Result SARS_CoV_2 Y144del 81 88 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. For K417T in B.1.351 lineage, no significant alterations were observed. 2021 Current research in structural biology Result SARS_CoV_2 K417T 4 9 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. For the characteristic NTD mutations across VoCs (L18F, T19R, T20N, D80A, and T95I), we observed the MTR score of0.738 suggesting that these mutations show a neutral impact on the protein structure. 2021 Current research in structural biology Result SARS_CoV_2 D80A;T19R;T20N;T95I;L18F 68;56;62;78;50 72;60;66;82;54 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Further, for the characteristic RBD mutations across VoCs (K417 T/N, L452R, S477N, T478K, E484K, and N501Y), we observed MTR scores between 0.68 and 0.91, suggesting these substitutions to be tolerant. 2021 Current research in structural biology Result SARS_CoV_2 E484K;L452R;N501Y;S477N;T478K;K417N;K417T 90;69;101;76;83;59;59 95;74;106;81;88;67;67 RBD 32 35 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. In B.1.1.7 lineage, there is one critical mutation in the RBM namely- N501Y, which has been reported previously to enhance the interaction with the hACE2. 2021 Current research in structural biology Result SARS_CoV_2 N501Y 70 75 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. In early pandemic, L5F substitution in the signal peptide was present, alongwith D614G mutation in the linker. 2021 Current research in structural biology Result SARS_CoV_2 D614G;L5F 81;19 86;22 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. In the D614G trajectory, it corresponded to a relatively compact state with significantly less distance between the NTD and RBD (5.97 nm and 5.82 nm, respectively) as shown in. 2021 Current research in structural biology Result SARS_CoV_2 D614G 7 12 RBD 124 127 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Interestingly, five out of eight mutations of RBD are present in the epitope region, where L452Rand N501Y substitutions map to the RBD-loop epitope and S477N, T478K, and E484K are harboured in the RBD-ridge epitope. 2021 Current research in structural biology Result SARS_CoV_2 E484K;N501Y;S477N;T478K 170;100;152;159 175;105;157;164 RBD;RBD;RBD 46;131;197 49;134;200 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Interestingly, the connecting region between the NTD and RBD (N2R: 310-319) is not mutating. 2021 Current research in structural biology Result SARS_CoV_2 N2R 62 65 RBD 57 60 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Molecular dynamics simulations of full-length D614G spike showed structurally flexible regions. 2021 Current research in structural biology Result SARS_CoV_2 D614G 46 51 S 52 57 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Our analysis revealed increased stability of the D614G protein (0.89 +- 0.007 nm) as compared to the WT spike system. 2021 Current research in structural biology Result SARS_CoV_2 D614G 49 54 S 104 109 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Similarly, E484K is present in B.1.525 (Eta), P.1 (Gamma), and B.1.351 (Beta). 2021 Current research in structural biology Result SARS_CoV_2 E484K 11 16 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Similarly, P.1 and B.1.351 lineages have three key mutations in the RBM, namely- K417 T/N, E484K, and N501Y. 2021 Current research in structural biology Result SARS_CoV_2 E484K;K417N;K417T;N501Y 91;81;81;102 96;89;89;107 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Similarly, the recent B.1.617.2 lineage possess 4 NTD mutation combination (T19R, E156del, F157del, and R158G). 2021 Current research in structural biology Result SARS_CoV_2 E156del;F157del;R158G;T19R 82;91;104;76 89;98;109;80 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Specifically, L18F, T19R, and T20N are present in the N-terminus epitope, whereas G142D, W152 R/L/C, M153T, and F157 are present in the supersite beta-hairpin epitope. 2021 Current research in structural biology Result SARS_CoV_2 G142D;L18F;M153T;T19R;T20N;W152C;W152L;W152R 82;14;101;20;30;89;89;89 87;18;106;24;34;99;99;99 N 54 55 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Specifically, the RBM in D614G (0.72 +- 0.002 nm) is observed to be relatively stable as compared to that of the WT system (1.00 +- 0.009 nm). 2021 Current research in structural biology Result SARS_CoV_2 D614G 25 30 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Structural analysis of the WT and B.1.1.7 variant bound to hACE2 revealed the formation of a high number of contacts after N501Y substitution. 2021 Current research in structural biology Result SARS_CoV_2 N501Y 123 128 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. The combination of K417N, E484K, and N501Y substitutions was also present in B.1.351 (Beta) and P.1 (Gamma). 2021 Current research in structural biology Result SARS_CoV_2 E484K;K417N;N501Y 26;19;37 31;24;42 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. The linker region consists of variant stretches contributed from three prominent mutations A570D, H655Y, and P681 H/R along with D614G. 2021 Current research in structural biology Result SARS_CoV_2 A570D;D614G;H655Y;P681H;P681R 91;129;98;109;109 96;134;103;117;117 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. The linker region with P681R and H655Y along with D614G were the main amino acid co-occurring substitutions. 2021 Current research in structural biology Result SARS_CoV_2 D614G;H655Y;P681R 50;33;23 55;38;28 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. The N-terminal region of the NTD, namely L18F, T19R, T20N, evolved early during the pandemic. 2021 Current research in structural biology Result SARS_CoV_2 L18F;T19R;T20N 41;47;53 45;51;57 N 4 5 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. The RBD of B.1.617.2 harbors two defining mutations (L452R and T478K), out of which L452R substitution enhanced the local hydrogen bond networking by forming 3 bonds as compared to the one in WT. 2021 Current research in structural biology Result SARS_CoV_2 L452R;T478K;L452R 84;63;53 89;68;58 RBD 4 7 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. The S1 subunit harbours the prominent D614G mutation present in 99.84% of genomes. 2021 Current research in structural biology Result SARS_CoV_2 D614G 38 43 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. The T478K is present directly on the RBM, and the long side chain of K478 might impact the neighbouring ACE2 residues in contact with the RBD residues. 2021 Current research in structural biology Result SARS_CoV_2 T478K 4 9 RBD 138 141 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. This results in a compact conformation of the D614G and more importantly results in higher proximity with the hACE2 structure. 2021 Current research in structural biology Result SARS_CoV_2 D614G 46 51 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Within the NTD, five prominent variant stretches were observed, with Y144 deletion, G142D, E156-F157 deletion, and R158G segment as the largest contiguous patch. 2021 Current research in structural biology Result SARS_CoV_2 G142D;R158G 84;115 89;120 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. A538T, M809L, P314L, A8D, S220G, A88V and L629F were found to have a deleterious effect on RNA-dependent RNA polymerase. 2021 Informatics in medicine unlocked Result SARS_CoV_2 A88V;A8D;L629F;M809L;P314L;S220G;A538T 33;21;42;7;14;26;0 37;24;47;12;19;31;5 RdRp 91 119 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. Conversely, 3 missense mutations (D3L, L5F, and S97I) were found to largely increase (DDG value > 0.5) the structural stability of the corresponding proteins. 2021 Informatics in medicine unlocked Result SARS_CoV_2 L5F;S97I;D3L 39;48;34 42;52;37 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. Conversely, C3037T (F106F) mutation was found as a synonymous mutation in the region encoding NSP3, a viral predicted phosphoesterase whereas C241T mutation fall over non-coding regions (5' UTR). 2021 Informatics in medicine unlocked Result SARS_CoV_2 C241T;C3037T;F106F 142;12;20 147;18;25 5'UTR;Nsp3 187;94 193;98 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. D1118H and C1243Y mutations have a deleterious effect on Spike protein. 2021 Informatics in medicine unlocked Result SARS_CoV_2 C1243Y;D1118H 11;0 17;6 S 57 62 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. D3L, P13L, S183Y, S186Y, S194L, R262H, and D377Y have a deleterious effect on Nucleocapsid protein. 2021 Informatics in medicine unlocked Result SARS_CoV_2 D377Y;P13L;R262H;S183Y;S186Y;S194L;D3L 43;5;32;11;18;25;0 48;9;37;16;23;30;3 N 78 90 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. Furthermore, the monthly basis of sequence analysis revealed that D614G (spike protein), F106F (NSP3), P314L (NSP12b), and 5' UTR:241 mutations are at the top of the mutation analysis chart of every month from March 2020 to December 2020. 2021 Informatics in medicine unlocked Result SARS_CoV_2 D614G;F106F;P314L 66;89;103 71;94;108 5'UTR;S;Nsp3 123;73;96 129;78;100 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. Missense mutations [A890D, T1063I, G1433C, and T1456I], [N266I and H268L], R233C, [L89F, and V212F], F263S, [D315Y, A316T, and C444Y], [L183A, and G185E], T85I, L111K, and [A54T, and A74V] have a damaging effect on NSP3, NSP14, NSP6, NSP5, NSP15, NSP13, NSP16, NSP2, NSP4, and NSP8 proteins, respectively. 2021 Informatics in medicine unlocked Result SARS_CoV_2 A316T;A74V;C444Y;F263S;G1433C;G185E;H268L;L111K;R233C;T1063I;T1456I;T85I;V212F;A54T;A890D;D315Y;L183A;L89F;N266I 116;183;127;101;35;147;67;161;75;27;47;155;93;173;20;109;136;83;57 121;187;132;106;41;152;72;166;80;33;53;159;98;177;25;114;141;87;62 Nsp13;Nsp2;Nsp3;Nsp4;Nsp8;Nsp5;Nsp6 247;261;215;267;277;234;228 252;265;219;271;281;238;232 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. Mutations [L5F, and R80I], S97I, and [L46C, V48G, G49I, Q57H, W131R, G172V, Q185H, and Y206S] were identified to have a deleterious effect on ORF7a, ORF8, and ORF3a proteins, respectively. 2021 Informatics in medicine unlocked Result SARS_CoV_2 G172V;G49I;Q185H;Q57H;R80I;S97I;V48G;W131R;Y206S;L46C;L5F 69;50;76;56;20;27;44;62;87;38;11 74;54;81;60;24;31;48;67;92;42;14 ORF7a;ORF3a;ORF8 142;159;149 147;164;153 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. Other common identified mutations are GGG28881AAC (RG203KR, in the nucleocapsid protein), C22227T (L93L, in the membrane protein), G29645T (A222V, spike protein), G21255C (A199A, in the NSP16), C28932T (V30L, in the ORF10), and T445C (A220V, in the nucleocapsid protein). 2021 Informatics in medicine unlocked Result SARS_CoV_2 C22227T;C28932T;G21255C;G29645T;G28881A;G28881C;T445C;A199A;A220V;A222V;L93L;V30L 90;194;163;131;38;38;228;172;235;140;99;203 97;201;170;138;49;49;233;177;240;145;103;207 N;N;Membrane;S 67;249;112;147 79;261;120;152 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. Out of 46, 25 missense mutations (D1118H, S194L, R262H, M809L, P314L, A8D, S220G, A890D, G1433C, T1456I, R233C, F263S, L111K, A54T, A74V, L183A, A316T, V212F, L46C, V48G, Q57H, W131R, G172V, Q185H, and Y206S) were found to largely decrease (DDG value < -0.5) the structural stability of the corresponding proteins. 2021 Informatics in medicine unlocked Result SARS_CoV_2 A316T;A54T;A74V;A890D;A8D;F263S;G1433C;G172V;L111K;L183A;L46C;M809L;P314L;Q185H;Q57H;R233C;R262H;S194L;S220G;T1456I;V212F;V48G;W131R;Y206S;D1118H 145;126;132;82;70;112;89;184;119;138;159;56;63;191;171;105;49;42;75;97;152;165;177;202;34 150;130;136;87;73;117;95;189;124;143;163;61;68;196;175;110;54;47;80;103;157;169;182;207;40 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. The A23403G mutation causes a change from Aspartate (D) to Glycine (G) in protein position 614 (spike protein) which is responsible for the initial entry of the virus through the ACE2 receptor and is associated with the severity of COVID 19. 2021 Informatics in medicine unlocked Result SARS_CoV_2 A23403G 4 11 S 96 101 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. The C14408T mutation substitute Proline (P) with Leucine (L) in position 314 of non-structural protein 12b (NSP12b), a RNA-dependent RNA polymerase (RdRp). 2021 Informatics in medicine unlocked Result SARS_CoV_2 C14408T 4 11 RdRp;RdRP 119;149 147;153 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. Apparently, the Cys 15-Cys 136 disulfide bond is not absolutely essential for S glycoprotein function but may contribute to the stability of the functional spike. 2022 Journal of virology Result SARS_CoV_2 C15C 16 26 S;S 78;156 92;161 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. As the S1170F change does not alter a potential N-linked glycosylation site, it apparently affects other posttranslational modifications; as discussed above, resistance of the 63-kDa PNGase F product to O-glycosidase appears to rule out modification by core 1 or core 3 O-glycans. 2022 Journal of virology Result SARS_CoV_2 S1170F 7 13 N 48 49 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. Both the S1 and S2 glycoproteins of the wild-type and D614G SARS-CoV-2 strains migrated faster when expressed in the GALE/GALK2 293T cells compared with the migration of these glycoproteins expressed in 293T cells. 2022 Journal of virology Result SARS_CoV_2 D614G 54 59 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. Both the wild-type SARS-CoV-2 S glycoprotein and the prevalent D614G variant S glycoprotein were expressed in 293T cells and in the GALE/GALK2 293T cells. 2022 Journal of virology Result SARS_CoV_2 D614G 63 68 S;S 30;77 44;91 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. Despite this alteration, the C15F S glycoprotein was proteolytically processed nearly as efficiently as the wild-type S glycoprotein and exhibited wild-type association of the S1 and S2 subunits. 2022 Journal of virology Result SARS_CoV_2 C15F 29 33 S;S 34;118 48;132 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. However, after freeze-thawing, the relative infectivity of the C15F mutant virus decreased dramatically (data not shown). 2022 Journal of virology Result SARS_CoV_2 C15F 63 67 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. In contrast, the C301F and C379F changes, which eliminate the Cys 291-Cys 301 and Cys 379-Cys 432 disulfide bonds, respectively, located in the S1 N-terminal domain and receptor-binding domain, resulted in S glycoproteins that were not processed into S1 and S2 glycoproteins. 2022 Journal of virology Result SARS_CoV_2 C301F;C379F;C291C;C379C 17;27;62;82 22;32;73;93 S;N 206;147 221;148 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. In our study, the peptide containing Ser 659, Ser 673, Thr 676, Thr 678, and Ser 680 was found to be occupied by at least one O-linked glycan at a level of about 5%. 2022 Journal of virology Result SARS_CoV_2 S673T 46 56 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. The 63-kDa S2 glycoprotein band seen in PNGase F-treated lysates from 293T cells expressing the wild-type S glycoproteins was not evident in lysates from cells expressing the S1170F mutant. 2022 Journal of virology Result SARS_CoV_2 S1170F 175 181 S 106 121 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. The C15F change eliminates the Cys 15-Cys 136 disulfide bond in the S1 N-terminal domain. 2022 Journal of virology Result SARS_CoV_2 C15F;C15C 4;31 8;41 N 71 72 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. The expressed S glycoproteins mediated the formation of syncytia when human ACE2 (hACE2) was transiently coexpressed in the 293T-S cells. 2022 Journal of virology Result SARS_CoV_2 T293S 124 130 S 14 29 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. The infectivity of VSV vectors pseudotyped with the C15F S glycoproteins was approximately 31% of that of virus pseudotyped with the wild-type S glycoproteins. 2022 Journal of virology Result SARS_CoV_2 C15F 52 56 S;S 57;143 72;158 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. The S673I mutant was processed inefficiently and only supported the infection of pseudotyped VSV vectors at a very low level. 2022 Journal of virology Result SARS_CoV_2 S673I 4 9 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. The S676I and S1170F mutants supported the entry of VSV pseudotypes as efficiently as the wild-type S glycoprotein. 2022 Journal of virology Result SARS_CoV_2 S1170F;S676I 14;4 20;9 S 100 114 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. The T323I-pseudotyped viruses infected cells with approximately 41% of the efficiency of viruses pseudotyped with the wild-type S glycoproteins. 2022 Journal of virology Result SARS_CoV_2 T323I 4 9 S 128 143 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. The T323I, T676I, and S1170F mutants were processed nearly as efficiently as the wild-type S glycoprotein and exhibited good subunit association. 2022 Journal of virology Result SARS_CoV_2 S1170F;T323I;T676I 22;4;11 28;9;16 S 91 105 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. Thus, of these rare cysteine variants of the SARS-CoV-2 S glycoprotein, only one (C15F) allows partial, but unstable, infectivity. 2022 Journal of virology Result SARS_CoV_2 C15F 82 86 S 56 70 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. Viruses pseudotyped with the C301F and C379F S glycoproteins exhibited very low levels of infectivity. 2022 Journal of virology Result SARS_CoV_2 C301F;C379F 29;39 34;44 S 45 60 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. We examined the sensitivity of the two most replication-competent S glycoprotein mutants, T676I and S1170F, to neutralization by sACE2 and sera from convalescing SARS-CoV-2-infected individuals. 2022 Journal of virology Result SARS_CoV_2 S1170F;T676I 100;90 106;95 S 66 80 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Additionally, the Lambda variant demonstrated 1.6-fold enhanced infection of LLC-MK2 (P<0.0001) and showed significantly enhanced infectivity of L452Q, T76I and Del246/252+D253N pseudoviruses. 2022 Emerging microbes & infections Result SARS_CoV_2 L452Q;T76I;D253N 145;152;172 150;156;177 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Among them, mAb 9G11 showed a 41.7-fold reduction in neutralizing protection against Lambda variants, mainly caused by the F490S mutation, followed by L452Q. 2022 Emerging microbes & infections Result SARS_CoV_2 F490S;L452Q 123;151 128;156 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Conversely, the neutralizing effect of the sera against the T76I mutant strain was enhanced 1.5-fold, which was statistically significant (P=0.021). 2022 Emerging microbes & infections Result SARS_CoV_2 T76I 60 64 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Furthermore, the neutralizing effects of these sera against the T76I mutant strain were enhanced 2.7-fold, which was statistically significant (P=0.0002). 2022 Emerging microbes & infections Result SARS_CoV_2 T76I 64 68 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Furthermore, we found that T76I and T859N pseudoviruses were more easily neutralized by convalescent sera, both with 1.7-fold increased sensitivity (Figure 4B), which was statistically significant (P<0.0001). 2022 Emerging microbes & infections Result SARS_CoV_2 T76I;T859N 27;36 31;41 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Futhermore, the neutralization effects of these sera against the G75 V mutant strain were enhanced 1.5-fold, which was also statistically significant (P=0.038). 2022 Emerging microbes & infections Result SARS_CoV_2 G75V 65 70 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. However, no significant changes occurred in neutralization of the RBD amino acid mutant strains L452Q and F490S, which decreased 1.4-fold and 1.2-fold, respectively. 2022 Emerging microbes & infections Result SARS_CoV_2 F490S;L452Q 106;96 111;101 RBD 66 69 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. However, the Lambda variant showed no significant change in cell infection and was less infectious than G75 V and T859N pseudoviruses. 2022 Emerging microbes & infections Result SARS_CoV_2 G75V;T859N 104;114 109;119 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. However, we found that infection of T859N pseudovirus on 293T-ACE2, 293T-ACE2-TMPRSS2, and 293T-ACE2-CatL were all reduced by 1.7-fold, 1.8-fold, and 1.5-fold, respectively. 2022 Emerging microbes & infections Result SARS_CoV_2 T859N 36 41 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. In addition, the seven mAbs MWF, A001, CB6, X604, 9A8, M128, and 4E5 did not differ more than 4-fold in their neutralization of the Lambda variant compared with their neutralization of D614G, indicating that these seven mAbs provided good protection against the Lambda variant. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 185 190 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. In contrast, G75 V, T76I, and T869N pseudoviruses appeared to be more easily neutralized, with 1.5-fold (P=0.01), 1.6-fold (P=0.0007), and 2.0-fold (P<0.0001) enhanced neutralization, respectively, which were all statistically significant differences. 2022 Emerging microbes & infections Result SARS_CoV_2 G75V;T76I;T869N 13;20;30 18;24;35 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Meanwhile, no significant changes existed in the neutralization effect of vaccine-immunized sera against the L452Q, F490S and L452Q + F490S mutant strains, showing 1.5-fold, 1.6-fold, and 1.4-fold decreases, respectively. 2022 Emerging microbes & infections Result SARS_CoV_2 F490S;F490S;L452Q;L452Q 116;134;109;126 121;139;114;131 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Meanwhile, the neutralization effect against the L452Q + F490S combined amino acid mutant pseudovirus was decreased by 1.9-fold, which was statistically significant (P=0.044). 2022 Emerging microbes & infections Result SARS_CoV_2 F490S;L452Q 57;49 62;54 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Moreover, the convalescent sera's neutralizing effect against F490S was reduced by 1.5-fold, while the neutralizing protection against L452Q was unchanged (Figure 4B). 2022 Emerging microbes & infections Result SARS_CoV_2 F490S;L452Q 62;135 67;140 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Moreover, the infection of Calu-3 cells by L452Q, F490S, T76I and Del246/252+D253N pseudoviruses was enhanced 3.3-fold, 1.9-fold, 2.9-fold, and 2.4-fold, respectively. 2022 Emerging microbes & infections Result SARS_CoV_2 F490S;L452Q;T76I;D253N 50;43;57;77 55;48;61;82 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. No significant changes existed in the Lambda variant's ability to infect these four cell lines compared with the D614G pseudovirus. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 113 118 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Similarly, the neutralization effects against the L452Q, F490S and L452Q + F490S pseudoviruses were decreased by 3.2-fold, 3.5-fold and 3.8-fold, respectively(P<0.001). 2022 Emerging microbes & infections Result SARS_CoV_2 F490S;F490S;L452Q;L452Q 57;75;50;67 62;80;55;72 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Stemirna Company's mRNA vaccine-immunized sera showed a 1.5-fold decrease in neutralization against the Lambda variant and 1.5-fold and 1.6-fold decreases against the RBD region L452Q and F490S mutant pseudoviruses, respectively (Figure 5A, E). 2022 Emerging microbes & infections Result SARS_CoV_2 F490S;L452Q 188;178 193;183 RBD 167 170 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. The decreased neutralizing effect of these three mAbs resulted from a combination of L452Q and F490S mutations in the RBD region. 2022 Emerging microbes & infections Result SARS_CoV_2 F490S;L452Q 95;85 100;90 RBD 118 121 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. The neutralizing effect of the five Ad5 adenovirus-vectored vaccine-immunized sera against the Lambda variant decreased by an average of 2.5-fold, but this was not statistically different from the effect observed against D614G because of the large differences between samples (Figure 5D, H). 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 221 226 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. The neutralizing protection of mAb AM180 decreased more than 243-fold, an almost complete abrogation of protection, which was caused by the accumulated mutations of F490S and L452Q. 2022 Emerging microbes & infections Result SARS_CoV_2 F490S;L452Q 165;175 170;180 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. To study the Lambda variant and each individual amino acid mutation's effect on viral function, we constructed 10 pseudovirus strains using the pseudovirus technique, including the D614G mutation, G75 V, T76I, Del246/252+D253N (RSYLTPGD246-253N), L452Q, F490S, T859N, L452Q + F490S, G75V + T76I and Lambda variant based on the D614G background (Figure 1). 2022 Emerging microbes & infections Result SARS_CoV_2 D614G;D614G;F490S;F490S;G75V;G75V;L452Q;L452Q;T76I;T76I;T859N;D253N 181;327;254;276;197;283;247;268;204;290;261;221 186;332;259;281;202;287;252;273;208;294;266;226 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. We found a 1.4-fold enhancement in infection by the Lambda variant in Huh7 cells compared with the D614G mutant strain, but this was not statistically significant. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 99 104 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. We found no significant differences in the neutralization of Lambda compared with D614G by convalescent sera, with only an approximately 1.3-fold reduction (Figure 4B, C). 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 82 87 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. Both dTTP and dUTP systems have the same trend for wild-type and spike N501Y detection (Figure S20). 2021 Analytical chemistry Result SARS_CoV_2 N501Y 71 76 S 65 70 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. Doubling the LAMP reaction time, CRISPR-LAMP technology can even achieve 10 cp/muL (10 copies of template per reaction) in wild-type and spike N501Y detection (Figure 5C). 2021 Analytical chemistry Result SARS_CoV_2 N501Y 143 148 S 137 142 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. Here, we focus on spike N501Y mutation and compared the LAMP technology with the CRISPR-LAMP technology. 2021 Analytical chemistry Result SARS_CoV_2 N501Y 24 29 S 18 23 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. However, specific LAMP primers either for wild-type or spike N501Y cannot be designed. 2021 Analytical chemistry Result SARS_CoV_2 N501Y 61 66 S 55 60 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. Mutant SARS-CoV-2 Spike N501Y Detection Design. 2021 Analytical chemistry Result SARS_CoV_2 N501Y 24 29 S 18 23 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. Statistical data are shown in Table S3 that proposed CRISPR-LAMP technology can improve sensitivity to 100 times than LAMP technology and can precisely detect wild-type and spike N501Y, respectively. 2021 Analytical chemistry Result SARS_CoV_2 N501Y 179 184 S 173 178 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. We also found that CRISPR-LAMP technology can detect wild-type on the background of spike N501Y at the level of 1% (Figure 6). 2021 Analytical chemistry Result SARS_CoV_2 N501Y 90 95 S 84 89 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. With CRISPR-LAMP technology, we designed common LAMP primers, wild-type crRNA, and spike N501Y crRNA which are shown in Figure 5B. 2021 Analytical chemistry Result SARS_CoV_2 N501Y 89 94 S 83 88 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Analyses of the binding response curves indicate that the variants bound to ACE-2 faster (KaN439K = 4.15 x 105 M-1 s-1, KaN501Y = 4.76 x 105 M-1 s-1, Kawt = 3.34 x 105 M-1 s-1) and mostly the N501Y had noticeable slower dissociation rates (KdisN439K = 3.57 x 10-3 s-1, KdisN501Y = 1.06 x 10-3 s-1, Kdiswt = 5.9 x 10-3 s-1). 2021 eLife Result SARS_CoV_2 N501Y 192 197 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Determination of the evasion capacity of the N439K and N501Y variants in naturally induced antibody-mediated immunity. 2021 eLife Result SARS_CoV_2 N439K;N501Y 45;55 50;60 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. However, best-fit IC50 values from sera from mice immunized with spike differed slightly between strains, as 11% and 19% higher serum concentration was required for the N439K and N501Y variants, respectively, to achieve the same inhibition levels as for the wt RBD. 2021 eLife Result SARS_CoV_2 N439K;N501Y 169;179 174;184 S;RBD 65;261 70;264 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. In order to examine whether the increased affinity of the N501Y variant for ACE-2 was associated with a more efficient establishment of infection and development of disease, we challenged transgenic ACE-2 humanized K18-hACE2 mice with the early 2020 SARS-CoV2 B.1 (Freiburg isolate, FR-4248) and the B1.1.7 (alpha) strains. 2021 eLife Result SARS_CoV_2 N501Y 58 63 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Linear regression and Spearman correlation analyses of the mAbs with best-fit IC50s within the range of concentration tested (n = 8) showed that the N439K and N501Y mutations had very minor effects on the inhibition potency of the mAbs (N439K R2 = 0.9777, rho = 1, p < 0.0001; N501Y R2 = 0.9832, rho = 0.9762, p < 0.0001). 2021 eLife Result SARS_CoV_2 N439K;N501Y;N501Y;N439K 149;159;277;237 154;164;282;242 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. The inhibition potencies towards the wt and the variants had a highly significant correlation (rho = 0.9774 and rho = 0.9581 for N439K and N501Y, respectively, p < 0.0001), with the best-fit X-intercept ranging from 12.38 to 15.89 for the N439K and N501Y, respectively (Figure 3B, C). 2021 eLife Result SARS_CoV_2 N439K;N439K;N501Y;N501Y 129;239;139;249 134;244;144;254 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. The N439K variant bound with an approx. 2021 eLife Result SARS_CoV_2 N439K 4 9 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. There was a statistically significant reduction in the inhibition of the N439K and N501Y RBD compared to the wt (p < 0.0001 for both) (Figure 3A). 2021 eLife Result SARS_CoV_2 N439K;N501Y 73;83 78;88 RBD 89 92 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. This suggests that the N439K, but not the N501Y, has a moderately deleterious effect on the RBD stability. 2021 eLife Result SARS_CoV_2 N439K;N501Y 23;42 28;47 RBD 92 95 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. twofold higher affinity than the wt (8.6 vs 17 nM) (Figure 1D, E), while the N501Y variant did so with an eightfold higher affinity (2.23 vs 17 nM) (Figure 1F). 2021 eLife Result SARS_CoV_2 N501Y 77 82 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. We expressed recombinant SARS-CoV-2 RBD wild-type (wt) (Wuhan-hu-1), RBD N439K, and RBD N501Y in Expi293 HEK cells and performed thermal stability and binding kinetic analyses to determine the biophysical relevance of the RBD variants (Figure 1). 2021 eLife Result SARS_CoV_2 N439K;N501Y 73;88 78;93 RBD;RBD;RBD;RBD 36;69;84;222 39;72;87;225 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. We monitored the thermal unfolding using the intrinsic fluorescence ratio at 350 and 330 nm and observed a ~2.5 C reduction in the inflection temperature (Ti) for the N439K variant (Figure 1C). 2021 eLife Result SARS_CoV_2 N439K 167 172 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. As lysine is also a basic amino acid, the R203K mutation causes only a small change in the pI of the linker region. 2021 Cell host & microbe Result SARS_CoV_2 R203K 42 47 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Combined with the abovementioned findings that the R203K/G204R mutations could impact the local charge of the N protein, the R203K/G204R mutations may promote the binding of RNA by increasing the positive charge within the linker region to increase the RNP assembly efficiency, thereby accelerating the virus' replication. 2021 Cell host & microbe Result SARS_CoV_2 R203K;R203K;G204R;G204R 51;125;131;57 56;130;136;62 N 110 111 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Considering that pattern changes during diversification and that the spread of R203K/G204R is not continuous, we calculated the CLR m/t per month. 2021 Cell host & microbe Result SARS_CoV_2 R203K;G204R 79;85 84;90 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Correlation analyses of IF tracks between pairs of mutants in these three time intervals show that the evolution of R203K/G204R is independent of that of D614G (Figures S2A-S2D; for details, see STAR Methods). 2021 Cell host & microbe Result SARS_CoV_2 D614G;R203K;G204R 154;116;122 159;121;127 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. In contrast, G204R introduces an additional basic amino acid, leading to a more significant increase in the linker region pI. 2021 Cell host & microbe Result SARS_CoV_2 G204R 13 18 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. In intra-host single nucleotide variation (iSNVs) analyses, we again observed a significant increase in the IF of R203K/G204R (Figure S1C). 2021 Cell host & microbe Result SARS_CoV_2 R203K;G204R 114;120 119;125 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Moreover, the PFU titers and E sgRNA loads of the 203K/204R virus were significantly higher than those of the R203/G204 virus (Figures 5E and 5F), indicating that the R203K/G204R mutation increased the infectivity of SARS-CoV-2 in the human lung cell line. 2021 Cell host & microbe Result SARS_CoV_2 R203K;G204R 167;173 172;178 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Selection signatures of R203K/G204R. 2021 Cell host & microbe Result SARS_CoV_2 R203G;R203K;G204R 24;24;30 29;29;35 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Structural implications of the R203K/G204R mutations for RNP assembly. 2021 Cell host & microbe Result SARS_CoV_2 R203K;G204R 31;37 36;42 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. The corresponding amino acid changes at the protein level are co-occurring R203K/G204R substitutions in the N protein. 2021 Cell host & microbe Result SARS_CoV_2 R203K;G204R 75;81 80;86 N 108 109 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. The decrease of R203K/G204R in D and the increase in I2 are associated with the increase of A222V in D (correlation = -0.99, P value = 0.0004) and the increase of N501Y in I2 (correlation = 0.99, P value = 0.00016; Table S2A, Figures S2E-S2L, "Cor_mut.pdf" in Data S1; for details, see STAR Methods), respectively. 2021 Cell host & microbe Result SARS_CoV_2 A222V;N501Y;R203K;G204R 92;163;16;22 97;168;21;27 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. The global IF of R203K/G204R increased from nearly zero in January 2020 to more than 70% in March 2021 (Figures 2A and 2B). 2021 Cell host & microbe Result SARS_CoV_2 R203K;G204R 17;23 22;28 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. The lineages showing rapid increases (Figures S4A-S4H), including B.1.1.7, P.1, P.2 (Zeta), P.3 (Theta), and C.37 (Lambda), are all carrying R203K/G204R mutations (Tables S3A and S3B). 2021 Cell host & microbe Result SARS_CoV_2 R203K;G204R 141;147 146;152 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. The R203K/G204R mutations are located in the linker region of N. 2021 Cell host & microbe Result SARS_CoV_2 R203K;G204R 4;10 9;15 N 62 63 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. The rapid spread of R203K/G204R mutant viruses worldwide. 2021 Cell host & microbe Result SARS_CoV_2 R203K;G204R 20;26 25;31 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. The results suggested that the R203K/G204R mutant virus confers higher susceptibility to serum neutralization. 2021 Cell host & microbe Result SARS_CoV_2 R203K;G204R 31;37 36;42 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. These R203K/G204R signatures are similar to previous findings for D614G. 2021 Cell host & microbe Result SARS_CoV_2 D614G;R203K;G204R 66;6;12 71;11;17 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. These results, combined together, demonstrated that the R203K/G204R mutations enhanced viral replication efficiency and further increased the virion infectivity commonly. 2021 Cell host & microbe Result SARS_CoV_2 R203K;G204R 56;62 61;67 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Thus, the R203K/G204R mutations may impact virus RNP assembly. 2021 Cell host & microbe Result SARS_CoV_2 R203K;G204R 10;16 15;21 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. To investigate the impact of R203K/G204R on the tertiary structure of the nucleocapsid, we built a structural model of the N protein based on documented cryo-EM reports (; Figure 7 ). 2021 Cell host & microbe Result SARS_CoV_2 R203K;G204R 29;35 34;40 N;N 74;123 86;124 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. We found that R203K/G204R have rapidly spread worldwide. 2021 Cell host & microbe Result SARS_CoV_2 R203K;G204R 14;20 19;25 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. We tracked the IFs of the combinations (23 = 8) of the three sets of two-allele polymorphisms (A222V, N501Y, and R203K/G204R) and identified four dominant lineages (Figure 3 A). 2021 Cell host & microbe Result SARS_CoV_2 N501Y;R203K;A222V;G204R 102;113;95;119 107;118;100;124 34822912 Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR. 25 (3.9 %) showed amplification of genes for N501Y with K417 and therefore, were considered to belong to the alpha variant. 2022 Journal of virological methods Result SARS_CoV_2 N501Y 45 50 34822912 Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR. 638 (96.1 %) samples showed amplification for the genes targeting L452R and K417 and therefore, were considered to be the delta variant. 2022 Journal of virological methods Result SARS_CoV_2 L452R 66 71 34822912 Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR. We also tested 20 samples that were assigned the delta lineage by sequencing and the only genes targeting L452R was amplified. 2022 Journal of virological methods Result SARS_CoV_2 L452R 106 111 34822912 Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR. We randomly selected 20 samples identified as alpha during May 2021 by sequencing and all 20 of these samples had genes targeting N501Y and K417 were amplified whereas there was no amplification of other genes. 2022 Journal of virological methods Result SARS_CoV_2 N501Y 130 135 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. Two mutations in the protein coding region i.e., D614G in spike and P314L in NSP 12b; one extragenic mutation at 241 position of 5'UTR and one silent mutation at F106 NSP3. 2022 Virus research Result SARS_CoV_2 D614G;P314L 49;68 54;73 S;5'UTR;Nsp3 58;129;167 63;134;171 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Altogether, mutation of T403R allows RaTG13 S interaction with human ACE2 and proteolytic activation by furin and Cathepsins for both cell-cell fusion and RaTG13 S-mediated VSVpp entry. 2021 Nature communications Result SARS_CoV_2 T403R 24 29 S;S 44;162 45;163 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Both WT SARS-CoV-2 S and (to a lesser extent) R403T SARS-CoV-2 S proteins were also capable of using bat (Rhinolophus affinis) ACE2 for viral entry although the overall infection rates were low. 2021 Nature communications Result SARS_CoV_2 R403T 46 51 S;S 19;63 20;64 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Coexpression of the transmembrane serine protease 2 (TMPRSS2) enhanced infection mediated by the wildtype (WT) and R403T SARS-CoV-2 S proteins but had no significant effect on entry mediated by the RaTG13 T403R S. 2021 Nature communications Result SARS_CoV_2 R403T;T403R 115;205 120;210 S;S 132;211 133;212 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Engineered expression of human ACE2 rendered Lu 1 highly susceptible to infection mediated by SARS-CoV-2 and the T403R RaTG13 S proteins. 2021 Nature communications Result SARS_CoV_2 T403R 113 118 S 126 127 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Furin inhibitor 1 prevented and the Cathepsin inhibitor E64-d moderately reduced both SARS-CoV-2 and RaTG13 T403R S-mediated cell-cell fusion. 2021 Nature communications Result SARS_CoV_2 T403R 108 113 S 114 115 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. However, significant syncytia formation was observed for the T403R RaTG13 S. 2021 Nature communications Result SARS_CoV_2 T403R 61 66 S 74 75 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. In addition, the substitution of E37A reduced the levels of WT SARS-CoV-2 S-mediated infection to those mediated by R403T SARS-CoV-2 S. 2021 Nature communications Result SARS_CoV_2 E37A;R403T 33;116 37;121 S;S 74;133 75;134 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. In agreement with its reported broad antiviral activity, the fusion inhibitor EK-1 efficiently inhibited SARS-CoV-2, T403R RaTG13, as well as (to a much lesser extent) Pangolin CoV S-mediated infection. 2021 Nature communications Result SARS_CoV_2 T403R 117 122 S 181 182 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. In agreement with the in silico data, mutation of E37A in ACE2 abolished the enhancing effect of the T403R change on RaTG13 S-mediated VSVpp infection of HEK293T cells. 2021 Nature communications Result SARS_CoV_2 E37A;T403R 50;101 54;106 S 124 125 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. In comparison, entry via the R403T SARS-CoV-2 S was strongly attenuated and the WT and T403A RaTG13 S proteins were unable to mediate VSV-pp infection. 2021 Nature communications Result SARS_CoV_2 R403T;T403A 29;87 34;92 S;S 46;100 47;101 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. In comparison, mutation of D38A in ACE2 predicted to play little if any role in S interaction did not disrupt the enhancing effect of the T403R change on RaTG13 S-mediated VSVpp infection. 2021 Nature communications Result SARS_CoV_2 D38A;T403R 27;138 31;143 S;S 80;161 81;162 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. In contrast, the parental RaTG13 S protein did not mediate VSVpp entry, while the T403R S allowed significant infection of human intestinal cells. 2021 Nature communications Result SARS_CoV_2 T403R 82 87 S;S 33;88 34;89 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. In the case of SARS-CoV-2 R403T S this effect may be partly due to reduced S expression levels. 2021 Nature communications Result SARS_CoV_2 R403T 26 31 S;S 32;75 33;76 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Indeed, ACE2 coexpression induced processing of the WT and R403T SARS-CoV-2 as well as T403R RaTG13 S2 proteins to S2', while cleavage of the WT and T403A RaTG13 S proteins remained inefficient. 2021 Nature communications Result SARS_CoV_2 R403T;T403A;T403R 59;149;87 64;154;92 S 162 163 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Indeed, SARS-CoV-2 and T403R RaTG13 S-mediated VSVpp infection of ACE2-A549 cells was efficiently inhibited by the Cathepsin inhibitor E64-d but not by the TMPRSS2 inhibitor Camostat mesylate. 2021 Nature communications Result SARS_CoV_2 T403R 23 28 S 36 37 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Infection of Caco-2 cells at low MOI showed that the R403T SARS-CoV-2 mutant replicated with significantly lower efficiency than WT virus. 2021 Nature communications Result SARS_CoV_2 R403T 53 58 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Mutation of R403T in the SARS-CoV-2 S reduced CPE. 2021 Nature communications Result SARS_CoV_2 R403T 12 17 S 36 37 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Mutation of R403T reduced the ability of the SARS-CoV-2 S protein to mediate entry of VSVpp into the human colorectal adenocarcinoma cell line Caco-2 by 40%. 2021 Nature communications Result SARS_CoV_2 R403T 12 17 S 56 57 Colorectal adenocarcinoma 107 132 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Mutation of T403R allows RaTG13 S to use human ACE2 as entry receptor. 2021 Nature communications Result SARS_CoV_2 T403R 12 17 S 32 33 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Proteolytic processing of the T403R RaTG13 S protein. 2021 Nature communications Result SARS_CoV_2 T403R 30 35 S 43 44 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. R403T S was efficiently expressed and incorporated into viral particles, albeit at slightly reduced levels compared to the WT SARS-CoV-2 S. 2021 Nature communications Result SARS_CoV_2 R403T 0 5 S;S 6;137 7;138 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Sensitivity of T403R RaTG13 S to inhibitors and sera from vaccinated individuals. 2021 Nature communications Result SARS_CoV_2 T403R 15 20 S 28 29 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Sera from three individuals who had received prime-boost treatment with the Pfizer-BioNTech COVID-19 Vaccine neutralized the T403R RaTG13 S with higher efficiency than the SARS-CoV-2 S. 2021 Nature communications Result SARS_CoV_2 T403R 125 130 S;S 138;183 139;184 COVID-19 92 100 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Strikingly, the T403R change enhanced the infectiousness of Vesicular stomatitis virus pseudoparticles (VSVpp) carrying the RaTG13 S for Caco-2 cells ~30-fold, while substitution of T403A introduced as control had no enhancing effect. 2021 Nature communications Result SARS_CoV_2 T403A;T403R 182;16 187;21 S 131 132 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. The ability of T403R RaTG13 S to utilize ACE2 is species-specific. 2021 Nature communications Result SARS_CoV_2 T403R 15 20 S 28 29 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. The enhancing effect of T403R in RaTG13 S depends on E37 in ACE2. 2021 Nature communications Result SARS_CoV_2 T403R 24 29 S 40 41 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. The increased infectiousness of the T403R RaTG13 S enabled us to examine its sensitivity to therapeutic agents and serum neutralization. 2021 Nature communications Result SARS_CoV_2 T403R 36 41 S 49 50 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. The parental and T403A RaTG13 S did not lead to detectable fusion. 2021 Nature communications Result SARS_CoV_2 T403A 17 22 S 30 31 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. The parental SARS-CoV-2 S protein allowed efficient infection of gut organoids and the R403T change had modest attenuating effects. 2021 Nature communications Result SARS_CoV_2 R403T 87 92 S 24 25 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. The R403T change in SARS-CoV-2 S moderately reduced and the T403R substitution in RaTG13 S strongly enhanced the levels of S protein bound to ACE2. 2021 Nature communications Result SARS_CoV_2 R403T;T403R 4;60 9;65 S;S;S 31;89;123 32;90;124 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. The results agree with the previous finding that RaTG13 S is able to use human ACE2 to some extent if overexpressed but also confirm that the T403R change greatly enhances this function and is required for utilization of endogenously expressed human ACE2. 2021 Nature communications Result SARS_CoV_2 T403R 142 147 S 56 57 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. The T403R change in RaTG13 S, however, specifically enhanced ACE2 binding without affecting S expression levels. 2021 Nature communications Result SARS_CoV_2 T403R 4 9 S;S 27;92 28;93 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. The WT and T403A RaTG13 S were unable to complement SCoV-2DeltaS, while the T403R RaTG13 S resulted in significant CPE. 2021 Nature communications Result SARS_CoV_2 T403A;T403R 11;76 16;81 S;S 24;89 25;90 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. The WT SARS-CoV-2 and the T403R RaTG13 S proteins allowed efficient entry into cells overexpressing human ACE2, while the parental RaTG13 S protein was poorly active. 2021 Nature communications Result SARS_CoV_2 T403R 26 31 S;S 39;138 40;139 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. These analyses predicted that mutation of T403R significantly strengthens the ability of the RaTG13 S protein to bind human ACE2. 2021 Nature communications Result SARS_CoV_2 T403R 42 47 S 100 101 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Thus, activation of S2 to S2' during RaTG13 T403R-dependent infection of ACE2-A549 cells is mediated by Cathepsins. 2021 Nature communications Result SARS_CoV_2 T403R 44 49 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Thus, the enhancing effect of the T403R mutation on the ability of RaTG13 S to infect human cells seems to be due to increased interaction with ACE2 rather than the utilization of integrins. 2021 Nature communications Result SARS_CoV_2 T403R 34 39 S 74 75 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. To assess the relevance of R403 for SARS-CoV-2 replication, we reconstituted replication-competent SARS-CoV-2 using bacmids specifically containing the R403T mutation and coding for the yellow fluorescent protein (YFP) in place of ORF6. 2021 Nature communications Result SARS_CoV_2 R403T 152 157 ORF6 231 235 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. To assess whether the T403R change might allow the bat CoV RaTG13 to spread to human bs, we performed infection studies using intestinal organoids derived from pluripotent stem cells. 2021 Nature communications Result SARS_CoV_2 T403R 22 27 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. To assess which proteases are involved in cell-cell fusion mediated by the RaTG13 T403R S protein, we examined syncitia formation in the presence of specific inhibitors. 2021 Nature communications Result SARS_CoV_2 T403R 82 87 S 88 89 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. To further analyze the sensitivity of the T403R RaTG13 S to neutralization, we examined sera from 22 individuals who received heterologous ChAdOx1 nCoV-19/BNT162b2 prime-boost vaccination and nine individuals who received homologous BNT162b2 vaccination. 2021 Nature communications Result SARS_CoV_2 T403R 42 47 S 55 56 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. We found that all sera inhibited RaTG13 T403R S-mediated infection abeit with varying efficiency. 2021 Nature communications Result SARS_CoV_2 T403R 40 45 S 46 47 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. We found that R403 is highly conserved in SARS-CoV-2 S proteins: only 294 of ~3.4 million S sequences recorded on GSAID contain a conservative change of R403K and just 132 another amino acids: M (78), H (16), G (10), S (10), T (6), I (9), L (2), N (2), P (1) or W (1). 2021 Nature communications Result SARS_CoV_2 R403K 153 158 N;S;S 246;53;90 247;54;91 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. We found that the integrin inhibitor ATN-161 had no definitive effect on SARS-CoV-2 or T403R RaTG13 S-mediated infection of Caco-2 cells. 2021 Nature communications Result SARS_CoV_2 T403R 87 92 S 100 101 34828410 Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India. Except for the D614G mutation in the Spike protein, which is the defining feature of the B.1 lineage, no mutation was found to be shared between kappa and alpha variants. 2021 Genes Result SARS_CoV_2 D614G 15 20 S 37 42 34828410 Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India. In addition, P681R mutation in the spike protein of the kappa variant was significant in view of its location being adjacent to the furin cleavage site and thereby having the potential to influence viral entry into the host cell. 2021 Genes Result SARS_CoV_2 P681R 13 18 S 35 40 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. As in the direct ELISA, reduced CB6 binding was seen with the gamma and K417N RBDs. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 K417N 72 77 RBD 78 82 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. As these VBMs share the N501Y RBD mutation, and the alpha contains only the N501Y mutation, we also tested 2E8 binding to an N501Y RBD; no binding was observed (data not shown). 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 N501Y;N501Y;N501Y 24;76;125 29;81;130 RBD;RBD 30;131 33;134 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. In contrast, 2E8 binding to RBDs with a single K417N or E484K mutation was not impaired (Figure 3a). 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 E484K;K417N 56;47 61;52 RBD 28 32 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. K417N by itself significantly reduces binding (Figure 3b). 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 K417N 0 5 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. The 2E8 ELISA bound to L, delta, the K417N mutant, kappa, and epsilon but not to any of the Y501-containing variant proteins: alpha, beta, and gamma. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 K417N 37 42 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. This indicates that the 2E8 can distinguish between N501 and N501Y independent of changes affecting class I (K417) and class II (E484) neutralizing antibodies. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 N501Y 61 66 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. This is consistent with the observations of others and suggests that CB6 is useful to differentiate N501Y-containing variants alpha and gamma from beta in an ELISA. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 N501Y 100 105 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. We also tested RBDs corresponding to delta, kappa (B.1.617.1; L452R, E484Q), and the single mutant K417N. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 E484Q;K417N;L452R 69;99;62 74;104;67 RBD 15 19 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. We explored the difference between binding to the beta and gamma RBDs, which differ only at K417 (beta, K417N; gamma, K417T). 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 K417N;K417T 104;118 109;123 RBD 65 69 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. We tested the hybridoma-expressed mAb for binding to commercial antigens (spike S1, spike D614G, and nucleocapsid) and the VSV-G:S1. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 D614G 90 95 N;S;S 101;74;84 113;79;89 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. We used a direct ELISA to compare the binding of 2E8 and CB6 to recombinant S1 and RBD proteins, including S1 proteins corresponding to L, alpha, beta, gamma, and epsilon (B.1.429; L452R, E484Q) (Figure 3). 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 E484Q;L452R 188;181 193;186 RBD 83 86 34833135 Emerging Mutations Potentially Related to SARS-CoV-2 Immune Escape: The Case of a Long-Term Patient. Seven additional changes, unrelated to B.1.177.51 lineage, were also detected, with three of them occurring in the S protein (V143D, del144/145, E484K; Figure 1). 2021 Life (Basel, Switzerland) Result SARS_CoV_2 E484K;V143D 145;126 150;131 S 115 116 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. After the post-infection treatment, curcumin exerted an antiviral effect against SARS-CoV-2 D614G strain at 10 microg/mL of 84.4%, p = 0.0095, and at 5 microg/mL of 31.7%, p = 0.0095 (Figure 5). 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 D614G 92 97 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. As can be seen from Figure 6, the viral titer of D614G strain was significantly reduced through co-treatment strategy (incubation of curcumin with the virus prior to infection) at 10 (92%, p = 0.004), 5 (60.4%, p = 0.004), and 2.5 microg/mL (39.3%, p = 0.004) of curcumin (Figure 6). 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 D614G 49 54 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. By pre-post infection treatment (cells treatment with curcumin, prior and post to infection with SARS-CoV-2) curcumin exerted antiviral activity of 99.0% (p = 0.0095), 51.3% (p = 0.0095), 22.2% (p = 0.0095), and 27.8% (p = 0.0095) against SARS-CoV-2 D614G strain at concentrations of 10, 5, 2.5, and 1.25 microg/mL, respectively (Figure 3). 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 D614G 250 255 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. Curcumin Inhibited SARS-CoV-2 D614G Strain Infectivity under the Co-Treatment Condition. 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 D614G 30 35 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. Curcumin Inhibited the Early and Late Stages of SARS-CoV-2 D614G Strain. 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 D614G 59 64 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. The pre-infection treatment demonstrated that curcumin had an antiviral effect against SARS-CoV-2 D614G strain at 10 microg/mL of 99.2%, p = 0.0095 and at 5 microg/mL of 39.3%, p = 0.0095 (Figure 4). 2021 Molecules (Basel, Switzerland) Result SARS_CoV_2 D614G 98 103 34834948 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a Dog in Connecticut in February 2021. The B.1 and its sub-lineages that carry both D614G in spike and P323L in nsp12 substitutions have become the dominant variants across the world. 2021 Viruses Result SARS_CoV_2 D614G;P323L 45;64 50;69 S;Nsp12 54;73 59;78 34834948 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a Dog in Connecticut in February 2021. The D614G and P323L occurred in China on 24 January 2020 and in the U.K. 2021 Viruses Result SARS_CoV_2 D614G;P323L 4;14 9;19 34834948 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a Dog in Connecticut in February 2021. The virus from this CT dog did not contain mutations related to the South African variant B.1.351 (N501Y, E484K and K417N in Spike) or the U.K. 2021 Viruses Result SARS_CoV_2 E484K;K417N;N501Y 106;116;99 111;121;104 S 125 130 34834948 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a Dog in Connecticut in February 2021. variant B.1.1.7 (69/70 deletion, N501Y, and P681H in Spike). 2021 Viruses Result SARS_CoV_2 N501Y;P681H 33;44 38;49 S 53 58 34834948 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in a Dog in Connecticut in February 2021. We found amino acid substitutions in Spike (D614G), N (D377Y, P67S, P199L), NS3 (G172V, Q57H), NS8 (S24L) NSP2 (T85I), NSP4 (M458I), NSP5 (L89F), NSP12 (P323L), NSP14 (N129D), and NSP16 (R216C) proteins. 2021 Viruses Result SARS_CoV_2 P199L;P67S;Q57H;D377Y;D614G;G172V;L89F;M458I;N129D;P323L;R216C;S24L;T85I 68;62;88;55;44;81;139;125;168;153;187;100;112 73;66;92;60;49;86;143;130;173;158;192;104;116 S;Nsp12;Nsp2;Nsp4;Nsp5;NS3;N 37;146;106;119;133;76;52 42;151;110;123;137;79;53 34834983 High Individual Heterogeneity of Neutralizing Activities against the Original Strain and Nine Different Variants of SARS-CoV-2. A similar mechanism also accounts for all variants that display the E484K mutation, including the Beta (70% decrease) and Gamma (67% decrease) variants (Table 1). 2021 Viruses Result SARS_CoV_2 E484K 68 73 34834983 High Individual Heterogeneity of Neutralizing Activities against the Original Strain and Nine Different Variants of SARS-CoV-2. In the case of the Marseille-501/A.27 variant, the L452R mutation is associated with N501Y. 2021 Viruses Result SARS_CoV_2 L452R;N501Y 51;85 56;90 34834983 High Individual Heterogeneity of Neutralizing Activities against the Original Strain and Nine Different Variants of SARS-CoV-2. The case of the Delta variant is more puzzling, since, in this case, the substitution L452R is associated with T478K instead of N501Y. 2021 Viruses Result SARS_CoV_2 L452R;N501Y;T478K 86;128;111 91;133;116 34834983 High Individual Heterogeneity of Neutralizing Activities against the Original Strain and Nine Different Variants of SARS-CoV-2. The E484K substitution (Glu Lys substitution) in the Marseille-484K.V1/R.1 variant induces a dramatic rearrangement of the RBD surface that results in a complete lack of interaction with the bamlanivimab nAb (Figure 4A,B). 2021 Viruses Result SARS_CoV_2 E484K 4 9 RBD 125 128 34834983 High Individual Heterogeneity of Neutralizing Activities against the Original Strain and Nine Different Variants of SARS-CoV-2. The L452R substitution is present in both the Marseille-501/A.27 (Figure 4C) and the Delta (Figure 4D) variants, yet in a distinct mutational context. 2021 Viruses Result SARS_CoV_2 L452R 4 9 34834983 High Individual Heterogeneity of Neutralizing Activities against the Original Strain and Nine Different Variants of SARS-CoV-2. When T478 is substituted by K478 (T478K substitution), F486 is attracted by the cationic group of K478, preventing any contact with the aromatic amino acids Y32 and Y92 of the antibody (Figure 6B). 2021 Viruses Result SARS_CoV_2 T478K 34 39 34834987 The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City. The B.1.1.159 variant is characterized by 9 mutations (C203T, C222T, C3140T, C10954T, A11117G, C12789T, C21306T, C22995A, and C23604A), four ORF1a substitutions (P959S, T3255I, I3618V, and T4175I) and three spike substitutions (T478K, P681H, and T732A) (Figure 1C). 2021 Viruses Result SARS_CoV_2 A11117G;C10954T;C12789T;C21306T;C222T;C22995A;C23604A;C3140T;I3618V;P681H;T3255I;T4175I;T732A;C203T;P959S;T478K 86;77;95;104;62;113;126;69;177;235;169;189;246;55;162;228 93;84;102;111;67;120;133;75;183;240;175;195;251;60;167;233 ORF1a;S 141;207 146;212 34835101 Impact of the Double Mutants on Spike Protein of SARS-CoV-2 B.1.617 Lineage on the Human ACE2 Receptor Binding: A Structural Insight. The delta variant, which carried L452R and T478K mutations, also demonstrated a reduced affinity towards the LY-CoV555. 2021 Viruses Result SARS_CoV_2 L452R;T478K 33;43 38;48 34835101 Impact of the Double Mutants on Spike Protein of SARS-CoV-2 B.1.617 Lineage on the Human ACE2 Receptor Binding: A Structural Insight. The occurrence of L452R and E484Q mutations in the kappa variant severely impacted the affinity of LY-CoV555. 2021 Viruses Result SARS_CoV_2 E484Q;L452R 28;18 33;23 34835101 Impact of the Double Mutants on Spike Protein of SARS-CoV-2 B.1.617 Lineage on the Human ACE2 Receptor Binding: A Structural Insight. The reference complex structures along with the kappa (L452R, E484Q) and delta variant (L452R and T478K) models were subjected to two hundred nanoseconds of MD simulations. 2021 Viruses Result SARS_CoV_2 E484Q;T478K;L452R;L452R 62;98;55;88 67;103;60;93 34835288 Antibody Titer Kinetics and SARS-CoV-2 Infections Six Months after Administration with the BNT162b2 Vaccine. The highest AUC was observed for the D614G variant followed by the B.1.1.7 and the B.1.351 (Figure 4). 2021 Vaccines Result SARS_CoV_2 D614G 37 42 34835288 Antibody Titer Kinetics and SARS-CoV-2 Infections Six Months after Administration with the BNT162b2 Vaccine. We also evaluated the neutralizing activity at T2 and T3 of the 48 collected sera (diluted to 1:80 and 1:160) against three SARS-CoV-2 strains isolated in our laboratory and belonging to the variants D614G, B.1.1.7, and B.1.351 (hCoV-19/Italy/LOM-UniSR-1/2020; hCoV-19/Italy/LOM-UniSR7/2021, and hCoV-19/Italy/LOM-UniSR6/2021 all available on GISAID sequence database: (accessed on 3 November 2021)). 2021 Vaccines Result SARS_CoV_2 D614G 200 205 34836485 A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. And when we went back to sequence the viruses from earlier passages, only H655Y, which has also been found in other circulating variants such as P.1, and V1128A were found. 2022 Emerging microbes & infections Result SARS_CoV_2 H655Y;V1128A 74;154 79;160 34836485 A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Here we assessed 2-36 activity on more variants, including pseudoviruses representing the combination of key spike mutations of B.1.427/B.1.429, R.1, B.1.1.1, B.1.525, B.1.617.1, B.1.617.2 and B.1.1.7 with E484 K, as well as many pseudoviruses with single spike mutations which are naturally circulating in COVID-19 patients with high frequency and located in the N-terminal domain, RBD, or S2. 2022 Emerging microbes & infections Result SARS_CoV_2 E484K 206 212 S;S;RBD;N 109;256;383;364 114;261;386;365 COVID-19 307 315 34836485 A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Indeed, when these mutations were introduced into pseudoviruses and tested for their sensitivity to 2-36, only K378 T alone or in combination with the other mutations was found to be resistant to 2-36, whereas viruses with T284I, H655Y, or V1128A alone remained sensitive (Figure 4D). 2022 Emerging microbes & infections Result SARS_CoV_2 H655Y;K378T;T284I;V1128A 230;111;223;240 235;117;228;246 34836485 A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Interestingly, although the K378 position in SARS-CoV-2 spike can be mutated to other residues at very low frequency, we could not find any K378 T mutation circulating in patient viruses to date (Figure 4E), further demonstrating the conserved nature of the region recognized by 2-36. 2022 Emerging microbes & infections Result SARS_CoV_2 K378T 140 146 S 56 61 34836485 A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Sequence analyses of the passage 12 virus revealed four single point spike mutations (T284I, K378 T, H655Y, V1128A), all of which were found at 100% frequency. 2022 Emerging microbes & infections Result SARS_CoV_2 H655Y;K378T;V1128A;T284I 101;93;108;86 106;99;114;91 S 69 74 34836485 A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. The T284I and K378 T mutations appeared only in the 2-36-resistant virus (Figure 4B). 2022 Emerging microbes & infections Result SARS_CoV_2 K378T;T284I 14;4 20;9 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. Also, eight genomes were classified in the Marseille-501/A.27 lineage that was first detected in our institute in January 2021, accounted for 18 genomes in our database and which may or may not harbour Q677H substitution. 2022 Virus genes Result SARS_CoV_2 Q677H 202 207 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. Codon changes from CAG to CAT or CAC leading to this Q677H substitution deoptimise the viral codon usage relative to that of the human genome. 2022 Virus genes Result SARS_CoV_2 Q677H 53 58 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. Finally, viral neutralisation in the presence of a monoclonal conformation-dependent antibody targeting the spike receptor binding domain led to a 50% reduction in neutralisation of 677H-harbouring spike relative to 677Q-harbouring spike (wild type), and of Q677H/D614G-harbouring spike relative to D614G only-harbouring spike. 2022 Virus genes Result SARS_CoV_2 D614G;Q677H;D614G 299;258;264 304;263;269 RBD;S;S;S;S;S 114;108;198;232;281;321 137;113;203;237;286;326 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. In 76 patients (2.3%), a spike Q677H substitution was observed in the 3634 SARS-CoV-2 genomes obtained in our institute. 2022 Virus genes Result SARS_CoV_2 Q677H 31 36 S 25 30 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. In addition, two were classified in the Marseille-4/B.1.160 lineage that was first detected in our institute in July 2020 and accounted for 573 (17%) genomes in our database, although its members did not harbour this spike Q677H substitution before 19 January 2021. 2022 Virus genes Result SARS_CoV_2 Q677H 223 228 S 217 222 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. In addition, we report the presence of the spike Q677H substitution in the A.27/Marseille-501 variant, which is a A-like lineage. 2022 Virus genes Result SARS_CoV_2 Q677H 49 54 S 43 48 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. It has been hypothesised that histidine protonation in Q677H could induce a conformational switch that may affect the accessibility to protease of this site, which may enhance the cleavage at the S1/S2 junction and viral entry efficiency . 2022 Virus genes Result SARS_CoV_2 Q677H 55 60 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. Q677H is notably part of the substitutions that emerged in strains of the B.1.1.7 and B.1.351 variants of concern. 2022 Virus genes Result SARS_CoV_2 Q677H 0 5 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. reported the emergence late 2020 of variants harbouring substitutions Q677H/P in the spike of viruses that were classified into sublineages of Nextstrain clades 20B and 20G as well as into Nextstrain clade 20A, and the Q677H substitution has been identified in the B.1.525 lineage first described in Nigeria and as a fast growing mutation in variants of concern. 2022 Virus genes Result SARS_CoV_2 Q677H;Q677H;Q677P 219;70;70 224;77;77 S 85 90 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. The Q677H substitution in the SARS-CoV-2 spike protein is in the close vicinity of the polybasic RRAR furin-cleavage site of the spike S1/S2 boundary, possibly impacting binding between the spike receptor binding domain and ACE2 . 2022 Virus genes Result SARS_CoV_2 Q677H 4 9 RBD;S;S;S 196;41;129;190 219;46;134;195 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. Therefore, the spike Q677H substitution should be considered as another example of convergent evolution, in addition to spike amino acid substitutions N501Y, L452R, and L18F which also independently appeared in various lineages. 2022 Virus genes Result SARS_CoV_2 L18F;L452R;N501Y;Q677H 169;158;151;21 173;163;156;26 S;S 15;120 20;125 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. Thus, overall, the functional consequences of the spike Q677H substitution and its epistatic interactions with other amino acid substitutions located inside or outside the receptor binding domain of the spike protein are currently not precisely deciphered. 2022 Virus genes Result SARS_CoV_2 Q677H 56 61 RBD;S;S 172;50;203 195;55;208 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. used a luciferase-bearing lentiviral pseudotype-based neutralisation assay to assess the effect of this spike Q677H substitution. 2022 Virus genes Result SARS_CoV_2 Q677H 110 115 S 104 109 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. Worldwide, 13659 SARS-CoV-2 genomes were found to encode this amino acid substitution Q677H according to the CoV-GLUE online tool (http://cov-glue.cvr.gla.ac.uk/). 2022 Virus genes Result SARS_CoV_2 Q677H 86 91 34840498 Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021. In this study, D614G mutation was detected in 103 Indonesian SARS-CoV-2 isolates. 2021 Bulletin of the National Research Centre Result SARS_CoV_2 D614G 15 20 34841034 Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2. Notably, D614G is recorded for SARS-CoV and other human CoVs since 2004. 2021 One health (Amsterdam, Netherlands) Result SARS_CoV_2 D614G 9 14 34841034 Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2. The D614G mutation and its relationship with the reservoirs. 2021 One health (Amsterdam, Netherlands) Result SARS_CoV_2 D614G 4 9 34841034 Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2. The first noteworthy mutation that became prevalent as early as mid-2020 is D614G. 2021 One health (Amsterdam, Netherlands) Result SARS_CoV_2 D614G 76 81 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. 3b) and mutation in the ORF8 gene (28144T > C) was found only in this age group. 2021 Current research in microbial sciences Result SARS_CoV_2 T28144C 35 45 ORF8 24 28 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. A total of 12 mutations were found in Germany in which four mutations 241C > T, 3037C > T, 14408C > T and 23403A > G were found common and existed at a frequency of 87.38%, 89.32%, 77.62% and 88.35%, respectively. 2021 Current research in microbial sciences Result SARS_CoV_2 C14408T;A23403G;C241T;C3037T 91;106;70;80 101;116;78;89 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. According to the H-clades (Q57H), 71 South Asian samples (13.71%) were clustered where the samples of India (44) were found as the most dominant one. 2021 Current research in microbial sciences Result SARS_CoV_2 Q57H 27 31 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. According to the S-clade (L84S) mutations, only the samples of India were found to be clustered at a frequency of 11.63%. 2021 Current research in microbial sciences Result SARS_CoV_2 L84S 26 30 S 17 18 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Additionally, a unique SNP (1163A > T) was found only in the isolates of Bangladesh at a considerably higher frequency (78.80%). 2021 Current research in microbial sciences Result SARS_CoV_2 A1163T 28 37 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. After analyzing the samples of Brazil, a total of 12 mutations were found in which four of them (241C > T, 3037C > T, 14408C > T and 23403A > G) were identified at a frequency of 100%. 2021 Current research in microbial sciences Result SARS_CoV_2 C14408T;A23403G;C3037T;C241T 118;133;107;97 128;143;116;105 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Among all of these alterations originated from North America, South America and European regions, five SNPs (241C > T, 3037C > T, 14408C > T, 23403A > G and 28881GGG > AAC) were the most common and frequent which were also found in the samples of South Asia. 2021 Current research in microbial sciences Result SARS_CoV_2 C14408T;A23403G;G28881A;G28881C;C3037T;C241T 130;142;157;157;119;109 140;152;171;171;128;117 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Among all of these alterations, 4 SNPs (241C > T, 3037C > T, 14408C > T, and 23403A > G) were found to have the most occurrences (more than 300 times). 2021 Current research in microbial sciences Result SARS_CoV_2 C14408T;A23403G;C3037T;C241T 61;77;50;40 71;87;59;48 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Among these unique SNPs, 27299T > C and 29148T > C were recognized at a considerably high frequency of 66.02% and 65.05%, respectively (Supplementary Table 6). 2021 Current research in microbial sciences Result SARS_CoV_2 T27299C;T29148C 25;40 35;50 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Among those unique mutations, 1059C > T mutation was found at a considerable frequency of 46.60% (Supplementary Table 5). 2021 Current research in microbial sciences Result SARS_CoV_2 C1059T 30 39 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Comparing these records with the frequency of 1163A > T mutation obtained from our analysis, it can be predicted that the 1163A > T mutation, which was local to the structural protein NSP2, may be responsible for restraining the severity of SARS-CoV-2 serotypes found in Bangladesh. 2021 Current research in microbial sciences Result SARS_CoV_2 A1163T;A1163T 46;122 55;131 Nsp2 184 188 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Considering the F-clade (L3606F), 54 samples (13.17%) were clustered and majority of these samples (40) were listed from India. 2021 Current research in microbial sciences Result SARS_CoV_2 L3606F 25 31 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Following the V-clade (G251V) mutations, we could not find any samples to be clustered. 2021 Current research in microbial sciences Result SARS_CoV_2 G251V 23 28 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. However, 3 SNPs (2416C > T, 8371G > T, and 22477 C > T) in the samples of Pakistan were found to be unique in the South Asian region (Supplementary Table 1). 2021 Current research in microbial sciences Result SARS_CoV_2 C22477T;G8371T;C2416T 43;28;17 54;37;26 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. However, four other unique mutations (1059C > T, 6446G > A, 25550T > A and 27046C > T) were identified compared to the samples of South Asia though their frequency was quite low (<=14%) (Supplementary Table 4). 2021 Current research in microbial sciences Result SARS_CoV_2 T25550A;C27046T;G6446A;C1059T 60;75;49;38 70;85;58;47 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. In case of Italy, four mutations (241C > T, 3037C > T, 14408C > T and 23403A > G) were found at a frequency of 96.12% whereas 20268A > G and 26530A > G (unique mutation found in only Italian samples) were found at a very low frequency (<=11%) (Supplementary Table 3). 2021 Current research in microbial sciences Result SARS_CoV_2 C14408T;A20268G;A23403G;A26530G;C3037T;C241T 55;126;70;141;44;34 65;136;80;151;53;42 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. In the USA, out of 16 mutations, four mutations (241C > T, 3037C > T, 14408C > T and 23403A > G) were found at a frequency of 99.03%, meanwhile, nine unique mutations were identified but at a very low frequency (<=13%). 2021 Current research in microbial sciences Result SARS_CoV_2 C14408T;A23403G;C3037T;C241T 70;85;59;49 80;95;68;57 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. In this case, we used one of the most common and well-studied D614G mutation found in the spike protein as a control agent of this analysis. 2021 Current research in microbial sciences Result SARS_CoV_2 D614G 62 67 S 90 95 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Remarkably, among these unique SNPs, 1163A > T was found at a frequency >78% (Supplementary Table 1. 2021 Current research in microbial sciences Result SARS_CoV_2 A1163T 37 46 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. The largest clustered group of the samples was found based on the G-clade (D614G), containing 81.7% (335/410 samples) of the total sample count. 2021 Current research in microbial sciences Result SARS_CoV_2 D614G 75 80 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. To align this prediction, we analyzed the impact of 1163A > T mutation on the stability of NSP2 protein through homology modeling. 2021 Current research in microbial sciences Result SARS_CoV_2 A1163T 52 61 Nsp2 91 95 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. To assess the effect of the 1163A > T (I120F) mutation on NSP2 protein, different parameters such as Gibbs free energy, the difference in vibrational entropy between wild type and mutant NSP2, fluctuation and deformation energies were calculated by DynaMut tool. 2021 Current research in microbial sciences Result SARS_CoV_2 A1163T;I120F 28;39 37;44 Nsp2;Nsp2 58;187 62;191 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Upon comprehensive analysis of the genomic diversity in SARS-CoV-2, we found four common SNPs (241C > T, 3037C > T, 14408C > T and 23403 C > T) in the samples isolated from countries of South Asia, Europe, North America and South America which encountered frequent infections. 2021 Current research in microbial sciences Result SARS_CoV_2 C14408T;C23403T;C3037T;C241T 116;131;105;95 126;142;114;103 34842496 A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). Other mutations of concern such as E484K, usually observed in B.1.351, B.1.525, B.1.621, and P.1 lineages are currently being monitored as well as the gain of changes in the RBD (L452R and T478 K) reported on B.1.617.2 viruses. 2022 Emerging microbes & infections Result SARS_CoV_2 E484K;T478K;L452R 35;189;179 40;195;184 RBD 174 177 34842496 A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). The D614G (96.4%) substitution was observed in most viral genomes, in addition to multiple mutations defining lineages, such as the mutation set Delta69-70, Delta144, N501Y, A570D, P681H, T716I, S982A, and D1118H for B.1.1.7 viruses. 2022 Emerging microbes & infections Result SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 174;206;4;167;181;195;188 179;212;9;172;186;200;193 34842604 Fc-Independent Protection from SARS-CoV-2 Infection by Recombinant Human Monoclonal Antibodies. In order to diminish its Fc-dependent functions, MD65 was further engineered to include the additional triple mutation N297G/S298G/T299A (MD65-AG, Figure 1A). 2021 Antibodies (Basel, Switzerland) Result SARS_CoV_2 N297G;S298G;T299A 119;125;131 124;130;136 34842604 Fc-Independent Protection from SARS-CoV-2 Infection by Recombinant Human Monoclonal Antibodies. Maintaining the N-linked glycosylation while introducing double mutations at S298G/T299A was shown to specifically maintain binding to FcgammaRII while abolishing binding to all other FcgammaR. 2021 Antibodies (Basel, Switzerland) Result SARS_CoV_2 S298G;T299A 77;83 82;88 N 16 17 34842604 Fc-Independent Protection from SARS-CoV-2 Infection by Recombinant Human Monoclonal Antibodies. The MD65 antibody backbone includes the triple mutation M252Y/S254T/T256E (YTE) in the Fc region (schematically depicted in Figure 1A) aimed at increasing the antibody affinity towards the human FcRn at acidic pH, therefore, prolonging its serum half-life. 2021 Antibodies (Basel, Switzerland) Result SARS_CoV_2 M252Y;S254T;T256E 56;62;68 61;67;73 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. Again, the R310A and F426A replacements were found to fully abrogate virus replication, while H424A yielded a crippled phenotype in SARS-CoV-2. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 F426A;H424A;R310A 21;94;11 26;99;16 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. Conversely, a MERS-CoV ExoN knockout mutant (D90A/E92A), which was included as a control, was found to modestly impact N7-MTase activity. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D90A;E92A 45;50 49;54 Exon 23 27 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. Four of the five mutations (Y420A and H424A in SARS-CoV, and W292A and H420A in MERS-CoV) that affected ExoN activity mapped to the hinge region. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 H420A;H424A;W292A;Y420A 71;38;61;28 76;43;66;33 Exon 104 108 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. In contrast, the ExoN activity of SARS-CoV mutants R310A, Y420A, and H424A and MERS-CoV mutant W292A was strongly or partially affected, as indicated by the reduced amount of hydrolysis products at the bottom of the gel. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 H424A;R310A;W292A;Y420A 69;51;95;58 74;56;100;63 Exon 17 21 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. In the case of MERS-CoV nsp14, only mutants N418A and F422A retained partial N7-MTase activity, 34% and 70%, respectively, while again all other mutations rendered the enzymatic activity barely detectable. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 F422A;N418A 54;44 59;49 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. Interestingly, mutant D352A yielded a mixed-size plaque phenotype, suggesting rapid (pseudo)reversion in a minor fraction of this mutant's progeny. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D352A 22 27 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. Likewise, the viable but severely crippled (small plaque) virus phenotypes of motif I mutant W292A and motif VI mutant H424A were surprising. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 H424A;W292A 119;93 124;98 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. Meanwhile, incorporation of the H420A mutation completely abrogated MERS-CoV nsp14 ExoN activity. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 H420A 32 37 Exon 83 87 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. On the other hand, D331A was the only non-viable SARS-CoV mutant for which reversion to wild-type was occasionally observed, suggesting that a very low level of viral RNA synthesis remained possible despite this mutation (see also Discussion). 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D331A 19 24 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. Remarkably, SARS-CoV mutations N306A, K336A, and N422A in motifs II, III, and VI, respectively, were found to yield viruses with plaque phenotypes and progeny titers similar to those of the wild-type control. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 K336A;N306A;N422A 38;31;49 43;36;54 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. This was surprising in the case of MERS-CoV, given the fact that this mutation (F422A in MERS-CoV) allowed substantial N7-MTase activity in the in vitro assay. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 F422A 80 85 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. Thus, our data confirmed and extended a previous study and showed that N7-MTase activity is affected by mutations that either may inhibit SAM binding (W292A, D331A, G333A, K336A, and D352A in SARS-CoV) or likely interfere with RNA chain stabilization (N306A, R310A, Y420A, N422A, and F426A) in the catalytic pocket. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 D331A;D352A;F426A;G333A;K336A;N422A;R310A;Y420A;N306A;W292A 158;183;284;165;172;273;259;266;252;151 163;188;289;170;177;278;264;271;257;156 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. When SARS-CoV-2 emerged during the course of this study, the three mutations that produced a similar phenotype across SARS-CoV, MERS-CoV, and MHV (R310A, H424A, and F426A, using SARS-CoV numbering) were also engineered for this newly discovered CoV. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 F426A;H424A;R310A 165;154;147 170;159;152 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. With the exception of N306A (30% residual activity), N422A (53% residual activity), and H424A (40% remaining), all SARS-CoV mutations tested almost completely abrogated nsp14 N7-MTase activity. 2021 Proc Natl Acad Sci U S A Result SARS_CoV_2 H424A;N306A;N422A 88;22;53 93;27;58 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. All four of these designs share the same sets of V382I and F515W mutations directly underneath the recognition surface of CR3022, suggesting that this combination of mutations likely results in local perturbation of the CR3022 epitope. 2021 bioRxiv Result SARS_CoV_2 F515W;V382I 59;49 64;54 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. Expression of the aglycosylated constructs was induced at 22 C for 22 hours in M19G media (see Methods). 2021 bioRxiv Result SARS_CoV_2 M19G 79 83 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. RBD1 contains a Y365W; both Y and W are disfavored relative to smaller aliphatics without hydrogen bond acceptors or donors. 2021 bioRxiv Result SARS_CoV_2 Y365W 16 21 RBD 0 3 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. The five designs were ordered as synthetic genes, subcloned into a plasmid optimized for the protease susceptibility assay, and expressed using a yeast surface display platform (Fig 1D) previously demonstrated to display properly folded aglycosylated S RBD (Wuhan Hu-1 S RBD(333-537)-N343Q; wild-type or "WT") (Banach et al. 2021 bioRxiv Result SARS_CoV_2 N343Q 284 289 RBD;RBD;S;S 253;271;251;269 256;274;252;270 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. The forty hits are largely distal to the RBM with the exception of multiple aliphatic mutations at N501 (N501F/W/M) (Fig 2C, Fig 3A). 2021 bioRxiv Result SARS_CoV_2 N501F;N501M;N501W 105;105;105 114;114;114 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. There are a number of small to large aliphatic substitutions occurring at this pocket, including A363WPMILV, A397ML, I434F, and F392W. 2021 bioRxiv Result SARS_CoV_2 F392W;I434F 128;117 133;122 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. We neglected these hits as mutations at N501 are known to impact ACE2 affinity, including the N501Y mutation found in several Variants of Concern. 2021 bioRxiv Result SARS_CoV_2 N501Y 94 99 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. 5D-b), whereas sharp increases of IFN-beta1, TLR4 and TLR3 were observed with the DeltaG188 mutant. 2021 bioRxiv Result SARS_CoV_2 DeltaG188 82 91 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. A natural mutant variant (Q57H) that is associated with the ongoing Beta variant, and deletion of a highly conserved guanine residue (DeltaG188) were tested. 2021 bioRxiv Result SARS_CoV_2 Q57H 26 30 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. Both Q57H and DeltaG188 mutants were tested in comparison with the wildtype ORF3a. 2021 bioRxiv Result SARS_CoV_2 Q57H 5 9 ORF3a 76 81 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. Compared to wildtype ORF3a, the DeltaG188 mutant markedly increased apoptosis and necrosis, whereas the Q57H mutant showed reduced apoptosis and necrosis. 2021 bioRxiv Result SARS_CoV_2 DeltaG188;Q57H 32;104 41;108 ORF3a 21 26 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. In contract, the Q57H mutant showed slightly improved cellular growth, viability and reduced cell death. 2021 bioRxiv Result SARS_CoV_2 Q57H 17 21 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. Similar or slightly reduced activation of IFN-beta1, TLR4 and TLR3 was observed in the Q57H mutant compared with the wildtype ORF3a. 2021 bioRxiv Result SARS_CoV_2 Q57H 87 91 ORF3a 126 131 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. While the Q57H mutant showed a similar immune expression profile as the wildtype ORF3a. 2021 bioRxiv Result SARS_CoV_2 Q57H 10 14 ORF3a 81 86 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. 1c-f), suggesting N501Y mutant spike might impair meiotic spindle assembly in mouse oocytes. 2021 Reproductive sciences (Thousand Oaks, Calif.) Result SARS_CoV_2 N501Y 18 23 S 31 36 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. After 24-h maturation, the percentage of germinal vesicle breakdown (GVBD) and metaphase II (MII) oocytes were not significant different between control and N501Y treatment. 2021 Reproductive sciences (Thousand Oaks, Calif.) Result SARS_CoV_2 N501Y 157 162 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. However, the chromosome misalignment was comparable between the N501Y-treated groups and control group. 2021 Reproductive sciences (Thousand Oaks, Calif.) Result SARS_CoV_2 N501Y 64 69 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. Interestingly, the mean spindle length and the plate width were significantly increased in the N501Y-treated group compared to the control. 2021 Reproductive sciences (Thousand Oaks, Calif.) Result SARS_CoV_2 N501Y 95 100 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. MitoTracker staining in MII oocytes revealed a modest increase in clustered distribution of mitochondria in N501Y mutant spike protein-treated group. 2021 Reproductive sciences (Thousand Oaks, Calif.) Result SARS_CoV_2 N501Y 108 113 S 121 126 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. S1), suggesting that N501Y spike protein did not block the nuclear maturation in mice oocyte. 2021 Reproductive sciences (Thousand Oaks, Calif.) Result SARS_CoV_2 N501Y 21 26 S 27 32 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. The immuno-confocal microscopy of spindle and chromosomes revealed that N501Y mutant spike treated oocytes displayed the obvious spindle morphology defects. 2021 Reproductive sciences (Thousand Oaks, Calif.) Result SARS_CoV_2 N501Y 72 77 S 85 90 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. These results indicate that the N501Y treatment did not significantly alter the mitochondrial distribution of oocytes. 2021 Reproductive sciences (Thousand Oaks, Calif.) Result SARS_CoV_2 N501Y 32 37 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. To further determine whether N501Y spike protein can damage the cytoplasmic maturation of mouse oocytes, we assessed spindle and chromosome assembly of MII oocytes. 2021 Reproductive sciences (Thousand Oaks, Calif.) Result SARS_CoV_2 N501Y 29 34 S 35 40 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. 2(b) further validates the co-occurring mutations of concern mentioned above, particularly between T478K, P681H and T732A, from the dominant clade 20B of variant 20B/478K.V1. 2021 Microbial genomics Result SARS_CoV_2 P681H;T478K;T732A 106;99;116 111;104;121 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. 3c) could be explained by neutral mutations linked to a beneficial mutation, such as D614G, increasing their frequencies due to hitchhiking. 2021 Microbial genomics Result SARS_CoV_2 D614G 85 90 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. A similar scenario with multiple combinations at the codon level, within different lineages in Mexico, can be seen in the mutation of concern S477N/I. 2021 Microbial genomics Result SARS_CoV_2 S477I;S477N 142;142 149;149 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Among these results, although not at a high frequency, cases of T478K co-occurring with other spike protein mutations of concern could be detected, including: (i) K417N, which is present in 20h/501Y.V2 or B.1.351, identified in one sample (February 2021, GISAID EPI ISL 1137473); (ii) L18F, which is present in 20J/501Y.V3 or P.1, identified in one sequence from the State of Oaxaca, in the parental lineage B.1 (January 2021, GISAID EPI ISL 1168605); and (iii) the deletion of an amino acid in position 144, which occurs in 20I/501Y.V1 or B.1.1.7 and 20A/S.484K or B.1.525, in one sample from Mexico City (February 2020, GISAID EPI ISL 1181713). 2021 Microbial genomics Result SARS_CoV_2 K417N;L18F;T478K 163;285;64 168;289;69 S 94 99 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Analogous to the E484K mutation present in the parental lineage B.1.36 of scenario (ii), which has been implicated in regional outbreaks in India, the proposed new Mexican lineage of scenario (i) includes the two San Luis Potosi E484K-containing variants identified after RT-qPCR screening (lineages B.1 and B.1.319), and the Oaxaca E484Q variant appearing early on during the pandemic, which corresponds to lineage B.1.243. 2021 Microbial genomics Result SARS_CoV_2 E484K;E484K;E484Q 17;229;333 22;234;338 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. As expected from independently evolving VOC, mutation V1176F is absent from the two sequences from the State of San Luis Potosi. 2021 Microbial genomics Result SARS_CoV_2 V1176F 54 60 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Besides the conserved D614G mutation, sequences from the newly detected and proposed VOI 20B/478 K.V1 and 20B/P.4, share, in different combinations, mutations T478K, E484K, P681H/R with VOC alpha, gamma and delta (20I/B.1.1.7, 20J/P.1 and 21A/B.1.617.2). 2021 Microbial genomics Result SARS_CoV_2 D614G;E484K;P681H;P681R;T478K 22;166;173;173;159 27;171;180;180;164 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. By contrasting the allelic imbalance between symptomatic and asymptomatic hosts in a polymorphic site fashion, we found a single significant association of the C28854T mutation (ANOVA; F=20.5; P=0.003). 2021 Microbial genomics Result SARS_CoV_2 C28854T 160 167 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. For instance, mutation L18F is a mutation of concern as it occurs in variants 20h/501Y.V2 or B.1.351 and 20J/501Y.V3 or P.1 and has been implicated in antibody scape. 2021 Microbial genomics Result SARS_CoV_2 L18F 23 27 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. For this, we focused on S477N, E484K and D614G as previously identified mutations of concern; and in mutations T478K, P681H/R and T732A present in the proposed VOI 478 K.V1. 2021 Microbial genomics Result SARS_CoV_2 D614G;E484K;P681H;P681R;S477N;T478K;T732A 41;31;118;118;24;111;130 46;36;125;125;29;116;135 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Given that P.3 has accumulated six further dangerous mutations in the spike protein, including E484K, N501Y and P681H, further investigation of P.4 in Mexico due to its evolutionary potential is recommended. 2021 Microbial genomics Result SARS_CoV_2 E484K;N501Y;P681H 95;102;112 100;107;117 S 70 75 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. However, many different Pangolin lineages are annotated within the implicated N:S194L-containing 20A sub-clade of scenario (i). 2021 Microbial genomics Result SARS_CoV_2 S194L 80 85 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Importantly, we found the mutation T478K in four of the 31 San Luis Potosi genomes, but it was filtered out of the population genetic analyses due to its low population frequency (<5%). 2021 Microbial genomics Result SARS_CoV_2 T478K 35 40 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. In addition to the B.1 lineage within these two 20A sub-clades, lineage B.1.243, with 78 genome sequences sharing the point mutation N:S194L and the deletion NS9c:Q41* (22.8 % of total sequences within these two 20A clades and 5.1 % of the total genome sequences), were of note. 2021 Microbial genomics Result SARS_CoV_2 Q41X;S194L 163;135 167;140 N 133 134 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. In addition, the Mexican variant shows mutation T732A. 2021 Microbial genomics Result SARS_CoV_2 T732A 48 53 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Indeed, all Mexican sequences form a distinctive clade supported by the mutations ORF1a: V1071A, P1810L, S3149F (Figs 1c and S3). 2021 Microbial genomics Result SARS_CoV_2 P1810L;S3149F;V1071A 97;105;89 103;111;95 ORF1a 82 87 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. It is also interesting to note that mutations T478I/R, previously identified as dangerous, could not be found in Mexico during the period of analysis. 2021 Microbial genomics Result SARS_CoV_2 T478I;T478R 46;46 53;53 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Likewise, following the same approach, a total of nine independent samples containing the E484K mutant could be detected in samples from the State of Jalisco. 2021 Microbial genomics Result SARS_CoV_2 E484K 90 95 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. More specifically, the genome data generated by Mexican authorities and other laboratories include sequences with the mutation E484K in the context of known VOC or VOI. 2021 Microbial genomics Result SARS_CoV_2 E484K 127 132 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Motivated by these results, we analysed the prevalence of mutation N:S194L in the extended Nextstrain phylogeny, and found three major sub-clades within the 20A clade with high prevalence: (i) two closely related sub-clades dominated by the B.1 lineage, where most of the Mexican genomes are placed, including more than one-fifth of all sequences available for the period of analysis (342 out of 1554); and (ii) a mainly Asian sub-clade that includes the emerging lineage B.1.36.# (where # refers to many sub-lineages. 2021 Microbial genomics Result SARS_CoV_2 S194L 69 74 N 67 68 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Our phylogenomic analyses also revealed a different 484 mutation involving another amino acid substitution, E484Q, in the sequence Mexico/OAX-InDRE-61/2020 (August 2020, GISAID EPI ISL 576264). 2021 Microbial genomics Result SARS_CoV_2 E484Q 108 113 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Our samples contained SNVs in one of the early strain types (VI) that spread out of China (C241T, C3037T, C14408T and A23403G mutations) which has the haplotype of allelic associations 241T-3037T-14408T-23403G, detected in high frequency worldwide (December 2020), and that may be involved in increasing the fitness of the SARS-CoV-2 virus. 2021 Microbial genomics Result SARS_CoV_2 A23403G;C14408T;C3037T;C241T 118;106;98;91 125;113;104;96 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Overall, we found that most of the genomic variants (SNVs+indels) occur in low frequencies, except for a few point variants, such as P323L in the RdRp protein, E484K, D614G and V1176F spanning the spike protein region, and R203K and S194L in the nucleocapsid region. 2021 Microbial genomics Result SARS_CoV_2 D614G;E484K;P323L;R203K;S194L;V1176F 167;160;133;223;233;177 172;165;138;228;238;183 N;S;RdRP 246;197;146 258;202;150 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. P.1 and P.2 share mutations E484K, D614G and V1176F (the last appearing to be specific to these closely related emerging lineages), but not N501Y. 2021 Microbial genomics Result SARS_CoV_2 D614G;E484K;N501Y;V1176F 35;28;140;45 40;33;145;51 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. S2), places the States of San Luis Potosi and Jalisco as epicentres of E484K-containing SARS-CoV-2 VOI in Mexico. 2021 Microbial genomics Result SARS_CoV_2 E484K 71 76 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. S6b), mostly in Jalisco, which is probably explained by pre-screening of the E484K in this locality. 2021 Microbial genomics Result SARS_CoV_2 E484K 77 82 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Similar to the convergent evolution of E484K leading to the potential VOI from the State of San Luis Potosi, mutation T478K is not only present in the entire country, but the sequence Mexico/OAX-InDRE_535/2021 (January 2021, GISAID EPI ISL 1168605) has it, and belongs to 20B/B.1. 2021 Microbial genomics Result SARS_CoV_2 E484K;T478K 39;118 44;123 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. The above-mentioned scenarios (ii) and (iii), together with further E484K-containing variants identified by RT-qPCR screening. 2021 Microbial genomics Result SARS_CoV_2 E484K 68 73 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. The genome sequence of the associated SARS-CoV-2 virus was obtained by Mexican authorities (Mexico/SLP-InDRE_454/2021, GISAID EPI ISL 1219714), confirming the mutation E484K, and also, independently by us in this study, as the raw reads were required for our population genomics analysis. 2021 Microbial genomics Result SARS_CoV_2 E484K 168 173 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. The mutations D614G and P681H/R are found in the S1 protein subdomain near T732A, taking part in S2. 2021 Microbial genomics Result SARS_CoV_2 D614G;P681H;P681R;T732A 14;24;24;75 19;31;31;80 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. The potential for evolving the dangerous E484K/Q mutation within this Mexican lineage is supported by the recent detection of the sub-lineage B.1.243.1 in Arizona, USA, which includes mutation E484K. 2021 Microbial genomics Result SARS_CoV_2 E484K;E484K;E484Q 193;41;41 198;48;48 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. The prevalence of high-frequency polymorphisms in the JAL samples could be merely due to sampling bias, as the patients were pre-screened for the presence of the E484K mutation before the sequencing experiment, and it is the locality with the smallest sample size. 2021 Microbial genomics Result SARS_CoV_2 E484K 162 167 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. The sequence Mexico/JAL-InDRE_373/2021 includes the mutation R190M, an alternative version of mutation R190S present in the VOC P.1 or B.1.1.28.1, which may be signs of evolution in Mexico. 2021 Microbial genomics Result SARS_CoV_2 R190M;R190S 61;103 66;108 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. These analyses show that roughly 80% of the clade 19B sequences display the spike protein mutation H49Y, which appears to be unique to that clade. 2021 Microbial genomics Result SARS_CoV_2 H49Y 99 103 S 76 81 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. This observation identifies the sequences of scenario (iii) as closer to the recently identified E484K-containing lineage 20A/S.484K (B.1.525) and B.1.243.1, than to 20B/P.2 (B.1.1.28.2). 2021 Microbial genomics Result SARS_CoV_2 E484K 97 102 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. This SNV corresponds to the amino acid serine to leucine S194L, in the nucleocapsid region and has a population frequency of 30 % in Guanajuato. 2021 Microbial genomics Result SARS_CoV_2 S194L 57 62 N 71 83 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Three mutations of concern, S477N, T478K and E484K, are in direct vicinity with the human receptor ACE2, located within the RBM. 2021 Microbial genomics Result SARS_CoV_2 E484K;S477N;T478K 45;28;35 50;33;40 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Variant 20B/478K.V1 has in addition the mutation T732A. 2021 Microbial genomics Result SARS_CoV_2 T732A 49 54 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. We screened for the spike protein mutations E484K, N501Y and 69-70 deletion. 2021 Microbial genomics Result SARS_CoV_2 E484K;N501Y 44;51 49;56 S 20 25 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. With only 25 sequences available, this analysis also identified covariances between S13I, L452R and W152C of the VOI B.1.427/9. 2021 Microbial genomics Result SARS_CoV_2 L452R;S13I;W152C 90;84;100 95;88;105 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Worryingly, these lineages have in common between them - and with the recently designated VOC 21A/S:478K (B.1.617.2, delta, first identified in India and shown to undergo immune escape - mutations T478K and P681H/R. 2021 Microbial genomics Result SARS_CoV_2 P681H;P681R;T478K 207;207;197 214;214;202 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Among haplotype 2, haplotype 2A with the mutations at nsp12 P323L, Spike D614G, and N R203K, G204R, markedly increased from 9.1% post-6-month spread to 15.23% post-1-year spread, in which sub-haplotypes 2A _1 (13.33%) and 2A_2 (1.90%) belonged to Pangolin lineages B.1.1.7 (WHO label Alpha) and B1.1.519 variants, respectively. 2022 Infection, genetics and evolution Result SARS_CoV_2 D614G;G204R;P323L;R203K 73;93;60;86 78;98;65;91 S;Nsp12;N 67;54;84 72;59;85 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Among the sub-haplotypes of haplotype 2A variants, sub-haplotype 2A_1 was the most prevalent sub-haplotype in the partly vaccinated rate group, containing three mutations in nsp3 (T183I, A890D, I1412T), seven new mutations in Spike protein (V143del, N501Y, A570, P681H, T716I, D614G, S982A, D1118H), two mutations in ORF8 (R52I, Y73C), and one new mutation in N (S235F). 2022 Infection, genetics and evolution Result SARS_CoV_2 A890D;D1118H;D614G;I1412T;N501Y;P681H;S982A;T716I;Y73C;R52I;S235F;T183I;V143del 187;291;277;194;250;263;284;270;329;323;363;180;241 192;297;282;200;255;268;289;275;333;327;368;185;248 S;Nsp3;ORF8;N 226;174;317;360 231;178;321;361 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Haplotype 1 with the mutation at ORF8 L84S was prevalent post-6-month spread (25.34%) but rarely identified post-1-year pandemic (1.19%). 2022 Infection, genetics and evolution Result SARS_CoV_2 L84S 38 42 ORF8 33 37 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Haplotype 2B containing the mutations at nsp12 P323L, Spike D614G, ORF3a Q57H, and nsp2 I85I emerged post 6-month spread, evolved into five sub-haplotypes, such as additional mutations at nsp3 K837N, spike protein D80A and D215G in sub-haplotype 2B_1, spike L5F, T95I, D253G in sub-haplotype 2B_4, and spike N439K, P681R in sub-haplotype 2B_5. 2022 Infection, genetics and evolution Result SARS_CoV_2 D215G;D253G;D614G;D80A;I85I;K837N;L5F;N439K;P323L;P681R;Q57H;T95I 223;269;60;214;88;193;258;308;47;315;73;263 228;274;65;218;92;198;261;313;52;320;77;267 S;S;S;S;ORF3a;Nsp12;Nsp2;Nsp3 54;200;252;302;67;41;83;188 59;205;257;307;72;46;87;192 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Haplotype 2B containing the mutations at nsp12 P323L, spike D614G, ORF3a Q57H, nsp2 I85I, slightly increased from 36.21% post 6-month spread to 38.81% post 1-year spread, including 0.95% for sub-haplotype 2B_1 (Pangolin lineage B1.351, WHO label Beta), 4.05% for 2B_2 (Pangolin lineage B.1.429, WHO label Epsilon), 33.81% for 2B_3 (Pangolin lineage B.1.596), respectively. 2022 Infection, genetics and evolution Result SARS_CoV_2 D614G;I85I;P323L;Q57H 60;84;47;73 65;88;52;77 S;ORF3a;Nsp12;Nsp2 54;67;41;79 59;72;46;83 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Meanwhile, haplotype 2 with the mutations at nsp12 P323L and spike G614D was almost total post-1-year spread (98.81%). 2022 Infection, genetics and evolution Result SARS_CoV_2 G614D;P323L 67;51 72;56 S;Nsp12 61;45 66;50 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Significantly, haplotype 2C variant (66.8%) was leading in the partly vaccinated rate group, which sub-haplotype 2C_3 contained two unique mutations in spike protein (EFR156-158del, L452R, P681R), one mutation in ORF3a (S26L), and one mutation in N (R203M). 2022 Infection, genetics and evolution Result SARS_CoV_2 L452R;P681R;R203M;S26L 182;189;250;220 187;194;255;224 S;ORF3a;N 152;213;247 157;218;248 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Significantly, new sub-haplotypes 2A_1 and 2C_3 had meaningful amino acid substitutions like T478K, N501Y, and P681H in SARS-COV-2 spike protein, locating ACE2-specific recognition site and the neutralization epitopes, and near the protease cleavage site. 2022 Infection, genetics and evolution Result SARS_CoV_2 N501Y;P681H;T478K 100;111;93 105;116;98 S 131 136 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. The haplotype 2A variant contained four mutations at nsp12 P323L, Spike D614G, and N R203K, G204R merged post-6-month outbreak. 2022 Infection, genetics and evolution Result SARS_CoV_2 D614G;G204R;P323L;R203K 72;92;59;85 77;97;64;90 S;Nsp12;N 66;53;83 71;58;84 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. Among all mutations, the mutation N501Y, which is common to three mutants. 2021 Nature communications Result SARS_CoV_2 N501Y 34 39 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. As a summary, the mutation N501Y in the Alpha, Beta, and Gamma variants seems to strengthen the frequency of the Y501-Y41 contact. 2021 Nature communications Result SARS_CoV_2 N501Y 27 32 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. N501Y mutation is more dynamic and establishes more than one extra contact in VoCs that are not present in the WT. 2021 Nature communications Result SARS_CoV_2 N501Y 0 5 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. Such interaction is not disrupted in the Alpha variant by mutation N501Y; instead, a stabilizing hydrophobic contact, Y501-Y41 within the ACE2 is reformed (Supplementary Table 3). 2021 Nature communications Result SARS_CoV_2 N501Y 67 72 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. The Kappa variant that lacks the N501Y mutation shows similar energy to the WT SARS-CoV-2. 2021 Nature communications Result SARS_CoV_2 N501Y 33 38 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. The mutation E484K in RBD changes the residue charge from a negative to a positive value and is present in two VoC. 2021 Nature communications Result SARS_CoV_2 E484K 13 18 RBD 22 25 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. The same contact is more persistent in Alpha variant with freq ~ 0.9 and under mutations K417N and K417T in Beta and Gamma respectively, the contact frequency drops below 0.4, which correlates with the dramatic drop of the electrostatic contribution in the interfacial energy. 2021 Nature communications Result SARS_CoV_2 K417N;K417T 89;99 94;104 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. Analytical Performance of HV69/70, E484K, and N501Y Assays Using Well-Characterized RNA from SARS-CoV-2 VOCs. 2021 Analytical chemistry Result SARS_CoV_2 E484K;N501Y 35;46 40;51 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. At a viral RNA concentration of 10,000 cp/muL, the HV69/70, E484K, and N501Y genotypes were all correctly identified among wildtype, Alpha, Beta, and Gamma SARS-CoV-2 strains (Figure 3C). 2021 Analytical chemistry Result SARS_CoV_2 E484K;N501Y 60;71 65;76 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. At the same concentration for the N501Y assay, 5 out of 6 replicates (83%) were amplified. 2021 Analytical chemistry Result SARS_CoV_2 N501Y 34 39 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. Clinical Performance of HV69/70, E484K, and N501Y Detecting RT-qPCR Assays. 2021 Analytical chemistry Result SARS_CoV_2 E484K;N501Y 33;44 38;49 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. For the E-gene, HV69/70, and E484K assay, a detection rate of 100% was achieved at a viral RNA concentration as low as 10 cp/muL. 2021 Analytical chemistry Result SARS_CoV_2 E484K 29 34 E 8 9 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. High amplification efficiencies (>90%) were obtained for the E-gene, the HV69/70 and E484K assays on the Bio-Rad CFX96 platform, and for the E-gene and E484K assays on the peakPCR device. 2021 Analytical chemistry Result SARS_CoV_2 E484K;E484K 85;152 90;157 E;E 61;141 62;142 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. Mutation-specific assays for HV69/70 (Figure 2B), E484K (Figure 2C), and N501Y (Figure 2D) were run on both platforms, while wildtype-specific assays were solely run on the Bio-Rad CFX96 platform. 2021 Analytical chemistry Result SARS_CoV_2 E484K;N501Y 50;73 55;78 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. Similar to the E484K assay, a YYE-labeled probe detects the wildtype and a FAM-labeled probe the mutated sequence. 2021 Analytical chemistry Result SARS_CoV_2 E484K 15 20 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. The E484K assay accurately identified the 484K SNP in 43 samples with the Beta VOC and in one sample assigned to the B.1.620 lineage. 2021 Analytical chemistry Result SARS_CoV_2 E484K 4 9 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. The E484K mutation is only present in Beta and Gamma VOCs. 2021 Analytical chemistry Result SARS_CoV_2 E484K 4 9 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. The E484K-mutation assay did not result in amplification when run on RNA from wildtype non-VOC Wuhan Hu-1 lineage and Alpha VOC. 2021 Analytical chemistry Result SARS_CoV_2 E484K 4 9 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. The N501Y assay correctly identified the 501Y mutation in one confirmed Alpha VOC sample and 43 confirmed Beta VOC samples. 2021 Analytical chemistry Result SARS_CoV_2 N501Y 4 9 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. The N501Y mutation is present in Alpha, Beta, and Gamma VOCs. 2021 Analytical chemistry Result SARS_CoV_2 N501Y 4 9 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. The N501Y-mutation assay correctly detected all VOCs but not the wildtype non-VOC Wuhan Hu-1 lineage. 2021 Analytical chemistry Result SARS_CoV_2 N501Y 4 9 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. The second assay targets a nonsynonymous SNP in the spike gene (A23011G), leading to an amino-acid exchange at positions 484 (E484K). 2021 Analytical chemistry Result SARS_CoV_2 A23011G;E484K 64;126 71;131 S 52 57 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. The third assay targets a nonsynonymous SNP in the spike gene (A23063T), leading to an amino-acid exchange at positions 501 (N501Y). 2021 Analytical chemistry Result SARS_CoV_2 A23063T;N501Y 63;125 70;130 S 51 56 34855904 Niclosamide shows strong antiviral activity in a human airway model of SARS-CoV-2 infection and a conserved potency against the Alpha (B.1.1.7), Beta (B.1.351) and Delta variant (B.1.617.2). Importantly, niclosamide also blocked the replication of the European BavPat D614G, B.1.1.7, B.1.351 and B.1.617.2 variant with an IC50 of 0.06 muM, 0.08 muM, 0.07 muM, and 0.08 muM respectively (Fig 2). 2021 PloS one Result SARS_CoV_2 D614G 77 82 34855904 Niclosamide shows strong antiviral activity in a human airway model of SARS-CoV-2 infection and a conserved potency against the Alpha (B.1.1.7), Beta (B.1.351) and Delta variant (B.1.617.2). We then tested the activity of niclosamide against several variants of concern of SARS-CoV-2, including the BavPat1 strain (D614G), SARS-CoV-2 lineage B.1.1.7 (Alpha), SARS-CoV-2 Wuhan D614, SARS CoV-2 lineage B.1.351 (Beta) and SARS-CoV-2 lineage B.1.617.2 (Delta). 2021 PloS one Result SARS_CoV_2 D614G 124 129 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. Although our results are accordant with recently published studies, the reason why Kappa/Delta and Epsilon behaviors are distinctive remained to be further studied, and it might stem from the limitation in our model, as we only employed the L452R mutation in RBD for the Epsilon variant without a D614G mutation. 2021 Journal of chemical theory and computation Result SARS_CoV_2 D614G;L452R 297;241 302;246 RBD 259 262 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. As shown in Figure 2B and C, Alpha and Beta variants include the N501Y mutation, while the Beta variant involves two additional mutations, K417N and E484 K. 2021 Journal of chemical theory and computation Result SARS_CoV_2 E484K;K417N;N501Y 149;139;65 155;144;70 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. It should be noted that both Kappa/Delta and Epsilon share the L452R mutation. 2021 Journal of chemical theory and computation Result SARS_CoV_2 L452R 63 68 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. Newly reported Kappa and Delta variants involve the same L452R mutation as Epsilon, but each variant contains an additional mutation: E484Q (Kappa) or T478 K (Delta). 2021 Journal of chemical theory and computation Result SARS_CoV_2 E484Q;L452R;T478K 134;57;151 139;62;157 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. Note that L450 and L492 are positioned in different beta-strands (Figure S4B, D colored in green and orange, respectively), and the L452R mutation makes the RBD-ACE2 interface unstable by shortening each beta-strand (i.e., the length of interacting beta-strands of Epsilon variant is decreased by almost half). 2021 Journal of chemical theory and computation Result SARS_CoV_2 L452R 132 137 RBD 157 160 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. reported that a subtle reorientation of G496 in Delta induces stronger beta-strand interactions and that it could be due to the L452R mutation. 2021 Journal of chemical theory and computation Result SARS_CoV_2 L452R 128 133 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. Such contacts are decreased or even lost in the case of RBDWT or RBDEpsilon lacking the N501Y mutation (Figure 2A, D). 2021 Journal of chemical theory and computation Result SARS_CoV_2 N501Y 88 93 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. The Gamma variant also shows decreased contact numbers similar to Beta due to its K417T mutation (Figure S2A). 2021 Journal of chemical theory and computation Result SARS_CoV_2 K417T 82 87 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. The only difference between Gamma and Beta is the K417 mutation, i.e., K417T vs K417N. 2021 Journal of chemical theory and computation Result SARS_CoV_2 K417N;K417T 80;71 85;76 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. The weakened interactions of RBDBeta N417 and RBDGamma T417 could make them less contagious than the Alpha variant, while the N501Y mutation still allows them to have a strong enough potential to interact with ACE2. 2021 Journal of chemical theory and computation Result SARS_CoV_2 N501Y 126 131 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. To investigate the mechanism behind such a big difference, the contact analysis in between RBD residues was performed, where the influence of the L452R mutation was examined by checking its contacts with surrounding residues, L450 and L492 (Figure S4). 2021 Journal of chemical theory and computation Result SARS_CoV_2 L452R 146 151 RBD 91 94 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. Upon the T478 K mutation, it requires the highest force for the RBD-ACE2 complex to be completely dissociated at D = 78 A (Figure 1A). 2021 Journal of chemical theory and computation Result SARS_CoV_2 T478K 9 15 RBD 64 67 34856891 A second functional furin site in the SARS-CoV-2 spike protein. A single K77A point mutant and a combined mutations at position 77-78 were constructed. 2022 Emerging microbes & infections Result SARS_CoV_2 K77A 9 13 34856891 A second functional furin site in the SARS-CoV-2 spike protein. After the cells were treated with Cathepsin L inhibitor E64D, the infectivity of DeltaF was lower than that of WT (Figure 2H), suggesting that the increase of infectivity in the DeltaF mutant may be mediated by Cathepsin L. 2022 Emerging microbes & infections Result SARS_CoV_2 E64D 56 60 34856891 A second functional furin site in the SARS-CoV-2 spike protein. As the DeltaF and K814A mutations were close to the active sites of TMPRSS2 (685-686 and 815-816), we further determined the effects of these mutations by overexpression of TMPRSS2 in 293T-ACE2 cells. 2022 Emerging microbes & infections Result SARS_CoV_2 K814A 18 23 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Both the Delta682-686 and K814A mutants showed significantly decreased infectivity in the Calu-3 cells. 2022 Emerging microbes & infections Result SARS_CoV_2 K814A 26 31 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Compared with WT SARS-CoV-2, neither Cathepsin L enhancing SARS-CoV-2 infectivity nor E64D inhibiting SARS-CoV-2 infectivity was shown in the K814A mutant, suggesting that the K814 site may not be the functional site of Cathepsin L (Figure 2H). 2022 Emerging microbes & infections Result SARS_CoV_2 E64D;K814A 86;142 90;147 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Consistent with the microscopy observations, the Renilla luciferase reporter assay also showed that DeltaF significantly reduced cell-cell fusion, while the K814A mutation partially reduced cell-cell fusion (Figure 3C). 2022 Emerging microbes & infections Result SARS_CoV_2 K814A 157 162 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Effect of Delta682-686 and K814A mutation on Cathepsin L and TMPRSS2. 2022 Emerging microbes & infections Result SARS_CoV_2 K814A 27 32 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Effect of Delta682-686 and K814A mutation on furin-mediated S cleavage. 2022 Emerging microbes & infections Result SARS_CoV_2 K814A 27 32 S 60 61 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Effect of Delta682-686 and K814A mutations on antigenicity of SARS-CoV-2. 2022 Emerging microbes & infections Result SARS_CoV_2 K814A 27 32 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Effect of Delta682-686 and K814A mutations on SARS-CoV-2 infectivity of lung cell lines and human ACE2 transgenic mice. 2022 Emerging microbes & infections Result SARS_CoV_2 K814A 27 32 34856891 A second functional furin site in the SARS-CoV-2 spike protein. For the canonical polybasic cleavage site F1, we constructed with deletion of several amino acids (Delta682-686, Delta681-684, Delta681-685), and single point (R682S, R685A) mutants. 2022 Emerging microbes & infections Result SARS_CoV_2 R685A;R682S 167;160 172;165 34856891 A second functional furin site in the SARS-CoV-2 spike protein. For WT and K814A mutated S, no differences were observed when furin was expressed either in donor or recipient cells. 2022 Emerging microbes & infections Result SARS_CoV_2 K814A 11 16 S 25 26 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Furthermore, in the 293T-furin cell line, the proportion of S2' in the K814A mutant was lower than that of WT strain (line3 vs line 1), suggesting that K814A mutation affects S2' cleavage. 2022 Emerging microbes & infections Result SARS_CoV_2 K814A;K814A 71;152 76;157 34856891 A second functional furin site in the SARS-CoV-2 spike protein. However, DeltaF mutated S protein resulted in very little intercellular fusion (Figure 3A), while the fusion capacity of the K814A mutated S protein was significantly decreased compared with WT S (Figure 3A). 2022 Emerging microbes & infections Result SARS_CoV_2 K814A 125 130 S;S;S 24;139;194 25;140;195 34856891 A second functional furin site in the SARS-CoV-2 spike protein. In addition, natural mutations around this position (N74K, G75D, T76I, R78K, D80N) was also tested. 2022 Emerging microbes & infections Result SARS_CoV_2 D80N;G75D;R78K;T76I;N74K 77;59;71;65;53 81;63;75;69;57 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Interestingly, when the amino acids at the F2 site (positions 810-817) were mutated one by one, furin no longer enhanced the infectivity of 814-816 mutated SARS-CoV-2 strains (K814A, K814S, R815A, or S816A), whereas K811N and P812A partially affected the furin-enhanced infectivity (Figure 2B). 2022 Emerging microbes & infections Result SARS_CoV_2 K811N;K814S;P812A;R815A;S816A;K814A 216;183;226;190;200;176 221;188;231;195;205;181 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Moreover, furin inhibitor (dec-RVKR-CMK) prevented infection of 293T-ACE2-furin cells by wildtype (WT) SARS-CoV-2 as well as by the DeltaF mutated virus but not the K814A mutant (Figure 2E). 2022 Emerging microbes & infections Result SARS_CoV_2 K814A 165 170 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Mutants K810A/S of RaTG13, K806S of PCoV-GD, and K808A/S of PCoV-GX lost the ability to be enhanced by furin, which was similar to the result observed in SARS-CoV-2. 2022 Emerging microbes & infections Result SARS_CoV_2 K806S;K808A;K808S;K810A;K810S 27;49;49;8;8 32;56;56;15;15 34856891 A second functional furin site in the SARS-CoV-2 spike protein. The results indicated that the K814A mutation did not affect the increased infectivity caused by TMPRSS2 overexpression, while the DeltaF mutation slightly promoted the enhancement of infectivity caused by TMPRSS2 overexpression (Figure 2I). 2022 Emerging microbes & infections Result SARS_CoV_2 K814A 31 36 34856891 A second functional furin site in the SARS-CoV-2 spike protein. The results showed that the infectivity of the Delta682-686 and K814A mutants both decreased (Figure 6B and 6C). 2022 Emerging microbes & infections Result SARS_CoV_2 K814A 64 69 34856891 A second functional furin site in the SARS-CoV-2 spike protein. These results suggest that F2 (K814A) is a novel furin functional sites. 2022 Emerging microbes & infections Result SARS_CoV_2 K814A 31 36 34856891 A second functional furin site in the SARS-CoV-2 spike protein. These results suggest that the K814A mutation affects furin activity only, but not that of other enzymes, whereas the mutation of DeltaF not only interfered with the activity of furin, but also promoted the activity of TMPRSS2 and Cathepsin L to a certain extent. 2022 Emerging microbes & infections Result SARS_CoV_2 K814A 31 36 34856891 A second functional furin site in the SARS-CoV-2 spike protein. To explore whether Delta682-686 and K814A affect the antigenicity of SARS-CoV-2, the neutralization characteristics of nine monoclonal antibodies, 12 convalescent sera, and 14 animal immune sera against WT and mutant pseudovirus were tested. 2022 Emerging microbes & infections Result SARS_CoV_2 K814A 36 41 34856891 A second functional furin site in the SARS-CoV-2 spike protein. We also added the polybasic cleavage site RRAR to the S1/S2 junction of PCoV-GD or PCoV-GX pseudovirus on the K806S or K808A/S mutation background. 2022 Emerging microbes & infections Result SARS_CoV_2 K806S;K808A;K808S 110;119;119 115;126;126 34856891 A second functional furin site in the SARS-CoV-2 spike protein. We further examined whether K814A mutation would influence the function of Cathepsin L. 2022 Emerging microbes & infections Result SARS_CoV_2 K814A 28 33 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. In order to further corroborate whether these antibodies were also able to neutralize viral infection in a cell culture, we performed cVNT for lineage B SARS-CoV2 (D614G) and the Alpha, Gamma, and Delta variants. 2021 Frontiers in immunology Result SARS_CoV_2 D614G 164 169 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. The GMT values obtained by cVNT for D614G strain and the Alpha, Gamma, and Delta variants were 74.8 (95% CI 59.8-93.6), 32.1(95% CI 20.1-51.1), 15.8 (95% CI 9.5-26.2) and 7.9 (95% CI 5.2-12), respectively. 2021 Frontiers in immunology Result SARS_CoV_2 D614G 36 41 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. The results obtained showed that, as compared to the D614G strain, there was a 2.33-fold decrease in neutralizing antibodies against the Alpha variant, a 4.73-fold reduction against the Gamma variant and a 9.46-fold reduction against the Delta variant ( Figure 2A ). 2021 Frontiers in immunology Result SARS_CoV_2 D614G 53 58 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. The seropositivity rates of neutralizing antibodies for the Alpha, Gamma and Delta variants were 84.62%, 65.38% and 55.76% respectively, while for the D614G strain was 97.6% ( Figure 2B ). 2021 Frontiers in immunology Result SARS_CoV_2 D614G 151 156 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. This result suggests that CoronaVac induce the secretion of antibodies that can neutralize these variants, but at rates lower than those reported for the WT or the D614G strain. 2021 Frontiers in immunology Result SARS_CoV_2 D614G 164 169 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. A total of 34 nonsynonymous mutations were observed, with the spike D614G having the highest occurrence in 2400 genomes followed by the nsp12 P4715L mutation observed in 2254 genomes (Figure 1A). 2021 Frontiers in genetics Result SARS_CoV_2 D614G;P4715L 68;142 73;148 S;Nsp12 62;136 67;141 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. After D614G, P681R occurred in 1455 of the analyzed sequences. 2021 Frontiers in genetics Result SARS_CoV_2 D614G;P681R 6;13 11;18 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. All, except D614G, from the 9 non-synonymous mutations observed, had relatively more frequency in the Gujarat region compared to their global frequencies. 2021 Frontiers in genetics Result SARS_CoV_2 D614G 12 17 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. Also, there is a clear difference in frequency as observed for D614G which was comparatively much higher compared to global during early phase up to July 2020 (Supplementary Figure S2) and now the frequencies are almost the same. 2021 Frontiers in genetics Result SARS_CoV_2 D614G 63 68 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. Such difference currently is observed in the P681R mutation, which is the hallmark mutation of the Delta variant wherein the percentage occurrence is 20% higher in the Gujarat region compared to the global. 2021 Frontiers in genetics Result SARS_CoV_2 P681R 45 50 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. The P681R has outraced other major mutations in spike proteins and is the second major mutation. 2021 Frontiers in genetics Result SARS_CoV_2 P681R 4 9 S 48 53 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. These also reflect that D613G is the most spread, and further there are around 12 mutations that have >25% occurrence globally. 2021 Frontiers in genetics Result SARS_CoV_2 D613G 24 29 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. While D614G had almost similar frequency with its global value. 2021 Frontiers in genetics Result SARS_CoV_2 D614G 6 11 34866979 Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study. Other changes which were frequently identified include G25563T (G57H) and C26735T (silent) each of which occurred in 33 variants, followed by C18877T (silent), G28881A (S202N) and G28883C (G204R) which appeared in 32, 23 and 22 variants respectively. 2021 Saudi journal of biological sciences Result SARS_CoV_2 C18877T;C26735T;G25563T;G28881A;G28883C;G204R;G57H;S202N 142;74;55;160;180;189;64;169 149;81;62;167;187;194;68;174 34866979 Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study. Our analysis showed that the most frequently changed nucleotide were C3037T (silent mutation) and A23403G (D614G) each of which occurred in 57 variants out of 58, followed by C14408T (P4715L) and C241T (5'UTR) which were found in 56 and 55 variants, respectively. 2021 Saudi journal of biological sciences Result SARS_CoV_2 A23403G;C14408T;C241T;C3037T;D614G;P4715L 98;175;196;69;107;184 105;182;201;75;112;190 5'UTR 203 208 34866979 Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study. The coexistence of C241T (5'UTR), C3037T (ORF1ab), C14408T (ORF1ab) and A23403G (S gene) was observed in 55 variants. 2021 Saudi journal of biological sciences Result SARS_CoV_2 A23403G;C14408T;C241T;C3037T 72;51;19;34 79;58;24;40 ORF1ab;ORF1ab;5'UTR;S 42;60;26;81 48;66;31;82 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. However, occupancy analysis at sites such as N149 in the WA1 strain and N122 in D614G strains did not meet our criteria. 2021 Frontiers in chemistry Result SARS_CoV_2 D614G 80 85 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. In addition, four glycosites, N603, N616, N1158, and N1194, were not identified in the WA1 strain, while all four were identified in the D614G variant (Figures 6A,B, Supplementary Tables S6 and S7). 2021 Frontiers in chemistry Result SARS_CoV_2 D614G 137 142 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. In contrast, 12 of 13 N-linked glycosites were identified in the S1 domain of the D614G variant (Figure 6A and Supplementary Table S7). 2021 Frontiers in chemistry Result SARS_CoV_2 D614G 82 87 N 22 23 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Interestingly, in the recombinant S1 protein, most N-linked glycosites are dominated by complex-type N-glycans, while most glycosites in both the WA1 strain and the D614G variant produced in the virus were dominated by high-mannose-type glycans (Figure 6A). 2021 Frontiers in chemistry Result SARS_CoV_2 D614G 165 170 N;N 51;101 52;102 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. No O-linked glycosites were identified in the virus-derived spike from WA1 and D614G. 2021 Frontiers in chemistry Result SARS_CoV_2 D614G 79 84 S 60 65 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Site occupancy identified by the PNGase F deglycosylation methodology revealed that 10 S1 N-glycosites from the WA1 strain (N61, N122, N165, N234, N282, N331, N343, N603, N616, and N567) and 9 N-glycosites from the D614G variant (N61, N149, N165, N234, N331, N343, N603, N616, and N657) were almost 100% glycosylated (Supplementary Tables S8, S9). 2021 Frontiers in chemistry Result SARS_CoV_2 D614G 215 220 N;N 90;193 91;194 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Site-Specific Glycosylation of the Spike From the WA1 Strain and the D614G Variant. 2021 Frontiers in chemistry Result SARS_CoV_2 D614G 69 74 S 35 40 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. The D614G variant contains the spike protein amino acid change at 614 from D to G, which is more infectious and transmissible and has become the most prevalent form in the global pandemic since March 2021. 2021 Frontiers in chemistry Result SARS_CoV_2 D614G 4 9 S 31 36 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. The D614G variant presents more complex-type glycans at N331 but less complex-type glycans at N343 compared to the WA1 strain. 2021 Frontiers in chemistry Result SARS_CoV_2 D614G 4 9 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. The glycan changes at N343 in D614G compared to WA1 could, at least partially, account for D614G phenotype changes if similar shifts in glycosylation occur in nature. 2021 Frontiers in chemistry Result SARS_CoV_2 D614G;D614G 30;91 35;96 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. The most abundant glycoform at each N-glycosite was comparable between WA1 and D614G (Figure 7). 2021 Frontiers in chemistry Result SARS_CoV_2 D614G 79 84 N 36 37 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Therefore, the high percent of high-mannose-type glycans on WA1 and D614G grown in Vero E6 cells was not limited to the SARS-CoV-2 spike. 2021 Frontiers in chemistry Result SARS_CoV_2 D614G 68 73 S 131 136 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Three N-glycosites, N74, N122, and N282, were only identified in D614G with a single replicate in the site occupancy study; therefore, we were not able to determine site occupancy at these three sites. 2021 Frontiers in chemistry Result SARS_CoV_2 D614G 65 70 N 6 7 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. To determine the differences and similarities in glycosylation between the recombinant S1, produced in HEK293 cells, and that of the spike produced in the virus, we examined the spike derived from the intact virus from two strains, the WA1 strain and D614G, propagated in Vero E6 cells. 2021 Frontiers in chemistry Result SARS_CoV_2 D614G 251 256 S;S 133;178 138;183 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. WA1 and D614G strains were grown in Vero E6 cells which are derived from the African green monkey kidney, while the recombinant S1 protein was expressed by HEK293 cells which are derived from human embryonic kidney cells. 2021 Frontiers in chemistry Result SARS_CoV_2 D614G 8 13 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. When comparing the mutant form, D614G, with the original form, WA1, we observed a similar glycosylation pattern for most N-linked glycosites in both S1 and S2 domains (Figures 6A,B). 2021 Frontiers in chemistry Result SARS_CoV_2 D614G 32 37 N 121 122 34869681 Arterial and Venous Thrombosis Complicated in COVID-19: A Retrospective Single Center Analysis in Japan. As we have reported, the ratio of VOC/VOI carrying N501Y or E484K mutation rapidly increased in our hospital during the observation period, and the proportion of VOC/VOI reached 100% by the end of April in 2021 (Figure 3A). 2021 Frontiers in cardiovascular medicine Result SARS_CoV_2 E484K;N501Y 60;51 65;56 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. All mutations except L18F were distributed well in all four regions but the number of L18F mutations was close to zero in Turkey when compared to other continents (Fig 3B). 2021 PloS one Result SARS_CoV_2 L18F;L18F 21;86 25;90 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. All the spike mutations were found to be in medium proximity to the human ACE2 receptor binding motif (RBM), with the exception of Ala222Val. 2021 PloS one Result SARS_CoV_2 A222V 131 140 S 8 13 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Although the fluctuation intensities and the location of the fluctuations were similar, residues 474-488 of the Asp614Gly mutant were mapped to a relatively more upward extended conformation. 2021 PloS one Result SARS_CoV_2 D614G 112 121 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. As a statistically robust analysis method, ConSurf results demonstrated that all the described spike mutations occurred in moderate to highly variable regions except for the Asp614Gly mutation. 2021 PloS one Result SARS_CoV_2 D614G 174 183 S 95 100 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. However, the increase in the SASA of the Asp614Gly mutation was to a lesser extent. 2021 PloS one Result SARS_CoV_2 D614G 41 50 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Moreover, a SASA calculation for the residues between 439 to 501 (including the RBD region) indicates that SASA change was minimal for the Asp614Gly mutation, which implies a more compact, structureless surface exposed with respect to the other mutations and reference protein regarding this region. 2021 PloS one Result SARS_CoV_2 D614G 139 148 RBD 80 83 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Only one mutation (C241T) was in a non-coding region. 2021 PloS one Result SARS_CoV_2 C241T 19 24 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. The D614G was the most seen mutation in all four regions. 2021 PloS one Result SARS_CoV_2 D614G 4 9 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. The distribution of specific amino acid changes in Spike glycoprotein, which are already related with increasing in transmissibility, showed that the N501Y and D614G mutations were widely detected in Europe when compared to other regions (Fig 3B). 2021 PloS one Result SARS_CoV_2 D614G;N501Y 160;150 165;155 S 51 69 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. The most common mutations were C17690T (69.2%), C2113T (61.5%), C241T (53.8%) and G25563T (53.8%) and in 38.5% of the cases these mutations were detected together. 2021 PloS one Result SARS_CoV_2 C17690T;C2113T;C241T;G25563T 31;48;64;82 38;54;69;89 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. The mutation A23403G, known as D614G, was detected in genome sequences of two of our patients (ACUTG-1 and ACUTG-5). 2021 PloS one Result SARS_CoV_2 A23403G;D614G 13;31 20;36 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. The mutation Ala222Val was located in a region with the highest variability score. 2021 PloS one Result SARS_CoV_2 A222V 13 22 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Three consecutive mutations of the N gene (G28881A, G28882A, and G28883C) were observed in four (ACUTG-5, ACUTG-6, ACUTG-8, and ACUTG-13) of the 13 SARS-CoV-2 genome sequences. 2021 PloS one Result SARS_CoV_2 G28882A;G28883C;G28881A 52;65;43 59;72;50 N 35 36 34874953 1H, 13C and 15N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution. As it is shown in Fig 3D, the CSP observed in 1H-15N HSQC spectra of wild type nsp1 vs the H81P mutant (red bars) are evident. 2021 PloS one Result SARS_CoV_2 H81P 91 95 34874953 1H, 13C and 15N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution. For the H81P mutant, we see chemical shift changes for residues 10-17 and 120-127 belonging to the junctions between structured/unstructured regions (Fig 3D). 2021 PloS one Result SARS_CoV_2 H81P 8 12 34874953 1H, 13C and 15N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution. In the first, a single histidine in position 81 was replaced by proline (H81P). 2021 PloS one Result SARS_CoV_2 H81P;H81P 23;73 71;77 34874953 1H, 13C and 15N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution. In the second mutant, we introduced two aa substitutions: Lys129 and Asp48 were replaced by Gln (K129E and D48E). 2021 PloS one Result SARS_CoV_2 D48E;K129E 107;97 111;102 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. Based on the Cryo-EM structures, it has been proposed that S-D614G substitution allosterically leads to more "open" conformations or a higher percentage of RBD in a "up" position that facilitates the interaction of RBD with the ACE2 receptor. 2021 Scientific reports Result SARS_CoV_2 D614G 61 66 RBD;RBD;S 156;215;59 159;218;60 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. Considering the proximity of N603 to the S-D614G substitution site, the glycan variation on N603 might have similar effect as that on the N616. 2021 Scientific reports Result SARS_CoV_2 D614G 43 48 S 41 42 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. One is the adaptability of the N-glycan shielding layer to the structural changes in the original protein caused by the S-D614G substitution. 2021 Scientific reports Result SARS_CoV_2 D614G 122 127 N;S 31;120 32;121 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. The closest glycosylation site to the S-D614G substitution is N616, as it resides only two amino acid residues downstream of the substitution site. 2021 Scientific reports Result SARS_CoV_2 D614G 40 45 S 38 39 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. Variations occurred on two major oligomannoses, Man5 and Man6, but their mass spectral abundances were reduced by approximately eight- and four-fold, respectively, when the aspartic acid at 614 was substituted for a glycine residue. 2021 Scientific reports Result SARS_CoV_2 D614G 173 223 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. While 6 of 11 sequons, including N165, N282, N603, N616, N1098, and N1134, were occupied by more than fifty percent of the complex glycans present on the S-614D protein, only one of them (N282) maintained 65% population of complex glycans after the S-D614G substitution. 2021 Scientific reports Result SARS_CoV_2 D614G 251 256 S;S 154;249 155;250 34886945 Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020. Using the inferred value of sigma = 1.31, we estimated that the D614G mutation would increase the herd immunity threshold from 50% to 62%. 2021 Euro surveillance Result SARS_CoV_2 D614G 64 69 34888394 A Multidimensional Cross-Sectional Analysis of Coronavirus Disease 2019 Seroprevalence Among a Police Officer Cohort: The PoliCOV-19 Study. Antibodies from seropositive individuals demonstrated neutralization activity against D614G up to a dilution of 1:320 (Supplementary Figure D). 2021 Open forum infectious diseases Result SARS_CoV_2 D614G 86 91 34888394 A Multidimensional Cross-Sectional Analysis of Coronavirus Disease 2019 Seroprevalence Among a Police Officer Cohort: The PoliCOV-19 Study. Antibody titers of anti-NCP and anti-S antibodies correlated with the dilution titers showing the highest coefficient with dilution of D614G and the lowest coefficient with dilution of B.1.351 (Beta), with P<.001 in all pairs (Supplementary Table F). 2021 Open forum infectious diseases Result SARS_CoV_2 D614G 135 140 S 37 38 34888394 A Multidimensional Cross-Sectional Analysis of Coronavirus Disease 2019 Seroprevalence Among a Police Officer Cohort: The PoliCOV-19 Study. Similar to the overall results of neutralization assays, the neutralization capacity of serum against Alpha and Beta variants was poorer than it was against D614G, even with serum demonstrating both >37.5 U/mL COI anti-NCP antibodies and >65 U/mL anti-S antibodies. 2021 Open forum infectious diseases Result SARS_CoV_2 D614G 157 162 S 252 253 34888394 A Multidimensional Cross-Sectional Analysis of Coronavirus Disease 2019 Seroprevalence Among a Police Officer Cohort: The PoliCOV-19 Study. The dilutions were lower for B.1.1.7 (1:40 for anti-S antibodies and 1:80 for anti-NCP antibodies) and for B.1.351 variants (1:20) (Supplementary Figures E and F), indicating a poorer neutralization capacity toward virus variants in comparison to the main circulating virus expressing D614G. 2021 Open forum infectious diseases Result SARS_CoV_2 D614G 285 290 S 52 53 34888394 A Multidimensional Cross-Sectional Analysis of Coronavirus Disease 2019 Seroprevalence Among a Police Officer Cohort: The PoliCOV-19 Study. The median dilution titer was significantly higher in assays that used D614G than in those that used B.1.1.7 (P<.001) and B.1.351 (P<.001). 2021 Open forum infectious diseases Result SARS_CoV_2 D614G 71 76 34890524 The significant immune escape of pseudotyped SARS-CoV-2 variant Omicron. The ED50 of Alpha, Beta, and Gamma is reduced about 1.2, 2.8, and 1.6-fold, respectively, compared to the reference strain PV-D614G (Figure 1B-D), while the reduction of neutralization for Lambda and Mu variants is 1.7- and 4.5-fold, respectively (Figure 1F-G). 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 126 131 34890524 The significant immune escape of pseudotyped SARS-CoV-2 variant Omicron. The results indicated that the mean neutralization titre (50% effective dilution, ED50) of PV-Omicron was 66, which represented about 8.4-fold reduction of neutralization compared to the reference strain PV-D614G (ED50 = 556) (Figure 1H). 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 207 212 34890524 The significant immune escape of pseudotyped SARS-CoV-2 variant Omicron. There are 32 mutations on the Spike of Omicron, including the following sites: A67V, H69del-V70del, T95I, G142D-V143del-Y144del-Y145del, N211del-L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F. 2022 Emerging microbes & infections Result SARS_CoV_2 A67V;D614G;D796Y;E484A;G142D;G339D;G446S;G496S;H655Y;K417N;L981F;N440K;N501Y;N679K;N764K;N856K;N969K;P681H;Q493R;Q498R;Q954H;S371L;S373P;S375F;S477N;T478K;T547K;T95I;Y505H;L212I 79;275;310;226;106;163;205;240;282;191;342;198;254;289;303;317;331;296;233;247;324;170;177;184;212;219;268;100;261;145 83;280;315;231;111;168;210;245;287;196;347;203;259;294;308;322;336;301;238;252;329;175;182;189;217;224;273;104;266;150 S 30 35 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. 4C and D), higher than observed for N501Y detection and in a previous study. 2022 Biosensors & bioelectronics Result SARS_CoV_2 N501Y 36 41 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. All samples carried the D614G mutation. 2022 Biosensors & bioelectronics Result SARS_CoV_2 D614G 24 29 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. Because CRISPR/Cas12a has been reported to differentiate SNPs with single-base resolution, we used Cas12a to identify SARS-CoV-2 N501Y, D614G, and 69/70 deletion mutations; these are the key mutations of SARS-CoV-2 VOC (Table S1). 2022 Biosensors & bioelectronics Result SARS_CoV_2 D614G;N501Y 136;129 141;134 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. D614G detection is thus more suitable for samples when SARS-CoV-2 viral load is <10-14 M (approximately 6000 copies/muL), and appropriate dilution of samples should be considered for higher viral loads (Table S5). 2022 Biosensors & bioelectronics Result SARS_CoV_2 D614G 0 5 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. Furthermore, five samples carrying the N501Y mutation and two samples carrying the 69/70 deletion were identified. 2022 Biosensors & bioelectronics Result SARS_CoV_2 N501Y 39 44 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. However, 40 min is the most advisable for D614G detection. 2022 Biosensors & bioelectronics Result SARS_CoV_2 D614G 42 47 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. However, significant differences in fluorescence intensities between 614-crRNA-W and 614-crRNA-M were noted, and this slight activation had no impact on D614G discrimination. 2022 Biosensors & bioelectronics Result SARS_CoV_2 D614G 153 158 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. Notably, kinetic analyses showed N501Y and 69/70 deletion can be identified in as small duration as 5-10 min, indicating a shorter reaction time for mutation tracking. 2022 Biosensors & bioelectronics Result SARS_CoV_2 N501Y 33 38 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. RT-CORDS fluorescence assay for 69/70 deletion identification showed a sensitivity of 10-17 M, the same value as that achieved for N501Y. 2022 Biosensors & bioelectronics Result SARS_CoV_2 N501Y 131 136 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. RT-CORDS is a rapid, robust, and accurate method for the identification of SARS-CoV-2 N501Y, D614G, and 69/70 deletion mutations and may be used for additional tracking of spike mutations through a simple process in clinical diagnostics. 2022 Biosensors & bioelectronics Result SARS_CoV_2 D614G;N501Y 93;86 98;91 S 172 177 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. The abovementioned findings indicate that 501-crRNA-W and 501-crRNA-M can identify N501Y MT variants specifically. 2022 Biosensors & bioelectronics Result SARS_CoV_2 N501Y 83 88 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. The crRNAs for single-base mutation were designed by introducing a transition mismatch in the seed region to enhance specificity, such as U-T mismatch in N501Y and C-C mismatch in D614G detection. 2022 Biosensors & bioelectronics Result SARS_CoV_2 D614G;N501Y 180;154 185;159 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. The sensitivity for D614G detection was 10-17 M for RT-CORDS fluorescence and 10-15 M for RT-CORDS paper strip reporting systems. 2022 Biosensors & bioelectronics Result SARS_CoV_2 D614G 20 25 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. The sensitivity of RT-CORDS for N501Y detection was 10-15 M, the same sensitivity as that of CORDS, when lateral flow strips were used as final read out. 2022 Biosensors & bioelectronics Result SARS_CoV_2 N501Y 32 37 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. We also introduced a skillful mismatch into the seed region of 614-crRNA-W and 614-crRNA-M for D614G. 2022 Biosensors & bioelectronics Result SARS_CoV_2 D614G 95 100 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. We conclude that the specific crRNA-W and crRNA-M that we designed can successfully and specifically identify N501Y, D614G, and 69/70 deletion mutations in SARS-CoV-2 variants. 2022 Biosensors & bioelectronics Result SARS_CoV_2 D614G;N501Y 117;110 122;115 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. We designed 501-crRNA-W (N501-WT-specific crRNA) and 501-crRNA-M (Y501-MT-specific crRNA) to detect N501Y mutation (Table S2). 2022 Biosensors & bioelectronics Result SARS_CoV_2 N501Y 100 105 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. A total of 11 variants in Iran carry I210del mutation. 2022 Gene Result SARS_CoV_2 I210del 37 44 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Finally, main characteristics of the fifteen SARS-CoV-2 variants carrying A262T mutation in Iran are shown in Table 13 . 2022 Gene Result SARS_CoV_2 A262T 74 79 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Four of these nine sequences sampled from Yazd, in addition to indicator mutations of a Delta variant, also have a common E1202Q mutation in the HR2 subdomain, in which glutamine replaces glutamic acid at position 1202. 2022 Gene Result SARS_CoV_2 E1202Q;Q1202E 122;169 128;218 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. The shared characteristic feature of these three clades is S_D614G mutation, which may increase the infectivity of SARS-CoV-2. 2022 Gene Result SARS_CoV_2 D614G 61 66 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. There were also three sequences carrying D138Y+ S477N+ D614G triple mutations sampled from shiraz and Tehran. 2022 Gene Result SARS_CoV_2 D138Y;D614G;S477N 41;55;48 46;60;53 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Among 129 SARS-CoV-2 strains, 27 strains with additional S: E484K mutation also formed a sub-cluster that was presented in. 2022 Journal of infection and public health Result SARS_CoV_2 E484K 60 65 S 57 58 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Among 186 different mutations, Q18stop mutation in NS8 protein was found to occur with highest frequency (Table 2). 2022 Journal of infection and public health Result SARS_CoV_2 Q18X 31 38 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. By performing the whole genome mutational analysis of 8592 SARS-CoV-2 strains collected during August 2020 to October 2021 from India, we identified 126 SARS-CoV-2 strains having new set of 11 coexisting mutations among 7 different genes: D279N and L353F in NSP4; V26F in NSP8; P323L in NSP12; D614G, P681H and V1230L in S glycoprotein; G172C in NS3; V62L in NS8; and R203K and G204R in N gene. 2022 Journal of infection and public health Result SARS_CoV_2 D279N;D614G;G172C;G204R;L353F;P323L;P681H;R203K;V1230L;V26F;V62L 239;294;337;378;249;278;301;368;311;264;351 244;299;342;383;254;283;306;373;317;268;355 S;Nsp12;Nsp4;Nsp8;NS3;N 321;287;258;272;346;387 335;292;262;276;349;388 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. In addition to 12 coexisting mutations including E484K, 186 different mutations were also found throughout the genome of these 129 SARS-CoV-2 strains. 2022 Journal of infection and public health Result SARS_CoV_2 E484K 49 54 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Interestingly, among 129 sequences, 27 sequences also harbored E484K mutation along with D614G, P681H and V1230L in the S glycoprotein. 2022 Journal of infection and public health Result SARS_CoV_2 D614G;E484K;P681H;V1230L 89;63;96;106 94;68;101;112 S 120 134 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Phylogenetic analysis of 38 representative genomes of the new variant along with 73 reference genomes of different clades/variants by MEGA X revealed that genomes of this new variant formed a novel cluster that emerged from the GR clade (B.1.1) which is characterized by four coexisting signature mutations: D614G in S glycoprotein, P323L in NSP12, and R203K and G204R in N protein. 2022 Journal of infection and public health Result SARS_CoV_2 D614G;G204R;P323L;R203K 308;363;333;353 313;368;338;358 S;Nsp12;N 317;342;372 331;347;373 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. This novel cluster has evolved from the GR clade by acquiring S glycoprotein mutations V1230L and P681H, and has been depicted in. 2022 Journal of infection and public health Result SARS_CoV_2 P681H;V1230L 98;87 103;93 S 62 76 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. 14.5% presented the combination of NSP3 p.E405A (Orf1ab p.E1223A) and Orf7a p.V106L. 2021 PloS one Result SARS_CoV_2 E1223A;E405A;V106L;E405A;V106L 56;40;76;42;78 64;47;83;47;83 ORF1ab;ORF7a;Nsp3 49;70;35 55;75;39 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. 20% of viral genomes analyzed presented the NSP4 p.L206F (Orf1ab p.L2969F) in combination with N p.A156S. 2021 PloS one Result SARS_CoV_2 A156S;P156S;L206F;L2969F;A156S;L206F 97;97;49;65;99;51 104;104;56;73;104;56 ORF1ab;Nsp4;N 58;44;95 64;48;96 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. 39% of sequences harbored NSP12b p.P218L (Orf1ab p.P4619S), NSP14 p.P451S (Orf1ab p.P6376S), Orf6 p.D61L and Orf8 p.K68* mutations. 2021 PloS one Result SARS_CoV_2 D61L;P218L;P451S;P4619S;D61L;K68X;P218L;P451S 98;33;66;49;100;116;35;68 104;40;73;57;104;120;40;73 ORF1ab;ORF1ab;ORF6;ORF8 42;75;93;109 48;81;97;113 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. Among these mutations, only the NSP12b p.P218L is already indexed on the CovidMiner data portal with a frequency of 16% among the deposited sequences. 2021 PloS one Result SARS_CoV_2 P218L;P218L 39;41 46;46 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. Fig 1 panel A-D graphically represents the p.N501Y spread during January and February in our territory. 2021 PloS one Result SARS_CoV_2 N501Y;N501Y 43;45 50;50 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. Furthermore, the Nucleocapsid p.A156S substitution has been already discussed in the study of Rahman and colleagues, highlighting a mutation-induced shift in protein stability with a decrease in flexibility. 2021 PloS one Result SARS_CoV_2 A156S;P156S;A156S 30;30;32 37;37;37 N 17 29 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. In the first four time points, we only detected two SNPs that differs from the B.1.1.7-defining ones: the p.D138H substitution (N = 3) and the p.D796H (N = 1). 2021 PloS one Result SARS_CoV_2 D138H;D796H;D138H;D796H 106;143;108;145 113;150;113;150 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. Indeed, 99.1% of p.N501Y positivity was then reached in early April. 2021 PloS one Result SARS_CoV_2 N501Y;N501Y 17;19 24;24 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. Indeed, all of the SARS-CoV-2 B.1.1.7 genomes analyzed in our cohort contained all the so-called signature mutations in the Spike glycoprotein, including p.H69-V70del, p.Y144del, p.N501Y, p.A570D, p.P681H, p.T716I, p.S982A, and p.D1118H. 2021 PloS one Result SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;T716I;Y144del;A570D;N501Y;P681H;S982A;T716I 188;228;179;197;215;206;168;190;181;199;217;208 195;236;186;204;222;213;177;195;186;204;222;213 S 124 142 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. Noteworthy, two specimens collected in mid-February turned out to possess the p.E484K but not p.N501Y. 2021 PloS one Result SARS_CoV_2 E484K;N501Y;E484K;N501Y 78;94;80;96 85;101;85;101 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. Table 1 and Fig 1 panel E summarize the percentage of p.N501Y positive samples over the selected analytical time points. 2021 PloS one Result SARS_CoV_2 N501Y;N501Y 54;56 61;61 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. The presence of p.N501Y and p.E484K Spike mutations was assessed by high resolution melting (HRM). 2021 PloS one Result SARS_CoV_2 E484K;N501Y;E484K;N501Y 28;16;30;18 35;23;35;23 S 36 41 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. We witnessed a fast and exponential growth in the percentage of samples possessing the p.N501Y mutation. 2021 PloS one Result SARS_CoV_2 N501Y;N501Y 87;89 94;94 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. Because B.1.1.7 emerged after D614G became globally common, the absolute fitness of B.1.1.7 is likely greater. 2021 Nature communications Result SARS_CoV_2 D614G 30 35 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. D614G shows a very similar pattern in the UK and Netherlands where the mutant was spreading in a way that is nearly indistinguishable from the wild-type strains for a period of several weeks in the early epidemic period. 2021 Nature communications Result SARS_CoV_2 D614G 0 5 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. Estimates from our population-genetic model for this country do not disagree but have much larger uncertainty; across all countries, the estimate is close for D614G and lower for B.1.1.7. 2021 Nature communications Result SARS_CoV_2 D614G 159 164 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. For D614G and B.1.1.7, these estimates are quite similar. 2021 Nature communications Result SARS_CoV_2 D614G 4 9 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. In both cases, the mutant strain is much slower to rise, occurring over a period of months rather than weeks as was the case with D614G. 2021 Nature communications Result SARS_CoV_2 D614G 130 135 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. Not all SARS-CoV-2 variants of interest replace the background as clearly as in the case of D614G, Alpha, and Delta. 2021 Nature communications Result SARS_CoV_2 D614G 92 97 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. Previous work estimates an advantage of 0.1-0.3 for D614G in the UK (range across models, much broader for CIs of each model) and 0.4-0.9 for B.1.1.7 in England. 2021 Nature communications Result SARS_CoV_2 D614G 52 57 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. Similarly, the selective advantage of D614G was detectable once there were 2500 cases globally, and the estimate of s remained approximately the same over the next month as the number of cases increased to 12500. 2021 Nature communications Result SARS_CoV_2 D614G 38 43 S 116 117 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. The dynamics of B.1.1.7 in the UK and Netherlands are substantially different from both D614G and each other. 2021 Nature communications Result SARS_CoV_2 D614G 88 93 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. The overall stochastic model fits to D614G and B.1.1.7 for the UK and Netherlands are shown in Figs. 2021 Nature communications Result SARS_CoV_2 D614G 37 42 34909459 Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M(pro). Considering this fact, it is justified to expect that results of molecular docking simulation with SARS-CoV-2 Mpro and D614G give the same picture. 2021 ChemistrySelect Result SARS_CoV_2 D614G 119 124 34909459 Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M(pro). The binding modes of investigated ligands towards SARS-CoV-2 Mpro and D614G are given in Tables 1 and S3. 2021 ChemistrySelect Result SARS_CoV_2 D614G 70 75 34909459 Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M(pro). The molecular docking simulations are also performed for mutation of Spike protein D614G. 2021 ChemistrySelect Result SARS_CoV_2 D614G 83 88 S 69 74 34909459 Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M(pro). The obtained results of similar values of the binding energies as in the case of SARS-CoV-2 Mpro suggest that the mutation D614G has a significant role in COVID-19 epidemiology and the design of therapeutic treatment. 2021 ChemistrySelect Result SARS_CoV_2 D614G 123 128 COVID-19 155 163 34909459 Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M(pro). The results represented in Table S3 and Figure 3 refer to interactions accomplished in molecular docking simulations of studied compounds and mutation of Spike (S) protein D614G. 2021 ChemistrySelect Result SARS_CoV_2 D614G 172 177 S;S 154;161 159;162 34909459 Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M(pro). The values of the binding energies calculated for 1, 2, 3, and 4 presented in Table S3 indicate almost the same inhibition potency toward D614G. 2021 ChemistrySelect Result SARS_CoV_2 D614G 138 143 34909459 Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M(pro). This observation indicates studied compounds as potential inhibitors of D614G mutation. 2021 ChemistrySelect Result SARS_CoV_2 D614G 72 77 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. A recent study suggesting that S309 is tolerant of G339D in isolation is therefore reassuring [Cathcart 2021]. 2021 bioRxiv Result SARS_CoV_2 G339D 51 56 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. Additionally, mutations such as D614G have previously been linked to increased infectivity via destabilization of the RBD-down spike protein conformation. 2021 bioRxiv Result SARS_CoV_2 D614G 32 37 S;RBD 127;118 132;121 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. Further, we note the that Omicron mutations may also enhance escape depth from class 1 antibodies beyond that observed for the Beta variant due to accumulation of additional mutations in class 1 antibody epitopes beyond the shared Beta/Omicron mutation K417N. 2021 bioRxiv Result SARS_CoV_2 K417N 253 258 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. In contrast, the RBD mutations of the Beta and Delta variants are confined to sites within class 1 and 2 antibody epitopes, with the exception of Beta N501Y, which interacts indirectly with certain class 3 antibodies. 2021 bioRxiv Result SARS_CoV_2 N501Y 151 156 RBD 17 20 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. In particular, Zahradnik et al., identified enhanced ACE2 binding by RBD's bearing Q498R and S477N when combined with the N501Y mutation [Zahradnik et al]. 2021 bioRxiv Result SARS_CoV_2 N501Y;Q498R;S477N 122;83;93 127;88;98 RBD 69 72 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. Our network analysis ranks Omicron mutations N440K, G446S, G496S, and Q498R as most likely to confer enhanced class 3 antibody escape based on these sites having the strongest network interactions with the antibodies surveyed. 2021 bioRxiv Result SARS_CoV_2 G446S;G496S;N440K;Q498R 52;59;45;70 57;64;50;75 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. Rappazzo et al., further reported that Y505C/N/S knocked down ADG-2 binding potency. 2021 bioRxiv Result SARS_CoV_2 Y505C;Y505N;Y505S 39;39;39 48;48;48 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. Several Omicron subclades have been detected with R346S and R346K mutations. 2021 bioRxiv Result SARS_CoV_2 R346K;R346S 60;50 65;55 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. The loss of these bonds is reflected in the positive DeltaDeltaG for Y505H and S373P, yet partially compensated for by a more energetically favorable R403 environment. 2021 bioRxiv Result SARS_CoV_2 S373P;Y505H 79;69 84;74 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. The Omicron mutations occurring in class 4 antibody epitopes (G339D, S371L, S373P, S375F) are predominantly indirectly networked to class 4 antibodies. 2021 bioRxiv Result SARS_CoV_2 S371L;S373P;S375F;G339D 69;76;83;62 74;81;88;67 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. The RBD of PMS20, a variant that was designed to escape neutralization from most convalescent and polyclonal sera, features similar class 3 mutations to Omicron at sites 440 and 445, yet also features an R346K mutation that Omicron lacks. 2021 bioRxiv Result SARS_CoV_2 R346K 204 209 RBD 4 7 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. Using AAI networks to examine the local residue dependencies in this vicinity, we observe a network extending from the known synergistic pair 498+501 to position 505, suggesting Omicron H505 may modulate the synergistic ACE-2 binding effect for Q498R + N501Y. 2021 bioRxiv Result SARS_CoV_2 N501Y;Q498R 253;245 258;250 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. We find that Omicron has accumulated multiple tightly clustered mutations and therefore may have enhanced escape from matured polyclonal responses that are tolerant of certain class 1 antibody escape mutations such as K417N and N501Y (see Figure 1). 2021 bioRxiv Result SARS_CoV_2 K417N;N501Y 218;228 223;233 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. We therefore suspect that mutations S371L, S373P, and S375F may provide a fitness advantage other than escape. 2021 bioRxiv Result SARS_CoV_2 S371L;S373P;S375F 36;43;54 41;48;59 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. At the time of pre-vaccination sample collection D614G was the major circulating SARS-CoV-2 variant, while at the time off post-first dose and post-second dose D614G and Alpha were circulating, and at the six month time point Delta was the dominant strain. 2021 bioRxiv Result SARS_CoV_2 D614G;D614G 49;160 54;165 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. Following the first dose of mRNA vaccine, a strong nAb response was induced among HCWs compared to pre-vaccination across all variants (p < 0.001), which efficiently blocked virus entry; this was despite the huge variation in nAb titers of these individuals including against D614G (mean = 1140, 95% CI = 317-1963, range = 100-15954). 2021 bioRxiv Result SARS_CoV_2 D614G 276 281 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. In particular, following two vaccine doses, mRNA-1273 vaccinated HCWs exhibited 2.1-, 2.3-, 2.4-, and 1.3-fold higher nAb response compared to BNT162b2-vaccinated HCWs for D614G, Alpha, Beta, and Delta variants, respectively. 2021 bioRxiv Result SARS_CoV_2 D614G 172 177 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. Interestingly, we found that the differences in NT50 between anti-N positive and negative HCWs were greater and more statistically significant for D614G and Alpha compared with the Beta and Delta variants, likely due to the strong neutralization resistance of the latter VOCs. 2021 bioRxiv Result SARS_CoV_2 D614G 147 152 N 66 67 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. The mean NT50 values for Alpha, Beta, and Delta variants at six months were 1.3-, 1.7-, and 3.6-fold lower than that of D614G, respectively, although the differences in these low nAb titer groups were not statistically significant. 2021 bioRxiv Result SARS_CoV_2 D614G 120 125 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. This corresponded to an approximately 10-fold decline in NT50 for D614G, Alpha, and Delta (R2 = 0.0452-0.594, p < 0.0001) every ~22 weeks compared with Beta (R2 = 0.286, p < 0.001) every ~37 weeks. 2021 bioRxiv Result SARS_CoV_2 D614G 66 71 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. We did not find significant differences in pseudotyped lentivirus infectivity for the four variants (all containing D614G) tested. 2021 bioRxiv Result SARS_CoV_2 D614G 116 121 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. We found that, following two vaccine doses, the Alpha, Beta, and Delta VOCs exhibited a 1.3- (p < 0.001), 3.2- (p < 0.001), and 2.2-fold (p < 0.001) lower NT50 values compared to D614G, respectively. 2021 bioRxiv Result SARS_CoV_2 D614G 179 184 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. We observed no significant correlation for age and NT50 against D614G at any time point. 2021 bioRxiv Result SARS_CoV_2 D614G 64 69 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. We produced lentiviral pseudotypes expressing a Gaussia luciferase reporter gene and bearing SARS-CoV-2 spike derived from D614G, Alpha, Beta, or Delta. 2021 bioRxiv Result SARS_CoV_2 D614G 123 128 S 104 109 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. In summary, the study of Delta infections revealed that, compared to unvaccinated controls, breakthrough infections were associated with asymptomatic disease, lower rates of hospitalization, spike mutation S112L, nsp12 mutation F192V, and the absence of seven mutations across different regions of the SARS-CoV-2 full genome. 2021 medRxiv Result SARS_CoV_2 F192V;S112L 228;206 233;211 S;Nsp12 191;213 196;218 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. One of the two mutations that we found positively associated with Delta breakthrough (spike S112L) is situated in the middle of the spike NTD domain, an Omicron hotspot region that carries abundant mutations and deletions. 2021 medRxiv Result SARS_CoV_2 S112L 92 97 S;S 86;132 91;137 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. One of these clusters consisted of the Delta subvariant AY.25 that emerged recently and included sequences with spike mutation S112L. 2021 medRxiv Result SARS_CoV_2 S112L 127 132 S 112 117 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. The comparative spike mutation analysis exclusive for the subset of Delta sequences confirmed S112L as the only substantially enriched mutation among Delta breakthroughs (P<0.05. 2021 medRxiv Result SARS_CoV_2 S112L 94 99 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. The post-hoc analysis revealed that nine of these 10 sites were Delta-defining mutations, whilst one, S112L, is not Delta-defining but contributes to the array of Delta subvariant AY.25 mutations. 2021 medRxiv Result SARS_CoV_2 S112L 102 107 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. The S112L mutation locates at the surface-exposed top part of NTD, one of the major antigenic regions of the spike protein. 2021 medRxiv Result SARS_CoV_2 S112L 4 9 S 109 114 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. The S112L-positive AY.25 sub-cluster contained SARS-CoV-2 sequences from one unvaccinated and five vaccinated cases. 2021 medRxiv Result SARS_CoV_2 S112L 4 9 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. The second breakthrough-enriched mutation in Delta (nsp12 F192V) is located in the functionally relevant nsp12 domain, coding for the RdRp polymerase, which also entails the Omicron- and/or Delta-defining mutations P314L and G662S. 2021 medRxiv Result SARS_CoV_2 F192V;G662S;P314L 58;225;215 63;230;220 Nsp12;Nsp12;RdRP 52;105;134 57;110;138 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. Two mutations were enriched in breakthrough sequences compared to unvaccinated controls, which, besides spike mutation S112L included mutation F192V in nsp12, the RNA-dependent RNA polymerase (RdRp) gene. 2021 medRxiv Result SARS_CoV_2 F192V;S112L 143;119 148;124 RdRp;S;Nsp12;RdRP 163;104;152;193 191;109;157;197 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. However, in the Russian dataset, we find that the linkage between nsp2:K81N and ORF7a:P45L is nearly perfect, and these mutations cooccur in nearly all samples. 2021 medRxiv Result SARS_CoV_2 K81N;P45L 71;86 75;90 ORF7a;Nsp2 80;66 85;70 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. In addition to the mutations characteristic of Delta, 92.4% of the Delta samples carried the nsp2:K81N (ORF1a:K261N) mutation, and 91.8% carried the ORF7a:P45L mutation. 2021 medRxiv Result SARS_CoV_2 K261N;K81N;P45L 110;98;155 115;102;159 ORF1a;ORF7a;Nsp2 104;149;93 109;154;97 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. In the 26 regions with more than five samples of Delta, between 62% and 100% of samples carried the nsp2:K81N+ORF7a:P45L combination (Table S2). 2021 medRxiv Result SARS_CoV_2 K81N;P45L 105;116 109;120 ORF7a;Nsp2 110;100 115;104 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Moreover, the dynamics of the nsp2:K81N + ORF7a:P45L combination outside Russia also doesn't support its increased fitness. 2021 medRxiv Result SARS_CoV_2 K81N;P45L 35;48 39;52 ORF7a;Nsp2 42;30 47;34 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Most Russian Delta samples are characterized by the nsp2:K81N+ORF7a:P45L combination of mutations. 2021 medRxiv Result SARS_CoV_2 K81N;P45L 57;68 61;72 ORF7a;Nsp2 62;52 67;56 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Outside Russia, the nsp2:K81N and ORF7a:P45L mutations are not strongly linked, and many samples carry the first but not the second. 2021 medRxiv Result SARS_CoV_2 K81N;P45L 25;40 29;44 ORF7a;Nsp2 34;20 39;24 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Soon after its first detection, the nsp2:K81N+ORF7a:P45L combination has become prevalent throughout Russia. 2021 medRxiv Result SARS_CoV_2 K81N;P45L 41;52 45;56 ORF7a;Nsp2 46;36 51;40 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Strikingly, 91.2% of all samples descended from just a single import (hereafter referred to as the "main import") characterised by the nsp2:K81N+ORF7a:P45L combination of mutations. 2021 medRxiv Result SARS_CoV_2 K81N;P45L 140;151 144;155 ORF7a;Nsp2 145;135 150;139 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. The earliest nsp2:K81N+ORF7a:P45L sample in Russia dates to April 19th, and it was one of the first Delta samples obtained in Russia. 2021 medRxiv Result SARS_CoV_2 K81N;P45L 18;29 22;33 ORF7a;Nsp2 23;13 28;17 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. The frequency of the nsp2:K81N+ORF7a:P45L combination has been steadily high between April and October, and it remained the dominant clade throughout this period. 2021 medRxiv Result SARS_CoV_2 K81N;P45L 26;37 30;41 ORF7a;Nsp2 31;21 36;25 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. The nsp2:K81N+ORF7a:P45L combination is rare among GISAID Delta samples worldwide (2.3%); outside Russia, its frequency is the highest in Moldova (100%; 9 out of 9 samples), followed by Ecuador (86%; 76 out of 89 samples), Kazakhstan (76%; 32 out of 42 samples) and Latvia (73%; 52 out of 71 samples). 2021 medRxiv Result SARS_CoV_2 K81N;P45L 9;20 13;24 ORF7a;Nsp2 14;4 19;8 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. The ORF7a:P45L mutation has been gained and lost repeatedly according to the global UShER tree. 2021 medRxiv Result SARS_CoV_2 P45L 10 14 ORF7a 4 9 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. The presence of the nsp2:K81N mutation puts these 92.4% of Russian Delta samples in the recently designated AY.122 pango lineage. 2021 medRxiv Result SARS_CoV_2 K81N 25 29 Nsp2 20 24 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. The success of the AY.122+ORF7a:P45L combination is probably not due to increased fitness. 2021 medRxiv Result SARS_CoV_2 P45L 32 36 ORF7a 26 31 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. To explain the success of the nsp2:K81N+ORF7a:P45L combination in Russia, we hypothesized that it could arise from fitness advantage conferred by these two mutations. 2021 medRxiv Result SARS_CoV_2 K81N;P45L 35;46 39;50 ORF7a;Nsp2 40;30 45;34 34910734 Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. In the dog, cat, gorilla, lion, and tiger, Y505H and Y453F were the most common mutations followed by Y145del, Y144del, and V70I in S protein. 2021 PloS one Result SARS_CoV_2 V70I;Y144del;Y145del;Y453F;Y505H 124;111;102;53;43 128;118;109;58;48 S 132 133 34910734 Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. Mink variant mutation in spike protein (spike_Y453F) was more common in SARS-CoV-2 strains from American mink than that of European mink. 2021 PloS one Result SARS_CoV_2 Y453F 46 51 S;S 25;40 30;45 34910734 Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. Other commonly found mutations were Y453F (50.3%), S194L (49.4%), R203K (49.1%), and G204R (47.6%) in N protein of mink (Fig 13). 2021 PloS one Result SARS_CoV_2 G204R;R203K;S194L;Y453F 85;66;51;36 90;71;56;41 N 102 103 34910734 Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. Similarly, lions have some unique mutations like E583V, G496D, S50L, Q613R, A623T, Y505H, A623I (Fig 12). 2021 PloS one Result SARS_CoV_2 A623I;A623T;E583V;G496D;Q613R;S50L;Y505H 90;76;49;56;69;63;83 95;81;54;61;74;67;88 34910734 Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. Some mutations in S protein like L54F, P681L, L18F, S494P, Q613H, L560P, T299A, V1104L, L1063F, Q675R, D138Y, A522S, A845S were only detected in cat, not in any other animal species. 2021 PloS one Result SARS_CoV_2 A522S;A845S;D138Y;L1063F;L18F;L54F;L560P;P681L;Q613H;Q675R;S494P;T299A;V1104L 110;117;103;88;46;33;66;39;59;96;52;73;80 115;122;108;94;50;37;71;44;64;101;57;78;86 S 18 19 34910734 Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. The D614G in spike protein and P323L in non-structural protein 12 (NSP12) were the most prevalent (95.2%) mutations in minks. 2021 PloS one Result SARS_CoV_2 D614G;P323L 4;31 9;36 S;Nsp12 13;67 18;72 34912372 Hotspot Mutations in SARS-CoV-2. Also, the mutation T478K, which is unique to the Delta variant, is known to facilitate antibody escape. 2021 Frontiers in genetics Result SARS_CoV_2 T478K 19 24 34912372 Hotspot Mutations in SARS-CoV-2. For example, it can be seen from both the figures that both P681H and P681R, which are part of the variant of concerns Alpha or B.1.1.7 and Delta or B.1.617.2, have evolved over time globally and for India as well. 2021 Frontiers in genetics Result SARS_CoV_2 P681H;P681R 60;70 65;75 34912372 Hotspot Mutations in SARS-CoV-2. It can be observed from the figures that the popular mutation D614G, which is common in all the variants though predominant in the earlier months of the pandemic, has waned over time. 2021 Frontiers in genetics Result SARS_CoV_2 D614G 62 67 34912372 Hotspot Mutations in SARS-CoV-2. Please note that mutations like G28881A and G28883C may have an impact on antigenicity of Nucleocapsid protein. 2021 Frontiers in genetics Result SARS_CoV_2 G28881A;G28883C 32;44 39;51 N 90 102 34912372 Hotspot Mutations in SARS-CoV-2. Some important hotspot mutations like H69-, V70-, Y144-, A222V, N501Y, A570D, P681H, and P681R identified in this study are associated with the different SARS-CoV-2 variants of concern like Alpha, Beta, Gamma, and Delta. 2021 Frontiers in genetics Result SARS_CoV_2 A222V;A570D;N501Y;P681H;P681R 57;71;64;78;89 62;76;69;83;94 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Additionally, in March when the D614G mutation became predominant in Japan, there was an increase of cough searches much greater than the increase of searches of fever that continued in April (Fig 4F). 2021 PLoS computational biology Result SARS_CoV_2 D614G 32 37 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Because we observed that symptom order changes by viral variant between the initial outbreak in China and the subsequent outbreak in the USA and in Japan and studies link the D614G mutation with changes in disease pathology, we hypothesized that these changes in likely symptom order are not due to comorbidities of the patients. 2021 PLoS computational biology Result SARS_CoV_2 D614G 175 180 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Furthermore, the magnitudes of these changes indicate that more people were searching these terms in March 2020 than the previous year, as the number of D614G patients increased throughout Japan. 2021 PLoS computational biology Result SARS_CoV_2 D614G 153 158 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Given the evidence that the D614G variant affects symptom order, we tested the effect of potential confounding factors on symptom order. 2021 PLoS computational biology Result SARS_CoV_2 D614G 28 33 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. However, after the D614G mutation became prominent in Japan, the order of symptoms matched the USA. 2021 PLoS computational biology Result SARS_CoV_2 D614G 19 24 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. If the hypothesis that symptom order depends on D614G mutation is correct, the order of symptoms should change in a population as the D614G mutation becomes more prominent. 2021 PLoS computational biology Result SARS_CoV_2 D614G;D614G 48;134 53;139 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. In order to further elucidate the relationship between symptom order and the D614G mutation, we implemented the Stochastic Progression Model as we did above to model two datasets from two other geographical regions with available symptom frequency data. 2021 PLoS computational biology Result SARS_CoV_2 D614G 77 82 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Region does not seem to affect symptom order, as we have analyzed the symptom order in China, Hong Kong, and Japan for the Wuhan reference strain and in the USA and Brazil for the D614G variant (Figs 1, 3, and 4). 2021 PLoS computational biology Result SARS_CoV_2 D614G 180 185 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. So, we implemented the Stochastic Progression Model once again and created Hasse Diagrams to mathematically model a dataset from Japan from before the D614G mutation was prominent (Fig 4A) and a dataset from Japan that consisted of mostly cases after the D614G mutation emerged (Fig 4B). 2021 PLoS computational biology Result SARS_CoV_2 D614G;D614G 151;255 156;260 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Symptom order in Japan changes with introduction of D614G variant. 2021 PLoS computational biology Result SARS_CoV_2 D614G 52 57 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. The D614G mutation in SARS-CoV-2 has been linked to COVID-19 pathology, as it results in higher viral infectivity and antigenicity, so the mutation might also affect order and prevalence of symptoms. 2021 PLoS computational biology Result SARS_CoV_2 D614G 4 9 COVID-19 52 60 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. The datasets we analyzed report differing median and interquantile ranges (IQR) of the age of the patients, so we investigated the effect of age on likely symptom order using a dataset characterized by the Wuhan reference strain and one characterized by the D614G variant. 2021 PLoS computational biology Result SARS_CoV_2 D614G 258 263 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. The time of data collection for the dataset from Hong Kong was during a period of the Wuhan reference strain dominating the region, whereas the D614G variant was predominant in Brazil at the time of that study. 2021 PLoS computational biology Result SARS_CoV_2 D614G 144 149 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. The Wuhan reference strain was dominant in Asia during the China study, but the D614G mutation was highly prevalent in North America during the USA study. 2021 PLoS computational biology Result SARS_CoV_2 D614G 80 85 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Therefore, these results support the notion that the likely order of symptoms in COVID-19 predicted by our model is linked to the D614G mutation in SARS-CoV-2. 2021 PLoS computational biology Result SARS_CoV_2 D614G 130 135 COVID-19 81 89 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. These results support the notion that the D614G variant induces a different symptom order in symptomatic patients. 2021 PLoS computational biology Result SARS_CoV_2 D614G 42 47 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Thus, before the D614G mutation became prominent in Japan, the order of symptoms matched China. 2021 PLoS computational biology Result SARS_CoV_2 D614G 17 22 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Thus, for both the Wuhan reference strain (Fig 5C) and the D614G variant (S14 Fig), we found that the most likely order of symptom onset did not change by age group. 2021 PLoS computational biology Result SARS_CoV_2 D614G 59 64 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Uniquely, patients in Japan initially had the Wuhan reference strain until the D614G variant was first found there in early March. 2021 PLoS computational biology Result SARS_CoV_2 D614G 79 84 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Additionally, the positioning of K31 within ACE2 is shifted relative to the D614G spike, adopting a position within pi-cation bonding distance to Y489 within the RBD (Figure S4M). 2021 Cell reports Result SARS_CoV_2 D614G 76 81 S;RBD 82;162 87;165 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Analysis of the D614G + N501Y + E484K mutant spike in complex with ACE2 reveals local rearrangements resulting in unambiguous rotamer placement of both H34 within ACE2 and Q493 within the spike RBD (Figures 3C, S4G, and S4M). 2021 Cell reports Result SARS_CoV_2 D614G;E484K;N501Y 16;32;24 21;37;29 S;S;RBD 45;188;194 50;193;197 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Compared with wild-type (D614G), spikes harboring combinations of RBD mutations found in circulating variants exhibited increased ACE2 binding affinities. 2021 Cell reports Result SARS_CoV_2 D614G 25 30 S;RBD 33;66 39;69 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. D614G + L452R. 2021 Cell reports Result SARS_CoV_2 L452R;D614G 8;0 13;5 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. D614G + N501Y + E484K + K417T/N. 2021 Cell reports Result SARS_CoV_2 E484K;K417N;K417N;K417T;N501Y;D614G 16;24;24;24;8;0 21;30;31;31;13;5 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. D614G + N501Y + E484K. 2021 Cell reports Result SARS_CoV_2 E484K;N501Y;D614G 16;8;0 21;13;5 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. D614G + N501Y. 2021 Cell reports Result SARS_CoV_2 N501Y;D614G 8;0 13;5 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Figure S4R shows the increase in electropositivity at position 452 upon L452R substitution, with position 452 approximately 13 A away from the highly electronegative site on ACE2 centered at E35. 2021 Cell reports Result SARS_CoV_2 L452R 72 77 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. In addition to solvation effects, the L452R substitution introduces a positive charge at position 452 that may increase the electrostatic complementarity between the RBD and ACE2. 2021 Cell reports Result SARS_CoV_2 L452R 38 43 RBD 166 169 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. In contrast to the D614G + N501Y + E484K-ACE2 complex, H34 rotamer placement is ambiguous within these complexes, with the predominant densities corresponding to H34 facing toward the K484 interface. 2021 Cell reports Result SARS_CoV_2 D614G;E484K;N501Y 19;35;27 24;40;32 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. In order to assess if such patterns of evolution are due to incompatibility of these mutations, we constructed and expressed recombinant spike ectodomains combining L452R with the full complement of either B.1.351 and P.1 RBD mutations and evaluated ACE2 and antibody binding of these mutants (Figures S5A-S5C). 2021 Cell reports Result SARS_CoV_2 L452R 165 170 S;RBD 137;222 142;225 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Interestingly, the K417N mutation reduced ACE2 affinity to a greater extent than the K417T mutation (both in isolation and when combined with D614G + N510Y + E484K). 2021 Cell reports Result SARS_CoV_2 D614G;E484K;K417N;K417T;N510Y 142;158;19;85;150 147;163;24;90;155 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Mutations at the 417 position (K417N/T) decreased the affinity for ACE2 both in isolation (D614G + K417N/T) and when introduced into the D614G + N501Y + E484K construct. 2021 Cell reports Result SARS_CoV_2 D614G;E484K;K417N;K417T;N501Y;D614G;K417N;K417T 137;153;99;99;145;91;31;31 142;158;106;106;150;96;38;38 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Mutations E484K, L452R, and K417N/T facilitate decreased antibody binding. 2021 Cell reports Result SARS_CoV_2 E484K;K417N;K417T;L452R 10;28;28;17 15;35;35;22 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Similarly, the E484K mutation resulted in loss of binding to ab8 (class 2) and S2M11, highlighting the critical nature of E484 within the epitopes of these antibodies. 2021 Cell reports Result SARS_CoV_2 E484K 15 20 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Structural comparison of D614G-ACE2 and D614G + L452R-ACE2 complexes reveals no significant changes at the RBD-ACE2 interface (Figures 3F and S4P), indicating that the enhanced ACE2 affinity afforded by L452R is not due to modulation of direct ACE2 contacts. 2021 Cell reports Result SARS_CoV_2 D614G;D614G;L452R;L452R 25;40;48;203 30;45;53;208 RBD 107 110 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Taken together, these results demonstrate that the amalgamation of spike RBD mutations present in circulating VoC/VoIs enables increased ACE2 affinity, which is driven mainly by N501Y (B.1.1.7), L452R (B.1.427/B.1.429), and the combinatorial effect of both N501Y and E484K (P.1, B.1.351, and VOC 202102/02). 2021 Cell reports Result SARS_CoV_2 E484K;L452R;N501Y;N501Y 267;195;178;257 272;200;183;262 S;RBD 67;73 72;76 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. The addition of L452R to both constructs preserved the antibody-evasive properties for K417N/T against ab1 and E484K against both ab8 and S2M11 (Figure S5C). 2021 Cell reports Result SARS_CoV_2 E484K;K417N;K417T;L452R 111;87;87;16 116;94;94;21 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. The apo- and ACE2-complexed S protein structures show no significant global changes in secondary or quaternary structure as a result of the various mutations compared with D614G (Figure S4A). 2021 Cell reports Result SARS_CoV_2 D614G 172 177 S 28 29 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. The cryo-EM structure of ACE2 bound to the D614G + N501Y mutant spike (Figures 3B and S4C) shows the same features at the RBD-ACE2 interface as in our previously reported structure of the N501Y-ACE2 complex in the absence of the D614G mutation (Figures 3A and S4B). 2021 Cell reports Result SARS_CoV_2 D614G;D614G;N501Y;N501Y 43;229;51;188 48;234;56;193 S;RBD 64;122 69;125 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. The individual addition of N501Y, E484K, or L452R mutations increased ACE2 binding affinity, and the increased affinity conferred by the N501Y and E484K mutations in isolation was preserved in combination in the D614G + N501Y + E484K construct, yielding the highest affinity ACE2 binder. 2021 Cell reports Result SARS_CoV_2 D614G;E484K;E484K;E484K;L452R;N501Y;N501Y;N501Y 212;34;147;228;44;27;137;220 217;39;152;233;49;32;142;225 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. The N501Y, E484K, and L452R mutations drive increased S protein-ACE2 binding affinity. 2021 Cell reports Result SARS_CoV_2 E484K;L452R;N501Y 11;22;4 16;27;9 S 54 55 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. The resulting H34 rotamer yields space that accommodates an alternative Q493 rotamer closer to ACE2 relative to the D614G spike, allowing it to be positioned within hydrogen-bonding distance of the main chain carbonyl of H34. 2021 Cell reports Result SARS_CoV_2 D614G 116 121 S 122 127 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. These results indicate that although the L452R mutation is not mutually exclusive with the complement of RBD mutations in B.1.351 and P.1 variants with regard to reduction of neutralizing antibody binding, the increase in ACE2 binding affinity conferred by the L452R mutation in isolation (Figures 2A and 2B) is absent when combined with B.1.351 and P.1 RBD mutations. 2021 Cell reports Result SARS_CoV_2 L452R;L452R 41;261 46;266 RBD;RBD 105;354 108;357 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. These subtle changes in intermolecular interactions enabled upon H34 repositioning suggest a basis for the enhanced ACE2 affinity observed for the D614G + N501Y + E484K mutant spike relative to D614G + N501Y. 2021 Cell reports Result SARS_CoV_2 D614G;D614G;E484K;N501Y;N501Y 147;194;163;155;202 152;199;168;160;207 S 176 181 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Thus, in contrast to the local rearrangements observed at the RBD-ACE2 interface for the N501Y, E484K, and K417N/T mutations, the binding effect of the L452R mutation is likely mediated by solvation and/or electrostatic complementarity effects. 2021 Cell reports Result SARS_CoV_2 E484K;K417N;K417T;L452R;N501Y 96;107;107;152;89 101;114;114;157;94 RBD 62 65 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Variants harbouring N501Y exhibit a spectrum of additional RBD mutations (B.1.1.7: N501Y; VOC 202102/02: E484K, N501Y; B.1.351: E484K, N501Y, K417N; and P.1: E484K, N501Y, K417T), while variants containing L452R (B.1.427/B.1.429) seemingly exclude N501Y, K417N/T, and E484K mutations, though there has been a recent report of E484Q co-mutation with L452R in India (B.1.617.1). 2021 Cell reports Result SARS_CoV_2 E484K;E484K;E484K;E484K;E484Q;K417N;K417N;K417T;K417T;L452R;L452R;N501Y;N501Y;N501Y;N501Y;N501Y;N501Y 105;128;158;268;326;142;255;255;172;206;349;20;83;112;135;165;248 110;133;163;273;331;147;262;262;177;211;354;25;88;117;140;170;253 RBD 59 62 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. A root mean square deviation (RMSD) based clustering of the simulation trajectories for the three systems (Wild-type RBD-ACE2, N501Y RBD-ACE2, and E484K-ACE2) is shown in. 2022 International immunopharmacology Result SARS_CoV_2 E484K;N501Y 147;127 152;132 RBD;RBD 117;133 120;136 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Analysis of the solvent-accessible surface area (SASA) of RBD reveals that the interfacial areas packed between the mutants (N501Y and E484K) spike RBD and ACE2 are higher than the wild-type RBD. 2022 International immunopharmacology Result SARS_CoV_2 E484K;N501Y 135;125 140;130 S;RBD;RBD;RBD 142;58;148;191 147;61;151;194 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. As a result, the conformational ensemble sampled during the simulation timescale for the wild-type SARS-CoV2 RBD-B38, E484K RBD-B38, and N501Y RBD-B38 is different with almost no overlap. 2022 International immunopharmacology Result SARS_CoV_2 E484K;N501Y 118;137 123;142 RBD;RBD;RBD 109;124;143 112;127;146 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Binding affinity predictions of wild-type, E484K and N501Y RBD to B38 antibody using potential of mean force calculations. 2022 International immunopharmacology Result SARS_CoV_2 E484K;N501Y 43;53 48;58 RBD 59 62 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. But the E484K mutant RBD shows an increase in hydrogen bonding interactions with the L-chain during the simulation. 2022 International immunopharmacology Result SARS_CoV_2 E484K 8 13 RBD 21 24 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. E484K and N501Y mutants show higher binding affinity to hACE2 compared to wild-type RBD: Evidences from free-energy calculations. 2022 International immunopharmacology Result SARS_CoV_2 N501Y;E484K 10;0 15;5 RBD 84 87 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. E484K and N501Y mutations alter the interaction profiles of RBD-ACE2 interface. 2022 International immunopharmacology Result SARS_CoV_2 N501Y;E484K 10;0 15;5 RBD 60 63 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. E484K RBD-ACE2 complex visited the least number of clusters during the simulation, further indicating high stabilization of the complex. 2022 International immunopharmacology Result SARS_CoV_2 E484K 0 5 RBD 6 9 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Equilibrium molecular dynamics simulations have been used to underscore the effect of the E484K and N501Y RBD mutations on ACE2 recognition. 2022 International immunopharmacology Result SARS_CoV_2 E484K;N501Y 90;100 95;105 RBD 106 109 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Equilibrium simulations indicate that both N501Y and E484K mutations stabilize the RBM upon complexation with ACE2. 2022 International immunopharmacology Result SARS_CoV_2 E484K;N501Y 53;43 58;48 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Further RMSD based clustering is used to identify the most populated solution structure of wild-type, N501Y, and E484K RBD complexed with ACE2. 2022 International immunopharmacology Result SARS_CoV_2 E484K;N501Y 113;102 118;107 RBD 119 122 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. However, the N501Y RBD mutation alters interfacial packing. 2022 International immunopharmacology Result SARS_CoV_2 N501Y 13 18 RBD 19 22 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. However, the RBM of the N501Y mutant spike loses critical contact with the H-chain of the antibody due to the upward curvature of a loop region. 2022 International immunopharmacology Result SARS_CoV_2 N501Y 24 29 S 37 42 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. In contrast, N501Y mutant RBD forms less number of interfacial hydrogen bonds. 2022 International immunopharmacology Result SARS_CoV_2 N501Y 13 18 RBD 26 29 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. In the root mean square deviation (RMSD) and radius of gyration (Rg) space, wild-type RBD dynamics are confined rather narrowly compared to the N501Y mutant when complexed with the ACE2. 2022 International immunopharmacology Result SARS_CoV_2 N501Y 144 149 RBD 86 89 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Interactions of wild-type, N501Y and E484K mutant RBDs with a neutralizing antibody, B38: Insights from the equilibrium simulations. 2022 International immunopharmacology Result SARS_CoV_2 E484K;N501Y 37;27 42;32 RBD 50 54 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Interactions of wild-type, N501Y and E484K mutant RBDs with ACE2: Insights from equilibrium simulations. 2022 International immunopharmacology Result SARS_CoV_2 E484K;N501Y 37;27 42;32 RBD 50 54 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. N501Y mutant RBD forms a specific hydrogen bond involving Ser477 of the RBD. 2022 International immunopharmacology Result SARS_CoV_2 N501Y 0 5 RBD;RBD 13;72 16;75 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. N501Y mutation further decreases the hydrogen bonding interaction with the L-chain. 2022 International immunopharmacology Result SARS_CoV_2 N501Y 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. N501Y mutation in the RBD also mildly stabilizes this region. 2022 International immunopharmacology Result SARS_CoV_2 N501Y 0 5 RBD 22 25 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. N501Y mutation increases the number of clusters visited during the simulation. 2022 International immunopharmacology Result SARS_CoV_2 N501Y 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. On the other hand, the E484K RBD mutation significantly stabilizes the complex. 2022 International immunopharmacology Result SARS_CoV_2 E484K 23 28 RBD 29 32 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Particularly, the E484K RBD loses a higher number of hydrogen bonding interactions during the simulation. 2022 International immunopharmacology Result SARS_CoV_2 E484K 18 23 RBD 24 27 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Root mean square fluctuations also reveal that E484K mutation highly stabilized the RBM upon complexation with the ACE2. 2022 International immunopharmacology Result SARS_CoV_2 E484K 47 52 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The 4th, 5th, and 1st cluster conformations are the most stable during the simulation timescale for wild-type RBD-B38, E484K RBD-B38, and N501Y RBD-B38, respectively. 2022 International immunopharmacology Result SARS_CoV_2 E484K;N501Y 119;138 124;143 RBD;RBD;RBD 110;125;144 113;128;147 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The complex structure is used to explore the effect of both the E484K and N501Y RBM mutations on the B38 monoclonal antibody recognition. 2022 International immunopharmacology Result SARS_CoV_2 E484K;N501Y 64;74 69;79 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The conformational space sampled during the molecular dynamics simulations by the E484K spike mutant is more confined in RMSD and Rg space, reconfirming high stabilization of the complex. 2022 International immunopharmacology Result SARS_CoV_2 E484K 82 87 S 88 93 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The E484K mutant RBD loses all the pi-cation interactions in addition to the loss of several hydrogen-bonding interactions with the B38 antibody. 2022 International immunopharmacology Result SARS_CoV_2 E484K 4 9 RBD 17 20 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The E484K mutant RBD showed a remarkably higher affinity towards ACE2 with the calculated binding free energy of -210 kJ/mol. 2022 International immunopharmacology Result SARS_CoV_2 E484K 4 9 RBD 17 20 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The E484K mutation allows Lys484 of the RBM to form specific hydrogen bonds with ACE2. 2022 International immunopharmacology Result SARS_CoV_2 E484K 4 9 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The E484K mutation disrupts most of the hydrophobic interactions involved in ACE2 recognition. 2022 International immunopharmacology Result SARS_CoV_2 E484K 4 9 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The E484K RBD is packed tightly to the ACE2 PD surface during the simulation. 2022 International immunopharmacology Result SARS_CoV_2 E484K 4 9 RBD 10 13 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The gain in binding affinity for the N501Y mutant to the ACE2 is due to the improved pi-pi and pi-cation interactions. 2022 International immunopharmacology Result SARS_CoV_2 N501Y 37 42 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The N501Y mutant RBD interacts more strongly with the ACE2. 2022 International immunopharmacology Result SARS_CoV_2 N501Y 4 9 RBD 17 20 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The N501Y mutant RDB gains few pi-pi stacking and pi-cation interactions during antibody recognition. 2022 International immunopharmacology Result SARS_CoV_2 N501Y 4 9 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The N501Y mutation in spike RBM induces dynamics in the complex. 2022 International immunopharmacology Result SARS_CoV_2 N501Y 4 9 S 22 27 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The Phe486 of RBD creates additional pi-pi stacking interaction with Tyr83 of ACE2, which is also present in the N501Y RBD-ACE2 complex. 2022 International immunopharmacology Result SARS_CoV_2 N501Y 113 118 RBD;RBD 14;119 17;122 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The RBM forms many contacts with both the H and L chains, and E484K mutant RBM shows very similar protein-protein contacts with the binding interface of the B38 antibody. 2022 International immunopharmacology Result SARS_CoV_2 E484K 62 67 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The region from 480-486 is highly stabilized in E484K mutated RBD compared to the wild-type. 2022 International immunopharmacology Result SARS_CoV_2 E484K 48 53 RBD 62 65 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The wild-type and E484K RBD-ACE2 complexes show similar interfacial packing. 2022 International immunopharmacology Result SARS_CoV_2 E484K 18 23 RBD 24 27 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The work highlights that the E484K and N501Y are gain-of-function mutants. 2022 International immunopharmacology Result SARS_CoV_2 E484K;N501Y 29;39 34;44 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. These high-affinity interactions allow E484K mutant RBD to be firmly bound to the ACE2 interface. 2022 International immunopharmacology Result SARS_CoV_2 E484K 39 44 RBD 52 55 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. This intense encounter of E484K RBD to ACE2 allows the remodeling of few interfacial residues. 2022 International immunopharmacology Result SARS_CoV_2 E484K 26 31 RBD 32 35 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. This interaction is evident in the wild-type and N501Y mutant but lost upon E484K mutation. 2022 International immunopharmacology Result SARS_CoV_2 E484K;N501Y 76;49 81;54 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. This signifies tight interfacial packing between RBD and ACE2 in the case of both N501Y and E484K mutants. 2022 International immunopharmacology Result SARS_CoV_2 E484K;N501Y 92;82 97;87 RBD 49 52 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Thus, the loss of many hydrogen-bonding interactions with the antibody accounts for the reduced binding affinity of the N501Y mutant. 2022 International immunopharmacology Result SARS_CoV_2 N501Y 120 125 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Tyr449, Asn460, Ser494, Tyr495, Thr500, and Gly502 lose hydrogen bonding interactions with the antibody for the E484K mutant. 2022 International immunopharmacology Result SARS_CoV_2 E484K 112 117 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Upon N501Y mutation, the Tyr501 gains van der Waals contacts with the ACE2 interface. 2022 International immunopharmacology Result SARS_CoV_2 N501Y 5 10 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. A total of 545 sequences (including incomplete and low-quality sequences) were uploaded, of which 108 sequences had D614G mutation in the spike protein, and 96 sequences had P323L mutation in NSP12. 2021 Frontiers in medicine Result SARS_CoV_2 D614G;P323L 116;174 121;179 S;Nsp12 138;192 143;197 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. Among the latter, SARS-CoV-2 with the D614G spike protein mutation was the main input. 2021 Frontiers in medicine Result SARS_CoV_2 D614G 38 43 S 44 49 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. Eight single nucleotide polymorphisms (SNPs) were identified, including C242T, C313T, C3037T, C14408T, A23403G, G28881A, G28882A, and G28883C. 2021 Frontiers in medicine Result SARS_CoV_2 A23403G;C14408T;C242T;C3037T;C313T;G28881A;G28882A;G28883C 103;94;72;86;79;112;121;134 110;101;77;92;84;119;128;141 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. In addition, these mutations were expressed as amino acid changes in the spike (D614G), Nsp12 (P323L), and N proteins (R203K and G204R). 2021 Frontiers in medicine Result SARS_CoV_2 G204R;D614G;P323L;R203K 129;80;95;119 134;85;100;124 S;Nsp12;N 73;88;107 78;93;108 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. Previous studies found that SARS-CoV-2 sequences with the D614G mutation were predominant in European countries. 2021 Frontiers in medicine Result SARS_CoV_2 D614G 58 63 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. The mixed D614G mutation and other multiple mutations formed multiple branches. 2021 Frontiers in medicine Result SARS_CoV_2 D614G 10 15 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. We downloaded the complete high-quality SARS-CoV-2 sequences of all spike protein D614G mutations in Spain before March 11, and used them to construct a phylogenetic tree (Figure 3). 2021 Frontiers in medicine Result SARS_CoV_2 D614G 82 87 S 68 73 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. A large group of mAbs (Beta-6, -10, -23, -24, -30, -40, -54, -55, -56) showed good neutralization of Alpha, Beta, Gamma, and Alpha+ viruses, with either reduced or completely absent neutralization of Victoria, B.1.525 (E484K), and Delta viruses (Figure 2B). 2022 Cell host & microbe Result SARS_CoV_2 E484K 219 224 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Alpha, Beta, and Gamma have a single mutation in common, N501Y, and we propose that the presence of the N501Y mutation creates an epitope for RBD recognition in Beta infection. 2022 Cell host & microbe Result SARS_CoV_2 N501Y;N501Y 57;104 62;109 RBD 142 145 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. For example, Beta-44, sensitive to L452R/T478K mutations, is perched adjacent to residue 478, while mAbs, Beta-20, -22, and -29 suggested to recognize an epitope related to residue 417 are tightly clustered atop this residue. 2022 Cell host & microbe Result SARS_CoV_2 L452R;T478K 35;41 40;46 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Four representative mAbs from different epitope classes were selected: Beta-20, which recognizes the K417N/T mutation and can potently neutralize Beta and to a lesser extent Gamma, Beta-24, which is specific to the N501Y mutation present in Alpha, Beta, and Gamma, Beta-26, which recognizes the E484K mutation found in Beta and Gamma, and Beta-27, the IgVH3-53 fully cross-reactive mAb, which neutralizes all variants similarly. 2022 Cell host & microbe Result SARS_CoV_2 E484K;K417N;K417T;N501Y 295;101;101;215 300;108;108;220 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. However, Alpha also contains the mutation D614G, which is not found in Victoria/Wuhan, we therefore went back and tested neutralization of a version of the early pandemic virus (B.1) containing the additional D614G mutation, using 17 Alpha sera. 2022 Cell host & microbe Result SARS_CoV_2 D614G;D614G 42;209 47;214 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. MAb Beta-26 requires the Beta E484K mutation for potent neutralization but is also exquisitely sensitive to the L452R/T478K mutations found in Delta. 2022 Cell host & microbe Result SARS_CoV_2 E484K;L452R;T478K 30;112;118 35;117;123 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Of the point mutations in the NTD (L18F, D80A, D215G, and R246I) only L18F is part of the epitope. 2022 Cell host & microbe Result SARS_CoV_2 D215G;D80A;L18F;R246I;L18F 47;41;70;58;35 52;45;74;63;39 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. The E484K mutation disrupts the binding of many potent mAbs generated from cases infected with early pandemic viruses, and we expected Lys-484 to be recognized by Beta-neutralizing mAbs. 2022 Cell host & microbe Result SARS_CoV_2 E484K 4 9 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. The serological data shows good correlation with this (Figure 2D), H2 fails to reach Lys-484 hence this mutation has little impact on binding, whereas the N501Y mutation has a positive impact on binding but K417N/T is also required for effective neutralization. 2022 Cell host & microbe Result SARS_CoV_2 K417N;K417T;N501Y 207;207;155 214;214;160 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Three mAbs, Beta-20, -22, and -29 showed maximum activity toward Beta and Gamma, suggesting that they recognize an epitope related to the K417N/T changes in Beta and Gamma, respectively. 2022 Cell host & microbe Result SARS_CoV_2 K417N;K417T 138;138 145;145 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. We performed live virus neutralization assays using the following viruses, containing the indicated changes in the RBD: Victoria (an early Wuhan related strain), Alpha (N501Y), Beta (K417N, E484K, and N501Y), Gamma (K417T, E484K, and N501Y), Delta (L452R and T478K), Alpha+E484K (E484K and N501Y), and B.1.525 (E484K) (Figures 2A-2F; Table S1A). 2022 Cell host & microbe Result SARS_CoV_2 E484K;E484K;N501Y;N501Y;N501Y;T478K;E484K;E484K;K417N;K417T;L452R;N501Y;E484K 190;223;201;234;290;259;280;311;183;216;249;169;273 195;228;206;239;295;264;285;316;188;221;254;174;278 RBD 115 118 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. We propose Beta-44 is sensitive to L452R/T478K mutations while Beta-26, -34, and -51 recognize an epitope composed of Glu-484 + Leu-452/Thr-478 (Figures 2C and 2E). 2022 Cell host & microbe Result SARS_CoV_2 L452R;T478K 35;41 40;46 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. D260Y mutation enhanced the binding with TBK1. 2021 Frontiers in microbiology Result SARS_CoV_2 D260Y 0 5 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Except for a minor deviation between 20-22 and 46-50 ns, the overall dynamics of the D260Y mutant revealed a very stable behavior, with an average RMSD of 0.3A. 2021 Frontiers in microbiology Result SARS_CoV_2 D260Y 85 90 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Furthermore, the M429I mutant demonstrated similar deviations as the WT, P77L, and Q88H mutant. 2021 Frontiers in microbiology Result SARS_CoV_2 M429I;P77L;Q88H 17;73;83 22;77;87 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Gln588-Gly17, Arg228-Lys192, Lys584-Arg22, Arg405-His230, and Tyr592-Asn51 formed hydrogen bonds between TBK1 and E341D mutant (Figure 4A). 2021 Frontiers in microbiology Result SARS_CoV_2 E341D 114 119 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. In contrast, D260Y and E341D displayed a more stable dynamic trend than the other complexes. 2021 Frontiers in microbiology Result SARS_CoV_2 D260Y;E341D 13;23 18;28 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Indeed at amino acid position 77, NSP13 was mutated, i.e., P77L. 2021 Frontiers in microbiology Result SARS_CoV_2 P77L 59 63 Nsp13 34 39 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Moreover, its NSP13 protein also harbored mutation at amino acid 88, i.e., Q88H. 2021 Frontiers in microbiology Result SARS_CoV_2 Q88H 75 79 Nsp13 14 19 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. On the other hand, the P77L mutant also exhibits a similar pattern of RMSD to the WT. 2021 Frontiers in microbiology Result SARS_CoV_2 P77L 23 27 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Similarly, the Q88H exhibited more frequent fluctuations between 480 and 550. 2021 Frontiers in microbiology Result SARS_CoV_2 Q88H 15 19 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Similarly, with few structural deviations between 15-20, 32-40, and 41-42 ns, the mean RMSD was also reported to be 0.3A for E341D. 2021 Frontiers in microbiology Result SARS_CoV_2 E341D 125 130 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. The average RMSD for M429I was 0.65A; however, an increasing trend was reported - for instance, a previous study reported that mutations with increasing instability produce the function of radical protein, implying that these mutations have evolved with radical function and have increased infectivity. 2021 Frontiers in microbiology Result SARS_CoV_2 M429I 21 26 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. The average value for the Q88H was reported to be higher; however, the Rg remained unchanged after 10 ns. 2021 Frontiers in microbiology Result SARS_CoV_2 Q88H 26 30 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. The binding energies for NSP13 WT and mutant P77L, Q88H, D260Y, E341D, and M429I were -74.72, -84.64, -91.36, -90.80, -85.17, and -81.98 kcal/mol, respectively. 2021 Frontiers in microbiology Result SARS_CoV_2 D260Y;E341D;M429I;P77L;Q88H 57;64;75;45;51 62;69;80;49;55 Nsp13 25 30 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. The compactness of P77L was different from the WT. 2021 Frontiers in microbiology Result SARS_CoV_2 P77L 19 23 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. The D260Y and M429I demonstrated a similar behavior. 2021 Frontiers in microbiology Result SARS_CoV_2 D260Y;M429I 4;14 9;19 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. The E341D mutant reported lower Rg with continuous increase or decrease in the Rg value during the simulation period. 2021 Frontiers in microbiology Result SARS_CoV_2 E341D 4 9 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. The HDOCK docking score for P77L (TBK1-P77L) was -204 kcal/mol, the substitution of amino acid highly increased the interaction of NSP13 and TBK1, and 10 hydrogen bonds, one salt bridge, and 263 non-bonded contacts were formed (Figure 2B). 2021 Frontiers in microbiology Result SARS_CoV_2 P77L;P77L 28;39 32;43 Nsp13 131 136 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. The P77L mutation was found to increase the function of the NSP13 protein by binding to TBK1 more strongly compared to WT. 2021 Frontiers in microbiology Result SARS_CoV_2 P77L 4 8 Nsp13 60 65 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. The Q88H mutation was observed to bind more stringently to TBK1 compared to WT. 2021 Frontiers in microbiology Result SARS_CoV_2 Q88H 4 8 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. The residual flexibility demonstrated variations in different regions, i.e., 10-100 and 1,000-1,150, for all the complexes except Q88H at the position 1,000-1,150. 2021 Frontiers in microbiology Result SARS_CoV_2 Q88H 130 134 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. The results from 2,500 structural frames revealed that the average number of hydrogen bonds in WT was 554, 583 in P77L, 579 in Q88H, 565 in D260Y, 585 in E341D, and 578 in M429I complex, respectively. 2021 Frontiers in microbiology Result SARS_CoV_2 D260Y;E341D;M429I;P77L;Q88H 140;154;172;114;127 145;159;177;118;131 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Therefore, it could be deduced that P77L might suppress IFNss production more stringently and make this virus more pathogenic. 2021 Frontiers in microbiology Result SARS_CoV_2 P77L 36 40 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Therefore, we determined the docking score for this mutation and found that the HDOCK docking score for D260Y (TBK1-D260Y) was observed to be -227 kcal/mol. 2021 Frontiers in microbiology Result SARS_CoV_2 D260Y;D260Y 104;116 109;121 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. This variant also has a mutation in its NSP13 at amino acid position 341, i.e., E341D. 2021 Frontiers in microbiology Result SARS_CoV_2 E341D 80 85 Nsp13 40 45 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. This variant also has a mutation in its NSP13 at amino acid position 429, i.e., M429I. 2021 Frontiers in microbiology Result SARS_CoV_2 M429I 80 85 Nsp13 40 45 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. This variant also has a mutation in NSP13 at position 260, i.e., D260Y. 2021 Frontiers in microbiology Result SARS_CoV_2 D260Y 65 70 Nsp13 36 41 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. To determine whether NSP13 mutants, compared to their WT counterpart, could affect their interaction with TBK1, mutants P77L, Q88H, D260Y, E341D, and M429I were generated by Chimera (Figures 1A-F). 2021 Frontiers in microbiology Result SARS_CoV_2 D260Y;E341D;M429I;P77L;Q88H 132;139;150;120;126 137;144;155;124;130 Nsp13 21 26 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Unlike the WT and P77L, the Q88H complex demonstrated a higher structural instability. 2021 Frontiers in microbiology Result SARS_CoV_2 P77L;Q88H 18;28 22;32 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. We determined the docking score for this mutation and found that the HDOCK docking score for M429I (TBK1-M429I) was -229 kcal/M. 2021 Frontiers in microbiology Result SARS_CoV_2 M429I;M429I 93;105 98;110 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. We determined the docking score for this mutation and found that the predicted score of HDOCK for E341D (TBK1-E341D) was -245 kcal/mol. 2021 Frontiers in microbiology Result SARS_CoV_2 E341D;E341D 98;110 103;115 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. We first determined the docking score for this mutation and found that the HDOCK docking score for Q88H (TBK1-Q88H) was -210 kcal/mol. 2021 Frontiers in microbiology Result SARS_CoV_2 Q88H;Q88H 99;110 103;114 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. A reduced (but not statistically significant) titer of anti-RBD IgG antibodies against Alpha (B.1.1.7) variant was observed for the Ad-S-F135N/N137T-immunized group, as compared to the other four immunized groups ( Figure 4B ). 2021 Frontiers in immunology Result SARS_CoV_2 N137T;F135N 143;137 148;142 RBD;S 60;135 63;136 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. A reduced (but not statistically significant) titer of anti-RBD IgG antibodies was also observed for the Ad-S-F135N/N137T-immunized group, as compared to the other four immunized groups ( Figure 3B ). 2021 Frontiers in immunology Result SARS_CoV_2 N137T;F135N 116;110 121;115 RBD;S 60;108 63;109 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Antisera from the Ad-S-R158N/Y160T-immunized group showed increased neutralization potency, as compared to those of the Ad-S and Ad-S-N370/A372T-immunized groups, and the lower levels of the Ad-S-F135N/N137T and Ad-S-H519N/P521T-immunized groups ( Figure 3C ). 2021 Frontiers in immunology Result SARS_CoV_2 A372T;N137T;P521T;Y160T;F135N;H519N;R158N 139;202;223;29;196;217;23 144;207;228;34;201;222;28 S;S;S;S;S 21;123;132;194;215 22;124;133;195;216 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Both the Ad-S-F135N/N137T and Ad-S-R158N/Y160T-immunized groups elicited more potent pseudo-neutralization against the Delta (B.1.167.2) variant, as compared to the Ad-S, Ad-S-N370/A372T, and Ad-S-H519N/P521T-immunized groups, in the first set of immunization experiments ( Figure 6C ); an approximately 3.7-fold and 4.6-fold increase in the neutralization IC-50 titer was found for the glycan-masking Ad-S-F135N/N137T and Ad-S-R158N/Y160T groups, respectively ( Figure 6D ). 2021 Frontiers in immunology Result SARS_CoV_2 A372T;N137T;N137T;P521T;Y160T;Y160T;F135N;F135N;H519N;R158N;R158N 181;20;413;203;41;434;14;407;197;35;428 186;25;418;208;46;439;19;412;202;40;433 S;S;S;S;S;S;S 12;33;168;174;195;405;426 13;34;169;175;196;406;427 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Both the Ad-S-R158N/Y160T and Ad-S-N370/A372T groups showed increased potency for pseudo-neutralization against the Beta (B.1.351) variant, as compared to the three other groups (Ad-S, Ad-S-F135N/N137T, and Ad-S-H519N/P521T-immunized) ( Figure 5C ); the neutralization IC-50 titer was approximately 6.5-fold and 2.8-fold higher in the glycan-masking Ad-S-R158N/Y160T and Ad-S-N370/A372T-immunized groups, respectively ( Figure 5D ). 2021 Frontiers in immunology Result SARS_CoV_2 A372T;A372T;N137T;P521T;Y160T;Y160T;F135N;H519N;R158N;R158N 40;381;196;218;20;361;190;212;14;355 45;386;201;223;25;366;195;217;19;360 S;S;S;S;S;S;S 12;33;182;188;210;353;374 13;34;183;189;211;354;375 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Dose-dependent pseudo-neutralization curves were observed for the Ad-S, Ad-S-N370/K356T, Ad-S-G413N, and Ad-S-D428N-immunized groups, but not for the PBS-immunized control ( Figure 3G ). 2021 Frontiers in immunology Result SARS_CoV_2 K356T;D428N;G413N 82;110;94 87;115;99 S;S;S;S 69;75;92;108 70;76;93;109 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. However, the Ad-S-D428N-immunized group displayed more potent neutralization against the Alpha (B.1.1.7) variant than the three other groups ( Figure 4G ), resulting in a 3.0-fold increase in the neutralization IC-50 titer, as compared to that of the wild-type Ad-S-immunized group ( Figure 4H ). 2021 Frontiers in immunology Result SARS_CoV_2 D428N 18 23 S;S 16;264 17;265 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. In the case of Delta (B.1.617.2) variant, we found that the anti-S1 IgG titers in the Ad-S-F135N/N137T-immunized group were lower than the wild type Ad-S and Ad-S-R158N/Y160T,-immunized groups ( Figure 6A ). 2021 Frontiers in immunology Result SARS_CoV_2 N137T;Y160T;F135N;R158N 97;169;91;163 102;174;96;168 S;S;S 89;152;161 90;153;162 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. In the case of the Beta (B.1.351) variant in the first set of immunization experiments in the Ad-S, Ad-S-F135N/N137T, Ad-S-R158N/Y160T, Ad-S- N370/A372T, and Ad-S-H519N/P521T-immunizd groups, the Ad-S-F135N/N137T-immunized group had a significantly lower IgG titer of anti-S1 antibodies than those in the wild type Ad-S and Ad-S-N370/A372T-immunized groups ( Figure 5A ). 2021 Frontiers in immunology Result SARS_CoV_2 A372T;A372T;N137T;N137T;P521T;Y160T;F135N;F135N;H519N;R158N 147;334;111;207;169;129;105;201;163;123 152;339;116;212;174;134;110;206;168;128 S;S;S;S;S;S;S;S 97;103;121;139;161;199;318;327 98;104;122;140;162;200;319;328 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. In the first set of immunization experiments in the Ad-S, Ad-S-F135N/N137T, Ad-S-R158N/Y160T, Ad-S-N370/A372T, and Ad-S-H519N/P521T-immunized groups, we found that the anti-S1 IgG titers against Alpha (B.1.1.7) variant in the Ad-S-F135N/N137T-immunized group were lower than the wild type Ad-S and Ad-S- N370/A372T-immunized groups ( Figure 4A ). 2021 Frontiers in immunology Result SARS_CoV_2 A372T;A372T;N137T;N137T;P521T;Y160T;F135N;F135N;H519N;R158N 104;309;69;237;126;87;63;231;120;81 109;314;74;242;131;92;68;236;125;86 S;S;S;S;S;S;S;S 55;61;79;97;118;229;292;301 56;62;80;98;119;230;293;302 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. In the first set of immunization experiments, Ad-S, Ad-S-F135N/N137T, Ad-S-R158N/Y160T, Ad-S-N370/A372T, and Ad-S-H519N/P521T-immunized groups showed dose-response neutralization, while the PBS-immunized control group did not ( Figure 3C ). 2021 Frontiers in immunology Result SARS_CoV_2 A372T;N137T;P521T;Y160T;F135N;H519N;R158N 98;63;120;81;57;114;75 103;68;125;86;62;119;80 S;S;S;S;S 49;55;73;91;112 50;56;74;92;113 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. In the first set of immunization experiments, the neutralization IC-50 titers elicited in the glycan-masking Ad-S-R158N/Y160T-immunized group showed a 2.5-fold increase against the Wuhan-Hu-1 ancestral strain, a 1.8-fold increase against the Alpha (B.1.1.7) variant, a 1.2-fold increase against the Beta (B.1.351) variant, but a 0.6-fold decrease against the Delta (B.1.617.2) variant ( Figure 7A ). 2021 Frontiers in immunology Result SARS_CoV_2 Y160T;R158N 120;114 125;119 S 112 113 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. In the first set of immunization experiments, the results indicated that the anti-S IgG titer elicited in the Ad-S- F135N/N137T-immunized group was significantly lower than those elicited in the wild-type Ad-S and Ad-S-R158N/Y160T-immunized groups ( Figure 3A ). 2021 Frontiers in immunology Result SARS_CoV_2 F135N;N137T;Y160T;R158N 116;122;225;219 121;127;230;224 S;S;S;S 82;113;208;217 83;114;209;218 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. In the second set of immunization experiments among the Ad-S, Ad-S-N354/K356T, Ad-S-G413N, and Ad-S-D428N-immunized groups, the pseudo-neutralization curves of the three glycan-masking groups against the Delta (B.167.2) variant were less potent than that of the wild-type Ad-S-immunized group ( Figure 6G ) with a reduced IC-50 titers to 0.46, 0.23, and 0.46 fold, respectively ( Figure 6H ). 2021 Frontiers in immunology Result SARS_CoV_2 K356T;D428N;G413N 72;100;84 77;105;89 S;S;S;S;S 59;65;82;98;275 60;66;83;99;276 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. In the second set of immunization experiments in the Ad-S, Ad-S-N354/K356T, Ad-S-G413N, and Ad-S-D428N-immunized groups, no significant differences were observed in the anti-S1 and anti-RBD titers among these four Ad immunization groups ( Figures 4E, F ). 2021 Frontiers in immunology Result SARS_CoV_2 K356T;D428N;G413N 69;97;81 74;102;86 RBD;S;S;S;S 186;56;62;79;95 189;57;63;80;96 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. In the second set of immunization experiments in the Ad-S, Ad-S-N354/K356T, Ad-S-G413N, and Ad-S-D428N-immunized groups, no significant differences were observed in the anti-S1 and anti-RBD titers among these four Ad immunization groups ( Figures 5E, F ). 2021 Frontiers in immunology Result SARS_CoV_2 K356T;D428N;G413N 69;97;81 74;102;86 RBD;S;S;S;S 186;56;62;79;95 189;57;63;80;96 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. In the second set of immunization experiments, the neutralization IC-50 titers elicited in the Ad-S-D428N-immunized group showed a 2.7-fold increase against the Wuhan-Hu-1 ancestral strain, a 3.2-fold increase against the Alpha (B.1.1.7) variant, a 2.0-fold increase against the Beta (B.1.351) variant, but a 0.2-fold decrease against the Delta (B.1.617.2) variant ( Figure 7B ). 2021 Frontiers in immunology Result SARS_CoV_2 D428N 100 105 S 98 99 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. No significant differences were observed in the anti-S and anti-RBD titers in the second set of immunization experiments with the Ad-S, Ad-S-N354/K356T, Ad-S-G413N, and Ad-S-D428N-immunized groups ( Figures 3E, F ). 2021 Frontiers in immunology Result SARS_CoV_2 K356T;D428N;G413N 146;174;158 151;179;163 RBD;S;S;S;S;S 64;53;133;139;156;172 67;54;134;140;157;173 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Seven glycan-masking N-glycan sites were engineered in the Ad-S vector: (#1) Ad-S-F135N/N137T, (#2) Ad-S-R158N/Y160T, (#3) Ad-S-N370/A372T, (#4) Ad-S-H519N/P521T, (#5) Ad-S-N354/K356T, (#6) Ad-S-G413N, and (#7) Ad-S-D428N) ( Figure 1B ). 2021 Frontiers in immunology Result SARS_CoV_2 A372T;K356T;N137T;P521T;Y160T;D428N;F135N;G413N;H519N;R158N 133;178;88;156;111;216;82;195;150;105 138;183;93;161;116;221;87;200;155;110 N 21 22 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The Ad-S-D428N-immunized group was more potent in neutralizing the Beta (B.1.351) variant than the other three groups ( Figure 5G ), resulting in a 2.0-fold increase in the neutralization IC-50 titer, as compared to that of the wild-type Ad-S-immunized group ( Figure 5H ). 2021 Frontiers in immunology Result SARS_CoV_2 D428N 9 14 S;S 7;241 8;242 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The anti-RBD IgG titer in the Ad-S-F135N/N137T-immunized group was lower, as compared to the titers in the Ad-S-R158N/Y160T and Ad-S-H519N/P521T-immunizd groups ( Figure 5B ). 2021 Frontiers in immunology Result SARS_CoV_2 N137T;P521T;Y160T;F135N;H519N;R158N 41;139;118;35;133;112 46;144;123;40;138;117 RBD;S;S;S 9;33;110;131 12;34;111;132 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The corresponding IC-50 titer elicited in the Ad-S-R158N/Y160T-immunized group against the Wuhan-Hu-1 ancestral strain was approximately 2.4-fold higher than that elicited in the wild-type Ad-S-immunized group ( Figure 3D ). 2021 Frontiers in immunology Result SARS_CoV_2 Y160T;R158N 57;51 62;56 S;S 49;192 50;193 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The glycan-masking Ad-S-D428N in RBD also elicited more potent neutralizing antibodies against the Wuhan-Hu-1 ancestral strain but only increased the cross-neutralizing antibody titers against the Alpha (B.1.1.7) and Beta (B.1.351) variants. 2021 Frontiers in immunology Result SARS_CoV_2 D428N 24 29 RBD;S 33;22 36;23 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The IC-50 titers of the Ad-S-N354/K356T and Ad-S-D428N-immunized groups against the Wuhan-Hu-1 ancestral strain were approximately 2.5- and 2.8-fold higher, as compared to that of the wild-type Ad-S-immunized group ( Figure 3H ). 2021 Frontiers in immunology Result SARS_CoV_2 K356T;D428N 34;49 39;54 S;S;S 27;47;197 28;48;198 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The pseudovirus neutralization curve of the Ad-S-R158N/Y160T-immunized group against the Alpha (B.1.1.7) variant was more potent than those of the wild-type Ad-S-immunized group and the three other immunization groups ( Figure 4C ), with an approximately 2.8-fold increase in the neutralization IC-50 titer, as compared to that of the wild-type Ad-S-immunized group ( Figure 4D ). 2021 Frontiers in immunology Result SARS_CoV_2 Y160T;R158N 55;49 60;54 S;S;S 47;160;348 48;161;349 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The results indicated the presence of S and S1 in the cell lysates of HEK293A cells infected with Ad-S, Ad-S-F135N/N137T, Ad-S-R158N/Y160T, Ad-S-N354/K356T, Ad-S-N370/A372T, Ad-S-G413N, Ad-S-D428N, and Ad-S-H519N/P521T ( Figure 2 ). 2021 Frontiers in immunology Result SARS_CoV_2 A372T;K356T;N137T;P521T;Y160T;D428N;F135N;G413N;H519N;R158N 167;150;115;213;133;191;109;179;207;127 172;155;120;218;138;196;114;184;212;132 S;S;S;S;S;S;S;S 101;107;125;143;160;177;189;205 102;108;126;144;161;178;190;206 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The titer for the Ad-S-R158N/Y160T group against the Delta (B.1.617.2) variant was still higher than the titer of Ad-S against the Delta variant ( Figure 7A ). 2021 Frontiers in immunology Result SARS_CoV_2 Y160T;R158N 29;23 34;28 S;S 21;117 22;118 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Therefore, immunization with the glycan-masking Ad-S-R158N/Y160T in NTD and glycan-masking Ad-S-N370/A372T and Ad-S-D428N in RBD were more potent than that with the wild-type Ad-S in eliciting neutralizing antibodies against the Beta (B.1.351) variant. 2021 Frontiers in immunology Result SARS_CoV_2 A372T;Y160T;D428N;R158N 101;59;116;53 106;64;121;58 RBD;S;S;S;S 125;51;94;114;178 128;52;95;115;179 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Therefore, only the glycan-masking Ad-S-F135N/N137T and Ad-S-R158N/Y160T in NTD elicited more potent neutralizing antibody titers against the Delta (B.1.617.2) variant. 2021 Frontiers in immunology Result SARS_CoV_2 N137T;Y160T;F135N;R158N 46;67;40;61 51;72;45;66 S;S 38;59 39;60 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Therefore, the glycan-masking Ad-S-R158N/Y160T in NTD and glycan-masking Ad-S-D428N in RBD were found to elicit increased titers of neutralizing antibodies against the Alpha (B.1.1.7) variant. 2021 Frontiers in immunology Result SARS_CoV_2 Y160T;D428N;R158N 41;78;35 46;83;40 RBD;S;S 87;33;76 90;34;77 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Therefore, the glycan-masking Ad-S-R158N/Y160T in NTD elicited more potent neutralizing antibodies against the Wuhan-Hu-1 ancestral strain and increased the cross-neutralizing antibody titers against the Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2) variants. 2021 Frontiers in immunology Result SARS_CoV_2 Y160T;R158N 41;35 46;40 S 33 34 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. These results indicated that the glycan-masking Ad-S-R158N/Y160T in NTD and glycan-masking Ad-S-N354/K356T and Ad-S-D428N in RBD elicited a 2.4-, 2.5-, and 2.8-fold increase, respectively, in the pseudo-neutralization IC-50 titer against the Wuhan-Hu-1 ancestral strain. 2021 Frontiers in immunology Result SARS_CoV_2 K356T;Y160T;D428N;R158N 101;59;116;53 106;64;121;58 RBD;S;S;S 125;51;94;114 128;52;95;115 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Two separate sets of immunization experiments were conducted in this study: (i) with Ad-S, Ad-S- F135N/N137T, Ad-S-R158N/Y160T, Ad-S- N370/A372T, and Ad-S-H519N/P521T, and (ii) with Ad-S, Ad-S-N354/K356T, Ad-S-G413N, and Ad-S-D428N. 2021 Frontiers in immunology Result SARS_CoV_2 F135N;A372T;K356T;N137T;P521T;Y160T;D428N;G413N;H519N;R158N 97;139;198;103;161;121;226;210;155;115 102;144;203;108;166;126;231;215;160;120 S;S;S;S;S;S;S;S;S 88;94;113;131;153;185;191;208;224 89;95;114;132;154;186;192;209;225 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. Docking analysis of a kinase with N501Y mutation in SARS-CoV-2 lineages. 2022 Travel medicine and infectious disease Result SARS_CoV_2 N501Y 34 39 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. First, we calculated the binding affinities of the wild type PDB complex (7EKG) and dock complex of the mutant (N501Y) spike RBD against the hACE2 receptor as a control. 2022 Travel medicine and infectious disease Result SARS_CoV_2 N501Y 112 117 S;RBD 119;125 124;128 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. In addition to N501Y, we also performed prediction of other mutations of B.1.351 and B.1.1.7 lineages by potent phosphorylation using servers search as mentioned above. 2022 Travel medicine and infectious disease Result SARS_CoV_2 N501Y 15 20 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. It has been shown that N501Y alone can exert the function as a powerful driver for elevated transmission but not inducing immune disruption suggesting the vaccine escape is minimum. 2022 Travel medicine and infectious disease Result SARS_CoV_2 N501Y 23 28 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. Most recently, while we are revising the manuscript, a study was published on which N501Y mutation's superiority among different mutations tested for transmission. 2022 Travel medicine and infectious disease Result SARS_CoV_2 N501Y 84 89 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. Next, we employed docking tools to generate desired complexes of the EGFR with wild and N501Y spike RBD. 2022 Travel medicine and infectious disease Result SARS_CoV_2 N501Y 88 93 S;RBD 94;100 99;103 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. Omicron RBD contains 11 mutations, where 4 of them K417 N, E484A, G496S and N501Y were found on the interface region. 2022 Travel medicine and infectious disease Result SARS_CoV_2 E484A;G496S;K417N;N501Y 59;66;51;76 64;71;57;81 RBD 8 11 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. Our data also suggest that the mutated N501Y and other sites of the RBD has the potential to be phosphorylated by different kinases including EGFR. 2022 Travel medicine and infectious disease Result SARS_CoV_2 N501Y 39 44 RBD 68 71 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. Potent kinase inhibitors in treatment and prevention of the N501Y mutations induced gain of phosphorylation. 2022 Travel medicine and infectious disease Result SARS_CoV_2 N501Y 60 65 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. The experimental data by infected hamsters suggest that in addition to deletion 69-70, N501Y showed much more advantages of fitness compared with wild type in replication efficiency in the upper airway, and shedding in nasal cavity or secretions which are related to air-borne transmission. 2022 Travel medicine and infectious disease Result SARS_CoV_2 N501Y 87 92 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. The N501Y EGFR-RBD complex showed slightly higher affinity of -12.3 kcal/mol compared to -11.6 kcal/mol with wild type RBD. 2022 Travel medicine and infectious disease Result SARS_CoV_2 N501Y 4 9 RBD;RBD 15;119 18;122 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. The tested mutations include spike mutants of T716I, N501Y, A570D, P681H, D1118H, 982A, deletion 69-70, deletion 145, with lineage B.1.1.7 variant spike. 2022 Travel medicine and infectious disease Result SARS_CoV_2 A570D;D1118H;N501Y;P681H;T716I 60;74;53;67;46 65;80;58;72;51 S;S 29;147 34;152 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. These include gain of possible phosphorylation by mutations of the two lineages with mutations of I2230T, N501Y; or H2799Y, D4527Y, N501Y to gain phosphorylation, compared with wild type sequences. 2022 Travel medicine and infectious disease Result SARS_CoV_2 D4527Y;H2799Y;I2230T;N501Y;N501Y 124;116;98;106;132 130;122;104;111;137 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. Thus, through the two programs prediction, EGFR potentially interacts with and phosphorylates SARS-CoV-2 spike RBD at N501Y. 2022 Travel medicine and infectious disease Result SARS_CoV_2 N501Y 118 123 S;RBD 105;111 110;114 34931119 Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences. According to the results of the multiple sequence alignment, the mutations of the EPI_ISL_601443 variant were as follows: H69 deletion, V70 deletion, Y144 deletion, N501Y substitution, A570D substitution, D614G substitution, P681H substitution, T716I substitution, S982A substitution, and D1118H substitution. 2022 International journal of peptide research and therapeutics Result SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 185;289;205;165;225;265;245 190;295;210;170;230;270;250 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. 3C) suggests that three substitutions contribute favorably to the binding (with high consensus) while K417N leads to the loss of an interface hydrogen bond. 2021 bioRxiv Result SARS_CoV_2 K417N 102 107 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. 6A,6B) while E484A loses both a salt bridge and hydrogen bond. 2021 bioRxiv Result SARS_CoV_2 E484A 13 18 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. 9); S373P promotes adoption of an alpha-helical conformation (which likely influences the structural uncertainty for this region) while S375F eliminates its hydrogen bond with the polypeptide chain backbone. 2021 bioRxiv Result SARS_CoV_2 S373P;S375F 4;136 9;141 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. All four models of omRBD-C002 highlight the markedly destabilizing effects of K417N and E484A at the interface. 2021 bioRxiv Result SARS_CoV_2 E484A;K417N 88;78 93;83 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. All four of our models of omRDB-COVOX-222 indicate that Y505H is destabilizing at the interface. 2021 bioRxiv Result SARS_CoV_2 Y505H 56 61 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Conversely, Q493R permits the formation of two backbone hydrogen bonds. 2021 bioRxiv Result SARS_CoV_2 Q493R 12 17 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Finally, Q493R led to a 70-fold reduction in REGN10933 binding. 2021 bioRxiv Result SARS_CoV_2 Q493R 9 14 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. found an escape fraction of 0.551 for REGN10987 with N440K. 2021 bioRxiv Result SARS_CoV_2 N440K 53 58 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Furthermore, three of four models highlight the energetic unfavorability of Q493R for binding, which may result in the loss of two hydrogen bonds. 2021 bioRxiv Result SARS_CoV_2 Q493R 76 81 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. G339D may permit the formation of a novel sidechain interaction while N440K may allow an additional hydrogen bond with its backbone. 2021 bioRxiv Result SARS_CoV_2 N440K;G339D 70;0 75;5 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. However, the (low consensus) prediction of a stabilizing effect of N440K appears to be in contradiction with some previous experimental results. 2021 bioRxiv Result SARS_CoV_2 N440K 67 72 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. In our structural analysis, G339D and N440K were indicated to be energetically-favorable substitutions in two out of four omRBD-S309 models each. 2021 bioRxiv Result SARS_CoV_2 G339D;N440K 28;38 33;43 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Interestingly, N501Y has been documented to have a negligible impact (0.1-fold reduction) on CC12.3 binding. 2021 bioRxiv Result SARS_CoV_2 N501Y 15 20 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. K417N has been shown experimentally to lead to reduction in REGN10933 binding by various degrees, ranging from 4.4- to >100-fold reductions, while reduced binding by 0.8- to 6.7-fold has been reported for the cocktail with REGN10987. 2021 bioRxiv Result SARS_CoV_2 K417N 0 5 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. K417N is predicted to lose a salt bridge with C002. 2021 bioRxiv Result SARS_CoV_2 K417N 0 5 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. K417N results in the loss of one salt bridge and two hydrogen bonds. 2021 bioRxiv Result SARS_CoV_2 K417N 0 5 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Many of the substitutions or sites of substitutions in omRBD were observed individually in other variants (N501Y, first seen in Alpha and Gamma; K417N and E484K, first seen in Beta; T478K; first seen in Delta). 2021 bioRxiv Result SARS_CoV_2 E484K;K417N;T478K;N501Y 155;145;182;107 160;150;187;112 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Most of our models indicate that K417N is destabilizing, and one model finds that Q493R is stabilizing. 2021 bioRxiv Result SARS_CoV_2 K417N;Q493R 33;82 38;87 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Notably, among these substitutions is S373P, which would be expected to cause disruption or kinking of the alpha-helix compared to wild-type. 2021 bioRxiv Result SARS_CoV_2 S373P 38 43 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Notably, but as expected, the consensus among three out of four models is that K417N will evoke a destabilizing decrease in binding energy (consistent with the aforementioned antibody studies), likely due to the loss of two interactions made by K417: a salt bridge and hydrogen bond with CC12.3. 2021 bioRxiv Result SARS_CoV_2 K417N 79 84 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Other interfacial substitutions that may have a modest favorable effect (low consensus) on binding are G496S, Q498R, and (moderate consensus) N501Y. 2021 bioRxiv Result SARS_CoV_2 G496S;N501Y;Q498R 103;142;110 108;147;115 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Other potential consequences from the Omicron VOC include the stabilization by G496S according to one model due to the formation of novel sidechain interactions. 2021 bioRxiv Result SARS_CoV_2 G496S 79 84 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Our findings are consistent with a previous study which discovered that Omicron-relevant substituted residues retain high escape fraction values, specifically for E484A (1.0) and Q493R (0.979). 2021 bioRxiv Result SARS_CoV_2 E484A;Q493R 163;179 168;184 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Overall, our models indicate that G446S and Q498R in omRBD may lead to a loss of interactions (also by Y449) which is in agreement with previous findings with these individual substitutions. 2021 bioRxiv Result SARS_CoV_2 G446S;Q498R 34;44 39;49 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Overall, S373P and S375F appear to contribute favorable and unfavorable energetics, respectively. 2021 bioRxiv Result SARS_CoV_2 S373P;S375F 9;19 14;24 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Previous studies of S309, VIR-7831, or VIR-7832 have indicated that G339D and N440K have negligible effects on antibody-binding reduction, ranging from 0.5-1.2-fold reduction. 2021 bioRxiv Result SARS_CoV_2 G339D;N440K 68;78 73;83 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Previous studies range greatly in terms of quantified abrogation of binding of REGN10987 in the presence of N440K, ranging from 1.5- to 95.6-fold reduction. 2021 bioRxiv Result SARS_CoV_2 N440K 108 113 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. S477N was reported to lead to 0.9- to 3.4-fold reduction in REGN10933 binding and 1.5-fold reduction for the cocktail. 2021 bioRxiv Result SARS_CoV_2 S477N 0 5 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. The other two substituted residues (N501Y and Y505H) at the interface have a moderate impact (low consensus) on CC12.3 binding to the Omicron VOC Spike. 2021 bioRxiv Result SARS_CoV_2 Y505H;N501Y 46;36 51;41 S 146 151 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. This finding is consistent with other studies that document at least 100-fold reduction in antibody binding as a result of K417N. 2021 bioRxiv Result SARS_CoV_2 K417N 123 128 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. This result is consistent with findings of an escape fraction of 0.795 for G446S by Starr et al., and a 17-fold reduction in antibody neutralization of the (chemically similar) substitution Q498H noted in CoVDB. 2021 bioRxiv Result SARS_CoV_2 G446S;Q498H 75;190 80;195 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Three models reveal a destabilizing impact of Q498R, possibly due to loss of interactions with an adjacent tyrosine residue. 2021 bioRxiv Result SARS_CoV_2 Q498R 46 51 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. Two models display energetic favorability of N440K, likely due to the formation of two salt bridges with REGN10987. 2021 bioRxiv Result SARS_CoV_2 N440K 45 50 34931193 Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces. With regard to REGN10933, some substituted interface residues display unfavorable energy changes; K417N may result in a salt bridge loss while E484A and Q493R may lead to loss of hydrogen bonds. 2021 bioRxiv Result SARS_CoV_2 E484A;K417N;Q493R 143;98;153 148;103;158 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. The mutations p.Lys1191Asp (K1191D), p.Glu484Lys (E484K), p.Leu18Phe (L18F), p.Pro26Ser (P26S), p.His655Tyr (H655Y), p.Asp614Gly (D614G), that along with other nucleotide substitutions constitute some of the VOC and VOI, were also identified, but not necessarily defining a complete lineage of interest. 2022 Infection, genetics and evolution Result SARS_CoV_2 D614G;E484K;H655Y;L18F;K1191D;P26S;D614G;E484K;H655Y;K1191D;L18F;P26S;D614G;E484K;H655Y;L18F;P26S 117;37;96;58;14;77;130;50;109;28;70;89;119;39;98;60;79 128;48;107;68;26;87;135;55;114;34;74;93;128;48;107;68;87 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. The spike glycoprotein mutation D614G was found in the totality of the sequences obtained (Table 2 ). 2022 Infection, genetics and evolution Result SARS_CoV_2 D614G 32 37 S 4 22 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. We identified Q57H on ORF3a in 184 out of 386 (47.6%) samples; we also found and R203K, R203R, G204R on N gene, in 74 (19.1%), 72 (18.7%), and 72 (18.7%) out of 386 cases, respectively. 2022 Infection, genetics and evolution Result SARS_CoV_2 G204R;Q57H;R203K;R203R 95;14;81;88 100;18;86;93 ORF3a;N 22;104 27;105 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. As soon as the binding of the inhibitor to C145A Mpro went through two steps, the kinetic curves for the WT enzyme could be described by Scheme 4, which contains two equilibrium steps and one irreversible step (Table 3). 2021 Frontiers in pharmacology Result SARS_CoV_2 C145A 43 48 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. Furthermore, the elimination of the Mpro covalent binding with PF-00835231 by means of the C145A mutation also strongly decreased the change in Tm (to ~2.2 C) as compared to the covalently bound WT adduct (~14.0 C), consistently with the pre-steady-state data, which yielded an inhibition constant of 2.5 muM (Table 3). 2021 Frontiers in pharmacology Result SARS_CoV_2 C145A 91 96 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. Indeed, as shown in Figure 3A, the FRET signal during the interaction of C145A Mpro with the substrate increased up to time point of 5 s. 2021 Frontiers in pharmacology Result SARS_CoV_2 C145A 73 78 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. Interaction of Wild-Type Mpro and C145A Mpro with the Substrate. 2021 Frontiers in pharmacology Result SARS_CoV_2 C145A 34 39 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. Interaction of WT Mpro and C145A Mpro With PF-00835231. 2021 Frontiers in pharmacology Result SARS_CoV_2 C145A 27 32 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. It should be noted that in the case of the WT enzyme, the initial phase of the fluorescence intensity increase was significantly slower as compared with C145A Mpro, indicating that the Cys145 residue must play an important role in the formation of the initial complex. 2021 Frontiers in pharmacology Result SARS_CoV_2 C145A 153 158 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. It should be noted that the rate constants of the substrate binding were not affected by the C145A substitution. 2021 Frontiers in pharmacology Result SARS_CoV_2 C145A 93 98 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. Nevertheless, the total binding constant was approximately fivefold higher in the case of the C145A variant owing to a decrease in k -1. 2021 Frontiers in pharmacology Result SARS_CoV_2 C145A 94 99 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. Of note, the affinity of C145A Mpro for PF-00835231 even without the covalent binding was 2.5 muM, strongly supporting perfect complementarity between the inhibitor and the active site, as first revealed by X-ray crystallography. 2021 Frontiers in pharmacology Result SARS_CoV_2 C145A 25 30 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. The analysis of the PF-00835231 binding kinetics in the course of its interaction with WT or C145A Mpro was performed by the stopped-flow technique with detection of intrinsic florescence intensity of PF-00835231. 2021 Frontiers in pharmacology Result SARS_CoV_2 C145A 93 98 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. The association of C145A Mpro with PF-00835231 led to a two-phase increase in the fluorescence intensity up to time point 2 s (Figure 5A). 2021 Frontiers in pharmacology Result SARS_CoV_2 C145A 19 24 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. The C145A substitution led to complete elimination of the catalytic activity of the protease owing to a loss of the catalytic thiol group. 2021 Frontiers in pharmacology Result SARS_CoV_2 C145A 4 9 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. The interaction of C145A Mpro with the substrate can lead only to its binding and formation of a preincision complex. 2021 Frontiers in pharmacology Result SARS_CoV_2 C145A 19 24 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. The value of rate constant k 1 revealed that the formation of the initial complex is approximately 20-fold faster for C145A Mpro, eventually yielding a 10-fold difference in the equilibrium binding constant between the WT and C145A enzymes. 2021 Frontiers in pharmacology Result SARS_CoV_2 C145A;C145A 118;226 123;231 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. Although the fluorescent signal of chimeric crRNA was lower than that of regular crRNA (Fig 1C and 1D), it could differentiate the signal between the N501Y and the wild type spectrophotometrically and visually without compromising the LOD. 2021 PloS one Result SARS_CoV_2 N501Y 150 155 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. Compared with N501Y crRNA 20-nt, the N501Y chimeric crRNA 24-nt achieved the same LOD (100 copies /muL RNA) for detecting N501Y samples (Fig 1B and 1D). 2021 PloS one Result SARS_CoV_2 N501Y;N501Y;N501Y 14;37;122 19;42;127 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. In the detection of samples containing wild type N501, N501Y crRNA 20-nt produced a weak false positive in the CRISPR-Cas12a reaction after incubation of 30 min (Fig 2A and 2B). 2021 PloS one Result SARS_CoV_2 N501Y 55 60 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. N501Y chimeric crRNA 24-nt was designed according to the method by Kim et al. 2021 PloS one Result SARS_CoV_2 N501Y 0 5 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. Therefore, N501Y crRNA 24-nt was also designed to evaluate whether the length of crRNA influences the specificity. 2021 PloS one Result SARS_CoV_2 N501Y 11 16 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. Thus, the chimeric crRNA can improve the specificity of CRISPR-Cas12a without compromising its sensitivity in detecting N501Y. 2021 PloS one Result SARS_CoV_2 N501Y 120 125 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. To determine whether the specificity and sensitivity of N501Y chimeric crRNA 24-nt is significant for N501Y detection, the limit of detection (LOD) was evaluated compared to N501Y crRNA 20-nt using the tenfold serial dilutions of synthetic RNA containing gene fragments of SARS-CoV-2. 2021 PloS one Result SARS_CoV_2 N501Y;N501Y;N501Y 56;102;174 61;107;179 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. We have designed and compared three different types of N501Y crRNA, namely, N501Y crRNA 20-nt (20-nt spacer, designing 20-nt spacer crRNAs is the traditional strategy for genome editing and detection by CRISPR-Cas12a, and in accordance, this 20-nt crRNA has recently been used to detect N501Y in miSHERLOCK platform), N501Y chimeric crRNA 24-nt (24-nt spacer), and N501Y crRNA 24-nt (24-nt spacer) to determine the most efficient crRNA used for N501Y detection (The sequences of primers and crRNAs are given in Table 1). 2021 PloS one Result SARS_CoV_2 N501Y;N501Y;N501Y;N501Y;N501Y;N501Y 55;76;287;318;365;445 60;81;292;323;370;450 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. We observed similar results (LOD and false positive signal for N501Y crRNA 20-nt) using synthetic DNA containing gene fragments of SARS-CoV-2 (S1 Fig). 2021 PloS one Result SARS_CoV_2 N501Y 63 68 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. We observed that the chimeric crRNA works best to differentiate N501Y from wild type as there is no false positive signal compared with a strong false positive signal for wild type when using N501Y crRNA 20-nt and N501Y crRNA 24-nt (Fig 1A). 2021 PloS one Result SARS_CoV_2 N501Y;N501Y;N501Y 64;192;214 69;197;219 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. A105V variant, respectively (data not shown). 2021 Biology Result SARS_CoV_2 A105V 0 5 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. Additionally, C-reactive protein (CRP) levels were significantly higher (9.7 mg/dL) in patients infected with the A105V compared to control (5.6 mg/dL), indicating a higher inflammation status. 2021 Biology Result SARS_CoV_2 A105V 114 119 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. Approximately 47% of patients infected with ORF7a A105V variant developed a severe form of the disease, compared to only 22.2% infected with non-mutant variant. 2021 Biology Result SARS_CoV_2 A105V 50 55 ORF7a 44 49 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. Asymptomatic and mild effects accounted for 46.5% of patients infected with WT variant, compared to 29.3% in the A105V group. 2021 Biology Result SARS_CoV_2 A105V 113 118 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. Clinical Data and Putative Disease-Enhancing Role of ORF7a A105V. 2021 Biology Result SARS_CoV_2 A105V 59 64 ORF7a 53 58 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. Comorbidity patient data showed that three, out of four, deceased patients due to COVID-19 in the WT group had associated comorbidities while two, out of three, patients who died due to infection with SARS-CoV-2 ORF7a A105V had no associated comorbidities. 2021 Biology Result SARS_CoV_2 A105V 218 223 ORF7a 212 217 COVID-19 82 90 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. However, comparative clinical data showed that patients carrying viral RNA coding for ORF7a A105V exhibited an unusual clinical pattern characterized by both a lower number of associated comorbidities and lower viral copy number (based on PCR cycle threshold, Table 1). 2021 Biology Result SARS_CoV_2 A105V 92 97 ORF7a 86 91 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. However, the standard deviation of the RMSF in A105V mutant simulations was overall consistently smaller within the same region, compared to both WT and A105V (Figure 3D, green line). 2021 Biology Result SARS_CoV_2 A105V;A105V 47;153 52;158 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. However, this was not observed when comparing A106V to WT simulations (Figure 4A, green line). 2021 Biology Result SARS_CoV_2 A106V 46 51 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. However, visual representations of the absolute RMSF standard deviations per-residue revealed higher values for core residues (21-71) for both WT (Figure 3C) and A106V (Figure 3D) controls, in contrast with A105V. 2021 Biology Result SARS_CoV_2 A105V;A106V 207;162 212;167 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. Notably, most of these residues were found in the beta-sheet formed by the 39-56 strand, but also in the adjacent 26-30 loop (Figure 4C), 17 of which were statistically different when comparing A105V vs. 2021 Biology Result SARS_CoV_2 A105V 194 199 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. Out of 62 patients with viral sequences analyzed, 17 (27.5%) were infected with A105V recurrent mutation (average frequency in assembled reads 99.1%). 2021 Biology Result SARS_CoV_2 A105V 80 85 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. Overall, lung CT scans of A105V patients showed increased severity compared with controls, with large glass opacities (35% vs. 2021 Biology Result SARS_CoV_2 A105V 26 31 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. Patients infected with mutated SARS-CoV-2 ORF7a A105V exhibited twice the death rate when compared with the wild-type SARS-CoV-2 group. 2021 Biology Result SARS_CoV_2 A105V 48 53 ORF7a 42 47 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. The A105V ORF7a assumed a much higher conformational stability compared to both wild-type and the A106V control, thus revealing its potential role as a change-of-function mutation in the ORF7a protein. 2021 Biology Result SARS_CoV_2 A105V;A106V 4;98 9;103 ORF7a;ORF7a 10;187 15;192 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. The calculated means (SE) of the standard deviations in the 21-71 region accurately reflect the observed effects (WT: 0.99 +- 0.03, A105V: 0.42 +- 0.01, A106V: 1.14 +- 0.06). 2021 Biology Result SARS_CoV_2 A105V;A106V 132;153 137;158 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. The comparative examination of the three simulated proteins, based on the standard deviation calculated from the six replications (per-residue basis), showed that A105V mutation behaved differently compared to controls. 2021 Biology Result SARS_CoV_2 A105V 163 168 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. The low standard deviation of the RMSF (for A105V simulations) was due to similar protein dynamics in each of the six replica simulations. 2021 Biology Result SARS_CoV_2 A105V 44 49 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. The overall results from the MD comparative analyses suggest that the A105V mutation induces a very specific change in the dynamic behavior of the mutated ORF7a protein. 2021 Biology Result SARS_CoV_2 A105V 70 75 ORF7a 155 160 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. The standard deviation of the A106V RMSF simulation in the protein core displayed high variability, with both negative and positive values, relative to WT (Figure 3D, red line). 2021 Biology Result SARS_CoV_2 A106V 30 35 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. This was reflected in the "A105V vs. 2021 Biology Result SARS_CoV_2 A105V 27 32 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. Thus, we determined whether A105V mutation alters protein dynamics, which may be linked to changes in ORF7a interaction landscape, by performing molecular dynamics (MD) simulations on three different proteins: the WT ORF7a, A105V ORF7a, and A106V ORF7a, with the first and the last as controls. 2021 Biology Result SARS_CoV_2 A105V;A105V;A106V 28;224;241 33;229;246 ORF7a;ORF7a;ORF7a;ORF7a 102;217;230;247 107;222;235;252 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. To identify the residues that undergo changes in the A105V simulation, we performed pair-wise F-tests for variance. 2021 Biology Result SARS_CoV_2 A105V 53 58 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. WT" analysis (Figure 4A, blue line), but also when comparing A105V to A106V simulations (Figure 4A, red line). 2021 Biology Result SARS_CoV_2 A105V;A106V 61;70 66;75 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. Consequently, this shows that the specific mutations in the RBD (S477N-E484K) help the new variant to increase binding affinity and, consequently, infectivity. 2021 Biology Result SARS_CoV_2 S477N;E484K 65;71 70;76 RBD 60 63 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. Hence, a thorough investigation of the RBD-specific mutations, i.e., S477N and E484K, is required to reveal more information on this variant. 2021 Biology Result SARS_CoV_2 E484K;S477N 79;69 84;74 RBD 39 42 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. However, a particular mutation in the RBD, C432D, lessens ACE2-assisted entry into the cell using a spike trimer. 2021 Biology Result SARS_CoV_2 C432D 43 48 S;RBD 100;38 105;41 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. Recently, a new variant of concern, B.1.620, with 23 mutations in total, including S477N, E484K, D614G, and P681H, has been reported. 2021 Biology Result SARS_CoV_2 D614G;E484K;P681H;S477N 97;90;108;83 102;95;113;88 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. Seeing the higher applicability of the specified method, we projected the impact of new substitutions S477N-E484K in the RBD on the binding to the ACE2 receptor. 2021 Biology Result SARS_CoV_2 S477N;E484K 102;108 107;113 RBD 121 124 34943523 Low Represented Mutation Clustering in SARS-CoV-2 B.1.1.7 Sublineage Group with Synonymous Mutations in the E Gene. As for the remaining 15 E-wild type patients, 14 carried the A156S mutation, and four out of these 14 patients also carried the S137L and N439K mutations, while the remaining 12 did not. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 A156S;N439K;S137L 61;138;128 66;143;133 E 24 25 34943523 Low Represented Mutation Clustering in SARS-CoV-2 B.1.1.7 Sublineage Group with Synonymous Mutations in the E Gene. Correlation p-values were calculated considering the number of samples with or without a certain mutation (S137L, N439K, and A156S), each time comparing two populations, for a total of 3 combinations for each mutation: EHPI database vs. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 A156S;N439K;S137L 125;114;107 130;119;112 34943523 Low Represented Mutation Clustering in SARS-CoV-2 B.1.1.7 Sublineage Group with Synonymous Mutations in the E Gene. Of the 75 samples belonging to lineage B.1.1.7, 20 showed at least one out of these three mutations: S137L (Open Reading Frame 1ab gene), N439K (Spike gene), and A156S (Nucleocapsid Gene). 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 A156S;N439K;S137L 162;138;101 167;143;106 N;S 169;145 181;150 34943523 Low Represented Mutation Clustering in SARS-CoV-2 B.1.1.7 Sublineage Group with Synonymous Mutations in the E Gene. The five samples with the synonymous mutation (four samples delivered by the CDI and one from our database) belonged to lineage B.1.1.7 (WHO label Alpha), but it was observed that they all shared some "extra-lineage" mutations: S137L in the Orf1ab gene, N439K in the Spike gene and A156S in the N gene (except for the African sample). 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 A156S;N439K;S137L 282;254;228 287;259;233 ORF1ab;S;N 241;267;295 247;272;296 34943523 Low Represented Mutation Clustering in SARS-CoV-2 B.1.1.7 Sublineage Group with Synonymous Mutations in the E Gene. The outcomes of the sequencing in our laboratory reveal that all the samples that did not amplify in RT-qPCR harbor a synonymous mutation at the E gene level, namely in position c.2641 C > T (Reference Genome: NC_045512, TAC > TAT, Tyr > Tyr, Figure 2). 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 C2641T 178 190 E 145 146 34943523 Low Represented Mutation Clustering in SARS-CoV-2 B.1.1.7 Sublineage Group with Synonymous Mutations in the E Gene. The remaining sample, negative for the synonymous mutations, was also negative for A156S and S137L, whereas it was positive for N439K only (Figure 3). 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 A156S;N439K;S137L 83;128;93 88;133;98 34943523 Low Represented Mutation Clustering in SARS-CoV-2 B.1.1.7 Sublineage Group with Synonymous Mutations in the E Gene. When focusing our attention on the mutational profiles of the 5 E-mutated patients, 4 of these carried all three above-described mutations, while one (the patient returning from Africa) did not have the A156S mutation. 2021 Diagnostics (Basel, Switzerland) Result SARS_CoV_2 A156S 203 208 E 64 65 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. The mea observation period was significantly longer in the N501Y infection group than that of the wild-type 501N infection group (8.4 +- 3.0 days vs. 2021 Journal of clinical medicine Result SARS_CoV_2 N501Y 59 64 34953513 Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. As expected, none of the SARS-CoV-2-naive plasma samples collected at V0 were able to recognize the SARS-CoV-2 S (D614G) or any of the variants tested here (B.1.1.7, B.1.351, B.1.617.2, P.1, B.1.526) (Figures 2A-2C and S2A). 2022 Cell host & microbe Result SARS_CoV_2 D614G 114 119 S 111 112 34953513 Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. As observed with the D614G S, the neutralizing activity decreased at V4 for all VOCs tested (Figure S3E). 2022 Cell host & microbe Result SARS_CoV_2 D614G 21 26 S 27 28 34953513 Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. For all the variants tested, we observed a similar pattern to the D614G S, with neutralizing Abs mainly induced after the second dose in the naive group (Figures S3A-S3E). 2022 Cell host & microbe Result SARS_CoV_2 D614G 66 71 S 72 73 34953513 Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. For naive individuals, even if vaccination strongly increased the recognition of every VOC S tested, we observed that plasmas recognized the different SARS-CoV-2 variants less efficiently than D614G S, except for the B.1.1.7 S, after the second dose (Figure S2). 2022 Cell host & microbe Result SARS_CoV_2 D614G 193 198 S;S;S 91;199;225 92;200;226 34953513 Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. Plasma from short interval vaccinated individuals was significantly less efficient at recognizing the D614G S and all other S variants tested except for the B.1.526 S (Figure 5D). 2022 Cell host & microbe Result SARS_CoV_2 D614G 102 107 S;S;S 108;124;165 109;125;166 34953513 Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. Remarkably, the neutralization of pseudoviral particles bearing D614G or almost all the variant Ss tested was significantly lower for individuals that received the two doses with a short interval (Figure 5F). 2022 Cell host & microbe Result SARS_CoV_2 D614G 64 69 34953513 Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. The first dose of vaccine strongly enhanced the recognition of the full D614G S and all the tested variants in both groups (Figures 2A-2C and S2B). 2022 Cell host & microbe Result SARS_CoV_2 D614G 72 77 S 78 79 34953513 Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. To evaluate the vaccine neutralizing response over time, we measured the capacity of plasma samples to neutralize pseudoviral particles carrying the SARS-CoV-2 S D614G glycoprotein (Figure 3B). 2022 Cell host & microbe Result SARS_CoV_2 D614G 162 167 S 160 161 34953513 Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. We also noted that, with the exception of B.1.1.7, plasma from the PI group prior to vaccination (V0) neutralized all pseudoviral particles bearing variant Ss less efficiently than the D614G (Figure S3A). 2022 Cell host & microbe Result SARS_CoV_2 D614G 185 190 34953513 Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. When we compared S recognition between the SARS-CoV-2 variants, we observed that plasma from PI individuals before vaccination less efficiently recognized the different S variants than the D614G S (Figure S2A). 2022 Cell host & microbe Result SARS_CoV_2 D614G 189 194 S;S;S 17;169;195 18;170;196 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. Further, the MM/GBSA binding free energy of the complexes- Native Spike:ACE2, L452R Spike:ACE2, T478K Spike:ACE2 and N501Y Spike:ACE2 complexes were found to be -73.06 kcal/mol, -76.59 kcal/mol, -75.0 kcal/mol and -75.42 kcal/mol (Table 2 ). 2022 Journal of King Saud University. Science Result SARS_CoV_2 L452R;N501Y;T478K 78;117;96 83;122;101 S;S;S;S 66;84;102;123 71;89;107;128 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. Further, the Native Spike:ACE2, L452R Spike:ACE2, T478K Spike:ACE2 and N501Y Spike:ACE2 complexes were subjected to 75 ns MD simulations study in an aqueous solution. 2022 Journal of King Saud University. Science Result SARS_CoV_2 L452R;N501Y;T478K 32;71;50 37;76;55 S;S;S;S 20;38;56;77 25;43;61;82 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. In the ACE2 and L452R spike mutant model complex, there are 20:23 interface residues, an interface area of 1085:1059 A2, 2 salt bridges, 11 hydrogen bonds and 177 non-bonded contacts. 2022 Journal of King Saud University. Science Result SARS_CoV_2 L452R 16 21 S 22 27 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. Table 1), 6 (Asp38, Tyr41, Tyr83 in ACE2 and Tyr449, Tyr489, Tyr505 in L452R spike mutant) (Suppl. 2022 Journal of King Saud University. Science Result SARS_CoV_2 L452R 71 76 S 77 82 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. Table 2), 6 (Asp30, Asp38, Tyr41, Tyr83 in ACE2 and Tyr489, Tyr505 in T478K spike mutant) (Suppl. 2022 Journal of King Saud University. Science Result SARS_CoV_2 T478K 70 75 S 76 81 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. Table 3) and 6 (Asp38, Tyr41, Tyr83 in ACE2 and Tyr489, Tyr501, Tyr505 in N501Y spike mutant) (Suppl. 2022 Journal of King Saud University. Science Result SARS_CoV_2 N501Y 74 79 S 80 85 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The average number of hydrogen bonds in Native Spike:ACE2, L452R Spike:ACE2, T478K Spike:ACE2 and N501Y Spike:ACE2 complexes were 636.1970706 +- 14.63797953, 631.5473 +- 15.02665, 625.00 +- 14.01999 and 630.6005 +- 15.20264 respectively (Table 4). 2022 Journal of King Saud University. Science Result SARS_CoV_2 L452R;N501Y;T478K 59;98;77 64;103;82 S;S;S;S 47;65;83;104 52;70;88;109 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The average Rg values of Native Spike:ACE2, L452R Spike:ACE2, T478K Spike:ACE2 and N501Y Spike:ACE2 complexes were 3.116693675 +- 0.020677384 nm, 3.033101278 +- 0.030052667 nm, 3.035738 +- 0.034536 nm and 3.027204 +- 0.041179 nm (Table 4). 2022 Journal of King Saud University. Science Result SARS_CoV_2 L452R;N501Y;T478K 44;83;62 49;88;67 S;S;S;S 32;50;68;89 37;55;73;94 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The average RMSD values of the Native Spike:ACE2, L452R Spike:ACE2, T478K Spike:ACE2 and N501Y Spike:ACE2 complexes were 0.465537598 +- 0.086582959 nm, 0.378618486 +- 0.052506812 nm, 0.423504386 +- 0.075685 nm and 0.493888 +- 0.06266 nm respectively (Table 4). 2022 Journal of King Saud University. Science Result SARS_CoV_2 L452R;N501Y;T478K 50;89;68 55;94;73 S;S;S;S 38;56;74;95 43;61;79;100 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The average total SASA values of Native Spike:ACE2, L452R Spike:ACE2, T478K Spike:ACE2 and N501Y Spike:ACE2 complexes were 322.5054567 +- 6.129235 nm2, 323.1132277 +- 6.044326 nm2, 326.1164 +- 5.607122 nm2 and 322.6669 +- 6.344532 nm2 respectively (Table 4). 2022 Journal of King Saud University. Science Result SARS_CoV_2 L452R;N501Y;T478K 52;91;70 57;96;75 S;S;S;S 40;58;76;97 45;63;81;102 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The binding interactions between human ACE2 and these three mutant models of Spike (L452R, T478K and N501Y) were studied using protein-protein docking method. 2022 Journal of King Saud University. Science Result SARS_CoV_2 N501Y;T478K;L452R 101;91;84 106;96;89 S 77 82 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The decrease in the RMSD values in the mutant spike:ACE2 complex except for N501Y spike:ACE2 seems to suggest that the spike RBD mutations caused a decrease in the conformational stabilities in the protein-protein complexes. 2022 Journal of King Saud University. Science Result SARS_CoV_2 N501Y 76 81 S;S;S;RBD 46;82;119;125 51;87;124;128 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The HADDOCK scores for Native Spike:ACE2, L452R Spike:ACE2, T478K Spike:ACE2 and N501Y Spike:ACE2 complexes were -137.6 +- 2.8, -140.5 +- 10.2, -141.3 +- 1.0 and -140.3 +- 1.3 respectively. 2022 Journal of King Saud University. Science Result SARS_CoV_2 L452R;N501Y;T478K 42;81;60 47;86;65 S;S;S;S 30;48;66;87 35;53;71;92 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The increase in the binding affinity of L452R spike mutant to ACE2 can be attributed to an increase in the number of interface residues, interface area, salt bridges, hydrogen bonds and non-bonded contacts. 2022 Journal of King Saud University. Science Result SARS_CoV_2 L452R 40 45 S 46 51 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The increased binding affinity of N501Y spike mutant to ACE2 can be explained in terms of an increase in the number of interface residues, interface area, number of hydrogen bonds and number of non-bonded contacts. 2022 Journal of King Saud University. Science Result SARS_CoV_2 N501Y 34 39 S 40 45 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The increased binding affinity of T478K spike mutant to ACE2 can be explained in terms of increase in the number of interface residues, interface area, number of salt bridges and number of non-bonded contacts. 2022 Journal of King Saud University. Science Result SARS_CoV_2 T478K 34 39 S 40 45 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The interface between ACE2 and N501Y spike mutant has 19:19 residues, an interface area of 962:1020 A2, 1 salt bridge, 13 hydrogen bonds and 143 non-bonded contacts. 2022 Journal of King Saud University. Science Result SARS_CoV_2 N501Y 31 36 S 37 42 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The key residues majorly contributing towards the interaction between ACE2 and Spike L452R mutant includes Tyr41 (-4.27 kcal/mol), Thr27 (-3.04 kcal/mol), Leu45 (-2.94 kcal/mol), Tyr83 (-2.83 kcal/mol) and Gln24 (-2.77 kcal/mol) of ACE2 and Tyr505 (-6.45 kcal/mol), Lys417 (-4.72 kcal/mol), Phe486 (-4.62 kcal/mol), Gln493 (-4.2 kcal/mol) and Leu455 (-4.05 kcal/mol). 2022 Journal of King Saud University. Science Result SARS_CoV_2 L452R 85 90 S 79 84 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The residues such as Tyr83 (-4.16 kcal/mol), Tyr41 (-3.19 kcal/mol), Thr27 (-3.01 kcal/mol), Gln24 (-3.0 kcal/mol) and Lys31 (-2.76 kcal/mol) of ACE2 and Phe486 (-5.01 kcal/mol), Tyr505 (-4.41 kcal/mol), Gln493 (-4.26 kcal/mol), Lys417 (-4.21 kcal/mol) and Tyr489 (-4.17 kcal/mol) contribute significantly to the interaction between ACE2 and Spike T478K mutant. 2022 Journal of King Saud University. Science Result SARS_CoV_2 T478K 348 353 S 342 347 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The top 5 residues contributing considerably to the binding between ACE2 and Spike N501Y mutant includes Tyr41 (-5.08 kcal/mol), Gln24 (-3.11 kcal/mol), Thr27 (-2.96 kcal/mol), Gln42 (-2.75 kcal/mol) and Lys31 (-2.64 kcal/mol) of ACE2 and Tyr501 (-7.18 kcal/mol), Tyr505 (-5.01 kcal/mol), Tyr449 (-4.72 kcal/mol), Gln493 (-4.47 kcal/mol) and Phe486 (-4.22 kcal/mol). 2022 Journal of King Saud University. Science Result SARS_CoV_2 N501Y 83 88 S 77 82 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. The total number of hotspot residues in the interface region of Native Spike:ACE2, L452R Spike:ACE2, T478K Spike:ACE2 and N501Y Spike:ACE2 were 5 (Asp30, Tyr41, Tyr83 in ACE2 and Tyr489, Tyr505 in native spike protein) (Suppl. 2022 Journal of King Saud University. Science Result SARS_CoV_2 L452R;N501Y;T478K 83;122;101 88;127;106 S;S;S;S;S 71;89;107;128;204 76;94;112;133;209 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. Thus, the L452R, T478K and N501Y mutations in the spike increased binding affinity with ACE2. 2022 Journal of King Saud University. Science Result SARS_CoV_2 L452R;N501Y;T478K 10;27;17 15;32;22 S 50 55 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. We have selected three major mutations-L452R, T478K and N501Y that occur in the receptor-binding domain (RBD) of spike protein. 2022 Journal of King Saud University. Science Result SARS_CoV_2 N501Y;T478K;L452R 56;46;39 61;51;44 S;RBD 113;105 118;108 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. Antibody titers against four different SARS-CoV-2 spike versions (the full-length spike protein bearing the D614G substitution, the Spike-RBD, the RBD carrying the E484Q alteration, or the NTD) and the nucleocapsid protein (NCP) ( Table 2 ) were calculated using serum samples obtained from each cohort. 2021 Frontiers in immunology Result SARS_CoV_2 D614G;E484Q 108;164 113;169 N;S;S;S;RBD;RBD 202;50;82;132;138;147 214;55;87;137;141;150 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. As anticipated, treatment with bamlanivimab and etesevimab together resulted in significantly increased neutralization of spike E484Q pseudovirus compared with placebo (p<0.0001) with the median of the bamlanivimab and etesevimab together group 15.2-fold higher compared to the median of the placebo group, due to the presence of etesevimab in the serum ( Figure 3 ). 2021 Frontiers in immunology Result SARS_CoV_2 E484Q 128 133 S 122 127 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. Bamlanivimab treatment (all dose levels pooled) resulted in significantly smaller neutralization of spike E484Q pseudovirus compared with placebo (p=0.001) with the median of the bamlanivimab group 3.1-fold lower compared to the median of the placebo group. 2021 Frontiers in immunology Result SARS_CoV_2 E484Q 106 111 S 100 105 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. Compared to placebo, treatment with bamlanivimab monotherapy resulted in an attenuated increase in antibody titer changes from baseline from day 15 through day 85 against Spike-E484Q (ranging from 2.0 to 2.9 fold across bamlanivimab doses and time points), Spike-NTD (ranging from 2.5 to 4.1 fold), and NCP (ranging from 1.4 to 2.2 fold) ( Figure 2 ). 2021 Frontiers in immunology Result SARS_CoV_2 E484Q 177 182 S;S 171;257 176;262 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. Genotypic analysis of the SARS-CoV-2 virus present in baseline samples confirm absence of these SARS-CoV-2 variants in this cohort, with the majority of infecting viruses containing the D614G substitution in spike found in the B.1 pangolin lineages. 2021 Frontiers in immunology Result SARS_CoV_2 D614G 186 191 S 208 213 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. Next, we calculated the titer change from baseline at day 3, 15, 29, 60, and 85 against the Spike-NTD and NCP (i.e., proteins that bind neither bamlanivimab nor etesevimab), as well as Spike-RBD E484Q (a mutation that negatively impacts bamlanivimab binding) ( Figure 2 ). 2021 Frontiers in immunology Result SARS_CoV_2 E484Q 195 200 S;S;RBD 92;185;191 97;190;194 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. Similar neutralization activity was observed against the Spike E484K pseudovirus (data not shown). 2021 Frontiers in immunology Result SARS_CoV_2 E484K 63 68 S 57 62 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. Since bamlanivimab does not bind significantly to Spike RBD with alterations at residue E484, and as the epitopes for bamlanivimab and etesevimab lie within the spike RBD, titers against Spike RBD E484Q, NTD, or NCP proteins solely reflect the endogenous antibody response. 2021 Frontiers in immunology Result SARS_CoV_2 E484Q 197 202 S;S;S;RBD;RBD;RBD 50;161;187;56;167;193 55;166;192;59;170;196 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. The same patterns for Spike RBD E484Q, the NTD, and NCP titers were observed in the mAb-receiving cohorts. 2021 Frontiers in immunology Result SARS_CoV_2 E484Q 32 37 S;RBD 22;28 27;31 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. We assessed IC50 titers of serum samples against three different pseudoviruses, containing the E484Q or E484K substitutions in spike, as well as the beta-variant (B.1.351) which contains E484K and K417N substitutions that have been shown to significantly reduce the binding of both bamlanivimab and etesevimab. 2021 Frontiers in immunology Result SARS_CoV_2 E484K;E484K;E484Q;K417N 104;187;95;197 109;192;100;202 S 127 132 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. A possible explanation is that the missense mutations created Van der Waal clashes with neighboring atoms because of shorter distance; The missense mutation, T487Y, caused a differential Van der Waals of -0.449 kcal/mol, which led to a greater re-pulsion from nearby atoms. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 T487Y 158 163 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. As shown in Table 4, T487S and L472P were predicted to decrease or weaken SARS-CoV-1 S RBD affinity to ACE2 by Foldx, mCSM-PPI2, and MutaBind2. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 L472P;T487S 31;21 36;26 RBD;S 87;85 90;86 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Consistently, S443A in corresponding position of SARS-CoV-2 increase the S stability (G = -0.768 kcal/mol). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 S443A 14 19 S 73 74 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Conversely, S336V in-creases the G by 1.28 kcal/mol, thereby destabilizing the SARS-CoV-1 structure. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 S336V 12 17 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. D614G, the dominant variant of SARS-CoV-2, corresponds to D600G but was predicted to stabilize S (G = -0.784 kcal/mol). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D600G;D614G 58;0 63;5 S 95 96 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. For example, the missense mutation A430W had a large effect on both the stability of the RBD (Figure 4B) and the entire spike protein of the SARS-CoV-1. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 A430W 35 40 S;RBD 120;89 125;92 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. For example, the missense mutation, S336E, reduces the G by -1.93 kcal/mol, thereby stabilizing the SARS-CoV-1 spike protein. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 S336E 36 41 S 111 116 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Furthermore, the mutation L472P destabilizes SARS-CoV-1 (G = 1 kcal/mol). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 L472P 26 31 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. However, mis-sense mutation N479Q decreased theG by -0.607 kcal/mol and increased G by 1.91 kcal/mol. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N479Q 28 33 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. However, N479K predict-ed as a destabilizing mutation by Foldx, DynaMut, and I-mutant3. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N479K 9 14 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. However, N479K was predicted by mCSM-PPI2 and MutaBind2 to decrease the binding affinity of SARS-CoV-1 S RBD. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N479K 9 14 RBD;S 105;103 108;104 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. In contrast, N501T, on the SARS-CoV-2 decreasedG by -1.346 kcal/mol. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N501T 13 18 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Interestingly, SARS-CoV-1 D600G can destabilize S (G = 0.21 kcal/mol). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 D600G 26 31 S 48 49 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Meanwhile, DUET, mCSM, and SDM predicted N479K as a stabilizing mutation (Table 3). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N479K 41 46 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Of the four target destabilizing mutations predicted by Foldx, four other computational tools predicted G634W as a destabilizing mutation, while three other tools except, DynaMut and I-mutant3, predicted A430W, A430Y, and G839W as destabilizing mutations. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 A430W;A430Y;G634W;G839W 204;211;104;222 209;216;109;227 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Of the three mutations, only N479K increases the solvation energy by 0.29 kcal/mol, which indicate this mutation can increase the interaction force or binding affinity of the residue. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N479K 29 34 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Of the two target stabilizing mutations predicted by Foldx, only two other tools (DynaMut and SDM) predicted G981W and T1059F as stabilizing mutations. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 G981W;T1059F 109;119 114;125 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Recent SARS-CoV-2 variant L452R ( G = -0.395 kcal/mol; G = 0.021 kcal/mol) corresponds to SARS-CoV-1 K439R ( G = 0.247 kcal/mol; G = 0.41 kcal/mol). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 K439R;L452R 101;26 106;31 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. The change in residue from Lysine in SARS-CoV-1 S protein to Leucine in SARS-CoV-2 S protein may be responsible for the increase in binding affinity caused by L452R. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 L452R 159 164 S;S 48;83 49;84 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. The computed missense mutation T487N increased theG by 2.28 kcal/mol and decreased the G by -0.14. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 T487N 31 36 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. The residue change, N479K, would increase the binding affinity ( G = -1.008 kcal/mol) and reduced S stability (G = 1.52 kcal/mol). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N479K 20 25 S 98 99 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. The two most destabilizing missense mutations, A430W and A430F, cause energy changes at 66.18 kcal/mol and 56.4 kcal/mol, respectively. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 A430F;A430W 57;47 62;52 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. The two most stabilizing missense mutations, G981W and T1059F, reduced the free energy of the wildtype structure by -5.16 kcal/mol and -4.98 kcal/mol, respectively. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 G981W;T1059F 45;55 50;61 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Two mutations, L472P and T487S, decreased the binding affinity of S RBD-ACE2 by introducingG at 1.875 kcal/mol and 0.752 kcal/mol, respectively. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 L472P;T487S 15;25 20;30 RBD;S 68;66 71;67 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Two of the three key mutations (T487S and L472P) on 2002-2003 viral isolates were predicted to de-stabilize the protein S protein by four of the six prediction tools. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 L472P;T487S 42;32 47;37 S 120 121 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Tyrosine and Tryptophan have nonpolar aromatic chains therefore the missense mutations T487Y and T487W, had similar effects (decrease binding affinity) on corresponding residue on SARS-CoV-2, N501Y and N501W, respectively. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N501W;N501Y;T487W;T487Y 202;192;97;87 207;197;102;92 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. We observed that the missense mutation A430S destabilizes SARS-CoV-1 S protein by introducing the folding energy change at 1.8 kcal/mol. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 A430S 39 44 S 69 70 34959053 Isolation of SARS-CoV-2 B.1.1.28.2 (P2) variant and pathogenicity comparison with D614G variant in hamster model. EPI_ISL_2013029 isolate showed additional substitutions N Q9H, NS3 G44V and NSP 15 K12N. 2022 Journal of infection and public health Result SARS_CoV_2 G44V;K12N;Q9H 67;83;58 71;87;61 NS3;N 63;56 66;57 34959053 Isolation of SARS-CoV-2 B.1.1.28.2 (P2) variant and pathogenicity comparison with D614G variant in hamster model. The amino acid substitutions detected in both the isolates were D614G, E484K, V1176F in the spike, A119S, G204R, M234I, R203K in the N, L205V in NSP5, L71F in NSP7 and P32L in NSP 12. 2022 Journal of infection and public health Result SARS_CoV_2 A119S;D614G;E484K;G204R;N205V;L205V;L71F;M234I;P32L;R203K;V1176F 99;64;71;106;134;134;151;113;168;120;78 104;69;76;111;141;141;155;118;172;125;84 S;Nsp7;Nsp5 92;159;145 97;163;149 34960156 The Impact of Mutations on the Pathogenic and Antigenic Activity of SARS-CoV-2 during the First Wave of the COVID-19 Pandemic: A Comprehensive Immunoinformatics Analysis. Among these pathogenic mutations, D614G (score = 4) in the S region has already been reported to be associated with greater infectivity. 2021 Vaccines Result SARS_CoV_2 D614G 34 39 S 59 60 34960156 The Impact of Mutations on the Pathogenic and Antigenic Activity of SARS-CoV-2 during the First Wave of the COVID-19 Pandemic: A Comprehensive Immunoinformatics Analysis. Another highly prevalent mutation (P323L) in the RdRp region was found to be neutral (score = 2), whereas its infectivity has not been reported so far. 2021 Vaccines Result SARS_CoV_2 P323L 35 40 RdRP 49 53 34960156 The Impact of Mutations on the Pathogenic and Antigenic Activity of SARS-CoV-2 during the First Wave of the COVID-19 Pandemic: A Comprehensive Immunoinformatics Analysis. D614G (50%) and P323L (49%) mutations showed the highest frequency among the screened sequences. 2021 Vaccines Result SARS_CoV_2 P323L;D614G 16;0 21;5 34960156 The Impact of Mutations on the Pathogenic and Antigenic Activity of SARS-CoV-2 during the First Wave of the COVID-19 Pandemic: A Comprehensive Immunoinformatics Analysis. It was observed that the antigenicity of the epitope with the deleterious mutation D614G decreased. 2021 Vaccines Result SARS_CoV_2 D614G 83 88 34960156 The Impact of Mutations on the Pathogenic and Antigenic Activity of SARS-CoV-2 during the First Wave of the COVID-19 Pandemic: A Comprehensive Immunoinformatics Analysis. Moreover, the mutation frequencies of P323L (49%) and D614G (50%) were found to be similar within the period from 15 January 2020 to 15 July 2021. 2021 Vaccines Result SARS_CoV_2 D614G;P323L 54;38 59;43 34960694 Semi-Supervised Pipeline for Autonomous Annotation of SARS-CoV-2 Genomes. For example, we observed five protein sequences to contain the N501Y mutation from 13 genomes originating from Oceania (submitted 2 July 2020) and North America (submitted 1 June 2020). 2021 Viruses Result SARS_CoV_2 N501Y 63 68 34960694 Semi-Supervised Pipeline for Autonomous Annotation of SARS-CoV-2 Genomes. Our observations are consistent with the current understanding of multiple introduction events causing the emergence of the N501Y variants. 2021 Viruses Result SARS_CoV_2 N501Y 124 129 34960694 Semi-Supervised Pipeline for Autonomous Annotation of SARS-CoV-2 Genomes. Then in mid-April 2020, the notable variant D614G (orange line) with now known increased infectivity, due to interaction with the ACE2 receptor, overtakes the ancestral reference sequence (green line) in its abundance, achieving fixation. 2021 Viruses Result SARS_CoV_2 D614G 44 49 34960694 Semi-Supervised Pipeline for Autonomous Annotation of SARS-CoV-2 Genomes. These variants are also observed to contain the D614G mutation, but are not present with the 69-70 deletion present in the B.1.1.7 variant of concern (U.K.) or B.1.351 E484K mutation (South Africa). 2021 Viruses Result SARS_CoV_2 D614G;E484K 48;168 53;173 34960694 Semi-Supervised Pipeline for Autonomous Annotation of SARS-CoV-2 Genomes. This includes observations of deletions early in the S protein and differentiation between substitutions P681H, which is a mutation of interest, and P681R. 2021 Viruses Result SARS_CoV_2 P681H;P681R 105;149 110;154 S 53 54 34960694 Semi-Supervised Pipeline for Autonomous Annotation of SARS-CoV-2 Genomes. Two other differing sequences are observed at lower abundance in this genome cohort and correspond to P1140X (olive line) and S2 cleavage product (pink line). 2021 Viruses Result SARS_CoV_2 P1140X 102 108 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. A 1.4-fold reduction in titers was observed for pseudoviruses with only the L452Q and F490S substitutions, indicating that these RBD substitutions contribute to C.37 resistance. 2021 Viruses Result SARS_CoV_2 F490S;L452Q 86;76 91;81 RBD 129 132 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. A further reduction in neutralization titers was seen against pseudoviruses bearing both L452R and T478 substitutions in RBD displayed (GMT 192) compared to WT(D614G) (GMT 392). 2021 Viruses Result SARS_CoV_2 L452R;D614G 89;160 94;165 RBD 121 124 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. A modest 1.8-fold reduction in titers against C.37 pseudoviruses was observed compared to WT(D614G) pseudoviruses (GMT titers 222 and 392, respectively). 2021 Viruses Result SARS_CoV_2 D614G 93 98 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. A prior study showed that convalescent sera and vaccine-elicited antibody neutralization titers against pseudoviruses bearing spikes containing L452R-E484Q-P681R substitutions displayed 2-5-fold reduction, compared to the neutralization titers against WT(D614G) pseudoviruses. 2021 Viruses Result SARS_CoV_2 L452R;D614G;E484Q;P681R 144;255;150;156 149;260;155;161 S 126 132 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Again, pseudoviruses K417N, L452R, T478K, L452Q + F490S, and B.1.429 were close to WT(D614G) (0.05-0.51 AU). 2021 Viruses Result SARS_CoV_2 F490S;K417N;L452Q;L452R;T478K;D614G 50;21;42;28;35;86 55;26;47;33;40;91 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Against pseudoviruses bearing spikes with T478K substitution in RBD, neutralization titers (GMT 270) were also reduced compared to WT(D614G) (GMT 392). 2021 Viruses Result SARS_CoV_2 T478K;D614G 42;134 47;139 S;RBD 30;64 36;67 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. AY.1 pseudoviruses displayed similar resistance to the nAbs as B.1.617.2 pseudoviruses, except for complete resistance to one additional nAb (N) due to the K417N RBD substitution and one cnAb (S) (Figure 4C). 2021 Viruses Result SARS_CoV_2 K417N 156 161 RBD;S 162;193 165;194 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. B.1.1.7 and WT(D614G) pseudoviruses bearing P681H also displayed enhanced spike cleavage (Figure 5A), consistent with previous reports. 2021 Viruses Result SARS_CoV_2 P681H;D614G 44;15 49;20 S 74 79 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. B.1.429 pseudoviruses that lack P681R or P681H substitutions near the furin cleavage site displayed inefficient spike cleavage, whereas the furin cleavage site ( PRRA)-deleted spike lacked cleavage. 2021 Viruses Result SARS_CoV_2 P681H;P681R 41;32 46;37 S;S 112;176 117;181 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. B.1.617.1 was also slightly closer to WT(D614G) at 1.55 AU and was positioned adjacent to the other variants. 2021 Viruses Result SARS_CoV_2 D614G 41 46 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. B.1.617.2, C.37, and AY.1 clustered below WT(D614G) and slightly further away (1.14-1.60 AU), while L452R + T478K was also further away, but in the opposite direction (1.20 AU). 2021 Viruses Result SARS_CoV_2 L452R;T478K;D614G 100;108;45 105;113;50 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Because the convalescent sera came from individuals who were previously infected by different variants (Table 2), we also explored differences in the neutralization titers between those infected by D614G variants lacking L452R and those infected by variants containing L452R (all have L452R and D614G, except one lacking D614G). 2021 Viruses Result SARS_CoV_2 D614G;D614G;D614G;L452R;L452R;L452R 198;295;321;221;269;285 203;300;326;226;274;290 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Compared to the convalescent sera map, there was a larger antigenic difference between AY.1 and WT(D614G) on the vaccine-elicited sera map. 2021 Viruses Result SARS_CoV_2 D614G 99 104 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Compared to titers against WT(D614G) pseudoviruses (GMT 392), titers against B.1.617.1 (B) pseudoviruses were approximately four-fold lower (GMT 90), confirming and extending other reports. 2021 Viruses Result SARS_CoV_2 D614G 30 35 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Compared to WT(D614G), both B.1.617.1 and B.1.617.2 spikes induced significantly higher cell-cell fusion activity when controlled for spike cell surface expression (4000 MFI of spike protein on cell surface) (Figure 5B). 2021 Viruses Result SARS_CoV_2 D614G 15 20 S;S;S 52;134;177 58;139;182 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Consistent with previous observations, the B.1.351 variant (GMT 169 for Pfizer and 306 for Moderna) displayed ~7-fold lower titers compared to WT(D614G), whereas C.37, P.1, R.1, and B.1.526 variants displayed modestly reduced titers that are similar to the titers against B.1.617 pseudoviruses (GMT 452-707 for Pfizer and GMT 824-1332 for Moderna). 2021 Viruses Result SARS_CoV_2 D614G 146 151 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Each vaccine-elicited serum had high neutralization titers against WT(D614G) pseudoviruses, ranging between 578 and 3935 for Pfizer/BioNtech BNT162b2 and 651 and 5853 for Moderna mRNA-1273 (Figure 2A,B) (Pfizer/BioNtech BNT162b2 vs. 2021 Viruses Result SARS_CoV_2 D614G 70 75 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Fold changes in neutralization titers against B.1.617.1 (B) and AY.1 variants were 3.3 and 1.3, respectively, for the L452 group, compared to 5.2 and 2.5, respectively, for the WT(D614G) group (Figure 1B,C). 2021 Viruses Result SARS_CoV_2 D614G 180 185 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. For all pseudoviruses bearing the P681R spike substitution, including B.1.617.1, B.1.617.2, Wuhan-Hu-1 + P681R, and P681R (+D614G), spike cleavage as determined by higher cleaved S1 subunit to total S (S1 + S) ratios was enhanced compared to the respective original pseudoviruses (Figure 5A). 2021 Viruses Result SARS_CoV_2 P681R;P681R;P681R;D614G 34;105;116;124 39;110;121;129 S;S;S;S 40;132;199;207 45;137;200;208 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Further investigations of the role of P681H/R substitutions for virus transmissibility and cell-to-cell spread in in vivo animal models are needed. 2021 Viruses Result SARS_CoV_2 P681H;P681R 38;38 45;45 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Furthermore, continued surveillance is necessary as several independent lineages have recently emerged containing additional substitutions proximal to S1/S2 cleavage junction, such as the B.1.2 and B.1.525 with Q677H, C.37 and B.1.617.2 with Q675H, and C.1.2 with N679K substitutions. 2021 Viruses Result SARS_CoV_2 N679K;Q675H;Q677H 264;242;211 269;247;216 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Furthermore, vaccine-elicited sera saw a smaller difference between B.1.351 and WT(D614G) than the convalescent sera, which may have aligned AY.1 and B.1.351 closer together. 2021 Viruses Result SARS_CoV_2 D614G 83 88 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. However, E484Q and C.37 were both closer to WT(D614G) but were poorly coordinated and extended in elongated shapes around WT(D614G). 2021 Viruses Result SARS_CoV_2 E484Q;D614G;D614G 9;47;125 14;52;130 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. However, in the bootstrap confidence interval 2D map and 3D map, L452R + T478K and AY.1 had distinct positions, clustering together with B.1.617.2 and C.37 in the 3D map and together but with T478K on the bootstrap 2D map. 2021 Viruses Result SARS_CoV_2 L452R;T478K;T478K 65;73;192 70;78;197 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. However, pseudoviruses with only spike RBD substitutions (T478K, E484Q), as well as the B.1.617.1 (IC50:2.03 microg/mL) and AY.1 (IC50:1.97 microg/mL) spikes, displayed comparable IC50 to WT(D614G) (0.5-1.5-fold change) (Table 4 and Supplementary Figure S6). 2021 Viruses Result SARS_CoV_2 E484Q;D614G;T478K 65;191;58 70;196;63 S;S;RBD 33;151;39 38;157;42 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. In agreement with greater ACE2 affinity of L452R RBD compared to WT RBD as reported by others using surface plasmon resonance, pseudoviruses containing L452R (IC50:1.19 microg/mL; p < 0.05) and L452R + T478K (IC50:1.23 microg/mL; p < 0.001) displayed 2.4- and 2.3-fold higher sensitivity to inhibition by sACE2. 2021 Viruses Result SARS_CoV_2 L452R;L452R;L452R;T478K 43;152;194;202 48;157;199;207 RBD;RBD 49;68 52;71 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. In comparison with other variants, we found that titers against B.1.429 pseudoviruses (GMT 332) were comparable to WT(D614G), but titers against the B.1.351 pseudovirus were 16.3-fold reduced (GMT 24) compared to WT(D614G), consistent with prior reports showing marked reductions of cross-neutralization against this variant. 2021 Viruses Result SARS_CoV_2 D614G;D614G 118;216 123;221 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. In the group infected by D614G variants that lacked L452R, a 5.2-fold, 1.6-fold, and 2.5-fold reduction in cross-neutralization potency was seen against B.1.617.1 (B), B.1.617.2, and AY.1 pseudoviruses, respectively (Figure 1B). 2021 Viruses Result SARS_CoV_2 D614G;L452R 25;52 30;57 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. In this study, depending upon the infecting variant, convalescent sera displayed a modest 2-4-fold reduction in neutralization titers for B.1.617.1 compared to WT(D614G), while the vaccine-elicited sera displayed only 2.1-fold reduction. 2021 Viruses Result SARS_CoV_2 D614G 163 168 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Likewise, titers against K417N (GMT 1208 for Pfizer and 2070 for Moderna) and T478K (GMT 1046 for Pfizer and 2113 for Moderna) alone or in L452R + T478K combination (GMT 964 for Pfizer and 1796 for Moderna) remained comparable to GMTs of WT(D614G) (Figure 2 and Supplementary Figure S2). 2021 Viruses Result SARS_CoV_2 K417N;L452R;T478K;T478K;D614G 25;139;78;147;241 30;144;83;152;246 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Maps made with convalescent sera only from infection by WT(D614G) or only from infection by strains containing L452R mutation were not sufficiently robust for antigen positioning. 2021 Viruses Result SARS_CoV_2 L452R;D614G 111;59 116;64 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Neutralization titers against WT(D614G) and L452R pseudoviruses were comparable (GMT titers 392 and 364, respectively), while neutralization titers against E484Q pseudoviruses were lower (GMT 165). 2021 Viruses Result SARS_CoV_2 E484Q;L452R;D614G 156;44;33 161;49;38 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. None of the cnAbs and pnAbs tested showed the loss of neutralization potency against L452R, E484Q, and B.1.617.1 (Supplementary Figure S4). 2021 Viruses Result SARS_CoV_2 E484Q;L452R 92;85 97;90 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. On all maps, B.1.351 was the most distinct from WT(D614G) (4.90 AU), followed by B.1.617.1 (2.78 AU), positioned between B.1.617.2 and B.1.351, and E484Q (1.77 AU), which was between WT(D614G) and B.1.351. 2021 Viruses Result SARS_CoV_2 E484Q;D614G;D614G 148;51;186 153;56;191 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. On the convalescent sera antigenic map, most of the pseudoviruses clustered close to the WT(D614G) pseudovirus and the WT(D614G) sera and L452R sera, including K417N, L452R, T478K, L452Q + F490S, and B.1.429 (0.25 to 0.72 antigenic units (AU) from WT (Table 3). 2021 Viruses Result SARS_CoV_2 F490S;K417N;L452Q;L452R;L452R;T478K;D614G;D614G 189;160;181;138;167;174;92;122 194;165;186;143;172;179;97;127 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Our findings agree with a recent study that showed 3.0-, 2.4-, and 4.1-fold reduction of Pfizer/BioNtech BNT162b2-elicited plasma neutralization, and 4.1-, 2.6-, and 9.5-fold reduction of Moderna mRNA-1273-elicited plasma neutralization for B.1.617.1, B.1.617.2, and AY.1 pseudoviruses, respectively, compared to WT(D614G). 2021 Viruses Result SARS_CoV_2 D614G 316 321 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Our findings agree with several studies reporting enhanced furin cleavage efficiency of B.1.1.7 and B.1.617 spikes bearing P681H and P681R substitutions, respectively. 2021 Viruses Result SARS_CoV_2 P681H;P681R 123;133 128;138 S 108 114 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Our findings extend previous studies indicating that the P681R substitution increases spike proteolytic cleavage and facilitates cell-cell fusion. 2021 Viruses Result SARS_CoV_2 P681R 57 62 S 86 91 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Our findings using B.1.617.1 pseudoviruses with the full complement of spike substitutions rather than just the L452R-E484Q-P681R spike substitutions confirm and extend the prior findings. 2021 Viruses Result SARS_CoV_2 L452R;E484Q;P681R 112;118;124 117;123;129 S;S 71;130 76;135 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Overall, these findings show that the E484Q and L452R substitutions fully account for the resistance of B.1.617.1 against these nAbs, while 17 of 23 tested therapeutic antibodies retained neutralization potency against B.1.617.1 (Supplementary Figure S4). 2021 Viruses Result SARS_CoV_2 E484Q;L452R 38;48 43;53 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Previous studies demonstrated that L452R, and N501Y substitutions in RBD enhanced spike protein affinity to ACE2, which may have contributed to greater transmissibility of B.1.1.7, B.1.351, P.1, and B.1.427/429 variants. 2021 Viruses Result SARS_CoV_2 L452R;N501Y 35;46 40;51 S;RBD 82;69 87;72 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Prior reports indicated increased infectivity of pseudoviruses containing the L452R substitution in spike in 293T-ACE2.TMPRSS2 cells due to L452R conferring enhanced RBD affinity to ACE2. 2021 Viruses Result SARS_CoV_2 L452R;L452R 78;140 83;145 S;RBD 100;166 105;169 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Pseudoviruses with single L452R and T478K substitutions each conferred a similar fold change in resistance (1.3- and 1.5-fold, respectively) as B.1.617.2 (1.6-fold) compared to WT(D614G), although a 2.4-fold reduction was seen against the pseudoviruses with the dual L452R + T478K substitutions. 2021 Viruses Result SARS_CoV_2 L452R;L452R;T478K;T478K;D614G 26;267;36;275;180 31;272;41;280;185 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Sera from the group infected by variants that had the L452R substitution showed similar fold changes in neutralization titers as the group infected by WT(D614G) variants without the L452R except against B.1.617.1 (B) and AY.1 pseudoviruses. 2021 Viruses Result SARS_CoV_2 L452R;L452R;D614G 54;182;154 59;187;159 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Similarly, GMTs against B.1.1.7 (955 for Pfizer and 1917 for Moderna) and B.1.429 variant with the L452R substitution (1063 for Pfizer and 1799 for Moderna) were comparable to those against WT(D614G). 2021 Viruses Result SARS_CoV_2 L452R;D614G 99;193 104;198 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Since P681H enhanced proteolytic processing of B.1.1.7 spike, we next evaluated spike proteolytic processing of B.1.617 pseudovirus variants carrying the P681R substitution. 2021 Viruses Result SARS_CoV_2 P681H;P681R 6;154 11;159 S;S 55;80 60;85 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The average neutralization potency of Moderna mRNA-1273-elicited sera was 2-2.4-fold reduced against B.1.617.1 (GMT 1019 for B.1.617.1 (A); GMT 856 for B.1.617.1 (B)) compared to WT(D614G) (GMT2015) and 1.8-3.4-fold lower against B.1.617.2 pseudoviruses (GMT 1095 for B.1.617.2; GMT 597 for AY.1) (Figure 2B). 2021 Viruses Result SARS_CoV_2 D614G 182 187 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The average neutralization potency of Pfizer/BioNtech BNT162b2 vaccine-elicited sera was 2-2.5-fold lower against B.1.617.1 pseudoviruses (GMT 642 for B.1.617.1 (A); GMT 519 for B.1.617.1 (B)) compared to WT(D614G) (GMT 1310) and 1.9-2.8-fold lower for B.1.617.2 pseudoviruses (GMT 693 for B.1.617.2; GMT 469 for AY.1 pseudovirus) compared to WT(D614G) (GMT1310) (Figure 2A). 2021 Viruses Result SARS_CoV_2 D614G;D614G 208;346 213;351 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The B.1.617 variant pseudoviruses displayed efficient proteolytic processing of spike compared to Wuhan-Hu-1 (D614) and WT(D614G) as observed by the S1/S ratio (Figure 5A). 2021 Viruses Result SARS_CoV_2 D614G 123 128 S;S 80;152 85;153 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The C.37 variant also has a substitution at L452 residue (L452Q instead of L452R) along with F490S in the RBD. 2021 Viruses Result SARS_CoV_2 F490S;L452R;L452Q 93;75;58 98;80;63 RBD 106 109 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The E484Q substitution alone conferred complete resistance (>50-fold) to three nAbs (E, F, and G), and partial resistance to one nAb (C) as previously described. 2021 Viruses Result SARS_CoV_2 E484Q 4 9 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The E484Q substitution in B.1.617.1 (B) only partially contributed to escape from neutralization (GMT 215) with a 2.5-fold reduction in neutralization compared to WT(D614G). 2021 Viruses Result SARS_CoV_2 E484Q;D614G 4;166 9;171 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The fold reduction of neutralization titers against variants containing substitutions at L452 position, including B.1.617.2, AY.1, B.1.617.1, C.37, and L452R RBD substitution mutant, compared to WT(D614G) also trended lower in the group infected by the L452R variant compared to the group infected by the WT(D614G) variant. 2021 Viruses Result SARS_CoV_2 L452R;L452R;D614G;D614G 152;253;198;308 157;258;203;313 RBD 158 161 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The generally lower titers and small numbers of samples in the L452R group in our study may impact the fold changes. 2021 Viruses Result SARS_CoV_2 L452R 63 68 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The L452R is centrally located in the receptor-binding site and is a known resistance substitution for several mAbs. 2021 Viruses Result SARS_CoV_2 L452R 4 9 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The L452R substitution alone is responsible for the resistance of these nAbs (C, D, E, and H) as pseudoviruses bearing L452R alone or in combination with T478K (L452R + T478K) displayed identical patterns of resistance as B.1.617.2 pseudoviruses. 2021 Viruses Result SARS_CoV_2 L452R;L452R;T478K;T478K;L452R 4;119;154;169;161 9;124;159;174;166 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The L452R substitution also conferred complete resistance to four nAbs (C, D, E, and H), as previously described. 2021 Viruses Result SARS_CoV_2 L452R 4 9 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The P681H substitution in B.1.1.7 variants has been associated with enhanced virus transmissibility whereas the P681R substitution in B.1.617 variants has been associated with enhanced pathogenicity in a hamster model and transmissibility. 2021 Viruses Result SARS_CoV_2 P681H;P681R 4;112 9;117 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. These findings are in agreement with a prior report showing a 3.3-fold reduction of convalescent sera neutralization titer for C.37 pseudoviruses compared to WT(D614G), as well as L452Q and F490S single substitutions contributing to neutralization resistance. 2021 Viruses Result SARS_CoV_2 F490S;L452Q;D614G 190;180;161 195;185;166 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. These findings extend a prior study reporting that spike-binding titers in convalescent sera from unvaccinated persons were decreased 4- to 6-fold for B.1.617.2 when compared to B.1.1.7 and WT(D614G). 2021 Viruses Result SARS_CoV_2 D614G 193 198 S 51 56 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. These findings suggest that the full set of RBD substitutions in combination with substitutions outside the RBD contributes to antigenic difference of B.1.617.1, B.1.617.2, C.37, and B.1.351, while RBD substitutions alone in the WT(D614G) background do not reflect what is observed for each respective variant. 2021 Viruses Result SARS_CoV_2 D614G 232 237 RBD;RBD;RBD 44;108;198 47;111;201 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Titers against B.1.617.1 (B), AY.1, E484Q, and L452R + T478K pseudoviruses were significantly different from the titers against WT(D614G). 2021 Viruses Result SARS_CoV_2 E484Q;L452R;T478K;D614G 36;47;55;131 41;52;60;136 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Titers against B.1.617.2 (GMT 259) and AY.1 (GMT 203) pseudoviruses also showed a 1.5- and 1.9-fold reduction, respectively, compared to WT(D614G) pseudoviruses. 2021 Viruses Result SARS_CoV_2 D614G 140 145 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Titers against L452R (GMT 935 for Pfizer and 1781 for Moderna) and E484Q (GMT 798 for Pfizer and 1429 for Moderna) alone trended slightly lower. 2021 Viruses Result SARS_CoV_2 E484Q;L452R 67;15 72;20 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Unexpectedly, AY.1 was between B.1.617.2 and B.1.351 and was further away from WT(D614G) (1.89 AU) than in the convalescent sera map (1.60 AU), being positioned only slightly closer to WT(D614G) than B.1.351 was from WT(D614G) (3.02 AU). 2021 Viruses Result SARS_CoV_2 D614G;D614G;D614G 82;188;220 87;193;225 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. We also investigated the contribution of individual RBD substitutions of B.1.617.1 (L452R, E484Q) and B.1.617.2/AY.1 (K417N, L452R, T478K) on the D614G background. 2021 Viruses Result SARS_CoV_2 D614G;E484Q;L452R;T478K;K417N;L452R 146;91;125;132;118;84 151;96;130;137;123;89 RBD 52 55 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. We also note that in our study the titers of the sera from WT(D614G)-infected individuals are generally higher than the neutralization titers of the sera from L452R-infected individuals, but the small number of samples prevents a meaningful comparison. 2021 Viruses Result SARS_CoV_2 L452R;D614G 159;62 164;67 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. We found that the 50% inhibitory concentrations (IC50) of sACE2 against B.1.617.2 (IC50: 0.68 microg/mL; p < 0.01) was 4.2-fold lower, compared to WT(D614G) (IC50: 2.88 microg/mL) (Table 4 and Supplementary Figure S6). 2021 Viruses Result SARS_CoV_2 D614G 150 155 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. We further evaluated the effect of P681R substitution on furin cleavage of SARS-CoV-2 by introducing this substitution in Wuhan-Hu-1 (D614) and WT(D614G) spike backgrounds. 2021 Viruses Result SARS_CoV_2 P681R;D614G 35;147 40;152 S 154 159 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. We next assessed the neutralization potency of mRNA vaccine-elicited sera against WT(D614G) and B.1.617 variant pseudoviruses. 2021 Viruses Result SARS_CoV_2 D614G 85 90 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. We therefore investigated the impact of the B.1.617 spike substitutions on pseudovirus infectivity and found that B.1617.1, B.1.617.2, and AY.1 pseudoviruses, as well as pseudoviruses with single RBD L452R, T478K, and E484Q substitutions, displayed similar infectivity to WT(D614G) (Supplementary Figure S5). 2021 Viruses Result SARS_CoV_2 E484Q;L452R;T478K;D614G 218;200;207;275 223;205;212;280 S;RBD 52;196 57;199 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. As a confirmation of our hypothesis, we analyzed Q675H spike mutation occurrence in all the SARS-CoV-2 globally circulating lineages from the beginning of the pandemic. 2021 Viruses Result SARS_CoV_2 Q675H 49 54 S 55 60 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. As shown in Figure 1, in Italy, SARS-CoV-2 sequences carrying the Q675H mutation were uncovered for the first time in October 2020. 2021 Viruses Result SARS_CoV_2 Q675H 66 71 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. As shown in Figure 2, 5 sequences out of 11 displaying Q675H mutation we obtained gave rise to an independent cluster in the B.1 lineage. 2021 Viruses Result SARS_CoV_2 Q675H 55 60 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. As shown in Figure 7B, three active substrate conformations for Q675H and two for Q675 were selected considering arginines within the 682-RRAR-685 cleavage site: P1-S1 substrate conformation extends only the guanidine side chain of the R685 in position P1 into the S1 pocket; P1-S1/P3-S4 substrate conformation puts also the guanidine side chains of the R683 in position P3 in the S4 pocket; and P1-S1/P4-S4 substrate conformation extends R685 in position P1 and R682 in position P4 into the S1 and S4 pocket, respectively. 2021 Viruses Result SARS_CoV_2 Q675H 64 69 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Based on our findings, we hypothesize that SARS-CoV-2 Q675H spike mutation may enhance viral fitness and host adaptation. 2021 Viruses Result SARS_CoV_2 Q675H 54 59 S 60 65 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Biocomputational studies were performed to explore the role of Q675H mutation in the context of the furin binding pocket. 2021 Viruses Result SARS_CoV_2 Q675H 63 68 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Furin Has Greater Affinity for Q675H Than Q675 Substrate Conformations. 2021 Viruses Result SARS_CoV_2 Q675H 31 36 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Further analysis showed that Q675H forms a distinct H-bond network involving residues at position 676, 677, 678, and 679 that are localized near the Q675H residue (Figure 6). 2021 Viruses Result SARS_CoV_2 Q675H;Q675H 29;149 34;154 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Furthermore, the substrate conformations in the most populated clusters were distributed as follows: P1-S1 substrate conformation makes up 37% (Q675) and 30% (Q675H) of the A and B chains, respectively; P1-S1/P3-S4 substrate conformation makes up 50% (Q675) and 40% (Q675H) of the C and A chains, respectively; and P1-S1/P4-S4 substrate conformation makes up 60% (Q675H) of the chain C. 2021 Viruses Result SARS_CoV_2 Q675H;Q675H;Q675H 159;267;364 164;272;369 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. However, as shown in Figure 3, Q675H Spike mutation is documented in all the VOCs. 2021 Viruses Result SARS_CoV_2 Q675H 31 36 S 37 42 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. In B.1.438.2 and B.1.438.3 lineages, Q675H is documented in 100% of the sequences belonging to these lineages, highlighting that Q675H spike mutation is one of the characteristic mutations necessary to define these lineages. 2021 Viruses Result SARS_CoV_2 Q675H;Q675H 37;129 42;134 S 135 140 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. In fact, in September and October 2021, when B.1.617.2 lineage represented almost the totality of the circulating lineages, we observed the highest fraction of sequences carrying the Q675H spike mutation. 2021 Viruses Result SARS_CoV_2 Q675H 183 188 S 189 194 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. In order to accurately determine evolutionary relationships of the 11 SARS-CoV-2 Q675H mutants detected in Brescia within a similar European context, a maximum likelihood (ML) tree was employed. 2021 Viruses Result SARS_CoV_2 Q675H 81 86 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. In order to understand if the Q675H mutation had already occurred in Italy before our observation in Brescia, a retrospective analysis of genomes displaying this mutation was retrieved from GISAID. 2021 Viruses Result SARS_CoV_2 Q675H 30 35 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. In particular, in B.1.438.1, B.1.438.2, B.1.438.3, and B.1.1.385 lineages, Q675H and D614G are the sole mutations located in the spike protein. 2021 Viruses Result SARS_CoV_2 D614G;Q675H 85;75 90;80 S 129 134 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. In the wild-type sequences, the number of those displaying a Q675H mutation in the spike pocket for furin binding, was considerably noteworthy. 2021 Viruses Result SARS_CoV_2 Q675H 61 66 S 83 88 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Indeed, in the considered interval of time, Q675H mutants represented 40% of all the analyzed wild-type sequences, leading us to hypothesize a role of this mutation in SARS-CoV-2 adaptive evolution. 2021 Viruses Result SARS_CoV_2 Q675H 44 49 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. It is worth noting that Q675H sequences represented in the phylogenetic tree cluster in different clades, in accordance with their lineage of belonging. 2021 Viruses Result SARS_CoV_2 Q675H 24 29 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Moreover, as expected, sequences displaying the Q675H mutation were scattered across the phylogenetic tree of each VOC (Figure 4). 2021 Viruses Result SARS_CoV_2 Q675H 48 53 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Nonetheless, in B.1.617.2 lineage, the percentage of sequences carrying Q675H mutation increased with the prevalence of B.1.617.2 worldwide (Figure 3D). 2021 Viruses Result SARS_CoV_2 Q675H 72 77 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Occurrence of Q675H Mutation in Different VOCs. 2021 Viruses Result SARS_CoV_2 Q675H 14 19 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Of note, the Q675H mutation, among our samples, was found in the wild-type sequences only. 2021 Viruses Result SARS_CoV_2 Q675H 13 18 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Of note, up to 26 October 2021, eight SARS-CoV-2 lineages (B.1.438.2, B.1.438.3, B.1.438.1, B.1.1.385, P.6, P.1.9, B.1.599, B.1.544) are documented worldwide to carry the Q675H spike mutation in the majority of their sequences retrievable in GISAID. 2021 Viruses Result SARS_CoV_2 Q675H 171 176 S 177 182 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Overall, Q675H has a higher number of active substrate conformations than Q675. 2021 Viruses Result SARS_CoV_2 Q675H 9 14 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. P1-S1/P3-S4 of Q675 and P1-S1/P4-S4 of Q675H substrate conformations are those with the highest binding affinity to furin, and Figure 8 shows their binding poses in the context of furin cleavage site. 2021 Viruses Result SARS_CoV_2 Q675H 39 44 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Phylogenetic Analysis of SARS-CoV-2 Sequences Carrying Q675H Mutation. 2021 Viruses Result SARS_CoV_2 Q675H 55 60 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Q675H Confers a Lower Structural Variability to the Furin Cleavage Site Loop by Forming a Distinct H-Bond Network. 2021 Viruses Result SARS_CoV_2 Q675H 0 5 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Q675H mutation showed a positive (DeltaDeltaG value is 0.665 kcal/mol) and a negative (DeltaDeltaSVibENCoM value is -0.108 kcal.mol-1K-1) change in vibrational entropy energy between wild-type and mutant proteins. 2021 Viruses Result SARS_CoV_2 Q675H 0 5 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Reporting of SARS-CoV-2 Q675H Mutation. 2021 Viruses Result SARS_CoV_2 Q675H 24 29 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Since then, Q675H prevalence arose until December 2020, when it reached the highest occurrence. 2021 Viruses Result SARS_CoV_2 Q675H 12 17 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Stabilities of the trimeric form of the Q675 and Q675H were examined using the root mean square deviation (RMSD) of C alpha atoms. 2021 Viruses Result SARS_CoV_2 Q675H 49 54 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Substrate conformations of the Q675H have a higher binding affinity than Q675. 2021 Viruses Result SARS_CoV_2 Q675H 31 36 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. The 6 remaining clustered in the B.1.177 lineage with other European Q675H sequences, but scattered across the phylogenetic tree. 2021 Viruses Result SARS_CoV_2 Q675H 69 74 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. The binding affinity is minor for P1-S1 substrate conformation (-7,4 kcal mol-1 for Q675 and -8,5 Kcal mol-1 for Q675H), and increases for P1-S1/P3-S4 (-11,3 kcal mol-1 for Q675 and -11,18 kcal mol-1 for Q675H), and for P1-S1/P4-S4 (-15,6 kcal mol-1 for Q675H) substrate conformations (Figure 7B). 2021 Viruses Result SARS_CoV_2 Q675H;Q675H;Q675H 113;204;254 118;209;259 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. The P1-S1/P4-S4 substrate conformation was observed only for Q675H. 2021 Viruses Result SARS_CoV_2 Q675H 61 66 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. The Q675H mutation is located in the spike protein adjacent to the polybasic S1/S2 furin cleavage site 682-RRAR*S-686. 2021 Viruses Result SARS_CoV_2 Q675H 4 9 S 37 42 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. The RMSD plot shows that the three chains of the Q675 and Q675H have a similar deviation of about 4 A (Figure 5). 2021 Viruses Result SARS_CoV_2 Q675H 58 63 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. The visual inspection of the curvature (kappa) and torsion (tau) values observed on the furin cleavage site loop shows that compared to Q675 chains (Figure 6A-C), a lower structural variability in spanning residues ranging from 675 to 683 in the Q675H chains was observed (Figure 6D-F). 2021 Viruses Result SARS_CoV_2 Q675H 246 251 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Therefore, it is likely to assume that the gain of fitness of wild-type lineages prompted by Q675H spike mutation itself had to be modest compared to mutations in RBD displayed by B.1.1.7 and B.1.617.2 lineages, which are known to confer a higher binding affinity of spike to ACE2 and increase virus infectivity. 2021 Viruses Result SARS_CoV_2 Q675H 93 98 S;S;RBD 99;267;163 104;272;166 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. These findings further suggest that Q675H mutation may arise in phylogenetically distant VOCs by a homoplasy event. 2021 Viruses Result SARS_CoV_2 Q675H 36 41 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. This finding leads to the hypothesis of the emergence of Q675H mutation by homoplasy, a process of parallel evolution, in which different populations, in different countries, have acquired the same advantageous genome mutations, multiple times, independently and in separate evolutionary clades. 2021 Viruses Result SARS_CoV_2 Q675H 57 62 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. This is due to the fact that Q675H always presents a y-conformation with the three arginines alternatively arranged. 2021 Viruses Result SARS_CoV_2 Q675H 29 34 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. To attest to its role in virus adaptive evolution, we analyzed worldwide the occurrence of Q675H mutation in SARS-CoV-2 VOCs through GISAID available data ( accessed on 1 December 2021). 2021 Viruses Result SARS_CoV_2 Q675H 91 96 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. To further characterize the structural stability and dynamic features of spike expressing Q675 or Q675H, we performed 200 ns molecular dynamics (MDs) simulations starting from the 6VXX (close conformation) charm-gui model (aa 1-1146) without glycans. 2021 Viruses Result SARS_CoV_2 Q675H 98 103 S 73 78 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. To note, when B.1.1.7 and B.1.617.2 lineages firstly emerged, neither of them carried the Q675H spike mutation. 2021 Viruses Result SARS_CoV_2 Q675H 90 95 S 96 101 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. We found that Q675H mutation was due to a transition at nucleotide position 23,588 (G->C or G->T). 2021 Viruses Result SARS_CoV_2 Q675H 14 19 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Whole genome sequencing was performed successfully in our laboratory for 11 SARS-CoV-2 Q675H mutants. 2021 Viruses Result SARS_CoV_2 Q675H 87 92 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Worldwide Analysis of SARS-CoV-2 Lineages Carrying the Q675H Spike Mutation. 2021 Viruses Result SARS_CoV_2 Q675H 55 60 S 61 66 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. All the missed mutations were due to a lack of coverage (<10 reads) and were grouped on the same amplicon NC_045512.2:22903-23122 (missing mutations: N440K, S477N, T478K, E484K, N501Y, A522S). 2021 Viruses Result SARS_CoV_2 A522S;E484K;N440K;N501Y;S477N;T478K 185;171;150;178;157;164 190;176;155;183;162;169 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. For example, a variant harboring mutations S477N and D614G was identified as belonging to lineage B.1.160. 2021 Viruses Result SARS_CoV_2 D614G;S477N 53;43 58;48 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. Taken together, the most frequently missed mutations were G142D (n = 11), E156G, 157del, 158del (n = 6), N501Y (n = 6), S477N (n = 5), T95I (n = 3), V130F (n = 2), and E484K (n = 2). 2021 Viruses Result SARS_CoV_2 157del;158del;E156G;E484K;G142D;N501Y;S477N;T95I;V130F 81;89;74;168;58;105;120;135;149 87;95;79;173;63;110;125;139;154 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. The missing mutations were not located in the same region as previously, but rather over the amplicon NC_045512.2:21743-21961 (T95I, V130F, G142D, E156G, F157del, and R158del, A222V). 2021 Viruses Result SARS_CoV_2 A222V;E156G;F157del;G142D;R158del;V130F;T95I 176;147;154;140;167;133;127 181;152;161;145;174;138;131 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. The same minority variants were detected with both protocols in three samples and the resulting percentages were quite similar (L5F: 46.4% with PacBio and 25.6% with Illumina; L176F: 22.6% with PacBio and 37.5% with Illumina; and 27.4% with PacBio and 31.2% with Illumina). 2021 Viruses Result SARS_CoV_2 L176F;L5F 176;128 181;131 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. Among the mutated residues, R346A, K444A, G446A, and N450A resulted in a near loss of P36-5D2 binding ( Figures 3A, C ). 2021 Frontiers in immunology Result SARS_CoV_2 G446A;K444A;N450A;R346A 42;35;53;28 47;40;58;33 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. At a resolution of 3.1 A, we found that P36-5D2 recognized an epitope consisting of 11 residues (T345, R346, L441, K444, V445, G446, G447, Y449, N450, T470, and F490) on RBD, devoid of the three key mutant residues K417N, E484K, and N501Y that facilitated escape from the neutralization of many mAbs, including some approved for EUA ( Figure 2A ). 2021 Frontiers in immunology Result SARS_CoV_2 E484K;K417N;N501Y 222;215;233 227;220;238 RBD 170 173 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. Consistent with the crystal structure analysis, the cryo-EM structure clearly demonstrated that the mutant residues K417N, E484K, and N501Y were not involved in the P36-5D2 epitope. 2021 Frontiers in immunology Result SARS_CoV_2 E484K;K417N;N501Y 123;116;134 128;121;139 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. Furthermore, among the 11 pesudoviruses bearing alanine mutated spikes, nine were able to confer resistance to P36-5D2, while the remaining two (L441A and T470A) had a relatively weaker impact ( Figure 3F ). 2021 Frontiers in immunology Result SARS_CoV_2 T470A;L441A 155;145 160;150 S 64 70 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. In contrast, P36-1B7, like the class I mAb CB6, was substantially impacted by the SARS-CoV-2 Alpha, Beta, and Gamma variants, largely due to K417N/T and N501Y mutations. 2021 Frontiers in immunology Result SARS_CoV_2 K417N;K417T;N501Y 141;141;153 148;148;158 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. P36-1A3 appeared to be heavily affected by N501Y and K417-E484K-N501Y mutations. 2021 Frontiers in immunology Result SARS_CoV_2 N501Y;E484K;N501Y 43;58;64 48;63;69 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. P36-5D2 Binds to a Highly Conserved Epitope on RBD and Avoids Three Key Mutant Residues (K417N, E484K, and N501Y) 2021 Frontiers in immunology Result SARS_CoV_2 E484K;N501Y;K417N 96;107;89 101;112;94 RBD 47 50 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. P36-5D2 Binds to a Highly Conserved Epitope on RBD and Avoids Three Key Mutant Residues (K417N, E484K, and N501Y). 2021 Frontiers in immunology Result SARS_CoV_2 E484K;N501Y;K417N 96;107;89 101;112;94 RBD 47 50 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. P74-6D2 demonstrated reduced or loss of neutralizing activities to the three VOCs, which was largely attributed to E484K, similar to the class II control mAb BD368-2 and the class I control mAb REGN10933. 2021 Frontiers in immunology Result SARS_CoV_2 E484K 115 120 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. To reveal the molecular basis of the broad and potent neutralizing activity of P36-5D2, we determined the crystal structure of its antigen-binding fragment (Fab) bound to the RBD-3M carrying the K417N, E484K, and N501Y mutations initially identified in the SARS-CoV-2 Beta variant. 2021 Frontiers in immunology Result SARS_CoV_2 E484K;K417N;N501Y 202;195;213 207;200;218 RBD 175 178 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. Two resides, K444A and V445A, also resulted in a substantial reduction in REGN10987 binding ( Figure 3D ), consistent with the epitope residues defined by structural analysis. 2021 Frontiers in immunology Result SARS_CoV_2 K444A;V445A 13;23 18;28 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. According to Table 1, the binding free energy (DeltaG bind) of SpikeWT/Biliverdin (-18.60 kcal/mol) is stronger than that of SpikeR190K/Biliverdin (-15.39 kcal/mol), which is in line with the fact that the R190K mutant would increase the Km value from 9.8 to 1,500 nM. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 R190K 206 211 S 125 130 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. As mentioned above, the mutation of R190K reduced the affinities of the biliverdin to Arg102 and Lys190. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 R190K 36 41 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. In SpikeR190K/Biliverdin (Figure 5B), however, Lys190 could be simultaneously integrated with Ser94, Glu96, Asn99, and Ile101, forming six hydrogen bonds in total. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 R190K 8 13 S 3 8 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. Intriguingly, a strong Asn99-Asp178 hydrogen bond is formed in SpikeN121Q/Biliverdin (Figure 7C), which triggers the gate loop approaching and narrowing the binding pocket of the biliverdin. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N121Q 68 73 S 63 68 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. It is not hard to find that the N121Q mutation had the N-terminal residues of the gate (residues 175 to 178) dramatically changed in contrast to the other two systems (Figure 7A). 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N121Q 32 37 N 55 56 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. The N121Q mutant likely leads the biliverdin binding as a differential pose when concerning the wild-type state. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N121Q 4 9 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. To further investigate how the N121Q mutant affects biliverdin binding affinity, we draw attention to hydrogen bonds around residue 121 in all three systems. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N121Q 31 36 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. Unexpectedly, the calculated DeltaG bind of SpikeN121Q/Biliverdin is -18.45 kcal/mol, comparable to the case of WT, which is different from the previous findings that the N121Q mutant is more sensitive to the binding interaction of biliverdin to SARS-CoV-2 spike. 2021 Frontiers in molecular biosciences Result SARS_CoV_2 N121Q 171 176 S;S 44;257 49;262 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Although the surface detection level of the Lambda variant was comparable to those of the Lambda + N246-253RSYLTPGD derivative and other NTD mutants tested (T76I, GT75-76VI, and RSYLTPGD246-253N) (Figure 2K), the augmented enhancement of viral infectivity was specific for the Lambda S (Figure 2L). 2022 Cell reports Result SARS_CoV_2 T76I 157 161 S 284 285 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. As shown in Figure 2H, the G75V, T76I, GT75-76VI, and T859N mutations did not affect vaccine-induced neutralization. 2022 Cell reports Result SARS_CoV_2 G75V;T76I;T859N 27;33;54 31;37;59 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. As shown in Figures 2I and 2J, the 4A8 antibody detected the cell surface expression of S proteins of the parental virus, Lambda + N246-253RSYLTPGD derivative, G75V, T76I, and GT75-76VI and inhibited the infections of these pseudoviruses in a dose-dependent manner. 2022 Cell reports Result SARS_CoV_2 G75V;T76I 160;166 164;170 S 88 89 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. As the control of this experiment, the pseudoviruses with the S protein of the D614G-bearing isolate (B.1 lineage), which spread in the early pandemic (i.e., during early 2020 and before the emergence of VOCs/VOIs), were prepared, and this is referred to as "parental virus" in this study. 2022 Cell reports Result SARS_CoV_2 D614G 79 84 S 62 63 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Because an apparent enhancement of viral infectivity compared to the parental S pseudovirus was not observed in the substituted mutants (G75V, T76I, GT75-76VI, and RSYLTPGD246-253N) (Figure 2L), our data suggest that multiple mutations in the NTD of Lambda S are crucial for the augmented enhancement of viral infectivity. 2022 Cell reports Result SARS_CoV_2 T76I;G75V 143;137 147;141 S;S 78;257 79;258 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Evasion of vaccine-induced cellular immunity induced by the L452Q mutation. 2022 Cell reports Result SARS_CoV_2 L452Q 60 65 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Figure 2E shows that the G75V mutation significantly reduces viral infectivity (p = 0.0004, by Student's t test), while the T76I and GT75-76VI mutations significantly increase viral infectivity (p = 0.0011, T75I versus parental; p = 0.012, GT75-76TI versus parental by Student's t test). 2022 Cell reports Result SARS_CoV_2 G75V;T75I;T76I 25;207;124 29;211;128 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. However, the lower infectivity of the Alpha variant compared to the D614G-bearing early pandemic virus, analyzed by pseudovirus assay (Figure 2A), is consistent with a previous report. 2022 Cell reports Result SARS_CoV_2 D614G 68 73 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. However, the sister group of Lambda variants does not contain any of the 7 mutations, excluding D614G in their S proteins (Figure S1A). 2022 Cell reports Result SARS_CoV_2 D614G 96 101 S 111 112 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. However, there were no viral sequences harboring the G75V mutation without the T76I mutation (Figure S1A). 2022 Cell reports Result SARS_CoV_2 G75V;T76I 53;79 57;83 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. In addition, 91.5% (1,746/1,908) of the Lambda variant sequences had these 2 mutations, and the phylogenetic tree of the Lambda variant indicated that the variant harboring either G75V or T76I sporadically emerged during the epidemic of the Lambda variant (Figure S1A). 2022 Cell reports Result SARS_CoV_2 G75V;T76I 180;188 184;192 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. In addition, the binding affinity of the SARS-CoV-2 RBD to soluble ACE2 was significantly increased by the insertion of the L452Q mutation, but not the F490S mutation (Figure 2F: p = 0.0004, L452Q versus parental; p = 0.92, F490S versus parental; p = 0.0002, L452Q/F490S versus parental by Student's t test). 2022 Cell reports Result SARS_CoV_2 F490S;F490S;L452Q;L452Q;L452Q;F490S 152;224;124;191;259;265 157;229;129;196;264;270 RBD 52 55 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. In addition, we found that the L452Q and F490S mutations confer resistance to vaccine-induced antisera (Figure 2H). 2022 Cell reports Result SARS_CoV_2 F490S;L452Q 41;31 46;36 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. In contrast, the L452Q mutation not only increases viral infectivity (Figure 2E) and affinity to ACE2 (Figure 2F) but also augments resistance to the vaccine-induced antiviral cellular (Figure 2G) and humoral immunities (Figure 2H), suggesting that this mutation is critical for the viral dissemination in the human population. 2022 Cell reports Result SARS_CoV_2 L452Q 17 22 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. In sharp contrast, 2 substitutions of the NF9 peptide, NF9-L452R and NF9-L452Q, faintly activated the NF9-specific CTLs (Figures 2G and S2H). 2022 Cell reports Result SARS_CoV_2 L452Q;L452R 73;59 78;64 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. In the 1,908 sequences of the Lambda variant (C.37 lineage), the majority of the S protein sequence of the genuine Lambda variants contains 6 substitution mutations (G75V, T76I, L452Q, F490S, D614G, and T859N) and a 7-amino acid deletion in the NTD (RSYLTPGD246-253N) (Figure S1A). 2022 Cell reports Result SARS_CoV_2 D614G;F490S;L452Q;T76I;T859N;G75V 192;185;178;172;203;166 197;190;183;176;208;170 S 81 82 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Interestingly, we recently demonstrated that the L452R mutation, a hallmark mutation in the Delta and Epsilon variants, could induce evasion of the antiviral effects triggered by HLA-A24-restricted cytotoxic T lymphocytes (CTLs). 2022 Cell reports Result SARS_CoV_2 L452R 49 54 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Structural analysis showed that the 3 mutations, G75V, T76I, and RSYLTPGD246-253N, are in the NTD (Figure 2C), and the RSYLTPGD246-253N mutation is located in a loop structure, which was designated as loop 5 (residues 246-260) in a previous study (Figure 2D). 2022 Cell reports Result SARS_CoV_2 G75V;T76I 49;55 53;59 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. The finding that the F490S mutation does not affect viral infectivity (Figure 2E) but confers the resistance to the vaccine-induced antisera (Figure 2H) suggests that this mutant has acquired resistance to antiviral humoral immunity. 2022 Cell reports Result SARS_CoV_2 F490S 21 26 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. The G75V and T76I mutations are located at the flexible loop adjacent to loop 5 (Figure 2C). 2022 Cell reports Result SARS_CoV_2 G75V;T76I 4;13 8;17 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. The infectivity of the T859N mutation was also similar to that of the parental pseudovirus (Figure 2E). 2022 Cell reports Result SARS_CoV_2 T859N 23 28 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. The L452Q and F490S mutations are situated in the receptor-binding motif in the RBD (Figures 2C and 2D), but neither residue is in direct contact with the angiotensin-converting enzyme 2 (ACE2) receptor (Figure S2E). 2022 Cell reports Result SARS_CoV_2 F490S;L452Q 14;4 19;9 RBD 80 83 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. The T859N mutation is in the heptad repeat 1 of the S2 subunit (Figure 2C). 2022 Cell reports Result SARS_CoV_2 T859N 4 9 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. These findings suggest that T76I is a compensatory mutation to recover the decreased infectivity by the G75V mutation. 2022 Cell reports Result SARS_CoV_2 G75V;T76I 104;28 108;32 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. These results suggest that the NF9 peptide is an immunodominant epitope in HLA-A*24:02+ vaccinated individuals and that the L452Q mutation potentially results in evasion of HLA-A24-restricted cellular immunity. 2022 Cell reports Result SARS_CoV_2 L452Q 124 129 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. These results suggest that the T76I and L452Q mutations are responsible for the higher infectivity of Lambda S (Figure 2E). 2022 Cell reports Result SARS_CoV_2 L452Q;T76I 40;31 45;35 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. To address this possibility, we prepared two Lambda S derivatives, N246A and N246Q, which abolished the NLGS (Figure 3A). 2022 Cell reports Result SARS_CoV_2 N246A;N246Q 67;77 72;82 S 52 53 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. To determine whether the L452Q mutation in the Lambda variant can contribute to evasion of HLA-A24-restricted anti-SARS-CoV-2 cellular immunity, as in the case of the L452R mutation, we obtained peripheral blood mononuclear cells (PBMCs) from HLA-A*24:02+ individuals vaccinated with BNT162b2 and stimulated these cells with the NF9 peptide (Table S5). 2022 Cell reports Result SARS_CoV_2 L452Q;L452R 25;167 30;172 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. We next examined 6 substitution mutations (G75V, T76I, L452Q, F490S, D614G, and T859N) and a deletion mutation (RSYLTPGD246-253N) of the Lambda variant in the structure of the SARS-CoV-2 S protein. 2022 Cell reports Result SARS_CoV_2 D614G;F490S;L452Q;T76I;T859N;G75V 69;62;55;49;80;43 74;67;60;53;85;47 S 187 188 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. We then assessed whether the L452Q mutation evades the HLA-A24-restricted cellular immunity induced by BNT162b2 vaccination. 2022 Cell reports Result SARS_CoV_2 L452Q 29 34 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. When we focused on the effect of the mutations in the RBD, the L452Q and L452Q/F490S mutations significantly increased viral infectivity (p = 0.0011, L452Q versus parental; p = 0.0003, L452Q/F490S versus parental by Student's t test), while the F490S mutation did not (Figure 2E). 2022 Cell reports Result SARS_CoV_2 F490S;L452Q;L452Q;L452Q;L452Q;F490S;F490S 245;63;73;150;185;191;79 250;68;78;155;190;196;84 RBD 54 57 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. 2B) whereas Cys480, Asn481 and Gly482 in V367F MT. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 V367F 41 46 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. 2C), Ser477 in R408I. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 R408I 15 20 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. 2D), Cys480 and Asn481 in G476S. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S 26 31 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. 2E), Ala483 and Glu484 in V483A and Asn481, Gly482. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 V483A 26 31 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. 2F), Val483 and Glu484 in N501Y MT. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 N501Y 26 31 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. 3B), while an average of 378.9, 388.5, 387.8, 373.4, 391.2, and 383.6 H-bonds of WT, V367F, R408I, G476S, V483A and N501Y were formed with the solvent molecule, respectively. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 99;116;92;85;106 104;121;97;90;111 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. 5A and E), while downward motions have existed in the loop regions of V367F, R408I and G476S MTs. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;R408I;V367F 87;77;70 92;82;75 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Additionally, an extended loop was present near to C-terminal harboured 2 mutations such as G476S and V483A, while N501Y mutation was located near to the end of C-terminal. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;N501Y;V483A 92;115;102 97;120;107 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. All MTs and WT showed mean RMSFs in the range of 0.14-0.2, excluding extended loop segment WT, V367F, R408I, G476S, V483A and N501Y MTs, respectively. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 109;126;102;95;116 114;131;107;100;121 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. An average SASA (total) values of WT, V367F, R408I, G476S, V483A and N501Y MTs were 103.2, 106.8, 106, 104.6, 108.7 and 108.3 nm2, respectively. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 52;69;45;38;59 57;74;50;43;64 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Average values of hydrophobic SASA were lied in the range of 54.2 nm2 for WT (low)-58 nm2 for V483A (high). 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 V483A 94 99 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. During binding energy analysis, electrostatic energy had a major contribution in total binding energy which were -212.3 (+-27.8), -185.3 (+-29.3), -213.5 (+-14.2), -244.6 (+-9.7), -214.6 (+-18.2) and -210.4 (+-20.3) for ACE2-WT, -V367F, -R408I, -G476S, -V483A and -N501Y MT complexes, respectively (Table 2). 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 246;265;238;230;254 251;270;243;235;259 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. During H-bond analysis, we observed that MTs exhibited high number of intra and inter H-bonds than WT except for G476S MT, which formed a lesser number of inter H-bonds. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S 113 118 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. During the projection of PC1 vs PC2 analysis, N501Y occupied a larger sub space whereas the rest of MTs and WT engaged smaller subspaces. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 N501Y 46 51 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. ED results showed that N501Y MT exhibited a large conformational change at the extended loop and other random moieties of protein, implying that these regions might play a crucial role in acquiring the stable conformation. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 N501Y 23 28 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. HADDOCK results indicated that there are minor changes in the binding energies of all WT and MTs except R408I. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 R408I 104 109 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. HADDOCK score of topmost clusters for ACE2-WT, -V367F, -R408I, -G476S, -V483A and -N501Y MT complexes were -122.9 (+-3.3), -122 (+-2.2), -114.2 (+-2), -121.4 (+-2.6), -122.1 (+-2.3) and -124.4 (+-3.1), respectively. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 64;83;56;48;72 69;88;61;53;77 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. In case of N501Y, four residues, namely Valine 350, Tyrosine451, Tyrosine453 and Tyrosine495 (V350, Y451, Y453 and Y495) were had higher CB values. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 N501Y 11 16 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. It comprized ~26 amino acid long segment (470-495) showed an average RMSFs of ~0.37, ~0.70, ~0.39, ~0.38, ~0.32 and ~0.46 nm for WT, V367F, R408I, G476S, V483A and N501Y MTs, respectively. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 147;164;140;133;154 152;169;145;138;159 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Moreover, mixed motions were found in N501Y MT, as downward and upward motions exhibited by the extended loop and rotational motions were found in N-terminal region. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 N501Y 38 43 N 147 148 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Moreover, N501Y MT exhibited additional motions near N-terminal beside the motion at extended loop region. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 N501Y 10 15 N 53 54 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Moreover, V367F and R408I MTs displayed higher deviations, whereas G476S MT exhibited lower deviation then WT, V483A and N501Y MTs. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 67;121;20;10;111 72;126;25;15;116 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Out of which, the first 3 eigenvectors accompanied with maximum motions and their cumulative percentage were 77.04, 87.4, 65.27, 67.33, 63.26 and 68.62% for WT, V367F, R408I, G476S, V483A, and N501Y MTs, respectively. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 175;193;168;161;182 180;198;173;166;187 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Preliminary analyses of effects of different mutations on 3D structure were predicted through MUpro and I-mutant servers and found that all mutant except N501Y showed decreased structure stabilities (Tables S4 and S5). 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 N501Y 154 159 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Protein compactness or globularity was measured by employing the radius of gyration (Rg) and found that average Rg values of ~1.76, ~1.74, ~1.72, ~1.79, ~1.77 and ~1.78 nm were obtained for WT, V367F, R408I, G476S, V483A and N501Y MTs, respectively. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 208;225;201;194;215 213;230;206;199;220 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Rgs were slightly reduced in V367F and R408I MTs, whereas G476S, V483A and N501Y MTs showed slightly higher Rg then WT. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 58;75;39;29;65 63;80;44;34;70 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. The above results showed that N501Y mutant undergoes large conformational changes. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 N501Y 30 35 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. The upward motions were found in the extended loop of WT and V483A MT. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 V483A 61 66 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. To assess the structural stabilities of WT and MTs (V367F, R408I, G476S, V483A and N501Y), root mean square deviation (RMSD) of protein backbone with respect to equilibrium structures were calculated and found that average RMSD values of ~0.37 for WT, ~0.47 for V367F, ~0.48 for R408I, ~0.35 for G476S, ~0.43 for V483A and ~0.40 nm for N501Y MTs were existed. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;G476S;N501Y;N501Y;R408I;R408I;V367F;V483A;V483A;V367F 66;296;83;336;59;279;262;73;313;52 71;301;88;341;64;284;267;78;318;57 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Topmost clusters size of ACE2-WT, -V367F, -R408I, -G476S, -V483A and -N501Y MT complexes were had 168, 169, 127, 175, 176 and 62 structures, respectively (Table 2 ). 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 51;70;43;35;59 56;75;48;40;64 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. V367F and R408I MTs were present in between beta-sheets 1 and 2, beta-sheet 3 and 4, respectively. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 R408I;V367F 10;0 15;5 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. V367F, R408I and N501Y MTs displayed slightly higher RMSFs, whereas V483A MT displayed lower RMSF then WT, indicating that V367F, R408I and N501Y MTs were more flexible and V483A MT was less flexible or more rigid than WT. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 N501Y;N501Y;R408I;R408I;V367F;V483A;V483A;V367F 17;140;7;130;123;68;173;0 22;145;12;135;128;73;178;5 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Various MT models were generated in PyMOL by replacing Valine367 with Phenylalanine (V367F), Arginine408 with Isoleucine (R408I), Glutamine476 with Serine (G476S), Valine483 with Alanine (V483A) and Asparagine501 with Tyrosine (N501Y) in WT 3D structure. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 R408I;N501Y;Q476S;V367F;V483A;G476S;N501Y;R408I;V367F;V483A 93;199;130;55;164;156;228;122;85;188 120;226;154;83;186;161;233;127;90;193 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. We found that V367F and V483A MTs showed increased binding affinities while R408I, G476S and N501Y MTs exhibited decreased binding affinities (Table 3 ). 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 83;93;76;14;24 88;98;81;19;29 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. While hydrophilic SASA values were in the range of 49 nm2 for WT (low)-51.5 nm2 for N501Y (high). 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 N501Y 84 89 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. WT and other mutants such as V367F, R408I, G476S, and V483A showed only one residue (Tyrosine453) as par with threshold CB value which is located in the beta-sheet region of the protein. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;R408I;V367F;V483A 43;36;29;54 48;41;34;59 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. WT, V367F, R408I, G476S, V483A, and N501Y MTs exhibited an average of 112.3, 105.5, 106.4, 115, 107.1, and 109.4 intra H-Bonds, respectively. 2022 Computer methods and programs in biomedicine Result SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 18;36;11;4;25 23;41;16;9;30 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Among substitution, two in nsp1 (Q63L, G82S), seven in nsp2 (R197C, K261 N, F275L, K292E, V378I, D448 N, V627F) and one deletion at N449, Nine amino acids substitutions in nsp3 (L1174I, T1246I, K1308 N, T1754I, T2016K, T2408F, L2564F, A2619V, Q2702H), two substitutions (T2848I, P2926L and five amino acid deletion 3153-3157) in nsp4, four in nsp5 (G3278S, L3393F, K3353R, P3447S), Two in nsp6 (L3606F, A3656V), one in nsp8 (P4075S), four in nsp12 (A4489V, P4715L, A4921V, V4979L), two in nsp13 (T5451I, A5561T), one substitution (L6082F), seven amino acid deletion (6418-6424) in nsp14, one in nsp15 (V6600F) while no mutation was observed in nsp7, nsp9, nsp10, and nsp16. 2022 Computers in biology and medicine Result SARS_CoV_2 A2619V;A3656V;A4921V;A5561T;D448N;F275L;G82S;K1308N;K261N;K292E;K3353R;L2564F;L3393F;P2926L;P3447S;P4715L;Q2702H;T1246I;T1754I;T2016K;T2408F;V378I;V4979L;V627F;A4489V;G3278S;L1174I;L3606F;L6082F;P4075S;Q63L;R197C;T2848I;T5451I;V6600F 235;403;465;504;97;76;39;194;68;83;365;227;357;279;373;457;243;186;203;211;219;90;473;105;449;349;178;395;531;425;33;61;271;496;602 241;409;471;510;103;81;43;201;74;88;371;233;363;285;379;463;249;192;209;217;225;95;479;110;455;355;184;401;537;431;37;66;277;502;608 Nsp13;Nsp12;Nsp2;Nsp3;Nsp4;Nsp7;Nsp8;Nsp5;Nsp6 489;442;55;172;329;644;419;343;389 494;447;59;176;333;648;423;347;393 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Among the non-structural proteins, nsp3 have four mutation hotspots S944L (11%), T1246I (11%), K1305 N (8%), NSP12 have one P4715L (57%), NSP15 have one V6600F (5%) mutation hotspots in Pakistani isolates as compared with the reference (Wuhan NC_045512.2). 2022 Computers in biology and medicine Result SARS_CoV_2 K1305N;P4715L;S944L;T1246I;V6600F 95;124;68;81;153 102;130;73;87;159 Nsp12;Nsp3;N 109;35;101 114;39;102 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Among the NSPs, the mutation P4715L in NSP12 was observed in 172 countries globally, followed by L3606F in NSP3, which occurred in 134 countries. 2022 Computers in biology and medicine Result SARS_CoV_2 L3606F;P4715L 97;29 103;35 Nsp3 107 111 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Among the substation, two substations of nsp3 T1246I and K1308 N co-occurred with substitution G3278S and P4715L of nsp5 and nsp12, respectively in isolates MW031799.1, MW031800.1, MW031801.1, MW031802.1. 2022 Computers in biology and medicine Result SARS_CoV_2 G3278S;K1308N;P4715L;T1246I 95;57;106;46 101;64;112;52 Nsp12;Nsp3;Nsp5;N 125;41;116;63 130;45;120;64 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. As a result, the D614G, Q677H double mutant enhanced binding efficiency, and this mutant, as well as other interface residues, are important hotspots for therapeutic development against SARS-CoV-2 variants. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;Q677H 17;24 22;29 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. As given in Table 5 , the total binding energy for the D614G-Q677H variant was -75.78 kcal/mol followed by the D614G-S943T-V622F variant -75.17 kcal/mol and -73.84 kcal/mol for the N74K-D614G variant. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;D614G;N74K;D614G;Q677H;S943T;V622F 55;111;181;186;61;117;123 60;116;185;191;66;122;128 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. As previously stated, the D614G-V622F-S943F mutation is responsible for enhancing the dissemination and infectivity of the SARS-CoV-2 variant and increasing the binding affinity and infectivity. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;S943F;V622F 26;38;32 31;43;37 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Estimation of the KD revealed that D614G-S943T-V622F (2.0 E-10) variant binds stronger than all. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;S943T;V622F 35;41;47 40;46;52 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. In isolate MT500122 the substation D448 N has preceded a deletion of N449 amino acid in nsp2. 2022 Computers in biology and medicine Result SARS_CoV_2 D448N 35 41 Nsp2;N 88;40 92;41 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. In ORF10, single substitution V30L has been observed in two isolates MT 879619.1 and MW242667.1. 2022 Computers in biology and medicine Result SARS_CoV_2 V30L 30 34 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. In these SARS-COV2 isolates, a signature Q57H substitution in ORF3 protein was observed in 23 out of 50 samples which is the second frequent mutation in these Pakistani isolates. 2022 Computers in biology and medicine Result SARS_CoV_2 Q57H 41 45 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Interestingly, among all recurrent mutations in structural protein, the spike protein has one D614G (82%), nucleocapsid had three S194L (20%), R203K (14%), G204R (14%) R209I (25%) mutation hotspot. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;G204R;R203K;R209I;S194L 94;156;143;168;130 99;161;148;173;135 N;S 107;72 119;77 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Interestingly, in Pakistani SARS-COV-2 isolates, a new mutation in ORF8, W45L was observed in the present study, while 35 out of 50 isolates have the ORF8-L genotype. 2022 Computers in biology and medicine Result SARS_CoV_2 W45L 73 77 ORF8;ORF8 67;150 71;154 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Moreover, the strength of the wild type and mutants was ranked as D614G-Q677H variant (1.0 E-09), wild type (1.9 E-09) while for the N74K-D614G variant the predicted KD value was 2.2 E-09. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;N74K;D614G;Q677H 66;133;138;72 71;137;143;77 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Mutation R203K in nucleocapsid protein was observed in 151 countries. 2022 Computers in biology and medicine Result SARS_CoV_2 R203K 9 14 N 18 30 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. On the other hand, the D614G-S943T-V622F variant complex demonstrated unstable dynamics at different times interval thus corroborated with the servers' predicted results. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;S943T;V622F 23;29;35 28;34;40 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Recently reported mutations in the spike proteins of SARS-CoV-2 from South Africa (Lys417Asn, Glu484Lys, Asn501Tyr) (501Y.V2Variant) and Brazil (Lys417Asn, Glu484Lys, Asn501Tyr) had led these strains to evade the vaccines successfully. 2022 Computers in biology and medicine Result SARS_CoV_2 N501Y;N501Y;E484K;E484K;K417N;K417N 105;167;94;156;83;145 114;176;103;165;92;154 S 35 40 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Several mutations have been reported in the ORF8 protein, but L84S is a highly recurred mutation observed in 100 countries. 2022 Computers in biology and medicine Result SARS_CoV_2 L84S 62 66 ORF8 44 48 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Surprisingly, in the spike protein, the D614G substitution was associated with two consecutive series of two substitutions R203K, and G204R of the nucleocapsid phosphoprotein in five isolates (MW031799.1, MW031800.1, MW031801.1, MW0831802.1, and MW031803.1). 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;G204R;R203K 40;134;123 45;139;128 N;S 147;21 159;26 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The accessory protein the ORF3A has one mutation hotspot Q57H (63%). 2022 Computers in biology and medicine Result SARS_CoV_2 Q57H 57 61 ORF3a 26 31 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The binding comparison revealed significant variation in the spike RBD binding between the wild type, D614G-V622F-S943F, and D614G-Q677H double mutants. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;D614G;Q677H;S943F;V622F 102;125;131;114;108 107;130;136;119;113 S;RBD 61;67 66;70 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The D614G mutation in spike protein has been reported to strengthen the folding stability of the spike protein. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G 4 9 S;S 22;97 27;102 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The D614G mutation of the spike protein where Aspartic acid (D) with a polar negative side charged amino acid is substituted with Glycine (G) with a nonpolar side chain amino acid. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G 4 9 S 26 31 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The enhanced interaction is due to substituted residue D614G, V622F, S943F in the spike protein complex. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;S943F;V622F 55;69;62 60;74;67 S 82 87 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The HDOCK docking score for D614G-V622F-S943F (ACE2-spike RBD) was reported as -13.70 kcal/mol. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;S943F;V622F 28;40;34 33;45;39 S;RBD 52;58 57;61 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The HDOCK docking score for D614G, Q677H (ACE2-spike RBD), was -13.42 kcal/mol. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;Q677H 28;35 33;40 S;RBD 47;53 52;56 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The hydrogen bonds formed by the ACE2- N74K, D614G spike (RBD) include Gln493-Glu35, Gln493-Lys31, Tyr453-His34, Lys417-Asp30, Thr500-Tyr41, Tyr449-Asp38, Tyr505-Glu37, Gly502-Lys353, Tyr449- Lys353, Gln498-Lys353, and double hydrogen bond between Thr500-Tyr41(Fig. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;N74K 45;39 50;43 S;RBD 51;58 56;61 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The L1174I mutation in NSP3 was observed only in 2 countries. 2022 Computers in biology and medicine Result SARS_CoV_2 L1174I 4 10 Nsp3 23 27 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The other less common mutation that co-occurred with D614G was N74K, V622F, Q677H, S943T, and D1153G (Table 1). 2022 Computers in biology and medicine Result SARS_CoV_2 D1153G;D614G;N74K;Q677H;S943T;V622F 94;53;63;76;83;69 100;58;67;81;88;74 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The predicted score of HDOCK for the ACE2-N74K, D614G mutant spike protein was -12.50 which is comparable with the wild-type complex. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;N74K 48;42 53;46 S 61 66 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The prevalence of Q57H substitution in ORF3 protein was reported relatively high (62.7%) in South Africa. 2022 Computers in biology and medicine Result SARS_CoV_2 Q57H 18 22 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The Q57H substitution in ORF3 co-occurs with two other amino acids mutations K21 N and T223I, in isolates MW447644.1, MW447642.1 respectively. 2022 Computers in biology and medicine Result SARS_CoV_2 K21N;Q57H;T223I 77;4;87 82;8;92 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The spike protein of 29 out 50 samples of SARS-COV2 Pakistani isolates harbors a signature D614G mutation indicative of the widespread mutation in Pakistani isolates. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G 91 96 S 4 9 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Therefore, we used HDOCK to perform the docking of ACE2 with the wild-type and double mutant spike protein (D614G-V622F-S943F D614G-Q677H and N74K-D614G) to explain how these mutations led to the higher infectivity of SARS-CoV-2 variants. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;N74K;D614G;D614G;Q677H;S943F;V622F 126;142;108;147;132;120;114 131;146;113;152;137;125;119 S 93 98 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. This D614G mutation of spike protein has reported a critical mutation that makes the SARS-CoV-2 more contagious and enhances its infectivity. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G 5 10 S 23 28 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. This substitution of Q57H was first reported in Singapore and occurred in 70% of US Covid-19 cases. 2022 Computers in biology and medicine Result SARS_CoV_2 Q57H 21 25 COVID-19 84 92 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. To verify whether the binding affinity of the RBD domain for the human ACE2 can be affected by the six mutations present in the spike protein of Pakistani isolates, we made a double mutant, which consists of the N74K-D614G, N74K-Q677H, D614G-V622F, D614G-S943F, D614G-V622F-S943F, and D614G-Q677H. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;D614G;D614G;D614G;N74K;N74K;D614G;Q677H;Q677H;S943F;S943F;V622F;V622F 236;249;262;285;212;224;217;229;291;255;274;242;268 241;254;267;290;216;228;222;234;296;260;279;247;273 S;RBD 128;46 133;49 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Unlike the D614G-S943T-V622F variant, the other two variants i.e., D614G-Q677H and N74K-D614G reported a significantly destabilizing effect throughout the simulation. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G;D614G;N74K;D614G;Q677H;S943T;V622F 11;67;83;88;73;17;23 16;72;87;93;78;22;28 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Within spike, D614G was found to be mutated in 171 countries. 2022 Computers in biology and medicine Result SARS_CoV_2 D614G 14 19 S 7 12 34968879 SARS-CoV-2 wastewater surveillance in Germany: Long-term RT-digital droplet PCR monitoring, suitability of primer/probe combinations and biomarker stability. After the first detections of variants containing the N501Y mutation, the increase followed a trend that is comparable with the increase of N501Y-containing variants in patients in Baden-Wuerttemberg. 2022 Water research Result SARS_CoV_2 N501Y;N501Y 54;140 59;145 34968879 SARS-CoV-2 wastewater surveillance in Germany: Long-term RT-digital droplet PCR monitoring, suitability of primer/probe combinations and biomarker stability. In December 2020, the state of Baden-Wurttemberg reported the detection of the alpha variant (B.1.1.7) for the first time, corresponding to the first detection of N501Y in wastewater influent from Karlsruhe. 2022 Water research Result SARS_CoV_2 N501Y 163 168 34968879 SARS-CoV-2 wastewater surveillance in Germany: Long-term RT-digital droplet PCR monitoring, suitability of primer/probe combinations and biomarker stability. Overall, RT-ddPCR and NGS are complementary methods that provide important information on the distribution of N501Y and other relevant mutations at the community level through the analysis of RNA extracts from wastewater samples. 2022 Water research Result SARS_CoV_2 N501Y 110 115 34968879 SARS-CoV-2 wastewater surveillance in Germany: Long-term RT-digital droplet PCR monitoring, suitability of primer/probe combinations and biomarker stability. The earliest detection of N501Y was made in the wastewater sample of December 28, 2020. 2022 Water research Result SARS_CoV_2 N501Y 26 31 34968879 SARS-CoV-2 wastewater surveillance in Germany: Long-term RT-digital droplet PCR monitoring, suitability of primer/probe combinations and biomarker stability. The proportion of N501Y gradually increased to 97% on March 11, 2021, and then settled at around 86%. 2022 Water research Result SARS_CoV_2 N501Y 18 23 34968879 SARS-CoV-2 wastewater surveillance in Germany: Long-term RT-digital droplet PCR monitoring, suitability of primer/probe combinations and biomarker stability. The proportion of N501Y to wildtype sequences was compared with publicly available data from the diagnostic tests of infected persons. 2022 Water research Result SARS_CoV_2 N501Y 18 23 34968879 SARS-CoV-2 wastewater surveillance in Germany: Long-term RT-digital droplet PCR monitoring, suitability of primer/probe combinations and biomarker stability. The proportion of the N501Y mutation in wastewater follows the same course as the trend seen for infected persons. 2022 Water research Result SARS_CoV_2 N501Y 22 27 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. 3 A, and the structures of N501I, N501T and N501V mutants are given in. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T;N501V 27;34;44 32;39;49 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. According to these values, the N501I and N501T are strong binders of ACE2 than N501V, which is comparable to the wild type. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T;N501V 31;41;79 36;46;84 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Among the reported mutations, N501Y, E484K, K417 N, E484Q and L452R elevate the pathogenicity scale. 2022 Computers in biology and medicine Result SARS_CoV_2 E484K;E484Q;K417N;L452R;N501Y 37;52;44;62;30 42;57;50;67;35 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. By achieving a stable structural state red colour, these conformational levels were shown to be closer to each other, notably in wild type, N501I, and N501T, and were regarded an energetically stable conformational state. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T 140;151 145;156 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Compared to the above-mentioned variants, all three runs of the N501V variant produced considerably more stable RoG with few minor fluxes. 2022 Computers in biology and medicine Result SARS_CoV_2 N501V 64 69 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Furthermore, HDOCK predicted the docking scores for each complex was wild type (-302.84 kcal/mol), N501I (-317.32 kcal/mol), N501T (-315.66 kcal/mol), while for N501V, the docking score was reported to be -308.02 kcal/mol. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T;N501V 99;125;161 104;130;166 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. HADDOCK predicted the docking score -127.23 +- 1.2 for the ACE2-N501I complex. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I 64 69 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Hence, our results are corroborated with these previous findings as N501T shows strong positive fitness while the N501V failed in the experimental validation, which is also reported as a weak binding mutation. 2022 Computers in biology and medicine Result SARS_CoV_2 N501T;N501V 68;114 73;119 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Herein, a direct comparison revealed that the N510Y possess higher total binding energy than the reported variants here but the results here are extracted from long-run simulation cannot be compared with the previous report which performed only 100ns. 2022 Computers in biology and medicine Result SARS_CoV_2 N510Y 46 51 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. However, the results of wild type and N501V are comparable. 2022 Computers in biology and medicine Result SARS_CoV_2 N501V 38 43 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. In addition, a recent study based on in silico analysis also reported that the N501I mutation remained stable during the MD simulation in complex with ACE2. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I 79 84 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. In all triplicates, the wild-type complex is structurally more stable, shown consistent intermolecular affinity and firm chemical interactions profile as compared to the N501I, N501T, and N501V variants. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T;N501V 170;177;188 175;182;193 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. In case of N501T third run, snapshots at different nanoseconds like 25 ns, 40 ns, 145 ns, and 180 ns revealed an RMSD of 1.129 A after superimposition. 2022 Computers in biology and medicine Result SARS_CoV_2 N501T 11 16 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. In the case of the wild ACE2-RBD complex, the first three eigenvectors accounted for 43% of the overall observed motion, while N501I accounted for 33%, N501T for 36%, and N501V for 56%. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T;N501V 127;152;171 132;157;176 RBD 29 32 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. In the recently reported mutations, including B.1.1.7 (N501Y), B.1.351, P.1, B.1.617 and B.1.618, increased in the stability increased was strongly correlated with a stable evolution of the new variants and tighter binding. 2022 Computers in biology and medicine Result SARS_CoV_2 N501Y 55 60 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. In the wild type, the average hydrogen bonds were 382 while in N501I 387, 385, 381, in N501T 382, 386, 383 and in N501V 382, 381 and 382.This finding shows that the mutations in these three variants have altered their hydrogen-bonding network and may use a different strategy if they emerged as potential variants. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T;N501V 63;87;114 68;92;119 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. It can be further witnessed as a destabilizing mutation C432D has been reported to reduce the affinity for ACE2 and thus entry to the cell. 2022 Computers in biology and medicine Result SARS_CoV_2 C432D 56 61 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Like N501I, N501T variant behaves in different dynamics in the triplicate run. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T 5;12 10;17 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. N501I residues range: 170-175, 300-305,505-515, and residues at the C and N-terminal regions are more flexible in the first run, while these residues range were found more stable in the second and third run except the C- and N-terminal. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I 0 5 N;N 74;225 75;226 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. N501T second run RoG appears to be more compact than the first and third run as predicted by RMSD. 2022 Computers in biology and medicine Result SARS_CoV_2 N501T 0 5 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Next, to uncover the binding mechanism of the predicted variants (N501I, N501T and N501V), we used HADDOCK to bring off the protein-protein (ACE2-RBD) docking. 2022 Computers in biology and medicine Result SARS_CoV_2 N501T;N501V;N501I 73;83;66 78;88;71 RBD 146 149 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. On the other hand, the N501V are reported to stabilize the interactions. 2022 Computers in biology and medicine Result SARS_CoV_2 N501V 23 28 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. PDBsum interaction analysis revealed that both ACE2 and N501I structures form 10 hydrogen bonds and one salt bridge, while the non-bonded interaction between the two complexes were 121. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I 56 61 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Previously for the N501Y substitution reported in B.1.1.7 variant the total binding energy was also reported to have increased than the wild type. 2022 Computers in biology and medicine Result SARS_CoV_2 N501Y 19 24 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Recently a study based on sequence and structure-based predictions of the impact of mutations reported that the mutation N501I is a stabilizing mutation and affect the RBD binding by manifold. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I 121 126 RBD 168 171 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Recently our group also reported that E484K mutation alone in the RBD domain may increase Spike variant binding to ACE2 and hence enhance virus infectivity and transmissibility. 2022 Computers in biology and medicine Result SARS_CoV_2 E484K 38 43 S;RBD 90;66 95;69 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Same observations were made for the N501T in the first, where the regions highlighted for the first run of N501I follow the same pattern of fluctuations. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T 107;36 112;41 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Similarly conformational dynamics of various mutations in the RBD reported in a previous study revealed that the N501I mutations particularly (at 501 position) increases the flexibility. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I 113 118 RBD 62 65 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Superimposition of N501I three replica snapshots picked at different nanoseconds (20 ns,35 ns,55 ns,74 ns,115 ns,125 ns and 160 ns) over the control revealed an RMSD of 1.271 A. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I 19 24 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Taking into account the high significance of these methods, they were applied herein to shed light on the structure, function and interaction impact of N501I, N501T and N501V mutations on Spike RBD binding to ACE2 receptor. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T;N501V 152;159;169 157;164;174 S;RBD 188;194 193;197 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The average net MM/GBSA binding energy of N501I is -64.52 kcal/mol, while for N501T and N501V, the net energy is -55.64 kcal/mol and -45.74 kcal/mol, respectively. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T;N501V 42;78;88 47;83;93 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The binding affinity of N501T was comparable with the N501I mutant with a total of one salt bridge, 10 hydrogen bonds and 112 non-bonded contacts. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T 54;24 59;29 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The docking score for ACE2-N501T mutant was reported to be -125.52 +- 2.1 kcal/mol. 2022 Computers in biology and medicine Result SARS_CoV_2 N501T 27 32 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The first and second run N501V RMSD highly resemble each other, and the complexes are structurally highly stable till 140 ns without experiencing any major deviation. 2022 Computers in biology and medicine Result SARS_CoV_2 N501V 25 30 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The first and second run of the N501T variant is somewhat similar in terms RMSD deviations and considerably more stable with minor deviations until 85 ns. 2022 Computers in biology and medicine Result SARS_CoV_2 N501T 32 37 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The first run of N501I variant, unlike the second run, is more uniform up to 50 ns, then sharply reaches to ~6 A, then suddenly stable to ~2.5 A, followed by fluctuating RMSD >4 A until it became stable at 140 ns, which was seen till the simulation end. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I 17 22 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The HADDOCK docking score for N501V (ACE2-spike RBD) was reported to be -123.65 +- 3.2 kcal/mol. 2022 Computers in biology and medicine Result SARS_CoV_2 N501V 30 35 S;RBD 42;48 47;51 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The hydrogen bonds formed by the ACE2-N501I complex includes Gln493-Glu35, Asn487-Tyr83, Gly446-Gln42, Ala475-Ser19, Lys417-Glu30, Thr500-Tyr41, Gly496- Lys353, Gly496- Glu38, Gly502-Lys353 and Tyr505-Gln37. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I 38 43 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The KD scores are validated that the two mutations N501I and N501T particularly are strong binder than the wild type. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T 51;61 56;66 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The low net energy value demonstrates the high intermolecular complex formation by N501I with ACE2, which in turn indicates better interaction of the N501I with the host cells allowing the variant to spread rapidly compared to the wild type. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501I 83;150 88;155 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The N501I RoG in the third run is facing high structure deviations due to its non-compact nature. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I 4 9 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The N501I variant among all is the highly stable variant with respect to ACE2, followed by N501T and N501V. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T;N501V 4;91;101 9;96;106 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The N501I variant RMSD behaves differently in all three runs; the second run is more stable than the first and third. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I 4 9 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The N501T and N501V can also be interpreted as more infectious based on the net MM/GBSA binding energy considering the wild type net binding energy as reference. 2022 Computers in biology and medicine Result SARS_CoV_2 N501T;N501V 4;14 9;19 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The N501V variant residues are comparatively more stable than other variants in the first run but depicting more fluctuations, especially in the regions of 100-200 400-460. 2022 Computers in biology and medicine Result SARS_CoV_2 N501V 4 9 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The net binding energy of N501I is -8.63 kcal/mol, which is stable than N501T (-6.44 kcal/mol) and N501V (-4.84 kcal/mol). 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T;N501V 26;72;99 31;77;104 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The researchers found N501T SARS-CoV-2 variants in 11/11 experimentally infected ferrets, with a rising fraction of the virome demonstrated over time, indicating significant positive selection in ferrets. 2022 Computers in biology and medicine Result SARS_CoV_2 N501T 22 27 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The third run of N501I variant among all is the most unstable, with maximum RMSD reaching 8 A. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I 17 22 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The third run of N501T variant, in particular, is concluded as highly unstable complex and behaves very flexibly, especially after 40 ns. 2022 Computers in biology and medicine Result SARS_CoV_2 N501T 17 22 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The wild type shows two minima separated by a small subspace, while the mutant complexes N501I, N501T and N501V reached only one energy minima, thus demonstrates the global conformational differences accustomed by the mutant complexes in response to mutations. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T;N501V 89;96;106 94;101;111 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. These findings are consistent with the previous findings which reported that mutations at 501 position particularly N501I increased the binding free energy. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I 116 121 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. These findings reported previously confirms that N501T may produce destabilizing effect, however long run simulations (~microseconds) can confirm the findings in more details. 2022 Computers in biology and medicine Result SARS_CoV_2 N501T 49 54 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. This behaviour may explain the structural rearrangement due to the mutations, and thus it may empirically be proposed that the RBD interaction may stabilize the protein by reducing the dynamics of the active regions to a lower level, particularly in N501I and N501T complexes. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T 250;260 255;265 RBD 127 130 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Through molecular interaction analysis, it has been revealed that the substituted residue N501V decreases the binding of ACE2 with the spike RBD domain as compared to the N501I mutants. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501V 171;90 176;95 S;RBD 135;141 140;144 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Thus, our finding shows that N501I, N501T and N501V possess stable dynamics and may evolve stably subjected to fitness and their adaptive significance, which may further increase the unusual virulence consequently but the impact of different environmental conditions i.e. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T;N501V 29;36;46 34;41;51 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. wild type, N501I, N501T and N501V. 2022 Computers in biology and medicine Result SARS_CoV_2 N501I;N501T;N501V 11;18;28 16;23;33 34982246 Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing. A missense mutation (1139A > G) detected in the NSP2 protein of SARS-CoV2 in this study is a novel genetic variant. 2022 Current microbiology Result SARS_CoV_2 A1139G 21 30 Nsp2 48 52 34982246 Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing. A single mutation was identified in S gene 23929 C > T (codons TAC to TAT, synonymous mutation). 2022 Current microbiology Result SARS_CoV_2 C23929T 43 54 S 36 37 34982246 Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing. Out of total 10 variants, the following 5 mutations were identified in the ORF1ab region: 1139A > G (codons AAG to GAG, missense mutation), 2144G > T (codons GTC to TTC, missense mutation), 11083G > T (codons TTG to TTT, missense mutation), 13730C > T (codons: GCT to GTT, missense mutation), and 6312 C > A (codons ACA to AAA, missense mutation). 2022 Current microbiology Result SARS_CoV_2 G11083T;A1139G;C13730T;G2144T;C6312A 190;90;241;140;297 200;99;251;149;307 ORF1ab 75 81 34982246 Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing. Similarly, out of 10 mutations, 1139A > G, p.Lys292Glu (position 112 of NSP2 protein) was identified as a unique genetic variant. 2022 Current microbiology Result SARS_CoV_2 A1139G;K292E;K292E 32;43;45 41;54;54 Nsp2 72 76 34982509 Engineered small extracellular vesicles displaying ACE2 variants on the surface protect against SARS-CoV-2 infection. Notably, sACE2.v1 sEVs and sACE2.v2 sEVs blocked D614G mutant infection in a concentration-dependent manner and exhibited 95% inhibition even at 100 mug/ml, which is equivalent to 4.47 x 1010 particles/ml containing 6.82 ng/ml of ACE2 and 2.72 x 1010 particles/ml with 11.68 ng/ml of ACE2, respectively. 2022 Journal of extracellular vesicles Result SARS_CoV_2 D614G 49 54 34982509 Engineered small extracellular vesicles displaying ACE2 variants on the surface protect against SARS-CoV-2 infection. sACE2(WT) sEVs had marginal effects on the infectivity of D614G mutant pseudovirus compared with that by sACE2.v1 sEVs and sACE2.v2 sEVs (Figure 4c,d). 2022 Journal of extracellular vesicles Result SARS_CoV_2 D614G 58 63 34982509 Engineered small extracellular vesicles displaying ACE2 variants on the surface protect against SARS-CoV-2 infection. To test whether S mutations confer resistance against sACE2-loaded sEVs, we generated SARS-CoV-2 pseudovirus containing D614G mutant, RBD mutations in Beta variant-K417N, E484K, and N501Y, and mutations in Delta variant L452R, E484K, and D614G (Figure S3a, Supporting Information). 2022 Journal of extracellular vesicles Result SARS_CoV_2 D614G;D614G;E484K;E484K;L452R;N501Y;K417N 120;238;171;227;220;182;164 125;243;176;232;225;187;169 RBD;S 134;16 137;17 34982509 Engineered small extracellular vesicles displaying ACE2 variants on the surface protect against SARS-CoV-2 infection. We assessed the neutralization efficacy of engineered sEVs expressing sACE2.v1 with H34A, T92Q, Q325P, and A386L, as well as sACE2.v2 containing T27Y, L79T, N330Y, and A386L. 2022 Journal of extracellular vesicles Result SARS_CoV_2 A386L;A386L;L79T;N330Y;Q325P;T92Q 107;168;151;157;96;90 112;173;155;162;101;94 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. In addition, we recently searched the two mutations A570D and T19R on the public website https://ngdc.cncb.ac.cn/ncov/lineage. 2022 Microbiology spectrum Result SARS_CoV_2 A570D;T19R 52;62 57;66 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. It is worth noting that the hot spot amino acid substitutions currently of interest, such as N501Y, E484K, and P681R, were not unique or specific mutations able to differentiate the VOCs. 2022 Microbiology spectrum Result SARS_CoV_2 E484K;N501Y;P681R 100;93;111 105;98;116 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. The site mutations at the 1709th (position 23271 on the reference genome, A570D on the spike protein) and 56th (position 21681 on the reference genome, T19R on the spike protein) positions in the spike gene were chosen as the single targets for designing primer/probe sets for the ARMS-RT-qPCR to identify these two variants, respectively. 2022 Microbiology spectrum Result SARS_CoV_2 A570D;T19R 74;152 79;156 S;S;S 87;164;196 92;169;201 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. The unique mutations C1709A and C56G specific for the two VOCs (Alpha and Delta) were chosen for ARMS-RT-qPCR primer and probe design. 2022 Microbiology spectrum Result SARS_CoV_2 C1709A;C56G 21;32 27;36 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. Thus, these two unique mutations, A570D and T19R, can be considered conserved and unique in all lineages of Alpha and Delta, respectively. 2022 Microbiology spectrum Result SARS_CoV_2 A570D;T19R 34;44 39;48 34985974 Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2. after HEK293T-hACE2 cells were transduced with WT or D614G pseudotyped lentivirus carrying a green fluorescence protein (GFP) reporter, ~50% of cells were GFP positive, with D614G pseudovirus exhibiting a higher transduction efficacy than that of the WT. 2022 Applied and environmental microbiology Result SARS_CoV_2 D614G;D614G 53;174 58;179 34985974 Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2. Compared to RAC alone, Nb-CBD-immobilized columns increased the capture efficiency for WT and D614G pseudoviruses by ~3.5 times and ~8 times, respectively. 2022 Applied and environmental microbiology Result SARS_CoV_2 D614G 94 99 34985974 Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2. Indeed, using medium containing WT or D614G pseudoviruses. 2022 Applied and environmental microbiology Result SARS_CoV_2 D614G 38 43 34985974 Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2. Meanwhile, we calculated the titers of WT or D614G pseudotyped lentivirus and estimated that ~105 viral particle particles/mL were present in the culture medium. 2022 Applied and environmental microbiology Result SARS_CoV_2 D614G 45 50 34985974 Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2. Notably, epidemiology and molecular biology studies have demonstrated that the D614G mutant confers higher transmission and worse symptoms in humans. 2022 Applied and environmental microbiology Result SARS_CoV_2 D614G 79 84 34985974 Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2. Therefore, it is of particular interest to assess our fusion protein strategy in the context of both the WT and the D614G variant. 2022 Applied and environmental microbiology Result SARS_CoV_2 D614G 116 121 34985974 Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2. These findings agreed with the increased infectivity by the D614G mutation. 2022 Applied and environmental microbiology Result SARS_CoV_2 D614G 60 65 34985974 Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2. Using this system, we compared the original wild-type (WT) S protein to the D614G mutant, in which the 614th aspartate is converted to glycine in the S protein of SASR-CoV-2. 2022 Applied and environmental microbiology Result SARS_CoV_2 D614G 76 81 S;S 59;150 60;151 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. 4 weeks after the third dose of the D614G/B.1.351_RBD-NP vaccine, the rhesus macaque sera potently neutralized the pseudotyped viruses of current major SARS-CoV-2 variants, including B.1.1.7, B.1.351, P.1, B.1.429, B.1.526, and B.1.617.1 (Figure 4C). 2022 Cell reports Result SARS_CoV_2 D614G 36 41 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. All immunized hACE2 mice were challenged intranasally with 4 x 104 PFUs of the D614G or B.1.351 strains, respectively, and euthanized 5 days after challenge. 2022 Cell reports Result SARS_CoV_2 D614G 79 84 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. All immunized hACE2 mice were challenged intranasally with 4 x 104 plaque-forming units (PFUs) of the D614G or B.1.351 strains, respectively, and euthanized 5 days after challenge. 2022 Cell reports Result SARS_CoV_2 D614G 102 107 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Although the single dose of D614G/B.1.351_RBD-monomer had an average of 1.62 x 105 and 3.88 x 104 copies/mL for the D614G strain and 1.54 x 105 and 3.17 x 104 copies/mL for the B.1.351 strain in the lungs and trachea, respectively, all single-dose D614G/B.1.351_RBD-NP-immunized hACE2 mice had undetectable levels of viral RNA (Figures 3E and 3F). 2022 Cell reports Result SARS_CoV_2 D614G;D614G;D614G 28;116;248 33;121;253 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. As measured by FRNT50 assay against the D614G authentic virus, nAb titers in serum from immunized rhesus macaques were elicited 14 days after priming by the D614G_RBD-NP vaccine and peaked following another 14 days after the first boost. 2022 Cell reports Result SARS_CoV_2 D614G;D614G 40;157 45;162 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. BALB/c mice were immunized subcutaneously with 10 mug of B.1.351_RBD-NP or D614G/B.1.351_RBD-NP adjuvant with alhydrogel in a prime-boost manner. 2022 Cell reports Result SARS_CoV_2 D614G 75 80 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Because the prime-boost strategy of the NP vaccine has been carefully evaluated using a monomer as a control in our previous study, here we also set the D614G/B.1.351_RBD-monomer group as a control for the single-dose strategy. 2022 Cell reports Result SARS_CoV_2 D614G 153 158 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. By utilizing pseudovirus neutralization assays, the nAbs induced by D614G/B.1.351_RBD-NP strongly inhibited D614G and B.1.351 pseudotyped variants (Figure 1E). 2022 Cell reports Result SARS_CoV_2 D614G;D614G 68;108 73;113 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Compared with the D614G_RBD-NP vaccine group, the bivalent D614G/B.1.351_RBD-NP vaccine showed better protection, as demonstrated by lower levels of viral RNA in the lungs and a reduction of inflammation, as seen by histopathological examination of lung tissue (Figure 3L and 3M). 2022 Cell reports Result SARS_CoV_2 D614G;D614G 59;18 64;23 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Control hACE2 mice had an average of 5.84 x 105 and 6.10 x 104 copies/mL for D614G and 6.75 x 105 and 2.69 x 105 copies/mL for the B.1.351 strain in the lungs and trachea, respectively, whereas D614G/B.1.351_RBD-NP-immunized hACE2 mice had undetectable levels of viral RNA (Figures 2D and 2E). 2022 Cell reports Result SARS_CoV_2 D614G;D614G 77;194 82;199 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Fifteen convalescent sera, which were collected in Guangzhou and Zhuhai in South China before April 15, 2020 and therefore excluded existence of the epidemic variants of SARS-CoV-2 except for the D614 and D614G strains, were used as controls for the pseudovirus neutralizing assay against SARS-CoV-2 variants (Figure S4F). 2022 Cell reports Result SARS_CoV_2 D614G 205 210 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Finally, we assess the cross-protection of the updated bivalent D614G/B.1.351_RBD-NP vaccine as a third dose on previously immunized rhesus macaques. 2022 Cell reports Result SARS_CoV_2 D614G 64 69 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Five hACE2 mice were immunized with 10 mug of the D614G/B.1.351_RBD-NP vaccine or an equimolar amount of D614G/B.1.351_RBD-monomer as a control. 2022 Cell reports Result SARS_CoV_2 D614G;D614G 50;105 55;110 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Following the bivalent D614G/B.1.351_RBD-NP vaccine booster injection, the nAb titers against the authentic D614G virus increased significantly, exceeding the previously measured peak for the D614G_RBD-NP level. 2022 Cell reports Result SARS_CoV_2 D614G;D614G;D614G 23;108;192 28;113;197 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. hACE2 mice were immunized with 2 mug, 5 mug, and 10 mug of the bivalent vaccine and D614G_RBD-NP vaccine in a single-dose regimen. 2022 Cell reports Result SARS_CoV_2 D614G 84 89 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Here we evaluate the immunogenicity and in vivo protection ability of a single dose of the bivalent D614G/B.1.351_RBD-NP vaccine (Figure 3A). 2022 Cell reports Result SARS_CoV_2 D614G 100 105 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Histopathology examination indicated severe bronchopneumonia and interstitial pneumonia in the D614G/B.1.351_RBD-monomer group, with edema and bronchial epithelial cell desquamation and infiltration of lymphocytes within alveolar spaces. 2022 Cell reports Result SARS_CoV_2 D614G 95 100 Bronchopneumonia;Pneumonia 44;65 60;87 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. In contrast, only very mild bronchopneumonia was observed in the D614G/B.1.351_RBD-NP vaccine group (Figures 3G and 3H). 2022 Cell reports Result SARS_CoV_2 D614G 65 70 Bronchopneumonia 28 44 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. In line with the previous findings that serum from convalescent COVID-19 individuals showed reduced neutralization against the B.1.351 variant, the D614G_RBD-NP vaccine showed a reduction of nAbs to the B.1.351 variant in BALB/c mice (Figure 1E). 2022 Cell reports Result SARS_CoV_2 D614G 148 153 COVID-19 64 72 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. In the 50% focus reduction neutralizing test (FRNT50) assay, the D614G/B.1.351_RBD-NP vaccine elicited a similar robust neutralization response against the authentic D614G and B.1.351 strains, whereas a 9-fold decrease of neutralization against the B.1.351 strain was observed in D614G_RBD-NP-immunized hACE2 mice (Figure 2C). 2022 Cell reports Result SARS_CoV_2 D614G;D614G;D614G 65;166;280 70;171;285 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. In the FRNT50 assay, the D614G/B.1.351_RBD-NP vaccine produced higher nAb responses against the authentic B.1.351 strain in mice vaccinated with a dose of 5 mug and 10 mug (Figure 3K). 2022 Cell reports Result SARS_CoV_2 D614G 25 30 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Interestingly, serum from immunized animals showed consistently higher nAb titers against the D614G strain than the B.1.351 strain (Figure 4B). 2022 Cell reports Result SARS_CoV_2 D614G 94 99 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Interestingly, the third dose of D614G/B.1.351_RBD-NP immunization for rhesus macaques potently elicited nAbs against all viral variants we tested (Figure 4C). 2022 Cell reports Result SARS_CoV_2 D614G 33 38 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. RBD-specific IgG against the D614G and B.1.351 strains was detectable in all NP-immunized hACE2 mice (Figure 3B). 2022 Cell reports Result SARS_CoV_2 D614G 29 34 RBD 0 3 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Rhesus macaques were immunized with 50 mug of the D614G_RBD-NP vaccine on days 1 and 28, and the robustness of the nAbs against the authentic D614G and B.1.351 strains was monitored over the course of more than 8 months (Figure 4A). 2022 Cell reports Result SARS_CoV_2 D614G;D614G 142;50 147;55 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Similarly, immunohistochemistry assays detected the SARS-CoV-2 N antigen in the D614G/B.1.351_RBD-monomer group, but the SARS-CoV-2 N antigen was undetectable in lung tissue of the single-dose-immunized D614G/B.1.351_RBD-NP group (Figures 3I and 3J). 2022 Cell reports Result SARS_CoV_2 D614G;D614G 80;203 85;208 N;N 63;132 64;133 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The B.1.351_RBD-NP and D614G/B.1.351_RBD-NP vaccines induced RBD-specific immunoglobulin G (IgG) in serum at approximately 105 titer and RBD-specific IgA secretion in bronchoalveolar lavage fluid (BALF) specific for the D614G and B.1.351 variants (Figures 1C and 1D). 2022 Cell reports Result SARS_CoV_2 D614G;D614G 23;220 28;225 RBD;RBD 61;137 64;140 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The B.1.351_RBD-NP vaccine and the bivalent D614G/B.1.351_RBD-NP vaccine induced robust humoral and cellular immune responses with a high level of stability. 2022 Cell reports Result SARS_CoV_2 D614G 44 49 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The B.1.351_RBD-NP vaccine elicited higher neutralization titers against B.1.351 compared with that of D614G, whereas the bivalent D614G/B.1.351_RBD-NP induced a similar robust neutralization response against the authentic D614G and B.1.351 strains, with no significant difference in neutralization titers (Figure 1F). 2022 Cell reports Result SARS_CoV_2 D614G;D614G;D614G 103;131;223 108;136;228 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The convalescent sera were 10-fold less effective at neutralizing B.1.351 and 23-fold less effective for B.1.617.1 in comparison with its neutralization of the D614G strain (Figure S4F). 2022 Cell reports Result SARS_CoV_2 D614G 160 165 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The D614G_NP vaccine remained overall efficacious and delivered notable cross-protection against the B.1.351 variant (Figure 2E). 2022 Cell reports Result SARS_CoV_2 D614G 4 9 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The measured binding dissociation constants (KD) of the D614G_RBD-NP and B.1.351_RBD-NP with the hACE2 receptor were 8.67 x 10-9 and 3.23 x 10-9 M, respectively, indicating that the epitopes on the NPs are exposed and correctly folded and that the B.1.351_RBD-NP binds to human ACE2 with increased affinity (Figures 1B and S1D). 2022 Cell reports Result SARS_CoV_2 D614G 56 61 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The nAbs in all NP-vaccinated mice strongly inhibited replication of the authentic D614G and B.1.351 strains. 2022 Cell reports Result SARS_CoV_2 D614G 83 88 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The purified Gv-D614G_RBD and Gv-B.1.351_RBD were irreversibly covalently conjugated to the Sd-ferritin to generate D614G_RBD-nanoparticle (NP) and B.1.351_RBD-NP (Figure 1A). 2022 Cell reports Result SARS_CoV_2 D614G;D614G 116;16 121;21 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The RBD-specific IgG against the D614G and B.1.351 strains was quite high in all NP-immunized hACE2 mice 2 weeks after boost (Figure 2B). 2022 Cell reports Result SARS_CoV_2 D614G 33 38 RBD 4 7 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The RBD-specific IgG titers against the D614G and B.1.351 strains were quite high after a third dose of the vaccine, reaching approximately 105 titers (Figure S4D). 2022 Cell reports Result SARS_CoV_2 D614G 40 45 RBD 4 7 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The Sd-coding sequence was genetically fused at the N terminus of ferritin (Sd-ferritin), whereas the Gv-coding sequence was fused at the N-terminus of the D614G_RBD or B.1.351_RBD sequence (Figure 1A). 2022 Cell reports Result SARS_CoV_2 D614G 156 161 N;N 52;138 53;139 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The third dose of the D614G/B.1.351_RBD-NP vaccine increased the neutralization titers against the D614G and B.1.351 strains 15-fold and 65-fold, respectively (Figures 4B and S4E). 2022 Cell reports Result SARS_CoV_2 D614G;D614G 22;99 27;104 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Then we determined whether the D614G/B.1.351_RBD-NP vaccine booster elicited nAbs against other SARS-CoV-2 variants. 2022 Cell reports Result SARS_CoV_2 D614G 31 36 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. These data demonstrated that single-dose vaccination of the D614G/B.1.351_RBD-NP vaccine caused significant prevention of replication of the authentic D614G and B.1.351 strains in the lungs. 2022 Cell reports Result SARS_CoV_2 D614G;D614G 60;151 65;156 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. This new boost especially enhances the nAb titer for B.1.617.1 33-fold, which is still slightly lower than that of the D614G strain (Figure 4C). 2022 Cell reports Result SARS_CoV_2 D614G 119 124 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. To determine bivalent D614G/B.1.351_RBD-NP vaccine protection against D614G and B.1.351 variant infection, we immunized transgenic hACE2 mice, which expressed humanized ACE2, with NP vaccines (Figure 2A). 2022 Cell reports Result SARS_CoV_2 D614G;D614G 22;70 27;75 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. To determine the stability of NP vaccines, we stored the D614G/B.1.351_RBD-NP vaccine at -80 C, -20 C, 4 C, and 25 C for 2 weeks. 2022 Cell reports Result SARS_CoV_2 D614G 57 62 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. To evaluate the ability of the bivalent D614G/B.1.351_RBD-NP vaccine to boost pre-existing immunity and increase neutralization of the D614G and B.1.351 strains, a third dose of 50 mug of the bivalent D614G/B.1.351_RBD-NP vaccine was administered on day 282 (Figure 4A). 2022 Cell reports Result SARS_CoV_2 D614G;D614G;D614G 40;135;201 45;140;206 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. To evaluate the immunogenicity of these bivalent NP vaccines against the ancestral D614G and B.1.351 variants, BALB/c mice were immunized with these vaccines. 2022 Cell reports Result SARS_CoV_2 D614G 83 88 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. To study whether these nAbs could inhibit infection with authentic D614G and B.1.351 strains, a focus reduction neutralizing test (FRNT) was conducted. 2022 Cell reports Result SARS_CoV_2 D614G 67 72 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. We next assessed the resilience of the D614G/B.1.351_RBD-NP vaccine by challenging it with multiple rounds of freezing and thawing. 2022 Cell reports Result SARS_CoV_2 D614G 39 44 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. With the FRNT50 assay and pseudovirus neutralization assays, a single dose of the D614G/B.1.351_RBD-NP vaccine induced significantly higher neutralization titers against the pseudovirus and authentic D614G and B.1.351 variants compared with D614G/B.1.351_RBD-monomer (Figures 3C, 3D and, S4A). 2022 Cell reports Result SARS_CoV_2 D614G;D614G;D614G 82;200;241 87;205;246 34993157 Clinical, Virological, Immunological, and Genomic Characterization of Asymptomatic and Symptomatic Cases With SARS-CoV-2 Infection in India. Interestingly, D614G mutation of the spike protein was observed in patient numbers 7, 9, and 10, and the analysis revealed that it is mostly linked with increased replication efficiencies and severe SARS-CoV-2 infection as the patients containing this mutation had high viral load and two patients succumb to death. 2021 Frontiers in cellular and infection microbiology Result SARS_CoV_2 D614G 15 20 S 37 42 COVID-19 199 219 34998405 Different decay of antibody response and VOC sensitivity in naive and previously infected subjects at 15 weeks following vaccination with BNT162b2. As the IgG-RBD titers dropped at W15, median nAb titers against the D614G lineage decreased in both vaccinee's groups but remained higher in previously infected subjects (median ID50 of 800 for naive and 2893 for previously infected individuals). 2022 Journal of translational medicine Result SARS_CoV_2 D614G 68 73 RBD 11 14 34998405 Different decay of antibody response and VOC sensitivity in naive and previously infected subjects at 15 weeks following vaccination with BNT162b2. Compared with the D614G lineage, no statistically significant differences were found in the neutralization of B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta) and B.1.298 (Mink) in previously infected subjects, whereas neutralization ability toward the P.1 lineage was significantly impaired at W15 from the first dose (p = 0.0414). 2022 Journal of translational medicine Result SARS_CoV_2 D614G 18 23 34998405 Different decay of antibody response and VOC sensitivity in naive and previously infected subjects at 15 weeks following vaccination with BNT162b2. In subjects with prior SARS-CoV-2 infection, the first dose generated neutralizing antibody (nAb) titers to the D614G lineage about 12-fold higher than those raised by naive participants (p = 0.0020). 2022 Journal of translational medicine Result SARS_CoV_2 D614G 112 117 COVID-19 23 43 34998405 Different decay of antibody response and VOC sensitivity in naive and previously infected subjects at 15 weeks following vaccination with BNT162b2. These findings were confirmed by the strong correlations between binding IgG to RBD and nAb titers (for previously infected.: r = 0.8667, p = 0.0045 for D614G; r = 0.9500, p = 0.0004 for B.1.1.7; r = 0.9205, p = 0.0010; for P.1; r = 0.7833, p = 0172 for B.1.617.2; r = 0.8333, p = 0.0083 for B.1.298; for naive: r = 0.8506, p < 0.0001 for D614G; r = 0.5155, p = 0.0099 for B.1.1.7; r = 0.6788, p = 0.0003 for B.1.617.2; r = 0.8858, p < 0.0001 for B.1.298, see Additional file 2: Table S1 and Additional file 3: Table S2). 2022 Journal of translational medicine Result SARS_CoV_2 D614G;D614G 153;339 158;344 RBD 80 83 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. 1B), we did not find the N501Y mutation, which is a characteristic of the UK variant (and shared by the Brazil and SA variants), or the K417N mutation that is found in the Brazil/SA variants. 2022 Archives of virology Result SARS_CoV_2 K417N;N501Y 136;25 141;30 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Additionally, the E154K mutation was found in five and the V382L and D1153Y mutations were found in four of the six Kappa variants. 2022 Archives of virology Result SARS_CoV_2 D1153Y;E154K;V382L 69;18;59 75;23;64 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. All six Indian variants of the B.1.617.1 lineage exhibited five unique mutations: G142D, L452R, E484Q, P681R, and Q1071H. 2022 Archives of virology Result SARS_CoV_2 E484Q;G142D;L452R;P681R;Q1071H 96;82;89;103;114 101;87;94;108;120 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. As shown in Table 1, we identified the V382L mutation in 4.8% of NPS specimens in 2021. 2022 Archives of virology Result SARS_CoV_2 V382L 39 44 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. At that time, 34 variants contained L452R/E484Q (37%), while 54 sequences harboured L452R/T478K mutations (59%), characteristic of the Delta variant. 2022 Archives of virology Result SARS_CoV_2 L452R;L452R;E484Q;T478K 36;84;42;90 41;89;47;95 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. For the Delta variant, all six sequences belonged to B.1.617.2 lineage and had six unique mutations (T19R, G142D, L452R, T478K, P681R, and D950N). 2022 Archives of virology Result SARS_CoV_2 D950N;G142D;L452R;P681R;T478K;T19R 139;107;114;128;121;101 144;112;119;133;126;105 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Importantly, as compared to March (35/45), a significant rise in L452R mutants was seen in April (88/91, p = 0.001). 2022 Archives of virology Result SARS_CoV_2 L452R 65 70 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Importantly, P681H was present in the UK variant B.1.1.7 (Table 2). 2022 Archives of virology Result SARS_CoV_2 P681H 13 18 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. In addition, instead of the E484K mutation seen in strains from Brazil and South Africa, Indian strains exhibited an E484Q mutation, defined later as the Kappa variant. 2022 Archives of virology Result SARS_CoV_2 E484K;E484Q 28;117 33;122 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Interestingly, at the same time, the frequency of the T478K mutation increased dramatically from 4% in March to 59% in April (p < 0.001). 2022 Archives of virology Result SARS_CoV_2 T478K 54 59 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Like the Delta variant, the six Indian variants contained the unique mutation D63G. 2022 Archives of virology Result SARS_CoV_2 D63G 78 82 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Notably, the position of the P681R mutation in the Kappa and Delta variants is immediately adjacent to the furin cleavage site (682-685). 2022 Archives of virology Result SARS_CoV_2 P681R 29 34 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. One sequence each exhibited the N501Y mutation characteristic of the UK strain, an N440K mutation, and no mutation. 2022 Archives of virology Result SARS_CoV_2 N440K;N501Y 83;32 88;37 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Our results indicated that the dominant clade G virus strains in Pune seem to have been replaced by the variant of concern Delta (L452R/T478K) during the second wave of the disease. 2022 Archives of virology Result SARS_CoV_2 L452R;T478K 130;136 135;141 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Overall, in the month of March, 33 out of 45 samples (73%) harboured the India-specific L452R/E484Q mutations. 2022 Archives of virology Result SARS_CoV_2 L452R;E484Q 88;94 93;99 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Overall, the L452R mutation increased from 0/30 in December to 123/136 (90%) in April (p < 0.001). 2022 Archives of virology Result SARS_CoV_2 L452R 13 18 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Strikingly, 70% of the NPS specimens sequenced during the beginning of March 2021 and 83% of the NPS samples sequenced at the end of March contained the L452R mutation observed in the California variant. 2022 Archives of virology Result SARS_CoV_2 L452R 153 158 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The acquisition of A222V and K417N by the Delta variant (AY.2 lineage) was associated with an upsurge in COVID-19 cases in Europe and the USA, and importantly, these amino acid changes were not found in the Delta variants from this study. 2022 Archives of virology Result SARS_CoV_2 A222V;K417N 19;29 24;34 COVID-19 105 113 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The four mutations, C241T, C3037T, C14408T, and A23403G, were observed in all 20 genome sequences from the clade "G" isolates (named after the D614G mutation). 2022 Archives of virology Result SARS_CoV_2 A23403G;C14408T;C241T;C3037T;D614G 48;35;20;27;143 55;42;25;33;148 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The increasing frequency of the dominant mutation L452R/T478K continued in May and June 2021, but we experienced a significant decline in the number of patients seeking COVID-19 diagnosis at the hospital (Table 1). 2022 Archives of virology Result SARS_CoV_2 L452R;T478K 50;56 55;61 COVID-19 169 177 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The Indian Delta variant-specific mutations were G210T (5'UTR) Nsp2-P129L, Nsp3-P822L, Nsp4-A446V, Nsp6-V149A (Orf1a), Nsp12-P323L, Nsp12-G671S, Nsp13-P77L (Orf1b), S26L (Orf3a), I82T (M), V82A, T120I (Orf7a), and deletions of D119 and F120 in Orf8. 2022 Archives of virology Result SARS_CoV_2 G210T;I82T;S26L;T120I;V82A;A446V;G671S;P129L;P323L;P77L;P822L;V149A 49;179;165;195;189;92;138;68;125;151;80;104 54;183;169;200;193;97;143;73;130;155;85;109 ORF1a;ORF7a;ORF3a;Nsp13;5'UTR;Nsp12;Nsp12;Nsp2;Nsp3;Nsp4;Nsp6;ORF8 111;202;171;145;56;119;132;63;75;87;99;244 116;207;176;150;61;124;137;67;79;91;103;248 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The Indian variants were distinct in this protein as well (Table 3) and did not share the D3L and S236F mutations and the P80R mutation seen in the UK and Brazilian variants, respectively. 2022 Archives of virology Result SARS_CoV_2 D3L;P80R;S236F 90;122;98 93;126;103 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The Kappa-variant-specific mutations were Nsp3-T749I, Nsp6-T77A (Orf1a), Nsp12-P323L, Nsp13-M429I, Nsp15-K259R (Orf1b), S26L (Orf3a), I33T (Orf6), and V82A (Orf7a). 2022 Archives of virology Result SARS_CoV_2 I33T;S26L;V82A;K259R;M429I;P323L;T749I;T77A 134;120;151;105;92;79;47;59 138;124;155;110;97;84;52;63 ORF1a;ORF7a;ORF3a;Nsp13;Nsp12;ORF6;Nsp3;Nsp6 65;157;126;86;73;140;42;54 70;162;131;91;78;144;46;58 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The presence of the D614G mutation in all of the Indian sequences revealed that clade G continued to be the only clade circulating so far in Pune. 2022 Archives of virology Result SARS_CoV_2 D614G 20 25 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The R203M and D377Y mutations were observed in all twelve Kappa and Delta variants. 2022 Archives of virology Result SARS_CoV_2 D377Y;R203M 14;4 19;9 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The remaining Indian sequences continued to harbour the R203K and G204R mutations, which were present since May 2020. 2022 Archives of virology Result SARS_CoV_2 G204R;R203K 66;56 71;61 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Together with the substitution E156G, two deletions at F157 and R158 were identified. 2022 Archives of virology Result SARS_CoV_2 E156G 31 36 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Two isolates, CD210922 (MW969752) and CD210896 (EPI_ISL_1710598), had the unique mutations V143F, Q677H, and N440K (Table 2). 2022 Archives of virology Result SARS_CoV_2 N440K;Q677H;V143F 109;98;91 114;103;96 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Two of the 15 samples from December 2020 contained the N440K mutation. 2022 Archives of virology Result SARS_CoV_2 N440K 55 60 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Two sequences from 2021 (CD211295 [MW969753] and CD210761 [MZ021503]) belonging to the original prevalent lineage B.1.1.306 had four characteristic mutations, L18F, A27S, E484K, and Q675H, in the spike protein. 2022 Archives of virology Result SARS_CoV_2 A27S;E484K;L18F;Q675H 165;171;159;182 169;176;163;187 S 196 201 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Until December 2020, none of the samples exhibited the characteristic mutations (K417N/T, E484K, N501Y, T478K) found in the variants of concern that have been identified so far. 2022 Archives of virology Result SARS_CoV_2 E484K;N501Y;T478K;K417N;K417T 90;97;104;81;81 95;102;109;88;88 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. Both unmodified and H84T-BanLec CAR-NK cells were stimulated to secrete inflammatory mediators when co-cultured with pseudoviral particles and virally infected cells, including IFNgamma (mean pg/ml +/- SEM of NK cells at baseline vs. 2021 Frontiers in immunology Result SARS_CoV_2 H84T 20 24 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. H84T-BanLec CAR-NK Cells Are Strongly Activated by Virus. 2021 Frontiers in immunology Result SARS_CoV_2 H84T 0 4 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. H84T-BanLec CAR-NK Cells Decrease Cellular Pseudovirus Infection. 2021 Frontiers in immunology Result SARS_CoV_2 H84T 0 4 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. H84T-BanLec CAR-NK; 23.5 +/-2.7% vs. 2021 Frontiers in immunology Result SARS_CoV_2 H84T 0 4 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. H84T-BanLec CAR-NK; 35 +/-11% vs 64%+/- 6% for 1:1 effector-to-target ratio, p=0.054; 21+/-3% vs 31%+/- 3% for 1:2.5 effector-to-target ratio, p=0.034; Figure 3D ). 2021 Frontiers in immunology Result SARS_CoV_2 H84T 0 4 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. H84T-BanLec.4-1BB.zeta CAR Is Stably Expressed in Human NK Cells. 2021 Frontiers in immunology Result SARS_CoV_2 H84T 0 4 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. Our complete CAR was comprised of H84T-BanLec, CD8alpha hinge and transmembrane domains, and the intracellular domains of 4-1BB and the CD3zeta chain ( Figure 1A ). 2021 Frontiers in immunology Result SARS_CoV_2 H84T 34 38 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. This reduction, which is indicative of a decrease in the total number of virally infected human cells, was noted in both unmodified and H84T-CAR NK cells, but was more pronounced when CAR-NK cells were present (mean % BL reduction +/- SEM of hACE2.293T in cocultures with unmodified NK vs. 2021 Frontiers in immunology Result SARS_CoV_2 H84T 136 140 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. This suggests that background cytotoxicity may have contributed to lowered BL in the absence of H84T-BanLec viral binding. 2021 Frontiers in immunology Result SARS_CoV_2 H84T 96 100 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. We found that our hACE2.293T cells bound trimeric S-protein, the S-protein Receptor Binding Domain (RBD), and the D614G mutated S-protein ( Figure 2C ). 2021 Frontiers in immunology Result SARS_CoV_2 D614G 114 119 RBD;RBD;S;S;S 75;100;50;65;128 98;103;51;66;129 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. We next investigated whether H84T-BanLec CAR-NK cells could specifically target S-protein pseudoviral transduced hACE2.293T. 2021 Frontiers in immunology Result SARS_CoV_2 H84T 29 33 S 80 81 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. We observed a reduction in SARS-CoV-2 pseudoviral mediated bioluminescence emission from hACE2.293T cells when H84T-BanLec CAR-NK cells were present ( Figure 3D ). 2021 Frontiers in immunology Result SARS_CoV_2 H84T 111 115 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. We produced replication incompetent retrovirus carrying our CAR sequence and used this to generate H84T-BanLec CAR NK cells. 2021 Frontiers in immunology Result SARS_CoV_2 H84T 99 103 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. We synthesized the H84T-banana lectin (H84T-BanLec) sequence and subcloned this in place of the extracellular binding domain of an existing 4-1BB.zeta CAR. 2021 Frontiers in immunology Result SARS_CoV_2 H84T;H84T 19;39 23;43 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. We used SARS-CoV-2 envelope pseudotyping of a replication deficient lentiviral vector in order to evaluate whether H84T-BanLec CAR NK cells could mediate clearance of SARS-CoV-2. 2021 Frontiers in immunology Result SARS_CoV_2 H84T 115 119 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. We verified surface expression using flow cytometry and measured stable expression of the H84T-BanLec.4-1BB.zeta CAR on the surface of human NK cells over the tested period of two weeks (day 4 post-transduction: median [range], 67.5% CAR-positive [64.7-75%], day 14 post-transduction: 58.9% CAR-positive [43.6-66.7%], Figures 1D, E ). 2021 Frontiers in immunology Result SARS_CoV_2 H84T 90 94 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. Among which, the amino acid substitution of p.Asp614Gly (cor = 0.29, p < 0.001) was significantly positively correlated with the clinical severity of patients. 2021 Frontiers in public health Result SARS_CoV_2 D614G;D614G 44;46 55;55 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. As showed in Figure 3, two amino acid substitutions occurred in N gene, such as p.Gli204Arg substitution in 46 SARS-COV-2 samples (16%) and p.Arg203Lys in 46 SARS-COV-2 samples (17%). 2021 Frontiers in public health Result SARS_CoV_2 R203K;R203K 140;142 151;151 N 64 65 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. In addition to the above mutations, amino acid substitutions of p.Pro681His and p.Pro681Arg were found in the S gene in 27 and 27 SARS-COV-2 samples, respectively (Table 4). 2021 Frontiers in public health Result SARS_CoV_2 P681R;P681H;P681R;P681H 80;64;82;66 91;75;91;75 S 110 111 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. In S gene, 98 SARS-COV-2 samples (35%) had p.Asp614Gly substitution and 25 SARS-COV-2 samples (9%) had p.Asp501Tyr substitution. 2021 Frontiers in public health Result SARS_CoV_2 D501Y;D614G;D501Y;D614G 103;43;105;45 114;54;114;54 S 3 4 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. It is reported that the high predominance of the clades GR is mainly related to the occurrence of the amino acid substitution p.Asp614Gly that improved viral fitness. 2021 Frontiers in public health Result SARS_CoV_2 D614G;D614G 126;128 137;137 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. The amino acid replacements of p.Ser316Thr (cor = -0.16, p = 0.04) and p.Lu484Lys (cor = -0.28, p < 0.001) were significantly negatively correlated with the course of disease. 2021 Frontiers in public health Result SARS_CoV_2 S316T;S316T 31;33 42;42 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. The p.Glin57His substitution in open reading frame 3a (ORF3a) and the p.Leu84Ser substitution in open reading frame 8 (ORF8) was found in 33 (12%) and 32 (11%) SARS-COV-2 samples, respectively. 2021 Frontiers in public health Result SARS_CoV_2 L84S;L84S 70;72 80;80 ORF3a;ORF8 55;119 60;123 35007661 A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: Effects on proteolytic cleavage and ACE2 binding. 6 A, fbAB effectively blocked the cleavage of the wild type and P681R SARS-CoV-2 furin motif by purified furin enzyme at 8 ng/well. 2022 Immunology letters Result SARS_CoV_2 P681R 64 69 35007661 A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: Effects on proteolytic cleavage and ACE2 binding. A higher concentration (16 ng/well) of furin enzyme increased cleavage of the wild type and P681R SARS-CoV-2 furin cleavage site, and fbAB was found to effectively reduce the cleavage by furin at this concentration as well. 2022 Immunology letters Result SARS_CoV_2 P681R 92 97 35007661 A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: Effects on proteolytic cleavage and ACE2 binding. The KD associated with P681R mutation, R683Q mutation, and triple R deletion is 1.1, 1.8, and 1.5 nM, respectively, compared with 1.0 nM for wild type. 2022 Immunology letters Result SARS_CoV_2 P681R;R683Q 23;39 28;44 35007661 A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: Effects on proteolytic cleavage and ACE2 binding. The specificity of fbAB-spike interaction was assessed by incubating antibody in wells coated with either: SARS-CoV-2 spike protein containing the S1/S2 boundary furin site; peptides containing the wild type, mutant (P681R and R683Q), and triple R-deleted SARS-CoV-2-specific furin motif; or SARS-CoV-2 S1 RBD protein. 2022 Immunology letters Result SARS_CoV_2 R683Q;P681R 227;217 232;222 S;S;RBD 24;118;306 29;123;309 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Africa (N501Y_E484K_K417N) showing new aromatic interactions with the ACE2 Tyr41 and cation-pi interactions with the ACE2 Lys353 (Supplementary Table 1 and. 2022 The EPMA journal Result SARS_CoV_2 N501Y;E484K;K417N 8;14;20 13;19;25 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Africa (N501Y_E484K_K417N) VoC (Supplementary Table 1 and. 2022 The EPMA journal Result SARS_CoV_2 N501Y;E484K;K417N 8;14;20 13;19;25 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Although S494P, approximately located in the center of the "boat-hull" region (residues 491-496), and S477N, located on the tip of the "boat-bow" region (residues 468-490) do not produce a viewable local conformational change, it is well known that the replacement of a serine may confer a different flexibility to the local secondary structure elements hosting the investigated mutation, due to the different abilities of Ser/Pro/Asn/Thr residues in producing kink/hinge movements. 2022 The EPMA journal Result SARS_CoV_2 S477N;S494P 102;9 107;14 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. From an energetical point of view, the P.1 Japan/Brazil VoC, showing the three mutations N501Y_E484K_K417T at the RBD, has the highest binding affinity (- 21.37 kcal/mol or - 89.41 kJ/mol; Table 1) for ACE2 (increased of 4% with respect to the Wuhan spike RBD, - 20.51 kcal/mol or - 85.81 kJ/mol, Table 1), followed by the B.1.141-VoC showing the single N439K amino acid replacement at the RBD and the single mutant E484K firstly detected in the spike RBD of the P.1 Japan/Brazil VoC (Table 1). 2022 The EPMA journal Result SARS_CoV_2 E484K;N439K;N501Y;E484K;K417T 416;354;89;95;101 421;359;94;100;106 S;S;RBD;RBD;RBD;RBD 250;446;114;256;390;452 255;451;117;259;393;455 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Indeed, it is possible to count a slight increase in the hydrophobic interactions within a range of 5 A at the SARS-CoV-2 spike RBD/ACE2 interface in the B.1.1.7-UK (S494P_N501Y_E484K); in the P.1 Japan/Brazil (N501Y_E484K_K417T) or in the B.1.351 S. 2022 The EPMA journal Result SARS_CoV_2 N501Y;S494P;E484K;E484K;K417T;N501Y 211;166;178;217;223;172 216;171;183;222;228;177 S;RBD;S 122;128;248 127;131;249 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Indeed, side chain-side chain H-bonds decrease at the SARS-CoV-2 spike RBD/ACE2 interface in all the VoC with the exception of the B.1.427/B.1.429 California L452R VoC (Supplementary Table 1 and. 2022 The EPMA journal Result SARS_CoV_2 L452R 158 163 S;RBD 65;71 70;74 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Indian (E484Q_L452R) VoC, whereas the same interactions appear increased in number in the P.1 Japan/Brazil (N501Y_E484K_K417T) and in the B.1.141 VoC N439K (Supplementary Table 1 and. 2022 The EPMA journal Result SARS_CoV_2 N439K;E484Q;N501Y;E484K;K417T;L452R 150;8;108;114;120;14 155;13;113;119;125;19 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. More in detail, the investigated L452R and E484Q amino acid replacements cause a local re-arrangement that perturbs the small beta-sheet in the "hull" region of the boat-shaped RBM (residues 450-455. 2022 The EPMA journal Result SARS_CoV_2 E484Q;L452R 43;33 48;38 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. New protein-protein aromatic-aromatic interactions (within 4.5 and 7 A) and protein-protein cation-pi interactions are observed at the SARS-CoV-2 spike RBD/ACE2 interface in all the VoCs showing the N501Y amino acid replacement (with specific reference to B.1.1.7-UK (S494P_N501Y_E484K), P.1 Japan/Brazil (N501Y_E484K_K417T) and B.1.351 S. 2022 The EPMA journal Result SARS_CoV_2 N501Y;N501Y;S494P;E484K;E484K;K417T;N501Y 199;306;268;280;312;318;274 204;311;273;285;317;323;279 S;RBD;S 146;152;337 151;155;338 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Some variations are observed in the number of protein-protein main chain-side chain hydrogen bonds which are apparently decreased at the SARS-CoV-2 spike RBD/ACE2 interface in the B.1.1.7-UK (S494P_N501Y_E484K), in the B.1.617.1-India (E484Q_L452), in the B.1.427/B.1.429 California (L452R), and in the B.1.617. 2022 The EPMA journal Result SARS_CoV_2 E484Q;L452R;S494P;E484K;N501Y 236;284;192;204;198 241;289;197;209;203 S;RBD 148;154 153;157 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. That is, L452R is the mutant with the greater number of protein-protein ionic interactions (Supplementary Table 1 and. 2022 The EPMA journal Result SARS_CoV_2 L452R 9 14 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. The B.1.1.7-UK (S494P_N501Y_E484K) variant and the B.1.617-India (E484Q_L452R) VoC show the lowest number of interactions (27 and 29, respectively) at the RBD/ACE2 protein-protein interface, according to PIC estimations. 2022 The EPMA journal Result SARS_CoV_2 E484Q;S494P;E484K;L452R;N501Y 66;16;28;72;22 71;21;33;77;27 RBD 155 158 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. The replacement of the seven investigated residues (N501Y, yellow sticks; E484K/Q, green/pink sticks; N439K, orange sticks; K417N/T, cyan/teal sticks; L452R, dark-blue sticks; S477N, light pink sticks; S494P, hot-pink sticks. 2022 The EPMA journal Result SARS_CoV_2 E484K;E484Q;K417N;K417T;L452R;N439K;S477N;S494P;N501Y 74;74;124;124;151;102;176;202;52 81;81;131;131;156;107;181;207;57 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. whereas N501Y, K417N, E484K and N439K amino acid replacements cause a conformational change in an alpha-helix close to N501 and N439 in the "stern" region (residues 436-449 and 497-503). 2022 The EPMA journal Result SARS_CoV_2 E484K;K417N;N439K;N501Y 22;15;32;8 27;20;37;13 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. With the exception of the B.1.427/B.1.429 California VoC (L452R) and B.1.141 (N439K) showing one more interaction (39 interactions) with respect to the interactions detected at the Wuhan SARS-CoV-2 spike RBD/ACE2 protein-protein interface (38 residues), all the other investigated ACE2/RBD complexes showed a decrease in the number of detected interactions at the protein-protein interface caused by the investigated amino acid replacements. 2022 The EPMA journal Result SARS_CoV_2 L452R;N439K 58;78 63;83 S;RBD;RBD 198;204;286 203;207;289 35014989 COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis. Only 2.4% (7/299) were from the lineage A that lack the D614G mutation. 2021 JMIRx med Result SARS_CoV_2 D614G 56 61 35014989 COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis. Our sequencing data does inform us that the outcomes presented in this VA cohort are dominated by the impacts of the B lineage D614G mutation. 2021 JMIRx med Result SARS_CoV_2 D614G 127 132 35014989 COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis. We found the majority of our specimens (154/299, 51.5%) were from SARS-CoV-2 lineage B.1 or a sublineage of B.1 (eg, B.1.302, B.1.303, B.1.356; 137/299, 46%), all of which are defined by D614G substitution (Figure 3, Multimedia Appendix 1). 2021 JMIRx med Result SARS_CoV_2 D614G 187 192 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. Among the mutations in RBD, R346K, N440K, G446V, N450K, V483F, E484K, E484Q, F490S and S494P also showed change in ACE2 binding to the extent of 75% to 90%. 2021 Journal of global infectious diseases Result SARS_CoV_2 E484K;E484Q;F490S;G446V;N440K;N450K;R346K;S494P;V483F 63;70;77;42;35;49;28;87;56 68;75;82;47;40;54;33;92;61 RBD 23 26 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. Among these 557 mutations, D614G was present in 79.99% (n = 3461) of Indian strains followed by L54F (n = 111, 2.57%) isolates. 2021 Journal of global infectious diseases Result SARS_CoV_2 D614G;L54F 27;96 32;100 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. Figure 4 shows prevalent mutations such as D614G, Q677H and P681H originated during March, April and July respectively and their appearance was observed till the end of the year 2020. 2021 Journal of global infectious diseases Result SARS_CoV_2 D614G;P681H;Q677H 43;60;50 48;65;55 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. It is also observed that two of the study variants possess H69del, V70del and Y144del in NTD and N501Y in RBD suggesting the improved affinity as well as adhesive properties of S-protein due to the concomitant mutations in both regions that synergistically promote virus host interaction. 2021 Journal of global infectious diseases Result SARS_CoV_2 H69del;N501Y;V70del;Y144del 59;97;67;78 65;102;73;85 RBD;S 106;177 109;178 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. It is noteworthy that single amino acid changes such as Y145del, F490S, A831S and double amino acid changes including D614G+A879S, D614G+A879T, and D614G+M1237I were reported to be resistant to convalescent sera or these mutations could confer the S protein monoclonal antibody resistance, whereas V367F of the RBD was reported to have increased sensitivity to neutralizing antibodies. 2021 Journal of global infectious diseases Result SARS_CoV_2 A831S;D614G;D614G;D614G;F490S;V367F;Y145del;A879S;A879T;M1237I 72;118;131;148;65;298;56;124;137;154 77;123;136;153;70;303;63;129;142;160 RBD;S 311;248 314;249 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. L18F, H69del, V70del, D138Y and Y144del mutations were observed in NTD of S-protein of few isolates and these mutations could enhance the surface electropositivity of the S-protein and thereby facilitating the adhesion of virus to negatively charged lipid raft gangliosides of host cells. 2021 Journal of global infectious diseases Result SARS_CoV_2 D138Y;H69del;V70del;L18F 22;6;14;0 27;12;20;4 S;S 74;171 75;172 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. L18F, T19A, D80N, D138Y, Y144del, Y145del, K147E, N148S, W152 L, Q218H and S255F were found in NTD, and among them, L18F, Y144del, Y145del and N148S and W152 L were shown to display resistance to neutralizing antibodies. 2021 Journal of global infectious diseases Result SARS_CoV_2 D138Y;D80N;K147E;L18F;N148S;N148S;Q218H;S255F;T19A;W152L;W152L;Y144del;Y144del;Y145del;Y145del;L18F 18;12;43;116;50;143;65;75;6;57;153;25;122;34;131;0 23;16;48;120;55;148;70;80;10;63;159;32;129;41;138;4 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. Many amino acid mutations were observed to be region specific namely F32Y, T33K and G35Q mutations (in Karnataka); T29I and P681H (Maharashtra); and L7S, L54F, R78M, Q690H, A701T and A879S (Gujarat). 2021 Journal of global infectious diseases Result SARS_CoV_2 A701T;A879S;F32Y;G35Q;L54F;L7S;P681H;Q690H;R78M;T29I;T33K 173;183;69;84;154;149;124;166;160;115;75 178;188;73;88;158;152;129;171;164;119;79 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. On contrary, L54F as well as K77M and P812 L mutations emerged during April and June respectively but absent after few months of their appearance. 2021 Journal of global infectious diseases Result SARS_CoV_2 K77M;L54F;P812L 29;13;38 33;17;44 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. One variant (EPI_ISL_479737) had lost both OGS and NGS sites due to mutations such as T602 L and N603Y [Table 2]. 2021 Journal of global infectious diseases Result SARS_CoV_2 N603Y;T602L 97;86 102;92 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. Other mutations M153I, S254F, and S255F identified in the study are found to reduce the affinity between S-protein and antibodies. 2021 Journal of global infectious diseases Result SARS_CoV_2 M153I;S254F;S255F 16;23;34 21;28;39 S 105 106 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. Some distinct amino acid variants were observed in Gujarat and Maharashtra (G181A) and V622F in Telangana and Orissa. 2021 Journal of global infectious diseases Result SARS_CoV_2 V622F;G181A 87;76 92;81 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. There were two NGS present in RBD without any mutation; among the four OGS in RBD, only one glycosylation mutation (T323I) was observed. 2021 Journal of global infectious diseases Result SARS_CoV_2 T323I 116 121 RBD;RBD 30;78 33;81 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. Variants identified with mutations at sites such as E484 (E484Q), F490 (F490S), Q493 (Q493STOP), and S494 (S494P) in the RBD are presumed to have immune escape features. 2021 Journal of global infectious diseases Result SARS_CoV_2 E484Q;F490S;Q493X;S494P 58;72;86;107 63;77;94;112 RBD 121 124 35018385 Integrin/TGF-beta1 inhibitor GLPG-0187 blocks SARS-CoV-2 Delta and Omicron pseudovirus infection of airway epithelial cells which could attenuate disease severity. After drug treatment, cells were spin-infected with the D614G pseudovirus for 20 hours. 2022 medRxiv Result SARS_CoV_2 D614G 56 61 35018385 Integrin/TGF-beta1 inhibitor GLPG-0187 blocks SARS-CoV-2 Delta and Omicron pseudovirus infection of airway epithelial cells which could attenuate disease severity. In addition to D614G, several other SARS-CoV-2 pseudovirus variants were also tested including D614, N501Y, E484K, N501Y + E484K (N+E), N501Y + E484K + K417N (NEK), R685A. 2022 medRxiv Result SARS_CoV_2 D614G;E484K;E484K;E484K;K417N;N501Y;N501Y;N501Y;R685A 15;108;123;144;152;101;115;136;165 20;113;128;149;157;106;120;141;170 N 130 131 35018385 Integrin/TGF-beta1 inhibitor GLPG-0187 blocks SARS-CoV-2 Delta and Omicron pseudovirus infection of airway epithelial cells which could attenuate disease severity. Nevertheless, the integrin inhibitor GLPG-0187 effectively blocked D614G, Delta and Omicron pseudovirus infection of HSAE cells. 2022 medRxiv Result SARS_CoV_2 D614G 67 72 35018385 Integrin/TGF-beta1 inhibitor GLPG-0187 blocks SARS-CoV-2 Delta and Omicron pseudovirus infection of airway epithelial cells which could attenuate disease severity. The results suggest that Omicron pseudovirus was less capable of infecting the small airway epithelial cells than D614G or Delta variant pseudovirus, which is in agreement with a recent study by Meng et al. 2022 medRxiv Result SARS_CoV_2 D614G 114 119 35018385 Integrin/TGF-beta1 inhibitor GLPG-0187 blocks SARS-CoV-2 Delta and Omicron pseudovirus infection of airway epithelial cells which could attenuate disease severity. To test the inhibition of SARS-CoV-2 pseudovirus infection with the integrin inhibitor GLPG-0187, HSAE cells were pre-treated with 20 nM, 100 nM, 200 nM, or 1 muM GLPG-0187 for 2 hours followed by spin-infection with either a pseudovirus expressing the D614G spike protein variant or a VsVg positive control for 24 hours. 2022 medRxiv Result SARS_CoV_2 D614G 253 258 S 259 264 35018385 Integrin/TGF-beta1 inhibitor GLPG-0187 blocks SARS-CoV-2 Delta and Omicron pseudovirus infection of airway epithelial cells which could attenuate disease severity. Treatment with GLPG-0187 inhibited pseudovirus infection in a dose-dependent manner in the D614G variant (Figure 2A). 2022 medRxiv Result SARS_CoV_2 D614G 91 96 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. Although the abundancy of each intra-host mutant was sparse, we also found a few S-gene mutations that were repeated in several viral isolates from individual 3807 (nucleotide substitution A3300G and T1389C, Fig 2) and one mutation (C968T) repeated in two individuals (Individual 4000 and 48559). 2022 PLoS pathogens Result SARS_CoV_2 A3300G;T1389C;C968T 189;200;233 195;206;238 S 81 82 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. An additional mutation in an O-glycosylation site was identified in individual 3953 (A1807G, N603D). 2022 PLoS pathogens Result SARS_CoV_2 N603D;A1807G 93;85 98;91 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. By measuring the p24 levels in the cell supernatant and the luminescence in the infected cells, we noted that the N-protein mutations A119V, M411I, A414P and E62D increase the pseudovirus production and the luciferase expression in the infected cells (Fig 3C and 3D). 2022 PLoS pathogens Result SARS_CoV_2 A119V;A414P;E62D;M411I 134;148;158;141 139;153;162;146 N 114 115 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. Finally, when the NT50 values of all plasma samples were compared, a significant increase was seen in the NT50 values of plasma samples that were incubated with SARS-CoV-2 pseudoviruses carrying the L1197I mutation in comparison with plasma samples that were incubated with SARS-CoV-2 pseudoviruses that express an unmutated spike protein (Fig 6C). 2022 PLoS pathogens Result SARS_CoV_2 L1197I 199 205 S 325 330 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. Further analysis of SARS-CoV-2 sequences from individual 3120 revealed S-gene variants with nonsense mutations (C1687T) in which a glutamine amino acid was replaced with a premature stop codon. 2022 PLoS pathogens Result SARS_CoV_2 C1687T 112 118 S 71 72 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. In accordance with the SGS results, the variant calling analysis identified that all 5 individuals were infected with the A1841G (D614G variant) and also identified the A3300G (T1100) in individual 3807 (S2 Table). 2022 PLoS pathogens Result SARS_CoV_2 A1841G;A3300G;D614G 122;169;130 128;175;135 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. In addition, a variant that was identified in two separate individuals (individual 4000 and individual 48559) carried a mutation in the N-glycosylation site (C968T, T323I). 2022 PLoS pathogens Result SARS_CoV_2 T323I;C968T 165;158 170;163 N 136 137 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. Interestingly, an identical N-gene variant C168G was isolated from four different individuals (individual 3953, individual 3120, individual 3807 and individual 4000; Fig 3A and 3B). 2022 PLoS pathogens Result SARS_CoV_2 C168G 43 48 N 28 29 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. Interestingly, the A3029G mutation that appears in individual 48552 leads to amino acid substitution Q110R that was previously associated with SARS-CoV-2 escape from polyclonal antibodies. 2022 PLoS pathogens Result SARS_CoV_2 A3029G;Q110R 19;101 25;106 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. Notably, reduced neutralization activity of five out of the seven plasma samples from vaccinated individuals was seen against SARS-CoV-2 pseudoviruses that express the L1197I mutation at the HR2 domain of the spike S2 subunit (Fig 6A). 2022 PLoS pathogens Result SARS_CoV_2 L1197I 168 174 S 209 214 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. Of note, pseudoviruses that carry the mutation F543S at the S1 subunit and C840F mutation at the S2 subunit resulted in the most significant reduction in infection, while the RBD mutation that also removed an N-glycosylation site (T323I) resulted in the most modest reduction in infectivity in comparison to all other spike mutations. 2022 PLoS pathogens Result SARS_CoV_2 C840F;F543S;T323I 75;47;231 80;52;236 S;RBD;N 318;175;209 323;178;210 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. Similar to our S-gene analysis, most of the N-gene variants we have identified were yet to be documented, but the synonymous nucleotide substitution (G609A) we have identified was found in numerous SARS-CoV-2 isolates (S4B Fig). 2022 PLoS pathogens Result SARS_CoV_2 G609A 150 155 N;S 44;15 45;16 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. Similarly, reduction in the neutralization activity against the L1197I variant was also seen in the two convalescent plasma samples that were tested (Fig 6B). 2022 PLoS pathogens Result SARS_CoV_2 L1197I 64 70 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. Similarly, to the results presented in Fig 6C, the L1197I mutation led to a significant increase in the NT50 values (S7B Fig). 2022 PLoS pathogens Result SARS_CoV_2 L1197I 51 57 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. The neutralizing activity of these plasma samples against three of the spike variants that we have isolated from the infected individuals was tested and showed the highest infectivity capacity: L216P, T323I and L1197I. 2022 PLoS pathogens Result SARS_CoV_2 L1197I;L216P;T323I 211;194;201 217;199;206 S 71 76 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. The tenth variant carries two mutations, G339D at the RBD and G909T at the S2 subunit (Fig 4A). 2022 PLoS pathogens Result SARS_CoV_2 G339D;G909T 41;62 46;67 RBD 54 57 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. To further test these differences, we also repeated the neutralization assay using a newly generated SARS-CoV-2 pseudoviruses carrying the Wuhan-Hu-1 spike protein or the L1197I mutation and evaluated the NT50 values using 3-fold plasma dilutions (S7 Fig). 2022 PLoS pathogens Result SARS_CoV_2 L1197I 171 177 S 150 155 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. We selected ten spike variants with mutations that are located at different domains of the spike protein for further analysis: L303F, K300E and L216P mutations at the S1 N-Terminal Domain (NTD), T323I and C361F mutations located at the receptor binding domain (RBD(, L938P mutation located at heptad repeat 1 (HR1) and L1197I mutation at heptad repeat 2 (HR2) at S2, two other variants from undefined domains at the S1 and S2 subunits, F543S and C840F, respectively. 2022 PLoS pathogens Result SARS_CoV_2 C361F;C840F;F543S;K300E;L1197I;L216P;L303F;L938P;T323I 205;446;436;134;319;144;127;267;195 210;451;441;139;325;149;132;272;200 RBD;S;S;RBD;N 236;16;91;261;170 259;21;96;264;171 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. When pseudoviruses that express the mutated spike proteins L216P and T323I were incubated with 10-fold dilutions of convalescent plasma or the vaccinees' plasma, the neutralization activity that was observed was comparable to the neutralization activity against SARS-CoV-2 pseudoviruses that carry the Wuhan-Hu-1 spike protein (Fig 6A and 6B), and no significant different in the half-maximal neutralizing titer values (NT50) was observed (Fig 6C). 2022 PLoS pathogens Result SARS_CoV_2 L216P;T323I 59;69 64;74 S;S 44;313 49;318 35025877 A short plus long-amplicon based sequencing approach improves genomic coverage and variant detection in the SARS-CoV-2 genome. As shown, mutation, i.e.,Q57H in the genomic region that have good uniform sequencing coverage in both assays, was consistently picked up by both short (Panel 3A) as well as long-amplicon data (Panel 3B). 2022 PloS one Result SARS_CoV_2 Q57H 25 29 35025877 A short plus long-amplicon based sequencing approach improves genomic coverage and variant detection in the SARS-CoV-2 genome. However, a nonsynonymous mutation G172V in ORF3a gene at nt25907(G T), and a synonymous mutation A2A in M gene at nt26528(A G) located in the poorly captured region in ARTIC assay, were missed in short amplicon data (Panel A), whereas the long-amplicon data did detect G172V in samples NP1 and NP3, and A2A mutation in sample A10 (Panel B). 2022 PloS one Result SARS_CoV_2 A2A;A2A;G172V;G172V 99;307;34;273 102;310;39;278 ORF3a 43 48 35025877 A short plus long-amplicon based sequencing approach improves genomic coverage and variant detection in the SARS-CoV-2 genome. K417N, E484K, N501Y, P618H and variants of interest i.e. 2022 PloS one Result SARS_CoV_2 E484K;N501Y;P618H;K417N 7;14;21;0 12;19;26;5 35025877 A short plus long-amplicon based sequencing approach improves genomic coverage and variant detection in the SARS-CoV-2 genome. L18F, 69-70 Del, D80A, Y144Del, L242Del, A570D, A701V and T716I. 2022 PloS one Result SARS_CoV_2 A570D;A701V;D80A;T716I;L18F 41;48;17;58;0 46;53;21;63;4 35025877 A short plus long-amplicon based sequencing approach improves genomic coverage and variant detection in the SARS-CoV-2 genome. Long-amplicon data captured 20 key lineage defining mutations including spike gene variants of concern K417N, E484K, N501Y and P618H (S3 File). 2022 PloS one Result SARS_CoV_2 E484K;K417N;N501Y;P618H 110;103;117;127 115;108;122;132 S 72 77 35026305 SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021. All 77 spike variants had detectable spike mutations using the Variants I Assay, comprising 18 with HV69/70 deletion and N501Y mutation confirmed as lineage B.1.1.7 using NGS, and 59 positive for E484K and N501Y mutations confirmed as B.1.351 by NGS (Table 1). 2022 Journal of virological methods Result SARS_CoV_2 E484K;N501Y;N501Y 196;121;206 201;126;211 S;S 7;37 12;42 35026305 SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021. Similarly, the Variants I Assay showed similar Ct values of RdRp and HV69/70 deletion/E484K/N501Y, with average deviation of 1.0 cycles. 2022 Journal of virological methods Result SARS_CoV_2 E484K;N501Y 86;92 91;97 RdRP 60 64 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Alpha+S494P and Alpha+V367F also enhanced infectivity within fourfold (Figure 2A). 2022 Journal of medical virology Result SARS_CoV_2 S494P;V367F 6;22 11;27 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Among the possible Beta variants, the Beta+V367F pseudovirus variant showed nearly fourfold enhanced infectivity, especially in Huh7 and LLC-MK2 cells, and Beta+S494P and Beta+A520S showed similar effects (Figure 2B). 2022 Journal of medical virology Result SARS_CoV_2 A520S;S494P;V367F 176;161;43 181;166;48 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Among the possible Gamma variants, the Gamma+A520S variant showed the most significant increase in infectivity, approaching or even exceeding fourfold in all the cell lines (Figure 2C). 2022 Journal of medical virology Result SARS_CoV_2 A520S 45 50 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Among the three mutations, variants with A520S displayed a significant effect in increasing the cell-cell fusion. 2022 Journal of medical virology Result SARS_CoV_2 A520S 41 46 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Among them, neutralizing activity of aggregated single-point and multipoint mutations on the possible VOCs suggested that the neutralization differences between immunogenic guinea pig sera with diverse mutations were insignificant, of which the immunoprotective effect of D614G + E484K + N501Y immunogen was slightly better than the other three groups. 2022 Journal of medical virology Result SARS_CoV_2 D614G;E484K;N501Y 272;280;288 277;285;293 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. As indicated in Figure 4D, N501Y in the Gamma RBD induces little conformational change. 2022 Journal of medical virology Result SARS_CoV_2 N501Y 27 32 RBD 46 49 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Compared with the corresponding three VOCs, among the possible Alpha variants, Alpha+A520S showed a significant increase in infectivity of more than fourfold in LLC-MK2 and Vero cells. 2022 Journal of medical virology Result SARS_CoV_2 A520S 85 90 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. D614G + P384L + A522S and D614G + V367F + P384L + A522S also had a significantly higher neutralization effect on the mAbs compared with the D614G variant pseudovirus, suggesting the possible synergistic effect of both P384L and A522S on neutralization protection (Figure S2A). 2022 Journal of medical virology Result SARS_CoV_2 A522S;A522S;A522S;D614G;D614G;P384L;P384L;P384L;V367F;D614G 16;50;228;26;140;8;42;218;34;0 21;55;233;31;145;13;47;223;39;5 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Effect of S494P, A520S, and V367F substitutions on spike protein expression on pseudotyped virus and cell-cell fusion. 2022 Journal of medical virology Result SARS_CoV_2 A520S;S494P;V367F 17;10;28 22;15;33 S 51 56 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. For the possible aggregation of multiple mutated VOCs, the changes in their mean NT50 ratios relative to their respective parental VOCs were Ad5-Spike (1.15), mRNA-Spike (0.86), 2019-nCoV (1.28), D614G (1.04), D614G + E484K + N501Y (1.91), D614G + K417N + E484K + N501Y (1.42) (Figure 7). 2022 Journal of medical virology Result SARS_CoV_2 D614G;D614G;D614G;E484K;E484K;K417N;N501Y;N501Y 196;210;240;218;256;248;226;264 201;215;245;223;261;253;231;269 S;S 145;164 150;169 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Furthermore, among the results from 293T-ACE2 cells of different species that were zoophilic, three mutant variants:S494P, V367F, and A520S:were particularly enhanced in infectivity in cells expressing mouse ACE2, reaching or approaching four-fold (Figure S1B), and these mutant variants deserve extra attention to prevent the emergence of new zoonotic transmissions. 2022 Journal of medical virology Result SARS_CoV_2 A520S;V367F;S494P 134;123;116 139;128;121 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. However, it is noteworthy that the proportional decrease in the neutralization titer was more pronounced for the possible Beta multisite variants compared with the D614G strain combined with the second to tenth mutations, although the p values were not statistically significant (Figure 6B). 2022 Journal of medical virology Result SARS_CoV_2 D614G 164 169 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. However, when the combined mutations reached 6th-Y453F and beyond (Figure 2A), the infectivity decreased, with infectivity rebounding slightly when combined with the V367F mutation. 2022 Journal of medical virology Result SARS_CoV_2 V367F;Y453F 166;49 171;54 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Interestingly, on the basis of the neutralization results, we found that some of the mutation sites enhanced the neutralization effect of mAbs when stacked together, with the last three sites of the top 15 high-frequency mutations:V367F, P384L, and A522S:being particularly effective at enhancing the neutralization of DXP-604 and 09-4E5-1G2 mAbs (Figure 5). 2022 Journal of medical virology Result SARS_CoV_2 A522S;P384L;V367F 249;238;231 254;243;236 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. It is also noteworthy that the serum of vaccine volunteers (Ad5-Spike and mRNA-Spike) showed similar neutralization results to those of convalescent sera (Figure 6), with some possible multilocus aggregation variants of Beta showing near or slightly over a fourfold decrease in neutralization activity compared to the D614G strain due to a significant decrease in the Beta variant itself (Figure 7B). 2022 Journal of medical virology Result SARS_CoV_2 D614G 318 323 S;S 64;79 69;84 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Moreover, compared with the D614G variant, the above possible combined Alpha and Gamma variants also showed less than a fourfold decrease in neutralization and did not display immune escape. 2022 Journal of medical virology Result SARS_CoV_2 D614G 28 33 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Notably, Alpha+A520S, Alpha+S494P, Beta+V367F, and Gamma+A520S possible variant pseudoviruses were significantly more infectious in 293T cells with high ACE2 receptor expression in most species (Figure 3), suggesting that these variants deserve special attention if they occur in nature. 2022 Journal of medical virology Result SARS_CoV_2 A520S;A520S;S494P;V367F 15;57;28;40 20;62;33;45 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Pseudotyped viruses were also constructed by aggregating the amino acid mutations in the order of the first 13 high-frequency mutations in the three VOCs followed by N501Y, S477N, N439K, L452R, E484K, K417N, Y453F, S494P, A520S, T478K, V367F, P384L and A522S (Figure 1D). 2022 Journal of medical virology Result SARS_CoV_2 A520S;A522S;E484K;K417N;L452R;N439K;N501Y;P384L;S477N;S494P;T478K;V367F;Y453F 222;253;194;201;187;180;166;243;173;215;229;236;208 227;258;199;206;192;185;171;248;178;220;234;241;213 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Similar to the infectivity results for susceptible mammalian cell lines, the Alpha, Beta, and Gamma possible variants were significantly less infectious compared with the corresponding VOCs after combining multiple high-frequency mutations (Alpha possible variants superimposed to the 6th-Y453F mutation start to decline, Beta and Gamma possible variants superimposed to the 2nd-N439K mutation start to decline) (Figure 3). 2022 Journal of medical virology Result SARS_CoV_2 N439K;Y453F 379;289 384;294 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Some possible variants, such as Alpha+V367F and Gamma+L452R, even showed a better neutralization ability to the convalescent sera (Figure 6A,C). 2022 Journal of medical virology Result SARS_CoV_2 L452R;V367F 54;38 59;43 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Taken together, these may lead to enhanced infectivity of the possible Gamma+A520S virus. 2022 Journal of medical virology Result SARS_CoV_2 A520S 77 82 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The D614G strain has replaced the SARS-CoV-2 (2019-nCoV) variant as a globally prevalent variant, we used the D614G strain as the control reference in this study. 2022 Journal of medical virology Result SARS_CoV_2 D614G;D614G 4;110 9;115 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The largest decrease in neutralization protection among the possible Alpha and Gamma variants was seen for the Alpha strain combined with top 11 high-frequency RBD mutations, namely the Alpha+11muts (P384L) variant, which decreased only twofold relative to the Alpha variant (Figure 6A). 2022 Journal of medical virology Result SARS_CoV_2 P384L 200 205 RBD 160 163 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The neutralization results for the possible VOC single variants showed that the N501Y mutation escape the mAbs CB6 and 03-10D12-1C3, while the N501T substitution in the Alpha+N501T variant does not escape mAb 03-10D12-1C3 (Figure 5A); the mAbs BGB-DXP593, 05-9G11, MW07-LALA, AM128, AM180, and AbG3 were escaped by the E484K mutation, whereby DXP-593, 05-9G11, AM180, and AbG3 were also escaped by the L452R mutation; mAb DXP-604 was escaped by the K417N, but not the K417T mutation (Figure 5B); the mAb 09-4E5-1G2 was escaped by the N439K mutation; and the mAb 09-7B8 was escaped by the S477N, S477R, and T478K mutations. 2022 Journal of medical virology Result SARS_CoV_2 E484K;K417N;K417T;L452R;N439K;N501T;N501Y;S477N;S477R;T478K;N501T 319;449;468;402;534;143;80;588;595;606;175 324;454;473;407;539;148;85;593;600;611;180 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The results showed no significant changes in the neutralizing activity of either vaccine volunteer sera or guinea pig sera against the three groups of possible single point mutant strains of VOCs (Alpha, Beta, and Gamma), with mean neutralizing 50% of pseudotyped viral activity (NT50) ratios relative to the corresponding VOCs of Ad5-Spike (2.16), mRNA-Spike (1.30), 2019-nCoV (1.45), D614G (1.37), D614G + E484K + N501Y (1.83), and D614G + K417N + E484K + N501Y (1.69) (Figure 7). 2022 Journal of medical virology Result SARS_CoV_2 D614G;D614G;D614G;E484K;E484K;K417N;N501Y;N501Y 386;400;434;408;450;442;416;458 391;405;439;413;455;447;421;463 S;S 335;354 340;359 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The results showed no significant difference in the amount of spike protein on the pseudotyped virus compared with the D614G strain and the three corresponding VOCs (Figure 4A). 2022 Journal of medical virology Result SARS_CoV_2 D614G 119 124 S 62 67 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The results showed that in the neutralizing activity to the two mAbs, DXP-604 and 09-4E5-1G2, the D614G + V367F variant had a significantly higher neutralization effect compared with the D614G variant. 2022 Journal of medical virology Result SARS_CoV_2 D614G;D614G;V367F 98;187;106 103;192;111 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The results showed that the D614G + A520S possible variant had significantly enhanced infectivity in Calu-3 and Huh7 cells (Figure S1A). 2022 Journal of medical virology Result SARS_CoV_2 A520S;D614G 36;28 41;33 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The results showed that the S494P, A520S, and V367F mutant variants could enhance the intensity of intercellular fusion, with the A520S mutation, in particular, enhancing fusion more than twofold in the four mutant variant profiles of D614G, Alpha, Beta, and Gamma (Figure 4B). 2022 Journal of medical virology Result SARS_CoV_2 A520S;A520S;D614G;S494P;V367F 35;130;235;28;46 40;135;240;33;51 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The structure of Gamma-A520S RBD-hACE2 was similar to the WT RBD-hACE2 structure with a root-mean-square deviation (RMSD) of 0.323 A (for 737 Calpha atoms, PDB: 6LZG). 2022 Journal of medical virology Result SARS_CoV_2 A520S 23 28 RBD;RBD 29;61 32;64 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. These suggested that the increased infectivity of pseudovirus variants after the addition of S494P, A520S, and V367F mutations may be achieved through the pathway of cell-cell fusion enhancement. 2022 Journal of medical virology Result SARS_CoV_2 A520S;S494P;V367F 100;93;111 105;98;116 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Thus, we focused on the A520S. 2022 Journal of medical virology Result SARS_CoV_2 A520S 24 29 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. To further characterize the changes in neutralizing activity of three possible groups of VOCs against different human vaccine and antigen-immunized guinea pig sera, we detected two 2019-nCoV vaccine sera used in emergency trials or in clinical trials in China: the Ad5-Spike vaccine (n = 5) based on the adenoviral vector and the mRNA-Spike vaccine (n = 4), and also detected the sera from immunized guinea pig with four groups of immunogens: 2019-nCoV group (n = 4), D614G group (n = 4), D614G + E484K + N501Y group (n = 4), and D614G + K417N + E484K + N501Y group (n = 4). 2022 Journal of medical virology Result SARS_CoV_2 D614G;D614G;D614G;E484K;E484K;K417N;N501Y;N501Y 468;489;530;497;546;538;505;554 473;494;535;502;551;543;510;559 S;S 269;335 274;340 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. To further investigate the mechanism responsible for the change in infectivity of the S494P, A520S, and V367F mutations in the D614G, Alpha, Beta, and Gamma variants, we first examined the difference in the amount of spike protein under quantitative conditions for the pseudotyped virus. 2022 Journal of medical virology Result SARS_CoV_2 A520S;D614G;S494P;V367F 93;127;86;104 98;132;91;109 S 217 222 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. To further investigate whether there is a synergistic effect between these three sites on pseudotyped virus neutralization, we performed one-, two- and three-site aggregated mutations on the D614G variant to verify their effects on neutralization. 2022 Journal of medical virology Result SARS_CoV_2 D614G 191 196 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. To further verify the effect of the three mutations, S494P, V367F, and A520S, on infectivity, we introduced a single-site mutation into the D614G pseudovirus variants individually and explored the changes in infectivity in the above cell lines. 2022 Journal of medical virology Result SARS_CoV_2 A520S;D614G;S494P;V367F 71;140;53;60 76;145;58;65 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. We first evaluated the effect of A520S on the binding affinity to the human receptor. 2022 Journal of medical virology Result SARS_CoV_2 A520S 33 38 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. We then solved the complex structure of Gamma-A520S RBD with hACE2 at a resolution of 3.3 A. 2022 Journal of medical virology Result SARS_CoV_2 A520S 46 51 RBD 52 55 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. When A520S was incorporated into the three VOCs, the affinities to hACE2 were maintained at a similar level to their respective parental ones. 2022 Journal of medical virology Result SARS_CoV_2 A520S 5 10 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. When the complex structure of Gamma-A520S with hACE2 was superimposed with the Cryo-EM structure of S protein (PDB: 6VSB), the standing RBD S520 Calpha is 1.7 A closer to the adjacent NTD loop, compared with the A520 Calpha. 2022 Journal of medical virology Result SARS_CoV_2 A520S 36 41 RBD;S 136;100 139;101 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. Furthermore, for Cq over 25 no SARS-CoV-2 variant (K417N/T, E484K, and N501Y) sample was detected by RAT. 2021 Frontiers in public health Result SARS_CoV_2 E484K;N501Y;K417N;K417T 60;71;51;51 65;76;58;58 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. Interestingly, from the three SARS-CoV-2 (K417N/T, E484K, and N501Y) positive samples for RAT, two of them presented a band of low intensity (Table 2) compared to SARS-CoV-2 samples with no mutations identified, which present a high-intensity band in the range 20>=Cq <25 (Table 1). 2021 Frontiers in public health Result SARS_CoV_2 E484K;N501Y;K417N;K417T 51;62;42;42 56;67;49;49 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. When we evaluated these NPSs containing SARS-CoV-2 variants, we observed that the sensitivity of RAT decreased in the variants that carry K417N/T and E484K amino acid substitutions, even in samples with the lowest ranges of Cq (20 <= Cq <25). 2021 Frontiers in public health Result SARS_CoV_2 E484K;K417N;K417T 150;138;138 155;145;145 35055023 Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors. On the other hand, the E11V mutation gains an energy increase of only -0.73 kcal/mol at a local position in addition to its impact on the nearest neighbor AA (Y10) to get an extra -1.2 kcal/mol. 2022 International journal of molecular sciences Result SARS_CoV_2 E11V 23 27 35055023 Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors. The D17R mutation in M11-MD has a stronger binding of -5.36 kcal/mol than M3-MD (Table S1 or Figure 2). 2022 International journal of molecular sciences Result SARS_CoV_2 D17R 4 8 35055023 Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors. The D17T mutation tends to reduce the binding with RBD, but the other three mutations (D17E, D17R, and D17M) have the opposite trends because their sidechains are longer than D, thus promoting more interactions with the RBD. 2022 International journal of molecular sciences Result SARS_CoV_2 D17M;D17R;D17T;D17E 103;93;4;87 107;97;8;91 RBD;RBD 51;220 54;223 35055023 Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors. The stronger binding is primarily due to the D17R mutation, which provides a -4.15 kcal/mol energy boost. 2022 International journal of molecular sciences Result SARS_CoV_2 D17R 45 49 35055023 Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors. To further verify that the increase in binding comes from the substituted AAs, the key interacting AAs in M15-MD (E11V + D17R) are analyzed as shown in Figure S8c,d. 2022 International journal of molecular sciences Result SARS_CoV_2 D17R;E11V 121;114 125;118 35056548 Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan. All CA strains possessed the D614G amino acid substitution in the S protein, whilst all DP strains showed amino acid 614D. 2022 Microorganisms Result SARS_CoV_2 D614G 29 34 S 66 67 35056548 Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan. DP strains obtained mutations that resulted in the novel haplotypes DP-B (C18656T, corresponding to T206I in the NSP14 protein) and DP-C (C18656T+C29635T, C29635T was a synonymous mutation) on the cruise ship. 2022 Microorganisms Result SARS_CoV_2 C29635T;T206I;C18656T;C18656T;C29635T 155;100;74;138;146 162;105;81;145;153 35056548 Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan. FJ strains contained one original East Asian-type strain (FJ294), and all other FJ strains possessed a D614G substitution in the S protein. 2022 Microorganisms Result SARS_CoV_2 D614G 103 108 S 129 130 35056548 Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan. SARS-CoV-2 obtained novel haplotypes on the CA cruise ship to form the CA-B (G25437T, corresponding to L15F in the ORF3a protein) and CA-C clusters (G25437T+C23604A, corresponding to L15F+P681H in the ORF3a and S protein, respectively), finally obtaining a reversion mutation, T11195C, that was originally found in the Wuhan-Hu-1 strain (Figure 3a). 2022 Microorganisms Result SARS_CoV_2 L15F;L15F;T11195C;G25437T;G25437T;C23604A;P681H 103;183;277;77;149;157;188 107;187;284;84;156;164;193 ORF3a;ORF3a;S 115;201;211 120;206;212 35056592 SARS-CoV-2 Evolution and Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIV Immune Suppression. Genotypic tests revealed a non-B HIV subtype, variant F1, with 106 V > I substitution at the reverse transcriptase (RT). 2022 Microorganisms Result SARS_CoV_2 V106I 63 72 35056592 SARS-CoV-2 Evolution and Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIV Immune Suppression. Interestingly, 23012G > A (S:E484K) was already technically fixed (VAF > 0.95) at the first time point, but its frequency decreased at T2 and T3 going down to 0.49-0.72. 2022 Microorganisms Result SARS_CoV_2 G23012A;E484K 15;29 25;34 S 27 28 35056592 SARS-CoV-2 Evolution and Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIV Immune Suppression. Of note, 3045C > T (P927L) was already at a very low VAF (0.07) in T1. 2022 Microorganisms Result SARS_CoV_2 C3045T;P927L 9;20 18;25 35056592 SARS-CoV-2 Evolution and Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIV Immune Suppression. Only 3096C > T (ORF1a:S944L) is a bit more common, but still appears in a small number of cases (<0.5%). 2022 Microorganisms Result SARS_CoV_2 C3096T;S944L 5;22 14;27 ORF1a 16 21 35056592 SARS-CoV-2 Evolution and Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIV Immune Suppression. SARS-CoV-2 was classified as an Alpha variant (Phylogenetic Assignment of Named Global Outbreak Lineages-PANGO-lineage B.1.1.7), similar to the consensus sequences of dominant contemporaneous isolates circulating by the same time, and included the relevant mutation S:E484K. 2022 Microorganisms Result SARS_CoV_2 E484K 268 273 S 266 267 35056592 SARS-CoV-2 Evolution and Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIV Immune Suppression. Some intra-host mutations not detected in T1 appeared in T2 or T3: 13033T > A (ORF1a:N4256K), 15559C > T (ORF1b:L698F), 15619C > T (ORF1b:L718F), 17523G > T (ORF1b:M1352I), 21641G > T (S:A27S), 21701ins, 21982T > A (F140L), 22583ins, 23031T > C (F490S). 2022 Microorganisms Result SARS_CoV_2 T13033A;C15559T;C15619T;G17523T;G21641T;21701ins;T21982A;22583ins;T23031C;F140L;F490S;A27S;L698F;L718F;M1352I;N4256K 67;94;120;146;173;194;204;224;234;216;246;187;112;138;164;85 77;104;130;156;183;202;214;232;244;221;251;191;117;143;170;91 ORF1a;S 79;185 84;186 35056592 SARS-CoV-2 Evolution and Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIV Immune Suppression. The 184 M > V RT-mutation, associated with lamivudine resistance, was detected at week 12 after ART initiation with no integrase mutations. 2022 Microorganisms Result SARS_CoV_2 M184V 4 13 35056592 SARS-CoV-2 Evolution and Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIV Immune Suppression. These mutations were often detected at low VAFs, and did not reach fixation, except for 13033T > A (ORF1a:N4256K) and 23896C > T which increased through time up to very high VAFs. 2022 Microorganisms Result SARS_CoV_2 T13033A;C23896T;N4256K 88;118;106 98;128;112 ORF1a 100 105 35056592 SARS-CoV-2 Evolution and Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIV Immune Suppression. Three of the intra-host mutations inferred at T1 were not detected at T2 or T3: 3045C > T (P927L), 6814T > C and 23257T > C. 2022 Microorganisms Result SARS_CoV_2 T23257C;C3045T;T6814C;P927L 113;80;99;91 123;89;108;96 35056592 SARS-CoV-2 Evolution and Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIV Immune Suppression. Thus, six apparently intra-host mutations were maintained at a high VAF across the three time points: 3675_3677del, 69_70del, 144del, 28095A > T (K68*), 28271del and 29594A > G (I13V), suggesting they were probably fixed, invariable mutations. 2022 Microorganisms Result SARS_CoV_2 144del;A28095T;28271del;A29594G;I13V;K68X 126;134;153;166;178;146 132;144;161;176;182;150 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. In contrast, much fewer cell fusion was observed in the cells expressing the Omicron spike than the WT-D614G spike, indicating that the Omicron variant has reduced fusogenicity (Figure 1D). 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 103 108 S;S 85;109 90;114 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. Pseudovirus (PV) of WT-D614G was used as a reference virus as the D614G is critical for higher viral infectivity, which is also present in the two tested VOC. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G;D614G 66;23 71;28 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. The Delta variant carries only L452R and T478K mutations in its RBD region, while the Omicron carries as much as fifteen RBD mutations of G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H. 2022 Emerging microbes & infections Result SARS_CoV_2 E484A;G339D;G446S;G496S;K417N;L452R;N440K;N501Y;Q493R;Q498R;S371L;S373P;S375F;S477N;T478K;T478K;Y505H 201;138;180;215;166;31;173;229;208;222;145;152;159;187;41;194;236 206;143;185;220;171;36;178;234;213;227;150;157;164;192;46;199;241 RBD;RBD 64;121 67;124 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. The result showed that the infectivity of the Omicron variant is slightly higher than WT-D614G and the Delta variant at the same Median Tissue Culture Infectious Dose (TCID50) (Figure 1B). 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 89 94 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. The result showed that, compared with WT-D614G, there is a 10.14 fold decrease of neutralization activity against the Omicron variant, while the decrease against the Delta variant is 1.79 fold (Figure 2B). 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 41 46 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. To precisely evaluate the reduction of neutralization against the variants, we further tested the half neutralization titer (NT50) of the 24 sera showing the highest activity against the WT-D614G infection. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 190 195 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. To test the immune escape ability of the Omicron variant, we conducted the pseudovirus neutralization assay in BHK21-hACE2 cells using 180 sera collected from Wuhan convalescents one-year post-infection, all with confirmed anti-SARS-CoV-2 (WT-D614G) activity in our previous study. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 243 248 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. When the sera were applied at a 100-fold dilution, we observed a dramatic reduction of sera neutralizing activity against the Omicron variant, with the average neutralization of only 13% compared with 80% of WT-D614G. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 211 216 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. Comparing to the overall free binding energy of 212.5 kJ mol-1 between the wild-type RBD and ACE2 receptor, all single and double RBD mutants showed increased free binding energy, except for N501Y, which decreased to -204.6 kJ mol-1 (Table 1A). 2021 Viruses Result SARS_CoV_2 N501Y 191 196 RBD;RBD 85;130 88;133 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. Figure 5 demonstrated the independent binding sites of C121 on S protein, covering N439, N440, L455, G446, E484, and Q493, and confirmed that E484K altered the binding sites of the C121 structure. 2021 Viruses Result SARS_CoV_2 E484K 142 147 S 63 64 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. However, N501 became a top residue in two of the three RBD double mutants and four of the five RBD single mutants, highlighting that N501Y in the RBD double mutants and single RBD mutants played significant roles in enhancing the affinity between RBD mutants to the ACE2 receptor by enhancing the binding energy (Table 1B, Figure 4). 2021 Viruses Result SARS_CoV_2 N501Y 133 138 RBD;RBD;RBD;RBD;RBD 55;95;146;176;247 58;98;149;179;250 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. However, the top five residues in each RBD double mutant were mostly changed from the wild-type RBD and their corresponding single mutations: L452/T478K changed to Y505, F486, N501, Q493, and T500; L452R/E484Q to F486, Q493, Y505, Y489, and F456; and E484K/N501Y to Y501, Y505, Q493, T500, and F486. 2021 Viruses Result SARS_CoV_2 E484K;L452R;E484Q;N501Y;T478K 251;198;204;257;147 256;203;209;262;152 RBD;RBD 39;96 42;99 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. L452R induced conformational change at residue positions 474-485 and 517-526 (Figure 3B), whereas N501Y did so at residue positions 439-453 and 498-502 (Figure 3F). 2021 Viruses Result SARS_CoV_2 N501Y;L452R 98;0 103;5 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. L452R/E484Q was the most significant among the three RBD double mutants, followed by E484K/N501Y and L452R/T478K. 2021 Viruses Result SARS_CoV_2 E484K;L452R;E484Q;N501Y;T478K;L452R 85;101;6;91;107;0 90;106;11;96;112;5 RBD 53 56 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. L452R/T478K showed conformational change at residue positions 475-482 and 518-521 (Figure 3G), whereas both L452R/E484Q and E484K/N501Y were at residue position 475-485 (Figure 3H,I). 2021 Viruses Result SARS_CoV_2 E484K;L452R;E484Q;N501Y;T478K;L452R 124;108;114;130;6;0 129;113;119;135;11;5 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. L452R/T478K showed deviation up to ~30 ns and thereafter stabilized at ~0.3-0.4 nm; L452R/E484Q stabilized ~0.3-0.5 nm with a deviation at around 35 ns; E484K/N501Y reached the equilibrium distance at ~0.23 nm. 2021 Viruses Result SARS_CoV_2 E484K;L452R;E484Q;N501Y;T478K;L452R 153;84;90;159;6;0 158;89;95;164;11;5 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. N501Y had 0.5 nm between 80 and 100 ns. 2021 Viruses Result SARS_CoV_2 N501Y 0 5 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. Single mutants L452R, T478K, E484Q, and E484K, except for N501Y, showed stable configuration post 60 ns: L452R stabilized ~0.25 nm, T478K ~ 0.3 nm, E484Q ~ 0.2-0.3 nm, E484K ~ 0.3 nm. 2021 Viruses Result SARS_CoV_2 E484K;E484K;E484Q;E484Q;L452R;L452R;N501Y;T478K;T478K 40;168;29;148;15;105;58;22;132 45;173;34;153;20;110;63;27;137 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. T478K, E484K, and E484Q had higher Rg values than the wild-type RBD but lower than the double mutants, except for N501Y, which had a higher value, ~3.2-3.3 nm (Figure S2). 2021 Viruses Result SARS_CoV_2 E484K;E484Q;N501Y;T478K 7;18;114;0 12;23;119;5 RBD 64 67 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. The binding sites for the double mutants L452R/T478K, L452R/E484Q, and E484K/N501Y were altered. 2021 Viruses Result SARS_CoV_2 E484K;L452R;L452R;E484Q;N501Y;T478K 71;41;54;60;77;47 76;46;59;65;82;52 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. The conformational changes in double mutants comprising L452R and N501Y were very different from their corresponding single mutants. 2021 Viruses Result SARS_CoV_2 L452R;N501Y 56;66 61;71 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. The double mutant L452R/T478K showed a greater Rg value, ~3.2-3.25 nm, for the entire trajectory than the wild-type; L452R/E484Q had ~3.13-3.18 nm; E484K/N501Y had ~3.15-3.25 nm after 35 ns; L452R/E484Q and E484K/N501Y showed the change in Rg value ~80-100 ns and ~10-30 ns, respectively. 2021 Viruses Result SARS_CoV_2 E484K;E484K;L452R;L452R;L452R;E484Q;E484Q;N501Y;N501Y;T478K 148;207;18;117;191;123;197;154;213;24 153;212;23;122;196;128;202;159;218;29 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. The double mutants L452R/T478K, L452R/E484Q and E484K/N501Y showed average displacement values ~10.88, ~7.33, and ~9.06, respectively, lower than the wild-type but higher than those in the single mutants (Figure S4). 2021 Viruses Result SARS_CoV_2 E484K;L452R;L452R;E484Q;N501Y;T478K 48;19;32;38;54;25 53;24;37;43;59;30 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. The flexibility in the polypeptide chain through RMSF showed that double mutants L452R/E484Q, L452R/T478K, and E484K/N501Y had high to medium resilience ~ 0.4 nm, ~0.15 nm, and ~0.25 nm, respectively, at residue positions 360-380 and 470-490. 2021 Viruses Result SARS_CoV_2 E484K;L452R;L452R;E484Q;N501Y;T478K 111;81;94;87;117;100 116;86;99;92;122;105 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. The higher resilience in the double mutants L452R/E484Q and E484K/N501Y can be attributed to their differences in RMSD trajectory around residue positions 360-380 and 470-490. 2021 Viruses Result SARS_CoV_2 E484K;L452R;E484Q;N501Y 60;44;50;66 65;49;55;71 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. The SARS-CoV-2 neutralizing antibody (NAb) C121 (PDB ID: 7K8X) is a well-known neutralizing antibody to SARS-CoV-2 through its binding to S RBD and the cell-based infectivity assay showed that E484K is resistant to C121 binding. 2021 Viruses Result SARS_CoV_2 E484K 193 198 RBD;S 140;138 143;139 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. The wild-type RBD had a surface area of ~430 nm2; all the single mutants, L452R, T478K, E484K, E484Q, and N501Y, had decreased values of ~426 nm2, ~426 nm2, ~424 nm2, ~428 nm2 and ~429 nm2, respectively. 2021 Viruses Result SARS_CoV_2 E484K;E484Q;L452R;N501Y;T478K 88;95;74;106;81 93;100;79;111;86 RBD 14 17 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. To investigate the effects of double mutations on the RBD structure, we examined the conformational changes of the RBD double mutant-ACE2 receptor complex in RBD double mutants L452R/T478K, L452R/E484Q, and E484K/N501Y using MD simulations for 100 ns. 2021 Viruses Result SARS_CoV_2 E484K;L452R;L452R;E484Q;N501Y;T478K 207;177;190;196;213;183 212;182;195;201;218;188 RBD;RBD;RBD 54;115;158 57;118;161 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. We used the C121 neutralizing antibody and E484K structure as the model to test the relationship between RBD double mutants and antibody resistance binding sites through structural mapping at 100 ns. 2021 Viruses Result SARS_CoV_2 E484K 43 48 RBD 105 108 35062211 SARS-CoV-2 Spike Expression at the Surface of Infected Primary Human Airway Epithelial Cells. CV3-25 specifically bound to infected (N+) pAECs when the cells were infected with the authentic D614G (Figure 1B) or Alpha (B.1.1.7) variant of concern (Figure 1C). 2021 Viruses Result SARS_CoV_2 D614G 97 102 35062211 SARS-CoV-2 Spike Expression at the Surface of Infected Primary Human Airway Epithelial Cells. Representative flow cytometry contour plots of the specific recognition of (N+) pAECs infected with SARS-CoV-2 D614G (Figure 2B,D) or the Alpha variant (Figure 2C,E) are shown. 2021 Viruses Result SARS_CoV_2 D614G 111 116 35062211 SARS-CoV-2 Spike Expression at the Surface of Infected Primary Human Airway Epithelial Cells. This was observed for pAECs infected with both authentic D614G and Alpha variants. 2021 Viruses Result SARS_CoV_2 D614G 57 62 35062211 SARS-CoV-2 Spike Expression at the Surface of Infected Primary Human Airway Epithelial Cells. Vaccination of these individuals elicited antibodies that readily recognized pAECs infected with the D614G (Figure 2D,G) or the Alpha variant (Figure 2E,G). 2021 Viruses Result SARS_CoV_2 D614G 101 106 35062214 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. Cryo-electron microscopy structures have recently been reported that reveal the structural consequences of this mutation and provide a plausible mechanistic explanation for the increased infectivity of D614G-carrying variants. 2021 Viruses Result SARS_CoV_2 D614G 202 207 35062214 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. It is natural to name the haplotype T478K-D614G-P681H-T732A as a B.1.1.222. 2021 Viruses Result SARS_CoV_2 T478K;D614G;P681H;T732A 36;42;48;54 41;47;53;59 35062214 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. It is plausible that the P681H mutation increases the flexibility of the S1/S2 cleavage segment, which might lead to enhanced cleavage and infectivity. 2021 Viruses Result SARS_CoV_2 P681H 25 30 35062214 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. N501Y has also been shown to reduce susceptibility to some neutralizing antibodies (nAbs), although the B.1.1.7 variant appears to remain susceptible to some extent to natural infection-acquired and vaccine-induced nAbs. 2021 Viruses Result SARS_CoV_2 N501Y 0 5 35062214 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. Of the five remaining VRVs in the UK-VRV haplotype, A570, T716, and S982 seem relatively benign in that mutations at these positions are already decreasing in certain states/territories (this trend is also true to some extent for N501Y). 2021 Viruses Result SARS_CoV_2 N501Y 230 235 35062214 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. The D614G mutation observed in the UK-VRV haplotype has been associated with increased infectivity/transmissibility. 2021 Viruses Result SARS_CoV_2 D614G 4 9 35062214 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. The L452R mutation is situated in the RBD; homology modelling of the RBD-ACE2 complex shows that while R452 does not directly contact ACE2, the guanidinium side chain of R452 is surface-exposed and thus could potentially impact nAb binding (Figure 3G). 2021 Viruses Result SARS_CoV_2 L452R 4 9 RBD;RBD 38;69 41;72 35062214 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. The L452R mutation was recently shown to reduce binding affinity to some RBD-targeting monoclonal antibodies, as well as to reduce susceptibility to nAbs. 2021 Viruses Result SARS_CoV_2 L452R 4 9 RBD 73 76 35062214 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. The N501Y mutation (present in the B.1.1.7 variant) is located in the receptor-binding domain (RBD) and has been reported to enhance binding affinity to the angiotensin-converting enzyme-2. 2021 Viruses Result SARS_CoV_2 N501Y 4 9 RBD 95 98 35062214 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. The P681H mutation occurs in the S1/S2 cleavage segment of the Spike protein, which is typically not resolved in cryo-electron microscopy or X-ray diffraction experiments. 2021 Viruses Result SARS_CoV_2 P681H 4 9 S 63 68 35062214 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. The S13I and W152C mutations, which are situated in the N-terminal domain (NTD) of the Spike protein, have been implicated in escape from NTD-targeting monoclonal antibodies. 2021 Viruses Result SARS_CoV_2 S13I;W152C 4;13 8;18 S;N 87;56 92;57 35062214 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. The US variants also carry the D614G mutation. 2021 Viruses Result SARS_CoV_2 D614G 31 36 35062214 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. The VRV-haplotype S13I-W152C-L452R (ICR-3) appeared in Fall 2020 and is rapidly becoming dominant in states on the West Coast, as well as appearing in selected southwestern and southeastern states (Figure 3C-F). 2021 Viruses Result SARS_CoV_2 S13I;L452R;W152C 18;29;23 22;34;28 35062281 Intra-Host SARS-CoV-2 Evolution in the Gut of Mucosally-Infected Chlorocebus aethiops (African Green Monkeys). However, the R682L mutation has been noted before in stocks of this virus expanded in Vero E6 cells and likely eliminates the furin cleavage site in spike. 2022 Viruses Result SARS_CoV_2 R682L 13 18 S 149 154 35062281 Intra-Host SARS-CoV-2 Evolution in the Gut of Mucosally-Infected Chlorocebus aethiops (African Green Monkeys). In contrast, F79L and R682L mutations, present at approximately 60 and 80% in the virus stock, respectively, were completely absent in all rectal samples. 2022 Viruses Result SARS_CoV_2 F79L;R682L 13;22 17;27 35062281 Intra-Host SARS-CoV-2 Evolution in the Gut of Mucosally-Infected Chlorocebus aethiops (African Green Monkeys). Sequencing of these samples revealed a consistent pattern of evolution in vivo with three mutations arising in all three animals; ORF1a/b S2103F, spike D215G, and spike H655Y (Figure 1B). 2022 Viruses Result SARS_CoV_2 D215G;H655Y;S2103F 152;169;138 157;174;144 ORF1a;S;S 130;146;163 135;151;168 35062281 Intra-Host SARS-CoV-2 Evolution in the Gut of Mucosally-Infected Chlorocebus aethiops (African Green Monkeys). The D215G mutation rose from approximately 15% prevalence in the stock to near 100% in all three animals. 2022 Viruses Result SARS_CoV_2 D215G 4 9 35062281 Intra-Host SARS-CoV-2 Evolution in the Gut of Mucosally-Infected Chlorocebus aethiops (African Green Monkeys). The H655Y mutation lies immediately adjacent to the furin cleavage site (Figure 1C) and has been detected in multiple viral lineages, with the P.1 (gamma) and B.1.1.529 (omicron) lineages being most prominent (nextstrain.org). 2022 Viruses Result SARS_CoV_2 H655Y 4 9 35062281 Intra-Host SARS-CoV-2 Evolution in the Gut of Mucosally-Infected Chlorocebus aethiops (African Green Monkeys). The loss of the F79L mutation, present at a relatively low frequency in the inoculum and lost in vivo, may simply reflect the outgrowth of viral variants containing the wild type residue at this position rather than selection. 2022 Viruses Result SARS_CoV_2 F79L 16 20 35062281 Intra-Host SARS-CoV-2 Evolution in the Gut of Mucosally-Infected Chlorocebus aethiops (African Green Monkeys). The S2103F mutation in this protein has been detected at low frequency in human samples, including in India, but is not restricted to a particular clade and, through the course of the pandemic, has never been detected in greater than 1% of all sequenced isolates ( accessed on 29 November 2021). 2022 Viruses Result SARS_CoV_2 S2103F 4 10 35062281 Intra-Host SARS-CoV-2 Evolution in the Gut of Mucosally-Infected Chlorocebus aethiops (African Green Monkeys). These included two mutations in spike, F79L, and a high-frequency mutation that changed the arginine (R) at position 682 to a leucine (R682L) (Figure 1A). 2022 Viruses Result SARS_CoV_2 F79L;R682L;R682R 39;135;91 43;140;121 S 32 37 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. According to these observations, the subset including SNPs from R158G to T716I, sizing 1603 bp, would have been an excellent target for the test. 2022 Viruses Result SARS_CoV_2 R158G;T716I 64;73 69;78 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. Considering several parameters, including estimated informedness and amplicon lengths, we observed that the subset comprising the SNPs K417N, N439K, Y453F, S477N, T478K, E484K, N501Y, A570D, H655Y, Q677H, P681H, I692V, A701V, and716I, would lead to a test providing an acceptable compromise between informedness (0.76) and minimal amplicon length (896 bp). 2022 Viruses Result SARS_CoV_2 A570D;A701V;E484K;H655Y;I692V;K417N;N439K;N501Y;P681H;Q677H;S477N;T478K;Y453F 184;219;170;191;212;135;142;177;205;198;156;163;149 189;224;175;196;217;140;147;182;210;203;161;168;154 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. In any case, the A222V mutation, the only unique mutation for the Nextstrain Cluster 20A.EU.1" variant, can be sequenced using three primer combinations constantly provided in our work (FS-1F/FS-2R; FS-2F/FS-3R; and FS-3F/FS-4R). 2022 Viruses Result SARS_CoV_2 A222V 17 22 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. In fact, these mutations were characteristic of some specific variants (e.g., the A570D mutation for the Alpha variant) and, consequently, these mutations were more important in the process of recognizing the SARS-CoV-2 variants. 2022 Viruses Result SARS_CoV_2 A570D 82 87 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. It should be noted that, owing to the lack of the A222V mutation, the Nextstrain Cluster 20A.EU.1 variant was overlooked by that test, causing a drop to 0.84 in the estimated overall sensitivity. 2022 Viruses Result SARS_CoV_2 A222V 50 55 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. The exclusion of the R215D mutation, on the other hand, is compensated by other mutations characterizing the South African variant which were sequenced with our selected workflow (FS-4F/FS-5R). 2022 Viruses Result SARS_CoV_2 R215D 21 26 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. All Spikes tested bound significantly better to ACE2 compared to their D614G counterpart, with Beta presenting the higher binding (Figure 1A and Table S2). 2022 Viruses Result SARS_CoV_2 D614G 71 76 S 4 10 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. All the SARS-CoV-2 S variants were recognized less efficiently compared to D614G S with the Delta S presenting the most profound decrease in plasma recognition. 2022 Viruses Result SARS_CoV_2 D614G 75 80 S;S;S 19;81;98 20;82;99 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. Among the single mutations present in the tested variants, only the N501Y mutation (present in both B.1.351 and B.1.621) enhanced the affinity of RBD for ACE2. 2022 Viruses Result SARS_CoV_2 N501Y 68 73 RBD 146 149 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. As previously reported, the RBD N501Y for ACE2 exhibited an enhanced affinity for ACE2 at both 10 C and 25 C (21). 2022 Viruses Result SARS_CoV_2 N501Y 32 37 RBD 28 31 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. In contrast, introduction of the K417N mutation (present in the B.1.351) into RBD reduced affinity for ACE2 at both temperatures. 2022 Viruses Result SARS_CoV_2 K417N 33 38 RBD 78 81 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. The impact of cold temperature (4 C) on ACE2 binding was more pronounced for the D614G Spike (3.55-fold increase) comparatively to the Spikes from the variants tested (Beta, Delta, Mu and A.2.5) (1.76-1.99-fold increase). 2022 Viruses Result SARS_CoV_2 D614G 82 87 S;S 88;136 93;142 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. While the Delta, Mu and A.2.5 Spikes displayed increased ACE2 binding compared to the D614G Spike at 37 C, this phenotype was lost at 4 C. 2022 Viruses Result SARS_CoV_2 D614G 86 91 S;S 30;92 36;97 35062734 Immunogenicity of a Heterologous Prime-Boost COVID-19 Vaccination with mRNA and Inactivated Virus Vaccines Compared with Homologous Vaccination Strategy against SARS-CoV-2 Variants. At 6 months, the GMT against D614G in the Combo, BNT162b2 and CoronaVac groups reduced to 5.7 (95% CI, 5.0-6.4), 21.5 (95% CI, 17.0-27.2) and 5 (95% CI, 5-5), respectively. 2022 Vaccines Result SARS_CoV_2 D614G 29 34 35062734 Immunogenicity of a Heterologous Prime-Boost COVID-19 Vaccination with mRNA and Inactivated Virus Vaccines Compared with Homologous Vaccination Strategy against SARS-CoV-2 Variants. Besides WT, vMN titres against variants (D614G, alpha, beta, theta, delta) were also determined. 2022 Vaccines Result SARS_CoV_2 D614G 41 46 35062734 Immunogenicity of a Heterologous Prime-Boost COVID-19 Vaccination with mRNA and Inactivated Virus Vaccines Compared with Homologous Vaccination Strategy against SARS-CoV-2 Variants. For the D614G variant, the BNT162b2 group showed significantly higher results on day 56 GMT (81.4, 95% CI, 60.0-110.5) (p < 0.0001) than the Combo (13.1, 95% CI, 10.7-16.1) and CoronaVac groups (11.8, 95% CI, 9.6-14.5) (Table 2) (Figure 2b). 2022 Vaccines Result SARS_CoV_2 D614G 8 13 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Among them, six vaccinated cases showed one more G142D AA change, while the other two vaccinated cases did not exhibit this mutation. 2022 Microbial pathogenesis Result SARS_CoV_2 G142D 49 54 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Among these, forty-seven (47, 56.6%) sequences exhibiting eight nonsynonymous mutations (T19R, G142D, E156G, L452R, T478K, D614G, P681R and D950 N) and two deletions of F157del and R158del have shown two mutational group of with (twenty seven sequences) and without (twenty sequences) G142D mutation (Table 1). 2022 Microbial pathogenesis Result SARS_CoV_2 D614G;D950N;E156G;F157del;G142D;G142D;L452R;P681R;R158del;T478K;T19R 123;140;102;169;95;285;109;130;181;116;89 128;146;107;176;100;290;114;135;188;121;93 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. D950 N was detected in 64 cases with a frequency of 77.1%. 2022 Microbial pathogenesis Result SARS_CoV_2 D950N 0 6 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Delta variant exhibited L452R, T478K, D614G, P681R, and D950 N mutations in all seventeen cases, while the frequency of other mutations varied as T19R and G142D were detected in fourteen and four cases respectively. 2022 Microbial pathogenesis Result SARS_CoV_2 D614G;D950N;G142D;L452R;P681R;T19R;T478K 38;56;155;24;45;146;31 43;62;160;29;50;150;36 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. E156G and two deletions (F157del and R158del) were observed in ten patients infected by the Delta variant. 2022 Microbial pathogenesis Result SARS_CoV_2 R158del;F157del;E156G 37;25;0 44;32;5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Five (6.0%) sequences resembled Kappa variant (lineage B.1.617.1/clade G/452 R.V3) and exhibited changes of L452R, E484Q, D614G, and P681R. 2022 Microbial pathogenesis Result SARS_CoV_2 D614G;E484Q;L452R;P681R 122;115;108;133 127;120;113;138 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. In the rest six cases of different B.1 sublineages, the mutation of D614G was found in all cases, while N440K was found in three cases. 2022 Microbial pathogenesis Result SARS_CoV_2 D614G;N440K 68;104 73;109 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. L452R, T478K, and P681 H/R were seen in 69(83.1%), 65(78.3%), and 73(87.9%) sequences, respectively. 2022 Microbial pathogenesis Result SARS_CoV_2 P681H;P681R;T478K;L452R 18;18;7;0 26;26;12;5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. L452R, T478K, N501Y and A570D mutations were located in spike protein receptor binding domain (RBD). 2022 Microbial pathogenesis Result SARS_CoV_2 A570D;N501Y;T478K;L452R 24;14;7;0 29;19;12;5 RBD;S;RBD 70;56;95 93;61;98 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Mutations of P681 R/H, D950 N, T716I, S982A, Q1071H, and D1118H were located in proximity to the S1/S2 cleavage site. 2022 Microbial pathogenesis Result SARS_CoV_2 D1118H;D950N;P681R;Q1071H;S982A;T716I 57;23;13;45;38;31 63;29;21;51;43;36 N 28 29 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. N-terminal domain (NTD) region of these sequences harbored T19R, G142D, and E156G, respectively along with deletions of H69, V70, Y144, F157 and R158del. 2022 Microbial pathogenesis Result SARS_CoV_2 E156G;G142D;R158del;T19R 76;65;145;59 81;70;152;63 N 0 1 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Notable mutation D614G was identified distally to the furin cleavage site. 2022 Microbial pathogenesis Result SARS_CoV_2 D614G 17 22 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Notably, all variants showed P323L mutation in nonstructural protein (NSP) 12 encoding RNA dependent RNA polymerase (RdRP) gene, and Delta variant exclusively showed I82T mutation in membrane protein-encoding gene. 2022 Microbial pathogenesis Result SARS_CoV_2 I82T;P323L 166;29 170;34 RdRp;Membrane;RdRP 87;183;117 115;191;121 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. One case infected by B.1.1.326 harbored a sole mutation of D614G. 2022 Microbial pathogenesis Result SARS_CoV_2 D614G 59 64 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Overall, only D614 G mutation was found in all cases with 100% occurrence among eighty-three sequences. 2022 Microbial pathogenesis Result SARS_CoV_2 D614G 14 20 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Seventeen sequences (20.4%) harbored six nonsynonymous changes of T19R, L452R, T478K, D614G, P681R, and D950 N and no deletions. 2022 Microbial pathogenesis Result SARS_CoV_2 D614G;D950N;L452R;P681R;T19R;T478K 86;104;72;93;66;79 91;110;77;98;70;84 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Similarly, P681H mutation in B.1.1.7 also changed the furin cleavage site by substituting Proline to Histidine, a polar AA (imidazole group). 2022 Microbial pathogenesis Result SARS_CoV_2 P681H 11 16 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. The Delta variant in all eight cases harbored the nonsynonymous mutations of T19R, E156G, L452R, T478K, D614G, P681R, D950 N, and two deletions of F157del and R158del, respectively. 2022 Microbial pathogenesis Result SARS_CoV_2 D614G;D950N;E156G;F157del;L452R;P681R;R158del;T19R;T478K 104;118;83;147;90;111;159;77;97 109;124;88;154;95;116;166;81;102 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. The Delta variant in eighteen cases showed similar mutational pattern as described above except four cases without harbouring two deletions (F157del and R158del) and one nonsynonymous mutation of E156G, thirteen cases without G142D and one case without T19R mutation were observed (Table 1. 2022 Microbial pathogenesis Result SARS_CoV_2 E156G;G142D;R158del;T19R;F157del 196;226;153;253;141 201;231;160;257;148 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. The mutational analysis found that the Delta variant exhibited all designated mutational AA changes except G142D in twelve, T19R in twenty, and E156G and two deletions (F157del and R158del) were observed in fifteen cases respectively. 2022 Microbial pathogenesis Result SARS_CoV_2 E156G;G142D;R158del;T19R;F157del 144;107;181;124;169 149;112;188;128;176 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. The P681R mutation in B.1.617.2 appears to disrupt the cleavage site by changing the Proline, a non-polar AA (imino acid group), to Arginine, a polar positively charged AA (guanidino group). 2022 Microbial pathogenesis Result SARS_CoV_2 P681R 4 9 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. The remaining four cases infected with B.1 lineage have shown the sole common mutation of D614G. 2022 Microbial pathogenesis Result SARS_CoV_2 D614G 90 95 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. The rest of the other prominent mutations, namely T19R, G142D were observed in 59 (92.2%) and 28 (33.7%%) sequences, whereas E156G and two deletions (F157del and R158del), were detected in forty-seven (73.4%) sequences respectively. 2022 Microbial pathogenesis Result SARS_CoV_2 E156G;G142D;R158del;T19R;F157del 125;56;162;50;150 130;61;169;54;157 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. These sequences were relatively found with fewer variations as D614G was dominantly found in all sequences, and only four sequences showed additional changes of N440K while one sequence exhibited two more changes of P681R and D950 N (Table 1). 2022 Microbial pathogenesis Result SARS_CoV_2 D614G;D950N;N440K;P681R 63;226;161;216 68;232;166;221 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Three (3.6%) sequences belonged to the Alpha variant (lineage B.1.1.7/clade GR/501Y.V1) and showed a mutational pattern of N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, and three deletions of H69, V70, and Y144. 2022 Microbial pathogenesis Result SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 130;165;137;123;144;158;151 135;171;142;128;149;163;156 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. VOC B.1.1.7 (n = 3) and B.1.617.2 (n = 64) exhibited substitution of same codon residue by different AA namely P681H and P681R. 2022 Microbial pathogenesis Result SARS_CoV_2 P681H;P681R 111;121 116;126 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. Additionally, in the spike region of Delta AY.1 variant unique substitution at W258L was detected in 37.5% cases (n=3/8). 2021 Frontiers in medicine Result SARS_CoV_2 W258L 79 84 S 21 26 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. Further, an exceptional mutation was present at A222V among Delta, and K417N among Delta AY.1 variants. 2021 Frontiers in medicine Result SARS_CoV_2 A222V;K417N 48;71 53;76 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. However, the Kappa variants demonstrated signature substitution at E154K and E484Q. 2021 Frontiers in medicine Result SARS_CoV_2 E154K;E484Q 67;77 72;82 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. In the second wave of 38 cases, aa variation at T95I was detected in 71.4% cases (Delta = 12, Delta AY.1 = 6, and Kappa = 2). 2021 Frontiers in medicine Result SARS_CoV_2 T95I 48 52 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. Interestingly, all three Kappa variants had two unique mutations (T1567I and M5753I) in ORF1ab protein. 2021 Frontiers in medicine Result SARS_CoV_2 M5753I;T1567I 77;66 83;72 ORF1ab 88 94 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. Interestingly, an exceptional aa change was detected at position D574Y in two cases, one from GR clade and one from Delta variant with breakthrough infection, whereas another breakthrough infection from the Kappa variant conserved the aa change at position 95 (T) as in the Wuhan isolate. 2021 Frontiers in medicine Result SARS_CoV_2 D574Y 65 70 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. It is noteworthy that substitution D614G in spike (S) protein was found in all G and its variant clade GH and GR, while Q57H substitution located in ORF3a protein was only found in 15 cases distributed among GH (n = 9), GR (n = 5), and O (n = 1) clade from the first wave (Supplementary Table 3). 2021 Frontiers in medicine Result SARS_CoV_2 D614G;Q57H 35;120 40;124 S;ORF3a;S 44;149;51 49;154;52 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. Signature substitutions at positions L452R and P681R were commonly detected in the Delta, Delta AY.1, and Kappa variant whereas T19R, T478K, and D614G were confined to Delta and Delta AY.1 variant only. 2021 Frontiers in medicine Result SARS_CoV_2 D614G;L452R;P681R;T19R;T478K 145;37;47;128;134 150;42;52;132;139 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. The uncommon aa change D574Y was uniquely detected in two variants including GR clade (MCL-20-H-405) and Delta variant (MCL-21-6602). 2021 Frontiers in medicine Result SARS_CoV_2 D574Y 23 28 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. Two mutations in Spike (K417N and W258L) were exclusively present in the Delta Plus variant. 2021 Frontiers in medicine Result SARS_CoV_2 W258L;K417N 34;24 39;29 S 17 22 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. We also identified 8 substitution mutants in the SARS-CoV-2, K417N, G446V, L452R, S477N, T478K, E484Q, F490S, and A522V in the RNA binding domain (RBD) of S1 subunit of Spike protein. 2021 Frontiers in medicine Result SARS_CoV_2 A522V;E484Q;F490S;G446V;K417N;L452R;S477N;T478K 114;96;103;68;61;75;82;89 119;101;108;73;66;80;87;94 S;RBD 169;147 174;150 35074352 Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. Additionally, in the middle of February 2021 at the MIR WWTP, two replacements located in the RBD (S477N and A522S) were identified in one amplicon, meaning that both mutations co-occurred within the same genome molecule. 2022 Environmental research Result SARS_CoV_2 A522S;S477N 109;99 114;104 RBD 94 97 35074352 Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. Additionally, the replacement E584K has also been associated with some Alpha sequences. 2022 Environmental research Result SARS_CoV_2 E584K 30 35 35074352 Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. Compared to the Wuhan-Hu-1 variant, VOC Alpha is characterized by the occurrence of 9 genetic markers in the S gene (69-70del, 144del, N501Y, A570D, D614G, P681H, T716I, S928A and D118H). 2022 Environmental research Result SARS_CoV_2 144del;A570D;D118H;D614G;N501Y;P681H;S928A;T716I 127;142;180;149;135;156;170;163 133;147;185;154;140;161;175;168 S 109 110 35074352 Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. Moreover, these two mutations are likely to be associated with the 69-70del and 144del in the proportion's ratio heat map (Figure S3), suggesting the occurrence of an Alpha variant sequence harboring additional mutations. 2022 Environmental research Result SARS_CoV_2 144del 80 86 35074352 Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. Replacements T73A and D253N, which are in the N2 and N5 loops of the NTD, respectively, were already detected at the beginning of February 2021 and were still present at the end of April in the VDP WWTP (Table 4). 2022 Environmental research Result SARS_CoV_2 D253N;T73A 22;13 27;17 35074352 Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. Seven of these mutations (L5F, T73A, S98F, S155I, L216F, D253N and D290Y) were located in the amino terminal domain (NTD) of the spike glycoprotein S, two (S477N and A522S) were located in the receptor binding domain (RBD), and nine (G669V, A706V, K854N, S940A, Q1071L, H1083R, D1084R, G1085R and G1267V) outside relevant regions. 2022 Environmental research Result SARS_CoV_2 A522S;A706V;D1084R;D253N;D290Y;G1085R;G1267V;H1083R;K854N;L216F;Q1071L;S155I;S940A;S98F;T73A;G669V;L5F;S477N 166;241;278;57;67;286;297;270;248;50;262;43;255;37;31;234;26;156 171;246;284;62;72;292;303;276;253;55;268;48;260;41;35;239;29;161 RBD;S;RBD;S 193;129;218;148 216;147;221;149 35074352 Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. The relative abundance of each marker from most to least abundant was D614G > A570D > 69-70del and 144del > D1118H > S982A > P681H and T716I > N501Y > E584K (Table 2). 2022 Environmental research Result SARS_CoV_2 144del;A570D;D1118H;D614G;E584K;N501Y;P681H;S982A;T716I 99;78;108;70;151;143;125;117;135 105;83;114;75;156;148;130;122;140 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. It is of interest to note that a single SNV a23403, coding for the well-known D614G, appeared to have no association with the COVID-19 hospitalization risk in unadjusted or adjusted analysis (p = 0.39 and 0.29, respectively). 2022 Scientific reports Result SARS_CoV_2 D614G 78 83 COVID-19 126 134 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. 6-fold) against the B.1.617.2 variant, most likely due to the T478K mutation in the RBD domain of Spike. 2022 EBioMedicine Result SARS_CoV_2 T478K 62 67 S;RBD 98;84 103;87 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. AX290ch maintained its picomolar affinity to all mutants except those containing K417N mutation alone or in combination N501Y/E484K/K417N (3-fold and 2-fold decrease in the affinity, respectively). 2022 EBioMedicine Result SARS_CoV_2 K417N;N501Y;E484K;K417N 81;120;126;132 86;125;131;137 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. AX677ch binds N501Y mutation, with 1 4-fold higher affinity than wild type RBD, reaching picomolar value (Figure 6b, Figure S6). 2022 EBioMedicine Result SARS_CoV_2 N501Y 14 19 RBD 75 78 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. Binding of AX290ch was reduced, most likely due to the mutation S477N. 2022 EBioMedicine Result SARS_CoV_2 S477N 64 69 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. E484K and N501Y made the highest impact on the binding of these mAbs to RBD containing the triple mutation N501Y/E484K/K417N present in the variant B.1.351. 2022 EBioMedicine Result SARS_CoV_2 N501Y;N501Y;E484K;K417N;E484K 10;107;113;119;0 15;112;118;124;5 RBD 72 75 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. E484K, however, reduced binding of AX322, AX175 and partially also AX67 to RBD. 2022 EBioMedicine Result SARS_CoV_2 E484K 0 5 RBD 75 78 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. Furthermore, this positive effect of the N501Y mutation is propagated into the triple mutant, which combines mutations N501, E484K, and K417N, and binds AX677ch with higher affinity than either of the single mutants E484K and K417N, and even wild type RBD (1 4-, 1 7- and 1 2-fold, respectively). 2022 EBioMedicine Result SARS_CoV_2 E484K;E484K;K417N;K417N;N501Y 125;216;136;226;41 130;221;141;231;46 RBD 252 255 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. In order to test the ability of the selected mAbs to bind RBD with the mutations that appear in the current SARS-CoV-2 VOCs, B.1.1.7 (N501Y) and B.1.351 (K417N/E484K/N501Y), we screened the mutated RBDs by ELISA (Figure 3a, b). 2022 EBioMedicine Result SARS_CoV_2 K417N;N501Y;E484K;N501Y 154;134;160;166 159;139;165;171 RBD;RBD 58;198 61;202 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. Individual mutations N501Y, K417N and E484K, and N439K mutation (widespread in Europe), had only a marginal impact on the antibody binding. 2022 EBioMedicine Result SARS_CoV_2 E484K;K417N;N439K;N501Y 38;28;49;21 43;33;54;26 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. Sequence analysis of the viruses that escaped from the neutralization by the individual antibodies revealed only one mutation in the S protein per antibody: S477R substitution for AX290, and T345N substitution for AX677 (Figure 5b). 2022 EBioMedicine Result SARS_CoV_2 S477R;T345N 157;191 162;196 S 133 134 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. The alternative substitution S477N that is more widespread in circulating viruses (1.482%) was not found in the sequenced viral genomes. 2022 EBioMedicine Result SARS_CoV_2 S477N 29 34 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. The analyses showed that T345N greatly reduced replication capacity of the virus and was almost eliminated from the pool (Figure 5d, Table S2, Mutant B11). 2022 EBioMedicine Result SARS_CoV_2 T345N 25 30 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. The AX290 escape virus (Mutant A1, containing the S477R mutation in the Spike protein) showed only slight decline in viral fitness indicated by a slight reduction in the proportion of the mutant in the mixture after the cultivation. 2022 EBioMedicine Result SARS_CoV_2 S477R 50 55 S 72 77 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. The combination K417N/E484K/N501Y exhibited either no or only minor influence on the binding of the antibodies of the Epitope I group. 2022 EBioMedicine Result SARS_CoV_2 K417N;E484K;N501Y 16;22;28 21;27;33 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. The mutation T345N present in the virus mutant that escaped from AX677 is positioned close to the peptides protected by the antibody in the HDX-MS experiment, but not directly within their sequence (Figure 5c). 2022 EBioMedicine Result SARS_CoV_2 T345N 13 18 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. The S477R substitution that allowed escape of the virus from AX290 is located in the region of RBD that was identified by HDX as the contact site of the antibody (Figure 5c). 2022 EBioMedicine Result SARS_CoV_2 S477R 4 9 RBD 95 98 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. The T345N escape mutation has been identified previously using an S-typed VSV pseudovirus for antibody 2H04, which also did not compete with ACE2 for binding to the S protein. 2022 EBioMedicine Result SARS_CoV_2 T345N 4 9 S;S 66;165 67;166 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. We have performed a test of binding of chimeric antibodies AX677ch and AX290ch to the ectodomain trimer of the Omicron S protein (carrying mutations A67V, HV69-70del, T95I, G142D, VYY143-145del, N211del, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F) in ELISA (Figure 6d). 2022 EBioMedicine Result SARS_CoV_2 A67V;D614G;D796Y;E484A;G142D;G339D;G446S;G496S;H655Y;K417N;L212I;L981F;N211del;N440K;N501Y;N679K;N764K;N856K;N969K;P681H;Q493R;Q498R;Q954H;S371L;S373P;S375F;S477N;T478K;T547K;T95I;Y505H 149;334;369;285;173;222;264;299;341;250;204;397;195;257;313;348;362;376;390;355;292;306;383;229;236;243;271;278;327;167;320 153;339;374;290;178;227;269;304;346;255;209;402;202;262;318;353;367;381;395;360;297;311;388;234;241;248;276;283;332;171;325 S 119 120 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. 5), indicating that the values of the monomer-dimer dissociation constants were comparable between WT and P108S mutant proteins within the given concentration ranges. 2022 Scientific reports Result SARS_CoV_2 P108S 106 111 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. 6a-d), suggesting that the P108S mutation perturbs the pocket that is behind and distant from the mutation. 2022 Scientific reports Result SARS_CoV_2 P108S 27 32 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Based on the results described above, because 3CLpro has been well characterized as a critical function for viral replication by biochemical and pharmacological analyses, and because the phylogenic tree analysis in Japan showed that the Pro151Leu mutation in nucleocapsid protein occurred earlier than the Pro108Ser mutation. 2022 Scientific reports Result SARS_CoV_2 P108S;P151L 306;237 315;246 N 259 271 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. By contrast, amino acid residues at and around Ser543Pro in the PLpro (NSP3) and Ala423Val in RNA-dependent RNA polymerase (RdRp, NSP12) were only weakly conserved. 2022 Scientific reports Result SARS_CoV_2 A423V;S543P 81;47 90;56 RdRp;Nsp12;Nsp3;RdRP 94;130;71;124 122;135;75;128 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Of the six mutations, four were non-synonymous: c.4346 U > C (Ser543Pro in papain-like protease [PLpro]), c.10376 C > U (Pro108Ser in 3CLpro), c.14708 C > U (Ala423Val in RNA-dependent RNA polymerase [RdRp]), and c.28725 C > U (Pro151Leu in nucleocapsid protein); the remaining two other mutations did not affect the amino acid translation of the viral proteins. 2022 Scientific reports Result SARS_CoV_2 A423V;P108S;P151L;S543P 158;121;228;62 167;130;237;71 RdRp;N;RdRP 171;241;201 199;253;205 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. On the other hand, the inhibitory effect of GC376 on the P108S mutant was decreased (Ki = 3.74 mumol/l. 2022 Scientific reports Result SARS_CoV_2 P108S 57 62 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. On the other hand, the serine in the PLpro at residue 543 and the Ala at residue 423 in RdRp were substituted with proline and valine in some beta-coronaviruses; both of these mutations were observed in Clade 20B-T, suggesting that Ser543Pro in the PLpro and Ala423Val in RdRp are likely to be functionally neutral. 2022 Scientific reports Result SARS_CoV_2 A423V;S543P 259;232 268;241 RdRP;RdRP 88;272 92;276 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. P108S 3CLpro reduces the catalytic activity and attenuates the sensitivity to GC376. 2022 Scientific reports Result SARS_CoV_2 P108S 0 5 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Pro108Ser in the 3CLpro and Pro151Leu in the nucleocapsid protein can therefore be considered as plausible candidate amino acid mutations in Clade 20B-T (B.1.1.284) that are functionally relevant and may explain the milder clinical course observed among patients infected with Clade 20B. 2022 Scientific reports Result SARS_CoV_2 P151L;P108S 28;0 37;9 N 45 57 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Since previous studies of SARS-CoV 3CLpro have indicated that the dimerization of 3CLpro activates its enzymatic activity, we analyzed the dimeric states of SARS-CoV-2 3CLpro WT and P108S using sedimentation velocity analytical ultracentrifugation (SV-AUC). 2022 Scientific reports Result SARS_CoV_2 P108S 182 187 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Studies of the conservation of the amino acid residues around the non-synonymous mutations in Clade 20B-T indicated that residues at and around Pro108Ser in the 3CLpro (NSP5) and those at and around Pro151Leu in the nucleocapsid protein were highly conserved among beta-coronaviruses. 2022 Scientific reports Result SARS_CoV_2 P108S;P151L 144;199 153;208 N;Nsp5 216;169 228;173 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. The B.1.1.214 lineage is characterized by the addition of 3 single nucleotide mutations with the basic haplotype of Clade 20B: c.18167 C > U (Pro43Leu in 3'-5' endonuclease), c.21518 G > U (Arg287Ile in 2'-O ribose methyltransferase), and c.28975 G > U (Met234Ile in nucleocapsid protein). 2022 Scientific reports Result SARS_CoV_2 R287I;M234I;P43L 190;254;142 199;263;150 N 267 279 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. The enzymatic activity of the P108S was significantly suppressed, compared with that of the WT. 2022 Scientific reports Result SARS_CoV_2 P108S 30 35 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. The Km value of P108S (215.7 mumol/l) was lower than that of the WT (110.3 mumol/l), and the activity also decreased by 58%, as determined by a comparison of the Kcat/Km values for the WT and P108S 3CLpro enzymes. 2022 Scientific reports Result SARS_CoV_2 P108S;P108S 16;192 21;197 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. These results suggest that the P108S mutation interferes with the ability of the enzyme to allow substrate binding. 2022 Scientific reports Result SARS_CoV_2 P108S 31 36 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. we focused on the function-structure relationship of the Pro108Ser mutant of 3CLpro for further investigation. 2022 Scientific reports Result SARS_CoV_2 P108S 57 66 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. We further examined the sensitivity of the P108S mutant against a competitive 3CLpro inhibitor GC376. 2022 Scientific reports Result SARS_CoV_2 P108S 43 48 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. We prepared recombinant proteins of WT and P108S of SARS-CoV-2 3CLpro to determine their enzymatic activities using a fluorescence-based cleavage assay. 2022 Scientific reports Result SARS_CoV_2 P108S 43 48 35079901 Trypsin enhances SARS-CoV-2 infection by facilitating viral entry. At positions 418 and 419 in N, the QA-DEL arose from a C-to-T substitution (C1252T) at position 1252 in ORF9 (nt 29,497 at the genome level). 2022 Archives of virology Result SARS_CoV_2 C1252T;C1252T 76;54 82;101 ORF9;N 104;28 108;29 35079901 Trypsin enhances SARS-CoV-2 infection by facilitating viral entry. Notably, one aa mutation (R685S) was found in the S1/S2 furin cleavage site (FCS), which contains multiple basic amino acids (681PRRAR685) (Table 3), which occurred in P10(-). 2022 Archives of virology Result SARS_CoV_2 R685S 26 31 35079901 Trypsin enhances SARS-CoV-2 infection by facilitating viral entry. The S-A-DEL resulted from a C-to-A substitution (C92A) at position 92 in ORF7b (nt 27,819 at the genome level). 2022 Archives of virology Result SARS_CoV_2 C92A 49 53 ORF7b 73 78 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. Each test can detect six targets (RBD, D614G, N501Y, E484K, L452R/E484Q-mutants, and 1 blank) of seven samples. 2022 Analytical chemistry Result SARS_CoV_2 D614G;E484K;L452R;N501Y;E484Q 39;53;60;46;66 44;58;65;51;71 RBD 34 37 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. Higher antibodies against RBD and D614G-mutant show higher antibodies against N501Y, E484K, and L452R/E484Q-mutants. 2022 Analytical chemistry Result SARS_CoV_2 D614G;E484K;L452R;N501Y;E484Q 34;85;96;78;102 39;90;101;83;107 RBD 26 29 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. The antibodies against N501Y, E484K, and L452R/E484Q-mutants were less than RBD and D614G-mutant. 2022 Analytical chemistry Result SARS_CoV_2 D614G;E484K;L452R;N501Y;E484Q 84;30;41;23;47 89;35;46;28;52 RBD 76 79 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. The concentration of antibodies for the D614G-mutant is the highest compared with other variants. 2022 Analytical chemistry Result SARS_CoV_2 D614G 40 45 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. The concentrations of antibodies against RBD, D614G, N501Y, E484K, and L452R/E484Q-mutants of serum 1, serum 2, and serum 3 were also analyzed by our multiplexed lab-on-a-chip immunoassays. 2022 Analytical chemistry Result SARS_CoV_2 D614G;E484K;L452R;N501Y;E484Q 46;60;71;53;77 51;65;76;58;82 RBD 41 44 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. The concentrations of antibodies for RBD, D614G, N501Y, E484K, and L452R/E484Q-mutants are 6.6 +- 3.6, 8.7 +- 4.6, 3.4 +- 2.8, 3.8 +- 2.8, and 2.8 +- 2.3 ng/mL, respectively (Figure 3b). 2022 Analytical chemistry Result SARS_CoV_2 D614G;E484K;L452R;N501Y;E484Q 42;56;67;49;73 47;61;72;54;78 RBD 37 40 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. The vaccinated volunteers have a high concentration of antibodies, especially for RBD and D614G-mutant spike protein. 2022 Analytical chemistry Result SARS_CoV_2 D614G 90 95 S;RBD 103;82 108;85 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. Among the mutant strains that appeared in Portugal in December, UK strain B.1.1.7 accounted for 73.1%; this strain possessed the L216F and M740V double mutation. 2022 Archives of virology Result SARS_CoV_2 L216F;M740V 129;139 134;144 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. As shown in Figure 5, the epidemic strain S477N+D614G (accounting for 5.0% of strains) and its corresponding single-site mutant strain isolated in Portugal can evade mAb 09-7B8. 2022 Archives of virology Result SARS_CoV_2 S477N;D614G 42;48 47;53 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. At the same time, variant B.1.258, along with B.1.258+L1063F and B.1.258+N751Y, also appeared. 2022 Archives of virology Result SARS_CoV_2 L1063F;N751Y 54;73 60;78 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. Compared with the neutralizing effects of L1063F+D614G and N751Y+D614G, immune escape may be due to a mutation in B.1.258. 2022 Archives of virology Result SARS_CoV_2 L1063F;N751Y;D614G;D614G 42;59;49;65 48;64;54;70 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. Figure 3 shows that in cells expressing ACE2 receptors of different species, the infectivity of the individual mutant pseudovirus did not differ by more than fourfold from that of D614G. 2022 Archives of virology Result SARS_CoV_2 D614G 180 185 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. From December 31, 2020, to March 3, 2021, D614G remained the most frequent mutation (94.9%), followed by A222V+D614G (24.0%), B.1.1.7 (15.5%), D839Y+D614G (7.3%), P1162R+D614G+A222V (5.2%), S477N+D614G (5.0%), and L176F+D614G (1.3%). 2022 Archives of virology Result SARS_CoV_2 A222V;D614G;D839Y;L176F;P1162R;S477N;A222V;D614G;D614G;D614G;D614G;D614G 105;42;143;214;163;190;176;111;149;170;196;220 110;47;148;219;169;195;181;116;154;175;201;225 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. Immune escape may therefore be attributed to the S477N mutation (using D614G as the standard and a reduction in neutralizing activity of >4 times as the threshold for immune escape). 2022 Archives of virology Result SARS_CoV_2 D614G;S477N 71;49 76;54 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. In all four types of cells, the RLU values for D839Y+D614G and B.1.258 were lower than those for D614G, and the infectivity of P1162R+D614G+A222V and L216F+B.1.1.7 was about two times higher than that of D614G. 2022 Archives of virology Result SARS_CoV_2 D614G;D614G;D839Y;L216F;P1162R;A222V;D614G;D614G 97;204;47;150;127;140;53;134 102;209;52;155;133;145;58;139 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. In general, the infectivity of the 11 natural mutants was similar to that of D614G (setting a four-fold increase as the threshold for a significant difference). 2022 Archives of virology Result SARS_CoV_2 D614G 77 82 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. The frequencies of D839Y+D614G and L176F+D614G in Portugal showed a decreasing trend, and the prevalence of the B.1.1.7+L216F, B.1.1.7+M740V, B.1.258, B.1.258+L1063F, and B.1.258+N751Y variants did not increase. 2022 Archives of virology Result SARS_CoV_2 D839Y;L176F;D614G;D614G;L1063F;L216F;M740V;N751Y 19;35;25;41;159;120;135;179 24;40;30;46;165;125;140;184 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. The frequencies of the variants D614G, A222V+D614G, B.1.1.7, S477N+D614G, and P1162R+D614G+A222V showed an increasing trend, with the increase in B.1.1.7 being second only to D614G. 2022 Archives of virology Result SARS_CoV_2 A222V;D614G;D614G;P1162R;S477N;A222V;D614G;D614G;D614G 39;32;175;78;61;91;45;67;85 44;37;180;84;66;96;50;72;90 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. The serum neutralized 11 pseudoviruses with no immune escape detected (defined as a fourfold reduction in the ID50 value compared with that for D614G). 2022 Archives of virology Result SARS_CoV_2 D614G 144 149 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. The single amino acid substitutions with the highest frequencies were D614G (91.5%), D839Y (12.8%), A222V (12.3%), P1162R (3.5%), S477N (1.6%), and L176F (1.6%). 2022 Archives of virology Result SARS_CoV_2 A222V;D614G;D839Y;L176F;P1162R;S477N 100;70;85;148;115;130 105;75;90;153;121;135 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. Therefore, the impact of the N439K, S477N, N501Y, and A570D mutations on protection by mAbs was evaluated. 2022 Archives of virology Result SARS_CoV_2 A570D;N439K;N501Y;S477N 54;29;43;36 59;34;48;41 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. To identify specific sites affecting the antigenicity of the viruses circulating in Portugal, we constructed seven pseudoviruses: S477N, D839Y, L176F, L216F+D614G, M740V+D614G, L1063F+D614G, and N751Y+D614G. 2022 Archives of virology Result SARS_CoV_2 D839Y;L1063F;L176F;L216F;M740V;N751Y;S477N;D614G;D614G;D614G;D614G 137;177;144;151;164;195;130;157;170;184;201 142;183;149;156;169;200;135;162;175;189;206 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. Using the neutralization ID50 (50% infective dose) titers for the D614G pseudovirus and different mouse sera for reference, the neutralization activity was evaluated for the other 11 pseudoviruses. 2022 Archives of virology Result SARS_CoV_2 D614G 66 71 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. We also found that the UK epidemic strain B.1.1.7 and its variants can escape mAbs 03-1F9, 2H10, 03-10D12- 1C3, 03-10F9-1A2, 11D12-1, CB6, and HB27, but M740V+D614G and L216F+D614G cannot. 2022 Archives of virology Result SARS_CoV_2 L216F;M740V;D614G;D614G 169;153;159;175 174;158;164;180 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. Among participants in the per-protocol analysis set who were non-naive at day 1 or day 22, or both, neutralising antibody titres (figure 3B; appendix pp 24-25) and binding antibody concentrations (figure 4B) to the D614G variant increased more than ten times in both age strata 21 days after a single injection (day 22) in all antigen dose groups, such that in each antigen dose group the day 22 titres in participants who were non-naive were higher than those reached among participants who were naive after two doses (day 36). 2022 The Lancet. Infectious diseases Result SARS_CoV_2 D614G 215 220 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. Among participants in the per-protocol analysis set who were SARS-CoV-2 naive, neutralising antibody GMTs to the D614G variant 14 days after the second injection (day 36) were 2189 (95% CI 1744-2746) in the low-dose group, 2269 (1792-2873) in the medium-dose group, and 2895 (2294-3654) in the high-dose group. 2022 The Lancet. Infectious diseases Result SARS_CoV_2 D614G 113 118 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. Among participants who were SARS-CoV-2 naive with at least one high-risk medical condition, neutralising antibody titres to the D614G variant were similar across antigen-dose groups in both age strata. 2022 The Lancet. Infectious diseases Result SARS_CoV_2 D614G 128 133 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. In naive participants in the per-protocol analysis set, GMTs were similar between the low-dose and medium-dose groups, and slightly higher in the high-dose group, with titres approximately ten times lower than for the D614G variant. 2022 The Lancet. Infectious diseases Result SARS_CoV_2 D614G 218 223 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. The pattern of neutralising antibody responses to the beta variant with age was similar to that observed with responses to the D614G variant, with higher titres in younger adults than older adults. 2022 The Lancet. Infectious diseases Result SARS_CoV_2 D614G 127 132 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. A nearby substitution, L452M, which has also appeared in at least one mink farm outbreak has no effect, suggesting this is not a specific adaptation to mink (Figure 3A). 2022 Cell reports Result SARS_CoV_2 L452M 23 28 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. A number of these variants have RBD mutations such as L452R, E484K, and/or N501Y, which are thought to promote human ACE2 binding. 2022 Cell reports Result SARS_CoV_2 E484K;L452R;N501Y 61;54;75 66;59;80 RBD 32 35 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Again, we observed that the Y453F-containing Cluster 5 was outcompeted, constituting only ~10% of reads by 24 h postinfection (Figure 4B). 2022 Cell reports Result SARS_CoV_2 Y453F 28 33 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Again, we saw the Y453F-containing virus was more readily neutralized by 7 of the 10 vaccinee sera, although the difference was not significant (Figure 5B). 2022 Cell reports Result SARS_CoV_2 Y453F 18 23 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Although the Y453F-containing virus is highly similar to that which circulated in mink early in the pandemic, the most prominent zoonotic spillover from mink was the Cluster 5 virus, which further contained D614G and Delta69-70. 2022 Cell reports Result SARS_CoV_2 D614G;Y453F 207;13 212;18 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. As with the ferret-adapted P2 virus and Cluster 5 isolate we saw that the Y453F + D614G RG virus produced less infectious virus upon replication in the primary human airway cells as compared with the otherwise isogenic WT (D614G) virus, significantly so at 24 h postinfection (Figure 4C). 2022 Cell reports Result SARS_CoV_2 D614G;Y453F;D614G 82;74;223 87;79;228 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. At days 1 to 2, the mean titer of Y453F virus shed in nasal washes was significantly higher than that of the parental virus, as determined by both E gene copy number and median tissue culture infectious dose (TCID50) (Figures 2B and 2C). 2022 Cell reports Result SARS_CoV_2 Y453F 34 39 E 147 148 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. B.1.1.7/E484K, Iota/B.1.526 + E484K (first associated with infections in New York), Eta/B.1.525 (a variant with associations with West Africa), and L452R (in multiple variants of concern, including Epsilon/B.1.427/B.1.429, first associated with infections in California, and Delta/B.1.617.2, which is currently replacing all other SARS-CoV-2 lineages globally) all allowed pseudovirus to use ferret ACE2 for cell entry to almost the same degree as human ACE2. 2022 Cell reports Result SARS_CoV_2 E484K;L452R;E484K 30;148;8 35;153;13 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Both groups of ferrets showed comparable patterns of fever during infection, peaking between days 2 and 4, and the Y453F-infected ferrets trended toward more weight loss over the course of the experiment (Figures 2D and 2E). 2022 Cell reports Result SARS_CoV_2 Y453F 115 120 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Both Y453F and N501T have previously been associated with experimental ferret adaptation of SARS-CoV-2. 2022 Cell reports Result SARS_CoV_2 N501T;Y453F 15;5 20;10 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. D614G and Delta69-70 are thought to potentially enhance virus infectivity in some backgrounds. 2022 Cell reports Result SARS_CoV_2 D614G 0 5 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Deep sequencing of the virus from the ferrets inoculated with the Y453F-containing ferret P2 virus showed the Y453F substitution was maintained in all four animals throughout the course of infection (Figure 2F). 2022 Cell reports Result SARS_CoV_2 Y453F;Y453F 66;110 71;115 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Finally, to further confirm that the attenuation in human cells of the Y453F-containing viruses, particularly the ferret-adapted strain, was not due to other changes in the genome (such as E S6L described above), we generated by reverse genetics (RG) two isogenic viruses on a Wuhan-hu-1 backbone, both carrying the D614G mutation in spike, WT (D614G), while the other additionally contained Y453F (D614G + Y453F). 2022 Cell reports Result SARS_CoV_2 D614G;Y453F;Y453F;Y453F;D614G;D614G 316;71;392;407;345;399 321;76;397;412;350;404 S 334 339 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. For example, Spike-Y453F lies close to ACE2-34 (histidine in human ACE2, tyrosine in mustelid), Spike-N501T lies close to ACE2-354, and Spike-F486L lies between ACE2 residues 79, 82, and 24 (Figure 3D). 2022 Cell reports Result SARS_CoV_2 F486L;N501T;Y453F 142;102;19 147;107;24 S;S;S 13;96;136 18;101;141 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. In donor animal #1, the virus rapidly gained majority N501T, with Y453F as a minor variant. 2022 Cell reports Result SARS_CoV_2 N501T;Y453F 54;66 59;71 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. In Donor/Contact pair #2, again both mutations were detected, but N501T predominated across both animals at all time points tested. 2022 Cell reports Result SARS_CoV_2 N501T 66 71 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. In the initial virus inoculum, N501T was detected at levels below 1% of total reads while Y453F was not detected at all (read depth 7,000). 2022 Cell reports Result SARS_CoV_2 N501T;Y453F 31;90 36;95 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. In the matched contact animal (contact #1), the transmitted virus population included a mixture of Y453F with a minority of N501T and Y453F continued to predominate between days 4 and 6. 2022 Cell reports Result SARS_CoV_2 N501T;Y453F;Y453F 124;99;134 129;104;139 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Interestingly, by investigating all SARS-CoV-2 sequences isolated from mink reported on the Global Initiative on Sharing All Influenza Data (GISAID), we and others noted that N501T, Y453F, as well as F486L have independently arisen multiple times in mink, and in multiple lineages, as illustrated in Figure 1B. 2022 Cell reports Result SARS_CoV_2 F486L;N501T;Y453F 200;175;182 205;180;187 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. It appears L452R, E484K, and N501Y may promote use of ferret ACE2, while K417N/T may result in a greater reduction in ferret ACE2 usage relative to human ACE2. 2022 Cell reports Result SARS_CoV_2 E484K;K417N;K417T;L452R;N501Y 18;73;73;11;29 23;80;80;16;34 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. N501T alone predominated in the day 2 nasal washes from the two donor animals that did not transmit to their direct contacts (98% in one, 94% in the other), with remaining reads showing WT spike. 2022 Cell reports Result SARS_CoV_2 N501T 0 5 S 189 194 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Next, we tested whether Y453F and the other mustelid-associated spike mutations improved the use of the otherwise suboptimal ferret ACE2. 2022 Cell reports Result SARS_CoV_2 Y453F 24 29 S 64 69 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Of all the mink-adapting substitutions, Y453F has been more frequently associated with spillback from mink into humans, including Cluster 5 in Denmark. 2022 Cell reports Result SARS_CoV_2 Y453F 40 45 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Of the two transmitted virus isolates, at the consensus level, one had gained N501T in the spike protein while the other had a mixture of Y453F and N501T. 2022 Cell reports Result SARS_CoV_2 N501T;N501T;Y453F 78;148;138 83;153;143 S 91 96 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Overall, these data suggest that Y453F adapts the virus to ferret infection, but also further adaptations may arise during ongoing adaptation in mustelid hosts. 2022 Cell reports Result SARS_CoV_2 Y453F 33 38 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Several further substitutions, all present at very low levels in the inoculum, rapidly grew to fixation in all four Y453F-infected ferrets. 2022 Cell reports Result SARS_CoV_2 Y453F 116 121 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Spike D614N may exert a similar effect to the ubiquitous SARS-CoV-2 human adaptation D614G, to nonspecifically enhance ACE2 binding by promoting the spike open conformation. 2022 Cell reports Result SARS_CoV_2 D614G;D614N 85;6 90;11 S;S 0;149 5;154 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Surprisingly, Y453F-containing "Ferret P2" virus was significantly more easily neutralized by convalescent first-wave antisera than WT requiring only 0.6 as much antisera for a 50% neutralization titer (Figure 5A). 2022 Cell reports Result SARS_CoV_2 Y453F 14 19 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. The effect of Y453F was not dependent on the presence or absence of D614G, as Y453F in a 614D background showed a similar effect (Figure 3C). 2022 Cell reports Result SARS_CoV_2 D614G;Y453F;Y453F 68;14;78 73;19;83 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. The titer of parental virus shed and fever in parental virus-infected animals approached that in the ferret P2 infected animals by days 3 to 4, likely because the parental virus had gained ferret-adapting mutations, such as Y453F or N501T, by this point (see Figure 1A). 2022 Cell reports Result SARS_CoV_2 N501T;Y453F 233;224 238;229 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. The Vero-grown virus stock was, in the majority, Y453F (~96%) with very minor variants, N501T and WT RBD also present (<5%). 2022 Cell reports Result SARS_CoV_2 N501T;Y453F 88;49 93;54 RBD 101 104 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. The WT virus significantly outcompeted Y453F, with less than ~5% of reads by 48 h postinfection containing Y453F. 2022 Cell reports Result SARS_CoV_2 Y453F;Y453F 39;107 44;112 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Therefore, we performed a similar competition experiment between a mixed inoculum of 40% Cluster 5 isolate and 60% early B.1 lineage, D614G containing virus ("WT"; IC19). 2022 Cell reports Result SARS_CoV_2 D614G 134 139 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. These encoded mutations in spike at D614N, in N protein at R68P, and in the NSP2 protein at T632I (Figure 2G). 2022 Cell reports Result SARS_CoV_2 D614N;R68P;T632I 36;59;92 41;63;97 S;Nsp2;N 27;76;46 32;80;47 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. To assess the impact of the Y453F mutation on the replication of virus in human airway epithelium, we infected primary human bronchial cells cultured at an air-liquid interface with a mix of the parental and ferret P2 viruses at a low multiplicity of infection (MOI) of around 0.1 (Figure 4A). 2022 Cell reports Result SARS_CoV_2 Y453F 28 33 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. To further investigate the effects of the Y453F substitution, we isolated virus from contact #1 from day 6 in Vero cells ("Ferret P2") and validated that the sequence change was maintained in the titrated virus stock (Figure 2A). 2022 Cell reports Result SARS_CoV_2 Y453F 42 47 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. To investigate whether a mustelid-adapted SARS-CoV-2 crossing back into the human population would have a large impact on re-infections or vaccine-breakthrough, we next tested whether the mutation at Y453F facilitated escape from antibody neutralization. 2022 Cell reports Result SARS_CoV_2 Y453F 200 205 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. To investigate whether the Y453F-containing virus showed greater replication in ferrets, we intranasally inoculated four naive ferrets with ferret P2 virus and compared levels of virus shed from the nose with four ferrets previously inoculated with the same infectious titer of parental England/2/2020 virus (the same donors from Figure 1A). 2022 Cell reports Result SARS_CoV_2 Y453F 27 32 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Virus with Y453F shows enhanced replication and trended toward higher morbidity in ferrets. 2022 Cell reports Result SARS_CoV_2 Y453F 11 16 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Viruses containing Y453F mutation are attenuated for replication in primary human airway epithelial cells. 2022 Cell reports Result SARS_CoV_2 Y453F 19 24 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. We found that nearly all variants of concern tested could better use mink ACE2 than WT (D614G only) pseudovirus. 2022 Cell reports Result SARS_CoV_2 D614G 88 93 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. We further investigated the relative antigenicity of Y453F, this time using the above-described RG viruses and antisera from health care workers who had received two doses the of Pfizer-BioNtech- BNT162b2 vaccine. 2022 Cell reports Result SARS_CoV_2 Y453F 53 58 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. While WT (D614G) spike uses ferret ACE2 poorly for entry (>10-fold less well than human ACE2), the adaptations Y453F, N501T, or F486L, as well as full Cluster 5 spike (Delta69/70, Y453F, D614G, I692V, M1229I), all allowed SARS-CoV-2 spike expressing pseudoviruses to enter into human or ferret, but not rat, ACE2-expressing cells with much greater efficiency (Figures 3A and 3B). 2022 Cell reports Result SARS_CoV_2 D614G;F486L;I692V;M1229I;N501T;Y453F;Y453F;D614G 187;128;194;201;118;111;180;10 192;133;199;207;123;116;185;15 S;S;S 17;161;233 22;166;238 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Y435F and N501T substitutions in the spike are detected in viruses transmitted between ferrets. 2022 Cell reports Result SARS_CoV_2 N501T;Y435F 10;0 15;5 S 37 42 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Y453F enhances cell entry using the mustelid ACE2 receptor. 2022 Cell reports Result SARS_CoV_2 Y453F 0 5 35095814 A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands. Additionally, in summer 2021, three consensus genome sequences were assigned to lineage B.1 (EPI_ISL_3087129, EPI_ISL_2626134, and EPI_ISL_2626162) and showed some interesting additional spike mutations, including S:L452R and S:E484Q; these three genomes have been reassigned to recently described lineage B.1.630. 2021 Frontiers in microbiology Result SARS_CoV_2 E484Q;L452R 228;216 233;221 S;S;S 187;214;226 192;215;227 35095814 A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands. During first half of 2021, substitutions at position E484 in the spike protein, naturally occurring in B.1.351 and P.1 lineages, have been detected in 3 genome sequences ascribed to lineages B.1.1.7 (S:E484K, n = 2) and B.1.617.2 (S:E484G, n = 1). 2021 Frontiers in microbiology Result SARS_CoV_2 E484G;E484K 233;202 238;207 S;S;S 65;200;231 70;201;232 35095814 A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands. Moreover, up to 31 genomes ascribed to lineage B.1.1.7 harbored the spike substitution S:R287K, a rare mutation with unknown biological effect. 2021 Frontiers in microbiology Result SARS_CoV_2 R287K 89 94 S;S 68;87 73;88 35095814 A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands. Of note, since July 2021, mutation S:Q613H present in lineage A.23.1 has been detected in a relative high number of genomes belonging to the P.1 (n = 1) and B.1.617.2/AY.X (n = 24) lineages, mutation which could provide some biological advantages. 2021 Frontiers in microbiology Result SARS_CoV_2 Q613H 37 42 S 35 36 35095814 A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands. S:P681R-defining mutation of PANGO lineages B.1.617.2 and AY.X, have been detected in 2 genomes belonging to lineages B.1 and B.1.1.7. 2021 Frontiers in microbiology Result SARS_CoV_2 P681R 2 7 S 0 1 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. A marked difference could also be observed for substitutions T696I, S884C, and Y144F. 2021 Frontiers in microbiology Result SARS_CoV_2 S884C;T696I;Y144F 68;61;79 73;66;84 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. All the other substitutions were confined to 1 or 2 sequences only, with the only exception of T4418I, present in 6 cases (16.2%) of the III wave. 2021 Frontiers in microbiology Result SARS_CoV_2 T4418I 95 101 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. Almost all sequences in the three waves displayed the ubiquitous substitution P4712L, with only one exception, in the Nsp12 gene. 2021 Frontiers in microbiology Result SARS_CoV_2 P4712L 78 84 Nsp12 118 123 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. Besides the ubiquitous P4715L, no other substitution found in our dataset displayed a percentage frequency higher than 1% in the global GISAID dataset. 2021 Frontiers in microbiology Result SARS_CoV_2 P4715L 23 29 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. In addition, other two widespread variants emerged during the II wave, A222V and P272L with frequencies of 52.4 and 50%, respectively. 2021 Frontiers in microbiology Result SARS_CoV_2 A222V;P272L 71;81 76;86 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. Some significant deviations in our sequences, compared to the global values, are observed, such as A156S, S187A, and A220V. 2021 Frontiers in microbiology Result SARS_CoV_2 A156S;A220V;S187A 99;117;106 104;122;111 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. Spike Y144F substitution was found in a subset of Nuoro samples that formed a supported subcluster among 20A clade members, and this internal subcluster was even further divided into two groups of sequences, attributed to the II (n = 5) and the III wave (n = 6), respectively. 2021 Frontiers in microbiology Result SARS_CoV_2 Y144F 6 11 S 0 5 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. Substitutions A222V, A262S, and P272L significantly deviated from the global distribution, demonstrating a higher prevalence in our dataset. 2021 Frontiers in microbiology Result SARS_CoV_2 A222V;A262S;P272L 14;21;32 19;26;37 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. Table 4 also reports the global percentage frequencies, which showed that D3L, R203_G204delinsKR, and S235F were the most globally frequent ones, among the substitutions found in our dataset. 2021 Frontiers in microbiology Result SARS_CoV_2 D3L;S235F 74;102 77;107 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. The analysis of the S, N, and Nsp12 missense mutations highlighted how the Y144F sequences coming from the two waves also formed two sets in terms of mutations, where all the sequences from the III wave were characterized by the same missense mutations of the sequences from the II wave, with the addition of substitution T4418I in the RdRp and Y837H in the spike protein. 2021 Frontiers in microbiology Result SARS_CoV_2 T4418I;Y144F;Y837H 322;75;345 328;80;350 S;Nsp12;RdRP;N;S 358;30;336;23;20 363;35;340;24;21 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. The II wave was also characterized by the appearance of the A220V substitution in 78.6% of cases. 2021 Frontiers in microbiology Result SARS_CoV_2 A220V 60 65 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. The III wave saw the introduction of the substitutions D3L and S235F. 2021 Frontiers in microbiology Result SARS_CoV_2 D3L;S235F 55;63 58;68 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. The III wave was characterized by the appearance of the subset of mutations that distinguish the B.1.1.7 lineage such as H69_V70del, Y144del, N501Y, A570D, P681H, T716I, S982A, and D1118H. 2021 Frontiers in microbiology Result SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;T716I;Y144del 149;181;142;156;170;163;133 154;187;147;161;175;168;140 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. The most common amino acid substitution in the S gene, detected in every analyzed sequence of this dataset, was D614G (Table 4). 2021 Frontiers in microbiology Result SARS_CoV_2 D614G 112 117 S 47 48 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. This conflicts with the observation that the B.1.1.7 lineage was otherwise always associated with 20I/501Y.V1 in our dataset, as expected considering the presence of the N501Y amino acid substitution -among all other typical ones- in the S protein. 2021 Frontiers in microbiology Result SARS_CoV_2 N501Y 170 175 S 238 239 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. 6B shows that the T-cell propensity did not change significantly for peptides under the D614G mutation, while the S939F displays a small but significant effect. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D614G;S939F 88;114 93;119 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Altogether our findings represent the first evidence of a SARS-CoV-2 variant carrying double Spike D614G/S939F in Italy. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D614G;S939F 99;105 104;110 S 93 98 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. For example in the case of the S939F, we could identify some alleles where some new strongly binding peptides emerged in the mutated protein (e.g. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 S939F 31 36 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Furthermore, we investigated dynamic patterns of SARS-CoV-2 genomic variants S939F and D614G independently, across different sampling locations over time. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D614G;S939F 87;77 92;82 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Here we aim to estimate the effects of the D614G/S939F mutations on the immune response. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D614G;S939F 43;49 48;54 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. HLA-A26:01 or HLA-A32:01), while for the D614G mutation the presence of isolated strongly binding peptides was not affected by the mutation (see HLA-A02:01, HLA-A02:03 and HLA-A02:06). 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D614G 41 46 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Identification of a SARS-CoV-2 double Spike mutation D614G/S939F. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D614G;S939F 53;59 58;64 S 38 43 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. In particular, S939F variant, due to nucleotide change C to T in position 24378 of Spike gene, resulted to be about three hundred times less frequent than D614G variant, due to nucleotide change A to G in position 23403 (3853 versus 1218522 counts), determining an evidence level of IV for S939F versus I for D614G. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 A23403G;C24378T;D614G;D614G;S939F;S939F 195;55;155;309;15;290 219;79;160;314;20;295 S 83 88 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. S939F variant frequency slightly increased over time, reaching 0.0032 at the beginning of June 2021, while D614G variant frequency dramatically increased from 0 at the end of February 2020 to 0.98 at the beginning of June 2021, indicating that this mutated genotype might have higher transmissibility. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D614G;S939F 107;0 112;5 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Similar to the analysis performed by Korber and collaborators for the global distribution of D614G variant, we interrogated GISAID to assess S939F variant distribution in Europe. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D614G;S939F 93;141 98;146 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Subsequently we assessed S939F variant distribution in Europe. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 S939F 25 30 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. The Spike D614G/S939F double mutation is poorly studied and consequently its impact on host infection and patient clinical implications are scarcely known. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D614G;S939F 10;16 15;21 S 4 9 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. The two point mutations D614G and S939F only affected a limited number of peptides, and due to their distance along the sequence no peptide can have more than one mutation. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D614G;S939F 24;34 29;39 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. To figure out where S939F and D614G variants were globally located over time, we interrogated COVID-19 CoV Genetics browser. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D614G;S939F 30;20 35;25 COVID-19 94 102 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. To further analyze the features of the identified SARS-CoV-2 double mutation, we investigated more in detail each single variant S939F and D614G. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D614G;S939F 139;129 144;134 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Unlike D614G, S939F affects T-cell propensity. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D614G;S939F 7;14 12;19 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. we can identify a small number of peptides that are either present exclusively in the reference protein (16 for D614G and 20 for S939F) or in the mutated protein (16 for D614G and 12 for S939F) (Table S2). 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D614G;D614G;S939F;S939F 112;170;129;187 117;175;134;192 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. We found that S939F variant was detected in Sweden and Denmark when we evidenced S939F-D614G double mutation in our patient samples. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 S939F;S939F;D614G 14;81;87 19;86;92 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Worldwide geographically distribution of double Spike mutation D614G/S939F. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D614G;S939F 63;69 68;74 S 48 53 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. 2 , D35 GMTs against variants with the E484K/Q mutation were lower than those against D614 by 13.9- and 34.8-fold to Beta and by 8.4- and 20.5-fold to Gamma for Groups 1 and 2, respectively. 2022 Vaccine Result SARS_CoV_2 E484K;E484Q 39;39 46;46 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. At D35, neutralizing titers against Alpha, Delta, and Epsilon variants, without the key E484K/Q mutation, were comparable to those against D614 with GMTs to D614, Alpha, and Epsilon all around the order of 3.3-3.5 log10. 2022 Vaccine Result SARS_CoV_2 E484K;E484Q 88;88 95;95 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. collectively demonstrated that the third booster vaccination, even with the vaccines containing the original D614 Spike protein sequence, can effectively improve the quality of vaccine-induced neutralizing antibody responses by expanding the breadth of coverage against VoC, especially those harboring the key E484K/Q mutation. 2022 Vaccine Result SARS_CoV_2 E484K;E484Q 310;310 317;317 S 114 119 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. For the variants with the E484K/Q mutation (Beta and Gamma), lower GMTs compared to D614 were demonstrated at D35 with GMTs to Beta at 78 (21.7-fold) and 31 (35.2-fold) and to Gamma at 76 (22.1-fold) and 58 (18.7-fold) for Groups A and B, respectively. 2022 Vaccine Result SARS_CoV_2 E484K;E484Q 26;26 33;33 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. The pre-boost NAb GMTs at D35, against variants lacking the E484K/Q mutation (D614, Alpha, Delta, and Epsilon) were generally comparable to each other, with GMTs to D614, Alpha, and Epsilon on the order of 3 log10. 2022 Vaccine Result SARS_CoV_2 E484K;E484Q 60;60 67;67 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. These results collectively demonstrated the benefit of a third vaccine dose in expanding the coverage breadth against the SARS-CoV-2 variants, regardless of the key E484K/Q mutation, and to a lesser extent NAbs to SARS-CoV-1. 2022 Vaccine Result SARS_CoV_2 E484K;E484Q 165;165 172;172 35104067 Neutralizing Antibodies and Cytokines in Breast Milk After Coronavirus Disease 2019 (COVID-19) mRNA Vaccination. Milk neutralizing antibodies to spike and four variants of concern (D614G, Alpha, Beta, and Gamma) were evaluated. 2022 Obstetrics and gynecology Result SARS_CoV_2 D614G 68 73 S 32 37 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. A dated phylogeny of global samples showed that samples with the R203K/G204R SNPs are predominantly found in Nextstrain clades 20A, 20B, and 20C, and do not form a monophyletic group. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 65;71 70;76 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. A genome-wide association study between SARS-CoV-2 SNPs and patient mortality identified the three consecutive SNPs (G28881A, G28882A, G28883C) underlying the R203K/G204R mutations. 2022 Nature communications Result SARS_CoV_2 G28882A;G28883C;R203K;G28881A;G204R 126;135;159;117;165 133;142;164;124;170 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. A positive significant association was also observed for the C14408T SNP, and a negative association for the C241T SNP (Supplementary Table S5). 2022 Nature communications Result SARS_CoV_2 C14408T;C241T 61;109 68;114 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. A significant negative association was found for the C3037T C14408T, and G25563T SNPs (Supplementary Table S9). 2022 Nature communications Result SARS_CoV_2 C14408T;C3037T;G25563T 60;53;73 67;59;80 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. For mortality and severity, we first fitted a logistic linear model using R203K/G204R SNPs as a covariate and adjusting by sex, age, comorbidities, hospital, and other SNPs. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 74;80 79;85 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. From this adjusted regression we found a positive and statistically significant relationship between R203K/G204R SNPs and log10(viral copy number), with the mean of log10(viral copy number) values increasing by 1.33 units (95% CI 0.72-1.93) (Supplementary Table S9). 2022 Nature communications Result SARS_CoV_2 R203K;G204R 101;107 106;112 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. However, after adjusting for time as a variable, there was no longer any association between R203K/G204R SNPs and mortality (log-odds: 0.58, 95% CI -0.41-1.56) (Supplementary Table S8). 2022 Nature communications Result SARS_CoV_2 R203K;G204R 93;99 98;104 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. In our samples, no other SNPs co-occur with the R203K/G204R SNPs. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 48;54 53;59 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. In the global data, the peak in R203K/G204R frequency is slightly delayed compared to samples from Saudi Arabia. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 32;38 37;43 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. In the time-adjusted model, the log-odds for the R203K/G204R SNPs increased to 1.38, 95% CI 0.28-2.48 (Supplementary Table S6). 2022 Nature communications Result SARS_CoV_2 R203K;G204R 49;55 54;60 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. In this model, the C241T SNP again displayed a significant negative association, and a positive association was now observed for the C1887T SNP (Supplementary Table S6). 2022 Nature communications Result SARS_CoV_2 C1887T;C241T 133;19 139;24 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. It is therefore not clear if the phylogenetic distribution of samples with R203K/G204R SNPs reflects multiple independent origins of the SNPs, although it is evident that the R203K/G204R SNPs appeared early in the pandemic spread. 2022 Nature communications Result SARS_CoV_2 R203K;R203K;G204R;G204R 75;175;81;181 80;180;86;186 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Origin of R203K/G204R SNPs. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 10;16 15;21 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Protein cross-linking shows that N mutant protein (with the R203K/G204R mutations) has higher oligomerization potential compared to the control N protein (without the changed amino acids) at low protein concentration. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 60;66 65;71 N;N 33;144 34;145 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Protein structure predictions have shown that the R203K/G204R mutations result in significant changes in protein structure, theoretically destabilizing the N structure, and potentially enhancing the protein's ability to bind RNA and alter its response to serine phosphorylation events. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 50;56 55;61 N 156 157 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Similarly, the model showed a positive significant association between the SNPs A23403G (Spike protein D614G) and C26735T SNPs and log10(viral copy number), the former being consistent with earlier reports. 2022 Nature communications Result SARS_CoV_2 A23403G;C26735T;D614G 80;114;103 87;121;108 S 89 94 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Taken together, these results suggest that the R203K/G204R mutations in the N protein may enhance its function in provoking a hyper-expression of interferon-related genes that contribute to the cytokine storm in exacerbating COVID-19 pathogenesis. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 47;53 52;58 N 76 77 COVID-19 225 233 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. The A23403G mutation results in the Spike protein D614G SNP that is associated with higher viral load. 2022 Nature communications Result SARS_CoV_2 A23403G;D614G 4;50 11;55 S 36 41 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. The frequency of the R203K/G204R SNPs is markedly higher in samples from Jeddah, where the observed frequency of 0.38 is more than 10-fold higher than the average of the other cities (Supplementary Table S1). 2022 Nature communications Result SARS_CoV_2 R203K;G204R 21;27 26;32 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. The initial global peak is observed in July 2020 followed by a decline until the fall of 2020, where the R203K/G204R SNPs once again increased along with the Spike protein Y501N mutation in the B1.1.17 lineage. 2022 Nature communications Result SARS_CoV_2 R203K;Y501N;G204R 105;172;111 110;177;116 S 158 163 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. The N mutant (R203K/G204R) induces overexpression of interferon-related genes in transfected host cells. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 14;20 19;25 N 4 5 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. The phylogeny highlighted the clade 20A that all carried the nucleocapsid (N) protein R203K/G204R mutations with high incidences of ICU hospitalizations. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 86;92 91;97 N;N 61;75 73;76 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. The positive and statistically significant association of R203K/G204R SNPs with higher viral load in critical COVID-19 patients. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 58;64 63;69 COVID-19 110 118 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. The R203K/G204R mutations in the N protein affect its interaction with host proteins. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 4;10 9;15 N 33 34 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. The R203K/G204R mutations in the SARS-CoV-2 N protein are within the linkage region (LKR) containing the serine/arginine-rich motif (SR-rich motif). 2022 Nature communications Result SARS_CoV_2 R203K;G204R 4;10 9;15 N 44 45 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. The relationship between mortality and R203K/G204R SNPs was positive and statistically significant in the model that did not include time with log-odds equal to 1.04, 95% 0.16-1.92. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 39;45 44;50 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Therefore, we decided to investigate how the two amino acids substitution (R203K and G204R) in the N protein impact its functional interaction with the host that could modulate viral pathogenesis and rewiring of host cell pathways and processes. 2022 Nature communications Result SARS_CoV_2 G204R;R203K 85;75 90;80 N 99 100 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. These include the Spike protein D614G (A23403G) and three consecutive SNPs (G28881A, G28882A, and G28883C) causing the R203K and G204R changes in the nucleocapsid protein. 2022 Nature communications Result SARS_CoV_2 D614G;G204R;G28882A;G28883C;R203K;A23403G;G28881A 32;129;85;98;119;39;76 37;134;92;105;124;46;83 N;S 150;18 162;23 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. To understand whether the R203K/G204R mutations in the N gene affect host cell transcriptome, we transfected Calu-3 cells (4 biological replicates) with plasmids expressing the full-length N-control and N-mutant protein along with mock-transfection control. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 26;32 31;37 N;N;N 55;189;203 56;190;204 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Using first a logistic regression model that did not include time, we observed a positive and statistically significant association between R203K/G204R SNPs and severity. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 140;146 145;151 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Using multivariable regression, we next evaluated the effect of the R203K/G204R SNPs on mortality, severity, and viral load in our COVID-19 patient samples for which a limited amount of clinical meta-datasets were available. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 68;74 73;79 COVID-19 131 139 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. We included 12 additional SNPs (C241T, C1191T, C3037T, G10427A, C14408T, C15352T, C18877T, A23403G, G25563T, C26735T, T27484C, and C28139T) that co-occurred with the R203K/G204R SNPs in at least five samples in the model. 2022 Nature communications Result SARS_CoV_2 A23403G;C1191T;C14408T;C15352T;C18877T;C26735T;C28139T;C3037T;G10427A;G25563T;R203K;T27484C;C241T;G204R 91;39;64;73;82;109;131;47;55;100;166;118;32;172 98;45;71;80;89;116;138;53;62;107;171;125;37;177 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. We then tested if R203K/G204R SNPs were associated with higher viral copy numbers as indicated by the cycle threshold (Ct) values obtained through quantitative PCRs. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 18;24 23;29 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Within our sampling window we observe an apparent transient increase in the frequency of R203K/G204R SNPs. 2022 Nature communications Result SARS_CoV_2 R203K;G204R 89;95 94;100 35113647 Divergent SARS-CoV-2 Omicron-reactive T and B cell responses in COVID-19 vaccine recipients. Antibody functionality was measured using an infectious virus neutralization assay with passage 3 SARS-CoV-2 viruses D614G (WT), B.1.351 (Beta), B.1617.2 (Delta) and B.1.1.529 (Omicron). 2022 Science immunology Result SARS_CoV_2 D614G 117 122 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. Both subclones showed a complete recovery of binding affinity against RBD-B.1.351 and RBD-L452R (Figures 7A and 7B; Table S7). 2022 Cell reports Result SARS_CoV_2 L452R 90 95 RBD;RBD 70;86 73;89 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. E484K:an escape mutant found in many different variants, including B.1.351 and A.VOI.V2 :did, however, reduce the binding affinity of N-612-017 by 6- to 10-fold (Figures 6A and 6B). 2022 Cell reports Result SARS_CoV_2 E484K 0 5 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. Furthermore, the L452R mutation found in CA.20C (also known as B.1.1.427 and B.1.1.429) completely abolished the binding of RBD by N-612-017. 2022 Cell reports Result SARS_CoV_2 L452R 17 22 RBD;N 124;131 127;132 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. Generation of E484K- and L452R-resistant N-612-017. 2022 Cell reports Result SARS_CoV_2 E484K;L452R 14;25 19;30 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. Interestingly, both N-612-017-01 and N-612-017-03 subclones not only exhibited restored binding affinity against E484K-expressing RBD variants, but they had 10- to 20-fold enhanced affinity against wild-type RBD (Figures 7A and 7B; Table S7). 2022 Cell reports Result SARS_CoV_2 E484K 113 118 RBD;RBD 130;208 133;211 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. N-612-017 and N-612-056 were then evaluated in a pseudovirus neutralization assay using wild-type (containing D614G), B.1.1.7, and B.1.351 pseudoviruses. 2022 Cell reports Result SARS_CoV_2 D614G 110 115 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. N-612-017 neutralized wild-type (D614G) and B.1.1.7 pseudoviruses with IC50 = 0.09-0.25 mug/mL but failed to neutralize B.1.351. 2022 Cell reports Result SARS_CoV_2 D614G 33 38 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. N-612-017-5B02 containing 4 additional VH mutations (A33T/S54W/G54Delta/S55T) and N-612-017-5B05 containing 4 additional VH mutations (S31P/A33V/R96E/D97E) were tested by BLI for their binding of B.1.351 and RBD-L452R. 2022 Cell reports Result SARS_CoV_2 A33T;S31P;A33V;D97E;R96E;S54W;S55T;L452R 53;135;140;150;145;58;72;212 57;139;144;154;149;62;76;217 RBD;N 208;82 211;83 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. Neither N501Y (the only RBD mutation in B.1.1.7 and one of 3 RBD mutations in B.1.351) nor K417N (one of 3 RBD mutations in B.1.351) disrupted the binding affinity of N-612-017. 2022 Cell reports Result SARS_CoV_2 K417N;N501Y 91;8 96;13 RBD;RBD;RBD 24;61;107 27;64;110 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. Subsequently, we used N-612-017-001 in affinity maturation against RBD-L452R and identified 2 clones with restored affinity against RBD-L452R. 2022 Cell reports Result SARS_CoV_2 L452R;L452R 71;136 76;141 RBD;RBD 67;132 70;135 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. The binding affinity of N-612-014 and N-612-004 against the recombinant S1 domain containing B.1.1.7 mutations was tested, and it was determined that 69-70del and Y144del on NTD did not affect the binding affinity of N-612-014 for S1, whereas these mutations moderately lowered (by about 3-fold) the binding affinity of N-612-004 for S1 (Figures S5B and S5C). 2022 Cell reports Result SARS_CoV_2 Y144del 163 170 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. The N-612-017 subclone N-612-017-01 containing a single VH:R71S mutation and subclone N-612-017-03 containing double VH:R71S/D97E mutations were tested by BLI for their binding of RBD-B.1.351 and RBD-L452R. 2022 Cell reports Result SARS_CoV_2 D97E;R71S;R71S;L452R 125;59;120;200 129;63;124;205 RBD;RBD 180;196 183;199 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. These subclones were then tested in a live virus neutralization assay against wild-type (D614G) and B.1.351 viruses and showed neutralization activity against both, whereas the parent N-612-017 did not show neutralization activity against B.1.351 (Figures 7C and 7D). 2022 Cell reports Result SARS_CoV_2 D614G 89 94 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. To assess the relative affinity of RBD-binding nAbs N-612-017 and N-612-056 against a series of variants, BLI was performed using RBD variants B.1.1.7 (N501Y), B.1.351 (K417N/E484K/N501Y), CAL.20C (L452R), and A.VOI.V2 (T478R/E484K) with single or combined mutations. 2022 Cell reports Result SARS_CoV_2 K417N;L452R;N501Y;T478R;E484K;E484K;N501Y 169;198;152;220;175;226;181 174;203;157;225;180;231;186 RBD;RBD 35;130 38;133 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. To improve potency of N-612-056, we utilized mRNA display for affinity maturation and identified N-612-056-21 containing a single point mutation in VH CDR3 (Ser 99 Pro) that resulted in a 10-fold improvement in binding affinity (K D = 0.41 nM) (Figure 7E). 2022 Cell reports Result SARS_CoV_2 S99P 157 169 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. To recover N-612-017 binding against RBD with the E484K substitution (RBD-E484K), we used an mRNA-doped library for affinity maturation and identified mutations on VH framework 3 (Arg 71 Ser) and CDR H3 (Asp 97 Glu) that restored binding affinity against RBD-E484K. 2022 Cell reports Result SARS_CoV_2 E484K;R71S;D97E;E484K;E484K 50;180;206;74;263 55;192;218;79;268 RBD;RBD;RBD 37;70;259 40;73;262 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. While neither subclone displayed a complete recovery of binding affinity against RBD-L452R, affinity was relatively enhanced (K D = 33.1-58.7 nM). 2022 Cell reports Result SARS_CoV_2 L452R 85 90 RBD 81 84 35115523 Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. All four of these lineages were found to be fully functional and produced transduction-competent lentiviral pseudoviruses with titers similar to the parent strain (D614G). 2022 Nature communications Result SARS_CoV_2 D614G 164 169 35115523 Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. As of November 30, 2021, there were only 35 SARS-CoV-2 sequences in GISAID that contained the polymorphism Q498H (eight in the USA), and none that contained Q498Y. 2022 Nature communications Result SARS_CoV_2 Q498H;Q498Y 107;157 112;162 35115523 Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. Each of these lineages contained at least five polymorphisms; the most divergent was WNY4, which contained 16 amino acid changes in its RBD including a deletion at position 484. 2022 Nature communications Result SARS_CoV_2 del 484 152 176 RBD 136 139 35115523 Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. For example, one of the lineages from WWTF 10 added the polymorphism F486P at later sampling dates. 2022 Nature communications Result SARS_CoV_2 F486P 69 74 35115523 Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. Interestingly, all four WNY lineages contained a polymorphism at spike protein residue 498 (Q498H or Q498Y). 2022 Nature communications Result SARS_CoV_2 Q498Y;Q498H 101;92 106;97 S 65 70 35115523 Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. N501Y+A570D), this observation cannot be taken as evidence that these lineages were derived from such a host. 2022 Nature communications Result SARS_CoV_2 N501Y;A570D 0;6 5;11 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. Compared to WT, the Omicron Q493K/R present increased force profiles evidenced by both the first (D = 53 A) and second maximum (D = 79 A) peaks (Figure 1A). 2022 bioRxiv Result SARS_CoV_2 Q493K;Q493R 28;28 35;35 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. Figure 2B,C show the two-dimensional contact maps of Omicron Q493K and Q493R. 2022 bioRxiv Result SARS_CoV_2 Q493K;Q493R 61;71 66;76 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. Figure 3D shows the number of contact analysis between RBD Omicron Q493K/R and selected residues in ACE2. 2022 bioRxiv Result SARS_CoV_2 Q493K;Q493R 67;67 74;74 RBD 55 58 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. From the initial state (about D = 50 A), Q493R displays more contacts with ACE2 than Q493K up to D = 58 A. 2022 bioRxiv Result SARS_CoV_2 Q493K;Q493R 85;41 90;46 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. Herein, we measured the binding affinity between ACE2 and the Omicron RBD bearing the Q493R mutation (Figure 4A). 2022 bioRxiv Result SARS_CoV_2 Q493R 86 91 RBD 70 73 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. N501Y mutation of the Omicron results in increased maximum force. 2022 bioRxiv Result SARS_CoV_2 N501Y 0 5 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. Omicron variants (Q493K/R) have shown unprecedented transmissibility compared to any other SARS-CoV-2 variants, and the force profile in Figure 1A confirms that the Omicron Q493K/R, compared to WT, present increased force profiles around D = 80 A as well as D = 53 A. 2022 bioRxiv Result SARS_CoV_2 Q493K;Q493R;Q493K;Q493R 173;173;18;18 180;180;25;25 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. Our results showing enhanced RBDOmicrons-ACE2 binding are consistent with the previous experimental and computational studies, and explain the differential interactions of Omicron Q493K/R, although we only considered single RBD out of trimeric SARS-CoV-2 S protein. 2022 bioRxiv Result SARS_CoV_2 Q493K;Q493R 180;180 187;187 RBD;S 224;255 227;256 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. Pulling force analysis was performed (Figure 1A) as a function of distance, D, between COMs of RBDOmicrons and ACE2 to obtain molecular-level insight into the Omicron variants (Q493K/R). 2022 bioRxiv Result SARS_CoV_2 Q493K;Q493R 177;177 184;184 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. Recent studies report that the Omicron contains either Q493K or Q493R, while other mutations remain the same. 2022 bioRxiv Result SARS_CoV_2 Q493K;Q493R 55;64 60;69 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. The force profiles of Omicron Q493K at D = 53 A (Figure 1A) present weaker maximum forces than Omicron Q493R, although both show higher forces than WT at the same distance. 2022 bioRxiv Result SARS_CoV_2 Q493K;Q493R 30;103 35;108 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. The Omicron presents enhanced second maximum force by T478K mutation. 2022 bioRxiv Result SARS_CoV_2 T478K 54 59 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. The Omicron Q493R mutation also induces reinforced RBD-ACE2 interface. 2022 bioRxiv Result SARS_CoV_2 Q493R 12 17 RBD 51 54 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. The stronger R493 interaction of Omicron Q493R further brings about increased contacts between RBD (F456, A475, G476, and N477) and ACE2 (S19, Q24, and T27) compared to WT or Omicron Q493K (Figure 2C). 2022 bioRxiv Result SARS_CoV_2 Q493K;Q493R 183;41 188;46 RBD 95 98 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. Therefore, we built up two independent Omicron model systems retaining Q493K or Q493R to address both cases (Figure 2D). 2022 bioRxiv Result SARS_CoV_2 Q493K;Q493R 71;80 76;85 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. This difference induces the gap in the number of contact analysis (Figure 3D) and makes RBDOmicron-Q493R-ACE2 interface stronger than RBDOmicron-Q493K-ACE2 interface. 2022 bioRxiv Result SARS_CoV_2 Q493K;Q493R 145;99 150;104 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. This indicates that the Omicron Q493R mutation contributes to having a reinforced RBD-ACE2 interface. 2022 bioRxiv Result SARS_CoV_2 Q493R 32 37 RBD 82 85 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. To analyze the contact frequency, the number of contacts was calculated between RBD residue 501 (N501 for WT; Y501 for Omicron Q493K/R) and ACE2 in Figure 3A. 2022 bioRxiv Result SARS_CoV_2 Q493K;Q493R 127;127 134;134 RBD 80 83 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. Y501 of Alpha and Omicron variants (Q493K/R) contain more contacts (about 40%) than N501 of WT and Delta. 2022 bioRxiv Result SARS_CoV_2 Q493K;Q493R 36;36 43;43 35118474 Breadth of SARS-CoV-2 Neutralization and Protection Induced by a Nanoparticle Vaccine. In the RBD-scNP and S2P-scNP immunized animals, neutralizing antibodies against SARS-CoV-2 D614G pseudovirus were detected after the first dose and were boosted after the second dose at week 6 (Figure 4C). 2022 bioRxiv Result SARS_CoV_2 D614G 91 96 RBD 7 10 35118474 Breadth of SARS-CoV-2 Neutralization and Protection Induced by a Nanoparticle Vaccine. Serum antibodies induced by three doses of RBD-scNP immunization neutralized both the D614G (ID50=16,531, ID80=5,484) and Omicron (ID50=3,858, ID80=980) pseudoviruses. 2022 bioRxiv Result SARS_CoV_2 D614G 86 91 RBD 43 46 35118474 Breadth of SARS-CoV-2 Neutralization and Protection Induced by a Nanoparticle Vaccine. To determine if the B.1.1.529 (Omicron) variant could escape RBD-scNP-induced neutralizing antibodies, we compared immune sera for capacity to neutralize the D614G and Omicron variants in a 293T-ACE2 pseudovirus assay. 2022 bioRxiv Result SARS_CoV_2 D614G 158 163 RBD 61 64 35123044 Clinical and genomic data of sars-cov-2 detected in maternal-fetal interface during the first wave of infection in Brazil. An additional aa change was also present in S2 subunit HRP2 region (V1176F) of MT21774/2020 (Figure 3C). 2022 Microbes and infection Result SARS_CoV_2 V1176F 68 74 35123044 Clinical and genomic data of sars-cov-2 detected in maternal-fetal interface during the first wave of infection in Brazil. In this study, the detected Spike aa changes were located in the S1 subunit (D614G) of both sequences, and in the RDB of MT21770/2020 (F490S) (Figure 3 A and 3B). 2022 Microbes and infection Result SARS_CoV_2 D614G;F490S 77;135 82;140 S 28 33 35123044 Clinical and genomic data of sars-cov-2 detected in maternal-fetal interface during the first wave of infection in Brazil. Sequences from this study also share four nonsynonymous mutations, P314L (Nsp12), D614G (Spike), R203K and G204R (Nucleocapsid), with these placenta sequences, in addition to two synonymous mutations (214C>T, 3037 C>T). 2022 Microbes and infection Result SARS_CoV_2 C3037T;D614G;G204R;P314L;R203K;C214T 209;82;107;67;97;201 217;87;112;72;102;207 N;S;Nsp12 114;89;74 126;94;79 35123263 The function of SARS-CoV-2 spike protein is impaired by disulfide-bond disruption with mutation at cysteine-488 and by thiol-reactive N-acetyl-cysteine and glutathione. and C488A spike mutant, in which the Cys-488 was substituted with alanine, did not induce syncytium formation. 2022 Biochemical and biophysical research communications Result SARS_CoV_2 C488A;C488A 4;37 9;73 S 10 15 35123263 The function of SARS-CoV-2 spike protein is impaired by disulfide-bond disruption with mutation at cysteine-488 and by thiol-reactive N-acetyl-cysteine and glutathione. and the pseudotyped virus infection assay showed that the C488A mutant pseudotyped virus lost apparent infectious activity. 2022 Biochemical and biophysical research communications Result SARS_CoV_2 C488A 58 63 35123263 The function of SARS-CoV-2 spike protein is impaired by disulfide-bond disruption with mutation at cysteine-488 and by thiol-reactive N-acetyl-cysteine and glutathione. Microscopic analysis showed that C488A mutant spike lost syncytium formation and cell-cell fusion activities. 2022 Biochemical and biophysical research communications Result SARS_CoV_2 C488A 33 38 S 46 51 35123263 The function of SARS-CoV-2 spike protein is impaired by disulfide-bond disruption with mutation at cysteine-488 and by thiol-reactive N-acetyl-cysteine and glutathione. Other spike expressions of the Wuhan-type, D614G, F486A, and C488A mutant were confirmed. 2022 Biochemical and biophysical research communications Result SARS_CoV_2 C488A;D614G;F486A 61;43;50 66;48;55 S 6 11 35126106 Antidepressant and Antipsychotic Drugs Reduce Viral Infection by SARS-CoV-2 and Fluoxetine Shows Antiviral Activity Against the Novel Variants in vitro. We found that fluoxetine (10 microM) treatment for 24 h was effective against pseudotyped viruses carrying single point mutations in their S protein (N501Y, K417N, or E484K) (Figures 5A,B), and also a triple mutant harboring combination of these three point mutations (N501Y/K417N/E484K) (Figure 5C). 2021 Frontiers in pharmacology Result SARS_CoV_2 E484K;K417N;N501Y;N501Y;E484K;K417N 167;157;150;269;281;275 172;162;155;274;286;280 S 139 140 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. 2 shows the locations of D155Y and D155'Y (red spheres) and S171L and S171'L (cyan spheres). 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y;S171L 25;60 30;65 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. A list of the clusters and their constituent residues has been provided for the WT and the two mutants (D155Y and S171L) in Table S4. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 S171L;D155Y 114;104 119;109 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. From these values, it is evident that the binding affinity of caveolin-1 is considerably less in D155Y mutant compared to WT and S171L. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y;S171L 97;129 102;134 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. However, Arg68 features as the second most contributory residue in D155Y mutant, whereas in the S171L mutant, it has the fourth position. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y;S171L 67;96 72;101 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. However, for the D155Y system, the protein complex showed a lot more fluctuation and deviation from the starting structure. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y 17 22 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. In D155Y, the top three residue pairs forming the hydrogen bonds with maximum occupancy are Tyr212'-Thr164', Ser205'-Asn144' and Ser205-Asn144. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y 3 8 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. In the mutant S171L, the top three residue pairs forming hydrogen bonds with maximum occupancy are Leu203-Asp210, Thr89'-Leu85' and Leu203'-Asp210'. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 S171L 14 19 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. Interestingly, in the D155Y variant, the residue showed higher flexibility compared to the WT (5.75 for WT, 9.12 for D155Y and 7.73 for WT, 10.60 for the D155Y at positions 155 and 155' respectively). 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y;D155Y;D155Y 22;120;159 27;125;164 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. Note that the frequency of D155Y and S171L substitutions in India were 2.27 and 0.82, which were comparable to Asia. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y;S171L 27;37 32;42 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. Similarly, in the S171L variant, the flexibility of the residue was higher than the WT (10.62 for WT, 14.67 for S171L and 22.06 for WT, 26.97 for S171L at positions 171 and 171' respectively). 2022 Computational and structural biotechnology journal Result SARS_CoV_2 S171L;S171L;S171L 18;115;151 23;120;156 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. So it can be concluded that the substitution at D155Y or S171L does not cause a major conformational change of ORF3a from the WT. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y;S171L 48;57 53;62 ORF3a 111 116 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. Stability of the two ORF3a variants, D155Y and S171L. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y;S171L 37;47 42;52 ORF3a 21 26 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. The change in hydrogen bonding, salt bridge pattern and hydrophobic interaction pattern associated with D155Y substitution may have contributed to the weakened interaction between D155Y ORF3a and caveolin-1. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y;D155Y 104;180 109;185 ORF3a 186 191 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. The loss of salt bridge interaction in D155Y may play a significant role in the binding affinity of the interacting partner of the ORF3a protein at this region. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y 39 44 ORF3a 131 136 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. The overall fluctuation in RMSD was also greater in S171L compared to the WT and D155Y. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y;S171L 81;52 86;57 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. The S171L mutant with a free energy of -5376.51 ( 19.34) kcal/mol was the most stable, followed by WT (-5356.85 12.95 kcal/mol) and D155Y mutant (-5266.41 12.56 kcal/mol). 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y;S171L 132;4 137;9 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. The substitutions D155Y and S171L on each monomer were modelled on the WT structure separately using Swiss PDB Viewer. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y;S171L 18;28 23;33 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. The values for WT, D155Y and S171L were -37.64 (8.32) kcal/mol, -20.31 (8.60) kcal/mol and -28.39 (0.71) kcal/mol, respectively. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y;S171L 19;29 24;34 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. This indicates a not-so-stable complex structure, which is further supported by the lower PROVEAN score of D155Y (Table S6). 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y 107 112 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. This indicates that S171L substitution causes more deviation. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 S171L 20 25 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. This indicates that the mutants D155Y and S171L can also exist independently just like the WT ORF3a protein. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y;S171L 32;42 37;47 ORF3a 94 99 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. This is in corroboration with the unstable protein protein complex in the D155Y system. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y 74 79 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. Thus, the D155Y substitution interferes with the caveolin binding activity of ORF3a protein. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y 10 15 ORF3a 78 83 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. We also calculated the salt bridge interactions for the WT and the two mutant proteins and tabulated the list in Table S3, which shows that D155Y forms lesser number of salt bridges compared to the WT and the S171L (n = 24 for D155Y and n = 31 for WT and S171L). 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y;D155Y;S171L;S171L 140;227;209;255 145;232;214;260 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. We observed that the WT and the S171L are stable having an average RMSD value of around 15A. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 S171L 32 37 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. Worldwide prevalence of D155Y substitution of ORF3a. 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y 24 29 ORF3a 46 51 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. WT and D155Y (black and red profiles, respectively) showed lesser RMSD (the final RMSD being 2.25) and lesser fluctuation, whereas the S171L (green profile) variant showed higher RMSD (the final RMSD being 2.75). 2022 Computational and structural biotechnology journal Result SARS_CoV_2 D155Y;S171L 7;135 12;140 35128118 SARS-CoV-2 in Egypt: epidemiology, clinical characterization and bioinformatics analysis. Four mutations detected together in all 144 sequences were E_V5F, Spike_D614G, NS3_Q57H, and NSP12_G823S. 2022 Heliyon Result SARS_CoV_2 D614G;G823S;Q57H 72;99;83 77;104;87 S;Nsp12;NS3 66;93;79 71;98;82 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. 6B and Table S7), the most notably enriched substitution was N501Y, which showed an odds ratio of 2.04 (95% credible interval of 1.25-3.18). 2022 mBio Result SARS_CoV_2 N501Y 61 66 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. Among non-spike substitutions, the P199L substitution in the nucleocapsid showed notable depletion (Table S7). 2022 mBio Result SARS_CoV_2 P199L 35 40 N;S 61;10 73;15 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. Several additional substitutions in spike were potentially enriched (D614G, P681R, D950N), but the 95% credible interval included one, so the evidence for enrichment was weaker (Table S7). 2022 mBio Result SARS_CoV_2 D950N;P681R;D614G 83;76;69 88;81;74 S 36 41 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. Stepping back, these findings together emphasize the potential importance of the N501Y substitution in vaccine breakthrough. 2022 mBio Result SARS_CoV_2 N501Y 81 86 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. The N501Y substitution is found in multiple VBM, including alpha, beta, and gamma, and is reported to increase the affinity of spike protein binding to the ACE2 receptor and to diminish binding of some human antibodies to spike. 2022 mBio Result SARS_CoV_2 N501Y 4 9 S;S 127;222 132;227 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. The spike substitution P681H was also slightly enriched; this substitution is near the furin cleavage site and may promote efficient proteolysis. 2022 mBio Result SARS_CoV_2 P681H 23 28 S 4 9 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. Two other closely studied spike substitutions, E484K and L452R, were not notably enriched among vaccine breakthrough cases, and the D253G substitution was modestly depleted. 2022 mBio Result SARS_CoV_2 D253G;E484K;L452R 132;47;57 137;52;62 S 26 31 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Among them, F490S and L452Q are the key RBD mutations in Lambda making Lambda a more dangerous emerging variant than Delta. 2022 ACS infectious diseases Result SARS_CoV_2 F490S;L452Q 12;22 17;27 RBD 40 43 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Considering the BFE change and antibody disruptive count of comutation set [N501Y, A520S] is 0.699 and 27, we suggest monitoring this variant in IN and BE. 2022 ACS infectious diseases Result SARS_CoV_2 A520S;N501Y 83;76 88;81 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. First, the 10 most observed or fast-growing RBD mutations are N501Y, L452R, T478K, E484K, K417T, S477N, N439K, K417N, F490S, and S494P, as shown in Table 1. 2022 ACS infectious diseases Result SARS_CoV_2 E484K;F490S;K417N;K417T;L452R;N439K;N501Y;S477N;S494P;T478K 83;118;111;90;69;104;62;97;129;76 88;123;116;95;74;109;67;102;134;81 RBD 44 47 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. For 4 comutations in Figure 2c, [P384L, K417N, E484K, N501Y] (Beta plus) could penetrate all vaccines due to its highest antibody disruption count of 101. 2022 ACS infectious diseases Result SARS_CoV_2 E484K;K417N;N501Y;P384L 47;40;54;33 52;45;59;38 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Four RBD mutations, N501Y, L452R, F490S, and L452Q, appear in both lists and are key mutations in WHO's VOC and VOI lists. 2022 ACS infectious diseases Result SARS_CoV_2 F490S;L452Q;L452R;N501Y 34;45;27;20 39;50;32;25 RBD 5 8 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. From Figure 2, 3 comutation sets [R345K, E484K, N501Y] (Mu), [K417T, E484K, N501Y] (Gamma), and [K417N, E484K, N501Y] (Beta) draw our attention. 2022 ACS infectious diseases Result SARS_CoV_2 E484K;E484K;E484K;N501Y;N501Y;N501Y;K417N;K417T;R345K 41;69;104;48;76;111;97;62;34 46;74;109;53;81;116;102;67;39 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. From Figure 2, RBD 2 comutation set [L452R, T478K] (Delta variant) has the highest frequency (219 362) and the highest BFE change (1.575 kcal/mol). 2022 ACS infectious diseases Result SARS_CoV_2 T478K;L452R 44;37 49;42 RBD 15 18 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Further, [R346K, E484K, N501Y] (Mu variant) has a BFE change of 0.768 kcal/mol and high antibody disruption count (60). 2022 ACS infectious diseases Result SARS_CoV_2 E484K;N501Y;R346K 17;24;10 22;29;15 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Furthermore, high-frequency 2 comutation sets [E484K, N501Y], [F490S, N501Y], and [S494P, N501Y] are all considered to be the emerging variants that have the potential to escape vaccines. 2022 ACS infectious diseases Result SARS_CoV_2 N501Y;N501Y;N501Y;E484K;F490S;S494P 54;70;90;47;63;83 59;75;95;52;68;88 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Furthermore, the comutation set [K417N, T470N, E484K, N501T] that was first found in BR on April 06, 2020 has a BFE change of 0.625 kcal/mol and antibody disruption count 84 is an emerging vaccine breakthrough comutation in Brazil. 2022 ACS infectious diseases Result SARS_CoV_2 E484K;N501T;T470N;K417N 47;54;40;33 52;59;45;38 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. In addition, comutation set [L452Q, F490S] (cyan lines) on Lambda variant was recently drawing much attention due to its potential ability to resist vaccines and enhance the infectivity, which is consistent with our predictions that comutation set [L452Q, F490S] has a relatively significant BFE change of S protein and ACE2 (1.421 kcal/mol) and would reduce the RBD binding with 59 antibodies. 2022 ACS infectious diseases Result SARS_CoV_2 F490S;F490S;L452Q;L452Q 36;256;29;249 41;261;34;254 RBD;S 363;306 366;307 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. It can be seen that mutations L452R, E484K, K417T, K417N, F490S, and S494P disrupt more than 30% of antibody-RBD complexes, while mutations E484K and K417T may disrupt nearly 30% antibody-RBD complexes, indicating their disruptive ability to the efficacy and reliability of antibody therapies and vaccines. 2022 ACS infectious diseases Result SARS_CoV_2 E484K;E484K;F490S;K417N;K417T;K417T;L452R;S494P 37;140;58;51;44;150;30;69 42;145;63;56;49;155;35;74 RBD;RBD 109;188 112;191 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Later on, in early March 2021, the UK, US, DK, DE, NL, SE, IT, FR, BE reported the appearance of [L452R, T478K] in early March 2021, and eventually [L452R, T478K] became a dominant comutation, which is consistent to the finding that Delta variant remains largely susceptible to infection. 2022 ACS infectious diseases Result SARS_CoV_2 T478K;T478K;L452R;L452R 105;156;98;149 110;161;103;154 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Moreover, [L452Q, F490S] (Lambda) is another comutation with high frequency, high BFE changes (1.421 kcal/mol), and high antibody disruption count (59). 2022 ACS infectious diseases Result SARS_CoV_2 F490S;L452Q 18;11 23;16 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Moreover, comutation set [N501Y, A520S] has quickly increased IN and BE since April 16, 2021. 2022 ACS infectious diseases Result SARS_CoV_2 A520S;N501Y 33;26 38;31 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Notably, comutaion set [G446V, L452R, T478K] in the UK with BFE change of 1.733 kcal/mol and 46 antibody disruption counts appears to be a dangerous set of comutations that may affect the infectivity and vaccine/antibodies efficacy shortly. 2022 ACS infectious diseases Result SARS_CoV_2 L452R;T478K;G446V 31;38;24 36;43;29 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Note that high-frequency mutation S477N does not significantly weaken any antibody and RBD binding and thus does not appear in any prevailing variants. 2022 ACS infectious diseases Result SARS_CoV_2 S477N 34 39 RBD 87 90 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Second, among the top 25 most observed RBD mutations, T478K, L452Q, N440K, L452R, N501Y, N501T, F490S, A475V, and P384L are the 8 most infectious ones judged by their ability to strengthen the binding with ACE2, as shown in Figure 1c. 2022 ACS infectious diseases Result SARS_CoV_2 A475V;F490S;L452Q;L452R;N440K;N501T;N501Y;P384L;T478K 103;96;61;75;68;89;82;114;54 108;101;66;80;73;94;87;119;59 RBD 39 42 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. The BFE changes of S protein and ACE2 for mutation T478K is nearly 1.00 kcal/mol, which strongly enhances the binding of the RBD-ACE2 complex. 2022 ACS infectious diseases Result SARS_CoV_2 T478K 51 56 RBD;S 125;19 128;20 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. The comutation set [K417T, E484K, N501Y] (Gamma) with BFE change of 0.656 kcal/mol was first found in Brazil in early January 2021 and then it became the most dominant comutation in Brazil and Canada, and the second dominant comutation in the US, NL, SE, IT, FR, IN, and BE. 2022 ACS infectious diseases Result SARS_CoV_2 E484K;N501Y;K417T 27;34;20 32;39;25 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. The cyan line is for the RBD comutation set [L452Q, F490S] on the Lambda variant, which is more penetrative to vaccines than the Delta. 2022 ACS infectious diseases Result SARS_CoV_2 F490S;L452Q 52;45 57;50 RBD 25 28 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. The RBD comutation set [L452R, T478K] (Delta) with 1.575 kcal/mol BFE change was first found in IN in early January 2021, and the number of this variant increases rapidly around the world in a short period. 2022 ACS infectious diseases Result SARS_CoV_2 T478K;L452R 31;24 36;29 RBD 4 7 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Third, among the top 25 most observed RBD mutations, Y449S, S494P, K417N, F490S, L452R, E484K, K417T, E484Q, L452Q, and N501Y are the 10 most antibody disruptive ones, judged by their interactions with 130 antibodies shown in Figure 1c. 2022 ACS infectious diseases Result SARS_CoV_2 E484K;E484Q;F490S;K417N;K417T;L452Q;L452R;N501Y;S494P;Y449S 88;102;74;67;95;109;81;120;60;53 93;107;79;72;100;114;86;125;65;58 RBD 38 41 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Together with L452R (BFE change: 0.58 kcal/mol), T478K makes Delta the most infectious variant in VOCs. 2022 ACS infectious diseases Result SARS_CoV_2 L452R;T478K 14;49 19;54 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. We anticipate that although comutation sets [V401L, L452R, T478K], [L452R, T478K, N501Y], [A411S, L452R, T478K], and [L452R, T478K, E484K, N501Y] have relatively low frequencies at this point, they may become dangerous variants soon due to their large BFE changes and antibody disruption counts. 2022 ACS infectious diseases Result SARS_CoV_2 E484K;L452R;L452R;N501Y;N501Y;T478K;T478K;T478K;T478K;A411S;L452R;L452R;V401L 132;52;98;82;139;59;75;105;125;91;68;118;45 137;57;103;87;144;64;80;110;130;96;73;123;50 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. We would like to address that all of the comutation sets, except for [Y449S, N501Y] in Figure 2, have positive BFE changes, following the natural selection. 2022 ACS infectious diseases Result SARS_CoV_2 N501Y;Y449S 77;70 82;75 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. With a BFE change of 1.4 kcal/mol and antibody disruption count of 82, comutation set [K417N, L452R, T478K] (Delta plus) appears to be more dangerous than all of the current VOCs and VOIs. 2022 ACS infectious diseases Result SARS_CoV_2 L452R;T478K;K417N 94;101;87 99;106;92 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Further, the Delta variant lysine substitution at position 478 (T478K) extends its positively charged sidechain towards an electronegative region on ACE2 (centred at position E87). 2022 Nature communications Result SARS_CoV_2 T478K 64 69 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. However, the enhanced electrostatic complementarity afforded by the accompanying L452R mutation, as described previously, may present a compensatory mutation accounting for the lost E484-K31 interaction. 2022 Nature communications Result SARS_CoV_2 L452R 81 86 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Interestingly, we observed enhanced potency of ab1 for both Kappa and Delta variant spikes relative to wild-type, despite the presence of the Kappa T478K mutation which falls within the ab1 footprint. 2022 Nature communications Result SARS_CoV_2 T478K 148 153 S 84 90 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Precedence for compensatory mutations towards increasing ACE2 affinity while decreasing antibody binding has been reported for the N501Y and K417N/T mutational combinations found in the Beta and Gamma variants. 2022 Nature communications Result SARS_CoV_2 K417N;K417T;N501Y 141;141;131 148;148;136 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The combination of these two opposing mutations, one diminishing ACE2 affinity (E484Q), and the other increasing ACE2 binding (L452R), is consistent with the unchanged overall affinity of the Kappa S protein-ACE2 binding interaction. 2022 Nature communications Result SARS_CoV_2 E484Q;L452R 80;127 85;132 S 198 199 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The cryo-EM 3D reconstruction of the Delta spike reveals no large-scale structural changes, with the predominant conformation having one RBD in the up position, as found in the wild-type (D614G) construct. 2022 Nature communications Result SARS_CoV_2 D614G 188 193 S;RBD 43;137 48;140 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The cryo-EM reconstruction of Q484A spikes revealed no evidence of dimer-of-trimer assemblies, consistent with our previous results for wild-type and other variant of concern (VoC) spikes. 2022 Nature communications Result SARS_CoV_2 Q484A 30 35 S;S 36;181 42;187 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The cryo-EM reconstruction yielded a dimer-of-trimers phenotype for the Kappa + Q484I S protein variant, yet, with a reduced number of picked particles comprising the dimer class (46%), relative to the original Kappa variant with Q484 (74%). 2022 Nature communications Result SARS_CoV_2 Q484I 80 85 S 86 87 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The Delta variant lacks the E484Q substitution which preserves the E484-K31 electrostatic interaction, while the common L452R mutation may increase ACE2 binding by enhancing electrostatic complementarity. 2022 Nature communications Result SARS_CoV_2 E484Q;L452R 28;120 33;125 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The Kappa and Kappa + Q484I dimer-of-trimers are structurally very similar, with RMSD values of 0.262 A and 0.705 A for the global and focus-refined atomic models, respectively. 2022 Nature communications Result SARS_CoV_2 Q484I 22 27 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The Kappa variant E484Q mutation results in the loss of an electrostatic interaction between residue E484 and residue K31 within ACE2, likely resulting in a weaker interaction at this site. 2022 Nature communications Result SARS_CoV_2 E484Q 18 23 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The oligomerization state of S proteins harbouring charged residues at 484 (E484, K484), along with the Q484A and Q484I mutations demonstrate that abrogation of charge at position 484 is necessary but not sufficient to permit dimerisation. 2022 Nature communications Result SARS_CoV_2 Q484A;Q484I 104;114 109;119 S 29 30 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Therefore, the combination of enhanced electrostatic complementarity afforded by the L452R and T478K Delta variant substitutions likely accounts for the moderate increase in ACE2 affinity. 2022 Nature communications Result SARS_CoV_2 L452R;T478K 85;95 90;100 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. This latter interaction at position 484 is of particular interest as it is uniquely mutated from glutamic acid to glutamine (E484Q) in the Kappa variant. 2022 Nature communications Result SARS_CoV_2 E484Q 125 130 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. To test this, we performed site-directed mutagenesis to substitute an alanine at position 484 (Q484A) in the Kappa S protein, purified the trimer, and performed structural studies. 2022 Nature communications Result SARS_CoV_2 Q484A 95 100 S 115 116 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. We have previously demonstrated the sensitivity of ab8 and S2M11 to the E484K mutation, wherein both antibodies were fully escaped. 2022 Nature communications Result SARS_CoV_2 E484K 72 77 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. We therefore hypothesised that charge neutrality at position 484 (as seen in the Q484, but not E484 or the recently emerged K484 S proteins) may be sufficient to reduce charge-charge repulsion at this site and therefore allow dimerisation. 2022 Nature communications Result SARS_CoV_2 K484S 124 130 S 129 130 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. While total escape of ab8 was achieved by the E484Q-bearing Kappa variant spike, binding and neutralisation of S2M11 was attenuated but not abolished. 2022 Nature communications Result SARS_CoV_2 E484Q 46 51 S 74 79 35136839 Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike. DM2 with Y489S T500S showed same number of interacting sites as compared to SM3. 2022 Translational medicine communications Result SARS_CoV_2 T500S;Y489S 15;9 20;14 35136839 Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike. DM3 with Y489S T500Y, DM4 with Y489S T500Y and DM5 with Y453S T500Y, all showed fewer interacting sites as compared to DM2 (S Table 3) with no interaction at the mutated sites (S. 2022 Translational medicine communications Result SARS_CoV_2 T500Y;T500Y;T500Y;Y453S;Y489S;Y489S 15;37;62;56;9;31 20;42;67;61;14;36 S;S 124;177 125;178 35136839 Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike. Double Mutation 1(DM1) with Y489S Y453S showed no interaction at the mutated site and comparatively at lesser interacting sites as compared to SM3 hence, those were rejected for further study. 2022 Translational medicine communications Result SARS_CoV_2 Y453S;Y489S 34;28 39;33 35136839 Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike. In single mutation Y489S, Y453S and T500Y did not show proper interactions (S Table 3) and hence were rejected for further study. 2022 Translational medicine communications Result SARS_CoV_2 T500Y;Y453S;Y489S 36;26;19 41;31;24 S 76 77 35136839 Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike. TM2 with Y489S, Y453S, T500Y though had same number of interacting sites as TM1 (S. 2022 Translational medicine communications Result SARS_CoV_2 T500Y;Y453S;Y489S 23;16;9 28;21;14 S 81 82 35136839 Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike. Triple Mutation 1(TM1) with Y489S Y453S T500S mutation also showed no interaction at the mutation site hence not considered for further study. 2022 Translational medicine communications Result SARS_CoV_2 T500S;Y453S;Y489S 40;34;28 45;39;33 35136839 Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike. Whereas, T500S mutation showed hydrogen bonding with TYR41 of ACE2, which mimicked the actual ACE2-nCOV2 spike-binding features. 2022 Translational medicine communications Result SARS_CoV_2 T500S 9 14 S 105 110 35139271 Final Analysis of Efficacy and Safety of Single-Dose Ad26.COV2.S. Vaccine efficacy against severe-critical Covid-19 was 93.1% (95% CI, 54.4 to 99.8) for the reference strain; 71.8% (95% CI, 56.3 to 82.3) for non-reference strain SARS-CoV-2 lineages, including "other" sequences with the E484K mutation; 78.4% (95% CI, 34.5 to 94.7) for the beta variant; 63.6% (95% CI, 18.8 to 85.1) for the gamma variant; 67.6% (95% CI, -29.8 to 94.4) for the lambda variant; and 79.5% (95% CI, 38.5 to 94.9) for the mu variant. 2022 The New England journal of medicine Result SARS_CoV_2 E484K 221 226 COVID-19 41 49 35139271 Final Analysis of Efficacy and Safety of Single-Dose Ad26.COV2.S. Vaccine efficacy was 70.2% (95% CI, 35.3 to 87.6) against moderate to severe-critical Covid-19 caused by the B.1.1.7 (alpha) variant; 69.0% (95% CI, 59.1 to 76.8) against moderate to severe-critical Covid-19 caused by SARS-CoV-2 classified as "other," with efficacy remaining stable through 195 days of follow-up; and 58.2% (95% CI, 35.0 to 73.7) against moderate to severe-critical Covid-19 caused by the reference strain (B.1.D614G). 2022 The New England journal of medicine Result SARS_CoV_2 D614G 428 433 COVID-19;COVID-19;COVID-19 86;199;383 94;207;391 35139368 Long-term, infection-acquired immunity against the SARS-CoV-2 Delta variant in a hamster model. A prototypical virus (SARS-CoV-2/UT-HP095-1N/Human/2020/Tokyo; HP095 S-614G) with only the D614G substitution in its spike protein was used as a reference virus to compare changes in neutralization titers against an isolate of the Delta variant (hCoV-19/USA/WI-UW-5250/2021). 2022 Cell reports Result SARS_CoV_2 D614G 91 96 S;S 117;69 122;70 35139368 Long-term, infection-acquired immunity against the SARS-CoV-2 Delta variant in a hamster model. Hamsters (female, 1 month old; n = 8) were infected via intranasal inoculation with 1,000 plaque-forming units (pfu) of SARS-CoV-2 USA-WA1/2020, an early isolate with an aspartic acid (D) at amino acid position 614 of the spike protein (WA-1 S-614D). 2022 Cell reports Result SARS_CoV_2 D614D 169 215 S;S 222;242 227;243 35139811 Linked nosocomial COVID-19 outbreak in three facilities for people with intellectual and developmental disabilities due to SARS-CoV-2 variant B.1.1.519 with spike mutation T478K in the Netherlands. Since the B1.1.519 lineage harbors a few mutations of interest in the spike protein including the T478K mutation (Additional file 1: Figure S1) and the P681H mutation as established in several other lineages, including the B.1.1.7 variant, we studied whether samples harboring this genotype contained higher viral loads compared to isolates belonging to the B.1.1.7 or other variants. 2022 BMC infectious diseases Result SARS_CoV_2 P681H;T478K 152;98 157;103 S 70 75 35140714 Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. Among 15 substituted amino acids, K417N and Y505H exhibited a slight reduction in binding energy due to the breakage of salt bridges between K417 of the RBD and D30 of ACE2; nonetheless, this breakage was compensated by the salt bridge between E35 of ACE2 and Q493K substitution in RBDOmic ( Figure 2C , right panel). 2021 Frontiers in immunology Result SARS_CoV_2 K417N;Q493K;Y505H 34;260;44 39;265;49 RBD 153 156 35140714 Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. By contrast, N501Y slightly strengthens the binding, establishing a hydrogen bond with D57 in CDRH2 ( Figure 4B ). 2021 Frontiers in immunology Result SARS_CoV_2 N501Y 13 18 35140714 Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. However, by performing endpoint molecular mechanics generalized born surface area (MMGBSA) binding free energy calculation, we could demonstrate a substantial increase in the binding affinity by T478K, Q493K, and Q498R, leading to an overall increase in the binding affinity of the RBDOmic with ACE2 (DeltaGWT = -64.65 kcal/mol < DeltaGOmic = -83.79 kcal/mol; Supplementary Figure 1A ). 2021 Frontiers in immunology Result SARS_CoV_2 Q493K;Q498R;T478K 202;213;195 207;218;200 35140714 Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. In addition, energy perturbation per amino acid could confirm that the four amino acids, i.e., N440K, T478K, Q493K, and Q498R, directly contribute to the change of the total energy and the electrostatic potential, whereas K417N and E484A compensate the energy change ( Figure 2C ). 2021 Frontiers in immunology Result SARS_CoV_2 E484A;K417N;N440K;Q493K;Q498R;T478K 232;222;95;109;120;102 237;227;100;114;125;107 35140714 Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. Similarly, the hotspots in CDRL1 and CDRH3 lost their bindings due to the mutations of E484A, Q493K, and Y505H in RBDOmic. 2021 Frontiers in immunology Result SARS_CoV_2 E484A;Q493K;Y505H 87;94;105 92;99;110 35140714 Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. To investigate how sotrovimab retains its neutralization efficacy, we constructed the RBDOmic-sotrovimab model and found that sotrovimab binds to a highly conserved epitope on the RBD and, among 15 mutations in the RBDOmic, faces only G339D mutation. 2021 Frontiers in immunology Result SARS_CoV_2 G339D 235 240 RBD 180 183 35140714 Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. We also investigated the change in electrostatic potential of the RBDOmic relative to that of RBDWT because the five residues in the RBM region of RBD are mutated from the polar to the positively charged residues (i.e., N440K, T478K, Q493K, Q498R, and Y505H). 2021 Frontiers in immunology Result SARS_CoV_2 N440K;Q493K;Q498R;T478K;Y505H 220;234;241;227;252 225;239;246;232;257 RBD 147 150 35140714 Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. We observed that two hotspots, i.e., R96 in CDRL3 and R50 in CDRH2 of bamlanivimab, established highly stable salt bridges with the E484 of RBDWT, losing their binding entirely upon E484A mutation in RBDOmic ( Figure 4A ). 2021 Frontiers in immunology Result SARS_CoV_2 E484A 182 187 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. Comparing the number of HLA-I alleles predicted to bind REF and VOI-derived peptides, we observed that peptides derived from the two deletions in S (69-70del, Y144del) lack the ability to bind to the HLA alleles set (Supplementary Table S3. 2022 Infection, genetics and evolution Result SARS_CoV_2 Y144del 159 166 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. Importantly, six out of the 22 remaining nsSNVs in protein S generated fewer peptide:HLA pairs when compared to the REF sequence, and two of them (A570D and D614G) generated less than half the number of binders compared to the respective REF sequences. 2022 Infection, genetics and evolution Result SARS_CoV_2 D614G;A570D 157;147 162;152 S 59 60 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. In contrast, a significantly stronger binding (lower %Rank) was observed for peptides derived from the nsSNVs D138Y and N501Y. 2022 Infection, genetics and evolution Result SARS_CoV_2 D138Y;N501Y 110;120 115;125 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. In contrast, nsSNVs T205I and Y144del showed lower antigenicity scores. 2022 Infection, genetics and evolution Result SARS_CoV_2 T205I;Y144del 20;30 25;37 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. In contrast, peptides derived from E484K exhibited weaker binding compared to the respective REF-derived peptides. 2022 Infection, genetics and evolution Result SARS_CoV_2 E484K 35 40 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. Notably, the nsSNV N501Y generated four times more binders than the REF sequence. 2022 Infection, genetics and evolution Result SARS_CoV_2 N501Y 19 24 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. We observed that the nsSNVs P80R, A701V, K417N, K417T, L18F, and R246I had greater antigenicity scores in regard to the REF sequence. 2022 Infection, genetics and evolution Result SARS_CoV_2 A701V;K417N;K417T;L18F;P80R;R246I 34;41;48;55;28;65 39;46;53;59;32;70 35151002 Rapid biosensing SARS-CoV-2 antibodies in vaccinated healthy donors. FO-BLI biosensors for detection of SARS-CoV-2-specific BAbs towards RBD, S-ECD, and RBD-N501Y in 100-fold diluted serum. 2022 Biosensors & bioelectronics Result SARS_CoV_2 N501Y 88 93 RBD;RBD;S 68;84;73 71;87;74 35151002 Rapid biosensing SARS-CoV-2 antibodies in vaccinated healthy donors. The assay conditions of the FO-BLI biosensors for the detection of SARS-CoV-2-specific BAbs towards S-ECD, RBD, and RBD-N501Y, respectively, in both buffer and serum, are summarized in Table 1 , with the principles elaborated in. 2022 Biosensors & bioelectronics Result SARS_CoV_2 N501Y 120 125 RBD;RBD;S 107;116;100 110;119;101 35151002 Rapid biosensing SARS-CoV-2 antibodies in vaccinated healthy donors. Using these defined parameters, calibration curves for specific anti-RBD, anti-ECD, and anti-RBD N501Y BAbs were generated by spiking a series of concentrations of MA-RBD S309 ranging from 0 to 500 ng/mL into 100-fold serum. 2022 Biosensors & bioelectronics Result SARS_CoV_2 N501Y 97 102 RBD;RBD;RBD 69;93;167 72;96;170 35155280 The Impact of Accumulated Mutations in SARS-CoV-2 Variants on the qPCR Detection Efficiency. Among the 5 main epidemic strains, we also found that G22813T was in Beta and Omicron variant, A22812C was in Gamma variant, and C21762T was in Omicron variant, accounting for 92.6%, 99.6% and 98.5% respectively. 2022 Frontiers in cellular and infection microbiology Result SARS_CoV_2 A22812C;C21762T;G22813T 95;129;54 102;136;61 35155280 The Impact of Accumulated Mutations in SARS-CoV-2 Variants on the qPCR Detection Efficiency. In the currently most prevalent SARS-CoV-2 variant, the Delta variant, we found that there are 166809 sequences where the G at position 28916 was mutated to T, among the 211740 sequences in total, accounting for 78.78%. 2022 Frontiers in cellular and infection microbiology Result SARS_CoV_2 G28916T 122 158 35155280 The Impact of Accumulated Mutations in SARS-CoV-2 Variants on the qPCR Detection Efficiency. Meanwhile, mutation G28913T and C28849T were found in Lambda variant, accounting for 96.52% and 26.38% respectively, which also affect the detection efficiency of CP4 and CP5 ( Table 1 ). 2022 Frontiers in cellular and infection microbiology Result SARS_CoV_2 C28849T;G28913T 32;20 39;27 35155280 The Impact of Accumulated Mutations in SARS-CoV-2 Variants on the qPCR Detection Efficiency. Mutation C23604A was found in Alpha, Omicron and Mu variants, mutation C23604G was found in Delta variant, and mutation T23599G was found in Omicron variant, accounting for more than 99% of the total sequences. 2022 Frontiers in cellular and infection microbiology Result SARS_CoV_2 C23604A;C23604G;T23599G 9;71;120 16;78;127 35155280 The Impact of Accumulated Mutations in SARS-CoV-2 Variants on the qPCR Detection Efficiency. The G28916T Mutation in the Delta Variant Severely Affected the Detection Efficiency and Detection Limit of the Primer/Probe Set of CP4 and CP5. 2022 Frontiers in cellular and infection microbiology Result SARS_CoV_2 G28916T 4 11 35155280 The Impact of Accumulated Mutations in SARS-CoV-2 Variants on the qPCR Detection Efficiency. Therefore, we generated the G28916T mutation on the N gene template. 2022 Frontiers in cellular and infection microbiology Result SARS_CoV_2 G28916T 28 35 N 52 53 35155280 The Impact of Accumulated Mutations in SARS-CoV-2 Variants on the qPCR Detection Efficiency. This showed that the mutation of G28916T in Delta variant increases the detection limit of the N gene primer/probe set of CP4 and CP5 by 10 times. 2022 Frontiers in cellular and infection microbiology Result SARS_CoV_2 G28916T 33 40 N 95 96 35155280 The Impact of Accumulated Mutations in SARS-CoV-2 Variants on the qPCR Detection Efficiency. We found that if the G28916T was matched with primer sequence, the detection efficiency of qPCR was not affected ( Figures 3A, B ). 2022 Frontiers in cellular and infection microbiology Result SARS_CoV_2 G28916T 21 28 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. 3 , the analysis of residues found no drastic effects of the mutation S:T1117I on the spike in a co-evolutionary context using mutual information and residues conservation models. 2022 Gene reports Result SARS_CoV_2 T1117I 72 78 S;S 86;70 91;71 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. A total of 1155 SARS-CoV-2 sequences were found with the mutation S:T1117I in 54 countries worldwide until April 30th, 2020. 2022 Gene reports Result SARS_CoV_2 T1117I 68 74 S 66 67 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. Due to Costa Rica is part of the top 3 countries reporting more genomes with S:T1117I (with 126 sequences), those genomes are part of the local lineage B.1.1.389, and the last was the predominant group according to the cumulative prevalence in this country during 2020 and early 2021, we followed our analysis studying this genotype and this mutation. 2022 Gene reports Result SARS_CoV_2 T1117I 79 85 S 77 78 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. Finally, to describe the effect of the mutation S:T1117I on the immune activity, an immunoinformatic approach to study peptides was performed. 2022 Gene reports Result SARS_CoV_2 T1117I 50 56 S 48 49 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. However, among all the sequenced genomes for the United States and England, the cumulative prevalence for genomes carrying S:T1117I is <0.5%, whereas for Costa Rica represents 22% of the sequenced cases up to April 30th, 2020. 2022 Gene reports Result SARS_CoV_2 T1117I 125 131 S 123 124 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. In order to analyze the evolutionary context of the mutation S:T1117I and its relation with all the available genomes, we aligned all the 407 spike sequences from SARS-CoV-2 genomes from Costa Rica (with or without the mutation). 2022 Gene reports Result SARS_CoV_2 T1117I 63 69 S;S 142;61 147;62 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. In this sense, the corrected Mutual Information (MI) was used to identify correlations between positions and the possible effect on the structure or function of the protein, revealing that the most impacted region (orange connections) are part of the RBD (positions 319-541), including the case of the mutation N501Y. 2022 Gene reports Result SARS_CoV_2 N501Y 311 316 RBD 251 254 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. including the D614G and T1117I in the spike. 2022 Gene reports Result SARS_CoV_2 D614G;T1117I 14;24 19;30 S 38 43 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. Mutation S:T1117I found in the Costa Rican lineage B.1.1.389 is product of natural selection, with some effects on the activity of the function and interactions of the spike protein. 2022 Gene reports Result SARS_CoV_2 T1117I 11 17 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. SARS-CoV-2 genomes harboring the mutation S:T1117I define a polyphyletic group with multiple lineages around the world, including the lineage B.1.1.389 as a local genotype. 2022 Gene reports Result SARS_CoV_2 T1117I 44 50 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. Tellingly, the sites 501 and 1118, corresponding to the mutations S:N501Y and S:D1118H present in the lineage B.1.1.7, and 1117, site of the mutation of our interest, were included. 2022 Gene reports Result SARS_CoV_2 D1118H;N501Y 80;68 86;73 S;S 66;78 67;79 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. The WT sequence and the mutated version with both mutations S:D614 and S:T1117I (spike sequence for the B.1.1.389 genomes) were considered for the docking with nelfinavir drug as ligand. 2022 Gene reports Result SARS_CoV_2 T1117I 73 79 S;S;S 81;60;71 86;61;72 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. Similarly, we also found that the I82T mutation in the Data ref: Membrane protein, is highly conserved across 92 homologous protein sequences from coronaviruses. 2022 Molecular systems biology Result SARS_CoV_2 I82T 34 38 Membrane 65 73 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. Strikingly, all these mutations except P323L in NSP12 are nearly exclusive to the Delta variant compared to other variants of concern (Alpha, Beta, and Gamma variants of SARS-CoV-2) (mean prevalenceDelta = 99.74%, mean prevalenceotherVariantsofConcern = 0.12%) (Fig EV2, Appendix Table S1). 2022 Molecular systems biology Result SARS_CoV_2 P323L 39 44 Nsp12 48 53 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. The mutations in the functionally important positions in DeltaUnitedStates:Spike G142D, E156G, DeltaF157, DeltaR158 mutations:map to the antigenic supersite (Cerutti et al,), possibly lead to immune evasion, and thus increase the virulence of this variant. 2022 Molecular systems biology Result SARS_CoV_2 DeltaF157;E156G;G142D 95;88;81 104;93;86 S 75 80 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. We found the R203 M mutation in the Nucleocapsid protein to be highly conserved across 139 homologous protein sequences from coronaviruses. 2022 Molecular systems biology Result SARS_CoV_2 R203M 13 19 N 36 48 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. We found the T492I mutation in the Nsp4C domain (possibly involved in protein-protein interactions; Data ref: Annotation rule,) of the NSP4 protein is highly conserved across 139 homologous protein sequences from coronaviruses. 2022 Molecular systems biology Result SARS_CoV_2 T492I 13 18 Nsp4 135 139 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. We identified seven highly prevalent mutations in the following proteins of the Delta variant: Membrane (I82T: 99.9%), Nucleocapsid (R203 M: 99.9%, D377Y: 99.6%), NSP12 (P323L: 99.9%), NS3 (S26L: 99.9%), and NS7a (V82A: 99.4%, T120I: 99.7%). 2022 Molecular systems biology Result SARS_CoV_2 D377Y;T120I;I82T;P323L;R203M;S26L;V82A 148;227;105;170;133;190;214 153;232;109;175;139;194;218 N;Membrane;Nsp12;NS3 119;95;163;185 131;103;168;188 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. Within the Spike protein, there are four such mutations (T19R, L452R, T478K, and P681R) as well (mean prevalenceDelta = 99.86%, mean prevalenceotherVariantsofConcern = 0.04%). 2022 Molecular systems biology Result SARS_CoV_2 L452R;P681R;T478K;T19R 63;81;70;57 68;86;75;61 S 11 16 35162151 Shorter Incubation Period among Unvaccinated Delta Variant Coronavirus Disease 2019 Patients in Japan. In 120 symptomatic patients with the L452R variant from 72 infectors, the mean incubation period was 3.7 days, and in 100 symptomatic patients with non-Delta strains, the mean incubation period was 4.9 days; the difference was significant (p-value = 0.000). 2022 International journal of environmental research and public health Result SARS_CoV_2 L452R 37 42 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. According to our analysis, there is a greater degree of mutational and conformational plasticity near the D614G position that could allow for greater variability and diversity of the open states. 2022 International journal of molecular sciences Result SARS_CoV_2 D614G 106 111 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Although modifications of A570D are generally destabilizing, the range of free-energy changes associated with this position suggested a moderate level of residual energetic frustration and suboptimal interactions (Figure 8). 2022 International journal of molecular sciences Result SARS_CoV_2 A570D 26 31 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Another interesting observation is the emergence of A570D and D614G mutational sites as the key inter-protomer hinges that can orchestrate functional movements in the S-B.1.1.7 conformations (Figure 6C,D). 2022 International journal of molecular sciences Result SARS_CoV_2 A570D;D614G 52;62 57;67 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. At the same time, E484K and N501Y sites are prominently featured among local maxima for the S-B.1.351 profiles (Figure 5E,F) and may experience functional changes due to movements of the RBDs. 2022 International journal of molecular sciences Result SARS_CoV_2 E484K;N501Y 18;28 23;33 RBD;S 187;92 191;93 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. At the same time, structural maps for the S-B.1.351 conformations (Figure 6E,F) highlighted the role of the NTD sites (L18F, D80A, D215G) and especially RBD sites (K417N, E484K, N501Y) that belong to the moving regions in slow motions. 2022 International journal of molecular sciences Result SARS_CoV_2 D215G;D80A;E484K;N501Y;K417N;L18F 131;125;171;178;164;119 136;129;176;183;169;123 RBD 153 156 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. At the same time, the functional RBD sites K417, E484, and N501Y become solvent-exposed, particularly E484 and N501Y positions with RSA > 70% (Figure 4C,D). 2022 International journal of molecular sciences Result SARS_CoV_2 N501Y;N501Y 59;111 64;116 RBD 33 36 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. At the same time, the key hinge position A570D showed a similar relative density of neutral and minimal frustration. 2022 International journal of molecular sciences Result SARS_CoV_2 A570D 41 46 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Collective Modes of the SARS-CoV-2 S Protein Variants Reveal Role of A570D and D614G in the Hinge Regions Controlling Transitions between Open and Closed States. 2022 International journal of molecular sciences Result SARS_CoV_2 A570D;D614G 69;79 74;84 S 35 36 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Combined with modulation of the inter-protomer hinge regions by A570D and D614G positions, the local frustration in the RBD mutational sites could drive dynamical transitions between closed and open states, accompanied by local adjustments of the RBD residues. 2022 International journal of molecular sciences Result SARS_CoV_2 A570D;D614G 64;74 69;79 RBD;RBD 120;247 123;250 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Combined with the collective dynamics analysis, these observations suggest that moderately-to-minimally frustrated A570 and A570D hinge positions may allow for conformational switches at the inter-protomer interfaces that drive functional transitions. 2022 International journal of molecular sciences Result SARS_CoV_2 A570D 124 129 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Functional dynamics analysis of slow modes confirmed the role of A570D as a potential regulatory switch that controls RBD movements. 2022 International journal of molecular sciences Result SARS_CoV_2 A570D 65 70 RBD 118 121 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Furthermore, the minimal frustration density distributions for A570D in the open state of the S-B.1.1.7 variant (Figure 7D-F) are also very similar to the corresponding frustration densities for A570 in the S-G614 open state (Figure 7A-C). 2022 International journal of molecular sciences Result SARS_CoV_2 A570D 63 68 S 207 208 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. In agreement with the experimental studies, N501Y may become less frustrated in the open state of the S-B.1.351 variant (Figure 9B) and allow for more optimal interactions of the RBD-up protomer with the host receptor. 2022 International journal of molecular sciences Result SARS_CoV_2 N501Y 44 49 RBD;S 179;102 182;103 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. In both states of S-B.1.351 variant, we observed appreciable destabilization changes induced by modifications in the D614G position (Figure 9). 2022 International journal of molecular sciences Result SARS_CoV_2 D614G 117 122 S 18 19 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. In particular, we found that S-G614 and S-B.1.1.7 conformations displayed a broad stabilization in both S1 and S2 subunits but pointed to plasticity at the inter-protomer interfaces particularly near D614G site. 2022 International journal of molecular sciences Result SARS_CoV_2 D614G 200 205 S;S 29;40 30;41 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. In some contrast, mutations in the functional RBD positions (K417, E484) and modifications of mutational variant sites T716I, S982A and D1118H resulted in minor energy changes in both closed (Figure 8A) and open S-B.1.1.7 conformations (Figure 8B). 2022 International journal of molecular sciences Result SARS_CoV_2 D1118H;S982A;T716I 136;126;119 142;131;124 RBD 46 49 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. In the closed S-B.1.1.7 states A570D can form the inter-protomer interactions with K964 and N856 that together comprise an important hinge cluster. 2022 International journal of molecular sciences Result SARS_CoV_2 A570D 31 36 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. In this S-B.1.1.7-specific switch, A570D forms the inter-protomer salt bridges with K854 and K964 that compensate for the loss of the salt bridge between D614 and K854 due to the D614G mutation. 2022 International journal of molecular sciences Result SARS_CoV_2 A570D;D614G 35;179 40;184 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Indeed, for the S-B.1.1.7 conformations, mutational positions D614G, S982A, D1118H are mostly neutrally frustrated (Figure 7E). 2022 International journal of molecular sciences Result SARS_CoV_2 D1118H;D614G;S982A 76;62;69 82;67;74 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Interestingly, mutational scanning of A570D and D614G produced relatively few destabilization changes in the open state (Figure 8B). 2022 International journal of molecular sciences Result SARS_CoV_2 A570D;D614G 38;48 43;53 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Interestingly, S982A substitution in the S-B.1.1.7 conformations abolished hydrogen bonding between central helices of the S2 domain and the CTD1 region. 2022 International journal of molecular sciences Result SARS_CoV_2 S982A 15 20 S 41 42 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Interestingly, substitutions in the D614G position are more destabilizing in both closed and open S-B.1.1.7 states (Figure 8), pointing to dynamic rearrangements near D614G position. 2022 International journal of molecular sciences Result SARS_CoV_2 D614G;D614G 36;167 41;172 S 98 99 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Interestingly, there is a clear difference in the mutational map for the N501Y position (Figure 9). 2022 International journal of molecular sciences Result SARS_CoV_2 N501Y 73 78 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Moderate free-energy changes are also seen for K417N and E484K sites in the closed and open states. 2022 International journal of molecular sciences Result SARS_CoV_2 E484K;K417N 57;47 62;52 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Mutational scanning maps for variant positions in the S-B.1.351 conformations showed similar and moderate stabilization changes for the NTD variant L18F, D80A, and D215G. 2022 International journal of molecular sciences Result SARS_CoV_2 D215G;D80A;L18F 164;154;148 169;158;152 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Mutational Scanning of Protein Stability of the SARS-CoV-2 S-614 Conformational States Reveals Energetic Effects of the D614G Mutation. 2022 International journal of molecular sciences Result SARS_CoV_2 D614G 120 125 S 59 60 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Mutational site A701V is located in the surface-exposed region of S2 and caused minimal structural changes. 2022 International journal of molecular sciences Result SARS_CoV_2 A701V 16 21 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Notably, the degree of solvent exposure for the mutated RBD sites K417N, E484K, and N501Y appreciably increased in the S-B.1.351 states, particularly in the open form featuring RSA = 96% for E484K and RSA = 68% for N501Y positions (Figure 4E,F). 2022 International journal of molecular sciences Result SARS_CoV_2 E484K;E484K;K417N;N501Y;N501Y 73;191;66;84;215 78;196;71;89;220 RBD;S 56;119 59;120 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Strikingly, in both closed and open states of the S-B.1.1.7 variant, A570D and S982A positions remain completely buried, featuring RSA < 10% (Figure 4C,D). 2022 International journal of molecular sciences Result SARS_CoV_2 A570D;S982A 69;79 74;84 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Strikingly, the positions of mutational changes A570D, D614G, T716I, S982A in the S-B.1.1.7 states (Figure 5C,D) and positions D614G and A701V in the S-B.1.351 conformations (Figure 5E,F) are aligned with the local minima along slow mode displacement profiles and correspond to immobilized positions in slow motions. 2022 International journal of molecular sciences Result SARS_CoV_2 A570D;A701V;D614G;D614G;S982A;T716I 48;137;55;127;69;62 53;142;60;132;74;67 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. The increased mobility of mutational sites is particularly apparent in the open state of the S-B.1.351 variant (Figure 3F), where all the modified positions L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G, and A701V displayed a significant plasticity. 2022 International journal of molecular sciences Result SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;L18F;N501Y;R246I 215;169;204;163;190;183;157;197;176 220;174;209;167;195;188;161;202;181 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. The mutational cartography analysis revealed that A570D and D614G mutational positions in the S-B.1.1.7 conformations are the most sensitive to modifications that result in more significant destabilizing changes (Figure 8). 2022 International journal of molecular sciences Result SARS_CoV_2 A570D;D614G 50;60 55;65 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. The results of mutational scanning are supportive of the local frustration analysis that displayed neutral-to-minimal frustration densities for A570D and D614G positions in the S-B.1.1.7 state. 2022 International journal of molecular sciences Result SARS_CoV_2 A570D;D614G 144;154 149;159 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. The results offer an interesting rationale for the important role of A570D and D614G mutational sites in the S-B.1.1.7 and S-B.1.351 variants. 2022 International journal of molecular sciences Result SARS_CoV_2 A570D;D614G 69;79 74;84 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. The S-B.1.1.7 open state featured a salt bridge involving interactions of A570D with K854 of the other protomer. 2022 International journal of molecular sciences Result SARS_CoV_2 A570D 74 79 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. These findings are consistent with a series of structural studies showing a moderate degree of conformational heterogeneity in the interprotomer interactions formed by A570D in different substates of the S-B.1.1.7 protein. 2022 International journal of molecular sciences Result SARS_CoV_2 A570D 168 173 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. These results are also consistent with the experiments showing that N501Y, T716I and D1118H mutations induce only minimal local conformational changes without affecting stability of the S protein. 2022 International journal of molecular sciences Result SARS_CoV_2 D1118H;N501Y;T716I 85;68;75 91;73;80 S 186 187 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. This is consistent with the experimental structural studies showing that A570D and D614G favor the acquisition of the open S-B.1.1.7 state. 2022 International journal of molecular sciences Result SARS_CoV_2 A570D;D614G 73;83 78;88 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. This is consistent with the experimental studies showing that A570D and D614G hinge positions in the S-B.1.1.7 protein form a molecular switch that incurs allosteric structural changes that can enhance the RBD motions. 2022 International journal of molecular sciences Result SARS_CoV_2 A570D;D614G 62;72 67;77 RBD 206 209 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. This minimal-to-neutral frustration level for A570D and D614G substitutions in the S-B.1.1.7 and S-B.1.351 conformations could allow for some mutational adaptability in the hinge position, which retains its regulatory role in the S variants, as confirmed by the structural and functional studies. 2022 International journal of molecular sciences Result SARS_CoV_2 A570D;D614G 46;56 51;61 S 230 231 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Together, A570D and D614G sites are involved in the inter-protomer interactions in the S-B.1.1.7 states and contribute to the hinge clusters that modulate RBD motions. 2022 International journal of molecular sciences Result SARS_CoV_2 A570D;D614G 10;20 15;25 RBD 155 158 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. We found that these K417N, E484K and N501Y sites can afford greater mutational tolerance and conformational plasticity in the S-B.1.351 conformations. 2022 International journal of molecular sciences Result SARS_CoV_2 E484K;K417N;N501Y 27;20;37 32;25;42 S 126 127 35164548 Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. A natural mutant variant (Q57H) that is associated with the ongoing Beta variant and deletion of a highly conserved glycine residue (DeltaG188) were tested. 2022 mBio Result SARS_CoV_2 Q57H 26 30 35164548 Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. Both Q57H and DeltaG188 mutants were tested in comparison with the wild-type ORF3a. 2022 mBio Result SARS_CoV_2 Q57H 5 9 ORF3a 77 82 35164548 Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. Compared with wild-type ORF3a, the DeltaG188 mutant markedly increased apoptosis and necrosis, whereas the Q57H mutant showed slightly reduced apoptosis and necrosis. 2022 mBio Result SARS_CoV_2 Q57H 107 111 ORF3a 24 29 35164548 Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. In contrast, the Q57H mutant showed slightly improved cellular growth and viability and reduced cell death. 2022 mBio Result SARS_CoV_2 Q57H 17 21 35164548 Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. Similar or slightly reduced activation of IFN-beta1, TLR4, and TLR3 was observed in the Q57H mutant compared with the wild-type ORF3a. 2022 mBio Result SARS_CoV_2 Q57H 88 92 ORF3a 128 133 35164548 Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. While the Q57H mutant showed a similar immune expression profile as the wild-type ORF3a. 2022 mBio Result SARS_CoV_2 Q57H 10 14 ORF3a 82 87 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. 1C); E484K was later adopted by the Alpha variant after the emergence of the Beta and Gamma variants. 2022 mBio Result SARS_CoV_2 E484K 5 10 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. All three S variants, SAlpha (later strain), SBeta, and SGamma, share both N501Y and E484K substitutions. 2022 mBio Result SARS_CoV_2 E484K;N501Y 85;75 90;80 S 10 11 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. Analysis of hACE2-bound SAlpha+E484K. 2022 mBio Result SARS_CoV_2 E484K 31 36 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. D614G substitution induces a conformational shift of virus-associated spikes toward receptor-accessible states. 2022 mBio Result SARS_CoV_2 D614G 0 5 S 70 76 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. E484K and N501Y reside in the RBM of spike that directly contacts the receptor hACE2. 2022 mBio Result SARS_CoV_2 N501Y;E484K 10;0 15;5 S 37 42 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. E484K substitution exhibited a noticeable effect of reducing the occupancy of ligand-free spike variant in the 0.5-FRET state and increasing the 0.3-FRET state occupancy. 2022 mBio Result SARS_CoV_2 E484K 0 5 S 90 95 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. E484K-carrying SAlpha resides predominately in partially open one/two-RBD-up receptor-accessible conformations. 2022 mBio Result SARS_CoV_2 E484K 0 5 RBD 70 73 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. Increasing experimental evidence indicates that E484K enables immune evasion, while N501Y may foster increased virus transmissibility by enhancing hACE2 binding. 2022 mBio Result SARS_CoV_2 E484K;N501Y 48;84 53;89 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. Lentivirus particles used for smFRET imaging were prepared by transfecting 293T cells with a 20-fold excess of plasmid encoding SD614, SG614, SAlpha, or SAlpha+E484K over their corresponding 427-Q3/556-A4 plasmid. 2022 mBio Result SARS_CoV_2 E484K 160 165 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. Similarly, the E484K-containing SAlpha variant also exhibits a higher frequency of spikes occupying the one/two-RBD-up intermediates (0.3-FRET) state than wild-type SAlpha. 2022 mBio Result SARS_CoV_2 E484K 15 20 S;RBD 83;112 89;115 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. The ligand-free SG614 and SAlpha+E484K spikes primarily occupy the one/two-RBD-up partially open state (0.3-FRET), which presents the lowest relative free energy among all four FRET-defined states. 2022 mBio Result SARS_CoV_2 E484K 33 38 S;RBD 39;75 45;78 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. The observation that E484K renders S variants adopting more one/two-RBD-up conformations agrees with all existing high-resolution cryo-EM structural results of E484K carrying SBeta and SGamma. 2022 mBio Result SARS_CoV_2 E484K;E484K 21;160 26;165 RBD;S 68;35 71;36 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. The overall conformational landscape of ligand-free SAlpha+E484K. 2022 mBio Result SARS_CoV_2 E484K 59 64 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. The similarity between overall conformational distributions (FRET histograms) of SAlpha+E484K and SG614 is also in line with the structural and biochemical observations that highlighted the consistency between the structural and biochemical profiles of the E484K-containing SBeta and SG614 variants. 2022 mBio Result SARS_CoV_2 E484K;E484K 257;88 262;93 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. This finding implies that the D614G substitution does not alter the sequence of events that constitute the conformational dynamics of the spike, although it does induce shifting of the conformational landscape/distribution. 2022 mBio Result SARS_CoV_2 D614G 30 35 S 138 143 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. This suggests that E484K stabilizes the S variants toward the one/two-RBD-up conformation by reducing the all-RBD-down conformation. 2022 mBio Result SARS_CoV_2 E484K 19 24 RBD;RBD;S 70;110;40 73;113;41 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. Thus, D614G substitution shifts the conformational landscape of the original SD614 from hACE2-inaccessible all-RBD-down conformation dominance to predominately hACE2-accessible conformations. 2022 mBio Result SARS_CoV_2 D614G 6 11 RBD 111 114 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. To determine whether D614G substitution on S would influence the conformational profiles of spike proteins, we next performed smFRET analyses of SG614 on lentivirus particles compared to the original SD614. 2022 mBio Result SARS_CoV_2 D614G 21 26 S;S 92;43 97;44 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. To further assess the conformational effects of E484K in the context of SBeta, SGamma, and SAlpha (SAlpha later adopted E484K), we next performed smFRET studies using E484K-carrying SAlpha+484K. 2022 mBio Result SARS_CoV_2 E484K;E484K;E484K 48;120;167 53;125;172 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. Virus particles bearing SG614, SG614+N501Y, SG614+E484K, SG614+E484K+N501Y, SAlpha, or E484K-carrying SAlpha (SAlpha+E484K) variants had a discernible increase in infectivity compared to viruses bearing the parental SD614. 2022 mBio Result SARS_CoV_2 E484K;E484K;E484K;E484K;N501Y;N501Y 87;50;63;117;37;69 92;55;68;122;42;74 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. In April 2021, 65%, 29% and 6% were B.1.1.7 (Alpha), E484K mutations and other forms of mutation. 2022 Scientific reports Result SARS_CoV_2 E484K 53 58 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. In March 2021, 67% were B.1.1.7 (Alpha) and the rest were single E484K mutation. 2022 Scientific reports Result SARS_CoV_2 E484K 65 70 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. The other forms of mutation include single mutation at N501S, I584V, R481K, F515L, P521L, T553S, N606S, A609G, double mutation at K557E and Q613R, and the triple mutation at L513F, Q580R and V615A. 2022 Scientific reports Result SARS_CoV_2 A609G;F515L;I584V;K557E;L513F;N501S;N606S;P521L;Q580R;Q613R;R481K;T553S;V615A 104;76;62;130;174;55;97;83;181;140;69;90;191 109;81;67;135;179;60;102;88;186;145;74;95;196 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. D614G is the most frequent mutation in the FCS region of S protein of SARS-CoV-2 found in this study. 2022 International microbiology Result SARS_CoV_2 D614G 0 5 S 57 58 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. Other variants S680P and Q675H were observed from Central Java with 1.92% of each in June and October 2020, respectively. 2022 International microbiology Result SARS_CoV_2 Q675H;S680P 25;15 30;20 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. The distribution of D614G mutation in Indonesia. 2022 International microbiology Result SARS_CoV_2 D614G 20 25 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. The phylodynamics of D614G mutation in Special Region of Yogyakarta and Central Java. 2022 International microbiology Result SARS_CoV_2 D614G 21 26 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. The time dynamics of D614G mutations among SARS-CoV-2 that circulated in the two provinces were also analyzed. 2022 International microbiology Result SARS_CoV_2 D614G 21 26 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. These mutations are co-segregated with D614G. 2022 International microbiology Result SARS_CoV_2 D614G 39 44 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. This finding is parallel with the time dynamics of D614G in Indonesian SARS-CoV-2 isolates. 2022 International microbiology Result SARS_CoV_2 D614G 51 56 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. Two sequences (3.85%) came from Yogyakarta containing Q677H mutation as of August 2020. 2022 International microbiology Result SARS_CoV_2 Q677H 54 59 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. We detected several mutations accompanying the D614G variant, i.e., Q675H, Q677H, S680P, and silent mutation in 23,557 C > T. 2022 International microbiology Result SARS_CoV_2 C23557T;D614G;Q675H;Q677H;S680P 112;47;68;75;82 124;52;73;80;87 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. A fraction of HCWs exhibited NT50 values below the detection limit (NT50 less than 100) against D614G (7 of 48), Alpha (17 of 48), Beta (22 of 48), and Delta (14 of 48) following the first dose of vaccine. 2022 Science translational medicine Result SARS_CoV_2 D614G 96 101 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. At the time of pre-vaccination sample collection, D614G was the major circulating SARS-CoV-2 variant, whereas at the time of post-first dose and post-second dose sample collections, D614G and Alpha were the major circulating variants. 2022 Science translational medicine Result SARS_CoV_2 D614G;D614G 50;182 55;187 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. D614G was selected to serve as the control virus because this mutation emerged very early in the pandemic, is present in nearly all circulating SARS-CoV-2 variants, and substantially impacts neutralization sensitivity. 2022 Science translational medicine Result SARS_CoV_2 D614G 0 5 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. Following the first dose of mRNA vaccine, a strong nAb response was induced among HCWs compared to pre-vaccination across all variants except for Omicron; this was observed despite extensive variation in nAb titers of these individuals, including against D614G (mean = 1140, 95% CI = 317-1963, range = 100-15954). 2022 Science translational medicine Result SARS_CoV_2 D614G 255 260 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. In light of this, comparisons of neutralization sensitivity to true wild-type SARS-CoV-2 would be confounded by the presence of the D614G mutation in all major SARS-CoV-2 variants. 2022 Science translational medicine Result SARS_CoV_2 D614G 132 137 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. In particular, following two vaccine doses, mRNA-1273 vaccinated HCWs exhibited significantly higher nAb titers than BNT162b2-vaccinated HCWs for the D614G (p < 0.001) and Alpha (p < 0.01) variants, respectively. 2022 Science translational medicine Result SARS_CoV_2 D614G 150 155 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. Interestingly, we found that the differences in NT50 between anti-N protein positive and negative HCWs were greater for D614G and Alpha compared with the Beta, Delta, and Omicron variants, possibly due to the stronger neutralization resistance of the latter VOCs. 2022 Science translational medicine Result SARS_CoV_2 D614G 120 125 N 66 67 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. Overall, we found that, following two vaccine doses, the Alpha, Beta, Delta, and Omicron VOCs exhibited a 1.3- (p < 0.01), 3.2- (p < 0.001), 2.2- (p < 0.001), and 28.6-fold (p < 0.001) lower NT50 values compared to D614G, respectively. 2022 Science translational medicine Result SARS_CoV_2 D614G 215 220 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. The below-detection rates fell to 0.0% (0 of 48) to 4.2% (2 of 48) for all variants except Omicron following a second vaccine dose, with a 2 to 3-fold increase in mean nAb titers compared to the first dose (p < 0.001 for D614G, Alpha, Beta, and Delta). 2022 Science translational medicine Result SARS_CoV_2 D614G 221 226 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. The mean NT50 values for Alpha, Beta, Delta, and Omicron variants at six months were 1.3-, 1.7-, 3.6-, and 10.2-fold lower than that of D614G, respectively. 2022 Science translational medicine Result SARS_CoV_2 D614G 136 141 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. This corresponded to an approximately 10-fold decline in NT50 for D614G, Alpha, and Delta (R2 = 0.0452 to 0.594, p < 0.0001) every 22 weeks compared with Beta (R2 = 0.286, p < 0.001) every 37 weeks. 2022 Science translational medicine Result SARS_CoV_2 D614G 66 71 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. We found that pseudotyped virus infectivity was reasonably comparable for all variants, with modest reductions seen for Alpha and Delta compared to D614G. 2022 Science translational medicine Result SARS_CoV_2 D614G 148 153 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. We observed no significant correlation for age and NT50 against D614G at any time point (p > 0.05. 2022 Science translational medicine Result SARS_CoV_2 D614G 64 69 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. We produced pseudotyped lentiviruses expressing a Gaussia luciferase reporter gene and bearing SARS-CoV-2 spike proteins derived from D614G, Alpha, Beta, Delta, or Omicron. 2022 Science translational medicine Result SARS_CoV_2 D614G 134 139 S 106 111 35168024 Development of SARS-CoV-2 variant protein microarray for profiling humoral immunity in vaccinated subjects. In D614G, B.1.1.7, P.1, B.1.617, B.1.617.1, and B.1.617.3 spike variants, the surrogate neutralizing activities were M2 >= M1 >= AZ2 > AZ1 > UN. 2022 Biosensors & bioelectronics Result SARS_CoV_2 D614G 3 8 S 58 63 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. 2.4 more open than that (69.1 ) of the parental strain D614G (termed G614) S-open (PDB 7KRR). 2022 Nature communications Result SARS_CoV_2 D614G 56 61 S 76 77 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. 4b), which clearly depicts the side-chain densities of the mutated RBM L452R and T478K. 2022 Nature communications Result SARS_CoV_2 L452R;T478K 71;81 76;86 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. 5c), revealing side chain densities in the interaction interface and the substituted L452R and T478K. 2022 Nature communications Result SARS_CoV_2 L452R;T478K 85;95 90;100 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. 5i), and considering 3C1 could adopt varied orientations to associate with RBD, 3C1 is likely not or minimally affected by the N501Y mutation and therefore remains effective against Beta and Kappa variants in the neutralization experiment. 2022 Nature communications Result SARS_CoV_2 N501Y 127 132 RBD 75 78 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Another mutation in the Delta variant RBD, L452R, is not involved in the interaction with ACE2. 2022 Nature communications Result SARS_CoV_2 L452R 43 48 RBD 38 41 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. As for 2H2 and 3C1 MAbs, the Delta L452R and T478K substitutions are not located in their neutralizing epitopes on RBD. 2022 Nature communications Result SARS_CoV_2 L452R;T478K 35;45 40;50 RBD 115 118 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Collectively, this Delta variant RBM T478K substitution could stabilize and induce conformational change of the RBM loop473-490 and strengthen the interaction with ACE2 receptor. 2022 Nature communications Result SARS_CoV_2 T478K 37 42 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Further inspection of the surface property showed that the T478K substitution makes the substituted site more positively charged and hydrophilic, which may strengthen RBM interaction with the negatively charged and hydrophilic ACE2 in the interaction interface. 2022 Nature communications Result SARS_CoV_2 T478K 59 64 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. In contrast, mutations in the Beta and Kappa S proteins, especially the E484K or E484Q substitution, may greatly impact RBM-targeting neutralizing MAbs. 2022 Nature communications Result SARS_CoV_2 E484K;E484Q 72;81 77;86 S 45 46 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. In fact, the RBM-targeting MAb 2H2 was greatly affected by the RBM mutations (K417N, E484K, and N501Y) in the Beta variant. 2022 Nature communications Result SARS_CoV_2 E484K;N501Y;K417N 85;96;78 90;101;83 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Inspection of the RBD-1-ACE2 interaction interface revealed that the RBM loop473-490, which plays important roles in the interactions with ACE2 receptor and neutralizing MAbs, exhibits observable conformational change induced by T478K substitution. 2022 Nature communications Result SARS_CoV_2 T478K 229 234 RBD 18 21 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Moreover, for 2H2, the other mutations, including K417N, E484K/Q, and N501Y mostly from the Beta and Kappa variants (N501Y also presented in the Alpha variant), all reside in its neutralizing epitopes on RBD. 2022 Nature communications Result SARS_CoV_2 E484K;E484Q;K417N;N501Y;N501Y 57;57;50;70;117 64;64;55;75;122 RBD 204 207 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. SARS-CoV-2 variants other than Delta harbor up to three distinct mutations in their RBD regions, e.g., Alpha (N501Y), Beta (K417N, E484K, and N501Y), and Kappa (L452R and E484Q). 2022 Nature communications Result SARS_CoV_2 E484K;E484Q;N501Y;K417N;L452R;N501Y 131;171;142;124;161;110 136;176;147;129;166;115 RBD 84 87 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. The Delta variant bears two mutations (T478K and L452R) in the RBD region compared with the WT strain. 2022 Nature communications Result SARS_CoV_2 L452R;T478K 49;39 54;44 RBD 63 66 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. The S trimer of the G614 variant, which only carries a D614G mutation relative to the WT strain, was also analyzed for ACE2 binding for comparison purpose. 2022 Nature communications Result SARS_CoV_2 D614G 55 60 S 4 5 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. While for the 3C1, only the N501Y substitution from Beta (also Alpha) variant resides in the edge of its epitope on the RBD. 2022 Nature communications Result SARS_CoV_2 N501Y 28 33 RBD 120 123 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. Accompanied solely by mutations in ORF1ab and ORF7b, it quickly outcompeted any variants not containing G215C to assume worldwide dominance. 2022 bioRxiv Result SARS_CoV_2 G215C 104 109 ORF1ab;ORF7b 35;46 41;51 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. An overlay of sedimentation coefficient distributions of the N:D63G and N:G215C mutants, as well as the quadruple N:D63G,R203M,G215C,D377Y mutant reflecting the full set of canonical mutations in 21J Delta variant is shown in. 2022 bioRxiv Result SARS_CoV_2 D377Y;G215C;R203M;D63G;D63G;G215C 133;127;121;63;116;74 138;132;126;67;120;79 N;N;N 61;72;114 62;73;115 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. Apparently, elementary features of NA binding are not substantially affected by the G215C mutation. 2022 bioRxiv Result SARS_CoV_2 G215C 84 89 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. As of November 29, 2021, 49.6 % of sequences in the data base contain the G215C mutation, but these describe only 34.9% of unique sequences (,720), consistent with the shorter period of time since the 21J clade has emerged. 2022 bioRxiv Result SARS_CoV_2 G215C 74 79 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. below the transition temperature) Nref and N:G215C only exhibited small differences, with slightly larger droplets observed for reduced N:G215C compared to Nref (SI Appendix. 2022 bioRxiv Result SARS_CoV_2 G215C;G215C 45;138 50;143 N;N 43;136 44;137 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. Compared to the ancestral Nref, N:G215C sediments much faster at 7.3 S. 2022 bioRxiv Result SARS_CoV_2 G215C 34 39 N 32 33 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. Finally, we used mass photometry (MP) to obtain an independent direct measurement of the molecular weight distribution of N:G215C in solution. 2022 bioRxiv Result SARS_CoV_2 G215C 124 129 N 122 123 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. However, at the much higher muM concentrations in SV, reduced N:G215C shows much different behavior. 2022 bioRxiv Result SARS_CoV_2 G215C 64 69 N 62 63 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. However, N:G215C exhibits much steeper transitions, and at a lower transition temperature, as may be discerned from the temperature-dependent particle size in DLS. 2022 bioRxiv Result SARS_CoV_2 G215C 11 16 N 9 10 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. In summary, N:G215C forms a tightly bound, compact tetramer via disulfide crosslinks of non-covalent dimers. 2022 bioRxiv Result SARS_CoV_2 G215C 14 19 N 12 13 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. In the case of N:G215C, we find this co-assembly significantly augmented. 2022 bioRxiv Result SARS_CoV_2 G215C 17 22 N 15 16 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. Interestingly, while for Nref a lower phase transition temperature is achieved in the presence of T10, the same transition temperature is observed for N:G215C already without any NA, and addition of T10 to N:G215C does not lead to a further shift. 2022 bioRxiv Result SARS_CoV_2 G215C;G215C 153;208 158;213 N;N 151;206 152;207 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. Structural Basis of Protected Islands in Disordered Regions and Effects of the G215C mutation. 2022 bioRxiv Result SARS_CoV_2 G215C 79 84 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. Such diminished disorder is consistent with the more compact hydrodynamic shape of N:G215C. 2022 bioRxiv Result SARS_CoV_2 G215C 85 90 N 83 84 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. The earlier R203K/G204R was shown experimentally to enhance the ability of N-protein to form condensates, and R203M - prevalent in the Delta variant - was recently reported to enhance viral replication. 2022 bioRxiv Result SARS_CoV_2 R203K;R203M;G204R 12;110;18 17;115;23 N 75 76 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. The most recent mutation G215C is located in the linker between the SR-rich and leucine rich regions. 2022 bioRxiv Result SARS_CoV_2 G215C 25 30 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. These can be expected to differ from protein/NA and protein-protein interactions that stabilize the discrete oligomeric co-assemblies observed above, including the tetramerization property augmented by the G215C mutation. 2022 bioRxiv Result SARS_CoV_2 G215C 206 211 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. This is accompanied by structural transitions by CD, which we similarly observe for N:G215C (SI Appendix. 2022 bioRxiv Result SARS_CoV_2 G215C 86 91 N 84 85 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. This is consistent with the experimentally observed enhanced dimer-dimer interactions of the N:G215C under reduced conditions and the possibility of forming disulfide bonds across different protomers. 2022 bioRxiv Result SARS_CoV_2 G215C 95 100 N 93 94 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. This shows cooperativity or an avidity advantage of N:G215C in the earliest steps of assembly with NA, presumably due to its ability to constitutively tetramerize. 2022 bioRxiv Result SARS_CoV_2 G215C 54 59 N 52 53 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. Thus, the G215C mutation induces conformational alterations that create, or significantly enhance, a non-covalent dimer-dimer protein interaction interface outside the CTD, even in the absence of covalent disulfide bonds. 2022 bioRxiv Result SARS_CoV_2 G215C 10 15 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. To assess the impact of the G215C mutation, we studied the disordered stretch 210-246 in the central linker containing the leucine-rich region. 2022 bioRxiv Result SARS_CoV_2 G215C 28 33 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. To complement the study of coarse-grained aspects of N-protein size and shape, we examined the secondary structure content of N:G215C by circular dichroism spectroscopy (CD). 2022 bioRxiv Result SARS_CoV_2 G215C 128 133 N;N 53;126 54;127 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. To comprehensively examine the altered state we focus on N:G215C, in light of its unique epidemiological impact, and to enable clear structural attribution of changes to a single residue substitution. 2022 bioRxiv Result SARS_CoV_2 G215C 59 64 N 57 58 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. Up to a decanucleotide T10, a length that spans the binding grove of the NTD, we observed similar binding affinities of NA for N:G215C as previously determined for Nref (SI Appendix. 2022 bioRxiv Result SARS_CoV_2 G215C 129 134 N 127 128 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. Whereas the spectrum of Nref is dominated by a large negative ellipticity at 200 nm that is characteristic for disordered chains, N:G215C shows much reduced negative 200 nm signal and instead stronger ellipticity in the range 220-230 nm typical for helical structures. 2022 bioRxiv Result SARS_CoV_2 G215C 132 137 N 130 131 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. While N:D63G sediments similar to Nref, indicating no change in size, shape, or self-association properties, both N:G215C and the quadruple mutant sediment much faster, at a rate that demonstrates the formation of tetramers at low micromolar concentrations. 2022 bioRxiv Result SARS_CoV_2 D63G;G215C 8;116 12;121 N;N 6;114 7;115 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. While this may be expected for disulfide-linked N:G215C tetramer, even in the reduced conditions N:G215C exhibits significantly stronger hetero-oligomerization. 2022 bioRxiv Result SARS_CoV_2 G215C;G215C 50;99 55;104 N;N 48;97 49;98 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Accuracy:positive percent agreement and negative percent agreement for N501Y detection. 2022 Microbiology spectrum Result SARS_CoV_2 N501Y 71 76 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. All specimens with a known A23063T substitution in the Sanger chromatogram produced a positive signal for N501Y with the rRT-PCR SNP assay (57/57, 100%) and were confirmed to be of the B.1.1.7 lineage by Sanger sequencing analysis. 2022 Microbiology spectrum Result SARS_CoV_2 A23063T;N501Y 27;106 34;111 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Eighty-eight specimens had been confirmed by WGS to have the N501Y SNP; 87 specimens were B.1.1.7 and 1 specimen was B.1.351. 2022 Microbiology spectrum Result SARS_CoV_2 N501Y 61 66 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Excellent intrarun repeatability and interrun reproducibility was documented down to 15 copies/reaction or 599.4 copies/mL of primary specimen for the N501Y specimens and down to 25 copies/reaction or 999 copies/mL of primary specimen for the N501 wild-type specimens. 2022 Microbiology spectrum Result SARS_CoV_2 N501Y 151 156 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Of 899 that were N501Y positive using our assay, 897 (99.8%) specimens were confirmed to have the N501Y SNP through WGS. 2022 Microbiology spectrum Result SARS_CoV_2 N501Y;N501Y 17;98 22;103 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. On 11 March 2021, 1,138 specimens were screened with our N501Y rRT-PCR assay. 2022 Microbiology spectrum Result SARS_CoV_2 N501Y 57 62 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. One of the 57 N501Y-positive specimens contained a mixed result on Sanger sequencing, indicating the presence of both wild-type N501 and mutant N501Y. 2022 Microbiology spectrum Result SARS_CoV_2 N501Y;N501Y 14;144 19;149 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Our N501Y SNP assay was validated using primer and probe sets from two vendors, LGC, Biosearch Technologies (Middlesex, UK) and Thermo Fisher Scientific (MA, USA). 2022 Microbiology spectrum Result SARS_CoV_2 N501Y 4 9 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Our rRT-PCR N501Y SNP assay has been instituted for surveillance testing across Ontario, allowing notification to public health at least 1 to 7 days earlier than relying on Sanger sequencing or WGS. 2022 Microbiology spectrum Result SARS_CoV_2 N501Y 12 17 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The 95% limit of detection (LOD) for the N501Y target was determined to be 5.67 (95% confidence interval [95% CI] of 1.98 to 16.24) copies/reaction, which represents 226.71 (95% CI of 79.15 to 649.33) copies/mL of primary specimen. 2022 Microbiology spectrum Result SARS_CoV_2 N501Y 41 46 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The analysis of interlaboratory reproducibility was done with replicates of a panel of nine N501Y samples, five wild-type samples, one mixed N501Y/N501 sample, and five negative samples. 2022 Microbiology spectrum Result SARS_CoV_2 N501Y;N501Y 92;141 97;146 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The CT values of the N501 target are more clustered around the mean, demonstrating more agreement with the E gene CT than with the N501Y target. 2022 Microbiology spectrum Result SARS_CoV_2 N501Y 131 136 E 107 108 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The E gene CT values are strongly correlated with CT values of both SNP rRT-PCR assay targets, with an r value of 0.99 for the N501 target, which is slightly higher than the N501Y target with an r value of 0.96. 2022 Microbiology spectrum Result SARS_CoV_2 N501Y 174 179 E 4 5 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The mean envelope (E) gene and N501Y SNP rRT-PCR assay cycle threshold (CT) values of all VOC specimens in this study were 19.15 (standard deviation [SD] of 3.76) and 21.88 (SD of 3.80), respectively. 2022 Microbiology spectrum Result SARS_CoV_2 N501Y 31 36 E 19 20 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. To analyze the performance of the N501Y SNP assay, a panel of 160 specimens, including 57 specimens with N501Y detected by Sanger sequencing and 103 wild-type N501 specimens, were tested. 2022 Microbiology spectrum Result SARS_CoV_2 N501Y;N501Y 34;105 39;110 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. To understand the provincial prevalence of VOCs in Ontario, 2,570 SARS-CoV-2-positive specimens reported on 20 January 2021 across the province were sent for screening using our rRT-PCR N501Y SNP assay, and 113 (4.4%) had a N501Y mutation detected. 2022 Microbiology spectrum Result SARS_CoV_2 N501Y;N501Y 186;224 191;229 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. We observed comparable results for both primer and probe sets, as there were no meaningful differences in average CT values or number of N501Y specimens detected. 2022 Microbiology spectrum Result SARS_CoV_2 N501Y 137 142 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. Another P.1 nondefining mutation was found in the Spike gene (D614G, n = 41, 38.7%). 2022 Microbiology spectrum Result SARS_CoV_2 D614G 62 67 S 50 55 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. Five specimens (6_LABRESIS, 101_LABRESIS, 195_LABRESIS, 198_LABRESIS, and 211_LABRESIS) were assigned as a P.1.2 sublineage, as they had two synonymous defining mutations (C1912T, and C28789T) tree missense defining mutations (D762G, T1820I, D155Y). 2022 Microbiology spectrum Result SARS_CoV_2 C28789T;D155Y;T1820I;C1912T;D762G 184;242;234;172;227 191;247;240;178;232 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. From the five P.1.2 sublineage-defining mutations, three resulted in amino acid substitutions: one in the ORF1ab (D762G/A2550G), one in the ORF3a (T1820I/C5724T), and one in the Nucleocapsid gene (D155Y/G25855T). 2022 Microbiology spectrum Result SARS_CoV_2 D155Y;D762G;T1820I;A2550G;C5724T;G25855T 197;114;147;120;154;203 202;119;153;126;160;210 N;ORF1ab;ORF3a 178;106;140 190;112;145 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. From the two specimens assigned as a P.1.1 sublineage by Pangolin, the specimen 76_LABRESIS presented all the 22 P.1 lineage-defining mutations while the 77_LABRESIS specimen lacked the T733C, C21614T (L18F), and G22132T (R190S) mutations. 2022 Microbiology spectrum Result SARS_CoV_2 C21614T;G22132T;T733C;L18F;R190S 193;213;186;202;222 200;220;191;206;227 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. In addition, five P.1 nondefining mutations were found in all of the P.1 sequences: two in the ORF1ab (C3037T and P314L) and three in the Nucleocapsid (A28877T, G28878C and R203K/G204R). 2022 Microbiology spectrum Result SARS_CoV_2 G28878C;P314L;R203K;A28877T;C3037T;G204R 161;114;173;152;103;179 168;119;178;159;109;184 N;ORF1ab 138;95 150;101 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. Noteworthy, two sequences did not present the P.1 lineage-defining mutation N501Y in the Spike protein, RBD domain. 2022 Microbiology spectrum Result SARS_CoV_2 N501Y 76 81 S;RBD 89;104 94;107 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. Of the 106 P.1 sequences (98 P.1, six P.1.2, two P.1.1), 99 (93.4%) presented most of the 22 P.1 lineage-defining mutations, with exception of one synonymous mutation in the ORF1ab (C12778T) and one missense mutation in the Spike (R190S), which were present in 44 (41.5%) and 79 (74.5%) sequences, respectively (Table 1). 2022 Microbiology spectrum Result SARS_CoV_2 C12778T;R190S 182;231 189;236 ORF1ab;S 174;224 180;229 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. Other specimen assigned as P.1.2 (90_LABRESIS) had all of them except the T1820I mutation. 2022 Microbiology spectrum Result SARS_CoV_2 T1820I 74 80 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. The subclade 1, comprising sequences that carried the mutations C2973T (A903V), A4314G (K1350R), C5796T (T1844I), C12439T, and G18816T in the ORF1ab and C25516T (P42S) in the Spike protein. 2022 Microbiology spectrum Result SARS_CoV_2 A4314G;C12439T;C25516T;C2973T;C5796T;G18816T;A903V;K1350R;P42S;T1844I 80;114;153;64;97;127;72;88;162;105 86;121;160;70;103;134;77;94;166;111 ORF1ab;S 142;175 148;180 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. The subclade 2, comprising sequences that carried the mutations T8908C, C11882T (L3873F) in the ORF1ab, A22991T, G22992C, G25305T (C1248F) in the Spike, and G28287T (G5V) in the Nucleocapsid. 2022 Microbiology spectrum Result SARS_CoV_2 A22991T;C11882T;G22992C;G25305T;G28287T;T8908C;C1248F;G5V;L3873F 104;72;113;122;157;64;131;166;81 111;79;120;129;164;70;137;169;87 N;ORF1ab;S 178;96;146 190;102;151 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. The subclade 3, comprising sequences that carried the mutations C1420T and G5063A (D1600N) in the ORF1ab. 2022 Microbiology spectrum Result SARS_CoV_2 C1420T;G5063A;D1600N 64;75;83 70;81;89 ORF1ab 98 104 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. The subclade 5, comprising sequences that carried the mutations C1545T (A427V) in the ORF1ab, C23413T and G24872T (V1104L) in the Spike. 2022 Microbiology spectrum Result SARS_CoV_2 C1545T;C23413T;G24872T;A427V;V1104L 64;94;106;72;115 70;101;113;77;121 ORF1ab;S 86;130 92;135 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. Three sequences from the subclade 5 presented one more mutation in the ORF1ab (G10979A-V3572M). 2022 Microbiology spectrum Result SARS_CoV_2 G10979A;V3572M 79;87 86;93 ORF1ab 71 77 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. However, p.Asn501Tyr variant and other 8 of the 17 variants (3267C>T p.Thr1001Ile, 6954T>C p.Ile2230Thr in the ORF1ab gene; 23063A>T, 23271 C>A p.Ala570Asp, 23604C>A p.Pro681His, 23709C>T p.Thr716Ile in the S gene; 27972C>T p.Gln27*, 28048G>T p.Arg52Ile in the Orf8 gene; 28977C>T p.Ser235Phe in the N gene) were observed only in a few sequences in our dataset, but never in linkage with each other, suggesting a synergistic effect of the variants in this new viral strain (S3 Table). 2022 PloS one Result SARS_CoV_2 A23063T;C23271A;C23604A;C23709T;C27972T;G28048T;C28977T;T6954C;N501Y;C3267T;A570D;R52I;N501Y;P681H;S235F;T1001I;T716I;N27X;I2230T 124;134;157;179;215;234;272;83;9;61;146;245;11;168;283;71;190;228;92 132;141;164;186;223;241;279;89;20;67;155;253;20;177;292;81;199;232;101 ORF1ab;ORF8;N;S 111;261;300;207 117;265;301;208 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. However, the variant does not seem to be associated with an increased disease severity, despite what was initially inferred from the correlation of mortality rate and prevalence of p.Asp614Gly in different countries. 2022 PloS one Result SARS_CoV_2 D614G;D614G 181;183 192;192 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. However, we confirmed the missense variant p.Asp614Gly in S protein as the most frequent (found in 57820 sequences, 77% of the total) (Table 2), as described in previous studies. 2022 PloS one Result SARS_CoV_2 D614G;D614G 43;45 54;54 S 58 59 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. In particular p.Asn501Tyr was observed in 2 sequences at the beginning of April, one in Brazil and the other in USA. 2022 PloS one Result SARS_CoV_2 N501Y;N501Y 14;16 25;25 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. Indeed, in the large majority of cases p.Asp614Gly occurs concomitantly with other variants, in particular with three variants, all characterized by similar frequency and located in the ORF1ab gene: the missense p.Pro4715Leu, the synonymous p.Phe924Phe and the c.-25C>T in the 5' untranslated region. 2022 PloS one Result SARS_CoV_2 C25T;D614G;F924F;P4715L;D614G;F924F 261;39;241;212;41;243 269;50;252;224;50;252 ORF1ab 186 192 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. It has been demonstrated that the p.Asp614Gly variant confers higher infectivity, competitive fitness and improved transmission in human primary cells and animal models. 2022 PloS one Result SARS_CoV_2 D614G;D614G 34;36 45;45 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. It is relevant to notice that, focusing on the 53 most frequent variants, we found the p.Asp614Gly variant as a single mutation in three patients only, suggesting that this variant alone does not provide a significant selective advantage to the virus. 2022 PloS one Result SARS_CoV_2 D614G;D614G 87;89 98;98 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. Moreover, we determined that the most frequent variant, the missense variant p.Asp614Gly in the S protein, is in strong linkage with three additional variants, suggesting a potential functional cooperation in providing a selective advantage to the virus. 2022 PloS one Result SARS_CoV_2 D614G;D614G 77;79 88;88 S 96 97 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. One of these mutations, the p.Asn501Tyr mutation located at the RBD of the S protein, has been previously reported to be an adaptive mutation in a mouse model subjected to serial passages of a human SARS-CoV-2 by means of intranasal inoculations. 2022 PloS one Result SARS_CoV_2 N501Y;N501Y 28;30 39;39 RBD;S 64;75 67;76 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. The 22992 missense variant, leading to a S477A aminoacidic change, has been associated to a stronger transmission capacity and higher infectivity, perhaps due to an improved binding of the S protein RBD (receptor-binding domain) to the ACE receptor. 2022 PloS one Result SARS_CoV_2 S477A 41 46 RBD;S 199;189 202;190 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. Although all 22 C29197T mutants were eventually classified as lineage B.1.1.519, 4 of them were originally classified as B.1.1.222 by an earlier Pango lineage classification (Table 1). 2022 PloS one Result SARS_CoV_2 C29197T 16 23 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. As a result, phylogenetic analysis was performed to further evaluate the C29197T mutants. 2022 PloS one Result SARS_CoV_2 C29197T 73 80 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. Both shared a single point mutation, C29197T. 2022 PloS one Result SARS_CoV_2 C29197T 37 44 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. For the most part, the 22 C29197T mutants are relatively diverse and vary genetically in multiple ways from the root of the clade (Fig 2B). 2022 PloS one Result SARS_CoV_2 C29197T 26 33 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. In addition, there was 1 C29197T mutant that shared an address with another and therefore removed from the prevalence count (Table 1). 2022 PloS one Result SARS_CoV_2 C29197T 25 32 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. In order to refine our estimate of the proportion of C29197T mutants that were circulating among the community, household clusters were identified and eliminated. 2022 PloS one Result SARS_CoV_2 C29197T 53 60 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. Of note, all 22 C29197T mutants demonstrated NGTF upon secondary testing on the Xpert Xpress SARS-CoV-2 assay (Table 1). 2022 PloS one Result SARS_CoV_2 C29197T 16 23 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. Out of these 312 sequences, 22 (7.1%) of them contained the C29197T mutation. 2022 PloS one Result SARS_CoV_2 C29197T 60 67 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. The resulting proportion was very similar and slightly higher, with 21 samples with the C29197T mutation circulating in the community out of the 284 remaining samples (7.4%). 2022 PloS one Result SARS_CoV_2 C29197T 88 95 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. To investigate the impact of this mutation further, 312 residual upper respiratory SARS-CoV-2 real-time polymerase chain reaction (RT-PCR) samples collected between January 3, 2021 and May 8, 2021 that were sequenced as part of baseline surveillance activities (see S1 Table) were evaluated to determine if they contained the C29197T mutation. 2022 PloS one Result SARS_CoV_2 C29197T 326 333 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. As more N501Y RBD has a higher affinity to ACE2, there were far more absolute amount of N501Y RBD bound to ACE2 than the WT in the presence of COVID-19 convalescent antisera (P < 0.0001, N = 41. 2022 Scientific reports Result SARS_CoV_2 N501Y;N501Y 8;88 13;93 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. However, we observed dramatic differences in the ability of the WT and N501Y RBD to bind ACE2. 2022 Scientific reports Result SARS_CoV_2 N501Y 71 76 RBD 77 80 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. mRNA vaccination results in much more effective neutralization than natural immunity against N501Y RBD from binding to ACE2. 2022 Scientific reports Result SARS_CoV_2 N501Y 93 98 RBD 99 102 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. N501Y RBD significantly increased ACE2 binding and attenuated the neutralization ability of COVID-19 convalescent antisera. 2022 Scientific reports Result SARS_CoV_2 N501Y 0 5 RBD 6 9 COVID-19 92 100 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. Results from five consecutive experiments showed that N501Y RBD bound to ACE2 at an average of 5.1-fold higher rate than the WT RBD (range 4.1 to 6.1-fold). 2022 Scientific reports Result SARS_CoV_2 N501Y 54 59 RBD;RBD 60;128 63;131 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. suggesting the antisera from COVID-19 convalescent donors bind both the WT and N501Y RBD proteins equally well. 2022 Scientific reports Result SARS_CoV_2 N501Y 79 84 RBD 85 88 COVID-19 29 37 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. The clinical validation study of the test was performed using 41 serum samples from 33 convalescent donors (Supplementary Table 1) with documented history of COVID-19 prior to September 1, 2020, months prior to the first reported alpha variant which contains RBD mutation N501Y and from 171 healthy donors collected before January 2020. 2022 Scientific reports Result SARS_CoV_2 N501Y 272 277 RBD 259 262 COVID-19 158 166 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. The neutralization assay against RBD-N501Y and ACE2 binding was both very sensitive and specific with AUC of ROC analysis of 0.948. 2022 Scientific reports Result SARS_CoV_2 N501Y 37 42 RBD 33 36 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. The results with the convalescent donor blood samples showed strong linear correlation between antibodies recognizing both the WT and the N501Y proteins (r2 = 0.927). 2022 Scientific reports Result SARS_CoV_2 N501Y 138 143 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. There was further a strong linear correlation between neutralization activity against the WT and the N501Y RBD in ACE2 binding with a slope of 1.03 (r2 = 0.896, n = 41; Supplementary. 2022 Scientific reports Result SARS_CoV_2 N501Y 101 106 RBD 107 110 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. There were 31.7% convalescent and 0% of vaccinated samples retained over 50% N501Y RBD and ACE2 binding, a difference that is highly significant. 2022 Scientific reports Result SARS_CoV_2 N501Y 77 82 RBD 83 86 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. Thus, COVID-19 antisera neutralize WT and N501Y RBD with an equal potency. 2022 Scientific reports Result SARS_CoV_2 N501Y 42 47 RBD 48 51 COVID-19 6 14 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. Thus, it can be concluded that N501Y RBD has a much higher affinity to ACE2. 2022 Scientific reports Result SARS_CoV_2 N501Y 31 36 RBD 37 40 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. Thus, natural immunity from the original SARS-CoV-2 infections could not consistently provide sufficient neutralization against N501Y RBD variant from binding to the cellular ACE2 receptor. 2022 Scientific reports Result SARS_CoV_2 N501Y 128 133 RBD 134 137 COVID-19 41 62 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. Thus, the mRNA vaccinated blood is far more effective in neutralizing the high affinity N501Y RBD from binding to ACE2. 2022 Scientific reports Result SARS_CoV_2 N501Y 88 93 RBD 94 97 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. Thus, the substantially elevated antibody levels in the mRNA vaccine group appeared to be the primary driver of better neutralization activities against the high affinity N501Y RBD. 2022 Scientific reports Result SARS_CoV_2 N501Y 171 176 RBD 177 180 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. To further determine the difference between natural immunity and mRNA vaccination, we selected five samples that had median levels of anti-RDB antibody of each group, and performed dilutions and neutralization studies against N501Y binding to ACE2. 2022 Scientific reports Result SARS_CoV_2 N501Y 226 231 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. To investigate the ability of antisera from convalescent patient to recognize the B.1.1.7 N501Y variant (alpha), we purified N501Y RBD protein and labeled it with the Ru-tag for electro-chemiluminescence assay. 2022 Scientific reports Result SARS_CoV_2 N501Y;N501Y 90;125 95;130 RBD 131 134 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. We derived a scheme to compare the levels of antibodies against either the WT or N501Y RBD in the same samples. 2022 Scientific reports Result SARS_CoV_2 N501Y 81 86 RBD 87 90 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. We further analyzed the ability of COVID-19 convalescent antisera to neutralize the binding of the N501Y RBD to ACE2, as in the case of the WT RBD. 2022 Scientific reports Result SARS_CoV_2 N501Y 99 104 RBD;RBD 105;143 108;146 COVID-19 35 43 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. We further examined the absolute level of the WT and the N501Y RBD bound to ACE2 in the presence of COVID-19 antisera. 2022 Scientific reports Result SARS_CoV_2 N501Y 57 62 RBD 63 66 COVID-19 100 108 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. When tested for neutralizing N501Y RBD against ACE2 binding, the mRNA vaccinated blood was far more effective compared to convalescent samples to achieve minimum ACE2 binding (P < 0.0001. 2022 Scientific reports Result SARS_CoV_2 N501Y 29 34 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. While the antisera neutralized both the WT and N501Y RBD at a similar rate, there was four times (slope = 3.99, N = 41) more N501Y RBD bound to ACE2 in the presence of the convalescent antisera. 2022 Scientific reports Result SARS_CoV_2 N501Y;N501Y 47;125 52;130 RBD;RBD 53;131 56;134 35176330 Evolutionary shift from purifying selection towards divergent selection of SARS-CoV2 favors its invasion into multiple human organs. But the present data of SARS-CoV2 mutation profile does not support that this region is refractory to nucleotide changes to generate nonsynonymous mutation as and identified numerous nonsynonymous mutations (C480F, Y495S, L517F and G476S, V483A,Y508H respectively) in this region in SARS-CoV2. 2022 Virus research Result SARS_CoV_2 G476S;L517F;V483A;Y495S;C480F;Y508H 232;222;239;215;208;245 237;227;244;220;213;250 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. A C > T transition at nt 22,000 did not result in an amino acid change. 2022 Scientific reports Result SARS_CoV_2 C22000T 2 32 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. A direct comparison of RNA-seq data from patients infected with the Alpha or Alpha+E484K variant revealed the differential expression of 266 genes, with 122 being induced in the Alpha+E484K patients by at least two-fold. 2022 Scientific reports Result SARS_CoV_2 E484K;E484K 83;184 88;189 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. A total of 24 patients (18 Alpha patients and 6 Alpha+E484K patients) were homozygous for the OAS1 mutation (Supplementary Table 13). 2022 Scientific reports Result SARS_CoV_2 E484K 54 59 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. A total of 36 hospitalized patients infected with the Alpha variant and 13 patients infected with the Alpha+E484K variant participated in this study (for detailed information see Table 1 and Supplementary Table 1). 2022 Scientific reports Result SARS_CoV_2 E484K 108 113 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. BCs were isolated from the 36 hospitalized Alpha patients and 13 hospitalized Alpha+E484K patients and RNA-seq was conducted with an average of 215 million reads per sample passing quality control. 2022 Scientific reports Result SARS_CoV_2 E484K 84 89 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Expression of a total of 387 genes was significantly induced in Alpha patients and 1143 genes were upregulated in Alpha+E484K patients. 2022 Scientific reports Result SARS_CoV_2 E484K 120 125 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. First, we generated transcriptomes from 28 Alpha patients and 10 Alpha+E484K patients after their discharge from the hospital, on average 25 days after first symptomology (Supplementary Tables 8, 9). 2022 Scientific reports Result SARS_CoV_2 E484K 71 76 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. For this study we had also recruited three hospitalized patients infected with the Gamma variant and a total of 48 genes were significantly higher expressed in all three E484K variants. 2022 Scientific reports Result SARS_CoV_2 E484K 170 175 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. For this, we directly compared the transcriptomes from the Alpha and the Alpha+E484K cohorts at approximately 25 days after first symptomology and again after an additional three weeks during convalescence. 2022 Scientific reports Result SARS_CoV_2 E484K 79 84 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Gene module linked to the E484K escape mutation. 2022 Scientific reports Result SARS_CoV_2 E484K 26 31 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Here, we investigated the bearing of the E484K escape mutation on the immune response and analyzed the Buffy Coat (BC) transcriptomes of patients infected with the SARS-CoV-2 Alpha variant and the Alpha variant carrying the E484K escape mutation. 2022 Scientific reports Result SARS_CoV_2 E484K;E484K 41;224 46;229 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. However, since there were no significant differences in clinical severity between the Alpha and Alpha+E484K groups reported (Supplementary Table 1), these genes might be part of a module particularly sensitive to SARS-CoV-2 E484K variants. 2022 Scientific reports Result SARS_CoV_2 E484K;E484K 224;102 229;107 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Immune transcriptome responses of hospitalized patients infected with the SARS-CoV-2 Alpha and Alpha+E484K variants. 2022 Scientific reports Result SARS_CoV_2 E484K 101 106 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. In contrasts, the decline was 2% between T1 and T2 and 10% between T1 and T3 in the Alpha+E484K cohort. 2022 Scientific reports Result SARS_CoV_2 E484K 90 95 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Initially, we investigated the immune transcriptomes of patients infected with either the Alpha+E484K or the Alpha parent variant within 10 days after the onset of COVID-19 symptomology. 2022 Scientific reports Result SARS_CoV_2 E484K 96 101 COVID-19 164 172 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Next, we investigated the immune transcriptome in five Alpha patients and seven Alpha+E484K during convalescence, on average 45 days post first symptomology. 2022 Scientific reports Result SARS_CoV_2 E484K 86 91 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. No pathway assignment was obtained for genes whose expression was reduced in Alpha+E484K patients (Supplementary Table 5). 2022 Scientific reports Result SARS_CoV_2 E484K 83 88 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Our study demonstrated that the acquisition of the E484K escape mutation in the Alpha background is associated with a heightened expression of a subset of immune-associated genes suggesting a distinct host response to the E484K variant. 2022 Scientific reports Result SARS_CoV_2 E484K;E484K 51;222 56;227 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Out of the 122 genes overexpressed in the Alpha+E484K patients, 67 were also overexpressed in Beta patients (Supplementary Table 7). 2022 Scientific reports Result SARS_CoV_2 E484K 48 53 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Six out of the 36 patients infected with the Alpha variant and 4 out of the 13 patients infected with the Alpha+E484K variant died within 2-4 weeks after first symptomology (Supplementary Table 1). 2022 Scientific reports Result SARS_CoV_2 E484K 112 117 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Specifically, we investigated the temporal fate of the 48 gene E484K module in the Alpha and Alpha+E484K cohorts. 2022 Scientific reports Result SARS_CoV_2 E484K;E484K 63;99 68;104 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. These findings suggest that the E484K mutation elicits a more prolonged activation of immune pathways. 2022 Scientific reports Result SARS_CoV_2 E484K 32 37 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. This finding begged the question whether this E484K module was specific to patients infected with the Alpha variant or also present in patients infected with other variants carrying the E484K mutation, such as Beta (formerly B.1.351) and Gamma (formerly P.1). 2022 Scientific reports Result SARS_CoV_2 E484K;E484K 46;186 51;191 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. To address whether or not any additional polymorphisms in the viral genome tracked with the E484K mutation we examined the full viral sequences from all individuals for which the data was available (Supplementary Table 2). 2022 Scientific reports Result SARS_CoV_2 E484K 92 97 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. We did not identify any additional amino acid mutations specific to the Alpha+E484K variant. 2022 Scientific reports Result SARS_CoV_2 E484K 78 83 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. We specifically addressed whether patients infected with the Alpha+E484K variant would retain a gene expression signature distinct from patients infected with the parent Alpha variant. 2022 Scientific reports Result SARS_CoV_2 E484K 67 72 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. While hospitalized patients infected with the Alpha+E484K variant displayed a more expansive immune transcriptome than the Alpha parent variant, it was not known whether the variants influenced the longitudinal progression of immune transcriptomes. 2022 Scientific reports Result SARS_CoV_2 E484K 52 57 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. While there is extensive information on genetic pathways activated in immune cells of hospitalized COVID-19 patients, the impact of different variants, in particular those carrying the E484K escape mutation, is not clear. 2022 Scientific reports Result SARS_CoV_2 E484K 185 190 COVID-19 99 107 35187580 Impaired detection of omicron by SARS-CoV-2 rapid antigen tests. The expanded delta isolate (GISAID 3233464) carries the D63G, R203M and D377Y mutations in the nucleocapsid protein as well as the commonly reported G215C mutation. 2022 Medical microbiology and immunology Result SARS_CoV_2 D377Y;D63G;G215C;R203M 72;56;149;62 77;60;154;67 N 95 107 35187580 Impaired detection of omicron by SARS-CoV-2 rapid antigen tests. The expanded omicron isolate (GISAID 7808190; BA.1 sublineage) carries the expected P13L, del31/33, R203K and G204R mutations. 2022 Medical microbiology and immunology Result SARS_CoV_2 G204R;P13L;R203K 110;84;100 115;88;105 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. At days 25 and 41 a novel haplotype (Hap B.2), characterized by SNVs 18211A > C (M5983L) in the ORF1a gene and 25771C > T (L127F) in the ORF3a gene, was detected with a frequency of 34%. 2022 Infection, genetics and evolution Result SARS_CoV_2 A18211C;C25771T;L127F;M5983L 69;111;123;81 79;121;128;87 ORF1a;ORF3a 96;137 101;142 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Four major SNVs were identified in single patients: 3157C > T (A964A) in the ORF1ab, 21,575C > T (L5F) in the S gene, 26555 A > G (E11E) and 26,774 G > T (M84I) in the M gene. 2022 Infection, genetics and evolution Result SARS_CoV_2 A26555G;C3157T;A964A;E11E;L5F;M84I;C575T;G774T 118;52;63;131;98;155;88;144 129;61;68;135;101;159;96;153 ORF1ab;S 77;110 83;111 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Hap A was characterized by 6 major SNVs [241C > T in the 5'-UTR region, 3037C > T (F924F) in the Orf1ab gene, 14,408C > T (P4715L) in the Orf1ab gene, 16,456 T > C (S5398P) in the Orf1ab gene, 23,403 A > G (D614G) in the S gene, and 26,681C > T (F53F) in the N gene]. 2022 Infection, genetics and evolution Result SARS_CoV_2 C3037T;D614G;F53F;F924F;P4715L;S5398P;A403G;C408T;T456C;C681T;C241T 72;207;246;83;123;165;196;113;154;236;41 81;212;250;88;129;171;205;121;163;244;49 ORF1ab;ORF1ab;ORF1ab;N;S 97;138;180;259;221 103;144;186;260;222 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Hap A was the founder haplotype; Hap B was characterized by the SNV 26057 A > C (D222A) in the ORF3a; Hap B1 was characterized by the SNV 26057 A > C (D222A) in the ORF3a gene and 5765 G > A (G1834S) and 5766 G > C (G1834A) in the ORF1a gene. 2022 Infection, genetics and evolution Result SARS_CoV_2 A26057C;A26057C;G5765A;G5766C;D222A;D222A;G1834A;G1834S 68;138;180;204;81;151;216;192 79;149;190;214;86;156;222;198 ORF1a;ORF3a;ORF3a 231;95;165 236;100;170 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Haplotype Hap C was characterized by SNV 21575C > T (L5F) in the S gene while haplotype Hap C.1 was characterized by SNVs 21,575C > T (L5F) in the S gene and C1684T (I473I) in the ORF1ab gene. 2022 Infection, genetics and evolution Result SARS_CoV_2 C21575T;C1684T;I473I;L5F;L5F;C575T 41;158;166;53;135;125 51;164;171;56;138;133 ORF1ab;S;S 180;65;147 186;66;148 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. It is of note that 10 out of 12 minor SNVs were specific of a single patient while the remaining 2 (5765 G > A (G1834T) in the ORF1ab gene and 26,057 A > C (D222A) in the ORF3a gene) were shared between patients #7 and #25. 2022 Infection, genetics and evolution Result SARS_CoV_2 G5765A;D222A;G1834T 100;157;112 110;162;118 ORF1ab;ORF3a 127;171 133;176 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. It is of note that patient #26 (isolate 39) carried 3 SNVs that reverted to the sequence corresponding to Whuan-H-1 (ntT241C, P5398S and G614D) (Hap F). 2022 Infection, genetics and evolution Result SARS_CoV_2 G614D;P5398S;T241C 137;126;117 142;132;124 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Six major SNVs were common to all samples at baseline, except for patient #26 (viral isolate 39): 241C > T in the 5'-UTR region, 3037C > T (F924F) in the Orf1ab gene, 14,408C > T (P4715L) in the Orf1ab gene, 16,456 T > C (S5398P) in the Orf1ab gene, 23,403 A > G (D614G) in the S gene and 26,681C > T (F53F) in the N gene. 2022 Infection, genetics and evolution Result SARS_CoV_2 C241T;C3037T;D614G;F53F;F924F;P4715L;S5398P;A403G;C408T;T456C;C681T 98;129;264;302;140;180;222;253;170;211;292 106;138;269;306;145;186;228;262;178;220;300 ORF1ab;ORF1ab;ORF1ab;N;S 154;195;237;315;278 160;201;243;316;279 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. SNVs in the Orf1ab gene were 1684C > T (I473I), 4898C > T (H1545Y), 5765 G > A (G1834T), 7594C > T (G2443G), 8208C > A (T2648N) and 18,211 A > C (M5983L); SNVs in the ORF3a gene were 25,945C > A (Q185K), 25,771C > T (L127F) and 26,057 A > C (D222A); SNVs in the ORF6, M and N were 27,354 A > G (Q51Q), 27,138 T > C (L206L) and 29,067C > T (T265I), respectively. 2022 Infection, genetics and evolution Result SARS_CoV_2 C1684T;C4898T;G5765A;C7594T;C8208A;D222A;G1834T;G2443G;H1545Y;I473I;L127F;L206L;M5983L;Q185K;Q51Q;T2648N;T265I;C067T;T138C;A211C;A354G;C771T;C945A 29;48;68;89;109;242;80;100;59;40;217;316;146;196;295;120;340;330;305;135;284;207;186 38;57;78;98;118;247;86;106;65;45;222;321;152;201;299;126;345;338;314;144;293;215;194 ORF1ab;ORF3a;ORF6;N 12;167;262;274 18;172;266;275 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. The cluster of the B.1 lineage in the viral isolates of this study was characterized by the presence of three SNVs: ntC241T in the 5' untranslated region, D614G in the S gene and P4715L in the Orf1ab (NSP12) gene, in agreement with epidemiological data available in March and early April 2020 in Europe. 2022 Infection, genetics and evolution Result SARS_CoV_2 D614G;C241T;P4715L 155;116;179 160;123;185 ORF1ab;Nsp12;S 193;201;168 199;206;169 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. The isolates from 2 patients (#10, and #38) were each characterized by the additional presence of 1 synonymous SNV (Hap D: E11E in the M gene; Hap H: A964A in the ORF1ab gene, respectively); 5 isolates (patients #4, #6, #7, #41 and #46) were characterized by the presence of 1 non-synonymous SNV (Hap E: T2648N in ORF1ab; Hap C: L5F in the S gene; Hap B: D222A in ORF3a gene; Hap J: T265I in the N gene; Hap K: M84I in the M gene); the haplotype of patient #34 (Hap G) was characterized by 1 non-synonymous SNV in the ORF1ab gene (L5022F) and by a 3-nt deletion (ntG26155, ntT26156, ntT26157) in the ORF3a gene that results in the deletion of V255; the haplotype of patient #39 (Hap I) presented two non-synonymous SNVs in the ORF1ab gene (L3606F, P3613L). 2022 Infection, genetics and evolution Result SARS_CoV_2 A964A;D222A;E11E;L5F;M84I;P3613L;T2648N;T265I;L3606F;L5022F 150;355;123;329;411;748;304;383;740;531 155;360;127;332;415;754;310;388;746;537 ORF1ab;ORF1ab;ORF1ab;ORF1ab;ORF3a;ORF3a;E;N;S 163;314;518;727;364;600;301;396;340 169;320;524;733;369;605;302;397;341 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. The remaining 4 major SNVs were found in 2 additional patients: patient #39 carried 2 SNVs in ORF1a gene (11,083 G > T: L3606F and 11,103C > T: P3613L) while patient #34 carried a SNV in ORF1a (15,328C > T: L5022F) and a SNV in del255 in ORF3a gene. 2022 Infection, genetics and evolution Result SARS_CoV_2 L3606F;L5022F;P3613L;G083T;C103T;C328T 120;207;144;109;134;197 126;213;150;118;142;205 ORF1a;ORF1a;ORF3a 94;187;238 99;192;243 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. The SNVs in the coding regions of Orf1ab gene were both synonymous (3037C > T:A964A; 3157C > T: A964A) and non-synonymous (11,083 G > T: L3606F; 11,103C > T: P3613L; 14,408C > T: P4715L; 15,328C > T: L5022F; 16,456 T > C: S5398P); the 2 SNVs in the coding regions of S gene were non-synonymous (21,575C > T: L5F; 23,403 A > G: D614G); the small indel 26,155 G > d (V255-) in the Orf3a gene was a 1-bp deletion; the 3 SNVs in the coding regions of M gene were both synonymous (26,555 A > G: E11E; 26,681C > T: F53F) and non-synonymous (26,774 G > T: M84I) while the remaining SNV located in the 5'-UTR was non-coding (ntC241T). 2022 Infection, genetics and evolution Result SARS_CoV_2 C3157T;A964A;D614G;E11E;F53F;L3606F;L5022F;L5F;M84I;P3613L;P4715L;S5398P;C3037T;C241T;G083T;C103T;C328T;A403G;C408T;T456C;A555G;C575T;C681T;G774T;A964A 85;96;327;490;509;137;200;308;549;158;179;222;68;617;126;148;190;316;169;211;479;298;499;538;78 94;101;332;494;513;143;206;311;553;164;185;228;77;624;135;156;198;325;177;220;488;306;507;547;83 ORF1ab;ORF3a;S 34;379;267 40;384;268 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. 2F) and K417T-E484K-N501Y. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 K417T;E484K;N501Y 8;14;20 13;19;25 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. A total of 8 H-bonds with 136 non-bonded contacts were observed in K417T-E484K-N501Y variant. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 K417T;E484K;N501Y 67;73;79 72;78;84 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. A total of 9 H-bonds, and 145 non-bonded contacts were reported in triple variant K417N-E484K-N501Y. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 K417N;E484K;N501Y 82;88;94 87;93;99 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. Also, the higher docking score and binding affinity displayed by L452R-E484Q indicates that it could possess the similar infectivity potential as the triple variants. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 L452R;E484Q 65;71 70;76 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. As can be seen, the Es for WT RBD-heparin complex was - 129.55 kJ/mol which was much higher than L452R and K417N/T-E484K-N501Y variants (Table 1). 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 K417N;K417T;L452R;E484K;N501Y 107;107;97;115;121 114;114;102;120;126 RBD 30 33 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. Both the L452R and E484Q variant formed 9 H-bonds and 1 salt bridge with the similar interfacial contacts between WT RBD/ACE2 in the presence of heparin. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484Q;L452R 19;9 24;14 RBD 117 120 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. Compared to WT RBD, the L452R-E484Q mutant complex form unique H-bonds with residues F347, Y351, Y449, and R452 along with the loss of H-bond from residues T345, V445, N448, Y451, and R509. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 L452R;E484Q 24;30 29;35 RBD 15 18 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. For L452R-E484Q mutant, the binding pocket has residues involved in H-bonding are R346, S349, Y351, K444, G447, Y449, N450, and R452 (Supporting information. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 L452R;E484Q 4;10 9;15 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. However, the triple variants, K417N-E484K-N501Y (Supporting information. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 K417N;E484K;N501Y 30;36;42 35;41;47 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. In addition, K444 forms an additional H-bond in E484Q variant along with an unfavorable acceptor-acceptor interaction by T345. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484Q 48 53 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. In case of K417N substitution, Y451 failed to form H-bond but form an extra salt bridge and an extra H-bond formed by Y449 and R346 (Supporting information. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 K417N 11 16 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. Interestingly, for the structural model of cluster 1 obtained from Cluspro, the intermolecular interactions in RBD-heparin complexes are similar to WT RBD for the variants N501Y, L452R, E484Q, K417N, and K417T (Supporting information. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484Q;K417N;K417T;L452R;N501Y 186;193;204;179;172 191;198;209;184;177 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. K417N>K417T> K417N-E484K-N501Y~ K417T-E484K-N501Y> L452R-E484Q > E484K~ L452R ~E484Q > N501Y >WT RBD (Table 2). 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484K;K417N;K417T;L452R;L452R;N501Y;E484Q;K417T;E484K;E484K;E484Q;K417N;N501Y;N501Y 65;13;32;51;72;87;79;6;19;38;57;0;25;44 70;18;37;56;77;92;84;11;24;43;62;5;30;49 RBD 97 100 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. N501Y> >L452R-E484Q>E484K>K417N~WT~417 T > E484Q>L452R> >K417N-E484K-N501Y~ K417N-E484K-N501Y. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484Q;K417N;E484K;K417N;K417N;L452R;L452R;E484K;E484K;E484Q;N501Y;N501Y;N501Y 43;76;20;26;57;8;49;63;82;14;0;69;88 48;81;25;31;62;13;54;68;87;19;5;74;93 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. N501Y> K417T-E484K-N501Y>L452R-E484Q> K417N-E484K-N501Y> E484K > L452R> K417N > E484Q> K417T >WT RBD (Table 2). 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484K;E484Q;K417N;K417N;K417T;K417T;L452R;L452R;E484K;E484K;E484Q;N501Y;N501Y;N501Y 57;80;38;72;7;87;65;25;13;44;31;0;19;50 62;85;43;77;12;92;70;30;18;49;36;5;24;55 RBD 97 100 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. Notably, the similar binding affinity of WT and N501Y variant to ACE2 in the presence of heparin suggests that the N501Y behave similarly to the WT and the already developed COVID-19 vaccines might work against the N501Y Alpha variant. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 N501Y;N501Y;N501Y 48;115;215 53;120;220 COVID-19 174 182 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. S3A) and K417T-E484K-N501Y (Supporting information. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 K417T;E484K;N501Y 9;15;21 14;20;26 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. Similarly, in case of K417T, R346 failed to form H-bond but form an extra salt bridge (Supporting information. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 K417T 22 27 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. Similarly, the binding pocket of E484K is also very much similar to the pocket obtained from other structure model (Supporting information. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484K 33 38 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The decrease in heparin binding affinity was observed for triple variants K417N/T-E484K-N501Y. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 K417N;K417T;E484K;N501Y 74;74;82;88 81;81;87;93 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The docking study thus revealed that L452R variant has stronger heparin binding affinity compared to WT RBD. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 L452R 37 42 RBD 104 107 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The E484K mutation binds to heparin at a site which is not overlapping to the ACE2 binding region. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484K 4 9 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The E484K RBD form 8 hydrogen bonds, 1 salt bridge, and 120 nonbonded contacts with ACE2 in the presence of heparin. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484K 4 9 RBD 10 13 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The E484K substitution results in stronger binding of heparin to RBD as indicated by the formation of H-bond from a different set of residues including S349, K444, Y453, K484 Q493, and S494, along with different salt bridge forming residues K484 and Y453. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484K 4 9 RBD 65 68 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The E484K variant leads to high transmissibility and infectivity of SARS-CoV-2. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484K 4 9 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The E484Q substitution behaves overall similar to WT RBD except that Y449 form two H-bonds and a loss of H-bond from V445. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484Q 4 9 RBD 53 56 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The higher binding affinity of ACE2 to L452R-E484Q mutant can be explained by the presence of 10 H-bonds, 1 salt bridge, and 180 non-bonded contacts in the RBD/ACE2 interface. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 L452R;E484Q 39;45 44;50 RBD 156 159 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The interaction clearly suggests that N501Y binds to ACE2 in a completely different binding pocket where all the H-bond interactions observed in case of WT/ACE2 interactions were lost. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 N501Y 38 43 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The intermolecular interactions of N501Y RBD-heparin complex revealed increase in number of H-bonds and salt bridges as compared to WT RBD. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 N501Y 35 40 RBD;RBD 41;135 44;138 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The intermolecular non-bonded contacts in L452R and E484Q mutant complex were 169 and 159, respectively. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484Q;L452R 52;42 57;47 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The K417 single substitution variant, K417N and K417T formed 8 H-bonds and 153 non-bonded contacts with similar interfacial residues (Supporting information. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 K417N;K417T 38;48 43;53 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The L452R reported in epsilon variant (B.1.427and B.1.429) exhibited a similar extent of heparin binding as in N501Y. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 L452R;N501Y 4;111 9;116 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The L452R substitution is evident with the formation of an extra H-bond and two salt bridges from the substituted residue R452. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 L452R 4 9 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The L452R-E484Q mutant SARS-CoV-2 variants binds strongly with ACE2 (-297.18 kcal/mol) as compared to the docking scores of triple mutants, K417T-E484K-N501Y (-295.93 kcal/mol), and K417N-E484K-N501Y (-293.04 kcal/mol). 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 K417N;K417T;L452R;E484K;E484K;E484Q;N501Y;N501Y 182;140;4;146;188;10;152;194 187;145;9;151;193;15;157;199 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The lesser binding of ACE2 to N501Y in the presence of heparin was explored through the PDBsum analysis of intermolecular interactions of the mutant RBD and ACE2 structures. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 N501Y 30 35 RBD 149 152 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The maximum ET for the K417N-E484K-N501Y, K417T-E484K-N501Y, and L452R-E484Q RBD/ACE2 complex in the presence of heparin was - 182.88, - 168.91, and - 158.78 kJ/mol, respectively (Table 2). 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 K417N;K417T;L452R;E484K;E484K;E484Q;N501Y;N501Y 23;42;65;29;48;71;35;54 28;47;70;34;53;76;40;59 RBD 77 80 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The mutation N501Y (Alpha variant) also increases the infectivity and has increased the COVID-19 cases. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 N501Y 13 18 COVID-19 88 96 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The other RBD variants exhibited higher Es than WT RBD, with the maximum value was seen in L452R-E484Q, E484K, and N501Y. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484K;L452R;N501Y;E484Q 104;91;115;97 109;96;120;102 RBD;RBD 10;51 13;54 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The other three single RBD mutants, E484Q, L452R, and E484K also displayed reduced binding affinity to ACE2 in the presence of heparin. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484K;E484Q;L452R 54;36;43 59;41;48 RBD 23 26 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The overall interactions suggest that the L452R-E484Q binds to heparin with a similar extent to WT RBD. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 L452R;E484Q 42;48 47;53 RBD 99 102 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The significant decrease in binding affinity of ACE2 to RBD decrease in case of N501Y, indicating the more protective behavior of heparin. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 N501Y 80 85 RBD 56 59 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The triple variants, K417N-E484K-N501Y. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 K417N;E484K;N501Y 21;27;33 26;32;38 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The UK variant N501Y reported to form 5 H-bonds, 1 salt bridge, and 192 non-bonded contacts with the ACE2 in the presence of heparin . 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 N501Y 15 20 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The WT RBD-heparin complex showed a binding affinity (DeltaG) of - 7.7 kcal/mol, whereas the mutant RBD showed comparable binding affinity towards heparin, with the strongest binding affinity exhibited by E484K, N501Y and L452R-E484Q (Table 1). 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484K;L452R;N501Y;E484Q 205;222;212;228 210;227;217;233 RBD;RBD 7;100 10;103 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. This could further explain by the fact that heparin binds more strongly to N501Y mutants as compared to other variants. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 N501Y 75 80 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. This could lead to the inability of heparin to inhibit the RBD-ACE2 interaction in case of E484K variant. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484K 91 96 RBD 59 62 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. To investigate the heparin binding to L452R-E484Q RBD, we generated the structural model of L452R-E484Q mutant and studied its docking to heparin. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 L452R;L452R;E484Q;E484Q 38;92;44;98 43;97;49;103 RBD 50 53 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. Whereas, K417N and K417T showed maximum binding affinity to ACE2 in the presence of heparin. 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 K417N;K417T 9;19 14;24 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. WT< N501Y< E484Q < L452R < E484K< L452R-E484Q< K417T-E484K-N501Y< K417N-E484K-N501Y< K417T< K417N (Table 2). 2022 Process biochemistry (Barking, London, England) Result SARS_CoV_2 E484K;E484Q;K417N;K417N;K417T;K417T;L452R;L452R;N501Y;E484K;E484K;E484Q;N501Y;N501Y 27;11;66;92;47;85;19;34;4;53;72;40;59;78 32;16;71;97;52;90;24;39;9;58;77;45;64;83 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. 6A) and mutations S:P681H/R, that exchange neutral/nonpolar residues with basic amino acids close to the cleavage site, enhance the S1/S2 cleavability. 2022 Microbiology spectrum Result SARS_CoV_2 P681H;P681R 20;20 27;27 S 18 19 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. AA deletions covering in the NTD region (Delta144, Delta141-144 and Delta138-143) and substitutions at the S1/S2 junction (N679K, P681H and P681R), however, were particularly prevalent and sharply increase from January to May 2021. 2022 Microbiology spectrum Result SARS_CoV_2 P681H;P681R;N679K 130;140;123 135;145;128 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. During June-July 2021, the proportion of P.1+N679K genomes continued to increase up to 76.9%, the relative frequency of P.1+P681H genomes increased up to 37.1% in June and then decrease to 13.5% in July, while the frequency of variants P.1+NTDdel dropped to 2.1%. 2022 Microbiology spectrum Result SARS_CoV_2 N679K;P681H 45;124 50;129 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Inspection of P.1 sequences available at EpiCoV database in the GISAID (https://www.gisaid.org/ 4) on July 22nd, 2021, also detected an increased frequency of variants P.1+NTDdel, P.1+N679K, P.1+P681H/R in other Brazilian states, but in a much lower prevalence than in the Amazonas. 2022 Microbiology spectrum Result SARS_CoV_2 N679K;P681H;P681H;P681R 184;195;195;195 189;200;202;202 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Interestingly, lineages P.1.4 and P.1.5 displayed the same lineage-defining AA substitution (N679K) but different nucleotide mutations (T23599G and T23599A). 2022 Microbiology spectrum Result SARS_CoV_2 T23599A;N679K;T23599G 148;93;136 155;98;143 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Lineage P.1.4 comprises most P.1+N679K sequences from the Amazonas state (n = 187/197, 95%) and three P.1+N679K sequences from Rio de Janeiro. 2022 Microbiology spectrum Result SARS_CoV_2 N679K;N679K 33;106 38;111 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Lineage P.1.5 comprises the remaining P.1+N679K sequences from the Amazonas state (n = 10/197, 5%) and two P.1+N679K sequences from Roraima and Sao Paulo states. 2022 Microbiology spectrum Result SARS_CoV_2 N679K;N679K 42;111 47;116 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Lineage P.1.6 comprises most P.1+P681H sequences from the Amazonas state (n = 208/209, 99%) and one P.1+P681H sequence from Rio de Janeiro. 2022 Microbiology spectrum Result SARS_CoV_2 P681H;P681H 33;104 38;109 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Most P.1+ sub-clades displayed only one AA lineage-defining mutation in the S protein, except P.1.8 that displayed three mutations (T470N, P681R, and C1235F). 2022 Microbiology spectrum Result SARS_CoV_2 C1235F;P681R;T470N 150;139;132 156;144;137 S 76 77 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Our analyses also revealed two major well-supported (aLRT = 76-99%) P.1+ lineages designated P.1.7 and P.1.8 that comprises most P.1+P681H (n = 227/234, 97%) and P.1+P681R (n = 13/20, 65%) sequences detected outside the Amazonas state, respectively. 2022 Microbiology spectrum Result SARS_CoV_2 P681H;P681R 133;166 138;171 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. The Maximum Likelihood (ML) phylogenetic analysis supports that NTD deletions around position Y144 arose multiple (n > 20) times during the evolution of lineage P.1 in Brazil, in agreement with our previous observations, as well as mutations S:N679K (n > 5), S:P681H (n > 4) and S:P681R (n > 3). 2022 Microbiology spectrum Result SARS_CoV_2 N679K;P681H;P681R 244;261;281 249;266;286 S;S;S 242;259;279 243;260;280 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. The P.1+NTDdel variants increased from 1.6% in January to 12.4% in May 2021, while the P.1+N679K and P.1+P681H variants increased from 0% to 25.4% and 17.6%, respectively, in the same period. 2022 Microbiology spectrum Result SARS_CoV_2 N679K;P681H 91;105 96;110 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. To determine if the most frequent P.1 mutations detected in Brazil resulted from independent convergent mutations events, we combined the Amazonian P.1 sequences generated in this and previous studies with P.1+NTDdel (Delta144, Delta143-144, and Delta141-144), P.1+N679K and P.1+P681H/R sequences detected in other Brazilian states that were available at the EpiCoV database in GISAID (https://www.gisaid.org/). 2022 Microbiology spectrum Result SARS_CoV_2 N679K;P681H;P681R 265;279;279 270;286;286 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. We hypothesize that mutation S:N679K may also benefit the enzyme-substrate coupling. 2022 Microbiology spectrum Result SARS_CoV_2 N679K 31 36 S 29 30 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. Using the LightCycler 96 Thermocycler (Roche, Mannheim, Germany), the LoD obtained from the 20 replicate tests was 30 copies/muL for the mutant N501Y and 60 copies/muL for the mutants DeltaHV 69/70, K417N, E484K, L452R, and P681R (Table 1). 2022 Microbiology spectrum Result SARS_CoV_2 E484K;K417N;L452R;N501Y;P681R 206;199;213;144;224 211;204;218;149;229 35197485 An adjuvanted subunit SARS-CoV-2 spike protein vaccine provides protection against Covid-19 infection and transmission. Next, sera were assessed for neutralizing activity against wild-type D614G or the delta variant of SARS-CoV-2 virus. 2022 NPJ vaccines Result SARS_CoV_2 D614G 69 74 35197485 An adjuvanted subunit SARS-CoV-2 spike protein vaccine provides protection against Covid-19 infection and transmission. Responses in vaccinated animals were compared to serum samples collected 21 days post-infection of unvaccinated hamsters with wild-type D614G SARS-CoV-2 virus (WT convalescent sera). 2022 NPJ vaccines Result SARS_CoV_2 D614G 136 141 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. As expected, A23056C, C26309A, and C26351T mutations emerged in P1, and the proportion of Q498H (S), A22D (E), and A36V (E) mutations and other four mutations (ORF 1a) in aged BALB/c mouse-adapted virus gradually increased following the subsequent passages ( Figures 1D, E ), so did the Q498H (S), A22D (E), and other four mutations (ORF 1a) in aged C57BL/6N mouse-adapted virus ( Figures 1F, G ). 2022 Frontiers in immunology Result SARS_CoV_2 A22D;A22D;A23056C;A36V;C26309A;C26351T;Q498H;Q498H 101;298;13;115;22;35;90;287 105;302;20;119;29;42;95;292 E;E;E;E;S;S 107;121;271;304;97;294 108;122;272;305;98;295 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. Five mutations, including T819I (nsp2), L1790F (nsp3), I65S (nsp9), Q498H (S), and A22D (E), emerged in both strains. 2022 Frontiers in immunology Result SARS_CoV_2 A22D;I65S;L1790F;Q498H;T819I 83;55;40;68;26 87;59;46;73;31 Nsp2;Nsp3;E;S 33;48;89;75 37;52;90;76 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. In addition, the BMA8 variant had two more mutations at T67A (nsp9) and A36V (E), and C57MA14 variant had one more mutation at P252L (nsp5) ( Figure 1C ). 2022 Frontiers in immunology Result SARS_CoV_2 A36V;P252L;T67A 72;127;56 76;132;60 Nsp5;E 134;78 138;79 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. In sum, these data indicated that the increased virulence of BMA8 and C57MA14 in mice was likely related to the emergence of Q498H substitution in the RBD of SARS-CoV-2 BMA8 and C57MA14 variants and enhanced binding affinity between RBD containing Q498H mutation and mACE2 receptor. 2022 Frontiers in immunology Result SARS_CoV_2 Q498H;Q498H 125;248 130;253 RBD;RBD 151;233 154;236 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. The A23056C mutation resulted in a Q498H amino acid substitution in the RBD of the S protein; structural remodeling suggested that the Q498H substitution in the RBD of SARS-CoV-2 S protein increased the binding affinity of the protein to mACE2 ( Figure 6B ). 2022 Frontiers in immunology Result SARS_CoV_2 A23056C;Q498H;Q498H 4;35;135 11;40;140 RBD;RBD;S;S 72;161;83;179 75;164;84;180 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. 450 nM) (Table 1), whereas the S339F variant had a marginal increase affinity at cleavage site two (KD, 20 nM vs. 2022 Life (Basel, Switzerland) Result SARS_CoV_2 S339F 31 36 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. Another variant that established direct contact with the S protein was S339F, where it formed a hydrogen bond with Q872. 2022 Life (Basel, Switzerland) Result SARS_CoV_2 S339F 71 76 S 57 58 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. Interestingly, although D435, S460 and G462 residues are important for the substrate binding, D435Y, S460R and G462D/G462S variants were all carried by European population only. 2022 Life (Basel, Switzerland) Result SARS_CoV_2 D435Y;G462D;S460R;G462S 94;111;101;117 99;116;106;122 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. Particularly, all nine populations carried V160M variants with high allele frequency. 2022 Life (Basel, Switzerland) Result SARS_CoV_2 V160M 43 48 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. Similar to the interactions at cleavage site one above, we predicted that the natural G462D and G462S variants would change the binding affinity to the S protein in similar fashions discussed above. 2022 Life (Basel, Switzerland) Result SARS_CoV_2 G462D;G462S 86;96 91;101 S 152 153 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. Similarly, the G462S variant had a decreased affinity at both sites (KD, 620 nM and 36 nM at cleavage sites one and two, respectively). 2022 Life (Basel, Switzerland) Result SARS_CoV_2 G462S 15 20 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. the C297S variant showed marginally lower predicted affinity for the S protein at cleavage site two (KD, 32 nM vs. 2022 Life (Basel, Switzerland) Result SARS_CoV_2 C297S 4 9 S 69 70 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. The C297S variant, however, had completely abolished the disulphide bond but retained the contacts with the S protein, and the bonds were longer. 2022 Life (Basel, Switzerland) Result SARS_CoV_2 C297S 4 9 S 108 109 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. The effect of natural S460R polymorphism, which replaced serine with the longer side-chained arginine had introduced a positive charge and therefore might contribute to an optimal interaction. 2022 Life (Basel, Switzerland) Result SARS_CoV_2 S460R 22 27 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. The effects of D435Y and S460R variants, similar to the interactions at cleavage site one, were increased hydrophobicity at position 435 and the introduction of a positive charge at position 460, respectively. 2022 Life (Basel, Switzerland) Result SARS_CoV_2 D435Y;S460R 15;25 20;30 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. The G462S variant had maintained its hydrogen bond with camostat mesylate (Figure 6a) and no interaction with nafamostat (Figure 6b) was observed. 2022 Life (Basel, Switzerland) Result SARS_CoV_2 G462S 4 9 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. The natural C297S variant, however, which completely abolished this bond by introducing a serine, established new several polar contacts with its adjacent residues. 2022 Life (Basel, Switzerland) Result SARS_CoV_2 C297S 12 17 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. The predicted effect of the D435Y variant was increased hydrophobicity at the protein interface by replacing the negatively-charged aspartate with a hydrophobic residue, which could contribute to a change in binding affinity. 2022 Life (Basel, Switzerland) Result SARS_CoV_2 D435Y 28 33 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. The S460R variant, on the other hand, did not interact with camostat mesylate but instead caused disruption to the polar contact between W461 and the oxygen atom of camostat mesylate (Figure 6a). 2022 Life (Basel, Switzerland) Result SARS_CoV_2 S460R 4 9 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. We found that both the G462D and G462S variants had an apparent decrease in predicted binding affinity for the S protein at both cleavage sites. 2022 Life (Basel, Switzerland) Result SARS_CoV_2 G462D;G462S 23;33 28;38 S 111 112 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. According to the corresponding experimental results, for templates containing L452R and L452P mutations and no mutations, the detection signal is HEX, no signal detection, and FAM. 2022 Micromachines Result SARS_CoV_2 L452P;L452R 88;78 93;83 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. The cDNA was added to the PARMS PCR system containing the detection of L452R and K417N mutation sites, and each group was repeated 3 times to quickly detect and type the SARS-CoV-2 strain. 2022 Micromachines Result SARS_CoV_2 K417N;L452R 81;71 86;76 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. The L452R site was screened, and one strain was detected with HEX fluorescence signal, which was judged to be the Delta strain, and the FAM signal was detected in other samples, which was consistent with the sequencing results; The K417N site was also screened, a HEX fluorescent signal was detected in a certain strain, and it was judged to be a Beta strain. 2022 Micromachines Result SARS_CoV_2 K417N;L452R 232;4 237;9 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. To test the sensitivity of PARMS technology, add 3 SARS-CoV-2 plasmid fragments containing L452R, E484K, and N501Y mutation sites to the pre-prepared PARMS PCR system containing 452, 484, and 501 labeled primers at a concentration of 1.28 x 1010-1.28 copies/muL from high to low, doing 3 repetitions for each concentration gradient at the same time, repeating 3 groups respectively. 2022 Micromachines Result SARS_CoV_2 E484K;L452R;N501Y 98;91;109 103;96;114 35208270 Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. To test the specificity of PARMS technology, take the 452 site as an example, add the three neocorona plasmid fragments containing L452R, L452P mutation, and no mutation at a concentration of 1.28 x 105 copies/muL into the pre-prepared PARMS PCR system containing L452R labeled primers, and do 3 repeats at the same time. 2022 Micromachines Result SARS_CoV_2 L452P;L452R;L452R 138;131;264 143;136;269 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. In particular, in the former assay, L452R mutations were observed for two samples positive for E484K. 2022 Microorganisms Result SARS_CoV_2 E484K;L452R 95;36 100;41 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. In the latter assay, one sample was identified as wild type instead of Delta (B.1.617.2) for the L452R mutation, and in another sample, Gamma (P.1) was only positive for N501Y with a drop-out for the E484K mutation. 2022 Microorganisms Result SARS_CoV_2 E484K;L452R;N501Y 200;97;170 205;102;175 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? A similar occurrence was also detected for the nucleotide cytosine in position (3037) (C3037T) affecting 1433 (87.91%) genomes causing an amino acid changing mutation in P314L, affecting the NSP12 (non-structural protein 12) and the viral RNA-dependent RNA polymerase (Figure 6 and Figure 7). 2022 Microorganisms Result SARS_CoV_2 P314L;C3037T 170;87 175;93 RdRp;Nsp12 239;191 267;196 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? In addition, fifteen other substitutions affect the spike protein including Q954H, N764K, H655Y, K417N, G339D, N211K, Q493R, S371L, S373P, S375F, S477N, T478K, E484A, N440K and G446S were detected as the most frequent mutation events in more than 84% of total genomes. 2022 Microorganisms Result SARS_CoV_2 E484A;G339D;G446S;H655Y;K417N;N211K;N440K;N764K;Q493R;Q954H;S371L;S373P;S375F;S477N;T478K 160;104;177;90;97;111;167;83;118;76;125;132;139;146;153 165;109;182;95;102;116;172;88;123;81;130;137;144;151;158 S 52 57 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? In addition, mutations affecting other protein sequences appeared frequently including; N:RG203KR and N:G212V (Nucleocapsid protein N) with (636 genomes, 39.01%) and (339 genomes, 20.79%), respectively, M:I82T (Membrane protein) (411 genomes, 25, 25%), NSP3:T428I (phosphoesterase, papain-like proteinase) (400, genomes, 24.53%), ORF3a protein (ORF3a:Q57H) (350 genomes, 21, 47%), S:N501Y (Spike protein) (163 genomes, 10.0%), and E:V5F (Envelope protein) with a lower occurrence (2.21%) of total SARS-CoV-2 genomes (Figure 7). 2022 Microorganisms Result SARS_CoV_2 G212V;I82T;N501Y;Q57H;T428I;V5F 104;205;383;351;258;433 109;209;388;355;263;436 N;Membrane;S;ORF3a;ORF3a;Nsp3;E;N;N;N;S 111;211;390;330;345;253;431;88;102;132;381 123;219;395;335;350;257;432;89;103;133;382 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? Overall, the C>T transition presents the most common events accounting for 42.63% with 18,198 in total, followed by G>T transversion at 16.81% with 7178 occurrence, A>G transition with 4449 events (10.42%) and G>A transition with 2071 (6.83%) of all observed viral mutations. 2022 Microorganisms Result SARS_CoV_2 A4449G;G2071A 165;210 189;234 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? The amino acid substitutions (D614G, D614G, D796Y, T547K, N856K, N679K, N969K, P681H, L981F) in the spike protein, P314L, A1892T, T492I, I189V and A1892T in the non-structural proteins (NSP3, NSP4, NPS6, and NSP12b) occurred in 100% of analyzed SARS-CoV-2 genomes. 2022 Microorganisms Result SARS_CoV_2 A1892T;A1892T;D614G;D796Y;I189V;L981F;N679K;N856K;N969K;P314L;P681H;T492I;T547K;D614G 122;147;37;44;137;86;65;58;72;115;79;130;51;30 128;153;42;49;142;91;70;63;77;120;84;135;56;35 S;Nsp3;Nsp4 100;186;192 105;190;196 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? The effects of mutations on the protein sequences of SARS-CoV-2 highlighted similar profiles in the North African countries with a mutation affecting the nucleotide adenosine in position (23,403) transformed into a guanosine (A23403G) causing a D614G spike (S) variant as the most common amino acid change occurring in 1553 (95.27%) of total SARS-CoV-2 genomes. 2022 Microorganisms Result SARS_CoV_2 D614G;A23403G 245;226 250;233 S;S 251;258 256;259 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? The time course of the phylogenetic analysis and clade distribution showed that clades G (Variant S-D614G), GH (Variant ORF3a-Q57H) and GR (Variant N-G204R) were the most prevalent in the first and second waves of viral introductions. 2022 Microorganisms Result SARS_CoV_2 D614G;G204R;Q57H 100;150;126 105;155;130 ORF3a;N;S 120;148;98 125;149;99 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? Two other silent mutations were noted including C241T (92.57%) and C14408T (87.91%), targeting the 5'UTR and the NSP3 (a viral predicted phosphoesterase) in position 14408. 2022 Microorganisms Result SARS_CoV_2 C14408T;C241T 67;48 74;53 5'UTR;Nsp3 99;113 104;117 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. A separate phylogenetic analysis was conducted with neigbouring representative sequences (in Nextstrain clade tree) of African, Indonesian and Malaysian lineages (Fig 2C) with Pahang SARS-CoV-2 D614G variants genomes. 2022 PloS one Result SARS_CoV_2 D614G 194 199 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Amino acid mutations in spike protein of the Pahang- D614G variant SARS-CoV-2. 2022 PloS one Result SARS_CoV_2 D614G 53 58 S 24 29 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Based on the GISAID database analysis, there were 41 lineages of D614G variant dispersed throughout Malaysia. 2022 PloS one Result SARS_CoV_2 D614G 65 70 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Evolution of D614G variant of SARS-CoV-2 in the Malaysian population. 2022 PloS one Result SARS_CoV_2 D614G 13 18 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Genomes of Pahang SARS-CoV-2 D614G variants were found congregrated into African, Indonesian and Malaysian lineages (Fig 2B and 2C). 2022 PloS one Result SARS_CoV_2 D614G 29 34 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. In addition to D614G mutation, B.1.524 also carries A701V mutation in the spike protein. 2022 PloS one Result SARS_CoV_2 A701V;D614G 52;15 57;20 S 74 79 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. In addition, PROVEAN and SNAP2 predicted decrease stability due to G1223C mutation in spike protein (Table 3). 2022 PloS one Result SARS_CoV_2 G1223C 67 73 S 86 91 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. In order to further resolve the phylogenetic analyses of the D614G variant actively spreading in Pahang. 2022 PloS one Result SARS_CoV_2 D614G 61 66 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. It appeared that of the six D614G variant clades (GH, G, GR, GRY, O and GV), GH makes up the largest clade with 760 of genomes from different lineages (Fig 1B). 2022 PloS one Result SARS_CoV_2 D614G 28 33 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Next, we investigated the frequency of D614G variant clades circulating in Malaysia until July 2021. 2022 PloS one Result SARS_CoV_2 D614G 39 44 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Of note, mCSM-PPI2 is unable to predict the change in protein interaction affinity in deletions, hence analysis on L241del, L242del and A243del were not included in Table 2. 2022 PloS one Result SARS_CoV_2 A243del;L241del;L242del 136;115;124 143;122;131 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Of the 1,502 SARS-CoV-2 complete genomes deposited to GISAID database, 1,356 contained spike D614G mutation in their genomes. 2022 PloS one Result SARS_CoV_2 D614G 93 98 S 87 92 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Of these two, B.1.524, which was first detected in September, 2020, had silently caused the largest local transmission of the D614G variant in Malaysia (n = 419), followed by AU.2 (n = 311). 2022 PloS one Result SARS_CoV_2 D614G 126 131 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Our analysis revealed that all of Pahang's SARS-CoV-2 isolates has a unique substitution mutation of Glycine (G) to Cysteine (C) at position 1223 (G1223C) which was not found in the other 976 genomes (Fig 3). 2022 PloS one Result SARS_CoV_2 G1223C 147 153 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Our findings on genomic surveillance in depicting local transmission and evolution of the D614G variant revealed that two of the variants had emerged locally: B.1.524, and AU.2, (S2 Table, highlighted in grey) here referred to as Malaysian lineages. 2022 PloS one Result SARS_CoV_2 D614G 90 95 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Taken together, the missense mutations, L18F, N501Y, A701V and G1223C seem to have increased the binding affinity of the spike protein, whereas mutations D80A, D215G, K417N, N439K, E484K and A688S had the opposite effect. 2022 PloS one Result SARS_CoV_2 A688S;A701V;D215G;D80A;E484K;G1223C;K417N;L18F;N439K;N501Y 191;53;160;154;181;63;167;40;174;46 196;58;165;158;186;69;172;44;179;51 S 121 126 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. To analyse the impact of G1223C mutation in the TM region of spike protein, a 3D structure model of the SARS-CoV-2 spike protein TM domain (7LC8) was retrieved from RCSB Protein Data Bank and was uploaded to mCSM-PPI2 server. 2022 PloS one Result SARS_CoV_2 G1223C 25 31 S;S 61;115 66;120 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. To better characterize the local distribution of lineages that may contribute to the constant increase in COVID-19 cases in Malaysia, Fig 1 summarizes the distribution of the D614G variant lineages throughout the country since it was first detected on March 21, 2020. 2022 PloS one Result SARS_CoV_2 D614G 175 180 COVID-19 106 114 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. To infer the origin of the D614G variant that was responsible in causing widespread COVID-19 infections in Pahang this year, we built a NJ phylogenetic tree using complete genomes of D614G variant of Malaysian origin retrieved from GISAID along with sequence data from this study. 2022 PloS one Result SARS_CoV_2 D614G;D614G 27;183 32;188 COVID-19 84 92 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Unique mutation, G1223C, does not cause significant structural rearrangement of the TM domain, except for the gain in salt bridge between C1223 and G1219 (Fig 4). 2022 PloS one Result SARS_CoV_2 G1223C 17 23 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Using Nextclade v.1.5.2 for clade assignment, mutation calling and sequence quality checks (https://clades.nextstrain.org), 1356 complete genomes of the D614G variant were analysed for sequence quality and mutations. 2022 PloS one Result SARS_CoV_2 D614G 153 158 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Whereas, AU.2 carries a mutation at positions N439K, P681R and G1251V. 2022 PloS one Result SARS_CoV_2 G1251V;N439K;P681R 63;46;53 69;51;58 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. While the B.1.524 may have contributed heavily to the active spreading of D614G lineage locally, the data suggest that the AU.2 lineage, which was first detected on January 3, 2021 (S2 Table, highlighted grey), is currently taking its place as the major D614G variant contributor in spreading the disease. 2022 PloS one Result SARS_CoV_2 D614G;D614G 74;254 79;259 35215765 Versatile SARS-CoV-2 Reverse-Genetics Systems for the Study of Antiviral Resistance and Replication. Additionally, we investigated two low prevalence variants found in the GenBank database, A97V, and N491S. 2022 Viruses Result SARS_CoV_2 A97V;N491S 89;99 93;104 35215765 Versatile SARS-CoV-2 Reverse-Genetics Systems for the Study of Antiviral Resistance and Replication. Among natural nsp12 polymorphisms, we investigated the P323L mutation, known as the major polymorphic site of nsp12 (>90% prevalence found in GISAID EpiCov database accessed 10 May 2021). 2022 Viruses Result SARS_CoV_2 P323L 55 60 Nsp12;Nsp12 14;110 19;115 35215765 Versatile SARS-CoV-2 Reverse-Genetics Systems for the Study of Antiviral Resistance and Replication. However, as previously demonstrated, the virus evolves in cell culture and a single change in the S coding region (S247R) was already detected in over 40% of the viral population (Table 2). 2022 Viruses Result SARS_CoV_2 S247R 115 120 S 98 99 35215765 Versatile SARS-CoV-2 Reverse-Genetics Systems for the Study of Antiviral Resistance and Replication. Our patient-isolate already carried an L in contrast to the Wuhan-1 reference sequence (NC_045512), which carried a P, thus we generated the L323P mutant. 2022 Viruses Result SARS_CoV_2 L323P 141 146 35215765 Versatile SARS-CoV-2 Reverse-Genetics Systems for the Study of Antiviral Resistance and Replication. These results indicate that neither the identified nsp12 polymorphic changes nor the previously described coronavirus resistance-associated substitutions V557L and F480L significantly affect SARS-CoV-2 drug susceptibility under our experimental conditions. 2022 Viruses Result SARS_CoV_2 F480L;V557L 164;154 169;159 Nsp12 51 56 35215765 Versatile SARS-CoV-2 Reverse-Genetics Systems for the Study of Antiviral Resistance and Replication. To verify whether the nsp12 mutations F480L and V557L conferring SARS-CoV resistance to remdesivir (6-fold increase in EC50) in cell culture, would in fact also confer SARS-CoV-2 resistance, we engineered these mutations into our full-length clone both individually and in combination. 2022 Viruses Result SARS_CoV_2 F480L;V557L 38;48 43;53 Nsp12 22 27 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. All the patients recovered from COVID-19, except the two patients with the Q493R-acquired mutations. 2022 Viruses Result SARS_CoV_2 Q493R 75 80 COVID-19 32 40 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. At baseline, the E484K mutation was detected in only one sample issued from patient P6, and Sanger sequencing confirmed the presence of a Variant of Concern (VOC), the Gamma (20J/501Y.V3) variant. 2022 Viruses Result SARS_CoV_2 E484K 17 22 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. Clinically, in both of them, the presence of the Q493R mutation was associated with a relapse of COVID-19 with a distress respiratory syndrome. 2022 Viruses Result SARS_CoV_2 Q493R 49 54 COVID-19;Acute respiratory distress syndrome 97;113 105;142 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. In total, five mutations (A67V, E406E/G, D427D/Y, Q493R and G1204G/E) appeared in the S gene in samples taken from four patients (P2, P3, P5 and P6), three of whom were receiving bamlanivimab therapy (one as a monotherapy and two in combination) and one a combination of casirivimab/imdevimab. 2022 Viruses Result SARS_CoV_2 D427D;D427Y;E406E;E406G;G1204G;G1204E;Q493R;A67V 41;41;32;32;60;60;50;26 48;48;39;39;68;68;55;30 S 86 87 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. On day 68, the S gene sequencing revealed the acquisition of two news mutations, A67V and mixed D427D/Y (Figure 1). 2022 Viruses Result SARS_CoV_2 A67V;D427D;D427Y 81;96;96 85;103;103 S 15 16 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. One patient was infected with a SARS-CoV-2 variant reported in Belgium in March 2021, which was associated with four mutations (Q414K, N450K, D614G and T716I) and an insertion of three amino acids at position 213 (TDR) in the S gene. 2022 Viruses Result SARS_CoV_2 D614G;ins 213;N450K;T716I;Q414K 142;166;135;152;128 147;212;140;157;133 S 226 227 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. The emergence of Q493R was associated with a rise in the SARS-CoV-2 viral load in nasopharyngeal samples (P5: Ct value from 26 on day 19 to 18 on day 68 and P2: Ct from 28 before acquisition of the Q493Q/R to 22 on day 6), as opposed to the mutations G1204E and E406G (Table 1). 2022 Viruses Result SARS_CoV_2 E406G;G1204E;Q493Q;Q493R;Q493R 262;251;198;198;17 267;257;205;205;22 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. The mutation Q493R was identified in two patients; in patient P2, a mixture of Q493Q/R was detected in the sample collected after the administration of bamlanivimab monotherapy, while in patient P5, four samples harbored the mutation Q493R after the administration of the bamlanivimab/etesevimab combination. 2022 Viruses Result SARS_CoV_2 Q493Q;Q493R;Q493R;Q493R 79;79;13;234 86;86;18;239 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. The mutations G1204E and E406G were identified in the mixed population with the wild amino acid and were absent in the following sample. 2022 Viruses Result SARS_CoV_2 E406G;G1204E 25;14 30;20 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. The patient P2 died about two weeks after the emergence of the Q493R, while the patient P5 died about 7 weeks after. 2022 Viruses Result SARS_CoV_2 Q493R 63 68 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. Twelve days after the second injection (D19), the viral load increased again, and this was associated with the appearance of the mutation Q493R, which remained present in all the following samples (D25, D52 and D68). 2022 Viruses Result SARS_CoV_2 Q493R 138 143 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. Two of them also harbored polymorphism mutations (P12: K182R and P13: S98F) which remained present during the follow-up (Table 1). 2022 Viruses Result SARS_CoV_2 K182R;S98F 55;70 60;74 35215823 Characterization of a Broadly Neutralizing Monoclonal Antibody against SARS-CoV-2 Variants. Furthermore, based on the sequence analysis, purified virus plaque with a single amino acid mutation at Val 483 Phe (SARS-CoV-2WT/em483) or Tyr 489 His (SARS-CoV-2WT/em489) was assessed by virus neutralization assay. 2022 Viruses Result SARS_CoV_2 Y489H;V483F 140;104 151;115 35215823 Characterization of a Broadly Neutralizing Monoclonal Antibody against SARS-CoV-2 Variants. Of the 5,343,811 available sequences, the mutation V483F appeared in 2699 sequences (0.0005%), and V483A appeared in 328 sequences, while 99.93% of the sequences were invariant. 2022 Viruses Result SARS_CoV_2 V483A;V483F 99;51 104;56 35215823 Characterization of a Broadly Neutralizing Monoclonal Antibody against SARS-CoV-2 Variants. Our study revealed that the amino acid residues V483F and Y489H within the RBD of an S protein might have an impact on ACE2 binding. 2022 Viruses Result SARS_CoV_2 V483F;Y489H 48;58 53;63 RBD;S 75;85 78;86 35215823 Characterization of a Broadly Neutralizing Monoclonal Antibody against SARS-CoV-2 Variants. The sequences of S from plaque-purified viruses carried single-point mutations at amino acid position V483F (Val to Phe) or Y489H (Tyr to His). 2022 Viruses Result SARS_CoV_2 V483F;Y489H 102;124 107;129 S 17 18 35215911 Ferristatin II Efficiently Inhibits SARS-CoV-2 Replication in Vero Cells. Due to the significant differences in the RBD proteins of the Wuhan D614G and the Omicron SARS-CoV-2 variants, the latter could not be detected in cell-based ELISA using the available anti-RBD antibody, as it was raised to the RBD of original SARS-CoV-2 strain. 2022 Viruses Result SARS_CoV_2 D614G 68 73 RBD;RBD;RBD 42;189;227 45;192;230 35215911 Ferristatin II Efficiently Inhibits SARS-CoV-2 Replication in Vero Cells. The detection of viral antigen in cell-base ELISA found that the IC50 values for ferristatin II were 26.5 and 40.4 microM for the Wuhan D614G and Delta viruses, respectively (Figure 2A). 2022 Viruses Result SARS_CoV_2 D614G 136 141 35215911 Ferristatin II Efficiently Inhibits SARS-CoV-2 Replication in Vero Cells. The quantification of the virus titers in culture media confirmed that the release of the virus from the infected cells into the culture medium was inhibited by ferristatin II, starting from 25 microM concentration, and IC50 values calculated from the reduction in TCID50 titers were 24.0 and 25.2 microM for the Wuhan D614G and Delta viruses, respectively. 2022 Viruses Result SARS_CoV_2 D614G 319 324 35215911 Ferristatin II Efficiently Inhibits SARS-CoV-2 Replication in Vero Cells. Therefore, the selectivity indices (determined as a ration of CC50 to IC50 values) for ferristatin II were >10, >15 and >64 for Wuhan D614G, Delta and Omicron SARS-CoV-2 strains, respectively. 2022 Viruses Result SARS_CoV_2 D614G 134 139 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Additionally, we noticed a convergent mutation of L37 in E, detecting two mutations resulting in L37F and L37R. 2022 Viruses Result SARS_CoV_2 L37F;L37R 97;106 101;110 E 57 58 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Analysing mutations in the PHE passage series, we identified four changes (C8782T; T18488T; T28144C; A29596G) relative to Wuhan-Hu-1 consistently at ~100% at all passages, likely reflecting fixation in the original virus stock (Figure 2a). 2022 Viruses Result SARS_CoV_2 A29596G;T18488T;T28144C;C8782T 101;83;92;75 108;90;99;81 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Deletion of the PBCS ablated the T23605G synonymous variant in the process. 2022 Viruses Result SARS_CoV_2 T23605G 33 40 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Like PHE, we also detected minor variants (nine), including G1251V and S1252C in Spike. 2022 Viruses Result SARS_CoV_2 G1251V;S1252C 60;71 66;77 S 81 86 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Like PHE, we identified mutations arising rapidly upon consecutive passage in Vero cells (i.e., were not detected at P2), including the non-synonymous mutations T293I in NSP12 and P812R in Spike. 2022 Viruses Result SARS_CoV_2 P812R;T293I 180;161 185;166 S;Nsp12 189;170 194;175 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. PHE is from clade A and does not contain the D614G substitution in Spike (Supplementary Table S1). 2022 Viruses Result SARS_CoV_2 D614G 45 50 S 67 72 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Similar to passage in Vero cells, we identified two mutations in Spike (G1251V and S1252C), which appeared at low frequencies (<10%) and never increased (Table S1). 2022 Viruses Result SARS_CoV_2 S1252C;G1251V 83;72 89;78 S 65 70 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. These changes included, but were not limited to, D614G in Spike; R203K and G204K in N; and an out-of-frame deletion of five nucleotides in ORF7A, leading to its premature truncation. 2022 Viruses Result SARS_CoV_2 D614G;G204K;R203K 49;75;65 54;80;70 ORF7a;S;N 139;58;84 144;63;85 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. This strain represents an isolate from the UK's "first wave" and is a representative of clade B that contains the D614G mutation in Spike (Table S1). 2022 Viruses Result SARS_CoV_2 D614G 114 119 S 132 137 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. To test this hypothesis, we focused subsequent analysis on PHE and BT20.1 Vero P4 stocks with clear genetic differences between them, including the PHE PBCS deletion in Spike, and the P812R (Spike) and NSP12 mutations in BT20.1. 2022 Viruses Result SARS_CoV_2 P812R 184 189 S;S;Nsp12 169;191;202 174;196;207 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Two of these Spike NTD mutations were similar to mutations occurring in VOCs: D215G and an out-of-frame deletion of 24 nucleotides (GCTATACATGTCTCTGGGACCAATGGTA21761G), resulting in a loss of nine amino acids IHVSGTNGT (aa67-76). 2022 Viruses Result SARS_CoV_2 D215G 78 83 S 13 18 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. With the core changes described above, two major mutations were observed: a synonymous (T23605G) and non-synonymous out-of-frame deletion (deletion of 24 nucleotides AATTCTCCTCGGCGGGCACGTAGTG 23597A; resulting in the replacement of nine amino acids (679-687; NSPRRARSV) in Spike with an isoleucine (I)) mapping to the polybasic cleavage site (PBCS) (Figure 2a). 2022 Viruses Result SARS_CoV_2 T23605G 88 95 S 273 278 35215963 Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic. All seven SARS-CoV-2 isolates showed similar growth kinetic profiles in Vero cells, with no significant difference in the viral replication slope, regardless of the presence or absence of the D614G amino acid substitution in the spike gene (Figure 7A). 2022 Viruses Result SARS_CoV_2 D614G 192 197 S 229 234 35215963 Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic. Finally, the seven SARS-CoV-2 isolates carried a variety of single nucleotide polymorphisms (SNP) relative to the reference sequence (SARS-CoV-2 isolate Wuhan-Hu-1 NC_045512), including a total of 27 non-synonymous mutations across the genome in different non-structural proteins (nsp), mainly in the RdRp (D54Y and P314L), the papain-like proteinase (nsp3, S126L and T1335I), and nucleocapsid (D22G, S183Y, and D377G) genes (Figure 5). 2022 Viruses Result SARS_CoV_2 D377G;P314L;S126L;S183Y;T1335I;D22G;D54Y 412;316;358;401;368;395;307 417;321;363;406;374;399;311 N;Nsp3;RdRP 381;352;301 393;356;305 35215963 Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic. Interestingly, although the SARS-CoV-2 spike neutralizing mAb was able to block the replication of all seven SARS-CoV-2 isolates, viruses carrying the D614G mutation in the spike gene (NZ3, NZ4, NZ5, and NZ7) were 2.4-fold more susceptible to the mAb than the wild-type viruses (median EC50 of 0.07 and 0.17 microg/mL, p < 0.0001, respectively; Figure 8). 2022 Viruses Result SARS_CoV_2 D614G 151 156 S;S 39;173 44;178 35215963 Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic. Perhaps the most relevant amino acid substitution, i.e., the D614G in the spike gene, was observed in the sequence of four out of seven SARS-CoV-2 isolates (NZ3, NZ4, NZ5, and NZ7; Figure 5). 2022 Viruses Result SARS_CoV_2 D614G 61 66 S 74 79 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. According to the phylogenetic and MSN reconstructions, only one sequence, "VO_SR_65" (haplotype G11083T, G26144T, C22088T), shares a private mutation with a Polish sequence, EPI_ISL_455452 (haplotypes C4338T, T9743C, G11083T, G26144T, and C22088T). 2022 Viruses Result SARS_CoV_2 C22088T;C22088T;C4338T;G11083T;G11083T;G26144T;G26144T;T9743C 114;239;201;96;217;105;226;209 121;246;207;103;224;112;233;215 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. All the viral sequences were characterized by two mutations, G11083T and G26144T (from here on reported as the ancestor haplotype, AH). 2022 Viruses Result SARS_CoV_2 G11083T;G26144T 61;73 68;80 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. At the gene level, G26144T mutation leads to an NS3:G251V amino acid change, which was reported to increase disease severity by 4.4 times. 2022 Viruses Result SARS_CoV_2 G26144T;G251V 19;52 26;57 NS3 48 51 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. Conversely, the G11083T mutation appears in recently collected sequences belonging to different lineages, suggesting that this is another example of homoplasy (Figure S1). 2022 Viruses Result SARS_CoV_2 G11083T 16 23 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. G11083T (NSP6:L37F), on the other hand, has been hypothesized to prevent the fusion of the autophagosomes to the cell lysosomes, affecting viral replication and evasion from cellular immunity. 2022 Viruses Result SARS_CoV_2 L37F;G11083T 14;0 18;7 Nsp6 9 13 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. G26144T was mostly associated with G11083T in lineage B and disappeared in April 2021 after reaching a peak at the beginning of the pandemic (February-April 2020). 2022 Viruses Result SARS_CoV_2 G11083T;G26144T 35;0 42;7 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. Household 456, where one household member was characterized by the AH (haplotype G11083T and G26144T), the second one acquired a novel private mutation (haplotype G11083T, G26144T, and C27972A), and the third one further acquired another private mutation (haplotype G11083T, G26144T, C27972A, and C26936T), likely reflects the direction of transmission and the sequential viral evolution during transmission among household members. 2022 Viruses Result SARS_CoV_2 C26936T;C27972A;C27972A;G11083T;G11083T;G11083T;G26144T;G26144T;G26144T 297;185;284;81;163;266;93;172;275 304;192;291;88;170;273;100;179;282 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. Households 838 and 219, where 2 out of 2 and 3 out of 3 family members shared the same haplotypes (G11083T, G26144T, T2248C, and C21575T and G11083T, G26144T, G1944A, T9731C, G15957T, and G20378T, respectively), exemplify this phenomenon. 2022 Viruses Result SARS_CoV_2 C21575T;G11083T;G15957T;G1944A;G20378T;G26144T;G26144T;T2248C;T9731C;G11083T 129;141;175;159;188;108;150;117;167;99 136;148;182;165;195;115;157;123;173;106 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. Interestingly, the mutation Spike:L5F (C21575T), which characterized the viral haplotype of two subjects in Vo', emerged from January 2021 to August 2021 as part of the mutation pattern defining the B.1.526 lineage (Iota variant), prevalent in the USA (Figure S2). 2022 Viruses Result SARS_CoV_2 C21575T;L5F 39;34 46;37 S 28 33 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. Of the 42 unique point mutations defining the different haplotypes (including G11083T and G26144T) mapped along different regions of the viral sequence, 1 was in the 5'-UTR (2.4%), 15 were synonymous (35.7%), and 26 were non-synonymous (61.9%). 2022 Viruses Result SARS_CoV_2 G11083T;G26144T 78;90 85;97 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. Studies on Spike:L5F highlighted the increase in the protein folding and assembly of virions, as well as the increase in CD8 T cell recognition and killing. 2022 Viruses Result SARS_CoV_2 L5F 17 20 S 11 16 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. The sequencing data indicate that the B lineage haplotypes introduced in the Veneto region, like the ones identified in Vo', derive from the AH, carrying G11083T and G26144T mutations that further developed new additional mutations. 2022 Viruses Result SARS_CoV_2 G11083T;G26144T 154;166 161;173 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. According to our data, most of these mutations, particularly G496S, Y505H, S371L, and S373P, could indeed adversely affect protein stability and binding affinity with Nb6 nanobody (Figure 7A,B). 2022 International journal of molecular sciences Result SARS_CoV_2 G496S;S371L;S373P;Y505H 61;75;86;68 66;80;91;73 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. According to the recent study, the Omicron variant can escape the neutralization of many monoclonal antibodies, where the K417N, Q493R, and E484A Omicron mutations affect the recognition of class 1 and 2 antibodies targeting the ACE2 binding epitope. 2022 International journal of molecular sciences Result SARS_CoV_2 E484A;K417N;Q493R 140;122;129 145;127;134 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. For VHH E binding, the large binding affinity loss resulted from E484A, Q493R, G496S, and N501Y mutations (Figure 7C,D). 2022 International journal of molecular sciences Result SARS_CoV_2 E484A;G496S;N501Y;Q493R 65;79;90;72 70;84;95;77 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. Hence, multiple Omicron RBD mutations (such as Q493R, G496S, Q498R, N501Y, Y505H) may have a measurable effect on allosteric couplings in the complexes with Nb6 and VHH E nanobodies, which would likely render some level of resistance to nanobody-induced neutralization. 2022 International journal of molecular sciences Result SARS_CoV_2 G496S;N501Y;Q493R;Q498R;Y505H 54;68;47;61;75 59;73;52;66;80 RBD 24 27 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. Importantly, some of the Omicron mutations could significantly affect Nb6 binding, particularly G446S, E484A, G496S, and Y505H modifications (Figure 7A,B). 2022 International journal of molecular sciences Result SARS_CoV_2 E484A;G446S;G496S;Y505H 103;96;110;121 108;101;115;126 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. In agreement with the experiments, mutations at the VHH E interface Y449H/D/N, F490S, S494P/S, G496S, and Y508H produced destabilizing DeltaDeltaG changes exceeding 2.0 kcal/mol (Figure 6). 2022 International journal of molecular sciences Result SARS_CoV_2 F490S;G496S;S494P;S494S;Y449D;Y449H;Y449N;Y508H 79;95;86;86;68;68;68;106 84;100;93;93;77;77;77;111 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. In particular, it was experimentally determined that Nb6 binding could be severely impeded by E484K mutation. 2022 International journal of molecular sciences Result SARS_CoV_2 E484K 94 99 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. In this case, a noticeable reduction of binding affinity was observed only for E484A, Q493R, and G496S mutations. 2022 International journal of molecular sciences Result SARS_CoV_2 E484A;G496S;Q493R 79;97;86 84;102;91 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. Instructively, nanobody binding can be partly escaped by mutations Y369H, S371P, F377L, and K378Q/N, even though these modifications are not currently circulating. 2022 International journal of molecular sciences Result SARS_CoV_2 F377L;K378N;K378Q;S371P;Y369H 81;92;92;74;67 86;99;99;79;72 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. Interestingly, our results also showed that VHH E/VHH V nanobody binding could be potentially less sensitive to Q498R, N501Y, and Y505H mutations (Figure 7E,F) as compared to binding of a single nanobody VHH E (Figure 7C,D). 2022 International journal of molecular sciences Result SARS_CoV_2 N501Y;Q498R;Y505H 119;112;130 124;117;135 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. It appeared that K417N and N501Y mutations only moderately affected nanobody binding. 2022 International journal of molecular sciences Result SARS_CoV_2 K417N;N501Y 17;27 22;32 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. Moreover, it was proposed that K417N, T478K, G496S, Y505H, and the mutations at the cryptic epitope S371L, S373P, S375F can reduce affinity to ACE2 while driving immune evasion. 2022 International journal of molecular sciences Result SARS_CoV_2 G496S;K417N;S371L;S373P;S375F;T478K;Y505H 45;31;100;107;114;38;52 50;36;105;112;119;43;57 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. Moreover, mutations at the E484 position (E484A, E484G, E484D, and E484K) confer partial resistance to the convalescent plasma, showing that E484 is also one of the dominant epitopes of spike protein. 2022 International journal of molecular sciences Result SARS_CoV_2 E484D;E484G;E484K;E484A 56;49;67;42 61;54;72;47 S 186 191 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. Moreover, structural studies showed that Omicron mutations E484A, Q493R, and Q498R are largely responsible for immune escape from monoclonal antibodies. 2022 International journal of molecular sciences Result SARS_CoV_2 E484A;Q493R;Q498R 59;66;77 64;71;82 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. Movements of these positions may affect the fidelity of nanobody binding, and mutations in these positions, particularly E484K, can escape the nanobody effect owing to the inherent functional plasticity in this region. 2022 International journal of molecular sciences Result SARS_CoV_2 E484K 121 126 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. Nb6 binding could be severely compromised by the E484K mutation, while other sites of nanobody-escaping mutations are likely to be suppressed by the nanobody. 2022 International journal of molecular sciences Result SARS_CoV_2 E484K 49 54 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. Recent studies also showed that Omicron mutations S477N, Q498R, and N501Y could increase ACE2 affinity anchoring the RBD to ACE2. 2022 International journal of molecular sciences Result SARS_CoV_2 N501Y;Q498R;S477N 68;57;50 73;62;55 RBD 117 120 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. The escaping mutations Y369H, S371P, F374I/V, T376I, F377L, and K378Q/N at the VHH U interface resulted in considerable destabilization losses (Figure 6). 2022 International journal of molecular sciences Result SARS_CoV_2 F374I;F374V;F377L;K378N;K378Q;S371P;T376I;Y369H 37;37;53;64;64;30;46;23 44;44;58;71;71;35;51;28 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. The fact that only the tip of the RBM region and E484/F486 remain more prone to changes could allow for E484K mutation to escape Nb6 binding and adopt a conformation evading efficient nanobody interactions. 2022 International journal of molecular sciences Result SARS_CoV_2 E484K 104 109 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. The mutational scanning analysis supported the notion that E484A mutation can have a significant detrimental effect on nanobody binding and result in Omicron-induced escape from nanobody neutralization. 2022 International journal of molecular sciences Result SARS_CoV_2 E484A 59 64 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. The mutational sensitivity map also sheds some light on the structure-functional role of sites targeted by common resistant mutations (F490S, E484K, Q493K/R, F490L, F486S, F486L, and Y508H) that evade many individual nanobodies. 2022 International journal of molecular sciences Result SARS_CoV_2 E484K;F486L;F486S;F490L;Q493K;Q493R;Y508H;F490S 142;172;165;158;149;149;183;135 147;177;170;163;156;156;188;140 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. We also examined the effect of Omicron mutations in the RBD (G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H) on binding of Nb6, VHH E, and VHH E/VHH V nanobodies (Figure 7). 2022 International journal of molecular sciences Result SARS_CoV_2 E484A;G446S;G496S;K417N;N440K;N501Y;Q493R;Q498R;S371L;S373P;S375F;S477N;T478K;Y505H;G339D 124;103;138;89;96;152;131;145;68;75;82;110;117;159;61 129;108;143;94;101;157;136;150;73;80;87;115;122;164;66 RBD 56 59 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. We specifically examined the effect of mutations present in the S-B.1.1.7 variant (N501Y) and S-B1.351 variant (K417N, E484K, N501Y on Nb6 and VHH E binding. 2022 International journal of molecular sciences Result SARS_CoV_2 E484K;N501Y;K417N;N501Y 119;126;112;83 124;131;117;88 S;S 64;94 65;95 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. Strikingly, this increased neutralization was more pronounced for the Omicron Spike (8.9-fold increase) compared with the other emerging variant Spikes (D614G, Beta, and Delta) (2.2- to 4.2-fold increase). 2022 Cell reports Result SARS_CoV_2 D614G 153 158 S;S 78;145 83;151 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. The 16-week interval regimen elicited significantly better neutralization activity against pseudoviral particles bearing the D614G, Beta, Delta, and Omicron Spikes (Figure 2C). 2022 Cell reports Result SARS_CoV_2 D614G 125 130 S 157 163 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. The antigenic profile of D614G, Alpha, Beta, Gamma, Delta, and Omicron Spikes was assessed with plasma collected 3 weeks (V3) and 4 months (V4) after the second dose of the BNT162b2 mRNA vaccine administered with a 16-week interval between doses (Figure 1 A). 2022 Cell reports Result SARS_CoV_2 D614G 25 30 S 71 77 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. 3B) on the LMM52630 models (which includes the B.1.91 lineage model only, and the B.1.91 lineage associated with the RBD substitutions: C379W, V395A and non-reported Y380Q, found exclusively in this participant) compared to the ancestral monomer sequence model. 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 C379W;V395A;Y380Q 136;143;166 141;148;171 RBD 117 120 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. A structural investigation of more than 20 crystals of viral spike protein from PDB, revealed that the mutations C379W, Y380Q and V395A are in a contact area complexed with antibodies in the RBD region. 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 C379W;V395A;Y380Q 113;130;120 118;135;125 S;RBD 61;191 66;194 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. Altered residues in the RBD region, especially the C379W and Y380Q mutations, are located close to each other and likely gain strength, thus providing an overall shift to hydrophilic profile. 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 C379W;Y380Q 51;61 56;66 RBD 24 27 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. Spike protein mutations and INDELs were found, including one mutation (Y380Q) that have never been reported (Table 1 ). 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 Y380Q 71 76 S 0 5 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. The C379W mutation changed the direction from highly hydrophobic (2.5) to hydrophilic (-0.9). 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 C379W 4 9 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. The participant that presented the novel Y380Q mutation was hospitalized for 18 days, including 8 days in ICU, requiring the use of mechanical ventilation. 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 Y380Q 41 46 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. Genome sequencing of 46 samples confirmed with 100% accuracy the S gene deletion in addition to B.1.617.2 characteristic L452R, T478K, P681R, and D950N mutations located in the spike protein. 2022 Pathology Result SARS_CoV_2 D950N;L452R;P681R;T478K 146;121;135;128 151;126;140;133 S;S 177;65 182;66 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. In addition, non-synonymous mutations C>G (T19R), T>G (L452R), C>A (T478K), C>G (P681R) and G>A G (D950N) were identified. 2022 Pathology Result SARS_CoV_2 D950N;L452R;P681R;T19R;T478K 99;55;81;43;68 104;60;86;47;73 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. The analysis detected both the expected deletion and the additional characteristic N501Y and P681H mutations, as shown in. 2022 Pathology Result SARS_CoV_2 N501Y;P681H 83;93 88;98 35223905 Molecular and Epidemiological Characterization of Emerging Immune-Escape Variants of SARS-CoV-2. At 1 week after vaccination, strong neutralization (hiVNT score > 70) of all variants was observed in most of the sera samples, ranging from the highest (95.2%) in D614G to the lowest in the Beta variant (70.6 %) (Figure 3). 2022 Frontiers in medicine Result SARS_CoV_2 D614G 164 169 35223905 Molecular and Epidemiological Characterization of Emerging Immune-Escape Variants of SARS-CoV-2. Delta + E484K + N501Y and Mu showed a pattern similar to that of Beta, with 73.8% and 78.6% of the samples strongly neutralized, respectively. 2022 Frontiers in medicine Result SARS_CoV_2 E484K;N501Y 8;16 13;21 35223905 Molecular and Epidemiological Characterization of Emerging Immune-Escape Variants of SARS-CoV-2. Delta + E484K + N501Y was detected only in Turkey from week 26, Mu was prevalent in South America from week 14, and C.1.2 was prevalent in South Africa from week 26 (Figure 4). 2022 Frontiers in medicine Result SARS_CoV_2 E484K;N501Y 8;16 13;21 35223905 Molecular and Epidemiological Characterization of Emerging Immune-Escape Variants of SARS-CoV-2. Etesevimab was still effective against Delta, but the effect was reduced in Delta + E484K + N501Y. 2022 Frontiers in medicine Result SARS_CoV_2 E484K;N501Y 84;92 89;97 35223905 Molecular and Epidemiological Characterization of Emerging Immune-Escape Variants of SARS-CoV-2. However, at 6 months after vaccination, strong neutralizing activity was significantly reduced against all mutant strains, ranging from the highest (60.2%) in the Lambda to the lowest in the Delta + E484K + N501Y variant (15.3 %) (Figure 3). 2022 Frontiers in medicine Result SARS_CoV_2 E484K;N501Y 199;207 204;212 35223905 Molecular and Epidemiological Characterization of Emerging Immune-Escape Variants of SARS-CoV-2. However, four variants, namely Beta and Delta derivatives (Delta+E484Q, Delta+E484K+N501Y), Mu, and C.1.2, showed relatively low hiVNT scores (Figure 1B), suggesting that the neutralizing activity of post-vaccination sera against these variants might be weak. 2022 Frontiers in medicine Result SARS_CoV_2 E484K;E484Q;N501Y 78;65;84 83;70;89 35223905 Molecular and Epidemiological Characterization of Emerging Immune-Escape Variants of SARS-CoV-2. Our epidemiological analysis demonstrated that the frequency of Delta + E484Q increased since week 24 of 2021 and the strain is still detected worldwide. 2022 Frontiers in medicine Result SARS_CoV_2 E484Q 72 77 35223905 Molecular and Epidemiological Characterization of Emerging Immune-Escape Variants of SARS-CoV-2. The geometric mean titers (GMTs) were 225 for D614G, 38 for Beta, and 37 for Delta + E484K + N501Y (Figure 2A), suggesting that the sera had 6-fold reduced neutralization efficacy against the Beta and Delta variants. 2022 Frontiers in medicine Result SARS_CoV_2 D614G;E484K;N501Y 46;85;93 51;90;98 35223905 Molecular and Epidemiological Characterization of Emerging Immune-Escape Variants of SARS-CoV-2. The highest occurrence of nAb escape (including weak and non-neutralizing activity, i.e., hiVNT score < 70) was noted with Beta (29.4%), followed by Delta + E484K + N501Y (26.2%) and Mu (21.4%). 2022 Frontiers in medicine Result SARS_CoV_2 E484K;N501Y 157;165 162;170 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. Accordingly, while we cannot exclude the possibility that this E484K substrain was pre-existing at a very low level, our intense yet incomplete surveillance did not find any evidence of it. 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 E484K 63 68 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. Firstly, despite widespread regional surveillance, we did not detect this B.1.311/E484K lineage in any patient except those associated with this particular household. 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 E484K 82 87 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. In addition to the E484K described in our Minnesota cluster, we found examples in New York (1 sequenced case) and California (2 cases), and an E484Q case in Maryland. 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 E484K;E484Q 19;143 24;148 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. Lineage analysis using Pangolin assigned it to B.1.311, a lineage in which Spike:E484K had not been previously detected. 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 E484K 81 86 S 75 80 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. No additional genomes on the Minnesota E484K sub-lineage were detected in this analysis or our own longitudinal surveillance. 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 E484K 39 44 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. No residual specimen was available from P2 or P4, but the sample from P3 was sequenced as part of our regional surveillance, and was found to have the E484K-encoding mutation. 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 E484K 151 156 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. Secondly, we sequenced a case from an adjacent county (WI-GMF-48798) which was the immediate viral ancestor on the B.1.311 lineage to this new E484K containing strain (i.e., it was identical to the 3 sequenced genomes with the exception of the G23012A mutation encoding E484K and the subsequently acquired variants that distinguished the 3 household contacts. 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 E484K;E484K;G23012A 143;270;244 148;275;251 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. Sequencing confirmed that both P5 and P6 had the same B.1.311/E484K substrain. 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 E484K 62 67 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. The observed transmission pattern was consistent with the possibility that the E484K variant emerged in P1 following bamlanivimab treatment, however unambiguously demonstrating this was not possible as we lacked a specimen from this case for sequencing. 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 E484K 79 84 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. Thus, while we cannot formally exclude the possibility that the E484K substrain and its immediate ancestor BOTH emerged elsewhere and arrived in our region in parallel, it seemed plausible that the E484K containing variant of this lineage may have originated locally. 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 E484K;E484K 64;198 69;203 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. To more rigorously evaluate whether there was evidence of the E484K substrain outside of this household we used rapid assays (see Methods; discrimination power of Taqman assay shown in. 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 E484K 62 67 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. While performing SARS-CoV-2 surveillance, we sequenced a case from Houston County, Minnesota sampled in late December 2020 which contained a genomic variant, G23012A, encoding an E484K mutation in the Spike protein. 2022 Diagnostic microbiology and infectious disease Result SARS_CoV_2 E484K;G23012A 179;158 184;165 S 201 206 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. Some other common synonymous mutations were also observed such as in the M gene at the position C26735T and the S gene at the position C22444T occurring as 288/546 (52.7%) and 233/546 (42.7%), respectively) Table 3 ). 2022 Saudi journal of biological sciences Result SARS_CoV_2 C22444T;C26735T 135;96 142;103 S 112 113 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. The most common synonymous mutation 493/546 (90.3%) occurred in the 5'UTR region at the position C241T, followed by several common mutations in ORF1 a/b at the positions C3037T, C17788T, and C2836T which displayed the following frequencies- 456/546 (83.5%), 297/546 (54.4%), and 216/546 (39.6%) respectively. 2022 Saudi journal of biological sciences Result SARS_CoV_2 C17788T;C241T;C2836T;C3037T 178;97;191;170 185;102;197;176 5'UTR 68 73 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. The most frequent non-synonymous mutation 486/546 (89.01%) occurred in the S gene at position 23,403 where A changed to G leading to the replacement of aspartic acid by glycine in position (D614G)) Table 3 and. 2022 Saudi journal of biological sciences Result SARS_CoV_2 D614G 190 195 S 75 76 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. The mutations C241T, A23403G, C14408T, and C3037T appeared together in 83 % of Indian SARC-CoV-2 variants. 2022 Saudi journal of biological sciences Result SARS_CoV_2 A23403G;C14408T;C241T;C3037T 21;30;14;43 28;37;19;49 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. The second most dominant non-synonymous mutation 465/546 (85.2%) occurred in ORF1 a/b at position 14,408 where C changed to T which changed the amino acid in RNA-dependent RNA polymerase (RdRp/ P323L)) Table 3 and. 2022 Saudi journal of biological sciences Result SARS_CoV_2 P323L 194 199 RdRp;RdRP 158;188 186;192 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. The third common mutation- 299/546 (54.8%) occurred in ORF3a at position 25,563 where G changed to T leading to- Q75H, followed by a mutation in N gene at position 28,854 where C changed to T leading to S194L) Table 3 and. 2022 Saudi journal of biological sciences Result SARS_CoV_2 Q75H;S194L 113;203 117;208 ORF3a;N 55;145 60;146 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. A23-58.1, B1-182.1, A19-46.1, and A19-61.1 have previously been shown to bind D614G and Beta equivalently, and showed similar ADCP, ADCC, ADCD, and ADCT activity against both D614G and Beta (Figure S1). 2022 Cell reports. Medicine Result SARS_CoV_2 D614G;D614G 78;175 83;180 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. Although Fc effector function elicited by the original D614G virus was not completely abrogated against Beta, the significant decrease in activity suggests that NTD and RBD, mutated in Beta, are substantial targets. 2022 Cell reports. Medicine Result SARS_CoV_2 D614G 55 60 RBD 169 172 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. Although wave 1 viral sequences were not obtained, these samples were collected several months prior to the emergence of Beta and were assumed to have been D614G infections (Figure 1A). 2022 Cell reports. Medicine Result SARS_CoV_2 D614G 156 161 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. an NTD mAb for which neutralization and binding are escaped by Beta (L18F, D80A, D215G, and 242-244 del), showed ADCC activity against the original variant but not Beta RBD (Figure 3B). 2022 Cell reports. Medicine Result SARS_CoV_2 D215G;D80A;L18F 81;75;69 86;79;73 RBD 169 172 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. As Beta-elicited plasma showed enhanced cross-reactivity for the original variants, we assessed a larger panel of VOCs (D614G and Alpha, Beta, Gamma, Delta, and SARS-1). 2022 Cell reports. Medicine Result SARS_CoV_2 D614G 120 125 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. As expected, Spearman's correlations >0.5 were noted between FcgammaRIIa binding and ADCP score, and between FcgammaRIIIa binding and ADCC against original D614G spike (Figures S2A and S2B). 2022 Cell reports. Medicine Result SARS_CoV_2 D614G 156 161 S 162 167 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. As for full spike (Figure S1), CR3022 ADCC against the RBD was unaffected by Beta RBD mutations (K417N, E484K, and N501Y), while ADCC mediated by P2B-2F6 was abrogated (Figure 3A). 2022 Cell reports. Medicine Result SARS_CoV_2 E484K;N501Y;K417N 104;115;97 109;120;102 S;RBD;RBD 12;55;82 17;58;85 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. Comparison of immunoglobulin (Ig) A and IgG binding from wave 1 plasma to the original (D614G) or Beta spikes showed a significant decrease in binding to Beta (Figures 1B and C). 2022 Cell reports. Medicine Result SARS_CoV_2 D614G 88 93 S 103 109 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. In contrast, neutralization titers in plasma from wave 1 decreased 14.7-fold against Beta, while wave 2 titers of Beta were 5.1-fold higher than those of D614G (Figure 1C), as we previously showed. 2022 Cell reports. Medicine Result SARS_CoV_2 D614G 154 159 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. In contrast, wave 2 plasma showed similar ADCC levels for VOCs (Figure 4B), with Gamma-specific ADCC showing the highest level (median 284), followed by Beta, Delta, Alpha, and D614G (250, 198, 159, and 138 respectively). 2022 Cell reports. Medicine Result SARS_CoV_2 D614G 177 182 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. Plasma from wave 1 participants showed a significantly decreased ability to mediate ADCP, ADCC, ADCD, and ADCT of Beta, compared with the original D614G spike, although all retained some activity against Beta (Figure 2A). 2022 Cell reports. Medicine Result SARS_CoV_2 D614G 147 152 S 153 158 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. The first wave was dominated by Wuhan D614G, the second by the Beta variant, and the third wave by Delta. 2022 Cell reports. Medicine Result SARS_CoV_2 D614G 38 43 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. Therefore, NTD and RBD are targets of ADCC responses in convalescent plasma, but mutations in these regions that confer neutralization escape in original (D614G) infections only slightly affect ADCC. 2022 Cell reports. Medicine Result SARS_CoV_2 D614G 155 160 RBD 19 22 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. Thus, Beta-elicited ADCC activity is cross-reactive for other VOCs, whereas ADCC in response to the original (D614G) variant was substantially less cross-reactive. 2022 Cell reports. Medicine Result SARS_CoV_2 D614G 110 115 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. To validate these assays, we tested monoclonal antibodies previously characterized for cell surface spike binding to D614G and Beta. 2022 Cell reports. Medicine Result SARS_CoV_2 D614G 117 122 S 100 105 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. We determined the contribution to ADCC of antibodies to NTD and RBD by measuring FcgammaRIIIa signaling as a result of crosslinking to NTD or RBD proteins from the D614G and Beta variants. 2022 Cell reports. Medicine Result SARS_CoV_2 D614G 164 169 RBD;RBD 64;142 67;145 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. We next measured whether Fc effector functions elicited by the original D614G variant or the Beta variant were equivalent in magnitude and cross-reactivity. 2022 Cell reports. Medicine Result SARS_CoV_2 D614G 72 77 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. We used convalescent plasma from the first two waves (first wave n = 27; second wave n = 21) to determine its ability to bind and neutralize original (D614G) or Beta. 2022 Cell reports. Medicine Result SARS_CoV_2 D614G 151 156 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. While wave 2 plasma samples mediated ADCP, ADCD, and ADCT to similar levels against D614G and Beta spikes, ADCC was significantly higher against Beta (Figure 2A) (median D614G ADCC = 138, Beta ADCC = 249, 1.8-fold difference). 2022 Cell reports. Medicine Result SARS_CoV_2 D614G;D614G 84;170 89;175 S 99 105 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. Bat CoV RaTG13 and pangolin CoV GX-P5L are both phylogenetically placed in the SARS-CoV-2 clade, which are more distantly related to SARS-CoV-2 than Omicron with 90.1% and 86.6% amino acid sequence identity, respectively, of the RBD sequence in comparison to Omicron at 93.3% (Fig 1b, c). 2022 Research square Result SARS_CoV_2 P5L 35 38 RBD 229 232 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. Clade-2 viruses include the ancestral SARS-CoV-2 virus (Wuhan-hu-1), variants of concern or interest (Alpha, Delta, Beta, Gamma, Delta plus, Lambda, Mu, and Omicron) and pre-emergent bat (RaTG13) and pangolin (GX-P5L) sarbecoviruses. 2022 Research square Result SARS_CoV_2 P5L 213 216 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. Consistent with our earlier observation, Omicron is more antigenic distant to SARS-CoV-2 than GX-P5L or RaTG13. 2022 Research square Result SARS_CoV_2 P5L 97 100 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. Generated from neutralization titer 50% of the examined 187 sera on all 16 sarbecoviruses (Supplementary Data Table 1), the antigenic map showed the clustering of SARS-CoV-2 clade and the antigenic distance between the SARS-CoV-2 and other clade 2 sarbecoviruses in the following descending order: Delta plus, Delta, Lambda, Alpha, Gamma, Mu, RaTG13, Beta, GX-P5L and Omicron (Extended Data Fig 2a). 2022 Research square Result SARS_CoV_2 P5L 360 363 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. In comparison to the SARS-CoV-2 ancestral RBD, the other 15 RBDs have the following rank of sequence relatedness (from high to low): Alpha, Delta, Lambda, Beta, Gamma, Delta plus, Mu, Omicron, RaTG13, GX-P5L, RsSHC014, WIV-1, Rs2018B, LYRa11 and SARS-CoV-1. 2022 Research square Result SARS_CoV_2 P5L 204 207 RBD;RBD 42;60 45;64 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. In contrast, Omicron showed an almost complete NAb escape against these sera, with a 64.8-fold and 33.2-fold reduction, respectively, against the RaTG13 and GX-P5L hyper immune sera (Extended Data Fig 3a, b), again demonstrating the greater NAb escape ability unique to Omicron in the context of RBD mutations or sequence relatedness. 2022 Research square Result SARS_CoV_2 P5L 160 163 RBD 296 299 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. Sera raised against RaTG13 and GX-P5L RBDs had highest NAb titer to their homologous viruses in the 16-plex sVNT and displayed a 6.8-fold and 4.1-fold NAb titer reduction, respectively, to SARS-CoV-2 (Extended Data Fig 3a, b). 2022 Research square Result SARS_CoV_2 P5L 34 37 RBD 38 42 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. To further dissect the differential level of NAb escape in relation to RBD aa mutations, we employed a panel of hyperimmune rabbit sera raised against recombinant RBD proteins of different clade-2 sarbecoviruses, including human SARS-CoV-2, bat CoV RaTG13, pangolin CoV GX-P5L, and two non-ACE2 binding RBDs from bat CoV RmYN02 and bat CoV SL-ZC45. 2022 Research square Result SARS_CoV_2 P5L 273 276 RBD;RBD;RBD 71;163;303 74;166;307 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. When the level of NAb titers were examined side by side, it was found that Omicron had a more significant NAb escape than either RaTG13 or GX-P5L (Fig 2a-d, Fig 3a, Supplementary Data Fig 1a-d), indicating that Omicron is antigenically more distant than the two pre-emergent sarbecoviruses despite the fact that there are 15 aa differences in Omicron RBD in comparison to 22 and 30 aa differences in the RBD of RaTG13 and GX-P5L, respectively. 2022 Research square Result SARS_CoV_2 P5L;P5L 142;425 145;428 RBD;RBD 351;404 354;407 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. Across all outcomes, infection with the Delta VOC was associated with higher effect estimates relative to N501Y-positive infections. 2022 Clinical infectious diseases Result SARS_CoV_2 N501Y 106 111 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. Among all reported cases, 64.6% were infections with the N501Y-positive VOC; 19.1% were classified as probable Delta infections. 2022 Clinical infectious diseases Result SARS_CoV_2 N501Y 57 62 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. By contrast, significant heterogeneity in risk estimates was seen for hospitalization risk across age groups with the N501Y-positive VOC and for hospitalization, ICU admission , and death risk with the Delta VOC (Figures 1 and 2). 2022 Clinical infectious diseases Result SARS_CoV_2 N501Y 118 123 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. For the N501Y-positive VOC, odds ratios could not be estimated for ICU admission in children aged <10 years or for death in those aged <20 years due to the rarity of these outcomes (Figure 1). 2022 Clinical infectious diseases Result SARS_CoV_2 N501Y 8 13 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. However, there was no significant linear association between age and relative risk of severe outcomes for either N501Y-positive variants or for the Delta variant (Table 2). 2022 Clinical infectious diseases Result SARS_CoV_2 N501Y 113 118 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. ICU admission risk was higher with N501Y-positive infection than with non-VOC infection in all groups aged >=30 years. 2022 Clinical infectious diseases Result SARS_CoV_2 N501Y 35 40 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. In random effects meta-analyses, we found no significant heterogeneity in odds ratios across age groups for death and ICU admission risk with the N501Y-positive VOC. 2022 Clinical infectious diseases Result SARS_CoV_2 N501Y 146 151 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. N501Y-positive VOC infection was associated with a significant increase in hospitalization among people aged >=20 years relative to infection with non-VOC SARS-CoV-2 strains. 2022 Clinical infectious diseases Result SARS_CoV_2 N501Y 0 5 35235585 Travel ban effects on SARS-CoV-2 transmission lineages in the UAE as inferred by genomic epidemiology. Apart from the S protein, an Abu Dhabi specific, monophyletic amino acid mutation in ORF1a (V1887I), which preserves physico-chemical properties (both are aliphatic, BLOSUM62 score of 3) was detected. 2022 PloS one Result SARS_CoV_2 V1887I 92 98 ORF1a;S 85;15 90;16 35235585 Travel ban effects on SARS-CoV-2 transmission lineages in the UAE as inferred by genomic epidemiology. In addition to the above-mentioned D614G mutation, we observe four cases of a nearby E583D mutation, that could be of diagnostic or clinical relevance (transmissibility and severity). 2022 PloS one Result SARS_CoV_2 D614G;E583D 35;85 40;90 35235585 Travel ban effects on SARS-CoV-2 transmission lineages in the UAE as inferred by genomic epidemiology. Prevalence shift of D614G variants. 2022 PloS one Result SARS_CoV_2 D614G 20 25 35235585 Travel ban effects on SARS-CoV-2 transmission lineages in the UAE as inferred by genomic epidemiology. We also observed a shift of prevalence for strains with D614G mutations in the viral Spike (S) protein. 2022 PloS one Result SARS_CoV_2 D614G 56 61 S;S 85;92 90;93 35235585 Travel ban effects on SARS-CoV-2 transmission lineages in the UAE as inferred by genomic epidemiology. We discovered one case of Q613H, directly adjacent to position 614 in S, almost unique to the UAE. 2022 PloS one Result SARS_CoV_2 Q613H 26 31 S 70 71 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. The neutralization of authentic SARS-CoV-2 wt (with D614G mutation), Delta, and Omicron was analyzed using sera of 2x BNT162b-vaccinated and BNT162b2 boost-vaccinated individuals. 2022 BMC medicine Result SARS_CoV_2 D614G 52 57 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. Analysis of the variant frequencies found in the respective samples showed a ~60% variant frequency for the G11083T substitution in the ORF1ab after isolation. 2022 Nature communications Result SARS_CoV_2 G11083T 108 115 ORF1ab 136 142 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. Both regions are targets for neutralizing antibodies and L18F and L452R have been previously associated with antibody escape and L452R additionally with increased infectivity. 2022 Nature communications Result SARS_CoV_2 L18F;L452R;L452R 57;66;129 61;71;134 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. Furthermore, N501Y was suggested to enhance the binding affinity to ACE2. 2022 Nature communications Result SARS_CoV_2 N501Y 13 18 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. L18F is present in the VOCs B.1.351 and P.1, the L452R substitution is found in high frequencies in B.1.617.2 and related AY lineages, and N501Y is known from B.1.1.7, B.1.351 and P.1. 2022 Nature communications Result SARS_CoV_2 L452R;N501Y;L18F 49;139;0 54;144;4 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. Lineage A.27 has two mutations in its RBD that translate to L452R and N501Y. 2022 Nature communications Result SARS_CoV_2 L452R;N501Y 60;70 65;75 RBD 38 41 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. One of the hallmarks of A.27 is the absence of the S D614G substitution present in the globally dominating B.1-derieved lineages, indicating an independent acquisition of the other spike mutations. 2022 Nature communications Result SARS_CoV_2 D614G 53 58 S;S 181;51 186;52 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. The A.27 Black Forest isolate reached similar titres in both VeroE6 and Calu3 cells, comparable with a prototypic B.1 isolate (Muc-IMB-1) that only harbors the S D614G substitution in its viral genome and four different VOCs. 2022 Nature communications Result SARS_CoV_2 D614G 162 167 S 160 161 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. The L18F amino acid substitution is found within the first of five loops of the NTD supersite and the L452R and N501Y mutations are located in the receptor-binding motif (RBM) which interacts with the human ACE2 protein. 2022 Nature communications Result SARS_CoV_2 L18F;L452R;N501Y 4;102;112 8;107;117 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. The potential escape was assessed by comparing the A.27 Black Forest isolate to the prototypic B.1 isolate that harbors the D614G mutation. 2022 Nature communications Result SARS_CoV_2 D614G 124 129 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. Three of the seven S substitutions, L18F, L452R, and N501Y, are of particular interest. 2022 Nature communications Result SARS_CoV_2 L18F;L452R;N501Y 36;42;53 40;47;58 S 19 20 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. A single branch of the B.1.36+B.1.468 clade (n=4, 3 of which were imported) had an additional amino acid replacement F490S in the RBD ( Figure 2B). 2021 Wellcome open research Result SARS_CoV_2 F490S 117 122 RBD 130 133 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. All 45 sequences with N440K are grouped into the B.1.36+B.1.468 clade ( Figure 2B). 2021 Wellcome open research Result SARS_CoV_2 N440K 22 27 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. Although only the D614G and N440K were present in an appreciable number (>50%) of sequences (extended data S7 . 2021 Wellcome open research Result SARS_CoV_2 D614G;N440K 18;28 23;33 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. Of the six sequences from a cluster of cases (Outbreak), only a single sequence carried the mutation resulting in the N440K change ( Figure 2B). 2021 Wellcome open research Result SARS_CoV_2 N440K 118 123 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. Of these, five (S477N, E484K, E484Q, S494L, S494P) were found in viruses circulating in Bengaluru, and the amino acid replacement V483A was from an imported case. 2021 Wellcome open research Result SARS_CoV_2 E484K;E484Q;S494L;S494P;V483A;S477N 23;30;37;44;130;16 28;35;42;49;135;21 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. The N440K mutation was present in 45/162 (27.7%) of the sequences. 2021 Wellcome open research Result SARS_CoV_2 N440K 4 9 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. The N440K was found in 37/65 (56.92%) of B.1.36 sequences (extended data S7 ). 2021 Wellcome open research Result SARS_CoV_2 N440K 4 9 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. The N501Y change was confined to the B.1.1.7 lineage. 2021 Wellcome open research Result SARS_CoV_2 N501Y 4 9 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. 7) show a sixfold increase in binding strength for Alpha spike, and a twofold increase for Beta spike (compared to Wuhan) arising from the shared substitution N501Y in the RBD. 2022 Nature communications Result SARS_CoV_2 N501Y 159 164 S;S;RBD 57;96;172 62;101;175 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. A similar observation has been made in studies of spike material isolated directly from the Alpha variant virus and the same P681H substitution has also been observed in the recent B.1.1.529 (Omicron) variant spike. 2022 Nature communications Result SARS_CoV_2 P681H 125 130 S;S 50;209 55;214 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. In the same way that G614 is a prerequisite for realising tighter receptor binding by the substitution N501Y described above, it may also enable spike protein from the Beta virus to achieve an open conformation as a result of the K417N substitution. 2022 Nature communications Result SARS_CoV_2 K417N;N501Y 230;103 235;108 S 145 150 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. Inspection of the sequence of the Beta spike and comparison of its structure with that of the closed form of Wuhan spike and the open and closed forms of G614 spikes, suggests that the opening of Beta spike could be driven by the substitution K417N on the background of G614 (both also observed in the Omicron variant spike). 2022 Nature communications Result SARS_CoV_2 K417N 243 248 S;S;S;S;S 39;115;159;201;318 44;120;165;206;323 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. Our binding data on the variants and engineered constructs show that the D614G substitution is a prerequisite for the tighter receptor binding of changes in RBD, like N501Y, but do not explain how it facilitates the increase in affinity. 2022 Nature communications Result SARS_CoV_2 D614G;N501Y 73;167 78;172 RBD 157 160 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. Our data suggest that this substitution P681R in Kappa and Delta spikes, as well as P681H in Omicron spike, will also increase stability of the receptor-bound form of these spikes, accounting at least in part for their increased transmissibility. 2022 Nature communications Result SARS_CoV_2 P681H;P681R 84;40 89;45 S;S;S 65;101;173 71;106;179 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. Similarly, we also show that the Y453F substitution in the RBD of mink spike, a structure of which we also report here (Supplementary Figures 4-6), only increases affinity for human ACE2 if residue 614 is a glycine but not if it is an aspartic acid. 2022 Nature communications Result SARS_CoV_2 Y453F 33 38 S;RBD 71;59 76;62 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. The engineered G614D Alpha spike (Y501, D614) shows the same binding affinity as Wuhan (N501, D614). 2022 Nature communications Result SARS_CoV_2 G614D 15 20 S 27 32 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. The recent variants of concern B.1.617 (Kappa) and B.1.617.2 (Delta) contain the substitution P681R, which also results in full cleavage. 2022 Nature communications Result SARS_CoV_2 P681R 94 99 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. The substitution D614G (relative to Wuhan) occurred earlier in the evolution of SARS-CoV-2, became the predominant global form of the virus and continues to be present in the Alpha and Beta variant forms of the virus. 2022 Nature communications Result SARS_CoV_2 D614G 17 22 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. the trimeric state of the receptor-bound form of the Alpha variant spike might be further stabilised by the substitutions D1118H and A570D on the inter-monomer interfaces. 2022 Nature communications Result SARS_CoV_2 A570D;D1118H 133;122 138;128 S 67 72 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. They follow D614G substitution which was acquired early in the pandemic and similarly acted to increase the spike stability. 2022 Nature communications Result SARS_CoV_2 D614G 12 17 S 108 113 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. This observation is consistent with one of the changes in the Alpha spike being the substitution P681H, which generates an even more basic furin-cleavage site (HRRAR). 2022 Nature communications Result SARS_CoV_2 P681H 97 102 S 68 73 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. We suggest that one of effects of the more open conformation promoted by the D614G substitution is to increase the proportion of accessible RBD-binding sites, thus enhancing the avidity of virus binding to host cells. 2022 Nature communications Result SARS_CoV_2 D614G 77 82 RBD 140 143 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. 2 shows that the G94D average structure did not fit well onto the wild-type protein. 2022 Informatics in medicine unlocked Result SARS_CoV_2 G94D 17 21 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. Finally, for the H80A variant, because it replaced the histidine with an alanine, we explored the alanine positioning. 2022 Informatics in medicine unlocked Result SARS_CoV_2 H80A 17 21 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. For the Y96"X" variants, Y96C and Y96W, again unremarkable, other than the Y96 residue. 2022 Informatics in medicine unlocked Result SARS_CoV_2 Y96C;Y96W 25;34 29;38 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. For the Y96F variant, that was the only notable change except for the F96 residue itself. 2022 Informatics in medicine unlocked Result SARS_CoV_2 Y96F 8 12 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. For Y96F, it should be noted that this variant is also found in many other coronavirus sequences and was the only variant with increased MTase activity. 2022 Informatics in medicine unlocked Result SARS_CoV_2 Y96F 4 8 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. G94D is one of only two variant peptides from the literature that resulted in zero methyltransferase. 2022 Informatics in medicine unlocked Result SARS_CoV_2 G94D 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. However, the Y96F variant has an almost identical structural alignment. 2022 Informatics in medicine unlocked Result SARS_CoV_2 Y96F 13 17 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. In all cases except for the Y96"X" variants, the H80 residues displayed the same rotation of H80 into a similar position as the G94D and K93E variants. 2022 Informatics in medicine unlocked Result SARS_CoV_2 G94D;K93E 128;137 132;141 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. In the other variants, Y96V, Y96I, and Y96A, the A71 residue changed, also protruding out further. 2022 Informatics in medicine unlocked Result SARS_CoV_2 Y96A;Y96I;Y96V 39;29;23 43;33;27 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. In the variants containing a Y96"X" change, Y96V, Y96I, Y96A, T96F, the H80 residue did not shift. 2022 Informatics in medicine unlocked Result SARS_CoV_2 T96F;Y96A;Y96I;Y96V 62;56;50;44 66;60;54;48 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. It was discovered that the H80 residue in both G94D and K93E shifted clockwise approximately 90 to an almost identical position in each variant. 2022 Informatics in medicine unlocked Result SARS_CoV_2 G94D;K93E 47;56 51;60 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. Notably, variants G94D and Y96F modulated the MTase activity to be very low and very high, respectively. 2022 Informatics in medicine unlocked Result SARS_CoV_2 G94D;Y96F 18;27 22;31 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. The WT, Y96F, and G94A were designated as having "high" MTase activity and we classified all other variants as "low." For the newly proposed variants, we performed an additional PCA analysis, one that included all variants and was plotted for visual analysis. 2022 Informatics in medicine unlocked Result SARS_CoV_2 G94A;Y96F 18;8 22;12 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. We began by viewing the overlays of G94D and K93E, both having complete zero methyltransferase activity, and used a space filling model to identify any residues that changed in both peptide simulations. 2022 Informatics in medicine unlocked Result SARS_CoV_2 G94D;K93E 36;45 40;49 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. We calculated this effect to produce ~2.5 A alteration of these residues in the variants R78A and R78G. 2022 Informatics in medicine unlocked Result SARS_CoV_2 R78A;R78G 89;98 93;102 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. We observed that all Y96"X" variants displayed an S72 residue that protrudes further than wild type, including Y96F. 2022 Informatics in medicine unlocked Result SARS_CoV_2 Y96F 111 115 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. Y96C is quite a bit smaller than Y96, and Y96W, as per the R group is larger than Y96. 2022 Informatics in medicine unlocked Result SARS_CoV_2 Y96W;Y96C 42;0 46;4 35255849 Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. Detection of de novo N501Y emergence within a skilled nursing facility outbreak. 2022 BMC public health Result SARS_CoV_2 N501Y 21 26 35255849 Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. Genomic surveillance of the outbreak in Facility A also revealed the emergence and eradication of a lineage that had a de novo asparagine to tyrosine substitution in site 501 of the Spike protein (N501Y). 2022 BMC public health Result SARS_CoV_2 N501Y;N501Y 127;197 174;202 S 182 187 35255849 Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. In total, 38 whole genome sequences were generated that grouped together within a clade defined by two substitutions (C18744T and G25699T). 2022 BMC public health Result SARS_CoV_2 G25699T;C18744T 130;118 137;125 35255849 Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. Notably, N501Y is present in three "variant of concern" lineages: B.1.1.7, B.1.351, and P.1. 2022 BMC public health Result SARS_CoV_2 N501Y 9 14 35255849 Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. Of 89 samples sequenced during this outbreak, 16 samples shared this N501Y substitution. 2022 BMC public health Result SARS_CoV_2 N501Y 69 74 35255849 Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. One virus had an additional C to T substitution at site 19,273 which yielded a proline to serine substitution at site 1936 in ORF1b. 2022 BMC public health Result SARS_CoV_2 P1936S 79 122 35255849 Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. The first sample containing this N501Y substitution was collected on November 29, 2020. 2022 BMC public health Result SARS_CoV_2 N501Y 33 38 35255849 Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. Within this clade, 14 of the 16 sequences differed from the primary outbreak strain in Facility A by only the A23063T substitution that yielded the N501Y change. 2022 BMC public health Result SARS_CoV_2 A23063T;N501Y 110;148 117;153 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. At the same time, the strain count for K417N mutation was 43,172; this mutation was first reported in Qatar. 2022 GeroScience Result SARS_CoV_2 K417N 39 44 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. K417N, E484A, Q493K, Q498R, N501Y, and Y505H were in the antibody-binding region, and S477N, T478K, G496S, G446S, and N440K were near the antibody-binding region. 2022 GeroScience Result SARS_CoV_2 E484A;G446S;G496S;N440K;N501Y;Q493K;Q498R;S477N;T478K;Y505H;K417N 7;107;100;118;28;14;21;86;93;39;0 12;112;105;123;33;19;26;91;98;44;5 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. Mutations previously reported as important in different variants were N501Y, D614G, H655Y, N679K, and P681H. 2022 GeroScience Result SARS_CoV_2 D614G;H655Y;N501Y;N679K;P681H 77;84;70;91;102 82;89;75;96;107 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. Significant mutations in the RBD include Q493K, G496S, Q498R, S477N, G466S, N440K, and Y505H, whereas those in the NTD included Delta143-145, A67V, T95I, L212I, and Delta211. 2022 GeroScience Result SARS_CoV_2 A67V;G466S;G496S;L212I;N440K;Q493K;Q498R;S477N;T95I;Y505H 142;69;48;154;76;41;55;62;148;87 146;74;53;159;81;46;60;67;152;92 RBD 29 32 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. Similarly, D796Y was identified as a new mutation in fusion protein (FP). 2022 GeroScience Result SARS_CoV_2 D796Y 11 16 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. The E484A mutation destabilized binding between the antibody and S-glycoprotein RBD. 2022 GeroScience Result SARS_CoV_2 E484A 4 9 S;RBD 65;80 79;83 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. The K417N mutation destabilized the S-glycoprotein. 2022 GeroScience Result SARS_CoV_2 K417N 4 9 S 36 50 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. The strain count for the E484A was 319, and this variant was first reported in Spain. 2022 GeroScience Result SARS_CoV_2 E484A 25 30 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. The strain count for the N501Y mutation was 1,353,726, and this variant was first recorded in Spain. 2022 GeroScience Result SARS_CoV_2 N501Y 25 30 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. The strain count for the T478K mutation was observed as 1,585,374, and this variant (K417N) was first reported in the USA. 2022 GeroScience Result SARS_CoV_2 T478K;K417N 25;85 30;90 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. The T478K mutation destabilized the interaction between the antibody and S-glycoprotein. 2022 GeroScience Result SARS_CoV_2 T478K 4 9 S 73 87 35262011 Use of amplicon melt temperature to detect SARS-CoV-2 Lineage B.1.1.7 variant through the G28048T mutation in the ORF 8 gene. In this case, a second (A28058G) mutation (synonymous) was also present which raised the melt temperature back up to the same as the original. 2021 Journal of clinical virology plus Result SARS_CoV_2 A28058G 24 31 35262011 Use of amplicon melt temperature to detect SARS-CoV-2 Lineage B.1.1.7 variant through the G28048T mutation in the ORF 8 gene. Nine out of the ten samples had sequences as predicted, but one sample (#9, high melt), which was predicted to be an 'original variant' also had the G28048T mutation. 2021 Journal of clinical virology plus Result SARS_CoV_2 G28048T 149 156 35262087 Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites. Amplification failure was expected and occurred for strains lacking both reference and mutation sequences at the locus (e.g., B.1.351 lacks both alleles at K417T, B.1.351 and P.1 lack both alleles at E484Q, and B.1.617.1 lacks both alleles at E484K) which indicates high specificity of all assays performed on synthetic RNA. 2022 medRxiv Result SARS_CoV_2 E484K;E484Q;K417T 243;200;156 248;205;161 35262087 Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites. Based on current circulating strains, we performed the L452R assay and identified 13 samples with reference sequence at this site. 2022 medRxiv Result SARS_CoV_2 L452R 55 60 35262087 Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites. Furthermore, due to possible non-specific binding in the SNP assays, sample results with relative fluorescent output (RFU) values outside of the 99% confidence interval (95% for L452R) of allele-specific RFU were also considered inconclusive (Supplemental Files 4 and 5, logic shown in Supplemental Figure 3). 2022 medRxiv Result SARS_CoV_2 L452R 178 183 35262087 Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites. Furthermore, of the 96 replicates that produced an inconclusive result, 74 were due to the presence of an alternate allele: 70 replicates containing E484K (B.1.351 and P.1 lineages) were inconclusive on E484Q, 4 replicates containing K417N were inconclusive for K417T (B.1.351 lineage and AY.2 sublineage) (Supplemental File 3). 2022 medRxiv Result SARS_CoV_2 E484K;E484Q;K417N;K417T 149;203;234;262 154;208;239;267 35262087 Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites. LoDs for ORF1aDelta3675-3677, K417T, E484K, E484Q, and L452R were 4 genome copies/assay. 2022 medRxiv Result SARS_CoV_2 E484K;E484Q;K417T;L452R 37;44;30;55 42;49;35;60 35262087 Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites. We assessed analytical specificity by performing K417T, E484K, E484Q, and L452R assays on synthetic RNA from six characteristic SARS-CoV-2 strains at 4 104 genome copies/assay (Figure 2). 2022 medRxiv Result SARS_CoV_2 E484K;E484Q;K417T;L452R 56;63;49;74 61;68;54;79 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. At 3 months after the vaccination, all vaccinees still had neutralizing antibodies against D614G, Alpha, and Eta variants, while Beta was neutralized by 84.6% (44/52) and Delta by 96.2% (50/52) of vaccinees' sera (Table 1). 2022 Microbiology spectrum Result SARS_CoV_2 D614G 91 96 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. despite different assay settings, sera from all vaccinees neutralized ancestral D614G (B.1) (laboratory A) and original Wuhan-like (B) (laboratory B) strains 6 weeks (GMT 441, CI 359-543, against D614G, and GMT 304, CI 239-388, against original strain) and 3 months (GMT 229, CI 180-292, against D614G and GMT 137, CI 110-172, against original strain) after vaccination. 2022 Microbiology spectrum Result SARS_CoV_2 D614G;D614G;D614G 80;196;296 85;201;301 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. Despite the decrease in the levels of neutralizing antibodies, sera of all vaccinees continued to neutralize D614G and Alpha, and 84.6% (44/52) neutralized Delta variant 6 months postvaccination (Table 1). 2022 Microbiology spectrum Result SARS_CoV_2 D614G 109 114 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. FIN1-20 (B) used in this study represented the original Wuhan-like strain despite H49Y substitution and DeltaQTQTN675-679 deletion from cell culture adaptation in the spike protein. 2022 Microbiology spectrum Result SARS_CoV_2 H49Y 82 86 S 167 172 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. FIN25-20 (B.1) had D614G substitution along with DeltaYQTQT674-678 and R682W changes near the furin cleavage site. 2022 Microbiology spectrum Result SARS_CoV_2 D614G;R682W 19;71 24;76 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. For D614G the fold-reduction was 2.8 in the moderate and 5.4 in the high titer group, whereas the fold-reductions were 2.5 and 5.1 for Alpha, and 4.0 and 11.8 for Delta. 2022 Microbiology spectrum Result SARS_CoV_2 D614G 4 9 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. GMTs were 354 (CI 288-435) and 441 (CI 359-543) against D614G, and 255 (CI 209-312) and 288 (CI 231-360) against Alpha (B.1.1.7) with 3- and 4-day incubation, respectively, indicating that longer incubation time increased neutralization titers slightly. 2022 Microbiology spectrum Result SARS_CoV_2 D614G 56 61 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. However, high neutralization titers against D614G, Alpha and Eta were not necessarily associated with high titers against Delta and Beta variants. 2022 Microbiology spectrum Result SARS_CoV_2 D614G 44 49 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. In addition to comparison of MNTs performed in two laboratories, we tested 3- and 4-day incubation times for MNT in laboratory A for D614G and Alpha variants. 2022 Microbiology spectrum Result SARS_CoV_2 D614G 133 138 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. In addition, neutralization titers against Eta (B.1.525) and Beta (B.1.351) correlated with each other (r = 0.764, P < 0.0001) and moderately with D614G (r = 0.611 for Eta and r = 0.508 for Beta, P < 0.0001). 2022 Microbiology spectrum Result SARS_CoV_2 D614G 147 152 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. including N501Y in both Alpha and Beta, E484K in Eta and Beta, K417N in Beta, and L452R and T478K only in Delta. 2022 Microbiology spectrum Result SARS_CoV_2 E484K;K417N;L452R;N501Y;T478K 40;63;82;10;92 45;68;87;15;97 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. Isolates representing Alpha (B.1.1.7), Eta (B.1.525), Beta (B.1.351), and Delta (B.1.617.2) variants had typical aa changes that define the lineages, and Alpha and Eta had R682W substitution from cell culture adaptation in all the sequence reads. 2022 Microbiology spectrum Result SARS_CoV_2 R682W 172 177 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. MNT for D614G was performed with both 3-day and 4-day incubations. 2022 Microbiology spectrum Result SARS_CoV_2 D614G 8 13 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. Neutralization titers against Alpha (B.1.1.7) and Delta (B.1.617.2) variants had a strong correlation with each other (r = 0.753, P < 0.0001) and even stronger correlation with ancestral D614G strain (r = 0.786 and r = 0.861, respectively, P < 0.0001). 2022 Microbiology spectrum Result SARS_CoV_2 D614G 187 192 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. SARS-CoV-2 isolates FIN1-20, FIN25-20, FIN35-21, FIN33-21, FIN32-21, and FIN37-21 representing original Wuhan-like strain, ancestral D614G strain, and variants Alpha, Eta, Beta, and Delta, respectively, were propagated in cells and sequenced to determine the amino acid (aa) changes compared to Wuhan Hu-1 isolate. 2022 Microbiology spectrum Result SARS_CoV_2 D614G 133 138 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. Since Beta was replaced by Delta variant at the end of June 2021 and Eta was subsequently reclassified from VOI to VBM, we continued to monitor the neuralization efficacy of sera against the ancestral D614G variant and the circulating variants in Finland, Alpha and Delta. 2022 Microbiology spectrum Result SARS_CoV_2 D614G 201 206 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. Six months postvaccination the fold-reduction of neutralizing antibody titers was increased to 3.9, 3.1, and 3.8 against D614G, Alpha, and Delta, respectively. 2022 Microbiology spectrum Result SARS_CoV_2 D614G 121 126 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. Six weeks after the first vaccine dose (and 3 weeks after the second dose), all vaccinated HCWs had high neutralization titers against D614G (GMT 354, CI 288-435 with 3-day incubation and GMT 441, CI 359-543 with 4-day incubation), Alpha (GMT 288, CI 231-360), and Eta (GMT 242, CI 192-305), while the neutralization titers against Beta (GMT 61, CI 50-76) and Delta (GMT 117, CI 96-143) were reduced 5.8-fold and 3.8-fold compared to B.1, respectively. 2022 Microbiology spectrum Result SARS_CoV_2 D614G 135 140 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. The ability of BNT162b2 vaccine-induced antibodies to neutralize SARS-CoV-2 variants D614G (B.1), Alpha (B.1.1.7; circulating in Finland during the first half of the year 2021), Eta (B.1.525), Beta (B.1.351), and Delta (B.1.617.2; circulating in Finland at the time of this study, summer and autumn 2021) was analyzed with microneutralization test (MNT). 2022 Microbiology spectrum Result SARS_CoV_2 D614G 85 90 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. Three months after vaccination, neutralizing antibody titers declined and the neutralization of D614G, Alpha, Eta, Beta, and Delta was reduced by 1.9-2.6-, 1.6-, 2.1-, 2.0-, and 1.8-fold, respectively, compared to the titers at 6 weeks. 2022 Microbiology spectrum Result SARS_CoV_2 D614G 96 101 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. Vaccinees were grouped with moderate (ID50 60-320) and high (ID50 >320) neutralization titers, and the fold-reduction for D614G, Alpha, and Delta (6 wk versus 6 mo) was calculated. 2022 Microbiology spectrum Result SARS_CoV_2 D614G 122 127 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. 6A), whereas lower density was noticed for the mutations L452R, E484Q and L452R-E484Q, with a range of 3.14 nm-3, 2.74 nm-3 and 2.94 nm-3, respectively. 2022 3 Biotech Result SARS_CoV_2 E484Q;L452R;L452R;E484Q 64;57;74;80 69;62;79;85 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. However, mutants including L452R, E484Q and L452R-E484Q had more expansive basins and numerous meta-stable conformations associated with multiple energy minima. 2022 3 Biotech Result SARS_CoV_2 E484Q;L452R;L452R;E484Q 34;27;44;50 39;32;49;55 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. However, the average PDF-Rg analysis indicates a higher drift on L452R, with 1.77 nm, E484Q with 1.77 nm, L452R-E484Q with 1.78 nm, whereas WT with 1.84 nm (Figure S1B and Table S1). 2022 3 Biotech Result SARS_CoV_2 E484Q;L452R;L452R;E484Q 86;65;106;112 91;70;111;117 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. Noticeably, the mutant L452R shows a fluctuation of 0.27 nm, and E484Q showed a drift of 0.26 nm, followed by maximum drift in L452R-E484Q with 0.41 nm (Figure S1A). 2022 3 Biotech Result SARS_CoV_2 E484Q;L452R;L452R;E484Q 65;23;127;133 70;28;132;138 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. The amplitude and the intensity of WT were magnified with a value of 0.080nm2 (Figure S2A), whereas a high difference is observed in the mutants L452R, E484Q and L452R-E484Q, with a range of 0.258nm2, 0.239nm2 and 0.239nm2, respectively (Figure S2B-D). 2022 3 Biotech Result SARS_CoV_2 E484Q;L452R;L452R;E484Q 152;145;162;168 157;150;167;173 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. The dynamic behavior of WT and mutants were compared with the clustering parameters and the results revealed that the clusters are well defined in the WT structures by covering the minimum region, whereas the L452R, E484Q and L452R-E484Q mutants occupied maximum regions with a wider cluster. 2022 3 Biotech Result SARS_CoV_2 E484Q;L452R;L452R;E484Q 216;209;226;232 221;214;231;237 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. The overall analysis showed that the L452R consists of 118.84 H-bonds, E484Q with 125.32, L452R-E484Q with 123.93, whereas WT with 119.59 H-bonds. 2022 3 Biotech Result SARS_CoV_2 E484Q;L452R;L452R;E484Q 71;37;90;96 76;42;95;101 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. The PDF analysis of SASA on mutants revealed an unsteady change with the values of 117.18nm2 for L452R, 109.98nm2 for E484Q, and 109.43nm2 for L452R-E484Q (Figure S1C and Table S1). 2022 3 Biotech Result SARS_CoV_2 E484Q;L452R;L452R;E484Q 118;97;143;149 123;102;148;154 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. The POLYPHEN scores for L452R and E484Q were high, reflecting deleterious effects on the native protein and a deviation from its WT activity. 2022 3 Biotech Result SARS_CoV_2 E484Q;L452R 34;24 39;29 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. The results found minimal fluctuations on the WT with a value of ~0.1 nm and the residual displacement of mutants L452R, E484Q and L452R-E484Q revealed maximum Calpha-RMSF fluctuation with ~0.2 nm, ~0.4 nm, and ~0.3 nm, respectively. 2022 3 Biotech Result SARS_CoV_2 E484Q;L452R;L452R;E484Q 121;114;131;137 126;119;136;142 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. The results revealed that L452R, E484Q, L452R_E484Q mutations showed increased fluctuation than WT SARS-CoV-2 RBD. 2022 3 Biotech Result SARS_CoV_2 E484Q;L452R;L452R 33;26;40 38;31;45 RBD 110 113 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. The results revealed that the mutants L452R, E484Q and L452R-E484Q showed a decrease in Rg with a maximum reduction in E484Q compared with WT. 2022 3 Biotech Result SARS_CoV_2 E484Q;E484Q;L452R;L452R;E484Q 45;119;38;55;61 50;124;43;60;66 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. The results revealed that the mutations L452R and E484Q are predicted to produce functional impact by destabilizing effect on the spike glycoprotein. 2022 3 Biotech Result SARS_CoV_2 E484Q;L452R 50;40 55;45 S 130 148 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. The RMSD analysis revealed that the mutations L452R, E484Q and L452R-E484Q were unstable with a RMSD range of ~0.2 to 0.5 nm compared with WT, which was stable with ~0.15 nm. 2022 3 Biotech Result SARS_CoV_2 E484Q;L452R;L452R;E484Q 53;46;63;69 58;51;68;74 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. The study was hypothesized to understand the underlying mechanism and molecular basis of SARS-CoV-2 mutations L452R, E484Q, L452R-E484Q on the receptor stability. 2022 3 Biotech Result SARS_CoV_2 E484Q;L452R;L452R;E484Q 117;110;124;130 122;115;129;135 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. 1A and C), potentially optimizing the furin cleavage site, which prompted us to examine the effect of the P681R substitution on furin cleavage. 2022 mBio Result SARS_CoV_2 P681R 106 111 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. As shown, the binding efficiencies of the RBDs of Kappa (L452R E484Q) (98.88%), Delta (L452R T478K) (99.04%), B.1.618 (E484K) (98.76%), L452R (98.90%), and E484Q (98.48%) were higher than that of the WT (89.6%), suggesting the RBDs of variants bind human ACE2 with a higher affinity. 2022 mBio Result SARS_CoV_2 E484Q;E484Q;L452R;T478K;E484K;L452R;L452R 63;156;136;93;119;57;87 68;161;141;98;124;62;92 RBD;RBD 42;227 46;231 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. Besides HeLa-mouse ACE2, Delta also exhibited significantly enhanced cell entry into HeLa-marmoset and HeLa-koala cells, which are contributed to by L452R and T478K mutations. 2022 mBio Result SARS_CoV_2 L452R;T478K 149;159 154;164 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. Collectively, these results suggest that P681R substitution in the Kappa and Delta variants could enhance spike cleavage and promote cell fusion. 2022 mBio Result SARS_CoV_2 P681R 41 46 S 106 111 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. Compared to WT spike, Delta and B.1.618 spike proteins gained an increased ability to mediate viral entry into HeLa-human ACE2 cells, which was contributed to by the T478K (Delta), P681R (Delta), Delta145-146 (B.1.618), and E484K (B.1.618) variants. 2022 mBio Result SARS_CoV_2 E484K;P681R;T478K 224;181;166 229;186;171 S;S 15;40 20;45 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. In addition, the N501Y mutation in the spike has been demonstrated to have gained the ability to utilize mouse ACE2 for cell entry, and our data suggested that the N501Y mutant specifically gained the ability to utilize mouse ACE2 for cell entry, with an efficiency approximately 4-fold higher than that of Delta; however, the N501Y mutation has a negligible effect on utilization of marmoset or koala ACE2 for cell entry. 2022 mBio Result SARS_CoV_2 N501Y;N501Y;N501Y 17;164;327 22;169;332 S 39 44 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. In contrast, Kappa did not increase cell entry into HeLa-marmoset or HeLa-koala cells, and B.1.618 only showed enhanced entry into HeLa-koala cells, which is attributable to E484K. 2022 mBio Result SARS_CoV_2 E484K 174 179 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. Interestingly, our data showed significantly increased cleavage of the full-length spike protein (S0) into the S1 and S2 fragments in Kappa spike and P681R spike pseudotyped viruses compared with WT spike. 2022 mBio Result SARS_CoV_2 P681R 150 155 S;S;S;S 83;140;156;199 88;145;161;204 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. Kappa and Delta variants contain a P681R substitution. 2022 mBio Result SARS_CoV_2 P681R 35 40 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. Our results showed that spike proteins from Kappa, Delta, and B.1.618 could significantly enhance cell entry into HeLa-mouse ACE2 cells, as a result of the T478K (Delta), E484Q (Kappa), and E484K (B.1.618) mutations. 2022 mBio Result SARS_CoV_2 E484K;E484Q;T478K 190;171;156 195;176;161 S 24 29 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. P681R mutation in Kappa and Delta variants with enhanced spike protein cleavage and increased cell fusion activity. 2022 mBio Result SARS_CoV_2 P681R 0 5 S 57 62 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. The cleaved S1/S0 ratio was 2.1-fold (Kappa) or 3.0-fold (P681R) higher than that of the WT, and the cleaved S2/S0 ratio was 2.4-fold (Kappa) or 1.8-fold (P681R) higher than that of the WT. 2022 mBio Result SARS_CoV_2 P681R;P681R 58;155 63;160 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. The extent of fusion was then quantified by measuring the GFP+ area: the spike proteins of the P681R, Kappa, and Delta variants were more active at cell fusion than the WT at both early and late time points. 2022 mBio Result SARS_CoV_2 P681R 95 100 S 73 78 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. The results showed that Kappa, Delta, and B.1.618 exhibited 1.8-, 3.0-, and 3.3-fold resistance to neutralization by convalescent-phase sera, respectively, which is conferred by E484Q, L452R E484Q, T478K, Delta145-146, and E484K. 2022 mBio Result SARS_CoV_2 E484K;E484Q;E484Q;L452R;T478K 223;178;191;185;198 228;183;196;190;203 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. The spike protein of Kappa exhibited comparable ability to mediate viral entry: even an E484Q or P681R mutation in its spike could significantly promote viral entry individually. 2022 mBio Result SARS_CoV_2 E484Q;P681R 88;97 93;102 S;S 4;119 9;124 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. To do this, we produced murine leukemia virus (MLV) viral particles pseudotyped with WT, Kappa, or P681R spike. 2022 mBio Result SARS_CoV_2 P681R 99 104 S 105 110 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. To further examine the biological impact of these mutations on cell entry, we produced pseudotyped virus particles containing a firefly luciferase reporter gene and expressing on their surface with the spike proteins of WT (D614G), Kappa, Delta, and B.1.618 variants. 2022 mBio Result SARS_CoV_2 D614G 224 229 S 202 207 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. To this end, we used an SARS-CoV-2 transcription- and replication-competent virus-like particle (trVLP) cell culture system, which recapitulates the entire viral life cycle in Caco-2-N cells, to engineer the desired mutations in the spike proteins of Kappa, Delta, and B.1.618 variants into an SARS-CoV-2 isolate, Wuhan-Hu-1, with a D614G (WT) backbone, and examined the sensitivity of trVLP of Kappa, Delta, and B.1.618 to inhibition of ACE2-Ig. 2022 mBio Result SARS_CoV_2 D614G 333 338 S 233 238 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. For example, H_5 originated from a non-synonymous mutational step (position 10525 of the RNA sequence/ H3509Y) from H_1 of ORF1a (Figure S1 C). 2022 Genetics and molecular biology Result SARS_CoV_2 H3509Y 103 109 ORF1a 123 128 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. For example, the synonymous substitution C1818T in the RNA sequence is recurrent in S and causes several reticulations (Figure S1 A), but we do not know if it represents a natural SARS-CoV-2 genomic mutational hotspot, or a simple annotation or sequencing error. 2022 Genetics and molecular biology Result SARS_CoV_2 C1818T 41 47 S 84 85 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. Haplotypes 5 and 23 (H_5 and H_23, Figure S1 A) have the selected sites A845S and L5F in the S. 2022 Genetics and molecular biology Result SARS_CoV_2 A845S;L5F 72;82 77;85 S 93 94 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. It is noteworthy that the positive selection signal was not lost when considering the derived lineages (Table 4), similar to what happens with the ORF3 selected sites L83F and D27Y; ORF1a selected sites G150S, G519S, P2046T/L, and K3353R, as well as ORF1b selected sites L314P, D1264E, and T1774I (Table 4),all of which were present in haplotypes with some level of expansion (Figure S1 B: H_2, H_36; Figure S1 C: H_64, H_222, H_79, H_89; Figure S1 D: H_11, H_60, H_261, respectively). 2022 Genetics and molecular biology Result SARS_CoV_2 D1264E;D27Y;G150S;G519S;K3353R;L314P;L83F;P2046T;T1774I 278;176;203;210;231;271;167;217;290 284;180;208;215;237;276;171;225;296 ORF1a 182 187 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. Notably, in our analysis, a number of these sites (e.g., E484K) did not exhibit evidence of positive selection. 2022 Genetics and molecular biology Result SARS_CoV_2 E484K 57 62 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. Notably, some critical diagnostic sites, whose positive selection signals were detected by us (Table S1), did not seem to be relevant in the networks, indicating no apparent sign of expansion (according to our criteria), at least so far (e.g., ORF1a T1820I and ORF3 D155Y diagnostic sites of P.1.2). 2022 Genetics and molecular biology Result SARS_CoV_2 D155Y;T1820I 266;250 271;256 ORF1a 244 249 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. ORF1b also presented positively selected sites under these conditions (H_32, 5484,5483/K1828T; H_65, 652/ P218L; H_117, 246/ K82N). 2022 Genetics and molecular biology Result SARS_CoV_2 K82N;P218L;K1828T 125;106;87 129;111;93 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. Table 4 shows the sites that met these criteria in both datasets [Gamma and Gamma/P1.1/P.1.2; S (L5F, T572I, A845S), ORF3 (L83F, K16N, L85F, D27Y), ORF1a (G150S, G519S, P2046T, L642F, K3353R), ORF1b (L314P, A1643V, D1264E, T1774I)], while others were unique to one or another dataset, suggesting potentially different evolutionary pathways from the ancestor (Gamma) and its two more recently derived lineages. 2022 Genetics and molecular biology Result SARS_CoV_2 A1643V;A845S;A845S;D1264E;D27Y;D27Y;G519S;G519S;K16N;K16N;K3353R;L642F;L642F;L85F;L85F;P2046T;T1774I;T572I;T572I;G150S;G150S;L314P;L314P;L5F;L5F;L83F;L83F 207;110;109;215;142;141;163;162;130;129;184;178;177;136;135;169;223;103;102;156;155;201;200;98;97;124;123 213;114;114;221;145;145;167;167;133;133;190;182;182;139;139;175;229;107;107;160;160;205;205;100;100;127;127 ORF1a;S 148;94 153;95 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. This result suggested that H3509Y of ORF1a occurred after P.1.2 had dispersed from the S to the southwest (SW) and northeast (NE) regions. 2022 Genetics and molecular biology Result SARS_CoV_2 H3509Y 27 33 ORF1a;S 37;87 42;88 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. 94 cases were detected in the CY5.5 channel for the mutant type of D614G and L452R mutations. 2022 Journal of virological methods Result SARS_CoV_2 D614G;L452R 67;77 72;82 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. In the CY5 channel, the wild type of E484Q and E484K were amplified in the 94 samples. 2022 Journal of virological methods Result SARS_CoV_2 E484K;E484Q 47;37 52;42 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. Sequencing results overlapped with the results of the Primer-Probe assay, 94 samples had the D614G and L452R mutations with 5 samples encompassing Del69/70. 2022 Journal of virological methods Result SARS_CoV_2 D614G;L452R 93;103 98;108 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. The 5 samples had detected by the Primer-Probe UK variant had the same melting curves that differed from 89 cases containing D614G, L452R, and T478K mutations. 2022 Journal of virological methods Result SARS_CoV_2 D614G;L452R;T478K 125;132;143 130;137;148 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. The 89 cases for L452R had the same patterns. 2022 Journal of virological methods Result SARS_CoV_2 L452R 17 22 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. The only one sample which was not detected, sequencing results confirmed it as Delta variant along with V483F mutation. 2022 Journal of virological methods Result SARS_CoV_2 V483F 104 109 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. The same 89 cases had similar patterns for T478K. 2022 Journal of virological methods Result SARS_CoV_2 T478K 43 48 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. The same melting curves patterns were detected in all cases for the D614G. 2022 Journal of virological methods Result SARS_CoV_2 D614G 68 73 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. Those samples with negative results for E484K, E484Q, and positive results for D614G, L452R were screened by HRM analysis plus T478K mutation specified for the Delta variant. 2022 Journal of virological methods Result SARS_CoV_2 D614G;E484K;E484Q;L452R;T478K 79;40;47;86;127 84;45;52;91;132 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. After treatment of the cells with 100-300 mug/mL GB-1, the number of 293 T cells with low binding to the RBD with N501Y mutation was significantly increased in both ACE2-positive cells and the top population in a dose-dependent manner . 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 N501Y 114 119 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. After treatment of the cells with GB-1, the number of 293 T cells with high binding to the RBD with L452R-T478K mutation was significantly decreased in both ACE2-positive cells and the top population in GB-1 treatment group . 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 L452R;T478K 100;106 105;111 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. After treatment of the cells with the indicated concentration of GB-1, the number of 293 T cells with high binding to the RBD with K417N mutation was not increased in both ACE2-positive cells and the top population . 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N 131 136 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. After treatment of the cells with the indicated concentration of GB-1, the number of 293 T cells with high binding to the RBD with K417T-E484K-N501Y mutation was decreased in both ACE2-positive cells and the top population in the 200-300 mug/mL GB-1 treatment group . 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417T;E484K;N501Y 131;137;143 136;142;148 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. After treatment of the cells with the indicated concentration of GB-1, the number of 293 T cells with low binding to the RBD with E484K mutation was significantly increased in both ACE2-positive cells and the top population . 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 E484K 130 135 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. After treatment of the cells with the indicated concentration of GB-1, the number of 293 T cells with low binding to the RBD with K417N-E484K-N501Y mutation was significantly increased in both ACE2-positive cells and the top population in the 200-300 mug/mL GB-1 treatment group . 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 130;136;142 135;141;147 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Despite the loss in the binding affinity between RBD and ACE2, the K417N mutation can escape neutralization by several monoclonal antibodies and decreases the efficiency of some vaccines. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N 67 72 RBD 49 52 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Effect of GB-1 on the binding between ACE2 and RBD with K417N-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 56;62;68 61;67;73 RBD 47 50 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Effect of GB-1 on the binding between ACE2 and RBD with K417T-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417T;E484K;N501Y 56;62;68 61;67;73 RBD 47 50 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Effect of GB-1 on the binding between ACE2 and RBD with L452R-T478K mutation. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 L452R;T478K 56;62 61;67 RBD 47 50 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Effect of GB-1 on the interaction between ACE2 and RBD with E484K mutation. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 E484K 60 65 RBD 51 54 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Effect of GB-1 on the interaction between ACE2 and RBD with K417N mutation. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N 60 65 RBD 51 54 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Effect of GB-1 on the interaction between ACE2 and RBD with N501Y mutation. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 N501Y 60 65 RBD 51 54 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. For this reason, we investigated the effect of GB-1 on the interaction between ACE2 and RBD with K417N mutation of RBD through dual-color flow cytometric analysis. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N 97 102 RBD;RBD 88;115 91;118 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. However, 50 mug/mL glycyrrhizic acid cannot affect the binding between ACE2 and RBD with K417N-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 89;95;101 94;100;106 RBD 80 83 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. However, the number of 293 T cells with high binding to the RBD with K417N-E484K-N501Y mutation was not increased in both ACE2-positive cells and the top population after 50 mug/mL glycyrrhizic acid treatment . 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 69;75;81 74;80;86 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. In our previous results, GB-1 could inhibit the binding between ACE2 and RBD with K417N-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 82;88;94 87;93;99 RBD 73 76 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. is the reference compound of Glycyrrhiza uralensis Our results indicated that GB-1 blocked the binding between ACE2 and RBD with Wuhan type or K417N-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 143;149;155 148;154;160 RBD 120 123 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. K417N can block the hydrogen bond with ACE2-reducing affinity. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N 0 5 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. K417N usually co-occurs with E484K and N501Y in both Beta variant and Gamma variant. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 E484K;N501Y;K417N 29;39;0 34;44;5 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. L452R and T478K mutations of RBD in delta variant could induce a strong immune escape ability. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 T478K;L452R 10;0 15;5 RBD 29 32 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Next, we investigated the effect of GB-1 on the binding between ACE2 and RBD with K417N-E484K-N501Y mutation through dual-color flow cytometric analysis. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 82;88;94 87;93;99 RBD 73 76 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Next, we investigated the effect of GB-1 on the binding between ACE2 and RBD with K417T-E484K-N501Y mutation through dual-color flow cytometric analysis. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417T;E484K;N501Y 82;88;94 87;93;99 RBD 73 76 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Next, we investigated the effect of GB-1 on the binding between ACE2 and RBD with L452R-T478K mutation through dual-color flow cytometric analysis. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 L452R;T478K 82;88 87;93 RBD 73 76 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Next, we investigated the effect of GB-1 on the interaction between ACE2 and RBD with E484K mutation through dual-color flow cytometric analysis. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 E484K 86 91 RBD 77 80 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Next, we investigated the effect of GB-1 on the interaction between ACE2 and RBD with N501Y mutation through dual-color flow cytometric analysis. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 N501Y 86 91 RBD 77 80 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Next, we investigated the effect of glycyrrhizic acid on the interaction between ACE2 and RBD with Wuhan type or K417N-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 113;119;125 118;124;130 RBD 90 93 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Previous reports have demonstrated that RBD with N501Y mutation promoted binding to the ACE2 receptor more than did the Wuhan type and increased the infectivity of SARS-CoV-2. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 N501Y 49 54 RBD 40 43 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Studies have reported that mutations (K417N, E484K and N501Y) in the RBD in SARS-CoV-2 are associated with higher infectivity and resistance to neutralization of several antibodies. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 E484K;N501Y;K417N 45;55;38 50;60;43 RBD 69 72 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The number of 293 T cells with high binding to the RBD with E484K mutation was also decreased in both ACE2-positive cells and the top population. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 E484K 60 65 RBD 51 54 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The number of 293 T cells with high binding to the RBD with K417N-E484K-N501Y mutation was also decreased in ACE2-positive cells and the top population in the 200-300 mug/mL GB-1 treatment group. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 60;66;72 65;71;77 RBD 51 54 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The number of 293 T cells with high binding to the RBD with N501Y mutation was also decreased in both ACE2-positive cells and the top population in a dose-dependent manner. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 N501Y 60 65 RBD 51 54 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The number of 293 T cells with low binding to the RBD with K417N mutation was decreased in both ACE2-positive cells and the top population. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N 59 64 RBD 50 53 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The number of 293 T cells with low binding to the RBD with K417N-E484K-N501Y mutation was not affected in both ACE2-positive cells and the top population after 50 mug/mL glycyrrhizic acid treatment. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 59;65;71 64;70;76 RBD 50 53 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The number of 293 T cells with low binding to the RBD with K417T-E484K-N501Y mutation was decreased in ACE2-positive cells and the top population in the 200 mug/mL GB-1 treatment group. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417T;E484K;N501Y 59;65;71 64;70;76 RBD 50 53 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The number of 293 T cells with low binding to the RBD with L452R-T478K mutation was also increased in ACE2-positive cells and the top population in the 200-300 mug/mL GB-1 treatment group. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 L452R;T478K 59;65 64;70 RBD 50 53 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The previous studies showed that E484K mutation can completely abolish the binding of RBD to bamlanivimab. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 E484K 33 38 RBD 86 89 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The RBD in gamma variant contain N501Y, E484K and K417T mutations. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 E484K;K417T;N501Y 40;50;33 45;55;38 RBD 4 7 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. These results suggested that 100-300 mug/mL GB-1 cannot affect the binding between ACE2 and RBD with K417N mutation. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N 101 106 RBD 92 95 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. These results suggested that 100-300 mug/mL GB-1 inhibited the binding between ACE2 and RBD with N501Y mutation. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 N501Y 97 102 RBD 88 91 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. These results suggested that 200-300 mug/mL GB-1 blocked the binding between ACE2 and RBD with K417N-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417N;E484K;N501Y 95;101;107 100;106;112 RBD 86 89 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. These results suggested that 200-300 mug/mL GB-1 blocked the binding between ACE2 and RBD with L452R-T478K mutation. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 L452R;T478K 95;101 100;106 RBD 86 89 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. These results suggested that 300 mug/mL GB-1 significantly inhibited the binding between ACE2 and RBD with E484K mutation. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 E484K 107 112 RBD 98 101 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. These results suggested that GB-1 can partially affect the binding between ACE2 and RBD with K417T-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Result SARS_CoV_2 K417T;E484K;N501Y 93;99;105 98;104;110 RBD 84 87 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. Among 42 patients, sera from 28 patients showed long-lasting neutralizing activities on the three VOCs (five out of fifteen mild: P6, P7, P9, P10, and P13, and all moderate to critical), in addition to D614G. 2022 Frontiers in immunology Result SARS_CoV_2 D614G 202 207 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. However, many patients in 'patients without pneumonia' could not acquire or maintain the Nab titers for D614G and three VOCs. 2022 Frontiers in immunology Result SARS_CoV_2 D614G 104 109 Pneumonia 44 53 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. Longevity of Neutralizing Activity Against D614G and VOCs. 2022 Frontiers in immunology Result SARS_CoV_2 D614G 43 48 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. Next, we analyzed the Nab titers among D614G and three VOCs by two severity groups. 2022 Frontiers in immunology Result SARS_CoV_2 D614G 39 44 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The median Nab titer (log2) with IQR against D614G, B.1.1.7, P.1, and B.1.351 at 1-3 months post onset were 5 (5-6), 5 (4-5), 4 (4-5), and 3 (2-4), respectively. 2022 Frontiers in immunology Result SARS_CoV_2 D614G 45 50 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The median Nab titer (log2) with IQR against D614G, B.1.1.7, P.1, and B.1.351 at 3-6 months post onset were 4 (4-5.5), 4 (3-5), 5 (4-6), and 3 (2-4), respectively. 2022 Frontiers in immunology Result SARS_CoV_2 D614G 45 50 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The median Nab titer (log2) with IQR against D614G, B.1.1.7, P.1, and B.1.351 at 6-8 months post onset were 4 (2-5), 5 (3-6), 4 (3-6), and 3 (2-3), respectively. 2022 Frontiers in immunology Result SARS_CoV_2 D614G 45 50 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The Nab titer against B.1.351 was significantly lower than that against the other three variants, and the Nab titer against P.1 was significantly lower than that against D614G. 2022 Frontiers in immunology Result SARS_CoV_2 D614G 170 175 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The Nab titer against D614G significantly decreased at 6-8 months post onset compared to 1-3 months post onset. 2022 Frontiers in immunology Result SARS_CoV_2 D614G 22 27 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The proportion of patients with ND for P.1 was the second-highest but without significant difference from D614G and B.1.1.7. 2022 Frontiers in immunology Result SARS_CoV_2 D614G 106 111 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The proportions of patients with ND for D614G, B.1.1.7, and P.1 at 1-3 months post onset were 0%, 11.8%, and 17.6%, respectively. 2022 Frontiers in immunology Result SARS_CoV_2 D614G 40 45 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The proportions of patients with ND for D614G, B.1.1.7, P.1 and B.1.351 at 3-6 months post onset were 5.3%, 15.8%, 26.3%, and 68.4%, respectively. 2022 Frontiers in immunology Result SARS_CoV_2 D614G 40 45 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The proportions of patients with ND for D614G, B.1.1.7, P.1, and B.1.351 at 6-8 months post onset were 20%, 20%, 30%, and 60%, respectively. 2022 Frontiers in immunology Result SARS_CoV_2 D614G 40 45 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. Then, we analyzed the trend of ND (not detected, that is, Nab titer under one) among D614G and three VOCs by two severity groups in Figure 2B . 2022 Frontiers in immunology Result SARS_CoV_2 D614G 85 90 35283546 SARS-CoV-2 infection after vaccination in Italian health care workers: a case report. The genotyping performed first by Real-time PCR and then confirmed by direct sequencing proved the presence of del69/70, N501Y, A570D, and 1841A > G (D614G) variants, indicative of VOC 202,012/01-lineage B.1.1.7, in all samples suggesting a common source of infection. 2022 National Academy science letters. National Academy of Sciences, India Result SARS_CoV_2 A1841G;A570D;N501Y;D614G 139;128;121;150 148;133;126;155 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. As a result, for the Alpha variant, we identified nine mutations in the spike gene: S:Delta69/70, S:Delta144, S:N510Y, S:A570D, S:D614G, S:P681H, S:T716I, S:S982A, and S:D1118H. 2022 Applied and environmental microbiology Result SARS_CoV_2 A570D;D1118H;D614G;N510Y;P681H;S982A;T716I 121;170;130;112;139;157;148 126;176;135;117;144;162;153 S;S;S;S;S;S;S;S;S;S 72;84;98;110;119;128;137;146;155;168 77;85;99;111;120;129;138;147;156;169 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. For the Alpha variant, we found three acceptable mutations, S:A570D, S:T716I, and S:S982A. 2022 Applied and environmental microbiology Result SARS_CoV_2 A570D;S982A;T716I 62;84;71 67;89;76 S;S;S 60;69;82 61;70;83 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. For the Delta variant, we found three mutations, S:L452R, S:P681R, and S:Delta156/157, in GISAID samples from the state of Illinois. 2022 Applied and environmental microbiology Result SARS_CoV_2 L452R;P681R 51;60 56;65 S;S;S 49;58;71 50;59;72 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. For the Delta variant, we identified seven mutations: S:T19R, S:Delta156/157, S:L452R, S:T484K, S:D614G, S:P681R, and S:D950N. 2022 Applied and environmental microbiology Result SARS_CoV_2 D614G;D950N;L452R;P681R;T19R;T484K 98;120;80;107;56;89 103;125;85;112;60;94 S;S;S;S;S;S;S 54;62;78;87;96;105;118 55;63;79;88;97;106;119 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. However, if we look at all GISAID samples from the United States, the sensitivity for the S:L452R and S:Delta156/157 mutations to characterize the Delta variant drops below 0.97. 2022 Applied and environmental microbiology Result SARS_CoV_2 L452R 92 97 S;S 90;102 91;103 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. Importantly, this mutation has higher sensitivity and specificity in both regions of interest than the mutation S:T478K (sensitivity is 0.99 and specificity is 0.97 in Illinois, while sensitivity is only 0.96 and specificity is only 0.98 in the United State [Fig. 2022 Applied and environmental microbiology Result SARS_CoV_2 T478K 114 119 S 112 113 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. S2b), and we chose the S:A570D mutation because the PCR assay targeting S:A570D has already been verified to work for sewage samples; we adopted this mutation in our analysis. 2022 Applied and environmental microbiology Result SARS_CoV_2 A570D;A570D 25;74 30;79 S;S 23;72 24;73 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. Since our goal was to develop PCR assays that are also effective in other states in the United States, we instead chose S:P681R, which has high sensitivity and specificity in both Illinois (sensitivity is 0.99, and specificity is 0.99) and the United States (sensitivity is 0.99, and specificity is 0.99). 2022 Applied and environmental microbiology Result SARS_CoV_2 P681R 122 127 S 120 121 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. Therefore, our analysis shows that the PCR assay targeting S:T478K would estimate that the Delta variant was dominant from January 2021 to October 2021, when in reality, Delta variant sequences were collected and later deposited in GISAID starting in May 2021. 2022 Applied and environmental microbiology Result SARS_CoV_2 T478K 61 66 S 59 60 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. This lineage accounted for only around 1.2% of sequences from the United States (n = 1,187,412, from January 2021 to October 2021), so the PCR assay targeting S:T478K was expected to work well for Illinois, USA, showing an estimated sensitivity of 0.94 and an estimated specificity of 0.97. 2022 Applied and environmental microbiology Result SARS_CoV_2 T478K 161 166 S 159 160 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. To further confirm whether the RT-qPCR results were correct, we conducted NGS analysis to examine eight mutation markers for the Alpha variant (S:Delta69/70, S:Delta144, S:N501Y, S:A570D, S:P681H, S:T716I, S:S982A, and S:D1118H) and six mutation markers for the Delta variant (S:T19R, S:Delta156/157, S:L452R, S:T478K, S:P681R, and S:D950N) on the spike gene of two sewage samples (samples 5 and 6) and three synthetic RNA controls (WT, Alpha variant, and Delta variant). 2022 Applied and environmental microbiology Result SARS_CoV_2 A570D;D1118H;D950N;L452R;N501Y;P681H;P681R;S982A;T19R;T478K;T716I 181;221;334;303;172;190;321;208;279;312;199 186;227;339;308;177;195;326;213;283;317;204 S;S;S;S;S;S;S;S;S;S;S;S;S;S;S 348;144;158;170;179;188;197;206;219;277;285;301;310;319;332 353;145;159;171;180;189;198;207;220;278;286;302;311;320;333 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. We demonstrate this by considering a recent PCR assay targeting mutation S:T478K of the Delta and Delta plus lineages. 2022 Applied and environmental microbiology Result SARS_CoV_2 T478K 75 80 S 73 74 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. Accordingly, a specific reaction was designed to detect that deletion, denoted S157del reaction hereafter, by using a probe that can only bind to the mutated sequence (21987 probe). 2022 Microbiology spectrum Result SARS_CoV_2 S157del 79 86 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. Although the Cq values obtained with the ORF8119del reaction were 2 to 3 cycles higher than those of the S157del reaction in this test, all samples were correctly identified. 2022 Microbiology spectrum Result SARS_CoV_2 S157del 105 112 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. As detailed in Table S3, all lineages were negative for both the S157del and Orf8119del reactions. 2022 Microbiology spectrum Result SARS_CoV_2 S157del 65 72 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. Both the S157del and the Orf8119del reactions were very specific and did not give a positive signal in non-Delta samples. 2022 Microbiology spectrum Result SARS_CoV_2 S157del 9 16 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. Comparison of the PCR results with the Illumina WGS analysis showed that of the 62 samples randomly selected, 19 were not classified by the WGS analysis but were positive for the Delta-specific deletions (the S157del, Orf8119del, or both) (Table 2). 2022 Microbiology spectrum Result SARS_CoV_2 S157del 209 216 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. Design of the S157del and Orf8119del reactions. 2022 Microbiology spectrum Result SARS_CoV_2 S157del 14 21 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. Each sample was sequenced in the S157del region and the Orf8119del region. 2022 Microbiology spectrum Result SARS_CoV_2 S157del 33 40 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. However, in these cases, the Cq values of the E-sarbeco reaction and the S157del reaction (in Delta samples) were always at least 10 cycles earlier than those of the ND3L reaction, thereby clearly indicating that the sample was not of the Alpha lineage. 2022 Microbiology spectrum Result SARS_CoV_2 S157del 73 80 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. In order to exclude a possible mutual effect of the four reactions combined together, serial dilutions of Delta RNA from cultured cells were tested, showing similar sensitivity of both the E-sarbeco and S157del reactions, thus confirming the maintained sensitivity of the Alpha-Delta multiplex. 2022 Microbiology spectrum Result SARS_CoV_2 S157del 203 210 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. In order to facilitate detection of SC-2 RNA regardless of the lineage and identify the Alpha or Delta lineages in a single test, the three SC-2-targeting reactions (i.e., E-sarbeco, ND3L, and S157del) were combined in one multiplex assay termed "Alpha-Delta assay." A control reaction detecting the human RNAse P gene was also included in the multiplex assay for an endogenous control, as was performed previously. 2022 Microbiology spectrum Result SARS_CoV_2 S157del 193 200 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. Sequencing of the C-terminal domain (CTD) of the Orf8 gene from the same four samples classified by the S157del assay as Delta confirmed the presence of the Orf8 119 to 120 deletion, which is the target of the Orf8119del reaction. 2022 Microbiology spectrum Result SARS_CoV_2 S157del 104 111 ORF8;ORF8 49;157 53;161 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. The Cq values of the ND3L and S157del reactions, when positive, were comparable to those of the E-sarbeco reaction, demonstrating sufficient sensitivity of these reactions with RNA extraction of wastewater. 2022 Microbiology spectrum Result SARS_CoV_2 S157del 30 37 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. The limit of detection (LOD) for the SC-2 targets was determined to be 12 copies/reaction for the E-sarbeco reaction, 50 copies for the ND3L reaction, and less than 10 copies for the S157del reaction. 2022 Microbiology spectrum Result SARS_CoV_2 S157del 183 190 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. These data suggest that the positive identification of both the Orf8119del and the S157del mutations by the qPCR assay enable a more definite classification of these samples, even in the absence of a complete sequencing coverage. 2022 Microbiology spectrum Result SARS_CoV_2 S157del 83 90 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. These samples, which were classified as "Delta-suspected" by the Alpha-Delta assay, were positive for the Orf8 119 to 120 deletion, but the S157del region was not fully sequenced. 2022 Microbiology spectrum Result SARS_CoV_2 S157del 140 147 ORF8 106 110 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. Altogether, these results indicate that the T95I, Y145H and A222V mutations are not associated with significant changes in recognition of the spike by a panel of 24 monoclonal antibodies and by sera from vaccine recipients. 2022 EBioMedicine Result SARS_CoV_2 A222V;T95I;Y145H 60;44;50 65;48;55 S 142 147 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. As previously reported, the D614G and Alpha spike variants were less fusogenic than the Delta spike (Figure 2a, b, Figure S2). 2022 EBioMedicine Result SARS_CoV_2 D614G 28 33 S;S 44;94 49;99 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. In particular, the spike protein contains the 3 expected mutations in the NTD (T95I, Y145H and A222V) when compared to the Delta strain used here as a reference. 2022 EBioMedicine Result SARS_CoV_2 A222V;Y145H;T95I 95;85;79 100;90;83 S 19 24 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. It contains several mutations outside of the spike, all of them are characteristic of the AY.4.2.3 sublineage, except for nsp14 G143R (Figure S3a). 2022 EBioMedicine Result SARS_CoV_2 G143R 128 133 S 45 50 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. The 95 and 222 residues are buried in the NTD, while the Y145H is exposed on the surface of the NTD, in an epitope which is known to be targeted by neutralizing antibodies. 2022 EBioMedicine Result SARS_CoV_2 Y145H 57 62 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. The combination of T95I, Y145H and A222V substitutions did not modify the fusogenic activity of the Delta spike (Figure 2a). 2022 EBioMedicine Result SARS_CoV_2 A222V;T95I;Y145H 35;19;25 40;23;30 S 106 111 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. To characterize the function of the AY.4.2 spike, we introduced the T95I, Y145H and A222V signature mutations in an expression plasmid coding for the Delta spike protein. 2022 EBioMedicine Result SARS_CoV_2 A222V;T95I;Y145H 84;68;74 89;72;79 S;S 43;156 48;161 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. We previously reported using this assay that the spike protein of Alpha had the highest affinity to ACE2, followed by Delta and then by D614G. 2022 EBioMedicine Result SARS_CoV_2 D614G 136 141 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. We thus analyzed the fusogenic activity of the AY.4.2 spike and compared it to the D614G, Alpha and Delta spikes. 2022 EBioMedicine Result SARS_CoV_2 D614G 83 88 S;S 54;106 59;112 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Additionally, the mouse-adapted mutants N501Y, Q493K, and Q498H of the SARS-CoV-2 RBD also showed significantly increased binding affinity towards mouse ACE2. 2022 Emerging microbes & infections Result SARS_CoV_2 N501Y;Q493K;Q498H 40;47;58 45;52;63 RBD 82 85 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Additionally, the mutations L452R, T478K, and E484Q are far from the binding site with the mAb CB6; thus, they do not directly affect its neutralization interactions (Figure 4(B-D)). 2022 Emerging microbes & infections Result SARS_CoV_2 E484Q;L452R;T478K 46;28;35 51;33;40 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Additionally, we compared the E484Q and E484K mutations. 2022 Emerging microbes & infections Result SARS_CoV_2 E484K;E484Q 40;30 45;35 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Although the viral infectivity for other species did not change over 4-fold among B.1.617 sub-lineages, the L452R+T478K, L452R+E484Q, T95I, G142D, Q1071H, and H1101D mutations led to increased infectivity in most species (Figures 2(B) and S1). 2022 Emerging microbes & infections Result SARS_CoV_2 G142D;H1101D;L452R;L452R;Q1071H;T95I;E484Q;T478K 140;159;108;121;147;134;127;114 145;165;113;126;153;138;132;119 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Analysis of immunized sera suggested that antisera obtained by immunization with B.1.351 and B.1.429 immunogens showed no decreased neutralization activities against B.1.617 variants, compared with the D614G reference strain (Figure 6(B)). 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 202 207 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. As for patients infected with D614G variant, the B.1.617.1-H/L and B.1.617.3-H/L variants reduced the neutralization activities of convalescent sera by 1.6-2.5-fold, while B.1.617.2-H/L variants reduced the neutralization activities of convalescent sera by 1.2-2.0-fold. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 30 35 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. As shown in Figure 3(B), the S2 proportion was not significantly increased in B.1.617 variants, RBD single mutants, or P681R mutants, compared with the D614G reference strain. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G;P681R 152;119 157;124 RBD 96 99 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. B.1.617 variants contain a P681R mutation, which is located adjacent to this cleavage site; structural prediction has suggested that the S1-S2 clearance rate of B.1.617 might be affected. 2022 Emerging microbes & infections Result SARS_CoV_2 P681R 27 32 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. B.1.617.2-H/L, which exhibited L452R and T478K mutations in the RBD region, reduced the neutralization effects of the X593, 9G11, 7B8, AbG3, and AM180 mAbs. 2022 Emerging microbes & infections Result SARS_CoV_2 L452R;T478K 31;41 36;46 RBD 64 67 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Because all B.1.617 variants carry the P681R mutation, adjacent to the proteolytic site, we investigated the influence of protease overexpression (using multiple proteases) on viral infectivity. 2022 Emerging microbes & infections Result SARS_CoV_2 P681R 39 44 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. By using the dual split reporter system, we found a twofold greater tendency for fusion in B.1.617 variants, compared with the D614G reference strain. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 127 132 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Compared with D614G, the neutralization effects against B.1.617.1-H/L and B.1.617.3-H/L variants were reduced by 1.5-2.3-fold, while the neutralization effects against B.1.617.2-H/L variants were reduced by 1.3-1.4-fold (Figure 5(A)). 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 14 19 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Compared with the D614G reference strain, the B.1.617.1-H/L, B.1.617.2-H/L, and B.1.617.3-H/L variants reduced the neutralization activities of inactivated vaccine-immunized sera by 1.4-2.1, 1.4-2.3, and 1.6-2.4-fold, respectively; and reduced the neutralization activities of adenovirus vaccine-immunized sera by 1.2-1.7, 0.9-1.4, and 1.4-1.7-fold, respectively. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 18 23 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. D614G, B.1.351, and B.1.429) were also tested. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 0 5 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. E484K-mediated immune escape has been reported by many groups; this comprises a key mutation in many VOCs and VOIs (e.g. 2022 Emerging microbes & infections Result SARS_CoV_2 E484K 0 5 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Further analyses based on single mutations suggested that the P681R single mutation also enhanced cell-cell spread (Figure 3(D)). 2022 Emerging microbes & infections Result SARS_CoV_2 P681R 62 67 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Furthermore, E484Q induced neutralization resistance to an extent comparable with the resistance induced by E484K. 2022 Emerging microbes & infections Result SARS_CoV_2 E484K;E484Q 108;13 113;18 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Furthermore, T19R and G142D mutants were found to escape from several NTD-specific mAbs by McCallum et al. 2022 Emerging microbes & infections Result SARS_CoV_2 G142D;T19R 22;13 27;17 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. In conclusion, our findings indicate that the host range of B.1.617 variants may not considerably differ from the D614G reference strain, although the mouse transmission characteristics showed notable differences. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 114 119 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. In our study, we tested 16 mAbs; the effects of four were reduced by all B.1.617 sub-lineages, whereas the effects of two were abolished by either B.1.617.1 and B.1.617.3 or B.1.617.2 variants because of differences involving T478K and E484Q mutations. 2022 Emerging microbes & infections Result SARS_CoV_2 E484Q;T478K 236;226 241;231 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. In patients infected with the D614G reference strain or the B.1.1.7 variant, convalescent serum neutralization activities are decreased by approximately two-fold. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 30 35 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Investigation of single mutations indicated that the Q1071H and H1101D single mutations and the combinations of L452R with T478K or E484Q could slightly enhance infectivity (Figure 2(A)). 2022 Emerging microbes & infections Result SARS_CoV_2 E484Q;H1101D;L452R;Q1071H;T478K 132;64;112;53;123 137;70;117;59;128 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Mutation of E484Q creates a charge leads to disruption of the interaction, while mutation of L452R affects the hydrophobic interactions. 2022 Emerging microbes & infections Result SARS_CoV_2 E484Q;L452R 12;93 17;98 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Mutation of T478K destroys the hydrophobic environment, thus affecting the RBD-antibody interaction. 2022 Emerging microbes & infections Result SARS_CoV_2 T478K 12 17 RBD 75 78 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Notably, although E484Q and E484K both involve an identical mutation site, E484K allowed escape from the AM128 mAb, whereas E484Q did not. 2022 Emerging microbes & infections Result SARS_CoV_2 E484K;E484K;E484Q;E484Q 28;75;18;124 33;80;23;129 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Notably, only one antibody (A261-262) exhibited distinct reactions to L452R and E484Q, which indicated that the two mutations may be located in nearby epitopes. 2022 Emerging microbes & infections Result SARS_CoV_2 E484Q;L452R 80;70 85;75 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Notably, similar as K417N, N501Y, and E484K in the B.1.351 variant, RBD mutations in the B.1.617 variants also showed enhanced infectivity in mouse cells. 2022 Emerging microbes & infections Result SARS_CoV_2 E484K;K417N;N501Y 38;20;27 43;25;32 RBD 68 71 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Our mutation analysis results also suggested that the E484Q mutation had a greater effect on neutralization than the T478K mutation. 2022 Emerging microbes & infections Result SARS_CoV_2 E484Q;T478K 54;117 59;122 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Previous studies concern SARS-CoV-2 mutations and a structural analysis of B.1.617 major mutations (L452R, E484Q, and P681R) suggested increased ACE2 binding by these variants. 2022 Emerging microbes & infections Result SARS_CoV_2 E484Q;P681R;L452R 107;118;100 112;123;105 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. reported that P681R enhances viral fusion, and the P681R mutant virus exhibited higher pathogenicity compared with its parental strain in infected hamsters. 2022 Emerging microbes & infections Result SARS_CoV_2 P681R;P681R 14;51 19;56 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Single RBD mutations analysis suggested that L452R or E484Q mutations (including L452R combined with E484Q or T478K mutations) were related to the reduced neutralization effect. 2022 Emerging microbes & infections Result SARS_CoV_2 E484Q;E484Q;L452R;L452R;T478K 54;101;45;81;110 59;106;50;86;115 RBD 7 10 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Single-mutation analyses indicated that E484Q was the main source of neutralization resistance, whereas the L452R and T478K mutations showed weaker effects. 2022 Emerging microbes & infections Result SARS_CoV_2 E484Q;L452R;T478K 40;108;118 45;113;123 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. The D614G single point mutation based on the original strain was used as the reference sequence (Figure 1(B)). 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 4 9 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. The fluorescence signals were 1.2-2.3-fold higher in B.1.617 variant-infected cells than in D614G reference strain (Figure 3(D)). 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 92 97 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. The increased infectivities by furin overexpression in B.1.617 variants were slightly greater than that of the D614G reference strain (Figure 3(A)). 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 111 116 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. The L452R mutation has also been discovered in some VOIs, such as B.1.427 and B.1.429; it reportedly reduces or abolishes the neutralization activities of several mAbs, allowing escape from vaccine-immunized sera. 2022 Emerging microbes & infections Result SARS_CoV_2 L452R 4 9 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. The L452R mutation may produce a charge conflict with R64, resulting in reduced affinity. 2022 Emerging microbes & infections Result SARS_CoV_2 L452R 4 9 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. The mAb 7B8 was the only antibody from which T478K could escape in this study. 2022 Emerging microbes & infections Result SARS_CoV_2 T478K 45 50 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. The results revealed that the immune sera did not reduce neutralization activity against the B.1.617 variants, compared with the D614G reference strain, suggesting that key mutation sites (e.g. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G 129 134 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. The results suggested that the RBD-specific mutations L452R, T478K, and E484Q significantly enhanced viral infectivity of mouse ACE2-overexpressing cells, compared with the D614G reference strain. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G;E484Q;L452R;T478K 173;72;54;61 178;77;59;66 RBD 31 34 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Their neutralization activities were significantly reduced (by 3-4-fold) against all B.1.617 variants, as well as the L452R, T478K, and E484Q single or double mutants. 2022 Emerging microbes & infections Result SARS_CoV_2 E484Q;L452R;T478K 136;118;125 141;123;130 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. These effects were presumably caused by a L452R and E484Q double mutation in the RBD region. 2022 Emerging microbes & infections Result SARS_CoV_2 E484Q;L452R 52;42 57;47 RBD 81 84 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. These findings were verified by analyses of pseudotyped viruses with single and combined mutations of L452R and E484Q in the RBD region. 2022 Emerging microbes & infections Result SARS_CoV_2 E484Q;L452R 112;102 117;107 RBD 125 128 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. To examine whether the S proteins of B.1.617 variants and the P681R mutant influenced cell-cell fusion characteristics, a dual reporter system consisting of a pair of split Renilla luciferase (spRL) fused to split green fluorescent protein (spGFP) was used. 2022 Emerging microbes & infections Result SARS_CoV_2 P681R 62 67 S 23 24 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. To predict whether the vaccine based on B.1.429 or B.1.351 variants or previous infection of these variants would provide protections against B.1.617, mice were immunized using pseudoviruses of B.1.429(containing L452R), B.1.351 (containing E484K) and D614G. 2022 Emerging microbes & infections Result SARS_CoV_2 D614G;E484K;L452R 252;241;213 257;246;218 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. We did not observe considerable synergistic effects between L452R and E484Q or T478K and E484Q. 2022 Emerging microbes & infections Result SARS_CoV_2 E484Q;E484Q;L452R;T478K 70;89;60;79 75;94;65;84 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. While the 9G11, AbG3, and AM128 mAbs were affected more by the E484K mutation, the X593 and AM180 mAbs reacted similarly to viruses containing either mutation. 2022 Emerging microbes & infections Result SARS_CoV_2 E484K 63 68 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. According to the Delta mutation heat map (Figure 1D), R203M, D63G, and D377Y mutations were found in 98.6%, 96.9% and 97.8% of Delta variants, respectively, which rarely occurred in other VOC or VOI variants (<= 0.1%). 2022 Emerging microbes & infections Result SARS_CoV_2 D377Y;D63G;R203M 71;61;54 76;65;59 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. As reported in Figure 4B, the RT-LAMP assay at a Cq ratio cutoff of 1.80 achieved superior diagnostic performance (AUC = 1.00) (Figure 4C), indicating that the rapid and inexpensive RT-LAMP assay was competent at identifying the R203M mutation in clinical samples as confirmed by sequencing. 2022 Emerging microbes & infections Result SARS_CoV_2 R203M 229 234 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. As shown in from Figure 3A, the time gap between the R203M type and the wild type always maintained a sufficient difference in the RT-LAMP reaction with different concentrations of the template (from 103 copies/mL to 108 copies/mL). 2022 Emerging microbes & infections Result SARS_CoV_2 R203M 53 58 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Because the SNP allele sits in the loop domain of the RT-LAMP products, the G to T transition of R203M could lead to an amplified Cq change for the R203M mutation while barely affecting the Cq value of the conserved fragment of the N gene; R203M consequently alters the ratio of the Cq value for the mutant-harboring fragment to the Cq for the conserved sequence of the N gene. 2022 Emerging microbes & infections Result SARS_CoV_2 R203M;R203M;R203M 97;148;240 102;153;245 N;N 232;370 233;371 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Dilution experiments with RNA from wild-type and R203M mutant-type samples templates were performed to determine the 95% limit of detection (LOD 95) of the developed RT-LAMP assay. 2022 Emerging microbes & infections Result SARS_CoV_2 R203M 49 54 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Due to the difference in amplification efficiency between the two reactions, the R203M genotyping could be performed using the time gap, which could be visually reported in a fluorescent Cq-difference way. 2022 Emerging microbes & infections Result SARS_CoV_2 R203M 81 86 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. However, near the R203M mutation site, the other common mutations in VOC and VOI were primarily R203K/G204R and T205I, and their base changes in the gene sequence are shown in Figure 1E. 2022 Emerging microbes & infections Result SARS_CoV_2 R203K;R203M;T205I;G204R 96;18;112;102 101;23;117;107 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. In addition, when the extracted nucleic acid was as low as 15-60 copies/reaction, the two sets of primers retained detection rate of approximately 50% for the clinical sample and achieved a single reaction differentiation for the R203M mutant-containing template from the wild-type target. 2022 Emerging microbes & infections Result SARS_CoV_2 R203M 230 235 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. It is critical to select the LP to obtain the ideal discrimination, and the R203M discrimination ability of these primer sets was subsequently tested with RT-LAMP reactions using both wild-type and R203M mutant-type plasmids at the same template concentration of 108 copies/mL (Figure 2B, Supplemental Table 1 and Supplemental Figure 1). 2022 Emerging microbes & infections Result SARS_CoV_2 R203M;R203M 76;198 81;203 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. It is worth noting that among the 114 non-Delta-positive samples, 4 did not yield the effective Cq value of the R203M primer (the corresponding conserved primer Cq value in the red dotted circle in Figure 4A). 2022 Emerging microbes & infections Result SARS_CoV_2 R203M 112 117 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. One RT-LAMP primer set was ultimately selected as the optimal primer (R203M primer, for short, Table 1, Figure 1C, Figure 2B), which could provide a minimum Cq-gap of 10 min (the amplification conditions were set to 1 min per cycle). 2022 Emerging microbes & infections Result SARS_CoV_2 R203M 70 75 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. R203M primer design and screening. 2022 Emerging microbes & infections Result SARS_CoV_2 R203M 0 5 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Reaction mixtures containing template SARS-CoV-2 N gene DNA (wild-type, R203M mutant-type, R203K/G204R mutant-type and T205I mutant-type) yielded positive results, whereas all other reaction mixtures, including a DEPC water negative control, yielded negative results (Figure 2C), supporting the specificity of this assay for SARS-CoV-2 and Delta. 2022 Emerging microbes & infections Result SARS_CoV_2 R203K;R203M;T205I;G204R 91;72;119;97 96;77;124;102 N 49 50 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Six primer sets were initially designed, each consisting of two outer primers (F3/B3), two inner primers (FIP/BIP) and a single loop primer (LF or LB) that corresponds to the allelic type of R203M (Supplemental Table 1). 2022 Emerging microbes & infections Result SARS_CoV_2 R203M 191 196 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Taken together, R203M of the N gene was chosen as a well-positioned candidate to distinguish Delta from other SARS-CoV-2 variants in the subsequent RT-LAMP experiment. 2022 Emerging microbes & infections Result SARS_CoV_2 R203M 16 21 N 29 30 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The actual detection was also beneficial for the resolution of this mutation and the identification of Delta by the R203M LAMP primer. 2022 Emerging microbes & infections Result SARS_CoV_2 R203M 116 121 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The BLAST results indicated that RT-LAMP primers for SARS-CoV-2 (Conserved and R203M primers) were specific and had a substantial nucleotide mismatch with SARS, MERS, and other viruses (Figure 2A). 2022 Emerging microbes & infections Result SARS_CoV_2 R203M 79 84 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The Cq ratios of the wild-type and R203M mutation types were significantly different, which demonstrated the feasibility of this method in identifying the R203M mutation. 2022 Emerging microbes & infections Result SARS_CoV_2 R203M;R203M 35;155 40;160 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The difference between the R203K/G204R, T205I, and Delta variants are more noticeable when compared to the wild-type N gene. 2022 Emerging microbes & infections Result SARS_CoV_2 R203K;T205I;G204R 27;40;33 32;45;38 N 117 118 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The position of the SNP should also be considered for primer design; R203M (G T, 28881nt) was located in the middle of the N gene sequence, which was conducive to primer design and screening for RT-LAMP of SNP detection, whereas the terminally located D63G and D377Y (28461nt and 29402nt) inherently restricted the primer design and selection for this developed method. 2022 Emerging microbes & infections Result SARS_CoV_2 D377Y;D63G;R203M 261;252;69 266;256;74 N 123 124 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The RNA of non-Delta variants contains different types sequenced as 20A, 20I (Alpha, V1) and 20H (Beta, V2), including common gene sequence types near the R203M mutation (Supplemental Table 3). 2022 Emerging microbes & infections Result SARS_CoV_2 R203M 155 160 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The same concentration of R203K/G204R and the T205I mutant N gene plasmids yielded higher Cq values than the wild-type under the amplification of the R203M primer set, indicating that the R203M primer set distinguishes Delta from other common variants. 2022 Emerging microbes & infections Result SARS_CoV_2 R203K;R203M;R203M;T205I;G204R 26;150;188;46;32 31;155;193;51;37 N 59 60 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. This observation indicates that when the concentration of the unknown positive sample is close to the detection limit, the Delta sample can be judged by the ratio normally, while the non-Delta sample may not be able to amplify the R203M primer due to the sequence difference, but it also shows that the gene sequence does not match the R203M mutation. 2022 Emerging microbes & infections Result SARS_CoV_2 R203M;R203M 231;336 236;341 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. We designed R203M allele loop primers and their respective inner and outer primers based on the LAMP principle (Figure 1A). 2022 Emerging microbes & infections Result SARS_CoV_2 R203M 12 17 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. We developed the Cq ratio-based RT-LAMP method using R203M mutant-type and wild-type plasmids in triplicate experiments with different concentrations. 2022 Emerging microbes & infections Result SARS_CoV_2 R203M 53 58 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. When the Cq ratio was less than 1.80, the nucleic acid template for RT-LAMP detection was judged to contain the R203M mutation; correspondingly, when the Cq ratio was greater than 1.80, the nucleic acid template should not contain the mutation. 2022 Emerging microbes & infections Result SARS_CoV_2 R203M 112 117 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Although E156G/Delta157-158 and L452R alone had an indiscernible effect on syncytium formation compared to the reference D614G, the area after cell-to-cell fusion was increased ~2-fold (P-values of <0.0001 from one-way ANOVA) when the cells expressing D614G spike bearing L452R and the E156G/Delta157-158 mutations were cocultured with ACE2-positive cells (Fig 5A and B). 2022 Life science alliance Result SARS_CoV_2 D614G;D614G;E156G;E156G;L452R;L452R 121;252;9;286;32;272 126;257;14;291;37;277 S 258 263 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Altogether, these results suggest the contribution of the NTD-specific mutations, in addition to the RBD-specific L452R, in conferring resistance to neutralization and promotion of infectivity. 2022 Life science alliance Result SARS_CoV_2 L452R 114 119 RBD 101 104 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Altogether, we observed that these mutations in NTD, particularly E156G/Delta157-158, cooperated with the seeding changes in the RBD, like L452R, for neutralizing antibody escape. 2022 Life science alliance Result SARS_CoV_2 E156G;L452R 66;139 71;144 RBD 129 132 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. E156G/Delta157-158 and L452R additively effects immune escape and increased infectivity. 2022 Life science alliance Result SARS_CoV_2 L452R;E156G 23;0 28;5 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. E156G/Delta157-158 contributed to attenuated neutralization susceptibility and increased infectivity. 2022 Life science alliance Result SARS_CoV_2 E156G 0 5 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Furthermore, to understand the effect of these mutations on spike protein structure, we predicted the structure of NTD-bearing E156G/Delta157-158 using the AlphaFold. 2022 Life science alliance Result SARS_CoV_2 E156G 127 132 S 60 65 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Furthermore, when we combined RBD-specific L452R and E484Q with NTD-specific E156G/Delta157-158, the magnitude of the cell-cell fusion was similar to that of the ICS-05/-03 spike. 2022 Life science alliance Result SARS_CoV_2 E156G;E484Q;L452R 77;53;43 82;58;48 S;RBD 173;30 178;33 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Given the higher prevalence (Fig 1D and F), we hypothesized the virological significance of these non-RBD mutations E156G/Delta157-158. 2022 Life science alliance Result SARS_CoV_2 E156G 116 121 RBD 102 105 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. In agreement with previous findings, whereas the RBD-specific mutation E484Q did not significantly confer infectivity advantage to the spike particles, the L452R mutation increased the infectivity more than twofold in these conditions (Fig 2B). 2022 Life science alliance Result SARS_CoV_2 E484Q;L452R 71;156 76;161 S;RBD 135;49 140;52 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. In comparison, the remaining NTD-specific mutations examined (T19R, T95I, and T19R/T95I) did not significantly confer infectivity advantage (Fig 2B). 2022 Life science alliance Result SARS_CoV_2 T19R;T95I;T19R;T95I 78;68;62;83 82;72;66;87 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Interestingly, mapping of E156G/Delta157-158 on the structure of wild-type spike protein implies that the mutated region is surface exposed, which might be a good target for antibodies (Fig 1G). 2022 Life science alliance Result SARS_CoV_2 E156G 26 31 S 75 80 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Interestingly, the spike E156G/Delta157-158 mutation (present in the NTD) conferred infectivity advantage almost equal to that of L452R (present in the RBD) (P-value of <0.0001 from one-way ANOVA). 2022 Life science alliance Result SARS_CoV_2 E156G;L452R 25;130 30;135 S;RBD 19;152 24;155 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Interestingly, we observed a six-nucleotide deletion that resulted in the loss of two amino acids at 157 and 158 positions and a change of glutamic acid at 156 positions to glycine (E156G/Delta157-158) (Fig S1). 2022 Life science alliance Result SARS_CoV_2 E156G 182 187 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Notably, the delta variant (B.1.617.2) that dominated the second wave in the country and caused 25.3% of breakthrough infections ( Preprint) shares all spike mutations with B.1.617.3 except T478K (Fig 1B and C). 2022 Life science alliance Result SARS_CoV_2 T478K 190 195 S 152 157 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Notably, the reduced susceptibility to neutralization observed for the ICS-05/-03 spike (11-fold) was mostly explained by a combination spike mutant that harbored E156G/Delta157-158 and L452R (sevenfold less susceptible to neutralization) (Fig 3E; P-values of <0.01 from Wilcoxon signed-rank test). 2022 Life science alliance Result SARS_CoV_2 E156G;L452R 163;186 168;191 S;S 82;136 87;141 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Our analysis revealed that E156G/Delta157-158 together with L452R conferred most of the resistance to antiviral immunity elicited by vaccination. 2022 Life science alliance Result SARS_CoV_2 E156G;L452R 27;60 32;65 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Our observations with the E156G/Delta157-158 mutation in reducing the PV sensitivity to neutralization are coherent. 2022 Life science alliance Result SARS_CoV_2 E156G 26 31 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Regardless of the background (E484Q or the L452R), the NTD-specific mutation E156G/Delta157-158 increased the infectivity ~4-fold for the spike-pseudotyped lentiviral particles in HEK293T ACE2 cells (Fig 3B; P-value <0.0001 from one-way ANOVA). 2022 Life science alliance Result SARS_CoV_2 E156G;L452R;E484Q 77;43;30 82;48;35 S 138 143 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. The E156G/ 157-158 mutation, first detected on 7 August 2020, subsequently became 35% prevalent worldwide (Fig 1D), and by October 2021, it was found in more than 90% of reported sequences from the USA and UK, with a downward trend from India (Fig 1F). 2022 Life science alliance Result SARS_CoV_2 E156G 4 9 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. The other indicated mutations, however, did not confer noticeable resistance in these conditions except the L452R mutant-bearing PV that required a 2.36-fold higher plasma for neutralization (P-values < 0.01 from Wilcoxon signed-rank test), which is consistent with the previous findings (Fig 2D). 2022 Life science alliance Result SARS_CoV_2 L452R 108 113 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. The presence of the mutations in regions ranging from 144 to 158, comprising the deletion mutation E156G/Delta157-158, therefore could impair the binding by such neutralizing antibodies while maintaining the ACE affinity and help the virus escape from immune surveillance. 2022 Life science alliance Result SARS_CoV_2 E156G 99 104 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Therefore, we combined the NTD-specific change E156G/Delta157-158 with E484Q and L452R (Fig 3A) and performed the infectivity and neutralization assays. 2022 Life science alliance Result SARS_CoV_2 E156G;E484Q;L452R 47;71;81 52;76;86 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. To appraise the exact potential of the NTD bearing E156G/Delta157-158 and the changes found in the region important for receptor binding, we introduced indicated mutations on the parental D614G (B.1) spike gene by site-directed mutagenesis (Fig 2A). 2022 Life science alliance Result SARS_CoV_2 D614G;E156G 188;51 193;56 S 200 205 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. To evaluate if the presence of TMPRSS2 in the target cells would impact the phenotype, we infected ACE2- and TMPRSS2-expressing A549 target cells with the indicated viruses and found a similar trend when spike harbored E156G/Delta157-158 and L452R mutations (Fig S4B). 2022 Life science alliance Result SARS_CoV_2 E156G;L452R 219;242 224;247 S 204 209 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. We first examined the spike protein in the structural context of E156G/Delta157-158 for clues regarding the alteration of epitopes. 2022 Life science alliance Result SARS_CoV_2 E156G 65 70 S 22 27 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Whereas E156G/Delta157-158 mutation alone did not show a significant difference in ACE2 binding affinity, spike PV bearing E156G/Delta157-158/L452 exhibited increased affinity almost equivalent to that of ICS-05 towards hACE2 (Fig 3D). 2022 Life science alliance Result SARS_CoV_2 E156G;E156G 8;123 13;128 S 106 111 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Whereas the ability of spike E484Q and L452R to evade BNT162b2 Pfizer mRNA vaccine-elicited antibodies has been established recently, we investigated if the indicated mutations acted in synergy in the antibody evasion process. 2022 Life science alliance Result SARS_CoV_2 E484Q;L452R 29;39 34;44 S 23 28 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. While the E156G/ 157-158 mutation was underrepresented in parental B.1 lineage, it was detected with high frequency in at least 157 countries in B.1.617.2 and B.1.617.3 lineage and was found in multiple PANGO lineages, including the AY lineage (; https://outbreak.info/) (Fig 1E). 2022 Life science alliance Result SARS_CoV_2 E156G 10 15 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. With the D614G as a reference, the NT50 values (see the Materials and Methods section for details for NT50) obtained showed that spike PV carrying the E156G/Delta157-158 mutation was 4.85-fold less susceptible (P-value <0.01 from Wilcoxon signed-rank test) to vaccine-elicited polyclonal antibodies (Fig 2D), indicating the role of this mutation in escaping the vaccine-elicited antiviral immunity in addition to promoting virion infectivity. 2022 Life science alliance Result SARS_CoV_2 D614G;E156G 9;151 14;156 S 129 134 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. A mutation at D484Y has been reported in a post- treatment sample from an immunocompromised patient who failed RDV therapy, but the RDV resistance phenotype associated with this mutation, whose location is distal to the active site, has not been confirmed. 2022 Nature communications Result SARS_CoV_2 D484Y 14 19 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Although RDV therapy has been widely administered to patients during the pandemic, E802D and all substitutions at residue 802 have been found in 131 and 297, respectively, of the 4.8 M genome sequences obtained from patient isolates in the GISAID database (www.gisaid.org; accessed 11/07/21). 2022 Nature communications Result SARS_CoV_2 E802D 83 88 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Analysis of assembled viral genomes identified a mutation, E802D, in nsp12, whose detection in patient specimens was temporally associated with RDV therapy. 2022 Nature communications Result SARS_CoV_2 E802D 59 64 Nsp12 69 74 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Consistent with the observation of a fitness cost, the allele frequency of E802D in nasopharyngeal specimens from the patient decreased from 22.6% to <1% between the period (day 160-162) after completion of RDV therapy and prior to casirivimab-imdevimab administration. 2022 Nature communications Result SARS_CoV_2 E802D 75 80 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Continued surveillance will thus be needed to elaborate whether the occurrence of E802D, as well as other substitutions at this residue, will be limited because of an underlying fitness cost or alternatively, emerge to pose a broader risk for RDV resistance. 2022 Nature communications Result SARS_CoV_2 E802D 82 87 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. E802D has been identified in an in vitro RDV resistance selection experiment and was found to confer a ~2.5-fold increase in IC50 to the drug. 2022 Nature communications Result SARS_CoV_2 E802D 0 5 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. E802D was not identified at an allele frequency above 1% in either the specimen obtained during the initial phase of illness (day 36) or in specimens collected during the first 5 days (days 148-152) of RDV therapy. 2022 Nature communications Result SARS_CoV_2 E802D 0 5 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Emergence of the nsp12 E802D mutation during remdesivir therapy. 2022 Nature communications Result SARS_CoV_2 E802D 23 28 Nsp12 17 22 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Furthermore, analysis of the 131 genomic sequences that have been found in GISAID to contain the E802D mutation identified two instances where sequences were geographically and temporally clustered, suggesting that local transmission of E802D variants may have occurred. 2022 Nature communications Result SARS_CoV_2 E802D;E802D 97;237 102;242 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. However, A504V in nsp14 was present (allele frequency 85.1%) in a specimen obtained during her initial phase of illness (day 36). 2022 Nature communications Result SARS_CoV_2 A504V 9 14 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. I115L in nsp15 was not detected in the early-phase specimen; we therefore cannot exclude the possibility that this mutation in the endoRNAse gene may contribute to RDV resistance. 2022 Nature communications Result SARS_CoV_2 I115L 0 5 EndoRNAse 131 140 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. In addition, further investigation is needed to evaluate whether epistatic interactions influence the expression of a remdesivir resistance phenotype beyond the isolated contribution of substitutions at E802D in nsp12. 2022 Nature communications Result SARS_CoV_2 E802D 203 208 Nsp12 212 217 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. In the presence of high concentrations of RDV (5 microM), the E802D mutant replicated to higher titers than the parental virus. 2022 Nature communications Result SARS_CoV_2 E802D 62 67 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. In vitro validation of nsp12 E802D as a remdesivir resistance mutation. 2022 Nature communications Result SARS_CoV_2 E802D 29 34 Nsp12 23 28 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. RDV dose-response curves demonstrated that E802D and E802A mutants had significant increases in IC50 values (4.2 muM and 2.7 muM, respectively), relative to parental icSARS-CoV-2-mNG (0.7 muM). 2022 Nature communications Result SARS_CoV_2 E802A;E802D 53;43 58;48 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Replication kinetics of the E802D and E802A mutants in Vero-E6 cells revealed decreased viral replication relative to parental icSARS-CoV-2-mNG. 2022 Nature communications Result SARS_CoV_2 E802A;E802D 38;28 43;33 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. To validate the resistance phenotype of E802D, we engineered this mutation and an E802A mutation, which had been also shown to confer RDV resistance, into an infectious molecular clone of SARS-CoV-2/WA01 (icSARS-CoV-2-mNG), which expresses the mNeon Green reporter and is ORF7a depleted. 2022 Nature communications Result SARS_CoV_2 E802A;E802D 82;40 87;45 ORF7a 272 277 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Together, the temporality of E802D emergence in the patient, its location in nsp12 and the in vitro identification of the same mutation with a RDV resistance phenotype support the plausibility that that RDV treatment of the patient selected for variants with the E802D mutation, which in turn contributed to the observed rebound viral shedding. 2022 Nature communications Result SARS_CoV_2 E802D;E802D 29;263 34;268 Nsp12 77 82 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. We identified two additional mutations, A504V in nsp14 (exonuclease) and I115L in nsp15 (endoRNAse), whose allele frequencies increased during and after RDV treatment. 2022 Nature communications Result SARS_CoV_2 A504V;I115L 40;73 45;78 Exonuclease;EndoRNAse 56;89 67;98 35301412 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. Comparison of this novel variant with genome signature of B.1.1.291 indicates that this novel variant contains two unique mutations (ORF8 Q27stop, NSP15 V127F) that other B.1.1.291 variants do not have, while lack of some other mutations (ORF1ab F106F, ORF1ab Y831Y, ORF1ab N73N, noncoding C29784T, and noncoding C241T) in Pango Lineage B.1.1.291 (Table 1). 2022 Scientific reports Result SARS_CoV_2 C241T;C29784T;F106F;N73N;Q27X;V127F;Y831Y 313;290;246;274;138;153;260 318;297;251;278;145;158;265 ORF1ab;ORF1ab;ORF1ab;ORF8 239;253;267;133 245;259;273;137 35301412 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. Interestingly, the only nonsynonymous mutation in this novel variant different from other Pango Lineage B.1.1.291 is the ORF8 Q27stop mutation, while all other differences are either synonymous mutations, or nonsynonymous mutations in non-coding region (Table 1). 2022 Scientific reports Result SARS_CoV_2 Q27X 126 133 ORF8 121 125 35301412 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. Note there is a new point mutation (NSP15 V127F) in EPI_ISL_525725, which does not exist in hCoV-19/USA/AK-PHL676/2020 (EPI_ISL_586254). 2022 Scientific reports Result SARS_CoV_2 V127F 42 47 35304093 Tracking SARS-CoV-2 variants by entire S-gene analysis using long-range RT-PCR and Sanger sequencing. All of the sequenced samples had S:D614G mutation. 2022 Clinica chimica acta; international journal of clinical chemistry Result SARS_CoV_2 D614G 35 40 S 33 34 35304093 Tracking SARS-CoV-2 variants by entire S-gene analysis using long-range RT-PCR and Sanger sequencing. Almost all Delta variants analyzed in this study were estimated AY.29 sub-lineage because of detection of the S:T95I and S:G142D mutations. 2022 Clinica chimica acta; international journal of clinical chemistry Result SARS_CoV_2 G142D;T95I 123;112 128;116 S;S 110;121 111;122 35304093 Tracking SARS-CoV-2 variants by entire S-gene analysis using long-range RT-PCR and Sanger sequencing. Almost all Omicron variants analyzed in this study were estimated BA.1.1 sub-lineage because of detection of the S:R346K mutations. 2022 Clinica chimica acta; international journal of clinical chemistry Result SARS_CoV_2 R346K 115 120 S 113 114 35304093 Tracking SARS-CoV-2 variants by entire S-gene analysis using long-range RT-PCR and Sanger sequencing. Samples that could not determine the lineage of SARS-CoV-2 because of the lack of specific mutation patterns except for S:D614G were classified as "Undetermined." To assess the dynamic of circulating SARS-CoV-2, we compared our data with the reported lineages in Chiba University Hospital. 2022 Clinica chimica acta; international journal of clinical chemistry Result SARS_CoV_2 D614G 122 127 S 120 121 35304531 In vitro evaluation of therapeutic antibodies against a SARS-CoV-2 Omicron B.1.1.529 isolate. The ancestral D614G BavPat1 European strain (B.1 lineage) was used as a reference to calculate the fold change between the EC50s determined for each virus. 2022 Scientific reports Result SARS_CoV_2 D614G 14 19 35305699 Neutralisation sensitivity of the SARS-CoV-2 omicron (B.1.1.529) variant: a cross-sectional study. However, the parent antibody of sotrovimab, S309, maintained its activity, with only a two-fold reduction in potency against the omicron variant compared with ancestral B.1 (D614G) virus (table 2), which is likely to be attributable to the location of the epitope that sotrovimab binds to being outside of the highly mutated receptor binding motif. 2022 The Lancet. Infectious diseases Result SARS_CoV_2 D614G 174 179 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. According to the A20268G mutation, the nucleotide change produces a stop codon lost for a tryptophan amino acid. 2022 Frontiers in microbiology Result SARS_CoV_2 A20268G 17 24 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. Also, two changes were identified in the receptor-binding domain (RBD): E484Q and S494. 2022 Frontiers in microbiology Result SARS_CoV_2 E484Q 72 77 RBD 66 69 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. Analysis of minority variants population revealed the presence of mutations T95I and S494L as viral subpopulations with a frequency <25%. 2022 Frontiers in microbiology Result SARS_CoV_2 S494L;T95I 85;76 90;80 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. Mutation D614G was found in the first virus analyzed in accordance with the lineage B.1. 2022 Frontiers in microbiology Result SARS_CoV_2 D614G 9 14 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. Mutation I770V reached almost 75% of the viral population in the sample taken from day 128 and 100% in the virus from sample collected on day 237. 2022 Frontiers in microbiology Result SARS_CoV_2 I770V 9 14 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. Remarkable, mutation E484Q was documented from day 132 onward. 2022 Frontiers in microbiology Result SARS_CoV_2 E484Q 21 26 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. Since the initial samples, 6 different amino acids appeared: A1105V, T540I, K977Q, S370L, E746A, and T820I. 2022 Frontiers in microbiology Result SARS_CoV_2 A1105V;E746A;K977Q;S370L;T540I;T820I 61;90;76;83;69;101 67;95;81;88;74;106 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. Specifically, two events related to the emergence and re-emergence of three changes (T95I, S494L, and Delta143/144 or Delta143/145) were identified in virus from samples from days 128 and 237. 2022 Frontiers in microbiology Result SARS_CoV_2 S494L;T95I 91;85 96;89 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. Supplementary Figure S5 showed the 7 amino acid changes in the Spike of virus detected in the last sample: S12F, T95I, L141F, E484Q, S494L, D614G, and I770V. 2022 Frontiers in microbiology Result SARS_CoV_2 D614G;E484Q;I770V;L141F;S12F;S494L;T95I 140;126;151;119;107;133;113 145;131;156;124;111;138;117 S 63 68 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. The patient presented 6 nucleotide mutations and 2 amino acid changes from the reference sequence Wuhan-1 (GenBank accession number: NC_045512): C96T, C241T, G12769T, C14408T, A20268G, A23403G, being present in the 12 consensus sequences analyzed from the patient. 2022 Frontiers in microbiology Result SARS_CoV_2 A20268G;A23403G;C14408T;C241T;C96T;G12769T 176;185;167;151;145;158 183;192;174;156;149;165 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. The Spike structure showed a signal peptide mutation, S12F, and two changes in the N-terminal domain (NTD), T95I and L141F. 2022 Frontiers in microbiology Result SARS_CoV_2 L141F;S12F;T95I 117;54;108 122;58;112 S;N 4;83 9;84 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? Mutation D138Y has been associated with a decrease in neutralizing monoclonal antibodies. 2022 Frontiers in microbiology Result SARS_CoV_2 D138Y 9 14 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? Notably, the low-frequency mutation H655Y was reported to naturally evolve in SARS-CoV-2 in positive selection and has been reported in multiple cohorts. 2022 Frontiers in microbiology Result SARS_CoV_2 H655Y 36 41 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? One study reported that mutation P1263L was associated with decreased transmission of the virus A study also reported a stabilizing effect of the mutation T362I using in silico studies. 2022 Frontiers in microbiology Result SARS_CoV_2 P1263L;T362I 33;155 39;160 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? Similarly, mutation of aspartic acid into histidine at position 144 in the nucleocapsid protein resulted in the formation of coil at the mutant location instead of the turn observed in the wild type (Figure 3B). 2022 Frontiers in microbiology Result SARS_CoV_2 D144H 23 67 N 75 87 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? The conversion of aspartic acid into tyrosine at position 138 in the spike protein showed the conversion of turn in the wild type to sheet in the mutant protein (Figure 3A). 2022 Frontiers in microbiology Result SARS_CoV_2 D138Y 18 61 S 69 74 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? We observed that the D144H and N7D mutations in the nucleocapsid region and the D138Y and H655Y mutations in the spike protein showed changes in extinction coefficient and net charge at pH 7 (Zce) (Supplementary Table 3). 2022 Frontiers in microbiology Result SARS_CoV_2 D138Y;D144H;H655Y;N7D 80;21;90;31 85;26;95;34 N;S 52;113 64;118 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? We observed that two low-frequency mutations, D138Y in the spike protein and D144H in the nucleocapsid protein, showed secondary structural changes. 2022 Frontiers in microbiology Result SARS_CoV_2 D138Y;D144H 46;77 51;82 N;S 90;59 102;64 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. 2'-OMe modifications of gRNA increased the specificity for the SARS-CoV-2 D614G mutant detection. 2022 Chemical science Result SARS_CoV_2 D614G 74 79 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. Accordingly, we designed one unmodified gRNA complementary to the SARS-CoV-2 D614G mutant (ugRNA-D614G). 2022 Chemical science Result SARS_CoV_2 D614G;D614G 77;97 82;102 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. all unmodified and modified gRNAs-D614G possessed high specificity even in the complex sample, demonstrating the stability of the Cas12a based D614G mutant biosensing platform. 2022 Chemical science Result SARS_CoV_2 D614G;D614G 143;34 148;39 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. For target DNA at 1 nM and 0.1 nM, the final DF values of mgRNA-D614G-3' (1.43 +- 0.08 and 1.8 +- 0.1 for 1 nM and 0.1 nM, respectively) were about two-fold higher than those of ugRNA-D614G (0.94 +- 0.04 and 1.04 +- 0.08, respectively), illustrating that 2'-OMe modifications improved the Cas12a's specificity for D614G mutant detection even at low target concentrations. 2022 Chemical science Result SARS_CoV_2 D614G;D614G;D614G 314;64;184 319;69;189 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. Furthermore, to explore the performance of the Cas12a system in a complex sample, we mixed the SARS-CoV-2 D614G mutant DNA (200 pM per reaction) with HBV B-type DNA (600 pM per reaction) and analysed the fluorescence intensity readout. 2022 Chemical science Result SARS_CoV_2 D614G 106 111 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. Moreover, to investigate the sensitivity of the Cas12a based D614G mutant detection system, we used D614G mutant DNA (concentrations varying from 0 to 10 nM) as input DNA. 2022 Chemical science Result SARS_CoV_2 D614G;D614G 61;100 66;105 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. the LOD of mgRNA-D614G-3' (10 pM) was lower than that of ugRNA-D614G, mgRNA-D614G-5' and mgRNA-D614G-m (50 pM), indicating that 2'-OMe modifications at the 3'-end of gRNA enhanced the Cas12a's sensitivity for D614G mutant detection. 2022 Chemical science Result SARS_CoV_2 D614G;D614G;D614G;D614G;D614G 209;17;63;76;95 214;22;68;81;100 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide pandemic and the mutant strain with one amino acid change at position 614 (D614G) has been reported to be dominant. 2022 Chemical science Result SARS_CoV_2 D614G 163 168 COVID-19 11 51 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. Then, to validate the versatility of the 2'-OMe modifications to improve the Cas12a's specificity for different applications, we developed a SARS-CoV-2 D614G mutant detection platform. 2022 Chemical science Result SARS_CoV_2 D614G 152 157 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. Three modified gRNAs (mgRNAs) with 2'-OMe modifications at various positions were also designed (5'-end modifications for mgRNA-D614G-5', the middle region for mgRNA-D614G-m and 5'-end for mgRNA-D614G-3', respectively). 2022 Chemical science Result SARS_CoV_2 D614G;D614G;D614G 128;166;195 133;171;200 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. we selected the 20 nt sequence containing the D614G mutant from the S1 subunit of the SARS-CoV-2 genome as the target site. 2022 Chemical science Result SARS_CoV_2 D614G 46 51 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. Applying a genetic divergence threshold and manual verification using available epidemiological data, a total of 128 phylogenetic clusters were determined across all samples, of which 70 belonged to lineage B.1-C15324T. 2022 Virus evolution Result SARS_CoV_2 C15324T 211 218 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. Figure 3D also shows the dynamic change in social interaction contribution to B.1-C15324T case numbers. 2022 Virus evolution Result SARS_CoV_2 C15324T 82 89 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. S7), with 247 genomes (60.0 per cent) belonging to the B.1-C15324T variant. 2022 Virus evolution Result SARS_CoV_2 C15324T 59 66 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. Unreported cases appeared to be a driving force of the transmission (88 per cent for the sequenced B.1-C15324T variant). 2022 Virus evolution Result SARS_CoV_2 C15324T 103 110 35311662 Reduced DMPC and PMPC in lung surfactant promote SARS-CoV-2 infection in obesity. D614G, the common mutation of the SARS-CoV-2 Spike protein in alpha, beta, gamma, and delta SARS-CoV-2 variants, has been reported to enhance virus replication and transmission. 2022 Metabolism Result SARS_CoV_2 D614G 0 5 S 45 50 35311662 Reduced DMPC and PMPC in lung surfactant promote SARS-CoV-2 infection in obesity. DMPC and PMPC also potently inhibited infection of SARS-CoV-2 pseudovirus harboring Spike D614G mutation in HEK293T-ACE2 and Vero E6 cells. 2022 Metabolism Result SARS_CoV_2 D614G 90 95 S 84 89 35311662 Reduced DMPC and PMPC in lung surfactant promote SARS-CoV-2 infection in obesity. Importantly, trimyristin treatment also inhibited D614G mutant SARS-CoV-2 infection. 2022 Metabolism Result SARS_CoV_2 D614G 50 55 COVID-19 63 83 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. Among the 15 mutation sites in the S protein of the Omicron variant, S375F was a common mutation site showing the interaction to be weakened with four monoclonal antibodies, and not with sotrovimab, among the antibodies that had significantly differing PIE from that of the wild type (Table 5). 2022 Journal of chemical information and modeling Result SARS_CoV_2 S375F 69 74 S 35 36 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. Among the seven mutation residues in the Omicron variant, six mutation residues in the Omicron variant except for S375F had a stronger electrostatic energy than those in the wild type. 2022 Journal of chemical information and modeling Result SARS_CoV_2 S375F 114 119 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. Another study shows the binding affinity between hACE2 and the RBD of the Omicron variant containing Q493K to be stronger than that of the wild type. 2022 Journal of chemical information and modeling Result SARS_CoV_2 Q493K 101 106 RBD 63 66 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. As all RBD structures of the Omicron variant containing the Q493R mutation obtained by superimposition were seen to overlap with hACE2, we used the RBD structures of the wild type and the Omicron variant containing the Q493K mutation for molecular dynamics but excluded those of the Omicron variant containing the Q493R mutation. 2022 Journal of chemical information and modeling Result SARS_CoV_2 Q493K;Q493R;Q493R 219;60;314 224;65;319 RBD;RBD 7;148 10;151 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. Comparing the results of protein-protein docking simulations and molecular dynamics for binding affinity prediction showed S371L or G496S to be residues with significant differences in PIE. 2022 Journal of chemical information and modeling Result SARS_CoV_2 G496S;S371L 132;123 137;128 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. Excluding three out of the total eight monoclonal antibodies analyzed, the binding affinity did not show a significant difference for four among five monoclonal antibodies and was lower for the Omicron variant containing the Q493R mutation than for the Delta variant. 2022 Journal of chemical information and modeling Result SARS_CoV_2 Q493R 225 230 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. For median PIEs between the residues of the RBD and hACE2, S375F showed a stronger interaction with hACE2 in the Omicron variant than that in the wild type. 2022 Journal of chemical information and modeling Result SARS_CoV_2 S375F 59 64 RBD 44 47 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. In N501Y, the difference of dispersion energy between the crystal structure of the wild type and the Omicron variant was calculated to be 4.3 kcal/mol, which is the biggest among the other residues due to the T-shaped pi-pi stacking interaction between Tyr41 in hACE2 and Tyr501 in the S protein of the Omicron variant (Figure S2). 2022 Journal of chemical information and modeling Result SARS_CoV_2 N501Y 3 8 S 286 287 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. In the crystal structure, S375F, N440K, S477N, T478K, E484A, Q493R, G496S, Q498R, and N501Y interacted more strongly with the omicron variant than with the wild type (Table 2). 2022 Journal of chemical information and modeling Result SARS_CoV_2 E484A;G496S;N440K;N501Y;Q493R;Q498R;S375F;S477N;T478K 54;68;33;86;61;75;26;40;47 59;73;38;91;66;80;31;45;52 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. Only S375F in the Omicron variant had a stronger solvation energy than that in the wild type. 2022 Journal of chemical information and modeling Result SARS_CoV_2 S375F 5 10 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. Our results showed 96 binding poses in the wild type, 98 in the Delta variant, 90 in the Omicron variant containing the Q493K mutation, and 85 in the Omicron variant containing the Q493R mutation. 2022 Journal of chemical information and modeling Result SARS_CoV_2 Q493K;Q493R 120;181 125;186 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. PIE values for S375F, N440K, T478K, E484A, Q493K/R, and Q498R in the RBD of the two Omicron variants indicated that they had a stronger interaction than the corresponding residues in the wild type (Table 1). 2022 Journal of chemical information and modeling Result SARS_CoV_2 E484A;N440K;Q493K;Q493R;Q498R;S375F;T478K 36;22;43;43;56;15;29 41;27;50;50;61;20;34 RBD 69 72 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The G339D, S373P, K417N, G446S, S477N, G496S, and N501Y fragments of the two Omicron variants were found to have weaker interactions than the corresponding residues of the wild type (Table 1). 2022 Journal of chemical information and modeling Result SARS_CoV_2 G339D;G446S;G496S;K417N;N501Y;S373P;S477N 4;25;39;18;50;11;32 9;30;44;23;55;16;37 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The highest RMSDs of the three types of RBDs were 7.852 A for the wild type, 7.488 A for the Delta variant, and 3.253 A for the Omicron variant containing the Q493R mutation. 2022 Journal of chemical information and modeling Result SARS_CoV_2 Q493R 159 164 RBD 40 44 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The lowest RMSDs of the three types of RBDs were 2.292 A for the wild type, 1.701 A for the Delta variant, and 2.505 A for the Omicron variant containing the Q493R mutation. 2022 Journal of chemical information and modeling Result SARS_CoV_2 Q493R 158 163 RBD 39 43 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The lowest values of RMSD among those obtained with the crystal structures were 2.996 A for the wild type, 2.932 A for the Delta variant, and 2.963 A for the Omicron variant containing the Q493R mutation. 2022 Journal of chemical information and modeling Result SARS_CoV_2 Q493R 189 194 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The median PIE was -759.9 kcal/mol for the wild type, -1164.1 kcal/mol for the Delta variant, and -1553.4 kcal/mol for the Omicron variant containing the Q493K mutation (Figure 2a). 2022 Journal of chemical information and modeling Result SARS_CoV_2 Q493K 154 159 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The median values of pair interaction energies were 340.0 kcal/mol for the wild type, 25.2 kcal/mol for the Delta variant, and -382.1 and -196.4 kcal/mol for the Omicron variants containing the Q493K and Q493R mutations, respectively. 2022 Journal of chemical information and modeling Result SARS_CoV_2 Q493K;Q493R 194;204 199;209 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The P-values obtained by the Kruskal-Wallis rank-sum test were 2.940 x 10-15 and 1.140 x 10-11 for the Omicron variants containing the Q493K and Q493R mutations, respectively, indicating that the median interaction energies for each RBD type were significantly different. 2022 Journal of chemical information and modeling Result SARS_CoV_2 Q493K;Q493R 135;145 140;150 RBD 233 236 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The PIE value of the S371L fragment, which was only present in the RBD of the Omicron variant containing the Q493R mutation, indicated the fragment to have a significantly stronger interaction than the corresponding residues of the wild type. 2022 Journal of chemical information and modeling Result SARS_CoV_2 Q493R;S371L 109;21 114;26 RBD 67 70 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The residues G339D, S373P, K417N, G446S, S477N, and N501Y showed significantly weaker interactions in the Omicron variant than the corresponding residues in the wild type (Table 3). 2022 Journal of chemical information and modeling Result SARS_CoV_2 G339D;G446S;K417N;N501Y;S373P;S477N 13;34;27;52;20;41 18;39;32;57;25;46 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The residues S371L, S375F, N440K, T478K, E484A, Q493K, and Q498R showed significantly stronger interactions in the Omicron variant than the corresponding residues in the wild type (Table 3). 2022 Journal of chemical information and modeling Result SARS_CoV_2 E484A;N440K;Q493K;Q498R;S371L;S375F;T478K 41;27;48;59;13;20;34 46;32;53;64;18;25;39 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The RMSD for the Omicron variant containing Q493K could not be calculated since Gln493 was substituted with a different residue in the structure generated using AlphaFold than that present in the original crystal structure. 2022 Journal of chemical information and modeling Result SARS_CoV_2 Q493K 44 49 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The six residues apart from S371L that were predicted to have strong interactions with hACE2 in protein-protein docking simulations also showed strong interactions with hACE2 in the Omicron variant than those in the wild type when analyzed experimentally. 2022 Journal of chemical information and modeling Result SARS_CoV_2 S371L 28 33 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The strongly interacting residues obtained by the protein-protein docking simulations formed a subset of those obtained by molecular dynamics, and S371L, which did not show significant differences in PIE obtained from protein-protein docking simulations between the wild type and the Omicron variant, was newly identified as a strongly interacting residue. 2022 Journal of chemical information and modeling Result SARS_CoV_2 S371L 147 152 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. The Y505H residue did not show a significant difference in PIE between the two prediction methods. 2022 Journal of chemical information and modeling Result SARS_CoV_2 Y505H 4 9 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. Therefore, the S375F mutation can be associated with increased infectivity and immune escape ability. 2022 Journal of chemical information and modeling Result SARS_CoV_2 S375F 15 20 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. Tixagevimab showed significantly lower binding affinity to the Omicron variant containing the Q493R mutation but not to the one containing the Q493K mutation, compared to the wild type and the Delta variant. 2022 Journal of chemical information and modeling Result SARS_CoV_2 Q493K;Q493R 143;94 148;99 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. We obtained 258 calculable complex structures, of which 81 were those of the wild type, 90 were of the Delta variant, and 87 were of the Omicron variants containing the Q493K mutation. 2022 Journal of chemical information and modeling Result SARS_CoV_2 Q493K 169 174 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). L452R-RT-LAMP-BART assay. 2022 PloS one Result SARS_CoV_2 L452R 0 5 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). Of the six SARS-CoV-2 RNAs, including those from two wild-type viruses and four variants (B.1.1.7, B.1.351, P1, and B.1.617.2), only B.1.617.2 RNA was detected by the L452R-RT-LAMP-BART assay (Table 1). 2022 PloS one Result SARS_CoV_2 L452R 167 172 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). The 3'-end of the F1 region matched the L452R (T1355G) sequence (S4 Fig), and the other sequences were identical to those expected (S3 Fig). 2022 PloS one Result SARS_CoV_2 L452R;T1355G 40;47 45;53 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). We demonstrated that 5x104 copies of the L452R sequence could be detected around 10 minutes whereas 5x106 copies of wild-type remained undetected after 30 minutes (Fig 2A). 2022 PloS one Result SARS_CoV_2 L452R 41 46 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). Within 25 min, we detected down to 102 RNA copies per reaction of the L452R sequence using the L452R-RT-LAMP-BART assay (Fig 2B). 2022 PloS one Result SARS_CoV_2 L452R;L452R 70;95 75;100 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. As expected, Delta breakthrough infection resulted in higher neutralizing titers against both D614G (by ~4.8-fold) and Delta (by ~3.8-fold) spikes than 2x BNT162b2 alone. 2022 bioRxiv Result SARS_CoV_2 D614G 94 99 S 140 146 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. As expected, the 2x BNT162b2 and Delta breakthrough plasmas most potently neutralized the D614G spike, and primary Delta infection plasmas most potently neutralized the Delta spike (Fig 6 and S7). 2022 bioRxiv Result SARS_CoV_2 D614G 90 95 S;S 96;175 101;180 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. Compared to the Wuhan-Hu-1 prototypical early 2020 virus, Delta has multiple mutations in the spike protein: T19R, Delta157-158, L452R, T478K, D614G (which fixed in circulating SARS-CoV-2 isolates in mid-2020), P681R, and D950N (Fig 1A). 2022 bioRxiv Result SARS_CoV_2 D614G;D950N;L452R;P681R;T19R;T478K 143;222;129;211;109;136 148;227;134;216;113;141 S 94 99 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. Delta + E484K has an ~8-fold effect on neutralization for primary Delta-infection elicited antibodies, but only a ~3-fold effect for mRNA vaccination- or Delta breakthrough infection-elicited antibodies, comparable to the effect of Delta + K417N mutation. 2022 bioRxiv Result SARS_CoV_2 E484K;K417N 8;240 13;245 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. In some cases, E484K alone can reduce neutralization to almost the same degree as removal of all RBD-binding antibodies (Fig 6A). 2022 bioRxiv Result SARS_CoV_2 E484K 15 20 RBD 97 100 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. In the D614G background, the E484K mutation has a large effect on antibody neutralization for early 2020 and mRNA vaccination-elicited plasmas. 2022 bioRxiv Result SARS_CoV_2 D614G;E484K 7;29 12;34 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. K417N has a larger effect on neutralization in the Delta than in the D614G spike. 2022 bioRxiv Result SARS_CoV_2 D614G;K417N 69;0 74;5 S 75 80 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. Notably, sublineages of the Delta variant, AY.1 and AY.2, colloquially referred to as "Delta+" lineages, contain the K417N mutation. 2022 bioRxiv Result SARS_CoV_2 K417N 117 122 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. Relative to Wuhan-Hu-1, the Delta RBD contains mutations in or proximal to the class 1 and 3 epitopes (T478K and L452R, respectively) (Fig 3A). 2022 bioRxiv Result SARS_CoV_2 L452R;T478K 113;103 118;108 RBD 34 37 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. The Delta + K417N mutation resulted in a ~3-fold reduction in neutralization for 2x BNT162b2 and Delta breakthrough plasmas when compared to the Delta spike. 2022 bioRxiv Result SARS_CoV_2 K417N 12 17 S 151 156 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. The L452R mutation likely disrupts binding of some 484-binding antibodies, probably explaining why the E484K mutation has a relatively smaller effect in the L452R-containing Delta spike. 2022 bioRxiv Result SARS_CoV_2 E484K;L452R;L452R 103;4;157 108;9;162 S 180 185 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. The neutralizing antibody activities elicited by a Delta breakthrough infection against the D614G and Delta spikes are also primarily focused on the RBD (Fig 2B, second and fourth panels from left, respectively). 2022 bioRxiv Result SARS_CoV_2 D614G 92 97 S;RBD 108;149 114;152 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. The primary Delta infection plasmas also had a ~2-fold reduced neutralization potency against Delta + K417N compared to Delta spike. 2022 bioRxiv Result SARS_CoV_2 K417N 102 107 S 126 131 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. The SARS-CoV-2 Beta variant (B.1.351) spike, which we also examine here, also has a number of mutations, including K417N, E484K, and N501Y mutations in the RBD (Fig 1B). 2022 bioRxiv Result SARS_CoV_2 E484K;K417N;N501Y 122;115;133 127;120;138 S;RBD 38;156 43;159 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. These results are consistent with other reports that K417N alone has little effect in the D614G background, although its effect can be unmasked when it is found in conjunction with mutations in more immunodominant sites such as E484K or L452R. 2022 bioRxiv Result SARS_CoV_2 D614G;E484K;K417N;L452R 90;228;53;237 95;233;58;242 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. This interpretation is supported by findings from other groups that the L452R and E484Q mutations in the Kappa variant have a less-than-additive effect on neutralization. 2022 bioRxiv Result SARS_CoV_2 E484Q;L452R 82;72 87;77 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. This is in contrast to the lack of effect of the K417N mutation in the D614G spike background for early 2020 infection- or vaccine-elicited plasmas (Fig 6B). 2022 bioRxiv Result SARS_CoV_2 D614G;K417N 71;49 76;54 S 77 82 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. Thus, mutations that further erode early 2020 infection and vaccine-elicited immunity (i.e., the K417N mutation) and mutations that erode Delta-elicited immunity (i.e., those to site 484) may have been under continued antigenic selection when the Delta variant was dominant. 2022 bioRxiv Result SARS_CoV_2 K417N 97 102 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. To determine whether the effects of mutations in the class 1 and 2 epitopes on antibody binding correspond to reductions in neutralization, we tested plasma neutralization against the canonical class 1 and 2 antibody-escape mutations K417N and E484K in the Delta RBD background. 2022 bioRxiv Result SARS_CoV_2 E484K;K417N 244;234 249;239 RBD 263 266 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. To understand the effect of a Delta breakthrough infection after mRNA vaccination, serum samples from individuals who had completed a two-dose series of BNT162b2 vaccination (hereafter referred to as 2x BNT162b2 vaccination) or who had a Delta breakthrough infection were depleted of D614G or Delta RBD-binding antibodies and assessed for neutralizing activity against the homologous spike. 2022 bioRxiv Result SARS_CoV_2 D614G 284 289 S;RBD 384;299 389;302 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. Two of these mutations, L452R and T478K, are in the spike RBD. 2022 bioRxiv Result SARS_CoV_2 L452R;T478K 24;34 29;39 S;RBD 52;58 57;61 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. We compared these results to the neutralization of D614G (early 2020) and Delta spike-pseudotyped lentiviral particles. 2022 bioRxiv Result SARS_CoV_2 D614G 51 56 S 80 85 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. While Delta breakthrough infection does boost modest non-RBD neutralizing activity against the D614G spike (Fig 2B, second panel from left), the Delta spike-reactive neutralizing activity is entirely directed towards the RBD (Fig 2B, fourth panel from left). 2022 bioRxiv Result SARS_CoV_2 D614G 95 100 S;S;RBD;RBD 101;151;57;221 106;156;60;224 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. While the L452R and T478K mutations affect binding and neutralization of some antibodies elicited by early 2020 viruses, only mutations to site K478, and not R452, sometimes strongly affect antibody binding of primary Delta infection-elicited plasmas (Fig 3). 2022 bioRxiv Result SARS_CoV_2 L452R;T478K 10;20 15;25 35314694 Genetic alteration of human MYH6 is mimicked by SARS-CoV-2 polyprotein: mapping viral variants of cardiac interest. Interestingly, one specific 8-mer from the SARS-CoV-2 Replicase polyprotein 1a/1ab (KIALKGGK) is identical to a mutant peptide encoded by the c.5410 C > A(Gln1804Lys) variation in human MYH6 (KIALKGGK), which is a subunit of a cardiac motor protein. 2022 Cell death discovery Result SARS_CoV_2 C5410A;A1804K;Q1804K 142;155;155 154;165;165 35317858 SARS-CoV-2 NSP13 helicase suppresses interferon signaling by perturbing JAK1 phosphorylation of STAT1. To this end, we created two mutants of NSP13, nucleic acid binding-defective mutant K345A K347A and NTP binding-defective mutant E375A. 2022 Cell & bioscience Result SARS_CoV_2 E375A;K345A;K347A 129;84;90 134;89;95 Nsp13 39 44 35317858 SARS-CoV-2 NSP13 helicase suppresses interferon signaling by perturbing JAK1 phosphorylation of STAT1. Whereas K345A K347A mutant of NSP13 failed to suppress IFN-beta-induced STAT1 phosphorylation, E375A mutant exhibited a partial suppressive effect on STAT1 phosphorylation after prolonged treatment with IFN-beta for 20 min. 2022 Cell & bioscience Result SARS_CoV_2 E375A;K345A;K347A 95;8;14 100;13;19 Nsp13 30 35 35321335 Omicron Variant of SARS-CoV-2 Virus: In Silico Evaluation of the Possible Impact on People Affected by Diabetes Mellitus. Although in the Omicron variant this lysine mutates into an arginine, Thr478 mutates into lysine (T478K), forming another glycation site on the ACE2 interface. 2022 Frontiers in endocrinology Result SARS_CoV_2 T478K;T478K 70;98 96;103 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Fitting led to determination of diffusion times for unbound ACE2 (taufree = 0.48+-0.02 ms), and ACE2 bound to SDeltaTM D614 (tauD614-bound = 4.53+-0.11 ms) or to the D614G variant (tauD614G-bound = 4.32+-0.15 ms). 2022 eLife Result SARS_CoV_2 D614G;D614G 166;184 171;189 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. For SDeltaTM D614G, 4A8 had only a minor effect on RBD-up occupancy or kinetics, again suggesting that the mAb binds without affecting the conformational equilibrium (Figure 4C-D). 2022 eLife Result SARS_CoV_2 D614G 13 18 RBD 51 54 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. However, the unbound SDeltaTM D614G displayed greater occupancy in the RBD-up conformation (59% +- 3%), and the overall level of dynamics was reduced as compared to D614 (Figure 3G-H). 2022 eLife Result SARS_CoV_2 D614G 30 35 RBD 71 74 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. In contrast, none of the mAbs stabilized the RBD-up conformation for SDeltaTM D614G to a significant extent (Figure 4C-D), suggesting that the effect of the D614G mutation is sufficient to enable mAb binding without further conformational changes. 2022 eLife Result SARS_CoV_2 D614G;D614G 78;157 83;162 RBD 45 48 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. In contrast, S309 had no significant effect on ACE2 binding to SDeltaTM D614G, and 4A8 had a slight inhibition of ACE2 binding, again consistent with their modulation of RBD conformation. 2022 eLife Result SARS_CoV_2 D614G 72 77 RBD 170 173 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Incubation of SDeltaTM D614 or D614G with MAb362IgA1 or REGN10987 resulted in statistically significant reductions in ACE2 binding that are consistent with previous reports at comparable concentrations (; Figure 5A, B). 2022 eLife Result SARS_CoV_2 D614G 31 36 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Of note, the stalk-targeting 1A9 and 2G12 mAbs induced the greatest enhancement of ACE2 binding to SDeltaTM D614 and D614G, consistent with their allosteric modulation of RBD conformation. 2022 eLife Result SARS_CoV_2 D614G 117 122 RBD 171 174 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Purified homo-trimers with either D614 or D614G were validated through two different approaches: (1) evaluation of their binding to ACE2 and (2) evaluation of their antigenic characteristics compared with untagged SDeltaTM. 2022 eLife Result SARS_CoV_2 D614G 42 47 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. These data indicate that the S2 stalk-targeting mAbs studied here allosterically induce transition of the RDB to the up conformation on both the D614 and D614G spikes. 2022 eLife Result SARS_CoV_2 D614G 154 159 S 160 166 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Thus, consistent with structural studies, the D614G mutation shifted the conformational equilibrium in favor of the RBD-up conformation. 2022 eLife Result SARS_CoV_2 D614G 46 51 RBD 116 119 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. To monitor the conformational dynamics of SDeltaTM D614 and D614G, we purified SDeltaTM hetero-trimers, formed by co-transfection of 161/345A4-tagged and untagged SDeltaTM plasmids at a 1:2 ratio. 2022 eLife Result SARS_CoV_2 D614G 60 65 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. We first sought to use our smFRET imaging approach to explore the effect of RBD-directed mAbs on SDeltaTM dynamics for both the D614 and D614G variants. 2022 eLife Result SARS_CoV_2 D614G 137 142 RBD 76 79 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. We next sought to determine the effect of the D614G mutation on the conformational dynamics of SDeltaTM. 2022 eLife Result SARS_CoV_2 D614G 46 51 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. We observed the same two FRET states for SDeltaTM D614G as for the ancestral D614 spike (Figure 3F). 2022 eLife Result SARS_CoV_2 D614G 50 55 S 82 87 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. We therefore applied our FCS assay for ACE2 binding after pre-treating SDeltaTM D614 or D614G with mAbs. 2022 eLife Result SARS_CoV_2 D614G 88 93 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. We therefore explored the conformational dynamics of both SDeltaTM D614 and D614G pre-treated with the NTD-targeting mAb 4A8, and with the S2 stalk-directed mAbs 1A9 and 2G12. 2022 eLife Result SARS_CoV_2 D614G 76 81 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. All of the strains in the 6B.1A5A + 187V/A cluster had the two amino acid substitutions of D187A and Q189E. 2022 Tropical medicine and infectious disease Result SARS_CoV_2 D187A;Q189E 91;101 96;106 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. An additional substitution of K209M was detected in this subclade, and the strains that carried K209M formed a distinct subclade with tMRCA of 2019.73 (PP = 0.94). 2022 Tropical medicine and infectious disease Result SARS_CoV_2 K209M;K209M 30;96 35;101 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. Eighteen strains registered in 2020 and the four strains of the present study belonged to subclade 6B.1A5A, which was further phylogenetically classified into three genetic groups: (1) two strains (9.1%) were related to the parental subclade 6B.1A5A strain; (2) five strains (22.7%) belonged to the 6B.1A5A + 187V/A subclade with the vaccine viruses of Guangdong-Maonan/SWL1536/2019 and Hawaii/70/2019 carrying the specific amino acid mutations of D187V/A and Q189E; and (3) 15 strains (68.2%), including the four strains obtained in the present study, belonged to the 6B.1A5A + 156K subclade with the vaccine viruses Wisconsin/588/2019 and Victoria/2570/2019 with N156K. 2022 Tropical medicine and infectious disease Result SARS_CoV_2 D187A;D187V;N156K;Q189E 448;448;665;460 455;455;670;465 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. In addition, 136 sequences contained K209M (37.99% of subclade 6B.1A5A + 156K and 17.48% of all H1N1 strains; Supplementary Table S4). 2022 Tropical medicine and infectious disease Result SARS_CoV_2 K209M 37 42 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. NA segment analysis indicated that all four sequences from the present study lacked the H275Y amino acid substitution (Supplementary Table S5) that confers oseltamivir resistance. 2022 Tropical medicine and infectious disease Result SARS_CoV_2 H275Y 88 93 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. On the other hand, 15 of Bangladesh 2020 6B.1A5A + 156K strains fell into the 6B.1A5A + 156K cluster carrying K130N, N156K, L161I, and V250A with a tMRCA of 2019.54 (PP = 1). 2022 Tropical medicine and infectious disease Result SARS_CoV_2 K130N;L161I;N156K;V250A 110;124;117;135 115;129;122;140 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. Results showed that 122 of 2018 strains were clustered with Ireland/84630/2018, the reference strain of the subclade 6B.1A6 defined by the amino acid substitutions T120A and S183P (Figure 2). 2022 Tropical medicine and infectious disease Result SARS_CoV_2 S183P;T120A 174;164 179;169 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. The H275Y mutation was found only one strain (A/Bangladesh/4005 2019 EPI ISL 395161 NA) in the Bangladesh strains registered in the GISAID database between January 2018 and March 2021 (Supplementary Table S5); however, it was found in seven (five 6B.1A5A + 156K, one 6B.1A5A + 187V/A, and one non-6B clade) of the 737 strains registered from all over the world between March 2020 and March 2021 (Supplementary Table S6). 2022 Tropical medicine and infectious disease Result SARS_CoV_2 H275Y 4 9 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. The sequences of the four isolates were all classified into subclade 6B.1A, as they possessed amino acid substitutions S74R, S164T, and I295V in HA1 as compared to the prototype A/Michigan/45/2015. 2022 Tropical medicine and infectious disease Result SARS_CoV_2 I295V;S164T;S74R 136;125;119 141;130;123 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. They also carried K130N, N156K, L161I, V250A, and E506D (N156K and L161I were in the Sa antigenic site), which are specific to subclade 6B.1A5A + 156K (Figure 1, Supplementary Table S3). 2022 Tropical medicine and infectious disease Result SARS_CoV_2 E506D;K130N;L161I;L161I;N156K;V250A;N156K 50;18;32;67;25;39;57 55;23;37;72;30;44;62 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. They were further classified into subclade 6B.1A5A by the presence of the additional amino acid substitutions of S183P, N129D, T185I, and N260D (T185I was in the Sb antigenic site). 2022 Tropical medicine and infectious disease Result SARS_CoV_2 N129D;N260D;S183P;T185I;T185I 120;138;113;127;145 125;143;118;132;150 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. A single mutation P77L in NSP13 was detected in all genomic isolates (N = 18). 2022 Genes Result SARS_CoV_2 P77L 18 22 Nsp13 26 31 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Among the unique mutation, NS3_I118L was detected in 14 isolates (Table 4). 2022 Genes Result SARS_CoV_2 I118L 31 36 NS3 27 30 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Among these, the most common were N_D377Y, N_R203M, and N_D63G have been detected in all 18 samples (Table 3). 2022 Genes Result SARS_CoV_2 D377Y;R203M 36;45 41;50 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Delta variant harbors L452R, P681R, and T478K in S protein. 2022 Genes Result SARS_CoV_2 L452R;P681R;T478K 22;29;40 27;34;45 S 49 50 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Forty-one mutations were detected in NSP14, including five non-synonymous mutations in which NSP14_A394V (N = 17) NSP14_M72I (N = 6) were the most common. 2022 Genes Result SARS_CoV_2 A394V;M72I 99;120 104;124 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Four mutations were detected in NSP6 in which T77A was detected with the highest frequency (N = 17). 2022 Genes Result SARS_CoV_2 T77A 46 50 Nsp6 32 36 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Mutations E554K (S1 domain of S), K1086Q, and C1250W (S2 domain of S) (Figure 1) were unique to S protein, and in GISAID, present in samples 1, 11, and 19. 2022 Genes Result SARS_CoV_2 C1250W;E554K;K1086Q 46;10;34 52;15;40 S;S;S 30;67;96 31;68;97 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Mutations NSP12_G671S (N = 18) and NSP12_P323L (N = 16) were the most common, present in the interface and RdRp domain (Figure 6). 2022 Genes Result SARS_CoV_2 G671S;P323L 16;41 21;46 Nsp12;Nsp12;RdRP 10;35;107 15;40;111 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Mutations with a single frequency at position L862F, P822L, and H920Y were detected in the PLpro domain of NSP3 (Figure 6D). 2022 Genes Result SARS_CoV_2 H920Y;L862F;P822L 64;46;53 69;51;58 Nsp3 107 111 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Mutations, spike_D950N and spike_T95I were present in twelve samples each. 2022 Genes Result SARS_CoV_2 D950N;T95I 17;33 22;37 S;S 11;27 16;32 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. No mutation was detected in the envelope the protein where the membrane (M) protein harbored only two non-synonymous mutations (I82T (N = 18) and V70F (N = 1)) in the transmembrane domain. 2022 Genes Result SARS_CoV_2 V70F;I82T 146;128 150;132 Membrane 63 71 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. NSP4 harbors four mutations in which V167L in NTD and T492I in CTD were present in 17 isolates. 2022 Genes Result SARS_CoV_2 T492I;V167L 54;37 59;42 Nsp4 0 4 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The D63G was present in N-terminal domain (NTD) of N protein, which is also called RNA-binding domain (RBD) (Figure 1 and Figure 2). 2022 Genes Result SARS_CoV_2 D63G 4 8 RBD;N;N 103;24;51 106;25;52 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The highest frequency of mutations was detected in virus NSP3 (Table 2) in which P1469S (N = 17), A488S (N = 17), and P1228L (N = 17) were the most common. 2022 Genes Result SARS_CoV_2 A488S;P1228L;P1469S 98;118;81 103;124;87 Nsp3 57 61 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The highest number of unique mutations were detected in NSP3 (N = 10), followed by NSP5 (V86L), NSP12 (F313Y), and NS3 (I118L). 2022 Genes Result SARS_CoV_2 F313Y;I118L;V86L 103;120;89 108;125;93 Nsp12;Nsp3;Nsp5;NS3 96;56;83;115 101;60;87;118 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The most common non-synonymous and indel mutations, present in all complete genome samples were spike_T478K, spike_T19R, spike_L452R, spike_F157del, spike_E156G, spike_P681R, spike_D614G, spike_R158del, and spike_G142D (Table 3). 2022 Genes Result SARS_CoV_2 D614G;E156G;F157del;G142D;L452R;P681R;R158del;T19R;T478K 181;155;140;213;127;168;194;115;102 186;160;147;218;132;173;201;119;107 S;S;S;S;S;S;S;S;S 96;109;121;134;149;162;175;188;207 101;114;126;139;154;167;180;193;212 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The spike_G142D mutant exhibited a little destabilizing affect (0.206 kcal/mole when compared with T478K (0.584 kcal/mol), E156G (0.049 kcal/mol), L452R (0.059 kcal/mol), P681R (0.503 kcal/mol), and T19R (0.403 kcal/mol). 2022 Genes Result SARS_CoV_2 E156G;L452R;P681R;T19R;T478K;G142D 123;147;171;199;99;10 128;152;176;203;104;15 S 4 9 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Two mutations, N_R203M and N_G215C, were present in SR-Linker region of N proteins and one D377Y in C-terminal domain (CTD). 2022 Genes Result SARS_CoV_2 D377Y;G215C;R203M 91;29;17 96;34;22 N 72 73 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. Compared to the neutralisation titres against PVs bearing the ancestral Spike, we observed the following geometric mean fold changes in neutralisation titres: B.1.1.298: 1.1 fold decrease, B.1.1.7: 1.8 fold decrease, B.1.617.2 K417N: 3.1 fold decrease, B.1.617.2: 4.8 fold decrease, B.1.617.1: 4.9 fold decrease, P.1: 8.2 fold decrease and lastly, B.1.351: 8.3 fold decrease. 2022 Frontiers in immunology Result SARS_CoV_2 K417N 227 232 S 72 77 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. Lastly, we found that the K417N mutation in the B.1.617.2 Delta Plus increased the neutralisation titres compared to B.1.617.2 delta VOC. 2022 Frontiers in immunology Result SARS_CoV_2 K417N 26 31 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. VOI B.1.617.1 and VOCs B.1.617.2 and VOC B.1.617.2 K417N IC50 values were not calibrated as we were unable to demonstrate parallelism between the curves as described in the methods section. 2022 Frontiers in immunology Result SARS_CoV_2 K417N 51 56 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. Also, entry of mutant S686G was significantly augmented by directed CTSL expression, suggesting that insufficient endogenous CTSL levels limit Calu-3 cell entry of this mutant. 2022 PloS one Result SARS_CoV_2 S686G 22 27 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. Exogenous cathepsin L expression rescues Calu-3 cell entry of SARS-CoV-2 S mutant S686G. 2022 PloS one Result SARS_CoV_2 S686G 82 87 S 73 74 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. Finally, we sought to obtain initial insights into why mutation S686G reduced viral entry into Calu-3 cells. 2022 PloS one Result SARS_CoV_2 S686G 64 69 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. In contrast, five mutations (P681H [cleavage efficiency: 52.3% +/- 1.7%], P681L [49.9% +/- 3.4%], A684S [53.4% +/- 1.4%], S686G [40.1% +/- 1.8%] and V687L [50.0% +/- 4.4%]) were found to cause a significant decrease (~1.34- to 1.80-fold) in S protein cleavage compared to the WT SARS-CoV-2 S (71.4% +/- 3.7%) (Fig 1C and 1D). 2022 PloS one Result SARS_CoV_2 A684S;P681L;S686G;V687L;P681H 98;74;122;149;29 103;79;127;154;34 S;S 241;290 242;291 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. Mutants Q675R, Q677H, P681H, P681L, A684S, A684T, A684V and V687L facilitated entry into all cell lines tested with comparable or up to two-fold enhanced/decreased efficiency compared to WT SARS-CoV-2 S (Fig 4A). 2022 PloS one Result SARS_CoV_2 A684S;A684T;A684V;P681H;P681L;Q675R;Q677H;V687L 36;43;50;22;29;8;15;60 41;48;55;27;34;13;20;65 S 201 202 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. Mutation S686G attenuated entry into Calu-3 and Caco-2 cells by roughly 2.5- and 3.5-fold, respectively, while entry into Vero and A549-ACE2 cells was enhanced by 1.8- and 4.5-fold, respectively. 2022 PloS one Result SARS_CoV_2 S686G 9 14 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. Mutation S686G slightly augments ACE2 binding. 2022 PloS one Result SARS_CoV_2 S686G 9 14 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. Mutations P681H, P681L, A684S, S686G and V687L reduce S protein cleavage. 2022 PloS one Result SARS_CoV_2 A684S;P681H;P681L;S686G;V687L 24;10;17;31;41 29;15;22;36;46 S 54 55 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. Out of the ten S protein mutants tested, one (S686G) showed variable and cell line-dependent phenotypes when compared to WT SARS-CoV-2 S. 2022 PloS one Result SARS_CoV_2 S686G 46 51 S;S 15;135 16;136 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. S686G modulates SARS-CoV-2 S-driven entry in a cell line-dependent manner. 2022 PloS one Result SARS_CoV_2 S686G 0 5 S 27 28 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. The only exception was mutation S686G, which caused a moderate but significant increase in ACE2 binding (Fig 2). 2022 PloS one Result SARS_CoV_2 S686G 32 37 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. The remaining mutations under study include Q675R, Q677H, S686G, V687L and A688V (Fig 1B). 2022 PloS one Result SARS_CoV_2 A688V;Q675R;Q677H;S686G;V687L 75;44;51;58;65 80;49;56;63;70 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. Three mutations are located within the S1/S2 cleavage motif 682-RRAR-685 (A684S, A684T or A684V), while two mutations affect the proline residue that directly precedes the cleavage motif (P681H, P681L) and one of them is present in the B.1.1.7 variant and B.1.1.529 variants (P681H). 2022 PloS one Result SARS_CoV_2 A684T;A684V;P681L;A684S;P681H;P681H 81;90;195;74;188;276 86;95;200;79;193;281 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. Thus, P681H and several other naturally-occurring polymorphisms can modulate S protein cleavage efficiency. 2022 PloS one Result SARS_CoV_2 P681H 6 11 S 77 78 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. We found that all S protein mutants were robustly incorporated into particles and no significant differences in S protein incorporation between WT and mutant SARS-CoV-2 S were observed, except for mutant A684S, for which particle incorporation was slightly (factor: 1.4 +/- 0.1) increased (Fig 1C). 2022 PloS one Result SARS_CoV_2 A684S 204 209 S;S;S 18;112;169 19;113;170 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). A total of 6 out of 32 (18.8%) sequences showed a nucleotide point mutation leading to a synonymous amino acid substitution, while 4/32 (12.5%) sequences carried a total of 5 nucleotide mutations, 3 of which (C22879A) led to the N439K amino acid substitution and 1 of which (G22992A) led to the S477N amino acid substitution. 2022 Microorganisms Result SARS_CoV_2 N439K;S477N;C22879A;G22992A 229;295;209;275 234;300;216;282 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). Briefly, in all sequences (32/32, 100%), the D614G substitution was detected, lineage B.1. 2022 Microorganisms Result SARS_CoV_2 D614G 45 50 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). Finally, 1/32 sequence was the Omicron strain, with the following mutations in the RBD domain: T22882G (N440K), G22898A (G446S), G22992A (S477N), C22995A (T478K), A23013C (E484A), A23040G (Q493R), G23048A (G496S), A23055G (Q498R), A23063T (N501Y), T23075C (Y505H), C23202A (T547K), A23403G (D614G), C23525T (H655Y), T23599G (N679K), C23604A (P681H). 2022 Microorganisms Result SARS_CoV_2 A23013C;A23040G;A23055G;A23063T;A23403G;C22995A;C23202A;C23525T;C23604A;G22898A;G22992A;G23048A;T22882G;T23075C;T23599G;D614G;E484A;G446S;G496S;H655Y;N440K;N501Y;N679K;P681H;Q493R;Q498R;S477N;T478K;T547K;Y505H 163;180;214;231;282;146;265;299;333;112;129;197;95;248;316;291;172;121;206;308;104;240;325;342;189;223;138;155;274;257 170;187;221;238;289;153;272;306;340;119;136;204;102;255;323;296;177;126;211;313;109;245;330;347;194;228;143;160;279;262 RBD 83 86 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). Full genome sequences obtained by the NGS of a single SARS-CoV-2 isolated strain, N439K, and a single Delta-like strain, which were deposited at GISAID (N439K: EPI_ISL_7208675; Delta: EPI_ISL_7698448). 2022 Microorganisms Result SARS_CoV_2 N439K;N439K 82;153 87;158 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). In addition, the Delta-like (EPI_ISL_7698448) strain was compared to the reference SARS-CoV-2 genome isolate (Wuhan-Hu-1, NC_045512.2) (Table 5), and it was assigned to the lineage B.1.617.2 + AY.43 strain using the Pangolin tool based on the presence of the nonsynonymous mutations or deletions A1306S, A1809V, P2046L, P2287S, V2930L, T3255I, T3646A, P4715L, G5063S, L5230I, P5401L, and A6319V in the ORF1ab gene; T19R, G142D, EFR156G (F157Delta, R158Delta), L452R, T478K, D614G, P681R, and D950N in the S gene; S26L in the ORF3a gene; I82T in the M gene; V82A and T120I in the ORF7a gene, T40I in the ORF7b gene; C37R, D119Delta, and F120Delta in the ORF8 gene; and Q9L, D63G, R203M, G215C, and D377Y in the N gene. 2022 Microorganisms Result SARS_CoV_2 A1306S;A1809V;A6319V;C37R;D377Y;D614G;D63G;D950N;G142D;G215C;G5063S;I82T;L452R;L5230I;P2046L;P2287S;P4715L;P5401L;P681R;Q9L;R203M;S26L;T120I;T19R;T3255I;T3646A;T40I;T478K;V2930L;V82A 296;304;388;615;697;474;673;492;421;686;360;537;460;368;312;320;352;376;481;668;679;513;566;415;336;344;591;467;328;557 302;310;394;619;702;479;677;497;426;691;366;541;465;374;318;326;358;382;486;671;684;517;571;419;342;350;595;472;334;561 ORF1ab;ORF7a;ORF7b;ORF3a;ORF8;N;S 402;579;603;525;653;710;505 408;584;608;530;657;711;506 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). In total, 7/32 (21.8%) strains showed the presence of 3 nucleotide mutations (T22917G, C22995A, C23604G), leading to the L452R, T478K, and P681R amino acid substitutions, all typical of a Delta-like variant. 2022 Microorganisms Result SARS_CoV_2 C22995A;C23604G;L452R;P681R;T478K;T22917G 87;96;121;139;128;78 94;103;126;144;133;85 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). The N439K (EPI_ISL_7208675) strain was compared to the reference SARS-CoV-2 genome isolate (Wuhan-Hu-1, NC_045512.2) (Table 4), and it was assigned to lineage B.1.258 ( H69/ V70) using Phylogenetic Assignment of Named Global Outbreak Lineages (pangolin) based on the presence of the nonsynonymous mutations or deletions R207H, K1895N, I2501T, M4241I, P4715L, V5112I, H5614Y, and A5922S in the ORF1ab gene; H69del, V70del, G75V, N439K, and D614G in the S gene; and G38stop in the ORF7a gene. 2022 Microorganisms Result SARS_CoV_2 A5922S;D614G;G38X;G75V;H5614Y;H69del;I2501T;K1895N;M4241I;N439K;N439K;P4715L;R207H;V5112I;V70del 379;439;464;422;367;406;335;327;343;4;428;351;320;359;414 385;444;471;426;373;412;341;333;349;9;433;357;325;365;420 ORF1ab;ORF7a;S 393;479;452 399;484;453 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). We decided to perform the full genome sequencing of the viral strains that were more represented in the sampled population: the N439K, present in 3/32 patients, and the Delta-like, present in 7/32 patients. 2022 Microorganisms Result SARS_CoV_2 N439K 128 133 35336868 Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens. A gain of an SNV expand was observed at the E gene (G26293A (V17I)) of P-1 Vero CCL-81 isolate, while it was absent in clinical as well as hamster sequences. 2022 Viruses Result SARS_CoV_2 G26293A;V17I 52;61 59;65 E 44 45 35336868 Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens. Further, an SNV was also observed at M gene (C26577G (Q19E)) of hamster P-1 which was not observed in the clinical sample, Vero CCL-81 P-1, or hamster P-2. 2022 Viruses Result SARS_CoV_2 C26577G;Q19E 45;54 52;58 35336868 Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens. Further, the studies have reported that the N440K strains have the capability of escaping the neutralization. 2022 Viruses Result SARS_CoV_2 N440K 44 49 35336868 Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens. The frequency of the N440K amino acid change was observed in the hamster sequences (100%) and in the human clinical sequences (68.5%). 2022 Viruses Result SARS_CoV_2 N440K 21 26 35336868 Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens. The variation in the frequency of the N440K in human clinical specimens, hamster specimens, and Vero CCL-81 passages could be due to the adaptive mutations in different host species. 2022 Viruses Result SARS_CoV_2 N440K 38 43 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. In addition, Table S2 also lists two HR1-CH models in the Delta variant: (e) wild type (WT) D950 and (f) mutated D950N (N950). 2022 Viruses Result SARS_CoV_2 D950N 113 118 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. Most of these studies focus on the clinical or experimental observations to demonstrate the danger of mutations, especially the P681R near the furin cleavage site in the SD2-FP domain of the S-protein, but, to the best of our knowledge, no theoretical explanation or computational studies have been reported so far. 2022 Viruses Result SARS_CoV_2 P681R 128 133 S 191 192 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. Table S2 lists the structure information from VASP optimization for the four SD2-FP models in the Delta variant: (a) wild type (WT), (b) mutated P681R (R681), (c) mutated D614G (G614), and (d) double mutation (DM) labeled as G614-R681. 2022 Viruses Result SARS_CoV_2 D614G;P681R 171;145 176;150 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. In addition, a S:E484Q mutation was detected in the spike protein of all seven sequences. 2022 Viruses Result SARS_CoV_2 E484Q 17 22 S;S 52;15 57;16 35336922 Multiorgan and Vascular Tropism of SARS-CoV-2. All SARS-CoV-2 genomes detected showed that the virus belonged to the clade 20A.EU2, with the presence of the characteristic S477N and the D614G mutations on the spike protein. 2022 Viruses Result SARS_CoV_2 D614G;S477N 139;125 144;130 S 162 167 35336922 Multiorgan and Vascular Tropism of SARS-CoV-2. For the spike protein, the Q526* mutation (ORF1a) was only detected in the mesenteric artery, and the F3271L, absent in the initial nasopharyngeal swab, was detected in pleura (14.4%), trachea (12.5%), myocardium (13.3%), stomach lining (10.5%) and testicle (9.6%). 2022 Viruses Result SARS_CoV_2 F3271L;Q526X 102;27 108;32 ORF1a;S 43;8 48;13 35336922 Multiorgan and Vascular Tropism of SARS-CoV-2. Furthermore, the E787V mutation (ORF1b) was detected in the totality of the analyzed tissues (8.0 to 25.6% of the viral quasispecies), but was undetected in the initial nasopharyngeal swab. 2022 Viruses Result SARS_CoV_2 E787V 17 22 35336922 Multiorgan and Vascular Tropism of SARS-CoV-2. Regarding the spike protein, specific mutations were observed in vascular tissues, the H655R and the V341A in vena cava (30.8% and 18.3%, respectively), as well as the E654A (44.0%), which was also poorly detected in other tissues in which the E654G was highly represented (trachea, myocardium, stomach lining, carotid and mesenteric artery) (Table 1). 2022 Viruses Result SARS_CoV_2 E654A;E654G;H655R;V341A 168;244;87;101 173;249;92;106 S 14 19 35336922 Multiorgan and Vascular Tropism of SARS-CoV-2. Various mutations were present in the stomach lining biopsy, especially the Q57H (ORF3a), reaching 98.6%, but were not detected in other tissues. 2022 Viruses Result SARS_CoV_2 Q57H 76 80 ORF3a 82 87 35336952 Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. Figure 3 shows the most frequent amino acid substitutions in the RBD (G339D, R346K, K417N, S371L, S373P, S375F, N440K, Q498R, and N501Y). 2022 Viruses Result SARS_CoV_2 K417N;N440K;N501Y;Q498R;R346K;S371L;S373P;S375F;G339D 84;112;130;119;77;91;98;105;70 89;117;135;124;82;96;103;110;75 RBD 65 68 35336952 Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. In addition, a group of five substitutions (A67V, del69/70, T95I, G142D, del143/145) had the highest prevalence values in all countries analyzed (92-100%), except in the United Kingdom and India (60-71%). 2022 Viruses Result SARS_CoV_2 G142D;T95I;A67V 66;60;44 71;64;48 35336952 Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. Interestingly, samples with R346K in Mexico City clustered in a monophyletic branch in a phylogenetic analysis (Supplementary Figure S1). 2022 Viruses Result SARS_CoV_2 R346K 28 33 35336952 Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. K417N/T is present in the Alpha and Gamma variants, and both mutations facilitate immune escape for monoclonal antibodies (bamlanivimab/LY-CoV555), escape from neutralization by convalescent plasma, and escape by sera from BNT162b2-vaccinated individuals. 2022 Viruses Result SARS_CoV_2 K417N;K417T 0;0 7;7 35336952 Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. N501Y is present in the Alpha, Beta, and Gamma variants, and this substitution increases binding affinity to angiotensin-converting enzyme receptor 2 (ACE2), playing an essential role in the higher rate of transmission of SARS-CoV-2 variants. 2022 Viruses Result SARS_CoV_2 N501Y 0 5 35336952 Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. Neutralization studies on the B.1.1.529+R346K pseudovirus showed that 18 of the 19 monoclonal antibodies (mAbs) tested lost neutralizing activity completely or partially. 2022 Viruses Result SARS_CoV_2 R346K 40 45 35336952 Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. On the other hand, the prevalence of eleven substitutions (S371L, S373P, S375F, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, and Y505H) was lower in Mexico City and Mexico outside of Mexico City, Israel, the United Kingdom, and India (32-70%) than in Australia, Canada, Japan, and the USA (91-100%) (Figure 4). 2022 Viruses Result SARS_CoV_2 E484A;G496S;N501Y;Q493R;Q498R;S373P;S375F;S477N;T478K;Y505H;S371L 94;108;122;101;115;66;73;80;87;133;59 99;113;127;106;120;71;78;85;92;138;64 35336952 Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. Prevalence of the R346K Substitution. 2022 Viruses Result SARS_CoV_2 R346K 18 23 35336952 Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. R346K was presented for the first time in the Mu variant B.1.621 and is now present in the Omicron variant. 2022 Viruses Result SARS_CoV_2 R346K 0 5 35336952 Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. The prevalence of R346K was 42% in Mexico City and 46% in the rest of the country; other countries with high prevalence were the USA (42%) and Japan (52%). 2022 Viruses Result SARS_CoV_2 R346K 18 23 35336952 Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. There are mAB-based therapies that have demonstrated efficacy in neutralizing Omicron+R346K, such as STI-9167 from Sorrento Therapeutics, sotrovimab by GSK, and Vir Biotechnology. 2022 Viruses Result SARS_CoV_2 R346K 86 91 35336952 Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. We found that the substitutions R346K, K417N, and N440K were more prevalent in Mexico City, Mexico outside of Mexico City, the USA, and Japan (42-52%). 2022 Viruses Result SARS_CoV_2 K417N;N440K;R346K 39;50;32 44;55;37 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. Analytic LoD was determined by 2-fold dilution series (8 steps, 8 repeats) as 19.0 IU/mL (CI95%: 12.9-132.2 IU/mL) for target 1: A67V + del-HV69-70; 105.0 IU/mL (CI95%: 80.7-129.3 IU/mL) for target 2: P681R; 193.9 IU/mL (CI95%: 144.7-334.7 IU/mL) for target 3: E484A; and 35.5 IU/mL (CI95%: 23.3-158.0 IU/mL) for target 4: N679K +P681H (See Table 3). 2022 Viruses Result SARS_CoV_2 A67V;E484A;N679K;P681R;P681H 129;261;323;201;330 133;266;328;206;335 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. The clinical sample set notably included SARS-CoV-2 lineages with P681H (non-N679K), Del-HV69-70 (non-A67V), E484K and E484Q sequence variances (e.g., B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.1 (Kappa)). 2022 Viruses Result SARS_CoV_2 E484K;E484Q;P681H;A67V;N679K 109;119;66;102;77 114;124;71;106;82 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. 1.1.7 and N501Y primer set, the assays for P1 and B.1.617.2 VOC were found specific with the RT-qPCR method. 2022 Viruses Result SARS_CoV_2 N501Y 10 15 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. Additionally, the N501Y primer set did not target the B.1.617.2. 2022 Viruses Result SARS_CoV_2 N501Y 18 23 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. As discussed earlier, the N501Y primer set should yield in a positive signal for the different VOC lineages containing the N501Y mutation (i.e., B.1.1.7, B.1.351 and P.1), while this primer set should be negative for the Wuhan strain and B.1.617.2 strain. 2022 Viruses Result SARS_CoV_2 N501Y;N501Y 26;123 31;128 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. As illustrated in Figure 2, the use of the N501Y primer sets also resulted in a positive signal in the reaction well containing the Wuhan strain. 2022 Viruses Result SARS_CoV_2 N501Y 43 48 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. Finally, the N501Y primer set targets the N501Y mutation in the spike region of the SARS-CoV-2 genome, which is present in the B.1.1.7, the B.1.351 and P.1 strain. 2022 Viruses Result SARS_CoV_2 N501Y;N501Y 13;42 18;47 S 64 69 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. For this reason, the dPCR assay is capable of measuring a combined signal of all VOC lineages containing the N501Y mutation through the use of this primer set. 2022 Viruses Result SARS_CoV_2 N501Y 109 114 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. For this reason, this primer set was excluded from the assay, and the occurrence of the P.1 VOC was measured through the application of the N501Y assay specifically. 2022 Viruses Result SARS_CoV_2 N501Y 140 145 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. Further optimization of the N501Y primer sets was, therefore, required. 2022 Viruses Result SARS_CoV_2 N501Y 28 33 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. However, it should be noted that the N501Y assay was negative in most cases. 2022 Viruses Result SARS_CoV_2 N501Y 37 42 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. In addition, the N501Y primer set was selective for the VOC lineages containing the N501Y mutation and did not result in a positive signal for the Wuhan strain (see Figure 3). 2022 Viruses Result SARS_CoV_2 N501Y;N501Y 17;84 22;89 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. In conclusion, the final assay is able to distinguish between the wild-type, B.1.1.7, B.1351, B.1.617.2 and other lineages containing the N501Y mutation (e.g., P.1) in the spike genome of SARS-CoV-2. 2022 Viruses Result SARS_CoV_2 N501Y 138 143 S 172 177 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. It should be noted that the sensitivity of the N501Y assay was only tested on the RNA control of B.1.1.7 lineage and not on the B.1.351 and P.1 strains. 2022 Viruses Result SARS_CoV_2 N501Y 47 52 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. Overall, native concentrations found with the N501Y primer set were also lower compared to the primer sets targeting the E gene, the B1.1.7 and the B.1.617.2 lineage. 2022 Viruses Result SARS_CoV_2 N501Y 46 51 E 121 122 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. RNA concentrations for the E gene in late 2020 most likely originate from the presence of the wild type in IWW since the majority of samples were negative for the B1.1.7, the B1.351 and the N501Y primer set. 2022 Viruses Result SARS_CoV_2 N501Y 190 195 E 27 28 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. The lower sensitivity of N501Y in IWW could potentially also be linked to the complexity of the wastewater matrix. 2022 Viruses Result SARS_CoV_2 N501Y 25 30 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. The N501Y assay is characteristic for genomic variants containing this mutation. 2022 Viruses Result SARS_CoV_2 N501Y 4 9 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. The N501Y assay targets all VOC strains that contain this respective mutation, for example, B.1.1.7, B.1.351 and P.1. 2022 Viruses Result SARS_CoV_2 N501Y 4 9 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. The N501Y primer sets could potentially be influenced to a larger extent, compared to the other PCR primers. 2022 Viruses Result SARS_CoV_2 N501Y 4 9 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. The same experimental design was conducted with dPCR to further investigate the applicability of the N501Y, B.1.1.7, P.1 and B.1.617.2 primer sets. 2022 Viruses Result SARS_CoV_2 N501Y 101 106 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. The use of the B.1.1.7, N501Y and B.1.351 primer sets did not give a positive test result for the B.1.617.2, further indicating the specificity of the different primer sets for the different VOC lineages. 2022 Viruses Result SARS_CoV_2 N501Y 24 29 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. 5D) and the Delta L452R mutant. 2022 The Journal of biological chemistry Result SARS_CoV_2 L452R 18 23 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. 5D), Alpha N501Y. 2022 The Journal of biological chemistry Result SARS_CoV_2 N501Y 11 16 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. 5F), and Gamma K417T/E484K/N501Y. 2022 The Journal of biological chemistry Result SARS_CoV_2 K417T;E484K;N501Y 15;21;27 20;26;32 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. Delta L452R. 2022 The Journal of biological chemistry Result SARS_CoV_2 L452R 6 11 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. Fractions Fr1-Fr4 showed strong binding affinity for the Alpha N501Y mutant. 2022 The Journal of biological chemistry Result SARS_CoV_2 N501Y 63 68 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. Heparin binding to the N501Y mutant lacked any interaction with Y501. 2022 The Journal of biological chemistry Result SARS_CoV_2 N501Y 23 28 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. In addition, through the competitive SPR assay (Table 4), it is also demonstrated that the native BoSG has stronger binding affinities for the N501Y-containing RBDs than for the single L452R mutant or wild type RBD. 2022 The Journal of biological chemistry Result SARS_CoV_2 L452R;N501Y 185;143 190;148 RBD;RBD 160;211 164;214 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. Molecular docking of BoSG-derived disaccharide constructs to N501Y RBD. 2022 The Journal of biological chemistry Result SARS_CoV_2 N501Y 61 66 RBD 67 70 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. Overall, from the docking poses of the RBD-BoSG disaccharides, it could be seen that residues Y501, Y449, Q498, R403, Q493 and Y453 play key roles in binding with the S-protein RBD N501Y mutant. 2022 The Journal of biological chemistry Result SARS_CoV_2 N501Y 181 186 RBD;RBD;S 39;177;167 42;180;168 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. some affinity for the Gamma K417T/E484K/N501Y mutant. 2022 The Journal of biological chemistry Result SARS_CoV_2 K417T;E484K;N501Y 28;34;40 33;39;45 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. The best-scoring docked pose of the heparin disaccharide to the N501Y mutant S-protein RBD indicated that its IdoA is oriented towards R408 and its O3 and O4 hydroxyl groups interact with D405 and R408, respectively. 2022 The Journal of biological chemistry Result SARS_CoV_2 N501Y 64 69 RBD;S 87;77 90;78 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. The binding affinities of BoSG to the Alpha and Gamma variants (N501Y-containing strains) were approximately two-fold higher than those of UFH (Table 4). 2022 The Journal of biological chemistry Result SARS_CoV_2 N501Y 64 69 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. The binding site examined in this study was the same one previously used for the holothurian sulfated glycans in binding analyses to the wild type and the N501Y mutant S-protein RBDs. 2022 The Journal of biological chemistry Result SARS_CoV_2 N501Y 155 160 RBD;S 178;168 182;169 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. These results indicate that the BoSG derivatives have strong affinity for the RBDs that contain the N501Y mutation. 2022 The Journal of biological chemistry Result SARS_CoV_2 N501Y 100 105 RBD 78 82 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. To define the contributions of different BoSG sulfation patterns to binding with the S-protein RBD, four possible BoSG (monosulfated/monosaccharide) disaccharides were constructed and computationally docked to the binding site close to the N501Y mutation in Alpha S-protein, which had the highest affinity observed by SPR. 2022 The Journal of biological chemistry Result SARS_CoV_2 N501Y 240 245 RBD;S;S 95;85;264 98;86;265 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Alongside the breach in the spike-antibody complex caused by the E484K transformation, the effects also go further when evaluating the spike-ACE2 interaction. 2022 PeerJ Result SARS_CoV_2 E484K 65 70 S;S 28;135 33;140 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Beyond this single point mutation, the entire set of alterations on the viral RBD such as E484K, N501Y, and K417N stabilize the VOCs as epidemiologically dominant. 2022 PeerJ Result SARS_CoV_2 E484K;K417N;N501Y 90;108;97 95;113;102 RBD 78 81 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Forbye the Alpha lineage, we show the posing of the E484K and K417N, present in the Alpha and the Beta strains, taking shape into the graphs as a constant repulsive interaction amongst the spike-antibody complexes scrutinized. 2022 PeerJ Result SARS_CoV_2 E484K;K417N 52;62 57;67 S 189 194 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Moreover, in the SARS-CoV-2 RBD, the N501Y mutation is convergent in the three VOCs here evaluated. 2022 PeerJ Result SARS_CoV_2 N501Y 37 42 RBD 28 31 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. The E484K mutation jeopardized a key contact for the antibody neutralization, which could partially explain the diminishing, without terminating, immune response as studied by. 2022 PeerJ Result SARS_CoV_2 E484K 4 9 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. we highlighted the E484K mutant, which causes a change in the interaction from attractive to repulsive. 2022 PeerJ Result SARS_CoV_2 E484K 19 24 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. Notably, a total 199 out of 202 viruses (99.9%) that we sequenced carried the S_D614G and NSP12_P323L non-synonymous mutations. 2022 PeerJ Result SARS_CoV_2 D614G;P323L 80;96 85;101 Nsp12 90 95 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. The L clade is an early marker belonging to the MN908947.3 reference sequence and designated for B.56 in this study, while GR and GH clades were previously known as the G clade marked with an S_D614G change that mainly consists of several lineages in the first wave. 2022 PeerJ Result SARS_CoV_2 D614G 194 199 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. Unique changes were found in Indonesian lineages belonging to B.1.1.398 (N_G204R and N_R203K), B.1.470 (NSP_12_P227L) and B.1.466.2 (S_N439K and NSP6_L75F) lineages. 2022 PeerJ Result SARS_CoV_2 G204R;L75F;N439K;P227L;R203K 75;150;135;111;87 80;154;140;116;92 Nsp6 145 149 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. We also observed that Delta variants carried various amino acid changes that differ from the first wave, which included changes within the spike protein, namely S_T19R, S_G142D, S_E156G, S_F157del, S_R158del, S_L452R, S_T478K, and S_D950N. 2022 PeerJ Result SARS_CoV_2 F157del;R158del;D950N;E156G;G142D;L452R;T19R;T478K 188;199;233;180;171;211;163;220 196;207;238;185;176;216;167;225 S 139 144 35341060 An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. Besides, the P15 variant with the Q27STOP mutation in the B.1.1.7 lineage was found in Africa, Asia, Europe and South America with a frequency of 108, 99, 156, and 1, respectively. 2022 PeerJ Result SARS_CoV_2 Q27X 34 41 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. Conversely, the I71D and I76D mutants showed similar hIL-17RA binding activity but drastically reduced hIL-17RC binding activity compared to the WT. 2022 mBio Result SARS_CoV_2 I71D;I76D 16;25 20;29 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. Correspondingly, the L84S variant failed to induce CCL20, CXCL1, and IL6 expression, whereas the V62L and S24L variants induced detectably lower expression of CCL20, CXCL1, and IL6 compared to WT ORF8. 2022 mBio Result SARS_CoV_2 L84S;S24L;V62L 21;106;97 25;110;101 ORF8 196 200 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. Finally, PLA showed that compared to ORF8 WT, the Y42H, I71D, I76D, and E106P mutants induced marked reduction of hIL-17RA/C heterodimerization. 2022 mBio Result SARS_CoV_2 E106P;I71D;I76D;Y42H 72;56;62;50 77;60;66;54 ORF8 37 41 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. Intriguingly, when 293T cells expressing hIL-17RA or hIL-17RC were used in the binding assay, the Y42H and E106P mutants showed the complete loss of hIL-17RA binding activity but maintained hIL-17RC binding activity compared with the WT. 2022 mBio Result SARS_CoV_2 E106P;Y42H 107;98 112;102 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. PLA showed that the L84S variant, which is predicted to be located near the Y42 and E106 residues at the ORF8-IL-17RA binding interface, also induced dramatically reduced hIL-17RA/C heterodimerization compared to WT ORF8. 2022 mBio Result SARS_CoV_2 L84S 20 24 ORF8;ORF8 105;216 109;220 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. The S24L and V62L variants also showed detectable reduction of the surface binding activity to THP-1 and hIL-17RA-expressing 293T cells but minor changes of the surface binding activity to hIL-17RC-expressing 293T cells. 2022 mBio Result SARS_CoV_2 S24L;V62L 4;13 8;17 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. These results demonstrate that the L84S change, among the most frequently emerged ORF8 variations, leads to reduced hIL-17RA binding activity and thereby attenuated inflammation, suggesting a potential mechanistic explanation of mild COVID-19 symptoms of patients infected with the ORF8 L84S variant. 2022 mBio Result SARS_CoV_2 L84S;L84S 35;287 39;291 ORF8;ORF8 82;282 86;286 COVID-19 234 242 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. Three variants, S24L, V62L, and L84S, the most frequently emerged ORF8 variants in America. 2022 mBio Result SARS_CoV_2 L84S;S24L;V62L 32;16;22 36;20;26 ORF8 66 70 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. We identified four ORF8 mutants (Y42H, E106P, I71D and I76D) that showed markedly decreased binding to hIL-17R on THP1 cells. 2022 mBio Result SARS_CoV_2 E106P;I71D;I76D;Y42H 39;46;55;33 44;50;59;37 ORF8 19 23 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. When hIL-17RA-expressing or hIL-17RC-expressing 293T cells and THP-1 cells were incubated with purified the ORF8 WT or one of the L84S, V62L, and S24L variants, the L84S variant displayed the most drastic reduction of the surface binding activity to THP-1 cells and hIL-17RA-expressing 293T cells but not hIL-17RC-expressing 293T cells compared with WT ORF8. 2022 mBio Result SARS_CoV_2 L84S;L84S;S24L;V62L 130;165;146;136 134;169;150;140 ORF8;ORF8 108;353 112;357 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. 21 (75%) of 28 patients with a titre of 1/10 to 1/20 (p=0 047), 21 (49%) of 43 patients with a titre of 1/20 to 1/32 (p<0 0001), and five (11%) of 44 patients with a titre of 1/32 or more (p=0 0001) lost neutralising activity to the D614G variant at 12 months. 2022 The Lancet. Microbe Result SARS_CoV_2 D614G 233 238 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. By contrast, only 68 (48%) had neutralising antibodies against D614G, 32 (23%) had neutralising antibodies against the beta variant, and 69 (49%) had neutralising antibody responses against the delta variant (all p<0 0001; figure 4A ). 2022 The Lancet. Microbe Result SARS_CoV_2 D614G 63 68 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. Moreover, the neutralising antibody titres against the D614G and delta variants were similar (p=0 42), and both were higher than those against the beta variant (p=0 036 for D614G vs beta and p=0 0019 for delta vs beta; figure 4A). 2022 The Lancet. Microbe Result SARS_CoV_2 D614G;D614G 55;173 60;178 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. The D614G (p=0 36) and beta (p=0 82) variants escaped from neutralising antibodies against the original strain, and there were no differences between age cohorts (appendix p 19). 2022 The Lancet. Microbe Result SARS_CoV_2 D614G 4 9 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. The neutralising antibody titres were significantly lower for the D614G (median 1/5 0 [IQR 1/5 0-1/14 1]; p<0 0001), beta (1/5 0 [1/5 0-1/5 0]; p<0 0001), and delta (1/5 0 [1/5 0-1/15 8]; p<0 0001) variants than for the original strain (1/25 1 [1/12 6-1/40 0]). 2022 The Lancet. Microbe Result SARS_CoV_2 D614G 66 71 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. To establish whether plasma from recovered patients can neutralise circulating SARS-CoV-2 variants, we tested plasma from 141 recovered patients against authentic viruses of the D614G, beta, and delta variants using microneutralisation assays. 2022 The Lancet. Microbe Result SARS_CoV_2 D614G 178 183 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. Again, consistent with a second wave infection, she had higher pseudovirus neutralisation titres against the beta variant than the D614G variant (ID50 414 vs 219). 2022 BMC medicine Result SARS_CoV_2 D614G 131 136 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. Anti-Spike seropositive sera from individuals infected during the first wave were assessed for neutralisation activity against the D614G variant, while that from individuals infected in the second wave was tested against the beta variant. 2022 BMC medicine Result SARS_CoV_2 D614G 131 136 S 5 10 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. Consistent with the time of reinfection (second wave), he had higher pseudovirus neutralisation titres against the beta variant than D614G (ID50 91 vs 37). 2022 BMC medicine Result SARS_CoV_2 D614G 133 138 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. Her last visit before reinfection was day 180, at which she had low pseudovirus neutralisation activity (D614G, ID50 46, beta, ID50 < 20) and anti-Spike and anti-RBD IgG antibody levels of 669.8 BAU/ml and 778.7 BAU/ml, respectively. 2022 BMC medicine Result SARS_CoV_2 D614G 105 110 S;RBD 147;162 152;165 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. His last visit before PCR-confirmed reinfection was day 240, at which he had undetectable pseudovirus neutralisation activity (D614G, ID50 < 20, beta, ID50 < 20) and anti-Spike and anti-RBD IgG antibody levels of 5.9 BAU/ml and 0.8 BAU/ml, respectively. 2022 BMC medicine Result SARS_CoV_2 D614G 127 132 S;RBD 171;186 176;189 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. Moreover, even in those that had no pre-vaccination pseudovirus neutralisation activity against the D614G (pre-vac 29% vs. 2022 BMC medicine Result SARS_CoV_2 D614G 100 105 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. Pseudovirus neutralisation activity was increased against D614G (p = 0.0156), beta (p = 0.0078), and delta (p = 0.0156) variants. 2022 BMC medicine Result SARS_CoV_2 D614G 58 63 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. These data showed that vaccination improved pseudovirus neutralisation activity not only against the infecting variant (beta variant) but also the original D614G and delta variants. 2022 BMC medicine Result SARS_CoV_2 D614G 156 161 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. To ascertain enhanced neutralisation activity after vaccination, sera from individuals who were infected during the second wave and subsequently vaccinated was tested for pseudovirus neutralisation activity against both the D614G, beta, and delta variants. 2022 BMC medicine Result SARS_CoV_2 D614G 224 229 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. We grouped the data into three tertiles based on the antibody concentrations, low (<= 25th centile), medium (> 25th < 75th centile) and high (>= 75th centile), and then assessed the level of pseudovirus neutralisation activity against D614G in these three groups. 2022 BMC medicine Result SARS_CoV_2 D614G 235 240 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. We observed a 2-fold (p = 0.0031) and 4-fold (p < 0.0001) increase in the levels of anti-Spike and RBD IgG antibodies against the original D614G variant following vaccination, respectively. 2022 BMC medicine Result SARS_CoV_2 D614G 139 144 S;RBD 89;99 94;102 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. We tested reactivity against D614G, alpha, beta, gamma, and delta variants in pre-vaccination and post-vaccination serum. 2022 BMC medicine Result SARS_CoV_2 D614G 29 34 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. We tested the longevity of the neutralising activity in convalescent serum using a pseudovirus neutralising assay against the original D614G variant and the beta variant. 2022 BMC medicine Result SARS_CoV_2 D614G 135 140 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. 2A, B and C) were 75.3 C (target: G22578A mutation), 72.7 C (target: T22917G mutation) and 73.2 C (target: G23948T mutation). 2022 Biochemical and biophysical research communications Result SARS_CoV_2 G22578A;G23948T;T22917G 35;110;71 42;117;78 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. 2A, B and C) were 75.5 C (target: G22578A mutation), 73.2 C (target: T22917G mutation) and 73.7 C (target: G23948T mutation). 2022 Biochemical and biophysical research communications Result SARS_CoV_2 G22578A;G23948T;T22917G 35;110;71 42;117;78 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. Additionally, the Tm value (73.3 C) of the RBD Delta variant to detect the L452R variation (T22917G mutation) was distinct from the others (72.8-72.9 C). 2022 Biochemical and biophysical research communications Result SARS_CoV_2 L452R;T22917G 76;93 81;100 RBD 44 47 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. For the detection of mutation T22917G, HRM curves derived from O1 specimens were similar to HRM curves of wt Isolate Wuhan-Hu-1 RBD and Omicron variant RBD. 2022 Biochemical and biophysical research communications Result SARS_CoV_2 T22917G 30 37 RBD;RBD 128;152 131;155 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. For the detection of the mutation T22917G, there were no significant differences in the HRM curve between the Omicron variant RBD and the other variants, except for the Delta variant RBD. 2022 Biochemical and biophysical research communications Result SARS_CoV_2 T22917G 34 41 RBD;RBD 126;183 129;186 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. In the detection of mutations G22578A and G23948T. 2022 Biochemical and biophysical research communications Result SARS_CoV_2 G22578A;G23948T 30;42 37;49 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. Normalized HRM curves for cDNA fragments of the Omicron variant RBD showed significant differences from the other curves for the detection of mutations G22578A and G23948T. 2022 Biochemical and biophysical research communications Result SARS_CoV_2 G22578A;G23948T 152;164 159;171 RBD 64 67 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. The Tm values of the amplicon from the Omicron variant RBD were 75.1 and 73.3 C in HRM analyses designed to target G339D and D796Y variations (G22578A and G23948T mutations), as shown in Table 1. 2022 Biochemical and biophysical research communications Result SARS_CoV_2 D796Y;G23948T;G339D;G22578A 126;156;116;144 131;163;121;151 RBD 55 58 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. Besides the Omicron variant; the Beta strain, Beta+R346K, and the Gamma strain exhibited resistance to casirivimab; however, imdevimab retained efficacy to these strains, excluding the Omicron variant, as shown in Figure 3C. 2022 Future microbiology Result SARS_CoV_2 R346K 51 56 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. Furthermore, none of the additional mutations K417N and R346K to the Delta variant altered its NT50 values. 2022 Future microbiology Result SARS_CoV_2 K417N;R346K 46;56 51;61 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. On the contrary, no substantial decrease in neutralization antibody titer was observed for Mu+K417N as compared with the original Mu strain. 2022 Future microbiology Result SARS_CoV_2 K417N 94 99 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. Since Beta+R346K and Mu+K417N share the same haplotype within the RBD of the spike protein, the authors expected that the neutralization antibody titer would substantially drop for Mu+K417N. 2022 Future microbiology Result SARS_CoV_2 K417N;K417N;R346K 24;184;11 29;189;16 S;RBD 77;66 82;69 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. The Beta, the Delta with spike protein mutations R346K and K417N (Delta+R346K+K417N) and the Mu were considered partially immunity-escaping with NT50 values of 38, 113 and 46, respectively. 2022 Future microbiology Result SARS_CoV_2 K417N;R346K;K417N;R346K 59;49;78;72 64;54;83;77 S 25 30 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. The contribution of R346K mutation was more apparent in the positive rate of neutralizing antibodies in vaccinated sera, as shown in Figure 3B. 2022 Future microbiology Result SARS_CoV_2 R346K 20 25 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. The NT50 of the Beta+R346K strain was found to be substantially lower than any strains found prior to Omicron variant, as shown in Figure 3A. 2022 Future microbiology Result SARS_CoV_2 R346K 21 26 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. The NT50 value of the Beta+R346K was much lower, with a value of 29, indicating that infection with this variant can occur even when vaccination effectiveness is at its prime. 2022 Future microbiology Result SARS_CoV_2 R346K 27 32 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. While R346K mutation barely contributed to the Mu or the Delta variant, a notable difference was observed for the Beta variant. 2022 Future microbiology Result SARS_CoV_2 R346K 6 11 35355624 Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. Along with these attractive interactions, it was confirmed that the binding energy including both statistical correction and desolvation (SC+Desolv) of the ACE2 with the mutant S-protein (N501Y) was further strengthened by ca. 2021 Chemical science Result SARS_CoV_2 N501Y 188 193 S 177 178 35355624 Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. analyzed the complex between the SARS-CoV-2 S-protein of the N501Y variant and a neutralizing antibody by cryo-electron microscopy (not yet published at February 7, 2021). 2021 Chemical science Result SARS_CoV_2 N501Y 61 66 S 44 45 35355624 Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. Currently, the highly transmissible variants of the United Kingdom (N501Y) and South Africa (N501Y, E484K, and K417N) are prevalent in various regions. 2021 Chemical science Result SARS_CoV_2 E484K;K417N;N501Y;N501Y 100;111;68;93 105;116;73;98 35355624 Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. Here, we investigated a mutation N501Y of RBD in common between S-protein variants of the United Kingdom and South Africa to understand the mutation effect by using modeling structure (FMODB ID: 7J11K), as seen in Section S7. 2021 Chemical science Result SARS_CoV_2 N501Y 33 38 RBD;S 42;64 45;65 35355624 Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. It was confirmed that the N501Y mutation of the S-protein attractively enhances the DI energy of Y41ACE2 on the peptide motif (E37-Q42), which was essential for recognizing the S-protein, as proposed by Larue et al. 2021 Chemical science Result SARS_CoV_2 N501Y 26 31 S;S 48;177 49;178 35355624 Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. Mutation effect of the SARS-CoV-2 S-protein (N501Y) 2021 Chemical science Result SARS_CoV_2 N501Y 45 50 S 34 35 35355624 Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. Mutation effect of the SARS-CoV-2 S-protein (N501Y). 2021 Chemical science Result SARS_CoV_2 N501Y 45 50 S 34 35 35355624 Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. S7 ), the N501Y mutation of the S-protein enhanced the attractive interaction because of the hydrogen bond and the XH/pi interactions with Y41ACE2 and K353ACE2 more than a wild type of the S-protein. 2021 Chemical science Result SARS_CoV_2 N501Y 10 15 S;S 32;189 33;190 35355624 Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. The complex structure of the mutant N501Y of the S-protein, similar to the variants that were first recognized in the United Kingdom and South Africa, had not yet been published as of February 1, 2021. 2021 Chemical science Result SARS_CoV_2 N501Y 36 41 S 49 50 35355624 Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. Their results are in good agreement with our FMO results using the modeling structure of the complex between the S-protein of the N501Y variant and the ACE2. 2021 Chemical science Result SARS_CoV_2 N501Y 130 135 S 113 114 35355624 Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. These FMO results may explain one of the reasons for the high infectivity of the mutant (N501Y). 2021 Chemical science Result SARS_CoV_2 N501Y;N501Y 90;89 94;94 35355624 Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. Thus, the IFIE and binding energy between the N501Y S-protein and the ACE2 were investigated with the aid of computer modeling, as seen in Section S7. 2021 Chemical science Result SARS_CoV_2 N501Y 46 51 S 52 53 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. Count of mutations in the spike was followed by RNA dependent RNA polymerase (rdrp) (n = 4,142) constituting A1892T, I189V, P314L, K38R, T492I, V57V in all omicron genomes analyzed (figure 3 and table 3). 2022 Virus research Result SARS_CoV_2 A1892T;I189V;K38R;P314L;T492I;V57V 109;117;131;124;137;144 115;122;135;129;142;148 RdRp;S;RdRP 48;26;78 76;31;82 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. Remaining 2903 mutations were detected in rest of the coding genomic region (table 2 , 3 , and supplementary table 1), where M19M in ORF6, and RG203KR in nucleocapsid protein are amongst the most prevalent mutations in omicron (figure 3). 2022 Virus research Result SARS_CoV_2 M19M 125 129 N;ORF6 154;133 166;137 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. The majority of spike protein mutations encompass A67, T547K, D614G, H655Y, N679K, P681H, D796Y, N856K, Q954H, which are reported in all the omicron genomes analysed (table 3). 2022 Virus research Result SARS_CoV_2 D614G;D796Y;H655Y;N679K;N856K;P681H;Q954H;T547K 62;90;69;76;97;83;104;55 67;95;74;81;102;88;109;60 S 16 21 35369437 Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China. To other sequences except 200327-84, 200328-142 and 200328-143, the D614G amino acid change in the S protein occurred by an A23403G nucleotide mutation, which confirmed to be associated with greater infectivity (Figure 2B). 2022 Frontiers in microbiology Result SARS_CoV_2 A23403G;D614G 124;68 131;73 S 99 100 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. As shown in Figure 6, ATV inhibited significantly the SARS-CoV-2 D614G strain in Caco-2 at 7.8 muM (52.7%, p = 0.03), by pre-post treatment (EC50 = 7.4 muM, SI = 8.7). 2022 Frontiers in microbiology Result SARS_CoV_2 D614G 65 70 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. ATV Exhibited Antiviral Effects Against SARS-CoV-2 D614G Strain in a Dose-Dependent Manner. 2022 Frontiers in microbiology Result SARS_CoV_2 D614G 51 56 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. ATV Inhibited D614G Strain Through Post-infection Treatment. 2022 Frontiers in microbiology Result SARS_CoV_2 D614G 14 19 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. ATV inhibited the D614G strain RNA at 31.2 muM (30.17%, p = 0.03) and 15.6 muM (84.8%, p = 0.03; Figure 4). 2022 Frontiers in microbiology Result SARS_CoV_2 D614G 18 23 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. ATV showed inhibition percentages for D614G strain of 79% (p = 0.002), 54.8% (p = 0.002), 22.6% (p = 0.04), and 25% (p = 0.03) at 31.2, 15.6, 7.8, and 3.9 muM concentrations, respectively (Figure 2). 2022 Frontiers in microbiology Result SARS_CoV_2 D614G 38 43 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. By pre-infection treatment, Heparin inhibited SARS-CoV-2 D614G strain at 100 mug/ml (80.6%, p = 0.028), 50 mug/ml (82.9%, p = 0.028), 25 mug/ml (87.3%, p = 0.028), and 12.5 mug/ml (79.9%, p = 0.028; Supplementary Figure 1B). 2022 Frontiers in microbiology Result SARS_CoV_2 D614G 57 62 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. Chloroquine (positive inhibition control) exhibited antiviral activity against D614G strain at 100 muM (100%, p = 0.002), 50 muM (99.9%, p = 0.002), 25 muM (97.5%, p = 0.002), and 12.5 muM (55.7%, p = 0.002; Supplementary Figure 1A). 2022 Frontiers in microbiology Result SARS_CoV_2 D614G 79 84 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. Considering that ATV showed inhibition against the D614G strain, this compound was evaluated against the SARS-CoV-2 Delta and Mu variants in Vero E6 cells. 2022 Frontiers in microbiology Result SARS_CoV_2 D614G 51 56 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. In comparison, as shown in Figures 3D-F, the viral titer of D614G strain was significantly reduced through post-infection treatment with ATV at all evaluated concentrations. 2022 Frontiers in microbiology Result SARS_CoV_2 D614G 60 65 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. On the other hand, as shown in Supplementary Figure 1C, CQ significantly inhibited D614G strain at 100, 50, 25, and 12.5 muM, with inhibition percentages of 99.2% (p = 0.009), 98.3% (p = 0.009), 74.8% (p = 0.009), and 23.6% (p = 0.033), respectively, by post-infection treatment (EC50 = 12.8, SI > 7.8). 2022 Frontiers in microbiology Result SARS_CoV_2 D614G 83 88 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. Once an antiviral effect against the SARS-CoV-2 D614G strain was observed by pre-post treatment in Vero E6, the pre-infection and post-infection treatments were done separately to infer the step of the viral replicative cycle affected by the ATV treatment. 2022 Frontiers in microbiology Result SARS_CoV_2 D614G 48 53 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. To evaluate the antiviral activity of ATV against the SARS-CoV-2 D614G strain, a pre-post treatment strategy was performed on Vero E6 cells. 2022 Frontiers in microbiology Result SARS_CoV_2 D614G 65 70 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. A few RBD variants have already shown to affect the vaccine efficacy as documented earlier by wet lab and dry lab results (S2 Table), however, the vaccine efficacy against the B.1.617 and K417G variants is yet to be elucidated. 2022 Indian journal of medical microbiology Result SARS_CoV_2 K417G 188 193 RBD 6 9 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. Our in-silico study suggests that the B.1.617 and K417G variants may affect vaccine efficacy. 2022 Indian journal of medical microbiology Result SARS_CoV_2 K417G 50 55 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. Out of seven variants, B.1.617 (B.1.617 G (p.D614G) variant in the European population may cause antigenic drift, resulting in vaccine mismatches that offer little protection to that group of patients. 2020 Pathogens (Basel, Switzerland) Conclusion SARS_CoV_2 A23403G;D614G;D614G 21;31;33 29;38;38 32742818 RdRp mutations are associated with SARS-CoV-2 genome evolution. Our study sheds light on the effects RdRp mutations, particularly 14408C>T mutation, on the mutability and possibly transmissibility of SARS-CoV-2. 2020 PeerJ Conclusion SARS_CoV_2 C14408T 66 74 RdRP 37 41 32818213 Characterizing SARS-CoV-2 mutations in the United States. We found that one of the top mutations, 27964C>T- (S24L on ORF8), has an unusually strong gender dependence. 2020 Research square Conclusion SARS_CoV_2 C27964T;S24L 40;51 48;55 ORF8 59 63 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). The D48E variant (from sample EPI_ISL_425242) leads to a novel "TSEEMLN" motif at the substrate binding flap, which may have repercussions on the efficiency and specificity of substrate binding. 2020 Journal of chemical information and modeling Conclusion SARS_CoV_2 D48E 4 8 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. SARS-CoV-2 strain with both RdRp 14408 C> T and S 23403 A>G mutations, which became dominant in Europe and US first, differed and continued accumulating both synonymous and non-synonymous mutations after Day 100, particularly in the S and Orf1a genes. 2020 PeerJ Conclusion SARS_CoV_2 C14408T;A23403G;S23403A;S23403G 33;48;48;48 43;59;59;59 ORF1a;RdRP;S;S 239;28;48;233 244;32;49;234 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. Mutation R408I in spike protein of Indian strain has significant influence on RBD domain of spike protein and this point mutation has a stabilization effect on the spike protein. 2020 PloS one Conclusion SARS_CoV_2 R408I 9 14 S;S;S;RBD 18;92;164;78 23;97;169;81 32933378 Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach. Sequence analysis revealed that about 70.42% (Ugurel et al.,) of Nsp12 sequences bear conserved P323L mutation in the cleft where Nsp8 binds. 2022 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 P323L 96 101 Nsp12;Nsp8 65;130 70;134 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. Amino acid changes were found in the S and N proteins of SARS-CoV-2 circulating in South America, the most frequent being D614G in S and R203K-G204R and I292T in N. 2020 Infection, genetics and evolution Conclusion SARS_CoV_2 D614G;I292T;R203K;G204R 122;153;137;143 127;158;142;148 N;N;S;S 43;162;37;131 44;163;38;132 32980406 Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13). These mutations (P504L and Y541C) caused important exchanges in functional domain 2A of Nsp13 (helicase), a critical enzyme in the life cycle of the virus. 2020 International journal of biological macromolecules Conclusion SARS_CoV_2 Y541C;P504L 27;17 32;22 Helicase;Nsp13 95;88 103;93 32989130 Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation. The "mutant spike" is thus devoid of the unique character that would be otherwise endowed by the polybasic insert P681RRA and adjacent cleavage site R685S, and the high reactivity of R682RAR685 may have eluded these studies. 2020 Proc Natl Acad Sci U S A Conclusion SARS_CoV_2 R685S 149 154 S 12 17 32989130 Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation. We show that the mutation D839Y found in a European strain of SARS-CoV-2 enhances the binding affinity of the SAg motif to the TCR. 2020 Proc Natl Acad Sci U S A Conclusion SARS_CoV_2 D839Y 26 31 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. Combined genetic, structural, and epidemiological data suggest that the D614G switch may cause increased prevalence of chemosensory deficits as observed during the pandemic progression from East Asia to Western countries. 2020 ACS chemical neuroscience Conclusion SARS_CoV_2 D614G 72 77 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. The spike protein mutation D614G became dominant in the SARS-CoV-2 virus during the COVID-19 pandemic. 2020 ACS chemical neuroscience Conclusion SARS_CoV_2 D614G 27 32 S 4 9 COVID-19 84 92 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. To gain more insights, future studies will need to examine the binding and the entry of D614G SARS-CoV-2 variants as well as SARS-CoV-1/NL63 specifically in ACE2-expressing cells of the olfactory epithelium such as sustentacular cells. 2020 ACS chemical neuroscience Conclusion SARS_CoV_2 D614G 88 93 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. The dominant pandemic viral variation, D614G, can stabilize the entire S protein. 2021 Briefings in bioinformatics Conclusion SARS_CoV_2 D614G 39 44 S 71 72 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. We analyzed 384 viral variations and identified that D614G in 5703 virus strains can stabilize SARS-Cov-2 entire S protein. 2021 Briefings in bioinformatics Conclusion SARS_CoV_2 D614G 53 58 S 113 114 33140034 Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein. Simulations of the N165A/N234A and of N234A mutants of the S protein highlight their critical structural role in stabilizing the RBD "up" conformation. 2020 ACS central science Conclusion SARS_CoV_2 N165A;N234A;N234A 19;38;25 24;43;30 RBD;S 129;59 132;60 33140034 Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein. To confirm our simulation results, biolayer interferometry experiments conducted on N165A and N234A variants show a reduced ACE2 binding when these glycans are removed, revealing an RBD conformational shift toward the "down" state, with a larger effect for N234A. 2020 ACS central science Conclusion SARS_CoV_2 N165A;N234A;N234A 84;94;257 89;99;262 RBD 182 185 33252670 SARS-CoV-2 Among Military and Civilian Patients, Metro Manila, Philippines. In this study, we found the D614G mutation in the majority of the sequences from specimens collected from the end of June 2020. 2021 Military medicine Conclusion SARS_CoV_2 D614G 28 33 33252670 SARS-CoV-2 Among Military and Civilian Patients, Metro Manila, Philippines. Sequencing results showed the presence of the D614G mutation in the spike protein in the majority of specimens collected from the end of June to July 2020, and this finding was associated with a sharp increase of SARS-CoV-2 cases seen at VLMC and in the entire Philippines starting July 2020. 2021 Military medicine Conclusion SARS_CoV_2 D614G 46 51 S 68 73 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Comparisons of selection sites reveal three RBM population variants G476S, V483A, and S494P that are in close contact with the ACE2 binding region. 2021 Biochemical and biophysical research communications Conclusion SARS_CoV_2 G476S;S494P;V483A 68;86;75 73;91;80 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. In V367F, the reorientation of Lys31 facilitates two additional hydrogen bonds formation which enhances its binding free energy contribution. 2021 Biochemical and biophysical research communications Conclusion SARS_CoV_2 V367F 3 8 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Interestingly, the V367F and S494P population variants display a higher binding affinity towards human ACE2. 2021 Biochemical and biophysical research communications Conclusion SARS_CoV_2 S494P;V367F 29;19 34;24 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. The enhanced binding affinity of S494P is attributed to strong interfacial complementarity during ACE2 recognition, while the V367F variant interacts with the ACE2 mediated by a higher number of hydrogen bonds. 2021 Biochemical and biophysical research communications Conclusion SARS_CoV_2 S494P;V367F 33;126 38;131 33330626 Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM. DeltaDeltaGbind for mutants, I40A, V104A, and R86A are comparatively high, suggesting the significance of these residues. 2020 Frontiers in molecular biosciences Conclusion SARS_CoV_2 I40A;R86A;V104A 29;46;35 33;50;40 33330626 Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM. The CAS study reveals that residues I40A, V104A, R86A, V78A, V44A, M247A, and Q87A of nsp16 were considered as hot spot residues for the association of nsp16-nsp10. 2020 Frontiers in molecular biosciences Conclusion SARS_CoV_2 I40A;M247A;Q87A;R86A;V104A;V44A;V78A 36;67;78;49;42;61;55 40;72;82;53;47;65;59 33336251 Multisystem Inflammatory Syndrome in Children in February 2020 and Implications of Genomic Sequencing for SARS-CoV-2. The assembled genome was consistent with Global Initiative on Sharing Avian Influenza Data (GISAID) clade GR (D614G and N-G204R) and has been deposited on GISAID (EPI ISL 644823). 2021 Journal of the Pediatric Infectious Diseases Society Conclusion SARS_CoV_2 D614G;G204R 110;122 115;127 N 120 121 33385461 Development of new vaccine target against SARS-CoV2 using envelope (E) protein: An evolutionary, molecular modeling and docking based study. Through an evolutionary analysis of SARS-CoV-2 E-protein, four novel mutations (T55S, V56F, E69R and G70del) were observed to occur in E-protein of SARS-CoV-2 when compared to the consensus E-protein of other related viruses. 2021 International journal of biological macromolecules Conclusion SARS_CoV_2 E69R;G70del;V56F;T55S 92;101;86;80 96;107;90;84 E;E;E 47;135;190 48;136;191 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. Further study with a larger sample size is necessary to investigate whether the dominating SARS-CoV-2 bearing the D614G mutation is due to a positive selection or a founder effect or some other mechanism and to explore the role of the D614G mutation in the pathogenesis and virulence of SARS-CoV-2. 2020 PeerJ Conclusion SARS_CoV_2 D614G;D614G 114;235 119;240 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. SARS-CoV-2 with the D614G mutation appears to become the major circulating virus in Indonesia, which is concurrent with the COVID-19 situation worldwide. 2020 PeerJ Conclusion SARS_CoV_2 D614G 20 25 COVID-19 124 132 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. Altogether, higher infectivity of D614G might be related to these structural changes, however, further studies are granted. 2021 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 D614G 34 39 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. In the present study, using bioinformatics tools, we showed that the D614G mutation causes extensive structural changes in the mutation region of spike protein. 2021 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 D614G 69 74 S 146 151 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. RMSF, SASA, energy content, immunogenicity values of mutant have decreased in comparison to wild type while Rg value of it has increased and it could be interfered (at least partially) that local and overall structural stability of D614G has increased. 2021 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 D614G 232 237 33475020 Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. The experimental stability analysis, binding pattern, and immunogenicity assay studies of D614G might be of great interest to follow to learn in depth about function, feature, and unclear aspects of this more pathogenic mutant of COVID-19 for finding a specific treatment against it in the next future. 2021 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 D614G 90 95 COVID-19 230 238 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. In the current study, we demonstrated that the D614G variant of SARS-CoV-2 appears to be taking over COVID-19 epidemic in the MENA, similar to what have been reported in other regions around the globe. 2021 Heliyon Conclusion SARS_CoV_2 D614G 47 52 COVID-19 101 109 33498225 Biological and Clinical Consequences of Integrin Binding via a Rogue RGD Motif in the SARS CoV-2 Spike Protein. The emergence of the highly infectious variant, B.1.1.7 (or VUI 202012/01), which includes a receptor-binding domain amino acid replacement, N501Y, directly adjacent to the RGD motif, highlights the possibility that further viral evolution could generate variants with enhanced virion-integrin interactions and expanded biological and clinical impact. 2021 Viruses Conclusion SARS_CoV_2 N501Y 141 146 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. However, D614G might change the viral conformational plasticity and hence a potential viral fitness gain. 2021 Biochemistry and biophysics reports Conclusion SARS_CoV_2 D614G 9 14 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. However, the highest mutation frequency in our study, with 62% of samples, showed aspartate substitution to glycine at D614G is consistent with other reports for samples collected in Europe at the same time of our sample collection, in March 2020. 2021 Biochemistry and biophysics reports Conclusion SARS_CoV_2 D614G 119 124 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. In this study, the mutation D614G was the dominant local mutation in Jordan. 2021 Biochemistry and biophysics reports Conclusion SARS_CoV_2 D614G 28 33 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. We expected that the four reported amino acid variants, especially tyrosine deletion at Y144 located in the SARS-CoV-like_Spike_S1_NTD and the aspartate substitution to glycine at D614G located in the SARS-CoV-2_Spike_S1_RBD to have an expliciteffect on the function of the spike protein in the Jordanian population collectively. 2021 Biochemistry and biophysics reports Conclusion SARS_CoV_2 D614G 180 185 S 274 279 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. Thus, the CRISPR-Cas13-based amplification strategy was accommodated to profile the clinically significant mutation, D614G, of SARS-CoV-2 variants. 2021 Analytical chemistry Conclusion SARS_CoV_2 D614G 117 122 33530355 One Year of SARS-CoV-2: How Much Has the Virus Changed? The first period was critical for some previously described mutations that overtook the entire globe, such as the D614G and P323L in the Spike and NSP12, respectively. 2021 Biology Conclusion SARS_CoV_2 D614G;P323L 114;124 119;129 S;Nsp12 137;147 142;152 33532796 The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. However, human sera with high neutralization titers against the USA-WA1/2020 strain were still able to neutralize the E484K rSARS-CoV-2. 2021 medRxiv Conclusion SARS_CoV_2 E484K 118 123 33532796 The E484K mutation in the SARS-CoV-2 spike protein reduces but does not abolish neutralizing activity of human convalescent and post-vaccination sera. These data indicate that the E484K mutation present in circulating SARS-CoV-2 strains that belong to the B.1.351 and P.1 lineages reduces the neutralizing activity of human polyclonal sera induced in convalescent (infected with previous strains) and vaccinated individuals. 2021 medRxiv Conclusion SARS_CoV_2 E484K 29 34 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. An additional neutrophil elastase cleavage site in Spike protein of SARS-CoV-2 was introduced by D614G mutation. 2021 Infection, genetics and evolution Conclusion SARS_CoV_2 D614G 97 102 S 51 56 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Alternatively, 4 distinct mutations have potential to change relative solvent accessibility: L37H, L37R, D72Y and L73F. 2021 Scientific reports Conclusion SARS_CoV_2 D72Y;L37H;L37R;L73F 105;93;99;114 109;97;103;118 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Alternatively, 6 mutations have the solvent accessibility change potential: N113B, P123L, P132S, H155Y, D190N and T208I. 2021 Scientific reports Conclusion SARS_CoV_2 D190N;H155Y;P123L;P132S;T208I 104;97;83;90;114 109;102;88;95;119 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Alternatively, mutations H146Y (24 cases), V483A (11 cases), E554D (14 cases), P681L (16 cases) and S939F (11 cases) all occur only in USA or mutation L8V (4 cases) occurs only in Hong Kong (refer to the spreadsheet data, which can be found in the Data Availability section). 2021 Scientific reports Conclusion SARS_CoV_2 E554D;H146Y;L8V;P681L;S939F;V483A 61;25;151;79;100;43 66;30;154;84;105;48 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Alternatively, the mutation Y453F occurs in 5 sequences all in Netherlands but the first collected date was on 2020-04-25 and the latest collected date was on 2020-04-29. 2021 Scientific reports Conclusion SARS_CoV_2 Y453F 28 33 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Among the nonsynonymous mutations, mutation D614G is extremely common as it happens in 3089 sequences, majorly collected in USA (2340), India (210) and Australia (132). 2021 Scientific reports Conclusion SARS_CoV_2 D614G 44 49 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Among these, 10 mutations are likely to make changes in protein secondary structure: C64F, A69S, A69V, V70F, N113B, R158L, V170I, D190N, D209Y and S214I. 2021 Scientific reports Conclusion SARS_CoV_2 A69S;A69V;C64F;D190N;D209Y;R158L;S214I;V170I;V70F 91;97;85;130;137;116;147;123;103 95;101;89;135;142;121;152;128;107 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Distinct nonsynonymous mutations (10 of them) include F19L, F28Y, F30L, S31L, L32F, T40I, C41F, C41S, H42Y and A43T. 2021 Scientific reports Conclusion SARS_CoV_2 A43T;C41F;C41S;F19L;F28Y;F30L;H42Y;L32F;S31L;T40I 111;90;96;54;60;66;102;78;72;84 115;94;100;58;64;70;106;82;76;88 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Five distinct nonsynonymous mutations in gene E have protein structure change potential: S68C, S68F, P71L, D72Y and L73F. 2021 Scientific reports Conclusion SARS_CoV_2 D72Y;L73F;P71L;S68C;S68F 107;116;101;89;95 111;120;105;93;99 E 46 47 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). In the RBD region, S477G [CBCTT(S)CCCCC CBCTT(S)CCCEC], P479L [CTTSC(C)CCCCC CTTSC(C)CECCC], V483A [CCCCC(C)CTTTC CCCCC(C)CCTTC], and F486L [CCCCT(T)TCBCS CCCEC(T)TCBCS] are four mutations having protein structure change potential. 2021 Scientific reports Conclusion SARS_CoV_2 F486L;P479L;S477G;V483A 134;56;19;93 139;61;24;98 RBD 7 10 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). It is however important to note that the first patient having the D614G mutation and his/her location may never be known because genome of that patient might not be sequenced and reported. 2021 Scientific reports Conclusion SARS_CoV_2 D614G 66 71 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Likewise, the mutation G476S occurs in 6 isolates all collected in USA: WA from 2020-03-10 to 2020-03-25. 2021 Scientific reports Conclusion SARS_CoV_2 G476S 23 28 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Mutation H146Y occurs in 24 cases and mutation P681L occurs in 16 cases, which are all collected in USA. 2021 Scientific reports Conclusion SARS_CoV_2 H146Y;P681L 9;47 14;52 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). N113B and D190N are thus two mutations having potential to change both protein structure and solvent accessibility in gene M. 2021 Scientific reports Conclusion SARS_CoV_2 D190N 10 15 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Notable mutation in this gene is L84S, which occurs in 1000 sequences with the first case collected at the beginning of the pandemic in China: Wuhan on 2019-12-30 and the latest case in Australia: Victoria on 2020-05-27. 2021 Scientific reports Conclusion SARS_CoV_2 L84S 33 37 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Notable mutation in this region is V483A occurring in 11 isolates all collected in USA. 2021 Scientific reports Conclusion SARS_CoV_2 V483A 35 40 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Notable mutations are P4715L occurring in 2576 sequences and T265I occurring in 1344 sequences. 2021 Scientific reports Conclusion SARS_CoV_2 P4715L;T265I 22;61 28;66 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Notable mutations are R203K occurring in 871 sequences and G204R occurring in 433 sequences. 2021 Scientific reports Conclusion SARS_CoV_2 G204R;R203K 59;22 64;27 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Notably, the mutation Q57H occurs in 2795 sequences collected in many countries. 2021 Scientific reports Conclusion SARS_CoV_2 Q57H 22 26 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Note that the difference of these ratios is partly due to the large number of D614G mutations (3089), which is outside the RBD region. 2021 Scientific reports Conclusion SARS_CoV_2 D614G 78 83 RBD 123 126 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Of these, only three mutations are in the RBD region: V483A [eebbb(b)bebeb eebbb(b)bbbeb], G485R [bbbbb(e)bebee bbbbb(b)bebee], and F486L [bbbbe(b)ebeeb bbbbb(e)ebeeb]. 2021 Scientific reports Conclusion SARS_CoV_2 F486L;G485R;V483A 132;91;54 137;96;59 RBD 42 45 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). On the other hand, there are 37 A829T mutations that all occur in Thailand. 2021 Scientific reports Conclusion SARS_CoV_2 A829T 32 37 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). The current data show that either of the following sequences, which have the D614G mutation, was first collected: MT326173 in USA in 2020, or MT270104, MT270105, MT270108 and MT270109 all in Germany: Bavaria in 2020-01, or MT503006 in Thailand on 2020-01-04. 2021 Scientific reports Conclusion SARS_CoV_2 D614G 77 82 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). The first and latest collected dates of these isolates were respectively 2020-03-05 and 2020-04-05, suggesting that the first isolate may have spread to others having the same mutation V483A. 2021 Scientific reports Conclusion SARS_CoV_2 V483A 185 190 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). The first collected date of the D614G mutation cannot be identified precisely because some sequences deposited to the NCBI GenBank did not record the full date details. 2021 Scientific reports Conclusion SARS_CoV_2 D614G 32 37 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). The most common mutation D614G does not have the potential to change either protein secondary structure or relative solvent accessibility. 2021 Scientific reports Conclusion SARS_CoV_2 D614G 25 30 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). The mutation D614G in protein S is unlikely to change either protein secondary structure or relative solvent accessibility based on the prediction results. 2021 Scientific reports Conclusion SARS_CoV_2 D614G 13 18 S 30 31 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). The mutation G251V occurring in 206 sequences is also a prevalent mutation in the ORF3a protein. 2021 Scientific reports Conclusion SARS_CoV_2 G251V 13 18 ORF3a 82 87 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). There are 15 mutations in this protein having the potential to change both protein structure and solvent accessibility, including G18V, D22Y, G34W, R40C, R40L, R185C, A211S, P365H, T391I, T393I, A398S, D399E, D399H, D401Y and D402Y. 2021 Scientific reports Conclusion SARS_CoV_2 A211S;A398S;D22Y;D399E;D399H;D401Y;D402Y;G18V;G34W;P365H;R185C;R40C;R40L;T391I;T393I 167;195;136;202;209;216;226;130;142;174;160;148;154;181;188 172;200;140;207;214;221;231;134;146;179;165;152;158;186;193 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). There are 8 distinct nonsynonymous mutations, including I4L, A8V, S23F, R24L, R24C, A28V, D31Y and V33I. 2021 Scientific reports Conclusion SARS_CoV_2 A28V;A8V;D31Y;I4L;R24C;R24L;S23F;V33I 84;61;90;56;78;72;66;99 88;64;94;59;82;76;70;103 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Therefore, D72Y and L73F are two mutations in gene E that have a potential to change both protein structure and solvent accessibility. 2021 Scientific reports Conclusion SARS_CoV_2 D72Y;L73F 11;20 15;24 E 51 52 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). These dates are too close, indicating that all the reported Y453F cases may have been infected from another case, whose genome had not been sequenced and reported to the NCBI GenBank. 2021 Scientific reports Conclusion SARS_CoV_2 Y453F 60 65 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). This may indicate that the first case had probably transmitted to other cases having the same mutation A829T in Thailand. 2021 Scientific reports Conclusion SARS_CoV_2 A829T 103 108 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Two mutations V483A and F486L are thus likely to make changes in both protein secondary structure and relative solvent accessibility in the RBD region. 2021 Scientific reports Conclusion SARS_CoV_2 F486L;V483A 24;14 29;19 RBD 140 143 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Comparisons of selection sites reveal three RBM population variants G476S, V483A, and S494P that are in close contact with the ACE2 binding region. 2021 Biochemical and biophysical research communications Conclusion SARS_CoV_2 G476S;S494P;V483A 68;86;75 73;91;80 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. In V367F, the reorientation of Lys31 facilitates two additional hydrogen bonds formation which enhances its binding free energy contribution. 2021 Biochemical and biophysical research communications Conclusion SARS_CoV_2 V367F 3 8 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Interestingly, the V367F and S494P population variants display a higher binding affinity towards human ACE2. 2021 Biochemical and biophysical research communications Conclusion SARS_CoV_2 S494P;V367F 29;19 34;24 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. The enhanced binding affinity of S494P is attributed to strong interfacial complementarity during ACE2 recognition, while the V367F variant interacts with the ACE2 mediated by a higher number of hydrogen bonds. 2021 Biochemical and biophysical research communications Conclusion SARS_CoV_2 S494P;V367F 33;126 38;131 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. Notably, presence of D614G mutation in the S gene was found in all the isolates. 2020 Frontiers in genetics Conclusion SARS_CoV_2 D614G 21 26 S 43 44 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. The impact of the mutation E484K is still not fully understood; however, its strong association with escaping neutralizing antibodies highlights the necessity for development studies to better establish mechanisms of viral infection. 2021 Virus research Conclusion SARS_CoV_2 E484K 27 32 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. The present work demonstrates a pervasive spread of B.1.1.28 (E484K), the possibility of occurrences of co-infection events and emergence of a novel SARS-CoV-2 lineage (VUI-NP13L) across the state of Rio Grande do Sul. 2021 Virus research Conclusion SARS_CoV_2 E484K 62 67 33634309 A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. Recent solution of S protein trimer structure with LA bound shows that monomer-monomer packing and interactions adjacent to the D398-R355 pair are structurally coupled to those around D614, as well as the environment of A570 (relevant to the B.1.1.7 variant of SARS-CoV-2 that carries the A570D mutation). 2021 Briefings in bioinformatics Conclusion SARS_CoV_2 A570D 289 294 S 19 20 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. A better understanding of the molecular basis of the evolutionary differences between these two genes/gene regions and the rest of the genome, as well as the effects of S D614G and RdRp P323L mutations, could lead to more effective strategies in combating COVID-19. 2021 Infection, genetics and evolution Conclusion SARS_CoV_2 D614G;P323L 171;186 176;191 RdRP;S 181;169 185;170 COVID-19 256 264 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. This hypothesis is supported by the recent observation of a new ORF8-deficient lineage (Q18 stop) in a lymphoma patient with long-term COVID-19, also associated with several spike mutations. 2021 Biochemical and biophysical research communications Conclusion SARS_CoV_2 Q18X 88 96 S;ORF8 174;64 179;68 COVID-19;Lymphoma 135;103 143;111 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. D614G mutation in Spike protein enabled Pahang/IIUM91 to increase its stability and fitness, thus contributing to a massive increase in COVID-19 positive cases detected in Pahang. 2022 Materials today. Proceedings Conclusion SARS_CoV_2 D614G 0 5 S 18 23 COVID-19 136 144 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. Here we report that COVID-19 with D614G mutation has been circulating in our society earlier than the case reported by MOH. 2022 Materials today. Proceedings Conclusion SARS_CoV_2 D614G 34 39 COVID-19 20 28 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. In conclusion, increases trend of positive COVID-19 in Malaysia may be contributed by major SARS-CoV-2 lineage B.5 which harbour D614G mutation in Spike protein. 2022 Materials today. Proceedings Conclusion SARS_CoV_2 D614G 129 134 S 147 152 COVID-19 43 51 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. This virus was not related to the mutant D614G virus introduced by Sivagangga cluster. 2022 Materials today. Proceedings Conclusion SARS_CoV_2 D614G 41 46 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. We also reported that D614G mutated Pahang/IIUM91 virus was circulating in Pahang since April 2020. 2022 Materials today. Proceedings Conclusion SARS_CoV_2 D614G 22 27 33714462 Pyrococcus furiosus Argonaute coupled with modified ligase chain reaction for detection of SARS-CoV-2 and HPV. The ability to detect single-base differences opens the opportunity for using PLCR to detect the novel coronavirus and its mutant spike D614G which is more infectious. 2021 Talanta Conclusion SARS_CoV_2 D614G 136 141 S 130 135 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. 197 Given the reported reduced neutralisation by vaccine-elicited antibodies against single to triple K417N + E484K + N501Y mutants, 96 it is likely that vaccines may need to be updated periodically to avoid potential loss of clinical efficacy, and in this regard mRNA vaccines are likely the easiest to be remanufactured. 2021 Reviews in medical virology Conclusion SARS_CoV_2 E484K;K417N;N501Y 111;103;119 116;108;124 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. The results of this study indicate that SII above 40% is associated with the emergence of SARS-CoV-2 E484K variants and P.1 lineage in the state of Amazonas, Brazil, whereas this correlation has not been found in overall Brazil during the period analyzed. 2021 Cureus Conclusion SARS_CoV_2 E484K 101 106 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. Apparently, the N501Y mutation in sRBD provides significant edges for the virus to proliferate; therefore, continued studies on the interaction between sRBD and hACE2 are warranted for the development of treatments against COVID-19. 2021 FEBS letters Conclusion SARS_CoV_2 N501Y 16 21 COVID-19 223 231 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. In a more recent study [14], it was further validated that N501Y together with N501F, N501W and N501V exhibited enhanced binding affinity between sRBD and hACE2 in vitro. 2021 FEBS letters Conclusion SARS_CoV_2 N501F;N501V;N501W;N501Y 79;96;86;59 84;101;91;64 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. In summary, our in silico studies suggest that the N501Y mutation can enhance sRBD binding affinity with hACE2 and potentially cause the virus to evade antibody neutralization. 2021 FEBS letters Conclusion SARS_CoV_2 N501Y 51 56 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. It only took the parental strain one passage to start exhibiting and accumulating the N501Y variant and, by the third passage, the N501Y strain took over 93% of the viral population, suggesting a much more favorable adaptation to the host than the wild-type strain, presumably as a result of enhanced sRBD interaction with hACE2. 2021 FEBS letters Conclusion SARS_CoV_2 N501Y;N501Y 86;131 91;136 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. Prior to July, 2020, it had been already discovered that the N501Y mutation could be generated de novo from an adaptive murine model using only the parental wild-type virus strain (IMEBJ05) first isolated in Beijing [13]. 2021 FEBS letters Conclusion SARS_CoV_2 N501Y 61 66 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. Regarding the polymorphism of hACE2, two mutations, K26R and I468V, in hACE2 (and close to the bound sRBD) can occur frequently in non-Finnish Europeans and East Asians [35] respectively; however, these residues (26 and 468) in hACE2 are not close to the residue 501 in sRBD. 2021 FEBS letters Conclusion SARS_CoV_2 I468V;K26R 61;52 66;56 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. The N501Y mutation only requires one mutation (A23063T [6]), whereas the codon requirement for N501 converting to F, W or V requires at least two bases to mutate simultaneously, which is much less likely to occur directly from the wild-type strain. 2021 FEBS letters Conclusion SARS_CoV_2 N501Y;A23063T 4;47 9;54 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. Therefore, it is much easier for N501Y to occur naturally by evolution and selection. 2021 FEBS letters Conclusion SARS_CoV_2 N501Y 33 38 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. Therefore, the molecular mechanism of the N501Y mutation revealed above is not altered by the known polymorphisms of hACE2. 2021 FEBS letters Conclusion SARS_CoV_2 N501Y 42 47 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. These results are consistent with the fact that N501Y is a naturally occurring and selected mutation [13]. 2021 FEBS letters Conclusion SARS_CoV_2 N501Y 48 53 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. We discovered that, after the N501Y mutation, Y501 in sRBD can simultaneously form hydrophobic interactions with Y41 and K353 in hACE2, yielding an enhanced interfacial binding. 2021 FEBS letters Conclusion SARS_CoV_2 N501Y 30 35 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. As could be anticipated, most of the studied mutations act as protein-protein interface destabilizers; however, a non-negligible number of mis-sense variations are predicted to enhance ACE2/S-RBDCoV-2 binding; in particular, the variants Q24T, T27D/K/W, D30E, H34S/T/K, E35D, Q42K, L79I/W, R357K, and R393K on ACE2 and L455D/W, F456 K/W, Q493K, N501T, and Y505W on the S-protein receptor binding domain, respectively, are expected to increase the affinity of each mutant isoforms for the corresponding protein counterpart. 2021 ACS nano Conclusion SARS_CoV_2 L455D;L455W;L79I;L79W;N501T;Q493K;Y505W 319;319;282;282;345;338;356 326;326;288;288;350;343;361 RBD;S;S 379;190;369 402;191;370 33738620 Clinical characteristics of SARS-CoV-2 by re-infection vs. reactivation: a case series from Iran. Both sequences had L139L non-synonymous mutation, novel mutation in nucleotide position 28688. 2021 European journal of clinical microbiology & infectious diseases Conclusion SARS_CoV_2 L139L 19 24 33738620 Clinical characteristics of SARS-CoV-2 by re-infection vs. reactivation: a case series from Iran. Moreover, the viral sequencing also revealed a D614G mutation of S gene from the second obtained sample. 2021 European journal of clinical microbiology & infectious diseases Conclusion SARS_CoV_2 D614G 47 52 S 65 66 33738620 Clinical characteristics of SARS-CoV-2 by re-infection vs. reactivation: a case series from Iran. The viral sequencing revealed a D614G mutation of S gene from the second isolated sample. 2021 European journal of clinical microbiology & infectious diseases Conclusion SARS_CoV_2 D614G 32 37 S 50 51 33746914 Global Geographic and Temporal Analysis of SARS-CoV-2 Haplotypes Normalized by COVID-19 Cases During the Pandemic. Why mutations R203K and G204R have such frequencies in most of the continents, why in North America, those mutations were not so successful and why currently Europe is dominated by OTU_2 are open questions. 2021 Frontiers in microbiology Conclusion SARS_CoV_2 G204R;R203K 24;14 29;19 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. A single novel mutation N228K detected in Mpro, located in domain III, may have catalytic consequences, which need to be validated through experimental approaches. 2021 ACS omega Conclusion SARS_CoV_2 N228K 24 29 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. However, E93K and W45L exhibited increased flexibility compared to L84S. 2021 ACS omega Conclusion SARS_CoV_2 E93K;L84S;W45L 9;67;18 13;71;22 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Mutation S327L in CTD of N increases the flexibility, while it stabilizes the structure. 2021 ACS omega Conclusion SARS_CoV_2 S327L 9 14 N 25 26 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Point mutations (L84S, E93K, and W45L) in NS8 (ORF8) have a destabilizing effect on the structure. 2021 ACS omega Conclusion SARS_CoV_2 E93K;W45L;L84S 23;33;17 27;37;21 ORF8 47 51 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Some novel mutations have been detected in NSP2 (D268del), NSP5 (N228K), and NS3 (F105S). 2021 ACS omega Conclusion SARS_CoV_2 D268del;F105S;N228K 49;82;65 56;87;70 Nsp2;Nsp5;NS3 43;59;77 47;63;80 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. The 20A/G clades are characterized by D614G mutation in spike protein, suggesting increased transmissibility but not pathogenicity. 2021 ACS omega Conclusion SARS_CoV_2 D614G 38 43 S 56 61 33750399 Modelling the association between COVID-19 transmissibility and D614G substitution in SARS-CoV-2 spike protein: using the surveillance data in California as an example. Our findings show a link between the molecular-level mutation activity of SARS-CoV-2 and population-level COVID-19 transmission to provide further evidence for a positive association between the D614G substitution and Rt. 2021 Theoretical biology & medical modelling Conclusion SARS_CoV_2 D614G 195 200 COVID-19 106 114 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. The main reason of this discrepancy is probably the use in previous work of the F318W mutant of PALS1, instead of the wild-type protein, as we have demonstrated that the Trp substituent is actively perturbing the mechanism of interaction with the viral peptides, being less crucial for the CRB1 binding mechanism. 2021 Computational and structural biotechnology journal Conclusion SARS_CoV_2 F318W 80 85 33777333 Specific epitopes form extensive hydrogen-bonding networks to ensure efficient antibody binding of SARS-CoV-2: Implications for advanced antibody design. Two single site mutations, VH V98E and VL G68D in antibody are proposed to imitate the interactions between SARS-CoV-2 RBD and the receptor. 2021 Computational and structural biotechnology journal Conclusion SARS_CoV_2 G68D;V98E 42;30 46;34 RBD 119 122 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Among seven mutations in three proteins (E, N and S), four mutations (L13H in E, R203K and P344S in N and D614G in S) were predicted neutral while, remaining three (P13L, S197L and G204R) found to have deleterious effects on protein functions. 2021 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 D614G;G204R;P344S;R203K;S197L;L13H;P13L 106;181;91;81;171;70;165 111;186;96;86;176;74;169 E;E;N;N;S;S 41;78;44;100;50;115 42;79;45;101;51;116 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. D614G mutation opens up the spike protein which though might lead to destabilization of protein but might lead to enhanced viral infections. 2021 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 D614G 0 5 S 28 33 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Discrete molecular dynamics and all-atom molecular dynamics results revealed that three mutations (P13L, S197L and R203K) in N protein give stability to the parent proteins. 2021 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 R203K;S197L;P13L 115;105;99 120;110;103 N 125 126 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. However, two mutations (G204R and P344S) in N protein and D614G in S protein destabilize the parent proteins. 2021 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 D614G;P344S;G204R 58;34;24 63;39;29 N;S 44;67 45;68 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Though our analysis of D614G mutation in Spike protein predicted destabilization of the protein, several experimental studies have shown that the mutation contributes towards enhanced infectivity of the virus. 2021 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 D614G 23 28 S 41 46 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. As shown here, the N501Y mutation in all three variants may enhance ACE2 affinity but might not confer antibody resistance individually or neutralizing effects by convalescent plasma and vaccine sera. 2021 Viruses Conclusion SARS_CoV_2 N501Y 19 24 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. In the 501Y.V1 variant, we hypothesized that R52I mutation could affect multimer assembly of the ORF8 protein, however another Q27Stop deletion apparently showed no effect on viral transcription. 2021 Viruses Conclusion SARS_CoV_2 Q27X;R52I 127;45 134;49 ORF8 97 101 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. The N501Y mutation, in particular, leads to stronger interaction with human ACE2 compared to its wildtype, although other co-occurring mutations along with N501Y might have a different overall effect. 2021 Viruses Conclusion SARS_CoV_2 N501Y;N501Y 4;156 9;161 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. It is strongly recommended to further sequence the VoCs and not stop at the identification of the N501Y mutations. 2021 Microorganisms Conclusion SARS_CoV_2 N501Y 98 103 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. The Swiss model, to monitor in a first phase with epidemiological and microbiological case definitions and in a second phase with a specific PCR, allowed the rapid screening of isolates and identification of the N501Y mutation as a surrogate marker for a potentially more transmissible variant. 2021 Microorganisms Conclusion SARS_CoV_2 N501Y 212 217 33810168 Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa. Subsequent local transmission in a supermarket cluster showed that a new lineage with a specific mutation 5209A>G was first identified in Cape Town. 2021 Viruses Conclusion SARS_CoV_2 A5209G 106 113 33851162 A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. However, two B.1.x sequences isolated from travelers returning to the UK also contain E484K, and the effect of S494P is not as well characterized. 2021 bioRxiv Conclusion SARS_CoV_2 E484K;S494P 86;111 91;116 33851162 A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. If this sublineage expands, or if other sublineages secondarily acquire E484K or other mutations that enhance viral fitness, B.1.x may become more likely to impose a global health threat. 2021 bioRxiv Conclusion SARS_CoV_2 E484K 72 77 33851162 A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. In particular, none of the isolates except for two from the UK contain E484K, which is present in other VOCs P.1, B.1.351 and in sublineages of B.1.1.7. 2021 bioRxiv Conclusion SARS_CoV_2 E484K 71 76 33860605 Polysulfates Block SARS-CoV-2 Uptake through Electrostatic Interactions*. With the MD simulations, we were further able to demonstrate that LPGS can bind to the RBD of virus variants, and conclude that LPGS might inhibit infection by variants carrying the E484K and N501Y mutations. 2021 Angewandte Chemie (International ed. in English) Conclusion SARS_CoV_2 E484K;N501Y 182;192 187;197 RBD 87 90 33868743 COVID-19 and mutations a threat level assessment. E484K being the most concerning as it aids in immune evasion and drastically causes the efficacy of the current vaccines to be reduced by large margins. 2021 Nepal journal of epidemiology Conclusion SARS_CoV_2 E484K 0 5 33868743 COVID-19 and mutations a threat level assessment. It is evident that the SARS-CoV-2 variants pose an international health risk, the mutations of E484K and N501Y are the two most implicated mutations. 2021 Nepal journal of epidemiology Conclusion SARS_CoV_2 E484K;N501Y 95;105 100;110 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. In conclusion, through the use of MM-PBSA binding free energy estimation in correlation with known experimental binding affinities of both wild-type and mutant versions of hACE2 proteins, we have been able to reasonably predict the binding affinities of the recently reported N501Y mutant of SARS-CoV-2 spike protein with both the hACE2 and the recently reported miniproteins. 2021 The journal of physical chemistry. B Conclusion SARS_CoV_2 N501Y 276 281 S 303 308 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. Particularly, the N501Y mutation has markedly increased the ACE2-spike protein binding affinity (Kd) from 22 nM (for the wild-type spike) to 0.4 nM (for the N501Y mutant spike), which could partially explain why the UK variant of SARS-CoV-2 (with N501Y mutation on the spike protein) is more infectious. 2021 The journal of physical chemistry. B Conclusion SARS_CoV_2 N501Y;N501Y;N501Y 18;157;247 23;162;252 S;S;S;S 65;131;170;269 70;136;175;274 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. The N501Y mutation is also predicted to decrease the binding affinity of a hACE2 decoy (CTC-445.2) binding with the spike protein. 2021 The journal of physical chemistry. B Conclusion SARS_CoV_2 N501Y 4 9 S 116 121 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. From the DCCM and vector field collective motion analysis, we demonstrated that our lead compound's molecular docking (SCHEMBL20144212) tolerates the effect of the P323L mutation and could act as an effective inhibitor against SARS-nCoV-2's RdRp. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 P323L 164 169 RdRP 241 245 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. Thus, this compound should be further validated through in vitro experiments as an alternative to Remdesivir to bypass the resistant effect of the P323L mutation. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 P323L 147 152 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. In summary, the phylogenetic and variant patterns are similar to those observed worldwide, such as the high prevalence of variant D614G in the Spike and low frequency of L84S in the ORF8, as well as the arrangement by clades. 2021 Infection, genetics and evolution Conclusion SARS_CoV_2 D614G;L84S 130;170 135;174 S;ORF8 143;182 148;186 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Interestingly, the variant T1117I in the Spike has increased its frequency along time from March to November 2020. 2021 Infection, genetics and evolution Conclusion SARS_CoV_2 T1117I 27 33 S 41 46 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. The Spike variant T1117I must be closely surveyed to see if it will become the predominant circulating variant in our country. 2021 Infection, genetics and evolution Conclusion SARS_CoV_2 T1117I 18 24 S 4 9 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. This work suggested that most of published nAbs with diverse recognizing epitopes still neutralized the SARS-CoV-2_N501Y as similar potencies as that of the wild type virus, except a few of nAbs which targeted the N501 residual directly. 2021 Virology journal Conclusion SARS_CoV_2 N501Y 115 120 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. Out of the 7.5 million possible 2-point mutation combinations, we found that the (R355D K424E) mutation produces one of the most stable spike proteins and should be included in the testing of possible vaccines and molecular inhibitors of SARS-CoV-2. 2021 Scientific reports Conclusion SARS_CoV_2 K424E;R355D 88;82 93;87 S 136 141 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. We also aim to explore mutations that appear outside the RBD region, such as the D614G mutation located in position 614 highlighted in. 2021 Scientific reports Conclusion SARS_CoV_2 D614G 81 86 RBD 57 60 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. In this study we identified the emergence of a new VOI (S:E484K) within lineage B.1.1.33 circulating in Brazil. 2021 Viruses Conclusion SARS_CoV_2 E484K 58 63 S 56 57 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. Mutation S:E484K has been identified as one of the most important substitutions that could contribute to immune evasion as confers resistance to several monoclonal antibodies and also reduces the neutralization potency of some polyclonal sera from convalescent and vaccinated individuals. 2021 Viruses Conclusion SARS_CoV_2 E484K 11 16 S 9 10 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. Mutation S:E484K has emerged independently in multiple VOCs (P.1, B.1.351 and B.1.1.7) and VOIs (P.2 and B.1.526) spreading around the world, and it is probably an example of convergent evolution and ongoing adaptation of the virus to the human host. 2021 Viruses Conclusion SARS_CoV_2 E484K 11 16 S 9 10 33919314 A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil. We predict that the Brazilian COVID-19 epidemic during 2021 will be dominated by a complex array of B.1.1.28 (S:E484K), including P.1 and P.2, and B.1.1.33 (S:E484K) variants that will completely replace the parental 484E lineages that drove the epidemic in 2020. 2021 Viruses Conclusion SARS_CoV_2 E484K;E484K 112;159 117;164 S;S 110;157 111;158 COVID-19 30 38 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. This study uncovered that mutations in VOC have a favorable contribution to the total binding energy, particularly due to N501Y and E484K mutations, underlying the higher affinity of novel VOC for hACE2 compared to the WT isolate. 2021 Microorganisms Conclusion SARS_CoV_2 E484K;N501Y 132;122 137;127 33975397 Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines? Unfortunately, the mutation frequency of the S protein is very high, and some mutations (such as E484K, N501Y, and K417N) affect the transmission and neutralization of the SARS-CoV-2 virus. 2021 Journal of Korean medical science Conclusion SARS_CoV_2 E484K;K417N;N501Y 97;115;104 102;120;109 S 45 46 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. More specifically, we found that mutations N501Y, E484K, and K417N in the United Kingdom (UK), South Africa, or Brazil variants, L452R and E484Q in the India, as well as mutations N439K, S477N, S477R, and N501T are all associated with the enhancement of the BFE of the S protein and ACE2, confirming the earlier speculation. 2021 Genomics Conclusion SARS_CoV_2 E484K;E484Q;K417N;L452R;N439K;N501T;N501Y;S477N;S477R 50;139;61;129;180;205;43;187;194 55;144;66;134;185;210;48;192;199 S 269 270 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Note that L452R in the California variant B.1.427 is as infectious as N501Y and as disruptive as E484K. 2021 Genomics Conclusion SARS_CoV_2 E484K;L452R;N501Y 97;10;70 102;15;75 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. We report that rapidly growing mutations S494P, Q493L, K417N, F486L, F490S, R403K, E484K, K417T, L452R, E484Q, A475S, and F490L are more likely to disrupt existing vaccines and many antibody drugs. 2021 Genomics Conclusion SARS_CoV_2 A475S;E484K;E484Q;F486L;F490L;F490S;K417N;K417T;L452R;Q493L;R403K;S494P 111;83;104;62;122;69;55;90;97;48;76;41 116;88;109;67;127;74;60;95;102;53;81;46 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. We show that four fast-growing mutations N439K, S477N, S477R, and N501T in addition to all known infectious variants containing N501Y, L452R, E484Q, E484K, and K417N, deserve the world's attention. 2021 Genomics Conclusion SARS_CoV_2 E484K;E484Q;K417N;L452R;N439K;N501T;N501Y;S477N;S477R 149;142;160;135;41;66;128;48;55 154;147;165;140;46;71;133;53;60 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. While mutations Q493R, R408I, Q493H, P384S, and N501T can also be disruptive, but mutations N439K, V367F, and S477R are not as disruptive as other rapidly growing ones. 2021 Genomics Conclusion SARS_CoV_2 N439K;N501T;P384S;Q493H;Q493R;R408I;S477R;V367F 92;48;37;30;16;23;110;99 97;53;42;35;21;28;115;104 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. Two mutants, R408I and W436R were found to decrease and enhance the structural stability, respectively. 2021 Briefings in bioinformatics Conclusion SARS_CoV_2 R408I;W436R 13;23 18;28 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. Two mutants, V367F and N354D/D364Y, were predicted to have significantly higher binding affinities, and the prediction was validated by experiment and the virus epidemiology. 2021 Briefings in bioinformatics Conclusion SARS_CoV_2 N354D;V367F;D364Y 23;13;29 28;18;34 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. E484K), and may be able to effectively establish infections in animals that are routinely in close proximity to humans. 2021 Clinical microbiology and infection Conclusion SARS_CoV_2 E484K 0 5 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. In many ways this mirrors the early independent emergence and spread of D614G mutations. 2021 Clinical microbiology and infection Conclusion SARS_CoV_2 D614G 72 77 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. N501Y), with some ability to escape previous immunity (e.g. 2021 Clinical microbiology and infection Conclusion SARS_CoV_2 N501Y 0 5 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. In particular, to our best knowledge, we described the earliest SARS-CoV-2 sequences harboring E484K in Southern Brazil. 2021 BMC genomics Conclusion SARS_CoV_2 E484K 95 100 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. Our results provide a comprehensive view of SARS-CoV-2 mutations from a time- and age-representative sample from May to October 2020, highlighting two frequent mutations in spike glycoprotein (D614G and V1176F), an emergent mutation in spike RBD (E484K) characteristic of B.1.351 and P.1 lineages, and the adjacent replacement of 2 amino acids in Nucleocapsid phosphoprotein (R203K and G204R). 2021 BMC genomics Conclusion SARS_CoV_2 G204R;V1176F;D614G;E484K;R203K 386;203;193;247;376 391;209;198;252;381 S;N;S;RBD 173;347;236;242 191;359;241;245 34043733 Molecular dynamics analysis of N-acetyl-D-glucosamine against specific SARS-CoV-2's pathogenicity factors. Our results confirmed and highlighted the strong binding of D-GlcNAc to the domain region of the selected proteins on aggressive mutant variants (D614G). 2021 PloS one Conclusion SARS_CoV_2 D614G 146 151 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. The two mutations E484K and N501Y in the spike RBD of SARS-CoV-2 of the new variants (UK, South African, and Brazilian) imbalance the weight in viral spike recognition through either ACE2 or CS-GRP78. 2021 Biochemical and biophysical research communications Conclusion SARS_CoV_2 E484K;N501Y 18;28 23;33 S;S;RBD 41;150;47 46;155;50 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. The D614G substitution in the SARS-CoV-2 spike protein, which is being intensively studied across the globe for COVID-19 prophylaxis and treatment, is under positive selection in the ongoing pandemic. 2021 Bioinformation Conclusion SARS_CoV_2 D614G 4 9 S 41 46 COVID-19 112 120 34092964 D614G substitution at the hinge region enhances the stability of trimeric SARS-CoV-2 spike protein. This computational study demonstrates that D614G substitution occurs at the hinge region and potentially influences the conformational transition essential for human ACE2 receptor binding. 2021 Bioinformation Conclusion SARS_CoV_2 D614G 43 48 34099945 First importations of SARS-CoV-2 P.1 and P.2 variants from Brazil to Spain and early community transmission. The P.2 variant carrying the E484K concern mutation is also reported here, imported by two other travellers who remained asymptomatic. 2022 Enfermedades infecciosas y microbiologia clinica Conclusion SARS_CoV_2 E484K 29 34 34114829 Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study. Our most promising stapled peptides showed stable profiles in the MD simulation and could retain important interactions with the RBD even in the presence of the E484K RBD mutation. 2021 The journal of physical chemistry. B Conclusion SARS_CoV_2 E484K 161 166 RBD;RBD 129;167 132;170 34119951 Examining the interactions scorpion venom peptides (HP1090, Meucin-13, and Meucin-18) with the receptor binding domain of the coronavirus spike protein to design a mutated therapeutic peptide. Mutation 1 (A9T) is even better than native meucin-18 and can be considered as a potential drug for COVID-19 infection; because these peptides can bind to the spike protein and inhibit all downstream processes of the SARS-CoV-2 to enter the cells and create cells' infection. 2021 Journal of molecular graphics & modelling Conclusion SARS_CoV_2 A9T 12 15 S 159 164 COVID-19 100 108 34119951 Examining the interactions scorpion venom peptides (HP1090, Meucin-13, and Meucin-18) with the receptor binding domain of the coronavirus spike protein to design a mutated therapeutic peptide. The results showed that mutation 1 (A9T) or (FFGHLFKLTTKIIPSLFQ) had the most negative binding energy and this mutation can prevent interaction RBD domain of spike protein with ACE2 receptor. 2021 Journal of molecular graphics & modelling Conclusion SARS_CoV_2 A9T 36 39 S;RBD 158;144 163;147 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. The mutants of H:V106R and H:V106R/H:P107Y might have more potent neutralizing activity against both wild type SARS-CoV-2 as well as the alarming variant of N501Y. 2021 Computers in biology and medicine Conclusion SARS_CoV_2 N501Y;P107Y;V106R;V106R;V106H 157;37;17;29;29 162;42;22;36;36 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Our results suggest that functional effects of the globally circulating D614G mutation may be determined by confluence of both local and global stability changes that collectively exert control over conformational transformations and differential thermodynamic stabilization of closed and open states. 2021 ACS omega Conclusion SARS_CoV_2 D614G 72 77 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. The differential stabilization of the S-G614 closed and open forms may help to reconcile mechanisms of mutation-induced preferences toward the open state and the reduced S1 shedding scenario underlying functional effects of the D614G circulating mutation. 2021 ACS omega Conclusion SARS_CoV_2 D614G 228 233 S 38 39 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. The results of this study provide an insight into the molecular mechanisms underlying the effect of the D614G mutation by examining the SARS-CoV-2 S protein as an allosteric regulatory machine. 2021 ACS omega Conclusion SARS_CoV_2 D614G 104 109 S 147 148 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Using mutational sensitivity analysis of the SARS-CoV-2 S-D614 and S-G614 proteins, we demonstrated the improved stability of the D614G mutant as compared to the S-D614 protein. 2021 ACS omega Conclusion SARS_CoV_2 D614G 130 135 S;S;S 56;67;162 57;68;163 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. We combined simulation-based approaches with dynamic network modeling and community analysis to quantify the effect of the D614G mutation on dynamics, stability, and network organization of the SARS-CoV-2 S proteins. 2021 ACS omega Conclusion SARS_CoV_2 D614G 123 128 S 205 206 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. Evidence from different researchers worldwide shows that the next emerging mutation after D614G can severely enhance the infection rate. 2021 Future virology Conclusion SARS_CoV_2 D614G 90 95 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. The V483A mutation represents one of the major emerging mutations of the current COVID-19 pandemic crisis. 2021 Future virology Conclusion SARS_CoV_2 V483A 4 9 COVID-19 81 89 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. V483A is not directly related to the virus-host cell interaction, but it can improve the protein-protein complex's binding stability and binding capacity. 2021 Future virology Conclusion SARS_CoV_2 V483A 0 5 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. We observed that the V483A mutation was first observed in the North American region. 2021 Future virology Conclusion SARS_CoV_2 V483A 21 26 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. However, further human and cell-based functional studies are required to elucidate the clinical importance of administering RDV to patients carrying the SARS-CoV-2 P323L-RdRp mutation. 2021 Biomolecules Conclusion SARS_CoV_2 P323L 164 169 RdRP 170 174 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Since, the effect of the most prevalent mutations, A97V and P323L, found in the RdRp of SARS-CoV-2 have been less examined, we used MD simulations to elucidate the effects of the mutations on the structure and stability of RdRp, in addition to the effect of binding of RDV. 2021 Biomolecules Conclusion SARS_CoV_2 A97V;P323L 51;60 55;65 RdRP;RdRP 80;223 84;227 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. The findings of this study demonstrated that RDV has a more favourable binding to mutant P323L-RdRp in comparison to WT-RdRp. 2021 Biomolecules Conclusion SARS_CoV_2 P323L 89 94 RdRP;RdRP 95;120 99;124 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Therefore, we postulate that administering RDV to patients carrying the SARS-CoV-2 P323L-RdRp mutation may have a more favorable chance of alleviating SARS-CoV-2 illness in comparison to WT-RdRp carriers. 2021 Biomolecules Conclusion SARS_CoV_2 P323L 83 88 RdRP;RdRP 89;190 93;194 COVID-19 151 169 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Another critical mutation, N501Y has been identified in several SARS-CoV-2 VOC. 2021 Virology Conclusion SARS_CoV_2 N501Y 27 32 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. However, increased RBD stability, high ACE2 binding affinity and no deleterious effect on protein function were observed for mutations N501I, N501S, N501Y, Q493L, Q493H and K417R. 2021 Virology Conclusion SARS_CoV_2 K417R;N501I;N501S;N501Y;Q493H;Q493L 173;135;142;149;163;156 178;140;147;154;168;161 RBD 19 22 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Initially a SARS-CoV-2 variant with mutation D614G in the S protein circulated across the globe and became the predominant form of the virus with increased infectivity and transmissibility. 2021 Virology Conclusion SARS_CoV_2 D614G 45 50 S 58 59 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. The variation N501Y occurs in the S-RBD, more specifically at the hotspot stabilizing residue of the RBM. 2021 Virology Conclusion SARS_CoV_2 N501Y 14 19 RBD;S 36;34 39;35 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. We predicted that the mutation N501Y might increase the RBD stability and its binding affinity for ACE2. 2021 Virology Conclusion SARS_CoV_2 N501Y 31 36 RBD 56 59 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. D614G that is located in of the spike genome, has become the most common mutation worldwide and generates high infectivity of the virus and this finding suggested it is associated with CFR on a country by country basis. 2021 Biomedical journal Conclusion SARS_CoV_2 D614G 0 5 S 32 37 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. Clearly, despite the dramatic reduction in global travel, the evolution of SARS-Cov-2 is partly shaped by globalizing factors, including the increased virus fitness conferred by S D614G, N R203K&G204R, and other positively selected amino acid substitutions. 2021 Proc Natl Acad Sci U S A Conclusion SARS_CoV_2 D614G;R203K;G204R 180;189;195 185;194;200 N;S 187;178 188;179 34304682 An overview of the preclinical discovery and development of bamlanivimab for the treatment of novel coronavirus infection (COVID-19): reasons for limited clinical use and lessons for the future. First, the emergence and expansion of E484K-carrying SARS-CoV-2 variants resistant to bamlanivimab had been at least partially underestimated. 2021 Expert opinion on drug discovery Conclusion SARS_CoV_2 E484K 38 43 34304682 An overview of the preclinical discovery and development of bamlanivimab for the treatment of novel coronavirus infection (COVID-19): reasons for limited clinical use and lessons for the future. The strategy of antibody cocktails could represent a temporary solution (cocktails cannot escape resistance for long time if occurrence of variants is too frequent), although their economic sustainability should be carefully considered: resistance to the bamlanivimab-etesevimab cocktail due to Q493R mutation has indeed already been reported, although fitness of such strain remains unconfirmed. 2021 Expert opinion on drug discovery Conclusion SARS_CoV_2 Q493R 295 300 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Most patients infected with the virus containing the specific ORF7 A105V mutation presented severe forms of the disease, including increased inflammatory markers. 2021 Frontiers in microbiology Conclusion SARS_CoV_2 A105V 67 72 ORF7 62 66 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Up to our best knowledge, this is the first assay developed specifically for exploring SARS CoV-2 D614G mutation using specific primers and probes for detecting D614G mutant by using real-time, conventional PCR and restriction endonuclease. 2021 Meta gene Conclusion SARS_CoV_2 D614G;D614G 98;161 103;166 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. 5' UTR interactions with host factors were studied and it was concluded that C241T changes the SL4, which overall changes the folding of RNA. 2021 Informatics in medicine unlocked Conclusion SARS_CoV_2 C241T 77 82 5'UTR 0 6 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Henceforth, we analyzed the S-protein-B.1.1.7 structure in complex with furin and compared it with the S-protein P681H complex to ascertain if the variant affected the furin binding P681H mutation affected furin cleavage using computational modelling and structural-dynamics approaches. 2021 Virus research Conclusion SARS_CoV_2 P681H;P681H 113;182 118;187 S;S 28;103 29;104 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Here in this study, we used biomolecular docking and simulation approaches to compare the binding affinities of furin to S-protein P681H and B.1.1.7 variant structures. 2021 Virus research Conclusion SARS_CoV_2 P681H 131 136 S 121 122 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. The B.1.1.7 variant demonstrated seven mutations and three deletions, with mutation P681H on the furin cleavage site. 2021 Virus research Conclusion SARS_CoV_2 P681H 84 89 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. According to the calculations of the binding free energies, the binding affinities of 501Y.V1, N439K, and 501Y.V2 variants were significantly increased by 36.8%, 29.5%, and 19.6%, respectively. 2021 Computational and structural biotechnology journal Conclusion SARS_CoV_2 N439K 95 100 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. For example, both the 501Y.V1 and N439K variants were able to form new hydrogen bonds, thus enhancing their binding affinity with hACE2. 2021 Computational and structural biotechnology journal Conclusion SARS_CoV_2 N439K 34 39 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. In conclusion, we investigated the binding affinity and mechanisms of the three most widespread SARS-CoV-2 variants (501Y.V1, 501Y.V2, N439K) based on molecular dynamics simulations and sequence analysis. 2021 Computational and structural biotechnology journal Conclusion SARS_CoV_2 N439K 135 140 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. Moreover, three MTs (S68F, P71S, and L73F) were analyzed through MD simulations and exhibited a stabilizing effect on the E protein structure. 2021 Informatics in medicine unlocked Conclusion SARS_CoV_2 L73F;P71S;S68F 37;27;21 41;31;25 E 122 123 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. In conclusion, the conformational variability of the mutation sites for B.1.617.2, B.1.617.1, B.1.427/429, P.1, B.1.351, B.1.1.7, S477N, and the wild-type strain has been assessed using SSSCPreds. 2021 ACS omega Conclusion SARS_CoV_2 S477N 130 135 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. K417N with the more flexible SSSC sequence from the SSSCPreds data of K417T (P.1) and K417N (B.1.351) can escape neutralization more effectively. 2021 ACS omega Conclusion SARS_CoV_2 K417N;K417T;K417N 86;70;0 91;75;5 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The increased rigidity of the amino acid sequence YRYRLFR for the L452R mutation stabilizes the RBM structure of B.1.427/429 and contributes to the high expression observed by the quantitative deep mutational scanning. 2021 ACS omega Conclusion SARS_CoV_2 L452R 66 71 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. The SSSCPreds data of the D614G mutation suggest that although the G614-induced conformation is stabilized in the same way as found in a LH alpha-helix, the D614 conformation is flexible without the hydrogen bonding latch between D614 and T859. 2021 ACS omega Conclusion SARS_CoV_2 D614G 26 31 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. On the other hand, the stabilizing nonsynonymous mutations (H49Y, S50L, N501Y, D614G, A845V, and P1143L) show greater interaction with the ACE2 receptor than native and destabilizing nonsynonymous mutations of the S-protein. 2021 Computers in biology and medicine Conclusion SARS_CoV_2 A845V;D614G;N501Y;P1143L;S50L;H49Y 86;79;72;97;66;60 91;84;77;103;70;64 S 214 215 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The docking and free binding energy (ddG) scores exhibited destabilizing nonsynonymous mutations (L8V, L8W, L18F, Y145H, M153T, F157S, G476S, L611F, A879S, C1247F, and C1254F) show lower interaction with the ACE2 receptor compared to native S-protein. 2021 Computers in biology and medicine Conclusion SARS_CoV_2 A879S;C1247F;C1254F;F157S;G476S;L18F;L611F;L8W;M153T;Y145H;L8V 149;156;168;128;135;108;142;103;121;114;98 154;162;174;133;140;112;147;106;126;119;101 S 241 242 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Thus, the MD simulation of stabilizing nonsynonymous mutations (N501Y and D614G) undergo structural changes and might influence interaction with ACE2. 2021 Computers in biology and medicine Conclusion SARS_CoV_2 D614G;N501Y 74;64 79;69 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. A new strain containing N501Y first appeared in the UK, the recent Delta+ strain (AY.1) containing K417N is now on the rise at the time of writing. 2021 PLoS computational biology Conclusion SARS_CoV_2 K417N;N501Y 99;24 104;29 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. After this work first became available as a preprint in December 2020, extensive molecular dynamics simulations totalling 20 mus and investigating the effect of the D614G mutation on conformational dynamics have been conducted with the full complement of glycans. 2021 PLoS computational biology Conclusion SARS_CoV_2 D614G 165 170 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Both studies come to the same conclusion as ours, namely that the open state is favoured on the D614G mutant. 2021 PLoS computational biology Conclusion SARS_CoV_2 D614G 96 101 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Namely, complementary computational molecular dynamics simulations as well as experimental work for the single mutant D614G as well as experimental work on the UK, SA and Brazil variants. 2021 PLoS computational biology Conclusion SARS_CoV_2 D614G 118 123 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Our results explain the behaviour of the D614G strain, the increased infectivity of SARS-CoV-2 relative to SARS-CoV as well as offer a possible explanation for the rise of new strains such as those harboring the N501Y mutation. 2021 PLoS computational biology Conclusion SARS_CoV_2 D614G;N501Y 41;212 46;217 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. The A222V mutation, reportedly responsible for many infections, emerged in Spain during the Summer of 2020 and since then has spread to neighbor countries; In Denmark, new strains related to SARS-CoV-2 transmission in mink farms were confirmed in early October by the WHO and shown to be caused by specific mutations not previously observed with the novelty of back-and-forth transmission between minks and humans. 2021 PLoS computational biology Conclusion SARS_CoV_2 A222V 4 9 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Two studies determined the structures of the D614G mutant in open and closed states via cryo electron microscopy (cryo-EM) in the open and closed states were published and came to our attention after this manuscript was published as a preprint. 2021 PLoS computational biology Conclusion SARS_CoV_2 D614G 45 50 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. Among the identified mutations, NSP2_T153M, NSP14_I42V and Spike_L18F mutations showed positive correlation to CFR, while NSP13_Y541C, NSP3_T73I and NSP3_Q180H showed a negative correlation. 2021 Genes Conclusion SARS_CoV_2 I42V;L18F;Q180H;T153M;T73I;Y541C 50;65;154;37;140;128 54;69;159;42;144;133 S;Nsp13;Nsp2;Nsp3;Nsp3 59;122;32;135;149 64;127;36;139;153 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. NSP12_P323L and Spike_D614G mutations showed positive correlation to number of cases per million, while NS8_L84S and NSP12_A97V mutations showed negative correlation. 2021 Genes Conclusion SARS_CoV_2 A97V;D614G;L84S;P323L 123;22;108;6 127;27;112;11 S;Nsp12;Nsp12 16;0;117 21;5;122 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The mutations having the highest frequencies among continents were Spike_D614G and NSP12_P323L. 2021 Genes Conclusion SARS_CoV_2 D614G;P323L 73;89 78;94 S;Nsp12 67;83 72;88 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The Spike_D614G and NSP12_P323L mutations showed positive correlation to deaths per million, while NSP3_T1198K, NS8_L84S and NSP12_A97V mutations showed negative correlation. 2021 Genes Conclusion SARS_CoV_2 A97V;D614G;L84S;P323L;T1198K 131;10;116;26;104 135;15;120;31;110 S;Nsp12;Nsp12;Nsp3 4;20;125;99 9;25;130;103 34358019 Antibodies Targeting Two Epitopes in SARS-CoV-2 Neutralize Pseudoviruses with the Spike Proteins from Different Variants. (N501Y) mutation:to more than 80%. 2021 Pathogens (Basel, Switzerland) Conclusion SARS_CoV_2 N501Y 0 6 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. The data obtained indicate no significant differences in VNA against B.1.1.7, B.1.617.3, and local genetic lineages B.1.1.141 (T385I), B.1.1.317 (S477N, A522S) with RBD mutations. 2021 Vaccines Conclusion SARS_CoV_2 A522S;S477N;T385I 153;146;127 158;151;132 RBD 165 168 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. g., E484K, N501Y), and the emergence of P.1, arguably one of the most potentially concerning lineages identified worldwide up to February 2021. 2021 Virus research Conclusion SARS_CoV_2 E484K;N501Y 4;11 9;16 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. A cell-cell fusion assay was used to mimic the SARS-CoV-2 virus spreading among ACE2-expressing cells, thus the V367F and Q498A mutant displayed a significantly increased luciferase activity. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 Q498A;V367F 122;112 127;117 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. Except for that of the N354D system, the binding free energy of the other three mutation systems is enhanced, and the electrostatic energy provides the greatest contribution. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 N354D 23 28 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. However, the V367F system of the non-RBM group is similar to the Q498A system. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 Q498A;V367F 65;13 70;18 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. In the three-dimensional motion diagram of PCA, the movement direction of the RMB region in the N354D system is disordered and the motion amplitude is very low. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 N354D 96 101 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The chargeability of the base acid before and after the mutation in the N354D system and the D364Y system is different, which makes the electrostatic energy of the mutation site greatly changed, so the energy contribution change at this site is the main reason for the overall binding free energy change. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 D364Y;N354D 93;72 98;77 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The D364Y, V367F, and Q498A systems show little difference in the movement of the RBM region compared with the WT system. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 D364Y;Q498A;V367F 4;22;11 9;27;16 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The secondary structure of the random coil Pro384-Asp389 of the N354D system and the V367F system has changed, which may indirectly affect the conformation of the RBM region. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 N354D;V367F 64;85 69;90 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. We also found a region (Ala475-Gly485) with obvious contrast, the secondary structure of the non-RBM group in this region was mostly changed from bend + coil to turn, whereas the Q498A system remained unchanged. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 Q498A 179 184 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. In conclusion, we found a number of high frequency SARS-CoV-2 RBD mutations with improved binding affinities to the ACE2 receptor including S477N, N439K, V367F, and N501Y. 2021 Antibody therapeutics Conclusion SARS_CoV_2 N439K;N501Y;S477N;V367F 147;165;140;154 152;170;145;159 RBD 62 65 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. We show that S477N and N439K mutations represent high frequency mutations in Australia and England, respectively. 2021 Antibody therapeutics Conclusion SARS_CoV_2 N439K;S477N 23;13 28;18 34389380 EGCG as an anti-SARS-CoV-2 agent: Preventive versus therapeutic potential against original and mutant virus. In vitro and in silico data indicate that EGCG binds the N501Y spike mutant slightly more efficiently than the original protein and should be considered as a protective agent against infection with "UK Variant" SARS-CoV-2. 2021 Biochimie Conclusion SARS_CoV_2 N501Y 57 62 S 63 68 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. A remarkable difference found in B.1.1.44 is an additional V1176F substitution besides the highly disseminated D614G amino acid substitution prevalent worldwide; increased number of mutations in S protein are also reported in other reinfection episodes (Table 2). 2021 Diagnostic microbiology and infectious disease Conclusion SARS_CoV_2 D614G;V1176F 111;59 116;65 S 195 196 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. In addition, both sequences presented the R203K and G204R aminoacid change in the nucleocapsid (N) protein. 2021 Diagnostic microbiology and infectious disease Conclusion SARS_CoV_2 G204R;R203K 52;42 57;47 N;N 82;96 94;97 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. In comparison with the WIV04-sequence, mutations were identified in S, N and NSP proteins of both genomes, but reinfection case (lineage B.1.44) presented an additional V1176F mutation in S protein (Table 1 ). 2021 Diagnostic microbiology and infectious disease Conclusion SARS_CoV_2 V1176F 169 175 N;S;S 71;68;188 72;69;189 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. Mutation in the spike S2 domain V1176F is recognized to be the second more frequent in SARS-CoV-2 from South America, but its frequency is <3% in available viral genomes. 2021 Diagnostic microbiology and infectious disease Conclusion SARS_CoV_2 V1176F 32 38 S 16 21 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. Mutations found only in EPI_ISL_708530 included NSP2 V577F, NSP7 L71F, NSP12 P323L, and NSP16 R216N. 2021 Diagnostic microbiology and infectious disease Conclusion SARS_CoV_2 L71F;P323L;R216N;V577F 65;77;94;53 69;82;99;58 Nsp12;Nsp2;Nsp7 71;48;60 76;52;64 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. On the other hand, only the EPI_ISL_708529 sequence presented the I292T and P383L in N protein, besides an I33T change in NS6 - Accessory protein 6 (NS6). 2021 Diagnostic microbiology and infectious disease Conclusion SARS_CoV_2 I292T;I33T;P383L 66;107;76 71;111;81 N 85 86 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. We detected mutations reported in clinical data, including those in variants of concern, such as the N501Y mutation in the surface glycoprotein. 2021 The Science of the total environment Conclusion SARS_CoV_2 N501Y 101 106 S 123 143 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. Even though a conserved salt bridge is absent, the E484Q mutation could favor the open conformation of RBD that aids in enhanced hACE2 binding and immune escape. 2021 Biomolecules Conclusion SARS_CoV_2 E484Q 51 56 RBD 103 106 34439910 Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant. The L452R mutation enhances the electrostatics of the binding surface and aids electrostatic attraction between hACE2 and the S protein. 2021 Biomolecules Conclusion SARS_CoV_2 L452R 4 9 S 126 127 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Our analysis indicated the high prevalence of the D614G and P323L missense mutations within S and RdRP genes, respectively; the growing trend of Q57H mutation in ORF3a; and the overrepresentation of R203K with G204R or G204L mutations in nucleocapsid phosphoprotein. 2021 International journal of molecular sciences Conclusion SARS_CoV_2 D614G;G204L;G204R;P323L;Q57H;R203K 50;219;210;60;145;199 55;224;215;65;149;204 N;ORF3a;RdRP;S 238;162;98;92 250;167;102;93 34452356 Rise and Fall of SARS-CoV-2 Lineage A.27 in Germany. One of these rare genomes combines a D614G background and several mutations of concern and should therefore also be monitored. 2021 Viruses Conclusion SARS_CoV_2 D614G 37 42 34454120 The low contagiousness and new A958D mutation of SARS-CoV-2 in children: An observational cohort study. This study indicates that (1) children have a lower ability to spread COVID-19 and that the first-generation case of cluster outbreaks among children is usually an adult, as opposed to a child; (2) pediatric COVID-19 may have long fecal virus nucleic acid shedding times, but the stool is not a source of infection after throat swab PCR becomes negative; and (3) the new A958D mutation of the spike protein improves SARS-CoV-2 thermostability and affects cell-cell fusion potentially after viral attachment to the host cell receptor. 2021 International journal of infectious diseases Conclusion SARS_CoV_2 A958D 371 376 S 393 398 COVID-19;COVID-19 70;208 78;216 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. The relevance of a polar environment influenced by N501Y and E484K mutations in the S protein binding regions of SARS-CoV-2 variants was also highlighted as observed in the reinforcement of affinity of highly polar ligands. 2021 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 E484K;N501Y 61;51 66;56 S 84 85 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Unreported V90T missense mutation in the N-terminal domain of SARS-CoV-2 spike protein was identified. 2021 Meta gene Conclusion SARS_CoV_2 V90T 11 15 S;N 73;41 78;42 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. V90T mutation showed positive affirmation towards escaping 2-51 neutralizing antibody. 2021 Meta gene Conclusion SARS_CoV_2 V90T 0 4 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. The non-synonymous SARS-CoV-2 SNV NSP3 D218E is inversely associated with the humoral response to S subunits 1 and 2. 2021 GeroScience Conclusion SARS_CoV_2 D218E 39 44 Nsp3;S 34;98 38;99 34493762 Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. Our analysis presents evidence that the high-frequency mutation N501Y is more transmissible (showed for its greater effective reproduction number) than not-N501Y, but also that control measures do not significantly favor the growth of any one in particular. 2021 Scientific reports Conclusion SARS_CoV_2 N501Y;N501Y 64;156 69;161 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Consistent with our molecular dynamics study, it was reported that especially the K417N + E484K + N501Y (B.1.351) variant of the RBD was more successful in avoiding neutralizing antibodies, and this was due to the high plasticity of the SARS-CoV-2 S and ACE2 interfaces (Hoffmann et al.,). 2021 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 E484K;K417N;N501Y 90;82;98 95;87;103 RBD;S 129;248 132;249 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). However, the investigated three SARS-CoV-2 variants of concern (E484K, N501Y and triple mutant) in this study have significantly increased the binding affinity of all the mutant spike glycoproteins against ACE2, for which we believe that could pose a potential danger to the efficacy of the currently launched anti-SARS-CoV-2 vaccines. 2021 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 N501Y;E484K 71;64 76;69 S 178 197 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). In addition, E484K alone or the triple mutant RBD (K417N + E484K + N501Y) abolished binding of the potent class 2 RBD neutralizing antibodies (nAbs) (Wibmer et al.,). 2021 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 E484K;E484K;N501Y;K417N 13;59;67;51 18;64;72;56 RBD;RBD 46;114 49;117 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). It is clear that the selection pressure on SARS-CoV-2 further increases the RBD-ACE2 stabilization of variants (Fernandez,; Nelson et al.,), and the E484K alone or in combination with K417N and N501Y, potentially results in an 'escape' phenotype (Franceschi, Ferrareze et al.,; Hu et al.,). 2021 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 E484K;K417N;N501Y 149;184;194 154;189;199 RBD 76 79 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Thus, we are of the opinion that E484K and the triple mutant most likely distort the native conformation of the RBD tip, thereby blocking the binding of RBD-directed SARS-CoV-2 antibodies to this domain, and hence the virus may escape from the vaccine-induced immune response. 2021 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 E484K 33 38 RBD;RBD 112;153 115;156 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). We also showed that among variants, E484K and triple mutant triggered the strongest changes in both the binding energy and the conformation. 2021 Journal of biomolecular structure & dynamics Conclusion SARS_CoV_2 E484K 36 41 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. First, the role of the emerging variants, especially the D614G, on the overall 3D structure of the spike protein should lead to change the way how vaccine developers evaluate the neutralization activities of the antibodies that have been previously produced by the immune system of the vaccinated people by the current vaccine. 2021 Biochimie Conclusion SARS_CoV_2 D614G 57 62 S 99 104 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. Previous studies have reported that D614G impacts the SARS-CoV-2 viral fitness and transmissibility by increasing the 'up' conformation in the RBD region of the spike protein. 2021 Biochimie Conclusion SARS_CoV_2 D614G 36 41 S;RBD 161;143 166;146 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The results of this study have also revealed the impact of another critical associated mutation with D614G, which is Q675H; that has a considerable superimposition change at the 3D structure before the Furin cleavage site of the spike protein of SARS-CoV-2, where it has a thermodynamic effect in destabilizing the spike protein with increasing its flexibility. 2021 Biochimie Conclusion SARS_CoV_2 D614G;Q675H 101;117 106;122 S;S 229;315 234;320 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The thermodynamics prediction results in this study have exhibited the stabilizing role of D614G and other variants and their role in increasing the spike protein. 2021 Biochimie Conclusion SARS_CoV_2 D614G 91 96 S 149 154 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. Through the analysis of 79,269 (the UK) and 139,703 (Europe) SARS-CoV-2 genomes, the same 27 candidate key mutation sites were found, including the N501Y mutation on the S protein, and the N501Y mutation was found completely linked to the other 16 specific sites. 2021 Computational and structural biotechnology journal Conclusion SARS_CoV_2 N501Y;N501Y 148;189 153;194 S 170 171 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. For example, the mutations Leu452Arg and Thr478Lys have an effect on the increased affinity of the spike proteins for the ACE2 receptor, which explains the greater pathogenicity of the variant. 2021 Cureus Conclusion SARS_CoV_2 L452R;T478K 27;41 36;50 S 99 104 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. The E484K mutation leads to a very strong K484(S) E75(ACE2) salt bridge described by an OC interaction arising from a orbital interaction. 2022 Chembiochem Conclusion SARS_CoV_2 E484K 4 9 S 47 48 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. The K417N, K417T mutations lead to long range weak N417(S) D30(ACE2) and T417(S) D30(ACE2) interactions. 2022 Chembiochem Conclusion SARS_CoV_2 K417N;K417T 4;11 9;16 S;S 56;80 57;81 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. The N501Y mutation leads to a Y484(S) K353(ACE2) contact described by a collection of orbital interactions, second in strength only to the interactions arising because of the E484K replacement. 2022 Chembiochem Conclusion SARS_CoV_2 E484K;N501Y 180;4 185;9 S 35 36 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. The S477N mutation leads to two N477(S) S19(ACE2) persistent primary hydrogen bonds. 2022 Chembiochem Conclusion SARS_CoV_2 S477N 4 9 S 37 38 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. To summarize, we offer a dissection of the explicit residue to residue intermolecular interactions resulting from the specific S477N, N501Y, K417N, K417T, E484K mutations in the receptor binding domain of the spike protein in the wild-type SARS-COV-2 virus that have led to the highly concerning B.1.160, B.1.1.7 (alpha), B.1.351 (beta), P.1 (gamma), and P.2 (zeta) variants. 2022 Chembiochem Conclusion SARS_CoV_2 E484K;K417N;K417T;N501Y;S477N 155;141;148;134;127 160;146;153;139;132 RBD;S 178;209 201;214 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. Our analysis identifies enhanced prevalence of chemosensory dysfunction as a novel, previously unrecognized phenotype of the now dominant virus with the D614G mutation. 2021 ACS chemical neuroscience Conclusion SARS_CoV_2 D614G 153 158 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. Our analysis shows an increased prevalence of olfactory dysfunction in COVID-19 patients infected with the D614G SARS-CoV-2 virus when compared with patients infected with the original D614 virus. 2021 ACS chemical neuroscience Conclusion SARS_CoV_2 D614G 107 112 COVID-19 71 79 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. Although SARS-CoV-2 is less diverse and adaptable, the D614G variant and the K203/R204 and Delta variants have emerged by either nucleotide mutation or homologous recombination during the rapid, global spread of the virus and do appear to have functional impact. 2021 Pathogens & immunity Conclusion SARS_CoV_2 D614G 55 60 34544043 Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants. At the time of writing, 109 BV-1-like genomes of B.1.1.7 lineage with a Q493R mutation have been reported to GISAID, with the earliest cases reported in the United Kingdom in January 2021, followed by appearances in the rest of Europe, Canada, Brazil, and 12 US states. 2021 The American journal of tropical medicine and hygiene Conclusion SARS_CoV_2 Q493R 72 77 34544043 Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants. Based on this, it is inferred that the Q493R mutation of BV-1 may confer resistance to some neutralizing antibodies, though we have not directly tested the neutralizing activity. 2021 The American journal of tropical medicine and hygiene Conclusion SARS_CoV_2 Q493R 39 44 34544043 Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants. BV-1 is genetically distinct from previously reported B.1.1.7/Q493R variants, forming a new cluster along with 45 other non-Q493R B.1.1.7 sequences, collected January 25 to March 11 from the same on-campus population. 2021 The American journal of tropical medicine and hygiene Conclusion SARS_CoV_2 Q493R;Q493R 62;124 67;129 34544043 Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants. It was recently reported that there are four major epitope classes on the SARS-CoV-2 spike protein receptor-binding domain where neutralizing antibodies bind, and that Q493R (BV-1) and E484K (not found in BV-1, but important in B.1.351 and B.1.617 variants) mediate roughly equivalent levels of resistance to only class-2 neutralizing antibodies, as defined in that study. 2021 The American journal of tropical medicine and hygiene Conclusion SARS_CoV_2 E484K;Q493R 185;168 190;173 S 85 90 34544043 Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants. Mutations of Q493 resulting in an amino acid change to either arginine (R) or lysine (K) have been reported as an adaptation associated with resistance to monoclonal neutralizing antibodies in laboratory tests and Q493K confers resistance to the Regeneron antibody cocktail and bamlanivimab. 2021 The American journal of tropical medicine and hygiene Conclusion SARS_CoV_2 Q493K 214 219 34544043 Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants. Of these, 56 (60%) sequences were of B.1.1.7/20I/501Y.V1 lineage; four isolated from early February through mid-March were of a B.1.1.519/20B lineage including three sequences with the T478K mutation that has been reported from the designated BV-2 (hCoV-19/USA/GHRC-BV2-EQ04518823/2021, hCOV-19/USA/GHRC-BV2-EQ04526485/2021 and hCoV-19/USA/GHRC-BV2-EQ04531246/2021), a lineage was first detected in the United States, but subsequently became common in Canada and Mexico with a peak near the end of March 2021; 22 were B.1.2/20G including BV-3, a genome very similar to other local 20G lineage sequences, except for the addition of a cluster of four spike mutations (P681H, T716I, S982A, and D1118H) that were not present in any local 20G lineage genomes, but were all present on all local 20I/501Y.V1 lineages, suggesting BV-3 arose from a recombination of a partial spike gene from a 20I/501Y.V1 strain on a 20G background (hCoV-19/USA/GHRC-BV3-EQ04527243/2021); five were B.1.596/20G; two were B.1.234/20A; two were B.1.243/20A; and one was B.1/20A (Figure 1). 2021 The American journal of tropical medicine and hygiene Conclusion SARS_CoV_2 D1118H;S982A;T478K;T716I;P681H 691;680;185;673;666 697;685;190;678;671 S;S 649;867 654;872 34544043 Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants. The B.1.1.7/Q493R sequences form 12 clusters, each arising from a non-Q493R lineage, suggesting that Q493R is either more accessible or may have greater adaptive value on a B.1.1.7 background. 2021 The American journal of tropical medicine and hygiene Conclusion SARS_CoV_2 Q493R;Q493R;Q493R 101;12;70 106;17;75 34544043 Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants. Whole-genome sequencing of the initial sample revealed a novel variant B.1.1.7 genetic background, plus an additional mutation in the spike protein gene that would change glutamine 493 to arginine (Q493R). 2021 The American journal of tropical medicine and hygiene Conclusion SARS_CoV_2 Q493R;Q493R 171;198 196;203 S 134 139 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. A good example is the phenomenon of the D614G mutation, which is associated with increased virus transmissibility in the absence of enhanced binding to ACE2. 2022 Journal of pharmaceutical analysis Conclusion SARS_CoV_2 D614G 40 45 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. We forecast that a few co-mutation sets, including [A411S, L452R, T478K], [L452R, T478K, N501Y], [K417N, L452R, T478K], [L452R, T478K, E484K, N501Y], and [P384L, K417N, E484K, N501Y], have a great potential to grow into unprecedentedly dangerous new SARS-CoV-2 variants. 2021 ArXiv Conclusion SARS_CoV_2 E484K;E484K;K417N;L452R;L452R;N501Y;N501Y;N501Y;T478K;T478K;T478K;T478K;A411S;K417N;L452R;L452R;P384L 135;169;162;59;105;89;142;176;66;82;112;128;52;98;75;121;155 140;174;167;64;110;94;147;181;71;87;117;133;57;103;80;126;160 34545334 Review of the mechanisms of SARS-CoV-2 evolution and transmission. We identify that an infectivity-weakening RBD co-mutation set [Y449S, N501Y] stands out among heavily vaccinated populations because it has an exceptionally strong ability to break through existing vaccines, signaling a new mechanism of SARS-CoV-2 evolution and transmission. 2021 ArXiv Conclusion SARS_CoV_2 N501Y;Y449S 70;63 75;68 RBD 42 45 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. In addition, the binding of known inhibitor; GRL0617 to SARS-CoV-2 PLPro might be affected by these mutations to some extent due to the large flexibility around the active site, particularly with the D108G mutation. 2022 Saudi journal of biological sciences Conclusion SARS_CoV_2 D108G 200 205 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. In this study, two mutations within SARS-CoV-2 PLPro were identified including D108G and A249V by analyzing 58 Saudi isolates in comparison to the first sequence reported in Wuhan, China. 2022 Saudi journal of biological sciences Conclusion SARS_CoV_2 A249V;D108G 89;79 94;84 34549097 Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran. The mutation D614G which became the most predominant form in pandemic from May 2020 globally was only found in one of the genome sequences of this study. 2021 Heliyon Conclusion SARS_CoV_2 D614G 13 18 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. However, the immune evasion caused by the mutation of SARS-CoV-2 spike protein, such as the B.1.351 harboring E484K, may reinfect the survivors, weaken or even invalidate the efficacy of mAbs and vaccines. 2022 Briefings in bioinformatics Conclusion SARS_CoV_2 E484K 110 115 S 65 70 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Overall, this work sheds light on the impact of the E484K mutation on mAb efficacy and predicts other potential residue mutations with risk of immune evasion, which may serve as an alarm for future mAb and vaccine development. 2022 Briefings in bioinformatics Conclusion SARS_CoV_2 E484K 52 57 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. The recently identified SARS-CoV-2 variants harboring E484K mutation was found to have great resistance to numerous mAbs. 2022 Briefings in bioinformatics Conclusion SARS_CoV_2 E484K 54 59 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. The results reveal that the E484K mutation impairs most of mAbs (~85%) to bind to the spike RBD. 2022 Briefings in bioinformatics Conclusion SARS_CoV_2 E484K 28 33 S;RBD 86;92 91;95 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. To understand the underlined mechanism, we calculated and analyzed the binding affinities of 26 mAbs to WT spike protein and to the E484K mutant, respectively. 2022 Briefings in bioinformatics Conclusion SARS_CoV_2 E484K 132 137 S 107 112 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. Twenty-two mAbs (85% of all the studied mAbs) have significantly decreased binding affinity to E484K mutant, indicating that E484K mutant is likely resistant to most mAbs. 2022 Briefings in bioinformatics Conclusion SARS_CoV_2 E484K;E484K 95;125 100;130 34553217 Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations. We calculated the binding free energy of current 26 mAbs to WT spike protein and its E484K mutant, respectively. 2022 Briefings in bioinformatics Conclusion SARS_CoV_2 E484K 85 90 S 63 68 34553696 Molecular docking studies of Indian variants of pathophysiological proteins of SARS-CoV-2 with selected drug candidates. With respect to the Spike protein, the most frequent mutation seen is the D614G followed by T572I. 2021 Journal of genetics Conclusion SARS_CoV_2 D614G 74 79 S 20 25 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Additionally, in order to explore the impacts of the E484K mutation on the recognition of neutralizing antibodies/nanobodies to RBD, six different neutralizing antibodies and nanobodies complexed with RBD were studied, in which the changes of the binding free energy induced by the mutation were also calculated by using MD simulations with MMGBSA method. 2021 Journal of molecular graphics & modelling Conclusion SARS_CoV_2 E484K 53 58 RBD;RBD 128;201 131;204 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Besides that, the E484K mutation also causes conformational rearrangements of the local structure around the mutant residue, which results in tighter binding interface of RBD with hACE2 and formation of some new hydrogen bonds. 2021 Journal of molecular graphics & modelling Conclusion SARS_CoV_2 E484K 18 23 RBD 171 174 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. However, serious attentions have been paid to the E484K mutation shared by both the 501Y.V2 and 501Y.V3 variants initially discovered respectively in the United Kingdom and Brazil, which is considered to be potentially associated with improved transmissibility as well as decreased neutralization activity of the present antibodies. 2021 Journal of molecular graphics & modelling Conclusion SARS_CoV_2 E484K 50 55 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In the present work, MD simulations combined with MMGBSA method were employed to evaluate the receptor binding free energy both for the wild-type RBD and the E484K mutant, and then the effects of the mutation on the binding affinity of RBD with the receptor hACE2 were investigated. 2021 Journal of molecular graphics & modelling Conclusion SARS_CoV_2 E484K 158 163 RBD;RBD 146;236 149;239 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The calculation results revealed that for most of the neutralizing antibodies and nanobodies, the E484K mutation significantly reduces the binding affinities between RBD and these antibodies/nanobodies, which may weaken the effectiveness of these antibodies/nanobodies and even evade the immune response. 2021 Journal of molecular graphics & modelling Conclusion SARS_CoV_2 E484K 98 103 RBD 166 169 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The calculation results show that upon the substitution of Glu484 with Lys, the unfavorable gas-phase electrostatic interactions between E484 and the negatively charged residues in hACE2 are converted to be favorable, which significantly contributes to the improved binding affinity of RBD with hACE2. 2021 Journal of molecular graphics & modelling Conclusion SARS_CoV_2 E484K 59 74 RBD 286 289 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The tighter RBD-receptor binding affinity caused by the mutation may be responsible for the more transmissibility of the E484K-containing SARS-CoV-2 variants. 2021 Journal of molecular graphics & modelling Conclusion SARS_CoV_2 E484K 121 126 RBD 12 15 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. Understanding the molecular mechanism behind the impacts of the E484K mutation on the binding affinities of RBD with the receptor hACE2 as well as with various neutralizing antibodies/nanobodies is of great significance for the developments of effective vaccines and antibody/nanobody drugs. 2021 Journal of molecular graphics & modelling Conclusion SARS_CoV_2 E484K 64 69 RBD 108 111 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Mutations in N501Y, N439K, and E484K RBDs showed insignificant changes in flexibility. 2021 Biomolecules Conclusion SARS_CoV_2 E484K;N439K;N501Y 31;20;13 36;25;18 RBD 37 41 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. The higher flexibility in S477N and L452R RBDs did not significantly affect the conformations, since the FEL analysis showed relatively local minima for each. 2021 Biomolecules Conclusion SARS_CoV_2 L452R;S477N 36;26 41;31 RBD 42 46 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. We identified that the essential motion of E484K, N439K, S477N, and L452R RBDs were mainly in the loop Y473-C489, which is located at the binding interface with ACE2 receptor. 2021 Biomolecules Conclusion SARS_CoV_2 E484K;L452R;N439K;S477N 43;68;50;57 48;73;55;62 RBD 74 78 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. In addition, the calculated structure of C145A, whose structure has been obtained experimentally, did not change significantly, despite mutation of the active center residue, consistent with experimental results. 2021 International journal of molecular sciences Conclusion SARS_CoV_2 C145A 41 46 34576002 Virtual Alanine Scan of the Main Protease Active Site in Severe Acute Respiratory Syndrome Coronavirus 2. In SARS-CoV-2 Mpro, mutations H163A and E166A affected ligand recognition but did not change the structure of the catalytic dyad, suggesting that these mutants may weaken the affinity of the inhibitor without a loss in enzymatic activity. 2021 International journal of molecular sciences Conclusion SARS_CoV_2 E166A;H163A 40;30 45;35 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. SARS-CoV-2 Kappa variant harboring E484Q mediate resistance to casirivimab while the substitution T478K present in Delta results in limited neutralization by imdevimab. 2021 Viruses Conclusion SARS_CoV_2 E484Q;T478K 35;98 40;103 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. Considering the current trend of COVID-19 incidence and fatality across the globe (covid19.who.int), we can deduce that these mutations confer a selective advantage of higher virulence and transmissibility of the virus, but might not really be the major player in fatality and higher severity of the disease considering the low fatality due to COVID-19 in Africa despite having the highest prevalence of the most recurrent mutations (P4715L and D614G) observed. 2021 Infection, genetics and evolution Conclusion SARS_CoV_2 D614G;P4715L 445;434 450;440 COVID-19;COVID-19 33;344 41;352 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. We report statistical evidence of the transmission advantage associated with the D614G substitution in SARS-CoV-2. 2021 BMC infectious diseases Conclusion SARS_CoV_2 D614G 81 86 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. In this study, clone 1741-LALA showed a broad neutralizing activity against SARS-CoV-2 D614G and B.1.351 variants, suggesting this mAb may protect against other SARS-CoV-2 variants. 2021 Antiviral research Conclusion SARS_CoV_2 D614G 87 92 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. These include mutations S13I and W152C, decreasing antibody binding, N460K, increasing RDB affinity, or Q498R, positively affecting both properties . 2021 International journal of molecular sciences Conclusion SARS_CoV_2 N460K;Q498R;S13I;W152C 69;104;24;33 74;109;28;38 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. These include mutations S13I and W152C, decreasing antibody binding, N460K, increasing RDB affinity, or Q498R, positively affecting both properties. 2021 International journal of molecular sciences Conclusion SARS_CoV_2 N460K;Q498R;S13I;W152C 69;104;24;33 74;109;28;38 34642638 The evolution of the mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America. However, since late March 2021, once vaccines had provided protection to highly vaccinated populations, several vaccine-resistant mutations such as Y449S and Y449H have been observed relatively frequently. 2021 ArXiv Conclusion SARS_CoV_2 Y449H;Y449S 158;148 163;153 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. In conclusion, the current study revealed the binding differences of some reported variants (N439K, S477 N, and T478K) of the SARS-CoV-2. 2021 Computers in biology and medicine Conclusion SARS_CoV_2 S477N;T478K;N439K 100;112;93 106;117;98 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Our results yield that N439K, S477 N, and T478K variants have a higher binding affinity towards the ACE2 receptor. 2021 Computers in biology and medicine Conclusion SARS_CoV_2 N439K;S477N;T478K 23;30;42 28;36;47 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. Mutations at amino acid positions 121 to 124 exhibited a high frequency of destabilization, with the exception of V121I, V121W, and L122I, present in very low frequencies. 2021 Pathogens (Basel, Switzerland) Conclusion SARS_CoV_2 L122I;V121I;V121W 132;114;121 137;119;126 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. The observation of mutations L452R and E484Q associated with B.1.617.1 variant lineage in similar period of declaration as variant of concern provides a conclusive evidence of WBE as early warning system. 2022 The Science of the total environment Conclusion SARS_CoV_2 E484Q;L452R 39;29 44;34 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. The prevalence of clinically unreported mutations, such as S:P1140del, NSP3:L550del, NSP14:C279F and S:C480R, in circulation from wastewater data, provide conclusive evidence for the potential utilization of wastewater as early warning system. 2022 The Science of the total environment Conclusion SARS_CoV_2 C279F;C480R;L550del;P1140del 91;103;76;61 96;108;83;69 Nsp3;S;S 71;59;101 75;60;102 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. We also report novel mutations such as NSP13:G206F (NSP13), which conclude the capability of wastewater sequencing data to provide mutations in circulation before they are observed clinically. 2022 The Science of the total environment Conclusion SARS_CoV_2 G206F 45 50 Nsp13;Nsp13 39;52 44;57 34705425 Gold-Nanostar-Chitosan-Mediated Delivery of SARS-CoV-2 DNA Vaccine for Respiratory Mucosal Immunization: Development and Proof-of-Principle. The antibody response results in high levels of IgG and IgA, which show a strong neutralizing effect against pseudoviruses expressing different spike variants of SC2 (Wuhan, D614G and beta mutant). 2021 ACS nano Conclusion SARS_CoV_2 D614G 174 179 S 144 149 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. The most frequent substitutions identified have been described globally, such as the G614-carrying virus and V1176F, enhancing viral transmissibility and infectivity. 2021 Microbial genomics Conclusion SARS_CoV_2 V1176F 109 115 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. All the mutant variants declared as VOI/VOC by the WHO and CDC had the D614G mutation common. 2021 Applied microbiology and biotechnology Conclusion SARS_CoV_2 D614G 71 76 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. More studies on the changes in molecular mechanism and virulence of the variants due to the D614G mutation will help future researchers develop proper therapeutics and vaccines, helping to end the pandemic soon. 2021 Applied microbiology and biotechnology Conclusion SARS_CoV_2 D614G 92 97 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Still, some cases of re-infection confirmed the presence of D614G mutation in the genome of these isolates. 2021 Applied microbiology and biotechnology Conclusion SARS_CoV_2 D614G 60 65 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The D614G mutant became predominant across the world within a brief period. 2021 Applied microbiology and biotechnology Conclusion SARS_CoV_2 D614G 4 9 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The virulence was alarming, and therefore, understanding the changes in the molecular mechanism of the variants due to D614G mutation and how it affects their virulence is a prerequisite. 2021 Applied microbiology and biotechnology Conclusion SARS_CoV_2 D614G 119 124 34774600 Structural and functional significance of the amino acid differences Val35Thr, Ser46Ala, Asn65Ser, and Ala94Ser in 3C-like proteinases from SARS-CoV-2 and SARS-CoV. The 3D structures of (Chymo)trypsin-like 3CLpro from SARS-CoV-2 and SARS-CoV have different amino acid residues at 8 positions of their amino acid sequences: Val35Thr, Ser46Ala, Asn65Ser, Val86Leu, Lys88Arg, Ala94Ser, Phe134His, and Asn180Lys. 2021 International journal of biological macromolecules Conclusion SARS_CoV_2 A94S;N180K;N65S;K88R;F134H;S46A;V35T;V86L 208;233;178;198;218;168;158;188 216;242;186;206;227;176;166;196 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Due to the N501Y mutation effect on the immunogenicity of the virus induces immune responses, we recommend that more attention be paid to the identification of SARS-CoV-2 lineage during the admittance of COVID-19 patients. 2022 Journal of cellular biochemistry Conclusion SARS_CoV_2 N501Y 11 16 COVID-19 204 212 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Our team in this current study uses various computational biology approaches examining the significant effects on the function of the spike molecular behavior due to the N501Y mutation. 2022 Journal of cellular biochemistry Conclusion SARS_CoV_2 N501Y 170 175 S 134 139 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. So far, many mutations (E484K, Q493N, and N501T) have been identified in the RBD domain of this protein. 2022 Journal of cellular biochemistry Conclusion SARS_CoV_2 N501T;Q493N;E484K 42;31;24 47;36;29 RBD 77 80 34786352 Gasless laparoendoscopic single-site surgery for management of unruptured tubal pregnancy in a woman with moderate COVID-19 pneumonia after administration of remdesivir and casirivimab-imdevimab: A case report. Real-time reverse transcription polymerase chain reaction assay (RT-PCR) was positive for SARS-CoV-2, which was subsequently shown to be an L452R variant. 2022 Case reports in women's health Conclusion SARS_CoV_2 L452R 140 145 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. We also detected the occurrence of an additional mutation S:(E661D) in the Gamma variant genomes. 2021 Virology journal Conclusion SARS_CoV_2 E661D 61 66 S 58 59 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. The recent development of the DARPin ensovibep (comprising the N-Cap Asp17Leu mutation) in less than 9 months from idea conception to entry into the clinics underlines this huge potential. 2022 The Journal of biological chemistry Conclusion SARS_CoV_2 D17L 69 77 N 63 64 34794434 SARS-CoV-2 exposure in Malawian blood donors: an analysis of seroprevalence and variant dynamics between January 2020 and July 2021. We report a dramatic rise in SARS-CoV-2 seroprevalence from 18.5% in October 2020 to 64.9% in May 2021 in healthy blood donors as Malawi experienced the first and second COVID-19 epidemic waves, likely driven initially by the original variant (D614G WT) and then the beta variant. 2021 BMC medicine Conclusion SARS_CoV_2 D614G 244 249 COVID-19 170 178 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. It is great period to prepare a vaccine or a neutralizing antibody against SARS-CoV-2 delta variant to prevent another wave of SARS-CoV-2 pandemic although there is no experimental evidence to confirm the significance of the T478K mutation in the SARS-CoV-2 delta variant. 2021 Immune network Conclusion SARS_CoV_2 T478K 225 230 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. The analysis of mutation sites in the critical RBM of spike protein on the SARS-CoV-2 variants ascertained a distinct T478K mutation in the SARS-CoV-2 delta variant. 2021 Immune network Conclusion SARS_CoV_2 T478K 118 123 S 54 59 34804549 Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography. We describe details of the co-crystal structure of SARS-CoV-2 Mpro bearing an active-site C145A mutation in complex with an octapeptide substrate corresponding to the natural nsp4/nsp5 junction sequence which Mpro autoprocesses prior to its C-terminal junction (nsp5/nsp6 site) during its maturation from the polyprotein precursor (Hsu et al., 2005; Chen, Jonas et al., 2010; Muramatsu et al., 2013). 2021 IUCrJ Conclusion SARS_CoV_2 C145A 90 95 Nsp4;Nsp5;Nsp5;Nsp6 175;180;262;267 179;184;266;271 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. Among all of the considered mutations that showed positive allosteric modulation, K417N was found to have the largest effects on the allostery and thereby holds the highest binding affinity with ACE2, providing an explanation as to why the delta variant shows higher transmissibility. 2021 ACS omega Conclusion SARS_CoV_2 K417N 82 87 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. We have described structural and functional significance of SARS-CoV-2 variant-specific spike (S) protein RBD mutations, E484K, K417N, L452Q, L452R, N501Y, and T478K, which characterize and differentiate several variants of interest/concern (VOIs/VOCs) as reported by the World Health Organization (WHO). 2021 ACS omega Conclusion SARS_CoV_2 E484K;K417N;L452Q;L452R;N501Y;T478K 121;128;135;142;149;160 126;133;140;147;154;165 S;RBD;S 88;106;95 93;109;96 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. A CRISPR-LAMP assay for SARS-CoV-2 B.1.1.7 variant major point mutation spike N501Y has also been developed. 2021 Analytical chemistry Conclusion SARS_CoV_2 N501Y 78 83 S 72 77 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. Combined with common LAMP primers, CRISPR-LAMP technology can efficiently detect point mutation with 10 copies of template which can even detect wild-type at 1% levels on the background of spike N501Y template. 2021 Analytical chemistry Conclusion SARS_CoV_2 N501Y 195 200 S 189 194 34829998 SARS-CoV-2 Variants, RBD Mutations, Binding Affinity, and Antibody Escape. Variant-induced risk of breakthrough infections among vaccinated people was attributed to the L452R mutations, decreasing the binding affinity of many antibodies. 2021 International journal of molecular sciences Conclusion SARS_CoV_2 L452R 94 99 34835101 Impact of the Double Mutants on Spike Protein of SARS-CoV-2 B.1.617 Lineage on the Human ACE2 Receptor Binding: A Structural Insight. This study concludes that the occurrence of kappa (L452R, E484Q) and delta (L452R + T478K) variants were more stable than the wt SARS-CoV-2 S protein. 2021 Viruses Conclusion SARS_CoV_2 E484Q;T478K;L452R;L452R 58;84;51;76 63;89;56;81 S 140 141 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. In this study, through analyzing the patterns and localizations of both genomic and proteomic mutations in SARS-CoV-2 isolates from the South Asian regions, we found that the D614G (G-clade) mutation was the most prominent mutation (81.7%; 335/410 samples) in the South Asian isolates. 2021 Current research in microbial sciences Conclusion SARS_CoV_2 D614G 175 180 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. We also identified a missense mutation (1163A > T) which was unique to only Bangladeshi isolates. 2021 Current research in microbial sciences Conclusion SARS_CoV_2 A1163T 40 49 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Following self-sampling, screening of mutations of concern, and a combined phylogenomic and population genetics pipeline of the SARS-CoV-2 virus, we reveal the appearance of specific mutations of concern in the spike protein that define the postulated variants of interest P.4 (B.1.1.28.4) and 20B/478K.V1 (B.1.1.222, leading to B.1.1.519), and in the nucleocapsid protein, N:S194L, in Mexico during the pre-vaccination stage. 2021 Microbial genomics Conclusion SARS_CoV_2 S194L 376 381 N;S;N 352;211;374 364;216;375 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. The mutation S194L in the nucleocapsid was found to associate with symptomatic patients versus asymptomatic carriers in the population investigated. 2021 Microbial genomics Conclusion SARS_CoV_2 S194L 13 18 N 26 38 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. In addition, the Epsilon variant is relatively more easily dissociated from ACE2 than others due to its destabilized RBD structure upon the L452R mutation. 2021 Journal of chemical theory and computation Conclusion SARS_CoV_2 L452R 140 145 RBD 117 120 34856802 Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. K417N/T mutations of Beta and Gamma appear to make the RBD-ACE2 interactions less strong compared to the Alpha variant. 2021 Journal of chemical theory and computation Conclusion SARS_CoV_2 K417N;K417T 0;0 7;7 RBD 55 58 34866979 Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study. The SARS CoV-2 variants isolated in Saudi Arabia showed high homology compared to original strain (Wuhan strain) and revealed characterized pattern of coexisting mutations (C241T, C3037T, C14408T and A23403G). 2021 Saudi journal of biological sciences Conclusion SARS_CoV_2 A23403G;C14408T;C3037T;C241T 200;188;180;173 207;195;186;178 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Glycan modification at most N-glycosites is very similar between WA1 and D614G and primarily high-mannose, with significant differences at N343. 2021 Frontiers in chemistry Conclusion SARS_CoV_2 D614G 73 78 N 28 29 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Glycan modification at most N-glycosites is very similar between WA1 and D614G, with significant differences at N343. 2021 Frontiers in chemistry Conclusion SARS_CoV_2 D614G 73 78 N 28 29 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. In this study, we characterized the site-specific glycosylation of the spike protein from recombinant RBD and S1 domains and from two intact viruses, the WA1 strain and the D614G variant. 2021 Frontiers in chemistry Conclusion SARS_CoV_2 D614G 173 178 S;RBD 71;102 76;105 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Our results also revealed different patterns of glycan modification among the recombinant S1 protein, recombinant RBD, and the WA1 and D614G strains, which implies that these spike proteins may perform differently in vitro and in vivo. 2021 Frontiers in chemistry Conclusion SARS_CoV_2 D614G 135 140 S;RBD 175;114 180;117 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. The D614G variant, carrying the protein amino acid change at 614 from aspartate(D) to glycine(G), is now prevalent in the circulating SARS-CoV-2 virus and is carried by all recently identified and highly concerning SARS-CoV-2 variants. 2021 Frontiers in chemistry Conclusion SARS_CoV_2 D614G 4 9 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. We also analyzed the glycan modification of whole viruses, the WA1 strain, and the D614G variant. 2021 Frontiers in chemistry Conclusion SARS_CoV_2 D614G 83 88 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. We found different patterns of glycan modification among the recombinant S1 protein, recombinant RBD, and WA1 and D614G strains. 2021 Frontiers in chemistry Conclusion SARS_CoV_2 D614G 114 119 RBD 97 100 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. Here, we performed genome-wide association analyses on all SARS-CoV-2 genomes in the GISAID database, and found that a mutation at genomic position 11 083, namely the 11083G>T mutation, located in the coding region of non-structural protein 6, is significantly associated with asymptomatic COVID-19, adjusted for various confounders and covariates, including virus phylogenetic relatedness, patient age, gender and country. 2021 Microbial genomics Conclusion SARS_CoV_2 G11083T 167 175 COVID-19 290 298 34876033 Emergence of SARS-CoV-2 resistance mutations in a patient who received anti-SARS-COV2 spike protein monoclonal antibodies: a case report. It showed a typical B1.1.7 variant on the first sample (April 13th); double populations: K417K/N, E484E/K and Q493Q/R on the 2nd sample (28th April), and E484K and K417N on the 3rd sample (May 8th). 2021 BMC infectious diseases Conclusion SARS_CoV_2 E484E;E484K;E484K;K417K;K417N;K417N;Q493Q;Q493R 98;98;154;89;89;164;110;110 105;105;159;96;96;169;117;117 34876033 Emergence of SARS-CoV-2 resistance mutations in a patient who received anti-SARS-COV2 spike protein monoclonal antibodies: a case report. The first main peak had a melting temperature compatible with the wild type 484, and a second smaller peak had a melting temperature compatible with substitution E484K. 2021 BMC infectious diseases Conclusion SARS_CoV_2 E484K 162 167 34876033 Emergence of SARS-CoV-2 resistance mutations in a patient who received anti-SARS-COV2 spike protein monoclonal antibodies: a case report. This time, the highest peak had a melting temperature compatible with the E484K substitution, while the smaller one was compatible with the wild type 484. 2021 BMC infectious diseases Conclusion SARS_CoV_2 E484K 74 79 34876033 Emergence of SARS-CoV-2 resistance mutations in a patient who received anti-SARS-COV2 spike protein monoclonal antibodies: a case report. Variant screening with TaqPath assay (ThermoFisher, Waltham, Massachusetts, USA) and VirSNiP SARS-CoV-2 Spike 484K-501Y assay (TIB Molbiol, Berlin, Germany) allowed the detection of a B.1.1.7 variant further confirmed by Sanger sequencing (69-70 and 144 deletions, and N501Y mutation on the S gene) with glutamic acid on position 484 (wild type). 2021 BMC infectious diseases Conclusion SARS_CoV_2 N501Y 269 274 S;S 104;291 109;292 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. The results of this study revealed that the single D614G substitution had impacts on the glycosylation of the spike protein and half of the N-glycosylation sequons in the S showed a difference in the distribution of various glycan forms between the S-614D and S-614G variants. 2021 Scientific reports Conclusion SARS_CoV_2 D614G 51 56 S;N;S;S;S 110;140;171;249;260 115;141;172;250;261 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. We analyzed the N-glycosylation profiles of the SARS-CoV-2 spike D614G variant and its ancestor protein using advanced EThcD mass spectrometry. 2021 Scientific reports Conclusion SARS_CoV_2 D614G 65 70 S;N 59;16 64;17 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. The presented data provide further support for continuous monitoring of E484K within emerging Delta sub-lineages, such as the Delta strain examined here. 2021 Euro surveillance Conclusion SARS_CoV_2 E484K 72 77 34886945 Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020. It is also important to acquire a thorough understanding of viral phenotypes, clinical and epidemiological characteristics of emerging SARS-CoV-2mutants such as D614G, such that surveillance and disease control measures could be adjusted dynamically to counter the evolving risks posed by dominant mutant clades. 2021 Euro surveillance Conclusion SARS_CoV_2 D614G 161 166 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. In summary, we report that the RT-CORDS is an accurate and sensitive system for identifying single-base mutations (N501Y and D614G) and a small deletion (69/70 deletion) mutation in SARS-CoV-2 variants using CRISPR/Cas12a. 2022 Biosensors & bioelectronics Conclusion SARS_CoV_2 D614G;N501Y 125;115 130;120 34909459 Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M(pro). Also, molecular docking simulations are performed to predict the potential inhibitory potency of compounds 1-4 toward SARS-CoV-2 main protease Mpro and mutation of SARS-CoV-2 Spike (S) Protein D614G. 2021 ChemistrySelect Conclusion SARS_CoV_2 D614G 193 198 S;S 175;182 180;183 34909459 Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M(pro). As regard molecular docking simulations with Spike (S) Protein D614G, the prominent inhibitory potency shows OPG, while examined adamantly- isothiourea derivatives possess similar inhibitory potential between each other. 2021 ChemistrySelect Conclusion SARS_CoV_2 D614G 63 68 S;S 45;52 50;53 34909459 Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M(pro). The important thermodynamical parameters from docking simulations with D614G, Table S4. 2021 ChemistrySelect Conclusion SARS_CoV_2 D614G 71 76 34909634 Severe breakthrough COVID-19 with a heavily mutated variant in a multiple myeloma patient 10 weeks after vaccination. Both mutations in the receptor-binding domain (RBD) of spike, N440K and E484Q, were in only our patient's strain. 2022 Clinical infection in practice Conclusion SARS_CoV_2 E484Q;N440K 72;62 77;67 S;RBD 55;47 60;50 34912372 Hotspot Mutations in SARS-CoV-2. Finally, SSIPe is used to report the binding affinity between the RBD of Spike protein and human ACE2 protein by considering L452R, T478K, E484Q, and N501Y hotspot mutations in that region. 2021 Frontiers in genetics Conclusion SARS_CoV_2 E484Q;L452R;N501Y;T478K 139;125;150;132 144;130;155;137 S;RBD 73;66 78;69 34912372 Hotspot Mutations in SARS-CoV-2. Some important mutations in such sequences pertaining to the Delta variant of SARS-CoV-2 are T19R, G142D, E156-, F157-, L452R, T478K, and P681R. 2021 Frontiers in genetics Conclusion SARS_CoV_2 G142D;L452R;P681R;T19R;T478K 99;120;138;93;127 104;125;143;97;132 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. Keeping the fact of EGFR kinase activity, this report suggests the possibility of phosphorylating N501Y mutation that is located on the interface region to further potentiate its importance. 2022 Travel medicine and infectious disease Conclusion SARS_CoV_2 N501Y 98 103 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. Also, we found important mutations such as E484K, L18F, and D614G, which impact on viral transmissibility, host immunity, and disease severity. 2022 Infection, genetics and evolution Conclusion SARS_CoV_2 D614G;E484K;L18F 60;43;50 65;48;54 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. Simulations of the D614G spike show that this mutation affects communication between the FA site and the FPPR and the S2' cleavage site. 2021 Computational and structural biotechnology journal Conclusion SARS_CoV_2 D614G 19 24 S 25 30 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. The D614G mutant shows reduced response of the FPPR and a slower rate of signal propagation to the S2' cleavage site compared to the wild-type protein (Movie 2). 2021 Computational and structural biotechnology journal Conclusion SARS_CoV_2 D614G 4 9 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. These results indicate that the D614G mutation affects the allosteric behaviour and the response to LA of the spike, which may be related to the changes in viral fitness associated with this mutation. 2021 Computational and structural biotechnology journal Conclusion SARS_CoV_2 D614G 32 37 S 110 115 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. An interaction of the catalytically inactive mutant enzyme (C145A Mpro) with the same substrate revealed that the enzyme normally induces conformational changes in the peptide during the complex formation. 2021 Frontiers in pharmacology Conclusion SARS_CoV_2 C145A 60 65 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. Indeed, the interaction of PF-00835231 in the active site of C145A Mpro, which is incapable of a covalent binding with this compound, revealed that there are only two reversible steps of binding-complex formation. 2021 Frontiers in pharmacology Conclusion SARS_CoV_2 C145A 61 66 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. The analysis of kinetics using the WT enzyme together with its catalytically inactive mutant, C145A, enabled us to identify the mechanism of action of the inhibitors and gave an opportunity to hypothesize the therapeutic potential of a model drug. 2021 Frontiers in pharmacology Conclusion SARS_CoV_2 C145A 94 99 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. Analysis of the clinical and genomic data revealed a strong link between disease severity and mortality and a particular mutation in the ORF7a protein, A105V. 2021 Biology Conclusion SARS_CoV_2 A105V 152 157 ORF7a 137 142 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. Structural computational analyses showed that A105V changed the conformational landscape most likely by altering the binding affinity of ORF7a protein. 2021 Biology Conclusion SARS_CoV_2 A105V 46 51 ORF7a 137 142 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. The study demonstrates the importance of ORF7a mutation A105V as a gain-of-function protein and paves the way for further work in determining its precise biological impact at cellular level that plays an important role in COVID-19 pathogenesis. 2021 Biology Conclusion SARS_CoV_2 A105V 56 61 ORF7a 41 46 COVID-19 222 230 34943225 Insights into the Binding of Receptor-Binding Domain (RBD) of SARS-CoV-2 Wild Type and B.1.620 Variant with hACE2 Using Molecular Docking and Simulation Approaches. The current findings based on protein complex modeling and bio-simulation methods revealed the atomic features of the B.1.620 variant harboring S477N and E484K mutations in the RBD. 2021 Biology Conclusion SARS_CoV_2 E484K;S477N 154;144 159;149 RBD 177 180 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. Using computational simulation approaches, we presented the probable mechanisms of increase in the binding affinity of spike mutants (L452R, T478K, and N501Y) to human ACE2 receptor. 2022 Journal of King Saud University. Science Conclusion SARS_CoV_2 N501Y;T478K;L452R 152;141;134 157;146;139 S 119 124 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. In addition, T487S and L472P weakened the binding affinity of SARS-CoV-1 S RBD. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 L472P;T487S 23;13 28;18 RBD;S 75;73 78;74 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. The analysis of viral isolates from 2002 to 2003 and 2003-2004 showed that residue changes N479K, L472P, and F360S destabilized the S protein of 2003-2004 viral isolate leading to a reduction in infection rate. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 F360S;L472P;N479K 109;98;91 114;103;96 S 132 133 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Here we show that pseudoviruses bearing B.1.617.1 spike with L452R and E484Q substitutions, and B.1.617.2 spike with K417N, L452R and T478K substitutions, have modestly reduced susceptibility to neutralization by Pfizer/BioNtech BNT162b2 or Moderna mRNA-1273 vaccine-elicited sera and convalescent sera compared to pseudoviruses bearing WT(D614G) spike. 2021 Viruses Conclusion SARS_CoV_2 E484Q;K417N;L452R;L452R;T478K;D614G 71;117;61;124;134;340 76;122;66;129;139;345 S;S;S 50;106;347 55;111;352 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. Resistance to the remaining therapeutic neutralizing antibodies is due to RBD substitutions, K417N, L452R, and E484Q, but not T478K. 2021 Viruses Conclusion SARS_CoV_2 E484Q;K417N;L452R;T478K 111;93;100;126 116;98;105;131 RBD 74 77 34960755 SARS-CoV-2 Delta Variant Displays Moderate Resistance to Neutralizing Antibodies and Spike Protein Properties of Higher Soluble ACE2 Sensitivity, Enhanced Cleavage and Fusogenic Activity. The individual L452R, T478K, E484Q, and dual L452R + T478K substitutions accounted for most but not all of the reduction in neutralization potency of the sera, suggesting contributions from substitutions in the NTD/CTD. 2021 Viruses Conclusion SARS_CoV_2 E484Q;L452R;L452R;T478K;T478K 29;15;45;22;53 34;20;50;27;58 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. However, in the case of N121Q mutation, although Q121 still maintained hydrogen bond interaction with biliverdin, the overall binding mode deviated significantly under the reversal of the benzene ring of the Phe175 side chain compared with WT. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 N121Q 24 29 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. However, the R190K mutation had little influence on the gate loop and could also make the structural change of the gate loop similar to WT. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 R190K 13 18 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. In addition, N121Q significantly promoted the gate loop deviating to the biliverdin binding site and compressed the site so that biliverdin could not maintain the binding mode of WT. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 N121Q 13 18 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. Moreover, we found that R190K and N121Q mutants would stabilize the lip loop. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 N121Q;R190K 34;24 39;29 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. Our simulations confirmed that the R190K mutation causes amino acid 190 to form six hydrogen bonds with surrounding residues Ser94, Glu96, Asn99, and Ile101, which, guided by Asn99 and Ile101, brings Lys190 closer to Arg102 and Asn121, thereby weakening the interaction energy between biliverdin and Ile101 as well as Lys190. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 R190K 35 40 34966787 Computational Insights Into the Effects of the R190K and N121Q Mutations on the SARS-CoV-2 Spike Complex With Biliverdin. Previous studies have reported the crystal structure of the SARS-CoV-2 spike and biliverdin and have come up with the idea that two single-site mutations, R190K and N121Q, will weaken the binding affinity of the biliverdin although the potential molecular mechanism is still unknown. 2021 Frontiers in molecular biosciences Conclusion SARS_CoV_2 N121Q;R190K 165;155 170;160 S 71 76 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. The data revealed that the D614G mutation particularly contributes to the enhanced infectivity. 2022 Computers in biology and medicine Conclusion SARS_CoV_2 D614G 27 32 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. We discovered that N501I and N501T might potentially cause unusual virulence if they emerged in the near future. 2022 Computers in biology and medicine Conclusion SARS_CoV_2 N501I;N501T 19;29 24;34 35041639 A 48-Year-Old Immunocompetent Female Resident of Southern Florida with Confirmed Reinfection with P.1 (Gamma) Variant of SARS-CoV-2. WGS of viral RNA from the patient's second infection showed the viral strain to be P.1 variant containing the E484K spike protein substitution, which is considered a substitution of therapeutic concern (SOTC) by the CDC. 2022 The American journal of case reports Conclusion SARS_CoV_2 E484K 110 115 S 116 121 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. On the other hand, the rapid test reduces its detection sensitivity compared to samples positive for SARS-CoV-2, but that present the mutations K417N/T, E484K, and N501Y observing a detection capacity of 42% in ranges of 20 <= Cq <25. 2021 Frontiers in public health Conclusion SARS_CoV_2 E484K;K417N;K417T;N501Y 153;144;144;164 158;151;151;169 35055023 Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors. Additionally, amino acid substitutions at residues 11 and 17 of MP3 enhance its binding more, especially D17R. 2022 International journal of molecular sciences Conclusion SARS_CoV_2 D17R 105 109 35055023 Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors. The D17R substitution shows significant change in PC, which could be the reason behind their enhanced binding. 2022 International journal of molecular sciences Conclusion SARS_CoV_2 D17R 4 8 35062214 Tracking SARS-CoV-2 Spike Protein Mutations in the United States (January 2020-March 2021) Using a Statistical Learning Strategy. However, we note that our analyses also identified a haplotype N6 (Table 2) that exhibits the subsequently well-documented mutation P681R, characteristic of the Delta variant that has dominated infections world-wide during the latter half of 2021. 2021 Viruses Conclusion SARS_CoV_2 P681R 132 137 35062281 Intra-Host SARS-CoV-2 Evolution in the Gut of Mucosally-Infected Chlorocebus aethiops (African Green Monkeys). Second, the combination of the three mutations identified (ORF1a/b S2103F, spike D215G, and spike H655Y) may represent an adaptation to AGM or to NHP generally. 2022 Viruses Conclusion SARS_CoV_2 D215G;H655Y;S2103F 81;98;67 86;103;73 ORF1a;S;S 59;75;92 64;80;97 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. The breakthrough infections showed unique mutational changes at position S:D574Y in cases of the Delta variant, whereas from the Kappa variant conserved aa change at position 95 (T) as in the Wuhan isolate. 2021 Frontiers in medicine Conclusion SARS_CoV_2 D574Y 75 80 S 73 74 35074352 Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. In this study, we have identified the co-occurrence of two pairs of mutations (T73 A/D253N, and S477N/A522S) which could be of concern, reinforcing the importance of the WBE for the early detection of potential novel variants. 2022 Environmental research Conclusion SARS_CoV_2 S477N;A522S;D253N;A253N 96;102;83;83 101;107;90;90 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. The antibodies against N501Y, E484K, and L452R/E484Q-mutants were less effective than RBD and D614G-mutant. 2022 Analytical chemistry Conclusion SARS_CoV_2 D614G;E484K;L452R;N501Y;E484Q 94;30;41;23;47 99;35;46;28;52 RBD 86 89 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. The concentrations of antibodies against RBD, D614G, N501Y, E484K, and L452R/E484Q-mutants are measured by our platform. 2022 Analytical chemistry Conclusion SARS_CoV_2 D614G;E484K;L452R;N501Y;E484Q 46;60;71;53;77 51;65;76;58;82 RBD 41 44 35115239 Persistent viral shedding of severe acute respiratory syndrome coronavirus 2 after treatment with bendamustine and rituximab: A case report. The NPS tested positive for the SARS-CoV-2, N501Y variant, with a cycle threshold (Ct) value of 29.3. 2022 Journal of infection and chemotherapy Conclusion SARS_CoV_2 N501Y 44 49 35115239 Persistent viral shedding of severe acute respiratory syndrome coronavirus 2 after treatment with bendamustine and rituximab: A case report. The specimen tested positive for SARS-CoV-2, N501Y variant with a Ct value of 21.3; the patient tested negative for both SARS-CoV-2 total antibody and SARS-CoV-2 spike protein antibody, which were measured using the electrochemiluminescent immunoassay test (Elecsys Anti-SARS-CoV-2 S, Roche Diagnostics K.K., Tokyo, Japan). 2022 Journal of infection and chemotherapy Conclusion SARS_CoV_2 N501Y 45 50 S;S 162;282 167;283 35115239 Persistent viral shedding of severe acute respiratory syndrome coronavirus 2 after treatment with bendamustine and rituximab: A case report. Two weeks after the diagnosis, PCR testing of a NPS demonstrated persistent positivity for the N501Y variant; the Ct value was 32.6. 2022 Journal of infection and chemotherapy Conclusion SARS_CoV_2 N501Y 95 100 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. Compared to the WT virus, the N501Y, Q493K/R, and T478K mutations are responsible for the higher force for RBDOmicrons-ACE2 dissociation. 2022 bioRxiv Conclusion SARS_CoV_2 N501Y;Q493K;Q493R;T478K 30;37;37;50 35;44;44;55 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. Our analysis shows that the Omicron variants exhibit unique interaction patterns reminiscing the features of previously dominated Alpha (N501Y) and Delta (L452R and T478K) variants. 2022 bioRxiv Conclusion SARS_CoV_2 T478K;L452R;N501Y 165;155;137 170;160;142 35118473 Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. This study characterizes interactions between ACE2 and the Omicron RBDs (Q493K or Q493R). 2022 bioRxiv Conclusion SARS_CoV_2 Q493R;Q493K 82;73 87;78 RBD 67 71 35128118 SARS-CoV-2 in Egypt: epidemiology, clinical characterization and bioinformatics analysis. All Egyptian variants showed a unique mutation (D614G/Q57H/V5F/G823S) pattern. 2022 Heliyon Conclusion SARS_CoV_2 D614G;G823S;Q57H;V5F 48;63;54;59 53;68;58;62 35136839 Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike. Amongst all the mutations, the single T500S mutation was found to be most effective. 2022 Translational medicine communications Conclusion SARS_CoV_2 T500S 38 43 35136839 Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike. It was further noticed that single mutation- T500S, double mutations- Y489S/T500S and triple mutations- Y489S/Y453S/T500Y could be great universal ACE2 blockers. 2022 Translational medicine communications Conclusion SARS_CoV_2 T500S;Y489S;Y489S;T500S;T500Y;Y453S 45;70;104;76;116;110 50;75;109;81;121;115 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. An in vitro analysis of post-vaccination sera from different vaccines simultaneously showed significantly decreased activity against the variants of concern containing E484K. 2022 Infection and drug resistance Conclusion SARS_CoV_2 E484K 168 173 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K can be selected when a culture recombinant virus expressing SARS-CoV-2 S is treated with antibody cocktails, and new variants with novel mutations are on the rise. 2022 Infection and drug resistance Conclusion SARS_CoV_2 E484K 0 5 S 77 78 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K escapes the neutralizing effect of several monoclonal antibodies, convalescent plasma, and post-vaccine sera. 2022 Infection and drug resistance Conclusion SARS_CoV_2 E484K 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K has emerged frequently in several SARS-CoV-2 variants of concern/interest. 2022 Infection and drug resistance Conclusion SARS_CoV_2 E484K 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K mutation also reduced neutralization of post-vaccination sera. 2022 Infection and drug resistance Conclusion SARS_CoV_2 E484K 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K reduced the susceptibility to casirivimab (25-fold), but retained susceptibility when casirivimab was combined with imdevimab. 2022 Infection and drug resistance Conclusion SARS_CoV_2 E484K 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. In January 2021, Moderna developed a modified vaccine, a boosting dose of mRNA-1273.351, targeting the beta variant and three mutations (E484K, N501Y, and K417N). 2022 Infection and drug resistance Conclusion SARS_CoV_2 K417N;N501Y;E484K 155;144;137 160;149;142 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Monoclonal antibodies derived from convalescent patients were further studied, and class 2 antibodies, which bind to RBD both in "up" and "down" conformations of the spike, were proved to be resistant to the E484K mutation. 2022 Infection and drug resistance Conclusion SARS_CoV_2 E484K 208 213 S;RBD 166;117 171;120 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Other monoclonal antibodies, such as sotrovimab, AZD7442, regdanvimab, and REGN-COV2, also retained their activity against E484K in vitro. 2022 Infection and drug resistance Conclusion SARS_CoV_2 E484K 123 128 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. Several studies have revealed that the E484K mutation reduces the neutralization of convalescent sera, as proved by a pseudoviral assay. 2022 Infection and drug resistance Conclusion SARS_CoV_2 E484K 39 44 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. The impact of E484K on the susceptibility to monoclonal antibodies were assessed. 2022 Infection and drug resistance Conclusion SARS_CoV_2 E484K 14 19 35151002 Rapid biosensing SARS-CoV-2 antibodies in vaccinated healthy donors. A detailed protocol was developed to detect BAbs against the RBD-N501Y variant, which helps to study the efficacy of new vaccines and therapeutic antibodies against coronavirus mutants. 2022 Biosensors & bioelectronics Conclusion SARS_CoV_2 N501Y 65 70 RBD 61 64 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. In conclusion, this work analyzed the mutation T1117I in the spike protein of the SARS-CoV-2. 2022 Gene reports Conclusion SARS_CoV_2 T1117I 47 53 S 61 66 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. S:T1117I is found in the lineage B.1.1.389 and its positive selection affected the spread of genomes carrying this mutation in Costa Rica. 2022 Gene reports Conclusion SARS_CoV_2 T1117I 2 8 S 0 1 35157870 Detection of SARS-CoV-2 RNA in wastewater, river water, and hospital wastewater of Nepal. N501Y mutation was also detected in one of the influent samples, highlighting the applicability of WBE in detecting variants of SARS-CoV-2. 2022 The Science of the total environment Conclusion SARS_CoV_2 N501Y 0 5 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. By combining conformational dynamics and local frustration analysis with the ensemble-based mutational scanning, our analysis demonstrated that A570D and D614G mutational sites emerge as key inter-protomer hinges that control functional movements and allosteric conformational changes in the S-B.1.1.7 variant (Figure 6C,D). 2022 International journal of molecular sciences Conclusion SARS_CoV_2 A570D;D614G 144;154 149;159 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. Collective dynamics of the S protein variants confirmed a critical regulatory role of the A570D and D614G positions acting as components of hinge clusters controlling the transitions between closed and open forms. 2022 International journal of molecular sciences Conclusion SARS_CoV_2 A570D;D614G 90;100 95;105 S 27 28 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. The results suggest that mutational variants target key residues of the spike protein that coordinate an allosteric cross-talk between rigid hinge sites (A570D, D614G) and more flexible RBD mutational sites (K417N, E484K, and N501Y). 2022 International journal of molecular sciences Conclusion SARS_CoV_2 D614G;E484K;N501Y;A570D;K417N 161;215;226;154;208 166;220;231;159;213 S;RBD 72;186 77;189 35163572 Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. We found that K417N, E484K and N501Y sites are relatively tolerant to modifications in the S-B.1.351 closed and open conformations. 2022 International journal of molecular sciences Conclusion SARS_CoV_2 E484K;K417N;N501Y 21;14;31 26;19;36 S 91 92 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. We also found that the most frequent variant, the missense p.Asp614Gly in the S protein, occurs almost exclusively in concomitance with three other variants, suggesting a high linkage and a potential cooperative effect on the virus fitness. 2022 PloS one Conclusion SARS_CoV_2 D614G;D614G 59;61 70;70 S 78 79 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. In conclusion, sufficient neutralizing antibodies in Japanese participants after BNT162b2 vaccination were produced against the original, R.1 lineage, and Alpha variants of SARS-CoV-2, while an insufficient humoral immunity was observed against the Beta and Delta variants, indicating that the E484K mutation is not the sole factor contributing toward a weakened humoral response. 2022 Vaccine Conclusion SARS_CoV_2 E484K 294 299 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. The maximum heparin binding affinity is observed in Alpha variant, N501Y. 2022 Process biochemistry (Barking, London, England) Conclusion SARS_CoV_2 N501Y 67 72 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. After our finding, we performed a search of Mu strains with the K417N mutation on Nextstrain (https://nextstrain.org/), where we found that sequences matching these criteria had already been included in the database since June 2021. 2022 Archives of virology Conclusion SARS_CoV_2 K417N 64 69 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. The appearance of a Mu variant with a K417N mutation requires the adaptation of the characterization workflow used in our laboratory, since Mu and Beta have the same mutations that had been used for Beta characterization. 2022 Archives of virology Conclusion SARS_CoV_2 K417N 38 43 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. To distinguish between these two variants, we propose the detection of the P681H mutation (i.e., VirSNiP Assays, TIB MOLBIOL, Germany) when the initial screening cannot distinguish between the Mu and Beta variants, as this mutation is present in Mu but not in Beta. 2022 Archives of virology Conclusion SARS_CoV_2 P681H 75 80 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. Two months later, in August 2021, a Mu variant harboring the K417N mutation was described for the first time in three different samples in our region. 2022 Archives of virology Conclusion SARS_CoV_2 K417N 61 66 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. Using rRT-PCR to detect mutations, we encountered a misidentification problem regarding the B.1.621 variant, which contains a K417N mutation. 2022 Archives of virology Conclusion SARS_CoV_2 K417N 126 131 35206580 Classical and Next-Generation Vaccine Platforms to SARS-CoV-2: Biotechnological Strategies and Genomic Variants. In laboratory tests, SARS-CoV-2 variants containing the L452R or E484K substitution in the spike protein cause a marked reduction in susceptibility to bamlanivimab and possibly also etesevimab and casirivimab. 2022 International journal of environmental research and public health Conclusion SARS_CoV_2 E484K;L452R 65;56 70;61 S 91 96 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. We also found that G462D, C297S and S460R variants had possibly altered the interactions with the two potential protease inhibitors, camostat mesylate and nafamostat. 2022 Life (Basel, Switzerland) Conclusion SARS_CoV_2 C297S;G462D;S460R 26;19;36 31;24;41 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Furthermore, the N439K mutation that observed in RBD of AU.2 deserves additional attention and monitoring due to its capability to increase virus infectivity while evading antibody-mediated immunity. 2022 PloS one Conclusion SARS_CoV_2 N439K 17 22 RBD 49 52 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Whereby the mutation at G1223C is under reported and further large-scale studies are warranted. 2022 PloS one Conclusion SARS_CoV_2 G1223C 24 30 35215963 Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic. We analyzed their whole-genome sequences using two different but complementary deep sequencing platforms, which allowed for the classification in clades/lineages and the identification of key amino acid substitutions, such as the D614G, associated with significant phenotypic characteristics. 2022 Viruses Conclusion SARS_CoV_2 D614G 230 235 35216287 Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. The mutational scanning analysis supported the notion that E484A mutation can have a significant detrimental effect on nanobody binding and result in Omicron-induced escape from nanobody neutralization. 2022 International journal of molecular sciences Conclusion SARS_CoV_2 E484A 59 64 35235585 Travel ban effects on SARS-CoV-2 transmission lineages in the UAE as inferred by genomic epidemiology. Moreover, we report a prevalence shift in D614G, but attribute it to change of import origins rather than higher transmissibility of the G-variant. 2022 PloS one Conclusion SARS_CoV_2 D614G 42 47 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. For example, the H80R variant peptide is predicted to attenuate MTase activity and is a potential candidate for an anti-MTase peptide. 2022 Informatics in medicine unlocked Conclusion SARS_CoV_2 H80R 17 21 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. Summarily, the RBD mutants L452R, E484Q and L452R-E484Q displayed a destabilizing and deleterious impact on the RBD native structure. 2022 3 Biotech Conclusion SARS_CoV_2 E484Q;L452R;L452R;E484Q 34;27;44;50 39;32;49;55 RBD;RBD 15;112 18;115 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. The RBD mutants, namely L452R, E484Q and L452R-E484Q, are predicted to have a significant deleterious impact on SARS-CoV-2 spike protein. 2022 3 Biotech Conclusion SARS_CoV_2 E484Q;L452R;L452R;E484Q 31;24;41;47 36;29;46;52 S;RBD 123;4 128;7 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. Secondly, HBV genotyping and SARS-CoV-2 D614G mutant biosensing platforms were established to validate the high specificity and versatility of the Cas12a system. 2022 Chemical science Conclusion SARS_CoV_2 D614G 40 45 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. S375F was found to be a residue that commonly increases the binding affinity of hACE2 with the RBD of the Omicron variant, and it can be considered as a residue that majorly affects the immune escape capability of SARS-CoV-2. 2022 Journal of chemical information and modeling Conclusion SARS_CoV_2 S375F 0 5 RBD 95 98 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. We described the emergence of a new SARS-CoV-2 variant, the B.1.617.2 lineage with the S:E484Q mutation, and its rapid spread and immune escape in vaccinated individuals. 2022 Viruses Conclusion SARS_CoV_2 E484Q 89 94 S 87 88 35337017 Optimization and Application of a Multiplex Digital PCR Assay for the Detection of SARS-CoV-2 Variants of Concern in Belgian Influent Wastewater. Primer sets targeting the N501Y were also included to monitor the occurrence of remaining lineages containing this mutation (e.g., P.1, B.1.1.7, and B.1.351). 2022 Viruses Conclusion SARS_CoV_2 N501Y 26 31 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. On the other hand, the neutralization titer against Mu+K417N, which shares the same haplotype in the spike RBD, did not changed. 2022 Future microbiology Conclusion SARS_CoV_2 K417N 55 60 S;RBD 101;107 106;110 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. This study identified Beta+R346K as exhibiting the highest vaccine-escaping capacity among the strains prior to the Omicron variant. 2022 Future microbiology Conclusion SARS_CoV_2 R346K 27 32 35355624 Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. In addition, we investigated IFIE and binding energy between the ACE2 and the mutant N501Y on the SARS-CoV-2 S-protein regarding the mutation in common of the variants between the United Kingdom and South Africa, and our results can explain the high infectivity of the mutant. 2021 Chemical science Conclusion SARS_CoV_2 N501Y 85 90 S 109 110 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. Atorvastatin demonstrated in vitro antiviral activity against the ancestral SARS-CoV-2 D614G strain and two emerging variants (Delta and Mu), with an independent effect of the cell line. 2022 Frontiers in microbiology Conclusion SARS_CoV_2 D614G 87 92 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. Results of the present study suggest that the B.1.617 strain and K417G within the receptor-binding site could reduce the vaccine efficacy and increase the chances of reinfection by affecting the SARS-CoV-2 interaction with the CR3022 antibody and ACE2 receptor. 2022 Indian journal of medical microbiology Conclusion SARS_CoV_2 K417G 65 70 35408761 Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor. Further analysis is required to completely unveil the consequences associated with the N501Y mutation. 2022 Molecules (Basel, Switzerland) Conclusion SARS_CoV_2 N501Y 87 92 35408761 Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor. However, the consequences associated with N501Y are more convoluted. 2022 Molecules (Basel, Switzerland) Conclusion SARS_CoV_2 N501Y 42 47 35408761 Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor. In principle, these losses and gains of interactions should imprint a near zero change in binding energy associated with mutation N501Y. 2022 Molecules (Basel, Switzerland) Conclusion SARS_CoV_2 N501Y 130 135 35408761 Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor. Several research groups, employing distinct experimental and computational techniques, have reached the conclusion that the mutation N501Y confers to the virus a higher binding affinity for the hACE2 receptor. 2022 Molecules (Basel, Switzerland) Conclusion SARS_CoV_2 N501Y 133 138 35408761 Molecular Dynamics and MM-PBSA Analysis of the SARS-CoV-2 Gamma Variant in Complex with the hACE-2 Receptor. This work provides further evidence, based on free energy estimations, that supports the notion that the mutations K417T and E484K are compensatory. 2022 Molecules (Basel, Switzerland) Conclusion SARS_CoV_2 E484K;K417T 125;115 130;120 35419205 Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. Assuming that the D614G genotype is better adapted than its ancestor in Vero cells, this observation is consistent with the hypothesis that fitter genotypes adapt at a slower pace. 2022 Evolution, medicine, and public health Conclusion SARS_CoV_2 D614G 18 23 35419205 Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. Here, we followed the evolution in cells of two strains of SARS-CoV-2: one with the original spike protein (CoV-2-D) and one carrying the D614G mutation (CoV-2-G), a variant that emerged in the early phase of the pandemic and soon became prevalent. 2022 Evolution, medicine, and public health Conclusion SARS_CoV_2 D614G 138 143 S 93 98 35419205 Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. The two genomic backgrounds shared several de novo mutations, suggesting that the D614G mutation on the spike protein did not substantially alter the mutational path of the viral populations. 2022 Evolution, medicine, and public health Conclusion SARS_CoV_2 D614G 82 87 S 104 109 35419205 Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. This occurred only in the lines carrying the D614G mutation (CoV-2-G strain), but we cannot discard the null hypothesis that this happened in such genomic background simply by chance. 2022 Evolution, medicine, and public health Conclusion SARS_CoV_2 D614G 45 50 35421842 Split T7 promoter-based isothermal transcription amplification for one-step fluorescence detection of SARS-CoV-2 and emerging variants. Finally, (v) broad applicability was verified through the multiplex detection of the SARS-CoV-2 variants (D614G mutation) as well as through the direct detection of bacterial 16S rRNA without the need for additional nucleic acid purification. 2022 Biosensors & bioelectronics Conclusion SARS_CoV_2 D614G 106 111 35430092 Prolonged shedding of infectious viruses with haplotype switches of SARS-CoV-2 in an immunocompromised patient. From haplotype 4 through haplotype 7, diversity was observed mainly in the S gene, and two of them (E484Q and S494P) were additional mutations in the receptor-binding motif of the receptor-binding domain (RBD). 2022 Journal of infection and chemotherapy Conclusion SARS_CoV_2 S494P;E484Q 110;100 115;105 RBD;S 205;75 208;76 35430092 Prolonged shedding of infectious viruses with haplotype switches of SARS-CoV-2 in an immunocompromised patient. Haplotype 3 acquired additional four non-synonymous mutations (ORF1a, S gene, and N gene), a single deletion (S gene), and a synonymous mutation; however, it lost two previous non-synonymous mutations including V658I. 2022 Journal of infection and chemotherapy Conclusion SARS_CoV_2 V658I 211 216 ORF1a;N;S;S 63;82;70;110 68;83;71;111 35430092 Prolonged shedding of infectious viruses with haplotype switches of SARS-CoV-2 in an immunocompromised patient. One of the non-synonymous mutations, V658I, was located in nsp12, which encodes RdRp. 2022 Journal of infection and chemotherapy Conclusion SARS_CoV_2 V658I 37 42 Nsp12;RdRP 59;80 64;84 35430092 Prolonged shedding of infectious viruses with haplotype switches of SARS-CoV-2 in an immunocompromised patient. When haplotype 1 was compared with Wuhan-Hu-1/2019 (GenBank accession number; MN908947), it had ten non-synonymous (ORF1a:Q2702H and S2981F, ORF1b:P314L, T1404 M, P1567L, and R2684I, S gene:D614G, N gene:R203K, G204R, and M234I) and five synonymous mutations. 2022 Journal of infection and chemotherapy Conclusion SARS_CoV_2 G204R;M234I;P1567L;R2684I;S2981F;T1404M;D614G;P314L;Q2702H;R203K 211;222;163;175;133;154;190;147;122;204 216;227;169;181;139;161;195;152;128;209 ORF1a;N;S 116;197;183 121;198;184 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. The neutralization resistance occurred due to E484K and N501Y mutations in the RBD of the spike. 2022 Frontiers in cellular and infection microbiology Conclusion SARS_CoV_2 E484K;N501Y 46;56 51;61 S;RBD 90;79 95;82 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. The two most commonly occurring mutations, Spike_D614G and Nsp12_P314L, were structurally modeled, which showed that these mutations had the potential to enhance viral entry and replication, respectively. 2022 Frontiers in cellular and infection microbiology Conclusion SARS_CoV_2 D614G;P314L 49;65 54;70 S;Nsp12 43;59 48;64 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. Till now, five variants designated as variants of concern (VOCs) by ECDC have been detected, namely, the Alpha (B.1.1.7), Alpha+E484K (B.1.1.7+E484K), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2), and seven SARS-CoV-2 variants are considered variants of interest (VOIs) . 2022 Frontiers in cellular and infection microbiology Conclusion SARS_CoV_2 E484K;E484K 128;143 133;148 35454161 Mutational Effect of Some Major COVID-19 Variants on Binding of the S Protein to ACE2. Our calculations show that these mutations can enhance the binding affinity of the complex, except for K417N and Y505H mutations. 2022 Biomolecules Conclusion SARS_CoV_2 K417N;Y505H 103;113 108;118 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. According to our results, mutations in the S477N position produce very minor destabilizing changes, while the T478K and E484A sites contribute insignificantly to the binding interface, thereby allowing for virus flexibility to produce mutations that evade neutralizing antibodies without compromising the binding affinity with ACE2. 2022 International journal of molecular sciences Conclusion SARS_CoV_2 E484A;S477N;T478K 120;43;110 125;48;115 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. Our results show that N501Y is the most critical binding affinity hotspot in the S Omicron RBD complex with ACE2 and the supporting energy hotspots in this region (S496, R498 and H505) collectively form the dominant interfacial cluster with ACE2. 2022 International journal of molecular sciences Conclusion SARS_CoV_2 N501Y 22 27 RBD;S 91;81 94;82 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. We found that the RBD-Delta mutational sites L452R and T478K have a minor effect on the binding affinity, while a greater contribution of the neighboring Y453, L455 and F456 residues to protein stability and RBD-ACE2 interactions may offer a moderately improved binding of the Delta variant. 2022 International journal of molecular sciences Conclusion SARS_CoV_2 L452R;T478K 45;55 50;60 RBD;RBD 18;208 21;211 35457196 Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. We showed that a constellation of mutational sites (G496S, Q498R, N501Y and Y505H) correspond to key binding energy hotspots and also contribute decisively to the key interfacial communities that mediate the allosteric communications between S-RBD and ACE2. 2022 International journal of molecular sciences Conclusion SARS_CoV_2 N501Y;Q498R;Y505H;G496S 66;59;76;52 71;64;81;57 RBD;S 244;242 247;243 35464398 Case Report: X-Linked SASH3 Deficiency Presenting as a Common Variable Immunodeficiency. To date only three SASH3 variants have been reported, two nonsense and one missense, with p.Gln169* being the most N-terminal one (Figure 1A). 2022 Frontiers in immunology Conclusion SARS_CoV_2 N169X 94 99 N 115 116 35464398 Case Report: X-Linked SASH3 Deficiency Presenting as a Common Variable Immunodeficiency. We found a novel hemizygous variant in SASH3, consisting of a single nucleotide change (c.505C>T) leading to a premature STOP codon (p.Gln169*). 2022 Frontiers in immunology Conclusion SARS_CoV_2 C505T;N169X 88;137 96;142 35464398 Case Report: X-Linked SASH3 Deficiency Presenting as a Common Variable Immunodeficiency. Western blot of the patient's PBMCs using a polyclonal antibody targeting the N-terminus of SASH3 showed complete absence of protein, thus confirming the LOF nature of the c.505C>T/p.Gln169* variant (Figure 1C). 2022 Frontiers in immunology Conclusion SARS_CoV_2 C505T;C505T;N169X 172;174;185 180;180;190 N 78 79 32300673 Genomic characterization of a novel SARS-CoV-2. 104T>A 2020 Gene reports Table SARS_CoV_2 T104A 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. 11083G>T 2020 Gene reports Table SARS_CoV_2 G11083T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 11083T>G 2020 Gene reports Table SARS_CoV_2 T11083G 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 111T>C 2020 Gene reports Table SARS_CoV_2 T111C 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. 112T>G 2020 Gene reports Table SARS_CoV_2 T112G 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. 11557G>T 2020 Gene reports Table SARS_CoV_2 G11557T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 11749T>A 2020 Gene reports Table SARS_CoV_2 T11749A 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 11764T>A 2020 Gene reports Table SARS_CoV_2 T11764A 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 119C>G 2020 Gene reports Table SARS_CoV_2 C119G 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. 120T>C 2020 Gene reports Table SARS_CoV_2 T120C 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. 124G>A 2020 Gene reports Table SARS_CoV_2 G124A 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. 13225C>G 2020 Gene reports Table SARS_CoV_2 C13225G 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 13226T>C 2020 Gene reports Table SARS_CoV_2 T13226C 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 1497G>A 2020 Gene reports Table SARS_CoV_2 G1497A 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 15324C>T 2020 Gene reports Table SARS_CoV_2 C15324T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 1548G>A 2020 Gene reports Table SARS_CoV_2 G1548A 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 15597T>C 2020 Gene reports Table SARS_CoV_2 T15597C 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 16467A>G 2020 Gene reports Table SARS_CoV_2 A16467G 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 16C>T 2020 Gene reports Table SARS_CoV_2 C16T 0 5 32300673 Genomic characterization of a novel SARS-CoV-2. 17423A>G 2020 Gene reports Table SARS_CoV_2 A17423G 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 18060C>T 2020 Gene reports Table SARS_CoV_2 C18060T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 18512C>T 2020 Gene reports Table SARS_CoV_2 C18512T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 1912C>T 2020 Gene reports Table SARS_CoV_2 C1912T 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 20679G>A 2020 Gene reports Table SARS_CoV_2 G20679A 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 21137A>G 2020 Gene reports Table SARS_CoV_2 A21137G 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 21316G>A 2020 Gene reports Table SARS_CoV_2 G21316A 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 21386C>T 2020 Gene reports Table SARS_CoV_2 C21386T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 21386insT 2020 Gene reports Table SARS_CoV_2 21386insT 0 9 32300673 Genomic characterization of a novel SARS-CoV-2. 22432C>T 2020 Gene reports Table SARS_CoV_2 C22432T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 23185C>T 2020 Gene reports Table SARS_CoV_2 C23185T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 23952T>G 2020 Gene reports Table SARS_CoV_2 T23952G 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 24034C>T 2020 Gene reports Table SARS_CoV_2 C24034T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 241C>T 2020 Gene reports Table SARS_CoV_2 C241T 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. 24292A>G 2020 Gene reports Table SARS_CoV_2 A24292G 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 24325A>G 2020 Gene reports Table SARS_CoV_2 A24325G 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 25810C>G 2020 Gene reports Table SARS_CoV_2 C25810G 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 26144G>T 2020 Gene reports Table SARS_CoV_2 G26144T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 2662C>T 2020 Gene reports Table SARS_CoV_2 C2662T 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 26729T>C 2020 Gene reports Table SARS_CoV_2 T26729C 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 27493C>T 2020 Gene reports Table SARS_CoV_2 C27493T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 28077G>C 2020 Gene reports Table SARS_CoV_2 G28077C 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 28144T>C 2020 Gene reports Table SARS_CoV_2 T28144C 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 28253C>T 2020 Gene reports Table SARS_CoV_2 C28253T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 28792A>C 2020 Gene reports Table SARS_CoV_2 A28792C 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 28854C>T 2020 Gene reports Table SARS_CoV_2 C28854T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 29095C>T 2020 Gene reports Table SARS_CoV_2 C29095T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 29303C>T 2020 Gene reports Table SARS_CoV_2 C29303T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 29642C>T 2020 Gene reports Table SARS_CoV_2 C29642T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 29705G>T 2020 Gene reports Table SARS_CoV_2 G29705T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 29854C>T 2020 Gene reports Table SARS_CoV_2 C29854T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 29856T>A 2020 Gene reports Table SARS_CoV_2 T29856A 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 29869del 2020 Gene reports Table SARS_CoV_2 29869del 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. 3177C>T 2020 Gene reports Table SARS_CoV_2 C3177T 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 3778A>G 2020 Gene reports Table SARS_CoV_2 A3778G 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 3792C>T 2020 Gene reports Table SARS_CoV_2 C3792T 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 490T>A 2020 Gene reports Table SARS_CoV_2 T490A 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. 4A>T 2020 Gene reports Table SARS_CoV_2 A4T 0 4 32300673 Genomic characterization of a novel SARS-CoV-2. 6031C>T 2020 Gene reports Table SARS_CoV_2 C6031T 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 6035A>G 2020 Gene reports Table SARS_CoV_2 A6035G 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 6968C>A 2020 Gene reports Table SARS_CoV_2 C6968A 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 6996T>C 2020 Gene reports Table SARS_CoV_2 T6996C 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 7016G>A 2020 Gene reports Table SARS_CoV_2 G7016A 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 75C>A 2020 Gene reports Table SARS_CoV_2 C75A 0 5 32300673 Genomic characterization of a novel SARS-CoV-2. 7866G>T 2020 Gene reports Table SARS_CoV_2 G7866T 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 8001A>C 2020 Gene reports Table SARS_CoV_2 A8001C 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 8388A>G 2020 Gene reports Table SARS_CoV_2 A8388G 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 8782C>T 2020 Gene reports Table SARS_CoV_2 C8782T 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 8987T>A 2020 Gene reports Table SARS_CoV_2 T8987A 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. 9534C>T 2020 Gene reports Table SARS_CoV_2 C9534T 0 7 32300673 Genomic characterization of a novel SARS-CoV-2. A1176V 2020 Gene reports Table SARS_CoV_2 A1176V 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. D2579A 2020 Gene reports Table SARS_CoV_2 D2579A 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. D75E 2020 Gene reports Table SARS_CoV_2 D75E 0 4 32300673 Genomic characterization of a novel SARS-CoV-2. E3764D 2020 Gene reports Table SARS_CoV_2 E3764D 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. F2908I 2020 Gene reports Table SARS_CoV_2 F2908I 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. G2251S 2020 Gene reports Table SARS_CoV_2 G2251S 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. G251V 2020 Gene reports Table SARS_CoV_2 G251V 0 5 32300673 Genomic characterization of a novel SARS-CoV-2. G2534V 2020 Gene reports Table SARS_CoV_2 G2534V 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. I2244T 2020 Gene reports Table SARS_CoV_2 I2244T 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. L140V 2020 Gene reports Table SARS_CoV_2 L140V 0 5 32300673 Genomic characterization of a novel SARS-CoV-2. L2235I 2020 Gene reports Table SARS_CoV_2 L2235I 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. L3606F 2020 Gene reports Table SARS_CoV_2 L3606F 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. L39del 2020 Gene reports Table SARS_CoV_2 L39del 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. L84S 2020 Gene reports Table SARS_CoV_2 L84S 0 4 32300673 Genomic characterization of a novel SARS-CoV-2. N2708S 2020 Gene reports Table SARS_CoV_2 N2708S 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. N3833K 2020 Gene reports Table SARS_CoV_2 N3833K 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. P344S 2020 Gene reports Table SARS_CoV_2 P344S 0 5 32300673 Genomic characterization of a novel SARS-CoV-2. P34S 2020 Gene reports Table SARS_CoV_2 P34S 0 4 32300673 Genomic characterization of a novel SARS-CoV-2. P971L 2020 Gene reports Table SARS_CoV_2 P971L 0 5 32300673 Genomic characterization of a novel SARS-CoV-2. S194L 2020 Gene reports Table SARS_CoV_2 S194L 0 5 32300673 Genomic characterization of a novel SARS-CoV-2. S428N 2020 Gene reports Table SARS_CoV_2 S428N 0 5 32300673 Genomic characterization of a novel SARS-CoV-2. T3090I 2020 Gene reports Table SARS_CoV_2 T3090I 0 6 32300673 Genomic characterization of a novel SARS-CoV-2. V62L 2020 Gene reports Table SARS_CoV_2 V62L 0 4 32300673 Genomic characterization of a novel SARS-CoV-2. Y5720C 2020 Gene reports Table SARS_CoV_2 Y5720C 0 6 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. 241C>T 2020 American journal of clinical pathology Table SARS_CoV_2 C241T 0 6 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. D614G 2020 American journal of clinical pathology Table SARS_CoV_2 D614G 0 5 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. L3083I 2020 American journal of clinical pathology Table SARS_CoV_2 L3083I 0 6 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. L3606F 2020 American journal of clinical pathology Table SARS_CoV_2 L3606F 0 6 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. P314L 2020 American journal of clinical pathology Table SARS_CoV_2 P314L 0 5 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. Q57H 2020 American journal of clinical pathology Table SARS_CoV_2 Q57H 0 4 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. T265I 2020 American journal of clinical pathology Table SARS_CoV_2 T265I 0 5 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. T739I 2020 American journal of clinical pathology Table SARS_CoV_2 T739I 0 5 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. A3220V 2020 The Indian journal of medical research Table SARS_CoV_2 A3220V 0 6 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. C18060T 2020 The Indian journal of medical research Table SARS_CoV_2 C18060T 0 7 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. C29095T 2020 The Indian journal of medical research Table SARS_CoV_2 C29095T 0 7 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. D614G 2020 The Indian journal of medical research Table SARS_CoV_2 D614G 0 5 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. G251V 2020 The Indian journal of medical research Table SARS_CoV_2 G251V 0 5 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. L3606F 2020 The Indian journal of medical research Table SARS_CoV_2 L3606F 0 6 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. L84S 2020 The Indian journal of medical research Table SARS_CoV_2 L84S 0 4 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. P314L 2020 The Indian journal of medical research Table SARS_CoV_2 P314L 0 5 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. S202N 2020 The Indian journal of medical research Table SARS_CoV_2 S202N 0 5 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. T514C 2020 The Indian journal of medical research Table SARS_CoV_2 T514C 0 5 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. V378I 2020 The Indian journal of medical research Table SARS_CoV_2 V378I 0 5 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. A88V 2020 Journal of biosciences Table SARS_CoV_2 A88V 0 4 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. D614G 2020 Journal of biosciences Table SARS_CoV_2 D614G 0 5 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. G1124V 2020 Journal of biosciences Table SARS_CoV_2 G1124V 0 6 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. G204R 2020 Journal of biosciences Table SARS_CoV_2 G204R 0 5 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. G251V 2020 Journal of biosciences Table SARS_CoV_2 G251V 0 5 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. H286Y 2020 Journal of biosciences Table SARS_CoV_2 H286Y 0 5 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. L84S 2020 Journal of biosciences Table SARS_CoV_2 L84S 0 4 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. P287T 2020 Journal of biosciences Table SARS_CoV_2 P287T 0 5 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. P323L 2020 Journal of biosciences Table SARS_CoV_2 P323L 0 5 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. R203K 2020 Journal of biosciences Table SARS_CoV_2 R203K 0 5 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. V32L 2020 Journal of biosciences Table SARS_CoV_2 V32L 0 4 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. A16577G 2020 Emerging microbes & infections Table SARS_CoV_2 A16577G 0 7 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. A59D 2020 Emerging microbes & infections Table SARS_CoV_2 A59D 0 4 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. C176A 2020 Emerging microbes & infections Table SARS_CoV_2 C176A 0 5 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. C595T 2020 Emerging microbes & infections Table SARS_CoV_2 C595T 0 5 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. C8517T 2020 Emerging microbes & infections Table SARS_CoV_2 C8517T 0 6 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. F817L 2020 Emerging microbes & infections Table SARS_CoV_2 F817L 0 5 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. H49Y 2020 Emerging microbes & infections Table SARS_CoV_2 H49Y 0 4 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. K5526R 2020 Emerging microbes & infections Table SARS_CoV_2 K5526R 0 6 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. P199S 2020 Emerging microbes & infections Table SARS_CoV_2 P199S 0 5 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. S884F 2020 Emerging microbes & infections Table SARS_CoV_2 S884F 0 5 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. T17459C 2020 Emerging microbes & infections Table SARS_CoV_2 T17459C 0 7 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. V5820A 2020 Emerging microbes & infections Table SARS_CoV_2 V5820A 0 6 32595352 An updated analysis of variations in SARS-CoV-2 genome. D614G 2020 Turkish journal of biology Table SARS_CoV_2 D614G 0 5 32595352 An updated analysis of variations in SARS-CoV-2 genome. G205R 2020 Turkish journal of biology Table SARS_CoV_2 G205R 0 5 32595352 An updated analysis of variations in SARS-CoV-2 genome. L36F 2020 Turkish journal of biology Table SARS_CoV_2 L36F 0 4 32595352 An updated analysis of variations in SARS-CoV-2 genome. P323L 2020 Turkish journal of biology Table SARS_CoV_2 P323L 0 5 32595352 An updated analysis of variations in SARS-CoV-2 genome. Q57H 2020 Turkish journal of biology Table SARS_CoV_2 Q57H 0 4 32595352 An updated analysis of variations in SARS-CoV-2 genome. R204K 2020 Turkish journal of biology Table SARS_CoV_2 R204K 0 5 32595352 An updated analysis of variations in SARS-CoV-2 genome. T266I 2020 Turkish journal of biology Table SARS_CoV_2 T266I 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A1006V 2020 Turkish journal of biology Table SARS_CoV_2 A1006V 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A1106T 2020 Turkish journal of biology Table SARS_CoV_2 A1106T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A1119C 2020 Turkish journal of biology Table SARS_CoV_2 A1119C 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A1134T 2020 Turkish journal of biology Table SARS_CoV_2 A1134T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A13376G 2020 Turkish journal of biology Table SARS_CoV_2 A13376G 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A1475C 2020 Turkish journal of biology Table SARS_CoV_2 A1475C 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A20268G 2020 Turkish journal of biology Table SARS_CoV_2 A20268G 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A22964G 2020 Turkish journal of biology Table SARS_CoV_2 A22964G 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A23403G 2020 Turkish journal of biology Table SARS_CoV_2 A23403G 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A23734T 2020 Turkish journal of biology Table SARS_CoV_2 A23734T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A2475T 2020 Turkish journal of biology Table SARS_CoV_2 A2475T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A27354G 2020 Turkish journal of biology Table SARS_CoV_2 A27354G 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A2932G 2020 Turkish journal of biology Table SARS_CoV_2 A2932G 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A9514G 2020 Turkish journal of biology Table SARS_CoV_2 A9514G 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C10202T 2020 Turkish journal of biology Table SARS_CoV_2 C10202T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C1059T 2020 Turkish journal of biology Table SARS_CoV_2 C1059T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C10702T 2020 Turkish journal of biology Table SARS_CoV_2 C10702T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C1101T 2020 Turkish journal of biology Table SARS_CoV_2 C1101T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C11074T 2020 Turkish journal of biology Table SARS_CoV_2 C11074T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C11232T 2020 Turkish journal of biology Table SARS_CoV_2 C11232T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C1225A 2020 Turkish journal of biology Table SARS_CoV_2 C1225A 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C12700T 2020 Turkish journal of biology Table SARS_CoV_2 C12700T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C12741T 2020 Turkish journal of biology Table SARS_CoV_2 C12741T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C12809T 2020 Turkish journal of biology Table SARS_CoV_2 C12809T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C1314T 2020 Turkish journal of biology Table SARS_CoV_2 C1314T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C13476T 2020 Turkish journal of biology Table SARS_CoV_2 C13476T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C13481T 2020 Turkish journal of biology Table SARS_CoV_2 C13481T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C13492T 2020 Turkish journal of biology Table SARS_CoV_2 C13492T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C1397T 2020 Turkish journal of biology Table SARS_CoV_2 C1397T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C14178T 2020 Turkish journal of biology Table SARS_CoV_2 C14178T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C1420T 2020 Turkish journal of biology Table SARS_CoV_2 C1420T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C14286T 2020 Turkish journal of biology Table SARS_CoV_2 C14286T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C1437T 2020 Turkish journal of biology Table SARS_CoV_2 C1437T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C14407A 2020 Turkish journal of biology Table SARS_CoV_2 C14407A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C14408T 2020 Turkish journal of biology Table SARS_CoV_2 C14408T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C1473T 2020 Turkish journal of biology Table SARS_CoV_2 C1473T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C14763A 2020 Turkish journal of biology Table SARS_CoV_2 C14763A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C15101A 2020 Turkish journal of biology Table SARS_CoV_2 C15101A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C15240T 2020 Turkish journal of biology Table SARS_CoV_2 C15240T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C16247T 2020 Turkish journal of biology Table SARS_CoV_2 C16247T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C16616T 2020 Turkish journal of biology Table SARS_CoV_2 C16616T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C17690T 2020 Turkish journal of biology Table SARS_CoV_2 C17690T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C1825T 2020 Turkish journal of biology Table SARS_CoV_2 C1825T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C18877T 2020 Turkish journal of biology Table SARS_CoV_2 C18877T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C19170T 2020 Turkish journal of biology Table SARS_CoV_2 C19170T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C19484T 2020 Turkish journal of biology Table SARS_CoV_2 C19484T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C19763A 2020 Turkish journal of biology Table SARS_CoV_2 C19763A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C2113T 2020 Turkish journal of biology Table SARS_CoV_2 C2113T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C21304A 2020 Turkish journal of biology Table SARS_CoV_2 C21304A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C21789T 2020 Turkish journal of biology Table SARS_CoV_2 C21789T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C22444T 2020 Turkish journal of biology Table SARS_CoV_2 C22444T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C228T 2020 Turkish journal of biology Table SARS_CoV_2 C228T 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C23874T 2020 Turkish journal of biology Table SARS_CoV_2 C23874T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C2416T 2020 Turkish journal of biology Table SARS_CoV_2 C2416T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C241T 2020 Turkish journal of biology Table SARS_CoV_2 C241T 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C2455T 2020 Turkish journal of biology Table SARS_CoV_2 C2455T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C24865T 2020 Turkish journal of biology Table SARS_CoV_2 C24865T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C24T 2020 Turkish journal of biology Table SARS_CoV_2 C24T 0 4 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C25275T 2020 Turkish journal of biology Table SARS_CoV_2 C25275T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C25549T 2020 Turkish journal of biology Table SARS_CoV_2 C25549T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C26256T 2020 Turkish journal of biology Table SARS_CoV_2 C26256T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C26340T 2020 Turkish journal of biology Table SARS_CoV_2 C26340T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C26549T 2020 Turkish journal of biology Table SARS_CoV_2 C26549T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C26735T 2020 Turkish journal of biology Table SARS_CoV_2 C26735T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C26753T 2020 Turkish journal of biology Table SARS_CoV_2 C26753T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C27103T 2020 Turkish journal of biology Table SARS_CoV_2 C27103T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C28054T 2020 Turkish journal of biology Table SARS_CoV_2 C28054T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C28854T 2020 Turkish journal of biology Table SARS_CoV_2 C28854T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C29563T 2020 Turkish journal of biology Table SARS_CoV_2 C29563T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C29741T 2020 Turkish journal of biology Table SARS_CoV_2 C29741T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C2997T 2020 Turkish journal of biology Table SARS_CoV_2 C2997T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C3037T 2020 Turkish journal of biology Table SARS_CoV_2 C3037T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C3117T 2020 Turkish journal of biology Table SARS_CoV_2 C3117T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C3903T 2020 Turkish journal of biology Table SARS_CoV_2 C3903T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C4084T 2020 Turkish journal of biology Table SARS_CoV_2 C4084T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C4524T 2020 Turkish journal of biology Table SARS_CoV_2 C4524T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C5477T 2020 Turkish journal of biology Table SARS_CoV_2 C5477T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C5736T 2020 Turkish journal of biology Table SARS_CoV_2 C5736T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C5826A 2020 Turkish journal of biology Table SARS_CoV_2 C5826A 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C6402T 2020 Turkish journal of biology Table SARS_CoV_2 C6402T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C7392T 2020 Turkish journal of biology Table SARS_CoV_2 C7392T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C7765T 2020 Turkish journal of biology Table SARS_CoV_2 C7765T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C7834T 2020 Turkish journal of biology Table SARS_CoV_2 C7834T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C8683A 2020 Turkish journal of biology Table SARS_CoV_2 C8683A 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C8782T 2020 Turkish journal of biology Table SARS_CoV_2 C8782T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C884T 2020 Turkish journal of biology Table SARS_CoV_2 C884T 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C8964T 2020 Turkish journal of biology Table SARS_CoV_2 C8964T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. D614G 2020 Turkish journal of biology Table SARS_CoV_2 D614G 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G11083T 2020 Turkish journal of biology Table SARS_CoV_2 G11083T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G11234A 2020 Turkish journal of biology Table SARS_CoV_2 G11234A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G1156A 2020 Turkish journal of biology Table SARS_CoV_2 G1156A 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G1210A 2020 Turkish journal of biology Table SARS_CoV_2 G1210A 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G12248T 2020 Turkish journal of biology Table SARS_CoV_2 G12248T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G1397A 2020 Turkish journal of biology Table SARS_CoV_2 G1397A 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G14122T 2020 Turkish journal of biology Table SARS_CoV_2 G14122T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G14310A 2020 Turkish journal of biology Table SARS_CoV_2 G14310A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G14430A 2020 Turkish journal of biology Table SARS_CoV_2 G14430A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G14443T 2020 Turkish journal of biology Table SARS_CoV_2 G14443T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G1470A 2020 Turkish journal of biology Table SARS_CoV_2 G1470A 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G14710A 2020 Turkish journal of biology Table SARS_CoV_2 G14710A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G14773T 2020 Turkish journal of biology Table SARS_CoV_2 G14773T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G15958A 2020 Turkish journal of biology Table SARS_CoV_2 G15958A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G19285A 2020 Turkish journal of biology Table SARS_CoV_2 G19285A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G204R 2020 Turkish journal of biology Table SARS_CoV_2 G204R 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G21305A 2020 Turkish journal of biology Table SARS_CoV_2 G21305A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G21452T 2020 Turkish journal of biology Table SARS_CoV_2 G21452T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G22468T 2020 Turkish journal of biology Table SARS_CoV_2 G22468T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G2250A 2020 Turkish journal of biology Table SARS_CoV_2 G2250A 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G23876A 2020 Turkish journal of biology Table SARS_CoV_2 G23876A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G25314T 2020 Turkish journal of biology Table SARS_CoV_2 G25314T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G2549C 2020 Turkish journal of biology Table SARS_CoV_2 G2549C 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G25563T 2020 Turkish journal of biology Table SARS_CoV_2 G25563T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G2591A 2020 Turkish journal of biology Table SARS_CoV_2 G2591A 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G2612C 2020 Turkish journal of biology Table SARS_CoV_2 G2612C 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G26718T 2020 Turkish journal of biology Table SARS_CoV_2 G26718T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G26720C 2020 Turkish journal of biology Table SARS_CoV_2 G26720C 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G2715T 2020 Turkish journal of biology Table SARS_CoV_2 G2715T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G28109T 2020 Turkish journal of biology Table SARS_CoV_2 G28109T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G28878A 2020 Turkish journal of biology Table SARS_CoV_2 G28878A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G28881A 2020 Turkish journal of biology Table SARS_CoV_2 G28881A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G28882A 2020 Turkish journal of biology Table SARS_CoV_2 G28882A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G28883C 2020 Turkish journal of biology Table SARS_CoV_2 G28883C 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G29742T 2020 Turkish journal of biology Table SARS_CoV_2 G29742T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G309C 2020 Turkish journal of biology Table SARS_CoV_2 G309C 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G779C 2020 Turkish journal of biology Table SARS_CoV_2 G779C 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G8371T 2020 Turkish journal of biology Table SARS_CoV_2 G8371T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G8653T 2020 Turkish journal of biology Table SARS_CoV_2 G8653T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G881A 2020 Turkish journal of biology Table SARS_CoV_2 G881A 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G944A 2020 Turkish journal of biology Table SARS_CoV_2 G944A 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G9479T 2020 Turkish journal of biology Table SARS_CoV_2 G9479T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. L37F 2020 Turkish journal of biology Table SARS_CoV_2 L37F 0 4 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. M33I 2020 Turkish journal of biology Table SARS_CoV_2 M33I 0 4 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. P323L 2020 Turkish journal of biology Table SARS_CoV_2 P323L 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. Q57H 2020 Turkish journal of biology Table SARS_CoV_2 Q57H 0 4 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. R203K 2020 Turkish journal of biology Table SARS_CoV_2 R203K 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. R27C 2020 Turkish journal of biology Table SARS_CoV_2 R27C 0 4 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. S188P 2020 Turkish journal of biology Table SARS_CoV_2 S188P 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. S194L 2020 Turkish journal of biology Table SARS_CoV_2 S194L 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. S485L 2020 Turkish journal of biology Table SARS_CoV_2 S485L 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T1100G 2020 Turkish journal of biology Table SARS_CoV_2 T1100G 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T1359C 2020 Turkish journal of biology Table SARS_CoV_2 T1359C 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T14394A 2020 Turkish journal of biology Table SARS_CoV_2 T14394A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T14682G 2020 Turkish journal of biology Table SARS_CoV_2 T14682G 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T14740C 2020 Turkish journal of biology Table SARS_CoV_2 T14740C 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T14808A 2020 Turkish journal of biology Table SARS_CoV_2 T14808A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T15102C 2020 Turkish journal of biology Table SARS_CoV_2 T15102C 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T15119A 2020 Turkish journal of biology Table SARS_CoV_2 T15119A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T19839C 2020 Turkish journal of biology Table SARS_CoV_2 T19839C 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T23559A 2020 Turkish journal of biology Table SARS_CoV_2 T23559A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T2586A 2020 Turkish journal of biology Table SARS_CoV_2 T2586A 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T26396A 2020 Turkish journal of biology Table SARS_CoV_2 T26396A 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T26551C 2020 Turkish journal of biology Table SARS_CoV_2 T26551C 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T28144C 2020 Turkish journal of biology Table SARS_CoV_2 T28144C 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T28688C 2020 Turkish journal of biology Table SARS_CoV_2 T28688C 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T28835C 2020 Turkish journal of biology Table SARS_CoV_2 T28835C 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T5182C 2020 Turkish journal of biology Table SARS_CoV_2 T5182C 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T580A 2020 Turkish journal of biology Table SARS_CoV_2 T580A 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T6202A 2020 Turkish journal of biology Table SARS_CoV_2 T6202A 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. T946A 2020 Turkish journal of biology Table SARS_CoV_2 T946A 0 5 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. V10A 2020 Turkish journal of biology Table SARS_CoV_2 V10A 0 4 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. V198I 2020 Turkish journal of biology Table SARS_CoV_2 V198I 0 5 32693089 Mortality in COVID-19 disease patients: Correlating the association of major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants. L84S 2020 International journal of infectious diseases Table SARS_CoV_2 L84S 0 4 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. D614G 2020 Cell Table SARS_CoV_2 D614G 0 5 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. M0491S 2020 Cell Table SARS_CoV_2 M0491S 0 6 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. A348T 2020 Cell Table SARS_CoV_2 A348T 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. A435S 2020 Cell Table SARS_CoV_2 A435S 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. A475V 2020 Cell Table SARS_CoV_2 A475V 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. A520S 2020 Cell Table SARS_CoV_2 A520S 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. A522S 2020 Cell Table SARS_CoV_2 A522S 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. A522V 2020 Cell Table SARS_CoV_2 A522V 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. A831V 2020 Cell Table SARS_CoV_2 A831V 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. A845S 2020 Cell Table SARS_CoV_2 A845S 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. A879S 2020 Cell Table SARS_CoV_2 A879S 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. D364Y 2020 Cell Table SARS_CoV_2 D364Y 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. D405V 2020 Cell Table SARS_CoV_2 D405V 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. D467V 2020 Cell Table SARS_CoV_2 D467V 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. D614G 2020 Cell Table SARS_CoV_2 D614G 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. D839E 2020 Cell Table SARS_CoV_2 D839E 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. D839Y 2020 Cell Table SARS_CoV_2 D839Y 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. D936Y 2020 Cell Table SARS_CoV_2 D936Y 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. F338L 2020 Cell Table SARS_CoV_2 F338L 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. F490L 2020 Cell Table SARS_CoV_2 F490L 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. G1124V 2020 Cell Table SARS_CoV_2 G1124V 0 6 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. G446V 2020 Cell Table SARS_CoV_2 G446V 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. G476S 2020 Cell Table SARS_CoV_2 G476S 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. H49Y 2020 Cell Table SARS_CoV_2 H49Y 0 4 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. H519P 2020 Cell Table SARS_CoV_2 H519P 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. H519Q 2020 Cell Table SARS_CoV_2 H519Q 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. I434K 2020 Cell Table SARS_CoV_2 I434K 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. I468F 2020 Cell Table SARS_CoV_2 I468F 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. I468T 2020 Cell Table SARS_CoV_2 I468T 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. I472V 2020 Cell Table SARS_CoV_2 I472V 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. K378R 2020 Cell Table SARS_CoV_2 K378R 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. K458N 2020 Cell Table SARS_CoV_2 K458N 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. K458R 2020 Cell Table SARS_CoV_2 K458R 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. L452R 2020 Cell Table SARS_CoV_2 L452R 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. M1229I 2020 Cell Table SARS_CoV_2 M1229I 0 6 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. M1237I 2020 Cell Table SARS_CoV_2 M1237I 0 6 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N1074Q 2020 Cell Table SARS_CoV_2 N1074Q 0 6 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N1098Q 2020 Cell Table SARS_CoV_2 N1098Q 0 6 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N1134Q 2020 Cell Table SARS_CoV_2 N1134Q 0 6 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N1158Q 2020 Cell Table SARS_CoV_2 N1158Q 0 6 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N1173Q 2020 Cell Table SARS_CoV_2 N1173Q 0 6 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N1194Q 2020 Cell Table SARS_CoV_2 N1194Q 0 6 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N122Q 2020 Cell Table SARS_CoV_2 N122Q 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N149H 2020 Cell Table SARS_CoV_2 N149H 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N149Q 2020 Cell Table SARS_CoV_2 N149Q 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N165Q 2020 Cell Table SARS_CoV_2 N165Q 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N17Q 2020 Cell Table SARS_CoV_2 N17Q 0 4 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N234Q 2020 Cell Table SARS_CoV_2 N234Q 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N282Q 2020 Cell Table SARS_CoV_2 N282Q 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N331Q 2020 Cell Table SARS_CoV_2 N331Q 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N343Q 2020 Cell Table SARS_CoV_2 N343Q 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N354D 2020 Cell Table SARS_CoV_2 N354D 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N354K 2020 Cell Table SARS_CoV_2 N354K 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N439K 2020 Cell Table SARS_CoV_2 N439K 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N603Q 2020 Cell Table SARS_CoV_2 N603Q 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N616Q 2020 Cell Table SARS_CoV_2 N616Q 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N61Q 2020 Cell Table SARS_CoV_2 N61Q 0 4 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N657Q 2020 Cell Table SARS_CoV_2 N657Q 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N709Q 2020 Cell Table SARS_CoV_2 N709Q 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N717Q 2020 Cell Table SARS_CoV_2 N717Q 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N74K 2020 Cell Table SARS_CoV_2 N74K 0 4 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N74Q 2020 Cell Table SARS_CoV_2 N74Q 0 4 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. N801Q 2020 Cell Table SARS_CoV_2 N801Q 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. P1263L 2020 Cell Table SARS_CoV_2 P1263L 0 6 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. P384L 2020 Cell Table SARS_CoV_2 P384L 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. P491R 2020 Cell Table SARS_CoV_2 P491R 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. P521S 2020 Cell Table SARS_CoV_2 P521S 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Q239K 2020 Cell Table SARS_CoV_2 Q239K 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Q321L 2020 Cell Table SARS_CoV_2 Q321L 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Q409E 2020 Cell Table SARS_CoV_2 Q409E 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Q414E 2020 Cell Table SARS_CoV_2 Q414E 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Q414P 2020 Cell Table SARS_CoV_2 Q414P 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Q675H 2020 Cell Table SARS_CoV_2 Q675H 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. R408I 2020 Cell Table SARS_CoV_2 R408I 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. R509K 2020 Cell Table SARS_CoV_2 R509K 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. S359N 2020 Cell Table SARS_CoV_2 S359N 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. S438F 2020 Cell Table SARS_CoV_2 S438F 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. S939F 2020 Cell Table SARS_CoV_2 S939F 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. S943R 2020 Cell Table SARS_CoV_2 S943R 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. S943T 2020 Cell Table SARS_CoV_2 S943T 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. T478I 2020 Cell Table SARS_CoV_2 T478I 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. T719A 2020 Cell Table SARS_CoV_2 T719A 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. V341I 2020 Cell Table SARS_CoV_2 V341I 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. V367F 2020 Cell Table SARS_CoV_2 V367F 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. V483A 2020 Cell Table SARS_CoV_2 V483A 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. V483I 2020 Cell Table SARS_CoV_2 V483I 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. V503F 2020 Cell Table SARS_CoV_2 V503F 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. V510L 2020 Cell Table SARS_CoV_2 V510L 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. V615L 2020 Cell Table SARS_CoV_2 V615L 0 5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Y145del 2020 Cell Table SARS_CoV_2 Y145del 0 7 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Y508H 2020 Cell Table SARS_CoV_2 Y508H 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. A320V 2020 Bulletin of the World Health Organization Table SARS_CoV_2 A320V 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. A876T/A 2020 Bulletin of the World Health Organization Table SARS_CoV_2 A876A;A876T 0;0 7;7 32742035 Variant analysis of SARS-CoV-2 genomes. D128D 2020 Bulletin of the World Health Organization Table SARS_CoV_2 D128D 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. D268del 2020 Bulletin of the World Health Organization Table SARS_CoV_2 D268del 0 7 32742035 Variant analysis of SARS-CoV-2 genomes. D448del 2020 Bulletin of the World Health Organization Table SARS_CoV_2 D448del 0 7 32742035 Variant analysis of SARS-CoV-2 genomes. D614G 2020 Bulletin of the World Health Organization Table SARS_CoV_2 D614G 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. D614G/Q 2020 Bulletin of the World Health Organization Table SARS_CoV_2 D614G;D614Q 0;0 7;7 32742035 Variant analysis of SARS-CoV-2 genomes. F3071Y/F 2020 Bulletin of the World Health Organization Table SARS_CoV_2 F3071F;F3071Y 0;0 8;8 32742035 Variant analysis of SARS-CoV-2 genomes. F924F/F 2020 Bulletin of the World Health Organization Table SARS_CoV_2 F924F 0 7 32742035 Variant analysis of SARS-CoV-2 genomes. G196V 2020 Bulletin of the World Health Organization Table SARS_CoV_2 G196V 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. G251V 2020 Bulletin of the World Health Organization Table SARS_CoV_2 G251V 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. G392D 2020 Bulletin of the World Health Organization Table SARS_CoV_2 G392D 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. G392D/G 2020 Bulletin of the World Health Organization Table SARS_CoV_2 G392D;G392G 0;0 7;7 32742035 Variant analysis of SARS-CoV-2 genomes. H83H/H 2020 Bulletin of the World Health Organization Table SARS_CoV_2 H83H 0 6 32742035 Variant analysis of SARS-CoV-2 genomes. I739V/I 2020 Bulletin of the World Health Organization Table SARS_CoV_2 I739I;I739V 0;0 7;7 32742035 Variant analysis of SARS-CoV-2 genomes. L139L 2020 Bulletin of the World Health Organization Table SARS_CoV_2 L139L 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. L216L 2020 Bulletin of the World Health Organization Table SARS_CoV_2 L216L 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. L280L 2020 Bulletin of the World Health Organization Table SARS_CoV_2 L280L 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. L3606F 2020 Bulletin of the World Health Organization Table SARS_CoV_2 L3606F 0 6 32742035 Variant analysis of SARS-CoV-2 genomes. L3606F/G 2020 Bulletin of the World Health Organization Table SARS_CoV_2 L3606F;L3606G 0;0 8;8 32742035 Variant analysis of SARS-CoV-2 genomes. L3606F/L 2020 Bulletin of the World Health Organization Table SARS_CoV_2 L3606F;L3606L 0;0 8;8 32742035 Variant analysis of SARS-CoV-2 genomes. L3606F/V 2020 Bulletin of the World Health Organization Table SARS_CoV_2 L3606F;L3606V 0;0 8;8 32742035 Variant analysis of SARS-CoV-2 genomes. L5932L/L 2020 Bulletin of the World Health Organization Table SARS_CoV_2 L5932L 0 8 32742035 Variant analysis of SARS-CoV-2 genomes. L84S 2020 Bulletin of the World Health Organization Table SARS_CoV_2 L84S 0 4 32742035 Variant analysis of SARS-CoV-2 genomes. N5020N/N 2020 Bulletin of the World Health Organization Table SARS_CoV_2 N5020N 0 8 32742035 Variant analysis of SARS-CoV-2 genomes. N824N 2020 Bulletin of the World Health Organization Table SARS_CoV_2 N824N 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. P13L 2020 Bulletin of the World Health Organization Table SARS_CoV_2 P13L 0 4 32742035 Variant analysis of SARS-CoV-2 genomes. P4715L/P 2020 Bulletin of the World Health Organization Table SARS_CoV_2 P4715L;P4715P 0;0 8;8 32742035 Variant analysis of SARS-CoV-2 genomes. P5828L 2020 Bulletin of the World Health Organization Table SARS_CoV_2 P5828L 0 6 32742035 Variant analysis of SARS-CoV-2 genomes. P5828L/P 2020 Bulletin of the World Health Organization Table SARS_CoV_2 P5828L;P5828P 0;0 8;8 32742035 Variant analysis of SARS-CoV-2 genomes. P765S 2020 Bulletin of the World Health Organization Table SARS_CoV_2 P765S 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. P765S/P 2020 Bulletin of the World Health Organization Table SARS_CoV_2 P765P;P765S 0;0 7;7 32742035 Variant analysis of SARS-CoV-2 genomes. P971L/T 2020 Bulletin of the World Health Organization Table SARS_CoV_2 P971L;P971T 0;0 7;7 32742035 Variant analysis of SARS-CoV-2 genomes. Q57H 2020 Bulletin of the World Health Organization Table SARS_CoV_2 Q57H 0 4 32742035 Variant analysis of SARS-CoV-2 genomes. R5661R/R 2020 Bulletin of the World Health Organization Table SARS_CoV_2 R5661R 0 8 32742035 Variant analysis of SARS-CoV-2 genomes. S194L 2020 Bulletin of the World Health Organization Table SARS_CoV_2 S194L 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. S197L 2020 Bulletin of the World Health Organization Table SARS_CoV_2 S197L 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. S24L 2020 Bulletin of the World Health Organization Table SARS_CoV_2 S24L 0 4 32742035 Variant analysis of SARS-CoV-2 genomes. S2839S/S 2020 Bulletin of the World Health Organization Table SARS_CoV_2 S2839S 0 8 32742035 Variant analysis of SARS-CoV-2 genomes. S3884L/S 2020 Bulletin of the World Health Organization Table SARS_CoV_2 S3884L;S3884S 0;0 8;8 32742035 Variant analysis of SARS-CoV-2 genomes. T175M 2020 Bulletin of the World Health Organization Table SARS_CoV_2 T175M 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. T265I 2020 Bulletin of the World Health Organization Table SARS_CoV_2 T265I 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. T265I/T 2020 Bulletin of the World Health Organization Table SARS_CoV_2 T265I;T265T 0;0 7;7 32742035 Variant analysis of SARS-CoV-2 genomes. V13L 2020 Bulletin of the World Health Organization Table SARS_CoV_2 V13L 0 4 32742035 Variant analysis of SARS-CoV-2 genomes. V378I/V 2020 Bulletin of the World Health Organization Table SARS_CoV_2 V378I;V378V 0;0 7;7 32742035 Variant analysis of SARS-CoV-2 genomes. V62L 2020 Bulletin of the World Health Organization Table SARS_CoV_2 V62L 0 4 32742035 Variant analysis of SARS-CoV-2 genomes. Y4847Y/Y 2020 Bulletin of the World Health Organization Table SARS_CoV_2 Y4847Y 0 8 32742035 Variant analysis of SARS-CoV-2 genomes. Y5865C/Y 2020 Bulletin of the World Health Organization Table SARS_CoV_2 Y5865C;Y5865Y 0;0 8;8 32742035 Variant analysis of SARS-CoV-2 genomes. Y717Y/Y 2020 Bulletin of the World Health Organization Table SARS_CoV_2 Y717Y 0 7 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. N487A 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 N487A 0 5 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. N489A 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 N489A 0 5 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. N501A 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 N501A 0 5 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. Y449A 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 Y449A 0 5 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. Y505A 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 Y505A 0 5 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. A17858G 2020 Frontiers in microbiology Table SARS_CoV_2 A17858G 0 7 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. A20268G 2020 Frontiers in microbiology Table SARS_CoV_2 A20268G 0 7 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. A23403G 2020 Frontiers in microbiology Table SARS_CoV_2 A23403G 0 7 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. A2480G 2020 Frontiers in microbiology Table SARS_CoV_2 A2480G 0 6 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. C1059T 2020 Frontiers in microbiology Table SARS_CoV_2 C1059T 0 6 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. C14408T 2020 Frontiers in microbiology Table SARS_CoV_2 C14408T 0 7 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. C14805T 2020 Frontiers in microbiology Table SARS_CoV_2 C14805T 0 7 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. C17747T 2020 Frontiers in microbiology Table SARS_CoV_2 C17747T 0 7 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. C18060T 2020 Frontiers in microbiology Table SARS_CoV_2 C18060T 0 7 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. C23731T 2020 Frontiers in microbiology Table SARS_CoV_2 C23731T 0 7 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. C241T 2020 Frontiers in microbiology Table SARS_CoV_2 C241T 0 5 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. C2558T 2020 Frontiers in microbiology Table SARS_CoV_2 C2558T 0 6 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. C3037T 2020 Frontiers in microbiology Table SARS_CoV_2 C3037T 0 6 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. C8782T 2020 Frontiers in microbiology Table SARS_CoV_2 C8782T 0 6 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. D614G 2020 Frontiers in microbiology Table SARS_CoV_2 D614G 0 5 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. F106F 2020 Frontiers in microbiology Table SARS_CoV_2 F106F 0 5 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. G10097A 2020 Frontiers in microbiology Table SARS_CoV_2 G10097A 0 7 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. G11083T 2020 Frontiers in microbiology Table SARS_CoV_2 G11083T 0 7 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. G15S 2020 Frontiers in microbiology Table SARS_CoV_2 G15S 0 4 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. G251V 2020 Frontiers in microbiology Table SARS_CoV_2 G251V 0 5 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. G25563T 2020 Frontiers in microbiology Table SARS_CoV_2 G25563T 0 7 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. G26144T 2020 Frontiers in microbiology Table SARS_CoV_2 G26144T 0 7 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. I559V 2020 Frontiers in microbiology Table SARS_CoV_2 I559V 0 5 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. L216L 2020 Frontiers in microbiology Table SARS_CoV_2 L216L 0 5 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. L37F 2020 Frontiers in microbiology Table SARS_CoV_2 L37F 0 4 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. L84S 2020 Frontiers in microbiology Table SARS_CoV_2 L84S 0 4 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. P314L 2020 Frontiers in microbiology Table SARS_CoV_2 P314L 0 5 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. P504L 2020 Frontiers in microbiology Table SARS_CoV_2 P504L 0 5 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. P585S 2020 Frontiers in microbiology Table SARS_CoV_2 P585S 0 5 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Q57H 2020 Frontiers in microbiology Table SARS_CoV_2 Q57H 0 4 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. S76S 2020 Frontiers in microbiology Table SARS_CoV_2 S76S 0 4 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. T28144C 2020 Frontiers in microbiology Table SARS_CoV_2 T28144C 0 7 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. T723T 2020 Frontiers in microbiology Table SARS_CoV_2 T723T 0 5 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. T85I 2020 Frontiers in microbiology Table SARS_CoV_2 T85I 0 4 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Y446Y 2020 Frontiers in microbiology Table SARS_CoV_2 Y446Y 0 5 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. Y541C 2020 Frontiers in microbiology Table SARS_CoV_2 Y541C 0 5 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. D614G 2020 Scientific reports Table SARS_CoV_2 D614G 0 5 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. A930V 2022 Journal of biomolecular structure & dynamics Table SARS_CoV_2 A930V 0 5 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. D936Y 2022 Journal of biomolecular structure & dynamics Table SARS_CoV_2 D936Y 0 5 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. F486L 2022 Journal of biomolecular structure & dynamics Table SARS_CoV_2 F486L 0 5 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. L455Y 2022 Journal of biomolecular structure & dynamics Table SARS_CoV_2 L455Y 0 5 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. N501T 2022 Journal of biomolecular structure & dynamics Table SARS_CoV_2 N501T 0 5 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. Q493N 2022 Journal of biomolecular structure & dynamics Table SARS_CoV_2 Q493N 0 5 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. Q498Y 2022 Journal of biomolecular structure & dynamics Table SARS_CoV_2 Q498Y 0 5 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. R408I 2022 Journal of biomolecular structure & dynamics Table SARS_CoV_2 R408I 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). A116V 2020 Journal of chemical information and modeling Table SARS_CoV_2 A116V 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). A129V 2020 Journal of chemical information and modeling Table SARS_CoV_2 A129V 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). A173V 2020 Journal of chemical information and modeling Table SARS_CoV_2 A173V 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). A191V 2020 Journal of chemical information and modeling Table SARS_CoV_2 A191V 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). A193V 2020 Journal of chemical information and modeling Table SARS_CoV_2 A193V 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). A234V 2020 Journal of chemical information and modeling Table SARS_CoV_2 A234V 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). A255V 2020 Journal of chemical information and modeling Table SARS_CoV_2 A255V 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). A260V 2020 Journal of chemical information and modeling Table SARS_CoV_2 A260V 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). A266V 2020 Journal of chemical information and modeling Table SARS_CoV_2 A266V 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). A70T 2020 Journal of chemical information and modeling Table SARS_CoV_2 A70T 0 4 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). C160S 2020 Journal of chemical information and modeling Table SARS_CoV_2 C160S 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). D248E 2020 Journal of chemical information and modeling Table SARS_CoV_2 D248E 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). D48E 2020 Journal of chemical information and modeling Table SARS_CoV_2 D48E 0 4 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). G15D 2020 Journal of chemical information and modeling Table SARS_CoV_2 G15D 0 4 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). G15S 2020 Journal of chemical information and modeling Table SARS_CoV_2 G15S 0 4 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). G71S 2020 Journal of chemical information and modeling Table SARS_CoV_2 G71S 0 4 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). I136V 2020 Journal of chemical information and modeling Table SARS_CoV_2 I136V 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). I259T 2020 Journal of chemical information and modeling Table SARS_CoV_2 I259T 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). K236R 2020 Journal of chemical information and modeling Table SARS_CoV_2 K236R 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). K61R 2020 Journal of chemical information and modeling Table SARS_CoV_2 K61R 0 4 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). K90R 2020 Journal of chemical information and modeling Table SARS_CoV_2 K90R 0 4 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). L220F 2020 Journal of chemical information and modeling Table SARS_CoV_2 L220F 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). L232F 2020 Journal of chemical information and modeling Table SARS_CoV_2 L232F 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). L89F 2020 Journal of chemical information and modeling Table SARS_CoV_2 L89F 0 4 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). M17I 2020 Journal of chemical information and modeling Table SARS_CoV_2 M17I 0 4 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). M49I 2020 Journal of chemical information and modeling Table SARS_CoV_2 M49I 0 4 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). N151D 2020 Journal of chemical information and modeling Table SARS_CoV_2 N151D 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). N274D 2020 Journal of chemical information and modeling Table SARS_CoV_2 N274D 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). P108S 2020 Journal of chemical information and modeling Table SARS_CoV_2 P108S 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). P132L 2020 Journal of chemical information and modeling Table SARS_CoV_2 P132L 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). P184L 2020 Journal of chemical information and modeling Table SARS_CoV_2 P184L 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). P184S 2020 Journal of chemical information and modeling Table SARS_CoV_2 P184S 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). P99L 2020 Journal of chemical information and modeling Table SARS_CoV_2 P99L 0 4 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). R105H 2020 Journal of chemical information and modeling Table SARS_CoV_2 R105H 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). R279C 2020 Journal of chemical information and modeling Table SARS_CoV_2 R279C 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). R60C 2020 Journal of chemical information and modeling Table SARS_CoV_2 R60C 0 4 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). S301L 2020 Journal of chemical information and modeling Table SARS_CoV_2 S301L 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). T135I 2020 Journal of chemical information and modeling Table SARS_CoV_2 T135I 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). T190I 2020 Journal of chemical information and modeling Table SARS_CoV_2 T190I 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). T196M 2020 Journal of chemical information and modeling Table SARS_CoV_2 T196M 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). T198I 2020 Journal of chemical information and modeling Table SARS_CoV_2 T198I 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). T201A 2020 Journal of chemical information and modeling Table SARS_CoV_2 T201A 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). T45I 2020 Journal of chemical information and modeling Table SARS_CoV_2 T45I 0 4 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). V157I 2020 Journal of chemical information and modeling Table SARS_CoV_2 V157I 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). V157L 2020 Journal of chemical information and modeling Table SARS_CoV_2 V157L 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). V20L 2020 Journal of chemical information and modeling Table SARS_CoV_2 V20L 0 4 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). V261A 2020 Journal of chemical information and modeling Table SARS_CoV_2 V261A 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). Y101C 2020 Journal of chemical information and modeling Table SARS_CoV_2 Y101C 0 5 32853525 Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M(pro). Y237H 2020 Journal of chemical information and modeling Table SARS_CoV_2 Y237H 0 5 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. A406V 2020 PloS one Table SARS_CoV_2 A406V 0 5 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. F797C 2020 PloS one Table SARS_CoV_2 F797C 0 5 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. G251V 2020 PloS one Table SARS_CoV_2 G251V 0 5 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. H49Y 2020 PloS one Table SARS_CoV_2 H49Y 0 4 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. L140V 2020 PloS one Table SARS_CoV_2 L140V 0 5 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. L37H 2020 PloS one Table SARS_CoV_2 L37H 0 4 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. P344S 2020 PloS one Table SARS_CoV_2 P344S 0 5 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. R408I 2020 PloS one Table SARS_CoV_2 R408I 0 5 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. R60C 2020 PloS one Table SARS_CoV_2 R60C 0 4 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. S221W 2020 PloS one Table SARS_CoV_2 S221W 0 5 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. S247R 2020 PloS one Table SARS_CoV_2 S247R 0 5 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. W128L 2020 PloS one Table SARS_CoV_2 W128L 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 21723G>C 2020 Journal of laboratory physicians Table SARS_CoV_2 G21723C 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 21723T>G 2020 Journal of laboratory physicians Table SARS_CoV_2 T21723G 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 21726T>A 2020 Journal of laboratory physicians Table SARS_CoV_2 T21726A 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 21774C>T 2020 Journal of laboratory physicians Table SARS_CoV_2 C21774T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 21893G>A 2020 Journal of laboratory physicians Table SARS_CoV_2 G21893A 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22033C>A 2020 Journal of laboratory physicians Table SARS_CoV_2 C22033A 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22436G>T 2020 Journal of laboratory physicians Table SARS_CoV_2 G22436T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22437C>T 2020 Journal of laboratory physicians Table SARS_CoV_2 C22437T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22439C>A 2020 Journal of laboratory physicians Table SARS_CoV_2 C22439A 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22439C>G 2020 Journal of laboratory physicians Table SARS_CoV_2 C22439G 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22441C>A 2020 Journal of laboratory physicians Table SARS_CoV_2 C22441A 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22441C>G 2020 Journal of laboratory physicians Table SARS_CoV_2 C22441G 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22441T>G 2020 Journal of laboratory physicians Table SARS_CoV_2 T22441G 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22443A>T 2020 Journal of laboratory physicians Table SARS_CoV_2 A22443T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22444C>A 2020 Journal of laboratory physicians Table SARS_CoV_2 C22444A 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22445C>T 2020 Journal of laboratory physicians Table SARS_CoV_2 C22445T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22446C>A 2020 Journal of laboratory physicians Table SARS_CoV_2 C22446A 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22448C>T 2020 Journal of laboratory physicians Table SARS_CoV_2 C22448T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22450C>T 2020 Journal of laboratory physicians Table SARS_CoV_2 C22450T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22452C>G 2020 Journal of laboratory physicians Table SARS_CoV_2 C22452G 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22453A>G 2020 Journal of laboratory physicians Table SARS_CoV_2 A22453G 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22530C>T 2020 Journal of laboratory physicians Table SARS_CoV_2 C22530T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22592G>T 2020 Journal of laboratory physicians Table SARS_CoV_2 G22592T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22604G>A 2020 Journal of laboratory physicians Table SARS_CoV_2 G22604A 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22661G>T 2020 Journal of laboratory physicians Table SARS_CoV_2 G22661T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22782G>T 2020 Journal of laboratory physicians Table SARS_CoV_2 G22782T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 22988G>A 2020 Journal of laboratory physicians Table SARS_CoV_2 G22988A 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 23004T>C 2020 Journal of laboratory physicians Table SARS_CoV_2 T23004C 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 23119T>A 2020 Journal of laboratory physicians Table SARS_CoV_2 T23119A 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 23120G>T 2020 Journal of laboratory physicians Table SARS_CoV_2 G23120T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 23125G>T 2020 Journal of laboratory physicians Table SARS_CoV_2 G23125T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 23147A>G 2020 Journal of laboratory physicians Table SARS_CoV_2 A23147G 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 23402A>G 2020 Journal of laboratory physicians Table SARS_CoV_2 A23402G 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 23521C>T 2020 Journal of laboratory physicians Table SARS_CoV_2 C23521T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 24353C>T 2020 Journal of laboratory physicians Table SARS_CoV_2 C24353T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 24368G>T 2020 Journal of laboratory physicians Table SARS_CoV_2 G24368T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 25064G>C 2020 Journal of laboratory physicians Table SARS_CoV_2 G25064C 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 25311G>A 2020 Journal of laboratory physicians Table SARS_CoV_2 G25311A 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. 25311G>T 2020 Journal of laboratory physicians Table SARS_CoV_2 G25311T 0 8 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. A292S 2020 Journal of laboratory physicians Table SARS_CoV_2 A292S 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. A344S 2020 Journal of laboratory physicians Table SARS_CoV_2 A344S 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. A348T 2020 Journal of laboratory physicians Table SARS_CoV_2 A348T 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. A419S 2020 Journal of laboratory physicians Table SARS_CoV_2 A419S 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. A520S 2020 Journal of laboratory physicians Table SARS_CoV_2 A520S 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. A522S 2020 Journal of laboratory physicians Table SARS_CoV_2 A522S 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. A653V 2020 Journal of laboratory physicians Table SARS_CoV_2 A653V 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. A930V 2020 Journal of laboratory physicians Table SARS_CoV_2 A930V 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. C1250F 2020 Journal of laboratory physicians Table SARS_CoV_2 C1250F 0 6 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. C1250Y 2020 Journal of laboratory physicians Table SARS_CoV_2 C1250Y 0 6 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. D111N 2020 Journal of laboratory physicians Table SARS_CoV_2 D111N 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. D1168H 2020 Journal of laboratory physicians Table SARS_CoV_2 D1168H 0 6 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. D294E 2020 Journal of laboratory physicians Table SARS_CoV_2 D294E 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. D294I 2020 Journal of laboratory physicians Table SARS_CoV_2 D294I 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. D614G 2020 Journal of laboratory physicians Table SARS_CoV_2 D614G 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. D936Y 2020 Journal of laboratory physicians Table SARS_CoV_2 D936Y 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. F157L 2020 Journal of laboratory physicians Table SARS_CoV_2 F157L 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. F55I 2020 Journal of laboratory physicians Table SARS_CoV_2 F55I 0 4 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. G476S 2020 Journal of laboratory physicians Table SARS_CoV_2 G476S 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. H519Q 2020 Journal of laboratory physicians Table SARS_CoV_2 H519Q 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. K529E 2020 Journal of laboratory physicians Table SARS_CoV_2 K529E 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. L293M 2020 Journal of laboratory physicians Table SARS_CoV_2 L293M 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. L293V 2020 Journal of laboratory physicians Table SARS_CoV_2 L293V 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. L296F 2020 Journal of laboratory physicians Table SARS_CoV_2 L296F 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. L54F 2020 Journal of laboratory physicians Table SARS_CoV_2 L54F 0 4 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. L54W 2020 Journal of laboratory physicians Table SARS_CoV_2 L54W 0 4 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. P295S 2020 Journal of laboratory physicians Table SARS_CoV_2 P295S 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. R408I 2020 Journal of laboratory physicians Table SARS_CoV_2 R408I 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. S297W 2020 Journal of laboratory physicians Table SARS_CoV_2 S297W 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. S71F 2020 Journal of laboratory physicians Table SARS_CoV_2 S71F 0 4 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. T323I 2020 Journal of laboratory physicians Table SARS_CoV_2 T323I 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. V367F 2020 Journal of laboratory physicians Table SARS_CoV_2 V367F 0 5 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. V483A 2020 Journal of laboratory physicians Table SARS_CoV_2 V483A 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. A10058G 2020 Sustainable cities and society Table SARS_CoV_2 A10058G 0 7 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. A17594G 2020 Sustainable cities and society Table SARS_CoV_2 A17594G 0 7 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. A1841G 2020 Sustainable cities and society Table SARS_CoV_2 A1841G 0 6 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. A2024G 2020 Sustainable cities and society Table SARS_CoV_2 A2024G 0 6 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. A2215G 2020 Sustainable cities and society Table SARS_CoV_2 A2215G 0 6 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. C11651T 2020 Sustainable cities and society Table SARS_CoV_2 C11651T 0 7 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. C14144T 2020 Sustainable cities and society Table SARS_CoV_2 C14144T 0 7 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. C14541T 2020 Sustainable cities and society Table SARS_CoV_2 C14541T 0 7 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. C17483T 2020 Sustainable cities and society Table SARS_CoV_2 C17483T 0 7 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. C17796T 2020 Sustainable cities and society Table SARS_CoV_2 C17796T 0 7 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. C18734T 2020 Sustainable cities and society Table SARS_CoV_2 C18734T 0 7 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. C2293T 2020 Sustainable cities and society Table SARS_CoV_2 C2293T 0 6 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. C242T 2020 Sustainable cities and society Table SARS_CoV_2 C242T 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. C2772T 2020 Sustainable cities and society Table SARS_CoV_2 C2772T 0 6 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. C2912T 2020 Sustainable cities and society Table SARS_CoV_2 C2912T 0 6 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. C296T 2020 Sustainable cities and society Table SARS_CoV_2 C296T 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. C524T 2020 Sustainable cities and society Table SARS_CoV_2 C524T 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. C581T 2020 Sustainable cities and society Table SARS_CoV_2 C581T 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. C590T 2020 Sustainable cities and society Table SARS_CoV_2 C590T 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. C794T 2020 Sustainable cities and society Table SARS_CoV_2 C794T 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. C8517T 2020 Sustainable cities and society Table SARS_CoV_2 C8517T 0 6 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. D614G 2020 Sustainable cities and society Table SARS_CoV_2 D614G 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G10818T 2020 Sustainable cities and society Table SARS_CoV_2 G10818T 0 7 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G1132A 2020 Sustainable cities and society Table SARS_CoV_2 G1132A 0 6 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G1175A 2020 Sustainable cities and society Table SARS_CoV_2 G1175A 0 6 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G171T 2020 Sustainable cities and society Table SARS_CoV_2 G171T 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G184C 2020 Sustainable cities and society Table SARS_CoV_2 G184C 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G184T 2020 Sustainable cities and society Table SARS_CoV_2 G184T 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G19420T 2020 Sustainable cities and society Table SARS_CoV_2 G19420T 0 7 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G200S 2020 Sustainable cities and society Table SARS_CoV_2 G200S 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G2025C 2020 Sustainable cities and society Table SARS_CoV_2 G2025C 0 6 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G204R 2020 Sustainable cities and society Table SARS_CoV_2 G204R 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G251V 2020 Sustainable cities and society Table SARS_CoV_2 G251V 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G2626A 2020 Sustainable cities and society Table SARS_CoV_2 G2626A 0 6 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G578T 2020 Sustainable cities and society Table SARS_CoV_2 G578T 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G587T 2020 Sustainable cities and society Table SARS_CoV_2 G587T 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G605A 2020 Sustainable cities and society Table SARS_CoV_2 G605A 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G752T 2020 Sustainable cities and society Table SARS_CoV_2 G752T 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. G9832A 2020 Sustainable cities and society Table SARS_CoV_2 G9832A 0 6 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. L3606F 2020 Sustainable cities and society Table SARS_CoV_2 L3606F 0 6 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. L84S 2020 Sustainable cities and society Table SARS_CoV_2 L84S 0 4 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. N192K 2020 Sustainable cities and society Table SARS_CoV_2 N192K 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. P13L 2020 Sustainable cities and society Table SARS_CoV_2 P13L 0 4 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. P199L 2020 Sustainable cities and society Table SARS_CoV_2 P199L 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. P199S 2020 Sustainable cities and society Table SARS_CoV_2 P199S 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. P199T 2020 Sustainable cities and society Table SARS_CoV_2 P199T 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. P4715L 2020 Sustainable cities and society Table SARS_CoV_2 P4715L 0 6 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. P5828L 2020 Sustainable cities and society Table SARS_CoV_2 P5828L 0 6 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. Q57H 2020 Sustainable cities and society Table SARS_CoV_2 Q57H 0 4 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. Q675H 2020 Sustainable cities and society Table SARS_CoV_2 Q675H 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. Q675R 2020 Sustainable cities and society Table SARS_CoV_2 Q675R 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. R185C 2020 Sustainable cities and society Table SARS_CoV_2 R185C 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. R191C 2020 Sustainable cities and society Table SARS_CoV_2 R191C 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. R195K 2020 Sustainable cities and society Table SARS_CoV_2 R195K 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. R203K 2020 Sustainable cities and society Table SARS_CoV_2 R203K 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. S183Y 2020 Sustainable cities and society Table SARS_CoV_2 S183Y 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. S186F 2020 Sustainable cities and society Table SARS_CoV_2 S186F 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. S186Y 2020 Sustainable cities and society Table SARS_CoV_2 S186Y 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. S188L 2020 Sustainable cities and society Table SARS_CoV_2 S188L 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. S188P 2020 Sustainable cities and society Table SARS_CoV_2 S188P 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. S190I 2020 Sustainable cities and society Table SARS_CoV_2 S190I 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. S193I 2020 Sustainable cities and society Table SARS_CoV_2 S193I 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. S194L 2020 Sustainable cities and society Table SARS_CoV_2 S194L 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. S197L 2020 Sustainable cities and society Table SARS_CoV_2 S197L 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. S202N 2020 Sustainable cities and society Table SARS_CoV_2 S202N 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. S943P 2020 Sustainable cities and society Table SARS_CoV_2 S943P 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. T18472C 2020 Sustainable cities and society Table SARS_CoV_2 T18472C 0 7 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. T198I 2020 Sustainable cities and society Table SARS_CoV_2 T198I 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. T225A 2020 Sustainable cities and society Table SARS_CoV_2 T225A 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. T251C 2020 Sustainable cities and society Table SARS_CoV_2 T251C 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. T265I 2020 Sustainable cities and society Table SARS_CoV_2 T265I 0 5 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. T9212A 2020 Sustainable cities and society Table SARS_CoV_2 T9212A 0 6 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. Y5865C 2020 Sustainable cities and society Table SARS_CoV_2 Y5865C 0 6 32905045 Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. D614G 2020 Cell reports. Medicine Table SARS_CoV_2 D614G 0 5 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. D614G 2020 bioRxiv Table SARS_CoV_2 D614G 0 5 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. A20268G 2020 Zoological research Table SARS_CoV_2 A20268G 0 7 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. A23403G 2020 Zoological research Table SARS_CoV_2 A23403G 0 7 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. C14408T 2020 Zoological research Table SARS_CoV_2 C14408T 0 7 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. C14805T 2020 Zoological research Table SARS_CoV_2 C14805T 0 7 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. C241T 2020 Zoological research Table SARS_CoV_2 C241T 0 5 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. C28657T 2020 Zoological research Table SARS_CoV_2 C28657T 0 7 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. C28863T 2020 Zoological research Table SARS_CoV_2 C28863T 0 7 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. C29144T 2020 Zoological research Table SARS_CoV_2 C29144T 0 7 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. C3037T 2020 Zoological research Table SARS_CoV_2 C3037T 0 6 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. G25979T 2020 Zoological research Table SARS_CoV_2 G25979T 0 7 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. G29734C 2020 Zoological research Table SARS_CoV_2 G29734C 0 7 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. T28144C 2020 Zoological research Table SARS_CoV_2 T28144C 0 7 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A222P 2021 Transboundary and emerging diseases Table SARS_CoV_2 A222P 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A222S 2021 Transboundary and emerging diseases Table SARS_CoV_2 A222S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A222V 2021 Transboundary and emerging diseases Table SARS_CoV_2 A222V 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A263S 2021 Transboundary and emerging diseases Table SARS_CoV_2 A263S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A263T 2021 Transboundary and emerging diseases Table SARS_CoV_2 A263T 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A263V 2021 Transboundary and emerging diseases Table SARS_CoV_2 A263V 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A27S 2021 Transboundary and emerging diseases Table SARS_CoV_2 A27S 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A27T 2021 Transboundary and emerging diseases Table SARS_CoV_2 A27T 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A27V 2021 Transboundary and emerging diseases Table SARS_CoV_2 A27V 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A570D 2021 Transboundary and emerging diseases Table SARS_CoV_2 A570D 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A570S 2021 Transboundary and emerging diseases Table SARS_CoV_2 A570S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A570T 2021 Transboundary and emerging diseases Table SARS_CoV_2 A570T 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A570V 2021 Transboundary and emerging diseases Table SARS_CoV_2 A570V 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A623V 2021 Transboundary and emerging diseases Table SARS_CoV_2 A623V 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A684S 2021 Transboundary and emerging diseases Table SARS_CoV_2 A684S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A684T 2021 Transboundary and emerging diseases Table SARS_CoV_2 A684T 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A684V 2021 Transboundary and emerging diseases Table SARS_CoV_2 A684V 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A831S 2021 Transboundary and emerging diseases Table SARS_CoV_2 A831S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A831T 2021 Transboundary and emerging diseases Table SARS_CoV_2 A831T 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A831V 2021 Transboundary and emerging diseases Table SARS_CoV_2 A831V 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A845D 2021 Transboundary and emerging diseases Table SARS_CoV_2 A845D 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A845S 2021 Transboundary and emerging diseases Table SARS_CoV_2 A845S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A845V 2021 Transboundary and emerging diseases Table SARS_CoV_2 A845V 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A879S 2021 Transboundary and emerging diseases Table SARS_CoV_2 A879S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A879T 2021 Transboundary and emerging diseases Table SARS_CoV_2 A879T 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A879V 2021 Transboundary and emerging diseases Table SARS_CoV_2 A879V 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A930S 2021 Transboundary and emerging diseases Table SARS_CoV_2 A930S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A930T 2021 Transboundary and emerging diseases Table SARS_CoV_2 A930T 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. A930V 2021 Transboundary and emerging diseases Table SARS_CoV_2 A930V 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D1146E 2021 Transboundary and emerging diseases Table SARS_CoV_2 D1146E 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D1146H 2021 Transboundary and emerging diseases Table SARS_CoV_2 D1146H 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D1146N 2021 Transboundary and emerging diseases Table SARS_CoV_2 D1146N 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D1146Y 2021 Transboundary and emerging diseases Table SARS_CoV_2 D1146Y 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D1153A 2021 Transboundary and emerging diseases Table SARS_CoV_2 D1153A 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D1153H 2021 Transboundary and emerging diseases Table SARS_CoV_2 D1153H 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D1153Y 2021 Transboundary and emerging diseases Table SARS_CoV_2 D1153Y 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D215G 2021 Transboundary and emerging diseases Table SARS_CoV_2 D215G 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D215H 2021 Transboundary and emerging diseases Table SARS_CoV_2 D215H 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D215N 2021 Transboundary and emerging diseases Table SARS_CoV_2 D215N 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D215Y 2021 Transboundary and emerging diseases Table SARS_CoV_2 D215Y 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D80A 2021 Transboundary and emerging diseases Table SARS_CoV_2 D80A 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D80N 2021 Transboundary and emerging diseases Table SARS_CoV_2 D80N 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D80Y 2021 Transboundary and emerging diseases Table SARS_CoV_2 D80Y 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D839E 2021 Transboundary and emerging diseases Table SARS_CoV_2 D839E 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D839N 2021 Transboundary and emerging diseases Table SARS_CoV_2 D839N 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. D839Y 2021 Transboundary and emerging diseases Table SARS_CoV_2 D839Y 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. E654D 2021 Transboundary and emerging diseases Table SARS_CoV_2 E654D 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. E654K 2021 Transboundary and emerging diseases Table SARS_CoV_2 E654K 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. E654Q 2021 Transboundary and emerging diseases Table SARS_CoV_2 E654Q 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. E780D 2021 Transboundary and emerging diseases Table SARS_CoV_2 E780D 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. E780Q 2021 Transboundary and emerging diseases Table SARS_CoV_2 E780Q 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. E780V 2021 Transboundary and emerging diseases Table SARS_CoV_2 E780V 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. F32I 2021 Transboundary and emerging diseases Table SARS_CoV_2 F32I 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. F32L 2021 Transboundary and emerging diseases Table SARS_CoV_2 F32L 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. F32V 2021 Transboundary and emerging diseases Table SARS_CoV_2 F32V 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. F32Y 2021 Transboundary and emerging diseases Table SARS_CoV_2 F32Y 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G1085E 2021 Transboundary and emerging diseases Table SARS_CoV_2 G1085E 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G1085L 2021 Transboundary and emerging diseases Table SARS_CoV_2 G1085L 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G1085R 2021 Transboundary and emerging diseases Table SARS_CoV_2 G1085R 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G142A 2021 Transboundary and emerging diseases Table SARS_CoV_2 G142A 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G142D 2021 Transboundary and emerging diseases Table SARS_CoV_2 G142D 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G142S 2021 Transboundary and emerging diseases Table SARS_CoV_2 G142S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G142V 2021 Transboundary and emerging diseases Table SARS_CoV_2 G142V 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G261D 2021 Transboundary and emerging diseases Table SARS_CoV_2 G261D 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G261R 2021 Transboundary and emerging diseases Table SARS_CoV_2 G261R 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G261S 2021 Transboundary and emerging diseases Table SARS_CoV_2 G261S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G261V 2021 Transboundary and emerging diseases Table SARS_CoV_2 G261V 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G72E 2021 Transboundary and emerging diseases Table SARS_CoV_2 G72E 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G72R 2021 Transboundary and emerging diseases Table SARS_CoV_2 G72R 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G72W 2021 Transboundary and emerging diseases Table SARS_CoV_2 G72W 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G75D 2021 Transboundary and emerging diseases Table SARS_CoV_2 G75D 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G75R 2021 Transboundary and emerging diseases Table SARS_CoV_2 G75R 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G75V 2021 Transboundary and emerging diseases Table SARS_CoV_2 G75V 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G838D 2021 Transboundary and emerging diseases Table SARS_CoV_2 G838D 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G838S 2021 Transboundary and emerging diseases Table SARS_CoV_2 G838S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. G838V 2021 Transboundary and emerging diseases Table SARS_CoV_2 G838V 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. H146N 2021 Transboundary and emerging diseases Table SARS_CoV_2 H146N 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. H146Q 2021 Transboundary and emerging diseases Table SARS_CoV_2 H146Q 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. H146R 2021 Transboundary and emerging diseases Table SARS_CoV_2 H146R 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. H146Y 2021 Transboundary and emerging diseases Table SARS_CoV_2 H146Y 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. I468F 2021 Transboundary and emerging diseases Table SARS_CoV_2 I468F 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. I468T 2021 Transboundary and emerging diseases Table SARS_CoV_2 I468T 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. I468V 2021 Transboundary and emerging diseases Table SARS_CoV_2 I468V 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. I870S 2021 Transboundary and emerging diseases Table SARS_CoV_2 I870S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. I870T 2021 Transboundary and emerging diseases Table SARS_CoV_2 I870T 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. I870V 2021 Transboundary and emerging diseases Table SARS_CoV_2 I870V 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. K529E 2021 Transboundary and emerging diseases Table SARS_CoV_2 K529E 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. K529M 2021 Transboundary and emerging diseases Table SARS_CoV_2 K529M 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. K529N 2021 Transboundary and emerging diseases Table SARS_CoV_2 K529N 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. K529R 2021 Transboundary and emerging diseases Table SARS_CoV_2 K529R 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. K558N 2021 Transboundary and emerging diseases Table SARS_CoV_2 K558N 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. K558Q 2021 Transboundary and emerging diseases Table SARS_CoV_2 K558Q 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. K558R 2021 Transboundary and emerging diseases Table SARS_CoV_2 K558R 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. K97E 2021 Transboundary and emerging diseases Table SARS_CoV_2 K97E 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. K97N 2021 Transboundary and emerging diseases Table SARS_CoV_2 K97N 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. K97R 2021 Transboundary and emerging diseases Table SARS_CoV_2 K97R 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. L752F 2021 Transboundary and emerging diseases Table SARS_CoV_2 L752F 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. L752I 2021 Transboundary and emerging diseases Table SARS_CoV_2 L752I 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. L752R 2021 Transboundary and emerging diseases Table SARS_CoV_2 L752R 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. M153I 2021 Transboundary and emerging diseases Table SARS_CoV_2 M153I 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. M153T 2021 Transboundary and emerging diseases Table SARS_CoV_2 M153T 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. M153V 2021 Transboundary and emerging diseases Table SARS_CoV_2 M153V 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. N148K 2021 Transboundary and emerging diseases Table SARS_CoV_2 N148K 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. N148S 2021 Transboundary and emerging diseases Table SARS_CoV_2 N148S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. N148Y 2021 Transboundary and emerging diseases Table SARS_CoV_2 N148Y 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. N354D 2021 Transboundary and emerging diseases Table SARS_CoV_2 N354D 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. N354K 2021 Transboundary and emerging diseases Table SARS_CoV_2 N354K 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. N354S 2021 Transboundary and emerging diseases Table SARS_CoV_2 N354S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. P1162A 2021 Transboundary and emerging diseases Table SARS_CoV_2 P1162A 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. P1162L 2021 Transboundary and emerging diseases Table SARS_CoV_2 P1162L 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. P1162S 2021 Transboundary and emerging diseases Table SARS_CoV_2 P1162S 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. P1162T 2021 Transboundary and emerging diseases Table SARS_CoV_2 P1162T 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. P251H 2021 Transboundary and emerging diseases Table SARS_CoV_2 P251H 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. P251L 2021 Transboundary and emerging diseases Table SARS_CoV_2 P251L 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. P251S 2021 Transboundary and emerging diseases Table SARS_CoV_2 P251S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. P26L 2021 Transboundary and emerging diseases Table SARS_CoV_2 P26L 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. P26R 2021 Transboundary and emerging diseases Table SARS_CoV_2 P26R 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. P26S 2021 Transboundary and emerging diseases Table SARS_CoV_2 P26S 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. P681H 2021 Transboundary and emerging diseases Table SARS_CoV_2 P681H 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. P681L 2021 Transboundary and emerging diseases Table SARS_CoV_2 P681L 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. P681S 2021 Transboundary and emerging diseases Table SARS_CoV_2 P681S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. P812L 2021 Transboundary and emerging diseases Table SARS_CoV_2 P812L 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. P812S 2021 Transboundary and emerging diseases Table SARS_CoV_2 P812S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. P812T 2021 Transboundary and emerging diseases Table SARS_CoV_2 P812T 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q183H 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q183H 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q183L 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q183L 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q183R 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q183R 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q218E 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q218E 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q218L 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q218L 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q218R 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q218R 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q239H 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q239H 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q239K 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q239K 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q239R 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q239R 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q414K 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q414K 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q414P 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q414P 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q414R 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q414R 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q675H 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q675H 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q675K 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q675K 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q675R 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q675R 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q677H 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q677H 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q677R 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q677R 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q677Y 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q677Y 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q836H 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q836H 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q836L 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q836L 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. Q836P 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q836P 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R102G 2021 Transboundary and emerging diseases Table SARS_CoV_2 R102G 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R102I 2021 Transboundary and emerging diseases Table SARS_CoV_2 R102I 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R102S 2021 Transboundary and emerging diseases Table SARS_CoV_2 R102S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R21I 2021 Transboundary and emerging diseases Table SARS_CoV_2 R21I 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R21K 2021 Transboundary and emerging diseases Table SARS_CoV_2 R21K 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R21T 2021 Transboundary and emerging diseases Table SARS_CoV_2 R21T 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R246I 2021 Transboundary and emerging diseases Table SARS_CoV_2 R246I 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R246K 2021 Transboundary and emerging diseases Table SARS_CoV_2 R246K 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R246S 2021 Transboundary and emerging diseases Table SARS_CoV_2 R246S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R273M 2021 Transboundary and emerging diseases Table SARS_CoV_2 R273M 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R273S 2021 Transboundary and emerging diseases Table SARS_CoV_2 R273S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R765C 2021 Transboundary and emerging diseases Table SARS_CoV_2 R765C 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R765H 2021 Transboundary and emerging diseases Table SARS_CoV_2 R765H 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R765L 2021 Transboundary and emerging diseases Table SARS_CoV_2 R765L 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R847I 2021 Transboundary and emerging diseases Table SARS_CoV_2 R847I 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R847K 2021 Transboundary and emerging diseases Table SARS_CoV_2 R847K 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. R847T 2021 Transboundary and emerging diseases Table SARS_CoV_2 R847T 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. S1170P 2021 Transboundary and emerging diseases Table SARS_CoV_2 S1170P 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. S1170T 2021 Transboundary and emerging diseases Table SARS_CoV_2 S1170T 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. S1170Y 2021 Transboundary and emerging diseases Table SARS_CoV_2 S1170Y 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. S247I 2021 Transboundary and emerging diseases Table SARS_CoV_2 S247I 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. S247N 2021 Transboundary and emerging diseases Table SARS_CoV_2 S247N 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. S247R 2021 Transboundary and emerging diseases Table SARS_CoV_2 S247R 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. S477G 2021 Transboundary and emerging diseases Table SARS_CoV_2 S477G 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. S477I 2021 Transboundary and emerging diseases Table SARS_CoV_2 S477I 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. S477N 2021 Transboundary and emerging diseases Table SARS_CoV_2 S477N 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. S477R 2021 Transboundary and emerging diseases Table SARS_CoV_2 S477R 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. S750I 2021 Transboundary and emerging diseases Table SARS_CoV_2 S750I 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. S750N 2021 Transboundary and emerging diseases Table SARS_CoV_2 S750N 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. S750R 2021 Transboundary and emerging diseases Table SARS_CoV_2 S750R 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T19I 2021 Transboundary and emerging diseases Table SARS_CoV_2 T19I 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T19P 2021 Transboundary and emerging diseases Table SARS_CoV_2 T19P 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T19S 2021 Transboundary and emerging diseases Table SARS_CoV_2 T19S 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T22A 2021 Transboundary and emerging diseases Table SARS_CoV_2 T22A 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T22I 2021 Transboundary and emerging diseases Table SARS_CoV_2 T22I 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T22N 2021 Transboundary and emerging diseases Table SARS_CoV_2 T22N 0 4 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T747A 2021 Transboundary and emerging diseases Table SARS_CoV_2 T747A 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T747I 2021 Transboundary and emerging diseases Table SARS_CoV_2 T747I 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T747N 2021 Transboundary and emerging diseases Table SARS_CoV_2 T747N 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T778A 2021 Transboundary and emerging diseases Table SARS_CoV_2 T778A 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T778I 2021 Transboundary and emerging diseases Table SARS_CoV_2 T778I 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T778N 2021 Transboundary and emerging diseases Table SARS_CoV_2 T778N 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T778S 2021 Transboundary and emerging diseases Table SARS_CoV_2 T778S 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T791A 2021 Transboundary and emerging diseases Table SARS_CoV_2 T791A 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T791I 2021 Transboundary and emerging diseases Table SARS_CoV_2 T791I 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T791K 2021 Transboundary and emerging diseases Table SARS_CoV_2 T791K 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. T791P 2021 Transboundary and emerging diseases Table SARS_CoV_2 T791P 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. V1129A 2021 Transboundary and emerging diseases Table SARS_CoV_2 V1129A 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. V1129I 2021 Transboundary and emerging diseases Table SARS_CoV_2 V1129I 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. V1129L 2021 Transboundary and emerging diseases Table SARS_CoV_2 V1129L 0 6 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. V483A 2021 Transboundary and emerging diseases Table SARS_CoV_2 V483A 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. V483F 2021 Transboundary and emerging diseases Table SARS_CoV_2 V483F 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. V483I 2021 Transboundary and emerging diseases Table SARS_CoV_2 V483I 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. V615F 2021 Transboundary and emerging diseases Table SARS_CoV_2 V615F 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. V615I 2021 Transboundary and emerging diseases Table SARS_CoV_2 V615I 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. V615L 2021 Transboundary and emerging diseases Table SARS_CoV_2 V615L 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. V622A 2021 Transboundary and emerging diseases Table SARS_CoV_2 V622A 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. V622F 2021 Transboundary and emerging diseases Table SARS_CoV_2 V622F 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. V622I 2021 Transboundary and emerging diseases Table SARS_CoV_2 V622I 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. V622L 2021 Transboundary and emerging diseases Table SARS_CoV_2 V622L 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. V772A 2021 Transboundary and emerging diseases Table SARS_CoV_2 V772A 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. V772I 2021 Transboundary and emerging diseases Table SARS_CoV_2 V772I 0 5 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. V772L 2021 Transboundary and emerging diseases Table SARS_CoV_2 V772L 0 5 32972934 Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh. D614G 2020 Microbiology resource announcements Table SARS_CoV_2 D614G 0 5 32972934 Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh. G204R 2020 Microbiology resource announcements Table SARS_CoV_2 G204R 0 5 32972934 Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh. G339S 2020 Microbiology resource announcements Table SARS_CoV_2 G339S 0 5 32972934 Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh. I120F 2020 Microbiology resource announcements Table SARS_CoV_2 I120F 0 5 32972934 Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh. K59N 2020 Microbiology resource announcements Table SARS_CoV_2 K59N 0 4 32972934 Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh. P323L 2020 Microbiology resource announcements Table SARS_CoV_2 P323L 0 5 32972934 Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh. P822S 2020 Microbiology resource announcements Table SARS_CoV_2 P822S 0 5 32972934 Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh. Q172R 2020 Microbiology resource announcements Table SARS_CoV_2 Q172R 0 5 32972934 Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh. R203K 2020 Microbiology resource announcements Table SARS_CoV_2 R203K 0 5 32972934 Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh. V480I 2020 Microbiology resource announcements Table SARS_CoV_2 V480I 0 5 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. D614G 2020 Cell Table SARS_CoV_2 D614G 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. A393W 2021 Briefings in bioinformatics Table SARS_CoV_2 A393W 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. A397L 2021 Briefings in bioinformatics Table SARS_CoV_2 A397L 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. A520G 2021 Briefings in bioinformatics Table SARS_CoV_2 A520G 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. A520P 2021 Briefings in bioinformatics Table SARS_CoV_2 A520P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. A520S 2021 Briefings in bioinformatics Table SARS_CoV_2 A520S 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. D355G 2021 Briefings in bioinformatics Table SARS_CoV_2 D355G 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. D355Y 2021 Briefings in bioinformatics Table SARS_CoV_2 D355Y 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. D38G 2021 Briefings in bioinformatics Table SARS_CoV_2 D38G 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. D614G 2021 Briefings in bioinformatics Table SARS_CoV_2 D614G 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. D614P 2021 Briefings in bioinformatics Table SARS_CoV_2 D614P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. D936F 2021 Briefings in bioinformatics Table SARS_CoV_2 D936F 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. D936P 2021 Briefings in bioinformatics Table SARS_CoV_2 D936P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. D936Y 2021 Briefings in bioinformatics Table SARS_CoV_2 D936Y 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. E75D 2021 Briefings in bioinformatics Table SARS_CoV_2 E75D 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. E75K 2021 Briefings in bioinformatics Table SARS_CoV_2 E75K 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. F497G 2021 Briefings in bioinformatics Table SARS_CoV_2 F497G 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. F497W 2021 Briefings in bioinformatics Table SARS_CoV_2 F497W 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G1124M 2021 Briefings in bioinformatics Table SARS_CoV_2 G1124M 0 6 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G1124P 2021 Briefings in bioinformatics Table SARS_CoV_2 G1124P 0 6 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G1124V 2021 Briefings in bioinformatics Table SARS_CoV_2 G1124V 0 6 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G326K 2021 Briefings in bioinformatics Table SARS_CoV_2 G326K 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G35A 2021 Briefings in bioinformatics Table SARS_CoV_2 G35A 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G35Y 2021 Briefings in bioinformatics Table SARS_CoV_2 G35Y 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G376P 2021 Briefings in bioinformatics Table SARS_CoV_2 G376P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G431A 2021 Briefings in bioinformatics Table SARS_CoV_2 G431A 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G431W 2021 Briefings in bioinformatics Table SARS_CoV_2 G431W 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G476D 2021 Briefings in bioinformatics Table SARS_CoV_2 G476D 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G476F 2021 Briefings in bioinformatics Table SARS_CoV_2 G476F 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G476S 2021 Briefings in bioinformatics Table SARS_CoV_2 G476S 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G496P 2021 Briefings in bioinformatics Table SARS_CoV_2 G496P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G496W 2021 Briefings in bioinformatics Table SARS_CoV_2 G496W 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G502L 2021 Briefings in bioinformatics Table SARS_CoV_2 G502L 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G502P 2021 Briefings in bioinformatics Table SARS_CoV_2 G502P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G504E 2021 Briefings in bioinformatics Table SARS_CoV_2 G504E 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G504W 2021 Briefings in bioinformatics Table SARS_CoV_2 G504W 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G526A 2021 Briefings in bioinformatics Table SARS_CoV_2 G526A 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G526C 2021 Briefings in bioinformatics Table SARS_CoV_2 G526C 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G526H 2021 Briefings in bioinformatics Table SARS_CoV_2 G526H 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G526Y 2021 Briefings in bioinformatics Table SARS_CoV_2 G526Y 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G648A 2021 Briefings in bioinformatics Table SARS_CoV_2 G648A 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. G648W 2021 Briefings in bioinformatics Table SARS_CoV_2 G648W 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. H49P 2021 Briefings in bioinformatics Table SARS_CoV_2 H49P 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. H49W 2021 Briefings in bioinformatics Table SARS_CoV_2 H49W 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. H49Y 2021 Briefings in bioinformatics Table SARS_CoV_2 H49Y 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. K26D 2021 Briefings in bioinformatics Table SARS_CoV_2 K26D 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. K26R 2021 Briefings in bioinformatics Table SARS_CoV_2 K26R 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. K353I 2021 Briefings in bioinformatics Table SARS_CoV_2 K353I 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. L452D 2021 Briefings in bioinformatics Table SARS_CoV_2 L452D 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. L452P 2021 Briefings in bioinformatics Table SARS_CoV_2 L452P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. L452R 2021 Briefings in bioinformatics Table SARS_CoV_2 L452R 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. L45H 2021 Briefings in bioinformatics Table SARS_CoV_2 L45H 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. L45N 2021 Briefings in bioinformatics Table SARS_CoV_2 L45N 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. N330D 2021 Briefings in bioinformatics Table SARS_CoV_2 N330D 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. N330F 2021 Briefings in bioinformatics Table SARS_CoV_2 N330F 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. N394P 2021 Briefings in bioinformatics Table SARS_CoV_2 N394P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. N394W 2021 Briefings in bioinformatics Table SARS_CoV_2 N394W 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. N439E 2021 Briefings in bioinformatics Table SARS_CoV_2 N439E 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. N439F 2021 Briefings in bioinformatics Table SARS_CoV_2 N439F 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. N439I 2021 Briefings in bioinformatics Table SARS_CoV_2 N439I 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. N439K 2021 Briefings in bioinformatics Table SARS_CoV_2 N439K 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. N439L 2021 Briefings in bioinformatics Table SARS_CoV_2 N439L 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. N439P 2021 Briefings in bioinformatics Table SARS_CoV_2 N439P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. N439R 2021 Briefings in bioinformatics Table SARS_CoV_2 N439R 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. N501E 2021 Briefings in bioinformatics Table SARS_CoV_2 N501E 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. N501Y 2021 Briefings in bioinformatics Table SARS_CoV_2 N501Y 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. P507A 2021 Briefings in bioinformatics Table SARS_CoV_2 P507A 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. P507W 2021 Briefings in bioinformatics Table SARS_CoV_2 P507W 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Q24L 2021 Briefings in bioinformatics Table SARS_CoV_2 Q24L 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Q24Y 2021 Briefings in bioinformatics Table SARS_CoV_2 Q24Y 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Q414E 2021 Briefings in bioinformatics Table SARS_CoV_2 Q414E 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Q414K 2021 Briefings in bioinformatics Table SARS_CoV_2 Q414K 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Q414P 2021 Briefings in bioinformatics Table SARS_CoV_2 Q414P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Q414W 2021 Briefings in bioinformatics Table SARS_CoV_2 Q414W 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Q42D 2021 Briefings in bioinformatics Table SARS_CoV_2 Q42D 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Q42R 2021 Briefings in bioinformatics Table SARS_CoV_2 Q42R 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Q498D 2021 Briefings in bioinformatics Table SARS_CoV_2 Q498D 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Q498I 2021 Briefings in bioinformatics Table SARS_CoV_2 Q498I 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S19G 2021 Briefings in bioinformatics Table SARS_CoV_2 S19G 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S19H 2021 Briefings in bioinformatics Table SARS_CoV_2 S19H 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S438C 2021 Briefings in bioinformatics Table SARS_CoV_2 S438C 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S438F 2021 Briefings in bioinformatics Table SARS_CoV_2 S438F 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S438H 2021 Briefings in bioinformatics Table SARS_CoV_2 S438H 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S438K 2021 Briefings in bioinformatics Table SARS_CoV_2 S438K 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S438V 2021 Briefings in bioinformatics Table SARS_CoV_2 S438V 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S438Y 2021 Briefings in bioinformatics Table SARS_CoV_2 S438Y 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S50G 2021 Briefings in bioinformatics Table SARS_CoV_2 S50G 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S50L 2021 Briefings in bioinformatics Table SARS_CoV_2 S50L 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S514F 2021 Briefings in bioinformatics Table SARS_CoV_2 S514F 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S514P 2021 Briefings in bioinformatics Table SARS_CoV_2 S514P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S735M 2021 Briefings in bioinformatics Table SARS_CoV_2 S735M 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S735P 2021 Briefings in bioinformatics Table SARS_CoV_2 S735P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S943I 2021 Briefings in bioinformatics Table SARS_CoV_2 S943I 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S943K 2021 Briefings in bioinformatics Table SARS_CoV_2 S943K 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S943V 2021 Briefings in bioinformatics Table SARS_CoV_2 S943V 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. T385E 2021 Briefings in bioinformatics Table SARS_CoV_2 T385E 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. T385H 2021 Briefings in bioinformatics Table SARS_CoV_2 T385H 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. T385P 2021 Briefings in bioinformatics Table SARS_CoV_2 T385P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. T385W 2021 Briefings in bioinformatics Table SARS_CoV_2 T385W 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. T500G 2021 Briefings in bioinformatics Table SARS_CoV_2 T500G 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. T500W 2021 Briefings in bioinformatics Table SARS_CoV_2 T500W 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. T724G 2021 Briefings in bioinformatics Table SARS_CoV_2 T724G 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. T724I 2021 Briefings in bioinformatics Table SARS_CoV_2 T724I 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. T724M 2021 Briefings in bioinformatics Table SARS_CoV_2 T724M 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V341F 2021 Briefings in bioinformatics Table SARS_CoV_2 V341F 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V341I 2021 Briefings in bioinformatics Table SARS_CoV_2 V341I 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V341P 2021 Briefings in bioinformatics Table SARS_CoV_2 V341P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V341R 2021 Briefings in bioinformatics Table SARS_CoV_2 V341R 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V367F 2021 Briefings in bioinformatics Table SARS_CoV_2 V367F 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V367P 2021 Briefings in bioinformatics Table SARS_CoV_2 V367P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V367Q 2021 Briefings in bioinformatics Table SARS_CoV_2 V367Q 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V483A 2021 Briefings in bioinformatics Table SARS_CoV_2 V483A 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V483D 2021 Briefings in bioinformatics Table SARS_CoV_2 V483D 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V483K 2021 Briefings in bioinformatics Table SARS_CoV_2 V483K 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V483P 2021 Briefings in bioinformatics Table SARS_CoV_2 V483P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V483R 2021 Briefings in bioinformatics Table SARS_CoV_2 V483R 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V503D 2021 Briefings in bioinformatics Table SARS_CoV_2 V503D 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V503F 2021 Briefings in bioinformatics Table SARS_CoV_2 V503F 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V503H 2021 Briefings in bioinformatics Table SARS_CoV_2 V503H 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V503P 2021 Briefings in bioinformatics Table SARS_CoV_2 V503P 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V503W 2021 Briefings in bioinformatics Table SARS_CoV_2 V503W 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. V976D 2021 Briefings in bioinformatics Table SARS_CoV_2 V976D 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Y41P 2021 Briefings in bioinformatics Table SARS_CoV_2 Y41P 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Y41W 2021 Briefings in bioinformatics Table SARS_CoV_2 Y41W 0 4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Y495G 2021 Briefings in bioinformatics Table SARS_CoV_2 Y495G 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Y495L 2021 Briefings in bioinformatics Table SARS_CoV_2 Y495L 0 5 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. A1078S 2020 Frontiers in immunology Table SARS_CoV_2 A1078S 0 6 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. A706V 2020 Frontiers in immunology Table SARS_CoV_2 A706V 0 5 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. A831V 2020 Frontiers in immunology Table SARS_CoV_2 A831V 0 5 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. D839Y 2020 Frontiers in immunology Table SARS_CoV_2 D839Y 0 5 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. D936Y 2020 Frontiers in immunology Table SARS_CoV_2 D936Y 0 5 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. G476S 2020 Frontiers in immunology Table SARS_CoV_2 G476S 0 5 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. H49Y 2020 Frontiers in immunology Table SARS_CoV_2 H49Y 0 4 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. P1263L 2020 Frontiers in immunology Table SARS_CoV_2 P1263L 0 6 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. Q239K 2020 Frontiers in immunology Table SARS_CoV_2 Q239K 0 5 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. Q675H 2020 Frontiers in immunology Table SARS_CoV_2 Q675H 0 5 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. S943P 2020 Frontiers in immunology Table SARS_CoV_2 S943P 0 5 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. T29I 2020 Frontiers in immunology Table SARS_CoV_2 T29I 0 4 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. V367F 2020 Frontiers in immunology Table SARS_CoV_2 V367F 0 5 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. V483A 2020 Frontiers in immunology Table SARS_CoV_2 V483A 0 5 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. A17858G 2020 Heliyon Table SARS_CoV_2 A17858G 0 7 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. A23403G 2020 Heliyon Table SARS_CoV_2 A23403G 0 7 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. A2480G 2020 Heliyon Table SARS_CoV_2 A2480G 0 6 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. ATG1605del 2020 Heliyon Table SARS_CoV_2 ATG1605del 0 10 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. C1059T 2020 Heliyon Table SARS_CoV_2 C1059T 0 6 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. C14408T 2020 Heliyon Table SARS_CoV_2 C14408T 0 7 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. C14805T 2020 Heliyon Table SARS_CoV_2 C14805T 0 7 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. C17747T 2020 Heliyon Table SARS_CoV_2 C17747T 0 7 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. C18060T 2020 Heliyon Table SARS_CoV_2 C18060T 0 7 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. C2558T 2020 Heliyon Table SARS_CoV_2 C2558T 0 6 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. C3037T 2020 Heliyon Table SARS_CoV_2 C3037T 0 6 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. C8782T 2020 Heliyon Table SARS_CoV_2 C8782T 0 6 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. D614G 2020 Heliyon Table SARS_CoV_2 D614G 0 5 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. G11083T 2020 Heliyon Table SARS_CoV_2 G11083T 0 7 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. G1440A 2020 Heliyon Table SARS_CoV_2 G1440A 0 6 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. G212D 2020 Heliyon Table SARS_CoV_2 G212D 0 5 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. G251V 2020 Heliyon Table SARS_CoV_2 G251V 0 5 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. G25563T 2020 Heliyon Table SARS_CoV_2 G25563T 0 7 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. G26144T 2020 Heliyon Table SARS_CoV_2 G26144T 0 7 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. GGG28881AAC 2020 Heliyon Table SARS_CoV_2 G28881A;G28881C 0;0 11;11 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. I559V 2020 Heliyon Table SARS_CoV_2 I559V 0 5 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. L37F 2020 Heliyon Table SARS_CoV_2 L37F 0 4 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. L84S 2020 Heliyon Table SARS_CoV_2 L84S 0 4 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. P314L 2020 Heliyon Table SARS_CoV_2 P314L 0 5 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. P504L 2020 Heliyon Table SARS_CoV_2 P504L 0 5 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. P585S 2020 Heliyon Table SARS_CoV_2 P585S 0 5 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. Q57H 2020 Heliyon Table SARS_CoV_2 Q57H 0 4 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. T17247C 2020 Heliyon Table SARS_CoV_2 T17247C 0 7 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. T28144C 2020 Heliyon Table SARS_CoV_2 T28144C 0 7 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. T85I 2020 Heliyon Table SARS_CoV_2 T85I 0 4 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. Y541C 2020 Heliyon Table SARS_CoV_2 Y541C 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. A1906V 2020 Microbes and infection Table SARS_CoV_2 A1906V 0 6 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. A31T 2020 Microbes and infection Table SARS_CoV_2 A31T 0 4 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. A3203V 2020 Microbes and infection Table SARS_CoV_2 A3203V 0 6 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. A4297G 2020 Microbes and infection Table SARS_CoV_2 A4297G 0 6 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. A930V 2020 Microbes and infection Table SARS_CoV_2 A930V 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. D364Y 2020 Microbes and infection Table SARS_CoV_2 D364Y 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. D58E 2020 Microbes and infection Table SARS_CoV_2 D58E 0 4 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. E955K 2020 Microbes and infection Table SARS_CoV_2 E955K 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. F1657L 2020 Microbes and infection Table SARS_CoV_2 F1657L 0 6 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. F4304L 2020 Microbes and infection Table SARS_CoV_2 F4304L 0 6 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. F797C 2020 Microbes and infection Table SARS_CoV_2 F797C 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. G196V 2020 Microbes and infection Table SARS_CoV_2 G196V 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. G2374R 2020 Microbes and infection Table SARS_CoV_2 G2374R 0 6 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. G4227R 2020 Microbes and infection Table SARS_CoV_2 G4227R 0 6 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. H93Y 2020 Microbes and infection Table SARS_CoV_2 H93Y 0 4 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. I1216T 2020 Microbes and infection Table SARS_CoV_2 I1216T 0 6 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. I292T 2020 Microbes and infection Table SARS_CoV_2 I292T 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. L121H 2020 Microbes and infection Table SARS_CoV_2 L121H 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. L952P 2020 Microbes and infection Table SARS_CoV_2 L952P 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. N1559T 2020 Microbes and infection Table SARS_CoV_2 N1559T 0 6 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. N354D 2020 Microbes and infection Table SARS_CoV_2 N354D 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. P1263L 2020 Microbes and infection Table SARS_CoV_2 P1263L 0 6 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. P4715L 2020 Microbes and infection Table SARS_CoV_2 P4715L 0 6 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. Q675H 2020 Microbes and infection Table SARS_CoV_2 Q675H 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. R416I 2020 Microbes and infection Table SARS_CoV_2 R416I 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. S1498F 2020 Microbes and infection Table SARS_CoV_2 S1498F 0 6 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. S193I 2020 Microbes and infection Table SARS_CoV_2 S193I 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. S197L 2020 Microbes and infection Table SARS_CoV_2 S197L 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. S438F 2020 Microbes and infection Table SARS_CoV_2 S438F 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. S81L 2020 Microbes and infection Table SARS_CoV_2 S81L 0 4 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. T148I 2020 Microbes and infection Table SARS_CoV_2 T148I 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. T175M 2020 Microbes and infection Table SARS_CoV_2 T175M 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. T791I 2020 Microbes and infection Table SARS_CoV_2 T791I 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. V1973L 2020 Microbes and infection Table SARS_CoV_2 V1973L 0 6 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. V62L 2020 Microbes and infection Table SARS_CoV_2 V62L 0 4 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. V74F 2020 Microbes and infection Table SARS_CoV_2 V74F 0 4 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. V88L 2020 Microbes and infection Table SARS_CoV_2 V88L 0 4 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. Y145del 2020 Microbes and infection Table SARS_CoV_2 Y145del 0 7 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. Y232C 2020 Microbes and infection Table SARS_CoV_2 Y232C 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. Y508H 2020 Microbes and infection Table SARS_CoV_2 Y508H 0 5 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. D614G 2021 International journal of infectious diseases Table SARS_CoV_2 D614G 0 5 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. A1938V 2021 Genomics Table SARS_CoV_2 A1938V 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. A287V 2021 Genomics Table SARS_CoV_2 A287V 0 5 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. A3270V 2021 Genomics Table SARS_CoV_2 A3270V 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. A540V 2021 Genomics Table SARS_CoV_2 A540V 0 5 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. C4703F 2021 Genomics Table SARS_CoV_2 C4703F 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. D614G 2021 Genomics Table SARS_CoV_2 D614G 0 5 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. E2089D 2021 Genomics Table SARS_CoV_2 E2089D 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. F3444L 2021 Genomics Table SARS_CoV_2 F3444L 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. G204R 2021 Genomics Table SARS_CoV_2 G204R 0 5 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. I2501V 2021 Genomics Table SARS_CoV_2 I2501V 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. I2511V 2021 Genomics Table SARS_CoV_2 I2511V 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. K2208stop 2021 Genomics Table SARS_CoV_2 K2208X 0 9 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. K2798R 2021 Genomics Table SARS_CoV_2 K2798R 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. L3199R 2021 Genomics Table SARS_CoV_2 L3199R 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. L3606F 2021 Genomics Table SARS_CoV_2 L3606F 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. L54F 2021 Genomics Table SARS_CoV_2 L54F 0 4 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. L73F 2021 Genomics Table SARS_CoV_2 L73F 0 4 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. M153I 2021 Genomics Table SARS_CoV_2 M153I 0 5 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. M177R 2021 Genomics Table SARS_CoV_2 M177R 0 5 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. M2796I 2021 Genomics Table SARS_CoV_2 M2796I 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. M2796L 2021 Genomics Table SARS_CoV_2 M2796L 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. N2006V 2021 Genomics Table SARS_CoV_2 N2006V 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. N2878Y 2021 Genomics Table SARS_CoV_2 N2878Y 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. P4715L 2021 Genomics Table SARS_CoV_2 P4715L 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. P84S 2021 Genomics Table SARS_CoV_2 P84S 0 4 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. Q22R 2021 Genomics Table SARS_CoV_2 Q22R 0 4 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. Q4011L 2021 Genomics Table SARS_CoV_2 Q4011L 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. Q4012L 2021 Genomics Table SARS_CoV_2 Q4012L 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. Q57H 2021 Genomics Table SARS_CoV_2 Q57H 0 4 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. R203K 2021 Genomics Table SARS_CoV_2 R203K 0 5 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. R207C 2021 Genomics Table SARS_CoV_2 R207C 0 5 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. R5346I 2021 Genomics Table SARS_CoV_2 R5346I 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. S1978Y 2021 Genomics Table SARS_CoV_2 S1978Y 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. S2797F 2021 Genomics Table SARS_CoV_2 S2797F 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. S4910L 2021 Genomics Table SARS_CoV_2 S4910L 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. T2007N 2021 Genomics Table SARS_CoV_2 T2007N 0 6 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. V378I 2021 Genomics Table SARS_CoV_2 V378I 0 5 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. V62D 2021 Genomics Table SARS_CoV_2 V62D 0 4 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. A1031E 2020 Microbiology resource announcements Table SARS_CoV_2 A1031E 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. A1049V 2020 Microbiology resource announcements Table SARS_CoV_2 A1049V 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. A10912G 2020 Microbiology resource announcements Table SARS_CoV_2 A10912G 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. A12G 2020 Microbiology resource announcements Table SARS_CoV_2 A12G 0 4 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. A1643V 2020 Microbiology resource announcements Table SARS_CoV_2 A1643V 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. A19767G 2020 Microbiology resource announcements Table SARS_CoV_2 A19767G 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. A2282V 2020 Microbiology resource announcements Table SARS_CoV_2 A2282V 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. A23403G 2020 Microbiology resource announcements Table SARS_CoV_2 A23403G 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. A27224C 2020 Microbiology resource announcements Table SARS_CoV_2 A27224C 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. A3070V 2020 Microbiology resource announcements Table SARS_CoV_2 A3070V 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. A3938C 2020 Microbiology resource announcements Table SARS_CoV_2 A3938C 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. A88V 2020 Microbiology resource announcements Table SARS_CoV_2 A88V 0 4 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. A903V 2020 Microbiology resource announcements Table SARS_CoV_2 A903V 0 5 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. A9782G 2020 Microbiology resource announcements Table SARS_CoV_2 A9782G 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C10138T 2020 Microbiology resource announcements Table SARS_CoV_2 C10138T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C11572T 2020 Microbiology resource announcements Table SARS_CoV_2 C11572T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C12053T 2020 Microbiology resource announcements Table SARS_CoV_2 C12053T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C13051T 2020 Microbiology resource announcements Table SARS_CoV_2 C13051T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C13730T 2020 Microbiology resource announcements Table SARS_CoV_2 C13730T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C14408T 2020 Microbiology resource announcements Table SARS_CoV_2 C14408T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C16559A 2020 Microbiology resource announcements Table SARS_CoV_2 C16559A 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C16726T 2020 Microbiology resource announcements Table SARS_CoV_2 C16726T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C18395T 2020 Microbiology resource announcements Table SARS_CoV_2 C18395T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C18828T 2020 Microbiology resource announcements Table SARS_CoV_2 C18828T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C18877T 2020 Microbiology resource announcements Table SARS_CoV_2 C18877T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C19983T 2020 Microbiology resource announcements Table SARS_CoV_2 C19983T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C20133T 2020 Microbiology resource announcements Table SARS_CoV_2 C20133T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C20312T 2020 Microbiology resource announcements Table SARS_CoV_2 C20312T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C21575T 2020 Microbiology resource announcements Table SARS_CoV_2 C21575T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C21597T 2020 Microbiology resource announcements Table SARS_CoV_2 C21597T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C22120T 2020 Microbiology resource announcements Table SARS_CoV_2 C22120T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C23929T 2020 Microbiology resource announcements Table SARS_CoV_2 C23929T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C23934T 2020 Microbiology resource announcements Table SARS_CoV_2 C23934T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C26224T 2020 Microbiology resource announcements Table SARS_CoV_2 C26224T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C26305T 2020 Microbiology resource announcements Table SARS_CoV_2 C26305T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C26464T 2020 Microbiology resource announcements Table SARS_CoV_2 C26464T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C26607T 2020 Microbiology resource announcements Table SARS_CoV_2 C26607T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C28093T 2020 Microbiology resource announcements Table SARS_CoV_2 C28093T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C28308G 2020 Microbiology resource announcements Table SARS_CoV_2 C28308G 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C28311T 2020 Microbiology resource announcements Table SARS_CoV_2 C28311T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C29144T 2020 Microbiology resource announcements Table SARS_CoV_2 C29144T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C2973T 2020 Microbiology resource announcements Table SARS_CoV_2 C2973T 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C3037T 2020 Microbiology resource announcements Table SARS_CoV_2 C3037T 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C3411T 2020 Microbiology resource announcements Table SARS_CoV_2 C3411T 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C4039T 2020 Microbiology resource announcements Table SARS_CoV_2 C4039T 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C539T 2020 Microbiology resource announcements Table SARS_CoV_2 C539T 0 5 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C5575T 2020 Microbiology resource announcements Table SARS_CoV_2 C5575T 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C593T 2020 Microbiology resource announcements Table SARS_CoV_2 C593T 0 5 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C6312A 2020 Microbiology resource announcements Table SARS_CoV_2 C6312A 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C6525T 2020 Microbiology resource announcements Table SARS_CoV_2 C6525T 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C6726T 2020 Microbiology resource announcements Table SARS_CoV_2 C6726T 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C7086T 2020 Microbiology resource announcements Table SARS_CoV_2 C7086T 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C7165T 2020 Microbiology resource announcements Table SARS_CoV_2 C7165T 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C7735T 2020 Microbiology resource announcements Table SARS_CoV_2 C7735T 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C8818T 2020 Microbiology resource announcements Table SARS_CoV_2 C8818T 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. C9474T 2020 Microbiology resource announcements Table SARS_CoV_2 C9474T 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. D614G 2020 Microbiology resource announcements Table SARS_CoV_2 D614G 0 5 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. E1126K 2020 Microbiology resource announcements Table SARS_CoV_2 E1126K 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G11083T 2020 Microbiology resource announcements Table SARS_CoV_2 G11083T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G14414T 2020 Microbiology resource announcements Table SARS_CoV_2 G14414T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G16808A 2020 Microbiology resource announcements Table SARS_CoV_2 G16808A 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G17278T 2020 Microbiology resource announcements Table SARS_CoV_2 G17278T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G17347T 2020 Microbiology resource announcements Table SARS_CoV_2 G17347T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G204R 2020 Microbiology resource announcements Table SARS_CoV_2 G204R 0 5 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G212V 2020 Microbiology resource announcements Table SARS_CoV_2 G212V 0 5 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G25088T 2020 Microbiology resource announcements Table SARS_CoV_2 G25088T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G27632C 2020 Microbiology resource announcements Table SARS_CoV_2 G27632C 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G27816A 2020 Microbiology resource announcements Table SARS_CoV_2 G27816A 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G28378A 2020 Microbiology resource announcements Table SARS_CoV_2 G28378A 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G28881A 2020 Microbiology resource announcements Table SARS_CoV_2 G28881A 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G28882A 2020 Microbiology resource announcements Table SARS_CoV_2 G28882A 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G28883C 2020 Microbiology resource announcements Table SARS_CoV_2 G28883C 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G28899T 2020 Microbiology resource announcements Table SARS_CoV_2 G28899T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G28908T 2020 Microbiology resource announcements Table SARS_CoV_2 G28908T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G29540T 2020 Microbiology resource announcements Table SARS_CoV_2 G29540T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G29543T 2020 Microbiology resource announcements Table SARS_CoV_2 G29543T 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G29654A 2020 Microbiology resource announcements Table SARS_CoV_2 G29654A 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G3641A 2020 Microbiology resource announcements Table SARS_CoV_2 G3641A 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G5924A 2020 Microbiology resource announcements Table SARS_CoV_2 G5924A 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G6943T 2020 Microbiology resource announcements Table SARS_CoV_2 G6943T 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G7042T 2020 Microbiology resource announcements Table SARS_CoV_2 G7042T 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. G942A 2020 Microbiology resource announcements Table SARS_CoV_2 G942A 0 5 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. H1087Y 2020 Microbiology resource announcements Table SARS_CoV_2 H1087Y 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. H110Y 2020 Microbiology resource announcements Table SARS_CoV_2 H110Y 0 5 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. L21F 2020 Microbiology resource announcements Table SARS_CoV_2 L21F 0 4 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. L29F 2020 Microbiology resource announcements Table SARS_CoV_2 L29F 0 4 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. L3606F 2020 Microbiology resource announcements Table SARS_CoV_2 L3606F 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. L3930F 2020 Microbiology resource announcements Table SARS_CoV_2 L3930F 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. L92F 2020 Microbiology resource announcements Table SARS_CoV_2 L92F 0 4 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. M2259I 2020 Microbiology resource announcements Table SARS_CoV_2 M2259I 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. P13L 2020 Microbiology resource announcements Table SARS_CoV_2 P13L 0 4 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. P314L 2020 Microbiology resource announcements Table SARS_CoV_2 P314L 0 5 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. R203K 2020 Microbiology resource announcements Table SARS_CoV_2 R203K 0 5 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. R209I 2020 Microbiology resource announcements Table SARS_CoV_2 R209I 0 5 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. R226K 2020 Microbiology resource announcements Table SARS_CoV_2 R226K 0 5 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. R80T 2020 Microbiology resource announcements Table SARS_CoV_2 R80T 0 4 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. S1114N 2020 Microbiology resource announcements Table SARS_CoV_2 S1114N 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. S12F 2020 Microbiology resource announcements Table SARS_CoV_2 S12F 0 4 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. S206Y 2020 Microbiology resource announcements Table SARS_CoV_2 S206Y 0 5 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. S316I 2020 Microbiology resource announcements Table SARS_CoV_2 S316I 0 5 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. S3173G 2020 Microbiology resource announcements Table SARS_CoV_2 S3173G 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. S67F 2020 Microbiology resource announcements Table SARS_CoV_2 S67F 0 4 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. T2016K 2020 Microbiology resource announcements Table SARS_CoV_2 T2016K 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. T2087I 2020 Microbiology resource announcements Table SARS_CoV_2 T2087I 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. T21198C 2020 Microbiology resource announcements Table SARS_CoV_2 T21198C 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. T2154I 2020 Microbiology resource announcements Table SARS_CoV_2 T2154I 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. T21775G 2020 Microbiology resource announcements Table SARS_CoV_2 T21775G 0 7 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. T2274I 2020 Microbiology resource announcements Table SARS_CoV_2 T2274I 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. T791I 2020 Microbiology resource announcements Table SARS_CoV_2 T791I 0 5 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. V1176F 2020 Microbiology resource announcements Table SARS_CoV_2 V1176F 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. V1271L 2020 Microbiology resource announcements Table SARS_CoV_2 V1271L 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. V1294F 2020 Microbiology resource announcements Table SARS_CoV_2 V1294F 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. V1887I 2020 Microbiology resource announcements Table SARS_CoV_2 V1887I 0 6 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. V21I 2020 Microbiology resource announcements Table SARS_CoV_2 V21I 0 4 33093050 Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines. V33I 2020 Microbiology resource announcements Table SARS_CoV_2 V33I 0 4 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. D614G 2021 Nature Table SARS_CoV_2 D614G 0 5 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. M0300L 2020 Cell reports Table SARS_CoV_2 M0300L 0 6 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. D614G 2020 Emerging microbes & infections Table SARS_CoV_2 D614G 0 5 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. D839E 2020 Emerging microbes & infections Table SARS_CoV_2 D839E 0 5 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. D839G 2020 Emerging microbes & infections Table SARS_CoV_2 D839G 0 5 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. D839N 2020 Emerging microbes & infections Table SARS_CoV_2 D839N 0 5 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. D839Y 2020 Emerging microbes & infections Table SARS_CoV_2 D839Y 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. A211V 2020 PloS one Table SARS_CoV_2 A211V 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. A58T 2020 PloS one Table SARS_CoV_2 A58T 0 4 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. C1250F 2020 PloS one Table SARS_CoV_2 C1250F 0 6 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. D161V 2020 PloS one Table SARS_CoV_2 D161V 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. D477N 2020 PloS one Table SARS_CoV_2 D477N 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. D614G 2020 PloS one Table SARS_CoV_2 D614G 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. G15S 2020 PloS one Table SARS_CoV_2 G15S 0 4 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. G204R 2020 PloS one Table SARS_CoV_2 G204R 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. G212D 2020 PloS one Table SARS_CoV_2 G212D 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. G251V 2020 PloS one Table SARS_CoV_2 G251V 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. G730D 2020 PloS one Table SARS_CoV_2 G730D 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. I103del 2020 PloS one Table SARS_CoV_2 I103del 0 7 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. I559V 2020 PloS one Table SARS_CoV_2 I559V 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. K1186R 2020 PloS one Table SARS_CoV_2 K1186R 0 6 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. L37F 2020 PloS one Table SARS_CoV_2 L37F 0 4 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. L54F 2020 PloS one Table SARS_CoV_2 L54F 0 4 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. L672F 2020 PloS one Table SARS_CoV_2 L672F 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. L96F 2020 PloS one Table SARS_CoV_2 L96F 0 4 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. M1901I 2020 PloS one Table SARS_CoV_2 M1901I 0 6 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. P1103L 2020 PloS one Table SARS_CoV_2 P1103L 0 6 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. P134S 2020 PloS one Table SARS_CoV_2 P134S 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. P323L 2020 PloS one Table SARS_CoV_2 P323L 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. P585S 2020 PloS one Table SARS_CoV_2 P585S 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. Q283H 2020 PloS one Table SARS_CoV_2 Q283H 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. Q57H 2020 PloS one Table SARS_CoV_2 Q57H 0 4 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. R203K 2020 PloS one Table SARS_CoV_2 R203K 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. R595S 2020 PloS one Table SARS_CoV_2 R595S 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. R646W 2020 PloS one Table SARS_CoV_2 R646W 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. S180I 2020 PloS one Table SARS_CoV_2 S180I 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. S254F 2020 PloS one Table SARS_CoV_2 S254F 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. S81L 2020 PloS one Table SARS_CoV_2 S81L 0 4 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. T140I 2020 PloS one Table SARS_CoV_2 T140I 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. T40I 2020 PloS one Table SARS_CoV_2 T40I 0 4 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. T428I 2020 PloS one Table SARS_CoV_2 T428I 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. T85I 2020 PloS one Table SARS_CoV_2 T85I 0 4 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. V320L 2020 PloS one Table SARS_CoV_2 V320L 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. V338F 2020 PloS one Table SARS_CoV_2 V338F 0 5 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. V70F 2020 PloS one Table SARS_CoV_2 V70F 0 4 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. 1059C>T 2021 Clinical infectious diseases Table SARS_CoV_2 C1059T 0 7 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. 12810T>C 2021 Clinical infectious diseases Table SARS_CoV_2 T12810C 0 8 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. 14805C>T 2021 Clinical infectious diseases Table SARS_CoV_2 C14805T 0 8 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. 16580C>T 2021 Clinical infectious diseases Table SARS_CoV_2 C16580T 0 8 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. 26060C>T 2021 Clinical infectious diseases Table SARS_CoV_2 C26060T 0 8 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. 28768A>G 2021 Clinical infectious diseases Table SARS_CoV_2 A28768G 0 8 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. 4951G>C 2021 Clinical infectious diseases Table SARS_CoV_2 G4951C 0 7 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. 526G>T 2021 Clinical infectious diseases Table SARS_CoV_2 G526T 0 6 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. 5572G>T 2021 Clinical infectious diseases Table SARS_CoV_2 G5572T 0 7 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. 5822C>T 2021 Clinical infectious diseases Table SARS_CoV_2 C5822T 0 7 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. 6262T>C 2021 Clinical infectious diseases Table SARS_CoV_2 T6262C 0 7 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. 635C>T 2021 Clinical infectious diseases Table SARS_CoV_2 C635T 0 6 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. 6719A>G 2021 Clinical infectious diseases Table SARS_CoV_2 A6719G 0 7 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. 9773delT 2021 Clinical infectious diseases Table SARS_CoV_2 9773delT 0 8 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. 9996C>T 2021 Clinical infectious diseases Table SARS_CoV_2 C9996T 0 7 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. D614G 2021 Clinical infectious diseases Table SARS_CoV_2 D614G 0 5 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. G251V 2021 Clinical infectious diseases Table SARS_CoV_2 G251V 0 5 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. L1035F 2021 Clinical infectious diseases Table SARS_CoV_2 L1035F 0 6 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. L37F 2021 Clinical infectious diseases Table SARS_CoV_2 L37F 0 4 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. L42P 2021 Clinical infectious diseases Table SARS_CoV_2 L42P 0 4 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. L744F 2021 Clinical infectious diseases Table SARS_CoV_2 L744F 0 5 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. M951I 2021 Clinical infectious diseases Table SARS_CoV_2 M951I 0 5 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. P323L 2021 Clinical infectious diseases Table SARS_CoV_2 P323L 0 5 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. Q57H 2021 Clinical infectious diseases Table SARS_CoV_2 Q57H 0 4 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. Q87D 2021 Clinical infectious diseases Table SARS_CoV_2 Q87D 0 4 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. R124C 2021 Clinical infectious diseases Table SARS_CoV_2 R124C 0 5 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. S481L 2021 Clinical infectious diseases Table SARS_CoV_2 S481L 0 5 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. T115I 2021 Clinical infectious diseases Table SARS_CoV_2 T115I 0 5 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. T1334A 2021 Clinical infectious diseases Table SARS_CoV_2 T1334A 0 6 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. T223I 2021 Clinical infectious diseases Table SARS_CoV_2 T223I 0 5 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. T85I 2021 Clinical infectious diseases Table SARS_CoV_2 T85I 0 4 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. A639V 2020 Virology journal Table SARS_CoV_2 A639V 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. A656S 2020 Virology journal Table SARS_CoV_2 A656S 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. A656T 2020 Virology journal Table SARS_CoV_2 A656T 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. A656V 2020 Virology journal Table SARS_CoV_2 A656V 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. A660S 2020 Virology journal Table SARS_CoV_2 A660S 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. A699S 2020 Virology journal Table SARS_CoV_2 A699S 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. A716S 2020 Virology journal Table SARS_CoV_2 A716S 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. D684G 2020 Virology journal Table SARS_CoV_2 D684G 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. D711Y 2020 Virology journal Table SARS_CoV_2 D711Y 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. D717Y 2020 Virology journal Table SARS_CoV_2 D717Y 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. D736G 2020 Virology journal Table SARS_CoV_2 D736G 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. D738Y 2020 Virology journal Table SARS_CoV_2 D738Y 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. E729D 2020 Virology journal Table SARS_CoV_2 E729D 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. E744D 2020 Virology journal Table SARS_CoV_2 E744D 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. G670C 2020 Virology journal Table SARS_CoV_2 G670C 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. G670S 2020 Virology journal Table SARS_CoV_2 G670S 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. G671S 2020 Virology journal Table SARS_CoV_2 G671S 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. G671V 2020 Virology journal Table SARS_CoV_2 G671V 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. G678C 2020 Virology journal Table SARS_CoV_2 G678C 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. G683V 2020 Virology journal Table SARS_CoV_2 G683V 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. G712S 2020 Virology journal Table SARS_CoV_2 G712S 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. G712V 2020 Virology journal Table SARS_CoV_2 G712V 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. H642N 2020 Virology journal Table SARS_CoV_2 H642N 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. H725Y 2020 Virology journal Table SARS_CoV_2 H725Y 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. H752Q 2020 Virology journal Table SARS_CoV_2 H752Q 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. K718N 2020 Virology journal Table SARS_CoV_2 K718N 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. K718R 2020 Virology journal Table SARS_CoV_2 K718R 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. L630F 2020 Virology journal Table SARS_CoV_2 L630F 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. L636F 2020 Virology journal Table SARS_CoV_2 L636F 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. L636I 2020 Virology journal Table SARS_CoV_2 L636I 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. L638F 2020 Virology journal Table SARS_CoV_2 L638F 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. L648F 2020 Virology journal Table SARS_CoV_2 L648F 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. L727F 2020 Virology journal Table SARS_CoV_2 L727F 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. L749M 2020 Virology journal Table SARS_CoV_2 L749M 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. M629I 2020 Virology journal Table SARS_CoV_2 M629I 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. M633T 2020 Virology journal Table SARS_CoV_2 M633T 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. M666I 2020 Virology journal Table SARS_CoV_2 M666I 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. M668I 2020 Virology journal Table SARS_CoV_2 M668I 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. N705D 2020 Virology journal Table SARS_CoV_2 N705D 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. N734T 2020 Virology journal Table SARS_CoV_2 N734T 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. N734Y 2020 Virology journal Table SARS_CoV_2 N734Y 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. N743S 2020 Virology journal Table SARS_CoV_2 N743S 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. P627S 2020 Virology journal Table SARS_CoV_2 P627S 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. R640H 2020 Virology journal Table SARS_CoV_2 R640H 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. R640S 2020 Virology journal Table SARS_CoV_2 R640S 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. R651H 2020 Virology journal Table SARS_CoV_2 R651H 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. R721H 2020 Virology journal Table SARS_CoV_2 R721H 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. R733K 2020 Virology journal Table SARS_CoV_2 R733K 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. R750C 2020 Virology journal Table SARS_CoV_2 R750C 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. R750H 2020 Virology journal Table SARS_CoV_2 R750H 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. S647I 2020 Virology journal Table SARS_CoV_2 S647I 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. T643I 2020 Virology journal Table SARS_CoV_2 T643I 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. T644M 2020 Virology journal Table SARS_CoV_2 T644M 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. T739I 2020 Virology journal Table SARS_CoV_2 T739I 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. V637L 2020 Virology journal Table SARS_CoV_2 V637L 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. V667I 2020 Virology journal Table SARS_CoV_2 V667I 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. V675F 2020 Virology journal Table SARS_CoV_2 V675F 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. V700A 2020 Virology journal Table SARS_CoV_2 V700A 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. V700I 2020 Virology journal Table SARS_CoV_2 V700I 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. V720F 2020 Virology journal Table SARS_CoV_2 V720F 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. V742A 2020 Virology journal Table SARS_CoV_2 V742A 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. V742G 2020 Virology journal Table SARS_CoV_2 V742G 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. V742M 2020 Virology journal Table SARS_CoV_2 V742M 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. Y674H 2020 Virology journal Table SARS_CoV_2 Y674H 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. Y719C 2020 Virology journal Table SARS_CoV_2 Y719C 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. Y748F 2020 Virology journal Table SARS_CoV_2 Y748F 0 5 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. Y748N 2020 Virology journal Table SARS_CoV_2 Y748N 0 5 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. D614G 2020 Nature communications Table SARS_CoV_2 D614G 0 5 33262895 Genomic characterization of SARS-CoV-2 in Egypt. c.-25C>T 2021 Journal of advanced research Table SARS_CoV_2 C25T 0 8 33262895 Genomic characterization of SARS-CoV-2 in Egypt. c.12269C>T 2021 Journal of advanced research Table SARS_CoV_2 C12269T 0 10 33262895 Genomic characterization of SARS-CoV-2 in Egypt. c.14144C>T 2021 Journal of advanced research Table SARS_CoV_2 C14144T 0 10 33262895 Genomic characterization of SARS-CoV-2 in Egypt. c.171G>T 2021 Journal of advanced research Table SARS_CoV_2 G171T 0 8 33262895 Genomic characterization of SARS-CoV-2 in Egypt. c.1841A>G 2021 Journal of advanced research Table SARS_CoV_2 A1841G 0 9 33262895 Genomic characterization of SARS-CoV-2 in Egypt. c.18613C>T 2021 Journal of advanced research Table SARS_CoV_2 C18613T 0 10 33262895 Genomic characterization of SARS-CoV-2 in Egypt. c.2169C>T 2021 Journal of advanced research Table SARS_CoV_2 C2169T 0 9 33262895 Genomic characterization of SARS-CoV-2 in Egypt. c.2772C>T 2021 Journal of advanced research Table SARS_CoV_2 C2772T 0 9 33262895 Genomic characterization of SARS-CoV-2 in Egypt. c.3108C>A 2021 Journal of advanced research Table SARS_CoV_2 C3108A 0 9 33262895 Genomic characterization of SARS-CoV-2 in Egypt. c.3737C>T 2021 Journal of advanced research Table SARS_CoV_2 C3737T 0 9 33262895 Genomic characterization of SARS-CoV-2 in Egypt. p.Asp1036Glu 2021 Journal of advanced research Table SARS_CoV_2 D1036E 0 12 33262895 Genomic characterization of SARS-CoV-2 in Egypt. p.Asp614Gly 2021 Journal of advanced research Table SARS_CoV_2 D614G 0 11 33262895 Genomic characterization of SARS-CoV-2 in Egypt. p.Gln57His 2021 Journal of advanced research Table SARS_CoV_2 Q57H 0 10 33262895 Genomic characterization of SARS-CoV-2 in Egypt. p.Phe924Phe 2021 Journal of advanced research Table SARS_CoV_2 F924F 0 11 33262895 Genomic characterization of SARS-CoV-2 in Egypt. p.Pro4715Leu 2021 Journal of advanced research Table SARS_CoV_2 P4715L 0 12 33262895 Genomic characterization of SARS-CoV-2 in Egypt. p.Thr1246Ile 2021 Journal of advanced research Table SARS_CoV_2 T1246I 0 12 33262895 Genomic characterization of SARS-CoV-2 in Egypt. p.Thr4090Ile 2021 Journal of advanced research Table SARS_CoV_2 T4090I 0 12 33292056 Sensing the interactions between carbohydrate-binding agents and N-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies. H84T 2020 Journal of biomolecular structure & dynamics Table SARS_CoV_2 H84T 0 4 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. D614G 2020 PloS one Table SARS_CoV_2 D614G 0 5 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. G1124V 2020 PloS one Table SARS_CoV_2 G1124V 0 6 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. D614G 2021 Cell host & microbe Table SARS_CoV_2 D614G 0 5 33319124 Mutational insights into the envelope protein of SARS-CoV-2. A22V,A 2021 Gene reports Table SARS_CoV_2 A22V 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. A41S,A 2021 Gene reports Table SARS_CoV_2 A41S 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. C43F,C 2021 Gene reports Table SARS_CoV_2 C43F 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. D72H 2021 Gene reports Table SARS_CoV_2 D72H 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. D72H,D 2021 Gene reports Table SARS_CoV_2 D72H 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. D72V,D 2021 Gene reports Table SARS_CoV_2 D72V 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. D72Y,D 2021 Gene reports Table SARS_CoV_2 D72Y 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. E7Q,E 2021 Gene reports Table SARS_CoV_2 E7Q 0 5 33319124 Mutational insights into the envelope protein of SARS-CoV-2. E8D,E 2021 Gene reports Table SARS_CoV_2 E8D 0 5 33319124 Mutational insights into the envelope protein of SARS-CoV-2. F20I,F 2021 Gene reports Table SARS_CoV_2 F20I 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. G10C,G 2021 Gene reports Table SARS_CoV_2 G10C 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. I46V,I 2021 Gene reports Table SARS_CoV_2 I46V 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. L19S,L 2021 Gene reports Table SARS_CoV_2 L19S 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. L21F 2021 Gene reports Table SARS_CoV_2 L21F 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. L21F,L 2021 Gene reports Table SARS_CoV_2 L21F 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. L27F,L 2021 Gene reports Table SARS_CoV_2 L27F 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. L31P,L 2021 Gene reports Table SARS_CoV_2 L31P 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. L37H,L 2021 Gene reports Table SARS_CoV_2 L37H 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. L37R 2021 Gene reports Table SARS_CoV_2 L37R 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. L51F,L 2021 Gene reports Table SARS_CoV_2 L51F 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. L73F 2021 Gene reports Table SARS_CoV_2 L73F 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. L73F,L 2021 Gene reports Table SARS_CoV_2 L73F 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. L74P,L 2021 Gene reports Table SARS_CoV_2 L74P 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. N64K,N 2021 Gene reports Table SARS_CoV_2 N64K 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. N66T,N 2021 Gene reports Table SARS_CoV_2 N66T 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. P71H 2021 Gene reports Table SARS_CoV_2 P71H 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. P71L 2021 Gene reports Table SARS_CoV_2 P71L 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. P71L,P 2021 Gene reports Table SARS_CoV_2 P71L 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. R61H,R 2021 Gene reports Table SARS_CoV_2 R61H 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. R61L 2021 Gene reports Table SARS_CoV_2 R61L 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. R69I 2021 Gene reports Table SARS_CoV_2 R69I 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. R69I,R 2021 Gene reports Table SARS_CoV_2 R69I 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. S16N,S 2021 Gene reports Table SARS_CoV_2 S16N;S16S 0;0 6;6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. S50I,S 2021 Gene reports Table SARS_CoV_2 S50I;S50S 0;0 6;6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. S55F 2021 Gene reports Table SARS_CoV_2 S55F 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. S68F 2021 Gene reports Table SARS_CoV_2 S68F 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. S68F,S 2021 Gene reports Table SARS_CoV_2 S68F;S68S 0;0 6;6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. S68Y 2021 Gene reports Table SARS_CoV_2 S68Y 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. T30I 2021 Gene reports Table SARS_CoV_2 T30I 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. T30I,T 2021 Gene reports Table SARS_CoV_2 T30I 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V17L,V 2021 Gene reports Table SARS_CoV_2 V17L 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V24A 2021 Gene reports Table SARS_CoV_2 V24A 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V24M 2021 Gene reports Table SARS_CoV_2 V24M 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V24M,V 2021 Gene reports Table SARS_CoV_2 V24M 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V47F,V 2021 Gene reports Table SARS_CoV_2 V47F 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V52E 2021 Gene reports Table SARS_CoV_2 V52E 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V52I,V 2021 Gene reports Table SARS_CoV_2 V52I 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V58A 2021 Gene reports Table SARS_CoV_2 V58A 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V58F 2021 Gene reports Table SARS_CoV_2 V58F 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V58F,V 2021 Gene reports Table SARS_CoV_2 V58F 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V5A,V 2021 Gene reports Table SARS_CoV_2 V5A 0 5 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V62F 2021 Gene reports Table SARS_CoV_2 V62F 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V62F,V 2021 Gene reports Table SARS_CoV_2 V62F 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V70A 2021 Gene reports Table SARS_CoV_2 V70A 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V70F,V 2021 Gene reports Table SARS_CoV_2 V70F 0 6 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V75L 2021 Gene reports Table SARS_CoV_2 V75L 0 4 33319124 Mutational insights into the envelope protein of SARS-CoV-2. V75L,V 2021 Gene reports Table SARS_CoV_2 V75L 0 6 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. D614G 2020 Cell reports Table SARS_CoV_2 D614G 0 5 33330626 Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM. I40A 2020 Frontiers in molecular biosciences Table SARS_CoV_2 I40A 0 4 33330626 Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM. M247A 2020 Frontiers in molecular biosciences Table SARS_CoV_2 M247A 0 5 33330626 Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM. Q87A 2020 Frontiers in molecular biosciences Table SARS_CoV_2 Q87A 0 4 33330626 Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM. R86A 2020 Frontiers in molecular biosciences Table SARS_CoV_2 R86A 0 4 33330626 Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM. V104A 2020 Frontiers in molecular biosciences Table SARS_CoV_2 V104A 0 5 33330626 Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM. V44A 2020 Frontiers in molecular biosciences Table SARS_CoV_2 V44A 0 4 33330626 Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM. V78A 2020 Frontiers in molecular biosciences Table SARS_CoV_2 V78A 0 4 33335187 CoV2-ID, a MIQE-compliant sub-20-min 5-plex RT-PCR assay targeting SARS-CoV-2 for the diagnosis of COVID-19. D614G 2020 Scientific reports Table SARS_CoV_2 D614G 0 5 33359807 SARS-Cov-2 ORF3a: Mutability and function. A54S 2021 International journal of biological macromolecules Table SARS_CoV_2 A54S 0 4 33359807 SARS-Cov-2 ORF3a: Mutability and function. A99V 2021 International journal of biological macromolecules Table SARS_CoV_2 A99V 0 4 33359807 SARS-Cov-2 ORF3a: Mutability and function. F207L 2021 International journal of biological macromolecules Table SARS_CoV_2 F207L 0 5 33359807 SARS-Cov-2 ORF3a: Mutability and function. G172V 2021 International journal of biological macromolecules Table SARS_CoV_2 G172V 0 5 33359807 SARS-Cov-2 ORF3a: Mutability and function. G196V 2021 International journal of biological macromolecules Table SARS_CoV_2 G196V 0 5 33359807 SARS-Cov-2 ORF3a: Mutability and function. K75N 2021 International journal of biological macromolecules Table SARS_CoV_2 K75N 0 4 33359807 SARS-Cov-2 ORF3a: Mutability and function. L108F 2021 International journal of biological macromolecules Table SARS_CoV_2 L108F 0 5 33359807 SARS-Cov-2 ORF3a: Mutability and function. L46F 2021 International journal of biological macromolecules Table SARS_CoV_2 L46F 0 4 33359807 SARS-Cov-2 ORF3a: Mutability and function. Q57H 2021 International journal of biological macromolecules Table SARS_CoV_2 Q57H 0 4 33359807 SARS-Cov-2 ORF3a: Mutability and function. R126S 2021 International journal of biological macromolecules Table SARS_CoV_2 R126S 0 5 33359807 SARS-Cov-2 ORF3a: Mutability and function. S58N 2021 International journal of biological macromolecules Table SARS_CoV_2 S58N 0 4 33359807 SARS-Cov-2 ORF3a: Mutability and function. T223I 2021 International journal of biological macromolecules Table SARS_CoV_2 T223I 0 5 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. S477N 2020 Journal of translational medicine Table SARS_CoV_2 S477N 0 5 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. A372V 2020 PeerJ Table SARS_CoV_2 A372V 0 5 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. G261D 2020 PeerJ Table SARS_CoV_2 G261D 0 5 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. L219V 2020 PeerJ Table SARS_CoV_2 L219V 0 5 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. A54V 2020 PeerJ Table SARS_CoV_2 A54V 0 4 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. A656S 2020 PeerJ Table SARS_CoV_2 A656S 0 5 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. A99S 2020 PeerJ Table SARS_CoV_2 A99S 0 4 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. D614G 2020 PeerJ Table SARS_CoV_2 D614G 0 5 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. H73Y 2020 PeerJ Table SARS_CoV_2 H73Y 0 4 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. M49I 2020 PeerJ Table SARS_CoV_2 M49I 0 4 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. M576I 2020 PeerJ Table SARS_CoV_2 M576I 0 5 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. P323L 2020 PeerJ Table SARS_CoV_2 P323L 0 5 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. P679S 2020 PeerJ Table SARS_CoV_2 P679S 0 5 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. P822L 2020 PeerJ Table SARS_CoV_2 P822L 0 5 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. Q160R 2020 PeerJ Table SARS_CoV_2 Q160R 0 5 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. Q57H 2020 PeerJ Table SARS_CoV_2 Q57H 0 4 33407987 Impact of population density and weather on COVID-19 pandemic and SARS-CoV-2 mutation frequency in Bangladesh. D614G 2021 Epidemiology and infection Table SARS_CoV_2 D614G 0 5 33412089 COVID-19-neutralizing antibodies predict disease severity and survival. D614G 2021 Cell Table SARS_CoV_2 D614G 0 5 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. A1708D 2021 Euro surveillance Table SARS_CoV_2 A1708D 0 6 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. A570D 2021 Euro surveillance Table SARS_CoV_2 A570D 0 5 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. D1118H 2021 Euro surveillance Table SARS_CoV_2 D1118H 0 6 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. H2357Y 2021 Euro surveillance Table SARS_CoV_2 H2357Y 0 6 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. I2230T 2021 Euro surveillance Table SARS_CoV_2 I2230T 0 6 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. N501Y 2021 Euro surveillance Table SARS_CoV_2 N501Y 0 5 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. P3395L 2021 Euro surveillance Table SARS_CoV_2 P3395L 0 6 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. P681H 2021 Euro surveillance Table SARS_CoV_2 P681H 0 5 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. R52I 2021 Euro surveillance Table SARS_CoV_2 R52I 0 4 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. S235F 2021 Euro surveillance Table SARS_CoV_2 S235F 0 5 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. S944L 2021 Euro surveillance Table SARS_CoV_2 S944L 0 5 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. S982A 2021 Euro surveillance Table SARS_CoV_2 S982A 0 5 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. T1001I 2021 Euro surveillance Table SARS_CoV_2 T1001I 0 6 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. T14I 2021 Euro surveillance Table SARS_CoV_2 T14I 0 4 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. T716I 2021 Euro surveillance Table SARS_CoV_2 T716I 0 5 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. Y73C 2021 Euro surveillance Table SARS_CoV_2 Y73C 0 4 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. D614G 2021 Cell reports Table SARS_CoV_2 D614G 0 5 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. P0877L 2021 Cell reports Table SARS_CoV_2 P0877L 0 6 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. 1163A>T 2021 PloS one Table SARS_CoV_2 A1163T 0 7 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. 23403A>G 2021 PloS one Table SARS_CoV_2 A23403G 0 8 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. 25563G>T 2021 PloS one Table SARS_CoV_2 G25563T 0 8 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. 28881G>A 2021 PloS one Table SARS_CoV_2 G28881A 0 8 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. 28882G>A 2021 PloS one Table SARS_CoV_2 G28882A 0 8 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. 28883G>C 2021 PloS one Table SARS_CoV_2 G28883C 0 8 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. Arg203ARG 2021 PloS one Table SARS_CoV_2 R203R 0 9 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. Arg203Lys 2021 PloS one Table SARS_CoV_2 R203K 0 9 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. Asp614Gly 2021 PloS one Table SARS_CoV_2 D614G 0 9 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. D614G 2021 PloS one Table SARS_CoV_2 D614G 0 5 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. G204A 2021 PloS one Table SARS_CoV_2 G204A 0 5 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. Gln57His 2021 PloS one Table SARS_CoV_2 Q57H 0 8 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. Gly204Arg 2021 PloS one Table SARS_CoV_2 G204R 0 9 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. I300F 2021 PloS one Table SARS_CoV_2 I300F 0 5 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. Ile300Phe 2021 PloS one Table SARS_CoV_2 I300F 0 9 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. P4715L 2021 PloS one Table SARS_CoV_2 P4715L 0 6 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. R203L 2021 PloS one Table SARS_CoV_2 R203L 0 5 33478625 Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020. D614G 2021 Euro surveillance Table SARS_CoV_2 D614G 0 5 33478625 Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020. D80Y 2021 Euro surveillance Table SARS_CoV_2 D80Y 0 4 33478625 Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020. H146Y 2021 Euro surveillance Table SARS_CoV_2 H146Y 0 5 33478625 Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020. N439K 2021 Euro surveillance Table SARS_CoV_2 N439K 0 5 33478625 Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020. S477N 2021 Euro surveillance Table SARS_CoV_2 S477N 0 5 33478625 Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020. V401L 2021 Euro surveillance Table SARS_CoV_2 V401L 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. A1174V 2021 Heliyon Table SARS_CoV_2 A1174V 0 6 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. A262T 2021 Heliyon Table SARS_CoV_2 A262T 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. A263V 2021 Heliyon Table SARS_CoV_2 A263V 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. A288T 2021 Heliyon Table SARS_CoV_2 A288T 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. A344S 2021 Heliyon Table SARS_CoV_2 A344S 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. A522V 2021 Heliyon Table SARS_CoV_2 A522V 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. A570S 2021 Heliyon Table SARS_CoV_2 A570S 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. A653V 2021 Heliyon Table SARS_CoV_2 A653V 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. A67S 2021 Heliyon Table SARS_CoV_2 A67S 0 4 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. A684V 2021 Heliyon Table SARS_CoV_2 A684V 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. A871S 2021 Heliyon Table SARS_CoV_2 A871S 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. A958S 2021 Heliyon Table SARS_CoV_2 A958S 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. aspartic acid by glycine at position 614 2021 Heliyon Table SARS_CoV_2 D614G 0 40 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. C1243F 2021 Heliyon Table SARS_CoV_2 C1243F 0 6 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. D1139Y 2021 Heliyon Table SARS_CoV_2 D1139Y 0 6 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. D1146Y 2021 Heliyon Table SARS_CoV_2 D1146Y 0 6 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. D1153A 2021 Heliyon Table SARS_CoV_2 D1153A 0 6 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. D614G 2021 Heliyon Table SARS_CoV_2 D614G 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. D936Y 2021 Heliyon Table SARS_CoV_2 D936Y 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. G1167S 2021 Heliyon Table SARS_CoV_2 G1167S 0 6 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. G311E 2021 Heliyon Table SARS_CoV_2 G311E 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. G75S 2021 Heliyon Table SARS_CoV_2 G75S 0 4 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. H1101Y 2021 Heliyon Table SARS_CoV_2 H1101Y 0 6 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. I850F 2021 Heliyon Table SARS_CoV_2 I850F 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. L1063F 2021 Heliyon Table SARS_CoV_2 L1063F 0 6 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. M1237I 2021 Heliyon Table SARS_CoV_2 M1237I 0 6 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. M153I 2021 Heliyon Table SARS_CoV_2 M153I 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. M177I 2021 Heliyon Table SARS_CoV_2 M177I 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. M731I 2021 Heliyon Table SARS_CoV_2 M731I 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. P138H 2021 Heliyon Table SARS_CoV_2 P138H 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. P499H 2021 Heliyon Table SARS_CoV_2 P499H 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. P621S 2021 Heliyon Table SARS_CoV_2 P621S 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. Q314R 2021 Heliyon Table SARS_CoV_2 Q314R 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. Q677H 2021 Heliyon Table SARS_CoV_2 Q677H 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. R21I 2021 Heliyon Table SARS_CoV_2 R21I 0 4 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. R408I 2021 Heliyon Table SARS_CoV_2 R408I 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. S12F 2021 Heliyon Table SARS_CoV_2 S12F 0 4 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. S13I 2021 Heliyon Table SARS_CoV_2 S13I 0 4 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. S255F 2021 Heliyon Table SARS_CoV_2 S255F 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. S459F 2021 Heliyon Table SARS_CoV_2 S459F 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. S477R 2021 Heliyon Table SARS_CoV_2 S477R 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. S514Y 2021 Heliyon Table SARS_CoV_2 S514Y 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. S939F 2021 Heliyon Table SARS_CoV_2 S939F 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. T22I 2021 Heliyon Table SARS_CoV_2 T22I 0 4 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. T29I 2021 Heliyon Table SARS_CoV_2 T29I 0 4 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. T732S 2021 Heliyon Table SARS_CoV_2 T732S 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. T859I 2021 Heliyon Table SARS_CoV_2 T859I 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. T95I 2021 Heliyon Table SARS_CoV_2 T95I 0 4 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. V1176F 2021 Heliyon Table SARS_CoV_2 V1176F 0 6 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. V1228L 2021 Heliyon Table SARS_CoV_2 V1228L 0 6 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. V622I/F 2021 Heliyon Table SARS_CoV_2 V622F;V622I 0;0 7;7 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. Y279N 2021 Heliyon Table SARS_CoV_2 Y279N 0 5 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. Y28H 2021 Heliyon Table SARS_CoV_2 Y28H 0 4 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. 11083G>T 2020 JMIR bioinformatics and biotechnology Table SARS_CoV_2 G11083T 0 8 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. 13730C>T 2020 JMIR bioinformatics and biotechnology Table SARS_CoV_2 C13730T 0 8 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. 23929C>T 2020 JMIR bioinformatics and biotechnology Table SARS_CoV_2 C23929T 0 8 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. 241C>T 2020 JMIR bioinformatics and biotechnology Table SARS_CoV_2 C241T 0 6 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. 28311C>T 2020 JMIR bioinformatics and biotechnology Table SARS_CoV_2 C28311T 0 8 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. 6310C>A 2020 JMIR bioinformatics and biotechnology Table SARS_CoV_2 C6310A 0 7 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. 6312C>A 2020 JMIR bioinformatics and biotechnology Table SARS_CoV_2 C6312A 0 7 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. A97V 2020 JMIR bioinformatics and biotechnology Table SARS_CoV_2 A97V 0 4 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. L37F 2020 JMIR bioinformatics and biotechnology Table SARS_CoV_2 L37F 0 4 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. P13L 2020 JMIR bioinformatics and biotechnology Table SARS_CoV_2 P13L 0 4 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. S1197R 2020 JMIR bioinformatics and biotechnology Table SARS_CoV_2 S1197R 0 6 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. T1198K 2020 JMIR bioinformatics and biotechnology Table SARS_CoV_2 T1198K 0 6 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. Y789Y 2020 JMIR bioinformatics and biotechnology Table SARS_CoV_2 Y789Y 0 5 33502471 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Replication and Tropism in the Lungs, Airways, and Vascular Endothelium of Patients With Fatal Coronavirus Disease 2019: An Autopsy Case Series. D614G 2021 The Journal of infectious diseases Table SARS_CoV_2 D614G 0 5 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. D1139Y 2021 Biochemistry and biophysics reports Table SARS_CoV_2 D1139Y 0 6 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. D614G 2021 Biochemistry and biophysics reports Table SARS_CoV_2 D614G 0 5 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. G1167S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G1167S 0 6 33509990 Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq. A23403G 2021 Microbiology resource announcements Table SARS_CoV_2 A23403G 0 7 33509990 Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq. C10078T 2021 Microbiology resource announcements Table SARS_CoV_2 C10078T 0 7 33509990 Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq. C12318T 2021 Microbiology resource announcements Table SARS_CoV_2 C12318T 0 7 33509990 Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq. C18877T 2021 Microbiology resource announcements Table SARS_CoV_2 C18877T 0 7 33509990 Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq. C241T 2021 Microbiology resource announcements Table SARS_CoV_2 C241T 0 5 33509990 Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq. C3037T 2021 Microbiology resource announcements Table SARS_CoV_2 C3037T 0 6 33509990 Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq. G25563T 2021 Microbiology resource announcements Table SARS_CoV_2 G25563T 0 7 33509990 Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq. G28916A 2021 Microbiology resource announcements Table SARS_CoV_2 G28916A 0 7 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A103S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A103S 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A103V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A103V 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A110S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A110S 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A110V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A110V 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A143S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A143S 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A143V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A143V 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A23S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A23S 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A31T 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A31T 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A33E 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A33E 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A33S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A33S 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A39T 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A39T 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A51S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A51S 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A54S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A54S 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A54T 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A54T 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A54V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A54V 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A59V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A59V 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A72S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A72S 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A99S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A99S 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A99T 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A99T 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. A99V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 A99V 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. C133F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 C133F 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. C148S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 C148S 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. C148Y 2021 Biochemistry and biophysics reports Table SARS_CoV_2 C148Y 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. C153Y 2021 Biochemistry and biophysics reports Table SARS_CoV_2 C153Y 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. D155Y 2021 Biochemistry and biophysics reports Table SARS_CoV_2 D155Y 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. D210Y 2021 Biochemistry and biophysics reports Table SARS_CoV_2 D210Y 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. D222G 2021 Biochemistry and biophysics reports Table SARS_CoV_2 D222G 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. D22Y 2021 Biochemistry and biophysics reports Table SARS_CoV_2 D22Y 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. D238E 2021 Biochemistry and biophysics reports Table SARS_CoV_2 D238E 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. D238N 2021 Biochemistry and biophysics reports Table SARS_CoV_2 D238N 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. D27H 2021 Biochemistry and biophysics reports Table SARS_CoV_2 D27H 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. D27Y 2021 Biochemistry and biophysics reports Table SARS_CoV_2 D27Y 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. E191K 2021 Biochemistry and biophysics reports Table SARS_CoV_2 E191K 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. E194Q 2021 Biochemistry and biophysics reports Table SARS_CoV_2 E194Q 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. E239D 2021 Biochemistry and biophysics reports Table SARS_CoV_2 E239D 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. E239G 2021 Biochemistry and biophysics reports Table SARS_CoV_2 E239G 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. E241A 2021 Biochemistry and biophysics reports Table SARS_CoV_2 E241A 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. E242A 2021 Biochemistry and biophysics reports Table SARS_CoV_2 E242A 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. F105L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 F105L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. F114C 2021 Biochemistry and biophysics reports Table SARS_CoV_2 F114C 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. F120L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 F120L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. F43Y 2021 Biochemistry and biophysics reports Table SARS_CoV_2 F43Y 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. F56C 2021 Biochemistry and biophysics reports Table SARS_CoV_2 F56C 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. F87L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 F87L 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G100C 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G100C 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G100F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G100F 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G100L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G100L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G100V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G100V 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G172C 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G172C 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G172V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G172V 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G174D 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G174D 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G188C 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G188C 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G18C 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G18C 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G18D 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G18D 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G18S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G18S 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G18V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G18V 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G196R 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G196R 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G196V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G196V 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G224C 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G224C 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G224V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G224V 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G251C 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G251C 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G251V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G251V 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G254R 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G254R 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G44V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G44V 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G49D 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G49D 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G49S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G49S 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. G49V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 G49V 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. H182Y 2021 Biochemistry and biophysics reports Table SARS_CoV_2 H182Y 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. H247Y 2021 Biochemistry and biophysics reports Table SARS_CoV_2 H247Y 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. H78Q 2021 Biochemistry and biophysics reports Table SARS_CoV_2 H78Q 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. H78Y 2021 Biochemistry and biophysics reports Table SARS_CoV_2 H78Y 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. H93Y 2021 Biochemistry and biophysics reports Table SARS_CoV_2 H93Y 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. I118V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 I118V 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. I123V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 I123V 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. I158V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 I158V 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. I20T 2021 Biochemistry and biophysics reports Table SARS_CoV_2 I20T 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. I263M 2021 Biochemistry and biophysics reports Table SARS_CoV_2 I263M 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. I35T 2021 Biochemistry and biophysics reports Table SARS_CoV_2 I35T 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. K16N 2021 Biochemistry and biophysics reports Table SARS_CoV_2 K16N 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. K21N 2021 Biochemistry and biophysics reports Table SARS_CoV_2 K21N 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. K21Q 2021 Biochemistry and biophysics reports Table SARS_CoV_2 K21Q 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. K66N 2021 Biochemistry and biophysics reports Table SARS_CoV_2 K66N 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. K67N 2021 Biochemistry and biophysics reports Table SARS_CoV_2 K67N 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. K67R 2021 Biochemistry and biophysics reports Table SARS_CoV_2 K67R 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. K75E 2021 Biochemistry and biophysics reports Table SARS_CoV_2 K75E 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. K75R 2021 Biochemistry and biophysics reports Table SARS_CoV_2 K75R 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L101F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L101F 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L106F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L106F 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L108F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L108F 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L111S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L111S 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L127F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L127F 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L127I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L127I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L129F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L129F 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L140F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L140F 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L140I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L140I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L147F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L147F 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L15F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L15F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L219F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L219F 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L219S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L219S 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L219V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L219V 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L41F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L41F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L41H 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L41H 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L41I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L41I 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L46F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L46F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L52F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L52F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L52I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L52I 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L53F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L53F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L53H 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L53H 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L65F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L65F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L73F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L73F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L83F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L83F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L85F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L85F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L86W 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L86W 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L94F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L94F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L94I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L94I 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L94P 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L94P 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L95F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L95F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. L96F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 L96F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. M125I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 M125I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. M260I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 M260I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. M260K 2021 Biochemistry and biophysics reports Table SARS_CoV_2 M260K 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. N119H 2021 Biochemistry and biophysics reports Table SARS_CoV_2 N119H 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. N144Y 2021 Biochemistry and biophysics reports Table SARS_CoV_2 N144Y 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. N152I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 N152I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. N152S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 N152S 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. N257S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 N257S 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. P104L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 P104L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. P104S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 P104S 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. P178S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 P178S 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. P240L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 P240L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. P240S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 P240S 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. P25L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 P25L 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. P25S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 P25S 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. P262L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 P262L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. P262S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 P262S 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. P267L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 P267L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. P267S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 P267S 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. P36L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 P36L 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. P42L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 P42L 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. P42R 2021 Biochemistry and biophysics reports Table SARS_CoV_2 P42R 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. P42S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 P42S 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Q116H 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Q116H 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Q17R 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Q17R 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Q185H 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Q185H 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Q213H 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Q213H 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Q218R 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Q218R 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Q245L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Q245L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Q38E 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Q38E 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Q38P 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Q38P 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Q57H 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Q57H 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Q57Y 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Q57Y 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. R122I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 R122I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. R122K 2021 Biochemistry and biophysics reports Table SARS_CoV_2 R122K 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. R126S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 R126S 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. R134C 2021 Biochemistry and biophysics reports Table SARS_CoV_2 R134C 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. R134H 2021 Biochemistry and biophysics reports Table SARS_CoV_2 R134H 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. R134L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 R134L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. R68I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 R68I 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S135P 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S135P 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S165F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S165F 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S165I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S165I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S166L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S166L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S171L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S171L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S177I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S177I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S195Y 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S195Y 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S216P 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S216P 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S220N 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S220N 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S26L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S26L 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S26P 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S26P 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S272I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S272I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S40L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S40L 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S40P 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S40P 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S74F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S74F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S74P 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S74P 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. S92L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 S92L 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T12N 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T12N 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T14I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T14I 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T151I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T151I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T170S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T170S 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T175I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T175I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T175K 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T175K 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T176I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T176I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T208A 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T208A 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T217A 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T217A 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T223I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T223I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T229I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T229I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T268K 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T268K 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T268M 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T268M 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T269M 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T269M 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T271I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T271I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T32I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T32I 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T34A 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T34A 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T64I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T64I 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T89I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T89I 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. T9K 2021 Biochemistry and biophysics reports Table SARS_CoV_2 T9K 0 3 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V112F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V112F 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V112L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V112L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V13A 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V13A 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V13I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V13I 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V13L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V13L 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V163L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V163L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V168I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V168I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V197I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V197I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V197L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V197L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V201I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V201I 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V202L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V202L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V225F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V225F 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V225L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V225L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V237A 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V237A 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V237F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V237F 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V259E 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V259E 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V259L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V259L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V273L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V273L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V48F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V48F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V50A 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V50A 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V50I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V50I 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V55F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V55F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V55G 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V55G 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V77F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V77F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V77I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V77I 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V88A 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V88A 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V88L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V88L 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V90F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V90F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V90I 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V90I 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V97A 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V97A 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. V97F 2021 Biochemistry and biophysics reports Table SARS_CoV_2 V97F 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. W128L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 W128L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. W131L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 W131L 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. W131R 2021 Biochemistry and biophysics reports Table SARS_CoV_2 W131R 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. W131S 2021 Biochemistry and biophysics reports Table SARS_CoV_2 W131S 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. W131V 2021 Biochemistry and biophysics reports Table SARS_CoV_2 W131V 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. W193R 2021 Biochemistry and biophysics reports Table SARS_CoV_2 W193R 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. W45L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 W45L 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. W45R 2021 Biochemistry and biophysics reports Table SARS_CoV_2 W45R 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. W69L 2021 Biochemistry and biophysics reports Table SARS_CoV_2 W69L 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. W69R 2021 Biochemistry and biophysics reports Table SARS_CoV_2 W69R 0 4 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Y154C 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Y154C 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Y160H 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Y160H 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Y184H 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Y184H 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Y189C 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Y189C 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Y211C 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Y211C 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Y215H 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Y215H 0 5 33527091 Variations in Orf3a protein of SARS-CoV-2 alter its structure and function. Y264C 2021 Biochemistry and biophysics reports Table SARS_CoV_2 Y264C 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. A18V 2021 Antiviral research Table SARS_CoV_2 A18V 0 4 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. A320V 2021 Antiviral research Table SARS_CoV_2 A320V 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. A446D 2021 Antiviral research Table SARS_CoV_2 A446D 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. A449V 2021 Antiviral research Table SARS_CoV_2 A449V 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. A598S 2021 Antiviral research Table SARS_CoV_2 A598S 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. A97V 2021 Antiviral research Table SARS_CoV_2 A97V 0 4 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. D135Y 2021 Antiviral research Table SARS_CoV_2 D135Y 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. E23G 2021 Antiviral research Table SARS_CoV_2 E23G 0 4 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. E244D 2021 Antiviral research Table SARS_CoV_2 E244D 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. E261D 2021 Antiviral research Table SARS_CoV_2 E261D 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. F233L 2021 Antiviral research Table SARS_CoV_2 F233L 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. I258V 2021 Antiviral research Table SARS_CoV_2 I258V 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. K460R 2021 Antiviral research Table SARS_CoV_2 K460R 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. M124I 2021 Antiviral research Table SARS_CoV_2 M124I 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. M196I 2021 Antiviral research Table SARS_CoV_2 M196I 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. M501I 2021 Antiviral research Table SARS_CoV_2 M501I 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. P227L 2021 Antiviral research Table SARS_CoV_2 P227L 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. P323L 2021 Antiviral research Table SARS_CoV_2 P323L 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. P47L 2021 Antiviral research Table SARS_CoV_2 P47L 0 4 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. P504L 2021 Antiviral research Table SARS_CoV_2 P504L 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. P78S 2021 Antiviral research Table SARS_CoV_2 P78S 0 4 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. Q24R 2021 Antiviral research Table SARS_CoV_2 Q24R 0 4 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. R392C 2021 Antiviral research Table SARS_CoV_2 R392C 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. S25A 2021 Antiviral research Table SARS_CoV_2 S25A 0 4 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. S25L 2021 Antiviral research Table SARS_CoV_2 S25L 0 4 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. S33N 2021 Antiviral research Table SARS_CoV_2 S33N 0 4 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. S913A 2021 Antiviral research Table SARS_CoV_2 S913A 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. T141I 2021 Antiviral research Table SARS_CoV_2 T141I 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. T293I 2021 Antiviral research Table SARS_CoV_2 T293I 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. T351I 2021 Antiviral research Table SARS_CoV_2 T351I 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. T588I 2021 Antiviral research Table SARS_CoV_2 T588I 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. T739I 2021 Antiviral research Table SARS_CoV_2 T739I 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. T803I 2021 Antiviral research Table SARS_CoV_2 T803I 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. T85I 2021 Antiviral research Table SARS_CoV_2 T85I 0 4 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. Y541C 2021 Antiviral research Table SARS_CoV_2 Y541C 0 5 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. A3220V 2021 Infection, genetics and evolution Table SARS_CoV_2 A3220V 0 6 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. C18060T 2021 Infection, genetics and evolution Table SARS_CoV_2 C18060T 0 7 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. C29095T 2021 Infection, genetics and evolution Table SARS_CoV_2 C29095T 0 7 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. D614G 2021 Infection, genetics and evolution Table SARS_CoV_2 D614G 0 5 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. G251V 2021 Infection, genetics and evolution Table SARS_CoV_2 G251V 0 5 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. L3606F 2021 Infection, genetics and evolution Table SARS_CoV_2 L3606F 0 6 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. L84S 2021 Infection, genetics and evolution Table SARS_CoV_2 L84S 0 4 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. P314L 2021 Infection, genetics and evolution Table SARS_CoV_2 P314L 0 5 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. S202N 2021 Infection, genetics and evolution Table SARS_CoV_2 S202N 0 5 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. T28144C 2021 Infection, genetics and evolution Table SARS_CoV_2 T28144C 0 7 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. T514C 2021 Infection, genetics and evolution Table SARS_CoV_2 T514C 0 5 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. V378I 2021 Infection, genetics and evolution Table SARS_CoV_2 V378I 0 5 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. D614G 2021 Biosafety and health Table SARS_CoV_2 D614G 0 5 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. G204R 2021 Biosafety and health Table SARS_CoV_2 G204R 0 5 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. P323L 2021 Biosafety and health Table SARS_CoV_2 P323L 0 5 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. R203K 2021 Biosafety and health Table SARS_CoV_2 R203K 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). A208G 2021 Scientific reports Table SARS_CoV_2 A208G 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). A262T 2021 Scientific reports Table SARS_CoV_2 A262T 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). A51S 2021 Scientific reports Table SARS_CoV_2 A51S 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). A520S 2021 Scientific reports Table SARS_CoV_2 A520S 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). A65S 2021 Scientific reports Table SARS_CoV_2 A65S 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). A829T 2021 Scientific reports Table SARS_CoV_2 A829T 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). D138H 2021 Scientific reports Table SARS_CoV_2 D138H 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). D22G 2021 Scientific reports Table SARS_CoV_2 D22G 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). D253G 2021 Scientific reports Table SARS_CoV_2 D253G 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). D34E 2021 Scientific reports Table SARS_CoV_2 D34E 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). D53G 2021 Scientific reports Table SARS_CoV_2 D53G 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). D53Y 2021 Scientific reports Table SARS_CoV_2 D53Y 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). D61K 2021 Scientific reports Table SARS_CoV_2 D61K 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). D61Y 2021 Scientific reports Table SARS_CoV_2 D61Y 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). D75E 2021 Scientific reports Table SARS_CoV_2 D75E 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). D80Y 2021 Scientific reports Table SARS_CoV_2 D80Y 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). E110G 2021 Scientific reports Table SARS_CoV_2 E110G 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). E1209D 2021 Scientific reports Table SARS_CoV_2 E1209D 0 6 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). E554D 2021 Scientific reports Table SARS_CoV_2 E554D 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). E583D 2021 Scientific reports Table SARS_CoV_2 E583D 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). E95K 2021 Scientific reports Table SARS_CoV_2 E95K 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). F190L 2021 Scientific reports Table SARS_CoV_2 F190L 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). F26L 2021 Scientific reports Table SARS_CoV_2 F26L 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). F30L 2021 Scientific reports Table SARS_CoV_2 F30L 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). F32L 2021 Scientific reports Table SARS_CoV_2 F32L 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). G18C 2021 Scientific reports Table SARS_CoV_2 G18C 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). G196V 2021 Scientific reports Table SARS_CoV_2 G196V 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). G204R 2021 Scientific reports Table SARS_CoV_2 G204R 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). G251V 2021 Scientific reports Table SARS_CoV_2 G251V 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). G261D 2021 Scientific reports Table SARS_CoV_2 G261D 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). G44V 2021 Scientific reports Table SARS_CoV_2 G44V 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). G476S 2021 Scientific reports Table SARS_CoV_2 G476S 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). G485R 2021 Scientific reports Table SARS_CoV_2 G485R 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). G66C 2021 Scientific reports Table SARS_CoV_2 G66C 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). H112Q 2021 Scientific reports Table SARS_CoV_2 H112Q 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). H146Y 2021 Scientific reports Table SARS_CoV_2 H146Y 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). H519Q 2021 Scientific reports Table SARS_CoV_2 H519Q 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). I110T 2021 Scientific reports Table SARS_CoV_2 I110T 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). I121S 2021 Scientific reports Table SARS_CoV_2 I121S 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). I33T 2021 Scientific reports Table SARS_CoV_2 I33T 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). K42N 2021 Scientific reports Table SARS_CoV_2 K42N 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). L18F 2021 Scientific reports Table SARS_CoV_2 L18F 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). L3606F 2021 Scientific reports Table SARS_CoV_2 L3606F 0 6 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). L54F 2021 Scientific reports Table SARS_CoV_2 L54F 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). L65F 2021 Scientific reports Table SARS_CoV_2 L65F 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). L73F 2021 Scientific reports Table SARS_CoV_2 L73F 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). L84S 2021 Scientific reports Table SARS_CoV_2 L84S 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). M58T 2021 Scientific reports Table SARS_CoV_2 M58T 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). P1162L 2021 Scientific reports Table SARS_CoV_2 P1162L 0 6 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). P1263L 2021 Scientific reports Table SARS_CoV_2 P1263L 0 6 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). P13L 2021 Scientific reports Table SARS_CoV_2 P13L 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). P36L 2021 Scientific reports Table SARS_CoV_2 P36L 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). P36S 2021 Scientific reports Table SARS_CoV_2 P36S 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). P5828L 2021 Scientific reports Table SARS_CoV_2 P5828L 0 6 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). P681L 2021 Scientific reports Table SARS_CoV_2 P681L 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). P71L 2021 Scientific reports Table SARS_CoV_2 P71L 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). P971L 2021 Scientific reports Table SARS_CoV_2 P971L 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). P99S 2021 Scientific reports Table SARS_CoV_2 P99S 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Q185H 2021 Scientific reports Table SARS_CoV_2 Q185H 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Q57H 2021 Scientific reports Table SARS_CoV_2 Q57H 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). R146H 2021 Scientific reports Table SARS_CoV_2 R146H 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). R203K 2021 Scientific reports Table SARS_CoV_2 R203K 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). R24L 2021 Scientific reports Table SARS_CoV_2 R24L 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). R408I 2021 Scientific reports Table SARS_CoV_2 R408I 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). R78M 2021 Scientific reports Table SARS_CoV_2 R78M 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S183Y 2021 Scientific reports Table SARS_CoV_2 S183Y 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S194L 2021 Scientific reports Table SARS_CoV_2 S194L 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S197L 2021 Scientific reports Table SARS_CoV_2 S197L 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S202N 2021 Scientific reports Table SARS_CoV_2 S202N 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S221L 2021 Scientific reports Table SARS_CoV_2 S221L 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S23F 2021 Scientific reports Table SARS_CoV_2 S23F 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S24L 2021 Scientific reports Table SARS_CoV_2 S24L 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S254F 2021 Scientific reports Table SARS_CoV_2 S254F 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S31L 2021 Scientific reports Table SARS_CoV_2 S31L 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S36F 2021 Scientific reports Table SARS_CoV_2 S36F 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S3884L 2021 Scientific reports Table SARS_CoV_2 S3884L 0 6 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S494P 2021 Scientific reports Table SARS_CoV_2 S494P 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S67F 2021 Scientific reports Table SARS_CoV_2 S67F 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S68F 2021 Scientific reports Table SARS_CoV_2 S68F 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S69L 2021 Scientific reports Table SARS_CoV_2 S69L 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S81L 2021 Scientific reports Table SARS_CoV_2 S81L 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S939F 2021 Scientific reports Table SARS_CoV_2 S939F 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). S98F 2021 Scientific reports Table SARS_CoV_2 S98F 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). T11A 2021 Scientific reports Table SARS_CoV_2 T11A 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). T11K 2021 Scientific reports Table SARS_CoV_2 T11K 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). T14I 2021 Scientific reports Table SARS_CoV_2 T14I 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). T175I 2021 Scientific reports Table SARS_CoV_2 T175I 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). T175M 2021 Scientific reports Table SARS_CoV_2 T175M 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). T205I 2021 Scientific reports Table SARS_CoV_2 T205I 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). T265I 2021 Scientific reports Table SARS_CoV_2 T265I 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). T29I 2021 Scientific reports Table SARS_CoV_2 T29I 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). T362I 2021 Scientific reports Table SARS_CoV_2 T362I 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). T40I 2021 Scientific reports Table SARS_CoV_2 T40I 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). T572I 2021 Scientific reports Table SARS_CoV_2 T572I 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). T676I 2021 Scientific reports Table SARS_CoV_2 T676I 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). T76I 2021 Scientific reports Table SARS_CoV_2 T76I 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). T95I 2021 Scientific reports Table SARS_CoV_2 T95I 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). V114F 2021 Scientific reports Table SARS_CoV_2 V114F 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). V29L 2021 Scientific reports Table SARS_CoV_2 V29L 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). V367F 2021 Scientific reports Table SARS_CoV_2 V367F 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). V483A 2021 Scientific reports Table SARS_CoV_2 V483A 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). V62L 2021 Scientific reports Table SARS_CoV_2 V62L 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). V70F 2021 Scientific reports Table SARS_CoV_2 V70F 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). V70I 2021 Scientific reports Table SARS_CoV_2 V70I 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). V71I 2021 Scientific reports Table SARS_CoV_2 V71I 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). V93F 2021 Scientific reports Table SARS_CoV_2 V93F 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). W258L 2021 Scientific reports Table SARS_CoV_2 W258L 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). W27L 2021 Scientific reports Table SARS_CoV_2 W27L 0 4 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Y453F 2021 Scientific reports Table SARS_CoV_2 Y453F 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Y5865C 2021 Scientific reports Table SARS_CoV_2 Y5865C 0 6 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. D614G 2021 eLife Table SARS_CoV_2 D614G 0 5 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. A1812D 2021 Microbiology resource announcements Table SARS_CoV_2 A1812D 0 6 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. A18253G 2021 Microbiology resource announcements Table SARS_CoV_2 A18253G 0 7 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. A23403G 2021 Microbiology resource announcements Table SARS_CoV_2 A23403G 0 7 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. A24774T 2021 Microbiology resource announcements Table SARS_CoV_2 A24774T 0 7 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. A28055G 2021 Microbiology resource announcements Table SARS_CoV_2 A28055G 0 7 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. A3143V 2021 Microbiology resource announcements Table SARS_CoV_2 A3143V 0 6 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. A4372G 2021 Microbiology resource announcements Table SARS_CoV_2 A4372G 0 6 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. A5608G 2021 Microbiology resource announcements Table SARS_CoV_2 A5608G 0 6 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. C14408T 2021 Microbiology resource announcements Table SARS_CoV_2 C14408T 0 7 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. C16626T 2021 Microbiology resource announcements Table SARS_CoV_2 C16626T 0 7 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. C18555T 2021 Microbiology resource announcements Table SARS_CoV_2 C18555T 0 7 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. C18877T 2021 Microbiology resource announcements Table SARS_CoV_2 C18877T 0 7 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. C23230T 2021 Microbiology resource announcements Table SARS_CoV_2 C23230T 0 7 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. C241T 2021 Microbiology resource announcements Table SARS_CoV_2 C241T 0 5 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. C24784T 2021 Microbiology resource announcements Table SARS_CoV_2 C24784T 0 7 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. C26010T 2021 Microbiology resource announcements Table SARS_CoV_2 C26010T 0 7 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. C2695T 2021 Microbiology resource announcements Table SARS_CoV_2 C2695T 0 6 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. C3037T 2021 Microbiology resource announcements Table SARS_CoV_2 C3037T 0 6 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. C313T 2021 Microbiology resource announcements Table SARS_CoV_2 C313T 0 5 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. C5700A 2021 Microbiology resource announcements Table SARS_CoV_2 C5700A 0 6 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. C9693T 2021 Microbiology resource announcements Table SARS_CoV_2 C9693T 0 6 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. D614G 2021 Microbiology resource announcements Table SARS_CoV_2 D614G 0 5 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. G204R 2021 Microbiology resource announcements Table SARS_CoV_2 G204R 0 5 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. G21468T 2021 Microbiology resource announcements Table SARS_CoV_2 G21468T 0 7 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. G28881A 2021 Microbiology resource announcements Table SARS_CoV_2 G28881A 0 7 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. G28882A 2021 Microbiology resource announcements Table SARS_CoV_2 G28882A 0 7 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. G28883C 2021 Microbiology resource announcements Table SARS_CoV_2 G28883C 0 7 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. G50N 2021 Microbiology resource announcements Table SARS_CoV_2 G50N 0 4 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. G8371T 2021 Microbiology resource announcements Table SARS_CoV_2 G8371T 0 6 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. G9190T 2021 Microbiology resource announcements Table SARS_CoV_2 G9190T 0 6 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. M15967V 2021 Microbiology resource announcements Table SARS_CoV_2 M15967V 0 7 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. M2667I 2021 Microbiology resource announcements Table SARS_CoV_2 M2667I 0 6 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. P314L 2021 Microbiology resource announcements Table SARS_CoV_2 P314L 0 5 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. Q1071L 2021 Microbiology resource announcements Table SARS_CoV_2 Q1071L 0 6 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. Q2702H 2021 Microbiology resource announcements Table SARS_CoV_2 Q2702H 0 6 33574104 Coding-Complete Genome Sequences of NITMA1086 and NITMA1139, Two SARS-CoV-2 Isolates from Belagavi District, Karnataka State, India, Harboring the D614G Mutation. R203K 2021 Microbiology resource announcements Table SARS_CoV_2 R203K 0 5 33579792 The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2. D614G 2021 Proc Natl Acad Sci U S A Table SARS_CoV_2 D614G 0 5 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. A23403G 2021 Briefings in bioinformatics Table SARS_CoV_2 A23403G 0 7 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. A208G 2021 Microbial pathogenesis Table SARS_CoV_2 A208G 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. A320V 2021 Microbial pathogenesis Table SARS_CoV_2 A320V 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. A361V 2021 Microbial pathogenesis Table SARS_CoV_2 A361V 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. A994D 2021 Microbial pathogenesis Table SARS_CoV_2 A994D 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. D614G 2021 Microbial pathogenesis Table SARS_CoV_2 D614G 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. D75E 2021 Microbial pathogenesis Table SARS_CoV_2 D75E 0 4 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. E204D 2021 Microbial pathogenesis Table SARS_CoV_2 E204D 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. F233L 2021 Microbial pathogenesis Table SARS_CoV_2 F233L 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. G15S 2021 Microbial pathogenesis Table SARS_CoV_2 G15S 0 4 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. G204R 2021 Microbial pathogenesis Table SARS_CoV_2 G204R 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. G212V 2021 Microbial pathogenesis Table SARS_CoV_2 G212V 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. G243C 2021 Microbial pathogenesis Table SARS_CoV_2 G243C 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. G25C 2021 Microbial pathogenesis Table SARS_CoV_2 G25C 0 4 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. G44V 2021 Microbial pathogenesis Table SARS_CoV_2 G44V 0 4 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. L37F 2021 Microbial pathogenesis Table SARS_CoV_2 L37F 0 4 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. L84S 2021 Microbial pathogenesis Table SARS_CoV_2 L84S 0 4 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. M129I 2021 Microbial pathogenesis Table SARS_CoV_2 M129I 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. M666I 2021 Microbial pathogenesis Table SARS_CoV_2 M666I 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. P109L 2021 Microbial pathogenesis Table SARS_CoV_2 P109L 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. P153L 2021 Microbial pathogenesis Table SARS_CoV_2 P153L 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. P236S 2021 Microbial pathogenesis Table SARS_CoV_2 P236S 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. P323L 2021 Microbial pathogenesis Table SARS_CoV_2 P323L 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. P412S 2021 Microbial pathogenesis Table SARS_CoV_2 P412S 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. Q57H 2021 Microbial pathogenesis Table SARS_CoV_2 Q57H 0 4 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. Q677H 2021 Microbial pathogenesis Table SARS_CoV_2 Q677H 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. R203K 2021 Microbial pathogenesis Table SARS_CoV_2 R203K 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. R51H 2021 Microbial pathogenesis Table SARS_CoV_2 R51H 0 4 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. S1147L 2021 Microbial pathogenesis Table SARS_CoV_2 S1147L 0 6 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. S193I 2021 Microbial pathogenesis Table SARS_CoV_2 S193I 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. S194L 2021 Microbial pathogenesis Table SARS_CoV_2 S194L 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. S25L 2021 Microbial pathogenesis Table SARS_CoV_2 S25L 0 4 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. S481L 2021 Microbial pathogenesis Table SARS_CoV_2 S481L 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. T1482I 2021 Microbial pathogenesis Table SARS_CoV_2 T1482I 0 6 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. T148I 2021 Microbial pathogenesis Table SARS_CoV_2 T148I 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. T393I 2021 Microbial pathogenesis Table SARS_CoV_2 T393I 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. T428I 2021 Microbial pathogenesis Table SARS_CoV_2 T428I 0 5 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. T73I 2021 Microbial pathogenesis Table SARS_CoV_2 T73I 0 4 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. T85I 2021 Microbial pathogenesis Table SARS_CoV_2 T85I 0 4 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. T95I 2021 Microbial pathogenesis Table SARS_CoV_2 T95I 0 4 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. V62L 2021 Microbial pathogenesis Table SARS_CoV_2 V62L 0 4 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. 1059C>T 2021 Communications biology Table SARS_CoV_2 C1059T 0 7 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. 14408C>T 2021 Communications biology Table SARS_CoV_2 C14408T 0 8 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. 17747C>T 2021 Communications biology Table SARS_CoV_2 C17747T 0 8 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. 17858A>G 2021 Communications biology Table SARS_CoV_2 A17858G 0 8 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. 23403A>G 2021 Communications biology Table SARS_CoV_2 A23403G 0 8 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. 25563G>T 2021 Communications biology Table SARS_CoV_2 G25563T 0 8 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. 27964C>T 2021 Communications biology Table SARS_CoV_2 C27964T 0 8 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. 28144T>C 2021 Communications biology Table SARS_CoV_2 T28144C 0 8 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. 28881G>A 2021 Communications biology Table SARS_CoV_2 G28881A 0 8 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. 28882G>A 2021 Communications biology Table SARS_CoV_2 G28882A 0 8 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. 28883G>C 2021 Communications biology Table SARS_CoV_2 G28883C 0 8 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. D614G 2021 Communications biology Table SARS_CoV_2 D614G 0 5 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. G204R 2021 Communications biology Table SARS_CoV_2 G204R 0 5 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. L84S 2021 Communications biology Table SARS_CoV_2 L84S 0 4 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. P323L 2021 Communications biology Table SARS_CoV_2 P323L 0 5 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. P504L 2021 Communications biology Table SARS_CoV_2 P504L 0 5 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Q57H 2021 Communications biology Table SARS_CoV_2 Q57H 0 4 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. R203K 2021 Communications biology Table SARS_CoV_2 R203K 0 5 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. S24L 2021 Communications biology Table SARS_CoV_2 S24L 0 4 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. T85I 2021 Communications biology Table SARS_CoV_2 T85I 0 4 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Y541C 2021 Communications biology Table SARS_CoV_2 Y541C 0 5 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. A13498G 2020 Frontiers in genetics Table SARS_CoV_2 A13498G 0 7 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. A23403G 2020 Frontiers in genetics Table SARS_CoV_2 A23403G 0 7 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. C10376T 2020 Frontiers in genetics Table SARS_CoV_2 C10376T 0 7 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. C14408T 2020 Frontiers in genetics Table SARS_CoV_2 C14408T 0 7 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. C27476T 2020 Frontiers in genetics Table SARS_CoV_2 C27476T 0 7 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. C28854T 2020 Frontiers in genetics Table SARS_CoV_2 C28854T 0 7 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. D614G 2020 Frontiers in genetics Table SARS_CoV_2 D614G 0 5 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. G1167V 2020 Frontiers in genetics Table SARS_CoV_2 G1167V 0 6 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. G19069T 2020 Frontiers in genetics Table SARS_CoV_2 G19069T 0 7 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. G204R 2020 Frontiers in genetics Table SARS_CoV_2 G204R 0 5 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. G25062T 2020 Frontiers in genetics Table SARS_CoV_2 G25062T 0 7 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. G25563T 2020 Frontiers in genetics Table SARS_CoV_2 G25563T 0 7 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. G28179C 2020 Frontiers in genetics Table SARS_CoV_2 G28179C 0 7 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. G28881A 2020 Frontiers in genetics Table SARS_CoV_2 G28881A 0 7 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. G28882A 2020 Frontiers in genetics Table SARS_CoV_2 G28882A 0 7 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. G28883C 2020 Frontiers in genetics Table SARS_CoV_2 G28883C 0 7 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. G96R 2020 Frontiers in genetics Table SARS_CoV_2 G96R 0 4 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. P3371S 2020 Frontiers in genetics Table SARS_CoV_2 P3371S 0 6 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. P4715L 2020 Frontiers in genetics Table SARS_CoV_2 P4715L 0 6 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. Q57H 2020 Frontiers in genetics Table SARS_CoV_2 Q57H 0 4 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. R203K 2020 Frontiers in genetics Table SARS_CoV_2 R203K 0 5 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. S194L 2020 Frontiers in genetics Table SARS_CoV_2 S194L 0 5 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. T28I 2020 Frontiers in genetics Table SARS_CoV_2 T28I 0 4 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. T4412A 2020 Frontiers in genetics Table SARS_CoV_2 T4412A 0 6 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. S477G 2021 Scientific reports Table SARS_CoV_2 S477G 0 5 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. S477N 2021 Scientific reports Table SARS_CoV_2 S477N 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. A123T 2021 medRxiv Table SARS_CoV_2 A123T 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. C136G/Y 2021 medRxiv Table SARS_CoV_2 C136G;C136Y 0;0 7;7 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. C136Y 2021 medRxiv Table SARS_CoV_2 C136Y 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. C15F 2021 medRxiv Table SARS_CoV_2 C15F 0 4 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. C15S 2021 medRxiv Table SARS_CoV_2 C15S 0 4 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. C15W 2021 medRxiv Table SARS_CoV_2 C15W 0 4 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. E484K 2021 medRxiv Table SARS_CoV_2 E484K 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. E484Q 2021 medRxiv Table SARS_CoV_2 E484Q 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. F140C 2021 medRxiv Table SARS_CoV_2 F140C 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. F140S 2021 medRxiv Table SARS_CoV_2 F140S 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. F490L 2021 medRxiv Table SARS_CoV_2 F490L 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. F490S 2021 medRxiv Table SARS_CoV_2 F490S 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. G142C/D 2021 medRxiv Table SARS_CoV_2 G142C;G142D 0;0 7;7 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. G142D 2021 medRxiv Table SARS_CoV_2 G142D 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. G252C 2021 medRxiv Table SARS_CoV_2 G252C 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. G476S 2021 medRxiv Table SARS_CoV_2 G476S 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. H146Y 2021 medRxiv Table SARS_CoV_2 H146Y 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. K147Q/T 2021 medRxiv Table SARS_CoV_2 K147Q;K147T 0;0 7;7 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. K147T 2021 medRxiv Table SARS_CoV_2 K147T 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. K147T/Q 2021 medRxiv Table SARS_CoV_2 K147Q;K147T 0;0 7;7 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. L141S 2021 medRxiv Table SARS_CoV_2 L141S 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. L18P 2021 medRxiv Table SARS_CoV_2 L18P 0 4 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. L244S 2021 medRxiv Table SARS_CoV_2 L244S 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. L455F 2021 medRxiv Table SARS_CoV_2 L455F 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. P251L 2021 medRxiv Table SARS_CoV_2 P251L 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. R158G 2021 medRxiv Table SARS_CoV_2 R158G 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. R246A 2021 medRxiv Table SARS_CoV_2 R246A 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. R246G 2021 medRxiv Table SARS_CoV_2 R246G 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. S12P 2021 medRxiv Table SARS_CoV_2 S12P 0 4 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. S494P 2021 medRxiv Table SARS_CoV_2 S494P 0 5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Y144C/N 2021 medRxiv Table SARS_CoV_2 Y144C;Y144N 0;0 7;7 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Y144del 2021 medRxiv Table SARS_CoV_2 Y144del 0 7 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Y28C 2021 medRxiv Table SARS_CoV_2 Y28C 0 4 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Y449N 2021 medRxiv Table SARS_CoV_2 Y449N 0 5 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. E3006E 2021 Cell Table SARS_CoV_2 E3006E 0 6 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. N439K 2021 Cell Table SARS_CoV_2 N439K 0 5 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. P0702L 2021 Cell Table SARS_CoV_2 P0702L 0 6 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. P0704L 2021 Cell Table SARS_CoV_2 P0704L 0 6 33628442 Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. D614G 2021 Clinical & translational immunology Table SARS_CoV_2 D614G 0 5 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. D614G 2021 Scientific reports Table SARS_CoV_2 D614G 0 5 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. H49Y 2021 Scientific reports Table SARS_CoV_2 H49Y 0 4 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. T573I 2021 Scientific reports Table SARS_CoV_2 T573I 0 5 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. A191V 2021 Saudi journal of biological sciences Table SARS_CoV_2 A191V 0 5 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. N142S 2021 Saudi journal of biological sciences Table SARS_CoV_2 N142S 0 5 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. T190I 2021 Saudi journal of biological sciences Table SARS_CoV_2 T190I 0 5 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. Y54C 2021 Saudi journal of biological sciences Table SARS_CoV_2 Y54C 0 4 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. D614G 2021 Cell Table SARS_CoV_2 D614G 0 5 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. E2621X 2021 Cell Table SARS_CoV_2 E2621X 0 6 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. M0491L 2021 Cell Table SARS_CoV_2 M0491L 0 6 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. D614G 2021 Biochemical and biophysical research communications Table SARS_CoV_2 D614G 0 5 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. E106stop 2021 Biochemical and biophysical research communications Table SARS_CoV_2 E106X 0 8 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. E110stop 2021 Biochemical and biophysical research communications Table SARS_CoV_2 E110X 0 8 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. E64stop 2021 Biochemical and biophysical research communications Table SARS_CoV_2 E64X 0 7 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. P1263L 2021 Biochemical and biophysical research communications Table SARS_CoV_2 P1263L 0 6 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. V367F 2021 Biochemical and biophysical research communications Table SARS_CoV_2 V367F 0 5 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. Y145H 2021 Biochemical and biophysical research communications Table SARS_CoV_2 Y145H 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. A23138G 2021 Infection, genetics and evolution Table SARS_CoV_2 A23138G 0 7 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. A829T 2021 Infection, genetics and evolution Table SARS_CoV_2 A829T 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. C14540T 2021 Infection, genetics and evolution Table SARS_CoV_2 C14540T 0 7 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. C17482T 2021 Infection, genetics and evolution Table SARS_CoV_2 C17482T 0 7 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. C28589T 2021 Infection, genetics and evolution Table SARS_CoV_2 C28589T 0 7 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. C28598T 2021 Infection, genetics and evolution Table SARS_CoV_2 C28598T 0 7 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. C2912T 2021 Infection, genetics and evolution Table SARS_CoV_2 C2912T 0 6 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. C794T 2021 Infection, genetics and evolution Table SARS_CoV_2 C794T 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. D614G 2021 Infection, genetics and evolution Table SARS_CoV_2 D614G 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. D75E 2021 Infection, genetics and evolution Table SARS_CoV_2 D75E 0 4 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. F308Y 2021 Infection, genetics and evolution Table SARS_CoV_2 F308Y 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. G10818T 2021 Infection, genetics and evolution Table SARS_CoV_2 G10818T 0 7 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. G196V 2021 Infection, genetics and evolution Table SARS_CoV_2 G196V 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. G19869T 2021 Infection, genetics and evolution Table SARS_CoV_2 G19869T 0 7 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. G204R 2021 Infection, genetics and evolution Table SARS_CoV_2 G204R 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. G23782A 2021 Infection, genetics and evolution Table SARS_CoV_2 G23782A 0 7 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. G25298T 2021 Infection, genetics and evolution Table SARS_CoV_2 G25298T 0 7 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. G25714T 2021 Infection, genetics and evolution Table SARS_CoV_2 G25714T 0 7 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. G25879T 2021 Infection, genetics and evolution Table SARS_CoV_2 G25879T 0 7 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. G27812C 2021 Infection, genetics and evolution Table SARS_CoV_2 G27812C 0 7 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. L37F 2021 Infection, genetics and evolution Table SARS_CoV_2 L37F 0 4 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. L84S 2021 Infection, genetics and evolution Table SARS_CoV_2 L84S 0 4 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. P153L 2021 Infection, genetics and evolution Table SARS_CoV_2 P153L 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. P504L 2021 Infection, genetics and evolution Table SARS_CoV_2 P504L 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Q57H 2021 Infection, genetics and evolution Table SARS_CoV_2 Q57H 0 4 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. R203K 2021 Infection, genetics and evolution Table SARS_CoV_2 R203K 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. S194L 2021 Infection, genetics and evolution Table SARS_CoV_2 S194L 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. S197L 2021 Infection, genetics and evolution Table SARS_CoV_2 S197L 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. T225A 2021 Infection, genetics and evolution Table SARS_CoV_2 T225A 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. T27879C 2021 Infection, genetics and evolution Table SARS_CoV_2 T27879C 0 7 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. T442I 2021 Infection, genetics and evolution Table SARS_CoV_2 T442I 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. T455I 2021 Infection, genetics and evolution Table SARS_CoV_2 T455I 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. T85I 2021 Infection, genetics and evolution Table SARS_CoV_2 T85I 0 4 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. T9212A 2021 Infection, genetics and evolution Table SARS_CoV_2 T9212A 0 6 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. V172L 2021 Infection, genetics and evolution Table SARS_CoV_2 V172L 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. V251F 2021 Infection, genetics and evolution Table SARS_CoV_2 V251F 0 5 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. V62L 2021 Infection, genetics and evolution Table SARS_CoV_2 V62L 0 4 33680867 COVID-19 outbreak in Malaysia: Decoding D614G mutation of SARS-CoV-2 virus isolated from an asymptomatic case in Pahang. D614G 2022 Materials today. Proceedings Table SARS_CoV_2 D614G 0 5 33681755 The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant. N501Y 2021 Medicine in drug discovery Table SARS_CoV_2 N501Y 0 5 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. A152S 2021 Computers in biology and medicine Table SARS_CoV_2 A152S 0 5 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. A1812D 2021 Computers in biology and medicine Table SARS_CoV_2 A1812D 0 6 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. A4489V 2021 Computers in biology and medicine Table SARS_CoV_2 A4489V 0 6 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. A4798V 2021 Computers in biology and medicine Table SARS_CoV_2 A4798V 0 6 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. A930V 2021 Computers in biology and medicine Table SARS_CoV_2 A930V 0 5 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. D614G 2021 Computers in biology and medicine Table SARS_CoV_2 D614G 0 5 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. F1089V 2021 Computers in biology and medicine Table SARS_CoV_2 F1089V 0 6 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. G204R 2021 Computers in biology and medicine Table SARS_CoV_2 G204R 0 5 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. G519S 2021 Computers in biology and medicine Table SARS_CoV_2 G519S 0 5 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. H1088R 2021 Computers in biology and medicine Table SARS_CoV_2 H1088R 0 6 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. I476V 2021 Computers in biology and medicine Table SARS_CoV_2 I476V 0 5 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. I671T 2021 Computers in biology and medicine Table SARS_CoV_2 I671T 0 5 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. L204F 2021 Computers in biology and medicine Table SARS_CoV_2 L204F 0 5 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. L3606F 2021 Computers in biology and medicine Table SARS_CoV_2 L3606F 0 6 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. L54F 2021 Computers in biology and medicine Table SARS_CoV_2 L54F 0 4 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. L84S 2021 Computers in biology and medicine Table SARS_CoV_2 L84S 0 4 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. N5928H 2021 Computers in biology and medicine Table SARS_CoV_2 N5928H 0 6 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. P13L 2021 Computers in biology and medicine Table SARS_CoV_2 P13L 0 4 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. P2144S 2021 Computers in biology and medicine Table SARS_CoV_2 P2144S 0 6 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. P2739L 2021 Computers in biology and medicine Table SARS_CoV_2 P2739L 0 6 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. P42R 2021 Computers in biology and medicine Table SARS_CoV_2 P42R 0 4 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. P4715L 2021 Computers in biology and medicine Table SARS_CoV_2 P4715L 0 6 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. P5624L 2021 Computers in biology and medicine Table SARS_CoV_2 P5624L 0 6 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Q57H 2021 Computers in biology and medicine Table SARS_CoV_2 Q57H 0 4 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Q677H 2021 Computers in biology and medicine Table SARS_CoV_2 Q677H 0 5 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. R203K 2021 Computers in biology and medicine Table SARS_CoV_2 R203K 0 5 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. R407I 2021 Computers in biology and medicine Table SARS_CoV_2 R407I 0 5 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. S194L 2021 Computers in biology and medicine Table SARS_CoV_2 S194L 0 5 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. S2015R 2021 Computers in biology and medicine Table SARS_CoV_2 S2015R 0 6 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. T2016K 2021 Computers in biology and medicine Table SARS_CoV_2 T2016K 0 6 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. T5538I 2021 Computers in biology and medicine Table SARS_CoV_2 T5538I 0 6 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. V3475F 2021 Computers in biology and medicine Table SARS_CoV_2 V3475F 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. A119S 2021 Reviews in medical virology Table SARS_CoV_2 A119S 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. A12964G 2021 Reviews in medical virology Table SARS_CoV_2 A12964G 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. A1708D 2021 Reviews in medical virology Table SARS_CoV_2 A1708D 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. A23063T 2021 Reviews in medical virology Table SARS_CoV_2 A23063T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. A23403G 2021 Reviews in medical virology Table SARS_CoV_2 A23403G 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. A2529V 2021 Reviews in medical virology Table SARS_CoV_2 A2529V 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. A27853C 2021 Reviews in medical virology Table SARS_CoV_2 A27853C 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. A28111G 2021 Reviews in medical virology Table SARS_CoV_2 A28111G 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. A5648C 2021 Reviews in medical virology Table SARS_CoV_2 A5648C 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. A570D 2021 Reviews in medical virology Table SARS_CoV_2 A570D 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. A598S 2021 Reviews in medical virology Table SARS_CoV_2 A598S 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. A6319G 2021 Reviews in medical virology Table SARS_CoV_2 A6319G 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. A6613G 2021 Reviews in medical virology Table SARS_CoV_2 A6613G 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. A701V 2021 Reviews in medical virology Table SARS_CoV_2 A701V 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C1059T 2021 Reviews in medical virology Table SARS_CoV_2 C1059T 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C12778T 2021 Reviews in medical virology Table SARS_CoV_2 C12778T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C13860T 2021 Reviews in medical virology Table SARS_CoV_2 C13860T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C14408T 2021 Reviews in medical virology Table SARS_CoV_2 C14408T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C174G 2021 Reviews in medical virology Table SARS_CoV_2 C174G 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C19602T 2021 Reviews in medical virology Table SARS_CoV_2 C19602T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C23271A 2021 Reviews in medical virology Table SARS_CoV_2 C23271A 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C23604A 2021 Reviews in medical virology Table SARS_CoV_2 C23604A 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C23709T 2021 Reviews in medical virology Table SARS_CoV_2 C23709T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C241T 2021 Reviews in medical virology Table SARS_CoV_2 C241T 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C2749T 2021 Reviews in medical virology Table SARS_CoV_2 C2749T 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C27972T 2021 Reviews in medical virology Table SARS_CoV_2 C27972T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C28512G 2021 Reviews in medical virology Table SARS_CoV_2 C28512G 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C28977T 2021 Reviews in medical virology Table SARS_CoV_2 C28977T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C29722T 2021 Reviews in medical virology Table SARS_CoV_2 C29722T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C29754T 2021 Reviews in medical virology Table SARS_CoV_2 C29754T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C3037T 2021 Reviews in medical virology Table SARS_CoV_2 C3037T 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C3267T 2021 Reviews in medical virology Table SARS_CoV_2 C3267T 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C3828T 2021 Reviews in medical virology Table SARS_CoV_2 C3828T 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C6573T 2021 Reviews in medical virology Table SARS_CoV_2 C6573T 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C7600T 2021 Reviews in medical virology Table SARS_CoV_2 C7600T 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C7851T 2021 Reviews in medical virology Table SARS_CoV_2 C7851T 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. C8782T 2021 Reviews in medical virology Table SARS_CoV_2 C8782T 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. D1118H 2021 Reviews in medical virology Table SARS_CoV_2 D1118H 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. D138Y 2021 Reviews in medical virology Table SARS_CoV_2 D138Y 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. D215G 2021 Reviews in medical virology Table SARS_CoV_2 D215G 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. D614G 2021 Reviews in medical virology Table SARS_CoV_2 D614G 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. D80A 2021 Reviews in medical virology Table SARS_CoV_2 D80A 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. E33A 2021 Reviews in medical virology Table SARS_CoV_2 E33A 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. E484K 2021 Reviews in medical virology Table SARS_CoV_2 E484K 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. E92K 2021 Reviews in medical virology Table SARS_CoV_2 E92K 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. F106F 2021 Reviews in medical virology Table SARS_CoV_2 F106F 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. F3605L 2021 Reviews in medical virology Table SARS_CoV_2 F3605L 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. F490S 2021 Reviews in medical virology Table SARS_CoV_2 F490S 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. G11083T 2021 Reviews in medical virology Table SARS_CoV_2 G11083T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. G1264T 2021 Reviews in medical virology Table SARS_CoV_2 G1264T 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. G17259T 2021 Reviews in medical virology Table SARS_CoV_2 G17259T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. G19656T 2021 Reviews in medical virology Table SARS_CoV_2 G19656T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. G24914C 2021 Reviews in medical virology Table SARS_CoV_2 G24914C 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. G251V 2021 Reviews in medical virology Table SARS_CoV_2 G251V 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. G25563T 2021 Reviews in medical virology Table SARS_CoV_2 G25563T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. G26144T 2021 Reviews in medical virology Table SARS_CoV_2 G26144T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. G28048T 2021 Reviews in medical virology Table SARS_CoV_2 G28048T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. G28628T 2021 Reviews in medical virology Table SARS_CoV_2 G28628T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. G28975T 2021 Reviews in medical virology Table SARS_CoV_2 G28975T 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. GGG28881AAC 2021 Reviews in medical virology Table SARS_CoV_2 G28881A;G28881C 0;0 11;11 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. H655Y 2021 Reviews in medical virology Table SARS_CoV_2 H655Y 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. I2230T 2021 Reviews in medical virology Table SARS_CoV_2 I2230T 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. I692V 2021 Reviews in medical virology Table SARS_CoV_2 I692V 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. K1655N 2021 Reviews in medical virology Table SARS_CoV_2 K1655N 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. K1795Q 2021 Reviews in medical virology Table SARS_CoV_2 K1795Q 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. K417N 2021 Reviews in medical virology Table SARS_CoV_2 K417N 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. K417T 2021 Reviews in medical virology Table SARS_CoV_2 K417T 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. L18F 2021 Reviews in medical virology Table SARS_CoV_2 L18F 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. L3468V 2021 Reviews in medical virology Table SARS_CoV_2 L3468V 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. L37F 2021 Reviews in medical virology Table SARS_CoV_2 L37F 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. L452R 2021 Reviews in medical virology Table SARS_CoV_2 L452R 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. L84S 2021 Reviews in medical virology Table SARS_CoV_2 L84S 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. M1229I 2021 Reviews in medical virology Table SARS_CoV_2 M1229I 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. M234I 2021 Reviews in medical virology Table SARS_CoV_2 M234I 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. M541V 2021 Reviews in medical virology Table SARS_CoV_2 M541V 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. N439K 2021 Reviews in medical virology Table SARS_CoV_2 N439K 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. N501Y 2021 Reviews in medical virology Table SARS_CoV_2 N501Y 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. P26S 2021 Reviews in medical virology Table SARS_CoV_2 P26S 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. P314L 2021 Reviews in medical virology Table SARS_CoV_2 P314L 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. P681H 2021 Reviews in medical virology Table SARS_CoV_2 P681H 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. P71L 2021 Reviews in medical virology Table SARS_CoV_2 P71L 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. P80R 2021 Reviews in medical virology Table SARS_CoV_2 P80R 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. Q57H 2021 Reviews in medical virology Table SARS_CoV_2 Q57H 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. Q77E 2021 Reviews in medical virology Table SARS_CoV_2 Q77E 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. R190S 2021 Reviews in medical virology Table SARS_CoV_2 R190S 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. R246I 2021 Reviews in medical virology Table SARS_CoV_2 R246I 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. R52I 2021 Reviews in medical virology Table SARS_CoV_2 R52I 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. S1188L 2021 Reviews in medical virology Table SARS_CoV_2 S1188L 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. S13I 2021 Reviews in medical virology Table SARS_CoV_2 S13I 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. S2103F 2021 Reviews in medical virology Table SARS_CoV_2 S2103F 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. S235F 2021 Reviews in medical virology Table SARS_CoV_2 S235F 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. S477N 2021 Reviews in medical virology Table SARS_CoV_2 S477N 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. S494P 2021 Reviews in medical virology Table SARS_CoV_2 S494P 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. S5665I 2021 Reviews in medical virology Table SARS_CoV_2 S5665I 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. S76S 2021 Reviews in medical virology Table SARS_CoV_2 S76S 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. S982A 2021 Reviews in medical virology Table SARS_CoV_2 S982A 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. T1001I 2021 Reviews in medical virology Table SARS_CoV_2 T1001I 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. T1027I 2021 Reviews in medical virology Table SARS_CoV_2 T1027I 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. T10667G 2021 Reviews in medical virology Table SARS_CoV_2 T10667G 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. T11078C 2021 Reviews in medical virology Table SARS_CoV_2 T11078C 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. T205I 2021 Reviews in medical virology Table SARS_CoV_2 T205I 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. T20N 2021 Reviews in medical virology Table SARS_CoV_2 T20N 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. T24506G 2021 Reviews in medical virology Table SARS_CoV_2 T24506G 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. T253G 2021 Reviews in medical virology Table SARS_CoV_2 T253G 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. T28144C 2021 Reviews in medical virology Table SARS_CoV_2 T28144C 0 7 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. T4532I 2021 Reviews in medical virology Table SARS_CoV_2 T4532I 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. T716I 2021 Reviews in medical virology Table SARS_CoV_2 T716I 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. T733C 2021 Reviews in medical virology Table SARS_CoV_2 T733C 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. T85I 2021 Reviews in medical virology Table SARS_CoV_2 T85I 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. T95I 2021 Reviews in medical virology Table SARS_CoV_2 T95I 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. V1176F 2021 Reviews in medical virology Table SARS_CoV_2 V1176F 0 6 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. V49L 2021 Reviews in medical virology Table SARS_CoV_2 V49L 0 4 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. V720I 2021 Reviews in medical virology Table SARS_CoV_2 V720I 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. W152C 2021 Reviews in medical virology Table SARS_CoV_2 W152C 0 5 33724631 Neutralising antibody escape of SARS-CoV-2 spike protein: Risk assessment for antibody-based Covid-19 therapeutics and vaccines. Y73C 2021 Reviews in medical virology Table SARS_CoV_2 Y73C 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. A159V 2021 Briefings in bioinformatics Table SARS_CoV_2 A159V 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. A1769G 2021 Briefings in bioinformatics Table SARS_CoV_2 A1769G 0 6 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. A320V 2021 Briefings in bioinformatics Table SARS_CoV_2 A320V 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. A380V 2021 Briefings in bioinformatics Table SARS_CoV_2 A380V 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. A58T 2021 Briefings in bioinformatics Table SARS_CoV_2 A58T 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. A97V 2021 Briefings in bioinformatics Table SARS_CoV_2 A97V 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. A994D 2021 Briefings in bioinformatics Table SARS_CoV_2 A994D 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. D1121G 2021 Briefings in bioinformatics Table SARS_CoV_2 D1121G 0 6 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. D614G 2021 Briefings in bioinformatics Table SARS_CoV_2 D614G 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. E583D 2021 Briefings in bioinformatics Table SARS_CoV_2 E583D 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. F308Y 2021 Briefings in bioinformatics Table SARS_CoV_2 F308Y 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. F506L 2021 Briefings in bioinformatics Table SARS_CoV_2 F506L 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. G15S 2021 Briefings in bioinformatics Table SARS_CoV_2 G15S 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. G196V 2021 Briefings in bioinformatics Table SARS_CoV_2 G196V 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. G204R 2021 Briefings in bioinformatics Table SARS_CoV_2 G204R 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. G212D 2021 Briefings in bioinformatics Table SARS_CoV_2 G212D 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. G251V 2021 Briefings in bioinformatics Table SARS_CoV_2 G251V 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. G339S 2021 Briefings in bioinformatics Table SARS_CoV_2 G339S 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. I559V 2021 Briefings in bioinformatics Table SARS_CoV_2 I559V 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. K77M 2021 Briefings in bioinformatics Table SARS_CoV_2 K77M 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. L329I 2021 Briefings in bioinformatics Table SARS_CoV_2 L329I 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. L37F 2021 Briefings in bioinformatics Table SARS_CoV_2 L37F 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. L54F 2021 Briefings in bioinformatics Table SARS_CoV_2 L54F 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. L84S 2021 Briefings in bioinformatics Table SARS_CoV_2 L84S 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. M33I 2021 Briefings in bioinformatics Table SARS_CoV_2 M33I 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. N298H 2021 Briefings in bioinformatics Table SARS_CoV_2 N298H 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. N298I 2021 Briefings in bioinformatics Table SARS_CoV_2 N298I 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. N298T 2021 Briefings in bioinformatics Table SARS_CoV_2 N298T 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. P13L 2021 Briefings in bioinformatics Table SARS_CoV_2 P13L 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. P153L 2021 Briefings in bioinformatics Table SARS_CoV_2 P153L 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. P323L 2021 Briefings in bioinformatics Table SARS_CoV_2 P323L 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. P504L 2021 Briefings in bioinformatics Table SARS_CoV_2 P504L 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. P585S 2021 Briefings in bioinformatics Table SARS_CoV_2 P585S 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. Q198H 2021 Briefings in bioinformatics Table SARS_CoV_2 Q198H 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. Q57H 2021 Briefings in bioinformatics Table SARS_CoV_2 Q57H 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. Q677H 2021 Briefings in bioinformatics Table SARS_CoV_2 Q677H 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. R203K 2021 Briefings in bioinformatics Table SARS_CoV_2 R203K 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. R27C 2021 Briefings in bioinformatics Table SARS_CoV_2 R27C 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. R78M 2021 Briefings in bioinformatics Table SARS_CoV_2 R78M 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. S1197R 2021 Briefings in bioinformatics Table SARS_CoV_2 S1197R 0 6 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. S194L 2021 Briefings in bioinformatics Table SARS_CoV_2 S194L 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. S197L 2021 Briefings in bioinformatics Table SARS_CoV_2 S197L 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. S202T 2021 Briefings in bioinformatics Table SARS_CoV_2 S202T 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. S24L 2021 Briefings in bioinformatics Table SARS_CoV_2 S24L 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. S25L 2021 Briefings in bioinformatics Table SARS_CoV_2 S25L 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. S301F 2021 Briefings in bioinformatics Table SARS_CoV_2 S301F 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. S507G 2021 Briefings in bioinformatics Table SARS_CoV_2 S507G 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. S697F 2021 Briefings in bioinformatics Table SARS_CoV_2 S697F 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. S716I 2021 Briefings in bioinformatics Table SARS_CoV_2 S716I 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. T1198K 2021 Briefings in bioinformatics Table SARS_CoV_2 T1198K 0 6 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. T175M 2021 Briefings in bioinformatics Table SARS_CoV_2 T175M 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. T295I 2021 Briefings in bioinformatics Table SARS_CoV_2 T295I 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. T315N 2021 Briefings in bioinformatics Table SARS_CoV_2 T315N 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. T572I 2021 Briefings in bioinformatics Table SARS_CoV_2 T572I 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. T85I 2021 Briefings in bioinformatics Table SARS_CoV_2 T85I 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. V13L 2021 Briefings in bioinformatics Table SARS_CoV_2 V13L 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. V198I 2021 Briefings in bioinformatics Table SARS_CoV_2 V198I 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. V62L 2021 Briefings in bioinformatics Table SARS_CoV_2 V62L 0 4 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. V880I 2021 Briefings in bioinformatics Table SARS_CoV_2 V880I 0 5 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. Y541C 2021 Briefings in bioinformatics Table SARS_CoV_2 Y541C 0 5 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. E484K 2021 Cureus Table SARS_CoV_2 E484K 0 5 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. N501Y 2021 FEBS letters Table SARS_CoV_2 N501Y 0 5 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. E484K 2021 Cell Table SARS_CoV_2 E484K 0 5 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. K417N 2021 Cell Table SARS_CoV_2 K417N 0 5 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. N501Y 2021 Cell Table SARS_CoV_2 N501Y 0 5 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. A701V 2021 Cell Table SARS_CoV_2 A701V 0 5 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. D215G 2021 Cell Table SARS_CoV_2 D215G 0 5 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. D614G 2021 Cell Table SARS_CoV_2 D614G 0 5 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. E484K 2021 Cell Table SARS_CoV_2 E484K 0 5 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. K417N 2021 Cell Table SARS_CoV_2 K417N 0 5 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. L18F 2021 Cell Table SARS_CoV_2 L18F 0 4 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. L242H 2021 Cell Table SARS_CoV_2 L242H 0 5 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. N501Y 2021 Cell Table SARS_CoV_2 N501Y 0 5 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. R246I 2021 Cell Table SARS_CoV_2 R246I 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. A348S 2021 International journal of infectious diseases Table SARS_CoV_2 A348S 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. A454V 2021 International journal of infectious diseases Table SARS_CoV_2 A454V 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. A81V 2021 International journal of infectious diseases Table SARS_CoV_2 A81V 0 4 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. A94V 2021 International journal of infectious diseases Table SARS_CoV_2 A94V 0 4 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. D176D 2021 International journal of infectious diseases Table SARS_CoV_2 D176D 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. D614G 2021 International journal of infectious diseases Table SARS_CoV_2 D614G 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. E145E 2021 International journal of infectious diseases Table SARS_CoV_2 E145E 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. E19D 2021 International journal of infectious diseases Table SARS_CoV_2 E19D 0 4 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. E261D 2021 International journal of infectious diseases Table SARS_CoV_2 E261D 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. F106F 2021 International journal of infectious diseases Table SARS_CoV_2 F106F 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. F274F 2021 International journal of infectious diseases Table SARS_CoV_2 F274F 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. F430S 2021 International journal of infectious diseases Table SARS_CoV_2 F430S 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. I156I 2021 International journal of infectious diseases Table SARS_CoV_2 I156I 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. K1191N 2021 International journal of infectious diseases Table SARS_CoV_2 K1191N 0 6 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. K1804N 2021 International journal of infectious diseases Table SARS_CoV_2 K1804N 0 6 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. K270R 2021 International journal of infectious diseases Table SARS_CoV_2 K270R 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. L297L 2021 International journal of infectious diseases Table SARS_CoV_2 L297L 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. L828I 2021 International journal of infectious diseases Table SARS_CoV_2 L828I 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. M271K 2021 International journal of infectious diseases Table SARS_CoV_2 M271K 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. N1337N 2021 International journal of infectious diseases Table SARS_CoV_2 N1337N 0 6 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. N297D 2021 International journal of infectious diseases Table SARS_CoV_2 N297D 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. N619N 2021 International journal of infectious diseases Table SARS_CoV_2 N619N 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. P13L 2021 International journal of infectious diseases Table SARS_CoV_2 P13L 0 4 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. P314L 2021 International journal of infectious diseases Table SARS_CoV_2 P314L 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. P365L 2021 International journal of infectious diseases Table SARS_CoV_2 P365L 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. Q181K 2021 International journal of infectious diseases Table SARS_CoV_2 Q181K 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. Q57H 2021 International journal of infectious diseases Table SARS_CoV_2 Q57H 0 4 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. R217M 2021 International journal of infectious diseases Table SARS_CoV_2 R217M 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. S1038S 2021 International journal of infectious diseases Table SARS_CoV_2 S1038S 0 6 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. S116S 2021 International journal of infectious diseases Table SARS_CoV_2 S116S 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. S183Y 2021 International journal of infectious diseases Table SARS_CoV_2 S183Y 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. S71F 2021 International journal of infectious diseases Table SARS_CoV_2 S71F 0 4 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. T113I 2021 International journal of infectious diseases Table SARS_CoV_2 T113I 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. T205I 2021 International journal of infectious diseases Table SARS_CoV_2 T205I 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. V108V 2021 International journal of infectious diseases Table SARS_CoV_2 V108V 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. V228A 2021 International journal of infectious diseases Table SARS_CoV_2 V228A 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. Y285Y 2021 International journal of infectious diseases Table SARS_CoV_2 Y285Y 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. Y451Y 2021 International journal of infectious diseases Table SARS_CoV_2 Y451Y 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. Y537Y 2021 International journal of infectious diseases Table SARS_CoV_2 Y537Y 0 5 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. Y80Y 2021 International journal of infectious diseases Table SARS_CoV_2 Y80Y 0 4 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. Y88Y 2021 International journal of infectious diseases Table SARS_CoV_2 Y88Y 0 4 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. A602S 2021 Virus research Table SARS_CoV_2 A602S 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. A889V 2021 Virus research Table SARS_CoV_2 A889V 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. D1108N 2021 Virus research Table SARS_CoV_2 D1108N 0 6 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. D1774H 2021 Virus research Table SARS_CoV_2 D1774H 0 6 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. D179N 2021 Virus research Table SARS_CoV_2 D179N 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. D614 G 2021 Virus research Table SARS_CoV_2 D614G 0 6 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. D85E 2021 Virus research Table SARS_CoV_2 D85E 0 4 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. E120K 2021 Virus research Table SARS_CoV_2 E120K 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. E194Q 2021 Virus research Table SARS_CoV_2 E194Q 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. E242A 2021 Virus research Table SARS_CoV_2 E242A 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. E42A 2021 Virus research Table SARS_CoV_2 E42A 0 4 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. F217I 2021 Virus research Table SARS_CoV_2 F217I 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. G1691C 2021 Virus research Table SARS_CoV_2 G1691C 0 6 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. G42V 2021 Virus research Table SARS_CoV_2 G42V 0 4 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. G773A 2021 Virus research Table SARS_CoV_2 G773A 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. H145N 2021 Virus research Table SARS_CoV_2 H145N 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. I569S 2021 Virus research Table SARS_CoV_2 I569S 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. K84T 2021 Virus research Table SARS_CoV_2 K84T 0 4 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. L22I 2021 Virus research Table SARS_CoV_2 L22I 0 4 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. L373M 2021 Virus research Table SARS_CoV_2 L373M 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. N377D 2021 Virus research Table SARS_CoV_2 N377D 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. N39Y 2021 Virus research Table SARS_CoV_2 N39Y 0 4 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. P104R 2021 Virus research Table SARS_CoV_2 P104R 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. P38R 2021 Virus research Table SARS_CoV_2 P38R 0 4 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. Q62E 2021 Virus research Table SARS_CoV_2 Q62E 0 4 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. T80I 2021 Virus research Table SARS_CoV_2 T80I 0 4 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. V120L 2021 Virus research Table SARS_CoV_2 V120L 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. V121D 2021 Virus research Table SARS_CoV_2 V121D 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. V31E 2021 Virus research Table SARS_CoV_2 V31E 0 4 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. V469A 2021 Virus research Table SARS_CoV_2 V469A 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. V56A 2021 Virus research Table SARS_CoV_2 V56A 0 4 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. V843F 2021 Virus research Table SARS_CoV_2 V843F 0 5 33737154 Global and local mutations in Bangladeshi SARS-CoV-2 genomes. Y660F 2021 Virus research Table SARS_CoV_2 Y660F 0 5 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.-25C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C25T 0 8 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.-94C>A 2021 Microbiology resource announcements Table SARS_CoV_2 C94A 0 8 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.*4350G>C 2021 Microbiology resource announcements Table SARS_CoV_2 G4350C 0 10 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.11262G>T 2021 Microbiology resource announcements Table SARS_CoV_2 G11262T 0 10 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.12723G>T 2021 Microbiology resource announcements Table SARS_CoV_2 G12723T 0 10 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.1317C>A 2021 Microbiology resource announcements Table SARS_CoV_2 C1317A 0 9 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.14144C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C14144T 0 10 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.15334G>A 2021 Microbiology resource announcements Table SARS_CoV_2 G15334A 0 10 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.16840C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C16840T 0 10 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.17764G>T 2021 Microbiology resource announcements Table SARS_CoV_2 G17764T 0 10 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.1841A>G 2021 Microbiology resource announcements Table SARS_CoV_2 A1841G 0 9 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.20004A>G 2021 Microbiology resource announcements Table SARS_CoV_2 A20004G 0 10 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.20187C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C20187T 0 10 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.262C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C262T 0 8 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.2772C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C2772T 0 9 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.3348T>C 2021 Microbiology resource announcements Table SARS_CoV_2 T3348C 0 9 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.3388A>G 2021 Microbiology resource announcements Table SARS_CoV_2 A3388G 0 9 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.450T>C 2021 Microbiology resource announcements Table SARS_CoV_2 T450C 0 8 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.7502T>C 2021 Microbiology resource announcements Table SARS_CoV_2 T7502C 0 9 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. c.7782C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C7782T 0 9 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. p.Ala5922Ser 2021 Microbiology resource announcements Table SARS_CoV_2 A5922S 0 12 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. p.Arg150Arg 2021 Microbiology resource announcements Table SARS_CoV_2 R150R 0 11 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. p.Asn439Lys 2021 Microbiology resource announcements Table SARS_CoV_2 N439K 0 11 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. p.Asp614Gly 2021 Microbiology resource announcements Table SARS_CoV_2 D614G 0 11 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. p.His5614Tyr 2021 Microbiology resource announcements Table SARS_CoV_2 H5614Y 0 12 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. p.Ile1130Val 2021 Microbiology resource announcements Table SARS_CoV_2 I1130V 0 12 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. p.Ile2501Thr 2021 Microbiology resource announcements Table SARS_CoV_2 I2501T 0 12 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. p.Leu3754Phe 2021 Microbiology resource announcements Table SARS_CoV_2 L3754F 0 12 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. p.Leu88Leu 2021 Microbiology resource announcements Table SARS_CoV_2 L88L 0 10 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. p.Met4241Ile 2021 Microbiology resource announcements Table SARS_CoV_2 M4241I 0 12 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. p.Phe924Phe 2021 Microbiology resource announcements Table SARS_CoV_2 F924F 0 11 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. p.Pro4715Leu 2021 Microbiology resource announcements Table SARS_CoV_2 P4715L 0 12 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. p.Thr1116Thr 2021 Microbiology resource announcements Table SARS_CoV_2 T1116T 0 12 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. p.Tyr2594Tyr 2021 Microbiology resource announcements Table SARS_CoV_2 Y2594Y 0 12 33737349 First Report of a SARS-CoV-2 Genome Sequence with a Spike His69-Val70 Deletion and an Asn439Lys Mutation in Morocco. p.Val5112Ile 2021 Microbiology resource announcements Table SARS_CoV_2 V5112I 0 12 33738620 Clinical characteristics of SARS-CoV-2 by re-infection vs. reactivation: a case series from Iran. D614G 2021 European journal of clinical microbiology & infectious diseases Table SARS_CoV_2 D614G 0 5 33738620 Clinical characteristics of SARS-CoV-2 by re-infection vs. reactivation: a case series from Iran. L139L 2021 European journal of clinical microbiology & infectious diseases Table SARS_CoV_2 L139L 0 5 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. D614G 2021 PLoS pathogens Table SARS_CoV_2 D614G 0 5 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. D614G 2021 Cell Table SARS_CoV_2 D614G 0 5 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. E484K 2021 Cell Table SARS_CoV_2 E484K 0 5 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. K417N 2021 Cell Table SARS_CoV_2 K417N 0 5 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. N501Y 2021 Cell Table SARS_CoV_2 N501Y 0 5 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. A237T 2021 ACS omega Table SARS_CoV_2 A237T 0 5 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. D268del 2021 ACS omega Table SARS_CoV_2 D268del 0 7 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. D614G 2021 ACS omega Table SARS_CoV_2 D614G 0 5 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. D830A 2021 ACS omega Table SARS_CoV_2 D830A 0 5 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. E92K 2021 ACS omega Table SARS_CoV_2 E92K 0 4 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. F105S 2021 ACS omega Table SARS_CoV_2 F105S 0 5 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. L270F 2021 ACS omega Table SARS_CoV_2 L270F 0 5 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. L37F 2021 ACS omega Table SARS_CoV_2 L37F 0 4 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. L84S 2021 ACS omega Table SARS_CoV_2 L84S 0 4 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. M86I 2021 ACS omega Table SARS_CoV_2 M86I 0 4 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. N228K 2021 ACS omega Table SARS_CoV_2 N228K 0 5 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. P202L 2021 ACS omega Table SARS_CoV_2 P202L 0 5 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. P323L 2021 ACS omega Table SARS_CoV_2 P323L 0 5 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Q1884H 2021 ACS omega Table SARS_CoV_2 Q1884H 0 6 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Q57H 2021 ACS omega Table SARS_CoV_2 Q57H 0 4 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. R27C 2021 ACS omega Table SARS_CoV_2 R27C 0 4 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. S202N 2021 ACS omega Table SARS_CoV_2 S202N 0 5 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. S327L 2021 ACS omega Table SARS_CoV_2 S327L 0 5 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. T250I 2021 ACS omega Table SARS_CoV_2 T250I 0 5 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. V198I 2021 ACS omega Table SARS_CoV_2 V198I 0 5 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. W45L 2021 ACS omega Table SARS_CoV_2 W45L 0 4 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. E484K 2021 Journal of cellular physiology Table SARS_CoV_2 E484K 0 5 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. K417N 2021 Journal of cellular physiology Table SARS_CoV_2 K417N 0 5 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. K417T 2021 Journal of cellular physiology Table SARS_CoV_2 K417T 0 5 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. N501Y 2021 Journal of cellular physiology Table SARS_CoV_2 N501Y 0 5 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 10738T>A 2021 PloS one Table SARS_CoV_2 T10738A 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 11083G>T 2021 PloS one Table SARS_CoV_2 G11083T 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 11230G>T 2021 PloS one Table SARS_CoV_2 G11230T 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 14408C>T 2021 PloS one Table SARS_CoV_2 C14408T 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 1613C>T 2021 PloS one Table SARS_CoV_2 C1613T 0 7 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 18603T>C 2021 PloS one Table SARS_CoV_2 T18603C 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 18788C>T 2021 PloS one Table SARS_CoV_2 C18788T 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 22477C>T 2021 PloS one Table SARS_CoV_2 C22477T 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 23403A>G 2021 PloS one Table SARS_CoV_2 A23403G 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 24051A>C 2021 PloS one Table SARS_CoV_2 A24051C 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 2416C>T 2021 PloS one Table SARS_CoV_2 C2416T 0 7 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 241C>T 2021 PloS one Table SARS_CoV_2 C241T 0 6 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 2461T>C 2021 PloS one Table SARS_CoV_2 T2461C 0 7 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 25563G>T 2021 PloS one Table SARS_CoV_2 G25563T 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 25706T>C 2021 PloS one Table SARS_CoV_2 T25706C 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 26313C>T 2021 PloS one Table SARS_CoV_2 C26313T 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 28027G>T 2021 PloS one Table SARS_CoV_2 G28027T 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 28144T>C 2021 PloS one Table SARS_CoV_2 T28144C 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 28167G>A 2021 PloS one Table SARS_CoV_2 G28167A 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 28378G>C 2021 PloS one Table SARS_CoV_2 G28378C 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 28878G>A 2021 PloS one Table SARS_CoV_2 G28878A 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 29696C>T 2021 PloS one Table SARS_CoV_2 C29696T 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 29742G>A 2021 PloS one Table SARS_CoV_2 G29742A 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 29868G>A 2021 PloS one Table SARS_CoV_2 G29868A 0 8 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 3037C>T 2021 PloS one Table SARS_CoV_2 C3037T 0 7 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 355C>T 2021 PloS one Table SARS_CoV_2 C355T 0 6 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 3613T>C 2021 PloS one Table SARS_CoV_2 T3613C 0 7 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 8371G>T 2021 PloS one Table SARS_CoV_2 G8371T 0 7 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. 8782C>T 2021 PloS one Table SARS_CoV_2 C8782T 0 7 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. D614G 2021 PloS one Table SARS_CoV_2 D614G 0 5 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. D830A 2021 PloS one Table SARS_CoV_2 D830A 0 5 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. E92K 2021 PloS one Table SARS_CoV_2 E92K 0 4 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. F105S 2021 PloS one Table SARS_CoV_2 F105S 0 5 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. L3606F 2021 PloS one Table SARS_CoV_2 L3606F 0 6 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. L450F 2021 PloS one Table SARS_CoV_2 L450F 0 5 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. L84S 2021 PloS one Table SARS_CoV_2 L84S 0 4 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. M3655I 2021 PloS one Table SARS_CoV_2 M3655I 0 6 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. N3491K 2021 PloS one Table SARS_CoV_2 N3491K 0 6 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. P4715L 2021 PloS one Table SARS_CoV_2 P4715L 0 6 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. Q2702H 2021 PloS one Table SARS_CoV_2 Q2702H 0 6 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. Q57H 2021 PloS one Table SARS_CoV_2 Q57H 0 4 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. S202N 2021 PloS one Table SARS_CoV_2 S202N 0 5 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. W45L 2021 PloS one Table SARS_CoV_2 W45L 0 4 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. A475V 2021 Heliyon Table SARS_CoV_2 A475V 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. E484A 2021 Heliyon Table SARS_CoV_2 E484A 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. E484D 2021 Heliyon Table SARS_CoV_2 E484D 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. E484K 2021 Heliyon Table SARS_CoV_2 E484K 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. E484Q 2021 Heliyon Table SARS_CoV_2 E484Q 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. F456L 2021 Heliyon Table SARS_CoV_2 F456L 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. F490L 2021 Heliyon Table SARS_CoV_2 F490L 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. F490S 2021 Heliyon Table SARS_CoV_2 F490S 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. G446A 2021 Heliyon Table SARS_CoV_2 G446A 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. G446S 2021 Heliyon Table SARS_CoV_2 G446S 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. G476A 2021 Heliyon Table SARS_CoV_2 G476A 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. G476S 2021 Heliyon Table SARS_CoV_2 G476S 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. G496C 2021 Heliyon Table SARS_CoV_2 G496C 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. K417N 2021 Heliyon Table SARS_CoV_2 K417N 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. K444R 2021 Heliyon Table SARS_CoV_2 K444R 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. L455F 2021 Heliyon Table SARS_CoV_2 L455F 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. L455I 2021 Heliyon Table SARS_CoV_2 L455I 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. N439K 2021 Heliyon Table SARS_CoV_2 N439K 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. N487L 2021 Heliyon Table SARS_CoV_2 N487L 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. N501Y 2021 Heliyon Table SARS_CoV_2 N501Y 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Q493L 2021 Heliyon Table SARS_CoV_2 Q493L 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Q493R 2021 Heliyon Table SARS_CoV_2 Q493R 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. R403K 2021 Heliyon Table SARS_CoV_2 R403K 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. S494L 2021 Heliyon Table SARS_CoV_2 S494L 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. S494P 2021 Heliyon Table SARS_CoV_2 S494P 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. T478I 2021 Heliyon Table SARS_CoV_2 T478I 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. V445I 2021 Heliyon Table SARS_CoV_2 V445I 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. V483A 2021 Heliyon Table SARS_CoV_2 V483A 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. V483F 2021 Heliyon Table SARS_CoV_2 V483F 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. V483I 2021 Heliyon Table SARS_CoV_2 V483I 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. V503F 2021 Heliyon Table SARS_CoV_2 V503F 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Y449N 2021 Heliyon Table SARS_CoV_2 Y449N 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Y489H 2021 Heliyon Table SARS_CoV_2 Y489H 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Y495N 2021 Heliyon Table SARS_CoV_2 Y495N 0 5 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Y505W 2021 Heliyon Table SARS_CoV_2 Y505W 0 5 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. A570D 2021 bioRxiv Table SARS_CoV_2 A570D 0 5 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. D1118H 2021 bioRxiv Table SARS_CoV_2 D1118H 0 6 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. N501Y 2021 bioRxiv Table SARS_CoV_2 N501Y 0 5 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. P681H 2021 bioRxiv Table SARS_CoV_2 P681H 0 5 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. S982A 2021 bioRxiv Table SARS_CoV_2 S982A 0 5 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. T716I 2021 bioRxiv Table SARS_CoV_2 T716I 0 5 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Asn479Ala 2021 Scientific reports Table SARS_CoV_2 N479A 0 9 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Gln493Ala 2021 Scientific reports Table SARS_CoV_2 Q493A 0 9 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Leu443Ala 2021 Scientific reports Table SARS_CoV_2 L443A 0 9 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Leu455Ala 2021 Scientific reports Table SARS_CoV_2 L455A 0 9 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Phe456Ala 2021 Scientific reports Table SARS_CoV_2 F456A 0 9 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Tyr440Ala 2021 Scientific reports Table SARS_CoV_2 Y440A 0 9 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Tyr442Ala 2021 Scientific reports Table SARS_CoV_2 Y442A 0 9 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Tyr453Ala 2021 Scientific reports Table SARS_CoV_2 Y453A 0 9 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. N501Y 2021 Journal of virological methods Table SARS_CoV_2 N501Y 0 5 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. D614G 2021 Infection, genetics and evolution Table SARS_CoV_2 D614G 0 5 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. D614G 2021 Gene reports Table SARS_CoV_2 D614G 0 5 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. G476S/V 2021 Gene reports Table SARS_CoV_2 G476S;G476V 0;0 7;7 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. H49Y 2021 Gene reports Table SARS_CoV_2 H49Y 0 4 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. H519Q/A 2021 Gene reports Table SARS_CoV_2 H519A;H519Q 0;0 7;7 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. D614G 2021 Virus research Table SARS_CoV_2 D614G 0 5 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. F506L 2021 Virus research Table SARS_CoV_2 F506L 0 5 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. G204R 2021 Virus research Table SARS_CoV_2 G204R 0 5 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. P323H 2021 Virus research Table SARS_CoV_2 P323H 0 5 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. P323L 2021 Virus research Table SARS_CoV_2 P323L 0 5 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. Q57H 2021 Virus research Table SARS_CoV_2 Q57H 0 4 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. R203K 2021 Virus research Table SARS_CoV_2 R203K 0 5 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. R203M 2021 Virus research Table SARS_CoV_2 R203M 0 5 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. R203S 2021 Virus research Table SARS_CoV_2 R203S 0 5 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. S507C 2021 Virus research Table SARS_CoV_2 S507C 0 5 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. S507G 2021 Virus research Table SARS_CoV_2 S507G 0 5 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. S507R 2021 Virus research Table SARS_CoV_2 S507R 0 5 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. T315I 2021 Virus research Table SARS_CoV_2 T315I 0 5 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. T315N 2021 Virus research Table SARS_CoV_2 T315N 0 5 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. T315S 2021 Virus research Table SARS_CoV_2 T315S 0 5 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. T85I 2021 Virus research Table SARS_CoV_2 T85I 0 4 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. E484K 2021 Cell host & microbe Table SARS_CoV_2 E484K 0 5 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. K417N 2021 Cell host & microbe Table SARS_CoV_2 K417N 0 5 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. M0202S 2021 Cell host & microbe Table SARS_CoV_2 M0202S 0 6 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. N501Y 2021 Cell host & microbe Table SARS_CoV_2 N501Y 0 5 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. R0138S 2021 Cell host & microbe Table SARS_CoV_2 R0138S 0 6 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. R0145S 2021 Cell host & microbe Table SARS_CoV_2 R0145S 0 6 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. D614G 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 D614G 0 5 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. G204R 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 G204R 0 5 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. L37H 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 L37H 0 4 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. P13L 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 P13L 0 4 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. P344S 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 P344S 0 5 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. R203K 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 R203K 0 5 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. S197L 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 S197L 0 5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. A1818T 2021 Journal, genetic engineering & biotechnology Table SARS_CoV_2 A1818T 0 6 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. A889V 2021 Journal, genetic engineering & biotechnology Table SARS_CoV_2 A889V 0 5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. D614G 2021 Journal, genetic engineering & biotechnology Table SARS_CoV_2 D614G 0 5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. G1691C 2021 Journal, genetic engineering & biotechnology Table SARS_CoV_2 G1691C 0 6 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. G204R 2021 Journal, genetic engineering & biotechnology Table SARS_CoV_2 G204R 0 5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. I120F 2021 Journal, genetic engineering & biotechnology Table SARS_CoV_2 I120F 0 5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. L122I 2021 Journal, genetic engineering & biotechnology Table SARS_CoV_2 L122I 0 5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. R203K 2021 Journal, genetic engineering & biotechnology Table SARS_CoV_2 R203K 0 5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. V121D 2021 Journal, genetic engineering & biotechnology Table SARS_CoV_2 V121D 0 5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. V843F 2021 Journal, genetic engineering & biotechnology Table SARS_CoV_2 V843F 0 5 33798491 Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant. N501Y 2021 Cell host & microbe Table SARS_CoV_2 N501Y 0 5 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. D614G 2021 Pathogens (Basel, Switzerland) Table SARS_CoV_2 D614G 0 5 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. E484K 2021 Pathogens (Basel, Switzerland) Table SARS_CoV_2 E484K 0 5 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. K417N 2021 Pathogens (Basel, Switzerland) Table SARS_CoV_2 K417N 0 5 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. N501Y 2021 Pathogens (Basel, Switzerland) Table SARS_CoV_2 N501Y 0 5 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. P681H 2021 Pathogens (Basel, Switzerland) Table SARS_CoV_2 P681H 0 5 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. A16512G 2021 Frontiers in genetics Table SARS_CoV_2 A16512G 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. A20268G 2021 Frontiers in genetics Table SARS_CoV_2 A20268G 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. A2292C 2021 Frontiers in genetics Table SARS_CoV_2 A2292C 0 6 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. A23403G 2021 Frontiers in genetics Table SARS_CoV_2 A23403G 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C1059T 2021 Frontiers in genetics Table SARS_CoV_2 C1059T 0 6 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C13730T 2021 Frontiers in genetics Table SARS_CoV_2 C13730T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C14408T 2021 Frontiers in genetics Table SARS_CoV_2 C14408T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C14805T 2021 Frontiers in genetics Table SARS_CoV_2 C14805T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C15324T 2021 Frontiers in genetics Table SARS_CoV_2 C15324T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C18568T 2021 Frontiers in genetics Table SARS_CoV_2 C18568T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C18877T 2021 Frontiers in genetics Table SARS_CoV_2 C18877T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C19154T 2021 Frontiers in genetics Table SARS_CoV_2 C19154T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C22444T 2021 Frontiers in genetics Table SARS_CoV_2 C22444T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C23277T 2021 Frontiers in genetics Table SARS_CoV_2 C23277T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C23929T 2021 Frontiers in genetics Table SARS_CoV_2 C23929T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C241T 2021 Frontiers in genetics Table SARS_CoV_2 C241T 0 5 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C25528T 2021 Frontiers in genetics Table SARS_CoV_2 C25528T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C26735T 2021 Frontiers in genetics Table SARS_CoV_2 C26735T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C28311T 2021 Frontiers in genetics Table SARS_CoV_2 C28311T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C2836T 2021 Frontiers in genetics Table SARS_CoV_2 C2836T 0 6 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C28854T 2021 Frontiers in genetics Table SARS_CoV_2 C28854T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C29750T 2021 Frontiers in genetics Table SARS_CoV_2 C29750T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C3037T 2021 Frontiers in genetics Table SARS_CoV_2 C3037T 0 6 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C313T 2021 Frontiers in genetics Table SARS_CoV_2 C313T 0 5 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C3634T 2021 Frontiers in genetics Table SARS_CoV_2 C3634T 0 6 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C4084T 2021 Frontiers in genetics Table SARS_CoV_2 C4084T 0 6 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C5700A 2021 Frontiers in genetics Table SARS_CoV_2 C5700A 0 6 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C6312A 2021 Frontiers in genetics Table SARS_CoV_2 C6312A 0 6 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C6573T 2021 Frontiers in genetics Table SARS_CoV_2 C6573T 0 6 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C8782T 2021 Frontiers in genetics Table SARS_CoV_2 C8782T 0 6 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. C8917T 2021 Frontiers in genetics Table SARS_CoV_2 C8917T 0 6 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. G11083T 2021 Frontiers in genetics Table SARS_CoV_2 G11083T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. G16078A 2021 Frontiers in genetics Table SARS_CoV_2 G16078A 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. G21724T 2021 Frontiers in genetics Table SARS_CoV_2 G21724T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. G23311T 2021 Frontiers in genetics Table SARS_CoV_2 G23311T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. G25088T 2021 Frontiers in genetics Table SARS_CoV_2 G25088T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. G25563T 2021 Frontiers in genetics Table SARS_CoV_2 G25563T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. G25770T 2021 Frontiers in genetics Table SARS_CoV_2 G25770T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. G26144T 2021 Frontiers in genetics Table SARS_CoV_2 G26144T 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. G29868A 2021 Frontiers in genetics Table SARS_CoV_2 G29868A 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. G4300T 2021 Frontiers in genetics Table SARS_CoV_2 G4300T 0 6 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. G4354A 2021 Frontiers in genetics Table SARS_CoV_2 G4354A 0 6 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. T12503C 2021 Frontiers in genetics Table SARS_CoV_2 T12503C 0 7 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. T28144C 2021 Frontiers in genetics Table SARS_CoV_2 T28144C 0 7 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. A570D 2021 bioRxiv Table SARS_CoV_2 A570D 0 5 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. A701V 2021 bioRxiv Table SARS_CoV_2 A701V 0 5 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. D1118H 2021 bioRxiv Table SARS_CoV_2 D1118H 0 6 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. D215G 2021 bioRxiv Table SARS_CoV_2 D215G 0 5 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. D614G 2021 bioRxiv Table SARS_CoV_2 D614G 0 5 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. D80A 2021 bioRxiv Table SARS_CoV_2 D80A 0 4 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. E484K 2021 bioRxiv Table SARS_CoV_2 E484K 0 5 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. K417N 2021 bioRxiv Table SARS_CoV_2 K417N 0 5 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. L18F 2021 bioRxiv Table SARS_CoV_2 L18F 0 4 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. N501Y 2021 bioRxiv Table SARS_CoV_2 N501Y 0 5 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. P681H 2021 bioRxiv Table SARS_CoV_2 P681H 0 5 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. R246I 2021 bioRxiv Table SARS_CoV_2 R246I 0 5 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. S982A 2021 bioRxiv Table SARS_CoV_2 S982A 0 5 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. T716I 2021 bioRxiv Table SARS_CoV_2 T716I 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. A225D 2022 Transboundary and emerging diseases Table SARS_CoV_2 A225D 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. A225S 2022 Transboundary and emerging diseases Table SARS_CoV_2 A225S 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. A225T 2022 Transboundary and emerging diseases Table SARS_CoV_2 A225T 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. A23403G 2022 Transboundary and emerging diseases Table SARS_CoV_2 A23403G 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. A344S 2022 Transboundary and emerging diseases Table SARS_CoV_2 A344S 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. A706V 2022 Transboundary and emerging diseases Table SARS_CoV_2 A706V 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. C14408T 2022 Transboundary and emerging diseases Table SARS_CoV_2 C14408T 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. C21627T 2022 Transboundary and emerging diseases Table SARS_CoV_2 C21627T 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. C23679T 2022 Transboundary and emerging diseases Table SARS_CoV_2 C23679T 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. C241T 2022 Transboundary and emerging diseases Table SARS_CoV_2 C241T 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. C28388G 2022 Transboundary and emerging diseases Table SARS_CoV_2 C28388G 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. C28830T 2022 Transboundary and emerging diseases Table SARS_CoV_2 C28830T 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. C3037T 2022 Transboundary and emerging diseases Table SARS_CoV_2 C3037T 0 6 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. C884T 2022 Transboundary and emerging diseases Table SARS_CoV_2 C884T 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. D614G 2022 Transboundary and emerging diseases Table SARS_CoV_2 D614G 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. E180K 2022 Transboundary and emerging diseases Table SARS_CoV_2 E180K 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. F106F 2022 Transboundary and emerging diseases Table SARS_CoV_2 F106F 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. G11083T 2022 Transboundary and emerging diseases Table SARS_CoV_2 G11083T 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. G1397A 2022 Transboundary and emerging diseases Table SARS_CoV_2 G1397A 0 6 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. G18712A 2022 Transboundary and emerging diseases Table SARS_CoV_2 G18712A 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. G20887A 2022 Transboundary and emerging diseases Table SARS_CoV_2 G20887A 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. G22100A 2022 Transboundary and emerging diseases Table SARS_CoV_2 G22100A 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. G22592T 2022 Transboundary and emerging diseases Table SARS_CoV_2 G22592T 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. G24348T 2022 Transboundary and emerging diseases Table SARS_CoV_2 G24348T 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. G25249T 2022 Transboundary and emerging diseases Table SARS_CoV_2 G25249T 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. G25563T 2022 Transboundary and emerging diseases Table SARS_CoV_2 G25563T 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. G29742T 2022 Transboundary and emerging diseases Table SARS_CoV_2 G29742T 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. G6461A 2022 Transboundary and emerging diseases Table SARS_CoV_2 G6461A 0 6 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. G77R 2022 Transboundary and emerging diseases Table SARS_CoV_2 G77R 0 4 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. G8653T 2022 Transboundary and emerging diseases Table SARS_CoV_2 G8653T 0 6 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. L139L 2022 Transboundary and emerging diseases Table SARS_CoV_2 L139L 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. L37F 2022 Transboundary and emerging diseases Table SARS_CoV_2 L37F 0 4 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. M1229I 2022 Transboundary and emerging diseases Table SARS_CoV_2 M1229I 0 6 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. M33I 2022 Transboundary and emerging diseases Table SARS_CoV_2 M33I 0 4 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. P323L 2022 Transboundary and emerging diseases Table SARS_CoV_2 P323L 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Q39E 2022 Transboundary and emerging diseases Table SARS_CoV_2 Q39E 0 4 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Q39H 2022 Transboundary and emerging diseases Table SARS_CoV_2 Q39H 0 4 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Q39L 2022 Transboundary and emerging diseases Table SARS_CoV_2 Q39L 0 4 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Q39R 2022 Transboundary and emerging diseases Table SARS_CoV_2 Q39R 0 4 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Q57H 2022 Transboundary and emerging diseases Table SARS_CoV_2 Q57H 0 4 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. R27C 2022 Transboundary and emerging diseases Table SARS_CoV_2 R27C 0 4 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. S186F 2022 Transboundary and emerging diseases Table SARS_CoV_2 S186F 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. S403A 2022 Transboundary and emerging diseases Table SARS_CoV_2 S403A 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. S403L 2022 Transboundary and emerging diseases Table SARS_CoV_2 S403L 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. S403P 2022 Transboundary and emerging diseases Table SARS_CoV_2 S403P 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. S929I 2022 Transboundary and emerging diseases Table SARS_CoV_2 S929I 0 5 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. T22I 2022 Transboundary and emerging diseases Table SARS_CoV_2 T22I 0 4 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. T28688C 2022 Transboundary and emerging diseases Table SARS_CoV_2 T28688C 0 7 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. T3926C 2022 Transboundary and emerging diseases Table SARS_CoV_2 T3926C 0 6 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. V1248G 2022 Transboundary and emerging diseases Table SARS_CoV_2 V1248G 0 6 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. V1248L 2022 Transboundary and emerging diseases Table SARS_CoV_2 V1248L 0 6 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. V1248M 2022 Transboundary and emerging diseases Table SARS_CoV_2 V1248M 0 6 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. V198I 2022 Transboundary and emerging diseases Table SARS_CoV_2 V198I 0 5 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. E484K 2021 Cell Table SARS_CoV_2 E484K 0 5 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. K417N 2021 Cell Table SARS_CoV_2 K417N 0 5 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. K417T 2021 Cell Table SARS_CoV_2 K417T 0 5 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. N501Y 2021 Cell Table SARS_CoV_2 N501Y 0 5 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. D614G 2021 Cell reports Table SARS_CoV_2 D614G 0 5 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. I692V 2021 Cell reports Table SARS_CoV_2 I692V 0 5 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. M1229I 2021 Cell reports Table SARS_CoV_2 M1229I 0 6 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Y453F 2021 Cell reports Table SARS_CoV_2 Y453F 0 5 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. N501Y 2021 The journal of physical chemistry. B Table SARS_CoV_2 N501Y 0 5 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.-25C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C25T 0 8 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.10012C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C10012T 0 10 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.14144C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C14144T 0 10 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.14412C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C14412T 0 10 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.14661C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C14661T 0 10 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.15015C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C15015T 0 10 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.1501A>T 2021 Microbiology resource announcements Table SARS_CoV_2 A1501T 0 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.155G>T 2021 Microbiology resource announcements Table SARS_CoV_2 G155T 0 8 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.15912T>C 2021 Microbiology resource announcements Table SARS_CoV_2 T15912C 0 10 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.1709C>A 2021 Microbiology resource announcements Table SARS_CoV_2 C1709A 0 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.17351A>G 2021 Microbiology resource announcements Table SARS_CoV_2 A17351G 0 10 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.1841A>G 2021 Microbiology resource announcements Table SARS_CoV_2 A1841G 0 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.2042C>A 2021 Microbiology resource announcements Table SARS_CoV_2 C2042A 0 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.2147C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C2147T 0 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.218A>G 2021 Microbiology resource announcements Table SARS_CoV_2 A218G 0 8 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.2772C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C2772T 0 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.2944T>G 2021 Microbiology resource announcements Table SARS_CoV_2 T2944G 0 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.3002C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C3002T 0 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.3352G>C 2021 Microbiology resource announcements Table SARS_CoV_2 G3352C 0 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.5123C>A 2021 Microbiology resource announcements Table SARS_CoV_2 C5123A 0 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.5721C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C5721T 0 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.608G>A 2021 Microbiology resource announcements Table SARS_CoV_2 G608A 0 8 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.609G>A 2021 Microbiology resource announcements Table SARS_CoV_2 G609A 0 8 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.610G>C 2021 Microbiology resource announcements Table SARS_CoV_2 G610C 0 8 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.648C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C648T 0 8 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.6689T>C 2021 Microbiology resource announcements Table SARS_CoV_2 T6689C 0 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.704C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C704T 0 8 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.79C>T 2021 Microbiology resource announcements Table SARS_CoV_2 C79T 0 7 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.7G>C 2021 Microbiology resource announcements Table SARS_CoV_2 G7C 0 6 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.8A>T 2021 Microbiology resource announcements Table SARS_CoV_2 A8T 0 6 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. c.9T>A 2021 Microbiology resource announcements Table SARS_CoV_2 T9A 0 6 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Ala1708Asp 2021 Microbiology resource announcements Table SARS_CoV_2 A1708D 0 12 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Ala570Asp 2021 Microbiology resource announcements Table SARS_CoV_2 A570D 0 11 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Arg203Arg 2021 Microbiology resource announcements Table SARS_CoV_2 R203R 0 11 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Arg203Lys 2021 Microbiology resource announcements Table SARS_CoV_2 R203K 0 11 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Arg52Ile 2021 Microbiology resource announcements Table SARS_CoV_2 R52I 0 10 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Asn501Tyr 2021 Microbiology resource announcements Table SARS_CoV_2 N501Y 0 11 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Asp1118His 2021 Microbiology resource announcements Table SARS_CoV_2 D1118H 0 12 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Asp3Glu 2021 Microbiology resource announcements Table SARS_CoV_2 D3E 0 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Asp3His 2021 Microbiology resource announcements Table SARS_CoV_2 D3H 0 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Asp3Val 2021 Microbiology resource announcements Table SARS_CoV_2 D3V 0 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Asp614Gly 2021 Microbiology resource announcements Table SARS_CoV_2 D614G 0 11 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Gly204Arg 2021 Microbiology resource announcements Table SARS_CoV_2 G204R 0 11 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.His5005His 2021 Microbiology resource announcements Table SARS_CoV_2 H5005H 0 12 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Ile2230Thr 2021 Microbiology resource announcements Table SARS_CoV_2 I2230T 0 12 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Leu3338Phe 2021 Microbiology resource announcements Table SARS_CoV_2 L3338F 0 12 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Lys5784Arg 2021 Microbiology resource announcements Table SARS_CoV_2 K5784R 0 12 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Phe1907Phe 2021 Microbiology resource announcements Table SARS_CoV_2 F1907F 0 12 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Phe924Phe 2021 Microbiology resource announcements Table SARS_CoV_2 F924F 0 11 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Pro4715Leu 2021 Microbiology resource announcements Table SARS_CoV_2 P4715L 0 12 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Pro4804Pro 2021 Microbiology resource announcements Table SARS_CoV_2 P4804P 0 12 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Pro681His 2021 Microbiology resource announcements Table SARS_CoV_2 P681H 0 11 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Ser216Ser 2021 Microbiology resource announcements Table SARS_CoV_2 S216S 0 11 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Ser235Phe 2021 Microbiology resource announcements Table SARS_CoV_2 S235F 0 11 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Ser982Ala 2021 Microbiology resource announcements Table SARS_CoV_2 S982A 0 11 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Thr1001Ile 2021 Microbiology resource announcements Table SARS_CoV_2 T1001I 0 12 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Thr5304Thr 2021 Microbiology resource announcements Table SARS_CoV_2 T5304T 0 12 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Thr716Ile 2021 Microbiology resource announcements Table SARS_CoV_2 T716I 0 11 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Tyr145del 2021 Microbiology resource announcements Table SARS_CoV_2 Y145del 0 9 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Tyr73Cys 2021 Microbiology resource announcements Table SARS_CoV_2 Y73C 0 10 33888505 Report of SARS-CoV-2 B1.1.7 Lineage in Morocco. p.Val4887Val 2021 Microbiology resource announcements Table SARS_CoV_2 V4887V 0 12 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. A1180G 2021 Emerging microbes & infections Table SARS_CoV_2 A1180G 0 6 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. A23403G 2021 Emerging microbes & infections Table SARS_CoV_2 A23403G 0 7 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. A6851C 2021 Emerging microbes & infections Table SARS_CoV_2 A6851C 0 6 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. C10029T 2021 Emerging microbes & infections Table SARS_CoV_2 C10029T 0 7 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. C1059T 2021 Emerging microbes & infections Table SARS_CoV_2 C1059T 0 6 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. C11514T 2021 Emerging microbes & infections Table SARS_CoV_2 C11514T 0 7 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. C14408T 2021 Emerging microbes & infections Table SARS_CoV_2 C14408T 0 7 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. C16375T 2021 Emerging microbes & infections Table SARS_CoV_2 C16375T 0 7 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. C23604A 2021 Emerging microbes & infections Table SARS_CoV_2 C23604A 0 7 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. C23709T 2021 Emerging microbes & infections Table SARS_CoV_2 C23709T 0 7 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. C241T 2021 Emerging microbes & infections Table SARS_CoV_2 C241T 0 5 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. C28887T 2021 Emerging microbes & infections Table SARS_CoV_2 C28887T 0 7 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. C29719T 2021 Emerging microbes & infections Table SARS_CoV_2 C29719T 0 7 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. C3037T 2021 Emerging microbes & infections Table SARS_CoV_2 C3037T 0 6 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. C6730T 2021 Emerging microbes & infections Table SARS_CoV_2 C6730T 0 6 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. C6936T 2021 Emerging microbes & infections Table SARS_CoV_2 C6936T 0 6 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. D614G 2021 Emerging microbes & infections Table SARS_CoV_2 D614G 0 5 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. F28L 2021 Emerging microbes & infections Table SARS_CoV_2 F28L 0 4 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. F924F 2021 Emerging microbes & infections Table SARS_CoV_2 F924F 0 5 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. G25563T 2021 Emerging microbes & infections Table SARS_CoV_2 G25563T 0 7 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. I48V 2021 Emerging microbes & infections Table SARS_CoV_2 I48V 0 4 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. I82T 2021 Emerging microbes & infections Table SARS_CoV_2 I82T 0 4 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. M84T 2021 Emerging microbes & infections Table SARS_CoV_2 M84T 0 4 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. N2155N 2021 Emerging microbes & infections Table SARS_CoV_2 N2155N 0 6 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. P305P 2021 Emerging microbes & infections Table SARS_CoV_2 P305P 0 5 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. P4715L 2021 Emerging microbes & infections Table SARS_CoV_2 P4715L 0 6 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. P5371S 2021 Emerging microbes & infections Table SARS_CoV_2 P5371S 0 6 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. P681H 2021 Emerging microbes & infections Table SARS_CoV_2 P681H 0 5 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. Q57H 2021 Emerging microbes & infections Table SARS_CoV_2 Q57H 0 4 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. S2224F 2021 Emerging microbes & infections Table SARS_CoV_2 S2224F 0 6 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. S494P 2021 Emerging microbes & infections Table SARS_CoV_2 S494P 0 5 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. T205I 2021 Emerging microbes & infections Table SARS_CoV_2 T205I 0 5 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. T20748C 2021 Emerging microbes & infections Table SARS_CoV_2 T20748C 0 7 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. T2196P 2021 Emerging microbes & infections Table SARS_CoV_2 T2196P 0 6 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. T23042C 2021 Emerging microbes & infections Table SARS_CoV_2 T23042C 0 7 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. T265I 2021 Emerging microbes & infections Table SARS_CoV_2 T265I 0 5 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. T26767C 2021 Emerging microbes & infections Table SARS_CoV_2 T26767C 0 7 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. T3255I 2021 Emerging microbes & infections Table SARS_CoV_2 T3255I 0 6 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. T3750I 2021 Emerging microbes & infections Table SARS_CoV_2 T3750I 0 6 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. T716I 2021 Emerging microbes & infections Table SARS_CoV_2 T716I 0 5 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. V70L 2021 Emerging microbes & infections Table SARS_CoV_2 V70L 0 4 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. P323L 2021 Frontiers in molecular biosciences Table SARS_CoV_2 P323L 0 5 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. c.10075C>T 2021 Infection, genetics and evolution Table SARS_CoV_2 C10075T 0 10 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. c.10095G>A 2021 Infection, genetics and evolution Table SARS_CoV_2 G10095A 0 10 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. c.14144C>T 2021 Infection, genetics and evolution Table SARS_CoV_2 C14144T 0 10 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. c.16746C>T 2021 Infection, genetics and evolution Table SARS_CoV_2 C16746T 0 10 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. c.1841A>G 2021 Infection, genetics and evolution Table SARS_CoV_2 A1841G 0 9 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. c.2451C>T 2021 Infection, genetics and evolution Table SARS_CoV_2 C2451T 0 9 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. c.3350C>T 2021 Infection, genetics and evolution Table SARS_CoV_2 C3350T 0 9 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. c.433C>T 2021 Infection, genetics and evolution Table SARS_CoV_2 C433T 0 8 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. c.608G>A 2021 Infection, genetics and evolution Table SARS_CoV_2 G608A 0 8 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. c.609G>A 2021 Infection, genetics and evolution Table SARS_CoV_2 G609A 0 8 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. c.610G>C 2021 Infection, genetics and evolution Table SARS_CoV_2 G610C 0 8 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. c.7217C>T 2021 Infection, genetics and evolution Table SARS_CoV_2 C7217T 0 9 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. c.751G>A 2021 Infection, genetics and evolution Table SARS_CoV_2 G751A 0 8 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. c.794C>T 2021 Infection, genetics and evolution Table SARS_CoV_2 C794T 0 8 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. c.8307G>T 2021 Infection, genetics and evolution Table SARS_CoV_2 G8307T 0 9 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. c.871C>T 2021 Infection, genetics and evolution Table SARS_CoV_2 C871T 0 8 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. D614G 2021 Infection, genetics and evolution Table SARS_CoV_2 D614G 0 5 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. G204R 2021 Infection, genetics and evolution Table SARS_CoV_2 G204R 0 5 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. G251S 2021 Infection, genetics and evolution Table SARS_CoV_2 G251S 0 5 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. G817G 2021 Infection, genetics and evolution Table SARS_CoV_2 G817G 0 5 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. H145Y 2021 Infection, genetics and evolution Table SARS_CoV_2 H145Y 0 5 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. I5582I 2021 Infection, genetics and evolution Table SARS_CoV_2 I5582I 0 6 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. K3365K 2021 Infection, genetics and evolution Table SARS_CoV_2 K3365K 0 6 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. L291L 2021 Infection, genetics and evolution Table SARS_CoV_2 L291L 0 5 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. p.Arg203Arg 2021 Infection, genetics and evolution Table SARS_CoV_2 R203R 0 11 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. p.Arg203Lys 2021 Infection, genetics and evolution Table SARS_CoV_2 R203K 0 11 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. p.Asp614Gly 2021 Infection, genetics and evolution Table SARS_CoV_2 D614G 0 11 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. p.Gly204Arg 2021 Infection, genetics and evolution Table SARS_CoV_2 G204R 0 11 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. p.Gly251Ser 2021 Infection, genetics and evolution Table SARS_CoV_2 G251S 0 11 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. p.Gly817Gly 2021 Infection, genetics and evolution Table SARS_CoV_2 G817G 0 11 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. p.His145Tyr 2021 Infection, genetics and evolution Table SARS_CoV_2 H145Y 0 11 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. p.Ile5582Ile 2021 Infection, genetics and evolution Table SARS_CoV_2 I5582I 0 12 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. p.Leu291Leu 2021 Infection, genetics and evolution Table SARS_CoV_2 L291L 0 11 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. p.Lys3365Lys 2021 Infection, genetics and evolution Table SARS_CoV_2 K3365K 0 12 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. p.Pro3359Ser 2021 Infection, genetics and evolution Table SARS_CoV_2 P3359S 0 12 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. p.Pro4715Leu 2021 Infection, genetics and evolution Table SARS_CoV_2 P4715L 0 12 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. p.Ser2406Leu 2021 Infection, genetics and evolution Table SARS_CoV_2 S2406L 0 12 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. p.Thr1117Ile 2021 Infection, genetics and evolution Table SARS_CoV_2 T1117I 0 12 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. p.Thr265Ile 2021 Infection, genetics and evolution Table SARS_CoV_2 T265I 0 11 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. p.Trp2769Cys 2021 Infection, genetics and evolution Table SARS_CoV_2 W2769C 0 12 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. P3359S 2021 Infection, genetics and evolution Table SARS_CoV_2 P3359S 0 6 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. P4715L 2021 Infection, genetics and evolution Table SARS_CoV_2 P4715L 0 6 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. R203K 2021 Infection, genetics and evolution Table SARS_CoV_2 R203K 0 5 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. R203R 2021 Infection, genetics and evolution Table SARS_CoV_2 R203R 0 5 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. S2406L 2021 Infection, genetics and evolution Table SARS_CoV_2 S2406L 0 6 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. T1117I 2021 Infection, genetics and evolution Table SARS_CoV_2 T1117I 0 6 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. T265I 2021 Infection, genetics and evolution Table SARS_CoV_2 T265I 0 5 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. W2769C 2021 Infection, genetics and evolution Table SARS_CoV_2 W2769C 0 6 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. A222V 2021 Epidemiology and infection Table SARS_CoV_2 A222V 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. A97V 2021 Epidemiology and infection Table SARS_CoV_2 A97V 0 4 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. D268del 2021 Epidemiology and infection Table SARS_CoV_2 D268del 0 7 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. E484K 2021 Epidemiology and infection Table SARS_CoV_2 E484K 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. E780Q 2021 Epidemiology and infection Table SARS_CoV_2 E780Q 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. G15S 2021 Epidemiology and infection Table SARS_CoV_2 G15S 0 4 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. G204R 2021 Epidemiology and infection Table SARS_CoV_2 G204R 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. G251V 2021 Epidemiology and infection Table SARS_CoV_2 G251V 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. H69del 2021 Epidemiology and infection Table SARS_CoV_2 H69del 0 6 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. I292T 2021 Epidemiology and infection Table SARS_CoV_2 I292T 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. I559V 2021 Epidemiology and infection Table SARS_CoV_2 I559V 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. K417N 2021 Epidemiology and infection Table SARS_CoV_2 K417N 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. L18F 2021 Epidemiology and infection Table SARS_CoV_2 L18F 0 4 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. L37F 2021 Epidemiology and infection Table SARS_CoV_2 L37F 0 4 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. L84S 2021 Epidemiology and infection Table SARS_CoV_2 L84S 0 4 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. N439K 2021 Epidemiology and infection Table SARS_CoV_2 N439K 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. N501Y 2021 Epidemiology and infection Table SARS_CoV_2 N501Y 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. P13L 2021 Epidemiology and infection Table SARS_CoV_2 P13L 0 4 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. P323L 2021 Epidemiology and infection Table SARS_CoV_2 P323L 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. P504L 2021 Epidemiology and infection Table SARS_CoV_2 P504L 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. P585S 2021 Epidemiology and infection Table SARS_CoV_2 P585S 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. Q57H 2021 Epidemiology and infection Table SARS_CoV_2 Q57H 0 4 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. R203K 2021 Epidemiology and infection Table SARS_CoV_2 R203K 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. S194L 2021 Epidemiology and infection Table SARS_CoV_2 S194L 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. S24L 2021 Epidemiology and infection Table SARS_CoV_2 S24L 0 4 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. S477N 2021 Epidemiology and infection Table SARS_CoV_2 S477N 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. T1198K 2021 Epidemiology and infection Table SARS_CoV_2 T1198K 0 6 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. T20N 2021 Epidemiology and infection Table SARS_CoV_2 T20N 0 4 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. T478I 2021 Epidemiology and infection Table SARS_CoV_2 T478I 0 5 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. T85I 2021 Epidemiology and infection Table SARS_CoV_2 T85I 0 4 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. V1176F 2021 Epidemiology and infection Table SARS_CoV_2 V1176F 0 6 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. V13L 2021 Epidemiology and infection Table SARS_CoV_2 V13L 0 4 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. Y145del 2021 Epidemiology and infection Table SARS_CoV_2 Y145del 0 7 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. Y541C 2021 Epidemiology and infection Table SARS_CoV_2 Y541C 0 5 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. N501Y 2021 Virology journal Table SARS_CoV_2 N501Y 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. A344S 2021 Scientific reports Table SARS_CoV_2 A344S 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. A348P 2021 Scientific reports Table SARS_CoV_2 A348P 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. A348S 2021 Scientific reports Table SARS_CoV_2 A348S 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. A352S 2021 Scientific reports Table SARS_CoV_2 A352S 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. A372T 2021 Scientific reports Table SARS_CoV_2 A372T 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. A411S 2021 Scientific reports Table SARS_CoV_2 A411S 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. A435S 2021 Scientific reports Table SARS_CoV_2 A435S 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. A520S 2021 Scientific reports Table SARS_CoV_2 A520S 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. C432F 2021 Scientific reports Table SARS_CoV_2 C432F 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. D364Y 2021 Scientific reports Table SARS_CoV_2 D364Y 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. D405C 2021 Scientific reports Table SARS_CoV_2 D405C 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. D467V 2021 Scientific reports Table SARS_CoV_2 D467V 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. E340K 2021 Scientific reports Table SARS_CoV_2 E340K 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. F347I 2021 Scientific reports Table SARS_CoV_2 F347I 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. F490L 2021 Scientific reports Table SARS_CoV_2 F490L 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. G339D 2021 Scientific reports Table SARS_CoV_2 G339D 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. G404K 2021 Scientific reports Table SARS_CoV_2 G404K 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. G413E 2021 Scientific reports Table SARS_CoV_2 G413E 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. G413V 2021 Scientific reports Table SARS_CoV_2 G413V 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. G431S 2021 Scientific reports Table SARS_CoV_2 G431S 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. G504D 2021 Scientific reports Table SARS_CoV_2 G504D 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. H519Q 2021 Scientific reports Table SARS_CoV_2 H519Q 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. I402V 2021 Scientific reports Table SARS_CoV_2 I402V 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. I410V 2021 Scientific reports Table SARS_CoV_2 I410V 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. I468F 2021 Scientific reports Table SARS_CoV_2 I468F 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. I468V 2021 Scientific reports Table SARS_CoV_2 I468V 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. K386D 2021 Scientific reports Table SARS_CoV_2 K386D 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. K386E 2021 Scientific reports Table SARS_CoV_2 K386E 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. K424D 2021 Scientific reports Table SARS_CoV_2 K424D 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. K424E 2021 Scientific reports Table SARS_CoV_2 K424E 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. N354D 2021 Scientific reports Table SARS_CoV_2 N354D 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. N354K 2021 Scientific reports Table SARS_CoV_2 N354K 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. N388T 2021 Scientific reports Table SARS_CoV_2 N388T 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. N439K 2021 Scientific reports Table SARS_CoV_2 N439K 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. P384L 2021 Scientific reports Table SARS_CoV_2 P384L 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. P384S 2021 Scientific reports Table SARS_CoV_2 P384S 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. P463S 2021 Scientific reports Table SARS_CoV_2 P463S 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. P491L 2021 Scientific reports Table SARS_CoV_2 P491L 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. P507H 2021 Scientific reports Table SARS_CoV_2 P507H 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. P507S 2021 Scientific reports Table SARS_CoV_2 P507S 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. P521S 2021 Scientific reports Table SARS_CoV_2 P521S 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. Q414K 2021 Scientific reports Table SARS_CoV_2 Q414K 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. Q506H 2021 Scientific reports Table SARS_CoV_2 Q506H 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. R346K 2021 Scientific reports Table SARS_CoV_2 R346K 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. R355D 2021 Scientific reports Table SARS_CoV_2 R355D 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. R355E 2021 Scientific reports Table SARS_CoV_2 R355E 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. R403K 2021 Scientific reports Table SARS_CoV_2 R403K 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. R408I 2021 Scientific reports Table SARS_CoV_2 R408I 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. R509K 2021 Scientific reports Table SARS_CoV_2 R509K 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. S359N 2021 Scientific reports Table SARS_CoV_2 S359N 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. S399A 2021 Scientific reports Table SARS_CoV_2 S399A 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. S399P 2021 Scientific reports Table SARS_CoV_2 S399P 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. S494P 2021 Scientific reports Table SARS_CoV_2 S494P 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. T430N 2021 Scientific reports Table SARS_CoV_2 T430N 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. V367F 2021 Scientific reports Table SARS_CoV_2 V367F 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. V382L 2021 Scientific reports Table SARS_CoV_2 V382L 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. V407G 2021 Scientific reports Table SARS_CoV_2 V407G 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. V510L 2021 Scientific reports Table SARS_CoV_2 V510L 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. Y505H 2021 Scientific reports Table SARS_CoV_2 Y505H 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. Y508H 2021 Scientific reports Table SARS_CoV_2 Y508H 0 5 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. Y508N 2021 Scientific reports Table SARS_CoV_2 Y508N 0 5 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. N501Y 2021 PLoS biology Table SARS_CoV_2 N501Y 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. A105S 2021 Epidemiology and infection Table SARS_CoV_2 A105S 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. A106S 2021 Epidemiology and infection Table SARS_CoV_2 A106S 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. A435S 2021 Epidemiology and infection Table SARS_CoV_2 A435S 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. A449V 2021 Epidemiology and infection Table SARS_CoV_2 A449V 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. A475V 2021 Epidemiology and infection Table SARS_CoV_2 A475V 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. A570D 2021 Epidemiology and infection Table SARS_CoV_2 A570D 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. A65V 2021 Epidemiology and infection Table SARS_CoV_2 A65V 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. A831V 2021 Epidemiology and infection Table SARS_CoV_2 A831V 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. A97V 2021 Epidemiology and infection Table SARS_CoV_2 A97V 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. C64Y 2021 Epidemiology and infection Table SARS_CoV_2 C64Y 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. D103Y 2021 Epidemiology and infection Table SARS_CoV_2 D103Y 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. D1118H 2021 Epidemiology and infection Table SARS_CoV_2 D1118H 0 6 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. D173Y 2021 Epidemiology and infection Table SARS_CoV_2 D173Y 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. D31Y 2021 Epidemiology and infection Table SARS_CoV_2 D31Y 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. D3G 2021 Epidemiology and infection Table SARS_CoV_2 D3G 0 3 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. D614G 2021 Epidemiology and infection Table SARS_CoV_2 D614G 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. D63Y 2021 Epidemiology and infection Table SARS_CoV_2 D63Y 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. E106Q 2021 Epidemiology and infection Table SARS_CoV_2 E106Q 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. E92D 2021 Epidemiology and infection Table SARS_CoV_2 E92D 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. F120L 2021 Epidemiology and infection Table SARS_CoV_2 F120L 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. F193L 2021 Epidemiology and infection Table SARS_CoV_2 F193L 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. F32I 2021 Epidemiology and infection Table SARS_CoV_2 F32I 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. F490L 2021 Epidemiology and infection Table SARS_CoV_2 F490L 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. G204R 2021 Epidemiology and infection Table SARS_CoV_2 G204R 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. G251V 2021 Epidemiology and infection Table SARS_CoV_2 G251V 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. G66S 2021 Epidemiology and infection Table SARS_CoV_2 G66S 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. G78C 2021 Epidemiology and infection Table SARS_CoV_2 G78C 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. H49Y 2021 Epidemiology and infection Table SARS_CoV_2 H49Y 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. H519P 2021 Epidemiology and infection Table SARS_CoV_2 H519P 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. H93Y 2021 Epidemiology and infection Table SARS_CoV_2 H93Y 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. I121L 2021 Epidemiology and infection Table SARS_CoV_2 I121L 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. I292T 2021 Epidemiology and infection Table SARS_CoV_2 I292T 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. I472V 2021 Epidemiology and infection Table SARS_CoV_2 I472V 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. I52T 2021 Epidemiology and infection Table SARS_CoV_2 I52T 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. I76F 2021 Epidemiology and infection Table SARS_CoV_2 I76F 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. I9T 2021 Epidemiology and infection Table SARS_CoV_2 I9T 0 3 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. K16N 2021 Epidemiology and infection Table SARS_CoV_2 K16N 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. K458R 2021 Epidemiology and infection Table SARS_CoV_2 K458R 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. L127I 2021 Epidemiology and infection Table SARS_CoV_2 L127I 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. L129F 2021 Epidemiology and infection Table SARS_CoV_2 L129F 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. L452R 2021 Epidemiology and infection Table SARS_CoV_2 L452R 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. L73F 2021 Epidemiology and infection Table SARS_CoV_2 L73F 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. L84S 2021 Epidemiology and infection Table SARS_CoV_2 L84S 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. L94F 2021 Epidemiology and infection Table SARS_CoV_2 L94F 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. N439K 2021 Epidemiology and infection Table SARS_CoV_2 N439K 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. P13L 2021 Epidemiology and infection Table SARS_CoV_2 P13L 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. P25L 2021 Epidemiology and infection Table SARS_CoV_2 P25L 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. P30S 2021 Epidemiology and infection Table SARS_CoV_2 P30S 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. P323L 2021 Epidemiology and infection Table SARS_CoV_2 P323L 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. P344S 2021 Epidemiology and infection Table SARS_CoV_2 P344S 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. P36S 2021 Epidemiology and infection Table SARS_CoV_2 P36S 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. P57L 2021 Epidemiology and infection Table SARS_CoV_2 P57L 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. P681H 2021 Epidemiology and infection Table SARS_CoV_2 P681H 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Q239K 2021 Epidemiology and infection Table SARS_CoV_2 Q239K 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Q57H 2021 Epidemiology and infection Table SARS_CoV_2 Q57H 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Q72H 2021 Epidemiology and infection Table SARS_CoV_2 Q72H 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Q91K 2021 Epidemiology and infection Table SARS_CoV_2 Q91K 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. R101L 2021 Epidemiology and infection Table SARS_CoV_2 R101L 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. R158C 2021 Epidemiology and infection Table SARS_CoV_2 R158C 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. R203K 2021 Epidemiology and infection Table SARS_CoV_2 R203K 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. R52T 2021 Epidemiology and infection Table SARS_CoV_2 R52T 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. R78H 2021 Epidemiology and infection Table SARS_CoV_2 R78H 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. S188L 2021 Epidemiology and infection Table SARS_CoV_2 S188L 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. S194L 2021 Epidemiology and infection Table SARS_CoV_2 S194L 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. S197L 2021 Epidemiology and infection Table SARS_CoV_2 S197L 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. S202N 2021 Epidemiology and infection Table SARS_CoV_2 S202N 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. S247R 2021 Epidemiology and infection Table SARS_CoV_2 S247R 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. S4777N 2021 Epidemiology and infection Table SARS_CoV_2 S4777N 0 6 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. S943T 2021 Epidemiology and infection Table SARS_CoV_2 S943T 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. S982A 2021 Epidemiology and infection Table SARS_CoV_2 S982A 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. T141I 2021 Epidemiology and infection Table SARS_CoV_2 T141I 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. T148I 2021 Epidemiology and infection Table SARS_CoV_2 T148I 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. T175I 2021 Epidemiology and infection Table SARS_CoV_2 T175I 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. T175M 2021 Epidemiology and infection Table SARS_CoV_2 T175M 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. T21I 2021 Epidemiology and infection Table SARS_CoV_2 T21I 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. T339I 2021 Epidemiology and infection Table SARS_CoV_2 T339I 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. T716I 2021 Epidemiology and infection Table SARS_CoV_2 T716I 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. T7I 2021 Epidemiology and infection Table SARS_CoV_2 T7I 0 3 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. T9I 2021 Epidemiology and infection Table SARS_CoV_2 T9I 0 3 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. V1176F 2021 Epidemiology and infection Table SARS_CoV_2 V1176F 0 6 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. V24M 2021 Epidemiology and infection Table SARS_CoV_2 V24M 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. V341I 2021 Epidemiology and infection Table SARS_CoV_2 V341I 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. V483A 2021 Epidemiology and infection Table SARS_CoV_2 V483A 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. V58F 2021 Epidemiology and infection Table SARS_CoV_2 V58F 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. W128L 2021 Epidemiology and infection Table SARS_CoV_2 W128L 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. W131C 2021 Epidemiology and infection Table SARS_CoV_2 W131C 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. W149L 2021 Epidemiology and infection Table SARS_CoV_2 W149L 0 5 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Y20N 2021 Epidemiology and infection Table SARS_CoV_2 Y20N 0 4 33928885 SARS-CoV-2 mutations: the biological trackway towards viral fitness. Y508H 2021 Epidemiology and infection Table SARS_CoV_2 Y508H 0 5 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. A65V 2021 Journal of medical virology Table SARS_CoV_2 A65V 0 4 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. D614G 2021 Journal of medical virology Table SARS_CoV_2 D614G 0 5 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. D950N 2021 Journal of medical virology Table SARS_CoV_2 D950N 0 5 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. E154A 2021 Journal of medical virology Table SARS_CoV_2 E154A 0 5 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. I49V 2021 Journal of medical virology Table SARS_CoV_2 I49V 0 4 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. L452R 2021 Journal of medical virology Table SARS_CoV_2 L452R 0 5 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. P141S 2021 Journal of medical virology Table SARS_CoV_2 P141S 0 5 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. P314L 2021 Journal of medical virology Table SARS_CoV_2 P314L 0 5 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. P681H 2021 Journal of medical virology Table SARS_CoV_2 P681H 0 5 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. P681R 2021 Journal of medical virology Table SARS_CoV_2 P681R 0 5 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. Q418H 2021 Journal of medical virology Table SARS_CoV_2 Q418H 0 5 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. T19R 2021 Journal of medical virology Table SARS_CoV_2 T19R 0 4 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. T35I 2021 Journal of medical virology Table SARS_CoV_2 T35I 0 4 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. T44I 2021 Journal of medical virology Table SARS_CoV_2 T44I 0 4 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. T478K 2021 Journal of medical virology Table SARS_CoV_2 T478K 0 5 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. T492I 2021 Journal of medical virology Table SARS_CoV_2 T492I 0 5 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. T732A 2021 Journal of medical virology Table SARS_CoV_2 T732A 0 5 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 046.C > T 2021 Transboundary and emerging diseases Table SARS_CoV_2 C046T 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 059.C > T 2021 Transboundary and emerging diseases Table SARS_CoV_2 C059T 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 060.C > T 2021 Transboundary and emerging diseases Table SARS_CoV_2 C060T 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 083.G > T 2021 Transboundary and emerging diseases Table SARS_CoV_2 G083T 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 144.T > C 2021 Transboundary and emerging diseases Table SARS_CoV_2 T144C 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 324.C > T 2021 Transboundary and emerging diseases Table SARS_CoV_2 C324T 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 540.G > A 2021 Transboundary and emerging diseases Table SARS_CoV_2 G540A 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 553.G > A 2021 Transboundary and emerging diseases Table SARS_CoV_2 G553A 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 563.G > T 2021 Transboundary and emerging diseases Table SARS_CoV_2 G563T 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 711.G > T 2021 Transboundary and emerging diseases Table SARS_CoV_2 G711T 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 747.C > T 2021 Transboundary and emerging diseases Table SARS_CoV_2 C747T 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 782.C > T 2021 Transboundary and emerging diseases Table SARS_CoV_2 C782T 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 858.A > G 2021 Transboundary and emerging diseases Table SARS_CoV_2 A858G 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 877.C > T 2021 Transboundary and emerging diseases Table SARS_CoV_2 C877T 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 881.G > A 2021 Transboundary and emerging diseases Table SARS_CoV_2 G881A 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 882.G > A 2021 Transboundary and emerging diseases Table SARS_CoV_2 G882A 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 883.G > C 2021 Transboundary and emerging diseases Table SARS_CoV_2 G883C 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 916.C > T 2021 Transboundary and emerging diseases Table SARS_CoV_2 C916T 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 964.C > T 2021 Transboundary and emerging diseases Table SARS_CoV_2 C964T 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. 998.C > T 2021 Transboundary and emerging diseases Table SARS_CoV_2 C998T 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. Arg203Lys 2021 Transboundary and emerging diseases Table SARS_CoV_2 R203K 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. Gln57His 2021 Transboundary and emerging diseases Table SARS_CoV_2 Q57H 0 8 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. Gly204Arg 2021 Transboundary and emerging diseases Table SARS_CoV_2 G204R 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. Leu3606Phe 2021 Transboundary and emerging diseases Table SARS_CoV_2 L3606F 0 10 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. Leu84Ser 2021 Transboundary and emerging diseases Table SARS_CoV_2 L84S 0 8 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. Met5865Val 2021 Transboundary and emerging diseases Table SARS_CoV_2 M5865V 0 10 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. Ser24Leu 2021 Transboundary and emerging diseases Table SARS_CoV_2 S24L 0 8 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. Ser3884Leu 2021 Transboundary and emerging diseases Table SARS_CoV_2 S3884L 0 10 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. Ser5932Phe 2021 Transboundary and emerging diseases Table SARS_CoV_2 S5932F 0 10 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. Thr175Met 2021 Transboundary and emerging diseases Table SARS_CoV_2 T175M 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. Thr265Ile 2021 Transboundary and emerging diseases Table SARS_CoV_2 T265I 0 9 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. Thr5020Ile 2021 Transboundary and emerging diseases Table SARS_CoV_2 T5020I 0 10 33975021 A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern. E484K 2021 Infection, genetics and evolution Table SARS_CoV_2 E484K 0 5 33975021 A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern. K417N 2021 Infection, genetics and evolution Table SARS_CoV_2 K417N 0 5 33975021 A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern. K417T 2021 Infection, genetics and evolution Table SARS_CoV_2 K417T 0 5 33975021 A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern. L452R 2021 Infection, genetics and evolution Table SARS_CoV_2 L452R 0 5 33975021 A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern. N501Y 2021 Infection, genetics and evolution Table SARS_CoV_2 N501Y 0 5 33975021 A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern. S477N 2021 Infection, genetics and evolution Table SARS_CoV_2 S477N 0 5 33983915 Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant - New York City, New York, January 1-April 5, 2021. E484K 2021 MMWR. Morbidity and mortality weekly report Table SARS_CoV_2 E484K 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. A348S 2021 Genomics Table SARS_CoV_2 A348S 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. A352S 2021 Genomics Table SARS_CoV_2 A352S 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. A475S 2021 Genomics Table SARS_CoV_2 A475S 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. A475V 2021 Genomics Table SARS_CoV_2 A475V 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. A520S 2021 Genomics Table SARS_CoV_2 A520S 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. A522S 2021 Genomics Table SARS_CoV_2 A522S 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. A522V 2021 Genomics Table SARS_CoV_2 A522V 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. D427N 2021 Genomics Table SARS_CoV_2 D427N 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. E406Q 2021 Genomics Table SARS_CoV_2 E406Q 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. E471Q 2021 Genomics Table SARS_CoV_2 E471Q 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. E484K 2021 Genomics Table SARS_CoV_2 E484K 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. E484Q 2021 Genomics Table SARS_CoV_2 E484Q 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. F486L 2021 Genomics Table SARS_CoV_2 F486L 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. F490L 2021 Genomics Table SARS_CoV_2 F490L 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. F490S 2021 Genomics Table SARS_CoV_2 F490S 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. F494P 2021 Genomics Table SARS_CoV_2 F494P 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. G446V 2021 Genomics Table SARS_CoV_2 G446V 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. G496S 2021 Genomics Table SARS_CoV_2 G496S 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. I410V 2021 Genomics Table SARS_CoV_2 I410V 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. K356R 2021 Genomics Table SARS_CoV_2 K356R 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. K378N 2021 Genomics Table SARS_CoV_2 K378N 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. K417N 2021 Genomics Table SARS_CoV_2 K417N 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. K417T 2021 Genomics Table SARS_CoV_2 K417T 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. K444N 2021 Genomics Table SARS_CoV_2 K444N 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. L452M 2021 Genomics Table SARS_CoV_2 L452M 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. L452R 2021 Genomics Table SARS_CoV_2 L452R 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. L455F 2021 Genomics Table SARS_CoV_2 L455F 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. N439K 2021 Genomics Table SARS_CoV_2 N439K 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. N440K 2021 Genomics Table SARS_CoV_2 N440K 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. N450K 2021 Genomics Table SARS_CoV_2 N450K 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. N501T 2021 Genomics Table SARS_CoV_2 N501T 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. N501Y 2021 Genomics Table SARS_CoV_2 N501Y 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. P330S 2021 Genomics Table SARS_CoV_2 P330S 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. P384L 2021 Genomics Table SARS_CoV_2 P384L 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. P384S 2021 Genomics Table SARS_CoV_2 P384S 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. P479S 2021 Genomics Table SARS_CoV_2 P479S 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Q414K 2021 Genomics Table SARS_CoV_2 Q414K 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Q414R 2021 Genomics Table SARS_CoV_2 Q414R 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Q493H 2021 Genomics Table SARS_CoV_2 Q493H 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Q493L 2021 Genomics Table SARS_CoV_2 Q493L 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Q493R 2021 Genomics Table SARS_CoV_2 Q493R 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. R346K 2021 Genomics Table SARS_CoV_2 R346K 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. R346S 2021 Genomics Table SARS_CoV_2 R346S 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. R357K 2021 Genomics Table SARS_CoV_2 R357K 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. R403K 2021 Genomics Table SARS_CoV_2 R403K 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. R408I 2021 Genomics Table SARS_CoV_2 R408I 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. S459Y 2021 Genomics Table SARS_CoV_2 S459Y 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. S477I 2021 Genomics Table SARS_CoV_2 S477I 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. S477N 2021 Genomics Table SARS_CoV_2 S477N 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. S477R 2021 Genomics Table SARS_CoV_2 S477R 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. S490L 2021 Genomics Table SARS_CoV_2 S490L 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. S494P 2021 Genomics Table SARS_CoV_2 S494P 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. T385I 2021 Genomics Table SARS_CoV_2 T385I 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. T385N 2021 Genomics Table SARS_CoV_2 T385N 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. T478I 2021 Genomics Table SARS_CoV_2 T478I 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. T478K 2021 Genomics Table SARS_CoV_2 T478K 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. V362F 2021 Genomics Table SARS_CoV_2 V362F 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. V367F 2021 Genomics Table SARS_CoV_2 V367F 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. V382L 2021 Genomics Table SARS_CoV_2 V382L 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. V483A 2021 Genomics Table SARS_CoV_2 V483A 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. V483F 2021 Genomics Table SARS_CoV_2 V483F 0 5 34004284 Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries. Y453F 2021 Genomics Table SARS_CoV_2 Y453F 0 5 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. A435S 2021 Briefings in bioinformatics Table SARS_CoV_2 A435S 0 5 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. D364Y 2021 Briefings in bioinformatics Table SARS_CoV_2 D364Y 0 5 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. F342L 2021 Briefings in bioinformatics Table SARS_CoV_2 F342L 0 5 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. G476S 2021 Briefings in bioinformatics Table SARS_CoV_2 G476S 0 5 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. N354D 2021 Briefings in bioinformatics Table SARS_CoV_2 N354D 0 5 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. R408I 2021 Briefings in bioinformatics Table SARS_CoV_2 R408I 0 5 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. V341I 2021 Briefings in bioinformatics Table SARS_CoV_2 V341I 0 5 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. V367F 2021 Briefings in bioinformatics Table SARS_CoV_2 V367F 0 5 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. V483A 2021 Briefings in bioinformatics Table SARS_CoV_2 V483A 0 5 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. W436R 2021 Briefings in bioinformatics Table SARS_CoV_2 W436R 0 5 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. E484K 2021 Clinical microbiology and infection Table SARS_CoV_2 E484K 0 5 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. E484Q 2021 Clinical microbiology and infection Table SARS_CoV_2 E484Q 0 5 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. K417N 2021 Clinical microbiology and infection Table SARS_CoV_2 K417N 0 5 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. K417T 2021 Clinical microbiology and infection Table SARS_CoV_2 K417T 0 5 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. L452R 2021 Clinical microbiology and infection Table SARS_CoV_2 L452R 0 5 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. N501Y 2021 Clinical microbiology and infection Table SARS_CoV_2 N501Y 0 5 34015535 Novel SARS-CoV-2 variants: the pandemics within the pandemic. N510Y 2021 Clinical microbiology and infection Table SARS_CoV_2 N510Y 0 5 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. E484K 2021 Journal of molecular biology Table SARS_CoV_2 E484K 0 5 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. E484K/N 2021 Journal of molecular biology Table SARS_CoV_2 E484K;E484N 0;0 7;7 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. K417N 2021 Journal of molecular biology Table SARS_CoV_2 K417N 0 5 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. N501Y 2021 Journal of molecular biology Table SARS_CoV_2 N501Y 0 5 34039497 An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose. D614G 2021 Vaccine Table SARS_CoV_2 D614G 0 5 34039497 An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose. K986P 2021 Vaccine Table SARS_CoV_2 K986P 0 5 34039497 An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose. V987P 2021 Vaccine Table SARS_CoV_2 V987P 0 5 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. N501Y 2021 Clinical microbiology and infection Table SARS_CoV_2 N501Y 0 5 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. A119S 2021 Infection, genetics and evolution Table SARS_CoV_2 A119S 0 5 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. A12964G 2021 Infection, genetics and evolution Table SARS_CoV_2 A12964G 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. A22812C 2021 Infection, genetics and evolution Table SARS_CoV_2 A22812C 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. A23063T 2021 Infection, genetics and evolution Table SARS_CoV_2 A23063T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. A2529V 2021 Infection, genetics and evolution Table SARS_CoV_2 A2529V 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. A27853C 2021 Infection, genetics and evolution Table SARS_CoV_2 A27853C 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. A5648C 2021 Infection, genetics and evolution Table SARS_CoV_2 A5648C 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. A6319G 2021 Infection, genetics and evolution Table SARS_CoV_2 A6319G 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. A6613G 2021 Infection, genetics and evolution Table SARS_CoV_2 A6613G 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C100T 2021 Infection, genetics and evolution Table SARS_CoV_2 C100T 0 5 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C11824T 2021 Infection, genetics and evolution Table SARS_CoV_2 C11824T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C12778T 2021 Infection, genetics and evolution Table SARS_CoV_2 C12778T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C13860T 2021 Infection, genetics and evolution Table SARS_CoV_2 C13860T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C19602T 2021 Infection, genetics and evolution Table SARS_CoV_2 C19602T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C21614T 2021 Infection, genetics and evolution Table SARS_CoV_2 C21614T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C21621A 2021 Infection, genetics and evolution Table SARS_CoV_2 C21621A 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C21638T 2021 Infection, genetics and evolution Table SARS_CoV_2 C21638T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C23525T 2021 Infection, genetics and evolution Table SARS_CoV_2 C23525T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C24642T 2021 Infection, genetics and evolution Table SARS_CoV_2 C24642T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C2749T 2021 Infection, genetics and evolution Table SARS_CoV_2 C2749T 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C28253T 2021 Infection, genetics and evolution Table SARS_CoV_2 C28253T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C28512G 2021 Infection, genetics and evolution Table SARS_CoV_2 C28512G 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C29722T 2021 Infection, genetics and evolution Table SARS_CoV_2 C29722T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C29754T 2021 Infection, genetics and evolution Table SARS_CoV_2 C29754T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C3828T 2021 Infection, genetics and evolution Table SARS_CoV_2 C3828T 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C6573T 2021 Infection, genetics and evolution Table SARS_CoV_2 C6573T 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C7600T 2021 Infection, genetics and evolution Table SARS_CoV_2 C7600T 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. C7851T 2021 Infection, genetics and evolution Table SARS_CoV_2 C7851T 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. D138Y 2021 Infection, genetics and evolution Table SARS_CoV_2 D138Y 0 5 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. E33A 2021 Infection, genetics and evolution Table SARS_CoV_2 E33A 0 4 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. E484K 2021 Infection, genetics and evolution Table SARS_CoV_2 E484K 0 5 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. E92K 2021 Infection, genetics and evolution Table SARS_CoV_2 E92K 0 4 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. F120F 2021 Infection, genetics and evolution Table SARS_CoV_2 F120F 0 5 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. F3605L 2021 Infection, genetics and evolution Table SARS_CoV_2 F3605L 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. G1264T 2021 Infection, genetics and evolution Table SARS_CoV_2 G1264T 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. G17259T 2021 Infection, genetics and evolution Table SARS_CoV_2 G17259T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. G19656T 2021 Infection, genetics and evolution Table SARS_CoV_2 G19656T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. G21974T 2021 Infection, genetics and evolution Table SARS_CoV_2 G21974T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. G22132T 2021 Infection, genetics and evolution Table SARS_CoV_2 G22132T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. G23012A 2021 Infection, genetics and evolution Table SARS_CoV_2 G23012A 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. G28167A 2021 Infection, genetics and evolution Table SARS_CoV_2 G28167A 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. G28628T 2021 Infection, genetics and evolution Table SARS_CoV_2 G28628T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. G28975T 2021 Infection, genetics and evolution Table SARS_CoV_2 G28975T 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. H655Y 2021 Infection, genetics and evolution Table SARS_CoV_2 H655Y 0 5 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. K1795Q 2021 Infection, genetics and evolution Table SARS_CoV_2 K1795Q 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. K417T 2021 Infection, genetics and evolution Table SARS_CoV_2 K417T 0 5 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. L18F 2021 Infection, genetics and evolution Table SARS_CoV_2 L18F 0 4 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. L3468V 2021 Infection, genetics and evolution Table SARS_CoV_2 L3468V 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. M234I 2021 Infection, genetics and evolution Table SARS_CoV_2 M234I 0 5 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. N501Y 2021 Infection, genetics and evolution Table SARS_CoV_2 N501Y 0 5 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. P26S 2021 Infection, genetics and evolution Table SARS_CoV_2 P26S 0 4 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. P80R 2021 Infection, genetics and evolution Table SARS_CoV_2 P80R 0 4 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. R190S 2021 Infection, genetics and evolution Table SARS_CoV_2 R190S 0 5 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. S1188L 2021 Infection, genetics and evolution Table SARS_CoV_2 S1188L 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. S2103F 2021 Infection, genetics and evolution Table SARS_CoV_2 S2103F 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. S253P 2021 Infection, genetics and evolution Table SARS_CoV_2 S253P 0 5 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. S5665I 2021 Infection, genetics and evolution Table SARS_CoV_2 S5665I 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. T1027I 2021 Infection, genetics and evolution Table SARS_CoV_2 T1027I 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. T10667G 2021 Infection, genetics and evolution Table SARS_CoV_2 T10667G 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. T11078C 2021 Infection, genetics and evolution Table SARS_CoV_2 T11078C 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. T20N 2021 Infection, genetics and evolution Table SARS_CoV_2 T20N 0 4 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. T26149C 2021 Infection, genetics and evolution Table SARS_CoV_2 T26149C 0 7 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. T4532I 2021 Infection, genetics and evolution Table SARS_CoV_2 T4532I 0 6 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. T733C 2021 Infection, genetics and evolution Table SARS_CoV_2 T733C 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. A249T 2021 Microbial pathogenesis Table SARS_CoV_2 A249T 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. A274S 2021 Microbial pathogenesis Table SARS_CoV_2 A274S 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. A994D 2021 Microbial pathogenesis Table SARS_CoV_2 A994D 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. A99V 2021 Microbial pathogenesis Table SARS_CoV_2 A99V 0 4 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. C83F 2021 Microbial pathogenesis Table SARS_CoV_2 C83F 0 4 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. D614G 2021 Microbial pathogenesis Table SARS_CoV_2 D614G 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. D614G,N 2021 Microbial pathogenesis Table SARS_CoV_2 D614G 0 7 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. E1213A 2021 Microbial pathogenesis Table SARS_CoV_2 E1213A 0 6 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. E156D 2021 Microbial pathogenesis Table SARS_CoV_2 E156D 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. E210K 2021 Microbial pathogenesis Table SARS_CoV_2 E210K 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. E484K 2021 Microbial pathogenesis Table SARS_CoV_2 E484K 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. F1503I 2021 Microbial pathogenesis Table SARS_CoV_2 F1503I 0 6 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. G142del 2021 Microbial pathogenesis Table SARS_CoV_2 G142del 0 7 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. G1433C 2021 Microbial pathogenesis Table SARS_CoV_2 G1433C 0 6 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. G204R,N 2021 Microbial pathogenesis Table SARS_CoV_2 G204R 0 7 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. H119Q 2021 Microbial pathogenesis Table SARS_CoV_2 H119Q 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. I120F 2021 Microbial pathogenesis Table SARS_CoV_2 I120F 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. I358V 2021 Microbial pathogenesis Table SARS_CoV_2 I358V 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. I385T 2021 Microbial pathogenesis Table SARS_CoV_2 I385T 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. I76T,N 2021 Microbial pathogenesis Table SARS_CoV_2 I76T 0 6 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. L141del 2021 Microbial pathogenesis Table SARS_CoV_2 L141del 0 7 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. L513F 2021 Microbial pathogenesis Table SARS_CoV_2 L513F 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. L57F 2021 Microbial pathogenesis Table SARS_CoV_2 L57F 0 4 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. L84S,N 2021 Microbial pathogenesis Table SARS_CoV_2 L84S 0 6 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. M184I 2021 Microbial pathogenesis Table SARS_CoV_2 M184I 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. M209I 2021 Microbial pathogenesis Table SARS_CoV_2 M209I 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. N209del 2021 Microbial pathogenesis Table SARS_CoV_2 N209del 0 7 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. P109L 2021 Microbial pathogenesis Table SARS_CoV_2 P109L 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. P236S 2021 Microbial pathogenesis Table SARS_CoV_2 P236S 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. P323L 2021 Microbial pathogenesis Table SARS_CoV_2 P323L 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. Q1884H 2021 Microbial pathogenesis Table SARS_CoV_2 Q1884H 0 6 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. Q229R 2021 Microbial pathogenesis Table SARS_CoV_2 Q229R 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. Q57H 2021 Microbial pathogenesis Table SARS_CoV_2 Q57H 0 4 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. Q57H,N 2021 Microbial pathogenesis Table SARS_CoV_2 Q57H 0 6 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. R118I 2021 Microbial pathogenesis Table SARS_CoV_2 R118I 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. R203K 2021 Microbial pathogenesis Table SARS_CoV_2 R203K 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. R370H 2021 Microbial pathogenesis Table SARS_CoV_2 R370H 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. S115A 2021 Microbial pathogenesis Table SARS_CoV_2 S115A 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. S1682F 2021 Microbial pathogenesis Table SARS_CoV_2 S1682F 0 6 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. S193I 2021 Microbial pathogenesis Table SARS_CoV_2 S193I 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. S243I 2021 Microbial pathogenesis Table SARS_CoV_2 S243I 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. S36P 2021 Microbial pathogenesis Table SARS_CoV_2 S36P 0 4 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. S99F 2021 Microbial pathogenesis Table SARS_CoV_2 S99F 0 4 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. T12I,N 2021 Microbial pathogenesis Table SARS_CoV_2 T12I 0 6 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. T143I 2021 Microbial pathogenesis Table SARS_CoV_2 T143I 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. T217I 2021 Microbial pathogenesis Table SARS_CoV_2 T217I 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. T229I,N 2021 Microbial pathogenesis Table SARS_CoV_2 T229I 0 7 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. T271I 2021 Microbial pathogenesis Table SARS_CoV_2 T271I 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. T45I 2021 Microbial pathogenesis Table SARS_CoV_2 T45I 0 4 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. T73I 2021 Microbial pathogenesis Table SARS_CoV_2 T73I 0 4 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. V1164A 2021 Microbial pathogenesis Table SARS_CoV_2 V1164A 0 6 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. V1264L 2021 Microbial pathogenesis Table SARS_CoV_2 V1264L 0 6 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. V143del 2021 Microbial pathogenesis Table SARS_CoV_2 V143del 0 7 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. V160I 2021 Microbial pathogenesis Table SARS_CoV_2 V160I 0 5 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. W64L 2021 Microbial pathogenesis Table SARS_CoV_2 W64L 0 4 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. Y144del 2021 Microbial pathogenesis Table SARS_CoV_2 Y144del 0 7 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. A570D 2021 mBio Table SARS_CoV_2 A570D 0 5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. A701V 2021 mBio Table SARS_CoV_2 A701V 0 5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. D1118H 2021 mBio Table SARS_CoV_2 D1118H 0 6 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. D215G 2021 mBio Table SARS_CoV_2 D215G 0 5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. D614G 2021 mBio Table SARS_CoV_2 D614G 0 5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. D80A 2021 mBio Table SARS_CoV_2 D80A 0 4 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. E484K 2021 mBio Table SARS_CoV_2 E484K 0 5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. F486S 2021 mBio Table SARS_CoV_2 F486S 0 5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. I692V 2021 mBio Table SARS_CoV_2 I692V 0 5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. K417N 2021 mBio Table SARS_CoV_2 K417N 0 5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. L18F 2021 mBio Table SARS_CoV_2 L18F 0 4 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. M1229I 2021 mBio Table SARS_CoV_2 M1229I 0 6 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. N501Y 2021 mBio Table SARS_CoV_2 N501Y 0 5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. P681H 2021 mBio Table SARS_CoV_2 P681H 0 5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. R246I 2021 mBio Table SARS_CoV_2 R246I 0 5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. S1147L 2021 mBio Table SARS_CoV_2 S1147L 0 6 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. S982A 2021 mBio Table SARS_CoV_2 S982A 0 5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. T716I 2021 mBio Table SARS_CoV_2 T716I 0 5 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Y453F 2021 mBio Table SARS_CoV_2 Y453F 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. A1179V 2021 BMC medical genomics Table SARS_CoV_2 A1179V 0 6 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. A119S 2021 BMC medical genomics Table SARS_CoV_2 A119S 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. A205V 2021 BMC medical genomics Table SARS_CoV_2 A205V 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. A21T 2021 BMC medical genomics Table SARS_CoV_2 A21T 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. A231V 2021 BMC medical genomics Table SARS_CoV_2 A231V 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. A54V 2021 BMC medical genomics Table SARS_CoV_2 A54V 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. A656S 2021 BMC medical genomics Table SARS_CoV_2 A656S 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. A97V 2021 BMC medical genomics Table SARS_CoV_2 A97V 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. A99S 2021 BMC medical genomics Table SARS_CoV_2 A99S 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. D222Y 2021 BMC medical genomics Table SARS_CoV_2 D222Y 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. D270D 2021 BMC medical genomics Table SARS_CoV_2 D270D 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. D284D 2021 BMC medical genomics Table SARS_CoV_2 D284D 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. D418D 2021 BMC medical genomics Table SARS_CoV_2 D418D 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. D614G 2021 BMC medical genomics Table SARS_CoV_2 D614G 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. E115E 2021 BMC medical genomics Table SARS_CoV_2 E115E 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. F106F 2021 BMC medical genomics Table SARS_CoV_2 F106F 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. F1354C 2021 BMC medical genomics Table SARS_CoV_2 F1354C 0 6 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. F150F 2021 BMC medical genomics Table SARS_CoV_2 F150F 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. F1640F 2021 BMC medical genomics Table SARS_CoV_2 F1640F 0 6 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. G204R 2021 BMC medical genomics Table SARS_CoV_2 G204R 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. H337Y 2021 BMC medical genomics Table SARS_CoV_2 H337Y 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. H73Y 2021 BMC medical genomics Table SARS_CoV_2 H73Y 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. H75H 2021 BMC medical genomics Table SARS_CoV_2 H75H 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. H892Y 2021 BMC medical genomics Table SARS_CoV_2 H892Y 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. I157I 2021 BMC medical genomics Table SARS_CoV_2 I157I 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. I168I 2021 BMC medical genomics Table SARS_CoV_2 I168I 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. I258I 2021 BMC medical genomics Table SARS_CoV_2 I258I 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. K12R 2021 BMC medical genomics Table SARS_CoV_2 K12R 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. L205L 2021 BMC medical genomics Table SARS_CoV_2 L205L 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. L280L 2021 BMC medical genomics Table SARS_CoV_2 L280L 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. L321L 2021 BMC medical genomics Table SARS_CoV_2 L321L 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. L37F 2021 BMC medical genomics Table SARS_CoV_2 L37F 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. L42F 2021 BMC medical genomics Table SARS_CoV_2 L42F 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. L60L 2021 BMC medical genomics Table SARS_CoV_2 L60L 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. L775L 2021 BMC medical genomics Table SARS_CoV_2 L775L 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. L877L 2021 BMC medical genomics Table SARS_CoV_2 L877L 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. L93L 2021 BMC medical genomics Table SARS_CoV_2 L93L 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. M234I 2021 BMC medical genomics Table SARS_CoV_2 M234I 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. M49I 2021 BMC medical genomics Table SARS_CoV_2 M49I 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. M576I 2021 BMC medical genomics Table SARS_CoV_2 M576I 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. M906V 2021 BMC medical genomics Table SARS_CoV_2 M906V 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. N151N 2021 BMC medical genomics Table SARS_CoV_2 N151N 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. N154N 2021 BMC medical genomics Table SARS_CoV_2 N154N 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. N30N 2021 BMC medical genomics Table SARS_CoV_2 N30N 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. N435N 2021 BMC medical genomics Table SARS_CoV_2 N435N 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. N811I 2021 BMC medical genomics Table SARS_CoV_2 N811I 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. P116P 2021 BMC medical genomics Table SARS_CoV_2 P116P 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. P13L 2021 BMC medical genomics Table SARS_CoV_2 P13L 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. P1665L 2021 BMC medical genomics Table SARS_CoV_2 P1665L 0 6 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. P184S 2021 BMC medical genomics Table SARS_CoV_2 P184S 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. P199S 2021 BMC medical genomics Table SARS_CoV_2 P199S 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. P203L 2021 BMC medical genomics Table SARS_CoV_2 P203L 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. P227L 2021 BMC medical genomics Table SARS_CoV_2 P227L 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. P323L 2021 BMC medical genomics Table SARS_CoV_2 P323L 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. P53P 2021 BMC medical genomics Table SARS_CoV_2 P53P 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. P679S 2021 BMC medical genomics Table SARS_CoV_2 P679S 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. P822L 2021 BMC medical genomics Table SARS_CoV_2 P822L 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Q160R 2021 BMC medical genomics Table SARS_CoV_2 Q160R 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Q321K 2021 BMC medical genomics Table SARS_CoV_2 Q321K 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Q57H 2021 BMC medical genomics Table SARS_CoV_2 Q57H 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Q677H 2021 BMC medical genomics Table SARS_CoV_2 Q677H 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. R195S 2021 BMC medical genomics Table SARS_CoV_2 R195S 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. R203K 2021 BMC medical genomics Table SARS_CoV_2 R203K 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. R569R 2021 BMC medical genomics Table SARS_CoV_2 R569R 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. S193I 2021 BMC medical genomics Table SARS_CoV_2 S193I 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. S312S 2021 BMC medical genomics Table SARS_CoV_2 S312S 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. S60S 2021 BMC medical genomics Table SARS_CoV_2 S60S 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. S74S 2021 BMC medical genomics Table SARS_CoV_2 S74S 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. T1022I 2021 BMC medical genomics Table SARS_CoV_2 T1022I 0 6 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. T1198K 2021 BMC medical genomics Table SARS_CoV_2 T1198K 0 6 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. T127I 2021 BMC medical genomics Table SARS_CoV_2 T127I 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. T151I 2021 BMC medical genomics Table SARS_CoV_2 T151I 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. T153I 2021 BMC medical genomics Table SARS_CoV_2 T153I 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. T248I 2021 BMC medical genomics Table SARS_CoV_2 T248I 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. T256I 2021 BMC medical genomics Table SARS_CoV_2 T256I 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. V169F 2021 BMC medical genomics Table SARS_CoV_2 V169F 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. V213A 2021 BMC medical genomics Table SARS_CoV_2 V213A 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. V247A 2021 BMC medical genomics Table SARS_CoV_2 V247A 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. V299A 2021 BMC medical genomics Table SARS_CoV_2 V299A 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. V62V 2021 BMC medical genomics Table SARS_CoV_2 V62V 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. V83L 2021 BMC medical genomics Table SARS_CoV_2 V83L 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. W258R 2021 BMC medical genomics Table SARS_CoV_2 W258R 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Y222C 2021 BMC medical genomics Table SARS_CoV_2 Y222C 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Y235Y 2021 BMC medical genomics Table SARS_CoV_2 Y235Y 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Y71Y 2021 BMC medical genomics Table SARS_CoV_2 Y71Y 0 4 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Y789Y 2021 BMC medical genomics Table SARS_CoV_2 Y789Y 0 5 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. E484K 2021 The journal of physical chemistry letters Table SARS_CoV_2 E484K 0 5 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. F456L 2021 The journal of physical chemistry letters Table SARS_CoV_2 F456L 0 5 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. G476S 2021 The journal of physical chemistry letters Table SARS_CoV_2 G476S 0 5 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. K417N 2021 The journal of physical chemistry letters Table SARS_CoV_2 K417N 0 5 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. K417V 2021 The journal of physical chemistry letters Table SARS_CoV_2 K417V 0 5 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. L455Y 2021 The journal of physical chemistry letters Table SARS_CoV_2 L455Y 0 5 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. N439R 2021 The journal of physical chemistry letters Table SARS_CoV_2 N439R 0 5 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. N501T 2021 The journal of physical chemistry letters Table SARS_CoV_2 N501T 0 5 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. N501Y 2021 The journal of physical chemistry letters Table SARS_CoV_2 N501Y 0 5 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. Q498Y 2021 The journal of physical chemistry letters Table SARS_CoV_2 Q498Y 0 5 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. R403K 2021 The journal of physical chemistry letters Table SARS_CoV_2 R403K 0 5 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. V367F 2021 The journal of physical chemistry letters Table SARS_CoV_2 V367F 0 5 34086459 Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. V483A 2021 The journal of physical chemistry letters Table SARS_CoV_2 V483A 0 5 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. D614G 2021 PLoS pathogens Table SARS_CoV_2 D614G 0 5 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. E484K 2021 PLoS pathogens Table SARS_CoV_2 E484K 0 5 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. G1362R 2021 PLoS pathogens Table SARS_CoV_2 G1362R 0 6 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. G204R 2021 PLoS pathogens Table SARS_CoV_2 G204R 0 5 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. G769V 2021 PLoS pathogens Table SARS_CoV_2 G769V 0 5 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. P1936H 2021 PLoS pathogens Table SARS_CoV_2 P1936H 0 6 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. P314L 2021 PLoS pathogens Table SARS_CoV_2 P314L 0 5 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. Q418H 2021 PLoS pathogens Table SARS_CoV_2 Q418H 0 5 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. R203K 2021 PLoS pathogens Table SARS_CoV_2 R203K 0 5 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. S187L 2021 PLoS pathogens Table SARS_CoV_2 S187L 0 5 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. W152L 2021 PLoS pathogens Table SARS_CoV_2 W152L 0 5 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. E191A 2021 Cell & bioscience Table SARS_CoV_2 E191A 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. A1043V 2021 European journal of medical research Table SARS_CoV_2 A1043V 0 6 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. A23403G 2021 European journal of medical research Table SARS_CoV_2 A23403G 0 7 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. A344S 2021 European journal of medical research Table SARS_CoV_2 A344S 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. A348V 2021 European journal of medical research Table SARS_CoV_2 A348V 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. A419S 2021 European journal of medical research Table SARS_CoV_2 A419S 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. A520S 2021 European journal of medical research Table SARS_CoV_2 A520S 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. A522S 2021 European journal of medical research Table SARS_CoV_2 A522S 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. A876T 2021 European journal of medical research Table SARS_CoV_2 A876T 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. A930V 2021 European journal of medical research Table SARS_CoV_2 A930V 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. A97V 2021 European journal of medical research Table SARS_CoV_2 A97V 0 4 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. A994D 2021 European journal of medical research Table SARS_CoV_2 A994D 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. Asp614Gly 2021 European journal of medical research Table SARS_CoV_2 D614G 0 9 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. C14408T 2021 European journal of medical research Table SARS_CoV_2 C14408T 0 7 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. C18060T 2021 European journal of medical research Table SARS_CoV_2 C18060T 0 7 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. C28144T 2021 European journal of medical research Table SARS_CoV_2 C28144T 0 7 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. C28854T 2021 European journal of medical research Table SARS_CoV_2 C28854T 0 7 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. C29095T 2021 European journal of medical research Table SARS_CoV_2 C29095T 0 7 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. C8782T 2021 European journal of medical research Table SARS_CoV_2 C8782T 0 6 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. D103Y 2021 European journal of medical research Table SARS_CoV_2 D103Y 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. D1121G 2021 European journal of medical research Table SARS_CoV_2 D1121G 0 6 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. D1168H 2021 European journal of medical research Table SARS_CoV_2 D1168H 0 6 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. D294D 2021 European journal of medical research Table SARS_CoV_2 D294D 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. D448del 2021 European journal of medical research Table SARS_CoV_2 D448del 0 7 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. D614G 2021 European journal of medical research Table SARS_CoV_2 D614G 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. D936Y 2021 European journal of medical research Table SARS_CoV_2 D936Y 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. E1207E 2021 European journal of medical research Table SARS_CoV_2 E1207E 0 6 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. E1207V 2021 European journal of medical research Table SARS_CoV_2 E1207V 0 6 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. E484K 2021 European journal of medical research Table SARS_CoV_2 E484K 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. E484Q 2021 European journal of medical research Table SARS_CoV_2 E484Q 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. E583D 2021 European journal of medical research Table SARS_CoV_2 E583D 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. F3071Y 2021 European journal of medical research Table SARS_CoV_2 F3071Y 0 6 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. G196V 2021 European journal of medical research Table SARS_CoV_2 G196V 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. G204R 2021 European journal of medical research Table SARS_CoV_2 G204R 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. G238C 2021 European journal of medical research Table SARS_CoV_2 G238C 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. G251V 2021 European journal of medical research Table SARS_CoV_2 G251V 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. G25563T 2021 European journal of medical research Table SARS_CoV_2 G25563T 0 7 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. G26144T 2021 European journal of medical research Table SARS_CoV_2 G26144T 0 7 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. G3334S 2021 European journal of medical research Table SARS_CoV_2 G3334S 0 6 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. G339S 2021 European journal of medical research Table SARS_CoV_2 G339S 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. G392D 2021 European journal of medical research Table SARS_CoV_2 G392D 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. G476S 2021 European journal of medical research Table SARS_CoV_2 G476S 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. G571S 2021 European journal of medical research Table SARS_CoV_2 G571S 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. G716I 2021 European journal of medical research Table SARS_CoV_2 G716I 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. H49Y 2021 European journal of medical research Table SARS_CoV_2 H49Y 0 4 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. H519Q 2021 European journal of medical research Table SARS_CoV_2 H519Q 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. K417N 2021 European journal of medical research Table SARS_CoV_2 K417N 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. K417T 2021 European journal of medical research Table SARS_CoV_2 K417T 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. K529E 2021 European journal of medical research Table SARS_CoV_2 K529E 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. K77M 2021 European journal of medical research Table SARS_CoV_2 K77M 0 4 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. L329I 2021 European journal of medical research Table SARS_CoV_2 L329I 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. L3606F 2021 European journal of medical research Table SARS_CoV_2 L3606F 0 6 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. L452R 2021 European journal of medical research Table SARS_CoV_2 L452R 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. L54F 2021 European journal of medical research Table SARS_CoV_2 L54F 0 4 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. L84S 2021 European journal of medical research Table SARS_CoV_2 L84S 0 4 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. N2894D 2021 European journal of medical research Table SARS_CoV_2 N2894D 0 6 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. N501Y 2021 European journal of medical research Table SARS_CoV_2 N501Y 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. P314L 2021 European journal of medical research Table SARS_CoV_2 P314L 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. P323L 2021 European journal of medical research Table SARS_CoV_2 P323L 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. Q57H 2021 European journal of medical research Table SARS_CoV_2 Q57H 0 4 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. Q677H 2021 European journal of medical research Table SARS_CoV_2 Q677H 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. R191C 2021 European journal of medical research Table SARS_CoV_2 R191C 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. R203K 2021 European journal of medical research Table SARS_CoV_2 R203K 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. R408I 2021 European journal of medical research Table SARS_CoV_2 R408I 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. R78M 2021 European journal of medical research Table SARS_CoV_2 R78M 0 4 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. S1197R 2021 European journal of medical research Table SARS_CoV_2 S1197R 0 6 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. S194L 2021 European journal of medical research Table SARS_CoV_2 S194L 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. S197L 2021 European journal of medical research Table SARS_CoV_2 S197L 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. S301F 2021 European journal of medical research Table SARS_CoV_2 S301F 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. T175M 2021 European journal of medical research Table SARS_CoV_2 T175M 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. T265I 2021 European journal of medical research Table SARS_CoV_2 T265I 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. T28144C 2021 European journal of medical research Table SARS_CoV_2 T28144C 0 7 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. T323I 2021 European journal of medical research Table SARS_CoV_2 T323I 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. T708I 2021 European journal of medical research Table SARS_CoV_2 T708I 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. T749I 2021 European journal of medical research Table SARS_CoV_2 T749I 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. T8782C 2021 European journal of medical research Table SARS_CoV_2 T8782C 0 6 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. V367F 2021 European journal of medical research Table SARS_CoV_2 V367F 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. V483A 2021 European journal of medical research Table SARS_CoV_2 V483A 0 5 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. V880I 2021 European journal of medical research Table SARS_CoV_2 V880I 0 5 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. -144delY 2021 Journal of veterinary diagnostic investigation Table SARS_CoV_2 144delY 0 8 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. D614G 2021 Journal of veterinary diagnostic investigation Table SARS_CoV_2 D614G 0 5 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. F486L 2021 Journal of veterinary diagnostic investigation Table SARS_CoV_2 F486L 0 5 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. G142D 2021 Journal of veterinary diagnostic investigation Table SARS_CoV_2 G142D 0 5 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. N501T 2021 Journal of veterinary diagnostic investigation Table SARS_CoV_2 N501T 0 5 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. T23045C 2021 Journal of veterinary diagnostic investigation Table SARS_CoV_2 T23045C 0 7 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. T23047G 2021 Journal of veterinary diagnostic investigation Table SARS_CoV_2 T23047G 0 7 34119826 Therapeutic effect of CT-P59 against SARS-CoV-2 South African variant. E484K 2021 Biochemical and biophysical research communications Table SARS_CoV_2 E484K 0 5 34119826 Therapeutic effect of CT-P59 against SARS-CoV-2 South African variant. K417N 2021 Biochemical and biophysical research communications Table SARS_CoV_2 K417N 0 5 34119826 Therapeutic effect of CT-P59 against SARS-CoV-2 South African variant. N501Y 2021 Biochemical and biophysical research communications Table SARS_CoV_2 N501Y 0 5 34119951 Examining the interactions scorpion venom peptides (HP1090, Meucin-13, and Meucin-18) with the receptor binding domain of the coronavirus spike protein to design a mutated therapeutic peptide. A9T 2021 Journal of molecular graphics & modelling Table SARS_CoV_2 A9T 0 3 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A1020V 2021 Bioinformatics and biology insights Table SARS_CoV_2 A1020V 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A1078V 2021 Bioinformatics and biology insights Table SARS_CoV_2 A1078V 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A262S 2021 Bioinformatics and biology insights Table SARS_CoV_2 A262S 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A262T 2021 Bioinformatics and biology insights Table SARS_CoV_2 A262T 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A288T 2021 Bioinformatics and biology insights Table SARS_CoV_2 A288T 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A570S 2021 Bioinformatics and biology insights Table SARS_CoV_2 A570S 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A570V 2021 Bioinformatics and biology insights Table SARS_CoV_2 A570V 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A626V 2021 Bioinformatics and biology insights Table SARS_CoV_2 A626V 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A647V 2021 Bioinformatics and biology insights Table SARS_CoV_2 A647V 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A653V 2021 Bioinformatics and biology insights Table SARS_CoV_2 A653V 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A684V 2021 Bioinformatics and biology insights Table SARS_CoV_2 A684V 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A706S 2021 Bioinformatics and biology insights Table SARS_CoV_2 A706S 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A783S 2021 Bioinformatics and biology insights Table SARS_CoV_2 A783S 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A829T 2021 Bioinformatics and biology insights Table SARS_CoV_2 A829T 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A845D 2021 Bioinformatics and biology insights Table SARS_CoV_2 A845D 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A845S 2021 Bioinformatics and biology insights Table SARS_CoV_2 A845S 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A845V 2021 Bioinformatics and biology insights Table SARS_CoV_2 A845V 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A846V 2021 Bioinformatics and biology insights Table SARS_CoV_2 A846V 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A879S 2021 Bioinformatics and biology insights Table SARS_CoV_2 A879S 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A892S 2021 Bioinformatics and biology insights Table SARS_CoV_2 A892S 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A892V 2021 Bioinformatics and biology insights Table SARS_CoV_2 A892V 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. A930V 2021 Bioinformatics and biology insights Table SARS_CoV_2 A930V 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. C1243F 2021 Bioinformatics and biology insights Table SARS_CoV_2 C1243F 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. C379F 2021 Bioinformatics and biology insights Table SARS_CoV_2 C379F 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. D1153Y 2021 Bioinformatics and biology insights Table SARS_CoV_2 D1153Y 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. D1163G 2021 Bioinformatics and biology insights Table SARS_CoV_2 D1163G 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. D1260N 2021 Bioinformatics and biology insights Table SARS_CoV_2 D1260N 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. D138H 2021 Bioinformatics and biology insights Table SARS_CoV_2 D138H 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. D253G 2021 Bioinformatics and biology insights Table SARS_CoV_2 D253G 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. D294I 2021 Bioinformatics and biology insights Table SARS_CoV_2 D294I 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. D574Y 2021 Bioinformatics and biology insights Table SARS_CoV_2 D574Y 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. D614G 2021 Bioinformatics and biology insights Table SARS_CoV_2 D614G 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. D936Y 2021 Bioinformatics and biology insights Table SARS_CoV_2 D936Y 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. E1195Q 2021 Bioinformatics and biology insights Table SARS_CoV_2 E1195Q 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. E132D 2021 Bioinformatics and biology insights Table SARS_CoV_2 E132D 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. E156D 2021 Bioinformatics and biology insights Table SARS_CoV_2 E156D 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. E471Q 2021 Bioinformatics and biology insights Table SARS_CoV_2 E471Q 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. E554D 2021 Bioinformatics and biology insights Table SARS_CoV_2 E554D 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. E583D 2021 Bioinformatics and biology insights Table SARS_CoV_2 E583D 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. F1109L 2021 Bioinformatics and biology insights Table SARS_CoV_2 F1109L 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. F220L 2021 Bioinformatics and biology insights Table SARS_CoV_2 F220L 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. F32L 2021 Bioinformatics and biology insights Table SARS_CoV_2 F32L 0 4 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. F486L 2021 Bioinformatics and biology insights Table SARS_CoV_2 F486L 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. F797C 2021 Bioinformatics and biology insights Table SARS_CoV_2 F797C 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. F86S 2021 Bioinformatics and biology insights Table SARS_CoV_2 F86S 0 4 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. G1124V 2021 Bioinformatics and biology insights Table SARS_CoV_2 G1124V 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. G1219V 2021 Bioinformatics and biology insights Table SARS_CoV_2 G1219V 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. G143V 2021 Bioinformatics and biology insights Table SARS_CoV_2 G143V 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. G261D 2021 Bioinformatics and biology insights Table SARS_CoV_2 G261D 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. G261R 2021 Bioinformatics and biology insights Table SARS_CoV_2 G261R 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. G485R 2021 Bioinformatics and biology insights Table SARS_CoV_2 G485R 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. G75V 2021 Bioinformatics and biology insights Table SARS_CoV_2 G75V 0 4 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. G769V 2021 Bioinformatics and biology insights Table SARS_CoV_2 G769V 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. G838D 2021 Bioinformatics and biology insights Table SARS_CoV_2 G838D 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. H1083Q 2021 Bioinformatics and biology insights Table SARS_CoV_2 H1083Q 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. H1101Y 2021 Bioinformatics and biology insights Table SARS_CoV_2 H1101Y 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. H245R 2021 Bioinformatics and biology insights Table SARS_CoV_2 H245R 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. H49Y 2021 Bioinformatics and biology insights Table SARS_CoV_2 H49Y 0 4 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. H519Q 2021 Bioinformatics and biology insights Table SARS_CoV_2 H519Q 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. H655Y 2021 Bioinformatics and biology insights Table SARS_CoV_2 H655Y 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. H69Y 2021 Bioinformatics and biology insights Table SARS_CoV_2 H69Y 0 4 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. I128F 2021 Bioinformatics and biology insights Table SARS_CoV_2 I128F 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. I197V 2021 Bioinformatics and biology insights Table SARS_CoV_2 I197V 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. I468T 2021 Bioinformatics and biology insights Table SARS_CoV_2 I468T 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. K1181R 2021 Bioinformatics and biology insights Table SARS_CoV_2 K1181R 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. K1191N 2021 Bioinformatics and biology insights Table SARS_CoV_2 K1191N 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. K188N 2021 Bioinformatics and biology insights Table SARS_CoV_2 K188N 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. K558R 2021 Bioinformatics and biology insights Table SARS_CoV_2 K558R 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. K786N 2021 Bioinformatics and biology insights Table SARS_CoV_2 K786N 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. K795Q 2021 Bioinformatics and biology insights Table SARS_CoV_2 K795Q 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. L1141F 2021 Bioinformatics and biology insights Table SARS_CoV_2 L1141F 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. L176F 2021 Bioinformatics and biology insights Table SARS_CoV_2 L176F 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. L176I 2021 Bioinformatics and biology insights Table SARS_CoV_2 L176I 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. L229F 2021 Bioinformatics and biology insights Table SARS_CoV_2 L229F 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. L293M 2021 Bioinformatics and biology insights Table SARS_CoV_2 L293M 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. L54F 2021 Bioinformatics and biology insights Table SARS_CoV_2 L54F 0 4 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. L611F 2021 Bioinformatics and biology insights Table SARS_CoV_2 L611F 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. L922F 2021 Bioinformatics and biology insights Table SARS_CoV_2 L922F 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. M153I 2021 Bioinformatics and biology insights Table SARS_CoV_2 M153I 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. M177I 2021 Bioinformatics and biology insights Table SARS_CoV_2 M177I 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. M731I 2021 Bioinformatics and biology insights Table SARS_CoV_2 M731I 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. M740I 2021 Bioinformatics and biology insights Table SARS_CoV_2 M740I 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. N148Y 2021 Bioinformatics and biology insights Table SARS_CoV_2 N148Y 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. N188D 2021 Bioinformatics and biology insights Table SARS_CoV_2 N188D 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. N211Y 2021 Bioinformatics and biology insights Table SARS_CoV_2 N211Y 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. N354K 2021 Bioinformatics and biology insights Table SARS_CoV_2 N354K 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. N501T 2021 Bioinformatics and biology insights Table SARS_CoV_2 N501T 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. N751D 2021 Bioinformatics and biology insights Table SARS_CoV_2 N751D 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. P1079S 2021 Bioinformatics and biology insights Table SARS_CoV_2 P1079S 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. P1162S 2021 Bioinformatics and biology insights Table SARS_CoV_2 P1162S 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. P1263L 2021 Bioinformatics and biology insights Table SARS_CoV_2 P1263L 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. P295H 2021 Bioinformatics and biology insights Table SARS_CoV_2 P295H 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. P330S 2021 Bioinformatics and biology insights Table SARS_CoV_2 P330S 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. P384L 2021 Bioinformatics and biology insights Table SARS_CoV_2 P384L 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. P507H 2021 Bioinformatics and biology insights Table SARS_CoV_2 P507H 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. P507S 2021 Bioinformatics and biology insights Table SARS_CoV_2 P507S 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. P561L 2021 Bioinformatics and biology insights Table SARS_CoV_2 P561L 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. P621S 2021 Bioinformatics and biology insights Table SARS_CoV_2 P621S 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. P631L 2021 Bioinformatics and biology insights Table SARS_CoV_2 P631L 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. P809S 2021 Bioinformatics and biology insights Table SARS_CoV_2 P809S 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. P812S 2021 Bioinformatics and biology insights Table SARS_CoV_2 P812S 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Q1002E 2021 Bioinformatics and biology insights Table SARS_CoV_2 Q1002E 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Q115R 2021 Bioinformatics and biology insights Table SARS_CoV_2 Q115R 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Q1201K 2021 Bioinformatics and biology insights Table SARS_CoV_2 Q1201K 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Q14H 2021 Bioinformatics and biology insights Table SARS_CoV_2 Q14H 0 4 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Q173H 2021 Bioinformatics and biology insights Table SARS_CoV_2 Q173H 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Q271R 2021 Bioinformatics and biology insights Table SARS_CoV_2 Q271R 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Q314R 2021 Bioinformatics and biology insights Table SARS_CoV_2 Q314R 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Q506H 2021 Bioinformatics and biology insights Table SARS_CoV_2 Q506H 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Q613H 2021 Bioinformatics and biology insights Table SARS_CoV_2 Q613H 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Q675H 2021 Bioinformatics and biology insights Table SARS_CoV_2 Q675H 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Q677H 2021 Bioinformatics and biology insights Table SARS_CoV_2 Q677H 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Q677R 2021 Bioinformatics and biology insights Table SARS_CoV_2 Q677R 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Q701H 2021 Bioinformatics and biology insights Table SARS_CoV_2 Q701H 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Q836L 2021 Bioinformatics and biology insights Table SARS_CoV_2 Q836L 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Q836P 2021 Bioinformatics and biology insights Table SARS_CoV_2 Q836P 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. R1091L 2021 Bioinformatics and biology insights Table SARS_CoV_2 R1091L 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. R158S 2021 Bioinformatics and biology insights Table SARS_CoV_2 R158S 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. R214L 2021 Bioinformatics and biology insights Table SARS_CoV_2 R214L 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. R273S 2021 Bioinformatics and biology insights Table SARS_CoV_2 R273S 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. R408I 2021 Bioinformatics and biology insights Table SARS_CoV_2 R408I 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. R682Q 2021 Bioinformatics and biology insights Table SARS_CoV_2 R682Q 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. R682W 2021 Bioinformatics and biology insights Table SARS_CoV_2 R682W 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. R765L 2021 Bioinformatics and biology insights Table SARS_CoV_2 R765L 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. R78M 2021 Bioinformatics and biology insights Table SARS_CoV_2 R78M 0 4 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. S12F 2021 Bioinformatics and biology insights Table SARS_CoV_2 S12F 0 4 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. S13I 2021 Bioinformatics and biology insights Table SARS_CoV_2 S13I 0 4 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. S162I 2021 Bioinformatics and biology insights Table SARS_CoV_2 S162I 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. S221L 2021 Bioinformatics and biology insights Table SARS_CoV_2 S221L 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. S221W 2021 Bioinformatics and biology insights Table SARS_CoV_2 S221W 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. S247R 2021 Bioinformatics and biology insights Table SARS_CoV_2 S247R 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. S254F 2021 Bioinformatics and biology insights Table SARS_CoV_2 S254F 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. S50L 2021 Bioinformatics and biology insights Table SARS_CoV_2 S50L 0 4 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. S640A 2021 Bioinformatics and biology insights Table SARS_CoV_2 S640A 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. S704L 2021 Bioinformatics and biology insights Table SARS_CoV_2 S704L 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. S884F 2021 Bioinformatics and biology insights Table SARS_CoV_2 S884F 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. S922F 2021 Bioinformatics and biology insights Table SARS_CoV_2 S922F 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. S939Y 2021 Bioinformatics and biology insights Table SARS_CoV_2 S939Y 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. T1120I 2021 Bioinformatics and biology insights Table SARS_CoV_2 T1120I 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. T22I 2021 Bioinformatics and biology insights Table SARS_CoV_2 T22I 0 4 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. T240I 2021 Bioinformatics and biology insights Table SARS_CoV_2 T240I 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. T29I 2021 Bioinformatics and biology insights Table SARS_CoV_2 T29I 0 4 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. T345S 2021 Bioinformatics and biology insights Table SARS_CoV_2 T345S 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. T393P 2021 Bioinformatics and biology insights Table SARS_CoV_2 T393P 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. T553N 2021 Bioinformatics and biology insights Table SARS_CoV_2 T553N 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. T572I 2021 Bioinformatics and biology insights Table SARS_CoV_2 T572I 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. T676I 2021 Bioinformatics and biology insights Table SARS_CoV_2 T676I 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. T732A 2021 Bioinformatics and biology insights Table SARS_CoV_2 T732A 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. T76I 2021 Bioinformatics and biology insights Table SARS_CoV_2 T76I 0 4 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. T791I 2021 Bioinformatics and biology insights Table SARS_CoV_2 T791I 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. T827I 2021 Bioinformatics and biology insights Table SARS_CoV_2 T827I 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. T95I 2021 Bioinformatics and biology insights Table SARS_CoV_2 T95I 0 4 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. V1104L 2021 Bioinformatics and biology insights Table SARS_CoV_2 V1104L 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. V1122L 2021 Bioinformatics and biology insights Table SARS_CoV_2 V1122L 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. V1129A 2021 Bioinformatics and biology insights Table SARS_CoV_2 V1129A 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. V1228L 2021 Bioinformatics and biology insights Table SARS_CoV_2 V1228L 0 6 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. V213L 2021 Bioinformatics and biology insights Table SARS_CoV_2 V213L 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. V267L 2021 Bioinformatics and biology insights Table SARS_CoV_2 V267L 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. V367F 2021 Bioinformatics and biology insights Table SARS_CoV_2 V367F 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. V382E 2021 Bioinformatics and biology insights Table SARS_CoV_2 V382E 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. V772I 2021 Bioinformatics and biology insights Table SARS_CoV_2 V772I 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. W258L 2021 Bioinformatics and biology insights Table SARS_CoV_2 W258L 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Y28N 2021 Bioinformatics and biology insights Table SARS_CoV_2 Y28N 0 4 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Y453F 2021 Bioinformatics and biology insights Table SARS_CoV_2 Y453F 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Y508N 2021 Bioinformatics and biology insights Table SARS_CoV_2 Y508N 0 5 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. Y789D 2021 Bioinformatics and biology insights Table SARS_CoV_2 Y789D 0 5 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. E484K 2021 Frontiers in cellular and infection microbiology Table SARS_CoV_2 E484K 0 5 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. E484K/N 2021 Frontiers in cellular and infection microbiology Table SARS_CoV_2 E484K;E484N 0;0 7;7 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. K417N 2021 Frontiers in cellular and infection microbiology Table SARS_CoV_2 K417N 0 5 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. D178H 2021 Emerging microbes & infections Table SARS_CoV_2 D178H 0 5 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. V70L 2021 Emerging microbes & infections Table SARS_CoV_2 V70L 0 4 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. A21683G 2021 mSystems Table SARS_CoV_2 A21683G 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. A21779G 2021 mSystems Table SARS_CoV_2 A21779G 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. A21894G 2021 mSystems Table SARS_CoV_2 A21894G 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. A21975G 2021 mSystems Table SARS_CoV_2 A21975G 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. A22994G 2021 mSystems Table SARS_CoV_2 A22994G 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. A23063T 2021 mSystems Table SARS_CoV_2 A23063T 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. A23201G 2021 mSystems Table SARS_CoV_2 A23201G 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. A67S 2021 mSystems Table SARS_CoV_2 A67S 0 4 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. C21727T 2021 mSystems Table SARS_CoV_2 C21727T 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. C21846T 2021 mSystems Table SARS_CoV_2 C21846T 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. C21855T 2021 mSystems Table SARS_CoV_2 C21855T 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. C21867A 2021 mSystems Table SARS_CoV_2 C21867A 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. C22995G 2021 mSystems Table SARS_CoV_2 C22995G 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. C23202A 2021 mSystems Table SARS_CoV_2 C23202A 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. C23271A 2021 mSystems Table SARS_CoV_2 C23271A 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. D111G 2021 mSystems Table SARS_CoV_2 D111G 0 5 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. D138G 2021 mSystems Table SARS_CoV_2 D138G 0 5 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. D574Y 2021 mSystems Table SARS_CoV_2 D574Y 0 5 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. F490S 2021 mSystems Table SARS_CoV_2 F490S 0 5 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. F515L 2021 mSystems Table SARS_CoV_2 F515L 0 5 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. G21761T 2021 mSystems Table SARS_CoV_2 G21761T 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. G23282T 2021 mSystems Table SARS_CoV_2 G23282T 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. I100T 2021 mSystems Table SARS_CoV_2 I100T 0 5 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. I68T 2021 mSystems Table SARS_CoV_2 I68T 0 4 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. K41E 2021 mSystems Table SARS_CoV_2 K41E 0 4 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. L54S 2021 mSystems Table SARS_CoV_2 L54S 0 4 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. R102K 2021 mSystems Table SARS_CoV_2 R102K 0 5 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. S494P 2021 mSystems Table SARS_CoV_2 S494P 0 5 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. S50P 2021 mSystems Table SARS_CoV_2 S50P 0 4 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. S56F 2021 mSystems Table SARS_CoV_2 S56F 0 4 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. S98F 2021 mSystems Table SARS_CoV_2 S98F 0 4 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. T21710C 2021 mSystems Table SARS_CoV_2 T21710C 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. T21723C 2021 mSystems Table SARS_CoV_2 T21723C 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. T21765C 2021 mSystems Table SARS_CoV_2 T21765C 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. T21831C 2021 mSystems Table SARS_CoV_2 T21831C 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. T21861C 2021 mSystems Table SARS_CoV_2 T21861C 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. T21990C 2021 mSystems Table SARS_CoV_2 T21990C 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. T23031C 2021 mSystems Table SARS_CoV_2 T23031C 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. T23042C 2021 mSystems Table SARS_CoV_2 T23042C 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. T23075C 2021 mSystems Table SARS_CoV_2 T23075C 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. T23105C 2021 mSystems Table SARS_CoV_2 T23105C 0 7 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. T478A 2021 mSystems Table SARS_CoV_2 T478A 0 5 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. T478R 2021 mSystems Table SARS_CoV_2 T478R 0 5 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. T547A 2021 mSystems Table SARS_CoV_2 T547A 0 5 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. T547I 2021 mSystems Table SARS_CoV_2 T547I 0 5 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. T73A 2021 mSystems Table SARS_CoV_2 T73A 0 4 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. T95I 2021 mSystems Table SARS_CoV_2 T95I 0 4 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. V143A 2021 mSystems Table SARS_CoV_2 V143A 0 5 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. V90A 2021 mSystems Table SARS_CoV_2 V90A 0 4 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. Y505H 2021 mSystems Table SARS_CoV_2 Y505H 0 5 34134034 Rapid and simultaneous identification of three mutations by the Novaplex SARS-CoV-2 variants I assay kit. E484K 2021 Journal of clinical virology Table SARS_CoV_2 E484K 0 5 34134034 Rapid and simultaneous identification of three mutations by the Novaplex SARS-CoV-2 variants I assay kit. N501Y 2021 Journal of clinical virology Table SARS_CoV_2 N501Y 0 5 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. A570D 2021 Frontiers in public health Table SARS_CoV_2 A570D 0 5 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. D614G 2021 Frontiers in public health Table SARS_CoV_2 D614G 0 5 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. H655P 2021 Frontiers in public health Table SARS_CoV_2 H655P 0 5 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. I716T 2021 Frontiers in public health Table SARS_CoV_2 I716T 0 5 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. K444R 2021 Frontiers in public health Table SARS_CoV_2 K444R 0 5 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. N501Y 2021 Frontiers in public health Table SARS_CoV_2 N501Y 0 5 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. P681H 2021 Frontiers in public health Table SARS_CoV_2 P681H 0 5 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. V445L 2021 Frontiers in public health Table SARS_CoV_2 V445L 0 5 34138474 High-resolution melting curve FRET-PCR rapidly identifies SARS-CoV-2 mutations. A23403G 2021 Journal of medical virology Table SARS_CoV_2 A23403G 0 7 34138474 High-resolution melting curve FRET-PCR rapidly identifies SARS-CoV-2 mutations. C14408T 2021 Journal of medical virology Table SARS_CoV_2 C14408T 0 7 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. E484K/N 2021 Computers in biology and medicine Table SARS_CoV_2 E484K;E484N 0;0 7;7 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. K417N/E 2021 Computers in biology and medicine Table SARS_CoV_2 K417E;K417N 0;0 7;7 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. L452R 2021 Computers in biology and medicine Table SARS_CoV_2 L452R 0 5 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. N439K 2021 Computers in biology and medicine Table SARS_CoV_2 N439K 0 5 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. N501Y 2021 Computers in biology and medicine Table SARS_CoV_2 N501Y 0 5 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. S477N 2021 Computers in biology and medicine Table SARS_CoV_2 S477N 0 5 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. S494P 2021 Computers in biology and medicine Table SARS_CoV_2 S494P 0 5 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. T478K 2021 Computers in biology and medicine Table SARS_CoV_2 T478K 0 5 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. V106R 2021 Computers in biology and medicine Table SARS_CoV_2 V106R 0 5 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. V106R/H 2021 Computers in biology and medicine Table SARS_CoV_2 V106H;V106R 0;0 7;7 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. C110A 2021 Frontiers in immunology Table SARS_CoV_2 C110A 0 5 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. C119A 2021 Frontiers in immunology Table SARS_CoV_2 C119A 0 5 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. C135A 2021 Frontiers in immunology Table SARS_CoV_2 C135A 0 5 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. C144A 2021 Frontiers in immunology Table SARS_CoV_2 C144A 0 5 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. A23403G 2021 Journal of infection and chemotherapy Table SARS_CoV_2 A23403G 0 7 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. C241T 2021 Journal of infection and chemotherapy Table SARS_CoV_2 C241T 0 5 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. C3037T 2021 Journal of infection and chemotherapy Table SARS_CoV_2 C3037T 0 6 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. C8782T 2021 Journal of infection and chemotherapy Table SARS_CoV_2 C8782T 0 6 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. D614G 2021 Journal of infection and chemotherapy Table SARS_CoV_2 D614G 0 5 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. G11083T 2021 Journal of infection and chemotherapy Table SARS_CoV_2 G11083T 0 7 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. G204R 2021 Journal of infection and chemotherapy Table SARS_CoV_2 G204R 0 5 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. G251V 2021 Journal of infection and chemotherapy Table SARS_CoV_2 G251V 0 5 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. G25563T 2021 Journal of infection and chemotherapy Table SARS_CoV_2 G25563T 0 7 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. G26144T 2021 Journal of infection and chemotherapy Table SARS_CoV_2 G26144T 0 7 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. G28882A 2021 Journal of infection and chemotherapy Table SARS_CoV_2 G28882A 0 7 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. L37F 2021 Journal of infection and chemotherapy Table SARS_CoV_2 L37F 0 4 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. L84S 2021 Journal of infection and chemotherapy Table SARS_CoV_2 L84S 0 4 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. Q57H 2021 Journal of infection and chemotherapy Table SARS_CoV_2 Q57H 0 4 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. T28144C 2021 Journal of infection and chemotherapy Table SARS_CoV_2 T28144C 0 7 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. 1059C>T 2021 Computers in biology and medicine Table SARS_CoV_2 C1059T 0 7 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. 13730C>T 2021 Computers in biology and medicine Table SARS_CoV_2 C13730T 0 8 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. 14408C>T 2021 Computers in biology and medicine Table SARS_CoV_2 C14408T 0 8 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. 16732T>G 2021 Computers in biology and medicine Table SARS_CoV_2 T16732G 0 8 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. 23403A>G 2021 Computers in biology and medicine Table SARS_CoV_2 A23403G 0 8 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. 25563G>T 2021 Computers in biology and medicine Table SARS_CoV_2 G25563T 0 8 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. 26144G>T 2021 Computers in biology and medicine Table SARS_CoV_2 G26144T 0 8 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. 26467G>T 2021 Computers in biology and medicine Table SARS_CoV_2 G26467T 0 8 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. 28311C>T 2021 Computers in biology and medicine Table SARS_CoV_2 C28311T 0 8 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. 28881G>A 2021 Computers in biology and medicine Table SARS_CoV_2 G28881A 0 8 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. 28882G>A 2021 Computers in biology and medicine Table SARS_CoV_2 G28882A 0 8 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. 28883G>C 2021 Computers in biology and medicine Table SARS_CoV_2 G28883C 0 8 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. A4489V 2021 Computers in biology and medicine Table SARS_CoV_2 A4489V 0 6 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. A97V 2021 Computers in biology and medicine Table SARS_CoV_2 A97V 0 4 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. D614G 2021 Computers in biology and medicine Table SARS_CoV_2 D614G 0 5 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. G204R 2021 Computers in biology and medicine Table SARS_CoV_2 G204R 0 5 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. G251V 2021 Computers in biology and medicine Table SARS_CoV_2 G251V 0 5 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. P13L 2021 Computers in biology and medicine Table SARS_CoV_2 P13L 0 4 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. P323L 2021 Computers in biology and medicine Table SARS_CoV_2 P323L 0 5 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. P4715L 2021 Computers in biology and medicine Table SARS_CoV_2 P4715L 0 6 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. Q57H 2021 Computers in biology and medicine Table SARS_CoV_2 Q57H 0 4 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. R203K 2021 Computers in biology and medicine Table SARS_CoV_2 R203K 0 5 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. S166A 2021 Computers in biology and medicine Table SARS_CoV_2 S166A 0 5 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. S5490A 2021 Computers in biology and medicine Table SARS_CoV_2 S5490A 0 6 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. T265I 2021 Computers in biology and medicine Table SARS_CoV_2 T265I 0 5 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. T85I 2021 Computers in biology and medicine Table SARS_CoV_2 T85I 0 4 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. V75F 2021 Computers in biology and medicine Table SARS_CoV_2 V75F 0 4 34158771 Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study. A930V 2021 Ethiopian journal of health sciences Table SARS_CoV_2 A930V 0 5 34158771 Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study. D614G 2021 Ethiopian journal of health sciences Table SARS_CoV_2 D614G 0 5 34158771 Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study. N74K 2021 Ethiopian journal of health sciences Table SARS_CoV_2 N74K 0 4 34158771 Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study. R408I 2021 Ethiopian journal of health sciences Table SARS_CoV_2 R408I 0 5 34158771 Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study. S247R 2021 Ethiopian journal of health sciences Table SARS_CoV_2 S247R 0 5 34158771 Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study. S50L 2021 Ethiopian journal of health sciences Table SARS_CoV_2 S50L 0 4 34158771 Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study. V1065L 2021 Ethiopian journal of health sciences Table SARS_CoV_2 V1065L 0 6 34158771 Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study. V772I 2021 Ethiopian journal of health sciences Table SARS_CoV_2 V772I 0 5 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. M3003L 2021 Cell reports Table SARS_CoV_2 M3003L 0 6 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. P07E 2021 Immunity Table SARS_CoV_2 P07E 0 4 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. 145del 2021 Journal of medical virology Table SARS_CoV_2 145del 0 6 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. N501Y 2021 Journal of medical virology Table SARS_CoV_2 N501Y 0 5 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. S982A 2021 Journal of medical virology Table SARS_CoV_2 S982A 0 5 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. D614G 2021 Cell host & microbe Table SARS_CoV_2 D614G 0 5 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. L452M 2021 Cell host & microbe Table SARS_CoV_2 L452M 0 5 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. L452Q 2021 Cell host & microbe Table SARS_CoV_2 L452Q 0 5 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. L452R 2021 Cell host & microbe Table SARS_CoV_2 L452R 0 5 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. L452R/L 2021 Cell host & microbe Table SARS_CoV_2 L452L;L452R 0;0 7;7 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. N450K 2021 Cell host & microbe Table SARS_CoV_2 N450K 0 5 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. N501Y 2021 Cell host & microbe Table SARS_CoV_2 N501Y 0 5 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. R1089S 2021 Cell host & microbe Table SARS_CoV_2 R1089S 0 6 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. R3198L 2021 Cell host & microbe Table SARS_CoV_2 R3198L 0 6 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. S13I 2021 Cell host & microbe Table SARS_CoV_2 S13I 0 4 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Y453F 2021 Cell host & microbe Table SARS_CoV_2 Y453F 0 5 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. D399N 2021 Journal of clinical virology Table SARS_CoV_2 D399N 0 5 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. T205I 2021 Journal of clinical virology Table SARS_CoV_2 T205I 0 5 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. N501Y 2021 Journal of clinical virology Table SARS_CoV_2 N501Y 0 5 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. D614G 2021 Cell host & microbe Table SARS_CoV_2 D614G 0 5 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. E484K 2021 Cell host & microbe Table SARS_CoV_2 E484K 0 5 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. N501Y 2021 Cell host & microbe Table SARS_CoV_2 N501Y 0 5 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. E406Q 2021 Cell Table SARS_CoV_2 E406Q 0 5 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. E484K 2021 Cell Table SARS_CoV_2 E484K 0 5 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. F486A 2021 Cell Table SARS_CoV_2 F486A 0 5 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. M0314L 2021 Cell Table SARS_CoV_2 M0314L 0 6 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. N417V 2021 Cell Table SARS_CoV_2 N417V 0 5 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. N439K 2021 Cell Table SARS_CoV_2 N439K 0 5 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. N439K/Y 2021 Cell Table SARS_CoV_2 N439K;N439Y 0;0 7;7 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. N440K 2021 Cell Table SARS_CoV_2 N440K 0 5 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. N487R 2021 Cell Table SARS_CoV_2 N487R 0 5 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. Q493R 2021 Cell Table SARS_CoV_2 Q493R 0 5 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. V49H 2021 Cell Table SARS_CoV_2 V49H 0 4 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. Y453F 2021 Cell Table SARS_CoV_2 Y453F 0 5 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. V483A 2021 Future virology Table SARS_CoV_2 V483A 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. A188S 2021 Scientific reports Table SARS_CoV_2 A188S 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. A231V 2021 Scientific reports Table SARS_CoV_2 A231V 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. A360V 2021 Scientific reports Table SARS_CoV_2 A360V 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. A361V 2021 Scientific reports Table SARS_CoV_2 A361V 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. A522V 2021 Scientific reports Table SARS_CoV_2 A522V 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. A68S 2021 Scientific reports Table SARS_CoV_2 A68S 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. D102Y 2021 Scientific reports Table SARS_CoV_2 D102Y 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. D1148N 2021 Scientific reports Table SARS_CoV_2 D1148N 0 6 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. D1184N 2021 Scientific reports Table SARS_CoV_2 D1184N 0 6 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. D1214N 2021 Scientific reports Table SARS_CoV_2 D1214N 0 6 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. D614G 2021 Scientific reports Table SARS_CoV_2 D614G 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. E223G 2021 Scientific reports Table SARS_CoV_2 E223G 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. F1659L 2021 Scientific reports Table SARS_CoV_2 F1659L 0 6 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. F565L 2021 Scientific reports Table SARS_CoV_2 F565L 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. G1011X 2021 Scientific reports Table SARS_CoV_2 G1011X 0 6 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. G142C 2021 Scientific reports Table SARS_CoV_2 G142C 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. G204R 2021 Scientific reports Table SARS_CoV_2 G204R 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. G34W 2021 Scientific reports Table SARS_CoV_2 G34W 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. G44D 2021 Scientific reports Table SARS_CoV_2 G44D 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. G638S 2021 Scientific reports Table SARS_CoV_2 G638S 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. H73R 2021 Scientific reports Table SARS_CoV_2 H73R 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. I1672S 2021 Scientific reports Table SARS_CoV_2 I1672S 0 6 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. I47F 2021 Scientific reports Table SARS_CoV_2 I47F 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. K110N 2021 Scientific reports Table SARS_CoV_2 K110N 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. K1191N 2021 Scientific reports Table SARS_CoV_2 K1191N 0 6 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. K460R 2021 Scientific reports Table SARS_CoV_2 K460R 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. K90R 2021 Scientific reports Table SARS_CoV_2 K90R 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. L35F 2021 Scientific reports Table SARS_CoV_2 L35F 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. L37F 2021 Scientific reports Table SARS_CoV_2 L37F 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. L89F 2021 Scientific reports Table SARS_CoV_2 L89F 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. M17I 2021 Scientific reports Table SARS_CoV_2 M17I 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. M755I 2021 Scientific reports Table SARS_CoV_2 M755I 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. P108L 2021 Scientific reports Table SARS_CoV_2 P108L 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. P122H 2021 Scientific reports Table SARS_CoV_2 P122H 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. P159S 2021 Scientific reports Table SARS_CoV_2 P159S 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. P191S 2021 Scientific reports Table SARS_CoV_2 P191S 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. P192H 2021 Scientific reports Table SARS_CoV_2 P192H 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. P236S 2021 Scientific reports Table SARS_CoV_2 P236S 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. P238S 2021 Scientific reports Table SARS_CoV_2 P238S 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. P323L 2021 Scientific reports Table SARS_CoV_2 P323L 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. P34S 2021 Scientific reports Table SARS_CoV_2 P34S 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. P807R 2021 Scientific reports Table SARS_CoV_2 P807R 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. P812L 2021 Scientific reports Table SARS_CoV_2 P812L 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. Q203H 2021 Scientific reports Table SARS_CoV_2 Q203H 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. Q208H 2021 Scientific reports Table SARS_CoV_2 Q208H 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. Q229H 2021 Scientific reports Table SARS_CoV_2 Q229H 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. Q57H 2021 Scientific reports Table SARS_CoV_2 Q57H 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. Q77H 2021 Scientific reports Table SARS_CoV_2 Q77H 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. R203K 2021 Scientific reports Table SARS_CoV_2 R203K 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. R214C 2021 Scientific reports Table SARS_CoV_2 R214C 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. R21I 2021 Scientific reports Table SARS_CoV_2 R21I 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. S177L 2021 Scientific reports Table SARS_CoV_2 S177L 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. S183Y 2021 Scientific reports Table SARS_CoV_2 S183Y 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. S194L 2021 Scientific reports Table SARS_CoV_2 S194L 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. S24L 2021 Scientific reports Table SARS_CoV_2 S24L 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. S312N 2021 Scientific reports Table SARS_CoV_2 S312N 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. S33R 2021 Scientific reports Table SARS_CoV_2 S33R 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. S702F 2021 Scientific reports Table SARS_CoV_2 S702F 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. T1288I 2021 Scientific reports Table SARS_CoV_2 T1288I 0 6 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. T175I 2021 Scientific reports Table SARS_CoV_2 T175I 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. T1830I 2021 Scientific reports Table SARS_CoV_2 T1830I 0 6 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. T286I 2021 Scientific reports Table SARS_CoV_2 T286I 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. T85I 2021 Scientific reports Table SARS_CoV_2 T85I 0 4 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. V116M 2021 Scientific reports Table SARS_CoV_2 V116M 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. V117F 2021 Scientific reports Table SARS_CoV_2 V117F 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. V287F 2021 Scientific reports Table SARS_CoV_2 V287F 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. V294F 2021 Scientific reports Table SARS_CoV_2 V294F 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. V308L 2021 Scientific reports Table SARS_CoV_2 V308L 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. Y144X 2021 Scientific reports Table SARS_CoV_2 Y144X 0 5 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. Y28H 2021 Scientific reports Table SARS_CoV_2 Y28H 0 4 34211709 The emerging SARS-CoV-2 variants of concern. E484K 2021 Therapeutic advances in infectious disease Table SARS_CoV_2 E484K 0 5 34211709 The emerging SARS-CoV-2 variants of concern. L452R 2021 Therapeutic advances in infectious disease Table SARS_CoV_2 L452R 0 5 34211709 The emerging SARS-CoV-2 variants of concern. N439K 2021 Therapeutic advances in infectious disease Table SARS_CoV_2 N439K 0 5 34211709 The emerging SARS-CoV-2 variants of concern. N501Y 2021 Therapeutic advances in infectious disease Table SARS_CoV_2 N501Y 0 5 34211709 The emerging SARS-CoV-2 variants of concern. Y453F 2021 Therapeutic advances in infectious disease Table SARS_CoV_2 Y453F 0 5 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. E64D 2021 Cell reports Table SARS_CoV_2 E64D 0 4 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. A475V 2021 Virology Table SARS_CoV_2 A475V 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. F456L 2021 Virology Table SARS_CoV_2 F456L 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. F456Y 2021 Virology Table SARS_CoV_2 F456Y 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. F486I 2021 Virology Table SARS_CoV_2 F486I 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. F486L 2021 Virology Table SARS_CoV_2 F486L 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. G446D 2021 Virology Table SARS_CoV_2 G446D 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. G446S 2021 Virology Table SARS_CoV_2 G446S 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. G446V 2021 Virology Table SARS_CoV_2 G446V 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. K417N 2021 Virology Table SARS_CoV_2 K417N 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. K417R 2021 Virology Table SARS_CoV_2 K417R 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. L455F 2021 Virology Table SARS_CoV_2 L455F 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. N501I 2021 Virology Table SARS_CoV_2 N501I 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. N501S 2021 Virology Table SARS_CoV_2 N501S 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. N501T 2021 Virology Table SARS_CoV_2 N501T 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. N501Y 2021 Virology Table SARS_CoV_2 N501Y 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Q493H 2021 Virology Table SARS_CoV_2 Q493H 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Q493K 2021 Virology Table SARS_CoV_2 Q493K 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Q493L 2021 Virology Table SARS_CoV_2 Q493L 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. T500S 2021 Virology Table SARS_CoV_2 T500S 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Y449F 2021 Virology Table SARS_CoV_2 Y449F 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Y453F 2021 Virology Table SARS_CoV_2 Y453F 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Y489H 2021 Virology Table SARS_CoV_2 Y489H 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Y495F 2021 Virology Table SARS_CoV_2 Y495F 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Y505C 2021 Virology Table SARS_CoV_2 Y505C 0 5 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Y505H 2021 Virology Table SARS_CoV_2 Y505H 0 5 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. D614G 2021 Human vaccines & immunotherapeutics Table SARS_CoV_2 D614G 0 5 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. E484K 2021 Human vaccines & immunotherapeutics Table SARS_CoV_2 E484K 0 5 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. N501Y 2021 Human vaccines & immunotherapeutics Table SARS_CoV_2 N501Y 0 5 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. S477N 2021 Human vaccines & immunotherapeutics Table SARS_CoV_2 S477N 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. A570D 2022 Allergy Table SARS_CoV_2 A570D 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. D111D 2022 Allergy Table SARS_CoV_2 D111D 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. D138Y 2022 Allergy Table SARS_CoV_2 D138Y 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. D215G 2022 Allergy Table SARS_CoV_2 D215G 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. D614G 2022 Allergy Table SARS_CoV_2 D614G 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. D80A 2022 Allergy Table SARS_CoV_2 D80A 0 4 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. E484K 2022 Allergy Table SARS_CoV_2 E484K 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. E484Q 2022 Allergy Table SARS_CoV_2 E484Q 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. G412D 2022 Allergy Table SARS_CoV_2 G412D 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. H655Y 2022 Allergy Table SARS_CoV_2 H655Y 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. K417N 2022 Allergy Table SARS_CoV_2 K417N 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. K417T 2022 Allergy Table SARS_CoV_2 K417T 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. L18F 2022 Allergy Table SARS_CoV_2 L18F 0 4 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. L452R 2022 Allergy Table SARS_CoV_2 L452R 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. N501Y 2022 Allergy Table SARS_CoV_2 N501Y 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. P26S 2022 Allergy Table SARS_CoV_2 P26S 0 4 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. P681H 2022 Allergy Table SARS_CoV_2 P681H 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. P681R 2022 Allergy Table SARS_CoV_2 P681R 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. R190S 2022 Allergy Table SARS_CoV_2 R190S 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. R246I 2022 Allergy Table SARS_CoV_2 R246I 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. S982A 2022 Allergy Table SARS_CoV_2 S982A 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. T1027I 2022 Allergy Table SARS_CoV_2 T1027I 0 6 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. T20N 2022 Allergy Table SARS_CoV_2 T20N 0 4 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. T716I 2022 Allergy Table SARS_CoV_2 T716I 0 5 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. V1176F 2022 Allergy Table SARS_CoV_2 V1176F 0 6 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. V70del 2022 Allergy Table SARS_CoV_2 V70del 0 6 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. Y144del 2022 Allergy Table SARS_CoV_2 Y144del 0 7 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. A3070V 2021 Bulletin of the World Health Organization Table SARS_CoV_2 A3070V 0 6 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. F157L 2021 Bulletin of the World Health Organization Table SARS_CoV_2 F157L 0 5 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. G181V 2021 Bulletin of the World Health Organization Table SARS_CoV_2 G181V 0 5 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. G215S 2021 Bulletin of the World Health Organization Table SARS_CoV_2 G215S 0 5 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. K1860N 2021 Bulletin of the World Health Organization Table SARS_CoV_2 K1860N 0 6 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. L3606F 2021 Bulletin of the World Health Organization Table SARS_CoV_2 L3606F 0 6 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. L3829F 2021 Bulletin of the World Health Organization Table SARS_CoV_2 L3829F 0 6 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. P1158S 2021 Bulletin of the World Health Organization Table SARS_CoV_2 P1158S 0 6 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. P46S 2021 Bulletin of the World Health Organization Table SARS_CoV_2 P46S 0 4 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. Q998H 2021 Bulletin of the World Health Organization Table SARS_CoV_2 Q998H 0 5 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. T2124I 2021 Bulletin of the World Health Organization Table SARS_CoV_2 T2124I 0 6 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. T945I 2021 Bulletin of the World Health Organization Table SARS_CoV_2 T945I 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. A1803V 2021 Virus genes Table SARS_CoV_2 A1803V 0 6 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. A1819S 2021 Virus genes Table SARS_CoV_2 A1819S 0 6 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. A602S 2021 Virus genes Table SARS_CoV_2 A602S 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. A69V 2021 Virus genes Table SARS_CoV_2 A69V 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. A889V 2021 Virus genes Table SARS_CoV_2 A889V 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. A94V 2021 Virus genes Table SARS_CoV_2 A94V 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. D1108N 2021 Virus genes Table SARS_CoV_2 D1108N 0 6 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. D36G 2021 Virus genes Table SARS_CoV_2 D36G 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. D85E 2021 Virus genes Table SARS_CoV_2 D85E 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. E425G 2021 Virus genes Table SARS_CoV_2 E425G 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. E516Q 2021 Virus genes Table SARS_CoV_2 E516Q 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. E68D 2021 Virus genes Table SARS_CoV_2 E68D 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. F140del 2021 Virus genes Table SARS_CoV_2 F140del 0 7 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. F20L 2021 Virus genes Table SARS_CoV_2 F20L 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. G1691C 2021 Virus genes Table SARS_CoV_2 G1691C 0 6 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. G42V 2021 Virus genes Table SARS_CoV_2 G42V 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. H145N 2021 Virus genes Table SARS_CoV_2 H145N 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. I106S 2021 Virus genes Table SARS_CoV_2 I106S 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. I1672S 2021 Virus genes Table SARS_CoV_2 I1672S 0 6 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. I258T 2021 Virus genes Table SARS_CoV_2 I258T 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. K1130R 2021 Virus genes Table SARS_CoV_2 K1130R 0 6 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. K270E 2021 Virus genes Table SARS_CoV_2 K270E 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. K462R 2021 Virus genes Table SARS_CoV_2 K462R 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. L22I 2021 Virus genes Table SARS_CoV_2 L22I 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. L373M 2021 Virus genes Table SARS_CoV_2 L373M 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. L518I 2021 Virus genes Table SARS_CoV_2 L518I 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. L7G 2021 Virus genes Table SARS_CoV_2 L7G 0 3 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. M209T 2021 Virus genes Table SARS_CoV_2 M209T 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. M85del 2021 Virus genes Table SARS_CoV_2 M85del 0 6 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. N1337S 2021 Virus genes Table SARS_CoV_2 N1337S 0 6 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. N211Y 2021 Virus genes Table SARS_CoV_2 N211Y 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. N377D 2021 Virus genes Table SARS_CoV_2 N377D 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. N39Y 2021 Virus genes Table SARS_CoV_2 N39Y 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. N51D 2021 Virus genes Table SARS_CoV_2 N51D 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. P38R 2021 Virus genes Table SARS_CoV_2 P38R 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. P96S 2021 Virus genes Table SARS_CoV_2 P96S 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Q224K 2021 Virus genes Table SARS_CoV_2 Q224K 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Q38E 2021 Virus genes Table SARS_CoV_2 Q38E 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Q470R 2021 Virus genes Table SARS_CoV_2 Q470R 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Q62E 2021 Virus genes Table SARS_CoV_2 Q62E 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Q83R 2021 Virus genes Table SARS_CoV_2 Q83R 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. R188S 2021 Virus genes Table SARS_CoV_2 R188S 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. R883G 2021 Virus genes Table SARS_CoV_2 R883G 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. S1038F 2021 Virus genes Table SARS_CoV_2 S1038F 0 6 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. S180T 2021 Virus genes Table SARS_CoV_2 S180T 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. S54P 2021 Virus genes Table SARS_CoV_2 S54P 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. S607I 2021 Virus genes Table SARS_CoV_2 S607I 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. S939Y 2021 Virus genes Table SARS_CoV_2 S939Y 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. T101I 2021 Virus genes Table SARS_CoV_2 T101I 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. T1363I 2021 Virus genes Table SARS_CoV_2 T1363I 0 6 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. T81A 2021 Virus genes Table SARS_CoV_2 T81A 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. V120L 2021 Virus genes Table SARS_CoV_2 V120L 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. V121D 2021 Virus genes Table SARS_CoV_2 V121D 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. V308M 2021 Virus genes Table SARS_CoV_2 V308M 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. V459I 2021 Virus genes Table SARS_CoV_2 V459I 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. V469A 2021 Virus genes Table SARS_CoV_2 V469A 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. V56A 2021 Virus genes Table SARS_CoV_2 V56A 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. V594F 2021 Virus genes Table SARS_CoV_2 V594F 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. V5T 2021 Virus genes Table SARS_CoV_2 V5T 0 3 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. V843F 2021 Virus genes Table SARS_CoV_2 V843F 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. W69R 2021 Virus genes Table SARS_CoV_2 W69R 0 4 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Y145del 2021 Virus genes Table SARS_CoV_2 Y145del 0 7 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Y198H 2021 Virus genes Table SARS_CoV_2 Y198H 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Y246C 2021 Virus genes Table SARS_CoV_2 Y246C 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Y248H 2021 Virus genes Table SARS_CoV_2 Y248H 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Y272H 2021 Virus genes Table SARS_CoV_2 Y272H 0 5 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Y660F 2021 Virus genes Table SARS_CoV_2 Y660F 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. A684del 2021 Archives of virology Table SARS_CoV_2 A684del 0 7 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. A684E 2021 Archives of virology Table SARS_CoV_2 A684E 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. A684S 2021 Archives of virology Table SARS_CoV_2 A684S 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. A684T 2021 Archives of virology Table SARS_CoV_2 A684T 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. A684V 2021 Archives of virology Table SARS_CoV_2 A684V 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. A688del 2021 Archives of virology Table SARS_CoV_2 A688del 0 7 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. A688S 2021 Archives of virology Table SARS_CoV_2 A688S 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. A688V 2021 Archives of virology Table SARS_CoV_2 A688V 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. P681del 2021 Archives of virology Table SARS_CoV_2 P681del 0 7 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. P681H 2021 Archives of virology Table SARS_CoV_2 P681H 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. P681L 2021 Archives of virology Table SARS_CoV_2 P681L 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. P681R 2021 Archives of virology Table SARS_CoV_2 P681R 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. P681S 2021 Archives of virology Table SARS_CoV_2 P681S 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. R682del 2021 Archives of virology Table SARS_CoV_2 R682del 0 7 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. R682G 2021 Archives of virology Table SARS_CoV_2 R682G 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. R682Q 2021 Archives of virology Table SARS_CoV_2 R682Q 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. R682W 2021 Archives of virology Table SARS_CoV_2 R682W 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. R683del 2021 Archives of virology Table SARS_CoV_2 R683del 0 7 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. R683G 2021 Archives of virology Table SARS_CoV_2 R683G 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. R683P 2021 Archives of virology Table SARS_CoV_2 R683P 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. S680del 2021 Archives of virology Table SARS_CoV_2 S680del 0 7 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. S680F 2021 Archives of virology Table SARS_CoV_2 S680F 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. S680P 2021 Archives of virology Table SARS_CoV_2 S680P 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. S686del 2021 Archives of virology Table SARS_CoV_2 S686del 0 7 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. S686R 2021 Archives of virology Table SARS_CoV_2 S686R 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. S689I 2021 Archives of virology Table SARS_CoV_2 S689I 0 5 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. V687del 2021 Archives of virology Table SARS_CoV_2 V687del 0 7 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. V687I 2021 Archives of virology Table SARS_CoV_2 V687I 0 5 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? E484K 2021 Journal of medical virology Table SARS_CoV_2 E484K 0 5 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? E484Q 2021 Journal of medical virology Table SARS_CoV_2 E484Q 0 5 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? K417N 2021 Journal of medical virology Table SARS_CoV_2 K417N 0 5 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? K417T 2021 Journal of medical virology Table SARS_CoV_2 K417T 0 5 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? L452R 2021 Journal of medical virology Table SARS_CoV_2 L452R 0 5 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? N501Y 2021 Journal of medical virology Table SARS_CoV_2 N501Y 0 5 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? T478K 2021 Journal of medical virology Table SARS_CoV_2 T478K 0 5 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. A15S 2021 Frontiers in medicine Table SARS_CoV_2 A15S 0 4 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. A27253G 2021 Frontiers in medicine Table SARS_CoV_2 A27253G 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. A28272T 2021 Frontiers in medicine Table SARS_CoV_2 A28272T 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. C1060T 2021 Frontiers in medicine Table SARS_CoV_2 C1060T 0 6 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. C16694T 2021 Frontiers in medicine Table SARS_CoV_2 C16694T 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. C241T 2021 Frontiers in medicine Table SARS_CoV_2 C241T 0 5 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. C26681T 2021 Frontiers in medicine Table SARS_CoV_2 C26681T 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. C27442T 2021 Frontiers in medicine Table SARS_CoV_2 C27442T 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. C27741T 2021 Frontiers in medicine Table SARS_CoV_2 C27741T 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. C28887T 2021 Frontiers in medicine Table SARS_CoV_2 C28887T 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. C5221T 2021 Frontiers in medicine Table SARS_CoV_2 C5221T 0 6 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. E484K 2021 Frontiers in medicine Table SARS_CoV_2 E484K 0 5 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. G10523C 2021 Frontiers in medicine Table SARS_CoV_2 G10523C 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. G17211T 2021 Frontiers in medicine Table SARS_CoV_2 G17211T 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. G17721T 2021 Frontiers in medicine Table SARS_CoV_2 G17721T 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. G21295A 2021 Frontiers in medicine Table SARS_CoV_2 G21295A 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. G21296A 2021 Frontiers in medicine Table SARS_CoV_2 G21296A 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. G23012A 2021 Frontiers in medicine Table SARS_CoV_2 G23012A 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. G2610N 2021 Frontiers in medicine Table SARS_CoV_2 G2610N 0 6 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. G27798T 2021 Frontiers in medicine Table SARS_CoV_2 G27798T 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. G29781T 2021 Frontiers in medicine Table SARS_CoV_2 G29781T 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. I18V 2021 Frontiers in medicine Table SARS_CoV_2 I18V 0 4 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. L1248F 2021 Frontiers in medicine Table SARS_CoV_2 L1248F 0 6 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. L249S 2021 Frontiers in medicine Table SARS_CoV_2 L249S 0 5 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. T1076I 2021 Frontiers in medicine Table SARS_CoV_2 T1076I 0 6 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. T205I 2021 Frontiers in medicine Table SARS_CoV_2 T205I 0 5 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. T21294A 2021 Frontiers in medicine Table SARS_CoV_2 T21294A 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. T22308C 2021 Frontiers in medicine Table SARS_CoV_2 T22308C 0 7 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. T5213C 2021 Frontiers in medicine Table SARS_CoV_2 T5213C 0 6 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. V2365F 2021 Frontiers in medicine Table SARS_CoV_2 V2365F 0 6 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. V3420L 2021 Frontiers in medicine Table SARS_CoV_2 V3420L 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. A1316A 2021 Microbiology resource announcements Table SARS_CoV_2 A1316A 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. A1708D 2021 Microbiology resource announcements Table SARS_CoV_2 A1708D 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. A27S 2021 Microbiology resource announcements Table SARS_CoV_2 A27S 0 4 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. A570D 2021 Microbiology resource announcements Table SARS_CoV_2 A570D 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. A701V 2021 Microbiology resource announcements Table SARS_CoV_2 A701V 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. C952C 2021 Microbiology resource announcements Table SARS_CoV_2 C952C 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. D1118H 2021 Microbiology resource announcements Table SARS_CoV_2 D1118H 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. D1501D 2021 Microbiology resource announcements Table SARS_CoV_2 D1501D 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. D2129D 2021 Microbiology resource announcements Table SARS_CoV_2 D2129D 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. D215G 2021 Microbiology resource announcements Table SARS_CoV_2 D215G 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. D614G 2021 Microbiology resource announcements Table SARS_CoV_2 D614G 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. D644N 2021 Microbiology resource announcements Table SARS_CoV_2 D644N 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. D80A 2021 Microbiology resource announcements Table SARS_CoV_2 D80A 0 4 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. E1370E 2021 Microbiology resource announcements Table SARS_CoV_2 E1370E 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. E1871G 2021 Microbiology resource announcements Table SARS_CoV_2 E1871G 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. E3965G 2021 Microbiology resource announcements Table SARS_CoV_2 E3965G 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. E484K 2021 Microbiology resource announcements Table SARS_CoV_2 E484K 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. F120F 2021 Microbiology resource announcements Table SARS_CoV_2 F120F 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. F1907F 2021 Microbiology resource announcements Table SARS_CoV_2 F1907F 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. F318N 2021 Microbiology resource announcements Table SARS_CoV_2 F318N 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. F924F 2021 Microbiology resource announcements Table SARS_CoV_2 F924F 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. G204R 2021 Microbiology resource announcements Table SARS_CoV_2 G204R 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. G3617S 2021 Microbiology resource announcements Table SARS_CoV_2 G3617S 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. G3849G 2021 Microbiology resource announcements Table SARS_CoV_2 G3849G 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. G392G 2021 Microbiology resource announcements Table SARS_CoV_2 G392G 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. G50N 2021 Microbiology resource announcements Table SARS_CoV_2 G50N 0 4 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. H604H 2021 Microbiology resource announcements Table SARS_CoV_2 H604H 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. I121L 2021 Microbiology resource announcements Table SARS_CoV_2 I121L 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. I2230T 2021 Microbiology resource announcements Table SARS_CoV_2 I2230T 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. I2278V 2021 Microbiology resource announcements Table SARS_CoV_2 I2278V 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. K1383R 2021 Microbiology resource announcements Table SARS_CoV_2 K1383R 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. K1655N 2021 Microbiology resource announcements Table SARS_CoV_2 K1655N 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. K3353R 2021 Microbiology resource announcements Table SARS_CoV_2 K3353R 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. K417N 2021 Microbiology resource announcements Table SARS_CoV_2 K417N 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. L1627L 2021 Microbiology resource announcements Table SARS_CoV_2 L1627L 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. L219I 2021 Microbiology resource announcements Table SARS_CoV_2 L219I 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. L3915F 2021 Microbiology resource announcements Table SARS_CoV_2 L3915F 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. L4126I 2021 Microbiology resource announcements Table SARS_CoV_2 L4126I 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. L52F 2021 Microbiology resource announcements Table SARS_CoV_2 L52F 0 4 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. L65L 2021 Microbiology resource announcements Table SARS_CoV_2 L65L 0 4 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. L820F 2021 Microbiology resource announcements Table SARS_CoV_2 L820F 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. L849L 2021 Microbiology resource announcements Table SARS_CoV_2 L849L 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. N501Y 2021 Microbiology resource announcements Table SARS_CoV_2 N501Y 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. N543N 2021 Microbiology resource announcements Table SARS_CoV_2 N543N 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. P314L 2021 Microbiology resource announcements Table SARS_CoV_2 P314L 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. P403P 2021 Microbiology resource announcements Table SARS_CoV_2 P403P 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. P681H 2021 Microbiology resource announcements Table SARS_CoV_2 P681H 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. P71L 2021 Microbiology resource announcements Table SARS_CoV_2 P71L 0 4 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. Q57H 2021 Microbiology resource announcements Table SARS_CoV_2 Q57H 0 4 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. R184H 2021 Microbiology resource announcements Table SARS_CoV_2 R184H 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. R203K 2021 Microbiology resource announcements Table SARS_CoV_2 R203K 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. R24R 2021 Microbiology resource announcements Table SARS_CoV_2 R24R 0 4 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. R52I 2021 Microbiology resource announcements Table SARS_CoV_2 R52I 0 4 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. S171L 2021 Microbiology resource announcements Table SARS_CoV_2 S171L 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. S216S 2021 Microbiology resource announcements Table SARS_CoV_2 S216S 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. S235F 2021 Microbiology resource announcements Table SARS_CoV_2 S235F 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. S37F 2021 Microbiology resource announcements Table SARS_CoV_2 S37F 0 4 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. S67F 2021 Microbiology resource announcements Table SARS_CoV_2 S67F 0 4 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. S982A 2021 Microbiology resource announcements Table SARS_CoV_2 S982A 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. T1001I 2021 Microbiology resource announcements Table SARS_CoV_2 T1001I 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. T12I 2021 Microbiology resource announcements Table SARS_CoV_2 T12I 0 4 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. T205I 2021 Microbiology resource announcements Table SARS_CoV_2 T205I 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. T265I 2021 Microbiology resource announcements Table SARS_CoV_2 T265I 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. T572I 2021 Microbiology resource announcements Table SARS_CoV_2 T572I 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. T716I 2021 Microbiology resource announcements Table SARS_CoV_2 T716I 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. T734T 2021 Microbiology resource announcements Table SARS_CoV_2 T734T 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. T903T 2021 Microbiology resource announcements Table SARS_CoV_2 T903T 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. V320F 2021 Microbiology resource announcements Table SARS_CoV_2 V320F 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. Y123Y 2021 Microbiology resource announcements Table SARS_CoV_2 Y123Y 0 5 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. Y3098Y 2021 Microbiology resource announcements Table SARS_CoV_2 Y3098Y 0 6 34264104 Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines. Y73C 2021 Microbiology resource announcements Table SARS_CoV_2 Y73C 0 4 34267528 Detection of Representative Mutant Strains and a Case of Prolonged Infection by SARS-CoV-2 with Spike 69/70 Deletion in Japan. E484K 2021 Infection and drug resistance Table SARS_CoV_2 E484K 0 5 34267528 Detection of Representative Mutant Strains and a Case of Prolonged Infection by SARS-CoV-2 with Spike 69/70 Deletion in Japan. N501Y 2021 Infection and drug resistance Table SARS_CoV_2 N501Y 0 5 34267528 Detection of Representative Mutant Strains and a Case of Prolonged Infection by SARS-CoV-2 with Spike 69/70 Deletion in Japan. P681H 2021 Infection and drug resistance Table SARS_CoV_2 P681H 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. A829T 2021 Biomedical journal Table SARS_CoV_2 A829T 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. A930V 2021 Biomedical journal Table SARS_CoV_2 A930V 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. D614G 2021 Biomedical journal Table SARS_CoV_2 D614G 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. E583D 2021 Biomedical journal Table SARS_CoV_2 E583D 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. E96G 2021 Biomedical journal Table SARS_CoV_2 E96G 0 4 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. F86S 2021 Biomedical journal Table SARS_CoV_2 F86S 0 4 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. G1219V 2021 Biomedical journal Table SARS_CoV_2 G1219V 0 6 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. G261D 2021 Biomedical journal Table SARS_CoV_2 G261D 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. H49Y 2021 Biomedical journal Table SARS_CoV_2 H49Y 0 4 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. L1063F 2021 Biomedical journal Table SARS_CoV_2 L1063F 0 6 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. N1187K 2021 Biomedical journal Table SARS_CoV_2 N1187K 0 6 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. N185K 2021 Biomedical journal Table SARS_CoV_2 N185K 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. N188K 2021 Biomedical journal Table SARS_CoV_2 N188K 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. P25L 2021 Biomedical journal Table SARS_CoV_2 P25L 0 4 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Q1002E 2021 Biomedical journal Table SARS_CoV_2 Q1002E 0 6 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. R682Q 2021 Biomedical journal Table SARS_CoV_2 R682Q 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. R682W 2021 Biomedical journal Table SARS_CoV_2 R682W 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. S13I 2021 Biomedical journal Table SARS_CoV_2 S13I 0 4 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. S151G 2021 Biomedical journal Table SARS_CoV_2 S151G 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. S221W 2021 Biomedical journal Table SARS_CoV_2 S221W 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. S247R 2021 Biomedical journal Table SARS_CoV_2 S247R 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. S50L 2021 Biomedical journal Table SARS_CoV_2 S50L 0 4 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. T22I 2021 Biomedical journal Table SARS_CoV_2 T22I 0 4 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. T29I 2021 Biomedical journal Table SARS_CoV_2 T29I 0 4 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. T553N 2021 Biomedical journal Table SARS_CoV_2 T553N 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. T572I 2021 Biomedical journal Table SARS_CoV_2 T572I 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. T791I 2021 Biomedical journal Table SARS_CoV_2 T791I 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. T95I 2021 Biomedical journal Table SARS_CoV_2 T95I 0 4 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. V213L 2021 Biomedical journal Table SARS_CoV_2 V213L 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. V367F 2021 Biomedical journal Table SARS_CoV_2 V367F 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Y279N 2021 Biomedical journal Table SARS_CoV_2 Y279N 0 5 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Y38C 2021 Biomedical journal Table SARS_CoV_2 Y38C 0 4 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Y453F 2021 Biomedical journal Table SARS_CoV_2 Y453F 0 5 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. E484K 2021 The Lancet regional health. Europe Table SARS_CoV_2 E484K 0 5 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. E484Q 2021 The Lancet regional health. Europe Table SARS_CoV_2 E484Q 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. A220V 2021 mBio Table SARS_CoV_2 A220V 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. A222V 2021 mBio Table SARS_CoV_2 A222V 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. A262S 2021 mBio Table SARS_CoV_2 A262S 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. A398V 2021 mBio Table SARS_CoV_2 A398V 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. A520S 2021 mBio Table SARS_CoV_2 A520S 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. A626S 2021 mBio Table SARS_CoV_2 A626S 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. A688V 2021 mBio Table SARS_CoV_2 A688V 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. A879S 2021 mBio Table SARS_CoV_2 A879S 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. D103Y 2021 mBio Table SARS_CoV_2 D103Y 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. D1084Y 2021 mBio Table SARS_CoV_2 D1084Y 0 6 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. D1163Y 2021 mBio Table SARS_CoV_2 D1163Y 0 6 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. D215H 2021 mBio Table SARS_CoV_2 D215H 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. D253G 2021 mBio Table SARS_CoV_2 D253G 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. D574Y 2021 mBio Table SARS_CoV_2 D574Y 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. D614G 2021 mBio Table SARS_CoV_2 D614G 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. D80Y 2021 mBio Table SARS_CoV_2 D80Y 0 4 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. D839Y 2021 mBio Table SARS_CoV_2 D839Y 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. D936Y 2021 mBio Table SARS_CoV_2 D936Y 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. E583D 2021 mBio Table SARS_CoV_2 E583D 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. G1124V 2021 mBio Table SARS_CoV_2 G1124V 0 6 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. G1167V 2021 mBio Table SARS_CoV_2 G1167V 0 6 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. G15S 2021 mBio Table SARS_CoV_2 G15S 0 4 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. G204R 2021 mBio Table SARS_CoV_2 G204R 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. G251V 2021 mBio Table SARS_CoV_2 G251V 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. G261V 2021 mBio Table SARS_CoV_2 G261V 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. G769V 2021 mBio Table SARS_CoV_2 G769V 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. H146Y 2021 mBio Table SARS_CoV_2 H146Y 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. H49Y 2021 mBio Table SARS_CoV_2 H49Y 0 4 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. H655Y 2021 mBio Table SARS_CoV_2 H655Y 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. I120F 2021 mBio Table SARS_CoV_2 I120F 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. K1073N 2021 mBio Table SARS_CoV_2 K1073N 0 6 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. L176F 2021 mBio Table SARS_CoV_2 L176F 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. L18F 2021 mBio Table SARS_CoV_2 L18F 0 4 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. L37F 2021 mBio Table SARS_CoV_2 L37F 0 4 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. L54F 2021 mBio Table SARS_CoV_2 L54F 0 4 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. L84S 2021 mBio Table SARS_CoV_2 L84S 0 4 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. M234I 2021 mBio Table SARS_CoV_2 M234I 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. N439K 2021 mBio Table SARS_CoV_2 N439K 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. N501Y 2021 mBio Table SARS_CoV_2 N501Y 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. P1263L 2021 mBio Table SARS_CoV_2 P1263L 0 6 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. P13L 2021 mBio Table SARS_CoV_2 P13L 0 4 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. P199L 2021 mBio Table SARS_CoV_2 P199L 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. P25S 2021 mBio Table SARS_CoV_2 P25S 0 4 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. P272L 2021 mBio Table SARS_CoV_2 P272L 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. P323L 2021 mBio Table SARS_CoV_2 P323L 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. P71S 2021 mBio Table SARS_CoV_2 P71S 0 4 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. Q57H 2021 mBio Table SARS_CoV_2 Q57H 0 4 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. Q675H 2021 mBio Table SARS_CoV_2 Q675H 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. Q677H 2021 mBio Table SARS_CoV_2 Q677H 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. R203K 2021 mBio Table SARS_CoV_2 R203K 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. R21I 2021 mBio Table SARS_CoV_2 R21I 0 4 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. S183Y 2021 mBio Table SARS_CoV_2 S183Y 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. S188L 2021 mBio Table SARS_CoV_2 S188L 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. S194L 2021 mBio Table SARS_CoV_2 S194L 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. S197L 2021 mBio Table SARS_CoV_2 S197L 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. S255F 2021 mBio Table SARS_CoV_2 S255F 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. S477N 2021 mBio Table SARS_CoV_2 S477N 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. S939F 2021 mBio Table SARS_CoV_2 S939F 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. S98F 2021 mBio Table SARS_CoV_2 S98F 0 4 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. T175M 2021 mBio Table SARS_CoV_2 T175M 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. T29I 2021 mBio Table SARS_CoV_2 T29I 0 4 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. T723I 2021 mBio Table SARS_CoV_2 T723I 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. T85I 2021 mBio Table SARS_CoV_2 T85I 0 4 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. T95I 2021 mBio Table SARS_CoV_2 T95I 0 4 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. V1068F 2021 mBio Table SARS_CoV_2 V1068F 0 6 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. V1176F 2021 mBio Table SARS_CoV_2 V1176F 0 6 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. V622F 2021 mBio Table SARS_CoV_2 V622F 0 5 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. W1214G 2021 mBio Table SARS_CoV_2 W1214G 0 6 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. Y453F 2021 mBio Table SARS_CoV_2 Y453F 0 5 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. E484K 2021 Journal of clinical microbiology Table SARS_CoV_2 E484K 0 5 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. N501Y 2021 Journal of clinical microbiology Table SARS_CoV_2 N501Y 0 5 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. A372T 2021 Cell Table SARS_CoV_2 A372T 0 5 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. D614G 2021 Cell Table SARS_CoV_2 D614G 0 5 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. G1114A 2021 Cell Table SARS_CoV_2 G1114A 0 6 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. N501Y 2021 Cell Table SARS_CoV_2 N501Y 0 5 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. V08H 2021 Cell Table SARS_CoV_2 V08H 0 4 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. p.Ala105Val 2021 Frontiers in microbiology Table SARS_CoV_2 A105V 0 11 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. p.Asp614Gly 2021 Frontiers in microbiology Table SARS_CoV_2 D614G 0 11 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. p.Thr987Asn 2021 Frontiers in microbiology Table SARS_CoV_2 T987N 0 11 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. D614G 2021 Meta gene Table SARS_CoV_2 D614G 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A1020D 2021 Virusdisease Table SARS_CoV_2 A1020D 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A1020S 2021 Virusdisease Table SARS_CoV_2 A1020S 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A1020V 2021 Virusdisease Table SARS_CoV_2 A1020V 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A1078S 2021 Virusdisease Table SARS_CoV_2 A1078S 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A1078V 2021 Virusdisease Table SARS_CoV_2 A1078V 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A222V 2021 Virusdisease Table SARS_CoV_2 A222V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A243P 2021 Virusdisease Table SARS_CoV_2 A243P 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A243S 2021 Virusdisease Table SARS_CoV_2 A243S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A263S 2021 Virusdisease Table SARS_CoV_2 A263S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A263V 2021 Virusdisease Table SARS_CoV_2 A263V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A27S 2021 Virusdisease Table SARS_CoV_2 A27S 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A27V 2021 Virusdisease Table SARS_CoV_2 A27V 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A344S 2021 Virusdisease Table SARS_CoV_2 A344S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A344T 2021 Virusdisease Table SARS_CoV_2 A344T 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A348S 2021 Virusdisease Table SARS_CoV_2 A348S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A411S 2021 Virusdisease Table SARS_CoV_2 A411S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A435S 2021 Virusdisease Table SARS_CoV_2 A435S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A475V 2021 Virusdisease Table SARS_CoV_2 A475V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A502S 2021 Virusdisease Table SARS_CoV_2 A502S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A520S 2021 Virusdisease Table SARS_CoV_2 A520S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A522S 2021 Virusdisease Table SARS_CoV_2 A522S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A570D 2021 Virusdisease Table SARS_CoV_2 A570D 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A570T 2021 Virusdisease Table SARS_CoV_2 A570T 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A570V 2021 Virusdisease Table SARS_CoV_2 A570V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A623S 2021 Virusdisease Table SARS_CoV_2 A623S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A623V 2021 Virusdisease Table SARS_CoV_2 A623V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A626S 2021 Virusdisease Table SARS_CoV_2 A626S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A647S 2021 Virusdisease Table SARS_CoV_2 A647S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A653S 2021 Virusdisease Table SARS_CoV_2 A653S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A653V 2021 Virusdisease Table SARS_CoV_2 A653V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A653V,H 2021 Virusdisease Table SARS_CoV_2 A653V 0 7 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A67S 2021 Virusdisease Table SARS_CoV_2 A67S 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A67V 2021 Virusdisease Table SARS_CoV_2 A67V 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A684V 2021 Virusdisease Table SARS_CoV_2 A684V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A688V 2021 Virusdisease Table SARS_CoV_2 A688V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A706S 2021 Virusdisease Table SARS_CoV_2 A706S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A706V 2021 Virusdisease Table SARS_CoV_2 A706V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A771V 2021 Virusdisease Table SARS_CoV_2 A771V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A829T 2021 Virusdisease Table SARS_CoV_2 A829T 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A831S 2021 Virusdisease Table SARS_CoV_2 A831S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A845S 2021 Virusdisease Table SARS_CoV_2 A845S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A845T 2021 Virusdisease Table SARS_CoV_2 A845T 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A845V 2021 Virusdisease Table SARS_CoV_2 A845V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A846V 2021 Virusdisease Table SARS_CoV_2 A846V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A854S 2021 Virusdisease Table SARS_CoV_2 A854S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A871S 2021 Virusdisease Table SARS_CoV_2 A871S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A879S 2021 Virusdisease Table SARS_CoV_2 A879S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A879T 2021 Virusdisease Table SARS_CoV_2 A879T 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A892S 2021 Virusdisease Table SARS_CoV_2 A892S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A892V 2021 Virusdisease Table SARS_CoV_2 A892V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A899S 2021 Virusdisease Table SARS_CoV_2 A899S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A924S 2021 Virusdisease Table SARS_CoV_2 A924S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A924V 2021 Virusdisease Table SARS_CoV_2 A924V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A930T 2021 Virusdisease Table SARS_CoV_2 A930T 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. A93S 2021 Virusdisease Table SARS_CoV_2 A93S 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. C1243F 2021 Virusdisease Table SARS_CoV_2 C1243F 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. C1248F 2021 Virusdisease Table SARS_CoV_2 C1248F 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. C1248S 2021 Virusdisease Table SARS_CoV_2 C1248S 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. C1250F 2021 Virusdisease Table SARS_CoV_2 C1250F 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. C379F 2021 Virusdisease Table SARS_CoV_2 C379F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. C432F 2021 Virusdisease Table SARS_CoV_2 C432F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D1084Y 2021 Virusdisease Table SARS_CoV_2 D1084Y 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D1118Y 2021 Virusdisease Table SARS_CoV_2 D1118Y 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D1146E 2021 Virusdisease Table SARS_CoV_2 D1146E 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D1162G 2021 Virusdisease Table SARS_CoV_2 D1162G 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D1163Y 2021 Virusdisease Table SARS_CoV_2 D1163Y 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D1259H 2021 Virusdisease Table SARS_CoV_2 D1259H 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D1259Y 2021 Virusdisease Table SARS_CoV_2 D1259Y 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D1260N 2021 Virusdisease Table SARS_CoV_2 D1260N 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D1260Y 2021 Virusdisease Table SARS_CoV_2 D1260Y 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D138H 2021 Virusdisease Table SARS_CoV_2 D138H 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D164G 2021 Virusdisease Table SARS_CoV_2 D164G 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D198G 2021 Virusdisease Table SARS_CoV_2 D198G 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D198Y 2021 Virusdisease Table SARS_CoV_2 D198Y 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D215G 2021 Virusdisease Table SARS_CoV_2 D215G 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D215H 2021 Virusdisease Table SARS_CoV_2 D215H 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D215Y 2021 Virusdisease Table SARS_CoV_2 D215Y 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D253G 2021 Virusdisease Table SARS_CoV_2 D253G 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D261G 2021 Virusdisease Table SARS_CoV_2 D261G 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D290Y 2021 Virusdisease Table SARS_CoV_2 D290Y 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D364Y 2021 Virusdisease Table SARS_CoV_2 D364Y 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D574H 2021 Virusdisease Table SARS_CoV_2 D574H 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D574Y 2021 Virusdisease Table SARS_CoV_2 D574Y 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D614G 2021 Virusdisease Table SARS_CoV_2 D614G 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D645G 2021 Virusdisease Table SARS_CoV_2 D645G 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D745G 2021 Virusdisease Table SARS_CoV_2 D745G 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D80N 2021 Virusdisease Table SARS_CoV_2 D80N 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D80Y 2021 Virusdisease Table SARS_CoV_2 D80Y 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D830G 2021 Virusdisease Table SARS_CoV_2 D830G 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D839Y 2021 Virusdisease Table SARS_CoV_2 D839Y 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D936Y 2021 Virusdisease Table SARS_CoV_2 D936Y 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D950H 2021 Virusdisease Table SARS_CoV_2 D950H 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D950Y 2021 Virusdisease Table SARS_CoV_2 D950Y 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E1150D 2021 Virusdisease Table SARS_CoV_2 E1150D 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E1182K 2021 Virusdisease Table SARS_CoV_2 E1182K 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E1202A 2021 Virusdisease Table SARS_CoV_2 E1202A 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E1202D 2021 Virusdisease Table SARS_CoV_2 E1202D 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E1207D 2021 Virusdisease Table SARS_CoV_2 E1207D 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E1262G 2021 Virusdisease Table SARS_CoV_2 E1262G 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E156D 2021 Virusdisease Table SARS_CoV_2 E156D 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E224G 2021 Virusdisease Table SARS_CoV_2 E224G 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E298G 2021 Virusdisease Table SARS_CoV_2 E298G 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E298K 2021 Virusdisease Table SARS_CoV_2 E298K 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E309Q 2021 Virusdisease Table SARS_CoV_2 E309Q 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E471Q 2021 Virusdisease Table SARS_CoV_2 E471Q 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E554D 2021 Virusdisease Table SARS_CoV_2 E554D 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E583D 2021 Virusdisease Table SARS_CoV_2 E583D 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E780Q 2021 Virusdisease Table SARS_CoV_2 E780Q 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E780V 2021 Virusdisease Table SARS_CoV_2 E780V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E868K 2021 Virusdisease Table SARS_CoV_2 E868K 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E96D 2021 Virusdisease Table SARS_CoV_2 E96D 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. E990A 2021 Virusdisease Table SARS_CoV_2 E990A 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. F1103L 2021 Virusdisease Table SARS_CoV_2 F1103L 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. F275Y 2021 Virusdisease Table SARS_CoV_2 F275Y 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. F32I 2021 Virusdisease Table SARS_CoV_2 F32I 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. F32V 2021 Virusdisease Table SARS_CoV_2 F32V 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. F32Y 2021 Virusdisease Table SARS_CoV_2 F32Y 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. F338L 2021 Virusdisease Table SARS_CoV_2 F338L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. F562Y 2021 Virusdisease Table SARS_CoV_2 F562Y 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. F797C 2021 Virusdisease Table SARS_CoV_2 F797C 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. F92L 2021 Virusdisease Table SARS_CoV_2 F92L 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. F970S 2021 Virusdisease Table SARS_CoV_2 F970S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G1085R 2021 Virusdisease Table SARS_CoV_2 G1085R 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G1093A 2021 Virusdisease Table SARS_CoV_2 G1093A 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G1124C 2021 Virusdisease Table SARS_CoV_2 G1124C 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G1124V 2021 Virusdisease Table SARS_CoV_2 G1124V 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G1167V 2021 Virusdisease Table SARS_CoV_2 G1167V 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G1171V 2021 Virusdisease Table SARS_CoV_2 G1171V 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G1219C 2021 Virusdisease Table SARS_CoV_2 G1219C 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G1219V 2021 Virusdisease Table SARS_CoV_2 G1219V 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G1251V 2021 Virusdisease Table SARS_CoV_2 G1251V 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G142A 2021 Virusdisease Table SARS_CoV_2 G142A 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G142V 2021 Virusdisease Table SARS_CoV_2 G142V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G181R 2021 Virusdisease Table SARS_CoV_2 G181R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G181V 2021 Virusdisease Table SARS_CoV_2 G181V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G261A 2021 Virusdisease Table SARS_CoV_2 G261A 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G261R 2021 Virusdisease Table SARS_CoV_2 G261R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G261S 2021 Virusdisease Table SARS_CoV_2 G261S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G339D 2021 Virusdisease Table SARS_CoV_2 G339D 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G413E 2021 Virusdisease Table SARS_CoV_2 G413E 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G446V 2021 Virusdisease Table SARS_CoV_2 G446V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G485R 2021 Virusdisease Table SARS_CoV_2 G485R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G652A 2021 Virusdisease Table SARS_CoV_2 G652A 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G75D 2021 Virusdisease Table SARS_CoV_2 G75D 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G75V 2021 Virusdisease Table SARS_CoV_2 G75V 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G769A 2021 Virusdisease Table SARS_CoV_2 G769A 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G769V 2021 Virusdisease Table SARS_CoV_2 G769V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G838S 2021 Virusdisease Table SARS_CoV_2 G838S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G838V 2021 Virusdisease Table SARS_CoV_2 G838V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G842S 2021 Virusdisease Table SARS_CoV_2 G842S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G857C 2021 Virusdisease Table SARS_CoV_2 G857C 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G932D 2021 Virusdisease Table SARS_CoV_2 G932D 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. G946R 2021 Virusdisease Table SARS_CoV_2 G946R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. H1058Y 2021 Virusdisease Table SARS_CoV_2 H1058Y 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. H1101Y 2021 Virusdisease Table SARS_CoV_2 H1101Y 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. H1201Y 2021 Virusdisease Table SARS_CoV_2 H1201Y 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. H146Y 2021 Virusdisease Table SARS_CoV_2 H146Y 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. H245R 2021 Virusdisease Table SARS_CoV_2 H245R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. H245Y 2021 Virusdisease Table SARS_CoV_2 H245Y 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. H49Y 2021 Virusdisease Table SARS_CoV_2 H49Y 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. H519P 2021 Virusdisease Table SARS_CoV_2 H519P 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. H625Q 2021 Virusdisease Table SARS_CoV_2 H625Q 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. H625R 2021 Virusdisease Table SARS_CoV_2 H625R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. H655Y 2021 Virusdisease Table SARS_CoV_2 H655Y 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. H675H 2021 Virusdisease Table SARS_CoV_2 H675H 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. H69Y 2021 Virusdisease Table SARS_CoV_2 H69Y 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. I1130L 2021 Virusdisease Table SARS_CoV_2 I1130L 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. I1132V 2021 Virusdisease Table SARS_CoV_2 I1132V 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. I1179N 2021 Virusdisease Table SARS_CoV_2 I1179N 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. I119V 2021 Virusdisease Table SARS_CoV_2 I119V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. I1216T 2021 Virusdisease Table SARS_CoV_2 I1216T 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. I1227M 2021 Virusdisease Table SARS_CoV_2 I1227M 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. I197V 2021 Virusdisease Table SARS_CoV_2 I197V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. I402L 2021 Virusdisease Table SARS_CoV_2 I402L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. I468V 2021 Virusdisease Table SARS_CoV_2 I468V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. I670M 2021 Virusdisease Table SARS_CoV_2 I670M 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. I692F 2021 Virusdisease Table SARS_CoV_2 I692F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. I720V 2021 Virusdisease Table SARS_CoV_2 I720V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. I788M 2021 Virusdisease Table SARS_CoV_2 I788M 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. I805M 2021 Virusdisease Table SARS_CoV_2 I805M 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. I818S 2021 Virusdisease Table SARS_CoV_2 I818S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. I934M 2021 Virusdisease Table SARS_CoV_2 I934M 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. K1086R 2021 Virusdisease Table SARS_CoV_2 K1086R 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. K1191N 2021 Virusdisease Table SARS_CoV_2 K1191N 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. K1205N 2021 Virusdisease Table SARS_CoV_2 K1205N 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. K300N 2021 Virusdisease Table SARS_CoV_2 K300N 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. K378R 2021 Virusdisease Table SARS_CoV_2 K378R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. K417N 2021 Virusdisease Table SARS_CoV_2 K417N 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. K558N 2021 Virusdisease Table SARS_CoV_2 K558N 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. K558R 2021 Virusdisease Table SARS_CoV_2 K558R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. K776T 2021 Virusdisease Table SARS_CoV_2 K776T 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. K77M 2021 Virusdisease Table SARS_CoV_2 K77M 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L1063F 2021 Virusdisease Table SARS_CoV_2 L1063F 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L10I 2021 Virusdisease Table SARS_CoV_2 L10I 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L118F 2021 Virusdisease Table SARS_CoV_2 L118F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L1200F 2021 Virusdisease Table SARS_CoV_2 L1200F 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L1203F 2021 Virusdisease Table SARS_CoV_2 L1203F 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L1244F 2021 Virusdisease Table SARS_CoV_2 L1244F 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L1265P 2021 Virusdisease Table SARS_CoV_2 L1265P 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L18F 2021 Virusdisease Table SARS_CoV_2 L18F 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L216F 2021 Virusdisease Table SARS_CoV_2 L216F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L244F 2021 Virusdisease Table SARS_CoV_2 L244F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L249S 2021 Virusdisease Table SARS_CoV_2 L249S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L276I 2021 Virusdisease Table SARS_CoV_2 L276I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L296H 2021 Virusdisease Table SARS_CoV_2 L296H 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L54F 2021 Virusdisease Table SARS_CoV_2 L54F 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L5F 2021 Virusdisease Table SARS_CoV_2 L5F 0 3 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L611F 2021 Virusdisease Table SARS_CoV_2 L611F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L752F 2021 Virusdisease Table SARS_CoV_2 L752F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L752R 2021 Virusdisease Table SARS_CoV_2 L752R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L754F 2021 Virusdisease Table SARS_CoV_2 L754F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L828P 2021 Virusdisease Table SARS_CoV_2 L828P 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L841I 2021 Virusdisease Table SARS_CoV_2 L841I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L849F 2021 Virusdisease Table SARS_CoV_2 L849F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L861K 2021 Virusdisease Table SARS_CoV_2 L861K 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L938F 2021 Virusdisease Table SARS_CoV_2 L938F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L938I 2021 Virusdisease Table SARS_CoV_2 L938I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L948R 2021 Virusdisease Table SARS_CoV_2 L948R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. M1050I 2021 Virusdisease Table SARS_CoV_2 M1050I 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. M1050V 2021 Virusdisease Table SARS_CoV_2 M1050V 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. M1229I 2021 Virusdisease Table SARS_CoV_2 M1229I 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. M1233I 2021 Virusdisease Table SARS_CoV_2 M1233I 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. M1237I 2021 Virusdisease Table SARS_CoV_2 M1237I 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. M1237T 2021 Virusdisease Table SARS_CoV_2 M1237T 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. M153I 2021 Virusdisease Table SARS_CoV_2 M153I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. M153T 2021 Virusdisease Table SARS_CoV_2 M153T 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. M153V 2021 Virusdisease Table SARS_CoV_2 M153V 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. M177I 2021 Virusdisease Table SARS_CoV_2 M177I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. M731I 2021 Virusdisease Table SARS_CoV_2 M731I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. M731R 2021 Virusdisease Table SARS_CoV_2 M731R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. M900I 2021 Virusdisease Table SARS_CoV_2 M900I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N1074H 2021 Virusdisease Table SARS_CoV_2 N1074H 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N1194S 2021 Virusdisease Table SARS_CoV_2 N1194S 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N121T 2021 Virusdisease Table SARS_CoV_2 N121T 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N125H 2021 Virusdisease Table SARS_CoV_2 N125H 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N148K 2021 Virusdisease Table SARS_CoV_2 N148K 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N148S 2021 Virusdisease Table SARS_CoV_2 N148S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N149H 2021 Virusdisease Table SARS_CoV_2 N149H 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N17K 2021 Virusdisease Table SARS_CoV_2 N17K 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N188I 2021 Virusdisease Table SARS_CoV_2 N188I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N317D 2021 Virusdisease Table SARS_CoV_2 N317D 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N354D 2021 Virusdisease Table SARS_CoV_2 N354D 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N354S 2021 Virusdisease Table SARS_CoV_2 N354S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N439K 2021 Virusdisease Table SARS_CoV_2 N439K 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N501Y 2021 Virusdisease Table SARS_CoV_2 N501Y 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N658D 2021 Virusdisease Table SARS_CoV_2 N658D 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N679K 2021 Virusdisease Table SARS_CoV_2 N679K 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N703S 2021 Virusdisease Table SARS_CoV_2 N703S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N717T 2021 Virusdisease Table SARS_CoV_2 N717T 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N801K 2021 Virusdisease Table SARS_CoV_2 N801K 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N914S 2021 Virusdisease Table SARS_CoV_2 N914S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. N969S 2021 Virusdisease Table SARS_CoV_2 N969S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P1079S 2021 Virusdisease Table SARS_CoV_2 P1079S 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P1079T 2021 Virusdisease Table SARS_CoV_2 P1079T 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P1143L 2021 Virusdisease Table SARS_CoV_2 P1143L 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P1162A 2021 Virusdisease Table SARS_CoV_2 P1162A 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P1162L 2021 Virusdisease Table SARS_CoV_2 P1162L 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P1162S 2021 Virusdisease Table SARS_CoV_2 P1162S 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P1263L 2021 Virusdisease Table SARS_CoV_2 P1263L 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P25S 2021 Virusdisease Table SARS_CoV_2 P25S 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P26S 2021 Virusdisease Table SARS_CoV_2 P26S 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P272T 2021 Virusdisease Table SARS_CoV_2 P272T 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P384L 2021 Virusdisease Table SARS_CoV_2 P384L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P384S 2021 Virusdisease Table SARS_CoV_2 P384S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P385L 2021 Virusdisease Table SARS_CoV_2 P385L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P491R 2021 Virusdisease Table SARS_CoV_2 P491R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P579Q 2021 Virusdisease Table SARS_CoV_2 P579Q 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P588S 2021 Virusdisease Table SARS_CoV_2 P588S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P631S 2021 Virusdisease Table SARS_CoV_2 P631S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P681H 2021 Virusdisease Table SARS_CoV_2 P681H 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P681L 2021 Virusdisease Table SARS_CoV_2 P681L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P809S 2021 Virusdisease Table SARS_CoV_2 P809S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P812L 2021 Virusdisease Table SARS_CoV_2 P812L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P812T 2021 Virusdisease Table SARS_CoV_2 P812T 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. P82L 2021 Virusdisease Table SARS_CoV_2 P82L 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Q1180H 2021 Virusdisease Table SARS_CoV_2 Q1180H 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Q1208H 2021 Virusdisease Table SARS_CoV_2 Q1208H 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Q183L 2021 Virusdisease Table SARS_CoV_2 Q183L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Q239K 2021 Virusdisease Table SARS_CoV_2 Q239K 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Q271R 2021 Virusdisease Table SARS_CoV_2 Q271R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Q409E 2021 Virusdisease Table SARS_CoV_2 Q409E 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Q498H 2021 Virusdisease Table SARS_CoV_2 Q498H 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Q613H 2021 Virusdisease Table SARS_CoV_2 Q613H 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Q675H 2021 Virusdisease Table SARS_CoV_2 Q675H 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Q675K 2021 Virusdisease Table SARS_CoV_2 Q675K 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Q675R 2021 Virusdisease Table SARS_CoV_2 Q675R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Q677H 2021 Virusdisease Table SARS_CoV_2 Q677H 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Q935H 2021 Virusdisease Table SARS_CoV_2 Q935H 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Q954K 2021 Virusdisease Table SARS_CoV_2 Q954K 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. R102I 2021 Virusdisease Table SARS_CoV_2 R102I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. R190K 2021 Virusdisease Table SARS_CoV_2 R190K 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. R211I 2021 Virusdisease Table SARS_CoV_2 R211I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. R214L 2021 Virusdisease Table SARS_CoV_2 R214L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. R21I 2021 Virusdisease Table SARS_CoV_2 R21I 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. R273M 2021 Virusdisease Table SARS_CoV_2 R273M 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. R357K 2021 Virusdisease Table SARS_CoV_2 R357K 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. R634S 2021 Virusdisease Table SARS_CoV_2 R634S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. R682Q 2021 Virusdisease Table SARS_CoV_2 R682Q 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. R682W 2021 Virusdisease Table SARS_CoV_2 R682W 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. R765L 2021 Virusdisease Table SARS_CoV_2 R765L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. R78K 2021 Virusdisease Table SARS_CoV_2 R78K 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. R78M 2021 Virusdisease Table SARS_CoV_2 R78M 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S1021F 2021 Virusdisease Table SARS_CoV_2 S1021F 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S1097T 2021 Virusdisease Table SARS_CoV_2 S1097T 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S1161P 2021 Virusdisease Table SARS_CoV_2 S1161P 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S1242I 2021 Virusdisease Table SARS_CoV_2 S1242I 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S1252F 2021 Virusdisease Table SARS_CoV_2 S1252F 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S13I 2021 Virusdisease Table SARS_CoV_2 S13I 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S151I 2021 Virusdisease Table SARS_CoV_2 S151I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S155T 2021 Virusdisease Table SARS_CoV_2 S155T 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S162I 2021 Virusdisease Table SARS_CoV_2 S162I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S221L 2021 Virusdisease Table SARS_CoV_2 S221L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S247N 2021 Virusdisease Table SARS_CoV_2 S247N 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S247R 2021 Virusdisease Table SARS_CoV_2 S247R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S254F 2021 Virusdisease Table SARS_CoV_2 S254F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S31F 2021 Virusdisease Table SARS_CoV_2 S31F 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S359N 2021 Virusdisease Table SARS_CoV_2 S359N 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S373L 2021 Virusdisease Table SARS_CoV_2 S373L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S477G 2021 Virusdisease Table SARS_CoV_2 S477G 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S477I 2021 Virusdisease Table SARS_CoV_2 S477I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S494P 2021 Virusdisease Table SARS_CoV_2 S494P 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S49L 2021 Virusdisease Table SARS_CoV_2 S49L 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S50L 2021 Virusdisease Table SARS_CoV_2 S50L 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S594P 2021 Virusdisease Table SARS_CoV_2 S594P 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S640A 2021 Virusdisease Table SARS_CoV_2 S640A 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S640F 2021 Virusdisease Table SARS_CoV_2 S640F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S659L 2021 Virusdisease Table SARS_CoV_2 S659L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S680F 2021 Virusdisease Table SARS_CoV_2 S680F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S686G 2021 Virusdisease Table SARS_CoV_2 S686G 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S689I 2021 Virusdisease Table SARS_CoV_2 S689I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S691F 2021 Virusdisease Table SARS_CoV_2 S691F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S704P 2021 Virusdisease Table SARS_CoV_2 S704P 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S708F 2021 Virusdisease Table SARS_CoV_2 S708F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S750I 2021 Virusdisease Table SARS_CoV_2 S750I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S750R 2021 Virusdisease Table SARS_CoV_2 S750R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S789I 2021 Virusdisease Table SARS_CoV_2 S789I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S929T 2021 Virusdisease Table SARS_CoV_2 S929T 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S939F 2021 Virusdisease Table SARS_CoV_2 S939F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S940F 2021 Virusdisease Table SARS_CoV_2 S940F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S943I 2021 Virusdisease Table SARS_CoV_2 S943I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S943P 2021 Virusdisease Table SARS_CoV_2 S943P 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S94F 2021 Virusdisease Table SARS_CoV_2 S94F 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S967R 2021 Virusdisease Table SARS_CoV_2 S967R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. S98F 2021 Virusdisease Table SARS_CoV_2 S98F 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T1027I 2021 Virusdisease Table SARS_CoV_2 T1027I 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T1077A 2021 Virusdisease Table SARS_CoV_2 T1077A 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T1117I 2021 Virusdisease Table SARS_CoV_2 T1117I 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T1120I 2021 Virusdisease Table SARS_CoV_2 T1120I 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T1160K 2021 Virusdisease Table SARS_CoV_2 T1160K 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T1273S 2021 Virusdisease Table SARS_CoV_2 T1273S 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T20S 2021 Virusdisease Table SARS_CoV_2 T20S 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T22A 2021 Virusdisease Table SARS_CoV_2 T22A 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T22I 2021 Virusdisease Table SARS_CoV_2 T22I 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T240I 2021 Virusdisease Table SARS_CoV_2 T240I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T274I 2021 Virusdisease Table SARS_CoV_2 T274I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T299I 2021 Virusdisease Table SARS_CoV_2 T299I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T29I 2021 Virusdisease Table SARS_CoV_2 T29I 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T302L 2021 Virusdisease Table SARS_CoV_2 T302L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T307I 2021 Virusdisease Table SARS_CoV_2 T307I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T323I 2021 Virusdisease Table SARS_CoV_2 T323I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T553I 2021 Virusdisease Table SARS_CoV_2 T553I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T553N 2021 Virusdisease Table SARS_CoV_2 T553N 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T572I 2021 Virusdisease Table SARS_CoV_2 T572I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T572I,T 2021 Virusdisease Table SARS_CoV_2 T572I 0 7 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T573I 2021 Virusdisease Table SARS_CoV_2 T573I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T602I 2021 Virusdisease Table SARS_CoV_2 T602I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T618I 2021 Virusdisease Table SARS_CoV_2 T618I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T630S 2021 Virusdisease Table SARS_CoV_2 T630S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T673P 2021 Virusdisease Table SARS_CoV_2 T673P 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T676I 2021 Virusdisease Table SARS_CoV_2 T676I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T676P 2021 Virusdisease Table SARS_CoV_2 T676P 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T678I 2021 Virusdisease Table SARS_CoV_2 T678I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T732I 2021 Virusdisease Table SARS_CoV_2 T732I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T761S 2021 Virusdisease Table SARS_CoV_2 T761S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T76I 2021 Virusdisease Table SARS_CoV_2 T76I 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T778I 2021 Virusdisease Table SARS_CoV_2 T778I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T778N 2021 Virusdisease Table SARS_CoV_2 T778N 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T791K 2021 Virusdisease Table SARS_CoV_2 T791K 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T859I 2021 Virusdisease Table SARS_CoV_2 T859I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T941I 2021 Virusdisease Table SARS_CoV_2 T941I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T95I 2021 Virusdisease Table SARS_CoV_2 T95I 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. T961M 2021 Virusdisease Table SARS_CoV_2 T961M 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V1040F 2021 Virusdisease Table SARS_CoV_2 V1040F 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V1060F 2021 Virusdisease Table SARS_CoV_2 V1060F 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V1068A 2021 Virusdisease Table SARS_CoV_2 V1068A 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V1068F 2021 Virusdisease Table SARS_CoV_2 V1068F 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V1094F 2021 Virusdisease Table SARS_CoV_2 V1094F 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V1104L 2021 Virusdisease Table SARS_CoV_2 V1104L 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V1129L 2021 Virusdisease Table SARS_CoV_2 V1129L 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V1133F 2021 Virusdisease Table SARS_CoV_2 V1133F 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V1175F 2021 Virusdisease Table SARS_CoV_2 V1175F 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V1176F 2021 Virusdisease Table SARS_CoV_2 V1176F 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V1177A 2021 Virusdisease Table SARS_CoV_2 V1177A 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V11F 2021 Virusdisease Table SARS_CoV_2 V11F 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V11I 2021 Virusdisease Table SARS_CoV_2 V11I 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V120F 2021 Virusdisease Table SARS_CoV_2 V120F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V120I 2021 Virusdisease Table SARS_CoV_2 V120I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V1228L 2021 Virusdisease Table SARS_CoV_2 V1228L 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V127F 2021 Virusdisease Table SARS_CoV_2 V127F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V143D 2021 Virusdisease Table SARS_CoV_2 V143D 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V143F 2021 Virusdisease Table SARS_CoV_2 V143F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V159I 2021 Virusdisease Table SARS_CoV_2 V159I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V193L 2021 Virusdisease Table SARS_CoV_2 V193L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V213L 2021 Virusdisease Table SARS_CoV_2 V213L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V289I 2021 Virusdisease Table SARS_CoV_2 V289I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V367F 2021 Virusdisease Table SARS_CoV_2 V367F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V382E 2021 Virusdisease Table SARS_CoV_2 V382E 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V395I 2021 Virusdisease Table SARS_CoV_2 V395I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V445A 2021 Virusdisease Table SARS_CoV_2 V445A 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V483F 2021 Virusdisease Table SARS_CoV_2 V483F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V503F 2021 Virusdisease Table SARS_CoV_2 V503F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V615L 2021 Virusdisease Table SARS_CoV_2 V615L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V620I 2021 Virusdisease Table SARS_CoV_2 V620I 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V622F 2021 Virusdisease Table SARS_CoV_2 V622F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V70F 2021 Virusdisease Table SARS_CoV_2 V70F 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V83F 2021 Virusdisease Table SARS_CoV_2 V83F 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V860F 2021 Virusdisease Table SARS_CoV_2 V860F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V860Q 2021 Virusdisease Table SARS_CoV_2 V860Q 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V90F 2021 Virusdisease Table SARS_CoV_2 V90F 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. V952F 2021 Virusdisease Table SARS_CoV_2 V952F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. W1102L 2021 Virusdisease Table SARS_CoV_2 W1102L 0 6 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. W152L 2021 Virusdisease Table SARS_CoV_2 W152L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. W152R 2021 Virusdisease Table SARS_CoV_2 W152R 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. W258L 2021 Virusdisease Table SARS_CoV_2 W258L 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Y144F 2021 Virusdisease Table SARS_CoV_2 Y144F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Y145H 2021 Virusdisease Table SARS_CoV_2 Y145H 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Y200S 2021 Virusdisease Table SARS_CoV_2 Y200S 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Y28H 2021 Virusdisease Table SARS_CoV_2 Y28H 0 4 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Y453F 2021 Virusdisease Table SARS_CoV_2 Y453F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Y508H 2021 Virusdisease Table SARS_CoV_2 Y508H 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Y636F 2021 Virusdisease Table SARS_CoV_2 Y636F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Y674F 2021 Virusdisease Table SARS_CoV_2 Y674F 0 5 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Y837L 2021 Virusdisease Table SARS_CoV_2 Y837L 0 5 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. C241T 2021 Informatics in medicine unlocked Table SARS_CoV_2 C241T 0 5 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. D614G 2021 mBio Table SARS_CoV_2 D614G 0 5 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. E484K 2021 mBio Table SARS_CoV_2 E484K 0 5 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. S477N 2021 mBio Table SARS_CoV_2 S477N 0 5 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. E484K 2021 Nature communications Table SARS_CoV_2 E484K 0 5 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. K986P 2021 Nature communications Table SARS_CoV_2 K986P 0 5 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. V987P 2021 Nature communications Table SARS_CoV_2 V987P 0 5 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. P681H 2021 Virus research Table SARS_CoV_2 P681H 0 5 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. A222V 2021 mSphere Table SARS_CoV_2 A222V 0 5 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. A2431V 2021 mSphere Table SARS_CoV_2 A2431V 0 6 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. A34V 2021 mSphere Table SARS_CoV_2 A34V 0 4 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. C21771T 2021 mSphere Table SARS_CoV_2 C21771T 0 7 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. D614G 2021 mSphere Table SARS_CoV_2 D614G 0 5 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. I114T 2021 mSphere Table SARS_CoV_2 I114T 0 5 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. L95F 2021 mSphere Table SARS_CoV_2 L95F 0 4 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. N87S 2021 mSphere Table SARS_CoV_2 N87S 0 4 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. P314L 2021 mSphere Table SARS_CoV_2 P314L 0 5 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. R42K 2021 mSphere Table SARS_CoV_2 R42K 0 4 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. S1375F 2021 mSphere Table SARS_CoV_2 S1375F 0 6 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. S2193F 2021 mSphere Table SARS_CoV_2 S2193F 0 6 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. S2285F 2021 mSphere Table SARS_CoV_2 S2285F 0 6 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. S50L 2021 mSphere Table SARS_CoV_2 S50L 0 4 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. T21570G 2021 mSphere Table SARS_CoV_2 T21570G 0 7 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. T295I 2021 mSphere Table SARS_CoV_2 T295I 0 5 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. T3058I 2021 mSphere Table SARS_CoV_2 T3058I 0 6 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. T30I 2021 mSphere Table SARS_CoV_2 T30I 0 4 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. T39S 2021 mSphere Table SARS_CoV_2 T39S 0 4 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. L84S 2021 Frontiers in microbiology Table SARS_CoV_2 L84S 0 4 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. S24L 2021 Frontiers in microbiology Table SARS_CoV_2 S24L 0 4 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. V62L 2021 Frontiers in microbiology Table SARS_CoV_2 V62L 0 4 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. W45L 2021 Frontiers in microbiology Table SARS_CoV_2 W45L 0 4 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. N439K 2021 Computational and structural biotechnology journal Table SARS_CoV_2 N439K 0 5 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. P71L 2021 Informatics in medicine unlocked Table SARS_CoV_2 P71L 0 4 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. R69I 2021 Informatics in medicine unlocked Table SARS_CoV_2 R69I 0 4 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. S55F 2021 Informatics in medicine unlocked Table SARS_CoV_2 S55F 0 4 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. V62F 2021 Informatics in medicine unlocked Table SARS_CoV_2 V62F 0 4 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. A262T 2021 Computers in biology and medicine Table SARS_CoV_2 A262T 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. A706V 2021 Computers in biology and medicine Table SARS_CoV_2 A706V 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. A831V 2021 Computers in biology and medicine Table SARS_CoV_2 A831V 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. A845S 2021 Computers in biology and medicine Table SARS_CoV_2 A845S 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. A845V 2021 Computers in biology and medicine Table SARS_CoV_2 A845V 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. A846V 2021 Computers in biology and medicine Table SARS_CoV_2 A846V 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. A852V 2021 Computers in biology and medicine Table SARS_CoV_2 A852V 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. A879S 2021 Computers in biology and medicine Table SARS_CoV_2 A879S 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. C1247F 2021 Computers in biology and medicine Table SARS_CoV_2 C1247F 0 6 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. C1254F 2021 Computers in biology and medicine Table SARS_CoV_2 C1254F 0 6 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. D1163G 2021 Computers in biology and medicine Table SARS_CoV_2 D1163G 0 6 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. D138Y 2021 Computers in biology and medicine Table SARS_CoV_2 D138Y 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. D215H 2021 Computers in biology and medicine Table SARS_CoV_2 D215H 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. D614G 2021 Computers in biology and medicine Table SARS_CoV_2 D614G 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. D839Y 2021 Computers in biology and medicine Table SARS_CoV_2 D839Y 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. D936H 2021 Computers in biology and medicine Table SARS_CoV_2 D936H 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. D936Y 2021 Computers in biology and medicine Table SARS_CoV_2 D936Y 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. F157S 2021 Computers in biology and medicine Table SARS_CoV_2 F157S 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. G181V 2021 Computers in biology and medicine Table SARS_CoV_2 G181V 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. G476S 2021 Computers in biology and medicine Table SARS_CoV_2 G476S 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. H49Y 2021 Computers in biology and medicine Table SARS_CoV_2 H49Y 0 4 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. I1216T 2021 Computers in biology and medicine Table SARS_CoV_2 I1216T 0 6 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. L176F 2021 Computers in biology and medicine Table SARS_CoV_2 L176F 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. L18F 2021 Computers in biology and medicine Table SARS_CoV_2 L18F 0 4 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. L54F 2021 Computers in biology and medicine Table SARS_CoV_2 L54F 0 4 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. L611F 2021 Computers in biology and medicine Table SARS_CoV_2 L611F 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. M1229I 2021 Computers in biology and medicine Table SARS_CoV_2 M1229I 0 6 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. M1237I 2021 Computers in biology and medicine Table SARS_CoV_2 M1237I 0 6 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. M1237L 2021 Computers in biology and medicine Table SARS_CoV_2 M1237L 0 6 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. M153T 2021 Computers in biology and medicine Table SARS_CoV_2 M153T 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. N501Y 2021 Computers in biology and medicine Table SARS_CoV_2 N501Y 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. P1143L 2021 Computers in biology and medicine Table SARS_CoV_2 P1143L 0 6 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. P1162L 2021 Computers in biology and medicine Table SARS_CoV_2 P1162L 0 6 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. P1263L 2021 Computers in biology and medicine Table SARS_CoV_2 P1263L 0 6 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. P809S 2021 Computers in biology and medicine Table SARS_CoV_2 P809S 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Q239K 2021 Computers in biology and medicine Table SARS_CoV_2 Q239K 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Q675H 2021 Computers in biology and medicine Table SARS_CoV_2 Q675H 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Q675R 2021 Computers in biology and medicine Table SARS_CoV_2 Q675R 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. S221L 2021 Computers in biology and medicine Table SARS_CoV_2 S221L 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. S221W 2021 Computers in biology and medicine Table SARS_CoV_2 S221W 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. S247R 2021 Computers in biology and medicine Table SARS_CoV_2 S247R 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. S254F 2021 Computers in biology and medicine Table SARS_CoV_2 S254F 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. S438F 2021 Computers in biology and medicine Table SARS_CoV_2 S438F 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. S50L 2021 Computers in biology and medicine Table SARS_CoV_2 S50L 0 4 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. S71F 2021 Computers in biology and medicine Table SARS_CoV_2 S71F 0 4 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. S939F 2021 Computers in biology and medicine Table SARS_CoV_2 S939F 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. S940F 2021 Computers in biology and medicine Table SARS_CoV_2 S940F 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. S940T 2021 Computers in biology and medicine Table SARS_CoV_2 S940T 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. S943P 2021 Computers in biology and medicine Table SARS_CoV_2 S943P 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. T76I 2021 Computers in biology and medicine Table SARS_CoV_2 T76I 0 4 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. T791I 2021 Computers in biology and medicine Table SARS_CoV_2 T791I 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. T941A 2021 Computers in biology and medicine Table SARS_CoV_2 T941A 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. V1040F 2021 Computers in biology and medicine Table SARS_CoV_2 V1040F 0 6 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. V120I 2021 Computers in biology and medicine Table SARS_CoV_2 V120I 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. V367F 2021 Computers in biology and medicine Table SARS_CoV_2 V367F 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. V483A 2021 Computers in biology and medicine Table SARS_CoV_2 V483A 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. W258L 2021 Computers in biology and medicine Table SARS_CoV_2 W258L 0 5 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Y145H 2021 Computers in biology and medicine Table SARS_CoV_2 Y145H 0 5 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. A570D 2021 Microbiology spectrum Table SARS_CoV_2 A570D 0 5 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. D614G 2021 Microbiology spectrum Table SARS_CoV_2 D614G 0 5 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. N501Y 2021 Microbiology spectrum Table SARS_CoV_2 N501Y 0 5 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. P681H 2021 Microbiology spectrum Table SARS_CoV_2 P681H 0 5 34351228 Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia. A23403G 2021 Microbiology resource announcements Table SARS_CoV_2 A23403G 0 7 34351228 Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia. C241T 2021 Microbiology resource announcements Table SARS_CoV_2 C241T 0 5 34351228 Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia. C3037T 2021 Microbiology resource announcements Table SARS_CoV_2 C3037T 0 6 34351228 Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia. D614G 2021 Microbiology resource announcements Table SARS_CoV_2 D614G 0 5 34351228 Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia. G25563T 2021 Microbiology resource announcements Table SARS_CoV_2 G25563T 0 7 34351228 Near-Complete Genome Sequences of Nine SARS-CoV-2 Strains Harboring the D614G Mutation in Malaysia. Q57H 2021 Microbiology resource announcements Table SARS_CoV_2 Q57H 0 4 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. D467P 2021 PLoS computational biology Table SARS_CoV_2 D467P 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. D467W 2021 PLoS computational biology Table SARS_CoV_2 D467W 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. D467Y 2021 PLoS computational biology Table SARS_CoV_2 D467Y 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. G252C 2021 PLoS computational biology Table SARS_CoV_2 G252C 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. G252D 2021 PLoS computational biology Table SARS_CoV_2 G252D 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. G252E 2021 PLoS computational biology Table SARS_CoV_2 G252E 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. G252H 2021 PLoS computational biology Table SARS_CoV_2 G252H 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. G252M 2021 PLoS computational biology Table SARS_CoV_2 G252M 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. G252P 2021 PLoS computational biology Table SARS_CoV_2 G252P 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. G252Q 2021 PLoS computational biology Table SARS_CoV_2 G252Q 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. G252S 2021 PLoS computational biology Table SARS_CoV_2 G252S 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. G252T 2021 PLoS computational biology Table SARS_CoV_2 G252T 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. G252W 2021 PLoS computational biology Table SARS_CoV_2 G252W 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. G404W 2021 PLoS computational biology Table SARS_CoV_2 G404W 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. G413M 2021 PLoS computational biology Table SARS_CoV_2 G413M 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. G416E 2021 PLoS computational biology Table SARS_CoV_2 G416E 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. G416Y 2021 PLoS computational biology Table SARS_CoV_2 G416Y 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. G504I 2021 PLoS computational biology Table SARS_CoV_2 G504I 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. G72W 2021 PLoS computational biology Table SARS_CoV_2 G72W 0 4 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. I468T 2021 PLoS computational biology Table SARS_CoV_2 I468T 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. K417D 2021 PLoS computational biology Table SARS_CoV_2 K417D 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. K417E 2021 PLoS computational biology Table SARS_CoV_2 K417E 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. K417G 2021 PLoS computational biology Table SARS_CoV_2 K417G 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. K417P 2021 PLoS computational biology Table SARS_CoV_2 K417P 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. N501W 2021 PLoS computational biology Table SARS_CoV_2 N501W 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Q14C 2021 PLoS computational biology Table SARS_CoV_2 Q14C 0 4 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. R34Y 2021 PLoS computational biology Table SARS_CoV_2 R34Y 0 4 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. R355F 2021 PLoS computational biology Table SARS_CoV_2 R355F 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. R403S 2021 PLoS computational biology Table SARS_CoV_2 R403S 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. S161F 2021 PLoS computational biology Table SARS_CoV_2 S161F 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. S161I 2021 PLoS computational biology Table SARS_CoV_2 S161I 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. S161Y 2021 PLoS computational biology Table SARS_CoV_2 S161Y 0 5 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. T73F 2021 PLoS computational biology Table SARS_CoV_2 T73F 0 4 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. D614-R 2021 Virus research Table SARS_CoV_2 D614R 0 6 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. G614-F 2021 Virus research Table SARS_CoV_2 G614F 0 6 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. G614-R 2021 Virus research Table SARS_CoV_2 G614R 0 6 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. A119S 2021 Virus research Table SARS_CoV_2 A119S 0 5 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. D138Y 2021 Virus research Table SARS_CoV_2 D138Y 0 5 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. D156D 2021 Virus research Table SARS_CoV_2 D156D 0 5 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. D614G 2021 Virus research Table SARS_CoV_2 D614G 0 5 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. D828D 2021 Virus research Table SARS_CoV_2 D828D 0 5 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. E484K 2021 Virus research Table SARS_CoV_2 E484K 0 5 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. E92K 2021 Virus research Table SARS_CoV_2 E92K 0 4 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. F120F 2021 Virus research Table SARS_CoV_2 F120F 0 5 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. F924F 2021 Virus research Table SARS_CoV_2 F924F 0 5 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. G4233G 2021 Virus research Table SARS_CoV_2 G4233G 0 6 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. H655Y 2021 Virus research Table SARS_CoV_2 H655Y 0 5 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. I292T 2021 Virus research Table SARS_CoV_2 I292T 0 5 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. I33T 2021 Virus research Table SARS_CoV_2 I33T 0 4 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. I3853I 2021 Virus research Table SARS_CoV_2 I3853I 0 6 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. K1795Q 2021 Virus research Table SARS_CoV_2 K1795Q 0 6 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. L18F 2021 Virus research Table SARS_CoV_2 L18F 0 4 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. L3468V 2021 Virus research Table SARS_CoV_2 L3468V 0 6 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. L3930F 2021 Virus research Table SARS_CoV_2 L3930F 0 6 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. L4715L 2021 Virus research Table SARS_CoV_2 L4715L 0 6 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. M234I 2021 Virus research Table SARS_CoV_2 M234I 0 5 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. N501Y 2021 Virus research Table SARS_CoV_2 N501Y 0 5 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. P2018P 2021 Virus research Table SARS_CoV_2 P2018P 0 6 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. P26S 2021 Virus research Table SARS_CoV_2 P26S 0 4 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. P80R 2021 Virus research Table SARS_CoV_2 P80R 0 4 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. R190S 2021 Virus research Table SARS_CoV_2 R190S 0 5 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. S253P 2021 Virus research Table SARS_CoV_2 S253P 0 5 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. S5665I 2021 Virus research Table SARS_CoV_2 S5665I 0 6 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. T1027I 2021 Virus research Table SARS_CoV_2 T1027I 0 6 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. T20N 2021 Virus research Table SARS_CoV_2 T20N 0 4 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. T4532I 2021 Virus research Table SARS_CoV_2 T4532I 0 6 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. V1176F 2021 Virus research Table SARS_CoV_2 V1176F 0 6 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. V2116V 2021 Virus research Table SARS_CoV_2 V2116V 0 6 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. Y4171Y 2021 Virus research Table SARS_CoV_2 Y4171Y 0 6 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. A67V 2021 Nature communications Table SARS_CoV_2 A67V 0 4 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. A701V 2021 Nature communications Table SARS_CoV_2 A701V 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. D253G 2021 Nature communications Table SARS_CoV_2 D253G 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. D614G 2021 Nature communications Table SARS_CoV_2 D614G 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. E484K 2021 Nature communications Table SARS_CoV_2 E484K 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. F157L 2021 Nature communications Table SARS_CoV_2 F157L 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. F888L 2021 Nature communications Table SARS_CoV_2 F888L 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. G769V 2021 Nature communications Table SARS_CoV_2 G769V 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. K417N 2021 Nature communications Table SARS_CoV_2 K417N 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. K417T 2021 Nature communications Table SARS_CoV_2 K417T 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. L452R 2021 Nature communications Table SARS_CoV_2 L452R 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. N501Y 2021 Nature communications Table SARS_CoV_2 N501Y 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. P681H 2021 Nature communications Table SARS_CoV_2 P681H 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. P681R 2021 Nature communications Table SARS_CoV_2 P681R 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Q52R 2021 Nature communications Table SARS_CoV_2 Q52R 0 4 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Q613H 2021 Nature communications Table SARS_CoV_2 Q613H 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Q677H 2021 Nature communications Table SARS_CoV_2 Q677H 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. R102I 2021 Nature communications Table SARS_CoV_2 R102I 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. T95I 2021 Nature communications Table SARS_CoV_2 T95I 0 4 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. V1176F 2021 Nature communications Table SARS_CoV_2 V1176F 0 6 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. V367F 2021 Nature communications Table SARS_CoV_2 V367F 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. W152C 2021 Nature communications Table SARS_CoV_2 W152C 0 5 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. W152L 2021 Nature communications Table SARS_CoV_2 W152L 0 5 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. C21774T 2021 Microbiology spectrum Table SARS_CoV_2 C21774T 0 7 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. N501Y 2021 Microbiology spectrum Table SARS_CoV_2 N501Y 0 5 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. A570V 2021 Journal of clinical microbiology Table SARS_CoV_2 A570V 0 5 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. E484K 2021 Journal of clinical microbiology Table SARS_CoV_2 E484K 0 5 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. G482V 2021 Journal of clinical microbiology Table SARS_CoV_2 G482V 0 5 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. G566S 2021 Journal of clinical microbiology Table SARS_CoV_2 G566S 0 5 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. L452R 2021 Journal of clinical microbiology Table SARS_CoV_2 L452R 0 5 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. L455F 2021 Journal of clinical microbiology Table SARS_CoV_2 L455F 0 5 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. P463S 2021 Journal of clinical microbiology Table SARS_CoV_2 P463S 0 5 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. S13I 2021 Journal of clinical microbiology Table SARS_CoV_2 S13I 0 4 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. S494P 2021 Journal of clinical microbiology Table SARS_CoV_2 S494P 0 5 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. T470N 2021 Journal of clinical microbiology Table SARS_CoV_2 T470N 0 5 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. T478K 2021 Journal of clinical microbiology Table SARS_CoV_2 T478K 0 5 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. T572I 2021 Journal of clinical microbiology Table SARS_CoV_2 T572I 0 5 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. W152C 2021 Journal of clinical microbiology Table SARS_CoV_2 W152C 0 5 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. D364Y 2021 Frontiers in molecular biosciences Table SARS_CoV_2 D364Y 0 5 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. N354D 2021 Frontiers in molecular biosciences Table SARS_CoV_2 N354D 0 5 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. Q498A 2021 Frontiers in molecular biosciences Table SARS_CoV_2 Q498A 0 5 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. V367F 2021 Frontiers in molecular biosciences Table SARS_CoV_2 V367F 0 5 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. E484K 2021 Antibody therapeutics Table SARS_CoV_2 E484K 0 5 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. E484Q 2021 Antibody therapeutics Table SARS_CoV_2 E484Q 0 5 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. N354S 2021 Antibody therapeutics Table SARS_CoV_2 N354S 0 5 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. N439K 2021 Antibody therapeutics Table SARS_CoV_2 N439K 0 5 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. N440K 2021 Antibody therapeutics Table SARS_CoV_2 N440K 0 5 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. N501Y 2021 Antibody therapeutics Table SARS_CoV_2 N501Y 0 5 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Q493L 2021 Antibody therapeutics Table SARS_CoV_2 Q493L 0 5 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. S359N 2021 Antibody therapeutics Table SARS_CoV_2 S359N 0 5 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. S477N 2021 Antibody therapeutics Table SARS_CoV_2 S477N 0 5 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. V367F 2021 Antibody therapeutics Table SARS_CoV_2 V367F 0 5 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Y453F 2021 Antibody therapeutics Table SARS_CoV_2 Y453F 0 5 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Y505W 2021 Antibody therapeutics Table SARS_CoV_2 Y505W 0 5 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Y508H 2021 Antibody therapeutics Table SARS_CoV_2 Y508H 0 5 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. A1146T 2021 Journal of autoimmunity Table SARS_CoV_2 A1146T 0 6 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. A1306S 2021 Journal of autoimmunity Table SARS_CoV_2 A1306S 0 6 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. A1927V 2021 Journal of autoimmunity Table SARS_CoV_2 A1927V 0 6 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. A3209V 2021 Journal of autoimmunity Table SARS_CoV_2 A3209V 0 6 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. D377Y 2021 Journal of autoimmunity Table SARS_CoV_2 D377Y 0 5 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. D63G 2021 Journal of autoimmunity Table SARS_CoV_2 D63G 0 4 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. G215C 2021 Journal of autoimmunity Table SARS_CoV_2 G215C 0 5 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. G671S 2021 Journal of autoimmunity Table SARS_CoV_2 G671S 0 5 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. I82T 2021 Journal of autoimmunity Table SARS_CoV_2 I82T 0 4 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. P1009L 2021 Journal of autoimmunity Table SARS_CoV_2 P1009L 0 6 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. P1640L 2021 Journal of autoimmunity Table SARS_CoV_2 P1640L 0 6 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. P2046L 2021 Journal of autoimmunity Table SARS_CoV_2 P2046L 0 6 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. P2287S 2021 Journal of autoimmunity Table SARS_CoV_2 P2287S 0 6 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. P323L 2021 Journal of autoimmunity Table SARS_CoV_2 P323L 0 5 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. R203M 2021 Journal of autoimmunity Table SARS_CoV_2 R203M 0 5 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. S26L 2021 Journal of autoimmunity Table SARS_CoV_2 S26L 0 4 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. T120I 2021 Journal of autoimmunity Table SARS_CoV_2 T120I 0 5 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. T1299I 2021 Journal of autoimmunity Table SARS_CoV_2 T1299I 0 6 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. T3255I 2021 Journal of autoimmunity Table SARS_CoV_2 T3255I 0 6 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. T3646A 2021 Journal of autoimmunity Table SARS_CoV_2 T3646A 0 6 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. T3750I 2021 Journal of autoimmunity Table SARS_CoV_2 T3750I 0 6 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. T40I 2021 Journal of autoimmunity Table SARS_CoV_2 T40I 0 4 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. T60A 2021 Journal of autoimmunity Table SARS_CoV_2 T60A 0 4 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. V2930L 2021 Journal of autoimmunity Table SARS_CoV_2 V2930L 0 6 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. V3718A 2021 Journal of autoimmunity Table SARS_CoV_2 V3718A 0 6 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. V82A 2021 Journal of autoimmunity Table SARS_CoV_2 V82A 0 4 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. A11451G 2021 Infection, genetics and evolution Table SARS_CoV_2 A11451G 0 7 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. A21993C 2021 Infection, genetics and evolution Table SARS_CoV_2 A21993C 0 7 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. A21996C 2021 Infection, genetics and evolution Table SARS_CoV_2 A21996C 0 7 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. A23063T 2021 Infection, genetics and evolution Table SARS_CoV_2 A23063T 0 7 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. A3428G 2021 Infection, genetics and evolution Table SARS_CoV_2 A3428G 0 6 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. C14408T 2021 Infection, genetics and evolution Table SARS_CoV_2 C14408T 0 7 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. C17491T 2021 Infection, genetics and evolution Table SARS_CoV_2 C17491T 0 7 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. C21846T 2021 Infection, genetics and evolution Table SARS_CoV_2 C21846T 0 7 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. C21997T 2021 Infection, genetics and evolution Table SARS_CoV_2 C21997T 0 7 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. C23604A 2021 Infection, genetics and evolution Table SARS_CoV_2 C23604A 0 7 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. C28005T 2021 Infection, genetics and evolution Table SARS_CoV_2 C28005T 0 7 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. C28093T 2021 Infection, genetics and evolution Table SARS_CoV_2 C28093T 0 7 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. C4878T 2021 Infection, genetics and evolution Table SARS_CoV_2 C4878T 0 6 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. G22599A 2021 Infection, genetics and evolution Table SARS_CoV_2 G22599A 0 7 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. G23012A 2021 Infection, genetics and evolution Table SARS_CoV_2 G23012A 0 7 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. G25563T 2021 Infection, genetics and evolution Table SARS_CoV_2 G25563T 0 7 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. ins146N 2021 Infection, genetics and evolution Table SARS_CoV_2 ins146N 0 7 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. N257X 2021 Infection, genetics and evolution Table SARS_CoV_2 N257X 0 5 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. T21992A 2021 Infection, genetics and evolution Table SARS_CoV_2 T21992A 0 7 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. A570D 2021 Frontiers in public health Table SARS_CoV_2 A570D 0 5 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. D1118H 2021 Frontiers in public health Table SARS_CoV_2 D1118H 0 6 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. D138Y 2021 Frontiers in public health Table SARS_CoV_2 D138Y 0 5 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. H655Y 2021 Frontiers in public health Table SARS_CoV_2 H655Y 0 5 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. L452R 2021 Frontiers in public health Table SARS_CoV_2 L452R 0 5 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. N501Y 2021 Frontiers in public health Table SARS_CoV_2 N501Y 0 5 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. P681H 2021 Frontiers in public health Table SARS_CoV_2 P681H 0 5 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. Q677H 2021 Frontiers in public health Table SARS_CoV_2 Q677H 0 5 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. R190S 2021 Frontiers in public health Table SARS_CoV_2 R190S 0 5 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. S982A 2021 Frontiers in public health Table SARS_CoV_2 S982A 0 5 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. T1027I 2021 Frontiers in public health Table SARS_CoV_2 T1027I 0 6 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. T20N 2021 Frontiers in public health Table SARS_CoV_2 T20N 0 4 34409009 The Emergence and Spread of Novel SARS-CoV-2 Variants. T716I 2021 Frontiers in public health Table SARS_CoV_2 T716I 0 5 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. D893Y 2021 Archives of microbiology Table SARS_CoV_2 D893Y 0 5 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. E802A 2021 Archives of microbiology Table SARS_CoV_2 E802A 0 5 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. Q822H 2021 Archives of microbiology Table SARS_CoV_2 Q822H 0 5 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. R118C 2021 Archives of microbiology Table SARS_CoV_2 R118C 0 5 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. T148I 2021 Archives of microbiology Table SARS_CoV_2 T148I 0 5 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. V880I 2021 Archives of microbiology Table SARS_CoV_2 V880I 0 5 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. Y149C 2021 Archives of microbiology Table SARS_CoV_2 Y149C 0 5 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. N439K 2021 Frontiers in cell and developmental biology Table SARS_CoV_2 N439K 0 5 34417165 Effectiveness of BNT162b2 and mRNA-1273 covid-19 vaccines against symptomatic SARS-CoV-2 infection and severe covid-19 outcomes in Ontario, Canada: test negative design study. E484K 2021 BMJ (Clinical research ed.) Table SARS_CoV_2 E484K 0 5 34417349 SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. D614G 2021 Proc Natl Acad Sci U S A Table SARS_CoV_2 D614G 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. A367T 2021 Infectious diseases of poverty Table SARS_CoV_2 A367T 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. A372S 2021 Infectious diseases of poverty Table SARS_CoV_2 A372S 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. A435S 2021 Infectious diseases of poverty Table SARS_CoV_2 A435S 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. A475V 2021 Infectious diseases of poverty Table SARS_CoV_2 A475V 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. A520S 2021 Infectious diseases of poverty Table SARS_CoV_2 A520S 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. A522E 2021 Infectious diseases of poverty Table SARS_CoV_2 A522E 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. A522S 2021 Infectious diseases of poverty Table SARS_CoV_2 A522S 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. A522V 2021 Infectious diseases of poverty Table SARS_CoV_2 A522V 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. D364Y 2021 Infectious diseases of poverty Table SARS_CoV_2 D364Y 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. D405V 2021 Infectious diseases of poverty Table SARS_CoV_2 D405V 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. D467V 2021 Infectious diseases of poverty Table SARS_CoV_2 D467V 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. E484K 2021 Infectious diseases of poverty Table SARS_CoV_2 E484K 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. E516Q 2021 Infectious diseases of poverty Table SARS_CoV_2 E516Q 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. F338L 2021 Infectious diseases of poverty Table SARS_CoV_2 F338L 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. F490L 2021 Infectious diseases of poverty Table SARS_CoV_2 F490L 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. F490S 2021 Infectious diseases of poverty Table SARS_CoV_2 F490S 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. G446V 2021 Infectious diseases of poverty Table SARS_CoV_2 G446V 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. G476S 2021 Infectious diseases of poverty Table SARS_CoV_2 G476S 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. H519P 2021 Infectious diseases of poverty Table SARS_CoV_2 H519P 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. H519Q 2021 Infectious diseases of poverty Table SARS_CoV_2 H519Q 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. I468F 2021 Infectious diseases of poverty Table SARS_CoV_2 I468F 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. I468T 2021 Infectious diseases of poverty Table SARS_CoV_2 I468T 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. I472V 2021 Infectious diseases of poverty Table SARS_CoV_2 I472V 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. K378R 2021 Infectious diseases of poverty Table SARS_CoV_2 K378R 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. K417R 2021 Infectious diseases of poverty Table SARS_CoV_2 K417R 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. K458N 2021 Infectious diseases of poverty Table SARS_CoV_2 K458N 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. K458R 2021 Infectious diseases of poverty Table SARS_CoV_2 K458R 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. N354D 2021 Infectious diseases of poverty Table SARS_CoV_2 N354D 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. N354K 2021 Infectious diseases of poverty Table SARS_CoV_2 N354K 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. N354S 2021 Infectious diseases of poverty Table SARS_CoV_2 N354S 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. N439K 2021 Infectious diseases of poverty Table SARS_CoV_2 N439K 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. N501T 2021 Infectious diseases of poverty Table SARS_CoV_2 N501T 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. P384S 2021 Infectious diseases of poverty Table SARS_CoV_2 P384S 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. P491R 2021 Infectious diseases of poverty Table SARS_CoV_2 P491R 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. P521R 2021 Infectious diseases of poverty Table SARS_CoV_2 P521R 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. Q409E 2021 Infectious diseases of poverty Table SARS_CoV_2 Q409E 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. Q414A 2021 Infectious diseases of poverty Table SARS_CoV_2 Q414A 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. Q414E 2021 Infectious diseases of poverty Table SARS_CoV_2 Q414E 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. R346K 2021 Infectious diseases of poverty Table SARS_CoV_2 R346K 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. R408I 2021 Infectious diseases of poverty Table SARS_CoV_2 R408I 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. R408K 2021 Infectious diseases of poverty Table SARS_CoV_2 R408K 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. R509K 2021 Infectious diseases of poverty Table SARS_CoV_2 R509K 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. S373L 2021 Infectious diseases of poverty Table SARS_CoV_2 S373L 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. S438F 2021 Infectious diseases of poverty Table SARS_CoV_2 S438F 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. S459Y 2021 Infectious diseases of poverty Table SARS_CoV_2 S459Y 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. S469P 2021 Infectious diseases of poverty Table SARS_CoV_2 S469P 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. S477G 2021 Infectious diseases of poverty Table SARS_CoV_2 S477G 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. S477N 2021 Infectious diseases of poverty Table SARS_CoV_2 S477N 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. S494P 2021 Infectious diseases of poverty Table SARS_CoV_2 S494P 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. S514F 2021 Infectious diseases of poverty Table SARS_CoV_2 S514F 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. T385I 2021 Infectious diseases of poverty Table SARS_CoV_2 T385I 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. T478K 2021 Infectious diseases of poverty Table SARS_CoV_2 T478K 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. V341I 2021 Infectious diseases of poverty Table SARS_CoV_2 V341I 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. V367F 2021 Infectious diseases of poverty Table SARS_CoV_2 V367F 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. V382L 2021 Infectious diseases of poverty Table SARS_CoV_2 V382L 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. V483A 2021 Infectious diseases of poverty Table SARS_CoV_2 V483A 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. V483I 2021 Infectious diseases of poverty Table SARS_CoV_2 V483I 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. V510L 2021 Infectious diseases of poverty Table SARS_CoV_2 V510L 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. Y508H 2021 Infectious diseases of poverty Table SARS_CoV_2 Y508H 0 5 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. N501Y 2021 EBioMedicine Table SARS_CoV_2 N501Y 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. A222V 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 A222V 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. D138Y 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 D138Y 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. D614G 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 D614G 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. E484K 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 E484K 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. E780Q 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 E780Q 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. G1219C 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 G1219C 0 6 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. G204R 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 G204R 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. H655Y 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 H655Y 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. I292T 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 I292T 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. I33T 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 I33T 0 4 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. K417T 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 K417T 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. L18F 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 L18F 0 4 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. L54F 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 L54F 0 4 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. L71F 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 L71F 0 4 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. M153I 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 M153I 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. N501Y 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 N501Y 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. P26S 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 P26S 0 4 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. P323L 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 P323L 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. P383L 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 P383L 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. R190S 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 R190S 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. R203K 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 R203K 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. R216N 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 R216N 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. S929I 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 S929I 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. T1027I 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 T1027I 0 6 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. T20N 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 T20N 0 4 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. T572I 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 T572I 0 5 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. V1176F 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 V1176F 0 6 34425504 SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil. V577F 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 V577F 0 5 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. E484K 2021 Nature Table SARS_CoV_2 E484K 0 5 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. N501Y 2021 Nature Table SARS_CoV_2 N501Y 0 5 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. E484K 2021 iScience Table SARS_CoV_2 E484K 0 5 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. K417N 2021 iScience Table SARS_CoV_2 K417N 0 5 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. N0315S 2021 iScience Table SARS_CoV_2 N0315S 0 6 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. N501Y 2021 iScience Table SARS_CoV_2 N501Y 0 5 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. E484K 2021 eLife Table SARS_CoV_2 E484K 0 5 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. K26R 2021 eLife Table SARS_CoV_2 K26R 0 4 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. K417N 2021 eLife Table SARS_CoV_2 K417N 0 5 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. K417T 2021 eLife Table SARS_CoV_2 K417T 0 5 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. N501Y 2021 eLife Table SARS_CoV_2 N501Y 0 5 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. S477N 2021 eLife Table SARS_CoV_2 S477N 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. 144del 2021 The Science of the total environment Table SARS_CoV_2 144del 0 6 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. 156del 2021 The Science of the total environment Table SARS_CoV_2 156del 0 6 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. 157del 2021 The Science of the total environment Table SARS_CoV_2 157del 0 6 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. 241del 2021 The Science of the total environment Table SARS_CoV_2 241del 0 6 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. 242del 2021 The Science of the total environment Table SARS_CoV_2 242del 0 6 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. 243del 2021 The Science of the total environment Table SARS_CoV_2 243del 0 6 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. 69del 2021 The Science of the total environment Table SARS_CoV_2 69del 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. 70del 2021 The Science of the total environment Table SARS_CoV_2 70del 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. A1105T 2021 The Science of the total environment Table SARS_CoV_2 A1105T 0 6 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. A67V 2021 The Science of the total environment Table SARS_CoV_2 A67V 0 4 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. A701V 2021 The Science of the total environment Table SARS_CoV_2 A701V 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. D138Y 2021 The Science of the total environment Table SARS_CoV_2 D138Y 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. D215G 2021 The Science of the total environment Table SARS_CoV_2 D215G 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. D253G 2021 The Science of the total environment Table SARS_CoV_2 D253G 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. D614G 2021 The Science of the total environment Table SARS_CoV_2 D614G 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. D950N 2021 The Science of the total environment Table SARS_CoV_2 D950N 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. E484K 2021 The Science of the total environment Table SARS_CoV_2 E484K 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. F888L 2021 The Science of the total environment Table SARS_CoV_2 F888L 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. G142D 2021 The Science of the total environment Table SARS_CoV_2 G142D 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. H655Y 2021 The Science of the total environment Table SARS_CoV_2 H655Y 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. K417N 2021 The Science of the total environment Table SARS_CoV_2 K417N 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. K417T 2021 The Science of the total environment Table SARS_CoV_2 K417T 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. L18F 2021 The Science of the total environment Table SARS_CoV_2 L18F 0 4 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. L452R 2021 The Science of the total environment Table SARS_CoV_2 L452R 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. L822F 2021 The Science of the total environment Table SARS_CoV_2 L822F 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. L858F 2021 The Science of the total environment Table SARS_CoV_2 L858F 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. L912F 2021 The Science of the total environment Table SARS_CoV_2 L912F 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. M101V 2021 The Science of the total environment Table SARS_CoV_2 M101V 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. M1788I 2021 The Science of the total environment Table SARS_CoV_2 M1788I 0 6 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. M458I 2021 The Science of the total environment Table SARS_CoV_2 M458I 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. N501Y 2021 The Science of the total environment Table SARS_CoV_2 N501Y 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. P26S 2021 The Science of the total environment Table SARS_CoV_2 P26S 0 4 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. P681R 2021 The Science of the total environment Table SARS_CoV_2 P681R 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. Q677H 2021 The Science of the total environment Table SARS_CoV_2 Q677H 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. Q920K 2021 The Science of the total environment Table SARS_CoV_2 Q920K 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. R158G 2021 The Science of the total environment Table SARS_CoV_2 R158G 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. R190S 2021 The Science of the total environment Table SARS_CoV_2 R190S 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. S13I 2021 The Science of the total environment Table SARS_CoV_2 S13I 0 4 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. S477N 2021 The Science of the total environment Table SARS_CoV_2 S477N 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. S884F 2021 The Science of the total environment Table SARS_CoV_2 S884F 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. S939F 2021 The Science of the total environment Table SARS_CoV_2 S939F 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. T1027I 2021 The Science of the total environment Table SARS_CoV_2 T1027I 0 6 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. T19R 2021 The Science of the total environment Table SARS_CoV_2 T19R 0 4 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. T20N 2021 The Science of the total environment Table SARS_CoV_2 T20N 0 4 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. T455I 2021 The Science of the total environment Table SARS_CoV_2 T455I 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. T478K 2021 The Science of the total environment Table SARS_CoV_2 T478K 0 5 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. T95I 2021 The Science of the total environment Table SARS_CoV_2 T95I 0 4 34438144 Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling. Y38F 2021 The Science of the total environment Table SARS_CoV_2 Y38F 0 4 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. A11117G 2021 Archives of virology Table SARS_CoV_2 A11117G 0 7 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. A23403G 2021 Archives of virology Table SARS_CoV_2 A23403G 0 7 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. A23756G 2021 Archives of virology Table SARS_CoV_2 A23756G 0 7 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. C10029T 2021 Archives of virology Table SARS_CoV_2 C10029T 0 7 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. C10954T 2021 Archives of virology Table SARS_CoV_2 C10954T 0 7 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. C12789T 2021 Archives of virology Table SARS_CoV_2 C12789T 0 7 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. C14408T 2021 Archives of virology Table SARS_CoV_2 C14408T 0 7 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. C203T 2021 Archives of virology Table SARS_CoV_2 C203T 0 5 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. C21306T 2021 Archives of virology Table SARS_CoV_2 C21306T 0 7 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. C222T 2021 Archives of virology Table SARS_CoV_2 C222T 0 5 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. C22995A 2021 Archives of virology Table SARS_CoV_2 C22995A 0 7 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. C23604A 2021 Archives of virology Table SARS_CoV_2 C23604A 0 7 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. C241T 2021 Archives of virology Table SARS_CoV_2 C241T 0 5 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. C29197T 2021 Archives of virology Table SARS_CoV_2 C29197T 0 7 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. C3037T 2021 Archives of virology Table SARS_CoV_2 C3037T 0 6 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. C3140T 2021 Archives of virology Table SARS_CoV_2 C3140T 0 6 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. D614G 2021 Archives of virology Table SARS_CoV_2 D614G 0 5 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. G204R 2021 Archives of virology Table SARS_CoV_2 G204R 0 5 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. G28881A 2021 Archives of virology Table SARS_CoV_2 G28881A 0 7 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. G28882A 2021 Archives of virology Table SARS_CoV_2 G28882A 0 7 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. G28883C 2021 Archives of virology Table SARS_CoV_2 G28883C 0 7 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. I49V 2021 Archives of virology Table SARS_CoV_2 I49V 0 4 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. P141S 2021 Archives of virology Table SARS_CoV_2 P141S 0 5 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. P323L 2021 Archives of virology Table SARS_CoV_2 P323L 0 5 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. P681H 2021 Archives of virology Table SARS_CoV_2 P681H 0 5 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. R203K 2021 Archives of virology Table SARS_CoV_2 R203K 0 5 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. T19839C 2021 Archives of virology Table SARS_CoV_2 T19839C 0 7 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. T478K 2021 Archives of virology Table SARS_CoV_2 T478K 0 5 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. T492I 2021 Archives of virology Table SARS_CoV_2 T492I 0 5 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. T732A 2021 Archives of virology Table SARS_CoV_2 T732A 0 5 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. E484K 2022 Allergy Table SARS_CoV_2 E484K 0 5 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. E484Q 2022 Allergy Table SARS_CoV_2 E484Q 0 5 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. L452R 2022 Allergy Table SARS_CoV_2 L452R 0 5 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 10323A>G 2021 Heliyon Table SARS_CoV_2 A10323G 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 11083G>T 2021 Heliyon Table SARS_CoV_2 G11083T 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 1163A>T 2021 Heliyon Table SARS_CoV_2 A1163T 0 7 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 14408C>T 2021 Heliyon Table SARS_CoV_2 C14408T 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 15324C>T 2021 Heliyon Table SARS_CoV_2 C15324T 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 15738C>T 2021 Heliyon Table SARS_CoV_2 C15738T 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 18877C>T 2021 Heliyon Table SARS_CoV_2 C18877T 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 19723G>T 2021 Heliyon Table SARS_CoV_2 G19723T 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 2040C>T 2021 Heliyon Table SARS_CoV_2 C2040T 0 7 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 21575C>T 2021 Heliyon Table SARS_CoV_2 C21575T 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 21855C>T 2021 Heliyon Table SARS_CoV_2 C21855T 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 22444C>T 2021 Heliyon Table SARS_CoV_2 C22444T 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 23403A>G 2021 Heliyon Table SARS_CoV_2 A23403G 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 2388C>T 2021 Heliyon Table SARS_CoV_2 C2388T 0 7 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 241C>T 2021 Heliyon Table SARS_CoV_2 C241T 0 6 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 25494G>T 2021 Heliyon Table SARS_CoV_2 G25494T 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 25504C>G 2021 Heliyon Table SARS_CoV_2 C25504G 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 25563G>T 2021 Heliyon Table SARS_CoV_2 G25563T 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 26735C>T 2021 Heliyon Table SARS_CoV_2 C26735T 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 26895C>T 2021 Heliyon Table SARS_CoV_2 C26895T 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 2836C>T 2021 Heliyon Table SARS_CoV_2 C2836T 0 7 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 28854C>T 2021 Heliyon Table SARS_CoV_2 C28854T 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 28881G>A 2021 Heliyon Table SARS_CoV_2 G28881A 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 28882G>A 2021 Heliyon Table SARS_CoV_2 G28882A 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 2910C>T 2021 Heliyon Table SARS_CoV_2 C2910T 0 7 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 29403A>G 2021 Heliyon Table SARS_CoV_2 A29403G 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 29848T>A 2021 Heliyon Table SARS_CoV_2 T29848A 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 29850A>T 2021 Heliyon Table SARS_CoV_2 A29850T 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 29852A>T 2021 Heliyon Table SARS_CoV_2 A29852T 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 29853G>A 2021 Heliyon Table SARS_CoV_2 G29853A 0 8 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 3037C>T 2021 Heliyon Table SARS_CoV_2 C3037T 0 7 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 3961C>T 2021 Heliyon Table SARS_CoV_2 C3961T 0 7 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 4444G>T 2021 Heliyon Table SARS_CoV_2 G4444T 0 7 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 683C>T 2021 Heliyon Table SARS_CoV_2 C683T 0 6 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 8026A>G 2021 Heliyon Table SARS_CoV_2 A8026G 0 7 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 8371G>T 2021 Heliyon Table SARS_CoV_2 G8371T 0 7 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. 9502C>T 2021 Heliyon Table SARS_CoV_2 C9502T 0 7 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. D377G 2021 Heliyon Table SARS_CoV_2 D377G 0 5 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. D614G 2021 Heliyon Table SARS_CoV_2 D614G 0 5 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. G204R 2021 Heliyon Table SARS_CoV_2 G204R 0 5 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. H125Y 2021 Heliyon Table SARS_CoV_2 H125Y 0 5 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. I300F 2021 Heliyon Table SARS_CoV_2 I300F 0 5 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. K3353R 2021 Heliyon Table SARS_CoV_2 K3353R 0 6 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. L3606F 2021 Heliyon Table SARS_CoV_2 L3606F 0 6 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. Q2702H 2021 Heliyon Table SARS_CoV_2 Q2702H 0 6 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. Q38E 2021 Heliyon Table SARS_CoV_2 Q38E 0 4 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. Q57H 2021 Heliyon Table SARS_CoV_2 Q57H 0 4 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. R203K 2021 Heliyon Table SARS_CoV_2 R203K 0 5 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. S194L 2021 Heliyon Table SARS_CoV_2 S194L 0 5 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. S98F 2021 Heliyon Table SARS_CoV_2 S98F 0 4 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. T592I 2021 Heliyon Table SARS_CoV_2 T592I 0 5 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. T708I 2021 Heliyon Table SARS_CoV_2 T708I 0 5 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. T882I 2021 Heliyon Table SARS_CoV_2 T882I 0 5 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. A20262G 2021 bioRxiv Table SARS_CoV_2 A20262G 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. A23604G 2021 bioRxiv Table SARS_CoV_2 A23604G 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. A28111G 2021 bioRxiv Table SARS_CoV_2 A28111G 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. A28271del 2021 bioRxiv Table SARS_CoV_2 A28271del 0 9 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. A28461G 2021 bioRxiv Table SARS_CoV_2 A28461G 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C1191T 2021 bioRxiv Table SARS_CoV_2 C1191T 0 6 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C1267T 2021 bioRxiv Table SARS_CoV_2 C1267T 0 6 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C14408T 2021 bioRxiv Table SARS_CoV_2 C14408T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C14676T 2021 bioRxiv Table SARS_CoV_2 C14676T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C15279T 2021 bioRxiv Table SARS_CoV_2 C15279T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C16466T 2021 bioRxiv Table SARS_CoV_2 C16466T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C20320T 2021 bioRxiv Table SARS_CoV_2 C20320T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C210T 2021 bioRxiv Table SARS_CoV_2 C210T 0 5 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C21618G 2021 bioRxiv Table SARS_CoV_2 C21618G 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C22995A 2021 bioRxiv Table SARS_CoV_2 C22995A 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C241T 2021 bioRxiv Table SARS_CoV_2 C241T 0 5 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C24745T 2021 bioRxiv Table SARS_CoV_2 C24745T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C25469T 2021 bioRxiv Table SARS_CoV_2 C25469T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C27739T 2021 bioRxiv Table SARS_CoV_2 C27739T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C27752T 2021 bioRxiv Table SARS_CoV_2 C27752T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C27972T 2021 bioRxiv Table SARS_CoV_2 C27972T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C28144T 2021 bioRxiv Table SARS_CoV_2 C28144T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C28977T 2021 bioRxiv Table SARS_CoV_2 C28977T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C29762T 2021 bioRxiv Table SARS_CoV_2 C29762T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C3037T 2021 bioRxiv Table SARS_CoV_2 C3037T 0 6 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C3177T 2021 bioRxiv Table SARS_CoV_2 C3177T 0 6 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C3267T 2021 bioRxiv Table SARS_CoV_2 C3267T 0 6 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C5184T 2021 bioRxiv Table SARS_CoV_2 C5184T 0 6 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C5388A 2021 bioRxiv Table SARS_CoV_2 C5388A 0 6 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C5986T 2021 bioRxiv Table SARS_CoV_2 C5986T 0 6 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C6539T 2021 bioRxiv Table SARS_CoV_2 C6539T 0 6 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C913T 2021 bioRxiv Table SARS_CoV_2 C913T 0 5 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. C9891T 2021 bioRxiv Table SARS_CoV_2 C9891T 0 6 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. G15451A 2021 bioRxiv Table SARS_CoV_2 G15451A 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. G21987A 2021 bioRxiv Table SARS_CoV_2 G21987A 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. G24410A 2021 bioRxiv Table SARS_CoV_2 G24410A 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. G28048T 2021 bioRxiv Table SARS_CoV_2 G28048T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. G28881T 2021 bioRxiv Table SARS_CoV_2 G28881T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. G29402T 2021 bioRxiv Table SARS_CoV_2 G29402T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. G29427A 2021 bioRxiv Table SARS_CoV_2 G29427A 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. G29742T 2021 bioRxiv Table SARS_CoV_2 G29742T 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. T11418C 2021 bioRxiv Table SARS_CoV_2 T11418C 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. T12946C 2021 bioRxiv Table SARS_CoV_2 T12946C 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. T14444C 2021 bioRxiv Table SARS_CoV_2 T14444C 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. T16176C 2021 bioRxiv Table SARS_CoV_2 T16176C 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. T22917G 2021 bioRxiv Table SARS_CoV_2 T22917G 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. T26767C 2021 bioRxiv Table SARS_CoV_2 T26767C 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. T27638C 2021 bioRxiv Table SARS_CoV_2 T27638C 0 7 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. T6954C 2021 bioRxiv Table SARS_CoV_2 T6954C 0 6 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. T8782C 2021 bioRxiv Table SARS_CoV_2 T8782C 0 6 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. E484K 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 E484K 0 5 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. K417N 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 K417N 0 5 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. K417T 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 K417T 0 5 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. N501Y 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 N501Y 0 5 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. D614G 2021 Immunity Table SARS_CoV_2 D614G 0 5 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. N501Y 2021 Diagnostic microbiology and infectious disease Table SARS_CoV_2 N501Y 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. 156del 2021 mBio Table SARS_CoV_2 156del 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. 157del 2021 mBio Table SARS_CoV_2 157del 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. A119S 2021 mBio Table SARS_CoV_2 A119S 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. A12G 2021 mBio Table SARS_CoV_2 A12G 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. A1708D 2021 mBio Table SARS_CoV_2 A1708D 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. A570D 2021 mBio Table SARS_CoV_2 A570D 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. A67V 2021 mBio Table SARS_CoV_2 A67V 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. A701V 2021 mBio Table SARS_CoV_2 A701V 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. D1118H 2021 mBio Table SARS_CoV_2 D1118H 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. D138Y 2021 mBio Table SARS_CoV_2 D138Y 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. D215G 2021 mBio Table SARS_CoV_2 D215G 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. D253G 2021 mBio Table SARS_CoV_2 D253G 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. D614G 2021 mBio Table SARS_CoV_2 D614G 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. D80A 2021 mBio Table SARS_CoV_2 D80A 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. D950N 2021 mBio Table SARS_CoV_2 D950N 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. E484K 2021 mBio Table SARS_CoV_2 E484K 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. E5665D 2021 mBio Table SARS_CoV_2 E5665D 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. E92K 2021 mBio Table SARS_CoV_2 E92K 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. F888L 2021 mBio Table SARS_CoV_2 F888L 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. G142D 2021 mBio Table SARS_CoV_2 G142D 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. G204R 2021 mBio Table SARS_CoV_2 G204R 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. H655Y 2021 mBio Table SARS_CoV_2 H655Y 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. I2230T 2021 mBio Table SARS_CoV_2 I2230T 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. I82T 2021 mBio Table SARS_CoV_2 I82T 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. K1655N 2021 mBio Table SARS_CoV_2 K1655N 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. K1795Q 2021 mBio Table SARS_CoV_2 K1795Q 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. K417N 2021 mBio Table SARS_CoV_2 K417N 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. K417T 2021 mBio Table SARS_CoV_2 K417T 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. L18F 2021 mBio Table SARS_CoV_2 L18F 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. L3201P 2021 mBio Table SARS_CoV_2 L3201P 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. L3468V 2021 mBio Table SARS_CoV_2 L3468V 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. L3930F 2021 mBio Table SARS_CoV_2 L3930F 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. L452R 2021 mBio Table SARS_CoV_2 L452R 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. M234I 2021 mBio Table SARS_CoV_2 M234I 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. N501Y 2021 mBio Table SARS_CoV_2 N501Y 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. P26S 2021 mBio Table SARS_CoV_2 P26S 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. P314F 2021 mBio Table SARS_CoV_2 P314F 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. P314L 2021 mBio Table SARS_CoV_2 P314L 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. P42L 2021 mBio Table SARS_CoV_2 P42L 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. P681H 2021 mBio Table SARS_CoV_2 P681H 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. P681R 2021 mBio Table SARS_CoV_2 P681R 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. P71L 2021 mBio Table SARS_CoV_2 P71L 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. P80R 2021 mBio Table SARS_CoV_2 P80R 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Q1011H 2021 mBio Table SARS_CoV_2 Q1011H 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Q57H 2021 mBio Table SARS_CoV_2 Q57H 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Q677H 2021 mBio Table SARS_CoV_2 Q677H 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. R158G 2021 mBio Table SARS_CoV_2 R158G 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. R190S 2021 mBio Table SARS_CoV_2 R190S 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. R203K 2021 mBio Table SARS_CoV_2 R203K 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. R246I 2021 mBio Table SARS_CoV_2 R246I 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. R52I 2021 mBio Table SARS_CoV_2 R52I 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. R81C 2021 mBio Table SARS_CoV_2 R81C 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. S1188L 2021 mBio Table SARS_CoV_2 S1188L 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. S235F 2021 mBio Table SARS_CoV_2 S235F 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. S982A 2021 mBio Table SARS_CoV_2 S982A 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. T1001I 2021 mBio Table SARS_CoV_2 T1001I 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. T1027I 2021 mBio Table SARS_CoV_2 T1027I 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. T11I 2021 mBio Table SARS_CoV_2 T11I 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. T19R 2021 mBio Table SARS_CoV_2 T19R 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. T2007I 2021 mBio Table SARS_CoV_2 T2007I 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. T205I 2021 mBio Table SARS_CoV_2 T205I 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. T20N 2021 mBio Table SARS_CoV_2 T20N 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. T265I 2021 mBio Table SARS_CoV_2 T265I 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. T478K 2021 mBio Table SARS_CoV_2 T478K 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. T716I 2021 mBio Table SARS_CoV_2 T716I 0 5 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. T95I 2021 mBio Table SARS_CoV_2 T95I 0 4 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. V1176F 2021 mBio Table SARS_CoV_2 V1176F 0 6 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Y73C 2021 mBio Table SARS_CoV_2 Y73C 0 4 34467913 An innovative approach for the non-invasive surveillance of communities and early detection of SARS-CoV-2 via solid waste analysis. A222V 2021 The Science of the total environment Table SARS_CoV_2 A222V 0 5 34467913 An innovative approach for the non-invasive surveillance of communities and early detection of SARS-CoV-2 via solid waste analysis. P521S 2021 The Science of the total environment Table SARS_CoV_2 P521S 0 5 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. D218E 2021 GeroScience Table SARS_CoV_2 D218E 0 5 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. E253A 2021 GeroScience Table SARS_CoV_2 E253A 0 5 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. Q444H 2021 GeroScience Table SARS_CoV_2 Q444H 0 5 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. S177I 2021 GeroScience Table SARS_CoV_2 S177I 0 5 34488546 Impact of the Delta variant on vaccine efficacy and response strategies. D614G 2021 Expert review of vaccines Table SARS_CoV_2 D614G 0 5 34492088 Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination. A879S 2021 PLoS pathogens Table SARS_CoV_2 A879S 0 5 34492088 Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination. D614G 2021 PLoS pathogens Table SARS_CoV_2 D614G 0 5 34492088 Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination. G1254V 2021 PLoS pathogens Table SARS_CoV_2 G1254V 0 6 34492088 Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination. P812L 2021 PLoS pathogens Table SARS_CoV_2 P812L 0 5 34492088 Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination. S1252C 2021 PLoS pathogens Table SARS_CoV_2 S1252C 0 6 34492088 Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination. V227L 2021 PLoS pathogens Table SARS_CoV_2 V227L 0 5 34492088 Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination. Y453F 2021 PLoS pathogens Table SARS_CoV_2 Y453F 0 5 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). E484K 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 E484K 0 5 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). K417N 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 K417N 0 5 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). N501Y 2021 Journal of biomolecular structure & dynamics Table SARS_CoV_2 N501Y 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. A222V 2021 Biochimie Table SARS_CoV_2 A222V 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. A262S 2021 Biochimie Table SARS_CoV_2 A262S 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. A701V 2021 Biochimie Table SARS_CoV_2 A701V 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. D1163Y 2021 Biochimie Table SARS_CoV_2 D1163Y 0 6 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. D614G 2021 Biochimie Table SARS_CoV_2 D614G 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. E484K 2021 Biochimie Table SARS_CoV_2 E484K 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. E484Q 2021 Biochimie Table SARS_CoV_2 E484Q 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. E583D 2021 Biochimie Table SARS_CoV_2 E583D 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. G1167V 2021 Biochimie Table SARS_CoV_2 G1167V 0 6 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. L18F 2021 Biochimie Table SARS_CoV_2 L18F 0 4 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. L452R 2021 Biochimie Table SARS_CoV_2 L452R 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. N439K 2021 Biochimie Table SARS_CoV_2 N439K 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. N501T 2021 Biochimie Table SARS_CoV_2 N501T 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. N501Y 2021 Biochimie Table SARS_CoV_2 N501Y 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. P272L 2021 Biochimie Table SARS_CoV_2 P272L 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. P681H 2021 Biochimie Table SARS_CoV_2 P681H 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. P681R 2021 Biochimie Table SARS_CoV_2 P681R 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. Q675H 2021 Biochimie Table SARS_CoV_2 Q675H 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. Q675P 2021 Biochimie Table SARS_CoV_2 Q675P 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. Q677H 2021 Biochimie Table SARS_CoV_2 Q677H 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. Q677P 2021 Biochimie Table SARS_CoV_2 Q677P 0 5 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. S98F 2021 Biochimie Table SARS_CoV_2 S98F 0 4 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. V1176F 2021 Biochimie Table SARS_CoV_2 V1176F 0 6 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. Y453F 2021 Biochimie Table SARS_CoV_2 Y453F 0 5 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. 1001T>I 2021 Computational and structural biotechnology journal Table SARS_CoV_2 T1001I 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. 172G>V 2021 Computational and structural biotechnology journal Table SARS_CoV_2 G172V 0 6 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. 222A>V 2021 Computational and structural biotechnology journal Table SARS_CoV_2 A222V 0 6 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. 2230I>T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 I2230T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. 235S>F 2021 Computational and structural biotechnology journal Table SARS_CoV_2 S235F 0 6 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. 265T>I 2021 Computational and structural biotechnology journal Table SARS_CoV_2 T265I 0 6 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. 330L>F 2021 Computational and structural biotechnology journal Table SARS_CoV_2 L330F 0 6 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. 356S>AS 2021 Computational and structural biotechnology journal Table SARS_CoV_2 S356S 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. 444S>PS 2021 Computational and structural biotechnology journal Table SARS_CoV_2 S444S 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. 4715P>L 2021 Computational and structural biotechnology journal Table SARS_CoV_2 P4715L 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. 5784K>R 2021 Computational and structural biotechnology journal Table SARS_CoV_2 K5784R 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. 614D>G 2021 Computational and structural biotechnology journal Table SARS_CoV_2 D614G 0 6 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. 716T>I 2021 Computational and structural biotechnology journal Table SARS_CoV_2 T716I 0 6 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. 73Y>C 2021 Computational and structural biotechnology journal Table SARS_CoV_2 Y73C 0 5 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. 807D>VX 2021 Computational and structural biotechnology journal Table SARS_CoV_2 D807X 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. A17615G 2021 Computational and structural biotechnology journal Table SARS_CoV_2 A17615G 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. A18424G 2021 Computational and structural biotechnology journal Table SARS_CoV_2 A18424G 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. A23063T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 A23063T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. A23403G 2021 Computational and structural biotechnology journal Table SARS_CoV_2 A23403G 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. A28111G 2021 Computational and structural biotechnology journal Table SARS_CoV_2 A28111G 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C10319T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C10319T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C1059T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C1059T 0 6 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C14408T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C14408T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C14676T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C14676T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C15279T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C15279T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C21304T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C21304T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C22227T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C22227T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C23604A 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C23604A 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C23709T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C23709T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C241T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C241T 0 5 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C26801G 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C26801G 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C27964T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C27964T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C27972T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C27972T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C28472T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C28472T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C28869T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C28869T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C28977T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C28977T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C3037T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C3037T 0 6 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C3267T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C3267T 0 6 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C5388A 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C5388A 0 6 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C5986T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C5986T 0 6 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C6286T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C6286T 0 6 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. C913T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 C913T 0 5 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. G24914C 2021 Computational and structural biotechnology journal Table SARS_CoV_2 G24914C 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. G25563T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 G25563T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. G25907T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 G25907T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. G28048T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 G28048T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. G29645T 2021 Computational and structural biotechnology journal Table SARS_CoV_2 G29645T 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. T16176C 2021 Computational and structural biotechnology journal Table SARS_CoV_2 T16176C 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. T24506G 2021 Computational and structural biotechnology journal Table SARS_CoV_2 T24506G 0 7 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. T445C 2021 Computational and structural biotechnology journal Table SARS_CoV_2 T445C 0 5 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. T6954C 2021 Computational and structural biotechnology journal Table SARS_CoV_2 T6954C 0 6 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. K417N 2022 Chembiochem Table SARS_CoV_2 K417N 0 5 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. K417T 2022 Chembiochem Table SARS_CoV_2 K417T 0 5 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. N501Y 2021 Cell Table SARS_CoV_2 N501Y 0 5 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. E484K 2022 Clinical microbiology and infection Table SARS_CoV_2 E484K 0 5 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. E484Q 2022 Clinical microbiology and infection Table SARS_CoV_2 E484Q 0 5 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. H655Y 2022 Clinical microbiology and infection Table SARS_CoV_2 H655Y 0 5 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. L452R 2022 Clinical microbiology and infection Table SARS_CoV_2 L452R 0 5 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. N501Y 2022 Clinical microbiology and infection Table SARS_CoV_2 N501Y 0 5 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. P681R 2022 Clinical microbiology and infection Table SARS_CoV_2 P681R 0 5 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. A475V 2021 Frontiers in immunology Table SARS_CoV_2 A475V 0 5 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. D614G 2021 Frontiers in immunology Table SARS_CoV_2 D614G 0 5 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. E484Q 2021 Frontiers in immunology Table SARS_CoV_2 E484Q 0 5 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. S309H 2021 Frontiers in immunology Table SARS_CoV_2 S309H 0 5 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. A23403G 2021 Iranian journal of microbiology Table SARS_CoV_2 A23403G 0 7 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. A352S 2021 Iranian journal of microbiology Table SARS_CoV_2 A352S 0 5 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. A672V 2021 Iranian journal of microbiology Table SARS_CoV_2 A672V 0 5 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. A67V 2021 Iranian journal of microbiology Table SARS_CoV_2 A67V 0 4 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. C1254F 2021 Iranian journal of microbiology Table SARS_CoV_2 C1254F 0 6 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. C241T 2021 Iranian journal of microbiology Table SARS_CoV_2 C241T 0 5 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. C3037T 2021 Iranian journal of microbiology Table SARS_CoV_2 C3037T 0 6 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. C8782T 2021 Iranian journal of microbiology Table SARS_CoV_2 C8782T 0 6 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. D614G 2021 Iranian journal of microbiology Table SARS_CoV_2 D614G 0 5 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. G11083T 2021 Iranian journal of microbiology Table SARS_CoV_2 G11083T 0 7 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. G204R 2021 Iranian journal of microbiology Table SARS_CoV_2 G204R 0 5 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. G251V 2021 Iranian journal of microbiology Table SARS_CoV_2 G251V 0 5 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. G25563T 2021 Iranian journal of microbiology Table SARS_CoV_2 G25563T 0 7 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. G26144T 2021 Iranian journal of microbiology Table SARS_CoV_2 G26144T 0 7 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. G28882A 2021 Iranian journal of microbiology Table SARS_CoV_2 G28882A 0 7 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. L37F 2021 Iranian journal of microbiology Table SARS_CoV_2 L37F 0 4 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. L822F 2021 Iranian journal of microbiology Table SARS_CoV_2 L822F 0 5 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. L84S 2021 Iranian journal of microbiology Table SARS_CoV_2 L84S 0 4 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. N185Y 2021 Iranian journal of microbiology Table SARS_CoV_2 N185Y 0 5 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Q57H 2021 Iranian journal of microbiology Table SARS_CoV_2 Q57H 0 4 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Q677H 2021 Iranian journal of microbiology Table SARS_CoV_2 Q677H 0 5 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. R214L 2021 Iranian journal of microbiology Table SARS_CoV_2 R214L 0 5 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. S116C 2021 Iranian journal of microbiology Table SARS_CoV_2 S116C 0 5 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. S477I 2021 Iranian journal of microbiology Table SARS_CoV_2 S477I 0 5 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. T22I 2021 Iranian journal of microbiology Table SARS_CoV_2 T22I 0 4 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. T22P 2021 Iranian journal of microbiology Table SARS_CoV_2 T22P 0 4 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. T259I 2021 Iranian journal of microbiology Table SARS_CoV_2 T259I 0 5 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. T28144C 2021 Iranian journal of microbiology Table SARS_CoV_2 T28144C 0 7 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. T572I 2021 Iranian journal of microbiology Table SARS_CoV_2 T572I 0 5 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. T76I 2021 Iranian journal of microbiology Table SARS_CoV_2 T76I 0 4 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. T95I 2021 Iranian journal of microbiology Table SARS_CoV_2 T95I 0 4 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. V622F 2021 Iranian journal of microbiology Table SARS_CoV_2 V622F 0 5 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. A23403G 2021 Frontiers in medicine Table SARS_CoV_2 A23403G 0 7 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. C21365T 2021 Frontiers in medicine Table SARS_CoV_2 C21365T 0 7 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. C21789T 2021 Frontiers in medicine Table SARS_CoV_2 C21789T 0 7 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. C23191T 2021 Frontiers in medicine Table SARS_CoV_2 C23191T 0 7 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. E484K 2021 Frontiers in medicine Table SARS_CoV_2 E484K 0 5 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. G21624C 2021 Frontiers in medicine Table SARS_CoV_2 G21624C 0 7 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. G22093C 2021 Frontiers in medicine Table SARS_CoV_2 G22093C 0 7 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. N477S 2021 Frontiers in medicine Table SARS_CoV_2 N477S 0 5 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. N501Y 2021 Frontiers in medicine Table SARS_CoV_2 N501Y 0 5 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. E484K 2021 The Journal of biological chemistry Table SARS_CoV_2 E484K 0 5 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. K417N 2021 The Journal of biological chemistry Table SARS_CoV_2 K417N 0 5 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. K417T 2021 The Journal of biological chemistry Table SARS_CoV_2 K417T 0 5 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. N501Y 2021 The Journal of biological chemistry Table SARS_CoV_2 N501Y 0 5 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. S477N 2021 The Journal of biological chemistry Table SARS_CoV_2 S477N 0 5 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. S494P 2021 The Journal of biological chemistry Table SARS_CoV_2 S494P 0 5 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. T478I 2021 The Journal of biological chemistry Table SARS_CoV_2 T478I 0 5 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Y453F 2021 The Journal of biological chemistry Table SARS_CoV_2 Y453F 0 5 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. D614G 2022 Journal of pharmaceutical analysis Table SARS_CoV_2 D614G 0 5 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. E484K 2022 Journal of pharmaceutical analysis Table SARS_CoV_2 E484K 0 5 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. N439K 2022 Journal of pharmaceutical analysis Table SARS_CoV_2 N439K 0 5 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. N501Y 2022 Journal of pharmaceutical analysis Table SARS_CoV_2 N501Y 0 5 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. Y453F 2022 Journal of pharmaceutical analysis Table SARS_CoV_2 Y453F 0 5 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. D138Y 2021 Biochemical and biophysical research communications Table SARS_CoV_2 D138Y 0 5 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. D614G 2021 Biochemical and biophysical research communications Table SARS_CoV_2 D614G 0 5 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. E154K 2021 Biochemical and biophysical research communications Table SARS_CoV_2 E154K 0 5 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. E484K 2021 Biochemical and biophysical research communications Table SARS_CoV_2 E484K 0 5 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. E484Q 2021 Biochemical and biophysical research communications Table SARS_CoV_2 E484Q 0 5 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. G142D 2021 Biochemical and biophysical research communications Table SARS_CoV_2 G142D 0 5 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. K417T 2021 Biochemical and biophysical research communications Table SARS_CoV_2 K417T 0 5 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. L452R 2021 Biochemical and biophysical research communications Table SARS_CoV_2 L452R 0 5 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. N501Y 2021 Biochemical and biophysical research communications Table SARS_CoV_2 N501Y 0 5 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. P681H 2021 Biochemical and biophysical research communications Table SARS_CoV_2 P681H 0 5 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. P681R 2021 Biochemical and biophysical research communications Table SARS_CoV_2 P681R 0 5 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. Q1071H 2021 Biochemical and biophysical research communications Table SARS_CoV_2 Q1071H 0 6 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. R158G 2021 Biochemical and biophysical research communications Table SARS_CoV_2 R158G 0 5 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. R190S 2021 Biochemical and biophysical research communications Table SARS_CoV_2 R190S 0 5 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. S13I 2021 Biochemical and biophysical research communications Table SARS_CoV_2 S13I 0 4 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. T19R 2021 Biochemical and biophysical research communications Table SARS_CoV_2 T19R 0 4 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. T478K 2021 Biochemical and biophysical research communications Table SARS_CoV_2 T478K 0 5 34547629 The in vitro and in vivo efficacy of CT-P59 against Gamma, Delta and its associated variants of SARS-CoV-2. W152C 2021 Biochemical and biophysical research communications Table SARS_CoV_2 W152C 0 5 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. A249V 2022 Saudi journal of biological sciences Table SARS_CoV_2 A249V 0 5 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. D108G 2022 Saudi journal of biological sciences Table SARS_CoV_2 D108G 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. A570D 2021 Journal of virology Table SARS_CoV_2 A570D 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. A67V 2021 Journal of virology Table SARS_CoV_2 A67V 0 4 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. A701V 2021 Journal of virology Table SARS_CoV_2 A701V 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. D1118H 2021 Journal of virology Table SARS_CoV_2 D1118H 0 6 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. D138Y 2021 Journal of virology Table SARS_CoV_2 D138Y 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. D215G 2021 Journal of virology Table SARS_CoV_2 D215G 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. D253G 2021 Journal of virology Table SARS_CoV_2 D253G 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. D253N 2021 Journal of virology Table SARS_CoV_2 D253N 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. D614G 2021 Journal of virology Table SARS_CoV_2 D614G 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. D80A 2021 Journal of virology Table SARS_CoV_2 D80A 0 4 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. D80Y 2021 Journal of virology Table SARS_CoV_2 D80Y 0 4 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. D950N 2021 Journal of virology Table SARS_CoV_2 D950N 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. E154K 2021 Journal of virology Table SARS_CoV_2 E154K 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. E156G 2021 Journal of virology Table SARS_CoV_2 E156G 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. E471Q 2021 Journal of virology Table SARS_CoV_2 E471Q 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. E484K 2021 Journal of virology Table SARS_CoV_2 E484K 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. E484Q 2021 Journal of virology Table SARS_CoV_2 E484Q 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. F157L 2021 Journal of virology Table SARS_CoV_2 F157L 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. F490S 2021 Journal of virology Table SARS_CoV_2 F490S 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. F888L 2021 Journal of virology Table SARS_CoV_2 F888L 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. G142D 2021 Journal of virology Table SARS_CoV_2 G142D 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. G75V 2021 Journal of virology Table SARS_CoV_2 G75V 0 4 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. H1101D 2021 Journal of virology Table SARS_CoV_2 H1101D 0 6 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. H655Y 2021 Journal of virology Table SARS_CoV_2 H655Y 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. ins146N 2021 Journal of virology Table SARS_CoV_2 ins146N 0 7 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. K417N 2021 Journal of virology Table SARS_CoV_2 K417N 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. K417T 2021 Journal of virology Table SARS_CoV_2 K417T 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. L18F 2021 Journal of virology Table SARS_CoV_2 L18F 0 4 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. L249M 2021 Journal of virology Table SARS_CoV_2 L249M 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. L452Q 2021 Journal of virology Table SARS_CoV_2 L452Q 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. L452R 2021 Journal of virology Table SARS_CoV_2 L452R 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. N501Y 2021 Journal of virology Table SARS_CoV_2 N501Y 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. P26S 2021 Journal of virology Table SARS_CoV_2 P26S 0 4 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. P681H 2021 Journal of virology Table SARS_CoV_2 P681H 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. P681R 2021 Journal of virology Table SARS_CoV_2 P681R 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Q1071H 2021 Journal of virology Table SARS_CoV_2 Q1071H 0 6 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Q52R 2021 Journal of virology Table SARS_CoV_2 Q52R 0 4 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Q613H 2021 Journal of virology Table SARS_CoV_2 Q613H 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Q677H 2021 Journal of virology Table SARS_CoV_2 Q677H 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Q957H 2021 Journal of virology Table SARS_CoV_2 Q957H 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. R102I 2021 Journal of virology Table SARS_CoV_2 R102I 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. R190S 2021 Journal of virology Table SARS_CoV_2 R190S 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. R246I 2021 Journal of virology Table SARS_CoV_2 R246I 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. R346K 2021 Journal of virology Table SARS_CoV_2 R346K 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. S13I 2021 Journal of virology Table SARS_CoV_2 S13I 0 4 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. S982A 2021 Journal of virology Table SARS_CoV_2 S982A 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. T1027I 2021 Journal of virology Table SARS_CoV_2 T1027I 0 6 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. T19R 2021 Journal of virology Table SARS_CoV_2 T19R 0 4 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. T20N 2021 Journal of virology Table SARS_CoV_2 T20N 0 4 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. T478K 2021 Journal of virology Table SARS_CoV_2 T478K 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. T478R 2021 Journal of virology Table SARS_CoV_2 T478R 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. T63I 2021 Journal of virology Table SARS_CoV_2 T63I 0 4 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. T716I 2021 Journal of virology Table SARS_CoV_2 T716I 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. T76I 2021 Journal of virology Table SARS_CoV_2 T76I 0 4 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. T859N 2021 Journal of virology Table SARS_CoV_2 T859N 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. T95I 2021 Journal of virology Table SARS_CoV_2 T95I 0 4 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. V1176F 2021 Journal of virology Table SARS_CoV_2 V1176F 0 6 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. V367F 2021 Journal of virology Table SARS_CoV_2 V367F 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. W152C 2021 Journal of virology Table SARS_CoV_2 W152C 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. W258L 2021 Journal of virology Table SARS_CoV_2 W258L 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Y144T 2021 Journal of virology Table SARS_CoV_2 Y144T 0 5 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Y145S 2021 Journal of virology Table SARS_CoV_2 Y145S 0 5 34553696 Molecular docking studies of Indian variants of pathophysiological proteins of SARS-CoV-2 with selected drug candidates. D614G 2021 Journal of genetics Table SARS_CoV_2 D614G 0 5 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. A161S 2021 PeerJ Table SARS_CoV_2 A161S 0 5 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. A320V 2021 PeerJ Table SARS_CoV_2 A320V 0 5 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. D614G 2021 PeerJ Table SARS_CoV_2 D614G 0 5 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. F1141X 2021 PeerJ Table SARS_CoV_2 F1141X 0 6 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. I266L 2021 PeerJ Table SARS_CoV_2 I266L 0 5 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. L177F 2021 PeerJ Table SARS_CoV_2 L177F 0 5 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. M436L 2021 PeerJ Table SARS_CoV_2 M436L 0 5 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. P1403S 2021 PeerJ Table SARS_CoV_2 P1403S 0 6 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. P323L 2021 PeerJ Table SARS_CoV_2 P323L 0 5 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. Q57H 2021 PeerJ Table SARS_CoV_2 Q57H 0 4 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. R1449G 2021 PeerJ Table SARS_CoV_2 R1449G 0 6 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. S183Y 2021 PeerJ Table SARS_CoV_2 S183Y 0 5 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. S25L 2021 PeerJ Table SARS_CoV_2 S25L 0 4 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. T85I 2021 PeerJ Table SARS_CoV_2 T85I 0 4 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. V58F 2021 PeerJ Table SARS_CoV_2 V58F 0 4 34560289 SARS-CoV-2 B.1.1.7 lineage rapidly spreads and replaces R.1 lineage in Japan: Serial and stationary observation in a community. E484K 2021 Infection, genetics and evolution Table SARS_CoV_2 E484K 0 5 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. E484K 2021 Journal of molecular graphics & modelling Table SARS_CoV_2 E484K 0 5 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. K99Y 2021 Journal of molecular graphics & modelling Table SARS_CoV_2 K99Y 0 4 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. D614G 2021 The Journal of biological chemistry Table SARS_CoV_2 D614G 0 5 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. A4489V 2021 Infection, genetics and evolution Table SARS_CoV_2 A4489V 0 6 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. D448del 2021 Infection, genetics and evolution Table SARS_CoV_2 D448del 0 7 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. D614G 2021 Infection, genetics and evolution Table SARS_CoV_2 D614G 0 5 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. G204R 2021 Infection, genetics and evolution Table SARS_CoV_2 G204R 0 5 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. G251V 2021 Infection, genetics and evolution Table SARS_CoV_2 G251V 0 5 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. G3278S 2021 Infection, genetics and evolution Table SARS_CoV_2 G3278S 0 6 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. I292T 2021 Infection, genetics and evolution Table SARS_CoV_2 I292T 0 5 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. L3606F 2021 Infection, genetics and evolution Table SARS_CoV_2 L3606F 0 6 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. L84S 2021 Infection, genetics and evolution Table SARS_CoV_2 L84S 0 4 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. P13L 2021 Infection, genetics and evolution Table SARS_CoV_2 P13L 0 4 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. P4715L 2021 Infection, genetics and evolution Table SARS_CoV_2 P4715L 0 6 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. P5828L 2021 Infection, genetics and evolution Table SARS_CoV_2 P5828L 0 6 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. Q57H 2021 Infection, genetics and evolution Table SARS_CoV_2 Q57H 0 4 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. R203K 2021 Infection, genetics and evolution Table SARS_CoV_2 R203K 0 5 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. S194L 2021 Infection, genetics and evolution Table SARS_CoV_2 S194L 0 5 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. S24L 2021 Infection, genetics and evolution Table SARS_CoV_2 S24L 0 4 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. T2016K 2021 Infection, genetics and evolution Table SARS_CoV_2 T2016K 0 6 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. T265I 2021 Infection, genetics and evolution Table SARS_CoV_2 T265I 0 5 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. Y5865C 2021 Infection, genetics and evolution Table SARS_CoV_2 Y5865C 0 6 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. N501Y 2021 CMAJ Table SARS_CoV_2 N501Y 0 5 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. D1118H 2021 Microbiology spectrum Table SARS_CoV_2 D1118H 0 6 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. D215G 2021 Microbiology spectrum Table SARS_CoV_2 D215G 0 5 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. E484K 2021 Microbiology spectrum Table SARS_CoV_2 E484K 0 5 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. K417N 2021 Microbiology spectrum Table SARS_CoV_2 K417N 0 5 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. K837N 2021 Microbiology spectrum Table SARS_CoV_2 K837N 0 5 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. N501Y 2021 Microbiology spectrum Table SARS_CoV_2 N501Y 0 5 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. S242del 2021 Microbiology spectrum Table SARS_CoV_2 S242del 0 7 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. D128D 2021 F1000Research Table SARS_CoV_2 D128D 0 5 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. D128Y 2021 F1000Research Table SARS_CoV_2 D128Y 0 5 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. D215D 2021 F1000Research Table SARS_CoV_2 D215D 0 5 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. D215Y 2021 F1000Research Table SARS_CoV_2 D215Y 0 5 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. D614D 2021 F1000Research Table SARS_CoV_2 D614D 0 5 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. D614G 2021 F1000Research Table SARS_CoV_2 D614G 0 5 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. E484D 2021 F1000Research Table SARS_CoV_2 E484D 0 5 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. E484E 2021 F1000Research Table SARS_CoV_2 E484E 0 5 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. G66G 2021 F1000Research Table SARS_CoV_2 G66G 0 4 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. G66X 2021 F1000Research Table SARS_CoV_2 G66X 0 4 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. K68K 2021 F1000Research Table SARS_CoV_2 K68K 0 4 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. K68X 2021 F1000Research Table SARS_CoV_2 K68X 0 4 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. N1047D 2021 F1000Research Table SARS_CoV_2 N1047D 0 6 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. N1047N 2021 F1000Research Table SARS_CoV_2 N1047N 0 6 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. P218L 2021 F1000Research Table SARS_CoV_2 P218L 0 5 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. P218P 2021 F1000Research Table SARS_CoV_2 P218P 0 5 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. P314L 2021 F1000Research Table SARS_CoV_2 P314L 0 5 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. P314P 2021 F1000Research Table SARS_CoV_2 P314P 0 5 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. Q57H 2021 F1000Research Table SARS_CoV_2 Q57H 0 4 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. Q57Q 2021 F1000Research Table SARS_CoV_2 Q57Q 0 4 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. V345L 2021 F1000Research Table SARS_CoV_2 V345L 0 5 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. V345V 2021 F1000Research Table SARS_CoV_2 V345V 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). 156del 2021 Journal of clinical virology Table SARS_CoV_2 156del 0 6 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). 157del 2021 Journal of clinical virology Table SARS_CoV_2 157del 0 6 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). A570D 2021 Journal of clinical virology Table SARS_CoV_2 A570D 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). A67V 2021 Journal of clinical virology Table SARS_CoV_2 A67V 0 4 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). A701V 2021 Journal of clinical virology Table SARS_CoV_2 A701V 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). D1118H 2021 Journal of clinical virology Table SARS_CoV_2 D1118H 0 6 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). D138Y 2021 Journal of clinical virology Table SARS_CoV_2 D138Y 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). D215G 2021 Journal of clinical virology Table SARS_CoV_2 D215G 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). D253G 2021 Journal of clinical virology Table SARS_CoV_2 D253G 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). D614G 2021 Journal of clinical virology Table SARS_CoV_2 D614G 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). D950N 2021 Journal of clinical virology Table SARS_CoV_2 D950N 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). E154K 2021 Journal of clinical virology Table SARS_CoV_2 E154K 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). E484K 2021 Journal of clinical virology Table SARS_CoV_2 E484K 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). E484Q 2021 Journal of clinical virology Table SARS_CoV_2 E484Q 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). F565L 2021 Journal of clinical virology Table SARS_CoV_2 F565L 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). F888L 2021 Journal of clinical virology Table SARS_CoV_2 F888L 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). G142D 2021 Journal of clinical virology Table SARS_CoV_2 G142D 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). G145D 2021 Journal of clinical virology Table SARS_CoV_2 G145D 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). H655Y 2021 Journal of clinical virology Table SARS_CoV_2 H655Y 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). K1191N 2021 Journal of clinical virology Table SARS_CoV_2 K1191N 0 6 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). K417N 2021 Journal of clinical virology Table SARS_CoV_2 K417N 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). K417T 2021 Journal of clinical virology Table SARS_CoV_2 K417T 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). L18F 2021 Journal of clinical virology Table SARS_CoV_2 L18F 0 4 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). L452R 2021 Journal of clinical virology Table SARS_CoV_2 L452R 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). N501Y 2021 Journal of clinical virology Table SARS_CoV_2 N501Y 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). P26S 2021 Journal of clinical virology Table SARS_CoV_2 P26S 0 4 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). P681H 2021 Journal of clinical virology Table SARS_CoV_2 P681H 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). P681R 2021 Journal of clinical virology Table SARS_CoV_2 P681R 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). Q1071H 2021 Journal of clinical virology Table SARS_CoV_2 Q1071H 0 6 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). Q675H 2021 Journal of clinical virology Table SARS_CoV_2 Q675H 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). Q677H 2021 Journal of clinical virology Table SARS_CoV_2 Q677H 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). R158G 2021 Journal of clinical virology Table SARS_CoV_2 R158G 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). R190S 2021 Journal of clinical virology Table SARS_CoV_2 R190S 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). S477N 2021 Journal of clinical virology Table SARS_CoV_2 S477N 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). S494P 2021 Journal of clinical virology Table SARS_CoV_2 S494P 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). S982A 2021 Journal of clinical virology Table SARS_CoV_2 S982A 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). T1027I 2021 Journal of clinical virology Table SARS_CoV_2 T1027I 0 6 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). T19R 2021 Journal of clinical virology Table SARS_CoV_2 T19R 0 4 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). T20N 2021 Journal of clinical virology Table SARS_CoV_2 T20N 0 4 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). T478K 2021 Journal of clinical virology Table SARS_CoV_2 T478K 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). T716I 2021 Journal of clinical virology Table SARS_CoV_2 T716I 0 5 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). T95I 2021 Journal of clinical virology Table SARS_CoV_2 T95I 0 4 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). V1176F 2021 Journal of clinical virology Table SARS_CoV_2 V1176F 0 6 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. E484K 2021 FASEB journal Table SARS_CoV_2 E484K 0 5 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. N501Y 2021 FASEB journal Table SARS_CoV_2 N501Y 0 5 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. A23403G 2021 Infection, genetics and evolution Table SARS_CoV_2 A23403G 0 7 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. C241T 2021 Infection, genetics and evolution Table SARS_CoV_2 C241T 0 5 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. C3037T 2021 Infection, genetics and evolution Table SARS_CoV_2 C3037T 0 6 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. C8782T 2021 Infection, genetics and evolution Table SARS_CoV_2 C8782T 0 6 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. G11083T 2021 Infection, genetics and evolution Table SARS_CoV_2 G11083T 0 7 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. G26144T 2021 Infection, genetics and evolution Table SARS_CoV_2 G26144T 0 7 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. T28144C 2021 Infection, genetics and evolution Table SARS_CoV_2 T28144C 0 7 34643437 Shared Mutations in Emerging SARS-CoV-2 Circulating Variants May Lead to Reverse Transcription-PCR (RT-PCR)-Based Misidentification of B.1.351 and P.1 Variants of Concern. E484Q 2021 Microbiology spectrum Table SARS_CoV_2 E484Q 0 5 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. E484Q 2021 Journal of chemical information and modeling Table SARS_CoV_2 E484Q 0 5 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. F490S 2021 Journal of chemical information and modeling Table SARS_CoV_2 F490S 0 5 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. L452Q 2021 Journal of chemical information and modeling Table SARS_CoV_2 L452Q 0 5 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. L452R 2021 Journal of chemical information and modeling Table SARS_CoV_2 L452R 0 5 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. T478K 2021 Journal of chemical information and modeling Table SARS_CoV_2 T478K 0 5 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. 19del 2021 Cell reports Table SARS_CoV_2 19del 0 5 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. D614G 2021 Cell reports Table SARS_CoV_2 D614G 0 5 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. E484K 2021 Cell reports Table SARS_CoV_2 E484K 0 5 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. E484Q 2021 Cell reports Table SARS_CoV_2 E484Q 0 5 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. K417N 2021 Cell reports Table SARS_CoV_2 K417N 0 5 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. L452R 2021 Cell reports Table SARS_CoV_2 L452R 0 5 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. N501Y 2021 Cell reports Table SARS_CoV_2 N501Y 0 5 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. A352S 2021 Emerging microbes & infections Table SARS_CoV_2 A352S 0 5 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. C1248F 2021 Emerging microbes & infections Table SARS_CoV_2 C1248F 0 6 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. G769V 2021 Emerging microbes & infections Table SARS_CoV_2 G769V 0 5 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. K854N 2021 Emerging microbes & infections Table SARS_CoV_2 K854N 0 5 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. R158G 2021 Emerging microbes & infections Table SARS_CoV_2 R158G 0 5 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. S71F 2021 Emerging microbes & infections Table SARS_CoV_2 S71F 0 4 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. T250I 2021 Emerging microbes & infections Table SARS_CoV_2 T250I 0 5 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. T572I 2021 Emerging microbes & infections Table SARS_CoV_2 T572I 0 5 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. N439K 2021 Computers in biology and medicine Table SARS_CoV_2 N439K 0 5 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. S439K 2021 Computers in biology and medicine Table SARS_CoV_2 S439K 0 5 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. S477N 2021 Computers in biology and medicine Table SARS_CoV_2 S477N 0 5 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. T478K 2021 Computers in biology and medicine Table SARS_CoV_2 T478K 0 5 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. A136G 2021 Frontiers in public health Table SARS_CoV_2 A136G 0 5 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. A15932G 2021 Frontiers in public health Table SARS_CoV_2 A15932G 0 7 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. A220V 2021 Frontiers in public health Table SARS_CoV_2 A220V 0 5 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. A23720G 2021 Frontiers in public health Table SARS_CoV_2 A23720G 0 7 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. A28271C 2021 Frontiers in public health Table SARS_CoV_2 A28271C 0 7 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. A3143V 2021 Frontiers in public health Table SARS_CoV_2 A3143V 0 6 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. A516T 2021 Frontiers in public health Table SARS_CoV_2 A516T 0 5 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. C11450A 2021 Frontiers in public health Table SARS_CoV_2 C11450A 0 7 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. C12008T 2021 Frontiers in public health Table SARS_CoV_2 C12008T 0 7 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. C12880T 2021 Frontiers in public health Table SARS_CoV_2 C12880T 0 7 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. C20436T 2021 Frontiers in public health Table SARS_CoV_2 C20436T 0 7 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. C22079A 2021 Frontiers in public health Table SARS_CoV_2 C22079A 0 7 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. C23673T 2021 Frontiers in public health Table SARS_CoV_2 C23673T 0 7 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. C28253T 2021 Frontiers in public health Table SARS_CoV_2 C28253T 0 7 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. C28932T 2021 Frontiers in public health Table SARS_CoV_2 C28932T 0 7 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. C3177T 2021 Frontiers in public health Table SARS_CoV_2 C3177T 0 6 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. C9693T 2021 Frontiers in public health Table SARS_CoV_2 C9693T 0 6 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. G142V 2021 Frontiers in public health Table SARS_CoV_2 G142V 0 5 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. G1811A 2021 Frontiers in public health Table SARS_CoV_2 G1811A 0 6 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. G18756T 2021 Frontiers in public health Table SARS_CoV_2 G18756T 0 7 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. G21987T 2021 Frontiers in public health Table SARS_CoV_2 G21987T 0 7 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. G25540A 2021 Frontiers in public health Table SARS_CoV_2 G25540A 0 7 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. I720V 2021 Frontiers in public health Table SARS_CoV_2 I720V 0 5 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. L3201P 2021 Frontiers in public health Table SARS_CoV_2 L3201P 0 6 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. L3915F 2021 Frontiers in public health Table SARS_CoV_2 L3915F 0 6 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. L452R 2021 Frontiers in public health Table SARS_CoV_2 L452R 0 5 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. N164K 2021 Frontiers in public health Table SARS_CoV_2 N164K 0 5 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. P971L 2021 Frontiers in public health Table SARS_CoV_2 P971L 0 5 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. Q173K 2021 Frontiers in public health Table SARS_CoV_2 Q173K 0 5 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. Q3729K 2021 Frontiers in public health Table SARS_CoV_2 Q3729K 0 6 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. S704L 2021 Frontiers in public health Table SARS_CoV_2 S704L 0 5 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. T22054G 2021 Frontiers in public health Table SARS_CoV_2 T22054G 0 7 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. T22917G 2021 Frontiers in public health Table SARS_CoV_2 T22917G 0 7 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. T9867C 2021 Frontiers in public health Table SARS_CoV_2 T9867C 0 6 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. V50I 2021 Frontiers in public health Table SARS_CoV_2 V50I 0 4 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. Y822C 2021 Frontiers in public health Table SARS_CoV_2 Y822C 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. A570D 2021 Journal of medical virology Table SARS_CoV_2 A570D 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. A890D 2021 Journal of medical virology Table SARS_CoV_2 A890D 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. D1118H 2021 Journal of medical virology Table SARS_CoV_2 D1118H 0 6 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. D614G 2021 Journal of medical virology Table SARS_CoV_2 D614G 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. F108del 2021 Journal of medical virology Table SARS_CoV_2 F108del 0 7 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. G107del 2021 Journal of medical virology Table SARS_CoV_2 G107del 0 7 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. G204R 2021 Journal of medical virology Table SARS_CoV_2 G204R 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. H69del 2021 Journal of medical virology Table SARS_CoV_2 H69del 0 6 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. I1412T 2021 Journal of medical virology Table SARS_CoV_2 I1412T 0 6 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. N501Y 2021 Journal of medical virology Table SARS_CoV_2 N501Y 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. P323L 2021 Journal of medical virology Table SARS_CoV_2 P323L 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. P681H 2021 Journal of medical virology Table SARS_CoV_2 P681H 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. R203K 2021 Journal of medical virology Table SARS_CoV_2 R203K 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. R27C 2021 Journal of medical virology Table SARS_CoV_2 R27C 0 4 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. R52I 2021 Journal of medical virology Table SARS_CoV_2 R52I 0 4 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. S106del 2021 Journal of medical virology Table SARS_CoV_2 S106del 0 7 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. S235F 2021 Journal of medical virology Table SARS_CoV_2 S235F 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. S982A 2021 Journal of medical virology Table SARS_CoV_2 S982A 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. T183I 2021 Journal of medical virology Table SARS_CoV_2 T183I 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. T716I 2021 Journal of medical virology Table SARS_CoV_2 T716I 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. V70del 2021 Journal of medical virology Table SARS_CoV_2 V70del 0 6 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Y144del 2021 Journal of medical virology Table SARS_CoV_2 Y144del 0 7 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Y73C 2021 Journal of medical virology Table SARS_CoV_2 Y73C 0 4 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. A220V 2021 Journal of medical virology Table SARS_CoV_2 A220V 0 5 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. D614G 2021 Journal of medical virology Table SARS_CoV_2 D614G 0 5 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. P323L 2021 Journal of medical virology Table SARS_CoV_2 P323L 0 5 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. Q57H 2021 Journal of medical virology Table SARS_CoV_2 Q57H 0 4 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. A701V 2021 Cell host & microbe Table SARS_CoV_2 A701V 0 5 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. D215G 2021 Cell host & microbe Table SARS_CoV_2 D215G 0 5 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. D614G 2021 Cell host & microbe Table SARS_CoV_2 D614G 0 5 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. D80A 2021 Cell host & microbe Table SARS_CoV_2 D80A 0 4 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. D950N 2021 Cell host & microbe Table SARS_CoV_2 D950N 0 5 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. E484K 2021 Cell host & microbe Table SARS_CoV_2 E484K 0 5 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. K417N 2021 Cell host & microbe Table SARS_CoV_2 K417N 0 5 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. L18F 2021 Cell host & microbe Table SARS_CoV_2 L18F 0 4 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. L452R 2021 Cell host & microbe Table SARS_CoV_2 L452R 0 5 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. N501Y 2021 Cell host & microbe Table SARS_CoV_2 N501Y 0 5 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. P681R 2021 Cell host & microbe Table SARS_CoV_2 P681R 0 5 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. R158G 2021 Cell host & microbe Table SARS_CoV_2 R158G 0 5 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. T19R 2021 Cell host & microbe Table SARS_CoV_2 T19R 0 4 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. T478K 2021 Cell host & microbe Table SARS_CoV_2 T478K 0 5 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. C279C 2022 The Science of the total environment Table SARS_CoV_2 C279C 0 5 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. C279F 2022 The Science of the total environment Table SARS_CoV_2 C279F 0 5 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. D614G 2022 The Science of the total environment Table SARS_CoV_2 D614G 0 5 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. D63G 2022 The Science of the total environment Table SARS_CoV_2 D63G 0 4 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. D950N 2022 The Science of the total environment Table SARS_CoV_2 D950N 0 5 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. E484Q 2022 The Science of the total environment Table SARS_CoV_2 E484Q 0 5 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. H80H 2022 The Science of the total environment Table SARS_CoV_2 H80H 0 4 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. L452R 2022 The Science of the total environment Table SARS_CoV_2 L452R 0 5 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. M429I 2022 The Science of the total environment Table SARS_CoV_2 M429I 0 5 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. P1140del 2022 The Science of the total environment Table SARS_CoV_2 P1140del 0 8 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. P314L 2022 The Science of the total environment Table SARS_CoV_2 P314L 0 5 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. P681R 2022 The Science of the total environment Table SARS_CoV_2 P681R 0 5 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. P822L 2022 The Science of the total environment Table SARS_CoV_2 P822L 0 5 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. Q1071H 2022 The Science of the total environment Table SARS_CoV_2 Q1071H 0 6 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. R203M 2022 The Science of the total environment Table SARS_CoV_2 R203M 0 5 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. S26L 2022 The Science of the total environment Table SARS_CoV_2 S26L 0 4 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. S97I 2022 The Science of the total environment Table SARS_CoV_2 S97I 0 4 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. T77A 2022 The Science of the total environment Table SARS_CoV_2 T77A 0 4 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. V10A 2022 The Science of the total environment Table SARS_CoV_2 V10A 0 4 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. V82A 2022 The Science of the total environment Table SARS_CoV_2 V82A 0 4 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. A222V 2021 Frontiers in microbiology Table SARS_CoV_2 A222V 0 5 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. A394V 2021 Frontiers in microbiology Table SARS_CoV_2 A394V 0 5 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. C206G 2021 Frontiers in microbiology Table SARS_CoV_2 C206G 0 5 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. D63G 2021 Frontiers in microbiology Table SARS_CoV_2 D63G 0 4 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. D77G 2021 Frontiers in microbiology Table SARS_CoV_2 D77G 0 4 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. G142D 2021 Frontiers in microbiology Table SARS_CoV_2 G142D 0 5 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. G215C 2021 Frontiers in microbiology Table SARS_CoV_2 G215C 0 5 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. G671S 2021 Frontiers in microbiology Table SARS_CoV_2 G671S 0 5 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. H1101D/Y 2021 Frontiers in microbiology Table SARS_CoV_2 H1101D;H1101Y 0;0 8;8 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. I95T 2021 Frontiers in microbiology Table SARS_CoV_2 I95T 0 4 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. K154E 2021 Frontiers in microbiology Table SARS_CoV_2 K154E 0 5 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. L37F 2021 Frontiers in microbiology Table SARS_CoV_2 L37F 0 4 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. P13T 2021 Frontiers in microbiology Table SARS_CoV_2 P13T 0 4 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. Q1071H 2021 Frontiers in microbiology Table SARS_CoV_2 Q1071H 0 6 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. R134N 2021 Frontiers in microbiology Table SARS_CoV_2 R134N 0 5 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. R216N 2021 Frontiers in microbiology Table SARS_CoV_2 R216N 0 5 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. R452L 2021 Frontiers in microbiology Table SARS_CoV_2 R452L 0 5 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. S647I 2021 Frontiers in microbiology Table SARS_CoV_2 S647I 0 5 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. S943P 2021 Frontiers in microbiology Table SARS_CoV_2 S943P 0 5 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. T135I 2021 Frontiers in microbiology Table SARS_CoV_2 T135I 0 5 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. V1264L 2021 Frontiers in microbiology Table SARS_CoV_2 V1264L 0 6 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. A23403G 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 A23403G 0 7 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. C13536T 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 C13536T 0 7 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. C13730T 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 C13730T 0 7 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. C14408T 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 C14408T 0 7 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. C18877T 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 C18877T 0 7 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. C23731T 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 C23731T 0 7 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. C23929T 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 C23929T 0 7 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. C2416T 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 C2416T 0 6 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. C26735T 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 C26735T 0 7 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. C28311T 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 C28311T 0 7 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. C3037T 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 C3037T 0 6 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. C313T 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 C313T 0 5 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. C4002T 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 C4002T 0 6 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. C6312A 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 C6312A 0 6 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. G10097A 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 G10097A 0 7 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. G11083T 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 G11083T 0 7 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. G25563T 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 G25563T 0 7 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. G28881A 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 G28881A 0 7 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. G28882A 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 G28882A 0 7 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. G28883C 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 G28883C 0 7 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. G8371T 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 G8371T 0 6 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. L3606F 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 L3606F 0 6 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. Q2702H 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 Q2702H 0 6 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. T1246I 2021 Genomics, proteomics & bioinformatics Table SARS_CoV_2 T1246I 0 6 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. A1020S 2021 mBio Table SARS_CoV_2 A1020S 0 6 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. A1078S 2021 mBio Table SARS_CoV_2 A1078S 0 6 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. A222V 2021 mBio Table SARS_CoV_2 A222V 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. A262S 2021 mBio Table SARS_CoV_2 A262S 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. A27S 2021 mBio Table SARS_CoV_2 A27S 0 4 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. A653V 2021 mBio Table SARS_CoV_2 A653V 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. A67V/S 2021 mBio Table SARS_CoV_2 A67S;A67V 0;0 6;6 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. A688V/T 2021 mBio Table SARS_CoV_2 A688T;A688V 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. A701V/S 2021 mBio Table SARS_CoV_2 A701S;A701V 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. A845S/V 2021 mBio Table SARS_CoV_2 A845S;A845V 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. A846V/S 2021 mBio Table SARS_CoV_2 A846S;A846V 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. A879S/V 2021 mBio Table SARS_CoV_2 A879S;A879V 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. D178H/N 2021 mBio Table SARS_CoV_2 D178H;D178N 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. D614G 2021 mBio Table SARS_CoV_2 D614G 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. D80A 2021 mBio Table SARS_CoV_2 D80A 0 4 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. E484D 2021 mBio Table SARS_CoV_2 E484D 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. E484K/Q 2021 mBio Table SARS_CoV_2 E484K;E484Q 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. E488D 2021 mBio Table SARS_CoV_2 E488D 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. G1167V/A 2021 mBio Table SARS_CoV_2 G1167A;G1167V 0;0 8;8 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. G1219C/V 2021 mBio Table SARS_CoV_2 G1219C;G1219V 0;0 8;8 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. G142V/D 2021 mBio Table SARS_CoV_2 G142D;G142V 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. G261V/R 2021 mBio Table SARS_CoV_2 G261R;G261V 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. G75R/V 2021 mBio Table SARS_CoV_2 G75R;G75V 0;0 6;6 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. H49Y 2021 mBio Table SARS_CoV_2 H49Y 0 4 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. H655Y 2021 mBio Table SARS_CoV_2 H655Y 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. K1191N 2021 mBio Table SARS_CoV_2 K1191N 0 6 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. L176F 2021 mBio Table SARS_CoV_2 L176F 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. L18F 2021 mBio Table SARS_CoV_2 L18F 0 4 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. L452P 2021 mBio Table SARS_CoV_2 L452P 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. L452R/Q 2021 mBio Table SARS_CoV_2 L452Q;L452R 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. N439S 2021 mBio Table SARS_CoV_2 N439S 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. N501K 2021 mBio Table SARS_CoV_2 N501K 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. N501Y/T 2021 mBio Table SARS_CoV_2 N501T;N501Y 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. P251S/L 2021 mBio Table SARS_CoV_2 P251L;P251S 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. P26S 2021 mBio Table SARS_CoV_2 P26S 0 4 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. P384L/S 2021 mBio Table SARS_CoV_2 P384L;P384S 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. P681H/R 2021 mBio Table SARS_CoV_2 P681H;P681R 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Q677H/P 2021 mBio Table SARS_CoV_2 Q677H;Q677P 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. S1252F/P 2021 mBio Table SARS_CoV_2 S1252F;S1252P 0;0 8;8 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. S12F 2021 mBio Table SARS_CoV_2 S12F 0 4 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. S254F 2021 mBio Table SARS_CoV_2 S254F 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. S255F/Y 2021 mBio Table SARS_CoV_2 S255F;S255Y 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. S477G 2021 mBio Table SARS_CoV_2 S477G 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. S477N/R 2021 mBio Table SARS_CoV_2 S477N;S477R 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. S640F 2021 mBio Table SARS_CoV_2 S640F 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. S939F 2021 mBio Table SARS_CoV_2 S939F 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. S943P/T 2021 mBio Table SARS_CoV_2 S943P;S943T 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. S98F 2021 mBio Table SARS_CoV_2 S98F 0 4 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. T1027I 2021 mBio Table SARS_CoV_2 T1027I 0 6 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. T478S 2021 mBio Table SARS_CoV_2 T478S 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. T572I 2021 mBio Table SARS_CoV_2 T572I 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. T76I/N 2021 mBio Table SARS_CoV_2 T76I;T76N 0;0 6;6 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. T859I 2021 mBio Table SARS_CoV_2 T859I 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. T95I 2021 mBio Table SARS_CoV_2 T95I 0 4 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. V1176F 2021 mBio Table SARS_CoV_2 V1176F 0 6 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. V143F/D 2021 mBio Table SARS_CoV_2 V143D;V143F 0;0 7;7 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. V622F/I 2021 mBio Table SARS_CoV_2 V622F;V622I 0;0 7;7 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A161V 2021 Journal of medical virology Table SARS_CoV_2 A161V 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A16V 2021 Journal of medical virology Table SARS_CoV_2 A16V 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A222V 2021 Journal of medical virology Table SARS_CoV_2 A222V 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A27S 2021 Journal of medical virology Table SARS_CoV_2 A27S 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A308G 2021 Journal of medical virology Table SARS_CoV_2 A308G 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A34V 2021 Journal of medical virology Table SARS_CoV_2 A34V 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A375V 2021 Journal of medical virology Table SARS_CoV_2 A375V 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A394V 2021 Journal of medical virology Table SARS_CoV_2 A394V 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A43V 2021 Journal of medical virology Table SARS_CoV_2 A43V 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A446V 2021 Journal of medical virology Table SARS_CoV_2 A446V 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A488S 2021 Journal of medical virology Table SARS_CoV_2 A488S 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A570V 2021 Journal of medical virology Table SARS_CoV_2 A570V 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A67V 2021 Journal of medical virology Table SARS_CoV_2 A67V 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A701V 2021 Journal of medical virology Table SARS_CoV_2 A701V 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A879S 2021 Journal of medical virology Table SARS_CoV_2 A879S 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. A92V 2021 Journal of medical virology Table SARS_CoV_2 A92V 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. D1163Y 2021 Journal of medical virology Table SARS_CoV_2 D1163Y 0 6 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. D178Y 2021 Journal of medical virology Table SARS_CoV_2 D178Y 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. D215G 2021 Journal of medical virology Table SARS_CoV_2 D215G 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. D35Y 2021 Journal of medical virology Table SARS_CoV_2 D35Y 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. D377Y 2021 Journal of medical virology Table SARS_CoV_2 D377Y 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. D614G 2021 Journal of medical virology Table SARS_CoV_2 D614G 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. D63G 2021 Journal of medical virology Table SARS_CoV_2 D63G 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. D80A 2021 Journal of medical virology Table SARS_CoV_2 D80A 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. D950N 2021 Journal of medical virology Table SARS_CoV_2 D950N 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. E341D 2021 Journal of medical virology Table SARS_CoV_2 E341D 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. E442G 2021 Journal of medical virology Table SARS_CoV_2 E442G 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. E484K 2021 Journal of medical virology Table SARS_CoV_2 E484K 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. E484Q 2021 Journal of medical virology Table SARS_CoV_2 E484Q 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. E92K 2021 Journal of medical virology Table SARS_CoV_2 E92K 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. F106L 2021 Journal of medical virology Table SARS_CoV_2 F106L 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. F120L 2021 Journal of medical virology Table SARS_CoV_2 F120L 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. F157S 2021 Journal of medical virology Table SARS_CoV_2 F157S 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. F79L 2021 Journal of medical virology Table SARS_CoV_2 F79L 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. G142D 2021 Journal of medical virology Table SARS_CoV_2 G142D 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. G172C 2021 Journal of medical virology Table SARS_CoV_2 G172C 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. G181V 2021 Journal of medical virology Table SARS_CoV_2 G181V 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. G215C 2021 Journal of medical virology Table SARS_CoV_2 G215C 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. G219S 2021 Journal of medical virology Table SARS_CoV_2 G219S 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. G229C 2021 Journal of medical virology Table SARS_CoV_2 G229C 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. G307V 2021 Journal of medical virology Table SARS_CoV_2 G307V 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. G30R 2021 Journal of medical virology Table SARS_CoV_2 G30R 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. G439E 2021 Journal of medical virology Table SARS_CoV_2 G439E 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. G662S 2021 Journal of medical virology Table SARS_CoV_2 G662S 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. H1274Y 2021 Journal of medical virology Table SARS_CoV_2 H1274Y 0 6 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. H234Y 2021 Journal of medical virology Table SARS_CoV_2 H234Y 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. H300Y 2021 Journal of medical virology Table SARS_CoV_2 H300Y 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. H49Y 2021 Journal of medical virology Table SARS_CoV_2 H49Y 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. H655Y 2021 Journal of medical virology Table SARS_CoV_2 H655Y 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. I118T 2021 Journal of medical virology Table SARS_CoV_2 I118T 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. I121L 2021 Journal of medical virology Table SARS_CoV_2 I121L 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. I82T 2021 Journal of medical virology Table SARS_CoV_2 I82T 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. I84V 2021 Journal of medical virology Table SARS_CoV_2 I84V 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. K111E 2021 Journal of medical virology Table SARS_CoV_2 K111E 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. K182N 2021 Journal of medical virology Table SARS_CoV_2 K182N 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. K34Q 2021 Journal of medical virology Table SARS_CoV_2 K34Q 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. K387N 2021 Journal of medical virology Table SARS_CoV_2 K387N 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. K417N 2021 Journal of medical virology Table SARS_CoV_2 K417N 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. K417T 2021 Journal of medical virology Table SARS_CoV_2 K417T 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. K42E 2021 Journal of medical virology Table SARS_CoV_2 K42E 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. K444R 2021 Journal of medical virology Table SARS_CoV_2 K444R 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. K565N 2021 Journal of medical virology Table SARS_CoV_2 K565N 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. K77N 2021 Journal of medical virology Table SARS_CoV_2 K77N 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. K837N 2021 Journal of medical virology Table SARS_CoV_2 K837N 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. L116F 2021 Journal of medical virology Table SARS_CoV_2 L116F 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. L139F 2021 Journal of medical virology Table SARS_CoV_2 L139F 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. L18F 2021 Journal of medical virology Table SARS_CoV_2 L18F 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. L445V 2021 Journal of medical virology Table SARS_CoV_2 L445V 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. L452R 2021 Journal of medical virology Table SARS_CoV_2 L452R 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. L56F 2021 Journal of medical virology Table SARS_CoV_2 L56F 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. L820F 2021 Journal of medical virology Table SARS_CoV_2 L820F 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. M210I 2021 Journal of medical virology Table SARS_CoV_2 M210I 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. M809V 2021 Journal of medical virology Table SARS_CoV_2 M809V 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. N192K 2021 Journal of medical virology Table SARS_CoV_2 N192K 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. N501T 2021 Journal of medical virology Table SARS_CoV_2 N501T 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. N501Y 2021 Journal of medical virology Table SARS_CoV_2 N501Y 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. N52K 2021 Journal of medical virology Table SARS_CoV_2 N52K 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. P1228L 2021 Journal of medical virology Table SARS_CoV_2 P1228L 0 6 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. P129L 2021 Journal of medical virology Table SARS_CoV_2 P129L 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. P13S 2021 Journal of medical virology Table SARS_CoV_2 P13S 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. P151S 2021 Journal of medical virology Table SARS_CoV_2 P151S 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. P314L 2021 Journal of medical virology Table SARS_CoV_2 P314L 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. P365L 2021 Journal of medical virology Table SARS_CoV_2 P365L 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. P395S 2021 Journal of medical virology Table SARS_CoV_2 P395S 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. P46L 2021 Journal of medical virology Table SARS_CoV_2 P46L 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. P681R 2021 Journal of medical virology Table SARS_CoV_2 P681R 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. P71L 2021 Journal of medical virology Table SARS_CoV_2 P71L 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. P77L 2021 Journal of medical virology Table SARS_CoV_2 P77L 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. P80A 2021 Journal of medical virology Table SARS_CoV_2 P80A 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. P80R 2021 Journal of medical virology Table SARS_CoV_2 P80R 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. P812S 2021 Journal of medical virology Table SARS_CoV_2 P812S 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. P822L 2021 Journal of medical virology Table SARS_CoV_2 P822L 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Q194P 2021 Journal of medical virology Table SARS_CoV_2 Q194P 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Q57H 2021 Journal of medical virology Table SARS_CoV_2 Q57H 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. R19S 2021 Journal of medical virology Table SARS_CoV_2 R19S 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. R203M 2021 Journal of medical virology Table SARS_CoV_2 R203M 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. R27C 2021 Journal of medical virology Table SARS_CoV_2 R27C 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. R385K 2021 Journal of medical virology Table SARS_CoV_2 R385K 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. R392C 2021 Journal of medical virology Table SARS_CoV_2 R392C 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. S1061V 2021 Journal of medical virology Table SARS_CoV_2 S1061V 0 6 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. S12F 2021 Journal of medical virology Table SARS_CoV_2 S12F 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. S163A 2021 Journal of medical virology Table SARS_CoV_2 S163A 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. S171L 2021 Journal of medical virology Table SARS_CoV_2 S171L 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. S194L 2021 Journal of medical virology Table SARS_CoV_2 S194L 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. S235P 2021 Journal of medical virology Table SARS_CoV_2 S235P 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. S26L 2021 Journal of medical virology Table SARS_CoV_2 S26L 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. S287L 2021 Journal of medical virology Table SARS_CoV_2 S287L 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. S400G 2021 Journal of medical virology Table SARS_CoV_2 S400G 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. S794L 2021 Journal of medical virology Table SARS_CoV_2 S794L 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. S93F 2021 Journal of medical virology Table SARS_CoV_2 S93F 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. T1027I 2021 Journal of medical virology Table SARS_CoV_2 T1027I 0 6 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. T120I 2021 Journal of medical virology Table SARS_CoV_2 T120I 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. T141S 2021 Journal of medical virology Table SARS_CoV_2 T141S 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. T181I 2021 Journal of medical virology Table SARS_CoV_2 T181I 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. T19R 2021 Journal of medical virology Table SARS_CoV_2 T19R 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. T205I 2021 Journal of medical virology Table SARS_CoV_2 T205I 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. T20N 2021 Journal of medical virology Table SARS_CoV_2 T20N 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. T217I 2021 Journal of medical virology Table SARS_CoV_2 T217I 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. T24I 2021 Journal of medical virology Table SARS_CoV_2 T24I 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. T271I 2021 Journal of medical virology Table SARS_CoV_2 T271I 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. T362I 2021 Journal of medical virology Table SARS_CoV_2 T362I 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. T40I 2021 Journal of medical virology Table SARS_CoV_2 T40I 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. T478K 2021 Journal of medical virology Table SARS_CoV_2 T478K 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. T492I 2021 Journal of medical virology Table SARS_CoV_2 T492I 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. T588I 2021 Journal of medical virology Table SARS_CoV_2 T588I 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. T85I 2021 Journal of medical virology Table SARS_CoV_2 T85I 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. V112F 2021 Journal of medical virology Table SARS_CoV_2 V112F 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. V1176F 2021 Journal of medical virology Table SARS_CoV_2 V1176F 0 6 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. V149A 2021 Journal of medical virology Table SARS_CoV_2 V149A 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. V161L 2021 Journal of medical virology Table SARS_CoV_2 V161L 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. V167L 2021 Journal of medical virology Table SARS_CoV_2 V167L 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. V169F 2021 Journal of medical virology Table SARS_CoV_2 V169F 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. V345E 2021 Journal of medical virology Table SARS_CoV_2 V345E 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. V613I 2021 Journal of medical virology Table SARS_CoV_2 V613I 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. V728F 2021 Journal of medical virology Table SARS_CoV_2 V728F 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. V77I 2021 Journal of medical virology Table SARS_CoV_2 V77I 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. V82A 2021 Journal of medical virology Table SARS_CoV_2 V82A 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. W153C 2021 Journal of medical virology Table SARS_CoV_2 W153C 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. W29L 2021 Journal of medical virology Table SARS_CoV_2 W29L 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. W69L 2021 Journal of medical virology Table SARS_CoV_2 W69L 0 4 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Y138H 2021 Journal of medical virology Table SARS_CoV_2 Y138H 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Y154H 2021 Journal of medical virology Table SARS_CoV_2 Y154H 0 5 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Y49H 2021 Journal of medical virology Table SARS_CoV_2 Y49H 0 4 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. A376T 2021 Frontiers in microbiology Table SARS_CoV_2 A376T 0 5 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. A812D 2021 Frontiers in microbiology Table SARS_CoV_2 A812D 0 5 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. D377Y 2021 Frontiers in microbiology Table SARS_CoV_2 D377Y 0 5 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. D614G 2021 Frontiers in microbiology Table SARS_CoV_2 D614G 0 5 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. I300F 2021 Frontiers in microbiology Table SARS_CoV_2 I300F 0 5 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. I4683T 2021 Frontiers in microbiology Table SARS_CoV_2 I4683T 0 6 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. K4576N 2021 Frontiers in microbiology Table SARS_CoV_2 K4576N 0 6 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. L3606F 2021 Frontiers in microbiology Table SARS_CoV_2 L3606F 0 6 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. L5129F 2021 Frontiers in microbiology Table SARS_CoV_2 L5129F 0 6 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. L84S 2021 Frontiers in microbiology Table SARS_CoV_2 L84S 0 4 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. M234I 2021 Frontiers in microbiology Table SARS_CoV_2 M234I 0 5 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. M3087I 2021 Frontiers in microbiology Table SARS_CoV_2 M3087I 0 6 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. N5542D 2021 Frontiers in microbiology Table SARS_CoV_2 N5542D 0 6 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. P13L 2021 Frontiers in microbiology Table SARS_CoV_2 P13L 0 4 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. Q57H 2021 Frontiers in microbiology Table SARS_CoV_2 Q57H 0 4 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. S194L 2021 Frontiers in microbiology Table SARS_CoV_2 S194L 0 5 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. S202N 2021 Frontiers in microbiology Table SARS_CoV_2 S202N 0 5 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. S477N 2021 Frontiers in microbiology Table SARS_CoV_2 S477N 0 5 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. S5585I 2021 Frontiers in microbiology Table SARS_CoV_2 S5585I 0 6 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. T2016K 2021 Frontiers in microbiology Table SARS_CoV_2 T2016K 0 6 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. V30L 2021 Frontiers in microbiology Table SARS_CoV_2 V30L 0 4 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. W131C 2021 Frontiers in microbiology Table SARS_CoV_2 W131C 0 5 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. X5167Y 2021 Frontiers in microbiology Table SARS_CoV_2 X5167Y 0 6 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. A701V 2021 Infection and drug resistance Table SARS_CoV_2 A701V 0 5 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. D614G 2021 Infection and drug resistance Table SARS_CoV_2 D614G 0 5 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. E484K 2021 Infection and drug resistance Table SARS_CoV_2 E484K 0 5 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. E484Q 2021 Infection and drug resistance Table SARS_CoV_2 E484Q 0 5 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. K417N 2021 Infection and drug resistance Table SARS_CoV_2 K417N 0 5 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. K417T 2021 Infection and drug resistance Table SARS_CoV_2 K417T 0 5 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. L452R 2021 Infection and drug resistance Table SARS_CoV_2 L452R 0 5 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. N501Y 2021 Infection and drug resistance Table SARS_CoV_2 N501Y 0 5 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. P681R 2021 Infection and drug resistance Table SARS_CoV_2 P681R 0 5 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. T20N 2021 Infection and drug resistance Table SARS_CoV_2 T20N 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. A119S 2022 Virus research Table SARS_CoV_2 A119S 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. A320V 2022 Virus research Table SARS_CoV_2 A320V 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. D138Y 2022 Virus research Table SARS_CoV_2 D138Y 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. D614G 2022 Virus research Table SARS_CoV_2 D614G 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. E341D 2022 Virus research Table SARS_CoV_2 E341D 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. E484K 2022 Virus research Table SARS_CoV_2 E484K 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. E92K 2022 Virus research Table SARS_CoV_2 E92K 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. F108L 2022 Virus research Table SARS_CoV_2 F108L 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. G107S 2022 Virus research Table SARS_CoV_2 G107S 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. G204R 2022 Virus research Table SARS_CoV_2 G204R 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. G251V 2022 Virus research Table SARS_CoV_2 G251V 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. G88E 2022 Virus research Table SARS_CoV_2 G88E 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. H655Y 2022 Virus research Table SARS_CoV_2 H655Y 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. I292T 2022 Virus research Table SARS_CoV_2 I292T 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. I33T 2022 Virus research Table SARS_CoV_2 I33T 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. K110R 2022 Virus research Table SARS_CoV_2 K110R 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. K417T 2022 Virus research Table SARS_CoV_2 K417T 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. K534N 2022 Virus research Table SARS_CoV_2 K534N 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. K982Q 2022 Virus research Table SARS_CoV_2 K982Q 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. L18F 2022 Virus research Table SARS_CoV_2 L18F 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. L205V 2022 Virus research Table SARS_CoV_2 L205V 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. L37F 2022 Virus research Table SARS_CoV_2 L37F 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. L71F 2022 Virus research Table SARS_CoV_2 L71F 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. M234I 2022 Virus research Table SARS_CoV_2 M234I 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. N256S 2022 Virus research Table SARS_CoV_2 N256S 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. N501Y 2022 Virus research Table SARS_CoV_2 N501Y 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. N74K 2022 Virus research Table SARS_CoV_2 N74K 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. P26S 2022 Virus research Table SARS_CoV_2 P26S 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. P323L 2022 Virus research Table SARS_CoV_2 P323L 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. P383L 2022 Virus research Table SARS_CoV_2 P383L 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. P80R 2022 Virus research Table SARS_CoV_2 P80R 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. P96H 2022 Virus research Table SARS_CoV_2 P96H 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. Q57H 2022 Virus research Table SARS_CoV_2 Q57H 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. R190S 2022 Virus research Table SARS_CoV_2 R190S 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. R203K 2022 Virus research Table SARS_CoV_2 R203K 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. R216N 2022 Virus research Table SARS_CoV_2 R216N 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. S106T 2022 Virus research Table SARS_CoV_2 S106T 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. S138L 2022 Virus research Table SARS_CoV_2 S138L 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. S171L 2022 Virus research Table SARS_CoV_2 S171L 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. S1740F 2022 Virus research Table SARS_CoV_2 S1740F 0 6 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. S184N 2022 Virus research Table SARS_CoV_2 S184N 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. S202T 2022 Virus research Table SARS_CoV_2 S202T 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. S253P 2022 Virus research Table SARS_CoV_2 S253P 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. S25L 2022 Virus research Table SARS_CoV_2 S25L 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. S375L 2022 Virus research Table SARS_CoV_2 S375L 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. T1027I 2022 Virus research Table SARS_CoV_2 T1027I 0 6 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. T16A 2022 Virus research Table SARS_CoV_2 T16A 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. T17I 2022 Virus research Table SARS_CoV_2 T17I 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. T20N 2022 Virus research Table SARS_CoV_2 T20N 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. T528I 2022 Virus research Table SARS_CoV_2 T528I 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. T85I 2022 Virus research Table SARS_CoV_2 T85I 0 4 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. V1176F 2022 Virus research Table SARS_CoV_2 V1176F 0 6 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. V577F 2022 Virus research Table SARS_CoV_2 V577F 0 5 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. Y235N 2022 Virus research Table SARS_CoV_2 Y235N 0 5 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. E484K 2021 Scientific reports Table SARS_CoV_2 E484K 0 5 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. K417N 2021 Scientific reports Table SARS_CoV_2 K417N 0 5 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. N501Y 2021 Scientific reports Table SARS_CoV_2 N501Y 0 5 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. D614G 2021 iScience Table SARS_CoV_2 D614G 0 5 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. E0554S 2021 iScience Table SARS_CoV_2 E0554S 0 6 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. P0703L 2021 iScience Table SARS_CoV_2 P0703L 0 6 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. P0704L 2021 iScience Table SARS_CoV_2 P0704L 0 6 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. A11506T 2021 PloS one Table SARS_CoV_2 A11506T 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. A21550C 2021 PloS one Table SARS_CoV_2 A21550C 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. A21551T 2021 PloS one Table SARS_CoV_2 A21551T 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. A23403G 2021 PloS one Table SARS_CoV_2 A23403G 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. A27379G 2021 PloS one Table SARS_CoV_2 A27379G 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. A27383T 2021 PloS one Table SARS_CoV_2 A27383T 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. A398S 2021 PloS one Table SARS_CoV_2 A398S 0 5 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. A98S 2021 PloS one Table SARS_CoV_2 A98S 0 4 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. C11758T 2021 PloS one Table SARS_CoV_2 C11758T 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. C11986T 2021 PloS one Table SARS_CoV_2 C11986T 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. C14408T 2021 PloS one Table SARS_CoV_2 C14408T 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. C15324T 2021 PloS one Table SARS_CoV_2 C15324T 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. C20483T 2021 PloS one Table SARS_CoV_2 C20483T 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. C21380T 2021 PloS one Table SARS_CoV_2 C21380T 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. C27213T 2021 PloS one Table SARS_CoV_2 C27213T 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. C27879T 2021 PloS one Table SARS_CoV_2 C27879T 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. C3037T 2021 PloS one Table SARS_CoV_2 C3037T 0 6 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. C3093T 2021 PloS one Table SARS_CoV_2 C3093T 0 6 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. C5986T 2021 PloS one Table SARS_CoV_2 C5986T 0 6 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. D614G 2021 PloS one Table SARS_CoV_2 D614G 0 5 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. G10523A 2021 PloS one Table SARS_CoV_2 G10523A 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. G11083T 2021 PloS one Table SARS_CoV_2 G11083T 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. G1397A 2021 PloS one Table SARS_CoV_2 G1397A 0 6 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. G16117A 2021 PloS one Table SARS_CoV_2 G16117A 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. G18984C 2021 PloS one Table SARS_CoV_2 G18984C 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. G22770A 2021 PloS one Table SARS_CoV_2 G22770A 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. G25684T 2021 PloS one Table SARS_CoV_2 G25684T 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. G27382C 2021 PloS one Table SARS_CoV_2 G27382C 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. G29465T 2021 PloS one Table SARS_CoV_2 G29465T 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. H42Y 2021 PloS one Table SARS_CoV_2 H42Y 0 4 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. I263M 2021 PloS one Table SARS_CoV_2 I263M 0 5 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. I60V 2021 PloS one Table SARS_CoV_2 I60V 0 4 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. L3606F 2021 PloS one Table SARS_CoV_2 L3606F 0 6 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. M1839I 2021 PloS one Table SARS_CoV_2 M1839I 0 6 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. P314L 2021 PloS one Table SARS_CoV_2 P314L 0 5 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. P943L 2021 PloS one Table SARS_CoV_2 P943L 0 5 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. S2339F 2021 PloS one Table SARS_CoV_2 S2339F 0 6 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. T26181G 2021 PloS one Table SARS_CoV_2 T26181G 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. T27384C 2021 PloS one Table SARS_CoV_2 T27384C 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. T28688C 2021 PloS one Table SARS_CoV_2 T28688C 0 7 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. T3873C 2021 PloS one Table SARS_CoV_2 T3873C 0 6 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. V3420I 2021 PloS one Table SARS_CoV_2 V3420I 0 6 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. V378I 2021 PloS one Table SARS_CoV_2 V378I 0 5 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Y453F 2021 PLoS pathogens Table SARS_CoV_2 Y453F 0 5 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. D614G 2021 Applied microbiology and biotechnology Table SARS_CoV_2 D614G 0 5 34756912 RT-qPCR detection of SARS-CoV-2 mutations S 69-70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples. N501Y 2022 The Science of the total environment Table SARS_CoV_2 N501Y 0 5 34758391 SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance. G204R 2022 International journal of infectious diseases Table SARS_CoV_2 G204R 0 5 34758391 SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance. R203K 2022 International journal of infectious diseases Table SARS_CoV_2 R203K 0 5 34758391 SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance. S235F 2022 International journal of infectious diseases Table SARS_CoV_2 S235F 0 5 34758391 SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance. T135I 2022 International journal of infectious diseases Table SARS_CoV_2 T135I 0 5 34759999 Epidemiology of COVID-19: An updated review. A570D 2021 Journal of research in medical sciences Table SARS_CoV_2 A570D 0 5 34759999 Epidemiology of COVID-19: An updated review. D1118H 2021 Journal of research in medical sciences Table SARS_CoV_2 D1118H 0 6 34759999 Epidemiology of COVID-19: An updated review. D138Y 2021 Journal of research in medical sciences Table SARS_CoV_2 D138Y 0 5 34759999 Epidemiology of COVID-19: An updated review. D614G 2021 Journal of research in medical sciences Table SARS_CoV_2 D614G 0 5 34759999 Epidemiology of COVID-19: An updated review. E484K 2021 Journal of research in medical sciences Table SARS_CoV_2 E484K 0 5 34759999 Epidemiology of COVID-19: An updated review. H655Y 2021 Journal of research in medical sciences Table SARS_CoV_2 H655Y 0 5 34759999 Epidemiology of COVID-19: An updated review. K417T 2021 Journal of research in medical sciences Table SARS_CoV_2 K417T 0 5 34759999 Epidemiology of COVID-19: An updated review. L18F 2021 Journal of research in medical sciences Table SARS_CoV_2 L18F 0 4 34759999 Epidemiology of COVID-19: An updated review. N501Y 2021 Journal of research in medical sciences Table SARS_CoV_2 N501Y 0 5 34759999 Epidemiology of COVID-19: An updated review. P26S 2021 Journal of research in medical sciences Table SARS_CoV_2 P26S 0 4 34759999 Epidemiology of COVID-19: An updated review. P681H 2021 Journal of research in medical sciences Table SARS_CoV_2 P681H 0 5 34759999 Epidemiology of COVID-19: An updated review. R190S 2021 Journal of research in medical sciences Table SARS_CoV_2 R190S 0 5 34759999 Epidemiology of COVID-19: An updated review. S982A 2021 Journal of research in medical sciences Table SARS_CoV_2 S982A 0 5 34759999 Epidemiology of COVID-19: An updated review. T1027I 2021 Journal of research in medical sciences Table SARS_CoV_2 T1027I 0 6 34759999 Epidemiology of COVID-19: An updated review. T20N 2021 Journal of research in medical sciences Table SARS_CoV_2 T20N 0 4 34759999 Epidemiology of COVID-19: An updated review. T716I 2021 Journal of research in medical sciences Table SARS_CoV_2 T716I 0 5 34759999 Epidemiology of COVID-19: An updated review. V1176F 2021 Journal of research in medical sciences Table SARS_CoV_2 V1176F 0 6 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. A4489V 2021 PeerJ Table SARS_CoV_2 A4489V 0 6 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. A701V 2021 PeerJ Table SARS_CoV_2 A701V 0 5 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. D614G 2021 PeerJ Table SARS_CoV_2 D614G 0 5 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. L3606F 2021 PeerJ Table SARS_CoV_2 L3606F 0 6 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. L5752F 2021 PeerJ Table SARS_CoV_2 L5752F 0 6 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. P13L 2021 PeerJ Table SARS_CoV_2 P13L 0 4 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. P4715L 2021 PeerJ Table SARS_CoV_2 P4715L 0 6 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. S194L 2021 PeerJ Table SARS_CoV_2 S194L 0 5 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. T2016I 2021 PeerJ Table SARS_CoV_2 T2016I 0 6 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. T2016K 2021 PeerJ Table SARS_CoV_2 T2016K 0 6 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. T2791I 2021 PeerJ Table SARS_CoV_2 T2791I 0 6 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. T3287A 2021 PeerJ Table SARS_CoV_2 T3287A 0 6 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. A10124G 2021 Scientific reports Table SARS_CoV_2 A10124G 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. A23403G 2021 Scientific reports Table SARS_CoV_2 A23403G 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. A28133T 2021 Scientific reports Table SARS_CoV_2 A28133T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. A29086T 2021 Scientific reports Table SARS_CoV_2 A29086T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. A29426G 2021 Scientific reports Table SARS_CoV_2 A29426G 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. A318V 2021 Scientific reports Table SARS_CoV_2 A318V 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. A701V 2021 Scientific reports Table SARS_CoV_2 A701V 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. A97V 2021 Scientific reports Table SARS_CoV_2 A97V 0 4 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C10604T 2021 Scientific reports Table SARS_CoV_2 C10604T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C11752T 2021 Scientific reports Table SARS_CoV_2 C11752T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C11941T 2021 Scientific reports Table SARS_CoV_2 C11941T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C13329T 2021 Scientific reports Table SARS_CoV_2 C13329T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C13730T 2021 Scientific reports Table SARS_CoV_2 C13730T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C14408T 2021 Scientific reports Table SARS_CoV_2 C14408T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C14805T 2021 Scientific reports Table SARS_CoV_2 C14805T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C17518T 2021 Scientific reports Table SARS_CoV_2 C17518T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C1758T 2021 Scientific reports Table SARS_CoV_2 C1758T 0 6 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C18877T 2021 Scientific reports Table SARS_CoV_2 C18877T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C19170A 2021 Scientific reports Table SARS_CoV_2 C19170A 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C19524T 2021 Scientific reports Table SARS_CoV_2 C19524T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C20823T 2021 Scientific reports Table SARS_CoV_2 C20823T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C21365T 2021 Scientific reports Table SARS_CoV_2 C21365T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C21516T 2021 Scientific reports Table SARS_CoV_2 C21516T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C21622A 2021 Scientific reports Table SARS_CoV_2 C21622A 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C21627T 2021 Scientific reports Table SARS_CoV_2 C21627T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C21658T 2021 Scientific reports Table SARS_CoV_2 C21658T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C23664T 2021 Scientific reports Table SARS_CoV_2 C23664T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C23929T 2021 Scientific reports Table SARS_CoV_2 C23929T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C241T 2021 Scientific reports Table SARS_CoV_2 C241T 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C24616G 2021 Scientific reports Table SARS_CoV_2 C24616G 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C2508A 2021 Scientific reports Table SARS_CoV_2 C2508A 0 6 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C25549T 2021 Scientific reports Table SARS_CoV_2 C25549T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C26607T 2021 Scientific reports Table SARS_CoV_2 C26607T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C28311T 2021 Scientific reports Table SARS_CoV_2 C28311T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C28854T 2021 Scientific reports Table SARS_CoV_2 C28854T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C29218T 2021 Scientific reports Table SARS_CoV_2 C29218T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C3037T 2021 Scientific reports Table SARS_CoV_2 C3037T 0 6 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C401T 2021 Scientific reports Table SARS_CoV_2 C401T 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C6310A 2021 Scientific reports Table SARS_CoV_2 C6310A 0 6 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C6312A 2021 Scientific reports Table SARS_CoV_2 C6312A 0 6 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C6312T 2021 Scientific reports Table SARS_CoV_2 C6312T 0 6 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C8637T 2021 Scientific reports Table SARS_CoV_2 C8637T 0 6 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. C8782T 2021 Scientific reports Table SARS_CoV_2 C8782T 0 6 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. D614G 2021 Scientific reports Table SARS_CoV_2 D614G 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. E55D 2021 Scientific reports Table SARS_CoV_2 E55D 0 4 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. F377L 2021 Scientific reports Table SARS_CoV_2 F377L 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. G11083T 2021 Scientific reports Table SARS_CoV_2 G11083T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. G114T 2021 Scientific reports Table SARS_CoV_2 G114T 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. G1467A 2021 Scientific reports Table SARS_CoV_2 G1467A 0 6 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. G204R 2021 Scientific reports Table SARS_CoV_2 G204R 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. G221D 2021 Scientific reports Table SARS_CoV_2 G221D 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. G251V 2021 Scientific reports Table SARS_CoV_2 G251V 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. G25429T 2021 Scientific reports Table SARS_CoV_2 G25429T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. G25563T 2021 Scientific reports Table SARS_CoV_2 G25563T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. G26144T 2021 Scientific reports Table SARS_CoV_2 G26144T 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. G28881A 2021 Scientific reports Table SARS_CoV_2 G28881A 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. G28882A 2021 Scientific reports Table SARS_CoV_2 G28882A 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. G28883C 2021 Scientific reports Table SARS_CoV_2 G28883C 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. G970T 2021 Scientific reports Table SARS_CoV_2 G970T 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. I1018M 2021 Scientific reports Table SARS_CoV_2 I1018M 0 6 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. L29F 2021 Scientific reports Table SARS_CoV_2 L29F 0 4 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. L37F 2021 Scientific reports Table SARS_CoV_2 L37F 0 4 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. L428F 2021 Scientific reports Table SARS_CoV_2 L428F 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. L46F 2021 Scientific reports Table SARS_CoV_2 L46F 0 4 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. L53F 2021 Scientific reports Table SARS_CoV_2 L53F 0 4 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. L84S 2021 Scientific reports Table SARS_CoV_2 L84S 0 4 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. P184S 2021 Scientific reports Table SARS_CoV_2 P184S 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. P236L 2021 Scientific reports Table SARS_CoV_2 P236L 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. P323L 2021 Scientific reports Table SARS_CoV_2 P323L 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. P38L 2021 Scientific reports Table SARS_CoV_2 P38L 0 4 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. P568H 2021 Scientific reports Table SARS_CoV_2 P568H 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. Q37H 2021 Scientific reports Table SARS_CoV_2 Q37H 0 4 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. R203K 2021 Scientific reports Table SARS_CoV_2 R203K 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. R385G 2021 Scientific reports Table SARS_CoV_2 R385G 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. S1197R 2021 Scientific reports Table SARS_CoV_2 S1197R 0 6 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. S194L 2021 Scientific reports Table SARS_CoV_2 S194L 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. T102I 2021 Scientific reports Table SARS_CoV_2 T102I 0 5 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. T1198I 2021 Scientific reports Table SARS_CoV_2 T1198I 0 6 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. T1198K 2021 Scientific reports Table SARS_CoV_2 T1198K 0 6 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. T22I 2021 Scientific reports Table SARS_CoV_2 T22I 0 4 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. T24A 2021 Scientific reports Table SARS_CoV_2 T24A 0 4 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. T28144C 2021 Scientific reports Table SARS_CoV_2 T28144C 0 7 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. T28I 2021 Scientific reports Table SARS_CoV_2 T28I 0 4 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. T7621C 2021 Scientific reports Table SARS_CoV_2 T7621C 0 6 34764315 Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave. V13L 2021 Scientific reports Table SARS_CoV_2 V13L 0 4 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. A38S 2021 PLoS pathogens Table SARS_CoV_2 A38S 0 4 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. D614G 2021 PLoS pathogens Table SARS_CoV_2 D614G 0 5 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. G37E 2021 PLoS pathogens Table SARS_CoV_2 G37E 0 4 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. H182Y 2021 PLoS pathogens Table SARS_CoV_2 H182Y 0 5 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. K113T 2021 PLoS pathogens Table SARS_CoV_2 K113T 0 5 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. N501T 2021 PLoS pathogens Table SARS_CoV_2 N501T 0 5 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. P323L 2021 PLoS pathogens Table SARS_CoV_2 P323L 0 5 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. Q289H 2021 PLoS pathogens Table SARS_CoV_2 Q289H 0 5 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. Q57H 2021 PLoS pathogens Table SARS_CoV_2 Q57H 0 4 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. S1206L 2021 PLoS pathogens Table SARS_CoV_2 S1206L 0 6 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. T205I 2021 PLoS pathogens Table SARS_CoV_2 T205I 0 5 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. T85I 2021 PLoS pathogens Table SARS_CoV_2 T85I 0 4 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. T91M 2021 PLoS pathogens Table SARS_CoV_2 T91M 0 4 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. V187I 2021 PLoS pathogens Table SARS_CoV_2 V187I 0 5 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. D614G 2021 Scientific reports Table SARS_CoV_2 D614G 0 5 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. E484K 2021 Scientific reports Table SARS_CoV_2 E484K 0 5 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. N501Y 2021 Scientific reports Table SARS_CoV_2 N501Y 0 5 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Y453F 2021 Scientific reports Table SARS_CoV_2 Y453F 0 5 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. A3303G 2021 PLoS pathogens Table SARS_CoV_2 A3303G 0 6 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. A652C 2021 PLoS pathogens Table SARS_CoV_2 A652C 0 5 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. C1913T 2021 PLoS pathogens Table SARS_CoV_2 C1913T 0 6 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. D614G 2021 PLoS pathogens Table SARS_CoV_2 D614G 0 5 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. G2035T 2021 PLoS pathogens Table SARS_CoV_2 G2035T 0 6 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. G28881A 2021 PLoS pathogens Table SARS_CoV_2 G28881A 0 7 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. G28882A 2021 PLoS pathogens Table SARS_CoV_2 G28882A 0 7 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. G28883C 2021 PLoS pathogens Table SARS_CoV_2 G28883C 0 7 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. G488A 2021 PLoS pathogens Table SARS_CoV_2 G488A 0 5 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. H182Y 2021 PLoS pathogens Table SARS_CoV_2 H182Y 0 5 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. K129N 2021 PLoS pathogens Table SARS_CoV_2 K129N 0 5 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. L590F 2021 PLoS pathogens Table SARS_CoV_2 L590F 0 5 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. P314L 2021 PLoS pathogens Table SARS_CoV_2 P314L 0 5 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. P3395S 2021 PLoS pathogens Table SARS_CoV_2 P3395S 0 6 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. R550C 2021 PLoS pathogens Table SARS_CoV_2 R550C 0 5 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. S194L 2021 PLoS pathogens Table SARS_CoV_2 S194L 0 5 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. S2430I 2021 PLoS pathogens Table SARS_CoV_2 S2430I 0 6 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. T1873C 2021 PLoS pathogens Table SARS_CoV_2 T1873C 0 6 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. T730I 2021 PLoS pathogens Table SARS_CoV_2 T730I 0 5 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. Y453F 2021 PLoS pathogens Table SARS_CoV_2 Y453F 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. A119T 2022 Virus research Table SARS_CoV_2 A119T 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. A136V 2022 Virus research Table SARS_CoV_2 A136V 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. A15S 2022 Virus research Table SARS_CoV_2 A15S 0 4 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. A43S 2022 Virus research Table SARS_CoV_2 A43S 0 4 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. D614G 2022 Virus research Table SARS_CoV_2 D614G 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. E484K 2022 Virus research Table SARS_CoV_2 E484K 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. G105S 2022 Virus research Table SARS_CoV_2 G105S 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. G213N 2022 Virus research Table SARS_CoV_2 G213N 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. I114T 2022 Virus research Table SARS_CoV_2 I114T 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. I18V 2022 Virus research Table SARS_CoV_2 I18V 0 4 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. K90R 2022 Virus research Table SARS_CoV_2 K90R 0 4 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. L17F 2022 Virus research Table SARS_CoV_2 L17F 0 4 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. L249S 2022 Virus research Table SARS_CoV_2 L249S 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. L325F 2022 Virus research Table SARS_CoV_2 L325F 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. L84S 2022 Virus research Table SARS_CoV_2 L84S 0 4 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. M234I 2022 Virus research Table SARS_CoV_2 M234I 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. P323L 2022 Virus research Table SARS_CoV_2 P323L 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Q57H 2022 Virus research Table SARS_CoV_2 Q57H 0 4 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. S1285F 2022 Virus research Table SARS_CoV_2 S1285F 0 6 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. T153I 2022 Virus research Table SARS_CoV_2 T153I 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. T205I 2022 Virus research Table SARS_CoV_2 T205I 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. T223I 2022 Virus research Table SARS_CoV_2 T223I 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. T859I 2022 Virus research Table SARS_CoV_2 T859I 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. V157L 2022 Virus research Table SARS_CoV_2 V157L 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. V314F 2022 Virus research Table SARS_CoV_2 V314F 0 5 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. W152R 2022 Virus research Table SARS_CoV_2 W152R 0 5 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. A13433G 2021 Nature communications Table SARS_CoV_2 A13433G 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. A13947T 2021 Nature communications Table SARS_CoV_2 A13947T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. A18179G 2021 Nature communications Table SARS_CoV_2 A18179G 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. A22920T 2021 Nature communications Table SARS_CoV_2 A22920T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. A23063T 2021 Nature communications Table SARS_CoV_2 A23063T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. A2325V 2021 Nature communications Table SARS_CoV_2 A2325V 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. A2637V 2021 Nature communications Table SARS_CoV_2 A2637V 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. A27574T 2021 Nature communications Table SARS_CoV_2 A27574T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. A28336T 2021 Nature communications Table SARS_CoV_2 A28336T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. A29424G 2021 Nature communications Table SARS_CoV_2 A29424G 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. A36V 2021 Nature communications Table SARS_CoV_2 A36V 0 4 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. A440V 2021 Nature communications Table SARS_CoV_2 A440V 0 5 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. A5405G 2021 Nature communications Table SARS_CoV_2 A5405G 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. A8387G 2021 Nature communications Table SARS_CoV_2 A8387G 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. A9737G 2021 Nature communications Table SARS_CoV_2 A9737G 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C10369T 2021 Nature communications Table SARS_CoV_2 C10369T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C11008T 2021 Nature communications Table SARS_CoV_2 C11008T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C12439T 2021 Nature communications Table SARS_CoV_2 C12439T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C12513T 2021 Nature communications Table SARS_CoV_2 C12513T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C14786T 2021 Nature communications Table SARS_CoV_2 C14786T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C14937T 2021 Nature communications Table SARS_CoV_2 C14937T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C15222T 2021 Nature communications Table SARS_CoV_2 C15222T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C16092T 2021 Nature communications Table SARS_CoV_2 C16092T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C17004T 2021 Nature communications Table SARS_CoV_2 C17004T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C1862T 2021 Nature communications Table SARS_CoV_2 C1862T 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C18979T 2021 Nature communications Table SARS_CoV_2 C18979T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C2094T 2021 Nature communications Table SARS_CoV_2 C2094T 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C21789T 2021 Nature communications Table SARS_CoV_2 C21789T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C24642T 2021 Nature communications Table SARS_CoV_2 C24642T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C26333T 2021 Nature communications Table SARS_CoV_2 C26333T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C26351T 2021 Nature communications Table SARS_CoV_2 C26351T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C29200T 2021 Nature communications Table SARS_CoV_2 C29200T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C29592T 2021 Nature communications Table SARS_CoV_2 C29592T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C7239T 2021 Nature communications Table SARS_CoV_2 C7239T 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C7279T 2021 Nature communications Table SARS_CoV_2 C7279T 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C8175T 2021 Nature communications Table SARS_CoV_2 C8175T 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C9438T 2021 Nature communications Table SARS_CoV_2 C9438T 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. C9491T 2021 Nature communications Table SARS_CoV_2 C9491T 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. E918D 2021 Nature communications Table SARS_CoV_2 E918D 0 5 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. F2328V 2021 Nature communications Table SARS_CoV_2 F2328V 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. G1068A 2021 Nature communications Table SARS_CoV_2 G1068A 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. G22363T 2021 Nature communications Table SARS_CoV_2 G22363T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. G22661T 2021 Nature communications Table SARS_CoV_2 G22661T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. G23782A 2021 Nature communications Table SARS_CoV_2 G23782A 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. G24316T 2021 Nature communications Table SARS_CoV_2 G24316T 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. G268E 2021 Nature communications Table SARS_CoV_2 G268E 0 5 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. G29744A 2021 Nature communications Table SARS_CoV_2 G29744A 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. H1838Y 2021 Nature communications Table SARS_CoV_2 H1838Y 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. H3076Y 2021 Nature communications Table SARS_CoV_2 H3076Y 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. I1714T 2021 Nature communications Table SARS_CoV_2 I1714T 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. I1714V 2021 Nature communications Table SARS_CoV_2 I1714V 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. K1571R 2021 Nature communications Table SARS_CoV_2 K1571R 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. L533F 2021 Nature communications Table SARS_CoV_2 L533F 0 5 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. M4390G 2021 Nature communications Table SARS_CoV_2 M4390G 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. M740I 2021 Nature communications Table SARS_CoV_2 M740I 0 5 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. N2708D 2021 Nature communications Table SARS_CoV_2 N2708D 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. N501Y 2021 Nature communications Table SARS_CoV_2 N501Y 0 5 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. P4058L 2021 Nature communications Table SARS_CoV_2 P4058L 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. Q384R 2021 Nature communications Table SARS_CoV_2 Q384R 0 5 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. S3158G 2021 Nature communications Table SARS_CoV_2 S3158G 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. S610L 2021 Nature communications Table SARS_CoV_2 S610L 0 5 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T1027I 2021 Nature communications Table SARS_CoV_2 T1027I 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T13417C 2021 Nature communications Table SARS_CoV_2 T13417C 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T18024C 2021 Nature communications Table SARS_CoV_2 T18024C 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T18678C 2021 Nature communications Table SARS_CoV_2 T18678C 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T18750C 2021 Nature communications Table SARS_CoV_2 T18750C 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T2149C 2021 Nature communications Table SARS_CoV_2 T2149C 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T24450C 2021 Nature communications Table SARS_CoV_2 T24450C 0 7 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T3058I 2021 Nature communications Table SARS_CoV_2 T3058I 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T30I 2021 Nature communications Table SARS_CoV_2 T30I 0 4 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T322A 2021 Nature communications Table SARS_CoV_2 T322A 0 5 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T34M 2021 Nature communications Table SARS_CoV_2 T34M 0 4 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T4083M 2021 Nature communications Table SARS_CoV_2 T4083M 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T5395A 2021 Nature communications Table SARS_CoV_2 T5395A 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T5406C 2021 Nature communications Table SARS_CoV_2 T5406C 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T61S 2021 Nature communications Table SARS_CoV_2 T61S 0 4 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T7247G 2021 Nature communications Table SARS_CoV_2 T7247G 0 6 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. T76I 2021 Nature communications Table SARS_CoV_2 T76I 0 4 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. V367F 2021 Nature communications Table SARS_CoV_2 V367F 0 5 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. V963A 2021 Nature communications Table SARS_CoV_2 V963A 0 5 34785663 Organ-specific genome diversity of replication-competent SARS-CoV-2. Y453F 2021 Nature communications Table SARS_CoV_2 Y453F 0 5 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. C29197T 2021 Microbiology spectrum Table SARS_CoV_2 C29197T 0 7 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. C29200T 2021 Microbiology spectrum Table SARS_CoV_2 C29200T 0 7 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. A570D 2021 Microbiology spectrum Table SARS_CoV_2 A570D 0 5 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. D614G 2021 Microbiology spectrum Table SARS_CoV_2 D614G 0 5 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. E484K 2021 Microbiology spectrum Table SARS_CoV_2 E484K 0 5 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. E484Q 2021 Microbiology spectrum Table SARS_CoV_2 E484Q 0 5 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. F490S 2021 Microbiology spectrum Table SARS_CoV_2 F490S 0 5 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. K417N 2021 Microbiology spectrum Table SARS_CoV_2 K417N 0 5 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. K417T 2021 Microbiology spectrum Table SARS_CoV_2 K417T 0 5 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. L452Q 2021 Microbiology spectrum Table SARS_CoV_2 L452Q 0 5 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. L452R 2021 Microbiology spectrum Table SARS_CoV_2 L452R 0 5 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. N501Y 2021 Microbiology spectrum Table SARS_CoV_2 N501Y 0 5 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. T478K 2021 Microbiology spectrum Table SARS_CoV_2 T478K 0 5 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. D614G 2021 Microbiology spectrum Table SARS_CoV_2 D614G 0 5 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. E484K 2021 Microbiology spectrum Table SARS_CoV_2 E484K 0 5 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. E484K/Q 2021 Microbiology spectrum Table SARS_CoV_2 E484K;E484Q 0;0 7;7 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. E484Q 2021 Microbiology spectrum Table SARS_CoV_2 E484Q 0 5 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. K417N 2021 Microbiology spectrum Table SARS_CoV_2 K417N 0 5 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. L452R 2021 Microbiology spectrum Table SARS_CoV_2 L452R 0 5 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. N501Y 2021 Microbiology spectrum Table SARS_CoV_2 N501Y 0 5 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. P681H 2021 Microbiology spectrum Table SARS_CoV_2 P681H 0 5 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. P681H/R 2021 Microbiology spectrum Table SARS_CoV_2 P681H;P681R 0;0 7;7 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. P681R 2021 Microbiology spectrum Table SARS_CoV_2 P681R 0 5 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. D138Y 2021 Virology journal Table SARS_CoV_2 D138Y 0 5 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. D614G 2021 Virology journal Table SARS_CoV_2 D614G 0 5 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. E1264D 2021 Virology journal Table SARS_CoV_2 E1264D 0 6 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. E484K 2021 Virology journal Table SARS_CoV_2 E484K 0 5 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. E661D 2021 Virology journal Table SARS_CoV_2 E661D 0 5 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. E92K 2021 Virology journal Table SARS_CoV_2 E92K 0 4 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. G204R 2021 Virology journal Table SARS_CoV_2 G204R 0 5 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. H655Y 2021 Virology journal Table SARS_CoV_2 H655Y 0 5 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. K1795Q 2021 Virology journal Table SARS_CoV_2 K1795Q 0 6 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. K417T 2021 Virology journal Table SARS_CoV_2 K417T 0 5 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. L18F 2021 Virology journal Table SARS_CoV_2 L18F 0 4 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. N501Y 2021 Virology journal Table SARS_CoV_2 N501Y 0 5 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. P26S 2021 Virology journal Table SARS_CoV_2 P26S 0 4 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. P314L 2021 Virology journal Table SARS_CoV_2 P314L 0 5 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. P80R 2021 Virology journal Table SARS_CoV_2 P80R 0 4 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. Q77E 2021 Virology journal Table SARS_CoV_2 Q77E 0 4 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. R190S 2021 Virology journal Table SARS_CoV_2 R190S 0 5 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. R203K 2021 Virology journal Table SARS_CoV_2 R203K 0 5 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. S1188L 2021 Virology journal Table SARS_CoV_2 S1188L 0 6 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. S253P 2021 Virology journal Table SARS_CoV_2 S253P 0 5 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. T1027I 2021 Virology journal Table SARS_CoV_2 T1027I 0 6 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. T20N 2021 Virology journal Table SARS_CoV_2 T20N 0 4 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. V1176F 2021 Virology journal Table SARS_CoV_2 V1176F 0 6 34790342 On the association between SARS-COV-2 variants and COVID-19 mortality during the second wave of the pandemic in Europe. D614G 2021 Journal of market access & health policy Table SARS_CoV_2 D614G 0 5 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. D17L 2022 The Journal of biological chemistry Table SARS_CoV_2 D17L 0 4 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. A222V 2021 Immune network Table SARS_CoV_2 A222V 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. A243del 2021 Immune network Table SARS_CoV_2 A243del 0 7 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. A570D 2021 Immune network Table SARS_CoV_2 A570D 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. A67V 2021 Immune network Table SARS_CoV_2 A67V 0 4 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. A701V 2021 Immune network Table SARS_CoV_2 A701V 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. D1118H 2021 Immune network Table SARS_CoV_2 D1118H 0 6 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. D138Y 2021 Immune network Table SARS_CoV_2 D138Y 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. D215G 2021 Immune network Table SARS_CoV_2 D215G 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. D253G 2021 Immune network Table SARS_CoV_2 D253G 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. D614G 2021 Immune network Table SARS_CoV_2 D614G 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. D80A 2021 Immune network Table SARS_CoV_2 D80A 0 4 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. D80G 2021 Immune network Table SARS_CoV_2 D80G 0 4 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. D950H 2021 Immune network Table SARS_CoV_2 D950H 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. D950N 2021 Immune network Table SARS_CoV_2 D950N 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. E154K 2021 Immune network Table SARS_CoV_2 E154K 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. E156del 2021 Immune network Table SARS_CoV_2 E156del 0 7 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. E484K 2021 Immune network Table SARS_CoV_2 E484K 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. E484Q 2021 Immune network Table SARS_CoV_2 E484Q 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. F157del 2021 Immune network Table SARS_CoV_2 F157del 0 7 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. F157S 2021 Immune network Table SARS_CoV_2 F157S 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. F565L 2021 Immune network Table SARS_CoV_2 F565L 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. F888L 2021 Immune network Table SARS_CoV_2 F888L 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. G142D 2021 Immune network Table SARS_CoV_2 G142D 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. H655Y 2021 Immune network Table SARS_CoV_2 H655Y 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. H69del 2021 Immune network Table SARS_CoV_2 H69del 0 6 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. K1191N 2021 Immune network Table SARS_CoV_2 K1191N 0 6 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. K417N 2021 Immune network Table SARS_CoV_2 K417N 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. K417T 2021 Immune network Table SARS_CoV_2 K417T 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. L18F 2021 Immune network Table SARS_CoV_2 L18F 0 4 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. L241del 2021 Immune network Table SARS_CoV_2 L241del 0 7 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. L242del 2021 Immune network Table SARS_CoV_2 L242del 0 7 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. L452R 2021 Immune network Table SARS_CoV_2 L452R 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. N501Y 2021 Immune network Table SARS_CoV_2 N501Y 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. P26S 2021 Immune network Table SARS_CoV_2 P26S 0 4 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. P681H 2021 Immune network Table SARS_CoV_2 P681H 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. P681R 2021 Immune network Table SARS_CoV_2 P681R 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. Q1071H 2021 Immune network Table SARS_CoV_2 Q1071H 0 6 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. Q677H 2021 Immune network Table SARS_CoV_2 Q677H 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. Q957R 2021 Immune network Table SARS_CoV_2 Q957R 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. R158G 2021 Immune network Table SARS_CoV_2 R158G 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. R190S 2021 Immune network Table SARS_CoV_2 R190S 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. S13I 2021 Immune network Table SARS_CoV_2 S13I 0 4 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. S477N 2021 Immune network Table SARS_CoV_2 S477N 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. S494P 2021 Immune network Table SARS_CoV_2 S494P 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. S982A 2021 Immune network Table SARS_CoV_2 S982A 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. T1027I 2021 Immune network Table SARS_CoV_2 T1027I 0 6 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. T19R 2021 Immune network Table SARS_CoV_2 T19R 0 4 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. T20N 2021 Immune network Table SARS_CoV_2 T20N 0 4 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. T478K 2021 Immune network Table SARS_CoV_2 T478K 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. T716I 2021 Immune network Table SARS_CoV_2 T716I 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. T859N 2021 Immune network Table SARS_CoV_2 T859N 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. T95I 2021 Immune network Table SARS_CoV_2 T95I 0 4 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. V1176F 2021 Immune network Table SARS_CoV_2 V1176F 0 6 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. V70del 2021 Immune network Table SARS_CoV_2 V70del 0 6 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. V70F 2021 Immune network Table SARS_CoV_2 V70F 0 4 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. W152C 2021 Immune network Table SARS_CoV_2 W152C 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. W258L 2021 Immune network Table SARS_CoV_2 W258L 0 5 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. Y144del 2021 Immune network Table SARS_CoV_2 Y144del 0 7 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. D614G 2021 Infection, genetics and evolution Table SARS_CoV_2 D614G 0 5 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. D796Y 2021 Infection, genetics and evolution Table SARS_CoV_2 D796Y 0 5 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. E484K 2021 Infection, genetics and evolution Table SARS_CoV_2 E484K 0 5 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. W152G 2021 Infection, genetics and evolution Table SARS_CoV_2 W152G 0 5 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. D614G 2021 Frontiers in immunology Table SARS_CoV_2 D614G 0 5 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. E484K 2021 Frontiers in immunology Table SARS_CoV_2 E484K 0 5 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. G142D 2021 Frontiers in immunology Table SARS_CoV_2 G142D 0 5 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. L452R 2021 Frontiers in immunology Table SARS_CoV_2 L452R 0 5 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. N501Y 2021 Frontiers in immunology Table SARS_CoV_2 N501Y 0 5 34804022 Implication of SARS-CoV-2 Immune Escape Spike Variants on Secondary and Vaccine Breakthrough Infections. P681R 2021 Frontiers in immunology Table SARS_CoV_2 P681R 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. 144del 2021 ACS omega Table SARS_CoV_2 144del 0 6 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. 156del 2021 ACS omega Table SARS_CoV_2 156del 0 6 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. 157del 2021 ACS omega Table SARS_CoV_2 157del 0 6 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. 241del 2021 ACS omega Table SARS_CoV_2 241del 0 6 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. 242del 2021 ACS omega Table SARS_CoV_2 242del 0 6 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. 243del 2021 ACS omega Table SARS_CoV_2 243del 0 6 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. 69del 2021 ACS omega Table SARS_CoV_2 69del 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. 70del 2021 ACS omega Table SARS_CoV_2 70del 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. A570D 2021 ACS omega Table SARS_CoV_2 A570D 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. A67V 2021 ACS omega Table SARS_CoV_2 A67V 0 4 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. A701V 2021 ACS omega Table SARS_CoV_2 A701V 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. D1118H 2021 ACS omega Table SARS_CoV_2 D1118H 0 6 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. D138Y 2021 ACS omega Table SARS_CoV_2 D138Y 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. D215G 2021 ACS omega Table SARS_CoV_2 D215G 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. D253G 2021 ACS omega Table SARS_CoV_2 D253G 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. D614G 2021 ACS omega Table SARS_CoV_2 D614G 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. D950N 2021 ACS omega Table SARS_CoV_2 D950N 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. E154K 2021 ACS omega Table SARS_CoV_2 E154K 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. E417K 2021 ACS omega Table SARS_CoV_2 E417K 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. E484K 2021 ACS omega Table SARS_CoV_2 E484K 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. E484Q 2021 ACS omega Table SARS_CoV_2 E484Q 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. F490S 2021 ACS omega Table SARS_CoV_2 F490S 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. F888L 2021 ACS omega Table SARS_CoV_2 F888L 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. G142D 2021 ACS omega Table SARS_CoV_2 G142D 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. G75V 2021 ACS omega Table SARS_CoV_2 G75V 0 4 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. H655Y 2021 ACS omega Table SARS_CoV_2 H655Y 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. K417N 2021 ACS omega Table SARS_CoV_2 K417N 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. K417T 2021 ACS omega Table SARS_CoV_2 K417T 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. L18F 2021 ACS omega Table SARS_CoV_2 L18F 0 4 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. L452Q 2021 ACS omega Table SARS_CoV_2 L452Q 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. L452R 2021 ACS omega Table SARS_CoV_2 L452R 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. N501Y 2021 ACS omega Table SARS_CoV_2 N501Y 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. P26S 2021 ACS omega Table SARS_CoV_2 P26S 0 4 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. P681H 2021 ACS omega Table SARS_CoV_2 P681H 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. P681R 2021 ACS omega Table SARS_CoV_2 P681R 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. Q1071H 2021 ACS omega Table SARS_CoV_2 Q1071H 0 6 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. Q677H 2021 ACS omega Table SARS_CoV_2 Q677H 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. R158G 2021 ACS omega Table SARS_CoV_2 R158G 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. R190S 2021 ACS omega Table SARS_CoV_2 R190S 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. S982A 2021 ACS omega Table SARS_CoV_2 S982A 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. T1027I 2021 ACS omega Table SARS_CoV_2 T1027I 0 6 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. T19R 2021 ACS omega Table SARS_CoV_2 T19R 0 4 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. T20N 2021 ACS omega Table SARS_CoV_2 T20N 0 4 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. T478K 2021 ACS omega Table SARS_CoV_2 T478K 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. T716I 2021 ACS omega Table SARS_CoV_2 T716I 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. T76I 2021 ACS omega Table SARS_CoV_2 T76I 0 4 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. T859N 2021 ACS omega Table SARS_CoV_2 T859N 0 5 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. T95I 2021 ACS omega Table SARS_CoV_2 T95I 0 4 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. T676Q 2022 Journal of virology Table SARS_CoV_2 T676Q 0 5 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. E1601L 2021 Cell host & microbe Table SARS_CoV_2 E1601L 0 6 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. R0734L 2021 Cell host & microbe Table SARS_CoV_2 R0734L 0 6 34822912 Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR. N501Y 2022 Journal of virological methods Table SARS_CoV_2 N501Y 0 5 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. A23403G 2022 Virus research Table SARS_CoV_2 A23403G 0 7 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. C14408T 2022 Virus research Table SARS_CoV_2 C14408T 0 7 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. C16466T 2022 Virus research Table SARS_CoV_2 C16466T 0 7 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. C21618G 2022 Virus research Table SARS_CoV_2 C21618G 0 7 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. C22995A 2022 Virus research Table SARS_CoV_2 C22995A 0 7 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. C23604G 2022 Virus research Table SARS_CoV_2 C23604G 0 7 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. C241T 2022 Virus research Table SARS_CoV_2 C241T 0 5 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. C25469T 2022 Virus research Table SARS_CoV_2 C25469T 0 7 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. C27752T 2022 Virus research Table SARS_CoV_2 C27752T 0 7 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. C3037T 2022 Virus research Table SARS_CoV_2 C3037T 0 6 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. G210T 2022 Virus research Table SARS_CoV_2 G210T 0 5 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. G24410A 2022 Virus research Table SARS_CoV_2 G24410A 0 7 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. G28881T 2022 Virus research Table SARS_CoV_2 G28881T 0 7 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. G29402T 2022 Virus research Table SARS_CoV_2 G29402T 0 7 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. G29742T 2022 Virus research Table SARS_CoV_2 G29742T 0 7 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. G662S 2022 Virus research Table SARS_CoV_2 G662S 0 5 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. T22917G 2022 Virus research Table SARS_CoV_2 T22917G 0 7 34822953 Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study. T26767C 2022 Virus research Table SARS_CoV_2 T26767C 0 7 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. 1163 A>T 2021 Current research in microbial sciences Table SARS_CoV_2 A1163T 0 8 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. 1163A > T 2021 Current research in microbial sciences Table SARS_CoV_2 A1163T 0 9 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. 14408C > T 2021 Current research in microbial sciences Table SARS_CoV_2 C14408T 0 10 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. 23403A > G 2021 Current research in microbial sciences Table SARS_CoV_2 A23403G 0 10 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. 241C > T 2021 Current research in microbial sciences Table SARS_CoV_2 C241T 0 8 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. 3037C > T 2021 Current research in microbial sciences Table SARS_CoV_2 C3037T 0 9 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. D614G 2021 Current research in microbial sciences Table SARS_CoV_2 D614G 0 5 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. F106F 2021 Current research in microbial sciences Table SARS_CoV_2 F106F 0 5 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. F924F 2021 Current research in microbial sciences Table SARS_CoV_2 F924F 0 5 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. G251V 2021 Current research in microbial sciences Table SARS_CoV_2 G251V 0 5 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. I120F 2021 Current research in microbial sciences Table SARS_CoV_2 I120F 0 5 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. I300F 2021 Current research in microbial sciences Table SARS_CoV_2 I300F 0 5 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. L3606F 2021 Current research in microbial sciences Table SARS_CoV_2 L3606F 0 6 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. L84S 2021 Current research in microbial sciences Table SARS_CoV_2 L84S 0 4 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. P323L 2021 Current research in microbial sciences Table SARS_CoV_2 P323L 0 5 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. P4715L 2021 Current research in microbial sciences Table SARS_CoV_2 P4715L 0 6 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Q57H 2021 Current research in microbial sciences Table SARS_CoV_2 Q57H 0 4 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. S194L 2021 Microbial genomics Table SARS_CoV_2 S194L 0 5 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. T478K 2021 Microbial genomics Table SARS_CoV_2 T478K 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. 119del 2022 Infection, genetics and evolution Table SARS_CoV_2 119del 0 6 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. A222V 2022 Infection, genetics and evolution Table SARS_CoV_2 A222V 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. A446V 2022 Infection, genetics and evolution Table SARS_CoV_2 A446V 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. A570D 2022 Infection, genetics and evolution Table SARS_CoV_2 A570D 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. A890D 2022 Infection, genetics and evolution Table SARS_CoV_2 A890D 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. D1118H 2022 Infection, genetics and evolution Table SARS_CoV_2 D1118H 0 6 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. D138Y 2022 Infection, genetics and evolution Table SARS_CoV_2 D138Y 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. D215G 2022 Infection, genetics and evolution Table SARS_CoV_2 D215G 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. D253G 2022 Infection, genetics and evolution Table SARS_CoV_2 D253G 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. D377Y 2022 Infection, genetics and evolution Table SARS_CoV_2 D377Y 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. D614G 2022 Infection, genetics and evolution Table SARS_CoV_2 D614G 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. D63G 2022 Infection, genetics and evolution Table SARS_CoV_2 D63G 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. D80A 2022 Infection, genetics and evolution Table SARS_CoV_2 D80A 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. E341D 2022 Infection, genetics and evolution Table SARS_CoV_2 E341D 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. E484K 2022 Infection, genetics and evolution Table SARS_CoV_2 E484K 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. E92K 2022 Infection, genetics and evolution Table SARS_CoV_2 E92K 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. G121V 2022 Infection, genetics and evolution Table SARS_CoV_2 G121V 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. G1251V 2022 Infection, genetics and evolution Table SARS_CoV_2 G1251V 0 6 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. G15S 2022 Infection, genetics and evolution Table SARS_CoV_2 G15S 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. G204del 2022 Infection, genetics and evolution Table SARS_CoV_2 G204del 0 7 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. G204R 2022 Infection, genetics and evolution Table SARS_CoV_2 G204R 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. G212V 2022 Infection, genetics and evolution Table SARS_CoV_2 G212V 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. G671S 2022 Infection, genetics and evolution Table SARS_CoV_2 G671S 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. H655Y 2022 Infection, genetics and evolution Table SARS_CoV_2 H655Y 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. H69del 2022 Infection, genetics and evolution Table SARS_CoV_2 H69del 0 6 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. I1412T 2022 Infection, genetics and evolution Table SARS_CoV_2 I1412T 0 6 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. I49V 2022 Infection, genetics and evolution Table SARS_CoV_2 I49V 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. I82T 2022 Infection, genetics and evolution Table SARS_CoV_2 I82T 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. K259R 2022 Infection, genetics and evolution Table SARS_CoV_2 K259R 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. K417T 2022 Infection, genetics and evolution Table SARS_CoV_2 K417T 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. K837N 2022 Infection, genetics and evolution Table SARS_CoV_2 K837N 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. K977Q 2022 Infection, genetics and evolution Table SARS_CoV_2 K977Q 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. L18F 2022 Infection, genetics and evolution Table SARS_CoV_2 L18F 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. L21F 2022 Infection, genetics and evolution Table SARS_CoV_2 L21F 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. L438P 2022 Infection, genetics and evolution Table SARS_CoV_2 L438P 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. L452R 2022 Infection, genetics and evolution Table SARS_CoV_2 L452R 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. L75F 2022 Infection, genetics and evolution Table SARS_CoV_2 L75F 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. L84S 2022 Infection, genetics and evolution Table SARS_CoV_2 L84S 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. L89F 2022 Infection, genetics and evolution Table SARS_CoV_2 L89F 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. M429I 2022 Infection, genetics and evolution Table SARS_CoV_2 M429I 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. N129D 2022 Infection, genetics and evolution Table SARS_CoV_2 N129D 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. N439K 2022 Infection, genetics and evolution Table SARS_CoV_2 N439K 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. N501Y 2022 Infection, genetics and evolution Table SARS_CoV_2 N501Y 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. P141S 2022 Infection, genetics and evolution Table SARS_CoV_2 P141S 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. P199L 2022 Infection, genetics and evolution Table SARS_CoV_2 P199L 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. P26S 2022 Infection, genetics and evolution Table SARS_CoV_2 P26S 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. P323L 2022 Infection, genetics and evolution Table SARS_CoV_2 P323L 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. P42L 2022 Infection, genetics and evolution Table SARS_CoV_2 P42L 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. P67S 2022 Infection, genetics and evolution Table SARS_CoV_2 P67S 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. P681H 2022 Infection, genetics and evolution Table SARS_CoV_2 P681H 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. P681R 2022 Infection, genetics and evolution Table SARS_CoV_2 P681R 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. P77L 2022 Infection, genetics and evolution Table SARS_CoV_2 P77L 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. P80R 2022 Infection, genetics and evolution Table SARS_CoV_2 P80R 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. P822L 2022 Infection, genetics and evolution Table SARS_CoV_2 P822L 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Q57H 2022 Infection, genetics and evolution Table SARS_CoV_2 Q57H 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Q677H 2022 Infection, genetics and evolution Table SARS_CoV_2 Q677H 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. R203K 2022 Infection, genetics and evolution Table SARS_CoV_2 R203K 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. R203M 2022 Infection, genetics and evolution Table SARS_CoV_2 R203M 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. R216C 2022 Infection, genetics and evolution Table SARS_CoV_2 R216C 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. R52I 2022 Infection, genetics and evolution Table SARS_CoV_2 R52I 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. S126L 2022 Infection, genetics and evolution Table SARS_CoV_2 S126L 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. S171L 2022 Infection, genetics and evolution Table SARS_CoV_2 S171L 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. S235F 2022 Infection, genetics and evolution Table SARS_CoV_2 S235F 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. S24L 2022 Infection, genetics and evolution Table SARS_CoV_2 S24L 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. S253P 2022 Infection, genetics and evolution Table SARS_CoV_2 S253P 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. S259L 2022 Infection, genetics and evolution Table SARS_CoV_2 S259L 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. S261A 2022 Infection, genetics and evolution Table SARS_CoV_2 S261A 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. S26L 2022 Infection, genetics and evolution Table SARS_CoV_2 S26L 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. S370L 2022 Infection, genetics and evolution Table SARS_CoV_2 S370L 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. S982A 2022 Infection, genetics and evolution Table SARS_CoV_2 S982A 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T1027I 2022 Infection, genetics and evolution Table SARS_CoV_2 T1027I 0 6 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T11I 2022 Infection, genetics and evolution Table SARS_CoV_2 T11I 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T148I 2022 Infection, genetics and evolution Table SARS_CoV_2 T148I 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T181I 2022 Infection, genetics and evolution Table SARS_CoV_2 T181I 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T183I 2022 Infection, genetics and evolution Table SARS_CoV_2 T183I 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T19R 2022 Infection, genetics and evolution Table SARS_CoV_2 T19R 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T205I 2022 Infection, genetics and evolution Table SARS_CoV_2 T205I 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T20N 2022 Infection, genetics and evolution Table SARS_CoV_2 T20N 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T350I 2022 Infection, genetics and evolution Table SARS_CoV_2 T350I 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T35I 2022 Infection, genetics and evolution Table SARS_CoV_2 T35I 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T428I 2022 Infection, genetics and evolution Table SARS_CoV_2 T428I 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T478K 2022 Infection, genetics and evolution Table SARS_CoV_2 T478K 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T492I 2022 Infection, genetics and evolution Table SARS_CoV_2 T492I 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T716I 2022 Infection, genetics and evolution Table SARS_CoV_2 T716I 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T732A 2022 Infection, genetics and evolution Table SARS_CoV_2 T732A 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T749I 2022 Infection, genetics and evolution Table SARS_CoV_2 T749I 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T77A 2022 Infection, genetics and evolution Table SARS_CoV_2 T77A 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T85I 2022 Infection, genetics and evolution Table SARS_CoV_2 T85I 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. T95I 2022 Infection, genetics and evolution Table SARS_CoV_2 T95I 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. V1176F 2022 Infection, genetics and evolution Table SARS_CoV_2 V1176F 0 6 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. V143del 2022 Infection, genetics and evolution Table SARS_CoV_2 V143del 0 7 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. V149A 2022 Infection, genetics and evolution Table SARS_CoV_2 V149A 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. V70L 2022 Infection, genetics and evolution Table SARS_CoV_2 V70L 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. V82A 2022 Infection, genetics and evolution Table SARS_CoV_2 V82A 0 4 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. W152C 2022 Infection, genetics and evolution Table SARS_CoV_2 W152C 0 5 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Y73C 2022 Infection, genetics and evolution Table SARS_CoV_2 Y73C 0 4 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. E484K 2021 Analytical chemistry Table SARS_CoV_2 E484K 0 5 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. N501Y 2021 Analytical chemistry Table SARS_CoV_2 N501Y 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. A1049V 2021 Microbiology resource announcements Table SARS_CoV_2 A1049V 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. A1306S 2021 Microbiology resource announcements Table SARS_CoV_2 A1306S 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. A1918V 2021 Microbiology resource announcements Table SARS_CoV_2 A1918V 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. A540V 2021 Microbiology resource announcements Table SARS_CoV_2 A540V 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. A576V 2021 Microbiology resource announcements Table SARS_CoV_2 A576V 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. A583V 2021 Microbiology resource announcements Table SARS_CoV_2 A583V 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. A845S 2021 Microbiology resource announcements Table SARS_CoV_2 A845S 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. C2691V 2021 Microbiology resource announcements Table SARS_CoV_2 C2691V 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. D1869Y 2021 Microbiology resource announcements Table SARS_CoV_2 D1869Y 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. D2429Y 2021 Microbiology resource announcements Table SARS_CoV_2 D2429Y 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. E1377G 2021 Microbiology resource announcements Table SARS_CoV_2 E1377G 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. E148G 2021 Microbiology resource announcements Table SARS_CoV_2 E148G 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. F116L 2021 Microbiology resource announcements Table SARS_CoV_2 F116L 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. F1504L 2021 Microbiology resource announcements Table SARS_CoV_2 F1504L 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. F15L 2021 Microbiology resource announcements Table SARS_CoV_2 F15L 0 4 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. G519S 2021 Microbiology resource announcements Table SARS_CoV_2 G519S 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. H1067Y 2021 Microbiology resource announcements Table SARS_CoV_2 H1067Y 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. H2571Y 2021 Microbiology resource announcements Table SARS_CoV_2 H2571Y 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. I2689S 2021 Microbiology resource announcements Table SARS_CoV_2 I2689S 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. I76F 2021 Microbiology resource announcements Table SARS_CoV_2 I76F 0 4 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. K1230N 2021 Microbiology resource announcements Table SARS_CoV_2 K1230N 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. K385R 2021 Microbiology resource announcements Table SARS_CoV_2 K385R 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. L139F 2021 Microbiology resource announcements Table SARS_CoV_2 L139F 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. L140F 2021 Microbiology resource announcements Table SARS_CoV_2 L140F 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. L1640P 2021 Microbiology resource announcements Table SARS_CoV_2 L1640P 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. L230F 2021 Microbiology resource announcements Table SARS_CoV_2 L230F 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. L2687I 2021 Microbiology resource announcements Table SARS_CoV_2 L2687I 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. L2695N 2021 Microbiology resource announcements Table SARS_CoV_2 L2695N 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. L2780F 2021 Microbiology resource announcements Table SARS_CoV_2 L2780F 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. L309P 2021 Microbiology resource announcements Table SARS_CoV_2 L309P 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. L3330S 2021 Microbiology resource announcements Table SARS_CoV_2 L3330S 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. L3829F 2021 Microbiology resource announcements Table SARS_CoV_2 L3829F 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. L60F 2021 Microbiology resource announcements Table SARS_CoV_2 L60F 0 4 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. L73F 2021 Microbiology resource announcements Table SARS_CoV_2 L73F 0 4 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. M1586I 2021 Microbiology resource announcements Table SARS_CoV_2 M1586I 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. P10S 2021 Microbiology resource announcements Table SARS_CoV_2 P10S 0 4 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. P2046L 2021 Microbiology resource announcements Table SARS_CoV_2 P2046L 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. P2287S 2021 Microbiology resource announcements Table SARS_CoV_2 P2287S 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. P3359S 2021 Microbiology resource announcements Table SARS_CoV_2 P3359S 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. P3504L 2021 Microbiology resource announcements Table SARS_CoV_2 P3504L 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. P45L 2021 Microbiology resource announcements Table SARS_CoV_2 P45L 0 4 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. P809S 2021 Microbiology resource announcements Table SARS_CoV_2 P809S 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. Q2615R 2021 Microbiology resource announcements Table SARS_CoV_2 Q2615R 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. R1383K 2021 Microbiology resource announcements Table SARS_CoV_2 R1383K 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. R2692L 2021 Microbiology resource announcements Table SARS_CoV_2 R2692L 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. S2690D 2021 Microbiology resource announcements Table SARS_CoV_2 S2690D 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. S2693V 2021 Microbiology resource announcements Table SARS_CoV_2 S2693V 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. S477I 2021 Microbiology resource announcements Table SARS_CoV_2 S477I 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. S759G 2021 Microbiology resource announcements Table SARS_CoV_2 S759G 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. T14I 2021 Microbiology resource announcements Table SARS_CoV_2 T14I 0 4 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. T284I 2021 Microbiology resource announcements Table SARS_CoV_2 T284I 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. T3058I 2021 Microbiology resource announcements Table SARS_CoV_2 T3058I 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. T3255I 2021 Microbiology resource announcements Table SARS_CoV_2 T3255I 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. T3646A 2021 Microbiology resource announcements Table SARS_CoV_2 T3646A 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. T40I 2021 Microbiology resource announcements Table SARS_CoV_2 T40I 0 4 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. V1122L 2021 Microbiology resource announcements Table SARS_CoV_2 V1122L 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. V2694N 2021 Microbiology resource announcements Table SARS_CoV_2 V2694N 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. V273M 2021 Microbiology resource announcements Table SARS_CoV_2 V273M 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. V2930L 2021 Microbiology resource announcements Table SARS_CoV_2 V2930L 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. V3209A 2021 Microbiology resource announcements Table SARS_CoV_2 V3209A 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. V3690L 2021 Microbiology resource announcements Table SARS_CoV_2 V3690L 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. V62F 2021 Microbiology resource announcements Table SARS_CoV_2 V62F 0 4 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. W131C 2021 Microbiology resource announcements Table SARS_CoV_2 W131C 0 5 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. W45L 2021 Microbiology resource announcements Table SARS_CoV_2 W45L 0 4 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. Y2092H 2021 Microbiology resource announcements Table SARS_CoV_2 Y2092H 0 6 34854728 Coding-Complete Genome Sequences of Alpha and Delta SARS-CoV-2 Variants from Kamphaeng Phet Province, Thailand, from May to July 2021. Y2285H 2021 Microbiology resource announcements Table SARS_CoV_2 Y2285H 0 6 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. D614G 2021 Frontiers in immunology Table SARS_CoV_2 D614G 0 5 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. A423V 2021 Microbial genomics Table SARS_CoV_2 A423V 0 5 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. D614G 2021 Microbial genomics Table SARS_CoV_2 D614G 0 5 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. K204R 2021 Microbial genomics Table SARS_CoV_2 K204R 0 5 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. L37F 2021 Microbial genomics Table SARS_CoV_2 L37F 0 4 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. L84S 2021 Microbial genomics Table SARS_CoV_2 L84S 0 4 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. M234I 2021 Microbial genomics Table SARS_CoV_2 M234I 0 5 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. P108S 2021 Microbial genomics Table SARS_CoV_2 P108S 0 5 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. P151L 2021 Microbial genomics Table SARS_CoV_2 P151L 0 5 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. P323L 2021 Microbial genomics Table SARS_CoV_2 P323L 0 5 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. P43H 2021 Microbial genomics Table SARS_CoV_2 P43H 0 4 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. P43L 2021 Microbial genomics Table SARS_CoV_2 P43L 0 4 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. Q57H 2021 Microbial genomics Table SARS_CoV_2 Q57H 0 4 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. R203K 2021 Microbial genomics Table SARS_CoV_2 R203K 0 5 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. R287I 2021 Microbial genomics Table SARS_CoV_2 R287I 0 5 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. S543P 2021 Microbial genomics Table SARS_CoV_2 S543P 0 5 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. T85I 2021 Microbial genomics Table SARS_CoV_2 T85I 0 4 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. V70F 2021 Microbial genomics Table SARS_CoV_2 V70F 0 4 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. V70I 2021 Microbial genomics Table SARS_CoV_2 V70I 0 4 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. V70L 2021 Microbial genomics Table SARS_CoV_2 V70L 0 4 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Ala222Val 2021 PloS one Table SARS_CoV_2 A222V 0 9 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Arg204Lys 2021 PloS one Table SARS_CoV_2 R204K 0 9 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Asp614Gly 2021 PloS one Table SARS_CoV_2 D614G 0 9 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Gln57His 2021 PloS one Table SARS_CoV_2 Q57H 0 8 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Gly205Arg 2021 PloS one Table SARS_CoV_2 G205R 0 9 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Ile436Ile 2021 PloS one Table SARS_CoV_2 I436I 0 9 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Leu13Phe 2021 PloS one Table SARS_CoV_2 L13F 0 8 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Leu280Leu 2021 PloS one Table SARS_CoV_2 L280L 0 9 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Leu42Phe 2021 PloS one Table SARS_CoV_2 L42F 0 8 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Met429Ile 2021 PloS one Table SARS_CoV_2 M429I 0 9 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Phe106Phe 2021 PloS one Table SARS_CoV_2 F106F 0 9 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Pro323Leu 2021 PloS one Table SARS_CoV_2 P323L 0 9 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Pro412Pro 2021 PloS one Table SARS_CoV_2 P412P 0 9 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Ser1682Ser 2021 PloS one Table SARS_CoV_2 S1682S 0 10 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. Ser485Leu 2021 PloS one Table SARS_CoV_2 S485L 0 9 34871906 Highly sensitive and specific detection of the SARS-CoV-2 Delta variant by double-mismatch allele-specific real time reverse transcription PCR. D614G 2022 Journal of clinical virology Table SARS_CoV_2 D614G 0 5 34876606 N-glycosylation profiles of the SARS-CoV-2 spike D614G mutant and its ancestral protein characterized by advanced mass spectrometry. D614G 2021 Scientific reports Table SARS_CoV_2 D614G 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. A653V 2021 Infection and drug resistance Table SARS_CoV_2 A653V 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. A701V 2021 Infection and drug resistance Table SARS_CoV_2 A701V 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. D614G 2021 Infection and drug resistance Table SARS_CoV_2 D614G 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. E484K 2021 Infection and drug resistance Table SARS_CoV_2 E484K 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. E484Q 2021 Infection and drug resistance Table SARS_CoV_2 E484Q 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. E516Q 2021 Infection and drug resistance Table SARS_CoV_2 E516Q 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. F490S 2021 Infection and drug resistance Table SARS_CoV_2 F490S 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. G669S 2021 Infection and drug resistance Table SARS_CoV_2 G669S 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. H655Y 2021 Infection and drug resistance Table SARS_CoV_2 H655Y 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. K417N 2021 Infection and drug resistance Table SARS_CoV_2 K417N 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. K417T 2021 Infection and drug resistance Table SARS_CoV_2 K417T 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. L452Q 2021 Infection and drug resistance Table SARS_CoV_2 L452Q 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. L452R 2021 Infection and drug resistance Table SARS_CoV_2 L452R 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. N439K 2021 Infection and drug resistance Table SARS_CoV_2 N439K 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. N450K 2021 Infection and drug resistance Table SARS_CoV_2 N450K 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. N501T 2021 Infection and drug resistance Table SARS_CoV_2 N501T 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. N501Y 2021 Infection and drug resistance Table SARS_CoV_2 N501Y 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. N679K 2021 Infection and drug resistance Table SARS_CoV_2 N679K 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. P384L 2021 Infection and drug resistance Table SARS_CoV_2 P384L 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. P681H 2021 Infection and drug resistance Table SARS_CoV_2 P681H 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. P681R 2021 Infection and drug resistance Table SARS_CoV_2 P681R 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. Q414K 2021 Infection and drug resistance Table SARS_CoV_2 Q414K 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. Q613H 2021 Infection and drug resistance Table SARS_CoV_2 Q613H 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. Q677H 2021 Infection and drug resistance Table SARS_CoV_2 Q677H 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. R346K 2021 Infection and drug resistance Table SARS_CoV_2 R346K 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. S477N 2021 Infection and drug resistance Table SARS_CoV_2 S477N 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. S494P 2021 Infection and drug resistance Table SARS_CoV_2 S494P 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. T478K 2021 Infection and drug resistance Table SARS_CoV_2 T478K 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. V367F 2021 Infection and drug resistance Table SARS_CoV_2 V367F 0 5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. V483A 2021 Infection and drug resistance Table SARS_CoV_2 V483A 0 5 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. D614G 2021 Euro surveillance Table SARS_CoV_2 D614G 0 5 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. E484K 2021 Euro surveillance Table SARS_CoV_2 E484K 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. A243del 2022 Gene Table SARS_CoV_2 A243del 0 7 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. A262T 2022 Gene Table SARS_CoV_2 A262T 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. A570D 2022 Gene Table SARS_CoV_2 A570D 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. A672P 2022 Gene Table SARS_CoV_2 A672P 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. A701V 2022 Gene Table SARS_CoV_2 A701V 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. C1250R 2022 Gene Table SARS_CoV_2 C1250R 0 6 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. C617R 2022 Gene Table SARS_CoV_2 C617R 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D1118H 2022 Gene Table SARS_CoV_2 D1118H 0 6 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D111N 2022 Gene Table SARS_CoV_2 D111N 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D1257E 2022 Gene Table SARS_CoV_2 D1257E 0 6 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D138Y 2022 Gene Table SARS_CoV_2 D138Y 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D215G 2022 Gene Table SARS_CoV_2 D215G 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D287Y 2022 Gene Table SARS_CoV_2 D287Y 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D467N 2022 Gene Table SARS_CoV_2 D467N 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D574N 2022 Gene Table SARS_CoV_2 D574N 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D574Y 2022 Gene Table SARS_CoV_2 D574Y 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D586E 2022 Gene Table SARS_CoV_2 D586E 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D614G 2022 Gene Table SARS_CoV_2 D614G 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D796H 2022 Gene Table SARS_CoV_2 D796H 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D796N 2022 Gene Table SARS_CoV_2 D796N 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D80A 2022 Gene Table SARS_CoV_2 D80A 0 4 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D843E 2022 Gene Table SARS_CoV_2 D843E 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D843G 2022 Gene Table SARS_CoV_2 D843G 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D936Y 2022 Gene Table SARS_CoV_2 D936Y 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. D950N 2022 Gene Table SARS_CoV_2 D950N 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. E1202Q 2022 Gene Table SARS_CoV_2 E1202Q 0 6 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. E484K 2022 Gene Table SARS_CoV_2 E484K 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. E583A 2022 Gene Table SARS_CoV_2 E583A 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. E661K 2022 Gene Table SARS_CoV_2 E661K 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. F1256L 2022 Gene Table SARS_CoV_2 F1256L 0 6 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. G142D 2022 Gene Table SARS_CoV_2 G142D 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. G181V 2022 Gene Table SARS_CoV_2 G181V 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. G485S 2022 Gene Table SARS_CoV_2 G485S 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. G652R 2022 Gene Table SARS_CoV_2 G652R 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. G932A 2022 Gene Table SARS_CoV_2 G932A 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. H49Y 2022 Gene Table SARS_CoV_2 H49Y 0 4 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. H519Y 2022 Gene Table SARS_CoV_2 H519Y 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. H655Y 2022 Gene Table SARS_CoV_2 H655Y 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. H66L 2022 Gene Table SARS_CoV_2 H66L 0 4 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. H69del 2022 Gene Table SARS_CoV_2 H69del 0 6 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. I100T 2022 Gene Table SARS_CoV_2 I100T 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. I210del 2022 Gene Table SARS_CoV_2 I210del 0 7 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. I726F 2022 Gene Table SARS_CoV_2 I726F 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. K150I 2022 Gene Table SARS_CoV_2 K150I 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. K182N 2022 Gene Table SARS_CoV_2 K182N 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. K417N 2022 Gene Table SARS_CoV_2 K417N 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. K417N/T 2022 Gene Table SARS_CoV_2 K417N;K417T 0;0 7;7 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. K417T 2022 Gene Table SARS_CoV_2 K417T 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. K77N 2022 Gene Table SARS_CoV_2 K77N 0 4 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. K77T 2022 Gene Table SARS_CoV_2 K77T 0 4 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. K811N 2022 Gene Table SARS_CoV_2 K811N 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. K835N 2022 Gene Table SARS_CoV_2 K835N 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. L1141W 2022 Gene Table SARS_CoV_2 L1141W 0 6 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. L176F 2022 Gene Table SARS_CoV_2 L176F 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. L179P 2022 Gene Table SARS_CoV_2 L179P 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. L212I 2022 Gene Table SARS_CoV_2 L212I 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. L242del 2022 Gene Table SARS_CoV_2 L242del 0 7 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. L244del 2022 Gene Table SARS_CoV_2 L244del 0 7 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. L452R 2022 Gene Table SARS_CoV_2 L452R 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. L54F 2022 Gene Table SARS_CoV_2 L54F 0 4 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. L699I 2022 Gene Table SARS_CoV_2 L699I 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. L841I 2022 Gene Table SARS_CoV_2 L841I 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. L938F 2022 Gene Table SARS_CoV_2 L938F 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. M177I 2022 Gene Table SARS_CoV_2 M177I 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. N211del 2022 Gene Table SARS_CoV_2 N211del 0 7 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. N439K 2022 Gene Table SARS_CoV_2 N439K 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. N460I 2022 Gene Table SARS_CoV_2 N460I 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. N487H 2022 Gene Table SARS_CoV_2 N487H 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. N487I 2022 Gene Table SARS_CoV_2 N487I 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. N501T 2022 Gene Table SARS_CoV_2 N501T 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. N501Y 2022 Gene Table SARS_CoV_2 N501Y 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. N536K 2022 Gene Table SARS_CoV_2 N536K 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. N542T 2022 Gene Table SARS_CoV_2 N542T 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. N603K 2022 Gene Table SARS_CoV_2 N603K 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. N606Y 2022 Gene Table SARS_CoV_2 N606Y 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. N641K 2022 Gene Table SARS_CoV_2 N641K 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. N74H 2022 Gene Table SARS_CoV_2 N74H 0 4 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. N925Y 2022 Gene Table SARS_CoV_2 N925Y 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. P1263L 2022 Gene Table SARS_CoV_2 P1263L 0 6 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. P225T 2022 Gene Table SARS_CoV_2 P225T 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. P412S 2022 Gene Table SARS_CoV_2 P412S 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. P479L 2022 Gene Table SARS_CoV_2 P479L 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. P499T 2022 Gene Table SARS_CoV_2 P499T 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. P681H 2022 Gene Table SARS_CoV_2 P681H 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. P681R 2022 Gene Table SARS_CoV_2 P681R 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. P863H 2022 Gene Table SARS_CoV_2 P863H 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Q115H 2022 Gene Table SARS_CoV_2 Q115H 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Q23H 2022 Gene Table SARS_CoV_2 Q23H 0 4 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Q271R 2022 Gene Table SARS_CoV_2 Q271R 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Q314R 2022 Gene Table SARS_CoV_2 Q314R 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Q498Y 2022 Gene Table SARS_CoV_2 Q498Y 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Q675H 2022 Gene Table SARS_CoV_2 Q675H 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Q675R 2022 Gene Table SARS_CoV_2 Q675R 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Q677H 2022 Gene Table SARS_CoV_2 Q677H 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. R158G 2022 Gene Table SARS_CoV_2 R158G 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. R21K 2022 Gene Table SARS_CoV_2 R21K 0 4 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. R246I 2022 Gene Table SARS_CoV_2 R246I 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. R328T 2022 Gene Table SARS_CoV_2 R328T 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. R408K 2022 Gene Table SARS_CoV_2 R408K 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. R44K 2022 Gene Table SARS_CoV_2 R44K 0 4 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. S1021P 2022 Gene Table SARS_CoV_2 S1021P 0 6 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. S112P 2022 Gene Table SARS_CoV_2 S112P 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. S254F 2022 Gene Table SARS_CoV_2 S254F 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. S459Y 2022 Gene Table SARS_CoV_2 S459Y 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. S477N 2022 Gene Table SARS_CoV_2 S477N 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. S758I 2022 Gene Table SARS_CoV_2 S758I 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. S982A 2022 Gene Table SARS_CoV_2 S982A 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. T19R 2022 Gene Table SARS_CoV_2 T19R 0 4 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. T22N 2022 Gene Table SARS_CoV_2 T22N 0 4 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. T478K 2022 Gene Table SARS_CoV_2 T478K 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. T602K 2022 Gene Table SARS_CoV_2 T602K 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. T716I 2022 Gene Table SARS_CoV_2 T716I 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. T716P 2022 Gene Table SARS_CoV_2 T716P 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. T791P 2022 Gene Table SARS_CoV_2 T791P 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. T827A 2022 Gene Table SARS_CoV_2 T827A 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. T874P 2022 Gene Table SARS_CoV_2 T874P 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. T941P 2022 Gene Table SARS_CoV_2 T941P 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. T95I 2022 Gene Table SARS_CoV_2 T95I 0 4 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. V11I 2022 Gene Table SARS_CoV_2 V11I 0 4 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. V171L 2022 Gene Table SARS_CoV_2 V171L 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. V289E 2022 Gene Table SARS_CoV_2 V289E 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. V407L 2022 Gene Table SARS_CoV_2 V407L 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. V620F 2022 Gene Table SARS_CoV_2 V620F 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. V620I 2022 Gene Table SARS_CoV_2 V620I 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. V70del 2022 Gene Table SARS_CoV_2 V70del 0 6 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. V781F 2022 Gene Table SARS_CoV_2 V781F 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. V976F 2022 Gene Table SARS_CoV_2 V976F 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. V987F 2022 Gene Table SARS_CoV_2 V987F 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Y144D 2022 Gene Table SARS_CoV_2 Y144D 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Y144del 2022 Gene Table SARS_CoV_2 Y144del 0 7 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Y200N 2022 Gene Table SARS_CoV_2 Y200N 0 5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Y873N 2022 Gene Table SARS_CoV_2 Y873N 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A110V 2022 Journal of infection and public health Table SARS_CoV_2 A110V 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A129V 2022 Journal of infection and public health Table SARS_CoV_2 A129V 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A150V 2022 Journal of infection and public health Table SARS_CoV_2 A150V 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A152V 2022 Journal of infection and public health Table SARS_CoV_2 A152V 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A15V 2022 Journal of infection and public health Table SARS_CoV_2 A15V 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A1711V 2022 Journal of infection and public health Table SARS_CoV_2 A1711V 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A171V 2022 Journal of infection and public health Table SARS_CoV_2 A171V 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A174T 2022 Journal of infection and public health Table SARS_CoV_2 A174T 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A243del 2022 Journal of infection and public health Table SARS_CoV_2 A243del 0 7 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A274S 2022 Journal of infection and public health Table SARS_CoV_2 A274S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A296S 2022 Journal of infection and public health Table SARS_CoV_2 A296S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A318S 2022 Journal of infection and public health Table SARS_CoV_2 A318S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A34V 2022 Journal of infection and public health Table SARS_CoV_2 A34V 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A35V 2022 Journal of infection and public health Table SARS_CoV_2 A35V 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A476V 2022 Journal of infection and public health Table SARS_CoV_2 A476V 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A614V 2022 Journal of infection and public health Table SARS_CoV_2 A614V 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A690V 2022 Journal of infection and public health Table SARS_CoV_2 A690V 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A81V 2022 Journal of infection and public health Table SARS_CoV_2 A81V 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A845S 2022 Journal of infection and public health Table SARS_CoV_2 A845S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. A861S 2022 Journal of infection and public health Table SARS_CoV_2 A861S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. C102F 2022 Journal of infection and public health Table SARS_CoV_2 C102F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. C133F 2022 Journal of infection and public health Table SARS_CoV_2 C133F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. C1392F 2022 Journal of infection and public health Table SARS_CoV_2 C1392F 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. D128H 2022 Journal of infection and public health Table SARS_CoV_2 D128H 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. D128Y 2022 Journal of infection and public health Table SARS_CoV_2 D128Y 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. D135Y 2022 Journal of infection and public health Table SARS_CoV_2 D135Y 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. D144G 2022 Journal of infection and public health Table SARS_CoV_2 D144G 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. D201Y 2022 Journal of infection and public health Table SARS_CoV_2 D201Y 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. D265Y 2022 Journal of infection and public health Table SARS_CoV_2 D265Y 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. D279N 2022 Journal of infection and public health Table SARS_CoV_2 D279N 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. D300N 2022 Journal of infection and public health Table SARS_CoV_2 D300N 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. D402H 2022 Journal of infection and public health Table SARS_CoV_2 D402H 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. D614G 2022 Journal of infection and public health Table SARS_CoV_2 D614G 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. E156G 2022 Journal of infection and public health Table SARS_CoV_2 E156G 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. E157del 2022 Journal of infection and public health Table SARS_CoV_2 E157del 0 7 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. E484K 2022 Journal of infection and public health Table SARS_CoV_2 E484K 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. E583Q 2022 Journal of infection and public health Table SARS_CoV_2 E583Q 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. E919D 2022 Journal of infection and public health Table SARS_CoV_2 E919D 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. F184V 2022 Journal of infection and public health Table SARS_CoV_2 F184V 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. G11R 2022 Journal of infection and public health Table SARS_CoV_2 G11R 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. G132D 2022 Journal of infection and public health Table SARS_CoV_2 G132D 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. G172C 2022 Journal of infection and public health Table SARS_CoV_2 G172C 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. G184V 2022 Journal of infection and public health Table SARS_CoV_2 G184V 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. G204R 2022 Journal of infection and public health Table SARS_CoV_2 G204R 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. G251C 2022 Journal of infection and public health Table SARS_CoV_2 G251C 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. G265C 2022 Journal of infection and public health Table SARS_CoV_2 G265C 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. G277R 2022 Journal of infection and public health Table SARS_CoV_2 G277R 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. G277S 2022 Journal of infection and public health Table SARS_CoV_2 G277S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. G30R 2022 Journal of infection and public health Table SARS_CoV_2 G30R 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. G38S 2022 Journal of infection and public health Table SARS_CoV_2 G38S 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. G38V 2022 Journal of infection and public health Table SARS_CoV_2 G38V 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. G44C 2022 Journal of infection and public health Table SARS_CoV_2 G44C 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. G72R 2022 Journal of infection and public health Table SARS_CoV_2 G72R 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. H290Y 2022 Journal of infection and public health Table SARS_CoV_2 H290Y 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. H31Y 2022 Journal of infection and public health Table SARS_CoV_2 H31Y 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. H49Y 2022 Journal of infection and public health Table SARS_CoV_2 H49Y 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. H78Y 2022 Journal of infection and public health Table SARS_CoV_2 H78Y 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. I1130M 2022 Journal of infection and public health Table SARS_CoV_2 I1130M 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. I224T 2022 Journal of infection and public health Table SARS_CoV_2 I224T 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. I273T 2022 Journal of infection and public health Table SARS_CoV_2 I273T 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. I587S 2022 Journal of infection and public health Table SARS_CoV_2 I587S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. I76M 2022 Journal of infection and public health Table SARS_CoV_2 I76M 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. K109N 2022 Journal of infection and public health Table SARS_CoV_2 K109N 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. K1181N 2022 Journal of infection and public health Table SARS_CoV_2 K1181N 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. K1191N 2022 Journal of infection and public health Table SARS_CoV_2 K1191N 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. K160R 2022 Journal of infection and public health Table SARS_CoV_2 K160R 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. K182N 2022 Journal of infection and public health Table SARS_CoV_2 K182N 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. K525R 2022 Journal of infection and public health Table SARS_CoV_2 K525R 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. K67N 2022 Journal of infection and public health Table SARS_CoV_2 K67N 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. K90R 2022 Journal of infection and public health Table SARS_CoV_2 K90R 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. K91R 2022 Journal of infection and public health Table SARS_CoV_2 K91R 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L1137F 2022 Journal of infection and public health Table SARS_CoV_2 L1137F 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L1200F 2022 Journal of infection and public health Table SARS_CoV_2 L1200F 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L1259F 2022 Journal of infection and public health Table SARS_CoV_2 L1259F 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L126F 2022 Journal of infection and public health Table SARS_CoV_2 L126F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L152I 2022 Journal of infection and public health Table SARS_CoV_2 L152I 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L198F 2022 Journal of infection and public health Table SARS_CoV_2 L198F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L244del 2022 Journal of infection and public health Table SARS_CoV_2 L244del 0 7 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L264F 2022 Journal of infection and public health Table SARS_CoV_2 L264F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L353F 2022 Journal of infection and public health Table SARS_CoV_2 L353F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L37F 2022 Journal of infection and public health Table SARS_CoV_2 L37F 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L451F 2022 Journal of infection and public health Table SARS_CoV_2 L451F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L49I 2022 Journal of infection and public health Table SARS_CoV_2 L49I 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L53F 2022 Journal of infection and public health Table SARS_CoV_2 L53F 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L54F 2022 Journal of infection and public health Table SARS_CoV_2 L54F 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L58F 2022 Journal of infection and public health Table SARS_CoV_2 L58F 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L620F 2022 Journal of infection and public health Table SARS_CoV_2 L620F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L689G 2022 Journal of infection and public health Table SARS_CoV_2 L689G 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. L95F 2022 Journal of infection and public health Table SARS_CoV_2 L95F 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. M1788T 2022 Journal of infection and public health Table SARS_CoV_2 M1788T 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. M196I 2022 Journal of infection and public health Table SARS_CoV_2 M196I 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. M330T 2022 Journal of infection and public health Table SARS_CoV_2 M330T 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. M829V 2022 Journal of infection and public health Table SARS_CoV_2 M829V 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. N1263T 2022 Journal of infection and public health Table SARS_CoV_2 N1263T 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P1044S 2022 Journal of infection and public health Table SARS_CoV_2 P1044S 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P122L 2022 Journal of infection and public health Table SARS_CoV_2 P122L 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P1292S 2022 Journal of infection and public health Table SARS_CoV_2 P1292S 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P129S 2022 Journal of infection and public health Table SARS_CoV_2 P129S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P133S 2022 Journal of infection and public health Table SARS_CoV_2 P133S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P13L 2022 Journal of infection and public health Table SARS_CoV_2 P13L 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P153L 2022 Journal of infection and public health Table SARS_CoV_2 P153L 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P240S 2022 Journal of infection and public health Table SARS_CoV_2 P240S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P262S 2022 Journal of infection and public health Table SARS_CoV_2 P262S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P26S 2022 Journal of infection and public health Table SARS_CoV_2 P26S 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P279L 2022 Journal of infection and public health Table SARS_CoV_2 P279L 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P297S 2022 Journal of infection and public health Table SARS_CoV_2 P297S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P323L 2022 Journal of infection and public health Table SARS_CoV_2 P323L 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P340L 2022 Journal of infection and public health Table SARS_CoV_2 P340L 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P36S 2022 Journal of infection and public health Table SARS_CoV_2 P36S 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P384L 2022 Journal of infection and public health Table SARS_CoV_2 P384L 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P393S 2022 Journal of infection and public health Table SARS_CoV_2 P393S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P589S 2022 Journal of infection and public health Table SARS_CoV_2 P589S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P597S 2022 Journal of infection and public health Table SARS_CoV_2 P597S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P681H 2022 Journal of infection and public health Table SARS_CoV_2 P681H 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P71S 2022 Journal of infection and public health Table SARS_CoV_2 P71S 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P80A 2022 Journal of infection and public health Table SARS_CoV_2 P80A 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P822S 2022 Journal of infection and public health Table SARS_CoV_2 P822S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. P84L 2022 Journal of infection and public health Table SARS_CoV_2 P84L 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Q134K 2022 Journal of infection and public health Table SARS_CoV_2 Q134K 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Q173H 2022 Journal of infection and public health Table SARS_CoV_2 Q173H 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Q213K 2022 Journal of infection and public health Table SARS_CoV_2 Q213K 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Q383R 2022 Journal of infection and public health Table SARS_CoV_2 Q383R 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Q675H 2022 Journal of infection and public health Table SARS_CoV_2 Q675H 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Q90R 2022 Journal of infection and public health Table SARS_CoV_2 Q90R 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Q913H 2022 Journal of infection and public health Table SARS_CoV_2 Q913H 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. R119H 2022 Journal of infection and public health Table SARS_CoV_2 R119H 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. R203K 2022 Journal of infection and public health Table SARS_CoV_2 R203K 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. R222C 2022 Journal of infection and public health Table SARS_CoV_2 R222C 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. R39G 2022 Journal of infection and public health Table SARS_CoV_2 R39G 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. R52I 2022 Journal of infection and public health Table SARS_CoV_2 R52I 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. S106F 2022 Journal of infection and public health Table SARS_CoV_2 S106F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. S118L 2022 Journal of infection and public health Table SARS_CoV_2 S118L 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. S196L 2022 Journal of infection and public health Table SARS_CoV_2 S196L 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. S261L 2022 Journal of infection and public health Table SARS_CoV_2 S261L 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. S26L 2022 Journal of infection and public health Table SARS_CoV_2 S26L 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. S284G 2022 Journal of infection and public health Table SARS_CoV_2 S284G 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. S288Y 2022 Journal of infection and public health Table SARS_CoV_2 S288Y 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. S430A 2022 Journal of infection and public health Table SARS_CoV_2 S430A 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. S609I 2022 Journal of infection and public health Table SARS_CoV_2 S609I 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. S60T 2022 Journal of infection and public health Table SARS_CoV_2 S60T 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. S67F 2022 Journal of infection and public health Table SARS_CoV_2 S67F 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T1004I 2022 Journal of infection and public health Table SARS_CoV_2 T1004I 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T1184M 2022 Journal of infection and public health Table SARS_CoV_2 T1184M 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T1189I 2022 Journal of infection and public health Table SARS_CoV_2 T1189I 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T11I 2022 Journal of infection and public health Table SARS_CoV_2 T11I 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T131I 2022 Journal of infection and public health Table SARS_CoV_2 T131I 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T1335I 2022 Journal of infection and public health Table SARS_CoV_2 T1335I 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T1348I 2022 Journal of infection and public health Table SARS_CoV_2 T1348I 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T1379I 2022 Journal of infection and public health Table SARS_CoV_2 T1379I 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T148I 2022 Journal of infection and public health Table SARS_CoV_2 T148I 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T151I 2022 Journal of infection and public health Table SARS_CoV_2 T151I 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T153M 2022 Journal of infection and public health Table SARS_CoV_2 T153M 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T196M 2022 Journal of infection and public health Table SARS_CoV_2 T196M 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T217I 2022 Journal of infection and public health Table SARS_CoV_2 T217I 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T21I 2022 Journal of infection and public health Table SARS_CoV_2 T21I 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T24I 2022 Journal of infection and public health Table SARS_CoV_2 T24I 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T295I 2022 Journal of infection and public health Table SARS_CoV_2 T295I 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T39I 2022 Journal of infection and public health Table SARS_CoV_2 T39I 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T45I 2022 Journal of infection and public health Table SARS_CoV_2 T45I 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T481M 2022 Journal of infection and public health Table SARS_CoV_2 T481M 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T681A 2022 Journal of infection and public health Table SARS_CoV_2 T681A 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T724I 2022 Journal of infection and public health Table SARS_CoV_2 T724I 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T91M 2022 Journal of infection and public health Table SARS_CoV_2 T91M 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. T936I 2022 Journal of infection and public health Table SARS_CoV_2 T936I 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V1048I 2022 Journal of infection and public health Table SARS_CoV_2 V1048I 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V1104I 2022 Journal of infection and public health Table SARS_CoV_2 V1104I 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V112I 2022 Journal of infection and public health Table SARS_CoV_2 V112I 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V1230L 2022 Journal of infection and public health Table SARS_CoV_2 V1230L 0 6 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V125F 2022 Journal of infection and public health Table SARS_CoV_2 V125F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V149F 2022 Journal of infection and public health Table SARS_CoV_2 V149F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V163L 2022 Journal of infection and public health Table SARS_CoV_2 V163L 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V190F 2022 Journal of infection and public health Table SARS_CoV_2 V190F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V210I 2022 Journal of infection and public health Table SARS_CoV_2 V210I 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V213L 2022 Journal of infection and public health Table SARS_CoV_2 V213L 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V256F 2022 Journal of infection and public health Table SARS_CoV_2 V256F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V26F 2022 Journal of infection and public health Table SARS_CoV_2 V26F 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V382L 2022 Journal of infection and public health Table SARS_CoV_2 V382L 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V435I 2022 Journal of infection and public health Table SARS_CoV_2 V435I 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V477F 2022 Journal of infection and public health Table SARS_CoV_2 V477F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V480D 2022 Journal of infection and public health Table SARS_CoV_2 V480D 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V594F 2022 Journal of infection and public health Table SARS_CoV_2 V594F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V622F 2022 Journal of infection and public health Table SARS_CoV_2 V622F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V62F 2022 Journal of infection and public health Table SARS_CoV_2 V62F 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V62L 2022 Journal of infection and public health Table SARS_CoV_2 V62L 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V94L 2022 Journal of infection and public health Table SARS_CoV_2 V94L 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V952F 2022 Journal of infection and public health Table SARS_CoV_2 V952F 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. W258S 2022 Journal of infection and public health Table SARS_CoV_2 W258S 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. W27L 2022 Journal of infection and public health Table SARS_CoV_2 W27L 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. W450C 2022 Journal of infection and public health Table SARS_CoV_2 W450C 0 5 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. W45L 2022 Journal of infection and public health Table SARS_CoV_2 W45L 0 4 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Y126stop 2022 Journal of infection and public health Table SARS_CoV_2 Y126X 0 8 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. L452R 2021 Medicine in drug discovery Table SARS_CoV_2 L452R 0 5 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. T478K 2021 Medicine in drug discovery Table SARS_CoV_2 T478K 0 5 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.A67V 2021 PloS one Table SARS_CoV_2 A67V 0 6 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.A694V 2021 PloS one Table SARS_CoV_2 A694V 0 7 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.D1153H 2021 PloS one Table SARS_CoV_2 D1153H 0 8 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.D138H 2021 PloS one Table SARS_CoV_2 D138H 0 7 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.D215Y 2021 PloS one Table SARS_CoV_2 D215Y 0 7 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.E484K 2021 PloS one Table SARS_CoV_2 E484K 0 7 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.E583D 2021 PloS one Table SARS_CoV_2 E583D 0 7 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.H1101Y 2021 PloS one Table SARS_CoV_2 H1101Y 0 8 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.L18F 2021 PloS one Table SARS_CoV_2 L18F 0 6 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.L5F 2021 PloS one Table SARS_CoV_2 L5F 0 5 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.L922F 2021 PloS one Table SARS_CoV_2 L922F 0 7 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.N501Y 2021 PloS one Table SARS_CoV_2 N501Y 0 7 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.N658K 2021 PloS one Table SARS_CoV_2 N658K 0 7 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.N751S 2021 PloS one Table SARS_CoV_2 N751S;P751S 0;0 7;7 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.P1079S 2021 PloS one Table SARS_CoV_2 P1079S 0 8 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.P26L 2021 PloS one Table SARS_CoV_2 P26L 0 6 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.P330S 2021 PloS one Table SARS_CoV_2 P330S 0 7 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.P384S 2021 PloS one Table SARS_CoV_2 P384S 0 7 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.T19I 2021 PloS one Table SARS_CoV_2 T19I 0 6 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.V1065L 2021 PloS one Table SARS_CoV_2 V1065L 0 8 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.V1104L 2021 PloS one Table SARS_CoV_2 V1104L 0 8 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.V1264L 2021 PloS one Table SARS_CoV_2 V1264L 0 8 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.V608I 2021 PloS one Table SARS_CoV_2 V608I 0 7 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.V70F 2021 PloS one Table SARS_CoV_2 V70F 0 6 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.V772I 2021 PloS one Table SARS_CoV_2 V772I 0 7 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. Y145del 2021 PloS one Table SARS_CoV_2 Y145del 0 7 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. 143del 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 143del 0 6 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. 144del 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 144del 0 6 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. A570D 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 A570D 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. A67V 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 A67V 0 4 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. A701V 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 A701V 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. D1118H 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 D1118H 0 6 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. D138Y 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 D138Y 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. D215G 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 D215G 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. D253G 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 D253G 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. D614G 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 D614G 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. D796Y 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 D796Y 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. D80A 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 D80A 0 4 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. D950N 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 D950N 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. E154K 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 E154K 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. E484K 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 E484K 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. E484Q 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 E484Q 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. F157L 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 F157L 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. G142D 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 G142D 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. H655Y 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 H655Y 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. K417N 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 K417N 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. K417T 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 K417T 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. L18F 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 L18F 0 4 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. L212I 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 L212I 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. L452R 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 L452R 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. L981F 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 L981F 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. N501Y 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 N501Y 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. N679K 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 N679K 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. N764K 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 N764K 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. N856K 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 N856K 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. N969K 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 N969K 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. P26S 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 P26S 0 4 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. P681H 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 P681H 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. P681R 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 P681R 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. Q1071H 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 Q1071H 0 6 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. Q677H 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 Q677H 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. Q954H 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 Q954H 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. R158G 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 R158G 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. R190S 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 R190S 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. R246I 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 R246I 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. S13I 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 S13I 0 4 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. S477N 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 S477N 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. S929I 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 S929I 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. S982A 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 S982A 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. T1027I 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 T1027I 0 6 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. T19R 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 T19R 0 4 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. T20N 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 T20N 0 4 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. T478K 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 T478K 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. T547K 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 T547K 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. T716I 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 T716I 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. T95I 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 T95I 0 4 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. V1176F 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 V1176F 0 6 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. W152C 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 W152C 0 5 34906769 Efficacy of mRNA, adenoviral vector, and perfusion protein COVID-19 vaccines. Y145D 2022 Biomedicine & pharmacotherapy Table SARS_CoV_2 Y145D 0 5 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. D614G 2021 Nature communications Table SARS_CoV_2 D614G 0 5 34912372 Hotspot Mutations in SARS-CoV-2. A11201G 2021 Frontiers in genetics Table SARS_CoV_2 A11201G 0 7 34912372 Hotspot Mutations in SARS-CoV-2. A20396G 2021 Frontiers in genetics Table SARS_CoV_2 A20396G 0 7 34912372 Hotspot Mutations in SARS-CoV-2. A222V 2021 Frontiers in genetics Table SARS_CoV_2 A222V 0 5 34912372 Hotspot Mutations in SARS-CoV-2. A23063T 2021 Frontiers in genetics Table SARS_CoV_2 A23063T 0 7 34912372 Hotspot Mutations in SARS-CoV-2. A24775T 2021 Frontiers in genetics Table SARS_CoV_2 A24775T 0 7 34912372 Hotspot Mutations in SARS-CoV-2. A28111G 2021 Frontiers in genetics Table SARS_CoV_2 A28111G 0 7 34912372 Hotspot Mutations in SARS-CoV-2. A28281T 2021 Frontiers in genetics Table SARS_CoV_2 A28281T 0 7 34912372 Hotspot Mutations in SARS-CoV-2. A28461G 2021 Frontiers in genetics Table SARS_CoV_2 A28461G 0 7 34912372 Hotspot Mutations in SARS-CoV-2. A446V 2021 Frontiers in genetics Table SARS_CoV_2 A446V 0 5 34912372 Hotspot Mutations in SARS-CoV-2. A570D 2021 Frontiers in genetics Table SARS_CoV_2 A570D 0 5 34912372 Hotspot Mutations in SARS-CoV-2. A890D 2021 Frontiers in genetics Table SARS_CoV_2 A890D 0 5 34912372 Hotspot Mutations in SARS-CoV-2. A994D 2021 Frontiers in genetics Table SARS_CoV_2 A994D 0 5 34912372 Hotspot Mutations in SARS-CoV-2. C1191T 2021 Frontiers in genetics Table SARS_CoV_2 C1191T 0 6 34912372 Hotspot Mutations in SARS-CoV-2. C16466T 2021 Frontiers in genetics Table SARS_CoV_2 C16466T 0 7 34912372 Hotspot Mutations in SARS-CoV-2. C21618G 2021 Frontiers in genetics Table SARS_CoV_2 C21618G 0 7 34912372 Hotspot Mutations in SARS-CoV-2. C21846T 2021 Frontiers in genetics Table SARS_CoV_2 C21846T 0 7 34912372 Hotspot Mutations in SARS-CoV-2. C22227T 2021 Frontiers in genetics Table SARS_CoV_2 C22227T 0 7 34912372 Hotspot Mutations in SARS-CoV-2. C22995A 2021 Frontiers in genetics Table SARS_CoV_2 C22995A 0 7 34912372 Hotspot Mutations in SARS-CoV-2. C23271A 2021 Frontiers in genetics Table SARS_CoV_2 C23271A 0 7 34912372 Hotspot Mutations in SARS-CoV-2. C23604A 2021 Frontiers in genetics Table SARS_CoV_2 C23604A 0 7 34912372 Hotspot Mutations in SARS-CoV-2. C23604G 2021 Frontiers in genetics Table SARS_CoV_2 C23604G 0 7 34912372 Hotspot Mutations in SARS-CoV-2. C23709T 2021 Frontiers in genetics Table SARS_CoV_2 C23709T 0 7 34912372 Hotspot Mutations in SARS-CoV-2. C25469T 2021 Frontiers in genetics Table SARS_CoV_2 C25469T 0 7 34912372 Hotspot Mutations in SARS-CoV-2. C27752T 2021 Frontiers in genetics Table SARS_CoV_2 C27752T 0 7 34912372 Hotspot Mutations in SARS-CoV-2. C28854T 2021 Frontiers in genetics Table SARS_CoV_2 C28854T 0 7 34912372 Hotspot Mutations in SARS-CoV-2. C28977T 2021 Frontiers in genetics Table SARS_CoV_2 C28977T 0 7 34912372 Hotspot Mutations in SARS-CoV-2. C3267T 2021 Frontiers in genetics Table SARS_CoV_2 C3267T 0 6 34912372 Hotspot Mutations in SARS-CoV-2. C4965T 2021 Frontiers in genetics Table SARS_CoV_2 C4965T 0 6 34912372 Hotspot Mutations in SARS-CoV-2. C5184T 2021 Frontiers in genetics Table SARS_CoV_2 C5184T 0 6 34912372 Hotspot Mutations in SARS-CoV-2. C5388A 2021 Frontiers in genetics Table SARS_CoV_2 C5388A 0 6 34912372 Hotspot Mutations in SARS-CoV-2. C5700A 2021 Frontiers in genetics Table SARS_CoV_2 C5700A 0 6 34912372 Hotspot Mutations in SARS-CoV-2. C9891T 2021 Frontiers in genetics Table SARS_CoV_2 C9891T 0 6 34912372 Hotspot Mutations in SARS-CoV-2. D1118H 2021 Frontiers in genetics Table SARS_CoV_2 D1118H 0 6 34912372 Hotspot Mutations in SARS-CoV-2. D377Y 2021 Frontiers in genetics Table SARS_CoV_2 D377Y 0 5 34912372 Hotspot Mutations in SARS-CoV-2. D63G 2021 Frontiers in genetics Table SARS_CoV_2 D63G 0 4 34912372 Hotspot Mutations in SARS-CoV-2. D950N 2021 Frontiers in genetics Table SARS_CoV_2 D950N 0 5 34912372 Hotspot Mutations in SARS-CoV-2. E484Q 2021 Frontiers in genetics Table SARS_CoV_2 E484Q 0 5 34912372 Hotspot Mutations in SARS-CoV-2. G142D 2021 Frontiers in genetics Table SARS_CoV_2 G142D 0 5 34912372 Hotspot Mutations in SARS-CoV-2. G15451A 2021 Frontiers in genetics Table SARS_CoV_2 G15451A 0 7 34912372 Hotspot Mutations in SARS-CoV-2. G17523T 2021 Frontiers in genetics Table SARS_CoV_2 G17523T 0 7 34912372 Hotspot Mutations in SARS-CoV-2. G204R 2021 Frontiers in genetics Table SARS_CoV_2 G204R 0 5 34912372 Hotspot Mutations in SARS-CoV-2. G21987A 2021 Frontiers in genetics Table SARS_CoV_2 G21987A 0 7 34912372 Hotspot Mutations in SARS-CoV-2. G22022A 2021 Frontiers in genetics Table SARS_CoV_2 G22022A 0 7 34912372 Hotspot Mutations in SARS-CoV-2. G23012C 2021 Frontiers in genetics Table SARS_CoV_2 G23012C 0 7 34912372 Hotspot Mutations in SARS-CoV-2. G24410A 2021 Frontiers in genetics Table SARS_CoV_2 G24410A 0 7 34912372 Hotspot Mutations in SARS-CoV-2. G24914C 2021 Frontiers in genetics Table SARS_CoV_2 G24914C 0 7 34912372 Hotspot Mutations in SARS-CoV-2. G25563T 2021 Frontiers in genetics Table SARS_CoV_2 G25563T 0 7 34912372 Hotspot Mutations in SARS-CoV-2. G28048T 2021 Frontiers in genetics Table SARS_CoV_2 G28048T 0 7 34912372 Hotspot Mutations in SARS-CoV-2. G28280C 2021 Frontiers in genetics Table SARS_CoV_2 G28280C 0 7 34912372 Hotspot Mutations in SARS-CoV-2. G28881A 2021 Frontiers in genetics Table SARS_CoV_2 G28881A 0 7 34912372 Hotspot Mutations in SARS-CoV-2. G28881T 2021 Frontiers in genetics Table SARS_CoV_2 G28881T 0 7 34912372 Hotspot Mutations in SARS-CoV-2. G28883C 2021 Frontiers in genetics Table SARS_CoV_2 G28883C 0 7 34912372 Hotspot Mutations in SARS-CoV-2. G29402T 2021 Frontiers in genetics Table SARS_CoV_2 G29402T 0 7 34912372 Hotspot Mutations in SARS-CoV-2. G671S 2021 Frontiers in genetics Table SARS_CoV_2 G671S 0 5 34912372 Hotspot Mutations in SARS-CoV-2. I1412T 2021 Frontiers in genetics Table SARS_CoV_2 I1412T 0 6 34912372 Hotspot Mutations in SARS-CoV-2. I82S 2021 Frontiers in genetics Table SARS_CoV_2 I82S 0 4 34912372 Hotspot Mutations in SARS-CoV-2. K259R 2021 Frontiers in genetics Table SARS_CoV_2 K259R 0 5 34912372 Hotspot Mutations in SARS-CoV-2. L452R 2021 Frontiers in genetics Table SARS_CoV_2 L452R 0 5 34912372 Hotspot Mutations in SARS-CoV-2. M429I 2021 Frontiers in genetics Table SARS_CoV_2 M429I 0 5 34912372 Hotspot Mutations in SARS-CoV-2. N501Y 2021 Frontiers in genetics Table SARS_CoV_2 N501Y 0 5 34912372 Hotspot Mutations in SARS-CoV-2. P129L 2021 Frontiers in genetics Table SARS_CoV_2 P129L 0 5 34912372 Hotspot Mutations in SARS-CoV-2. P681H 2021 Frontiers in genetics Table SARS_CoV_2 P681H 0 5 34912372 Hotspot Mutations in SARS-CoV-2. P681R 2021 Frontiers in genetics Table SARS_CoV_2 P681R 0 5 34912372 Hotspot Mutations in SARS-CoV-2. P77L 2021 Frontiers in genetics Table SARS_CoV_2 P77L 0 4 34912372 Hotspot Mutations in SARS-CoV-2. P822L 2021 Frontiers in genetics Table SARS_CoV_2 P822L 0 5 34912372 Hotspot Mutations in SARS-CoV-2. Q1071H 2021 Frontiers in genetics Table SARS_CoV_2 Q1071H 0 6 34912372 Hotspot Mutations in SARS-CoV-2. Q57H 2021 Frontiers in genetics Table SARS_CoV_2 Q57H 0 4 34912372 Hotspot Mutations in SARS-CoV-2. R203M 2021 Frontiers in genetics Table SARS_CoV_2 R203M 0 5 34912372 Hotspot Mutations in SARS-CoV-2. R52I 2021 Frontiers in genetics Table SARS_CoV_2 R52I 0 4 34912372 Hotspot Mutations in SARS-CoV-2. S194L 2021 Frontiers in genetics Table SARS_CoV_2 S194L 0 5 34912372 Hotspot Mutations in SARS-CoV-2. S235F 2021 Frontiers in genetics Table SARS_CoV_2 S235F 0 5 34912372 Hotspot Mutations in SARS-CoV-2. S26L 2021 Frontiers in genetics Table SARS_CoV_2 S26L 0 4 34912372 Hotspot Mutations in SARS-CoV-2. S982A 2021 Frontiers in genetics Table SARS_CoV_2 S982A 0 5 34912372 Hotspot Mutations in SARS-CoV-2. T11418C 2021 Frontiers in genetics Table SARS_CoV_2 T11418C 0 7 34912372 Hotspot Mutations in SARS-CoV-2. T120I 2021 Frontiers in genetics Table SARS_CoV_2 T120I 0 5 34912372 Hotspot Mutations in SARS-CoV-2. T183I 2021 Frontiers in genetics Table SARS_CoV_2 T183I 0 5 34912372 Hotspot Mutations in SARS-CoV-2. T19R 2021 Frontiers in genetics Table SARS_CoV_2 T19R 0 4 34912372 Hotspot Mutations in SARS-CoV-2. T22917G 2021 Frontiers in genetics Table SARS_CoV_2 T22917G 0 7 34912372 Hotspot Mutations in SARS-CoV-2. T24506G 2021 Frontiers in genetics Table SARS_CoV_2 T24506G 0 7 34912372 Hotspot Mutations in SARS-CoV-2. T26767G 2021 Frontiers in genetics Table SARS_CoV_2 T26767G 0 7 34912372 Hotspot Mutations in SARS-CoV-2. T27638C 2021 Frontiers in genetics Table SARS_CoV_2 T27638C 0 7 34912372 Hotspot Mutations in SARS-CoV-2. T28282A 2021 Frontiers in genetics Table SARS_CoV_2 T28282A 0 7 34912372 Hotspot Mutations in SARS-CoV-2. T478K 2021 Frontiers in genetics Table SARS_CoV_2 T478K 0 5 34912372 Hotspot Mutations in SARS-CoV-2. T6954C 2021 Frontiers in genetics Table SARS_CoV_2 T6954C 0 6 34912372 Hotspot Mutations in SARS-CoV-2. T716I 2021 Frontiers in genetics Table SARS_CoV_2 T716I 0 5 34912372 Hotspot Mutations in SARS-CoV-2. T749I 2021 Frontiers in genetics Table SARS_CoV_2 T749I 0 5 34912372 Hotspot Mutations in SARS-CoV-2. T77A 2021 Frontiers in genetics Table SARS_CoV_2 T77A 0 4 34912372 Hotspot Mutations in SARS-CoV-2. T95I 2021 Frontiers in genetics Table SARS_CoV_2 T95I 0 4 34912372 Hotspot Mutations in SARS-CoV-2. V149A 2021 Frontiers in genetics Table SARS_CoV_2 V149A 0 5 34912372 Hotspot Mutations in SARS-CoV-2. V82A 2021 Frontiers in genetics Table SARS_CoV_2 V82A 0 4 34912372 Hotspot Mutations in SARS-CoV-2. Y73C 2021 Frontiers in genetics Table SARS_CoV_2 Y73C 0 4 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. D614G 2021 Cell reports Table SARS_CoV_2 D614G 0 5 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. E0554S 2021 Cell reports Table SARS_CoV_2 E0554S 0 6 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. E484K 2021 Cell reports Table SARS_CoV_2 E484K 0 5 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. K417N 2021 Cell reports Table SARS_CoV_2 K417N 0 5 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. K417T 2021 Cell reports Table SARS_CoV_2 K417T 0 5 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. L452R 2021 Cell reports Table SARS_CoV_2 L452R 0 5 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. N501Y 2021 Cell reports Table SARS_CoV_2 N501Y 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. A475V 2022 International immunopharmacology Table SARS_CoV_2 A475V 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. E340K 2022 International immunopharmacology Table SARS_CoV_2 E340K 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. E484K 2022 International immunopharmacology Table SARS_CoV_2 E484K 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. E484Q 2022 International immunopharmacology Table SARS_CoV_2 E484Q 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. F486L 2022 International immunopharmacology Table SARS_CoV_2 F486L 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. F490S 2022 International immunopharmacology Table SARS_CoV_2 F490S 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. G446V 2022 International immunopharmacology Table SARS_CoV_2 G446V 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. G476S 2022 International immunopharmacology Table SARS_CoV_2 G476S 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. K417N 2022 International immunopharmacology Table SARS_CoV_2 K417N 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. K417T 2022 International immunopharmacology Table SARS_CoV_2 K417T 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. L452R 2022 International immunopharmacology Table SARS_CoV_2 L452R 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. N343A 2022 International immunopharmacology Table SARS_CoV_2 N343A 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. N439K 2022 International immunopharmacology Table SARS_CoV_2 N439K 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. N440Y 2022 International immunopharmacology Table SARS_CoV_2 N440Y 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. N450K 2022 International immunopharmacology Table SARS_CoV_2 N450K 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. N501Y 2022 International immunopharmacology Table SARS_CoV_2 N501Y 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Q493L 2022 International immunopharmacology Table SARS_CoV_2 Q493L 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. R346S 2022 International immunopharmacology Table SARS_CoV_2 R346S 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. R408I 2022 International immunopharmacology Table SARS_CoV_2 R408I 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. S477G 2022 International immunopharmacology Table SARS_CoV_2 S477G 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. S477N 2022 International immunopharmacology Table SARS_CoV_2 S477N 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. S494P 2022 International immunopharmacology Table SARS_CoV_2 S494P 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. T345I 2022 International immunopharmacology Table SARS_CoV_2 T345I 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. T478I 2022 International immunopharmacology Table SARS_CoV_2 T478I 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. V367F 2022 International immunopharmacology Table SARS_CoV_2 V367F 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Y453F 2022 International immunopharmacology Table SARS_CoV_2 Y453F 0 5 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Y505W 2022 International immunopharmacology Table SARS_CoV_2 Y505W 0 5 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. E484K 2022 Cell host & microbe Table SARS_CoV_2 E484K 0 5 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. K417N 2022 Cell host & microbe Table SARS_CoV_2 K417N 0 5 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. N501Y 2022 Cell host & microbe Table SARS_CoV_2 N501Y 0 5 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. D260Y 2021 Frontiers in microbiology Table SARS_CoV_2 D260Y 0 5 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. E341D 2021 Frontiers in microbiology Table SARS_CoV_2 E341D 0 5 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. M429I 2021 Frontiers in microbiology Table SARS_CoV_2 M429I 0 5 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. P77L 2021 Frontiers in microbiology Table SARS_CoV_2 P77L 0 4 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Q88H 2021 Frontiers in microbiology Table SARS_CoV_2 Q88H 0 4 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. N501Y 2022 Travel medicine and infectious disease Table SARS_CoV_2 N501Y 0 5 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. D614G 2022 Infection, genetics and evolution Table SARS_CoV_2 D614G 0 5 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. E484K 2022 Infection, genetics and evolution Table SARS_CoV_2 E484K 0 5 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. H655Y 2022 Infection, genetics and evolution Table SARS_CoV_2 H655Y 0 5 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. K1191D 2022 Infection, genetics and evolution Table SARS_CoV_2 K1191D 0 6 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. L18F 2022 Infection, genetics and evolution Table SARS_CoV_2 L18F 0 4 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. p.Asp614Gly 2022 Infection, genetics and evolution Table SARS_CoV_2 D614G 0 11 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. p.Glu484Lys 2022 Infection, genetics and evolution Table SARS_CoV_2 E484K 0 11 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. p.His655Tyr 2022 Infection, genetics and evolution Table SARS_CoV_2 H655Y 0 11 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. p.Leu18Phe 2022 Infection, genetics and evolution Table SARS_CoV_2 L18F 0 10 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. p.Lys1191Asp 2022 Infection, genetics and evolution Table SARS_CoV_2 K1191D 0 12 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. p.Pro26Ser 2022 Infection, genetics and evolution Table SARS_CoV_2 P26S 0 10 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. P26S 2022 Infection, genetics and evolution Table SARS_CoV_2 P26S 0 4 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. C to A in position 23615 2022 Nature Table SARS_CoV_2 C23615A 0 24 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. S614G 2022 Nature Table SARS_CoV_2 S614G 0 5 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. C145A 2021 Frontiers in pharmacology Table SARS_CoV_2 C145A 0 5 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. N501Y 2021 PloS one Table SARS_CoV_2 N501Y 0 5 34953513 Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. D614G 2022 Cell host & microbe Table SARS_CoV_2 D614G 0 5 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. L452R 2022 Journal of King Saud University. Science Table SARS_CoV_2 L452R 0 5 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. N501Y 2022 Journal of King Saud University. Science Table SARS_CoV_2 N501Y 0 5 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. T478K 2022 Journal of King Saud University. Science Table SARS_CoV_2 T478K 0 5 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. A701V 2021 Frontiers in immunology Table SARS_CoV_2 A701V 0 5 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. D215G 2021 Frontiers in immunology Table SARS_CoV_2 D215G 0 5 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. D614G 2021 Frontiers in immunology Table SARS_CoV_2 D614G 0 5 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. E484K 2021 Frontiers in immunology Table SARS_CoV_2 E484K 0 5 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. E484Q 2021 Frontiers in immunology Table SARS_CoV_2 E484Q 0 5 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. L18F,D 2021 Frontiers in immunology Table SARS_CoV_2 L18F 0 6 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. A260C 2021 Frontiers in molecular biosciences Table SARS_CoV_2 A260C 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. A260T 2021 Frontiers in molecular biosciences Table SARS_CoV_2 A260T 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. A430F 2021 Frontiers in molecular biosciences Table SARS_CoV_2 A430F 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. A430S 2021 Frontiers in molecular biosciences Table SARS_CoV_2 A430S 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. A430Y 2021 Frontiers in molecular biosciences Table SARS_CoV_2 A430Y 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. A475D 2021 Frontiers in molecular biosciences Table SARS_CoV_2 A475D 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. A475P 2021 Frontiers in molecular biosciences Table SARS_CoV_2 A475P 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. D480G 2021 Frontiers in molecular biosciences Table SARS_CoV_2 D480G 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. D600G 2021 Frontiers in molecular biosciences Table SARS_CoV_2 D600G 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. D614G 2021 Frontiers in molecular biosciences Table SARS_CoV_2 D614G 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. F360S 2021 Frontiers in molecular biosciences Table SARS_CoV_2 F360S 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. G482E 2021 Frontiers in molecular biosciences Table SARS_CoV_2 G482E 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. G488P 2021 Frontiers in molecular biosciences Table SARS_CoV_2 G488P 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. G496E 2021 Frontiers in molecular biosciences Table SARS_CoV_2 G496E 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. G502P 2021 Frontiers in molecular biosciences Table SARS_CoV_2 G502P 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. G634W 2021 Frontiers in molecular biosciences Table SARS_CoV_2 G634W 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. G648W 2021 Frontiers in molecular biosciences Table SARS_CoV_2 G648W 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. G839W 2021 Frontiers in molecular biosciences Table SARS_CoV_2 G839W 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. G857W 2021 Frontiers in molecular biosciences Table SARS_CoV_2 G857W 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. G981F 2021 Frontiers in molecular biosciences Table SARS_CoV_2 G981F 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. G981W 2021 Frontiers in molecular biosciences Table SARS_CoV_2 G981W 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. G999F 2021 Frontiers in molecular biosciences Table SARS_CoV_2 G999F 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. G999W 2021 Frontiers in molecular biosciences Table SARS_CoV_2 G999W 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. K344R 2021 Frontiers in molecular biosciences Table SARS_CoV_2 K344R 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. L472P 2021 Frontiers in molecular biosciences Table SARS_CoV_2 L472P 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. N479K 2021 Frontiers in molecular biosciences Table SARS_CoV_2 N479K 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. N479M 2021 Frontiers in molecular biosciences Table SARS_CoV_2 N479M 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. N479Q 2021 Frontiers in molecular biosciences Table SARS_CoV_2 N479Q 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. N501T 2021 Frontiers in molecular biosciences Table SARS_CoV_2 N501T 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. N501W 2021 Frontiers in molecular biosciences Table SARS_CoV_2 N501W 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. N501Y 2021 Frontiers in molecular biosciences Table SARS_CoV_2 N501Y 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. P462A 2021 Frontiers in molecular biosciences Table SARS_CoV_2 P462A 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. P462D 2021 Frontiers in molecular biosciences Table SARS_CoV_2 P462D 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Q493M 2021 Frontiers in molecular biosciences Table SARS_CoV_2 Q493M 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Q493N 2021 Frontiers in molecular biosciences Table SARS_CoV_2 Q493N 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. S432V 2021 Frontiers in molecular biosciences Table SARS_CoV_2 S432V 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. S432Y 2021 Frontiers in molecular biosciences Table SARS_CoV_2 S432Y 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. S443A 2021 Frontiers in molecular biosciences Table SARS_CoV_2 S443A 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. S443F 2021 Frontiers in molecular biosciences Table SARS_CoV_2 S443F 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. S443W 2021 Frontiers in molecular biosciences Table SARS_CoV_2 S443W 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. S443Y 2021 Frontiers in molecular biosciences Table SARS_CoV_2 S443Y 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. S500W 2021 Frontiers in molecular biosciences Table SARS_CoV_2 S500W 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. S514W 2021 Frontiers in molecular biosciences Table SARS_CoV_2 S514W 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. T1059F 2021 Frontiers in molecular biosciences Table SARS_CoV_2 T1059F 0 6 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. T1077F 2021 Frontiers in molecular biosciences Table SARS_CoV_2 T1077F 0 6 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. T247A 2021 Frontiers in molecular biosciences Table SARS_CoV_2 T247A 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. T247C 2021 Frontiers in molecular biosciences Table SARS_CoV_2 T247C 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. T487N 2021 Frontiers in molecular biosciences Table SARS_CoV_2 T487N 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. T487S 2021 Frontiers in molecular biosciences Table SARS_CoV_2 T487S 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. T487W 2021 Frontiers in molecular biosciences Table SARS_CoV_2 T487W 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. T487Y 2021 Frontiers in molecular biosciences Table SARS_CoV_2 T487Y 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. V445S 2021 Frontiers in molecular biosciences Table SARS_CoV_2 V445S 0 5 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. V445Y 2021 Frontiers in molecular biosciences Table SARS_CoV_2 V445Y 0 5 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. D614G 2022 Cell reports Table SARS_CoV_2 D614G 0 5 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. F490S 2022 Cell reports Table SARS_CoV_2 F490S 0 5 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. G75V 2022 Cell reports Table SARS_CoV_2 G75V 0 4 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. L452Q 2022 Cell reports Table SARS_CoV_2 L452Q 0 5 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. L452R 2022 Cell reports Table SARS_CoV_2 L452R 0 5 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. L5Q 2022 Cell reports Table SARS_CoV_2 L5Q 0 3 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. N246A 2022 Cell reports Table SARS_CoV_2 N246A 0 5 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. N246Q 2022 Cell reports Table SARS_CoV_2 N246Q 0 5 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. R0136S 2022 Cell reports Table SARS_CoV_2 R0136S 0 6 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. R0142S 2022 Cell reports Table SARS_CoV_2 R0142S 0 6 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. R050A 2022 Cell reports Table SARS_CoV_2 R050A 0 5 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. R0599S 2022 Cell reports Table SARS_CoV_2 R0599S 0 6 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. R1089S 2022 Cell reports Table SARS_CoV_2 R1089S 0 6 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. T76I 2022 Cell reports Table SARS_CoV_2 T76I 0 4 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. G476S 2022 Computer methods and programs in biomedicine Table SARS_CoV_2 G476S 0 5 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. N501Y 2022 Computer methods and programs in biomedicine Table SARS_CoV_2 N501Y 0 5 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. R408I 2022 Computer methods and programs in biomedicine Table SARS_CoV_2 R408I 0 5 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. V367F 2022 Computer methods and programs in biomedicine Table SARS_CoV_2 V367F 0 5 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. V483A 2022 Computer methods and programs in biomedicine Table SARS_CoV_2 V483A 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. A2618V 2022 Computers in biology and medicine Table SARS_CoV_2 A2618V 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. A2956V 2022 Computers in biology and medicine Table SARS_CoV_2 A2956V 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. A4489L 2022 Computers in biology and medicine Table SARS_CoV_2 A4489L 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. A4921V 2022 Computers in biology and medicine Table SARS_CoV_2 A4921V 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. A5561T 2022 Computers in biology and medicine Table SARS_CoV_2 A5561T 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. D614G 2022 Computers in biology and medicine Table SARS_CoV_2 D614G 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. F275L 2022 Computers in biology and medicine Table SARS_CoV_2 F275L 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. G204R 2022 Computers in biology and medicine Table SARS_CoV_2 G204R 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. G3278S 2022 Computers in biology and medicine Table SARS_CoV_2 G3278S 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. G82S 2022 Computers in biology and medicine Table SARS_CoV_2 G82S 0 4 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. G934C 2022 Computers in biology and medicine Table SARS_CoV_2 G934C 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. H125Y 2022 Computers in biology and medicine Table SARS_CoV_2 H125Y 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. H25Y 2022 Computers in biology and medicine Table SARS_CoV_2 H25Y 0 4 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. K292E 2022 Computers in biology and medicine Table SARS_CoV_2 K292E 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. K3353R 2022 Computers in biology and medicine Table SARS_CoV_2 K3353R 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. L1175I 2022 Computers in biology and medicine Table SARS_CoV_2 L1175I 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. L2564F 2022 Computers in biology and medicine Table SARS_CoV_2 L2564F 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. L3293F 2022 Computers in biology and medicine Table SARS_CoV_2 L3293F 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. L3606F 2022 Computers in biology and medicine Table SARS_CoV_2 L3606F 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. L84S 2022 Computers in biology and medicine Table SARS_CoV_2 L84S 0 4 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. N74K 2022 Computers in biology and medicine Table SARS_CoV_2 N74K 0 4 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. P13L 2022 Computers in biology and medicine Table SARS_CoV_2 P13L 0 4 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. P2965L 2022 Computers in biology and medicine Table SARS_CoV_2 P2965L 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. P3447S 2022 Computers in biology and medicine Table SARS_CoV_2 P3447S 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. P4075S 2022 Computers in biology and medicine Table SARS_CoV_2 P4075S 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. P4715L 2022 Computers in biology and medicine Table SARS_CoV_2 P4715L 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. P4716L 2022 Computers in biology and medicine Table SARS_CoV_2 P4716L 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Q2702H 2022 Computers in biology and medicine Table SARS_CoV_2 Q2702H 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Q57H 2022 Computers in biology and medicine Table SARS_CoV_2 Q57H 0 4 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Q63L 2022 Computers in biology and medicine Table SARS_CoV_2 Q63L 0 4 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Q677H 2022 Computers in biology and medicine Table SARS_CoV_2 Q677H 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. R203K 2022 Computers in biology and medicine Table SARS_CoV_2 R203K 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. R207C 2022 Computers in biology and medicine Table SARS_CoV_2 R207C 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. R209I 2022 Computers in biology and medicine Table SARS_CoV_2 R209I 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. S194L 2022 Computers in biology and medicine Table SARS_CoV_2 S194L 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. S318I 2022 Computers in biology and medicine Table SARS_CoV_2 S318I 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. S327L 2022 Computers in biology and medicine Table SARS_CoV_2 S327L 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. S943T 2022 Computers in biology and medicine Table SARS_CoV_2 S943T 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. S944L 2022 Computers in biology and medicine Table SARS_CoV_2 S944L 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. T1246I 2022 Computers in biology and medicine Table SARS_CoV_2 T1246I 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. T1754I 2022 Computers in biology and medicine Table SARS_CoV_2 T1754I 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. T2016K 2022 Computers in biology and medicine Table SARS_CoV_2 T2016K 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. T2018K 2022 Computers in biology and medicine Table SARS_CoV_2 T2018K 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. T205I 2022 Computers in biology and medicine Table SARS_CoV_2 T205I 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. T223I 2022 Computers in biology and medicine Table SARS_CoV_2 T223I 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. T2408I 2022 Computers in biology and medicine Table SARS_CoV_2 T2408I 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. T2846I 2022 Computers in biology and medicine Table SARS_CoV_2 T2846I 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. T5451I 2022 Computers in biology and medicine Table SARS_CoV_2 T5451I 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. V2133A 2022 Computers in biology and medicine Table SARS_CoV_2 V2133A 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. V30L 2022 Computers in biology and medicine Table SARS_CoV_2 V30L 0 4 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. V378I 2022 Computers in biology and medicine Table SARS_CoV_2 V378I 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. V4979L 2022 Computers in biology and medicine Table SARS_CoV_2 V4979L 0 6 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. V622F 2022 Computers in biology and medicine Table SARS_CoV_2 V622F 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. V627F 2022 Computers in biology and medicine Table SARS_CoV_2 V627F 0 5 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. W45L 2022 Computers in biology and medicine Table SARS_CoV_2 W45L 0 4 34968879 SARS-CoV-2 wastewater surveillance in Germany: Long-term RT-digital droplet PCR monitoring, suitability of primer/probe combinations and biomarker stability. N501Y 2022 Water research Table SARS_CoV_2 N501Y 0 5 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. N501I 2022 Computers in biology and medicine Table SARS_CoV_2 N501I 0 5 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. N501T 2022 Computers in biology and medicine Table SARS_CoV_2 N501T 0 5 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. N501V 2022 Computers in biology and medicine Table SARS_CoV_2 N501V 0 5 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. N501Y 2022 Computers in biology and medicine Table SARS_CoV_2 N501Y 0 5 34982246 Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing. 23929(C > T) 2022 Current microbiology Table SARS_CoV_2 C23929T 0 12 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. A570D 2022 Microbiology spectrum Table SARS_CoV_2 A570D 0 5 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. C1709A 2022 Microbiology spectrum Table SARS_CoV_2 C1709A 0 6 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. C56G 2022 Microbiology spectrum Table SARS_CoV_2 C56G 0 4 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. D1118H 2022 Microbiology spectrum Table SARS_CoV_2 D1118H 0 6 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. D215G 2022 Microbiology spectrum Table SARS_CoV_2 D215G 0 5 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. D80A 2022 Microbiology spectrum Table SARS_CoV_2 D80A 0 4 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. D950N 2022 Microbiology spectrum Table SARS_CoV_2 D950N 0 5 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. K417N 2022 Microbiology spectrum Table SARS_CoV_2 K417N 0 5 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. K417T 2022 Microbiology spectrum Table SARS_CoV_2 K417T 0 5 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. P26S 2022 Microbiology spectrum Table SARS_CoV_2 P26S 0 4 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. S982A 2022 Microbiology spectrum Table SARS_CoV_2 S982A 0 5 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. T19R 2022 Microbiology spectrum Table SARS_CoV_2 T19R 0 4 34985323 Developing an Amplification Refractory Mutation System-Quantitative Reverse Transcription-PCR Assay for Rapid and Sensitive Screening of SARS-CoV-2 Variants of Concern. T20N 2022 Microbiology spectrum Table SARS_CoV_2 T20N 0 4 34985974 Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2. D614G 2022 Applied and environmental microbiology Table SARS_CoV_2 D614G 0 5 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. D614G 2022 Cell reports Table SARS_CoV_2 D614G 0 5 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. E484K 2022 Archives of virology Table SARS_CoV_2 E484K 0 5 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. E484Q 2022 Archives of virology Table SARS_CoV_2 E484Q 0 5 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. L18F 2022 Archives of virology Table SARS_CoV_2 L18F 0 4 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. L452R 2022 Archives of virology Table SARS_CoV_2 L452R 0 5 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. N440K 2022 Archives of virology Table SARS_CoV_2 N440K 0 5 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. N501Y 2022 Archives of virology Table SARS_CoV_2 N501Y 0 5 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. S494P 2022 Archives of virology Table SARS_CoV_2 S494P 0 5 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. T478K 2022 Archives of virology Table SARS_CoV_2 T478K 0 5 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. V382L 2022 Archives of virology Table SARS_CoV_2 V382L 0 5 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. A222V 2021 Frontiers in public health Table SARS_CoV_2 A222V 0 5 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. D614G 2021 Frontiers in public health Table SARS_CoV_2 D614G 0 5 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. E484K 2021 Frontiers in public health Table SARS_CoV_2 E484K 0 5 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. E484Q 2021 Frontiers in public health Table SARS_CoV_2 E484Q 0 5 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. K417N 2021 Frontiers in public health Table SARS_CoV_2 K417N 0 5 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. L452Q 2021 Frontiers in public health Table SARS_CoV_2 L452Q 0 5 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. L452R 2021 Frontiers in public health Table SARS_CoV_2 L452R 0 5 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. N501Y 2021 Frontiers in public health Table SARS_CoV_2 N501Y 0 5 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. P681H 2021 Frontiers in public health Table SARS_CoV_2 P681H 0 5 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. P681R 2021 Frontiers in public health Table SARS_CoV_2 P681R 0 5 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. V70F 2021 Frontiers in public health Table SARS_CoV_2 V70F 0 4 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. W258L 2021 Frontiers in public health Table SARS_CoV_2 W258L 0 5 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. E484K 2022 The EPMA journal Table SARS_CoV_2 E484K 0 5 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. E484Q 2022 The EPMA journal Table SARS_CoV_2 E484Q 0 5 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. K417N 2022 The EPMA journal Table SARS_CoV_2 K417N 0 5 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. K417T 2022 The EPMA journal Table SARS_CoV_2 K417T 0 5 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. L452R 2022 The EPMA journal Table SARS_CoV_2 L452R 0 5 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. N439K 2022 The EPMA journal Table SARS_CoV_2 N439K 0 5 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. N501Y 2022 The EPMA journal Table SARS_CoV_2 N501Y 0 5 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. S477N 2022 The EPMA journal Table SARS_CoV_2 S477N 0 5 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. S494P 2022 The EPMA journal Table SARS_CoV_2 S494P 0 5 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. N1074D 2021 Journal of global infectious diseases Table SARS_CoV_2 N1074D 0 6 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. N149G 2021 Journal of global infectious diseases Table SARS_CoV_2 N149G 0 5 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. N165S 2021 Journal of global infectious diseases Table SARS_CoV_2 N165S 0 5 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. N234Y 2021 Journal of global infectious diseases Table SARS_CoV_2 N234Y 0 5 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. N603Y 2021 Journal of global infectious diseases Table SARS_CoV_2 N603Y 0 5 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. N709K 2021 Journal of global infectious diseases Table SARS_CoV_2 N709K 0 5 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. S221F 2021 Journal of global infectious diseases Table SARS_CoV_2 S221F 0 5 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. S813I 2021 Journal of global infectious diseases Table SARS_CoV_2 S813I 0 5 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. S982A 2021 Journal of global infectious diseases Table SARS_CoV_2 S982A 0 5 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. T1077I 2021 Journal of global infectious diseases Table SARS_CoV_2 T1077I 0 6 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. T323I 2021 Journal of global infectious diseases Table SARS_CoV_2 T323I 0 5 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. T602I 2021 Journal of global infectious diseases Table SARS_CoV_2 T602I 0 5 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. T602L 2021 Journal of global infectious diseases Table SARS_CoV_2 T602L 0 5 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. T73I 2021 Journal of global infectious diseases Table SARS_CoV_2 T73I 0 4 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. A28461G 2022 Microbiology spectrum Table SARS_CoV_2 A28461G 0 7 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. A308S 2022 Microbiology spectrum Table SARS_CoV_2 A308S 0 5 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. D377Y 2022 Microbiology spectrum Table SARS_CoV_2 D377Y 0 5 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. D63G 2022 Microbiology spectrum Table SARS_CoV_2 D63G 0 4 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. G215C 2022 Microbiology spectrum Table SARS_CoV_2 G215C 0 5 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. G28881T 2022 Microbiology spectrum Table SARS_CoV_2 G28881T 0 7 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. G28916T 2022 Microbiology spectrum Table SARS_CoV_2 G28916T 0 7 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. G29195T 2022 Microbiology spectrum Table SARS_CoV_2 G29195T 0 7 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. G29402T 2022 Microbiology spectrum Table SARS_CoV_2 G29402T 0 7 35019683 SARS-CoV-2 N Gene G29195T Point Mutation May Affect Diagnostic Reverse Transcription-PCR Detection. R203M 2022 Microbiology spectrum Table SARS_CoV_2 R203M 0 5 35026305 SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021. N501Y 2022 Journal of virological methods Table SARS_CoV_2 N501Y 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. A1708D 2022 New microbes and new infections Table SARS_CoV_2 A1708D 0 6 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. A2249V 2022 New microbes and new infections Table SARS_CoV_2 A2249V 0 6 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. A3209V 2022 New microbes and new infections Table SARS_CoV_2 A3209V 0 6 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. A565V 2022 New microbes and new infections Table SARS_CoV_2 A565V 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. A570D 2022 New microbes and new infections Table SARS_CoV_2 A570D 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. D1118H 2022 New microbes and new infections Table SARS_CoV_2 D1118H 0 6 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. D377Y 2022 New microbes and new infections Table SARS_CoV_2 D377Y 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. D614G 2022 New microbes and new infections Table SARS_CoV_2 D614G 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. D63G 2022 New microbes and new infections Table SARS_CoV_2 D63G 0 4 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. D950N 2022 New microbes and new infections Table SARS_CoV_2 D950N 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. G204R 2022 New microbes and new infections Table SARS_CoV_2 G204R 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. G662S 2022 New microbes and new infections Table SARS_CoV_2 G662S 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. H2285Y 2022 New microbes and new infections Table SARS_CoV_2 H2285Y 0 6 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. I2230T 2022 New microbes and new infections Table SARS_CoV_2 I2230T 0 6 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. I82T 2022 New microbes and new infections Table SARS_CoV_2 I82T 0 4 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. K1073Q 2022 New microbes and new infections Table SARS_CoV_2 K1073Q 0 6 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. L116F 2022 New microbes and new infections Table SARS_CoV_2 L116F 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. L139F 2022 New microbes and new infections Table SARS_CoV_2 L139F 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. L452R 2022 New microbes and new infections Table SARS_CoV_2 L452R 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. N501Y 2022 New microbes and new infections Table SARS_CoV_2 N501Y 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. P1000L 2022 New microbes and new infections Table SARS_CoV_2 P1000L 0 6 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. P1640L 2022 New microbes and new infections Table SARS_CoV_2 P1640L 0 6 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. P309L 2022 New microbes and new infections Table SARS_CoV_2 P309L 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. P314L 2022 New microbes and new infections Table SARS_CoV_2 P314L 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. P681H 2022 New microbes and new infections Table SARS_CoV_2 P681H 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. P681R 2022 New microbes and new infections Table SARS_CoV_2 P681R 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. Q1129R 2022 New microbes and new infections Table SARS_CoV_2 Q1129R 0 6 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. Q229H 2022 New microbes and new infections Table SARS_CoV_2 Q229H 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. R14C 2022 New microbes and new infections Table SARS_CoV_2 R14C 0 4 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. R158G 2022 New microbes and new infections Table SARS_CoV_2 R158G 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. R203K 2022 New microbes and new infections Table SARS_CoV_2 R203K 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. R203M 2022 New microbes and new infections Table SARS_CoV_2 R203M 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. R385K 2022 New microbes and new infections Table SARS_CoV_2 R385K 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. R52I 2022 New microbes and new infections Table SARS_CoV_2 R52I 0 4 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. S235F 2022 New microbes and new infections Table SARS_CoV_2 S235F 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. S255A 2022 New microbes and new infections Table SARS_CoV_2 S255A 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. S26L 2022 New microbes and new infections Table SARS_CoV_2 S26L 0 4 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. S944L 2022 New microbes and new infections Table SARS_CoV_2 S944L 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. S982A 2022 New microbes and new infections Table SARS_CoV_2 S982A 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. T1001I 2022 New microbes and new infections Table SARS_CoV_2 T1001I 0 6 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. T120I 2022 New microbes and new infections Table SARS_CoV_2 T120I 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. T19R 2022 New microbes and new infections Table SARS_CoV_2 T19R 0 4 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. T478K 2022 New microbes and new infections Table SARS_CoV_2 T478K 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. T60A 2022 New microbes and new infections Table SARS_CoV_2 T60A 0 4 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. T716I 2022 New microbes and new infections Table SARS_CoV_2 T716I 0 5 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. V3718A 2022 New microbes and new infections Table SARS_CoV_2 V3718A 0 6 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. V82A 2022 New microbes and new infections Table SARS_CoV_2 V82A 0 4 35035981 Genetic variations from successive whole genome sequencing during COVID-19 treatment in five individuals. Y73C 2022 New microbes and new infections Table SARS_CoV_2 Y73C 0 4 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. E484K 2021 Frontiers in public health Table SARS_CoV_2 E484K 0 5 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. K417N/T 2021 Frontiers in public health Table SARS_CoV_2 K417N;K417T 0;0 7;7 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. N501Y 2021 Frontiers in public health Table SARS_CoV_2 N501Y 0 5 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. A222V 2022 Viruses Table SARS_CoV_2 A222V 0 5 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. A570D 2022 Viruses Table SARS_CoV_2 A570D 0 5 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. A701V 2022 Viruses Table SARS_CoV_2 A701V 0 5 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. D215G 2022 Viruses Table SARS_CoV_2 D215G 0 5 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. F888L 2022 Viruses Table SARS_CoV_2 F888L 0 5 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. H655Y 2022 Viruses Table SARS_CoV_2 H655Y 0 5 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. I692V 2022 Viruses Table SARS_CoV_2 I692V 0 5 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. K417N 2022 Viruses Table SARS_CoV_2 K417N 0 5 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. N439K 2022 Viruses Table SARS_CoV_2 N439K 0 5 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. P681H 2022 Viruses Table SARS_CoV_2 P681H 0 5 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. Q52R 2022 Viruses Table SARS_CoV_2 Q52R 0 4 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. Q677H 2022 Viruses Table SARS_CoV_2 Q677H 0 5 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. S477N 2022 Viruses Table SARS_CoV_2 S477N 0 5 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. S982A 2022 Viruses Table SARS_CoV_2 S982A 0 5 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. T716I 2022 Viruses Table SARS_CoV_2 T716I 0 5 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. Y453F 2022 Viruses Table SARS_CoV_2 Y453F 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. A446V 2022 Microbial pathogenesis Table SARS_CoV_2 A446V 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. A570D 2022 Microbial pathogenesis Table SARS_CoV_2 A570D 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. A890D 2022 Microbial pathogenesis Table SARS_CoV_2 A890D 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. D1118H 2022 Microbial pathogenesis Table SARS_CoV_2 D1118H 0 6 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. D377Y 2022 Microbial pathogenesis Table SARS_CoV_2 D377Y 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. D614G 2022 Microbial pathogenesis Table SARS_CoV_2 D614G 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. D63G 2022 Microbial pathogenesis Table SARS_CoV_2 D63G 0 4 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. E154K 2022 Microbial pathogenesis Table SARS_CoV_2 E154K 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. E156G 2022 Microbial pathogenesis Table SARS_CoV_2 E156G 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. E484Q 2022 Microbial pathogenesis Table SARS_CoV_2 E484Q 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. F157del 2022 Microbial pathogenesis Table SARS_CoV_2 F157del 0 7 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. G107del 2022 Microbial pathogenesis Table SARS_CoV_2 G107del 0 7 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. G142D 2022 Microbial pathogenesis Table SARS_CoV_2 G142D 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. G206C 2022 Microbial pathogenesis Table SARS_CoV_2 G206C 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. G671S 2022 Microbial pathogenesis Table SARS_CoV_2 G671S 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. H69del 2022 Microbial pathogenesis Table SARS_CoV_2 H69del 0 6 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. I82S 2022 Microbial pathogenesis Table SARS_CoV_2 I82S 0 4 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. I82T 2022 Microbial pathogenesis Table SARS_CoV_2 I82T 0 4 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. K259R 2022 Microbial pathogenesis Table SARS_CoV_2 K259R 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. L116F 2022 Microbial pathogenesis Table SARS_CoV_2 L116F 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. L452R 2022 Microbial pathogenesis Table SARS_CoV_2 L452R 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. M429I 2022 Microbial pathogenesis Table SARS_CoV_2 M429I 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. N440K 2022 Microbial pathogenesis Table SARS_CoV_2 N440K 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. N501Y 2022 Microbial pathogenesis Table SARS_CoV_2 N501Y 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. P129L 2022 Microbial pathogenesis Table SARS_CoV_2 P129L 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. P323L 2022 Microbial pathogenesis Table SARS_CoV_2 P323L 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. P46L 2022 Microbial pathogenesis Table SARS_CoV_2 P46L 0 4 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. P681R 2022 Microbial pathogenesis Table SARS_CoV_2 P681R 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. P77L 2022 Microbial pathogenesis Table SARS_CoV_2 P77L 0 4 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. P822L 2022 Microbial pathogenesis Table SARS_CoV_2 P822L 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Q1071H 2022 Microbial pathogenesis Table SARS_CoV_2 Q1071H 0 6 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. R158del 2022 Microbial pathogenesis Table SARS_CoV_2 R158del 0 7 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. R385K 2022 Microbial pathogenesis Table SARS_CoV_2 R385K 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. S106del 2022 Microbial pathogenesis Table SARS_CoV_2 S106del 0 7 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. S261A 2022 Microbial pathogenesis Table SARS_CoV_2 S261A 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. S26L 2022 Microbial pathogenesis Table SARS_CoV_2 S26L 0 4 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. S982A 2022 Microbial pathogenesis Table SARS_CoV_2 S982A 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. T120I 2022 Microbial pathogenesis Table SARS_CoV_2 T120I 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. T19R 2022 Microbial pathogenesis Table SARS_CoV_2 T19R 0 4 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. T478K 2022 Microbial pathogenesis Table SARS_CoV_2 T478K 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. T716I 2022 Microbial pathogenesis Table SARS_CoV_2 T716I 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. T749I 2022 Microbial pathogenesis Table SARS_CoV_2 T749I 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. T77A 2022 Microbial pathogenesis Table SARS_CoV_2 T77A 0 4 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. V149A 2022 Microbial pathogenesis Table SARS_CoV_2 V149A 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. V70del 2022 Microbial pathogenesis Table SARS_CoV_2 V70del 0 6 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. V82A 2022 Microbial pathogenesis Table SARS_CoV_2 V82A 0 4 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Y144del 2022 Microbial pathogenesis Table SARS_CoV_2 Y144del 0 7 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. A222V 2021 Frontiers in medicine Table SARS_CoV_2 A222V 0 5 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. A522V 2021 Frontiers in medicine Table SARS_CoV_2 A522V 0 5 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. D574Y 2021 Frontiers in medicine Table SARS_CoV_2 D574Y 0 5 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. D614G 2021 Frontiers in medicine Table SARS_CoV_2 D614G 0 5 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. E154K 2021 Frontiers in medicine Table SARS_CoV_2 E154K 0 5 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. E484Q 2021 Frontiers in medicine Table SARS_CoV_2 E484Q 0 5 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. E583D 2021 Frontiers in medicine Table SARS_CoV_2 E583D 0 5 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. F490S 2021 Frontiers in medicine Table SARS_CoV_2 F490S 0 5 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. G446V 2021 Frontiers in medicine Table SARS_CoV_2 G446V 0 5 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. K417N 2021 Frontiers in medicine Table SARS_CoV_2 K417N 0 5 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. K558N 2021 Frontiers in medicine Table SARS_CoV_2 K558N 0 5 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. L18R 2021 Frontiers in medicine Table SARS_CoV_2 L18R 0 4 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. L24S 2021 Frontiers in medicine Table SARS_CoV_2 L24S 0 4 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. L452R 2021 Frontiers in medicine Table SARS_CoV_2 L452R 0 5 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. L585H 2021 Frontiers in medicine Table SARS_CoV_2 L585H 0 5 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. P681R 2021 Frontiers in medicine Table SARS_CoV_2 P681R 0 5 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. S477N 2021 Frontiers in medicine Table SARS_CoV_2 S477N 0 5 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. T19R 2021 Frontiers in medicine Table SARS_CoV_2 T19R 0 4 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. T478K 2021 Frontiers in medicine Table SARS_CoV_2 T478K 0 5 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. T95I 2021 Frontiers in medicine Table SARS_CoV_2 T95I 0 4 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. T95S 2021 Frontiers in medicine Table SARS_CoV_2 T95S 0 4 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. W258L 2021 Frontiers in medicine Table SARS_CoV_2 W258L 0 5 35071665 Infection spread simulation technology in a mixed state of multi variant viruses. L452R 2022 AIMS public health Table SARS_CoV_2 L452R 0 5 35071665 Infection spread simulation technology in a mixed state of multi variant viruses. N501Y 2022 AIMS public health Table SARS_CoV_2 N501Y 0 5 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. D614G 2022 Scientific reports Table SARS_CoV_2 D614G 0 5 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. F106F 2022 Scientific reports Table SARS_CoV_2 F106F 0 5 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. G204R 2022 Scientific reports Table SARS_CoV_2 G204R 0 5 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. L216L 2022 Scientific reports Table SARS_CoV_2 L216L 0 5 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. N73N 2022 Scientific reports Table SARS_CoV_2 N73N 0 4 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. Q57H 2022 Scientific reports Table SARS_CoV_2 Q57H 0 4 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. R203K 2022 Scientific reports Table SARS_CoV_2 R203K 0 5 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. R203R 2022 Scientific reports Table SARS_CoV_2 R203R 0 5 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. R203S 2022 Scientific reports Table SARS_CoV_2 R203S 0 5 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. S194L 2022 Scientific reports Table SARS_CoV_2 S194L 0 5 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. S24L 2022 Scientific reports Table SARS_CoV_2 S24L 0 4 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. T85I 2022 Scientific reports Table SARS_CoV_2 T85I 0 4 35079901 Trypsin enhances SARS-CoV-2 infection by facilitating viral entry. C1252T 2022 Archives of virology Table SARS_CoV_2 C1252T 0 6 35079901 Trypsin enhances SARS-CoV-2 infection by facilitating viral entry. C92A 2022 Archives of virology Table SARS_CoV_2 C92A 0 4 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. 145del 2022 Archives of virology Table SARS_CoV_2 145del 0 6 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. A222V 2022 Archives of virology Table SARS_CoV_2 A222V 0 5 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. A570D 2022 Archives of virology Table SARS_CoV_2 A570D 0 5 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. D1118H 2022 Archives of virology Table SARS_CoV_2 D1118H 0 6 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. D614G 2022 Archives of virology Table SARS_CoV_2 D614G 0 5 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. D839Y 2022 Archives of virology Table SARS_CoV_2 D839Y 0 5 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. L1063F 2022 Archives of virology Table SARS_CoV_2 L1063F 0 6 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. L176F 2022 Archives of virology Table SARS_CoV_2 L176F 0 5 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. L216F 2022 Archives of virology Table SARS_CoV_2 L216F 0 5 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. M740V 2022 Archives of virology Table SARS_CoV_2 M740V 0 5 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. N439K 2022 Archives of virology Table SARS_CoV_2 N439K 0 5 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. N501Y 2022 Archives of virology Table SARS_CoV_2 N501Y 0 5 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. N751Y 2022 Archives of virology Table SARS_CoV_2 N751Y 0 5 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. P1162R 2022 Archives of virology Table SARS_CoV_2 P1162R 0 6 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. P681H 2022 Archives of virology Table SARS_CoV_2 P681H 0 5 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. S477N 2022 Archives of virology Table SARS_CoV_2 S477N 0 5 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. S982A 2022 Archives of virology Table SARS_CoV_2 S982A 0 5 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. T716I 2022 Archives of virology Table SARS_CoV_2 T716I 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. A1812D 2022 Microbiology resource announcements Table SARS_CoV_2 A1812D 0 6 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. A3497V 2022 Microbiology resource announcements Table SARS_CoV_2 A3497V 0 6 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. A51V 2022 Microbiology resource announcements Table SARS_CoV_2 A51V 0 4 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. C20F 2022 Microbiology resource announcements Table SARS_CoV_2 C20F 0 4 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. D294Y 2022 Microbiology resource announcements Table SARS_CoV_2 D294Y 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. D3042N 2022 Microbiology resource announcements Table SARS_CoV_2 D3042N 0 6 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. D614G 2022 Microbiology resource announcements Table SARS_CoV_2 D614G 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. D936Y 2022 Microbiology resource announcements Table SARS_CoV_2 D936Y 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. G204R 2022 Microbiology resource announcements Table SARS_CoV_2 G204R 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. G2180V 2022 Microbiology resource announcements Table SARS_CoV_2 G2180V 0 6 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. H1838Y 2022 Microbiology resource announcements Table SARS_CoV_2 H1838Y 0 6 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. H243R 2022 Microbiology resource announcements Table SARS_CoV_2 H243R 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. I121L 2022 Microbiology resource announcements Table SARS_CoV_2 I121L 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. K3577R 2022 Microbiology resource announcements Table SARS_CoV_2 K3577R 0 6 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. L18F 2022 Microbiology resource announcements Table SARS_CoV_2 L18F 0 4 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. M187I 2022 Microbiology resource announcements Table SARS_CoV_2 M187I 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. M3752I 2022 Microbiology resource announcements Table SARS_CoV_2 M3752I 0 6 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. P104L 2022 Microbiology resource announcements Table SARS_CoV_2 P104L 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. P10S 2022 Microbiology resource announcements Table SARS_CoV_2 P10S 0 4 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. P1207L 2022 Microbiology resource announcements Table SARS_CoV_2 P1207L 0 6 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. P13L 2022 Microbiology resource announcements Table SARS_CoV_2 P13L 0 4 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. P2144S 2022 Microbiology resource announcements Table SARS_CoV_2 P2144S 0 6 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. P240S 2022 Microbiology resource announcements Table SARS_CoV_2 P240S 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. P255S 2022 Microbiology resource announcements Table SARS_CoV_2 P255S 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. P309S 2022 Microbiology resource announcements Table SARS_CoV_2 P309S 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. P314L 2022 Microbiology resource announcements Table SARS_CoV_2 P314L 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. P3504H 2022 Microbiology resource announcements Table SARS_CoV_2 P3504H 0 6 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. Q57H 2022 Microbiology resource announcements Table SARS_CoV_2 Q57H 0 4 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. R102G 2022 Microbiology resource announcements Table SARS_CoV_2 R102G 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. R195T 2022 Microbiology resource announcements Table SARS_CoV_2 R195T 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. R203K 2022 Microbiology resource announcements Table SARS_CoV_2 R203K 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. S318L 2022 Microbiology resource announcements Table SARS_CoV_2 S318L 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. S58I 2022 Microbiology resource announcements Table SARS_CoV_2 S58I 0 4 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. T76I 2022 Microbiology resource announcements Table SARS_CoV_2 T76I 0 4 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. W131C 2022 Microbiology resource announcements Table SARS_CoV_2 W131C 0 5 35084216 Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India. Y1759H 2022 Microbiology resource announcements Table SARS_CoV_2 Y1759H 0 6 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. D614G 2022 The Lancet. Infectious diseases Table SARS_CoV_2 D614G 0 5 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. D614G 2022 Cell reports Table SARS_CoV_2 D614G 0 5 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. S1330S 2022 Cell reports Table SARS_CoV_2 S1330S 0 6 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ala156Ser 2021 Frontiers in microbiology Table SARS_CoV_2 A156S 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ala182Ser 2021 Frontiers in microbiology Table SARS_CoV_2 A182S 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ala220Val 2021 Frontiers in microbiology Table SARS_CoV_2 A220V 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ala222Val 2021 Frontiers in microbiology Table SARS_CoV_2 A222V 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ala262Ser 2021 Frontiers in microbiology Table SARS_CoV_2 A262S 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ala414Ser 2021 Frontiers in microbiology Table SARS_CoV_2 A414S 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ala4918Val 2021 Frontiers in microbiology Table SARS_CoV_2 A4918V 0 12 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ala4921Val 2021 Frontiers in microbiology Table SARS_CoV_2 A4921V 0 12 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ala570Asp 2021 Frontiers in microbiology Table SARS_CoV_2 A570D 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ala67Val 2021 Frontiers in microbiology Table SARS_CoV_2 A67V 0 10 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ala684Val 2021 Frontiers in microbiology Table SARS_CoV_2 A684V 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ala701Val 2021 Frontiers in microbiology Table SARS_CoV_2 A701V 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ala899Ser 2021 Frontiers in microbiology Table SARS_CoV_2 A899S 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Arg1091Cys 2021 Frontiers in microbiology Table SARS_CoV_2 R1091C 0 12 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Arg237Lys 2021 Frontiers in microbiology Table SARS_CoV_2 R237K 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Arg346Ser 2021 Frontiers in microbiology Table SARS_CoV_2 R346S 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Asn440Lys 2021 Frontiers in microbiology Table SARS_CoV_2 N440K 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Asn4480Ser 2021 Frontiers in microbiology Table SARS_CoV_2 N4480S 0 12 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Asn501Tyr 2021 Frontiers in microbiology Table SARS_CoV_2 N501Y 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Asp1118His 2021 Frontiers in microbiology Table SARS_CoV_2 D1118H 0 12 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Asp215Gly 2021 Frontiers in microbiology Table SARS_CoV_2 D215G 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Asp377Tyr 2021 Frontiers in microbiology Table SARS_CoV_2 D377Y 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Asp3Leu 2021 Frontiers in microbiology Table SARS_CoV_2 D3L 0 9 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Asp574Tyr 2021 Frontiers in microbiology Table SARS_CoV_2 D574Y 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Asp614Gly 2021 Frontiers in microbiology Table SARS_CoV_2 D614G 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Asp63Tyr 2021 Frontiers in microbiology Table SARS_CoV_2 D63Y 0 10 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Asp80Ala 2021 Frontiers in microbiology Table SARS_CoV_2 D80A 0 10 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Asp80Tyr 2021 Frontiers in microbiology Table SARS_CoV_2 D80Y 0 10 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Asp98Asn 2021 Frontiers in microbiology Table SARS_CoV_2 D98N 0 10 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Gln229His 2021 Frontiers in microbiology Table SARS_CoV_2 Q229H 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Gln677His 2021 Frontiers in microbiology Table SARS_CoV_2 Q677H 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Glu484Lys 2021 Frontiers in microbiology Table SARS_CoV_2 E484K 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Glu5136Asp 2021 Frontiers in microbiology Table SARS_CoV_2 E5136D 0 12 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Gly212Val 2021 Frontiers in microbiology Table SARS_CoV_2 G212V 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Gly932Val 2021 Frontiers in microbiology Table SARS_CoV_2 G932V 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.His145Tyr 2021 Frontiers in microbiology Table SARS_CoV_2 H145Y 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Leu18Phe 2021 Frontiers in microbiology Table SARS_CoV_2 L18F 0 10 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Leu452Arg 2021 Frontiers in microbiology Table SARS_CoV_2 L452R 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Leu5030Phe 2021 Frontiers in microbiology Table SARS_CoV_2 L5030F 0 12 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Lys1073Asn 2021 Frontiers in microbiology Table SARS_CoV_2 K1073N 0 12 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Lys417Asn 2021 Frontiers in microbiology Table SARS_CoV_2 K417N 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Pro13Ser 2021 Frontiers in microbiology Table SARS_CoV_2 P13S 0 10 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Pro272Leu 2021 Frontiers in microbiology Table SARS_CoV_2 P272L 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Pro326Leu 2021 Frontiers in microbiology Table SARS_CoV_2 P326L 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Pro4656Thr 2021 Frontiers in microbiology Table SARS_CoV_2 P4656T 0 12 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Pro46Ser 2021 Frontiers in microbiology Table SARS_CoV_2 P46S 0 10 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Pro4715Leu 2021 Frontiers in microbiology Table SARS_CoV_2 P4715L 0 12 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Pro681His 2021 Frontiers in microbiology Table SARS_CoV_2 P681H 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Pro812Ser 2021 Frontiers in microbiology Table SARS_CoV_2 P812S 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ser1147Leu 2021 Frontiers in microbiology Table SARS_CoV_2 S1147L 0 12 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ser12Phe 2021 Frontiers in microbiology Table SARS_CoV_2 S12F 0 10 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ser180Ile 2021 Frontiers in microbiology Table SARS_CoV_2 S180I 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ser186Tyr 2021 Frontiers in microbiology Table SARS_CoV_2 S186Y 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ser187Ala 2021 Frontiers in microbiology Table SARS_CoV_2 S187A 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ser197Thr 2021 Frontiers in microbiology Table SARS_CoV_2 S197T 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ser235Phe 2021 Frontiers in microbiology Table SARS_CoV_2 S235F 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ser416Leu 2021 Frontiers in microbiology Table SARS_CoV_2 S416L 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ser884Cys 2021 Frontiers in microbiology Table SARS_CoV_2 S884C 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Ser982Ala 2021 Frontiers in microbiology Table SARS_CoV_2 S982A 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Thr1027Ile 2021 Frontiers in microbiology Table SARS_CoV_2 T1027I 0 12 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Thr148Ala 2021 Frontiers in microbiology Table SARS_CoV_2 T148A 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Thr205Ile 2021 Frontiers in microbiology Table SARS_CoV_2 T205I 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Thr24Ile 2021 Frontiers in microbiology Table SARS_CoV_2 T24I 0 10 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Thr379Ile 2021 Frontiers in microbiology Table SARS_CoV_2 T379I 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Thr417Ser 2021 Frontiers in microbiology Table SARS_CoV_2 T417S 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Thr4418Ile 2021 Frontiers in microbiology Table SARS_CoV_2 T4418I 0 12 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Thr4477Ile 2021 Frontiers in microbiology Table SARS_CoV_2 T4477I 0 12 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Thr4644Ile 2021 Frontiers in microbiology Table SARS_CoV_2 T4644I 0 12 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Thr4794Ile 2021 Frontiers in microbiology Table SARS_CoV_2 T4794I 0 12 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Thr696Ile 2021 Frontiers in microbiology Table SARS_CoV_2 T696I 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Thr716Ile 2021 Frontiers in microbiology Table SARS_CoV_2 T716I 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Thr732Ala 2021 Frontiers in microbiology Table SARS_CoV_2 T732A 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Thr76Ile 2021 Frontiers in microbiology Table SARS_CoV_2 T76I 0 10 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Trp152Arg 2021 Frontiers in microbiology Table SARS_CoV_2 W152R 0 11 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Tyr144del 2021 Frontiers in microbiology Table SARS_CoV_2 Y144del 0 9 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. p.Tyr144Phe 2021 Frontiers in microbiology Table SARS_CoV_2 Y144F 0 11 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. A570D 2022 Vaccine Table SARS_CoV_2 A570D 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. A701V 2022 Vaccine Table SARS_CoV_2 A701V 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. D1118H 2022 Vaccine Table SARS_CoV_2 D1118H 0 6 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. D138Y 2022 Vaccine Table SARS_CoV_2 D138Y 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. D215G 2022 Vaccine Table SARS_CoV_2 D215G 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. D614G 2022 Vaccine Table SARS_CoV_2 D614G 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. D80A 2022 Vaccine Table SARS_CoV_2 D80A 0 4 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. D950N 2022 Vaccine Table SARS_CoV_2 D950N 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. E156G 2022 Vaccine Table SARS_CoV_2 E156G 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. E484K 2022 Vaccine Table SARS_CoV_2 E484K 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. G142D 2022 Vaccine Table SARS_CoV_2 G142D 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. H655Y 2022 Vaccine Table SARS_CoV_2 H655Y 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. K417N 2022 Vaccine Table SARS_CoV_2 K417N 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. K417T 2022 Vaccine Table SARS_CoV_2 K417T 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. L18F 2022 Vaccine Table SARS_CoV_2 L18F 0 4 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. L452R 2022 Vaccine Table SARS_CoV_2 L452R 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. N501Y 2022 Vaccine Table SARS_CoV_2 N501Y 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. P26S 2022 Vaccine Table SARS_CoV_2 P26S 0 4 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. P681H 2022 Vaccine Table SARS_CoV_2 P681H 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. P681R 2022 Vaccine Table SARS_CoV_2 P681R 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. R190S 2022 Vaccine Table SARS_CoV_2 R190S 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. R246I 2022 Vaccine Table SARS_CoV_2 R246I 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. S13I 2022 Vaccine Table SARS_CoV_2 S13I 0 4 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. S982A 2022 Vaccine Table SARS_CoV_2 S982A 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. T1027I 2022 Vaccine Table SARS_CoV_2 T1027I 0 6 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. T19R 2022 Vaccine Table SARS_CoV_2 T19R 0 4 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. T20N 2022 Vaccine Table SARS_CoV_2 T20N 0 4 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. T478K 2022 Vaccine Table SARS_CoV_2 T478K 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. T716I 2022 Vaccine Table SARS_CoV_2 T716I 0 5 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. W152C 2022 Vaccine Table SARS_CoV_2 W152C 0 5 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. E2621L 2022 Cell reports Table SARS_CoV_2 E2621L 0 6 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. R32A 2022 Cell reports Table SARS_CoV_2 R32A 0 4 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. V08H 2022 Cell reports Table SARS_CoV_2 V08H 0 4 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. D155Y 2022 Computational and structural biotechnology journal Table SARS_CoV_2 D155Y 0 5 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. G172C 2022 Computational and structural biotechnology journal Table SARS_CoV_2 G172C 0 5 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. G172V 2022 Computational and structural biotechnology journal Table SARS_CoV_2 G172V 0 5 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. Q57H 2022 Computational and structural biotechnology journal Table SARS_CoV_2 Q57H 0 4 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. S171L 2022 Computational and structural biotechnology journal Table SARS_CoV_2 S171L 0 5 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. W131C 2022 Computational and structural biotechnology journal Table SARS_CoV_2 W131C 0 5 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. W131R 2022 Computational and structural biotechnology journal Table SARS_CoV_2 W131R 0 5 35130474 Amplification Artifact in SARS-CoV-2 Omicron Sequences Carrying P681R Mutation, New York, USA. P681R 2022 Emerging infectious diseases Table SARS_CoV_2 P681R 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. A475V 2022 ACS infectious diseases Table SARS_CoV_2 A475V 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. A520S 2022 ACS infectious diseases Table SARS_CoV_2 A520S 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. A522S 2022 ACS infectious diseases Table SARS_CoV_2 A522S 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. D427N 2022 ACS infectious diseases Table SARS_CoV_2 D427N 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. E484K 2022 ACS infectious diseases Table SARS_CoV_2 E484K 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. E484Q 2022 ACS infectious diseases Table SARS_CoV_2 E484Q 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. F490S 2022 ACS infectious diseases Table SARS_CoV_2 F490S 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. K417N 2022 ACS infectious diseases Table SARS_CoV_2 K417N 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. K417T 2022 ACS infectious diseases Table SARS_CoV_2 K417T 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. L452Q 2022 ACS infectious diseases Table SARS_CoV_2 L452Q 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. L452R 2022 ACS infectious diseases Table SARS_CoV_2 L452R 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. N439K 2022 ACS infectious diseases Table SARS_CoV_2 N439K 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. N440K 2022 ACS infectious diseases Table SARS_CoV_2 N440K 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. N440S 2022 ACS infectious diseases Table SARS_CoV_2 N440S 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. N501T 2022 ACS infectious diseases Table SARS_CoV_2 N501T 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. N501Y 2022 ACS infectious diseases Table SARS_CoV_2 N501Y 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. P384L 2022 ACS infectious diseases Table SARS_CoV_2 P384L 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. R346K 2022 ACS infectious diseases Table SARS_CoV_2 R346K 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. R346S 2022 ACS infectious diseases Table SARS_CoV_2 R346S 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. R357K 2022 ACS infectious diseases Table SARS_CoV_2 R357K 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. S477N 2022 ACS infectious diseases Table SARS_CoV_2 S477N 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. S494P 2022 ACS infectious diseases Table SARS_CoV_2 S494P 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. T478K 2022 ACS infectious diseases Table SARS_CoV_2 T478K 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. V367F 2022 ACS infectious diseases Table SARS_CoV_2 V367F 0 5 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Y449S 2022 ACS infectious diseases Table SARS_CoV_2 Y449S 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. D614G 2022 Infection and drug resistance Table SARS_CoV_2 D614G 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484A 2022 Infection and drug resistance Table SARS_CoV_2 E484A 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484D 2022 Infection and drug resistance Table SARS_CoV_2 E484D 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484G 2022 Infection and drug resistance Table SARS_CoV_2 E484G 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K 2022 Infection and drug resistance Table SARS_CoV_2 E484K 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. K417N 2022 Infection and drug resistance Table SARS_CoV_2 K417N 0 5 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. N501Y 2022 Infection and drug resistance Table SARS_CoV_2 N501Y 0 5 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. A701V 2022 Infection, genetics and evolution Table SARS_CoV_2 A701V 0 5 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. D138Y 2022 Infection, genetics and evolution Table SARS_CoV_2 D138Y 0 5 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. E484K 2022 Infection, genetics and evolution Table SARS_CoV_2 E484K 0 5 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. K417T 2022 Infection, genetics and evolution Table SARS_CoV_2 K417T 0 5 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. L18F 2022 Infection, genetics and evolution Table SARS_CoV_2 L18F 0 4 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. N501Y 2022 Infection, genetics and evolution Table SARS_CoV_2 N501Y 0 5 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. P80R 2022 Infection, genetics and evolution Table SARS_CoV_2 P80R 0 4 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. R246I 2022 Infection, genetics and evolution Table SARS_CoV_2 R246I 0 5 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. T205I 2022 Infection, genetics and evolution Table SARS_CoV_2 T205I 0 5 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. Y144del 2022 Infection, genetics and evolution Table SARS_CoV_2 Y144del 0 7 35151002 Rapid biosensing SARS-CoV-2 antibodies in vaccinated healthy donors. N501Y 2022 Biosensors & bioelectronics Table SARS_CoV_2 N501Y 0 5 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. D614G 2022 Gene reports Table SARS_CoV_2 D614G 0 5 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. T1117I 2022 Gene reports Table SARS_CoV_2 T1117I 0 6 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. D377Y 2022 Molecular systems biology Table SARS_CoV_2 D377Y 0 5 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. D614G 2022 Molecular systems biology Table SARS_CoV_2 D614G 0 5 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. E156G 2022 Molecular systems biology Table SARS_CoV_2 E156G 0 5 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. I82T 2022 Molecular systems biology Table SARS_CoV_2 I82T 0 4 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. L452R 2022 Molecular systems biology Table SARS_CoV_2 L452R 0 5 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. P323L 2022 Molecular systems biology Table SARS_CoV_2 P323L 0 5 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. P681R 2022 Molecular systems biology Table SARS_CoV_2 P681R 0 5 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. S26L 2022 Molecular systems biology Table SARS_CoV_2 S26L 0 4 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. T120I 2022 Molecular systems biology Table SARS_CoV_2 T120I 0 5 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. T19R 2022 Molecular systems biology Table SARS_CoV_2 T19R 0 4 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. T478K 2022 Molecular systems biology Table SARS_CoV_2 T478K 0 5 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. V82A 2022 Molecular systems biology Table SARS_CoV_2 V82A 0 4 35157870 Detection of SARS-CoV-2 RNA in wastewater, river water, and hospital wastewater of Nepal. N501Y 2022 The Science of the total environment Table SARS_CoV_2 N501Y 0 5 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. N501Y 2022 Microbiology spectrum Table SARS_CoV_2 N501Y 0 5 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. A22812C 2022 Microbiology spectrum Table SARS_CoV_2 A22812C 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. A23063T 2022 Microbiology spectrum Table SARS_CoV_2 A23063T 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. A23403G 2022 Microbiology spectrum Table SARS_CoV_2 A23403G 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. A28877T 2022 Microbiology spectrum Table SARS_CoV_2 A28877T 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. A5648C 2022 Microbiology spectrum Table SARS_CoV_2 A5648C 0 6 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. C12778T 2022 Microbiology spectrum Table SARS_CoV_2 C12778T 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. C13860T 2022 Microbiology spectrum Table SARS_CoV_2 C13860T 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. C14408T 2022 Microbiology spectrum Table SARS_CoV_2 C14408T 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. C21614T 2022 Microbiology spectrum Table SARS_CoV_2 C21614T 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. C21621A 2022 Microbiology spectrum Table SARS_CoV_2 C21621A 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. C21638T 2022 Microbiology spectrum Table SARS_CoV_2 C21638T 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. C23525T 2022 Microbiology spectrum Table SARS_CoV_2 C23525T 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. C241T 2022 Microbiology spectrum Table SARS_CoV_2 C241T 0 5 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. C24642T 2022 Microbiology spectrum Table SARS_CoV_2 C24642T 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. C2749T 2022 Microbiology spectrum Table SARS_CoV_2 C2749T 0 6 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. C28512G 2022 Microbiology spectrum Table SARS_CoV_2 C28512G 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. C3037T 2022 Microbiology spectrum Table SARS_CoV_2 C3037T 0 6 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. C3828T 2022 Microbiology spectrum Table SARS_CoV_2 C3828T 0 6 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. D138Y 2022 Microbiology spectrum Table SARS_CoV_2 D138Y 0 5 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. D614G 2022 Microbiology spectrum Table SARS_CoV_2 D614G 0 5 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. E1264D 2022 Microbiology spectrum Table SARS_CoV_2 E1264D 0 6 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. E484K 2022 Microbiology spectrum Table SARS_CoV_2 E484K 0 5 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. E92K 2022 Microbiology spectrum Table SARS_CoV_2 E92K 0 4 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. G17259T 2022 Microbiology spectrum Table SARS_CoV_2 G17259T 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. G204R 2022 Microbiology spectrum Table SARS_CoV_2 G204R 0 5 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. G21974T 2022 Microbiology spectrum Table SARS_CoV_2 G21974T 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. G22132T 2022 Microbiology spectrum Table SARS_CoV_2 G22132T 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. G23012A 2022 Microbiology spectrum Table SARS_CoV_2 G23012A 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. G28167A 2022 Microbiology spectrum Table SARS_CoV_2 G28167A 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. G28878C 2022 Microbiology spectrum Table SARS_CoV_2 G28878C 0 7 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. H655Y 2022 Microbiology spectrum Table SARS_CoV_2 H655Y 0 5 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. K1795Q 2022 Microbiology spectrum Table SARS_CoV_2 K1795Q 0 6 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. K417T 2022 Microbiology spectrum Table SARS_CoV_2 K417T 0 5 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. L18F 2022 Microbiology spectrum Table SARS_CoV_2 L18F 0 4 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. N501Y 2022 Microbiology spectrum Table SARS_CoV_2 N501Y 0 5 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. P26S 2022 Microbiology spectrum Table SARS_CoV_2 P26S 0 4 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. P314L 2022 Microbiology spectrum Table SARS_CoV_2 P314L 0 5 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. P80R 2022 Microbiology spectrum Table SARS_CoV_2 P80R 0 4 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. R190S 2022 Microbiology spectrum Table SARS_CoV_2 R190S 0 5 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. R203K 2022 Microbiology spectrum Table SARS_CoV_2 R203K 0 5 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. S1188L 2022 Microbiology spectrum Table SARS_CoV_2 S1188L 0 6 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. T1027I 2022 Microbiology spectrum Table SARS_CoV_2 T1027I 0 6 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. T20N 2022 Microbiology spectrum Table SARS_CoV_2 T20N 0 4 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. T733C 2022 Microbiology spectrum Table SARS_CoV_2 T733C 0 5 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.-25C>T 2022 PloS one Table SARS_CoV_2 C25T 0 8 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.10818G>T 2022 PloS one Table SARS_CoV_2 G10818T 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.1175G>A 2022 PloS one Table SARS_CoV_2 G1175A 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.13466C>T 2022 PloS one Table SARS_CoV_2 C13466T 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.14144C>T 2022 PloS one Table SARS_CoV_2 C14144T 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.1430G>A 2022 PloS one Table SARS_CoV_2 G1430A 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.14541C>T 2022 PloS one Table SARS_CoV_2 C14541T 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.15060C>T 2022 PloS one Table SARS_CoV_2 C15060T 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.16383G>T 2022 PloS one Table SARS_CoV_2 G16383T 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.16983T>C 2022 PloS one Table SARS_CoV_2 T16983C 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.171G>T 2022 PloS one Table SARS_CoV_2 G171T 0 8 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.17483C>T 2022 PloS one Table SARS_CoV_2 C17483T 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.17594A>G 2022 PloS one Table SARS_CoV_2 A17594G 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.17796C>T 2022 PloS one Table SARS_CoV_2 C17796T 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.18291C>T 2022 PloS one Table SARS_CoV_2 C18291T 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.1839G>A 2022 PloS one Table SARS_CoV_2 G1839A 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.1841A>G 2022 PloS one Table SARS_CoV_2 A1841G 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.18613C>T 2022 PloS one Table SARS_CoV_2 C18613T 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.19575T>C 2022 PloS one Table SARS_CoV_2 T19575C 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.20004A>G 2022 PloS one Table SARS_CoV_2 A20004G 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.2151C>T 2022 PloS one Table SARS_CoV_2 C2151T 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.2169C>T 2022 PloS one Table SARS_CoV_2 C2169T 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.2215A>G 2022 PloS one Table SARS_CoV_2 A2215G 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.2293C>T 2022 PloS one Table SARS_CoV_2 C2293T 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.2367C>T 2022 PloS one Table SARS_CoV_2 C2367T 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.251T>C 2022 PloS one Table SARS_CoV_2 T251C 0 8 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.2626G>A 2022 PloS one Table SARS_CoV_2 G2626A 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.2772C>T 2022 PloS one Table SARS_CoV_2 C2772T 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.307G>T 2022 PloS one Table SARS_CoV_2 G307T 0 8 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.37G>T 2022 PloS one Table SARS_CoV_2 G37T 0 7 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.384C>T 2022 PloS one Table SARS_CoV_2 C384T 0 8 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.38C>T 2022 PloS one Table SARS_CoV_2 C38T 0 7 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.48C>T 2022 PloS one Table SARS_CoV_2 C48T 0 7 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.581C>T 2022 PloS one Table SARS_CoV_2 C581T 0 8 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.587G>T 2022 PloS one Table SARS_CoV_2 G587T 0 8 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.590C>T 2022 PloS one Table SARS_CoV_2 C590T 0 8 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.6047C>A 2022 PloS one Table SARS_CoV_2 C6047A 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.608G>A 2022 PloS one Table SARS_CoV_2 G608A 0 8 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.609G>A 2022 PloS one Table SARS_CoV_2 G609A 0 8 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.610G>C 2022 PloS one Table SARS_CoV_2 G610C 0 8 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.71C>T 2022 PloS one Table SARS_CoV_2 C71T 0 7 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.7275T>C 2022 PloS one Table SARS_CoV_2 T7275C 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.752G>T 2022 PloS one Table SARS_CoV_2 G752T 0 8 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.794C>T 2022 PloS one Table SARS_CoV_2 C794T 0 8 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.8517C>T 2022 PloS one Table SARS_CoV_2 C8517T 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.898A>T 2022 PloS one Table SARS_CoV_2 A898T 0 8 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.9212T>A 2022 PloS one Table SARS_CoV_2 T9212A 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. c.9832G>A 2022 PloS one Table SARS_CoV_2 G9832A 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Ala4489Val 2022 PloS one Table SARS_CoV_2 A4489V 0 12 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Ala876Thr 2022 PloS one Table SARS_CoV_2 A876T 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Arg203Arg 2022 PloS one Table SARS_CoV_2 R203R 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Arg203Lys 2022 PloS one Table SARS_CoV_2 R203K 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Arg5661Arg 2022 PloS one Table SARS_CoV_2 R5661R 0 12 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Asn5020Asn 2022 PloS one Table SARS_CoV_2 N5020N 0 12 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Asp103Tyr 2022 PloS one Table SARS_CoV_2 D103Y 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Asp128Asp 2022 PloS one Table SARS_CoV_2 D128D 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Asp448del 2022 PloS one Table SARS_CoV_2 D448del 0 9 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Asp614Gly 2022 PloS one Table SARS_CoV_2 D614G 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Gln57His 2022 PloS one Table SARS_CoV_2 Q57H 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Gln613Gln 2022 PloS one Table SARS_CoV_2 Q613Q 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Gly196Val 2022 PloS one Table SARS_CoV_2 G196V 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Gly204Arg 2022 PloS one Table SARS_CoV_2 G204R 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Gly251Val 2022 PloS one Table SARS_CoV_2 G251V 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Gly3278Ser 2022 PloS one Table SARS_CoV_2 G3278S 0 12 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Gly392Asp 2022 PloS one Table SARS_CoV_2 G392D 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Ile300Phe 2022 PloS one Table SARS_CoV_2 I300F 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Ile739Val 2022 PloS one Table SARS_CoV_2 I739V 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Leu16Leu 2022 PloS one Table SARS_CoV_2 L16L 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Leu3606Phe 2022 PloS one Table SARS_CoV_2 L3606F 0 12 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Leu5932Leu 2022 PloS one Table SARS_CoV_2 L5932L 0 12 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Leu84Ser 2022 PloS one Table SARS_CoV_2 L84S 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Phe3071Tyr 2022 PloS one Table SARS_CoV_2 F3071Y 0 12 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Phe924Phe 2022 PloS one Table SARS_CoV_2 F924F 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Pro13Leu 2022 PloS one Table SARS_CoV_2 P13L 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Pro4715Leu 2022 PloS one Table SARS_CoV_2 P4715L 0 12 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Pro5828Leu 2022 PloS one Table SARS_CoV_2 P5828L 0 12 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Pro765Ser 2022 PloS one Table SARS_CoV_2 P765S 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Ser194Leu 2022 PloS one Table SARS_CoV_2 S194L 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Ser197Leu 2022 PloS one Table SARS_CoV_2 S197L 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Ser24Leu 2022 PloS one Table SARS_CoV_2 S24L 0 10 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Ser2839Ser 2022 PloS one Table SARS_CoV_2 S2839S 0 12 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Ser477Asn 2022 PloS one Table SARS_CoV_2 S477N 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Thr2016Lys 2022 PloS one Table SARS_CoV_2 T2016K 0 12 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Thr2425Thr 2022 PloS one Table SARS_CoV_2 T2425T 0 12 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Thr265Ile 2022 PloS one Table SARS_CoV_2 T265I 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Thr5461Thr 2022 PloS one Table SARS_CoV_2 T5461T 0 12 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Thr723Thr 2022 PloS one Table SARS_CoV_2 T723T 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Tyr4847Tyr 2022 PloS one Table SARS_CoV_2 Y4847Y 0 12 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Tyr5865Cys 2022 PloS one Table SARS_CoV_2 Y5865C 0 12 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Tyr717Tyr 2022 PloS one Table SARS_CoV_2 Y717Y 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Tyr789Tyr 2022 PloS one Table SARS_CoV_2 Y789Y 0 11 35171928 Worldwide SARS-CoV-2 haplotype distribution in early pandemic. p.Val13Leu 2022 PloS one Table SARS_CoV_2 V13L 0 10 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. C29197T 2022 PloS one Table SARS_CoV_2 C29197T 0 7 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. G29227T 2022 PloS one Table SARS_CoV_2 G29227T 0 7 35178586 Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. E484K 2022 Archives of virology Table SARS_CoV_2 E484K 0 5 35178586 Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. E484Q 2022 Archives of virology Table SARS_CoV_2 E484Q 0 5 35178586 Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. L452R 2022 Archives of virology Table SARS_CoV_2 L452R 0 5 35178586 Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. N501Y 2022 Archives of virology Table SARS_CoV_2 N501Y 0 5 35178586 Emergence in southern France of a new SARS-CoV-2 variant harbouring both N501Y and E484K substitutions in the spike protein. P681H 2022 Archives of virology Table SARS_CoV_2 P681H 0 5 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. E484K 2022 Scientific reports Table SARS_CoV_2 E484K 0 5 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. A964A 2022 Infection, genetics and evolution Table SARS_CoV_2 A964A 0 5 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. C241T 2022 Infection, genetics and evolution Table SARS_CoV_2 C241T 0 5 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. D222A 2022 Infection, genetics and evolution Table SARS_CoV_2 D222A 0 5 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. D614G 2022 Infection, genetics and evolution Table SARS_CoV_2 D614G 0 5 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. E11E 2022 Infection, genetics and evolution Table SARS_CoV_2 E11E 0 4 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. F53F 2022 Infection, genetics and evolution Table SARS_CoV_2 F53F 0 4 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. F924F 2022 Infection, genetics and evolution Table SARS_CoV_2 F924F 0 5 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. G614D 2022 Infection, genetics and evolution Table SARS_CoV_2 G614D 0 5 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. L3606F 2022 Infection, genetics and evolution Table SARS_CoV_2 L3606F 0 6 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. L5022F 2022 Infection, genetics and evolution Table SARS_CoV_2 L5022F 0 6 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. M84I 2022 Infection, genetics and evolution Table SARS_CoV_2 M84I 0 4 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. P3613L 2022 Infection, genetics and evolution Table SARS_CoV_2 P3613L 0 6 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. P4715L 2022 Infection, genetics and evolution Table SARS_CoV_2 P4715L 0 6 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. P5398S 2022 Infection, genetics and evolution Table SARS_CoV_2 P5398S 0 6 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. S5398P 2022 Infection, genetics and evolution Table SARS_CoV_2 S5398P 0 6 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. T241C 2022 Infection, genetics and evolution Table SARS_CoV_2 T241C 0 5 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. T2648N 2022 Infection, genetics and evolution Table SARS_CoV_2 T2648N 0 6 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. T265I 2022 Infection, genetics and evolution Table SARS_CoV_2 T265I 0 5 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. E484K 2022 Process biochemistry (Barking, London, England) Table SARS_CoV_2 E484K 0 5 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. E484Q 2022 Process biochemistry (Barking, London, England) Table SARS_CoV_2 E484Q 0 5 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. K417T 2022 Process biochemistry (Barking, London, England) Table SARS_CoV_2 K417T 0 5 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. L452R 2022 Process biochemistry (Barking, London, England) Table SARS_CoV_2 L452R 0 5 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. N501Y 2022 Process biochemistry (Barking, London, England) Table SARS_CoV_2 N501Y 0 5 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. A21801C 2022 Archives of virology Table SARS_CoV_2 A21801C 0 7 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. A21993C 2022 Archives of virology Table SARS_CoV_2 A21993C 0 7 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. A22206G 2022 Archives of virology Table SARS_CoV_2 A22206G 0 7 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. A23063T 2022 Archives of virology Table SARS_CoV_2 A23063T 0 7 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. A23403G 2022 Archives of virology Table SARS_CoV_2 A23403G 0 7 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. A701V 2022 Archives of virology Table SARS_CoV_2 A701V 0 5 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. C21846T 2022 Archives of virology Table SARS_CoV_2 C21846T 0 7 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. C23604A 2022 Archives of virology Table SARS_CoV_2 C23604A 0 7 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. C23664T 2022 Archives of virology Table SARS_CoV_2 C23664T 0 7 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. D215G 2022 Archives of virology Table SARS_CoV_2 D215G 0 5 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. D614G 2022 Archives of virology Table SARS_CoV_2 D614G 0 5 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. D80A 2022 Archives of virology Table SARS_CoV_2 D80A 0 4 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. D950N 2022 Archives of virology Table SARS_CoV_2 D950N 0 5 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. E484K 2022 Archives of virology Table SARS_CoV_2 E484K 0 5 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. G22599A 2022 Archives of virology Table SARS_CoV_2 G22599A 0 7 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. G22813T 2022 Archives of virology Table SARS_CoV_2 G22813T 0 7 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. G23012A 2022 Archives of virology Table SARS_CoV_2 G23012A 0 7 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. G24410A 2022 Archives of virology Table SARS_CoV_2 G24410A 0 7 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. N501Y 2022 Archives of virology Table SARS_CoV_2 N501Y 0 5 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. P681H 2022 Archives of virology Table SARS_CoV_2 P681H 0 5 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. R346K 2022 Archives of virology Table SARS_CoV_2 R346K 0 5 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. T21995A 2022 Archives of virology Table SARS_CoV_2 T21995A 0 7 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. T95I 2022 Archives of virology Table SARS_CoV_2 T95I 0 4 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. Y144S 2022 Archives of virology Table SARS_CoV_2 Y144S 0 5 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. Y145N 2022 Archives of virology Table SARS_CoV_2 Y145N 0 5 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. A3209V 2022 Microbiology spectrum Table SARS_CoV_2 A3209V 0 6 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. H17Y 2022 Microbiology spectrum Table SARS_CoV_2 H17Y 0 4 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. N679K 2022 Microbiology spectrum Table SARS_CoV_2 N679K 0 5 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. P681H 2022 Microbiology spectrum Table SARS_CoV_2 P681H 0 5 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. P909L 2022 Microbiology spectrum Table SARS_CoV_2 P909L 0 5 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. T23599G 2022 Microbiology spectrum Table SARS_CoV_2 T23599G 0 7 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. T951I 2022 Microbiology spectrum Table SARS_CoV_2 T951I 0 5 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. A22812A 2022 Microbiology spectrum Table SARS_CoV_2 A22812A 0 7 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. A22812C 2022 Microbiology spectrum Table SARS_CoV_2 A22812C 0 7 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. A23063A 2022 Microbiology spectrum Table SARS_CoV_2 A23063A 0 7 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. A23063T 2022 Microbiology spectrum Table SARS_CoV_2 A23063T 0 7 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. C23604A 2022 Microbiology spectrum Table SARS_CoV_2 C23604A 0 7 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. C23604C 2022 Microbiology spectrum Table SARS_CoV_2 C23604C 0 7 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. C23604G 2022 Microbiology spectrum Table SARS_CoV_2 C23604G 0 7 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. E484E 2022 Microbiology spectrum Table SARS_CoV_2 E484E 0 5 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. E484K 2022 Microbiology spectrum Table SARS_CoV_2 E484K 0 5 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. E484Q 2022 Microbiology spectrum Table SARS_CoV_2 E484Q 0 5 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. G22813T 2022 Microbiology spectrum Table SARS_CoV_2 G22813T 0 7 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. G23012A 2022 Microbiology spectrum Table SARS_CoV_2 G23012A 0 7 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. G23012C 2022 Microbiology spectrum Table SARS_CoV_2 G23012C 0 7 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. G23012G 2022 Microbiology spectrum Table SARS_CoV_2 G23012G 0 7 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. K417K 2022 Microbiology spectrum Table SARS_CoV_2 K417K 0 5 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. K417N 2022 Microbiology spectrum Table SARS_CoV_2 K417N 0 5 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. K417T 2022 Microbiology spectrum Table SARS_CoV_2 K417T 0 5 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. L452L 2022 Microbiology spectrum Table SARS_CoV_2 L452L 0 5 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. L452R 2022 Microbiology spectrum Table SARS_CoV_2 L452R 0 5 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. N501N 2022 Microbiology spectrum Table SARS_CoV_2 N501N 0 5 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. N501Y 2022 Microbiology spectrum Table SARS_CoV_2 N501Y 0 5 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. P681H 2022 Microbiology spectrum Table SARS_CoV_2 P681H 0 5 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. P681P 2022 Microbiology spectrum Table SARS_CoV_2 P681P 0 5 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. P681R 2022 Microbiology spectrum Table SARS_CoV_2 P681R 0 5 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. T22917G 2022 Microbiology spectrum Table SARS_CoV_2 T22917G 0 7 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. T22917T 2022 Microbiology spectrum Table SARS_CoV_2 T22917T 0 7 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. D614G 2022 PloS one Table SARS_CoV_2 D614G 0 5 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. G1223C 2022 PloS one Table SARS_CoV_2 G1223C 0 6 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. D614G 2022 Cell reports Table SARS_CoV_2 D614G 0 5 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. D614G 2022 Diagnostic microbiology and infectious disease Table SARS_CoV_2 D614G 0 5 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. D839Y 2022 Diagnostic microbiology and infectious disease Table SARS_CoV_2 D839Y 0 5 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. F133S 2022 Diagnostic microbiology and infectious disease Table SARS_CoV_2 F133S 0 5 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. G232A 2022 Diagnostic microbiology and infectious disease Table SARS_CoV_2 G232A 0 5 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. K77N 2022 Diagnostic microbiology and infectious disease Table SARS_CoV_2 K77N 0 4 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. R78M 2022 Diagnostic microbiology and infectious disease Table SARS_CoV_2 R78M 0 4 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. T768N 2022 Diagnostic microbiology and infectious disease Table SARS_CoV_2 T768N 0 5 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. T76I 2022 Diagnostic microbiology and infectious disease Table SARS_CoV_2 T76I 0 4 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. V1176F 2022 Diagnostic microbiology and infectious disease Table SARS_CoV_2 V1176F 0 6 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. V395A 2022 Diagnostic microbiology and infectious disease Table SARS_CoV_2 V395A 0 5 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. Y1272F 2022 Diagnostic microbiology and infectious disease Table SARS_CoV_2 Y1272F 0 6 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. Y380Q 2022 Diagnostic microbiology and infectious disease Table SARS_CoV_2 Y380Q 0 5 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. p.D614G 2022 Pathology Table SARS_CoV_2 D614G 0 7 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. p.D63G 2022 Pathology Table SARS_CoV_2 D63G 0 6 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. p.D950N 2022 Pathology Table SARS_CoV_2 D950N 0 7 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. p.G5063S 2022 Pathology Table SARS_CoV_2 G5063S;P5063S 0;0 8;8 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. p.I82T 2022 Pathology Table SARS_CoV_2 I82T 0 6 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. p.L452R 2022 Pathology Table SARS_CoV_2 L452R 0 7 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. p.P681R 2022 Pathology Table SARS_CoV_2 P681R 0 7 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. p.R1467S 2022 Pathology Table SARS_CoV_2 P1467S;R1467S 0;0 8;8 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. p.S1468C 2022 Pathology Table SARS_CoV_2 S1468C 0 8 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. p.S538A 2022 Pathology Table SARS_CoV_2 S538A 0 7 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. p.T19R 2022 Pathology Table SARS_CoV_2 T19R 0 6 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. p.T478K 2022 Pathology Table SARS_CoV_2 T478K 0 7 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. p.V4072A 2022 Pathology Table SARS_CoV_2 V4072A 0 8 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. A46R 2022 Frontiers in immunology Table SARS_CoV_2 A46R 0 4 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. A99V 2022 Frontiers in immunology Table SARS_CoV_2 A99V 0 4 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. D614G 2022 Frontiers in immunology Table SARS_CoV_2 D614G 0 5 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. E484K 2022 Frontiers in immunology Table SARS_CoV_2 E484K 0 5 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. G196V 2022 Frontiers in immunology Table SARS_CoV_2 G196V 0 5 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. G252V 2022 Frontiers in immunology Table SARS_CoV_2 G252V 0 5 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. K444R 2022 Frontiers in immunology Table SARS_CoV_2 K444R 0 5 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. L37F 2022 Frontiers in immunology Table SARS_CoV_2 L37F 0 4 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. L452R 2022 Frontiers in immunology Table SARS_CoV_2 L452R 0 5 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. N439K 2022 Frontiers in immunology Table SARS_CoV_2 N439K 0 5 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. N501Y 2022 Frontiers in immunology Table SARS_CoV_2 N501Y 0 5 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. P681R 2022 Frontiers in immunology Table SARS_CoV_2 P681R 0 5 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Q57H 2022 Frontiers in immunology Table SARS_CoV_2 Q57H 0 4 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. T85I 2022 Frontiers in immunology Table SARS_CoV_2 T85I 0 4 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. V13L 2022 Frontiers in immunology Table SARS_CoV_2 V13L 0 4 35222380 A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Y453F 2022 Frontiers in immunology Table SARS_CoV_2 Y453F 0 5 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. A23403G 2022 Saudi journal of biological sciences Table SARS_CoV_2 A23403G 0 7 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. C14408T 2022 Saudi journal of biological sciences Table SARS_CoV_2 C14408T 0 7 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. C18877T 2022 Saudi journal of biological sciences Table SARS_CoV_2 C18877T 0 7 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. C22444T 2022 Saudi journal of biological sciences Table SARS_CoV_2 C22444T 0 7 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. C241T 2022 Saudi journal of biological sciences Table SARS_CoV_2 C241T 0 5 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. C26735T 2022 Saudi journal of biological sciences Table SARS_CoV_2 C26735T 0 7 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. C28854T 2022 Saudi journal of biological sciences Table SARS_CoV_2 C28854T 0 7 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. D614G 2022 Saudi journal of biological sciences Table SARS_CoV_2 D614G 0 5 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. G25563T 2022 Saudi journal of biological sciences Table SARS_CoV_2 G25563T 0 7 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. P4715L 2022 Saudi journal of biological sciences Table SARS_CoV_2 P4715L 0 6 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. Q57H 2022 Saudi journal of biological sciences Table SARS_CoV_2 Q57H 0 4 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. S194L 2022 Saudi journal of biological sciences Table SARS_CoV_2 S194L 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. A570D 2022 Cell reports. Medicine Table SARS_CoV_2 A570D 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. A701V 2022 Cell reports. Medicine Table SARS_CoV_2 A701V 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. D1118H 2022 Cell reports. Medicine Table SARS_CoV_2 D1118H 0 6 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. D138Y 2022 Cell reports. Medicine Table SARS_CoV_2 D138Y 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. D215G 2022 Cell reports. Medicine Table SARS_CoV_2 D215G 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. D614G 2022 Cell reports. Medicine Table SARS_CoV_2 D614G 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. D950N 2022 Cell reports. Medicine Table SARS_CoV_2 D950N 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. E484K 2022 Cell reports. Medicine Table SARS_CoV_2 E484K 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. H655Y 2022 Cell reports. Medicine Table SARS_CoV_2 H655Y 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. K417N 2022 Cell reports. Medicine Table SARS_CoV_2 K417N 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. K417T 2022 Cell reports. Medicine Table SARS_CoV_2 K417T 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. L18F 2022 Cell reports. Medicine Table SARS_CoV_2 L18F 0 4 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. L452R 2022 Cell reports. Medicine Table SARS_CoV_2 L452R 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. N501Y 2022 Cell reports. Medicine Table SARS_CoV_2 N501Y 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. P26S 2022 Cell reports. Medicine Table SARS_CoV_2 P26S 0 4 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. P681H 2022 Cell reports. Medicine Table SARS_CoV_2 P681H 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. P681R 2022 Cell reports. Medicine Table SARS_CoV_2 P681R 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. R158G 2022 Cell reports. Medicine Table SARS_CoV_2 R158G 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. R190S 2022 Cell reports. Medicine Table SARS_CoV_2 R190S 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. S982A 2022 Cell reports. Medicine Table SARS_CoV_2 S982A 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. T1027I 2022 Cell reports. Medicine Table SARS_CoV_2 T1027I 0 6 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. T19R 2022 Cell reports. Medicine Table SARS_CoV_2 T19R 0 4 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. T20N 2022 Cell reports. Medicine Table SARS_CoV_2 T20N 0 4 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. T478K 2022 Cell reports. Medicine Table SARS_CoV_2 T478K 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. T716I 2022 Cell reports. Medicine Table SARS_CoV_2 T716I 0 5 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. V1176F 2022 Cell reports. Medicine Table SARS_CoV_2 V1176F 0 6 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. N501Y 2022 Clinical infectious diseases Table SARS_CoV_2 N501Y 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. E484A 2022 BMC medicine Table SARS_CoV_2 E484A 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. E484K 2022 BMC medicine Table SARS_CoV_2 E484K 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. G339D 2022 BMC medicine Table SARS_CoV_2 G339D 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. G446S 2022 BMC medicine Table SARS_CoV_2 G446S 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. G496S 2022 BMC medicine Table SARS_CoV_2 G496S 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. K417N 2022 BMC medicine Table SARS_CoV_2 K417N 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. L452R 2022 BMC medicine Table SARS_CoV_2 L452R 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. N440K 2022 BMC medicine Table SARS_CoV_2 N440K 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. N501Y 2022 BMC medicine Table SARS_CoV_2 N501Y 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. Q493K 2022 BMC medicine Table SARS_CoV_2 Q493K 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. Q498R 2022 BMC medicine Table SARS_CoV_2 Q498R 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. S371L 2022 BMC medicine Table SARS_CoV_2 S371L 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. S373P 2022 BMC medicine Table SARS_CoV_2 S373P 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. S375F 2022 BMC medicine Table SARS_CoV_2 S375F 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. S477N 2022 BMC medicine Table SARS_CoV_2 S477N 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. T478K 2022 BMC medicine Table SARS_CoV_2 T478K 0 5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. Y505H 2022 BMC medicine Table SARS_CoV_2 Y505H 0 5 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. A11217G 2022 Nature communications Table SARS_CoV_2 A11217G 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. A18366G 2022 Nature communications Table SARS_CoV_2 A18366G 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. A20262G 2022 Nature communications Table SARS_CoV_2 A20262G 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. A23063T 2022 Nature communications Table SARS_CoV_2 A23063T 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. A28273T 2022 Nature communications Table SARS_CoV_2 A28273T 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. A361G 2022 Nature communications Table SARS_CoV_2 A361G 0 5 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. A653V 2022 Nature communications Table SARS_CoV_2 A653V 0 5 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. A9204G 2022 Nature communications Table SARS_CoV_2 A9204G 0 6 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. C1122T 2022 Nature communications Table SARS_CoV_2 C1122T 0 6 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. C16293T 2022 Nature communications Table SARS_CoV_2 C16293T 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. C16466T 2022 Nature communications Table SARS_CoV_2 C16466T 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. C21614T 2022 Nature communications Table SARS_CoV_2 C21614T 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. C23520T 2022 Nature communications Table SARS_CoV_2 C23520T 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. C23525T 2022 Nature communications Table SARS_CoV_2 C23525T 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. C27247T 2022 Nature communications Table SARS_CoV_2 C27247T 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. C8782T 2022 Nature communications Table SARS_CoV_2 C8782T 0 6 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. D2980G 2022 Nature communications Table SARS_CoV_2 D2980G 0 6 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. D796Y 2022 Nature communications Table SARS_CoV_2 D796Y 0 5 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. G1219V 2022 Nature communications Table SARS_CoV_2 G1219V 0 6 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. G22468T 2022 Nature communications Table SARS_CoV_2 G22468T 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. G23948T 2022 Nature communications Table SARS_CoV_2 G23948T 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. G25218T 2022 Nature communications Table SARS_CoV_2 G25218T 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. G28878A 2022 Nature communications Table SARS_CoV_2 G28878A 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. G29742A 2022 Nature communications Table SARS_CoV_2 G29742A 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. H655Y 2022 Nature communications Table SARS_CoV_2 H655Y 0 5 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. L18F 2022 Nature communications Table SARS_CoV_2 L18F 0 4 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. L452R 2022 Nature communications Table SARS_CoV_2 L452R 0 5 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. L84S 2022 Nature communications Table SARS_CoV_2 L84S 0 4 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. N3651S 2022 Nature communications Table SARS_CoV_2 N3651S 0 6 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. N501Y 2022 Nature communications Table SARS_CoV_2 N501Y 0 5 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. P286L 2022 Nature communications Table SARS_CoV_2 P286L 0 5 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. P5401L 2022 Nature communications Table SARS_CoV_2 P5401L 0 6 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. S202N 2022 Nature communications Table SARS_CoV_2 S202N 0 5 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. T22917G 2022 Nature communications Table SARS_CoV_2 T22917G 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. T25541C 2022 Nature communications Table SARS_CoV_2 T25541C 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. T28144C 2022 Nature communications Table SARS_CoV_2 T28144C 0 7 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. V50A 2022 Nature communications Table SARS_CoV_2 V50A 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. C73I 2022 Informatics in medicine unlocked Table SARS_CoV_2 C73I 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. C73V 2022 Informatics in medicine unlocked Table SARS_CoV_2 C73V 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. C79A 2022 Informatics in medicine unlocked Table SARS_CoV_2 C79A 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. F68Y 2022 Informatics in medicine unlocked Table SARS_CoV_2 F68Y 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. G70A 2022 Informatics in medicine unlocked Table SARS_CoV_2 G70A 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. G94A 2022 Informatics in medicine unlocked Table SARS_CoV_2 G94A 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. G94D 2022 Informatics in medicine unlocked Table SARS_CoV_2 G94D 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. H80A 2022 Informatics in medicine unlocked Table SARS_CoV_2 H80A 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. H80R 2022 Informatics in medicine unlocked Table SARS_CoV_2 H80R 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. K78A 2022 Informatics in medicine unlocked Table SARS_CoV_2 K78A 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. K78G 2022 Informatics in medicine unlocked Table SARS_CoV_2 K78G 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. K93A 2022 Informatics in medicine unlocked Table SARS_CoV_2 K93A 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. K93E 2022 Informatics in medicine unlocked Table SARS_CoV_2 K93E 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. K93R 2022 Informatics in medicine unlocked Table SARS_CoV_2 K93R 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. K95A 2022 Informatics in medicine unlocked Table SARS_CoV_2 K95A 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. L92F 2022 Informatics in medicine unlocked Table SARS_CoV_2 L92F 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. L92Y 2022 Informatics in medicine unlocked Table SARS_CoV_2 L92Y 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. R78A 2022 Informatics in medicine unlocked Table SARS_CoV_2 R78A 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. R78G 2022 Informatics in medicine unlocked Table SARS_CoV_2 R78G 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. S72A 2022 Informatics in medicine unlocked Table SARS_CoV_2 S72A 0 4 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. Y96F 2022 Informatics in medicine unlocked Table SARS_CoV_2 Y96F 0 4 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. D614G 2022 GeroScience Table SARS_CoV_2 D614G 0 5 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. H655Y 2022 GeroScience Table SARS_CoV_2 H655Y 0 5 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. N501Y 2022 GeroScience Table SARS_CoV_2 N501Y 0 5 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. N679K 2022 GeroScience Table SARS_CoV_2 N679K 0 5 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. P681H 2022 GeroScience Table SARS_CoV_2 P681H 0 5 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. P681R 2022 GeroScience Table SARS_CoV_2 P681R 0 5 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. Q498R 2022 GeroScience Table SARS_CoV_2 Q498R 0 5 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. D614G 2022 Microbiology spectrum Table SARS_CoV_2 D614G 0 5 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. L452R 2022 3 Biotech Table SARS_CoV_2 L452R 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. A1643V 2022 Genetics and molecular biology Table SARS_CoV_2 A1643V 0 6 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. A27V 2022 Genetics and molecular biology Table SARS_CoV_2 A27V 0 4 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. A3209V 2022 Genetics and molecular biology Table SARS_CoV_2 A3209V 0 6 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. A33S 2022 Genetics and molecular biology Table SARS_CoV_2 A33S 0 4 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. A54V 2022 Genetics and molecular biology Table SARS_CoV_2 A54V 0 4 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. A845S 2022 Genetics and molecular biology Table SARS_CoV_2 A845S 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. D1264E 2022 Genetics and molecular biology Table SARS_CoV_2 D1264E 0 6 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. D138Y 2022 Genetics and molecular biology Table SARS_CoV_2 D138Y 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. D27Y 2022 Genetics and molecular biology Table SARS_CoV_2 D27Y 0 4 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. D614G 2022 Genetics and molecular biology Table SARS_CoV_2 D614G 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. E484K 2022 Genetics and molecular biology Table SARS_CoV_2 E484K 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. E5665D 2022 Genetics and molecular biology Table SARS_CoV_2 E5665D 0 6 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. E92K 2022 Genetics and molecular biology Table SARS_CoV_2 E92K 0 4 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. G150S 2022 Genetics and molecular biology Table SARS_CoV_2 G150S 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. G519S 2022 Genetics and molecular biology Table SARS_CoV_2 G519S 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. G614D 2022 Genetics and molecular biology Table SARS_CoV_2 G614D 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. H3509Y 2022 Genetics and molecular biology Table SARS_CoV_2 H3509Y 0 6 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. H655Y 2022 Genetics and molecular biology Table SARS_CoV_2 H655Y 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. K16N 2022 Genetics and molecular biology Table SARS_CoV_2 K16N 0 4 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. K1795Q 2022 Genetics and molecular biology Table SARS_CoV_2 K1795Q 0 6 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. K3353R 2022 Genetics and molecular biology Table SARS_CoV_2 K3353R 0 6 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. K417T 2022 Genetics and molecular biology Table SARS_CoV_2 K417T 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. K82N 2022 Genetics and molecular biology Table SARS_CoV_2 K82N 0 4 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. L18F 2022 Genetics and molecular biology Table SARS_CoV_2 L18F 0 4 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. L314P 2022 Genetics and molecular biology Table SARS_CoV_2 L314P 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. L642F 2022 Genetics and molecular biology Table SARS_CoV_2 L642F 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. L83F 2022 Genetics and molecular biology Table SARS_CoV_2 L83F 0 4 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. L85F 2022 Genetics and molecular biology Table SARS_CoV_2 L85F 0 4 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. N501Y 2022 Genetics and molecular biology Table SARS_CoV_2 N501Y 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. P2046T 2022 Genetics and molecular biology Table SARS_CoV_2 P2046T 0 6 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. P218L 2022 Genetics and molecular biology Table SARS_CoV_2 P218L 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. P26S 2022 Genetics and molecular biology Table SARS_CoV_2 P26S 0 4 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. P80R 2022 Genetics and molecular biology Table SARS_CoV_2 P80R 0 4 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. R190S 2022 Genetics and molecular biology Table SARS_CoV_2 R190S 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. S1188L 2022 Genetics and molecular biology Table SARS_CoV_2 S1188L 0 6 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. S12F 2022 Genetics and molecular biology Table SARS_CoV_2 S12F 0 4 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. T1027I 2022 Genetics and molecular biology Table SARS_CoV_2 T1027I 0 6 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. T175I 2022 Genetics and molecular biology Table SARS_CoV_2 T175I 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. T1774I 2022 Genetics and molecular biology Table SARS_CoV_2 T1774I 0 6 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. T20N 2022 Genetics and molecular biology Table SARS_CoV_2 T20N 0 4 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. T4174I 2022 Genetics and molecular biology Table SARS_CoV_2 T4174I 0 6 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. T572I 2022 Genetics and molecular biology Table SARS_CoV_2 T572I 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. T733C 2022 Genetics and molecular biology Table SARS_CoV_2 T733C 0 5 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. V202L 2022 Genetics and molecular biology Table SARS_CoV_2 V202L 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. A570D 2022 Journal of virological methods Table SARS_CoV_2 A570D 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. A701V 2022 Journal of virological methods Table SARS_CoV_2 A701V 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. D1118H 2022 Journal of virological methods Table SARS_CoV_2 D1118H 0 6 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. D138Y 2022 Journal of virological methods Table SARS_CoV_2 D138Y 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. D215G 2022 Journal of virological methods Table SARS_CoV_2 D215G 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. D614G 2022 Journal of virological methods Table SARS_CoV_2 D614G 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. D80A 2022 Journal of virological methods Table SARS_CoV_2 D80A 0 4 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. D950N 2022 Journal of virological methods Table SARS_CoV_2 D950N 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. E154K 2022 Journal of virological methods Table SARS_CoV_2 E154K 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. E484K 2022 Journal of virological methods Table SARS_CoV_2 E484K 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. E484Q 2022 Journal of virological methods Table SARS_CoV_2 E484Q 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. H655Y 2022 Journal of virological methods Table SARS_CoV_2 H655Y 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. K417N 2022 Journal of virological methods Table SARS_CoV_2 K417N 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. K417T 2022 Journal of virological methods Table SARS_CoV_2 K417T 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. L18F 2022 Journal of virological methods Table SARS_CoV_2 L18F 0 4 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. L452R 2022 Journal of virological methods Table SARS_CoV_2 L452R 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. N501Y 2022 Journal of virological methods Table SARS_CoV_2 N501Y 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. P26S 2022 Journal of virological methods Table SARS_CoV_2 P26S 0 4 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. P681H 2022 Journal of virological methods Table SARS_CoV_2 P681H 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. P681R 2022 Journal of virological methods Table SARS_CoV_2 P681R 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. Q1071H 2022 Journal of virological methods Table SARS_CoV_2 Q1071H 0 6 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. R158G 2022 Journal of virological methods Table SARS_CoV_2 R158G 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. R190S 2022 Journal of virological methods Table SARS_CoV_2 R190S 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. S982A 2022 Journal of virological methods Table SARS_CoV_2 S982A 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. T1027I 2022 Journal of virological methods Table SARS_CoV_2 T1027I 0 6 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. T19R 2022 Journal of virological methods Table SARS_CoV_2 T19R 0 4 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. T20N 2022 Journal of virological methods Table SARS_CoV_2 T20N 0 4 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. T478K 2022 Journal of virological methods Table SARS_CoV_2 T478K 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. T716I 2022 Journal of virological methods Table SARS_CoV_2 T716I 0 5 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. V1176F 2022 Journal of virological methods Table SARS_CoV_2 V1176F 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. A1708D 2022 Frontiers in medicine Table SARS_CoV_2 A1708D 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. A243del 2022 Frontiers in medicine Table SARS_CoV_2 A243del 0 7 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. A2710T 2022 Frontiers in medicine Table SARS_CoV_2 A2710T 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. A29del 2022 Frontiers in medicine Table SARS_CoV_2 A29del 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. A570D 2022 Frontiers in medicine Table SARS_CoV_2 A570D 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. A63T 2022 Frontiers in medicine Table SARS_CoV_2 A63T 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. A67V 2022 Frontiers in medicine Table SARS_CoV_2 A67V 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. A701V 2022 Frontiers in medicine Table SARS_CoV_2 A701V 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. D1118H 2022 Frontiers in medicine Table SARS_CoV_2 D1118H 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. D119del 2022 Frontiers in medicine Table SARS_CoV_2 D119del 0 7 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. D138Y 2022 Frontiers in medicine Table SARS_CoV_2 D138Y 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. D215G 2022 Frontiers in medicine Table SARS_CoV_2 D215G 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. D377Y 2022 Frontiers in medicine Table SARS_CoV_2 D377Y 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. D3G 2022 Frontiers in medicine Table SARS_CoV_2 D3G 0 3 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. D614G 2022 Frontiers in medicine Table SARS_CoV_2 D614G 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. D63G 2022 Frontiers in medicine Table SARS_CoV_2 D63G 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. D796Y 2022 Frontiers in medicine Table SARS_CoV_2 D796Y 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. D80A 2022 Frontiers in medicine Table SARS_CoV_2 D80A 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. D950N 2022 Frontiers in medicine Table SARS_CoV_2 D950N 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. E1264D 2022 Frontiers in medicine Table SARS_CoV_2 E1264D 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. E156del 2022 Frontiers in medicine Table SARS_CoV_2 E156del 0 7 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. E27del 2022 Frontiers in medicine Table SARS_CoV_2 E27del 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. E31del 2022 Frontiers in medicine Table SARS_CoV_2 E31del 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. E484A 2022 Frontiers in medicine Table SARS_CoV_2 E484A 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. E484K 2022 Frontiers in medicine Table SARS_CoV_2 E484K 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. E484K/Q 2022 Frontiers in medicine Table SARS_CoV_2 E484K;E484Q 0;0 7;7 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. E92K 2022 Frontiers in medicine Table SARS_CoV_2 E92K 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. F120del 2022 Frontiers in medicine Table SARS_CoV_2 F120del 0 7 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. F157del 2022 Frontiers in medicine Table SARS_CoV_2 F157del 0 7 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. F3677del 2022 Frontiers in medicine Table SARS_CoV_2 F3677del 0 8 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. G142del 2022 Frontiers in medicine Table SARS_CoV_2 G142del 0 7 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. G204R 2022 Frontiers in medicine Table SARS_CoV_2 G204R 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. G339D 2022 Frontiers in medicine Table SARS_CoV_2 G339D 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. G3676del 2022 Frontiers in medicine Table SARS_CoV_2 G3676del 0 8 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. G446S 2022 Frontiers in medicine Table SARS_CoV_2 G446S 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. G496S 2022 Frontiers in medicine Table SARS_CoV_2 G496S 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. G662S 2022 Frontiers in medicine Table SARS_CoV_2 G662S 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. H655Y 2022 Frontiers in medicine Table SARS_CoV_2 H655Y 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. H69del 2022 Frontiers in medicine Table SARS_CoV_2 H69del 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. I1566V 2022 Frontiers in medicine Table SARS_CoV_2 I1566V 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. I2230T 2022 Frontiers in medicine Table SARS_CoV_2 I2230T 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. I3758V 2022 Frontiers in medicine Table SARS_CoV_2 I3758V 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. I82T 2022 Frontiers in medicine Table SARS_CoV_2 I82T 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. K1655N 2022 Frontiers in medicine Table SARS_CoV_2 K1655N 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. K1795Q 2022 Frontiers in medicine Table SARS_CoV_2 K1795Q 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. K3353R 2022 Frontiers in medicine Table SARS_CoV_2 K3353R 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. K417N/T 2022 Frontiers in medicine Table SARS_CoV_2 K417N;K417T 0;0 7;7 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. K417T 2022 Frontiers in medicine Table SARS_CoV_2 K417T 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. K856R 2022 Frontiers in medicine Table SARS_CoV_2 K856R 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. L18F 2022 Frontiers in medicine Table SARS_CoV_2 L18F 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. L2084I 2022 Frontiers in medicine Table SARS_CoV_2 L2084I 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. L212I 2022 Frontiers in medicine Table SARS_CoV_2 L212I 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. L241del 2022 Frontiers in medicine Table SARS_CoV_2 L241del 0 7 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. L242del 2022 Frontiers in medicine Table SARS_CoV_2 L242del 0 7 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. L3674del 2022 Frontiers in medicine Table SARS_CoV_2 L3674del 0 8 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. L452R 2022 Frontiers in medicine Table SARS_CoV_2 L452R 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. L981F 2022 Frontiers in medicine Table SARS_CoV_2 L981F 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. N211del 2022 Frontiers in medicine Table SARS_CoV_2 N211del 0 7 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. N28del 2022 Frontiers in medicine Table SARS_CoV_2 N28del 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. N440K 2022 Frontiers in medicine Table SARS_CoV_2 N440K 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. N679K 2022 Frontiers in medicine Table SARS_CoV_2 N679K 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. N764K 2022 Frontiers in medicine Table SARS_CoV_2 N764K 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. N856K 2022 Frontiers in medicine Table SARS_CoV_2 N856K 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. N969K 2022 Frontiers in medicine Table SARS_CoV_2 N969K 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. P1000L 2022 Frontiers in medicine Table SARS_CoV_2 P1000L 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. P10S 2022 Frontiers in medicine Table SARS_CoV_2 P10S 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. P13L 2022 Frontiers in medicine Table SARS_CoV_2 P13L 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. P26S 2022 Frontiers in medicine Table SARS_CoV_2 P26S 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. P314L 2022 Frontiers in medicine Table SARS_CoV_2 P314L 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. P3395H 2022 Frontiers in medicine Table SARS_CoV_2 P3395H 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. P681H 2022 Frontiers in medicine Table SARS_CoV_2 P681H 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. P681R 2022 Frontiers in medicine Table SARS_CoV_2 P681R 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. P71L 2022 Frontiers in medicine Table SARS_CoV_2 P71L 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. P80R 2022 Frontiers in medicine Table SARS_CoV_2 P80R 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Q19E 2022 Frontiers in medicine Table SARS_CoV_2 Q19E 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Q493K 2022 Frontiers in medicine Table SARS_CoV_2 Q493K 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Q493R 2022 Frontiers in medicine Table SARS_CoV_2 Q493R 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Q498R 2022 Frontiers in medicine Table SARS_CoV_2 Q498R 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Q57H 2022 Frontiers in medicine Table SARS_CoV_2 Q57H 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Q677P/H 2022 Frontiers in medicine Table SARS_CoV_2 Q677H;Q677P 0;0 7;7 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Q954H 2022 Frontiers in medicine Table SARS_CoV_2 Q954H 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. R158G 2022 Frontiers in medicine Table SARS_CoV_2 R158G 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. R190S 2022 Frontiers in medicine Table SARS_CoV_2 R190S 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. R203K 2022 Frontiers in medicine Table SARS_CoV_2 R203K 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. R203M 2022 Frontiers in medicine Table SARS_CoV_2 R203M 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. R32del 2022 Frontiers in medicine Table SARS_CoV_2 R32del 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. R52I 2022 Frontiers in medicine Table SARS_CoV_2 R52I 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. S1188L 2022 Frontiers in medicine Table SARS_CoV_2 S1188L 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. S2083del 2022 Frontiers in medicine Table SARS_CoV_2 S2083del 0 8 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. S235F 2022 Frontiers in medicine Table SARS_CoV_2 S235F 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. S253P 2022 Frontiers in medicine Table SARS_CoV_2 S253P 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. S26L 2022 Frontiers in medicine Table SARS_CoV_2 S26L 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. S33del 2022 Frontiers in medicine Table SARS_CoV_2 S33del 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. S3675del 2022 Frontiers in medicine Table SARS_CoV_2 S3675del 0 8 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. S371L 2022 Frontiers in medicine Table SARS_CoV_2 S371L 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. S373P 2022 Frontiers in medicine Table SARS_CoV_2 S373P 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. S375F 2022 Frontiers in medicine Table SARS_CoV_2 S375F 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. S477N 2022 Frontiers in medicine Table SARS_CoV_2 S477N 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. S982A 2022 Frontiers in medicine Table SARS_CoV_2 S982A 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. T1001I 2022 Frontiers in medicine Table SARS_CoV_2 T1001I 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. T1027I 2022 Frontiers in medicine Table SARS_CoV_2 T1027I 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. T120I 2022 Frontiers in medicine Table SARS_CoV_2 T120I 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. T19R 2022 Frontiers in medicine Table SARS_CoV_2 T19R 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. T205I 2022 Frontiers in medicine Table SARS_CoV_2 T205I 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. T20N 2022 Frontiers in medicine Table SARS_CoV_2 T20N 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. T265I 2022 Frontiers in medicine Table SARS_CoV_2 T265I 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. T3255I 2022 Frontiers in medicine Table SARS_CoV_2 T3255I 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. T478K 2022 Frontiers in medicine Table SARS_CoV_2 T478K 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. T547K 2022 Frontiers in medicine Table SARS_CoV_2 T547K 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. T60A 2022 Frontiers in medicine Table SARS_CoV_2 T60A 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. T716I 2022 Frontiers in medicine Table SARS_CoV_2 T716I 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. T95I 2022 Frontiers in medicine Table SARS_CoV_2 T95I 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. V1176F 2022 Frontiers in medicine Table SARS_CoV_2 V1176F 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. V143del 2022 Frontiers in medicine Table SARS_CoV_2 V143del 0 7 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. V70del 2022 Frontiers in medicine Table SARS_CoV_2 V70del 0 6 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. V82A 2022 Frontiers in medicine Table SARS_CoV_2 V82A 0 4 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Y144del 2022 Frontiers in medicine Table SARS_CoV_2 Y144del 0 7 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Y145D 2022 Frontiers in medicine Table SARS_CoV_2 Y145D 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Y505H 2022 Frontiers in medicine Table SARS_CoV_2 Y505H 0 5 35273977 SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Y73C 2022 Frontiers in medicine Table SARS_CoV_2 Y73C 0 4 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. S157del 2022 Microbiology spectrum Table SARS_CoV_2 S157del 0 7 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. R203M 2022 Emerging microbes & infections Table SARS_CoV_2 R203M 0 5 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. A67V 2022 Life science alliance Table SARS_CoV_2 A67V 0 4 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. D138Y 2022 Life science alliance Table SARS_CoV_2 D138Y 0 5 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. D215G 2022 Life science alliance Table SARS_CoV_2 D215G 0 5 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. D80A 2022 Life science alliance Table SARS_CoV_2 D80A 0 4 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. E156G 2022 Life science alliance Table SARS_CoV_2 E156G 0 5 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. G142D 2022 Life science alliance Table SARS_CoV_2 G142D 0 5 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. G75V 2022 Life science alliance Table SARS_CoV_2 G75V 0 4 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. L18F 2022 Life science alliance Table SARS_CoV_2 L18F 0 4 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. N211I 2022 Life science alliance Table SARS_CoV_2 N211I 0 5 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. P26S 2022 Life science alliance Table SARS_CoV_2 P26S 0 4 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. R190S 2022 Life science alliance Table SARS_CoV_2 R190S 0 5 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. R246N 2022 Life science alliance Table SARS_CoV_2 R246N 0 5 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. T19R 2022 Life science alliance Table SARS_CoV_2 T19R 0 4 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. T20N 2022 Life science alliance Table SARS_CoV_2 T20N 0 4 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. T76I 2022 Life science alliance Table SARS_CoV_2 T76I 0 4 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. T95I 2022 Life science alliance Table SARS_CoV_2 T95I 0 4 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Y144S 2022 Life science alliance Table SARS_CoV_2 Y144S 0 5 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Y145N 2022 Life science alliance Table SARS_CoV_2 Y145N 0 5 35301412 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. C241T 2022 Scientific reports Table SARS_CoV_2 C241T 0 5 35301412 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. C29784T 2022 Scientific reports Table SARS_CoV_2 C29784T 0 7 35301412 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. D614G 2022 Scientific reports Table SARS_CoV_2 D614G 0 5 35301412 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. E244D 2022 Scientific reports Table SARS_CoV_2 E244D 0 5 35301412 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. F106F 2022 Scientific reports Table SARS_CoV_2 F106F 0 5 35301412 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. G204R 2022 Scientific reports Table SARS_CoV_2 G204R 0 5 35301412 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. N73N 2022 Scientific reports Table SARS_CoV_2 N73N 0 4 35301412 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. P323L 2022 Scientific reports Table SARS_CoV_2 P323L 0 5 35301412 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. R203K 2022 Scientific reports Table SARS_CoV_2 R203K 0 5 35301412 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. V127F 2022 Scientific reports Table SARS_CoV_2 V127F 0 5 35301412 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. Y831Y 2022 Scientific reports Table SARS_CoV_2 Y831Y 0 5 35305699 Neutralisation sensitivity of the SARS-CoV-2 omicron (B.1.1.529) variant: a cross-sectional study. D614G 2022 The Lancet. Infectious diseases Table SARS_CoV_2 D614G 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? A11201G 2022 Frontiers in microbiology Table SARS_CoV_2 A11201G 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? A1708D 2022 Frontiers in microbiology Table SARS_CoV_2 A1708D 0 6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? A23063T 2022 Frontiers in microbiology Table SARS_CoV_2 A23063T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? A23403G 2022 Frontiers in microbiology Table SARS_CoV_2 A23403G 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? A28111G 2022 Frontiers in microbiology Table SARS_CoV_2 A28111G 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? A28295G 2022 Frontiers in microbiology Table SARS_CoV_2 A28295G 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? A28461G 2022 Frontiers in microbiology Table SARS_CoV_2 A28461G 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? A570D 2022 Frontiers in microbiology Table SARS_CoV_2 A570D 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C10029T 2022 Frontiers in microbiology Table SARS_CoV_2 C10029T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C13620T 2022 Frontiers in microbiology Table SARS_CoV_2 C13620T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C14262T 2022 Frontiers in microbiology Table SARS_CoV_2 C14262T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C14408T 2022 Frontiers in microbiology Table SARS_CoV_2 C14408T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C14790T 2022 Frontiers in microbiology Table SARS_CoV_2 C14790T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C15240T 2022 Frontiers in microbiology Table SARS_CoV_2 C15240T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C16466T 2022 Frontiers in microbiology Table SARS_CoV_2 C16466T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C17135T 2022 Frontiers in microbiology Table SARS_CoV_2 C17135T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C21618G 2022 Frontiers in microbiology Table SARS_CoV_2 C21618G 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C21855T 2022 Frontiers in microbiology Table SARS_CoV_2 C21855T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C22995A 2022 Frontiers in microbiology Table SARS_CoV_2 C22995A 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C23271A 2022 Frontiers in microbiology Table SARS_CoV_2 C23271A 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C23525T 2022 Frontiers in microbiology Table SARS_CoV_2 C23525T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C23604G 2022 Frontiers in microbiology Table SARS_CoV_2 C23604G 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C241T 2022 Frontiers in microbiology Table SARS_CoV_2 C241T 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C25339T 2022 Frontiers in microbiology Table SARS_CoV_2 C25339T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C25350T 2022 Frontiers in microbiology Table SARS_CoV_2 C25350T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C25469T 2022 Frontiers in microbiology Table SARS_CoV_2 C25469T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C29358T 2022 Frontiers in microbiology Table SARS_CoV_2 C29358T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C29738T 2022 Frontiers in microbiology Table SARS_CoV_2 C29738T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C3037T 2022 Frontiers in microbiology Table SARS_CoV_2 C3037T 0 6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C3267T 2022 Frontiers in microbiology Table SARS_CoV_2 C3267T 0 6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C344T 2022 Frontiers in microbiology Table SARS_CoV_2 C344T 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C5388A 2022 Frontiers in microbiology Table SARS_CoV_2 C5388A 0 6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C6573T 2022 Frontiers in microbiology Table SARS_CoV_2 C6573T 0 6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? C913T 2022 Frontiers in microbiology Table SARS_CoV_2 C913T 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? D1118H 2022 Frontiers in microbiology Table SARS_CoV_2 D1118H 0 6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? D1259D 2022 Frontiers in microbiology Table SARS_CoV_2 D1259D 0 6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? D138Y 2022 Frontiers in microbiology Table SARS_CoV_2 D138Y 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? D144H 2022 Frontiers in microbiology Table SARS_CoV_2 D144H 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? D265D 2022 Frontiers in microbiology Table SARS_CoV_2 D265D 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? D377Y 2022 Frontiers in microbiology Table SARS_CoV_2 D377Y 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? D51D 2022 Frontiers in microbiology Table SARS_CoV_2 D51D 0 4 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? D614G 2022 Frontiers in microbiology Table SARS_CoV_2 D614G 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? D63G 2022 Frontiers in microbiology Table SARS_CoV_2 D63G 0 4 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? D950N 2022 Frontiers in microbiology Table SARS_CoV_2 D950N 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? G1219V 2022 Frontiers in microbiology Table SARS_CoV_2 G1219V 0 6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? G12940T 2022 Frontiers in microbiology Table SARS_CoV_2 G12940T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? G210T 2022 Frontiers in microbiology Table SARS_CoV_2 G210T 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? G21974C 2022 Frontiers in microbiology Table SARS_CoV_2 G21974C 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? G24410A 2022 Frontiers in microbiology Table SARS_CoV_2 G24410A 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? G24914C 2022 Frontiers in microbiology Table SARS_CoV_2 G24914C 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? G25218T 2022 Frontiers in microbiology Table SARS_CoV_2 G25218T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? G28280C 2022 Frontiers in microbiology Table SARS_CoV_2 G28280C 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? G28703T 2022 Frontiers in microbiology Table SARS_CoV_2 G28703T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? G28881T 2022 Frontiers in microbiology Table SARS_CoV_2 G28881T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? G29402T 2022 Frontiers in microbiology Table SARS_CoV_2 G29402T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? G29742T 2022 Frontiers in microbiology Table SARS_CoV_2 G29742T 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? H655Y 2022 Frontiers in microbiology Table SARS_CoV_2 H655Y 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? I441I 2022 Frontiers in microbiology Table SARS_CoV_2 I441I 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? I82T/S 2022 Frontiers in microbiology Table SARS_CoV_2 I82S;I82T 0;0 6;6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? L27F 2022 Frontiers in microbiology Table SARS_CoV_2 L27F 0 4 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? L425R 2022 Frontiers in microbiology Table SARS_CoV_2 L425R 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? N501Y 2022 Frontiers in microbiology Table SARS_CoV_2 N501Y 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? N591N 2022 Frontiers in microbiology Table SARS_CoV_2 N591N 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? P1000L 2022 Frontiers in microbiology Table SARS_CoV_2 P1000L 0 6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? P1223L 2022 Frontiers in microbiology Table SARS_CoV_2 P1223L 0 6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? P1263L 2022 Frontiers in microbiology Table SARS_CoV_2 P1263L 0 6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? P314L 2022 Frontiers in microbiology Table SARS_CoV_2 P314L 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? P681R 2022 Frontiers in microbiology Table SARS_CoV_2 P681R 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? R203K 2022 Frontiers in microbiology Table SARS_CoV_2 R203K 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? S2103F 2022 Frontiers in microbiology Table SARS_CoV_2 S2103F 0 6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? S26L 2022 Frontiers in microbiology Table SARS_CoV_2 S26L 0 4 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? S982A 2022 Frontiers in microbiology Table SARS_CoV_2 S982A 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? S98F 2022 Frontiers in microbiology Table SARS_CoV_2 S98F 0 4 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? T1001I 2022 Frontiers in microbiology Table SARS_CoV_2 T1001I 0 6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? T19R 2022 Frontiers in microbiology Table SARS_CoV_2 T19R 0 4 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? T22917G 2022 Frontiers in microbiology Table SARS_CoV_2 T22917G 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? T24506G 2022 Frontiers in microbiology Table SARS_CoV_2 T24506G 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? T26767C 2022 Frontiers in microbiology Table SARS_CoV_2 T26767C 0 7 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? T3255I 2022 Frontiers in microbiology Table SARS_CoV_2 T3255I 0 6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? T362I 2022 Frontiers in microbiology Table SARS_CoV_2 T362I 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? T3646A 2022 Frontiers in microbiology Table SARS_CoV_2 T3646A 0 6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? T478K 2022 Frontiers in microbiology Table SARS_CoV_2 T478K 0 5 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? V4225V 2022 Frontiers in microbiology Table SARS_CoV_2 V4225V 0 6 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? Y73C 2022 Frontiers in microbiology Table SARS_CoV_2 Y73C 0 4 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. E484A 2022 Journal of chemical information and modeling Table SARS_CoV_2 E484A 0 5 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. E484R 2022 Journal of chemical information and modeling Table SARS_CoV_2 E484R 0 5 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. G339D 2022 Journal of chemical information and modeling Table SARS_CoV_2 G339D 0 5 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. G446S 2022 Journal of chemical information and modeling Table SARS_CoV_2 G446S 0 5 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. G496S 2022 Journal of chemical information and modeling Table SARS_CoV_2 G496S 0 5 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. K417N 2022 Journal of chemical information and modeling Table SARS_CoV_2 K417N 0 5 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. N440K 2022 Journal of chemical information and modeling Table SARS_CoV_2 N440K 0 5 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. N501Y 2022 Journal of chemical information and modeling Table SARS_CoV_2 N501Y 0 5 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. Q493K 2022 Journal of chemical information and modeling Table SARS_CoV_2 Q493K 0 5 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. Q493R 2022 Journal of chemical information and modeling Table SARS_CoV_2 Q493R 0 5 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. Q498R 2022 Journal of chemical information and modeling Table SARS_CoV_2 Q498R 0 5 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. S371L 2022 Journal of chemical information and modeling Table SARS_CoV_2 S371L 0 5 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. S373P 2022 Journal of chemical information and modeling Table SARS_CoV_2 S373P 0 5 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. S375F 2022 Journal of chemical information and modeling Table SARS_CoV_2 S375F 0 5 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. S477N 2022 Journal of chemical information and modeling Table SARS_CoV_2 S477N 0 5 35312321 Interaction Analysis of the Spike Protein of Delta and Omicron Variants of SARS-CoV-2 with hACE2 and Eight Monoclonal Antibodies Using the Fragment Molecular Orbital Method. T478K 2022 Journal of chemical information and modeling Table SARS_CoV_2 T478K 0 5 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). L452R 2022 PloS one Table SARS_CoV_2 L452R 0 5 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). T1355G 2022 PloS one Table SARS_CoV_2 T1355G 0 6 35314694 Genetic alteration of human MYH6 is mimicked by SARS-CoV-2 polyprotein: mapping viral variants of cardiac interest. p.Arg380Cys 2022 Cell death discovery Table SARS_CoV_2 R380C 0 11 35314694 Genetic alteration of human MYH6 is mimicked by SARS-CoV-2 polyprotein: mapping viral variants of cardiac interest. p.Gly215Val 2022 Cell death discovery Table SARS_CoV_2 G215V 0 11 35314694 Genetic alteration of human MYH6 is mimicked by SARS-CoV-2 polyprotein: mapping viral variants of cardiac interest. p.Lys519Arg 2022 Cell death discovery Table SARS_CoV_2 K519R 0 11 35314694 Genetic alteration of human MYH6 is mimicked by SARS-CoV-2 polyprotein: mapping viral variants of cardiac interest. p.Val1732Leu 2022 Cell death discovery Table SARS_CoV_2 V1732L 0 12 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. D614G 2022 eLife Table SARS_CoV_2 D614G 0 5 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. E0554S 2022 eLife Table SARS_CoV_2 E0554S 0 6 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. 144del 2022 Frontiers in immunology Table SARS_CoV_2 144del 0 6 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. 241del 2022 Frontiers in immunology Table SARS_CoV_2 241del 0 6 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. 242del 2022 Frontiers in immunology Table SARS_CoV_2 242del 0 6 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. 243del 2022 Frontiers in immunology Table SARS_CoV_2 243del 0 6 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. 69del 2022 Frontiers in immunology Table SARS_CoV_2 69del 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. 70del 2022 Frontiers in immunology Table SARS_CoV_2 70del 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. A222V 2022 Frontiers in immunology Table SARS_CoV_2 A222V 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. A570D 2022 Frontiers in immunology Table SARS_CoV_2 A570D 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. A701V 2022 Frontiers in immunology Table SARS_CoV_2 A701V 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. D1118H 2022 Frontiers in immunology Table SARS_CoV_2 D1118H 0 6 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. D138Y 2022 Frontiers in immunology Table SARS_CoV_2 D138Y 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. D215G 2022 Frontiers in immunology Table SARS_CoV_2 D215G 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. D614G 2022 Frontiers in immunology Table SARS_CoV_2 D614G 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. D80A 2022 Frontiers in immunology Table SARS_CoV_2 D80A 0 4 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. D950N 2022 Frontiers in immunology Table SARS_CoV_2 D950N 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. E154K 2022 Frontiers in immunology Table SARS_CoV_2 E154K 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. E484K 2022 Frontiers in immunology Table SARS_CoV_2 E484K 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. E484Q 2022 Frontiers in immunology Table SARS_CoV_2 E484Q 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. G142D 2022 Frontiers in immunology Table SARS_CoV_2 G142D 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. H655Y 2022 Frontiers in immunology Table SARS_CoV_2 H655Y 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. I692V 2022 Frontiers in immunology Table SARS_CoV_2 I692V 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. K1191N 2022 Frontiers in immunology Table SARS_CoV_2 K1191N 0 6 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. K417N 2022 Frontiers in immunology Table SARS_CoV_2 K417N 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. K417T 2022 Frontiers in immunology Table SARS_CoV_2 K417T 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. L18F 2022 Frontiers in immunology Table SARS_CoV_2 L18F 0 4 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. L452R 2022 Frontiers in immunology Table SARS_CoV_2 L452R 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. M1229I 2022 Frontiers in immunology Table SARS_CoV_2 M1229I 0 6 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. N501Y 2022 Frontiers in immunology Table SARS_CoV_2 N501Y 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. P26S 2022 Frontiers in immunology Table SARS_CoV_2 P26S 0 4 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. P681H 2022 Frontiers in immunology Table SARS_CoV_2 P681H 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. P681R 2022 Frontiers in immunology Table SARS_CoV_2 P681R 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. Q1071H 2022 Frontiers in immunology Table SARS_CoV_2 Q1071H 0 6 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. R158G 2022 Frontiers in immunology Table SARS_CoV_2 R158G 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. R190S 2022 Frontiers in immunology Table SARS_CoV_2 R190S 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. S494P 2022 Frontiers in immunology Table SARS_CoV_2 S494P 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. S982A 2022 Frontiers in immunology Table SARS_CoV_2 S982A 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. T1027I 2022 Frontiers in immunology Table SARS_CoV_2 T1027I 0 6 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. T19R 2022 Frontiers in immunology Table SARS_CoV_2 T19R 0 4 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. T20N 2022 Frontiers in immunology Table SARS_CoV_2 T20N 0 4 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. T478K 2022 Frontiers in immunology Table SARS_CoV_2 T478K 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. T716I 2022 Frontiers in immunology Table SARS_CoV_2 T716I 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. T95I 2022 Frontiers in immunology Table SARS_CoV_2 T95I 0 4 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. V70F 2022 Frontiers in immunology Table SARS_CoV_2 V70F 0 4 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. W258L 2022 Frontiers in immunology Table SARS_CoV_2 W258L 0 5 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. Y453F 2022 Frontiers in immunology Table SARS_CoV_2 Y453F 0 5 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. E484K 2022 The Journal of biological chemistry Table SARS_CoV_2 E484K 0 5 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. K417T 2022 The Journal of biological chemistry Table SARS_CoV_2 K417T 0 5 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. L452R 2022 The Journal of biological chemistry Table SARS_CoV_2 L452R 0 5 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. N501Y 2022 The Journal of biological chemistry Table SARS_CoV_2 N501Y 0 5 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. E484K 2022 PeerJ Table SARS_CoV_2 E484K 0 5 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. N501Y 2022 PeerJ Table SARS_CoV_2 N501Y 0 5 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. D796Y 2022 Biochemical and biophysical research communications Table SARS_CoV_2 D796Y 0 5 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. G22578A 2022 Biochemical and biophysical research communications Table SARS_CoV_2 G22578A 0 7 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. G23948T 2022 Biochemical and biophysical research communications Table SARS_CoV_2 G23948T 0 7 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. G339D 2022 Biochemical and biophysical research communications Table SARS_CoV_2 G339D 0 5 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. L452R 2022 Biochemical and biophysical research communications Table SARS_CoV_2 L452R 0 5 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. T22917G 2022 Biochemical and biophysical research communications Table SARS_CoV_2 T22917G 0 7 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. A1892T 2022 Virus research Table SARS_CoV_2 A1892T 0 6 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. A63T 2022 Virus research Table SARS_CoV_2 A63T 0 4 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. A889A 2022 Virus research Table SARS_CoV_2 A889A 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. D1146D 2022 Virus research Table SARS_CoV_2 D1146D 0 6 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. D614G 2022 Virus research Table SARS_CoV_2 D614G 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. D796Y 2022 Virus research Table SARS_CoV_2 D796Y 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. E484A 2022 Virus research Table SARS_CoV_2 E484A 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. F106F 2022 Virus research Table SARS_CoV_2 F106F 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. G339D 2022 Virus research Table SARS_CoV_2 G339D 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. G446S 2022 Virus research Table SARS_CoV_2 G446S 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. G496S 2022 Virus research Table SARS_CoV_2 G496S 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. H655Y 2022 Virus research Table SARS_CoV_2 H655Y 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. I189V 2022 Virus research Table SARS_CoV_2 I189V 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. I42V 2022 Virus research Table SARS_CoV_2 I42V 0 4 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. K38R 2022 Virus research Table SARS_CoV_2 K38R 0 4 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. K417N 2022 Virus research Table SARS_CoV_2 K417N 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. L17L 2022 Virus research Table SARS_CoV_2 L17L 0 4 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. L212C 2022 Virus research Table SARS_CoV_2 L212C 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. L981F 2022 Virus research Table SARS_CoV_2 L981F 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. M19M 2022 Virus research Table SARS_CoV_2 M19M 0 4 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. N211K 2022 Virus research Table SARS_CoV_2 N211K 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. N440K 2022 Virus research Table SARS_CoV_2 N440K 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. N501Y 2022 Virus research Table SARS_CoV_2 N501Y 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. N591N 2022 Virus research Table SARS_CoV_2 N591N 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. N679K 2022 Virus research Table SARS_CoV_2 N679K 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. N764K 2022 Virus research Table SARS_CoV_2 N764K 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. N856K 2022 Virus research Table SARS_CoV_2 N856K 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. N969K 2022 Virus research Table SARS_CoV_2 N969K 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. P132H 2022 Virus research Table SARS_CoV_2 P132H 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. P13L 2022 Virus research Table SARS_CoV_2 P13L 0 4 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. P314L 2022 Virus research Table SARS_CoV_2 P314L 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. P681H 2022 Virus research Table SARS_CoV_2 P681H 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. Q19E 2022 Virus research Table SARS_CoV_2 Q19E 0 4 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. Q493R 2022 Virus research Table SARS_CoV_2 Q493R 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. Q498R 2022 Virus research Table SARS_CoV_2 Q498R 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. Q954H 2022 Virus research Table SARS_CoV_2 Q954H 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. R214R 2022 Virus research Table SARS_CoV_2 R214R 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. S371L 2022 Virus research Table SARS_CoV_2 S371L 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. S373P 2022 Virus research Table SARS_CoV_2 S373P 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. S375F 2022 Virus research Table SARS_CoV_2 S375F 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. S477N 2022 Virus research Table SARS_CoV_2 S477N 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. T478K 2022 Virus research Table SARS_CoV_2 T478K 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. T492I 2022 Virus research Table SARS_CoV_2 T492I 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. T547K 2022 Virus research Table SARS_CoV_2 T547K 0 5 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. T64T 2022 Virus research Table SARS_CoV_2 T64T 0 4 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. T95I 2022 Virus research Table SARS_CoV_2 T95I 0 4 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. V57V 2022 Virus research Table SARS_CoV_2 V57V 0 4 35367284 Mutational cascade of SARS-CoV-2 leading to evolution and emergence of omicron variant. Y505H 2022 Virus research Table SARS_CoV_2 Y505H 0 5 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. D614G 2022 Frontiers in microbiology Table SARS_CoV_2 D614G 0 5 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. A570D 2022 Indian journal of medical microbiology Table SARS_CoV_2 A570D 0 5 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. E484K 2022 Indian journal of medical microbiology Table SARS_CoV_2 E484K 0 5 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. E484Q 2022 Indian journal of medical microbiology Table SARS_CoV_2 E484Q 0 5 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. F486L 2022 Indian journal of medical microbiology Table SARS_CoV_2 F486L 0 5 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. K417G 2022 Indian journal of medical microbiology Table SARS_CoV_2 K417G 0 5 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. L452R 2022 Indian journal of medical microbiology Table SARS_CoV_2 L452R 0 5 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. L455Y 2022 Indian journal of medical microbiology Table SARS_CoV_2 L455Y 0 5 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. N439K 2022 Indian journal of medical microbiology Table SARS_CoV_2 N439K 0 5 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. N501T 2022 Indian journal of medical microbiology Table SARS_CoV_2 N501T 0 5 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. N501Y 2022 Indian journal of medical microbiology Table SARS_CoV_2 N501Y 0 5 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. Q493N 2022 Indian journal of medical microbiology Table SARS_CoV_2 Q493N 0 5 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. Q498Y 2022 Indian journal of medical microbiology Table SARS_CoV_2 Q498Y 0 5 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. R408I 2022 Indian journal of medical microbiology Table SARS_CoV_2 R408I 0 5 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. A99V 2022 Scientific reports Table SARS_CoV_2 A99V 0 4 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. D614G 2022 Scientific reports Table SARS_CoV_2 D614G 0 5 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. F3753I 2022 Scientific reports Table SARS_CoV_2 F3753I 0 6 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. G204R 2022 Scientific reports Table SARS_CoV_2 G204R 0 5 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. G251V 2022 Scientific reports Table SARS_CoV_2 G251V 0 5 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. G3278S 2022 Scientific reports Table SARS_CoV_2 G3278S 0 6 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. G50R 2022 Scientific reports Table SARS_CoV_2 G50R 0 4 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. L3606F 2022 Scientific reports Table SARS_CoV_2 L3606F 0 6 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. M3752L 2022 Scientific reports Table SARS_CoV_2 M3752L 0 6 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. M3752T 2022 Scientific reports Table SARS_CoV_2 M3752T 0 6 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. P314L 2022 Scientific reports Table SARS_CoV_2 P314L 0 5 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. Q57H 2022 Scientific reports Table SARS_CoV_2 Q57H 0 4 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. R203K 2022 Scientific reports Table SARS_CoV_2 R203K 0 5 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. T1246I 2022 Scientific reports Table SARS_CoV_2 T1246I 0 6 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. T1543I 2022 Scientific reports Table SARS_CoV_2 T1543I 0 6 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. T265I 2022 Scientific reports Table SARS_CoV_2 T265I 0 5 35396165 A self-amplifying RNA vaccine protects against SARS-CoV-2 (D614G) and Alpha variant of concern (B.1.1.7) in a transmission-challenge hamster model. D614G 2022 Vaccine Table SARS_CoV_2 D614G 0 5 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. D614G 2022 Journal of applied genetics Table SARS_CoV_2 D614G 0 5 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. F486L 2022 Journal of applied genetics Table SARS_CoV_2 F486L 0 5 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. N501T 2022 Journal of applied genetics Table SARS_CoV_2 N501T 0 5 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Y453F 2022 Journal of applied genetics Table SARS_CoV_2 Y453F 0 5 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. D64G 2022 Cell reports Table SARS_CoV_2 D64G 0 4 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. E0554S 2022 Cell reports Table SARS_CoV_2 E0554S 0 6 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. E55D 2022 Cell reports Table SARS_CoV_2 E55D 0 4 35399374 Unique peptide signatures of SARS-ComicronV-2 virus against human proteome reveal variants' immune escape and infectiveness. A701V 2022 Heliyon Table SARS_CoV_2 A701V 0 5 35399374 Unique peptide signatures of SARS-ComicronV-2 virus against human proteome reveal variants' immune escape and infectiveness. P681H 2022 Heliyon Table SARS_CoV_2 P681H 0 5 35399374 Unique peptide signatures of SARS-ComicronV-2 virus against human proteome reveal variants' immune escape and infectiveness. P681R 2022 Heliyon Table SARS_CoV_2 P681R 0 5 35421378 Efficacy of vaccination and previous infection against the Omicron BA.1 variant in Syrian hamsters. S-614D 2022 Cell reports Table SARS_CoV_2 S614D 0 6 35421378 Efficacy of vaccination and previous infection against the Omicron BA.1 variant in Syrian hamsters. S-614G 2022 Cell reports Table SARS_CoV_2 S614G 0 6 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. A67V 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 A67V 0 4 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. D138Y 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 D138Y 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. D614G 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 D614G 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. D796Y 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 D796Y 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. D950N 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 D950N 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. E484A 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 E484A 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. E484K 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 E484K 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. F924F 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 F924F 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. G204R 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 G204R 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. G251V 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 G251V 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. G339D 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 G339D 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. G446S 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 G446S 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. G496S 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 G496S 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. H655Y 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 H655Y 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. I692V 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 I692V 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. K417N 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 K417N 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. K417T 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 K417T 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. L18F 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 L18F 0 4 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. L212I 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 L212I 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. L3606F 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 L3606F 0 6 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. L452R 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 L452R 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. L4715L 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 L4715L 0 6 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. L84S 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 L84S 0 4 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. L981F 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 L981F 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. M1229I 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 M1229I 0 6 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. M5865V 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 M5865V 0 6 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. N440K 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 N440K 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. N501Y 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 N501Y 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. N679K 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 N679K 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. N764K 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 N764K 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. N856K 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 N856K 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. N969K 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 N969K 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. P26S 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 P26S 0 4 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. P4715L 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 P4715L 0 6 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. P681H 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 P681H 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. P681R 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 P681R 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. Q493R 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 Q493R 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. Q498R 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 Q498R 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. Q57H 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 Q57H 0 4 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. Q954H 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 Q954H 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. R158G 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 R158G 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. R190S 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 R190S 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. R203K 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 R203K 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. S371L 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 S371L 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. S373P 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 S373P 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. S375F 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 S375F 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. S477N 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 S477N 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. S5932F 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 S5932F 0 6 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. T1027I 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 T1027I 0 6 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. T19R 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 T19R 0 4 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. T20N 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 T20N 0 4 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. T265I 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 T265I 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. T478K 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 T478K 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. T547K 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 T547K 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. T95I 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 T95I 0 4 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. Y145D 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 Y145D 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. Y453F 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 Y453F 0 5 35433495 Role of the Microbiome in the Pathogenesis of COVID-19. Y505H 2022 Frontiers in cellular and infection microbiology Table SARS_CoV_2 Y505H 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. A222V 2022 MedComm Table SARS_CoV_2 A222V 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. A27S 2022 MedComm Table SARS_CoV_2 A27S 0 4 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. A570D 2022 MedComm Table SARS_CoV_2 A570D 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. A67V 2022 MedComm Table SARS_CoV_2 A67V 0 4 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. A701V 2022 MedComm Table SARS_CoV_2 A701V 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. C136F 2022 MedComm Table SARS_CoV_2 C136F 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. D1118H 2022 MedComm Table SARS_CoV_2 D1118H 0 6 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. D1139H 2022 MedComm Table SARS_CoV_2 D1139H 0 6 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. D138Y 2022 MedComm Table SARS_CoV_2 D138Y 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. D215G 2022 MedComm Table SARS_CoV_2 D215G 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. D215H 2022 MedComm Table SARS_CoV_2 D215H 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. D253N 2022 MedComm Table SARS_CoV_2 D253N 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. D405N 2022 MedComm Table SARS_CoV_2 D405N 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. D614G 2022 MedComm Table SARS_CoV_2 D614G 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. D796Y 2022 MedComm Table SARS_CoV_2 D796Y 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. D80A 2022 MedComm Table SARS_CoV_2 D80A 0 4 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. D936H 2022 MedComm Table SARS_CoV_2 D936H 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. D950N 2022 MedComm Table SARS_CoV_2 D950N 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. E484A 2022 MedComm Table SARS_CoV_2 E484A 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. E484K 2022 MedComm Table SARS_CoV_2 E484K 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. E484Q 2022 MedComm Table SARS_CoV_2 E484Q 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. E96Q 2022 MedComm Table SARS_CoV_2 E96Q 0 4 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. F490R 2022 MedComm Table SARS_CoV_2 F490R 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. F490S 2022 MedComm Table SARS_CoV_2 F490S 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. G142D 2022 MedComm Table SARS_CoV_2 G142D 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. G339D 2022 MedComm Table SARS_CoV_2 G339D 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. G446S 2022 MedComm Table SARS_CoV_2 G446S 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. G496S 2022 MedComm Table SARS_CoV_2 G496S 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. G75V 2022 MedComm Table SARS_CoV_2 G75V 0 4 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. H655Y 2022 MedComm Table SARS_CoV_2 H655Y 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. I210T 2022 MedComm Table SARS_CoV_2 I210T 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. K417N 2022 MedComm Table SARS_CoV_2 K417N 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. K417T 2022 MedComm Table SARS_CoV_2 K417T 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. L18F 2022 MedComm Table SARS_CoV_2 L18F 0 4 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. L212I 2022 MedComm Table SARS_CoV_2 L212I 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. L452Q 2022 MedComm Table SARS_CoV_2 L452Q 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. L452R 2022 MedComm Table SARS_CoV_2 L452R 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. L981F 2022 MedComm Table SARS_CoV_2 L981F 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. N394S 2022 MedComm Table SARS_CoV_2 N394S 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. N440K 2022 MedComm Table SARS_CoV_2 N440K 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. N501Y 2022 MedComm Table SARS_CoV_2 N501Y 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. N679K 2022 MedComm Table SARS_CoV_2 N679K 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. N764K 2022 MedComm Table SARS_CoV_2 N764K 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. N856K 2022 MedComm Table SARS_CoV_2 N856K 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. N969K 2022 MedComm Table SARS_CoV_2 N969K 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. P26S 2022 MedComm Table SARS_CoV_2 P26S 0 4 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. P681H 2022 MedComm Table SARS_CoV_2 P681H 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. P681R 2022 MedComm Table SARS_CoV_2 P681R 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. P9L 2022 MedComm Table SARS_CoV_2 P9L 0 3 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Q493R 2022 MedComm Table SARS_CoV_2 Q493R 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Q498R 2022 MedComm Table SARS_CoV_2 Q498R 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Q954H 2022 MedComm Table SARS_CoV_2 Q954H 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. R158G 2022 MedComm Table SARS_CoV_2 R158G 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. R190S 2022 MedComm Table SARS_CoV_2 R190S 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. R346K 2022 MedComm Table SARS_CoV_2 R346K 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. R346S 2022 MedComm Table SARS_CoV_2 R346S 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. R408S 2022 MedComm Table SARS_CoV_2 R408S 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. S371F 2022 MedComm Table SARS_CoV_2 S371F 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. S371L 2022 MedComm Table SARS_CoV_2 S371L 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. S373P 2022 MedComm Table SARS_CoV_2 S373P 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. S375F 2022 MedComm Table SARS_CoV_2 S375F 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. S477N 2022 MedComm Table SARS_CoV_2 S477N 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. S982A 2022 MedComm Table SARS_CoV_2 S982A 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. T1027I 2022 MedComm Table SARS_CoV_2 T1027I 0 6 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. T19I 2022 MedComm Table SARS_CoV_2 T19I 0 4 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. T19R 2022 MedComm Table SARS_CoV_2 T19R 0 4 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. T20N 2022 MedComm Table SARS_CoV_2 T20N 0 4 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. T376A 2022 MedComm Table SARS_CoV_2 T376A 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. T478K 2022 MedComm Table SARS_CoV_2 T478K 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. T478R 2022 MedComm Table SARS_CoV_2 T478R 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. T547K 2022 MedComm Table SARS_CoV_2 T547K 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. T716I 2022 MedComm Table SARS_CoV_2 T716I 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. T76I 2022 MedComm Table SARS_CoV_2 T76I 0 4 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. T859N 2022 MedComm Table SARS_CoV_2 T859N 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. T95I 2022 MedComm Table SARS_CoV_2 T95I 0 4 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. V1176F 2022 MedComm Table SARS_CoV_2 V1176F 0 6 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. V213G 2022 MedComm Table SARS_CoV_2 V213G 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Y144S 2022 MedComm Table SARS_CoV_2 Y144S 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Y145N 2022 MedComm Table SARS_CoV_2 Y145N 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Y449H 2022 MedComm Table SARS_CoV_2 Y449H 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Y449N 2022 MedComm Table SARS_CoV_2 Y449N 0 5 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Y505H 2022 MedComm Table SARS_CoV_2 Y505H 0 5 35461811 Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. G15S 2022 The Journal of biological chemistry Table SARS_CoV_2 G15S 0 4 35461811 Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. K90R 2022 The Journal of biological chemistry Table SARS_CoV_2 K90R 0 4 35461811 Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. P132H 2022 The Journal of biological chemistry Table SARS_CoV_2 P132H 0 5 35464398 Case Report: X-Linked SASH3 Deficiency Presenting as a Common Variable Immunodeficiency. p.R288* 2022 Frontiers in immunology Table SARS_CoV_2 R288X 0 7 35464398 Case Report: X-Linked SASH3 Deficiency Presenting as a Common Variable Immunodeficiency. p.R347C 2022 Frontiers in immunology Table SARS_CoV_2 R347C 0 7 32464271 Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? The mutation observed at the S protein of the SARS-COV-2, D614G in white color, may create conformational changes mimicking the open status and facilitate the cleavage domain's exposure to proteases FURIN or TMPRSS2 and could be sufficient to speed up the cleavage. 2020 International journal of infectious diseases Figure SARS_CoV_2 D614G 58 63 S 29 30 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. (A) 24933 G/T (G1124V) mutation in the Spike protein coding gene in Clustal Omega. 2020 Journal of biosciences Figure SARS_CoV_2 G1124V 15 21 S 39 44 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. (B) 28881-3 GGG/AAC (R203K and G204R)) mutations in the nucleocapside protein coding gene in Clustal Omega. 2020 Journal of biosciences Figure SARS_CoV_2 G204R;R203K 31;21 36;26 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. (Bottom) This panel shows the domain organization of the variant SARS-CoV-2 N-protein with mutations at position 203 and 204 (R203K, G204R). 2020 Journal of biosciences Figure SARS_CoV_2 G204R;R203K 133;126 138;131 N 76 77 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. (C) 13730 C/T (A88V) mutation in the RdRp gene in Clustal Omega. 2020 Journal of biosciences Figure SARS_CoV_2 A88V 15 19 RdRP 37 41 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Taiwanese strains are located in 4 different clades I, II, III and IV, including (B) and clade I with ORF8-L84S, (C) clade II with ORF3a-G251V, (D) clade IV with ORF1ab-V378I, and (E) clade III with S-D614G. 2020 Emerging microbes & infections Figure SARS_CoV_2 D614G;G251V;L84S;V378I 201;137;107;169 206;142;111;174 ORF1ab;ORF3a;ORF8;S 162;131;102;199 168;136;106;200 32595352 An updated analysis of variations in SARS-CoV-2 genome. SARS-CoV-2 isolate numbers carrying the variations Green: Isolate numbers carrying C14408T, Blue: Isolate numbers carrying A23403G, Red: Isolate numbers carrying G25563T and Yellow: Isolate numbers carrying GGG to AAC variations between 28881-28883. 2020 Turkish journal of biology Figure SARS_CoV_2 A23403G;C14408T;G25563T 123;83;162 130;90;169 32693089 Mortality in COVID-19 disease patients: Correlating the association of major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants. In the countries that submitted more than 100 sequences where the proportion is different: in China, 38% SARS-CoV-2 sequences account for ORF8 (S84L), in Spain 43%, in the USA 32% and in Canada 31%. 2020 International journal of infectious diseases Figure SARS_CoV_2 S84L 144 148 ORF8 138 142 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. (A) Spike sites of interest (with a minimum frequency of 0.3% variant amino acids) are mapped onto a parsimony tree (for D614G; Figure S6). 2020 Cell Figure SARS_CoV_2 D614G 121 126 S 4 9 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. (B) D614G status was not statistically associated with hospitalization status (outpatient [OP], inpatient [IP], or ICU) as a marker of disease severity, but age was highly correlated. 2020 Cell Figure SARS_CoV_2 D614G 4 9 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. (C) Examples of exploratory plots showing A829T in Thailand and D839Y in New Zealand. 2020 Cell Figure SARS_CoV_2 A829T;D839Y 42;64 47;69 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. A829T is found in a single lineage. 2020 Cell Figure SARS_CoV_2 A829T 0 5 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. As an example, in this tree, the region from approximately 12:30 to 3 o'clock represents GISAID's "GR" clade, defined both by mutations we are tracking in this paper that carry the G614 variant (the GISAID G clade, defined by mutations A23403G, C14408T, C3037T, and a mutation in the 5' UTR (C241T, not shown here), and an additional 3-position polymorphism: G28881A + G28882A + G28883C. 2020 Cell Figure SARS_CoV_2 A23403G;C14408T;C3037T;G28881A;G28882A;G28883C;C241T 236;245;254;359;369;379;292 243;252;260;366;376;386;297 5'UTR 284 290 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Branch ends representing sequence isolates bearing the D614G change are decorated with a gray square; sectors of the tree containing that mutation are subtended by a dark blue arc in the inner element; other mutations are denoted by different colors. 2020 Cell Figure SARS_CoV_2 D614G 55 60 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Clinical Status and D614G Associations Based on 999 Subjects with COVID-19 and Linked Sequence and Clinical Data Were Sampled in Sheffield, England. 2020 Cell Figure SARS_CoV_2 D614G 20 25 COVID-19 66 74 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Distribution of A23403G (D614G) Mutation and Other Mutations on an Approximate Phylogenetic Tree Using Parsimony, Related to Figure 7. 2020 Cell Figure SARS_CoV_2 A23403G;D614G 16;25 23;30 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Investigation of S943P, Related to Figure 7. 2020 Cell Figure SARS_CoV_2 S943P 17 22 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. L5F recurs throughout the tree and is often clustered in small local clades. 2020 Cell Figure SARS_CoV_2 L5F 0 3 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Of note, the TTCG form did not expand, and it lacked the RdRp P323L change, raising the possibility that the P323L change may contribute to a selective advantage of the haplotype. 2020 Cell Figure SARS_CoV_2 P323L;P323L 62;109 67;114 RdRP 57 61 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. One is in the RdRp protein (nucleotide C14408T resulting in a P323L amino acid change), one in Spike (nucleotide A23403G resulting in the D614G amino acid change) and one is silent (C3037T). 2020 Cell Figure SARS_CoV_2 A23403G;C14408T;D614G;P323L;C3037T 113;39;138;62;182 120;46;143;67;188 S;RdRP 95;14 100;18 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Raw data from amplicon 81 contains a portion of adaptor sequence which is homologous to the reference genome, apart from the C variants which lead to a S943P mutation call. 2020 Cell Figure SARS_CoV_2 S943P 152 157 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. The Ct levels for the two PCR methods (nucleic acid extraction versus simple heat inactivation) differ, and so we used a GLM to evaluate the statistical effect of D614G across methods. 2020 Cell Figure SARS_CoV_2 D614G 163 168 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. The frequency of the GR clade appears to be increased in the UK and Europe as a subset of the regional G clade expansion, given that both carry G614D. 2020 Cell Figure SARS_CoV_2 G614D 144 149 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. The Increasing Frequency of the D614G Variant over Time in Australia and Asia, Related to Figures 1 and 2. 2020 Cell Figure SARS_CoV_2 D614G 32 37 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. The Increasing Frequency of the D614G Variant over Time in North America, Related to Figure 1. 2020 Cell Figure SARS_CoV_2 D614G 32 37 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. The other mutation is in the 5' UTR (C241T), and tallies based on all 4 positions are done separately, as they are based on an alignment with fewer sequences. 2020 Cell Figure SARS_CoV_2 C241T 37 42 5'UTR 29 35 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. These base substitutions are contiguous and result two amino acid changes, including N-G204R, hence GISAID's "GR clade" name. 2020 Cell Figure SARS_CoV_2 G204R 87 92 N 85 86 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Viral Infectivity and D614G Associations. 2020 Cell Figure SARS_CoV_2 D614G 22 27 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. b Correlation analysis between frequencies of S 614G variant of SARS-CoV-2 and fatality rates in BCG+ and BCG- countries. 2020 Journal of human genetics Figure SARS_CoV_2 S614G 46 52 S 46 47 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. b, c Correlation analysis between frequencies of SARS-CoV-2 ORF1ab 4715L (b) or S 614G variants (c) and fatality rates. 2020 Journal of human genetics Figure SARS_CoV_2 S614G 80 86 ORF1ab;S 60;80 66;81 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. Correlation analysis of variant frequencies of SARS-CoV-2 ORF1ab 4715L (a) or S 614G (b) with fatality rates of COVID-19 among 28 countries. 2020 Journal of human genetics Figure SARS_CoV_2 S614G 78 84 ORF1ab;S 58;78 64;79 COVID-19 112 120 32703419 Proteasome activator PA28gamma-dependent degradation of coronavirus disease (COVID-19) nucleocapsid protein. (C) Cells were transient transfected with the same amount of HA-nCoV-N, FRT-PA28gamma wild-type, FRT-PA28gamma N151Y, HA-pSG5 vector, and FRT vector using Lipo2000 transfection reagent for 48 h. 2020 Biochemical and biophysical research communications Figure SARS_CoV_2 N151Y 111 116 N 69 70 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. (A) Variants and combined variants with D614G across the entire S gene excluding the RBD region. 2020 Cell Figure SARS_CoV_2 D614G 40 45 RBD;S 85;64 88;65 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. This group include mutations we introduced at all 22 putative glycosylation sites (N to Q), a combination of two glycosylation site mutations in RBD, and three naturally occurring variants, N74K, N149H, and T719A, with ablated glycosylation sites. 2020 Cell Figure SARS_CoV_2 N149H;N74K;T719A 196;190;207 201;194;212 RBD 145 148 32732280 Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. (D) The proportion of A23063T mutation in each passage. 2020 Science (New York, N.Y.) Figure SARS_CoV_2 A23063T 22 29 32732280 Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. Amino acid sequences of the parental IME-BJ05 strain and the MASCp6 strain adjacent to the N501Y mutation are shown. 2020 Science (New York, N.Y.) Figure SARS_CoV_2 N501Y 91 96 32756549 SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness. Comparisons between D614 and D614G were made by two-sided Mann-Whitney test within each study, and no significance was detected. 2020 Nature Figure SARS_CoV_2 D614G 29 34 32756549 SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness. mRNA-1273 elicits robust pseudovirus neutralizing antibody responses to SARS-CoV-2_D614G. 2020 Nature Figure SARS_CoV_2 D614G 83 88 32756549 SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness. Sera were collected 2 weeks post-boost and assessed for neutralizing antibodies against homotypic SARS-CoV-2_D614 pseudovirus (filled circles) or SARS-CoV-2_D614G (unfilled circles). 2020 Nature Figure SARS_CoV_2 D614G 157 162 32762417 Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. (B) Intermolecular contacts of mutant N487, Y489A, N501 and Y505A complex systems. 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 Y489A;Y505A 44;60 49;65 32779780 Atomistic simulation reveals structural mechanisms underlying D614G spike glycoprotein-enhanced fitness in SARS-COV-2. (a) Communities evolved by the wild type (b) and D614G mutant during simulation. 2020 Journal of computational chemistry Figure SARS_CoV_2 D614G 49 54 32779780 Atomistic simulation reveals structural mechanisms underlying D614G spike glycoprotein-enhanced fitness in SARS-COV-2. (c) Surface representation of spike glycoprotein trimer showing the optimal communication path between residue 614 and T500 (RBD) in wild type and D614G mutant (d) [Color figure can be viewed at wileyonlinelibrary.com] 2020 Journal of computational chemistry Figure SARS_CoV_2 D614G 147 152 S;RBD 30;125 48;128 32779780 Atomistic simulation reveals structural mechanisms underlying D614G spike glycoprotein-enhanced fitness in SARS-COV-2. (c) Surface representation of spike glycoprotein trimer showing the optimal communication path between residue 614 and T500 (RBD) in wild type and D614G mutant (d) [Color figure can be viewed at wileyonlinelibrary.com]. 2020 Journal of computational chemistry Figure SARS_CoV_2 D614G 147 152 S;RBD 30;125 48;128 32779780 Atomistic simulation reveals structural mechanisms underlying D614G spike glycoprotein-enhanced fitness in SARS-COV-2. Sampled population and dynamics of wild type and D614G SARS-COV-2 spike glycoprotein . 2020 Journal of computational chemistry Figure SARS_CoV_2 D614G 49 54 S 66 84 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. (B) Dot-bracket notation of minimum free energy prediction of the secondary structure of SARS-CoV-2 5'UTR (nt 1-265), WT (left) and C241T variant (right). 2020 Frontiers in microbiology Figure SARS_CoV_2 C241T 132 137 5'UTR 100 105 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. Estimated Molecular Dating of Evolutionary History of 442 Representative Global SARS-CoV-2 Sequences (Late-December 2019-Mid-March 2020) and the Emergence of the D614G Clade. 2020 Scientific reports Figure SARS_CoV_2 D614G 162 167 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. Global Distribution of SARS-CoV-2 Genome Sequences Possessing the Spike Protein D614G Mutation. 2020 Scientific reports Figure SARS_CoV_2 D614G 80 85 S 66 71 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. Node colors indicate continents of isolation; x-axis indicating dates by year and days in decimal notation; D614G clade sequences are highlighted in a yellow box. 2020 Scientific reports Figure SARS_CoV_2 D614G 108 113 32820179 Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide. These four contacts are destabilizing and create a hydrophilic-hydrophobic repelling effect that is lost upon replacement of aspartate by glycine in the D614G mutation (see Table 1). 2020 Scientific reports Figure SARS_CoV_2 D614G 153 158 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. (B) Phylogenetic tree reconstructed from all of the ORFs showing the linkage between D614G in S and P4715L in ORF1ab. 2020 Proc Natl Acad Sci U S A Figure SARS_CoV_2 D614G;P4715L 85;100 90;106 ORF1ab;S 110;94 116;95 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. (C) Overall number of sequences with D614 or D614G across continents; the predominance of D614G in Europe is suggestive of a founder event. 2020 Proc Natl Acad Sci U S A Figure SARS_CoV_2 D614G;D614G 45;90 50;95 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. The MRCA and Wuhan-Hu-1 reference sequences were identical, while the consensus derived from all circulating sequences showed a mutation (D614G). 2020 Proc Natl Acad Sci U S A Figure SARS_CoV_2 D614G 138 143 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. The mutation D614G was found in 69% of sequences sampled globally as of May 18, 2020, the second most frequent mutation in S was only found in ~2% of sequences. 2020 Proc Natl Acad Sci U S A Figure SARS_CoV_2 D614G 13 18 S 123 124 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. The S mutation D614G quickly became dominant. 2020 Proc Natl Acad Sci U S A Figure SARS_CoV_2 D614G 15 20 S 4 5 32879797 Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp. Mutation density has a strong correlation with time in isolates carrying both 14408 C >T and 23403 A >G mutations. 2020 PeerJ Figure SARS_CoV_2 C14408T;A23403G 78;93 88;103 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. (A) The hydrogen bond network of the Mpro (WT) and R60C mutant. 2020 PloS one Figure SARS_CoV_2 R60C 51 55 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. (B) The Structure of WT and R60C mutant Mpro. 2020 PloS one Figure SARS_CoV_2 R60C 28 32 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. Green color indicates the SARS-CoV-2 Mpro while the cyan color indicates the R60C mutant Mpro. 2020 PloS one Figure SARS_CoV_2 R60C 77 81 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. Molecular dynamics of complexed SARS-CoV-2 Mpro and the R60C mutant. 2020 PloS one Figure SARS_CoV_2 R60C 56 60 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. Two Major clades A and B are formed due to the most prevalent mutations D614G. 2020 Journal of laboratory physicians Figure SARS_CoV_2 D614G 72 77 32895623 Crystal structure of SARS-CoV-2 papain-like protease. (A) Ribbon model of the unliganded SARS-CoV-2 PLpro containing C111S mutation. 2021 Acta pharmaceutica Sinica. B Figure SARS_CoV_2 C111S 63 68 32895623 Crystal structure of SARS-CoV-2 papain-like protease. (C) Superimposition of the unliganded SARS-CoV-2 PLpro (yellow, PDB ID: 7CJD, C111S mutant) with SARS-CoV-2 PLpro (blue) complexed by peptide inhibitor VIR251 (magenta). 2021 Acta pharmaceutica Sinica. B Figure SARS_CoV_2 C111S 78 83 32895623 Crystal structure of SARS-CoV-2 papain-like protease. (D) The unliganded SARS-CoV-2 PLpro (yellow, PDB ID: 7CJD, C111S mutant) is superimposed with the structures of PLpro complexed by VIR251 (light blue, PDB ID: 6WX4) and by GRL0617 (green, PDB ID: 7CMD, complexed by GRL0617). 2021 Acta pharmaceutica Sinica. B Figure SARS_CoV_2 C111S 59 64 32895623 Crystal structure of SARS-CoV-2 papain-like protease. The catalytic triads C111S-H272-D286, and other catalytically important residues W93 W106, D108 and N109 are shown with stick model. 2021 Acta pharmaceutica Sinica. B Figure SARS_CoV_2 C111S 21 26 32895643 Genomic characterization of SARS-CoV-2 identified in a reemerging COVID-19 outbreak in Beijing's Xinfadi market in 2020. nt23403(A G) is a nonsynonymous substitution in S gene, which leads to D614G mutation of S protein (indicated in red). 2020 Biosafety and health Figure SARS_CoV_2 D614G 71 76 S;S 48;89 49;90 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. SARS-CoV (AY291315.1), SARS-CoV-2_referential (EPI_ISL_402119), SARS-CoV-2_NSP13-P504L_Y541C (EPI_ISL_413456), Bat-CoV RaTG13 (MN996532.1), Bat-CoV_RmYN02 (EPI_ISL_412977), Pangolin-CoV (EPI_ISL_410721), MERS-CoV (KC875821.1). 2020 Sustainable cities and society Figure SARS_CoV_2 Y541C;P504L 87;81 92;86 32905045 Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. Longitudinal Antibody Responses in Patients Infected with D614G Mutant SARS-CoV-2 Detected by Rapid Lateral Flow and Neutralization Assays. 2020 Cell reports. Medicine Figure SARS_CoV_2 D614G 58 63 32905045 Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. Spike D614G Characterization in the Phase 1 Clinical Cohort (A) Genome map of SARS-CoV-2, with overall topography of Spike expanded. 2020 Cell reports. Medicine Figure SARS_CoV_2 D614G 6 11 S;S 0;117 5;122 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. D614G substitution significantly enhances SARS-CoV-2 replication in primary human airway tissues from a different donor. 2020 bioRxiv Figure SARS_CoV_2 D614G 0 5 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. The D614G mutation was introduced into a mNeonGreen reporter SARS-CoV-2 using the method as described previously. 2020 bioRxiv Figure SARS_CoV_2 D614G 4 9 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. (A) Analysis of ExoN activity in the presence of increasing amounts of nsp10, using wt MERS-CoV-nsp14 (left) and the ExoN double-knockout mutant (DM; D90A/E92A; right). 2020 Journal of virology Figure SARS_CoV_2 D90A;E92A 150;155 154;159 Exon;Exon 16;117 20;121 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. (A) Plaque phenotypes of wt SARS-CoV (left) and SARS-CoV-2 (right) and their corresponding ExoN motif I knockout double mutants (DM; D90A/E92A) in Vero E6 cells. 2020 Journal of virology Figure SARS_CoV_2 D90A;E92A 133;138 137;142 Exon 91 95 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. (C) Plaque phenotype in HuH7 cells of rMERS-CoV nsp14-E191D and wt control in the absence or presence of the mutagenic agent 5-FU. 2020 Journal of virology Figure SARS_CoV_2 E191D 54 59 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. (D) Dose-response curve of wt and E191D mutant MERS-CoV in the presence of 5-FU concentrations up to 400 muM (MOI, 0.1; n = 4; means +- SD). 2020 Journal of virology Figure SARS_CoV_2 E191D 34 39 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. (Left) wt virus; (middle) DM mutant; (right) H229C mutant. 2020 Journal of virology Figure SARS_CoV_2 H229C 45 50 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Characterization of growth kinetics of rMERS-nsp14-E191D and its sensitivity to 5-FU treatment. 2020 Journal of virology Figure SARS_CoV_2 E191D 51 56 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Plaque assays were performed using supernatants harvested from transfected cell cultures at 3 dpt, which were diluted 10-4 for wt and mutant E191D and used in undiluted form for the D90A/E92A ExoN knockout double mutant (DM) and the H229C ZF1 mutant. 2020 Journal of virology Figure SARS_CoV_2 D90A;E191D;H229C;E92A 182;141;233;187 186;146;238;191 Exon 192 196 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. The ExoN activity of different recombinant nsp14 proteins (wt, D90A/E92A, E191D, and H229C) was evaluated by incubating 200 nM nsp14 and 800 nM nsp10 for 0, 5, 30, 60, and 90 min at 37 C. 2020 Journal of virology Figure SARS_CoV_2 D90A;E191D;H229C;E92A 63;74;85;68 67;79;90;72 Exon 4 8 32941419 Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization. The relative abundance of variants of the D614G spike protein mutation (position 14 in our ISM and position 23403 in the reference genome). 2020 PLoS computational biology Figure SARS_CoV_2 D614G 42 47 S 48 53 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. Spatiotemporal distribution of the D614G substitution in the Spike protein of SARS-CoV-2 in South America. 2020 Infection, genetics and evolution Figure SARS_CoV_2 D614G 35 40 S 61 66 32954666 Comprehensive annotations of the mutational spectra of SARS-CoV-2 spike protein: a fast and accurate pipeline. We found two core shared aa mutations at residue position 5 (L5F) and 614 (D614G) in Asia, Europe, Africa, Australia, North America and South America, and two core shared mutations at residue positions of 614 (D614G) and 936 (D936Y) in continental, diverse, dry, tropical and temperate climatic conditions. 2021 Transboundary and emerging diseases Figure SARS_CoV_2 D614G;D614G;D936Y;L5F 75;210;226;61 80;215;231;64 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. RNA synthesis catalyzed by SARS-CoV-2 RdRp WT and the V557L mutant complex on Template R. 2020 The Journal of biological chemistry Figure SARS_CoV_2 V557L 54 59 RdRP 38 42 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. RNA synthesis catalyzed by SARS-CoV-2 RdRp WT, S861G, S861A, and S861P mutant complexes on an RNA template containing single U for RDV-TP incorporation. 2020 The Journal of biological chemistry Figure SARS_CoV_2 S861A;S861G;S861P 54;47;65 59;52;70 RdRP 38 42 32980406 Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13). a) SARS-CoV-2 wild type helicase b) SARS-CoV-2 mutant (P504L and Y541C) helicase. 2020 International journal of biological macromolecules Figure SARS_CoV_2 Y541C;P504L 65;55 70;60 Helicase;Helicase 24;72 32;80 32980406 Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13). The representation in the hexagon is the ATP-binding site and the active residues are shown in yellow, two mutations (P504L and Y541C) are shown in red. 2020 International journal of biological macromolecules Figure SARS_CoV_2 Y541C;P504L 128;118 133;123 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (A and B) Vero cells were challenged with pVSV-SARS-CoV-2-S-mNeon pseudoparticles encoding either D614 (A) or D614G (B) S protein variants in the presence of serial dilutions of the indicated human monoclonal antibodies targeting the SARS-CoV-2 S protein receptor-binding domain or IgG1 isotype control. 2020 Cell Figure SARS_CoV_2 D614G 110 115 S;S;S 58;120;245 59;121;246 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (A-D) SPR measurement of D614-ACE2 binding ([A] and [C]) and D614G-ACE2 binding ([B] and [D]) at 25 C ([A] and [B]) or 37 C ([C] and [D]). 2020 Cell Figure SARS_CoV_2 D614G 61 66 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (A) Cryo-EM density maps of the two conformations of D614G protomer. 2020 Cell Figure SARS_CoV_2 D614G 53 58 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (A) D614G envelope from the three-dimensional reconstruction. 2020 Cell Figure SARS_CoV_2 D614G 4 9 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (A) Lentiviral virions bearing either GFP or Luciferase transgenes, and pseudotyped with either SARS-CoV-2 D614 or D614G S proteins, were produced by transfection of HEK293 cells and used to transduce human Calu3 lung cells, Caco2 colon cells, and either HEK293 or SupT1 cells stably expressing ACE2 and TMPRSS2. 2020 Cell Figure SARS_CoV_2 D614G 115 120 S 121 122 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (A) Size exclusion column elution profiles of D614G (blue line) and D614 (red line). 2020 Cell Figure SARS_CoV_2 D614G 46 51 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (A) The global frequency of the S protein D614G variant over time in the GISAID SARS-CoV-2 database as of June 25, 2020. 2020 Cell Figure SARS_CoV_2 D614G 42 47 S 32 33 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (B) Atomic models for the closed (left) and open (right) conformations for the two D614G protomers shown in (A). 2020 Cell Figure SARS_CoV_2 D614G 83 88 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (B) Lentiviral virions bearing a luciferase transgene, pseudotyped with either SARS-CoV-2 D614 or D614G S proteins, were produced by transfection of HEK293 cells and used to transduce human HEK293 cells transiently transfected with plasmids encoding the indicated ACE2 orthologs. 2020 Cell Figure SARS_CoV_2 D614G 98 103 S 104 105 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (B) The frequency of the D614G variant over time (blue) in sequences collected from six continental regions, using the same dataset as in (A), plotted as a seven-day rolling average. 2020 Cell Figure SARS_CoV_2 D614G 25 30 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (C) Comparison of the two D614G protomer S1 subunit conformations with the corresponding conformations of the D614 protomer S1 subunit. 2020 Cell Figure SARS_CoV_2 D614G 26 31 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (C) Neutralization potency (IC50) of individual monoclonals and of combinations of monoclonals, against the SARS-CoV-2 D614G and D614G S protein variants, as indicated. 2020 Cell Figure SARS_CoV_2 D614G;D614G 119;129 124;134 S 135 136 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (D) 2D-clustering of trimeric D614G particles. 2020 Cell Figure SARS_CoV_2 D614G 30 35 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (D) Atomic model for D614G without the receptor-binding domain. 2020 Cell Figure SARS_CoV_2 D614G 21 26 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (D) The D614G S protein trimer adopts four conformations. 2020 Cell Figure SARS_CoV_2 D614G 8 13 S 14 15 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (E and F) Comparison of the D614G S1 subunit with the closed conformation (E) and open conformation (F) of the D614 S1 subunit. 2020 Cell Figure SARS_CoV_2 D614G 28 33 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (E) Fourier shell correlation diagram for D614G (unmasked). 2020 Cell Figure SARS_CoV_2 D614G 42 47 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (H and I) Substitution of Asp614 with glycine changes hydrogen bonding around residue 614. 2020 Cell Figure SARS_CoV_2 D614G 26 45 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. (H) Local resolution of the ensemble map for Spike D614G. 2020 Cell Figure SARS_CoV_2 D614G 51 56 S 45 50 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Arrows indicate the relative movement of the S1 subunit of D614G. 2020 Cell Figure SARS_CoV_2 D614G 59 64 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. D614G binds ACE2 5-fold weaker than D614 at both temperatures tested. 2020 Cell Figure SARS_CoV_2 D614G 0 5 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. D614G Populates More Open Conformations Than Does the Ancestral S Protein. 2020 Cell Figure SARS_CoV_2 D614G 0 5 S 64 65 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. For D614G (I), the Asp614-Thr859 hydrogen bond is eliminated, and interaction with intradomain Ala647 is strengthened. 2020 Cell Figure SARS_CoV_2 D614G 4 9 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. In addition to the all-closed and one open conformation detected with the D614 S protein trimer, the D614G S protein trimer adopts two-open and three-open conformations. 2020 Cell Figure SARS_CoV_2 D614G 101 106 S;S 79;107 80;108 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Neutralization Potency of Monoclonal Antibodies Targeting the SARS-CoV-2 S Protein Receptor-Binding Domain Is Not Attenuated by D614G. 2020 Cell Figure SARS_CoV_2 D614G 128 133 S 73 74 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Relative infectivity of D614G versus D614, with D614 set at one, was determined based on bulk luciferase activity. 2020 Cell Figure SARS_CoV_2 D614G 24 29 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Relative infectivity of D614G versus D614, with D614 set at one, was determined based on flow cytometry for percent GFP positivity or on bulk luciferase activity. 2020 Cell Figure SARS_CoV_2 D614G 24 29 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. SARS-CoV-2 D614G S Protein Variant Binds ACE2 Weaker than the Ancestral Protein. 2020 Cell Figure SARS_CoV_2 D614G 11 16 S 17 18 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. SARS-CoV-2 D614G S Protein Variant Enhances Infectivity of Pseudotyped Lentiviruses in Cell Culture. 2020 Cell Figure SARS_CoV_2 D614G 11 16 S 17 18 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Structural Determination of Spike D614G, Related to Figure 6. 2020 Cell Figure SARS_CoV_2 D614G 34 39 S 28 33 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Structural Determination of Spike D614G. 2020 Cell Figure SARS_CoV_2 D614G 34 39 S 28 33 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The filled blue plot represents a seven-day rolling average of the fraction of sequences bearing the D614G variant for each collection date. 2020 Cell Figure SARS_CoV_2 D614G 101 106 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The Frequency of the SARS-CoV-2 S Protein D614G Variant over the Course of the Pandemic Has Increased Nearly to Fixation. 2020 Cell Figure SARS_CoV_2 D614G 42 47 S 32 33 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The overlaid black line shows the cumulative frequency of D614G in sequences collected up to and including each date. 2020 Cell Figure SARS_CoV_2 D614G 58 63 32997488 Chemosensory Dysfunction in COVID-19: Integration of Genetic and Epidemiological Data Points to D614G Spike Protein Variant as a Contributing Factor. The D614G substitution, even though it is not located within the RBD (so it will not change the affinity of pure RBD to hACE2), changes the interprotomer spike energetics and enhances RBD exposure, thus favoring the likelihood of binding of the G614-spike protein to hACE2 as compared with the D614 variant. 2020 ACS chemical neuroscience Figure SARS_CoV_2 D614G 4 9 S;S;RBD;RBD;RBD 154;250;65;113;184 159;255;68;116;187 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Viral common variation D614G located in D614 is closed to N-linked glycosylation site N616. 2021 Briefings in bioinformatics Figure SARS_CoV_2 D614G 23 28 N 58 59 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. A total of 18 relatively high frequency sites were screened out (frequency > 10-3), including a highest frequency substitution site D614G. 2020 Frontiers in immunology Figure SARS_CoV_2 D614G 132 137 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. All of them had two variations, except one with T29I, D614G, and G1124V. 2020 Frontiers in immunology Figure SARS_CoV_2 D614G;G1124V;T29I 54;65;48 59;71;52 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. The highest frequency substitution site D614G widely distributes around the world and spreads through the whole transmission process. 2020 Frontiers in immunology Figure SARS_CoV_2 D614G 40 45 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. (a) B-cell epitope in non-mutated RdRp (left) and P4715L mutant (right). 2020 Microbes and infection Figure SARS_CoV_2 P4715L 50 56 RdRP 34 38 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. (a) Effect of P4715L mutation in RdRp. 2020 Microbes and infection Figure SARS_CoV_2 P4715L 14 20 RdRP 33 37 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. (b) Epitope loss linked with ORF3a G251V. 2020 Microbes and infection Figure SARS_CoV_2 G251V 35 40 ORF3a 29 34 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. (c) Epitope loss linked with S1498F in the papain-like protease domain of NSP3 in the ORF1a region. 2020 Microbes and infection Figure SARS_CoV_2 S1498F 29 35 ORF1a;Nsp3 86;74 91;78 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. G251V mutant (right) causes loss of DGSSGVV(250....256aa). 2020 Microbes and infection Figure SARS_CoV_2 G251V 0 5 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. P4715L RdRp and D614G spike variants show co-occurrence. 2020 Microbes and infection Figure SARS_CoV_2 D614G;P4715L 16;0 21;6 S;RdRP 22;7 27;11 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. The B-cell epitope of wildtype sample (left), S1498F mutation causes the loss YKDWS (right). 2020 Microbes and infection Figure SARS_CoV_2 S1498F 46 52 33067385 Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals. (A) Pseudoviral particles coding for the luciferase reporter gene and bearing SARS-CoV-2 S glycoprotein or its D614G counterpart, SARS-CoV S glycoprotein, or VSV-G glycoprotein were used to infect 293T-ACE2 cells. 2020 mBio Figure SARS_CoV_2 D614G 111 116 S;S 89;139 103;153 33067385 Decline of Humoral Responses against SARS-CoV-2 Spike in Convalescent Individuals. (D to F) Cell surface staining of 293T cells expressing full-length Spike (S) from different HCoVs, including (D) SARS-CoV-2 or its D614G counterpart; (E) SARS-CoV; and (F) OC43, NL63, and 229E with plasma samples recovered at baseline (6 weeks after the onset of symptoms) and 1 month later. 2020 mBio Figure SARS_CoV_2 D614G 132 137 S;S 68;75 73;76 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. (B) D614G mutant S protein monomer. 2021 International journal of infectious diseases Figure SARS_CoV_2 D614G 4 9 S 17 18 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. (B) This hydrogen bond can be disrupted with the D614G substitution, altering the activity of the protein. 2021 International journal of infectious diseases Figure SARS_CoV_2 D614G 49 54 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. Furin bound to WT D614 S protein is depicted in green and bound to the D614G mutant is depicted in purple. 2021 International journal of infectious diseases Figure SARS_CoV_2 D614G 71 76 S 23 24 33075532 Higher binding affinity of furin for SARS-CoV-2 spike (S) protein D614G mutant could be associated with higher SARS-CoV-2 infectivity. The red region of the protein depicts the more flexible region of the protein due to the D614G substitution with decreased stability of DeltaDeltaG = -0.086 kcal mol-1 and an increase in vibrational entropy (DeltaDeltaSVib) of 0.137 kcal mol -1 K-1. 2021 International journal of infectious diseases Figure SARS_CoV_2 D614G 89 94 33083031 Experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. A D614G mutation is expected to disrupt both these interactions. 2020 NPJ vaccines Figure SARS_CoV_2 D614G 2 7 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. Bars show the incidences of Q57H (A) and G251V (B) in Orf3a, S194L (C) and R203K/G204R (D) in N at different time periods or in the top five countries and globe (total), as of September 1st, 2020. 2021 Journal of medical virology Figure SARS_CoV_2 G251V;Q57H;R203K;S194L;G204R 41;28;75;61;81 46;32;80;66;86 ORF3a;N 54;94 59;95 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. The aligned structures of control ones and Q57H Orf3a (A), G251V Orf3a (B), S194L N (C), and R203K/G204R N (D) are shown in blue (control, Ctrl) and warm pink (mutant) with the value of RMSD below. 2021 Journal of medical virology Figure SARS_CoV_2 G251V;Q57H;R203K;S194L;G204R 59;43;93;76;99 64;47;98;81;104 ORF3a;ORF3a;N;N 48;65;82;105 53;70;83;106 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. The hot spots in Ctrl Orf3a-S (A), Q57H Orf3a-S (B), G251V Orf3a-S (C), Ctrl Orf3a-Orf8 (D), or Q57H Orf3a-Orf8 (E) complexes are shown as sticks. 2021 Journal of medical virology Figure SARS_CoV_2 G251V;Q57H;Q57H 53;35;96 58;39;100 ORF3a;ORF3a;ORF3a;ORF3a;ORF3a;ORF8;ORF8;S;S;S 22;40;59;77;101;83;107;28;46;65 27;45;64;82;106;87;111;29;47;66 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. D614G substitution significantly enhances SARS-CoV-2 replication in primary human airway tissues from a different donor. 2021 Nature Figure SARS_CoV_2 D614G 0 5 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. The D614G mutation was introduced into a mNeonGreen reporter SARS-CoV-2 using the method as described previously. 2021 Nature Figure SARS_CoV_2 D614G 4 9 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. Founder effect of D614-variants in Spain and selective advantage of D614G substitution. 2021 Journal of virology Figure SARS_CoV_2 D614G 68 73 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. Increased infectivity of D614G pseudoviruses. 2021 Journal of virology Figure SARS_CoV_2 D614G 25 30 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. The red star indicates the sequence associated with the Contamines-Monjoie cluster, and "V" indicates the presence of the G251V mutation in ORF3a protein. 2021 Journal of virology Figure SARS_CoV_2 G251V 122 127 ORF3a 140 145 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. (B) Radial maximum likelihood phylogenetic tree showing the high proportion of genomes with the Spike D839Y mutation detected in Portugal [about 20% of all sequences collected until the end of March (255/1275) or the end of April (287/1500)]. 2020 Emerging microbes & infections Figure SARS_CoV_2 D839Y 102 107 S 96 101 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. As detailed in Table S2, the D839Y sequence from Estonia indicates March 2020 as the date of collection (31 March 2020 was assumed in this plot). 2020 Emerging microbes & infections Figure SARS_CoV_2 D839Y 29 34 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Detection and circulation of the SARS-CoV-2 Spike D839Y mutation worldwide. 2020 Emerging microbes & infections Figure SARS_CoV_2 D839Y 50 55 S 44 49 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. The bar graph in the upper right corner displays the proportion of D839Y sequences in the total number of Spike amino acid sequences available per country. 2020 Emerging microbes & infections Figure SARS_CoV_2 D839Y 67 72 S 106 111 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. The main plot displays the country and data of collection of 92 Spike sequences with the D839Y mutation (detailed in Table S2). 2020 Emerging microbes & infections Figure SARS_CoV_2 D839Y 89 94 S 64 69 33140034 Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein. N234A and N165A mutations of the spike reducebinding to ACE2.(A) Representative biolayer interferometry sensorgramsshowing binding of ACE2 to spike variants. 2020 ACS central science Figure SARS_CoV_2 N165A;N234A 10;0 15;5 S;S 33;142 38;147 33140034 Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein. N234A and N165Amutations show increased instability of RBD-A inthe "up" state. 2020 ACS central science Figure SARS_CoV_2 N234A 0 5 RBD 55 58 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. G22017T spike gene mutation in patient HKU-IHCE0511-006. 2021 Clinical microbiology and infection Figure SARS_CoV_2 G22017T 0 7 S 8 13 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. A comparison of the different mutants and reference viral strain with a delta score revealed that mutations G196V and G251V decreased disorder. 2020 Evolutionary bioinformatics online Figure SARS_CoV_2 G196V;G251V 108;118 113;123 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. A comparison of the R203K mutant and reference viral strain with a delta score revealed that the mutation increased disorder. 2020 Evolutionary bioinformatics online Figure SARS_CoV_2 R203K 20 25 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. A similar outcome was obtained with the G204R mutant. 2020 Evolutionary bioinformatics online Figure SARS_CoV_2 G204R 40 45 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. DALI structural neighborhood analysis of PDB entry 6JYT (1356 structures) showed C541Y is in regions of the molecule that are structurally conserved, while the L504P region was variable at both sequence and structure levels. 2020 Evolutionary bioinformatics online Figure SARS_CoV_2 C541Y;L504P 81;160 86;165 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. Examining the SARS-CoV-2 structure in complex with NSP7 and 8 cofactors (PDB entry 6M71) revealed that the P323L mutation sits in an 'interface' region (spanning residues 250-365) between the N-terminal nidovirus-unique NiRAN domain with nucleotidyltransferase activity and the C-terminal polymerase domain that harbors the fingers, palm and thumb subdomains. 2020 Evolutionary bioinformatics online Figure SARS_CoV_2 P323L 107 112 Nsp7;N 51;192 55;193 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. L504P and C541Y are in loop regions located on the surface of the middle of the 2B domain. 2020 Evolutionary bioinformatics online Figure SARS_CoV_2 C541Y;L504P 10;0 15;5 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. Mutation G197V forms part of a loop at the surface of the CD. 2020 Evolutionary bioinformatics online Figure SARS_CoV_2 G197V 9 14 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. Mutation Q57H is located in the first of the 3 transmembrane helices at the major hydrophilic constriction of the pore important for channel activity. 2020 Evolutionary bioinformatics online Figure SARS_CoV_2 Q57H 9 13 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. The SARS-CoV-2 atomic model of a dimer (PDB entry 6VXX) shows the D614G mutation of the S1 domain eliminates a hydrogen bonding interaction with site 859 of the S2 domain of another protomer (colored in orange in the inset). 2020 Evolutionary bioinformatics online Figure SARS_CoV_2 D614G 66 71 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. (A) The align of Korean COVID-19 and wild ype SARS-CoV2 spike gene amino acid sequence revealed three new mutations (G504D/V524D/P579L) highlighted by green with red letter. 2020 Immune network Figure SARS_CoV_2 G504D;P579L;V524D 117;129;123 122;134;128 S 56 61 COVID-19 24 32 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. The known mutation (D614G) marked by blue with red letter. 2020 Immune network Figure SARS_CoV_2 D614G 20 25 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. The representative chromatography of D614G (A), G504D (B), V524D (C), and P579L (D) mutation was shown from the DNA sequencing results of four Korean COVID-19 patients. 2020 Immune network Figure SARS_CoV_2 D614G;G504D;P579L;V524D 37;48;74;59 42;53;79;64 COVID-19 150 158 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. Average variation counts per sample for C3037T (F924F), C14408T (P4715L), A23403G (D614G), and C23575T (C671C) first coobserved in EPI_ISL_422425 in China are displayed since January 24, 2020. 2020 Proc Natl Acad Sci U S A Figure SARS_CoV_2 A23403G;C14408T;C23575T;C3037T;C671C;D614G;F924F;P4715L 74;56;95;40;104;83;48;65 81;63;102;46;109;88;53;71 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. The moving-window proportion on a sample collection date was calculated by dividing the number of variations (e.g., allele G for A23403G) by the number of strains within four closest sample collection dates on each side. 2020 Proc Natl Acad Sci U S A Figure SARS_CoV_2 A23403G 129 136 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. The TTG signature SNVs persisted, but C23575T was lost immediately in the samples. 2020 Proc Natl Acad Sci U S A Figure SARS_CoV_2 C23575T 38 45 33185784 Comparison of Binding Site of Remdesivir and Its Metabolites with NSP12-NSP7-NSP8, and NSP3 of SARS CoV-2 Virus and Alternative Potential Drugs for COVID-19 Treatment. Superimposition of the crystal structure of the metabolite of Remdesivir (PDB: 7BV2) in wild type (purple) and V557L (orange) with UTP (Uridine phosphate, green) (Color figure online) 2020 The protein journal Figure SARS_CoV_2 V557L 111 116 33185784 Comparison of Binding Site of Remdesivir and Its Metabolites with NSP12-NSP7-NSP8, and NSP3 of SARS CoV-2 Virus and Alternative Potential Drugs for COVID-19 Treatment. Superimposition of the crystal structure of the metabolite of Remdesivir (PDB: 7BV2) in wild type (purple) and V557L (orange) with UTP (Uridine phosphate, green) (Color figure online). 2020 The protein journal Figure SARS_CoV_2 V557L 111 116 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. (A) Highlight of the Q57H substitution in orf3a and the introduction of premature stop codon in orf3b. 2020 Emerging microbes & infections Figure SARS_CoV_2 Q57H 21 25 ORF3b;ORF3a 96;42 101;47 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. SARS-CoV-2 orf3a Q57H substitution creates early stop codon of orf3b. 2020 Emerging microbes & infections Figure SARS_CoV_2 Q57H 17 21 ORF3b;ORF3a 63;11 68;16 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. a 2mFo-DFc electron density (contoured at 1.0sigma) in chain B of the C145A mutant shows presence of the bound C-terminal product of symmetry-related molecule B'. 2020 Nature communications Figure SARS_CoV_2 C145A 70 75 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. a CPK molecular surface of SARS-CoV-1 C145A catalytic mutant ES complex (PDB 5B60), including C-terminal cleavage site P6-P4' (P1'-P3' with green carbons). 2020 Nature communications Figure SARS_CoV_2 C145A 38 43 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. b 2mFo-DFc electron density (1.0sigma) of empty protomer, chain A, of the same C145A mutant structure shows presence of a highly ordered water molecule hydrogen bonded to Nepsilon2 of His41, consistent with a general base role of the latter and coincident in position with the Wcat weakly observed in the acyl-enzyme complex as in c and. 2020 Nature communications Figure SARS_CoV_2 C145A 79 84 33208735 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site. C145A SARS-CoV-2 Mpro product complex at 2.0 A resolution. 2020 Nature communications Figure SARS_CoV_2 C145A 0 5 33208827 Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19. Inhibition of pseudoviruses carrying D614D (wild-type) or D614G (variant) versions of the spike protein by mice immunized with S-2P with CpG 1018 and aluminum hydroxide. 2020 Scientific reports Figure SARS_CoV_2 D614D;D614G 37;58 42;63 S;S 90;127 95;128 33208827 Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19. Neutralization assays were performed with pseudoviruses with either D616D or D614G spike proteins. 2020 Scientific reports Figure SARS_CoV_2 D614G;D616D 77;68 82;73 S 83 88 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Schematic comparison of two independent models explaining increased infectivity by SARS-CoV-2 isolates possessing D614G mutant spike. 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 D614G 114 119 S 127 132 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. b A representation of the SARS-CoV-2 S protein (top) and D/G variation at residue 614 presented in logo plots at different time points between January 1st and May 30th, 2020 (bottom). 2020 Nature communications Figure SARS_CoV_2 D614G 57 85 S 37 38 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. The D614G mutation is associated with enhanced infectivity. 2020 Nature communications Figure SARS_CoV_2 D614G 4 9 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. The D614G mutation neither increases S protein affinity for ACE2 nor makes PV more resistant to neutralization. 2020 Nature communications Figure SARS_CoV_2 D614G 4 9 S 37 38 33259879 Evolution and genetic diversity of SARS-CoV-2 in Africa using whole genome sequences. The red shaded region represents the receptor binding domain; the blue shaded box represents the D614G motive, while the empty red box represents the polybasic cleavage site bordering the S1/S2 sub-unit. 2021 International journal of infectious diseases Figure SARS_CoV_2 D614G 97 102 RBD 37 60 33272568 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Variations of root mean square deviation (RMSD) (A), Distribution of RBD-ACE2 distances (B), Distribution of RBD-ACE2 interfacial area (C), number of hydrogen bonds (D), van der Waals interaction energy (E), and electrostatic interactions energy (F) between RBD and ACE2 obtained from the molecular dynamics simulations for wild-type, V367F and S494P variant of RBD are shown. 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 S494P;V367F 345;335 350;340 RBD;RBD;RBD;RBD 69;109;258;362 72;112;261;365 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. A single P384A substitution increases CR3022 affinity to the SARS-CoV-2 RBD. 2020 PLoS pathogens Figure SARS_CoV_2 P384A 9 14 RBD 72 75 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. The neutralizing activity of CR3022 IgG or Fab to SARS-CoV, SARS-CoV-2, and SARS-CoV-2 P384A mutant was measured in a pseudovirus neutralization assay. 2020 PLoS pathogens Figure SARS_CoV_2 P384A 87 92 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Clinical Severity in Patients in Association with the D614G Polymorphism and Age. 2021 Cell Figure SARS_CoV_2 D614G 54 59 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Maximum Likelihood Phylogeny Estimated from a Representative Set of 900 SARS-CoV-2 Genome Sequences, Showing global Lineage Assignments and the Origins of the Spike Protein D614G Mutation, which Seeded Many Introductions in the United Kingdom. 2021 Cell Figure SARS_CoV_2 D614G 173 178 S 159 164 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Putative reversions to 614D and independently arising D614G mutations are shown as large circles. 2021 Cell Figure SARS_CoV_2 D614G 54 59 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. The D614N genomes shown as red circles indicated two independent clusters in the United Kingdom. 2021 Cell Figure SARS_CoV_2 D614N 4 9 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. This shows the early stages of emergence of D614G into Europe from China. 2021 Cell Figure SARS_CoV_2 D614G 44 49 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. In bovine tissues, D614G replicated significantly at higher magnitude compared to D614 at 48 hpi (p < 0.05) in tracheal EVOCs; 48 hpi (p <0.01) and 72 hpi (p < 0.05) in lung EVOCs. 2021 Veterinary microbiology Figure SARS_CoV_2 D614G 19 24 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. Number of RNA copies of SARS-CoV-2 in EVOC supernatants infected with a dose of 103 TCID50/mL of the D614 and D614G strains increased significantly in bovine and ovine EVOCs from 1 to 72 hpi (p < 0.05). 2021 Veterinary microbiology Figure SARS_CoV_2 D614G 110 115 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. Quantification of RNA copies in EVOC supernatants revealed more evident differences between D614 and D614G. 2021 Veterinary microbiology Figure SARS_CoV_2 D614G 101 106 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. (C) Volcano plot of parameters associated with the presence of D614G mutation in spike proteins of study participants' infecting SARS-CoV-2 viruses. 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 63 68 S 81 86 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. Clade and clinical correlation analysis and study parameters associated with lethal outcome and spike D614G mutation. 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 102 107 S 96 101 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. The introduction of the spike D614G mutation is indicated by a red arrowhead. 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 30 35 S 24 29 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. (A) In this alpha-complementation assay, 293T target cells expressing ACE2 only or ACE2+TMPRSS2 were incubated with ilomastat and marimastat at the indicated concentration for 2 h before cocultivation with effector cells expressing wild-type or D614G S gp for 4 h. 2020 Journal of virology Figure SARS_CoV_2 D614G 245 250 S 251 252 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. (A) Lentivirus particles pseudotyped with the wild-type or D614G S glycoproteins were incubated with various concentrations (0 to 300 nM) of soluble ACE2 (sACE2) for 1 h on ice. 2020 Journal of virology Figure SARS_CoV_2 D614G 59 64 S 65 80 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. (B) Lentivirus particles pseudotyped with the wild-type or D614G glycoproteins were incubated with the indicated concentrations of sACE2 for 1 h at 37 C. 2020 Journal of virology Figure SARS_CoV_2 D614G 59 64 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. (C and D) VSV vectors pseudotyped with the wild-type, FurinMut, or D614G S gp variants were used to infect 293T-ACE2 cells after incubation with different dilutions/concentrations of NYP01, NYP21, and NYP22 convalescent-phase sera or soluble ACE2 (sACE2). 2020 Journal of virology Figure SARS_CoV_2 D614G 67 72 S 73 74 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. (C) Lentivirus particles pseudotyped with the wild-type or D614G S glycoproteins were incubated at 37 C for the indicated number of days, after which the lentivirus particles were pelleted, lysed, and Western blotted. 2020 Journal of virology Figure SARS_CoV_2 D614G 59 64 S 65 80 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. (D) Lysates from 293T cells transiently expressing the His6-tagged wild-type or D614G glycoproteins were incubated at the indicated temperatures for 1 h. 2020 Journal of virology Figure SARS_CoV_2 D614G 80 85 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. D614G alteration increases S gp sensitivity to soluble ACE2 and S1-trimer association. 2020 Journal of virology Figure SARS_CoV_2 D614G 0 5 S 27 28 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. The D614G and FurinMut changes influence virus infectivity, cold sensitivity, and sensitivity to soluble ACE2 and neutralizing antisera. 2020 Journal of virology Figure SARS_CoV_2 D614G 4 9 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. The wild-type, FurinMut, and D614G S glycoproteins are positioned along the pathway according to their phenotypes. 2020 Journal of virology Figure SARS_CoV_2 D614G 29 34 S 35 50 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. (A) Serially diluted soluble ACE2, ACE2, and ACE2.H345A microbody proteins were incubated for 30 min with SARS-CoV-2 Delta19.S pseudotyped virus and then added to ACE2.293T cells. 2020 Cell reports Figure SARS_CoV_2 Delta19 117 124 S 125 126 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. (A) The domain structure of the SARS-CoV-2 D614G Delta19 S expression vector is diagrammed above. 2020 Cell reports Figure SARS_CoV_2 D614G 43 48 S 57 58 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. (B) A panel of cell lines was infected with equivalent amounts (MOI = 0.2) of wild-type and D614G Delta19 spike protein pseudotyped virus. 2020 Cell reports Figure SARS_CoV_2 D614G 92 97 S 106 111 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. (C) Serially diluted soluble ACE2 and ACE2 microbody proteins were mixed with D614G Delta19 spike protein pseudotyped virus and added to target cells. 2020 Cell reports Figure SARS_CoV_2 D614G 78 83 S 92 97 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. ACE2 Microbody Blocks Entry of the D614G Variant Spike Protein Pseudotyped Virus Infection and ACE2 Using beta Coronavirus Spike Proteins. 2020 Cell reports Figure SARS_CoV_2 D614G 35 40 S;S 49;123 54;128 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. Red star indicates the D614G mutation in the spike protein. 2020 Cell reports Figure SARS_CoV_2 D614G 23 28 S 45 50 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. SARS-CoV-2 Delta19.S pseudotyped virus was added to ACE2.293T cells. 2020 Cell reports Figure SARS_CoV_2 Delta19 11 18 S 19 20 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. (I) The hydrogen bond is lost as a result of D614G mutation. 2020 Frontiers in microbiology Figure SARS_CoV_2 D614G 45 50 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. D614G change in Spike protein enhanced TMPRSS2 protease interaction that might be responsible for increased virus infectivity. 2020 Frontiers in microbiology Figure SARS_CoV_2 D614G 0 5 S 16 21 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. D614G in Spike gene increases infectivity portrayed by Ct values as a surrogate for viral load. 2020 Frontiers in microbiology Figure SARS_CoV_2 D614G 0 5 S 9 14 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Pro323Leu is a frequent mutation in nsp12. 2020 Genome biology Figure SARS_CoV_2 P323L 0 9 Nsp12 36 41 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. The mutation Asp614Gly is quite frequent (62% of sequences analyzed have it) (PDB id 6xr8). 2020 Genome biology Figure SARS_CoV_2 D614G 13 22 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. The mutation Ser25Leu in nsp7 is fairly frequent. 2020 Genome biology Figure SARS_CoV_2 S25L 13 21 Nsp7 25 29 33357233 Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. The mutations Val483Gly, Val483Ala, and Val483Asp were identified in SARS-CoV-2. 2020 Genome biology Figure SARS_CoV_2 V483A;V483D;V483G 25;40;14 34;49;23 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. c Evolution of S447N and N439K in space and time. 2020 Journal of translational medicine Figure SARS_CoV_2 N439K;S447N 25;15 30;20 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. All G clades (G, GH and GR) carried the D614G mutation. 2020 PeerJ Figure SARS_CoV_2 D614G 40 45 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. Clade distribution of SARS-CoV-2 genomes in Indonesia until the submission date of September 2020, showing that 65% contained the D614G mutation. 2020 PeerJ Figure SARS_CoV_2 D614G 130 135 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. (A) Detection of the D614G mutation at the protein level. 2021 Trends in genetics Figure SARS_CoV_2 D614G 21 26 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. (B) Detection of the D614G mutation at the gene level. 2021 Trends in genetics Figure SARS_CoV_2 D614G 21 26 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Biosensing Technologies for the Detection of the D614G Mutation. 2021 Trends in genetics Figure SARS_CoV_2 D614G 49 54 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Promising approaches for the recognition of the D614G mutation at the gene level include loop-mediated isothermal amplification (LAMP), restriction enzymes, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas, nanopore, and oligo probe hybridization. 2021 Trends in genetics Figure SARS_CoV_2 D614G 48 53 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. Specific signal generated by these biorecognition techniques can be then used for the detection of the D614G mutation using a variety of detection principles, such as electrochemical and optical techniques, lateral flow strips, sequencing, or microarrays. 2021 Trends in genetics Figure SARS_CoV_2 D614G 103 108 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. The D614G mutation at the protein level can be identified using angiotensin-converting enzyme 2 (ACE2) protein, aptamers, antibodies, or nanobodies. 2021 Trends in genetics Figure SARS_CoV_2 D614G 4 9 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. The D614G mutation in severe acute respiratory coronavirus 2 (SARS-CoV-2) spike protein corresponds to the alteration of an adenine to a guanine at genomic position 23 403. 2021 Trends in genetics Figure SARS_CoV_2 D614G 4 9 S 74 79 33402270 Biosensing Detection of the SARS-CoV-2 D614G Mutation. The D614G Mutation in Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) Spike Protein. 2021 Trends in genetics Figure SARS_CoV_2 D614G 4 9 S 74 79 33412089 COVID-19-neutralizing antibodies predict disease severity and survival. (A) A schematic of the SARS-CoV-2 and WIV1-CoV spike proteins, including full-length, truncated (Delta18), and mutant (D614G) forms is shown; ERRS denotes putative ER retention signal. 2021 Cell Figure SARS_CoV_2 D614G 119 124 S 47 52 33412089 COVID-19-neutralizing antibodies predict disease severity and survival. (B) Expression of full-length, Delta18, and Delta18 D614G SARS-CoV-2 spike constructs in 293T cells in comparison to empty vector (neg. 2021 Cell Figure SARS_CoV_2 D614G 52 57 S 69 74 33412089 COVID-19-neutralizing antibodies predict disease severity and survival. (C) Cross-neutralization of serum samples from COVID-19 patients that were non-hospitalized (green, n = 16), hospitalized (yellow, n = 67), intubated (red, n = 43), deceased (gray, n = 15), or immunosuppressed (blue, n = 21) and healthy blood donors (n = 35) was measured for wild-type versus D614G mutant SARS-CoV-2 Delta18 spike pseudovirus. 2021 Cell Figure SARS_CoV_2 D614G 293 298 S 325 330 COVID-19 47 55 33412089 COVID-19-neutralizing antibodies predict disease severity and survival. SARS-CoV-2-infected patient sera cross-neutralizes both wild-type and D614G mutant SARS-CoV-2 spike but not the highly homologous pre-emergent bat coronavirus WIV1-CoV. 2021 Cell Figure SARS_CoV_2 D614G 70 75 S 94 99 33412089 COVID-19-neutralizing antibodies predict disease severity and survival. Several constructs of spike were tested: codon-optimized full-length spike from SARS-CoV-2, a truncated version with 18 amino acids deleted from the cytoplasmic tail (Delta18), and a truncated version that also includes a D614G mutation. 2021 Cell Figure SARS_CoV_2 D614G 222 227 S;S 22;69 27;74 33413610 An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets. a-c High frequency non-synonymous spike D614G, NSP12 N314L and orf3A Q57H mutations found in SARS-CoV-2 plotted weekly by continent. 2021 Genome medicine Figure SARS_CoV_2 D614G;N314L;Q57H 40;53;69 45;58;73 S;ORF3a;Nsp12 34;63;47 39;68;52 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (A) (Left) SEC elution profile on a Superose 6 10/300 column of the S-GSAS/D614G (blue) ectodomain. 2021 Cell reports Figure SARS_CoV_2 D614G 75 80 S 68 69 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (A) SEC elution profile of the S-RRAR (in red) and S-RRAR/D614G (in blue) ectodomains. 2021 Cell reports Figure SARS_CoV_2 D614G 58 63 S;S 31;51 32;52 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (A) SEC elution profile on a Superose 6 10/300 column of the S-HRV3C (red) and S-HRV3C/D614G (blue) ectodomains. 2021 Cell reports Figure SARS_CoV_2 D614G 87 92 S;S 61;79 62;80 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (A) Side view of the cryo-EM reconstruction of the 1-RBD-up (EMD: 22824) and the 3-RBD-down (EMD: 22823) states of the furin-cleaved S-RRAR/D614G ectodomain colored by chain. 2021 Cell reports Figure SARS_CoV_2 D614G 140 145 RBD;RBD;S 53;83;133 56;86;134 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (B) Binding of ACE2 receptor ectodomain (RBD-directed), CR3022 (RBD-directed neutralizing antibody), 2G12 (S2-directed), Ab712199 (RBD-directed neutralizing antibody), and Ab511584 (S2-directed non-neutralizing antibody) to S-GSAS/D614G (in blue) and the furin-cleaved S-RRAR/D614G ectodomain (in green) measured by ELISA. 2021 Cell reports Figure SARS_CoV_2 D614G;D614G 231;276 236;281 RBD;RBD;RBD;S;S 41;64;131;224;269 44;67;134;225;270 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (B) Representative NSEM micrograph of S-GSAS/D614G and 2D class averages (related to Data S2). 2021 Cell reports Figure SARS_CoV_2 D614G 45 50 S 38 39 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (C and D) Representative NSEM micrograph of (C) S-HRV3C and (D) S-HRV3C/D614G ectodomains and 2D class averages (related to Data S4). 2021 Cell reports Figure SARS_CoV_2 D614G 72 77 S;S 48;64 49;65 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (C and D) Representative NSEM micrograph of (C) S-RRAR and (D) S-RRAR/D614G ectodomains and 2D class averages (related to Data S5). 2021 Cell reports Figure SARS_CoV_2 D614G 70 75 S;S 48;63 49;64 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (C) Side view of the cryo-EM reconstruction of the 1-RBD-up (EMD: 22826) and the 3-RBD-down (EMD: 22825) states of the S-GSAS/D614G ectodomain colored by chain. 2021 Cell reports Figure SARS_CoV_2 D614G 126 131 RBD;RBD;S 53;83;119 56;86;120 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (D) (Left) The protomers of the 1-RBD-up structure of the furin-cleaved S-RRAR/D614G ectodomain superimposed using residues 908-1,035 and colored by the color of their NTD as depicted in (A). 2021 Cell reports Figure SARS_CoV_2 D614G 79 84 RBD;S 34;72 37;73 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (E and F) SDS-PAGE of an HRV3C digestion of the (E) S-HRV3C and (F) S-HRV3C/D614G engineered ectodomains at 25 C for 24 h in the presence of 0.03 U of enzyme per microgram of ectodomain. 2021 Cell reports Figure SARS_CoV_2 D614G 76 81 S;S 52;68 53;69 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (E) SDS-PAGE of furin digestion of the S-RRAR and S-RRAR/D614G ectodomains at 25 C for 3 h in the presence of 0.3 U of enzyme per microgram of ectodomain in buffer containing 0.2 mM CaCl2. 2021 Cell reports Figure SARS_CoV_2 D614G 57 62 S;S 39;50 40;51 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (F) SEC elution profile of the S-RRAR/D614G furin digested (in blue). 2021 Cell reports Figure SARS_CoV_2 D614G 38 43 S 31 32 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (G) Quantification of S protomer (200 kDa) band intensity on SDS-PAGE at the time points presented on (E) and (F) (S-HRV3C in red, S-HRV3C/D614G in blue). 2021 Cell reports Figure SARS_CoV_2 D614G 139 144 S;S;S 22;115;131 23;116;132 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (G) SDS-PAGE of the S-RRAR/D614G furin digested and SEC purified ectodomain. 2021 Cell reports Figure SARS_CoV_2 D614G 27 32 S 20 21 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (H) Representative NSEM micrograph and 2D class averages of the S-RRAR/D614G furin digested and SEC purified following digestion. 2021 Cell reports Figure SARS_CoV_2 D614G 71 76 S 64 65 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. (right) Differential scanning fluorimetry (DSF) of S-GSAS/D614G (blue). 2021 Cell reports Figure SARS_CoV_2 D614G 58 63 S 51 52 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Biophysics and Structure of the S-GSAS/D614G Ectodomain. 2021 Cell reports Figure SARS_CoV_2 D614G 39 44 S 32 33 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Domain Motions in the S-GSAS/D614G Ectodomain. 2021 Cell reports Figure SARS_CoV_2 D614G 29 34 S 22 23 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Each inset corresponds to the S regions understudy and is highlighted in red on the trimeric structure (K986P-V987P, D614G, and the furin protease cleavage site). 2021 Cell reports Figure SARS_CoV_2 D614G;K986P;V987P 117;104;110 122;109;115 S 30 31 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. SARS-CoV-2 Spike (S) Protein Ectodomain Platform for Characterizing the Structures, Antigenicity, and Protease Susceptibility of the S Protein and D614G Mutant. 2021 Cell reports Figure SARS_CoV_2 D614G 147 152 S;S;S 11;18;133 16;19;134 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Structure and Antigenicity of the Furin-Cleaved S-RRAR/D614G Ectodomain. 2021 Cell reports Figure SARS_CoV_2 D614G 55 60 S 48 49 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. The D614G mutation is in the SD2 domain (yellow star, green contour). 2021 Cell reports Figure SARS_CoV_2 D614G 4 9 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. The Engineered S-HRV3C/D614G Ectodomain Is More Susceptible to S1/S2 Cleavage by the HRV3C Protease Than S-HRV3C. 2021 Cell reports Figure SARS_CoV_2 D614G 23 28 S;S 15;105 16;106 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. The K986P-V987P mutations between the HR1 and CH domains are indicated by a yellow star (red contour) on the S-GSAS/PP template. 2021 Cell reports Figure SARS_CoV_2 K986P;V987P 4;10 9;15 S 109 110 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. The S-RRAR/D614G Ectodomain Is More Susceptible to S1/S2 Cleavage by Furin Than S-RRAR. 2021 Cell reports Figure SARS_CoV_2 D614G 11 16 S;S 4;80 5;81 33429204 PfAgo-based detection of SARS-CoV-2. Identifying SARS-CoV-2 and its D614G mutants with PAND in clinical samples. 2021 Biosensors & bioelectronics Figure SARS_CoV_2 D614G 31 36 33433004 Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure. A steric clash is observed between nsp8 M129 and RdRp N386, which is abolished in the nsp8 M129I mutant. 2021 Journal of medical virology Figure SARS_CoV_2 M129I 91 96 Nsp8;Nsp8;RdRP 35;86;49 39;90;53 33433004 Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure. The P323L mutation in RdRp leads to a H-bond formation with nsp8 N118, which is not observed when native RdRp interacts with nsp8. 2021 Journal of medical virology Figure SARS_CoV_2 P323L 4 9 Nsp8;Nsp8;RdRP;RdRP 60;125;22;105 64;129;26;109 33433004 Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure. The S25L mutation in nsp7 leads to a H-bond formation between nsp7 S26 and nsp8 D163, which is not observed in the native RdRp-nsp7-nsp8 supercomplex. 2021 Journal of medical virology Figure SARS_CoV_2 S25L 4 8 Nsp7;Nsp7;Nsp7;Nsp8;Nsp8;RdRP 21;62;127;75;132;122 25;66;131;79;136;126 33436577 A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein. a Serial twofold-diluted CT-P59 were incubated with SARS-CoV-2 live viruses; wild type (blue) and D614G (red). 2021 Nature communications Figure SARS_CoV_2 D614G 98 103 33468695 SARS-CoV-2 Infection Severity Is Linked to Superior Humoral Immunity against the Spike. (a and b) Endpoint titers of total Ig antibodies binding to the WT (D614) and mutant (D614G) SARS-CoV-2 spike protein from the acute (a) (n = 35) and convalescent (b) (n = 105) cohorts. 2021 mBio Figure SARS_CoV_2 D614G 86 91 S 104 109 33468695 SARS-CoV-2 Infection Severity Is Linked to Superior Humoral Immunity against the Spike. (c) Correlation of total Ig endpoint titers against the WT (D614) and mutant (D614G) spike from the convalescent cohort (n = 105). 2021 mBio Figure SARS_CoV_2 D614G 78 83 S 85 90 33471859 In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh. Circle 1 exhibits the location and distribution of genome sequences; circle 2 demonstrates GISAID clades based on some specific mutations, and circle 3 represents the D614G classification. 2021 PloS one Figure SARS_CoV_2 D614G 167 172 33478625 Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020. The 21765-21770 deletion in the S gene results in deletion of amino-acid residues 69 and 70 in the S protein; on each side of the 21765-21770 deletion in the nt sequence, the remaining ATC (21764-21771-21772) encodes an isoleucine amino acid (I). 2021 Euro surveillance Figure SARS_CoV_2 del 69 50 84 S;S 32;99 33;100 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. A: L84S; B: S24L and C: V62L. 2021 Gene reports Figure SARS_CoV_2 L84S;S24L;V62L 3;12;24 7;16;28 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. A: ORF8 DNA of Human SARS-CoV-2 (SARS CoV2 ORF8) (gene ID: 43740577), and the 269 variants sequences and 2 deletions' sequences (G66-S67del, K68E, L7-I121del) were analyzed. 2021 Gene reports Figure SARS_CoV_2 K68E 141 145 ORF8;ORF8 3;43 7;47 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. L84S is highly present in USA, Spain, Australia and United Kingdom. 2021 Gene reports Figure SARS_CoV_2 L84S 0 4 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. S24L is highly present in USA, followed by Australia and Canada. 2021 Gene reports Figure SARS_CoV_2 S24L 0 4 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. Some variants were found at conserved amino acids and were located in beta-strands like Q23X(H), C25F(S), P30S (L,Q,T), W45S(L,C,X), R48G, I88T (F,V), C90F, G96V(S,C), R101(L,C) and C102F(Y), D113Y, V116A, V117F and L118X(V,S,F). 2021 Gene reports Figure SARS_CoV_2 C102F;C25F;C90F;D113Y;G96V;I88T;L118X;P30S;Q23X;R101L;R48G;V116A;V117F;W45S 182;97;151;192;157;139;216;106;88;168;133;199;206;120 187;101;155;197;161;143;221;110;92;177;137;204;211;124 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. United Kingdom has the highest V62L representation worldwide. 2021 Gene reports Figure SARS_CoV_2 V62L 31 35 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. A) The upper MCC tree with sequences having the D614G mutation. 2021 Heliyon Figure SARS_CoV_2 D614G 48 53 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. Temporal change in the prevalence of D614G in the Middle East and North Africa stratified by months of SARS-CoV-2 sequence collection. 2021 Heliyon Figure SARS_CoV_2 D614G 37 42 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. The relative proportions of D614 and D614G mutation in the Middle East and North Africa stratified by countries of SARS-CoV-2 sequence collection. 2021 Heliyon Figure SARS_CoV_2 D614G 37 42 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Analyses plots for N protein mutation at position 28311 (P13L). 2021 PloS one Figure SARS_CoV_2 P13L 57 61 N 19 20 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Analyses plots for ORF3a protein mutation at position 25563 (Q57H). 2021 PloS one Figure SARS_CoV_2 Q57H 61 65 ORF3a 19 24 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Boxplot distributions with and without the P13L mutation. 2021 PloS one Figure SARS_CoV_2 P13L 43 47 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Boxplot distributions with and without the Q57H mutation. 2021 PloS one Figure SARS_CoV_2 Q57H 43 47 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Cases per million for countries with the P13L mutation and the reference mutation including response time separation. 2021 PloS one Figure SARS_CoV_2 P13L 41 45 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Cases per million for countries with the P13L mutation and the reference mutation. 2021 PloS one Figure SARS_CoV_2 P13L 41 45 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Cases per million for countries with the Q57H mutation and the reference mutation including response time separation. 2021 PloS one Figure SARS_CoV_2 Q57H 41 45 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Cases per million for countries with the Q57H mutation and the reference mutation. 2021 PloS one Figure SARS_CoV_2 Q57H 41 45 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Deaths per million for countries with the P13L mutation and the reference mutation including response time separation. 2021 PloS one Figure SARS_CoV_2 P13L 42 46 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Deaths per million for countries with the P13L mutation and the reference mutation. 2021 PloS one Figure SARS_CoV_2 P13L 42 46 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Deaths per million for countries with the Q57H mutation and the reference mutation including response time separation. 2021 PloS one Figure SARS_CoV_2 Q57H 42 46 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Deaths per million for countries with the Q57H mutation and the reference mutation. 2021 PloS one Figure SARS_CoV_2 Q57H 42 46 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Detailed molecular structural conformational changes of ORF3a protein showing the REF-Q57H. 2021 PloS one Figure SARS_CoV_2 Q57H 86 90 ORF3a 56 61 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Mutations of interest, P13L and Q57H, are labelled in the plot together with the D614G mutation for comparison. 2021 PloS one Figure SARS_CoV_2 D614G;P13L;Q57H 81;23;32 86;27;36 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. P13L transmission in months from its first occurrence in Asia (Korea) to its transmission across other countries and continents. 2021 PloS one Figure SARS_CoV_2 P13L 0 4 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Q57H transmission in months from its first occurrence in Europe (France) to its transmission across the globe. 2021 PloS one Figure SARS_CoV_2 Q57H 0 4 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. REF-P13L complexes colored in red, ALT-P13L complexes colored in green. 2021 PloS one Figure SARS_CoV_2 P13L;P13L 4;39 8;43 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. REF-P13L complexes colored in red; ALT-P13L complexes colored in green. 2021 PloS one Figure SARS_CoV_2 P13L;P13L 4;39 8;43 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Same molecular analysis for the structure with ALT-Q57H. 2021 PloS one Figure SARS_CoV_2 Q57H 51 55 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Structural prediction with ALT-Q57H. 2021 PloS one Figure SARS_CoV_2 Q57H 31 35 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Structural prediction with REF-Q57H. 2021 PloS one Figure SARS_CoV_2 Q57H 31 35 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. (Phyre2) Mutational sensitivity (a) the locations of single amino acid variants del Y144 (left side) & D614G (right side) on spike protein as they have the highest mutation sensitivity scores. 2021 Biochemistry and biophysics reports Figure SARS_CoV_2 D614G 103 108 S 125 130 33506644 Genotype-phenotype correlation identified a novel SARS-CoV-2 variant possibly linked to severe disease. Two mutations, Q271R and R41R in the S and N genes, respectively, were found in severely sick patients only (p = .055, two tailed t-test) 2022 Transboundary and emerging diseases Figure SARS_CoV_2 Q271R;R41R 15;25 20;29 N;S 43;37 44;38 33506644 Genotype-phenotype correlation identified a novel SARS-CoV-2 variant possibly linked to severe disease. Two mutations, Q271R and R41R in the S and N genes, respectively, were found in severely sick patients only (p = .055, two tailed t-test). 2022 Transboundary and emerging diseases Figure SARS_CoV_2 Q271R;R41R 15;25 20;29 N;S 43;37 44;38 33508515 Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. A total of 53 variants were used to construct the haplotypes and the nucleotide and amino acid differences in comparison with NC_045512 among the major clades Lv(RdRp:A97V), G, GHv [C18887U, C26735U] and GR with the 48,881-48,883(GGG-AAC, N:R203K, G204R) variants are mentioned. 2021 Infection, genetics and evolution Figure SARS_CoV_2 G204R;A97V;R203K 248;167;241 253;171;246 RdRP;N 162;239 166;240 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. (A) Illustration of the position of D614G mutations using a series of presubstrate probes (1-6), sequencing result of mutated and wild SARS-CoV-2, and design of presubstrate probes (1-6) for identifying D614G mutations; (B) fluorescence response (F0 - F) toward mutated and wild SARS-CoV-2 using presubstrate probes 1-6. 2021 Analytical chemistry Figure SARS_CoV_2 D614G;D614G 36;203 41;208 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. F0 and F indicate the fluorescence intensity in the absence and presence of RNA virus, respectively; (C) discrimination rates for detecting D614G mutations using presubstrate probes 1-6; (D) fluorescence response toward wild and mutated SARS-CoV-2 virus using presubstrate probes 3. 2021 Analytical chemistry Figure SARS_CoV_2 D614G 140 145 33511840 Detection of SARS-CoV-2 and Its Mutated Variants via CRISPR-Cas13-Based Transcription Amplification. Identify D614G mutations of SARS-CoV-2 variants. 2021 Analytical chemistry Figure SARS_CoV_2 D614G 9 14 33513449 Different SARS-CoV-2 haplotypes associate with geographic origin and case fatality rates of COVID-19 patients. COVID case severity versus the D614G mutation (Sum of ranks: G 7913.5, D 997.5; p = 0.031085). 2021 Infection, genetics and evolution Figure SARS_CoV_2 D614G 31 36 COVID-19 0 5 33513449 Different SARS-CoV-2 haplotypes associate with geographic origin and case fatality rates of COVID-19 patients. Minimum spanning tree covering haplotype diversity at the D614G level in association with disease severity. 2021 Infection, genetics and evolution Figure SARS_CoV_2 D614G 58 63 33529260 Clinical and whole genome characterization of SARS-CoV-2 in India. Comparison of predicted docking origination of ACE2 interaction with (A) RK100 (Y28H) interacts with ACE2 through its residues 623 to 639 along with 293 Leu and 28 His; (B, D) KN443, RK1090 and RR1191 interacting ACE2 through its residues 152 to 184; (C) KN318, TC469 and KP1125 (D614G) interreacts ACE2 through its residues 623 to 639. 2021 PloS one Figure SARS_CoV_2 D614G;Y28H 280;80 285;84 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. (A) Plaque assays were performed to isolate the VSV-SARS-CoV-2-S wild-type, E484A, E484K, and F486S escape mutant on Vero E6 TMPRSS2 cells in the present of the indicated mAb in the overlay. 2021 Cell host & microbe Figure SARS_CoV_2 E484A;E484K;F486S 76;83;94 81;88;99 S 63 64 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. (B) Representative neutralization curves of wild-type, S477N, and E484A mutant with four different human sera. 2021 Cell host & microbe Figure SARS_CoV_2 E484A;S477N 66;55 71;60 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. (C) Representative neutralization curves of wild-type and F486S mutant VSV-SARS-CoV-2 with hACE2-Fc and mACE2-Fc. 2021 Cell host & microbe Figure SARS_CoV_2 F486S 58 63 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. 2B04 escape mutants including E484A, E484K, and F486S are indicated in green. 2021 Cell host & microbe Figure SARS_CoV_2 E484A;E484K;F486S 30;37;48 35;42;53 33545711 SARS-CoV-2 evolution during treatment of chronic infection. Amino acid variant and corresponding nucleotide position: S:W64G = 21752, S:Delta69 = 21765-21770, S:Y200H = 22160, S:T240I = 22281, S:P330S = 22550, S:D795H = 23948. 2021 Nature Figure SARS_CoV_2 D795H;P330S;T240I;W64G;Y200H 152;135;118;60;101 157;140;123;64;106 S;S;S;S;S;S 58;74;99;116;133;150 59;75;100;117;134;151 33545711 SARS-CoV-2 evolution during treatment of chronic infection. Classes of RBD binding antibodies and fold changes for Spike mutations D796H or DeltaH69/V70 are indicated based Bouwer et al. 2021 Nature Figure SARS_CoV_2 D796H 71 76 S;RBD 55;11 60;14 33545711 SARS-CoV-2 evolution during treatment of chronic infection. Lentivirus pseudotyped with SARS-CoV-2 Spike protein: WT (D614G background), D796H, DeltaH69/V70, D796H+DeltaH69/V70 were produced in 293T cells and used to infect target Hela cells stably expressing ACE2 in the presence of serial dilutions of indicated monoclonal antibodies. 2021 Nature Figure SARS_CoV_2 D796H;D796H;D614G 77;98;58 82;103;63 S 39 44 33545711 SARS-CoV-2 evolution during treatment of chronic infection. Location of Spike mutations DeltaH69/Y70 and D796H. 2021 Nature Figure SARS_CoV_2 D796H 45 50 S 12 17 33545711 SARS-CoV-2 evolution during treatment of chronic infection. Neutralization potency of a panel of monoclonal antibodies targeting the RBD is not impacted by Spike mutations D796H or DeltaH69/V70. 2021 Nature Figure SARS_CoV_2 D796H 112 117 S;RBD 96;73 101;76 33545711 SARS-CoV-2 evolution during treatment of chronic infection. The global prevalence of each of the six spike mutations W64G, DeltaH69/V70, Y200H, T240I, P330S and D796H were assessed by viewing the multiple sequence alignment in AliView, sorting by the column of interest, and counting the number of mutations. 2021 Nature Figure SARS_CoV_2 D796H;P330S;T240I;W64G;Y200H 101;91;84;57;77 106;96;89;61;82 S 41 46 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. (c) An additional neutrophil elastase (elastase -2) cleavage site around S1-S2 junction was introduced due to the D614G mutation in SARS-CoV-2; the Glycine at 614th position is predicted to be the nearest substrate site for neutrophil elastase to perform proteolytic cleavage in the adjacent residue. 2021 Infection, genetics and evolution Figure SARS_CoV_2 D614G 114 119 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. The 614th amino acid position in the S protein was found to be conserved among species, until the occurrence of the D614G mutation. 2021 Infection, genetics and evolution Figure SARS_CoV_2 D614G 116 121 S 37 38 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Binding affinity between dimeric ACE2 and trimeric SARS2-S WT (a, c, and e) or D614G variant (b, d, and f) (two-fold serially diluted from 71.4 nM to 1.12 nM) was evaluated at 25 C (a and b), 30 C (c and d), or 37 C (e and f) using Octet RED96 instrument. 2021 Nature communications Figure SARS_CoV_2 D614G 79 84 S 57 58 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. d Structural difference between WT and D614G SARS-CoV-2 S proteins. 2021 Nature communications Figure SARS_CoV_2 D614G 39 44 S 56 57 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. D614G (right); the short nonpolar side chain of glycine (G614), which does not bind to T859 and K854, provides flexible space between the two protomers. 2021 Nature communications Figure SARS_CoV_2 D614G 0 5 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. D614G; details are depicted in. 2021 Nature communications Figure SARS_CoV_2 D614G 0 5 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. from seven independent experiments (except for that of G476S, n = 6 with three technical replicates); compared with WT using one-way ANOVA with Dunnett's multiple comparison test. 2021 Nature communications Figure SARS_CoV_2 G476S 55 60 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. G476S; the substitution at position 476 in the RBD results in a protruded surface, which appears to interfere with the ACE2-RBD interaction. 2021 Nature communications Figure SARS_CoV_2 G476S 0 5 RBD;RBD 47;124 50;127 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. H49Y; as the histidine at position 49 is located distant from the RBD and putative cleavage sites, the effect of this mutation on S's function is likely limited. 2021 Nature communications Figure SARS_CoV_2 H49Y 0 4 RBD;S 66;130 69;131 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Lentiviruses pseudotyped with either the WT or D614G mutant SARS2-S were preincubated with two-fold serially diluted human sera (80-fold to 10, 240-fold) obtained from a healthy donor (Ctrl) or collected at 15-30 days post-symptom onset from confirmed case patients (#1-#5) infected with the prototypic viruses. 2021 Nature communications Figure SARS_CoV_2 D614G 47 52 S 66 67 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. SARS-2 S WT and D614G proteins are similarly neutralized by patient sera. 2021 Nature communications Figure SARS_CoV_2 D614G 16 21 S 7 8 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. SARS2-S D614G protein binds ACE2 with higher affinity than WT S protein. 2021 Nature communications Figure SARS_CoV_2 D614G 8 13 S;S 6;62 7;63 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. SARS2-S D614G protein shows the prominent structural difference. 2021 Nature communications Figure SARS_CoV_2 D614G 8 13 S 6 7 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. SARS2-S D614G variant protein display highest levels of entry activity. 2021 Nature communications Figure SARS_CoV_2 D614G 8 13 S 6 7 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. V367F; the substitution from a valine to a phenylalanine at position 367 in the RBD introduces a larger side chain at a protomer-protomer interface, which might provide a more rigid RBD structure. 2021 Nature communications Figure SARS_CoV_2 V367F;V367F 31;0 72;5 RBD;RBD 80;182 83;185 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. V483A; both valine and alanine residues have short side chains, likely sharing similar phenotypes. 2021 Nature communications Figure SARS_CoV_2 V483A 0 5 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). A spike at location D614G (3089) while other regions of the protein are stable. 2021 Scientific reports Figure SARS_CoV_2 D614G 20 25 S 2 7 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). One synonymous mutation D61K and two insertions - 62R and - 63T at the end of isolate USA/MA_MGH_00184/2020 (MT520188) is interesting while there is a high chance that HKG/VM20001061/2020 has spread to USA/VA-DCLS-0294/2020. 2021 Scientific reports Figure SARS_CoV_2 D61K 24 28 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Protein ORF3a: two spikes at Q57H (2795) and G251V (206); protein ORF8: two spikes at S24L (320) and L84S (1000); protein N: R203K (876) and G204R (433); Other proteins E, M, ORF6, ORF7a, ORF7b and ORF10 are almost entirely stable. 2021 Scientific reports Figure SARS_CoV_2 G204R;G251V;L84S;Q57H;R203K;S24L 141;45;101;29;125;86 146;50;105;33;130;90 ORF7a;ORF7b;S;S;ORF3a;ORF6;ORF8;E;N 181;188;19;76;8;175;66;169;122 186;193;25;82;13;179;70;170;123 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Spikes at locations: T265I (1344), L3606F (271), P4715L (2576), P5828L (475) and Y5865C (476). 2021 Scientific reports Figure SARS_CoV_2 L3606F;P4715L;P5828L;T265I;Y5865C 35;49;64;21;81 41;55;70;26;87 S 0 6 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. (a) Prevalence of D614G-containing SARS-CoV-2 genomes over time. 2021 eLife Figure SARS_CoV_2 D614G 18 23 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. Change in MHC binding affinity for peptides near the D614G mutation in the SARS-CoV-2 Spike protein. 2021 eLife Figure SARS_CoV_2 D614G 53 58 S 86 91 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. Increased infection of SARS-CoV-2 virus with the Spike D614G variant in human cells. 2021 eLife Figure SARS_CoV_2 D614G 55 60 S 49 54 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. SARS-CoV-2 Spike D614G-pseudotyped lentivirus results in increased transduction of human lung, liver, and colon cell lines. 2021 eLife Figure SARS_CoV_2 D614G 17 22 S 11 16 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. The SARS-CoV-2 D614G mutation has spread rapidly and is correlated with increased fatality and higher viral load. 2021 eLife Figure SARS_CoV_2 D614G 15 20 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. The SARS-CoV-2 Spike D614G variant displays similar ACE2 binding kinetics but altered proteolytic cleavage. 2021 eLife Figure SARS_CoV_2 D614G 21 26 S 15 20 33583326 Structural genetics of circulating variants affecting the SARS-CoV-2 spike/human ACE2 complex. The D614G variant, located outside the RBD, is also indicated. 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 D614G 4 9 RBD 39 42 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Here, the red rectangle marks the Q57H position with its neighborhoods. 2021 Communications biology Figure SARS_CoV_2 Q57H 34 38 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. One high-frequency mutation 25563G>T-(Q57H) locates on the ORF3a protein. 2021 Communications biology Figure SARS_CoV_2 G25563T;Q57H 28;38 36;42 ORF3a 59 64 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The high-frequency mutation 25563G>T-(Q57H) on ORF3a is marked in color. 2021 Communications biology Figure SARS_CoV_2 G25563T;Q57H 28;38 36;42 ORF3a 47 52 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The mutation with the highest frequency is D614G. 2021 Communications biology Figure SARS_CoV_2 D614G 43 48 33589648 Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. The RBD is displayed in green, the ACE2 is given in red, and mutation D614G is highlighted in red. 2021 Communications biology Figure SARS_CoV_2 D614G 70 75 RBD 4 7 33602511 Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity. Variations of root mean square deviation (RMSD) (A), Distribution of RBD-ACE2 distances (B), Distribution of RBD-ACE2 interfacial area (C), number of hydrogen bonds (D), van der Waals interaction energy (E), and electrostatic interactions energy (F) between RBD and ACE2 obtained from the molecular dynamics simulations for wild-type, V367F and S494P variant of RBD are shown. 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 S494P;V367F 345;335 350;340 RBD;RBD;RBD;RBD 69;109;258;362 72;112;261;365 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. (A) Change in interactions within spike protein due to D614G mutation: The mutation is located in the RBD of the spike protein. 2020 Frontiers in genetics Figure SARS_CoV_2 D614G 55 60 S;S;RBD 34;113;102 39;118;105 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. (A) The mutations S194L, R203K, and G204R are located in the highly conserved linker region as indicated in panel. 2020 Frontiers in genetics Figure SARS_CoV_2 G204R;R203K;S194L 36;25;18 41;30;23 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. (B) Location of G1167V mutation in spike protein: Two alternate computational models are shown, as the structure of the full-length spike protein has not been solved so far. 2020 Frontiers in genetics Figure SARS_CoV_2 G1167V 16 22 S;S 35;132 40;137 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. The mutation D614G causes loss of all these interactions. 2020 Frontiers in genetics Figure SARS_CoV_2 D614G 13 18 33613621 SARS-CoV-2 Genomes From Oklahoma, United States. The mutation G1167V may affect the alpha helical region as well as the bending motion of the stalk region. 2020 Frontiers in genetics Figure SARS_CoV_2 G1167V 13 19 33619331 Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. Native RBD and the variants S477G and S477N are shown as grey cartoon representations with residue 477 highlighted in yellow. 2021 Scientific reports Figure SARS_CoV_2 S477G;S477N 28;38 33;43 RBD 7 10 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. (a-b) Vaccine sera dilution for 50% neutralization against WT and Spike mutant with N501Y, A570D, DeltaH69/V70. 2021 medRxiv Figure SARS_CoV_2 A570D;N501Y 91;84 96;89 S 66 71 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. (c-d) Convalescent sera dilution for 50% neutralization against WT and Spike mutant with N501Y, A570D, DeltaH69/V70. 2021 medRxiv Figure SARS_CoV_2 A570D;N501Y 96;89 101;94 S 71 76 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. a-b, Binding to WT (black) and E484K (red) RBD by 27 RBM-targeting (a) and 19 non-RBM-targeting (b) mAbs. 2021 medRxiv Figure SARS_CoV_2 E484K 31 36 RBD 43 46 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. a-b, Binding to WT (black) and N501Y (blue) RBD by 22 RBM-targeting (a) and 21 non-RBM-targeting (b) mAbs. 2021 medRxiv Figure SARS_CoV_2 N501Y 31 36 RBD 44 47 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Binding of human ACE2 to SARS-CoV-2 WT, N501Y, TM (N501Y, E484K, K417N) RBDs. 2021 medRxiv Figure SARS_CoV_2 E484K;K417N;N501Y;N501Y 58;65;40;51 63;70;45;56 RBD 72 76 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. e, Representative curves of convalescent serum log10 inverse dilution against % neutralization for WT v N501Y, A570D, DeltaH69/V70. 2021 medRxiv Figure SARS_CoV_2 A570D;N501Y 111;104 116;109 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Kinetics of binding to WT and E484K SARS-CoV-2 RBD of 46 RBD-specific mAbs. 2021 medRxiv Figure SARS_CoV_2 E484K 30 35 RBD;RBD 47;57 50;60 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Kinetics of binding to WT and N501Y SARS-CoV-2 RBD of 43 RBD-specific mAbs. 2021 medRxiv Figure SARS_CoV_2 N501Y 30 35 RBD;RBD 47;57 50;60 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Neutralisation of WT (D614G), B.1.1.7 and TM (N501Y, E484K, K417N) SARS-CoV-2 Spike pseudotyped virus by a panel of 57 monoclonal antibodies (mAbs). 2021 medRxiv Figure SARS_CoV_2 E484K;K417N;D614G;N501Y 53;60;22;46 58;65;27;51 S 78 83 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Neutralization by first dose BNT162b2 vaccine and convalescent sera against wild type and mutant (N501Y, A570D, DeltaH69/V70) SARS-CoV-2 pseudotyped viruses. 2021 medRxiv Figure SARS_CoV_2 A570D;N501Y 105;98 110;103 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Representative neutralization curves of BNT162b2 vaccine sera against pseudovirus virus bearing eight Spike mutations present in B.1.1.7 versus wild type (all In Spike D614G background). 2021 medRxiv Figure SARS_CoV_2 D614G 168 173 S;S 102;162 107;167 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. (A) Image downloaded from the Compare SNVs tab of covidcg.org on December 29, 2020: SARS-CoV-2 variants bearing the spike S477N mutation (also known as the G22992A SNV; depicted in purple), the majority of which lie in the B.1.1.25 lineage, had become the most prevalent form of SARS-CoV-2 in Australia in June through September 2020. 2021 eLife Figure SARS_CoV_2 G22992A;S477N 156;122 163;127 S 116 121 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. (A) The G29140T mutation has been demonstrated to impact the NIID_2019-nCOV_N_F2 primer sensitivity. 2021 eLife Figure SARS_CoV_2 G29140T 8 15 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. (B) Image downloaded from the Compare Locations tab of covidcg.org on December 29, 2020: the cumulative percent of sequences carrying the S477N mutation in Australia and the United Kingdom. 2021 eLife Figure SARS_CoV_2 S477N 138 143 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. (C) Images downloaded from the Compare NT SNVs tab of covidcg.org on December 29, 2020: co-occurring SNVs of G22992A (spike S477N) in Australia, all time versus prior to May 2020, versus in the United Kingdom. 2021 eLife Figure SARS_CoV_2 G22992A;S477N 109;124 116;129 S 118 123 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. Frequency of the spike S477N mutation in Australia over time. 2021 eLife Figure SARS_CoV_2 S477N 23 28 S 17 22 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. Population dynamics of spike D614G in different regions. 2021 eLife Figure SARS_CoV_2 D614G 29 34 S 23 28 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. The S439N mutant had not been previously detected in Ireland. 2021 eLife Figure SARS_CoV_2 S439N 4 9 33620031 COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. The S477N mutant constituted only 1.05% of the Australian SARS-CoV-2 genomes on GISAID prior to June. 2021 eLife Figure SARS_CoV_2 S477N 4 9 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. (A and B) Binding of serum and plasma samples from 442 SARS-CoV-2 infected individuals against WT and N439K RBD plotted as (A) ELISA ED50 for each RBD (cut-off for positive binding to WT set at 30) and (B) fold change relative to WT. 2021 Cell Figure SARS_CoV_2 N439K 102 107 RBD;RBD 108;147 111;150 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. (A-C) X-ray structures of the SARS-CoV (A), SARS-CoV-2 WT (B), and SARS-CoV-2 N439K (C) RBD in complex with hACE2 (based on 2AJF, 6M0J, and current work, respectively). 2021 Cell Figure SARS_CoV_2 N439K 78 83 RBD 88 91 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. (A) Epidemiological growth of the N439/D614, N439/D614G, or N439K/D614G virus in the National Health Service (NHS) Greater Glasgow and Clyde (GGC) Health Board area relative to sampling time in epidemiological (epi) weeks (top) and their relative contributions (bottom) for 1,918 patients whose diagnostic samples were sequenced. 2021 Cell Figure SARS_CoV_2 N439K;D614G;D614G 60;50;66 65;55;71 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. (A) Phylogenetic tree (de-duplicated and down-sampled) showing the relationship among representative global SARS-CoV-2 variants, with N439K variants highlighted in color. 2021 Cell Figure SARS_CoV_2 N439K 134 139 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. (B) Comparison of clinical severity between D614/N439, D614G/N439 and D614G/N439K genotypes by patient age group for 1591 patients whose diagnostic samples were sequenced. 2021 Cell Figure SARS_CoV_2 D614G;D614G;D614N;N439K 55;70;55;76 60;75;60;81 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. (B) Frequency of N439K variants relative to sampling time and their geographical area of occurrence (see key): Africa (Morocco, Nigeria), Americas (Brazil, USA), Asia (Japan, Singapore, South Korea), the European countries Denmark, England, Republic of Ireland and Scotland and other European countries (Belgium, Bosnia-Herzegovina, Croatia, Czech Republic, Faroe Islands, Finland, France, Germany, Hungary, Italy, Luxembourg, Netherlands, Northern Ireland, Norway, Poland, Romania, Slovakia, Sweden, Switzerland, Wales), and Oceania (Australia, New Zealand). 2021 Cell Figure SARS_CoV_2 N439K 17 22 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. (B) Top: real-time PCR data for N439/D614, N439/D614G, and N439K/D614G groups, same patient population as in (A). 2021 Cell Figure SARS_CoV_2 N439K;D614G;D614G 59;48;65 64;53;70 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. (C and D) Binding of 140 mAbs from SARS-CoV-2 infected individuals and four clinical-stage or EUA-approved mAbs against WT, N439K, K417V, and N439K/K417V RBD, plotted as (C) ELISA AUC for each RBD and (D) fold change relative to WT. 2021 Cell Figure SARS_CoV_2 K417V;N439K;N439K;K417V 131;124;142;148 136;129;147;153 RBD;RBD 154;193 157;196 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. (C) Frequency of the two N439K lineages (same colors as A) over time relative to all sequences for that country (gray) and their normalized contributions (lower panels) in Scotland, England, Republic of Ireland, and Denmark. 2021 Cell Figure SARS_CoV_2 N439K 25 30 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. (C) Top: neutralization IC50 of the D614G virus determined as the geometric mean of three biological replicates. 2021 Cell Figure SARS_CoV_2 D614G 36 41 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. (D) Growth curves for GLA1 (N439/D614G) or GLA2 (N439K/D614G) virus isolates in Vero E6 cells with ACE2 and TMPRSS2 overexpression (+TMPRSS2 +ACE2), ACE2 overexpression (+ACE2), or no overexpression. 2021 Cell Figure SARS_CoV_2 N439K;D614G;D614G 49;33;55 54;38;60 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. All spike ECD contain the D614G mutation. 2021 Cell Figure SARS_CoV_2 D614G 26 31 S 4 9 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Binding of 13 selected mAbs to RBD WT (gray), N439K (blue), K417V (yellow) and N439K/K417V (red) as measured by BLI. 2021 Cell Figure SARS_CoV_2 K417V;N439K;N439K;K417V 60;46;79;85 65;51;84;90 RBD 31 34 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Blue dots indicate sera with at least 2-fold loss of binding to the N439K RBD variant as compared to WT in both replicates. 2021 Cell Figure SARS_CoV_2 N439K 68 73 RBD 74 77 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Bottom: neutralization results for all mAbs tested, expressed as a fold-change relative to D614G (all variants are in the background of D614G) (Data S1). 2021 Cell Figure SARS_CoV_2 D614G;D614G 91;136 96;141 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Clinical outcomes and virological evaluation of N439K lineage i indicate maintenance of fitness relative to WT virus. 2021 Cell Figure SARS_CoV_2 N439K 48 53 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. ELISA binding of 80 out of the 144 mAbs to RBD WT (gray), N439K (blue), K417V (yellow) and N439K/K417V (red). 2021 Cell Figure SARS_CoV_2 K417V;N439K;N439K;K417V 72;58;91;97 77;63;96;102 RBD 43 46 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. ELISA binding of the 33 human sera with a > 2-fold reduction of binding to RBD N439K (A) and of the 6 sera of individuals infected with SARS-CoV-2 N439K viruses (B) to RBD WT (gray), N439K (blue), K417V (yellow) and N439K/K417V (red). 2021 Cell Figure SARS_CoV_2 K417V;N439K;N439K;N439K;N439K;K417V 197;79;147;183;216;222 202;84;152;188;221;227 RBD;RBD 75;168 78;171 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. N439K creates a new RBD:hACE2 salt bridge and enhances RBD:hACE2 affinity. 2021 Cell Figure SARS_CoV_2 N439K 0 5 RBD;RBD 20;55 23;58 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Ordinal regression analysis indicated that the N439K viral genotype was associated with similar clinical outcomes compared to the N439 genotype (posterior mean of N439K/D614G genotype effect: 0.06, 95% CI: -1.21, 1.33). 2021 Cell Figure SARS_CoV_2 N439K;N439K;D614G 47;163;169 52;168;174 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Purple dots indicate sera from individuals infected with SARS-CoV-2 N439K variant. 2021 Cell Figure SARS_CoV_2 N439K 68 73 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Quantification of each virus was performed by tracking the frequency of N439K within the spike gene using metagenomic NGS. 2021 Cell Figure SARS_CoV_2 N439K 72 77 S 89 94 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The N439K genotype was associated with marginally lower Ct values than the N439 genotype (posterior mean Ct value difference between N439K/D614G and N439/D614G: -0.65, 95% CI: -1.22, -0.07). 2021 Cell Figure SARS_CoV_2 N439K;N439K;D614G;D614G 4;133;139;154 9;138;144;159 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The N439K mutation has also emerged independently on at least seven occasions (red circles show four of these) bringing the total country count to 34. 2021 Cell Figure SARS_CoV_2 N439K 4 9 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The N439K RBM mutation has arisen independently multiple times, twice forming significant lineages. 2021 Cell Figure SARS_CoV_2 N439K 4 9 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The Scottish N439K lineage i (which co-occurs with D614G) is indicated in black along with whether wild-type N439 lineages are D614 (red) or D614G (blue). 2021 Cell Figure SARS_CoV_2 D614G;D614G;N439K 51;141;13 56;146;18 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Two significant N439K lineages, one in Scotland (>500 sequences, blue circles) and one in 32 countries (>6,000 sequences, yellow circles) were detected as of January 6, 2021. 2021 Cell Figure SARS_CoV_2 N439K 16 21 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Vertical bars indicate global lineage, the presence of N439K (same colors as tree), D614G (orange) or D614N (dark gray). 2021 Cell Figure SARS_CoV_2 D614G;D614N;N439K 84;102;55 89;107;60 33622851 Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2. (A) In silico receptor-ligand docking analysis for mutated S-protein (D614G) from SARS-CoV-2 and ACE2 protein present in human. 2021 mSystems Figure SARS_CoV_2 D614G 70 75 S 59 60 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. (A) 3D Structural conformation of D614G (pink) next, the zoom of the amino acid G614 is shown in pink while the WT residue is indicated in blue. 2021 Scientific reports Figure SARS_CoV_2 D614G 34 39 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. (A) WT, (B) D614G, (C) H49Y, and (D) T573I. 2021 Scientific reports Figure SARS_CoV_2 D614G;H49Y;T573I 12;23;37 17;27;42 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. (B) 3D structure of H49Y (purple), the zoom of the amino acid variant Y49 is shown in purple, the WT residue is shown in the sticks in blue. 2021 Scientific reports Figure SARS_CoV_2 H49Y 20 24 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. (C) 3D structure of T573I (cyan) the zoom of the residue variant I573 is shown cyan while the WT residue T573 is indicated in blue sticks. 2021 Scientific reports Figure SARS_CoV_2 T573I 20 25 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Also, the interactions are between cepharanthine (wheat sticks) with (D) wild type spike protein, (E) D614G, (F) H49Y and (G) T573I; and hydroxychloroquine (orange sticks) with (H) wild type spike protein, (I) D614G, (J) H49Y and (K) T573I; and nelfinavir (raspberry sticks) with (L) wild type spike protein, (M) D614G, (N) H49Y and (O) T573I. 2021 Scientific reports Figure SARS_CoV_2 D614G;D614G;D614G;H49Y;H49Y;H49Y;T573I;T573I;T573I 102;210;313;113;221;324;126;234;337 107;215;318;117;225;328;131;239;342 S;S;S;N 83;191;294;321 88;196;299;322 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. General view of the binding pose obtained by docking of (A) cepharanthine, (B) hydroxychloroquine, (C) nelfinavir with wild type spike protein (green ribbon), D614G (cyan ribbon), H49Y (magenta ribbon) and T573I (yellow ribbon). 2021 Scientific reports Figure SARS_CoV_2 D614G;H49Y;T573I 159;180;206 164;184;211 S 129 134 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. PC1) of T573I. 2021 Scientific reports Figure SARS_CoV_2 T573I 8 13 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. PC1) of the D614G, (E) projection of the motion in the phase space along the first and second eigenvectors (PC2 vs. 2021 Scientific reports Figure SARS_CoV_2 D614G 12 17 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. PC1) of the H49Y, (F) projection of the motion in the phase space along the first and second eigenvectors (PC2 vs. 2021 Scientific reports Figure SARS_CoV_2 H49Y 12 16 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Representation of the two extreme projections along the first eigenvector of MD simulation of (A) WT spike protein, (B) D614G, (C) H49Y and (D) T573I. 2021 Scientific reports Figure SARS_CoV_2 D614G;H49Y;T573I 120;131;144 125;135;149 S 101 106 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. The NCI isosurfaces (drawn at 0.5) of (A) Cepharanthine-D614G, (B) Cepharanthine-H49Y, (C) Cepharanthine-T573I, (D) Cepharanthine-WT, (E) Hydroxychloroquine-H49Y, (F) Hydroxychloroquine-T573I, (G) Nelfinavir-H49Y, (H) Nelfinavir-T573I and (I) Nelfinavir-WT complexes. 2021 Scientific reports Figure SARS_CoV_2 D614G;H49Y;H49Y;H49Y;T573I;T573I;T573I 56;81;157;208;105;186;229 61;85;161;212;110;191;234 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. The trajectories of the WT are shown in navy blue, D614G are shown in purple, H49Y are shown in blue and T573I are shown in yellow. 2021 Scientific reports Figure SARS_CoV_2 D614G;H49Y;T573I 51;78;105 56;82;110 33633229 Structural insights into SARS-CoV-2 spike protein and its natural mutants found in Mexican population. Wild type spike protein is depicted in black, D614G in red, H49Y in green, and T573I in purple. 2021 Scientific reports Figure SARS_CoV_2 D614G;H49Y;T573I 46;60;79 51;64;84 S 10 15 33634309 A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. In the absence of a known structure for interfacial regions in an S trimer bearing the A570D mutation, the degree of packing at monomer:monomer sites is unknown, as shown. 2021 Briefings in bioinformatics Figure SARS_CoV_2 A570D 87 92 S 66 67 33634309 A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. In the horizontal centre are tube cartoon representations of 6zp2 and 7a98, alongside 6zp1 (closed, no LA) and 7kdk (closed, D614G), drawn for regions within 10 A of R355 (upper), A570 (centre) and D614 (lower). 2021 Briefings in bioinformatics Figure SARS_CoV_2 D614G 125 130 33639276 The role of A-to-I RNA editing in infections by RNA viruses: Possible implications for SARS-CoV-2 infection. One such example is the D614G substitution (A-to-G point mutation; unknown origin) which has increased viral infectivity by ~10-fold. 2021 Clinical immunology (Orlando, Fla.) Figure SARS_CoV_2 D614G 24 29 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. Molecular dynamics results of the Imiglitazir-WT Mpro complex (Black), PF-03715455-Y54C (red), Salvianolic acidA-N142S (green), Salvianolic acidA-T190I (blue) and Montelukast-A191V (Yellow). 2021 Saudi journal of biological sciences Figure SARS_CoV_2 A191V;N142S;T190I;Y54C 175;113;146;83 180;118;151;87 33649700 Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19. The binding of top scoring compounds (A) Binding of Imiglitazar within the active site of Mpro (WT) (B) Binding of PF-03715455 within the active site of Mpro (Y54C) (C) Binding of Salvianolic acid A within the active site of Mpro (N142S) (D) Mpro (T190I) (E) Binding of Montelukast within the active site of Mpro (A191V). 2021 Saudi journal of biological sciences Figure SARS_CoV_2 A191V;N142S;T190I;Y54C 314;231;248;159 319;236;253;163 E 256 257 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. ((Top panels) Immune or vaccine-derived sera from mice, hamsters, NHP, or humans (see Figures 2, 3, and 4) were incubated with deep-sequenced confirmed p0 (Vero cell-produced) or p1 (Vero-hACE2-TMPRSS2 cell-produced) versions of K417N/E484K/N501Y/D614G virus and then subjected to a FRNT in Vero-hACE2-TMPRSS2 recipient cells. 2021 Nature medicine Figure SARS_CoV_2 K417N;D614G;E484K;N501Y 229;247;235;241 234;252;240;246 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. (Middle panels) Serum neutralization curves with K417N/E484K/N501Y/D614G virus (p0, generated in Vero E6 cells; p1, generated in Vero-hACE2-TMPRSS2 cells) using a FRNT and Vero-hACE2-TMPRSS2 cells. 2021 Nature medicine Figure SARS_CoV_2 K417N;D614G;E484K;N501Y 49;67;55;61 54;72;60;66 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Inset shows top-down view of the RBD with B.1.1.248 RBD substitutions (K417T/E484K/N501Y) shaded red and contextualized with the receptor binding motif. 2021 Nature medicine Figure SARS_CoV_2 K417T;E484K;N501Y 71;77;83 76;82;88 RBD;RBD 33;52 36;55 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Red hexagon depicts approximate location of R190S, which is obscured in this view. 2021 Nature medicine Figure SARS_CoV_2 R190S 44 49 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Red star indicates approximate location of T1027I, which is obscured in this view. 2021 Nature medicine Figure SARS_CoV_2 T1027I 43 49 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Serum from individuals (n = 10) who had been infected with SARS-CoV-2 (~ 1-month time point) or vaccinated with the Pfizer-BioNTech mRNA vaccine (n = 10) were tested for neutralization of the indicated SARS-CoV-2 strains (D614G, B.1.1.7, Wash SA-B.1.351, Wash BR-B.1.248) using a FRNT and Vero-TMPRSS2 cells. 2021 Nature medicine Figure SARS_CoV_2 D614G 222 227 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Substitutions seen in the B.1.1.248 Brazilian variant (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, and V1176F) are shaded red. 2021 Nature medicine Figure SARS_CoV_2 D138Y;D614G;E484K;H655Y;K417T;N501Y;P26S;R190S;T1027I;T20N;V1176F;L18F 73;108;94;115;87;101;67;80;122;61;134;55 78;113;99;120;92;106;71;85;128;65;140;59 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. V1176F is not shown, as it exists beyond the C-terminus of this model, which ends at residue D1146. 2021 Nature medicine Figure SARS_CoV_2 V1176F 0 6 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. (A-D) Graphs show the neutralizing activities of 14 selected nAbs with different SARS-CoV-2 S-protein binding profiles against SARS-CoV-2, SARS-CoV-2 D614G, SARS-CoV and MERS-CoV pseudotypes respectively. 2021 Cell Figure SARS_CoV_2 D614G 150 155 S 92 93 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. (D-F) Neutralization curves for selected antibodies were shown as percentage of viral neutralization against the authentic SARS-CoV-2 wild type (D), D614G variant (E), and the emerging variant B.1.1.7 (F). 2021 Cell Figure SARS_CoV_2 D614G 149 154 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. (G-I) Neutralization potency of 14 selected antibodies against the authentic SARS-CoV-2 wild type (G), D614G variant (H), and the emerging variant B.1.1.7 (I). 2021 Cell Figure SARS_CoV_2 D614G 103 108 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. (I-K) Neutralization curves against the authentic SARS-CoV-2 wild type, the D614G variant and the B.1.1.7 emerging variant for J08-MUT, I14-MUT and F05-MUT shown in blue, green and red respectively. 2021 Cell Figure SARS_CoV_2 D614G 76 81 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. A) The main cluster with E64stop variants in clade 20B is identified by a blue box. 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 E64X 25 32 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. C) SARS-CoV-2 phylogeny highlighting the ORF8-deficient variants resulting from the nonsense mutation Q18stop. 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 Q18X 102 109 ORF8 41 45 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. SARS-CoV-2 phylogeny highlighting the ORF8-deficient variants resulting from the nonsense mutation E64stop. 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 E64X 99 106 ORF8 38 42 33676232 SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring. The cluster with variants harbouring both Q18stop and E110stop is identified by a blue box. 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 E110X;Q18X 54;42 62;49 33681755 The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant. (b) Residues at position 501 for both of WT and N501Y mutated structures and interacting residue in the vicinity of position 501.The WT RBD and ACE2 are shown in Blue while the N501Y mutated RBD and ACE2 are shown in Green. 2021 Medicine in drug discovery Figure SARS_CoV_2 N501Y;N501Y 48;177 53;182 RBD;RBD 136;191 139;194 33681755 The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant. Representation of a selected favorable Electrostatic and vdW interactions in both of WT and N501Y complexes. 2021 Medicine in drug discovery Figure SARS_CoV_2 N501Y 92 97 33681755 The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant. Salt-bridges between RBD and ACE2 in both of WT and N501Y mutated structure. 2021 Medicine in drug discovery Figure SARS_CoV_2 N501Y 52 57 RBD 21 24 33681755 The new SARS-CoV-2 strain shows a stronger binding affinity to ACE2 due to N501Y mutant. The WT RBD and ACE2 are shown in Blue while the N501Y mutated RBD and ACE2 are shown in Green. 2021 Medicine in drug discovery Figure SARS_CoV_2 N501Y 48 53 RBD;RBD 7;62 10;65 33692211 SARS-CoV-2 rapidly adapts in aged BALB/c mice and induces typical pneumonia. LG isolated in infected aged mice acquired Q498H in RBD. 2021 Journal of virology Figure SARS_CoV_2 Q498H 43 48 RBD 52 55 33714462 Pyrococcus furiosus Argonaute coupled with modified ligase chain reaction for detection of SARS-CoV-2 and HPV. (B) The ability of PLCR to distinguish wild type SARS-CoV-2 and its spike D614G mutant. 2021 Talanta Figure SARS_CoV_2 D614G 74 79 S 68 73 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. A, comparison of the best-fit IC50 of polyclonal sera from mice immunized with SARS-CoV-2 WT RBD (RBD imm.) or spike (spike imm.) against WT RBD (black symbols) and the Y453F variant (gray symbols). 2021 The Journal of biological chemistry Figure SARS_CoV_2 Y453F 169 174 S;S;RBD;RBD;RBD 111;118;93;98;141 116;123;96;101;144 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. A, distribution of the inhibition potency of COVID-19 patient sera against WT and Y453F RBD (n = 141), analyzed using the Mann-Whitney test. 2021 The Journal of biological chemistry Figure SARS_CoV_2 Y453F 82 87 RBD 88 91 COVID-19 45 53 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. ACE-2-Fc was immobilized onto anti-human IgG Fc capture sensors and dipped into serial dilutions of RBD (5-point 2-fold dilutions starting at 100 nM [WT] or 60 nM [Y453F]). 2021 The Journal of biological chemistry Figure SARS_CoV_2 Y453F 164 169 RBD 100 103 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. B, linear regression and Spearman rank correlation analyses of the inhibition potency (log[IC50]) of the WT and Y453F RBD using individual mAbs raised against WT RBD (n = 10) or WT spike (n = 8). 2021 The Journal of biological chemistry Figure SARS_CoV_2 Y453F 112 117 S;RBD;RBD 181;118;162 186;121;165 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. B, thermal denaturation curves of the WT and Y453F RBD. 2021 The Journal of biological chemistry Figure SARS_CoV_2 Y453F 45 50 RBD 51 54 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. Biophysical characterization of WT and Y453F RBD.A, details of the binding interface of SARS-COV-2 RBD (orange) and the human ACE-2 receptor (green). 2021 The Journal of biological chemistry Figure SARS_CoV_2 Y453F 39 44 RBD;RBD 45;99 48;102 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. C and D, WT (C) and Y453F (D) RBD binding response curves to ACE-2 determined by biolayer interferometry. 2021 The Journal of biological chemistry Figure SARS_CoV_2 Y453F 20 25 RBD 30 33 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. Inhibition potency of COVID-19 convalescent patient sera against the WT and Y453F RBD. 2021 The Journal of biological chemistry Figure SARS_CoV_2 Y453F 76 81 RBD 82 85 COVID-19 22 30 33727252 Structural impact on SARS-CoV-2 spike protein by D614G substitution. Close-up views of the D614G substitution. 2021 Science (New York, N.Y.) Figure SARS_CoV_2 D614G 22 27 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Social Isolation Index and prevalence of E484K variants in the following week, according to the level of SII, for the state of Amazonas. 2021 Cureus Figure SARS_CoV_2 E484K 41 46 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Social Isolation Index and prevalence of the E484K variant in the following week, when below 40% and when above 40%, in the state of Amazonas, Brazil. 2021 Cureus Figure SARS_CoV_2 E484K 45 50 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. The percentage of all E484K variants (A) and P.1 lineage (B) in the state of Amazonas and in Brazil. 2021 Cureus Figure SARS_CoV_2 E484K 22 27 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. (B) The bound state between the mutated sRBD (N501Y) and hACE2. 2021 FEBS letters Figure SARS_CoV_2 N501Y 46 51 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. Effects of the N501Y mutation on the binding between the neutralizing mAb CB6 and sRBD. 2021 FEBS letters Figure SARS_CoV_2 N501Y 15 20 33728680 Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations. Illustration of a thermodynamic cycle used in the FEP calculations with the mutation N501Y. 2021 FEBS letters Figure SARS_CoV_2 N501Y 85 90 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. (A and B) BLI plots showing a titration series of binding to ACE2 (see STAR Methods) for (A) Wuhan RBD and (B) K417N, E484K, and N501Y B.1.351 RBD. 2021 Cell Figure SARS_CoV_2 E484K;K417N;N501Y 118;111;129 123;116;134 RBD;RBD 99;143 102;146 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. (C and D) KD of RBD/mAb interaction measured by BLI for WT Wuhan RBD (left dots) and K417N, E484K, and N501Y B.1.351 RBD (right dots). 2021 Cell Figure SARS_CoV_2 E484K;K417N;N501Y 92;85;103 97;90;108 RBD;RBD;RBD 16;65;117 19;68;120 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. (C) Structure plot showing distribution of mutations of South African variant sequences as defined by N501Y and deletion 241-243; point mutations are marked in yellow and the deletions in dark gray. 2021 Cell Figure SARS_CoV_2 N501Y 102 107 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. (E) Positions of the K417N, E484K, and N501Y (yellow) mutations within the ACE2 interaction surface (dark green) of RBD. 2021 Cell Figure SARS_CoV_2 E484K;K417N;N501Y 28;21;39 33;26;44 RBD 116 119 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. (G) The K417N mutation is modeled in the RBD/CB6 complex. 2021 Cell Figure SARS_CoV_2 K417N 8 13 RBD 41 44 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. Black dots refer to mapped antibodies not included in this analysis; dark green to RBD ACE2-binding surface; and yellow to mutated K417N, E484K, and N501Y. 2021 Cell Figure SARS_CoV_2 E484K;K417N;N501Y 138;131;149 143;136;154 RBD 83 86 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. Note the strain used in this report does not have L18F and R246I mutations. 2021 Cell Figure SARS_CoV_2 L18F;R246I 50;59 54;64 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. (C) Main interactions involving the S-RBDCoV-2 Q493K mutant at the interface with ACE2 as obtained from the relevant equilibrated MD simulations. 2021 ACS nano Figure SARS_CoV_2 Q493K 47 52 S 36 37 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. (D) Main interactions involving the S-RBDCoV-2 N501T mutant at the interface with ACE2 as obtained from the relevant equilibrated MD simulations. 2021 ACS nano Figure SARS_CoV_2 N501T 47 52 S 36 37 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. (D) Main interactions involving the S-RBDCoV-2 Y453K mutant at the interface with ACE2 as obtained from the relevant equilibrated MD simulations. 2021 ACS nano Figure SARS_CoV_2 Y453K 47 52 S 36 37 33733740 Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence. (D) Main interactions involving the S-RBDCoV-2 Y505W mutant at the interface with ACE2 as obtained from the relevant equilibrated MD simulations. 2021 ACS nano Figure SARS_CoV_2 Y505W 47 52 S 36 37 33738620 Clinical characteristics of SARS-CoV-2 by re-infection vs. reactivation: a case series from Iran. The sequences of first and second infections are identical even at c.28688 T>C (p.L139L). 2021 European journal of clinical microbiology & infectious diseases Figure SARS_CoV_2 T28688C;L139L;L139L 67;80;82 78;87;87 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. Potential ski-holiday related cluster (C1059T) with seven samples had confirmed associations with skiing destinations. 2021 PLoS pathogens Figure SARS_CoV_2 C1059T 39 45 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. Proportion of B.1-C15324T genomes among all publicly available genomes per country from the five countries in which this variant was first registered to March 23rd. 2021 PLoS pathogens Figure SARS_CoV_2 C15324T 18 25 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. (C) SEC profiles of three SApNPs presenting the SARS-CoV-2 S2GDeltaHR2 spike, from left to right, S2GDeltaHR2-5GS-FR, S2GDeltaHR2-5GS-E2p-LD4-PADRE (or E2p-L4P), and S2GDeltaHR2-10GS-I3-01v9-LD7-PADRE (or I3-01v9-L7P). 2021 Science advances Figure SARS_CoV_2 L4P;L7P 156;213 159;216 S 71 76 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. (L and M) SEC profiles and EM images of SARS-CoV-1/2 RBD-5GS-SPY-5GS-I3-01v9-LD7-PADRE (or I3-01v9-L7P) SApNPs produced by supernatant mix. 2021 Science advances Figure SARS_CoV_2 L7P 99 102 RBD 53 56 33741598 Single-component, self-assembling, protein nanoparticles presenting the receptor binding domain and stabilized spike as SARS-CoV-2 vaccine candidates. The approximate position for the unstructured HR2 stalk, or, in this case, a 5-amino acid (aa) G4S linker, is highlighted with a dashed line box. 2021 Science advances Figure SARS_CoV_2 G4S 95 98 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. (A and B) Pseudovirus neutralization (pNT50) is plotted for all individuals that received one dose (bottom panels) or two full doses (upper panels) of either the BNT162b2 (A) or mRNA-1273 (B) vaccines for each of the following SARS-CoV-2 pseudoviruses: wild-type, D614G, B.1.1.7, B.1.1.298, B.1.429, P.2, P.1, and three variants of the B.1.351 lineage denoted as B.1.351 v1, v2, and v3. 2021 Cell Figure SARS_CoV_2 D614G 264 269 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. (B) Representative pseudovirus neutralization curves are shown for an individual >=7 days out from the second dose of BNT162b2 vaccine comparing wild-type SARS-CoV-2 pseudovirus to the following variant pseudoviruses: D614G (pink); B.1.1.7 (purple); B.1.1.298 (blue); B.1.429 (green); P.2 (yellow); P.1 (orange); B.1.351 v1, v2, and v3 (red); SARS-CoV (brown); and WIV1-CoV (black). 2021 Cell Figure SARS_CoV_2 D614G 218 223 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. (B) World map depicting the locations where the variants of these lineages were first described: original wild-type virus from A lineage (gray) in Wuhan, China; D614G variant (pink) in Europe that became dominant circulating strain; B.1.1.7 lineage (purple) in the United Kingdom; B.1.1.298 (blue) in Denmark; B.1.429 (green) in California, United States; P.2 (yellow) in Brazil and Japan; P.1 (orange) in Brazil and Japan; and B.1.351 (red) in South Africa. 2021 Cell Figure SARS_CoV_2 D614G 161 166 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. (C) Correlations between pseudovirus neutralization titer of D614G and B.1.351 chimeric viruses are shown. 2021 Cell Figure SARS_CoV_2 D614G 61 66 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. (D) Pseudovirus neutralization (pNT50) of K417N+E484K+N501Y mutant pseudovirus is correlated to wild-type pseudovirus. 2021 Cell Figure SARS_CoV_2 K417N;E484K;N501Y 42;48;54 47;53;59 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. (E) Total antibodies that bind RBD harboring the B.1.351 mutations (anti-RBDK417N+E484K+N501Y total antibodies) were measured by a quantitative ELISA and correlated to pseudovirus neutralization (pNT50) of K417N+E484K+N501Y mutant pseudovirus. 2021 Cell Figure SARS_CoV_2 K417N;E484K;E484K;N501Y;N501Y 206;82;212;88;218 211;87;217;93;223 RBD;RBD 31;73 34;76 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Schematic of mutations in the spike protein sequence of the following SARS-CoV-2 variants are illustrated: wild type (gray), D614G (pink), B.1.1.7 (purple), B.1.1.298 (blue), B.1.1.429 (green), P.2 (yellow), P.1 (orange), three variants of B.1.351 (red; v1, v2, and v3), SARS-CoV (brown), and WIV1-CoV (black). 2021 Cell Figure SARS_CoV_2 D614G 125 130 S 30 35 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Sera was also tested against pseudovirus bearing only RBD mutations found in B.1.351 (K417N, E484K, and N501Y). 2021 Cell Figure SARS_CoV_2 E484K;N501Y;K417N 93;104;86 98;109;91 RBD 54 57 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. (A) Decrease in RdRp flexibility (blue region).The effect of P323L seems stabilizing on the protein structure. 2021 ACS omega Figure SARS_CoV_2 P323L 61 66 RdRP 16 20 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. (A) Increasein molecular flexibility (red region) due to D614G point mutation.The total energy calculated for mutants (MT) shows a stabilizing effecton the protein structure. 2021 ACS omega Figure SARS_CoV_2 D614G 57 62 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. E93K and W45L exhibited an increase in flexibilitywhile L84S shows decrease. 2021 ACS omega Figure SARS_CoV_2 L84S;W45L;E93K 56;9;0 60;13;4 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Effect of point mutation (D614G) on spike proteindynamics.DeltaDeltaG; Free energy difference. 2021 ACS omega Figure SARS_CoV_2 D614G 26 31 S 36 41 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Effect of pointmutation(P323L) on NSP12 (RdRp) dynamics. 2021 ACS omega Figure SARS_CoV_2 P323L 24 29 Nsp12;RdRP 34;41 39;45 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Effect of pointmutations (L84S, E93K, and W45L)on NS8 (ORF8) structure and dynamics. 2021 ACS omega Figure SARS_CoV_2 E93K;W45L;L84S 32;42;26 36;46;30 ORF8 55 59 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Effect of S327L mutationon N protein structureand dynamics (PDB ID 6yun). 2021 ACS omega Figure SARS_CoV_2 S327L 10 15 N 27 28 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. L84S, E93K, and W45L have adestabilizing effect. 2021 ACS omega Figure SARS_CoV_2 E93K;W45L;L84S 6;16;0 10;20;4 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Mutation (N228K) in NSP5 (main protease) andits dynamic effect. 2021 ACS omega Figure SARS_CoV_2 N228K 10 15 Nsp5 20 24 33748571 SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. Mutation in NSP13 (Helicase) at position A237Tand its dynamic effect. 2021 ACS omega Figure SARS_CoV_2 A237T 41 46 Helicase;Nsp13 19;12 27;17 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. (a) represent the binding interface of the N501Y complex along with its stick representation of the key hydrogen interactions. 2021 Journal of cellular physiology Figure SARS_CoV_2 N501Y 43 48 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. (b) shows the binding interface and stick representation of the key hydrogen bonding interactions of the E484K mutant. 2021 Journal of cellular physiology Figure SARS_CoV_2 E484K 105 110 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. (b) shows the binding interface and stick representation of the key hydrogen bonding interactions of the E484K- N501Y mutant. 2021 Journal of cellular physiology Figure SARS_CoV_2 E484K;N501Y 105;112 110;117 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. (c, d) represent the 2D interactions representation including hydrogen, salt bridges and nonbonded interactions in N501Y and E484K- N501Y complex. 2021 Journal of cellular physiology Figure SARS_CoV_2 E484K;N501Y;N501Y 125;115;132 130;120;137 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. (c, d) represent the 2D interactions representation including hydrogen, salt bridges, and nonbonded interactions in wild type and E484K complex. 2021 Journal of cellular physiology Figure SARS_CoV_2 E484K 130 135 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. (c) show the individual residue flexibility, that is, K417N, K417T, E48K, and N501Y. 2021 Journal of cellular physiology Figure SARS_CoV_2 E48K;K417N;K417T;N501Y 68;54;61;78 72;59;66;83 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. (c) wild type, (d) E484K, (e) N501Y, and (f) E484K-N501Y, (g) K417N-E484K-N501Y, and (h) shows the K417T-E484K-N501Y structure of the spike RBD. 2021 Journal of cellular physiology Figure SARS_CoV_2 E484K;E484K;K417N;K417T;N501Y;E484K;E484K;N501Y;N501Y;N501Y 19;45;62;99;30;68;105;51;74;111 24;50;67;104;35;73;110;56;79;116 S;RBD 134;140 139;143 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Docking representation of the N501Y and E484K- N501Y mutant complexes. 2021 Journal of cellular physiology Figure SARS_CoV_2 E484K;N501Y;N501Y 40;30;47 45;35;52 33755190 Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Docking representation of the Wild type and E484K mutant complexes. 2021 Journal of cellular physiology Figure SARS_CoV_2 E484K 44 49 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. A, B, C Interaction histograms of SARS-CoV-2, SARS-CoV-1 and CRB1 E-SLiM peptides against PALS1 F318W mutant. 2021 Computational and structural biotechnology journal Figure SARS_CoV_2 F318W 96 101 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. B, binding isotherm of PALS1 F318 W and SARS-CoV-1 E peptide, C, binding isotherm of of PALS1 F318W variant and CRB1, D, binding isotherm of PALS1 wild type and SARS-CoV-2 E peptide E, binding isotherm of PALS1 F318W variant and SARS-CoV-1 E peptide, F, binding isotherm of PALS1 wild type and CRB1 peptide. 2021 Computational and structural biotechnology journal Figure SARS_CoV_2 F318W;F318W;F318W 29;94;211 35;99;216 E;E;E;E 51;172;182;240 52;173;183;241 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. B, F318W protein. 2021 Computational and structural biotechnology journal Figure SARS_CoV_2 F318W 3 8 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. D, E, F) Most representative conformations of SARS-CoV-2, SARS-CoV-1 and CRB1 are reported in purple, where only the last 8 residues are shown, in complex with PALS1 F318W. 2021 Computational and structural biotechnology journal Figure SARS_CoV_2 F318W 166 171 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. Data point were obtained at the following concentration [PALS1_F318W] = 120, 60, 15, 7.5, 3.75 and 1.875 muM and [PALS1_wt] = 60, 30, 15, 7.5, 3.75 and 1.875 muM. 2021 Computational and structural biotechnology journal Figure SARS_CoV_2 F318W 63 68 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. In purple the closed position of F318 in green the open one, D, the 3D model of PALS1 F318W variant showing the two different conformation of W318, keeping the same color code of panel C. 2021 Computational and structural biotechnology journal Figure SARS_CoV_2 F318W 86 91 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. Molecular Dynamics simulation of the free PALS1 wild type and F318W variant. 2021 Computational and structural biotechnology journal Figure SARS_CoV_2 F318W 62 67 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. Panel A, binding isotherm of PALS1 F318 W and SARS-CoV-2 E peptide. 2021 Computational and structural biotechnology journal Figure SARS_CoV_2 F318W 35 41 E 57 58 33758649 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. Scatchard plots of the interactions between immobilized tetradecapeptides and the analytes, PALS1 F318W and PALS1 wild-type at T = 25C. 2021 Computational and structural biotechnology journal Figure SARS_CoV_2 F318W 98 103 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Schematic representation of RBD mutant location on RBD complexed with ACE-2 Receptor A) The RMSDs of the backbone atoms of both RBD-ACE-2 complex; B) The RMSFs of Calpha atoms of both RBD-ACE2 complexes C) Binding free energies of SARS-CoV-2 RBD ACE-2 (including wild and mutant at N439K) D) Ribbon diagram structure of hydrogen bonds between SARS-CoV-2 and h-ACE2 receptor wild type E) Ribbon diagram structure of hydrogen bonds between SARS-CoV-2 and h-ACE2 receptor mutant N439K type. 2021 Heliyon Figure SARS_CoV_2 N439K;N439K 282;476 287;481 RBD;RBD;RBD;RBD;RBD 28;51;128;184;242 31;54;131;187;245 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. a-c, The N501Y variant was mixed with wt virus and inoculated intranasally into hamsters. 2021 bioRxiv Figure SARS_CoV_2 N501Y 9 14 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. a-f, The wt, N501Y and UK-8x mutant viruses were inoculated on Vero E6 (a,c,e) and calu-3 cells (b,d,f) respectively. 2021 bioRxiv Figure SARS_CoV_2 N501Y 13 18 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. a-h, Eight SARS-CoV-2 spike mutants: Delta69-70 (a), Delta145 (b), A570D (c), P681H (d), T716I (e), S982A (f), D1118H (g) and UK-8x (h) were mixed with wt virus at a ratio of approximately 1:1. 2021 bioRxiv Figure SARS_CoV_2 A570D;D1118H;P681H;S982A;T716I 67;111;78;100;89 72;117;83;105;94 S 22 27 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. a, The reverse genetic construction design of all the individual and combined mutations on the wt D614G backbone. 2021 bioRxiv Figure SARS_CoV_2 D614G 98 103 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. a,b, The ratios of mixed viruses in the nasal washes (a), tracheae and lungs (b) of recipient hamsters were compared to the ratios of N501Y:wt measured on the day 1 nasal wash of donor hamsters to assess fitness for transmission to and early replication in the recipient hamsters. 2021 bioRxiv Figure SARS_CoV_2 N501Y 134 139 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. b, The location of all 8 UK B.1.1.7 substitutions and D614G on the SARS-CoV-2 spike protein trimer. 2021 bioRxiv Figure SARS_CoV_2 D614G 54 59 S 78 83 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. b, Weight change in hamsters following infection by the N501Y (n=5) and UK-8x (n=5) mutants compared to the wt (n=5). 2021 bioRxiv Figure SARS_CoV_2 N501Y 56 61 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. c-h, The infection of N501Y and UK-8x mutants compared to the wt in the nasal washes (c-e) collected 1, 2, 3, or 5 days post-infection and in the organs (f-h) 2 days post-infection. 2021 bioRxiv Figure SARS_CoV_2 N501Y 22 27 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. No significant differences were seen between the N501Y/UK-8x and wt groups. 2021 bioRxiv Figure SARS_CoV_2 N501Y 49 54 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. The replication kinetics of N501Y/wt mixed viruses in the competition assay in hamsters. 2021 bioRxiv Figure SARS_CoV_2 N501Y 28 33 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. The replication kinetics of the N501Y and UK-8x mutants on Vero E6 and calu-3 cells. 2021 bioRxiv Figure SARS_CoV_2 N501Y 32 37 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. The spike N501Y substitution benefits viral infection of hamster upper airways. 2021 bioRxiv Figure SARS_CoV_2 N501Y 10 15 S 4 9 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. The wt, N501Y and UK-8x viruses were intranasally inoculated into hamsters at a titer of 104 PFU per hamster. 2021 bioRxiv Figure SARS_CoV_2 N501Y 8 13 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. (b) Neutralizing Ab titers against wildtype (D614G) SARS-CoV-2 S, B.1.1.7, and B.1.351 S HIV pseudoviruses from NHPs immunized with 12GS-RBD-NP at day 56 (two immunizations, filled symbols) and 196 (three immunizations, open symbols) (c) Cladogram based on sarbecovirus RBD amino acid sequences. 2021 bioRxiv Figure SARS_CoV_2 D614G 45 50 RBD;RBD;S;S 137;270;63;87 140;273;64;88 33761008 Diverse SARS-CoV-2 variants preceded the initial COVID-19 outbreak in Croatia. Position of the V13I mutation in the structure of the SARS-Cov-2 Mpro protease with an inhibitor bound in the active site. 2021 Archives of virology Figure SARS_CoV_2 V13I 16 20 33761008 Diverse SARS-CoV-2 variants preceded the initial COVID-19 outbreak in Croatia. The crystal structure of the protease (PDB:6XR3) was used to show the position of the V13I mutation. 2021 Archives of virology Figure SARS_CoV_2 V13I 86 90 33761008 Diverse SARS-CoV-2 variants preceded the initial COVID-19 outbreak in Croatia. The following clades are highlighted in different colors: clade G (substitutions C214T, C3037T, A23403G), GH (C214T, C3037T, A23403G, G25563T), GR (C241T, C3037T, A23403G, G28882A), and L (C241, C3037, A23403, C8782, G11083, G26144, T28144). 2021 Archives of virology Figure SARS_CoV_2 A23403G;A23403G;A23403G;C214T;C3037T;C3037T;C3037T;G25563T;G28882A;C214T;C241T 96;125;163;81;88;117;155;134;172;110;148 103;132;170;86;94;123;161;141;179;115;153 33767200 The effect of SARS-CoV-2 D614G mutation on BNT162b2 vaccine-elicited neutralization. The effect of spike D614G substitution on SARS-CoV-2 neutralization. 2021 NPJ vaccines Figure SARS_CoV_2 D614G 20 25 S 14 19 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. a) Variant discrimination assay plot: samples with sequence confirmed SARS-CoV-2 wild strain (N501) in blue, N501Y variants in either red, and mixed variants in green. 2021 Journal of virological methods Figure SARS_CoV_2 N501Y 109 114 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. b) Graph of variant amplification assay: amplification of wild type variant in green and N501Y variants in blue (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article). 2021 Journal of virological methods Figure SARS_CoV_2 N501Y 89 94 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. (a) RMSD plot of the wild-type, D614G and open-state S-proteins. 2021 Infection, genetics and evolution Figure SARS_CoV_2 D614G 32 37 S 53 54 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. (b) Conformation of the RBD in the wild-type, D614G and open-state S-proteins. 2021 Infection, genetics and evolution Figure SARS_CoV_2 D614G 46 51 RBD;S 24;67 27;68 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Residual energy contributions to interaction between the wild-type or D614G S-protein with (a) CB6 (b) P2B-2F6 (c) 4A8 are shown. 2021 Infection, genetics and evolution Figure SARS_CoV_2 D614G 70 75 S 76 77 33778179 Mutational analysis of structural proteins of SARS-CoV-2. b) Single amino acid substitution E8K in the E protein (QKO24093.1 isolate) resulted in a PKC site at position 6-9 position. 2021 Heliyon Figure SARS_CoV_2 E8K 34 37 E 45 46 33778179 Mutational analysis of structural proteins of SARS-CoV-2. d) In addition to the above mentioned modification sites in the M protein, a single point mutation D3G in QIZ16332.1 isolate resulted in a N myristoylation site at 3-8 position. 2021 Heliyon Figure SARS_CoV_2 D3G 99 102 N 139 140 33778179 Mutational analysis of structural proteins of SARS-CoV-2. D614 amino acid in the chain A of SARS-CoV-2 S protein (with up-RBD confirmation), interacted with T869 and K854 of adjacent chains while in the D614G mutant, G614 in chain A did not establish interaction with any nearby residue. 2021 Heliyon Figure SARS_CoV_2 D614G 145 150 RBD;S 64;45 67;46 33778179 Mutational analysis of structural proteins of SARS-CoV-2. e) Similarly, a single amino acid substitution V10A in the M protein sequence of QLF97810.1 isolate resulted in an N myristoylation site at 6-11 position. 2021 Heliyon Figure SARS_CoV_2 V10A 47 51 N 115 116 33778179 Mutational analysis of structural proteins of SARS-CoV-2. f) Furthermore a CK II phosphorylation site was observed at 9-12 position due to a single amino acid substitution P132S in the sequence of QKG90089.1 isolate. 2021 Heliyon Figure SARS_CoV_2 P132S 114 119 33778179 Mutational analysis of structural proteins of SARS-CoV-2. Interacting amino acids between a) V483A-RBD: ACE-2; b) N501Y-RBD: ACE-2. 2021 Heliyon Figure SARS_CoV_2 N501Y;V483A 56;35 61;40 RBD;RBD 41;62 44;65 33778179 Mutational analysis of structural proteins of SARS-CoV-2. Interacting amino acids between a) Wild Type-RBD: ACE-2; b) S477N-RBD: ACE-2. 2021 Heliyon Figure SARS_CoV_2 S477N 60 65 RBD;RBD 45;66 48;69 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. In the global frequency (A), the overlaid black line indicates the cumulative frequency of D614G in sequences collected up to and including each date. 2021 Gene reports Figure SARS_CoV_2 D614G 91 96 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. The frequency of the S protein D614G (blue) over time in sequences collected from worldwide (n = 113,381) (A), North America (n = 29,198) (B), Europe (n = 62,006) (C), Asia (6665) (D), and Korea (n = 834) (E) in the public databases as of September 30, 2020. 2021 Gene reports Figure SARS_CoV_2 D614G 31 36 S 21 22 33789085 SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Pseudoviruses displaying wild-type or mutant SARS-CoV-2 spike from UK-N50Y or SA-N501Y/K417N/E484K variants were used in neutralization assays. 2021 Cell host & microbe Figure SARS_CoV_2 E484K;K417N;N501Y;N50Y 93;87;81;70 98;92;86;74 S 56 61 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. (A) Conformations of WT (cyan), P13L (green), S197L (pink), R203K (red), G204R (orange) populated at 50 ns timestep. 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 G204R;P13L;R203K;S197L 73;32;60;46 78;36;65;51 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. (A) Showing dynamics in the structure of WT and P344S mutant at different intervals of time. 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 P344S 48 53 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. (B) Rg plot of WT (green) and P344S mutant (yellow) displays their compactness. 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 P344S 30 35 33797336 In silico characterization of mutations circulating in SARS-CoV-2 structural proteins. Stability analysis of crystallized N protein CTD and its mutant (P344S). 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 P344S 65 70 N 35 36 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. (A) Variation frequency curve of ORF1ab p.5828P > L (NSP13: P504L) and ORF1ab p.5865Y > C (NSP13: Y541C), black line chart indicates variation frequency, green histogram indicates SARS-CoV-2 strains. 2021 Infection, genetics and evolution Figure SARS_CoV_2 P504L;Y541C 60;98 65;103 ORF1ab;ORF1ab;Nsp13;Nsp13 33;71;53;91 39;77;58;96 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. COVID-19 outcomes in states with different proportions of strains containing variation in NSP13: P504L and NSP13: Y541C. 2021 Infection, genetics and evolution Figure SARS_CoV_2 P504L;Y541C 97;114 102;119 Nsp13;Nsp13 90;107 95;112 COVID-19 0 8 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Effects of NSP13: P504L and NSP13: Y541C on NSP13 function. 2021 Infection, genetics and evolution Figure SARS_CoV_2 P504L;Y541C 18;35 23;40 Nsp13;Nsp13;Nsp13 11;28;44 16;33;49 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. ORF1ab variations (NSP13: P504L and NSP13: Y541C) in SARS-CoV-2. 2021 Infection, genetics and evolution Figure SARS_CoV_2 P504L;Y541C 26;43 31;48 ORF1ab;Nsp13;Nsp13 0;19;36 6;24;41 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Prediction results of ORF1ab variations (NSP13: P504L and NSP13: Y541C) based on PolyPhen-2 (C), and PROVEAN v1.1 (D). 2021 Infection, genetics and evolution Figure SARS_CoV_2 P504L;Y541C 48;65 53;70 ORF1ab;Nsp13;Nsp13 22;41;58 28;46;63 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. Distinct cluster of the viral isolate with mutation C28854T/Ser194Leu/N gene in Gujarat SARS-CoV-2 genomes. 2021 Frontiers in genetics Figure SARS_CoV_2 C28854T;S194L 52;60 59;69 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. The top mutations included C241T, C3037T, C14408T/Pro314Leu, C18877T, A23403G/Asp614Gly, G25563T/Gln57His, and C26735T with frequency >55%. 2021 Frontiers in genetics Figure SARS_CoV_2 A23403G;C14408T;C18877T;C241T;C26735T;C3037T;G25563T;A614G;D614G;G57H;Q57H;P314L 70;42;61;27;111;34;89;78;78;97;97;50 77;49;68;32;118;40;96;87;87;105;105;59 33834012 Comparison of Clinical Features and Outcomes of Medically Attended COVID-19 and Influenza Patients in a Defined Population in the 2020 Respiratory Virus Season. Stimulation shown the residue S477N binding with ACE2 Sernine19. 2021 Frontiers in public health Figure SARS_CoV_2 S477N 30 35 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. (b-e) Thermal dynamic cycle to obtain the binding free energy change induced by the K417N mutation. 2022 Journal of medicinal chemistry Figure SARS_CoV_2 K417N 84 89 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. MD simulation of the RBD-ACE2 complex with the N501Y, K417N, and E484K mutations in the RBD. 2022 Journal of medicinal chemistry Figure SARS_CoV_2 E484K;K417N;N501Y 65;54;47 70;59;52 RBD;RBD 21;88 24;91 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. The frequency of D614G mutation during March-October interval in Iranian SARS-CoV-2 outbreak. 2022 Transboundary and emerging diseases Figure SARS_CoV_2 D614G 17 22 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. c Immunoblot analysis of the Dox-induced expression of NR203/G204-mEGFP and NR203K/G204R-mEGFP proteins in H1299 cells. 2021 Nature communications Figure SARS_CoV_2 G204R 83 88 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. f, g Time-lapse imaging of NR203/G204-mEGFP and NR203K/G204R-mEGFP proteins (20 muM) in the presence of Cy5-labeled 60-nt vRNA (40 ng/mul) (f), and the partition coefficient (n = 8 randomly selected views) of total fluorescence intensity in each view (g). 2021 Nature communications Figure SARS_CoV_2 G204R 55 60 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. Foci of NR203/G204-mEGFP and NR203K/G204R-mEGFP proteins per cell were quantified, n = 100 biologically independent cells (e). 2021 Nature communications Figure SARS_CoV_2 G204R 36 41 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. Foci of NR203/G204-mEGFP and NR203K/G204R-mEGFP proteins per cell were quantified, n = 100 biologically independent cells (h). 2021 Nature communications Figure SARS_CoV_2 G204R 36 41 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. NR203K/G204R gained greater ability to undergo RNA-induced LLPS. 2021 Nature communications Figure SARS_CoV_2 G204R 7 12 33842902 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. (B) Literature measurements of the effects of K417N, E484K, and N501Y on neutralization by LY-CoV555 and LY-CoV016. 2021 Cell reports. Medicine Figure SARS_CoV_2 E484K;K417N;N501Y 53;46;64 58;51;69 33842902 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. Mutations with notable frequencies are labeled, and those discussed in the text are colored to key with (B) or to highlight observed cocktail escape mutations (Q493K/R). 2021 Cell reports. Medicine Figure SARS_CoV_2 Q493K;Q493R 160;160 167;167 33842902 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. These measurements validate our maps, which suggest that K417N specifically escapes LY-CoV016, E484K specifically escapes LY-CoV555, and N501Y affects neither antibody. 2021 Cell reports. Medicine Figure SARS_CoV_2 E484K;K417N;N501Y 95;57;137 100;62;142 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. (D) Depiction of the RBD as a gray surface with the location of the three mutations (K417T, E484K, and N501Y) (magenta); the ACE2 binding surface of RBD is colored green. 2021 Cell Figure SARS_CoV_2 E484K;N501Y;K417T 92;103;85 97;108;90 RBD;RBD 21;149 24;152 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. (E and F) K417N/T interactions with Fab 222 (E) and N501Y interactions with Fab 222 (F) in the K417N (cyan), K417T (magenta), P.1 (blue), and P.1.351 (teal) RBD-Fab 222 complex structures compared with the WT RBD-Fab 222 (gray) complex by superimposing the RBD. 2021 Cell Figure SARS_CoV_2 K417N;K417N;K417T;K417T;N501Y 95;10;10;109;52 100;17;17;114;57 RBD;RBD;RBD 157;209;257 160;212;260 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. (F and G) Effect of E484K mutation on the electrostatic surface. 2021 Cell Figure SARS_CoV_2 E484K 20 25 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. Sliding 7-day window depicting proportion of sequences containing K417T, related to Figure 1. 2021 Cell Figure SARS_CoV_2 K417T 66 71 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. Yellow marks mutated K417T, E484K, and N501Y. 2021 Cell Figure SARS_CoV_2 E484K;K417T;N501Y 28;21;39 33;26;44 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Legend: a = reference sequences, b = 36/219 sequences carry additional L452M mutation; Abbreviations: H. 2021 Cell reports Figure SARS_CoV_2 L452M 71 76 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Statistical significance of differences in NT50 values between SARS-CoV-2 S harboring D614G alone or in conjunction with Y453F was analyzed by paired Student's t test (p = 0.0212). 2021 Cell reports Figure SARS_CoV_2 D614G;Y453F 86;121 91;126 S 74 75 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Y453F reduces neutralization by convalescent sera and monoclonal antibodies. 2021 Cell reports Figure SARS_CoV_2 Y453F 0 5 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. (D) Effect of D614G substitution on FP coverage. 2021 Science advances Figure SARS_CoV_2 D614G 14 19 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. D614G substitution alters inter-protomer interactions between S1 and S2 subunits. 2021 Science advances Figure SARS_CoV_2 D614G 0 5 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. Here, only one of the three D614G sites is shown. 2021 Science advances Figure SARS_CoV_2 D614G 28 33 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. The white dashed circle indicates a D614G site. 2021 Science advances Figure SARS_CoV_2 D614G 36 41 33875719 Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology. The emergence of D614G mutation is marked by a red asterisk. 2021 Scientific reports Figure SARS_CoV_2 D614G 17 22 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. (A) Overview of the wild-type spike/LCB1 binding region, with wild-type mutated residues N501Y represented as balls and sticks. 2021 The journal of physical chemistry. B Figure SARS_CoV_2 N501Y 89 94 S 30 35 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. (B) Energy-minimized binding mode of the N501Y mutant spike protein and hACE2 with mutated spike protein residue Y501. 2021 The journal of physical chemistry. B Figure SARS_CoV_2 N501Y 41 46 S;S 54;91 59;96 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. (B) Overview of the N501Y Spike/LCB1 binding region with mutated residues highlighted with balls and sticks. 2021 The journal of physical chemistry. B Figure SARS_CoV_2 N501Y 20 25 S 26 31 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. (D) Binding mode of the N501Y spike protein and LCB1, with mutated residues visualized with balls in sticks, the N501Y residue change removes a hydrogen bond with E22, resulting in the loss of binding affinity. 2021 The journal of physical chemistry. B Figure SARS_CoV_2 N501Y;N501Y 24;113 29;118 S 30 35 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. (D) Interactions of N501Y mutant with the hACE2 protein. 2021 The journal of physical chemistry. B Figure SARS_CoV_2 N501Y 20 25 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. (E) Overview of the wild-type spike/LCB3 binding region, with wild-type mutated residues N501Y represented as balls and sticks. 2021 The journal of physical chemistry. B Figure SARS_CoV_2 N501Y 89 94 S 30 35 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. (F) Overview of the N501Y spike/LCB3 binding region with mutated residues highlighted with balls and sticks. 2021 The journal of physical chemistry. B Figure SARS_CoV_2 N501Y 20 25 S 26 31 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. (H) Binding mode of ACE2.v2.4 with the wild-type spike protein; while the introduction of N330Y still contributes hydrophobic interactions with G496, the loss of the A386L mutation results in the loss of the strengthened hydrogen bonds between R403 and E37 seen in ACE2.v2. 2021 The journal of physical chemistry. B Figure SARS_CoV_2 A386L;N330Y 166;90 171;95 S 49 54 33881861 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates. (H) Binding mode of the N501Y spike protein and LCB3, with mutated residues visualized with balls in sticks; the N501Y residue change removes a hydrogen bond with N1, resulting in a similar loss of calculated binding affinity as with the LCB3 with N501Y spike. 2021 The journal of physical chemistry. B Figure SARS_CoV_2 N501Y;N501Y;N501Y 24;113;248 29;118;253 S;S 30;254 35;259 33886690 The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways. Study panel of wild-type and S1/S2 site mutant spikes, and the D614G mutant of SARS-2-S. 2021 PLoS pathogens Figure SARS_CoV_2 D614G 63 68 S;S 47;86 53;87 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. (C) Neutralization of WT or N501Y D614G SARS-CoV-2 using the MNV and PRNT assay. 2021 Proc Natl Acad Sci U S A Figure SARS_CoV_2 D614G;N501Y 34;28 39;33 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. (D) Inhibition of WT and N501Y D614G SARS-CoV-2 virus using PRNT. 2021 Proc Natl Acad Sci U S A Figure SARS_CoV_2 D614G;N501Y 31;25 36;30 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. After 24 h, mice were challenged with SARS-CoV-2 N501Y D614G virus via the Glas-col nebulization inhalation system. 2021 Proc Natl Acad Sci U S A Figure SARS_CoV_2 D614G;N501Y 55;49 60;54 33894500 Screening of potent phytochemical inhibitors against SARS-CoV-2 protease and its two Asian mutants. Interactions of protease mutant (a) R60C (b) I152V with top-scored ligand (NPC474104). 2021 Computers in biology and medicine Figure SARS_CoV_2 I152V;R60C 45;36 50;40 33894500 Screening of potent phytochemical inhibitors against SARS-CoV-2 protease and its two Asian mutants. Shows the comparative Gibbs binging free energy of the wild (green), mutant R60C (blue) and mutant I152V (orange) proteases with Kazinol T. 2021 Computers in biology and medicine Figure SARS_CoV_2 I152V;R60C 99;76 104;80 33894500 Screening of potent phytochemical inhibitors against SARS-CoV-2 protease and its two Asian mutants. The above plot shows the RMSD evolution of a (wild) b (R60C) and c (I152V) proteases (left Y-axis). 2021 Computers in biology and medicine Figure SARS_CoV_2 I152V;R60C 68;55 73;59 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. Detailed view of phylogenetic tree of viral genomes carrying missense M mutations coloured by the genotypes at M:82 (I: green; T: yellow), demonstrating proposed new clade B.1 M:I82T (middle), falling between B.1.375 clade that carries M:I48V (top) and B.1.525 clade that also carries M:I82T (bottom). 2021 Emerging microbes & infections Figure SARS_CoV_2 I48V;I82T;I82T 238;178;287 242;182;291 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. (A) RdRp-Remdesivir; (B) RdRp-SCHEMBL20144212; (C) P323L-Remdesivir; (D) P323L-SCHEMBL20144212. 2021 Frontiers in molecular biosciences Figure SARS_CoV_2 P323L;P323L 51;73 56;78 RdRP;RdRP 4;25 8;29 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. Depiction of cross-correlation networks: (A) RdRp-Remdesivir; (C) RdRp-SCHEMBL20144212; (E) P323L-Remdesivir; (G) P323L-SCHEMBL20144212. 2021 Frontiers in molecular biosciences Figure SARS_CoV_2 P323L;P323L 92;114 97;119 RdRP;RdRP 45;66 49;70 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. Depiction of vector field collective motions: (B) RdRp-Remdesivir; (D) RdRp-SCHEMBL20144212; (F) P323L-Remdesivir; (H) P323L-SCHEMBL20144212. 2021 Frontiers in molecular biosciences Figure SARS_CoV_2 P323L;P323L 97;119 102;124 RdRP;RdRP 50;71 54;75 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. GISAID clades were further clustered into 2 clade groups depending on the presence of the G614D spike glycoprotein variant (black dashed line). 2021 JAMA network open Figure SARS_CoV_2 G614D 90 95 S 96 114 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. The observed P812R mutation is highlighted in orange. 2021 Antimicrobial agents and chemotherapy Figure SARS_CoV_2 P812R 13 18 33905891 Spike protein mutational landscape in India during the complete lockdown phase: Could Muller's ratchet be a future game-changer for COVID-19? Stability index (i.e., docking score or HADDOCK score) plot of S-R complexes for spike protein variants emerging from (a) Ancestor 1 (Wuhan-Hu-1/2019 variant) and (b) Ancestor 2 (D614G variant). 2021 Infection, genetics and evolution Figure SARS_CoV_2 D614G 179 184 S;S 81;63 86;64 33905891 Spike protein mutational landscape in India during the complete lockdown phase: Could Muller's ratchet be a future game-changer for COVID-19? The black arrows lead to the variants for which the docking scores could not be determined either because of the presence of at least one variation outside the available template region for docking, or due to non-existing isolate in the lone hypothetical node with H1083Q mutation denoted by black color. 2021 Infection, genetics and evolution Figure SARS_CoV_2 H1083Q 265 271 33905891 Spike protein mutational landscape in India during the complete lockdown phase: Could Muller's ratchet be a future game-changer for COVID-19? This black node signifies a variant with no available isolate in our dataset, while it gives rise to two derived variants, H1083Q:R78M and H1083Q:E583D, for which representative isolates were available. 2021 Infection, genetics and evolution Figure SARS_CoV_2 H1083Q;H1083Q;E583D;R78M 123;139;146;130 129;145;151;134 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. D614G could affect the interaction with the host, as well as the immune response (vaccines), but real effects remain unclear. 2021 Infection, genetics and evolution Figure SARS_CoV_2 D614G 0 5 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Frequency of T1117I in the spike along time in Costa Rica and the world. 2021 Infection, genetics and evolution Figure SARS_CoV_2 T1117I 13 19 S 27 32 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. The most frequent variants (Spike D614G and ORF1a P4715L) are present in 183 (98.9%) genomes (arrow). 2021 Infection, genetics and evolution Figure SARS_CoV_2 D614G;P4715L 34;50 39;56 ORF1a;S 44;28 49;33 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. The variant T1117I is a variant very scarcely reported in the world (0.08%, GISAID), but the frequency in Costa Rica is 29.2%. 2021 Infection, genetics and evolution Figure SARS_CoV_2 T1117I 12 18 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Variant D614G is present in 98.6% of the genomes in this study, which is also predominant worldwide (>90%, GISAID). 2021 Infection, genetics and evolution Figure SARS_CoV_2 D614G 8 13 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Variant T1117I in the spike is present in 54 genomes, which belong to a separated monophyletic cluster (dark-blue). 2021 Infection, genetics and evolution Figure SARS_CoV_2 T1117I 8 14 S 22 27 33906967 Noncanonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9. (E) Specific detection of the D614G point mutation within the spike protein of SARS-CoV-2. 2021 Science (New York, N.Y.) Figure SARS_CoV_2 D614G 30 35 S 62 67 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. (a) Examples of binding affinities of CB6 to spike RBD of Wuhan strain (WT) or the N501Y mutant. 2021 Virology journal Figure SARS_CoV_2 N501Y 83 88 S;RBD 45;51 50;54 33910569 Impact of the N501Y substitution of SARS-CoV-2 Spike on neutralizing monoclonal antibodies targeting diverse epitopes. (a) Examples of neutralization of indicated mAbs against pseudovirus bearing the spike of Wuhan strain (WT) or the N501Y mutant. 2021 Virology journal Figure SARS_CoV_2 N501Y 115 120 S 81 86 33911163 Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. Full 50ns MD Simulation of the non-mutant native spike (blue) and the (R355D K424E) mutant structure (orange). 2021 Scientific reports Figure SARS_CoV_2 K424E;R355D 77;71 82;76 S 49 54 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. (A) Atomic model for the structure of the complex of VH ab8 (blue) with the N501Y mutant spike protein ectodomain (gray). 2021 PLoS biology Figure SARS_CoV_2 N501Y 76 81 S 89 94 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. (A) ELISA analysis of antibody interactions with either N501Y or unmutated spike ectodomain. 2021 PLoS biology Figure SARS_CoV_2 N501Y 56 61 S 75 80 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. (B) N501Y or unmutated SARS-CoV-2 S pseudotyped virus neutralization by either VH Fc ab8 or IgG ab1. 2021 PLoS biology Figure SARS_CoV_2 N501Y 4 9 S 34 35 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. (C and D) ELISA analysis of N501Y or unmutated SARS-CoV-2 spike ectodomain binding by soluble ACE2-mFc in the presence of serial dilutions of either (C) IgG ab1 or (D) VH Fc ab8. 2021 PLoS biology Figure SARS_CoV_2 N501Y 28 33 S 58 63 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. (C) Density map in the region near 501 for the N501Y mutant spike protein ectodomain showing density for residues Q498, Y501, and Y505. 2021 PLoS biology Figure SARS_CoV_2 N501Y 47 52 S 60 65 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. (D) Density map in the region near 501 for the N501Y mutant spike protein ectodomain showing density for residues Q498, Y501, and Y505 in the spike protein and a loop in Fab ab1 that includes S30, the residue closest to Y501. 2021 PLoS biology Figure SARS_CoV_2 N501Y 47 52 S;S 60;142 65;147 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. (E) Zoomed-in view of the interface, showing a superposition of the structures of unmutated and N501Y mutant spike proteins in complex with ACE2. 2021 PLoS biology Figure SARS_CoV_2 N501Y 96 101 S 109 114 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Analysis of VH Fc ab8 and IgG ab1 interactions with N501Y and unmutated spike. 2021 PLoS biology Figure SARS_CoV_2 N501Y 52 57 S 72 77 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Ribbon diagram with superposition of the unmutated and N501Y RBD-ACE2 complex (PDB ID 7KMB). 2021 PLoS biology Figure SARS_CoV_2 N501Y 55 60 RBD 61 64 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Structure of Fab ab1 bound to the N501Y mutant spike protein trimer. 2021 PLoS biology Figure SARS_CoV_2 N501Y 34 39 S 47 52 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to the ACE2 ectodomain. 2021 PLoS biology Figure SARS_CoV_2 N501Y 28 33 S 41 46 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Structure of VH ab8 bound to the N501Y mutant spike protein trimer. 2021 PLoS biology Figure SARS_CoV_2 N501Y 33 38 S 46 51 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. The carbon atoms of residues in the N501Y mutant and ACE2 in our structure are colored in cyan and pale red, respectively, while those in the structure of the complex between unmutated spike protein and ACE2 are in light gray. 2021 PLoS biology Figure SARS_CoV_2 N501Y 36 41 S 185 190 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. Ability of RBD to block WT (a), 19del (b), or 19del + D614G (c) pseudovirus infection. 2021 Journal of biomedical science Figure SARS_CoV_2 19del;19del;D614G 32;46;54 37;51;59 RBD 11 14 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. Following preincubation with RBD protein, hACE2 expressing 293TT cells were infected with WT, 19del, or 19del + D614G SARS-CoV-2 pseudoviruses (quantified as 25ng of HIV Gag p24 protein). 2021 Journal of biomedical science Figure SARS_CoV_2 19del;19del;D614G 94;104;112 99;109;117 RBD 29 32 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. hACE2 expressing 293TT cells were infected with wild-type, 19del, or 19del + D614G SARS-CoV-2 pseudoviruses (quantified as 25ng of HIV Gag p24 protein) for 72 h. 2021 Journal of biomedical science Figure SARS_CoV_2 19del;19del;D614G 59;69;77 64;74;82 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. Infectivity of wild-type (WT), 19del, and 19del + D614G SARS-CoV-2 pseudoviruses. 2021 Journal of biomedical science Figure SARS_CoV_2 D614G 50 55 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. one hour before 19del or 19del + D614G pseudovirus infection. 2021 Journal of biomedical science Figure SARS_CoV_2 D614G 33 38 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. Quantification of bioluminescence signal of mice infected with 19del (c) or 19del + D614G (d) pseudovirus with or without RBD blocking showing significantly lower infection in mice treated with RBD protein compared to unblocked control. 2021 Journal of biomedical science Figure SARS_CoV_2 19del;19del;D614G 63;76;84 68;81;89 RBD;RBD 122;194 125;197 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. Representative bioluminescence and kinetics of mouse infection with 19del or 19del + D614G pseudoviruses (c). 2021 Journal of biomedical science Figure SARS_CoV_2 19del;19del;D614G 68;77;85 73;82;90 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. Representative bioluminescence images of mice infected with 19del or 19del + D614G pseudovirus with or without RBD blocking (b). 2021 Journal of biomedical science Figure SARS_CoV_2 D614G 77 82 RBD 111 114 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. (A,B) miRFP signals (top) and neutralization curves and NT50 titers (bottom) to pseudoviruses Str and D614G at 72 h post-infection in HEK-293T-hACE2 cells of a convalescent-phase serum sample from a confirmed COVID-19 case (A) and neutralization curves and NT50 titers of other 4 confirmed COVID-19 cases (B). 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 102 107 COVID-19;COVID-19 209;290 217;298 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. (A) Quantification of viral RNA copies of three pseudoviruses (Str, D614G, AAAR) and miRFP vector only by qRT-PCR with primers targeting the HIV-1 pol gene. 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 68 73 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. (A) Schematic drawing of plasmids expressing full-length (S) and truncated (Str) SARS-CoV-2 S proteins, truncated S proteins with mutations (D614G and AAAR), and VSV-G protein as well as co-transfection with pNL43 R-E-miRFP (miRFP) to generate different pseudoviruses containing miRFP reporter, infection of target cells, one-step imagining and various applications. 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 141 146 S;S;S 58;92;114 59;93;115 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. (B,C) Western blot analysis of three pseudovirus particles (Str, D614G, AAAR) and miRFP vector only purified from sucrose cushion ultracentrifugation using HIV-1 positive sera (B,C bottom) and rabbit sera to S protein (B top) and a human mAb CR3022 to RBD (C top) of SARS-CoV-1. 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 65 70 RBD;S 252;208 255;209 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. (C) Comparison between NT50 titers to pseudoviruses Str and D614G for 15 confirmed COVID-19 cases. 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 60 65 COVID-19 83 91 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. (E-J) Relationship between NT50 titers to pseudoviruses Str and PRNT50 (E), PRNT80 (F) or PRNT90 (G) titers to SARS-CoV-2 USA-WA-1 strain (containing D614) and relationship between NT50 titers to pseudoviruses D614G and PRNT50 (H), PRNT80 (I) or PRNT90 (J) titers to SARS-CoV-2 USA-WA-1 strain. 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 210 215 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. Infection kinectics of three SARS-CoV-2 pseudoviruses (Str, D614G, AAAR) in HEK-293T-hACE2 cells with miRFP signals (A) and quantification (B), and cellular tropism in different cells with miRFP quantification from 24 h to 120 h post-infection (C). 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 60 65 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. SARS-CoV-2 phylogeny highlighting D614G split and cases through time in Washington State. 2021 Science translational medicine Figure SARS_CoV_2 D614G 34 39 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. (A) Number of sequenced SARS-CoV-2 genomes carrying S:T478K mutation over time, measured weekly. 2021 Journal of medical virology Figure SARS_CoV_2 T478K 54 59 S 52 53 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. (A) Prevalence of Spike mutation T478K in PANGO lineages. 2021 Journal of medical virology Figure SARS_CoV_2 T478K 33 38 S 18 23 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. (B) Frequency of sequenced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes carrying the S:T478K mutation, divided into 10 years age ranges. 2021 Journal of medical virology Figure SARS_CoV_2 T478K 111 116 S 109 110 COVID-19 34 74 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. (B) Prevalence over time of S:T478K in the SARS-CoV-2 population, measured as the number of S:T478K genomes over the total number of sequenced genomes. 2021 Journal of medical virology Figure SARS_CoV_2 T478K;T478K 30;94 35;99 S;S 28;92 29;93 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. (C) 3D detail of structural superposition of WT SARS-CoV-2 RBD and S:T478K. 2021 Journal of medical virology Figure SARS_CoV_2 T478K 69 74 RBD;S 59;67 62;68 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. (C) Pie chart showing the distribution of S:T478K by patient sex. 2021 Journal of medical virology Figure SARS_CoV_2 T478K 44 49 S 42 43 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. (C) Prevalence over time of S:N501Y in the SARS-CoV-2 population. 2021 Journal of medical virology Figure SARS_CoV_2 N501Y 30 35 S 28 29 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. (D) Number of S:T478K samples over total samples sequenced from each country. 2021 Journal of medical virology Figure SARS_CoV_2 T478K 16 21 S 14 15 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. (D) Prevalence over time of S:D614G in the SARS-CoV-2 population. 2021 Journal of medical virology Figure SARS_CoV_2 D614G 30 35 S 28 29 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. (E) Geographic global projection of S:T478K cases detected in each country. 2021 Journal of medical virology Figure SARS_CoV_2 T478K 38 43 S 36 37 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. Discrete numbers of S:T478K are reported on top of each bar. 2021 Journal of medical virology Figure SARS_CoV_2 T478K 22 27 S 20 21 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. Most S:T478K-carrying samples are classified in the B.1.1.519 lineage. 2021 Journal of medical virology Figure SARS_CoV_2 T478K 7 12 S 5 6 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. The color scale indicates the number of SARS-CoV-2 genomes carrying the S:T478K mutation, in logarithm-10 scale. 2021 Journal of medical virology Figure SARS_CoV_2 T478K 74 79 S 72 73 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. The discrete number of S:T478K is reported on top of each bar. 2021 Journal of medical virology Figure SARS_CoV_2 T478K 25 30 S 23 24 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. The top 10 lineages are reported, sorted by number of S:T478K samples over a total number of lineage samples. 2021 Journal of medical virology Figure SARS_CoV_2 T478K 56 61 S 54 55 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. The total number of S:T478K patients for the specified age range is reported on top of the bars. 2021 Journal of medical virology Figure SARS_CoV_2 T478K 22 27 S 20 21 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. (a) The time-dependent accumulating plot for frequencies of the two SNPs (1,059.C > T & 25,563.G > T) between continents. 2021 Transboundary and emerging diseases Figure SARS_CoV_2 C059T;G563T 76;91 85;100 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. Retrospectively tracing the early SARS-CoV-2 isolates with SNPs (1,059.C > T & 25,563.G > T) of all continents and North American lineage B.1. 2021 Transboundary and emerging diseases Figure SARS_CoV_2 C059T;G563T 67;82 76;91 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. (A) shows the surface binding of the HS molecule to the S247R mutation and residue R683 of the PRRARS domain. 2021 Computational and structural biotechnology journal Figure SARS_CoV_2 S247R 56 61 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. The left hand side presents the face containing the PRRARS furin cleavage site and 245H-S247R site, while the right hand side is the opposite face. 2021 Computational and structural biotechnology journal Figure SARS_CoV_2 S247R 88 93 33968333 Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain. The PRRARS site is in orange, and the 247H-S247R is in green. 2021 Computational and structural biotechnology journal Figure SARS_CoV_2 S247R 43 48 33968806 SARS CoV-2 Nucleoprotein Enhances the Infectivity of Lentiviral Spike Particles. n=3 +- SD (G) Comparison between the infectivity of both wild-type spike and the D614G mutant, with and without N protein co-transfection, normalized to the wild-type spike-only condition n=6 +- SD. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 D614G 81 86 S;S;N 67;167;112 72;172;113 33975021 A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern. Sections from the electropherograms obtained by Sanger sequencing showing the E484K and N501Y VOC-associated mutations (C). 2021 Infection, genetics and evolution Figure SARS_CoV_2 E484K;N501Y 78;88 83;93 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. c Spike D614G evolutionary context. 2021 Nature communications Figure SARS_CoV_2 D614G 8 13 S 2 7 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Sarbecovirus alignment (text) surrounding spike-protein D614G amino-acid-changing SNV, which rose in frequency in multiple geographic locations suggesting increased transmissibility. 2021 Nature communications Figure SARS_CoV_2 D614G 56 61 S 42 47 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. This A-to-G SNV disrupts a perfectly conserved nucleotide (bold font, A-to-G), which disrupts a perfectly conserved amino-acid (red box, D-to-G), in a perfectly conserved 11-amino-acid region (dotted black box, light-green = synonymous-substitutions) across bat-host sarbecoviruses, suggesting D614G might represent a human-host-adaptive mutation. 2021 Nature communications Figure SARS_CoV_2 D614G 294 299 33977858 A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. Melting profiles for E484WT and E484K (left panel), and those for N501WT and N501Y (right panel). 2021 Emerging microbes & infections Figure SARS_CoV_2 E484K;N501Y 32;77 37;82 33983915 Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant - New York City, New York, January 1-April 5, 2021. Number of specimens undergoing whole genome sequencing* (A) and percentage of specimens with B1.526 variant with or without E484K mutation, B.1.1.7 variant, and other variants of concern or interest (B), by week of specimen collection : New York City, New York, January 1-April 5, 2021. 2021 MMWR. Morbidity and mortality weekly report Figure SARS_CoV_2 E484K 124 129 33983915 Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant - New York City, New York, January 1-April 5, 2021. This two-part figure includes a bar graph and line graph showing, by week, the total number of specimens undergoing whole genome sequencing in New York City, New York, during January 1-April 5, 2021, and the percentage of specimens with the B.1.1.7 variant, the B1.526 variant with or without the E484K mutation, and other variants of concern. 2021 MMWR. Morbidity and mortality weekly report Figure SARS_CoV_2 E484K 297 302 33991677 Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage. Map of the nucleotide and aa substitutions and deletions of the new variant along the SARS-CoV-2 genome (a) and three-dimensional structure of the spike protein showing aa substitutions and deletions in various spike N501Y variants (b). 2021 Clinical microbiology and infection Figure SARS_CoV_2 N501Y 217 222 S;S 147;211 152;216 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. E484K/Q are present in the GSAID database; other unlabeled bars have not been observed in nature. 2021 Journal of molecular biology Figure SARS_CoV_2 E484K;E484Q 0;0 7;7 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Local conformational distortions induced by single Spike mutations N440K (a) and G476S (b) and their associated normalized affinities. 2021 Journal of molecular biology Figure SARS_CoV_2 G476S;N440K 81;67 86;72 S 51 56 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Mutations L472F, L472P and Y442F/L472F produced local conformational distortions at the interaction interface (S-cyan, hACE2-green), whereas mutations Y442, N479K, D480G, and T487S do not structurally perturb the wild-type complex (S, wheat; hACE2, yellow). 2021 Journal of molecular biology Figure SARS_CoV_2 D480G;L472F;L472P;N479K;T487S;Y442F;L472F 164;10;17;157;175;27;33 169;15;22;162;180;32;38 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. (b) WBP-1 RBD (Q493K/Q498H-RBD) interacts human ACE2. 2021 EBioMedicine Figure SARS_CoV_2 Q493K;Q498H 15;21 20;26 RBD;RBD 10;27 13;30 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. (d) Modelling of WBP-1 RBD (Q493K/Q498H-RBD) shows interaction with mouse ACE2. 2021 EBioMedicine Figure SARS_CoV_2 Q493K;Q498H 28;34 33;39 RBD;RBD 23;40 26;43 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. The sensors were dipped in hACE2-hFC and functionalized sensorgrams captured upon incubation of Q493K-RBD (i), Q498H-RBD (j), Q493K/Q498H-RBD (k), and WT-RBD (l) at 50 (black), 100 (blue), 200 (green), and 400 nM (red). 2021 EBioMedicine Figure SARS_CoV_2 Q493K;Q493K;Q498H;Q498H 96;126;111;132 101;131;116;137 RBD;RBD;RBD;RBD 102;117;138;154 105;120;141;157 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. The sensors were dipped in mACE2-hFC and functionalized sensorgrams captured upon incubation of Q493K-RBD (e), Q498H-RBD (f), Q493K/Q498H-RBD (g), and WT-RBD (h) at 6.25 (black), 12.5 (blue), 25 (green), and 50 nM (red). 2021 EBioMedicine Figure SARS_CoV_2 Q493K;Q493K;Q498H;Q498H 96;126;111;132 101;131;116;137 RBD;RBD;RBD;RBD 102;117;138;154 105;120;141;157 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. (A and B) 1H/15N HSQC NMR spectra of N15A and V25F mutant E proteins (red contours) superimposed on those from the wild-type E protein (black contours), respectively. 2021 PLoS pathogens Figure SARS_CoV_2 N15A;V25F 37;46 41;50 E;E 58;125 59;126 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. (A and B) 1H/15N HSQC NMR spectra of N15A and V25F mutants of E protein in the absence (black contours) and presence (red contours) of HMA, respectively. 2021 PLoS pathogens Figure SARS_CoV_2 N15A;V25F 37;46 41;50 E 62 63 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. (C and D) Chemical shift perturbation plots for the N15A and V25F mutants of E protein, respectively. 2021 PLoS pathogens Figure SARS_CoV_2 N15A;V25F 52;61 56;65 E 77 78 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. (C and D) Chemical shift perturbation plots of the effects of HMA binding to the N15A and V25F mutants of E protein, respectively. 2021 PLoS pathogens Figure SARS_CoV_2 N15A;V25F 81;90 85;94 E 106 107 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. (D) PFO-PAGE of wild-type, N15A mutant, and V25F mutant E proteins. 2021 PLoS pathogens Figure SARS_CoV_2 N15A;V25F 27;44 31;48 E 56 57 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. Comparison of NMR data of N15A and V25F mutants of E protein. 2021 PLoS pathogens Figure SARS_CoV_2 N15A;V25F 26;35 30;39 E 51 52 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. Comparisons of the effects of HMA binding on the NMR spectra of N15A and V25F mutants of E protein. 2021 PLoS pathogens Figure SARS_CoV_2 N15A;V25F 64;73 68;77 E 89 90 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. For E protein, * indicates the N15A mutant and ** indicates the V25F mutant. 2021 PLoS pathogens Figure SARS_CoV_2 N15A;V25F 31;64 35;68 E 4 5 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. The dotted lines indicate 1.5 times the average chemical shift changes of V25F EF by HMA. 2021 PLoS pathogens Figure SARS_CoV_2 V25F 74 78 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. The introduction of P.2 lineage (E484K mutation) is indicated. 2021 BMC genomics Figure SARS_CoV_2 E484K 33 38 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. (C) Neutralization of CV38-142 and COVA1-16 against SARS-CoV-2 wild type, K417N or E484K pseudoviruses. 2021 Science (New York, N.Y.) Figure SARS_CoV_2 E484K;K417N 83;74 88;79 34016740 Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. (D) Neutralization of pseudotyped SARS-CoV-2 virus and variants carrying K417N or E484K mutations. 2021 Science (New York, N.Y.) Figure SARS_CoV_2 E484K;K417N 82;73 87;78 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. Flow cytometric assay of the SARS-CoV-2 RBD and its mutants (K417R, Q498H, and K417R-Q498H) binding to human, mouse, rat, and European hedgehog ACE2s expressed on the cell surface of BHK21 cells. 2021 The EMBO journal Figure SARS_CoV_2 K417R;Q498H;K417R;Q498H 79;68;61;85 84;73;66;90 RBD 40 43 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. Residue Q498H substitution in GD/1/2019 RBD and GX/P2V/2017 RBD strengthens the interaction with the receptor compared with the SARS-CoV-2 RBD. 2021 The EMBO journal Figure SARS_CoV_2 Q498H 8 13 RBD;RBD;RBD 40;60;139 43;63;142 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. The mFc-tagged ACE2s from human, mouse, rat, and European hedgehog were captured by anti-mIgG Fc antibodies immobilized on the CM5 chip, and sequentially tested the binding with serially diluted SARS-CoV-2 RBD and its mutants (K417R, Q498H, and K417R-Q498H). 2021 The EMBO journal Figure SARS_CoV_2 K417R;Q498H;K417R;Q498H 245;234;227;251 250;239;232;256 RBD 206 209 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. a NT50 values for COVID-19 convalescent plasma (CE) and CoronaVac vaccinee plasma (I) using D614G mutant pseudovirus neutralization assay. 2021 Cell research Figure SARS_CoV_2 D614G 92 97 COVID-19 18 26 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. a NT50 values for ZF2001 vaccinee plasma/sera using D614G mutant pseudovirus neutralization assay. 2021 Cell research Figure SARS_CoV_2 D614G 52 57 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. a VSV-pseudovirus neutralization assays measuring neutralizing ability of convalescent plasma against D614G (blue), RBD.V2 (red), and 501Y.V2 (yellow) mutants. 2021 Cell research Figure SARS_CoV_2 D614G 102 107 RBD 116 119 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. b VSV-pseudovirus neutralization assays measuring neutralizing ability of CoronaVac vaccinee plasma against D614G (blue), RBD.V2 (red), and 501Y.V2 (yellow) mutants. 2021 Cell research Figure SARS_CoV_2 D614G 108 113 RBD 122 125 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. c Comparison of anti-IgG ELISA AUC values among RBD.V2 (triangle), D614G (circle), and 242-244Delta (diamond) mutants of S1. 2021 Cell research Figure SARS_CoV_2 D614G 67 72 RBD 48 51 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. c The IC50 values of six potent anti-NTD NAbs against pseudovirus carrying D614G or 242-244Delta. 2021 Cell research Figure SARS_CoV_2 D614G 75 80 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. d NT50 fold-change from D614G to 501Y.V2 for convalescent and CoronaVac vaccinee plasma by pseudovirus neutralization assay. 2021 Cell research Figure SARS_CoV_2 D614G 24 29 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. d NT50 fold-change from D614G to 501Y.V2 for ZF2001 vaccinee plasma/sera by pseudovirus neutralization assay. 2021 Cell research Figure SARS_CoV_2 D614G 24 29 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. f Comparison of NT50 values by pseudovirus or authentic virus neutralization assay between WT/D614G and the indicated mutants for CoronaVac vaccinee plasma samples. 2021 Cell research Figure SARS_CoV_2 D614G 94 99 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. f Comparison of NT50 values by pseudovirus or authentic virus neutralization assay between WT/D614G and the indicated mutants for ZF2001 vaccinee plasma samples. 2021 Cell research Figure SARS_CoV_2 D614G 94 99 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. g Comparison of NT50 values by pseudovirus or authentic virus neutralization assay between WT/D614G and the indicated mutants for CE samples. 2021 Cell research Figure SARS_CoV_2 D614G 94 99 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. g Summary of the fold change of NT50 for the indicated mutants from D614G. 2021 Cell research Figure SARS_CoV_2 D614G 68 73 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. h Summary of the fold change of NT50 for the indicated mutants from D614G. 2021 Cell research Figure SARS_CoV_2 D614G 68 73 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. Pseudovirus neutralization assays measuring plasma neutralizing ability against D614G (blue), RBD.V2 (red), and 501Y.V2 (yellow) mutants. 2021 Cell research Figure SARS_CoV_2 D614G 80 85 RBD 94 97 34033650 SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. (A) 3D structure of the RNA-dependent RNA polymerase where the blue region depicts a more rigid structure due to P323L mutation with an increase in stability of DeltaDeltaG: 0.717 kcal/mol and a decrease in vibrational entropy to DeltaDeltaSVib ENCoM: -0.301 kcal.mol-1.K-1. 2021 PloS one Figure SARS_CoV_2 P323L 113 118 RdRp 24 52 34033650 SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. (A) S protein monomer 6VSB with D614G mutation, the red region of the protein depicts the more flexible region of the protein due to the D614G mutation with a decrease in stability of DeltaDeltaG: -0.086 kcal/mol and an increase in vibrational entropy to DeltaDeltaSVib 0.137 kcal.mol-1.K-1. 2021 PloS one Figure SARS_CoV_2 D614G;D614G 32;137 37;142 S 4 5 34033650 SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. (B) The suggested hydrogen bond can be disrupted with the D614G mutation altering the activity of the protein. 2021 PloS one Figure SARS_CoV_2 D614G 58 63 34033650 SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. 3D modelling of P323L mutation. 2021 PloS one Figure SARS_CoV_2 P323L 16 21 34039497 An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose. (a) Graphical representation of linear DNA construct for mRNA transcription, (b) IVT optimization where Lane 4 is the optimized condition, (c) DNA sequencing electropherogram data of D614G sequence in the target, (d) Identification of purified capped mRNA by SEC-HPLC, (e) size distribution of mRNA-LNP dose formulation. 2021 Vaccine Figure SARS_CoV_2 D614G 183 188 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. Legend to figure: 20AS: clade 20A strain, M1V: Marseille-1 variant, V: Marseille-4 variant, N501YV: N501Y variant. 2021 Clinical microbiology and infection Figure SARS_CoV_2 M1V;N501Y 42;100 45;105 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. The grey zone corresponds to the extrapolated number of cases with other genotypes than clade 20A strain, Marseille-1, Marseille-4 and N501Y variants. 2021 Clinical microbiology and infection Figure SARS_CoV_2 N501Y 135 140 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Bayesian phylogenetic inference of the 134 Brazilian E484K mutated genomes. 2021 Infection, genetics and evolution Figure SARS_CoV_2 E484K 53 58 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Distribution of genomes harboring E484K mutation across different lineages (A) and Brazilian states (B) from October to December 2020. 2021 Infection, genetics and evolution Figure SARS_CoV_2 E484K 34 39 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Histogram of frequent mutations observed in the Brazilian SARS-CoV-2 genomes harboring E484K mutation. 2021 Infection, genetics and evolution Figure SARS_CoV_2 E484K 87 92 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Monthly presence of the E484K mutation considering worldwide available data (A) and Brazilian genomes (B). 2021 Infection, genetics and evolution Figure SARS_CoV_2 E484K 24 29 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. The enlarged panel on the right side shows the interacting residues in colored sticks in which WT RBD is blue, while the E484K mutant variant in magenta. 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 E484K 121 126 RBD 98 101 34049205 Recognition through GRP78 is enhanced in the UK, South African, and Brazilian variants of SARS-CoV-2; An in silico perspective. The superposition of the docked complexes of GRP78 (green) to ACE2 (cyan)-SARS-CoV-2 Spike RBD (red) complex WT and Mutated (E484K). 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 E484K 125 130 S;RBD 85;91 90;94 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. Identification of E484K mutation on the genome of the six isolates as represented by the multiple sequence alignment and Single Nucleotide Polymorphisms analysis. 2021 Microbial pathogenesis Figure SARS_CoV_2 E484K 18 23 34059617 A core-shell structured COVID-19 mRNA vaccine with favorable biodistribution pattern and promising immunity. b Titers of NAbs for neutralizing ability against pseudotype SARS-CoV-2 with indicated mutation points in S protein or were tested against live D614G mutant and wide-type strain (Wuhan/IVDC-HB-01/2019) using plaque reduction neutralization test. 2021 Signal transduction and targeted therapy Figure SARS_CoV_2 D614G 144 149 S 106 107 34059617 A core-shell structured COVID-19 mRNA vaccine with favorable biodistribution pattern and promising immunity. c, e Serum collected at week 5 from two-dose SW0123-immunized mice (n = 5 for each strain) were tested for neutralizing ability against pseudotype SARS-CoV-2 with indicated mutation points in S protein or were tested against live D614G mutant and wide-type strain (Wuhan/IVDC-HB-01/2019) using plaque reduction neutralization test. 2021 Signal transduction and targeted therapy Figure SARS_CoV_2 D614G 230 235 S 192 193 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. (A) Neutralization of B.1.1.7 (Delta69-70/N501Y/P681H), B.1.351, B.1.1.248, mink cluster 5, and COH.20G/677H pseudotypes (top left); individual B.1.1.7 mutations (top right); individual B.1.351 mutations (bottom left); and mink cluster 5 mutation pseudotyped viruses (bottom right) by REGN10987. 2021 mBio Figure SARS_CoV_2 N501Y;P681H 42;48 47;53 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. (B) Neutralization by convalescent-phase donor serum of viruses pseudotyped by N501Y, Delta69-70, B.1.1.7 (Delta69-70/N501Y/P681H), COH.20G/677H, 20A.EU2, and mink cluster 5 spike proteins compared to D614G. 2021 mBio Figure SARS_CoV_2 D614G;N501Y;N501Y;P681H 201;79;118;124 206;84;123;129 S 174 179 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. (B) Neutralization curves of D614G, B.1.1.7 (Delta69-70/N501Y/P681H), B.1.351, B.1.1.248, mink cluster 5, and COH.20G/677H (top left); individual B.1.1.7 mutations (top right); individual B.1.351 mutations (bottom left); and mink cluster 5 mutation pseudotyped viruses (bottom right) by REGN10933. 2021 mBio Figure SARS_CoV_2 D614G;N501Y;P681H 29;56;62 34;61;67 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. (B) Neutralization IC50s of D614G, N501Y, S982A, B.1.1.7 (Delta69-70/N501Y/P681H), COH.20G/677H, 20A.EU2, B.1.351, and B.1.1.248 pseudotypes. 2021 mBio Figure SARS_CoV_2 D614G;N501Y;S982A;N501Y;P681H 28;35;42;69;75 33;40;47;74;80 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. (C, left) Neutralization of virus pseudotyped by the D614G, B.1.351, or E484K spike proteins by convalescent-phase sera. 2021 mBio Figure SARS_CoV_2 D614G;E484K 53;72 58;77 S 78 83 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. (C) Neutralization of D614G, B.1.1.7 (Delta69-70/N501Y/P681H), B.1.351, B.1.1.248, COH.20G/677H, and mink cluster 5 pseudotyped viruses by a 1:1 mixture of REGN10933 and REGN10987. 2021 mBio Figure SARS_CoV_2 D614G;N501Y;P681H 22;49;55 27;54;60 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. (D) Infectivity of D614G; European 20A.EU2; Columbus, OH, COH.20G/677H; and Brazilian B.1.1.248 spike protein-pseudotyped viruses. 2021 mBio Figure SARS_CoV_2 D614G 19 24 S 96 101 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. (D) Neutralization of virus pseudotyped by the D614G and B.1.1.248 spike proteins by convalescent-phase sera. 2021 mBio Figure SARS_CoV_2 D614G 47 52 S 67 72 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. (Right) Comparison of neutralization of B.1.351 spike protein-pseudotyped virus with neutralization of the E484K pseudotype. 2021 mBio Figure SARS_CoV_2 E484K 107 112 S 48 53 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Arrows indicate RBD amino acid residues 417, 453, 484, 486, and 501 and the Delta69-70 and D614G mutations. 2021 mBio Figure SARS_CoV_2 D614G 91 96 RBD 16 19 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Expression vectors for the variant spike proteins or with the individual mutations were generated, each with the D614G mutation and deleted for the carboxy-terminal 19 amino acids. 2021 mBio Figure SARS_CoV_2 D614G 113 118 S 35 40 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The data represent percent infectivities, at each concentration of sACE2, of the spike variants plotted against sACE2 neutralization of D614G pseudotyped virus. 2021 mBio Figure SARS_CoV_2 D614G 136 141 S 81 86 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The neutralization of D614G, B.1.1.7, B.1.351, B.1.1.248, and mink cluster 5 pseudotyped viruses by REGN10933 and REGN10987 was measured. 2021 mBio Figure SARS_CoV_2 D614G 22 27 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. (B) Detection of wild-type ORF8 and its L84S variant via Coomassie brilliant blue staining without dithiothreitol. 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 L84S 40 44 ORF8 27 31 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. (D) 1H nuclear magnetic resonance (NMR) spectra of wild-type ORF8 (WT) and its L84S variant (L84S). 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 L84S;L84S 79;93 83;97 ORF8 61 65 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Detection of wild-type ORF8 and its L84S variant via Coomassie brilliant blue staining. 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 L84S 36 40 ORF8 23 27 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Wild-type ORF8 (left) and the L84S variant (right) were analyzed. 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 L84S 30 34 ORF8 10 14 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. WT, wild-type ORF8; L84S, L84S variant. 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 L84S;L84S 20;26 24;30 ORF8 14 18 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. XVE, transcriptional activator that responds to estrogen; SP, signal peptide of Arabidopsis chitinase; 8His, 8 x His-tag; ORF8; mature ORF8 coding sequence (CDS); ORF8(L84S), ORF8 L84S variant CDS; LBS, LexA binding site; PG10-90, synthetic constitutive promoter; PLexA-46, fusion promoter controlled by XVE; dMP, partial movement protein; SRz, ribozyme sequence from tobacco ringspot virus satellite RNA; 35ST, 35S terminator; RB, right border; and LB, left border. 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 L84S;L84S 180;168 184;172 ORF8;ORF8;ORF8;ORF8;S 122;135;163;175;58 126;139;167;179;60 34087220 Synthetic proteins for COVID-19 diagnostics. Three circulating human variants in the JS7 sequence, L452R (recent California), E484K and N501Y are indicated by red arrows, yellow side chains in the structure above. 2021 Peptides Figure SARS_CoV_2 E484K;L452R;N501Y 81;54;91 86;59;96 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. An allelic discrimination plot of the results, showing the spike variants with W152L (upper), E484K (middle), and G769V (lower). 2021 PLoS pathogens Figure SARS_CoV_2 E484K;G769V;W152L 94;114;79 99;119;84 S 59 64 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. The R.1 lineage acquired its spike W152L and G769V mutations at the root. 2021 PLoS pathogens Figure SARS_CoV_2 G769V;W152L 45;35 50;40 S 29 34 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. The sublineage harbors an ORF1b G814C mutation. 2021 PLoS pathogens Figure SARS_CoV_2 G814C 32 37 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. We analyzed samples of R.1 lineage SARS-CoV-2 (n = 3), which harbors a spike variant with the W152L/E484K/G769V mutations and samples of SARS-CoV-2 without these three mutations (n = 5) using a TaqMan assay. 2021 PLoS pathogens Figure SARS_CoV_2 W152L;E484K;G769V 94;100;106 99;105;111 S 71 76 34098567 Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. Pseudotyped viruses containing E484K or K417N, E484K and N501Y (KEN) also contain the R683G substitution. 2021 Nature Figure SARS_CoV_2 E484K;E484K;K417N;N501Y;R683G 31;47;40;57;86 36;52;45;62;91 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. a, b Multi-step growth curves of recombinant PEDVs (E191A-P1, E191A-P4, and the parental icPC22A) in Vero cells using an MOI of 0.01. 2021 Cell & bioscience Figure SARS_CoV_2 E191A;E191A 62;52 67;57 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Due to the very low infectious titers of E191A-P1, the RNA titers presented in b was employed to interpret the growth kinetics of recombinant PEDVs; c plaques of recombinant PEDVs in Vero cells overlayed with 1.5% agarose. 2021 Cell & bioscience Figure SARS_CoV_2 E191A 41 46 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Genetic instability of E191A mutant. 2021 Cell & bioscience Figure SARS_CoV_2 E191A 23 28 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. In vitro Characterization of the recombinant nsp14-ExoN mutant E191A. 2021 Cell & bioscience Figure SARS_CoV_2 E191A 63 68 Exon 51 55 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Induction of partial protection by E191A-P1 mutant in Gn pigs against icPC22A challenge. 2021 Cell & bioscience Figure SARS_CoV_2 E191A 35 40 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Sanger sequencing showed that E191A-P4 and the fecal sample collected at 2 dpi from the E191A-P1-inoculated pig#8 reverted to wildtype ExoN (GAG) 2021 Cell & bioscience Figure SARS_CoV_2 E191A;E191A 30;88 35;93 Exon 135 139 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Sanger sequencing showed that E191A-P4 and the fecal sample collected at 2 dpi from the E191A-P1-inoculated pig#8 reverted to wildtype ExoN (GAG). 2021 Cell & bioscience Figure SARS_CoV_2 E191A;E191A 30;88 35;93 Exon 135 139 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. The brown signals, indicated by arrows, represented the PEDV antigens in enterocytes and were observed in the icPC22A- and E191A-P1-inoculated, but not in mock piglets. 2021 Cell & bioscience Figure SARS_CoV_2 E191A 123 128 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. (A) Comparison of the binding affinity of prototype S protein and V367F mutant to human ACE2 receptor by ligand-receptor binding ELISA. 2021 Journal of virology Figure SARS_CoV_2 V367F 66 71 S 52 53 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. (B) Comparison of the binding affinity of prototype S protein and V367F mutant to human ACE2 protein by SPR. 2021 Journal of virology Figure SARS_CoV_2 V367F 66 71 S 52 53 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. (C) Quantification of the genome copy number of the V367F mutant versus the prototype using pseudovirus infection assay. 2021 Journal of virology Figure SARS_CoV_2 V367F 52 57 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. All 34 V367F mutants were included. 2021 Journal of virology Figure SARS_CoV_2 V367F 7 12 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Experimental validation of the enhanced affinity and infectivity of the V367F mutant. 2021 Journal of virology Figure SARS_CoV_2 V367F 72 77 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The peak signals of D614G and the other dominant mutations are marked in red. 2021 Journal of virology Figure SARS_CoV_2 D614G 20 25 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The relative fold increases of viruses infecting the cells are shown by the pseudoviral DNA copy number of the V367F mutant in both Vero and Caco-2 cells at 24 h p.i. 2021 Journal of virology Figure SARS_CoV_2 V367F 111 116 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. V367F mutants are marked with red triangles; sampled referenced sequences are annotated in different colors by clades using Figtree 1.4.4 (https://github.com/rambaut/figtree/releases). 2021 Journal of virology Figure SARS_CoV_2 V367F 0 5 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. V367F mutants with the enhanced binding affinity were found on all of the four continents and are marked in red. 2021 Journal of virology Figure SARS_CoV_2 V367F 0 5 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. (A) Schematic showing the application of RAY for distinguishing variants WT and N501Y using electrophoresis, key steps in the process are shown. 2021 eLife Figure SARS_CoV_2 N501Y 80 85 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. (B) Reproducibility in output on multiple runs of RAY on the same samples (WT or N501Y) showing high concordance between assays (n = 10 RAY replicates from same sample). 2021 eLife Figure SARS_CoV_2 N501Y 81 86 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. (B) Schematic for detecting the N501Y through a single amplicon RAY on a lateral flow assay is shown. 2021 eLife Figure SARS_CoV_2 N501Y 32 37 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. (E) Representative image showing the limit of detection of RAY for serial dilutions of patient samples (N501Y or WT as indicated). 2021 eLife Figure SARS_CoV_2 N501Y 104 109 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. (F) Graph showing the distribution of sequenced confirmed WT (cyan dot) and N501Y (red triangle) containing patient samples detected through RAY. 2021 eLife Figure SARS_CoV_2 N501Y 76 81 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. (G) RAY outcomes on E484K and T716I mutations from patient samples. 2021 eLife Figure SARS_CoV_2 E484K;T716I 20;30 25;35 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. (H) Outcome of RAY showing minimal cross-reactivity of N501Y sgRNA on the E484K amplicon. 2021 eLife Figure SARS_CoV_2 E484K;N501Y 74;55 79;60 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. (I) Increased signal intensity of N501Y RAY on patient samples upon using phosphorothioate modified synthetic sgRNA as compared to in vitro synthesized sgRNA. 2021 eLife Figure SARS_CoV_2 N501Y 34 39 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Adaptation of RAY for identification of N501Y mutation. 2021 eLife Figure SARS_CoV_2 N501Y 40 45 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Distinct bands on the streptavidin line (test line) characterize CoV-2 negative, CoV-2 wild type and CoV2 N501Y variants. 2021 eLife Figure SARS_CoV_2 N501Y 106 111 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Dotted line depicts the cut-off for N501Y sgRNA. 2021 eLife Figure SARS_CoV_2 N501Y 36 41 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Positions of primers and sgRNAs for the N501Y sgRNA and WT S-gene sgRNA are shown. 2021 eLife Figure SARS_CoV_2 N501Y 40 45 S 59 60 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. Red dotted box shows the optimal amplification conditions for successful discrimination of WT and N501Y samples. 2021 eLife Figure SARS_CoV_2 N501Y 98 103 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. The N501Y mutation position is shown in raised font. 2021 eLife Figure SARS_CoV_2 N501Y 4 9 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. The uncleaved band represents the amplicon from either the WT or N501Y sample, cleavage occurs only in the N501Y sample. 2021 eLife Figure SARS_CoV_2 N501Y;N501Y 65;107 70;112 34109885 SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. Timeline of emergence of human-derived (above the timeline) and mink-derived (below the timeline) SARS-CoV2 spike protein N501T-G142D and N501T-G142D-F486L variants in the United States. 2021 Journal of veterinary diagnostic investigation Figure SARS_CoV_2 N501T;N501T;F486L;G142D;G142D 122;138;150;128;144 127;143;155;133;149 S 108 113 34114829 Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study. Detailing of the aspartic acid 30 substitution by glutamic acid in modification 15. 2021 The journal of physical chemistry. B Figure SARS_CoV_2 D30E 17 63 34114829 Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study. Most persistent interactions (>10% of simulation time) from modification 11 (A) and modification 15 (B) with viral RBD containing the mutation E484K. 2021 The journal of physical chemistry. B Figure SARS_CoV_2 E484K 143 148 RBD 115 118 34119826 Therapeutic effect of CT-P59 against SARS-CoV-2 South African variant. In addition, serially diluted CT-P59 mixed with D614G (black circle) or 501Y.V2 (red rectangle) variant pseudovirus. 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 D614G 48 53 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. (A) SARS-CoV-2 pseudovirus neutralization assay of four RmAbs (9H1, 1H1, 5E1 and 7G5) against wild type (WT) strain, the D614G variant, the B.1.1.7 variant, the B.1.429 variant, the P.1 variant, the B.1.526 variant, and the B.1.351 variant. 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 121 126 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. (B) RmAbs have different recognition of RBD and RBD mutants including RBD N501Y, RBD K417N, RBD E484K, and RBD N501Y/K417N/E481K. 2021 Emerging microbes & infections Figure SARS_CoV_2 E484K;K417N;N501Y;N501Y;E481K;K417N 96;85;74;111;123;117 101;90;79;116;128;122 RBD;RBD;RBD;RBD;RBD;RBD 40;48;70;81;92;107 43;51;73;84;95;110 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. The Phylogenetic tree of one mutation (T393P, in blue color) predicted to may play a role in structure damage according to Genome Detective Coronavirus Typing Tool is shown. 2021 Bioinformatics and biology insights Figure SARS_CoV_2 T393P 39 44 34121839 Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2. These mutations are D614G(A), T393P(B), M177I(C), P507S(D), P295H(E), L293M(F), G75V(G), G143V)(H), T95I(I) respectively.According to bioinformatics analysis, these mutations might affect the structure of the spike protein. 2021 Bioinformatics and biology insights Figure SARS_CoV_2 D614G;G143V;G75V;L293M;M177I;P295H;P507S;T393P;T95I 20;89;80;70;40;60;50;30;100 25;94;84;75;45;65;55;35;104 S 209 214 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. (A) Shows the alignment for the 69/70 deletion assay; (B) shows the alignment for the K417N mutation assay; (C) shows the alignment for the E484K/N501Y assay. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 E484K;K417N;N501Y 140;86;146 145;91;151 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. (A) The curves of four independent reactions are shown; the purple curves with a lower Cq value show the forward primer amplification directed to the sequence without K417N mutation (Reaction 1) in a sample of COVID-19 patients or control C+ without-Mut. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 K417N 167 172 COVID-19 210 218 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. (A) The green curve shows the amplification of the probe directed to the sequence without the E484K mutation (FAM), while the signal by the probe directed to the sequence that presents the mutation remains without amplification signal; (B) the orange curve shows the amplification of the probe directed to the E484K mutation (CFR 610), while the probe directed to the sequence without mutation remains without amplification signal; (C) the blue curve shows the amplification of the probe directed to the sequence without mutation N501Y (HEX), while the probe directed to the sequence with the mutation remains without amplification signal; (D) the purple curve shows the amplification of the probe directed to the mutation N501Y (Quasar670) with the control containing the mutation (C+ Mut484-501-417), while the probe directed to the sequence without the mutation remains without amplification signal. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 E484K;E484K;N501Y;N501Y 94;310;530;723 99;315;535;728 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. (B) The purple curves with a lower Cq value show the amplification of the forward primer directed to the K417N mutation (417N Fw) (Reaction 2) using synthetic control C+ Mut484-501-417 (which contains the mutation). 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 K417N 105 110 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Amplification curves for the K417N assay. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 K417N 29 34 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Amplification curves of the E484K/N501Y Assay. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 E484K;N501Y 28;34 33;39 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Detection of E484K and N501Y mutations. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 E484K;N501Y 13;23 18;28 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. The first 4 samples show the E484K mutation, and the fifth is a wild-type sample. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 E484K 29 34 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. The green curve corresponds to the probe that detects the sequence without the E484K mutation (Probe 484E); the red curve corresponds to the probe that detects the sequence with the E484K mutation (Probe 484K); the blue curve corresponds to the probe that detects the sequence without the N501Y mutation, and the purple curve corresponds to the probe that detects the sequence with the N501Y mutation. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 E484K;E484K;N501Y;N501Y 79;182;289;386 84;187;294;391 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. (A) Percentages of B.1.1.7 (blue) or B.1.1.7-M:V70L (orange) isolates that carried the S:D178H mutation from January to April 2021 in US and globally, respectively. 2021 Emerging microbes & infections Figure SARS_CoV_2 D178H;V70L 89;47 94;51 S 87 88 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. (B) Percentages of B.1.1.7 isolates that carried the S:D178H mutation from September 2020 to April 2021 in California. 2021 Emerging microbes & infections Figure SARS_CoV_2 D178H 55 60 S 53 54 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. (C) Percentages of B.1.1.7 isolates that carried the S:D178H mutation from January 2021 to April 2021 in Washington. 2021 Emerging microbes & infections Figure SARS_CoV_2 D178H 55 60 S 53 54 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Branching off a sub-lineage of B.1.1.7 that is distinguished by the M:V40L mutation because of the emergence of the S:D178H mutation on 23 January 2021 as estimated. 2021 Emerging microbes & infections Figure SARS_CoV_2 D178H;V40L 118;70 123;74 S 116 117 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. D178H is in close proximity to other amino acids in the NTD that are affected in the B.1.1.7 lineage, HV69-70del and Y144/Y145del (top right). 2021 Emerging microbes & infections Figure SARS_CoV_2 D178H 0 5 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Prevalence of the B.1.1.7 sub-lineage carrying mutation S:D178H Globally, US, Washington, and California. 2021 Emerging microbes & infections Figure SARS_CoV_2 D178H 58 63 S 56 57 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Structural location of the D178H and other spike protein mutations in the B.1.1.7 lineage. 2021 Emerging microbes & infections Figure SARS_CoV_2 D178H 27 32 S 43 48 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. The inset provides more information about the branching S:D178H mutation, namely the genomic position, the inferred date, the data confidence interval, and the likely states of origin. 2021 Emerging microbes & infections Figure SARS_CoV_2 D178H 58 63 S 56 57 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Transmission of the 1026 B.1.1.7-MV70L-S:D178H isolates across the US. 2021 Emerging microbes & infections Figure SARS_CoV_2 D178H 41 46 S 39 40 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. (A) Deletion of nucleotides 21765 to 21770 (deletion of amino acids HV69-70); (B) deletion of nucleotides 21991 to 21993 (deletion of amino acid Y144); (C) mutation A23063T (amino acid change N501Y); (D) mutation C23271A (amino acid change A570D). 2021 mSystems Figure SARS_CoV_2 A23063T;A570D;C23271A;N501Y 165;240;213;192 172;245;220;197 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. The location of selected amino acid substitutions found in SARS-CoV-2 B.1.1.7 variant are shown in red; mutations found at low frequency in viral RNAs from sewage are indicated in pink, and the position of mutation E484K present in B.1.351 and P.1 VOCs is shown in yellow. 2021 mSystems Figure SARS_CoV_2 E484K 215 220 34129831 Antibody Responses After mRNA-Based COVID-19 Vaccination in Residential Older Adults: Implications for Reopening. Spearman correlation scatter plot of Beckman Coulter extinction coefficients (x-axis) by D614 G NT50 pseudovirus (left side, y-axis) and B.1.1.7 (UK) NT50 pseudovirus (right side, y-axis). 2021 Journal of the American Medical Directors Association Figure SARS_CoV_2 D614G 89 95 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. (B) District wise distribution of SGTF cases which are sequenced and having N501Y mutation. 2021 Frontiers in public health Figure SARS_CoV_2 N501Y 76 81 34138474 High-resolution melting curve FRET-PCR rapidly identifies SARS-CoV-2 mutations. (B) RT FRET-PCRs of the clinical samples from a cat and people all had a T m of around 54.3 C with this RT FRET-PCR indicating the presence of the C14408T mutation. 2021 Journal of medical virology Figure SARS_CoV_2 C14408T 147 154 34138474 High-resolution melting curve FRET-PCR rapidly identifies SARS-CoV-2 mutations. (B) RT FRET-PCRs of the clinical samples from a cat and people all had a T m of around 58.2 C indicating the presence of the A23403G mutation. 2021 Journal of medical virology Figure SARS_CoV_2 A23403G 125 132 34138474 High-resolution melting curve FRET-PCR rapidly identifies SARS-CoV-2 mutations. Melting temperature (T m) analysis of SARS-CoV-2 controls and feline and human isolates with an RT-FRET-PCR for the A23403G mutation. 2021 Journal of medical virology Figure SARS_CoV_2 A23403G 116 123 34138474 High-resolution melting curve FRET-PCR rapidly identifies SARS-CoV-2 mutations. Melting temperature (T m) analysis of SARS-CoV-2 controls and feline and human isolates with an RT-FRET-PCR for the C14408T mutation. 2021 Journal of medical virology Figure SARS_CoV_2 C14408T 116 123 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. For RBD K417N vs WT, p = 0.0495; vs L452R, p = 0.0451; and vs E484K/K417N/N501Y, p = 0.0128. 2021 Scientific reports Figure SARS_CoV_2 E484K;K417N;L452R;K417N;N501Y 62;8;36;68;74 67;13;41;73;79 RBD 4 7 34141447 Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2. (F)MHV-A59 (NC_048217.1); aHuCoV-HKU1 (NC_006577.2); bBCoV-2014-13 (KX982264.1); cDromedary camel CoV (DcCoV)-HKU23; dHuCoV-OC43-ATCC/VR759 (NC_006213.1); eEqCoV-NC99 (EF446615.1); fRbCoV-HKU14 (NC_017083.1); gMHV-3 (FJ647224.1); hBetaCoV-HKU24-R05005I (NC_026011.1). 2021 Virus evolution Figure SARS_CoV_2 R05005I 245 252 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Among these mutations, the most representative ones are substitution mutations such as D614G, N501Y, Y453F, N439K/R, P681H, K417N/T, and E484K, and deletion mutations of DeltaH69/V70 and Delta242-244. 2021 Infection, genetics and evolution Figure SARS_CoV_2 D614G;E484K;K417N;K417T;N439K;N439R;N501Y;P681H;Y453F 87;137;124;124;108;108;94;117;101 92;142;131;131;115;115;99;122;106 34146731 Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic. Three mutations, D614G, N501Y, and E484K, confer the virus with enhanced infectivity, transmissibility, and resistance to neutralization. 2021 Infection, genetics and evolution Figure SARS_CoV_2 D614G;E484K;N501Y 17;35;24 22;40;29 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. B-H) Global distribution of (represented by percentage frequency) highly recurring mutations: B) Nsp2:T85I, C) Nsp6:L37F, D) Nsp12:P323L, E) Spike:D614G, F) ORF3a:Q57H, G) N protein:R203K and H) N protein:G204R. 2021 Infection, genetics and evolution Figure SARS_CoV_2 D614G;G204R;L37F;P323L;Q57H;R203K;T85I 147;205;116;131;163;182;102 152;210;120;136;167;187;106 S;ORF3a;Nsp12;Nsp2;Nsp6;N;N 141;157;125;97;111;172;195 146;162;130;101;115;173;196 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. Binding interactions around residue 106 in the heavy chain of P2B-2F6 WT (A) and H:V106R (B), H:V106R/H:P107Y (C) mutants with SARS-CoV-2 RBD. 2021 Computers in biology and medicine Figure SARS_CoV_2 P107Y;V106R;V106H;V106R 104;83;96;96 109;88;103;103 RBD 138 141 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. P2B-2F6, H:V106R and H:V106R/H:P107Y mutants are shown in cyan, purple and yellow, respectively. 2021 Computers in biology and medicine Figure SARS_CoV_2 P107Y;V106R;V106R;V106H 31;11;23;23 36;16;30;30 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. The hydrophobic patches in the CDR regions of WT P2B-2F6 (A), H:V106R (B) and H:V106R/H:P107Y (C) mutants. 2021 Computers in biology and medicine Figure SARS_CoV_2 P107Y;V106R;V106R;V106H 88;64;80;80 93;69;87;87 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. The horizontal red line highlights the RBD variants (K417T, E484K, and N501Y) that disrupt the binding of the largest number of NAbs. 2021 Frontiers in immunology Figure SARS_CoV_2 E484K;N501Y;K417T 60;71;53 65;76;58 RBD 39 42 34161095 Allosteric Cross-Talk among Spike's Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor. The three N501Y, E484K, and K417N mutations sites are circled in red, yellow, and black, respectively. 2021 The journal of physical chemistry letters Figure SARS_CoV_2 E484K;K417N;N501Y 17;28;10 22;33;15 34161337 SARS-CoV-2 uses major endothelial integrin alphavbeta3 to cause vascular dysregulation in-vitro during COVID-19. Sequence comparison between SARS-CoV and SARS-CoV-2 highlights the novel K403R mutagenesis. 2021 PloS one Figure SARS_CoV_2 K403R 73 78 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. (A and B) Maximum-likelihood phylogeny of global sequences carrying Spike mutant (A) N439K and (B) Y453F. 2021 Cell reports Figure SARS_CoV_2 N439K;Y453F 85;99 90;104 S 68 73 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. (A) Maximum-likelihood phylogeny of global SARS-CoV-2 whole-genome sequences, highlighting those with specific mutations in spike: DeltaH69/V70, N439K, Y453F, and N501Y. 2021 Cell reports Figure SARS_CoV_2 N439K;N501Y;Y453F 145;163;152 150;168;157 S 124 129 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. (B and C) Cumulative occurrences of SARS-CoV-2 sequences with DeltaH69/V70 by month for (B) DeltaH69/V70 with or without N439K/Y453F and (C) DeltaH69/V70 with N501Y. 2021 Cell reports Figure SARS_CoV_2 N439K;N501Y;Y453F 121;159;127 126;164;132 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. (B) Representative infectivity of B.1.1.7 with replacement of H69 and V70 versus B.1.1.7 containing spike DeltaH69/V70 and WT (D614G) spike; single-round infection by luciferase-expressing lentiviruses pseudotyped with SARS-CoV-2 spike protein on HeLa cells transduced with ACE2. 2021 Cell reports Figure SARS_CoV_2 D614G 127 132 S;S;S 100;134;230 105;139;235 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. (C-E) Western blots and quantification of virions with infectivity shown in (B) and of cell lysates of HEK293T producer cells following transfection with plasmids expressing lentiviral vectors and SARS-CoV-2 S DeltaH69/V70 versus the WT (all with D614G), probed with antibodies for HIV-1 p24 and SARS-Cov-2 S2 (C). 2021 Cell reports Figure SARS_CoV_2 D614G 247 252 S 208 209 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. (C) Neutralization of spike DeltaH69/V70 PV and WT (D614G background) by convalescent sera from 15 donors. 2021 Cell reports Figure SARS_CoV_2 D614G 52 57 S 22 27 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. (D) Infectivity of spike (D614G) DeltaH69/V70 in the absence and presence of spike RBD mutations. 2021 Cell reports Figure SARS_CoV_2 D614G 26 31 S;S;RBD 19;77;83 24;82;86 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. (F and G) Densitometric quantification of the (F) spike:p24 and (G) cleaved S2 spike:FL spike ratios for spike (D614G) DeltaH69/V70 in the absence and presence of spike RBD mutations across multiple experiments in pelleted viruses. 2021 Cell reports Figure SARS_CoV_2 D614G 112 117 S;S;S;S;S;RBD 50;79;88;105;163;169 55;84;93;110;168;172 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. (G) Western blots of virions and cell lysates of H1299 lung epithelial producer cells following transfection with plasmids expressing lentiviral vectors and SARS-CoV-2 S DeltaH69/V70 versus the WT (all with D614G). 2021 Cell reports Figure SARS_CoV_2 D614G 207 212 S 168 169 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. All sequences in the GISAID database containing S:439K or S:Y453F (February 18, 2021) were downloaded, realigned to Wuhan-Hu-1 using MAFFT, and deduplicated. 2021 Cell reports Figure SARS_CoV_2 Y453F 60 65 S;S 48;58 49;59 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. DeltaH69/V70 appears after spike N439K and Y453F and compensates for their reduced infectivity. 2021 Cell reports Figure SARS_CoV_2 N439K;Y453F 33;43 38;48 S 27 32 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Grey bars on the right show the presence or absence of the DeltaH69/V70 and amino acid variants N439K, Y453F, and N501Y. 2021 Cell reports Figure SARS_CoV_2 N439K;N501Y;Y453F 96;114;103 101;119;108 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. In target cells, camostat inhibits TMPRSS2 and, therefore, cell fusion at the plasma membrane, and E64D blocks cathepsins and targets endocytic viral entry (right panel). 2021 Cell reports Figure SARS_CoV_2 E64D 99 103 Membrane 85 93 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. S pseudotyped lentiviruses bearing WT S, DeltaH69/V70 S, or VSV-G were used to transduce 293T-ACE2 or 293T-ACE2/TMPRSS2 cells in the presence of E64D or camostat at different drug concentrations. 2021 Cell reports Figure SARS_CoV_2 E64D 145 149 S;S;S 0;38;54 1;39;55 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. (C and D) The fold changes in neutralizing activity, measured by half-maximal inhibitory concentration (IC50) (C), and in binding activity, measured by mean fluorescence intensity (MFI), relative to that of WT D614G. 2021 Immunity Figure SARS_CoV_2 D614G 210 215 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The fold change in ID50 between mutant and WT D614G pseudoviruses is shown by overall average at the top in (A) or individually in (C). 2021 Immunity Figure SARS_CoV_2 D614G 46 51 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. The values show the fold changes in luciferase activity for each indicated mutant pseudovirus variant compared with WT D614G. 2021 Immunity Figure SARS_CoV_2 D614G 119 124 34168138 The architecture of the SARS-CoV-2 RNA genome inside virion. b The A-to-G transition (D614G mutant) at 23,403 nt remodels two bulge structures into a single six-nucleotide bulge. 2021 Nature communications Figure SARS_CoV_2 D614G 25 30 34168138 The architecture of the SARS-CoV-2 RNA genome inside virion. c-e The D614G accompanying mutations have no influence on duplexes except for the C14408U transition (e). 2021 Nature communications Figure SARS_CoV_2 D614G 8 13 34168138 The architecture of the SARS-CoV-2 RNA genome inside virion. D614G and the accompanying mutations on structure remodeling. 2021 Nature communications Figure SARS_CoV_2 D614G 0 5 34168138 The architecture of the SARS-CoV-2 RNA genome inside virion. The C241U, C3037U, C14408U, and A23403G (D614G) mutants are marked as solid lines. 2021 Nature communications Figure SARS_CoV_2 A23403G;D614G 32;41 39;46 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. (E) Positive control demonstrates amplification for AA69-70del and N501Y mutation and (G) B.1.1.7 Negative control (Non-B.1.1.7 SARS-CoV-2 and water) shows no amplification for AA69-70del and N501Y mutation for RT-ddPCR amplicon set 1. 2021 Journal of medical virology Figure SARS_CoV_2 N501Y;N501Y 67;192 72;197 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. (F) Positive control demonstrates amplification for AA145 deletion and S982A mutation and (H) B.1.1.7 Negative control (Non-B.1.1.7 SARS-CoV-2 and water) shows no amplification for AA145 deletion and S982A mutation for RT-ddPCR amplicon set 2. 2021 Journal of medical virology Figure SARS_CoV_2 S982A;S982A 71;200 76;205 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. Both SGTF samples that genotyped as B.1.1.7 lineage by RT-ddPCR were also sequenced and clustered with N501Y.V1 clades in the United States. 2021 Journal of medical virology Figure SARS_CoV_2 N501Y 103 108 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. Variant Sample #2 (55545) have amplification for AA145 deletion and S982A mutation. 2021 Journal of medical virology Figure SARS_CoV_2 S982A 68 73 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. Variant Sample #2 (55545) have amplification for AA69-70del and N501Y mutation. 2021 Journal of medical virology Figure SARS_CoV_2 N501Y 64 69 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. (A and C) Distribution of the L452R and Y453F mutants during the pandemic. 2021 Cell host & microbe Figure SARS_CoV_2 L452R;Y453F 30;40 35;45 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. (B and D) Epidemic dynamics of the L452R-harboring B.1.427/429 lineage in California, USA (B, top) and the USA (B, bottom), and the Y453F-harboring B.1.1.298 lineage in Denmark (D). 2021 Cell host & microbe Figure SARS_CoV_2 L452R;Y453F 35;132 40;137 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. (G) Distribution of the L452R and Y453F mutants during the pandemic. 2021 Cell host & microbe Figure SARS_CoV_2 L452R;Y453F 24;34 29;39 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. (G) Gain of electrostatic complementarity by the L452R substitution. 2021 Cell host & microbe Figure SARS_CoV_2 L452R 49 54 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Chromatograms of nucleotide positions 22,913-22,924 (left) and 23,060-23,068 (right) of parental SARS-CoV-2 (strain WK-521; GISAID ID: EPI_ISL_408667) and the L452R (T22917G in nucleotide), Y453F (A22920T in nucleotide), and N501Y (A23063T in nucleotide) mutants are shown. 2021 Cell host & microbe Figure SARS_CoV_2 L452R;N501Y;Y453F;A22920T;A23063T;T22917G 159;225;190;197;232;166 164;230;195;204;239;173 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. HLA-A24-positive CTL lines of eight COVID-19 convalescent donors were stimulated with 1 nM NF9 peptide or its derivatives: NF9-L452R (NYNYRYRLF) and NF9-Y453F (NYNYLFRLF). 2021 Cell host & microbe Figure SARS_CoV_2 L452R;Y453F 127;153 132;158 COVID-19 36 44 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. In (E and F), statistically significant differences (*p < 0.05) versus parental S (E) and the D614G mutant (F) at the same dose were determined by Student's t test. 2021 Cell host & microbe Figure SARS_CoV_2 D614G 94 99 S 80 81 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Note that an L452R variant isolated from gorillas and three Y453F variants isolated from cats are not included. 2021 Cell host & microbe Figure SARS_CoV_2 L452R;Y453F 13;60 18;65 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Parental SARS-CoV-2 and the L452R, Y453F, and N501Y mutants (100 plaque-forming units [PFU]) were inoculated into HEK293-ACE2 cells (I and J), A549-ACE2 cells (K), and VeroE6/TMPRSS2 cells (L), and the copy number of viral RNA in the culture supernatant was quantified by real-time PCR. 2021 Cell host & microbe Figure SARS_CoV_2 L452R;N501Y;Y453F 28;46;35 33;51;40 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Parental virus and the L452R mutant were mixed at a 1:1 ratio based on PFU, and the mixture was inoculated into HEK293-ACE2 cells. 2021 Cell host & microbe Figure SARS_CoV_2 L452R 23 28 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Right: Coulombic surface coloring of the structures of SARS-CoV-2 S and ACE2 (PDB: 6M17) (top) and a model of the L452R substitution (bottom). 2021 Cell host & microbe Figure SARS_CoV_2 L452R 114 119 S 66 67 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Shown are the top five countries where variants harboring the L452R (top) and Y453F (bottom) mutations are found. 2021 Cell host & microbe Figure SARS_CoV_2 L452R;Y453F 62;78 67;83 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. The HIV-1-based reporter virus pseudotyped with the parental SARS-CoV-2 S or its derivatives (E, L452R, Y453F, and N501Y; F, D614G, B.1.429 [S13I/W152C/L452R/D614G], and B.1.1.298 [HV69-70del/Y453F/D614G]) was inoculated into HEK293 cells transiently expressing human ACE2 and TMPRSS2 at four different doses (1, 3, 5, and 10 ng p24 antigens). 2021 Cell host & microbe Figure SARS_CoV_2 D614G;L452R;N501Y;Y453F;D614G;D614G;L452R;W152C;Y453F;S13I 125;97;115;104;158;198;152;146;192;141 130;102;120;109;163;203;157;151;197;145 S 72 73 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. The PANGO lineages harboring L452R (A and B) and Y453F (C and D) and their epidemic dynamics are summarized. 2021 Cell host & microbe Figure SARS_CoV_2 L452R;Y453F 29;49 34;54 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. The percentage of L452R mutant at each time point was analyzed as described in STAR Methods. 2021 Cell host & microbe Figure SARS_CoV_2 L452R 18 23 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. The top five PANGO lineages (https://cov-lineages.org/index.html) that harbor the L452R (A) and Y453F (C) mutations are shown. 2021 Cell host & microbe Figure SARS_CoV_2 L452R;Y453F 82;96 87;101 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. A) Distribution of deposited GISAID genomes with the D399N mutation across the globe. 2021 Journal of clinical virology Figure SARS_CoV_2 D399N 53 58 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. B) Distribution of deposited GISAID genomes with the D399N mutation over time. 2021 Journal of clinical virology Figure SARS_CoV_2 D399N 53 58 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. D399N in the context of other N gene mutations in deposited GISAID consensus sequences. 2021 Journal of clinical virology Figure SARS_CoV_2 D399N 0 5 N 30 31 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Highlighted in orange are the genomes with D399N without any co-occurring N gene mutations. 2021 Journal of clinical virology Figure SARS_CoV_2 D399N 43 48 N 74 75 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Matrix shows co-occurrences of D399N with other N gene mutations, sorted in descending frequency from left to right, with frequencies plotted above as a bar plot. 2021 Journal of clinical virology Figure SARS_CoV_2 D399N 31 36 N 48 49 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Prevalence of D399N mutations in deposited GISAID consensus sequences. 2021 Journal of clinical virology Figure SARS_CoV_2 D399N 14 19 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. To evaluate N protein expression, total protein normalized lysates from 293T cells transfected with N Wuhan-Hu-1 (WT), N T205I, N D399N, N T205I/D399M, or empty vector and either 250 ng, 125 ng, or 62.5 ng of recombinant N were subjected to SDS-PAGE followed by alphaN western blot. 2021 Journal of clinical virology Figure SARS_CoV_2 D399N;T205I;T205I;D399M 130;121;139;145 135;126;144;150 N;N;N;N;N;N 12;100;119;128;137;221 13;101;120;129;138;222 34179666 Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Community analysis and structural community maps in the SARS-CoV-2 S-D614 and S-D614G mutant structures. 2021 ACS omega Figure SARS_CoV_2 D614G 80 85 S;S 67;78 68;79 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. The SARS-CoV-2 N501YPCR targeting the receptor binding domain (RBD) is specifically designed for detecting the N501Y SNP. 2021 Journal of clinical virology Figure SARS_CoV_2 N501Y 111 116 RBD;RBD 38;63 61;66 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. A Neutralization titres of initially seronegative vaccinees (n = 169) for D614G variants FIN-25 and SR121, and 85HEL (B.1.1.7) and HEL12-102 (B.1.351) variants before (0d), three (3wk), and six weeks (6wk) after the first dose of BNT162b2 vaccine and neutralization titres of convalescent sera of non-hospitalized patients (Conv, n = 50). 2021 Nature communications Figure SARS_CoV_2 D614G 74 79 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. Comparison between two D614G virus isolates, FIN-25 and SR121, was done with sera from 86 BNT162b2 vaccinees. 2021 Nature communications Figure SARS_CoV_2 D614G 23 28 34184982 Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. Weekly numbers of genomes with the wild type genome (D614) or the D614G mutant in the spike protein. 2021 Microbial genomics Figure SARS_CoV_2 D614G 66 71 S 86 91 34188167 Activation of NF-kappaB and induction of proinflammatory cytokine expressions mediated by ORF7a protein of SARS-CoV-2. Single amino acid change (G251V) was identified in clade V. 2021 Scientific reports Figure SARS_CoV_2 G251V 26 31 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. inoculation with 103 PFU of WA1/2020-E484K/N501Y/D614G. 2021 Cell host & microbe Figure SARS_CoV_2 D614G;N501Y;E484K 49;43;37 54;48;42 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. LCB1v1.3 protects mice against B.1.1.7 variant and WA1/2020 E484K/N501Y/D614G strains. 2021 Cell host & microbe Figure SARS_CoV_2 E484K;D614G;N501Y 60;72;66 65;77;71 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. (B) Mutant V483A. 2021 Future virology Figure SARS_CoV_2 V483A 11 16 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. (B) The docked pose of mutant V483A RBD interacting with human ACE2 receptor helix 1. 2021 Future virology Figure SARS_CoV_2 V483A 30 35 RBD 36 39 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. (C & D) Represents the ball and stick model of interacting amino acids of wild-type and V483A mutant, respectively, where aa in blue belongs to S protein, and green belongs to human ACE2 receptor. 2021 Future virology Figure SARS_CoV_2 V483A 88 93 S 144 145 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. The wild strain from China, Wuhan got mutated and transmitted to various parts of the world as a V483A variant. 2021 Future virology Figure SARS_CoV_2 V483A 97 102 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. SARS-CoV-2 S-protein D614G variant shows increased infectivity. 2021 Scientific reports Figure SARS_CoV_2 D614G 21 26 S 11 12 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Structural implications of the D614G mutation in S-protein. 2021 Scientific reports Figure SARS_CoV_2 D614G 31 36 S 49 50 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Structural implications of the D614G mutation in the S-protein. 2021 Scientific reports Figure SARS_CoV_2 D614G 31 36 S 53 54 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Temporal and spatial distribution of the four possible D614G and P323L combinations. 2021 Scientific reports Figure SARS_CoV_2 D614G;P323L 55;65 60;70 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Temporal evolution of the four possible D614G and P323L variants in different countries. 2021 Scientific reports Figure SARS_CoV_2 D614G;P323L 40;50 45;55 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Two major protein variants of SARS-CoV-2: S protein D614G and RNA-dependent polymerase P323L. 2021 Scientific reports Figure SARS_CoV_2 D614G;P323L 52;87 57;92 S 42 43 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. All 25 sequences were classified as G clade with mutations P323L in NSP12 (RdRP) and D614G in S protein (grey circle). 2021 Scientific reports Figure SARS_CoV_2 D614G;P323L 85;59 90;64 Nsp12;RdRP;S 68;75;94 73;79;95 34211709 The emerging SARS-CoV-2 variants of concern. 20H and 20I include two variants of concern (VOCs) emerging from N501Y; 501Y.V2 in South Africa and 501Y.V1 in the UK while 20J has the VOC 501Y.V3 or P1 which emerged from Brazil and Japan. 2021 Therapeutic advances in infectious disease Figure SARS_CoV_2 N501Y 65 70 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. (A) H522 cells were pre-treated with bafilomycin A, SGC-AAK1-1, E64D, apilimod, or camostat mesylate for 1 h and then infected with SARS-CoV-2 at an MOI of 1 in the presence of the inhibitors. 2021 Cell reports Figure SARS_CoV_2 E64D 64 68 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. (E) Quantification of vRNA in H522 cells infected with WT SARS-CoV-2 and SARS-CoV-2 containing the E484D S substitution. 2021 Cell reports Figure SARS_CoV_2 E484D 99 104 S 105 106 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. The SARS-CoV-2 S protein is necessary for viral entry in H522 cells, and the E484D mutation enhances infection. 2021 Cell reports Figure SARS_CoV_2 E484D 77 82 S 15 16 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. (a) Dimplot showing the interactions between the RBD (WT and mutant N501I, N501Y) and ACE2. 2021 Virology Figure SARS_CoV_2 N501I;N501Y 68;75 73;80 RBD 49 52 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. (b) Dimplot showing the interactions between the RBD (mutant Q493L, Q493H and K417R) and ACE2. 2021 Virology Figure SARS_CoV_2 K417R;Q493H;Q493L 78;68;61 83;73;66 RBD 49 52 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. (d) N501Y, (e) WT, (f) Q493L, (g) N501I, (h) K417R and (i) Q493H. 2021 Virology Figure SARS_CoV_2 K417R;N501I;N501Y;Q493H;Q493L 45;34;4;59;23 50;39;9;64;28 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Per residue energy decomposition for (a) N501, N501Y and N501I, (b) K417 and K417R, (c) Q493, Q493L and Q493H. 2021 Virology Figure SARS_CoV_2 K417R;N501I;N501Y;Q493H;Q493L 77;57;47;104;94 82;62;52;109;99 34217923 Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. WT (Black); magenta (K417R); green (Q493H); cyan (Q493L); blue (N501I); red (N501Y). 2021 Virology Figure SARS_CoV_2 K417R;N501I;N501Y;Q493H;Q493L 21;64;77;36;50 26;69;82;41;55 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. (B) Structure modeling of the mutation N501Y in S1 and S982A in S2 based on "6VXX". 2021 Frontiers in immunology Figure SARS_CoV_2 N501Y;S982A 39;55 44;60 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Scatter plot of (A-F) showing the neutralization ID50 ratio of each variant to that of D614G. 2021 Frontiers in immunology Figure SARS_CoV_2 D614G 87 92 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. The data represent the ID50 ratio of each variant to that of D614G. 2021 Frontiers in immunology Figure SARS_CoV_2 D614G 61 66 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. D Neutralization activities of F61 and H121 towards mutations K417N, E484K, and N501Y on S protein were measured by pseudovirus. 2021 Virologica Sinica Figure SARS_CoV_2 E484K;K417N;N501Y 69;62;80 74;67;85 S 89 90 34225487 Replicative Fitness of a SARS-CoV-2 20I/501Y.V1 Variant from Lineage B.1.1.7 in Human Reconstituted Bronchial Epithelium. In vitro and ex vivo replication ability of a 20I/501Y.V1 (B.1.1.7) variant in comparison with a lineage B.1 D614G strain. 2021 mBio Figure SARS_CoV_2 D614G 109 114 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. (A-G) Sera with series of dilution inhibited infection of pseudovirus with or without mutation (WT, B.1.351, P.1, B.1.1.7, D614G, N501Y, E484K). 2021 MedComm Figure SARS_CoV_2 D614G;E484K;N501Y 123;137;130 128;142;135 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. (C-F) Inhibition rate of RBD(WT), RBD(K417N), RBD(E484K), RBD(N501Y) binding to cell surface ACE2 receptor. 2021 MedComm Figure SARS_CoV_2 E484K;K417N;N501Y 50;38;62 55;43;67 RBD;RBD;RBD;RBD 25;34;46;58 28;37;49;61 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. (c) PRNT80 titers against the Munich SARS-CoV-2 P3 strain (Spike D614G) for a negative control pAb and SAB-185 Lot 1, Lot 5, and Lot 6. 2021 Human vaccines & immunotherapeutics Figure SARS_CoV_2 D614G 65 70 S 59 64 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. Mutations E484K and N501K occur on the RBM segments (dark purple ribbon), while K417N occurs on helix alpha4 of RBD. 2022 Allergy Figure SARS_CoV_2 E484K;K417N;N501K 10;80;20 15;85;25 RBD 112 115 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. d Comparison of public antibodies' neutralization against pseudovirus bearing WT, K417R, K417A, K417E, K417N, or K417T mutant SARS-CoV-2 spike on the pseudovirus. 2021 Nature communications Figure SARS_CoV_2 K417A;K417E;K417N;K417R;K417T 89;96;103;82;113 94;101;108;87;118 S 137 142 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. (A) S:A222V, (B) S:L18F, (C) ORF10:V30F, (D) N:A220V, (E) nsp7:L71F, (F) nsp14:A320V, (G) S:V1176F, (H) Ratios of nonsynonymous SNVs in the whole region or IDR of proteins, S, ORF1ab, and ORF3a, (I) Hydrophobic scores before (REF) and after alternations (ALT) of nonsynonymous SNVs in the IDRs of proteins, S, ORF1ab, and ORF3a. 2021 Journal of medical virology Figure SARS_CoV_2 A220V;A222V;A320V;L18F;L71F;V1176F;V30F 47;6;79;19;63;92;35 52;11;84;23;67;98;39 ORF1ab;ORF1ab;ORF3a;ORF3a;Nsp7;N;S;S;S;S;S 176;310;188;322;58;45;4;17;90;173;307 182;316;193;327;62;46;5;18;91;174;308 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. EPI_ISL_415539U) as it is the first sample with both 11083G > T and 26326C > T. 2021 Bulletin of the World Health Organization Figure SARS_CoV_2 G11083T;C26326T 53;68 63;78 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. (D) The location of the Y453F substitution in the receptor binding domain complexed with a host ACE2 receptor (blue) [PBD: 6LZG]. 2021 Frontiers in microbiology Figure SARS_CoV_2 Y453F 24 29 RBD 50 73 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. The regions encompassing the S1147L and M1229I substitutions are not within the crystal structure; however, their relative positions are indicated. 2021 Frontiers in microbiology Figure SARS_CoV_2 M1229I;S1147L 40;29 46;35 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. However, the single chromatographic peak of the C145S variant was shifted to an earlier retention volume, which represents a higher oligomeric state than the dimeric state of the WT enzyme. 2021 Frontiers in chemistry Figure SARS_CoV_2 C145S 48 53 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. Similarly, the chromatographic peak of the C145A variant exhibited a single peak that aligned with the dimeric peak of the WT enzyme. 2021 Frontiers in chemistry Figure SARS_CoV_2 C145A 43 48 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. B, Stacked area plot showing the number of GISAID genomes (n = 250) that are B.1.1.7 (20I/501Y.V1) and have the E484K spike mutation over time in the United States and globally. 2021 Open forum infectious diseases Figure SARS_CoV_2 E484K 112 117 S 118 123 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Diversity of SARS-CoV-2 in Philadelphia and global diversity of sequenced B.1.1.7+E484K genomes. 2021 Open forum infectious diseases Figure SARS_CoV_2 E484K 82 87 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Maximum likelihood tree of the B.1.1.7+E484K isolates. 2021 Open forum infectious diseases Figure SARS_CoV_2 E484K 39 44 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. SNP-based phylogeny showing the independent acquisitions of E484K in the B.1.1.7 lineage. 2021 Open forum infectious diseases Figure SARS_CoV_2 E484K 60 65 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. Stacked area plot showing relative abundance of circulating CCs for the 236 B.1.1.7+E484K isolates (typed by GNUVID). 2021 Open forum infectious diseases Figure SARS_CoV_2 E484K 84 89 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. The PA B.1.1.7+E484K isolates are represented with red stars. 2021 Open forum infectious diseases Figure SARS_CoV_2 E484K 15 20 34254040 Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates. The red branches represent ancestral reconstruction of the E484K mutation in the B.1.1.7 lineage. 2021 Open forum infectious diseases Figure SARS_CoV_2 E484K 59 64 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. (d, f, h) RT-PCR assays to evaluate the suppression of ancestral and D614G SARS-CoV-2 strains in VERO cells expressing either non-targeting (NT), NCP-1, or tiled crRNAs targeting the D614G mutation hotspot in the Spike genomic and subgenomic RNA 1 h (d), 24 h (f), and 48 h (h) post-transfection, N = 4; Data are normalized means and errors are SD; Results are analysed by one-way ANOVA test (95% confidence interval). 2021 Nature communications Figure SARS_CoV_2 D614G;D614G 69;183 74;188 S 213 218 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. 48 h post-transfection, cells were infected with either ancestral or D614G SARS-CoV-2 for 1 h, and the kinetics of viral replication was assessed in supernatant collected at 1 h (initial viral load), 24 h, and 48 h post-infection via quantification of viral RNA in the supernatant using RT-PCR. 2021 Nature communications Figure SARS_CoV_2 D614G 69 74 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. a Fluorescence-based reporter assay to assess the silencing efficiency of the D614G Spike transcripts with 6 tiled crRNAs harbouring a single-nucleotide mismatch with the target at various spacer positions; Data points in the graphs are mean fluorescence from 4 representative fields of view per condition imaged; N = 3. 2021 Nature communications Figure SARS_CoV_2 D614G 78 83 S 84 89 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. a-c Fluorescence-based reporter assay to assess the silencing efficiency of the D614G Spike transcripts with 18 tiled crRNAs harbouring a G-U (a), G-G (b) single-nucleotide mismatch, or G-C full match (c) with the target at various spacer positions; Data points in the graphs are mean fluorescence from 4 representative fields of view per condition imaged; N = 3. 2021 Nature communications Figure SARS_CoV_2 D614G 80 85 S 86 91 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. b Schematic of infection assays to assess pspCas13b-mediated suppression of both ancestral and D614G replication-competent SARS-CoV-2 in infected VERO cells. 2021 Nature communications Figure SARS_CoV_2 D614G 95 100 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. c, e, g RT-PCR assays to evaluate relative viral loads (ancestral versus D614G) in control VERO cells expressing non-targeting (NT) crRNA at timepoints 1 hr to estimate the initial viral input (c), 24 h (e), and 48 h (g) post-infection, N = 4; Data are normalized means and errors are SD; Results are analysed by unpaired two-tailed Student's t-test (95% confidence interval). 2021 Nature communications Figure SARS_CoV_2 D614G 73 78 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. Single crRNAs targeting the D614 genomic mutation hotspot can silence both ancestral and D614G variants in infected cells through single-nucleotide mismatch tolerance. 2021 Nature communications Figure SARS_CoV_2 D614G 89 94 34257311 Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance. Single crRNAs targeting the D614 genomic mutation hotspot can silence D614G variant's RNA through the single-nucleotide mismatch tolerance. 2021 Nature communications Figure SARS_CoV_2 D614G 70 75 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. Phylogenetic tree of SARS-CoV-2 and B.1+L249S+E484K emergence. 2021 Frontiers in medicine Figure SARS_CoV_2 E484K;L249S 46;40 51;45 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. (e) Asn501Tyr (N501Y) mutation shifts the binding pocket of tauro-alpha-muricholic acid (orange) and (f) tilivalline (yellow). 2021 Chembiochem Figure SARS_CoV_2 N501Y;N501Y 4;15 13;20 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. Asn501Tyr (N501Y) mutation abolishes the binding pocket of bile acids and NRPs in the WT-RBD. 2021 Chembiochem Figure SARS_CoV_2 N501Y;N501Y 11;0 16;9 RBD 89 92 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. The Asn501Tyr (N501Y) mutation is seen among many variants. 2021 Chembiochem Figure SARS_CoV_2 N501Y;N501Y 4;15 13;20 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. The N501Y mutation or other mutations interfere with the binding of NPs with the RBD and/or increase the interaction of RBD with the ACD2 receptor. 2021 Chembiochem Figure SARS_CoV_2 N501Y 4 9 RBD;RBD 81;120 84;123 34265150 Hidden in Plain Sight: Natural Products of Commensal Microbiota as an Environmental Selection Pressure for the Rise of New Variants of SARS-CoV-2. The new binding pocket has a significantly lower affinity for these NPs (Supporting Table S1) and in this pocket the interference of (g) tauro-alpha-muricholic acid (orange) and (h) tilivalline with the N501Y-RBD binding to the ACE2 receptor is minimized as observed by aligning the predicted binding site with the solved structure of RBD-ACE2 receptor (PDB Code: 7NXC). 2021 Chembiochem Figure SARS_CoV_2 N501Y 203 208 RBD;RBD 209;335 212;338 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. (A) D614 Mutation (B) A829T (C) E96G and (D) P25L Mutation. 2021 Biomedical journal Figure SARS_CoV_2 A829T;E96G;P25L 22;32;45 27;36;49 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Europe is the region that had the most D614G amino acid mutation cases over time (n = 49) and Australia is the region that had the least D614G amino acid mutation cases over time (n = 4). 2021 Biomedical journal Figure SARS_CoV_2 D614G;D614G 39;137 44;142 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. March 2020 had the most D614G amino acid mutations that occurred in all five regions. 2021 Biomedical journal Figure SARS_CoV_2 D614G 24 29 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Monthly distribution of A1841G mutation in Spike protein of SARS-CoV-2 in different regions. 2021 Biomedical journal Figure SARS_CoV_2 A1841G 24 30 S 43 48 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Monthly distribution of D614G mutation in Spike protein of SARS-CoV-2 in different region. 2021 Biomedical journal Figure SARS_CoV_2 D614G 24 29 S 42 47 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. The type of mutation that had the highest number and occurred in all five areas was the A1841G mutation. 2021 Biomedical journal Figure SARS_CoV_2 A1841G 88 94 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. The type of mutation that had the highest number and occurred in all five areas was the D614G mutation. 2021 Biomedical journal Figure SARS_CoV_2 D614G 88 93 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. There is no D614G amino acid mutation in December 2019. 2021 Biomedical journal Figure SARS_CoV_2 D614G 12 17 34271432 Natto extract, a Japanese fermented soybean food, directly inhibits viral infections including SARS-CoV-2 in vitro. (C) The recombinant RBD protein of SARS-CoV-2 carrying a point mutation (N501Y) was incubated with the heated or unheated natto extract. 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 N501Y 73 78 RBD 20 23 34271432 Natto extract, a Japanese fermented soybean food, directly inhibits viral infections including SARS-CoV-2 in vitro. Lane 1: protein marker, Lane 2: RBD protein (N501Y) treated with PBS, Lane 3: RBD protein (N501Y) treated with unheated-natto extract, Lane 4: RBD protein (N501Y) treated with heated-natto extract, Lane 5: PBS treated with unheated-natto extract, Lane 6: PBS treated with heated-natto extract. 2021 Biochemical and biophysical research communications Figure SARS_CoV_2 N501Y;N501Y;N501Y 45;91;156 50;96;161 RBD;RBD;RBD 32;78;143 35;81;146 34278277 SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high risk variants into the United Kingdom. Variants of Concern B.1.1.7 (n = 1317), B.1.1.7 with E484K (n = 3), B.1.351 (n = 69), B.1.617.2 (n = 28), and P.1 (n = 6) are highlighted in orange, Variants under Investigation B.1.617.1 (n = 49), B.1.617 (n = 9), B.1.617.3 (n = 3), B.1.525 (n = 34), and B.1.318 (n = 7) are highlighted in yellow and Variants under Monitoring A.27, B.1.214.2, B.1.526 and R.1 (all n = 1) are highlighted in blue (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.). 2021 EClinicalMedicine Figure SARS_CoV_2 E484K 53 58 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. Bamla, bamlanivimab; CP, convalescent plasma; RDV, remdesivir; REGN, REGN:COV2, casirivimab/imdevimab; CTx, chemotherapy; HTx heart transplantation; PRDL, prednisolone; DXM, dexamethasone; MMF, mycophenolate mofetil; TAC, tacrolimus; CsA, cyclosporin A; AZA, azathioprine; CCL, chronic lymphocytic leukemia; E484K, substitution in the receptor-binding domain (RDB) associated with immune escape. 2021 The Lancet regional health. Europe Figure SARS_CoV_2 E484K 308 313 B cell chronic leukemia 278 306 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. Selection of E484K in SARS-CoV-2 infected patients with severe immunosuppression. 2021 The Lancet regional health. Europe Figure SARS_CoV_2 E484K 13 18 COVID-19 22 41 34278671 Efficient Inhibition of SARS-CoV-2 Using Chimeric Antisense Oligonucleotides through RNase L Activation*. Efficiently inhibited infection of three mutated SARS-CoV-2 pseudoviruses, N501Y, DeltaH69/DeltaV70 and their combined mutants (Dual) in HEK293T-hACE2 cells after Chimera-S4 treatment (40 nM, 48 h), as measured by luciferase assay. 2021 Angewandte Chemie (International ed. in English) Figure SARS_CoV_2 N501Y 75 80 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. (A) SPR binding kinetics of ACE2(HH:NN) WT Fc, LALA-PG Fc, LY-CoV555, REGN10933, and REGN10987 against SARS-CoV-1, SARS-CoV-2 variants (Wuhan, D614G, B1.1.7, B.1.351, and P.1), and HCoV-NL63 S1 domains. 2021 Journal of virology Figure SARS_CoV_2 D614G 143 148 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. (C) Kinetic affinity of catalytically active ACE2-Fc with SARS-CoV-2 S1 WT, D614G, B1.1.7, B.1.351, and P.1. 2021 Journal of virology Figure SARS_CoV_2 D614G 76 81 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. (D) Neutralization assay of SARS-CoV-1, SARS-CoV-2 Wuhan, SARS-CoV-2 D614G, SARS-CoV-2 B1.1.7, and SARS-CoV-2 B1.351 pseudotyped vectors with ACE2(HH:NN)-Fc (LALA-PG), LY-CoV-55, REGN10933/REGN10987 cocktail, REGN10933, and REGN10987. 2021 Journal of virology Figure SARS_CoV_2 D614G 69 74 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. Physical particle number determined via p24 ELISA (D) and infectious viral titer (E) comparison for SARS-CoV-1, SARS-CoV-2 Wuhan, SARS-CoV-2 D614G, SARS-CoV-2 B1.1.7, and SARS-CoV-2 B1.351 pseudotyped vectors, showing comparable particle concentration but diverse infectivity capacity (mean +- standard deviation [SD]). 2021 Journal of virology Figure SARS_CoV_2 D614G 141 146 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. Prevalence of N501Y variant strains among the tested sample set over time. 2021 Journal of clinical microbiology Figure SARS_CoV_2 N501Y 14 19 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. The proportion of N501Y and E484K variants is shown for samples obtained during the periods of October to November (n = 9 tested with SMB-501/n = 3 tested with SMB-484), January (n = 16/n = 12), February (n = 15/n = 9), and the first week of March (n = 6/n = 2). 2021 Journal of clinical microbiology Figure SARS_CoV_2 E484K;N501Y 28;18 33;23 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. (A) Visualization of the T372 and D614G mutants. 2021 Cell Figure SARS_CoV_2 D614G 34 39 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. (B and C) Surface map of the WT S protein (B) and the N370-glycosylated T372 S protein (C), colored by the residue side-chain properties: green for hydrophobic, blue for positively charged, red for negatively charged, teal for polar uncharged, and gray for neutral. 2021 Cell Figure SARS_CoV_2 T372S 72 78 S;S 32;77 33;78 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. (B) Non-synonymous difference (Thr372Ala) between SARS-CoV-2 and four other Sarbecovirus members found in the putative selective sweep region (22,529-22,862). 2021 Cell Figure SARS_CoV_2 T372A 31 40 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. A372T substitution decreases SARS-CoV-2 replication on human lung epithelial cells. 2021 Cell Figure SARS_CoV_2 A372T 0 5 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Decreased binding of the A372T mutant to human ACE2. 2021 Cell Figure SARS_CoV_2 A372T 25 30 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Plates were coated with recombinant human ACE2 receptor (2 mug/mL at 100 muL/well) and then probed with varying concentrations (0.256-4000 ng/mL) of purified RBDs from WT SARS-CoV-2 (S A372), A372T, and N501Y (positive control). 2021 Cell Figure SARS_CoV_2 A372T;N501Y 192;203 197;208 RBD;S 158;183 162;184 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. The top panel shows the WT (A372) and T372 mutant, the center panel displays a glycosylated N370 T372 S protein with various rotamers of the GlcNAc-glycosylated N370, and the bottom panel shows the WT and G614 mutant. 2021 Cell Figure SARS_CoV_2 T372S 97 103 S 102 103 34292870 Inhalable nanocatchers for SARS-CoV-2 inhibition. (G) Pseudotyped wild-type SARS-CoV-2 and SARS-CoV-2 D614G variant neutralization curves by NCs or NVs, which were collected from 293T cells with hACE2 over-expression or wide-type 293T cells, respectively. 2021 Proc Natl Acad Sci U S A Figure SARS_CoV_2 D614G 52 57 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. (D) The frequency of S 614G, at least one NLS-associated variant (N 194L, N119L, N203K, N205I, and N220V), and at least one emerging spike variant (SI Appendix. 2021 Proc Natl Acad Sci U S A Figure SARS_CoV_2 N119L;N203K;N205I;N220V;S614G;N194L 74;81;88;99;21;66 79;86;93;104;27;72 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. Black nodes correspond to key amino acid substitutions S L18F, S A222V, S S477N, S N501Y, S D614G, S P681H, S T716I, N R203K, and N G204R. 2021 Proc Natl Acad Sci U S A Figure SARS_CoV_2 A222V;D614G;G204R;L18F;N501Y;P681H;R203K;S477N;T716I 65;92;132;57;83;101;119;74;110 70;97;137;61;88;106;124;79;115 N;N;S;S;S;S;S;S;S 117;130;55;63;72;81;90;99;108 118;131;56;64;73;82;91;100;109 34292871 Ongoing global and regional adaptive evolution of SARS-CoV-2. S23, excluding S 477N). 2021 Proc Natl Acad Sci U S A Figure SARS_CoV_2 S477N 15 21 S 15 16 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. Note that some annotation methods treat the E156G and del157-158 differently; we have used the GISAID annotation nomenclature. 2021 The American journal of pathology Figure SARS_CoV_2 E156G 44 49 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Amplification curves using AddProbe rRT PCR master mix (AddBio) using D614G IN primers and probes including D614 D-FAM and G614 G-HEX probes. 2021 Meta gene Figure SARS_CoV_2 D614D;D614G;G614G 108;70;123 114;75;129 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Both D614G Out F and R primers are also located. 2021 Meta gene Figure SARS_CoV_2 D614G 5 10 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. DNA sequencings of both SARS CoV-2 D614G and human cytochrome b used for RFLP: Panel (A) Nucleic acid sequences of SARS CoV-2 shows restriction site (GGATGNN) in the wild type D614 which is cleaved by BtsCI enzyme while G614 mutant sequence is not cut by the enzyme. 2021 Meta gene Figure SARS_CoV_2 D614G 35 40 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Lane 1 = undigested PCR product amplified by D614G Out primers. 2021 Meta gene Figure SARS_CoV_2 D614G 45 50 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Lanes 2 and 3 = PCR products amplified by D614G Out primers and incubated with BtsCI enzyme at 50C. 2021 Meta gene Figure SARS_CoV_2 D614G 42 47 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Locations of primers and probes in a specific region around D614G (A23403G) mutation in SARS CoV-2 isolate Wuhan-Hu-1, complete genome. 2021 Meta gene Figure SARS_CoV_2 D614G;A23403G 60;67 65;74 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. A: The differential heat map showing the base pair probability difference between the wild-type and mutant (C241T). 2021 Informatics in medicine unlocked Figure SARS_CoV_2 C241T 108 113 34307830 In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. Structural changes in the wild-type and mutant variant C241U (C241T) of 5' UTR of SARS-CoV-2. 2021 Informatics in medicine unlocked Figure SARS_CoV_2 C241T 62 67 5'UTR 72 78 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. (Bottom) Sequences of aa 612 to 617 in the wild-type and mutant D614G spike proteins. 2021 mBio Figure SARS_CoV_2 D614G 64 69 S 70 75 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. (E) Effects of treatment with CMK (50 muM) and the R682A mutation of S on syncytium formation induced by S-D614 or S-G614 protein. 2021 mBio Figure SARS_CoV_2 R682A 51 56 S;S;S 69;105;115 70;106;116 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. D614G substitution in the spike (S) protein enhanced viral production and increased cleavage of the S protein compared to that in wild-type spike in Calu-3 cells infected with SARS-CoV-2 isolates. 2021 mBio Figure SARS_CoV_2 D614G 0 5 S;S;S;S 26;140;33;100 31;145;34;101 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. The luciferase activity in cells expressing the SARS-CoV-2 S-D614/S-G614 protein or D614/R682A or G614/R682A protein with or without treatment with a furin/PC inhibitor (CMK, 50 muM) was assessed as indicated. 2021 mBio Figure SARS_CoV_2 R682A;R682A 89;103 94;108 S;S 59;66 60;67 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. (A) Neutralization of viruses with D614G, B.1.526 variant spikes by convalescent-phase sera (n = 6). 2021 mBio Figure SARS_CoV_2 D614G 35 40 S 58 64 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. (C) A 1:1 mixture of the two antibodies was measured on viruses pseudotyped with B.1.526, D614G and E484K variant spike proteins. 2021 mBio Figure SARS_CoV_2 D614G;E484K 90;100 95;105 S 114 119 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. IC50 (serum dilution) of sera from convalescent individuals (n = 6) against virus with B.1.526 and E484K variant spikes (right). 2021 mBio Figure SARS_CoV_2 E484K 99 104 S 113 119 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. IC50 values of neutralization of virus with D614G, B.1.1.7, B.1.351, and B.1.526 are shown. 2021 mBio Figure SARS_CoV_2 D614G 44 49 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. Neutralization curves of REGN10933, REGN10987, and a 1:1 mixture of REGN10933 and REGN10987 on viruses with the B.1.526, D614G and E484K variant spike proteins. 2021 mBio Figure SARS_CoV_2 D614G;E484K 121;131 126;136 S 145 150 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. The effect of the MAb ratio on neutralization of variant B.1.526 (E484K) was tested by holding REGN10933 constant at its IC50 and titrating in REGN10987 (left) or holding REGN10987 constant at its IC50 and titrating in REGN10933. 2021 mBio Figure SARS_CoV_2 E484K 66 71 34311587 B.1.526 SARS-CoV-2 Variants Identified in New York City are Neutralized by Vaccine-Elicited and Therapeutic Monoclonal Antibodies. The locations of the mutations in the two B.1.526 spike proteins are diagrammed below with the distinguishing E484K and S477N mutations in bold. 2021 mBio Figure SARS_CoV_2 E484K;S477N 110;120 115;125 S 50 55 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. (b) Neutralization activity of individual serum samples against rcVSV-CoV2-S with the WT (black circles), B.1.1.7 (blue circles), B.1.351 (red circles), or E484K (orange circles) spike proteins. 2021 Nature communications Figure SARS_CoV_2 E484K 156 161 S;S 179;75 184;76 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. All the variants and mutants have D614G. 2021 Nature communications Figure SARS_CoV_2 D614G 34 39 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Black, blue, red, and organe circles represent WT, B.1.1.7, B.1.351, and E484K viruses, respectively. 2021 Nature communications Figure SARS_CoV_2 E484K 73 78 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. c is a repeat of the experiment done in a with the E484K mutant using a different preparation of recombinant RBD-Fc (see methods). 2021 Nature communications Figure SARS_CoV_2 E484K 51 56 RBD 109 112 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. c rcVSV-CoV-2-S containing the prevailing WT (D614G) and VOC (B.1.1.7 and B.1.351) spikes were inoculated into one 6-well each of F8-2 cells (MOI 0.1) and subsequently overlaid with methylcellulose-DMEM to monitor syncytia formation. 2021 Nature communications Figure SARS_CoV_2 D614G 46 51 S;S 83;14 89;15 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Colored filled symbols represent the indicated viruses, open symbols in e represent assigned SNT values of 1.0 when no significant neutralization activity could be detected (SP012: B.1.351 and E484K). 2021 Nature communications Figure SARS_CoV_2 E484K 193 198 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Data points for one serum (SP012) against WT, B.1.351 and E484K could not be calculated because there was no best-fit value. 2021 Nature communications Figure SARS_CoV_2 E484K 58 63 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. The prevailing WT sequence now has a D614G substitution. 2021 Nature communications Figure SARS_CoV_2 D614G 37 42 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. (A) Overlay of the P681H S-protein (orange) and B.1.1.7 variant (teal), residue mutations are depicted in magenta and deleted residues in blue. 2021 Virus research Figure SARS_CoV_2 P681H 19 24 S 25 26 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. (B) Overlay of the modeled P681H S-protein (orange) and S-protein 6VSB (blue). 2021 Virus research Figure SARS_CoV_2 P681H 27 32 S;S 33;56 34;57 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. Molecular dynamic simulations RMSD plots at 100 ns simulations of S-protein (A) P681H-furin (orange) and (B) S-protein B.1.1.7-furin (teal). 2021 Virus research Figure SARS_CoV_2 P681H 80 85 S;S 66;109 67;110 34314772 Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity. RMSF plot of S-protein P681H-furin (orange) and S-protein B.1.1.7-Furin complex (teal). 2021 Virus research Figure SARS_CoV_2 P681H 23 28 S;S 13;48 14;49 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. The graphs are given in wild type, T2W, T2Y, L3R, and A5W sequence. 2021 Interdisciplinary sciences, computational life sciences Figure SARS_CoV_2 A5W;L3R;T2W;T2Y 54;45;35;40 57;48;38;43 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. The sequence is wild type, T2W, T2Y, L3R, and A5W. 2021 Interdisciplinary sciences, computational life sciences Figure SARS_CoV_2 A5W;L3R;T2W;T2Y 46;37;27;32 49;40;30;35 34324157 In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. Wild (black), T2W (blue), T2Y (Magenta), and L3R (navy), while the A5W is shown in red color. 2021 Interdisciplinary sciences, computational life sciences Figure SARS_CoV_2 A5W;L3R;T2W;T2Y 67;45;14;26 70;48;17;29 34326308 Structural and functional basis for pan-CoV fusion inhibitors against SARS-CoV-2 and its variants with preclinical evaluation. d-g Anti-SARS-CoV-2 efficacy of EK1 and EK1C4 on PsV infection mediated by the S protein with single mutations, including K417N (d), E484K (e), N501Y (f), or D614G (g), respectively on Caco2 cells. 2021 Signal transduction and targeted therapy Figure SARS_CoV_2 D614G;E484K;K417N;N501Y 158;133;122;144 163;138;127;149 S 79 80 34326308 Structural and functional basis for pan-CoV fusion inhibitors against SARS-CoV-2 and its variants with preclinical evaluation. h-k Antiviral efficacy of EK1 and EK1C4 against PsV infection mediated by the S protein with combinational mutations, including K417N/ E484K (h), N501Y/ K417N (i) N501Y/E484K (j), and N501Y/ K417N/E484K (k), respectively, on Caco2 cells. 2021 Signal transduction and targeted therapy Figure SARS_CoV_2 E484K;K417N;K417N;K417N;N501Y;N501Y;N501Y;E484K;E484K 135;128;153;191;146;163;184;169;197 140;133;158;196;151;168;189;174;202 S 78 79 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. (A) Key hydrogen bonding interactions of the V62L mutant with the IRF3 binding interface along with stick representation (left). 2021 Frontiers in microbiology Figure SARS_CoV_2 V62L 45 49 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. (A) ORF8 WT, (B) S24L, (C) W45L, (D) V62L, (E) L84S, (F) V62L, and L84S double mutant (G). 2021 Frontiers in microbiology Figure SARS_CoV_2 L84S;L84S;S24L;V62L;V62L;W45L 47;67;17;37;57;27 51;71;21;41;61;31 ORF8 4 8 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. (B) Key hydrogen bonding interactions of S24L mutant with the IRF3 binding interface along with stick representation (left). 2021 Frontiers in microbiology Figure SARS_CoV_2 S24L 41 45 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. (B) Key hydrogen bonding interactions of the L84S complex with the IRF3 binding interface along with stick representation of the ORF8 WT complex with IRF3 (left). 2021 Frontiers in microbiology Figure SARS_CoV_2 L84S 45 49 ORF8 129 133 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. (C) Key hydrogen bonding interactions of double mutants V62L and L84S with the IRF3 binding interface along with stick representation (left). 2021 Frontiers in microbiology Figure SARS_CoV_2 L84S;V62L 65;56 69;60 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. (C) Key hydrogen bonding interactions of the W45L complex with the IRF3 binding interface along with stick representation of the ORF8 WT complex with IRF3 (left). 2021 Frontiers in microbiology Figure SARS_CoV_2 W45L 45 49 ORF8 129 133 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. Docking of ORF8 WT, S24L, and W45L mutant complexes. 2021 Frontiers in microbiology Figure SARS_CoV_2 S24L;W45L 20;30 24;34 ORF8 11 15 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. Docking V62L, L84S, and V62L and L84S double-mutant complexes. 2021 Frontiers in microbiology Figure SARS_CoV_2 L84S;L84S;V62L;V62L 14;33;8;24 18;37;12;28 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. Superimposed structure of ORF8 WT (green) with S24L (light magenta), W45L (cyan), V62L (yellow), L84S (orange), and V62L, L84S (dark magenta). 2021 Frontiers in microbiology Figure SARS_CoV_2 L84S;L84S;S24L;V62L;V62L;W45L 97;122;47;82;116;69 101;126;51;86;120;73 ORF8 26 30 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. (a) Schematic domains of the wild-type SARS-CoV-2 spike monomer and the three variants (501Y.V1, 501Y.V2 and N439K), with the N501Y mutation appearing in both the 501Y.V1 and 501Y.V2 variants. 2021 Computational and structural biotechnology journal Figure SARS_CoV_2 N439K;N501Y 109;126 114;131 S 50 55 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. (a) Wild-type, (b) 501Y.V1, (c) 501Y.V2 and (d) N439K variants of SARS-CoV-2 RBD. 2021 Computational and structural biotechnology journal Figure SARS_CoV_2 N439K 48 53 RBD 77 80 34336146 Binding affinity and mechanisms of SARS-CoV-2 variants. Binding interfaces between (a) the wild-type, (b) the 501Y.V1 variant, (c) the 501Y.V2 variant, and (d) the N439K variant SARS-CoV-2 RBD and hACE2, including hydrogen bonds, salt bridges and residues with the dominant binding contributions. 2021 Computational and structural biotechnology journal Figure SARS_CoV_2 N439K 108 113 RBD 133 136 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. (A) The WT residue index and SSE along Y-axis shows differences at the 60-65ns MD simulations period; (B) S68F shows a little variation at 40-55ns; (C) P71S exhibits more variations at 45-68ns; (D) L73F also demonstrates variations when the WT is compared with P71S and S68F. 2021 Informatics in medicine unlocked Figure SARS_CoV_2 L73F;P71S;P71S;S68F;S68F 198;152;261;106;270 202;156;265;110;274 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. MT S68F shows more stability than WT based on the free energy landscape. 2021 Informatics in medicine unlocked Figure SARS_CoV_2 S68F 3 7 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. S68F, P71S, and L73F MTs have been compared with their WT on the left. 2021 Informatics in medicine unlocked Figure SARS_CoV_2 L73F;P71S;S68F 16;6;0 20;10;4 34337139 Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. WT exhibited more stability than P71S and L73F. 2021 Informatics in medicine unlocked Figure SARS_CoV_2 L73F;P71S 42;33 46;37 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. Sequence flexibility/rigidity map of the RBD regions of P.1, B.1.351,B.1.1.7, and the wild-type strain near K417N/T mutation sites. 2021 ACS omega Figure SARS_CoV_2 K417N;K417T 108;108 115;115 RBD 41 44 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. Sequence flexibility/rigidity map of the RBM regions of B.1.617.2,B.1.617.1, B.1.427/429, P.1, B.1.351, B.1.1.7, S477N, and the wild-typestrain. 2021 ACS omega Figure SARS_CoV_2 S477N 113 118 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. Sequence flexibility/rigidity maps of all of the single amino acidmutations at the D614G mutation site (blue: identical alpha-helix-typeconformations; red: identical beta-sheet-type conformations; andgreen: identical other-type conformations). 2021 ACS omega Figure SARS_CoV_2 D614G 83 88 34337269 Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds. Sequence flexibility/rigidity maps of all of the single amino acidmutations at the P681H/R mutation sites (blue: identical alpha-helix-typeconformations; red: identical beta-sheet-type conformations; andgreen: identical other-type conformations). 2021 ACS omega Figure SARS_CoV_2 P681H;P681R 83;83 90;90 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. (a) The native is depicted in black, the N501Y nonsynonymous mutant is depicted in green, and the D614G nonsynonymous mutant is depicted in yellow. 2021 Computers in biology and medicine Figure SARS_CoV_2 D614G;N501Y 98;41 103;46 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. a-e: The total energy, RMSD matrix, RMSF, SASA, and NH-bonds of native and nonsynonymous mutants (N501Y and D614G) of the S-protein versus time at 300 K. 2021 Computers in biology and medicine Figure SARS_CoV_2 D614G;N501Y 108;98 113;103 S 122 123 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. D614G nonsynonymous Mutant S-protein residue interaction with ACE-2 receptor prepared by Ligplot. 2021 Computers in biology and medicine Figure SARS_CoV_2 D614G 0 5 S 27 28 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. H49Y nonsynonymous mutant S-protein residue interaction with ACE-2 receptor prepared by Ligplot. 2021 Computers in biology and medicine Figure SARS_CoV_2 H49Y 0 4 S 26 27 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. N501Y nonsynonymous mutant S-protein residue interaction with ACE-2 receptor prepared by Ligplot. 2021 Computers in biology and medicine Figure SARS_CoV_2 N501Y 0 5 S 27 28 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Native and destabilizing nonsynonymous mutations (L8V, L8W, L18F, Y145H, M153T, F157S, G476S, L611F, A879S, C1247F, and C1254F) of S-protein interaction with ACE2 receptor. 2021 Computers in biology and medicine Figure SARS_CoV_2 A879S;C1247F;C1254F;F157S;G476S;L18F;L611F;L8W;M153T;Y145H;L8V 101;108;120;80;87;60;94;55;73;66;50 106;114;126;85;92;64;99;58;78;71;53 S 131 132 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Native and nonsynonymous stabilizing mutations (H49Y, S50L, N501Y, D614G, A845V, and P1143L) of S-protein interaction with ACE2 receptor. 2021 Computers in biology and medicine Figure SARS_CoV_2 A845V;D614G;N501Y;P1143L;S50L;H49Y 74;67;60;85;54;48 79;72;65;91;58;52 S 96 97 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. S50L nonsynonymous mutant S-protein residue interaction with ACE-2 receptor prepared by Ligplot. 2021 Computers in biology and medicine Figure SARS_CoV_2 S50L 0 4 S 26 27 34346744 SARS-CoV-2 Quasispecies Provides an Advantage Mutation Pool for the Epidemic Variants. Six current epidemic variant lineages are highlighted and evolved from a predominant variant with D614G mutations. 2021 Microbiology spectrum Figure SARS_CoV_2 D614G 98 103 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. Effects of the D614G mutation on the Dynamical Signature of the closed (purple) and open B chain RBD (blue) structures, measured by the difference between the calculated b-factors of D614 and G614. 2021 PLoS computational biology Figure SARS_CoV_2 D614G 15 20 RBD 97 100 34351895 Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants. The branches that comprehend most strains containing the D614G mutation are highlighted in red. 2021 PLoS computational biology Figure SARS_CoV_2 D614G 57 62 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. (F-I) Neutralization assays were performed against pseudoviruses displaying WT or S494P spike mutants, in the presence of serial dilutions of convalescent sera (F, G) or post-vaccination sera 1 month after the first and the second rounds of vaccination (H, I). 2021 PLoS pathogens Figure SARS_CoV_2 S494P 82 87 S 88 93 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. (F, H) Paired analysis of neutralizing activity of convalescent sera (F) or post-vaccination sera (H) against WT vs S494P, S494P/N501Y, E484K/S494P or E484K/S494P/N501Y mutants. 2021 PLoS pathogens Figure SARS_CoV_2 E484K;E484K;S494P;S494P;N501Y;N501Y;S494P;S494P 136;151;116;123;129;163;142;157 141;156;121;128;134;168;147;162 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. (G, I) Ratios of sera neutralization between S494P mutants and WT viruses. 2021 PLoS pathogens Figure SARS_CoV_2 S494P 45 50 34352360 A discernable increase in the severe acute respiratory syndrome coronavirus 2 R.1 lineage carrying an E484K spike protein mutation in Japan. The R.1 lineage carries the E484K mutation in the S protein; common genetic features are highlighted above the schematic representation of the SARS-CoV-2 genome structure. 2021 Infection, genetics and evolution Figure SARS_CoV_2 E484K 28 33 S 50 51 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. (A,D) profile of B.1.1.7 UK variant; (B,E) profile of B.1.1.7 variant with S71F mutation; (C,F) profile of P.1.351 or P.1 variants. 2021 Diagnostics (Basel, Switzerland) Figure SARS_CoV_2 S71F 75 79 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. * with or without S67A mutation, (D,E) were B.1.1.7 without E484K mutation. 2021 Diagnostics (Basel, Switzerland) Figure SARS_CoV_2 E484K;S67A 60;18 65;22 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. With the ID Solution kit, the green, blue and red curves correspond to SARS-CoV-2, N501Y and DeltaH69/DeltaV70, respectively. 2021 Diagnostics (Basel, Switzerland) Figure SARS_CoV_2 N501Y 83 88 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. With the PerkinElmer kit, the green, blue, red and orange curves correspond to SARS-CoV-2, N501Y, DeltaH69/DeltaV7 and E484K, respectively. 2021 Diagnostics (Basel, Switzerland) Figure SARS_CoV_2 E484K;N501Y 119;91 124;96 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. (A) SARS-CoV-2 genome map with the detailed sequence information of the designed crRNA targeting the D614G mutation. 2021 Virus research Figure SARS_CoV_2 D614G 101 106 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. (A) Schematic of the process for design of D614G specific primer with synthetic mismatch. 2021 Virus research Figure SARS_CoV_2 D614G 43 48 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. (B) Fluorescence signals of CRISPR/Cas12a-based detection of D614G mutation with crRNA-0. 2021 Virus research Figure SARS_CoV_2 D614G 61 66 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. (C) Schematic of the process for design of D614G specific spacers with synthetic mismatches. 2021 Virus research Figure SARS_CoV_2 D614G 43 48 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. (D) Fluorescence signals of CRISPR/Cas12a-based detection of D614G mutation with crRNAs design in (C). 2021 Virus research Figure SARS_CoV_2 D614G 61 66 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. crRNAs design and specificity of Cas12-based detection of SARS-CoV-2 D614G mutation. 2021 Virus research Figure SARS_CoV_2 D614G 69 74 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Sensitivity evaluation Cas12a-based detection of SARS-CoV-2 D614G mutation. 2021 Virus research Figure SARS_CoV_2 D614G 60 65 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Synthetic mismatches are placed in -3 to +3 position of the SNP (A23403G) site of D614G mutation. 2021 Virus research Figure SARS_CoV_2 D614G;A23403G 82;65 87;72 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Synthetic RNA of SARS-CoV-2 D614G detected by dsmCRISPR. 2021 Virus research Figure SARS_CoV_2 D614G 28 33 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. The 3' end of the forward primer is located at the SNP (A23403G) site of D614G mutation with a synthetic mismatch which is the same as that of crRNA-1. 2021 Virus research Figure SARS_CoV_2 D614G;A23403G 73;56 78;63 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Validation of primer mismatch amplification of SARS-CoV-2 D614G by PCR and Cas12-based detection. 2021 Virus research Figure SARS_CoV_2 D614G 58 63 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. (C) Plaque morphology of mutant D330A, Y414A and WT virus at passage 10 (P10). 2021 Emerging microbes & infections Figure SARS_CoV_2 D330A;Y414A 32;39 37;44 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. (D) The D330A and Y414A mutants were maintained after 10 rounds of passage. 2021 Emerging microbes & infections Figure SARS_CoV_2 D330A;Y414A 8;18 13;23 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. (E) One-step replication curves of D330A, Y414A, and WT virus were measured on Neuro 2a cells and L2 cells at an MOI of 0.01. 2021 Emerging microbes & infections Figure SARS_CoV_2 D330A;Y414A 35;42 40;47 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. Four-week-old C57BL/6 mice were immunized with 5x105 PFU D330A, Y414A, while the WT virus and DMEM were used as positive and mock control, respectively. 2021 Emerging microbes & infections Figure SARS_CoV_2 D330A;Y414A 57;64 62;69 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. (A) Quantitative data of the binding efficiency of S309-CAR-NKprimary to pseudotyped SARS-CoV-2 and D614G variant viral particles. 2021 Frontiers in immunology Figure SARS_CoV_2 D614G 100 105 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. (C) Expanded S309-CAR-NKprimary has increased killing activity against A549-Spike and A549-Spike D614G cells compared to CR3022-CAR-NKprimary. 2021 Frontiers in immunology Figure SARS_CoV_2 D614G 97 102 S;S 76;91 81;96 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. Briefly, effector cells were cocultured with A549, A549-Spike, or A549-Spike D614G for 4 hours at 37 C. 2021 Frontiers in immunology Figure SARS_CoV_2 D614G 77 82 S;S 56;71 61;76 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. Effector cells were blocked with anti-CD16 and anti-NKG2D prior to coculturing with A549-Spike or A549-Spike D614G target cells for 4 hours at 37 C. 2021 Frontiers in immunology Figure SARS_CoV_2 D614G 109 114 S;S 89;103 94;108 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. S309-CAR-NKprimary cells can also target SARS-CoV-2 D614G variant. 2021 Frontiers in immunology Figure SARS_CoV_2 D614G 52 57 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Detected copy numbers of WT and N501Y in mixtures containing ~600 copies WT and 2-fold dilution series of variant lineage B.1.351. 2021 The Science of the total environment Figure SARS_CoV_2 N501Y 32 37 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Detected copy numbers of WT and N501Y in mixtures containing ~700 copies variant lineage B.1.351WT and 2-fold dilution series of WT. 2021 The Science of the total environment Figure SARS_CoV_2 N501Y 32 37 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Proportion of Spike gene RNA fragments containing the N501Y mutation in wastewater from Amsterdam (A) and Utrecht (B) calculated as relative concentration of N501Y containing Spike gene fragments divided by the total concentration of S-gene fragments (WT + N501Y). 2021 The Science of the total environment Figure SARS_CoV_2 N501Y;N501Y;N501Y 54;158;257 59;163;262 S;S;S 14;175;234 19;180;235 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. The expected and detected proportion of N501Y (A) and WT (B) in artificial mixtures of WT and lineage B.1.351 as detected by ddPCR. 2021 The Science of the total environment Figure SARS_CoV_2 N501Y 40 45 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. The proportion of newly COVID-19 patients infected with N501Y containing variants (Pathogen genomic surveillance) are shown as (the proportional sum of lineages B.1.1.7, B.1.351 and P.1). 2021 The Science of the total environment Figure SARS_CoV_2 N501Y 56 61 COVID-19 24 32 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. a Pseudovirus with spike mutations L5F, T95I, D253G, E484K, D614G (B.1.526 v.1), and A701V. 2021 Nature communications Figure SARS_CoV_2 A701V;D253G;D614G;E484K;L5F;T95I 85;46;60;53;35;40 90;51;65;58;38;44 S 19 24 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. a Spaciotemporal pattern of B.1.526 E484K lineage in New York City (NYC). 2021 Nature communications Figure SARS_CoV_2 E484K 36 41 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Also displayed is the logistic regression for B.1.526 samples with E484K mutation (red dotted line) and without (blue dotted line). 2021 Nature communications Figure SARS_CoV_2 E484K 67 72 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. b Pseudovirus with spike mutations L5F, T95I, D253G, S477N, D614G, and Q957R (B.1.526 v.2). 2021 Nature communications Figure SARS_CoV_2 D253G;D614G;L5F;Q957R;S477N;T95I 46;60;35;71;53;40 51;65;38;76;58;44 S 19 24 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. b Spaciotemporal pattern of B.1.526 without E484K lineage in NYC. 2021 Nature communications Figure SARS_CoV_2 E484K 44 49 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Data represent 38 B.1.526 E484K variants out of 782 sequenced genomes in December 1, 2020-January 31, 2021, 1,755 B.1.526 E484K variants out of 8437 sequenced genomes in February 1-March 31, 2021 and 1,518 B.1.526 E484K variants identified out of a total of 6702 sequenced genomes in April 1-May 18, 2021. 2021 Nature communications Figure SARS_CoV_2 E484K;E484K;E484K 26;122;214 31;127;219 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Data represent 45 B.1.526 variants without E484K out of 782 sequenced genomes in December 1, 2020-January 31, 2021, 1,349 B.1.526 variants without E484K out of 8,437 sequenced genomes in February 1-March 31, 2021 and 927 B.1.526 variants without E484K identified out of a total of 6702 sequenced genomes in April 1-May 18, 2021. 2021 Nature communications Figure SARS_CoV_2 E484K;E484K;E484K 43;147;246 48;152;251 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Point density of B.1.526 variants with the E484K mutation geo-located by case address overlayed on a map of NYC delineated by zip code. 2021 Nature communications Figure SARS_CoV_2 E484K 43 48 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Point density of B.1.526 variants without the E484K mutation geo-located by case address overlayed on a map of NYC delineated by zip code. 2021 Nature communications Figure SARS_CoV_2 E484K 46 51 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The B.1.526 clade defined by the E484K mutation is highlighted in red. 2021 Nature communications Figure SARS_CoV_2 E484K 33 38 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The color indicates the estimated rolling mean of prevalence out of all samples for B.1.1.7 (green), B.1.526.1 (orange), B.1.526 E484K (red), B.1.526 E484 (blue). 2021 Nature communications Figure SARS_CoV_2 E484K 129 134 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The S477N site is also shown (label outlined) for the branch containing this mutation instead of the E484K mutation. 2021 Nature communications Figure SARS_CoV_2 E484K;S477N 101;4 106;9 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. The previous 7-day rolling average of SARS-CoV-2 positive specimens is represented in blue and the same day's previous 7-day rolling average of the number of specimens tested with both the DeltaH69/V70 and N501Y assays is represented in orange. 2021 Microbiology spectrum Figure SARS_CoV_2 N501Y 206 211 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Yellow circles, branches with L452R; blue, with L452Q; orange, with L452M. 2021 Journal of clinical microbiology Figure SARS_CoV_2 L452M;L452Q;L452R 68;48;30 73;53;35 34385423 Potent prophylactic and therapeutic efficacy of recombinant human ACE2-Fc against SARS-CoV-2 infection in vivo. c hACE2-Fc potently neutralized SARS-CoV-2 pp mutant bearing D614G or V367F. 2021 Cell discovery Figure SARS_CoV_2 D614G;V367F 61;70 66;75 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. (A) RMSD values in the WT system (red) and N354D system (blue). 2021 Frontiers in molecular biosciences Figure SARS_CoV_2 N354D 43 48 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. (B) N354D system. 2021 Frontiers in molecular biosciences Figure SARS_CoV_2 N354D 4 9 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. (B) Residues Asn134-Glu140 of ACE2 in the D364Y system. 2021 Frontiers in molecular biosciences Figure SARS_CoV_2 D364Y 42 47 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. (B) WT system and D364Y system (green). 2021 Frontiers in molecular biosciences Figure SARS_CoV_2 D364Y 18 23 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. (C) WT system and V367F system (purple). 2021 Frontiers in molecular biosciences Figure SARS_CoV_2 V367F 18 23 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. (D) Residues Pro384-Asp389 of RBD in the N354D system. 2021 Frontiers in molecular biosciences Figure SARS_CoV_2 N354D 41 46 RBD 30 33 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. (D) WT system and Q498A system (orange). 2021 Frontiers in molecular biosciences Figure SARS_CoV_2 Q498A 18 23 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. (E) Residues Pro384-Asp389 of RBD in the V367F system. 2021 Frontiers in molecular biosciences Figure SARS_CoV_2 V367F 41 46 RBD 30 33 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. RMSF values of ACE2 and RBD in the WT system (red), N354D system (blue), D364Y system (green), V367F system (blue) and Q498A system (orange). 2021 Frontiers in molecular biosciences Figure SARS_CoV_2 D364Y;N354D;Q498A;V367F 73;52;119;95 78;57;124;100 RBD 24 27 34386518 Non-RBM Mutations Impaired SARS-CoV-2 Spike Protein Regulated to the ACE2 Receptor Based on Molecular Dynamic Simulation. The arrow (green) plot of the first (PC1) motion modes for the RBM (blue) region in the WT system (A), N354D system (B), D364Y system (C), V367F system (D), and Q498A system (E). 2021 Frontiers in molecular biosciences Figure SARS_CoV_2 D364Y;N354D;Q498A;V367F 121;103;161;139 126;108;166;144 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. (b) Frequency of S477N mutations by country as a function of a total 6 974 S477N amino acid mutants. 2021 Antibody therapeutics Figure SARS_CoV_2 S477N;S477N 17;75 22;80 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. (c) Frequency of N439K mutations by country as a function of a total 629 N439K amino acid mutants. 2021 Antibody therapeutics Figure SARS_CoV_2 N439K;N439K 17;73 22;78 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. 293 T cells with pCEP4-MYC-ACE2 plasmid were incubated with RBD (K417N-E484K-N501Y)-sfGFP-containing medium and co-stained with fluorescent anti-MYC Alexa 647 to detect surface ACE2 by flow cytometry. 2021 Biomedicine & pharmacotherapy Figure SARS_CoV_2 K417N;E484K;N501Y 65;71;77 70;76;82 RBD 60 63 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. 293T cells with pCEP4-myc-ACE2 plasmid were incubated with RBD (N501Y(A), K417N(C), E484K(E) or L452R(G))-sfGFP-containing medium and co-stained with fluorescent anti-MYC Alexa 647 to detect surface ACE2 by flow cytometry. 2021 Biomedicine & pharmacotherapy Figure SARS_CoV_2 E484K;K417N;L452R;N501Y 84;74;96;64 89;79;101;69 RBD 59 62 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Effect of GB-2 on interaction between ACE2 and SARS-CoV-2 Spike (K417N-E484K-N501Y). 2021 Biomedicine & pharmacotherapy Figure SARS_CoV_2 K417N;E484K;N501Y 65;71;77 70;76;82 S 58 63 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Effect of GB-2 on interaction between ACE2 and SARS-CoV-2 Spike (K417N, E484K, N501Y or L452R). 2021 Biomedicine & pharmacotherapy Figure SARS_CoV_2 E484K;L452R;N501Y;K417N 72;88;79;65 77;93;84;70 S 58 63 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Then, two subsets of the ACE2-positive population were collected: the top population (nCoV-S-High sort, red gate) and the bottom population (nCoV-S-Low sort, green gate) based on the fluorescence of bound RBD (N501Y(A), K417N(C), E484K(E) or L452R(G))-sfGFP relative to ACE2 surface expression. 2021 Biomedicine & pharmacotherapy Figure SARS_CoV_2 E484K;K417N;L452R;N501Y 230;220;242;210 235;225;247;215 RBD;S;S 205;91;146 208;92;147 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Then, two subsets of the ACE2-positive population were collected: the top population (nCoV-S-High sort, red gate) and the bottom population (nCoV-S-Low sort, green gate) based on the fluorescence of bound RBD(K417N-E484K-N501Y)-sfGFP relative to ACE2 surface expression. 2021 Biomedicine & pharmacotherapy Figure SARS_CoV_2 K417N;E484K;N501Y 209;215;221 214;220;226 RBD;S;S 205;91;146 208;92;147 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. effect of mutation W258L on the geometry of antibody binding surface. 2021 Journal of autoimmunity Figure SARS_CoV_2 W258L 19 24 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Impact of G142D and R156G mutations, the steric clash between D142 and R158 is shown in the dotted line of 1.6 A length. 2021 Journal of autoimmunity Figure SARS_CoV_2 G142D;R156G 10;20 15;25 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Note that the mutation K417N (as in Delta Plus) would result in the loss of this interaction. 2021 Journal of autoimmunity Figure SARS_CoV_2 K417N 23 28 34399188 Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. Prevalence of five key mutations (T95I, G142D, R158G, L452R, T478K, and K417N) at different time points in Delta variant (n = 600) sequences and Delta Plus variant (n = 200) sequences. 2021 Journal of autoimmunity Figure SARS_CoV_2 G142D;K417N;L452R;R158G;T478K;T95I 40;72;54;47;61;34 45;77;59;52;66;38 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. (A) SARS-CoV-2/B.1.351 variants detected by ORF1ab and S484K assays. 2021 Chinese medical journal Figure SARS_CoV_2 S484K 55 60 ORF1ab 44 50 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. (B) SARS-CoV-2/B.1.1.7 variants detected by ORF1ab and S501Y assays. 2021 Chinese medical journal Figure SARS_CoV_2 S501Y 55 60 ORF1ab 44 50 34403732 Identification of natural compounds as SARS-CoV-2 entry inhibitors by molecular docking-based virtual screening with bio-layer interferometry. After 24 h, the hACE2 overexpressing cells were infected by RBD wild-type and mutant S-pseudotyped lentivirus (D614G, N501Y, N439K & Y453F) (green) in the presence of 0-100 muM EGCG. 2021 Pharmacological research Figure SARS_CoV_2 N439K;N501Y;Y453F;D614G 125;118;133;111 130;123;138;116 RBD;S 60;85 63;86 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. (A) Plaques formed by the early-passage (P1) isolate of CoV-2/UAB and the recombinant CoV-2/GFP-based variants, containing either the insertion in the NTD or S686G mutation or both modifications. 2021 Journal of virology Figure SARS_CoV_2 S686G 158 163 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. CoV-2/GFP acquires an S686G mutation in P1' of FCS. 2021 Journal of virology Figure SARS_CoV_2 S686G 22 27 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. The S686G mutation has negative effect on the ability of SARS-CoV-2 virus to form syncytia. 2021 Journal of virology Figure SARS_CoV_2 S686G 4 9 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. Interatomic interactions were altered by mutations at locus R118C, T148I, Y149C, E802A, Q822H, V880I and D893Y as shown in figure. 2021 Archives of microbiology Figure SARS_CoV_2 D893Y;E802A;Q822H;R118C;T148I;V880I;Y149C 105;81;88;60;67;95;74 110;86;93;65;72;100;79 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. (B) Characteristic dynamic fluctuations of both RBD-REGN10987 and RBD(N439K)-REGN10987 complexes. 2021 Frontiers in cell and developmental biology Figure SARS_CoV_2 N439K 70 75 RBD;RBD 48;66 51;69 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. (B) The RMSDs of the backbone atoms of both RBD-hACE2 complexes, the RBD-hACE2 is colored orange and RBD(N439K)-hACE2 is colored blue. 2021 Frontiers in cell and developmental biology Figure SARS_CoV_2 N439K 105 110 RBD;RBD;RBD 44;69;101 47;72;104 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. (C) The binding free energies for SARS-CoV-2 RBM-hACE2 (including wild type and variant N439K), using orange for wild-type and blue for mutant type. 2021 Frontiers in cell and developmental biology Figure SARS_CoV_2 N439K 88 93 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. (C) The RMSFs of Calphaatoms of both RBD-hACE2 complexes, where RBD-hACE2 is colored orange and RBD(N439K)-hACE2 is colored blue. 2021 Frontiers in cell and developmental biology Figure SARS_CoV_2 N439K 100 105 RBD;RBD;RBD 37;64;96 40;67;99 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. The N501Y, K417N, and E484K mutations are highlighted in red with a *. 2021 eLife Figure SARS_CoV_2 E484K;K417N;N501Y 22;11;4 27;16;9 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. Correlation of plasma IgG antibody binding to Wuhan-1 Asp614Gly wild-type vs beta (B.1.351) full-length spike protein in vaccine recipients. 2021 The lancet. HIV Figure SARS_CoV_2 D614G 54 63 S 104 109 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. Pseudovirus neutralisation responses to Wuhan-1 Asp614Gly wild-type on day 42 in vaccinees. 2021 The lancet. HIV Figure SARS_CoV_2 D614G 48 57 34417349 SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. (A) Heat map showing the neutralization activity of tested plasma samples to the SARS-CoV-2 WT and D614G and PT188-EM variants. 2021 Proc Natl Acad Sci U S A Figure SARS_CoV_2 D614G 99 104 34417349 SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. (D) In silico model of the PT188-EM spike RBD based on PDB ID code 6M17, where the E484K mutation is shown with licorice representation. 2021 Proc Natl Acad Sci U S A Figure SARS_CoV_2 E484K 83 88 S;RBD 36;42 41;45 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. Plots show correlations between SARS-CoV-2 WA-1 S-specific IgG, B.1.351 S-specific IgG, WA-1 RBD-specific IgG, B.1.351 RBD-specific IgG, D614G lentiviral-based pseudovirus neutralization, B.1.351 lentiviral-based pseudovirus neutralization, D614G VSV-based pseudovirus neutralization, B.1.351 VSV-based pseudovirus neutralization, D614G focus reduction neutralization, and B.1.351 focus reduction neutralization at week 12. 2021 Nature immunology Figure SARS_CoV_2 D614G;D614G;D614G 137;241;331 142;246;336 RBD;RBD;S;S 93;119;48;72 96;122;49;73 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. Sera collected at weeks 0, 2, 7, and 12 were assessed for SARS-CoV-2 D614G (A), and B.1.351 (B) lentiviral-based pseudovirus neutralization. 2021 Nature immunology Figure SARS_CoV_2 D614G 69 74 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. HEK293T-ACE2 cells were infected with the recombinant lentiviruses' pseudoviruses (0.37 microl, 1 x 107 TU/ml) with the indicated SARS-CoV-2 S protein (wild-type, N354D, or V367F). 2021 Infectious diseases of poverty Figure SARS_CoV_2 N354D;V367F 163;173 168;178 S 141 142 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. Pseudoviruses with the indicated SARS-CoV-2 S proteins (wild-type, N354D, or V367F) were incubated (1 h, room temperature) with different concentrations of neutralization antibody, before being inoculated into HEK293T-ACE2 cells. 2021 Infectious diseases of poverty Figure SARS_CoV_2 N354D;V367F 67;77 72;82 S 44 45 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. (a) WT vs N501Y RBD; (b) WT vs N501Y-E484K-K417N RBD. 2021 EBioMedicine Figure SARS_CoV_2 N501Y;N501Y;E484K;K417N 10;31;37;43 15;36;42;48 RBD;RBD 16;49 19;52 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Comparison of anti-RBD IgG for serum optical density values of 272 convalescent COVID-19 patients between wild type, N501Y, and N501Y-E484K-K417N RBD mutant. 2021 EBioMedicine Figure SARS_CoV_2 N501Y;N501Y;E484K;K417N 117;128;134;140 122;133;139;145 RBD;RBD 19;146 22;149 COVID-19 80 88 34423327 Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing. (D) Identification of a B.1.1.7 variant, characterized by the presence of an additional A522S (G23126T) mutation in the Spike protein. 2021 The Lancet regional health. Europe Figure SARS_CoV_2 A522S;G23126T 88;95 93;102 S 120 125 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. a, Neutralizing activities of 12 monoclonal antibodies against pseudoviruses containing E484K alone or all five signature B.1.526 mutations (L5F, T95I, D253G, A701V and E484K) (NYDelta5(E484K)), as well as against the authentic B.1.526-E484K. 2021 Nature Figure SARS_CoV_2 A701V;D253G;E484K;E484K;T95I;E484K;L5F;E484K 159;152;88;169;146;186;141;236 164;157;93;174;150;191;144;241 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. a, Neutralizing activities of 12 monoclonal antibodies against pseudoviruses containing S477N alone or all five signature B.1.526-S477N mutations (L5F, T95I, D253G, A701V, and S477N), termed NYDelta5(S477N). 2021 Nature Figure SARS_CoV_2 A701V;D253G;S477N;S477N;T95I;L5F;S477N;S477N 165;158;88;176;152;147;200;130 170;163;93;181;156;150;205;135 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. b, Fold change in virus-neutralizing activity of plasma from patients who have recovered from SARS-CoV-2 infection (convalescent plasma) (n = 20) and sera from vaccinated individuals (vaccinee sera) (n = 22) against the NYDelta5(E484K) pseudovirus compared with wild-type pseudovirus, as well as against authentic B.1.526-E484K and wild-type virus (WA1) (numbers shown above P-values). 2021 Nature Figure SARS_CoV_2 E484K;E484K 229;322 234;327 COVID-19 94 114 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. b, Neutralizing activities of convalescent plasma (n = 20) against NYDelta5(S477N) as well as against the authentic B.1.526 virus with S477N, and neutralizing activities of vaccinee sera (n = 22) against the NYDelta5(S477N) pseudovirus, compared to wild-type counterparts. 2021 Nature Figure SARS_CoV_2 S477N;S477N;S477N 135;76;217 140;81;222 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Left, PCR-based genotyping assays for E484K and N501Y (see Extended Data. 2021 Nature Figure SARS_CoV_2 E484K;N501Y 38;48 43;53 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Neutralization studies of B.1.526-E484K and comparative analyses. 2021 Nature Figure SARS_CoV_2 E484K 34 39 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Neutralization studies of B.1.526-S477N. 2021 Nature Figure SARS_CoV_2 S477N 34 39 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Phylogenetic tree based on whole-genome alignment of genomes sequenced from our hospital centre with at least one mutation of interest or concern (E484K, N501Y, S477N, or L452R) and unique spike protein mutation constellations (n = 64). 2021 Nature Figure SARS_CoV_2 L452R;N501Y;S477N;E484K 171;154;161;147 176;159;166;152 S 189 194 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Prevalence of E484K-harbouring SARS-CoV-2 and B.1.526. 2021 Nature Figure SARS_CoV_2 E484K 14 19 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Spike protein mutations are labelled on the tree, showing the stepwise accumulation of signature B.1.526 mutations T95I, D253G and L5F, and branching of B.1.526-E484K (orange) and two B.1.526-S477N sub-lineages (yellow, blue). 2021 Nature Figure SARS_CoV_2 D253G;L5F;T95I;E484K;S477N 121;131;115;161;192 126;134;119;166;197 S 0 5 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. The B.1.526-L452R sub-lineage (green) emerged in parallel. 2021 Nature Figure SARS_CoV_2 L452R 12 17 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. The D253G mutation resides in the antigenic supersite within the N-terminal domain (NTD), a target for neutralizing antibodies, E484K and S477N at the RBD interface with the cellular receptor ACE2, and A701V near the furin cleavage site. 2021 Nature Figure SARS_CoV_2 A701V;D253G;E484K;S477N 202;4;128;138 207;9;133;143 RBD;N 151;65 154;66 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. The earliest detected variant with the E484K mutation was collected in mid-November 2020. 2021 Nature Figure SARS_CoV_2 E484K 39 44 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. The prevalence of E484K (samples with E484K/total PCR-genotyped samples) subsequently increased over time, from 1.8% between 1 and 15 December 2020 to 26.1% between 1 and 15 March 2021. 2021 Nature Figure SARS_CoV_2 E484K;E484K 18;38 23;43 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Throughout late 2020 and early 2021, we identified fewer isolates with N501Y than with E484K, with a maximum of 5.9% of isolates containing N501Y in mid-February 2021. 2021 Nature Figure SARS_CoV_2 E484K;N501Y;N501Y 87;71;140 92;76;145 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. We identified a significant proportion of samples with E484K (11%), later confirmed through sequencing to primarily fall within the B.1.526 lineage, and a number of samples with N501Y (3.9%), primarily within the B.1.1.7 lineage. 2021 Nature Figure SARS_CoV_2 E484K;N501Y 55;178 60;183 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. (A and B) Total antibody binding (Max RU) of 1mg/mL for the six batches of hCoV-2IG (hCoV-2IG-1 to hCoV-2IG-6) to purified WA-1 RBD (RBD-wt) and RBD mutants: RBD-K417N, RBD-N501Y and RBD-E484K by SPR (A). 2021 iScience Figure SARS_CoV_2 E484K;K417N;N501Y 187;162;173 192;167;178 RBD;RBD;RBD;RBD;RBD;RBD 128;133;145;158;169;183 131;136;148;161;172;186 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. (B) The fold-decrease in antibody binding to mutants RBD-K417N, RBD-N501Y and RBD-E484K of hCoV-2IG in comparison with RBD-wt from WA-1 strain was calculated from the data in Panel A. 2021 iScience Figure SARS_CoV_2 E484K;K417N;N501Y 82;57;68 87;62;73 RBD;RBD;RBD;RBD 53;64;78;119 56;67;81;122 34433426 Investigation of Interaction between the Spike Protein of SARS-CoV-2 and ACE2-Expressing Cells Using an In Vitro Cell Capturing System. A S1 or D614G S1 variant was immobilized on 96 well microplates, and HEK293 cells stably expressing ACE2-GFP were incubated with ACE2-293 T cells. 2021 Biological procedures online Figure SARS_CoV_2 D614G 8 13 34433426 Investigation of Interaction between the Spike Protein of SARS-CoV-2 and ACE2-Expressing Cells Using an In Vitro Cell Capturing System. B FLAG-tagged ACE2 stable expressed cells lysate were incubate with Spike S1 or S1(D614G) proteins. 2021 Biological procedures online Figure SARS_CoV_2 D614G 83 88 34433426 Investigation of Interaction between the Spike Protein of SARS-CoV-2 and ACE2-Expressing Cells Using an In Vitro Cell Capturing System. Fluorescence intensity quantification of S1 or S1(D614G) indicated below each band were normalized by each input. 2021 Biological procedures online Figure SARS_CoV_2 D614G 50 55 34433426 Investigation of Interaction between the Spike Protein of SARS-CoV-2 and ACE2-Expressing Cells Using an In Vitro Cell Capturing System. The D614G mutation increases ACE2-expressing cell capturing ability of S protein. 2021 Biological procedures online Figure SARS_CoV_2 D614G 4 9 S 71 72 34433803 ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker. a-g 3E8 blocked infections of ACE2-overexpressing HEK293 cells by different pseudo-typed coronaviruses with Env-defective HIV-1 and full-length S-proteins from SARS-CoV-2, SARS-CoV-2-D614G, B.1.1.7, B.1.351, B.1.617.1, SARS-CoV, and HCoV-NL63. 2021 Signal transduction and targeted therapy Figure SARS_CoV_2 D614G 183 188 S 144 145 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. (A) N501Y has emerged independently in the three clades 501Y.V1, 501Y.V2, and 501Y.V3. 2021 eLife Figure SARS_CoV_2 N501Y 4 9 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. (B, C) Show the difference (DeltaDeltaDeltaG) between the measured and predicted DeltaDeltaG for S19P (B) and K26R (C) ACE2 variants binding to the indicated RBD variants, calculated from data in Table 2. 2021 eLife Figure SARS_CoV_2 K26R 110 114 RBD 158 161 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. (B) E484K has also been observed independently of its main progenitor clades 501Y.V2 and 501Y.V3. 2021 eLife Figure SARS_CoV_2 E484K 4 9 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. (C) S477N has been observed beyond clades 20 F and 20A.EU2. 2021 eLife Figure SARS_CoV_2 S477N 4 9 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. E484Q and E484G have also been observed. 2021 eLife Figure SARS_CoV_2 E484G;E484Q 10;0 15;5 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Overlay of traces showing association and dissociation of N501Y (A) and K417N (B) RBD variants when injected at a range of concentrations over immobilised WT ACE2. 2021 eLife Figure SARS_CoV_2 K417N;N501Y 72;58 77;63 RBD 82 85 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. The koff (A) and kon (B) for E484K/N501Y (UK2) RBD binding WT ACE2 at a range of surface immobilisations (n = 12). 2021 eLife Figure SARS_CoV_2 E484K;N501Y 29;35 34;40 RBD 47 50 34448936 Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. Viruses in the B.1.1.519 lineage were initially classified within the B.1.1.222 lineage, and they contain the mutations T478K, P681H, and T732A (green box). 2021 Archives of virology Figure SARS_CoV_2 P681H;T478K;T732A 127;120;138 132;125;143 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. BLI sensorgrams illustrating the interaction between ACE2 and (A) wild-type RBD (RBDWT); (B) E484K single-mutant RBD (RBDE484K); (C) L452R/E484Q double-mutant RBD (RBDL452R/E484Q; and (D)) N440 single-mutant RBD (RBDN440K) 2022 Allergy Figure SARS_CoV_2 E484K;E484Q;E484Q;E484K;L452R 93;139;173;121;167 98;144;178;126;172 RBD;RBD;RBD;RBD;RBD;RBD;RBD 76;113;118;159;164;208;213 79;116;121;162;167;211;216 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. BLI sensorgrams illustrating the interaction between ACE2 and (A) wild-type RBD (RBDWT); (B) E484K single-mutant RBD (RBDE484K); (C) L452R/E484Q double-mutant RBD (RBDL452R/E484Q; and (D)) N440 single-mutant RBD (RBDN440K). 2022 Allergy Figure SARS_CoV_2 E484K;L452R;E484Q;E484Q 93;133;139;173 98;138;144;178 RBD;RBD;RBD;RBD;RBD;RBD;RBD 76;113;118;159;164;208;213 79;116;121;162;167;211;216 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. Comparison of total anti-RBD IgG and RBD-ACE2-blocking antibodies between wild-type RBD and mutants E484K, L452R/E484Q, and N440K. 2022 Allergy Figure SARS_CoV_2 E484K;L452R;N440K;E484Q 100;107;124;113 105;112;129;118 RBD;RBD;RBD 25;37;84 28;40;87 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. Positions of mutations N440K, L452R, and E484Q. 2022 Allergy Figure SARS_CoV_2 E484Q;L452R;N440K 41;30;23 46;35;28 34454120 The low contagiousness and new A958D mutation of SARS-CoV-2 in children: An observational cohort study. C24435A and A19945G are missense variants; the others are synonymous variants. 2021 International journal of infectious diseases Figure SARS_CoV_2 A19945G;C24435A 12;0 19;7 34454120 The low contagiousness and new A958D mutation of SARS-CoV-2 in children: An observational cohort study. H) The structure and the A958D mutation of the spike protein. 2021 International journal of infectious diseases Figure SARS_CoV_2 A958D 25 30 S 47 52 34455390 Evolution of antibody responses up to 13 months after SARS-CoV-2 infection and risk of reinfection. (b) Neutralizing antibody titers (log IC50) against the D614G, B.1.1.7, and B.1.351 variants measured at M11-13. 2021 EBioMedicine Figure SARS_CoV_2 D614G 56 61 34455390 Evolution of antibody responses up to 13 months after SARS-CoV-2 infection and risk of reinfection. (c) Spearman correlation between anti-RBD IgG titers (log BAU/mL) and neutralizing antibody titer (log IC50) against D614G (green circles), B.1.1.7 (purple squares), and B.1.351 (orange triangles) variants measured at M11-13 in vaccinated (n = 13) and unvaccinated (n = 15) HCW. 2021 EBioMedicine Figure SARS_CoV_2 D614G 117 122 RBD 38 41 34455390 Evolution of antibody responses up to 13 months after SARS-CoV-2 infection and risk of reinfection. Neutralizing antibody titers against live-strains of D614G, B.1.1.7, and B.1.351 variants of SARS-CoV-2 were measured in sera collected at M11-13 for 13 single-dose vaccinated HCW and 15 unvaccinated HCW. 2021 EBioMedicine Figure SARS_CoV_2 D614G 53 58 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. Mutated amino acid positions shown in the human ACE2 receptor bound structure (PDB ID: 6acj) of SARS-CoV-2 spike protein (except L5F, S13I, Q14H, G75V, T76I, Y145del, H146Y, Q675 H/R, Q677H, N679K, I834V, R1185H and K1195N as the regions were not covered in the structure). 2021 Heliyon Figure SARS_CoV_2 G75V;H146Y;I834V;K1195N;L5F;N679K;Q14H;Q675H;Q675R;Q677H;R1185H;S13I;T76I;Y145del 146;167;198;216;129;191;140;174;174;184;205;134;152;158 150;172;203;222;132;196;144;182;182;189;211;138;156;165 S 107 112 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. GMTs and 95% CIs are indicated: D614G (75.1), alpha (18.5), gamma (10.05) variant. 2022 Journal of medical virology Figure SARS_CoV_2 D614G 32 37 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. Neutralization assays with D614G (lineage B, blue circles), alpha (lineage B.1.1.7, red circles) and gamma (lineage P.1, green circles) variants were done. 2022 Journal of medical virology Figure SARS_CoV_2 D614G 27 32 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. Neutralization assays with infectious D614G (lineage B), alpha (lineage B.1.1.7) and gamma (lineage P.1) variants were done. 2022 Journal of medical virology Figure SARS_CoV_2 D614G 38 43 34460119 Neutralization of alpha, gamma, and D614G SARS-CoV-2 variants by CoronaVac vaccine-induced antibodies. Patterns of neutralizing antibody titers of 44 CoronaVac-vaccinated human sera against infectious D614G, alpha and gamma SARS-CoV-2 variants. 2022 Journal of medical virology Figure SARS_CoV_2 D614G 98 103 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. The affinity of ACE2 to Alpha RBD (N501Y) is below the detection limit and is presented as <1.0x10-12. 2021 bioRxiv Figure SARS_CoV_2 N501Y 35 40 RBD 30 33 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Three dimensional (left) and schematic representations (right) of (a) chondramide C3 (1) against wild-type, (b) chondramide C (2) against N501Y, and (c) chondramide C (2) against E484K SARS-CoV-2 spike variants. 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 E484K;N501Y 179;138 184;143 S 196 201 34463219 Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein. Three dimensional (left) and schematic representations (right) of chondramide C (2) against (a) South African (N501Y-E484K-K417N) and (b) Brazilian (N501Y-E484K-K417T) SARS-CoV-2 variants. 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 N501Y;N501Y;E484K;E484K;K417N;K417T 111;149;117;155;123;161 116;154;122;160;128;166 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. (A-C) Percent weight change over time (A) and viral RNA (B) and infectious virus titer (C) in lung homogenates 4 dpi of hamsters that received 5 mg/kg isotype (black) or 2C08 (gray) one day prior to intranasal challenge with 5x105 FFU of D614G, (left), Wash-B.1.351 (center), or B.1.617.2 (right) SARS-CoV-2. 2021 Immunity Figure SARS_CoV_2 D614G 238 243 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. D614G data are from two experiments, n = 10 per condition; variant data are from one experiment, n = 5 per condition. 2021 Immunity Figure SARS_CoV_2 D614G 0 5 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. ELISA binding to D614G RBD previously reported in. 2021 Immunity Figure SARS_CoV_2 D614G 17 22 RBD 23 26 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. Results are from one experiment performed in duplicate (A, D614G and B.1.617.2) or in singlet (A, B.1.1.7, B.1.351, and B.1.1.28), or two experiments performed in duplicate (B). 2021 Immunity Figure SARS_CoV_2 D614G 59 64 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Structural landscape of the D614G mutation. 2021 mBio Figure SARS_CoV_2 D614G 28 33 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Structural landscape of the E484K mutation. 2021 mBio Figure SARS_CoV_2 E484K 28 33 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Structural landscape of the K417N mutation. 2021 mBio Figure SARS_CoV_2 K417N 28 33 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Structural landscape of the K417T mutation. 2021 mBio Figure SARS_CoV_2 K417T 28 33 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Structural landscape of the N501Y mutation. 2021 mBio Figure SARS_CoV_2 N501Y 28 33 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Adhesion frequency curves of ACE2 binding with SARS2-RBD mutants (Q493N and F486L) (d) and SARS2-S (SARS2-SWT and SARS2-SD614G) are shown (f). 2021 Cell research Figure SARS_CoV_2 F486L;Q493N;D614G 76;66;121 81;71;126 RBD;S 53;97 56;98 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. b, c Pseudovirus infection of SARS2 wild-type (WT) or mutants (Q493N, F486L and D614G). 2021 Cell research Figure SARS_CoV_2 D614G;F486L;Q493N 80;70;63 85;75;68 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Comparisons of the efficiencies of SARS2 pseudotyped viruses (WT, Q493N, and F486L) infecting ACE2-expressing cells (c). 2021 Cell research Figure SARS_CoV_2 F486L;Q493N 77;66 82;71 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. D614G variation further accelerates S1/S2 detachment under mechanical force. 2021 Cell research Figure SARS_CoV_2 D614G 0 5 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. i Comparison of S1/S2 detaching probability of SARS2-SWT with that of SARS2-SD614G under force. 2021 Cell research Figure SARS_CoV_2 D614G 77 82 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Impairment of inter-protomer interactions by the D614G variation not only strengthens force-dependent SARS2-S/ACE2 binding, but also accelerates force-induced S1/S2 detachment. 2021 Cell research Figure SARS_CoV_2 D614G 49 54 S 108 109 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. The probabilities of H-bond formation in WT and D614G mutant are compared (c). 2021 Cell research Figure SARS_CoV_2 D614G 48 53 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. The representative set of curves of ACE2 binding with SARS2-RBD mutants (WT (h), Q493N (i), and F486L (j)) are shown. 2021 Cell research Figure SARS_CoV_2 F486L;Q493N 96;81 101;86 RBD 60 63 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. B and C, binding kinetics between SARS-CoV-2 RBD (WT or N501Y) and sACE2 assessed by BLI at different temperatures. 2021 The Journal of biological chemistry Figure SARS_CoV_2 N501Y 56 61 RBD 45 48 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. B, pseudoviruses Luc+ bearing SARS-CoV-2 Spike (D614G, D614G N501Y or B.1.1.7), or VSV-G as a control, were used to infect 293T-ACE2 cells. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G;N501Y;D614G 55;61;48 60;66;53 S 41 46 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. C-E, cell-surface staining of transfected 293T cells expressing SARS-CoV-2 Spike (WT, D614G, Furin KO, D614G Furin KO, D614G N501Y, or B.1.1.7 variant) or SARS-CoV-1 Spike (WT) using (C) CV3-25 mAb or (D and E) ACE2-Fc. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G;D614G;D614G;N501Y 86;103;119;125 91;108;124;130 S;S 75;166 80;171 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. C, cell-to-cell fusion was measured between 293T effector cells expressing HIV-1 Tat and SARS-CoV-2 Spike (D614G or B.1.1.7), or HIV-1 EnvJRFL as a control, which were incubated at 37C or 4C for 1 h prior coculture with TZM-bl-ACE2 target cells. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G 107 112 S 100 105 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. D and E, pseudoviruses Luc+ bearing SARS-CoV-2 Spike (WT, D614G or B.1.1.7) were used to infect 293T-ACE2 cells in presence of increasing concentrations of sACE2 at 37C for 1 h prior infection of 293T-ACE2 cells. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G 58 63 S 47 52 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. Enhanced affinity of SARS-CoV-2 RBD for ACE2 at low temperatures.A, the thermodynamic parameters of sACE2 binding to SARS-CoV-2 RBD WT or N501Y measured by ITC at 10C, 15C, 25C, and 35C. 2021 The Journal of biological chemistry Figure SARS_CoV_2 N501Y 138 143 RBD;RBD 32;128 35;131 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. F, authentic SARS-CoV-2 D614G virus was used to infect reconstituted human airway epithelia. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G 24 29 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. F, cell-surface staining of Vero E6 or primary human AECs from two healthy donors infected with authentic SARS-CoV-2 viruses (D614G or B.1.1.7 variant) using ACE2-Fc. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G 126 131 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. SARS-CoV-2 viral attachment and infectivity is higher at low temperatures.A, pseudoviruses encoding the luciferase gene (Luc+) and bearing SARS-CoV-2 Spike (D614G or D614G N501Y) were tested for virus capture by ACE2-Fc at 37C or 4C. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G;N501Y;D614G 166;172;157 171;177;162 S 150 155 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. SARS-CoV-2Spike trimer "opens" at low temperatures.A and B, binding of sACE2 to SARS-CoV-2 Spike (A) D614G or (B) B.1.1.7 expressed on 293T cells was measured at 37C or 4C by flow cytometry. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G 101 106 S 91 96 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. Eight mutations (Y453F, L455F, F456L, A475V, A475S, T500S, N501Y, and Y505H) were in the RBD and hACE2 interaction region (RBD/hACE2); 10 mutations (V367I, V382L, R408G, N438K, L452Q, S477N, T478K, E484Q, S494P, and A520S) were in the RBD region but no interaction with hACE2 (RBD/Non-hACE2); 6 mutations (S98F, D614G, P681H, S982A, D1118H, and D1118Y) were not in the RBD region (Non-RBD). 2021 Frontiers in immunology Figure SARS_CoV_2 A475S;A475V;A520S;D1118H;D1118Y;D614G;E484Q;F456L;L452Q;L455F;N438K;N501Y;P681H;R408G;S477N;S494P;S982A;T478K;T500S;V382L;Y505H;S98F;V367I;Y453F 45;38;216;333;345;312;198;31;177;24;170;59;319;163;184;205;326;191;52;156;70;306;149;17 50;43;221;339;351;317;203;36;182;29;175;64;324;168;189;210;331;196;57;161;75;310;154;22 RBD;RBD;RBD;RBD;RBD;RBD 89;123;235;277;369;385 92;126;238;280;372;388 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. Neutralization analysis of RBD-specific mAbs (n = 3) against pseudoviruses with the Wuhan reference spike protein and variant spike protein A475V or E484Q. 2021 Frontiers in immunology Figure SARS_CoV_2 A475V;E484Q 140;149 145;154 S;S;RBD 100;126;27 105;131;30 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. Neutralization curves of three mAbs (CC12.1, (A); 2-4, (B); B38, (C) against the Wuhan reference pseudovirus, A475V variant pseudovirus, and E484Q variant pseudovirus in the HEK293T/hACE2 cells. 2021 Frontiers in immunology Figure SARS_CoV_2 A475V;E484Q 110;141 115;146 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. Paired neutralization analyses of five convalescent plasma samples against the Wuhan reference and variant pseudoviruses of A475V, E484Q, and D614G are shown in (B-D), respectively. 2021 Frontiers in immunology Figure SARS_CoV_2 A475V;D614G;E484Q 124;142;131 129;147;136 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. Paired neutralization analyses of three mAbs against the Wuhan reference and variant pseudoviruses of A475V and E484Q are shown in (D, E). 2021 Frontiers in immunology Figure SARS_CoV_2 A475V;E484Q 102;112 107;117 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? (A) The schematic diagram shows the D614G mutation in S-glycoprotein of all emerging variants of concern (VOC) and interest (VOI) of SARS-CoV-2. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 36 41 S 54 68 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? (A) The transmission pattern of the variants of SARS-CoV-2 with D614G mutation in Asia. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 64 69 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? (A) Transmission pattern of the variants of SARS-CoV-2 with D614G mutation in Louisiana, USA. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 60 65 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? (B) Phylodynamics of the variants of SARS-CoV-2 with D614G mutation in Asia. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 53 58 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? (B) Phylodynamics of the variants of SARS-CoV-2 with D614G mutation in Louisiana, USA. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 53 58 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? (C) Transmission pattern of the variants of SARS-CoV-2 with D614G mutation in Latin America and the Caribbean. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 60 65 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? (C) Transmission pattern of the variants of SARS-CoV-2 with D614G mutation in Oregon, USA. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 60 65 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? (D) Phylodynamics of the variants of SARS-CoV-2 with D614G mutation in Latin America and the Caribbean. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 53 58 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? (D) Phylodynamics of the variants of SARS-CoV-2 with D614G mutation in Oregon, USA. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 53 58 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? (E) Transmission pattern of the variants of SARS-CoV-2 with D614G mutation in West Africa. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 60 65 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? (F) Phylodynamics of the variants of SARS-CoV-2 with D614G mutation in West Africa. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 53 58 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? At the same time, the lowest frequency was noted in E583D mutation (0.0057). 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 E583D 52 57 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? D614G mutation eventuates in all VOI and VOC through positive selection and spread worldwide. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 0 5 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? D614G mutation occurs in the highest frequency compared to other mutations. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 0 5 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? From our previous analysis (Figure 1, Figure 2, Figure 3), finally, we have concluded by stating D614G mutation occurrence in all the emerging variants of concern (VOC) and interest (VOI) of SARS-CoV-2 with the highest frequency and circulating throughout the World. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 97 102 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? It also demonstrates the phylodynamics of the variants with D614G mutation from different parts of the United States. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 60 65 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? It also shows the phylodynamics of the variants with D614G mutation in different parts of the world other than the United States. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 53 58 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? Map of the transmission pattern of all regions with the variants of SARS-CoV-2 with D614G mutation and their phylodynamics of all area-specific variants showing D614G mutation circulating worldwide. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G;D614G 84;161 89;166 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? Map of the United States' transmission pattern with the variants of SARS-CoV-2 with D614G mutation and their phylodynamics of all area-specific variants showing D614G mutation circulating in all areas in the United States. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G;D614G 84;161 89;166 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? Significant features of D614G mutation gained through positive selection. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 24 29 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? The hypothetical diagram illustrates the positive selection of the D614G mutation. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 67 72 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? The model shows D614G mutation as the predominant one with the highest frequency (0.0486). 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 16 21 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? This figure shows that the variants of SARS-CoV-2 with D614G mutation have spread in different parts of the United States. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 55 60 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? This figure shows that the variants of SARS-CoV-2 with D614G mutation have spread in different parts of the world other than the United States. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 55 60 34484868 D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin? Through positive selection, D614G mutation emerges in all VOI and VOC and spreads worldwide. 2021 Molecular therapy. Nucleic acids Figure SARS_CoV_2 D614G 28 33 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. e, Neutralization of B.1.617 spike PV and WT (Wuhan-1 D614G) by vaccine sera (n = 33 ChAdOx1 or n = 32 BNT162b2). 2021 Nature Figure SARS_CoV_2 D614G 54 59 S 29 34 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. h, i, Western blots of PV virions (h) and cell lysates (i) of 293T producer cells following transfection with plasmids expressing lentiviral vectors and SARS-CoV-2 S B.1.617.1 and Delta variant B.1.617.2 versus WT (Wuhan-1 with D614G), probed with antibodies to HIV-1 p24 and SARS-Cov-2 S2. 2021 Nature Figure SARS_CoV_2 D614G 228 233 S 164 165 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. j, Calu-3 cell entry by spike B.1.617.2 and B.1.617.1 versus WT D614G parental plasmid PVs. 2021 Nature Figure SARS_CoV_2 D614G 64 69 S 24 29 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Red, L19R; green, del157/158; blue, L452R; yellow, T478K. 2021 Nature Figure SARS_CoV_2 L19R;L452R;T478K 5;36;51 9;41;56 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Single round infectivity on different cell targets by spike B.1.617.1 and B.1.617.1 versus WT (Wuhan-1 D614G) PV produced in 293T cells. 2021 Nature Figure SARS_CoV_2 D614G 103 108 S 54 59 34488225 SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. The white dotted box indicates the location of the D950N substitution (orange). 2021 Nature Figure SARS_CoV_2 D950N 51 56 34493762 Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. (a) Each panel shows the estimated effective reproduction number of SARS-CoV-2 bearing (blue) or not (grey) the HF mutation N501Y (HF or notHF, respectively) in different countries. 2021 Scientific reports Figure SARS_CoV_2 N501Y 124 129 34493762 Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures. (a) Statistical comparison between the bootstrap distribution of the Rt of SARS-CoV-2 bearing (blue) or not (grey) the HF mutation N501Y (HF or notHF, respectively) in different levels of stringency. 2021 Scientific reports Figure SARS_CoV_2 N501Y 131 136 34495697 A Bifluorescent-Based Assay for the Identification of Neutralizing Antibodies against SARS-CoV-2 Variants of Concern In Vitro and In Vivo. Sanger sequencing results of the rSARS-CoV-2 Venus strain (top) and the rSARS-CoV-2 mCherry SA with the K417N, E484K, and N501Y substitutions in the RBD of the S glycoprotein (bottom) are indicated. 2021 Journal of virology Figure SARS_CoV_2 E484K;K417N;N501Y 111;104;122 116;109;127 S;RBD 160;149 174;152 34495697 A Bifluorescent-Based Assay for the Identification of Neutralizing Antibodies against SARS-CoV-2 Variants of Concern In Vitro and In Vivo. The genome of a rSARS-CoV-2 Venus strain (top) and the rSARS-CoV-2 strain with the three mutations (K417N, E484K, and N501Y) present in the S RBD of the SA B.1.351 (beta) VoC expressing mCherry (bottom) is shown. 2021 Journal of virology Figure SARS_CoV_2 E484K;N501Y;K417N 107;118;100 112;123;105 RBD;S 142;140 145;141 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. Impact of D614G mutation is only observed with full-length Spike protein. 2021 Journal of virology Figure SARS_CoV_2 D614G 10 15 S 59 64 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). (a) Native (control) spike (red) and E484K variant (blue), (b) Native spike (red) and N501Y variant (yellow), (c) Native spike (red) and multiple (K417N + E484K + N501Y) spike variant (green). 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 E484K;E484K;N501Y;N501Y;K417N 37;155;86;163;147 42;160;91;168;152 S;S;S;S 21;70;121;170 26;75;126;175 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). (a) Native spike (red) and E484K (blue) variant, (b) Native spike (red) and N501Y variant (yellow), (c) Native spike and multiple (K417N + E484K + N501Y) spike variant (green). 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 E484K;E484K;N501Y;N501Y;K417N 27;139;76;147;131 32;144;81;152;136 S;S;S;S 11;60;111;154 16;65;116;159 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Note that the E484K (a) and multiple (c) spike variants show significant conformational changes relative to control (red). 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 E484K 14 19 S 41 46 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Sequence representation of the regions of the E484K, N501Y and K417N mutations corresponding to the amino acid sequence of the spike glycoprotein. 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 E484K;K417N;N501Y 46;63;53 51;68;58 S 127 145 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Superposed images of spike glycoproteins SARS-CoV-2 E484K mutant and wild-type SARS-CoV-2. 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 E484K 52 57 S 21 40 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Superposed images of spike glycoproteins SARS-CoV-2 K417N + E484K + N501Y mutant and wild-type SARS-CoV-2. 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 E484K;K417N;N501Y 60;52;68 65;57;73 S 21 40 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Superposed images of spike glycoproteins SARS-CoV-2 N501Y mutant and wild-type SARS-CoV-2. 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 N501Y 52 57 S 21 40 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). The E484K variant shows only a slight enhanced mobility at the residue 477 and the multiple variant also a very slight enhanced mobility in the residues 385, 390 and 480. 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 E484K 4 9 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). The N501Y variant shows enhanced mobility, compared to the wild spike, at the residues 448, 460-470 and 481. 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 N501Y 4 9 S 64 69 34495817 Understanding the molecular interaction of SARS-CoV-2 spike mutants with ACE2 (angiotensin converting enzyme 2). Time evolution of the structure and interactions in the complexes of A- Wild-type Spike/ACE2 (control), B- Spike_E484K/ACE2 C- Spike_N501Y/ACE2, and D- Spike_South_Africa_triple (K417N + E484K + N501Y)/ACE2 in molecular dynamics simulations. 2021 Journal of biomolecular structure & dynamics Figure SARS_CoV_2 E484K;N501Y;K417N;E484K;N501Y 187;195;179;113;133 192;200;184;118;138 S;S;S 82;107;127 87;112;132 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. * The codes on the x and y axes of the matrix include: s001A: 20A, s002A: 19A, s003A: 20A/S.A262S, s004A: 20A/S.A701V, s005A: 20A/S.D80A, s006A: 20A/S.E484K, s007A: 20A/S.E484Q, s008A: 20A/S.K417 N, s009A: 20A/S.L452R, s010A: 20A/S.N501T, s011A: 20A/S.N501Y, s012A: 20A/S.P681H, s013A: 20A/S.P681R, s014A: 20A/S.Q675H, s015A: 20A/S.Q675P, s016A: 20A/S.Q677H, s017A: 20A/S.Q677P, s018A: 20A/S.V1176F, s019A: 20A/S.A222V, s020A: 20A/S.L18F, s021A: 20A/S.S477 N, s022A: 20A/S.N439K, s023A: 20A/S.S98F, s024A: 20A/S.L5F, s025A: 20A/S.P272L, s026A: 20A/S.D1163Y, s027A: 20A/S.E583D, s028A: 20A/S.G1167V, s029A: 20A/S.Y453F, s030A: Beta, s031A: Iota, s032A: Delta, s033A: Gamma, s034A: Alpha, s035A: Epsilon, s036A: Lambda, s037A: Kappa, s038A: Eta, s039A: Theta. 2021 Biochimie Figure SARS_CoV_2 A222V;A262S;A701V;D1163Y;D80A;E484K;E484Q;E583D;G1167V;L18F;L452R;L5F;N439K;N501T;N501Y;P272L;P681H;P681R;Q675H;Q675P;Q677H;Q677P;S98F;V1176F;Y453F 413;92;112;550;132;151;171;571;591;433;212;512;473;232;252;530;272;292;312;332;352;372;493;392;612 418;97;117;556;136;156;176;576;597;437;217;515;478;237;257;535;277;297;317;337;357;377;497;398;617 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. 2D-difference distance matrix by SuperPose v.1.0 (on the left hand side) with the 3D visualization by the TM-align, v.20190822,for the spike protein with variant D614G (clade 20A; in blue) versus the wild type (clade 19A; in red). 2021 Biochimie Figure SARS_CoV_2 D614G 162 167 S 135 140 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. (A) One of the energetically allowed rotamers of the L452R mutations. 2021 Cureus Figure SARS_CoV_2 L452R 53 58 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. (A) The mutation of Glu 484 by Gln 484, and its position in the receptor-binding motif (RBM). 2021 Cureus Figure SARS_CoV_2 E484Q 20 34 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. The E484Q mutation. 2021 Cureus Figure SARS_CoV_2 E484Q 4 9 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. The L452R mutation. 2021 Cureus Figure SARS_CoV_2 L452R 4 9 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. The mutant T478K seems to stabilize the receptor binding by forming a strong H-bond with Gln 24 of angiotensin-converting enzyme 2 (ACE2). 2021 Cureus Figure SARS_CoV_2 T478K 11 16 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. The T478K mutation. 2021 Cureus Figure SARS_CoV_2 T478K 4 9 34515998 The first Italian outbreak of SARS-CoV-2 B.1.1.7 lineage in Corzano, Lombardy. SARS-CoV-2 B.1.1.7 sequences from Corzano are identified by red circles; SARS-CoV-2 B.1.1.7 sequences from Corzano which carry the Spike mutation V551F are identified by yellow circles; other SARS-CoV-2 B.1.1.7 sequences circulating in the Brescia area are identified by green circles; other Italian SARS-CoV-2 B.1.1.7 sequences are identified by gray circles. 2022 Journal of medical virology Figure SARS_CoV_2 V551F 146 151 S 131 136 34515998 The first Italian outbreak of SARS-CoV-2 B.1.1.7 lineage in Corzano, Lombardy. SARS-CoV-2 B.1.1.7 sequences from Corzano are identified by red circles; SARS-CoV-2 B.1.1.7 sequences from Corzano which carry the Spike mutation V551F are identified by yellow circles; other SARS-CoV-2 Italian sequences are identified by green circles; SARS-CoV-2 sequences from all over the world are identified by violet circles; SARS-CoV-2 B.1.1.7 sequences from all over the world which carry the Spike mutation V551F are identified by pink circles. 2022 Journal of medical virology Figure SARS_CoV_2 V551F;V551F 146;417 151;422 S;S 131;402 136;407 34519222 Improved SARS-CoV-2 PCR detection and genotyping with double-bubble primers. (A) 5% agarose gel showing detection of SARS-CoV-2 N501Y-mutated RNA extracted from nasopharyngeal swabs of patient VOC3 or wild-type viral RNA extracted from nasopharyngeal swabs from patient S1. 2021 BioTechniques Figure SARS_CoV_2 N501Y 51 56 34519222 Improved SARS-CoV-2 PCR detection and genotyping with double-bubble primers. Primer mixes: lanes 2 and 5: region 1 gene N primer mix #8 positive controls; lanes 3, 6, 9: region 3 gene S wild-type primer mix #11a + #11c; lanes 4, 7, 10: region 3 gene S N501Y mutation (MUT) primer mix #11b + #11c. 2021 BioTechniques Figure SARS_CoV_2 N501Y 175 180 N;S;S 43;107;173 44;108;174 34519222 Improved SARS-CoV-2 PCR detection and genotyping with double-bubble primers. Sense primer #11b has a point mutation 't' at the 3' end to detect the a t replacement of the N501Y mutation. 2021 BioTechniques Figure SARS_CoV_2 N501Y 94 99 34519222 Improved SARS-CoV-2 PCR detection and genotyping with double-bubble primers. Utilizing double-bubble primers in RT-qPCR to detect N501Y mutation using end point RT-PCR. 2021 BioTechniques Figure SARS_CoV_2 N501Y;N501Y 54;53 59;58 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. d, Neutralization of wild-type D614G 1 month after the primary series and neutralization of wild-type D614G, B.1.617.1 and B.1.617.2 immediately before the booster dose from sera samples collected from a subset of participants in the mRNA-1273 booster group (D614G, n = 20; B.1.617.1, n = 11; B.1.617.2, n = 11). 2021 Nature medicine Figure SARS_CoV_2 D614G;D614G;D614G 31;102;259 36;107;264 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. In a-d, the GMTs against the wild-type D614G and variants measured in participants before the booster dose or 2 weeks after the booster dose were evaluated versus peak titers measured against the wild-type D614G 1 month after the primary vaccination series. 2021 Nature medicine Figure SARS_CoV_2 D614G;D614G 39;206 44;211 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. n = 20 for wild-type D614G, B.1.351 and P.1 and n = 11 for B.1.427/B.1.429, B.1.526, B.1.617.1 and B.1.617.2. 2021 Nature medicine Figure SARS_CoV_2 D614G 21 26 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Neutralization of wild-type D614G and B.1.351 by participant serum collected immediately before and after boosters, as measured by the lentiviral-based PsVN assay. 2021 Nature medicine Figure SARS_CoV_2 D614G 28 33 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Neutralization of wild-type D614G and variants by participant serum collected 1 month after primary vaccination series and before and after boosters, as measured by the VSV-based PsVN assay. 2021 Nature medicine Figure SARS_CoV_2 D614G 28 33 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. The GMT fold change versus the peak titers against the wild-type D614G virus after the primary vaccination series are shown, with red indicating fold drop and blue indicating fold rise. 2021 Nature medicine Figure SARS_CoV_2 D614G 65 70 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Wild-type D614G neutralization (a) and B.1.351 neutralization (b) in a validated recombinant lentivirus-based SARS-CoV-2 pseudovirus assay by serum from participants (n = 20 participants per booster cohort). 2021 Nature medicine Figure SARS_CoV_2 D614G 10 15 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. E484K mutation. 2022 Chembiochem Figure SARS_CoV_2 E484K 0 5 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. K417N mutation. 2022 Chembiochem Figure SARS_CoV_2 K417N 0 5 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. K417T mutation. 2022 Chembiochem Figure SARS_CoV_2 K417T 0 5 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. N501Y mutation. 2022 Chembiochem Figure SARS_CoV_2 N501Y 0 5 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. S477N mutation. 2022 Chembiochem Figure SARS_CoV_2 S477N 0 5 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. The interacting fragments involving the mutated virus (K417N(T) mutations) are depicted in blue and green. 2022 Chembiochem Figure SARS_CoV_2 K417N 55 60 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. (e) Antibody screening using wild type RBD-Fc and variants containing the E484K, Y453F or N501Y mutations. 2021 Scientific reports Figure SARS_CoV_2 E484K;N501Y;Y453F 74;90;81 79;95;86 RBD 39 42 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. Data from 2 independent virus stocks with 2 replicates except for rSARS-CoV-2 and rNSP12-E802A. 2021 PLoS pathogens Figure SARS_CoV_2 E802A 89 94 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. The assay does not discriminate between rSARS-CoV-2 and rNSP12-E802D. 2021 PLoS pathogens Figure SARS_CoV_2 E802D 63 68 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. Three focused panels are WT (upper) and two potential confirmations of E802D. 2021 PLoS pathogens Figure SARS_CoV_2 E802D 71 76 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. VeroE6-ACE2-TMPRSS2 were infected with different ratios of rNSP12-E802D to rSARS-CoV-2. 2021 PLoS pathogens Figure SARS_CoV_2 E802D 66 71 34535691 Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020. We report the estimated temporal evolution of the frequency of the main spike mutations in the province of Liege (A), as well as the cartography of phylogenetic nodes and branches associated with the target mutations S98F (B), A222V (C), and S477N (D). 2021 Scientific reports Figure SARS_CoV_2 A222V;S477N;S98F 227;242;217 232;247;221 S 72 77 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. ACE2-Fc binding to (A) full Spikes variants or the (B) B.1.1.7, (C) B.1.351, (D) P.1, (E) B.1.429, and (F) B.1.526 Spike and its corresponding single mutations are presented as a ratio of ACE2 binding to D614G Spike normalized to CV3-25 binding. 2021 Virology Figure SARS_CoV_2 D614G 204 209 S;S;S 28;115;210 34;120;215 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. ACE2-Fc binding to the different Spike variants are presented as a ratio of ACE2 binding to D614G Spik, normalized to CV3-25 binding at 37 C (red) or at 4 C (blue). 2021 Virology Figure SARS_CoV_2 D614G 92 97 S 33 38 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. L452R. 2021 Virology Figure SARS_CoV_2 L452R 0 5 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. N, (D) K417T, (E) E484K, and (F) 2021 Virology Figure SARS_CoV_2 E484K;K417T 18;7 23;12 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. N, (D) K417T, (E) E484K, and (F). 2021 Virology Figure SARS_CoV_2 E484K;K417T 18;7 23;12 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. nM prior to dissociation for 300s for (A) WT, (B) N501Y, (C) K417. 2021 Virology Figure SARS_CoV_2 N501Y 50 55 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Plasma recognition of (A) full Spike variants (B) B.1.1.7, (C) B.1.351, (D) P.1, (E) B.1.429, (F) B.1.526 Spike and variant-specific Spike single mutations are presented as ratio of plasma binding to D614G Spike normalized CV3-25 binding. 2021 Virology Figure SARS_CoV_2 D614G 200 205 S;S;S;S 31;106;133;206 36;111;138;211 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Plasma recognition of (A) full Spike variants or the (B) B.1.1.7, (C) B.1.351, (D) P.1, (E) B.1.429, (F) B.1.526 Spikes and Spikes with their corresponding single mutations are presented as a ratio of plasma binding to D614G Spike normalized with CV3-25 binding. 2021 Virology Figure SARS_CoV_2 D614G 219 224 S;S;S;S 31;113;124;225 36;119;130;230 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Statistical analyses were used to compare each Spike at 4 C vs 37 C (black) or to compare variants Spike to D614G at 37 C (red) or at 4 C (blue). 2021 Virology Figure SARS_CoV_2 D614G 108 113 S;S 47;99 52;104 34537136 The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Also included for reference are sites previously detected to be evolving under positive selection such as S/614, the site of the D614G mutation that is present in all three of the 501Y lineages, S/5, and RdRp/P323L (ORF1b/314). 2021 Cell Figure SARS_CoV_2 D614G;P323L 129;209 134;214 RdRP;S;S 204;106;195 208;107;196 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. (B) deltaH/deltaH expansions 4.8-4.5/6.0-3.25 ppm in TOCSY spectrum covering the anomeric region of N-acetylgalactosamine (GalNAc) units, showing the presence of three spin systems (vertical dashed lines) correspondent to the non-, 6- and 4-sulfated GalNAc units labeled, respectively, as N0S, N6S and N4S. 2021 The Journal of biological chemistry Figure SARS_CoV_2 N4S;N6S 302;294 305;297 N 100 101 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. Bound glycan glycosidic torsional plots are shown in blue (WT) and orange (N501Y). 2021 The Journal of biological chemistry Figure SARS_CoV_2 N501Y 75 80 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. Predicted binding poses of sulfated glycans bound to wild-type (left panel) and N501Y mutant (right panel) of SARS-CoV2 S-protein RBD. 2021 The Journal of biological chemistry Figure SARS_CoV_2 N501Y 80 85 RBD;S 130;120 133;121 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. The bar plots (based on triplicate experiments for standard deviation) indicate normalized S-protein (A and D-F) or N501Y mutant (B) binding to surface heparin inhibited with different sulfated glycans and concentrations. 2021 The Journal of biological chemistry Figure SARS_CoV_2 N501Y 116 121 S 91 92 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. (B) Neutralization to D614G mutant pseudovirus. 2021 Frontiers in immunology Figure SARS_CoV_2 D614G 22 27 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. (C) Neutralization to E484Q mutant pseudovirus. 2021 Frontiers in immunology Figure SARS_CoV_2 E484Q 22 27 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. (D) Neutralization to A475V mutant pseudovirus. 2021 Frontiers in immunology Figure SARS_CoV_2 A475V 22 27 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. Surface plasmon resonance (SPR) demonstrated the binding and dissociation kinetics of the 9 antibodies (A: XG81; B: XG83; C: S309H-CV30L; D: S309; E: P2B-2F6; F: CB6; B: S309H-XG81L; H: CC12.1-XG83L; I: CB6H-XG83L) against S. 2021 Frontiers in immunology Figure SARS_CoV_2 S309H;S309H 125;170 130;175 E;S 147;223 148;224 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. (a) Site mutation of A352S is showed in black column. 2021 Iranian journal of microbiology Figure SARS_CoV_2 A352S 21 26 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. (a) The mutation of M49I is shown in black column. 2021 Iranian journal of microbiology Figure SARS_CoV_2 M49I 20 24 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. (a) The mutation of P77L is shown in black column. 2021 Iranian journal of microbiology Figure SARS_CoV_2 P77L 20 24 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. (b) Site mutation of S477I is shown in black column. 2021 Iranian journal of microbiology Figure SARS_CoV_2 S477I 21 26 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. (b) The mutation of L50F is shown in black column. 2021 Iranian journal of microbiology Figure SARS_CoV_2 L50F 20 24 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. (b) The mutation of V205I is shown in black column. 2021 Iranian journal of microbiology Figure SARS_CoV_2 V205I 20 25 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. (c) Site mutation of Q677H is showed in black column. 2021 Iranian journal of microbiology Figure SARS_CoV_2 Q677H 21 26 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Site mutation of D614G is showed in black column. 2021 Iranian journal of microbiology Figure SARS_CoV_2 D614G 17 22 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. The D614G (B.1) variant has become one of the dominant forms globally between January 2020 and January 2021. 2021 Pathogens & immunity Figure SARS_CoV_2 D614G 4 9 34541432 Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. The proportion of R203/G204 to K203/R204 sub-variants of the D614G variant differs in different regions between January 2020 and January 2021 with recent increases in the frequency of new variants. 2021 Pathogens & immunity Figure SARS_CoV_2 D614G 61 66 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. (A and B) SARS-CoV-2 and SARS-CoV-2(V367F) pseudovirus were incubated with threefold serially diluted mAbs. 2021 MedComm Figure SARS_CoV_2 V367F 36 41 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. (E and F) Triple-mAb and pair-mAb cocktails with threefold serial dilution were incubated with SARS-CoV-2(V367F) pseudovirus. 2021 MedComm Figure SARS_CoV_2 V367F 106 111 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. Four distinct antigenic sites of the RBD targeted by four groups of mAbs, which can make potent neutralizing cocktails against SARS-CoV-2 and SARS-CoV-2(V367F). 2021 MedComm Figure SARS_CoV_2 V367F 153 158 RBD 37 40 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. Neutralization of the SARS-CoV-2 pseudovirus and live virus and the SARS-CoV-2(V367F) pseudovirus by mAbs. 2021 MedComm Figure SARS_CoV_2 V367F 79 84 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. A double mutant (E484K/N501Y) and triple mutants corresponding to Beta variant (K417N/E484K/N501Y) and Gamma variant (K417T/E484K/N501Y) were also used. 2021 The Journal of biological chemistry Figure SARS_CoV_2 E484K;K417N;K417T;E484K;E484K;N501Y;N501Y;N501Y 17;80;118;86;124;23;92;130 22;85;123;91;129;28;97;135 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Panels A-I show the data for the wild-type RBD, single amino acid mutations K417N, Y453F, S477N, T478I, E484K, S494P, N501Y, and for the triple mutant K417T/E483K/N501Y, respectively. 2021 The Journal of biological chemistry Figure SARS_CoV_2 E484K;K417N;K417T;N501Y;S477N;S494P;T478I;Y453F;E483K;N501Y 104;76;151;118;90;111;97;83;157;163 109;81;156;123;95;116;102;88;162;168 RBD 43 46 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. The single mutants of RBD used in this study were K417N, N439K, Y453F, S477N, T478I, E484K, S494P and N501Y (Alpha variant). 2021 The Journal of biological chemistry Figure SARS_CoV_2 E484K;K417N;N439K;N501Y;S477N;S494P;T478I;Y453F 85;50;57;102;71;92;78;64 90;55;62;107;76;97;83;69 RBD 22 25 34544043 Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants. (B) Global reports of new genomes of BV-1-like viruses (B.1.1.7 + Q493R) per week, grouped by sampling date and location. 2021 The American journal of tropical medicine and hygiene Figure SARS_CoV_2 Q493R 66 71 34544043 Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants. (C) Global reports of new BV-2-like viruses (B.1.1.519 + T478K) per week. 2021 The American journal of tropical medicine and hygiene Figure SARS_CoV_2 T478K 57 62 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. a Genomic sequence comparison of the D614G variants used in this study to the reference genome (accession number: NC_0.45512.2). 2021 Communications biology Figure SARS_CoV_2 D614G 37 42 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. One non-D614G lineage variant (HK-15 (MT835141)) and three D614G lineage variants (HK-405, B.1.1.7 and HK-95) were used. 2021 Communications biology Figure SARS_CoV_2 D614G;D614G 59;8 64;13 34545191 Low dose inocula of SARS-CoV-2 Alpha variant transmits more efficiently than earlier variants in hamsters. Viral growth kinetics of Sars-CoV-2 D614G variants. 2021 Communications biology Figure SARS_CoV_2 D614G 36 41 34545316 Assessment of the binding interactions of SARS-CoV-2 spike glycoprotein variants. The variants used were (a) D614G, (b) N501Y, (c) N439K, (d) Y453F, and (e) E484K. 2022 Journal of pharmaceutical analysis Figure SARS_CoV_2 D614G;E484K;N439K;N501Y;Y453F 27;75;49;38;60 32;80;54;43;65 34545803 Genomic Sequencing of SARS-CoV-2 E484K Variant B.1.243.1, Arizona, USA. Emergence of E484K-harboring B.1.243.1 variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Arizona, United States. 2021 Emerging infectious diseases Figure SARS_CoV_2 E484K 13 18 COVID-19 57 97 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. (C and D) show the contribution of the interatomic interaction of wild-type and A249V of PLPro. 2022 Saudi journal of biological sciences Figure SARS_CoV_2 A249V 80 85 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. Effect of mutation on interactions between atoms within PLPro at the mutation site (A and B) show the contribution of the interatomic interaction of the wild-type and D108G of PLPro. 2022 Saudi journal of biological sciences Figure SARS_CoV_2 D108G 167 172 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. MD simulations of GRL0617 in complex with the wild-type PLPro, D108G, and A249V. 2022 Saudi journal of biological sciences Figure SARS_CoV_2 A249V;D108G 74;63 79;68 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. MD simulations of the wild-type PLPro, D108G, and A249V. 2022 Saudi journal of biological sciences Figure SARS_CoV_2 A249V;D108G 50;39 55;44 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. Ribbon representation showing the change in Delta Vibrational Entropy Energy between the wild-type and the mutants PLPro due to (A) D108G and (B) A249V mutation. 2022 Saudi journal of biological sciences Figure SARS_CoV_2 A249V;D108G 146;132 151;137 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. Surface representation showing the change in Delta Vibrational Entropy Energy between the wild-type and the mutant PLPro due to (C) D108G and (D) A249V mutation. 2022 Saudi journal of biological sciences Figure SARS_CoV_2 A249V;D108G 146;132 151;137 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Data for B.1.1.7 (Alpha), B.1.1.7+E484K (Alpha), P.1 (Gamma), and B.1.427/B.1.429 were published previously. 2021 Journal of virology Figure SARS_CoV_2 E484K 34 39 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. In panel B, the colored lines connect the D614G and variant neutralization titers in matched samples. 2021 Journal of virology Figure SARS_CoV_2 D614G 42 47 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. The GMT fold change over D614G for each variant is shown. 2021 Journal of virology Figure SARS_CoV_2 D614G 25 30 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. The pseudoviruses tested incorporated D614G or the spike substitutions present in B.1.1.7 (Alpha), B.1.1.7+E484K (Alpha), B.1.351-v1 (Beta), B.1.351-v2 (Beta), B.1.351-v3 (Beta), P.1 (Gamma), B.1.617.2-v1 (Delta), B.1.617.2-v2 (Delta), B.1.525 (Eta), B.1.526 (Iota), B.1.617.1-v1 (Kappa), B.1.617.1-v2 (Kappa), C.37-v1 (Lambda), C.37-v2 (Lambda), B.1.427/B.1.429, B.1.621 (Mu), A.23.1-v1, A.23.1-v2, and A.VOI.V2 (Table 1). 2021 Journal of virology Figure SARS_CoV_2 D614G;E484K 38;107 43;112 S 51 56 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. a ADCC activity in patients against D614G, B.1.1.7, B.1.351, and P.1. 2021 Signal transduction and targeted therapy Figure SARS_CoV_2 D614G 36 41 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. b ADCC activity in BALB/c mice infected with SARS-COV-2 pseudoviruses D614G, B.1.1.7, B.1.351, and P.1. 2021 Signal transduction and targeted therapy Figure SARS_CoV_2 D614G 70 75 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. Four SARS-COV-2 strains, which included D614G, B.1.1.7, B.1.351, and P.1, were used. 2021 Signal transduction and targeted therapy Figure SARS_CoV_2 D614G 40 45 34561887 Proteolytic activation of SARS-CoV-2 spike protein. Alteration of interprotomer interaction by D614G mutation. 2022 Microbiology and immunology Figure SARS_CoV_2 D614G 43 48 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. (a) The superposition of the average structure in the MD simulations between the wild-type complex and the E484K mutant. 2021 Journal of molecular graphics & modelling Figure SARS_CoV_2 E484K 107 112 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. In these figures, the residue E484K is located on RBD, and the other residues are from the antibodies/nanobodies, which dominantly contribute to the decreases of the binding affinity. 2021 Journal of molecular graphics & modelling Figure SARS_CoV_2 E484K 30 35 RBD 50 53 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The binding free energies contributed by each of the key residues on RBD (a) and hACE2 (b), which are responsible for the improvement of the RBD-hACE2 binding affinity caused by the E484K mutation. 2021 Journal of molecular graphics & modelling Figure SARS_CoV_2 E484K 182 187 RBD;RBD 69;141 72;144 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The charged residues on hACE2 locating nearby the mutated residue E484K are displayed with positively charged residues in blue and negatively charged residues in red, respectively. 2021 Journal of molecular graphics & modelling Figure SARS_CoV_2 E484K 66 71 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The distances between several pairwise residues across the binding interface in the wild-type complex structure (b), and those in the E484K mutant (c) are displayed, respectively, to detect the conformational changes caused by the mutation. 2021 Journal of molecular graphics & modelling Figure SARS_CoV_2 E484K 134 139 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The electrostatic energies contributed by each of the key residues responsible for the decreases of the binding affinity caused by the E484K mutation for the complex systems formed by RBD with the neutralizing antibody BD23 (a), the nanobody H11-D4 (b), the neutralizing antibody BD368-2(c), the nanobody Nb20 (d), the nanobody MR17-K99Y (e) and the neutralizing antibody S2M11 (f), respectively. 2021 Journal of molecular graphics & modelling Figure SARS_CoV_2 E484K;K99Y 135;333 140;337 RBD 184 187 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The electrostatic potential was calculated by using Adaptive Poisson-Boltzmann Solver (APBS) and displayed with UCSF Chimera package for wild-type RBD (a), the RBD with E484K mutation (b) and the surfaces of hACE2 (c). 2021 Journal of molecular graphics & modelling Figure SARS_CoV_2 E484K 169 174 RBD;RBD 147;160 150;163 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The local structural rearrangements of the RBD-hACE2 binding interface caused by the E484K mutation. 2021 Journal of molecular graphics & modelling Figure SARS_CoV_2 E484K 85 90 RBD 43 46 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The locations as well as the conformational rearrangements of the key residues responsible for the raising of the electrostatic energies caused by the E484K mutation for the complex systems formed by RBD with the neutralizing antibody BD23 (a), the nanobody H11-D4 (b), the neutralizing antibody BD368-2 (c), the nanobody Nb20 (d), the nanobody MR17-K99Y (e) and the neutralizing antibody S2M11 (f), respectively. 2021 Journal of molecular graphics & modelling Figure SARS_CoV_2 E484K;K99Y 151;350 156;354 RBD 200 203 34562851 E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies. The mutated residue E484K was labeled in the figure. 2021 Journal of molecular graphics & modelling Figure SARS_CoV_2 E484K 20 25 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. B, cartoon representative of the atomic model of the trimeric S-D614G with the domains colored in accordance with (A). 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G 64 69 S 62 63 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. B, DSC profiles S-D614 (dashed lines) and S-D614G (solid lines) at Day 0 (fresh; black), 37C for 6 days (orange) and 4C for 6 days (light blue). 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G 44 49 S;S 16;42 17;43 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. C, DSF profiles of S-D614 (dashed lines) and S-D614G (solid lines) as a function of pH values. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G 47 52 S;S 19;45 20;46 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. C, structural heterogeneity of S-D614G. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G 33 38 S 31 32 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Cryo-EM analysis of S-D614G.A, schematic domain architecture of S-D614G. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G;D614G 22;66 27;71 S;S 20;64 21;65 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. In contrast, S-D614G exhibited visible unfolding only by heat shock at 60C for 30 min 3D maps of the individual samples derived from the native-like particle images are shown on the upper right corner of each panel. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G 15 20 S 13 14 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Orthogonal views:side views and top views are shown on the top and bottom panels, respectively:of the five distinct clusters of S-D614G derived from 3DVA. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G 130 135 S 128 129 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Quantitative analyses of the thermal stabilities of S-D614 and S-D614G.A, histograms of the relative amounts of native-like particle images with respect to the fresh samples. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G 65 70 S;S 52;63 53;64 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Relative native-like particle number of S-D614G as a function of temperature. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G 42 47 S 40 41 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Representative NSEM micrographs of S-D614 (top panels) and S-D614G (bottom panels) after different temperature treatments. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G 61 66 S;S 35;59 36;60 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. S-D614G is highly stable over a broad range of temperatures. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G 2 7 S 0 1 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. The difference between S-D614G and S-D614 (Diff.) is derived by subtracting the values of S-D614 by those of S-D614G. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G;D614G 25;111 30;116 S;S;S;S 23;35;90;109 24;36;91;110 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. The open and filled curves correspond to S-D614 and S-D614G, respectively. 2021 The Journal of biological chemistry Figure SARS_CoV_2 D614G 54 59 S;S 41;52 42;53 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. The proportion of N501Y, Q493H, K417N mutations located on the RBD. 2021 Nature communications Figure SARS_CoV_2 K417N;N501Y;Q493H 32;18;25 37;23;30 RBD 63 66 34595399 Genomic epidemiological analysis of SARS-CoV-2 household transmission. A combination of two synonymous mutations separate the cluster from other B.1 lineage genomes from the region, with the acquisition of a further non-synonymous A-to-G mutation in the ORF encoding the spike protein (S:N30S) identified in Cases 1 and 7. 2021 Access microbiology Figure SARS_CoV_2 N30S 217 221 S;S 200;215 205;216 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Alpha and Beta SARS-CoV-2 S proteins induce more robust syncytia formation than D614G. 2021 The EMBO journal Figure SARS_CoV_2 D614G 80 85 S 26 27 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Bottom left Panel: Vero GFP-split cells were transfected with S plasmids containing each of the individual mutations associated with Alpha variant in the D614G background. 2021 The EMBO journal Figure SARS_CoV_2 D614G 154 159 S 62 63 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Data set for N501Y and D614G reference mutations are duplicated between bottom left and bottom right panels for presentation as these mutations are common to both variants. 2021 The EMBO journal Figure SARS_CoV_2 D614G;N501Y 23;13 28;18 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Data set for N501Y and D614G reference mutations are duplicated between left and right panels as mutations are common to both variants. 2021 The EMBO journal Figure SARS_CoV_2 D614G;N501Y 23;13 28;18 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Delta SARS-CoV-2 S protein induces more syncytia formation and binds more to ACE2 than D614G. 2021 The EMBO journal Figure SARS_CoV_2 D614G 87 92 S 17 18 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Effect of IFITMs and TMPRSS2 on the cell-cell fusion induced by different S proteins, (D) Wuhan, (E) D614G, (F) Alpha, and (G) Beta. 2021 The EMBO journal Figure SARS_CoV_2 D614G 101 106 S 74 75 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Left Panel: Fusion was quantified by GFP area/ number of nuclei and normalized to D614G for each of the transfected variant S proteins. 2021 The EMBO journal Figure SARS_CoV_2 D614G 82 87 S 124 125 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Left Panel: Fusion was quantified by GFP area/ number of nuclei and normalized to D614G for U2OS-ACE2 20 h post-infection at MOI 0.001. 2021 The EMBO journal Figure SARS_CoV_2 D614G 82 87 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Left Panel: Fusion was quantified by GFP area/number of nuclei and normalized to D614G for each of the transfected variant S proteins. 2021 The EMBO journal Figure SARS_CoV_2 D614G 81 86 S 123 124 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Left Panel: Quantified fusion of the Alpha + E484K variant S protein normalized to D614G S. 2021 The EMBO journal Figure SARS_CoV_2 D614G;E484K 83;45 88;50 S;S 59;89 60;90 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Left Panel: Representative ACE2 binding dilution curves for the Delta variant in relation to Alpha and D614G. 2021 The EMBO journal Figure SARS_CoV_2 D614G 103 108 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. One-way ANOVA compared with D614G reference, ns: non-significant, **P < 0.01, ***P < 0.001, ****P < 0.0001. 2021 The EMBO journal Figure SARS_CoV_2 D614G 28 33 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Quantification of median florescent intensity (MFI) of variant S protein at the cell surface and representative histograms of MFI of the Delta variant compared with the Alpha and D614G using mAb129. 2021 The EMBO journal Figure SARS_CoV_2 D614G 179 184 S 63 64 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Quantification of median florescent intensity (MFI) of variant S protein at the cell surface and representative histograms of MFI of the Wuhan, D614G, Alpha, Beta, and Alpha + E484K variants S protein using mAb10. 2021 The EMBO journal Figure SARS_CoV_2 D614G;E484K 144;176 149;181 S;S 63;191 64;192 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Quantification of median florescent intensity (MFI) of variant S protein at the cell surface and representative histograms of MFI of the Wuhan, D614G, Alpha, Beta, and Alpha + E484K variants S protein using mAb129. 2021 The EMBO journal Figure SARS_CoV_2 D614G;E484K 144;176 149;181 S;S 63;191 64;192 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Replication kinetics of D614G, Alpha, and Beta variants in cell culture. 2021 The EMBO journal Figure SARS_CoV_2 D614G 24 29 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Right Panel: Fusion quantification of at least three independent video microscopy experiments, 20 h post-transfection, normalized to D614G. 2021 The EMBO journal Figure SARS_CoV_2 D614G 133 138 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Right Panel: Fusion quantification of three independent video microscopy experiments, 20 h post-transfection, normalized to D614G. 2021 The EMBO journal Figure SARS_CoV_2 D614G 124 129 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Statistical analysis: mixed-effect analysis or two-way ANOVA compared with D614G reference, ns: non-significant, *P < 0. 2021 The EMBO journal Figure SARS_CoV_2 D614G 75 80 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Statistical analysis: one-way ANOVA compared with D614G reference or control plasmid transfection, ns: non-significant, *P < 0. 2021 The EMBO journal Figure SARS_CoV_2 D614G 50 55 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Statistical analysis: one-way ANOVA compared with D614G reference, *P < 0. 2021 The EMBO journal Figure SARS_CoV_2 D614G 50 55 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Statistical analysis: one-way ANOVA compared with D614G reference, ns: non-significant, **P < 0.01, ****P < 0.0001. 2021 The EMBO journal Figure SARS_CoV_2 D614G 50 55 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Statistical analysis: one-way ANOVA compared with D614G reference, ns: non-significant, *P < 0. 2021 The EMBO journal Figure SARS_CoV_2 D614G 50 55 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Statistical analysis: one-way ANOVA compared with D614G reference, ns: non-significant. 2021 The EMBO journal Figure SARS_CoV_2 D614G 50 55 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The amount of fusion was quantified at 20 h and normalized to D614G reference plasmid. 2021 The EMBO journal Figure SARS_CoV_2 D614G 62 67 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. U2OS-ACE2 GFP-split cells were infected at MOI 0.01 with the Wuhan, D614G, Alpha, and Beta strains for 20 h. 2021 The EMBO journal Figure SARS_CoV_2 D614G 68 73 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. (b) Infectivity of indicated VOCs with or without Q677H. 2021 mBio Figure SARS_CoV_2 Q677H 50 55 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. (e and f) NT50 values and NT50 values relative to the D614G virus were determined for 40 vaccinee serum samples collected 3 to 4 weeks after their second dose of Moderna (n = 20) or Pfizer (n = 20) vaccine with significance being determined by one-way repeated-measures analysis of variance (ANOVA) with Bonferroni posttest. 2021 mBio Figure SARS_CoV_2 D614G 54 59 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. against P1-501Y-V3 (Brazil), B.1.1.7 (United Kingdom), and B.1.351 (South Africa) variants with or without the introduction of the Q677H mutation. 2021 mBio Figure SARS_CoV_2 Q677H 131 136 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. All comparisons were made against D614G; *, P < 0.05; **, P < 0.01; ***, P < 0.001; ns, not significant. 2021 mBio Figure SARS_CoV_2 D614G 34 39 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Comparison of the neutralization of VOCs B.1.1.7, B.1.351, and P1 with their counterparts containing Q677H, as well as comparison of the Moderna and Pfizer neutralizing antibody responses against Q677H-bearing variants. 2021 mBio Figure SARS_CoV_2 Q677H;Q677H 101;196 106;201 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Key mutations E484K, N501Y, D614G, and Q677H are indicated. 2021 mBio Figure SARS_CoV_2 D614G;E484K;N501Y;Q677H 28;14;21;39 33;19;26;44 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Neutralization of Q677H-bearing SARS-CoV-2 spike-pseudotyped lentivirus by convalescent-phase and vaccinee sera. 2021 mBio Figure SARS_CoV_2 Q677H 18 23 S 43 48 34607452 Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H. Relative infectivity (also indicated on the top) was calculated by setting the value of D614G to 100. 2021 mBio Figure SARS_CoV_2 D614G 88 93 34607791 BNT162b2 vaccine-induced humoral and cellular responses against SARS-CoV-2 variants in systemic lupus erythematosus. (A) Comparison of serum anti-RBD IgG levels measured by photonic ring immunoassay with neutralising capacity against D614G SARS-CoV-2 (n=126). 2022 Annals of the rheumatic diseases Figure SARS_CoV_2 D614G 117 122 RBD 29 32 34607791 BNT162b2 vaccine-induced humoral and cellular responses against SARS-CoV-2 variants in systemic lupus erythematosus. (B) Serum neutralising activities against D614G SARS-CoV-2 measured as inhibitory dilution 50 (ID50) in 126 serum samples at D42. 2022 Annals of the rheumatic diseases Figure SARS_CoV_2 D614G 42 47 34607791 BNT162b2 vaccine-induced humoral and cellular responses against SARS-CoV-2 variants in systemic lupus erythematosus. (C) Comparison of serum neutralising activities measured as ID50 against D614G SARS-CoV-2 in patients with systemic lupus erythematosus (SLE) with baseline low (grey, n=19) or high (black, n=40) naive B cell frequency (arbitrary cut-off=42% of total B cells). 2022 Annals of the rheumatic diseases Figure SARS_CoV_2 D614G 73 78 Systemic lupus erythematosus;Systemic lupus erythematosus 137;107 140;135 34607791 BNT162b2 vaccine-induced humoral and cellular responses against SARS-CoV-2 variants in systemic lupus erythematosus. (D) Serum neutralising activities against D614G SARS-CoV-2 measured as ID50 in 59 patients with SLE classified according to their naive B cell counts. 2022 Annals of the rheumatic diseases Figure SARS_CoV_2 D614G 42 47 Systemic lupus erythematosus 96 99 34610919 Evaluation of the relative virulence of novel SARS-CoV-2 variants: a retrospective cohort study in Ontario, Canada. After May 1, 2021, all screened specimens not identified as an N501Y-positive VOC (N501Y+ VOC) or another variant were classified as probable Delta VOC infections. 2021 CMAJ Figure SARS_CoV_2 N501Y;N501Y 63;83 68;88 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. Two primers were designed to specifically complement the sequences containing the D215G mutation and the 242 to 244 deletion. 2021 Microbiology spectrum Figure SARS_CoV_2 D215G 82 87 34613786 Highly Efficient SARS-CoV-2 Infection of Human Cardiomyocytes: Spike Protein-Mediated Cell Fusion and Its Inhibition. (B) (Left panel) Gel analysis of CoV-2 S protein processing in the absence or presence of FI (20 muM) and of the processing of the CoV-2 S R682s furin cleavage mutant (R682S). 2021 Journal of virology Figure SARS_CoV_2 R682S 168 173 S;S 39;137 40;138 34613786 Highly Efficient SARS-CoV-2 Infection of Human Cardiomyocytes: Spike Protein-Mediated Cell Fusion and Its Inhibition. The 2nd to 4th panels show phase contrast images of hiPSC-CM expressing CoV-2 S in the absence or presence of 20 muM FI or of Vero cells expressing the R682S cleavage mutant, respectively, 72-h after transfection. 2021 Journal of virology Figure SARS_CoV_2 R682S 152 157 S 78 79 34613786 Highly Efficient SARS-CoV-2 Infection of Human Cardiomyocytes: Spike Protein-Mediated Cell Fusion and Its Inhibition. The 2nd to 4th panels show phase contrast images of Vero cells expressing CoV-2 S in the absence or presence of 20 muM FI or of Vero cells expressing the R682S cleavage mutant, respectively, 72-h after transfection. 2021 Journal of virology Figure SARS_CoV_2 R682S 154 159 S 80 81 34613786 Highly Efficient SARS-CoV-2 Infection of Human Cardiomyocytes: Spike Protein-Mediated Cell Fusion and Its Inhibition. The location of the furin cleavage mutant, R682S, is indicated. 2021 Journal of virology Figure SARS_CoV_2 R682S 43 48 34615860 Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil. An early sample from August 2020 was assigned to Gamma (P.1) to the presence of the K417T mutation. 2021 Nature communications Figure SARS_CoV_2 K417T 84 89 34615860 Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil. Phylogeographic analyses suggest emergence of the dominant P.1 lineage in November 2020, with a most recent common ancestor of all P.1-like (K417T) viruses estimated at August 2020. 2021 Nature communications Figure SARS_CoV_2 K417T 141 146 34615860 Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil. Therefore it is plausible that this sample was a precursor to likely 'true' Gamma (P.1) or a spontaneous K417T mutation. 2021 Nature communications Figure SARS_CoV_2 K417T 105 110 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. Four different groups where identified: Y453/D614, Y453F/D614, Y453/D614G, and Y453F/D614G. 2021 Frontiers in microbiology Figure SARS_CoV_2 Y453F;Y453F;D614G;D614G 51;79;68;85 56;84;73;90 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. The location of the variants Y453F and D164G is shown in red. 2021 Frontiers in microbiology Figure SARS_CoV_2 D164G;Y453F 39;29 44;34 34630410 A Barcoded Flow Cytometric Assay to Explore the Antibody Responses Against SARS-CoV-2 Spike and Its Variants. (A) Schematic drawing of the RBD-CD8 protein with either an WT (green), or an N501Y (blue), E484K (red) or G496I (grey) mutated RBD sequence. 2021 Frontiers in immunology Figure SARS_CoV_2 E484K;G496I;N501Y 92;107;78 97;112;83 RBD;RBD 29;128 32;131 34630410 A Barcoded Flow Cytometric Assay to Explore the Antibody Responses Against SARS-CoV-2 Spike and Its Variants. Shown is the IgG (left panel) and IgA (right panel) antibody response of the sera diluted 1:100 and analyzed for binding to Ramos cells expressing RBD-CD8 protein with either a WT (green), or an N501Y (blue), E484K (red) or G496I (grey) mutated RBD sequence. 2021 Frontiers in immunology Figure SARS_CoV_2 E484K;G496I;N501Y 209;224;195 214;229;200 RBD;RBD 147;245 150;248 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. Sera of 81 patients who had recovered from COVID-19 were tested for neutralizing activity against the SARS-CoV-2 variants D614G, B.1.1.7, P.1, and B.1.351. 2021 Open forum infectious diseases Figure SARS_CoV_2 D614G 122 127 COVID-19 43 51 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. The neutralizing antibody titer against (A) D614G, (B) B.1.1.7, (C) P.1, and (D) B.1.351 in patients' sera with different severity groups. 2021 Open forum infectious diseases Figure SARS_CoV_2 D614G 44 49 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. The neutralizing antibody titers of sera against D614G, B.1.1.7, P.1, and B.1.351 were compared in the first wave (from March 1 to June 2020) (A), second wave (from July 1 to October 2020) (B), third wave (from November 1, 2020, to February 2021) (C), and fourth wave (after March 1, 2021) (D). 2021 Open forum infectious diseases Figure SARS_CoV_2 D614G 49 54 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. (a) Binding responses of anti-SARS-CoV-2 S protein mAbs, S1D2-hIgG1, STI-1499-LALA and 1741-LALA to the S1 fragment of the S protein from SARS-CoV-2 variants, including 2019-nCoV, B.1.1.7 (HV69-70 deletion, Y144 deletion, N501Y, A570D, D614G, P681H)-, B.1.351 (K417N, E484K, N501Y, D614G)-, and B.1.617.2 (T19R, G142D, E156G, 157-158 deletion, L452R, T478K, D614G, P681R)- lineage. 2021 Antiviral research Figure SARS_CoV_2 A570D;D614G;D614G;D614G;E156G;E484K;G142D;L452R;N501Y;N501Y;P681H;P681R;T478K;K417N;T19R 229;236;282;358;319;268;312;344;222;275;243;365;351;261;306 234;241;287;363;324;273;317;349;227;280;248;370;356;266;310 S;S 41;123 42;124 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. Kinetic interaction between anti-SARS-CoV-2 Spike mAbs and variant spike protein, neutralization abilities of convalescent plasma and anti-SARS-CoV-2 spike mAbs against SARS-CoV-2 strains B.1.351, D614, and D614G. 2021 Antiviral research Figure SARS_CoV_2 D614G 207 212 S;S;S 44;67;150 49;72;155 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. Neutralization titers of (c) convalescent plasma from three different COVID-19 patients against SARS-CoV-2 D614 and PRNT50 curves of anti-SARS-CoV-2 spike mAbs against (d) D614 (e) D614G, and (f) B.1.351. 2021 Antiviral research Figure SARS_CoV_2 D614G 181 186 S 149 154 COVID-19 70 78 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. ELISA was used to determine EC50 values for ACE2 binding to S1-RBD, S1-RBD N501Y, or S1-RBD E484K. 2021 FASEB journal Figure SARS_CoV_2 E484K;N501Y 92;75 97;80 RBD;RBD;RBD 63;71;88 66;74;91 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. ELISA was used to determine EC50 values for individual VNAR-hFc antibodies to (A) S1, (B) S1-RBD, (C) S1-RBD N501Y, and (D) S1-RBD E484K. 2021 FASEB journal Figure SARS_CoV_2 E484K;N501Y 131;109 136;114 RBD;RBD;RBD 93;105;127 96;108;130 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. ELISA was used to determine IC50 blocking values for individual VNAR-hFc antibodies against (A) S1, (B) S1-RBD, (C) S1-RBD N501Y, and (D) S1-RBD E484K (blockers only). 2021 FASEB journal Figure SARS_CoV_2 E484K;N501Y 145;123 150;128 RBD;RBD;RBD 107;119;141 110;122;144 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The relative entry point of the C14805T and C14408T mutations in the tree, their area of influence (shaded area), the inferred node from which evolved the SS4 cluster and the central node at the root of the SS4 cluster (filled yellow circle) are shown. 2021 Infection, genetics and evolution Figure SARS_CoV_2 C14408T;C14805T 44;32 51;39 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Change in binding free energy (DeltaDeltaG = DeltaGWILD-TYPE - DeltaGMUTANT) predicted by computational mutagenesis of the S-RBDCoV-2 wild-type residues E484 (A), Q493 (B), S494P (C), V483 (D), F486 (E), Y489 (F), Y449 (G), L452 (H), T470 (I), and F490 (J) for the corresponding S-RBDCoV-2/LY-CoV555 mAb complexes. 2021 Scientific reports Figure SARS_CoV_2 S494P 173 178 S;S 123;279 124;280 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Images for all other circulating mutants (E484A/D/G/Q/V, Q493H/K/L, S494A/P/T, and L452M/Q) are shown in Figures S1-S3 and S8 (see also Tables S5-S7 and S12 for details). 2021 Scientific reports Figure SARS_CoV_2 L452M;L452Q;Q493H;Q493K;Q493L;S494A;S494P;S494T;E484A;E484D;E484G;E484Q;E484V 83;83;57;57;57;68;68;68;42;42;42;42;42 90;90;66;66;66;77;77;77;55;55;55;55;55 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Images for all other circulating mutants (K417E/R/T, D420G/, N460K/S/T, T415A/I/N/S and Y489C/F/H) are shown in Figures S11-S14 and S18 (see also Tables S19-S22 and S26 for details). 2021 Scientific reports Figure SARS_CoV_2 D420G;N460K;N460S;N460T;T415A;T415I;T415N;T415S;Y489C;Y489F;Y489H;K417E;K417R;K417T 53;61;61;61;72;72;72;72;88;88;88;42;42;42 58;70;70;70;83;83;83;83;97;97;97;51;51;51 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Main interactions involving the S-RBDCoV-2 E484K (A), Q3493R (B), S494R (C), and L452R (D) mutants at the interface with the LY-CoV555 (bamlanivimab) mAb as obtained from the relevant equilibrated MD simulations. 2021 Scientific reports Figure SARS_CoV_2 E484K;L452R;Q3493R;S494R 43;81;54;66 48;86;60;71 S 32 33 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Main interactions involving the S-RBDCoV-2 K417N (A), D420A (B), N460I (C), T415P (D), and Y489S (E) mutants at the interface with the LY-CoV016 (etesevimab) mAb as obtained from the relevant equilibrated MD simulations. 2021 Scientific reports Figure SARS_CoV_2 D420A;K417N;N460I;T415P;Y489S 54;43;65;76;91 59;48;70;81;96 S 32 33 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. b Structural modelling of the K417N/T, L452R, Y453F, S477N, E484K and N501Y mutations, based on 7chh for X593, RBD-7B8 for 7B8, RBD-Ab1 for 10D 12, and 7c01 for CB6. 2021 Communications biology Figure SARS_CoV_2 E484K;K417N;K417T;L452R;N501Y;S477N;Y453F 60;30;30;39;70;53;46 65;37;37;44;75;58;51 RBD;RBD 111;128 114;131 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. b the ID50 ratios, compared with the D614G reference strain, are displayed using dot plots. 2021 Communications biology Figure SARS_CoV_2 D614G 37 42 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. e Heat map of mean ID50 ratio, compared with D614G. 2021 Communications biology Figure SARS_CoV_2 D614G 45 50 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. e ID50 ratios of sera from inactived-vaccine, compared with the D614G reference strain, are displayed using dot plots. 2021 Communications biology Figure SARS_CoV_2 D614G 64 69 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. e RLU of cells infected with D614G virus. 2021 Communications biology Figure SARS_CoV_2 D614G 29 34 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. E484K-carrying variants are marked in red. 2021 Communications biology Figure SARS_CoV_2 E484K 0 5 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Each mutation in each SARS-CoV-2 variant is indicated relative to the reference D614G sequence. 2021 Communications biology Figure SARS_CoV_2 D614G 80 85 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. f ID50 ratios of sera from adenovirus-vaccine, compared with the D614G reference strain, are displayed using dot plots. 2021 Communications biology Figure SARS_CoV_2 D614G 65 70 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. f Neutralization ID50 values of different immunized serum samples against pseudotyped D614G virus. 2021 Communications biology Figure SARS_CoV_2 D614G 86 91 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. f-h Ratios by which enzyme overexpression induced enhanced infection, compared with D614G. 2021 Communications biology Figure SARS_CoV_2 D614G 84 89 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. ID50 ratios between the variants and the D614G reference strain are presented. 2021 Communications biology Figure SARS_CoV_2 D614G 41 46 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Neutralization analyses of convalescence sera from D614G-, B.1.1.7- and B.1.351- infected patients and vaccine-elicited sera. 2021 Communications biology Figure SARS_CoV_2 D614G 51 56 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Ratios between variants and the D614G reference strain were calculated. 2021 Communications biology Figure SARS_CoV_2 D614G 32 37 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Reduced neutralization, folds compared with the D614G reference strain, is labeled at the bottom of each plot. 2021 Communications biology Figure SARS_CoV_2 D614G 48 53 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Relative infectivities compared with the D614G reference strain are displayed as the RLU ratio to D614G. 2021 Communications biology Figure SARS_CoV_2 D614G;D614G 41;98 46;103 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Relative RLUs were compared with or without the indicated enzyme first, and then compared with the D614G reference strain. 2021 Communications biology Figure SARS_CoV_2 D614G 99 104 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. The heat map shows of mean ID50 ratio compared with D614G. 2021 Communications biology Figure SARS_CoV_2 D614G 52 57 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. (a) Illustrations of unfavorable interfacial coordinations for L452R. 2021 Journal of chemical information and modeling Figure SARS_CoV_2 L452R 63 68 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. (a) LY-CoV555 of different concentrations was added to pseudovirions bearing the wild type Wuhan-Huh-1 spike or sequences containing triple mutations found in the Kappa variant (L452R/E484Q/D614G). 2021 Journal of chemical information and modeling Figure SARS_CoV_2 L452R;D614G;E484Q 178;190;184 183;195;189 S 103 108 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. (b) Illustrations of unfavorable interfacial coordinations for E484Q. 2021 Journal of chemical information and modeling Figure SARS_CoV_2 E484Q 63 68 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. (b) Plaque reduction neutralization assays were performed to evaluate the neutralizing ability of LY-CoV555 against WA1/2020, recombinant virus containing L452R/E484Q/D614G or E484Q/D614G. 2021 Journal of chemical information and modeling Figure SARS_CoV_2 E484Q;L452R;D614G;D614G;E484Q 176;155;167;182;161 181;160;172;187;166 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. (c) Illustrations of interfacial coordinations for T478K. 2021 Journal of chemical information and modeling Figure SARS_CoV_2 T478K 51 56 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. (d) Illustrations of unfavorable interfacial coordinations for F490S. 2021 Journal of chemical information and modeling Figure SARS_CoV_2 F490S 63 68 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. L452R/E484Q confers escape from LY-CoV555 in the experiment. 2021 Journal of chemical information and modeling Figure SARS_CoV_2 E484Q;L452R 6;0 11;5 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. (A and B) In vitro infection assay of VSV PsVs, including N501Y + D614G, N501Y + L452R + D614G, and N501Y + K417N + E484K + D614G, on 293 cells transfected with human ACE2 (A) or mouse ACE2 (B). 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;D614G;E484K;K417N;L452R;N501Y;N501Y;N501Y 66;89;124;116;108;81;58;73;100 71;94;129;121;113;86;63;78;105 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. (A-E) Representative neutralization curves for the indicated COVID-19+ or vaccinated tier groups against the N501Y + D614G, N501Y + L452R + D614G, or N501Y + K417N + E484K + D614G PsVs. 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;D614G;E484K;K417N;L452R;N501Y;N501Y;N501Y 117;140;174;166;158;132;109;124;150 122;145;179;171;163;137;114;129;155 COVID-19 61 69 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. (A-F) In vivo neutralization of SARS-CoV-2 VSV PsVs carrying emerging L452R and K417N + E484K spike mutations by COVID-19+ or vaccinated human plasma samples. 2021 Cell reports Figure SARS_CoV_2 E484K;K417N;L452R 88;80;70 93;85;75 S 94 99 COVID-19 113 121 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. (A) In vitro infectivity of SARS-CoV-2 PsVs, including N501Y + D614G, N501Y + L452R + D614G, N501Y + K417N + E484K + D614G, and N501Y + L452R + K417N + E484Q + D614G, on 293 cells transfected with human ACE2. 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;D614G;D614G;E484K;E484Q;K417N;K417N;L452R;L452R;N501Y;N501Y;N501Y;N501Y 63;86;117;160;109;152;101;144;78;136;55;70;93;128 68;91;122;165;114;157;106;149;83;141;60;75;98;133 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. (C and D) Binding curves of the WT or N501Y variant RBD with 293 cells expressing hACE2 (C) or mACE2 (D). 2021 Cell reports Figure SARS_CoV_2 N501Y 38 43 RBD 52 55 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. (D and E) Quantification of signal in the lungs (D) and nasopharyngeal passage (E) of mice infected with N501Y + D614G SARS-CoV-2 VSV PsVs and blocked or vaccinated as indicated (n = 5). 2021 Cell reports Figure SARS_CoV_2 D614G;N501Y 113;105 118;110 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. (G and H) Comparison of neutralization ability of each indicated COVID-19+ or vaccinated group between (G) N501Y + K417N + E484K + D614G and N501Y + D614G PsV infection or (H) N501Y + L452R + D614G and N501Y + D614G PsV infection. 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;D614G;D614G;E484K;K417N;L452R;N501Y;N501Y;N501Y;N501Y 131;149;192;210;123;115;184;107;141;176;202 136;154;197;215;128;120;189;112;146;181;207 COVID-19 65 73 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. (G and H) Quantification of signal in the lungs (G) and nasopharyngeal passage (H) of mice transduced with AdV5-hACE2, infected with N501Y + D614G SARS-CoV-2 VSV PsVs, and blocked or vaccinated as indicated (n = 5). 2021 Cell reports Figure SARS_CoV_2 D614G;N501Y 141;133 146;138 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. (G) Quantification of nasopharyngeal signal in mice following primary infection with N501Y + D614G and then N501Y + D614G rechallenge compared with N501Y + D614G reference infection. 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;D614G;N501Y;N501Y;N501Y 93;116;156;85;108;148 98;121;161;90;113;153 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. (H) Quantification of nasopharyngeal signal in mice following primary infection with N501Y + D614G and then N501Y + K417N + E484K + D614G rechallenge compared with N501Y + K417N + E484K + D614G reference infection. 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;D614G;E484K;E484K;K417N;K417N;N501Y;N501Y;N501Y 93;132;188;124;180;116;172;85;108;164 98;137;193;129;185;121;177;90;113;169 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. (I-K) Plasma anti-SARS-CoV-2 spike levels represented via histogram (I) or bar graphs (J and K) in infection groups, including naive mice (normal plasma), primary infection with N501Y + D614G, reinfection with N501Y + D614G, and reinfection with N501Y + K417N + E484K + D614G. 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;D614G;E484K;K417N;N501Y;N501Y;N501Y 186;218;270;262;254;178;210;246 191;223;275;267;259;183;215;251 S 29 34 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. (L-N) WT versus N501Y + K417N + E484K + D614G RBD-specific (L) IgG, (M) IgM, and (N) IgA antibody levels from COVID-19+ or vaccinated individuals stratified by anti-SARS-CoV-2 spike tier groups. 2021 Cell reports Figure SARS_CoV_2 D614G;E484K;K417N;N501Y 40;32;24;16 45;37;29;21 S;RBD;N 176;46;82 181;49;83 COVID-19 110 118 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. 2 weeks later, mice were rechallenged with N501Y + D614G or N501Y + K417N + E484K + D614G PsVs. 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;E484K;K417N;N501Y;N501Y 51;84;76;68;43;60 56;89;81;73;48;65 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. All mice were administered anti-IFNAR1 24 h prior to infection with N501Y + D614G SARS-CoV-2 VSV PsVs intranasally. 2021 Cell reports Figure SARS_CoV_2 D614G;N501Y 76;68 81;73 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. All mice were administered anti-IFNAR1 24 h prior to infection with N501Y + D614G, N501Y + L452R + D614G, or N501Y + K417N + E484K + D614G SARS-CoV-2 VSV PsVs intranasally. 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;D614G;E484K;K417N;L452R;N501Y;N501Y;N501Y 76;99;133;125;117;91;68;83;109 81;104;138;130;122;96;73;88;114 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Application of SARS-CoV-2 N501Y variant VSV-based murine model to intervention studies. 2021 Cell reports Figure SARS_CoV_2 N501Y 26 31 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Bottom: the N501Y-RBD variant. 2021 Cell reports Figure SARS_CoV_2 N501Y 12 17 RBD 18 21 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Effect of L452R and K417N + E484K spike mutations on the ability of antibodies from COVID-19+ or vaccinated individuals to bind and neutralize SARS-CoV-2. 2021 Cell reports Figure SARS_CoV_2 E484K;K417N;L452R 28;20;10 33;25;15 S 34 39 COVID-19 84 92 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Hexa-Histidine (6HIS)-tagged WT or N501Y RBD proteins were titrated on a 2-fold scale according to values on the x axis. 2021 Cell reports Figure SARS_CoV_2 N501Y 35 40 RBD 41 44 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. In vivo neutralization of L452R and K417N + E484K variant PsVs by COVID-19+ or vaccinated plasma. 2021 Cell reports Figure SARS_CoV_2 E484K;K417N;L452R 44;36;26 49;41;31 COVID-19 66 74 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Infectivity and immune escape potential of the N501Y + L452R + K417 + E484Q + D614G India variant. 2021 Cell reports Figure SARS_CoV_2 D614G;E484Q;L452R;N501Y 78;70;55;47 83;75;60;52 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Infectivity and reinfection potential of L452R and K417N + E484K spike mutation bearing SARS-CoV-2 PsVs in vivo. 2021 Cell reports Figure SARS_CoV_2 E484K;K417N;L452R 59;51;41 64;56;46 S 65 70 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Kd for hACE2 binding: WT (Kd = 3.4 nM), N501Y (Kd = 2.1 nM). 2021 Cell reports Figure SARS_CoV_2 N501Y 40 45 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Kd for mACE2 binding: WT (Kd cannot be determined), N501Y (Kd = 47.6 nM). 2021 Cell reports Figure SARS_CoV_2 N501Y 52 57 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Luciferase-expressing N501Y + D614G PsVs were preincubated with COVID-19+ plasma, RBD-Fc-vaccinated mouse plasma, or species-matched control plasma at the indicated dilutions on the x axis over a 2-fold dilution range. 2021 Cell reports Figure SARS_CoV_2 D614G;N501Y 30;22 35;27 RBD 82 85 COVID-19 64 72 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Luciferase-expressing PsVs, including (E) N501Y + D614G, (F) N501Y + L452R + D614G, (G) N501Y + K417N + E484K + D614G, and (H) N501Y + L452R + K417N + E484Q + D614G, were preincubated with serially diluted low-, mid-, or high-tier COVID-19+ plasma prior to infection. 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;D614G;D614G;E484K;E484Q;K417N;K417N;L452R;L452R;N501Y;N501Y;N501Y;N501Y 50;77;112;159;104;151;96;143;69;135;42;61;88;127 55;82;117;164;109;156;101;148;74;140;47;66;93;132 COVID-19 231 239 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Luciferase-expressing PsVs, including N501Y + D614G, N501Y + L452R + D614G, and N501Y + K417N + E484K + D614G, were preincubated with 45 COVID-19+ plasma samples, 15 COVID-19-vaccinated plasma samples, or 4 control plasma samples over a 3-fold dilution range. 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;D614G;E484K;K417N;L452R;N501Y;N501Y;N501Y 46;69;104;96;88;61;38;53;80 51;74;109;101;93;66;43;58;85 COVID-19;COVID-19 137;166 145;174 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Luciferase-expressing SARS-CoV-2 variant Lenti PsVs, including (1) WT, (2) D614G, (3) N501Y, and (4) N501Y + D614G (all having a 19-amino-acid [aa] deletion) were normalized to the total amount of S protein via western blot, titrated across a 2-fold range as indicated on the x axis, and then added to hACE+, mACE2+, or non-transfected 293 cells that were seeded 24 h prior to infection. 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;N501Y;N501Y 75;109;86;101 80;114;91;106 S 197 198 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. MFI for each plasma samples was graphed against reciprocal log10IC50 for each plasma incubated with (I) N501Y + D614G, (J) N501Y + L452R + D614G, and (K) N501Y + K417N + E484K + D614G VSV PsVs. 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;D614G;E484K;K417N;L452R;N501Y;N501Y;N501Y 112;139;178;170;162;131;104;123;154 117;144;183;175;167;136;109;128;159 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Mice were first challenged with N501Y + D614G VSV PsVs. 2021 Cell reports Figure SARS_CoV_2 D614G;N501Y 40;32 45;37 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. SARS-CoV-2 VSV PsV infection groups include (1) WT, (2) D614G, (3) N501Y, and (4) N501Y + D614G. 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;N501Y;N501Y 56;90;67;82 61;95;72;87 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Shown are representative image and luminescence values for mice infected with (A and B) N501Y + D614G, (C and D) N501Y + L452R + D614G, and (E and F) N501Y + K417N + E484K + D614G VSV PsVs and transferred with the indicated human plasma samples. 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;D614G;E484K;K417N;L452R;N501Y;N501Y;N501Y 96;129;174;166;158;121;88;113;150 101;134;179;171;163;126;93;118;155 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. The SARS-CoV-2 N501Y variant VSV-based murine model. 2021 Cell reports Figure SARS_CoV_2 N501Y 15 20 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. The scale was set based on primary infection with N501Y + D614G or N501Y + K417N + E484K + D614G PsVs because this would indicate the predicted level of infection without preexisting immunity. 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;E484K;K417N;N501Y;N501Y 58;91;83;75;50;67 63;96;88;80;55;72 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Then mice were anesthetized with 2.5% vaporized isoflurane and administered normalized amounts of the indicated PsVs intranasally, including (1) WT, (2) D614G, (3) N501Y, and (4) N501Y + D614G . 2021 Cell reports Figure SARS_CoV_2 D614G;D614G;N501Y;N501Y 153;187;164;179 158;192;169;184 34649268 Genomic reconstruction of the SARS-CoV-2 epidemic in England. a, The observed relative frequency of other lineages (light grey), Alpha/B.1.1.7 (dark grey), E484K variants (orange) and Delta/B.1.617.2 (brown). 2021 Nature Figure SARS_CoV_2 E484K 94 99 34649268 Genomic reconstruction of the SARS-CoV-2 epidemic in England. Dynamics of E484K variants and Delta between January and June 2021. 2021 Nature Figure SARS_CoV_2 E484K 12 17 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. (a) domain organization of the Spike protein, (b) binding interface of Spike RBD and ACE2 receptor, (c) wild type RBD (d) N439K mutant RBD (e) S477 N mutant RBD (f) T478K mutant RBD (g-i) Superimposed structure of RBD WT (green) with N439K (orange), S477 N (magenta), T478K (cyan), L84S (orange). 2021 Computers in biology and medicine Figure SARS_CoV_2 L84S;N439K;N439K;S477N;S477N;T478K;T478K 282;122;234;143;250;165;268 286;127;239;149;256;170;273 S;S;RBD;RBD;RBD;RBD;RBD;RBD;N;N 31;71;77;114;135;157;178;214;148;255 36;76;80;117;138;160;181;217;149;256 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. (a) Represent the binding interface of the S477 N complex along with its stick representation of the key hydrogen interactions with ACE2. 2021 Computers in biology and medicine Figure SARS_CoV_2 S477N 43 49 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. (a) show the comparative Rg of the wild type and N439K, (b) show the comparative Rg of the wild type and S477 N while (c) show the comparative Rg of the wild type and T478K. 2021 Computers in biology and medicine Figure SARS_CoV_2 N439K;S477N;T478K 49;105;167 54;111;172 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. (a) show the comparative RMSD of the wild type and N439K, (b) show the comparative RMSD of the wild type and S477 N, while (c) show the comparative RMSD of the wild type and T478K. 2021 Computers in biology and medicine Figure SARS_CoV_2 N439K;S477N;T478K 51;109;174 56;115;179 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. (a) show the comparative total number of hydrogen bonds of the wild type and N439K, (b) show the comparative total number of hydrogen bonds of the wild type and S477 N while (c) show the comparative total number of hydrogen bonds of the wild type and T478K. 2021 Computers in biology and medicine Figure SARS_CoV_2 N439K;S477N;T478K 77;161;251 82;167;256 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. (b) The binding interface and stick representation of hydrogen bonding of the N439K mutant complex. 2021 Computers in biology and medicine Figure SARS_CoV_2 N439K 78 83 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. (b) The binding interface and stick representation of hydrogen bonding of the T478K mutant complex. 2021 Computers in biology and medicine Figure SARS_CoV_2 T478K 78 83 34655895 Bioinformatics analysis of the differences in the binding profile of the wild-type and mutants of the SARS-CoV-2 spike protein variants with the ACE2 receptor. Docking complexes of S477N and T478K mutants spike protein with ACE2. 2021 Computers in biology and medicine Figure SARS_CoV_2 S477N;T478K 21;31 26;36 S 45 50 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. (1 F) Amplification curves of Y501 (N501Y allele) for ten-fold serial dilutions of B.1.36.27. 2022 Journal of virological methods Figure SARS_CoV_2 N501Y 36 41 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. (1 G) Wildtype and N501Y containing SARS-CoV-2 RNA were mixed at ratios from 9:1 (allele frequency = 90 %) to 1:9 (allele frequency = 10 %). 2022 Journal of virological methods Figure SARS_CoV_2 N501Y 19 24 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. (1C) Amplification curves of Y501 (N501Y allele) for ten-fold serial dilutions of B.1.1.7. 2022 Journal of virological methods Figure SARS_CoV_2 N501Y 35 40 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. (1D) The concentration (copies/muL) of serial dilutions of B.1.36.27 (non-N501Y variant) sample. 2022 Journal of virological methods Figure SARS_CoV_2 N501Y 74 79 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. Determination of limit of detection (LoD) of the N501Y RT-qPCR and detection of low-frequency N501Y variants. 2022 Journal of virological methods Figure SARS_CoV_2 N501Y;N501Y 49;94 54;99 34656702 A low-cost TaqMan minor groove binder probe-based one-step RT-qPCR assay for rapid identification of N501Y variants of SARS-CoV-2. N501Y mutation was successfully detected at an allele frequency as low as 10 % in the RNA mixtures. 2022 Journal of virological methods Figure SARS_CoV_2 N501Y 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The comparison of general SARS-CoV-2 and N501Y mutation sequence. 2021 Journal of medical virology Figure SARS_CoV_2 N501Y 41 46 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. (A) The downstream (617-636) of D614G in wild (green) and mutant (red) S protein was focused. 2021 Journal of medical virology Figure SARS_CoV_2 D614G 32 37 S 71 72 34676891 Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. The effect on transmembrane channel pore of ORF3a viroporin due to p.Q57H mutation. 2021 Journal of medical virology Figure SARS_CoV_2 Q57H;Q57H 67;69 73;73 ORF3a 44 49 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. By immunohistochemistry for SARS-CoV-2 N protein, moderate amounts of antigen-positive pneumocytes (arrows) were detected in D614G-inoculated animals (G), whereas scattered numbers of antigen-positive pneumocytes (arrows) were detected in B.1.1.7- and B.1.351-inoculated animals (H and I). 2021 Science advances Figure SARS_CoV_2 D614G 125 130 N 39 40 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Differences in cytokine and chemokine levels in serum, BAL, and nose samples of rhesus macaques inoculated with D614G, B.1.1.7, or B.1.351. 2021 Science advances Figure SARS_CoV_2 D614G 112 117 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Differences in histopathological changes in lungs of rhesus macaques inoculated with D614G, B.1.1.7, or B.1.351. 2021 Science advances Figure SARS_CoV_2 D614G 85 90 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Milder disease observed in rhesus macaques inoculated with B.1.351 than with D614G or B.1.1.7. 2021 Science advances Figure SARS_CoV_2 D614G 77 82 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. No differences in virus shedding between D614G, B.1.1.7, and B.1.351. 2021 Science advances Figure SARS_CoV_2 D614G 41 46 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Three groups of six adult rhesus macaques were inoculated with SARS-CoV-2 variants D614G, B.1.1.7, or B.1.351. 2021 Science advances Figure SARS_CoV_2 D614G 83 88 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. A microarray heatmap represents 22 genes and selected control genes in HAECs in response to Spike D614G. 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Figure SARS_CoV_2 D614G 98 103 S 92 97 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. a) In the endothelialized microfluidic platform, HAECs were exposed to SARS-CoV-2, Lenti-S D614G, or Lipo-S in the presence or absence of Lipo-hACE2 or anti-IL-6 (scale bar = 100 microm). 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Figure SARS_CoV_2 D614G 91 96 S;S 89;106 90;107 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. a) Representative images of fibrin deposition (in magenta) and platelet-platelet aggregates (in green) in the HAEC-seeded microfluidic channels were compared with exposure to the live SARS-CoV-2 virus, the Spike proteins, and the Spike variant D614G via viral vector (scale bar = 100 microm). 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Figure SARS_CoV_2 D614G 244 249 S;S 206;230 211;235 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. b) Spike mutation D614G inflammatory effect was tested HAECs. 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Figure SARS_CoV_2 D614G 18 23 S 3 8 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. c) Immunocytochemical analysis showed Lenti-S D614G increasing protein level of IL-6 (in red). 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Figure SARS_CoV_2 D614G 46 51 S 44 45 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. Fibrin deposition was also significant in response to Spike and the Spike mutation D614G. 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Figure SARS_CoV_2 D614G 83 88 S;S 54;68 59;73 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. Fibrin nodules were observed as dense magenta aggregates in the center of the channels in the presence of SARS-CoV-2 and also confirmed in response to Lenti-Spike mutation D614G (n = 4). 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Figure SARS_CoV_2 D614G 172 177 S 157 162 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. (A) Neutralization of the SARS-CoV-2 D614G pseudovirus by plasma pre- and post-vaccination from participants with no prior infection (green, n = 19) and those infected in the first (blue, n = 20) and second waves (red, n = 19). 2021 Cell host & microbe Figure SARS_CoV_2 D614G 37 42 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. (B) Cross-reactive ADCC activity 28 days post-vaccination against D614G, Beta, and Delta. 2021 Cell host & microbe Figure SARS_CoV_2 D614G 66 71 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. (B) Cross-reactive neutralization post-vaccination against D614G, Beta, and Delta. 2021 Cell host & microbe Figure SARS_CoV_2 D614G 59 64 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. (B) Plasma samples from participants with no prior infection (green, n = 19), first-wave infection (blue, n = 20), or second-wave infection (red, n = 19) were tested for binding to D614G spike protein pre- and post-vaccination (OD450nm). 2021 Cell host & microbe Figure SARS_CoV_2 D614G 181 186 S 187 192 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. (C) Cross-reactivity of vaccine-induced antibody responses to D614G and Beta spike. 2021 Cell host & microbe Figure SARS_CoV_2 D614G 62 67 S 77 82 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. (C) Fold change of post-vaccination D614G ADCC levels relative to those of the Beta/Delta variants. 2021 Cell host & microbe Figure SARS_CoV_2 D614G 36 41 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. (C) Fold change of post-vaccination D614G neutralization titers relative to Beta or Delta. 2021 Cell host & microbe Figure SARS_CoV_2 D614G 36 41 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. Statistical analyses were performed with the Friedman test between groups and the Wilcoxon test for pre- and post-vaccine time points or D614G in comparison with Beta/Delta responses. 2021 Cell host & microbe Figure SARS_CoV_2 D614G 137 142 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. Statistical analyses were performed with the Mann-Whitney test between groups, and the Wilcoxon test was performed for pre- and post-vaccine time points or D614G in comparison with Beta responses. 2021 Cell host & microbe Figure SARS_CoV_2 D614G 156 161 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. The ancestral strain (D614G) is depicted in blue, and Beta is depicted in red. 2021 Cell host & microbe Figure SARS_CoV_2 D614G 22 27 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. (d-i) BHK21 cells transfected with empty vector, mouse ACE2, rat ACE2 or human ACE2 were inoculated with SARS-CoV-2-S-pseudoviruses with (d) B.1, (e) B.1.1.7, (f) B.1.351, (g) P.1, (h) B.1.617.2 or (i) WT and N501Y spike. 2021 EBioMedicine Figure SARS_CoV_2 N501Y 209 214 S;S 215;116 220;117 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. B.1.1.7 and other N501Y-carrying variants expanded tropism to infect Mus musculus. 2021 EBioMedicine Figure SARS_CoV_2 N501Y 18 23 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. SARS-CoV-2 B.1.1.7 and other N501Y-carrying variants efficiently utilize murine ACE2 for virus entry. 2021 EBioMedicine Figure SARS_CoV_2 N501Y 29 34 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. BLI binding response curves of RBD wt (A), K417N (B), K417T (C), E484K (D), N501Y (E), B.1.351 (N_K_Y) (F), and P.1 (T_K_Y) (G) to ACE-2-Fc immobilized unto AHC sensors. 2021 Frontiers in immunology Figure SARS_CoV_2 E484K;K417N;K417T;N501Y 65;43;54;76 70;48;59;81 RBD 31 34 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. Linear regression and Spearman correlation analyses of the logIC50 (n = 18) for RBD wt vs K417N (A), K417T (B), E484K (C), N501Y (D), B.1.351 (N_K_Y) (E), and P.1 (T_K_Y) (F). 2021 Frontiers in immunology Figure SARS_CoV_2 E484K;K417N;K417T;N501Y 112;90;101;123 117;95;106;128 RBD 80 83 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. N_K_Y, B.1.351 RBD (K417N + E484K + N501Y); T_K_Y, P.1 RBD (K417T + E484K + N501Y). 2021 Frontiers in immunology Figure SARS_CoV_2 E484K;E484K;N501Y;N501Y;K417N;K417T 28;68;36;76;20;60 33;73;41;81;25;65 RBD;RBD 15;55 18;58 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. (B) Protein models of S protein containing T478I/R/K or E484K/Q mutations together with D614G double mutations were superposed onto the prototype. 2021 mBio Figure SARS_CoV_2 D614G;E484K;E484Q;T478I;T478K;T478R 88;56;56;43;43;43 93;63;63;52;52;52 S 22 23 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. 614D, SARS-CoV-2 prototype; 614G, SARS-CoV-2 variant containing glycine at codon position 614 of S gene (S-D614G), except for the four VOCs (alpha, beta, gamma, and delta). 2021 mBio Figure SARS_CoV_2 D614G 107 112 S;S 97;105 98;106 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Note the D614G mutant is 50.53% identical to the prototype. 2021 mBio Figure SARS_CoV_2 D614G 9 14 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Note the T478R/K + D614G and E484Q + D614G double mutants are >93% identitical to the prototype, while the S1-RBD domain of T478I + D614G and E484K + D614G double mutants were not aligned with the prototype. 2021 mBio Figure SARS_CoV_2 D614G;D614G;D614G;D614G;E484K;E484Q;T478I;T478K;T478R 19;37;132;150;142;29;124;9;9 24;42;137;155;147;34;129;16;16 RBD 110 113 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. S protein in group 1 did not carry the D614G mutation, while S protein of groups 2, 3, and 4 contained D614G mutation. 2021 mBio Figure SARS_CoV_2 D614G;D614G 39;103 44;108 S;S 0;61 1;62 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. When superposing protein models of S-D614G mutant (mutated amino acid residue 614, indicated by a black arrow) onto the prototype, the aligned regions of the two models are indicated in light gray, while the regions where these two proteins are not aligning are indicated in blue (prototype) and red (S-D614G mutant). 2021 mBio Figure SARS_CoV_2 D614G;D614G 37;303 42;308 S;S 35;301 36;302 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. (b) Highest diversity is at the A23403G (D614G) substitution splitting the tree in the bottom (Chinese) and top (European) branch. 2021 Scientific reports Figure SARS_CoV_2 A23403G;D614G 32;41 39;46 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. All predominating variants in June 2021 also carried the D614G, besides their characteristic amino acid changes. 2021 Scientific reports Figure SARS_CoV_2 D614G 57 62 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. G22486T may reflect migration routes because in the nextstrain analysis of Africa as a whole there are also Tunisian samples in this branch (https://nextstrain.org/ncov/africa?f_region=Africa, accessed Jun 26th, 2020). 2021 Scientific reports Figure SARS_CoV_2 G22486T 0 7 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. Temporal course of clade distribution confirms gaining of share of the Europe-associated G-clades harboring the putatively more infectious D614G amino acid substitution (February-April 2020). 2021 Scientific reports Figure SARS_CoV_2 D614G 139 144 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. This plot was generated in June 2021 and confirms our previous analysis of samples from February 2020 to April 2020 predicting a rapid spread of the variants carrying the D614G amino acid substitution. 2021 Scientific reports Figure SARS_CoV_2 D614G 171 176 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. Within the clade S, there are putatively specific West-African mutations at the branches at C24370T and G22468T. 2021 Scientific reports Figure SARS_CoV_2 C24370T;G22468T 92;104 99;111 S 17 18 34705425 Gold-Nanostar-Chitosan-Mediated Delivery of SARS-CoV-2 DNA Vaccine for Respiratory Mucosal Immunization: Development and Proof-of-Principle. The relative inhibition in infectivity was performed against lentiviral particles engineered with (e) S protein SC2-Wuhan, (f) SC2-beta mutant, and (g) SC2-D614G mutant variants. 2021 ACS nano Figure SARS_CoV_2 D614G 156 161 S 102 103 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. Intermolecular interactions of ACE2 with SARS-CoV-2 RBD (S477I). 2021 Bioinformatics and biology insights Figure SARS_CoV_2 S477I 57 62 RBD 52 55 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. (A-C) Infectivity analysis of SARS-CoV-2 WT, D614G, N501Y.V1 and N501Y.V2 RBD entry into 293T-hACE2 (A), Caco2-hACE2 (B), and Vero (C) cells at 10 h, 14 h, 18 h, 24 h, and 36 h. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 D614G;N501Y;N501Y 45;52;65 50;57;70 RBD 74 77 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. (A-C) N501Y.V1 and N501Y.V2 RBD entry into host cells through CatB/L or TMPRSS2 activation was evaluated by adding E64d, Camostat or the combination of them (E64d + Camostat) to 293T-hACE2 cells 2 h prior to transduction. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 N501Y;N501Y 6;19 11;24 RBD 28 31 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. (A, B) SARS-CoV, SARS-CoV-2 WT, D614G, N501Y.V1 and N501Y.V2 RBD S pseudovirions were incubated in cell culture medium DMEM at 37 C (A) or 42 C (B) for the specified times (0 to 6 h). 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 D614G;N501Y;N501Y 32;39;52 37;44;57 RBD;S 61;65 64;66 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. (A) Construction of SARS-CoV-2 variants N501Y.V1, N501Y.V2, and N501Y.V2 RBD S protein. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 N501Y;N501Y;N501Y 40;50;64 45;55;69 RBD;S 73;77 76;78 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. (A) Infection efficiency of SARS-CoV-2 WT, D614G, N501Y.V1 and N501Y.V2 RBD variants in human and animal cell lines. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 D614G;N501Y;N501Y 43;50;63 48;55;68 RBD 72 75 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. (B) Analysis of S protein expression and particle incorporation of N501Y.V1 and N501Y.V2 RBD lineages. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 N501Y;N501Y 67;80 72;85 RBD;S 89;16 92;17 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. (B) Infectivity analysis of N501Y.V1 and N501Y.V2 RBD single-site mutants. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 N501Y;N501Y 28;41 33;46 RBD 50 53 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. (C-F) The single-site mutations of N501Y.V1 and N501Y.V2 RBD S pseudovirions were incubated in cell culture medium DMEM at 37 C for 4 h (C) and 6 h (D) or 42 C for 4 h (E) and 6 h (F). 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 N501Y;N501Y 35;48 40;53 RBD;S 57;61 60;62 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. (C) Analysis of the S protein expression of single-site mutation of spike protein in N501Y.V1 and N501Y.V2 lineages by western blot. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 N501Y;N501Y 85;98 90;103 S;S 68;20 73;21 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. (D-F) Inhibition of entry of SARS-CoV, SARS-CoV-2 WT, D614G, N501Y.V1 and N501Y.V2 RBD by adding endocytosis inhibitors Chloroquine, Tetradeine, and Apilimod to 293T-hACE2 cells 2 h prior to transduction. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 D614G;N501Y;N501Y 54;61;74 59;66;79 RBD 83 86 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. (D) Representative images of SARS-Cov-2 WT, D614G, N501Y.V1 and N501Y.V2 RBD entry into 293T-hACE2 cells at indicated time points. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 D614G;N501Y;N501Y 44;51;64 49;56;69 RBD 73 76 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Infection efficiency of SARS-CoV-2 variants N501Y.V1 and N501Y.V2 in mammalian cell lines. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 N501Y;N501Y 44;57 49;62 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Infection efficiency of SARS-CoV-2 variants N501Y.V1 and N501Y.V2 RBD in target cells at different time points. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 N501Y;N501Y 44;57 49;62 RBD 66 69 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. N501Y.V1 and N501Y.V2 RBD single-site mutants conducted in 293T-hACE2 (top), Caco2-hACE2 (middle) and Vero (bottom). 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 N501Y;N501Y 13;0 18;5 RBD 22 25 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. SARS-CoV-2 variants N501Y.V1 and N501Y.V2 RBD are more thermal stable than WT and D614G. 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 D614G;N501Y;N501Y 82;20;33 87;25;38 RBD 42 45 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. The S protein of N501Y.V1 include nine mutations (HV69-70 del, 144 del, N501Y, D614G, P681H, T716I, S982A, and D1118H), N501Y.V2 include ten mutations (L18F, D80A, D215G, 242-244 del, R246I, K417N, E484K, N501Y, D614G and A701V) and N501Y-V2 RBD include D614G and three major mutations in the RBD (K417N, E484K and N501Y). 2021 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 A701V;D1118H;D215G;D614G;D614G;D614G;D80A;E484K;E484K;K417N;N501Y;N501Y;N501Y;N501Y;N501Y;N501Y;P681H;R246I;S982A;T716I;K417N;L18F 222;111;164;79;212;254;158;198;305;191;17;72;120;205;233;315;86;184;100;93;298;152 227;117;169;84;217;259;162;203;310;196;22;77;125;210;238;320;91;189;105;98;303;156 RBD;RBD;S 242;293;4 245;296;5 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. (J) Immunoreactivity in bronchi of the D614G vs B.1.1.7 (M,N) (H&E and IHC magnifications (G_N) = 100x). 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 39 44 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. AGMs were infected with either the D614G or B.1.1.7 SARS-CoV-2 variant intranasally utilizing the Nasal Mucosal Atomization Device. 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 35 40 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Immunoreactivity in the trachea of D614G vs B.1.1.7. 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 35 40 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. L, respectively) Normal bronchi found in the D614G (I) vs bronchi with inflammation and cellular infiltrates found in the B.1.1.7. 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 45 50 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Minimally thickened and inflamed alveolar septa with multifocal pneumocyte immunoreactivity in the D614G and B.1.1.7 samples (H&E (D,F) and IHC (H,J) = 100x; H&E (E,G) and IHC I,K) = 400x.). 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 99 104 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Normal mucosa with multifocal mucosal immunoreactivity in the D614G challenged ileum (G,H,K,L) (HE G, IHC K, 20x; HE H, IHC L, 400x). 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 62 67 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Normal trachea found in the D614G (G) vs. 2021 Emerging microbes & infections Figure SARS_CoV_2 D614G 28 33 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. d Binding of Y58L mutations based on n3113.1-Fc to S protein of Delta variant. 2021 Signal transduction and targeted therapy Figure SARS_CoV_2 Y58L 13 17 S 51 52 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. f Neutralization profile of n3113.1-Fc (Y58L) against viruses pseudotyped with the S protein of WT, four VOCs, and one VOI. 2021 Signal transduction and targeted therapy Figure SARS_CoV_2 Y58L 40 44 S 83 84 34732694 A non-ACE2 competing human single-domain antibody confers broad neutralization against SARS-CoV-2 and circulating variants. N3113.1 (Y58L) maintains susceptivity to circulating SARS-CoV-2 variants. 2021 Signal transduction and targeted therapy Figure SARS_CoV_2 Y58L 9 13 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. (A) Orthogonal views of the low-pass filtered cryo-EM maps of S-D614G and S-Alpha with the visibly resolved stems of N-glycans (first two GlcNAc moieties extending from the sidechain of Asn) at specific regions highlighted in different colors. 2022 Glycobiology Figure SARS_CoV_2 D614G 64 69 N;S;S 117;62;74 118;63;75 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. (A) The trimeric prefusion S proteins analyzed in parallel for direct comparison were all stabilized by 2P mutations and RRAR to GSAS substitution at the furin cleavage site, with a foldon trimerization motif added for the wild type (fm2P), D614G and Alpha (B1.1.7) variants, but a stabilized wild type S protein (2P) retaining the furin cleavage site was also included. 2022 Glycobiology Figure SARS_CoV_2 D614G 241 246 S;S 27;303 28;304 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. (B) Orthogonal views of the superposition of the atomic models of the D614G and Alpha variants, which are shown in gray (PDB ID 7EAZ) and cyan (PDB ID 7EDF), respectively. 2022 Glycobiology Figure SARS_CoV_2 D614G 70 75 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. (B) Side view and top view of the trimeric S proteins based on our cryo-EM structure of S-D614G (PDB ID 7EAZ), highlighting a single protomer with another protomer (faded) in the background. 2022 Glycobiology Figure SARS_CoV_2 D614G 90 95 S;S 43;88 44;89 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. (C) The glycosylation bar charts for N122 on the S proteins of the D614G and Alpha variants, averaging data from triplicate analysis. 2022 Glycobiology Figure SARS_CoV_2 D614G 67 72 S 49 50 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. Data for S-fm2P, S-D614G and S-Alpha were generated in this work. 2022 Glycobiology Figure SARS_CoV_2 D614G 19 24 S;S;S 9;17;29 10;18;30 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. Overall site-specific glycosylation pattern of the recombinant trimeric spike proteins derived from the original SARS-CoV-2 strain and its mutated D614G and Alpha variants. 2022 Glycobiology Figure SARS_CoV_2 D614G 147 152 S 72 77 34735575 Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants. The expanded views of the NTD highlight the differences in the EM maps between the D614G and Alpha variants due to Delta69-70 and Delta144 in the latter. 2022 Glycobiology Figure SARS_CoV_2 D614G 83 88 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. (a) Binding energy between the RBD and the ACE2, for the wild type (WT), mutation MT1: N501Y, MT2: E484K/N501Y, MT3: K417N/E484K/N501Y, and L452R/T478K. 2021 Scientific reports Figure SARS_CoV_2 E484K;K417N;L452R;N501Y;E484K;N501Y;N501Y;T478K 99;117;141;87;123;105;129;147 104;122;146;92;128;110;134;152 RBD 31 34 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. These mutations include MT1: N501Y, MT2: E484K/N501Y, and MT3: K417N/E484K/N501Y. 2021 Scientific reports Figure SARS_CoV_2 E484K;K417N;N501Y;E484K;N501Y;N501Y 41;63;29;69;47;75 46;68;34;74;52;80 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. (C) Serum neutralization ID50 values of convalescent patient sera and Moderna vaccinee sera against VSV pseudoviruses (A) and authentic SARS-CoV-2 variants (B) were compared with those against D614G. 2021 iScience Figure SARS_CoV_2 D614G 193 198 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The average S1/S2 ratio was calculated and compared with that of D614G. 2021 iScience Figure SARS_CoV_2 D614G 65 70 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The cell-cell fusion activity of each SARS-CoV-2 variant S glycoprotein was compared with that of D614G. 2021 iScience Figure SARS_CoV_2 D614G 98 103 S 57 71 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The infectivity of each of the pseudoviruses was compared with that of the D614G variant. 2021 iScience Figure SARS_CoV_2 D614G 75 80 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The measured infectivity was normalized to that observed for the D614G variant. 2021 iScience Figure SARS_CoV_2 D614G 65 70 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The S1/S2 ratio for each variant was compared with that of D614G. 2021 iScience Figure SARS_CoV_2 D614G 59 64 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. (A) Schematic of testing the efficiency of ACE2 variants binding WT or Y453F viral spikes. 2021 PLoS pathogens Figure SARS_CoV_2 Y453F 71 76 S 83 89 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. (C) The binding kinetics of ACE2 proteins (ferret or stoat) with recombinant WT or Y453F SARS-CoV-2 RBD were obtained using the BIAcore. 2021 PLoS pathogens Figure SARS_CoV_2 Y453F 83 88 RBD 100 103 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. (E) Table summarizing biochemical results for ACE2 variants bound to WT or Y453F RBD. 2021 PLoS pathogens Figure SARS_CoV_2 Y453F 75 80 RBD 81 84 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Enhanced entry of Y453F spike pseudotyped virion by utilization of mink ACE2. 2021 PLoS pathogens Figure SARS_CoV_2 Y453F 18 23 S 24 29 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Increased binding of Y453F RBD protein to mink ACE2. 2021 PLoS pathogens Figure SARS_CoV_2 Y453F 21 26 RBD 27 30 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Increased binding of Y453F RBD protein to Mustelidae ACE2 orthologs. 2021 PLoS pathogens Figure SARS_CoV_2 Y453F 21 26 RBD 27 30 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Left: complex of Y453F RBD/mink ACE2. 2021 PLoS pathogens Figure SARS_CoV_2 Y453F 17 22 RBD 23 26 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Mink W/O Y453F: del69-70/I692V/M1229I; Mink: del69-70/Y453F/I692V/M1229I. 2021 PLoS pathogens Figure SARS_CoV_2 Y453F;I692V;I692V;M1229I;M1229I;Y453F 9;25;60;31;66;54 14;30;65;37;72;59 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. SARS-CoV-2 GFP/DeltaN trVLP (WT or Y453F) were produced as previously described. 2021 PLoS pathogens Figure SARS_CoV_2 Y453F 35 40 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Structural comparison of Y453F RBD/mink ACE2 and WT RBD/human ACE2 complexes. 2021 PLoS pathogens Figure SARS_CoV_2 Y453F 25 30 RBD;RBD 31;52 34;55 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. The mutation Y453F in SARS-CoV-2 spike protein is a potential genetic adaptation in minks. 2021 PLoS pathogens Figure SARS_CoV_2 Y453F 13 18 S 33 38 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. The transduced cells were incubated with the WT or Y453F S1 domain of SARS-CoV-2 C-terminally fused with a His tag and then stained anti-His-PE for flow cytometry analysis. 2021 PLoS pathogens Figure SARS_CoV_2 Y453F 51 56 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. The Y453F-RBD is shown in cyan and mink ACE2 in green. 2021 PLoS pathogens Figure SARS_CoV_2 Y453F 4 9 RBD 10 13 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Transduced cells were incubated with WT or Y453F S1 domain of SARS-CoV-2 C-terminally fused with His tag and then stained with anti-His-PE for flow cytometry analysis. 2021 PLoS pathogens Figure SARS_CoV_2 Y453F 43 48 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Y453F mutation in spike protein promote SARS-CoV-2 GFP/DeltaN trVLP infection of Caco-2ACE2KO cells expressing exogenous mink ACE2. 2021 PLoS pathogens Figure SARS_CoV_2 Y453F 0 5 S 18 23 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. A 3D model of S-glycoprotein stating the location of D614G mutation. 2021 Applied microbiology and biotechnology Figure SARS_CoV_2 D614G 53 58 S 14 28 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. A conceptual diagram illustrating the characteristics change of the SARS-CoV-2 variant due to the D614G mutation. 2021 Applied microbiology and biotechnology Figure SARS_CoV_2 D614G 98 103 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. D614G mutation location in the 3D model of S-glycoprotein and different conformational states of S-glycoprotein. 2021 Applied microbiology and biotechnology Figure SARS_CoV_2 D614G 0 5 S;S 43;97 57;111 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Researchers noted that D614G mutation favors the open conformation of S-glycoprotein and thus helps more interaction with the hACE2 receptor, which causes more infection and re-infection. 2021 Applied microbiology and biotechnology Figure SARS_CoV_2 D614G 23 28 S 70 84 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. Schematic diagram of the location of D614G amino acids where mutation occurs in S-glycoprotein. 2021 Applied microbiology and biotechnology Figure SARS_CoV_2 D614G 37 42 S 80 94 34755213 D614G mutation and SARS-CoV-2: impact on S-protein structure, function, infectivity, and immunity. The schematic diagram illustrates the D614G mutation causing more infectivity. 2021 Applied microbiology and biotechnology Figure SARS_CoV_2 D614G 38 43 34755818 SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil. Branches leading to the four "N.9-like / B.1.1.33 + E484K" genomes are also coloured in red. 2021 Memorias do Instituto Oswaldo Cruz Figure SARS_CoV_2 E484K 52 57 34755818 SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil. Each colored line represents a mutation that emerged during the diversification of B.1.1.33 lineage in Brazil originating the N.9 and "N.9-like / B.1.1.33 + E484K". 2021 Memorias do Instituto Oswaldo Cruz Figure SARS_CoV_2 E484K 157 162 34755818 SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil. evolutionary steps associated with the possible emergence of N.9 and "N.9-like / B.1.1.33 + E484K" lineages. 2021 Memorias do Instituto Oswaldo Cruz Figure SARS_CoV_2 E484K 92 97 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. (a) Substrate-Binding plots for ACE2 binding to original [D614] S1, original [D614] RBD, Mink [Y453F] RBD and alpha/beta/gamma [N501Y] RBD proteins. 2021 Scientific reports Figure SARS_CoV_2 N501Y;Y453F 128;95 133;100 RBD;RBD;RBD 84;102;135 87;105;138 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. (a) Substrate-binding plots for inhibition of ACE2 binding to beta [E484K] RBD by digitoxin, digoxin, ouabain, digitoxigenin and digoxigenin (30 nM). 2021 Scientific reports Figure SARS_CoV_2 E484K 68 73 RBD 75 78 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. (a) Substrate-Binding plots for original [D614] S1 spike (red), alpha/beta/gamma [D614G] S1 spike (blue), and original [D614] RBD (green) proteins. 2021 Scientific reports Figure SARS_CoV_2 D614G 82 87 S;S;RBD 51;92;126 56;97;129 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. (b-d) Eadie-Hoffstee plots of data in Part (a) for original [D614] RBD and S1 spike (b), original [D614] S1 spike and Mink [Y453F] RBD (c), and original [D614] S1 spike and alpha/beta/gamma [N501Y] RBD (d). 2021 Scientific reports Figure SARS_CoV_2 N501Y;Y453F 191;124 196;129 S;S;S;RBD;RBD;RBD 78;108;163;67;131;198 83;113;168;70;134;201 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. (b-d) Eadie-Hoffstee plots of data in Part (a) for original [D614] S1 spike (b), alpha/beta/gamma [D614G] S1 spike (c), and original [D614] RBD from the S1 spike (d). 2021 Scientific reports Figure SARS_CoV_2 D614G 99 104 S;S;S;RBD 70;109;156;140 75;114;161;143 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Binding kinetics for ACE2 to beta [E484K], Mink [Y453F], alpha/beta/gamma [N501Y], and original [D614] RBDs. 2021 Scientific reports Figure SARS_CoV_2 E484K;N501Y;Y453F 35;75;49 40;80;54 RBD 103 107 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Inhibition of ACE2 binding to beta [E484K] RBD by cardiac glycosides. 2021 Scientific reports Figure SARS_CoV_2 E484K 36 41 RBD 43 46 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Inhibition of ACE2 binding to the alpha/beta/gamma [D614G] S1 spike by cardiac glycoside drugs. 2021 Scientific reports Figure SARS_CoV_2 D614G 52 57 S 62 67 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Correlation of neutralizing titers against B.1+L249S+E484K in relation to SARS-CoV-2 lineages. 2022 Virus research Figure SARS_CoV_2 E484K;L249S 53;47 58;52 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Neutralizing titers of convalescent sera against SARS-CoV-2 A.1, B.1.420, B.1.111, and B.1+L249S+E484K lineages. 2022 Virus research Figure SARS_CoV_2 E484K;L249S 97;91 102;96 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. 2) reduces the structural fluctuations rate following the N501Y mutation. 2022 Journal of cellular biochemistry Figure SARS_CoV_2 N501Y 58 63 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Rosetta docking outputs for native and N501Y spike variants. 2022 Journal of cellular biochemistry Figure SARS_CoV_2 N501Y 39 44 S 45 50 34783057 SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. Schematic representation of the binding energy for native and N501Y carrying complexes. 2022 Journal of cellular biochemistry Figure SARS_CoV_2 N501Y 62 67 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. (A) World map showing the origin of SARS-CoV-2 (in China) and the appearance of the E484K mutation in the variants of concern Beta (in South Africa), Gamma (in Brazil), and evolved Alpha (in UK). 2021 ACS synthetic biology Figure SARS_CoV_2 E484K 84 89 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. CRISPR-Cas12a-based detection of SARS-CoV-2 harboring the E484K mutation. 2021 ACS synthetic biology Figure SARS_CoV_2 E484K 58 63 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. In the inset, fold change in fluorescence upon detection of the E484K mutation. 2021 ACS synthetic biology Figure SARS_CoV_2 E484K 64 69 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. On the bottom, structural model of the spike protein (mutation E484K colored in orange and pointed by an arrow). 2021 ACS synthetic biology Figure SARS_CoV_2 E484K 63 68 S 39 44 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. On the bottom, virus harboring the E484K mutation (patient P4). 2021 ACS synthetic biology Figure SARS_CoV_2 E484K 35 40 34783536 CRISPR-Cas12a-Based Detection of SARS-CoV-2 Harboring the E484K Mutation. The E484K mutation creates a PAM sequence for Cas12a recognition in the resulting dsDNA amplicon. 2021 ACS synthetic biology Figure SARS_CoV_2 E484K 4 9 34783635 Identification of the SARS-CoV-2 Delta variant C22995A using a high-resolution melting curve RT-FRET-PCR. (A) With the 6-FAM probe designed to match the area incorporating the C22995A mutation exactly, dilutions of a control SARS-CoV-2 Delta variant (positive control from Kansas State Veterinary Diagnostic Laboratory) used in the Delta RT-FRET-PCR had a Tm of around 56.1 C. 2022 Emerging microbes & infections Figure SARS_CoV_2 C22995A 70 77 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. Prevalence of E484K/Q and N501Y mutants among SARS-Cov-2 samples from nonvaccinated individuals from January to April 2021. 2021 Microbiology spectrum Figure SARS_CoV_2 E484K;E484Q;N501Y 14;14;26 21;21;31 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. Phylogenetic tree of SARS-CoV-2 showing the distribution of sequences containing the C29197T mutation (in blue). 2021 Microbiology spectrum Figure SARS_CoV_2 C29197T 85 92 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. Whole-genome sequencing of five samples with the C to T mutation at position 29200. 2021 Microbiology spectrum Figure SARS_CoV_2 C29200T 49 82 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. Whole-genome sequencing of five samples with the C to T mutation at position 34 of the Xpert cartridge amplicon and position 29197 of the reference sequence. 2021 Microbiology spectrum Figure SARS_CoV_2 C34T 49 79 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. Different concentrations of SARS-CoV-2 DNA were used as the template and amplified by PCR with the aforementioned forward primers followed by detection of CRISPR-Cas12a-mediated assay to detect the single nucleotide mutation of K417N (B and C), L452R (D), L452Q (E), and E484Q (F), respectively. 2021 Microbiology spectrum Figure SARS_CoV_2 E484Q;K417N;L452Q;L452R 271;228;256;245 276;233;261;250 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. (a) MS peaks of 9 MPE probes without extension; (b) target site peaks of the MPE probes extended to non-SARS-CoV-2 variants; (c) target site peaks of the MPE probes extended to SARS-CoV-2 S gene mutation plasmid 1 (containing the HV69-70del, K417N, E484K, N501Y, D614G, and P681H mutations); (d) target site peaks of the MPE probes extended to SARS-CoV-2 S gene mutation plasmid 2 (containing the L452R, E484Q, and P681R mutations). 2021 Microbiology spectrum Figure SARS_CoV_2 D614G;E484K;E484Q;K417N;L452R;N501Y;P681H;P681R 263;249;404;242;397;256;274;415 268;254;409;247;402;261;279;420 S;S 188;355 189;356 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. Highlighted in the boxes are the genomes of the Gamma-like-II lineage (green) and the Gamma -E661D mutation (golden). 2021 Virology journal Figure SARS_CoV_2 E661D 93 98 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. In addition, the SARS CoV-2 reference sequence, the Gamma-like-II sequence and the Gamma sequence group with the spike protein mutation S:E661D are highlighted. 2021 Virology journal Figure SARS_CoV_2 E661D 138 143 S;S 113;136 118;137 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. The lineage N.10 is highlighted in red; the Gamma-like-II genomes are highlighted in light green; Gamma sequences harboring S:E661D are highlighted in shadow golden and Wuhan-Hu-1 is highlighted in orange. 2021 Virology journal Figure SARS_CoV_2 E661D 126 131 S 124 125 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. The lineage N.10 is highlighted in red; the lineage P.2 is highlighted in light yellow; the Gamma-like-II genomes are highlighted in light green; Gamma sequences harboring S:E661D are highlighted in shadow golden and Wuhan-Hu-1 is highlighted in orange. 2021 Virology journal Figure SARS_CoV_2 E661D 174 179 S 172 173 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. B, the Asp17Leu mutant (N1C_v05) has a T m of 84.6 C and is strongly stabilized compared with N1C_v01 containing Asp17. 2022 The Journal of biological chemistry Figure SARS_CoV_2 D17L 7 15 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Thermal unfolding of DARPin domains followed by CD spectroscopy between 40 C and 95 C; all variants were measured at a concentration of 10 muM in PBS.A, N1C_v01 to N1C_v04: The measured T m values were 74.5 C for the control N1C (N1C_v01), 64.7 C for the N-Cap Leu4Ala mutant (N1C_v02), 74.3 C for the N-Cap Gly5Ala mutant (N1C_v03), and 82.4 C for the N-Cap Asp17Ala mutant (N1C_v04). 2022 The Journal of biological chemistry Figure SARS_CoV_2 D17A;G5A;L4A 365;313;265 373;320;272 N;N;N 259;307;359 260;308;360 34794434 SARS-CoV-2 exposure in Malawian blood donors: an analysis of seroprevalence and variant dynamics between January 2020 and July 2021. A Correlation of SARS-CoV-2 antibody neutralisation potency against D614G WT and beta variant. 2021 BMC medicine Figure SARS_CoV_2 D614G 68 73 34794434 SARS-CoV-2 exposure in Malawian blood donors: an analysis of seroprevalence and variant dynamics between January 2020 and July 2021. B Proportion of wave 1 or wave 2 sera with neutralisation activity against D614G WT or beta variant. 2021 BMC medicine Figure SARS_CoV_2 D614G 75 80 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. The common D614G in all ten variant (Table 1) was indicated by bold blue letter. 2021 Immune network Figure SARS_CoV_2 D614G 11 16 34796036 SARS-CoV-2 Delta (B.1.617.2) Variant: A Unique T478K Mutation in Receptor Binding Motif (RBM) of Spike Gene. The unique T478K mutation site of delta variant was indicated by a large red font with yellow highlight. 2021 Immune network Figure SARS_CoV_2 T478K 11 16 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Frequency of E484K mutation in complete genome sequences, excluding Alpha, Beta, Gamma, and Zeta variants. 2021 Infection, genetics and evolution Figure SARS_CoV_2 E484K 13 18 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Frequency of E484K mutation in the complete genome sequences available from worldwide in GISAID according to time. 2021 Infection, genetics and evolution Figure SARS_CoV_2 E484K 13 18 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. The analysis included 89 reported cases of reinfection worldwide, with SARS-CoV-2 genomes confirmed by sequencing, 41 of which were supported by a preprint or a peer-reviewed article: 13/89 (14.6%) of them harbored the mutation E484K, all of them from Brazil. 2021 Infection, genetics and evolution Figure SARS_CoV_2 E484K 228 233 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. 1 associated with the Alpha variant of concern first detected in the United Kingdom are H69_V70del, Y144del (identified as Y145del by alignment software), N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H. 2022 Infection, genetics and evolution Figure SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I;Y144del;Y145del 162;201;169;155;176;190;183;100;123 167;207;174;160;181;195;188;107;130 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. 1 associated with the Iota variant of interest are L5F, D253G, E484K, S477N, D614G, A701V). 2022 Infection, genetics and evolution Figure SARS_CoV_2 A701V;D253G;D614G;E484K;L5F;S477N 84;56;77;63;51;70 89;61;82;68;54;75 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. A222V is located on a loop region, as is the case with D614G (D). 2022 Infection, genetics and evolution Figure SARS_CoV_2 D614G;A222V 55;0 60;5 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. B) A ribbon diagram of the highly prevalent Nsp12: P323L substitution. 2022 Infection, genetics and evolution Figure SARS_CoV_2 P323L 51 56 Nsp12 44 49 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. C) A ribbon diagram visualizing the secondary structure of the A222V variant and surrounding residues. 2022 Infection, genetics and evolution Figure SARS_CoV_2 A222V 63 68 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. C) The mutations associated with the Gamma variant of concern appeared together in mid-December 2020; all mutations except for T20N and K417T were present separately before the emergence of the variant. 2022 Infection, genetics and evolution Figure SARS_CoV_2 K417T;T20N 136;127 141;131 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. D614G was observed in 90% of sequences analyzed globally by early May 2020. 2022 Infection, genetics and evolution Figure SARS_CoV_2 D614G 0 5 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Despite its distance from the receptor binding domain, D614G has been observed to alter the conformational state of the receptor binding domain by altering the conformation in the region surrounding codon 614, acting as a hinge. 2022 Infection, genetics and evolution Figure SARS_CoV_2 D614G 55 60 RBD;RBD 30;120 53;143 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Exceptions include the Nsp12 finger subdomain substitution A423V, which was common in Asia during July and August 2020, and the Nsp7 substitution L71F, which was common in South America during October and November 2020. 2022 Infection, genetics and evolution Figure SARS_CoV_2 A423V;L71F 59;146 64;150 Nsp12;Nsp7 23;128 28;132 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. L18F, E484K, N501Y, D614G, H655Y, and V1176F are associated with the Gamma variant of concern, and S13I, W152C, L452R are associated with the Epsilon variant of concern. 2022 Infection, genetics and evolution Figure SARS_CoV_2 D614G;E484K;H655Y;L452R;N501Y;S13I;V1176F;W152C;L18F 20;6;27;112;13;99;38;105;0 25;11;32;117;18;103;44;110;4 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Most mutations in the polymerase complex do not appear to persist, except for the Nsp12 substitutions P323L, V776L, A185S, and V720I. 2022 Infection, genetics and evolution Figure SARS_CoV_2 A185S;P323L;V720I;V776L 116;102;127;109 121;107;132;114 Nsp12 82 87 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Mutations associated with the Alpha variant of concern (H69_V70del, Y145del, N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H) have rapidly increased in prevalence since the appearance of the variant in mid-September 2020. 2022 Infection, genetics and evolution Figure SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I;Y145del 84;123;91;77;98;112;105;68 89;129;96;82;103;117;110;75 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Nearly all mutations besides the Nsp12 substitution P323L have either peaked and subsequently decreased in prevalence, or have plateaued at low prevalence values of 5-10%. 2022 Infection, genetics and evolution Figure SARS_CoV_2 P323L 52 57 Nsp12 33 38 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Some mutations are present in multiple variants: the RBD substitution E484K is also observed in the Beta, Gamma, and Iota variants, and the RBD substitution N501Y is also observed in the Alpha, Beta, and Gamma variants. 2022 Infection, genetics and evolution Figure SARS_CoV_2 E484K;N501Y 70;157 75;162 RBD;RBD 53;140 56;143 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Some mutations associated with the Beta variant of concern (H69_V70del, Y145del, N501Y, D614G, P681H, and T716I) were present separately before the emergence of the variant in mid-September 2020, while others (A570D, S982A, and D1118H) appeared together at this point. 2022 Infection, genetics and evolution Figure SARS_CoV_2 D1118H;D614G;N501Y;P681H;S982A;T716I;Y145del;A570D 228;88;81;95;217;106;72;210 234;93;86;100;222;111;79;215 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The combination and prevalence of mutations present varies by continent, with the Nsp12 substitution P323L being most common on all continents, and most other mutations present in less than 20% of samples from each continent. 2022 Infection, genetics and evolution Figure SARS_CoV_2 P323L 101 106 Nsp12 82 87 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The common Nsp12 substitution A656S is also shown. 2022 Infection, genetics and evolution Figure SARS_CoV_2 A656S 30 35 Nsp12 11 16 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The common variant Nsp7: S25L exists at the interface between Nsp7 and Nsp8. 2022 Infection, genetics and evolution Figure SARS_CoV_2 S25L 25 29 Nsp7;Nsp7;Nsp8 19;62;71 23;66;75 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The mutation Y453F would result in the loss of a hydroxyl group, which may reduce steric clashing with the histidine residue. 2022 Infection, genetics and evolution Figure SARS_CoV_2 Y453F 13 18 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The mutations D80A, L242_L244del, K417N, E484K, N501Y, D614G, A701V, L18F, and D215G are associated with the Beta variant of concern. 2022 Infection, genetics and evolution Figure SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;L18F;N501Y 62;79;55;14;41;34;69;48 67;84;60;18;46;39;73;53 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The substitution D614G was the first mutation to become highly prevalent on all continents. 2022 Infection, genetics and evolution Figure SARS_CoV_2 D614G 17 22 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The substitution E484K involves the replacement of a negatively charged glutamic acid residue with a positively charged lysine residue, which results in decreased efficacy of antibodies produced against wild-type E484 variants. 2022 Infection, genetics and evolution Figure SARS_CoV_2 E484K 17 22 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The substitution L452R is observed in the Epsilon variant of concern. 2022 Infection, genetics and evolution Figure SARS_CoV_2 L452R 17 22 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The substitutions L452R and S13I appeared separately before the emergence of the variant, while W152C did not. 2022 Infection, genetics and evolution Figure SARS_CoV_2 L452R;S13I;W152C 18;28;96 23;32;101 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Y144del sometimes appears as Y145del due to ambiguities in the alignment software with identical adjacent amino acids. 2022 Infection, genetics and evolution Figure SARS_CoV_2 Y145del;Y144del 29;0 36;7 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. (a) Fractional shift (X) variation in the compensatory mutation segments C1, C2, and C3induced by the RBD mutations, E484K, K417N, L452Q, L452R, N501Y, andT478K. 2021 ACS omega Figure SARS_CoV_2 E484K;K417N;L452Q;L452R;N501Y 117;124;131;138;145 122;129;136;143;150 RBD 102 105 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. (A) Snapshotsof the effects of the RBD mutations, N501Y, T478K, and K417N; interfaceinteractions and their distribution between ACE2 (red) and the RBD(blue) differed among the mutated states with different RBD movements,determining different dissociation constants Kd. 2021 ACS omega Figure SARS_CoV_2 K417N;N501Y;T478K 68;50;57 73;55;62 RBD;RBD;RBD 35;147;206 38;150;209 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. (B) Zoomed-in snapshots ofthe H-bond and salt bridge interactions with the K417N mutation. 2021 ACS omega Figure SARS_CoV_2 K417N 75 80 34805715 Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants. Among all six considered RBD mutations, K417N showed thelowest Kd. 2021 ACS omega Figure SARS_CoV_2 K417N 40 45 RBD 25 28 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. (C) Snapshots showing the dynamics of RBM with respect to the RBD and NTD in WT & D614G mutant spike protein as a function of time. 2021 Current research in structural biology Figure SARS_CoV_2 D614G 82 87 S;RBD 95;62 100;65 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Dynamics of the wild-type and D614G mutant spike. 2021 Current research in structural biology Figure SARS_CoV_2 D614G 30 35 S 43 48 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. The D614G present in the linker region is marked as a star for reference as it is now present in98% of the genomes. 2021 Current research in structural biology Figure SARS_CoV_2 D614G 4 9 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. The A23403G, C3037T, C14408T, and C241T are the most widespread mutations globally. 2021 Informatics in medicine unlocked Figure SARS_CoV_2 A23403G;C14408T;C241T;C3037T 4;21;34;13 11;28;39;19 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. The D614G, F106F, P314L, and C241T are the most widespread mutations globally. 2021 Informatics in medicine unlocked Figure SARS_CoV_2 C241T;D614G;F106F;P314L 29;4;11;18 34;9;16;23 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. (A) The wild-type SARS-CoV-2 S glycoprotein (D614, with an aspartic acid residue at 614) and the D614G variant (G614, with a glycine residue at 614) were expressed in wild-type 293T cells (wt) or in GALE/GALK2 293T cells (ko). 2022 Journal of virology Figure SARS_CoV_2 D614G 97 102 S 29 43 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. Characterization of wild-type and D614G S glycoproteins in GALE/GALK2 293T cells. 2022 Journal of virology Figure SARS_CoV_2 D614G 34 39 S 40 55 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. (C) Analysis of the ID50 values of neutralization reactions between the D614G reference and Lambda pseudoviruses to convalescent sera. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 72 77 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Analysis of the ID50 values of the neutralization reactions for vaccine-immunized sera between D614G and Lambda pseudoviruses (E, F, G, H). 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 95 100 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. One-way ANOVA and Dunnett's multiple comparisons test were employed to determine differences in infectivity between Lambda and D614G. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 127 132 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Structural modelling of the L452Q and F490S mutations, based on RBD-9G11 for 9G11 (B), and RBD-X593 for X593 (C). 2022 Emerging microbes & infections Figure SARS_CoV_2 F490S;L452Q 38;28 43;33 RBD;RBD 64;91 67;94 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. The ratio of ID50 value between Lambda and the D614G reference was calculated and analysed, followed by heatmap construction using HemI software. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 47 52 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. The ratio of ID50 values (mean of three independent experiments) between the Lambda variant and D614G reference was calculated and analysed, followed by construction of a heatmap using HemI software. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 96 101 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. The relative infectivity of the mutant pseudoviruses is presented as the ratio of relative luciferase units (RLU) for mutant/RLU for the D614G variant. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 137 142 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. (B) dTTP LAMP reaction was combined with CRISPR-LAMP assay using spike N501Y crRNA. 2021 Analytical chemistry Figure SARS_CoV_2 N501Y 71 76 S 65 70 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. (C) Statistical data of the wild-type and spike N501Y detection efficiency with prolonged LAMP reaction. 2021 Analytical chemistry Figure SARS_CoV_2 N501Y 48 53 S 42 47 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. (D) dUTP LAMP reaction was combined with CRISPR-LAMP assay using spike N501Y crRNA. 2021 Analytical chemistry Figure SARS_CoV_2 N501Y 71 76 S 65 70 34818890 Universally Stable and Precise CRISPR-LAMP Detection Platform for Precise Multiple Respiratory Tract Virus Diagnosis Including Mutant SARS-CoV-2 Spike N501Y. Detection of wild-type or spike N501Y as a fraction of the background target. 2021 Analytical chemistry Figure SARS_CoV_2 N501Y 32 37 S 26 31 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. (A) Inhibition of wild-type (wt), N439K, and N501Y receptor-binding domain (RBD) towards angiotensin-converting enzyme-2 (ACE-2) in serum from convalescent COVID-19 individuals (n = 140). 2021 eLife Figure SARS_CoV_2 N439K;N501Y 34;45 39;50 RBD 76 79 COVID-19 156 164 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. (C) Thermal denaturation curves of the RBD wild-type (wt), N439K, and N501Y variants. 2021 eLife Figure SARS_CoV_2 N439K;N501Y 59;70 64;75 RBD 39 42 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Biolayer interferometry (BLI) sensorgrams of RBD wt (D), N439K (E), and N501Y (F) binding to ACE-2-Fc immobilized in anti-human Fc capture (AHC) sensors. 2021 eLife Figure SARS_CoV_2 N439K;N501Y 57;72 62;77 RBD 45 48 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Comparison of the inhibition potency (log[IC50]) of mouse mAbs (n = 8) calculated from three independent experiments against RBD wt and RBD N439K (C) or RBD N501Y (D), analysed by linear regression and Spearman correlation. 2021 eLife Figure SARS_CoV_2 N439K;N501Y 140;157 145;162 RBD;RBD;RBD 125;136;153 128;139;156 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. IC50 comparison of the inhibition of polyclonal mice sera from an animal vaccine model based on RBD (A) or spike (B) challenged with RBD wt, N439K, and N501Y. 2021 eLife Figure SARS_CoV_2 N439K;N501Y 141;152 146;157 S;RBD;RBD 107;96;133 112;99;136 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Linear regression and Spearman correlation analyses for N439K vs wt (B) and N501Y vs wt (C). 2021 eLife Figure SARS_CoV_2 N439K;N501Y 56;76 61;81 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. (D) IFs of 203K/204R (orange) and R203K/G204 (gray) among continents. 2021 Cell host & microbe Figure SARS_CoV_2 R203G;R203K 34;34 39;39 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. (G-I) show that the R203K/G204R substitutions enhance SARS-CoV-2 replication in primary human airway tissues. 2021 Cell host & microbe Figure SARS_CoV_2 R203K;G204R 20;26 25;31 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Changes in the IF of 8 lineages including A222V (LG_4), N510Y (LG_5), and R203K/G204R (LG_3) and the distribution of lineages in the phylogenetic tree of all strains (H). 2021 Cell host & microbe Figure SARS_CoV_2 A222V;N510Y;R203K;G204R 42;56;74;80 47;61;79;85 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Effects of R203K/G204R on the severity of disease. 2021 Cell host & microbe Figure SARS_CoV_2 R203K;G204R 11;17 16;22 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Evidence showing the adaptation of R203K/G204R. 2021 Cell host & microbe Figure SARS_CoV_2 R203G;R203K;G204R 35;35;41 40;40;46 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Graphical overview of virology experiments to evaluate the impact of the R203K/G204R mutations on the infectivity and fitness of SARS-CoV-2. 2021 Cell host & microbe Figure SARS_CoV_2 R203K;G204R 73;79 78;84 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Rapid spread of R203K/G204R. 2021 Cell host & microbe Figure SARS_CoV_2 R203G;R203K;G204R 16;16;22 21;21;27 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. The study showed that the R203K/G204R substitutions result in increased virus infectivity and fitness in lung epithelial cells (A), a human airway tissue culture model (B), and the hamster upper airway (C). 2021 Cell host & microbe Figure SARS_CoV_2 R203K;G204R 26;32 31;37 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. (Lower left) The size distributions of plaque-like spots in D614G-infected and D614G/P681R-infected cultures. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 60;79;85 65;84;90 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. (Right) The size distributions of adherent GFP+ syncytia in the D614G mutant-infected (n = 147) and the D614G/P681R mutant-infected (n = 171) cultures. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 64;104;110 69;109;115 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. A B.1.617.2/Delta and a D614G-bearing B.1.1 were inoculated in cells, and the copy number of viral RNA in the supernatant was quantified using RT-qPCR. 2022 Nature Figure SARS_CoV_2 D614G 24 29 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. A statistically significant difference (*, P < 0.05) versus D614G S was determined by two-sided Student's t test. 2022 Nature Figure SARS_CoV_2 D614G 60 65 S 66 67 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. A statistically significant difference versus the D614G virus was determined by two-sided Wilcoxon matched-pairs signed rank test. 2022 Nature Figure SARS_CoV_2 D614G 50 55 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. a, (Left) Floating syncytia in VeroE6/TMPRSS2 cells infected with GFP-expressing D614G and D614G/P681R mutant viruses (100 TCID50) at 72 h.p.i. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 81;91;97 86;96;102 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Association of the P681R mutation with sensitivity to NAbs. 2022 Nature Figure SARS_CoV_2 P681R 19 24 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. b, Chromatograms of nucleotide positions 23,399-23,407 (left) and 23,600-23,608 (right) of parental SARS-CoV-2 (strain WK-521, PANGO lineage A; GISAID ID: EPI_ISL_408667) and the D614G (A23403G in nucleotide) and P681R (C23604G in nucleotide) mutations. 2022 Nature Figure SARS_CoV_2 D614G;P681R;A23403G;C23604G 179;213;186;220 184;218;193;227 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. b, Floating syncytia in VeroE6/TMPRSS2 cells infected with the D614G and D614G/P681R mutant viruses at 72 h.p.i. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 63;73;79 68;78;84 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. b, The GFP-expressing D614G and D614G/P681R mutant viruses (1,000 TCID50) were inoculated on the apical side of culture. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 22;32;38 27;37;43 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Bottom, the size distributions of floating syncytia in D614G-infected (n = 228) and D614G/P681R-infected (n = 164) cultures. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 55;84;90 60;89;95 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. c, Adherent syncytia in VeroE6/TMPRSS2 cells infected with GFP-expressing D614G- and D614G/P681R-mutant viruses at 24 h.p.i. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 74;85;91 79;90;96 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. CT severity score of D614G-infected (n = 4), D614G/P681R-infected (n = 4), and uninfected hamsters (n = 3) Syrian hamsters. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 21;45;51 26;50;56 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Enhanced pathogenicity by the P681R mutation in hamsters. 2022 Nature Figure SARS_CoV_2 P681R 30 35 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. In b, statistically significant differences (*P < 0.05) versus the D614G (black), B.1.1.7/Alpha (blue) or B.1.351/Beta (green) were determined by two-sided Student's t test. 2022 Nature Figure SARS_CoV_2 D614G 67 72 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. In c, the NT50 values of D614G S (black) and D614G/P681R S (orange) for each serum are indicated in each panel. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 25;45;51 30;50;56 S;S 31;57 32;58 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Note that D614G/P681R-infected animals had a higher average CT severity score compared to D614G-infected animals. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 10;90;16 15;95;21 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Note that larger plaque-like spots are observed in D614G/P681R-infected culture after 7 d.p.i. 2022 Nature Figure SARS_CoV_2 D614G;P681R 51;57 56;62 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Note that the S protein sequence of "D614G" is identical to that of B.1.1 isolate. 2022 Nature Figure SARS_CoV_2 D614G 37 42 S 14 15 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Rates of infectivity compared to the virus pseudotyped with parental S D614G (1,000 ng HIV-1 p24) in HOS-ACE2 cells are shown. 2022 Nature Figure SARS_CoV_2 D614G 71 76 S 69 70 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Representative IHC panels of the viral N proteins in the lung of hamsters infected with D614G-bearing B.1.1 isolate (left) and B.1.617.2/Delta isolates (right) are shown. 2022 Nature Figure SARS_CoV_2 D614G 88 93 N 39 40 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Representative pathological images of D614G- and D614G/P681R-infected lungs at 3 d.p.i. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 38;49;55 43;54;60 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Statistically significant differences (*P < 0.05) versus the D614G virus were determined by two-sided Student's t test. 2022 Nature Figure SARS_CoV_2 D614G 61 66 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Statistically significant differences between B.1.1 and B.1.617.2/Delta (a, *P < 0.05) and between D614G and D614G/P681R (c, *P < 0.05) were determined by two-sided Mann-Whitney U test. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 99;109;115 104;114;120 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Statistically significant differences versus D614G (*P < 0.05) and uninfected culture (#P < 0.05) were determined using two-sided unpaired Student's t-tests (a, d) or Mann-Whitney U-tests (b, c). 2022 Nature Figure SARS_CoV_2 D614G 45 50 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Statistically significant differences versus D614G (*P < 0.05) were determined by two-sided, unpaired Student's t test (b, upper left) or the Mann-Whitney U test (a, b, lower left). 2022 Nature Figure SARS_CoV_2 D614G 45 50 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Syrian hamsters were intranasally inoculated with the D614G and D614G/P681R viruses. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 54;64;70 59;69;75 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Target cells were prepared by transfecting the indicated amounts of human ACE2 expression plasmid, while Effector cells were prepared by transfecting SARS-CoV-2 S D614G expression plasmid. 2022 Nature Figure SARS_CoV_2 D614G 163 168 S 161 162 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. The D614G and D614G/P681R mutant viruses were generated by reverse genetics. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 4;14;20 9;19;25 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. The GFP-expressing D614G and D614G/P681R mutant viruses were generated by reverse genetics. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 19;29;35 24;34;40 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. The HIV-1-based reporter virus pseudotyped with SARS-CoV-2 S D614G or D614G/P681R was inoculated into HOS-ACE2 cells or HOS-ACE2/TMPRSS2 cells at 4 different doses (125, 250, 500 and 1,000 ng HIV-1 p24 antigen). 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 61;70;76 66;75;81 S 59 60 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. The P value of the comparison between D614G and D614G/P681R at each d.p.i. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 38;48;54 43;53;59 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. The size distributions of adherent GFP+ syncytia in the D614G-infected (n = 111) and D614G/P681R-infected (n = 126) cultures. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 56;85;91 61;90;96 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. VeroE6/TMPRSS2 cells were infected with the B.1.1 or B.1.617.2/Delta (a) or artificially generated D614G or D614G/P681R (b) viruses [multiplicity of infection (MOI) 0.01]. 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 99;108;114 104;113;119 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Virological features of the P681R-containing virus in vitro. 2022 Nature Figure SARS_CoV_2 P681R 28 33 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Virological phenotypes exhibited by the P681R mutation. 2022 Nature Figure SARS_CoV_2 P681R 40 45 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. with D614G-infected (n = 4), D614G/P681R-infected (n = 4), and uninfected hamsters (n = 3). 2022 Nature Figure SARS_CoV_2 D614G;D614G;P681R 5;29;35 10;34;40 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. c Exemplary energy curve of the reactive molecular dynamics simulation for SARS-CoV-2 S and SARS-CoV-2 S R403T (top panel) and RaTG13 and RaTG13 T430R spike with human ACE2 (bottom panel). 2021 Nature communications Figure SARS_CoV_2 R403T;T430R 105;145 110;150 S;S;S 151;86;103 156;87;104 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. g Replication kinetic of Caco-2 cells, infected with either SARS-CoV-2 d6-YFP wild type or SARS-CoV-2 d6-YFP R403T (MOI 0.005 or 0.02). 2021 Nature communications Figure SARS_CoV_2 R403T 109 114 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. SCoV-2 S and T403R RaTG13 S allow entry with human but not bat ACE2. 2021 Nature communications Figure SARS_CoV_2 T403R 13 18 S;S 7;26 8;27 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. T403R RaTG13 S is sensitive to EK-1 and sera from vaccinated individuals but not Casivirimab. 2021 Nature communications Figure SARS_CoV_2 T403R 0 5 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. The enhancing effect of T403R in RaTG13 S depends on E37 in ACE2. 2021 Nature communications Figure SARS_CoV_2 T403R 24 29 S 40 41 34839413 Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. Numbers of SARS-CoV-2 genomes harbouring the spike Q677H mutation worldwide according to timeline. 2022 Virus genes Figure SARS_CoV_2 Q677H 51 56 S 45 50 34840498 Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021. A Distribution of D614G mutation from various provinces in Indonesia; B 3D structure visualization of SARS-CoV-2 S protein. 2021 Bulletin of the National Research Centre Figure SARS_CoV_2 D614G 18 23 S 113 114 34841034 Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2. B) Diffusion of D614D/E/N/G substitution in bat, porcine and human coronavirus. 2021 One health (Amsterdam, Netherlands) Figure SARS_CoV_2 D614D;D614E;D614G;D614N 16;16;16;16 27;27;27;27 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Visual representation of the impact of 1163A > T mutation on the NSP2 protein structure. 2021 Current research in microbial sciences Figure SARS_CoV_2 A1163T 39 48 Nsp2 65 69 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. For MERS-CoV, ExoN knockout mutant D90A/E92A was included as a control. 2021 Proc Natl Acad Sci U S A Figure SARS_CoV_2 D90A;E92A 35;40 39;44 Exon 14 18 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. b Incidence of spindle and chromosome abnormalities in MII oocytes between control group and N501Y groups (control, n = 62; 20 mug/ml N501Y, n = 30; 50 mug/ml N501Y, n = 57). 2021 Reproductive sciences (Thousand Oaks, Calif.) Figure SARS_CoV_2 N501Y;N501Y;N501Y 93;134;159 98;139;164 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. d Statistical data of spindle length in control and N501Y-treated oocytes after cultured for 24 h (control, n = 12; 20 mug/ml N501Y, n = 10; 50 mug/ml N501Y, n = 8). 2021 Reproductive sciences (Thousand Oaks, Calif.) Figure SARS_CoV_2 N501Y;N501Y;N501Y 52;126;151 57;131;156 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. Effects of N501Y mutation spike protein on spindle assembly and chromosome aggregation in murine oocytes. 2021 Reproductive sciences (Thousand Oaks, Calif.) Figure SARS_CoV_2 N501Y 11 16 S 26 31 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. f Statistical result of MII plate width in control and N501Y-treated oocytes after cultured for 24 h (control, n = 11; 20 mug/ml N501Y, n = 11; 50 mug/ml N501Y, n = 7). 2021 Reproductive sciences (Thousand Oaks, Calif.) Figure SARS_CoV_2 N501Y;N501Y;N501Y 55;129;154 60;134;159 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. (a) Worldwide occurrence of the N:S194L mutation using NextStrain. 2021 Microbial genomics Figure SARS_CoV_2 S194L 34 39 N 32 33 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. (b) Same analysis highlighting only sequences from Mexico distributed in two sub-clades consisting of a broad diversity of Pangolin lineages, dominated by B.1 but also showing B.1.243 with the potential to evolve the E484K mutation. 2021 Microbial genomics Figure SARS_CoV_2 E484K 217 222 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. ORF1a and spike protein amino acid mutations (ORF1a: V1071A, P1810L, S3149F; S: R190M) are indicated with green stars. 2021 Microbial genomics Figure SARS_CoV_2 P1810L;R190M;S3149F;V1071A 61;80;69;53 67;85;75;59 ORF1a;ORF1a;S;S 0;46;10;77 5;51;15;78 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Presence of N:S194L in SARS-Cov-2 clades. 2021 Microbial genomics Figure SARS_CoV_2 S194L 14 19 N 12 13 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Right: positions of the important mutations S477N, T478K, E484K, D614G, P681H/R and T732A in two different regions. 2021 Microbial genomics Figure SARS_CoV_2 D614G;E484K;P681H;P681R;S477N;T478K;T732A 65;58;72;72;44;51;84 70;63;79;79;49;56;89 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Violin plots depict the distributions of the (e) genome-wide and (f) locus-specific (S194L) allelic imbalance for symptomatic and asymptomatic hosts within Guanajuato. 2021 Microbial genomics Figure SARS_CoV_2 S194L 85 90 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. (A) Identification of spike gene mutations using HV69/70, E484K, and N501Y RT-qPCR assays in 184 clinical samples collected in Equatorial Guinea from November 2020 to March 2021. 2021 Analytical chemistry Figure SARS_CoV_2 E484K;N501Y 58;69 63;74 S 22 27 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. (A) RT-qPCR amplification efficiency of the E-gene, HV69/70, E484K, and N501Y assays as determined by serial dilutions of RNA derived from four cell culture supernatant SARS-CoV-2 lineages. 2021 Analytical chemistry Figure SARS_CoV_2 E484K;N501Y 61;72 66;77 E 44 45 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. (A) SARS-CoV-2 E-gene reference assay, (B) HV69/70 assay, (C) E484K assay, and (D) N501Y assay. 2021 Analytical chemistry Figure SARS_CoV_2 E484K;N501Y 62;83 67;88 E 15 16 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. (B) Detection of N501Y-wt in serial dilution of Wuhan Hu-1 lineage, ranging from 1 to 10,000 cp/muL using the YYE channel of the Bio-Rad CFX96 instrument. 2021 Analytical chemistry Figure SARS_CoV_2 N501Y 17 22 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. (C) Detection of N501Y-mut in serial dilution of P.1 lineage, ranging from 1 to 1,000,000 cp/muL using the FAM channel of the Bio-Rad CFX96 instrument. 2021 Analytical chemistry Figure SARS_CoV_2 N501Y 17 22 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. Analytical performance of HV69/70, E484K, and N501Y detecting RT-qPCR assays. 2021 Analytical chemistry Figure SARS_CoV_2 E484K;N501Y 35;46 40;51 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. Rapid detection of SARS-CoV-2 VOC-associated mutations using HV69/70, E484K, and N501Y RT-qPCR assays. 2021 Analytical chemistry Figure SARS_CoV_2 E484K;N501Y 70;81 75;86 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Effect of Delta682-686 and K814A mutations on SARS-CoV-2 infectivity of lung cell line and human ACE2 transgenic mice. 2022 Emerging microbes & infections Figure SARS_CoV_2 K814A 27 32 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Infectivity analysis of F1 and F2 mutations in 293T-ACE2-furin cells, with and without cathepsin inhibitor (E64D). 2022 Emerging microbes & infections Figure SARS_CoV_2 E64D 108 112 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. The neutralizing titer was determinate for the last dilution where no viral cytopathic effect was found in cells against wild type (D614G), and Alpha, Gamma and Delta variants. 2021 Frontiers in immunology Figure SARS_CoV_2 D614G 132 137 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. (A) Pangolin-CoV, (B) SARS-CoV-2 (D614G) Variant, (C) Reference sequence at 614 position in spike glycoprotein sequence. 2021 Frontiers in genetics Figure SARS_CoV_2 D614G 34 39 S 92 110 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. (B) Amino acid sequence alignment of spike protein encompassing the D614G position. 2021 Frontiers in genetics Figure SARS_CoV_2 D614G 68 73 S 37 42 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. Comparison of the glycosylation pattern on the spike protein from recombinant S1, the WA1 strain, and the D614G variant. 2021 Frontiers in chemistry Figure SARS_CoV_2 D614G 106 111 S 47 52 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. The most abundant glycoform detected in Vero E6 cell-derived WA1 and the D614G strain spike N-glycosite was comparable but different from that detected in recombinant S1 produced in HEK293. 2021 Frontiers in chemistry Figure SARS_CoV_2 D614G 73 78 S;N 86;92 91;93 34869209 Site-Specific Glycosylation Patterns of the SARS-CoV-2 Spike Protein Derived From Recombinant Protein and Viral WA1 and D614G Strains. The most abundant glycoforms detected in Vero E6 cell-derived WA1 and D614G strain spike N-glycosites were comparable but different from that detected in recombinant S1 produced in HEK293. 2021 Frontiers in chemistry Figure SARS_CoV_2 D614G 70 75 S;N 83;89 88;90 34869681 Arterial and Venous Thrombosis Complicated in COVID-19: A Retrospective Single Center Analysis in Japan. Based on the results of the epidemiologic analysis in Tokyo, the variant carrying E484K alone, N501Y alone, and L452R alone were considered as R.1 lineage variant, alpha variant, and delta variant, respectively. 2021 Frontiers in cardiovascular medicine Figure SARS_CoV_2 E484K;L452R;N501Y 82;112;95 87;117;100 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. (A) RMSD of alpha carbon atoms of the reference SARS-CoV-2 spike protein (WT) and its single mutations (A222V, Y265C, and D614G) versus time at 310.15 K. 2021 PloS one Figure SARS_CoV_2 D614G;Y265C;A222V 122;111;104 127;116;109 S 59 64 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. (A) WT, reference trimeric spike protein, (B) A222V mutant, (C) Y265C mutant, and (D) D614G mutant. 2021 PloS one Figure SARS_CoV_2 A222V;D614G;Y265C 46;86;64 51;91;69 S 27 32 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. (B) RMSD of alpha carbon atoms of the reference SARS-CoV-2 spike protein (WT) and its single mutations (A222V, Y265C, D614G) versus time at 310.15 K around the ACE-2 Receptor Binding Domain residues. 2021 PloS one Figure SARS_CoV_2 D614G;Y265C;A222V 118;111;104 123;116;109 RBD;S 166;59 189;64 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. WT, reference trimeric spike protein, A222V mutant, Y265C mutant, and D614G mutant. 2021 PloS one Figure SARS_CoV_2 A222V;D614G;Y265C 38;70;52 43;75;57 S 23 28 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. (a) Distribution of vaccine-resistant mutation Y449S. 2021 The journal of physical chemistry letters Figure SARS_CoV_2 Y449S 47 52 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. (b) Time evolution of the vaccination rate and the frequency of Y449S in top 12 countries from December 26, 2020, to October 22, 2021. 2021 The journal of physical chemistry letters Figure SARS_CoV_2 Y449S 64 69 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. The blue chain represents the human ACE2; the pink chain represents the S protein, and the purple fragment on the S protein points out the two vaccine-resistant mutations Y449S and Y449H. 2021 The journal of physical chemistry letters Figure SARS_CoV_2 Y449H;Y449S 181;171 186;176 S;S 72;114 73;115 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. The color bar represents the log 10 frequency of Y449S in 14 countries: Denmark (DK), the United Kingdom (UK), France (FR), Bulgaria (BG), the United States (US), Argentina (AR), Brazil (BR), Sweden (SE), Canada (CA), Switzerland (CH), Germany (DE), Spain (ES), Romania (RO), and Belgium (BE). 2021 The journal of physical chemistry letters Figure SARS_CoV_2 Y449S 49 54 34873910 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America. The red line shows the frequency of mutation Y449S. 2021 The journal of physical chemistry letters Figure SARS_CoV_2 Y449S 45 50 34874953 1H, 13C and 15N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution. (D) Chemical shift deviations of Delta1H and Delta15N nuclei (ppm), obtained as distances , between wild type SARS-CoV-2 nsp1 protein and nsp1(H81P) (red) or nsp1(K129E, D48E) (blue) mutants. 2021 PloS one Figure SARS_CoV_2 D48E;H81P;K129E 170;143;163 174;147;168 34876033 Emergence of SARS-CoV-2 resistance mutations in a patient who received anti-SARS-COV2 spike protein monoclonal antibodies: a case report. B Naso-pharyngeal swab collected on April 28th: a double peak is observed for position 484: the main first peak at 51 C (wild type 484) and a second smaller one at 54.6 C (E484K); the third peak at 61 C is N501Y. 2021 BMC infectious diseases Figure SARS_CoV_2 N501Y;E484K 209;174 214;179 34876033 Emergence of SARS-CoV-2 resistance mutations in a patient who received anti-SARS-COV2 spike protein monoclonal antibodies: a case report. C Bronchoalveolar lavage collected on May 5th where a double peak is again observed: the main peak at 54.3 C (E484K) and a smaller one at 51.3 C (wild type 484); the N501Y peak at 61 C is unchanged. 2021 BMC infectious diseases Figure SARS_CoV_2 N501Y;E484K 168;111 173;116 34876033 Emergence of SARS-CoV-2 resistance mutations in a patient who received anti-SARS-COV2 spike protein monoclonal antibodies: a case report. No amplification for the negative control; wild type samples (E484E) segregate on the low right; E484K samples segregate at the top; sample collected from our patient is observed in an intermediate location between wild type samples and E484K samples. 2021 BMC infectious diseases Figure SARS_CoV_2 E484K;E484K;E484E 97;237;62 102;242;67 34878296 Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. (D) The fraction of B.1.617.2 sequences in GISAID with (blue) and without (orange) G142D through August 31, 2021. 2021 Microbiology spectrum Figure SARS_CoV_2 G142D 83 88 34878296 Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. (E) Frequency of L452R (gray), D950N (blue), and G142D (orange) amino acid substitutions observed in SARS-CoV-2-positive samples from April through August of 2021. 2021 Microbiology spectrum Figure SARS_CoV_2 D950N;G142D;L452R 31;49;17 36;54;22 34878296 Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. L452R, D950N, and G142D are hallmark amino acid substitutions of the Delta variant. 2021 Microbiology spectrum Figure SARS_CoV_2 D950N;G142D;L452R 7;18;0 12;23;5 34880635 Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants. The reference "wild-type'" virus B.1 was assumed (with no mutation D614G and other spike protein changes). 2021 Infection and drug resistance Figure SARS_CoV_2 D614G 67 72 S 83 88 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. Dark turquoise boxes indicate Delta lineage-defining spike mutations present in all Delta lineages/sub-lineages evaluated, light turquoise boxes indicate the AY.4 sub-lineage mutation, light cyan boxes indicate the AY.4.2 sub-lineage mutations, patterned boxes indicates other mutations present in the strains evaluated, and grey boxes indicates the D614G mutation that predominated globally since April 2020. 2021 Euro surveillance Figure SARS_CoV_2 D614G 350 355 S 53 58 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. Fold changes are relative to D614G. 2021 Euro surveillance Figure SARS_CoV_2 D614G 29 34 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. Fold changes are relative to the early pandemic strain D614G. 2021 Euro surveillance Figure SARS_CoV_2 D614G 55 60 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. Spike mutations of SARS-CoV-2 Delta variant clinical isolates sequenced in Denmark between 13 March 2020 (D614G) and 12 October 2021, which were used to evaluate virus neutralisation of an early pandemic strain D614G, and Delta variants B.1.617.2, AY.4, AY.4.2, and B.1.617.2 + E484K. 2021 Euro surveillance Figure SARS_CoV_2 D614G;E484K;D614G 211;278;106 216;283;111 S 0 5 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. Virus neutralisation for each serum sample was tested against clinical isolates representing an early pandemic strain (D614G), the parental Delta lineage (Pango lineage designation B.1.617.2), Delta lineage AY.4, Delta sub-lineage AY.4.2, and a Delta lineage B.1.617.2 bearing the neutralisation-resistant spike mutation E484K. 2021 Euro surveillance Figure SARS_CoV_2 E484K;D614G 321;119 326;124 S 306 311 34888394 A Multidimensional Cross-Sectional Analysis of Coronavirus Disease 2019 Seroprevalence Among a Police Officer Cohort: The PoliCOV-19 Study. Results of neutralization assays performed with serum of study participants (n=126) and isogenic severe acute respiratory syndrome coronavirus 2 viruses harboring either the D614G spike, the full-length B.1.1.7 spike (Alpha variant), or the full-length B.1.351 spike (Beta variant). 2021 Open forum infectious diseases Figure SARS_CoV_2 D614G 174 179 S;S;S 180;211;261 185;216;266 34890524 The significant immune escape of pseudotyped SARS-CoV-2 variant Omicron. The neutralization ED50 and ratio compared to the reference strain D614G was also displayed as indicated. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 67 72 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. (A, B) Sensitivity of N501Y detection using the RT-CORDS lateral flow strips system. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 N501Y 22 27 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. (A) D614G detection of SARS-CoV-2 variants using the RT-CORDS paper strip assay. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 D614G 4 9 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. (A) Sensitivity of N501Y detection using the CORDS fluorescence reporting assay after 10 min of Cas12a/crRNA sensing time. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 N501Y 19 24 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. (B, C, D) in vitro cleavage assay of N501Y, D614G and 69/70 deletion targets using Cas12a/crRNA-W and Cas12a-crRNA-M. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 D614G;N501Y 44;37 49;42 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. (B) N501Y detection of SARS-CoV-2 variants samples using the RT-CORDS paper strip assay. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 N501Y 4 9 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. (D, E) Sensitivity of 69/70 deletion and N501Y mutation detection using the CORDS strips assay. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 N501Y 41 46 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. (E, F, G) Identification of N501Y, D614G and 69/70 deletion targets through CRISPR/Cas12a trans-cleavage of the fluorescence reporter. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 D614G;N501Y 35;28 40;33 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. (E, F) Sensitivity of D614G detection using the RT-CORDS lateral flow strips system. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 D614G 22 27 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. Detection of N501Y and 69/70 deletion mutations in SARS-CoV-2 using the CORDS platform. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 N501Y 13 18 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. (C) The sub-branch of the new lineage (B.1.1.526) illustrating 27 strains with additional S: E484K mutation. 2022 Journal of infection and public health Figure SARS_CoV_2 E484K 93 98 S 90 91 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. a) and b) Depiction of vdW and electrostatic interaction energies, respectively, associated with each structure (wild type (magenta), T478K mutated structure (red), L452R (black), and structures with double mutations (blue). 2021 Medicine in drug discovery Figure SARS_CoV_2 L452R;T478K 165;134 170;139 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. RBDs of L452R, and T478K mutated structure are shown in Pink and Blue respectively, while ACE2 associated with these structures are shown in Yellow and Red, respectively. 2021 Medicine in drug discovery Figure SARS_CoV_2 L452R;T478K 8;19 13;24 RBD 0 4 34901826 The Delta Variant Mutations in the Receptor Binding Domain of SARS-CoV-2 Show Enhanced Electrostatic Interactions with the ACE2. The interactions between selected residues at the RBD/ACE2 interface in WT protein and protein structures with single RBD mutations (L452R and T478K) and double mutation. 2021 Medicine in drug discovery Figure SARS_CoV_2 T478K;L452R 143;133 148;138 RBD;RBD 50;118 53;121 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. A-D, p.N501Y spread in the province of Udine. 2021 PloS one Figure SARS_CoV_2 N501Y;N501Y 5;7 12;12 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. E, relative abundance of the p.N501Y positive samples in about 15 weeks. 2021 PloS one Figure SARS_CoV_2 N501Y;N501Y 29;31 36;36 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. Expansion of Spike p.N501Y positive samples in Friuli Venezia Giulia. 2021 PloS one Figure SARS_CoV_2 N501Y;N501Y 19;21 26;26 S 13 18 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. Green dots represent p.N501Y positive samples from January 1st to January 15th (A), from January 16th to January 31st (B), from February 1st to February 15th (C), from February 16th to February 28th (D). 2021 PloS one Figure SARS_CoV_2 N501Y;N501Y 21;23 28;28 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. A D614G in the United Kingdom; B B.1.1.7 in the United Kingdom; C R.1 in Japan; D D614G in the Netherlands; E B.1.1.7 in the Netherlands; and F B.1.351 in the Netherlands. 2021 Nature communications Figure SARS_CoV_2 D614G;D614G 2;82 7;87 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. Estimates of the selection parameter s for United Kingdom (UK), Netherlands (NL), and Japan (JP) and variants D614G, B.1.1.7, B.1.351, and R.1. 2021 Nature communications Figure SARS_CoV_2 D614G 110 115 S 37 38 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. Mechanistic model fit to D614G data in the Netherlands, and UK. 2021 Nature communications Figure SARS_CoV_2 D614G 25 30 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. Panels A and B show realizations of the prevalence of the background, Iwt, and D614G variant, Imt for the maximum-likelihood model fit. 2021 Nature communications Figure SARS_CoV_2 D614G 79 84 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. The number of days of data is measured from the time horizon back to a first day for each variant: 2020-01-04 for D614G, 2020-09-20 for B.1.1.7, 2020-10-01 for B.1.351, and 2020-10-24 for R.1. 2021 Nature communications Figure SARS_CoV_2 D614G 114 119 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. The total number of sequences used is 114690 for D614G, 466954 for B.1.1.7, 1147386 for B.1.351, and 942329 for R.1. 2021 Nature communications Figure SARS_CoV_2 D614G 49 54 34909459 Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M(pro). Structure of Spike (S) protein (D614G) and its interactions with OPG and compounds 1-4. 2021 ChemistrySelect Figure SARS_CoV_2 D614G 32 37 S;S 13;20 18;21 34910734 Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. Star (*) indicates mink variant mutation in spike protein (Spike_Y453F) reported in mink and humans. 2021 PloS one Figure SARS_CoV_2 Y453F 65 70 S;S 44;59 49;64 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. (The study used for symptom frequencies of COVID-19 patients after the outbreak of the D614G mutation reported symptoms of 2636 patients, except for cough, where only 2634 of the patients were recorded.) D) Abridged Hasse Diagram depicting the transition probabilities from no symptom to fever or cough before the D614G mutation became prominent. 2021 PLoS computational biology Figure SARS_CoV_2 D614G;D614G 87;314 92;319 COVID-19 43 51 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. A) The first (gold), second (silver), and third (bronze) likeliest paths of the order of discernible symptoms of COVID-19 patients before the D614G mutation became prominent. 2021 PLoS computational biology Figure SARS_CoV_2 D614G 142 147 COVID-19 113 121 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. B) The first, second, and third likeliest paths of the order of discernible symptoms of COVID-19 patients in Japan after the D614G mutation became prominent. 2021 PLoS computational biology Figure SARS_CoV_2 D614G 125 130 COVID-19 88 96 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. C) Table of raw frequency data specifying the number and the percentage of patients that experienced fever and cough in the datasets of Japan before and after the D614G mutation became prominent. 2021 PLoS computational biology Figure SARS_CoV_2 D614G 163 168 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. E) Abridged Hasse Diagram depicting the transition probabilities from no symptom to fever or cough after the D614G mutation became prominent. 2021 PLoS computational biology Figure SARS_CoV_2 D614G 109 114 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. The other columns are the most likely path of discernible symptom order of datasets representing, from left to right, Detroit, New York, and Atlanta in the USA, when the D614G variant was prominent. 2021 PLoS computational biology Figure SARS_CoV_2 D614G 170 175 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. The three likeliest paths of discernible symptom order in Japan before and after the D614G mutation became prominent. 2021 PLoS computational biology Figure SARS_CoV_2 D614G 85 90 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. (B) Area under the curve (AUC) fold changes in ELISA binding assays relative to D614G alone for Ab1, Ab8, CR3022, S309, and S2M11. 2021 Cell reports Figure SARS_CoV_2 D614G 80 85 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. (B) Relative fold change differences in S protein-ACE2 affinity (Kd) relative to D614G alone. 2021 Cell reports Figure SARS_CoV_2 D614G 81 86 S 40 41 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. All constructs contain the D614G mutation as background, and this was defined as the wild-type construct throughout the study. 2021 Cell reports Figure SARS_CoV_2 D614G 27 32 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. (A) 2-D scatter representation of the conformational ensemble of wild-type RBD-B38 (black), N501Y RBD-B38 (red), and E484K RBD-B38 (blue) complexes obtained from the equilibrium simulation in RMSD and Rg space. 2022 International immunopharmacology Figure SARS_CoV_2 E484K;N501Y 117;92 122;97 RBD;RBD;RBD 75;98;123 78;101;126 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. (A) Potential of mean force for the binding of wild-type (black), N501Y (red), and E484K (blue) RBD to ACE2. 2022 International immunopharmacology Figure SARS_CoV_2 E484K;N501Y 83;66 88;71 RBD 96 99 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. (A) Potential of mean force for the binding of wild-type (black), N501Y (red), and E484K (blue) RBD to B38 antibody. 2022 International immunopharmacology Figure SARS_CoV_2 E484K;N501Y 83;66 88;71 RBD 96 99 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. (A) Root mean square deviation (RMSD) based clustering of the SARS-CoV2 spike RBD-ACE2 complexes obtained from the simulation trajectories for the three systems (Wild-type RBD-ACE2, N501Y RBD-ACE2, and E484K-ACE2) is shown. 2022 International immunopharmacology Figure SARS_CoV_2 E484K;N501Y 202;182 207;187 S;RBD;RBD;RBD 72;78;172;188 77;81;175;191 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. (A) Time-evolution of conformational clusters evident from the RMSD based clustering of simulation trajectory of wild-type (black), N501Y (red), and E484K (blue) RBD complexed with ACE2. 2022 International immunopharmacology Figure SARS_CoV_2 E484K;N501Y 149;132 154;137 RBD 162 165 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. (B) Time-evolution of conformational clusters of wild-type (black), N501Y (red), and E484K (blue) RBD complexed with B38. 2022 International immunopharmacology Figure SARS_CoV_2 E484K;N501Y 85;68 90;73 RBD 98 101 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Unique interactions present in the wild-type RBD-ACE2 complex (B), N501Y RBD-ACE2 complex (C), and E484K RBD-ACE2 complex (D) are shown. 2022 International immunopharmacology Figure SARS_CoV_2 E484K;N501Y 99;67 104;72 RBD;RBD;RBD 45;73;105 48;76;108 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Wild-type, N501Y, and E484K RBD are colored gray, red, and blue. 2022 International immunopharmacology Figure SARS_CoV_2 E484K;N501Y 22;11 27;16 RBD 28 31 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Wild-type, N501Y, and E484K RBD complexed with ACE2 are colored as deep salmon, greenish-yellow, and blue, respectively. 2022 International immunopharmacology Figure SARS_CoV_2 E484K;N501Y 22;11 27;16 RBD 28 31 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. Phylogenetic tree of the SARS-CoV-2 spike protein sequence with the D614G mutation collected in Spain before March 11, 2020. 2021 Frontiers in medicine Figure SARS_CoV_2 D614G 68 73 S 36 41 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. (A-F) Neutralization assays performed against Victoria, Alpha (N501Y), Beta (K417N, E484K, and N501Y), Gamma (K417T, E484K, and N501Y), Delta (L452R and T478K), Alpha+E484K (E484K and N501Y), and B.1.525 (E484K) live viral isolates with 27 potent Beta-specific mAbs. 2022 Cell host & microbe Figure SARS_CoV_2 E484K;E484K;N501Y;N501Y;N501Y;T478K;E484K;E484K;K417N;K417T;L452R;N501Y;E484K 84;117;95;128;184;153;174;205;77;110;143;63;167 89;122;100;133;189;158;179;210;82;115;148;68;172 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. (G) FRNT50 titers of 17 Alpha convalescent sera against Alpha and B.1 (D614G), analysis used the Wilcoxon matched-pairs signed rank sum test, and two-tailed p values were calculated; geometric means are indicated above each column. 2022 Cell host & microbe Figure SARS_CoV_2 D614G 71 76 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Data are shown as mean +- SEM (A) Fully cross-reactive mAbs, (B) N501Y-dependent mAbs, (C) E484K-dependent mAbs, (D) K417N/T-dependent mAbs, (E) L452R/T478K-dependent mAbs, and (F) a single NTD-binding mAb. 2022 Cell host & microbe Figure SARS_CoV_2 E484K;K417N;K417T;L452R;N501Y;T478K 91;117;117;145;65;151 96;124;124;150;70;156 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. (A) E341D mutant and TBK1 key hydrogen bonding interactions and stick representations of bonds (left). 2021 Frontiers in microbiology Figure SARS_CoV_2 E341D 4 9 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. (A) NSP13 WT, (B) P77L, (C) Q88H, (D) D260Y, (E) E341D, and (F) M429I. 2021 Frontiers in microbiology Figure SARS_CoV_2 D260Y;E341D;M429I;P77L;Q88H 38;49;64;18;28 43;54;69;22;32 Nsp13 4 9 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. (A) Q88H mutant and TBK1 key hydrogen bonding interactions and representations of bonds by sticks (left). 2021 Frontiers in microbiology Figure SARS_CoV_2 Q88H 4 8 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. (B) D260Y mutant and TBK1 key hydrogen bonding interactions and representations of bonds by sticks (left). 2021 Frontiers in microbiology Figure SARS_CoV_2 D260Y 4 9 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. (B) P77L mutant and TBK1 key hydrogen bonding interactions along with their stick representation (left). 2021 Frontiers in microbiology Figure SARS_CoV_2 P77L 4 8 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. (G) Superimposed structure of NSP13 WT (green) with P77L (yellow), Q88H (cyan), D260Y (light magenta), E341D (orange), and M429I (dark magenta). 2021 Frontiers in microbiology Figure SARS_CoV_2 D260Y;E341D;M429I;P77L;Q88H 80;103;123;52;67 85;108;128;56;71 Nsp13 30 35 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. E341D and M429I mutant complex docking. 2021 Frontiers in microbiology Figure SARS_CoV_2 M429I;E341D 10;0 15;5 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Non-structural protein 13 WT and P77L mutant complex docking. 2021 Frontiers in microbiology Figure SARS_CoV_2 P77L 33 37 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Q88H and D260Y mutant complex docking. 2021 Frontiers in microbiology Figure SARS_CoV_2 D260Y;Q88H 9;0 14;4 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. (A) Fold-changes in the IC-50 NT titers against the Wuhan-Hu-1 ancestral strain in the first set of immunization experiments (5 x 107 pfu per dose) with the glycan-masking Ad-S-F135N/N137T, Ad-S-R158N/Y160T, Ad-S-N370/A372T, and Ad-S-H519N/P521T-immunized groups, as compared to the IC-50 titer of the wild-type Ad-S-immunized group; (B) Fold-changes in the IC-50 NT titers against the Wuhan-Hu-1 ancestral strain in the second set of immunization experiments (1 x108 pfu per dose) with the glycan-masking Ad-S-N354/K356T, Ad-S-G413N, and Ad-S-D428N-immunized groups, as compared to the IC-50 titer of the wild-type Ad-S-immunized group. 2021 Frontiers in immunology Figure SARS_CoV_2 A372T;K356T;N137T;P521T;Y160T;D428N;F135N;G413N;H519N;R158N 218;516;183;240;201;544;177;528;234;195 223;521;188;245;206;549;182;533;239;200 S;S;S;S;S;S;S;S;S 175;193;211;232;315;509;526;542;619 176;194;212;233;316;510;527;543;620 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Cell lysates of HEK-293A cells infected with Ad-S, Ad-S-F135N/N137T, Ad-S-R158N/Y160T, Ad-S-N354/K356T, Ad-S-N370/A372T, Ad-S-G413N, Ad-S-D428N, and Ad-S-H519N/P521T and analyzed using 8% SDS-PAGE and western blotting with an S1-specific polyclonal antibody. 2021 Frontiers in immunology Figure SARS_CoV_2 A372T;K356T;N137T;P521T;Y160T;D428N;F135N;G413N;H519N;R158N 114;97;62;160;80;138;56;126;154;74 119;102;67;165;85;143;61;131;159;79 S;S;S;S;S;S;S;S 48;54;72;90;107;124;136;152 49;55;73;91;108;125;137;153 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Domains of the full-length S protein: N-terminal domain (NTD), receptor binding domain (RBD), furin cleavage site (S1/S2), fusion peptide (FP), heptad repeat 1(HR1), heptad repeat 2 (HR2), transmembrane domain (TM), and cytoplasmic tail (CT); (B) The seven engineered N-linked glycan sites of (#1) F135N/N137T, (#2) R158N/Y160T, (#3) N354/K356T, (#4) N370/A372T, (#5) G413N, (#6) D428N, and (#7) H519N/P521T are shown in the intact trimeric S structure. 2021 Frontiers in immunology Figure SARS_CoV_2 D428N;F135N;G413N;H519N;R158N;A372T;K356T;N137T;P521T;Y160T 380;298;368;396;316;356;339;304;402;322 385;303;373;401;321;361;344;309;407;327 RBD;RBD;N;N;S;S 63;88;38;268;27;441 86;91;39;269;28;442 34929375 Omicron N501Y mutation among SARS-CoV-2 lineages: Insilico analysis of potent binding to tyrosine kinase and hypothetical repurposed medicine. Docked complexes of the Spike RBD wild type (pink) and N501Y (light green) are shown in cartoon representation with hACE2 receptor. 2022 Travel medicine and infectious disease Figure SARS_CoV_2 N501Y 55 60 S;RBD 24;30 29;33 34934478 The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour. Response of the wild-type and D614G spike to LA removal. 2021 Computational and structural biotechnology journal Figure SARS_CoV_2 D614G 30 35 S 36 41 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. (a-c) Syrian hamsters were inoculated with comparable genome equivalent mixture of either wt-S614G and Beta (a), Alpha and Beta (b), or wt-S614G and Alpha (c). 2022 Nature Figure SARS_CoV_2 S614G;S614G 93;139 98;144 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. (a-d) Groups hACE2-KI male mice were inoculated intranasally with 104 PFUs of SARS-CoV-2 wt-S614G, Alpha, wt-SAlpha and Beta (n = 8 mice/group). 2022 Nature Figure SARS_CoV_2 S614G 92 97 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. (a) Affinity between spike (S614G, SAlpha, and SBeta) protein trimers and hACE2 dimers determined by Bio-layer interferometry. 2022 Nature Figure SARS_CoV_2 S614G 28 33 S 21 26 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. (b-e) Representative micrographs of hematoxylin and eosin staining of 3 mum sections of nasal conchae of donor ferrets (n = 6) 6 dpi with wt-S614G and Alpha. 2022 Nature Figure SARS_CoV_2 S614G 141 146 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. (b, c) Data are presented as individual points with mean (line) and standard deviation; (b) n = 2 (Alpha and Beta), n = 4 (wt-S614G), (c) n = 3 independent biological replicates. 2022 Nature Figure SARS_CoV_2 S614G 126 131 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. (b) Pie chart colors illustrate the ratio of wt-S614G (orange) with Alpha (dark blue), or with wt-SAlpha (light blue) in corresponding experiments in lung homogenates of contact mice at 7 dpc (i.e., 8 dpi of donor mice). 2022 Nature Figure SARS_CoV_2 S614G 48 53 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. (b) Viral replication kinetics of SARS-CoV-2 Alpha, Beta, and wt-S614G (MOI 0.02) at 33 C and 37 C in primary human nasal airway epithelial cell (AEC) cultures. 2022 Nature Figure SARS_CoV_2 S614G 65 70 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. (d, e) Ferrets were inoculated intranasally with an equal mixture of wt-S614G and Alpha. 2022 Nature Figure SARS_CoV_2 S614G 72 77 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. (d) Affinity between spike (S614G, SAlpha) protein trimers with hamster ACE2 determined by Bio-layer interferometry. 2022 Nature Figure SARS_CoV_2 S614G 28 33 S 21 26 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. a-d, Groups of hACE2-KI male (a, c, d) and female (b) mice were inoculated with 1 x 104 PFU, determined by back titration and comprising a mixture of wt-S614G and Alpha at a 3:1 ratio (a, b), a mixture of wt-S614G and wt-SAlpha at a 1:1 ratio (c), and a mixture of wt-S614G and Beta at a 1:1.6 ratio (d). 2022 Nature Figure SARS_CoV_2 S614G;S614G;S614G 153;208;268 158;213;273 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. a, b, Two groups of four donor hACE2-K18Tg mice were inoculated with 1 x 104 PFU, determined by back titration and comprising a mixture of wt-S614G (orange) and Alpha (dark blue) at a 3:1 ratio (a), or a mixture of wt-S614G and wt-SAlpha (light blue) at a 1:1 ratio (b). 2022 Nature Figure SARS_CoV_2 S614G;S614G 142;218 147;223 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Competitive replication and transmission of Alpha and wt-S614G in Syrian hamsters. 2022 Nature Figure SARS_CoV_2 S614G 57 62 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Competitive replication and transmission of Beta and wt-S614G in Syrian hamsters. 2022 Nature Figure SARS_CoV_2 S614G 56 61 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. hACE2-K18Tg mice inoculated with a mixture of wt-S614G and Alpha, or wt-S614G and wt-SAlpha. 2022 Nature Figure SARS_CoV_2 S614G;S614G 49;72 54;77 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Replication and transmission of SARS-CoV-2 Alpha and wt-S614G in ferrets. 2022 Nature Figure SARS_CoV_2 S614G 56 61 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Replication of Alpha, wt-SAlpha, and Beta in competition with wt-S614G in hACE2-KI mice. 2022 Nature Figure SARS_CoV_2 S614G 65 70 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Replication of Alpha, wt-SAlpha, and wt-S614G in hACE2-K18Tg mice. 2022 Nature Figure SARS_CoV_2 S614G 40 45 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Six donor ferrets were each inoculated with a TCID50 of 105.9, determined by back titration and comprising a mixture of wt-S614G and Alpha at a 1:1.2 ratio, determined by RT-qPCR. 2022 Nature Figure SARS_CoV_2 S614G 123 128 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Six donor hamsters were each inoculated with a median tissue culture infectious dose (TCID50) of 104.25, determined by back titration and comprising a mixture of wt-S614G (orange) and Beta (green) at a 1:3.8 ratio, determined by quantitative PCR with reverse transcription (RT-qPCR). 2022 Nature Figure SARS_CoV_2 S614G 165 170 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Six donor hamsters were each inoculated with a TCID50 of 104.3, determined by back titration and comprising a mixture of wt-S614G and Alpha at a 1:1.6 ratio, determined by RT-qPCR. 2022 Nature Figure SARS_CoV_2 S614G 124 129 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Viral genome load in upper (URT) and lower (LRT) respiratory tract tissue of ferrets in the competitive transmission experiment between SARS-CoV-2 Alpha and wt-S614G. 2022 Nature Figure SARS_CoV_2 S614G 160 165 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. E: C145A Mpro, I: PF-00835231, (E I)i: enzyme-inhibitor noncovalent complexes. 2021 Frontiers in pharmacology Figure SARS_CoV_2 C145A 3 8 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. E: C145A Mpro, S: substrate, E S: enzyme-substrate complex. 2021 Frontiers in pharmacology Figure SARS_CoV_2 C145A 3 8 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. Experimental and theoretical (red) kinetic curves of changes in PF-00835231 fluorescence intensity during the interaction with C145A Mpro(A) or WT Mpro(B). 2021 Frontiers in pharmacology Figure SARS_CoV_2 C145A 127 132 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. Experimental and theoretical (smooth curves) kinetic curves for the FRET signal changes during the interaction of C145A Mpro(A) or WT Mpro(B) with FRET-S. 2021 Frontiers in pharmacology Figure SARS_CoV_2 C145A 114 119 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. The kinetic mechanism of the interaction between C145A Mpro and FRET-S. 2021 Frontiers in pharmacology Figure SARS_CoV_2 C145A 49 54 34938188 Pre-Steady-State Kinetics of the SARS-CoV-2 Main Protease as a Powerful Tool for Antiviral Drug Discovery. The kinetic mechanism of the interaction between C145A Mpro and PF-00835231. 2021 Frontiers in pharmacology Figure SARS_CoV_2 C145A 49 54 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. (A) Detection of N501Y variant and wild type using N501Y chimeric crRNA 24-nt, crRNA 24-nt, and crRNA 20-nt after incubation at 37C for 10 min. 2021 PloS one Figure SARS_CoV_2 N501Y;N501Y 17;51 22;56 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. (A) Detection of N501Y variant and wild type using N501Y crRNA 20-nt after incubation for 30 min. 2021 PloS one Figure SARS_CoV_2 N501Y;N501Y 17;51 22;56 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. (B) Table summarizing positive rate (visualization of the tube) of N501Y and wild type when using different crRNAs after incubation for 1 h. 2021 PloS one Figure SARS_CoV_2 N501Y 67 72 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. (B) Table summarizing positive rate (visualization of the tube) of N501Y and wild type when using N501Y crRNA 20-nt after incubation for 30 min. 2021 PloS one Figure SARS_CoV_2 N501Y;N501Y 67;98 72;103 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. (C) Detection of N501Y variant and wild type using N501Y chimeric crRNA 24-nt after incubation for 2 h. 2021 PloS one Figure SARS_CoV_2 N501Y;N501Y 17;51 22;56 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. (C) Detection of N501Y variant and wild type using N501Y crRNA 20-nt after incubation for 1 h. 2021 PloS one Figure SARS_CoV_2 N501Y;N501Y 17;51 22;56 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. (D) Detection of N501Y variant and wild type using N501Y chimeric crRNA 24-nt after incubation for 1 h. 2021 PloS one Figure SARS_CoV_2 N501Y;N501Y 17;51 22;56 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. (D) Table summarizing positive rate (visualization of the tube) of N501Y and wild type when using N501Y chimeric crRNA 24-nt after incubation for 2 h. 2021 PloS one Figure SARS_CoV_2 N501Y;N501Y 67;98 72;103 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. Schematic diagram of spike protein domains- N-terminal domain (NTD), receptor-binding domain (RBD), fusion peptide (FP), heptapeptide repeat sequence 1 (HR1), heptapeptide repeat sequence 2 (HR2), transmembrane region (TM) and cytoplasm domain (CT), and structural positions of mutations (T478K, L452R and N501Y on spike RBD region. 2022 Journal of King Saud University. Science Figure SARS_CoV_2 L452R;N501Y;T478K 296;306;289 301;311;294 S;S;RBD;RBD;N 21;315;94;321;44 26;320;97;324;45 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. Median of the reciprocals of IC50 titers against the spike E484Q were 225, 213, and 220, for sera collected from the bamlanivimab 700, 2800, and 7000 mg cohorts, respectively. 2021 Frontiers in immunology Figure SARS_CoV_2 E484Q 59 64 S 53 58 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. Neutralization activity of serum samples against spike E484Q and beta variant (B.1.351) at day 29. 2021 Frontiers in immunology Figure SARS_CoV_2 E484Q 55 60 S 49 54 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. The full-length spike protein carries the D614G substitution. 2021 Frontiers in immunology Figure SARS_CoV_2 D614G 42 47 S 16 21 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. Titers against Spike-RBD E484Q not shown for cohort receiving bamlanivimab and etesevimab together as etesevimab binds to this mutant protein. 2021 Frontiers in immunology Figure SARS_CoV_2 E484Q 25 30 S;RBD 15;21 20;24 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. (B) Structural representation of SARS-CoV-1 S RBD showing stabilizing (T363L) and destabilizing (A430W) mutations in red and their side chains. 2021 Frontiers in molecular biosciences Figure SARS_CoV_2 A430W;T363L 97;71 102;76 RBD;S 46;44 49;45 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. (A) The epitope of P36-5D2 (purple) is highlighted on the surface of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RBD-3M carrying K417T, E484K, and N501Y (cyan) (PDB: 7FJC). 2021 Frontiers in immunology Figure SARS_CoV_2 E484K;K417T;N501Y 153;146;164 158;151;169 RBD 130 133 COVID-19 76 116 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. (C-E) The relative mean fluorescence intensity (MFI) of mAbs or ACE2 binding was determined by comparing the total MFI in the selected gate between the spike variants and WT D614G. 2021 Frontiers in immunology Figure SARS_CoV_2 D614G 174 179 S 152 157 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. P36-5D2 binds to a highly conserved epitope on the receptor-binding domain (RBD) and avoids three key mutant residues: K417N, E484K, and N501Y. 2021 Frontiers in immunology Figure SARS_CoV_2 E484K;K417N;N501Y 126;119;137 131;124;142 RBD 76 79 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. The IC50 of antibodies against WT D614G are listed in (A). 2021 Frontiers in immunology Figure SARS_CoV_2 D614G 34 39 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. Values indicate the fold changes in half-maximal inhibitory concentrations (IC50) (A) and the mean fluorescence intensity (MFI) relative to that of wild-type (WT) D614G (B). 2021 Frontiers in immunology Figure SARS_CoV_2 D614G 163 168 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. HIV-1-based reporter viruses pseudotyped with SARS-CoV-2 S proteins bearing respective mutations of the Lambda variant in parental S (G75V, T76I, GT75-76VI, RSYLTPGD246-253N, L452Q, F490S, L452Q/F490S, or T859N) as well as the parental S were prepared. 2022 Cell reports Figure SARS_CoV_2 F490S;L452Q;L452Q;T76I;T859N;G75V;F490S 182;175;189;140;205;134;195 187;180;194;144;210;138;200 S;S;S 57;131;236 58;132;237 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. HLA-A24+ CTL lines established from 6 BNT162b2-vaccinated donors were stimulated with 1 nM NF9 peptide or its derivatives, NF9-L452Q (NYNYQYRLF) or NF9-L452R (NYNYRYRLF). 2022 Cell reports Figure SARS_CoV_2 L452Q;L452R 127;152 132;157 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. (A) ACE2-WT complex, (B) ACE2-V367F complex, (C) ACE2-R408I complex, (D) ACE2-G476S complex, (E) ACE2-V483A complex and (F) ACE2-N501Y complex. 2022 Computer methods and programs in biomedicine Figure SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 78;129;54;30;102 83;134;59;35;107 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. (A) Plot of first 20 eigenvectors with associated eigenvalues (solid lines) and their cumulative percentage (dotted lines) of WT, V367F, R408I and G476S MTs, (B) Plot of first 20 eigenvectors with associated eigenvalues (solid lines) and their cumulative percentage (dotted lines) of WT, V483A and N501Y MTs, (C) Projection of PC1 vs PC2 of WT, V367F, R408I and G476S MTs and (D) Projection of PC1 vs PC2 of WT, V483A and N501Y MTs. 2022 Computer methods and programs in biomedicine Figure SARS_CoV_2 G476S;G476S;N501Y;N501Y;R408I;R408I;V367F;V367F;V483A;V483A 147;362;298;422;137;352;130;345;288;412 152;367;303;427;142;357;135;350;293;417 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. (A) RMSF plot at function of amino acid residues, (B) Structure fluctuations of WT, (C) Structure fluctuations of V367F MT, (D) Structure fluctuations of R408I MT, (E) Structure fluctuations of G476S MT, (F) Structure fluctuations of V483A MT and (G) Structure fluctuation of N501Y MT. 2022 Computer methods and programs in biomedicine Figure SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 194;276;154;114;234 199;281;159;119;239 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. 30 frames of PC1 were sequentially superimposed and associated motions were depicted in porcupine structures of (A) WT, (B) V367F, (C) R408I, (D) G476S, (E) V483A and (F) N501Y. 2022 Computer methods and programs in biomedicine Figure SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 146;171;135;124;157 151;176;140;129;162 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. 3D structure of RBD was shown in cartoon mode with cyan color and different mutations V367F, R408I, G476S, V483A and N501Y were depicted in stick mode. 2022 Computer methods and programs in biomedicine Figure SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 100;117;93;86;107 105;122;98;91;112 RBD 16 19 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Betweenness centrality (CB) values of (A) WT, (B) V367F, (C) R408I, (D) G476S, (E) V483A and (F) N501Y. 2022 Computer methods and programs in biomedicine Figure SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 72;97;61;50;83 77;102;66;55;88 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. WT, V367F, R408I, G476S, V483A and N501Y MTs were labelled in black, red, green, blue, magenta and yellow color, respectively. 2022 Computer methods and programs in biomedicine Figure SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 18;35;11;4;25 23;40;16;9;30 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. (a, b, c) Superimposed structure of wild-type spike protein (green) with D614G-V622F-S943F (red), and D614G-Q677H (orange) and. 2022 Computers in biology and medicine Figure SARS_CoV_2 D614G;D614G;Q677H;S943F;V622F 73;102;108;85;79 78;107;113;90;84 S 46 51 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. (A) Among the Structural proteins, D614G mutation in spike protein was found the most reoccurring mutation in 171Countries while L84S in ORF8 was observed in 100 countries. 2022 Computers in biology and medicine Figure SARS_CoV_2 D614G;L84S 35;129 40;133 S;ORF8 53;137 58;141 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. (B) Among the Non-Structural proteins, the mutation P4715L in NSP12 was observed in 172 countries of the world, followed by L3606F in NSP3 which occurred in 134 countries while the L1174I mutation in NSP3 was observed only in 2 countries. 2022 Computers in biology and medicine Figure SARS_CoV_2 L1174I;L3606F;P4715L 181;124;52 187;130;58 Nsp12;Nsp3;Nsp3 62;134;200 67;138;204 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. (b) Docking complexes of D614G-Q677H spike protein with ACE2. 2022 Computers in biology and medicine Figure SARS_CoV_2 D614G;Q677H 25;31 30;36 S 37 42 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. (B) RMSD of D614G-S943T-V622F, (C) RMSD of D614G-Q677H and (D) RMSD N74K-D614G variant complex. 2022 Computers in biology and medicine Figure SARS_CoV_2 D614G;D614G;N74K;D614G;Q677H;S943T;V622F 12;43;68;73;49;18;24 17;48;72;78;54;23;29 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. (b) wild type spike protein, (c) D614G, V622F, S943T (d) D614G, Q677H (e) N74K, D614G. 2022 Computers in biology and medicine Figure SARS_CoV_2 D614G;D614G;D614G;N74K;Q677H;S943T;V622F 33;57;80;74;64;47;40 38;62;85;78;69;52;45 S 14 19 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Docking complexes of ACE2-N74K, D614G spike protein with ACE2. 2022 Computers in biology and medicine Figure SARS_CoV_2 D614G;N74K 32;26 37;30 S 38 43 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Docking complexes of D614G-V622F-S943F spike protein with ACE2. 2022 Computers in biology and medicine Figure SARS_CoV_2 D614G;S943F;V622F 21;33;27 26;38;32 S 39 44 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. N74K-D614 (blue). 2022 Computers in biology and medicine Figure SARS_CoV_2 N74K 0 4 34968862 Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using computational modelling and simulation approaches. Residual flexibility of the wild type, D614G-S943T-V622F, D614G-Q677H, and RMSD N74K-D614G variant complexes. 2022 Computers in biology and medicine Figure SARS_CoV_2 D614G;D614G;N74K;D614G;Q677H;S943T;V622F 39;58;80;85;64;45;51 44;63;84;90;69;50;56 34968879 SARS-CoV-2 wastewater surveillance in Germany: Long-term RT-digital droplet PCR monitoring, suitability of primer/probe combinations and biomarker stability. Concentration of N501Y mutation divided by the total gene copy numbers of the S-gene (ratio of wildtype and N501Y mutation) in wastewater, and ratios of variants of concern (VoC) in new COVID-19 patients in Baden-Wurttemberg by variant-specific PCR according to the Association of Accredited Laboratories in Medicine (ALM e.V). 2022 Water research Figure SARS_CoV_2 N501Y;N501Y 17;108 22;113 S 78 79 COVID-19 186 194 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. (B) (C) and (D) shows different mutations N501I, N501T and N501V. 2022 Computers in biology and medicine Figure SARS_CoV_2 N501I;N501T;N501V 42;49;59 47;54;64 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. (c) Represent the intra and inter residues bonding network of wild type while (d) (e) and (f) represent the intra and inter residues bonding network of the three mutants N501I, N501T and N501V. 2022 Computers in biology and medicine Figure SARS_CoV_2 N501I;N501T;N501V 170;177;187 175;182;192 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Docking representation of N501I and N501T mutant complexes. 2022 Computers in biology and medicine Figure SARS_CoV_2 N501I;N501T 26;36 31;41 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Docking representation of N501V mutant complexes. 2022 Computers in biology and medicine Figure SARS_CoV_2 N501V 26 31 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. Free Energy Landscape (FEL) of all the complexes i.e., wild type, N501I, N501T and N501V. 2022 Computers in biology and medicine Figure SARS_CoV_2 N501I;N501T;N501V 66;73;83 71;78;88 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The figure represents the binding interface of N501I (A) and N501T (B) complexes along with its stick representation of the key hydrogen interactions. 2022 Computers in biology and medicine Figure SARS_CoV_2 N501I;N501T 47;61 52;66 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. The figure represents the binding interface of N501V complex along with its stick representation of the key hydrogen interactions. 2022 Computers in biology and medicine Figure SARS_CoV_2 N501V 47 52 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. While the right panel shows the binding interface with key hydrogen bonding interactions of the N501V mutant. 2022 Computers in biology and medicine Figure SARS_CoV_2 N501V 96 101 34979405 Computational modelling of potentially emerging SARS-CoV-2 spike protein RBDs mutations with higher binding affinity towards ACE2: A structural modelling study. wild type, N501I, N501T and N501V. 2022 Computers in biology and medicine Figure SARS_CoV_2 N501I;N501T;N501V 11;18;28 16;23;33 34982509 Engineered small extracellular vesicles displaying ACE2 variants on the surface protect against SARS-CoV-2 infection. (c,d) Infectivity of pseudovirus bearing D614G S proteins (n = 3). 2022 Journal of extracellular vesicles Figure SARS_CoV_2 D614G 41 46 S 47 48 34982509 Engineered small extracellular vesicles displaying ACE2 variants on the surface protect against SARS-CoV-2 infection. (e,f) Infectivity of pseudovirus bearing Beta variant S (K417N, E484K, N501Y) proteins (n = 4). 2022 Journal of extracellular vesicles Figure SARS_CoV_2 E484K;N501Y;K417N 64;71;57 69;76;62 S 54 55 34982509 Engineered small extracellular vesicles displaying ACE2 variants on the surface protect against SARS-CoV-2 infection. (g,h) Infectivity of pseudovirus bearing Delta variant S (L452R, E484K, D614G) proteins (n = 4). 2022 Journal of extracellular vesicles Figure SARS_CoV_2 D614G;E484K;L452R 72;65;58 77;70;63 S 55 56 34985974 Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2. (b) Microscope images showing that the HEK293T-hACE2 cells expressed GFP after transduction with lentivirus pseudotyped with the wild-type (WT) SARS-CoV-2 spike protein or the D614G variant. 2022 Applied and environmental microbiology Figure SARS_CoV_2 D614G 176 181 S 155 160 34985974 Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2. (c) Representative flow cytometric analysis evaluating the transduction efficiency of SARS-CoV-2 WT and D614G pseudoviruses compared with two negative-control groups: HEK293T-hACE2 without any transduction and HEK293T transduced with SARS-CoV-2 WT pseudotyped lentivirus. 2022 Applied and environmental microbiology Figure SARS_CoV_2 D614G 104 109 34985974 Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2. After incubation of the pseudovirus with 200 muL of 10 mug/mL fusion protein Nb-CBD or Nb (negative control) immobilized on cellulose paper or free protein with equal concentrations, the titers of wild-type (WT) and D614G pseudoviruses were quantified by transducing HEK293T-hACE2 cells with the remaining viruses in the supernatant. 2022 Applied and environmental microbiology Figure SARS_CoV_2 D614G 216 221 34985974 Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2. Generation of wild-type and D614G pseudoviruses for functional assays by Nb (Ty1)-CBD-functionalized cellulose. 2022 Applied and environmental microbiology Figure SARS_CoV_2 D614G 28 33 34985974 Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2. The flowthrough samples from functionalized RAC columns were used to transduce HEK293T-hACE2 cells to quantify viral titers for WT and D614G SARS-CoV-2 pseudoviruses, respectively. 2022 Applied and environmental microbiology Figure SARS_CoV_2 D614G 135 140 34987509 An Intranasal OMV-Based Vaccine Induces High Mucosal and Systemic Protecting Immunity Against a SARS-CoV-2 Infection. Not shown: six stabilizing prolines in S2 at positions F817P, A892P, A899P, A942P, K986P, and V987P. 2021 Frontiers in immunology Figure SARS_CoV_2 A892P;A899P;A942P;F817P;K986P;V987P 62;69;76;55;83;94 67;74;81;60;88;99 34987509 An Intranasal OMV-Based Vaccine Induces High Mucosal and Systemic Protecting Immunity Against a SARS-CoV-2 Infection. S, signal sequence; NTD, N-terminal domain; RBD, receptor-binding domain; FP, fusion peptide; HR1-HR2, heptad repeat 1 and 2; FC, disrupted S1/S2 furin cleavage site (R682G, R684S, R685S). 2021 Frontiers in immunology Figure SARS_CoV_2 R684S;R685S;R682G 174;181;167 179;186;172 RBD;N;S 44;25;0 47;26;1 34987509 An Intranasal OMV-Based Vaccine Induces High Mucosal and Systemic Protecting Immunity Against a SARS-CoV-2 Infection. The aspartic acid at position 614 in the original HexaPro spike protein was replaced with a glycine (D614G). 2021 Frontiers in immunology Figure SARS_CoV_2 D614G 101 106 S 58 63 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. (A) Schematic of the bivalent D614G/B.1.351_RBD-NP. 2022 Cell reports Figure SARS_CoV_2 D614G 30 35 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. (B) D614G_RBD-specific and B.1.351_RBD-specific IgG antibody titers of serum were determined using ELISA by serial dilution and are represented as the reciprocal of the endpoint serum dilution. 2022 Cell reports Figure SARS_CoV_2 D614G 4 9 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. (B) D614G_RBD-specific and B1.351_RBD-specific IgG antibody titers of serum were determined using ELISA by serial dilution and are represented as the reciprocal of the endpoint serum dilution. 2022 Cell reports Figure SARS_CoV_2 D614G 4 9 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. (B) Representative BIAcore plots of D614G_RBD-NP and B.1.351_RBD-NP bound to hACE2. 2022 Cell reports Figure SARS_CoV_2 D614G 36 41 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. (B) The serum of each rhesus macaque at different times was 10-fold serially diluted and incubated with 500 ffu of authentic SARS-CoV-2 (D614G/B.1.351), followed by incubation with Vero E6 cells. 2022 Cell reports Figure SARS_CoV_2 D614G 137 142 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. (C and D) D614G_RBD- and B.1.351_RBD-specific IgG/IgA titers of immunized BALB/c mice were detected by ELISA. 2022 Cell reports Figure SARS_CoV_2 D614G 10 15 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. (C) The nAbs titer for SARS-CoV-2 pseudovirus (D614G/B.1.351) of vaccinated hACE2 mice by pseudotyped virus neutralization assay, represented as IC50. 2022 Cell reports Figure SARS_CoV_2 D614G 47 52 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. (C) The nAbs titer for the SARS-CoV-2 pseudovirus (D614G/D614/B.1.1.7/B.1.351/P.1/B.1.429/B.1.526/B.1.617.1) of rhesus macaques before and after the third boost with D614G/B.1.351_RBD-NP was determined by pseudotyped virus neutralization assay and is represented as IC50. 2022 Cell reports Figure SARS_CoV_2 D614G;D614D;D614G 166;51;51 171;56;56 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. (C) The serum of each mouse was 10-fold serially diluted and incubated with 500 focus-forming units (ffu) of authentic SARS-CoV-2 (D614G/B.1.351), followed by incubation with Vero E6 cells. 2022 Cell reports Figure SARS_CoV_2 D614G 131 136 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. (D) The serum of each mouse was 10-fold serially diluted and incubated with 500 ffu of authentic SARS-CoV-2 (D614G/B.1.351), followed by incubation with Vero E6 cells. 2022 Cell reports Figure SARS_CoV_2 D614G 109 114 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. (E) Groups of serially diluted serum were examined for nAbs against pseudotyped SARS-CoV-2 (D614G/B.1.351). 2022 Cell reports Figure SARS_CoV_2 D614G 92 97 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. (F) The nAbs titer of each vaccine group for the authentic SARS-CoV-2 (D614G/B.1.351) was determined by FRNT and is represented as half-maximal inhibitory concentration (IC50). 2022 Cell reports Figure SARS_CoV_2 D614G 71 76 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. (G and H) Immunoreactivity of bivalent D614G/B.1.351_RBD-NP for D614G_RBD and B.1.351_RBD, determined by ELISA after storage at various temperatures for 2 weeks (G) or after one to five cycles of freezing and thawing (H). 2022 Cell reports Figure SARS_CoV_2 D614G;D614G 39;64 44;69 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. A third dose of the bivalent D614G/B.1.351_RBD-NP vaccine in rhesus macaques previously vaccinated with two doses of D614G_RBD-NP induces cross-neutralization of viral variants. 2022 Cell reports Figure SARS_CoV_2 D614G;D614G 29;117 34;122 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Five mice in each group were primer-boost-vaccinated with the bivalent D614G/B.1.351_RBD-NP on day 0 and day 28. 2022 Cell reports Figure SARS_CoV_2 D614G 71 76 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Five mice in each group were vaccinated with a single dose of the bivalent D614G/B.1.351_RBD-NP on day 0. 2022 Cell reports Figure SARS_CoV_2 D614G 75 80 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Four rhesus macaques were first vaccinated with primer-boost D614G_RBD-NP on day 0 and day 28 and then vaccinated with bivalent D614G/B.1.351_RBD-NP on day 282. 2022 Cell reports Figure SARS_CoV_2 D614G 128 133 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. FRNT50 of nAbs of authentic SARS-CoV-2 (D614G/B.1.351) was determined by FRNT and plotted as a time-course curve. 2022 Cell reports Figure SARS_CoV_2 D614G 40 45 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Mice were challenged with authentic SARS-CoV-2 (D614G/B.1.351) on day 56. 2022 Cell reports Figure SARS_CoV_2 D614G 48 53 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Protection efficacy of a single dose of the bivalent D614G/B.1.351_RBD-NP vaccine against D614G and (B)1.351 variant infection in hACE2 mice. 2022 Cell reports Figure SARS_CoV_2 D614G;D614G 53;90 58;95 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The bivalent D614G/B.1.351_RBD-NP consists of Sd-ferritin, Gv-D614G_RBD, and Gv-B.1.351_RBD. 2022 Cell reports Figure SARS_CoV_2 D614G;D614G 13;62 18;67 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The bivalent D614G/B.1.351_RBD-NP vaccine elicits a robust immune responses in BALB/c mice and is thermostable and resilient. 2022 Cell reports Figure SARS_CoV_2 D614G 13 18 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The bivalent D614G/B.1.351_RBD-NP vaccine protects against D614G and (B)1.351 variant infection in hACE2 mice. 2022 Cell reports Figure SARS_CoV_2 D614G;D614G 13;59 18;64 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The ratio is 50/50 of D614G_RBD-NP and B.1.351_RBD-NP in bivalent D614G/B.1.351_RBD-NP. 2022 Cell reports Figure SARS_CoV_2 D614G;D614G 66;22 71;27 34998405 Different decay of antibody response and VOC sensitivity in naive and previously infected subjects at 15 weeks following vaccination with BNT162b2. Neutralizing antibody titers (expressed as ID50) against the D614G, B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta) and B.1.298 (Mink) SARS-CoV-2 lineages. 2022 Journal of translational medicine Figure SARS_CoV_2 D614G 61 66 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. H84T-Banana Lectin (BanLec) CAR-NK cells are activated by binding high mannose glycosites that decorate the SARS-CoV-2 envelope. 2021 Frontiers in immunology Figure SARS_CoV_2 H84T 0 4 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. H84T-BanLec CAR-NK cells decrease S-pseudotyped viral infection. 2021 Frontiers in immunology Figure SARS_CoV_2 H84T 0 4 S 34 35 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. H84T-BanLec.4-1BB.zeta CAR expression in human NK cells. 2021 Frontiers in immunology Figure SARS_CoV_2 H84T 0 4 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. UTD: untransduced NK cell lysate, CAR: H84T-BanLec CAR-NK cell lysate. 2021 Frontiers in immunology Figure SARS_CoV_2 H84T 39 43 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Africa VoC; G S494P in dark pink sticks; H the triple mutant E484K_S494P_N501Y detected in the B.1.1.7_UK variant; I N439K, orange sticks, observed in the B.1.141 VoC; J E484Q, light pink sticks; K L452R in dark-blue sticks, observed in the B.1.427/B.1.429 California VoC; L the double mutant E484Q_L452R observed in the B.1.617.1 India VoC; M K417T in teal sticks; N the triple mutant K417T_E484K_N501Y observed in the P.1 Japan/Brazil VoC; O S477N, brown sticks; P the two RBD mutations S477N_E484K, observed in the B.1.620 VoC. 2022 The EPMA journal Figure SARS_CoV_2 E484K;E484Q;E484Q;K417T;K417T;L452R;N439K;S477N;S477N;S494P;E484K;E484K;L452R;N501Y;N501Y;S494P 61;170;293;344;386;198;117;444;489;14;392;495;299;73;398;67 66;175;298;349;391;203;122;449;494;19;397;500;304;78;403;72 RBD;N 475;366 478;367 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. C N501Y, yellow sticks; D E484K, green sticks; E K417N cyan sticks, F the triple mutant N501Y_E484K_K417N, observed in the B.1.351 S. 2022 The EPMA journal Figure SARS_CoV_2 E484K;K417N;N501Y;N501Y;E484K;K417N 26;49;2;88;94;100 31;54;7;93;99;105 S 131 132 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. a, K417N escape scores and corresponding K417N pseudovirus neutralizing IC50 fold change compared to D614G pseudovirus of antibodies within epitope group A. 2022 Nature Figure SARS_CoV_2 D614G;K417N;K417N 101;3;41 106;8;46 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. a, SARS-CoV-2 D614G spike protein structure overlayed with Omicron mutations. 2022 Nature Figure SARS_CoV_2 D614G 14 19 S 20 25 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Annotations on the right side of heat maps represent the pseudovirus neutralizing IC50 fold change (FC) for Omicron and Beta compared to D614G. 2022 Nature Figure SARS_CoV_2 D614G 137 142 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. b, E484K/E484A escape scores and corresponding E484K pseudovirus neutralizing IC50 fold change compared to D614G pseudovirus of antibodies within epitope group C. 2022 Nature Figure SARS_CoV_2 D614G;E484K;E484K;E484A 107;3;47;9 112;8;52;14 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. c-e, The IC50 against D614G (c), Beta (d) and Omicron (e) variants for neutralizing antibodies in each epitope group (n = 66, 26, 57, 27, 39, 32 antibodies for epitope group A, B, C, D, E, F, respectively). 2022 Nature Figure SARS_CoV_2 D614G 22 27 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Fold-change of IC50 (VSV pseudovirus neutralization) compared to D614G by Beta and Omicron (BA.1) are shown for all 247 neutralizing antibodies tested. 2022 Nature Figure SARS_CoV_2 D614G 65 70 35016194 Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Shades of red show the fold change in IC50 compared with D614G for each antibody. 2022 Nature Figure SARS_CoV_2 D614G 57 62 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. D614G is predominant throughout the year with high frequency followed by L54F mutation. 2021 Journal of global infectious diseases Figure SARS_CoV_2 L54F;D614G 73;0 77;5 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. D614G, Q677H and P681H mutations originated during the first half of the year and their appearance was observed throughout the year; L54F, K77M and P812 L mutations emerged during the first half of the year but absent after few months of their appearance. 2021 Journal of global infectious diseases Figure SARS_CoV_2 K77M;L54F;P681H;P812L;Q677H;D614G 139;133;17;148;7;0 143;137;22;154;12;5 35025877 A short plus long-amplicon based sequencing approach improves genomic coverage and variant detection in the SARS-CoV-2 genome. Blue solid arrows point to examples of three mutations, Q57H, G172V and A2A mutations. 2022 PloS one Figure SARS_CoV_2 A2A;G172V;Q57H 72;62;56 75;67;60 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. (C) Schematic diagram of mutations in the D614G, Alpha, Beta, and Gamma variants, where the pentagon represents the amino acid mutations introduced on the pseudotyped virus spike protein in this study. 2022 Journal of medical virology Figure SARS_CoV_2 D614G 42 47 S 173 178 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. (D) The overall structure of Gamma A520S RBD-hACE2. 2022 Journal of medical virology Figure SARS_CoV_2 A520S 35 40 RBD 41 44 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. (E) Superimposition of Gamma A520S RBD in the complex on the Cryo-EM structure of SARS-CoV-2 spike glycoprotein (PDB: 6VSB) suggests that residue 520 in the RBD places in the interface with the adjacent NTD. 2022 Journal of medical virology Figure SARS_CoV_2 A520S 29 34 S;RBD;RBD 93;35;157 111;38;160 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. A fourfold difference was considered significant; the dashed lines in the graph represent a 0.25 or fourfold change compared with strain D614G, respectively. 2022 Journal of medical virology Figure SARS_CoV_2 D614G 137 142 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. A fourfold difference was considered significant; the dashed lines in the graph represent a 0.25- or 4-fold change compared with strain D614G, respectively. 2022 Journal of medical virology Figure SARS_CoV_2 D614G 136 141 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Analysis of the effects of S494P, A520S, and V367F mutations on the spike protein and cell-cell fusion of different mutant strains of pseudotyped viruses. 2022 Journal of medical virology Figure SARS_CoV_2 A520S;S494P;V367F 34;27;45 39;32;50 S 68 73 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. As an example of nomenclature, Alpha+2muts (N439K) represents the first two mutations with the highest mutation frequency introduced on the Alpha variant and the last site added is N439K. 2022 Journal of medical virology Figure SARS_CoV_2 N439K;N439K 181;44 186;49 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Finally, the WT, S494P, A520S, and V367F mutant pseudotyped viruses of the different mutant strains were diluted to the same particle number for an enzymw-linked immunosorbent assay assay to quantify the spike protein on the surface of the pseudotyped viruses. 2022 Journal of medical virology Figure SARS_CoV_2 A520S;S494P;V367F 24;17;35 29;22;40 S 204 209 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Gray was used to indicate the positions of amino acids (V367, P384, T478, L452, S494, A520S, and A522) in the RBD structure. 2022 Journal of medical virology Figure SARS_CoV_2 A520S 86 91 RBD 110 113 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Human ACE2, SARS-CoV-2 WT RBD, and Gamma A520S RBD were colored in green, gray, and magenta, respectively. 2022 Journal of medical virology Figure SARS_CoV_2 A520S 41 46 RBD;RBD 26;47 29;50 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Serially diluted WT RBD, Alpha RBD, Alpha A520S RBD, Beta RBD, Beta A520S RBD, Gamma RBD, and Gamma A520S RBD protein flowed through the chip, and response unit was recorded. 2022 Journal of medical virology Figure SARS_CoV_2 A520S;A520S;A520S 42;68;100 47;73;105 RBD;RBD;RBD;RBD;RBD;RBD;RBD 20;31;48;58;74;85;106 23;34;51;61;77;88;109 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The 15 most commonly observed mutations in the RBD were as follows: N501Y, S477N, N439K, L452R, E484K, K417N, Y453F, S494P, A520S, N501T, T478K, V367F, S477R, P384L, and A522S, which were located at 13 sites in the RBD. 2022 Journal of medical virology Figure SARS_CoV_2 A520S;A522S;E484K;K417N;L452R;N439K;N501T;N501Y;P384L;S477N;S477R;S494P;T478K;V367F;Y453F 124;170;96;103;89;82;131;68;159;75;152;117;138;145;110 129;175;101;108;94;87;136;73;164;80;157;122;143;150;115 RBD;RBD 47;215 50;218 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The 293T cells were transfected with GFP1-7 RLN plasmid and spike mutant plasmids of WT, S494P, A520S, and V367F of different mutant strain variants, and the 293T-ACE2 cells were transfected with GFP8-11 RLC plasmid. 2022 Journal of medical virology Figure SARS_CoV_2 A520S;S494P;V367F 96;89;107 101;94;112 S 60 65 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The Ad5-Spike vaccine (five cases) based on the adenoviral vector, the mRNA-Spike vaccine (four cases), the 2019-nCoV-spike vaccine guinea pig sera (four cases), D614G-spike vaccine guinea pig sera (four cases), (D614G + E484K + N501Y)-spike vaccine guinea pig sera (four cases), and (D614G + K417N + E484K + N501Y)-spike vaccine guinea pig sera (four cases) were inactivated. 2022 Journal of medical virology Figure SARS_CoV_2 D614G;E484K;E484K;K417N;N501Y;N501Y;D614G;D614G 162;221;301;293;229;309;213;285 167;226;306;298;234;314;218;290 S;S;S;S;S;S 8;76;118;168;236;316 13;81;123;173;241;321 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The complex structure of Gamma A520S RBD-hACE2 was superimposed on that of WT RBD-hACE2. 2022 Journal of medical virology Figure SARS_CoV_2 A520S 31 36 RBD;RBD 37;78 40;81 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The dashed lines in the graph represent a fourfold increase or decrease in neutralization capacity compared with strain D614G, respectively. 2022 Journal of medical virology Figure SARS_CoV_2 D614G 120 125 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The dotted graph indicates the change in neutralization for each inoculator serum, with the dashed lines in the graph representing a fourfold increase or decrease in neutralization capacity compared with the D614G strain, respectively. 2022 Journal of medical virology Figure SARS_CoV_2 D614G 208 213 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The EC50 ratio between the variants or possible mutant strains and the reference strain D614G was calculated and analyzed to generate a heat map using Hem I. 2022 Journal of medical virology Figure SARS_CoV_2 D614G 88 93 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The Gamma A520S RBD was colored magenta. 2022 Journal of medical virology Figure SARS_CoV_2 A520S 10 15 RBD 16 19 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The NT50 ratio between the variants or possible mutant strains and the reference strain D614G was calculated and analyzed to generate a heat map using Hem I. 2022 Journal of medical virology Figure SARS_CoV_2 D614G 88 93 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The RLU values, determined for the infected cells by detecting the variants and their possible mutant strains, were compared with the reference strain D614G. 2022 Journal of medical virology Figure SARS_CoV_2 D614G 151 156 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The uppermost and lowermost horizontal dashed lines indicate the threshold lines for a four-fold change in the neutralization level relative to the reference strain D614G. 2022 Journal of medical virology Figure SARS_CoV_2 D614G 165 170 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The variants and mutant strains were first diluted to the same number of viral particles by nucleic acid quantification and then infected with cells, and the RLU values of the infected cells of the variants and their possible mutant strains were compared with the reference strain D614G by an infection assay. 2022 Journal of medical virology Figure SARS_CoV_2 D614G 281 286 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Using D614G as the reference strain, the NT50 ratio of the variants or possible mutant strains relative to the reference strain D614G was calculated and analyzed, and the neutralization mean values for each group were generated by GraphPad Prism 8.0. 2022 Journal of medical virology Figure SARS_CoV_2 D614G;D614G 6;128 11;133 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Using D614G as the reference strain, the relative GFP expression ratio, which represents the differential change in fusion between cells, was calculated. 2022 Journal of medical virology Figure SARS_CoV_2 D614G 6 11 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. By contrast, in the other 15 positive samples we identified the SARS-CoV-2 variants K417N/T, E484K, and N501Y (gray arrows) (Group 2). 2021 Frontiers in public health Figure SARS_CoV_2 E484K;K417N;K417T;N501Y 93;84;84;104 98;91;91;109 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. RAT detection of SARS-CoV-2 variants which contain K417N/T, E484K, and N501Y mutations, from RT-qPCR positive samples with Cq value between 20>=Cq <25, 25>=Cq <30, 30>=Cq <35. 2021 Frontiers in public health Figure SARS_CoV_2 E484K;K417N;K417T;N501Y 60;51;51;71 65;58;58;76 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. BHK21-hACE2 and Vero-E6 Cells were transfected with plasmid vector or plasmids expressing spike proteins of the WT-D614G, Delta, or Omicron variants. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 115 120 S 90 95 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. The average sera neutralization efficiency against the WT-D614G, Delta, Omicron were 80%, 71%, 13%, respectively. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 58 63 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. The half neutralization titer of 24 sera against the WT-D614G, Delta, and Omicron variants, respectively. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 56 61 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. The heatmap of sera neutralization efficiency against the WT-D614G, Delta, and Omicron variants. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 61 66 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. The NT50 titer of the sera collected before or after the vaccine boosting was determined against the WT-D614G(C), the Delta (D), and the Omicron (E). 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 104 109 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Kappa VUM (D) B.1.617.2 Delta VOC and (E, F) Overlap substitutions shown in spike protein P681 H/R; Proline (orange), Histidine (red) and Arginine (green). 2022 Microbial pathogenesis Figure SARS_CoV_2 P681H;P681R 90;90 98;98 S 76 81 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. (a) Representative H&E images of lungs of hamsters infected with 103 TCID50 of BavPat (D614G) strain (n = 6) or the omicron (B.1.1.529) SARS-CoV-2 variant at day 4 post-infection (pi). 2022 Antiviral research Figure SARS_CoV_2 D614G 87 92 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. (b) Cumulative severity score from H&E stained slides of lungs from hamsters infected with the D614G strain or the omicron variant at day 4 pi. 2022 Antiviral research Figure SARS_CoV_2 D614G 95 100 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. (b) Viral RNA levels in the lungs of hamsters infected with 103 TCID50 of BavPat (D614G) strain (n = 6) or the omicron (B.1.1.529) SARS-CoV-2 variant (n = 6) on day 4 post-infection (pi) are expressed as log10 SARS-CoV-2 RNA copies per mg lung tissue. 2022 Antiviral research Figure SARS_CoV_2 D614G 82 87 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. (c) Infectious viral loads in the lungs of hamsters infected with the D614G strain or the omicron variant at day 4 pi are expressed as log10 TCID50 per mg lung tissue. 2022 Antiviral research Figure SARS_CoV_2 D614G 70 75 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. Characterization of the in vivo replication of the omicron SARS-CoV-2 variant versus the ancestral D614G strain. 2022 Antiviral research Figure SARS_CoV_2 D614G 99 104 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. Histopathology of lungs of Syrian hamsters infected with either the D614G strain or the omicron SARS-CoV-2 variant. 2022 Antiviral research Figure SARS_CoV_2 D614G 68 73 35066015 The omicron (B.1.1.529) SARS-CoV-2 variant of concern does not readily infect Syrian hamsters. The lungs of hamsters infected with the ancestral D614G strain (left picture) show significant bronchopneumonia (green arrows), perivascular inflammation with peri-vascular oedema (red arrows) and peri-bronchial inflammation (blue arrows), whereas the lungs of the omicron-infected hamsters (Right picture) appear normal with no peri-bronchial inflammation (blue arrows) or bronchopneumonia. 2022 Antiviral research Figure SARS_CoV_2 D614G 50 55 Bronchopneumonia;Bronchopneumonia 95;374 111;390 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. (a, b) Binding of the antibodies to the RBD carrying the individual mutations (N501Y, N439K, E484K, K417N) and RBD with triple mutation N501Y/E484K/K417N were analysed. 2022 EBioMedicine Figure SARS_CoV_2 E484K;K417N;N439K;N501Y;N501Y;E484K;K417N 93;100;86;136;79;142;148 98;105;91;141;84;147;153 RBD;RBD 40;111 43;114 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. ACE2 is shown in a green cartoon model, RBD as a grey surface model, mutations N439K (within AX677 binding site) and E484K (within AX290 binding site) are shown in red. 2022 EBioMedicine Figure SARS_CoV_2 E484K;N439K 117;79 122;84 RBD 40 43 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. (a) Recombinant WT or P108S of SARS-CoV2 3CLpro were analysed with SDS-PAGE visualizing using CBB staining. 2022 Scientific reports Figure SARS_CoV_2 P108S 22 27 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. (b) The enzymatic activities of SARS-CoV2 3CLpro WT (circle) and P108S (square) were determined using a FRET-based substrate with the cleavage site of SARS CoV-2 3CLpro (Dabcyl-KTSAVLQ SGFRKME-Edans). 2022 Scientific reports Figure SARS_CoV_2 P108S 65 70 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. (c) The kinetic parameters of enzyme activity of 3CLpro WT and P108S were determined using GraphPad Prism 8 software by initial rate measurement of the substrate cleavage. 2022 Scientific reports Figure SARS_CoV_2 P108S 63 68 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. (d) Inhibitory activities of SARS-CoV2 3CLpro WT and P108S by GC376 were analyzed using a FRET-based cleavage assay. 2022 Scientific reports Figure SARS_CoV_2 P108S 53 58 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Deuterium uptake curves for the peptides showing significant differences between WT (black) and P108S (red) proteins were presented. 2022 Scientific reports Figure SARS_CoV_2 P108S 96 101 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. HDX-MS results of SARS CoV-2 3CLpro WT and P108S. 2022 Scientific reports Figure SARS_CoV_2 P108S 43 48 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. HDX-MS showed more protected regions (magenta) and more exposed regions (cyan) in SARS-CoV-2 3CLpro Pro108Ser mutant compared to SARS-CoV-2 3CLpro. 2022 Scientific reports Figure SARS_CoV_2 P108S 100 109 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Multiple sequence alignments homologous proteins of 7 beta-coronaviruses at and around 3 non-synonymous mutations using Molecular Evolutionary Genetic Analysis software (MEGA, https://www.megasoftware.net/) and Microsoft power point 2019: Ser543Pro in the PLpro, Pro108Ser in the 3CLpro, and Ala423Val in the RdRp. 2022 Scientific reports Figure SARS_CoV_2 A423V;P108S;S543P 292;263;239 301;272;248 RdRP 309 313 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Multiple sequence alignments homologous proteins of 7 beta-coronaviruses at and around the non-synonymous mutation Pro151Leu in the nucleocapsid protein using Molecular Evolutionary Genetic Analysis software (MEGA, https://www.megasoftware.net/) and Microsoft power point 2019. 2022 Scientific reports Figure SARS_CoV_2 P151L 115 124 N 132 144 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. SARS-CoV-2 3CLpro P108S is declined its enzymatic activity by structural alteration. 2022 Scientific reports Figure SARS_CoV_2 P108S 18 23 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; 3CLpro, 3 chymotrypsin-like protease; WT, Wuhan-strain type; P108S, Pro108Ser mutant. 2022 Scientific reports Figure SARS_CoV_2 P108S;P108S 122;129 127;138 COVID-19 19 59 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; 3CLpro, 3 chymotrypsin-like protease; WT, Wuhan-strain type; P108S, Pro108Ser-strain type; SDS-PAGE, Sodium dodecyl sulfate-Polyacrylamide gel electrophoresis; CBB, Coomassie Brilliant Blue; FRET, fluorescence resonance energy transfer. 2022 Scientific reports Figure SARS_CoV_2 P108S 122 127 COVID-19 19 59 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. The Kcat/Km value of the P108S mutant enzyme was 42% of that of the WT enzyme, showing 58% reduction. 2022 Scientific reports Figure SARS_CoV_2 P108S 25 30 35079901 Trypsin enhances SARS-CoV-2 infection by facilitating viral entry. S1/S2 FCS represents the S1/S2 furin cleavage site (FCS), which contains multiple basic amino acids (681PRRAR685), and the vertical red bars indicate the R685S mutation in the S1/S2 FCS. 2022 Archives of virology Figure SARS_CoV_2 R685S 156 161 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. (b) Concentrations of antibodies against RBD, D614G, N501Y, E484K, and L452R/E484Q-mutants. 2022 Analytical chemistry Figure SARS_CoV_2 D614G;E484K;L452R;N501Y;E484Q 46;60;71;53;77 51;65;76;58;82 RBD 41 44 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. (c-g) Concentrations of antibodies against RBD, D614G, N501Y, E484K, and L452R/E484Q-mutants of serum 1, serum 2, and serum 3. 2022 Analytical chemistry Figure SARS_CoV_2 D614G;E484K;L452R;N501Y;E484Q 48;62;73;55;79 53;67;78;60;84 RBD 43 46 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. Each test can detect six targets (RBD, D614G, N501Y, E484K, L452R/E484Q-mutants, and 1 blank) of seven samples. 2022 Analytical chemistry Figure SARS_CoV_2 D614G;E484K;L452R;N501Y;E484Q 39;53;60;46;66 44;58;65;51;71 RBD 34 37 35080377 Multiplexed Lab-on-a-Chip Bioassays for Testing Antibodies against SARS-CoV-2 and Its Variants in Multiple Individuals. The receptor-binding domains (RBDs) of SARS-CoV-2 spike protein and its variants (E484K, N501Y, D614G, and L452R/E484Q-mutants) were used as an ELISA antigen to enhance the specificity of our assay. 2022 Analytical chemistry Figure SARS_CoV_2 D614G;L452R;N501Y;E484K;E484Q 96;107;89;82;113 101;112;94;87;118 S;RBD 50;30 55;34 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. (B-D) Comparison of the RLU values of the other 11 pseudoviruses to that of D614G. 2022 Archives of virology Figure SARS_CoV_2 D614G 76 81 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. B.1.1.7 contains the spike (S) protein mutations A570D, D614G, D1118H, H69-V70del, N501Y, P681H, S982A, T716I, and Y145del. 2022 Archives of virology Figure SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I;Y145del 49;63;56;83;90;97;104;115 54;69;61;88;95;102;109;122 S;S 21;28 26;29 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. B.1.258 contains the S protein mutations D614G, N439K, and H69-V70del. 2022 Archives of virology Figure SARS_CoV_2 D614G;N439K 41;48 46;53 S 21 22 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. Dotted lines at x = 0.25 represent a fourfold decrease in neutralization activity compared to D614G, and those at x = 4 represent a fourfold increase in neutralization activity. 2022 Archives of virology Figure SARS_CoV_2 D614G 94 99 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. The neutralization ID50 value for D614G was used as the standard, and neutralization ID50 values were calculated for the different mutant strains of the pseudoviruses and the 11 mAbs. 2022 Archives of virology Figure SARS_CoV_2 D614G 34 39 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. The RLU value of the mutant infection was measured and compared with that of reference strain D614G. 2022 Archives of virology Figure SARS_CoV_2 D614G 94 99 35083577 Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France. (B) Effect of the E484K mutation on the electrostatic surface potential of the RBD. 2022 Archives of virology Figure SARS_CoV_2 E484K 18 23 RBD 79 82 35083577 Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France. (C) Effect of the W152L mutation on the electrostatic surface potential of the NTD (upper panels). 2022 Archives of virology Figure SARS_CoV_2 W152L 18 23 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. Binding antibody response to D614G, following each injection, by SARS-CoV-2 naive status (per-protocol analysis set) 2022 The Lancet. Infectious diseases Figure SARS_CoV_2 D614G 29 34 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. Binding antibody response to D614G, following each injection, by SARS-CoV-2 naive status (per-protocol analysis set). 2022 The Lancet. Infectious diseases Figure SARS_CoV_2 D614G 29 34 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. Neutralising antibody response to D614G, after each injection, by SARS-CoV-2 naive status (per-protocol analysis set) 2022 The Lancet. Infectious diseases Figure SARS_CoV_2 D614G 34 39 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. Neutralising antibody response to D614G, after each injection, by SARS-CoV-2 naive status (per-protocol analysis set). 2022 The Lancet. Infectious diseases Figure SARS_CoV_2 D614G 34 39 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. (A and B) Live virus neutralization comparing WT or Y453F-containg ferret passage 2 (A) or the isogenic reverse genetics-derived WT (D614G) and D614G + Y453F-containing SARS-CoV-2 isolates (B) using N = 6 human convalescent antisera from the first UK wave (~April-June 2020); (A) or n = 10 double-dose BNT162b2 (Pfizer-BioNTech mRNA vaccine) human antisera (B). 2022 Cell reports Figure SARS_CoV_2 D614G;Y453F;Y453F;D614G 144;52;152;133 149;57;157;138 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. (A-C) Human primary airway epithelial cells cultured at air-liquid interface were infected at an MOI of approximately 0.1 with (A) a mixture of parental and ferret-adapted England/2 virus, (B) a mixture of mink-adapted "Cluster 5" virus and a D614G control, or (C) either isogenic WT (D614G) or D614G + Y453F -containing reverse genetics-derived virus isolates. 2022 Cell reports Figure SARS_CoV_2 D614G;D614G;Y453F;D614G 243;295;303;285 248;300;308;290 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. (B-E) RNA (B) and infectious virus (C) shedding dynamics of ferrets directly infected with either WT (orange circles; as previously described in ]) or Y453F (i.e., ferret passage 2; black and white squares) SARS-CoV-2. 2022 Cell reports Figure SARS_CoV_2 Y453F 151 156 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. (B) Maximum-likelihood phylogeny of SARS-CoV-2 genomes sampled from American mink (Neogale vison, formerly Neovison vison), highlighting the spike mutations 69-70, Y453F, F486L, or F486I, N501T, and D614G. 2022 Cell reports Figure SARS_CoV_2 D614G;F486I;F486L;N501T;Y453F 200;182;172;189;165 205;187;177;194;170 S 141 146 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Alpha also known as B.1.1.7; Beta also known as B.1.351; Gamma also known as P.1; Eta also known as B.1.525; Iota also known as B.1.526 + E484K. 2022 Cell reports Figure SARS_CoV_2 E484K 138 143 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Cells in orange indicate changes from WT/D614G. 2022 Cell reports Figure SARS_CoV_2 D614G 41 46 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Passage of SARS-CoV-2 in ferrets results in spontaneous emergence of the mink-associated mutations Y453F and N501T. 2022 Cell reports Figure SARS_CoV_2 N501T;Y453F 109;99 114;104 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Pseudovirus shown contain either D614G (B) or D614 (C). 2022 Cell reports Figure SARS_CoV_2 D614G 33 38 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. The common mink and ferret adaptation, Y453F, attenuates virus replication in primary human airway cells. 2022 Cell reports Figure SARS_CoV_2 Y453F 39 44 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. The spike mutation, Y453F, enhances replication and morbidity in ferrets. 2022 Cell reports Figure SARS_CoV_2 Y453F 20 25 S 4 9 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. D614G mutation. 2022 Computational and structural biotechnology journal Figure SARS_CoV_2 D614G 0 5 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. S939F (A) and D614G (B) mutations occurrence in the five continents of the world from 1 March 2020 to 31 January 2021 by COVID CG. 2022 Computational and structural biotechnology journal Figure SARS_CoV_2 D614G;S939F 14;0 19;5 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. S939F and D614G mutations genomic locations and characteristics by 2019nCoVR. 2022 Computational and structural biotechnology journal Figure SARS_CoV_2 D614G;S939F 10;0 15;5 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. S939F mutation distribution (indicated in yellow) in Europe at the indicated time intervals by GSAID. 2022 Computational and structural biotechnology journal Figure SARS_CoV_2 S939F 0 5 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. S939F mutation. 2022 Computational and structural biotechnology journal Figure SARS_CoV_2 S939F 0 5 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. The distribution of T-cell propensities estimated by NetTepi is not affected by the D614G mutation (p = 0.99 according to the Kolmogorov-Smirnov test) while a significant change is observed for the S939F mutation (p = 0.01 according to the Kolmogorov-Smirnov test). 2022 Computational and structural biotechnology journal Figure SARS_CoV_2 D614G;S939F 84;198 89;203 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. The figure shows the number of highly ranked peptides from the reference and the mutated (D614G and S939F) SARS-CoV-2 spike protein for a set of HLA alleles, estimated with NetTepi as discussed in the Methods section. 2022 Computational and structural biotechnology journal Figure SARS_CoV_2 S939F;D614G 100;90 105;95 S 118 123 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Time (upper panel) and Area (lower panel) frequencies of S939F (B) and D614G (C) mutations by 2019nCoVR are indicated. 2022 Computational and structural biotechnology journal Figure SARS_CoV_2 D614G;S939F 71;57 76;62 35104067 Neutralizing Antibodies and Cytokines in Breast Milk After Coronavirus Disease 2019 (COVID-19) mRNA Vaccination. D614G (B), Alpha (B.1.1.7) (C), Beta (B.1.351) (D), and Gamma (P.1) (E). 2022 Obstetrics and gynecology Figure SARS_CoV_2 D614G 0 5 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. a A schematic diagram showing the SARS-CoV-2 N protein different domains (Upper: control, Lower: mutant) and highlighting the mutation site (R203K and G204R) and the linker region (LKR) containing a serine-arginine rich motif (SR-motif). 2022 Nature communications Figure SARS_CoV_2 G204R;R203K 151;141 156;146 N 45 46 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. b Overview of the three SNPs underlying the N protein R203K/G204R changes. 2022 Nature communications Figure SARS_CoV_2 R203K;G204R 54;60 59;65 N 44 45 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Higher viral loads in samples with R203K/G204R SNPs. 2022 Nature communications Figure SARS_CoV_2 R203K;G204R 35;41 40;46 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. On both plots, lines show the fraction of samples having the R203K/G204R SNPs (red line), having both the R203K/G204R SNPs and the Spike protein N501Y SNP (blue line), and having the Spike protein D614G SNP (green line). 2022 Nature communications Figure SARS_CoV_2 D614G;N501Y;R203K;R203K;G204R;G204R 197;145;61;106;67;112 202;150;66;111;72;117 S;S 131;183 136;188 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Sketch showing part of SR-rich motif of SARS-CoV-2 N protein containing the KR mutation site (R203K and G204R) (Lower). 2022 Nature communications Figure SARS_CoV_2 G204R;R203K 104;94 109;99 N 51 52 35113647 Divergent SARS-CoV-2 Omicron-reactive T and B cell responses in COVID-19 vaccine recipients. Geometric mean titers are indicated above the graphs, fold change reductions are indicated and calculated by dividing the D614G GMT by the Omicron GMT. 2022 Science immunology Figure SARS_CoV_2 D614G 122 127 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. (B) BLI kinetic analysis of N-612-017 affinity-matured subclones against RBD-wild type, RBD-B.1.351, and RBD-L452R. 2022 Cell reports Figure SARS_CoV_2 L452R 109 114 RBD;RBD;RBD 73;88;105 76;91;108 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. (C and D) N-612-017 (C) and N-612-056 (D) against wild-type (D614G), (B)1.1.7, and (B)1.351 variants. 2022 Cell reports Figure SARS_CoV_2 D614G 61 66 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. N-612-017 binding curves against RBD mutants containing E484K were fit with a 1:1 binding model using a shorter dissociation time (30 s) to highlight weakened binding. 2022 Cell reports Figure SARS_CoV_2 E484K 56 61 RBD 33 36 35114688 ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. Each change is supported by weak bootstrap support values, and this hypothesis introduces a non-parsimonious history with respect to an indel at position 482. 2022 Nature Figure SARS_CoV_2 indel 482 136 157 35114688 ACE2 binding is an ancestral and evolvable trait of sarbecoviruses. Mutagenesis data explain the inefficient mouse infectivity of the SARS-CoV-2 B.1.1.7 isolate which incorporates the N501Y RBD mutation, relative to the efficient replication of the mouse-adapted SARS-CoV-2 isolate containing Q498Y or the pathogenic WBP-1 strain containing Q493K and Q498H. 2022 Nature Figure SARS_CoV_2 N501Y;Q493K;Q498H;Q498Y 116;273;283;225 121;278;288;230 RBD 122 125 35115523 Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. Lentiviral reporter pseudoviruses containing Gaussia luciferase were generated with parent (D614G), WNY1, WNY2, WNY3, or WNY4 Spike proteins. 2022 Nature communications Figure SARS_CoV_2 D614G 92 97 S 126 131 35115523 Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. Pseudoviruses containing SARS-COV-2 Spike with N501Y/A570D were used as a control as this is known to be capable of infecting rodent cells. 2022 Nature communications Figure SARS_CoV_2 N501Y;A570D 47;53 52;58 S 36 41 35115523 Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. WNY1 = E484A/F486P/S494P/Q498Y/H519N/F572N, WNY2 = Q493K/S494P/Q498Y/H519N/T572N, WNY3 = K417T/K444T/E484A/F590Y/Q498H, WNY4 = K417T/N439K/K444N/Y449R/L452R/N460K/S477N/Delta484/F486V/S494T/G496V/Q498Y/N501T/G504D/505H/H519Q. 2022 Nature communications Figure SARS_CoV_2 E484A;K417T;K417T;Q493K;E484A;F486P;F486V;F572N;F590Y;G496V;G504D;H519N;H519N;H519Q;K444N;K444T;L452R;N439K;N460K;N501T;Q498H;Q498Y;Q498Y;Q498Y;S477N;S494P;S494P;S494T;T572N;Y449R 7;89;127;51;101;13;178;37;107;190;208;31;69;219;139;95;151;133;157;202;113;25;63;196;163;19;57;184;75;145 12;94;132;56;106;18;183;42;112;195;213;36;74;224;144;100;156;138;162;207;118;30;68;201;168;24;62;189;80;150 35123044 Clinical and genomic data of sars-cov-2 detected in maternal-fetal interface during the first wave of infection in Brazil. Tridimensional structure of MT21770/2020 (A) and MT21774/2020 (B) Spike protein (grey) in complex with ACE2 receptor (green) showing the receptor binding domain (RBD) mutation F490S (blue) and the S1 mutation D614G (yellow). 2022 Microbes and infection Figure SARS_CoV_2 D614G;F490S 209;176 214;181 RBD;S;RBD 137;66;162 160;71;165 35123263 The function of SARS-CoV-2 spike protein is impaired by disulfide-bond disruption with mutation at cysteine-488 and by thiol-reactive N-acetyl-cysteine and glutathione. Disulfide bridges between Cys-480 and -488 are indicated.(C) C488A mutant spike expression did not induce syncytium formation. 2022 Biochemical and biophysical research communications Figure SARS_CoV_2 C488A 61 66 S 74 79 35123263 The function of SARS-CoV-2 spike protein is impaired by disulfide-bond disruption with mutation at cysteine-488 and by thiol-reactive N-acetyl-cysteine and glutathione. Expression of Wuhan type and C488A mutant spike proteins (Green signal) in Vero cells were probed in non-permeabilized cells. 2022 Biochemical and biophysical research communications Figure SARS_CoV_2 C488A 29 34 S 42 47 35123263 The function of SARS-CoV-2 spike protein is impaired by disulfide-bond disruption with mutation at cysteine-488 and by thiol-reactive N-acetyl-cysteine and glutathione. The lack of giant green adherent cells after treatment with the C488A mutant spike indicate a lack of cell-cell fusion between C488A mutant spike-expressing 293T cells and VeroE6/TMPRSS2 cells. 2022 Biochemical and biophysical research communications Figure SARS_CoV_2 C488A;C488A 64;127 69;132 S;S 77;140 82;145 35126106 Antidepressant and Antipsychotic Drugs Reduce Viral Infection by SARS-CoV-2 and Fluoxetine Shows Antiviral Activity Against the Novel Variants in vitro. Treatment with fluoxetine (10 muM, 24 h) significantly reduced the luciferase reporter activity in HEK293T-ACE2-TMPRSS2 cells infected with (A) WT (grey, n = 16), N501Y (blue, n = 18), K417N (red, n = 18), (B) E484K (green, n = 8-9) and (C) triple mutant (N501Y/K417N/E484K, orange, n = 13-16), viral particles. 2021 Frontiers in pharmacology Figure SARS_CoV_2 E484K;K417N;N501Y;N501Y;E484K;K417N 210;185;163;256;268;262 215;190;168;261;273;267 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. (a) Black: WT-caveolin-1, (b) Red: D155Y-caveolin-1 and (c) Green: S171L-caveolin-1. 2022 Computational and structural biotechnology journal Figure SARS_CoV_2 D155Y;S171L 35;67 40;72 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. Black, red and green lines denote WT, D155Y and S171L, respectively. 2022 Computational and structural biotechnology journal Figure SARS_CoV_2 D155Y;S171L 38;48 43;53 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. The different interactomes are shown for (a) WT, (b) D155Y and (c) S171L. 2022 Computational and structural biotechnology journal Figure SARS_CoV_2 D155Y;S171L 53;67 58;72 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. The global distribution of D155Y and S171L substitutions across the continents have been shown in blue and red respectively in (c). 2022 Computational and structural biotechnology journal Figure SARS_CoV_2 D155Y;S171L 27;37 32;42 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. (b) Comparison of experimental CT-P59 IC50 fold change (reduction) and predicted BFE changes induced by mutations L452R and T478K. 2022 ACS infectious diseases Figure SARS_CoV_2 L452R;T478K 114;124 119;129 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. (c) Comparison of predicted BFE changes and relative luciferase units for pseudovirus infection changes of ACE2 and S protein complex induced by mutations L452R and N501Y. 2022 ACS infectious diseases Figure SARS_CoV_2 L452R;N501Y 155;165 160;170 S 116 117 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Most mutations, except for vaccine-resistant Y449H and Y449S, strengthen the RBD binding with ACE2. 2022 ACS infectious diseases Figure SARS_CoV_2 Y449H;Y449S 45;55 50;60 RBD 77 80 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Notably, there are two blues lines in the panel of FR due to the same frequency of [K417N, E484K, N501Y] and [E484K, N501Y]. 2022 ACS infectious diseases Figure SARS_CoV_2 E484K;N501Y;N501Y;E484K;K417N 91;98;117;110;84 96;103;122;115;89 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. The cyan line is for the RBD comutation [L452Q, F490S] on the Lambda variant, and the other comutations are marked by light gray lines. 2022 ACS infectious diseases Figure SARS_CoV_2 F490S;L452Q 48;41 53;46 RBD 25 28 35133792 Emerging Vaccine-Breakthrough SARS-CoV-2 Variants. Y449S and K417N are highly disruptive to antibodies. 2022 ACS infectious diseases Figure SARS_CoV_2 K417N;Y449S 10;0 15;5 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. b Cryo-EM density maps for the Kappa + Q484A and Kappa + Q484I mutated S proteins. 2022 Nature communications Figure SARS_CoV_2 Q484A;Q484I 39;57 44;62 S 71 72 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. c SARS-CoV-2 amino acid sequence box plots for the wild-type (D614G) and B.1.617 sub-lineages. 2022 Nature communications Figure SARS_CoV_2 D614G 62 67 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The E484 surface potential was generated using the previously reported wild-type (D614G) + ACE2 focus-refined atomic model. 2022 Nature communications Figure SARS_CoV_2 D614G 82 87 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The K484 surface potential was generated using the previously reported D614G + N501Y + E484K focus-refined atomic model. 2022 Nature communications Figure SARS_CoV_2 D614G;E484K;N501Y 71;87;79 76;92;84 35136839 Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike. T500S mutation only replaced the larger structure of THR with SER but mode it convenient to form H-bond with ACE2-TYR41 due to presence of same -OH group (b) and stabilized the ACE2-CUT4 mutant binding. 2022 Translational medicine communications Figure SARS_CoV_2 T500S 0 5 35139368 Long-term, infection-acquired immunity against the SARS-CoV-2 Delta variant in a hamster model. Fold-changes in neutralization titers for the Delta variant (B; indicated in parentheses) using the same vaccine serum samples compared against the HP095 S-D614G virus. 2022 Cell reports Figure SARS_CoV_2 D614G 156 161 S 154 155 35139368 Long-term, infection-acquired immunity against the SARS-CoV-2 Delta variant in a hamster model. Neutralization assays were performed once with an isolate of SARS-CoV-2 with only the D614G mutation in the spike protein (HP095 S-614G) or with an isolate of the Delta variant. 2022 Cell reports Figure SARS_CoV_2 D614G 86 91 S;S 108;129 113;130 35140483 SARS-CoV-2 E484K Mutation Narrative Review: Epidemiology, Immune Escape, Clinical Implications, and Future Considerations. E484K Global Presence Rate. 2022 Infection and drug resistance Figure SARS_CoV_2 E484K 0 5 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. The nsSNV N:S235F did not generate any binder (Supplementary Table S2 and Supplementary Table S1). 2022 Infection, genetics and evolution Figure SARS_CoV_2 S235F 12 17 N 10 11 35151002 Rapid biosensing SARS-CoV-2 antibodies in vaccinated healthy donors. (C) Standard binding curves of the FO-BLI biosensors for anti-RBD BAbs, anti-S-ECD and anti-RBD N501Y in 100-fold diluted serum, respectively. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 N501Y 96 101 RBD;RBD;S 62;92;77 65;95;78 35151002 Rapid biosensing SARS-CoV-2 antibodies in vaccinated healthy donors. The BAbs are specific towards RBD, full length protein S-ECD and RBD mutation N501Y. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 N501Y 78 83 RBD;RBD;S 30;65;55 33;68;56 35155280 The Impact of Accumulated Mutations in SARS-CoV-2 Variants on the qPCR Detection Efficiency. (A, B) Ct values for testing of the standard plasmid and the G28916T mutant plasmid using CP3 and CP4 by qPCR. 2022 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 G28916T 61 68 35155280 The Impact of Accumulated Mutations in SARS-CoV-2 Variants on the qPCR Detection Efficiency. The G28916T mutation in the Delta variant severely affected the detection efficiency and detection limit of the primer/probe set of CP4 and CP5. 2022 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 G28916T 4 11 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. For the other residues, including the case of the mutation S:T1117I, no drastic effects are predicted according to the correlation metrics which are presented with gray connections. 2022 Gene reports Figure SARS_CoV_2 T1117I 61 67 S 59 60 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. In addition, B.1.1.389 is the only S:T1117I-carrying lineage with a relatively high prevalence of 22% in a specific location (Costa Rica), unlike other lineages with a prevalence <0.5% in other countries. 2022 Gene reports Figure SARS_CoV_2 T1117I 37 43 S 35 36 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. Phylogenetic tree of SARS-CoV-2 genome sequence carrying the mutation T1117 in the spike (S:T1117I) of all around the world. 2022 Gene reports Figure SARS_CoV_2 T1117I 92 98 S;S 83;90 88;91 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. The B.1.1.389 was the only lineage that carries the S:T1117I as a characteristic mutation (marker for the lineage), unlike the other groups in which this mutation is not widely found among the genomes of the lineage. 2022 Gene reports Figure SARS_CoV_2 T1117I 54 60 S 52 53 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. The drug was docked into the HR1 region of S2 domain in the spike, using the WT or the mutated (S:D614G and S:T1117I) proteins. 2022 Gene reports Figure SARS_CoV_2 D614G;T1117I 98;110 103;116 S;S;S 60;96;108 65;97;109 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. The lineage is characterized by the presence of eight mutations including two in the spike, the D614G and the T1117I variants. 2022 Gene reports Figure SARS_CoV_2 D614G;T1117I 96;110 101;116 S 85 90 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. The most impacted region (residues with orange connections) are part of the RBD (position 319-541), including the case of the mutation N501Y. 2022 Gene reports Figure SARS_CoV_2 N501Y 135 140 RBD 76 79 35156767 High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. Residues corresponding to Spike protein mutations T19R, T478K, and P681R are missing from the structure of the Spike protein and hence not shown here. 2022 Molecular systems biology Figure SARS_CoV_2 P681R;T19R;T478K 67;50;56 72;54;61 S;S 26;111 31;116 35164548 Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. 293T cells were transfected with plasmids harboring ORF3a wild type (WT), DeltaG188, or Q57H mutant variant. 2022 mBio Figure SARS_CoV_2 Q57H 88 92 ORF3a 52 57 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. (A to D) Free-energy models of parental SD614 (A) and variants SG614 (B), SAlpha (C), and SAlpha+E484K (D). 2022 mBio Figure SARS_CoV_2 E484K 97 102 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. (C) Domain organization of the parental full-length SARS-CoV-2 spike protein with D614G and E484K mutations. 2022 mBio Figure SARS_CoV_2 D614G;E484K 82;92 87;97 S 63 68 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. (C) Representative fluorescence traces (LD555, green; LD655, red) and quantified FRET traces of a single ligand-free E484K-carrying SAlpha variant (SAlpha+E484K) on lentivirus particles. 2022 mBio Figure SARS_CoV_2 E484K;E484K 117;155 122;160 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. (D) FRET histogram (left) and TDP (right) of ligand-free SAlpha+E484K on lentivirus particles. 2022 mBio Figure SARS_CoV_2 E484K 64 69 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. D614G and E484K substitutions render S on the virus in favor of RBD-up open conformations, which are slower in temporal transitions. 2022 mBio Figure SARS_CoV_2 E484K;D614G 10;0 15;5 RBD;S 64;37 67;38 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. D614G substitution shifts the conformational landscape of unbound spike from the ground state to asymmetrically configurated intermediate states. 2022 mBio Figure SARS_CoV_2 D614G 0 5 S 66 71 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. E484K stabilizes the SAlpha variant toward RBD-up conformations. 2022 mBio Figure SARS_CoV_2 E484K 0 5 RBD 43 46 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. The ligand-free D614G- and E484K-carrying spikes are dominated by the intermediate-FRET state (one/two-RBD-up), which exhibits the lowest relative free energy among all four FRET states. 2022 mBio Figure SARS_CoV_2 D614G;E484K 16;27 21;32 S;RBD 42;103 48;106 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. The bar graph described the prevalence of B.1.1.7 (Alpha), E484K and the other forms of mutation found in Hiroshima Japan. 2022 Scientific reports Figure SARS_CoV_2 E484K 59 64 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. The other forms of mutation include single mutations of N501S, I584V, R481K, F515L, P521L, T553S, N606S, A609G, double mutation of K557E and Q613R, and triple mutation of L513F, Q580R and V615A. 2022 Scientific reports Figure SARS_CoV_2 A609G;F515L;I584V;K557E;L513F;N501S;N606S;P521L;Q580R;Q613R;R481K;T553S;V615A 105;77;63;131;171;56;98;84;178;141;70;91;188 110;82;68;136;176;61;103;89;183;146;75;96;193 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. The red color represents B.1.1.7 (Alpha), the orange color shows E484K mutation, the green color for the other forms of mutation and the blue color for those having no mutation at targeted spike region. 2022 Scientific reports Figure SARS_CoV_2 E484K 65 70 S 189 194 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. Analysis of the maximum clade credibility (MCC) tree in the research samples and the Indonesian samples obtained from GISAID data showed the formation of five clusters from the FCS region, with S680P and Q677H in the same cluster. 2022 International microbiology Figure SARS_CoV_2 Q677H;S680P 204;194 209;199 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. maximum likelihood (ML) tree from furin cleavage site (FCS) region of research samples (red dot) with several FCS SARS-CoV-2 strains originating from the GeneBank (black dots were originated from Indonesia and blue dots were from another country) showed 4 different mutations in the FCS region, Q675H, Q677H, one mutation near the furin cleavage PRRAR was S680P, and one silent mutation in 23,557 C > T. 2022 International microbiology Figure SARS_CoV_2 Q675H;Q677H;S680P 295;302;356 300;307;361 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. The D614G mutant variant has been found in 25 provinces in Indonesia based on this study and GISAID data. 2022 International microbiology Figure SARS_CoV_2 D614G 4 9 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. The geographical distribution of the D614G variants reported in Indonesia from April 2020 to January 2021. 2022 International microbiology Figure SARS_CoV_2 D614G 37 42 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. The location of the D614G mutant variant reported in Indonesia from April 2020 to January 2021. 2022 International microbiology Figure SARS_CoV_2 D614G 20 25 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. The phylodynamic of D614G mutant in the Special Region of Yogyakarta and Central Java provinces. 2022 International microbiology Figure SARS_CoV_2 D614G 20 25 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. The proportion of D614G variant in Indonesia based on this study and GISAID data. 2022 International microbiology Figure SARS_CoV_2 D614G 18 23 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. (A) Schematic representations of the SARS-CoV-2 variant spike proteins tested are shown, including D614G, Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529). 2022 Science translational medicine Figure SARS_CoV_2 D614G 99 104 S 56 61 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. (C to G) Lentivirus pseudotyped with SARS-CoV-2 spike protein from D614G (C), Alpha (D), Beta (E), Delta (F), and Omicron (G) were neutralized with serum samples from health care workers (HCWs) (n = 48 biological replicates) collected pre-vaccination (Pre), post-vaccination with a first mRNA vaccine dose (Post 1st), post-vaccination with a second mRNA vaccine dose (Post 2nd), and six months post second dose (Six Months). 2022 Science translational medicine Figure SARS_CoV_2 D614G 67 72 S 48 53 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. (H to L) Log10-transformed NT50 values against D614G (H), Alpha (I), Beta (J), Delta (K), and Omicron (L) variants were plotted against days post-second vaccine dose of sample collection (n = 96 biological replicates). 2022 Science translational medicine Figure SARS_CoV_2 D614G 47 52 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. Media was harvested from infected cells 48 hours after infection and assayed for Gaussia luciferase activity to determine the relative infectivity of each variant pseudotyped virus; infectivity was measured as luminescence signal relative to D614G signal, relative units (ru). 2022 Science translational medicine Figure SARS_CoV_2 D614G 242 247 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. Significance relative to D614G was determined by one-way ANOVA with Bonferroni's correction (n >= 3 biological replicates); error bars represent means +- standard error. 2022 Science translational medicine Figure SARS_CoV_2 D614G 25 30 35168024 Development of SARS-CoV-2 variant protein microarray for profiling humoral immunity in vaccinated subjects. a The amino acid sequences of the ECD of spike proteins from wild type SARS-CoV-2 and their variants, including D614G, B.1.1.7, B.1.351, P.1, B.1.617, B.1.617.1, B.1.617.2, and B.1.617.3. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 D614G 112 117 S 41 46 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. e Zoomed-in view of the S-ACE2 interaction interface, showing the side chain densities of the substituted L452R and T478K were well resolved. 2022 Nature communications Figure SARS_CoV_2 L452R;T478K 106;116 111;121 S 24 25 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. (B) N501Y target CT values against E gene CT values. 2022 Microbiology spectrum Figure SARS_CoV_2 N501Y 4 9 E 35 36 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Scatterplot of N501 and N501Y SNP rRT-PCR target CT values against E gene CT values showing strong linear correlation. 2022 Microbiology spectrum Figure SARS_CoV_2 N501Y 24 29 E 67 68 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The N501 target is shown in red, and the N501Y target is shown in blue; N501, r = 0.99; N501Y, r = 0.96. 2022 Microbiology spectrum Figure SARS_CoV_2 N501Y;N501Y 41;88 46;93 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. (B) Genetic divergence of the C29197T clade, which was made up of both B.1.1.222 variants and B.1.1.519 variants in February before being resolved in April as containing exclusively variants classified as B.1.1.519. 2022 PloS one Figure SARS_CoV_2 C29197T 30 37 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. Nucleotide T at position 29197 denotes the mutation of interest, also referred to as C29197T mutants, highlighted in yellow. 2022 PloS one Figure SARS_CoV_2 C29197T 85 92 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. (A) Linearity of the anti-WT-RDB and anti-N501Y-RBD detected in the convalescent sera with a slope of 1.087 (r2 = 0.927). 2022 Scientific reports Figure SARS_CoV_2 N501Y 42 47 RBD 48 51 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. (C) Linear regression analysis of the ACE2 bound the WT and N501Y RBD detected using the COVID-19 convalescent sera with a slope of 3.99 (r2 = 0.896, N = 41). 2022 Scientific reports Figure SARS_CoV_2 N501Y 60 65 RBD 66 69 COVID-19 89 97 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. (C) Vaccinated blood samples more effective than convalescent ones to inhibit N501Y RBD in ACE2 binding (P < 0.0001). 2022 Scientific reports Figure SARS_CoV_2 N501Y 78 83 RBD 84 87 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. (D) Antibody concentration-dependent inhibition of N501Y RBD and ACE2 binding with blood samples from natural immunity (r2 = 0.926) and mRNA vaccination (r2 = 0.823). 2022 Scientific reports Figure SARS_CoV_2 N501Y 51 56 RBD 57 60 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. (D) N501Y RBD have much higher absolute ACE2 binding than the WT RBD in the presence of neutralizing convalescent sera (P < 0.0001, N = 41). 2022 Scientific reports Figure SARS_CoV_2 N501Y 4 9 RBD;RBD 10;65 13;68 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. Comparison of antibody levels and neutralization activities against both the wildtype RBD and N501Y RBD proteins with convalescent sera. 2022 Scientific reports Figure SARS_CoV_2 N501Y 94 99 RBD;RBD 86;100 89;103 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. mRNA vaccine far more effective than natural immunity in neutralizing N501Y RBD mutant in ACE2 binding. 2022 Scientific reports Figure SARS_CoV_2 N501Y 70 75 RBD 76 79 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. The convalescent sera had specific neutralizing activity against N501Y-RBD (P < 0.0001). 2022 Scientific reports Figure SARS_CoV_2 N501Y 65 70 RBD 71 74 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. (a) Heatmap shows the expression levels of 48 genes significantly induced by variants with the E484K mutation as compared to Non-COVID controls. 2022 Scientific reports Figure SARS_CoV_2 E484K 95 100 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. (d) Heatmaps showing relative fold change of 48 signature genes for the E484K mutation. 2022 Scientific reports Figure SARS_CoV_2 E484K 72 77 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Distinct immune transcriptome signature in COVID-19 patients infected by different SARS-CoV-2 variants carrying the E484K mutation. 2022 Scientific reports Figure SARS_CoV_2 E484K 116 121 COVID-19 43 51 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. Two-dimensional (2D) diagrams of heparin-RBD interactions for (A) E484K, (B) N501Y, (C) L452R, (D) E484Q, (E) L452R-E484Q, (F) K417N-E484K-N501Y, and (G) K417T-E484K-N501Y. 2022 Process biochemistry (Barking, London, England) Figure SARS_CoV_2 E484K;E484Q;K417N;K417T;L452R;L452R;N501Y;E484K;E484K;E484Q;N501Y;N501Y 66;99;127;154;88;110;77;133;160;116;139;166 71;104;132;159;93;115;82;138;165;121;144;171 RBD 41 44 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. Two-dimensional (2D) diagrams of RBD/ACE2 interactions in the presence of heparin for (A) L452R-E484Q, (B) K417N-E484K-N501Y, and (C) K417T-E484K-N501Y. 2022 Process biochemistry (Barking, London, England) Figure SARS_CoV_2 K417N;K417T;L452R;E484K;E484K;E484Q;N501Y;N501Y 107;134;90;113;140;96;119;146 112;139;95;118;145;101;124;151 RBD 33 36 35194375 In silico investigations of heparin binding to SARS-CoV-2 variants with a focus at the RBD/ACE2 interface. Two-dimensional (2D) diagrams of RBD/ACE2 interactions in the presence of heparin for (A) N501Y, (B) L452R (C) E484Q, and (D) E484K. 2022 Process biochemistry (Barking, London, England) Figure SARS_CoV_2 E484K;E484Q;L452R;N501Y 126;111;101;90 131;116;106;95 RBD 33 36 35194675 Misidentification of the SARS-CoV-2 Mu variant using commercial mutation screening assays. (a) Routine workflow before detection of Mu variants with the K417N mutation. 2022 Archives of virology Figure SARS_CoV_2 K417N 62 67 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Arrows indicate the native position of variant mutations N679K and P681H/R. 2022 Microbiology spectrum Figure SARS_CoV_2 N679K;P681H;P681R 57;67;67 62;74;74 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Maximum likelihood phylogenetic tree of P.1 Amazonian sequences and P.1+NTDdel, P.1+N679K, and P.1+P681H sequences detected outside Amazonas. 2022 Microbiology spectrum Figure SARS_CoV_2 N679K;P681H 84;99 89;104 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Temporal structure and phylogeographic reconstruction of the P.1+NTDdel, P.1+N679K, and P.1+P681H clades. 2022 Microbiology spectrum Figure SARS_CoV_2 N679K;P681H 77;92 82;97 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. (A) VOI (K417T and P681H) and VOC (DeltaHV69-79, K417N, L452R, E484K, E484Q, N501Y, and P681R). 2022 Microbiology spectrum Figure SARS_CoV_2 E484K;E484Q;K417N;L452R;N501Y;P681H;P681R;K417T 63;70;49;56;77;19;88;9 68;75;54;61;82;24;93;14 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. Yellow, DeltaHV69-70; light violet, K417N and 417T; green, L452R; brown, E484K and E484Q; gray, N5011Y; and pink, P681H and P681R. 2022 Microbiology spectrum Figure SARS_CoV_2 E484K;E484Q;K417N;L452R;N5011Y;P681H;P681R 73;83;36;59;96;114;124 78;88;41;64;102;119;129 35197485 An adjuvanted subunit SARS-CoV-2 spike protein vaccine provides protection against Covid-19 infection and transmission. Viral neutralizing antibodies were assessed against wild-type D614G (c) and delta variant (d) viruses. 2022 NPJ vaccines Figure SARS_CoV_2 D614G 62 67 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. Q498H substitution increased the binding affinity between receptor-binding domain (RBD) and murine angiotensin-converting enzyme 2 (mACE2). 2022 Frontiers in immunology Figure SARS_CoV_2 Q498H 0 5 RBD 83 86 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. (A) Distribution of lineages of SARS-CoV-2 D614G variant from Malaysia deposited in GISAID until July 5, 2021 (n = 1356). 2022 PloS one Figure SARS_CoV_2 D614G 43 48 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. (A) Nextstrain clade distribution (inset) of 986 complete genomes of Malaysia SARS-CoV-2 D614G variant (filled circles) (B) Nextstrain clade and lineage distribution (inset) of the Pahang SARS-CoV-2 D614G variants (filled circle). 2022 PloS one Figure SARS_CoV_2 D614G;D614G 89;199 94;204 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. (A) Nextstrain clade mutation analysis (vertical bars) of 986 Malaysian SARS-CoV-2 genomes, where Pahang SARS-CoV-2 D614G variants are highlighted in the box. 2022 PloS one Figure SARS_CoV_2 D614G 116 121 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. (B) Donut diagram showing clade distribution of D614G variants from Malaysia deposited in GISAID until July 19, 2021 (C) Lineages clustered in clade GH (D) Lineages clustered in clade G. 2022 PloS one Figure SARS_CoV_2 D614G 48 53 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Nonsynonymous mutations in the spike protein of Malaysian SARS-CoV-2 D614G variants. 2022 PloS one Figure SARS_CoV_2 D614G 69 74 S 31 36 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Note the presence of unique mutation at G1223C in only Pahang SARS-CoV-2 D614G variants (B) Enlarged view of the Pahang SARS-CoV-2 D614G variants box where amino acid substitutions are annotated in the different regions of spike protein, schematically represented at bottom. 2022 PloS one Figure SARS_CoV_2 D614G;D614G;G1223C 73;131;40 78;136;46 S 223 228 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Phylogenetic tree of 986 complete genomes of Malaysia SARS-CoV-2 D614G variants in 2021. 2022 PloS one Figure SARS_CoV_2 D614G 65 70 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Please see S2 File for the fully annotated tree (C) Phylogenetic relationship of the Pahang SARS-CoV-2 D614G variants (blue branches) with the selected neighbouring representatives (in Nextstrain clade tree) of SARS-CoV-2 genome sequences of African (green branches), Indonesian (red branches) and Malaysian lineages (yellow branches). 2022 PloS one Figure SARS_CoV_2 D614G 103 108 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. SARS-CoV-2 D614G variant lineages and clades distribution in Malaysia. 2022 PloS one Figure SARS_CoV_2 D614G 11 16 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. (B-G) 293T cells were transfected with the indicated full-length Spike from different SARS-CoV-2 variants (D614G in B, Alpha in C, Beta in D, Gamma in E, Delta in F, and Omicron in G) and stained with the CV3-25 Ab or with plasma collected 3 weeks (V3) or 4 months (V4) after a second dose administered with a 16-week interval. 2022 Cell reports Figure SARS_CoV_2 D614G 107 112 S 65 70 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. (B) 293T cells were transfected with the full-length Spike from different SARS-CoV-2 variants (D614G, Beta, Delta, and Omicron) and stained with the CV3-25 Ab or with plasma from naive donors who received a short (4 weeks, yellow) or long (16 weeks, red) interval between doses collected 3 weeks after the second dose (V3) and analyzed by flow cytometry. 2022 Cell reports Figure SARS_CoV_2 D614G 95 100 S 53 58 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. (C) Neutralizing activity was measured by incubating pseudoviruses bearing indicated SARS-CoV-2 Spikes (D614G, Beta, Delta, and Omicron), with serial dilutions of plasma for 1 h at 37 C before infecting 293T-ACE2 cells. 2022 Cell reports Figure SARS_CoV_2 D614G 104 109 S 96 102 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. Physicochemical modifications of mutations in the B.1.91 lineage and RBD region (C379W, Y380Q, V395A). 2022 Diagnostic microbiology and infectious disease Figure SARS_CoV_2 V395A;Y380Q;C379W 95;88;81 100;93;86 RBD 69 72 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. The neighbor residues C379 and Y380 are depicted together, while the V395* is buried and not perceptible at the surface. 2022 Diagnostic microbiology and infectious disease Figure SARS_CoV_2 V395X 69 74 35221043 Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant. Arrows indicate the deletion on the Spike protein at nucleotide positions 22029/71 (DeltaE156/DeltaF157), and representative mutations at positions 22917 (L452R), 22995 (T478K) and 24410 (D950N) of B.1.617.2 (Delta) variant (A), and the corresponding deletion and mutations corresponding to B.1.1.7 (Alpha) variant (B). 2022 Pathology Figure SARS_CoV_2 D950N;L452R;T478K 188;155;170 193;160;175 S 36 41 35223905 Molecular and Epidemiological Characterization of Emerging Immune-Escape Variants of SARS-CoV-2. Since these nAbs are treated as a cocktail, they are considered effective if the EC50 of either antibody is equivalent to or lower than that of the D614G control. 2022 Frontiers in medicine Figure SARS_CoV_2 D614G 148 153 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. Hierarchical relationship between sequenced B.1.311 genomes related to this transmission chain, Excerpt from phylogenetic tree showing acquisition of the E484K encoding mutation (G23012A) on the branch leading to this cluster (P3, P5, P6). 2022 Diagnostic microbiology and infectious disease Figure SARS_CoV_2 E484K;G23012A 154;179 159;186 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. Validation of rapid Taqman SNP genotyping assay for the G23012A polymorphism, Clear discrimination between the G allele (encoding E at Spike:484) and the A allele (encoding K at Spike:484) is shown. 2022 Diagnostic microbiology and infectious disease Figure SARS_CoV_2 G23012A 56 63 S;S;E 135;178;130 140;183;131 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. (A) ADCC of monoclonal antibodies CR3022, P2B-2FB, and palivizumab shown as RLU of signaling through FcgammaRIIIa expressing cells and crosslinking of original (white) or Beta (red) (K417N, E484K, and N501Y) RBD protein. 2022 Cell reports. Medicine Figure SARS_CoV_2 E484K;N501Y;K417N 190;201;183 195;206;188 RBD 208 211 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. (B and C) (B) IgA and (C) IgG-binding levels by ELISA of wave 1 or wave 2 samples against the original (D614G) (white) or Beta (red) spike. 2022 Cell reports. Medicine Figure SARS_CoV_2 D614G 104 109 S 133 138 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. (B) ADCC of monoclonal antibodies 4A8 and palivizumab against original (white) or Beta (red; L18F, D80A, D215G, 242-244 del) NTD protein. 2022 Cell reports. Medicine Figure SARS_CoV_2 D215G;D80A;L18F 105;99;93 110;103;97 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. (B) Fold difference of functions against Beta relative to the original variant for wave 1 and 2 samples where the dotted line indicates no change between variants (red = Beta > D614G; white = D614G < Beta). 2022 Cell reports. Medicine Figure SARS_CoV_2 D614G;D614G 177;192 182;197 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. (D) Neutralization of original (D614G) or Beta pseudoviruses by wave 1 and 2 plasma. 2022 Cell reports. Medicine Figure SARS_CoV_2 D614G 32 37 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. The percentage of total SARS-CoV-2 sequences over time (left y axis) is shown as a line plot where the proportions of the original D614G, Alpha, Beta, Gamma, Delta, Eta, Kappa, and C.1.2 lineages are shown. 2022 Cell reports. Medicine Figure SARS_CoV_2 D614G 131 136 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. Forest plot with adjusted ORs for hospitalization, ICU admission, and death by age group for N501Y-positive variant of concern (VOC) infection relative to non-VOC severe acute respiratory syndrome coronavirus 2 infection. 2022 Clinical infectious diseases Figure SARS_CoV_2 N501Y 93 98 COVID-19;COVID-19 155;170 220;220 35235585 Travel ban effects on SARS-CoV-2 transmission lineages in the UAE as inferred by genomic epidemiology. A shift of prevalence of strains with D614G mutations. 2022 PloS one Figure SARS_CoV_2 D614G 38 43 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. Neutralization of authentic SARS-CoV-2 wt (including D614G mutation), Delta, and Omicron using sera of 2x BNT162b-vaccinated (A) and BNT162b2 boost-vaccinated (B) individuals. 2022 BMC medicine Figure SARS_CoV_2 D614G 53 58 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. Neutralization of SARS-CoV-2 wild type (D614G), Delta, and Omicron. 2022 BMC medicine Figure SARS_CoV_2 D614G 40 45 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. a, Proportions of BA.1, BA.1+R346K and BA.2 in B.1.1.529 sequences on GISAID over the latter half of December 2021 and January 2022. 2022 Nature Figure SARS_CoV_2 R346K 29 34 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. b, Fold change in IC50 values relative to D614G of neutralization of Omicron variants, as well as point mutants unique to BA.2. 2022 Nature Figure SARS_CoV_2 D614G 42 47 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. b Plots of fractional saturation binding measurements with data for the Alpha variant shown in red, Alpha variant with G614D substitution in pink, and Wuhan (D614) spike in blue. 2022 Nature communications Figure SARS_CoV_2 G614D 119 124 S 164 169 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. b The K417N substitution present in the Beta variant likely destabilises the closed form of the protein by introducing a steric clash and interfering with the network of electrostatic interactions present at the trimer interface in the closed form of the Wuhan protein. 2022 Nature communications Figure SARS_CoV_2 K417N 6 11 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. d The N501Y substitution present in both the Beta and Alpha variants allows formation of a new hydrogen bond or a salt bridge. 2022 Nature communications Figure SARS_CoV_2 N501Y 6 11 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. e The K417N substitution present in the Beta variant eliminates a salt bridge between the RBD and ACE2. 2022 Nature communications Figure SARS_CoV_2 K417N 6 11 RBD 90 93 35246509 Evolution of the SARS-CoV-2 spike protein in the human host. Similar results were obtained for G614 vs D614 mink (Y453F) spike (Supplementary Figs. 2022 Nature communications Figure SARS_CoV_2 Y453F 53 58 S 60 65 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. (a) Histidine rotamer in G94D.(b) K93E, and (c) H80A turning approximately 90 . 2022 Informatics in medicine unlocked Figure SARS_CoV_2 G94D;H80A;K93E 25;48;34 29;52;38 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. (a) Wild type (green) and G94D (magenta) overlay displaying large differences in several positions, most notably F68, H80, I81. 2022 Informatics in medicine unlocked Figure SARS_CoV_2 G94D 26 30 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. (b) Wild type and Y96F (cyan) overlay exhibiting nearly complete structure homogeneity with a few subtle differences. 2022 Informatics in medicine unlocked Figure SARS_CoV_2 Y96F 18 22 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. (c.) Y96V white, Y96I magenta, Y96A orange, Y95F cyan, and WT green overlay showing the differences in the variants. 2022 Informatics in medicine unlocked Figure SARS_CoV_2 Y95F;Y96A;Y96I;Y96V 44;31;17;5 48;35;21;9 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. (c) enlarged view with notable positions F68, H80, I81, G94D, and Y96 shown. 2022 Informatics in medicine unlocked Figure SARS_CoV_2 G94D 56 60 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. For the Y96F variant, this was the only notable change except for the F96 residue itself. 2022 Informatics in medicine unlocked Figure SARS_CoV_2 Y96F 8 12 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. In the other variants Y96V, Y96I, and Y96A, the A71 residue did change, protruding out further. 2022 Informatics in medicine unlocked Figure SARS_CoV_2 Y96A;Y96I;Y96V 38;28;22 42;32;26 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. In the variants R78A (blue) and R78G (tv red) we observe that the 3 residues H80, I81 and D82 are shifted, with the furthest distance being 2.5 A. 2022 Informatics in medicine unlocked Figure SARS_CoV_2 R78A;R78G 16;32 20;36 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. Low value variants clustered together, and we can see qualitatively that the Y96F and WT distances were very close. 2022 Informatics in medicine unlocked Figure SARS_CoV_2 Y96F 77 81 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. New variants closest to the green cluster, Y96C and H80 were predicted by random forest to be candidates for future testing. 2022 Informatics in medicine unlocked Figure SARS_CoV_2 Y96C 43 47 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. Notable qualitative changes include the A71 residue protruding out further than the wild type in all variants, including Y96F. 2022 Informatics in medicine unlocked Figure SARS_CoV_2 Y96F 121 125 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. The WT and Y96F were designated as having "high" MTase activity, >90% (green). 2022 Informatics in medicine unlocked Figure SARS_CoV_2 Y96F 11 15 35255849 Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. *The parental B.1.311 lineage in this case gave rise to additional de novo mutations in Spike in some downstream members of this clade, including N501Y, and T95I. 2022 BMC public health Figure SARS_CoV_2 N501Y;T95I 146;157 151;161 S 88 93 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. In the figure, red arrows in a, c, e, and g show the K417N, T478K, E484A, and N501Y mutations found in the Omicron variant. 2022 GeroScience Figure SARS_CoV_2 E484A;K417N;N501Y;T478K 67;53;78;60 72;58;83;65 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. Red box in b, d, f, and h represents the county of origin of the K417N, T478K, E484A, and N501Y mutations. 2022 GeroScience Figure SARS_CoV_2 E484A;K417N;N501Y;T478K 79;65;90;72 84;70;95;77 35262011 Use of amplicon melt temperature to detect SARS-CoV-2 Lineage B.1.1.7 variant through the G28048T mutation in the ORF 8 gene. G28048T mutations were not observed in any other lineages. 2021 Journal of clinical virology plus Figure SARS_CoV_2 G28048T 0 7 35262011 Use of amplicon melt temperature to detect SARS-CoV-2 Lineage B.1.1.7 variant through the G28048T mutation in the ORF 8 gene. These were analysed using GISAID CoVsurver mutations App to highlight G28048T mutations (black dots). 2021 Journal of clinical virology plus Figure SARS_CoV_2 G28048T 70 77 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. (a) Neutralization titers against D614G (B.1), original Wuhan-like variant (B), and Delta variant (B.1.617.2) were analyzed in microneutralization test performed in two laboratories (A and B) that use different cell lines (VeroE6-TMPRRS2 versus VeroE6), virus amounts (50 TCID50 versus 100 TCID50), incubation times (4 days versus 3 days), and reference virus strains (B.1 versus B). 2022 Microbiology spectrum Figure SARS_CoV_2 D614G 34 39 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. (b) Comparison of MNTs performed with 3- and 4-day incubation times in laboratory A for D614G and Alpha variants (VeroE6-TMPRRS2 cells and 50 TCID50). 2022 Microbiology spectrum Figure SARS_CoV_2 D614G 88 93 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. Amino acid substitutions and deletions present in over 20% of the NGS-obtained sequence reads are indicated for the variants used in this study: original Wuhan-like strain (B), D614G (B.1), Alpha (B.1.1.7), Eta (B.1.525), Beta (B.1.351), and Delta (B.1.617.2) variants. 2022 Microbiology spectrum Figure SARS_CoV_2 D614G 177 182 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. MNT for D614G, Alpha, and Delta was performed with 4-day incubation (a) and for D614G, Beta, and Eta with 3-day incubation (b). 2022 Microbiology spectrum Figure SARS_CoV_2 D614G;D614G 8;80 13;85 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. Neutralization of variants (a) Alpha (B.1.1.7) and Delta (B.1.617.2) and (b) variants Eta (B.1.525) and Beta (B.1.351) compared with neutralization of ancestral D614G (B.1) in serum samples collected 6 weeks (a, b), 3 months (a, b), and 6 months (a) after the first vaccine dose from 2x BNT162b2 vaccinated HCWs (n = 52). 2022 Microbiology spectrum Figure SARS_CoV_2 D614G 161 166 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. Average Eigen RMSF values for WT-RBD and the L452R, E484Q and L452R-E484Q mutant systems (B) PC1 and (C) PC2. 2022 3 Biotech Figure SARS_CoV_2 E484Q;L452R;L452R;E484Q 52;45;62;68 57;50;67;73 RBD 33 36 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. Density distribution analysis plotted to understand the atomic orientation using densmap script for both WT and mutant compares on throughout MD simulations (A) WT-RBD, (B) L452R-RBD, (C) E484Q-RBD, and (C) L452R-E484Q-RBD. 2022 3 Biotech Figure SARS_CoV_2 E484Q;L452R;L452R;E484Q 188;173;207;213 193;178;212;218 RBD;RBD;RBD;RBD 164;179;194;219 167;182;197;222 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. FEL analysis plot displaying the direction of motion and magnitude analysis for (A) WT-RBD, (B) L452R-RBD, (C) E484Q-RBD, and (D) L452R-E484Q-RBD variants. 2022 3 Biotech Figure SARS_CoV_2 E484Q;L452R;L452R;E484Q 111;96;130;136 116;101;135;141 RBD;RBD;RBD;RBD 87;102;117;142 90;105;120;145 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. (C) Immunoblot analysis of spike protein cleavage of pseudovirus of the Kappa and P681R variants using polyclonal antibodies against spike. 2022 mBio Figure SARS_CoV_2 P681R 82 87 S;S 27;133 32;138 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. Luciferase activity was determined after 2 days of infection, and data were normalized to the WT (D614G) of the individual experiment. 2022 mBio Figure SARS_CoV_2 D614G 98 103 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. This experiment was repeated twice independently, and data were normalized to the WT (D614G) of the individual experiment. 2022 mBio Figure SARS_CoV_2 D614G 86 91 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. A) Amplification curves D614G using D614G primers and probes. 2022 Journal of virological methods Figure SARS_CoV_2 D614G;D614G 24;36 29;41 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. A) HRM analysis for D614G mutation: all samples had the same patterns B) HRM analysis for L452R mutation, UK variant plus 6 samples with different patterns compared to L452R and UK variant. 2022 Journal of virological methods Figure SARS_CoV_2 D614G;L452R;L452R 20;90;168 25;95;173 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. B) Amplification curves L452R using L452R primers and probes. 2022 Journal of virological methods Figure SARS_CoV_2 L452R;L452R 24;36 29;41 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. C) Amplification curves E484K using E484K primers and probes. 2022 Journal of virological methods Figure SARS_CoV_2 E484K;E484K 24;36 29;41 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. D) Amplification curves E484Q using E484Q primers and probes. 2022 Journal of virological methods Figure SARS_CoV_2 E484Q;E484Q 24;36 29;41 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. Schematic of the mutations del69-70, E484K, E484Q, D614G, L452R, and T478K that were selected for dominant variant screening.b. 2022 Journal of virological methods Figure SARS_CoV_2 D614G;E484K;E484Q;L452R;T478K 51;37;44;58;69 56;42;49;63;74 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. The presence of A) L452R mutation, B) T478K mutation, C) V483F mutation and D) D614G mutation in one sample that was not detected by RT-PCR. 2022 Journal of virological methods Figure SARS_CoV_2 D614G;L452R;T478K;V483F 79;19;38;57 84;24;43;62 35271889 A screening strategy for identifying the dominant variant of SARS-COV-2 in the fifth peak of Kurdistan- Iran population using HRM and Probe-based RT-PCR assay. We could not analyze these 6 samples by HRM analysis C) HRM analysis for T478K mutation. 2022 Journal of virological methods Figure SARS_CoV_2 T478K 73 78 35273217 A SARS-CoV-2 Wuhan spike virosome vaccine induces superior neutralization breadth compared to one using the Beta spike. (F) SARS-CoV-2 pseudovirus neutralization titers against Wuhan, D614G and all variants of concern at week 8 (n = 16 per group). 2022 Scientific reports Figure SARS_CoV_2 D614G 64 69 35273217 A SARS-CoV-2 Wuhan spike virosome vaccine induces superior neutralization breadth compared to one using the Beta spike. The beta immunogen contains the L242H and R246I substitutions that were present in early Beta strains, and not the the 242-244 deletion that later became dominant in the beta lineage. 2022 Scientific reports Figure SARS_CoV_2 L242H;R246I 32;42 37;47 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. (A) 293 T cells with pCEP4-myc-ACE2 plasmid were incubated with RBD (E484K)-sfGFP-containing medium and co-stained with fluorescent anti-MYC Alexa 647 to detect surface ACE2 by flow cytometry. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 E484K 69 74 RBD 64 67 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. (A) 293 T cells with pCEP4-myc-ACE2 plasmid were incubated with RBD (K417N)-sfGFP-containing medium and co-stained with fluorescent anti-MYC Alexa 647 to detect surface ACE2 by flow cytometry. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 K417N 69 74 RBD 64 67 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. (A) 293 T cells with pCEP4-myc-ACE2 plasmid were incubated with RBD (N501Y)-sfGFP-containing medium and co-stained with fluorescent anti-MYC Alexa 647 to detect surface ACE2 by flow cytometry. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 N501Y 69 74 RBD 64 67 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. 293 T cells with pCEP4-MYC-ACE2 plasmid were incubated with RBD (K417N-E484K-N501Y)-sfGFP-containing medium and co-stained with fluorescent anti-MYC Alexa 647 to detect surface ACE2 by flow cytometry. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 K417N;E484K;N501Y 65;71;77 70;76;82 RBD 60 63 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. 293 T cells with pCEP4-MYC-ACE2 plasmid were incubated with RBD (K417T-E484K-N501Y)-sfGFP-containing medium and co-stained with fluorescent anti-MYC Alexa 647 to detect surface ACE2 by flow cytometry. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 K417T;E484K;N501Y 65;71;77 70;76;82 RBD 60 63 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. 293 T cells with pCEP4-MYC-ACE2 plasmid were incubated with RBD (L452R-T478K)-sfGFP-containing medium and co-stained with fluorescent anti-MYC Alexa 647 to detect surface ACE2 by flow cytometry. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 L452R;T478K 65;71 70;76 RBD 60 63 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Effect of GB-1 on interaction between ACE2 and RBD with E484K mutation. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 E484K 56 61 RBD 47 50 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Effect of GB-1 on interaction between ACE2 and RBD with K417N-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 K417N;E484K;N501Y 56;62;68 61;67;73 RBD 47 50 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Effect of GB-1 on interaction between ACE2 and RBD with K417N. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 K417N 56 61 RBD 47 50 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Effect of GB-1 on interaction between ACE2 and RBD with K417T-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 K417T;E484K;N501Y 56;62;68 61;67;73 RBD 47 50 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Effect of GB-1 on interaction between ACE2 and RBD with L452R-T478K mutation. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 L452R;T478K 56;62 61;67 RBD 47 50 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Effect of GB-1 on interaction between ACE2 and RBD with N501Y mutation. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 N501Y 56 61 RBD 47 50 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Effect of glycyrrhizic acid on interaction between ACE2 and RBD with K417N-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 K417N;E484K;N501Y 69;75;81 74;80;86 RBD 60 63 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Then, two subsets of the ACE2-positive population were collected: the top population (nCoV-S-High sort, red gate) and the bottom population (nCoV-S-Low sort, green gate) based on the fluorescence of bound RBD (E484K)-sfGFP relative to ACE2 surface expression. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 E484K 210 215 RBD;S;S 205;91;146 208;92;147 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Then, two subsets of the ACE2-positive population were collected: the top population (nCoV-S-High sort, red gate) and the bottom population (nCoV-S-Low sort, green gate) based on the fluorescence of bound RBD (K417N-E484K-N501Y)-sfGFP relative to ACE2 surface expression. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 K417N;E484K;N501Y 210;216;222 215;221;227 RBD;S;S 205;91;146 208;92;147 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Then, two subsets of the ACE2-positive population were collected: the top population (nCoV-S-High sort, red gate) and the bottom population (nCoV-S-Low sort, green gate) based on the fluorescence of bound RBD (K417N)-sfGFP relative to ACE2 surface expression. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 K417N 210 215 RBD;S;S 205;91;146 208;92;147 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Then, two subsets of the ACE2-positive population were collected: the top population (nCoV-S-High sort, red gate) and the bottom population (nCoV-S-Low sort, green gate) based on the fluorescence of bound RBD (N501Y)-sfGFP relative to ACE2 surface expression. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 N501Y 210 215 RBD;S;S 205;91;146 208;92;147 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Then, two subsets of the ACE2-positive population were collected: the top population (nCoV-S-High sort, red gate) and the bottom population (nCoV-S-Low sort, green gate) based on the fluorescence of bound RBD(K417N-E484K-N501Y)-sfGFP relative to ACE2 surface expression. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 K417N;E484K;N501Y 209;215;221 214;220;226 RBD;S;S 205;91;146 208;92;147 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Then, two subsets of the ACE2-positive population were collected: the top population (nCoV-S-High sort, red gate) and the bottom population (nCoV-S-Low sort, green gate) based on the fluorescence of bound RBD(K417T-E484K-N501Y)-sfGFP relative to ACE2 surface expression. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 K417T;E484K;N501Y 209;215;221 214;220;226 RBD;S;S 205;91;146 208;92;147 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Then, two subsets of the ACE2-positive population were collected: the top population (nCoV-S-High sort, red gate) and the bottom population (nCoV-S-Low sort, green gate) based on the fluorescence of bound RBD(L452R-T478K)-sfGFP relative to ACE2 surface expression. 2022 Biomedicine & pharmacotherapy Figure SARS_CoV_2 L452R;T478K 209;215 214;220 RBD;S;S 205;91;146 208;92;147 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. Comparisons of neutralizing antibody titers among D614G and three VOCs by the timing of sampling are shown in (A). 2022 Frontiers in immunology Figure SARS_CoV_2 D614G 50 55 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. Comparisons of neutralizing antibody titers among D614G and three VOCs by the timing of sampling in 'patients without pneumonia' [1-3 months post onset (n=17), 3-6 months post onset (n=19), and 6-8 months post onset (n=10)] and those in 'patients with pneumonia' [1-3 months post onset (n=21), 3-6 months post onset (n=23), and 6-8 months post onset (n=7)] are shown in (A). 2022 Frontiers in immunology Figure SARS_CoV_2 D614G 50 55 Pneumonia;Pneumonia 118;252 127;261 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. Horizontal bars in (A) show the four variants (D614G mutation, B.1.1.7, P.1, and B.1.351) by the three groups of months post-onset (1-3m, 3-6m, and 6-8m). 2022 Frontiers in immunology Figure SARS_CoV_2 D614G 47 52 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. Horizontal bars in (B) show the three groups of months post-onset (1-3m, 3-6m, and 6-8m) for each of the four variants (D614G mutation, B.1.1.7, P.1, and B.1.351). 2022 Frontiers in immunology Figure SARS_CoV_2 D614G 120 125 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. Horizontal bars show the four variants (D614G mutation, B.1.1.7, P.1, and B.1.351) by the three groups of months post-onset (1-3m, 3-6m, and 6-8m). 2022 Frontiers in immunology Figure SARS_CoV_2 D614G 40 45 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. Horizontal bars show the four variants (D614G mutation, B.1.1.7, P.1, and B.1.351) by the three sampling times. 2022 Frontiers in immunology Figure SARS_CoV_2 D614G 40 45 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. Horizontal bars show the trend among patients at 1-3 months post onset, 3-6 months post onset, and 6-8 months post onset according to the four variants (D614G mutation, B.1.1.7, P.1, and B.1.351). 2022 Frontiers in immunology Figure SARS_CoV_2 D614G 153 158 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. Longitudinal analysis of neutralizing antibody titer by D614G and three VOCs in (B). 2022 Frontiers in immunology Figure SARS_CoV_2 D614G 56 61 35283546 SARS-CoV-2 infection after vaccination in Italian health care workers: a case report. Sections from the electropherograms showing the 69/70, N501Y, A570D, and D614G (a., b., c., d.) associated with SARS-CoV-2 Alfa Variant B.1.1.7. 2022 National Academy science letters. National Academy of Sciences, India Figure SARS_CoV_2 A570D;D614G;N501Y 62;73;55 67;78;60 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. (e and f) Estimated assignment of GISAID samples from Illinois (e) and the United States (f) to variants using the primer designed to target mutation S:P681R. 2022 Applied and environmental microbiology Figure SARS_CoV_2 P681R 152 157 S 150 151 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. In silico analysis of PCR assay targeting the S:T478K mutation to detect the Delta variant in the United States (n = 1,187,412) (a) and Mexico (n = 28,956) (b). 2022 Applied and environmental microbiology Figure SARS_CoV_2 T478K 48 53 S 46 47 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. Left Panel: Fusion was quantified by using the total GFP area/number of nuclei before normalizing to D614G for each experiment. 2022 EBioMedicine Figure SARS_CoV_2 D614G 101 106 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. Statistical analysis: One-way ANOVA, each strain is compared to D614G or delta. 2022 EBioMedicine Figure SARS_CoV_2 D614G 64 69 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Data show the neutralization ID50 ratio of each variant, compared with the D614G reference strain. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 75 80 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Fluorescence signals of GFP were normalized to the signal of the D614G reference strain after 1 h of co-incubation; values shown indicate means +- SEMs. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 65 70 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Neutralization activities of from animals immunized with D614G and other SARS-CoV-2 variants. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 57 62 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Normalized chemiluminescence signals (in RLUs) of target cells were calculated compared with the D614G reference strain. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 97 102 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Normalized ID50 ratios compared to D614G reference strain are shown. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 35 40 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Ratios of infectivity compared with the D614G reference strain were shown. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 40 45 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Reduced differences (compared with the D614G reference strain) are labelled at the bottom of each plot. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 39 44 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Relative RLUs were compared with or without the indicated enzyme first, then compared with the D614G reference strain. 2022 Emerging microbes & infections Figure SARS_CoV_2 D614G 95 100 35293847 Analysis of SARS-CoV-2 variants B.1.617: host tropism, proteolytic activation, cell-cell fusion, and neutralization sensitivity. Structural modelling of the L452R, T478K, and E484Q mutations, based on 7chh for X593, RBD-7B8 for 7B8, RBD-Ab5 for 9G11, and 7c01 for CB6. 2022 Emerging microbes & infections Figure SARS_CoV_2 E484Q;L452R;T478K 46;28;35 51;33;40 RBD;RBD 87;104 90;107 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. (A) Comparison of the Cq values for R203M and conserved primers on the amplification of clinical samples. 2022 Emerging microbes & infections Figure SARS_CoV_2 R203M 36 41 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. (A) Primer sequence comparisons for six viruses (SARS-CoV, MERS-CoV, Bat SARA CoV HKU3, H1N1, Influenza B, HPIV-1 and HRV-A66) The red "T" in the LF of the R203M primer set is the mutation site of R203M. 2022 Emerging microbes & infections Figure SARS_CoV_2 R203M;R203M 156;197 161;202 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. (A) The real-time quantitative fluorescent RT-LAMP result of the conserved and R203M primers over a range of templates from 103 -108 copies/mL. 2022 Emerging microbes & infections Figure SARS_CoV_2 R203M 79 84 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. (E) The specific differences in the R203M, R203K/G204R and T205I mutations in the N gene sequence. 2022 Emerging microbes & infections Figure SARS_CoV_2 R203K;R203M;T205I;G204R 43;36;59;49 48;41;64;54 N 82 83 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. *Low-concentration samples: The four low-concentration non-Delta samples circled by the red dotted line have no corresponding amplification Cq value using R203M primers. 2022 Emerging microbes & infections Figure SARS_CoV_2 R203M 155 160 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Numbers 1-4: the amplified curve of the R203M, R203K/G204R, T205I mutant-containing template and wild template using the conserved primer set. 2022 Emerging microbes & infections Figure SARS_CoV_2 R203K;R203M;T205I;G204R 47;40;60;53 52;45;65;58 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Numbers 21-32 refer to RT-LAMP reactions using the R203M primer set for these 12 pathogens. 2022 Emerging microbes & infections Figure SARS_CoV_2 R203M 51 56 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Numbers 33 and 34 were DEPC H2O (negative control) with the conserved primer set and the R203M primer set, respectively. 2022 Emerging microbes & infections Figure SARS_CoV_2 R203M 89 94 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Numbers 5-8: the amplified curve of the R203M, R203K/G204R, T205I mutant-containing template and wild template using the R203M primer set. 2022 Emerging microbes & infections Figure SARS_CoV_2 R203K;R203M;R203M;T205I;G204R 47;40;121;60;53 52;45;126;65;58 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. R203M primer screening, and the analytical specificity and detection limit of the two sets of RT-LAMP primers. 2022 Emerging microbes & infections Figure SARS_CoV_2 R203M 0 5 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The amplification curves: wild-type plasmid using the conserved primers (solid lines), wild-type plasmid using the mutant primers (dotted lines), and R203M mutant plasmid using mutant primers (dashed lines). 2022 Emerging microbes & infections Figure SARS_CoV_2 R203M 150 155 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The extracted RNA from clinical samples was amplified with two sets of primers (R203M and conserved primer). 2022 Emerging microbes & infections Figure SARS_CoV_2 R203M 80 85 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The LOD95 of the conserved region primer set (left) and the LOD95 of the R203M primer set (right). 2022 Emerging microbes & infections Figure SARS_CoV_2 R203M 73 78 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The R203M mutation (G to T transition) in the mutant primer is indicated in the black box, G refers to the wild allele and T is the mutant allele in the Delta (sequence from GenBank: MN908947.3). 2022 Emerging microbes & infections Figure SARS_CoV_2 R203M 4 9 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The selected LF4 shows the best distinguishing effect for R203M. 2022 Emerging microbes & infections Figure SARS_CoV_2 R203M 58 63 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. (D) The prevalence of E156G/ 157-158 mutation in the indicated countries and worldwide. 2022 Life science alliance Figure SARS_CoV_2 E156G 22 27 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. (E) Occurrence of E156G/ 157-158 in the PANGO lineages (https://cov-lineages.org/index.html). 2022 Life science alliance Figure SARS_CoV_2 E156G 18 23 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. (F) The numbers of sequences carrying E156G/ 157-158 were reported by indicated countries. 2022 Life science alliance Figure SARS_CoV_2 E156G 38 43 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. (H) Superimposition of WT NTD (green, PDB ID: 7DF3) and E156G/ 157-158 NTD (magenta) of the spike protein. 2022 Life science alliance Figure SARS_CoV_2 E156G 56 61 S 92 97 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. The affinity for the ACE2 receptor was normalized to the D614G-pseudotyped lentiviral particles. 2022 Life science alliance Figure SARS_CoV_2 D614G 57 62 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. The fold difference in response to the neutralizing plasma was measured compared to the reference D614G mutant spike PV (n = 14). 2022 Life science alliance Figure SARS_CoV_2 D614G 98 103 S 111 116 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. The fold difference in response to the neutralizing plasma was measured compared to the reference D614G mutant spike PV (n = 6). 2022 Life science alliance Figure SARS_CoV_2 D614G 98 103 S 111 116 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. The infectivity was normalized to the D614G-pseudotyped lentiviral particles. 2022 Life science alliance Figure SARS_CoV_2 D614G 38 43 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. The left Y-axis represents the total number (#) of SARS-CoV-2 genome sequences (blue dots), whereas the right Y-axis denotes the percentage of E156G/ 157-158 occurrence (red bars). 2022 Life science alliance Figure SARS_CoV_2 E156G 143 148 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. b Allele frequencies of E802D in nsp12 as ascertained by whole genome sequencing. 2022 Nature communications Figure SARS_CoV_2 E802D 24 29 Nsp12 33 38 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. d Viral growth curves from icSARS-CoV-2 mNG WT, E802D (patient), and E802A (control) nsp12 mutants on a ORF7a depleted backbone. 2022 Nature communications Figure SARS_CoV_2 E802A;E802D 69;48 74;53 ORF7a;Nsp12 104;85 109;90 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Significance between WT and E802D mutants was assessed by unpaired, two-sample t tests, **p < 0.01 (p = 0.002 at 24 h, p = 0.006 at 48 h). 2022 Nature communications Figure SARS_CoV_2 E802D 28 33 35301412 Identification of a novel SARS-CoV-2 variant with a truncated protein in ORF8 gene by next generation sequencing. A new point mutation (NSP15 V127F) occurred in EPI_ISL_525725 that was not exist in EPI_ISL_586254 (highlighted and crossed in red). 2022 Scientific reports Figure SARS_CoV_2 V127F 28 33 35304093 Tracking SARS-CoV-2 variants by entire S-gene analysis using long-range RT-PCR and Sanger sequencing. Undetermined includes various lineages of SARS-CoV-2 which could not be determined the lineages because of the lack of specific mutation patterns except for S:D614G. 2022 Clinica chimica acta; international journal of clinical chemistry Figure SARS_CoV_2 D614G 161 166 35304531 In vitro evaluation of therapeutic antibodies against a SARS-CoV-2 Omicron B.1.1.529 isolate. Dose response curves reporting the susceptibility of the SARS-CoV-2 BavPat1 D614G ancestral strain and Omicron variant to a panel of therapeutic monoclonal antibodies. 2022 Scientific reports Figure SARS_CoV_2 D614G 76 81 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? (A) Mutation D138Y in the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) showing the conversion of turn (blue) into sheet (green). 2022 Frontiers in microbiology Figure SARS_CoV_2 D138Y 13 18 S 26 31 COVID-19 50 90 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? (B) Mutation D144H in the nucleocapsid protein of SARS-CoV-2 showing the conversion of turn (blue) into coil (yellow). 2022 Frontiers in microbiology Figure SARS_CoV_2 D144H 13 18 N 26 38 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. (A) Principle of the Cas12a based SARS-CoV-2 D614G mutant detection platform. 2022 Chemical science Figure SARS_CoV_2 D614G 45 50 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. (C) Results of the Cas12a's specificity tests for the SARS-CoV-2 D614G mutant detection. 2022 Chemical science Figure SARS_CoV_2 D614G 65 70 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. (D) Results of the Cas12a's sensitivity tests for the D614G mutant detection. 2022 Chemical science Figure SARS_CoV_2 D614G 54 59 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. 2'-OMe modifications of gRNAs improved the Cas12a's specificity for SARS-CoV-2 D614G mutant detection. 2022 Chemical science Figure SARS_CoV_2 D614G 79 84 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. A 20 nt sequence in the S1 subunit of the SARS-CoV-2 genome containing the D614G mutant is selected as the target site. 2022 Chemical science Figure SARS_CoV_2 D614G 75 80 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. gRNA-D614G is designed for specific recognition of the SARS-CoV-2 D614G mutant, thus the wild type SARS-CoV-2 will not lead to the Cas12a's indiscriminate cleavage. 2022 Chemical science Figure SARS_CoV_2 D614G;D614G 66;5 71;10 35308857 2'-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. Three modified gRNAs (mgRNAs) with 2'-OMe modifications at various positions are designed (5'-end, the middle region and 3'-end for mgRNA-D614G-5', mgRNA-D614G-m and mgRNA-D614G-3', respectively). 2022 Chemical science Figure SARS_CoV_2 D614G;D614G;D614G 138;154;172 143;159;177 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. A) Spatial positive/negative case distribution throughout the city with the most dominant SARS-CoV-2 variant (B.1-C15324T), the focus of this study, highlighted in turquoise. 2022 Virus evolution Figure SARS_CoV_2 C15324T 114 121 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. B) Relative mean contribution of mobility to a socio-economic tertile's effective reproductive number associated with the major variant B.1-C15324T. 2022 Virus evolution Figure SARS_CoV_2 C15324T 140 147 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. C) Summary for inferred phylogenetic clusters within (1) all lineages and (2) the major variant B.1-C15324T in tertiles of median income. 2022 Virus evolution Figure SARS_CoV_2 C15324T 100 107 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. D) Smoothed relative temporal development of social interaction and mobility contribution to the effective reproductive number associated with the major variant B.1-C15324T. 2022 Virus evolution Figure SARS_CoV_2 C15324T 165 172 35311662 Reduced DMPC and PMPC in lung surfactant promote SARS-CoV-2 infection in obesity. BALF lipids from trimyristin-treated obese mice reverse the elevated D614G mutant SARS-CoV-2 infection in Vero E6 cells (n = 5). 2022 Metabolism Figure SARS_CoV_2 D614G 69 74 COVID-19 82 102 35311662 Reduced DMPC and PMPC in lung surfactant promote SARS-CoV-2 infection in obesity. DMPC and PMPC inhibit the infection of SARS-CoV-2 pseudovirus harboring Spike D614G mutation in 293T/ACE2 (N) and Vero E6 (O) cells (n = 6). 2022 Metabolism Figure SARS_CoV_2 D614G 78 83 S;N 72;107 77;108 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). Assayed samples were synthetic S gene RNA of SARS-CoV-2 with L452R (T1355G) (positive control, 5x104 RNA copies), SARS-CoV-2 RNA (wild-type, JPN/AI/1-004, 5x106 RNA copies), and DW. 2022 PloS one Figure SARS_CoV_2 L452R;T1355G 61;68 66;74 S 31 32 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). L452R-RT-LAMP-BART assay data derived via real-time monitoring the lights on the tube. 2022 PloS one Figure SARS_CoV_2 L452R 0 5 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). L452R-RT-LAMP-BART assay data with PNA and without PNA derived via real-time monitoring the lights on the tube using 3M Molecular Detection Instrument (MDS100, 3M, USA). 2022 PloS one Figure SARS_CoV_2 L452R 0 5 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). Serial 10-fold-diluted samples (synthetic S gene RNA of SARS-CoV-2 with L452R (T1355G); 5x104, 5x103, 5x102, 102, 5x10, and 5 RNA copies) were assayed. 2022 PloS one Figure SARS_CoV_2 L452R;T1355G 72;79 77;85 S 42 43 35317858 SARS-CoV-2 NSP13 helicase suppresses interferon signaling by perturbing JAK1 phosphorylation of STAT1. 1 were repeated with nucleic acid binding-defective mutant K345A K347A and NTP binding-defective mutant E375A of NSP13. 2022 Cell & bioscience Figure SARS_CoV_2 E375A;K345A;K347A 104;59;65 109;64;70 Nsp13 113 118 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. (A) Binding of ACE2 by (A) SDeltaTM D614 or (B) D614G spikes pre-incubated with the indicated monoclonal antibodies (mAbs) was measured by fluorescence correlation spectroscopy (FCS) as described in Materials and methods. 2022 eLife Figure SARS_CoV_2 D614G 48 53 S 54 60 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. (A) The D614G mutation and angiotensin-converting enzyme 2 (ACE2) have additive effects on the thermodynamic stabilization of the receptor-binding domain (RBD)-up conformation. 2022 eLife Figure SARS_CoV_2 D614G 8 13 RBD 155 158 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. (B) The same SEC data for SDeltaTM D614G and (C) ACE2. 2022 eLife Figure SARS_CoV_2 D614G 35 40 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. (C) RBD-up conformation occupancy data for SDeltaTM D614G displayed as in (A). 2022 eLife Figure SARS_CoV_2 D614G 52 57 RBD 4 7 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. (D) Kinetic data for SDeltaTM D614G displayed as in (B). 2022 eLife Figure SARS_CoV_2 D614G 30 35 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. (E) SEC purification, displayed as in (A), for LD550/650-labeled A4-tagged SDeltaTM D614 and (F) SDeltaTM D614G hetero-trimers. 2022 eLife Figure SARS_CoV_2 D614G 106 111 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. (F) FRET histograms for the unbound and ACE2-bound SDeltaTM D614G spike, displayed as in (B). 2022 eLife Figure SARS_CoV_2 D614G 60 65 S 66 71 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. (G) Violin plots indicating FRET state occupancies for the SDeltaTM D614G spike, displayed as in (C). 2022 eLife Figure SARS_CoV_2 D614G 68 73 S 74 79 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. (H) TDPs for the SDeltaTM D614G spike, displayed as in (D). 2022 eLife Figure SARS_CoV_2 D614G 26 31 S 32 37 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. (I) Rate constants for the unbound and ACE2-bound SDeltaTM D614G spike, displayed as in (E). 2022 eLife Figure SARS_CoV_2 D614G 59 64 S 65 70 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Angiotensin-converting enzyme 2 (ACE2)-binding modulates the receptor-binding domain (RBD) conformation of SDeltaTM D614 and D614G. 2022 eLife Figure SARS_CoV_2 D614G 125 130 RBD 86 89 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Data are shown for both the D614 and D614G spikes in the presence of the indicated mAbs and are presented exactly as in Figure 3. 2022 eLife Figure SARS_CoV_2 D614G 37 42 S 43 49 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Lane 1: SDeltaTM D614; lane 2: LD550/650-labeled SDeltaTM D614; lane 3: SDeltaTM D614G; LD550/650-labeled SDeltaTM D614G; and lane 5: unlabeled ACE2. 2022 eLife Figure SARS_CoV_2 D614G;D614G 81;115 86;120 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Model fitness was evaluated using both the SDeltaTM D614 and D614G data sets, which yielded equivalent results. 2022 eLife Figure SARS_CoV_2 D614G 61 66 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. The D614G mutation and ligands modulate the S energetic landscape. 2022 eLife Figure SARS_CoV_2 D614G 4 9 S 44 45 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. Neutralisation assays were carried out using pseudotypes expressing either ancestral spike or B.1.1.298, B.1.1.7, B.1.617.2 K417N, B.1.617.2, B.1.617.1, P.1 and B.1.351. 2022 Frontiers in immunology Figure SARS_CoV_2 K417N 124 129 S 85 90 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. S686G modulates SARS-CoV-2 S-driven entry in a cell line-dependent manner. 2022 PloS one Figure SARS_CoV_2 S686G 0 5 S 27 28 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. Delta variant sequences are expected to contain the P681R SNP (probe 2, "P681R") but not the other tested variances. 2022 Viruses Figure SARS_CoV_2 P681R;P681R 52;73 57;78 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. Omicron variant (Non-BA.2) sequences are expected to contain A67V + del-HV69-70 (probe 1, "SDEL2"), E484A (probe 3, "E484A") and N679K + P681H (probe 4, "P681H"). 2022 Viruses Figure SARS_CoV_2 A67V;E484A;N679K;P681H;E484A;P681H 61;100;129;137;117;154 65;105;134;142;122;159 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. Bar graphs indicate normalized binding of IIa (A), AT (B), or HCII (C), or S-protein RBDs of wild type Wuhan strain (D), or N501Y (E), L452R (F), or K417T/E484K/N501Y mutants (G) to surface-immobilized heparin. 2022 The Journal of biological chemistry Figure SARS_CoV_2 K417T;L452R;N501Y;E484K;N501Y 149;135;124;155;161 154;140;129;160;166 RBD;S 85;75 89;76 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. Docked (A) heparin, (B) BoSG [4S-3S], (C) BoSG [2S-3S], (D) BoSG [4S-2S], and (E) BoSG [2S-2S] disaccharides in N501Y mutant. 2022 The Journal of biological chemistry Figure SARS_CoV_2 N501Y 112 117 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. Predicted binding poses of heparin and BoSG (monosulfated/monosaccharide) disaccharides bound to N501Y of SARS-CoV2 S-protein RBD. 2022 The Journal of biological chemistry Figure SARS_CoV_2 N501Y 97 102 RBD;S 126;116 129;117 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. (A) Three attractive interactions lost in E484K. 2022 PeerJ Figure SARS_CoV_2 E484K 42 47 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. 1 (K417T, E484K, and N501Y). 2022 PeerJ Figure SARS_CoV_2 E484K;N501Y;K417T 10;21;3 15;26;8 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. The red signs are the two mutations placed at the RBM (E484K and N501Y). 2022 PeerJ Figure SARS_CoV_2 N501Y;E484K 65;55 70;60 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. We highlighted position 484: the E484K mutation changes the attractive interaction to a repulsive. 2022 PeerJ Figure SARS_CoV_2 E484K 33 38 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. One virus (hCoV-19/Indonesia/JK-LIPI135/2021) not shown in this figure was found to carry multiple amino acid changes, including S_D614G, S_P681R, S_T478K, S_L452R, NSP6_T77A, NSP3_P1228L, NSP12_P323L, NSP12_G671S, and NSP14_A394V. 2022 PeerJ Figure SARS_CoV_2 A394V;D614G;G671S;L452R;P1228L;P323L;P681R;T478K;T77A 225;131;208;158;181;195;140;149;170 230;136;213;163;187;200;145;154;174 Nsp12;Nsp12;Nsp3;Nsp6 189;202;176;165 194;207;180;169 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. The highest incidence of substitutions includes S_D614G (n = 199) and NSP12_P323L (n = 197). 2022 PeerJ Figure SARS_CoV_2 D614G;P323L 50;76 55;81 Nsp12 70 75 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. Two viruses from B.56 lineages were found to carry the least number of mutations (n = 4) and no S_D614G substitution. 2022 PeerJ Figure SARS_CoV_2 D614G 98 103 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. (F) L84S variant shows the loss of IL-17RA/RC heterodimerization. 2022 mBio Figure SARS_CoV_2 L84S 4 8 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. At 24 h posttransfection with HA-hIL-17RA and Myc-hIL-17RC, NIH 3T3 cells were treated with the ORF8 WT or L84S variant for 30 min, followed by PLA. 2022 mBio Figure SARS_CoV_2 L84S 107 111 ORF8 96 100 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. (A) Neutralising antibody titres against the original SARS-CoV-2 strain from Wuhan, China (IPBCAMS-WH-01/2019, number EPI_ISL_402123), and the D614G, beta (B.1.351), and delta (B.1.617.2) variants in 141 patients. 2022 The Lancet. Microbe Figure SARS_CoV_2 D614G 143 148 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. Humoral and cellular immune responses to the original SARS-CoV-2 strain, and the D614G, beta, and delta variants, in recovered patients 12 months after infection. 2022 The Lancet. Microbe Figure SARS_CoV_2 D614G 81 86 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. D Magnitude of neutralisation activity against the beta, D614G, and delta variants in pre- and post-vaccination sera. 2022 BMC medicine Figure SARS_CoV_2 D614G 57 62 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. E Number of individuals with neutralisation activity against Beta or D614G or Delta variants in pre- and post-vaccination sera. 2022 BMC medicine Figure SARS_CoV_2 D614G 69 74 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. Magnitude of neutralisation activity against the original variant (D614G) in first wave sera with varying concentrations of A anti-Spike IgG and B anti-RBD IgG antibodies. 2022 BMC medicine Figure SARS_CoV_2 D614G 67 72 S;RBD 131;152 136;155 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. The Spike and RBD protein antigens were from the original D614G variant. 2022 BMC medicine Figure SARS_CoV_2 D614G 58 63 S;RBD 4;14 9;17 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. (A) Normalized HRM curves of amplicons from the second amplification by nested PCR with the primer pair "Second G339D forward" and "Second G339D reverse" to detect the G22578A mutation. 2022 Biochemical and biophysical research communications Figure SARS_CoV_2 G22578A;G339D;G339D 168;112;139 175;117;144 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. (B) Normalized HRM curves of amplicons from the second amplification by nested PCR with the primer pair "Second L452R forward" and "Second L452R reverse" to detect the T22917G mutation. 2022 Biochemical and biophysical research communications Figure SARS_CoV_2 L452R;L452R;T22917G 112;139;168 117;144;175 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. (C) Normalized HRM curves of amplicons from the second amplification by nested PCR with the primer pair "Second D796Y forward" and "Second D796Y reverse" to detect the G23948T mutation. 2022 Biochemical and biophysical research communications Figure SARS_CoV_2 D796Y;D796Y;G23948T 112;139;168 117;144;175 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. (A) Neutralization titers of variant of concerns, variants of Interest, Beta+R346K, Delta+R346K+K417N and Mu+K417N. 2022 Future microbiology Figure SARS_CoV_2 K417N;K417N;R346K;R346K 96;109;77;90 101;114;82;95 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. Immune-escape features of Beta+R346K and Omicron variants. 2022 Future microbiology Figure SARS_CoV_2 R346K;R346K 32;31 37;36 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. The Beta does not harbor R346K, whereas the Mu lacks K417N in the receptor-binding domain. 2022 Future microbiology Figure SARS_CoV_2 K417N;R346K 53;25 58;30 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. (A) Reduction of D614G strain titer (PFU/ml) in Caco-2 cells supernatants after pre-post treatment with ATV (n = 4). 2022 Frontiers in microbiology Figure SARS_CoV_2 D614G 17 22 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. (B) Reduction of the D614G strain titer (PFU/ml) in Vero E6 supernatants after pre-infection treatment with ATV. 2022 Frontiers in microbiology Figure SARS_CoV_2 D614G 21 26 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. (B) Reduction of the D614G strain titer (PFU/ml) in Vero E6 supernatants after pre-post treatment with ATV (n = 4). 2022 Frontiers in microbiology Figure SARS_CoV_2 D614G 21 26 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. (B) Representative plaques of ATV treatment against the SARS-CoV-2 D614G are shown. 2022 Frontiers in microbiology Figure SARS_CoV_2 D614G 67 72 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. (C) Representative plaques of pre-infection treatment against the D614G strain are shown. 2022 Frontiers in microbiology Figure SARS_CoV_2 D614G 66 71 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. (E) Reduction of D614G strain titer (PFU/ml) in Vero E6 supernatants after post-infection treatment with ATV. 2022 Frontiers in microbiology Figure SARS_CoV_2 D614G 17 22 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. Atorvastatin exhibited an antiviral effect against the SARS-CoV-2 D614G strain in a dose-dependent manner. 2022 Frontiers in microbiology Figure SARS_CoV_2 D614G 66 71 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. ATV affected SARS-CoV-2 D614G replication. 2022 Frontiers in microbiology Figure SARS_CoV_2 D614G 24 29 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. ATV inhibited D614G strain during pre-infection and post-infection treatment. 2022 Frontiers in microbiology Figure SARS_CoV_2 D614G 14 19 35370361 CRISPR-Cas13a cascade-based viral RNA assay for detecting SARS-CoV-2 and its mutations in clinical samples. (A) Design of crRNA_S (1-5) for identifying N501Y mutations. 2022 Sensors and actuators. B, Chemical Figure SARS_CoV_2 N501Y 44 49 35370361 CRISPR-Cas13a cascade-based viral RNA assay for detecting SARS-CoV-2 and its mutations in clinical samples. (C) The Cas13C assay can detect the mutant N501Y in wild SARA-CoV-2 samples. 2022 Sensors and actuators. B, Chemical Figure SARS_CoV_2 N501Y 43 48 35370361 CRISPR-Cas13a cascade-based viral RNA assay for detecting SARS-CoV-2 and its mutations in clinical samples. Identify N501Y mutations of SARS-CoV-2 variants. 2022 Sensors and actuators. B, Chemical Figure SARS_CoV_2 N501Y 9 14 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. (A) Neutralization ID50 values of the vaccinated sera against SARS-CoV-2 D614G reference pseudovirus. 2022 Frontiers in immunology Figure SARS_CoV_2 D614G 73 78 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. (A) The fold changes in neutralizing activity (IC50) of the mAbs against SARS-CoV-2 variants pseudovirus relative to D614G. 2022 Frontiers in immunology Figure SARS_CoV_2 D614G 117 122 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. (B) The fold changes in binding activity [mean fluorescence intensity (MFI)] of the mAbs against SARS-CoV-2 variants pseudovirus relative to D614G. 2022 Frontiers in immunology Figure SARS_CoV_2 D614G 141 146 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. (E) The fold changes in half maximal inhibitory concentration (IC50) of inhibitors against SARS-CoV-2 variants pseudovirus relative to D614G. 2022 Frontiers in immunology Figure SARS_CoV_2 D614G 135 140 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. Fold changes of vaccine sera neutralization activity (ID50) between variants and D614G reference strain pseudoviruses, depicted in a heat map. 2022 Frontiers in immunology Figure SARS_CoV_2 D614G 81 86 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. Recombinant hACE2 protein binding percentages were calculated by the ratio between variants over D614G MFI normalized relative to that of S2 specific antibody. 2022 Frontiers in immunology Figure SARS_CoV_2 D614G 97 102 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. The geometric mean titer against each variant is indicated by a black horizontal line in panels (D, G) and a black curve in panels (E, H) The fold changes of ID50 between variant and D614G pseudoviruses are illustrated by the overall average at the top in (D, G). 2022 Frontiers in immunology Figure SARS_CoV_2 D614G 183 188 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. The infectivity of the D614G variant was used as a control. 2022 Frontiers in immunology Figure SARS_CoV_2 D614G 23 28 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. A) The fraction of the nsp2:K81N + ORF7a:P45L combination among all Delta samples from Russia in 15-day sliding window. 2022 Virus evolution Figure SARS_CoV_2 K81N;P45L 28;41 32;45 ORF7a;Nsp2 35;23 40;27 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. C, D) UShER tree of Delta (C) and its AY.122 + ORF7a:P45L sublineage (D). 2022 Virus evolution Figure SARS_CoV_2 P45L 53 57 ORF7a 47 52 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. The AY.122 + ORF7a:P45L sublineage is marked by an arrow. 2022 Virus evolution Figure SARS_CoV_2 P45L 19 23 ORF7a 13 18 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. The following mutations that characterize the major sublineage of B.1.617.2 ('21J' in Nextstrain nomenclature) and occur in >85 per cent of Delta samples both in Russia and globally are not shown: RdRp:G671S, exonuclease:A394V, nsp6:T77A, nsp3:A488S, nsp3:P1228L, nsp6:V120V, ORF7b:T40I, nsp3:P1469S, N:G215C, nsp4:D144D, nsp4:V167L, and nsp4:T492I. 2022 Virus evolution Figure SARS_CoV_2 A394V;A488S;D144D;G215C;G671S;P1228L;P1469S;T40I;T492I;T77A;V120V;V167L 221;244;315;303;202;256;293;282;343;233;269;327 226;249;320;308;207;262;299;286;348;237;274;332 Exonuclease;ORF7b;Nsp3;Nsp3;Nsp3;Nsp4;Nsp4;Nsp4;Nsp6;Nsp6;RdRP;N 209;276;239;251;288;310;322;338;228;264;197;301 220;281;243;255;292;314;326;342;232;268;201;302 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. The internal node corresponding to the main PII and which defines the AY.122 + ORF7a:P45L sublineage is marked by a red circle; branches leading to the Russian descendants of the main PII are colored in red; to other Russian sequences, in purple; to non-Russian sequences, in blue; internal branches, in gray. 2022 Virus evolution Figure SARS_CoV_2 P45L 85 89 ORF7a 79 84 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. (A to C) Neutralization curves against D614G (black) and Omicron (red) are shown for eleven monoclonal neutralizing antibodies (nAb) and one tri-specific antibody mimetic protein (DARPin) (A), five cocktail neutralizing antibody products (B), and two polyclonal antibody preparations (C). 2022 Science translational medicine Figure SARS_CoV_2 D614G 39 44 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. (A) Neutralization assays used lentiviral pseudoviruses bearing SARS-CoV-2 spike proteins from D614G, Delta, or Omicron. 2022 Science translational medicine Figure SARS_CoV_2 D614G 95 100 S 75 80 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. (D) IC50 values against D614G and Omicron are shown for all therapeutic antibodies. 2022 Science translational medicine Figure SARS_CoV_2 D614G 24 29 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. (E) Ratio of NT50 values after 3rd versus 2nd immunizations are shown for D614G, Delta, and Omicron. 2022 Science translational medicine Figure SARS_CoV_2 D614G 74 79 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. Antigenic cartography of convalescent and vaccinee serum samples against D614G, Delta, and Omicron variants. 2022 Science translational medicine Figure SARS_CoV_2 D614G 73 78 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. Arrows indicate decrease relative to D614G (for D614G, Alpha and Beta serum samples) or Delta (for Delta serum samples). 2022 Science translational medicine Figure SARS_CoV_2 D614G;D614G 37;48 42;53 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. B.1 and B.1.2 have no mutations in the receptor binding domain and were therefore considered D614G, whereas some of the AY mutants have additional non-RBD spike mutations relative to B.1.617.2. 2022 Science translational medicine Figure SARS_CoV_2 D614G 93 98 RBD;S;RBD 39;155;151 62;160;154 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. Black arrows indicate fold decrease relative to D614G after the 2nd or 3rd immunization. 2022 Science translational medicine Figure SARS_CoV_2 D614G 48 53 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. Black squares correspond to D614G variant. 2022 Science translational medicine Figure SARS_CoV_2 D614G 28 33 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. Black squares correspond to D614G, blue triangles correspond to Delta, and red circles correspond to Omicron. 2022 Science translational medicine Figure SARS_CoV_2 D614G 28 33 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. Squares correspond to D614G, triangles correspond to Delta, and circles correspond to Omicron. 2022 Science translational medicine Figure SARS_CoV_2 D614G 22 27 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. Structural changes during molecular dynamic simulation: (A) Superimposed root mean square deviation (RMSD) and root mean square fluctuation (RMSF) spectrum of wild-type (black) and mutant proteins [S194* (recovered) shown in green and S194L (mortality) shown in red] during 200 ns of molecular dynamics simulation period. 2022 Frontiers in cellular and infection microbiology Figure SARS_CoV_2 S194L;S194X 235;198 240;203 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. (A and B) HEK-293T cells in a 24-well plate were cotransfected with expression vectors encoding SARS-CoV-2 nsp5 (WT or S46A) (A) or SARS-CoV nsp5 (WT or A46S) (B) along with an IFN-beta reporter plasmid and a pRL-TK plasmid. 2022 Journal of virology Figure SARS_CoV_2 A46S;S46A 153;119 157;123 Nsp5;Nsp5 107;141 111;145 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. (A) We transfected 0.4 mug of plasmid expressing NEMO-truncated mutants (NEMO-K277A [1-152], NEMO-K277A [1-205], NEMO-K277A [1-231], NEMO-K277A [153-419], NEMO-K277A [206-419], and NEMO-K277A [232-419]) along with IFN-beta reporter plasmid and pRL-TK plasmid into HEK-293T cells for 28 h. 2022 Journal of virology Figure SARS_CoV_2 K277A;K277A;K277A;K277A;K277A;K277A 78;98;118;138;160;186 83;103;123;143;165;191 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. (C to E) HEK-293T cells were cotransfected with expression vectors encoding SARS-CoV-2 nsp5 and FLAG-tagged wild-type (WT) NEMO or NEMO mutants Q218A, Q229K, Q231A, Q236A/Q239A, or Q259A (C), NEMO mutants Q198A, Q201A, Q205A, or Q207A (D), or NEMO mutants Q120A, Q132A, Q133A, Q134A, Q145A, or Q154A (E). 2022 Journal of virology Figure SARS_CoV_2 Q120A;Q132A;Q133A;Q134A;Q145A;Q154A;Q198A;Q201A;Q205A;Q207A;Q218A;Q229K;Q231A;Q236A;Q259A;Q239A 256;263;270;277;284;294;205;212;219;229;144;151;158;165;181;171 261;268;275;282;289;299;210;217;224;234;149;156;163;170;186;176 Nsp5 87 91 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. (C) Schematic representation of SARS-CoV-2 nsp5 and its S46A mutant and SARS-CoV nsp5 and its A46S mutant. 2022 Journal of virology Figure SARS_CoV_2 A46S;S46A 94;56 98;60 Nsp5;Nsp5 43;81 47;85 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. (D) HEK-293T cells were cotransfected with expression vectors encoding FLAG-tagged NEMO and various amounts of expression plasmids encoding HA-tagged WT SARS-CoV-2 nsp5 (0.25 mug, 0.125 mug, 0.0625 mug, and 0.03125 mug) or SARS-CoV-2 nsp5 (S46A) (0.25 mug, 0.125 mug, 0.0625 mug, and 0.03125 mug). 2022 Journal of virology Figure SARS_CoV_2 S46A 240 244 Nsp5;Nsp5 164;234 168;238 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. (E) HEK-293T cells were cotransfected with expression vectors encoding FLAG-tagged NEMO and increasing amounts of plasmid encoding WT SARS-CoV nsp5 (1 mug, 0.5 mug, 0.25 mug, and 0.125 mug) or SARS-CoV nsp5 (A46S) (0.25 mug, 0.125 mug, 0.0625 mug, and 0.03125 mug). 2022 Journal of virology Figure SARS_CoV_2 A46S 208 212 Nsp5;Nsp5 143;202 147;206 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. (F) HEK-293T cells were cotransfected with expression vectors encoding FLAG-tagged WT NEMO or NEMO mutants (E137A/E152A/E155A) and a plasmid encoding SARS-CoV-2 nsp5. 2022 Journal of virology Figure SARS_CoV_2 E137A;E152A;E155A 108;114;120 113;119;125 Nsp5 161 165 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. (G) HEK-293T cells were cotransfected with expression vectors encoding FLAG-tagged WT NEMO or a NEMO triple mutant (E152A/Q205A/Q231A) and a plasmid encoding SARS-CoV-2 nsp5. 2022 Journal of virology Figure SARS_CoV_2 E152A;Q205A;Q231A 116;122;128 121;127;133 Nsp5 169 173 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. (H) HEK-293T cells were cotransfected with expression vectors encoding FLAG-tagged NEMO or NEMO mutants (E152A, Q205, Q231) and a plasmid encoding SARS-CoV nsp5. 2022 Journal of virology Figure SARS_CoV_2 E152A 105 110 Nsp5 156 160 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. (I) HEK-293T cells were cotransfected with expression vectors encoding FLAG-tagged WT NEMO or a NEMO triple mutant (E152A/Q205A/Q231A) and a plasmid encoding SARS-CoV nsp5. 2022 Journal of virology Figure SARS_CoV_2 E152A;Q205A;Q231A 116;122;128 121;127;133 Nsp5 167 171 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. 5B (C) HEK-293T cells seeded in a 24-well plate were transfected with equal amounts of plasmids encoding SARS-CoV-2 nsp5 (WT or S46A) or SARS-CoV nsp5 (WT or A46S) for 24 h and then treated as described in. 2022 Journal of virology Figure SARS_CoV_2 A46S;S46A 158;128 162;132 Nsp5;Nsp5 116;146 120;150 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. A fluorescence resonance energy transfer assay was conducted using 40 muM fluorogenic peptide substrate (Dabcyl-TSAVLQ SGFRKM-E-Edans, containing the N-terminal autocleavage site of SARS-CoV-2 3CLpro) and 50 nM SARS-CoV-2 nsp5 (WT and S46A) or SARS-CoV nsp5 (WT and A46S). 2022 Journal of virology Figure SARS_CoV_2 A46S;S46A 266;235 270;239 Nsp5;Nsp5;N 222;253;150 226;257;151 35396165 A self-amplifying RNA vaccine protects against SARS-CoV-2 (D614G) and Alpha variant of concern (B.1.1.7) in a transmission-challenge hamster model. (a)Weight loss in donor hamsters (n = 6 per group) directly inoculated on day 0 with 103 pfu WT D614G (B.1.238) (blue) or with Alpha VOC (B.1.1.7) (red). 2022 Vaccine Figure SARS_CoV_2 D614G 96 101 35396165 A self-amplifying RNA vaccine protects against SARS-CoV-2 (D614G) and Alpha variant of concern (B.1.1.7) in a transmission-challenge hamster model. (b) Weight loss in hamsters vaccinated with saRNA encoding influenza H1 HA (black) or SARS-CoV-2 S protein (green) and exposed to donors infected with WT D614G (B.1.238) SARS-CoV-2. 2022 Vaccine Figure SARS_CoV_2 D614G 154 159 S 97 98 35396165 A self-amplifying RNA vaccine protects against SARS-CoV-2 (D614G) and Alpha variant of concern (B.1.1.7) in a transmission-challenge hamster model. Infectious virus measured by plaque assay in Vero cells from lung homogenates of immunized hamsters exposed to donors infected with (a) WT D614G (B.1.238) or (b) Alpha VOC (B.1.1.7) SARS-CoV-2. 2022 Vaccine Figure SARS_CoV_2 D614G 139 144 35396165 A self-amplifying RNA vaccine protects against SARS-CoV-2 (D614G) and Alpha variant of concern (B.1.1.7) in a transmission-challenge hamster model. Two weeks after the second dose, immunized hamsters were cohoused with infected donor hamsters one day after they had been intranasally inoculated with 103 pfu SARS-CoV-2 either WT (D614G) variant (B.1.238) or Alpha VOC (B.1.1.7). 2022 Vaccine Figure SARS_CoV_2 D614G 182 187 35396511 Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage. c, d Neutralization activity of biologically independent plasma samples taken from donors previously vaccinated with either AZD1222 (N = 11), Ad26.COV.2.S (N = 10 for D614G, Beta and Delta and N = 9 for C.1.2) or BNT162b2 (N = 7 for C.1.2 and N = 6 for D614G, Beta, and Delta) (c) and patients previously infected during the first (N = 10 for D614G, N = 7 for C.1.2 and N = 5 for Beta and Delta), second (N = 10 for D614G, Beta, and Delta and N = 7 for C.1.2) or third (N = 9 for D614G, Beta, and Delta and N = 7 for C.1.2) waves in South Africa (d) against the wild-type (D614G), Beta, Delta, and C.1.2 variants. 2022 Nature communications Figure SARS_CoV_2 D614G;D614G;D614G;D614G;D614G;D614G 167;253;343;416;480;573 172;258;348;421;485;578 S 153 154 35396511 Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage. GMT and fold-change (FC) differences relative to D614G are given below the graph, with red representing decreased titer and green representing increased titer. 2022 Nature communications Figure SARS_CoV_2 D614G 49 54 35396511 Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage. Key mutations known/predicted to influence neutralization sensitivity (C136F and P25L, Delta144Y, Delta242L/243A, and E484K), or furin cleavage (H655Y and N679K) are indicated. 2022 Nature communications Figure SARS_CoV_2 E484K;N679K;P25L;C136F;H655Y 118;155;81;71;145 123;160;85;76;150 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Abbreviations stand for: CT, cytoplasmic domain; D614G, mutation in the S protein; F486L, mutation in the S protein; FP, fusion peptide; HR1, heptapeptide repeat sequence 1; HR2, heptapeptide repeat sequence 2; N501T, mutation in the S protein; NDT, N-terminal domain; PRRA, polybasic cleavage site; RBD, receptor-binding domain; S1, S1 subunit of the S protein; S2, S2 subunit of the S protein; TM, transmembrane domain; Y453F, mutation in the S protein. 2022 Journal of applied genetics Figure SARS_CoV_2 D614G;F486L;N501T;Y453F 49;83;211;422 54;88;216;427 RBD;N;S;S;S;S;S;S 300;250;72;106;234;352;385;445 303;251;73;107;235;353;386;446 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Boxes indicate substitutions (S32F, L50S, I76T, P218Q, D324E, T346R, T372A, T403R, K439N, H440N, I441L, A443S, E445V, F449Y, A459S, K478T, Q483V, T484E, L486F, Y490F, Y493Q, R494S, Y498Q, D501N, H505Y, N519H, A604T, S1125N, and I1228V) present in the compared genomes. 2022 Journal of applied genetics Figure SARS_CoV_2 A443S;A459S;A604T;D324E;D501N;E445V;F449Y;H440N;H505Y;I1228V;I441L;I76T;K439N;K478T;L486F;L50S;N519H;P218Q;Q483V;R494S;S1125N;T346R;T372A;T403R;T484E;Y490F;Y493Q;Y498Q;S32F 104;125;209;55;188;111;118;90;195;228;97;42;83;132;153;36;202;48;139;174;216;62;69;76;146;160;167;181;30 109;130;214;60;193;116;123;95;200;234;102;46;88;137;158;40;207;53;144;179;222;67;74;81;151;165;172;186;34 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (A) DiO-labeled pseudovirions of SARS-CoV-2 spike (WT) or D614G spike were incubated with proteoliposomes and coated with polyhistidine-tagged hACE2, NRP1-b1, and TMPRSS2 at desired pH and 0.5 mM CaCl2, as indicated. 2022 Cell reports Figure SARS_CoV_2 D614G 58 63 S;S 44;64 49;69 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (A) Fluorescence anisotropy assay design for probing fusion peptide binding to target membrane by incubating pseudovirions having SARS-CoV2-S* or SARS-CoV2-D614G-S* with the proteoliposome with ACE2/NRP1/TMPRSS2 during triggering with Ca2+ and low pH 4.6 (STAR Methods). 2022 Cell reports Figure SARS_CoV_2 D614G 156 161 Membrane;S;S 86;140;162 94;141;163 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (A) Fluorescence resonance energy transfer (FRET) assay design for probing spike (S) protein conformation change from pre-fusion to post-fusion state by incubating pseudovirions having SARS-CoV2-S** or SARS-CoV2-D614G-S** with the proteoliposome with ACE2/NRP1/TMPRSS2 during triggering with Ca2+ and low pH 4.6 (STAR Methods). 2022 Cell reports Figure SARS_CoV_2 D614G 212 217 S;S;S;S 75;82;195;218 80;83;196;219 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (A) Pseudovirions formed with SARS-CoV-2 WT spike or D614G spike were labeled with a self-quenching lipophilic fluorophore DiO (STAR Methods). 2022 Cell reports Figure SARS_CoV_2 D614G 53 58 S;S 44;59 49;64 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (B) Fluorescence dequenching was observed only in the presence of Ca2+ at pH 5 and 4.6 for both the WT (blue) and D614G spike (green) in presence of all receptors (Table S1). 2022 Cell reports Figure SARS_CoV_2 D614G 114 119 S 120 125 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (B) The change in anisotropy value in fusion peptide with time during membrane fusion in presence of Ca2+ and in absence of calcium at low pH 4.6 for WT and D614G spikes. 2022 Cell reports Figure SARS_CoV_2 D614G 157 162 Membrane;S 70;163 78;169 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (C and D) Fluorescence anisotropy measurements were performed at different Ca2+ concentrations, as indicated, for both WT and D614G spikes. 2022 Cell reports Figure SARS_CoV_2 D614G 126 131 S 132 138 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (C) FRET emission spectra for WT spike and D614G spike in presence and absence of Ca2+ at pH 4.6. 2022 Cell reports Figure SARS_CoV_2 D614G 43 48 S;S 33;49 38;54 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (C) Fusion efficacy at varying Ca2+ concentration for D614G spike and WT spike reflects the high Ca2+ sensitivity for D614G. 2022 Cell reports Figure SARS_CoV_2 D614G;D614G 54;118 59;123 S;S 60;73 65;78 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (C) Normalized fusion efficiency shows D614G spike virion is 2-fold fusogenic compared to the WT spike. 2022 Cell reports Figure SARS_CoV_2 D614G 39 44 S;S 45;97 50;102 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (C) The degree of fusion for WT and D614G with hACE2 at pH 4.6 in presence or absence of Ca2+ has been normalized to fusion efficiency in the presence of 1% Triton X, which was set to 100% (Table S1). 2022 Cell reports Figure SARS_CoV_2 D614G 36 41 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (D and E) The FRET emission spectra as a measure of conformational change was measured at different Ca2+ concentration for WT (D) and D614G spike (E). 2022 Cell reports Figure SARS_CoV_2 D614G 134 139 S 140 145 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (D) Comparative fusion efficacy after 20 min of the fusion reaction for D614G and WT spike in presence of all receptors, at indicated pH and calcium. 2022 Cell reports Figure SARS_CoV_2 D614G 72 77 S 85 90 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (E) Individual receptor's role in fusion efficacy between D614G and WT in presence of low pH and 0.5 mM CaCl2. 2022 Cell reports Figure SARS_CoV_2 D614G 58 63 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (E) Pre-triggering the D614G spike virions with low pH 4.6 (red), with 500 muM Ca2+ with neutral pH (cyan), and with 500 muM Ca2+ with low pH 4.6 (green) shows the role of calcium in pre-triggering the spike for inactivation. 2022 Cell reports Figure SARS_CoV_2 D614G 23 28 S;S 29;202 34;207 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (E) Pseudovirions of SARS-CoV-2 spike or D614G spike were mixed with liposomes coated with polyhistidine-tagged NRP1-b1, followed by adjustment to the desired pH, in the presence or absence of 0.5 mM CaCl2 into the reaction mixer. 2022 Cell reports Figure SARS_CoV_2 D614G 41 46 S;S 32;47 37;52 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (F) Fluorescence dequenching was observed only in the presence of Ca2+ with NRP1-b1 at pH 5 and 4.6 for both the WT (blue) and D614G spike (green). 2022 Cell reports Figure SARS_CoV_2 D614G 127 132 S 133 138 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (F) Quantification of the occupancies in the high-FRET pre-fusion and low-FRET post-fusion conformations at different at different Ca2+ concentration for WT spike (blue) and D614G spike (green) in the presence of liposomes, which was determined from FRET emission spectra. 2022 Cell reports Figure SARS_CoV_2 D614G 174 179 S;S 157;180 162;185 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (F) The fusion efficiency changes due to pre-triggering with Ca2+ at indicated conditions are plotted for D614G (green) and WT spike (red). 2022 Cell reports Figure SARS_CoV_2 D614G 106 111 S 127 132 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (G) D614G spike shows a high degree of fusion compared to WT in the presence of Ca2+ at low pH and NRP1-b1 (Table S1). 2022 Cell reports Figure SARS_CoV_2 D614G 4 9 S 10 15 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (G) Mechanistic model of fusion peptide translocation into membrane, where D614G spike variant can penetrate more into the target membrane due to efficient Ca2+ binding, compared to WT spike. 2022 Cell reports Figure SARS_CoV_2 D614G 75 80 Membrane;Membrane;S;S 59;130;81;185 67;138;86;190 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (H) The comparative fusion efficiency after 20 min of fusion reaction for WT and D614G at indicated pH and in presence or absence of Ca2+ (n = 4 independent experiments; error bar represents standard error of mean). 2022 Cell reports Figure SARS_CoV_2 D614G 81 86 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (I) Lipid mixing assay between SARS-CoV-2 spike or D614G spike pseudovirions and liposomes coated with polyhistidine-tagged TMPRSS2. 2022 Cell reports Figure SARS_CoV_2 D614G 51 56 S;S 42;57 47;62 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (J) Increment of fluorescence over initial fluorescence (F/F0) was observed only in the presence of Ca2+ at pH 5 and 4.6 for both the WT (blue) and D614G spike (green). 2022 Cell reports Figure SARS_CoV_2 D614G 148 153 S 154 159 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. (K) D614G spike variant has higher inner layer fusion efficacy in any circumstance. 2022 Cell reports Figure SARS_CoV_2 D614G 4 9 S 10 15 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. At 500 muM Ca2+, the fusion peptide binding to membrane is maximum for both the WT and D614G, but D614G spike fusion peptide shows 150% more binding efficiency compared to WT. 2022 Cell reports Figure SARS_CoV_2 D614G;D614G 87;98 92;103 Membrane;S 47;104 55;109 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Ca2+ drives the spike-mediated full fusion between virus and liposome, and D614G is highly fusogenic. 2022 Cell reports Figure SARS_CoV_2 D614G 75 80 S 16 21 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Ca2+ triggers robust SARS-CoV-2 D614G spike-mediated virus-liposome lipid mixing compared to WT spike at acidic pH. 2022 Cell reports Figure SARS_CoV_2 D614G 32 37 S;S 38;96 43;101 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Calcium concentration-dependent fusion efficiency of WT spike virions (A) and D614G virions (B) in presence of proteoliposomes having all the receptors. 2022 Cell reports Figure SARS_CoV_2 D614G 78 83 S 56 61 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. D614G spike demonstrates higher fusion efficiency (K) and fusion index (L) compared to WT spike (Table S1). 2022 Cell reports Figure SARS_CoV_2 D614G 0 5 S;S 6;90 11;95 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. D614G spike shows pronounced calcium concentration-dependent fusion efficiency, and its fusion efficacy is almost double at 500 muM Ca2+ (Table S3). 2022 Cell reports Figure SARS_CoV_2 D614G 0 5 S 6 11 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Dequenching was observed only in the presence of Ca2+ with hACE2 at pH 4.6 for both the WT (blue) and D614G spike (green). 2022 Cell reports Figure SARS_CoV_2 D614G 102 107 S 108 113 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Dynamic Ca2+ concentration-dependent stimulation of D614G spike-mediated fusion. 2022 Cell reports Figure SARS_CoV_2 D614G 52 57 S 58 63 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. For D614G spike, with increment of the Ca2+ concentration, the population for pre-fusion conformation decreases and the population for post-fusion conformation increases more compared to WT spike. 2022 Cell reports Figure SARS_CoV_2 D614G 4 9 S;S 10;190 15;195 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Maximal dequenching was observed for D614G (green). 2022 Cell reports Figure SARS_CoV_2 D614G 37 42 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Structural features of pre-fusion trimeric spike SARS-CoV-2 WT (PDB: 6XR8) and SARS-CoV-2 D614G spike (PDB: 7KRQ) and the close-up view of fusion peptide domain (S2816-855) for SARS-CoV-2 WT spike and SARS-CoV-2 D614G spike showing the conformational difference in the loop and different orientation of side chain of D810 and D839 amino acids. 2022 Cell reports Figure SARS_CoV_2 D614G;D614G 90;212 95;217 S;S;S;S 43;96;191;218 48;101;196;223 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. The comparative inner leaflet fusion efficiency in presence individual receptor ACE2, NRP1-b1, and TMPRSS2 with D614G spike virion (I) and WT spike virion (J) at pH 4.6 and 0.5 mM CaCl2 (Table S2). 2022 Cell reports Figure SARS_CoV_2 D614G 112 117 S;S 118;142 123;147 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. The full fusion and inner leaflet fusion kinetics were followed for 20 min for D614G virion (G) and WT spike virion (H) (Table S2). 2022 Cell reports Figure SARS_CoV_2 D614G 79 84 S 103 108 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. The maximum post-fusion conformation for D614G was found at 500 mum Ca2+ concentration. 2022 Cell reports Figure SARS_CoV_2 D614G 41 46 35399374 Unique peptide signatures of SARS-ComicronV-2 virus against human proteome reveal variants' immune escape and infectiveness. B) Set of C/H-CrUPs generated around the R685 S cleavage site of wild-type and mutant Spike protein forms. 2022 Heliyon Figure SARS_CoV_2 R685S 41 47 S;S 86;46 91;47 35399374 Unique peptide signatures of SARS-ComicronV-2 virus against human proteome reveal variants' immune escape and infectiveness. Blue lines indicate C/H-CrUPs derived from wild-type protein around the R685 S cleavage site. 2022 Heliyon Figure SARS_CoV_2 R685S 72 78 S 77 78 35399374 Unique peptide signatures of SARS-ComicronV-2 virus against human proteome reveal variants' immune escape and infectiveness. C) Amino acid sequences of the NF9 peptide between positions 448 and 456 in wild-type Spike protein, and after creation of the L452R and L452Q mutations. 2022 Heliyon Figure SARS_CoV_2 L452Q;L452R 137;127 142;132 S 86 91 35399374 Unique peptide signatures of SARS-ComicronV-2 virus against human proteome reveal variants' immune escape and infectiveness. C/H-CrUPs residing around the R685 S cleavage site and belonging to the NF9 peptide of Spike protein (SPIKE_SARS2, P0DTC2). 2022 Heliyon Figure SARS_CoV_2 R685S 30 36 S;S 87;35 92;36 35399374 Unique peptide signatures of SARS-ComicronV-2 virus against human proteome reveal variants' immune escape and infectiveness. D) Set of C/H-CrUPs residing in the NF9 peptide in wild-type, and L452R and L452Q mutated protein forms. 2022 Heliyon Figure SARS_CoV_2 L452Q;L452R 76;66 81;71 35399374 Unique peptide signatures of SARS-ComicronV-2 virus against human proteome reveal variants' immune escape and infectiveness. Green lines indicate the new created mutant C/H-CrUPs that derive from the P681H and P681R mutations in Alpha and Delta variants, respectively. 2022 Heliyon Figure SARS_CoV_2 P681H;P681R 75;85 80;90 35399374 Unique peptide signatures of SARS-ComicronV-2 virus against human proteome reveal variants' immune escape and infectiveness. Green lines indicate the new generated mutant collection of C/H-CrUPs derived from the L452R and L452Q mutations. 2022 Heliyon Figure SARS_CoV_2 L452Q;L452R 97;87 102;92 35399374 Unique peptide signatures of SARS-ComicronV-2 virus against human proteome reveal variants' immune escape and infectiveness. Purple blocks mark the point mutations around this position, while red outline indicates the Delta and Kappa variants carrying the critical mutation P681R. 2022 Heliyon Figure SARS_CoV_2 P681R 149 154 35399374 Unique peptide signatures of SARS-ComicronV-2 virus against human proteome reveal variants' immune escape and infectiveness. Red arrow denotes the Furin cleavage site R685 S. 2022 Heliyon Figure SARS_CoV_2 R685S 42 48 S 47 48 35399374 Unique peptide signatures of SARS-ComicronV-2 virus against human proteome reveal variants' immune escape and infectiveness. Red lines denote C/H-CrUPs produced by the P681H and P681R mutations. 2022 Heliyon Figure SARS_CoV_2 P681H;P681R 43;53 48;58 35399374 Unique peptide signatures of SARS-ComicronV-2 virus against human proteome reveal variants' immune escape and infectiveness. Red lines denote C/H-CrUPs that are produced by the L452R and L452Q mutations. 2022 Heliyon Figure SARS_CoV_2 L452Q;L452R 62;52 67;57 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. (a) SARS-CoV-2 Omicron (R346K) viral RNA load in a) Throat swab (n = 8, p = 0 0002 on 1DPI, p = 0 0019 on 3DPI, p = 0 0042 on 7DPI, Mann Whitney test), (b) Nasal wash (n = 8, p = 0 0002 on 1DPI, p = 0 0092 on 3DPI, p = 0 0044 on 5DPI, p = 0 019 on 7DPI, Mann-Whitney test) and viral sgRNA load in (c) Throat swab (n = 8, p = 0 0007 on 1DPI, p = 0 049 on 5DPI, p = 0 02 on 7DPI, Mann-Whitney test) and (d) Nasal wash (n = 8, p = 0 0002 on 1DPI, p = 0 0462 on 5DPI, Mann-Whitney test) in hamsters on 1,3,5,7,10 and 14 DPI post Omicron (R346K) infection. 2022 EBioMedicine Figure SARS_CoV_2 R346K;R346K 24;534 29;539 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. (a) The body weight changes in hamsters after SARS-CoV-2 Omicron (R346K) and Delta variant infection in comparison to that of age matched control animals. 2022 EBioMedicine Figure SARS_CoV_2 R346K 66 71 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. (d) Lungs sections showing bronchioles filled with exudates (arrow) and denuded epithelial cells as well as inflammatory cells, diffuse consolidation and alveolar septal thickening in the parenchyma as well as peribronchial and perivascular mononuclear cell infiltration post Omicron (R346K) infection, H& E, scale bar = 100 microm. 2022 EBioMedicine Figure SARS_CoV_2 R346K 285 290 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. (e) Lung section showing diffuse alveolar haemorrhages (arrows), peribronchial and perivascular mononuclear cell infiltration and bronchiolitis, post Omicron (R346K) infection, H& E, scale bar = 100 microm. 2022 EBioMedicine Figure SARS_CoV_2 R346K 159 164 Bronchiolitis 130 143 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. (e) Neutralizing antibody levels in Omicron (R346K) infected hamsters on 3,5,7,10 and 14 DPI against Omicron (R346K), B.1, Alpha, Beta and Delta variants. 2022 EBioMedicine Figure SARS_CoV_2 R346K;R346K 45;110 50;115 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. [n = 8 on 3, 5, 7 and 10 DPI and n = 4 on 14 DPI for Omicron (R346K) and Delta variant infected group, uninfected control (n = 4), Mann Whitney test]. 2022 EBioMedicine Figure SARS_CoV_2 R346K 62 67 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Lungs of hamsters infected with the Omicron (R346K) variant (a-c) showing varying degree of consolidation and haemorrhages, scale bar = 1 cm. 2022 EBioMedicine Figure SARS_CoV_2 R346K 45 50 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Viral load in organs of hamsters after the SARS-CoV-2 Omicron (R346K) and Delta variant infection. 2022 EBioMedicine Figure SARS_CoV_2 R346K 63 68 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Viral RNA load in organs of hamsters after the SARS-CoV-2 Omicron (R346K) and Delta variant infection. 2022 EBioMedicine Figure SARS_CoV_2 R346K 67 72 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Viral shedding in hamsters after the SARS-CoV-2 Omicron (R346K) and Delta variant infection. 2022 EBioMedicine Figure SARS_CoV_2 R346K 57 62 35421378 Efficacy of vaccination and previous infection against the Omicron BA.1 variant in Syrian hamsters. Virus replication of the S-614G isolate in the lungs (A) or nasal turbinates (NT) (C) or of the Omicron variant in the lungs (B) or NT (D) of naive hamsters or those vaccinated twice or once with the Moderna mRNA vaccine. 2022 Cell reports Figure SARS_CoV_2 S614G 25 31 S 25 26 35421378 Efficacy of vaccination and previous infection against the Omicron BA.1 variant in Syrian hamsters. Virus replication of the S-614G isolate or the Omicron variant in groups of naive hamsters (A and C, respectively) or groups of hamsters previously infected 7 months prior with an S-614G isolate (closed circles) or 22 months prior with an earlier S-614D isolate (open circles) and re-infected with the S-614G isolate (B) or the Omicron variant (D). 2022 Cell reports Figure SARS_CoV_2 S614D;S614G;S614G;S614G 247;25;180;302 253;31;186;308 S;S;S;S 25;180;247;302 26;181;248;303 35421842 Split T7 promoter-based isothermal transcription amplification for one-step fluorescence detection of SARS-CoV-2 and emerging variants. (A) Illustration of the STAR assay for the D614G mutation in the S gene of SARS-CoV-2. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 D614G 43 48 S 65 66 35421842 Split T7 promoter-based isothermal transcription amplification for one-step fluorescence detection of SARS-CoV-2 and emerging variants. (C) Limit of detection of STAR for the D614G mutation (*P < 0.05, ***P < 0.001). 2022 Biosensors & bioelectronics Figure SARS_CoV_2 D614G 39 44 35421842 Split T7 promoter-based isothermal transcription amplification for one-step fluorescence detection of SARS-CoV-2 and emerging variants. (D) Detection of the D614G mutation in mixtures of mutant/wild-type targets with different molar ratios (**P < 0.01). 2022 Biosensors & bioelectronics Figure SARS_CoV_2 D614G 21 26 35421842 Split T7 promoter-based isothermal transcription amplification for one-step fluorescence detection of SARS-CoV-2 and emerging variants. (E) Illustration of one-pot, multiplex STAR for simultaneous detection of the SARS-CoV-2 N gene and D614G mutation. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 D614G 100 105 N 89 90 35421842 Split T7 promoter-based isothermal transcription amplification for one-step fluorescence detection of SARS-CoV-2 and emerging variants. (G) Heatmap showing results of one-pot, multiplex detection of the N gene and D614G mutation. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 D614G 78 83 N 67 68 35421842 Split T7 promoter-based isothermal transcription amplification for one-step fluorescence detection of SARS-CoV-2 and emerging variants. (H) One-pot, multiplex detection of the N gene and D614G mutation at different concentrations. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 D614G 51 56 N 40 41 35421842 Split T7 promoter-based isothermal transcription amplification for one-step fluorescence detection of SARS-CoV-2 and emerging variants. Application of STAR for the multiplex detection of the SARS-CoV-2 D614G mutation. 2022 Biosensors & bioelectronics Figure SARS_CoV_2 D614G 66 71 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (A) Molecular association between the residues in the wild-type L452R mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 L452R 64 69 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (A) Molecular association between the residues in the wild-type N501Y mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 N501Y 64 69 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (B) The schematic diagram shows the molecular association between the residues in the wild-type L452R mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 L452R 96 101 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (B) The schematic diagram shows the molecular association between the residues in the wild-type N501Y mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 N501Y 96 101 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (C) Molecular association between the residues in the mutant type L452R mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 L452R 66 71 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (C) Molecular association between the residues in the mutant type N501Y mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 N501Y 66 71 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (D) The bottom zoom view of the interaction between RBD and hACE2 residues of B.1.1.7 variant and yellow color stick represent the mutation of N501Y. 2022 Infection, genetics and evolution Figure SARS_CoV_2 N501Y 143 148 RBD 52 55 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (D) The schematic diagram shows the molecular association between the residues in the mutant type N501Y mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 N501Y 98 103 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (D) The schematic diagram shows the molecular association between the residues of mutant type L452R mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 L452R 94 99 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (E) Molecular association between the residues in the wild-type D614G mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 D614G 64 69 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (E) Molecular association between the residues in the wild-type E484Q mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 E484Q 64 69 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (E) The top zoom view of the interaction between RBD and hACE2 residues of B.1.617.2 variant and yellow color stick represent the mutation of L452R and E484Q. 2022 Infection, genetics and evolution Figure SARS_CoV_2 E484Q;L452R 152;142 157;147 RBD 49 52 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (F) The schematic diagram shows the molecular association between the residues in the wild-type E484Q mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 E484Q 96 101 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (F) The schematic diagram shows the molecular association between the residues of wild type D614G mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 D614G 92 97 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (G) Molecular association between the residues in the mutant type D614G mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 D614G 66 71 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (G) Molecular association between the residues in the mutant type E484Q mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 E484Q 66 71 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (H) The schematic diagram shows the molecular association between the residues of mutant type D614G mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 D614G 94 99 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (H) The schematic diagram shows the molecular association between the residues of mutant type E484Q mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 E484Q 94 99 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (I) Molecular association between the residues in the wild-type P681R mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 P681R 64 69 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (J) The schematic diagram shows the molecular association between the residues in the wild-type P681R mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 P681R 96 101 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (K) Molecular association between the residues in the mutant type P681R mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 P681R 66 71 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. (L) The schematic diagram shows the molecular association between the residues of mutant type P681R mutation. 2022 Infection, genetics and evolution Figure SARS_CoV_2 P681R 94 99 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. The diagram shows significant mutations in B.1.1.7 (N501Y, D614G, and P681R) and B.1.617.2 (N501Y, D614G, L452R, E484Q, and P681R) (C). 2022 Infection, genetics and evolution Figure SARS_CoV_2 D614G;D614G;E484Q;L452R;P681R;P681R;N501Y;N501Y 59;99;113;106;70;124;52;92 64;104;118;111;75;129;57;97 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. (A) Heatmap of the neutralizing activity of 24 mAbs derived from infected or vaccine immunized persons against D614G and seven variant pseudoviruses. 2022 MedComm Figure SARS_CoV_2 D614G 111 116 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. (B) The heatmap represents the ratio of EC50 values between seven variants and D614G reference. 2022 MedComm Figure SARS_CoV_2 D614G 79 84 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Darker brown indicates higher neutralizing activity of mAbs against the variant compared with D614G. 2022 MedComm Figure SARS_CoV_2 D614G 94 99 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. In contrast, darker blue indicates lower neutralizing activity of mAbs against the variant compared with D614G. 2022 MedComm Figure SARS_CoV_2 D614G 105 110 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Neutralization curves of 24 mAbs against D614G and seven variant pseudoviruses. 2022 MedComm Figure SARS_CoV_2 D614G 41 46 35436320 Occurrence of a novel cleavage site for cathepsin G adjacent to the polybasic sequence within the proteolytically sensitive activation loop of the SARS-CoV-2 Omicron variant: The amino acid substitution N679K and P681H of the spike protein. 200 mug/ml SARS-CoV-2 N679K P681R (Omicron) peptide was incubated with equal amounts of CatG and NE (4 mug/ml, upper panel) or 4 mug/ml of CatG, furin, and NE for 2h at 37 C. 2022 PloS one Figure SARS_CoV_2 N679K;P681R 22;28 27;33 35436320 Occurrence of a novel cleavage site for cathepsin G adjacent to the polybasic sequence within the proteolytically sensitive activation loop of the SARS-CoV-2 Omicron variant: The amino acid substitution N679K and P681H of the spike protein. Potential cleavage sites of NE at the proteolytically sensitive activation loop of SARS-CoV-1, SARS-CoV-2 (Wuhan), SARS-CoV-2 P681H (Alpha), SARS-CoV-2 P681R (Delta), SARS-CoV-2 N679K (C.1.2), and SARS-CoV-2 N679K P681R (Omicron) peptides were mapped using "ExPASy peptide cutter". 2022 PloS one Figure SARS_CoV_2 N679K;N679K;P681H;P681R;P681R 178;208;126;152;214 183;213;131;157;219 35461042 Increased resistance of SARS-CoV-2 Lambda variant to antibody neutralization. (c, d) Changes in neutralizing titers of convalescent (c) and inactivated vaccine-elicited plasma (d) against Lambda variant, L452Q/F490S, L452Q, and F490S mutated viruses compared with those against the D614G-WT. 2022 Journal of clinical virology Figure SARS_CoV_2 D614G;F490S;L452Q;L452Q;F490S 204;150;126;139;132 209;155;131;144;137 35461811 Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. (a) Analytical size-exclusion profile using using Zenix SEC-300, 4.6 x 150 mM column (b) SDS-PAGE analysis: Lane 1, Marker; Lane 2, SARS-Cov2-Mpro wildtype; Lane 3, SARS-Cov2-Mpro G15S; Lane 4, SARS-Cov2-Mpro K90R; Lane 5, SARS-Cov2-Mpro P132H (c) Enzyme Kinetics of Mpro variants: The rate of cleavage of the FRET peptide substrate in the presence of indicated Mpro is monitored by increase in fluorescence over time with the fluorescent signal being converted to nM substrate cleaved by use of a standard curve generated from cleaved substrate. 2022 The Journal of biological chemistry Figure SARS_CoV_2 G15S;K90R;P132H 180;209;238 184;213;243 35461811 Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. Residual deuterium exchange plots indicate no significant differential uptake between wild-type and SARS-CoV-2-Mpro mutants; (a.) G15S, (b.) K90R and (c.) P132H. 2022 The Journal of biological chemistry Figure SARS_CoV_2 G15S;K90R;P132H 130;141;155 134;145;160 35461811 Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. Superposition of the x-ray crystal structures of nirmatrelvir bound to wildtype SARS-CoV-2-Mpro (grey) and (a.) SARS-Cov-2-Mpro P132H (in magenta and green); (b.) G15S (in cyan and green) and (c.) K90R (in orange and green). 2022 The Journal of biological chemistry Figure SARS_CoV_2 G15S;K90R;P132H 163;197;128 167;201;133 35464398 Case Report: X-Linked SASH3 Deficiency Presenting as a Common Variable Immunodeficiency. The location of the c.505C>T/p.Gln169* variant is indicated below in red and Sanger sequencing confirmation is shown. 2022 Frontiers in immunology Figure SARS_CoV_2 C505T;C505T;N169X 20;22;33 28;28;38 35480056 Safety and Immunogenicity of Inactivated COVID-19 Vaccines Among People Living with HIV in China. (A) Comparison of neutralizing antibodies to the D614G and Delta variants between PLWH and HDs. 2022 Infection and drug resistance Figure SARS_CoV_2 D614G 49 54 SARS-CoV-2-HIV coinfections 82 86 35480056 Safety and Immunogenicity of Inactivated COVID-19 Vaccines Among People Living with HIV in China. (C) Comparison of neutralizing antibody (NAb) titers between D614G and Delta variants in PLWH and HDs. 2022 Infection and drug resistance Figure SARS_CoV_2 D614G 61 66 SARS-CoV-2-HIV coinfections 89 93 35480056 Safety and Immunogenicity of Inactivated COVID-19 Vaccines Among People Living with HIV in China. Correlation between time since two doses of vaccines and the neutralization antibody titers against the D614G variant (A), Delta variant (B), and IgG (C). 2022 Infection and drug resistance Figure SARS_CoV_2 D614G 104 109 35480056 Safety and Immunogenicity of Inactivated COVID-19 Vaccines Among People Living with HIV in China. The difference in NAb titers against the D614G variant (A), the delta variant (B), and the concentration of SARS-Cov-2 IgG (C) between the two groups was shown. 2022 Infection and drug resistance Figure SARS_CoV_2 D614G 41 46 32300673 Genomic characterization of a novel SARS-CoV-2. 29095C>T is found in the subset of them. 2020 Gene reports Discussion SARS_CoV_2 C29095T 0 8 32300673 Genomic characterization of a novel SARS-CoV-2. Both 8782C>T and 29095C>T are synonymous; however, 28144T>C causes amino acid to change L84S in ORF8. 2020 Gene reports Discussion SARS_CoV_2 T28144C;C29095T;C8782T;L84S 51;17;5;88 59;25;12;92 ORF8 96 100 32300673 Genomic characterization of a novel SARS-CoV-2. It is notable that most of 8782C>T and 28144T>C variant substrains are found outside of Wuhan. 2020 Gene reports Discussion SARS_CoV_2 T28144C;C8782T 39;27 47;34 32300673 Genomic characterization of a novel SARS-CoV-2. Many researchers found the relationship between ORFs with COVID-19 i.e.8782C>T(ORF1ab) and 28144T>C (ORF8) are available among genomic databases. 2020 Gene reports Discussion SARS_CoV_2 T28144C;C8782T 91;71 99;78 ORF1ab;ORF8 79;101 85;105 COVID-19 58 66 32300673 Genomic characterization of a novel SARS-CoV-2. Moreover, multiple arrangements with different coronavirus ORF8 sequences propose that L84 related to 28144T>C (L84S) isn't preserved. 2020 Gene reports Discussion SARS_CoV_2 T28144C;L84S 102;112 110;116 ORF8 59 63 32300673 Genomic characterization of a novel SARS-CoV-2. Most common variants were 8782C>T(ORF1ab) in 13 samples, 28144T>C (ORF8) in 14 samples and 29095C>T (N) in 8 samples.The occurrences of 8782C>T and 28144T>C coincide. 2020 Gene reports Discussion SARS_CoV_2 T28144C;T28144C;C29095T;C8782T;C8782T 57;148;91;26;136 65;156;99;33;143 ORF1ab;ORF8;N 34;67;101 40;71;102 32357545 Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment. A recent report corroborated our findings of high prevalence of D614G in Europe. 2020 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D614G 64 69 32357545 Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment. However, given the small sample size, it is hard to ascertain whether D614G is the dominant strain in these countries. 2020 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D614G 70 75 32357545 Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment. In addition to the Netherlands, Switzerland, and France, our data indicate that the D614G sub-strain is frequently detected in Brazil, Finland, and Belgium. 2020 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D614G 84 89 32357545 Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment. In fact, we observed p.V615L in our data set, suggesting that a second or a third hit could occur in the same epitope while a vaccine is being developed. 2020 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 V615L;V615L 21;23 28;28 32357545 Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment. Intriguingly, in our data the D614G variant was detected only in 2 out of 151 Chinese patients analyzed. 2020 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D614G 30 35 32357545 Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment. Notably, these two samples do not share common variants besides p.D614G. 2020 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D614G 66 71 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. A study examining the transmission and evolution of SARS-CoV-2 in cruise quarantine suggests that the G11083T mutation can be transmitted via RNA recombination. 2020 American journal of clinical pathology Discussion SARS_CoV_2 G11083T 102 109 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. In this case we did observe other mutations not extensively described in previous genomic sequencing efforts, including point mutations C9515T, C23378T, and in-frame deletion 12137_12142del (Table 2). 2020 American journal of clinical pathology Discussion SARS_CoV_2 C23378T;C9515T 144;136 151;142 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. It has been suggested that the G11083T mutation is more common in regions (Italy and Brazil) with higher fatality rates. 2020 American journal of clinical pathology Discussion SARS_CoV_2 G11083T 31 38 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. Linkage disequilibrium analysis suggests that RNA recombination with a G11083T mutation may contribute to the increase of mutations among the viral progeny. 2020 American journal of clinical pathology Discussion SARS_CoV_2 G11083T 71 78 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. More studies are needed to determine if G11083T, or other mutations detected in this case, may increase the fitness of the carrier virus as a benefit allele in the future. 2020 American journal of clinical pathology Discussion SARS_CoV_2 G11083T 40 47 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. Sequencing of viral RNA from FFPE lung tissue from the case 1 autopsy showed mutations most consistent with a subset of the Western European Clade A2a (C3037T, C14408T, A23403G), with mutations enriched in New York State A2a cases (C1059T and G25563T). 2020 American journal of clinical pathology Discussion SARS_CoV_2 A23403G;C14408T;G25563T;C1059T;C3037T 169;160;243;232;152 176;167;250;238;158 32451533 Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases. The viral RNA from our cases also had G11083T mutation that to date has been described in only 2% (13/648) of the A2a clade that contain C1059T mutation. 2020 American journal of clinical pathology Discussion SARS_CoV_2 C1059T;G11083T 137;38 143;45 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. Further, this study also showed that two-amino acid substitutions (N479K/T487S) in the RBD of SARS-CoV had strong impact on the potential of the coronavirus to infect human cells expressing ACE2. 2020 The Indian journal of medical research Discussion SARS_CoV_2 N479K;T487S 67;73 72;78 RBD 87 90 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. In all countries, initially the ancestral type was the most frequent, possibly because of return of travellers from China but was replaced by the A2a type that is characterized by the D614G non-synonymous mutation located in the S1-S2 junction near the furin recognition site (R667) for the cleavage of S protein required for the entry of the virion into the host cell. 2020 The Indian journal of medical research Discussion SARS_CoV_2 D614G 184 189 S 303 304 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. It is not clear whether the derived allele producing glycine directly provides a selective/transmission advantage for the entry of the virion or whether the polymorphic locus (Orf1b:P314L. 2020 The Indian journal of medical research Discussion SARS_CoV_2 P314L 182 187 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. Many mutations that arose throughout the genome of the coronavirus rose to high frequency, among which D614G was notable. 2020 The Indian journal of medical research Discussion SARS_CoV_2 D614G 103 108 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. The A type defined by T29095C is a mutation that is possessed by all sequences of type B2 of this study. 2020 The Indian journal of medical research Discussion SARS_CoV_2 T29095C 22 29 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. The B type defined by C28144T (ORF8: L>S) and T8782C comprises the collection of B, B1, B2 and B4 types of this study. 2020 The Indian journal of medical research Discussion SARS_CoV_2 C28144T;T8782C 22;46 29;52 ORF8 31 35 32474553 Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type. The C type defined by G26144T (ORF3a:G251>V) is the A1a type of this study. 2020 The Indian journal of medical research Discussion SARS_CoV_2 G26144T;G251V 22;37 29;43 ORF3a 31 36 32478289 The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey. All three viral isolates carried the D614G marker variant indicating the isolates belong to clade G, which encompasses mostly European countries according to GISAID classification. 2020 Northern clinics of Istanbul Discussion SARS_CoV_2 D614G 37 42 32478289 The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey. Clades were named based on variants L84S in ORF8 (S clade), D614G in S gene (G clade), and G251V in ORF3a (V clade). 2020 Northern clinics of Istanbul Discussion SARS_CoV_2 D614G;G251V;L84S 60;91;36 65;96;40 ORF3a;ORF8;S;S 100;44;50;69 105;48;51;70 32478289 The origin of SARS-CoV-2 in Istanbul: Sequencing findings from the epicenter of the pandemic in Turkey. Three isolates in this analysis carried the D614G variant in the S gene, indicating they are all in G clade, which was mostly detected in European countries. 2020 Northern clinics of Istanbul Discussion SARS_CoV_2 D614G 44 49 S 65 66 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. In particular, the P323L was present in all A2a sequences in our samples. 2020 Journal of biosciences Discussion SARS_CoV_2 P323L 19 24 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. Instead, it harboured three different mutations resulting in two non-synonymous changes of H286Y, P287T and a synonymous mutation which were not found in any other sequences reported from India until date and are specific for the B4 clade. 2020 Journal of biosciences Discussion SARS_CoV_2 H286Y;P287T 91;98 96;103 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. Interestingly, the mutations D614G (in SD domain) is supposed to confer flexibility in the SD domain and the mutation G1124V might impart partial rigidity in the conformation of S2 domain. 2020 Journal of biosciences Discussion SARS_CoV_2 D614G;G1124V 29;118 34;124 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. Notably, the D614G mutation is close to the Furin recognition site for cleavage of the Spike protein, which plays an important role in virus entry. 2020 Journal of biosciences Discussion SARS_CoV_2 D614G 13 18 S 87 92 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. S2 and S3, who shared an identical sequence of the virus, also harboured one unique mutation resulting in the amino acid alteration of G1124V in the Spike protein. 2020 Journal of biosciences Discussion SARS_CoV_2 G1124V 135 141 S 149 154 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. S2, S3 and S5, shared rare set of three contiguous mutations in their genome which resulted in the consecutive alterations of R203K and G204R. 2020 Journal of biosciences Discussion SARS_CoV_2 G204R;R203K 136;126 141;131 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. Sequence obtained from one of the samples S10, which belonged to the clade B4, did not possess the P323L mutation. 2020 Journal of biosciences Discussion SARS_CoV_2 P323L 99 104 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. Sequences from two samples, S11 and S12, shared a unique RdRp mutation at A88V which has not been detected until date in rest of the sequences submitted from India or Worldwide. 2020 Journal of biosciences Discussion SARS_CoV_2 A88V 74 78 RdRP 57 61 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. The A2a clade is characterized by the signature nonsynonymous mutations leading to amino acid changes of P323L in the RdRp which is involved in replication of the viral genome and the change of D614G in the Spike glycoprotein which is essential for the entry of the virus in the host cell by binding to the ACE2 receptor. 2020 Journal of biosciences Discussion SARS_CoV_2 D614G;P323L 194;105 199;110 S;RdRP 207;118 225;122 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. Viral RNA sequences obtained from two samples S11 and S12 shared all mutations except a V32L mutation at ORF8 harboured by S11 and not by S12. 2020 Journal of biosciences Discussion SARS_CoV_2 V32L 88 92 ORF8 105 109 32515358 Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. We also analysed the predicted structural alterations in the viral nucleocapsid protein, which might be caused by consecutive alterations of R203K and G204R. 2020 Journal of biosciences Discussion SARS_CoV_2 G204R;R203K 151;141 156;146 N 67 79 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Clade IV featuring the ORF1ab-V378I mutation was highlighted, in which some infections may be associated with infections caused in the Middle East, including two Taiwanese (CGMH-CGU-10 and -11) strains having a travel history to Turkey, and some strains from Australia and Germany having a travel history to Iran. 2020 Emerging microbes & infections Discussion SARS_CoV_2 V378I 30 35 ORF1ab 23 29 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Moreover, these 5 genomes were phylogenetically designated to a clade harbouring the ORF1ab-V378I mutation, which is different from the 3 previously reported clades ORF8-L84S, ORF3a-G251V and S-D614G. 2020 Emerging microbes & infections Discussion SARS_CoV_2 D614G;G251V;L84S;V378I 194;182;170;92 199;187;174;97 ORF1ab;ORF3a;ORF8;S 85;176;165;192 91;181;169;193 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. The second-wave strains circulating in Taiwan (Figure 2E and 3E) are characterized by Asp to Gly mutation at position 614 of the S gene that encodes the spike protein required for viral entrance. 2020 Emerging microbes & infections Discussion SARS_CoV_2 D614G 86 121 S;S 153;129 158;130 32543353 SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East. Whether the receptor-binding activity or furin cleavage might be altered by D614G mutation remains to be investigated. 2020 Emerging microbes & infections Discussion SARS_CoV_2 D614G 76 81 32577641 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. As an example of the importance of correct annotations, we note that seven variants within ORF3c (T25473C, T25476C, G25494T, G25500A, G25500T, C25539T, C25572T) were classified by nextstrain as synonymous based on their predicted effect on ORF3a, but in fact cause amino acid changes in the ORF3c protein. 2020 bioRxiv Discussion SARS_CoV_2 C25539T;C25572T;G25494T;G25500A;G25500T;T25476C;T25473C 143;152;116;125;134;107;98 150;159;123;132;141;114;105 ORF3a 240 245 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. (2020), C8782T substitution, which is also a silent mutation, was present in 28 out of 95 samples, although this mutation was only present in 2 samples (EPI_ISL_428718 and EPI_ISL_437317) in our study, which indicates that this mutation is not as common as in Europe for the viral isolates in Turkey and may be related with isolates from other countries. 2020 Turkish journal of biology Discussion SARS_CoV_2 C8782T 8 14 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A recent study indicates that SARS-CoV-2 genomes which harbor C14408T mutation, are more likely to have mutations in the membrane (M) and envelope (E) proteins (Eskier et al., 2020). 2020 Turkish journal of biology Discussion SARS_CoV_2 C14408T 62 69 Membrane;E 121;148 129;149 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A23403G mutation in the spike glycoprotein coding region was also amongst the mostly seen mutations in viral isolates from Turkey (61%). 2020 Turkish journal of biology Discussion SARS_CoV_2 A23403G 0 7 S 24 42 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. A23403G substitution was found to be present in isolates from Europe and leads to an amino acid change from aspartate to glycine at position 614 (D614G) within the spike glycoprotein, where these amino acids differ by means of their isoelectric points (Pachetti et al., 2020). 2020 Turkish journal of biology Discussion SARS_CoV_2 D614G;D614G;A23403G 108;146;0 144;151;7 S 164 182 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. According to the linkage analysis, C241T, C3037T, C14408T and A23403G in Cluster 3 were in complete linkage and the TTTG haplotype was high in Europe and correlated with the death rate. 2020 Turkish journal of biology Discussion SARS_CoV_2 A23403G;C14408T;C241T;C3037T 62;50;35;42 69;57;40;48 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. Another mutation found within the spike protein encoding region was C22444T, which is a silent mutation and seen in 7 out of 62 isolates (Table 1). 2020 Turkish journal of biology Discussion SARS_CoV_2 C22444T 68 75 S 34 39 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. B-type variant have T8782C nonsynonymous and C28144T synonymous (Leu to Ser) substitution in addition to A-type and C-type variant have G26144T synonymous mutation (Gly to Val) in addition to B-type substitutions. 2020 Turkish journal of biology Discussion SARS_CoV_2 C28144T;G26144T;T8782C 45;136;20 52;143;26 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. Both C8782T and G11083T mutations were found to be mostly present in Oceania isolates, where followed by North America and Europe subsequently (Pachetti et al., 2020). 2020 Turkish journal of biology Discussion SARS_CoV_2 C8782T;G11083T 5;16 11;23 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C14408T mutation within the RNA-dependent RNA polymerase encoding region of ORF1b, which is a missense mutation that leads to an amino acid change from proline to leucine at position 323 (P323L) in RNA polymerase protein, was amongst the most commonly seenmutations [61% (38/62)] in isolates from Turkey. 2020 Turkish journal of biology Discussion SARS_CoV_2 P323L;P323L;C14408T 152;188;0 186;193;7 RdRp 28 56 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C28854T substitution in the nucleocapsid protein coding region, which leads to an amino acid change (S194L), was another missense mutation that also was seen in 6/95 samples in a previous study where 95 sequences from different countries were evaluated (Wang et al., 2020). 2020 Turkish journal of biology Discussion SARS_CoV_2 S194L;C28854T 101;0 106;7 N 28 40 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C3037T, C14408T and A23403G substitutions, which are present in Nsp3, RNA-dependent RNA polymerase and spike encoding regions respectively, were found to be the mostly seen mutations in Turkey SARS-CoV-2 isolates. 2020 Turkish journal of biology Discussion SARS_CoV_2 A23403G;C14408T;C3037T 20;8;0 27;15;6 RdRp;S;Nsp3 70;103;64 98;108;68 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. C8782T was previously seen in more than 10 isolates in Guangdong province of China (Lu et al., 2020) and proposed to be clade specific in a study performed on 313 SARS-CoV-2 genomes (Li, Li, Cui, and Wu, 2020). 2020 Turkish journal of biology Discussion SARS_CoV_2 C8782T 0 6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G11083T is the most common one among such sites across different countries and sequencing technologies, which might be an indicator of this position being either a site for frequent mutation or an artefact. 2020 Turkish journal of biology Discussion SARS_CoV_2 G11083T 0 7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G11083T, corresponding to the amino acid substitution L37F within Nsp6 protein, was present in 38% of the samples (24/62) and this mutation was previously seen in SARS-CoV-2 sequences analyzed from all over the world (Benvenuto et al., 2020; Wang et al., 2020). 2020 Turkish journal of biology Discussion SARS_CoV_2 L37F;G11083T 54;0 58;7 Nsp6 66 70 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G1397A substitution in Nsp2 encoding region of ORF1a, which was present in 33% (21/62) of the isolates, was mainly seen in viral isolates from Oceania, however was also present in minor amounts in isolates from Asia and North America (Pachetti et al., 2020). 2020 Turkish journal of biology Discussion SARS_CoV_2 G1397A 0 6 ORF1a;Nsp2 47;23 52;27 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G1397A, T28688C and G29742T substitutions were said to belong to a monophyletic group which is defined by the presence of these 3 mutations and were found to present in patients who were traveled to or are residents in Iran (Eden J et al., 2020) as well as in Australian and New Zealand isolates. 2020 Turkish journal of biology Discussion SARS_CoV_2 G29742T;T28688C;G1397A 20;8;0 27;15;6 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G28878A, which is present in the same isolate with C8782T, was observed in isolates from Australia and USA (Li et al., 2020). 2020 Turkish journal of biology Discussion SARS_CoV_2 C8782T;G28878A 51;0 57;7 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. G28881A, along with A23403G substitution in spike glycoprotein, seems to have occurred after February 16th, 2020 in Europe (Pachetti et al., 2020). 2020 Turkish journal of biology Discussion SARS_CoV_2 A23403G;G28881A 20;0 27;7 S 44 62 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. However, there are also isolates that harbor either C241T and not the other 3 mutations or vice versa. 2020 Turkish journal of biology Discussion SARS_CoV_2 C241T 52 57 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. In 11 out of 62 samples, C241T was also observed to be present together with C3037T, C14408T and A23403G. 2020 Turkish journal of biology Discussion SARS_CoV_2 A23403G;C14408T;C241T;C3037T 97;85;25;77 104;92;30;83 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. In a recent study which performed multivariate generalized linear model (GLM) analysis with outpatient and hospitalized patients in the Sheffield Teaching Hospitals NHS Foundation Trust as the outcome revealed that patients carrying G614 mutation had higher viral loads compared to D614, although D614G status did not significantly affect the hospitalization status (Korber et al., 2020). 2020 Turkish journal of biology Discussion SARS_CoV_2 D614G 297 302 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. In the viral isolates analyzed in this study, C3037T, C14408T and A23403G, which were the most common mutations (61%), exist together. 2020 Turkish journal of biology Discussion SARS_CoV_2 A23403G;C14408T;C3037T 66;54;46 73;61;52 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. It also seems that the viral isolates which carry D614G mutation increases in number across the world and this mutation was proposed to have effect on the viral infectivity either due to its presence on the spike protein promoter surface region which might affect hydrogen bonding properties with neighbouring promoter regions or due to be in a site surrounded by antibody-dependent enhancement targets, where antibody binding may lead to a confirmational change that might increase the ACE2 interaction. 2020 Turkish journal of biology Discussion SARS_CoV_2 D614G 50 55 S 207 212 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. The reason of not observing C241T in linkage with other mutations with the same percentage can be due to the absence of the first 265 nucleotides in 25 of the uploaded sequences to GISAID. 2020 Turkish journal of biology Discussion SARS_CoV_2 C241T 28 33 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. Therefore, the effect of D614G mutation on the transmission of the virus is still a debate. 2020 Turkish journal of biology Discussion SARS_CoV_2 D614G 25 30 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. These mutations were due to nucleotide substitutions in 3 nucleotides in order where 2 of them (G28881A and G28882A) results in arginine to lysine (R203K) substitution and the third one (G28883C) results in glycine to arginine (G204R) in the nucleocapsid phosphoprotein, where both substituted amino acids differ from their original amino acids in means of their isoelectric points (Pachetti et al., 2020) (Table 1). 2020 Turkish journal of biology Discussion SARS_CoV_2 G28882A;G204R;G28881A;G28883C;R203K 108;228;96;187;148 115;233;103;194;153 N 242 254 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. This substitution leads to an amino acid change from valine to isoleucine at the position 198 (V198I) within Nsp2 protein, where both amino acids have the same isoelectric points. 2020 Turkish journal of biology Discussion SARS_CoV_2 V198I;V198I 53;95 93;100 Nsp2 109 113 32595354 Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. When we consider the mutations in ORF1ab, nucleotide substitutions of C884T, G1397A, C3037T, G8653T, G11083T, C14408T, and C18877T were seen in more than 15% (11/62) of the samples. 2020 Turkish journal of biology Discussion SARS_CoV_2 C14408T;C18877T;C3037T;C884T;G11083T;G1397A;G8653T 110;123;85;70;101;77;93 117;130;91;75;108;83;99 ORF1ab 34 40 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Finally, the neutralization assays performed were based on sera from SARS-CoV-2 infected individuals with an unknown D614G status. 2020 Cell Discussion SARS_CoV_2 D614G 117 122 COVID-19 69 88 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Given that most G614 variants belong to the G clade lineage, phylogenetic methods that depend on recurrence of mutational events for their signal are poorly powered to resolve whether D614G is under positive selection. 2020 Cell Discussion SARS_CoV_2 D614G 184 189 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Infectiousness and transmissibility are not always synonymous, and more studies are needed to determine whether the D614G mutation actually led to an increase in number of infections and not just higher viral loads during infection. 2020 Cell Discussion SARS_CoV_2 D614G 116 121 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Our data show that, over the course of 1 month, the variant carrying the D614G Spike mutation became the globally dominant form of SARS-CoV-2. 2020 Cell Discussion SARS_CoV_2 D614G 73 78 S 79 84 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. The experimental approach taken here to acquire laboratory evidence of increased fitness of the D614G mutation is based on two different pseudovirus models of infection in established cell lines. 2020 Cell Discussion SARS_CoV_2 D614G 96 101 32697968 Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. The mutation that causes the D614G amino change is transmitted as part of a conserved haplotype defined by 4 mutations that almost always track together (Figures S5 and S6). 2020 Cell Discussion SARS_CoV_2 D614G 29 34 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. Concordant to our results, a few reports demonstrated that S 614G variant was associated with the mortality related to COVID-19. 2020 Journal of human genetics Discussion SARS_CoV_2 S614G 59 65 S 59 60 COVID-19 119 127 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. ORF1ab P4715L is located in Nsp12, which is important for viral RNA replication. 2020 Journal of human genetics Discussion SARS_CoV_2 P4715L 7 13 ORF1ab;Nsp12 0;28 6;33 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. ORF1ab P4715L is located in the epitope sequences of ORF1ab 4713-4721, FPPTSFGPL, ORF1ab 4713-4722, FPPTSFGPLV, and ORF1ab 4715-4724, PTSFGPLVRK, which were predicted to have strong binding affinities of 44, 41, and 45 nM to HLA-B*07:02, HLA-B*54:01, and HLA-A*11:01, respectively. 2020 Journal of human genetics Discussion SARS_CoV_2 P4715L 7 13 ORF1ab;ORF1ab;ORF1ab;ORF1ab 0;53;82;116 6;59;88;122 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. Similarly, S D614G is located in the epitope sequences of S606-615, NQVAVLYQDV, and S612-620, YQDVNCTEV. 2020 Journal of human genetics Discussion SARS_CoV_2 D614G 13 18 S 11 12 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. Structural analyses indicated that S protein having a D614G substitution is located on the surface of the virus and interacts with ACE2. 2020 Journal of human genetics Discussion SARS_CoV_2 D614G 54 59 S 35 36 32699345 SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. The D614G spike mutation is the mutation detected in Europe in the early phase and has widely spread around the globe, especially to European and North American countries. 2020 Journal of human genetics Discussion SARS_CoV_2 D614G 4 9 S 10 15 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. A475V reduced the sensitivity to 6 mAb out of the 13 mAb used in this study, whereas F490L reduced the sensitivity to neutralization by 3 mAbs. 2020 Cell Discussion SARS_CoV_2 F490L;A475V 85;0 90;5 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. An amino acid change (D614G) outside the RBD was found to be more infectious, but no evidence of being resistant to neutralizing antibodies has been demonstrated. 2020 Cell Discussion SARS_CoV_2 D614G 22 27 RBD 41 44 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Another important finding is that natural variants capable of affecting the reactivity to neutralizing mAbs were almost all located in the RBD region (except A831V) because all antibodies used in this study were targeting the RBD. 2020 Cell Discussion SARS_CoV_2 A831V 158 163 RBD;RBD 139;226 142;229 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Another RBD variant A475V sits in the binding epitope of RBD. 2020 Cell Discussion SARS_CoV_2 A475V 20 25 RBD;RBD 8;57 11;60 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. However, only V483A exceeded 0.1% in frequency at the beginning of the study, all of which were found in the United States, with 28 sequences reported as of May 6, 2020, and 36 up to July 3, 2020. 2020 Cell Discussion SARS_CoV_2 V483A 14 19 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. However, the increasing dominance of D614G particularly deserves attention. 2020 Cell Discussion SARS_CoV_2 D614G 37 42 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. In addition, only one sequence from France containing Y508H was deposited in GIRSAID as of May 6, whereas four sequences reported as of July 3, 2020, of which two originated from Netherlands, one from Sweden, and one from France. 2020 Cell Discussion SARS_CoV_2 Y508H 54 59 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. In this study, the other glycosylation mutant N234Q, which is also close to the RBD, is resistant to several mAbs. 2020 Cell Discussion SARS_CoV_2 N234Q 46 51 RBD 80 83 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Indeed, both L452R and F490L were natural variants, with decreased sensitivity to neutralization by P2B-2F6 mAb; because both L452R and F490L remain sensitive to P2C-1F11, suggesting this mAb is not derived from the same clone for P2B-2F6. 2020 Cell Discussion SARS_CoV_2 F490L;F490L;L452R;L452R 23;136;13;126 28;141;18;131 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Indeed, the Y508H was found to be resistant to this mAb. 2020 Cell Discussion SARS_CoV_2 Y508H 12 17 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. It is worth mentioning that D614G+I472V has shown increased infectivity and more resistance to neutralizing antibodies (Table 1), but only one sequence (originated from Canada) was reported in GISAID. 2020 Cell Discussion SARS_CoV_2 D614G;I472V 28;34 33;39 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Moreover, some variants, including N439K, L452R, A475V, V483A, F490L, and Y508H, do have decreased sensitivity to neutralizing mAbs. 2020 Cell Discussion SARS_CoV_2 A475V;F490L;L452R;N439K;V483A;Y508H 49;63;42;35;56;74 54;68;47;40;61;79 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Notably, some RBD variants such as A475V and F490L have been confirmed to have decreased sensitivity to both human sera and multiple neutralizing mAbs. 2020 Cell Discussion SARS_CoV_2 A475V;F490L 35;45 40;50 RBD 14 17 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Of all variants, D614G is of particular note. 2020 Cell Discussion SARS_CoV_2 D614G 17 22 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. P2C-1F11 and P2B-2F6 actually bind to overlapping epitope, with the latter being better characterized. 2020 Cell Discussion SARS_CoV_2 P2C 0 3 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. The A475V could weaken the hydrogen bond and hydrophobic interaction, whereas F490L may erode the hydrophobic interaction between molecules. 2020 Cell Discussion SARS_CoV_2 A475V;F490L 4;78 9;83 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. V483A in RBD is one of the two variants with a mutation frequency of over 0.1%. 2020 Cell Discussion SARS_CoV_2 V483A 0 5 RBD 9 12 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Variants containing N439K showed a significant increase in circulation, i.e., with 5 cases reported as of May 6, 2020 (all in the United Kingdom) to 47 by July 3, 2020 (45 in the United Kingdom and 2 in Romania). 2020 Cell Discussion SARS_CoV_2 N439K 20 25 32730807 The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. With regard to the glycosylation mutants analyzed in this study, N165Q increased the sensitivity to mAb P2b-2F6 whereas N234Q displayed resistance to neutralizing mAbs such CA1, CB6, 157, and others. 2020 Cell Discussion SARS_CoV_2 N165Q;N234Q 65;120 70;125 32732280 Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. The N501Y mutation seems to provide a more favorable interaction with mouse ACE2 for docking and entry, thus leading to the increased virulence phenotype in mice. 2020 Science (New York, N.Y.) Discussion SARS_CoV_2 N501Y 4 9 32732280 Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy. Whether the other three mutations, except for N501Y, also regulated viral infectivity remains to be determined. 2020 Science (New York, N.Y.) Discussion SARS_CoV_2 N501Y 46 51 32735992 Design of an engineered ACE2 as a novel therapeutics against COVID-19. Although the saturation mutation results proposed the Arginine 273 to Glycine mutation, we have preferred the experimentally approved Arginine to Glutamine mutation. 2020 Journal of theoretical biology Discussion SARS_CoV_2 R273G 54 77 32735992 Design of an engineered ACE2 as a novel therapeutics against COVID-19. Our results indicate that the threonine 27 to Arginine mutation does not have a drastic effect on the interaction orientation and the interacting amino acids. 2020 Journal of theoretical biology Discussion SARS_CoV_2 T27R 30 54 32735992 Design of an engineered ACE2 as a novel therapeutics against COVID-19. The first approach involved the mutation of amino acids with highest B factors (aspartate 427 to arginine). 2020 Journal of theoretical biology Discussion SARS_CoV_2 D427R 80 105 32735992 Design of an engineered ACE2 as a novel therapeutics against COVID-19. The Threonine 445 to Glycine mutation does the same regarding the hydrogen bond omission and preservation of the occupied volume by an equivalent sidechain. 2020 Journal of theoretical biology Discussion SARS_CoV_2 T445G 4 28 32735992 Design of an engineered ACE2 as a novel therapeutics against COVID-19. These results could be construed as stronger interactions between ACE2 and RBD with similar interaction orientation following the threonine 27 to Arginine mutation. 2020 Journal of theoretical biology Discussion SARS_CoV_2 T27R 130 154 RBD 75 78 32742035 Variant analysis of SARS-CoV-2 genomes. Almost all strains with D614G mutation also have a mutation in the protein responsible for replication (ORF1ab P4715L; RdRp P323L), which might affect replication speed of the virus. 2020 Bulletin of the World Health Organization Discussion SARS_CoV_2 D614G;P323L;P4715L 24;124;111 29;129;117 ORF1ab;RdRP 104;119 110;123 32742035 Variant analysis of SARS-CoV-2 genomes. Although amino acids are quite conserved in this epitope, we identified 14 other variants besides D614G. 2020 Bulletin of the World Health Organization Discussion SARS_CoV_2 D614G 98 103 32742035 Variant analysis of SARS-CoV-2 genomes. D614G was first observed in late January in China and became the largest clade in three months. 2020 Bulletin of the World Health Organization Discussion SARS_CoV_2 D614G 0 5 32742035 Variant analysis of SARS-CoV-2 genomes. The most common clade identified was the D614G variant, which is located in a B-cell epitope with a highly immunodominant region and may therefore affect vaccine effectiveness. 2020 Bulletin of the World Health Organization Discussion SARS_CoV_2 D614G 41 46 32742035 Variant analysis of SARS-CoV-2 genomes. The V367F and D364Y variants have been reported to enhance the structural stability of the spike protein facilitating more efficient binding to the ACE2 receptor. 2020 Bulletin of the World Health Organization Discussion SARS_CoV_2 D364Y;V367F 14;4 19;9 S 91 96 32742035 Variant analysis of SARS-CoV-2 genomes. V483A and G476S are primarily observed in samples from the United States, whereas V367F is found in samples from China, Hong Kong Special Administrative Region, France and the Netherlands. 2020 Bulletin of the World Health Organization Discussion SARS_CoV_2 G476S;V367F;V483A 10;82;0 15;87;5 32742035 Variant analysis of SARS-CoV-2 genomes. While the earliest samples from the United Stated appear to be derived from China, belonging either to basal or L84S clades, the European clades, such as D614G/Q57H, tend to associate with most of the subsequent increase in infected people in the United States. 2020 Bulletin of the World Health Organization Discussion SARS_CoV_2 D614G;L84S;Q57H 154;112;160 159;116;164 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. Given the location of the 614 residue within the S1 fragment distal to the RBD, it is also unlikely that the D614G mutation directly affects the ACE2 binding activity. 2020 bioRxiv Discussion SARS_CoV_2 D614G 109 114 RBD 75 78 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. Here, in the present report we find functional evidence that the Spike D614G mutant has modestly different biochemical properties consistent with positive selection of the D614G mutant SARS-CoV2 virus variant. 2020 bioRxiv Discussion SARS_CoV_2 D614G;D614G 71;172 76;177 S 65 70 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. Observational population genetics alone could not resolve whether this mutation and/or the frequently co-occurring ORF1b P314L allele alter biological activity or are just an epiphenomenon underlying a founder effect due to repeated introductions. 2020 bioRxiv Discussion SARS_CoV_2 P314L 121 126 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. The emergence of the SARS-CoV2 Spike D614G and its rapid increase in prevalence has been striking. 2020 bioRxiv Discussion SARS_CoV_2 D614G 37 42 S 31 36 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. The increase in cell entry activity of pseudotyped lentiviral vectors and cell fusion allowed us to dissect the Spike protein function in isolation and test the activity of the D614G point mutation. 2020 bioRxiv Discussion SARS_CoV_2 D614G 177 182 S 112 117 32743569 The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner. Thus, a biochemical basis for increased infectivity is observed in the SARS-CoV2 D614G mutant consistent with positive selection observed in the field. 2020 bioRxiv Discussion SARS_CoV_2 D614G 81 86 32764372 Comprehensive Analyses of SARS-CoV-2 Transmission in a Public Health Virology Laboratory. Depending upon whether these mutations are beneficial for the virus, they may survive and be transmitted over time, for example, as occurred with the emerging clade 20-associated mutation A23403G/D614G that changed aspartate (acidic group) to glycine (aliphatic group) in the spike protein which presumably provides better viral fitness. 2020 Viruses Discussion SARS_CoV_2 A23403G;D614G 188;196 195;201 S 276 281 32764372 Comprehensive Analyses of SARS-CoV-2 Transmission in a Public Health Virology Laboratory. Indeed, the A23403G mutation associated with clade 20, also referred to as D614G (numbering according to the position of the mutation in the spike protein amino acid sequence), was recently shown to have emerged in Europe and is now the most prevalent form worldwide. 2020 Viruses Discussion SARS_CoV_2 A23403G;D614G 12;75 19;80 S 141 146 32764372 Comprehensive Analyses of SARS-CoV-2 Transmission in a Public Health Virology Laboratory. S8 (S3's spouse), shared only one 20C clade mutation with other ICVL members:G25563T, while lacking the other:C1059T. 2020 Viruses Discussion SARS_CoV_2 C1059T;G25563T 110;77 116;84 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. The prevalent Spike D614G mutation does not seem to affect the interaction domain with ACE2 (Wang et al.,), responsible for the viral entry into epithelial cells (Guzzi et al.,), but other mutations are currently located in that domain, such as N439K, present in 0.7% of the sequenced SARS-CoV-2 genomes. 2020 Frontiers in microbiology Discussion SARS_CoV_2 D614G;N439K 20;245 25;250 S 14 19 32793182 Geographic and Genomic Distribution of SARS-CoV-2 Mutations. There is currently little evidence on the clinical and molecular differences between the circulating clades of SARS-CoV-2; for example, one study has shown that the D614G mutation in the Spike protein may be associated to higher case fatality rates (Becerra-Flores and Cardozo,). 2020 Frontiers in microbiology Discussion SARS_CoV_2 D614G 165 170 S 187 192 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. A mutation profile consisting in C3037T, C14408T, A23403G (mutation found in all the Romanian sequences), next to C241T was found to be specific to the Europe cluster and was initially associated with higher pathogenicity. 2020 Life (Basel, Switzerland) Discussion SARS_CoV_2 A23403G;C14408T;C241T;C3037T 50;41;114;33 57;48;119;39 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. A new mutation, K489E in Nsp2 protein, was identified in one of the strains circulating in BMA in a patient with a mild disease form. 2020 Life (Basel, Switzerland) Discussion SARS_CoV_2 K489E 16 21 Nsp2 25 29 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. A subsequent study reported that A23403G (D614G in S) is becoming prevalent worldwide and associated with severe disease cases. 2020 Life (Basel, Switzerland) Discussion SARS_CoV_2 A23403G;D614G 33;42 40;47 S 51 52 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. Although the unreported mutation (K489E) we have found in Nsp2 protein may not impact the virus replication, its interaction with the host mechanisms might influence the disease evolution. 2020 Life (Basel, Switzerland) Discussion SARS_CoV_2 K489E 34 39 Nsp2 58 62 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. However, only one of the isolated strains (EPI_ISL_468152) was associated with severe disease; this strain had an additional mutation Y397C in Nsp4 protein. 2020 Life (Basel, Switzerland) Discussion SARS_CoV_2 Y397C 134 139 Nsp4 143 147 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. It is plausible to presume that one of these cysteines would form a disulfide bridge if Y397C mutation occurs, therefore a fourth cysteine in that space could enhance the formation of the disulfide bridges in that region, which may affect the overall conformation of Nsp4. 2020 Life (Basel, Switzerland) Discussion SARS_CoV_2 Y397C 88 93 Nsp4 267 271 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. Some mutations have emerged as possible signatures for different outbreaks in Romania, thus A20268G is linked to north Romania (Suceava county), while sequences with G28881A, G28882A and G28883C are found in south-east Romania (BMA). 2020 Life (Basel, Switzerland) Discussion SARS_CoV_2 A20268G;G28881A;G28882A;G28883C 92;166;175;187 99;173;182;194 32823907 Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic. These sequences showcase one particular non-synonymous mutation, C16049T (T870I in Nsp12). 2020 Life (Basel, Switzerland) Discussion SARS_CoV_2 C16049T;T870I 65;74 72;79 Nsp12 83 88 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. Existing reports stated that the substitution of Ala to Val is one of the major causes of resistance in the mouse hepatitis coronavirus which was studied against HR1 and HR2 derived peptide inhibitors (Bosch et al.,), the spike protein mutation A930V of HR1 may also have a similar effect, which can be investigated further. 2022 Journal of biomolecular structure & dynamics Discussion SARS_CoV_2 A930V 245 250 S 222 227 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. Interestingly, in our study too, the RBD mutations L455Y, F486L, Q493N, and N501T were observed to have the highest deviations as compared to the WT structure. 2022 Journal of biomolecular structure & dynamics Discussion SARS_CoV_2 F486L;L455Y;N501T;Q493N 58;51;76;65 63;56;81;70 RBD 37 40 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. Most of the mutations like F486L, Q493N, L455Y, and Q498Y are known to interact and N501T was found in forming a hydrogen bond with ACE2 in the viral entry to the host cells. 2022 Journal of biomolecular structure & dynamics Discussion SARS_CoV_2 F486L;L455Y;N501T;Q493N;Q498Y 27;41;84;34;52 32;46;89;39;57 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The A930V and D936Y mutations of the HR1 domain play a significant role in the infection process as the domain is vital for the viral membrane fusion and host cell entry forming the helical bundles. 2022 Journal of biomolecular structure & dynamics Discussion SARS_CoV_2 A930V;D936Y 4;14 9;19 Membrane 134 142 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The analysis of the intramolecular hydrogen bonding profile revealed the least number of the bonds in mutant structures F486L, and Q498Y, whereas the mutations R408I, L455Y, Q493N, and N501T projected average intra-molecular hydrogen bonds when compared to WT. 2022 Journal of biomolecular structure & dynamics Discussion SARS_CoV_2 F486L;L455Y;N501T;Q493N;Q498Y;R408I 120;167;185;174;131;160 125;172;190;179;136;165 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The in silico methods revealed that the selected mutations R408I, L455Y, F486L, Q493N, Q498Y, N501T on RBD, and A930V, D936Y on HR1 are highly deleterious, damaging and majorly responsible for the destabilization of spike glycoprotein. 2022 Journal of biomolecular structure & dynamics Discussion SARS_CoV_2 A930V;D936Y;F486L;L455Y;N501T;Q493N;Q498Y;R408I 112;119;73;66;94;80;87;59 117;124;78;71;99;85;92;64 S;RBD 216;103 234;106 32851910 Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. The mutant R408I on the RBD domain persists a positive charge (Arg) which is substituted by an aliphatic uncharged (Iso) residue, this change in charge can affect the receptor binding. 2022 Journal of biomolecular structure & dynamics Discussion SARS_CoV_2 R408I 11 16 RBD 24 27 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. A mutation, S612L, that emerged in MERS-CoV after passaging the virus in the presence of two antibodies (in 5/15 clones after 20 passages) warrants the evaluation of the analogous D614G mutation in SARS-CoV-2 for its ability to interfere with the recognition of a distal epitope. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G;S612L 180;12 185;17 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. As such, on January 28, 2020, a virus carrying the D614G mutation, which was rare among sequences from China, was identified in Germany. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 51 56 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. As such, pseudoviruses with D614G were as susceptible to neutralization as those with the initial residue D614. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 28 33 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. For example, SARS-CoV mediates cell entry more efficiently than SARS-CoV-2 (with or without the D614G S mutation). 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 96 101 S 102 103 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Further analyses are needed to characterize the biologic mechanisms behind the spread of the D614G mutation. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 93 98 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Hence, it would be important to understand whether, controlling for epidemiological factors, there are higher reproduction numbers associated with viruses carrying the D614G mutation. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 168 173 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Importantly, we found no mutation in the RBD that was present in more than 1% of SARS-CoV-2 sequences (highest frequency was 0.2% N439K); such rare variants are unlikely to interfere with vaccine efficacy. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 N439K 130 135 RBD 41 44 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. In the context of rare SARS-CoV-2 mutations, the rapid spread of the D614G mutation is singular and has led authors to hypothesize that viruses with D614G may have enhanced fitness. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G;D614G 69;149 74;154 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. So far, no causal association has been identified between the presence of D614G and disease severity. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 74 79 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Specifically, an A82V mutation in the glycoprotein, which, like S for SARS-CoV-2, is critical for the virus entry into host cells, was associated with an increase in infectivity. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 A82V 17 21 S 64 65 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. The strongest evidence of a biological effect for this mutation comes from recent reports of an increase in in vitro infectivity or cell entry for pseudoviruses with D614G. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 166 171 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. These data indicate that epidemiologic factors could be sufficient to explain the global spread of mutations such as D614G. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 117 122 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Vaccine developers could consider designing a vaccine insert with the D614G mutation in S, as this mutation has become dominant worldwide. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 70 75 S 88 89 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. While a preliminary comparison of the lineages with either D or G in Washington State did not indicate an obvious advantage for D614G mutants, as they found similar maximal values for the effective reproduction number (https://github.com/blab/ncov-wa-phylodynamics), additional comparisons in different geographic locations should be informative. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 128 133 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. While mutations that become fixed are often linked to the host immune pressure, this seems unlikely for the SARS-CoV-2 mutation D614G. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 128 133 32868447 A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Yet, it is important to note that founder effects do not exclude that the D614G can confer distinguishing properties in terms of protein stability, infectivity, or transmissibility. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 74 79 32869023 SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution. As expected, the P323L change in the RNA-dependent RNA polymerase (RdRp), genetically linked to D614G, was also found in all our samples. 2020 bioRxiv Discussion SARS_CoV_2 D614G;P323L 96;17 101;22 RdRp;RdRP 37;67 65;71 32869023 SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution. In silico analysis showed that P323L may have an impact on the protein secondary structure, leading to a reduction in its molecular flexibility. 2020 bioRxiv Discussion SARS_CoV_2 P323L 31 36 32869023 SARS-CoV-2 genomic and quasispecies analyses in cancer patients reveal relaxed intrahost virus evolution. The spike (S) D614G mutation, found in all samples analyzed, has been associated with higher viral titers, suggesting increased viral infectivity. 2020 bioRxiv Discussion SARS_CoV_2 D614G 14 19 S;S 4;11 9;12 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. In addition, we also found 379C>A with a high prevalence in our study specimens compared to the subsampling of sequences from the United States and globally (Figure 6). 2020 medRxiv Discussion SARS_CoV_2 C379A 27 33 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. In this study 62 of the 133 specimens from Northern Nevada contain P323F. 2020 medRxiv Discussion SARS_CoV_2 P323F 67 72 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. It is possible that these measures, compounded by potential inherent transmission variability of some viral isolates, influenced the change in the frequency of D614G, clades and P323L/F that we noted during this time period within Nevada. 2020 medRxiv Discussion SARS_CoV_2 D614G;P323F;P323L 160;178;178 165;185;185 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. Of the 14,885 complete SARS-CoV-2 genomes currently available (as of August 14, 2020) in NCBI there are only 6 genomes that have the P323F variant (accession number: MT706208, LR860619, MT345877, MT627429, MT810889, MT811171). 2020 medRxiv Discussion SARS_CoV_2 P323F 133 138 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. That is 46% of specimens from Northern Nevada contain P323F compared to 0.04% of NCBI deposited SARS-CoV-2 isolates. 2020 medRxiv Discussion SARS_CoV_2 P323F 54 59 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. We find that the overall trend for D614G in Nevada during this time period was similar to what was observed in other states and internationally, with the exception of within Asia where the D614 allele had originated. 2020 medRxiv Discussion SARS_CoV_2 D614G 35 40 32869037 Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. We performed structural modeling of the P323L/F variation and did not find any significant change to the nsp12 conformation with either P323L or P323F, therefore this variant is most likely a neutral mutation and does not confer either a fitness advantage or disadvantage to transmission or pathogenicity of SARS-CoV-2. 2020 medRxiv Discussion SARS_CoV_2 P323F;P323L;P323F;P323L 145;136;40;40 150;141;47;47 Nsp12 105 110 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. A mutation P344S in nucleocapsid protein has been detected in SARS-CoV-2 Japan strain. 2020 PloS one Discussion SARS_CoV_2 P344S 11 16 N 20 32 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. Single amino acid mutation was observed in both Mpro (R60C) of SARS-CoV-2 Vietnam isolate and RdRp (A408V) of SARS-CoV-2 India isolate. 2020 PloS one Discussion SARS_CoV_2 A408V;R60C 100;54 105;58 RdRP 94 98 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. The Indian isolates were carrying the R408I on the spike protein while A406V on the RdRp and several mutations on the replicase polyprotein of SARS-CoV-2. 2020 PloS one Discussion SARS_CoV_2 A406V;R408I 71;38 76;43 S;RdRP 51;84 56;88 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. The P344S mutation on nucleocapsid was found to decrease the protein stability (DeltaDeltaG -1.2252261). 2020 PloS one Discussion SARS_CoV_2 P344S 4 9 N 22 34 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. The R60C mutant lies at helix adjacent to the short helix (H2) that forms the catalytic channel (Fig 5). 2020 PloS one Discussion SARS_CoV_2 R60C 4 8 32881907 Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. We detected one amino acid mutation L37H in transmembrane domain (TMD) of envelop protein of SARS-CoV-2 South Korea isolate. 2020 PloS one Discussion SARS_CoV_2 L37H 36 40 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. Hence the mutation A930V in HR1 domain and D1168H in HR2 domain found in our study might be relevant in explaining the pathogenesis of SARS-CoV-2. 2020 Journal of laboratory physicians Discussion SARS_CoV_2 A930V;A930V;D1168H 20;19;43 25;24;49 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. However, a previous study shows variations in HR1 domain which forms helical bundles with HR2 to facilitate fusion and entry of virus into the host and hypothesizes that the mutation A1168V in HR2 domain along with A930V mutation in HR1 domain confers peptide entry inhibitor resistance in mouse hepatitis coronaviruses. 2020 Journal of laboratory physicians Discussion SARS_CoV_2 A1168V;A930V;A930V 183;217;215 189;222;220 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. Out of 88 SNP clusters, D614G was found in 34 (38.6%) SARS-CoV-2 genomes. 2020 Journal of laboratory physicians Discussion SARS_CoV_2 D614G 25 30 32884216 Mutations in SARS-CoV-2 Leading to Antigenic Variations in Spike Protein: A Challenge in Vaccine Development. The amino acid change in 23403A>G variant (p.D614G) involves a change of large acidic residue D (aspartic acid) into small hydrophobic residue G (glycine). 2020 Journal of laboratory physicians Discussion SARS_CoV_2 A23403G;D614G 25;45 33;50 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. Among the triple linkage substitution hotspots of ORF1ab-277, ORF1ab-14144 and S-1841, ORF1ab-C2772T belongs to synonymous substitution, while ORF1ab-C14144T caused the aa change of NSP12-P323L in interface region which is a bridge section connecting NiRNA (nidovirus RdRp-associated nucleo-tidyltransferase) and Fingers of RdRp. 2020 Sustainable cities and society Discussion SARS_CoV_2 C14144T;C2772T;P323L 150;94;188 157;100;193 ORF1ab;ORF1ab;ORF1ab;ORF1ab;Nsp12;RdRP;RdRP;S 50;62;87;143;182;268;324;79 56;68;93;149;187;272;328;80 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. As for ORF3a-G752T (G251V), a recent analysis predicted that it was in an important functional domain and might be related to virulence, infectivity, ion channel formation and virus release. 2020 Sustainable cities and society Discussion SARS_CoV_2 G251V;G752T 20;13 25;18 ORF3a 7 12 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. For instance, S-Q675H and S-Q675R near furin cleavage region possibly influence the cleavage of RRAR, a critical step for virus entry. 2020 Sustainable cities and society Discussion SARS_CoV_2 Q675H;Q675R 16;28 21;33 S;S 14;26 15;27 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. For instance, the ORF1ab-C794T was located on NSP2 and NSP2 was reported to inhibit the host protein PHB1 and PHB2 which benefited viral replication, indicating that ORF1ab-C794T may affect viral replication. 2020 Sustainable cities and society Discussion SARS_CoV_2 C794T;C794T 25;173 30;178 ORF1ab;ORF1ab;Nsp2;Nsp2 18;166;46;55 24;172;50;59 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. In addition, we also detected a strain with the mutation of S-R408I located in the RBD (Table S2) which was reported to play an important role in virus-receptor binding by a recent study. 2020 Sustainable cities and society Discussion SARS_CoV_2 R408I 62 67 RBD;S 83;60 86;61 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. In SARS-CoV NSP13, the 541th aa was critical for the protein function and double mutations of S539A/Y541A showed higher unwinding activity for nucleic acids binding. 2020 Sustainable cities and society Discussion SARS_CoV_2 S539A;Y541A 94;100 99;105 Nsp13 12 17 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. Notably, the mutant strain of NSP13-541C first appeared in the United States (sampled on Feb 20, 2020), and the United States was the country with the largest number and extremely high proportion of this mutant strains (316, 78 % of all the 405 mutant strains with NSP13-Y541C). 2020 Sustainable cities and society Discussion SARS_CoV_2 Y541C 271 276 Nsp13;Nsp13 30;265 35;270 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. The latest study has discovered the strain with substitution of S-D614G could increases the infectivity of SARS-CoV-2. 2020 Sustainable cities and society Discussion SARS_CoV_2 D614G 66 71 S 64 65 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. The ORF3a-G171T (Q57H) was located at the transmembranous domain of the 3a protein. 2020 Sustainable cities and society Discussion SARS_CoV_2 Q57H;G171T 17;10 21;15 ORF3a 4 9 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. Therefore, we speculate that NSP13-Y541C improves the unwinding activity of NSP13 and promotes the replication of SARS-CoV-2, contributing to their rapid spread in the United States. 2020 Sustainable cities and society Discussion SARS_CoV_2 Y541C 35 40 Nsp13;Nsp13 29;76 34;81 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. This fact indicates that NSP13-Y541C has gone through less negative selection pressure and even this variation may be beneficial. 2020 Sustainable cities and society Discussion SARS_CoV_2 Y541C 31 36 Nsp13 25 30 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. Thus, ORF3a-G171T (Q57H) may affect the formation of ion channels and subsequently influence the viral replication. 2020 Sustainable cities and society Discussion SARS_CoV_2 Q57H;G171T 19;12 23;17 ORF3a 6 11 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. We also noted that among the 711 strains sampled in the United States on Feb 20, 2020 and beyond, strains with NSP13-Y541C accounted for almost half of these strains. 2020 Sustainable cities and society Discussion SARS_CoV_2 Y541C 117 122 Nsp13 111 116 32904401 BioAider: An efficient tool for viral genome analysis and its application in tracing SARS-CoV-2 transmission. We found that mutant strains with NSP12-323L & S-614G were popular in the world and owned more than half the frequency (52 %) in the population, indicating that this mutant was dominant in SARS-CoV-2. 2020 Sustainable cities and society Discussion SARS_CoV_2 S614G 47 53 Nsp12;S 34;47 39;48 32905045 Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. Demonstration that POC antibody LFA tests can detect the D614G spike mutant is therefore of importance. 2020 Cell reports. Medicine Discussion SARS_CoV_2 D614G 57 62 S 63 68 32905045 Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. Of critical importance is the fact that both POC antibody tests (and ELISA) were able to detect antibody responses in patients infected with the D614G Spike mutant and that the band intensity of POC testing increased with neutralization activity in these individuals. 2020 Cell reports. Medicine Discussion SARS_CoV_2 D614G 145 150 S 151 156 32905045 Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. The D614G Spike mutant has spread globally. 2020 Cell reports. Medicine Discussion SARS_CoV_2 D614G 4 9 S 10 15 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Although virions produced from Calu-3 cells had more complete S1/S2 cleavage than those produced form Vero E6 cells, no substantial differences in spike cleavage were detectable between the D614 and G614 virions produced from either cell type, suggesting that the enhanced virion infectivity is not likely due to the D614G-mediated spike cleavage difference. 2020 bioRxiv Discussion SARS_CoV_2 D614G 317 322 S;S 147;332 152;337 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Besides antisera, we also showed that, depending on the epitope locations on RBD, the neutralizing potency of certain mAbs may be affected by the D614G mutation. 2020 bioRxiv Discussion SARS_CoV_2 D614G 146 151 RBD 77 80 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. In summary, we have used authentic SARS-CoV-2 to demonstrate that spike substitution D614G enhances viral replication in the upper respiratory tract and increases neutralization susceptibility. 2020 bioRxiv Discussion SARS_CoV_2 D614G 85 90 S 66 71 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Mechanistically, two recent studies showed that the D614G mutation abolishes a hydrogen-bond interaction with T859 from a neighboring protomer of the spike trimer, which allosterically promotes the RDB domain to an "up" conformation for receptor ACE2 binding and fusion, leading to an enhanced virion infectivity. 2020 bioRxiv Discussion SARS_CoV_2 D614G 52 57 S 150 155 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Our results from authentic SARS-CoV-2 are in contrast with previous studies reporting that the D614G mutation changes the cleavage and shedding of spike protein when expressed alone or in the context of pseudotyped virions. 2020 bioRxiv Discussion SARS_CoV_2 D614G 95 100 S 147 152 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Patients infected with G614 virus developed higher levels of viral RNA in the nasopharyngeal swabs than those infected with D614 virus, but disease severity is not associated with the D614G mutation. 2020 bioRxiv Discussion SARS_CoV_2 D614G 184 189 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. Since current COVID-19 vaccines in clinical trials are based on the original D614 sequence, our neutralization result mitigates the concern that the D614G mutation might compromise the efficacy of vaccines against the circulating G614 virus. 2020 bioRxiv Discussion SARS_CoV_2 D614G 149 154 COVID-19 14 22 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. The higher viral loads of G614 in the upper airway of COVID-19 patients and infected hamsters support the role of D614G mutation in viral transmissibility. 2020 bioRxiv Discussion SARS_CoV_2 D614G 114 119 COVID-19 54 62 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. The increased susceptibility of G614 virus to serum neutralization generated by D614 seems counterintuitive, but could be explained by the D614G-mediated increase in the "up" conformation of the RDB for binding to ACE2 receptor. 2020 bioRxiv Discussion SARS_CoV_2 D614G 139 144 32908978 Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. We demonstrated that the spike substitution D614G enhanced SARS-CoV-2 replication in the upper respiratory tract through increased virion infectivity. 2020 bioRxiv Discussion SARS_CoV_2 D614G 44 49 S 25 30 32934770 Structural Impact of Mutation D614G in SARS-CoV-2 Spike Protein: Enhanced Infectivity and Therapeutic Opportunity. The structural, or rather epistructural, impact of the mutation D614G is consistent with established phenotypic differences between SG614 and SD614 in the sense that SG614 has a greater stability resulting from less S1 shedding and greater incorporation of the intact S protein into the pseudovirion. 2020 ACS medicinal chemistry letters Discussion SARS_CoV_2 D614G 64 69 S 268 269 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. In fact, the low frequency of this mutation in Spain is difficult to reconcile with the high incidence of the disease in the country, compared to other countries with lower disease incidence but a higher frequency of D614G. 2020 Zoological research Discussion SARS_CoV_2 D614G 217 222 32935498 Phylogeography of SARS-CoV-2 pandemic in Spain: a story of multiple introductions, micro-geographic stratification, founder effects, and super-spreaders. We found no evidence to support previous claims suggesting increased transmissibility of SARS-CoV-2 strains carrying the amino-acid mutation D614G (basically all A2 haplotypes; see phylogeny of Figure 1 and). 2020 Zoological research Discussion SARS_CoV_2 D614G 141 146 32937868 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. A23403G is one of the most prominent mutations; it occurs in the S protein at amino acid residue 614, where Aspartic acid is substituted by Glycine (D614G). 2020 Viruses Discussion SARS_CoV_2 D614G;A23403G 149;0 154;7 S 65 66 32937868 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. All MPs with the exception of MP1 had the basic genomic mutation A23403G. 2020 Viruses Discussion SARS_CoV_2 A23403G 65 72 32937868 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. Although the frequency of S936Y is low worldwide, increased frequency has been observed in Nordic countries: 69% (178/258, the number for mutant's appearance/total number of SARS-CoV-2) in Finland, 22% (116/531) in Sweden, and 11% (9/83) in Norway (data from 3 August, ). 2020 Viruses Discussion SARS_CoV_2 S936Y 26 31 32937868 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. et al., but with the additional mutations T265I on ORF1ab, Q57H on ORF3, and the four basic mutations (C241T, C3037T, C14408T, and A23403G). 2020 Viruses Discussion SARS_CoV_2 A23403G;C14408T;C3037T;Q57H;T265I;C241T 131;118;110;59;42;103 138;125;116;63;47;108 ORF1ab 51 57 32937868 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. For instance, a mutation in the Zika virus membrane region (prM-S139N) emerged in a viral lineage preceding the devastating epidemic in the Americas, while a single mutation (GP-A82V) in Ebola virus increased the infection rate of human cells. 2020 Viruses Discussion SARS_CoV_2 A82V;S139N 178;64 182;69 Membrane 43 51 32937868 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. found that the D614G/ D936Y co-occur on the S1/S2 protein, and their emergence was traced back to 15 March in Washington, USA, and later on spread to Wales, Iceland, and the Netherlands. 2020 Viruses Discussion SARS_CoV_2 D614G;D936Y 15;22 20;27 32937868 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. In Sweden, we found that on 14 May, the frequency of D614G on the S1 protein was 94.8% in the population. 2020 Viruses Discussion SARS_CoV_2 D614G 53 58 32937868 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. Our findings that D936Y in the S protein is under positive selection is consistent with antigenic drift playing a role for SARS-CoV-2 as well. 2020 Viruses Discussion SARS_CoV_2 D936Y 18 23 S 31 32 32937868 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. The D614G mutant strain is designated as the "G clade" by GISAID and originated in Europe, and further spread to North America and Oceania, then Asia. 2020 Viruses Discussion SARS_CoV_2 D614G 4 9 32937868 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. We found that the basis mutations, which contain C241T, C3037T, C14408T, and A23403G, combined with other mutations can be classified into 10 mutational profiles in Sweden. 2020 Viruses Discussion SARS_CoV_2 A23403G;C14408T;C241T;C3037T 77;64;49;56 84;71;54;62 32937868 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. We saw this co-occurrence of D614G/D936Y in our data-set with a frequency of 17.2%, which was the same frequency as MP6. 2020 Viruses Discussion SARS_CoV_2 D614G;D936Y 29;35 34;40 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Although the E191D mutant was somewhat more sensitive to the mutagenic agent 5-FU. 2020 Journal of virology Discussion SARS_CoV_2 E191D 13 18 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. As reported for MHV and SARS-CoV ExoN mutants, possible (late) reversion was observed for a few of our MERS-CoV ExoN active-site mutants, specifically, those with E191A, D273E, D273A, and in particular D90E, which had reverted by 6 dpt in four of eight experiments. 2020 Journal of virology Discussion SARS_CoV_2 D273A;D273E;D90E;E191A 177;170;202;163 182;175;206;168 Exon;Exon 33;112 37;116 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Biochemical assays revealed that the E191D-ExoN enzyme is able to hydrolyze a dsRNA substrate with an activity level approaching that of the wt protein. 2020 Journal of virology Discussion SARS_CoV_2 E191D 37 42 Exon 43 47 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Furthermore, in follow-up studies with the crippled H229C ZF1 mutant, a possible pseudorevertant carrying a second-site mutation (Q19R) in nsp8 was identified in three independently obtained progeny samples, providing genetic support for an interaction between nsp8 and nsp14, which may be relevant in the context of the association of nsp14 with the tripartite RdRp complex consisting of nsp7, nsp8, and nsp12. 2020 Journal of virology Discussion SARS_CoV_2 H229C;Q19R 52;130 57;134 Nsp12;Nsp7;Nsp8;Nsp8;Nsp8;RdRP 405;389;139;261;395;362 410;393;143;265;399;366 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Here, we demonstrate that the more conservative H229C replacement, which converts ZF1 from a nonclassical CCCH-type ZF motif into a classical CCCC type, was tolerated during recombinant protein expression and yielded an ExoN that is active in vitro. 2020 Journal of virology Discussion SARS_CoV_2 H229C 48 53 Exon 220 224 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. However, this did not change the negative outcome of our transfection experiments, which were repeated more than 10 times for several of the nonviable mutants, always using wt and E191D MERS-CoV as positive controls that proved to be consistently viable. 2020 Journal of virology Discussion SARS_CoV_2 E191D 180 185 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. In contrast, the corresponding TGEV mutant (ZF-C) was not strongly affected and could be stably maintained over several passages The reverse genetics data suggest that ZF2, which is in close proximity to ExoN catalytic residues, is equally important, although technical complications with expression of the C261A and H264R nsp14 mutants prevented us from performing in vitro activity assays. 2020 Journal of virology Discussion SARS_CoV_2 C261A;H264R 307;317 312;322 Exon 204 208 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. In previous ZF1 studies, a mutation equivalent to H229A caused solubility issues during expression of recombinant SARS-CoV nsp14 and resulted in a partially active ExoN in the case of white bream virus, a tobanivirus that also belongs to the order Nidovirales. 2020 Journal of virology Discussion SARS_CoV_2 H229A 50 55 Exon 164 168 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. In the only viable MERS-CoV ExoN active-site mutant obtained, E191D, the catalytic motif was changed from DEEDh to DEDDh, which is characteristic of all members of the exonuclease family that ExoN belongs to. 2020 Journal of virology Discussion SARS_CoV_2 E191D 62 67 Exonuclease;Exon;Exon 168;28;192 179;32;196 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Mutation of ExoN catalytic residues can alter ion binding or disturb the fragile chemical equilibrium, as shown for conservative mutations (corresponding to E191D and D273E) in the Klenow fragment, a member of the DEDDh exonuclease family, which reduced ExoN activity by >96%. 2020 Journal of virology Discussion SARS_CoV_2 D273E;E191D 167;157 172;162 Exonuclease;Exon;Exon 220;12;254 231;16;258 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. Nevertheless, its overall crippled phenotype and the nonviable phenotype of the C201H mutant clearly highlighted the general importance of ZF1 for virus replication. 2020 Journal of virology Discussion SARS_CoV_2 C201H 80 85 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. The growth of the E191D virus mutant was comparable to that of wt virus. 2020 Journal of virology Discussion SARS_CoV_2 E191D 18 23 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. The only exception was the conservative E191D mutant, which was found to exhibit near-wt ExoN activity. 2020 Journal of virology Discussion SARS_CoV_2 E191D 40 45 Exon 89 93 32938769 The Enzymatic Activity of the nsp14 Exoribonuclease Is Critical for Replication of MERS-CoV and SARS-CoV-2. This likely contributed to the fact that the H229C virus mutant retained a low level of viability. 2020 Journal of virology Discussion SARS_CoV_2 H229C 45 50 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. D614G was detected in 85% of sequences being present in most of the South American countries with available genomic information. 2020 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 0 5 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. On the other hand, the co-occurrence of R203K and G204R substitutions in the N protein, was identified in 34% of South American sequences. 2020 Infection, genetics and evolution Discussion SARS_CoV_2 G204R;R203K 50;40 55;45 N 77 78 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. Several studies have suggested a potential role of the D614G substitution in increase the virus infectivity, transmissibility, mortality rate and immune system evasion; However, the information regarding D614G substitution is still inconclusive and it there is not unquestionable evidence of the relation of this mutation with SARS-CoV-2 infectivity and transmission, also it was not possible to rule out the association with founder effects. 2020 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;D614G 55;204 60;209 32950697 Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America. This study evidenced the presence of the D614G substitution in the S protein in 89.6% (112/125) of Colombian SARS-CoV-2 sequences, by April 27, 2020, while the first introduced cases presented the conserved position reported in the Wuhan-Hu-1 reference genome. 2020 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 41 46 S 67 68 32967693 A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual. In agreement with the evidence that SARS-CoV-2 GZ69 isolate showed no relevant impairment in infectivity, we observed that it maintained a "wild type" S sequence; the fixed "european" D614G substitution was, in fact, the only difference detected with respect to Wuhan reference strain. 2020 Journal of translational medicine Discussion SARS_CoV_2 D614G 184 189 S 151 152 32967693 A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual. In particular, mutation S1188L is comprised within the SARS-CoV-2 macrodomain (Mac1, residues 1023-1197 of polyprotein 1a), a domain that is present in all coronaviruses. 2020 Journal of translational medicine Discussion SARS_CoV_2 S1188L 24 30 Mac1 66 77 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. Hence, the barrier to the selection of V557L might be even higher for SARS-CoV-2. 2020 The Journal of biological chemistry Discussion SARS_CoV_2 V557L 39 44 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. Here we demonstrate that the smaller S861G eliminates termination. 2020 The Journal of biological chemistry Discussion SARS_CoV_2 S861G 37 42 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. However, it is important to note that neither V557L nor F480L or any other RDV resistance-associated mutations in SARS-CoV-2 have been reported at this point. 2020 The Journal of biological chemistry Discussion SARS_CoV_2 F480L;V557L 56;46 61;51 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. In agreement with these observations, we demonstrate the V557L in SARS-CoV-2 RdRp diminishes efficiency of regular nucleotide incorporations and neutralizes its advantageous effects on UTP incorporation opposite RDV. 2020 The Journal of biological chemistry Discussion SARS_CoV_2 V557L 57 62 RdRP 77 81 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. It is therefore conceivable that the V557L facilitates incorporation of UTP through repositioning of the template strand. 2020 The Journal of biological chemistry Discussion SARS_CoV_2 V557L 37 42 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. It is therefore tempting to predict that the S861G mutant will eliminate or reduce pausing. 2020 The Journal of biological chemistry Discussion SARS_CoV_2 S861G 45 50 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. Moreover, incorporation of the adjacent NTP, immediately downstream of the newly added UTP is likewise inhibited and the effect of V557L is less pronounced at this position (stage 7). 2020 The Journal of biological chemistry Discussion SARS_CoV_2 V557L 131 136 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. The effect of V557L is specifically seen when RDV is present in the template. 2020 The Journal of biological chemistry Discussion SARS_CoV_2 V557L 14 19 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. The neighboring resistance-associated mutation V557L counteracts this effect. 2020 The Journal of biological chemistry Discussion SARS_CoV_2 V557L 47 52 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. The selection of the structural equivalent V553L MHV required a high number of passages and RNA levels in the presence of drug are still lower than RNA levels in the absence of drug. 2020 The Journal of biological chemistry Discussion SARS_CoV_2 V553L 43 48 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. This concentration is significantly lowered with the V557L mutant, which provides a mechanism for drug resistance. 2020 The Journal of biological chemistry Discussion SARS_CoV_2 V557L 53 58 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. This effect is also shown here even with the bulkier S861P substitution. 2020 The Journal of biological chemistry Discussion SARS_CoV_2 S861P 53 58 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. This hypothesis was supported by experiments with the S861A mutant that showed subtle reductions in efficiency of delayed chain termination. 2020 The Journal of biological chemistry Discussion SARS_CoV_2 S861A 54 59 32967965 Template-dependent inhibition of coronavirus RNA-dependent RNA polymerase by remdesivir reveals a second mechanism of action. WT and V557L mutant do not show significant differences regarding selective incorporation of RDV-TP or delayed chain termination. 2020 The Journal of biological chemistry Discussion SARS_CoV_2 V557L 7 12 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. According to these models, the well-populated all-open conformation of D614G (Figure 7D) would reflect an intermediate that is on-pathway to S-mediated membrane fusion. 2020 Cell Discussion SARS_CoV_2 D614G 71 76 Membrane;S 152;141 160;142 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Additional sequencing of archived samples, or of viruses currently circulating, could shed further light on the pandemic trajectory of D614G. 2020 Cell Discussion SARS_CoV_2 D614G 135 140 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Another complication of any epidemiologic study of human transmission is that D614G is generally accompanied by three other sequence variants. 2020 Cell Discussion SARS_CoV_2 D614G 78 83 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Another possible explanation for why D614G dominated the SARS-CoV-2 pandemic, but has not been detected in bats, is that unlike bats, humans are immunologically naive to Sarbecoviruses. 2020 Cell Discussion SARS_CoV_2 D614G 37 42 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Consistent with the increased ability of D614G to infect cells in tissue culture, several studies suggest that D614G is associated with increased viral load in people with COVID-19, although these studies quantitated SARS-CoV-2 RNA and did not measure infectious virus. 2020 Cell Discussion SARS_CoV_2 D614G;D614G 41;111 46;116 COVID-19 172 180 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. D614G exhibited striking conformational changes (Figures 6E, 6F, 7C, and 7D), all of which could be attributable to disruption of the interprotomer latch between D614 in S1 and T859 in S2 (Figures 6H and 6I). 2020 Cell Discussion SARS_CoV_2 D614G 0 5 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Data in which the presence of D614G correlates with increased rates of transmission through human populations would support this hypothesis. 2020 Cell Discussion SARS_CoV_2 D614G 30 35 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Despite the increased infectivity of D614G in tissue culture, and the increased viral load in infected people, increased COVID-19 disease severity has not been detected in association with D614G infection. 2020 Cell Discussion SARS_CoV_2 D614G;D614G 37;189 42;194 COVID-19 121 137 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Efforts are underway to compare the replication efficiency of D614G with that of D614 in the context of the nearly 30,000-nucleotide SARS-CoV-2 genome. 2020 Cell Discussion SARS_CoV_2 D614G 62 67 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Examination of the effect of D614G on native S protein will require electron cryotomography to directly visualize the S protein on virion-like particles. 2020 Cell Discussion SARS_CoV_2 D614G 29 34 S;S 45;118 46;119 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Finally, the structural determination of D614G performed here was with a widely used soluble version of the S protein that differs from the native protein in three aspects. 2020 Cell Discussion SARS_CoV_2 D614G 41 46 S 108 109 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Future prospective comparisons of D614G transmission to that of D614 seem unlikely given that D614G has gone to near fixation worldwide (Figure 1). 2020 Cell Discussion SARS_CoV_2 D614G;D614G 34;94 39;99 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. However, the SARS-CoV-2 genomes that have been sequenced are only a narrow snapshot of the pandemic and additional sequencing of archived samples might pinpoint the origin of D614G or better resolve the variant's trajectory. 2020 Cell Discussion SARS_CoV_2 D614G 175 180 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. If SARS-CoV-2 Spike D614G is an adaptive variant that was selected for increased human-to-human transmission after spillover from an animal reservoir, one might expect that increased infectivity would only be evident on cells bearing ACE2 orthologs similar to that in humans. 2020 Cell Discussion SARS_CoV_2 D614G 20 25 S 14 19 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. In contrast to the primate-specific increase in infectivity that was reported for the major clade-forming Ebola virus glycoprotein variant from the 2013-2016 West African outbreak, the increased infectivity of D614G was equally evident on cells bearing ACE2 orthologs from a range of mammalian species (Figure 2B). 2020 Cell Discussion SARS_CoV_2 D614G 210 215 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. In keeping with the fact that the location of D614G within the S protein is remote from the receptor-binding domain, that D614G affinity for ACE2 is less than that of D614 (Figure 4), and that the relatively better-concealed D614 receptor-binding domain is likely to be advantageous for immune evasion, the D614G and D614 variants are equally sensitive to neutralization by human monoclonal antibodies targeting the S protein RBD (Figure 5). 2020 Cell Discussion SARS_CoV_2 D614G;D614G;D614G 46;122;307 51;127;312 RBD;S;S 426;63;416 429;64;417 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Indirect evidence that D614G is more infectious was provided here by experiments with pseudotyped viruses showing that D614G transduces 3- to 9-fold more efficiently than does the ancestral S protein (Figure 2A). 2020 Cell Discussion SARS_CoV_2 D614G;D614G 23;119 28;124 S 190 191 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Insight into the mechanism by which D614G increases infectivity was gleaned from cryo-EM studies of the SARS-CoV-2 S protein trimer. 2020 Cell Discussion SARS_CoV_2 D614G 36 41 S 115 116 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Interestingly, when non-lung cells are challenged, disruption of the furin-cleavage site increases SARS-CoV-2 infectivity to the same extent as does D614G. 2020 Cell Discussion SARS_CoV_2 D614G 149 154 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Nonetheless, the pseudotype experiments presented here show a pronounced increase in infectivity with D614G in isolation, and the structural studies are consistent with conformational changes expected for a more infectious S protein variant. 2020 Cell Discussion SARS_CoV_2 D614G 102 107 S 223 224 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Perhaps there are fitness tradeoffs for D614G in vivo due to the more open conformation of its RBD (Figure 7), which potentially renders D614G more immunogenic. 2020 Cell Discussion SARS_CoV_2 D614G;D614G 40;137 45;142 RBD 95 98 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The current high frequency of D614G throughout the world suggests that this variant transmits person to person more efficiently than do viruses bearing D614, but demographically matched cohorts that might be used for comparing transmission likelihood of D614 versus D614G have been difficult to assemble. 2020 Cell Discussion SARS_CoV_2 D614G;D614G 30;266 35;271 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The fact that D614G was more infectious on cells expressing ACE2 orthologs from Chinese rufous horseshoe bat and Malayan pangolin raises the question of why D614G does not dominate the sequences of closely related Sarbecoviruses that circulate in these species. 2020 Cell Discussion SARS_CoV_2 D614G;D614G 14;157 19;162 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. The SARS-CoV-2 S protein variant D614G is one of only four SNPs, out of the more than 12,000 reported in GISAID, that has risen to high frequency (Figure 1). 2020 Cell Discussion SARS_CoV_2 D614G 33 38 S 15 16 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. These observations suggest not only that D614G increases infectivity in the presence of the furin cleavage site but also that D614G offers no selective advantage when transmission is possible in the absence of the furin site, as appears to be the case in bats and pangolins. 2020 Cell Discussion SARS_CoV_2 D614G;D614G 41;126 46;131 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. This suggests that D614G confers a replication advantage to SARS-CoV-2, such that it increases the likelihood of human-to-human transmission. 2020 Cell Discussion SARS_CoV_2 D614G 19 24 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Weakening of the interprotomer contacts results in increased distance between the protomers and a dramatic flip in the ratio of open to closed S protein particles, from 82% closed and 18% open for D614 to 42% closed and 58% open for D614G. 2020 Cell Discussion SARS_CoV_2 D614G 233 238 S 143 144 32991842 Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. When S protein trimers were examined more closely, in addition to the all-closed conformation and the one open conformation previously reported for D614, a significant fraction of D614G trimers populated a two-open conformation (39%) and an all-open state (20%). 2020 Cell Discussion SARS_CoV_2 D614G 180 185 S 5 6 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. However, despite having a low nM affinity to SARS-CoV-2 P384A RBD, CR3022 only weakly neutralizes SARS-CoV-2 P384A with an IC50 of 3.2 mug/ml and SARS-CoV with an IC50 of 5.2 mug/ml. 2020 bioRxiv Discussion SARS_CoV_2 P384A;P384A 56;109 61;114 RBD 62 65 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. The KD of CR3022 Fab to SARS-CoV-2 WT RBD is 68 nM, whereas to SARS-CoV-2 P384A RBD is 1 nM (Figure 1B-C), indicating that the affinity threshold for neutralization of SARS-CoV-2 to this epitope is in the low nM range. 2020 bioRxiv Discussion SARS_CoV_2 P384A 74 79 RBD;RBD 38;80 41;83 32995788 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. While CR3022 cannot neutralize SARS-CoV-2 WT in almost all studies, it can neutralize the SARS-CoV-2 P384A mutant. 2020 bioRxiv Discussion SARS_CoV_2 P384A 101 106 32995830 Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report. By day 42 nAb response showed a 1.5-fold increase to Wuhan pseudovirus, and a 2.6-fold increase to D614G pseudovirus. 2020 medRxiv Discussion SARS_CoV_2 D614G 99 104 32995830 Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report. Taken together, these findings suggest that poorly developed or waned antibodies against the D614 virus formed after primary infection in March were not protective against reinfection with the D614G spike variant acquired in July. 2020 medRxiv Discussion SARS_CoV_2 D614G 193 198 S 199 204 32995830 Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report. The spike variant D614G from Europe has now taken over as the predominant circulating strain. 2020 medRxiv Discussion SARS_CoV_2 D614G 18 23 S 4 9 32995830 Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report. The time course of InCoV139's two infections overlaps with the transition in Seattle to the newer D614G strain, supporting reinfection as opposed to intra-host evolution. 2020 medRxiv Discussion SARS_CoV_2 D614G 98 103 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. A prefusion-stabilized MERS-CoV S 2P protein was rationally designed by introducing two consecutive proline mutations V1060P and L1061P. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 L1061P;V1060P 129;118 135;124 S 32 33 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. A recent study showed that the patients with D614G strain had higher viral loads and suggested this mutation is important for RBD binding and enhance viral infection and production. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D614G 45 50 RBD 126 129 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Among all destabilizing mutations, G431W introduced the highest folding energy change on full-length S trimer, monomer and RBD, indicating this mutation can strongly reduce the protein stability. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 G431W 35 40 RBD;S 123;101 126;102 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. D614G has the minimum DeltaDeltaG at -0.7838 kcal/mol among all 19 possible mutations in this position (Figure 2). 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D614G 0 5 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. In addition, common viral mutations D936Y in 37 strains, V483A in 24 strains and V367F in 14 strains can also induce the stabilizing effects on SARS-Cov-2 full-length S or RBD (Table 3). 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D936Y;V367F;V483A 36;81;57 41;86;62 RBD;S 172;167 175;168 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. In addition, D614G is predicted to have neutral effect (SNAP = -52) on protein function, which would benefit the viral S protein function (Table 3). 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D614G 13 18 S 119 120 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. In G496s contact residue K353 of ACE2, mutation K353F has the minimum DeltaDeltaDeltaG at -1.937 kcal/mol. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 K353F 48 53 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Interestingly, a recent study showed that glycosylation deletion including N343 can reduce infectivity and N343Q cause 20-fold reduction in viral infectivity. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 N343Q 107 112 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Many mutations in N343 (DeltaDeltaG mean = 0.227 kcal/mol) including N343Q (DeltaDeltaG = 0.552 kcal/mol) induce the destabilizing effects on S protein stability that are unfavorable on virus function. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 N343Q 69 74 S 142 143 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Most mutation in RBD residue F497 can increase the RBD-ACE binding, and mutation F497W has the minimum DeltaDeltaDeltaG at -0.978 kcal/mol in this position. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 F497W 81 86 RBD;RBD 17;51 20;54 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Most of the mutations in F483 of SARS-Cov have not effects on binding affinity and F483R can weaken the interaction. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 F483R 83 88 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. One viral mutation T323I was identified on this site and this mutation can increase the protein stability (DeltaDeltaG = -0.827 kcal/mol). 2021 Briefings in bioinformatics Discussion SARS_CoV_2 T323I 19 24 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Particularly, D614G becomes the dominant pandemic form worldwide. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D614G 14 19 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Remarkably, both viral mutations N603K and T323I are not the mutations introducing the strongest stabilizing effects. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 N603K;T323I 33;43 38;48 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S50L in seven strains and V341I have the minimum DeltaDeltaG among all other possible mutations in their positions (Supplementary Figure 5). 2021 Briefings in bioinformatics Discussion SARS_CoV_2 V341I;S50L 26;0 31;4 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. S514F induce the strongest stabilizing effect on both full-length and RBD region. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 S514F 0 5 RBD 70 73 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. SARS-Cov-2 mutations K986P and V987P have the minimum DeltaDeltaG values at -0.839 and -1.999 kcal/mol, respectively. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 K986P;V987P 21;31 26;36 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. The mechanism of D614G infections is still unknown, but recent studies showed that D614G can increase infectivity in various cells lines and strengthen the interaction between S1 and S2 domains. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D614G;D614G 17;83 22;88 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. The results from these experiments and our analysis suggest that D614G make the S protein more stable, and this change is favorable for virus infection. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D614G 65 70 S 80 81 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. There have been four observed viral mutations (N74K, N149H, N603K and N1194S) to N-linked glycosylation sites. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 N1194S;N149H;N603K;N74K 70;53;60;47 76;58;65;51 N 81 82 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. Thus, D614G may enhance the fitness of SARS-Cov-2 through increasing S protein stability and participating in the N-linked glycosylation. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D614G 6 11 N;S 114;69 115;70 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. We calculated the folding energy changes and showed that V1060P and L1061P have the minimum DeltaDeltaG values at -2.225 and -0.821 kcal/mol in their positions, respectively. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 L1061P;V1060P 68;57 74;63 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. We can calculate the DeltaDeltaG of N603K at -0.5521 kcal/mol, indicating this mutation could increase full-length S stability. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 N603K 36 41 S 115 116 33006605 Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. We found that the most common variant D614G in 5703 strains can induce the stabilizing effects on SARS-Cov-2 full-length S at -0.7838 kcal/mol. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D614G 38 43 S 121 122 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. A study suggested that the D614G mutant may have originated either in China or Europe, but spread rapidly first in Europe, and then to other parts of the world. 2020 Frontiers in immunology Discussion SARS_CoV_2 D614G 27 32 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. Among them, the D614G mutant has aroused urgent concern recently, because of its extraordinarily high frequency. 2020 Frontiers in immunology Discussion SARS_CoV_2 D614G 16 21 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. Another study indicated that the D614G mutant was first collected on January 28, 2020 in Germany. 2020 Frontiers in immunology Discussion SARS_CoV_2 D614G 33 38 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. However, given the small sample size, it is hard to ascertain whether D614G is the dominant strain in these countries. 2020 Frontiers in immunology Discussion SARS_CoV_2 D614G 70 75 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. In comparison, we identified 3 amino acid substitutions (V367F, G476S, and V483A) in the RBD region, and V483A was in one epitope. 2020 Frontiers in immunology Discussion SARS_CoV_2 G476S;V483A;V483A;V367F 64;75;105;57 69;80;110;62 RBD 89 92 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. Interestingly, we also found that many sequences of variants had multi-variations, of note, most of which were combined with D614G mutant. 2020 Frontiers in immunology Discussion SARS_CoV_2 D614G 125 130 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. So far, of the 3 amino acid variations identified in the RBD of SARS-CoV-2, G476S was directly in an angiotensin-converting enzyme 2 contact residue. 2020 Frontiers in immunology Discussion SARS_CoV_2 G476S 76 81 RBD 57 60 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. The A831V located in a defined linear B cell epitope (amino acids 818-835) was a part of the fusion peptide of S protein. 2020 Frontiers in immunology Discussion SARS_CoV_2 A831V 4 9 S 111 112 33013929 Variations in SARS-CoV-2 Spike Protein Cell Epitopes and Glycosylation Profiles During Global Transmission Course of COVID-19. The binding affinity of some epitopes switched from strong to weak binder due to specific variations (including T29I, V367F, A706V, and A831V) in context of HLA alleles. 2020 Frontiers in immunology Discussion SARS_CoV_2 A706V;A831V;T29I;V367F 125;136;112;118 130;141;116;123 33015402 Characterization of local SARS-CoV-2 isolates and pathogenicity in IFNAR(-/-) mice. The most prominent variation is observed on the spike protein marker, resulting in the substitution D614G, with a prevalence of 56.2%. 2020 Heliyon Discussion SARS_CoV_2 D614G 100 105 S 48 53 33024961 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. This revealed that the Spike D614G substitution likely represents a new adaptation to human hosts, as it disrupts a Sarbecovirus-conserved residue in a strongly-conserved region of S1, and to interpret the likely functional impact of genetic variants co-inherited with D614G based on their evolutionary history. 2020 Research square Discussion SARS_CoV_2 D614G;D614G 29;269 34;274 S 23 28 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. D614G mutation in spike is the dominant pandemic form that may indicate a fitness advantage and related to severe reduced antigenic specificity. 2020 Microbes and infection Discussion SARS_CoV_2 D614G 0 5 S 18 23 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. For P4715L mutation in RdRp, a mixed outcome has been noticed. 2020 Microbes and infection Discussion SARS_CoV_2 P4715L 4 10 RdRP 23 27 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. However, careful examination of the cryoEM structure predicts that the interactions with the neighbouring protomer due to D614G mutation is disrupted in absence of negatively charged/hydrogen bond accepting group from the side chain of non-polar glycine. 2020 Microbes and infection Discussion SARS_CoV_2 D614G 122 127 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. However, it can be anticipated that the replacement of negatively charged Asp into non-polar Gly in D614G mutation of spike protein consequences from the replacement of hydrophilic to the hydrophobic residue. 2020 Microbes and infection Discussion SARS_CoV_2 D614G 100 105 S 118 123 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. Indian isolates from European origin show a new mutation S1498F in the papain-like protease domain of Nsp3 in the ORF1a region. 2020 Microbes and infection Discussion SARS_CoV_2 S1498F 57 63 ORF1a;Nsp3 114;102 119;106 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. Mutations that appeared at multiple times include D614G in spike glycoprotein and P4715L in RdRp. 2020 Microbes and infection Discussion SARS_CoV_2 D614G;P4715L 50;82 55;88 S;RdRP 59;92 77;96 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. R203K and G204R in nucleocapsid protein are found in SARS-CoV-2 of three Indian patients who traveled from Italy in April 2020. 2020 Microbes and infection Discussion SARS_CoV_2 G204R;R203K 10;0 15;5 N 19 31 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. SARS-CoV-2 genome sequences available at the public database of the Global Initiative on Sharing All Influenza Data (GISAID) till 02-10-2020 classifies the variants into several clades like (i) L-original lineage, (ii) G-variant of spike protein causing D614S mutation, (iii) S- variant ORF8 responsible for L84S mutation, (iv) V- variant of the ORF3a coding protein N3S responsible for G251V mutation, (v) GH- a G derivative characterized by ORF3a: Q57H mutation, (vi) GR-nucleocapsid gene mutations- R203K and G204R, (vii) O- other combinations that do match from the rest. 2020 Microbes and infection Discussion SARS_CoV_2 G204R;G251V;L84S;N3S;Q57H;R203K 512;387;308;367;450;502 517;392;312;370;454;507 N;S;ORF3a;ORF3a;ORF8;S 473;232;346;443;287;276 485;237;351;448;291;277 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. Spike D614G mutation site is not proximally situated to the RBD-Ace2 binding interface and unable to differentiate much in Ace2 interactions. 2020 Microbes and infection Discussion SARS_CoV_2 D614G 6 11 S;RBD 0;60 5;63 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. Such changes in the ORF3a-viroporin domain require further experimental outcomes to precisely understand the effect exerted.While trying to unravel the role of non-synonymous mutation from the Indian perspective, it has been found that the Indian SARS-CoV-2 samples isolated from the patient of Kerala state with travel history from Wuhan on January lack D614G mutation in their spike glycoprotein but additionally shows a neutral mutation R416I and an alteration of A930V with deleterious effect. 2020 Microbes and infection Discussion SARS_CoV_2 A930V;D614G;R416I 467;355;440 472;360;445 S;ORF3a 379;20 397;25 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. The bulletin from WHO on variant analysis of SARS-CoV-2 reported on June, 2020 described P4715L mutation in ORF1ab from 6319 samples. 2020 Microbes and infection Discussion SARS_CoV_2 P4715L 89 95 ORF1ab 108 114 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. The change of secondary structure from loop to helix linked to P4715L supports epitope loss as epitope antibody residues are enriched by loops and depleted of strands and helixes. 2020 Microbes and infection Discussion SARS_CoV_2 P4715L 63 69 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. The epitope loss linked with G251V in ORF3a might cause a change in flexibility due to the substitution of small hydrogen moiety of Gly (G) to the bulky branched side chain in Val (V). 2020 Microbes and infection Discussion SARS_CoV_2 G251V 29 34 ORF3a 38 43 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. The phenomenon of epitope loss due to P4715L in ORF1ab polyprotein is supported because Leu (L) is the hydrophobic residue which prefers normally to buried within the protein rather than to expose outside to act as an epitope for immunological interactions. 2020 Microbes and infection Discussion SARS_CoV_2 P4715L 38 44 ORF1ab 48 54 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. The second most common mutation is among these variants is P4715L of RdRp. 2020 Microbes and infection Discussion SARS_CoV_2 P4715L 59 65 RdRP 69 73 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. The tendency for epitopes to be depleted of small hydrophobic amino acids like Val supports the epitope loss associated with G251V. 2020 Microbes and infection Discussion SARS_CoV_2 G251V 125 130 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. This process may trigger the binding of S1 subunit to host cell receptors leading to enhanced pathogenicity due to D614G mutation. 2020 Microbes and infection Discussion SARS_CoV_2 D614G 115 120 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. Thus, it may be hypothecated that D614G mutation diminishes the interaction between the S1 and S2 units, facilitating the shedding of S1 from viral-membrane-bound S2. 2020 Microbes and infection Discussion SARS_CoV_2 D614G 34 39 Membrane 148 156 33049387 Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. V74F mutation appears in the ORF7a accessory protein among isolates from the COVID-19 patients of India who migrated from Iran. 2020 Microbes and infection Discussion SARS_CoV_2 V74F 0 4 ORF7a 29 34 COVID-19 77 85 33072699 Geographical Distribution of Genetic Variants and Lineages of SARS-CoV-2 in Chile. At the beginning of the outbreak, Chinese isolates were mainly variant O, the most related to the reference sequence NC_045512.2, but in mid-January 2020, variant S (T 28144 C) and few cases of V (G 26144 T) and G (A 23403 G) started to appear. 2020 Frontiers in public health Discussion SARS_CoV_2 A23403G;G26144T;T28144C 215;197;166 224;206;175 S 163 164 33080267 Designed variants of ACE2-Fc that decouple anti-SARS-CoV-2 activities from unwanted cardiovascular effects. On the other hand, the Arg273Ala single site mutant that is predicted to change the substrate pocket will likely have a milder impact on overall protein stability, which is an important parameter in pharmaceutical production. 2020 International journal of biological macromolecules Discussion SARS_CoV_2 R273A 23 32 33080267 Designed variants of ACE2-Fc that decouple anti-SARS-CoV-2 activities from unwanted cardiovascular effects. This double mutation, as well as our His378Ala and Glu402Ala single mutations of the zinc-binding pocket may potentially suffer protein instability problems. 2020 International journal of biological macromolecules Discussion SARS_CoV_2 E402A;H378A 51;37 60;46 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. 22 Therefore, the enhanced interaction between each SARS-CoV-2 N mutant (S194L or R203K/G204R) and E might promote virus release, while decreased binding affinity of S194L N-M might attenuate virus assembly. 2021 Journal of medical virology Discussion SARS_CoV_2 R203K;S194L;S194L;G204R 83;167;74;89 88;172;79;94 E;N;N 100;64;173 101;65;174 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. 25 Remarkably, the incidences of Q57H in Orf3a and R203K/G204R in N were quite high (15.12% and 17.84%), which could be a sign that these mutations are correlated with enhanced virulence, evolvability, and traits considered beneficial for the virus. 2021 Journal of medical virology Discussion SARS_CoV_2 Q57H;R203K;G204R 34;52;58 38;57;63 ORF3a;N 42;67 47;68 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. 33 Our results showed stronger binding affinities in Q57H Orf3a-M and Q57H Orf3a-S complexes, but weaker affinities in G251V Orf3a-M and G251V Orf3a-S complexes. 2021 Journal of medical virology Discussion SARS_CoV_2 G251V;G251V;Q57H;Q57H 120;138;54;71 125;143;58;75 ORF3a;ORF3a;ORF3a;ORF3a;S;S 59;76;126;144;82;150 64;81;131;149;83;151 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. 38 Previous experimental research showed that Y195A mutation in SARS-CoV M was found to disrupt its interaction with S, resulting in a declined ability of virus assembly. 2021 Journal of medical virology Discussion SARS_CoV_2 Y195A 47 52 S 118 119 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. After structural alignment, four protein mutants (Q57H Orf3a, G251V Orf3a, S194L N, and R203K/G204R N) were found displaying different structures from control ones, which corresponding mutations were located in the coding region of N and Orf3a known as essential proteins for coronavirus assembly 24 and cytotoxicity. 2021 Journal of medical virology Discussion SARS_CoV_2 G251V;R203K;S194L;Q57H;G204R 62;88;75;50;94 67;93;80;54;99 ORF3a;ORF3a;ORF3a;N;N;N 55;68;238;81;100;232 60;73;243;82;101;233 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. For instance, a study reported that D614G in S could lead to increased virus infectivity by eliminating side-chain hydrogen bond, which was only a tiny change in overall protein structure, 29 and our data also showed a slight structural difference between control and D614G mutant (RMSD = 2.33 A). 2021 Journal of medical virology Discussion SARS_CoV_2 D614G;D614G 36;269 41;274 S 45 46 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. However, it is interesting that some mutations, such as P323L in nsp12 and D614G in S, with even much higher occurrence rates (43.21% and 43.27%) were found with no significant impact on protein structure, which indicates they maybe could affect virus characteristics via altering RNA second structure, 26 protein stability, 27 or partial structure, 28 instead of integral protein structure. 2021 Journal of medical virology Discussion SARS_CoV_2 D614G;P323L 75;56 80;61 Nsp12;S 65;84 70;85 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. In addition, the single amino acid substitution would alter protein structure as well, and it has been reported that G104E mutation in SARS-CoV nsp9 could prevent viral replication via changing protein structure and further destroying the helix-helix interface. 2021 Journal of medical virology Discussion SARS_CoV_2 G104E 117 122 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. Meanwhile, considering the great disparity between the incidences of Q57H in Orf3a (15.12%) and G251V in Orf3a (2.25%), it could be speculated that the virus assembly and transmission would be disproportionately affected by different Orf3a mutations. 2021 Journal of medical virology Discussion SARS_CoV_2 G251V;Q57H 96;69 101;73 ORF3a;ORF3a;ORF3a 77;105;234 82;110;239 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. Take R203K/G204R in N as an example; this mutation combination with increased incidence was found mainly in Europe till March 2020, 46 , 47 while its high frequency also happened in Asian and African countries as of September 2020. 2021 Journal of medical virology Discussion SARS_CoV_2 R203K;G204R 5;11 10;16 N 20 21 33090512 Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions. What is more, the hot spots that play critical roles in protein-protein interactions can be used as drugs target, 37 and our results demonstrated that all these selected SARS-CoV-2 mutations (Q57H and G251V in Orf3a, S194L and R203K/G204R in N) had great influences on hot spots within protein combinations, which the changes could have strong impacts on clinical treatment. 2021 Journal of medical virology Discussion SARS_CoV_2 G251V;R203K;S194L;Q57H;G204R 202;228;218;193;234 207;233;223;197;239 ORF3a;N 211;243 216;244 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. Additional random mutation combinations mainly at the level of NSPs were found in three patients travelling from Iran and UK, namely mutations at position 884C > T; 1397G > A; 8653G > T and 11,083 T > G. 2021 Genomics Discussion SARS_CoV_2 G1397A;G8653T;C884T;T083G 165;176;155;193 174;185;163;202 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. Among structural proteins, we describe the presence as well of two mutations affecting the N gene in two positions, 28881G > A and 28883G > C, in two isolates from patients coming from France and UK. 2021 Genomics Discussion SARS_CoV_2 G28881A;G28883C 116;131 126;141 N 91 92 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. In our results, we detected a frequent missense mutation among 6 of our 11 isolates (25563G > T), and another deletion mutation belonging to the gene of the accessory protein ORF3. 2021 Genomics Discussion SARS_CoV_2 G25563T 85 95 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. Moreover, we reveal the identification of two extremely important novel mutations, a stop codon and a frameshift mutation affecting NSP 3 and NSP 4 at position 6887A > T and 8651/fs, respectively. 2021 Genomics Discussion SARS_CoV_2 A6887T 160 169 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. Near to these three domains is located the Q57H mutation, which may affect the inflammasome activation. 2021 Genomics Discussion SARS_CoV_2 Q57H 43 47 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. Of high interest in our variants was the co-existence of 3 mutations (23403A > G, 14408C > T and 25563G > T) in 8 out of the 11 sequences (with only two strains, lacking the 25563G > T mutation). 2021 Genomics Discussion SARS_CoV_2 C14408T;G25563T;G25563T;A23403G 82;97;174;70 92;107;184;80 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. Of those 18 mutations, sixteen missense mutations were found in different positions as follows; 6198C > A, 6281A > G/T, 6285C > A, 6887A > T and 7766A > C belonging to NSP 3, 8897A > T belonging to NSP 4, 10,595 T > C belonging to NSP 5, 12297A > T belonging to NSP 8, 14369G > T and 14993C > T belonging to NSP 12 (RdRp), 16301G > T belonging to NSP 13, 18670G > T and 19499A > C belonging to NSP 14, 22093G > T and 22425C > T belonging to S and 26428A > T belonging to E gene. 2021 Genomics Discussion SARS_CoV_2 A12297T;G14369T;C14993T;G16301T;G18670T;A19499C;G22093T;C22425T;A26428T;C6198A;C6285A;A6887T;A7766C;A8897T;T595C 238;269;284;323;355;370;402;417;447;96;120;131;145;175;208 248;279;294;333;365;380;412;427;457;105;129;140;154;184;217 RdRP;E;S 316;471;441 320;472;442 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. Such occurrence was statistically proved and correlated to the presence of the RdRp mutation at position 14408C > T. 2021 Genomics Discussion SARS_CoV_2 C14408T 105 115 RdRP 79 83 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. Two less frequently reported at positions 21724G > T and 22021G > T; and two additional novel mutations based on our analysis at positions 22093G > T, 22425C > T. 2021 Genomics Discussion SARS_CoV_2 G21724T;G22021T;G22093T;C22425T 42;57;139;151 52;67;149;161 33091548 Variant analysis of the first Lebanese SARS-CoV-2 isolates. We found a major mutation reported 76,294 times in GISAID database at position 23403A > G (D614G). 2021 Genomics Discussion SARS_CoV_2 A23403G;D614G 79;91 89;96 33097660 SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling. Notably, a mutant Orf6 protein (methionine-to-arginine substitution at residue 58) that is deficient in Nup98 binding. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 M58R 32 81 ORF6 18 22 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. Although virions produced from Calu-3 cells had more complete S1/S2 cleavage than those produced form Vero E6 cells, no substantial differences in spike cleavage were detectable between the D614 and G614 virions, suggesting that the enhanced virion infectivity is not likely due to a D614G-mediated spike cleavage difference. 2021 Nature Discussion SARS_CoV_2 D614G 284 289 S;S 147;299 152;304 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. Besides antisera, we also showed that, depending on the epitope locations on RBD, the neutralizing potency of certain mAbs may be affected by the D614G mutation. 2021 Nature Discussion SARS_CoV_2 D614G 146 151 RBD 77 80 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. Compared with D614, the G614 virus replicated to a higher level in the upper airway, but not in the lungs, of hamsters, suggesting that the D614G mutation may select against lung replication. 2021 Nature Discussion SARS_CoV_2 D614G 140 145 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. Future efforts are warranted to study other emerging mutations, including those that accompanied with the D614G substitution in SARS-CoV-2. 2021 Nature Discussion SARS_CoV_2 D614G 106 111 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. However, age-dependent impacts of D614G on SARS-CoV-2 infection, pathogenesis, and transmission remain to be studied. 2021 Nature Discussion SARS_CoV_2 D614G 34 39 COVID-19 43 63 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. In summary, we have used authentic SARS-CoV-2 to demonstrate that spike substitution D614G enhances viral replication in the upper respiratory tract and increases neutralization susceptibility. 2021 Nature Discussion SARS_CoV_2 D614G 85 90 S 66 71 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. Mechanistically, recent studies showed that the D614G mutation abolishes a hydrogen-bond interaction with T859 from a neighboring protomer of the spike trimer, which allosterically promotes the RDB domain to an "up" conformation for receptor ACE2 binding, leading to an enhanced virion infectivity. 2021 Nature Discussion SARS_CoV_2 D614G 48 53 S 146 151 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. Our results from authentic SARS-CoV-2 are in contrast with previous studies reporting that the D614G mutation changes the cleavage and shedding of spike protein when expressed alone on pseudotyped virions. 2021 Nature Discussion SARS_CoV_2 D614G 95 100 S 147 152 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. Since current COVID-19 vaccines in clinical trials are based on the original D614 sequence, our neutralization result mitigates the concern that the D614G mutation might compromise their efficacy. 2021 Nature Discussion SARS_CoV_2 D614G 149 154 COVID-19 14 22 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. The higher viral loads of G614 in the upper airway of COVID-19 patients and infected hamsters suggest the role of D614G mutation in viral transmissibility. 2021 Nature Discussion SARS_CoV_2 D614G 114 119 COVID-19 54 62 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. This seems counterintuitive, but could be explained by a D614G-mediated increase in the "up" conformation of the RDB. 2021 Nature Discussion SARS_CoV_2 D614G 57 62 33106671 Spike mutation D614G alters SARS-CoV-2 fitness. We demonstrated that the spike substitution D614G enhanced SARS-CoV-2 replication in the upper respiratory tract through increased virion infectivity. 2021 Nature Discussion SARS_CoV_2 D614G 44 49 S 25 30 33106822 COVID-19 neutralizing antibodies predict disease severity and survival. We found that one such mutation, D614G, which has now spread and become a dominant strain worldwide, does not affect the neutralizing ability of patient sera, reducing concerns for re-infection. 2020 medRxiv Discussion SARS_CoV_2 D614G 33 38 33108902 ACE2 and TMPRSS2 Potential Involvement in Genetic Susceptibility to SARS-COV-2 in Cancer Patients. In particular, the ACE2 variants S19P, exclusively present in Africans, and the E37 K in Finnish males, even if with a low frequency, could be protective factors to SARS-CoV-2. 2020 Cell transplantation Discussion SARS_CoV_2 E37K;S19P 80;33 85;37 33109270 Molecular detection of drug resistant polymorphisms in Plasmodium falciparum isolates from Southwest, Nigeria. Due to limited availability of sampled DNA and RNA, we were unable to repeat the detection of the suspected C580Y mutant or validate its presence using sequencing approaches. 2020 BMC research notes Discussion SARS_CoV_2 C580Y 108 113 33109270 Molecular detection of drug resistant polymorphisms in Plasmodium falciparum isolates from Southwest, Nigeria. However, a recent report from Rwanda confirmed de novo local emergence and spread of the Pfk13 R561H artemisinin resistance associated variant, though clinical cure rate remained > 95%. 2020 BMC research notes Discussion SARS_CoV_2 R561H 95 100 33109270 Molecular detection of drug resistant polymorphisms in Plasmodium falciparum isolates from Southwest, Nigeria. In the absence of repeated detection and confirmation by sequencing, the possibility of the detected Pfk13 C580Y mutants being as a result of contamination cannot be ruled out. 2020 BMC research notes Discussion SARS_CoV_2 C580Y 107 112 33109270 Molecular detection of drug resistant polymorphisms in Plasmodium falciparum isolates from Southwest, Nigeria. Only few cases of delayed clearance of malaria after ACT treatment have been reported in Africa and the C580Y is almost completely absent. 2020 BMC research notes Discussion SARS_CoV_2 C580Y 104 109 33109270 Molecular detection of drug resistant polymorphisms in Plasmodium falciparum isolates from Southwest, Nigeria. Other Pfk13 haplotypes containing mutations at positions A578S and V581F, close to the C580Y mutation, are known to circulate in Africa and could have emerged prior to the introduction of ACTs. 2020 BMC research notes Discussion SARS_CoV_2 A578S;C580Y;V581F 57;87;67 62;92;72 33109270 Molecular detection of drug resistant polymorphisms in Plasmodium falciparum isolates from Southwest, Nigeria. Other well-known characterized mutations in drug resistant genes such as Pfmdr1- N86Y and Y184F, and pfcrt- CVIET haplotype were also detected. 2020 BMC research notes Discussion SARS_CoV_2 N86Y;Y184F 81;90 85;95 33109270 Molecular detection of drug resistant polymorphisms in Plasmodium falciparum isolates from Southwest, Nigeria. Polymorphisms of Pfmdr1 (N86Y, Y184F, S1034C, N1042D, and D1246Y) and copy number amplifications modulate resistance to quinolones and other ACT partner drugs. 2020 BMC research notes Discussion SARS_CoV_2 D1246Y;N1042D;S1034C;Y184F;N86Y 58;46;38;31;25 64;52;44;36;29 33109270 Molecular detection of drug resistant polymorphisms in Plasmodium falciparum isolates from Southwest, Nigeria. The Pfk13 C580Y mutant is the most prevalent SNP associated with reduction in parasite susceptibility to ACTs. 2020 BMC research notes Discussion SARS_CoV_2 C580Y 10 15 33109270 Molecular detection of drug resistant polymorphisms in Plasmodium falciparum isolates from Southwest, Nigeria. Though genetic epidemiology and in vitro forward genetic approaches have clearly implicated C580Y and other Pfk13 mutations in delayed parasite clearance, the artemisinin resistance phenotype and associated molecular mechanisms may be different in African parasites lacking these Pfk13 variants. 2020 BMC research notes Discussion SARS_CoV_2 C580Y 92 97 33109270 Molecular detection of drug resistant polymorphisms in Plasmodium falciparum isolates from Southwest, Nigeria. Though Pfk13 C580Y mutant allele was suspected in two mixed infections, only wildtype mRNA was detected. 2020 BMC research notes Discussion SARS_CoV_2 C580Y 13 18 33109270 Molecular detection of drug resistant polymorphisms in Plasmodium falciparum isolates from Southwest, Nigeria. We also detected polymorphisms of PfATPase6, the R37K, A630S, I898I found in Brazil, double mutation E431K, A623E in Senegal, and H243Y in Central Africa. 2020 BMC research notes Discussion SARS_CoV_2 A623E;A630S;E431K;H243Y;I898I;R37K 108;55;101;130;62;49 113;60;106;135;67;53 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. Another European isolate (MT35638) had a G>T at 12,725, which is within the nCoV_IP2 forward primer. 2020 Cell reports Discussion SARS_CoV_2 G12725T 41 54 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. Given the increasing abundance of D614G SNVs, further research into its role in pathogenicity and clinical outcomes is warranted. 2020 Cell reports Discussion SARS_CoV_2 D614G 34 39 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. Multiple studies demonstrated superior infectivity of D614G-containing viruses or pseudotyped particles. 2020 Cell reports Discussion SARS_CoV_2 D614G 54 59 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. Of the 87 sequences that have the D614G mutation, 69 have the C214T mutation, 15 have the C3037T mutation, and 48 have the C14408T mutation. 2020 Cell reports Discussion SARS_CoV_2 C14408T;C214T;C3037T;D614G 123;62;90;34 130;67;96;39 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. reported on a clustering of genomes that harbor a D614G mutation in the S gene. 2020 Cell reports Discussion SARS_CoV_2 D614G 50 55 S 72 73 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. Several other mutations reportedly accompany the D614G mutation on the S gene and include C214T, C3037T, and the C14408T mutations, and together, these form the globally dominant strain of SARS-CoV-2. 2020 Cell reports Discussion SARS_CoV_2 C14408T;C214T;C3037T;D614G 113;90;97;49 120;95;103;54 S 71 72 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. SNV analysis documents the presence of a presumed high-pathogenicity variant D614G in 57% of the cases. 2020 Cell reports Discussion SARS_CoV_2 D614G 77 82 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. Studies of Russian isolates also have identified D614G, as well as additional mutations. 2020 Cell reports Discussion SARS_CoV_2 D614G 49 54 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. The association of the D614G SNV with specific clinical presentations, distinct biological properties, and high peak titers seems increasingly likely. 2020 Cell reports Discussion SARS_CoV_2 D614G 23 28 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. The D614G mutation dominates over the initial human strain defined by the SARS-CoV-2/human/CHN/Wuhan-01/2019 isolate. 2020 Cell reports Discussion SARS_CoV_2 D614G 4 9 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. Their analysis of 489 genomes derived from 32 countries reveals that genomes in clades A2 and A2a harboring the D614G mutation originate mainly from European and several South American countries, different from clade B, which contains genomes from mainland China. 2020 Cell reports Discussion SARS_CoV_2 D614G 112 117 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. These findings are consistent with ours, as most of the genomes containing the D614G mutation also carry additional mutations defining the G clade. 2020 Cell reports Discussion SARS_CoV_2 D614G 79 84 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. They observed on average higher genome copy numbers for the D614G isolate, similar to this study, but could not make a conclusive association with clinical outcomes. 2020 Cell reports Discussion SARS_CoV_2 D614G 60 65 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. While this article was under review, a large number of studies cemented the importance of the D614G SNV and its biological and clinical properties. 2020 Cell reports Discussion SARS_CoV_2 D614G 94 99 33113345 High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. Within the limitations presented by measuring viral loads within samples collected at unknown times past infection and with presumably differing clinical sampling efficiency, patients with the D614G SNV presented with higher SARS-CoV-2 genome loads. 2020 Cell reports Discussion SARS_CoV_2 D614G 193 198 33127745 A Founder Effect Led Early SARS-CoV-2 Transmission in Spain. A recent study also associated the D614G substitution with a decreased neutralization sensitivity to individual convalescent-phase sera. 2021 Journal of virology Discussion SARS_CoV_2 D614G 35 40 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Besides the potential functional role of D839Y mutation and its high prevalence in Portugal, its detection in 12 other countries from four continents, it's probable independent emergence in distinct times and genetic clades (20A and 20C) in some of these countries and its considerable relative weight (~5%) in the sampled genomes of three countries (besides Portugal) also indicate that the hypothesis of selective advantage is not implausible. 2020 Emerging microbes & infections Discussion SARS_CoV_2 D839Y 41 46 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. In another perspective, one cannot rule out that the high dissemination could have also been driven by fitness increase mediated by the D839Y mutation, which would be consistent with its estimated frequency increase from 13.3% to 33.1% in a 4-week period. 2020 Emerging microbes & infections Discussion SARS_CoV_2 D839Y 136 141 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. In the present study, we show that a SARS-CoV-2 variant with a Spike D839Y mutation was associated with ~25% of all COVID-19 cases in Portugal during the exponential phase of the epidemic, after its importation from Italy in mid-late February 2020. 2020 Emerging microbes & infections Discussion SARS_CoV_2 D839Y 69 74 S 63 68 COVID-19 116 124 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. In this hypothesis, this mutation would have posed "advantageous" structural changes in the Spike protein with potential impact on SARS-CoV-2 infectivity and, consequently, on its transmissibility, as suggested for D614G. 2020 Emerging microbes & infections Discussion SARS_CoV_2 D614G 215 220 S 92 97 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. It is still worth highlighting that the huge discrepancies in sequencing sampling between countries completely hampers a real knowledge of D839Y frequency regionally and globally. 2020 Emerging microbes & infections Discussion SARS_CoV_2 D839Y 139 144 33131453 Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. While D614G was hypothesized to increase SARS-CoV-2 infectivity by influencing the dynamics of the spatially proximal fusion peptide, D839Y, which itself falls within functional fusogenic element of Spike, could also have shaped this motif towards a better fitted fusion of SARS-CoV-2 with human cells. 2020 Emerging microbes & infections Discussion SARS_CoV_2 D614G;D839Y 6;134 11;139 S 199 204 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. However, since the introduction of the S-D614G change in early 2020, the SARS-CoV-2 S-614G variant has become globally prevalent. 2020 bioRxiv Discussion SARS_CoV_2 D614G 41 46 S;S 39;84 40;85 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. Our data are also in agreement with reported functional changes conferred by the D614G substitution in the S protein and infections studies using pseudotyped viruses demonstrating increased infection. 2020 bioRxiv Discussion SARS_CoV_2 D614G 81 86 S 107 108 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. Studies that employed isogenic SARS-CoV-2 D614G variants to assess the phenotype in the context of a SARS-CoV-2 infection were only very recently reported in preprints. 2020 bioRxiv Discussion SARS_CoV_2 D614G 42 47 COVID-19 101 121 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. The advantage provided by the D614G change becomes most prominent in competition and transmission experiments in hamsters and ferrets and must therefore be considered as a driving force leading to the global dominance of the SARS-CoV-2 614G variant. 2020 bioRxiv Discussion SARS_CoV_2 D614G 30 35 33140052 SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. We found the S1 or the monomeric S ectodomain with D614G substitution had increased affinity to hACE2, which may be another mechanism underlying the increased replication and transmission of the SARS-CoV-2 D614G variant. 2020 bioRxiv Discussion SARS_CoV_2 D614G;D614G 51;206 56;211 S 33 34 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. Although nucleotide changes are frequent, amino acid mutation is actually an infrequent event for the spike gene, except for D614G which now accounts for the majority of the SARS-CoV-2 reported worldwide. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 D614G 125 130 S 102 107 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. Fourth, for the patient with W152L mutation in the saliva specimen collected on day 9 after symptom onset, only sputum specimen was available on day 7 after symptom onset. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 W152L 29 34 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. However, out of 4000 bp sequenced, only W152L was found to be the predominant mutant. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 W152L 40 45 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. However, since usually only one viral sequence from each patient would be deposited into public databases, the prevalence of W152L mutation may have been underestimated. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 W152L 125 130 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. In one patient with severe disease, an important non-synonymous mutation G22017T, which results in W152L (tryptophan to leucine) mutation in the N-terminal domain of the spike gene, was present at a low frequency of <=5% in the sputum specimen but represented the predominant population (>=60%) in the saliva specimen collected 2 days later. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 G22017T;W152L 73;99 80;104 S;N 170;145 175;146 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. It is possible that W152L mutation is already present as a predominant population in the saliva of the patient on day 7 after symptom onset. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 W152L 20 25 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. Our patient with W152L mutation was treated with ribavirin and lopinavir-ritonavir which started between the collection of the first and second specimen. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 W152L 17 22 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. Since tryptophan has an aromatic side chain while leucine has an aliphatic side chain, the W152L mutation might change the structure of the N3 loop in the N-terminal domain, hence affecting the binding of neutralizing antibodies. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 W152L 91 96 N 155 156 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. The low prevalence of W152L mutation suggest that this mutation may confer reduced fitness or transmissibility. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 W152L 22 27 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. The presence of W152L from a minor population to become the predominant population suggests that this site may be under immune selection pressure in this patient. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 W152L 16 21 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. W152L is located within the binding site of a recently identified neutralizing antibody 4A8. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 W152L 0 5 33144203 Intra-host non-synonymous diversity at a neutralizing antibody epitope of SARS-CoV-2 spike protein N-terminal domain. W152L mutation is located at the N-terminal domain of the spike protein. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 W152L 0 5 S;N 58;33 63;34 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. (1) S-protein: As previously reported, our research exploration reveals the active fixation of the D614G mutation of the S-protein of the spike, which we also find has coordinated entropic trends associated with the P323L mutation of the NSP12 polymerase that mediates viral replication (Figure 3). 2020 Evolutionary bioinformatics online Discussion SARS_CoV_2 D614G;P323L 99;216 104;221 S;Nsp12;S;S 138;238;4;121 143;243;5;122 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. (2) NSP12 polymerase: As part of the 4-mutation haplotype, the P323L mutation of the NSP12 polymerase is also actively fixed (Table 1). 2020 Evolutionary bioinformatics online Discussion SARS_CoV_2 P323L 63 68 Nsp12;Nsp12 4;85 9;90 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. (3) NSP13 helicase: One novelty is that our analysis shows active fixation tendencies of 2 mutations in the NSP13 helicase protein that mediates viral RNA unwinding, L504P and C541Y (Figure 6c). 2020 Evolutionary bioinformatics online Discussion SARS_CoV_2 C541Y;L504P 176;166 181;171 Helicase;Helicase;Nsp13;Nsp13 10;114;4;108 18;122;9;113 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. In addition, a comparison of mutants V13L, Q57H, G196V and G251V and the reference viral strain with delta scores of disorder and binding revealed interesting patterns. 2020 Evolutionary bioinformatics online Discussion SARS_CoV_2 G196V;G251V;Q57H;V13L 49;59;43;37 54;64;47;41 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. In an earlier study, several mutations in the RBD were found to enhance SARS-CoV (K479N and S487T) and SARS-CoV-2 (493 and 501) interaction with human ACE2 binding hot spots Lys31 and Lys353, and mutations K479N and S487T played a critical role in the civet-to-human and human-to-human transmission, respectively. 2020 Evolutionary bioinformatics online Discussion SARS_CoV_2 K479N;S487T;S487T;K479N 206;92;216;82 211;97;221;87 RBD 46 49 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. In contrast, G196V in the loop region of CD and G251V in the C-terminus region induced significant decreases in disorder and increases in binding potential in regions as far away as 30 to 50 amino acids from the mutated residue. 2020 Evolutionary bioinformatics online Discussion SARS_CoV_2 G196V;G251V 13;48 18;53 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. In turn, low-entropy mutation G197V, which follows the entropic return mode (Figure 3), forms part of a loop at the surface of the CD region. 2020 Evolutionary bioinformatics online Discussion SARS_CoV_2 G197V 30 35 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. Note that D614G is part of a haplotype of 4 mutations (including those that alter NSP12, the 5' UTR, and silently NSP3), which constitute the G-clade that originated in China and was established in Europe. 2020 Evolutionary bioinformatics online Discussion SARS_CoV_2 D614G 10 15 5'UTR;Nsp12;Nsp3 93;82;114 99;87;118 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. P323L seats at the center of the interface domain, contacting the NiRAN and fingers domains of NSP12 and the second subunit of NSP8 (Figure 6b). 2020 Evolutionary bioinformatics online Discussion SARS_CoV_2 P323L 0 5 Nsp12;Nsp8 95;127 100;131 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. The coordinated rates of increase of the R203K and G204R mutations indicated mutations did not occur randomly. 2020 Evolutionary bioinformatics online Discussion SARS_CoV_2 G204R;R203K 51;41 56;46 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. The high-entropy mutation Q57H, which follows an entropy expansion mode (Figure 3), is located in the first transmembrane helix at the major hydrophilic constriction of the pore, which is important for ion channel activity. 2020 Evolutionary bioinformatics online Discussion SARS_CoV_2 Q57H 26 30 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. The long-range effect and magnitude of these mutations is significant, especially G251V, which is present in 13.8% of all proteomes examined and its entropic incidence is growing. 2020 Evolutionary bioinformatics online Discussion SARS_CoV_2 G251V 82 87 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. The R203K and G204R mutations spanned regions of high disorder and high binding ability. 2020 Evolutionary bioinformatics online Discussion SARS_CoV_2 G204R;R203K 14;4 19;9 33149541 New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. The sites of the L504P and C541Y mutations fall on the N-terminal region of the 2A domain and are located in loops at the surface of the domain structure (Figure 3c). 2020 Evolutionary bioinformatics online Discussion SARS_CoV_2 C541Y;L504P 27;17 32;22 N 55 56 33157300 SARS-CoV-2 spread across the Colombian-Venezuelan border. Additionally, the presence of substitution D614G in the spike protein of the three viruses from patients residing in the current hotspots of COVID-19 in Venezuela may correlate with the reported increased infectivity observed in SARS-CoV-2-infected patients in the state of Zulia (""). 2020 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 43 48 S 56 61 COVID-19;COVID-19 141;229 149;248 33159417 Humanized COVID-19 decoy antibody effectively blocks viral entry and prevents SARS-CoV-2 infection. Although infection of SARS-CoV-2 with D614G was shown to correlate with higher infectivity and viral load in study patients, our results demonstrated that ACE2-Fc could significantly reduce the entry of SARS-CoV-2 with D614G mutation (Fig 6). 2021 EMBO molecular medicine Discussion SARS_CoV_2 D614G;D614G 38;219 43;224 33159417 Humanized COVID-19 decoy antibody effectively blocks viral entry and prevents SARS-CoV-2 infection. Based on the efficient blocking of SARS-CoV-2 entry, including the D614G variant strains, in the human epithelial cells and the airway organoids, we believe that the prophylactic use of ACE2-Fc could prevent healthcare workers or people at high risk from SARS-CoV-2 infection. 2021 EMBO molecular medicine Discussion SARS_CoV_2 D614G 67 72 COVID-19 255 275 33159417 Humanized COVID-19 decoy antibody effectively blocks viral entry and prevents SARS-CoV-2 infection. In a recent report (Korber et al, 2020), the SARS-CoV-2 bearing the D614G mutation in Spike was adapted during the human-to-human transmission and has become the pandemic strain. 2021 EMBO molecular medicine Discussion SARS_CoV_2 D614G 68 73 S 86 91 33159417 Humanized COVID-19 decoy antibody effectively blocks viral entry and prevents SARS-CoV-2 infection. Notably, the presence of the A475V, L452R, V483A, and F490L mutations in the RBD domain of SARS-CoV-2 was shown to decrease the neutralizing activity of antibody and might impede the development of therapeutic antibodies (Li et al, 2020). 2021 EMBO molecular medicine Discussion SARS_CoV_2 A475V;F490L;L452R;V483A 29;54;36;43 34;59;41;48 RBD 77 80 33159417 Humanized COVID-19 decoy antibody effectively blocks viral entry and prevents SARS-CoV-2 infection. The SARS-CoV-2 Spike with D614G pseudotyped virus was shown to exhibit enhanced infectivity compared to their counter strain with D614 at Spike (Korber et al, 2020). 2021 EMBO molecular medicine Discussion SARS_CoV_2 D614G 26 31 S;S 15;138 20;143 33159417 Humanized COVID-19 decoy antibody effectively blocks viral entry and prevents SARS-CoV-2 infection. Three of six of our isolated SARS-CoV-2 strains harbored D614G mutation (Table EV1). 2021 EMBO molecular medicine Discussion SARS_CoV_2 D614G 57 62 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. A recent study reported a single point mutation in which amino acid residue aspartic acid 614 replaced by glycine (D614G) in S gene, resulting in enhanced infectivity of SARS-CoV2. 2020 Immune network Discussion SARS_CoV_2 D614G;D614G 76;115 113;120 S 125 126 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. A third P579L mutation is located near the known D614G mutation in SD2 but without known specific function. 2020 Immune network Discussion SARS_CoV_2 D614G;P579L 49;8 54;13 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. However, the D614G mutation is dominant all over the world between March 21-30, 2020. 2020 Immune network Discussion SARS_CoV_2 D614G 13 18 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. However, the significance of this mutation is uncertain since the D614G mutation is located in the SD2 - which has no known specific function - rather than the RBD of S gene. 2020 Immune network Discussion SARS_CoV_2 D614G 66 71 RBD;S 160;167 163;168 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. In addition, we found two additional mutations G504D/V524D within the critical RBD domain of S gene. 2020 Immune network Discussion SARS_CoV_2 G504D;V524D 47;53 52;58 RBD;S 79;93 82;94 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. Interestingly, the novel P579L mutation is close to S cleavage site that may influence the infectivity of SARS-CoV2 as reported in previous study. 2020 Immune network Discussion SARS_CoV_2 P579L 25 30 S 52 53 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. It is interesting that the D614G mutation exists in all four Korean COVID-19 patients. 2020 Immune network Discussion SARS_CoV_2 D614G 27 32 COVID-19 68 76 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. The analysis of DNA sequencing revealed the D614G mutation in all four Korean COVID-19 patients. 2020 Immune network Discussion SARS_CoV_2 D614G 44 49 COVID-19 78 86 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. The D614G and P579L mutations present in the SD2. 2020 Immune network Discussion SARS_CoV_2 D614G;P579L 4;14 9;19 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. The D614G mutation has been reported from different regions of the world including continental Europe, Asia, North America, and other continents with fewer number of COVID-19. 2020 Immune network Discussion SARS_CoV_2 D614G 4 9 COVID-19 166 174 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. The D614G mutation in the S gene of SARS-CoV2 dramatically increased after March 21, 2020 compared with before March 1, 2020 [18]. 2020 Immune network Discussion SARS_CoV_2 D614G 4 9 S 26 27 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. The D614G mutation was indicated on the top of spike gene with red letter. 2020 Immune network Discussion SARS_CoV_2 D614G 4 9 S 47 52 33163249 The Progression of SARS Coronavirus 2 (SARS-CoV2): Mutation in the Receptor Binding Domain of Spike Gene. There were many SARS-CoV2 isolates with the D614G mutation in Europe prior to March 1, 2020, but there are not many in China and North America. 2020 Immune network Discussion SARS_CoV_2 D614G 44 49 33163695 Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh. Among the mutations, the most frequent 2 mutations were D614G (Spike protein) and P323L (NSP12). 2020 Gene reports Discussion SARS_CoV_2 D614G;P323L 56;82 61;87 S;Nsp12 63;89 68;94 33163695 Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh. in 2020 identified a A930V mutation in the S glycoprotein, which was absent in our sequences. 2020 Gene reports Discussion SARS_CoV_2 A930V 21 26 S 43 57 33163695 Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh. in 2020 suggested that heavy alteration in the glycosylated spike protein might be resulted due to the D614G mutation. 2020 Gene reports Discussion SARS_CoV_2 D614G 103 108 S 60 65 33163695 Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh. In another study by, the most common variants were reported in ORF1ab (C8782T), ORF8 (T28144C) and N gene (C29095T). 2020 Gene reports Discussion SARS_CoV_2 C29095T;C8782T;T28144C 107;71;86 114;77;93 ORF1ab;ORF8;N 63;80;99 69;84;100 33163695 Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh. Moreover, D614G substitution may affect the structure of spike glycoprotein which helps the virus to enter into the host cell by binding to the ACE2 receptor. 2020 Gene reports Discussion SARS_CoV_2 D614G 10 15 S 57 75 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. All of the evaluated samples in their report have been isolated in the first three months of 2020, while our first D614G mutant isolated in June. 2020 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 115 120 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. D614G mutants began expanding in Europe and rapidly became dominant species. 2020 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 0 5 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. Regarding this and also the importance of D614G in comparison to other mutations, here we evaluated the rapid and inexpensive PCR-RFLP method for the detection of this mutation. 2020 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 42 47 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. reported the D614G mutation in Taiwanese patients and patients who had a history of travel to Europe, Turkey, and Iran. 2020 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 13 18 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. reported the viral genome sequences to include D614G mutation in the travelers who returned from Iran. 2020 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 47 52 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. The D614G mutation was first identified in Germany. 2020 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 4 9 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. This study is vital for us because of the lack of data about D614G mutation in Iran. 2020 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 61 66 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. To date, reports around the world indicate an increase in the prevalence of D614G mutation. 2020 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 76 81 33166683 Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. We hope that this method will provide more information on the prevalence and epidemiology of D614G mutations worldwide. 2020 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 93 98 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. (2020), of which the two positions 17858 (M5865V) and 18060 (S5932F) in orf1ab, and 28881 (R203K) in nucleocapside. 2020 PloS one Discussion SARS_CoV_2 M5865V;R203K;S5932F 42;91;61 48;96;67 ORF1ab 72 78 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. Among all the frequent mutations in this protein, the V483A mutation has been identified in this receptor and found mainly in SARS-CoV-2 genomes isolated from USA. 2020 PloS one Discussion SARS_CoV_2 V483A 54 59 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. Among them, eight identified as new mutations, including three in nsp12-RNA-dependent RNA polymerase (M4555T, T4847I and T5020I), three in nsp13-Helicase (V5661A, P5703L and M5865V) and two in nsp15-EndoRNAse (I6525T and Ter6668W). 2020 PloS one Discussion SARS_CoV_2 M5865V;P5703L;T4847I;T5020I;I6525T;M4555T;V5661A 174;163;110;121;210;102;155 180;169;116;127;216;108;161 RdRp;EndoRNAse;Helicase;Nsp13;Nsp12 72;199;145;139;66 100;208;153;144;71 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. Among them, position 11083 (L3606F) detected in nsp6, this protein works with nsp3 and nsp4 by forming double-membrane vesicles and convoluted membranes involved in viral replication. 2020 PloS one Discussion SARS_CoV_2 L3606F 28 34 Membrane;Membrane;Nsp3;Nsp4;Nsp6 110;143;78;87;48 118;152;82;91;52 33170902 Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geo-distribution and a rich genetic variations of hotspots mutations. Eight stains from china, USA and France harbored V367F mutation previously described to enhance the affinity with ACE2 receptor. 2020 PloS one Discussion SARS_CoV_2 V367F 49 54 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. Furthermore, the subtype VIb signature SNVs G28881A, G28882A, and G28883C exhibited strong pairwise allelic association of >0.997 and uprising trend in proportion in the type VI strains (more than 38.56%) in the dataset of n = 38,248. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 G28881A;G28882A;G28883C 44;53;66 51;60;73 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. However, in this study, we found that strains carrying the single SNV (A23403G) but not the other two signature SNVs (C3037T and C14408T) did not persist. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 C14408T;A23403G;C3037T 129;71;118 136;78;124 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. In addition, the strong allelic association among the long-distant variations C3037T (nsp3, F924F), C14408T (RdRp, P4715L), A23403G (S protein, D614G), and C241T (5' UTR) suggest a possible beneficial interaction either among the proteins or RNA regions/species. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 A23403G;C14408T;C241T;C3037T;D614G;F924F;P4715L 124;100;156;78;144;92;115 131;107;161;84;149;97;121 5'UTR;Nsp3;RdRP;S 163;86;109;133 169;90;113;134 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. Recent studies suggested that D614G in the S protein, caused by one of the signature SNVs (A23403G) in type VI, may increase infectivity of SARS-CoV-2. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G;A23403G 30;91 35;98 S 43 44 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. This also explains that the strong fitness of the type VI signature SNVs is hard to explain by a genetic hitchhiking with A23403G. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 A23403G 122 129 33184173 Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. This illustrates that the study focusing on D614G alone may be insufficient and must jointly consider other signature SNVs of type VI in order to reach a better understanding regarding the prevalence of COVID-19. 2020 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 44 49 COVID-19 203 211 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. Four new unique variants were detected in three SARS-CoV-2 genomes in our study, including C4733T (nsp3: L672F), A29122C (N: Q283H), deletion TT 27792..27793 (OFR7b: Leu14 frameshift) and deletion T 5514 (nsp3: Val931 frameshift). 2020 PloS one Discussion SARS_CoV_2 A29122C;C4733T;L672F;Q283H 113;91;105;125 120;97;110;130 Nsp3;Nsp3;N 99;205;122 103;209;123 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. Interestingly, these three variants always occurred together, and sometimes they were accompanied by a synonymous mutation C241T (in 39 genomes) or multiple nucleotide substitutions GGG28881..28883AAC (N: R203K, G204R; in 33 genomes), suggesting linkage of mutations among these strains. 2020 PloS one Discussion SARS_CoV_2 C241T;G204R;R203K 123;212;205 128;217;210 N 202 203 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. Of the SARS-CoV-2 genomes from the first two patients in Vietnam (one from Wuhan who transmitted to a second case), the D614G change was not found. 2020 PloS one Discussion SARS_CoV_2 D614G 120 125 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. The B.1 lineage and its sublineages have formed the majority of sequences from Vietnam since March 2020 (S1 Fig) and harbour D614G. 2020 PloS one Discussion SARS_CoV_2 D614G 125 130 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. The D614G mutation was first detected in a SARS-CoV-2 sequence from Germany in January 2020. 2020 PloS one Discussion SARS_CoV_2 D614G 4 9 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. The linkage of four changes (C241T, C3037T, C14408T, A23403T) has been described in a comprehensive study of Spike protein variants especially related to the D614G transition. 2020 PloS one Discussion SARS_CoV_2 A23403T;C14408T;C3037T;D614G;C241T 53;44;36;158;29 60;51;42;163;34 S 109 114 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. We characterised the three most prevalent variants detected in 40/44 completed genome sequences, namely C3037T (synonymous substitution) and two non-synonymous mutations C14408T (nsp12: P323L), A23403G (S: D614G). 2020 PloS one Discussion SARS_CoV_2 A23403G;C14408T;C3037T;D614G;P323L 194;170;104;206;186 201;177;110;211;191 Nsp12;S 179;203 184;204 33201914 Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam. We identified other mutations on the Spike protein (L54F, S254F, C1250F), however these changes did not occur in the receptor binding domain. 2020 PloS one Discussion SARS_CoV_2 C1250F;S254F;L54F 65;58;52 71;63;56 RBD;S 117;37 140;42 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. briefly mentioned a premature stop codon in SARS-CoV-2 orf3b at position 14 (E14) which is corresponding to the Q57H mutation in orf3a in their Extended Data Figure 1(b). 2020 Emerging microbes & infections Discussion SARS_CoV_2 Q57H 112 116 ORF3b;ORF3a 55;129 60;134 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. For the SARS-CoV-2 orf3a, more than 50 non-synonymous mutations have been identified and the most frequent and dominant one is Q57H. 2020 Emerging microbes & infections Discussion SARS_CoV_2 Q57H 127 131 ORF3a 19 24 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. It is also important to analyse any correlation of Delta3b/D614G genotype and clinical manifestation of COVID-19 patients. 2020 Emerging microbes & infections Discussion SARS_CoV_2 D614G 59 64 COVID-19 104 112 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. It will be of interest to understand whether loss of orf3b decreases the virulence and spike D614G substitution increases the transmissibility simultaneously. 2020 Emerging microbes & infections Discussion SARS_CoV_2 D614G 93 98 ORF3b;S 53;87 58;92 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. Most importantly, not only does the number of Delta3b sequences increases during the pandemic, but its emergence also coincides with the spike D614G viruses. 2020 Emerging microbes & infections Discussion SARS_CoV_2 D614G 143 148 S 137 142 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. One of the well-studied examples is spike protein D614G substitution, of which the G614 genotype is now dominant in circulating strains with higher infectivity. 2020 Emerging microbes & infections Discussion SARS_CoV_2 D614G 50 55 S 36 41 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. Since then, no further detailed analysis on the prevalence of orf3a Q57H and truncation of orf3b has been reported. 2020 Emerging microbes & infections Discussion SARS_CoV_2 Q57H 68 72 ORF3b;ORF3a 91;62 96;67 33205709 Loss of orf3b in the circulating SARS-CoV-2 strains. We have demonstrated a distinct clade where all sequences contain orf3a Q57H substitution. 2020 Emerging microbes & infections Discussion SARS_CoV_2 Q57H 72 76 ORF3a 66 71 33208827 Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19. In this study, we showed that in mice, two injections of a subunit vaccine consisting of the prefusion spike protein (S-2P) adjuvanted with CpG 1018 and alum were effective in inducing potent neutralization activity against both pseudovirus expressing wild-type and D614G variant spike proteins, and wild-type SARS-CoV-2. 2020 Scientific reports Discussion SARS_CoV_2 D614G 266 271 S;S;S 103;280;118 108;285;119 33208827 Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19. Our results of the pseudovirus neutralization assay showed cross-reaction of these antibodies with the dominant circulating strain D614G with similar titer levels. 2020 Scientific reports Discussion SARS_CoV_2 D614G 131 136 33208827 Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19. Strains harboring the D614G mutation in the spike protein were first observed in Europe in February 2020 and over time has become the global dominant variant. 2020 Scientific reports Discussion SARS_CoV_2 D614G 22 27 S 44 49 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. A recent study reported that 7% of sera from convalescent patients showed decreased antibody neutralization S D614G pseudovirus. 2021 Clinical infectious diseases Discussion SARS_CoV_2 D614G 110 115 S 108 109 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. At reinfection in our patient, S D614G variant, located in the external spike protein of SARS-CoV-2, was observed. 2021 Clinical infectious diseases Discussion SARS_CoV_2 D614G 33 38 S;S 72;31 77;32 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. In patient 1, we confirmed that viral RNA from the positive retest clustered in clade "G" as defined by the S D614G substitution, while the viral RNA from the initial infection was found to be clade "V," as defined by the ORF3a G251V substitution. 2021 Clinical infectious diseases Discussion SARS_CoV_2 D614G;G251V 110;228 115;233 ORF3a;S 222;108 227;109 33219681 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. In the viral RNA from the clinical specimen of patient 1 at reinfection, no read sequences containing substitutions 5'UTR 241C>T and nsp1 R124C, which represent reinfection, contained the substitution nsp1 Q87D initially detected in the initial infection and still observed with lowered VAF in reinfection (Supplementary Figure 3). 2021 Clinical infectious diseases Discussion SARS_CoV_2 C241T;Q87D;R124C 122;206;138 128;210;143 5'UTR 116 121 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Current literature makes it clear that the D614G variant in SARS-CoV-2 S protein significantly enhances infectivity and transmissibility of the virus. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 D614G 43 48 S 71 72 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. During the current pandemic, there has so far been only one mutation in the S protein, D614G, which confers an apparent fitness advantage to the virus. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 D614G 87 92 S 76 77 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. However, the furin cleavage site may have made the S protein less stable and therefore the virus may have acquired the D614G mutation to compensate for this instability. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 D614G 119 124 S 51 52 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. In addition to an incomplete understanding of the molecular mechanism by which the D614G mutation exerts its effect, the full health impacts of this mutation are also not yet clear. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 D614G 83 88 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Indeed, the single S protein mutation that did emerge, D614G, is buried within the S protein and does not have a significant impact on any critical antibody epitope. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 D614G 55 60 S;S 19;83 20;84 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. On the other hand, stabilization of intermolecular interactions between S1 and S2, which leads to decreased S1 shedding and more efficient spike incorporation onto virions, can explain the enhanced infectivity of D614G viruses by an avidity effect. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 D614G 213 218 S 139 144 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. Regardless, the predominance of D614G indicates that it, like the furin cleavage site, is beneficial to the virus. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 D614G 32 37 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. The acute selective pressure of S protein instability, which has been an Achilles' heel of the virus, was resolved by the D614G mutation. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 D614G 122 127 S 32 33 33220921 Functional importance of the D614G mutation in the SARS-CoV-2 spike protein. The clinical and epidemiological data reviewed above suggest that although the D614G mutation confers an advantage in transmissibility, its effect on disease severity is uncertain, partially because other mutations frequently co-occur. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 D614G 79 84 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. Among the missense mutations found on conserved domains, the frequency of 15438G > T was the highest (n = 34) which changes the last residue of cofactor nsp8 interaction site from methionine to isoleucine (M666I) and was predominantly found in Europe. 2020 Virology journal Discussion SARS_CoV_2 G15438T;M666I 74;206 84;211 Nsp8 153 157 33225958 Evaluation on the use of Nanopore sequencing for direct characterization of coronaviruses from respiratory specimens, and a study on emerging missense mutations in partial RdRP gene of SARS-CoV-2. Our data displayed the diversity of SNVs involving 114 bases (28.93%) in a short segment of 394 bp, and missense mutations generally occurred at low frequencies (ranged from 1 to 47 genomes) compared to 15324C > T synonymous mutation (n = 553). 2020 Virology journal Discussion SARS_CoV_2 C15324T 203 213 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Although our sample size is small, the convergent origination of S H655Y with E S67S in all index cats and the fixation of these variants following transmission in two contact cats signals a potentially important functional role for one or both of these variants in feline hosts, and points towards a potential selective bottleneck. 2021 bioRxiv Discussion SARS_CoV_2 H655Y;S67S 67;80 72;84 E;S 78;65 79;66 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Although we cannot easily test this, if the transmission bottleneck were large and S H655Y, in linkage with E S67S, were rapidly selected in contact hosts immediately following transmission we might see a similar pattern to what we observe in cats 4 and 6. 2021 bioRxiv Discussion SARS_CoV_2 H655Y;S67S 85;110 90;114 E;S 108;83 109;84 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Based on iSNV frequencies, S H655Y and E S67S appear to be in linkage with each other (see cat 2 and cat 5 in Fig 3 in particular), however with short sequence reads and sequencing approaches relying on amplicon PCR, we cannot rigorously assess the extent of linkage disequilibrium between these variants. 2021 bioRxiv Discussion SARS_CoV_2 H655Y;S67S 29;41 34;45 E;S 39;27 40;28 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. E S67S has not been documented elsewhere. 2021 bioRxiv Discussion SARS_CoV_2 S67S 2 6 E 0 1 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Furthermore, S H655Y with E S67S were transmitted and fixed in contact cats in two of the three transmission events evaluated here. 2021 bioRxiv Discussion SARS_CoV_2 H655Y;S67S 15;28 20;32 E;S 26;13 27;14 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. If S H655Y facilitates viral replication in cats, viruses with this variant in linkage with E S67S might have been positively selected in all index cats. 2021 bioRxiv Discussion SARS_CoV_2 H655Y;S67S 5;94 10;98 E;S 92;3 93;4 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. It may be that S H655Y arose on the genetic background of an existing S67S variant in envelope. 2021 bioRxiv Discussion SARS_CoV_2 H655Y;S67S 17;70 22;74 S 15 16 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. S H655Y and E S67S arose rapidly, despite being found at 0.85% and 0.34% in the stock, and were detectable at intermediate frequencies at the first-day post-inoculation in all three index cats. 2021 bioRxiv Discussion SARS_CoV_2 H655Y;S67S 2;14 7;18 E;S 12;0 13;1 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. S H655Y has been previously reported in other settings as well - natural SARS-CoV-2 infections in humans, transmission studies in a hamster model, as well as SARS-CoV-2 tissue culture experiments. 2021 bioRxiv Discussion SARS_CoV_2 H655Y 2 7 S 0 1 COVID-19 73 94 33236011 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. S H655Y is near the polybasic cleavage site, residing between the receptor binding domain and the fusion peptide, and is thought to modulate Spike glycoprotein fusion efficiency. 2021 bioRxiv Discussion SARS_CoV_2 H655Y 2 7 RBD;S;S 66;141;0 89;159;1 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Although evidence is still accumulating, the increasing predominance of D614G in humans raises the possibility that viruses with this mutation have a fitness advantage, perhaps allowing more efficient person-to-person transmission. 2020 Nature communications Discussion SARS_CoV_2 D614G 72 77 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. As we have shown in this study, there are two mechanisms with which SARS-CoV-2 could have enhanced its infectivity, namely, through D614G mutation or elimination of furin-cleavage site with an optimized replacement. 2020 Nature communications Discussion SARS_CoV_2 D614G 132 137 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. However, as the virus transmits in humans, it has clearly retained the furin site while compensating for this site with D614G mutation. 2020 Nature communications Discussion SARS_CoV_2 D614G 120 125 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. In summary, an S-protein mutation, D614G, that appears to promote SARS-CoV-2 transmission in humans also enhances functional S-protein incorporation into SARS-CoV-2 VLP and retroviral PV and increases PV infectivity. 2020 Nature communications Discussion SARS_CoV_2 D614G 35 40 S;S 15;125 16;126 33243994 SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. The strong phenotypic difference we observe here between D614 and G614 suggests that more studies on the impact of the D614G mutation on the course of disease may be warranted. 2020 Nature communications Discussion SARS_CoV_2 D614G 119 124 33252670 SARS-CoV-2 Among Military and Civilian Patients, Metro Manila, Philippines. Alternatively, this might have also facilitated the dissemination of strains such as GR/B.1.1 and GR/B1.1.28 with the D614G mutation, which led to the replacement of other circulating SARS-CoV-2 strains before June 2020. 2021 Military medicine Discussion SARS_CoV_2 D614G 118 123 33252670 SARS-CoV-2 Among Military and Civilian Patients, Metro Manila, Philippines. The D614G mutation has been associated with higher titers of SARS-CoV-2 pseudo viruses (a retrovirus that can integrate the envelope glycoprotein of another virus to form a virus with an exogenous viral envelope with the genome retaining the characteristics of the original retrovirus) and higher viral RNA levels in vitro as well as enhanced SARS-CoV-2 replication in the upper airway using a primary human airway tissue model, though further studies are still needed to definitely determine whether this mutation translates to an actual impact on transmission efficiency or disease severity. 2021 Military medicine Discussion SARS_CoV_2 D614G 4 9 33252670 SARS-CoV-2 Among Military and Civilian Patients, Metro Manila, Philippines. We detected the D614G mutation from SARS-CoV-2-positive specimens collected from the end of June to July in the majority (22/23) of the strains we sequenced. 2021 Military medicine Discussion SARS_CoV_2 D614G 16 21 33253226 SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia. Furthermore, public sharing of sequences contributed to identification of the C6310A (nsp3-S1197R) mutation affecting the sensitivity of a commercial diagnostic real-time PCR assay, leading to updated primers/probes. 2020 PLoS neglected tropical diseases Discussion SARS_CoV_2 C6310A;S1197R 78;91 84;97 Nsp3 86 90 33262895 Genomic characterization of SARS-CoV-2 in Egypt. 8782C > T(ORF1ab) and 28144 T > C (ORF8), has been identified among researchers in several genome databases. 2021 Journal of advanced research Discussion SARS_CoV_2 T28144C;C8782T 22;0 33;9 ORF1ab;ORF8 10;35 16;39 33262895 Genomic characterization of SARS-CoV-2 in Egypt. Asn1673 Asn) in 6 samples and finally, c.2772delC (p. 2021 Journal of advanced research Discussion SARS_CoV_2 2772delC 39 49 33262895 Genomic characterization of SARS-CoV-2 in Egypt. Asp614Gly), which also has a replication mutation in ORF1ab P4715L. 2021 Journal of advanced research Discussion SARS_CoV_2 P4715L;D614G 60;0 66;9 ORF1ab 53 59 33262895 Genomic characterization of SARS-CoV-2 in Egypt. C.2772delC (p. 2021 Journal of advanced research Discussion SARS_CoV_2 2772delC 2 10 33262895 Genomic characterization of SARS-CoV-2 in Egypt. In late January, in China, D614 G was first observed and in three months became the largest clade. 2021 Journal of advanced research Discussion SARS_CoV_2 D614G 27 33 33262895 Genomic characterization of SARS-CoV-2 in Egypt. In the current study, synonymous variations were detected in one position of E and one position of M genes: c.222G > C (p. 2021 Journal of advanced research Discussion SARS_CoV_2 G222C 108 118 E 77 78 33262895 Genomic characterization of SARS-CoV-2 in Egypt. In the current study, the missense variation was found in ORF3a c.171G > T (p.Gln57His), ORF7a c.21C > A (p.Phe7Leu), ORF8, and ORF10 genes. 2021 Journal of advanced research Discussion SARS_CoV_2 G171T;C21A;Q57H;F7L;Q57H 64;95;76;106;78 74;104;86;115;86 ORF7a;ORF3a;ORF8 89;58;118 94;63;122 33262895 Genomic characterization of SARS-CoV-2 in Egypt. Likewise the most common variation in the current study in the S gene is the missense mutation c.1841A > G (p. 2021 Journal of advanced research Discussion SARS_CoV_2 A1841G 95 106 S 63 64 33262895 Genomic characterization of SARS-CoV-2 in Egypt. One of these variations is the S-protein mutation, D614 G, in the carboxy(C)-terminal region of the S1 domain. 2021 Journal of advanced research Discussion SARS_CoV_2 D614G 51 57 S 31 32 33262895 Genomic characterization of SARS-CoV-2 in Egypt. Phe924Phe) (detected by 57/61 samples) was the highest mutation observed in NSP3, followed by c.5019C > T (p. 2021 Journal of advanced research Discussion SARS_CoV_2 C5019T;F924F 94;0 105;9 Nsp3 76 80 33262895 Genomic characterization of SARS-CoV-2 in Egypt. SARS-CoV-2 isolates are the most common SNP mutation in nsp8 proteins, where leucine (L) amino acid is mutated to serine(S) (28,144 T > C). 2021 Journal of advanced research Discussion SARS_CoV_2 T144C 128 137 Nsp8;S 56;121 60;122 33262895 Genomic characterization of SARS-CoV-2 in Egypt. Ser5398Leu), and c.137994A > G (p. 2021 Journal of advanced research Discussion SARS_CoV_2 A137994G 17 30 33262895 Genomic characterization of SARS-CoV-2 in Egypt. The analysis currently investigates the 10 variation in 56/61 samples, followed by c.16193C > T (p. 2021 Journal of advanced research Discussion SARS_CoV_2 C16193T 83 95 33262895 Genomic characterization of SARS-CoV-2 in Egypt. The most widely defined clade was a vaccine-based variation D614G, which is located in a B cell epitope with a highly immuno-dominant region. 2021 Journal of advanced research Discussion SARS_CoV_2 D614G 60 65 33262895 Genomic characterization of SARS-CoV-2 in Egypt. The previous research was carried out on 103 genomes of SARS-CoV-2 for both co-mutations (8782C > T and 28,144 T > C) which classified the virus as S / L types (Yin, 2020). 2021 Journal of advanced research Discussion SARS_CoV_2 C8782T;T144C 90;107 99;116 33262895 Genomic characterization of SARS-CoV-2 in Egypt. Ther4598Thr) for 3/61 samples in 10 RNA-dependent RNA Polymerase (RdRp) region (one missense variation c.14144C > T (p. 2021 Journal of advanced research Discussion SARS_CoV_2 C14144T 103 115 RdRp;RdRP 36;66 64;70 33262895 Genomic characterization of SARS-CoV-2 in Egypt. Tyr71Tyr), respectively. 2021 Journal of advanced research Discussion SARS_CoV_2 Y71Y 0 8 33262895 Genomic characterization of SARS-CoV-2 in Egypt. Virus replication speeds can also be affected by nearly all strains that have D614 G mutation in their protein responsible for Replication (Orf1ab P4715L; RdRp P323L). 2021 Journal of advanced research Discussion SARS_CoV_2 D614G;P323L;P4715L 78;160;147 84;165;153 ORF1ab;RdRP 140;155 146;159 33262895 Genomic characterization of SARS-CoV-2 in Egypt. While in this epitope the amino acids are well preserved, 14 other variations besides D614 G have been identified. 2021 Journal of advanced research Discussion SARS_CoV_2 D614G 86 92 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. However, despite having a low nM affinity to SARS-CoV-2 P384A RBD, CR3022 only weakly neutralizes SARS-CoV-2 P384A with an IC50 of 3.2 mug/ml and SARS-CoV with an IC50 of 5.2 mug/ml. 2020 PLoS pathogens Discussion SARS_CoV_2 P384A;P384A 56;109 61;114 RBD 62 65 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. The KD of CR3022 Fab to SARS-CoV-2 WT RBD is 68 nM, whereas to SARS-CoV-2 P384A RBD is 1 nM (Fig 1B and 1C), indicating that the affinity threshold for neutralization of SARS-CoV-2 to this epitope is in the low nM range. 2020 PLoS pathogens Discussion SARS_CoV_2 P384A 74 79 RBD;RBD 38;80 41;83 33275640 A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody. While CR3022 cannot neutralize SARS-CoV-2 WT in almost all studies, it can neutralize the SARS-CoV-2 P384A mutant. 2020 PLoS pathogens Discussion SARS_CoV_2 P384A 101 106 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Convergent molecular evolution (resulting in homoplasies) can present an alternative source of information about potentially beneficial virus mutations; however, such approaches lack sensitivity for the D614G as almost all circulating 614G genomes derive from a single ancestor. 2021 Cell Discussion SARS_CoV_2 D614G 203 208 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. In the case of D614G, a large increase in cellular infectivity results in a weak population-level signal that nonetheless produces a discernible effect on transmissibility. 2021 Cell Discussion SARS_CoV_2 D614G 15 20 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. One amino acid replacement is notable: RdRp P323L, which occurred almost concurrently with D614G and is in almost perfect linkage equilibrium with 614G. 2021 Cell Discussion SARS_CoV_2 D614G;P323L 91;44 96;49 RdRP 39 43 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Our discovery of co-occurring mutations in neighboring sites (615 and 613) and the D614N variant is suggestive of a more complex selective landscape in this region of the spike protein than was first indicated. 2021 Cell Discussion SARS_CoV_2 D614N 83 88 S 171 176 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. The observed association of patient age with D614G remains an unexplained and potentially important aspect of the epidemiology of this variant. 2021 Cell Discussion SARS_CoV_2 D614G 45 50 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. The rarity of independent occurrences of D614G and P323L make it impossible to evaluate the effects of these replacements epidemiologically, but experiments with pseudotyped virus have been carried out in the absence of P323L. 2021 Cell Discussion SARS_CoV_2 D614G;P323L;P323L 41;51;220 46;56;225 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Whether the current explosive epidemics across the world are to any degree being driven by D614G, or whether it is simply the beneficiary of being in the right place at the right time, it is now the dominant variant. 2021 Cell Discussion SARS_CoV_2 D614G 91 96 33275900 Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. While we believe an effect on SARS-CoV-2 transmissibility caused by D614G is likely to be present, it is important to note that the estimation of the absolute size of this effect is uncertain and much harder to predict. 2021 Cell Discussion SARS_CoV_2 D614G 68 73 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. Because the SARS-CoV-2/IZSAM/46419 isolate with D614G is accompanied by three additional mutations in the viral genome, it can be reasonably argued that the enhanced replicative capabilities observed here are not necessarily associated with D614G. 2021 Veterinary microbiology Discussion SARS_CoV_2 D614G;D614G 48;241 53;246 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. However, the effects of D614G on viral replication have recently been demonstrated in both human cells and hamsters. 2021 Veterinary microbiology Discussion SARS_CoV_2 D614G 24 29 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. Importantly, we demonstrated that a SARS-CoV-2 isolate containing the D614G mutation in the S protein possessed enhanced replicative capabilities compared to earlier strains, represented here by a SARS-CoV-2 strain collected from a Chinese tourist who visited Rome, Italy, in January 2020. 2021 Veterinary microbiology Discussion SARS_CoV_2 D614G 70 75 S 92 93 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. Nevertheless, additional studies are required to confirm the higher fitness and infectivity of D614G viruses in animal tissues. 2021 Veterinary microbiology Discussion SARS_CoV_2 D614G 95 100 33278734 SARS-CoV-2 replicates in respiratory ex vivo organ cultures of domestic ruminant species. We therefore speculate that D614G played a role by enhancing the replicative capabilities of SARS-CoV-2/IZSAM/46419 in the experiments we performed. 2021 Veterinary microbiology Discussion SARS_CoV_2 D614G 28 33 33292056 Sensing the interactions between carbohydrate-binding agents and N-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies. H84T of BanLec was seen to interact with SARS-CoV-2 S glycoprotein in both the complexes. 2020 Journal of biomolecular structure & dynamics Discussion SARS_CoV_2 H84T 0 4 S 52 66 33292056 Sensing the interactions between carbohydrate-binding agents and N-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies. Single amino acid substitution in wild-type BanLec, where replacement of histidine with threonine at 84th position (H84T) in BanLec abolishes its mitogenic activity and significantly retained its broad-range antiviral activity. 2020 Journal of biomolecular structure & dynamics Discussion SARS_CoV_2 H84T 116 120 33292056 Sensing the interactions between carbohydrate-binding agents and N-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies. Surprisingly, the point of mutation (H84T) was also seen to interact well with the S glycoprotein of SARS-CoV-2 in both the wild-type and mutant BanLec suggesting that the single amino acid substitution did not affect the binding property of BanLec. 2020 Journal of biomolecular structure & dynamics Discussion SARS_CoV_2 H84T 37 41 S 83 97 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. Also in this case, the Q493N mutation reduces the binding affinity of the full spike for ACE2. 2020 bioRxiv Discussion SARS_CoV_2 Q493N 23 28 S 79 84 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. Deep Scanning Mutagenesis indicates that the Q493N mutation reduces the avidity of the ACE2-RBD complex by a small amount, though it also indicates that the specific recognition of K31 and E35 might not be crucial, as mutations to hydrophobic residues (M, A, or Y) further increase the avidity. 2020 bioRxiv Discussion SARS_CoV_2 Q493N 45 50 RBD 92 95 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. Experiments have shown that the N501T reduces the binding strength of the full spike protein, although measurements probing the result for the RBD alone showed a small increase in avidity upon mutation. 2020 bioRxiv Discussion SARS_CoV_2 N501T 32 37 S;RBD 79;143 84;146 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. for the change in avidity of the mutant G502X as a function of the volume of the residue X. 2020 bioRxiv Discussion SARS_CoV_2 G502X 40 45 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. Free energy calculations showed that the mutant (G502P) complex is weakened by almost 3 kcal/mol (Table 1). 2020 bioRxiv Discussion SARS_CoV_2 G502P 49 54 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. In addition, computational studies report a DeltaDeltaG for the F486A mutation that is somewhat larger than our result for the F486L substitution. 2020 bioRxiv Discussion SARS_CoV_2 F486A;F486L 64;127 69;132 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. Interestingly, the inverse mutation, T487N, in SARS-CoV was also predicted via MD simulations to be favorable, which might highlight that changes to nearby or far-away groups contribute to selecting which amino acid increases stability. 2020 bioRxiv Discussion SARS_CoV_2 T487N 37 42 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. Interestingly, the values for the DeltaDeltaG of F486L in SARS-CoV-2 and L472F in SARS-CoV are in excellent agreement. 2020 bioRxiv Discussion SARS_CoV_2 F486L;L472F 49;73 54;78 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. Our prediction of the change in binding affinity when F486 is mutated to leucine is in agreement with experiments measuring the change in binding avidity for the same mutation, and with experiments and simulations showing that the L472F mutation in SARS-CoV resulted in a more stable complex. 2020 bioRxiv Discussion SARS_CoV_2 L472F 231 236 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. The inverse mutation on SARS-CoV, N479Q, was predicted to be favorable. 2020 bioRxiv Discussion SARS_CoV_2 N479Q 34 39 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. We found that the N501T mutation in SARS-CoV-2, which restores the SARS-CoV residue, increases the binding affinity of the RBD for ACE2. 2020 bioRxiv Discussion SARS_CoV_2 N501T 18 23 RBD 123 126 33299995 Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2. We provided structural characterization to explain these observations by studying the effect of the substitution of glycine 502 with proline using MD simulations. 2020 bioRxiv Discussion SARS_CoV_2 G502P 116 140 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. Although recent studies agreed that D614G mutation could enhance SARS-CoV-2 infectivity and promote its transmission, regarding its effect on virulence, one study reported that G614 virus infection was associated with higher mortality, while the other study concluded no obvious effect on disease severity. 2020 PloS one Discussion SARS_CoV_2 D614G 36 41 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. In contrast, the G1124V mutation appears to favor the virus to escape immune recognition as this mutation reduces epitope binding affinity of HLA alleles to a level that some are no longer able to bind (Table 3). 2020 PloS one Discussion SARS_CoV_2 G1124V 17 23 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. One potential explanation for these disparate clinical findings is that the prevalent HLAs of the infected subjects in the two studies differ, which leads to divergent anti-S protein CD8 T cell responses, either toward the epitopes containing the G614 mutation alone and/or in combination with other epitopes we identified, as D614G mutation can occur simultaneously with other mutations on the S protein (S1 Fig). 2020 PloS one Discussion SARS_CoV_2 D614G 327 332 S;S 173;395 174;396 33301503 CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention. Our data of mutational effect of L5F suggests that the evolution of SARS-CoV2 virus targeting L5 might be eventually unsuccessful as the mutated epitope could enhance CD8 T cell recognition and killing through the enhanced interaction with most of the HLA alleles (Table 2). 2020 PloS one Discussion SARS_CoV_2 L5F 33 36 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. According to the CoV-GLUE database, ORF8 L84S is the 8th most prevalent AA replacement to date. 2021 Emerging microbes & infections Discussion SARS_CoV_2 L84S 41 45 ORF8 36 40 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. After a controversial debate about the ancestry of L and S types and the functional impact of L84S, the still limited amount of data indicates that L84S might confer selection advantage and render the virus more virulent based on destabilizing the immuno- and replication-modulatory protein ORF8 and mitigating binding of ORF8 to human complement C3b. 2021 Emerging microbes & infections Discussion SARS_CoV_2 L84S;L84S 94;148 98;152 ORF8;ORF8;S 291;322;57 295;326;58 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. Although D614G serves as the clade G-defining mutation with likely effects on virus infectivity/transmissibility, D614G is governed by a very strict co-appearance with C241 T, C3037 T, and C14408 T, both in Uruguayan and global G variants (Figure 5, Figure S5). 2021 Emerging microbes & infections Discussion SARS_CoV_2 C14408T;C241T;C3037T;D614G;D614G 189;168;176;9;114 197;174;183;14;119 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. by D614G, even in asymptomatic cases) and limited clinical presentation (e.g. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 3 8 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. by P323L, decreasing the production of viral RNA) to eventually attenuate an aggressive virus that, as shown for MERS and SARS-CoV-1, is more vulnerable to viral clearance with lack of long-term epidemiological success. 2021 Emerging microbes & infections Discussion SARS_CoV_2 P323L 3 8 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. C17470 T, C25521 T, and C26088 T. 2021 Emerging microbes & infections Discussion SARS_CoV_2 C25521T;C26088T;C17470T 10;24;0 18;32;8 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. D614G alone or P323L alone have <=0.3 global prevalence, whereas D614G and P323L together have ~70% global prevalence as of August 2020. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G;P323L;P323L;D614G 65;15;75;0 70;20;80;5 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. Diverse structural and functional assays strongly suggest that the spike D614G mutation renders SARS-CoV-2 more infectious by stabilizing its structure. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 73 78 S 67 72 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. Furthermore, D614G triggers higher spike numbers on the virion surface and induces a more open, receptor-binding domain (RBD)-up spike conformation toward a receptor-binding and fusion-competent state. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 13 18 S;S;RBD 35;129;121 40;134;124 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. In an FDR-adjusted analysis, the presence of D614G mutation was coupled to other viral mutations, treatment of the infected patients in a regional healthcare institution, and late sampling, but not to clinical parameters (Figures 5 and 6, Figure S11). 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 45 50 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. In D614G spikes, binding to the angiotensin-converting enzyme 2 (ACE2) receptor is not increased, and SARS-CoV-2 viruses do not acquire D614G escape mutations in vitro under neutralizing antibody immune pressure. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G;D614G 3;136 8;141 S 9 15 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. Instead, D614G increases neutralization susceptibility of SARS-CoV-2, which assures high sensitivity to vaccination-induced neutralizing antibodies. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 9 14 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. More specifically, we studied pairwise correlations with the spike D614G mutation, which, because of perfectly matching mutation patterns, also represents correlation analyses for the RdRp P323L mutation or G-related clades (G, GR, and GH). 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G;P323L 67;189 72;194 S;RdRP 61;184 66;188 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. Notably, in addition to the D614G-causing A23403 G mutation in spike, C14408 T is responsible for the AA replacement P323L in the RdRp gene. 2021 Emerging microbes & infections Discussion SARS_CoV_2 A23403G;C14408T;D614G;P323L 42;70;28;117 50;78;33;122 S;RdRP 63;130 68;134 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. P323L, although not located in the active centre, possibly influences RdRp fidelity through allosteric effects at the nsp12 interface with the nsp8 cofactor and might increase the viral mutation rate. 2021 Emerging microbes & infections Discussion SARS_CoV_2 P323L 0 5 Nsp12;Nsp8;RdRP 118;143;70 123;147;74 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. There have been controversial reports of D614G being associated with higher fatality rates and/or severe illness in a few data sets, whereas more recent data suggests no correlations of D614G with clinical outcome, the latter supported by our findings. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G;D614G 41;186 46;191 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. Thus, the strong correlation patterns between key mutations in our Uruguayan data set, mirroring global patterns, allows us to hypothesize that coupled mutations, such as D614G in spike and P3233L in RdRp might synergize for the epidemiological success of the virus. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G;P3233L 171;190 176;196 S;RdRP 180;200 185;204 33306459 SARS-CoV-2 genomic characterization and clinical manifestation of the COVID-19 outbreak in Uruguay. Uruguayan clade S viruses are characterized by the key mutations T28144 C, causing the AA replacement L84S in ORF8, and C8782 T, in agreement with global clade S strains. 2021 Emerging microbes & infections Discussion SARS_CoV_2 C8782T;L84S;T28144C 120;102;65 127;106;73 ORF8;S;S 110;16;160 114;17;161 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. (4) Our experiments do not rule out possible differences in spike incorporation as another mechanism for the increased neutralization-susceptibility of the D614G spike pseudovirus. 2021 Cell host & microbe Discussion SARS_CoV_2 D614G 156 161 S;S 60;162 65;167 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. Although this soluble ectodomain has been shown to be a good mimic of the native spike, and the shift in the proportion of RBD "up" conformation between the D614 and G614 variants suggest an allosteric effect of the D614G mutation on the RBD conformations, the structures of the native spike could have some differences from what we observe in the context of the ectodomain. 2021 Cell host & microbe Discussion SARS_CoV_2 D614G 216 221 S;S;RBD;RBD 81;286;123;238 86;291;126;241 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. More recently, the D614G mutation was shown to render live SARS-CoV-2 virus more susceptible to neutralization by sera from D614 spike-immunized mice. 2021 Cell host & microbe Discussion SARS_CoV_2 D614G 19 24 S 129 134 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. Most of the immunogens in these trials were either derived from the initial D614 virus or contain D614G in the spike. 2021 Cell host & microbe Discussion SARS_CoV_2 D614G 98 103 S 111 116 33306985 D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. Our structural data demonstrate that, although the D614G mutation is located in the SD2 subdomain and distal from the RBD region, in the context of a soluble ectodomain construct, this mutation leads to an increased proportion of the 1-RBD-up conformation (Figure 4). 2021 Cell host & microbe Discussion SARS_CoV_2 D614G 51 56 RBD;RBD 118;236 121;239 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Based on the reported structures of the SARS-CoV-2 spike glycoprotein, several amino acid residues (Lys835, Gln836, and Lys854) are in close proximity to Asp614 and therefore could potentially influence D614G phenotypes. 2020 Journal of virology Discussion SARS_CoV_2 D614G 203 208 S 51 69 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. D614G retains an intact furin cleavage site but strengthens the association of S1 with the S trimer, possibly by improving S1 CTD2-S2 interactions. 2020 Journal of virology Discussion SARS_CoV_2 D614G 0 5 S 91 92 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. However, alanine substitutions of these residues did not abolish the observed D614G phenotypes (data not shown). 2020 Journal of virology Discussion SARS_CoV_2 D614G 78 83 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Of note, the D614G change partially compensates for the effects of acquisition of the furin cleavage site on virus infectivity and ACE2 responsiveness. 2020 Journal of virology Discussion SARS_CoV_2 D614G 13 18 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. Our results indicate that two key features of the SARS-CoV-2 S gp, the furin cleavage site presumably acquired during viral passage to humans from bat/intermediate hosts and the D614G change associated with increasing prevalence in human populations, influence related functions of the S gp. 2020 Journal of virology Discussion SARS_CoV_2 D614G 178 183 S;S 61;286 62;287 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. The D614G change increases virus infectivity and responsiveness to ACE2 but also results in moderate increases in sensitivity to neutralizing antisera. 2020 Journal of virology Discussion SARS_CoV_2 D614G 4 9 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. The more triggerable FurinMut and D614G mutants solve this potential problem in different ways. 2020 Journal of virology Discussion SARS_CoV_2 D614G 34 39 33310888 Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects. The resulting higher spike density allows FurinMut and D614G to take replicative advantage of increased triggerability in response to ACE2 binding. 2020 Journal of virology Discussion SARS_CoV_2 D614G 55 60 S 21 26 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. SARS-CoV-2 encoding the D614G spike protein has increased its frequency in the human population. 2020 Cell reports Discussion SARS_CoV_2 D614G 24 29 S 30 35 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. The ACE2 microbody maintained its ability to neutralize D614G spike protein pseudotyped virus and was able to neutralize diverse beta coronaviruses. 2020 Cell reports Discussion SARS_CoV_2 D614G 56 61 S 62 67 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. The D614G spike protein was found to be more resistant to shedding from the virion, adopting a conformation that favors ACE2 binding and lowers the energy barrier to cell fusion. 2020 Cell reports Discussion SARS_CoV_2 D614G 4 9 S 10 15 33326798 An ACE2 Microbody Containing a Single Immunoglobulin Fc Domain Is a Potent Inhibitor of SARS-CoV-2. The microbody was fully active against virus with the D614G spike protein, a variant of increasing prevalence with increased infectivity in vitro (Figure 6B), and was highly active against ACE2-specific spike proteins from other beta coronaviruses. 2020 Cell reports Discussion SARS_CoV_2 D614G 54 59 S;S 60;203 65;208 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. At the same time, several reports documented that 23,403 A > G (D614G) missense mutation in the Spike protein enhanced the infectivity rate of the virus. 2020 Frontiers in microbiology Discussion SARS_CoV_2 D614G;A403G 64;53 69;62 S 96 101 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. From initial observation, we have seen a 10.34% occurrence of C6312A, which has been associated with an India-specific clade called I/A3i. 2020 Frontiers in microbiology Discussion SARS_CoV_2 C6312A 62 68 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. We found that four common variants, i.e., 241 C > T in the UTR region, 3,037 C > T in NSP3 gene, 14,408 C > T in the NSP12, and 23,403 A > G in S gene coevolved mostly in the 20A and 20B clades. 2020 Frontiers in microbiology Discussion SARS_CoV_2 C241T;C037T;A403G;C408T 42;73;131;100 51;82;140;109 Nsp12;Nsp3;S 117;86;144 122;90;145 33329480 Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. We observed in our protein modeling analysis that TMPRSS2 binding to Spike protein is enhanced by this mutation of aspartic acid to glycine (D614G) as it resulted in increased hydrogen bonding interactions. 2020 Frontiers in microbiology Discussion SARS_CoV_2 D614G 141 146 S 69 74 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. (doi: 10.1101/2020.06.12.148726) concluded that the D614G mutation led to enhanced retention of S1. 2020 bioRxiv Discussion SARS_CoV_2 D614G 52 57 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. 2020 https://www.biorxiv.org/content/10.1101/2020.11.16.384594v1.full.pdf), we do not suggest that the effects of the D614G mutation are necessarily mediated by M6P receptors. 2020 bioRxiv Discussion SARS_CoV_2 D614G 118 123 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. Although it is at least formally possible that these various effect of the D614G mutation are unrelated, the more parsimonious hypothesis is that they are all reflections of a common mechanism. 2020 bioRxiv Discussion SARS_CoV_2 D614G 75 80 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. Given that the D614G mutation enhances viral fitness, it is important to consider how viral fitness might be promoted by an increase in the lysosomal sorting of spike and the accumulation of spike-containing punctae within lysosomes of SARS-CoV-2-infected cells. 2020 bioRxiv Discussion SARS_CoV_2 D614G 15 20 S;S 161;191 166;196 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. In addition, we observed that the D614G mutation induced a slight elevation in spike protein processing at the S1/S2 junction. 2020 bioRxiv Discussion SARS_CoV_2 D614G 34 39 S 79 84 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. The most obvious effect of the D614G mutation is the ~4-8-fold increase in a proxy marker of SARS-CoV-2 infection (an encoded luciferase) at 8 hours post-infection, suggestive of accelerated viral entry. 2020 bioRxiv Discussion SARS_CoV_2 D614G 31 36 COVID-19 93 113 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. This D614G-induced shift in spike protein trafficking was observed in human cells expressing the spike protein on its own, outside the context of a viral infection, where it appeared to enhance spike-induced lysosomes clustering. 2020 bioRxiv Discussion SARS_CoV_2 D614G 5 10 S;S;S 28;97;194 33;102;199 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. This may reflect a slight increase in the cleavage of G614 spike at the S1/S2 boundary, and since lysosomal proteases can catalyze this event it may be a consequence of enhanced lysosomal sorting of D614G spike proteins. 2020 bioRxiv Discussion SARS_CoV_2 D614G 199 204 S;S 59;205 64;210 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. To the best of our knowledge, the D614G-induced lysosomal shift in spike protein trafficking and slight elevation in spike processing represent the earliest cell biological and biochemical manifestations of the D614G mutation, raising the strong possibility that they may contribute to the pronounced effects of the D614G mutation on SARS-CoV-2 infectivity, viral load, and transmission. 2020 bioRxiv Discussion SARS_CoV_2 D614G;D614G;D614G 34;211;316 39;216;321 S;S 67;117 72;122 33330866 The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike. We show here that the spike D614G mutation alters spike protein sorting, enhancing its trafficking towards the lysosome and away from other intracellular compartments. 2020 bioRxiv Discussion SARS_CoV_2 D614G 28 33 S;S 22;50 27;55 33335187 CoV2-ID, a MIQE-compliant sub-20-min 5-plex RT-PCR assay targeting SARS-CoV-2 for the diagnosis of COVID-19. Nonetheless, a SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has replaced the original D614A variant in many locations. 2020 Scientific reports Discussion SARS_CoV_2 D614A;D614G 111;79 116;84 S 47 52 33335187 CoV2-ID, a MIQE-compliant sub-20-min 5-plex RT-PCR assay targeting SARS-CoV-2 for the diagnosis of COVID-19. These data certainly support the finding that this variant is ubiquitous, as all of the UK isolates tested back as early as 14th April carry the D614G mutation. 2020 Scientific reports Discussion SARS_CoV_2 D614G 145 150 33335187 CoV2-ID, a MIQE-compliant sub-20-min 5-plex RT-PCR assay targeting SARS-CoV-2 for the diagnosis of COVID-19. Two mutations within the N-gene probe binding site, one a G to T transversion at 5'-end nucleotide 3, the other a C to T transition at nucleotide 5 with respective frequencies of 0.053% and 0.029% also had no discernible effect on sensitivity. 2020 Scientific reports Discussion SARS_CoV_2 C5T;G5T 114;58 147;82 N 25 26 33336251 Multisystem Inflammatory Syndrome in Children in February 2020 and Implications of Genomic Sequencing for SARS-CoV-2. Development of MIS-C in this patient and not others, at a time when isolation of D614G was rare, suggests that the risk of developing MIS-C as a complication of SARS-CoV-2 infection may be associated with viral lineage. 2021 Journal of the Pediatric Infectious Diseases Society Discussion SARS_CoV_2 D614G 81 86 COVID-19 161 181 33336251 Multisystem Inflammatory Syndrome in Children in February 2020 and Implications of Genomic Sequencing for SARS-CoV-2. MIS-C cases were described when the circulation of D614G was increasing worldwide. 2021 Journal of the Pediatric Infectious Diseases Society Discussion SARS_CoV_2 D614G 51 56 33336251 Multisystem Inflammatory Syndrome in Children in February 2020 and Implications of Genomic Sequencing for SARS-CoV-2. The G clade, representing the D614G variant, was not identified in the United States until late February, but it quickly became the dominant lineage circulating within the United States by mid-March. 2021 Journal of the Pediatric Infectious Diseases Society Discussion SARS_CoV_2 D614G 30 35 33350913 Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China. However, our sequencing result demonstrated that the genome of case 66 was 100% identical to the first published SARS-CoV-2 genome, and all cases in cluster 1 did not harbor Orf3a-G251V, which was recognized as a hallmark of local cases with unknown source in our community. 2021 Emerging infectious diseases Discussion SARS_CoV_2 G251V 180 185 ORF3a 174 179 33350913 Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China. In concert with epidemiologic information, all 11 cases from cluster 4 shared 3 common missense mutations, namely S-L8V, Orf1ab-H3233Y, and Orf3a-G251V; 7 cases shared identical genomes. 2021 Emerging infectious diseases Discussion SARS_CoV_2 G251V;H3233Y;L8V 146;128;116 151;134;119 ORF1ab;ORF3a;S 121;140;114 127;145;115 33350913 Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China. It also harbored a common mutation at Orf3a-G251V, which accounted for 88.0% of cases in this study. 2021 Emerging infectious diseases Discussion SARS_CoV_2 G251V 44 49 ORF3a 38 43 33350913 Territorywide Study of Early Coronavirus Disease Outbreak, Hong Kong, China. Two missense mutations, Orf1ab-G295V and Orf1ab-L3606F, were unique to this cluster. 2021 Emerging infectious diseases Discussion SARS_CoV_2 G295V;L3606F 31;48 36;54 ORF1ab;ORF1ab 24;41 30;47 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. According to GISAID, this G71S common mutation was first reported in February 2020 in Germany (hCoV-19/Germany/BW-ChVir-1577/2020) and belongs to the B.1 lineage (G and GR clades) (https://www.gisaid.org/, 6-11-2020). 2021 International journal of infectious diseases Discussion SARS_CoV_2 G71S 26 30 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. Another commonly observed mutation in this study, P323L, was described as the most common in other countries; furthermore, the increasing ratio of P323L indicates that this type of mutation may favor and enhance the transmission capacity of SARS-CoV-2. 2021 International journal of infectious diseases Discussion SARS_CoV_2 P323L;P323L 50;147 55;152 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. Both D614G and P323L were prevalent and coexisted in this study with almost the same frequency. 2021 International journal of infectious diseases Discussion SARS_CoV_2 D614G;P323L 5;15 10;20 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. However, the mutation G71S is only present in Oman. 2021 International journal of infectious diseases Discussion SARS_CoV_2 G71S 22 26 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. showed that the D614G mutation appeared to be taking over COVID-19 infections in the Middle East and North Africa (MENA) region as a significant increase in the proportion was noticed from 63.0% in February 2020 to 98.5% in June 2020 (p < 0.001). 2021 International journal of infectious diseases Discussion SARS_CoV_2 D614G 16 21 COVID-19 58 66 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. The B1.1 lineage (GR) comprising both Spike D614G and nucleocapsid RG203KR mutations, was the major clade found in Oman, which is inconsistent with the current globally predominant clade in Europe, Asia, South America, and Africa. 2021 International journal of infectious diseases Discussion SARS_CoV_2 D614G 44 49 N;S 54;38 66;43 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. The D614G mutation in the Spike protein has been reported in 116 countries mostly of B1 lineages (GR, G, and GH clades). 2021 International journal of infectious diseases Discussion SARS_CoV_2 D614G 4 9 S 26 31 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. The D614G was found to be the second-highest mutation with a frequency of 92.6% (87/94) in our study. 2021 International journal of infectious diseases Discussion SARS_CoV_2 D614G 4 9 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. The I280V mutation has been reported in only three countries, Oman was the first to report this mutation from a strain (hCoV-19/Oman/11374/2020) collected on April 7, 2020 among the V cluster that was observed in Al Batinah South Governorate. 2021 International journal of infectious diseases Discussion SARS_CoV_2 I280V 4 9 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. The unique mutation NSP15-I280V detected in this study is in the endoRNAse of the NSP15 genomic region of SARS-CoV-2. 2021 International journal of infectious diseases Discussion SARS_CoV_2 I280V 26 31 EndoRNAse 65 74 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. Then clade G appeared at the end of January 2020 and the first appearance of its subclades, GR and GH (mutated in Spike D614G, ORF3a, and Q57H), emerged about three weeks later (February 20, 2020). 2021 International journal of infectious diseases Discussion SARS_CoV_2 D614G;Q57H 120;138 125;142 S;ORF3a 114;127 119;132 33359061 Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country. While infectiousness and transmissibility are closely related, they are not necessarily synonymous to one another, and therefore, detailed studies are needed to decide whether or not the D614G mutation has contributed to an increase in the number of infections and not simply higher viral loads during infection ( and). 2021 International journal of infectious diseases Discussion SARS_CoV_2 D614G 187 192 33359807 SARS-Cov-2 ORF3a: Mutability and function. According to the predictions, G196V is stabilizing the protein. 2021 International journal of biological macromolecules Discussion SARS_CoV_2 G196V 30 35 33359807 SARS-Cov-2 ORF3a: Mutability and function. By analogy, the mutations V13L and G252V, for which lack of spatial coordinates hinders predictions, can have also a similar effect. 2021 International journal of biological macromolecules Discussion SARS_CoV_2 G252V;V13L 35;26 40;30 33359807 SARS-Cov-2 ORF3a: Mutability and function. Considering the entire sample, the five most frequent mutations are V13L, Q57H, Q57H + A99V, G196V and G252V. 2021 International journal of biological macromolecules Discussion SARS_CoV_2 A99V;G196V;G252V;Q57H;Q57H;V13L 87;93;103;74;80;68 91;98;108;78;84;72 33359807 SARS-Cov-2 ORF3a: Mutability and function. Continuous monitoring of SARS-Cov-2 ORF3a evolution will indicate whether these changes can attribute the virus any advantage and become frequent in the population as observed for the change Q57H. 2021 International journal of biological macromolecules Discussion SARS_CoV_2 Q57H 191 195 ORF3a 36 41 33359807 SARS-Cov-2 ORF3a: Mutability and function. However, two mutations (K75N and R126S) remove two basic and positively charged residues from the proximity of the pore. 2021 International journal of biological macromolecules Discussion SARS_CoV_2 R126S;K75N 33;24 38;28 33359807 SARS-Cov-2 ORF3a: Mutability and function. Q57H is stabilizing according to DynaMut and slightly destabilizing from Duet calculations. 2021 International journal of biological macromolecules Discussion SARS_CoV_2 Q57H 0 4 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. A molecular virological study investigated the details of conformational changes between D614 and G614 variants, and showed that the D614G mutation shifts the S glycoprotein conformation to be more open, which could contribute to the increased efficiency of ACE2 binding and fusion. 2020 Genes Discussion SARS_CoV_2 D614G 133 138 S 159 173 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. Evidence showed that the S glycoprotein D614G mutation could enhance the infectivity of SARS-CoV-2 by incorporating more spike proteins to the viral envelope, which thereby increases the chance of viral attaching in populations with lower expression of ACE2 in host cells. 2020 Genes Discussion SARS_CoV_2 D614G 40 45 S;S 25;121 39;126 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. Further studies using reverse genetics are required to confirm the relevance of our findings, connecting the D614G mutation with different ACE2 expression levels. 2020 Genes Discussion SARS_CoV_2 D614G 109 114 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. In this study, we provided a possible explanation for the positive selection of the D614G mutation in SARS-CoV-2. 2020 Genes Discussion SARS_CoV_2 D614G 84 89 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. The D614G mutation in S glycoprotein is a potential example of how positive selection drives the adaptive evolution of SARS-CoV-2. 2020 Genes Discussion SARS_CoV_2 D614G 4 9 S 22 36 33374416 Impact of Genetic Variability in ACE2 Expression on the Evolutionary Dynamics of SARS-CoV-2 Spike D614G Mutation. The SARS-CoV-2 D614G mutation notably did not increase the binding affinity with ACE2. 2020 Genes Discussion SARS_CoV_2 D614G 15 20 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. Both the S477N and the second-most frequent RBD variation N439K lie in the RBM, suggesting a selective pressure on this locus. 2020 Journal of translational medicine Discussion SARS_CoV_2 N439K;S477N 58;9 63;14 RBD 44 47 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. From the polarity point of view, only the N439K switch has a change from Neutral to Polar; a recent structural topology article provided an in-depth analysis of the Energy free change of the most frequent single and clustered mutations, showing that the N439K has a strong increase of Binding Free Energy (BFE). 2020 Journal of translational medicine Discussion SARS_CoV_2 N439K;N439K 42;254 47;259 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. N439K was recently reported to reduce affinity to one of the described antibodies, H00S022, while no data is still available for S477N. 2020 Journal of translational medicine Discussion SARS_CoV_2 S477N;N439K 129;0 134;5 33380328 Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants. The S477N has only a slight BFE increase that does not seem to reflect its relative increase in frequency. 2020 Journal of translational medicine Discussion SARS_CoV_2 S477N 4 9 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. Analysis of ORF1ab nsp2 (638 aa from A181-G818) polyproteins of SARS-CoV-2 isolated from animals revealed six characteristic mutations, one in cat (H388Y) and five in mink (E352Q, A372V, R398C, A405T, and E743V) isolates. 2020 PeerJ Discussion SARS_CoV_2 A372V;A405T;E743V;R398C;E352Q;H388Y 180;194;205;187;173;148 185;199;210;192;178;153 ORF1ab;Nsp2 12;19 18;23 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. However, Q498H in mouse isolate may have a significant change in the properties of the amino acid residues because glutamine is neutral while histidine is positively charged, and both have significant differences in the structure of the side chain. 2020 PeerJ Discussion SARS_CoV_2 Q498H 9 14 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. In our study, all analyzed SARS-CoV-2 from animals had Q493 and N501 except mink isolates which had N501T. 2020 PeerJ Discussion SARS_CoV_2 N501T 100 105 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. In our study, the N protein had four amino acid substitutions: three in mink isolates (R41L, P80L, and P199Q) with a frequency of 2.7% each, and one in cat isolates (T247I) with a frequency of 16.7%. 2020 PeerJ Discussion SARS_CoV_2 P199Q;P80L;R41L;T247I 103;93;87;166 108;97;91;171 N 18 19 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. In S protein, for example, L452M involved leucine and methionine, and both are neutral and hydrophobic. 2020 PeerJ Discussion SARS_CoV_2 L452M 27 32 S 3 4 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. It was found that K479N and S487T of SARS-CoV are associated with human ACE2 receptor recognition. 2020 PeerJ Discussion SARS_CoV_2 K479N;S487T 18;28 23;33 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. Similarly, Y453F involved tyrosine and phenylalanine, and both are hydrophobic and aromatic. 2020 PeerJ Discussion SARS_CoV_2 Y453F 11 16 33384909 Mutational spectra of SARS-CoV-2 isolated from animals. The D614G mutation downstream of the RBD could be associated with higher transmission, pathogenicity, and evasion of immune interventions. 2020 PeerJ Discussion SARS_CoV_2 D614G 4 9 RBD 37 40 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. According to phylogenetic tree and sequence distribution analysis, it has been suggested that the dominating D614G globally is caused by a positive selection, while the dominating D614G in Europe is due to a founder effect. 2020 PeerJ Discussion SARS_CoV_2 D614G;D614G 109;180 114;185 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. All GH clade samples in the present study also contained P323L (Table 1). 2020 PeerJ Discussion SARS_CoV_2 P323L 57 62 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. An increase in SARS-CoV-2 detection conveys the D614G mutation concurrent with the recent global situation of COVID-19. 2020 PeerJ Discussion SARS_CoV_2 D614G 48 53 COVID-19 110 118 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. Further study with a larger sample size and involving risk factors for COVID-19 severity is mandatory to determine the association between the D614G mutation and the severity of COVID-19, particularly in Indonesia. 2020 PeerJ Discussion SARS_CoV_2 D614G 143 148 COVID-19;COVID-19 71;178 79;186 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. Interestingly, patients infected with SARS-CoV-2 bearing D614G mutations showed moderate COVID-19, while the patient without mutations suffered from mild symptoms. 2020 PeerJ Discussion SARS_CoV_2 D614G 57 62 COVID-19 89 97 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. It has already been reported that the D614G variant is almost always accompanied by three other variants: a C-T change in the 5'UTR, a silent c.3307C > T variant, and P323L. 2020 PeerJ Discussion SARS_CoV_2 C3307T;D614G;P323L 142;38;167 153;43;172 5'UTR 126 131 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. It has been reported that COVID-19 patients with the D614G mutation have a higher viral load than patients infected by SARS-CoV-2 without mutations. 2020 PeerJ Discussion SARS_CoV_2 D614G 53 58 COVID-19 26 34 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. The D614G mutation dominates globally approximately 77,818/96,215 (~81%) full genomes submitted at GISAID until 18 September 2020. 2020 PeerJ Discussion SARS_CoV_2 D614G 4 9 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. The patients with D614G had a CT value lower than one patient without the mutation (Table 1). 2020 PeerJ Discussion SARS_CoV_2 D614G 18 23 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. The virus with the D614G mutation in Indonesia was first detected in April 2020 in Surabaya, East Java, followed by other provinces, including Yogyakarta, Central Java, West Java and Banten. 2020 PeerJ Discussion SARS_CoV_2 D614G 19 24 33391880 Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. Three of four (75%) SARS-CoV-2 in our case series also consisted of D614G. 2020 PeerJ Discussion SARS_CoV_2 D614G 68 73 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. D796H, but not DeltaH69/DeltaV70, conferred reduction in susceptibility to polyclonal antibodies in the units of CP administered, though we cannot speculate as to their individual impacts on sera from other individuals. 2020 medRxiv Discussion SARS_CoV_2 D796H 0 5 33398302 Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. The deletion was observed contemporaneously with the rare S2 mutation D796H after two separate courses of CP, with other viral populations emerging. 2020 medRxiv Discussion SARS_CoV_2 D796H 70 75 33407987 Impact of population density and weather on COVID-19 pandemic and SARS-CoV-2 mutation frequency in Bangladesh. Among host factors, coinfections had strong correlation with frequency of mutations at ORF1ab- common mutation (rs = 0.485), rare mutation (rs = 0.642), at S-D614G (rs = 0.644) and common mutation at other protein (rs = 0.671). 2021 Epidemiology and infection Discussion SARS_CoV_2 D614G 158 163 ORF1ab;S 87;156 93;157 33407987 Impact of population density and weather on COVID-19 pandemic and SARS-CoV-2 mutation frequency in Bangladesh. This study reported common mutations at ORF1ab-P323L (NSP12) (88%) and I120F (NSP2) (72%); S-D614G (82%), N-R203K (73%) and G204R (73%) and other structural proteins with high frequency. 2021 Epidemiology and infection Discussion SARS_CoV_2 G204R;I120F;D614G;P323L;R203K 124;71;93;47;108 129;76;98;52;113 ORF1ab;Nsp12;Nsp2;N;S 40;54;78;106;91 46;59;82;107;92 33407987 Impact of population density and weather on COVID-19 pandemic and SARS-CoV-2 mutation frequency in Bangladesh. This study reported strong correlation between average temperature and mutation frequency at ORF1ab-common mutation (rs = 0.654), rare mutation (rs = 0.598) and at S- D614G (rs = 0.611); between maximum temperature and rare mutation at S (rs = 0.658). 2021 Epidemiology and infection Discussion SARS_CoV_2 D614G 167 172 ORF1ab;S;S 93;164;236 99;165;237 33408342 A longitudinal study of SARS-CoV-2-infected patients reveals a high correlation between neutralizing antibodies and COVID-19 severity. Among them, a variant with a single mutation at position 614 (D614G) has become the currently dominant circulating virus. 2021 Cellular & molecular immunology Discussion SARS_CoV_2 D614G 62 67 33412089 COVID-19-neutralizing antibodies predict disease severity and survival. We found that one such mutation, D614G, which has now spread and become a dominant strain worldwide, does not affect the neutralizing ability of patient sera, reducing concerns for re-infection. 2021 Cell Discussion SARS_CoV_2 D614G 33 38 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. Along with these two mutations, 241C>T in the 5' UTR and a silent mutation 3037C>T in the ORF1ab were predominantly found in severely affected group (the later not significantly), however, these mutations do not alter amino acid sequence in a protein. 2020 Genomics & informatics Discussion SARS_CoV_2 C241T;C3037T 32;75 38;82 5'UTR;ORF1ab 46;90 52;96 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. Although the 14408C>T (RdRp P323L) mutation was predominantly found in severely affected patients in the present study, further studies will be required to elucidate whether this RdRp mutation has any significant impact on the viability and infectivity of SARS-CoV-2 and the severity of COVID-19. 2020 Genomics & informatics Discussion SARS_CoV_2 C14408T;P323L 13;28 21;33 RdRP;RdRP 23;179 27;183 COVID-19 287 295 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. Among numerous mutations observed in this study, two missense mutations, 14408C>T and 23403A>G, affecting RdRp and spike protein genes, respectively, were found most predominantly in the severely affected group compared with mildly affected group. 2020 Genomics & informatics Discussion SARS_CoV_2 C14408T;A23403G 73;86 81;94 S;RdRP 115;106 120;110 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. As we found in the present study, previous studies also identified that the spike protein D614G mutation frequently accompanies a silent mutation 3037C>T and a missense mutation 14,408C>T in ORF1ab. 2020 Genomics & informatics Discussion SARS_CoV_2 C3037T;D614G 146;90 153;95 ORF1ab;S 191;76 197;81 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. Based on our findings, it may be concluded that the spike protein D614G and RdRp P323L mutations predominate in severely affected COVID-19 patients. 2020 Genomics & informatics Discussion SARS_CoV_2 D614G;P323L 66;81 71;86 S;RdRP 52;76 57;80 COVID-19 130 138 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. found that patients infected with spike protein D614G mutant form of SARS-CoV-2 had higher viral loads since fewer PCR cycles were needed for their diagnosis. 2020 Genomics & informatics Discussion SARS_CoV_2 D614G 48 53 S 34 39 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. Further studies will be required to explore whether spike protein D614G mutation or RdRp P323L mutation or the combination of both mutations can exert an impact on the severity of COVID-19. 2020 Genomics & informatics Discussion SARS_CoV_2 D614G;P323L 66;89 71;94 S;RdRP 52;84 57;88 COVID-19 180 188 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. Furthermore, in cell culture experiment, viral particles with spike protein D614G mutation was found to infect ACE2 expressing cells more efficiently, and this increased infectivity was found to correlate with less shedding of S1 domain of spike protein and more incorporation of spike protein in the virion. 2020 Genomics & informatics Discussion SARS_CoV_2 D614G 76 81 S;S;S 62;240;280 67;245;285 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. However, computer-based structural analysis of spike protein with D614G mutation suggested that the mutation is unlikely to alter its interaction with human ACE2 receptor. 2020 Genomics & informatics Discussion SARS_CoV_2 D614G 66 71 S 47 52 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. In spite of these facts, previous studies were unable to explore an association between the spike protein D614G mutation and disease severity due to relative lack of clinical data of the patients included in their studies. 2020 Genomics & informatics Discussion SARS_CoV_2 D614G 106 111 S 92 97 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. Several ways have been proposed through which spike protein D614G mutation may increase the infectivity of SARS-CoV-2. 2020 Genomics & informatics Discussion SARS_CoV_2 D614G 60 65 S 46 51 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. The 14408C>T mutation in ORF1ab replaces a proline (P) with leucine (L) at position 4715 (P4715L) of ORF1ab polyprotein which actually appears as a replacement of proline with leucine at position 323 (P323L) of RdRp enzyme. 2020 Genomics & informatics Discussion SARS_CoV_2 C14408T;P323L;P323L;P4715L 4;163;201;90 12;199;206;96 ORF1ab;ORF1ab;RdRP 25;101;211 31;107;215 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. The 23403A>G mutation in the genome of SARS-CoV-2 causes replacement of aspartic acid (D) with glycine (G) at position 614 (D614G) of the spike protein. 2020 Genomics & informatics Discussion SARS_CoV_2 A23403G;D614G 4;124 12;129 S 138 143 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. The presence of 14408C>T mutation in SARS-CoV-2 genome that causes RdRp P323L mutation was found to be associated with overall increase in mutation rate in the viral genome. 2020 Genomics & informatics Discussion SARS_CoV_2 C14408T;P323L 16;72 24;77 RdRP 67 71 33412760 Spike protein D614G and RdRp P323L: the SARS-CoV-2 mutations associated with severity of COVID-19. This D614G spike protein mutation appeared sometimes in late January 2020 and then it has spread initially in Europe and then all over the world. 2020 Genomics & informatics Discussion SARS_CoV_2 D614G 5 10 S 11 16 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. However, if this variant were also more transmissible, more studies would be necessary to investigate the multiple non-synonymous mutations shared or not shared with 501Y Variant 2, as well as how these mutations (such as Delta69/Delta70 and P681H of the spike protein) may account for the increased transmissibility. 2021 Euro surveillance Discussion SARS_CoV_2 P681H 242 247 S 255 260 33413740 Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. If the N501Y mutation would increase the binding to human ACE2, it might increase the susceptibility of children to 501Y Variant 2. 2021 Euro surveillance Discussion SARS_CoV_2 N501Y 7 12 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Also, this study does not investigate the effect of the D614G mutation on cleavage at the TMPRSS2 cleavage site, which remains an important question to be answered in future studies. 2021 Cell reports Discussion SARS_CoV_2 D614G 56 61 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. In addition to the D614G mutation, the SD2 subdomain also houses the multibasic furin cleavage site that demarcates the S1 and S2 subunits. 2021 Cell reports Discussion SARS_CoV_2 D614G 19 24 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. In this paper, we study the effect of the SARS-CoV-2 S D614G mutation on S structure, focusing on RBD conformation and changes in proteolytic susceptibility at the multibasic furin cleavage site at the S1/S2 junction. 2021 Cell reports Discussion SARS_CoV_2 D614G 55 60 RBD;S;S 98;53;73 101;54;74 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. Not only does the D614G mutation alter RBD up/down proportions, but it also results in increased furin cleavage susceptibility, which could be responsible for the increased transmissibility of the SARS-CoV-2 variant with the D614G mutation. 2021 Cell reports Discussion SARS_CoV_2 D614G;D614G 18;225 23;230 RBD 39 42 33417835 D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction. We provide evidence in this study that the D614G mutation enhances susceptibility of the SARS-CoV-2 S ectodomain to furin cleavage, thus raising the possibility that this is a contributor to increased fitness and transmissibility of D614G isolates. 2021 Cell reports Discussion SARS_CoV_2 D614G;D614G 43;233 48;238 S 100 101 33436577 A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein. For instance, V367F, W436R, and D364Y were reported to increase the binding affinity for ACE2, which might accelerate viral spread further perpetuating the pandemic. 2021 Nature communications Discussion SARS_CoV_2 D364Y;V367F;W436R 32;14;21 37;19;26 33436577 A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein. Importantly, CT-P59 significantly inhibited the viral replication of clinical isolates, wild-type, and D614G variant by in vitro PRNT. 2021 Nature communications Discussion SARS_CoV_2 D614G 103 108 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. According to the GISAID database, the P681H mutation is found worldwide in 5,955 strains reported as of December 31, 2020. 2021 bioRxiv Discussion SARS_CoV_2 P681H 38 43 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Additionally, a new variant in Nigeria (B.1.207)(EPI_ISL_729975) has been defined by the P681H mutation found in the two Hawaii strains. 2021 bioRxiv Discussion SARS_CoV_2 P681H 89 94 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Additionally, the proline in the P681H mutation is within the epitope found to be the highest-ranking B and T cell epitope based on the in silico long-term population-scale epitope prediction for vaccine development study. 2021 bioRxiv Discussion SARS_CoV_2 P681H 33 38 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. All of these original strains introduced to Hawaii were collected in March 2020, and 66.6% (8/12) have the D614G mutation. 2021 bioRxiv Discussion SARS_CoV_2 D614G 107 112 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Further studies are warranted to analyze the pathogenicity and virulence of the newly identified P681H mutation seen in the Hawaii strains and whether this is a viral evasion mechanism to deter antibody recognition or another increase in fitness. 2021 bioRxiv Discussion SARS_CoV_2 P681H 97 102 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Further, EPI_ISL_601443 shows the N501Y, A570D, D614G, P681H, and T716 mutations in the 969-bp region, while the two Hawaii strains, MW237663 and MW237664, display the D614G and P681H mutations. 2021 bioRxiv Discussion SARS_CoV_2 A570D;D614G;D614G;N501Y;P681H;P681H 41;48;168;34;55;178 46;53;173;39;60;183 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Interestingly, several mutations (nucleotide position 241 C T, position 3037 C T, and position 14408 C T, etc.) exist alongside the D614G mutation Similarly, in the both Hawaii SARS-CoV-2 strains the P681H mutation is also present alongside D614G. 2021 bioRxiv Discussion SARS_CoV_2 D614G;D614G;P681H 132;241;200 137;246;205 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Recent SARS-CoV-2 studies indicate that the P681H mutation is immediately juxtaposed to the amino acid 682-685, furin cleavage site, identified at the S1/S2 linkage site, which predicted enhance systemic infection, and increased membrane fusion. 2021 bioRxiv Discussion SARS_CoV_2 P681H 44 49 Membrane 229 237 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. Similar to the P681H, the S680C mutation is also within the epitope region of the B and T cell epitope in silico prediction model for vaccine development. 2021 bioRxiv Discussion SARS_CoV_2 P681H;S680C 15;26 20;31 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. That is, the sequence surrounding this P681H mutation is predictably the loci where the immune response is targeted. 2021 bioRxiv Discussion SARS_CoV_2 P681H 39 44 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The D614G mutation has become universal throughout the SARS-CoV-2 strains. 2021 bioRxiv Discussion SARS_CoV_2 D614G 4 9 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The D614G mutation is known to enhance infectivity, replication, and localize the virus to the upper respiratory tract to increase transmission. 2021 bioRxiv Discussion SARS_CoV_2 D614G 4 9 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The F797C mutation is seen alone in the Sweden strain (MT093571.1). 2021 bioRxiv Discussion SARS_CoV_2 F797C 4 9 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The N protein mutations are D3L and S235F. 2021 bioRxiv Discussion SARS_CoV_2 D3L;S235F 28;36 31;41 N 4 5 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The Orf8 mutations are Q27stop, R52I, and Y73C. 2021 bioRxiv Discussion SARS_CoV_2 Q27X;R52I;Y73C 23;32;42 30;36;46 ORF8 4 8 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The other non-synonymous SNPs found in this study - A522S, F543L, I584V, I726F, A771S, E780Q - are not as apparent in presenting drastic evolutionary change, but they too deserve further analysis. 2021 bioRxiv Discussion SARS_CoV_2 A522S;A771S;E780Q;F543L;I584V;I726F 52;80;87;59;66;73 57;85;92;64;71;78 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The P681H represents the loss of a proline residue and the gain instead of an imidazole-containing histidine residue. 2021 bioRxiv Discussion SARS_CoV_2 P681H 4 9 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The Pearson's correlation test of the logarithmic transformed P681H prevalence of the mutation versus time indicates that the P681H mutation is exponentially increasing worldwide and the sequences encompassing the P681H mutation is dominating significantly when compared to other SARS-CoV-2 strains. 2021 bioRxiv Discussion SARS_CoV_2 P681H;P681H;P681H 62;126;214 67;131;219 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The R577C and S680C mutations are present together in the strain from Australia (MT451798.1). 2021 bioRxiv Discussion SARS_CoV_2 R577C;S680C 4;14 9;19 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The R577C, S680C, and F797C mutations depicted in Table 1 are also very prominent mutations in that they present possible new disulfide bridges forming within and around the RBD. 2021 bioRxiv Discussion SARS_CoV_2 F797C;R577C;S680C 22;4;11 27;9;16 RBD 174 177 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The six ORF1ab mutations are T1001I, A1708D, I2230T, and DeltaS3675, DeltaG2676, and DeltaF3677. 2021 bioRxiv Discussion SARS_CoV_2 A1708D;I2230T;T1001I 37;45;29 43;51;35 ORF1ab 8 14 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The ten spike mutations are DeltaH69, DeltaV70, DeltaY145, N501Y, A570D, D614G, P681H, T716I, S982A, and D1118. 2021 bioRxiv Discussion SARS_CoV_2 A570D;D614G;N501Y;P681H;S982A;T716I 66;73;59;80;94;87 71;78;64;85;99;92 S 8 13 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. The two Hawaii strains analyzed in this study cluster together predictably due to the emerging P681H mutation. 2021 bioRxiv Discussion SARS_CoV_2 P681H 95 100 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. This observation indicates that, similar to D614G mutation the P681H mutation is becoming globally prevalent among SARS-CoV-2 sequences. 2021 bioRxiv Discussion SARS_CoV_2 D614G;P681H 44;63 49;68 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. This study demonstrates a partial sequence from the first SARS-CoV-2 strain possessing the P681H non-synonymous mutation. 2021 bioRxiv Discussion SARS_CoV_2 P681H 91 96 33442699 Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawaii Reveals the Worldwide Emerging P681H Mutation. When comparing the SNPs encompassing the 969-bp of two strains from this study to the reference genome for VOC202012/01, EPI_ISL_601443, we found two similar mutations, D614G and P681H. 2021 bioRxiv Discussion SARS_CoV_2 D614G;P681H 169;179 174;184 33447831 Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces shedding of SARS-CoV-2 D614G in rhesus macaques. Both hamster and NHP studies described here demonstrate clearly that the ChAdOx1 nCoV-19 vaccine protects against SARS-CoV-2 containing the D614G mutation. 2021 bioRxiv Discussion SARS_CoV_2 D614G 140 145 33447831 Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces shedding of SARS-CoV-2 D614G in rhesus macaques. Both strains contain the N501Y mutation in RBD. 2021 bioRxiv Discussion SARS_CoV_2 N501Y 25 30 RBD 43 46 33447831 Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces shedding of SARS-CoV-2 D614G in rhesus macaques. The most prevalent of the novel mutations is likely D614G in the S protein, which is present in the majority of circulating SARS-CoV-2 viruses. 2021 bioRxiv Discussion SARS_CoV_2 D614G 52 57 S 65 66 33447831 Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces shedding of SARS-CoV-2 D614G in rhesus macaques. This virus has one coding change in the S protein compared to the vaccine antigen; D614G. 2021 bioRxiv Discussion SARS_CoV_2 D614G 83 88 S 40 41 33447831 Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces shedding of SARS-CoV-2 D614G in rhesus macaques. We detected no difference in the ability of antibodies elicited by ChAdOx1 nCoV-19 vaccination to bind to N501Y mutant RBD. 2021 bioRxiv Discussion SARS_CoV_2 N501Y 106 111 RBD 119 122 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. Another study from central India reported that the D614G mutation (A2a clade/G clade) was the predominant type (~46%) followed by A4 and B clades. 2021 Indian journal of medical microbiology Discussion SARS_CoV_2 D614G 51 56 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. Both the 20A and 20B clades predominantly contains the D614G mutation (G clade) which now seems to be predominant in the state of Odisha, India too. 2021 Indian journal of medical microbiology Discussion SARS_CoV_2 D614G 55 60 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. By the end of June 2020, the predominant strain of SARS-CoV-2 worldwide had the D614G mutation known as the G-variant or G-clade. 2021 Indian journal of medical microbiology Discussion SARS_CoV_2 D614G 80 85 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. Further analysis using representative 32 whole genome sequence from January to May 2020, including strains of early L and S type, Clade G (D614G), B6/Type-L showed a distinct clade differentiation from the S-type strains which too formed a separate clade from the L-type strains. 2021 Indian journal of medical microbiology Discussion SARS_CoV_2 D614G 139 144 S;S 122;206 123;207 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. In February 2020, a group of researchers from China had initially classified the SARS-CoV-2 into two major strains, notably L and S based on a tightly linked SNPs between two widely separated nucleotides at location 8782 (ORF1ab T8517C) and position 28,144 (ORF8: C251T, codon S84L). 2021 Indian journal of medical microbiology Discussion SARS_CoV_2 C251T;S84L;T8517C 264;277;229 269;281;235 ORF1ab;ORF8;S 222;258;130 228;262;131 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. in their study analyzing 3636 complete genome sequences collected from 55 countries, have categorized the SARS-CoV-2 into 11 major clades based on temporal evolution and that the A2a (D614G) clade was spreading rapidly across the globe. 2021 Indian journal of medical microbiology Discussion SARS_CoV_2 D614G 184 189 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. Now world over, the S-type strains has been smoothly being replaced by the predominant L-type strains which have further diverged into Clade G or A2a (D614G) clade and other clades. 2021 Indian journal of medical microbiology Discussion SARS_CoV_2 D614G 151 156 S 20 21 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. There is a future role of TSP-PCR in rapidly classifying clades and sub-clades of SARS-CoV-2 including rapidly identifying the clade G (D614G) or other strains without the use nucleic acid sequencing data. 2021 Indian journal of medical microbiology Discussion SARS_CoV_2 D614G 136 141 33460733 TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2. They identified six-major clades and 14 subclades with the D614G variant clade (Clade G) as the most common clade. 2021 Indian journal of medical microbiology Discussion SARS_CoV_2 D614G 59 64 33467732 Intranasal Infection of Ferrets with SARS-CoV-2 as a Model for Asymptomatic Human Infection. Although the SARS-CoV-2 spike protein from human isolates is predicted to have low affinity for the mink and ferret ACE2 receptors, the emergence of the Y453F variant in both field and experimental infection of mink and ferrets may indicate that this mutation promotes a functional interaction between virus spike protein and mink or ferret ACE2 receptors. 2021 Viruses Discussion SARS_CoV_2 Y453F 153 158 S;S 24;308 29;313 33467732 Intranasal Infection of Ferrets with SARS-CoV-2 as a Model for Asymptomatic Human Infection. Another single nucleotide polymorphism corresponded to the spike protein Y453F variant that has emerged in mink in the Netherlands, as well as being present in the Cluster 5 variant of SARS-CoV-2 isolated from mink in Denmark and in isolated human clinical cases. 2021 Viruses Discussion SARS_CoV_2 Y453F 73 78 S 59 64 33467732 Intranasal Infection of Ferrets with SARS-CoV-2 as a Model for Asymptomatic Human Infection. In our study, the D614G polymorphism that has become globally dominant in humans was not detected. 2021 Viruses Discussion SARS_CoV_2 D614G 18 23 33467732 Intranasal Infection of Ferrets with SARS-CoV-2 as a Model for Asymptomatic Human Infection. In the hamster model, the D614G mutation significantly accelerated droplet transmission during the initial stages of infection, whilst in ferrets, it provided an advantage for viral replication and transmission but did not alter pathogenicity. 2021 Viruses Discussion SARS_CoV_2 D614G 26 31 33467732 Intranasal Infection of Ferrets with SARS-CoV-2 as a Model for Asymptomatic Human Infection. The Y453F polymorphism in the S protein has been identified in in vitro assays as a potential mutant that can escape neutralization by some therapeutic monoclonal antibodies. 2021 Viruses Discussion SARS_CoV_2 Y453F 4 9 S 30 31 33467732 Intranasal Infection of Ferrets with SARS-CoV-2 as a Model for Asymptomatic Human Infection. Whole genome sequencing analysis of single samples from the upper respiratory tracts of three ferrets revealed, in all samples, a L3606F polymorphism in the ORF1ab-encoded protein that has been attributed to a basal clade of SARS-CoV-2 isolates that emerged in China in January 2020, and was also identified sporadically in three of five clusters in the Netherlands. 2021 Viruses Discussion SARS_CoV_2 L3606F 130 136 ORF1ab 157 163 33468702 SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia. We find that all of the viral genomes recovered contained the spike D614G substitution suggested to promote spread among humans, and all contained the linked RdRp P314L substitution, marking them as the lineage B.1, Nextstrain clade 20A or 20C, GISAID clade G or GH, and clade A2a. 2021 mBio Discussion SARS_CoV_2 D614G;P314L 68;163 73;168 S;RdRP 62;158 67;162 33477951 Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. Although there has been talk about the role of D614G mutation and enhancement of infectivity, it is difficult to associate it to a single mutation. 2021 Viruses Discussion SARS_CoV_2 D614G 47 52 33477951 Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. However, the results of the temporal analysis of the mutation frequency of P323L (nsp12), and D614G (S-protein) show that P323L was consistently present in the viruses and started co-evolving with D614G sometime late January 2020. 2021 Viruses Discussion SARS_CoV_2 D614G;D614G;P323L;P323L 94;197;75;122 99;202;80;127 Nsp12;S 82;101 87;102 33477951 Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. Interestingly, there was a non-synonymous substitution (Proline to leucine; P323L) in RNA Dependent RNA Polymerase (RdRp) region next to the nsp8 binding site in majority of Saudi SARS-CoV-2 sequences. 2021 Viruses Discussion SARS_CoV_2 P323L 76 81 RdRp;Nsp8;RdRP 86;141;116 114;145;120 33477951 Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. Methionine to isoleucine (Spike, M731I) M to I substitution in HIV-1 reverse transcriptase provides resistance to nucleoside analog 2',3'-dideoxy-3'thiacytidine. 2021 Viruses Discussion SARS_CoV_2 M731I 33 38 33477951 Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. Substitution or deletion of residue 731 from its C-terminal is known to be associated with gradual down regulation of cyclooxygenase-2 (COX-2) promoter. 2021 Viruses Discussion SARS_CoV_2 del 731 16 39 33477951 Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. The co-existence of D614G (spike) and P323L (nsp12) might contribute to replication and infectivity along with host factors. 2021 Viruses Discussion SARS_CoV_2 D614G;P323L 20;38 25;43 S;Nsp12 27;45 32;50 33477951 Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. The most prevalent substitution found in orf3a (NS3) was Q57H, followed by A51S and S216P (Figure 4c). 2021 Viruses Discussion SARS_CoV_2 A51S;Q57H;S216P 75;57;84 79;61;89 ORF3a;NS3 41;48 46;51 33478625 Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020. In addition, it has been recently shown that the combined DeltaH69/V70 and D796H mutant was less sensitive to neutralising antibodies. 2021 Euro surveillance Discussion SARS_CoV_2 D796H 75 80 33478625 Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020. It should be underlined that N439K, Y453F or N501Y RBD mutations that can co-occur with DeltaH69/DeltaV70 might be associated with an increased affinity to angiotensin-converting enzyme 2 (ACE2) or reduced sensitivity to SARS-CoV-2 antibodies. 2021 Euro surveillance Discussion SARS_CoV_2 N439K;N501Y;Y453F 29;45;36 34;50;41 RBD 51 54 33478625 Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69-V70, France, August to December 2020. The N501Y mutation of the VOC 202012/01, in particular, might be also responsible of the higher transmissibility reported for this lineage. 2021 Euro surveillance Discussion SARS_CoV_2 N501Y 4 9 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. Among the 240 nonsynonymous mutations, L84S, the most frequent is located between C83 and P85. 2021 Gene reports Discussion SARS_CoV_2 L84S 39 43 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. It would be of great importance to decipher the effects of variants and deletions experimentally on ORF8 protein structure and function, and to analyze the effects of these mutations and their relations to viral infectivity and their impacts on disease severity and clinical features since D614G in the S protein seems to enhance infectivity but not disease severity, and the deletions close to the spike S1/S2 cleavage were more related to mild symptoms. 2021 Gene reports Discussion SARS_CoV_2 D614G 290 295 S;ORF8;S 399;100;303 404;104;304 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. Last but not least, this work revealed the effectiveness of COV-GLUE and its accuracy in detecting nonsynonymous mutations and deletions in ORF8 gene because only V62F was not documented, and P85T and F86S were not found among the 240 mutations. 2021 Gene reports Discussion SARS_CoV_2 F86S;P85T;V62F 201;192;163 205;196;167 ORF8 140 144 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. Likewise, S24L which is part of the beta1 strand and V62L come next in the order. 2021 Gene reports Discussion SARS_CoV_2 S24L;V62L 10;53 14;57 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. Mutations could be dynamic, as it has been proposed that some mutations like L84S are disappearing, and there is emergence of new ones that render the virus more infective, like S24L that was first sequenced in the USA. 2021 Gene reports Discussion SARS_CoV_2 L84S;S24L 77;178 81;182 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. Phylogenetic analysis of protein and DNA sequences of SARS-CoV-2 ORF8 variants, together with that of Bat and Pangolin, revealed that L84S (L84S, A65V) is closer to both of them. 2021 Gene reports Discussion SARS_CoV_2 A65V;L84S;L84S 146;134;140 150;138;144 ORF8 65 69 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. The absence of S24L (except one case in the United Kingdom) is probably the reason behind high Fst value between North America and Europe. 2021 Gene reports Discussion SARS_CoV_2 S24L 15 19 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. This also could explain the presence of deletions and mutations like M1I (T,V) and nonsense ones. 2021 Gene reports Discussion SARS_CoV_2 M1I 69 72 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. This could explain the weak signal of population expansion whose distribution of S24L, on a large number of sequences, and, at the same time, of L84S increased the Pi value and added some equilibrium with the low frequency of new mutations. 2021 Gene reports Discussion SARS_CoV_2 L84S;S24L 145;81 149;85 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. To note that, L84S clade is also dependent on another variant located in the ORF1ab at 8782C>T, and this makes the possibility that L84S clade could be more ancestral than the L clade especially with the presence of COVID19 asymptomatic patients. 2021 Gene reports Discussion SARS_CoV_2 C8782T;L84S;L84S 87;14;132 94;18;136 ORF1ab 77 83 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. To note, the highest value of the second and third pics that refer to North America is predominant in the United States of America (Data not shown) because of the double co mutation L84S and V62L. 2021 Gene reports Discussion SARS_CoV_2 L84S;V62L 182;191 186;195 33490718 Mutational analysis of SARS-CoV-2 ORF8 during six months of COVID-19 pandemic. Wang and colleagues showed that L84S decreases the function of ORF8, and thus is beneficial for human immune system, whilst S24L increases its function since it reinforces protein folding stability. 2021 Gene reports Discussion SARS_CoV_2 L84S;S24L 32;124 36;128 ORF8 63 67 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. estimated the global prevalence of D614G at 71.0%, whereas our estimate in the MENA was 78.7%, which appears reasonable, bearing in mind the protracted duration of sequence collection in this study. 2021 Heliyon Discussion SARS_CoV_2 D614G 35 40 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. Other amino acid replacements that were found in the study included Q677H (found only in Egypt), and L5F found in three different countries (Oman, Egypt, and Morocco). 2021 Heliyon Discussion SARS_CoV_2 L5F;Q677H 101;68 104;73 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. The emergence of D614G and its increasing prevalence have been reported by several published papers and preprints including a report from North Africa by Laamarti et al., albeit with a fewer number of sequences than the one analyzed in the current study. 2021 Heliyon Discussion SARS_CoV_2 D614G 17 22 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. The explanation for such an observation is most likely related to the association of D614G with a higher viral load and subsequent higher quantities of the virus shed by infected individuals, which increases the likelihood of infection by such a mutant, although an early founder effect of this variant cannot be ruled out. 2021 Heliyon Discussion SARS_CoV_2 D614G 85 90 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. The functional importance of Q677H replacement as not been determined yet despite a previous report describing its occurrence. 2021 Heliyon Discussion SARS_CoV_2 Q677H 29 34 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. The L5F replacement is located in the signal peptide domain of the spike glycoprotein and might be related to recurring sequencing errors. 2021 Heliyon Discussion SARS_CoV_2 L5F 4 7 S 67 85 33495741 Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa. The major result of this study was the demonstration of a temporal shift of SARS-CoV-2 from D614 into D614G variant, which dominated the most recent sequences collected in the region. 2021 Heliyon Discussion SARS_CoV_2 D614G 102 107 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. All the "minor group" mutations were novel among the Indian isolates, except 11083G>T (L37F, NSP6), which was previously reported as an infrequent mutation from Australia, Japan, Netherlands, and some other European countries. 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 G11083T;L37F 77;87 85;91 Nsp6 93 97 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. Certain strains in the "major group" displayed 22374A>G (Q271R), 24933G>T (G1124V), and 22444C>T (D294D) changes in the S gene, which were unique to India. 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 A22374G;C22444T;G24933T;D294D;G1124V;Q271R 47;88;65;98;75;57 55;96;73;103;81;62 S 120 121 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. Few infrequent mutations at position 1059 T>A (T85I) in NSP2 and 8782 C>T (S76S) in NSP4 observed here have also been reported to be prevalent in other countries. 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 T1059A;C8782T;S76S;T85I 37;65;75;47 45;73;79;51 Nsp2;Nsp4 56;84 60;88 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. Few strains from Europe and North America since February 2020 have shown the emergence of mutations like 3037C>T (F106F, NSP3), 23403A>G (D614G), and 28881-28883GGG>AAC (R203K and G204R, N) in the SARS-CoV-2 genome harboring the 14408C>T (P323L) mutation within the RdRP gene, suggesting a probable association or coexistence of 14408C>T (P323L) and the emerging higher number of novel point mutations compared to viral genomes from Asia. 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 C14408T;C14408T;A23403G;C3037T;G204R;G204N;D614G;F106F;P323L;P323L;R203K 229;329;128;105;180;180;138;114;239;339;170 237;337;136;112;187;187;143;119;244;344;175 Nsp3;RdRP 121;266 125;270 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. Hence, it is interesting to note the presence of a coexisting mutation 6312 C>A (T1198K) in NSP3 of the "minor group" strains, though the significance of this coexistence (L37F and T1198K) in context to the NSP6-NSP3 interaction can only be confirmed through association studies. 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 C6312A;T1198K;L37F;T1198K 71;181;172;81 79;187;176;87 Nsp3;Nsp3;Nsp6 92;212;207 96;216;211 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. In addition, A97V was found to be located in the nidovirus RdRP-associated nucleotidyl transferase domain whose function remains unknown. 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 A97V 13 17 RdRP 59 63 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. It was not surprising to observe the triple site mutation 28881-28883 GGG>AAC (R203K and G204R) in the N gene of 13 SARS-CoV-2 strains of the "major group." This has previously been reported from Mexico, South America, Australia, New Zealand, and a few Asian countries. 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 G204R;R203K 89;79 94;84 N 103 104 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. Missense mutations, Q271R and G1124V in the S protein, were found to reside around the N-linked glycosylation sites 282 and 1134, respectively, and these might affect the protein function. 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 G1124V;Q271R 30;20 36;25 N;S 87;44 88;45 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. Mutations observed in the NSP3 gene at positions 6310 C>A (S1197R), 7392 C>T (P1558L), and 6466 A>G (K1249K) were completely unique to Indian strains. 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 C6310A;A6466G;C7392T;K1249K;P1558L;S1197R 49;91;68;101;78;59 57;99;76;107;84;65 Nsp3 26 30 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. The "major group" of SARS-CoV-2 strains (66/95, 69.4%) represents the A2a clade reported previously from Africa, South America, Oceania, and South and West Asia, comprising of strains with coevolving mutations like 241 C>T (5' UTR), 3037 C>T (F106F, NSP3), 14403 C>T (P323L, RdRP/NSP12), and 23403 A>G (D614G, S glycoprotein). 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 C14403T;A23403G;C241T;C3037T;D614G;F106F;P323L 257;292;215;233;303;243;268 266;301;222;241;308;248;273 S;5'UTR;Nsp12;Nsp3;RdRP 310;224;280;250;275 324;230;285;254;279 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. The "minor group" of Indian SARS-CoV-2 (21/95, 22.1%) was comprised of strains with 5 coevolving mutations: 13730C>T (A97V, RdRP/NSP12), 23929C>T (Y789Y, S), 28311C>T (P13L, N), 6312C>A (T1198K, NSP3), and 11083G>T (L37F, NSP6). 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 G11083T;C13730T;C23929T;C28311T;C6312A;A97V;L37F;P13L;T1198K;Y789Y 206;108;137;158;178;118;216;168;187;147 214;116;145;166;185;122;220;172;193;152 Nsp12;Nsp3;Nsp6;RdRP;N;S 129;195;222;124;174;154 134;199;226;128;175;155 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. The 203/204 region is part of the SR dipeptide domain of the N protein (SRNSSRNSTPGSSRGTSPARMA) and changes in arginine at position 203 to lysine; and glycine at position 204 to arginine resulted in the insertion of a lysine residue between serine and arginine (SRNSSRNSTPGSSKRTSPARMA), which might interfere with the phosphorylation at serine residue required for normal functioning of the N protein. 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 R203K;G204R 111;151 145;186 N;N 61;391 62;392 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. The functional accuracy of RdRP is challenged due to the presence of the 13730 C>T (A97V) change, which was predicted to have significant effect on the secondary structure of RdRP. 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 C13730T;A97V 73;84 82;88 RdRP;RdRP 27;175 31;179 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. The L37F mutation strongly implies positive selection toward evolution of Betacoronaviruses, indicating a possible origin of the "minor group" out of this positive selection, with subsequent acquisition of mutations among the strains already harboring the 11083G>T change. 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 G11083T;L37F 256;4 264;8 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. The missense mutation 14408C>T (P323L) in RdRP was first observed in Italy (Lombardy) in February 2020. 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 C14408T;P323L 22;32 30;37 RdRP 42 46 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. The P13L mutation is located in the intrinsically disordered region of the N protein and might affect RND-binding activity of the N-terminal domain and C-terminal domain of the N protein. 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 P13L 4 8 N;N;N 75;130;177 76;131;178 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. Their study identified few recurrent mutations among isolates from Europe that were not detected among the viruses circulating within Asian countries, such as 3037C>T (F106F/NSP3 gene), 14408C>T (P323L/RdRP gene), 28881-28883GGG>AAC (R203K and G204R/N gene), and 23403A>G (D614G/S gene). 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 C14408T;A23403G;C3037T;G204R;G204N;D614G;F106F;P323L;R203K 186;263;159;244;244;273;168;196;234 194;271;166;251;251;280;173;201;239 Nsp3;RdRP;S;N 174;202;278;250 178;206;279;251 33496683 The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. Therefore, we can assume that two mutations, 14408C>T (P323L) and 13730C>T (A97V), which were found to have significant influence on the secondary structure of RdRP, could play key roles in the simultaneous establishment of "two groups" of SARS-CoV-2 with several characteristic "co-evolving mutations" in India (Asia). 2020 JMIR bioinformatics and biotechnology Discussion SARS_CoV_2 C13730T;C14408T;A97V;P323L 66;45;76;55 74;53;80;60 RdRP 160 164 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. A less frequent mutation, such as the P13L mutation on the N protein of SARS-CoV-2, is highlighted using the GLMs constructed in this study and shows a negative correlation with respect to country deaths and cases per million. 2021 PloS one Discussion SARS_CoV_2 P13L 38 42 N 59 60 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. D614G) that are directly correlated with a rapid increase in viral transmission, but also accompanied by increased deaths. 2021 PloS one Discussion SARS_CoV_2 D614G 0 5 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. D614G) that are positively correlated with both death rates and transmission rates. 2021 PloS one Discussion SARS_CoV_2 D614G 0 5 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Fitness for a viral mutation can be governed by factors such as increase of viral transmission, such as that observed for D614G. 2021 PloS one Discussion SARS_CoV_2 D614G 122 127 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Furthermore, investigation of the N-M interaction reveals that the ALT-P13L -M protein complex exhibited a decrease in binding affinity. 2021 PloS one Discussion SARS_CoV_2 P13L 71 75 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Moreover, structural analysis of the Q57H shows significant conformational changes in the ORF3a protein. 2021 PloS one Discussion SARS_CoV_2 Q57H 37 41 ORF3a 90 95 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Q57H and P13L) with increased transmission but decreased deaths. 2021 PloS one Discussion SARS_CoV_2 P13L;Q57H 9;0 13;4 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. RNA-protein docking performed in this study show a potential impact of the ALT-P13L on RNA binding affinity. 2021 PloS one Discussion SARS_CoV_2 P13L 79 83 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. Taking the frequently occurring D614G as an example it is evident that this mutation is becoming the dominant mutation across populations and its rapid spread denotes a natural selection pressure that shows increased fitness for this mutation. 2021 PloS one Discussion SARS_CoV_2 D614G 32 37 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. The more frequent but not so well studied Q57H mutation shows patterns that are in accordance to optimal viral fitness and persistence. 2021 PloS one Discussion SARS_CoV_2 Q57H 42 46 33497392 Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. This is exactly what is observed for the Q57H and P13L mutations, which provide a counter balance to mutations (e.g. 2021 PloS one Discussion SARS_CoV_2 P13L;Q57H 50;41 54;45 33498225 Biological and Clinical Consequences of Integrin Binding via a Rogue RGD Motif in the SARS CoV-2 Spike Protein. Further support for this hypothesis comes from the observation that the double deletion mutant Delta69-Delta70 often co-occurs with the replacements N501Y, N439K and Y453F. 2021 Viruses Discussion SARS_CoV_2 N439K;N501Y;Y453F 156;149;166 161;154;171 33498225 Biological and Clinical Consequences of Integrin Binding via a Rogue RGD Motif in the SARS CoV-2 Spike Protein. Of these sequence changes, only N501Y is located in the receptor-binding domain. 2021 Viruses Discussion SARS_CoV_2 N501Y 32 37 33498225 Biological and Clinical Consequences of Integrin Binding via a Rogue RGD Motif in the SARS CoV-2 Spike Protein. The variant is characterized by multiple mutations including three amino acid deletions (69-70 and 144) and seven single-amino-acid replacements in the spike protein (N501Y, A570D, D614G, P681H, T716I, S692A, D1118H). 2021 Viruses Discussion SARS_CoV_2 A570D;D1118H;D614G;P681H;S692A;T716I;N501Y 174;209;181;188;202;195;167 179;215;186;193;207;200;172 S 152 157 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. In silico analysis also predicted that the N501Y mutation would result in enhanced RBD affinity for the mACE-2 receptor. 2021 medRxiv Discussion SARS_CoV_2 N501Y 43 48 RBD 83 86 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. In this work we present two mouse models for studying enhanced illness during the outcome of SARS-CoV-2 infection in the context of these comorbidities with the MA-SARS-CoV-2 that has the N501Y mutation. 2021 medRxiv Discussion SARS_CoV_2 N501Y 188 193 COVID-19 93 113 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. Interestingly, the N501Y mutation in the RBD of the S protein is also found in the newly emerging 20B/501Y.V1 strain that was first detected in the UK but now is circulating worldwide with high transmissibility. 2021 medRxiv Discussion SARS_CoV_2 N501Y 19 24 RBD;S 41;52 44;53 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. The MA-SARS-CoV-2 has acquired an asparagine to tyrosine mutation at position 501 in the spike RBD (N501Y). 2021 medRxiv Discussion SARS_CoV_2 N501Y;N501Y 34;100 81;105 S;RBD 89;95 94;98 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. The N501Y mutation is the only mutation in the RBD of the S protein of the UK-origin 20B/501Y.V1 strains, and therefore, might impact its antigenicity. 2021 medRxiv Discussion SARS_CoV_2 N501Y 4 9 RBD;S 47;58 50;59 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. Viral escape from neutralizing antibodies has been shown in vitro using pseudoviruses (22) and there are strong concerns that monoclonal antibody therapies and vaccines that become currently available may have reduced efficacy against circulating strains with the N501Y mutation. 2021 medRxiv Discussion SARS_CoV_2 N501Y 264 269 33501468 The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera. We showed that convalescent and post-vaccination sera obtained from both mice and humans can still potently neutralize the MA-SARS-CoV-2 variant with N501Y mutation in its RBD. 2021 medRxiv Discussion SARS_CoV_2 N501Y 150 155 RBD 172 175 33502471 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Replication and Tropism in the Lungs, Airways, and Vascular Endothelium of Patients With Fatal Coronavirus Disease 2019: An Autopsy Case Series. Furthermore, we performed genetic characterization of SARS-CoV-2 from fixed tissues of fatal cases and identified D614G spike variant in 9 of 26 (35%) RT-PCR-positive case patients. 2021 The Journal of infectious diseases Discussion SARS_CoV_2 D614G 114 119 S 120 125 33502471 Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Replication and Tropism in the Lungs, Airways, and Vascular Endothelium of Patients With Fatal Coronavirus Disease 2019: An Autopsy Case Series. Nonetheless, a recent study showed a correlation between D614G and higher viral load. 2021 The Journal of infectious diseases Discussion SARS_CoV_2 D614G 57 62 33503420 The immunodominant and neutralization linear epitopes for SARS-CoV-2. Importantly, a shift of the immunodominant and neutralizing epitope region from S556-S570 to S675-689 was observed upon D614G mutation. 2021 Cell reports Discussion SARS_CoV_2 D614G 120 125 33503420 The immunodominant and neutralization linear epitopes for SARS-CoV-2. Moreover, S556-570 was no longer an immunodominant and neutralizing epitope in the G614 strain, and the antibodies induced by S675-689 inhibited G614 but not D614 pseudovirus entry into ACE2-expressing 293T cells, suggesting that antigenic drift was caused by the D614G mutation. 2021 Cell reports Discussion SARS_CoV_2 D614G 264 269 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. (2020) in nature structural & molecular biology, which suggests that the D614G substitution could play a role in two conformational states, 'up' and 'down.' On the other hand, our mutation sensitivity analysis by Phyre2 for D614G spike protein is consistent with a newly published article, on the 20th of August 2020, in nature scientific reports by Sandra Isabel and her colleagues. 2021 Biochemistry and biophysics reports Discussion SARS_CoV_2 D614G;D614G 73;224 78;229 S 230 235 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. (2020), which included that the D614G substitution might change the viral conformational plasticity and hence a potential viral fitness gain. 2021 Biochemistry and biophysics reports Discussion SARS_CoV_2 D614G 32 37 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. At last, with taking the analysis output from all servers applied in this study we draw an inference that what makes the D614G meaningful for the COVID-19 pandemic still unclear and agrees with a previous study; this is due to many reasons. 2021 Biochemistry and biophysics reports Discussion SARS_CoV_2 D614G 121 126 COVID-19 146 154 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. From PSIPRED analysis, the D614G mutation showed the substitution of aspartate, a coil amino acid, to glycine, an extracellular amino acid. 2021 Biochemistry and biophysics reports Discussion SARS_CoV_2 D614G 27 32 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. highlighted an inference that the D614G clade might have a most likely neutral effect on the affinity of spike protein with its human ACE2 receptors. 2021 Biochemistry and biophysics reports Discussion SARS_CoV_2 D614G 34 39 S 105 110 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. However, we have recently reported in Non-coding RNA Research that the 1841A > G substitution at the viral genomic RNA level (D614G at spike protein level) showed many named microRNA sequences in human cells (e.g., hsa-miR-4793-5p to hsa-miR-3620-3p). 2021 Biochemistry and biophysics reports Discussion SARS_CoV_2 A1841G;D614G 71;126 80;131 S 135 140 33506114 Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan. Our non-coding RNA findings support a new hypothesis of host non-coding RNA based response, which can directly bind and affect the viral RNA replication of the D614G spike protein. 2021 Biochemistry and biophysics reports Discussion SARS_CoV_2 D614G 160 165 S 166 171 33506644 Genotype-phenotype correlation identified a novel SARS-CoV-2 variant possibly linked to severe disease. Most of those strains (58/60) carried the D614G mutation previously associated with higher infectivity rates (Volz et al., 2020; Zhang et al., 2020). 2022 Transboundary and emerging diseases Discussion SARS_CoV_2 D614G 42 47 33506644 Genotype-phenotype correlation identified a novel SARS-CoV-2 variant possibly linked to severe disease. Our genotype-phenotype analysis suggests a possible association between the Q271R missense and R41R synonymous mutations in the S and N genes, respectively, and disease severity. 2022 Transboundary and emerging diseases Discussion SARS_CoV_2 Q271R;R41R 76;95 81;99 N;S 134;128 135;129 33506644 Genotype-phenotype correlation identified a novel SARS-CoV-2 variant possibly linked to severe disease. Our study has identified a missense (Q271R) and synonymous (R41R) mutation in the S and N proteins that might be associated with severe disease in otherwise healthy adults. 2022 Transboundary and emerging diseases Discussion SARS_CoV_2 Q271R;R41R 37;60 42;64 N;S 88;82 89;83 33506644 Genotype-phenotype correlation identified a novel SARS-CoV-2 variant possibly linked to severe disease. The Q271R missense mutation is located in the N-terminal domain of S protein, outside the receptor binding domain (RBD), and its effect on protein structure or function cannot be deciphered without additional functional analysis. 2022 Transboundary and emerging diseases Discussion SARS_CoV_2 Q271R 4 9 RBD;RBD;N;S 90;115;46;67 113;118;47;68 33506644 Genotype-phenotype correlation identified a novel SARS-CoV-2 variant possibly linked to severe disease. Thus, the closure of international flights and the strict community-based transmission between April - June 2020 in the UAE provides another epidemiological evidence that the D614G mutation increases infectivity (16, 17) (Figure S1). 2022 Transboundary and emerging diseases Discussion SARS_CoV_2 D614G 175 180 33508515 Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. Earlier reports have also attributed the occurrence of higher numbers of mutations to the presence of C14,408 U (RdRp: P323L) variant occurring in the interaction domain of RdRp thus impairing protein-protein interactions with NSP7, NSP8 and NSP14 resulting in altered proofreading and processivity as has been speculated in earlier reports. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P323L 119 124 Nsp7;Nsp8;RdRP;RdRP 227;233;113;173 231;237;117;177 33508515 Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. have shown these antivirals binding to the RdRp-NSP7-NSP8 complex through a hydrophobic groove involving amino acid residues F324, F325, F326 of the RdRp protein which is just next to the P323L variant site with potential to alter response to treatment with these antivirals which is in strong LD with the A23,403G (S:D614G) variant. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P323L;D614G 188;318 193;323 Nsp7;Nsp8;RdRP;RdRP;S 48;53;43;149;316 52;57;47;153;317 33508515 Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. This could be because of recent population expansions as has been observed in H1N1 populations involved in outbreaks and epidemics and the uniform negative Tajima's D values across all the SARS-CoV-2 ORFs could also be attributed to it and this finding has remained unchanged with increase in viral sequences numbers.The clade G (S:G614) viruses with the C14,408U (RdRp: P323L) variant were found to incur more number of variations leading to the emergence of a number of sub-clusters of viruses with increased branch lengths in comparison to the clade Lv viruses including clade GHv and GR. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P323L 371 376 RdRP;S 365;330 369;331 33508515 Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. This idea is reinforced with the recent emergence and rapid spread of the B.1.1.7 variant with multiple additional spike protein mutations [deletion 69-70 (diagnostic failure), deletion145, N501Y (increased hACE2 binding affinity), A570D, P681H (Furin cleavage site), T716I, S982A, D1118H) on the background of the G614 mutation. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;T716I 232;282;190;239;275;268 237;288;195;244;280;273 S 115 120 33513449 Different SARS-CoV-2 haplotypes associate with geographic origin and case fatality rates of COVID-19 patients. More recently, the D614G mutation was identified as a marker associated with fatality rate at a countrywide level. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 19 24 33513449 Different SARS-CoV-2 haplotypes associate with geographic origin and case fatality rates of COVID-19 patients. Recent studies demonstrated that in situ images of S trimer conformational changes were affected by the D614G substitution. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 104 109 S 51 52 33513449 Different SARS-CoV-2 haplotypes associate with geographic origin and case fatality rates of COVID-19 patients. The D614G mutation has received a great deal of attention with respect to its rapid global dissemination and its significant influence on the spike protein's affinity for the ACE2 receptor. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 4 9 S 142 147 33513449 Different SARS-CoV-2 haplotypes associate with geographic origin and case fatality rates of COVID-19 patients. Within this region, we showed a significant association between the D614G mutation and case severity. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 68 73 33524589 A global analysis of replacement of genetic variants of SARS-CoV-2 in association with containment capacity and changes in disease severity. Taken together, it is possible that both survival benefits and founder effect have accounted for the global predominance of lineage G* (S-D614G variants). 2021 Clinical microbiology and infection Discussion SARS_CoV_2 D614G 138 143 S 136 137 33524589 A global analysis of replacement of genetic variants of SARS-CoV-2 in association with containment capacity and changes in disease severity. The phenomenon of global replacement by lineage G* (S-D614G variants) as documented in this study could be due to its survival benefits or simply a founder effect. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 D614G 54 59 S 52 53 33524589 A global analysis of replacement of genetic variants of SARS-CoV-2 in association with containment capacity and changes in disease severity. The S-D614G mutation is a signature of variants of lineage G*, including clades G, GH and GR, which could induce conformational modification that facilitates exposure of the cleavage domain to proteases. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 D614G 6 11 S 4 5 33524589 A global analysis of replacement of genetic variants of SARS-CoV-2 in association with containment capacity and changes in disease severity. We observed that S-D614G replacement started in late February 2020, and was followed by the exponential upsurge in reported cases 2 weeks later in mid-March 2020. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 D614G 19 24 S 17 18 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. B.1.1.28 contains three mutations (K417T, E484K, and N501Y) at the same RBD residues as B.1.351. 2021 bioRxiv Discussion SARS_CoV_2 E484K;N501Y;K417T 42;53;35 47;58;40 RBD 72 75 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. N501Y is shared among viruses in these three lineages; while this mutation may confer enhanced binding to ACE2, its antigenic impact is limited to a few mAbs. 2021 bioRxiv Discussion SARS_CoV_2 N501Y 0 5 33532778 Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7. This relative resistance is largely due to E484K, a mutation shared by B.1.351 and B.1.1.28. 2021 bioRxiv Discussion SARS_CoV_2 E484K 43 48 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Additional analysis is required to determine how broad the resistance associated with S477N is, and to probe the mechanism by which it occurs. 2021 Cell host & microbe Discussion SARS_CoV_2 S477N 86 91 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Among our panel of mutants, we isolated a total of 14 substitutions at sites of glycosylation, including eight N-linked glycans sites: T345N, K444N, S477N, L441R, L517R, L452R, S477R, and K444R; and six O-linked glycans: F486S, T345S, F490S, P479S, F486Y, and N450Y. 2021 Cell host & microbe Discussion SARS_CoV_2 F486S;F486Y;F490S;K444N;K444R;L441R;L452R;L517R;N450Y;P479S;S477N;S477R;T345N;T345S 221;249;235;142;188;156;170;163;260;242;149;177;135;228 226;254;240;147;193;161;175;168;265;247;154;182;140;233 N 111 112 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. For the wild-type S sequence and some escape mutants (e.g., L441R, K444N, L452R, and S477N), we observed a modest increase in infectivity at increasing concentration of soluble mACE2. 2021 Cell host & microbe Discussion SARS_CoV_2 K444N;L441R;L452R;S477N 67;60;74;85 72;65;79;90 S 18 19 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Four variants at this position (E484A, E484D, E484G, and E484K) exhibited resistance to each of the human convalescent sera we tested. 2021 Cell host & microbe Discussion SARS_CoV_2 E484D;E484G;E484K;E484A 39;46;57;32 44;51;62;37 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Future studies that introduce F486S into an infectious cDNA clone of SARS-CoV-2 are needed to determine the significance of this change to hACE2 interactions in vivo. 2021 Cell host & microbe Discussion SARS_CoV_2 F486S 30 35 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. How S477N could confer such broad resistance is of interest, given its penetrance among clinical isolates (6.5%). 2021 Cell host & microbe Discussion SARS_CoV_2 S477N 4 9 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Substitution E484K is likely to increase in penetrance further as it linked together with N501Y and K417N changes that are present in variant 501.V2, which is believed to be more transmissible. 2021 Cell host & microbe Discussion SARS_CoV_2 E484K;K417N;N501Y 13;100;90 18;105;95 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Substitution F486S was particularly notable, as we were unable to attain 50% neutralization at the highest concentrations of soluble hACE2 tested (>20 mug/mL). 2021 Cell host & microbe Discussion SARS_CoV_2 F486S 13 18 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Substitution of S477N, the fourth most abundant S protein sequence variant in circulating human isolates of SARS-CoV-2, led to a degree of resistance to all of the mAbs we profiled, including 2B04 and 2H04. 2021 Cell host & microbe Discussion SARS_CoV_2 S477N 16 21 S 48 49 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. The broad mAb resistance observed here for S477N was not accompanied by resistance to neutralization by human convalescent sera, suggesting that other epitopes:such as those centered around E484:are more dominant in humans. 2021 Cell host & microbe Discussion SARS_CoV_2 S477N 43 48 33535027 Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. The finding of an antibody escape mutant mapping to a critical residue within the ACE2 binding site raises questions regarding possible receptor usage by viruses containing S proteins with F486S. 2021 Cell host & microbe Discussion SARS_CoV_2 F486S 189 194 S 173 174 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. A recent study suggested that D614G variants became the predominant type circulating worldwide; these strains account for 78% of total distribution as of May 2020 and are associated with increased infectivity and a high case-fatality rate. 2021 PloS one Discussion SARS_CoV_2 D614G 30 35 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. Additionally, we identified a predominant type of D614G variants with the concomitant silent mutations C241T, C313T, and C3037T in ORF1a; the P214L amino acid substitution in S; and double mutation of R202K and G203R in N. 2021 PloS one Discussion SARS_CoV_2 C241T;C3037T;C313T;D614G;G203R;P214L;R202K 103;121;110;50;211;142;201 108;127;115;55;216;147;206 ORF1a;N;S 131;220;175 136;221;176 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. By contrast, the European strains have higher infectivity, virulence, and replication rate than the Asian type, especially the D614G mutant variants. 2021 PloS one Discussion SARS_CoV_2 D614G 127 132 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. In addition to the D614G mutation, the spike region contained two different types of mutations, M153T in S65 and T76I in S66. 2021 PloS one Discussion SARS_CoV_2 D614G;M153T;T76I 19;96;113 24;101;117 S 39 44 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. In light of the alterations in infectivity and transmissibility of D614G variants, our findings provide important insights into clinical management of SARS-CoV-2, as well as how we might modify preventive and control strategies in the future. 2021 PloS one Discussion SARS_CoV_2 D614G 67 72 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. Moreover, four GR strains from the second wave had the same mutation at C28725T. 2021 PloS one Discussion SARS_CoV_2 C28725T 72 79 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. Notably, we found a mutation in the nucleocapsid protein in all seven GR strains from Hiroshima: a triple mutation (G28881A, G28882A, and G2888C) resulting in an amino acid change. 2021 PloS one Discussion SARS_CoV_2 G28882A;G2888C;G28881A 125;138;116 132;144;123 N 36 48 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. The full-length genomes obtained in our study revealed that all seven European strains were genotype GR (specifically, D614G variants). 2021 PloS one Discussion SARS_CoV_2 D614G 119 124 33544733 Molecular characterization and the mutation pattern of SARS-CoV-2 during first and second wave outbreaks in Hiroshima, Japan. The predominant D614G variants and a new form of ORF8 deletion also provide the clues for the role of viral factor in local outbreak of SARS-CoV-2 in Hiroshima. 2021 PloS one Discussion SARS_CoV_2 D614G 16 21 ORF8 49 53 33545711 SARS-CoV-2 evolution during treatment of chronic infection. D796H has been documented in 0.02% of global sequences and D796Y appears in 0.05% of global sequences (Extended data 9). 2021 Nature Discussion SARS_CoV_2 D796Y;D796H 59;0 64;5 33545711 SARS-CoV-2 evolution during treatment of chronic infection. D796H, but not DeltaH69/DeltaV70, conferred reduction in susceptibility to polyclonal antibodies in the units of CP administered, though we cannot speculate as to their individual impacts on sera from other individuals. 2021 Nature Discussion SARS_CoV_2 D796H 0 5 33545711 SARS-CoV-2 evolution during treatment of chronic infection. It is intriguing that the DeltaH69/DeltaV70 + D796H double mutant diminished in between CP courses, suggesting that there were other selective forces at play in the intervening period, possibly driven by the inflammation observed in the individual. 2021 Nature Discussion SARS_CoV_2 D796H 46 51 33545711 SARS-CoV-2 evolution during treatment of chronic infection. The deletion was observed contemporaneously with the rare S2 mutation D796H after two separate courses of CP, with other viral populations emerging. 2021 Nature Discussion SARS_CoV_2 D796H 70 75 33545711 SARS-CoV-2 evolution during treatment of chronic infection. This includes the possibility that the haplotype with DeltaH69/DeltaV70 + D796H may have carried mutations in other regions deleterious during that intervening period. 2021 Nature Discussion SARS_CoV_2 D796H 74 79 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. Each SARS-CoV-2 variant also contained one nsp13 substitution, K460R in B.1.1.7 and T588I in B.1.351, that are unlikely to affect RDV susceptibility. 2021 Antiviral research Discussion SARS_CoV_2 K460R;T588I 63;84 68;89 Nsp13 43 48 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. For instance, based on a recent study of Ebola virus resistance to RDV, focus on residues in the fingers domain, such as A449V observed in 0.57% of clinical isolates, and their potential impact on template dependent inhibition may be warranted. 2021 Antiviral research Discussion SARS_CoV_2 A449V 121 126 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. From cryo-EM structures, none of the observed substitutions, including nsp12 P323L, were determined to have any direct interaction with pre-incorporated RDV-TP, the site of delayed chain termination, or the site of template dependent inhibition. 2021 Antiviral research Discussion SARS_CoV_2 P323L 77 82 Nsp12 71 76 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. In the mink dataset, low variation was also observed in the RNA replication complex and nsp12 P323L was the most frequent amino acid substitution, consistent with the human data. 2021 Antiviral research Discussion SARS_CoV_2 P323L 94 99 Nsp12 88 93 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. Nsp12 P323L is the most frequent substitution observed, increasing in frequency over time. 2021 Antiviral research Discussion SARS_CoV_2 P323L 6 11 Nsp12 0 5 33549572 Genetic conservation of SARS-CoV-2 RNA replication complex in globally circulating isolates and recently emerged variants from humans and minks suggests minimal pre-existing resistance to remdesivir. Nsp12 P323L was observed in 100% of isolates from each lineage. 2021 Antiviral research Discussion SARS_CoV_2 P323L 6 11 Nsp12 0 5 33551188 Fast and cost-effective screening for SARS-CoV-2 variants in a routine diagnostic setting. In case of a positive test for SARS-CoV-2 and corresponding clinical and anamnestic indications, a second qPCR for the mutation N501Y can follow and deliver the result to public health authorities and to the treating physician within a few hours. 2021 Dental materials Discussion SARS_CoV_2 N501Y 128 133 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. One non-synonymous (Aspartic acid to Glycine) mutation at amino acid position 614 (D614G) of the Spike protein of the coronavirus stands out. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;D614G 20;83 81;88 S 97 102 33556558 SARS-CoV-2 mutation 614G creates an elastase cleavage site enhancing its spread in high AAT-deficient regions. The D614G mutation is near the S1-S2 junction on SARS-CoV-2 Spike (S) protein. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 4 9 S;S 60;67 65;68 33556653 The G614 pandemic SARS-CoV-2 variant is not more pathogenic than the original D614 form in adult Syrian hamsters. Although multiple studies, including ours, show the G614 variant grows to a higher titer, it is unclear whether the fixation of D614G spike mutation is the result of a founder effect as the SARS-CoV-2 pandemic spread to Europe and the Americas or a product of viral evolution in response to a new host or to some other selective pressure. 2021 Virology Discussion SARS_CoV_2 D614G 128 133 S 134 139 33556653 The G614 pandemic SARS-CoV-2 variant is not more pathogenic than the original D614 form in adult Syrian hamsters. Rather than use recombinant SARS-CoV-2, which would focus on the single D614G mutation, we chose two isolates from US patients that were collected at different time periods during the pandemic. 2021 Virology Discussion SARS_CoV_2 D614G 72 77 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. 291 changes in 165 of 222 M residues), S68F being the most prevalent, in only 0.2% of the global sequences. 2021 Viruses Discussion SARS_CoV_2 S68F 39 43 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. A recent study has reported that D614G increases infectivity in human lung cells or cells with bat or pangolin ACE2 receptor in cell cultures, and that D614G shifts the S protein conformation toward an ACE2-binding fusion-competent state. 2021 Viruses Discussion SARS_CoV_2 D614G;D614G 33;152 38;157 S 169 170 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. A recent study suggested that the co-occuring mutations R203K and G204R may decrease the overall structural flexibility of SARS-COV-2 N protein. 2021 Viruses Discussion SARS_CoV_2 G204R;R203K 66;56 71;61 N 134 135 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Although infrequent, most mutations with a global rate >=0.1% were found in the CTD, including S68F. 2021 Viruses Discussion SARS_CoV_2 S68F 95 99 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. D614G has been previously reported in several studies, some of them also including a large number of sequences, but its biological impact has not been elucidated yet. 2021 Viruses Discussion SARS_CoV_2 D614G 0 5 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Further analysis is needed to evaluate the impact of N SR-linker mutations in SARS-CoV-2 transmissibility and virulence, as well as of the observed global increase of the G204R and R203K combination. 2021 Viruses Discussion SARS_CoV_2 G204R;R203K 171;181 176;186 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. G204R and R203K are located in the SR-linker of the N protein (aa 180-210), as well as the other two aa changes found (S194L and S197L) with >1% global rate. 2021 Viruses Discussion SARS_CoV_2 R203K;S197L;S194L;G204R 10;129;119;0 15;134;124;5 N 52 53 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. However, other reports hypothesize that D614G enhances viral fitness. 2021 Viruses Discussion SARS_CoV_2 D614G 40 45 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. In most European countries, the G204R and R203K combination seemed to have steadily increased in time during the beginning of the pandemic, however, this upward trend may be disappearing in the last epiweeks for some countries. 2021 Viruses Discussion SARS_CoV_2 G204R;R203K 32;42 37;47 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. In the S protein, the most remarkable aa change was D614G, present in eight out of 10 global spike analyzed sequences. 2021 Viruses Discussion SARS_CoV_2 D614G 52 57 S;S 93;7 98;8 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. In this study, we found only 221 sequences of the total 101,376 E sequences (0.2%) with aa changes in the PBM, being L73F the most prevalent, and with no frequency increase over time. 2021 Viruses Discussion SARS_CoV_2 L73F 117 121 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. It has been reported that mutations in this region could have an important biological impact, including aa change S197L, present in 1686 N sequences in our study, and representing 1.7% of the complete sequence set. 2021 Viruses Discussion SARS_CoV_2 S197L 114 119 N 137 138 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Phosphorylation of this SR-link motif in SARS-CoV modulates nucleocapsid multimerization, translational inhibitory activity and cellular localization The main finding in this protein was the simultaneous increase in the frequency of both G204R and R203K, the most frequent mutations in the N protein (37% and 37.3%, respectively) at the global and regional levels. 2021 Viruses Discussion SARS_CoV_2 G204R;R203K 238;248 243;253 N;N 60;290 72;291 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. S197L is a phosphorylation site for kinases involved in the control of the cell cycle. 2021 Viruses Discussion SARS_CoV_2 S197L 0 5 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Some reports suggest that D614G spread could be explained by a founder effect, without the need for a selective advantage, especially at the beginning of an epidemic, when most individuals are susceptible. 2021 Viruses Discussion SARS_CoV_2 D614G 26 31 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. The D3G mutation belongs to the exposed NTD, whereas T175M is located in the CTD. 2021 Viruses Discussion SARS_CoV_2 D3G;T175M 4;53 7;58 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. The M protein was the most conserved protein (99.99%), but it also presented aa changes in the global approach, D3G and T175M being the most prevalent of the 291 aa changes found. 2021 Viruses Discussion SARS_CoV_2 D3G;T175M 112;120 115;125 33557213 Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. When analyzing each geographical region individually, different temporal trends of the G204R + R203K pair were observed according to the country of origin of the N sequences and even between epiweeks. 2021 Viruses Discussion SARS_CoV_2 G204R;R203K 87;95 92;100 N 162 163 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. According to the results of pseudovirus-based neutralization assays, we found that the SARS2-S WT and D614G mutant were similarly susceptible to all confirmed case patient sera raised against the prototypic viruses. 2021 Nature communications Discussion SARS_CoV_2 D614G 102 107 S 93 94 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Consequently, during its continuous transmission from human to human, the prototype might have acquired more widely prevalent phenotypes represented by the A2a clade that harbors the D614G mutation, possibly with enhanced speed of global transmission. 2021 Nature communications Discussion SARS_CoV_2 D614G 183 188 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Consistently, our experiments using biolayer interferometry technology demonstrate that the D614G protein trimer has an increased binding affinity for the ACE2 protein dimer in a temperature-dependent manner. 2021 Nature communications Discussion SARS_CoV_2 D614G 92 97 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Importantly, during and after the submission of our initial preprint, several groups also proved that the D614G mutant virus shows increased infectivity and retained neutralization sensitivity, by similarly conducting infectivity assays using S-protein-pseudotyped viruses. 2021 Nature communications Discussion SARS_CoV_2 D614G 106 111 S 243 244 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. In fact, the D614G mutation defines the clade A2a, which has overwhelmingly spread worldwide, accounting for 87% of sequenced cases in New York City (73 out of 84 in one study), 76% of cases in Iceland (438 out of 577, including A2a-derived haplotypes in a study), the vast majority of the recent cases in Japan, and almost all of the cases in Italy. 2021 Nature communications Discussion SARS_CoV_2 D614G 13 18 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. In striking contrast, the recent paper published during our revision process, where a surface plasmon resonance technique was used, showed that D614G rather decreased the affinity for ACE2. 2021 Nature communications Discussion SARS_CoV_2 D614G 144 149 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. More importantly, the D614G mutant displayed the highest entry activity among SARS2-S proteins tested in this study. 2021 Nature communications Discussion SARS_CoV_2 D614G 22 27 S 84 85 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. The aforementioned results indicate that the D614G variant has virological and structural differences from the WT strain. 2021 Nature communications Discussion SARS_CoV_2 D614G 45 50 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. This finding therefore suggests that the D614G mutant virus might be more transmissible from human to human than the prototype viruses, even though further investigations are necessary to determine the correlation between viral infectivity and transmissibility among humans. 2021 Nature communications Discussion SARS_CoV_2 D614G 41 46 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. This is particularly important in that the clade-defining D614G mutation will not hinder the current strategy for anti-SARS-CoV-2 drug/vaccine development due to the absence of antigenic alteration in the S protein. 2021 Nature communications Discussion SARS_CoV_2 D614G 58 63 S 205 206 33558493 SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. This result indeed reflects the structural prediction that the spatial flexibility of S protein is induced by the D614G mutation, which likely leads to enhanced ACE2-binding. 2021 Nature communications Discussion SARS_CoV_2 D614G 114 119 S 86 87 33558635 Potent neutralization of clinical isolates of SARS-CoV-2 D614 and G614 variants by a monomeric, sub-nanomolar affinity nanobody. Along these lines, a recent study has shown that the D614G trimer is constrained in a prefusion state likely to be a superior immunogen for eliciting protective neutralizing antibody responses. 2021 Scientific reports Discussion SARS_CoV_2 D614G 53 58 33558635 Potent neutralization of clinical isolates of SARS-CoV-2 D614 and G614 variants by a monomeric, sub-nanomolar affinity nanobody. The difference observed may be explained by structural impacts of the D614G mutation, which influence the dynamics of exposure of the RBD region. 2021 Scientific reports Discussion SARS_CoV_2 D614G 70 75 RBD 134 137 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. Among the missense mutations, Spike_D614G, NSP12_P323L, N_R203K and N_G204R occurred with high frequency worldwide. 2021 Biosafety and health Discussion SARS_CoV_2 D614G;G204R;P323L;R203K 36;70;49;58 41;75;54;63 S;Nsp12 30;43 35;48 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. Concerning the mutation Spike_M1237I, it's noteworthy that the spike surface glycoprotein is crucial for the virus binding to receptors on the host cell. 2021 Biosafety and health Discussion SARS_CoV_2 M1237I 30 36 S;S;S 69;24;63 89;29;68 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. Other missense mutations occurred either with small frequency like Spike_M1237I that was reported 11 times all over the world or those reported only once worldwide, like NSP12_M196I, NSP3_A1819V, M_L13F, NSP14_D324A, NSP14_T75I and NSP5_V125I. 2021 Biosafety and health Discussion SARS_CoV_2 A1819V;D324A;L13F;M1237I;M196I;T75I;V125I 188;210;198;73;176;223;237 194;215;202;79;181;227;242 S;Nsp12;Nsp3;Nsp5 67;170;183;232 72;175;187;236 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. The mutations NSP10_R134S, NSP15_D335N, NSP16_I169L, NSP3_L431H, NSP3_P1292L and Spike_V6F that occurred in the Moroccan sequences with no record in other sequences worldwide, should get careful attention and should be investigated to figure out their potential effects on the SARS-CoV-2 virulence, as well as their association with immunological and clinical symptoms. 2021 Biosafety and health Discussion SARS_CoV_2 D335N;I169L;L431H;P1292L;R134S 33;46;58;70;20 38;51;63;76;25 S;Nsp3;Nsp3 81;53;65 86;57;69 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. The Spike_D614G mutation manifested a major effect on the efficiency of the virus to infect hosts and showed a high ability to hinder the immune systems of hosts that already dealt with version of SARS-CoV-2 without the Spike_D614G mutation. 2021 Biosafety and health Discussion SARS_CoV_2 D614G;D614G 10;226 15;231 S;S 4;220 9;225 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. This might be because the change from proline to leucine amino-acid (P323L) did not change the protein function, as both amino-acids pertain to the non-polar aliphatic R groups. 2021 Biosafety and health Discussion SARS_CoV_2 P323L 69 74 33558859 Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. Though the mutation NSP12_P323L aroused the substitution of proline that plays a prominent role in protein folding and aggregation, neither increased the SARS-CoV-2's infectivity or its fitness regarding natural selection. 2021 Biosafety and health Discussion SARS_CoV_2 P323L 26 31 Nsp12 20 25 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. Among the experimental data reported in that study, we were particularly interested in the measured affinity of the Spike N501F protein mutant with ACE2 as it involves residue 501 and as the affinity was assessed in a purified binding assay (most of these other affinity evaluations were performed using high-throughput affinity measurements that could be less accurate than measurements carried out in purified systems). 2021 International journal of molecular sciences Discussion SARS_CoV_2 N501F 122 127 S 116 121 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. Another most likely alternative could be that, as ACE2 K26 makes a salt-bridge with ACE2 E22 and polar interactions with ACE2 N90, the K26R substitution stabilizes locally this region of ACE2 (possibly creating another salt-bridge with the nearby ACE2 E23, not possible when ACE2 at position 26 is a K) and this could contribute to a more favorable change in free energy of binding with the Spike protein. 2021 International journal of molecular sciences Discussion SARS_CoV_2 K26R 135 139 S 391 396 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. Experimentally, it was found that the Spike N501F protein has increased affinity for ACE2. 2021 International journal of molecular sciences Discussion SARS_CoV_2 N501F 44 49 S 38 43 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. For example, the Spike D614G substitution seems to increase the affinity with the ACE2 receptor although this residue is not present at the Spike-ACE2 interface but at a Spike protomer-protomer interface. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G 23 28 S;S;S 17;140;170 22;145;175 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. For the time being, we do not know if the N501Y alone could counterbalance the predicted unfavorable Spike K417N and E484K amino acid replacements. 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484K;K417N;N501Y 117;107;42 122;112;47 S 101 106 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. For the UK strain, it is possible that the enhanced affinity to ACE2 due to the N501Y substitution increases transmissibility but also contributes to disease severity (not only due to the increased number of infected individuals) as suggested after comparisons of the SARS-CoV-2 with other human coronaviruses. 2021 International journal of molecular sciences Discussion SARS_CoV_2 N501Y 80 85 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. From the simulations performed here it seems that the N501Y substitution or the N501Y, K417N, E484K replacements should not induce major conformational changes, suggesting that the newly developed vaccines should be efficient against these variants. 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484K;K417N;N501Y;N501Y 94;87;54;80 99;92;59;85 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. In our hands, it would seem that the ACE2 K26R may only have minor roles with regard to Spike binding. 2021 International journal of molecular sciences Discussion SARS_CoV_2 K26R 42 46 S 88 93 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. In that study, the authors found that two substitutions in ACE2 positions 19 and 26 could modulate the affinity for the Spike protein (ACE2 position 19, fully solvent exposed:the S19P is common in African people and the substitution was suggested to protect individuals (reduced affinity for Spike) and a cleavage site of the ACE2 precursor; ACE2 position 26, fully solvent exposed:the K26R is common in European people, the mutation may increase affinity of ACE2 towards Spike). 2021 International journal of molecular sciences Discussion SARS_CoV_2 K26R;S19P 386;179 390;183 S;S;S 120;292;472 125;297;477 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. Our observation applies essentially to the UK strain while additional work is required to gain insights into the South African strain because in our hands, looking only at the interface, it would seem that the K417N and E484K substitutions are not favorable for the interaction with ACE2. 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484K;K417N 220;210 225;215 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. The E484K replacement was not found to change the expression level, suggesting, as observed in our structural analysis, that a K could be present in this position of the Spike protein without creating major structural changes. 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484K 4 9 S 170 175 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. This observation is expected for the N501Y substitution although the measurements were not performed in purified system. 2021 International journal of molecular sciences Discussion SARS_CoV_2 N501Y 37 42 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. We noted, however, that the SPServer and pyDockEneRes tools were able to output values consistent with this high-quality N501F experimental result. 2021 International journal of molecular sciences Discussion SARS_CoV_2 N501F 121 126 33567580 In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface. Yet, when focusing only on the Spike RBD-ACE2 interface, the present in silico predictions and interactive structural analysis suggest that the key player residue in term of enhanced affinity is the N501Y replacement. 2021 International journal of molecular sciences Discussion SARS_CoV_2 N501Y 199 204 S;RBD 31;37 36;40 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Among 4434 sequences of the S protein, 3089 sequences have the mutation D614G, taking 69.67%. 2021 Scientific reports Discussion SARS_CoV_2 D614G 72 77 S 28 29 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). For example, in gene S (Table 10), the latest date of D614G was on 2020-06-05 (same as the latest collection date of the entire genome dataset used in this study), indicating that this mutation is still active. 2021 Scientific reports Discussion SARS_CoV_2 D614G 54 59 S 21 22 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). In particular, among 3089 D614G mutations, our prediction results show that none of these mutations is likely to make changes in the protein secondary structure and relative solvent accessibility. 2021 Scientific reports Discussion SARS_CoV_2 D614G 26 31 33568759 Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). The latest date of P681L was on 2020-04-03, showing that this mutation may no longer occur. 2021 Scientific reports Discussion SARS_CoV_2 P681L 19 24 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. In summary, we have demonstrated that the recent and now-dominant mutation in the SARS-CoV-2 Spike glycoprotein D614G increases the efficiency of cellular entry for the virus across a broad range of human cell types, including cells from lung, liver, and colon. 2021 eLife Discussion SARS_CoV_2 D614G 112 117 S 93 111 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. Several other groups have also reported that the D614G results in increased viral fitness and infection efficiency . 2021 eLife Discussion SARS_CoV_2 D614G 49 54 33570490 The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. Using bio-layer interferometry with purified SARS-CoV-2 Spike S1 fragment monomers and ACE2 proteins, we found no significant difference in binding kinetics with the ACE2 receptor resulting from the D614G mutation. 2021 eLife Discussion SARS_CoV_2 D614G 199 204 S 56 61 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. Additionally, we found a substitution in the S protein (S477N) with a high frequency in OC. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 S477N 56 61 S 45 46 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. Although the dN/dS values were positive for T85I, I120F, G614, L323, Q57H, G204R and S477N, only F120 and L323 presented statistical significance, indicating positive natural selection. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 G204R;I120F;Q57H;S477N;T85I 75;50;69;85;44 80;55;73;90;48 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. Another homoplasy event was the emergence of the mutation A23063T > N501Y in England and South Africa. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 A23063T;N501Y 58;68 65;73 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. Associations between the presence of the moderate and severe forms of COVID-19 in pediatric patients and P323L and D614G substitutions were also reported. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D614G;P323L 115;105 120;110 COVID-19 70 78 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. Initial studies have shown that the presence of the D614G substitution produces a reduction in the neutralization titers using antibodies from convalescent plasma obtained from patients with COVID-19. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D614G 52 57 COVID-19 191 199 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. Its rapid spread has been associated with the N501Y and P681H substitutions, which could be implicated in viral infectivity. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 N501Y;P681H 46;56 51;61 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. Meanwhile, the P323L substitution is located in a pocket that has been predicted as a possible druggable site; however, further research is needed to discover if the mutation could affect these properties. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 P323L 15 20 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. Moreover, P323L and D614G substitutions may correlate with higher fatality rates. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D614G;P323L 20;10 25;15 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. Recently, the British government reported two imported cases from South Africa; those genomes had the N501Y substitution but did not share the same mutations in the B1.1.7 linage. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 N501Y 102 107 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. Seven of them presented frequencies > 10% in the global SARS-CoV-2 population and were detected in nsp2 (T85I and I120F), nsp12 (P323L), S protein (D614G), ORF3a (Q57H) and N protein (R203K and G204R). 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 G204R;I120F;D614G;P323L;Q57H;R203K;T85I 194;114;148;129;163;184;105 199;119;153;134;167;189;109 ORF3a;Nsp12;Nsp2;N;S 156;122;99;173;137 161;127;103;174;138 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. The I120F substitution occurs in the N-terminal of nsp2, which is located in the extracellular region of the protein. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 I120F 4 9 Nsp2;N 51;37 55;38 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. The more significant changes in this strain were the mutations A23063T and C23604A, which resulted in substitutions of N501Y and P681H, respectively, in the S protein. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 A23063T;C23604A;N501Y;P681H 63;75;119;129 70;82;124;134 S 157 158 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. The P323L and D614G substitutions in the global SARS-CoV-2 population have increased dramatically in their frequency over time. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D614G;P323L 14;4 19;9 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. The P323L substitution is located in an interphase region of nsp12, and together with nsp7 and nsp8, it has been reported to play an important role in the formation of a protein complex, which provides structural stability to nsp12 for its processivity. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 P323L 4 9 Nsp12;Nsp12;Nsp7;Nsp8 61;226;86;95 66;231;90;99 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. The S447N substitution is located in the RBM and a recent study showed that S477 increases the affinity for the ACE-2 receptor. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 S447N 4 9 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. The variant (501Y.V2), which was first identified in South Africa in October 2020, also carries the N501Y substitution. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 N501Y 100 105 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. They found five dN substitutions in ORF8, nsp6, ORF3a, nsp4 and N protein related to mild disease, while 17 dN substitutions distributed in S protein, nsp12, ORF3a, N protein, nsp3, ORF6 and nsp7 were related to hospitalization and severe disease, including D614G, P323L, Q57H, R203K and G204R. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D614G;G204R;P323L;Q57H;R203K 258;288;265;272;278 263;293;270;276;283 ORF3a;ORF3a;Nsp12;ORF6;Nsp3;Nsp4;Nsp7;Nsp6;ORF8;N;N;S 48;158;151;182;176;55;191;42;36;64;165;140 53;163;156;186;180;59;195;46;40;65;166;141 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. To date, most serum samples from either volunteers in vaccines trials or patients recovering from COVID-19 have shown full or slightly diminished capacity to inactivate some of the more widespread SARS-CoV-2 variants, except for B.1.1.7 (N501Y substitution), 501Y.V2 (N501Y, K417N and E484K substitutions) and 501.V3 (N501Y and E484K substitutions), which have been able to cause a decrease in the neutralization assays using the aforementioned serum samples. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 E484K;E484K;K417N;N501Y;N501Y;N501Y 285;328;275;238;268;318 290;333;280;243;273;323 COVID-19 98 106 33572190 Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging. We found that the D614G substitutions in the S protein, P323L in nsp12, and R203K and G204R in the N protein had a significant association with the disease severity. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D614G;G204R;P323L;R203K 18;86;56;76 23;91;61;81 Nsp12;N;S 65;99;45 70;100;46 33579701 Insights into neutralizing antibody responses in individuals exposed to SARS-CoV-2 in Chile. Considering the high prevalence of the D614G spike variant in Chile (https://cov2.cl), we wanted to know whether antibodies present in clinical samples from actively sick and recovered patients were more potent in neutralizing the pseudotype carrying this mutation. 2021 Science advances Discussion SARS_CoV_2 D614G 39 44 S 45 50 33579701 Insights into neutralizing antibody responses in individuals exposed to SARS-CoV-2 in Chile. Hence, we identified two plasma samples having a significant increase in their neutralizing activity against the pseudotype carrying the D614G variant, but more importantly, we identified 12 of 38 samples having a significant reduction in their neutralization capacity against this predominant variant. 2021 Science advances Discussion SARS_CoV_2 D614G 137 142 33579701 Insights into neutralizing antibody responses in individuals exposed to SARS-CoV-2 in Chile. However, while we observed that the highly predominant D614G variant of the spike protein conferred increased infectivity to the pseudotype, we also observed that this occurred, altering the susceptibility to NAbs from some plasma samples. 2021 Science advances Discussion SARS_CoV_2 D614G 55 60 S 76 81 33579701 Insights into neutralizing antibody responses in individuals exposed to SARS-CoV-2 in Chile. These data provide further evidence for the relevance of the D614G mutation in the immune response, raising the possibility for the generation of NAbs targeting specific antigenic epitopes of this predominant variant and for an immune escape that requires further investigation. 2021 Science advances Discussion SARS_CoV_2 D614G 61 66 33579792 The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2. A number of biological features have been reported to distinguish the D614G mutant that may correlate with these differences in structure. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 70 75 33579792 The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2. As a consequence of the D614G substitution, a tightly closed structure observed for the D614 spike is not formed and the G614 spike assembly adopts a greater range of more open and flexible conformations than its D614 counterpart. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 24 29 S;S 93;126 98;131 33579792 The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2. At the same time, the more open conformation may result in the exposure of epitopes for additional neutralizing antibodies; indeed, recent reports suggest that the D614G substitution increases the susceptibility of SARS-CoV-2 to neutralization. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 164 169 33579792 The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2. suggest that the effect of the D614G substitution is mediated by the loss of a hydrogen bond to a threonine residue at position 859 of S2. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 31 36 33580132 Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada. A fifth polymorphic site (C25217T) was observed in four samples (S2, S4, S16, and S34,) and is a missense variant resulting in a glycine to cysteine substitution at the 1219th residue of the S protein. 2021 Scientific reports Discussion SARS_CoV_2 C25217T 26 33 S 191 192 33580132 Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada. A fourth polymorphic site at A23403G is a well described mutation that results in a D614G substitution in the S protein. 2021 Scientific reports Discussion SARS_CoV_2 A23403G;D614G 29;84 36;89 S 110 111 33580132 Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada. Clustering of shared mutations identified two samples (S21 and S23) that belong to A.1 lineage characterized by two polymorphic sites at C8782T and T28144C. 2021 Scientific reports Discussion SARS_CoV_2 C8782T;T28144C 137;148 143;155 33580132 Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada. The presence of three additional polymorphic sites at C17747T, A17858G, and C18060T exclusively present in North America provide support for the USA origin hypothesis described by our phylogenetic analysis. 2021 Scientific reports Discussion SARS_CoV_2 A17858G;C17747T;C18060T 63;54;76 70;61;83 33580132 Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada. This project identified three unique mutations in the coding region of the S protein, however all three are predicted to be synonymous and likely will not affect viral virulence or epitopes (Supplementary Table 2: C24382T, T24982C, and C25357T). 2021 Scientific reports Discussion SARS_CoV_2 C24382T;C25357T;T24982C 214;236;223 221;243;230 S 75 76 33580132 Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada. We also identified one heterozygous variant, C9994A, coding for a missense variant in ORF1a in S11. 2021 Scientific reports Discussion SARS_CoV_2 C9994A 45 51 ORF1a 86 91 33580132 Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada. Within the other twenty-five samples sharing the D614G substitution in the S protein, we observe three distinct lineages. 2021 Scientific reports Discussion SARS_CoV_2 D614G 49 54 S 75 76 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. A23403G were deemed as important mutations in spike protein. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 A23403G 0 7 S 46 51 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. Mutations C1059T and G25563T are first highlighted here. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 C1059T;G25563T 10;21 16;28 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. The A23403G mutation increases the spike-ACE2 interaction, and finally leads to the enhancement of its infectivity. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 A23403G 4 11 S 35 40 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. There T8782C, and C28144T were also identified by Peter et al. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 C28144T 18 25 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. Totally, we identified five dominant mutations T8782C, C28144T, C3037T, C14408T and A23403G and two potential dominant mutations C1059T and G25563T. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 A23403G;C1059T;C14408T;C28144T;C3037T;G25563T 84;129;72;55;64;140 91;135;79;62;70;147 33580783 Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. We analyzed the alteration of protein stability due to the dominant mutations and using I-Mutant and the alteration of spike-ACE2 binding affinity due to A23403G using PPA-Pred. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 A23403G 154 161 S 119 124 33588026 Variant analysis of SARS-CoV-2 genomes in the Middle East. On the basis of SNP analysis 10818delTinsG, 2772delCinsC, 14159delCinsC and 2789delAinsA are identified as high impact variants. 2021 Microbial pathogenesis Discussion SARS_CoV_2 10818delTinsG 29 42 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Additional S variants such as N439K and S477N also rapidly increased in frequency in Europe over the summer and into the fall of 2020. 2021 medRxiv Discussion SARS_CoV_2 N439K;S477N 30;40 35;45 S 11 12 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Although S477N reportedly increases affinity for the entry receptor, ACE2, and both mutations may impact antibody neutralization to some degree, neither shows any signature of increased transmissibility over the S: D614G background from which they emerged, and neither have become prominent in the United States. 2021 medRxiv Discussion SARS_CoV_2 D614G;S477N 215;9 220;14 S 212 213 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. At least two emergent lineages of concern, B.1.1.7 (501Y.V1), and a newer variant whose prevalence is on the rise in Uganda both contain amino acid substitutions affecting the first position of the polybasic cleavage site, S:P681H and S:P681R, respectively. 2021 medRxiv Discussion SARS_CoV_2 P681H;P681R 225;237 230;242 S;S 223;235 224;236 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Between August and November, 2020, seven independent lineages of SARS-CoV-2 with S:Q677H or S:Q677P mutations arose and gained in frequency. 2021 medRxiv Discussion SARS_CoV_2 Q677H;Q677P 83;94 88;99 S;S 81;92 82;93 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. For instance, the 20E (EU1) lineage characterized by an S: A222V polymorphism emerged suddenly in Europe over the summer, but has not been found to show any evidence for increased transmissibility and instead is thought to have been spread via holiday travel and relaxing summertime restrictions. 2021 medRxiv Discussion SARS_CoV_2 A222V 59 64 S 56 57 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Furthermore, a newly designated, emergent PANGO lineage, B.1.525, carries S: Q677H in addition to several mutations seen in B.1.1.7 (501Y.V1), such as S: del 69-70 and S: del 144, and also, S: E484K. 2021 medRxiv Discussion SARS_CoV_2 E484K;Q677H 193;77 198;82 S;S;S;S 74;151;168;190 75;152;169;191 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Given their relatively recent emergence, however, Q677P/H lineages may continue to rise as a percentage of total cases. 2021 medRxiv Discussion SARS_CoV_2 Q677P;Q677H 50;50 57;57 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. N501Y is therefore notably found in all three of the 'variants of concern'. 2021 medRxiv Discussion SARS_CoV_2 N501Y 0 5 33594385 Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. Remarkably, a 19B cluster harboring the ostensibly less fit, 'ancestral' D614 Spike, which has been circulating at <=2% of global frequency since August 2020, recently resurfaced as a newly re-emergent lineage carrying N501Y together with 677H. 2021 medRxiv Discussion SARS_CoV_2 N501Y 219 224 S 78 83 33606828 SARS-CoV-2 genetic diversity in Venezuela: Predominance of D614G variants and analysis of one outbreak. All the lineage B Venezuelan sequences bore the mutation C14408T, which produces the amino acid mutation P314L in the Nsp12 protein, the polymerase in the RdRP. 2021 PloS one Discussion SARS_CoV_2 C14408T;P314L 57;105 64;110 Nsp12;RdRP 118;155 123;159 33606828 SARS-CoV-2 genetic diversity in Venezuela: Predominance of D614G variants and analysis of one outbreak. Another non-synonymous mutation A23403G, yielding the mutation D614G in the Spike protein, has been widely described. 2021 PloS one Discussion SARS_CoV_2 A23403G;D614G 32;63 39;68 S 76 81 33606828 SARS-CoV-2 genetic diversity in Venezuela: Predominance of D614G variants and analysis of one outbreak. In conclusion, a high diversity of SARS-CoV-2 isolates was found circulating in Venezuela, with the predominance of the D614G isolates. 2021 PloS one Discussion SARS_CoV_2 D614G 120 125 33619506 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. variant, which contains an E484K mutation within the RBD region, was capable of significantly reducing neutralization potency of fully vaccinated individuals, in line with what has been suggested by deep mutational scanning. 2021 medRxiv Discussion SARS_CoV_2 E484K 27 32 RBD 53 56 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. against 501Y.V2 compared to the chimeric pseudotyped viral particle carrying only the RBD mutations K417N, E484K and N501Y. 2021 medRxiv Discussion SARS_CoV_2 E484K;K417N;N501Y 107;100;117 112;105;122 RBD 86 89 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Consistently, in this study we found that approximately 50% of the RBM mAbs tested lost neutralising activity against SARS-CoV-2 carrying E484K. 2021 medRxiv Discussion SARS_CoV_2 E484K 138 143 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. E484K has been shown to impact neutralisation by monoclonal antibodies or convalescent sera, especially in combination with N501Y and K417N. 2021 medRxiv Discussion SARS_CoV_2 K417N;N501Y;E484K 134;124;0 139;129;5 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Evidence for the importance role of NTD deletions in combination with E484K in immune escape is provided by Andreano et al. 2021 medRxiv Discussion SARS_CoV_2 E484K 70 75 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Finally, the role of NTD mutations (in particular, L18F, Delta242-244 and R246I) was further supported by the marked loss of neutralization observed by Wibmer et al. 2021 medRxiv Discussion SARS_CoV_2 L18F;R246I 51;74 55;79 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. have also recently reported the loss of neutralization of 501Y.V2 by the NTD-specific mAb 4A8, likely driven by the R246I mutation. 2021 medRxiv Discussion SARS_CoV_2 R246I 116 121 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. However, the contribution of N501Y to loss of neutralisation activity of polyclonal vaccine and convalescent sera is less clear, and interactions with other mutations likely. 2021 medRxiv Discussion SARS_CoV_2 N501Y 29 34 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. However, we demonstrated that a pseudovirus bearing S protein with the full set of mutations present in the B.1.1.7 variant (i.e., DeltaH69/V70, Delta144, N501Y, A570D, P681H, T716I, S982A, D1118H) did result in small reduction in neutralisation by sera from vaccinees that was more marked following the first dose than the second dose. 2021 medRxiv Discussion SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;T716I 162;190;155;169;183;176 167;196;160;174;188;181 S 52 53 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. In the study by Wang et al., 6 out 17 RDB-specific mAbs isolated from mRNA-1273 vaccinated individuals showed more than 100-fold neutralisation loss against N501Y mutant, a finding that is consistent with the loss of neutralisation by 5 out 29 RBM-specific mAbs described in this study. 2021 medRxiv Discussion SARS_CoV_2 N501Y 157 162 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Other major variants with E484K such as 501Y.V2 and V3 are also spreading regionally. 2021 medRxiv Discussion SARS_CoV_2 E484K 26 31 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Our data suggest that vaccine escape to current Spike directed vaccines designed against the Wuhan strain will be inevitable, particularly given that E484K is emerging independently and recurrently on a B.1.1.7 (501Y.V1) background, and given the rapid global spread of B.1.1.7. 2021 medRxiv Discussion SARS_CoV_2 E484K 150 155 S 48 53 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. The three mutations in S1 (N501Y, A570D, DeltaH69/V70) did not appear to impact neutralisation in a pseudovirus assay, consistent with data on N501Y having little effect on nuetralisation by convalescent and post vaccination sera. 2021 medRxiv Discussion SARS_CoV_2 A570D;N501Y;N501Y 34;143;27 39;148;32 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. This Delta140 mutant subsequently acquired E484K which resulted in a further 4-fold drop in neutralization titre indicating a two residue change across NTD and RBD represents an effective pathway of escape that can dramatically inhibit the polyclonal response. 2021 medRxiv Discussion SARS_CoV_2 E484K 43 48 RBD 160 163 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. using pseudoviruses carrying the N501Y mutation. 2021 medRxiv Discussion SARS_CoV_2 N501Y 33 38 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Wang et al also showed reduced neutralisation by mRNA vaccine sera against E484K bearing pseudovirus. 2021 medRxiv Discussion SARS_CoV_2 E484K 75 80 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. We measured further reduction neutralisation titers by vaccine sera when E484K was present alongside the B.1.1.7 S mutations. 2021 medRxiv Discussion SARS_CoV_2 E484K 73 78 S 113 114 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Worryingly, we have shown that there are multiple B.1.1.7 sequences in the UK bearing E484K with early evidence of transmission as well as independent aquisitions. 2021 medRxiv Discussion SARS_CoV_2 E484K 86 91 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Wu and co-authors have also shown that variants carrying the E484K mutation resulted in 3-to-6 fold reduction in neutralization by sera from mRNA-1273 vaccinated individuals. 2021 medRxiv Discussion SARS_CoV_2 E484K 61 66 33619509 SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Xie et al did not find an effect of N501Y alone in the context of BNT162b2 vaccine sera. 2021 medRxiv Discussion SARS_CoV_2 N501Y 36 41 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. A few other circulating RBM mutations have become prominent since N439K first emerged. 2021 Cell Discussion SARS_CoV_2 N439K 66 71 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Additionally, we observed no evidence for change in disease severity in a large cohort of individuals infected with N439K virus as compared to WT N439 virus, although we acknowledge some limitations in the data collection, including variations in testing guidelines and availability of testing during the course of the study. 2021 Cell Discussion SARS_CoV_2 N439K 116 121 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Additionally, we observed that two mutations together (N439K/K417V) conferred resistance in vitro to the two-mAb cocktail (Figure 7C). 2021 Cell Discussion SARS_CoV_2 N439K;K417V 55;61 60;66 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. For example, our data show that N439K can compensate for a mutation (K417V) that otherwise decreases receptor binding affinity (Figure 4D) and that several mAbs were more sensitive to these mutations in combination versus individually (Figure 6D; Data S1). 2021 Cell Discussion SARS_CoV_2 N439K;K417V 32;69 37;74 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Future retrospective studies will confirm whether these new RBM mutations fall into the same category as N439K: mutations that do not attenuate viral fitness or disease but cause immune evasion. 2021 Cell Discussion SARS_CoV_2 N439K 105 110 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Here, we describe an example of a circulating RBM mutation, N439K, which can evade antibody-mediated immunity without losing fitness relative to WT. 2021 Cell Discussion SARS_CoV_2 N439K 60 65 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. In our profile of immune escape from the N439K variant, we observed resistance to a mAb which is part of a two-mAb cocktail that recently received EAU. 2021 Cell Discussion SARS_CoV_2 N439K 41 46 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. In the final weeks of 2020, SARS-CoV-2 variants carrying multiple mutations in the S protein, in both the RBM and Domain A, have been observed including one variant carrying three simultaneous RBM mutations (K417N, E484K, and N501Y). 2021 Cell Discussion SARS_CoV_2 E484K;N501Y;K417N 215;226;208 220;231;213 S 83 84 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Last, the N501Y mutation has gained notice in the final weeks of 2020 for its association with high rates of infection, although further research is needed to determine the impact on immune escape. 2021 Cell Discussion SARS_CoV_2 N501Y 10 15 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. N439K was the first RBM amino acid replacement, relative to the ancestral SARS-CoV-2 variant used in vaccine preparations, to increase to high frequency and so can be viewed as a sentinel mutation for SARS-CoV-2 antigenic drift. 2021 Cell Discussion SARS_CoV_2 N439K 0 5 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. S477N appeared in the sequence databases in March 2020 but did not become the most prevalent RBD mutation until the summer (as of January 2021, it has >19,000 counts). 2021 Cell Discussion SARS_CoV_2 S477N 0 5 RBD 93 96 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The success of the N439K mutation is consistent with our findings that the RBM is a highly variable region of S. 2021 Cell Discussion SARS_CoV_2 N439K 19 24 S 110 111 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The success of variants with the N439K mutation is evidenced by their repeated emergence by convergent evolution on at least nine occasions, spread to 34 countries as of January 2021, significant representation in sampled genome sequences (indicative of high infection rates), the fact that the N439K RBD retains a high-affinity interaction with the hACE2 receptor, and efficient replication of N439K virus in cultured cells. 2021 Cell Discussion SARS_CoV_2 N439K;N439K;N439K 33;295;395 38;300;400 RBD 301 304 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. The Y453F mutation has become noteworthy recently for its association with virus circulating in mink farms and its transmission back to humans and the DMS measurement indicating it confers significantly increased hACE2 binding. 2021 Cell Discussion SARS_CoV_2 Y453F 4 9 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. This study presents the finding that the RBM is a highly variable region of the SARS-CoV-2 S protein, and we provide a thorough characterization of the N439K RBM amino acid replacement, and the ability of this mutation to confer immune evasion without attenuating (or enhancing) fitness or disease. 2021 Cell Discussion SARS_CoV_2 N439K 152 157 S 91 92 33621484 Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. To date, we know of only one example of published immune escape documented for Y453F, but more examples may arise as this new mutation is investigated further. 2021 Cell Discussion SARS_CoV_2 Y453F 79 84 33628442 Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. Overall, our study shows that the D614G mutation on the S protein does not impact SARS-CoV-2 neutralisation by the host antibody response, nor confer viral resistance against the humoral immunity. 2021 Clinical & translational immunology Discussion SARS_CoV_2 D614G 34 39 S 56 57 33628442 Human neutralising antibodies elicited by SARS-CoV-2 non-D614G variants offer cross-protection against the SARS-CoV-2 D614G variant. Recent studies have also demonstrated an overall equivalent sensitivity against both the D614 and G614 pseudotyped viruses, suggesting that the D614G mutation is not expected to hinder current vaccine development. 2021 Clinical & translational immunology Discussion SARS_CoV_2 D614G 144 149 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Although there are a few reported cases of reinfection, the possibility of co-infection by E484K adds a new factor to the complex interaction between immune response systems and SARS-CoV-2 Spike mutations. 2021 Virus research Discussion SARS_CoV_2 E484K 91 96 S 189 194 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Despite sharing the same variation, it is important to mention that 501Y.V2 harbors a different set of mutations than B.1.1.28 (E484K). 2021 Virus research Discussion SARS_CoV_2 E484K 128 133 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Finally, this is the first report of co-infection events caused by the simultaneous occurrence of B.1.1.28 (E484K) and other lineages. 2021 Virus research Discussion SARS_CoV_2 E484K 108 113 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Half of the genomes sequenced in our study belonged to the novel B.1.1.28 (E484K) lineage that recently emerged in Rio de Janeiro (clustered in C5). 2021 Virus research Discussion SARS_CoV_2 E484K 75 80 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Indeed, two recent studies confirmed re-infection cases in Brazil where the second infection was caused by the B.1.1.28 (E484K) lineage . 2021 Virus research Discussion SARS_CoV_2 E484K 121 126 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Interestingly, the E484K mutation appears to have arisen independently around the world, as demonstrated by sequences deposited in GISAID. 2021 Virus research Discussion SARS_CoV_2 E484K 19 24 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. No statistically significant difference was found in the CT values of VUI-NP13L when compared to the other clusters. 2021 Virus research Discussion SARS_CoV_2 P13L 75 79 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Over the course of the epidemic, we have observed a shift in the prevalence of lineages from B.1.1 (during the beginning of epidemic) to B.1.1.28 (E484K) given its rapid increase in frequency around the country. 2021 Virus research Discussion SARS_CoV_2 E484K 147 152 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Since the first report, two more mutations in orf1ab (U10667G > L3468V and C11824U > I3853I) emerged by the end of December. 2021 Virus research Discussion SARS_CoV_2 I3853I;L3468V 85;64 91;70 ORF1ab 46 52 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. The distinguished pattern in the intra-host frequencies of lineage-defining mutations from B.1.1.28 (E484K), B.1.1.248 and B.1.91 in both cases strongly support this findings. 2021 Virus research Discussion SARS_CoV_2 E484K 101 106 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. The P13L mutation also emerged in a cluster from India from stochastic events independent from the Brazilian lineage. 2021 Virus research Discussion SARS_CoV_2 P13L 4 8 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. The putative resistance-associated with E484K may play an important role in cases of co-infection as well as opening a new horizon to investigate changes in the severity of COVID-19 over the course of the infection. 2021 Virus research Discussion SARS_CoV_2 E484K 40 45 COVID-19 173 181 33631222 Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Whereas 501Y.V2 is distinguished by eight SNVs targeting Spike protein, the Brazilian lineage was initially described as having five mutations in the UTRs, orf8 and N besides the E484K in S. 2021 Virus research Discussion SARS_CoV_2 E484K 179 184 S;ORF8;N;S 57;156;165;188 62;160;166;189 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Alternatively, suppose viruses bearing S H655Y preferentially found infection in the recipient. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 41 46 S 39 40 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Although our sample size is small, the outgrowth of S H655Y with E S67S in all index cats, and the fixation of these variants in 2 of 3 contact cats, suggest that selection for one or both of these variants could have played a role in shaping genetic diversity recovered from contact cats. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y;S67S 54;67 59;71 E;S 65;52 66;53 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. As of 28 December, 2020, S H655Y has been detected in 1,070 human SARS-CoV-2 viruses across 18 different countries in sequences deposited in GISAID. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 27 32 S 25 26 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. At the time of writing, S H655Y was the 16th most common variant detected in Spike among publicly-available SARS-CoV-2 sequences. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 26 31 S;S 77;24 82;25 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Based on iSNV frequencies, S H655Y and E S67S appear to be in linkage with each other (see mirrored iSNV frequencies in cat 2 and cat 5 in Fig 3 in particular), however with short sequence reads and sequencing approaches relying on amplicon PCR, we cannot rigorously assess the extent of linkage disequilibrium between these variants. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y;S67S 29;41 34;45 E;S 39;27 40;28 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Because narrow transmission bottlenecks can result in the loss of even beneficial variants, the fact that S H655Y and E S67S failed to be transmitted in pair 2 does not exclude the possibility that these variants enhance viral fitness. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y;S67S 108;120 113;124 E;S 118;106 119;107 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Despite this, we observe the rapid outgrowth of S H655Y in all three index cats, suggesting that this site may be under positive selection in this system. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 50 55 S 48 49 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. E S67S has not been documented elsewhere. 2021 PLoS pathogens Discussion SARS_CoV_2 S67S 2 6 E 0 1 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. If S H655Y facilitates viral entry or replication in cats, viruses with this variant in linkage with E S67S might have been positively selected in all index cats. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y;S67S 5;103 10;107 E;S 101;3 102;4 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. If selection acts primarily within index hosts prior to transmission, S H655Y could have achieved a high enough frequency to be randomly drawn at the time of transmission. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 72 77 S 70 71 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. In spite of its location outside of the RBD, S H655Y has been shown to arise on the background of a vesicular stomatitis virus (VSV) pseudotyped virus expressing various SARS-CoV-2 spike variants and confer escape from multiple monoclonal human antibodies in cell culture. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 47 52 S;RBD;S 181;40;45 186;43;46 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Interestingly, S H655Y is not found in any of the 18 full-genome domestic cat, tiger, and lion SARS-CoV-2 sequences available on GISAID (S4 Fig). 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 17 22 S 15 16 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. It is possible S H655Y offers a similar advantage in human hosts and/or confers escape from some antibodies. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 17 22 S 15 16 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. It is unlikely S H655Y represents a site of antibody escape in these cats because they were specific pathogen-free and had undetectable IgG antibody titers against SARS-CoV-2 Spike and Nucleocapsid proteins on the day of infection. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 17 22 N;S;S 185;175;15 197;180;16 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. It may be that S H655Y arose on the genetic background of an existing S67S variant in envelope. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y;S67S 17;70 22;74 S 15 16 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Next, suppose that viruses bearing S H655Y are shed more efficiently from index animals. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 37 42 S 35 36 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Notably, S H655Y and E S67S are absent from contact cat 5 (pair 2), despite being detectable and even reaching consensus levels in the associated index animal. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y;S67S 11;23 16;27 E;S 21;9 22;10 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Our data alone cannot resolve the precise mechanisms by which SARS-CoV-2 diversity is reduced during transmission, but the trajectories of S H655Y and E S67S raise some interesting possibilities. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y;S67S 141;153 146;157 E;S 151;139 152;140 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Relatively little is known about the phenotypic impact of S H655Y in cats, humans, and other host species. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 60 65 S 58 59 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. S H655Y additionally persisted in vivo in rhesus macaques challenged with one of these stock viruses [BioProject PRJNA645906, experiment number SRX9287155]. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 2 7 S 0 1 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. S H655Y and E S67S were found at 0.85% and 0.34% in the stock, but were preferentially amplified in all three index cats and were detectable at intermediate frequencies at the first-day post-inoculation. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y;S67S 2;14 7;18 E;S 12;0 13;1 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. S H655Y has, however, been reported in a variety of other settings, including transmission studies in a hamster model, SARS-CoV-2 tissue culture experiments, and in a stock virus passaged on Vero E6 cells [BioProject PRJNA645906, experiment numbers SRX9287152 (p1), SRX9287151 (p2), SRX9287154 (p3a); BioProject PRJNA627977]. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 2 7 S 0 1 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Sequences containing S H655Y variant are found in two distinct European clusters, EU1 and EU2, suggesting it has arisen more than once (S5A Fig). 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 23 28 S 21 22 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. We did not do any experiments to elucidate the functional impact of this variant, but we speculate S H655Y could have improved Spike fusion efficiency and therefore host cell entry in cats. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 101 106 S;S 127;99 132;100 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. While S H655Y has not been found in mink and is not one of the defining B.1.1.7 mutations, another one of the defining B.1.1.7 mutations, Spike N501Y, has emerged independently in mouse models. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y;N501Y 8;144 13;149 S;S 138;6 143;7 33635912 Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. While these variants are lost during transmission in this pair, a variant in ORF1ab (Gly1756Gly), which was undetectable in index cat 2, became fixed in contact cat 5 following transmission. 2021 PLoS pathogens Discussion SARS_CoV_2 G1756G 85 95 ORF1ab 77 83 33662015 Genomic characterization and evolution of SARS-CoV-2 of a Canadian population. Among them, P1427I (ORF1b) and Y1464C (ORF1b) have been reported to be signature mutations in USA in comparison to ones in Asian and European continent. 2021 PloS one Discussion SARS_CoV_2 P1427I;Y1464C 12;31 18;37 33662015 Genomic characterization and evolution of SARS-CoV-2 of a Canadian population. In addition, replacement of Leucine with Serine at 84 position of ORF8 was found to have significant effect on the structure of the protein C-terminal which was possibly a phosphorylation target for the human Serine/Threonine kinases. 2021 PloS one Discussion SARS_CoV_2 L84S 28 62 ORF8 66 70 33662015 Genomic characterization and evolution of SARS-CoV-2 of a Canadian population. Interestingly, three substitutions: T8502C (ORF1a), T10506C (ORF1a), and C6071T (ORF1b) are only presented in viruses from this Canadian population but not in other populations in the world. 2021 PloS one Discussion SARS_CoV_2 C6071T;T10506C;T8502C 73;52;36 79;59;42 ORF1a;ORF1a 44;61 49;66 33662015 Genomic characterization and evolution of SARS-CoV-2 of a Canadian population. Over 50% of them changed coding sequences but only 3 mutations:P1427I (ORF1b), Y1464C (ORF1b), and Q57H (ORF3a), potentially affected the fitness of viruses. 2021 PloS one Discussion SARS_CoV_2 Q57H;Y1464C;P1427I 99;79;63 103;85;69 ORF3a 105 110 33662015 Genomic characterization and evolution of SARS-CoV-2 of a Canadian population. The binding may bring together the promoters of S1 and S2 units while D614G mutation possibly interrupts the interaction between the S1, and S2 units, blocking shedding of S1 from S2. 2021 PloS one Discussion SARS_CoV_2 D614G 70 75 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. As an example, recent studies with Vero E6 cell-derived SARS-CoV-2 with spike proteins containing some (E484K, N501Y, and D614G) or all of the South African mutations showed smaller 1.2 to 2.7-fold decreases in neutralization potency by BNT162b2 mRNA vaccine-elicited human immune sera. 2021 Nature medicine Discussion SARS_CoV_2 D614G;N501Y;E484K 122;111;104 127;116;109 S 72 77 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. However, several other highly neutralizing mAbs (e.g., COV2-2196, COV2-2381, COV2-3025, and S2E12) showed intact or only mildly diminished inhibitory activity against the suite of variant viruses we tested, possibly because they bind the RBM at sites other than the E484K residue (Table 1). 2021 Nature medicine Discussion SARS_CoV_2 E484K 266 271 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Indeed, similar findings with authentic SARS-CoV-2 viruses encoding E484K mutations were recently reported. 2021 Nature medicine Discussion SARS_CoV_2 E484K 68 73 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Moreover, they are consistent with studies showing loss of neutralization potency of human convalescent serum against VSV-SARS-CoV-2 chimeric virus variants containing the E484K mutation and selection of escape E484K mutants under serial passage of convalescent COVID-19 plasma. 2021 Nature medicine Discussion SARS_CoV_2 E484K;E484K 172;211 177;216 COVID-19 262 270 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Our results establishing the E484K substitution as a vulnerability for multiple neutralizing mAbs are consistent with deep mutational scanning or VSV-SARS-CoV-2-based neutralization escape screening campaigns. 2021 Nature medicine Discussion SARS_CoV_2 E484K 29 34 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Our studies with human sera from convalescent subjects and recipients of the BNT162b2 mRNA vaccine, and animal sera after immunization with a vaccine encoding a similar spike gene, demonstrate a lower potency of neutralization against E484K and N501Y-containing viruses (note: we did not perform studies with the single-mutation viruses, due to limited serum availability). 2021 Nature medicine Discussion SARS_CoV_2 E484K;N501Y 235;245 240;250 S 169 174 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Overall, our findings may have therapeutic implications, as immune plasma derived from individuals infected early during the pandemic might fail to protect patients infected with more recent isolates containing the E484K mutation. 2021 Nature medicine Discussion SARS_CoV_2 E484K 215 220 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Sequential infection and/or vaccination/infection studies in animals and analysis of vaccine efficacy in the setting of new variant infections ultimately will determine the impact of emerging SARS-CoV-2 lineages, especially those containing E484K mutations. 2021 Nature medicine Discussion SARS_CoV_2 E484K 241 246 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Some neutralizing mAbs targeting the base of the RBD or NTD showed reduced activity against the B.1.1.7 isolate, whereas others targeting the RBM or NTD failed to inhibit infection of Wash SA-B.1.351, Wash BR-B.1.1.248, or variants containing the E484K mutation. 2021 Nature medicine Discussion SARS_CoV_2 E484K 247 252 RBD 49 52 33664494 Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. When we compared neutralization of deep-sequenced confirmed p0 (Vero E6 cell-produced) and p1 (Vero-hACE2-TMPRSS2 cell-produced) K417N/E484K/N501Y/D614G viruses by immune serum from vaccinated animals or humans, or naturally infected humans in the same recipient Vero-hACE2-TMPRSS2 cells, the viruses produced in Vero E6 cells were neutralized more efficiently (2 to 3-fold, P < 0.05) than those propagated in Vero-hACE2-TMPRSS2 cells (Extended Data Fig 10). 2021 Nature medicine Discussion SARS_CoV_2 K417N;D614G;E484K;N501Y 129;147;135;141 134;152;140;146 33667349 Extremely potent human monoclonal antibodies from COVID-19 convalescent patients. Out of the 453 neutralizing antibodies that were tested and characterized, one antibody (J08) showed extremely high neutralization potency against both the WT SARS-CoV-2 virus isolated in Wuhan and emerging variants containing the D614G, E484K, and N501Y variants. 2021 Cell Discussion SARS_CoV_2 D614G;E484K;N501Y 231;238;249 236;243;254 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. As there are very few sequenced isolates carrying the D614G mutation but not the P323L mutation, or vice versa, there is not yet sufficient information to assess the individual impact of the mutations on genome replication fidelity or viral fitness. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;P323L 54;81 59;86 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. In this study, we show that viruses with the dominant 23403A>G (S D614G) and 14408C>T (RdRp P323L) mutations also have lower dN/dS ratios compared to those without these two mutations, particularly at the RdRp coding region and the Orf8 gene. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 C14408T;A23403G;D614G;P323L 77;54;66;92 85;62;71;97 ORF8;RdRP;RdRP;S 232;87;205;64 236;91;209;65 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. It is less clear how the D614G mutation in the S gene could affect the mutation rate; however, increased transmission across the population might lead to more permissive circumstances for novel mutations to arise. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 25 30 S 47 48 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. Less is known about its co-mutation in RdRp (P323L), however, it could be leading to altered mutational fidelity. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P323L 45 50 RdRP 39 43 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. On the other hand, as the pandemic progressed, S with the dominant D614G (23403A>G) mutation has become increasingly less tolerant to non-synonymous mutations. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;A23403G 67;74 72;82 S 47 48 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. One could speculate that RdRp with the P323L (14408C>T) mutation in the MT genomes has been relatively fit, and did not undergo significant changes in its dN/dS ratio over time. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P323L;C14408T 39;46 44;54 RdRP 25 29 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. One question that remains to be answered is whether the RdRp 14408C>T mutation has any effect on differential mutation rates observed between the S gene and the RdRp coding region of the two genotypes. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 C14408T 61 69 RdRP;RdRP;S 56;161;146 60;165;147 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. The double mutant D614G and P323L genotype significantly affects the evolution process, and mechanistic study of these mutations may lead to a clearer image of how and where future mutations might arise. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;P323L 18;28 23;33 33667722 Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations. The surface glycoprotein mutation D614G has been under spotlight since May 2020 and today it is widely accepted as causing a more transmissible form of SARS-CoV-2. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 34 39 S 4 24 33671631 Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants. In week 11, appeared a B.1 subgroup that carries the mutation G29734C and has been proposed to arise in Madrid (haplogroup A2a5c in ref.). 2021 Microorganisms Discussion SARS_CoV_2 G29734C 62 69 33671631 Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants. On the other hand, the frequency of the D614G mutation was low during the first two weeks but quickly became dominant, being over 80% for most of the studied period, again in contrast with the publicly available Spanish data (around 50%) and similar to other European countries. 2021 Microorganisms Discussion SARS_CoV_2 D614G 40 45 33672021 Molecular Epidemiological Investigation of a Nosocomial Cluster of C. auris: Evidence of Recent Emergence in Italy and Ease of Transmission during the COVID-19 Pandemic. All isolates characterized in this study showed a reduced susceptibility to voriconazole and were highly resistant to fluconazole, owing to the presence of missense mutations in the ERG11(K143R) and TAC1B(A640V) genetic loci, consistently with the recently reported association between high-level resistance to fluconazole and co-occurrence of these mutations. 2021 Journal of fungi (Basel, Switzerland) Discussion SARS_CoV_2 A640V;K143R 205;188 210;193 33672021 Molecular Epidemiological Investigation of a Nosocomial Cluster of C. auris: Evidence of Recent Emergence in Italy and Ease of Transmission during the COVID-19 Pandemic. auris genetic lineages, with the ERG11(Y132F or K143R) being primarily found within the South Asian clade. 2021 Journal of fungi (Basel, Switzerland) Discussion SARS_CoV_2 K143R;Y132F 48;39 53;44 33672021 Molecular Epidemiological Investigation of a Nosocomial Cluster of C. auris: Evidence of Recent Emergence in Italy and Ease of Transmission during the COVID-19 Pandemic. Different ERG11 hot-spot mutations (Y132F, K143R, and F126L or VF125AL) have been previously associated with different C. 2021 Journal of fungi (Basel, Switzerland) Discussion SARS_CoV_2 F126L;K143R;Y132F 54;43;36 59;48;41 33672021 Molecular Epidemiological Investigation of a Nosocomial Cluster of C. auris: Evidence of Recent Emergence in Italy and Ease of Transmission during the COVID-19 Pandemic. Interestingly, our findings underscored that a strong association between ERG11(K143R) and TAC1B(A640V) clearly subsists within the latter clade, corroborating the role of such mutations as lineage-specific resistance signatures. 2021 Journal of fungi (Basel, Switzerland) Discussion SARS_CoV_2 A640V;K143R 97;80 102;85 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Beside the amino acid substitutions occurred at SARS-CoV-2 nucleocapsid such as S194L, R203K and G204R in this study, Nucleocapsid RG103KR mutation was aforementioned as one genotype of current common variants in the global. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 G204R;R203K;S194L 97;87;80 102;92;85 N;N 59;118 71;130 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. In addition, Subclade 2C variants with the mutations Spike D614G, ORF3a Q57H, and Nucleocapsid S194L chiefly appeared in Asia area. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;Q57H;S194L 59;72;95 64;76;100 N;S;ORF3a 82;53;66 94;58;71 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Notably, Subclade 1C variants with the mutations ORF8 L84S and Helicase P504L was over 79% (842 out of 1072) within Clade 1. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 L84S;P504L 54;72 58;77 Helicase;ORF8 63;49 71;53 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Phylogenetic tree analysis highlighted that clade 2 with the amino acid change at Spike D614G was the most predominant and prevalent haplotype of SARS-CoV-2 variants since the first variant appeared in Germany lately on February. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 88 93 S 82 87 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Since Spike, ORF3a, and nsp2 were linked to virulence, infectivity, ion channel formation, and virus release, the mutations Spike D614G, ORF3a Q57H, and nsp2 T85I within Subclade 2B variants might alter the viral transmission and pathogenesis, which could correlate with the dominant spread of COVID-19 in USA. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;Q57H;T85I 130;143;158 135;147;162 S;S;ORF3a;ORF3a;Nsp2;Nsp2 6;124;13;137;24;153 11;129;18;142;28;157 COVID-19 294 302 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Subclade 2A identified based on distance and maximum-likelihood methods from NJ phylogeny that contains the haplotype Spike D614G, and Nucleocapsid R203K, G204R were more frequent in Europe, Asia, and Africa areas than Subclade 2B. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;G204R;R203K 124;155;148 129;160;153 N;S 135;118 147;123 33677109 The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread. Subclade 2B with the amino acid changes at nsp2 T85I, Spike D614G, and ORF3a Q57H was firstly reported on March 4, 2020 in United States of America, becoming the most frequent sub-haplogroup in the world (36.21%) and America (45.79%). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;Q57H;T85I 60;77;48 65;81;52 S;ORF3a;Nsp2 54;71;43 59;76;47 33688650 Ultrapotent miniproteins targeting the receptor-binding domain protect against SARS-CoV-2 infection and disease in mice. Based on the cryo-EM structure of the parent LCB1 binder in complex with SARS-CoV-2 RBD, only the N501Y mutation is expected to affect binding. 2021 bioRxiv Discussion SARS_CoV_2 N501Y 98 103 RBD 84 87 33688650 Ultrapotent miniproteins targeting the receptor-binding domain protect against SARS-CoV-2 infection and disease in mice. In comparison, LCB1v1.3 showed efficacy against historical (WA1/2020) and emerging (B.1.1.7 and E484K/N501Y/D614G) SARS-CoV-2 strains. 2021 bioRxiv Discussion SARS_CoV_2 E484K;D614G;N501Y 96;108;102 101;113;107 33688689 Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. A single case of the P.2 variant, which carries the E484K mutation, was detected in this study. 2021 medRxiv Discussion SARS_CoV_2 E484K 52 57 33688689 Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. At the time of this sampling, no instances of B.1.1.7, or independent N501Y mutations were detected in our sample population of 830, despite sporadic observations elsewhere in CA (approximately 3% [69/2423] of genomes reported in California during the January study period; accessed from GISAID Feb 24, 2021). 2021 medRxiv Discussion SARS_CoV_2 N501Y 70 75 33688689 Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco. In addition to the mutations associated with spike L452R in the West Coast variants, we observed, at lower frequencies, other mutations of interest, including those in spike at positions 677, and 681, both of which have been reported previously on their own, or in the case of 681, in the context of other mutations such as N501Y. 2021 medRxiv Discussion SARS_CoV_2 L452R;N501Y 51;324 56;329 S;S 45;168 50;173 33692211 SARS-CoV-2 rapidly adapts in aged BALB/c mice and induces typical pneumonia. In conclusion, the Q498H mutation in the RBD contributed to the different effects of WH-CD observed in older and younger mice. 2021 Journal of virology Discussion SARS_CoV_2 Q498H 19 24 RBD 41 44 33692211 SARS-CoV-2 rapidly adapts in aged BALB/c mice and induces typical pneumonia. Our WH-CD isolate acquired the mutations N74K and H655Y in the S protein after 4 in vitro passages, compared with the original SARS-CoV-2 isolate (WH-01). 2021 Journal of virology Discussion SARS_CoV_2 H655Y;N74K 50;41 55;45 S 63 64 33692211 SARS-CoV-2 rapidly adapts in aged BALB/c mice and induces typical pneumonia. The LG strain isolated from infected mice acquired the Q498H mutation in the RBD, which may have attributed to the mouse adaptation in a previous study. 2021 Journal of virology Discussion SARS_CoV_2 Q498H 55 60 RBD 77 80 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. D614G is a frequent and important mutation identified in global and Indian SARS-CoV-2 isolates. 2021 Computers in biology and medicine Discussion SARS_CoV_2 D614G 0 5 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. G14S mutation can influence the catalytic activity and folding rate of PLPro worldwide. 2021 Computers in biology and medicine Discussion SARS_CoV_2 G14S 0 4 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Genome variation analysis found a rare mutation, P1089V in the spike protein of Surat (GBRC275b) isolate, reflecting its clinical importance in COVID-19 patients. 2021 Computers in biology and medicine Discussion SARS_CoV_2 P1089V 49 55 COVID-19 144 152 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Interestingly, Surat (GBRC275b) and Gandhinagar (GBRC239) isolates have two unique mutations W6152R and N5928H in exonuclease, respectively. 2021 Computers in biology and medicine Discussion SARS_CoV_2 N5928H;W6152R 104;93 110;99 Exonuclease 114 125 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Our study also detected consecutive alterations of R203K and G204R in the viral nucleocapsid protein. 2021 Computers in biology and medicine Discussion SARS_CoV_2 G204R;R203K 61;51 66;56 N 80 92 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Our study found P2144S, A1812D, and S2015R mutations in PLPro affecting the structural characteristics of this enzyme in Kerala (IND/29) and Himachal Pradesh isolates. 2021 Computers in biology and medicine Discussion SARS_CoV_2 A1812D;P2144S;S2015R 24;16;36 30;22;42 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Our study revealed a phylogenetic discrepancy between two Kerala isolates as both isolates have typical mutations in spike (R407I/A930V; Nsp2: I671T/I476V), PLPro, RdRp, helicase, and Orf8. 2021 Computers in biology and medicine Discussion SARS_CoV_2 I671T;R407I;A930V;I476V 143;124;130;149 148;129;135;154 Helicase;S;Nsp2;ORF8;RdRP 170;117;137;184;164 178;122;141;188;168 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Some potential mutations (R407I, D614G, and F1089V) also identified in spike protein that can generate new antigenic variants to evade host immune surveillance. 2021 Computers in biology and medicine Discussion SARS_CoV_2 D614G;F1089V;R407I 33;44;26 38;50;31 S 71 76 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Spike-D614G, Nsp3-G251V, Nsp3: F106F, Nsp12b: P314L, ORF3a: Q57H, ORF8-L84S, N: RG203KR, and 5'UTR:241 were the most frequent mutations in global SARS-CoV-2 isolates similar to earlier analyses. 2021 Computers in biology and medicine Discussion SARS_CoV_2 F106F;P314L;Q57H;D614G;G251V;L84S 31;46;60;6;18;71 36;51;64;11;23;75 S;ORF3a;5'UTR;Nsp3;Nsp3;ORF8;N 0;53;93;13;25;66;77 5;58;98;17;29;70;78 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. Spike: A23403G and RdRp: C14408T identified as the dominant mutations in Gujarat isolate, which have shown to decrease patients at a frequency of 97.67-95.35%. 2021 Computers in biology and medicine Discussion SARS_CoV_2 A23403G;C14408T 7;25 14;32 S;RdRP 0;19 5;23 33705994 A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics. The P4715L mutation was located in a hydrophobic cleft of this protein providing the ability to hijack from remdesivir by the earlier work. 2021 Computers in biology and medicine Discussion SARS_CoV_2 P4715L 4 10 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. However, a thorough functional characterization of the impact of the Y453F RBD variant on immunity and ACE-2 interaction has so far not been conducted. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 Y453F 69 74 RBD 75 78 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. Recently, three new genetic mutations inducing residue changes in the RBD have been reported in Europe, that is, N439K, Y453F, and N501Y. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 N439K;N501Y;Y453F 113;131;120 118;136;125 RBD 70 73 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. The functional properties of the N501Y mutant variant are not yet established. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 N501Y 33 38 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. The N439K may make the virus more infectious because of an increased affinity toward ACE-2 and/or a reduced sensitivity to neutralizing antibodies. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 N439K 4 9 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. The N501Y mutant is a part of a novel strain, "Variant of Concern 202012/01"/B.1.1.7, that has accumulated 17 mutations:8 of them in the spike gene:and in some areas of England may account for most of the new cases at the time of writing. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 N501Y 4 9 S 137 142 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. The vast majority of these residue substitutions are located in the spike regions outside of the RBD with the D614G mutation being a common variant reported on all continents and which seems to be taking over likely because of selective advantages. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 D614G 110 115 S;RBD 68;97 73;100 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. The Y453F was first identified in Denmark in the summer of 2020 among farmed minks. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 Y453F 4 9 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. This follows in the line of the new UK discovered N501Y mutant that within a short time gained transmission dominance in many areas including London, where by mid-December represented more than 60% of the cases. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 N501Y 50 55 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. To further examine the possible inhibition differences between the two RBD variants, we used a traditional vaccine approach applying mice immunized with WT RBD or the full WT ectodomain spike and assessed the antibody titers and neutralization capacity of WT and Y453F RBD. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 Y453F 263 268 S;RBD;RBD;RBD 186;71;156;269 191;74;159;272 33716040 The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. When we challenged the RBD:ACE-2 interaction with COVID-19 convalescent sera from 141 qPCR-confirmed individuals that have been infected with the original SARS-CoV-2 variant, we found no reduction in the serum capacity to inhibit the binding of the Y453F variant to ACE-2. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 Y453F 249 254 RBD 23 26 COVID-19 50 58 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. Apart from A23403G, other significant SNPs which occur frequently include C3037T (Synonymous mutation) in NSP3 gene of ORF1ab and C14408T (P323L) in RdRp gene of ORF1ab in both global excluding India and Indian sequences. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 A23403G;C14408T;C3037T;P323L 11;130;74;139 18;137;80;144 ORF1ab;ORF1ab;Nsp3;RdRP 119;162;106;149 125;168;110;153 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. In addition to these mutation points, the most frequent (in more than 10% of virus population) and common mutation points between global excluding India and India are G11083T (L37F), T19557A (F506L), A19558G (S507G) and G25563T (Q57H) in NSP6, Exon and ORF3a respectively. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 A19558G;G11083T;G25563T;T19557A;F506L;L37F;Q57H;S507G 200;167;220;183;192;176;229;209 207;174;227;190;197;180;233;214 ORF3a;Exon;Nsp6 253;244;238 258;248;242 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. It is to be noted that these genomic coordinates have been identified as frequent mutation points in the literature as well, especially A23403G in virus genome that corresponds to D614G in Spike protein has been associated with enhancing viral replication in the upper respiratory tract, thereby increasing its susceptibility to neutralisation by antibodies. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 A23403G;D614G 136;180 143;185 S 189 194 33725111 Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. Similarly for India, the other most frequent mutation points are C6312A (T1198K), C13730T (A97V), C22506A (T315N) and C28311T (P13L) in NSP3, RdRp, Spike and ORF8 respectively. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 C13730T;C22506A;C28311T;C6312A;A97V;P13L;T1198K;T315N 82;98;118;65;91;127;73;107 89;105;125;71;95;131;79;112 S;Nsp3;ORF8;RdRP 148;136;158;142 153;140;162;146 33725432 Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. Neutralizing activity of the two mRNA vaccines against the B.1.351 variant has also been observed to be lower, by a factor of 8.6 (mRNA-1273 vaccine [Moderna]) or 6.5 (BNT-162b2 vaccine [Pfizer]) on pseudovirus neutralization assay, than activity against the D614G virus, whereas no difference was evident against the N510Y.V1 (B.1.1.7)-like mutant. 2021 The New England journal of medicine Discussion SARS_CoV_2 D614G;N510Y 259;318 264;323 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Data regarding level of SII and viral ability to mutate was consistent since both P.1 lineage and E484K variants were in general correlated with SII in a similar manner. 2021 Cureus Discussion SARS_CoV_2 E484K 98 103 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. However, at the best of our knowledge, this is the first attempt to correlate SII and emergence of E484K variants, including the new lineage P.1. 2021 Cureus Discussion SARS_CoV_2 E484K 99 104 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Indeed, other factors than SII may influence the emergence of new SARS-CoV-2 variants, in particular for the E484K mutations. 2021 Cureus Discussion SARS_CoV_2 E484K 109 114 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Specifically, E484K mutations seem particularly critical because its shifts the main site for interaction with the human membrane-attached angiotensin conversing enzyme-2 (ACE-2). 2021 Cureus Discussion SARS_CoV_2 E484K 14 19 Membrane 121 129 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. Three of these mutations - K4017T, E484K, and N501Y - are present in the receptor-binding domain, which is critical for ligand-receptor interaction, and were similar to the three mutations detected in the South African B1.351 lineage. 2021 Cureus Discussion SARS_CoV_2 E484K;K4017T;N501Y 35;27;46 40;33;51 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. While in Brazil, variants were mostly heterogeneous, reflecting a large number of independent acquisition events, E484K harboring mutations in detected in the state of Amazonas were mostly derived from a highly homogeneous P.1 lineage, possibly as a consequence of fewer multiple-mutation events possibly related to higher levels of SII. 2021 Cureus Discussion SARS_CoV_2 E484K 114 119 33728228 Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants. While the occurrence of P.1 and E484K variants were both positively correlated with SII in the state of Amazonas, neutral and negatively correlations were detected in Brazil. 2021 Cureus Discussion SARS_CoV_2 E484K 32 37 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. Furthermore, serial passage of virus in sub-neutralizing concentrations of immune plasma led to the emergence of the deletion of F140 and the creation of a new N-linked glycosylation sequon in the NTD together with the E484K RBD mutation. 2021 Cell Discussion SARS_CoV_2 E484K 219 224 RBD;N 225;160 228;161 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. Furthermore, since E484K appears to be such an important mutation with respect to antibody binding and neutralization, future studies may seek to define mAbs from individuals infected with E484K viruses to provide protection from these virus strains that are being pressured to emerge, we believe mainly through increased fitness imparted by the higher affinity of RBD for ACE2. 2021 Cell Discussion SARS_CoV_2 E484K;E484K 19;189 24;194 RBD 365 368 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. Interestingly, repeated use of plasma therapy in an immunocompromised individual led to the transient emergence of the N501Y mutation as well as the 69-70 deletion in the NTD, which is characteristic of B.1.1.7. 2021 Cell Discussion SARS_CoV_2 N501Y 119 124 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. Principal among these are N501Y found in all B.1.1.7, B.1.351, and P.1 lineages and E484K found in B.1.351 and P.1. 2021 Cell Discussion SARS_CoV_2 E484K;N501Y 84;26 89;31 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. The first theme involves the ACE2 interaction surface of the RBD: all share the N501Y mutation, while B.1.351 and P.1 share E484K and N501Y and both B.1.351 and P.1 have changes at 417, 417T in P.1 and 417N in B.1.351. 2021 Cell Discussion SARS_CoV_2 E484K;N501Y;N501Y 124;80;134 129;85;139 RBD 61 64 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. The possibility of escape from natural and vaccine-induced immunity has prompted a rush to understand the consequences of these changes and spurred a push to develop new vaccine constructs tailored to the variants, particularly incorporating the E484K mutation. 2021 Cell Discussion SARS_CoV_2 E484K 246 251 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. The widespread emergence of variant strains, particularly containing the E484K mutation, may make it prudent to develop mAbs to target the 484K change. 2021 Cell Discussion SARS_CoV_2 E484K 73 78 33730597 Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. These mutations increase the affinity of the RBD for ACE2 2.7-fold for B.1.1.7 and 19-fold for B.1.351, which is compatible with the observation that viruses carrying the E484K and N501Y mutations likely have increased transmissibility. 2021 Cell Discussion SARS_CoV_2 E484K;N501Y 171;181 176;186 RBD 45 48 33731300 Genetic modification to design a stable yeast-expressed recombinant SARS-CoV-2 receptor binding domain as a COVID-19 vaccine candidate. (2) Design: The C538A mutation was designed to prevent dimer formation via intermolecular disulfide bond bridging and to improve stability. 2021 Biochimica et biophysica acta. General subjects Discussion SARS_CoV_2 C538A 16 21 33731300 Genetic modification to design a stable yeast-expressed recombinant SARS-CoV-2 receptor binding domain as a COVID-19 vaccine candidate. Since it is unknown whether the C538A mutation may have a safety effect, it is important this is monitored in the clinical settings. 2021 Biochimica et biophysica acta. General subjects Discussion SARS_CoV_2 C538A 32 37 33731300 Genetic modification to design a stable yeast-expressed recombinant SARS-CoV-2 receptor binding domain as a COVID-19 vaccine candidate. The recently emerging SARS-CoV-2 South Africa variant (B.1.351) contains a concerning mutation, E484K, located in the RBM, which reduced the neutralizing ability of monoclonal antibodies and human convalescent sera raised against earlier SARS-CoV-2 variants and also negatively impacted the efficacy of several full-length S-protein vaccines. 2021 Biochimica et biophysica acta. General subjects Discussion SARS_CoV_2 E484K 96 101 S 323 324 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. All variants of 501Y.V2 harbor the E484K mutation, further supporting that this mutation can at least partially explain the observed decreased susceptibility to neutralization by convalescent sera. 2021 Cell Discussion SARS_CoV_2 E484K 35 40 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. Although H014 and P2C-1F11 neutralized all of the 501Y.V2 variants we tested in the present study, we previously showed that some other mutations in the RBD region lead to decreased neutralizing capability for P2C-1F11 (A475V) and H014 (A435S and Y508H). 2021 Cell Discussion SARS_CoV_2 Y508H;A435S;A475V 247;237;220 252;242;225 RBD 153 156 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. By contrast, the RBD binding surface with P2B-2F6, which cannot neutralize variants carrying the E484K mutation, includes only 14 residues. 2021 Cell Discussion SARS_CoV_2 E484K 97 102 RBD 17 20 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. Interestingly, our data from assays with convalescent sera indicate that the K417N mutation actually increases viral sensitivity to neutralization. 2021 Cell Discussion SARS_CoV_2 K417N 77 82 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. It is notable that residue 484 has mutated into a variety of different amino acids under pressure of SARS-CoV-2 convalescent sera (e.g., E484A, E484G, E448D, and E484K), and mutation at this site can cause immune resistance to different convalescent sera. 2021 Cell Discussion SARS_CoV_2 E448D;E484A;E484G;E484K 151;137;144;162 156;142;149;167 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. The K417N mutation increases the probability of conversion to the open conformation, thus enhancing the S protein's binding capacity for ACE2 and increasing viral infectivity. 2021 Cell Discussion SARS_CoV_2 K417N 4 9 S 104 105 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. The lethal variant is characterized by the superposition of two RBD mutations, Q493H and K417N, in the N501Y mutant background. 2021 Cell Discussion SARS_CoV_2 K417N;N501Y;Q493H 89;103;79 94;108;84 RBD 64 67 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. This enhanced adaptation to murine hosts is at least partially attributable to the occurrence of the N501Y mutation. 2021 Cell Discussion SARS_CoV_2 N501Y 101 106 33735608 SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. We found that multiple pseudotyped viruses harboring N501Y and K417N mutations (including 501Y.V2-2 and 501Y.V2-3) were significantly more infective toward HEK293T cells expressing murine ACE2 compared to the reference 614G variant. 2021 Cell Discussion SARS_CoV_2 K417N;N501Y 63;53 68;58 33737129 Genomic surveillance of SARS-CoV-2 in the Republic of Congo. All SARS-CoV-2 genomes carried the spike mutation D614G, which is associated with efficient replication ex vivo and transmission in vivo. 2021 International journal of infectious diseases Discussion SARS_CoV_2 D614G 50 55 S 35 40 33738124 SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity. As expected, the P323L change in the RNA-dependent RNA polymerase (RdRp), genetically linked to D614G, was also found in all our samples. 2021 Virus evolution Discussion SARS_CoV_2 D614G;P323L 96;17 101;22 RdRp;RdRP 37;67 65;71 33738124 SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity. In silico analysis showed that P323L may impact the protein secondary structure, leading to a reduction in its molecular flexibility. 2021 Virus evolution Discussion SARS_CoV_2 P323L 31 36 33738124 SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity. The spike (S) D614G mutation, found in all samples analyzed, has been associated with higher viral titers, suggesting increased viral infectivity. 2021 Virus evolution Discussion SARS_CoV_2 D614G 14 19 S;S 4;11 9;12 33738620 Clinical characteristics of SARS-CoV-2 by re-infection vs. reactivation: a case series from Iran. The amino acid change in the spike protein of the virus, D614G, has emerged early during the pandemic as the viruses harboring this mutation are now dominant in many places worldwide. 2021 European journal of clinical microbiology & infectious diseases Discussion SARS_CoV_2 D614G 57 62 S 29 34 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. Both V354F and V470A are also known to increase the entry of pseudoviruses into cells expressing ACE2. 2021 Zoological research Discussion SARS_CoV_2 V354F;V470A 5;15 10;20 33738989 Mutations in spike protein and allele variations in ACE2 impact targeted therapy strategies against SARS-CoV-2. Here, we found that SARS-CoV-2 with V354F or V470A substitutions of spike-S1 showed increased infectivity. 2021 Zoological research Discussion SARS_CoV_2 V354F;V470A 36;45 41;50 S 68 73 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. In conclusion, the start of the outbreak of SARS-CoV-2 in the Basel area was characterized by a dominant variant, B.1-C15324T, which we infer to have arisen in mid-February in our tri-national region. 2021 PLoS pathogens Discussion SARS_CoV_2 C15324T 118 125 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. In particular, the B.1-C15324T lineage variant dominated the early phase of the local spread causing approximately 70% of Basel cases. 2021 PLoS pathogens Discussion SARS_CoV_2 C15324T 23 30 33740028 SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. The Basel cluster virus variant 20A/C15324T was first detected in Europe on March 2nd in Switzerland and Germany simultaneously. 2021 PLoS pathogens Discussion SARS_CoV_2 C15324T 36 43 33743213 Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. variant, which contains an E484K mutation within the RBD region, was capable of significantly reducing neutralization potency of fully vaccinated individuals, in line with what has been suggested by deep mutational scanning. 2021 Cell Discussion SARS_CoV_2 E484K 27 32 RBD 53 56 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. Although the D614G mutation is increasingly reported in strains worldwide, we have found a novel mutation D830A (aspartic acid to alanine) in strains NIH-44905 and NIH-HAS001 of clade S. 2021 PloS one Discussion SARS_CoV_2 D614G;D830A 13;106 18;111 S 184 185 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. In vitro studies conducted by Li et al., involving pseudoviruses showed that the D614G mutation was responsible for increased infectivity. 2021 PloS one Discussion SARS_CoV_2 D614G 81 86 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. Moreover, experimental work by Hou et al., demonstrated that the D614G substitution enhances SARS-CoV-2 infectivity, competitive fitness, and transmission in primary human cells and animal models. 2021 PloS one Discussion SARS_CoV_2 D614G 65 70 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. Moreover, the D614G change was accompanied by three characteristic mutations: 241C>T, 3037C>T, and 14408C>T. 2021 PloS one Discussion SARS_CoV_2 C14408T;C241T;C3037T;D614G 99;78;86;14 107;84;93;19 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. Notably, we have found a D614G (aspartic acid to glycine) mutation in the envelope spike protein of indigenous strains (NIH-45090, NIH-45143, and NIH-45579). 2021 PloS one Discussion SARS_CoV_2 D614G 25 30 S 83 88 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. Since the detection and global spread of the G614 variant, a major concern has been on the impact of D614G mutation on the effectiveness of vaccines as most of the vaccines have been designed using the D614 virus (Lurie et al., 2020). 2021 PloS one Discussion SARS_CoV_2 D614G 101 106 33755704 Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. This concern has been addressed by the findings of Weissman et al., which showed that the variant with D614G mutation does not escape neutralization but rather is neutralized at a higher level by serum from vaccinated mice, non-human primates, and humans. 2021 PloS one Discussion SARS_CoV_2 D614G 103 108 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Despite of a total of 3895 mutational events observed in spike protein sequences, frequency of events and its occurrence is still low in total available sequences except for D641G. 2021 Heliyon Discussion SARS_CoV_2 D641G 174 179 S 57 62 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Distinctively, Indian isolates also did not displayed emergence of co-evolving mutations associated with mutant strain G25563T (ORF3a), C26735T (NSP14) and C18877T (M protein), which are observed globally. 2021 Heliyon Discussion SARS_CoV_2 C18877T;C26735T;G25563T 156;136;119 163;143;126 ORF3a 128 133 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. It was noted that D614G mutant strains in India increased rapidly during eight months of the pandemic and is present in more than 81% of the genome sequences reported from India. 2021 Heliyon Discussion SARS_CoV_2 D614G 18 23 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Notably, N439K mutant is reported to show increased affinity binding affinity with hACE2. 2021 Heliyon Discussion SARS_CoV_2 N439K 9 14 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Recently, the emergent UK variant strain named as VUI-202012/01 with defined as a set of 17 mutations, more significant N501Y was also observed and reported in India. 2021 Heliyon Discussion SARS_CoV_2 N501Y 120 125 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Single variant N439K at RBD region was observed in 0.52% (n = 293) of genomes. 2021 Heliyon Discussion SARS_CoV_2 N439K 15 20 RBD 24 27 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. The recent studies by Korber et al and WHO collaborating study in China demonstrated D614G strains are 10-fold more infectious than the original Wuhan-1 strain. 2021 Heliyon Discussion SARS_CoV_2 D614G 85 90 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. This led us to study the impact of observed N439K mutation within RBM region using computational docking and MD simulations approaches. 2021 Heliyon Discussion SARS_CoV_2 N439K 44 49 33758785 Pan-India novel coronavirus SARS-CoV-2 genomics and global diversity analysis in spike protein. Yet even in such states, the association with D614G could not be found. 2021 Heliyon Discussion SARS_CoV_2 D614G 46 51 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Although mutations in other parts of the genome could also contribute to this transmission phenotype, the N501Y substitution in the spike protein in particular appears to be a major determinant of efficient transmission. 2021 bioRxiv Discussion SARS_CoV_2 N501Y 106 111 S 132 137 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Combined with our data indicating that none except Delta69-70 and N501Y has a consistent phenotype, and some even show reduced fitness in our experimental results at certain timepoints, this suggests many if not all of the remaining mutations were not directly selected; these mutations probably occurred through drift mechanisms such as founder and hitchhiking effects, followed by maintenance via linkage to Delta69-70 and N501Y, or possibly via recombination, which occurs frequently during SARS-CoV-2 replication. 2021 bioRxiv Discussion SARS_CoV_2 N501Y;N501Y 66;425 71;430 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Fortunately, tests to date with N501Y substitution indicate minimal changes in susceptibility to in PRNT50 values suggesting little or no resistance to neutralization elicited by vaccines now in widespread use. 2021 bioRxiv Discussion SARS_CoV_2 N501Y 32 37 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. However, beginning in September, 2020, all 8 mutations, but especially N501Y (Extended Table 1 and. 2021 bioRxiv Discussion SARS_CoV_2 N501Y 71 76 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. However, the frequent co-occurrence of this deletion with N501Y suggests possible epistasis, which should be further examined. 2021 bioRxiv Discussion SARS_CoV_2 N501Y 58 63 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. Only the N501Y substitution and a deletion of codons 69-70 showed consistent fitness advantages for replication in the upper airway in the hamster model, with higher shedding in nasal secretions, as well as in primary human airway epithelial cells. 2021 bioRxiv Discussion SARS_CoV_2 N501Y 9 14 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. The first of these to appear in sequenced strains were the two deletions (69-70 and 145), followed by all of the substitutions except S982A by March, 2020 (Extended Data Table 1). 2021 bioRxiv Discussion SARS_CoV_2 S982A 134 139 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. The N501Y substitution alone had a phenotype similar to that of the combined 8 mutations, suggesting it is the major spike determinant driving increased transmission of the UK variant. 2021 bioRxiv Discussion SARS_CoV_2 N501Y 4 9 S 117 122 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. This finding corroborates our results indicating that this mutation has less impact on transmission potential than N501Y, as indicated by our in vivo and in vitro models. 2021 bioRxiv Discussion SARS_CoV_2 N501Y 115 120 33758836 The N501Y spike substitution enhances SARS-CoV-2 transmission. This substitution, also present in the South African and Brazilian variants, is likely a result of convergent evolution, suggesting that N501Y is a major adaptive spike mutation of current concern. 2021 bioRxiv Discussion SARS_CoV_2 N501Y 137 142 S 163 168 33758837 Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice. Consistent with previous studies that measured efficacy of mRNA-LNP vaccines for SARS-CoV-2 vaccines in mice, our monovalent SARS-CoV-2 vaccine elicited robust neutralizing antibody titers to the SARS-CoV-2 D614G variant. 2021 bioRxiv Discussion SARS_CoV_2 D614G 207 212 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. Although both SARS-CoV-2 RBD-NP and HexaPro-elicited sera robustly neutralize the B.1.1.7 S variant, which does not include the E484K substitution, neutralization of the B.1.351 variant was dampened, as was also the case with sera from individuals vaccinated twice with the Pfizer-BioNTech BNT162b2 mRNA. 2021 bioRxiv Discussion SARS_CoV_2 E484K 128 133 RBD;S 25;90 28;91 33758839 Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. The E484K mutation, however, leads to a ~5-fold reduction in neutralizing activity elicited by either RBD-NP or HexaPro in NHPs. 2021 bioRxiv Discussion SARS_CoV_2 E484K 4 9 RBD 102 105 33758853 Recombinant SARS-CoV-2 genomes are currently circulating at low levels. However, none of the seven other cdSNPs that differentiate these clades support recombination, suggesting C14805T is a homoplastic site. 2021 bioRxiv Discussion SARS_CoV_2 C14805T 106 113 33758853 Recombinant SARS-CoV-2 genomes are currently circulating at low levels. Over the last 4 months, clade 19 viruses have become progressively rarer while the D614G harboring clade 20 viruses have disproportionately driven waves of infection around the world. 2021 bioRxiv Discussion SARS_CoV_2 D614G 83 88 33758853 Recombinant SARS-CoV-2 genomes are currently circulating at low levels. Similarly, recent waves of infection driven by three clade 20 N501Y bearing lineages have further reduced our ability to detect recombinant genomes. 2021 bioRxiv Discussion SARS_CoV_2 N501Y 62 67 33758853 Recombinant SARS-CoV-2 genomes are currently circulating at low levels. The only site that does not strictly follow the pattern of vertical descent is C14805T, which occurs in both clades 19A-4 and 19B-4. 2021 bioRxiv Discussion SARS_CoV_2 C14805T 79 86 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. However, recent expansion of B.1.526, a lineage also featuring E484K but without N501Y in New York City, suggests that this fitness loss may be overcome by other, yet uncharacterized, changes in the virus as well. 2021 medRxiv Discussion SARS_CoV_2 E484K;N501Y 63;81 68;86 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. In contrast, introduction of E484K reduced the affinity by 4-fold which may explain why virus variants carrying only the E484K mutation have rarely spread efficiently, although viruses carrying E484K have been detected since the fall of 2020 in a handful of patients receiving care at the Mount Sinai Health System and have also been reported in immunocompromised patients. 2021 medRxiv Discussion SARS_CoV_2 E484K;E484K;E484K 29;121;194 34;126;199 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. In fact, the B.1.351 RBD, which carries N501Y and E484K (as well as N417K) showed binding to hACE2 that was similar to wild type RBD. 2021 medRxiv Discussion SARS_CoV_2 E484K;N417K;N501Y 50;68;40 55;73;45 RBD;RBD 21;129 24;132 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. Interestingly, binding of convalescent sera to the N501Y RBD was also increased, suggesting that changes that increase affinity for the receptor may also increase affinity of a set of antibodies that may mimic the receptor. 2021 medRxiv Discussion SARS_CoV_2 N501Y 51 56 RBD 57 60 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. Interestingly, N501Y increased the affinity by five-fold. 2021 medRxiv Discussion SARS_CoV_2 N501Y 15 20 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. It is tempting to speculate that the N501Y mutation enables the acquisition of E484K without a fitness loss. 2021 medRxiv Discussion SARS_CoV_2 E484K;N501Y 79;37 84;42 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. Our data indicate that reduction in binding to the E484K and B.1.351 variant RBDs was minor (often only 2-fold) compared to reported reduction in neutralization (which ranges from 6-8 fold to complete loss of neutralization). 2021 medRxiv Discussion SARS_CoV_2 E484K 51 56 RBD 77 81 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. Recently, B.1.1.7 variant strains carrying E484K, in addition to N501Y, have been isolated in the UK, providing evidence for the hypothesis that N501Y enables acquisition of mutations in the RBD that may be detrimental to receptor binding. 2021 medRxiv Discussion SARS_CoV_2 E484K;N501Y;N501Y 43;65;145 48;70;150 RBD 191 194 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. The reduced affinity of the E484K variant RBD for hACE2 could render the virus more susceptible to RBD binding mAbs. 2021 medRxiv Discussion SARS_CoV_2 E484K 28 33 RBD;RBD 42;99 45;102 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. These observations may explain why a reduction in neutralization against the viral variant of concern B.1.17 is seen in some studies despite the fact the N501Y substitution in the RBD of this variant does not significantly impact binding and neutralizing activity. 2021 medRxiv Discussion SARS_CoV_2 N501Y 154 159 RBD 180 183 33758878 The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies and targets both the NTD and the RBD. We also noted that the two neutralizing antibodies against the RBD showed some reduced binding to a mutant RBD carrying the E484K mutation while having similar or even increased neutralizing potency against a variant virus carrying the E484K mutation as the only change in its RBD. 2021 medRxiv Discussion SARS_CoV_2 E484K;E484K 124;236 129;241 RBD;RBD;RBD 63;107;277 66;110;280 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. In designing this assay, we took advantage of the fact that the N501Y mutation is common to the three major SARS-CoV-2 variants of concern. 2021 medRxiv Discussion SARS_CoV_2 N501Y 64 69 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. Thus, this assay has the potential for relatively inexpensive high throughput testing for rapid identification of N501Y variants. 2021 medRxiv Discussion SARS_CoV_2 N501Y 114 119 33758892 A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. Thus, we expect that our assay should continue to be able to identify N501Y variants even if additional mutations develop near this primary mutation once the specific Tm signatures of each new genotype are characterized. 2021 medRxiv Discussion SARS_CoV_2 N501Y 70 75 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. An alternative (but not mutually exclusive) possibility is that the additional mutations in B.1.427/B.1.429, especially the W152C and S13I mutations in the spike protein, may contribute to increased infectivity of the variant relative to lineages carrying the L452R mutation alone. 2021 medRxiv Discussion SARS_CoV_2 L452R;S13I;W152C 260;134;124 265;138;129 S 156 161 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Given our findings of increased infectivity of L452R pseudoviruses, it is unclear why surges in L452R-carrying lineages have not occurred earlier. 2021 medRxiv Discussion SARS_CoV_2 L452R;L452R 47;96 52;101 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. However, given that L452 is positioned in a hydrophobic patch of the spike RBD, it is plausible that the L452R mutation causes structural changes in the region that promote the interaction between the spike protein and its ACE2 receptor. 2021 medRxiv Discussion SARS_CoV_2 L452R 105 110 S;S;RBD 69;201;75 74;206;78 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. In the current study, we describe the spread of a novel B.1.427/B.1.429 variant in California carrying a characteristic triad of spike protein mutations (S13I, W152C, and L452R) that is predicted to have emerged in May 2020 and increased in frequency from 0% to >50% of sequenced cases from September 2020 to January 2021. 2021 medRxiv Discussion SARS_CoV_2 L452R;W152C;S13I 171;160;154 176;165;158 S 129 134 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Indeed, a reduction in neutralization associated with the L452R mutation has been reported following vaccination, although the observed decrease in neutralizing antibody titers was similar at 2.9-fold. 2021 medRxiv Discussion SARS_CoV_2 L452R 58 63 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Indeed, in the current study we observed smaller but statistically significant increases in infection of 293T cell and lung organoids by pseudoviruses carrying W152C. 2021 medRxiv Discussion SARS_CoV_2 W152C 160 165 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Notably, our findings reveal that the infectivity of L452R pseudoviruses was higher than D614G, but slightly reduced compared to that of N501Y pseudoviruses in 293T cells and human airway lung organoids. 2021 medRxiv Discussion SARS_CoV_2 D614G;L452R;N501Y 89;53;137 94;58;142 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Of note, a >4-fold decrease in neutralizing antibody titers in convalescent plasma suggest that immune selection pressure from a previously exposed population may be partly driving the emergence of L452R variants. 2021 medRxiv Discussion SARS_CoV_2 L452R 198 203 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Our findings of enhanced infection of 293T cells and lung organoids by pseudoviruses carrying L452R confirm these early predictions. 2021 medRxiv Discussion SARS_CoV_2 L452R 94 99 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Our neutralization findings are consistent with a prior report showing decreased binding of L452R-carrying pseudoviruses by antibodies from previously infected COVID-19 patients and escape from neutralization in 3 of 4 convalescent plasma samples. 2021 medRxiv Discussion SARS_CoV_2 L452R 92 97 COVID-19 160 168 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Prior studies have suggested that the L452R mutation may stabilize the interaction between the spike protein and its human ACE2 receptor and thereby increase infectivity. 2021 medRxiv Discussion SARS_CoV_2 L452R 38 43 S 95 100 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. The L452R mutation in the B.1.427/B.1.429 variant has been observed previously in rare, mostly singleton cases, first reported from Denmark on March 17, 2020, and also reported from multiple US states and the UK prior to September 1, 2020. 2021 medRxiv Discussion SARS_CoV_2 L452R 4 9 33758899 Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Thus, whether the L452R-carrying B.1.427/B.1.429 will continue to remain the predominant circulating strain in California, or whether it will eventually be replaced by the N501Y-carrying B.1.1.7 variant remains unclear. 2021 medRxiv Discussion SARS_CoV_2 L452R;N501Y 18;172 23;177 33760807 SARS-CoV-2 variants reveal features critical for replication in primary human cells. Furthermore, recent SARS-CoV-2 reverse genetics studies have also linked the single D614G substitution to increased infectivity and virus replication in primary human cells as well as in vivo models. 2021 PLoS biology Discussion SARS_CoV_2 D614G 84 89 33760807 SARS-CoV-2 variants reveal features critical for replication in primary human cells. Mechanistically, the D614G substitution appears to permit a more open ACE2-binding conformation of the S trimer, which may lead to increased virus fusion with host cell membranes. 2021 PLoS biology Discussion SARS_CoV_2 D614G 21 26 Membrane;S 169;103 178;104 33760807 SARS-CoV-2 variants reveal features critical for replication in primary human cells. Nevertheless, the Orf3a Q57H variant was acquired shortly after introduction into humans and is not found in early SARS-CoV-2 sequences or in related bat coronaviruses, potentially suggesting positive selection of this residue similar to S D614G. 2021 PLoS biology Discussion SARS_CoV_2 D614G;Q57H 240;24 245;28 ORF3a;S 18;238 23;239 33760807 SARS-CoV-2 variants reveal features critical for replication in primary human cells. Notably, the mutation leading to the Orf3a Q57H variant also changes the sequence of 2 other putative (and poorly characterized) overlapping reading frame products, Orf3c and Orf3d. 2021 PLoS biology Discussion SARS_CoV_2 Q57H 43 47 ORF3a 37 42 33760807 SARS-CoV-2 variants reveal features critical for replication in primary human cells. Recent structural studies have revealed that Q57 forms the major hydrophilic constriction in the SARS-CoV-2 Orf3a pore; however, the Q57H substitution does not appear to influence Orf3a channel activities. 2021 PLoS biology Discussion SARS_CoV_2 Q57H 133 137 ORF3a;ORF3a 108;180 113;185 33760807 SARS-CoV-2 variants reveal features critical for replication in primary human cells. Secondly, we uncovered an association between naturally occurring Orf3a (Q57H) and nsp2 (T85I) variants, and a cell-specific replication phenotype: SARS-CoV-2 isolates unique in harboring these variants replicated poorly in Vero-CCL81 cells, while maintaining efficient replicative capacity in primary human BEpCs. 2021 PLoS biology Discussion SARS_CoV_2 Q57H;T85I 73;89 77;93 ORF3a;Nsp2 66;83 71;87 33760807 SARS-CoV-2 variants reveal features critical for replication in primary human cells. Together with our results from naturally occurring SARS-CoV-2 isolates, these common findings using different experimental systems provide a clear basis to understand the rapid emergence and population-wide spread of the S D614G substitution. 2021 PLoS biology Discussion SARS_CoV_2 D614G 223 228 S 221 222 33760807 SARS-CoV-2 variants reveal features critical for replication in primary human cells. While Vero-CCL81 cells are clearly not a physiological substrate for SARS-CoV-2, it may be that the cell-specific replication capacities that we observe with isolates expressing Orf3a (Q57H) and nsp2 (T85I) variants also occurs in other, non-respiratory, cell types of the human body, potentially impacting disease pathogenesis. 2021 PLoS biology Discussion SARS_CoV_2 Q57H;T85I 185;201 189;205 ORF3a;Nsp2 178;195 183;199 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Also, mutation Asn479Gln located in the middle part of the receptor-binding motif of the spike protein, leading to a decrease in the binding free energy at this point in SARS-CoV-2 compared with SARS-CoV. 2021 Scientific reports Discussion SARS_CoV_2 N479Q 15 24 S 89 94 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Mutation Thr487Asn could explain the increment of the H-bond in region 334-339 in SARS-CoV-2 compared with SARS-CoV. 2021 Scientific reports Discussion SARS_CoV_2 T487N 9 18 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Mutations Thr487Asn could also be considered as a reason for increasing of the interaction number as well as interface area in region 327-353 of ACE2 when interacting with SARS-CoV-2 compared with SARS-CoV. 2021 Scientific reports Discussion SARS_CoV_2 T487N 10 19 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Ortega and colleagues also reported that mutation Thr487Asn may result in increasing binding affinity of SARS-CoV-2 with its cognate receptor. 2021 Scientific reports Discussion SARS_CoV_2 T487N 50 59 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Other mutations including Pro462Ala and Leu472Phe are located almost at the beginning and end of the loop region (residues 475-486). 2021 Scientific reports Discussion SARS_CoV_2 L472F;P462A 40;26 49;35 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Therefore, mutations Thr487Asn, Pro462Ala, Leu472Phe, and Asn479Gln could be considered as hotspot points in RBD of SARS-CoV2 and play an important role in the interaction of the virus with the two ends of the N-terminal domains of ACE2, leading to higher affinity of SARS-CoV-2 spike protein to its receptor compared with SARS-CoV. 2021 Scientific reports Discussion SARS_CoV_2 N479Q;L472F;P462A;T487N 58;43;32;21 67;52;41;30 S;RBD;N 279;109;210 284;112;211 33767306 In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. These mutations (Tyr442Leu, Leu443Phe, Pro462Ala, Leu472Phe, Asn479Gln and Thr487Asn) interact with Lys31 and Lys353 of ACE2 that were previously introduced as hotspot points in the spike-ACE2 interaction. 2021 Scientific reports Discussion SARS_CoV_2 N479Q;L443F;L472F;P462A;T487N;Y442L 61;28;50;39;75;17 70;37;59;48;84;26 S 182 187 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. Consistent with this, Abs (such as mAb 20) have modest IC50 and exhibit cross reactivity against SARS-CoV-2 with A520S and H49Y spike mutations. 2021 JCI insight Discussion SARS_CoV_2 A520S;H49Y 113;123 118;127 S 128 133 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. found that the D614G and the RBD A520S spike variant increased infectivity of pseudotyped viruses. 2021 JCI insight Discussion SARS_CoV_2 A520S;D614G 33;15 38;20 S;RBD 39;29 44;32 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. found that the D614G mutation increased virus infectivity, competitive fitness, and transmission in primary human cells and in animal models. 2021 JCI insight Discussion SARS_CoV_2 D614G 15 20 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. Our results indicate that D614G and A520S variants are more resistant to neutralizing Abs than viruses with the Wuhan Hu-1 spike, suggesting that immunity elicited against the Wuhan Hu-1 (the prevalent strain in Michigan at the time of sample collection) might fuel escape variants. 2021 JCI insight Discussion SARS_CoV_2 A520S;D614G 36;26 41;31 S 123 128 33769311 IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity. suggested a causal link between D614G variants and increased fatality in patients with COVID-19. 2021 JCI insight Discussion SARS_CoV_2 D614G 32 37 COVID-19 87 95 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. In 2020, the SARS-CoV-2 spike protein variant D614 G which replaced the original strains identified, was found to be associated with increased transmissibility and more serious pathology. 2021 Journal of virological methods Discussion SARS_CoV_2 D614G 46 52 S 24 29 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. In the other 63 samples (35 of them the N510Y variant), the correlation between the novel VD RT-PCR method and the sequencing method was complete. 2021 Journal of virological methods Discussion SARS_CoV_2 N510Y 40 45 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. N501Y variant was present in almost 30 % of these samples. 2021 Journal of virological methods Discussion SARS_CoV_2 N501Y 0 5 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. No differences in the presence of the N501Y variant were found in terms gender or mean age. 2021 Journal of virological methods Discussion SARS_CoV_2 N501Y 38 43 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. Recently, the newly identified SARS-CoV-2 variants B.1.1.7, B1.351, and B.1.1.28.1 have come under scrutiny because they can increase transmissibility and reduce neutralization.All of these variants share the spike protein mutation N501Y, which is involved in virus binding, and is principally found in mutations associated with virus transmission (; Virological, 2021). 2021 Journal of virological methods Discussion SARS_CoV_2 N501Y 232 237 S 209 214 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. Since the presence of these variants in our locality only began in early January, these results suggest that the N501Y variant can now replace circulating wild-type strains very early. 2021 Journal of virological methods Discussion SARS_CoV_2 N501Y 113 118 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. The eleven samples analyzed by NGS confirmed that the N501Y variant found was most similar to strain B.1.1.7. 2021 Journal of virological methods Discussion SARS_CoV_2 N501Y 54 59 33774075 A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants. The method developed in this work to identify N501Y SARS-CoV-2 variants is fast and simple, and can be performed in any basic laboratory in less than one hour. 2021 Journal of virological methods Discussion SARS_CoV_2 N501Y 46 51 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Analysis of the interaction energies between the S-protein and neutralizing antibodies show that the efficiency of neutralizing activity of the D614G variant is dependent on the neutralizing antibody. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 144 149 S 49 50 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. In another study, the D614G variant was more susceptible to neutralization by RBD monoclonal antibodies and convalescent sera from individuals infected with the virus. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 22 27 RBD 78 81 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. In summary, our results show that the D614G S-protein adopts a distinct conformational dynamics, which is skewed towards the open-state conformation more than the wild-type conformation. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 38 43 S 44 45 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. In this study, we used molecular dynamics simulation to explore the structural conformation of the wild-type and the D614G S-proteins of SARS-CoV-2 and provide a plausible description of the impact the mutation has on the molecular features of interaction with neutralization antibodies. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 117 122 S 123 124 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Our data also shows that there is an allosteric effect to the RBD structural conformation as a result of the D614G mutation. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 109 114 RBD 62 65 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. SARS-CoV-2 neutralizing assay data from Chile demonstrated that some samples from individuals exposed to the virus showed enhanced or decreased neutralizing activity against the D614G variant compared to the wild-type. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 178 183 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Several studies have reported that there is a similar neutralizing potency of the wild-type and D614G variant when treated with convalescent sera of individuals exposed to the virus. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 96 101 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The D614G S-protein interacted with the CB6 antibody better than the wild-type. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 4 9 S 10 11 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The D614G variant emerged around late January to mid-February 2020 and within 1 month, emerged as the dominant circulating strain in Europe and its environs. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 4 9 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The residue-specific variations in amino acid flexibility and domain-specific RMSD support our claim that the mutation of aspartate to glycine at position 614 in the CTD affects the conformational dynamics of the RBD. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 122 158 RBD 213 216 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The results of this study data show that the D614G S-protein adopts a conformation that is skewed towards the open-state conformation more than the wild-type conformation. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 45 50 S 51 52 33774178 Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. The results of this study have shed insights into the behaviour of the D614G S-protein at the molecular level and provided a glimpse of the neutralization mechanism of this variant. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 71 76 S 77 78 33778179 Mutational analysis of structural proteins of SARS-CoV-2. Also D614G mutation in the S protein resulted in a myristoylation site. 2021 Heliyon Discussion SARS_CoV_2 D614G 5 10 S 27 28 33778179 Mutational analysis of structural proteins of SARS-CoV-2. Both the variants carry N501Y mutation lying in the RBD region of S protein. 2021 Heliyon Discussion SARS_CoV_2 N501Y 24 29 RBD;S 52;66 55;67 33778179 Mutational analysis of structural proteins of SARS-CoV-2. In addition E8L mutation in the E protein resulted in a PKC site at 6-8 aa position. 2021 Heliyon Discussion SARS_CoV_2 E8L 12 15 E 32 33 33778179 Mutational analysis of structural proteins of SARS-CoV-2. The results also depicted the elimination of this intramolecular interaction on D614G mutation. 2021 Heliyon Discussion SARS_CoV_2 D614G 80 85 33778179 Mutational analysis of structural proteins of SARS-CoV-2. The widespread mutation D614G lies at the inner side at the S1-S2 junction of S protein and don't lead to any change on epitopes or surface structure of S protein and hence may not get impacted by vaccines. 2021 Heliyon Discussion SARS_CoV_2 D614G 24 29 S;S 78;153 79;154 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. A recent study has suggested that differences in ACE2 expression across different geographic regions may be a driving force for the positive selection of the D614G in the viral S protein. 2021 Gene reports Discussion SARS_CoV_2 D614G 158 163 S 177 178 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Also, our results support previous studies showing that the D614G variant can significantly enhance the viral infectivity and transmission compared to its D614 form. 2021 Gene reports Discussion SARS_CoV_2 D614G 60 65 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Although the D614G confers the viral infectivity and transmissibility, its effect on disease severity remains unclear because other mutations often co-occur. 2021 Gene reports Discussion SARS_CoV_2 D614G 13 18 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Among frequent mutations observed in the S protein, a non-synonymous mutation, V483A, which increases the binding with ACE2 receptor, was mainly identified in the viral genomes isolated from North Americans. 2021 Gene reports Discussion SARS_CoV_2 V483A 79 84 S 41 42 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Deficiency of the inhibitor facilitates entry of virus carrying the D614G into host cells. 2021 Gene reports Discussion SARS_CoV_2 D614G 68 73 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Furthermore, a recent study has suggested that the prevalent D614G and combined with other mutations such as L5F, V341I, K458R, I472V, D936Y, and S943T are more infectious. 2021 Gene reports Discussion SARS_CoV_2 D614G;D936Y;I472V;K458R;L5F;S943T;V341I 61;135;128;121;109;146;114 66;140;133;126;112;151;119 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. However, it has been shown that mutations in other viral genes of SARS-CoV-2 evolve along with the D614G. 2021 Gene reports Discussion SARS_CoV_2 D614G 99 104 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. In addition to the D614G mutation occurring in the S protein, structural and multi-omics studies revealed that D7611G in S protein, T265I in Nsp2, S1920P in Nsp3, L3605F in Nsp6, co-occurring P5731L and Y5768C in Nsp13 may play crucial roles in modulating the efficiency of the viral entry into host cells and its pathogenesis. 2021 Gene reports Discussion SARS_CoV_2 D614G;D7611G;L3605F;P5731L;S1920P;T265I;Y5768C 19;111;163;192;147;132;203 24;117;169;198;153;137;209 Nsp13;Nsp2;Nsp3;Nsp6;S;S 213;141;157;173;51;121 218;145;161;177;52;122 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. In Korea, SARS-CoV-2 strains with D614G have also become the most dominant form as of September 2020. 2021 Gene reports Discussion SARS_CoV_2 D614G 34 39 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. In this regard, further research is needed to clarify our understanding of the evolutionary mechanism of the SARS-CoV-2 D614G variant and the vaccine efficacy against the variant, which is rapidly spreading worldwide. 2021 Gene reports Discussion SARS_CoV_2 D614G 120 125 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. In this study, we used a PCR-based sequencing method to rapidly detect the 6 mutational hotspots in the S protein of SARS-CoV-2 isolates from different geographic origins, showing that there was only the D614G mutation in the samples. 2021 Gene reports Discussion SARS_CoV_2 D614G 204 209 S 104 105 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Interestingly, a recent study has revealed that the D614G makes a neutrophil elastase cleavage site increasing the viral spread in high alpha1-antitrypsin-deficient individuals. 2021 Gene reports Discussion SARS_CoV_2 D614G 52 57 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Interestingly, the study has also revealed that ACE2 expression is higher in Asians than in North Americans and Europeans, suggesting an association of the D614G with increased transmission of SARS-CoV-2 in specific populations with lower ACE2 expression. 2021 Gene reports Discussion SARS_CoV_2 D614G 156 161 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. More recently, analysis of prevalent clades by continents revealed that the clade GH (carrying 241C>T in 5' untranslated region, 3037C>T in nonstructural protein 3 (Nsp3), P314L in Nsp12b, Q57H in open reading frame 3a (Orf3a), and D614G in S protein) was most predominant in North America, followed by G (carrying 241C>T, 3037C>T, P314L, and D614G) and GR (carrying 241C>T, 3037C>T, P314L, RG203KR in N, and D614G). 2021 Gene reports Discussion SARS_CoV_2 C241T;C241T;C241T;C3037T;C3037T;C3037T;D614G;D614G;D614G;P314L;P314L;P314L;Q57H 95;315;367;129;323;375;232;343;409;172;332;384;189 101;321;373;136;330;382;237;348;414;177;337;389;193 ORF3a;Nsp3;N;S 220;165;402;241 225;169;403;242 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Moreover, the D614G showed the highest host entry activity among mutations such as V367F, G476S, V483A, and H49Y that frequently occur in the S protein. 2021 Gene reports Discussion SARS_CoV_2 D614G;G476S;H49Y;V367F;V483A 14;90;108;83;97 19;95;112;88;102 S 142 143 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Notable, the structure of the receptor-binding domain (RDB) in the S protein of SARS-CoV-2 carrying the D614G has more open conformations such as a two-open conformation and an all-open state, which may increase the efficiency of ACE2 binding and fusion. 2021 Gene reports Discussion SARS_CoV_2 D614G 104 109 S 67 68 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Our analysis of the publicly available sequences also supports recent studies showing that the D614G began in Europe and has spread to Asia through North America and Oceania. 2021 Gene reports Discussion SARS_CoV_2 D614G 95 100 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Our sequencing results showed a trend similar to the frequency of the rapidly increasing D614G mutation until September 30, 2020. 2021 Gene reports Discussion SARS_CoV_2 D614G 89 94 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. P1327L, Y1364C, and S2540F mutations in Orf1b protein involved in the viral RNA replication and processing have been also identified in strains from North America, suggesting that the viral replication processes have favorably evolved in North American populations. 2021 Gene reports Discussion SARS_CoV_2 S2540F;Y1364C;P1327L 20;8;0 26;14;6 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Positive selection resulting from the D614G in the S protein is closely related to the adaptive evolution of SARS-CoV-2. 2021 Gene reports Discussion SARS_CoV_2 D614G 38 43 S 51 52 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. The D614G increases cell entry with enhanced human receptor angiotensin-converting enzyme-2 (ACE2)-binding affinity, and the D614G-mediated cell entry is also highly dependent on transmembrane serine protease2 (TMPRSS2). 2021 Gene reports Discussion SARS_CoV_2 D614G;D614G 4;125 9;130 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. The D614G is frequently accompanied by a silent mutation 3037C>T and a missense mutation 14408C>T that causes P323L in viral RdRp in mild and severely affected patients. 2021 Gene reports Discussion SARS_CoV_2 C14408T;C3037T;D614G;P323L 89;57;4;110 97;64;9;115 RdRP 125 129 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. The effect of SARS-CoV-2 carrying the D614G on the viral transmission and vaccine effectiveness targeting the variant clinically remains unclear. 2021 Gene reports Discussion SARS_CoV_2 D614G 38 43 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. The predominance of the D614G across the globe suggests that the mutation enhances human-to-human transmission by conferring a replication advantage to SARS-CoV-2. 2021 Gene reports Discussion SARS_CoV_2 D614G 24 29 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Therefore, further studies are needed to elucidate the association of COVID-19 severity with the D614G mutation among human populations. 2021 Gene reports Discussion SARS_CoV_2 D614G 97 102 COVID-19 70 78 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Therefore, the virus carrying the D614G is more likely to infect and spread in North America and Europe than in East Asia, supporting the results in our study. 2021 Gene reports Discussion SARS_CoV_2 D614G 34 39 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. These results suggest that co-occurrence of D614G with other mutations may contribute to the adaptive evolution of SARS-CoV-2 under the current COVID-19 pandemic. 2021 Gene reports Discussion SARS_CoV_2 D614G 44 49 COVID-19 144 152 33778182 Comparative analysis of mutational hotspots in the spike protein of SARS-CoV-2 isolates from different geographic origins. Together with the sequencing results, geographical analysis of 113,381 sequences available from the public repositories as of September 30, 2020, showed that the D614G is the most prevalent form worldwide including North America, Europe, Asia, and South Korea, supporting previously reported studies. 2021 Gene reports Discussion SARS_CoV_2 D614G 162 167 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. For both Clusters 3 and 4, such damaging non-synonymous signature SNPs are F506L and S507C in Exon while Clusters 2 and 3 do not exhibit any such behaviour due to the absence of non-synonymous signature SNPs. 2021 Virus research Discussion SARS_CoV_2 F506L;S507C 75;85 80;90 Exon 94 98 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. From the consensus of both PROVEAN and PolyPhen-2, it can be seen from Table 6 that out of 16 unique non-synonymous signature SNPs, 5 are predicted to be deleterious or damaging, out of which T85I, Q57H and R203M are in NSP2, ORF3a and Nucleocapsid respectively for Cluster 1. 2021 Virus research Discussion SARS_CoV_2 Q57H;R203M;T85I 198;207;192 202;212;196 N;ORF3a;Nsp2 236;226;220 248;231;224 33781798 Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism. It is to be noted that although some mutations are neutral, their stability can decrease like D614G in Spike protein. 2021 Virus research Discussion SARS_CoV_2 D614G 94 99 S 103 108 33791702 Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2. B.1.1.7 entry in HeLa ACE2 cells, which express high levels of receptor, exceeded that of Wu-Hu-1 but was lower than Wu-Hu-1 D614G. 2021 bioRxiv Discussion SARS_CoV_2 D614G 125 130 33791702 Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2. By contrast, Wu-Hu-1 D614G and B.1.1.7 infection of HEK 293T cells were indistinguishable, both being ~10 fold greater than Wu-Hu-1. 2021 bioRxiv Discussion SARS_CoV_2 D614G 21 26 33791702 Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2. Our experiments demonstrate that the activity of B.1.1.7 spike is altered relative to both Wu-Hu-1 (representative of wave-one SARS-CoV-2) and Wu-Hu-1 D614G (representative of the previously dominant strain). 2021 bioRxiv Discussion SARS_CoV_2 D614G 151 156 S 57 62 33791702 Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2. Therefore, our data suggest that the D614G mutation represents adaptation to host and permits infection of poorly permissive cell types. 2021 bioRxiv Discussion SARS_CoV_2 D614G 37 42 33791702 Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2. Thus far, studies have focussed on the contribution made by RBD mutations, and with good reason; N501Y and E484K have been implicated in increased ACE2 affinity and escape from anti-RBD responses. 2021 bioRxiv Discussion SARS_CoV_2 E484K;N501Y 107;97 112;102 RBD;RBD 60;182 63;185 33791722 SARS-CoV-2 genome sequencing from COVID-19 in Ecuadorian patients: a whole country analysis. An example is A23403G mutation (D614G amino acid change) which was present in 95.79% of sequences from this study. 2021 medRxiv Discussion SARS_CoV_2 A23403G;D614G 14;32 21;37 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. A889V can change the compactness of the proteins since it showed a notably altered Rg during the MD simulation.There is a chance that these altered binding positions, RMSF, Rg, and RMSD can make the virus resistant against GRL0617. 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 A889V 0 5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. A889V occurred due to the most common C T transition; plausibly this mutation first appeared in the protein, and then V843F took place due to ROS. 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 V843F;A889V 120;0 125;5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. According to the clinical histories, V843F did not raise pathogenesis in the patients. 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 V843F 37 42 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. Although GRL0617-bound mutant PLPros showed similar RMSD at 50 ns, V843F + A889V double mutant demonstrated a slightly higher value at the end. 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 A889V;V843F 75;67 80;72 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. Amino acid substitution in V843F and G1691C took place due to G T transversion that was possibly introduced by Oxo-guanine generated from reactive oxygen species (ROS). 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 G1691C;V843F 37;27 43;32 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. Especially, V121D and V843F positions are highly conserved in the protein, and G1691C might reduce the essential flexibility of NSP-3 (Table 2). 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 G1691C;V121D;V843F 79;12;22 85;17;27 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. Here, V843F and A889V mutations were present in the PLPro domain of the NSP-3 protein. 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 A889V;V843F 16;6 21;11 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. However, the most frequent mutation V843F led to reduced binding affinity towards the ubiquitin-binding subsite 1 of SARS-CoV-2 PLPro. 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 V843F 36 41 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. In SARS-CoV-2 NIB-1, A889V substitution protected the protease from the damage of V843F. 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 A889V;V843F 21;82 26;87 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. Mutant A889V, V843F + A889V, and wild-type PLPro did not show any differences when docked against ISG-15. 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 A889V;A889V;V843F 7;22;14 12;27;19 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. SARS-CoV-2 NIB-1 has V121D and L122I amino acid substitutions in the NSP-1. 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 L122I;V121D 31;21 36;26 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. The novel mutations V121D, V843F, and G1691C occurred in SARS-CoV-2 NIB-1 isolate due to transversion substitutions that have the potentials to destabilize or alter the protein structure and functions (Table 2). 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 G1691C;V121D;V843F 38;20;27 44;25;32 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. Therefore, V121D and L122I mutations along with 93rd C T in 5' UTR did not change the pathogenicity of SARS-CoV-2 significantly. 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 L122I;V121D 21;11 26;16 5'UTR 62 68 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. Therefore, V843F can be assumed as a detrimental and destabilizing transversion mutation that reduced the degradation of ISG-15. 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 V843F 11 16 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. Through computational analysis, we have observed that V121D and L122I mutants might destabilize the structure of NSP-1 (Table 2 & Supplementary 2) yet with these two mutations, the virus caused mild fever, cough, and throat congestion in a young female patient. 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 L122I;V121D 64;54 69;59 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. V843F and A889V single mutants and V843F + A889V double mutant changed the binding site of GRL0617. 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 A889V;A889V;V843F;V843F 10;43;35;0 15;48;40;5 33797663 Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. V843F mutation can reduce this process and allow the host cells to halt viral replications. 2021 Journal, genetic engineering & biotechnology Discussion SARS_CoV_2 V843F 0 5 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Although the NSP13: P505L and NSP13: Y541C variants were identified in Cluster 3, mainly in the United States, Australia, and Canada, the fatality rate of Cluster 3 showed no statistical significance compared with Cluster 1 and Cluster 2. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P505L;Y541C 20;37 25;42 Nsp13;Nsp13 13;30 18;35 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. As the branches of a viral phylogenetic tree can explain viral dynamics across the globe, we found that strains containing p.5828P > L and p.5865Y > C (NSP13: P504L and NSP13: Y541C) were responsible for the phylogenetic branches. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P504L;Y541C 159;176 164;181 Nsp13;Nsp13 152;169 157;174 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. As Velazquez-Salinas's study identified that residue 5865 (NSP13: Y541C) was under directional selection, which is also shown by the datamonkey evolutionary server, the variants (NSP13: P504L and NSP13: Y541C) may be under experimenting positive selection. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P504L;Y541C;Y541C 186;66;203 191;71;208 Nsp13;Nsp13;Nsp13 59;179;196 64;184;201 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Haplotype mapping and phylogenetic tree analysis showed that amino acid variations in ORF1ab (p.5828P > L and p.5865Y > C, NSP13: P504L and NSP13: Y541C) were important characteristics of this clade. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P504L;Y541C 130;147 135;152 ORF1ab;Nsp13;Nsp13 86;123;140 92;128;145 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. However, outcomes in hosts infected with strains containing whether ORF1ab variations (NSP13: P504L and NSP13: Y541C) or not in the same States were missing, making it difficult to directly build the correlation between them. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P504L;Y541C 94;111 99;116 ORF1ab;Nsp13;Nsp13 68;87;104 74;92;109 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. However, we found that for mortality rate in Washington State was high, with 69.05% of strains containing ORF1ab variants (NSP13: P504L and NSP13: Y541C), whereas other states (e.g., Minnesota, Utah, Wisconsin, and California) that only contained a small proportion of strains with the ORF1ab variants, showed better disease outcomes. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P504L;Y541C 130;147 135;152 ORF1ab;ORF1ab;Nsp13;Nsp13 106;286;123;140 112;292;128;145 33798758 Molecular epidemiology analysis of early variants of SARS-CoV-2 reveals the potential impact of mutations P504L and Y541C (NSP13) in the clinical COVID-19 outcomes. Studies on mutation analysis of SARS-CoV-2 showed that NSP13: Y541C and NSP13: P504L were the top mutations in sequenced SARS-CoV-2 genomes, which were consistent with the NSP13 variants identified by our study. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P504L;Y541C 79;62 84;67 Nsp13;Nsp13;Nsp13 55;72;172 60;77;177 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. Although the Moderna COVID-19 vaccine (mRNA 1273) could be effective against the N501Y mutation, additional mutations in the South African variant (501Y.V2), Indian and Australian variants are likely to influence its S protein affinity to the host receptor and evading neutralization. 2021 Viruses Discussion SARS_CoV_2 N501Y 81 86 S 217 218 COVID-19 21 29 33803400 Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. on reduced sensitivity of the RT-PCR diagnostic assay owing to a single mutation (Q289H) in the forward N gene primer. 2021 Viruses Discussion SARS_CoV_2 Q289H 82 87 N 104 105 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. Among the 501Y.V2 genomes collected after 1 December 2020, the L18F substrain constitutes 41% genomes (127 out of 309), according to GISAID as of 12 February 2021). 2021 Viruses Discussion SARS_CoV_2 L18F 63 67 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. and McCallum et al., together with the increase of L18F variants in 501Y.V2, P.1, and VOC strains, suggests that the replicative advantage of L18F mutants can be partly associated with their ability to infect seroprevalent individuals, and thus depend on the fraction of seroprevalent individuals in given territory. 2021 Viruses Discussion SARS_CoV_2 L18F;L18F 51;142 55;146 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. As the global spread of the VOC strain is very likely, it is important to monitor mutations of this strain, with particular attention to mutations interfering with immune response including the fast spreading NTD mutation L18F, and RBM mutations E484K, F490S, and S494P that may decrease the efficacy of currently available vaccines. 2021 Viruses Discussion SARS_CoV_2 E484K;F490S;L18F;S494P 246;253;222;264 251;258;226;269 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. Based on GISAID data in England we estimated its replicative advantage over other non-VOC D614G English strains as 1.24 [95% CI: 1.22-1.27]. 2021 Viruses Discussion SARS_CoV_2 D614G 90 95 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. By systematic analysis of the propagation of VOC substrains we found that substrain(s) conferring L18F substitution is/are the most abundant and rapidly growing VOC substrain(s). 2021 Viruses Discussion SARS_CoV_2 L18F 98 102 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. Importantly, the L18F mutation has also expanded in the South African strain 501Y.V2 defined by three spike mutations K417N, E484K, N501Y (thus sharing with the VOC strain spike mutation N501Y). 2021 Viruses Discussion SARS_CoV_2 E484K;K417N;L18F;N501Y;N501Y 125;118;17;132;187 130;123;21;137;192 S;S 102;172 107;177 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. In addition to double deletion 69-70HV, substitution N501Y in the RBD of spike is considered the most important VOC mutation. 2021 Viruses Discussion SARS_CoV_2 N501Y 53 58 S;RBD 73;66 78;69 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. In Brazil, in strain P.1 defined by three spike mutations K417T, E484K, N501Y (differing from the South African strain 501Y.V2 by substitution K417T instead of K417N), mutation L18F has been found in 93% of genomes (69 out of 74) collected after 1 December 2020. 2021 Viruses Discussion SARS_CoV_2 E484K;K417N;K417T;K417T;L18F;N501Y 65;160;58;143;177;72 70;165;63;148;181;77 S 42 47 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. showed that L18F substitution compromises binding of neutralizing antibodies. 2021 Viruses Discussion SARS_CoV_2 L18F 12 16 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. shows that an African variant L18F, D80A, D215G, K417N, E484K, N501Y, D614G, A701V propagates much faster than a variant without L18F mutation in the presence of plasma antibodies collected from donors infected in the first wave of epidemic in South Africa (June-August 2020). 2021 Viruses Discussion SARS_CoV_2 A701V;D215G;D614G;D80A;E484K;K417N;L18F;L18F;N501Y 77;42;70;36;56;49;30;129;63 82;47;75;40;61;54;34;133;68 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. Substitution D614G in spike protein (first GISAID reported genome, EPI_ISL_913915, was collected on 2 January 2020, in Mexico) initiated a strain with replicative advantage over D614 strains estimated based on data from England as 1.42 [95% CI: 1.38-1.45]. 2021 Viruses Discussion SARS_CoV_2 D614G 13 18 S 22 27 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The 20A.EU1 strain, a substrain of D614G that harbors A222V mutation in spike, emerged in Spain in early summer, 2020, spread over Europe, becoming the dominating strain (more than half of sequenced genomes) in several countries (Spain, England, Scotland, Wales, Ireland and Italy) in November, 2020, but was nearly absent outside of Europe. 2021 Viruses Discussion SARS_CoV_2 A222V;D614G 54;35 59;40 S 72 77 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The D614G strain has spread worldwide nearly reaching fixation; it was present in more than 99% of genomes collected worldwide in January 2021. 2021 Viruses Discussion SARS_CoV_2 D614G 4 9 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The data collected in the five-week period of 7 December 2020-17 January 2021, in England suggest a replicative advantage of the L18F substrain in relation to the remaining VOC strains. 2021 Viruses Discussion SARS_CoV_2 L18F 129 133 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The replicative advantage of 501Y.V2 strains supports the conjecture that mutation N501Y increases infectiousness of SARS-CoV-2 by increasing the affinity of spike RBD to the angiotensin-converting enzyme 2 (ACE2). 2021 Viruses Discussion SARS_CoV_2 N501Y 83 88 S;RBD 158;164 163;167 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. The strain P.1, found in Brazil, that shares with VOC RBM mutation N501Y, caused recently the second (higher) wave of deaths in Manaus despite high seroprevalence of the population. 2021 Viruses Discussion SARS_CoV_2 N501Y 67 72 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. This data suggests a replicative advantage of L18F substrains within the VOC, 501Y.V2, and P.1 strains, in, respectively, England, South Africa, and Brazil. 2021 Viruses Discussion SARS_CoV_2 L18F 46 50 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. This replicative advantage of the VOC L18F substrain must be considered with caution until the mechanism promoting faster spread of strains containing L18F substitution is elucidated. 2021 Viruses Discussion SARS_CoV_2 L18F;L18F 38;151 42;155 33804556 SARS-CoV-2 Variant of Concern 202012/01 Has about Twofold Replicative Advantage and Acquires Concerning Mutations. With respect to L18F, an in vitro study by Cele et al. 2021 Viruses Discussion SARS_CoV_2 L18F 16 20 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. However, some laboratories have established a workflow including N501Y-specific PCR for all SARS-CoV-2 positive cases:this allowed us to monitor the increase in prevalence across tested samples in these individual laboratories. 2021 Microorganisms Discussion SARS_CoV_2 N501Y 65 70 33806013 SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. In order to efficiently select samples for subsequent sequencing, we have implemented a N501Y-specific PCR in many laboratories throughout Switzerland. 2021 Microorganisms Discussion SARS_CoV_2 N501Y 88 93 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. In line with several previous studies, genetic analysis of SARS-CoV-2 in Jordan showed the shift into B lineage, harboring the spike D614G amino acid substitution, with all sequences collected in Jordan harboring this substitution from July 2020 onwards. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D614G 133 138 S 127 132 33807556 Molecular Analysis of SARS-CoV-2 Genetic Lineages in Jordan: Tracking the Introduction and Spread of COVID-19 UK Variant of Concern at a Country Level. This proposed change in virus behavior can be related to enhanced binding between the spike glycoprotein of this lineage and its receptor; and this enhancement has been proposed to be the result of N501Y amino acid substitution. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 N501Y 198 203 S 86 104 33810168 Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa. Following the introduction of the Dutch variant into Cape Town, the virus further diversified with the acquisition of an additional mutation 5209A>G before causing a large outbreak in a supermarket (supermarkets were among the few essential services allowed to continue operating during lockdown level 5 in South Africa). 2021 Viruses Discussion SARS_CoV_2 A5209G 141 148 33810168 Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa. For Tygerberg_31, the most likely route of transmission was from China to Australia, then from Australia to the United States (defined by the 17247T>C mutation), and then onward to Cape Town. 2021 Viruses Discussion SARS_CoV_2 T17247C 142 150 33810168 Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa. The Dutch variant is defined by the common mutation 24862A>G relative to the Wuhan reference strain. 2021 Viruses Discussion SARS_CoV_2 A24862G 52 60 33810168 Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa. The reconstruction suggests transmission of a Spanish variant (20268A>G) to the U.K. 2021 Viruses Discussion SARS_CoV_2 A20268G 63 71 33810168 Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa. The Tygerberg_06 (lineage B.40) and Tygerberg_31 (lineage B.39) genotypes share two common mutations (26144G>T and 14805C>T) in relation to the Wuhan-Hu-1 reference stain. 2021 Viruses Discussion SARS_CoV_2 C14805T;G26144T 115;102 123;110 33810168 Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa. This variant, with a rare mutation 5209A>G, has been observed only in the supermarket outbreak in Cape Town. 2021 Viruses Discussion SARS_CoV_2 A5209G 35 42 33810168 Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa. Two mutations, 8782T>C and 28144C>T, define this lineage (, accessed 21 March 2021). 2021 Viruses Discussion SARS_CoV_2 C28144T;T8782C 27;15 35;22 33810168 Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa. variant (defined by the common mutation 10097G>A). 2021 Viruses Discussion SARS_CoV_2 G10097A 40 48 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. Another mutation, C14408T with a frequency of 96.83%, is present in the Orf1b gene encoding RNA-directed RNA polymerase (RDRP) non-structural protein (nsp12) with a p-value of 0.1440 in deceased versus recovered patients from Gujarat, while also being observed to be statistically significant in the global dataset with a p-value of 8.28E-05 with a frequency of 88.77%. 2021 Frontiers in genetics Discussion SARS_CoV_2 C14408T 18 25 Nsp12;RdRP 151;121 156;125 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. Moreover, C28854T is forming a distinct sub-cluster under 20A (A2a as per the old classification of the next strain) clade, highlighted in Figure 8. 2021 Frontiers in genetics Discussion SARS_CoV_2 C28854T 10 17 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. Mutation in the N gene at C28854T and mutation in the Orf3a gene at G25563T were found to be dominant among deceased patients from Gujarat. 2021 Frontiers in genetics Discussion SARS_CoV_2 C28854T;G25563T 26;68 33;75 ORF3a;N 54;16 59;17 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. Similarly, a comparison analysis of the global (n = 79,518), India (n = 1,821), and Gujarat datasets (n = 502), where the "n" is the number of genomes included in the analysis, indicates the overall dominance of C241T, C3037T, A23403G, C14408T, and G25563T. 2021 Frontiers in genetics Discussion SARS_CoV_2 A23403G;C14408T;C241T;C3037T;G25563T 227;236;212;219;249 234;243;217;225;256 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. The analysis of the dataset from the global deceased (n = 276) and recovered patients (n = 1,845) with known status from the metadata information available on the GISAID server with the complete genome sequences considered in the analysis indicates the dominance of the missense mutations at A23403G, C14408T, C1059T, and G25563T. 2021 Frontiers in genetics Discussion SARS_CoV_2 A23403G;C1059T;C14408T;G25563T 292;310;301;322 299;316;308;329 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. The dominant mutations in the deceased patients represented by the change in A23403G were observed at a frequency of 98.41% in the Gujarat genomes (p-value of 0.1640) and 74.28% in the global genomes with known patient status (p-value of 0.5223). 2021 Frontiers in genetics Discussion SARS_CoV_2 A23403G 77 84 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. The exclusive dominant mutations present in the population of Gujarat were G25563T and C28854T in the Orf3a and N genes, respectively. 2021 Frontiers in genetics Discussion SARS_CoV_2 C28854T;G25563T 87;75 94;82 ORF3a;N 102;112 107;113 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. The predicted SIFT score of the mutation G25563T in the Orf3a and C28854T in the N gene was classified to be deleterious in nature. 2021 Frontiers in genetics Discussion SARS_CoV_2 C28854T;G25563T 66;41 73;48 ORF3a;N 56;81 61;82 33815459 Genomic Variations in SARS-CoV-2 Genomes From Gujarat: Underlying Role of Variants in Disease Epidemiology. While in the case of mutation at position C28311T leading to change of amino acid proline to leucine, the enzyme lies in the N gene that has a role in virion assembly and release and plays a significant role in the formation of replication-transcription complexes. 2021 Frontiers in genetics Discussion SARS_CoV_2 C28311T 42 49 N 125 126 33821267 Ultrapotent bispecific antibodies neutralize emerging SARS-CoV-2 variants. Crucially, a potent bispecific antibody was efficacious against SARS-CoV-2 carrying the key variant mutation E484K in the hamster model. 2021 bioRxiv Discussion SARS_CoV_2 E484K 109 114 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. However, the infectivity of the T323I mutant was more sensitive to freeze-thawing than that of viruses pseudotyped with the wild-type S glycoprotein. 2021 bioRxiv Discussion SARS_CoV_2 T323I 32 37 S 134 148 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. However, we noted that the infectivity of the C15F mutant virus was compromised after freeze-thawing more than that of the wild-type virus. 2021 bioRxiv Discussion SARS_CoV_2 C15F 46 50 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. Of note, some of the expressed S glycoproteins formed a disulfide bond between Cys 131 and Cys 136, and therefore lacked two of the canonical disulfide bonds (Cys 15-Cys 136 and Cys 131-Cys 166) in the N-terminal domain. 2021 bioRxiv Discussion SARS_CoV_2 C131C;C15C 178;159 189;169 S;N 31;202 46;203 33821278 Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein. On the other hand, even though the S1170F change altered post-translational modification of the S2 glycoprotein, this mutant exhibited wild-type levels of infectivity and resistance to freeze-thawing. 2021 bioRxiv Discussion SARS_CoV_2 S1170F 35 41 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. found no support for a selective advantage of any of the variants they tested, including D614G. 2021 medRxiv Discussion SARS_CoV_2 D614G 89 94 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. Our analyses all point to very strong but heterogeneous selective advantages for the D614G and B.1.17 variants at the country level, even allowing for both migration and drift. 2021 medRxiv Discussion SARS_CoV_2 D614G 85 90 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. Several studies using other methods have similarly found D614G and B.1.1.7 to each have a selective advantage over other variants circulating contemporaneously. 2021 medRxiv Discussion SARS_CoV_2 D614G 57 62 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. Third, the UK has put effort into developing a representative sample of SARS-CoV-2 genomes in their country and the estimates for the selection effects in the UK for D614G and B.1.1.7 are very close and slightly above the population average for these lineages. 2021 medRxiv Discussion SARS_CoV_2 D614G 166 171 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. This means that the estimates of a fitness advantage of B.1.1.7 in many countries is relative to a background that consists mostly of D614G. 2021 medRxiv Discussion SARS_CoV_2 D614G 134 139 33821289 Estimating the strength of selection for new SARS-CoV-2 variants. Thus, the fitness of B.1.1.7 exceeds that of D614G, which itself exceeds the original genotype. 2021 medRxiv Discussion SARS_CoV_2 D614G 45 50 33834012 Comparison of Clinical Features and Outcomes of Medically Attended COVID-19 and Influenza Patients in a Defined Population in the 2020 Respiratory Virus Season. Adaptive mutations in SARS-COV-2 have also been reported, and the most important mutation in spike is D614G, which has attracted global attention. 2021 Frontiers in public health Discussion SARS_CoV_2 D614G 102 107 S 93 98 33834012 Comparison of Clinical Features and Outcomes of Medically Attended COVID-19 and Influenza Patients in a Defined Population in the 2020 Respiratory Virus Season. The D614G mutant began to spread in Europe in early February 2020 and became the mainstream strain worldwide by May 2020, accounting for nearly 70% of samples in Europe and North America. 2021 Frontiers in public health Discussion SARS_CoV_2 D614G 4 9 33834012 Comparison of Clinical Features and Outcomes of Medically Attended COVID-19 and Influenza Patients in a Defined Population in the 2020 Respiratory Virus Season. The N439K variants can maintain fitness but can evade the antibody-mediated immunity, it is unclear what the S477N mutation will bring to the vaccines and epidemics. 2021 Frontiers in public health Discussion SARS_CoV_2 N439K;S477N 4;109 9;114 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. Additionally, with the revealed mechanism underlying the K417N mutation, it is possible to design more efficacious antibody cocktails to treat COVID-19 patients infected with variant 501Y.V2 as well as the recently discovered variant P.1 in Brazil. 2022 Journal of medicinal chemistry Discussion SARS_CoV_2 K417N 57 62 COVID-19 143 151 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. Although it is counterintuitive to learn that the K417N mutation actually decreases the RBD's binding affinity with ACE2 by 1.48 kcal/mol, it is in fact beneficial for RBD to escape human antibody CB6 by dramatically reducing the binding affinity by 9.59 kcal/mol. 2022 Journal of medicinal chemistry Discussion SARS_CoV_2 K417N 50 55 RBD;RBD 88;168 91;171 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. Before the E484K mutation, E484 forms a hydrogen bond with F490 (Figure S5), which attaches the loop (residues 477-486) to the remainder of the RBD. 2022 Journal of medicinal chemistry Discussion SARS_CoV_2 E484K 11 16 RBD 144 147 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. In the South Africa variant (501Y.V2), actually there are two more mutations, N501Y and E484K. 2022 Journal of medicinal chemistry Discussion SARS_CoV_2 E484K;N501Y 88;78 93;83 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. Interestingly, the virus with the K417N mutation seems to sacrifice its binding affinity for ACE2 to survive the attack of the antibodies. 2022 Journal of medicinal chemistry Discussion SARS_CoV_2 K417N 34 39 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. More dramatically, the K417N mutation allows the variant to escape from many human antibodies other than CB6 by removing a salt bridge buried in the RBD-antibody interface. 2022 Journal of medicinal chemistry Discussion SARS_CoV_2 K417N 23 28 RBD 149 152 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. Therefore, the gain from the improved RBD-ACE2 binding that resulted from both N501Y and E484K mutations might be enough to compensate for the loss caused by the K417N mutation and is likely to yield an interaction with ACE2 even stronger than that of the wild-type virus. 2022 Journal of medicinal chemistry Discussion SARS_CoV_2 E484K;K417N;N501Y 89;162;79 94;167;84 RBD 38 41 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. Thus, the K417N mutation can weaken the binding of the RBD with CB6 much more than with ACE2. 2022 Journal of medicinal chemistry Discussion SARS_CoV_2 K417N 10 15 RBD 55 58 33834772 Insights into SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival. To explore their contributions, we carried out MD simulation for the RBD-ACE2 complex with all three mutations (K417N, N501Y, and E484K), as shown in Figure 5. 2022 Journal of medicinal chemistry Discussion SARS_CoV_2 E484K;N501Y;K417N 130;119;112 135;124;117 RBD 69 72 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Furthermore, the unique mutations and also haplotypes of [G20887A-C28830T-C21627T] or [G8653T-C884T] with [G1397A-T28688C-G29742T] were identified in low proportion of samples. 2022 Transboundary and emerging diseases Discussion SARS_CoV_2 G1397A;G20887A;G8653T;C21627T;C28830T;C884T;G29742T;T28688C 107;58;87;74;66;94;122;114 113;65;93;81;73;99;129;121 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Monitoring the spike mutations in Iranian SARS-CoV-2 genomes revealed no novel mutations in this genomic region, while determined two commonly known mutations, T22I and D614G. 2022 Transboundary and emerging diseases Discussion SARS_CoV_2 D614G;T22I 169;160 174;164 S 15 20 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Notably, in accordance with the increasing [B.1*/20A] clade among the viral isolates of the Iranian epidemic as of mid-May, the D614G variant is dominating in this population. 2022 Transboundary and emerging diseases Discussion SARS_CoV_2 D614G 128 133 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. The increase in frequency of D614G mutation and B.1* lineages from mid-May onwards predicts a rapid viral transmission followed by considerable change in the composition of viral lineages circulating in the country. 2022 Transboundary and emerging diseases Discussion SARS_CoV_2 D614G 29 34 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Variation tracking of SARS-CoV-2 has shown that some mutations:such as P323L and D614G:are distributed globally, while some others are accumulated in specific geographical regions (Kannan et al., 2020). 2022 Transboundary and emerging diseases Discussion SARS_CoV_2 D614G;P323L 81;71 86;76 33835709 SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. While the T22I mutation is less frequent in other regions, the D614G variant is now the most prevalent mutation in COVID-19 pandemic (Ahmadpour et al., 2020; Korber et al., 2020; Mercatelli and Giorgi, 2020). 2022 Transboundary and emerging diseases Discussion SARS_CoV_2 D614G;T22I 63;10 68;14 COVID-19 115 123 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. Although our results showed that NR203K/G204R has little effect on the death ratio of COVID-19 patients, future studies with patient clinical outcomes and the coupled SARS-CoV-2 genome sequences will provide important evidences regarding the effect of NR203K/G204R polymorphism on the biology of SARS-CoV-2. 2021 Nature communications Discussion SARS_CoV_2 G204R;G204R 40;259 45;264 COVID-19 86 94 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. By analyzing the reported genome sequences, we found that the NR203K/G204R variant, contained by ~37% of the total sequenced SARS-CoV-2 viruses, gained greater ability to undergo RNA-triggered LLPS. 2021 Nature communications Discussion SARS_CoV_2 G204R 69 74 33837182 GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. Interestingly, NR203K/G204R exhibited a higher propensity to undergo LLPS in the presence of RNAs and showed a greater effect on the inhibition of IFN expression. 2021 Nature communications Discussion SARS_CoV_2 G204R 22 27 33838638 Free SARS-CoV-2 Spike Protein S1 Particles May Play a Role in the Pathogenesis of COVID-19 Infection. However, there are no indications that the D614G mutation is associated with more severe COVID-19 infection symptoms. 2021 Biochemistry. Biokhimiia Discussion SARS_CoV_2 D614G 43 48 COVID-19 89 107 33838638 Free SARS-CoV-2 Spike Protein S1 Particles May Play a Role in the Pathogenesis of COVID-19 Infection. It was demonstrated that the D614G mutation decreases the stability of the S protein trimer and facilitates RBD transition into its open conformation. 2021 Biochemistry. Biokhimiia Discussion SARS_CoV_2 D614G 29 34 RBD;S 108;75 111;76 33838638 Free SARS-CoV-2 Spike Protein S1 Particles May Play a Role in the Pathogenesis of COVID-19 Infection. Our hypothesis suggests that the decreased S1 shedding may be one of the factors limiting the morbidity and mortality of the D614G SARS-CoV-2 infection despite a higher infectivity of the virus and higher viral loads observed for the mutant virus. 2021 Biochemistry. Biokhimiia Discussion SARS_CoV_2 D614G 125 130 COVID-19 131 151 33838638 Free SARS-CoV-2 Spike Protein S1 Particles May Play a Role in the Pathogenesis of COVID-19 Infection. Recently, SARS-CoV-2 isolates with the D614G mutation in the S protein were described. 2021 Biochemistry. Biokhimiia Discussion SARS_CoV_2 D614G 39 44 S 61 62 33838638 Free SARS-CoV-2 Spike Protein S1 Particles May Play a Role in the Pathogenesis of COVID-19 Infection. Surprisingly, despite the fact that this mutation destabilizes the trimer, it was shown that the S1 shedding from the lentiviruses pseudotyped with the D614G mutant SARS-CoV-2 S protein was significantly reduced compared to the wild-type D614 protein. 2021 Biochemistry. Biokhimiia Discussion SARS_CoV_2 D614G 152 157 S 176 177 33840632 Association of SARS-CoV-2 clades with clinical, inflammatory and virologic outcomes: An observational study. Higher SARS-CoV-2 viral load has been correlated with COVID-19 mortality, suggesting host immune response to G-clade infections may differ and be less pathogenic - either as a direct result of D614G or other genetic variation associated with this clade. 2021 EBioMedicine Discussion SARS_CoV_2 D614G 193 198 COVID-19 54 62 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. According to the haplotype subgroup epidemic trends and frequencies of the 10 sites, the previous H1 haplotype derived H1-2 and H1-3 haplotypes with new mutations and increasing trends, which indicated that the combined mutations of T445C, C6286T, C22227T, C26801G and G29645T at later stage or the single mutation of G25563T at earlier stage may have some influence on infectivity, pathogenicity or host adaptability of SARS-CoV-2. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 C22227T;C26801G;C6286T;G25563T;G29645T;T445C 248;257;240;318;269;233 255;264;246;325;276;238 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. Among the haplotypes of the 10 sites, H1-2 haplotype subgroup had 614D > G and 222A > V double mutation in S protein, which might be related to its rapid spread, should be further confirmed and verified. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 A222V;D614G 79;66 87;74 S 107 108 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. Among them, only C22227T, G25563T and G29645T caused amino acid changes of S, ORF3a and ORF10 proteins (Table 2), which indicated that these 3 sites might have more important contributions to infectivity, pathogenicity or host adaptability of SARS-CoV-2. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 C22227T;G25563T;G29645T 17;26;38 24;33;45 ORF3a;S 78;75 83;76 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. Among them, the frequency of N501Y mutation seems to reach 10% in the latest 28 days (13/11/2020-10/12/2020), whether the frequency of the mutation will increase over time should be monitored to further infer the significance of the mutation. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 N501Y 29 34 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. In addition, previous researchers identified several other mutations of N439K, Y453F and N501Y in the S protein, but we did not. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 N439K;N501Y;Y453F 72;89;79 77;94;84 S 102 103 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. Moreover, both the single mutation of A23403G or the combined mutations of C241T, C3037T and C14408T could influence the infectivity, pathogenicity or host adaptability of SARS-CoV-2, which further confirmed the 4 specific sites (C241T, C3037T, C14408T and A23403G) were important in the previous H1 haplotype. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 A23403G;A23403G;C14408T;C14408T;C241T;C3037T;C3037T;C241T 38;257;93;245;75;82;237;230 45;264;100;252;80;88;243;235 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. Our results showed that the early H1 haplotype subgroup with the 4 highly linked sites (C241T, C3037T, C14408T and A23403G) derived H1-2 subgroup had another 5 highly linked sites (T445C, C6286T, C22227T, C26801G and G29645T). 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 A23403G;C14408T;C22227T;C26801G;C3037T;C6286T;G29645T;C241T;T445C 115;103;196;205;95;188;217;88;181 122;110;203;212;101;194;224;93;186 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. The mutation of A23403G located in S genes resulted in amino acid change of 614D > G (Table 2), which has been proved to be related to infectivity by several in vitro experiments. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 D614G;A23403G 76;16 84;23 S 35 36 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. Then we focused on the 6 mutations (T445C, C6286T, C22227T, G25563T, C26801G and G29645T) with a frequency greater than 20% among 23 sites. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 C22227T;C26801G;C6286T;G25563T;G29645T;T445C 51;69;43;60;81;36 58;76;49;67;88;41 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. Therefore, it is strongly recommended that the A23403G mutation should be taken into account in the development of SARS-CoV-2 vaccines, especially RNA vaccines. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 A23403G 47 54 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. These 6 sites (T445C, C6286T, C22227T, G25563T, C26801G and G29645T) were located in ORF1ab, ORF1ab, S, ORF3a, M and ORF10 genes, respectively. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 C22227T;C26801G;C6286T;G25563T;G29645T;T445C 30;48;22;39;60;15 37;55;28;46;67;20 ORF1ab;ORF1ab;ORF3a;S 85;93;104;101 91;99;109;102 33841748 AutoVEM: An automated tool to real-time monitor epidemic trends and key mutations in SARS-CoV-2 evolution. This lineage had 222A > V (C22227T) mutation on the basis of 614D > G (A23403G) mutation, which was consistent with the results of the present study. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 A222V;D614G;A23403G;C22227T 17;61;71;27 25;69;78;34 33842902 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. After the posting of the original preprint version of our manuscript, the FDA confirmed that L452R abolishes LY-CoV555 neutralization. 2021 Cell reports. Medicine Discussion SARS_CoV_2 L452R 93 98 33842902 Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. confirmed that E484K and K417N abolish neutralization by LY-CoV555 and LY-CoV016, respectively. 2021 Cell reports. Medicine Discussion SARS_CoV_2 E484K;K417N 15;25 20;30 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. As explained for other variants (including D614G in humans and Y453F in mink ), we consider that the rise of P681H-containing viruses could be due to chance, with founder effects being responsible for rapid progression, or P681H may confer an advantage with regards transmissibility or cell-cell spread in vivo. 2021 bioRxiv Discussion SARS_CoV_2 D614G;P681H;P681H;Y453F 43;109;223;63 48;114;228;68 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. B.1.1.7 is certainly not the only SARS-CoV-2 variant with a P681H change in the spike protein; it is also present in B.1.243 (clade 20A), B.1.222 (clade 20B) and a lineage B.1 variant termed clade 20C, with these three variants recently reported in New York State, USA. 2021 bioRxiv Discussion SARS_CoV_2 P681H 60 65 S 80 85 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. However, it is important to note that the P681H change does not result in the formation of a consensus furin cleavage site (i.e., P4R-x-B-RP1), even at lowered pH. 2021 bioRxiv Discussion SARS_CoV_2 P681H 42 47 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. However, many other VOIs e.g., CAL.20C do not contain P681H. 2021 bioRxiv Discussion SARS_CoV_2 P681H 54 59 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Interestingly, B.1.243 comprised the majority of P681H-containing viruses and was the predominant variant in New York in November 2020, but had declined significantly by February 2021 (to be replaced by B.1.1.7 and B.1.222 among other variants):some of which do not contain P681H (e.g., B.1.429). 2021 bioRxiv Discussion SARS_CoV_2 P681H;P681H 49;274 54;279 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Likewise, we or show no differences in cell-cell fusion assays using the spike P681H-expressing cells. 2021 bioRxiv Discussion SARS_CoV_2 P681H 79 84 S 73 78 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. One interpretation of the appearance of the P681H mutation in circulating viruses is that SARS-CoV-2 is evolving to become a transmissible but relatively benign community-acquired respiratory (CAR) or "common cold" coronavirus, such as the betacoronaviruses HCoV-HKU1 and HCoV-OC43:both of which have very strong "polybasic" furin cleavage sites at the S1/S2 position. 2021 bioRxiv Discussion SARS_CoV_2 P681H 44 49 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Other examples of variants of interest (VOIs) containing P681H include A.VOI.V2 detected through travel surveillance in Angola, Africa, isolates from Hawaii and viruses originally classified under lineage B.1.1.28 in locations such as the Philippines. 2021 bioRxiv Discussion SARS_CoV_2 P681H 57 62 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Other variants containing mutations have been identified that have been proposed to impact S1/S2 cleavage, e.g., A688V, but we consider such mutations to be too distal to the cleavage site to have a direct impact on furin activity. 2021 bioRxiv Discussion SARS_CoV_2 A688V 113 118 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Our findings suggest that the introduction of P681H in the B.1.1.7 variant may increase spike cleavage by furin-like proteases, but this does not significantly impact viral entry or cell-cell spread. 2021 bioRxiv Discussion SARS_CoV_2 P681H 46 51 S 88 93 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. Overall, we show that the P681H mutation at the S1/S2 site of the SARS-CoV-2 spike protein may increase its cleavability by furin-like proteases, but that this does not translate into increased virus entry or membrane fusion. 2021 bioRxiv Discussion SARS_CoV_2 P681H 26 31 Membrane;S 209;77 217;82 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. The P681H mutation increases the number of basic residues to four (especially at lowered pH) and is predicted to result in a slightly increased cleavability based on ProP and Pitou scoring and peptide cleavage assays at pH 7.4. 2021 bioRxiv Discussion SARS_CoV_2 P681H 4 9 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. We performed functional assays using pseudo-typed particles harboring SARS-CoV-2 spike proteins and observed no significant transduction differences between Wuhan-Hu1 and B.1.1.7 spike-carrying pseudo-typed particles in VeroE6 or Vero-TMPRSS2 cells, despite the spikes containing P681H being more efficiently cleaved. 2021 bioRxiv Discussion SARS_CoV_2 P681H 280 285 S;S;S 81;179;262 86;184;268 33851153 Functional evaluation of the P681H mutation on the proteolytic activation the SARS-CoV-2 variant B.1.1.7 (Alpha) spike. While the VOCs B.1.351 and B.1.1.28.1 (P.1) are currently of high concern due to immune escape, B.1.1.7 is not presently a concern in this regard; however, the possible acquisition of "immune-escape" mutations such as E484K or N439K during widespread circulation in the population means that SARS-CoV-2 B.1.1.7 remains a significant concern. 2021 bioRxiv Discussion SARS_CoV_2 E484K;N439K 218;227 223;232 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. Among a number of mutations selected were the very same positions found in the recent variants of concern, namely E484K and N501Y, and less frequently, changes at residue 417 were also observed. 2021 Cell Discussion SARS_CoV_2 E484K;N501Y 114;124 119;129 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. Comparison of neutralization of pseudoviruses expressing only the three RBD mutations (K417N, E484K, and N501Y) of B.1.351 with pseudovirus expressing the full suite of mutations in B.1.351 spike shows that the non-RBD changes substantially increase escape from neutralization. 2021 Cell Discussion SARS_CoV_2 E484K;N501Y;K417N 94;105;87 99;110;92 S;RBD;RBD 190;72;215 195;75;218 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. This approach led to the identification of a number of potential antibody escape mutants, among them E484K, which is likely responsible for a proportion of the escape from antibody neutralization we describe for P.1. 2021 Cell Discussion SARS_CoV_2 E484K 101 106 33852911 Antibody evasion by the P.1 strain of SARS-CoV-2. Using convalescent serum, B.1.351 showed 13-fold reduction in neutralization compared to Victoria, while P.1 was only reduced 3.1-fold, comparable to the reduction seen with B.1.1.7, which only harbors the single N501Y change in the RBD. 2021 Cell Discussion SARS_CoV_2 N501Y 213 218 RBD 233 236 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Alternatively, Y453F might be the result of viral evasion of the antibody response, and a recent report on emergence of Y453F in a patient with long-term COVID-19 supports this possibility. 2021 Cell reports Discussion SARS_CoV_2 Y453F;Y453F 15;120 20;125 COVID-19 154 162 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Further, we did not investigate whether presence of Y453F in the SARS-CoV-2 S protein increases binding to mink ACE2. 2021 Cell reports Discussion SARS_CoV_2 Y453F 52 57 S 76 77 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. However, entry into certain cell lines was reduced when Y453F was combined with H69Delta, V70Delta, I692V, and M1229I, as found in the S protein of the SARS-CoV-2 cluster 5 variant. 2021 Cell reports Discussion SARS_CoV_2 I692V;M1229I;Y453F 100;111;56 105;117;61 S 135 136 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. In keeping with this finding, a combination of casirivimab/REGN10933 and imdevimab/REGN10987 efficiently blocked SARS-CoV-2 with Y453F in cell culture. 2021 Cell reports Discussion SARS_CoV_2 Y453F 129 134 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Indeed, mutation Y453F observed in mink may be an adaptation to efficient use of mink ACE2 for entry, since amino acid 453 is known to make direct contact with human ACE2 and mutation Y453F increases human ACE2 binding. 2021 Cell reports Discussion SARS_CoV_2 Y453F;Y453F 17;184 22;189 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Maybe more concerning is that Y453F diminished entry inhibition by human sera/plasma from convalescent COVID-19 patients. 2021 Cell reports Discussion SARS_CoV_2 Y453F 30 35 COVID-19 103 111 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Moreover, viruses bearing Y453F emerged during experimental infection of ferrets, and it has been speculated that Y453F might reflect adaptation of the S protein to ferret ACE2. 2021 Cell reports Discussion SARS_CoV_2 Y453F;Y453F 26;114 31;119 S 152 153 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. The other antibody, imdevimab/REGN10987, targets a different region in the S protein and inhibited S protein-driven entry with high efficiency regardless of the presence of Y453F. 2021 Cell reports Discussion SARS_CoV_2 Y453F 173 178 S;S 75;99 76;100 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. The presence of mutation Y453F alone or in combination with H69Delta and V70Delta did not compromise S protein-mediated entry into human cells and its inhibition by soluble ACE2. 2021 Cell reports Discussion SARS_CoV_2 Y453F 25 30 S 101 102 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. We employed pseudotyped particles instead of authentic SARS-CoV-2, and we did not determine whether Y453F affects viral inhibition by T cell responses raised against SARS-CoV-2. 2021 Cell reports Discussion SARS_CoV_2 Y453F 100 105 33857422 SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. Y453F markedly reduced the neutralizing potential of an antibody with an EUA (casirivimab/REGN10933). 2021 Cell reports Discussion SARS_CoV_2 Y453F 0 5 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. Since many neutralizing antibodies target this RBD region, it would also explain the enhanced sensitivity of the D614G form to neutralization activity in vaccine and convalescent sera. 2021 Science advances Discussion SARS_CoV_2 D614G 113 118 RBD 47 50 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. That study demonstrates that D614G substitution exhibits faster transmission phenotypes in vivo and shows increased replication in the nasal epithelium and large airway epithelium. 2021 Science advances Discussion SARS_CoV_2 D614G 29 34 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. The D614G substitution occurs on the inter-protomer interface of the Spike protein mediating critical contacts. 2021 Science advances Discussion SARS_CoV_2 D614G 4 9 S 69 74 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. There are no significant global changes coming from the D614G substitution on the ACE2 binding site exposure in RBD once the Spike trimer is in the one-up conformation. 2021 Science advances Discussion SARS_CoV_2 D614G 56 61 S;RBD 125;112 130;115 33863729 The SARS-CoV-2 Spike variant D614G favors an open conformational state. Therefore, a change toward a higher one-up state population is likely the dominant effect of the D614G substitution. 2021 Science advances Discussion SARS_CoV_2 D614G 97 102 33875719 Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology. About 93.5% of the genomes belonged to the clades with D614G mutation including the clades G, GH, GR and GV. 2021 Scientific reports Discussion SARS_CoV_2 D614G 55 60 33875719 Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology. Earlier in January, clade G characterized by spike D614G mutation was identified and rapidly predominated the pandemic. 2021 Scientific reports Discussion SARS_CoV_2 D614G 51 56 S 45 50 33875719 Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology. Such findings suggest higher transmission of viral strains whose genome belong to all clades with D614G mutation. 2021 Scientific reports Discussion SARS_CoV_2 D614G 98 103 33875719 Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology. This is in line with the previous finding of higher viral loads in patients infected by SARS-CoV-2 virus strains harboring D614G genomic mutations. 2021 Scientific reports Discussion SARS_CoV_2 D614G 123 128 33875719 Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology. Tracking the distribution of individual clades in different countries with respect to disease epidemiology parameters showed higher prevalence of all clades with D614G mutation among the group of countries that showed above median total number of cases than others. 2021 Scientific reports Discussion SARS_CoV_2 D614G 162 167 33882219 Vaccine Breakthrough Infections with SARS-CoV-2 Variants. In January 2021, Moderna announced clinical efforts to target a new variant of SARS-CoV-2 that was first identified in South Africa and includes three mutations (E484K, N501Y, and K417N) in the angiotensin-converting-enzyme 2 receptor-binding domain. 2021 The New England journal of medicine Discussion SARS_CoV_2 K417N;N501Y;E484K 180;169;162 185;174;167 33882219 Vaccine Breakthrough Infections with SARS-CoV-2 Variants. Some of the substitutions in Patient 1 (T95I, del144, E484K, A570D, D614G, P681H, and D796H) were shared with B.1.526 (T95I, E484K, and D614G), and three substitutions were shared with Patient 2 (in whom the variants T95I, G142V and del144, F220I, R190T, R237K, R246T, and D614G were detected). 2021 The New England journal of medicine Discussion SARS_CoV_2 A570D;D614G;D614G;D614G;D796H;E484K;E484K;F220I;G142V;P681H;R190T;R237K;R246T;T95I;T95I;T95I 61;68;136;273;86;54;125;241;223;75;248;255;262;217;40;119 66;73;141;278;91;59;130;246;228;80;253;260;267;221;44;123 33882219 Vaccine Breakthrough Infections with SARS-CoV-2 Variants. Whole viral genome sequencing revealed several additional substitutions, including D796H, present in a guanine-cytosine-rich region not identified by targeted PCR. 2021 The New England journal of medicine Discussion SARS_CoV_2 D796H 83 88 33883059 Severe Acute Respiratory Syndrome Coronavirus 2 P.2 Lineage Associated with Reinfection Case, Brazil, June-October 2020. The mutation E484K is located in the receptor-binding domain and has also been recently described in multiple SARS-CoV-2 VOI and variants of concern rapidly spreading in the Americas, Europe, and Africa. 2021 Emerging infectious diseases Discussion SARS_CoV_2 E484K 13 18 33883059 Severe Acute Respiratory Syndrome Coronavirus 2 P.2 Lineage Associated with Reinfection Case, Brazil, June-October 2020. The rapid dissemination of these variants, combined with the ability of viruses harboring the mutation E484K to potentially escape from neutralizing antibodies mounted for older lineages, should raise concern about the potential effect on infectivity, pathogenicity, and reinfection. 2021 Emerging infectious diseases Discussion SARS_CoV_2 E484K 103 108 33883059 Severe Acute Respiratory Syndrome Coronavirus 2 P.2 Lineage Associated with Reinfection Case, Brazil, June-October 2020. We demonstrate that this reinfection case in Brazil corresponds to a primary infection with the lineage B.1.1.33 and a reinfection with the VOI P.2, which harbors the mutation S-E484K. 2021 Emerging infectious diseases Discussion SARS_CoV_2 E484K 178 183 S 176 177 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. A similar explanation has also been proposed by other authors for the S494P spike protein variant (Chakraborty, 2021). 2021 EXCLI journal Discussion SARS_CoV_2 S494P 70 75 S 76 81 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. Additionally, as recently reported, the host antibodies generated after vaccination with the currently available mRNA vaccine could neutralize the N501Y variant (Xie et al., 2021). 2021 EXCLI journal Discussion SARS_CoV_2 N501Y 147 152 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. Although currently, the Y505W variant is not found frequently, it deserves further analysis for genomic surveillance over time as this mutation significantly increases the binding affinity to human ACE2. 2021 EXCLI journal Discussion SARS_CoV_2 Y505W 24 29 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. In addition, our results are in concordance with other reports indicating that the S477N mutation did not produce changes in the secondary structure of the SARS-CoV-2 spike protein. 2021 EXCLI journal Discussion SARS_CoV_2 S477N 83 88 S 167 172 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. In the most prevalent mutants such as N501Y and B.1.1.7, the substitution of Asp to Tyr resulted in a substantial conformational reorganization that led to an increased number of interactions and changed nature of these interactions between the spike protein and ACE2 receptor. 2021 EXCLI journal Discussion SARS_CoV_2 N501Y 38 43 S 245 250 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. It has been reported recently that the E484K mutant has a lower affinity to the neutralizing antibodies than the WT spike (Greaney et al., 2020). 2021 EXCLI journal Discussion SARS_CoV_2 E484K 39 44 S 116 121 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. Recently, the scientific and health community also has focused on the new variants called the South African (B.1.351) and Brazilian (P.1) variants that carry several mutations including both the N501Y and E484K (Tang et al., 2021; Toovey et al., 2021). 2021 EXCLI journal Discussion SARS_CoV_2 E484K;N501Y 205;195 210;200 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. The binding free energy of this mutant to ACE2 is lower than of the WT spike protein and both currently most prevalent variants, N501Y and B.1.1.7. 2021 EXCLI journal Discussion SARS_CoV_2 N501Y 129 134 S 71 76 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. The highest increase in the receptor binding affinity was obtained for Y505W. 2021 EXCLI journal Discussion SARS_CoV_2 Y505W 71 76 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. Thus, residue substitution in the Y505W mutant likely introduced the conformational rearrangements that allowed the surrounding residues to interact better with the ACE2 receptor. 2021 EXCLI journal Discussion SARS_CoV_2 Y505W 34 39 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. Thus, their high transmissibility is most likely related to increased binding affinity to the human host receptor through the N501Y mutation and reduced response to antibodies associated with the E484K mutation. 2021 EXCLI journal Discussion SARS_CoV_2 E484K;N501Y 196;126 201;131 33883984 Mutations in the SARS-CoV-2 spike protein modulate the virus affinity to the human ACE2 receptor, an in silico analysis. Whereas the mutation of N501Y resulted in the conformational rearrangements increasing its affinity to the human ACE2 receptor in comparison to the S477N variant (Mathavan, 2020). 2021 EXCLI journal Discussion SARS_CoV_2 N501Y;S477N 24;148 29;153 33885735 New framework for recombination and adaptive evolution analysis with application to the novel coronavirus SARS-CoV-2. As the virus mutated, the emergence of small clusters was replaced quickly, whereas others gradually became dominant because the mutations were fixed, such as the D614G mutation in the RBD region. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D614G 163 168 RBD 185 188 33885735 New framework for recombination and adaptive evolution analysis with application to the novel coronavirus SARS-CoV-2. It is worth noting that the D614G mutation always accompanies the two most frequent mutation sites in the ORF1ab (14408 in ORF1b and 3037 in ORF1a) region, which is in the spike region at position 23403 according to the network mutation analysis (Table S4). 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D614G 28 33 ORF1ab;ORF1a;S 106;141;172 112;146;177 33885735 New framework for recombination and adaptive evolution analysis with application to the novel coronavirus SARS-CoV-2. Moreover, researchers reported the substitution causing a D614G amino acid change that may advance the fitness of the virus by increasing its infectivity. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D614G 58 63 33885735 New framework for recombination and adaptive evolution analysis with application to the novel coronavirus SARS-CoV-2. There are other high-frequency mutations widely distributed on the genome whose effects are yet to be elucidated (for example, G11083T between Cluster 1 and Cluster 2 as well as C1059T and G15583T between Cluster 4 and Cluster 8). 2021 Briefings in bioinformatics Discussion SARS_CoV_2 C1059T;G11083T;G15583T 178;127;189 184;134;196 33886690 The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways. Besides, the superior cell entry of SG614 pseudovirus, seen in this and several other studies, was rationalized by structural evidence that the D614G substitution leads to a more open receptor binding conformation. 2021 PLoS pathogens Discussion SARS_CoV_2 D614G 144 149 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Furthermore, they bound to the N501Y RBD variant with the same antibody affinities compared to WT RBD and, more importantly, neutralized SARS-CoV-2 N501Y D614G virus at comparable potencies to WT SARS-CoV-2. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G;N501Y;N501Y 154;31;148 159;36;153 RBD;RBD 37;98 40;101 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Here, immunization of alpacas with recombinant spike and RBD proteins enabled the identification of potent neutralizing nanobodies against SARS-CoV-2 and the N501Y D614G variant. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G;N501Y 164;158 169;163 S;RBD 47;57 52;60 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. The K417N/T variants would disallow the formation of a salt bridge. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 K417N;K417T 4;4 11;11 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Using the RBD variant array in an ACE2 blocking assay, we show that our four WNbFc fusions blocked ACE2 interaction with the E484K RBD variant at a level comparable to WT RBD. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 E484K 125 130 RBD;RBD;RBD 10;131;171 13;134;174 33893175 Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice. Within the RBD, B.1.1.7 harbors the N501Y mutation, whereas B.1.351 has K417N, E484K, and N501Y, and B.1.1.248 has K417T, E484K, and N501Y. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 E484K;E484K;K417N;K417T;N501Y;N501Y;N501Y 79;122;72;115;36;90;133 84;127;77;120;41;95;138 RBD 11 14 33893880 Combined RT-qPCR and pyrosequencing of a Spike glycoprotein polybasic cleavage motif can uncover pediatric SARS-CoV-2 infections associated with heterogeneous presentation. In contrast, genotyping by pyrosequencing alone seems inprecise, since the solitary occurrence of N501Y or P681H is not sufficient for the detection of the currently emerging variants-of-concern. 2021 Molecular and cellular pediatrics Discussion SARS_CoV_2 N501Y;P681H 98;107 103;112 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. Given the rapid emergence of this mutation, and the role of the M protein in multiple viral functions, including viral host cell binding, innate immune and T cell responses in SARS and SARS-CoV-2, with possible immune evasion, and now potential alterations in glucose transport, this novel M:I82T clade warrants inclusion in ongoing SARS-CoV-2 genomic surveillance and further evaluation for potential increased geographic spread and pathogenicity. 2021 Emerging microbes & infections Discussion SARS_CoV_2 I82T 292 296 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. In addition, we note that the V70L undergoing rapid expansion in the UK and the I82T mutations, both of which are under increasing rapidly, involve the putative glucose transport transmembrane helices of the M protein. 2021 Emerging microbes & infections Discussion SARS_CoV_2 I82T;V70L 80;30 84;34 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. In particular, we identified the emergence of a novel M:I82T clade over the last three months in the eastern USA. 2021 Emerging microbes & infections Discussion SARS_CoV_2 I82T 56 60 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. Structural prediction, however, did not suggest significant impact of structural changes to be caused by the M:I82T mutation which is a hydrophobic to slightly polar amino acid change (Figure 2). 2021 Emerging microbes & infections Discussion SARS_CoV_2 I82T 111 115 33896413 Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. The M:I82T mutation falls in the third transmembrane helical domain. 2021 Emerging microbes & infections Discussion SARS_CoV_2 I82T 6 10 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. Also, in comparison to our identified lead compound (SCHEMBL20144212) with mutant RdRp (P323L) exhibited large correlative networks and could act as a sturdy inhibitor against mutant RdRp (Figure 3G). 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 P323L 88 93 RdRP;RdRP 82;183 86;187 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. From the above observations, we strongly believe that the molecular docking of SCHEMBL20144212 lead compound reduces the effect of P323L mutation and could act as an effective inhibitor against SARS-nCoV-2's RdRp. 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 P323L 131 136 RdRP 208 212 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. Furthermore, our results from DCCM showed the RdRp-SCHEMBL20144212 and P323L-SCHEMBL20144212 complexes exhibited strongly correlated motions (Figures 4B,D). 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 P323L 71 76 RdRP 46 50 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. However, upon introducing the P323L mutation, only four compounds were found to bind with a higher binding affinity than Remdesivir. 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 P323L 30 35 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. in 2020 identified the P323L mutation in the RdRp of SARS-CoV-2 (Pachetti et al.,). 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 P323L 23 28 RdRP 45 49 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. The RdRp and mutant RdRp (P323L) with SCHEMBL20144212 lead compound exhibited a rigid complex as seen in Figures 3D,H. 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 P323L 26 31 RdRP;RdRP 4;20 8;24 33898520 Structure-Based Virtual Screening to Identify Novel Potential Compound as an Alternative to Remdesivir to Overcome the RdRp Protein Mutations in SARS-CoV-2. The residue cross-correlation networks were obtained for all the docked complexes, and among them, the P323L-Remdesivir complex obtained less correlative network at the region from 5 to 120 residues (Figure 3E). 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 P323L 103 108 33900165 Susceptibility to SARS-CoV-2 of Cell Lines and Substrates Commonly Used to Diagnose and Isolate Influenza and Other Viruses. Herein, we showed that the spike D614G substitution does not alter susceptibility of the cell lines tested including those with low levels of human (A549), nonhuman primate (CV-1), mink (Mv1Lu), cat (CRFK), or dog (MDCK) ACE2. 2021 Emerging infectious diseases Discussion SARS_CoV_2 D614G 33 38 S 27 32 33900165 Susceptibility to SARS-CoV-2 of Cell Lines and Substrates Commonly Used to Diagnose and Isolate Influenza and Other Viruses. In addition, most circulating strains contain the D614G substitution in the spike protein, which could affect binding, entry, and species specificity; viruses with this change were not tested in previous studies. 2021 Emerging infectious diseases Discussion SARS_CoV_2 D614G 50 55 S 76 81 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. Although the clinical implications of these variants remain unclear, 1 study noted that the 11083G>T variant was associated with asymptomatic transmission. 2021 JAMA network open Discussion SARS_CoV_2 G11083T 92 100 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. Clade group 2 contains the D614G variant and has been associated with increased infectivity in several reports. 2021 JAMA network open Discussion SARS_CoV_2 D614G 27 32 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. Clade V is hallmarked by 2 nonsynonymous variants, 11083G>T (L37F ORF1ab) and 26144G>T (G251V ORF3a), leading to alterations in the NSP6 and NS3 proteins, respectively. 2021 JAMA network open Discussion SARS_CoV_2 G11083T;G26144T;G251V;L37F 51;78;88;61 59;86;93;65 ORF1ab;ORF3a;Nsp6;NS3 66;94;132;141 72;99;136;144 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. However, the 26144G>T variant has been associated with epitope loss due to decreased protein flexibility, which may influence pathogenesis through antibody escape. 2021 JAMA network open Discussion SARS_CoV_2 G26144T 13 21 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. Often, D614G genotype strains are disproportionately represented, impacting the ability to discern differences between clades in smaller studies. 2021 JAMA network open Discussion SARS_CoV_2 D614G 7 12 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. Reports show that strains containing D614G had higher viral loads in patient specimens, yet no difference in hospitalization outcomes. 2021 JAMA network open Discussion SARS_CoV_2 D614G 37 42 33900399 Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity. Similar to our findings, prevalent variants include 23403A>G (D614G Spike), 14408C>T (P323L ORF1ab), and 25563G>T (Q57H ORF3a). 2021 JAMA network open Discussion SARS_CoV_2 C14408T;A23403G;G25563T;D614G;P323L;Q57H 76;52;105;62;86;115 84;60;113;67;91;119 ORF1ab;S;ORF3a 92;68;120 98;73;125 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. A recent study showed decreased susceptibility to neutralization from COVID-19 convalescent-phase plasma and SARS-CoV-2 vaccine sera of the South African (B.1.351) SARS-CoV-2 variant, which harbors several spike protein mutations, including E484K. 2021 Antimicrobial agents and chemotherapy Discussion SARS_CoV_2 E484K 241 246 S 206 211 COVID-19 70 78 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. E484D, which appeared early during culture adaptation in Huh7.5 cells and during long-term infection of the original inoculated Vero E6 culture, is located in the receptor binding domain and interacts with K31 in the ACE2 receptor. 2021 Antimicrobial agents and chemotherapy Discussion SARS_CoV_2 E484D 0 5 RBD 163 186 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. Finally, Q954H was present at a low frequency in P1 but increased significantly in later passages in Huh7.5 cells, consistent with the maximum increase in viral infectivity. 2021 Antimicrobial agents and chemotherapy Discussion SARS_CoV_2 Q954H 9 14 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. Indeed, mutation E484D, which was the only common spike mutation in the two viruses that recapitulated the entire virus life cycle in unmodified A549 cells (adapted-SARS2 and the virus harvested on day 42 after inoculation of Vero E6 cells), might be a major contributor to culture adaptation in human cells, possibly through an increased binding affinity for ACE2. 2021 Antimicrobial agents and chemotherapy Discussion SARS_CoV_2 E484D 17 22 S 50 55 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. It is important to highlight that this phenotype is not shared by culture-adapted variants with E484D, as demonstrated here; thus, extensive reverse-genetics studies will be needed to elucidate which positions and residues are involved in viral immune evasion in vivo. 2021 Antimicrobial agents and chemotherapy Discussion SARS_CoV_2 E484D 96 101 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. Mutation E484D very often emerges during cell culture of SARS-CoV-2 (in both Vero E6 and human cells), versus E484K, which has been found in infected individuals, usually combined with N501Y. 2021 Antimicrobial agents and chemotherapy Discussion SARS_CoV_2 E484D;E484K;N501Y 9;110;185 14;115;190 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. Nevertheless, as adapted-SARS2 was still more efficient in replicating and propagating in human cells than the Vero E6 day 42 virus, other mutations found in adapted-SARS2 might significantly contribute to this phenotype, for instance, mutation P812R, which emerged only during the latest passages, when the virus exhibited maximum infectivity. 2021 Antimicrobial agents and chemotherapy Discussion SARS_CoV_2 P812R 245 250 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. Noticeably, an in silico study of E484D predicted a higher ACE2 binding affinity that could render a more infectious SARS-CoV-2 variant, which is further supported by our ACE2-blocking experiments in which more ACE2 antibody is needed to decrease the infectivity of the adapted virus. 2021 Antimicrobial agents and chemotherapy Discussion SARS_CoV_2 E484D 34 39 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. P812R changes the sequence "PSKR" to "RSKR," which corresponds to the furin consensus cleavage motif ("RX[K/R]R"); thus, a putative second furin cleavage site could have emerged at the S2'site. 2021 Antimicrobial agents and chemotherapy Discussion SARS_CoV_2 P812R 0 5 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. The acquisition of the furin cleavage site by substitution P812R, which could compensate for a putative low level of activation of spike due to inadequate TMPRRS2 expression, might represent another mechanism of culture adaptation meriting further investigation. 2021 Antimicrobial agents and chemotherapy Discussion SARS_CoV_2 P812R 59 64 S 131 136 33903110 Overcoming Culture Restriction for SARS-CoV-2 in Human Cells Facilitates the Screening of Compounds Inhibiting Viral Replication. Thus, the Q954H change may contribute to increased infectivity by enhancing fusion activity, in a manner similar to that suggested for other HR1 mutations. 2021 Antimicrobial agents and chemotherapy Discussion SARS_CoV_2 Q954H 10 15 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. According to GISAID (December 31st, 2020), T1117I occurred merely 213 times worldwide (0.08% of all samples with Spike sequence in the database) in only 19 countries, including Colombia and New Zealand. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 T1117I 43 49 S 113 118 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. According to GISAID, D614G already occurred worldwide in >90% of all samples. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 21 26 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Altogether, the variant calling analysis reveals that the patterns found in Costa Rica, with 283 distinct mutations, are similar to those observed worldwide (such as D614G in the Spike and L84S in the ORF8), except for the T1117I in the Spike. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;L84S;T1117I 166;189;223 171;193;229 S;S;ORF8 179;237;201 184;242;205 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. As observed also in Costa Rica (98.9%), D614G of the Spike protein is highly prevalent in the world, including America and Europe. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 40 45 S 53 58 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. As part of the RdRp, P4715L might affect the replication speed of the virus. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P4715L 21 27 RdRP 15 19 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Despite the relation between D614G and transmissibility, severity or mortality remains unclear. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 29 34 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Due to the location of the T1117I variant in the Spike. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 T1117I 27 33 S 49 54 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Genome sequences in this group have at least six variants, including the mutation A222V in the Spike protein and A220V in the nucleoprotein. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 A220V;A222V 113;82 118;87 S 95 100 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. However, as found for other variants, the functional significance of P4715L and other variants in the RdRp is yet unknown. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P4715L 69 75 RdRP 102 106 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. In Costa Rica, all the sequences with D614G also carry the P4715L, with 98.9% out of all the genomes included here. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;P4715L 38;59 43;65 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. In Costa Rica, T1117I was first reported in June 2020 in San Jose, and it increased in number during the June-December period (0%, 6.3%, 11.1%, 14.5%, 22.7%, 26.6%, and 29.2% from May to November 2020, respectively), mainly in the Central Valley. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 T1117I 15 21 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. In our study, this mutation co-occurs with the H145Y and L291L variants in the Nucleocapsid. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 H145Y;L291L 47;57 52;62 N 79 91 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. In patients, D614G has been associated with higher viral load, but without significant changes in the disease severity or vaccine effectiveness. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 13 18 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Interestingly, T1117I has been scarcely reported in other latitudes. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 T1117I 15 21 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. L84S, one out of the two variants that define the clade S (GISAID classification), has been reported mainly for Asian countries, with a lower frequency in European and American countries. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 L84S 0 4 S 56 57 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. None of the A222V in the Spike and the A220V in the nucleoprotein were found in our study. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 A220V;A222V 39;12 44;17 S 25 30 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Only two genomes (1.1%) in this study have the variant L84S in the ORF8. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 L84S 55 59 ORF8 67 71 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. ORF1ab - P4715L (RdRp - P323L) 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P323L;P4715L 24;9 29;15 ORF1ab;RdRP 0;17 6;21 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. ORF1ab - P4715L (RdRp - P323L). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P323L 24 29 ORF1ab;RdRP 0;17 6;21 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. ORF8-L84S. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 L84S 5 9 ORF8 0 4 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Other studies have shown that almost all sequences with the D614G (Spike) mutation also have the variant P4715L in the ORF1ab (RdRp, P323L). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;P323L;P4715L 60;133;105 65;138;111 ORF1ab;S;RdRP 119;67;127 125;72;131 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Our 54 sequences represent 25.3% out of all the available sequences with the T1117I variant worldwide. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 T1117I 77 83 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. Recently, a variant N501Y in the Spike has been reported in the United Kingdom, which is located in the RBD and the impact on the transmission or severity is not known. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 N501Y 20 25 S;RBD 33;104 38;107 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. T1117I in the Spike is the second variant found in frequency in the Spike protein (54 genomes, 29.2%). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 T1117I 0 6 S;S 14;68 19;73 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. The 54 sequences with the T1117I variant define a separated cluster with a monophyletic origin. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 T1117I 26 32 33905892 SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation. The most common variants were P4715L in the ORF1ab-RdRp and D614G in the Spike protein (both in the same 183 genomes, 98.9%). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;P4715L 60;30 65;36 ORF1ab;S;RdRP 44;73;51 50;78;55 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Continued monitoring for emerging variants with mutations such as E484K is important to maximize the impact of public health measures to mitigate the effects of the SARS-CoV-2 pandemic. 2021 bioRxiv Discussion SARS_CoV_2 E484K 66 71 33907745 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The presence of E484K mutation likely plays a key role in facilitating increased viral transmission and reducing antibody neutralizing titers, as previously shown in other studies. 2021 bioRxiv Discussion SARS_CoV_2 E484K 16 21 33907767 Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. In this cohort of PVSCs in HCP, L452R was much more prevalent. 2021 medRxiv Discussion SARS_CoV_2 L452R 32 37 33907767 Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. Isolated L452R mutation presumptive of infection with B.1.427/B.1.429 variant was associated with partially- and fully-vaccinated status on univariate analysis. 2021 medRxiv Discussion SARS_CoV_2 L452R 9 14 33907767 Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. N501Y in the absence of E484K could indicate B.1.1.7 (the UK variant), which is expected to be the dominant variant in the United States in Spring 2021. 2021 medRxiv Discussion SARS_CoV_2 E484K;N501Y 24;0 29;5 33907767 Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. Only three PVSCs with N501Y mutation alone were observed, and no E484K mutations were found. 2021 medRxiv Discussion SARS_CoV_2 E484K;N501Y 65;22 70;27 33907767 Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. The PVSCs with N501Y mutation occurred towards the end of the project in late March 2021. 2021 medRxiv Discussion SARS_CoV_2 N501Y 15 20 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. A previous study in Bangladesh has reported significant correlation between average temperature and mutation frequency at ORF1ab and at S- D614G. 2021 Epidemiology and infection Discussion SARS_CoV_2 D614G 139 144 ORF1ab;S 122;136 128;137 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. About all of the isolates in Japan contained D614G at spike proteins, N_S194L and N_R203K at the nucleocapsid region. 2021 Epidemiology and infection Discussion SARS_CoV_2 D614G;R203K;S194L 45;84;72 50;89;77 N;S 97;54 109;59 33908339 Impact of meteorological parameters and population density on variants of SARS-CoV-2 and outcome of COVID-19 pandemic in Japan. Variants with substitutions namely, K417N, T478I, N501Y, E484K, N439K and S477N at RBDs have been detected recently in Japan. 2021 Epidemiology and infection Discussion SARS_CoV_2 E484K;K417N;N439K;N501Y;S477N;T478I 57;36;64;50;74;43 62;41;69;55;79;48 RBD 83 87 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Negative stain experiments show that populations of spike proteins with 1, 2, or 3 ACE2 receptors bound are obtained (S6 Fig), and consistent with the binding studies, we find that a higher number of ACE2 receptors bind N501Y spikes as compared to unmutated spikes when the incubation is carried out under similar conditions. 2021 PLoS biology Discussion SARS_CoV_2 N501Y 220 225 S;S;S 52;226;258 57;232;264 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Our results suggest that despite the higher infectivity of SARS-CoV-2 viruses carrying the N501Y mutation, the availability of the extended epitope surface on the RBD enables effective neutralization by VH ab8 and Fab ab1. 2021 PLoS biology Discussion SARS_CoV_2 N501Y 91 96 RBD 163 166 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Our structural studies establish the molecular basis underpinning the observed increase in ACE2 binding efficiency conferred by the N501Y mutation. 2021 PLoS biology Discussion SARS_CoV_2 N501Y 132 137 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. Our studies with the N501Y mutant are consistent with the expectation that the rapid spread of the UK variant of SARS-CoV-2 is likely due to the virus being more infectious. 2021 PLoS biology Discussion SARS_CoV_2 N501Y 21 26 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. The footprints of these antibodies are comparable to those of other antibodies recently described (S2 Table), suggesting that at least some antibodies elicited by immunization with vaccines that are currently in production may also retain the ability to neutralize the N501Y mutant. 2021 PLoS biology Discussion SARS_CoV_2 N501Y 269 274 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. The location of residue 501 at the outer edge of the contact zone for the Fab ab1 complex and outside the zone of contact for VH ab8 complex provides a structural rationale for the findings we describe here on the differential effects of the N501Y mutation on binding and neutralization by these 2 antibodies (Fig 5). 2021 PLoS biology Discussion SARS_CoV_2 N501Y 242 247 33914735 Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies. While there can be multiple origins for the increased infectivity, our biochemical studies suggest that the N501Y mutation results in increased ACE2 binding efficiency, a finding that has been reproduced by several recent studies. 2021 PLoS biology Discussion SARS_CoV_2 N501Y 108 113 33918332 Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. During this study, we found one sequence with the N501Y substitution in the S protein that is not associated with a variant of concern lineage, but with lineage B.1.1.70. 2021 Microorganisms Discussion SARS_CoV_2 N501Y 50 55 S 76 77 33918332 Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. Immune evasion against monoclonal antibody preparations and reduced neutralization capacity against vaccine-elicited and convalescence sera have been described for variants carrying the E484K substitution, making these lineages of particular concern. 2021 Microorganisms Discussion SARS_CoV_2 E484K 186 191 33918332 Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. The typing PCRs commonly used for the identification of the B.1.1.7 and B.1.351 variants target the Delta69/70 deletion and the N501Y substitution in S. 2021 Microorganisms Discussion SARS_CoV_2 N501Y 128 133 S 150 151 33918332 Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. This observation further supports the evolutionary convergence of N501Y as an initial key event in different viral clades. 2021 Microorganisms Discussion SARS_CoV_2 N501Y 66 71 33918332 Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. We found no evidence for a circulating variant harboring the E484K mutation during this study period, which is present in the B.1.351 (first identified in South Africa), P.1, and P.2 (both originating from Brazil lineages). 2021 Microorganisms Discussion SARS_CoV_2 E484K 61 66 33918332 Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. We found the N501Y substitution in 610 sequences in clade B.1.1.70 (one from Germany, the majority from Wales). 2021 Microorganisms Discussion SARS_CoV_2 N501Y 13 18 33918332 Surveillance of SARS-CoV-2 in Frankfurt am Main from October to December 2020 Reveals High Viral Diversity Including Spike Mutation N501Y in B.1.1.70 and B.1.1.7. We show that nonvariant of concern sequences may also harbor the N501Y substitution, and may be common in Germany, suggesting that a positive typing PCR only for N501Y should be followed up by additional full-genome sequencing. 2021 Microorganisms Discussion SARS_CoV_2 N501Y;N501Y 65;162 70;167 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. A high prevalence of important variants, such as D614G (93.88%) in spike and P323L (93.74%) in NSP12, was confirmed by our large-scale study. 2021 Biomedicines Discussion SARS_CoV_2 D614G;P323L 49;77 54;82 S;Nsp12 67;95 72;100 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. Additionally, other variants like S25L in NSP7, S194L, R203K, G204R, and T205I in nucleocapsid, T85I and I120F in NSP2, S477N in spike, and Q57H in ORF3a have also been confirmed by previous studies. 2021 Biomedicines Discussion SARS_CoV_2 G204R;I120F;Q57H;R203K;S194L;S25L;S477N;T205I;T85I 62;105;140;55;48;34;120;73;96 67;110;144;60;53;38;125;78;100 N;S;ORF3a;Nsp2;Nsp7 82;129;148;114;42 94;134;153;118;46 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. Compared with wildtype D614, the D614G variant changes the dynamic structures of the viral spike to bind with human angiotensin-converting enzyme 2 and increases transmission fitness with enhanced viral loads in the upper respiratory tract of SARS-CoV-2 cases. 2021 Biomedicines Discussion SARS_CoV_2 D614G 33 38 S 91 96 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. Despite the proofreading activity of viral exoribonuclease, an increasing prevalence of key genetic variants, such as D614G in viral spike and P323L in NSP12, was observed in many countries and continents. 2021 Biomedicines Discussion SARS_CoV_2 D614G;P323L 118;143 123;148 S;Nsp12 133;152 138;157 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. Furthermore, D614G in spike is coevolving with P323L in NSP12, with strong allelic associations. 2021 Biomedicines Discussion SARS_CoV_2 D614G;P323L 13;47 18;52 S;Nsp12 22;56 27;61 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. In addition, D614G increases the replication fitness of SARS-CoV-2 in cell cultures and enhances viral transmission in hamsters. 2021 Biomedicines Discussion SARS_CoV_2 D614G 13 18 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. Spike variants such as D614G and N501Y, contained in the 20H/501Y.V2 and 20I/501Y.V1 clades, may lead to changes in viral antigenicity that are harmful to monoclonal antibody therapies and vaccine protection, thereby mediating potential escape from vaccine response. 2021 Biomedicines Discussion SARS_CoV_2 D614G;N501Y 23;33 28;38 S 0 5 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. The coexistence of D614G (spike), P323L (NSP12), and C241U (5'-UTR) may contribute to increased transmission fitness. 2021 Biomedicines Discussion SARS_CoV_2 D614G;P323L 19;34 24;39 S;Nsp12 26;41 31;46 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. The D614G variant is located at a region interfacing with the neighboring subunit, and it potentially alters the trimer stability of the viral spike to enhance membrane fusion and host entry. 2021 Biomedicines Discussion SARS_CoV_2 D614G 4 9 Membrane;S 160;143 168;148 33920487 Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. The P323L variant might alter the secondary and tertiary structures of NSP12 to interact with NSP8, thereby affecting viral replication. 2021 Biomedicines Discussion SARS_CoV_2 P323L 4 9 Nsp12;Nsp8 71;94 76;98 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Along with the N501Y mutation in UK-VOC, it is speculated that the combination of the P681H mutation in the furin cleavage site and deletion of two amino acids at positions 69-70, which can alter the homology of the S-protein, is likely enhancing the transmissibility of SARS-CoV-2 and resulting in increased patient numbers. 2021 Microorganisms Discussion SARS_CoV_2 N501Y;P681H 15;86 20;91 S 216 217 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Although all VOC investigated in this study have the N501Y mutation in common, it seems that they have emerged separately. 2021 Microorganisms Discussion SARS_CoV_2 N501Y 53 58 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Although it is demonstrated that the D614G does not impact on S-protein topology, variants with D614G mutation have a weaker interaction between S1 and S2 subunits of S-protein compared with WT variant, therefore, increase cleavage rate of S1-S2 subunits which facilitate virus entry into host cells. 2021 Microorganisms Discussion SARS_CoV_2 D614G;D614G 37;96 42;101 S;S 62;167 63;168 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. As it can be seen, neither L452 nor R452 have a significant contribution to the total binding energy, however, L452R mutation is slightly in favor of complex formation in CAL-20C by lowering the binding energy (Supplementary Figure S1). 2021 Microorganisms Discussion SARS_CoV_2 L452R 111 116 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Conversely, some variants (e.g., UK-VOC, SA-VOC, COH-VOC, and BR-VOC) with mutations known to enhanced transmissibility or infectivity (such as the N501Y mutation in the S-protein), confirmed by epidemiological data (rapid spread in human populations), are of particular concern. 2021 Microorganisms Discussion SARS_CoV_2 N501Y 148 153 S 170 171 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Conversely, the E484K mutation in BR-VOC potentially strengthens binding affinity of SARS-CoV-2 RBD to hACE2. 2021 Microorganisms Discussion SARS_CoV_2 E484K 16 21 RBD 96 99 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Even though, the mutation K417T in BR-VOC would indirectly favor complex formation in BR-VOC by changing the conformation of RBM at the flexible loop, where K484 in BR-VOC forms a strong H-bond with E75. 2021 Microorganisms Discussion SARS_CoV_2 K417T 26 31 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. For example, COH-VOC has the N501Y mutation similar to other VOC, and fell in clade GH with SA-VOC, but lacks most of the other S-protein mutations detected in SA-VOC, implying an independent evolutionary pathway. 2021 Microorganisms Discussion SARS_CoV_2 N501Y 29 34 S 128 129 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Furthermore, some variants such as mink SARS-CoV-2 variant with the Y453F mutation in RBD of S-protein known to escape neutralizing antibodies, however, with restricted geographical spread during outbreak (mainly detected in Denmark and the Netherlands), were also not considered as a variant of concern. 2021 Microorganisms Discussion SARS_CoV_2 Y453F 68 73 RBD;S 86;93 89;94 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Moreover, the SA-VOC with rapid spread contains the E484K mutation, in addition to N501Y, which can be also found in BR-VOC (highly mutated variant). 2021 Microorganisms Discussion SARS_CoV_2 E484K;N501Y 52;83 57;88 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Nevertheless, mutations at this residue seem to have a moderate impact on RBD-hACE2 binding affinity, as it is located in a region with a lower probability of contact, which is in line with a previous study describing the lower probability of contact in the K417N mutation. 2021 Microorganisms Discussion SARS_CoV_2 K417N 258 263 RBD 74 77 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Nevertheless, there are evidences that the E484K mutations may give the virus new features to evade antibodies that neutralize the SARS-CoV-2. 2021 Microorganisms Discussion SARS_CoV_2 E484K 43 48 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Our data is consistent with previous studies describing the possibility of strengthen infectivity following the of N501Y mutation. 2021 Microorganisms Discussion SARS_CoV_2 N501Y 115 120 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Since spring 2020, the SARS-CoV-2 clade G and then all its descendent clades 'GH, GR, GV' with D614G mutation have become dominant circulating variants worldwide. 2021 Microorganisms Discussion SARS_CoV_2 D614G 95 100 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. The CAL-20C with L452R mutation in RBD is thought to be a more transmissible variant mainly due to epidemiological data (37% of all samples collected in California in January 2021 was CAL-20C). 2021 Microorganisms Discussion SARS_CoV_2 L452R 17 22 RBD 35 38 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Therefore, combining data from FEB and molecular interface, this might be assumed that the K417N/T mutations disfavor complex formation between RBD and hACE2, which is consistent with a previous study on SA-VOC. 2021 Microorganisms Discussion SARS_CoV_2 K417N;K417T 91;91 98;98 RBD 144 147 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Therefore, combining FEB and molecular interaction data, the N501Y mutation in RBD strengthens binding affinity of SARS-CoV-2 RBD to hACE2. 2021 Microorganisms Discussion SARS_CoV_2 N501Y 61 66 RBD;RBD 79;126 82;129 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Therefore, in light of FEB and molecular interaction results, it seems that the E484K mutation in SA-VOC has no significant effect on binding affinity between SARS-CoV-2 RBD and hACE2. 2021 Microorganisms Discussion SARS_CoV_2 E484K 80 85 RBD 170 173 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. Thus, it makes sense to consider novel variants of SARS-CoV-2 as VOC if mutations in RBM significantly strengthen binding affinity (e.g., N501Y) in RBD-hACE2 complex (genetic data), while associated with rapid spread in human populations (epidemiological data). 2021 Microorganisms Discussion SARS_CoV_2 N501Y 138 143 RBD 148 151 33925854 Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern. We have not considered this variant as a VOC, since the increased number of infected cases with CAL-20C is not associated with any significant mutation signatures (e.g., N501Y and E484K) like what can be seen in other VOC. 2021 Microorganisms Discussion SARS_CoV_2 E484K;N501Y 180;170 185;175 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. administration of 19del or 19del + D614G SARS-CoV-2 pseudoviruses. 2021 Journal of biomedical science Discussion SARS_CoV_2 D614G 35 40 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. It is important to note that WT RBD protein and 19del + D614G PsVs were used in this experiment, suggesting that WT RBD protein administration could have efficacy in preventing infection by some mutant SARS-CoV-2 PsV. 2021 Journal of biomedical science Discussion SARS_CoV_2 19del;D614G 48;56 53;61 RBD;RBD 32;116 35;119 33926459 A novel pseudovirus-based mouse model of SARS-CoV-2 infection to test COVID-19 interventions. We utilized the D614G mutation, an amino acid change that mediates heightened infectivity and quickly became the most prevalent form of SARS-CoV-2 spreading during the COVID-19 pandemic, to enhance the infectivity of our PsVs. 2021 Journal of biomedical science Discussion SARS_CoV_2 D614G 16 21 COVID-19 168 176 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. Consistent with a previous report of pseudoviruses with tags at both N- and C-termini of S protein, our pseudovirus (without any tags in S protein) D614G had comparable viral RNA copies, less shedding and increased S1 protein density than pseudovirus Str; this may account for its higher infectivity (Figure 3). 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 148 153 N;S;S 69;89;137 70;90;138 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. Future studies involving all samples with known history of infection by D614 or D614G viruses are needed to clarify this discrepancy and provide possible explanations. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 80 85 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. Given the continuous surge of multiple variants of public health concerns, our method can be used to quickly generate different variant pseudoviruses containing mutations in the S protein as exemplified by our D614G pseudovirus and evaluate the sensitivity to neutralization by sera from individuals after natural infection or immunization with different vaccines. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 210 215 S 178 179 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. The positive correlations between the PRNT50, PRNT80 or PRNT90 titers to live virus and NT50 titers to pseudoviruses Str (D614) or D614G support the robustness of the assay. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 131 136 33929934 A real-time and high-throughput neutralization test based on SARS-CoV-2 pseudovirus containing monomeric infrared fluorescent protein as reporter. Third, NT50 titers to Str (D614) were generally higher than those to D614G (Figure 4(C)); this is agreement with a recent study but not with another reporting higher NT titers to D614G than to D614. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G;D614G 69;179 74;184 33930563 Assessment of basic reproduction number (R0), spatial and temporal epidemiological determinants, and genetic characterization of SARS-CoV-2 in Bangladesh. In S protein, the D614G mutation was also prevalent in Europe and North America. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 18 23 S 3 4 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. Another intriguing finding in the current study was the significant association between a missense mutation at 16457 encoding for nsp13/helicase-S5398L and an increase in fever duration and mean age of infected patients. 2021 Biochimica et biophysica acta. Molecular basis of disease Discussion SARS_CoV_2 S5398L 145 151 Helicase;Nsp13 136;130 144;135 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. E3909G-nsp7 was associated a shorter duration of symptoms, and E3073G-nsp4 along with E1363D-nsp3 were linked to a significant decrease in fever duration. 2021 Biochimica et biophysica acta. Molecular basis of disease Discussion SARS_CoV_2 E1363D;E3073G;E3909G 86;63;0 92;69;6 Nsp3;Nsp4;Nsp7 93;70;7 97;74;11 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. Four highly recurrent mutations (>85%) were observed in S-gene at 23,403 encoding for D614G-spike glycoprotein, in 241-5'UTR and in ORF1a at 3037 (F924*-nsp3) and 14,408 (P4715L-RdRp). 2021 Biochimica et biophysica acta. Molecular basis of disease Discussion SARS_CoV_2 D614G;F924X;P4715L 86;147;171 91;152;177 S;ORF1a;5'UTR;Nsp3;RdRP;S 92;132;119;153;178;56 110;137;124;157;182;57 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. In conclusion, we found that the most recurrent P4715L-RdRp and D614G-spike-glycoprotein amino acid alterations were not significantly associated with variations in clinical symptoms, indicating that these mutations are linked to viral spread and persistence within the host regardless of clinical symptoms. 2021 Biochimica et biophysica acta. Molecular basis of disease Discussion SARS_CoV_2 D614G;P4715L 64;48 69;54 S;RdRP 70;55 88;59 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. In contrast to previous findings in Europe that showed the co-occurrence of mutations in 14,408 encoding for RNA dependent RNA polymerase (RdRp) and G614 variants, no significant correlation was found between genomes isolated from our Egyptian patient's cohort harboring mutations in 14,408 (P4715L-RdRp) and 23,403 (D614G-spike glycoprotein). 2021 Biochimica et biophysica acta. Molecular basis of disease Discussion SARS_CoV_2 D614G;P4715L 317;292 322;298 RdRp;S;RdRP;RdRP 109;323;139;299 137;341;143;303 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. In line with this finding, we observed a missense mutation in 4354 of nsp3 resulting in amino acid change from glutamate to aspartate (E1363D). 2021 Biochimica et biophysica acta. Molecular basis of disease Discussion SARS_CoV_2 E1363D 135 141 Nsp3 70 74 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. In the current study, we observed a link between two synonymous mutations, 28,846 encoding R191* N-protein and 934 encoding D223*-nsp2, and clinical manifestations. 2021 Biochimica et biophysica acta. Molecular basis of disease Discussion SARS_CoV_2 D223X;R191X 124;91 129;96 N 97 98 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. In the present study, we found that E3909G nsp7replicase variant encoded by ORF1a at 11,991 was significantly more common among children (2-13 yrs.), affecting 100% of this age group while being absent in other age groups and being significantly associated with a reduction in duration of COVID 19 symptoms. 2021 Biochimica et biophysica acta. Molecular basis of disease Discussion SARS_CoV_2 E3909G 36 42 ORF1a 76 81 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. Korber, Fischer found that D614G status was significantly associated with higher viral loads without being significantly related to disease severity as indicated by hospitalization. 2021 Biochimica et biophysica acta. Molecular basis of disease Discussion SARS_CoV_2 D614G 27 32 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. Missense mutation leading to S5398L helicase was significantly associated with progressive fever. 2021 Biochimica et biophysica acta. Molecular basis of disease Discussion SARS_CoV_2 S5398L 29 35 Helicase 36 44 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. The E3073A-nsp4 variant was related to a significant reduction in fever duration. 2021 Biochimica et biophysica acta. Molecular basis of disease Discussion SARS_CoV_2 E3073A 4 10 Nsp4 11 15 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. The missense mutation in 23,403 (A to G) encoding for the spike glycoprotein resulted in an amino acid substitution D614G with a significantly different isoelectric point. 2021 Biochimica et biophysica acta. Molecular basis of disease Discussion SARS_CoV_2 D614G 116 121 S 58 76 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. The P4715L RdRPp variant was caused by a missense mutation in 14,408. 2021 Biochimica et biophysica acta. Molecular basis of disease Discussion SARS_CoV_2 P4715L 4 10 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. This could explain the lack of an association between variants with P4715L RdRp mutations and clinical manifestation variability. 2021 Biochimica et biophysica acta. Molecular basis of disease Discussion SARS_CoV_2 P4715L 68 74 RdRP 75 79 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. We found that a missense mutation in the 9483 encoding nsp4 resulted in an E3073A substitution within the amino terminal transmembrane domain of nsp4. 2021 Biochimica et biophysica acta. Molecular basis of disease Discussion SARS_CoV_2 E3073A 75 81 Nsp4;Nsp4 55;145 59;149 33932525 Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes. We hypothesize that the association of S5398L-nsp13 with longer fever duration and progressive fever observed in this study might be due to the fact that this variant is in a region that could enhance the replication transcription complex (RTC) to unwind more double-stranded nucleic acid, eventually leading to more virus self-reproduction. 2021 Biochimica et biophysica acta. Molecular basis of disease Discussion SARS_CoV_2 S5398L 39 45 Nsp13 46 51 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. However, we did not find evidence that D614G has an impact on risk of hospitalization although testing policy would bias toward finding a variant with greater virulence as hospitalized patients are overrepresented in the dataset. 2021 Science translational medicine Discussion SARS_CoV_2 D614G 39 44 33941621 Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. Our findings are broadly consistent with other analyses on the spike D614G substitution. 2021 Science translational medicine Discussion SARS_CoV_2 D614G 69 74 S 63 68 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. D936Y was the most frequent among the HR1 fusion core mutations on 25 February 2021. 2021 Molecules (Basel, Switzerland) Discussion SARS_CoV_2 D936Y 0 5 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. Experimental testing of the D936Y mutation, within a study comprising over 100 S protein variants or glycosylation site modifications, has shown a significant decrease of infectivity as compared to the Wuhan reference strain when it was the only variant. 2021 Molecules (Basel, Switzerland) Discussion SARS_CoV_2 D936Y 28 33 S 79 80 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. It demonstrated instead increased infectivity, as compared to the reference strain, when associated with the D614G variant, which was comparable to that of the strain presenting only the D614G mutation. 2021 Molecules (Basel, Switzerland) Discussion SARS_CoV_2 D614G;D614G 109;187 114;192 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. It is worth noticing that, for other frequent variants included in the same study, such as L5F and D839Y, infectivity was virtually unchanged. 2021 Molecules (Basel, Switzerland) Discussion SARS_CoV_2 D839Y;L5F 99;91 104;94 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. On 15 February 2021, D936Y was the most frequent mutation on the HR1 fusion core, followed by S939F and S929T. 2021 Molecules (Basel, Switzerland) Discussion SARS_CoV_2 D936Y;S929T;S939F 21;104;94 26;109;99 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. Such mutations, mainly localized in Europe and USA, are quite late ones, emerging starting from the end of February 2020, and are associated with the late G/GH/GR/GV clades, implying that they co-exist with the globally dominant D614G mutation. 2021 Molecules (Basel, Switzerland) Discussion SARS_CoV_2 D614G 229 234 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. The structural effect of the D936Y mutation, that we report here, may call for further functional and clinical studies to clarify its possible consequences on the SARS-CoV-2 virulence. 2021 Molecules (Basel, Switzerland) Discussion SARS_CoV_2 D936Y 29 34 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. We investigated the structural basis of such mutations, finding out that the D936Y mutation is the one expected to have the greatest structural impact. 2021 Molecules (Basel, Switzerland) Discussion SARS_CoV_2 D936Y 77 82 33946306 D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. While the geographical distribution of S929T, mostly from England, and of S939F, mostly from England, USA, and Denmark, may reflect the higher contribution of these countries to the genomic sequencing of SARS-CoV-2 (the three countries together covered roughly two-thirds of the sequences in GISAID on 15 February), D936Y was widespread. 2021 Molecules (Basel, Switzerland) Discussion SARS_CoV_2 D936Y;S929T;S939F 316;39;74 321;44;79 33948590 A broadly neutralizing antibody protects against SARS-CoV, pre-emergent bat CoVs, and SARS-CoV-2 variants in mice. In addition, the presence of the E484K mutation in many variants of concern, severely dampens the neutralization activity by more than 6-fold of the AstraZeneca COV2-2196 mAb, Brii BioSciences mAb Brii-198, and the Regeneron mAb REGN 10933. 2021 bioRxiv Discussion SARS_CoV_2 E484K 33 38 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. An in silico molecular dynamics study on the protein structure of Spike has predicted that the T478K mutation, substituting a non-charged amino acid (Threonine) with a positive one (Lysine) may significantly alter the electrostatic surface of the protein (Figure 3), and therefore the interaction with ACE2, drugs, or antibodies, 25 and that the effect can be increased if combined by other co-occurring Spike mutations (see Table 1). 2021 Journal of medical virology Discussion SARS_CoV_2 T478K 95 100 S;S 66;405 71;410 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. Another experiment showed that T478K and T478R mutants were enriched when SARS-CoV-2 viral cultures were tested against weak neutralizing antibodies, 26 highlighting, at least in vitro, a possible genetic route the virus can follow to escape immune recognition. 2021 Journal of medical virology Discussion SARS_CoV_2 T478K;T478R 31;41 36;46 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. Everything considered, we believe that the continued genetical and clinical monitoring of S:T478K and other Spike mutations are of paramount importance to better understand COVID-19 and be able to better counteract its future developments. 2021 Journal of medical virology Discussion SARS_CoV_2 T478K 92 97 S;S 108;90 113;91 COVID-19 173 181 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. In this short communication, we report the distribution of the Spike mutation S:T478K and its recent growth in prevalence in the SARS-CoV-2 population. 2021 Journal of medical virology Discussion SARS_CoV_2 T478K 80 85 S;S 63;78 68;79 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. T478K has been detected in other phylogenetically non-derived lineages from B.1.1.519, supporting the hypothesis that this mutation arose more than once in distinct events. 2021 Journal of medical virology Discussion SARS_CoV_2 T478K 0 5 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. The distribution of this mutation, which emerged from the B.1 lineage carrying S:D614G, but is independent of the S:N501Y mutation, is higher in North America, 24 but we could detect it also in several European countries. 2021 Journal of medical virology Discussion SARS_CoV_2 D614G;N501Y 81;116 86;121 S;S 79;114 80;115 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. The location of S:T478K in the interaction complex with human ACE2 may affect the affinity with human cells and therefore influence viral infectivity. 2021 Journal of medical virology Discussion SARS_CoV_2 T478K 18 23 S 16 17 33951211 Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K. While there is currently no report of association of this variant with clinical features, S:T478K's rapid growth may indicate an increased adaption of SARS-CoV-2 variants carrying it, particularly lineage B.1.1.519. 2021 Journal of medical virology Discussion SARS_CoV_2 T478K 92 97 S 90 91 33966351 Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2. It has been reported that SARS-CoV-2 with the D614G mutation in the S protein increases infectivity in human lung cells (Yurkovetskiy et al., 2020). 2021 Transboundary and emerging diseases Discussion SARS_CoV_2 D614G 46 51 S 68 69 33968806 SARS CoV-2 Nucleoprotein Enhances the Infectivity of Lentiviral Spike Particles. Our assessment of pseudoviruses generated from both N-exclusive and N-inclusive backgrounds directly implicates N as a potent enhancer of virion quality and infectivity, an effect which extends over both the wild-type spike protein as well as the D614G mutant. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G 247 252 S;N;N;N 218;52;68;112 223;53;69;113 33968806 SARS CoV-2 Nucleoprotein Enhances the Infectivity of Lentiviral Spike Particles. Similar to the proposed infectivity enhancing mechanism for the D614G variant, which relies on reduced S1 shedding and increased spike protein retainment in virions, the N-dependent enrichment of spike glycoprotein within viral fractions we demonstrated lends support to this hypothesis. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G 64 69 S;S;N 196;129;170 214;134;171 33969329 Interferon antagonism by SARS-CoV-2: a functional study using reverse genetics. A limitation of this study is that we did not construct further rSARS-CoV variants containing Gln51Glu and Gln56Glu mutations to confirm phenotypic relevance in the context of virus replication. 2021 The Lancet. Microbe Discussion SARS_CoV_2 Q51E;Q56E 94;107 102;115 33976134 SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Sarbecovirus evolutionary histories provided clues to the biology of spike-gene mutations D614G, N501Y, E484K, and K417N/T and allowed us to catalog co-inherited mutations likely to have functional consequences. 2021 Nature communications Discussion SARS_CoV_2 D614G;E484K;K417N;K417T;N501Y 90;104;115;115;97 95;109;122;122;102 S 69 74 33983915 Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant - New York City, New York, January 1-April 5, 2021. Although the SARS-CoV-2 B.1.526 variant emerged rapidly in NYC, early evidence suggests that this variant, even with the E484K mutation, does not lead to more severe disease and is not associated with increased risk for breakthrough infection or reinfection compared with other sequenced SARS-CoV-2 viruses. 2021 MMWR. Morbidity and mortality weekly report Discussion SARS_CoV_2 E484K 121 126 33983915 Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant - New York City, New York, January 1-April 5, 2021. Approximately one half of the B.1.526 variants identified were found to have the E484K mutation, which has been shown to attenuate antibody neutralization in vitro. 2021 MMWR. Morbidity and mortality weekly report Discussion SARS_CoV_2 E484K 81 86 33983915 Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant - New York City, New York, January 1-April 5, 2021. In NYC, evidence does not indicate a higher reinfection rate among persons infected with B.1.526 viruses carrying the E484K mutation compared with those with infections without the mutation, although this might reflect incomplete case ascertainment during early 2020 because of limited testing capacity. 2021 MMWR. Morbidity and mortality weekly report Discussion SARS_CoV_2 E484K 118 123 33983915 Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant - New York City, New York, January 1-April 5, 2021. Laboratory studies of B.1.526 variants carrying the E484K mutation showed that vaccine-induced antibodies against this virus had decreased neutralizing activity and that certain monoclonal antibodies had impaired activity . 2021 MMWR. Morbidity and mortality weekly report Discussion SARS_CoV_2 E484K 52 57 33983915 Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant - New York City, New York, January 1-April 5, 2021. The presence of the E484K mutation is concerning because it has been shown to attenuate antibody neutralization in vitro. 2021 MMWR. Morbidity and mortality weekly report Discussion SARS_CoV_2 E484K 20 25 33983915 Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant - New York City, New York, January 1-April 5, 2021. Whereas a slightly larger proportion of persons infected with the B.1.526 variant carrying the E484K mutation had a previous positive antibody test than those infected with B.1.526 without the mutation, the difference is not significant, and data are insufficient to conclude that there is an increased risk for reinfection. 2021 MMWR. Morbidity and mortality weekly report Discussion SARS_CoV_2 E484K 95 100 33991677 Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage. For instance, N501Y is part of several variants that belong to distinct lineages and have been detected worldwide in association with various combinations of mutations, while L18F has been reported in 20E strains in England, in a 20I/N501Y.V1 substrain with an increased replicative fitness, in 20H/501Y.V2 strains with a faster propagation in presence of convalescent plasma, and in a majority of 20J/501Y.V3 variants. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 L18F;N501Y;N501Y 175;14;234 179;19;239 33991677 Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage. Its spike protein harbors several aa substitutions recently reported to emerge in various lineages and/or to be associated with immune escape (L18F, L452R, N501Y, H655Y, Q677H) (Supplementary Material Data). 2021 Clinical microbiology and infection Discussion SARS_CoV_2 H655Y;L452R;N501Y;Q677H;L18F 163;149;156;170;143 168;154;161;175;147 S 4 9 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Indeed, identification of a stabilizing D614G mutation in the neck of the Spike protein that increases its density on viral particles highlights the need for further study of mutations outside of S RBD in the new SARS-CoV-2 lineages. 2021 Journal of molecular biology Discussion SARS_CoV_2 D614G 40 45 S;RBD;S 74;198;196 79;201;197 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Interestingly, our models predict that the triple mutation K417T/E484K/N501Y, which arose in the ancestral lineage E484K/N501Y, has about the same affinity as WT, although its frequency is increasing around the globe. 2021 Journal of molecular biology Discussion SARS_CoV_2 E484K;K417T;E484K;N501Y;N501Y 115;59;65;71;121 120;64;70;76;126 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Our analysis also predicts that the unobserved triple mutant S477N/E484K/N501Y has the highest affinity among all combinations of fast-spreading mutations examined. 2021 Journal of molecular biology Discussion SARS_CoV_2 S477N;E484K;N501Y 61;67;73 66;72;78 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Our predictive modeling of interface mutations in the S-hACE2 complex complements experimental studies and supports the emerging view that combinatorial mutations in SARS-CoV-2 can simultaneously maintain high-affinity binding to hACE2 and evade antibodies (e.g., by N440K, L452R, E484K/Q/R, K417N/T) in human hosts. 2021 Journal of molecular biology Discussion SARS_CoV_2 E484K;E484Q;E484R;K417N;K417T;L452R;N440K 281;281;281;292;292;274;267 290;290;290;299;299;279;272 S 54 55 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Our structural analysis suggests that the widespread N501Y mutation likely introduces stabilizing cation-pi interactions between S Y501 and hACE2 K353, whereas E484K enhances the solvation energy. 2021 Journal of molecular biology Discussion SARS_CoV_2 E484K;N501Y 160;53 165;58 S 129 130 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. Similarly, although the L452R/E484Q variant is not predicted to possess an enhanced affinity relative to WT, it carries two mutations that enable significant antibody escape (Figure 5(b)), which likely accounts for its spread. 2021 Journal of molecular biology Discussion SARS_CoV_2 L452R;E484Q 24;30 29;35 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The double mutants S477N/E484K and E484K/N501Y have very high affinities (~80% above WT), which correlates well with its rapid spread in multiple countries (e.g., Brazil, South Africa, UK, US). 2021 Journal of molecular biology Discussion SARS_CoV_2 E484K;S477N;E484K;N501Y 35;19;25;41 40;24;30;46 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. The high-confidence, high-affinity S mutations include N440K, S443A, G476S, E484R and G502P (Figure 5(c)), and among these N440K and E484K/R stand out for their ability to escape surveillance of some neutralizing antibodies (C135 and C121). 2021 Journal of molecular biology Discussion SARS_CoV_2 E484K;E484R;E484R;G476S;G502P;N440K;N440K;S443A 133;133;76;69;86;55;123;62 140;140;81;74;91;60;128;67 S 35 36 33992693 Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. We found that highly-transmissible S477N, E484K and N501Y mutations have greater average affinities than WT over known hACE2 variants. 2021 Journal of molecular biology Discussion SARS_CoV_2 E484K;N501Y;S477N 42;52;35 47;57;40 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. However, the I7T mutation is located in vesicular lumen, and therefore this mutation probably has little effect on its viral RNA replication. 2021 EBioMedicine Discussion SARS_CoV_2 I7T 13 16 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. In this study, the contributions of T77I in NSP9 to SARS-CoV-2 mouse adaptation or viral pathogenesis should be further investigated. 2021 EBioMedicine Discussion SARS_CoV_2 T77I 36 40 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. In this study, we experimentally determined the binding affinities and demonstrated for the first time that Q493K, Q498H, or both increased the interactive affinities of RBD with mACE2. 2021 EBioMedicine Discussion SARS_CoV_2 Q493K;Q498H 108;115 113;120 RBD 170 173 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. Interestingly, WBP-1 acquired both Q493K and Q498H mutations simultaneously. 2021 EBioMedicine Discussion SARS_CoV_2 Q493K;Q498H 35;45 40;50 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. It is worth noting that eight SARS-CoV-2 strains from several countries have naturally acquired Q493K mutation in RBD which may allow the virus to bind mACE2 and infect mice. 2021 EBioMedicine Discussion SARS_CoV_2 Q493K 96 101 RBD 114 117 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. Several mouse-adapted SARS-CoV-2 strains, such as MASCp6 (N501Y), MA10 (Q493K) and HRB26 (Q498H), increase virulence or replication in mice likely attributed to one of the mutations in the S protein. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y;Q493K;Q498H 58;72;90 63;77;95 S 189 190 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. The mutation F294L, which is located in helix 11, is ~30-A away from the catalytic active site and therefore should not affect proteolytic activity of 3CLpro . 2021 EBioMedicine Discussion SARS_CoV_2 F294L 13 18 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. The mutations N501Y, Q493K, or Q498H were predicted to enhance interactions with the mACE2 receptor. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y;Q493K;Q498H 14;21;31 19;26;36 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. Therefore, we propose that the Q493K and Q498H mutations in RBD could serve as an indicator for recognizing SARS-CoV-2 variants with potential public health risk that could emerge at the human-mouse interface. 2021 EBioMedicine Discussion SARS_CoV_2 Q493K;Q498H 31;41 36;46 RBD 60 63 33993052 Q493K and Q498H substitutions in Spike promote adaptation of SARS-CoV-2 in mice. We characterized the dynamics of the adaptive mutations in SARS-CoV-2 and demonstrated for the first time that the Q493K and Q498H mutations in the RBD of WBP-1 enhanced its interactive affinities with mACE2. 2021 EBioMedicine Discussion SARS_CoV_2 Q493K;Q498H 115;125 120;130 RBD 148 151 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. Although we do not observe changes in oligomeric states of N15A or V25F mutant E proteins under our experimental conditions, comparisons of their CSPs suggests that the N15A mutation but not the V25F mutation causes a significant change in the N-terminal region. 2021 PLoS pathogens Discussion SARS_CoV_2 N15A;N15A;V25F;V25F 59;169;67;195 63;173;71;199 E;N 79;244 80;245 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. Changes associated with the N15A and V25F mutations are suggestive of involvement of E protein's N-terminal domain in virus assembly and/or release. 2021 PLoS pathogens Discussion SARS_CoV_2 N15A;V25F 28;37 32;41 E;N 85;97 86;98 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. The N15A mutation affects the entire binding site and abolishes the interaction with HMA, demonstrating that residue N15 plays a key role in maintaining SARS-CoV-2 E protein's native conformation and its ability to interact with HMA. 2021 PLoS pathogens Discussion SARS_CoV_2 N15A 4 8 E 164 165 34003853 Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. The small CSPs induced by the V25F mutation are localized near the mutation site indicating that the conformation of the mutant E protein is preserved, which is consistent with its response to HMA being identical to that of the wild-type E protein. 2021 PLoS pathogens Discussion SARS_CoV_2 V25F 30 34 E;E 128;238 129;239 34011679 Shedding of Viable Virus in Asymptomatic SARS-CoV-2 Carriers. Sequencing analysis of the longitudinal nasopharyngeal samples collected from this patient revealed the emergence of two novel SNVs (C8626T transition and C18452T transition) in the sample collected on day 15 after initial PCR confirmation. 2021 mSphere Discussion SARS_CoV_2 C18452T;C8626T 155;133 162;139 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. According to our computational results, two mutant types showed significantly higher binding affinity than the prototype, V367F and N354D/D364Y. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 N354D;V367F;D364Y 132;122;138 137;127;143 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. As to the other mutants, most of them showed a comparable binding affinity with the prototype, and some specific types, such as F342L, R408I and G476S, showed lower binding affinity than the prototype. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 F342L;G476S;R408I 128;145;135 133;150;140 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. For mutant R408I and W436R, the RBD free energy was changed dramatically involved by a charged amino acid being mutated to a neutral one or vice versa. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 R408I;W436R 11;21 16;26 RBD 32 35 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. Interestingly, we found that the binding free energy of D364Y is much more potent than the prototype, while that of N354D is much less potent (Table 1). 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D364Y;N354D 56;116 61;121 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. Our prediction result showed that N354D/D364Y and V367F were two mutants with binding affinity significantly more potent than the prototype (-20.84 kcal/mol and - 20.66 kcal/mol versus -16.04 kcal/mol), while W436R was comparable with the prototype (-17.12 kcal/mol versus -16.04 kcal/mol). 2021 Briefings in bioinformatics Discussion SARS_CoV_2 N354D;V367F;W436R;D364Y 34;50;209;40 39;55;214;45 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. The trend of the measured binding affinities was: prototype < W436R < N354D/D364Y < V367F. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 N354D;V367F;W436R;D364Y 70;84;62;76 75;89;67;81 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. To understand the binding mechanism of N354D/D364Y, the only double-mutation system, we also performed simulations and conducted free energy calculations separately for N354D and D364Y. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D364Y;N354D;N354D;D364Y 179;39;169;45 184;44;174;50 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. V367F mutant was reported by multiple countries and found to be more potent than the prototype, agreeing with our prediction. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 V367F 0 5 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. V367F, W436R and N354D/D364Y, had more potent binding affinities than the prototype, and the findings agreed with the KD and EC50 values measured by different methods by ACRO biosystem (https://www.acrobiosystems.com). 2021 Briefings in bioinformatics Discussion SARS_CoV_2 N354D;W436R;D364Y;V367F 17;7;23;0 22;12;28;5 34013346 In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. We hypothesized that there is compensation mechanism governing the double mutations: too strong interaction between RBD and hACE2 in D364Y might actually prevent the sequential process of SARS-CoV2 entering host cells, and the N354D mutation attenuate the strong interaction between RBD and hACE2 to facilitate the viruses to enter the host cells. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D364Y;N354D 133;227 138;232 RBD;RBD 116;283 119;286 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. A mutation in S (D614G) was recently associated with higher viral loads, increased replication on human lung epithelial cells, and younger age of patients, but not with the disease severity. 2021 BMC genomics Discussion SARS_CoV_2 D614G 17 22 S 14 15 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. Also concerning the S protein, we identified the V1176F variant in 38.1% of our samples and in all of them there was a co-occurrence with D614G. 2021 BMC genomics Discussion SARS_CoV_2 D614G;V1176F 138;49 143;55 S 20 21 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. Also E484K could be related to enhanced infectivity, which may be associated with the rapid dissemination of these escape mutants. 2021 BMC genomics Discussion SARS_CoV_2 E484K 5 10 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. Another replacement in the RDB of S protein (E484K) was also assigned. 2021 BMC genomics Discussion SARS_CoV_2 E484K 45 50 S 34 35 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. As of 28 April, 2021, 38,436 genome sequences harbor this mutation, which are found in ~10% of the sequences generated to date on average (https://outbreak.info/situation-reports?muts=S%3AE484K) In Brazil, >90% of the sequenced samples since February 2021 carry this mutation, which is present in P.1 and P.2 emergent lineages (https://outbreak.info/situation-reports?muts=S%3AE484K&selected=BRA&loc=BRA). 2021 BMC genomics Discussion SARS_CoV_2 E484K;E484K 188;377 193;382 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. E484K also emerged independently in multiple lineages, including P.1, P.2 and B.1.1.33 firstly identified in Brazil between late 2020 and early 2021. 2021 BMC genomics Discussion SARS_CoV_2 E484K 0 5 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. Importantly, all these three sublineages harbor the E484K mutation, which arose independently in both of them and appear to be evolving under diversifying positive selection. 2021 BMC genomics Discussion SARS_CoV_2 E484K 52 57 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. Importantly, two sequences (9.5%) from this study had four of five shared mutations with a new lineage (subsequently called P.2) reported in the Rio de Janeiro state (synonymous C28253T (F120F; ORF8), missense G28628T (A119S) and G28975T (M234I) in N protein and C29754U (3 UTR)), in addition to E484K RBD replacement. 2021 BMC genomics Discussion SARS_CoV_2 C28253T;E484K;G28628T;G28975T;A119S;F120F;M234I 178;296;210;230;219;187;239 185;301;217;237;224;192;244 ORF8;RBD;N 194;302;249 198;305;250 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. Interestingly, the I33F and I292T mutations that were found in ORF6 and N, respectively, have been considered dominant mutations in the SARS-CoV-2 sequences from Brazil. 2021 BMC genomics Discussion SARS_CoV_2 I292T;I33F 28;19 33;23 ORF6;N 63;72 67;73 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. Recent evidence showed that E484K replacement enables viral escape from neutralizing monoclonal antibodies or polyclonal sera facilitating reinfection by emerging lineages harboring this mutation as reported in Brazil. 2021 BMC genomics Discussion SARS_CoV_2 E484K 28 33 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. Since the E484K mutation identified in this study has been associated with loss of neutralizing activity from convalescent plasma (immune evasion) and enhanced interaction with hACE-2, lineages containing this substitution must be the subject of intense surveillance. 2021 BMC genomics Discussion SARS_CoV_2 E484K 10 15 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. The missense mutation in ORF1ab (L3930F) was reported in other 429 sequences (125 from Brazil) and also in two sequences of lineage B.1.1.248 from the Philippines. 2021 BMC genomics Discussion SARS_CoV_2 L3930F 33 39 ORF1ab 25 31 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. The publication of a recent reinfection case of SARS-CoV-2 harboring E484K and the presence of this mutation in COVID-19 patients during the current second wave in Northern Brazil are highly suggestive that this mutation is critical for viral evolution and thus must be investigated thoroughly. 2021 BMC genomics Discussion SARS_CoV_2 E484K 69 74 COVID-19 112 120 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. Until mid-December 2020, 157 genomes have this mutation globally, 114 (72.6%) isolated from South Africa, where a new lineage (B.1.351 or 501Y.V2) characterized by three RBD mutations (K417N, E484K and N501Y) recently emerged. 2021 BMC genomics Discussion SARS_CoV_2 E484K;N501Y;K417N 192;202;185 197;207;190 RBD 170 173 34016042 Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil. We have found the ORF6:I33T mutation in 42.9% of our samples, raising its potential association with immune suppression. 2021 BMC genomics Discussion SARS_CoV_2 I33T 23 27 ORF6 18 22 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. According to our data, the SARS-CoV-2 RBD with Q498H increases the binding strength to hACE2 by 5-fold, suggesting the Q498H mutant is more ready to interact with human receptor than the wild type and highlighting the necessity for more strict control of virus and virus-infected animals. 2021 The EMBO journal Discussion SARS_CoV_2 Q498H;Q498H 47;119 52;124 RBD 38 41 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. Currently, the Q498H substitution has been found in the SARS-CoV-2 in two human samples (SA-lsf-27 and SA-lsf-37) from Iran. 2021 The EMBO journal Discussion SARS_CoV_2 Q498H 15 20 34018203 Molecular basis of cross-species ACE2 interactions with SARS-CoV-2-like viruses of pangolin origin. Notably, a recent report showed that HRB-26m, a mouse-adapted strain of the SARS-CoV-2, contains A81T in the nsp8, Q498H, and N969S, together with the deletion of QTQTN675-679 in the S protein. 2021 The EMBO journal Discussion SARS_CoV_2 A81T;N969S;Q498H 97;126;115 101;131;120 Nsp8;S 109;183 113;184 34019466 Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. Although we do not have any knowledge upon the nucleotide sequences of the primers and probe adopted by this kit, it is likely that this gene dropout only occurs when 28948C > T is coupled with 28932C > T, this latter present in all B.1.177.75 sequences available on public databases. 2021 Emerging microbes & infections Discussion SARS_CoV_2 C28932T;C28948T 194;167 204;177 34019466 Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. As we did not observe any +/+/- diagnostic pattern prior to 19 February 2021 and considering that IZSAM processes for SARS-CoV-2 RNA the vast majority (up to 65%) of swab samples of the entire Abruzzo region, we may speculate that mutation 28948C > T emerged with case 2021TE101854, a 3-year-old child who likely got infected from a B.1.177.75 N-positive individual, potentially including his teacher at daycare. 2021 Emerging microbes & infections Discussion SARS_CoV_2 C28948T 240 250 N 344 345 34019466 Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. In this regard, however, it is important to point out that, in support to our hypothesis, 28948C > T is the only mutation differentiating N-negative from N-positive B.1.177.75 samples and that, when N-negative samples are tested with a different N-based molecular test, all of them tested positive. 2021 Emerging microbes & infections Discussion SARS_CoV_2 C28948T 90 100 N;N;N;N 138;154;199;246 139;155;200;247 34019466 Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. It cannot be ruled out that, as a consequence of convergent evolution or homologous recombination events, the 28948C > T and 28932C > T mutations may emerge in other lineages, including B.1.1.7, and that could lead to substantial diagnostic problems. 2021 Emerging microbes & infections Discussion SARS_CoV_2 C28932T;C28948T 125;110 135;120 34019466 Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. Mutations 28948C > T and 28932C > T in the N gene are not novel within the plethora of mutations evidenced during SARS-CoV-2 evolution and adaptation to the human host. 2021 Emerging microbes & infections Discussion SARS_CoV_2 C28932T;C28948T 25;10 35;20 N 43 44 34019466 Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. Second, we did not demonstrate that the combination of 28948C > T and 28932C > T is, with certainty, responsible for the observed N-gene dropout. 2021 Emerging microbes & infections Discussion SARS_CoV_2 C28932T;C28948T 70;55 80;65 N 130 131 34019466 Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. This phenomenon is likely due to the onset, in the B.1.177.75 lineage, of the synonymous 28948C > T mutation. 2021 Emerging microbes & infections Discussion SARS_CoV_2 C28948T 89 99 34019466 Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR. Thus, 28948C > T is the sole mutation characterizing the N-negative B.1.177.75 samples with respect to N-positive strains belonging to the same lineage. 2021 Emerging microbes & infections Discussion SARS_CoV_2 C28948T 6 16 N;N 57;103 58;104 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. For example, a yeast screening experiment showed that the E406W mutation on RBD abolishes neutralization by both NAbs in the REGN-COV2 cocktail, although this residue does not directly interact with either of them. 2021 Cell research Discussion SARS_CoV_2 E406W 58 63 RBD 76 79 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. Fortunately, the new variant strains do not spread as rapidly as the D614G strain did, such that the rapid deployment of vaccines using WT antigens might be sufficient to stop the pandemic. 2021 Cell research Discussion SARS_CoV_2 D614G 69 74 34021265 Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. Nevertheless, the trend is the same; that is, E484K and 242-244Delta would greatly influence vaccine efficacy. 2021 Cell research Discussion SARS_CoV_2 E484K 46 51 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. It is therefore possible that the increased prevalence of lineage P.2, carrying only E484K in its RBD, is due to immune escape rather than increased transmissibility. 2021 Journal of molecular biology Discussion SARS_CoV_2 E484K 85 90 RBD 98 101 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. Synergy between the N501Y and E484K mutations in a cellular multivalent system seems to be more prominent than in our 1:1 system, and it would be worthwhile to unravel if this is a result of differences in experimental conditions or protein homogeneity or if this is caused by avidity. 2021 Journal of molecular biology Discussion SARS_CoV_2 E484K;N501Y 30;20 35;25 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. Taken together, our results show that receptor binding domains from rapidly spreading variants of SARS-CoV-2 bind with increased affinity to the hACE2 receptor and that this is predominantly caused by the N501Y mutation. 2021 Journal of molecular biology Discussion SARS_CoV_2 N501Y 205 210 RBD 38 62 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. The K417N mutation in B.1.351 has occurred as an independent event onto the E484K/N501Y combination before rapidly spreading into the population. 2021 Journal of molecular biology Discussion SARS_CoV_2 E484K;K417N;N501Y 76;4;82 81;9;87 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. The large increase in receptor binding strength of variants carrying N501Y, and a reported overall positive correlation between the stabilizing effect of mutations on receptor binding and their incidence in the population, indicate that affinity for the receptor may be one of the factors that determine viral transmission. 2021 Journal of molecular biology Discussion SARS_CoV_2 N501Y 69 74 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. The recently reported observation of the independent emergence of the E484K mutation into the more transmissible B.1.1.7 strain in for example the UK is of particular concern, as it combines the immune evasion properties of the E484K mutation with N501Y's high affinity, as shown here for the E484K/N501Y double mutant. 2021 Journal of molecular biology Discussion SARS_CoV_2 E484K;E484K;E484K;N501Y;N501Y 70;228;293;248;299 75;233;298;253;304 34023401 Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. While the E484K mutation does not have a large effect on affinity for the receptor, it seems to have a significant effect on immune response. 2021 Journal of molecular biology Discussion SARS_CoV_2 E484K 10 15 34029587 Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication. Amino acid substitutions R95K or R177K inhibited N protein RNA binding in cellulo to SARS-CoV-2 5'-UTR genomic RNA using a CLIP assay in HEK293 cells. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 R177K;R95K 33;25 38;29 N 49 50 34029587 Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication. How does arginine methylation of N protein regulate SG formation? Both R95K and R177K were defective in RNA binding to the SARS-CoV-2 5'-UTR RNA, and yet only R95K within the NTD was required for SG regulation. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 R177K;R95K;R95K 80;71;159 85;75;163 N 33 34 34029587 Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication. Interestingly, the only variant in N protein is R203K;G204R in the B.1.17 strain and T205I in B.1.351 strain, suggesting the RGT sequence is an important regulatory site. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 R203K;T205I;G204R 48;85;54 53;90;59 N 35 36 34033650 SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. The European strain carries additional mutations, notably the hotspot mutations R203K and G204R, that cluster in a serine-rich linker region at the RdRp. 2021 PloS one Discussion SARS_CoV_2 G204R;R203K 90;80 95;85 RdRP 148 152 34033650 SARS-CoV-2: Possible recombination and emergence of potentially more virulent strains. The structural analysis of the two European strain mutations, D614G located in the spike gene and P314L located in the RdRp gene, indicated that the former mutation may render the furin cleavage site more accessible while the latter would increase protein stability. 2021 PloS one Discussion SARS_CoV_2 D614G;P314L 62;98 67;103 S;RdRP 83;119 88;123 34039497 An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose. In other words, the D614G mutation in fact promotes the S1/S2 association and stabilize the spike. 2021 Vaccine Discussion SARS_CoV_2 D614G 20 25 S 92 97 34039497 An mRNA-based vaccine candidate against SARS-CoV-2 elicits stable immuno-response with single dose. On the contrary, structural modeling studies revealed that "the D614G substitution creates a sticky packing defect in subunit S1, promoting its association with subunit S2 as a means to stabilize the structure of S1 within the S1/S2 complex. 2021 Vaccine Discussion SARS_CoV_2 D614G 64 69 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. , 21 Therefore, it is possible that D614G facilitates the transmission of SARS-CoV-2 and may cause larger outbreaks. 2021 Journal of medical virology Discussion SARS_CoV_2 D614G 38 43 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. 20 Moreover, D614G mutation was found in the six SARS-CoV-2 strains isolated from the outbreak occurring in a bar. 2021 Journal of medical virology Discussion SARS_CoV_2 D614G 14 19 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. All 18 samples carrying D614G mutation were detected from March 14 onwards. 2021 Journal of medical virology Discussion SARS_CoV_2 D614G 24 29 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. D614G mutation has detected in many areas of the world. 2021 Journal of medical virology Discussion SARS_CoV_2 D614G 0 5 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. Eighteen samples had the signature mutation profile of A23403G which was related to the amino acid change, D614G. 2021 Journal of medical virology Discussion SARS_CoV_2 A23403G;D614G 55;107 62;112 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. However, current SARS-CoV-2 vaccine candidates are unlikely to be affected by D614G mutation. 2021 Journal of medical virology Discussion SARS_CoV_2 D614G 79 84 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. In our study, those with D614G mutation in the SARS-CoV-2 spike protein were more likely to have a lower C t (<25) in real-time RT-PCR tests than the original (D614). 2021 Journal of medical virology Discussion SARS_CoV_2 D614G 25 30 S 58 63 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. SARS-CoV-2 was also found to be silently transmitted in the community as early as March 2020, when the D614G strain was first detected and became dominant. 2021 Journal of medical virology Discussion SARS_CoV_2 D614G 103 108 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. the D614G mutation had not been detected in the samples sequenced before March 14, 2020, which were classified mainly into clade 19A and 19B. 2021 Journal of medical virology Discussion SARS_CoV_2 D614G 4 9 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. The D614G was reportedly associated with increased infectivity of SARS-CoV-2. 2021 Journal of medical virology Discussion SARS_CoV_2 D614G 4 9 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. There were three alterations in the spike region: A23403G, C23731T, and G24794T. 2021 Journal of medical virology Discussion SARS_CoV_2 A23403G;C23731T;G24794T 50;59;72 57;66;79 S 36 41 34042186 Genome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: Understanding the nature of the epidemic and role of the D614G mutation. We found that there was a mutation on ORF1ab-14408 that was inversely correlated with D614G. 2021 Journal of medical virology Discussion SARS_CoV_2 D614G 87 92 34043733 Molecular dynamics analysis of N-acetyl-D-glucosamine against specific SARS-CoV-2's pathogenicity factors. The findings of Cheng and colleagues provided a higher affinity to the human ACE2 receptor, among the mutations, are the N501Y, K417N, and E484K mutations. 2021 PloS one Discussion SARS_CoV_2 E484K;K417N;N501Y 139;128;121 144;133;126 34043733 Molecular dynamics analysis of N-acetyl-D-glucosamine against specific SARS-CoV-2's pathogenicity factors. Thereby, a molecular docking with the D614G variant of the virus (PDB: 7KDK) and the results did not include any loss of affinity (S5 Data). 2021 PloS one Discussion SARS_CoV_2 D614G 38 43 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. Patients infected with the M1V are clearly younger than those with the initial virus or those with the M4V and the N501YV. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 M1V;M4V 27;103 30;106 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. The severity is also different since the M1V was less severe than other lineages, the N501YV appears to be less severe than the M4V, which seems to have had the greatest severity compared to others. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 M1V;M4V 41;128 44;131 34044152 Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. This underlines the fact that COVID-19 presents a variability from July 2020, which is associated with epidemiological modifications such as the source (the M1V undoubtedly came from Africa, the 20AS from China, the N501YV from England and the source of M4V is unknown but is believed to be of European origin). 2021 Clinical microbiology and infection Discussion SARS_CoV_2 M1V;M4V 157;254 160;257 COVID-19 30 38 34044153 SARS-CoV-2 N gene dropout and N gene Ct value shift as indicator for the presence of B.1.1.7 lineage in a commercial multiplex PCR assay. For example, D3Y is present in the variant of interest B.1.525, which currently represents less than 1% of the SARS-CoV-2 population. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 D3Y 13 16 34044153 SARS-CoV-2 N gene dropout and N gene Ct value shift as indicator for the presence of B.1.1.7 lineage in a commercial multiplex PCR assay. These N gene dropouts or Ct value shifts were caused by a D3L mutation in the N gene of SARS-CoV-2 which was confirmed by reverse genetics. 2021 Clinical microbiology and infection Discussion SARS_CoV_2 D3L 58 61 N;N 6;78 7;79 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Arguably the effect of E484K could be particularly relevant. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 23 28 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Considering that E484K enhances escape from immune system antibodies, these may potentially lead to a viral advantage. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 17 22 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Even as an independent evolutionary event, the potential fixation of mutations such as E484K across lineages may indicate active mechanisms of adaptive selection and are very relevant in planning future therapeutic strategies (for example, newer vaccines and immunotherapy platforms). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 87 92 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. However, the fixation of these mutations, as well as Nsp12:P323L and D614G in all the E484K evaluated genomes may indicate a novel adaptive relationship among these modifications resulting in viral evolutionary success. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;E484K;P323L 69;86;59 74;91;64 Nsp12 53 58 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. However, we still do not know if this holds true for other sets of mutations associated with E484K. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 93 98 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. In summary, we have demonstrated widespread dissemination of mutants harboring E484K replacement in geographically diverse regions in Brazil, as well as the potential fixation of the E484K mutation despite a short time (three months) after its first arising. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K;E484K 79;183 84;188 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. It was structurally demonstrated that, at least in combination with K417N and N501Y, the substitution has profound impact in shifting the main site of contact between viral RBD and hACE-2 residues. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 K417N;N501Y 68;78 73;83 RBD 173 176 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. Moreover, in the study of, the combination of the mutations E484K +N501Y +D614G generated lower neutralization titers than the N501Y virus or the virus with three mutations from the UK variant (Delta69/70 + N501Y + D614G). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;E484K;N501Y;N501Y;D614G;N501Y 215;60;127;207;74;67 220;65;132;212;79;72 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. showed that the E484K affects the binding of serum polyclonal neutralizing antibodies and decreases the neutralization efficiency for serum with low or moderate IgG for the SARS-CoV-2 spike protein. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 16 21 S 184 189 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The analysis of the South African clade V501 V2 found some similar results for FUBAR evaluation, with the detection of adaptive selection at the sites 5 (L5F), 12 (S12F), and 484 (E484K). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K;L5F;S12F 180;154;164 185;157;168 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The fact that E484K was found in the context of different mutations and lineages is suggestive that this particular substitution may act as a common solution for viral evolution in different genotypes. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 14 19 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The occurrence of simultaneous mutations as N:R203K and N:G204R is already known in the SARS-CoV-2 literature. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 G204R;R203K 58;46 63;51 N;N 44;56 45;57 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The potential causality or influence of the E484K and other substitutions for the effectiveness of neutralizing antibodies that bind the N-terminal domain of the spike protein remains uncertain. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 44 49 S;N 162;137 167;138 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The presence of spike S:D614G, N:R203K, N:G204R, and Nsp12:P323L in all sequenced E484 mutated samples, reaching three different lineages, might suggest that these lineages show increased viral replication. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;G204R;P323L;R203K 24;42;59;33 29;47;64;38 S;Nsp12;N;N;S 16;53;31;40;22 21;58;32;41;23 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. The residues 155 and 677 are not associated with the E484K-presenting lineages, however, recent data found evidence of evolutionary convergence of this mutation in at least six distinct sub-lineages, which could improve proteolytic processing, cell tropism, and transmissibility. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 53 58 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. To the best of our knowledge, the impact of E484K in different lineages has not been deeply explored. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 44 49 34044192 E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil. When taken together, this growing body of evidence suggests that E484K should be the target of intense virologic surveillance. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 65 70 34058304 Identification of E484K and other novel SARS-COV-2 variants from the Kingdom of Bahrain. We have found two significant mutations (E484K and D614G) on the spike protein of Bahrain isolates. 2021 Microbial pathogenesis Discussion SARS_CoV_2 D614G;E484K 51;41 56;46 S 65 70 34059617 A core-shell structured COVID-19 mRNA vaccine with favorable biodistribution pattern and promising immunity. Although some of the mutations occurred in RBD region such as V367F, G476S, V483A, SW0123-elicited Abs were still able to neutralize these variants effectively, which suggested that diversified NAbs and non-RBD region functional Abs can be induced. 2021 Signal transduction and targeted therapy Discussion SARS_CoV_2 G476S;V367F;V483A 69;62;76 74;67;81 RBD;RBD 43;207 46;210 34059617 A core-shell structured COVID-19 mRNA vaccine with favorable biodistribution pattern and promising immunity. Of note, although E484K mutation causes escape from convalescent serum and monoclonal Abs, sera collected from SW0123-immunized BALB/c mice and rhesus macaques still maintained high neutralizing activity against this variant. 2021 Signal transduction and targeted therapy Discussion SARS_CoV_2 E484K 18 23 34059617 A core-shell structured COVID-19 mRNA vaccine with favorable biodistribution pattern and promising immunity. SARS-CoV-2 D614G has become a dominant variant worldwide, with remarkably enhanced infectivity and transmissibility. 2021 Signal transduction and targeted therapy Discussion SARS_CoV_2 D614G 11 16 34059617 A core-shell structured COVID-19 mRNA vaccine with favorable biodistribution pattern and promising immunity. The variants such as Y453F, N439K, N501Y, and E484K have shown either enhanced cross-species transmissibility or ability to escape neutralization by NAbs. 2021 Signal transduction and targeted therapy Discussion SARS_CoV_2 E484K;N439K;N501Y;Y453F 46;28;35;21 51;33;40;26 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. A single mutation, E406W, allowed escape from both antibodies, although the residue is not located within the epitope bound by either antibody. 2021 mBio Discussion SARS_CoV_2 E406W 19 24 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Convalescent-phase sera from individuals who had been infected prior to the emergence of the variants neutralized viruses with the B.1.1.7, COH.20G/677H, 20A.EU2, and mink cluster 5 spikes with titers close to that of the parental D614G and neutralized viruses pseudotyped with B.1.351 and B.1.1.248 spike proteins nearly as well, with a 1.7-fold decrease in titer. 2021 mBio Discussion SARS_CoV_2 D614G 231 236 S;S 182;300 188;305 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. found that BNT162b2 vaccine-elicited antibodies neutralized virus with E484K/N501Y mutations with a titer that was 0.8-fold lower compared to D614G. 2021 mBio Discussion SARS_CoV_2 D614G;E484K;N501Y 142;71;77 147;76;82 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. In addition, neutralization by REGN10933 was prevented by the nearby mutation F486S, a mutation that has been shown to affect ACE2 binding. 2021 mBio Discussion SARS_CoV_2 F486S 78 83 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. In our experiments, D614G caused a significant increase in infectivity, but the variants, all of which contain the mutation, showed either no increase or a small increase (1.1- to 1.6-fold) in infectivity (Delta69-70, S982A, and Delta69-70/N501Y/P681H). 2021 mBio Discussion SARS_CoV_2 D614G;S982A;N501Y;P681H 20;218;240;246 25;223;245;251 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The decrease in the neutralizing titer was attributable to the E484K mutation. 2021 mBio Discussion SARS_CoV_2 E484K 63 68 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The decrease in titer was the result of the E484K mutation, suggesting that a modified vaccine with this mutation might be required to provide a high degree of protection for such individuals. 2021 mBio Discussion SARS_CoV_2 E484K 44 49 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The escape was the result of the K417N and E484K mutations in the RBD, either of which prevents neutralization, consistent with the findings of Wang et al. 2021 mBio Discussion SARS_CoV_2 E484K;K417N 43;33 48;38 RBD 66 69 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The mutations that affected REGN10933 (E484K, K417N, and Y453F) cluster on the face of the RBD to which the antibody binds. 2021 mBio Discussion SARS_CoV_2 K417N;Y453F;E484K 46;57;39 51;62;44 RBD 91 94 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The vaccine-elicited antibodies neutralized virus pseudotyped with B.1.1.7, COH.20G/677H, and 20A.EU2 spike proteins with titers similar to that of D614G and neutralized the B.1.351 and B.1.1.248 spike proteins with a 3-fold decrease in titer, a titer that remained higher than that elicited by natural infection against D614G. 2021 mBio Discussion SARS_CoV_2 D614G;D614G 148;321 153;326 S;S 102;196 107;201 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. The variant spike proteins were expressed well in cells and efficiently incorporated into virions, with the exception of the B.1.1.7 spike protein and a spike protein with one of the constituent B.1.1.7 mutations, T716I. 2021 mBio Discussion SARS_CoV_2 T716I 214 219 S;S;S 12;133;153 17;138;158 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. Viruses pseudotyped with B.1.1.7 or B.1.351 were not more infectious than the parental D614G, although in an ACE2 binding assay, the N501Y mutation present in the B.1.1.7, B.1.351, and COH.20G/677H spike proteins caused an increase in the ACE2 binding affinity. 2021 mBio Discussion SARS_CoV_2 D614G;N501Y 87;133 92;138 S 198 203 34060334 Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes. We found that the B.1.351, B.1.1.7, and some of the variant point mutations caused a >2-fold increase in infectivity at 50 C compared to D614G, suggesting that the mutations increase the stability of the spike protein. 2021 mBio Discussion SARS_CoV_2 D614G 137 142 S 204 209 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Additionally, it is noteworthy that in BY-2 cells, the production of an ORF8 variant lacking the intermolecular disulfide bond (ORF8 C20S variant) was significantly lower than that of wild-type ORF8 and its L84S variant (Supplementary Table 2), probably because of reduced dimerizing ability. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 C20S;L84S 133;207 137;211 ORF8;ORF8;ORF8 72;128;194 76;132;198 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Furthermore, the L84S variant was more stable and soluble than the wild-type protein under weakly acidic conditions. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 L84S 17 21 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. However, no reports have described differences in the function of wild-type ORF8 and its L84S variant that would explain differences in disease severity. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 L84S 89 93 ORF8 76 80 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. In addition, the L84S variant, which is more soluble than the wild-type protein under weakly acidic conditions, is expected to cause less damage to acidic organelles. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 L84S 17 21 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Intriguingly, the L84S variant displayed slightly greater conformational stability against temperature and pH variation than wild-type ORF8. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 L84S 18 22 ORF8 135 139 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Modeling of the three-dimensional structure revealed no significant differences in the conformation of the wild-type ORF8 and its L84S variant. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 L84S 130 134 ORF8 117 121 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Patients infected with strain carrying the L84S variant exhibited significantly less severe illness than those infected with wild-type ORF8-expressing strain. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 L84S 43 47 ORF8 135 139 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. The L84S variant exhibited greater solubility than the wild-type protein under weakly acidic conditions. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 L84S 4 8 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. The wild-type and L84S variant proteins were purified and enriched, and their thermal and pH stability were evaluated using NMR. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 L84S 18 22 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. This might explain the low incidence of severe disease in patients infected with SARS-CoV-2 strains carrying the L84S variant. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 L84S 113 117 34062392 Similarities and differences in the conformational stability and reversibility of ORF8, an accessory protein of SARS-CoV-2, and its L84S variant. Using a BY-2 cell-based protein production system, we mass-produced wild-type ORF8 and its L84S variant with a single conformation. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 L84S 91 95 ORF8 78 82 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. According to this model, the gear-like domain (GLD):where D614G and T307I mutations are located-would convey the motion between NTD and RBD (Figure 5a). 2021 Viruses Discussion SARS_CoV_2 D614G;T307I 58;68 63;73 RBD 136 139 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Although this points out to a rather different effect of T307I in comparison with other reported mutations in the gear domain, it is possible that the loss of core compactness caused by A653V and I692V, and the change in hydrophobicity induced by H655Y could have similar dynamic effects as T307I. 2021 Viruses Discussion SARS_CoV_2 A653V;H655Y;I692V;T307I;T307I 186;247;196;57;291 191;252;201;62;296 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Amino acid 307 lies on the opposite side of D614G in the same folding domain being completely solvent-exposed. 2021 Viruses Discussion SARS_CoV_2 D614G 44 49 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Due to the putative role of spike mutations in virus spreading, we further investigated the effects of the T307I substitution on the spike protein structure. 2021 Viruses Discussion SARS_CoV_2 T307I 107 112 S;S 28;133 33;138 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Further supporting our model, the superposition of spike structures obtained by electron microscopy suggested a different rotation on the positioning of the GLD in the D614G compared to the WT. 2021 Viruses Discussion SARS_CoV_2 D614G 168 173 S 51 56 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. However, over a period of six weeks, a novel SARS-CoV-2 haplotype carrying the T307I spike mutation replaced all competing lineages that were previously established. 2021 Viruses Discussion SARS_CoV_2 T307I 79 84 S 85 90 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Mutation H655Y alters the hydrophobicity of an exposed residue, with a less evident effect. 2021 Viruses Discussion SARS_CoV_2 H655Y 9 14 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Mutation T307I is unique in its location and interaction with the alpha-helix of the gear domain. 2021 Viruses Discussion SARS_CoV_2 T307I 9 14 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Mutations A653V and I692V, located inside the hydrophobic core of the gear domain, probably cause loss of compactness of the beta-sandwich core. 2021 Viruses Discussion SARS_CoV_2 A653V;I692V 10;20 15;25 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Our analysis suggest that the conformational changes induced by the T30I mutation are analogous to those induced by pH as assessed by cryo-electron microscopy analysis. 2021 Viruses Discussion SARS_CoV_2 T30I 68 72 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Our findings contribute to the mechanistic view of Yurkovetskiy et al., who suggested that the D614G mutation unlocks a latch between this domain and the RBD. 2021 Viruses Discussion SARS_CoV_2 D614G 95 100 RBD 154 157 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Our simulations showed that the polar-to-hydrophobic T307I replacement pulls the preceding F306 and removes it from a highly conserved hydrophobic cavity of the N-terminal domain. 2021 Viruses Discussion SARS_CoV_2 T307I 53 58 N 161 162 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Recently, the United Kingdom has reported that a large proportion of new cases in South East England belonged to a new single phylogenetic cluster defined by multiple spike protein mutations (deletions 69-70 and 144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H). 2021 Viruses Discussion SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 224;259;231;217;238;252;245 229;265;236;222;243;257;250 S 167 172 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. The B1.525 variant harbors a Q677H mutation, the variant B1.1.7 reported in the United Kingdom carries A570D and P681H mutations, the P1 variant from Brazil shows the H655Y mutation, and the recently reported B.1.617 strain in India shows a P681R change. 2021 Viruses Discussion SARS_CoV_2 A570D;H655Y;P681H;P681R;Q677H 103;167;113;241;29 108;172;118;246;34 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. The rapid shift to a mutated strain with a novel spike protein variation (D614G/T307I) suggested an adaptive advantage. 2021 Viruses Discussion SARS_CoV_2 D614G;T307I 74;80 79;85 S 49 54 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. The T307I mutation may promote RBD-open conformations, similarly as proposed for D614G, or decouple the mechanic communication between N-terminal and RBD. 2021 Viruses Discussion SARS_CoV_2 D614G;T307I 81;4 86;9 RBD;RBD;N 31;150;135 34;153;136 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Three variants were located within the N-protein coding gene, two of these polymorphisms refer to amino acid changes (R203K and G204R), which have been associated earlier to increased fitness and adaptation. 2021 Viruses Discussion SARS_CoV_2 G204R;R203K 128;118 133;123 N 39 40 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. To substantiate this speculation, we performed coarse-grained molecular dynamics simulations of the spike trimer's soluble part introducing the T307I and D614G mutations. 2021 Viruses Discussion SARS_CoV_2 D614G;T307I 154;144 159;149 S 100 105 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Two threonine-isoleucine substitutions (T1246I, T1250I) were localized within Nsp3. 2021 Viruses Discussion SARS_CoV_2 T1250I;T1246I 48;40 54;46 Nsp3 78 82 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. We therefore postulate that upon T307I substitution, F306 is attracted to the mutated I307 to optimize hydrophobic interactions. 2021 Viruses Discussion SARS_CoV_2 T307I 33 38 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Whereas mutations emerging within the receptor binding domain such as N501Y and N440K might have a direct impact on ACE2 binding, our work further supports the idea that distant variations affecting RBD dynamics, such as D614G, must also be monitored. 2021 Viruses Discussion SARS_CoV_2 D614G;N440K;N501Y 221;80;70 226;85;75 RBD;RBD 38;199 61;202 34064904 Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Whether these mutations located within the same domain as T307I may induce a similar impact on the molecular dynamics warrants further investigation. 2021 Viruses Discussion SARS_CoV_2 T307I 58 63 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. Another significant S_E484K mutation at the RBD, called an escape mutant, has already been found in the South African variant (B.1.351), Brazilian variant (P.1), and UK variant (B.1.1.7) and was also observed in the current study in two Bangladeshi strains under lineage B.1.1.25. 2021 Microorganisms Discussion SARS_CoV_2 E484K 22 27 RBD 44 47 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. Bangladeshi strains exhibited other S protein mutations or variants, as well as combined variants, such as L5F, L18F, N354S, A520K, Q675H/R, P681H/R, L5F + D614G, and D614G + M1229Y, which have been previously linked with increased infectivity under experimental setups and may have significant biological properties in response to natural infection. 2021 Microorganisms Discussion SARS_CoV_2 A520K;D614G;D614G;L18F;L5F;L5F;M1229Y;N354S;P681H;P681R;Q675H;Q675R 125;156;167;112;107;150;175;118;141;141;132;132 130;161;172;116;110;153;181;123;148;148;139;139 S 36 37 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. Furthermore, mutations observed at Y789N, S803L, and N1074H in Bangladeshi strains that creating or deleting potential glycosylation sites, may also affect antigenic and other properties of the circulating strains. 2021 Microorganisms Discussion SARS_CoV_2 N1074H;S803L;Y789N 53;42;35 59;47;40 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. However, the introduction of lineage B.1.1.7/GRY (UK variant/S_N501Y mutation) in late December 2020 in Bangladesh was of particular concern. 2021 Microorganisms Discussion SARS_CoV_2 N501Y 63 68 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. In addition, some Bangladeshi strains had H69del + V70del, and Y144del or Y145del, which has shown a twofold higher infectivity than wild type, and has a decreased sensitivity to convalescent sera respectively. 2021 Microorganisms Discussion SARS_CoV_2 Y144del;Y145del 63;74 70;81 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. Many other missense and synonymous mutations found in respective proteins of Bangladeshi virus populations such as ORF1ab/nsp12_P323L, NS3_Q57H, NS8_R52I, N_S194L, N_R203K, and N_G204R, which are also common worldwide. 2021 Microorganisms Discussion SARS_CoV_2 G204R;P323L;Q57H;R203K;R52I;S194L 179;128;139;166;149;157 184;133;143;171;153;162 ORF1ab;Nsp12;NS3 115;122;135 121;127;138 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. Our study further stated the new introduction of the highly transmissible S_E484K mutant and presence of the variant B.1.1.7 strain in Bangladesh. 2021 Microorganisms Discussion SARS_CoV_2 E484K 76 81 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. The common distinctive feature of these three clades is S_D614G mutation. 2021 Microorganisms Discussion SARS_CoV_2 D614G 58 63 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. The GR clade, in which the N_G204R mutation in the nucleocapsid protein is combined with the widespread S_D614G mutation, accounted for around 83% of the Bangladeshi sequences. 2021 Microorganisms Discussion SARS_CoV_2 D614G;G204R 106;29 111;34 N 51 63 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. The mutation NSP12_P323L plays a prominent role in protein folding and aggregation. 2021 Microorganisms Discussion SARS_CoV_2 P323L 19 24 Nsp12 13 18 34065789 Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations. The mutation S_D614G has become globally prevalent, which may increase the infectivity of SARS-CoV-2 that has been observed in 95.12% of global sequences. 2021 Microorganisms Discussion SARS_CoV_2 D614G 15 20 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. Although MD simulation data on wt S protein RBDACE2 interaction has been reported, data on dynamic changes induced by the N501Y variant found in B.1.1.7 (British), B.1.351 (South African) and P.1 (Brazilian, Japanese) is lacking. 2021 Biomedicines Discussion SARS_CoV_2 N501Y 122 127 S 34 35 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. For tyrosine 501 from the S protein RBD, we found an increased van der Waals interaction with lysine 353 (ACE2) in the N501Y variant. 2021 Biomedicines Discussion SARS_CoV_2 N501Y 119 124 RBD;S 36;26 39;27 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. For variants carrying this D614G mutation, it has also been suggested that more functional S protein is incorporated into the virion membrane. 2021 Biomedicines Discussion SARS_CoV_2 D614G 27 32 Membrane;S 133;91 141;92 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. However, molecular mechanisms explaining the higher infectivity of the D614G mutation are still elusive. 2021 Biomedicines Discussion SARS_CoV_2 D614G 71 76 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. Our data, derived from simulations of the entire S trimer and comparing wt with B.1.1.7, reveal a rearrangement of salt bridges caused by the loss of interaction between position 614 due to the D614G mutation and lysine 854 in B.1.1.7. 2021 Biomedicines Discussion SARS_CoV_2 D614G 194 199 S 49 50 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. The newly formed salt bridge of aspartate 570 with lysine 964 does not compensate for the loss of aspartate 614 in terms of protein stability, but might weaken salt bridges formed by aspartate 568. 2021 Biomedicines Discussion SARS_CoV_2 D570K 32 57 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. These three variants also harbor the D614G mutation, which has previously been associated with higher infectivity and viral replication. 2021 Biomedicines Discussion SARS_CoV_2 D614G 37 42 34066729 Mutations in the B.1.1.7 SARS-CoV-2 Spike Protein Reduce Receptor-Binding Affinity and Induce a Flexible Link to the Fusion Peptide. This might also happen after cleavage at the S2' position by TMPRSS2 or allow faster entry into host cells after priming the S2' position by furin during protein secretion, especially as enhanced proteolytic cleavage was proposed for D614G S proteins. 2021 Biomedicines Discussion SARS_CoV_2 D614G 234 239 S 240 241 34067745 An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. Another immune escape mutation, the N440K amino acid in the spike protein, was also observed in Telangana (n = 7), Andhra Pradesh (n = 5), and Assam (n = 1) from May 2020. 2021 Viruses Discussion SARS_CoV_2 N440K 36 41 S 60 65 34067745 An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. Based on the analysis of this study, 84.6% of sequences in the unclassified cluster had the ORF1ab: L3606F mutation. 2021 Viruses Discussion SARS_CoV_2 L3606F 100 106 ORF1ab 92 98 34067745 An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. In addition, this study observed the presence of individual amino acid variants in the SARS-CoV-2 variants B.1.1.7 (S494P), B.1.525 (A67V, Q677H), B.1.526 (L5F, T95I, S477N), and P2 (V1176F) in the earlier samples. 2021 Viruses Discussion SARS_CoV_2 Q677H;S477N;T95I;A67V;L5F;S494P;V1176F 139;167;161;133;156;116;183 144;172;165;137;159;121;189 34067745 An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. Recently, a new PangoLIN lineage (B.1.617) was identified in Indian SARS-CoV-2 sequences, with the E484Q and L452R mutation (commonly known as a double mutant) in the spike protein of SARS-CoV-2, which is considered to have higher transmission rates. 2021 Viruses Discussion SARS_CoV_2 E484Q;L452R 99;109 104;114 S 167 172 34067745 An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. The amino acid mutation:L3606F in the NSP6 region of ORF1ab:is quite intriguing. 2021 Viruses Discussion SARS_CoV_2 L3606F 24 30 ORF1ab;Nsp6 53;38 59;42 34067745 An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India. The SARS-CoV-2 sequence analyses during the period between January and August 2020 revealed the presence of the E484Q mutation in the spike protein. 2021 Viruses Discussion SARS_CoV_2 E484Q 112 117 S 134 139 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. As an example of application, we have used the simulations as guide to evaluate how the novel N501Y mutation may modulate the affinity between virus and host (Figure 3). 2021 Viruses Discussion SARS_CoV_2 N501Y 94 99 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Here, by uncovering the prominent role of Asn90 glycan in forming contacts with RBD, our simulations indicate how Asn90-glycan sterics may impede the binding, as well as the unbinding of RBD. 2021 Viruses Discussion SARS_CoV_2 N90G 114 123 RBD;RBD 80;187 83;190 34067878 Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Specifically, our analysis suggests that N501Y leads to additional stabilizing interactions (i.e., with Y41 and K353 of host ACE2, see Figure 3b) that can facilitate virus binding. 2021 Viruses Discussion SARS_CoV_2 N501Y 41 46 34073577 Kinetics of Neutralizing Antibodies of COVID-19 Patients Tested Using Clinical D614G, B.1.1.7, and B 1.351 Isolates in Microneutralization Assays. The patients from which the paired samples in this study were collected with high likelihood experienced D614G infection in spring 2020. 2021 Viruses Discussion SARS_CoV_2 D614G 105 110 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. Besides bamlanivimab, E484K mutation has been reported to escape the recognition of more monoclonal antibodies targeting RBD region. 2021 mAbs Discussion SARS_CoV_2 E484K 22 27 RBD 121 124 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. However, these additional mutations within the RBD regions, such as E484K besides N501Y within both the South African and Brazilian variants, cause complete loss of efficacy of bamlanivimab. 2021 mAbs Discussion SARS_CoV_2 E484K;N501Y 68;82 73;87 RBD 47 50 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. Interestingly, detailed analysis showed that introduction of the E484K mutation alone within RBD (K484/Y5010-RBD) does not affect the binding affinity to ACE2, while a single mutation of K417N in the South African variant confers a dramatic drop of the binding affinity. 2021 mAbs Discussion SARS_CoV_2 E484K;K417N 65;187 70;192 RBD;RBD 93;109 96;112 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. On the other hand, although the E484K mutation does not affect the binding between RBD and ACE2, it completely abolishes the binding of RBD to bamlanivimab. 2021 mAbs Discussion SARS_CoV_2 E484K 32 37 RBD;RBD 83;136 86;139 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. The extent of escape should correlate with how much E484 contributes to the RBD and antibody interaction, as E484K mutation would not only lose the negatively charged glutamic acid side chain, but add positively charged lysine side chain. 2021 mAbs Discussion SARS_CoV_2 E484K 109 114 RBD 76 79 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. The introduction of K417T existing from the Brazilian variant should lead to the similar drop due to the loss of potential salt bridges. 2021 mAbs Discussion SARS_CoV_2 K417T 20 25 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. To our surprise, the additional K417N mutation within RBD region of the Spike from the South African variant lowers the binding affinity of this RBD (417 N/484 K/501Y-RBD) to ACE2 almost fivefold, although it remains ~ 2-fold higher than that of wildtype to ACE2. 2021 mAbs Discussion SARS_CoV_2 K417N 32 37 S;RBD;RBD;RBD 72;54;145;167 77;57;148;170 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. We found that a single mutation, N501Y, found in the United Kingdom variant, conferred an ~10-fold higher binding affinity of the RBD of the SARS-CoV-2 Spike protein to ACE2, the receptor from human host, compared to that of wildtype RBD and ACE2. 2021 mAbs Discussion SARS_CoV_2 N501Y 33 38 S;RBD;RBD 152;130;234 157;133;237 34074219 501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to bamlanivimab in vitro. We showed previously that higher concentrations of the antibody may be needed to treat COVID-19 patients infected with the United Kingdom variant compared to patients with wildtype virus, even though N501Y mutation does not affect the binding of bamlanivimab. 2021 mAbs Discussion SARS_CoV_2 N501Y 200 205 COVID-19 87 95 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. All samples from family cluster-1 revealed another spike protein mutation, V213A, besides D614G. 2021 BMC medical genomics Discussion SARS_CoV_2 D614G;V213A 90;75 95;80 S 51 56 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. B.1.1.7 variant (multiple spike protein mutations: deletion 69-70, deletion 144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H). 2021 BMC medical genomics Discussion SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 88;123;95;81;102;116;109 93;129;100;86;107;121;114 S 26 31 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Currently, besides the D614G variant, several mutations within the receptor binding domains (RBD) of the S protein have attracted most scientists' attention due to their increased frequency in certain countries, including S477N (Australia and some Central European), N439K (UK and European), and N501Y (part of the new UK variant B.1.1.7, the new South Africa variant 501.V2 and the new Brazil variant P.1). 2021 BMC medical genomics Discussion SARS_CoV_2 D614G;N439K;N501Y;S477N 23;267;296;222 28;272;301;227 RBD;RBD;S 67;93;105 91;96;106 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Double mutations of V213A and D614G on spike protein were detected in four patients, but three of them (75%) developed severe diseases causing critical conditions and two (50%) with fatal outcome. 2021 BMC medical genomics Discussion SARS_CoV_2 D614G;V213A 30;20 35;25 S 39 44 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Globally, D614G has been detected in ~ 97% samples in 182 countries. 2021 BMC medical genomics Discussion SARS_CoV_2 D614G 10 15 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. However, virus samples isolated from fatal disease outcomes carried V247A mutation in the NSP2 protein, while those from the recovered patient did not. 2021 BMC medical genomics Discussion SARS_CoV_2 V247A 68 73 Nsp2 90 94 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. In conjunction with D614G mutation, substitution of valine (V) to alanine (A) in position 247 and 213 of NSP2 and spike protein, respectively, were detected in the patients with fatal disease outcomes. 2021 BMC medical genomics Discussion SARS_CoV_2 D614G 20 25 S;Nsp2 114;105 119;109 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. L, G, GH, GR, and O, in the SARS-CoV-2 samples from Indonesia and most of them (~ 60%) contained D614G. 2021 BMC medical genomics Discussion SARS_CoV_2 D614G 97 102 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. L5F, V213A, W258R, Q677H, and K811I. 2021 BMC medical genomics Discussion SARS_CoV_2 K811I;Q677H;V213A;W258R;L5F 30;19;5;12;0 35;24;10;17;3 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Moreover, it is difficult to assess the convergent evolution of D614G mutation in our samples since all samples were from Yogyakarta and Central Java and D614G has been already found in most samples (97%) from all over the world. 2021 BMC medical genomics Discussion SARS_CoV_2 D614G;D614G 64;154 69;159 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. Noteworthy, the V213A variant was identified in all patients from family cluster-1. 2021 BMC medical genomics Discussion SARS_CoV_2 V213A 16 21 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. proposed a more complex selective landscape in the spike protein for the co-occurring variants between D614G and the neighbouring sites (615 and 613). 2021 BMC medical genomics Discussion SARS_CoV_2 D614G 103 108 S 51 56 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. The hypothesis of convergent evolution for D614G mutation is not supported by the sequence data since almost all 614G variants derived from the same ancestor. 2021 BMC medical genomics Discussion SARS_CoV_2 D614G 43 48 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. V213A was detected in 4/17 (23.5%) of our samples. 2021 BMC medical genomics Discussion SARS_CoV_2 V213A 0 5 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. While a recent study showed that D614G mutation is significantly associated with the increase of SARS-CoV-2 infectivity, competitive fitness, and transmission in primary human airway epithelial cells and hamsters, it does not associate with the clinical severity of COVID-19 patients. 2021 BMC medical genomics Discussion SARS_CoV_2 D614G 33 38 COVID-19 266 274 34074255 Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters. While both V and A, as well as G are in the non-polar hydrophobic amino acid group and no evidence shows that the double mutations of V213A and D614G affect the severity and lethality of COVID-19 patients, further investigations are necessary to determine whether these dual mutations (V213A and D614G in spike protein) or even triple mutations (V213A and D614G in spike protein and V47A in NS2) associated with increased risk of mortality in COVID-19 patients. 2021 BMC medical genomics Discussion SARS_CoV_2 D614G;D614G;D614G;V213A;V47A;V213A;V213A 144;296;356;134;383;286;346 149;301;361;139;387;291;351 S;S 305;365 310;370 COVID-19;COVID-19 443;187 451;195 34081630 Epitope-specific antibody responses differentiate COVID-19 outcomes and variants of concern. All 3 VOCs harbor an N501Y mutation within S-RBD, while the B.1.351 and P.1 variants contain 2 additional RBD changes, K417N/T and E484K. 2021 JCI insight Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y 131;119;119;21 136;126;126;26 RBD;RBD;S 45;106;43 48;109;44 34081630 Epitope-specific antibody responses differentiate COVID-19 outcomes and variants of concern. Besides the RBD, a P681H mutation located in the S1/S2 linker region of the spike has been detected in multiple VOCs. 2021 JCI insight Discussion SARS_CoV_2 P681H 19 24 S;RBD 76;12 81;15 34081630 Epitope-specific antibody responses differentiate COVID-19 outcomes and variants of concern. Nevertheless, we note that the P681H and S235F mutations only affected a few individuals in the cohort of patients examined herein while the majority of patients displayed no apparent antibody responses against the corresponding epitopes. 2021 JCI insight Discussion SARS_CoV_2 P681H;S235F 31;41 36;46 34081630 Epitope-specific antibody responses differentiate COVID-19 outcomes and variants of concern. We found that the P681H mutation in the spike and the S235F in the nucleocapsid rendered the corresponding epitopes completely incapable of binding antibodies generated against the original virus. 2021 JCI insight Discussion SARS_CoV_2 P681H;S235F 18;54 23;59 N;S 67;40 79;45 34081630 Epitope-specific antibody responses differentiate COVID-19 outcomes and variants of concern. While it remains to be determined whether these mutations mediate immune escape of the corresponding VOCs in some patients, our findings imply that the P681H mutation may render the WT spike mRNA-based vaccine less effective to those who employ S-671 (which encompasses the mutated residue) as a major epitope. 2021 JCI insight Discussion SARS_CoV_2 P681H 152 157 S;S 185;245 190;246 34087220 Synthetic proteins for COVID-19 diagnostics. Although the N501Y mutant did not alter neutralization by polyclonal antibodies in some test sera, other changes in this area at the interface of the RBD and its ACE2 receptor. 2021 Peptides Discussion SARS_CoV_2 N501Y 13 18 RBD 150 153 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. A comprehensive analysis of >12 300 SARS-CoV-2 genome sequences across 28 countries reported that mutation at P4715L and D614G may correlate with higher fatality rates. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G;P4715L 121;110 126;116 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. G25563T leads to the Q57H missense mutation ORF3a that is associated with host cell apoptosis and contributes to increased infectivity and virulence. 2021 Open forum infectious diseases Discussion SARS_CoV_2 Q57H;G25563T 21;0 25;7 ORF3a 44 49 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. Genomic evaluation of SARS-CoV-2 in this cohort demonstrated that nearly all of our isolates carried the D614G mutation in the spike protein. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G 105 110 S 127 132 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. ORF1ab P4715L is located in Nsp12, which is important for viral replication. 2021 Open forum infectious diseases Discussion SARS_CoV_2 P4715L 7 13 ORF1ab;Nsp12 0;28 6;33 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. The D614G mutation has been shown to have been rapidly fixed in isolates from Europe and North America and has been associated with lower Ct values in vitro and in vivo, but not with disease severity or case fatality rates. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G 4 9 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. The role of the D614G mutation in SARS-CoV-2 pathogenicity continues to be a focus of active investigation. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G 16 21 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. Two additional mutations (C1059T and G25563T) differentiate phylogenetic clade 20C from 20A and 20B, and at least 1 of these may potentially be associated with increased disease severity. 2021 Open forum infectious diseases Discussion SARS_CoV_2 G25563T;C1059T 37;26 44;32 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. We also identified the 2 common mutations (F924F and P4715L) alongside the D614G mutation in our isolates. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G;P4715L;F924F 75;53;43 80;59;48 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. We also observed an unexpectedly increased mutation rate (22.5 substitutions per year) in this cohort when compared with other SARS-CoV-2 cases from California without the D614G mutation during the same period (13.5 substitutions per year). 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G 172 177 34095334 High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19. We postulate that the increased transmissibility caused by D614G may have also led to this increased mutation rate. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G 59 64 34097003 Detecting SARS-CoV-2 and its variant strains with a full genome tiling array. Mutations like D614G cause immense concerns because they occur in the spike protein, which are the targets of current SARS-CoV-2 vaccines. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D614G 15 20 S 70 75 34097003 Detecting SARS-CoV-2 and its variant strains with a full genome tiling array. Of the eight samples, four had the D614G mutation in the spike protein. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D614G 35 40 S 57 62 34097003 Detecting SARS-CoV-2 and its variant strains with a full genome tiling array. Our samples were collected around May 2020, a few months after the outbreak in the United States; thus, it may suggest that the D614G variant was abundant from the start of the US outbreak. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D614G 128 133 34097003 Detecting SARS-CoV-2 and its variant strains with a full genome tiling array. The most infamous adverse mutation is D614G in the spike protein, which appeared first in eastern China and spread around the world soon after. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D614G 38 43 S 51 56 34097003 Detecting SARS-CoV-2 and its variant strains with a full genome tiling array. These two mutations might be populated at a lower frequency than the D614G mutation, as evidenced by only one of the eight samples. 2021 Briefings in bioinformatics Discussion SARS_CoV_2 D614G 69 74 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. Additionally, a patient who received the second shot of mRNA-1273 vaccine (Moderna) was infected with SARS-CoV-2 harboring the E484K mutation, despite having a serum neutralizing antibody titer that is normally sufficient to prevent infection. 2021 PLoS pathogens Discussion SARS_CoV_2 E484K 127 132 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. Furthermore, the W152L mutation is located in the N3 loop of the NTD and may be related to decreased antibody neutralization activity. 2021 PLoS pathogens Discussion SARS_CoV_2 W152L 17 22 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. In Brazil, a patient was re-infected with SARS-CoV-2 carrying the E484K mutation, indicating that this mutation is related to escape from neutralizing antibodies in recovered patients. 2021 PLoS pathogens Discussion SARS_CoV_2 E484K 66 71 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. In the present study, we observed an expansion in Japan of R.1 lineage SARS-CoV-2 harboring the spike RBD E484K and spike NTD W152L mutations, which have potential significance for immune escape. 2021 PLoS pathogens Discussion SARS_CoV_2 E484K;W152L 106;126 111;131 S;S;RBD 96;116;102 101;121;105 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. Previous reports showed that COVID-19 convalescent and mRNA vaccine-elicited sera/plasma have reduced neutralizing activity against SARS-CoV-2 harboring the E484K mutation. 2021 PLoS pathogens Discussion SARS_CoV_2 E484K 157 162 COVID-19 29 37 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. The new emergent lineage B.1.429, which has a substitution in the same codon 152 (W152C), was first identified in California, United States; this lineage is defined as a "Variant of Interest" by the US Centers for Disease Control and Prevention (CDC). 2021 PLoS pathogens Discussion SARS_CoV_2 W152C 82 87 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. The W152C mutation is located in the NTD antigenic supersite (designated site i) and is also associated with reduced recognition of the NTD by neutralizing monoclonal antibodies. 2021 PLoS pathogens Discussion SARS_CoV_2 W152C 4 9 34097716 Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan. Worryingly, the E484K mutation has been identified in SARS-CoV-2 "Variants of Concern", such as B.1.351 (South Africa) and P.1 (Brazil), and in SARS-CoV-2 "Variants of Interest", such as B.1.526 (New York, NY, USA), B.1.525 (United Kingdom/Nigeria), and P.2 (Brazil). 2021 PLoS pathogens Discussion SARS_CoV_2 E484K 16 21 34098567 Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. As this region lies outside the ACE2-binding motif, nanobody-RBD contacts are unaffected by the E484K or N501Y substitutions. 2021 Nature Discussion SARS_CoV_2 E484K;N501Y 96;105 101;110 RBD 61 64 34098567 Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants. First, similar to human antibodies, llama nanobodies (Nb15 and Nb56) hinder ACE2 binding to the spike of the original virus, but they are ineffective against viruses that carry E484K or N501Y substitutions. 2021 Nature Discussion SARS_CoV_2 E484K;N501Y 177;186 182;191 S 96 101 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Although the onset of diarrhea and viral shedding were slightly delayed in E191A-P4-inoculated pigs, it may be resulted from pigs of different day ages when being inoculated. 2021 Cell & bioscience Discussion SARS_CoV_2 E191A 75 80 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Among all 13 mutants they designed, only the one carrying E191D mutation could be recovered. 2021 Cell & bioscience Discussion SARS_CoV_2 E191D 58 63 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Both innate and adaptive immune responses may contribute to the partial protection provided by E191A-P1 infection. 2021 Cell & bioscience Discussion SARS_CoV_2 E191A 95 100 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Compared with wild type PEDV, E191A-P1 with deficient proofreading activity must have a higher mutation rate. 2021 Cell & bioscience Discussion SARS_CoV_2 E191A 30 35 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Eight recombinant PEDVs with inactivated nsp14 were designed and subjected for recovery, and only one bearing E191A mutation was rescued. 2021 Cell & bioscience Discussion SARS_CoV_2 E191A 110 115 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Even the reversion event occurred in pig#8 in E191A-P1 group, the pig did not develop watery diarrhea or high level of viral RNA shedding as virulent icPC22A inoculated pigs. 2021 Cell & bioscience Discussion SARS_CoV_2 E191A 46 51 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Five pigs initially inoculated with E191A-P1 without viral RNA shedding in feces or diarrhea by 3 dpi were re-inoculated with E191A-P4 (100 TCID50/pig) to characterize the pathogenesis of E191A-P4. 2021 Cell & bioscience Discussion SARS_CoV_2 E191A;E191A;E191A 36;126;188 41;131;193 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. If more pigs were tested, E191A-P1 reversion may occur at different dpi. 2021 Cell & bioscience Discussion SARS_CoV_2 E191A 26 31 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. In our study, partial protection from severe diarrhea and viral shedding was induced by E191A-P1 infection. 2021 Cell & bioscience Discussion SARS_CoV_2 E191A 88 93 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. In summary, we showed that the recombinant PEDV mutant E191A with deficient nsp14-ExoN was viable, but it replicated poorly in vitro and in vivo. 2021 Cell & bioscience Discussion SARS_CoV_2 E191A 55 60 Exon 82 86 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. In terms of adaptive immunity, although replicating poorly, E191A-P1 mutant elicited VN antibody titers by 15 dpi. 2021 Cell & bioscience Discussion SARS_CoV_2 E191A 60 65 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. In the four pigs inoculated with E191A-P1 mutant, three pigs (3/4, 75%) had positive viral RNA shedding in feces, and the mutant virus in pig #8 reverted at 2 dpi by sequence analyses. 2021 Cell & bioscience Discussion SARS_CoV_2 E191A 33 38 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. In vitro growth curve showed that the RNA level of E191A-P1 kept increasing even the infectious titer started to drop after 48 hpi. 2021 Cell & bioscience Discussion SARS_CoV_2 E191A 51 56 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. It suggested that RNA synthesis for E191A-P1 was competent but accumulated mutations caused the deficiency in generation of infectious progeny. 2021 Cell & bioscience Discussion SARS_CoV_2 E191A 36 41 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. It would be more informative if the enzymatic activity of nsp14-ExoN of E191A-P1 mutant is characterized. 2021 Cell & bioscience Discussion SARS_CoV_2 E191A 72 77 Exon 64 68 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. Possible reasons are listed here: (1) There were potential compensate mutations throughout the viral genome of the reverted virus, which were acquired during viral replication in the pig and may contribute to this attenuated phenotype; (2) local mucosal immune response elicited by limited E191A-P1 replication at the early stage of infection help protect the pig from severe diarrhea which could be caused by the reverted virus. 2021 Cell & bioscience Discussion SARS_CoV_2 E191A 290 295 34099051 Crucial mutation in the exoribonuclease domain of nsp14 of PEDV leads to high genetic instability during viral replication. The whole genome sequencing of it illustrated that the P4 of E191A mutant has lost the introduced E191A mutation. 2021 Cell & bioscience Discussion SARS_CoV_2 E191A;E191A 61;98 66;103 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. A small number of samples from individuals infected with (B.1.351) and without (B.1.177, B.1.1.163, B.1.258) the E484K mutation (B.1.351) were available for comparison. 2021 medRxiv Discussion SARS_CoV_2 E484K 113 118 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Cohort sizes were not sufficient for statistical analyses of significance but temporally-matched transcriptomes did show variation from B.1.1.7 and B.1.1.7+E484K. 2021 medRxiv Discussion SARS_CoV_2 E484K 156 161 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. Five and three individuals died in B.1.1.7 and B.1.1.7+E484K groups, respectively. 2021 medRxiv Discussion SARS_CoV_2 E484K 55 60 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. However, the significant differences in transcriptome response between B.1.1.7 and B.1.1.7+E484K infected individuals persisted even if these vaccinated individuals, documenting the reproducibility of the finding across clinical settings. 2021 medRxiv Discussion SARS_CoV_2 E484K 91 96 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. In summary, our study documents that the E484K mutation is sufficient to alter transcriptome response. 2021 medRxiv Discussion SARS_CoV_2 E484K 41 46 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. In this study the majority of this hospitalized population received corticosteroid treatment, which may have modified immune response, but as there were no significant differences in the percentage treated between B.1.1.7 and B.1.1.7+E484K patients, this was not the reason for the significant differences in transcriptome response found. 2021 medRxiv Discussion SARS_CoV_2 E484K 234 239 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. The RBD mutation, E484K, first detected in the B.1.351 variant, has evolved independently in infected individuals in different genetic SARS-CoV-2 backgrounds. 2021 medRxiv Discussion SARS_CoV_2 E484K 18 23 RBD 4 7 34100027 Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. There was no significant difference in deaths between B.1.1.7 and B.1.1.7+E484K infection. 2021 medRxiv Discussion SARS_CoV_2 E484K 74 79 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. After two mutations, including the synonymous mutation T8782C and the non-synonymous mutation C28144T, by replacing serine with leucine in type A, type B is formed. 2021 European journal of medical research Discussion SARS_CoV_2 C28144T;T8782C 94;55 101;61 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. Concurrently, a specific mutation (D614G) in the S protein might speed up the viral transmission. 2021 European journal of medical research Discussion SARS_CoV_2 D614G 35 40 S 49 50 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. Eke, one of the mutations in S protein (D614G), has been seen repeatedly in Europe and the United States since the onset of the infection, apparently because it has dramatically increased the transmission ability of SARS-CoV-2. 2021 European journal of medical research Discussion SARS_CoV_2 D614G 40 45 S 29 30 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. H49Y mutation in the S protein may also be responsible for local transmissions in earlier stages. 2021 European journal of medical research Discussion SARS_CoV_2 H49Y 0 4 S 21 22 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. In a survey conducted in mid-March in Mexico, evidence of local translocation of strains with an H49Y mutation in Spike protein strains was reported. 2021 European journal of medical research Discussion SARS_CoV_2 H49Y 97 101 S 114 119 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. In other words, the S variant (Type A) with two mutations at 8782C>T and 28144 T>C was mainly identified in East Asia. 2021 European journal of medical research Discussion SARS_CoV_2 T28144C;C8782T 73;61 82;68 S 20 21 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. Meanwhile, a unique mutation 24351C (A930V (T)) in the spike surface glycoprotein was reported in one of the Wuhan strains in India. 2021 European journal of medical research Discussion SARS_CoV_2 A930V 37 42 S;S 61;55 81;60 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. reported C14408T variant on Nsp12 and A23403G variation on S protein, and both cause significant mutations and changes in virus variants worldwide. 2021 European journal of medical research Discussion SARS_CoV_2 A23403G;C14408T 38;9 45;16 Nsp12;S 28;59 33;60 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. The role of QHD43416 p.Asp614Gly variant in many strains is controversial and not fully understood. 2021 European journal of medical research Discussion SARS_CoV_2 D614G;D614G 21;23 32;32 34103090 Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review. Type C is also derived from type B by the non-synonymous mutation G26144T, in which valine replaces glycine. 2021 European journal of medical research Discussion SARS_CoV_2 G26144T 66 73 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Among the six dominant mutation types, V367F mutants that emerged in Asia and Europe displayed enhanced structural stability of the spike protein along with higher binding affinities to the human ACE2 receptor. 2021 Journal of virology Discussion SARS_CoV_2 V367F 39 44 S 132 137 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Among them, V483A in MERS-CoV and N439K in SARS-CoV resulted in reduced host receptor binding. 2021 Journal of virology Discussion SARS_CoV_2 N439K;V483A 34;12 39;17 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. As RBD is conserved in SARS-CoV-2, the coincidence of V367F mutants across large geographic distances indicates that this mutation is more robust and that these variants originated as a novel sublineage, given the close isolation dates (22 and 23 January 2020, respectively). 2021 Journal of virology Discussion SARS_CoV_2 V367F 54 59 RBD 3 6 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. By tracking the V367F mutation type in the SARS-CoV-2 circulating strains, most of these mutants were first detected within the prototype D614 strains, then together with the G614 variants. 2021 Journal of virology Discussion SARS_CoV_2 V367F 16 21 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. By tracking these recent variants, we find that only the V367F mutation type was detected continually; the other enhanced mutations have disappeared. 2021 Journal of virology Discussion SARS_CoV_2 V367F 57 62 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Compared to that of the prototype strain Wuhan-Hu-1, the DeltaG of the V367F mutation decreased ~25%. 2021 Journal of virology Discussion SARS_CoV_2 V367F 71 76 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. D614G is distinct from the RBD mutations: it is not located in the RBD but enhances viral infectivity by elevating its sensitivity to proteases and increasing stability. 2021 Journal of virology Discussion SARS_CoV_2 D614G 0 5 RBD;RBD 27;67 30;70 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. For example, through deep mutation scanning, an assumed N501F mutation was confirmed to have enhanced binding efficiency while not emergent, but later, the N501Y mutation in the same position with a similar enhancing effect was frequently detected in emerging lineage B1.1.7 variants. 2021 Journal of virology Discussion SARS_CoV_2 N501F;N501Y 56;156 61;161 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Furthermore, D614G and V367F may function independently and have synergistic effects on viral infectivity. 2021 Journal of virology Discussion SARS_CoV_2 D614G;V367F 13;23 18;28 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Given the alanine shares similar chemical and structural properties with serine, the A344S variant was expected to have similar affinity to human ACE2 as the prototype strain, which was later confirmed through scanning. 2021 Journal of virology Discussion SARS_CoV_2 A344S 85 90 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Interestingly, we discovered some V367F variants combined with the D614G mutation. 2021 Journal of virology Discussion SARS_CoV_2 D614G;V367F 67;34 72;39 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Phylogenetic analysis of the genomes of V367F mutants showed that during the early transmission phase, most V367F mutants clustered more closely with the SARS-CoV-2 prototype strain than the dual-mutation variants (V367F+D614G) which emerged later and formed a distinct subcluster. 2021 Journal of virology Discussion SARS_CoV_2 V367F;V367F;V367F;D614G 40;108;215;221 45;113;220;226 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. Recombination is known to play an important role in natural coronavirus evolution, which may contribute to the convergence of dual enhancing mutants (D614G+V367F). 2021 Journal of virology Discussion SARS_CoV_2 D614G;V367F 150;156 155;161 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The emergence of dual mutants (V367F+D614G) and other combined mutations possibly due to recombination may hint toward the emergence of other variants with increased infectivity or with enhanced escape from the host immune response. 2021 Journal of virology Discussion SARS_CoV_2 V367F;D614G 31;37 36;42 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The mutant type V367F continuously circulating worldwide displayed higher binding affinity to human ACE2 due to the enhanced structural stabilization of the RBD beta-sheet scaffold. 2021 Journal of virology Discussion SARS_CoV_2 V367F 16 21 RBD 157 160 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The recent emerging variants B.1.1.7, B.1.351, and B.1.429, which are currently threatening the world, also partially harbor the V367F mutation, possibly deriving from other recombination events. 2021 Journal of virology Discussion SARS_CoV_2 V367F 129 134 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The V367F mutants were frequently found during the early transmission phase (Table 1). 2021 Journal of virology Discussion SARS_CoV_2 V367F 4 9 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. The V367F mutation was also confirmed with higher protein expression level and enhanced stability due to the higher melting temperature in mammalian-expressed purified RBD than the prototype RBD. 2021 Journal of virology Discussion SARS_CoV_2 V367F 4 9 RBD;RBD 168;191 171;194 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. This may be because they failed to compete with the dominant D614G variants. 2021 Journal of virology Discussion SARS_CoV_2 D614G 61 66 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. This may partly explain why V367F has not been dominant in the subsequent epidemic. 2021 Journal of virology Discussion SARS_CoV_2 V367F 28 33 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. This suggests that the V367F mutants are stable and have acquired increased infectivity for humans during the COVID-19 pandemic. 2021 Journal of virology Discussion SARS_CoV_2 V367F 23 28 COVID-19 110 118 34105996 V367F Mutation in SARS-CoV-2 Spike RBD Emerging during the Early Transmission Phase Enhances Viral Infectivity through Increased Human ACE2 Receptor Binding Affinity. V367F mutants were circulating along with the D614G mutants. 2021 Journal of virology Discussion SARS_CoV_2 D614G;V367F 46;0 51;5 34106048 FnCas9-based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV-2 variants on a paper strip. For example, determining whether a sample belongs to the South African lineage through E484K specific RAY can allow early quarantine of the patient and prevent the spreading of a highly transmissible variant. 2021 eLife Discussion SARS_CoV_2 E484K 87 92 34107326 SARS-CoV-2 reinfection with a virus harboring mutation in the Spike and the Nucleocapsid proteins in Panama. D215A in the NTD of Spike has not been described; however, D215G has been detected in the VOC B.1.351. 2021 International journal of infectious diseases Discussion SARS_CoV_2 D215G;D215A 59;0 64;5 S 20 25 34107326 SARS-CoV-2 reinfection with a virus harboring mutation in the Spike and the Nucleocapsid proteins in Panama. D614G mutation in S, with a higher affinity for ACE2 receptor, results in increased infectivity and higher virus transmission; probably explaining why this mutation, detected in most dominant variants, has overtaken the entire globe. 2021 International journal of infectious diseases Discussion SARS_CoV_2 D614G 0 5 S 18 19 34107326 SARS-CoV-2 reinfection with a virus harboring mutation in the Spike and the Nucleocapsid proteins in Panama. In the N protein, residues S194 and M234 are some of the most mutated, suggesting a purifying selection, and mutation P365S was associated with B cell epitopes, suggesting that it could also let to an immune escape phenotype. 2021 International journal of infectious diseases Discussion SARS_CoV_2 P365S 118 123 N 7 8 34107326 SARS-CoV-2 reinfection with a virus harboring mutation in the Spike and the Nucleocapsid proteins in Panama. SARS-CoV-2 genome analysis showed that both infections were induced by viruses from Panamanian endemic lineages, A.2.4 for the first, and A.2.5, containing Spike mutations D614G and L452R, for the second. 2021 International journal of infectious diseases Discussion SARS_CoV_2 D614G;L452R 172;182 177;187 S 156 161 34107326 SARS-CoV-2 reinfection with a virus harboring mutation in the Spike and the Nucleocapsid proteins in Panama. Spike mutation L452R, decreasing sensitivity to neutralizing antibodies, has been associated with immune escape and reinfection and is present in the variant of interest (VOI) B.1.526.1, and the variants of concern (VOC) B.1.427 and B.1.429. 2021 International journal of infectious diseases Discussion SARS_CoV_2 L452R 15 20 S 0 5 34107326 SARS-CoV-2 reinfection with a virus harboring mutation in the Spike and the Nucleocapsid proteins in Panama. The observed 3 amino acid deletion (L141del, G142del, V143del) in S was located in an epitope involved in the generation of neutralizing antibodies and Y144del detected in the VOC B.1.1.7. 2021 International journal of infectious diseases Discussion SARS_CoV_2 G142del;V143del;Y144del;L141del 45;54;152;36 52;61;159;43 S 66 67 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. In our study, in addition to SARS-CoV-2 wild type strain, we tested a panel of emerging SARS-CoV-2 variants using VSV-based SARS-CoV-2 pseudovirus neutralization assay, including the D614G variant, the United Kingdom B.1.1.7 variant, the California B.1.429 variant, the Brazil P.1 variant, the New York B.1.526 variant, and the Brazil B.1.351 variant. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 183 188 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. Notably, 1H1 was also able to neutralize all six emerging SARS-CoV-2 mutant variants tested including D614G, B.1.1.7, B.1.429, P.1, B.1.526 and B.1.351 variants. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 102 107 34120577 Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. Our vaccine-induced RBD-specific mAbs, 9H1, 7G5, 5E1 and 1H1, recognized not only RBD and S1 protein with high binding affinity, but also some recently emerging RBD variant proteins including RBD N501Y, RBD 417N, RBD E484K, and RBD N501Y/K47N/E484K. 2021 Emerging microbes & infections Discussion SARS_CoV_2 E484K;N501Y;N501Y;E484K;K47N 217;196;232;243;238 222;201;237;248;242 RBD;RBD;RBD;RBD;RBD;RBD;RBD 20;82;161;192;203;213;228 23;85;164;195;206;216;231 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Finding mutations with a clinical impact such as E484K might have significant implications for public health policies, surveillance, and immunization strategies; therefore, we consider that the world's health authorities should consider the intentional search for mutations with important biological effects. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 E484K 49 54 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. The E484K mutation is found within the RBD (a major target of neutralizing antibodies elicited during the primary exposure to SARS-CoV-2); thus, this mutation has been predicted to affect antibody neutralization. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 E484K 4 9 RBD 39 42 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. The full genome sequence showed the identification of the P.2 lineage through phylogenomic analysis in four samples whereas this E484K was detected with our RT-qPCR screening assay. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 E484K 129 134 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. The mutation E484K, first identified in march 2020 and then identified as a part of 501Y.V2 (B.1.351) and 484K.V1 (P.1) SARS-CoV-2 variants, has now been identified in the UK fast-spreading variant, prompting fears that the virus is evolving further and could become resistant to vaccines. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 E484K 13 18 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. This finding is important because in Mexico, previously, Hernandez-Huerta et al., only identified the D614G mutation in the spike protein and the L84S mutation in the ORF8 gene and Taboada et al., only reported that the lineages circulating in Mexico changed from late February to March from A2 to B1 but both two studies did not found new lineages establishment in this country. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G;L84S 102;146 107;150 S;ORF8 124;167 129;171 34123874 RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact. Through this directed approach, we were able to find the E484K mutation in our country, and this is a starting point to select these specific cases and study them in greater depth through sequencing. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 E484K 57 62 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. And finally, it should be noted that this NTD mutation co-exists with the previously reported M protein mutation M:V70L, suggesting that M protein mutations also contribute to enhanced biologic "fitness" or pathogenicity of this sub-lineage. 2021 Emerging microbes & infections Discussion SARS_CoV_2 V70L 115 119 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Dozens of SARS-CoV-2 genomes that carry the S:D178H mutation were reported before February, but none of these demonstrated the increased frequency seen when the mutation occurs in the context of the B.1.1.7 lineage. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D178H 46 51 S 44 45 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. In March 2021, the B.1.1.7-M:V70L-S:D178H lineage appeared abruptly at high prevalence (35.6%) in all reported B.1.1.7 isolates in Washington. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D178H;V70L 36;29 41;33 S 34 35 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. It is also of interest that this mutation occurs in the NTD, unlike most of the mutations associated with current VOC that are centred on the spike protein RBD, implying that NTD mutations beyond the original 69-70del and the 144del are of concern. 2021 Emerging microbes & infections Discussion SARS_CoV_2 144del 226 232 S;RBD 142;156 147;159 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. It may thus have a similar immune evasion effect as the HV69-70del and Y144del mutations, or it may further enhance that of the two other mutations, based on the 3D model. 2021 Emerging microbes & infections Discussion SARS_CoV_2 Y144del 71 78 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Phylogenetic analysis revealed a distinct and long branch leading to the new S:D178 branch after M:V70L. 2021 Emerging microbes & infections Discussion SARS_CoV_2 V70L 99 103 S 77 78 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Since the D178H falls in the NTD domain close to the N5 loop, it may alter NTD structure and antibody recognition. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D178H 10 15 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. The appearance of the S:D178H mutation in the context of the B.1.1.7 lineage is temporally associated with the increased incidence of COVID-19 in Washington. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D178H 24 29 S 22 23 COVID-19 134 142 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. The potential effect of the S:D178H mutation on immunity and vaccine "escape" also warrant further analysis. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D178H 30 35 S 28 29 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. The rapid increase in its prevalence, only after its acquisition by the B.1.1.7-M:V70L sub-lineage suggests this combination of mutations is associated with increased transmissibility. 2021 Emerging microbes & infections Discussion SARS_CoV_2 V70L 82 86 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. The S:D178H mutation arose independently again in the US on the B.1.1.7-M:V70L background. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D178H;V70L 6;74 11;78 S 4 5 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. The S:D178H mutation, while demonstrably associated here with the more pathogenic B.1.1.7 lineage, is not necessarily by itself more pathogenic. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D178H 6 11 S 4 5 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. These findings highlight the continued importance of active genomic surveillance to monitor the spread of this B.1.1.7-M:V70L-S:178H lineage. 2021 Emerging microbes & infections Discussion SARS_CoV_2 V70L 121 125 S 126 127 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. This is the same observed with other deleterious mutations like the N501Y and E484K mutations, both of which are now superimposed on distinct and separate more pathogenic lineages (https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html). 2021 Emerging microbes & infections Discussion SARS_CoV_2 E484K;N501Y 78;68 83;73 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Together, these observations suggest that the S:D178H mutation is recurrent, but only increased exponentially in the context of the more pathogenic B.1.1.7 lineage, which serves as an argument for its fitness. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D178H 48 53 S 46 47 34125658 Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. We found only 29 sequences belonging to the B.1.1.7 lineage, among which only one carried M:V70L and S:D178H mutations. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D178H;V70L 103;92 108;96 S 101 102 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. Mutations T478A, F490S, and S494P, in particular, are located very close to amino acid 484, known to have an effect on virus antigenicity, as discussed above. 2021 mSystems Discussion SARS_CoV_2 F490S;S494P;T478A 17;28;10 22;33;15 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. On the other hand, identification of locally circulating VOCs could be delayed using ES at sites that cover very large populations, and therefore community-based ES targeting smaller populations would increase the sensitivity for detection of such VOCs, e.g., current efforts to track down transmission of B.1.1.7 viruses harboring mutation E484K in England could be helped by community-based ES in areas where isolation of such viruses are known to have occurred. 2021 mSystems Discussion SARS_CoV_2 E484K 341 346 34128696 Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. The G23012A nucleotide substitution present in both B.1.351 and P.1 lineages and responsible for spike amino acid change E484K, thought to play a critical role at changing virus antigenicity and reducing human immune response to the virus and vaccine efficacy, was not detected in viral genomes from sewage. 2021 mSystems Discussion SARS_CoV_2 E484K;G23012A 121;4 126;11 S 97 102 34134034 Rapid and simultaneous identification of three mutations by the Novaplex SARS-CoV-2 variants I assay kit. In Japan, as of April 23, 2021, randomly selected COVID-19-positive samples were tested for the N501Y mutation at local public health institutes and affiliated hospitals, and the positive samples along with a few negative ones were sent to a central public health institute (National Institute of Infectious Diseases, Tokyo, Japan) for whole-genome sequencing. 2021 Journal of clinical virology Discussion SARS_CoV_2 N501Y 96 101 COVID-19 50 58 34134034 Rapid and simultaneous identification of three mutations by the Novaplex SARS-CoV-2 variants I assay kit. We detected two samples with the E484K mutation and without the N501Y mutation in this study. 2021 Journal of clinical virology Discussion SARS_CoV_2 E484K;N501Y 33;64 38;69 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. According to GISAID data (March 10, 2021), the amino acid change K444R has been detected in 36 sequences from 5 countries and the last strain with such a mutation was reported from England (EPI_ISL_777390) in December 2020. 2021 Frontiers in public health Discussion SARS_CoV_2 K444R 65 70 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. Notably, two SGTF samples (NIH-4490AB and NIH-5872BE) showed no such mutations whereas sample NIH-4774AE had two rare mutations K444R and V445L. 2021 Frontiers in public health Discussion SARS_CoV_2 K444R;V445L 128;138 133;143 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. Our study did not evaluate the functional impact of H655P mutation on the fusion efficiency of spike protein, however, highlights the importance of continuous monitoring of amino acid changes in the spike region of circulating strains. 2021 Frontiers in public health Discussion SARS_CoV_2 H655P 52 57 S;S 95;199 100;204 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. Previously, H655Y (655Histidine > Tyrosine) amino acid change has been shown to confer escape from monoclonal antibodies in cell culture systems. 2021 Frontiers in public health Discussion SARS_CoV_2 H655Y 12 17 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. Similarly, the V445L change has only been reported once in a strain collected on December 28, 2020 from Denmark (hCoV-19/Denmark/DCGC-24535/2020; EPI_ISL_795176). 2021 Frontiers in public health Discussion SARS_CoV_2 V445L 15 20 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. The emergence of B.1.1.7 lineage with S:E484K cases in the UK followed by its detection in other countries highlights the need for continuous surveillance in Pakistan. 2021 Frontiers in public health Discussion SARS_CoV_2 E484K 40 45 S 38 39 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. The sequencing results confirmed 93% (n = 29/31) cases as B.1.1.7, having the marker S protein mutations (N501Y, A570D, P681H, and T716I). 2021 Frontiers in public health Discussion SARS_CoV_2 A570D;P681H;T716I;N501Y 113;120;131;106 118;125;136;111 S 85 86 34136461 Proliferation of SARS-CoV-2 B.1.1.7 Variant in Pakistan-A Short Surveillance Account. We also found a novel mutation H655P (655Histidine > Proline) in one of our study sample NIH-5818BB (EPI_ISL_1173505). 2021 Frontiers in public health Discussion SARS_CoV_2 H655P 31 36 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. reported previously on the affinity of their ACE2-FC to S RBD with the D614G mutation. 2021 Scientific reports Discussion SARS_CoV_2 D614G 71 76 RBD;S 58;56 61;57 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. The greater affinity of ACE2 for S RBD with the N501Y substitution alone or in combination with E484K reported here is in alignment with our findings in Nelson et al., wherein we used MD simulation to predict that these mutations have a high probability of increasing affinity for ACE2. 2021 Scientific reports Discussion SARS_CoV_2 E484K;N501Y 96;48 101;53 RBD;S 35;33 38;34 34140558 An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants. To our knowledge, we are the first to report binding affinities of a recombinant mutant ACE2 decoy to the spike receptor binding domain expressing N501Y, E484K, N417Y, or L452R mutations; although we note Huang et al. 2021 Scientific reports Discussion SARS_CoV_2 E484K;L452R;N417Y;N501Y 154;171;161;147 159;176;166;152 RBD;S 112;106 135;111 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. 2 MR (ORF8:L84S and ORF3a:G251V. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 G251V;L84S 26;11 31;15 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Among all the highly recurring mutations, Nsp12:P323L and Spike:D614G are found in majority of the countries (~69%). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;P323L 64;48 69;53 S;Nsp12 58;42 63;47 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Among the moderately recurring mutations, M protein:T175M along with Spike:D614G occur above 25% in the Netherlands. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;T175M 75;52 80;57 S 69 74 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Among them, Clade 2 has originated from the moderately recurring mutation ORF8:L84S and Clade 5 mainly possesses low recurring mutations. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 L84S 79 83 ORF8 74 78 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. As SARS-CoV-2 variants having Spike:D614G mutation (which has enhanced infectivity and transmissibility) have conquered the wild-type across the globe, it is important to analyze the occurrence of high and moderate recurrent mutations along with Spike:D614G. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;D614G 36;252 41;257 S;S 30;246 35;251 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. For instance, Nsp2:T85I and ORF3a:Q57H (mostly occur together) along with Spike:D614G are found to be highly prevalent in USA (Nsp2:T85I and Spike:D614G = ~75% and ORF3a:Q57H and Spike:D614G = ~85%) and Denmark (Nsp2:T85I and Spike:D614G = ~72% and ORF3a:Q57H and Spike:D614G = ~76%) population. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;D614G;D614G;D614G;D614G;Q57H;Q57H;Q57H;T85I;T85I;T85I 80;147;185;232;270;34;170;255;19;132;217 85;152;190;237;275;38;174;259;23;136;221 S;S;S;S;S;ORF3a;ORF3a;ORF3a;Nsp2;Nsp2;Nsp2 74;141;179;226;264;28;164;249;14;127;212 79;146;184;231;269;33;169;254;18;131;216 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. However, Nsp6:L37F has led to Clade 1a and its sub-clade 1b (ORF3a:G251V). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 G251V;L37F 67;14 72;18 ORF3a;Nsp6 61;9 66;13 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. In general, the mutations in the replicase machinery, except Nsp12:P323L, occur with a low recurrence indicating their role in functional conservation and thus, could be potential therapeutic targets. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P323L 67 72 Nsp12 61 66 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Interestingly, 70% of proteome sequences are found under Clade 3 which encompasses 4 sub-clades emerging from Nsp12:P323L, ORF3a:Q57H, N protein:R203K & G204R and Nsp6:T85I mutations indicating their evolutionary advantage. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 G204R;P323L;Q57H;R203K;T85I 153;116;129;145;168 158;121;133;150;172 ORF3a;Nsp12;Nsp6;N 123;110;163;135 128;115;167;136 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Interestingly, R203K and G204R are co-occurring (dependent) mutations as they occur in nearly similar frequency in same countries. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 G204R;R203K 25;15 30;20 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Interestingly, Spike:D614G, Spike:D936Y and ORF3a:V13L mutations are observed in potential B-cell or T-cell epitope regions, thus, may have an influence on the host defence mechanisms. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;D936Y;V13L 21;34;50 26;39;54 S;S;ORF3a 15;28;44 20;33;49 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Intriguingly, some of these mutations are highly prevalent in certain countries compared to the rest of the mutations: P323L, D614G, R203K and G204R in England and P323L, D614G, Q57H and T85I in USA. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;D614G;G204R;P323L;P323L;Q57H;R203K;T85I 126;171;143;119;164;178;133;187 131;176;148;124;169;182;138;191 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Luckily, the availability of the mutations present in the SARS-CoV-2 proteome enables the understanding of the prevalence of certain mutations along with Spike:D614G (TableSD29.xlsx). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 160 165 S 154 159 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Not surprisingly, Spike:D614G and Nsp12:P323L are found together in all the countries with above 95%. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;P323L 24;40 29;45 S;Nsp12 18;34 23;39 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Occurrence of S25L mutation in Nsp7, which is in the proximity to Nsp7-Nsp8 binding interface and the proximity of Nsp12:P323L to the Nsp12-Nsp8 binding site indicate their possible role in modulating the viral replication mechanism. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 S25L;P323L 14;121 18;126 Nsp12;Nsp12;Nsp7;Nsp7;Nsp8;Nsp8 115;134;31;66;71;140 120;139;35;70;75;144 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Similarly, N protein:S194L and Spike:D614G occur ~25% in India. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;S194L 37;21 42;26 S;N 31;11 36;12 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Similarly, Nsp16:P134S located in the cavity that is in proximity to the SAM binding site may have a role in replication modulation (PDB ID: 7BQ7). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P134S 17 22 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. Similarly, Spike:D614G and the co-mutations N protein:R203K and N protein:G204R are highly recurring in countries like Greece (78%), Portugal (68%), Russia (65%), UK (52%), Netherlands (35%) etc. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;G204R;R203K 17;74;54 22;79;59 S;N;N 11;44;64 16;45;65 34147651 Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades. The highly recurring mutations include Nsp2:T85I, Nsp6:L37F, Nsp12:P323L, Spike:D614G, ORF3a:Q57H, N protein:R203K and N protein:G204R which are found across 47, 59, 71, 70, 51, 63 and 63 countries respectively. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;G204R;L37F;P323L;Q57H;R203K;T85I 80;129;55;67;93;109;44 85;134;59;72;97;114;48 S;ORF3a;Nsp12;Nsp2;Nsp6;N;N 74;87;61;39;50;99;119 79;92;66;43;54;100;120 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. Although N501Y mutation increases the binding affinity of SARS-CoV-2 RBD with host ACE2, it has little effect on the binding of antibodies investigated in this study. 2021 Computers in biology and medicine Discussion SARS_CoV_2 N501Y 9 14 RBD 69 72 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. From the binding interactions of P2B-2F6 with SARS-CoV-2, we speculate that the K417V, KVG444-446TST, LF455-6YL and TEI470-2NVP mutations have little effect on the neutralizing activity of P2B-2F6 and the optimized antibodies, but the L452K and S494D mutated pseudotyped virus might reduce the neutralizing activity of the antibodies. 2021 Computers in biology and medicine Discussion SARS_CoV_2 K417V;L452K;S494D 80;235;245 85;240;250 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. However, for other concerning mutations of E484K, E484K/N501Y and K417N/E484K/N501Y observed in some SARS-CoV-2 variants, the neutralizing activity of both the WT antibody and the optimized mutants might be significantly decreased due to the loss of interactions from E484 and the probable appearance of electrostatic repulsion with H:R112 and H:R106 of the antibodies when this glutamate mutates to lysine. 2021 Computers in biology and medicine Discussion SARS_CoV_2 E484K;E484K;K417N;E484K;N501Y;N501Y 43;50;66;72;56;78 48;55;71;77;61;83 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. The most alarming evolution is the newly detected spike mutation N501Y, common among B.1.1.7, B.1.351 and P.1 lineages, which has increased the infectivity of SARS-CoV-2. 2021 Computers in biology and medicine Discussion SARS_CoV_2 N501Y 65 70 S 50 55 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. Therefore, we propose that H:V106R and H:V106R/H:P107Y mutants of P2B-2F6 might have more potent neutralizing activity against SARS-CoV-2 than P2B-2F6. 2021 Computers in biology and medicine Discussion SARS_CoV_2 P107Y;V106R;V106R;V106H 49;29;41;41 54;34;48;48 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. Therefore, we speculate that the optimized antibodies also have high neutralizing activity against N501Y variant of SARS-CoV-2. 2021 Computers in biology and medicine Discussion SARS_CoV_2 N501Y 99 104 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. They found that some of the tested antibodies lost or exhibited less potency against the RBD-mutated pseudotyped virus, including K417V, KVG444-446TST, L452K, LF455-6YL, TEI470-2NVP, and S494D. 2021 Computers in biology and medicine Discussion SARS_CoV_2 K417V;L452K;S494D 130;152;187 135;157;192 RBD 89 92 34147856 Rational optimization of a human neutralizing antibody of SARS-CoV-2. We found that two potent P2B-2F6 mutants, H:V106R and H:V106R/H:P107Y, produce higher binding affinities with the RBD domain of SARS-CoV-2 than others. 2021 Computers in biology and medicine Discussion SARS_CoV_2 P107Y;V106R;V106H;V106R 64;44;56;56 69;49;63;63 RBD 114 117 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Analysis of RBD-variant/ACE2 binding affinity revealed that N501Y and E484K exhibited essentially WT affinity for ACE2, where WT corresponds to the Wuhan-1 SARS-CoV-2 RBD sequence. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;N501Y 70;60 75;65 RBD;RBD 12;167 15;170 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Combined, the 3 SARS-CoV-2 RBD variants (K417T, E484K, and N501Y) present in the P.1 Japan/Brazil and B.1.351 South Africa VoC significantly disrupted the binding of 65% of the NAbs tested. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;N501Y;K417T 48;59;41 53;64;46 RBD 27 30 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Furthermore, we find the C3 RGN10987 NAb is highly sensitive to the G446V variant, suggesting the virus has identified RBD variant residues that disrupt the binding of NAbs from each NAb class. 2021 Frontiers in immunology Discussion SARS_CoV_2 G446V 68 73 RBD 119 122 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. However, the K417T variant, as well as the G446V and A475V variants exhibit reduced (~2-fold) ACE2 binding affinity. 2021 Frontiers in immunology Discussion SARS_CoV_2 A475V;G446V;K417T 53;43;13 58;48;18 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. If increased ACE2 affinity is required for increasing viral infectivity, other mutations in the SARS-CoV-2 S, such as D614G, P681H, or several other changes, alone or together, must be responsible for enhanced ACE2 binding affinity. 2021 Frontiers in immunology Discussion SARS_CoV_2 D614G;P681H 118;125 123;130 S 107 108 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. In contrast, L452R exhibited a 2-fold increase in ACE2 affinity. 2021 Frontiers in immunology Discussion SARS_CoV_2 L452R 13 18 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Like N501Y and E484K, K417T also significantly disrupts NAb binding. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;K417T;N501Y 15;22;5 20;27;10 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Overall, our data suggests that N501Y and E484K (For E484K, this is inferred from the evaluation of the E484R mutation in our studies), enhance viral fitness predominantly by disrupting the host NAb response, but not by increasing ACE2 binding affinity. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;E484K;E484R;N501Y 42;53;104;32 47;58;109;37 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. RBD amino acid mutations found in the VoC, with the exception of the K417T mutation (K417T frequency = 0 in the analysis on 1-11-21), are found in the top 20 of most frequently observed mutations (frequency > 0.024%) in the GISAID. 2021 Frontiers in immunology Discussion SARS_CoV_2 K417T;K417T 69;85 74;90 RBD 0 3 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. RBD variants N440Y and T345I also exhibited ACE2 binding affinity similar to WT RBD. 2021 Frontiers in immunology Discussion SARS_CoV_2 N440Y;T345I 13;23 18;28 RBD;RBD 0;80 3;83 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. Recent data suggests that the D614G mutation stabilizes the S trimer and is necessary to observe the functional impact of the N501Y and L452R mutations on cell infectivity. 2021 Frontiers in immunology Discussion SARS_CoV_2 D614G;L452R;N501Y 30;136;126 35;141;131 S 60 61 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. The analysis found that E484K is the most disruptive mutation and impacted the greatest number of NAbs tested in our study (30%), with N501Y and K417T being slightly less disruptive, but still each impacting 25% of the NAbs evaluated. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;K417T;N501Y 24;145;135 29;150;140 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. The current VoC include B.1.1.7-UK (N501Y, S494P*, E484K*), P.1-Japan/Brazil (K417N/T, E484K, N501Y), B.1.351-South Africa (K417N, E484K, N501Y) B.1.427/B.1.429-California (L452R), where amino acid changes in the SARS-CoV-2 S RBD of these VoC are listed in parentheses. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;E484K;E484K;N501Y;N501Y;S494P;K417N;K417N;K417T;L452R;N501Y 51;87;131;94;138;43;124;78;78;173;36 56;92;136;99;143;48;129;85;85;178;41 RBD;S 226;224 229;225 34149735 Epitope Classification and RBD Binding Properties of Neutralizing Antibodies Against SARS-CoV-2 Variants of Concern. This suggests that neither N501Y and/or E484K variants increase infectivity, reported for the B.1.1.7 UK VoC, by increasing affinity for ACE2. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;N501Y 40;27 45;32 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. Indeed, HRM analysis correctly identified the genomic RNA of GISAID clade S virus to be A23403, G25563, G26144, T28144C, and G28882. 2021 Journal of infection and chemotherapy Discussion SARS_CoV_2 T28144C 112 119 S 74 75 34154921 Development of a genotyping platform for SARS-CoV-2 variants using high-resolution melting analysis. This technique has characterized five mutants (S, V, G, GH, and GR; Table 1), among which G, GH, and GR mutants possess an identical mutation site (D614G) in the spike protein's coding region. 2021 Journal of infection and chemotherapy Discussion SARS_CoV_2 D614G 148 153 S 162 167 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. Almost all viral strains with D614G, have also accumulated other variants like P333L (RNA-dependent RNA polymerase) and P4715L (ORF1ab) in proteins responsible for SARS-CoV-2 replication. 2021 Computers in biology and medicine Discussion SARS_CoV_2 D614G;P333L;P4715L 30;79;120 35;84;126 RdRp;ORF1ab 86;128 114;134 34157472 Multilevel systems biology analysis of lung transcriptomics data identifies key miRNAs and potential miRNA target genes for SARS-CoV-2 infection. In this study, variant D614G (spike), localized to highly conserved B-cell epitope is the most common clade identified in viral strains from Saudi Arabia, South Africa, USA, Russia and New Zealand. 2021 Computers in biology and medicine Discussion SARS_CoV_2 D614G 23 28 S 30 35 34158771 Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study. focused on D614G substitution as an urgent concern, proposing that this mutation began spreading in Europe in early February 2020. 2021 Ethiopian journal of health sciences Discussion SARS_CoV_2 D614G 11 16 34158771 Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study. In agreement with Korber's study, our results indicated the spread of D614G substitution. 2021 Ethiopian journal of health sciences Discussion SARS_CoV_2 D614G 70 75 34158771 Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study. Similar to our findings, substitution in amino acid 614 (D614G) was the most prevalent mutation (25%). 2021 Ethiopian journal of health sciences Discussion SARS_CoV_2 D614G 57 62 34158771 Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study. The results of the present study showed that the spike protein was highly conserved, and high prevalence mutation was detected only in one site (D614G). 2021 Ethiopian journal of health sciences Discussion SARS_CoV_2 D614G 145 150 S 49 54 34159627 Genome-wide association analysis of COVID-19 mortality risk in SARS-CoV-2 genomes identifies mutation in the SARS-CoV-2 spike protein that colocalizes with P.1 of the Brazilian strain. The V1176F mutation in S2 is located in the Heptad repeat 2 domain, which is involved in the viral fusion machinery. 2021 Genetic epidemiology Discussion SARS_CoV_2 V1176F 4 10 34161337 SARS-CoV-2 uses major endothelial integrin alphavbeta3 to cause vascular dysregulation in-vitro during COVID-19. A striking difference resides in the mutation from lysine to arginine at residue 403 within SARS-CoV-2. 2021 PloS one Discussion SARS_CoV_2 K403R 51 84 34161337 SARS-CoV-2 uses major endothelial integrin alphavbeta3 to cause vascular dysregulation in-vitro during COVID-19. This interaction is likely mediated through the evolutionary K403R motif within the spike protein that promotes binding to alphaVbeta3. 2021 PloS one Discussion SARS_CoV_2 K403R 61 66 S 84 89 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. As another example, a new VOC bearing DeltaH69/V70 with E484K was recently identified (B.1.525). 2021 Cell reports Discussion SARS_CoV_2 E484K 56 61 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. DeltaH69/V70 itself has frequently followed immune escape-associated amino acid replacements in the RBD (e.g., N439K and Y453F) and is specifically found in the B.1.1.7 variant, known to have higher transmissibility and, possibly, pathogenicity. 2021 Cell reports Discussion SARS_CoV_2 N439K;Y453F 111;121 116;126 RBD 100 103 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. However, recent reports from the United States and central Europe caution against use of SGTF as a sole marker for B.1.1.7 detection because a significant DeltaH69/V70 lineage without other mutations in spike is circulating in the United States, and a B.1.258 lineage with N439K with DeltaH69/V70 is circulating in Slovakia/Czech Republic. 2021 Cell reports Discussion SARS_CoV_2 N439K 273 278 S 203 208 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Importantly, we were able to recapitulate the DeltaH69/V70 phenotype in a spike protein that did not have the D614G mutation, indicating that D614G is not involved in the mechanism. 2021 Cell reports Discussion SARS_CoV_2 D614G;D614G 110;142 115;147 S 74 79 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. In addition, a recent report on the S1/S2 cleavage site mutation P681H demonstrated that enhanced cleavage of spike P681H was not associated with increased PV infectivity or cell fusion relative to the WT. 2021 Cell reports Discussion SARS_CoV_2 P681H;P681H 65;116 70;121 S 110 115 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Instead, our experimental results demonstrate that DeltaH69/V70 is able increase infectivity of the Wuhan-1 D614G spike PV as well as the PV bearing the additional RBD mutations N439K or Y453F, explaining why the deletion is often observed after these immune escape mutations that carry infectivity cost. 2021 Cell reports Discussion SARS_CoV_2 D614G;N439K;Y453F 108;178;187 113;183;192 S;RBD 114;164 119;167 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. We have found consistent differences in spike as well as cleaved spike in the producer cell and its incorporation into PV particles when comparing DeltaH69/V70 with a Wuhan-1 spike (both with D614G). 2021 Cell reports Discussion SARS_CoV_2 D614G 192 197 S;S;S 40;65;175 45;70;180 34166617 Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. We show that Alpha variant B.1.1.7 spike has similar infectivity as WT D614G spike, consistent with data on live B.1.1.7 virus in human airway epithelial cells but in contrast to another study that showed a difference in live virus with the 8 spike mutations. 2021 Cell reports Discussion SARS_CoV_2 D614G 71 76 S;S;S 35;77;243 40;82;248 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Because K417N/T also markedly reduced binding to soluble ACE2, this mutation may shift the balance in favor of binding to an antibody rather than to ACE2. 2021 Immunity Discussion SARS_CoV_2 K417N;K417T 8;8 15;15 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Considering that most class I antibodies with heavy-chain IGHV3-53/3-66 usage lost efficacy against the K417N mutation, the P2C-1F11 findings show the existence of class I antibodies that were not affected by the mutation. 2021 Immunity Discussion SARS_CoV_2 K417N 104 109 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. However, the same K417N and/or N501Y mutations found in mouse-adapted SARS-CoV-2 should raise enough concern about the potential spread of these new variants to mice and beyond. 2021 Immunity Discussion SARS_CoV_2 K417N;N501Y 18;31 23;36 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. More importantly, P2C-1F11, which is currently in therapeutic development, was virtually unaffected by the single K417N/T or the triple K417N-E484K-N501Y mutation. 2021 Immunity Discussion SARS_CoV_2 K417N;K417N;K417T;E484K;N501Y 136;114;114;142;148 141;121;121;147;153 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Most class I mAbs studied here were disrupted by the K417N/T mutation and those in class II by the E484K mutation. 2021 Immunity Discussion SARS_CoV_2 E484K;K417N;K417T 99;53;53 104;60;60 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Of note, we observed that the single K417N/T mutant tended to increase rather than decrease the neutralizing activity of non-class I mAbs. 2021 Immunity Discussion SARS_CoV_2 K417N;K417T 37;37 44;44 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Particularly B.1.351 had the NTD supersite mutation (242-244del) and triple K417N-E484K-N501Y RBD mutation, whereas P.1 had only the latter and B.1.1.7 only the former (Y144del) together with N501Y in the RBD (Figure 1A). 2021 Immunity Discussion SARS_CoV_2 K417N;N501Y;Y144del;E484K;N501Y 76;192;169;82;88 81;197;176;87;93 RBD;RBD 94;205 97;208 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Reduction or complete loss of neutralization activities were variably attributed to the 242-244del mutation in the NTD, E484K, and triple K417N-E484K-N501Y in the RBD, depending on the individual profiles of neutralizing antibodies. 2021 Immunity Discussion SARS_CoV_2 E484K;K417N;E484K;N501Y 120;138;144;150 125;143;149;155 RBD 163 166 34166623 Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. We identified K417N, E484K, and N501Y mutations in the RBD of the three variants that have profound consequences on antibody neutralization and interaction with mouse and mink ACE2. 2021 Immunity Discussion SARS_CoV_2 E484K;K417N;N501Y 21;14;32 26;19;37 RBD 55 58 34168138 The architecture of the SARS-CoV-2 RNA genome inside virion. Our model also provides novel insights on how some pathogenic SARS-CoV-2 variants, such as D614G might enable a viral fitness advantage at the RNA structure level. 2021 Nature communications Discussion SARS_CoV_2 D614G 91 96 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. One of the mutations thought to be responsible for this increased transmissibility, N501Y, is shared by other VOCs, such as B.1.351 and P.1, which include additional mutations in the S gene thought to reduce the neutralization capacity of antibodies generated against WT virus. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 84 89 S 183 184 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. Other assays targeted N501Y as well or used melt-curve analysis, but the ABI 7500 PCR machines we used for SGTF screening are not well-suited for melt-curve analysis, and N501Y alone is not sufficient to definitely characterize a SARS-CoV-2 lineage without sequence analysis. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y;N501Y 22;171 27;176 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. The large number of genomic mutations associated with B.1.1.7, including SNPs (A570D, D614G, P681H, T716I, S982A, and D1118H) highlight the need to rapidly distinguish these subtle mutations in emerging VOCs. 2021 Journal of medical virology Discussion SARS_CoV_2 D1118H;D614G;P681H;S982A;T716I;A570D 118;86;93;107;100;79 124;91;98;112;105;84 34170525 Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. Therefore, detection of the N501Y mutation flags samples that may harbor mutations associated with immune evasion as well as increased transmissibility. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 28 33 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Accordingly, variants, particularly those possessing the L452R mutation, such as the B.1.427/429 lineage, are a potential threat in countries and regions with a predominance of HLA-A24 individuals, and deep surveillance and tracing of the epidemic related to these variants are urgently required. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R 57 62 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Although it remains unclear whether the emergence of the Y453F mutant may be associated with evasion from acquired immunity in minks, we demonstrate here that this mutation does confer resistance to HLA-A24-restricted human cellular immunity. 2021 Cell host & microbe Discussion SARS_CoV_2 Y453F 57 62 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Although the effects of L452R and Y453F mutations on sensitivity to neutralizing antibodies are controversial, our data demonstrate that these mutations evade HLA-A24-mediated cellular immunity. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R;Y453F 24;34 29;39 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Another possibility is that the L452R mutant developed to evade HLA-A24-restricted cellular immunity: HLA-A24 is relatively predominant in East Asian individuals, and the proportion of Asian Americans in the USA is highest in California. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R 32 37 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. As suggested in previous reports, our data show that the B.1.1.298 variant possessing the Y453F substitution is closely associated with the outbreak among minks in Denmark. 2021 Cell host & microbe Discussion SARS_CoV_2 Y453F 90 95 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Because the B.1.427/429 variant harboring L452R mutation has been predominantly spreading in California, it may be assumed that the emergence of the L452R mutant (or the B.1.427/429 lineage) was driven by HLA-A24-mediated cellular immunity. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R;L452R 42;149 47;154 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Because the L452R mutation reinforces binding to human ACE2 and further enhances viral replication capacity, this variant might have emerged to improve viral fitness in humans. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R 12 17 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Because the Y453F mutation did not increase infection efficacy when using mink ACE2, our results suggest that the emergence of this mutation is not due to enhanced viral fitness in minks. 2021 Cell host & microbe Discussion SARS_CoV_2 Y453F 12 17 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. First, we hypothesized that the emergence of the L452R and Y453F mutations might be attributed to the immune pressure triggered by HLA-A24-mediated cellular immunity. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R;Y453F 49;59 54;64 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Furthermore, we demonstrate that the L452R mutation significantly improves viral replication capacity by increasing binding affinity to human ACE2 as well as S protein stability. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R 37 42 S 158 159 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Here, we demonstrate that the L452R and Y453F mutations contribute to escape from HLA-restricted cellular immunity. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R;Y453F 30;40 35;45 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Here, we demonstrated that the L452R mutation increases viral fusogenicity. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R 31 36 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. In addition to our findings, recent papers have documented that the L452R and Y453F substitutions may confer resistance to neutralizing antibodies, suggesting that these mutants can evade both humoral and HLA-restricted cellular immunity. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R;Y453F 68;78 73;83 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. In contrast to the B.1.1.298 variant, the B.1.427/429 variant harboring the L452R substitution appears to have emerged during spread in the human population. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R 76 81 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. In the present study, we demonstrate that at least two naturally occurring mutations in the SARS-CoV-2 RBM, L452R and Y453F, escape HLA-restricted cellular immunity and further promote affinity toward the viral receptor ACE2. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R;Y453F 108;118 113;123 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Nevertheless, we provide direct evidence suggesting that mutations in the RBM, including L452R (in the B.1.427/429 lineage) and Y453F (in the B1.1.298 lineage), may confer escape from HLA-A24-restricted cellular immunity, and furthermore, that the L452R mutant has increased replication capacity. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R;L452R;Y453F 89;248;128 94;253;133 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Notably, in addition to the B.1.427/429 lineage, the L452R mutation is a hallmark of the B.1.617 lineage. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R 53 58 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. On the other hand, a recent study has shown that the B.1.427/429 variant, which harbors the L452R mutation, is 2-6.7-fold more resistant to neutralizing antibodies than the non-L452R prototypic virus. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R;L452R 92;177 97;182 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Our data suggest that the L452R mutant escapes HLA-A24-restricted cellular immunity and further strengthens its infectivity. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R 26 31 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. performed a pseudovirus assay and showed that the L452R mutation increases viral infectivity. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R 50 55 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Previous papers have reported that the L452R and Y453F mutations had less effect on the sensitivity to neutralizing antibodies (e.g., convalescent/vaccinated sera and monoclonal antibodies). 2021 Cell host & microbe Discussion SARS_CoV_2 L452R;Y453F 39;49 44;54 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Therefore, the L452R mutation would be a mutation of concern and should be targeted by deep surveillance. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R 15 20 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Therefore, the L452R/Y453F mutations would more crucially impact HLA-A24-mediated cellular immunity than sensitivity to neutralizing antibodies. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R;Y453F 15;21 20;26 34171266 SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. We also demonstrate that the L452R mutation increases the stability of the S protein and viral infectivity and thereby enhances viral replication. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R 29 34 S 75 76 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. At this time, it is not clear whether the D399N mutation alters binding by the capture or the detection antibody. 2021 Journal of clinical virology Discussion SARS_CoV_2 D399N 42 47 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. Neither the T205I or D399N mutation recovered in our interrogated specimens occurred in these regions, nor could high-confidence models be created for these regions in HHPred. 2021 Journal of clinical virology Discussion SARS_CoV_2 D399N;T205I 21;12 26;17 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. The D399N mutation that affected the Quidel Sofia 2 assay performance seems to be of limited public health importance at this time given the few number of cases it has been detected in. 2021 Journal of clinical virology Discussion SARS_CoV_2 D399N 4 9 34171548 A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. We further characterized a single amino acid mutation (D399N) that affected the analytical sensitivity of the Quidel Sofia SARS Antigen FIA by approximately 1000-fold, when measured on the Sofia 2. 2021 Journal of clinical virology Discussion SARS_CoV_2 D399N 55 60 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. Furthermore, other lineages featuring the N501Y SNP, but lacking the deletion, (i.e., B.1.351 and P.1) may also be detected as abnormal for further investigation, though further validation is necessary regarding these two VOCs. 2021 Journal of clinical virology Discussion SARS_CoV_2 N501Y 42 47 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. Furthermore, while SARS-CoV-2 P1 lineage (first detected in Brazil) should be identifiable as suspicious (N501Y positive, del-HV69/70 negative) by the multiplex, we were unable to test this claim as there were no samples available. 2021 Journal of clinical virology Discussion SARS_CoV_2 N501Y 106 111 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. Mutations like N501Y have independently occurred multiple times in areas with high incidence rates, implying advantages in an environment of high background host-immunity. 2021 Journal of clinical virology Discussion SARS_CoV_2 N501Y 15 20 34182299 Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. The SCOV2_VAR_UCT is able to detect both the del-HV69/70 and N501Y mutations, relevant for B.1.1.7, B1.351 and P.1 and further adaptions can be implemented to also pick up new emerging SNPs if necessary. 2021 Journal of clinical virology Discussion SARS_CoV_2 N501Y 61 66 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. Immunity to a recent B.1.1.7 variant was equally good as compared to the D614G variant, whereas vaccine and SARS-CoV-2 infection induced immunity against B.1.351 variant was reduced. 2021 Nature communications Discussion SARS_CoV_2 D614G 73 78 COVID-19 108 128 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. In summary, in the present study we show that the Pfizer-BioNTech BNT162b2 COVID-19 mRNA vaccine is highly immunogenic, and particularly after two vaccine doses, all vaccinees showed a very high humoral immune response to D614G variant viruses. 2021 Nature communications Discussion SARS_CoV_2 D614G 222 227 COVID-19 75 83 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. The critical amino acid changes linked to escape from humoral immunity in the B.1.351 variant appear to be K417N, E484K, and N501Y. 2021 Nature communications Discussion SARS_CoV_2 E484K;K417N;N501Y 114;107;125 119;112;130 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. The D614G and B.1.1.7 variant viruses were readily neutralized by the vaccinees' sera, indicating that these mutations are unlikely to impair the neutralizing antibody capacity induced by vaccination or natural infection. 2021 Nature communications Discussion SARS_CoV_2 D614G 4 9 34183681 COVID-19 mRNA vaccine induced antibody responses against three SARS-CoV-2 variants. The vaccine induced good cross-reactivity to D614G and B.1.1.7 variants in all vaccinees and, albeit reduced levels, detectable neutralizing antibodies to B.1.351 variant in 92% of the vaccinees. 2021 Nature communications Discussion SARS_CoV_2 D614G 45 50 34184982 Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. An additional G >A mutation at position 20125 found in three of the outbreak genomes demonstrated that within the short period of time that the virus was circulating in the factory, some evolution with subsequent onward spread had occurred. 2021 Microbial genomics Discussion SARS_CoV_2 G20125A 14 45 34184982 Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. However there was a rapid fall in the proportion of samples with the wild type in April (10.7 %), and by May 95 % of samples had the D614G mutation. 2021 Microbial genomics Discussion SARS_CoV_2 D614G 133 138 34184982 Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. There is evidence that a mutation in the spike protein with an amino acid change of D to G at position 614 (D614G) increases the transmissibility of the virus, which is associated with an increased viral load in mutant-infected cases. 2021 Microbial genomics Discussion SARS_CoV_2 D614G;D614G 84;108 106;113 S 41 46 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. Based on the cryoelectron microscopy (cryo-EM) structure of the parent LCB1 binder in complex with SARS-CoV-2 RBD, only the N501Y mutation is expected to affect binding. 2021 Cell host & microbe Discussion SARS_CoV_2 N501Y 124 129 RBD 110 113 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. Because structural data suggested that the N501Y mutation might affect LCB1 binding, we tested LCB1v1.3 against a virus encoding this mutation in vivo. 2021 Cell host & microbe Discussion SARS_CoV_2 N501Y 43 48 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. In comparison, LCB1v1.3 showed efficacy against historical (WA1/2020) and emerging (B.1.1.7 and E484K/N501Y/D614G) SARS-CoV-2 strains. 2021 Cell host & microbe Discussion SARS_CoV_2 E484K;D614G;N501Y 96;108;102 101;113;107 34192518 Ultrapotent miniproteins targeting the SARS-CoV-2 receptor-binding domain protect against infection and disease. Treatment with LCB1v1.3 conferred high levels of protection against a B.1.1.7 isolate and a recombinant WA1/2020 strain encoding N501Y/E484K/D614G mutations. 2021 Cell host & microbe Discussion SARS_CoV_2 N501Y;D614G;E484K 129;141;135 134;146;140 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. However, recent expansion of B.1.526, a lineage also featuring E484K but without N501Y in New York City, suggests that this fitness loss may be overcome by other, yet uncharacterized, changes in the virus as well. 2021 Cell Discussion SARS_CoV_2 E484K;N501Y 63;81 68;86 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. In contrast, introduction of E484K reduced the affinity by 4-fold which may explain why virus variants carrying only the E484K mutation have rarely spread efficiently, although viruses carrying E484K have been detected since the fall of 2020 in a handful of patients receiving care at the Mount Sinai Health System and have also been reported in immunocompromised patients. 2021 Cell Discussion SARS_CoV_2 E484K;E484K;E484K 29;121;194 34;126;199 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. In fact, the B.1.351 RBD, which carries N501Y and E484K (as well as N417K) showed binding to hACE2 that was similar to wild-type RBD. 2021 Cell Discussion SARS_CoV_2 E484K;N417K;N501Y 50;68;40 55;73;45 RBD;RBD 21;129 24;132 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. Interestingly, binding of convalescent sera to the N501Y RBD was also increased, suggesting that changes that increase affinity for the receptor may also increase affinity of a set of antibodies that may mimic the receptor. 2021 Cell Discussion SARS_CoV_2 N501Y 51 56 RBD 57 60 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. Interestingly, N501Y increased the affinity by 5-fold. 2021 Cell Discussion SARS_CoV_2 N501Y 15 20 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. It is tempting to speculate that the N501Y mutation enables the acquisition of E484K without a fitness loss. 2021 Cell Discussion SARS_CoV_2 E484K;N501Y 79;37 84;42 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. Our data indicate that reduction in binding to the E484K and B.1.351 variant RBDs was minor (often only 2-fold) compared to reported reduction in neutralization (which ranges from 6- to 8-fold to complete loss of neutralization). 2021 Cell Discussion SARS_CoV_2 E484K 51 56 RBD 77 81 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. Recently, B.1.1.7 variant strains carrying E484K, in addition to N501Y, have been isolated in the UK, providing evidence for the hypothesis that N501Y enables acquisition of mutations in the RBD that may be detrimental to receptor binding. 2021 Cell Discussion SARS_CoV_2 E484K;N501Y;N501Y 43;65;145 48;70;150 RBD 191 194 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. The reduced affinity of the E484K variant RBD for hACE2 could render the virus more susceptible to RBD binding mAbs. 2021 Cell Discussion SARS_CoV_2 E484K 28 33 RBD;RBD 42;99 45;102 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. These observations may explain why a reduction in neutralization against the viral variant of concern B.1.1.7 is seen in some studies despite the fact the N501Y substitution in the RBD of this variant does not significantly impact binding and neutralizing activity. 2021 Cell Discussion SARS_CoV_2 N501Y 155 160 RBD 181 184 34192529 SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. We also noted that the two neutralizing antibodies against the RBD showed some reduced binding to a mutant RBD carrying the E484K mutation while having similar or even increased neutralizing potency against a variant virus carrying the E484K mutation as the only change in its RBD. 2021 Cell Discussion SARS_CoV_2 E484K;E484K 124;236 129;241 RBD;RBD;RBD 63;107;277 66;110;280 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. One such emerging mutation at the RBM is V483A. 2021 Future virology Discussion SARS_CoV_2 V483A 41 46 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. Other than V483A mutation, some other substitutional mutations like V483F, V483I, V483P, V483D, V483R and V483K at a lower frequency rate. 2021 Future virology Discussion SARS_CoV_2 V483A;V483D;V483F;V483I;V483K;V483P;V483R 11;89;68;75;106;82;96 16;94;73;80;111;87;101 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. The antigenicity study reveals that the V483A mutant can neutralize antibodies like X593, P2B-2F6, etc., and attain immune evasion. 2021 Future virology Discussion SARS_CoV_2 V483A 40 45 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. The V483A mutant favors higher solvent accessibility because the mutation is present at the surface of the RBD and is exposed to the solvent region. 2021 Future virology Discussion SARS_CoV_2 V483A 4 9 RBD 107 110 34194534 V483A: an emerging mutation hotspot of SARS-CoV-2. This review has highlighted all possible evidence that the V483A mutation at the RBM of SARS-CoV-2 may increase the virus's transmission rate. 2021 Future virology Discussion SARS_CoV_2 V483A 59 64 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. Additionally, no significant changes in the titer were needed for neutralization of the WT SARS-CoV-2 compared to a viral sample from the B.1.1.7 variant (in which P681H is one of its defining mutations), using sera from convalescent patients or individuals vaccinated with the Moderna mRNA-1273 vaccine from Moderna. 2021 Vaccines Discussion SARS_CoV_2 P681H 164 169 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. Although first detected in clinical samples in November 2020, the P681H mutation had already been identified in Israel in October 2020 via sequencing of sewage samples. 2021 Vaccines Discussion SARS_CoV_2 P681H 66 71 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. Herein, we report a novel local variant with the P681H mutation that emerged from the locally circulating B.1.1.50 lineage. 2021 Vaccines Discussion SARS_CoV_2 P681H 49 54 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. Overall, as the B.1.1.50 + P681H variant was efficiently neutralized by vaccine-derived antibodies, similarly to local unmutated circulating strains, it was not associated with escalated infection or spread, and in light of the P681H mutation being observed in additional SARS-CoV-2 strains worldwide not defined as VOCs, this emerging local variant is currently not defined as a VOC. 2021 Vaccines Discussion SARS_CoV_2 P681H;P681H 27;228 32;233 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. Previous serum neutralization assays for VSV-based SARS-CoV-2 pseudoviruses expressing the S protein with the P681H mutation demonstrated no significant changes in the titer required for neutralization compared to the unmutated S protein. 2021 Vaccines Discussion SARS_CoV_2 P681H 110 115 S;S 91;228 92;229 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. Similar to these reports, this study demonstrates comparable neutralization of the B.1.1.50 + P681H variant, an Israel WT strain and the B.1.1.7 variant, by sera from vaccinated individuals. 2021 Vaccines Discussion SARS_CoV_2 P681H 94 99 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. The P681H mutation was observed as early as March 2020 in samples worldwide and also characterizes the globally spreading B.1.1.7 variant. 2021 Vaccines Discussion SARS_CoV_2 P681H 4 9 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. The prevalence of the B.1.1.50 + P681H variant declined with time, from ~12% in November 2020 to 3.2% in January 2021 and 0.9% in February 2021 (out of 2843 randomly sequenced samples, data not shown). 2021 Vaccines Discussion SARS_CoV_2 P681H 33 38 34201088 A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel. This local B.1.1.50 + P681H variant was identified in 181 sequenced samples collected from November 2020 to January 2021 in Israel. 2021 Vaccines Discussion SARS_CoV_2 P681H 22 27 34203844 SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence. In addition, a new variant, L18F, has been recently reported with 1186 spike L18F VOC genomes in the UK. 2021 Journal of clinical medicine Discussion SARS_CoV_2 L18F;L18F 28;77 32;81 S 71 76 34203844 SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence. showed a lower rate of hospitalization associated with N501Y variants as compared to Clade 20A and the Marseille-4 variant. 2021 Journal of clinical medicine Discussion SARS_CoV_2 N501Y 55 60 34203844 SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence. The in vitro and in vivo studies to date showed that the mutation D614G in Spike protein was associated with higher viral loads and probably with enhanced transmissibility of the virus. 2021 Journal of clinical medicine Discussion SARS_CoV_2 D614G 66 71 S 75 80 34203844 SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence. The main effect of the D614G mutation is to increase the availability of spike trimer components in the conformation and permits enhancing the binding of the virus spike to the ACE2 receptor. 2021 Journal of clinical medicine Discussion SARS_CoV_2 D614G 23 28 S;S 73;164 78;169 34203844 SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence. The weekly growth rate of the L18F increased 1.75-fold, compared with the VOC genomes non-mutated at residue 18. 2021 Journal of clinical medicine Discussion SARS_CoV_2 L18F 30 34 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. D614G neutralization was significantly increased in both vaccinated and infected, compared to WH1. 2021 Viruses Discussion SARS_CoV_2 D614G 0 5 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. Finally, we show here that vaccinated individuals, as a whole, suffered a small reduction of cross-neutralizing activity against B.1.1.7 in comparison to D614G, as previously reported. 2021 Viruses Discussion SARS_CoV_2 D614G 154 159 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. The capacity of this group to neutralize B.1.1.7 in comparison to both WH1 and D614G was not statistically different from infected individuals tested after 6 months. 2021 Viruses Discussion SARS_CoV_2 D614G 79 84 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. The neutralizing response associated with the B.1.1.7 variant only showed a significant decrease when compared to the D614G mutant but not with the original WH1 spike. 2021 Viruses Discussion SARS_CoV_2 D614G 118 123 S 161 166 34204754 Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals. This is in agreement with recent reports showing that D614G mutation is associated with a more open (one-up) conformation which increases access to the RBD and results in both an increase in infectivity and an increase in sensitivity to neutralization. 2021 Viruses Discussion SARS_CoV_2 D614G 54 59 RBD 152 155 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. As for A97V-RdRp, RDV complex forms H-bonds with K545, S549, K551, T556, and S682. 2021 Biomolecules Discussion SARS_CoV_2 A97V 7 11 RdRP 12 16 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Furthermore, P323L-RdRp in complex with RDV presented a very tight and stable structure, depicted in Figure 3B, reflecting a tighter and more compact structure compared to RDV bound to WT and A97V. 2021 Biomolecules Discussion SARS_CoV_2 A97V;P323L 192;13 196;18 RdRP 19 23 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. However, in this study, mutations A97V and P323L are present in nsp12 and were far from the residues interacting with nsp8 and nsp7. 2021 Biomolecules Discussion SARS_CoV_2 A97V;P323L 34;43 38;48 Nsp12;Nsp7;Nsp8 64;127;118 69;131;122 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. In addition, the RMSD (Figure 3A,B) and RMSF (Figure 4A) of WT RdRp-A97V and P323L showed no effect of mutations on the overall structure and internal dynamics of the RdRp complex. 2021 Biomolecules Discussion SARS_CoV_2 P323L;A97V 77;68 82;72 RdRP;RdRP 63;167 67;171 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. In contrast, Chand et al., using the DynaMut structural stability prediction server P323L mutation, presented a stable RdRp structure (DeltaDeltaG: 0.717 kcal/mol). 2021 Biomolecules Discussion SARS_CoV_2 P323L 84 89 RdRP 119 123 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. In general, mutations of protein targets for vaccines can hinder the efficacy of a drug or even develop drug resistance, whereas, in this case, the P323L-RdRp mutation-bound RDV showed a higher binding. 2021 Biomolecules Discussion SARS_CoV_2 P323L 148 153 RdRP 154 158 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. In the apo state, WT-RdRp and A97V-RdRp RMSD and RMSF patterns were not significantly different, indicating that the mutation had no effect on the overall stability of the protein structure or the internal dynamics of the RdRp domain. 2021 Biomolecules Discussion SARS_CoV_2 A97V 30 34 RdRP;RdRP;RdRP 21;35;222 25;39;226 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. In the current study, the RMSD and RMSF values were compared between WT-RdRp, A97V, and P323L_RdrP mutants in the apo form and in complex with RDV (Figure 3 and Figure 4). 2021 Biomolecules Discussion SARS_CoV_2 A97V;P323L 78;88 82;93 RdRP 72 76 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Interestingly, RDV binding to A97V-RdRp showed a weaker affinity than to WT at 14.37 kcal/mol, although the RMSD dynamics and RMSF fluctuations showed similar patterns for both structures bound to RDV (Figure 3 and Figure 4). 2021 Biomolecules Discussion SARS_CoV_2 A97V 30 34 RdRP 35 39 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. MD simulations result established that RDV presents a higher affinity to P323L-RdRp, and we further corroborated our findings by demonstrating the H-bonding networks of RDV with RdRp WT, A97V, and P323L structures. 2021 Biomolecules Discussion SARS_CoV_2 A97V;P323L;P323L 187;73;197 191;78;202 RdRP;RdRP 79;178 83;182 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. On the other hand, the P323L-RDV complex demonstrated a tighter binding with an affinity of 24.14 kcal/mol, which is 60-fold higher than RDV bound to WT-RdRp. 2021 Biomolecules Discussion SARS_CoV_2 P323L 23 28 RdRP 153 157 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Out of these, A97V and P323L are the most prevalent mutations spreading across Europe, North America, and India. 2021 Biomolecules Discussion SARS_CoV_2 A97V;P323L 14;23 18;28 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. P323L mutation is positioned on the interface domain of RdRp (nsp12) between residues A250-R365. 2021 Biomolecules Discussion SARS_CoV_2 P323L 0 5 Nsp12;RdRP 62;56 67;60 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. R555 H-bonding with RDV, in particular, has been observed in recent modeling studies. 2021 Biomolecules Discussion SARS_CoV_2 R555H 0 6 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Since RDV has a very short half-life and its concentrations in cells are much lower than those of NTPs, administering RDV to patients infected with the P323L mutant might be more beneficial with greater outcomes. 2021 Biomolecules Discussion SARS_CoV_2 P323L 152 157 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Structural analysis has shown that residues S682 and N691 are involved in 2'OH recognition of the incoming nucleotide; therefore, the binding of RDV to S682 and N691 in the P323L-RdRp structure may block recognition of the incoming nucleotide. 2021 Biomolecules Discussion SARS_CoV_2 P323L 173 178 RdRP 179 183 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Subsequently, our results showed that the mutant P323L-RdRP has a stronger affinity to RDV; as such, it would possibly be favourable to administer it to patients carrying the P323L-RdRp SARS-CoV-2 mutation. 2021 Biomolecules Discussion SARS_CoV_2 P323L;P323L 49;175 54;180 RdRP;RdRP 55;181 59;185 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. The activity of a native protein may be affected due to mutations that do not essentially occur in active site moieties; whereby, both A97V-RdRp and P323L-RdRp mutations are far from the active site (Figure 1). 2021 Biomolecules Discussion SARS_CoV_2 A97V;P323L 135;149 139;154 RdRP;RdRP 140;155 144;159 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. The effect of the P323L mutation displayed by DynaMUT analysis is a fast snapshot of the effect of the protein dynamics, unlike the more rigorous approach of using 200 ns simulations. 2021 Biomolecules Discussion SARS_CoV_2 P323L 18 23 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. The H-bonding structure of RDV in P323L-RdRp is slightly different where it interacts with T556, S759, T680, S682, and N691. 2021 Biomolecules Discussion SARS_CoV_2 P323L 34 39 RdRP 40 44 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. The RMSD and RMSF values of A97V-RdRp in complex with RDV were comparable to the WT-RdRp bound to RDV, demonstrating the same fluctuation patterns on the overall structure and internal dynamics; thus, indicating that A97V mutation does not influence the binding of RDV to RdRp. 2021 Biomolecules Discussion SARS_CoV_2 A97V;A97V 28;217 32;221 RdRP;RdRP;RdRP 33;84;272 37;88;276 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Therefore, H-bond formation with RDV in the P323L-RdRp structure may hinder incoming NTP binding. 2021 Biomolecules Discussion SARS_CoV_2 P323L 44 49 RdRP 50 54 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Therefore, to further illustrate the effects of RdRp mutations, using MD simulations, we extrapolated the free binding energies (DeltaG) of RDV bound to A97V and P323L and compared them to WT. 2021 Biomolecules Discussion SARS_CoV_2 A97V;P323L 153;162 157;167 RdRP 48 52 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. This can indicate that A97V-RdRp increased resistance to RDV 20-fold. 2021 Biomolecules Discussion SARS_CoV_2 A97V 23 27 RdRP 28 32 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. Whereas, as observed from Figure 3B, P323L RMSD fluctuates at the end of the simulation, indicating a more dynamic structure. 2021 Biomolecules Discussion SARS_CoV_2 P323L 37 42 34206274 Remdesivir MD Simulations Suggest a More Favourable Binding to SARS-CoV-2 RNA Dependent RNA Polymerase Mutant P323L Than Wild-Type. With P323L-RdRp, the RMSD calculations demonstrated more structural mobility near the end of the 200 ns simulation time, whereas the RMSF fluctuations were similar to WT-RdRp. 2021 Biomolecules Discussion SARS_CoV_2 P323L 5 10 RdRP;RdRP 11;170 15;174 34207378 Anti-SARS-CoV-2 Vaccines and Monoclonal Antibodies Facing Viral Variants. More transmissible variants are currently circulating in France, such as 19B/501Y and 20C/655Y, which carry multiple mutations involved in immune escape (e.g., H655Y), or the CAL.20C variant, which carries the E484K and the L452R mutations. 2021 Viruses Discussion SARS_CoV_2 E484K;H655Y;L452R 210;160;224 215;165;229 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. Furthermore, one uncommon mutation, S477G, was identified in the RBD. 2021 Viruses Discussion SARS_CoV_2 S477G 36 41 RBD 65 68 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. Furthermore, the S98F (50%, 5/10) and S162G (40%, 4/10) substitutions were also found in our dataset, with relatively high frequencies, highlighting the possibility of the further accumulation of mutations (Table S2). 2021 Viruses Discussion SARS_CoV_2 S162G;S98F 38;17 43;21 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. In addition to D614G, the most common mutations identified in the B.1.177 lineage in this study were L18F and A222V (Figure 2). 2021 Viruses Discussion SARS_CoV_2 A222V;D614G;L18F 110;15;101 115;20;105 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. In one sequence in the B.1.258 lineage in this study, the K417N mutation was detected (Figure 2B). 2021 Viruses Discussion SARS_CoV_2 K417N 58 63 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. Interestingly, it has also been found that K417N weakens binding between the RBD and human ACE2, while other mutations, such as E484K, enhance binding. 2021 Viruses Discussion SARS_CoV_2 E484K;K417N 128;43 133;48 RBD 77 80 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. It is important to note that the only common mutation found in B.1.1.29 and the B.1 lineage was D614G (Figure 2). 2021 Viruses Discussion SARS_CoV_2 D614G 96 101 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. N439K lies within the RBD, has been reported to be associated with immune escape, and confers increased binding affinity upon the ACE2 receptor, resulting in infection with a similar clinical outcome and a marginally higher viral load. 2021 Viruses Discussion SARS_CoV_2 N439K 0 5 RBD 22 25 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. Namely, the uncommon G446V mutation has been reported to reduce serum binding and neutralization. 2021 Viruses Discussion SARS_CoV_2 G446V 21 26 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. Nonetheless, specifically for mutations such as G769V, mutational frequency data prompted the suggestion they do not impede the evolutionary stability of the virus. 2021 Viruses Discussion SARS_CoV_2 G769V 48 53 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. The following mutations within the S protein have been reported in this lineage: N501Y, A570D, P681H, T716I, S982A, D1118H, DeltaH69/V70 and DeltaY144. 2021 Viruses Discussion SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;T716I 88;116;81;95;109;102 93;122;86;100;114;107 S 35 36 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. The independent evolution of certain mutations and deletions (DeltaH69/V70, N439K and K417N) in different lineages highlights the importance of molecular epidemiology studies, in which known and dangerous mutations can be identified and monitored. 2021 Viruses Discussion SARS_CoV_2 K417N;N439K 86;76 91;81 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. The K417N amino acid substitution is part of a group of substitutions most frequently detected in South African lineage B.1.351 (N501Y, K417N and E484K) that possibly promote antibody evasion. 2021 Viruses Discussion SARS_CoV_2 E484K;K417N;K417N;N501Y 146;4;136;129 151;9;141;134 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. The L18F substitution, also found in the South African strain B.1.351, has been reported to confer antibody escape, and it has been speculated that A222V may contribute to spreading efficiency as well as immune evasion; however, this is still under investigation. 2021 Viruses Discussion SARS_CoV_2 A222V;L18F 148;4 153;8 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. The only common S protein mutation identified in the B.1.2 lineage in this study was D614G, while detected uncommon S protein mutations included G769V, A942V and S1170X (Tables S2 and S3). 2021 Viruses Discussion SARS_CoV_2 A942V;D614G;G769V;S1170X 152;85;145;162 157;90;150;168 S;S 16;116 17;117 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. The other mutation commonly detected in the sequences in this lineage was N439K (Figure 2 and Figure 3). 2021 Viruses Discussion SARS_CoV_2 N439K 74 79 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. The uncommon mutation S477G, on the other hand, has been reported to strengthen the interaction between ACE2 and the RBD, thereby highlighting the dangers of new evolutionary traits, even in lineages that do not normally harbor such mutations. 2021 Viruses Discussion SARS_CoV_2 S477G 22 27 RBD 117 120 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. These benefits allow viral lineages carrying the D614G mutation to outcompete those lacking it during transmission bottlenecks, explaining its dominance and prevalence. 2021 Viruses Discussion SARS_CoV_2 D614G 49 54 34207490 A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic. These two deletions are suspected to compensate for mutations such as N501Y that reduce infectivity. 2021 Viruses Discussion SARS_CoV_2 N501Y 70 75 34208912 Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. As for the E484K mutation, characteristic of the SA and BR P.1 variant RBDs, it was reported to be "associated with escape from neutralizing antibodies", which adversely affects the efficacy of spike protein-dependent COVID-19 vaccines. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 E484K 11 16 S;RBD 194;71 199;75 COVID-19 218 226 34208912 Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. Our results demonstrate that Ab5 exerts significantly reduced neutralizing activity against the UK, SA, and BR P.1 variant RBDs, suggesting that the shared N501Y mutation not only increased ACE2-RBD interaction, but it also contributed to the escape phenomenon of the neutralizing antibody. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 N501Y 156 161 RBD;RBD 123;195 127;198 34208912 Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. Since the neutralization activities of the bin A antibodies (Ab1 and Ab4) were not affected by the three mutations contained in the UK, SA, and BR P.1 variant RBDs, further investigation of the mechanism by which the E484K or K417N/T alters the binding and neutralizing activities of these antibodies may help in the identification of a better therapeutic epitope target. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 E484K;K417N;K417T 217;226;226 222;233;233 RBD 159 163 34208912 Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. The N501Y RBD mutation, first found in the UK variant, has been demonstrated to exhibit stronger interaction force with the ACE2 receptor, which is associated with the increased infectivity of the UK variant. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 N501Y 4 9 RBD 10 13 34208912 Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. This discriminative binding behavior to the four RBDs suggests that the E484K or K417N/T mutations likely induced conformational changes near the epitopes, where these antibodies bind in the SA and BR P.1 variant RBDs. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 E484K;K417N;K417T 72;81;81 77;88;88 RBD;RBD 49;213 53;217 34208912 Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. With regard to the impact of N501Y mutation on the escape of a neutralizing antibody, Supasa et al. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 N501Y 29 34 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Although more experiments are needed to understand the underlying biological relevance of the two mutations, we speculate that the P323L mutation attenuates the clinical presentation of the SARS-CoV-2. 2021 Scientific reports Discussion SARS_CoV_2 P323L 131 136 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Firstly, based on its location, we expect the P323L mutation to negatively impact the nsp8 association. 2021 Scientific reports Discussion SARS_CoV_2 P323L 46 51 Nsp8 86 90 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Here, we have analysed the structural and functional impact of the widely discussed S-protein mutation D614G and investigated whether it provides by itself an epidemiological advantage to the SARS-CoV-2. 2021 Scientific reports Discussion SARS_CoV_2 D614G 103 108 S 84 85 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. However, epidemiological data suggests that the D614G mutation is not exclusively responsible as a driver mutation of SARS-CoV-2. 2021 Scientific reports Discussion SARS_CoV_2 D614G 48 53 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. In the case of the RdRp, the P323L mutation is located far from the RNA binding domain, which lies within the finger-palm-thumb domains and, therefore, any direct effect of the mutation on the ability of the mutated RdRp to bind RNA should be excluded. 2021 Scientific reports Discussion SARS_CoV_2 P323L 29 34 RdRP;RdRP 19;216 23;220 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Moreover, experiments on the stability of the P323L variant are needed, since changes in the stability of the mutated nsp12 could alter its cellular concentration, which would subsequently affect the replication rate of the virus within the host cell. 2021 Scientific reports Discussion SARS_CoV_2 P323L 46 51 Nsp12 118 123 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Our data, however, are not compatible with the concept that the D614G S-protein mutation by itself is sufficient to explain the epidemiological success of the presently predominant SARS-CoV-2 strain. 2021 Scientific reports Discussion SARS_CoV_2 D614G 64 69 S 70 71 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Taken together, our study demonstrates that the mutation D614G in S-protein has high infectivity in cellular systems and provides a structural explanation of this effect through molecular modelling. 2021 Scientific reports Discussion SARS_CoV_2 D614G 57 62 S 66 67 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. The coevolution of the S-protein mutation with the P323L mutation of the RdRp is striking and appears to be crucial for the success of the viral strain. 2021 Scientific reports Discussion SARS_CoV_2 P323L 51 56 RdRP;S 73;23 77;24 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. The infectivity-enhancing D614G S-protein mutation would then counterbalance this initial decrease in virion production and allow transmission even by asymptomatic or presymptomatic individual. 2021 Scientific reports Discussion SARS_CoV_2 D614G 26 31 S 32 33 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. The level of association of nsp8 has been shown to be an important factor for obtaining high RNA polymerase activity in SARS-CoV-1, and thus P323L is likely to attenuate polymerase activity in SARS-CoV-2. 2021 Scientific reports Discussion SARS_CoV_2 P323L 141 146 Nsp8 28 32 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. The time series for the emergence of the D614G and P323L mutations indicates that the S-protein mutation (D614G) evolved simultaneously with P323L in RdRp. 2021 Scientific reports Discussion SARS_CoV_2 D614G;P323L;P323L;D614G 41;51;141;106 46;56;146;111 RdRP;S 150;86 154;87 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Therefore, the D614G mutation observed more prevalently in specific regions might help to reduce the energetic cost of the conformational transition needed to attach to the cell receptors. 2021 Scientific reports Discussion SARS_CoV_2 D614G 15 20 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. Thus, our data suggest that the P323L mutation of the polymerase plays an important role in the present epidemiological success of D614G and SARS-CoV-2 in general, possibly by providing a selective advantage as hypothesized by Korber et al. 2021 Scientific reports Discussion SARS_CoV_2 D614G;P323L 131;32 136;37 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. We demonstrate that indeed, this single amino acid substitution from aspartate to glycine at position 614 significantly enhances the infectivity of pseudotyped lentivectors. 2021 Scientific reports Discussion SARS_CoV_2 D614G 69 105 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. We provide a working hypothesis where the polymerase mutation attenuates the symptoms and severity of the infection, while the spike mutation improves the ability of the D614G spike variant to infect cells. 2021 Scientific reports Discussion SARS_CoV_2 D614G 170 175 S;S 127;176 132;181 34210996 Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant. We, therefore, speculate that the P323L RdRp mutation might decrease the production of viral RNA and hence increase the likelihood of asymptomatic infections and/or the time between infection and appearance of symptoms. 2021 Scientific reports Discussion SARS_CoV_2 P323L 34 39 RdRP 40 44 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. In addition to the G clade's other common mutation, NSP12-P323L, frequent mutations we observed include N-S194L, N-R203K, N-G204R, NSP2-T85I, and ORF3a-Q57H. 2021 Scientific reports Discussion SARS_CoV_2 G204R;P323L;Q57H;R203K;S194L;T85I 124;58;152;115;106;136 129;63;156;120;111;140 ORF3a;Nsp12;Nsp2;N;N;N 146;52;131;104;113;122 151;57;135;105;114;123 34211026 High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. The G clade and tis lineage have been dominant since late March, 2020 and its D614G mutation in the spike protein has been associated with increased transmissibility. 2021 Scientific reports Discussion SARS_CoV_2 D614G 78 83 S 100 105 34211709 The emerging SARS-CoV-2 variants of concern. According to various studies, B.1.617 is the prevalent variant devastating India, which carries L452R spike mutation, and another, referred to as a "double mutant" Y453F has an RBD which has seen an increased ACE2 binding. 2021 Therapeutic advances in infectious disease Discussion SARS_CoV_2 L452R;Y453F 96;166 101;171 S;RBD 102;179 107;182 34211709 The emerging SARS-CoV-2 variants of concern. D614G, like N501Y, is also suggestive of natural selection and has been seen to infect many geographic regions. 2021 Therapeutic advances in infectious disease Discussion SARS_CoV_2 N501Y;D614G 12;0 17;5 34211709 The emerging SARS-CoV-2 variants of concern. Furthermore, a newer variant referred to as B.1.1.248 lineage has several mutations in the S protein, including N501Y and E484K. 2021 Therapeutic advances in infectious disease Discussion SARS_CoV_2 E484K;N501Y 122;112 127;117 S 91 92 34211709 The emerging SARS-CoV-2 variants of concern. However, the study further showed that variants that carry K417N/T, E484K, and N501Y mutations, such as the UK (B1.1.7/501Y.V1), South African (501Y.V2), and Brazil (B1.1.28/501.V3) variants, can reduce the neutralization potency of vaccine plasma. 2021 Therapeutic advances in infectious disease Discussion SARS_CoV_2 E484K;K417N;K417N;K417T;K417T;N501Y 68;61;59;61;59;79 73;68;66;68;66;84 34211709 The emerging SARS-CoV-2 variants of concern. It is proposed that this mutation resulted from viruses harboring 614G leading to an outbreak of the D614G mutation, where the (D) stands for aspartic acid at residue 614 of the spike viral protein that converts to glycine (G). 2021 Therapeutic advances in infectious disease Discussion SARS_CoV_2 D614G 101 106 S 180 185 34211709 The emerging SARS-CoV-2 variants of concern. Moreover, spike D614G (G614 virus) from hamsters infected with SARS-CoV-2 revealed higher infectious titers in the upper versus lower respiratory tract, supporting the evidence of increased transmission within humans. 2021 Therapeutic advances in infectious disease Discussion SARS_CoV_2 D614G 16 21 S 10 15 34211709 The emerging SARS-CoV-2 variants of concern. N439K has a single amino acid change and has decreased sensitivity to neutralizing antibodies. 2021 Therapeutic advances in infectious disease Discussion SARS_CoV_2 N439K 0 5 34211709 The emerging SARS-CoV-2 variants of concern. N501Y rapidly spreads as part of the B.1.1.7 and 501.V2 clades with an affinity for ACE2 receptors in humans. 2021 Therapeutic advances in infectious disease Discussion SARS_CoV_2 N501Y 0 5 34211709 The emerging SARS-CoV-2 variants of concern. Sera from hamsters with D614G showed higher neutralization titers, which indicates that the efficacy of vaccines in clinical trials to protect against COVID-19 will not be compromised. 2021 Therapeutic advances in infectious disease Discussion SARS_CoV_2 D614G 24 29 COVID-19 151 159 34211709 The emerging SARS-CoV-2 variants of concern. Spike mutation E484K is present in about half of this lineage, with a smaller fraction having S477N instead of E484K. 2021 Therapeutic advances in infectious disease Discussion SARS_CoV_2 E484K;E484K;S477N 15;111;94 20;116;99 S 0 5 34211709 The emerging SARS-CoV-2 variants of concern. The variant isolate of E484K belonging to B.1.1.248, reported in the first week of 2021 in Brazil, also known as 501.V3 or P.1, is not identical to the new isolate identified in Japan, even though it is believed to have been carried via passengers aboard a flight from Brazil to Tokyo, Japan. 2021 Therapeutic advances in infectious disease Discussion SARS_CoV_2 E484K 23 28 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Despite the possible utilization of an alternative receptor, SARS-CoV-2 entry into H522 cells requires S, and the E484D S substitution appears to be specifically required for viral entry into H522 cells. 2021 Cell reports Discussion SARS_CoV_2 E484D 114 119 S;S 103;120 104;121 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. However, the low level of infectivity with the lentiviral pseudoparticles and the inability of the VSV-GFP-SARS-CoV-2 E484D to spread suggests that other factors, viral or cellular, may be required for efficient virus replication in H522 cells. 2021 Cell reports Discussion SARS_CoV_2 E484D 118 123 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. In a complementary experiment, inhibition of type I IFN signaling by ruxolitinib (a JAK1/2 inhibitor) did not facilitate the spread of VSV-GFP-SARS-CoV-2-SDelta21 or the E484D mutant (data not shown). 2021 Cell reports Discussion SARS_CoV_2 E484D 170 175 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Once the novel receptor mechanism is known, structural and biochemical studies of E484D S will be important. 2021 Cell reports Discussion SARS_CoV_2 E484D 82 87 S 88 89 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Our studies suggest that the E484D substitution may enable SARS-CoV-2 the ability to use an alternative receptor, either heparan sulfate alone or a modified host protein, without impacting ACE2-dependent entry. 2021 Cell reports Discussion SARS_CoV_2 E484D 29 34 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Substitutions within the E484 position, including E484D/K/Q/A/G, have been found in naturally circulating SARS-CoV-2 isolates as well as in clinical settings in response to mAb treatment. 2021 Cell reports Discussion SARS_CoV_2 E484A;E484D;E484G;E484K;E484Q 50;50;50;50;50 63;63;63;63;63 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. The striking requirement of the S E484D variant for infection of H522 cells establishes possible physiological relevance to these findings, which may reveal new facets of disease pathogenesis in vivo, particularly as it relates to variants. 2021 Cell reports Discussion SARS_CoV_2 E484D 34 39 S 32 33 34214467 Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. This study does not establish why the E484D variant enables ACE2-independent infection. 2021 Cell reports Discussion SARS_CoV_2 E484D 38 43 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. As it is located in the RBD, the N439K mutation is also resistant to neutralization by some mAbs. 2021 Frontiers in immunology Discussion SARS_CoV_2 N439K 33 38 RBD 24 27 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Both the D614G+L18F+A222V and D614G+A222V variants showed increased sensitivity to convalescent sera and sera elicited by inactivated-virus vaccines, which may be caused by the A222V mutation. 2021 Frontiers in immunology Discussion SARS_CoV_2 A222V;D614G;D614G;A222V;A222V;L18F 177;9;30;20;36;15 182;14;35;25;41;19 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. D614G+L18F+A222V and D614G+A222V were the main epidemic variants before the emergence of VOC-202012/01. 2021 Frontiers in immunology Discussion SARS_CoV_2 D614G;A222V;A222V;L18F;D614G 21;11;27;6;0 26;16;32;10;5 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Eight of the 17 mutations in the VOC-202012/01 variant are located in the spike protein, including 69-70del, 144/145del, N501Y, A570D, P681H, T716I, S982A, and D1118H. 2021 Frontiers in immunology Discussion SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;T716I 128;160;121;135;149;142 133;166;126;140;154;147 S 74 79 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Furthermore, as the P681H mutation is immediately adjacent to the Furin cleavage site, the proteolytic cleavage during viral maturation is assumed to be influenced. 2021 Frontiers in immunology Discussion SARS_CoV_2 P681H 20 25 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Furthermore, S477N was also resistant to neutralization by the human convalescent sera tested in this study, but not to vaccine-elicited sera. 2021 Frontiers in immunology Discussion SARS_CoV_2 S477N 13 18 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Furthermore, the L18F mutation is also present in variants B.1.351and P1, which are reported to exhibit a significant capacity to escape from mAbs and vaccines. 2021 Frontiers in immunology Discussion SARS_CoV_2 L18F 17 21 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Furthermore, the P681H mutant was also slightly less sensitive to neutralizing mAbs. 2021 Frontiers in immunology Discussion SARS_CoV_2 P681H 17 22 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. In addition, the introduction of a benzene ring formed a large steric effects, which may be one of the reasons for the decrease of neutralization activity of some mAbs caused by N501Y mutation. 2021 Frontiers in immunology Discussion SARS_CoV_2 N501Y 178 183 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. In Australia, 60% of the sequences uploaded up to January 2021 contained D614G+S477N. 2021 Frontiers in immunology Discussion SARS_CoV_2 D614G;S477N 73;79 78;84 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. In summary, this study found that the N501Y, N439K, and S477N mutations significantly decreased the neutralization activity of some monoclonal antibodies. 2021 Frontiers in immunology Discussion SARS_CoV_2 N439K;N501Y;S477N 45;38;56 50;43;61 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. It has also been suggested that the N501Y mutation increases the binding affinity of the spike protein to human ACE2. 2021 Frontiers in immunology Discussion SARS_CoV_2 N501Y 36 41 S 89 94 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. L18F and A222V are typical mutations of the B.1.177 lineage. 2021 Frontiers in immunology Discussion SARS_CoV_2 A222V;L18F 9;0 14;4 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. N439K is the representative mutation of lineage B.1.258, in which it always appears together with the 69-70del mutation. 2021 Frontiers in immunology Discussion SARS_CoV_2 N439K 0 5 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Our results showed that S477N escaped from neutralization by the mAb 7B8, which was consistent with the results of another study, which showed broad resistance of this mutant to a group of mAbs. 2021 Frontiers in immunology Discussion SARS_CoV_2 S477N 24 29 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Our results therefore indicate that the N501Y, P681H, and S982A mutations might be important antigenic sites of the VOC-202012/01 variant. 2021 Frontiers in immunology Discussion SARS_CoV_2 N501Y;P681H;S982A 40;47;58 45;52;63 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Our study of the neutralization susceptibility of these variants to a panel of mAbs showed that the N501Y mutation of VOC-202012/01 located in the RBD significantly decreased the neutralization activity of seven antibodies. 2021 Frontiers in immunology Discussion SARS_CoV_2 N501Y 100 105 RBD 147 150 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. S477N is the representative mutation site of the B.1.160, B.1.127, and B.1.526 lineages (COVID-19 CoV Genetics Browser, ). 2021 Frontiers in immunology Discussion SARS_CoV_2 S477N 0 5 COVID-19 89 97 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Since June 2020, a large number of S477N mutants have appeared and spread rapidly. 2021 Frontiers in immunology Discussion SARS_CoV_2 S477N 35 40 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. Since S477N is in the RBD region of S protein, it may slightly change the antigenicity of the virus. 2021 Frontiers in immunology Discussion SARS_CoV_2 S477N 6 11 RBD;S 22;36 25;37 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. The B.1.526 lineage that recently spread rapidly in New York City, USA, also contains the S477N mutation, which is speculated to significantly impact the epidemic. 2021 Frontiers in immunology Discussion SARS_CoV_2 S477N 90 95 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. The N501Y mutation in the RBD has been identified in a mouse-adapted strain, indicating that it is potentially associated with increased virulence in mice. 2021 Frontiers in immunology Discussion SARS_CoV_2 N501Y 4 9 RBD 26 29 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. The single mutation S982A at the S2 fragment of the spike protein also affected the neutralization activity of five mAbs, although not as significantly as N501Y. 2021 Frontiers in immunology Discussion SARS_CoV_2 N501Y;S982A 155;20 160;25 S 52 57 34220844 The Antigenicity of Epidemic SARS-CoV-2 Variants in the United Kingdom. This study showed that A222V was more sensitive to most mAbs, whereas L18F was slightly resistant to some mAbs. 2021 Frontiers in immunology Discussion SARS_CoV_2 A222V;L18F 23;70 28;74 34220870 Declining Levels of Neutralizing Antibodies Against SARS-CoV-2 in Convalescent COVID-19 Patients One Year Post Symptom Onset. Obviously, it would be of importance to conduct similar studies using a comprehensive panel of VOCs and virus under investigation (VUI), including variants harbouring the E484Q mutation such as B.1.617, which is currently very prevalent in India. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484Q 171 176 34222046 SARS-CoV-2: Origin, Evolution, and Targeting Inhibition. Recently, other mutations, such as E484Q and L452R, have emerged and have decreased the effect of the vaccine. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 E484Q;L452R 35;45 40;50 34222046 SARS-CoV-2: Origin, Evolution, and Targeting Inhibition. Unfortunately, the SARS-CoV-2 variant D614G is more infectious than the ancestral SARS-CoV-2. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G 38 43 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. F61 identified a linear epitope ranging from residues G446 to S494 on RBD, which included mutation site E484K in B.1.351. 2021 Virologica Sinica Discussion SARS_CoV_2 E484K 104 109 RBD 70 73 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. Furthermore, the unchanged neutralizing activity to N501Y, E484K, and L452R indicated that the gained antibodies may also neutralize the recent India endemic strain B.1.617, which revealed a broad neutralizing activity against SARS-CoV-2 variants. 2021 Virologica Sinica Discussion SARS_CoV_2 E484K;L452R;N501Y 59;70;52 64;75;57 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. Mutation L452R carried by the Indian variants B.1.617 could also be effectively neutralized by F61 and H121. 2021 Virologica Sinica Discussion SARS_CoV_2 L452R 9 14 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. Mutations K417N, E484K and N501Y in B.1.351 were not within the H121 epitope, therefore B.1.351 showed no resistance to the neutralizing activity of H121. 2021 Virologica Sinica Discussion SARS_CoV_2 E484K;K417N;N501Y 17;10;27 22;15;32 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. Pseudovirus with single-residue variants of K417N, L452R, A475V, E484K and N501Y on S protein could be efficiently neutralized by F61 and H121. 2021 Virologica Sinica Discussion SARS_CoV_2 A475V;E484K;K417N;L452R;N501Y 58;65;44;51;75 63;70;49;56;80 S 84 85 34224110 Antibody Cocktail Exhibits Broad Neutralization Activity Against SARS-CoV-2 and SARS-CoV-2 Variants. Variants of concern observed in the United Kingdom (B.1.1.7 with mutations N501Y), South Africa (B.1.351 with mutations K417N, E484K and N501Y), Brazil (P.1 with mutations K417T, E484K and N501Y) (Long et al.) and India (B.1.617 with mutations L452R and E484Q) (Cherian et al.) contain mutations K417N, L452R, A475V, E484K and N501Y. 2021 Virologica Sinica Discussion SARS_CoV_2 A475V;E484K;E484K;E484K;E484Q;K417N;K417N;K417T;L452R;L452R;N501Y;N501Y;N501Y;N501Y 310;127;179;317;254;120;296;172;244;303;75;137;189;327 315;132;184;322;259;125;301;177;249;308;80;142;194;332 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. Consistent with these studies, our results showed that S1-WT protein displayed lower neutralization titers against the mutant viruses containing E484K mutation, such as B.1.351 and P.1. 2021 MedComm Discussion SARS_CoV_2 E484K 145 150 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. Meanwhile, others discovered that the single E484K mutation impaired the binding ability of serum polyclonal neutralizing antibodies induced by previous SARS-CoV-2 strains infection or vaccines. 2021 MedComm Discussion SARS_CoV_2 E484K 45 50 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. Moreover, the neutralization antibodies induced by recombinant S1-WT displayed strong blockade on RBD-WT, while neutralization antibodies induced by S1-Mut protein displayed stronger blockade on RBD (E484K) and RBD-Mut, respectively. 2021 MedComm Discussion SARS_CoV_2 E484K 200 205 RBD;RBD;RBD 98;195;211 101;198;214 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. Thrillingly, we discovered that the sera from mice immunized with S1-Mut reduced the affinity between the ACE2 and RBD with E484K mutation, and S1-Mut recombinant protein induced strong protective immunity to block B.1.351 and P.1 pseudoviruses containing E484K mutation. 2021 MedComm Discussion SARS_CoV_2 E484K;E484K 124;256 129;261 RBD 115 118 34226895 A bivalent recombinant vaccine targeting the S1 protein induces neutralizing antibodies against both SARS-CoV-2 variants and wild-type of the virus. Wang et al reported that B.1.351 variant is refractory to neutralization by most NTD mAbs and multiple individual mAbs to RBD, which might be due to the E484K mutation in the S1 subunit of RBD. 2021 MedComm Discussion SARS_CoV_2 E484K 153 158 RBD;RBD 122;189 125;192 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. The potency seen for SAB-185 with the combination of E484K and N501Y likely reflects the fact that the hyperimmune IgG SAB-185 recognizes a broader swath of epitopes in S such that single substitutions are unlikely to escape neutralization. 2021 Human vaccines & immunotherapeutics Discussion SARS_CoV_2 E484K;N501Y 53;63 58;68 S 169 170 34228597 Human immunoglobulin from transchromosomic bovines hyperimmunized with SARS-CoV-2 spike antigen efficiently neutralizes viral variants. This finding contrasts with earlier work which shows that immune sera obtained from patients that have recovered from COVID-19 as well as several mAbs show significant reductions in neutralization potency in cell culture assays particularly against S substitutions E484K and S477N. 2021 Human vaccines & immunotherapeutics Discussion SARS_CoV_2 E484K;S477N 265;275 270;280 S 249 250 COVID-19 118 126 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. During the late spring of 2021, A.23.1 became extinct (1% prevalence on May 5th 2021), with this and other variants being replaced by VOC B.1.351 and VOI B.1.525 (without P681R), and increasingly B.1.617.2:which contains P681R (Figure 5). 2022 bioRxiv Discussion SARS_CoV_2 P681R;P681R 171;221 176;226 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. However, the A.23.1 variant pre-dated B.1.617 as a P681R-containing VOC/VOI by several months. 2022 bioRxiv Discussion SARS_CoV_2 P681R 51 56 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. Most recently, a new VOC B.1.617.2 has replaced B.1.1.7 as the dominant circulating virus globally, which (along with the other sub-lineages B.1.617.1 and B.1.617.3) has a P681R point mutation, and is more conventionally "polybasic" in the S1/S2 cleavage motif and suggested to enhance transmissibility and pathogenesis. 2022 bioRxiv Discussion SARS_CoV_2 P681R 172 177 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. Overall, this epidemiological data, suggests that while the P681R point mutation is important for furin-mediated cleavage, it is not the primary driver of virus transmissibility, a finding reinforced by the molecular studies described here. 2022 bioRxiv Discussion SARS_CoV_2 P681R 60 65 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. These variants appear to have expanded following the prior introduction of stabilizing mutations into the spike protein, such as D614G and Q613H. 2022 bioRxiv Discussion SARS_CoV_2 D614G;Q613H 129;139 134;144 S 106 111 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. This VOC is characterized by a P681H mutation in the spike S1/S2 "furin cleavage site" and has been linked to increased transmissibility due to the presence of the additional basic amino acid, histidine (H). 2022 bioRxiv Discussion SARS_CoV_2 P681H 31 36 S 53 58 34230931 Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda. While P681R does make the S1/S2 cleavage site more basic in nature, such variant cleavage sites are still not "ideal" for furin:as originally found in the prototype furin-cleaved virus mouse hepatitis virus (MHV) (RRARR S). 2022 bioRxiv Discussion SARS_CoV_2 P681R 6 11 34234758 A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3' Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity. Most of the amino acid changes in SARS-CoV-2 have already been characterized as energetically detrimental, and we agree with this fact in terms of structural dynamics, since recurrent changes in the Spike protein are capable of increasing (S477N, V1176F) or decreasing (A222V) the molecular dynamics of certain domains of the protein, implying that SARS-CoV-2 proteins are prone to evolve over time by variant accumulation. 2021 Frontiers in microbiology Discussion SARS_CoV_2 V1176F;A222V;S477N 247;270;240 253;275;245 S 199 204 34234758 A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3' Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity. Nevertheless, variants with minimal changes in fitness such as the mutation D614G in the early months of the pandemic shifts the S protein conformation toward an ACE2-binding fusion competent state, thereby increasing infectivity. 2021 Frontiers in microbiology Discussion SARS_CoV_2 D614G 76 81 S 129 130 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. A previous study has shown that serum neutralization is not compromised by N501Y (also found in the strain B.1.1.7). 2022 Allergy Discussion SARS_CoV_2 N501Y 75 80 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. In contrast, E484K (found B.1.1.7 and in P.1 strains) was associated with reduced neutralization by monoclonal antibodies and reduced recognition as shown here. 2022 Allergy Discussion SARS_CoV_2 E484K 13 18 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. The variant with the mutation N501Y shows enhanced affinity but almost normal recognition by convalescent antibodies. 2022 Allergy Discussion SARS_CoV_2 N501Y 30 35 34240429 Molecular definition of severe acute respiratory syndrome coronavirus 2 receptor-binding domain mutations: Receptor affinity versus neutralization of receptor interaction. When we investigated whether distinct mutations may affect receptor affinity, we found that N501Y mutation enhanced affinity for the viral receptor ACE2 both as a single mutation and as a triple mutation, while E484K mutation alone did not affect the interaction with ACE2. 2022 Allergy Discussion SARS_CoV_2 E484K;N501Y 211;92 216;97 34241897 Genomic monitoring unveil the early detection of the SARS-CoV-2 B.1.351 (beta) variant (20H/501Y.V2) in Brazil. Furthermore, a performed deep analysis of the mutational profile of this strain demonstrates that in comparison with the South African reference strain there were present three additional specific mutations in the spike genomic region (A262D, D614G, and C1247F). 2021 Journal of medical virology Discussion SARS_CoV_2 C1247F;D614G;A262D 254;243;236 260;248;241 S 214 219 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. Especially, K417N/T has already been identified in SA501Y.V2 and BR501Y.V3 mutant strains, decreasing or abolishing neutralizing activity of mAbs including those (CB6 and REGN10933) already approved for Emergency-Use-Administration, convalescent plasma from naturally infected patients, and immune sera from vaccinated individuals. 2021 Nature communications Discussion SARS_CoV_2 K417N;K417T 12;12 19;19 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. Further, K417N mutation has also been identified in mouse-adapted SARS-CoV-2 strains together with N501Y and Q493H. 2021 Nature communications Discussion SARS_CoV_2 K417N;N501Y;Q493H 9;99;109 14;104;114 34244522 Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. Importantly, virus escape studies identified K417N/T mutations conferring resistance to this class of antibodies, like those in class I or RBS-A indicated by previous studies. 2021 Nature communications Discussion SARS_CoV_2 K417N;K417T 45;45 52;52 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Although the majority of groups A and C SNVs were observed to be mutually exclusively with each other before June 2020, 95% of genomes harboring the representative SNV in the group C, G11083T (ORF1ab:L3606F), also carried group A SNVs after June 2020, confirming the ruling role of group A in current SARS-CoV-2 genomes. 2021 Journal of medical virology Discussion SARS_CoV_2 G11083T;L3606F 184;200 191;206 ORF1ab 193 199 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. For example, the occurrence ratios of group A.E1 SNVs, represented by C22227T (S:A222V), G29645T (ORF10:V30L), and C28932T (N:A220V), increased from 10% in August to 70% in November 2020, while the occurrence ratios of group A.E2, C27944T and G204T, and group A.E3, C21614T (S:L18F) and C24334T, elevated to about 60% and 50%, respectively, during the same time period. 2021 Journal of medical virology Discussion SARS_CoV_2 C21614T;C22227T;C24334T;C27944T;C28932T;G204T;G29645T;A220V;A222V;L18F;V30L 266;70;287;231;115;243;89;126;81;277;104 273;77;294;238;122;248;96;131;86;281;108 N;S;S 124;79;275 125;80;276 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Moreover, seven SNVs over-represented in the male were also specific to the age and mortality, including C5700A (nsp3:A994D), C6312A (nsp3:T1198K), C13730T (nsp12:A97V), C23929T (S:Y789Y), C28311T (ORF9:P13L), C19524T (nsp14:L495L), and G21724T (S:L54F). 2021 Journal of medical virology Discussion SARS_CoV_2 C13730T;C19524T;C23929T;C28311T;C5700A;C6312A;G21724T;A97V;A994D;L495L;L54F;P13L;T1198K;Y789Y 148;210;170;189;105;126;237;163;118;225;248;203;139;181 155;217;177;196;111;132;244;167;123;230;252;207;145;186 Nsp12;Nsp3;Nsp3;ORF9;S;S 157;113;134;198;179;246 162;117;138;202;180;247 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. Several emerging SNVs, for example, groups A.E1-E3, co-occurred with group A representative SNV, S:D614G, in the UK and other Northern European countries (Figure 1B,C). 2021 Journal of medical virology Discussion SARS_CoV_2 D614G 99 104 S 97 98 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. The logistic regression model used to predict mortality status explored that three critical nonsynonymous SNVs, S:V1176F, ORF7a:L31L, and T25A at the upstream of ORF1ab, in addition to ages above 40 years old, and the gender of male may have significant contributions to the death event. 2021 Journal of medical virology Discussion SARS_CoV_2 T25A;L31L;V1176F 138;128;114 142;132;120 ORF1ab;ORF7a;S 162;122;112 168;127;113 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. The set of signature variants includes 8 changes from S protein: deletion 69-70, deletion 144-145, N501Y (A23063T), A570D (C23271A), D614G, P681H (C23604A), T716I (C23709T), S982A (T24506G), D1118H (G24914C). 2021 Journal of medical virology Discussion SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I;A23063T;C23271A;C23604A;C23709T;G24914C;T24506G 116;191;133;99;140;174;157;106;123;147;164;199;181 121;197;138;104;145;179;162;113;130;154;171;206;188 S 54 55 34245452 Updated SARS-CoV-2 single nucleotide variants and mortality association. We further identified 41 and 30 SNVs with at least twofold higher occurrence rates in the death and nondeath group, respectively, including several mutations on the S protein, for example, G25088T (S:V1176F), G23401T (S:Q613H), G24197T (S:A879S), and T24811A (S:1083Q). 2021 Journal of medical virology Discussion SARS_CoV_2 G23401T;G24197T;G25088T;T24811A;A879S;Q613H;V1176F 209;228;189;251;239;220;200 216;235;196;258;244;225;206 S;S;S;S;S 165;198;218;237;260 166;199;219;238;261 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. Because this mutation was also later detected in other variants, in addition to UPHL-01, future studies should further investigate whether 11083G > T may increase the fitness of the carrier. 2021 Bulletin of the World Health Organization Discussion SARS_CoV_2 G11083T 139 149 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. Other studies have suggested the 11083G > T could be a beneficial mutation linked to asymptomatic infection. 2021 Bulletin of the World Health Organization Discussion SARS_CoV_2 G11083T 33 43 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. The RNA recombination of 11803G > T is also present in UPHL-01 variant, however, whether the carrier of the UPHL-01 acquired the variant from a cruise ship passenger or if the mutation appeared independently of cruise ship variants is unknown. 2021 Bulletin of the World Health Organization Discussion SARS_CoV_2 G11803T 25 35 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. The transmission started from either one or two primary cases with WIV04 sequence and/or 11083G > T mutation, then quickly separated into at least five subgroups based on new mutations. 2021 Bulletin of the World Health Organization Discussion SARS_CoV_2 G11083T 89 99 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. We have also reported the unique 29742G > A or 29742G > U substitutions in stem loop-II motif RNA in SARS-CoV-2 isolates in Australia. 2021 Bulletin of the World Health Organization Discussion SARS_CoV_2 G29742A 33 43 34248221 Viral transmission and evolution dynamics of SARS-CoV-2 in shipboard quarantine. Within 3 weeks, the genome, sampled from four infected individuals, had gained the same 11083G > T mutation, suggesting that RNA recombination also participated in viral evolution of the virus. 2021 Bulletin of the World Health Organization Discussion SARS_CoV_2 G11083T 88 98 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. Following the Cluster 5 discovery, a mink-associated SARS-CoV-2 variant with six spike protein changes appeared (L5F, DeltaH69/V70, Y453F, D614G, N751Y, and C1250F). 2021 Frontiers in microbiology Discussion SARS_CoV_2 C1250F;D614G;N751Y;Y453F;L5F 157;139;146;132;113 163;144;151;137;116 S 81 86 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. However, the Y453F substitution and DeltaH69/V70 were evaluated in other contexts. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F 13 18 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. Moreover, the Y453F variant also arose as a neutralization resistance mutation in the presence of some therapeutic neutralizing antibodies, as demonstrated for Regeneron's cocktail REGN10933 where Y453F reduced the neutralizing activity of an antibody by 29%. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F;Y453F 14;197 19;202 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. Potential causes may include: (i) reduced efficiency of viral entry due to the spike mutations; (ii) modulated viral replication resulting from amino acid changes and/or deletions in ORF1a (DeltaM85 and DeltaN2082) and ORF1b (P314L, T730I, and T2163I) that encode the viral replication and transcription complex; or (iii) altered virus induced apoptosis mediated by ORF3a in the presence of the H182Y change. 2021 Frontiers in microbiology Discussion SARS_CoV_2 H182Y;T2163I;T730I;P314L 395;244;233;226 400;250;238;231 ORF1a;S;ORF3a 183;79;366 188;84;371 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. Taken together, the Y453F and/or DeltaH69/V70 may have contributed to the observed reduced neutralization sensitivity of the Cluster 5 variant for COVID-19 convalescent plasma samples. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F 20 25 COVID-19 147 155 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. The NF9-Y453F epitope significantly reduces CD8+ T cell responses in HLA-A*24-positive COVID-19 convalescent samples. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F 8 13 COVID-19 87 95 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. The unhindered transmission and spread of mink-associated viruses in the community, together with the potential threat of new variants, necessitated an investigation of a newly emerged mink-associated variant (Cluster 5), which had four amino acid changes in the spike protein (DeltaH69/V70, Y453F, I692V, and M1229I) in addition to D614G. 2021 Frontiers in microbiology Discussion SARS_CoV_2 D614G;I692V;M1229I;Y453F 333;299;310;292 338;304;316;297 S 263 268 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. The Y453F substitution in the receptor binding domain appeared independently in SARS-CoV-2 infected mink in the Netherlands and in Denmark. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F 4 9 RBD 30 53 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. While infrequent in the Netherlands (4 out of 16 farms), Y453F became an established mink-associated spike mutation in Denmark. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F 57 62 S 101 106 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. While Y453F is potentially an adaptation to the mink ACE2 receptor, it also increases affinity for human ACE2. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F 6 11 34248922 In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. Y453F resides within an immunodominant HLA-A*24:02 restricted epitope NF9. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F 0 5 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. As a result, the serine substitution at Cys145 for 3CLpro did not exhibit any catalytic activity as it won't be able to be deprotonated by His145. 2021 Frontiers in chemistry Discussion SARS_CoV_2 S145C 17 46 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. Even though both aspartate and glutamate can in theory function as a general base and promote the 3CLpro-catalyzed reaction, the H41D and H41E variants were catalytically inactive. 2021 Frontiers in chemistry Discussion SARS_CoV_2 H41D;H41E 129;138 133;142 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. For the H41D variant, 3CLpro stability was reduced, with an increase in the DeltaH cal value. 2021 Frontiers in chemistry Discussion SARS_CoV_2 H41D 8 12 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. Further, the oligomeric state of the H41A and C145S variants was the same as that of the WT enzyme, with a pronounced dimeric form. 2021 Frontiers in chemistry Discussion SARS_CoV_2 C145S;H41A 46;37 51;41 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. Furthermore, the thermodynamic stability and T m value of the H41A variant decreased; however, it did change in the C145A variant. 2021 Frontiers in chemistry Discussion SARS_CoV_2 C145A;H41A 116;62 121;66 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. Hence, the lack of catalytic activity upon H41D or H41E substitution is not a result of a disturbed structural fold of the enzyme but, rather, it is related to overall change of the conformational fold of the enzyme. 2021 Frontiers in chemistry Discussion SARS_CoV_2 H41D;H41E 43;51 47;55 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. However, in cystine proteases as the case for 3CLpro, an aspartic residue is not present to bind His41 of the catalytic dyad to make it a strong nucleophile for the deprotonation of serine substitution at Cys145. 2021 Frontiers in chemistry Discussion SARS_CoV_2 S145C 182 211 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. Similar to the alanine substitution, the H41D and H41E variants did not exhibit any activity even at high enzyme concentration. 2021 Frontiers in chemistry Discussion SARS_CoV_2 H41D;H41E 41;50 45;54 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. The C145A variant was the only variant whose oligomeric state was higher than that of the WT enzyme. 2021 Frontiers in chemistry Discussion SARS_CoV_2 C145A 4 9 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. The catalytic activity of 3CLpro was abolished in the H41A or C145A variants although CD analysis revealed that the abolished catalytic activity of these variants was not caused by changes in their secondary structure. 2021 Frontiers in chemistry Discussion SARS_CoV_2 C145A;H41A 62;54 67;58 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. The lowest drop in the T m value was observed with the C145A mutant which is also the only mutant that possess an oligomeric state higher than the dimeric form of the WT enzyme. 2021 Frontiers in chemistry Discussion SARS_CoV_2 C145A 55 60 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. The oligomeric state of the C145S enzyme was similar to that of other variants, in that it preferentially adopted the dimeric state. 2021 Frontiers in chemistry Discussion SARS_CoV_2 C145S 28 33 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. The stability of 3CLpro C145S slightly increased, with a major increase in the DeltaH cal value, similar to the effect of H41E. 2021 Frontiers in chemistry Discussion SARS_CoV_2 C145S;H41E 24;122 29;126 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. The stability of 3CLpro was not affected by the H41E substitution and a considerable increase in the DeltaH cal value was noted for this variant. 2021 Frontiers in chemistry Discussion SARS_CoV_2 H41E 48 52 34249864 Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. This indicates that polar bonding interactions contribute the most to the stability of the H41E variant. 2021 Frontiers in chemistry Discussion SARS_CoV_2 H41E 91 95 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. A proportion of RBD-specific mAbs isolated from vaccinated individuals have also demonstrated significant neutralization loss (>50-fold) against N501Y mutants. 2021 JCI insight Discussion SARS_CoV_2 N501Y 145 150 RBD 16 19 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Although the E484K mutation has been associated with immune escape, predictions regarding its affinity to the ACE2 receptor are conflicting. 2021 JCI insight Discussion SARS_CoV_2 E484K 13 18 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Furthermore, F490L, which has been described to be remarkably resistant to mAbs, demonstrated weak binding to the panel of mAbs in comparison with the other variants in the multiplex assay, with RBD alanine mutation at this position confirming that this is a critical epitope for certain mAbs. 2021 JCI insight Discussion SARS_CoV_2 F490L 13 18 RBD 195 198 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. However, there were differences in particular with S477N, which had the second highest overall affinity (KD) for ACE2 (after N501Y) as determined via BLI but had weaker EC50 compared with Q493L and S494P, respectively. 2021 JCI insight Discussion SARS_CoV_2 N501Y;Q493L;S477N;S494P 125;188;51;198 130;193;56;203 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Indeed, the frequency and presence of the N501Y mutation in recently rapidly emerging SARS-CoV-2 lineages, B.1.1.7, B.1.351, B.1.1.70, and P.1, appear to further strengthen this hypothesis, as does the frequency of S477N and S494P, which we find bound ACE2 with an enhanced affinity (Figure 3, B and D). 2021 JCI insight Discussion SARS_CoV_2 N501Y;S477N;S494P 42;215;225 47;220;230 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. It has also been suggested that mutations of the RBD, such as N501Y, that increase the affinity of ACE2 are likely to tip the equilibrium away from mAb-RBD interaction toward RBD-ACE2, making the virus more difficult to neutralize. 2021 JCI insight Discussion SARS_CoV_2 N501Y 62 67 RBD;RBD;RBD 49;152;175 52;155;178 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. It is interesting to note, however, that unlike higher affinity N501Y and S477N variants, F490L and G446V demonstrated the weakest EC50 values in our ACE2 binding assay (Figure 3D), but were observed at relatively high frequencies (Figure 3B), supporting the hypothesis that modestly deleterious mutations may have the potential to rise in prevalence if they confer escape from selective pressures, such as the immune response. 2021 JCI insight Discussion SARS_CoV_2 F490L;G446V;N501Y;S477N 90;100;64;74 95;105;69;79 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. It is therefore plausible that factors in the assay design, including the orientation by which RBD may be being presented on the beads and the use of the RBD instead of the spike, may exaggerate the impact of the N501Y mutation due to its altered affinity. 2021 JCI insight Discussion SARS_CoV_2 N501Y 213 218 S;RBD;RBD 173;95;154 178;98;157 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. It is, however, generally thought that minimal or modest drops in neutralization do not indicate a biologically relevant change in neutralization activity, and there is presently no evidence for vaccine escape from the B.1.1.7 variant carrying the single RBD N501Y mutation. 2021 JCI insight Discussion SARS_CoV_2 N501Y 259 264 RBD 255 258 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Our findings for mAb C135 and C002 contrast those of others, which demonstrated little to no significant impact of the N501Y variant. 2021 JCI insight Discussion SARS_CoV_2 N501Y 119 124 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Our findings, which demonstrate a reduced affinity of E484K to ACE2, however, support the recent observations in which the E484K mutation has been found to prevent the formation of 2 salt bridges that help to form and stabilize the RBD-ACE2 complex, thus reducing ACE2 binding affinity. 2021 JCI insight Discussion SARS_CoV_2 E484K;E484K 54;123 59;128 RBD 232 235 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Similar findings to N501Y pseudotyped and chimeric viruses have been reported for some mAbs, with partial escape from COVA1-18 and COVA2-15 associated with the N501Y mutation. 2021 JCI insight Discussion SARS_CoV_2 N501Y;N501Y 20;160 25;165 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Specifically, within the mAb panel, we found variants at positions 446 and 484 (with the exception of E484D) were poorly neutralized. 2021 JCI insight Discussion SARS_CoV_2 E484D 102 107 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. This could be explained by the fact that compared with Q493L and S494P (which have a comparable KA to the WT), S477N has a much faster on rate, which results in a stronger overall KD. 2021 JCI insight Discussion SARS_CoV_2 Q493L;S477N;S494P 55;111;65 60;116;70 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Though the E484K variant has been associated with immune escape because it is situated in an immunodominant epitope targeted by most infected patients, several studies have found minimal to no pronounced effect of the N501Y mutation on the neutralizing activity of plasma from convalescent or vaccinated individuals. 2021 JCI insight Discussion SARS_CoV_2 E484K;N501Y 11;218 16;223 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. Unlike the previously described variants, which demonstrated escape from mAb recognition, N501Y was recognized at relatively high affinity by most mAbs. 2021 JCI insight Discussion SARS_CoV_2 N501Y 90 95 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. We also found S477N, and Q493L, a variant at a position that interfaces directly with ACE2, had enhanced affinity to ACE2, confirming observations from deep mutational scanning analysis. 2021 JCI insight Discussion SARS_CoV_2 Q493L;S477N 25;14 30;19 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. We also found variant G446V, which has demonstrated resistance to REGEN10987 and C135, to be poorly neutralized by our panel of mAbs. 2021 JCI insight Discussion SARS_CoV_2 G446V 22 27 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. We observed via BLI an almost 5-fold greater affinity of the N501Y variant to ACE2 compared with WT, confirming previous studies that describe the formation of 3 additional bonds that increase the affinity of this variant to the ACE2 receptor. 2021 JCI insight Discussion SARS_CoV_2 N501Y 61 66 34251356 Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay. When we profiled the polyclonal response of SARS-CoV-2 convalescent plasma to the RBD variants by multiplex, we observed a similar pattern in the attenuation of the inhibitory response to variants at position E484, as well as a pronounced reduction in the inhibitory response against N501Y (as well as Q493L, followed by N439K and S477N). 2021 JCI insight Discussion SARS_CoV_2 N439K;N501Y;Q493L;S477N 321;284;302;331 326;289;307;336 RBD 82 85 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. In this study, signature nonsynonymous mutations leading to amino acid changes of P323L in the RdRp was found (Supplementary Table ST2), which is involved in the replication of the viral genome. 2021 Virus genes Discussion SARS_CoV_2 P323L 82 87 RdRP 95 99 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Moreover, D614G in the spike glycoprotein is also predominant in Bangladesh-originated SARS-CoV-2 genome, which should be of urgent concern considering the dominance of this mutation globally since early February in Europe. 2021 Virus genes Discussion SARS_CoV_2 D614G 10 15 S 23 41 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Notably, few other previous studies although suggest the involvement of the diseases severity with the specific mutation (D614, P323L) in the SARS-CoV-2 genome. 2021 Virus genes Discussion SARS_CoV_2 P323L 128 133 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. Notably, the D614G mutation is close to the furin recognition site for cleavage of the spike protein, which plays an important role in virus entry. 2021 Virus genes Discussion SARS_CoV_2 D614G 13 18 S 87 92 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. On the other hand, the temporal analysis of mutation accumulation also showed mutations (P323L, I120F, D614G, R203K, G204R) that persist over a longer period of time. 2021 Virus genes Discussion SARS_CoV_2 D614G;G204R;I120F;R203K;P323L 103;117;96;110;89 108;122;101;115;94 34251592 Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh. So, mutations in S protein including D614G need to be evaluated carefully, as S protein is essential for the entry of the virus in the host cell by binding to the ACE2 receptor leading to the escape from antibody inhibition allowing infected and recovered patients to become infected again and these mutations may have resulted in the evolution of a new subtype with more transmissible ability. 2021 Virus genes Discussion SARS_CoV_2 D614G 37 42 S;S 17;78 18;79 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Although the P681H mutation was the most prevalent FCS mutation in human SARS-CoV-2 isolates, it was also detected in different animal species, including dog (n = 3), cat (n = 2), monkey (n = 2), lion (n = 1), tiger (n = 1), and leopard (n = 1), as well as in environmental samples (n = 167), indicating that this mutation may have an impact on virus transmissibility and fitness. 2021 Archives of virology Discussion SARS_CoV_2 P681H 13 18 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Deep analysis of SARS-CoV-2 S protein sequences revealed multiple substitutions, including S680P/F, P681H/R/S/L, R682G/Q/W, R683G/P, A684E/S/T/V, S686R, V687I, and A688S/V (Table 1). 2021 Archives of virology Discussion SARS_CoV_2 A684E;A684S;A684T;A684V;A688S;A688V;P681H;P681L;P681R;P681S;R682G;R682Q;R682W;R683G;R683P;S680F;S680P;S686R;V687I 133;133;133;133;164;164;100;100;100;100;113;113;113;124;124;91;91;146;153 144;144;144;144;171;171;111;111;111;111;122;122;122;131;131;98;98;151;158 S 28 29 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. However, we observed a slight increase in the frequency of some randomly chosen mutations (S680F, P681S, A684T, and V687I), particularly during the period of October 2020 to January 2021 compared to other time periods in 2020. 2021 Archives of virology Discussion SARS_CoV_2 A684T;P681S;V687I;S680F 105;98;116;91 110;103;121;96 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. In addition, seven single deletions (DeltaS680, DeltaP681, DeltaR682, DeltaR683, DeltaA684, DeltaS686, DeltaV687, and DeltaA688) were also found in the FCS of SARS-CoV-2 isolated from humans and animals. 2021 Archives of virology Discussion SARS_CoV_2 DeltaA688 118 127 34258664 Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals. Moreover, this mutation is also a characteristic of the newly emerged SARS-CoV-2 variants, which are defined by multiple mutations in the S glycoprotein (Delta69-70, Delta144, N501Y, A570D, D614G, P681H, T716I, S982A, and D1118H). 2021 Archives of virology Discussion SARS_CoV_2 A570D;D1118H;D614G;N501Y;P681H;S982A;T716I 183;222;190;176;197;211;204 188;228;195;181;202;216;209 S 138 152 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? In contrast, it lacks mutation E484Q which is present in the other two lineages and was initially suspected to confer a certain degree of resistance to antibody neutralization. 2021 Journal of medical virology Discussion SARS_CoV_2 E484Q 31 36 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? Our data indicate that most of the mutants are predicted to destabilize the RBD structure, except for E484K and T478K. 2021 Journal of medical virology Discussion SARS_CoV_2 E484K;T478K 102;112 107;117 RBD 76 79 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? Subvariants B.1.617.1 (kappa) and B.1.617.3 have both the double mutations E484Q and the L452R. 2021 Journal of medical virology Discussion SARS_CoV_2 E484Q;L452R 75;89 80;94 34260088 SARS-CoV-2 B.1.617 Indian variants: Are electrostatic potential changes responsible for a higher transmission rate? To further justify our assumption, we note that the intensely investigated D614G substitution of the spike protein, early reported in Italian isolates, and subsequently attributed with increased virus transmissibility was found to enhance the protein torsional ability and potentially affecting its stability. 2021 Journal of medical virology Discussion SARS_CoV_2 D614G 75 80 S 101 106 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. An obligatory question that arises from the current analysis of the novel lineage and the evidence of 67 other lineages with the evolutionary convergence at the Spike E484K is related to the context of the emergence of highly divergent lineages, and the selection of specific substitutions. 2021 Frontiers in medicine Discussion SARS_CoV_2 E484K 167 172 S 161 166 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. E484K has been suggested to be responsible for a considerably lower neutralizing activity in vitro from convalescent plasma, although the cell-mediated immunity could not be affected by the distinctive mutations. 2021 Frontiers in medicine Discussion SARS_CoV_2 E484K 0 5 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. In the present study, the emerging lineage is bearing the amino acid change E484K, located at the receptor binding domain (RBD) of the Spike protein. 2021 Frontiers in medicine Discussion SARS_CoV_2 E484K 76 81 RBD;S;RBD 98;135;123 121;140;126 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. In the same way, despite it has not been considered a critical amino acid change, S249L is located at the N-terminal domain (NTD), the second domain most frequently targeted by neutralizing antibodies. 2021 Frontiers in medicine Discussion SARS_CoV_2 S249L 82 87 N 106 107 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. It is mandatory to evaluate the impact of the genetic background of B.1+L249S+E484K in the neutralization efficacy of convalescent sera/plasma from acquired immunity. 2021 Frontiers in medicine Discussion SARS_CoV_2 E484K;L249S 78;72 83;77 34262921 Novel Highly Divergent SARS-CoV-2 Lineage With the Spike Substitutions L249S and E484K. The potential impact of E484K in concert with other amino acid chances has been suggested for the P.1 variant, therefore, its effect in combination to S249L or other changes in critical proteins for viral replication (e.g., Helicase, 2'-O-ribose methyltransferase, etc.) found in the here reported lineage is to be determined. 2021 Frontiers in medicine Discussion SARS_CoV_2 E484K;S249L 24;151 29;156 Helicase 224 232 34268528 SARS-CoV-2 Infections in mRNA Vaccinated Individuals are Biased for Viruses Encoding Spike E484K and Associated with Reduced Infectious Virus Loads that Correlate with Respiratory Antiviral IgG levels. Genomic analysis revealed that only 67 had genomic coverage of >= 90% and when compared to a random cohort of our characterized genomes from a matched time frame, there was a statistically significant increased representation of lineage B.1.526 as well as the Spike amino acid change S:E484K. 2021 medRxiv Discussion SARS_CoV_2 E484K 286 291 S;S 260;284 265;285 34268528 SARS-CoV-2 Infections in mRNA Vaccinated Individuals are Biased for Viruses Encoding Spike E484K and Associated with Reduced Infectious Virus Loads that Correlate with Respiratory Antiviral IgG levels. Our study shows that the S: E484K is significantly associated with breakthrough cases after vaccination in a well-controlled analysis that used a large cohort of controls from a matched time frame of sample collection. 2021 medRxiv Discussion SARS_CoV_2 E484K 28 33 S 25 26 34268528 SARS-CoV-2 Infections in mRNA Vaccinated Individuals are Biased for Viruses Encoding Spike E484K and Associated with Reduced Infectious Virus Loads that Correlate with Respiratory Antiviral IgG levels. The S: E484K independently emerged in multiple lineages in distant geographical locations including the B.1.351 and the P.1 and those lineages showed some reduction in neutralization by sera collected from immunized individuals as well as decreased susceptibility to certain therapeutic monoclonal antibodies. 2021 medRxiv Discussion SARS_CoV_2 E484K 7 12 S 4 5 34268528 SARS-CoV-2 Infections in mRNA Vaccinated Individuals are Biased for Viruses Encoding Spike E484K and Associated with Reduced Infectious Virus Loads that Correlate with Respiratory Antiviral IgG levels. The S: E484K is also present in some strains of lineage B.1.526, a lineage which was significantly associated with positives after vaccination in our cohort, even though in a previous study, it was not reported to associate with positives after vaccination. 2021 medRxiv Discussion SARS_CoV_2 E484K 7 12 S 4 5 34268528 SARS-CoV-2 Infections in mRNA Vaccinated Individuals are Biased for Viruses Encoding Spike E484K and Associated with Reduced Infectious Virus Loads that Correlate with Respiratory Antiviral IgG levels. This study is also the first to show the significant association of S: E484K with positives after full vaccination using a well-controlled analysis and a relatively large sample size. 2021 medRxiv Discussion SARS_CoV_2 E484K 71 76 S 68 69 34268528 SARS-CoV-2 Infections in mRNA Vaccinated Individuals are Biased for Viruses Encoding Spike E484K and Associated with Reduced Infectious Virus Loads that Correlate with Respiratory Antiviral IgG levels. Those variants were associated with an increase in transmissibility and in particular the S: E484K substitution was associated with a compromise in the neutralization by monoclonal antibodies rendering this change "of therapeutic concern". 2021 medRxiv Discussion SARS_CoV_2 E484K 93 98 S 90 91 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Additionally, another finding demonstrated that the increasing in CFR occurs as consequence of D614G mutation which results in an increase in the entry of virus cells that are harbored with this mutation leading to increased viral infectivity. 2021 Biomedical journal Discussion SARS_CoV_2 D614G 95 100 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Also, the D614G mutation is the dominant mutation among other mutations. 2021 Biomedical journal Discussion SARS_CoV_2 D614G 10 15 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Although it does not have antigenicity, the D614G mutation is very ubiquitous with a higher mortality rate than from COVID-19. 2021 Biomedical journal Discussion SARS_CoV_2 D614G 44 49 COVID-19 117 125 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Apart from D614G, we also identified other mutations in the S1 subunit namely L5F and S13I which are in the signal peptide (SP) domain. 2021 Biomedical journal Discussion SARS_CoV_2 D614G;L5F;S13I 11;78;86 16;81;90 S 124 126 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Based on statistical analysis, it is known that the genome group that has the A1841G mutation is more dominant than other mutations. 2021 Biomedical journal Discussion SARS_CoV_2 A1841G 78 84 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Following the findings of mutations in NTD, mutations were also found in CTD/RBD of the SARS-CoV-2 spike sequence including Y453F and V367F. 2021 Biomedical journal Discussion SARS_CoV_2 V367F;Y453F 134;124 139;129 S;RBD 99;77 104;80 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. Since we found several mutations that occur in these domains including T791I, A930V, N1187K and G1219V, the pattern suggests that they affect the membrane fusion process. 2021 Biomedical journal Discussion SARS_CoV_2 A930V;G1219V;N1187K;T791I 78;96;85;71 83;102;91;76 Membrane 146 154 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. The protein level also shows the same pattern, where the A1841G mutation causes a change in the aspartic acid at position 614 to Glycine. 2021 Biomedical journal Discussion SARS_CoV_2 A1841G;D614G 57;96 63;136 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. This D614G mutation does not change the antigenicity of SARS-CoV-2 because the position is not part of (the N-terminal domain [NTD] and the C-terminal domain [CTD]) which is the first priming of the SARS-CoV-2 antigen. 2021 Biomedical journal Discussion SARS_CoV_2 D614G 5 10 N 108 109 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. This study also shows that several genomes have a combination of mutations of A1841G and mutations of other types. 2021 Biomedical journal Discussion SARS_CoV_2 A1841G 78 84 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. We found 17 mutation types of total sequences located within the NTD including T22I, P25L, T29I, Y38C, H49Y, S50L, F86S, T95I, E96G, S151G, N185K, N188K, V213L, S221W, S247R, G261D and Y279N. 2021 Biomedical journal Discussion SARS_CoV_2 E96G;F86S;G261D;H49Y;N185K;N188K;P25L;S151G;S221W;S247R;S50L;T22I;T29I;T95I;V213L;Y279N;Y38C 127;115;175;103;140;147;85;133;161;168;109;79;91;121;154;185;97 131;119;180;107;145;152;89;138;166;173;113;83;95;125;159;190;101 34271250 Emerging mutation in SARS-CoV-2 spike: Widening distribution over time in different geographic areas. We noted that the nucleotide mutation A1841G is a mutation that was first introduced in January in the European region and subsequently spread so rapidly that it became the most common type of mutation in spike sequences worldwide over time. 2021 Biomedical journal Discussion SARS_CoV_2 A1841G 38 44 S 205 210 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. A regional variant was detected with increased prevalence in February 2021 that combined S: P681H and S: E484K. 2022 Clinical infectious diseases Discussion SARS_CoV_2 E484K;P681H 105;92 110;97 S;S 89;102 90;103 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. B.1.243 has substitution NSP3:G1300D, which was present in the genomes of all of the hospitalized patients, but in only about 80% of the total genomes of this lineage. 2022 Clinical infectious diseases Discussion SARS_CoV_2 G1300D 30 36 Nsp3 25 29 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. Earlier research proposed an association of the S:D614G with mortality; however, this might be difficult to interpret owing to this substitution's early global dominance. 2022 Clinical infectious diseases Discussion SARS_CoV_2 D614G 50 55 S 48 49 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. It was also the only lineage with the occasional co-occurrence of N:T205I and N:S194L, which were both seen in higher percentages of sequences from known hospitalized patients. 2022 Clinical infectious diseases Discussion SARS_CoV_2 S194L;T205I 80;68 85;73 N;N 66;78 67;79 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. Notably, the circulation of variants carrying S: E484K has been temporary and the prevalence of this change remains sparse. 2022 Clinical infectious diseases Discussion SARS_CoV_2 E484K 49 54 S 46 47 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. On the other hand, a global increase in S: P681H is notable as a part of B.1.1.7. 2022 Clinical infectious diseases Discussion SARS_CoV_2 P681H 43 48 S 40 41 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. Our data show that variants that carried S: E484K showed temporary circulation, in contrast to variants with S: P681H. 2022 Clinical infectious diseases Discussion SARS_CoV_2 E484K;P681H 44;112 49;117 S;S 41;109 42;110 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. Signature mutations in the B.1.1.7, P1 and B.1.351 variants, including S: N501Y, could affect binding to ACE2. 2022 Clinical infectious diseases Discussion SARS_CoV_2 N501Y 74 79 S 71 72 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. The most common amino acid substitutions were extra-spike and included stable changes (eg, NS3:Q57H) and changes that increased (multiple NSP3 and NS8 changes). 2022 Clinical infectious diseases Discussion SARS_CoV_2 Q57H 95 99 S;Nsp3;NS3 52;138;91 57;142;94 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. The S: E484K variants B.1.351 and P1, however, were more successful in South Africa and South America, respectively. 2022 Clinical infectious diseases Discussion SARS_CoV_2 E484K 7 12 S 4 5 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. The spike amino acid changes that were most common after S: D614G included N501Y and P681H, with a notable increase in diversity compared with March 2020. 2022 Clinical infectious diseases Discussion SARS_CoV_2 D614G;N501Y;P681H 60;75;85 65;80;90 S;S 4;57 9;58 34272947 An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern. This lineage shows amino acid substitutions NSP12:P323L, N:S194L,S:D614G, and S:P681H in >90% of specimens. 2022 Clinical infectious diseases Discussion SARS_CoV_2 D614G;P323L;P681H;S194L;S194S 67;50;80;59;59 72;55;85;64;64 Nsp12;N;S;S 44;57;65;78 49;58;66;79 34278277 SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high risk variants into the United Kingdom. B.1.617.1 also features E484Q, a similar mutation to the E484K SNP found in B.1.351, B.1.525 and P.1, which has been demonstrated to mediate immune escape. 2021 EClinicalMedicine Discussion SARS_CoV_2 E484K;E484Q 57;24 62;29 34278277 SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high risk variants into the United Kingdom. B.1.617.2 on the other hand contains T478K in place of E484Q. 2021 EClinicalMedicine Discussion SARS_CoV_2 E484Q;T478K 55;37 60;42 34278277 SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high risk variants into the United Kingdom. In relation to the B.1.617 lineage, spike L452R is notable for its ability to induce substantially reduced sensitivity to convalescent sera and for having the greatest increase in binding affinity to ACE2. 2021 EClinicalMedicine Discussion SARS_CoV_2 L452R 42 47 S 36 41 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. CP and casirivimab/imdevimab (REGN:COV2) appeared to remain at least partially effective from a clinical perspective when used in our patients with viral rebound even in the presence of E484K. 2021 The Lancet regional health. Europe Discussion SARS_CoV_2 E484K 186 191 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. Due to the complexity of the immunosuppressed patients treated with bamlanivimab, we treated them exclusively as inpatients in single rooms in a dedicated COVID-19 isolation ward with staff trained and highly experienced in PSA, and there was no evidence of transmission of these emerging viral strains harbouring E484K in this setting. 2021 The Lancet regional health. Europe Discussion SARS_CoV_2 E484K 314 319 COVID-19 155 163 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. Gottlieb and colleagues reported an emergence of escape mutants (E484K; E484Q; F490S and S494P) in 28/297 (9 4%) patients who received bamlanivimab monotherapy and even in 7/145 (4 8%) of patients receiving placebo in the phase 2/3 BLAZE-1 trial. 2021 The Lancet regional health. Europe Discussion SARS_CoV_2 E484Q;F490S;S494P;E484K 72;79;89;65 77;84;94;70 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. Indeed, there are already different reports that describe the E484K substitution in the context of B.1.1.7. 2021 The Lancet regional health. Europe Discussion SARS_CoV_2 E484K 62 67 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. It should also be mentioned that the recently described variant B.1.617.1 (first documented in India, WHO label Kappa) harbours the E484Q mutation, which was also selected in patient 1. 2021 The Lancet regional health. Europe Discussion SARS_CoV_2 E484Q 132 137 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. Remarkably, only 3 out of the 1270 available sequences presented the E484K mutation and were characterized as B.1.351 isolates. 2021 The Lancet regional health. Europe Discussion SARS_CoV_2 E484K 69 74 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. Similarly, the development of the immune escape mutation E484K during the course of the disease cannot conclusively explain the lack of timely response to mAb therapy in patients 2 and 3. 2021 The Lancet regional health. Europe Discussion SARS_CoV_2 E484K 57 62 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. The E484K mutation selected here in common SARS-CoV-2 variants is also present in different VOCs associated with immune evasion, including the variant B.1.351 initially described in South Africa (WHO label Beta) and the variants P1 (WHO label Gamma) and P2 (WHO label Zeta) detected in Brazil which are currently rare in Germany. 2021 The Lancet regional health. Europe Discussion SARS_CoV_2 E484K 4 9 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. The fact that we observed the occurrence of E484K in a much higher percentage (5/6; 83 3%) when treating severely immunosuppressed patients suggests a significantly higher risk of viral escape in this setting. 2021 The Lancet regional health. Europe Discussion SARS_CoV_2 E484K 44 49 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. This observation and the fact that all our patients harboured variants with the E484E mutation at baseline support our hypothesis that the E484K mutation was indeed newly selected under the specific immune pressure of bamlanivimab in five of six patients with impaired humoral and cell-mediated immunity. 2021 The Lancet regional health. Europe Discussion SARS_CoV_2 E484E;E484K 80;139 85;144 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. To investigate the local baseline prevalence of the E484K mutation, all SARS-CoV-2 whole genome sequences available from the Dusseldorf region at that time were screened. 2021 The Lancet regional health. Europe Discussion SARS_CoV_2 E484K 52 57 34278371 Emergence of the E484K mutation in SARS-COV-2-infected immunocompromised patients treated with bamlanivimab in Germany. While it was reported in vitro that SARS-CoV-2 variants harbouring the mutations E484K or E484Q are resistant against neutralization by the monoclonal antibody bamlanivimab, our clinical observation that these mutations newly emerged under bamlanivimab therapy and potentially impaired clinical outcomes of patients could have important implications not only for the clinical management of individual patients but also concerning epidemiological measures for pandemic control. 2021 The Lancet regional health. Europe Discussion SARS_CoV_2 E484K;E484Q 81;90 86;95 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. For example, many of the favorably selected variants, such as L18F, L5F (spike); R203K, G204R, and A220V (nucleocapsid), were found to be destabilizing the respective protein structure (Table 1). 2021 mBio Discussion SARS_CoV_2 A220V;G204R;L18F;L5F;R203K 99;88;62;68;81 104;93;66;71;86 N;S 106;73 118;78 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. In addition, we also observed a positive natural selection of Q57H (B.1.X), R203K/G204R (B.1.1.X), T85I (B.1.2-B.1.3), G15S+T428I (C.X), and I120F (D.X) variants. 2021 mBio Discussion SARS_CoV_2 G15S;I120F;Q57H;R203K;T85I;G204R;T428I 119;141;62;76;99;82;124 123;146;66;81;103;87;129 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. Our analysis confirmed previously recorded positive natural selection of the D614G, S477N, A222V, and V1176F variants and a global expansion of the PANGOLIN variant B.1. 2021 mBio Discussion SARS_CoV_2 A222V;D614G;S477N;V1176F 91;77;84;102 96;82;89;108 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. Recently generated experimental evidence suggests that leading vaccines (mRNA-1273, BNT162b1, and ChAdOx1 nCoV-19) and two potent neutralizing antibodies (REGN10987 and REGN10933) are unlikely to be affected by the dominant variant D614G. 2021 mBio Discussion SARS_CoV_2 D614G 232 237 34281387 Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations. The antigenic effect of key RBD mutations against the REGN-COV2 cocktail (REGN10933 and REGN10987) showed N439K and K444R variants escaped neutralization only by REGN10987, while E406W escaped both individual REGN-COV2 antibodies and the cocktail. 2021 mBio Discussion SARS_CoV_2 E406W;K444R;N439K 179;116;106 184;121;111 RBD 28 31 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. By analyzing kinetic of interactions, we determined that the antibodies LY-CoV555, REGN10933, and REGN10987 showed strong binding capacity for the SARS-CoV-2 Wuhan, D614G, and B.1.1.7 S1 domains. 2021 Journal of virology Discussion SARS_CoV_2 D614G 165 170 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. Despite the enhanced affinity of the S1 variants B.1.1.7 and P.1 for the ACE2 receptor and the increased infectivity of the pseudotyped vectors displaying the D614G, B.1.1.7, and B.1.351 S glycoproteins, the ACE2(HH:NN)-Fc LALA-PG decoy maintained efficient neutralization capacity toward all SARS-CoV-2 variants tested, showing enhanced potency driven by mutational drift. 2021 Journal of virology Discussion SARS_CoV_2 D614G 159 164 S 187 202 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. We also noticed a generally reduced neutralization capacity for the D614G variant, which is likely due to its enhanced infectious capacity compared to that of the Wuhan strain. 2021 Journal of virology Discussion SARS_CoV_2 D614G 68 73 34287040 Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants. While not yet present in naturally occurring variants, the single amino acid mutation E406W has recently been shown to be able to escape both antibodies in the REGN-COV2 cocktail, further highlighting the weakness of the MAb approach. 2021 Journal of virology Discussion SARS_CoV_2 E406W 86 91 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. Although in this study we have proposed the use of a combination of two probes per assay for increased accuracy, we expect that most SARS CoV-2 variants can be identified using only the MT probe alone, and future versions of our assay are likely to use a single SMB to identify mutations that are less critical than N501Y and E484K. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 E484K;N501Y 326;316 331;321 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. In designing this assay, we took advantage of the fact that the N501Y and E484K mutations are common in the major SARS-CoV-2 variants. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 E484K;N501Y 74;64 79;69 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. Thus, this assay has the potential for relatively inexpensive high-throughput testing for rapid identification of N501Y, E484K variants. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 E484K;N501Y 121;114 126;119 34288729 A Simple Reverse Transcriptase PCR Melting-Temperature Assay To Rapidly Screen for Widely Circulating SARS-CoV-2 Variants. Thus, we expect that our assay should continue to be able to identify N501Y and E484K variants even if additional mutations develop near this primary mutation within the probe-footprint region once the specific Tm signatures of each new genotype are characterized. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 E484K;N501Y 80;70 85;75 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Although the experimental data presented here clearly demonstrate the dramatic effect of the S protein A372T mutation on SARS-CoV-2 replication in human lung cells, we cannot definitively conclude that it enabled efficient human-to-human transmission or that it was necessary for cross-species transmission. 2021 Cell Discussion SARS_CoV_2 A372T 103 108 S 93 94 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Further, growth of the A372T S mutant was reduced greatly for multiple days, which may be indicative of an effect on viral shedding kinetics in humans. 2021 Cell Discussion SARS_CoV_2 A372T 23 28 S 29 30 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Indeed, molecular modeling of GlcNAc at N370 in an open conformation of T372 S protein shows a highly solvent accessible glycan site (Figure 2). 2021 Cell Discussion SARS_CoV_2 T372S 72 78 S 77 78 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. These data hint that, along with decreased receptor-binding, inefficient TMPRSS2 cleavage of A372T S could at least partially mediate the attenuation we observed. 2021 Cell Discussion SARS_CoV_2 A372T 93 98 S 99 100 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. used a reverse genetics system to generate the D614G S protein mutant and showed increased replication in cell culture and hamsters, highlighting the utility of using a live virus to characterize critical viral mutations. 2021 Cell Discussion SARS_CoV_2 D614G 47 52 S 53 54 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Using a reverse genetics system to generate a SARS-CoV-2 mutant containing the putative ancestral SNP, we show that the A372T S mutant virus replicates over 60-fold less efficiently than WT SARS-CoV-2 in Calu-3 human lung epithelial cells (Figure 4d). 2021 Cell Discussion SARS_CoV_2 A372T 120 125 S 126 127 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. We also generated the D614G S mutant here:reported widely to increase SARS-CoV-2 infectivity :which only increased viral titers by a maximum of 2.9-fold in Calu-3 cells compared with the WT, a finding that is consistent with previous results. 2021 Cell Discussion SARS_CoV_2 D614G 22 27 S 28 29 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. We also observed slight attenuation for the A372T S mutant in Vero E6 cells (3.8-fold lower titers compared with the WT 2 dpi). 2021 Cell Discussion SARS_CoV_2 A372T 44 49 S 50 51 34289344 A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. We determined experimentally that the RBD from the T372 variant bound hACE2 with lower affinity than WT SARS-CoV-2 RBD (A372; Figure 3); thus, open-close conformational dynamics cannot fully account for the difference in binding strength between WT and T372 S. 2021 Cell Discussion SARS_CoV_2 T372S 253 259 RBD;RBD;S 38;115;258 41;118;259 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. Consistent with other studies, this study identified the E484K change in several genetically distinct lineages of the virus, a finding likely attributable to convergent evolution, as noted previously by others. 2021 The American journal of pathology Discussion SARS_CoV_2 E484K 57 62 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. Identification of 22 patients with the B.1.617 family of variants and 11 patients with B.1.1.7 plus E484K in metropolitan Houston is cause for heightened concern. 2021 The American journal of pathology Discussion SARS_CoV_2 E484K 100 105 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. In the United Kingdom, genome sequencing efforts have identified the E484K change in some B.1.1.7 samples, although it remains a minor subpopulation (https://www.gov.uk/government/publications/covid-19-variants-genomically-confirmed-case-numbers/variants-distribution-of-cases-data, last accessed May 17, 2021). 2021 The American journal of pathology Discussion SARS_CoV_2 E484K 69 74 COVID-19 193 201 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. SARS-CoV-2 variants with the E484K amino acid replacement are of particular concern in many areas, including Brazil, South Africa, and India (Center for Infectious Disease Research and Policy, https://www.cidrap.umn.edu/news-perspective/2021/02/pfizer-moderna-vaccines-may-be-less-effective-against-b1351-variant, last accessed May 17, 2021). 2021 The American journal of pathology Discussion SARS_CoV_2 E484K 29 34 34303698 Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. The B.1.1.7 plus E484K variant has been reported infrequently elsewhere in the United States (Outbreak.info, https://outbreak.info/situation-reports?pango=b.1.1.7&muts=s%3ae484k, last accessed May 17, 2021). 2021 The American journal of pathology Discussion SARS_CoV_2 E484K 17 22 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Although 614 D > G mutation was associated with lower Ct values in RT-PCR analyses, our samples recorded a very large range of Cts, between 17 and 36, suggesting that several factors, probably both virus and host related, influence viral titers. 2021 Frontiers in microbiology Discussion SARS_CoV_2 D614G 9 18 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Among the most abundant observed mutations, 241 C > T belongs to the leader sequence, with significance for discontinuous sub-genomic replication. 2021 Frontiers in microbiology Discussion SARS_CoV_2 C241T 44 53 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Another non-synonymous recurrent mutation in a large number of our samples was A105V in ORF7a. 2021 Frontiers in microbiology Discussion SARS_CoV_2 A105V 79 84 ORF7a 88 93 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Another recurrent mutation in our samples associated with a large proportion of severe disease cases, was the T987N replacement in ORF1ab polyprotein. 2021 Frontiers in microbiology Discussion SARS_CoV_2 T987N 110 115 ORF1ab 131 137 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. As a consequence, a synonymous mutation in NSP3, a P323L mutation in RNA primase, and a mutation in spike glycoprotein (614 D > G) occurred. 2021 Frontiers in microbiology Discussion SARS_CoV_2 P323L;D614G 51;120 56;129 S;Nsp3 100;43 118;47 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. As such, a more stable ORF7, due to a A105V mutation, may reduce immune response and, consequently, more severe COVID symptoms. 2021 Frontiers in microbiology Discussion SARS_CoV_2 A105V 38 43 ORF7 23 27 COVID-19 112 117 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. As such, patients infected with A105V had higher values of CRP, compared with non-A105V infected patients. 2021 Frontiers in microbiology Discussion SARS_CoV_2 A105V;A105V 32;82 37;87 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Interestingly, the signature of another super spreader, which was less encountered in European genomes, namely the change in 11083 G > T was present in two of our samples. 2021 Frontiers in microbiology Discussion SARS_CoV_2 G11083T 125 136 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Mutation 20268 A > G was recorded in samples collected before 26 of May, in 45% of samples from Spain and was also present in most of our samples from Suceava. 2021 Frontiers in microbiology Discussion SARS_CoV_2 A20268G 9 20 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. One such mutation is 614 D > G, which, over the course of 1 month, became prevalent in viral strains worldwide. 2021 Frontiers in microbiology Discussion SARS_CoV_2 D614G 21 30 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Specifically, mutations at positions 241 (non-coding), 3037 C > T, 14408 C > T, 20268 20003A > G, and 23403 A > G are frequent in European samples and were identified early in the pandemic evolution, as a signature for one of the superspreaders that originated from Wuhan. 2021 Frontiers in microbiology Discussion SARS_CoV_2 C14408T;A20003G;A23403G;C3037T 67;86;102;55 78;96;113;65 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. Therefore, the replacement of alanine 105 residue to valine favors beta-sheet's secondary structure. 2021 Frontiers in microbiology Discussion SARS_CoV_2 A105V 30 59 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. This mutation co-evolved with other three major mutations, 3037 C > T, 14408 C > T, and 23403 A > G. 2021 Frontiers in microbiology Discussion SARS_CoV_2 C14408T;A23403G;C3037T 71;88;59 82;99;69 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. This mutation is associated with less shedding of S1 subdomain of the S protein, increased viral stability and transmission, although not necessarily with increased disease severity, while other studies associated 614 D > G and 4715 P > L with increased mortality. 2021 Frontiers in microbiology Discussion SARS_CoV_2 P4715L;D614G 228;214 238;223 S 70 71 34305826 Introduction and Characteristics of SARS-CoV-2 in North-East of Romania During the First COVID-19 Outbreak. When examining sampling dates for sequences from Suceava without 20268 A > G mutation, it appears that they were introduced in Suceava around April 16, possibly from the Czechia. 2021 Frontiers in microbiology Discussion SARS_CoV_2 A20268G 65 76 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Additionally, the researchers should be reminded that our methods are actually testing for the A23403G nucleotide mutation, which mostly encodes the D614G amino acid mutation. 2021 Meta gene Discussion SARS_CoV_2 A23403G;D614G 95;149 102;154 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. By 12 February 2021, the D614G (A23403G) is the most prevalent single nucleotide variations (SNVs) in the world that is about 439,559 sequences (95.5%). 2021 Meta gene Discussion SARS_CoV_2 D614G;A23403G 25;32 30;39 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Moreover, a UK variant, N501Y, has been emerged since October 2020 and currently spreading in the country and has become a public threat in more than 30 countries. 2021 Meta gene Discussion SARS_CoV_2 N501Y 24 29 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Other common mutations in the spike (S) protein, including A222V (C22227T), L81S (C21614T), and S477N (G22992A), are co-occurred with D614G in 100,401 sequences (21.8%), 45,943 sequences (10%) and 23,426 sequences (5.1%), respectively (Covid19 CG data: https://covidcg.org/?tab=group). 2021 Meta gene Discussion SARS_CoV_2 A222V;D614G;L81S;S477N;C21614T;C22227T;G22992A 59;134;76;96;82;66;103 64;139;80;101;89;73;110 S;S 30;37 35;38 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Studies showed that D614G mutation is associated with antigenic epitopes, antibody neutralizing sensitivity, infectivity, transmission and fatality. 2021 Meta gene Discussion SARS_CoV_2 D614G 20 25 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. There have been controversies around the impacts of D614G mutations on vaccine developments. 2021 Meta gene Discussion SARS_CoV_2 D614G 52 57 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. Therefore, future work should concentrate on these four mutations to see whether their co-occurrences with D614G are associated with disease severity, infectivity, transmissions, and antibody sensitivity. 2021 Meta gene Discussion SARS_CoV_2 D614G 107 112 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. We believe our methods are advantageous over SARS CoV-2 whole genome sequences, particularly in developing countries for tracking the D614G mutation and its association with severity, infectivity, and fatality which have been controversial in various studies. 2021 Meta gene Discussion SARS_CoV_2 D614G 134 139 34307051 Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation. We have recently developed methods for detecting N501Y mutation, which can be used with the methods of the current study to explore SARS CoV-2 reinfections. 2021 Meta gene Discussion SARS_CoV_2 N501Y 49 54 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. Among them the most appearance mutation is D614G, identified as high frequent mutation worldwide. 2021 Virusdisease Discussion SARS_CoV_2 D614G 43 48 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. D614G is an important mutation that causes structural changes which in turn increase the affinity towards ACE2 and leading to functional changes in SARS-CoV-2 spike protein. 2021 Virusdisease Discussion SARS_CoV_2 D614G 0 5 S 159 164 34307771 Mutational analysis in international isolates and drug repurposing against SARS-CoV-2 spike protein: molecular docking and simulation approach. L5F, T22I, T29I, H49Y, L54F, V90F, S98F, S221L, S254F, V367F, A520S, T572I, D614G, H655Y, P809S, A879S, D936Y, A1020S, A1078S, and H1101Y. 2021 Virusdisease Discussion SARS_CoV_2 A1020S;A1078S;A520S;A879S;D614G;D936Y;H1101Y;H49Y;H655Y;L54F;P809S;S221L;S254F;S98F;T22I;T29I;T572I;V367F;V90F;L5F 111;119;62;97;76;104;131;17;83;23;90;41;48;35;5;11;69;55;29;0 117;125;67;102;81;109;137;21;88;27;95;46;53;39;9;15;74;60;33;3 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. Based on these observations, the increased syncytium formation induced by the D614G substitution might increase the spreading of SARS-CoV-2. 2021 mBio Discussion SARS_CoV_2 D614G 78 83 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. Despite this, the effect of D614G might be confounded by other genetic variations among different virus isolates. 2021 mBio Discussion SARS_CoV_2 D614G 28 33 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. For example, the D614G mutation was noted to be associated with mutations in viral nsp3 and an ORF1b protein variant (P314L). 2021 mBio Discussion SARS_CoV_2 D614G;P314L 17;118 22;123 Nsp3 83 87 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. One structure change caused by the D614G substitution is the loss of the salt bridge between D614 and K854, which reduced the stability of the spike trimer in the closed form. 2021 mBio Discussion SARS_CoV_2 D614G 35 40 S 143 148 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. Our study here provides a possible mechanistic explanation in support of the notion that the D614G substitution can increase virus transmission through enhanced membrane fusion mediated by increased cleavage of the S protein by furin/PC proteases. 2021 mBio Discussion SARS_CoV_2 D614G 93 98 Membrane;S 161;215 169;216 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. Recently, several studies showed that the D614G variant SARS-CoV-2 replicates more efficiently in primary human proximal airway epithelial cells than the wild-type virus. 2021 mBio Discussion SARS_CoV_2 D614G 42 47 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. Regarding how the substitution may affect furin cleavage, through cryo-EM analysis, several studies well demonstrated the effects of the D614G substitution on the structure of spike protein. 2021 mBio Discussion SARS_CoV_2 D614G 137 142 S 176 181 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. The coexistence of D614G and P314L may suggest additional mechanisms for the selection advantage of viruses expressing S-G614 in terms of viral infectivity and warrant further investigation. 2021 mBio Discussion SARS_CoV_2 D614G;P314L 19;29 24;34 S 119 120 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. The current study further revealed that the D614G substitution in S might contribute to increase the cleavage by furin/PCs and thus increase the syncytium formation of S-G614-containing SARS-CoV-2 strains. 2021 mBio Discussion SARS_CoV_2 D614G 44 49 S;S 66;168 67;169 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. The finding that CMK treatment can further decrease the luciferase reporter activity of the R682A mutant, suggesting that CMK might have some other effect on reporter activity, independently of the cleavage by the furin/PCs, needs further investigation. 2021 mBio Discussion SARS_CoV_2 R682A 92 97 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. Therefore, the effect of enhanced furin cleavage of the spike protein caused by the D614G substitution might increase viral entry into the cells and contribute to higher virus titers after multiple infection cycles. 2021 mBio Discussion SARS_CoV_2 D614G 84 89 S 56 61 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. These structural changes caused by the D614G substitution might contribute to a higher affinity of the spike protein for the furin/PCs, which has been demonstrated by the computational prediction of furin binding to the RRAR motif of S-G614 versus S-D614 and is preliminarily supported by the results of an in vitro proteolytic assay. 2021 mBio Discussion SARS_CoV_2 D614G 39 44 S;S;S 103;234;248 108;235;249 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. They also provided in vivo evidence showing that the D614G variant exhibited significantly faster droplet transmission between hamsters than the wild-type virus at early stages after infection. 2021 mBio Discussion SARS_CoV_2 D614G 53 58 34311586 D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Virus Titer via Enhanced Furin-Mediated Spike Cleavage. Though the mechanism for the increased cleavage by furin/PCs by the D614G substitution was delineated in assays of cells expressing only the S protein, it has been well supported by virus-infected cells, as most S-G614-containing viruses show more evidence of the cleavage of S in association with higher virus titers. 2021 mBio Discussion SARS_CoV_2 D614G 68 73 S;S;S 141;212;276 142;213;277 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Although we stress that the Gameyla Sputnik V vaccine is likely to retain strong efficacy at preventing severe COVID-19, even in the case of infection by VOC, our data reveal a concerning potential of B.1.351, and to a lesser extent, any variant carrying the E484K substitution (e.g. 2021 Nature communications Discussion SARS_CoV_2 E484K 259 264 COVID-19 111 119 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. B.1.351 and P.1 have in common three RBD substitutions (K417N/T, E484K and N501Y) whereas B.1.351, P.1 and B.1.1.7 contain the N501Y substitution. 2021 Nature communications Discussion SARS_CoV_2 E484K;N501Y;N501Y;K417N;K417T 65;75;127;56;56 70;80;132;63;63 RBD 37 40 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. E484K is present not only as part of an ensemble of RBD mutations present in B.1.351 and P.1, but in many of the 17 lineages detected from South America that carry it, such as P.2, E484K is the only RBD substitution (Supplementary Table 1). 2021 Nature communications Discussion SARS_CoV_2 E484K;E484K 181;0 186;5 RBD;RBD 52;199 55;202 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Furthermore, three major classes of neutralizing antibodies (RBS-A, -B, and -C) identified from convalescent patients are sensitive to either the K417N (RBS-A) or E484K (RBS-B and -C) substitutions present in B.1.351. 2021 Nature communications Discussion SARS_CoV_2 E484K;K417N 163;146 168;151 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Here, we showed that sera from Sputnik vaccine recipients in Argentina had a median 6.1-fold and 2.8-fold reduction in GMT against B.1.351 and the E484K mutant spike, respectively. 2021 Nature communications Discussion SARS_CoV_2 E484K 147 152 S 160 165 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Moreover, in all cases thus far examined, these first generation vaccines are less effective against variants with certain non-synonymous substitutions in Spike, such as E484K. 2021 Nature communications Discussion SARS_CoV_2 E484K 170 175 S 155 160 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Nonetheless, our data show that resistance conferred by E484K mutation be overcome by higher titer antibodies present in undiluted patient sera. 2021 Nature communications Discussion SARS_CoV_2 E484K 56 61 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Our study shows a similar mean reduction in GMT (reciprocal IC50) against E484K and B.1.351 using 1-month post-Sputnik vaccine sera when compared to other vaccines. 2021 Nature communications Discussion SARS_CoV_2 E484K 74 79 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. The neutralization curves for B.1.351 in our study are not classically sigmodal and have significantly shallower slopes than WT, B.1.17 and E484K, which result in <= 90% neutralization for all but one sample when extrapolated to full serum strength. 2021 Nature communications Discussion SARS_CoV_2 E484K 140 145 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. The steep Hill slopes (>1.0) observed for E484K suggest such co-operative effects might be occurring. 2021 Nature communications Discussion SARS_CoV_2 E484K 42 47 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. These strains have substitutions in the RBD (L452R and E484K/Q) and elsewhere in the spike that might confer some degree of neutralization resistance in our in vitro assays. 2021 Nature communications Discussion SARS_CoV_2 E484K;E484Q;L452R 55;55;45 62;62;50 S;RBD 85;40 90;43 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. Three of the six COVID-19 vaccines currently in use worldwide, namely Moderna mRNA-1273, BioNTech BNT162b2, and Janssen Ad26.COV2.S, each express S harboring K986P and V987P substitutions (2P) within a loop abutting the central helix of the S2' membrane fusion machinery. 2021 Nature communications Discussion SARS_CoV_2 K986P;V987P 158;168 163;173 Membrane;S;S 245;130;146 253;131;147 COVID-19 17 25 34312390 Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variants. While the E484K substitution appears to be a common route of escape from many RBD-targeting monoclonal antibodies, it is somewhat surprising that a single mutation can confer a significant degree of neutralization resistance from polyclonal responses. 2021 Nature communications Discussion SARS_CoV_2 E484K 10 15 RBD 78 81 34314050 SARS-CoV-2 R.1 lineage variants that prevailed in Tokyo in March 2021. Just as the detection of the N501Y mutation and the survey of the B.1.1.7 variants are important, the detection of the E484K mutation and surveillance of the R.1 variants are still important for SARS-CoV-2 infection control. 2021 Journal of medical virology Discussion SARS_CoV_2 E484K;N501Y 119;29 124;34 COVID-19 195 215 34314050 SARS-CoV-2 R.1 lineage variants that prevailed in Tokyo in March 2021. The E484K mutation has been reported to cause immune escape. 2021 Journal of medical virology Discussion SARS_CoV_2 E484K 4 9 34314050 SARS-CoV-2 R.1 lineage variants that prevailed in Tokyo in March 2021. The preventive effects of antibodies produced by vaccination can be diminished by E484K mutations. 2021 Journal of medical virology Discussion SARS_CoV_2 E484K 82 87 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. A222V is also predicted to be located within one of the epitopes recognized by unexposed humans. 2021 mSphere Discussion SARS_CoV_2 A222V 0 5 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. Although no experimental data are available about the functional role of S50L (which falls within the spike N-terminal domain, NTD), recent computational analysis suggests that it might have strong stabilizing effects on SARS-Cov-2 full-length spike protein. 2021 mSphere Discussion SARS_CoV_2 S50L 73 77 S;S;N 102;244;108 107;249;109 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. Although the spike A222V mutation (within the NTD) has not yet been reported to recurrently emerge during long-term infections, it has been specially focused by the scientific community. 2021 mSphere Discussion SARS_CoV_2 A222V 19 24 S 13 18 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. Altogether, our results consolidate the expectation that A222V might have a still to be disclosed functional impact on spike host-interacting activities. 2021 mSphere Discussion SARS_CoV_2 A222V 57 62 S 119 124 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. Another relevant recurrent mutation detected in the present study is the spike S50L amino acid change, as it was also detected during prolonged COVID-19 in another lymphoma patient. 2021 mSphere Discussion SARS_CoV_2 S50L 79 83 S 73 78 COVID-19;Lymphoma 144;164 152;172 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. In addition, another spike A222V-bearing variant was the cause of one of the first reinfection cases reported worldwide. 2021 mSphere Discussion SARS_CoV_2 A222V 27 32 S 21 26 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. Notably, a spike mutation (L18F) affecting this region has shown strong signs of convergent evolution, being harbored by the variant of concern (VOC) P.1 and being present in a high proportion of VOC B.1.351 viruses. 2021 mSphere Discussion SARS_CoV_2 L18F 27 31 S 11 16 34319130 Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma. Outside spike, we highlight the SNP C9438T leading to a T295I amino acid change in NSP4 protein, as this exact mutation was detected during persistence and evolution of SARS-CoV-2 in another patient with non-Hodgkin diffuse B-cell lymphoma. 2021 mSphere Discussion SARS_CoV_2 C9438T;T295I 36;56 42;61 S;Nsp4 8;83 13;87 B cell lymphoma 224 239 34326308 Structural and functional basis for pan-CoV fusion inhibitors against SARS-CoV-2 and its variants with preclinical evaluation. In this study, we showed that EK1 peptides effectively blocked infection by pseudotyped SARS-CoV-2 variants B.1.1.7 and B.1.1.248 and the PsVs carrying single or multiple crucial mutations, such as N501Y, E484K, and N417N, in S proteins of the currently dominant variants. 2021 Signal transduction and targeted therapy Discussion SARS_CoV_2 E484K;N417N;N501Y 205;216;198 210;221;203 S 226 227 34332998 The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another. It distinguishes the VOC B.1.351 from the VOC P.1 by amplification of the K417N and K417T mutations respectively when both the N501Y and E484K mutations were found positive with the Variant I Assay. 2021 Journal of virological methods Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y 137;74;84;127 142;79;89;132 34332998 The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another. Nevertheless, one can not preclude a cross-reaction between the E484Q mutation and the detection of the E484K target available in the Variants I Assay. 2021 Journal of virological methods Discussion SARS_CoV_2 E484K;E484Q 104;64 109;69 34332998 The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another. Next, we select samples for which no mutation has been detected (to flush out L452R and W152C mutations), as well as samples with an isolated E484K mutation. 2021 Journal of virological methods Discussion SARS_CoV_2 E484K;L452R;W152C 142;78;88 147;83;93 34332998 The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another. Since early May 2021, a new NovaplexSARS-CoV-2 Variants II Assay has been available on the market to detect L452R, K417N, K417T and W152C mutations. 2021 Journal of virological methods Discussion SARS_CoV_2 K417N;K417T;L452R;W152C 115;122;108;132 120;127;113;137 34332998 The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another. The NovaplexSARS-CoV-2 Variants I Assay diagnoses the presence of E484K, N501Y mutations and H69/V70 deletion. 2021 Journal of virological methods Discussion SARS_CoV_2 E484K;N501Y 66;73 71;78 34332998 The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another. The other two targets of the Variant II Assay are the L452R and W152C mutations. 2021 Journal of virological methods Discussion SARS_CoV_2 L452R;W152C 54;64 59;69 34332998 The challenge of screening SARS-CoV-2 variants of concern with RT-qPCR: One variant can hide another. The Variant II Assay does not target the E484Q mutation that would have distinguished B.1.617.1 and B.1.617.3 from B.1.617.2. 2021 Journal of virological methods Discussion SARS_CoV_2 E484Q 41 46 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. Collectively, the HADDOCK scores, the bonding network, the RMSD, the Rg scores, and the binding free energies enhanced the binding of W45L with IRF3 compared to ORF8 WT and other mutants. 2021 Frontiers in microbiology Discussion SARS_CoV_2 W45L 134 138 ORF8 161 165 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. Even the double-mutant V62L/L84S did not significantly affect its binding with IRF3. 2021 Frontiers in microbiology Discussion SARS_CoV_2 V62L;L84S 23;28 27;32 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. Finally, hydrogen bonding (Figure 5B) and free energy binding (Table 1) affect the confirmation and structure of W45L that favors its strong binding with IRF3. 2021 Frontiers in microbiology Discussion SARS_CoV_2 W45L 113 117 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. In contrast, both the HADDOCK docking score and the binding free energy for L84S (IRF3-L84S) were close to the IRF3-ORF8 WT complex (Table 1), suggesting that this substitution may not enhance the binding of ORF8 with IRF3. 2021 Frontiers in microbiology Discussion SARS_CoV_2 L84S;L84S 76;87 80;91 ORF8;ORF8 116;208 120;212 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. In the current study, we adapted structural and biophysical analysis approaches to explore the impact of various mutations of ORF8, such as S24L, W45L, V62L, and L84S, on its ability to bind IRF3 and to evade the host immune system. 2021 Frontiers in microbiology Discussion SARS_CoV_2 L84S;S24L;V62L;W45L 162;140;152;146 166;144;156;150 ORF8 126 130 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. Our results are in line with the previous studies in which L84S substitution did not enhance the IFNss antagonism and the downregulation of MHC-I compared to ORF8 WT. 2021 Frontiers in microbiology Discussion SARS_CoV_2 L84S 59 63 ORF8 158 162 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. S24L is the second most frequent mutation in the SARS-CoV-2 ORF8 protein. 2021 Frontiers in microbiology Discussion SARS_CoV_2 S24L 0 4 ORF8 60 64 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. S24L was found to increase the folding stability of the ORF8 protein and is associated with the dissemination of SARS-CoV-2. 2021 Frontiers in microbiology Discussion SARS_CoV_2 S24L 0 4 ORF8 56 60 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The circulation of this mutant in different countries indicated that W45L mutation may affect the function of the ORF8 protein through increasing its binding to IRF3 and enhancing its function in antagonizing IFNss. 2021 Frontiers in microbiology Discussion SARS_CoV_2 W45L 69 73 ORF8 114 118 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The different mutations reported in ORF8 are S24L, W45L, V62L, L84S, V62L, and the V62L/L84S double mutant. 2021 Frontiers in microbiology Discussion SARS_CoV_2 L84S;S24L;V62L;V62L;V62L;W45L;L84S 63;45;57;69;83;51;88 67;49;61;73;87;55;92 ORF8 36 40 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The HADDOCK docking score for W45L (IRF3-ORF8) was significantly bigger than that for ORF8 WT (Figure 2C), while the free binding energy for W45L was the highest among the ORF8 WT and mutants analyzed (Table 1). 2021 Frontiers in microbiology Discussion SARS_CoV_2 W45L;W45L 30;141 34;145 ORF8;ORF8;ORF8 41;86;172 45;90;176 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The stability analysis revealed by RMSD showed that the system is most stable for the W45L mutant (Figure 4A). 2021 Frontiers in microbiology Discussion SARS_CoV_2 W45L 86 90 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. The W45L substitution in ORF8 was first reported in Saudi Arabia and then circulated in Pakistan to cause more severe COVID-19 disease. 2021 Frontiers in microbiology Discussion SARS_CoV_2 W45L 4 8 ORF8 25 29 COVID-19 118 134 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. We have found that the nuclear translocations of IRF3 by either overexpressing ORF8 WT or L84S in HEK293T cells were the same. 2021 Frontiers in microbiology Discussion SARS_CoV_2 L84S 90 94 ORF8 79 83 34335535 Mutations in SARS-CoV-2 ORF8 Altered the Bonding Network With Interferon Regulatory Factor 3 to Evade Host Immune System. When overexpressing using L84S, similar effects were observed in the downregulation of MHC-I. 2021 Frontiers in microbiology Discussion SARS_CoV_2 L84S 26 30 34336597 Lack of N2-gene amplification on the Cepheid Xpert Xpress SARS-CoV-2 assay and potential novel causative mutations: A case series from Auckland, New Zealand. Furthermore, a different SNP at the same position (C29200A) also causes failure of amplification of the Xpert N2-gene target. 2021 IDCases Discussion SARS_CoV_2 C29200A 51 58 34336597 Lack of N2-gene amplification on the Cepheid Xpert Xpress SARS-CoV-2 assay and potential novel causative mutations: A case series from Auckland, New Zealand. The C29200T SNP common to Cases A and B has already been described to cause loss of amplification of the N2-gene target of the Xpert assay. 2021 IDCases Discussion SARS_CoV_2 C29200T 4 11 34336597 Lack of N2-gene amplification on the Cepheid Xpert Xpress SARS-CoV-2 assay and potential novel causative mutations: A case series from Auckland, New Zealand. The remaining three SNPs found in the virus from Case C, C29197T, G29227T and G29321T, are not previously known to cause loss of amplification of the Xpert N2-gene target. 2021 IDCases Discussion SARS_CoV_2 C29197T;G29227T;G29321T 57;66;78 64;73;85 34336597 Lack of N2-gene amplification on the Cepheid Xpert Xpress SARS-CoV-2 assay and potential novel causative mutations: A case series from Auckland, New Zealand. The SNPs G28881A, G28882A and G28883C have been previously described, occurring at the 3' end of the Chinese CDC N-gene forward primer. 2021 IDCases Discussion SARS_CoV_2 G28881A;G28882A;G28883C 9;18;30 16;25;37 N 113 114 34336597 Lack of N2-gene amplification on the Cepheid Xpert Xpress SARS-CoV-2 assay and potential novel causative mutations: A case series from Auckland, New Zealand. Whilst the primers and probes utilised in the Xpert assay are proprietary, we postulate that the C29197T and G29227T SNPs are most likely to be responsible for loss of amplification of the N2-gene target since these SNPs are in close proximity to the previously described C29200T/C29200A SNPs, already shown to abolish N2-gene detection by the Xpert assay. 2021 IDCases Discussion SARS_CoV_2 C29197T;C29200A;C29200T;G29227T;C29200A 97;272;272;109;280 104;279;279;116;287 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. As a result, the mutant S-protein structures (N501Y and D614G) had a larger fluctuation in RMSD, RMSF, SASA, and PCA, indicating that the native S-protein is undergoing a major structural shift, which could be the reason for better ACE2 receptor interaction. 2021 Computers in biology and medicine Discussion SARS_CoV_2 D614G;N501Y 56;46 61;51 S;S 24;145 25;146 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Combination of both sequence and structure-based online servers predicted 11 (L8V, L8W, L18F, Y145H, M153T, F157S, G476S, L611F, A879S, C1247F, and C1254F) nonsynonymous mutations with decreased stability and six nonsynonymous mutations (H49Y, S50L, N501Y, D614G, A845V, and P1143L) with increased stability in the S-protein upon mutations (Table 1, Table 2). 2021 Computers in biology and medicine Discussion SARS_CoV_2 A845V;A879S;C1247F;C1254F;D614G;F157S;G476S;L18F;L611F;L8W;M153T;N501Y;P1143L;S50L;Y145H;H49Y;L8V 264;129;136;148;257;108;115;88;122;83;101;250;275;244;94;238;78 269;134;142;154;262;113;120;92;127;86;106;255;281;248;99;242;81 S 315 316 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. In the RMSD matrix plot, the mutant (N501Y and D614G) structures showed higher deviation values, whereas the native structure showed lower deviation values. 2021 Computers in biology and medicine Discussion SARS_CoV_2 D614G;N501Y 47;37 52;42 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. It defines that the N501Y and D614 nonsynonymous mutations have structural transitions on the conformational geometry of S-protein. 2021 Computers in biology and medicine Discussion SARS_CoV_2 N501Y 20 25 S 121 122 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Many recent studies reported that mainly the stabilizing nonsynonymous mutations N501Y and D614G have a better affinity with the ACE2 receptor. 2021 Computers in biology and medicine Discussion SARS_CoV_2 D614G;N501Y 91;81 96;86 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Mutant (N501Y and D614G) S-protein structures showed higher values of SASA with time, whereas native structure shows lower values of SASA with time. 2021 Computers in biology and medicine Discussion SARS_CoV_2 D614G;N501Y 18;8 23;13 S 25 26 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. On the other hand, the destabilizing nonsynonymous mutations of S-protein and ACE2 complexes (L8V-ACE2, L8W-ACE2, L18F-ACE2, Y145H-ACE2, M153T-ACE2, F157S-ACE2, G476S-ACE2, L611F-ACE2, A879S-ACE2, C1247F-ACE2, and C1254F-ACE2) show less negative value than the native complex and indicate a lower binding interaction with biological partners (Table 3a &. 2021 Computers in biology and medicine Discussion SARS_CoV_2 A879S;C1247F;C1254F;F157S;G476S;L18F;L611F;L8W;M153T;Y145H;L8V 185;197;214;149;161;114;173;104;137;125;94 190;203;220;154;166;118;178;107;142;130;97 S 64 65 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The MD simulation results confirm that the two advantageous stabilizing nonsynonymous mutations (N501Y and D614G) undergo the structural transitions and might be the reason for enhancing the interaction with ACE2. 2021 Computers in biology and medicine Discussion SARS_CoV_2 D614G;N501Y 107;97 112;102 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The Mutant (N501Y and D614G) -ACE2 complex structures show similar or more h-bonds than other destabilizing nonsynonymous mutations. 2021 Computers in biology and medicine Discussion SARS_CoV_2 D614G;N501Y 22;12 27;17 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The S-protein loses its interaction with the ACE2 receptor upon destabilizing nonsynonymous mutations (L8V, L8W, L18F, Y145H, M153T, F157S, G476S, L611F, A879S, C1247F, and C1254F), whereas the stabilizing nonsynonymous mutations (H49Y, S50L, N501Y, D614G, A845V, and P1143L) in the S-protein shows increased interaction with the ACE2 receptor (Table 3a, Table 3ba-b). 2021 Computers in biology and medicine Discussion SARS_CoV_2 A845V;A879S;C1247F;C1254F;D614G;F157S;G476S;L18F;L611F;L8W;M153T;N501Y;P1143L;S50L;Y145H;H49Y;L8V 257;154;161;173;250;133;140;113;147;108;126;243;268;237;119;231;103 262;159;167;179;255;138;145;117;152;111;131;248;274;241;124;235;106 S;S 4;283 5;284 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The stabilizing nonsynonymous mutations (H49Y, S50L, N501Y, D614G, A845V, and P1143L) of S-protein and ACE2 complexes show more binding free energy native complex (Table 4b). 2021 Computers in biology and medicine Discussion SARS_CoV_2 A845V;D614G;N501Y;P1143L;S50L;H49Y 67;60;53;78;47;41 72;65;58;84;51;45 S 89 90 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. The stabilizing nonsynonymous mutations (H49Y, S50L, N501Y, D614G, A845V, and P1143L) of the S-protein have a better binding affinity with ACE2 receptor complexes with the native complex (Table 4b). 2021 Computers in biology and medicine Discussion SARS_CoV_2 A845V;D614G;N501Y;P1143L;S50L;H49Y 67;60;53;78;47;41 72;65;58;84;51;45 S 93 94 34346317 Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. This principle is the destabilizing nonsynonymous mutations (L8V, L8W, L18F, Y145H, M153T, F157S, G476S, L611F, A879S, C1247F, and C1254F) have lost their binding affinity between the S-protein and the ACE2 receptor molecule, and this affects their function. 2021 Computers in biology and medicine Discussion SARS_CoV_2 A879S;C1247F;C1254F;F157S;G476S;L18F;L611F;L8W;M153T;Y145H;L8V 112;119;131;91;98;71;105;66;84;77;61 117;125;137;96;103;75;110;69;89;82;64 S 184 185 34346744 SARS-CoV-2 Quasispecies Provides an Advantage Mutation Pool for the Epidemic Variants. At the consensus genome level, a potential positive selection site, such as G999C, had also been identified in the CH domain. 2021 Microbiology spectrum Discussion SARS_CoV_2 G999C 76 81 34346744 SARS-CoV-2 Quasispecies Provides an Advantage Mutation Pool for the Epidemic Variants. The predominant mutation D614G showed potential resistance to the camostat mesilate through enhancing affinity between the S1-S2 hinge region and TMPRSS2 protease. 2021 Microbiology spectrum Discussion SARS_CoV_2 D614G 25 30 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. After the initial writing of this manuscript, the complete molecular structure of the D614G mutation of the Spike protein of SARS-CoV-2 was determined. 2021 Microbiology spectrum Discussion SARS_CoV_2 D614G 86 91 S 108 113 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. Biophysical computations demonstrated the configurational changes associated with D614G, where the arm length of the Down-state transitions to an Up-state value, despite no changes in the hinge angle. 2021 Microbiology spectrum Discussion SARS_CoV_2 D614G 82 87 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. On the other hand, D614G leads to a reduction in premature transitions compared to WT and increased infection rates. 2021 Microbiology spectrum Discussion SARS_CoV_2 D614G 19 24 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. Our methodologies directly identify two key mutations (D614G and N501Y) as possible configuration and ACE2 binding changes, respectively. 2021 Microbiology spectrum Discussion SARS_CoV_2 N501Y;D614G 65;55 70;60 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. Those authors also experimentally showed a significantly enhanced stability of the prefusion complex of D614G. 2021 Microbiology spectrum Discussion SARS_CoV_2 D614G 104 109 34346753 Transformations, Lineage Comparisons, and Analysis of Down-to-Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein, Including the UK Variant B.1.1.7. We further show that N501Y has a potential hACE2 glue point partner, 41Y, which may lead to a strong Y-Y hydrophobic residue pair interaction; this may be partially responsible for the higher infection rate of the UK (B.1.1.7) and SA (B.1.351) variants, although more studies are needed to verify this. 2021 Microbiology spectrum Discussion SARS_CoV_2 N501Y 21 26 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. At the moment, however, with the majority of the population still susceptible to viral infection, mutations that increase viral transmission, such as N501Y have a selective advantage. 2021 PLoS pathogens Discussion SARS_CoV_2 N501Y 150 155 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. Of note, current prevalence of B.1.351 and of P.1 is 1.9% and 0.47%, respectively, being in the same range as S494P. 2021 PLoS pathogens Discussion SARS_CoV_2 S494P 110 115 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. The fact that only mutations containing the E484K substitution promote immune escape, although this effect increases with synergic mutations that improve viral binding to ACE2 (K417N and N501Y), may be a consequence of lack in immunological selective pressure, a recognized driver of evolution, as a large proportion of the population remains susceptible to SARS-CoV-2 infection. 2021 PLoS pathogens Discussion SARS_CoV_2 E484K;N501Y;K417N 44;187;177 49;192;182 COVID-19 358 378 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. The mutation S494P has been found in nature with a prevalence of 0.81% of all sequenced genomes (March 2021, S1 Fig) and has already been observed in combination with mutation E484K (reported on the 22nd of October 2020). 2021 PLoS pathogens Discussion SARS_CoV_2 E484K;S494P 176;13 181;18 34352039 Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. We observed a similar pattern relative to the substitution L452R/Q in India, in which the E484Q mutation was acquired posteriorly. 2021 PLoS pathogens Discussion SARS_CoV_2 E484Q;L452Q;L452R 90;59;59 95;66;66 34354142 Entropy based analysis of SARS-CoV-2 spread in India using informative subtype markers. Moreover, we studied the role of D614G mutation in transmission of the infection. 2021 Scientific reports Discussion SARS_CoV_2 D614G 33 38 34354142 Entropy based analysis of SARS-CoV-2 spread in India using informative subtype markers. Previous studies reported that the S protein of SARS-CoV-2 produced an evolutionary mutation of K403R compared with the S protein of SARS-CoV, forming an adjacent RGD motif at the interaction surface. 2021 Scientific reports Discussion SARS_CoV_2 K403R 96 101 S;S 35;120 36;121 34354142 Entropy based analysis of SARS-CoV-2 spread in India using informative subtype markers. This can be because D614G is a dominant mutation which increases the infectivity of the virus. 2021 Scientific reports Discussion SARS_CoV_2 D614G 20 25 34354142 Entropy based analysis of SARS-CoV-2 spread in India using informative subtype markers. Thus, D614G mutation increases the infectivity, albeit the mortality rate remained stable across countries. 2021 Scientific reports Discussion SARS_CoV_2 D614G 6 11 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. According to our findings, The Spike_D614G mutation in the S2 domain has a positive correlation between viral infectivity and transmissibility. 2021 Genes Discussion SARS_CoV_2 D614G 37 42 S 31 36 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. In addition, NSP3_T1198K, NS8_L84S and NSP12_A97V mutations showed a significant negative correlation to the deaths per million. 2021 Genes Discussion SARS_CoV_2 A97V;L84S;T1198K 45;30;18 49;34;24 Nsp12;Nsp3 39;13 44;17 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. In addition, the NSP1_M85I, NSP3_E475D showed a significant positive correlation to the number of cases per million. 2021 Genes Discussion SARS_CoV_2 E475D;M85I 33;22 38;26 Nsp3 28 32 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. In line with previous studies, this study revealed that the Spike_D614G mutation showed a positive correlation with viral infectivity and enhanced transmissibility. 2021 Genes Discussion SARS_CoV_2 D614G 66 71 S 60 65 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. In our study, many genetic variants in non-structural proteins, including NSP3_T73I, NSP3_Q180H and NSP13_Y541C mutations showed a significant negative correlation to CFR. 2021 Genes Discussion SARS_CoV_2 Q180H;T73I;Y541C 90;79;106 95;83;111 Nsp13;Nsp3;Nsp3 100;74;85 105;78;89 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. In our study, NS8_L84S mutation showed a significant negative correlation to deaths per. 2021 Genes Discussion SARS_CoV_2 L84S 18 22 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. In our study, The Spike_L18F mutation showed a significant positive correlation to CFR. 2021 Genes Discussion SARS_CoV_2 L18F 24 28 S 18 23 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. In the current study, the mutations having the highest frequencies among continents were missense, including Spike_D614G and NSP12_P323L. 2021 Genes Discussion SARS_CoV_2 D614G;P323L 115;131 120;136 S;Nsp12 109;125 114;130 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. Moreover, the highest frequencies for Spike_D614G and NSP12_P323L mutations were among isolates from Europe with 98.99% and 98.35%, respectively. 2021 Genes Discussion SARS_CoV_2 D614G;P323L 44;60 49;65 S;Nsp12 38;54 43;59 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. NSP12_P323L mutation showed a positive correlation to deaths per million. 2021 Genes Discussion SARS_CoV_2 P323L 6 11 Nsp12 0 5 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. On the other hand, The Spike_D614G mutation showed a significant positive correlation to the number of cases per million and the number of deaths per million. 2021 Genes Discussion SARS_CoV_2 D614G 29 34 S 23 28 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. Our study indicated a significant correlation between the number of both the number of cases per million and the number of deaths per million, with the Spike_D614G mutation, which is a mutation outside the receptor-binding domain (RBD). 2021 Genes Discussion SARS_CoV_2 D614G 158 163 S;RBD 152;231 157;234 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The clades G, GH, GR and GV, which account for 98% of the genomes, were found to have the D614G mutation. 2021 Genes Discussion SARS_CoV_2 D614G 90 95 34356077 Correlates of SARS-CoV-2 Variants on Deaths, Case Incidence and Case Fatality Ratio among the Continents for the Period of 1 December 2020 to 15 March 2021. The NS8_L84S and NSP12_A97V mutations showed a negative correlation to number of cases per million. 2021 Genes Discussion SARS_CoV_2 A97V;L84S 23;8 27;12 Nsp12 17 22 34358019 Antibodies Targeting Two Epitopes in SARS-CoV-2 Neutralize Pseudoviruses with the Spike Proteins from Different Variants. could neutralize SARS-CoV-2 pseudoviral particles with spike proteins from four different SARS-CoV-2 variants (basal; D614G; Alpha variant; Beta variant) (Figure 3), but not from SARS-CoV (Figure 4). 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D614G 118 123 S 55 60 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. A significant percentage of the substitution variants that are becoming common is recorded: S477N + A522S (27.8%), N501Y (4.73%), E484K (3.55%), T385I (2.37%), E484K + S494P (1.77%), N439K (1.18%), Y508H (0.59%), T478K (0.59%), S477N (0.59%), N501T (0.59%). 2021 Vaccines Discussion SARS_CoV_2 A522S;E484K;E484K;N439K;N501T;N501Y;S477N;S477N;S494P;T385I;T478K;Y508H 100;130;160;183;243;115;92;228;168;145;213;198 105;135;165;188;248;120;97;233;173;150;218;203 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. A slightly more concerning mutation is N439K. 2021 Vaccines Discussion SARS_CoV_2 N439K 39 44 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. For example, the D614G mutation enhances binding affinity between RBD and ACE2 resulting in increased virus transmissibility. 2021 Vaccines Discussion SARS_CoV_2 D614G 17 22 RBD 66 69 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. For the K417N mutation, a positive effect on the interaction with ACE2 and a weakened interaction with the neutralizing antibody STE90-C11 were shown. 2021 Vaccines Discussion SARS_CoV_2 K417N 8 13 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. Fortunately, the increased transmissibility of D614G variants is not associated with increased pathogenicity, nor with antibody-neutralization effects, due to its remoteness from RBD fragment. 2021 Vaccines Discussion SARS_CoV_2 D614G 47 52 RBD 179 182 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. Similar to D614G this mutation leads to enhanced binding affinity between RBD and ACE2 but provides resistance to some monoclonal antibodies and eludes some polyclonal responses. 2021 Vaccines Discussion SARS_CoV_2 D614G 11 16 RBD 74 77 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. Since neither D614G nor N439K has shown the ability to increase the severity of the disease or to escape from neutralizing antibodies, the genetic lineages with these mutations are not classified as VOC. 2021 Vaccines Discussion SARS_CoV_2 D614G;N439K 14;24 19;29 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. Some of the mutation variants occur independently in different genetic lineages, i.e., N439K or the E484K mutation. 2021 Vaccines Discussion SARS_CoV_2 E484K;N439K 100;87 105;92 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. Specifically, N501Y is a well-known mutation of the UK strain B.1.1.7 that can increase interaction with ACE2 and contribute to the partial escape from the neutralizing effect of antibodies. 2021 Vaccines Discussion SARS_CoV_2 N501Y 14 19 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. Summarizing the obtained data, we can conclude that for the B.1.1.7, B.1.617.3, and local Moscow variants of genetic lineages B.1.1.141 (T385I) and B.1.1.317 (S477N, A522S) neutralizing properties of Sputnik V induced sera are not changed. 2021 Vaccines Discussion SARS_CoV_2 A522S;S477N;T385I 166;159;137 171;164;142 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. The D614G variants now dominate in most countries worldwide. 2021 Vaccines Discussion SARS_CoV_2 D614G 4 9 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. The E484K mutation is currently found in VOC B.1.351, P.1, P.2, and in the newly emerged Alpha strain B.1.1.7 with an additional E484K mutation. 2021 Vaccines Discussion SARS_CoV_2 E484K;E484K 4;129 9;134 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. The K417N mutation shows a more pronounced effect in combination with N501Y further amplified by the E484K mutation. 2021 Vaccines Discussion SARS_CoV_2 E484K;K417N;N501Y 101;4;70 106;9;75 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. There are 23 mutations in the genome B.1.1.7, including a mutation in RBD N501Y, which increases the affinity of binding ACE2 receptor. 2021 Vaccines Discussion SARS_CoV_2 N501Y 74 79 RBD 70 73 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. These data are in concordance with previously reported analysis for Russia where S477N, A522S, T385I, and E484K mutation rates were found extensively increasing according to GISAID. 2021 Vaccines Discussion SARS_CoV_2 A522S;E484K;S477N;T385I 88;106;81;95 93;111;86;100 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. This lineage is characterized by eight mutations in S protein, including three substitutions in the RBD (K417N, E484K, and N501Y) resulting in increased transmissibility and immune escape. 2021 Vaccines Discussion SARS_CoV_2 E484K;N501Y;K417N 112;123;105 117;128;110 RBD;S 100;52 103;53 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. Two mutations of RBD including T478K and E484Q differentiate these variants from each other. 2021 Vaccines Discussion SARS_CoV_2 E484Q;T478K 41;31 46;36 RBD 17 20 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. We assessed the virus-neutralizing effect of serum in the patients vaccinated with Sputnik V based on live virus isolates, which showed a non-significant decrease in the antibody-neutralizing effect against B.1.1.397 (T385I) and B.1.1.317 (S477N, A522S). 2021 Vaccines Discussion SARS_CoV_2 A522S;S477N;T385I 247;240;218 252;245;223 34358195 Neutralizing Activity of Sera from Sputnik V-Vaccinated People against Variants of Concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow Endemic SARS-CoV-2 Variants. We isolated two variants B.1.617.2 (S: T19R G142D E156G F157del R158del L452R T478K D614G P681R D950N) and B.1.617.3 (S: T19R G142D E156G F157del R158del L452R E484Q D614G P681R D950N). 2021 Vaccines Discussion SARS_CoV_2 D614G;D614G;D950N;D950N;E156G;E156G;E484Q;G142D;G142D;L452R;L452R;P681R;P681R;T19R;T19R;T478K 84;166;96;178;50;132;160;44;126;72;154;90;172;39;121;78 89;171;101;183;55;137;165;49;131;77;159;95;177;43;125;83 S;S 36;118 37;119 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Here, we showed that the PerkinElmer kit performed better than the ID Solution kit, avoiding the problem of mutation detection, notably the detection of E484K mutation. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 E484K 153 158 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. However, even if the PerkinElmer kit presented better performance in our study, we suggest that a similar problem of detection could be observed if a mutation was localized closed to the E484K target, impacting on the two RT-PCR screening kits assays. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 E484K 187 192 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Indeed, the SARS-CoV-2 genome sequencing of these samples highlighted the presence of two mutations, S71F and A67S, localized very closely to the targeted deletion (Figure 2), which could explain the lack of detection. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 A67S;S71F 110;101 114;105 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Moreover, we can hypothesize that the sequences of the PCR primers are different, even if they are not known by users, as we can detect the A67S mutation with the PerkinElmer kit. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 A67S 140 144 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. The detection of the E484K mutation has a clinical importance because it is associated with a reduced efficacy of the vaccine, or confers resistance to monoclonal antibodies or convalescent plasma. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 E484K 21 26 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Thus, we suspect that the PerkinElmer probes can bind more easily to the sequence genome, despite the presence of the S71F mutation. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 S71F 118 122 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Using the PerkinElmer kit, we observed a low fluorescence intensity in this targeted deletion (Figure 1E), but only in samples with the S71F mutation. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 S71F 136 140 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. When the RT-PCR using the ID Solution kit detected two targets (universal SARS-CoV-2 (N-gene) and N501Y (S-gene)), the manufacturer proposed to conclude that there is the presence of lineage B.1.351; however, the N501Y mutation is present in many variants (e.g., lineage A.27). 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 N501Y;N501Y 98;213 103;218 N;S 86;105 87;106 34359323 Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. With the evolution of VOCs and VOIs, the French recommendations evolved on 26 May 2021 to screen only E484K and two other mutations (E484Q, L452R), with an impact similar to E484K. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 E484K;E484K;L452R;E484Q 102;174;140;133 107;179;145;138 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. A recent report revealed that the L452R mutation reduced or abolished neutralizing activity of 14 out of 35 RBD-specific mAbs including three clinical stage mAbs. 2021 Microorganisms Discussion SARS_CoV_2 L452R 34 39 RBD 108 111 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. A recent study revealed increased infectivity of the B.1.617 spike protein that could be attributed to L452R which itself caused a 3.5-fold increase in infectivity and, in combination with E484Q, caused a 3-fold increase. 2021 Microorganisms Discussion SARS_CoV_2 E484Q;L452R 189;103 194;108 S 61 66 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Another recent study has demonstrated that the mutation L452R can escape from human leukocyte antigen (HLA) 24-restricted cellular immunity and can also increase viral infectivity, potentially promoting viral replication. 2021 Microorganisms Discussion SARS_CoV_2 L452R 56 61 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Another significant mutation, P681R, in the furin cleavage site resulted in enhancement of the basicity of the poly-basic stretch, and the likely facilitation of additional contacts with furin for S1-S2 cleavage. 2021 Microorganisms Discussion SARS_CoV_2 P681R 30 35 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. E484Q has also been reported in several sequences in the GISAID. 2021 Microorganisms Discussion SARS_CoV_2 E484Q 0 5 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. L452R has been noted earlier in lineages B.1.427 and B.1.429 while the E484K mutation is common to the two VOCs beta and gamma and two VUIs, zeta and eta. 2021 Microorganisms Discussion SARS_CoV_2 E484K;L452R 71;0 76;5 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Notably, D111D was found to be associated with the signature mutations of lineage B.1.1.617.1. 2021 Microorganisms Discussion SARS_CoV_2 D111D 9 14 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. On the other hand, the B.1.617.1 lineage possessing common signature mutations L452R, E484Q and P681R in the spike protein could be linked to the surge of cases in February 2021 in eastern Maharashtra. 2021 Microorganisms Discussion SARS_CoV_2 E484Q;L452R;P681R 86;79;96 91;84;101 S 109 114 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. P681H is one of the mutations in the VIC alpha, while P681R is one of the mutations in the lineage A.23.1, which is identified as a "variant under monitoring" (, Accessed on 14 June 2021). 2021 Microorganisms Discussion SARS_CoV_2 P681R;P681H 54;0 59;5 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Structural analysis further showed that the two RBD mutations L452R and E484Q may decrease the binding ability of REGN10933 and P2B-2F6 antibodies to the variant strains, compared to that in the wildtype strain. 2021 Microorganisms Discussion SARS_CoV_2 E484Q;L452R 72;62 77;67 RBD 48 51 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The combination of the two RBD mutations, L452R and E484Q, noted in this study could affect the neutralization of the select mAbs. 2021 Microorganisms Discussion SARS_CoV_2 E484Q;L452R 52;42 57;47 RBD 27 30 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The effect of the mutations L452R and T478K on ACE2 binding was also observed as enhanced stabilization of the RBD-ACE2 complex. 2021 Microorganisms Discussion SARS_CoV_2 L452R;T478K 28;38 33;43 RBD 111 114 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The new lineages B.1.617.1 and B.1.617.3 in this study are thus a unique combination of spike mutations L452R, E484Q and P681R. 2021 Microorganisms Discussion SARS_CoV_2 E484Q;L452R;P681R 111;104;121 116;109;126 S 88 93 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The P681R mutation caused a small increase in proteolytic processing that might have an effect on infectivity. 2021 Microorganisms Discussion SARS_CoV_2 P681R 4 9 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The structural analysis of the effect of RBD mutations L452R and E484Q towards ACE2 binding revealed a decrease in intramolecular and intermolecular contacts with respect to the wildtype. 2021 Microorganisms Discussion SARS_CoV_2 E484Q;L452R 65;55 70;60 RBD 41 44 34361977 SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. The T478K mutation in the spike protein in lineage B.1.617.2 has been seen in Mexican variant B.1.1.222. 2021 Microorganisms Discussion SARS_CoV_2 T478K 4 9 S 26 31 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Although Meng and colleagues recently reported a cas12a-based detection of D614G, our dsmCRISPR method is more effective as it could be extended to discriminate other SARS-CoV-2 variants with high specificity and sensitivity. 2021 Virus research Discussion SARS_CoV_2 D614G 75 80 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. In summary, dsmCRISPR system is an efficient and effective assay to detect the SARS-CoV-2 variant with D614G mutation. 2021 Virus research Discussion SARS_CoV_2 D614G 103 108 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Our dsmCRISPR assay utilized dual synthetic crRNA to enable sensitive, specific, and robust detection of D614G, the most dominant SARS-CoV-2 variant. 2021 Virus research Discussion SARS_CoV_2 D614G 105 110 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. The rapid spread of SARS-CoV-2 virus globally is reported to link with the occurrence of highly transmissive variants including D614G, E484Q, L452R, E484K etc. 2021 Virus research Discussion SARS_CoV_2 D614G;E484K;E484Q;L452R 128;149;135;142 133;154;140;147 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Therefore, dsmCRISPR can efficiently increase the detection specificity of D614G variant by 23.12-fold while isolated study reported to increase by 13-fold. 2021 Virus research Discussion SARS_CoV_2 D614G 75 80 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Therefore, in this study, a Cas12a-based detection system was established to detect SARS-CoV-2 D614G mutation. 2021 Virus research Discussion SARS_CoV_2 D614G 95 100 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. Therefore, we designed crRNAs with additional nucleotide mismatches from the -3 to +3 positions centered around the A23403G site. 2021 Virus research Discussion SARS_CoV_2 A23403G 116 123 34363850 dsmCRISPR: Dual synthetic mismatches CRISPR/Cas12a-based detection of SARS-CoV-2 D614G mutation. When coupled with a synthetic mismatch primer, whose 3' end is located at the D614G SNP (A23403G) site, the D614G mutation was selectively amplified. 2021 Virus research Discussion SARS_CoV_2 D614G;D614G;A23403G 78;108;89 83;113;96 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. Almost all Brazilian sequences harbor S:D614G, a hallmark of the ancestral B.1 lineage. 2021 Virus research Discussion SARS_CoV_2 D614G 40 45 S 38 39 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. g., N501Y) or immune evasion (e.g., E484K). 2021 Virus research Discussion SARS_CoV_2 E484K;N501Y 36;4 41;9 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. Molecular dynamic simulation reveals that E484K mutation enhances spike RBD-ACE2 affinity and the combination of E484K, K417N and N501Y mutations (501Y.V2 variant) induces a higher number of conformational changes than N501Y mutant alone, potentially resulting in an escape mutant. 2021 Virus research Discussion SARS_CoV_2 E484K;E484K;K417N;N501Y;N501Y 42;113;120;130;219 47;118;125;135;224 S;RBD 66;72 71;75 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. Of the 10 new amino acid mutations in the spike protein (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I) compared to its immediate ancestor (B.1.1.28), molecular selection analyses found evidence that 8 of these 10 mutations are under diversifying positive selection. 2021 Virus research Discussion SARS_CoV_2 D138Y;E484K;H655Y;K417T;N501Y;P26S;R190S;T1027I;T20N;L18F 75;96;110;89;103;69;82;117;63;57 80;101;115;94;108;73;87;123;67;61 S 42 47 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. Second, the fact that the set of mutations shared by P.1, B.1.1.7 and B.1.351 seem to have arisen independently, as previously demonstrated with emergence of E484K in others Brazilian lineages (P.2, B.1.1.28 and B.1.1.33), is suggestive of convergent molecular evolution. 2021 Virus research Discussion SARS_CoV_2 E484K 158 163 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. The E484K mutation seems to be of particular relevance, as its presence shifts the main interaction residue to this site. 2021 Virus research Discussion SARS_CoV_2 E484K 4 9 34363852 Mutation hotspots and spatiotemporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021. The emergence of a B.1.1.28-derived lineage carrying the E484K mutation (later named P.2) was dated in July 2020, however it began to appear more frequently and almost simultaneously in October 2020 in the Rio de Janeiro state and in the small municipality of Esteio, Rio Grande do Sul, suggesting its wide distribution in the Southern and Southeastern regions of Brazil and uncertainty regarding its origin. 2021 Virus research Discussion SARS_CoV_2 E484K 57 62 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. IFN-I is secreted and signals through the type I interferon receptor (IFNAR), followed by the establishment of host cell antiviral state, which might be the reason for the rapid clearance of D330A and Y414A in vivo. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D330A;Y414A 191;201 196;206 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. Moreover, D330A and Y414A can be rapidly cleared within 2 dpi after infecting mice, indicating that these mutants are highly attenuated and safe (Figure 2). 2021 Emerging microbes & infections Discussion SARS_CoV_2 D330A;Y414A 10;20 15;25 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. Our results showed that N7-MTase mutants, especially Y414A, can induce higher IFN-I production at the early stage of infection without any adjuvants (Figure 2), and can build strong neutralizing antibody responses and cellular immune responses after immunization (Figure 3). 2021 Emerging microbes & infections Discussion SARS_CoV_2 Y414A 53 58 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. Our results showed that the N7-MTase mutants MHV D330A and Y414A were replicative and stable in the cell culture, which indicates that it would be cheap and easy to prepare these mutants as LAVs in a short time. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D330A;Y414A 49;59 54;64 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. reported that N7-MTase deficient MHV (G332A) impairs viral replication, enhances sensitivity to the innate immune response, and reduces viral RNA translation efficiency in cell culture. 2021 Emerging microbes & infections Discussion SARS_CoV_2 G332A 38 43 34365904 Live attenuated coronavirus vaccines deficient in N7-Methyltransferase activity induce both humoral and cellular immune responses in mice. What's more, another group showed that N7-MTase deficient PEDV (D350A), which belongs to Alphacoronavirus, can induce higher IFN-I and IFN-III responses in cell culture. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D350A 64 69 34367128 CAR-NK Cells Effectively Target SARS-CoV-2-Spike-Expressing Cell Lines In Vitro. Furthermore, S309 NAb recognizes the N343 glycan that is located outside of the ACE2-binding site, and the acquired mutations of the emerging SARS-CoV-2 variants, including the N501Y, E484K, or K418T, are not within the S309 epitope. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;K418T;N501Y 184;194;177 189;199;182 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. Although more extensive research is needed to determine the limit of detection accurately, experiments on SARS-CoV-2 RNA from lineage B.1.351 (with mutation N501Y) and WT in different proportional mixtures demonstrated that proportions as low as 0,5% of lineage B.1.351 can be detected in a background of 700 RNA-copies of WT SARS-CoV-2. 2021 The Science of the total environment Discussion SARS_CoV_2 N501Y 157 162 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. At the onset of this study in January 2021, the threat of emergence of B 1.1.7 (the Alpha VOC) in the Netherlands was most imminent and our data show that the emergence of this VOC was detectable via N501Y monitoring of wastewater. 2021 The Science of the total environment Discussion SARS_CoV_2 N501Y 200 205 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. E484K, K417T, K417N or L452R) characteristic for various epidemiologically or immunologically relevant VoC's. 2021 The Science of the total environment Discussion SARS_CoV_2 K417N;K417T;L452R;E484K 14;7;23;0 19;12;28;5 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. N501Y containing B 1.1.7 variants were first detected on December 82,020 in Amsterdam and two weeks later in Utrecht. 2021 The Science of the total environment Discussion SARS_CoV_2 N501Y 0 5 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. The proportion of N501Y variants in the weekly samples increased to approximately 80% on March 1, 2021. 2021 The Science of the total environment Discussion SARS_CoV_2 N501Y 18 23 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. These experiments also demonstrated the linearity of the expected proportion and the measured proportion of B.1.351 in the mixtures and vice versa, indicating that this N501Y assay can be used to accurately determine the ratio between SARS-CoV-2 genomes containing N501Y and those containing the WT sequence. 2021 The Science of the total environment Discussion SARS_CoV_2 N501Y;N501Y 169;265 174;270 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. These results demonstrate the applicability of this RT-ddPCR assay to monitor the absolute quantities and ratios of WT viral sequences and sequences containing the N501Y mutation. 2021 The Science of the total environment Discussion SARS_CoV_2 N501Y 164 169 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. This assay can be used for sensitive and simultaneous detection of WT and the N501Y mutation in sewage. 2021 The Science of the total environment Discussion SARS_CoV_2 N501Y 78 83 34371414 Droplet digital RT-PCR to detect SARS-CoV-2 signature mutations of variants of concern in wastewater. This proof-of-principle demonstrates the value of RT-ddPCR to detect N501Y, and suggests RT-ddPCR can also be used for the detection of multiple signature mutations (like f.e. 2021 The Science of the total environment Discussion SARS_CoV_2 N501Y 69 74 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. A decrease in the prevalence of the N439K variant was the exception. 2021 Viruses Discussion SARS_CoV_2 N439K 36 41 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. As expected and suggested by the previous studies, D614G spike mutation has become fixed in the observed sequences as this variant was associated with in early sequences with transmission advantage and higher SARS-CoV-2 viral loads. 2021 Viruses Discussion SARS_CoV_2 D614G 51 56 S 57 62 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. As presented, during the first wave of the SARS-CoV-2 epidemic in Poland the virus was less diverse genetically, with practically only a D614G spike mutation observed in the analyzed genomes. 2021 Viruses Discussion SARS_CoV_2 D614G 137 142 S 143 148 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. Clade 3 was the PANGO B.1.221 (Nextstrain 20A) strain with S98F mutation. 2021 Viruses Discussion SARS_CoV_2 S98F 59 63 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. In comparison, N439K increases the binding affinity to ACE2 and may be responsible for the immune escape from the convalescent sera and monoclonal antibodies. 2021 Viruses Discussion SARS_CoV_2 N439K 15 20 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. In this period, we report an expansion of more virulent variants such as B.1.1.7 VOC and strains not associated with the increased transmissibility per se but containing the described above DeltaH69_V70, N439K, or P681H mutations. 2021 Viruses Discussion SARS_CoV_2 N439K;P681H 204;214 209;219 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. Interestingly, two genetically convergent strains (Clade 2 and 3) classified as B.1.258 and B.1.221 were responsible for almost 1/3 (29.2%) of the remaining infections in the analyzed period, with Clade 2 characterized by the conjunction of two spike mutations, DeltaH69_V70 and N439K. 2021 Viruses Discussion SARS_CoV_2 N439K 279 284 S 245 250 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. It has been indicated before that N439K co-occurs with DeltaH69_V70 in the PANGO B.1.258 clade, exactly as confirmed in the presented phylogenetic analysis. 2021 Viruses Discussion SARS_CoV_2 N439K 34 39 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. Our analysis shows that subsequently, three genetic lines of the SARS-CoV-2 molecular evolution have emerged, with the largest clade (Clade 1, lineages B.1.1.*) being the most diverse genetically, with a significant proportion (24.6% for this clade) of the VOC B.1.1.7 variant characterized by a signature combination of the DeltaY144, N501Y, A570D, S982A, D1118H, and T716I spike mutations. 2021 Viruses Discussion SARS_CoV_2 A570D;D1118H;DeltaY144;N501Y;S982A;T716I 343;357;325;336;350;369 348;363;334;341;355;374 S 375 380 34372500 Molecular Evolution and Epidemiological Characteristics of SARS COV-2 in (Northwestern) Poland. This was most likely due to the expansion of the B.1.1.7 variant, which does not contain N439K substitution, and a smaller proportion of the B.1.258 infections in early 2021. 2021 Viruses Discussion SARS_CoV_2 N439K 89 94 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. Continued monitoring for emerging variants with mutations such as E484K is important to maximize the impact of public health measures to mitigate the effects of the SARS-CoV-2 pandemic. 2021 Nature communications Discussion SARS_CoV_2 E484K 66 71 34373458 Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York. The presence of E484K mutation may play a key role in facilitating increased viral transmission and reducing antibody neutralizing titers, as previously shown in other studies. 2021 Nature communications Discussion SARS_CoV_2 E484K 16 21 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. Assays that target S gene mutations such as E484K, K417N, K417T, L452R, the Y144 deletion, and the 242 to 244 deletion, and the ORF1ab gene 3675 to 3677 deletion, are in development. 2021 Microbiology spectrum Discussion SARS_CoV_2 E484K;K417N;K417T;L452R 44;51;58;65 49;56;63;70 ORF1ab;S 128;19 134;20 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. Because the VOC assays presented only have the N501Y mutation as a marker for B.1.351 and P.1, this led to a low PPV for the VOC assays in detecting these non-B.1.1.7 VOCs (76.7%); thus, samples positive for N501Y alone required further analysis by nucleic acid sequencing, which significantly increases the turnaround time to confirm the lineage result. 2021 Microbiology spectrum Discussion SARS_CoV_2 N501Y;N501Y 47;208 52;213 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. describe the design and use of assays targeting N501Y, E484K, and L452R, which are all found in different VOCs; this approach allowed them to detect the rise of SARS-CoV-2 strains carrying L452R in the San Francisco Bay Area. 2021 Microbiology spectrum Discussion SARS_CoV_2 E484K;L452R;L452R;N501Y 55;66;189;48 60;71;194;53 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. Eight B.1.1.7 positive samples that were misclassified by the VOC assays as potential P.1/B.1.351 positive samples were found to have a mutation adjacent to the H69/V70 deletion region (C21774T), likely being the cause of the negative DeltaH69/V70 assay result. 2021 Microbiology spectrum Discussion SARS_CoV_2 C21774T 186 193 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. The combined approach of using both the DeltaH69/V70 and N501Y assays described in this report to quickly screen thousands of SARS-CoV-2-positive samples would have detected all VOCs described during the time period of the study and are much less costly, as they are in-house assays that use nonproprietary reagents. 2021 Microbiology spectrum Discussion SARS_CoV_2 N501Y 57 62 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. These rRT-PCR assays, targeting the H69/V70 deletion and N501Y mutation, allowed the rapid identification of B.1.1.7 and other VOCs so that public health contact tracers could rapidly follow up with cases (and contacts of cases) and apply a containment strategy to the variants. 2021 Microbiology spectrum Discussion SARS_CoV_2 N501Y 57 62 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. Very similar to the strategy implemented in our study, another group used commercially available assays to test for the H69/V70 deletion and N501Y in 35,208 SARS-CoV-2-positive samples in France to detect the rise of B.1.1.7 there. 2021 Microbiology spectrum Discussion SARS_CoV_2 N501Y 141 146 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. We found 585 samples with the H69/V70 deletion alone without the N501Y mutation, with the majority belonging to the B.1.525 lineage, which is not a VOC but considered a variant of interest in Canada. 2021 Microbiology spectrum Discussion SARS_CoV_2 N501Y 65 70 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. While a number of other jurisdictions have relied upon a readily available commercial assay (the TaqPath Thermo Fisher assay) to identify S gene target failures (SGTFs) and rapidly detect potential VOCs, this is an expensive and less-sensitive approach, since B.1.1.7 and B.1.1.7 + E484K are the only VOCs expected to demonstrate SGTFs. 2021 Microbiology spectrum Discussion SARS_CoV_2 E484K 282 287 S 138 139 34378966 Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance. While we also found some N501Y positive samples that were not VOCs, these only numbered 29 and the majority of these belonged to the B.1 lineage. 2021 Microbiology spectrum Discussion SARS_CoV_2 N501Y 25 30 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. Accordingly, the R408I mutation within RBD exhibiting low antigenicity which will eliminate the neutralization to SARS-CoV-2 by those antibodies. 2021 Biotechnology journal Discussion SARS_CoV_2 R408I 17 22 RBD 39 42 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. And some of them such as N501Y in the United Kingdom has been proven to increase the infectivity and became the dominant lineage. 2021 Biotechnology journal Discussion SARS_CoV_2 N501Y 25 30 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. For example, only HTS0483 bound with R408I and W436R mutant in RBD, suggesting that the binding of HTS0483 to RBD is independent of R481 and W436. 2021 Biotechnology journal Discussion SARS_CoV_2 R408I;W436R 37;47 42;52 RBD;RBD 63;110 66;113 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. Furthermore, only HTS0483 blocked the binding of both W436R and R408I mutants to ACE2 implied that the mutation in RBD may eliminate some antibodies mediated blocking. 2021 Biotechnology journal Discussion SARS_CoV_2 R408I;W436R 64;54 69;59 RBD 115 118 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. Interestingly, the mutations W436R and R408I were isolated from Wuhan and India, respectively. 2021 Biotechnology journal Discussion SARS_CoV_2 R408I;W436R 39;29 44;34 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. It has been demonstrated that N439K mutation which has been found in more than 30 countries confer resistance against several neutralizing monoclonal antibodies, including one authorized for emergency use by the FDA. 2021 Biotechnology journal Discussion SARS_CoV_2 N439K 30 35 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. Meanwhile, although the sequence of HTS0433 and HTS0466 is almost identical, with only three amino acids different in frame region, the affinity to mutant N501Y is totally different, which demonstrated that these amino acids in frame region of VL is critical to bind with N501Y. 2021 Biotechnology journal Discussion SARS_CoV_2 N501Y;N501Y 155;272 160;277 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. Then, the RBD sequence between SARS-CoV-2 and SARS-CoV was compared and we found that the W436R and R408I are same in both, which suggested that the binding to these sites couldn't distinguish SARS-CoV-2 and SARS-CoV. 2021 Biotechnology journal Discussion SARS_CoV_2 R408I;W436R 100;90 105;95 RBD 10 13 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. Therefore, the convalescent patients or vaccine immunized people without antibody to block the mutant virus may still have the possibility of SARS-COV-2 infection with W436R and R408I mutation. 2021 Biotechnology journal Discussion SARS_CoV_2 R408I;W436R 178;168 183;173 COVID-19 142 162 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. These data suggested that the W436R and R408I are essential for the bind of HTS0422, HTS0433 and HTS0446 (Figure S7b). 2021 Biotechnology journal Discussion SARS_CoV_2 R408I;W436R 40;30 45;35 34379353 Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. While the sequence of HTS0483 is totally different with the other 3 antibodies which may partially explain why only HTS0483 could blocking the entry of the mutants W436R and R408I. 2021 Biotechnology journal Discussion SARS_CoV_2 R408I;W436R 174;164 179;169 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. According to the sequence deposited in GISAID, the gorilla CAL.20A variant carries two additional point mutations, both in the ORF1ab nonstructural protein 2 (nsp2): a missense c810t (T183I) and synonymous c934t (unfortunately, several sequence stretches are missing in the genome). 2021 Journal of clinical microbiology Discussion SARS_CoV_2 T183I 184 189 ORF1ab;Nsp2 127;159 133;163 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Furthermore, it was shown that L452R confers viral escape from human leukocyte antigen (HLA)-restricted cellular immunity mediated by cytotoxic T lymphocytes. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 L452R 31 36 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. In particular, one study has shown that the L452R mutation reduced neutralizing activity of 14 of 34 RBD-specific monoclonal antibodies. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 L452R 44 49 RBD 101 104 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Interestingly, it appears that the selection for L452R became especially strong relatively recently. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 L452R 49 54 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Interestingly, the same study showed that the S13I and W152C mutations that are present in the S protein of the California-dominating B.1.427/B.1.429 lineage, but absent in CAL.20A, resulted in total loss of neutralization by all 10 N-terminal domain (NTD)-specific monoclonal antibodies tested. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 S13I;W152C 46;55 50;60 N;S 233;95 234;96 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. It is impossible to say at this point to what extent the isolation of the CAL.20A variant is connected to possibly distinctive biological properties of the strain and, specifically, the L452R mutation. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 L452R 186 191 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. It was found that L452R reduces multifold the spike protein reactivity with viral neutralizing antibodies and sera from convalescent patients. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 L452R 18 23 S 46 51 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Several recent studies investigated the potential effects of L452R and other mutations. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 L452R 61 66 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. Taken together, our results show that in late 2020 to early 2021, two independent nCoV variants emerged in the state of California that carry the L452R mutation in the spike protein: the previously defined and broadly expanded epsilon variant and the more recently emerged CAL.20A identified here. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 L452R 146 151 S 168 173 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. The fact that, according to the genome-wide analysis, emergence of both CAL.20A and the epsilon variant was triggered by the L452R mutation provides direct evidence for the adaptive significance of this mutation specifically and also creates a potential opportunity to isolate and functionally compare naturally occurring isogenic variants of nCoV with and without L452R. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 L452R;L452R 125;365 130;370 34379531 Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. This would indicate that other mutations in the epsilon variant, such as S13I and W152C in the N-terminal domain of the spike protein, might enhance the adaptive impact of L452R, i.e., that the genomic background of L452R plays a significant role as the target of positive selection. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 L452R;L452R;S13I;W152C 172;216;73;82 177;221;77;87 S;N 120;95 125;96 34382034 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Likewise, the only difference observed in our study between B.1.1.7 and D614G was in the innate immune response in the upper, but not lower respiratory tract. 2021 bioRxiv Discussion SARS_CoV_2 D614G 72 77 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Furthermore, there were a number of mutations that could significantly improve RBD-ACE2 binding but were either completely absent in our data or of extremely low frequency, including N501F, Y453F, T385R, Q493M, and Q414A, among others (Supplementary Table 3). 2021 Antibody therapeutics Discussion SARS_CoV_2 N501F;Q414A;Q493M;T385R;Y453F 183;215;204;197;190 188;220;209;202;195 RBD 79 82 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. It should be noted that antibody neutralization may vary based on certain mutations as shown with the E484K mutation, which in our dataset was found in 11 SARS-CoV-2 sequences. 2021 Antibody therapeutics Discussion SARS_CoV_2 E484K 102 107 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. Some of the highest frequency mutations with improved binding to the ACE2 receptor included S477N, N439K, V367F, and N501Y. 2021 Antibody therapeutics Discussion SARS_CoV_2 N439K;N501Y;S477N;V367F 99;117;92;106 104;122;97;111 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. The S477N mutation represented the highest frequency of all with N501Y displaying the highest binding affinity (Supplementary Table 1). 2021 Antibody therapeutics Discussion SARS_CoV_2 N501Y;S477N 65;4 70;9 34386694 SARS-CoV-2 receptor-binding mutations and antibody contact sites. This is perplexing as the Q498H, Q498Y, and Q498F all improve RBD expression and ACE2 binding; moreover, the Q498H mutation boasts the highest affinity for ACE2 of any RBD mutant. 2021 Antibody therapeutics Discussion SARS_CoV_2 Q498F;Q498H;Q498H;Q498Y 44;26;109;33 49;31;114;38 RBD;RBD 62;168 65;171 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. A previous study suggested that the K417N mutation minimally affects this binding between the RBD and the ACE2 receptor. 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 K417N 36 41 RBD 94 97 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Because these N501Y, K417N, E484K and L452R mutations in RBD play the important role in immune evasion, we focused on the effect of GB-2 on these mutations. 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 E484K;K417N;L452R;N501Y 28;21;38;14 33;26;43;19 RBD 57 60 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Both alpha and beta variants have the N501Y mutation. 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 N501Y 38 43 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. E484K can switch the charge on the flexible loop region of the RBD and induce the formation of new favorable contact. 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 E484K 0 5 RBD 63 66 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. For epsilon variant, the two B.1.427 and B.1.429 lineages have the same spike protein mutations, inclunding S13I and W152C in the NTD and L452R in the RBD. 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 L452R;S13I;W152C 138;108;117 143;112;122 S;RBD 72;151 77;154 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. For L452R, previous studies showed that the L452R mutation may stabilize the binding between the spike protein and human ACE2 to increase infectivity. 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 L452R;L452R 4;44 9;49 S 97 102 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. GB-2 can inhibit the binding between ACE2 and RBD with the triple mutation (K417N-E484K-N501Y). 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 K417N;E484K;N501Y 76;82;88 81;87;93 RBD 46 49 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. However, the combination of the E484K, K417N, and N501Y mutations could induce a higher degree of conformational alterations of the RBD when it was bound to the ACE2 receptor. 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 E484K;K417N;N501Y 32;39;50 37;44;55 RBD 132 135 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. In addition, beta variant has more mutations in the N-terminal domain region of the spike protein:including L18F, D80A, D215G, LAL 242-244 del, and R246I:within or near flexible variable loops without modifying the structure of the functional domains of the spike protein. 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 D215G;D80A;L18F;R246I 120;114;108;148 125;118;112;153 S;S;N 84;258;52 89;263;53 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. In conclusion, our results suggest that GB-2 could be a candidate for prophylaxis against SARS-CoV-2 different variants infection because of its inhibition of the binding between ACE2 and the RBD with K417N-E484K-N501Y mutations and L452R mutation. 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 K417N;L452R;E484K;N501Y 201;233;207;213 206;238;212;218 RBD 192 195 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. In our results, we also discovered that GB-2 can block the binding between ACE2 and the RBD with a single mutation (K417N). 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 K417N 116 121 RBD 88 91 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. In this study, we discovered that GB-2 blocks the binding between ACE2 and RBD with a triple mutation (K417N-E484K-N501Y) and L452R mutation. 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 L452R;K417N;E484K;N501Y 126;103;109;115 131;108;114;120 RBD 75 78 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. L452R mutation is the imporant mutatnt in RBD of epsilon variant. 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 L452R 0 5 RBD 42 45 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. Moreover, L452R mutation of epsilon variant reduced neutralizing activity of several RBD-specific monoclonal antibodies. 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 L452R 10 15 RBD 85 88 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. The N501Y mutation in the RBD domain of the spike protein increases both the binding affinity of the RBD to the ACE2 receptor and the viral transmission rate of both alpha and beta variants. 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 N501Y 4 9 S;RBD;RBD 44;26;101 49;29;104 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. The results suggested that GB-2 could decrease the viral transmission rate of both alpha and beta variants with the N501Y mutation. 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 N501Y 116 121 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. The results suggested that GB-2 may decrease infectivity of epsilon variant with L452R mutation. 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 L452R 81 86 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. This is possibly why GB-2 cannot affect the binding between ACE2 and the RBD with a single mutation (E484K). 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 E484K 101 106 RBD 73 76 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. We discovered that GB-2 can block the binding between ACE2 and RBD with a single mutation (N501Y). 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 N501Y 91 96 RBD 63 66 34388530 GB-2 blocking the interaction between ACE2 and wild type and mutation of spike protein of SARS-CoV-2. We found that GB-2 can block the binding between ACE2 and RBD with L452R mutation. 2021 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 L452R 67 72 RBD 58 61 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. In addition, there are some other significant mutations in SARS-CoV-2 variants, such as D614G, L452R, and E484Q, which can also be considered for specific detection with rRT-PCR assay; relevant research in our laboratory is in progress. 2021 Chinese medical journal Discussion SARS_CoV_2 D614G;E484Q;L452R 88;106;95 93;111;100 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. In addition, we developed S484K and S501Y assays. 2021 Chinese medical journal Discussion SARS_CoV_2 S484K;S501Y 26;36 31;41 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. The N501Y substitution in the S protein has been shown to increase ACE2 binding, potentially reducing susceptibility to neutralizing antibodies with the result of increased viral transmission advantage. 2021 Chinese medical journal Discussion SARS_CoV_2 N501Y 4 9 S 30 31 34402479 Real-time reverse transcription-polymerase chain reaction assay panel for the detection of severe acute respiratory syndrome coronavirus 2 and its variants. To conclude, we developed four rRT-PCR assays (RdRp, N, S484K, and S501Y) to detect SARS-CoV-2 variants and applied them to multiple virus strains. 2021 Chinese medical journal Discussion SARS_CoV_2 S484K;S501Y 56;67 61;72 RdRP;N 47;53 51;54 34403732 Identification of natural compounds as SARS-CoV-2 entry inhibitors by molecular docking-based virtual screening with bio-layer interferometry. These include N439K (B.1.141 "Scottish lineage"), Y453F (B.1.1.298 "mink variant"), N501Y (B.1.1.7, B.1.351 and P1) and D614G (found in most variants). 2021 Pharmacological research Discussion SARS_CoV_2 D614G;N439K;N501Y;Y453F 120;14;84;50 125;19;89;55 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. Conversely, the P681H substitution in the S1/S2 furin cleavage site, although increase spike cleavage by furin-like proteases does not significantly impact viral entry or cell-cell spread in vitro (Ord et al., 2020) neither with higher infection rate or higher prevalence. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P681H 16 21 S 87 92 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. The 69/70 deletion spike together with the E484K and N501Y substitutions decrease the ability to neutralize antibodies. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K;N501Y 43;53 48;58 S 19 24 34403832 Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2. The substitutions in the spike protein are common, however some distinctive substitutions have relevant characteristics for instance, the presence of E484K has been associated with lower neutralizing activity from convalescent plasma. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 150 155 S 25 30 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. 10), are also located relatively close to the above-described S247R. 2021 Journal of virology Discussion SARS_CoV_2 S247R 62 67 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. A small fraction of passaged WA1/2020 contained another mutation, S247R, which also contributes to an increase in the positive charge of the NTD surface. 2021 Journal of virology Discussion SARS_CoV_2 S247R 66 71 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Analysis of sequences submitted to GISAID's EpiCoV database revealed that accumulation of mutations that increase the positive charge of NTD upon passaging in Vero cells is quite common: N74K was detected in EPI_ISL_1039208, EPI_ISL_1190402, EPI_ISL_1718321, EPI_ISL_1707039, EPI_ISL_1785073, and EPI_ISL_1785076, and I68R/K was found in EPI_ISL_493139 and EPI_ISL_2226226. 2021 Journal of virology Discussion SARS_CoV_2 I68R;I68K;N74K 318;318;187 324;324;191 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Combining the positively charged insertion and S686G mutation in the same S protein did not detectably increase the affinity of infectious viral particles to heparin Sepharose above the level determined for CoV-2/GFP/ins. 2021 Journal of virology Discussion SARS_CoV_2 S686G 47 52 S 74 75 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. First, viruses with S686G are eluted from heparin Sepharose by lower concentrations of NaCl. 2021 Journal of virology Discussion SARS_CoV_2 S686G 20 25 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. However, it was likely less competitive than the S686G mutant and was eliminated from the viral pool within a few subsequent passages. 2021 Journal of virology Discussion SARS_CoV_2 S686G 49 54 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. However, the insertion- and/or S686G mutation-containing variants, which became adapted to cell culture, were eluted by NaCl at 0.35 and 0.3 concentrations. 2021 Journal of virology Discussion SARS_CoV_2 S686G 31 36 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Importantly, the recombinant single mutants continued to accumulate the second-site mutations, either R/K substitutions in NTD for CoV-2/GFP/G or the S686G mutation for CoV-2/GFP/ins. 2021 Journal of virology Discussion SARS_CoV_2 S686G 150 155 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Importantly, we observed that rapid adaptation of the recombinant, cDNA-derived virus, and the S686G mutation became dominant by passage 2 because it increased viral infectivity by 100-fold. 2021 Journal of virology Discussion SARS_CoV_2 S686G 95 100 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. In our study, at the early passages, we were able to detect another CoV-2/GFP variant with mutated positively charged aa in the furin cleavage site (R685H mutation). 2021 Journal of virology Discussion SARS_CoV_2 R685H 149 154 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. In our study, the selected recombinant viruses with the S686G mutation replicated to 2 orders of magnitude higher infectious titers in Vero cells than did the natural isolates and previously designed deletion mutants. 2021 Journal of virology Discussion SARS_CoV_2 S686G 56 61 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Second, in contrast to the insertion mutant, the originally selected CoV-2/GFP variant with the S686G mutation continued to evolve and attain additional mutations in the NTD, such as I68R and N74K. 2021 Journal of virology Discussion SARS_CoV_2 I68R;N74K;S686G 183;192;96 187;196;101 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Taken together, these data suggest that I68R and N74K additionally contribute to HS binding. 2021 Journal of virology Discussion SARS_CoV_2 I68R;N74K 40;49 44;53 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. The indicated I68R and N74K mutations, which additionally increase the positive charge of the NTD surface. 2021 Journal of virology Discussion SARS_CoV_2 I68R;N74K 14;23 18;27 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. The mutations leading to more efficient spread include (i) substitutions of single aa in the NTD by those positively charged, (ii) insertions of short peptides that contain basic aa, and (iii) an S686G substitution that likely transforms FCS into the HS-interacting peptide. 2021 Journal of virology Discussion SARS_CoV_2 S686G 196 201 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. The previously published data showed that the peptide representing FCS is often entirely or partially deleted during virus passaging, and the same S686G mutation was also detected after passaging of other SARS-CoV-2 isolates. 2021 Journal of virology Discussion SARS_CoV_2 S686G 147 152 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. The second mechanism of SARS-CoV-2 adaptation was based on the appearance of the S686G substitution in P1' position of the S1/S2 cleavage site, FCS. 2021 Journal of virology Discussion SARS_CoV_2 S686G 81 86 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. These results suggest that, in contrast to FCS deletion, inhibition of the S1/S2 processing by S686G is likely not the only advantage of the new variants. 2021 Journal of virology Discussion SARS_CoV_2 S686G 95 100 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. This was an indication that during viral infection, the introduced mutations, GLTSKRN insertion and S686G substitution, were able to function in either synergistic or additive modes. 2021 Journal of virology Discussion SARS_CoV_2 S686G 100 105 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Thus, the S686G mutant apparently produced higher infectious titers than other variants with mutated arginine-rich motifs. 2021 Journal of virology Discussion SARS_CoV_2 S686G 10 15 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Viral mutants with deleted FCS and R682L, S686G, and H655L mutations have been detected in the stock of the WA1/2020 isolate from the CDC. 2021 Journal of virology Discussion SARS_CoV_2 H655L;R682L;S686G 53;35;42 58;40;47 34406867 Natural and Recombinant SARS-CoV-2 Isolates Rapidly Evolve In Vitro to Higher Infectivity through More Efficient Binding to Heparan Sulfate and Reduced S1/S2 Cleavage. Viral spikes with S686G substitutions retained the entire polybasic motif, which was originally required for cleavage by furin protease. 2021 Journal of virology Discussion SARS_CoV_2 S686G 18 23 S 6 12 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. Further, the analysis showed that the mutations at Y149C and V880I did not alter the secondary structure whereas the mutations at R118C, T148I, Q822H and D893Y lead to noticeable changes in secondary structure of RdRp protein. 2021 Archives of microbiology Discussion SARS_CoV_2 D893Y;Q822H;R118C;T148I;V880I;Y149C 154;144;130;137;61;51 159;149;135;142;66;56 RdRP 213 217 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. Furthermore, the protein dynamics study revealed the occurrence of rigidness in the C- terminal region of the RdRp protein after mutation except for Y149C which leads to flexibility in the N-terminal region. 2021 Archives of microbiology Discussion SARS_CoV_2 Y149C 149 154 RdRP;N 110;189 114;190 34410443 Identification and characterization of mutations in the SARS-CoV-2 RNA-dependent RNA polymerase as a promising antiviral therapeutic target. The mutation at R118C occurs at the NiRAN domain and is an important structural block with five antiparallel beta strands and two helices and therefore, can influence the structural integrity of the virus (Gao et al.). 2021 Archives of microbiology Discussion SARS_CoV_2 R118C 16 21 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. A few other circulating RBD mutations have become prominent since N439K first emerged. 2021 Frontiers in cell and developmental biology Discussion SARS_CoV_2 N439K 66 71 RBD 24 27 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. Among the E484K, K417N, and N501Y mutations in the receptor-binding domain of Spike caused widespread escape from monoclonal antibodies. 2021 Frontiers in cell and developmental biology Discussion SARS_CoV_2 E484K;K417N;N501Y 10;17;28 15;22;33 S 78 83 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. Here, we describe a circulating RBD mutation N439K that maintains a high affinity with hACE2 while evading antibody-mediated immune response using bioinformatics method. 2021 Frontiers in cell and developmental biology Discussion SARS_CoV_2 N439K 45 50 RBD 32 35 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. In other words, N439K increases spike affinity for ACE2 significantly, which is consistent with the surface plasmon resonance (SPR) result. 2021 Frontiers in cell and developmental biology Discussion SARS_CoV_2 N439K 16 21 S 32 37 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. MD simulations and MM-PBSA results showed that the binding ability of the N439K-mutated RBD with hACE2 was enhanced. 2021 Frontiers in cell and developmental biology Discussion SARS_CoV_2 N439K 74 79 RBD 88 91 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. Meanwhile, the reduced binding of REGN10987 mAb to the variant N439K RBD, which was also confirmed by bio-layer interferometry analysis. 2021 Frontiers in cell and developmental biology Discussion SARS_CoV_2 N439K 63 68 RBD 69 72 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. Our study shows that the N439K influences the affinity of both RBD-hACE2 and RBD-mAbs complexes which is favored by the intermolecular van der Waals, electrostatic interactions, and polar solvation free energy. 2021 Frontiers in cell and developmental biology Discussion SARS_CoV_2 N439K 25 30 RBD;RBD 63;77 66;80 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. The B.1.1.7 variants with increased transmission have 9 amino-acid changes in Spike, including N501Y, and N501Y compromises neutralization by many antibodies with public V-region IGHV3-53. 2021 Frontiers in cell and developmental biology Discussion SARS_CoV_2 N501Y;N501Y 95;106 100;111 S 78 83 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. The N439K (ASN439 to LYS439) SARS-CoV-2 variant form a new salt bridge at the RBD-hACE2 interface through simulation calculation, which is consistent with the previous study. 2021 Frontiers in cell and developmental biology Discussion SARS_CoV_2 N439K;N439K 4;11 9;27 RBD 78 81 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. The Y435F mutation provides evidence of animal-to-human transmission in mink farms. 2021 Frontiers in cell and developmental biology Discussion SARS_CoV_2 Y435F 4 9 34414185 N439K Variant in Spike Protein Alter the Infection Efficiency and Antigenicity of SARS-CoV-2 Based on Molecular Dynamics Simulation. Thomson used SPR to evaluate binding of recombinant N439K RBD protein to recombinant hACE2, indicating that acquisition of the N439K mutation enhances hACE2 binding. 2021 Frontiers in cell and developmental biology Discussion SARS_CoV_2 N439K;N439K 52;127 57;132 RBD 58 61 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Additional mutations within the receptor-binding site (K417N and E484K) changed the amino acid sequence of the epitope and may contribute to the escape from antibody binding. 2021 eLife Discussion SARS_CoV_2 E484K;K417N 65;55 70;60 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. All of these methodologies suggested that, of the three mutations examined in this work, the N501Y mutation in the RBD has the most significant role in binding and dissociation from the ACE2 receptor . 2021 eLife Discussion SARS_CoV_2 N501Y 93 98 RBD 115 118 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Although they do not contain the N501Y mutation, other mutations in the RBD might increase the binding of the virus to the human receptor ACE2, leading to a similar effect. 2021 eLife Discussion SARS_CoV_2 N501Y 33 38 RBD 72 75 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. As confirmed by other simulation studies performed at various speeds, our simulations revealed that additional pi-pi and cation-pi interactions resulting from the N501Y mutation lead to the higher rupture force. 2021 eLife Discussion SARS_CoV_2 N501Y 163 168 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Consequently, we believe that N501Y is a critical mutation that affects the transmission of COVID-19 by strengthening the interaction between RBD and ACE2. 2021 eLife Discussion SARS_CoV_2 N501Y 30 35 RBD 142 145 COVID-19 92 100 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Here, we found that a RBD with the N501Y mutation has a 5-10 times higher affinity than wild-type RBD for ACE2. 2021 eLife Discussion SARS_CoV_2 N501Y 35 40 RBD;RBD 22;98 25;101 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Indeed, the alpha variant of SARS-CoV-2, which contains the N501Y mutation, had become the most common lineage in the United States by June 2020. 2021 eLife Discussion SARS_CoV_2 N501Y 60 65 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Indeed, the results from flow cytometry showed that E484K contributed less to the interaction increment than N501Y, whereas K417N even decreased the interaction. 2021 eLife Discussion SARS_CoV_2 E484K;K417N;N501Y 52;124;109 57;129;114 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Interestingly, three key mutations (N501Y, E484K, and K417T) are found in the RBD of the P.1 variant. 2021 eLife Discussion SARS_CoV_2 E484K;K417T;N501Y 43;54;36 48;59;41 RBD 78 81 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. It is noted that only a modest effect from the N501Y mutation was detected in the experimental data, such as the 10 pN difference in complex dissociation force between the wild-type and variants detected by AFM measurement. 2021 eLife Discussion SARS_CoV_2 N501Y 47 52 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. The effects of the E484K and K417N mutations may cancel each other out, and N501Y is the dominant site in affecting the interaction. 2021 eLife Discussion SARS_CoV_2 E484K;K417N;N501Y 19;29;76 24;34;81 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. The strong interaction of the N501Y mutant RBD leads to the tighter binding of SARS-CoV-2 to the host cell, allowing complete membrane fusion or the internalization of the receptor with the virus. 2021 eLife Discussion SARS_CoV_2 N501Y 30 35 Membrane;RBD 126;43 134;46 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. This will make the current vaccine less effective against SARS-CoV-2 variants that contain the N501Y mutation. 2021 eLife Discussion SARS_CoV_2 N501Y 95 100 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Thus, a higher vaccine-induced antibody titer or neutralizing antibodies of higher affinity are needed to compete for the RBDN501Y-ACE2 interaction. 2021 eLife Discussion SARS_CoV_2 N501Y 125 130 RBD 122 125 34414884 N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Thus, the results of SMD simulations are essential parts of our work, revealing that additional interactions are present for the N501Y mutant RBD and are responsible for the increased rupture force. 2021 eLife Discussion SARS_CoV_2 N501Y 129 134 RBD 142 145 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. Furthermore, in those vaccinated people with HIV who developed neutralising responses to Asp614Gly wild-type, neutralisation against the beta variant was retained in 50% of vaccinated participants, 80% of whom were RBD IgG seropositive at baseline, and in whom ChAdOx1 nCoV-19 induced high neutralising antibody titres against the original Asp614Gly wild-type strain. 2021 The lancet. HIV Discussion SARS_CoV_2 D614G;D614G 89;340 98;349 RBD 215 218 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. In our trial, development of neutralising titres against the Asp614Gly wild-type strain after priming and booster doses of ChAdOx1 nCoV-19 correlated with antibody responses to FLS and RBD viral antigens in HIV-negative participants and in people with HIV. 2021 The lancet. HIV Discussion SARS_CoV_2 D614G 61 70 RBD 185 188 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. Neutralising antibodies have been implicated as correlates of protection from COVID-19 in preclinical challenge studies and, in a previous clinical trial, neutralising antibodies developed against the Asp614Gly wild-type strain in more than 99% of participants after vaccination with ChAdOx1 nCoV-19, with higher levels in boosted than in non-boosted groups. 2021 The lancet. HIV Discussion SARS_CoV_2 D614G 201 210 COVID-19 78 86 34416193 Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 in people living with and without HIV in South Africa: an interim analysis of a randomised, double-blind, placebo-controlled, phase 1B/2A trial. Our findings also suggest that previous exposure to the ancestral SARS-CoV-2 virus, Asp614Gly wild-type, in people with HIV might result in a heightened immune response, including some preservation of neutralising antibody activity against the beta variant. 2021 The lancet. HIV Discussion SARS_CoV_2 D614G 84 93 34417165 Effectiveness of BNT162b2 and mRNA-1273 covid-19 vaccines against symptomatic SARS-CoV-2 infection and severe covid-19 outcomes in Ontario, Canada: test negative design study. Lastly, our finding that two doses of mRNA vaccines was not associated with appreciable vaccine escape by lineage alpha or variants with the E484K mutation (beta and gamma) is notable. 2021 BMJ (Clinical research ed.) Discussion SARS_CoV_2 E484K 141 146 34417349 SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. In the RBD, the possibility to escape is limited, and the mutation E484K that we found is one of the most frequent mutations to escape mAbs and among the most common RBD mutations described in experimental settings. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 E484K 67 72 RBD;RBD 7;166 10;169 34417349 SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. Remarkably, the evolution of the E484K substitution observed in our experimental setting was replicated a few months later in the real world by the emergence of E484K variants in South Africa, Brazil, and Japan. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 E484K;E484K 33;161 38;166 34417349 SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. The ability of the virus to adapt to the host immune system was also observed in clinical settings where an immunocompromised COVID-19 patient, after 154 d of infection, presented different variants of the virus, including the E484K substitution. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 E484K 227 232 COVID-19 126 134 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. Here, we show there was a dose-dependent increase in WA-1 and B.1.351 S- and RBD-specific antibody titers and D614G and B.1.351 neutralization titers. 2021 Nature immunology Discussion SARS_CoV_2 D614G 110 115 RBD;S 77;70 80;71 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. mRNA-1273 and BNT162b2 vaccines had ~95% efficacy in clinical trials performed in the US, when WA-1 and D614G variants circulated most widely. 2021 Nature immunology Discussion SARS_CoV_2 D614G 104 109 34417590 mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. The B.1.351 variant is one of greatest concern compared to WA-1, D614G, or B.1.1.7 based on the higher reduction in neutralization using vaccine sera and clinical trials showing lower efficacy against symptomatic infection. 2021 Nature immunology Discussion SARS_CoV_2 D614G 65 70 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. A520S was reported to be associated with low antigenicity. 2021 Infectious diseases of poverty Discussion SARS_CoV_2 A520S 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. Although V367F increases its binding affinity to ACE2, it increases the reactivity to neutralizing antibody. 2021 Infectious diseases of poverty Discussion SARS_CoV_2 V367F 9 14 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. E484K was associated with a decreased affinity (Table 2), which is consistent with a previous report. 2021 Infectious diseases of poverty Discussion SARS_CoV_2 E484K 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. For the first time, we demonstrated that the V367F mutant exhibits more sensitivity to the neutralizing antibody than wild-type counterpart (P < 0.001), possibly because this mutation increases the antigenicity. 2021 Infectious diseases of poverty Discussion SARS_CoV_2 V367F 45 50 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. However, E484K lead to immune evasion from both natural and vaccine-induced sera. 2021 Infectious diseases of poverty Discussion SARS_CoV_2 E484K 9 14 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. I468F, Q414E, V367F, A367T, A520S, N354D, and A435S were identified to be the early mutations with the affinity change of DeltaDeltaGwild-mutation > 0.1 kcal/mol (Table 1). 2021 Infectious diseases of poverty Discussion SARS_CoV_2 A367T;A435S;A520S;N354D;Q414E;V367F;I468F 21;46;28;35;7;14;0 26;51;33;40;12;19;5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. It was demonstrated that V367F and N354D mutants showed higher infectivity than wild-type counterpart. 2021 Infectious diseases of poverty Discussion SARS_CoV_2 N354D;V367F 35;25 40;30 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. N354D mutation increased the infectivity of SARS-CoV-2, but did not alter antibody neutralization. 2021 Infectious diseases of poverty Discussion SARS_CoV_2 N354D 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. Of those, E484K was the most frequent one (n = 86 585). 2021 Infectious diseases of poverty Discussion SARS_CoV_2 E484K 10 15 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. Of those, the sequences with I468F, Q414E, A367T, or A435S were not chosen due to only < 10 strains uploaded in 2020. 2021 Infectious diseases of poverty Discussion SARS_CoV_2 A367T;A435S;I468F;Q414E 43;53;29;36 48;58;34;41 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. S477N enhance the binding affinity. 2021 Infectious diseases of poverty Discussion SARS_CoV_2 S477N 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. S477N, a mutation mainly identified in the USA, Australia, and some European countries, also had a large number of uploaded sequences. 2021 Infectious diseases of poverty Discussion SARS_CoV_2 S477N 0 5 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. The neutralizing antibody applied in this study is a kind of monoclonal antibody targeting to the S1 protein, which has a higher reactivity to the V367F-related antigenic determinant. 2021 Infectious diseases of poverty Discussion SARS_CoV_2 V367F 147 152 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. Thus, rapid identification of emerging mutants with immune evasion including E484K and those with increased binding affinity such as S477N is important in tracing SARS-CoV-2 evolution. 2021 Infectious diseases of poverty Discussion SARS_CoV_2 E484K;S477N 77;133 82;138 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. Thus, V367F and N354D were selected for the in vitro experiments. 2021 Infectious diseases of poverty Discussion SARS_CoV_2 N354D;V367F 16;6 21;11 34419160 Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein. V367F was present at the early stage and thereafter. 2021 Infectious diseases of poverty Discussion SARS_CoV_2 V367F 0 5 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. A1056V is located in the S2 subunit, which is required for the fusion of host and viral membrane. 2021 EBioMedicine Discussion SARS_CoV_2 A1056V 0 6 Membrane 88 96 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. D614G causes conformation change of the spike protein, and therefore mutations in the S2 subunit may affect neutralization by allosteric mechanism. 2021 EBioMedicine Discussion SARS_CoV_2 D614G 0 5 S 40 45 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. D796H mutation in the S2 region has been proposed to reduce neutralization susceptibility by convalescent plasma and is found in the B.1.1.318. 2021 EBioMedicine Discussion SARS_CoV_2 D796H 0 5 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Furthermore, there is a possibility that second generation vaccines containing variant spike RBD may have reduced efficacy against non-N501Y strains. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y 135 140 S;RBD 87;93 92;96 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Most previous studies assessing the impact of N501Y variants on the antibody titer used only a single virus isolate in the variant lineage for the determination of neutralizing antibody titer. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y 46 51 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Our current study showed that N501Y variants may affect the time-to-seropositivity for anti-RBD IgG with the commercial assay, as 6 of the 7 anti-N IgG positive specimens tested negative for anti-RBD IgG. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y 30 35 RBD;RBD;N 92;196;146 95;199;147 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. The binding of antibody in convalescent sera were statistically significantly lower for N501Y RBD than for wild type RBD. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y 88 93 RBD;RBD 94;117 97;120 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. The difference between these two strains were located at nsp2 (S512Y), nsp13 (K460R), and the spike protein (A1056V). 2021 EBioMedicine Discussion SARS_CoV_2 A1056V;K460R;S512Y 109;78;63 115;83;68 S;Nsp13;Nsp2 94;71;57 99;76;61 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Therefore, anti-RBD IgG induced by infection with N501Y variant may not bind well to wild type RBD. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y 50 55 RBD;RBD 16;95 19;98 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. This study assessed the impact of N501Y variants on the neutralizing activity of convalescent sera from COVID-19 patients, and on anti-RBD immunoassays. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y 34 39 RBD 135 138 COVID-19 104 112 34419925 The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. Three SARS-CoV-2 variants with spike N501Y mutation, including B.1.1.7, B.1.351 and P.1, have been classified as "variants of concern" because of increased transmissibility, disease severity, or reduced susceptibility to neutralization by natural infection or vaccine-induced antibodies. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y 37 42 S 31 36 34423763 Severe Acute Respiratory Syndrome Coronavirus 2 in Farmed Mink (Neovison vison), Poland. The G75V mutation is localized in the N terminal domain and could be responsible for interactions with host receptors or stabilizing the spike protein in a constrained prefusion state. 2021 Emerging infectious diseases Discussion SARS_CoV_2 G75V 4 8 S;N 137;38 142;39 34423763 Severe Acute Respiratory Syndrome Coronavirus 2 in Farmed Mink (Neovison vison), Poland. Two mutations located in the spike protein (G75V and C1247F) were present in all isolates reported in this study. 2021 Emerging infectious diseases Discussion SARS_CoV_2 C1247F;G75V 53;44 59;48 S 29 34 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. By contrast, the S477N mutation, a key signature of another B.1.526 sub-lineage, did not have an impact on antibody neutralization. 2021 Nature Discussion SARS_CoV_2 S477N 17 22 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Furthermore, neutralizing activities of plasma from individuals who have recovered from SARS-CoV-2 infection or sera from vaccinated individuals were lower against B.1.526-E484K. 2021 Nature Discussion SARS_CoV_2 E484K 172 177 COVID-19 88 108 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. However, B.1.526 is one of the few lineages with E484K that has risen to prominence. 2021 Nature Discussion SARS_CoV_2 E484K 49 54 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. In addition, our PCR screen enabled us to obtain unbiased estimates of E484K and N501Y prevalence early on in the study. 2021 Nature Discussion SARS_CoV_2 E484K;N501Y 71;81 76;86 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Neutralization studies on B.1.526-E484K demonstrate that the activities of several antibodies are either impaired or lost with this variant, including two antibodies (Ly-CoV555 and REGN10933) that are already in clinical use. 2021 Nature Discussion SARS_CoV_2 E484K 34 39 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Similarly, although B.1.351 may pose the greatest antigenic challenge to antibodies and vaccines, the B.1.526-E484K sub-lineage also exhibits resistance to antibody neutralization. 2021 Nature Discussion SARS_CoV_2 E484K 110 115 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. This highlights that E484K can rapidly emerge in multiple clonal backgrounds and may warrant targeted screening for this key mutation in addition to robust genomic surveillance programs. 2021 Nature Discussion SARS_CoV_2 E484K 21 26 34428777 Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York. Together, our findings underscore the importance of the E484K mutation, which has emerged in at least 246 different lineages of SARS-CoV-2, a powerful illustration of convergent evolution. 2021 Nature Discussion SARS_CoV_2 E484K 56 61 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. A treatment approach could be to treat with a standard dose immediately, and if genotyping reveals a critical mutation, like the E484K, to adjust the hCoV-2IG dosing subsequently. 2021 iScience Discussion SARS_CoV_2 E484K 129 134 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. In contrast, the K417N had only minimal effect on RBD binding and the N501Y reduced binding of the hCoV-2IG by 2-fold. 2021 iScience Discussion SARS_CoV_2 K417N;N501Y 17;70 22;75 RBD 50 53 34430803 Epitope diversity of SARS-CoV-2 hyperimmune intravenous human immunoglobulins and neutralization of variants of concern. We found that the E484K mutation, which is shared between Brazil/JP P.1 VOC and SA B.1.351 VOC, significantly reduced binding of hCoV-2IG to the RBD (19-fold reduction) compared with RBD-wt. 2021 iScience Discussion SARS_CoV_2 E484K 18 23 RBD;RBD 145;183 148;186 34431691 Emergence of Multiple SARS-CoV-2 Antibody Escape Variants in an Immunocompromised Host Undergoing Convalescent Plasma Treatment. The patient then started to endogenously develop antibodies, including NAbs (day 19), displaying higher titers against a nonescape virus (e.g., Wuhan-Hu-1) but lower titers against antibody escape variants harboring E484K. 2021 mSphere Discussion SARS_CoV_2 E484K 216 221 34432488 Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern. Due to the rise of E484K and the inability of clinical labs to screen for this mutation, the Food and Drug Administration revoked the emergency use authorization of bamlanivimab when administered alone (https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-revokes-emergency-use-authorization-monoclonal-antibody-bamlanivimab). 2021 Journal of clinical microbiology Discussion SARS_CoV_2 E484K 19 24 COVID-19 267 275 34432488 Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern. Here, application of a E484K SNP assay could allow for the selection of appropriate monoclonal antibodies, akin to the role of HIV genotyping in antiretroviral regimen selection. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 E484K 23 28 34432488 Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern. In addition, sporadic E484K and N501Y mutations may be present and may not necessarily be indicative of VOC; however, these mutations are likely still of phenotypic significance. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 E484K;N501Y 22;32 27;37 34432488 Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern. In California, use of a targeted SNP assay allowed for real-time surveillance of the emergence of variants harboring the L452R mutation. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 L452R 121 126 34432488 Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern. In particular, N501Y has been shown to increase binding affinity to human ACE2, leading to increased infectivity, while E484K has been shown to decrease neutralization by monoclonal antibodies, as well as that by convalescent and postvaccine sera. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 E484K;N501Y 120;15 125;20 34432488 Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern. Mutations in the spike protein such as N501Y (present in B.1.1.7, B.1.351, and P.1) and E484K (present in B.1.351, B.1.525, B.1.526, B.1.620, B.1.621, P.1, P.2 and P.3), among others, are likely driving worrisome phenotypes seen with emerging variants (https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html). 2021 Journal of clinical microbiology Discussion SARS_CoV_2 E484K;N501Y 88;39 93;44 S 17 22 34432488 Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern. The simple design of the SNP assay provides consistent amplification of the target region, limits the potential for amplicon dropout from mutations in the primer sequences, and facilitates the addition of new probes to detect emerging mutations identified among SARS-CoV-2 variants (e.g., L452R). 2021 Journal of clinical microbiology Discussion SARS_CoV_2 L452R 289 294 34432488 Single-Amplicon Multiplex Real-Time Reverse Transcription-PCR with Tiled Probes To Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern. This is evidenced by repeated convergent evolution of tolerable mutations such as E484K and N501Y. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 E484K;N501Y 82;92 87;97 34433426 Investigation of Interaction between the Spike Protein of SARS-CoV-2 and ACE2-Expressing Cells Using an In Vitro Cell Capturing System. Using the in vitro cell capturing system, we showed that S protein variant with D614G mutation showed a higher cell capturing ability than wild type one, which is in line with its effect on infection efficiency and binding affinity. 2021 Biological procedures online Discussion SARS_CoV_2 D614G 80 85 S 57 58 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. A preliminary analysis suggests that the carriers of the K26R ACE allele might be at increased risk of severe disease, but the findings did not reach statistical significance, and further studies are required. 2021 eLife Discussion SARS_CoV_2 K26R 57 61 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Both lineages include the N501Y mutation, but this appears to have modest effects on antibody neutralisation. 2021 eLife Discussion SARS_CoV_2 N501Y 26 31 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Finally, a SARS-CoV-2 variant with the Spike mutation D614G, which increases its activity by stabilising it following furin cleavage, rapidly became dominant globally after it emerged. 2021 eLife Discussion SARS_CoV_2 D614G 54 59 S 39 44 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. In contrast, the E484K mutation, also present in both variants, potently disrupts antibody neutralisation. 2021 eLife Discussion SARS_CoV_2 E484K 17 22 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. In this case, the opposite effect of the RBD S477N mutation on its affinity for ACE2 S19P (decreased), compared with ACE2 WT (increased), suggests that this RBD variant may have a selective disadvantage amongst carriers of the ACE2 S19P variant, in contrast to those with ACE2 WT, where it appears to be advantageous. 2021 eLife Discussion SARS_CoV_2 S477N 45 50 RBD;RBD 41;157 44;160 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Indeed, mutations of K417 can block antibody neutralisation, albeit less effectively than E484K. 2021 eLife Discussion SARS_CoV_2 E484K 90 95 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. It is notable that these affinity-reducing K417N/T mutations have only emerged together with mutations (N501Y and E484K) that increase the affinity of RBD for ACE2, suggesting a cooperative effect between mutations that enhance immune escape and mutations that increase affinity. 2021 eLife Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y 114;43;43;104 119;50;50;109 RBD 151 154 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Our affinity and kinetic data on RBD variants are broadly consistent with some, but not all, recent reports on the K417T/N, N501Y, and E484K variants. 2021 eLife Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y 135;115;115;124 140;122;122;129 RBD 33 36 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Our finding that the K417N/T mutations present in Beta and Gamma variants decrease the affinity of RBD for ACE2 suggests that they were selected because they facilitate immune escape. 2021 eLife Discussion SARS_CoV_2 K417N;K417T 21;21 28;28 RBD 99 102 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Our finding that the N501Y, E484K, and S477N all increase the binding affinity of RBD for ACE2 raises the question as to whether this contributed to their selection. 2021 eLife Discussion SARS_CoV_2 E484K;N501Y;S477N 28;21;39 33;26;44 RBD 82 85 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Second, epidemiological studies have suggested that the Alpha variant, which has the N501Y mutation, has enhanced transmissibility. 2021 eLife Discussion SARS_CoV_2 N501Y 85 90 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Second, will combinations of existing mutations be selected because they further increase the affinity? While the appearance E484K, together with N501Y in three lineages (Alpha, Beta, and Gamma), supports this, it is also possible that E484K was selected because it disrupts antibody neutraliaation, as discussed below. 2021 eLife Discussion SARS_CoV_2 E484K;E484K;N501Y 125;236;146 130;241;151 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. Taken together, these findings suggest that the WT Spike/ACE2 interaction is limiting for transmission and that mutations that enhance it, including the N501Y, E484K, and S477N mutations, could provide a selective advantage by increasing transmissibility. 2021 eLife Discussion SARS_CoV_2 E484K;N501Y;S477N 160;153;171 165;158;176 S 51 56 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. The effect of the increased affinity for SARS-CoV-2 Spike RBD of the K26R and S19P ACE2 mutants is less clear. 2021 eLife Discussion SARS_CoV_2 K26R 69 73 S;RBD 52;58 57;61 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. The fact that ACE2 S19P mutation is largely confined to African/African-American populations, suggests that it is more recent than K26R and/or selected by pathogen(s) confined to the African continent. 2021 eLife Discussion SARS_CoV_2 K26R 131 135 34435953 Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. The interaction that we identified between the RBD S477N and ACE2 S19P mutants highlights the importance of considering variation in the host population when studying the evolution of viral variants. 2021 eLife Discussion SARS_CoV_2 S477N 51 56 RBD 47 50 34442775 Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally. Other important mutations, N501Y and P681H, specific for the emerging alpha variant of concern were found at a high percentage among the environmental strains. 2021 Microorganisms Discussion SARS_CoV_2 N501Y;P681H 27;37 32;42 34442775 Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally. The most common amino acid substitutions were D614G in the S glycoprotein of environmental strains that are commonly circulating among the clinical human samples. 2021 Microorganisms Discussion SARS_CoV_2 D614G 46 51 S 59 73 34442817 Impact of Full Vaccination with mRNA BNT162b2 on SARS-CoV-2 Infection: Genomic and Subgenomic Viral RNAs Detection in Nasopharyngeal Swab and Saliva of Health Care Workers. However, this previous study was limited to a single HCW: a 38 years old man, fully vaccinated with BNT162b2, who tested positive in NPS at 54 days after vaccination, and for the N501Y and HV69-70del mutations associated with the B.1.1.7 lineage. 2021 Microorganisms Discussion SARS_CoV_2 N501Y 179 184 34442817 Impact of Full Vaccination with mRNA BNT162b2 on SARS-CoV-2 Infection: Genomic and Subgenomic Viral RNAs Detection in Nasopharyngeal Swab and Saliva of Health Care Workers. Two others that were symptomatic (one with myalgia and the B.1.1.7 variant, and one with a fever 38.5 C, myalgia and nasal congestion, and the K417T mutation, common in P.1-type variants) only showed a persistent viral sgRNA in NPS. 2021 Microorganisms Discussion SARS_CoV_2 K417T 144 149 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Additionally, the reported worldwide growing trend of the Q57H mutation was confirmed in our samples, with a percentage of ~47% in samples collected during October/November 2020. 2021 International journal of molecular sciences Discussion SARS_CoV_2 Q57H 58 62 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Although H625R involves the substitution of two amino acids with positively charged polar side chains, the in silico structure analysis suggested significant changes in S protein folding. 2021 International journal of molecular sciences Discussion SARS_CoV_2 H625R 9 14 S 169 170 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Focusing on N gene, the declining trend of 28881G>A, 28882G>A, and 28883G>C substitutions was confirmed in our samples. 2021 International journal of molecular sciences Discussion SARS_CoV_2 G28881A;G28882A;G28883C 43;53;67 51;61;75 N 12 13 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. In this regard, specific monitoring of H625R along with other newly emerging mutants in COVID-19 patients and wastewater is necessary to conclude on their potential selective advantage and possible association with SARS-CoV-2 infectivity and effect on existing vaccines. 2021 International journal of molecular sciences Discussion SARS_CoV_2 H625R 39 44 COVID-19 88 96 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. In this regard, the D614G (23403A>G) missense mutation, which was initially identified in Europe, has emerged as the dominant pandemic form, likely due to a significant fitness advantage. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G;A23403G 20;27 25;35 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. In this regard, we have initially targeted five well-characterized missense mutations spanning different genomic regions of SARS-CoV-2, i.e., D614G (23403A>G), P323L (14408C>T), Q57H (25563G>T), R203K (28881G>A), and G204R (28883G>C), and specific nested PCR amplicons were sequenced using DNA-seq. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G;G204R;P323L;Q57H;R203K;C14408T;A23403G;G25563T;G28881A;G28883C 142;217;160;178;195;167;149;184;202;224 147;222;165;182;200;175;157;192;210;232 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Interestingly, a previously unknown missense mutation in the S gene, H625R (23436A>G), was identified in ~6% of September samples. 2021 International journal of molecular sciences Discussion SARS_CoV_2 H625R;A23436G 69;76 74;84 S 61 62 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Interestingly, the 28884G>A substitution, which reportedly has a ~1% prevalence worldwide, was overrepresented in Athen's samples (09/2020, 70% and 11/2020, 35%) and correlated significantly with 28883G>C, resulting in the G204L substitution of nucleocapsid protein. 2021 International journal of molecular sciences Discussion SARS_CoV_2 G28883C;G28884A;G204L 196;19;223 204;27;228 N 245 257 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Interestingly, the P323L (14408C>T) mutation has been reported to co-evolve with D614G worldwide; this adaptation of the virus might strengthen SARS-CoV-2 G614 strain replication rates and infectivity. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G;P323L;C14408T 81;19;26 86;24;34 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. Moreover, a novel variant originating from a simultaneous 4 nt deletion (28881_28884del) and a 4 nt insertion at position 28885 (28885_28886insACAT), was observed in our samples, leading to the R203K and G204H missense mutations of nucleocapsid protein. 2021 International journal of molecular sciences Discussion SARS_CoV_2 G204H;R203K 204;194 209;199 N 232 244 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. The D614G mutation has been strongly associated with higher upper track viral loads and higher rates of younger hosts' infection, as well as with increased replication and higher pseudotyped viral titers ex vivo. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G 4 9 34445204 Novel Nested-Seq Approach for SARS-CoV-2 Real-Time Epidemiology and In-Depth Mutational Profiling in Wastewater. This approach allowed the quantification of SARS-CoV-2 mutations/variations, and our data highlighted the significant prevalence (>99%) of D614G and P323L mutations in wastewater samples obtained from WWTP of Athens, Greece, during September-November 2020, in line with worldwide data based on COVID-19 patient samples. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G;P323L 139;149 144;154 COVID-19 294 302 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. compared the number of residues within interphase for the wild type and the D614G mutant using each closed-form and 1-open form without ACE2. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G 76 81 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. D614G is missing a side chain, which may affect flexibility more than D614A. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614A;D614G 70;0 75;5 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. In an investigation into Korean mutants obtained from the KDCA, the D614G mutant was confirmed as the most prevalent, as it is in other countries. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G 68 73 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. KDCA investigated S protein variants of SARS-CoV-2 in Korean patients using RT-PCR analysis and identified five major mutants (D614G, D614A, L455F, F456L, and Q787H) depending on domain region. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614A;F456L;L455F;Q787H;D614G 134;148;141;159;127 139;153;146;164;132 S 18 19 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. L455F and F456L are located in the RBD region, which interacts with ACE2. 2021 International journal of molecular sciences Discussion SARS_CoV_2 F456L;L455F 10;0 15;5 RBD 35 38 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. Our results suggest that the conformational importance of the D614G mutant in the CT2 domain was related more to the interactions between S protein chains than to the effects of other mutants. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G 62 67 S 138 139 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. The D614G mutant had lower distance fluctuations between the S protein chains, indicating the presence of protomers, and lower energy between the S protein and ACE2 in the 1-, 2-, and 3-complex forms than the wild type. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G 4 9 S;S 61;146 62;147 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. The D614G mutant has both distance and energy stability, according to the results of the V503 and N501 residue distance and MM/PBSA energy calculations. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G 4 9 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. The large prevalence of D614G is in Korea, and this could affect the worldwide pandemic. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G 24 29 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. The number of residues in the D614G mutant was higher in the open form than in the wild type, although there was no difference in the closed form. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G 30 35 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. The other mutants:D614A, L455F, F456L, and Q787H:show more stability than the wild type in some complexes and are more unstable than the wild type in other situations. 2021 International journal of molecular sciences Discussion SARS_CoV_2 F456L;L455F;Q787H;D614A 32;25;43;18 37;30;48;23 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. The Q787H region is in the S2 region and is cleaved by furin post fusion. 2021 International journal of molecular sciences Discussion SARS_CoV_2 Q787H 4 9 34445414 Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2. The results showed that the D614G mutation affected no neutralization by antibody but led to a more frequent transition from closed to open form than is observed in the wild type, causing higher viral infectivity. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G 28 33 34449757 An Autochthonous Outbreak of the SARS-CoV-2 P.1 Variant of Concern in Southern Italy, April 2021. Some studies demonstrated that samples of vaccinated and convalescent people exhibit lower neutralization activity against SARS-CoV-2 strains harboring the E484K spike mutation, showing the need to induce the highest neutralization titers through vaccination. 2021 Tropical medicine and infectious disease Discussion SARS_CoV_2 E484K 156 161 S 162 167 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. Additionally, B.1.1.7 carries the P681H substitution in the furin-cleavage site and multiple VOIs bear the L452R substitution. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 L452R;P681H 107;34 112;39 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. B.1.1.7, B.1.351, and P.1, the most studied VOCs, have the D614G and N501Y mutations in common. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D614G;N501Y 59;69 64;74 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. B.1.351 and P.1 share a mutation in the K417 site (K417N and K417T, respectively) and the E484K replacement, which is also observed in the P.2 lineage. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 E484K;K417T;K417N 90;61;51 95;66;56 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. Remarkably, our local sequences are more similar to genomes from other countries compared to the RJ cluster, which acquired at least four additional mutations (including S:A262S). 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 A262S 172 177 S 170 171 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. The emergence of a B.1.1.28 derived lineage carrying the S:E484K mutation (P.2) was dated, in a retrospective study, late February 2020 in the Southeast (Sao Paulo and Rio de Janeiro), followed by transmission to the South (especially RS). 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 E484K 59 64 S 57 58 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. The ORF3a:D155Y substitution is located near SARS-CoV caveolin-binding Domain IV. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D155Y 10 15 ORF3a 4 9 34451453 Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021. The VOC P.1 carries three deletions, four synonymous substitutions, a four base-pair nucleotide insertion, and at least 17 other lineage-defining replacements, including 10 missense mutations in the spike protein (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, and T1027I), 8 of which are subjected to positive selection. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D138Y;E484K;H655Y;K417T;N501Y;P26S;R190S;T1027I;T20N;L18F 232;253;267;246;260;226;239;278;220;214 237;258;272;251;265;230;244;284;224;218 S 199 204 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Herein, we report a novel variant carrying the S protein L452R mutation, which emerged from a local B.1.362 lineage. 2021 Vaccines Discussion SARS_CoV_2 L452R 57 62 S 47 48 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. However, with the penetration of the dominant Alpha variant in December 2020, all local lineages started to decline, including the B.1.362 lineage and the B.1.362+L452R variant. 2021 Vaccines Discussion SARS_CoV_2 L452R 163 168 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. In addition, as a result of the successful vaccination program in Israel that started already in December 2020, the number of overall infected individuals drastically declined, such that by April 2021 the B.1.362+L452R variant was completely diminished. 2021 Vaccines Discussion SARS_CoV_2 L452R 213 218 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. In addition, viral variants carrying the L452R mutation such as the Epsilon and Delta variants have been shown to have a 6.7 and a 5.8-fold reduction in neutralization against WT virus, respectively. 2021 Vaccines Discussion SARS_CoV_2 L452R 41 46 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. It is estimated to be 60% more transmissible than the Alpha variant, where the high transmissibility is attributed to the combination of three main mutations in the S protein: E484Q, L452R and P681R. 2021 Vaccines Discussion SARS_CoV_2 E484Q;L452R;P681R 176;183;193 181;188;198 S 165 166 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Similarly, this study demonstrated a X4-fold decrease in neutralization capacity of sera derived from fully vaccinated individuals against the B.1.362+L452R variant, suggesting that it is this mutation that accounts for the impact on the neutralization potential of the different variants that carry the L452R mutation. 2021 Vaccines Discussion SARS_CoV_2 L452R;L452R 304;151 309;156 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. Specifically, emerging variants carrying mutations that are known in VOC associated with increased infectivity and/or reduction in neutralization, such as L452R, and the accompanying concern that such variants will gain additional mutations facilitating enhanced and rapid spread:locally and worldwide. 2021 Vaccines Discussion SARS_CoV_2 L452R 155 160 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. The B.1.362 lineage from which the B.1.362+L452R variant emerged, was one of the two most prevalent SARS-CoV-2 lineages (along with B.1.1.50) in Israel since the start of the epidemic in Israel in March 2020. 2021 Vaccines Discussion SARS_CoV_2 L452R 43 48 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. The B.1.362+L452R variant is currently not defined as a variant of concern in Israel, despite the observed reduction in neutralization, as it is no longer observed via routine sequencing since April 2021. 2021 Vaccines Discussion SARS_CoV_2 L452R 12 17 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. The identification of this locally emerging variant carrying the L452R mutation, accompanied by additional independently emerging variants carrying the same mutation (Delta and additional B.1.617 lineage variants, Epsilon, A.27.1), emphasizes the relevance of the L452R mutation to the virus adaptiveness. 2021 Vaccines Discussion SARS_CoV_2 L452R;L452R 65;264 70;269 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. The S protein mutation L452R has been recently in the spotlight as one of the main mutations within the B.1.617 lineage variants originating in India, most notably the Delta variant which is currently uninhibitedly spreading worldwide and is suspected to be one of the most contagious SARS-CoV-2 variants yet. 2021 Vaccines Discussion SARS_CoV_2 L452R 23 28 S 4 5 34452062 The Rise and Fall of a Local SARS-CoV-2 Variant with the Spike Protein Mutation L452R. This is unlike the surge of the currently most successful variant carrying this same L452R substitution, the Delta variant, suggesting that this mutation by itself does not guarantee dominancy of such virus. 2021 Vaccines Discussion SARS_CoV_2 L452R 85 90 34452371 Intravenous, Intratracheal, and Intranasal Inoculation of Swine with SARS-CoV-2. This particular virus isolate contains the D614G mutation in the S gene, which was emerging in the US at the time of the outbreak in the animals and became the dominant genotype worldwide. 2021 Viruses Discussion SARS_CoV_2 D614G 43 48 S 65 66 34452390 The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect. Furthermore, lineage B.1, a large European clade corresponding approximately to the Italian outbreak, and the clade B.1.1 corresponding to a European lineage with three clear SNPs: G28881A, G28882A, G28883C were also identified amid the Algerian sequences. 2021 Viruses Discussion SARS_CoV_2 G28881A;G28882A;G28883C 181;190;199 188;197;206 34452390 The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect. In the sequence, Algeria/EPI_ISL_766874, the amino acid substitution A130V in the RdRp gene result in a harmful functional effect on the protein responsible for viral replication. 2021 Viruses Discussion SARS_CoV_2 A130V 69 74 RdRP 82 86 34452390 The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect. Likewise, a deleterious mutation results from the non-synonymous amino acid replacement N874H in Algeria/EPI_ISL_766875 in the NSP12 gene. 2021 Viruses Discussion SARS_CoV_2 N874H 88 93 Nsp12 127 132 34452390 The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect. Namely, the H69del, V70del, E484K, Y144del, and Q52R. 2021 Viruses Discussion SARS_CoV_2 E484K;H69del;Q52R;V70del;Y144del 28;12;48;20;35 33;18;52;26;42 34452390 The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect. Similarly, In the accessory gene ORF3a, which plays an important role in virulence, infectivity, and virus release, the deleterious mutation A23T was first reported from the USA and sampled sixty-two times in fifteen countries; thus, based on collection dates, the sequence Algeria/ EPI_ISL_766862 is related to sequences from Texas (USA).The last deleterious amino acid replacement, L129F, was found in the NS3 gene and detected for the first time in Algeria. 2021 Viruses Discussion SARS_CoV_2 A23T;L129F 141;384 145;389 ORF3a;NS3 33;408 38;411 34452390 The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect. The E681D amino acid replacement in the protease gene (NSP3) was first acknowledged in the Algerian genome EPI_ISL_766862 and occurring only in three samples worldwide demonstrated disease exportation from Algeria to Austria (EPI_ISL_853900) via the sample collection dates. 2021 Viruses Discussion SARS_CoV_2 E681D 4 9 Nsp3 55 59 34452390 The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect. The first in the exonuclease gene (NSP14), H26Y amino acid substitution originally discovered for the first time in the aforementioned Algerian sequence and right after in the Greek sequence EPI_ISL_437907, subsequently supporting relatedness of the two genomes. 2021 Viruses Discussion SARS_CoV_2 H26Y 43 47 Exonuclease 17 28 34452390 The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect. This included T85I in the nsp2 gene, P423L in the nsp12 gene, D614G in the S gene, and Q57H in the ORF3a gene. 2021 Viruses Discussion SARS_CoV_2 D614G;P423L;Q57H;T85I 62;37;87;14 67;42;91;18 ORF3a;Nsp12;Nsp2;S 99;50;26;75 104;55;30;76 34452390 The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect. To cite an example, the T1004I replacement in the nsp3 gene was detected in the sequence Algeria_EPI_ISL_420037. 2021 Viruses Discussion SARS_CoV_2 T1004I 24 30 Nsp3 50 54 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. All patients in this study were infected by the B.1.1.7 variant, which could increase the risk of E484A/K selection, as observed in the unique previous case report of bamlanivimab use on B.1.1.7. 2021 Viruses Discussion SARS_CoV_2 E484A;E484K 98;98 105;105 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. Along with other case report series, the clinical observation of high rates of resistance emergence under such antibody monotherapy raises the concern of accelerating the E484K spread, along with other mutations, at a population level. 2021 Viruses Discussion SARS_CoV_2 E484K 171 176 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. E484K and E484Q are rare without therapeutic antibody selective pressure, and several in vitro studies have reported that SARS-CoV-2 variants harboring these mutations are resistant to neutralization by the monoclonal antibody bamlanivimab. 2021 Viruses Discussion SARS_CoV_2 E484Q;E484K 10;0 15;5 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. Finally, all six patients presented a mutation associated with resistance or suspicion of resistance in the Spike protein, including E484A/K, but also S494P and Q493R. 2021 Viruses Discussion SARS_CoV_2 E484A;E484K;Q493R;S494P 133;133;161;151 140;140;166;156 S 108 113 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. In the same way, a rapid E484K disappearance was also observed for Patient 1, as in two previous report cases without bamlanivimab. 2021 Viruses Discussion SARS_CoV_2 E484K 25 30 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. In this work, we describe the selection of E484K mutations among five out of six patients at high risk of severe COVID-19 who were treated with bamlanivimab monotherapy. 2021 Viruses Discussion SARS_CoV_2 E484K 43 48 COVID-19 113 121 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. Of note, E484K and E484A mutations correspond to two separate nucleotide changes (i.e., GAA to AAA for E484K and GAA to GCA for E484A). 2021 Viruses Discussion SARS_CoV_2 E484A;E484A;E484K;E484K 19;128;9;103 24;133;14;108 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. The impact of mutation E484A, observed for Patient 2, remains to be explored. 2021 Viruses Discussion SARS_CoV_2 E484A 23 28 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. The mechanisms and determinants explaining the maintenance or disappearance of viral mutations or the switches between resistance mutations, such as between E484K and E484A in Patient 2, remain to be explored and understood. 2021 Viruses Discussion SARS_CoV_2 E484A;E484K 167;157 172;162 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. The very high level of E484K selection (5/6 patients) and other mutations observed emphasizes the importance of using combinations of monoclonal antibodies. 2021 Viruses Discussion SARS_CoV_2 E484K 23 28 34452507 Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. This study confirms the clinical and virological findings from another observational case series in Germany, which also found that five of six immunocompromised patients treated with bamlanivimab monotherapy developed an E484K resistance mutation. 2021 Viruses Discussion SARS_CoV_2 E484K 221 226 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. In this case, only mutant E484K evades recognition by anti-RBD antibodies, while all others exhibit IgG titers equivalent to those obtained for RBDWT (Figure 3C). 2022 Allergy Discussion SARS_CoV_2 E484K 26 31 RBD 59 62 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. Likewise point mutations conferred by L452R or E484Q alone have been shown to reduce sensitivity to antibodies elicited by BNT162b2 vaccine. 2022 Allergy Discussion SARS_CoV_2 E484Q;L452R 47;38 52;43 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. More interestingly though, inhibition of RBD-ACE2 interaction by vaccine-induced antibodies significantly falls for all mutants, most markedly for E484K and L452R/E484Q (Figure 3D), indicating that the increased receptor affinity renders neutralization more difficult. 2022 Allergy Discussion SARS_CoV_2 E484K;L452R;E484Q 147;157;163 152;162;168 RBD 41 44 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. Mutation N440K, on the other hand, has caused no significant effect on recognition of RBD by antibodies induced by infection (Figure 3A). 2022 Allergy Discussion SARS_CoV_2 N440K 9 14 RBD 86 89 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. Our data show that the affinity of RBD for ACE2 is fivefold increased by the point mutations L452R and E484Q (Figure 2C and Table 1), whereas mutation N440K has the effect of doubling this value, when compared to RBDWT. 2022 Allergy Discussion SARS_CoV_2 E484Q;L452R;N440K 103;93;151 108;98;156 RBD 35 38 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. Regarding the recognition of RBD by convalescent sera, a sharp decay is observed for mutants E484K and L452R/E484Q (Figure 3A). 2022 Allergy Discussion SARS_CoV_2 E484K;L452R;E484Q 93;103;109 98;108;114 RBD 29 32 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. This might lead to a lower binding recognition of antibodies to the E484K as it has been recently postulated by free energy calculation performed by Wu et al. 2022 Allergy Discussion SARS_CoV_2 E484K 68 73 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. This result is not surprising, as mutation E484K has already been shown to evade immunity in the context of variants B.1.351 and P.1. 2022 Allergy Discussion SARS_CoV_2 E484K 43 48 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. This result may be due to the change in charges (from negative to positive) that occur for E484K only, as the glutamine in E484Q is neutral at physiological pH. 2022 Allergy Discussion SARS_CoV_2 E484K;E484Q 91;123 96;128 34453338 In vitro data suggest that Indian delta variant B.1.617 of SARS-CoV-2 escapes neutralization by both receptor affinity and immune evasion. We are also tempted to speculate that mutation L452R contributes to the increased affinity observed for the double-mutant RBD mostly by stabilizing the RBM rather than by forming new bonds with the receptor. 2022 Allergy Discussion SARS_CoV_2 L452R 47 52 RBD 122 125 34454120 The low contagiousness and new A958D mutation of SARS-CoV-2 in children: An observational cohort study. Because A958 faces R1014 of the neighboring helix, we predict that the A958D mutation will inevitably lead to salt bridge formation between D958 and R1014, which will dramatically improve the thermostability of the spike protein. 2021 International journal of infectious diseases Discussion SARS_CoV_2 A958D 71 76 S 215 220 34454120 The low contagiousness and new A958D mutation of SARS-CoV-2 in children: An observational cohort study. Compared to the sequence isolated from throat swabs, the 24435C>A mutation detected in stool leads to a missense A958D mutation in the S2 domain of the spike protein. 2021 International journal of infectious diseases Discussion SARS_CoV_2 C24435A;A958D 57;113 65;118 S 152 157 34454120 The low contagiousness and new A958D mutation of SARS-CoV-2 in children: An observational cohort study. We deduce that the new A958D mutation might have been a potential reason for the long residence of SARS-CoV-2 in the infant's intestines without apparent symptoms. 2021 International journal of infectious diseases Discussion SARS_CoV_2 A958D 23 28 34455390 Evolution of antibody responses up to 13 months after SARS-CoV-2 infection and risk of reinfection. From M7, anti-RBD antibodies stabilize at a level that neutralizes infectious variants D614G and B.1.1.7, but less B.1.351, suggesting that most COVID-19 positive patients may be protected from reinfection by the former variants. 2021 EBioMedicine Discussion SARS_CoV_2 D614G 87 92 RBD 14 17 COVID-19 145 153 34455390 Evolution of antibody responses up to 13 months after SARS-CoV-2 infection and risk of reinfection. However, taken together our data demonstrate a long-term persistence of anti-RBD IgG titers that may reduce risk of reinfection in convalescent COVID-19 patients by variants D614G and B.1.1.7. 2021 EBioMedicine Discussion SARS_CoV_2 D614G 174 179 RBD 77 80 COVID-19 144 152 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. Among all 4 mutations the D614G is most studied and reported. 2021 Heliyon Discussion SARS_CoV_2 D614G 26 31 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. Considering these analyses it can be said that the current evidence is not clear about the impact of D614G mutation alone on the disease severity and mortality as multiple other stronger factors play role especially age and comorbidity. 2021 Heliyon Discussion SARS_CoV_2 D614G 101 106 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. One study mentioned that the Q57H mutation in ORF3a protein may decrease ion permeability by creating a tighter constriction in channel pore and possibly decrease viral release and immune response (Ul Alam et al.). 2021 Heliyon Discussion SARS_CoV_2 Q57H 29 33 ORF3a 46 51 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. One study predicted D614G mutation introduces a novel protease (elastase) cleavage site that may enhance the fusion of viral envelop to the host cell membrane hence further facilitate viral RNA entry into the host cell. 2021 Heliyon Discussion SARS_CoV_2 D614G 20 25 Membrane 150 158 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. Our analysis suggested the Q57H decreases protein stability with altered protein function may result in loss of a CD4+ T Cell epitope similar to other studies. 2021 Heliyon Discussion SARS_CoV_2 Q57H 27 31 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. Studies reported D614G mutation increases infectivity of the virus as it was found to be associated with higher viral load and higher infectious titre. 2021 Heliyon Discussion SARS_CoV_2 D614G 17 22 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. The 241C>T mutation was one of the most frequent (96%) we have observed in our study. 2021 Heliyon Discussion SARS_CoV_2 C241T 4 10 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. The I300F mutation (occurred in 78% isolates) was predicted to reduce the stability of NSP2 protein the function of which is not yet confirmed. 2021 Heliyon Discussion SARS_CoV_2 I300F 4 9 Nsp2 87 91 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. The P323L mutation in RdRp is reported to be associated with increased mutation rate. 2021 Heliyon Discussion SARS_CoV_2 P323L 4 9 RdRP 22 26 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. The S194L was predicted to have neutral effect in our study with a reduced DDG value and may attenuate viral assembly as reported in an earlier study. 2021 Heliyon Discussion SARS_CoV_2 S194L 4 9 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. The second most frequent mutation in our analysis was a tri-nucleotide change resulting in two amino acid changes which are R203K and G204R in N protein. 2021 Heliyon Discussion SARS_CoV_2 G204R;R203K 134;124 139;129 N 143 144 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. There have been concerns about the impact of D614G mutation on vaccine development but it is clear that the mutation does not take place in the receptor binding region of the spike protein which is the primary target of the neutralizing antibodies. 2021 Heliyon Discussion SARS_CoV_2 D614G 45 50 S 175 180 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. There two other functionally significant mutations which are Q57H in ORF3a and S194L in N protein. 2021 Heliyon Discussion SARS_CoV_2 Q57H;S194L 61;79 65;84 ORF3a;N 69;88 74;89 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. This finding is similar with other studies those reported R203K and G204R destabilizes N protein structure but may enhance interaction with SARS-CoV-2 Envelop protein that may promote viral release. 2021 Heliyon Discussion SARS_CoV_2 G204R;R203K 68;58 73;63 N 87 88 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. This may explain the spread of D614G or G clade in mostly Europe, America and recently in South Asia. 2021 Heliyon Discussion SARS_CoV_2 D614G 31 36 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. Those mutations include 3037C>T (98%), 14408C>T (98%) and 23403A>G (97%) where the last two are non-synonymous mutations (P4715L in ORF1ab or P323L in RdRp and D614G in Spike protein). 2021 Heliyon Discussion SARS_CoV_2 C14408T;A23403G;C3037T;D614G;P323L;P4715L 39;58;24;160;142;122 47;66;31;165;147;128 ORF1ab;S;RdRP 132;169;151 138;174;155 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. Though not in the receptor binding part of Spike protein, multiple studies reported that the D614G mutation provides the SARS-CoV-2 an evolutionary advantage for replication. 2021 Heliyon Discussion SARS_CoV_2 D614G 93 98 S 43 48 34458642 Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations. While some studies suggested that D614G mutation is associated with higher fatality rate, several other studies reported no significant association. 2021 Heliyon Discussion SARS_CoV_2 D614G 34 39 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. First, it accumulated a D614G mutation in the spike gene to enhance viral transmission. 2021 bioRxiv Discussion SARS_CoV_2 D614G 24 29 S 46 51 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Importantly, the unique P681R mutation plays a critical role in this fitness advantage and increases the processing of Delta spike to S1 and S2, most likely through an improved furin cleavage when newly assembled virions egress through the trans-Golgi network. 2021 bioRxiv Discussion SARS_CoV_2 P681R 24 29 S 125 130 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. In summary, using a reverse genetic system and primary human airway cultures, we have identified spike mutation P681R as a significant determinant for enhanced viral replication fitness of the Delta compared to the Alpha variant. 2021 bioRxiv Discussion SARS_CoV_2 P681R 112 117 S 97 102 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Subsequently, another spike mutation N501Y emerged independently in Alpha, Beta, and Gamma variants from the United Kingdom, South Africa, and Brazil, respectively. 2021 bioRxiv Discussion SARS_CoV_2 N501Y 37 42 S 22 27 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. The N501Y mutation further increases the binding affinity between the spike protein and ACE2, leading to additional improvement in viral transmission. 2021 bioRxiv Discussion SARS_CoV_2 N501Y 4 9 S 70 75 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. The P681R mutation enhances spike protein processing through the improved furin cleavage site. 2021 bioRxiv Discussion SARS_CoV_2 P681R 4 9 S 28 33 34462752 Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. The P681R substitution clearly augments spike processing and is likely the main driver of the fitness advantage observed in Delta variant. 2021 bioRxiv Discussion SARS_CoV_2 P681R 4 9 S 40 45 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. Five isolates with the ORF8 L84S mutation also had N gene S202N. 2021 PloS one Discussion SARS_CoV_2 L84S;S202N 28;58 32;63 ORF8;N 23;51 27;52 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. Interestingly, variant (241C > T) of the 5'UTR region often coexists with spike glycoprotein variant (S protein, D614G). 2021 PloS one Discussion SARS_CoV_2 D614G;C241T 113;24 118;32 S;5'UTR;S 74;41;102 92;46;103 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. L lineage isolates exhibiting L3606F mutations were first reported on January 2020 in China and associated with super spreader events in the USA, Singapore, Japan, and Europe. 2021 PloS one Discussion SARS_CoV_2 L3606F 30 36 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. L3606F is not typical of GH the clade, and is a transitory mutation defining L to S clade divergence, possibly identifying further evolutionary transitions in this isolate. 2021 PloS one Discussion SARS_CoV_2 L3606F 0 6 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. N gene P13L was present in both S clade and A lineage isolates in this study, it has been previously reported from the UK and Australia. 2021 PloS one Discussion SARS_CoV_2 P13L 7 11 N;S 0;32 1;33 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. One strain had two S gene mutations, D614G and L5F. 2021 PloS one Discussion SARS_CoV_2 D614G;L5F 37;47 42;50 S 19 20 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. P4715L and D614G containing isolates have shown significant positive correlations with fatality rates in many countries. 2021 PloS one Discussion SARS_CoV_2 D614G;P4715L 11;0 16;6 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. Recently reported spectrum of mutations mainly spike 69/70 deletion, E484K and N501Y variants in B.1 lineage strains, have revealed a role for mutations in driving virulence of the virus by impacting host infection, transmission, diagnostics and vaccine escape. 2021 PloS one Discussion SARS_CoV_2 E484K;N501Y 69;79 74;84 S 47 52 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. Recently reported spectrum of mutations mainly spike 69/70 deletion, E484K and N501Y variants in B.1 lineage strains, have revealed a role for mutations in driving virulence of the virus by impacting host infection, transmission, diagnostics, and vaccine escape. 2021 PloS one Discussion SARS_CoV_2 E484K;N501Y 69;79 74;84 S 47 52 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. The 241C > T mutation has been reported to result in the strong binding of TARDBP (RNA/DNA-binding protein) to the 5'UTR region of the SARS CoV2 virus. 2021 PloS one Discussion SARS_CoV_2 C241T 4 12 5'UTR 115 120 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. The D614G mutation has also been associated with greater mortality observed in Belgium, Spain, Italy, France, Netherlands and Switzerland. 2021 PloS one Discussion SARS_CoV_2 D614G 4 9 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. The D614G mutation in S gene was present in the majority (76%) of the genomes studied here and reported globally. 2021 PloS one Discussion SARS_CoV_2 D614G 4 9 S 22 23 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. The frequency of P4715L has been shown to differ between SARS-CoV-2 genomes isolated from the USA (63.0%) and China (11.2%) and have been attributed to the differential efficacy observed in the clinical trials of the antiviral agent Remdesivir. 2021 PloS one Discussion SARS_CoV_2 P4715L 17 23 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. The L84S mutation is common amongst S clade isolates found in Europe where it was found to co-evolve with mutations such as P323L. 2021 PloS one Discussion SARS_CoV_2 L84S;P323L 4;124 8;129 S 36 37 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. The most common non-synonymous variants observed were S D614G, Orf1ab RdRp gene P4715L and, Orf3a Q57H which have previously been reported from Europe and the United States. 2021 PloS one Discussion SARS_CoV_2 D614G;P4715L;Q57H 56;80;98 61;86;102 ORF1ab;ORF3a;RdRP;S 63;92;70;54 69;97;74;55 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. The RdRp variant P4715L was present in 72% of all isolates. 2021 PloS one Discussion SARS_CoV_2 P4715L 17 23 RdRP 4 8 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. This coexistence is also evident in our study as we found 4 GH clade strains and a V clade strain to have the 5' UTR variant +241 C>T. 2021 PloS one Discussion SARS_CoV_2 C241T 125 133 5'UTR 110 116 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. Two S clade strains had the 3' UTR + 29742 G>A. 2021 PloS one Discussion SARS_CoV_2 G29742A 37 46 3'UTR;S 28;4 34;5 34464419 Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. We observed a GH isolate from May to have Orf1ab L3606F mutation co-occurring with P323L. 2021 PloS one Discussion SARS_CoV_2 L3606F;P323L 49;83 55;88 ORF1ab 42 48 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. Although mutations such as these that abrogate 2C08 binding currently are rare among clinical isolates, viruses carrying the F486L mutation have been isolated from farmed mink and could be transmitted to humans. 2021 Immunity Discussion SARS_CoV_2 F486L 125 130 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. Indeed, we found that virus recovered from the lungs of the B.1.351-challenged hamster with the highest viral titer in the 2C08-treated group had developed a G476S mutation. 2021 Immunity Discussion SARS_CoV_2 G476S 158 163 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. One possibility is that 2C08 more readily selected for a partial escape mutant among viruses displaying the B.1.351 variant spike than the WA1/2020 D614G or B.1.617.2 spikes. 2021 Immunity Discussion SARS_CoV_2 D614G 148 153 S;S 124;167 129;173 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. Several have been shown to bind RBD and neutralize D614G as well as the B.1.1.7 and B.1.351 variants. 2021 Immunity Discussion SARS_CoV_2 D614G 51 56 RBD 32 35 34464596 A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. We note that somewhat higher levels of lung viral RNA were recovered from the 2C08-treated animals challenged with the Wash-B.1.351 variant compared with those challenged with the D614G or B.1.617.2 strains. 2021 Immunity Discussion SARS_CoV_2 D614G 180 185 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. In other variants of concern, such as the B 1.351 and P.1 variants, the main mutations in the N protein are non-synonymous ones, such as T205I and P80R, respectively. 2021 Diagnostic microbiology and infectious disease Discussion SARS_CoV_2 P80R;T205I 147;137 151;142 N 94 95 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. In our series, the two cases positive for N501Y that were considered non-suspected cases by the VirSNiP assay could be a new or emerging variant, such as B.1.351 or P.1. 2021 Diagnostic microbiology and infectious disease Discussion SARS_CoV_2 N501Y 42 47 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. Other mutations detected in all samples analyzed, such as M1X, R203K and G204R, could affect the amplification efficiency of the N-gene target. 2021 Diagnostic microbiology and infectious disease Discussion SARS_CoV_2 G204R;M1X;R203K 73;58;63 78;61;68 N 129 130 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. The mutations most frequently detected in the N protein of VOC B.1.1.7 are D3L and S235F. 2021 Diagnostic microbiology and infectious disease Discussion SARS_CoV_2 D3L;S235F 75;83 78;88 N 46 47 34464903 Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. Two studies found that the C29200A mutation may be responsible for failure of amplification of the N gene by Cepheid's Xpert assay. 2021 Diagnostic microbiology and infectious disease Discussion SARS_CoV_2 C29200A 27 34 N 99 100 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. It is a known fact that the E484K mutation affects neutralization by convalescent-phase sera or monoclonal antibodies (MAbs). 2021 mBio Discussion SARS_CoV_2 E484K 28 33 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. Similarly, the combination mutation of K417N and N501Y affects neutralization by MAbs and convalescent-phase sera. 2021 mBio Discussion SARS_CoV_2 K417N;N501Y 39;49 44;54 34465019 Evolution, Mode of Transmission, and Mutational Landscape of Newly Emerging SARS-CoV-2 Variants. We have also evaluated the structural landscape of several significant mutations (E484K, K417T/N, N501Y, and D614G) in the emerging variants. 2021 mBio Discussion SARS_CoV_2 D614G;K417N;K417T;N501Y;E484K 109;89;89;98;82 114;96;96;103;87 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Also, we can hardly rule out the possibility that D614G variation may cause a larger extent of force-induced rotational conformational changes of RBD, thereby resulting in a longer force-dependent bond lifetime of SARS2-S/ACE2 binding. 2021 Cell research Discussion SARS_CoV_2 D614G 50 55 RBD;S 146;220 149;221 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Another alternative explanation is that ACE2 sequentially binds with each up RBD of SARS2-SD614G via sliding-rebinding mechanism. 2021 Cell research Discussion SARS_CoV_2 D614G 91 96 RBD 77 80 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. As the D614G variation disrupts stable contact between inter-protomers to allosterically favor more SARS2-RBD up conformation, this enhancement of force-dependent recognition might be due to the synergistic effect of two or three up RBDs in a single SARS2-S trimer. 2021 Cell research Discussion SARS_CoV_2 D614G 7 12 RBD;RBD;S 106;233;256 109;237;257 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Impairment of inter-protomer interactions by the D614G variation not only strengthens force-dependent SARS2-S/ACE2 binding, but more importantly, induces S1/S2 detachment much faster than in the WT protein under force, providing a new molecular explanation for the high infectivity of the SARS2 D614G variant. 2021 Cell research Discussion SARS_CoV_2 D614G;D614G 49;295 54;300 S 108 109 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. One plausible explanation is that the S1 subunits of all three protomers in the D614G variant are more flexible such that it may release the spatial restriction to allow more than one RBD binding with ACE2 dimer simultaneously. 2021 Cell research Discussion SARS_CoV_2 D614G 80 85 RBD 184 187 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. Second, we propose that the D614G variation of SARS2-S could allosterically strengthen its binding with ACE2 under force and simultaneously enhance the force-accelerated S1/S2 detachment, which might favor effective viral infection. 2021 Cell research Discussion SARS_CoV_2 D614G 28 33 S 53 54 34465913 Mechanical activation of spike fosters SARS-CoV-2 viral infection. To conclude, we demonstrate that mechanical force counter-intuitively impedes SARS2-S/ACE2 dissociation and induces subsequent S1/S2 rapid detachment for effective viral infection, and that D614G variation further enhances this mechano-regulation to increase SARS2 infectivity. 2021 Cell research Discussion SARS_CoV_2 D614G 190 195 S 84 85 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. (1) a bit more distant linkage for variant V18 was also correctly predicted by assigning V18 to cluster C8, such as variant V18 might have evolved (directly or indirectly) from V1 upon substitutions: L18F and P812L. 2021 Meta gene Discussion SARS_CoV_2 L18F;P812L 200;209 204;214 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. As variant V20 lost D614G mutation which is the key mutation that is associated to enhanced SARS-CoV-2 replication in human lung epithelial cells and primary human airway tissues, reduced infectivity may be associated to V20. 2021 Meta gene Discussion SARS_CoV_2 D614G 20 25 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Given that P681H mutation enhances SARS-CoV-2 binding affinity towards the cell that results in increased infectivity, the absence of P681H mutation for V22, V9 and V23 may result in reduced infectivity. 2021 Meta gene Discussion SARS_CoV_2 P681H;P681H 11;134 16;139 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Given that V10 emerged from V5, then D1118H deletion must had occurred in V5. 2021 Meta gene Discussion SARS_CoV_2 D1118H 37 43 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Here I suggest that variant V12 emerged upon D614G deletion in V1, variant V13 upon E96D substitution in V1, variant V15 upon P809S substitution in V1 and variant V19 upon L5F substitution in N-terminal domain of V1. 2021 Meta gene Discussion SARS_CoV_2 D614G;E96D;L5F;P809S 45;84;172;126 50;88;175;131 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. In particular, variant V3 replacedV70 with V70I and most likely the absence ofV70 in the commonly found B.1.1.7HV [69, 70] spike deletion pair was compensated by deletion of Isoleucine at the nearby position 68:I68. 2021 Meta gene Discussion SARS_CoV_2 V70I 43 47 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. In this case variant V8 is suggested as likely parental strain for variants: V16, V21 and V24, such as: V16 is predicted to emerged from V8 upon S943I substitution in V8, V21 upon E96D substitution in V8 and V24 upon A653V substitution in V8. 2021 Meta gene Discussion SARS_CoV_2 A653V;E96D;S943I 217;180;145 222;184;150 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. In this case, variant V2 is suggested as likely parental strain for variant V6, as variant V6 might have been transformed from variant V2 upon S155G substitution. 2021 Meta gene Discussion SARS_CoV_2 S155G 143 148 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. On the other hand, given that V10 emerged from V7, then S982A deletion must had occurred in V7. 2021 Meta gene Discussion SARS_CoV_2 S982A 56 61 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. On the other hand, variant V20 profiles most deletions of defining amino acid substitutions: A570D, D614G and T716I. 2021 Meta gene Discussion SARS_CoV_2 A570D;D614G;T716I 93;100;110 98;105;115 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Reduced infectivity may be associated to V12, as variant V12 lost D614G mutation. 2021 Meta gene Discussion SARS_CoV_2 D614G 66 71 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Since A570D mutation eases close to open spike conformational update, no amplification of infectivity than already introduced by D614G mutation can be attached to variants: V24, V21, V8 and V16. 2021 Meta gene Discussion SARS_CoV_2 A570D;D614G 6;129 11;134 S 41 46 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Suggestion that variant V23 might have been transformed from V9 upon E96D substitution is made. 2021 Meta gene Discussion SARS_CoV_2 E96D 69 73 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. The absence of P681H mutation in this case can be associated to decreased SARS-CoV-2 binding affinity towards host cell, what is expected to result in reduced infectivity and mild up to moderate clinical presentation. 2021 Meta gene Discussion SARS_CoV_2 P681H 15 20 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Variant V11 is predicted to emerged from V4 upon deletion of defining P681H substitution. 2021 Meta gene Discussion SARS_CoV_2 P681H 70 75 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Variants assigned to cluster C5 are missing A570D defining mutation. 2021 Meta gene Discussion SARS_CoV_2 A570D 44 49 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. Variants V22, V9 and V23 are missing P681H defining substitution. 2021 Meta gene Discussion SARS_CoV_2 P681H 37 42 34466389 Phylogenicity of B.1.1.7 surface glycoprotein, novel distance function and first report of V90T missense mutation in SARS-CoV-2 surface glycoprotein. while V22 can be also linked to V9, but two alterations must had happened: L18F non-defining substitution and deletion of S982A defining substitution. 2021 Meta gene Discussion SARS_CoV_2 L18F;S982A 75;122 79;127 34466655 Furin and the adaptive mutation of SARS-COV2: a computational framework. Presence of D614G mutation (video S1). 2021 Modeling earth systems and environment Discussion SARS_CoV_2 D614G 12 17 34467913 An innovative approach for the non-invasive surveillance of communities and early detection of SARS-CoV-2 via solid waste analysis. A222V is characteristic of clade GV, lineage B.1.177 (GISAID) or 20E.EU1 (Nexstrain), which emerged in the early summer of 2020 in Spain and subsequently spread to multiple locations in Europe, possibly introduced into other countries by summer tourists. 2021 The Science of the total environment Discussion SARS_CoV_2 A222V 0 5 34467913 An innovative approach for the non-invasive surveillance of communities and early detection of SARS-CoV-2 via solid waste analysis. Instead, based on GISAID data, the amino acid mutation P521S has only been detected 119 times (0.01% of all samples with spike sequences) in 25 countries to date. 2021 The Science of the total environment Discussion SARS_CoV_2 P521S 55 60 S 121 126 34467913 An innovative approach for the non-invasive surveillance of communities and early detection of SARS-CoV-2 via solid waste analysis. The spike amino acid mutation A222V is common in SARS-CoV-2 sequences. 2021 The Science of the total environment Discussion SARS_CoV_2 A222V 30 35 S 4 9 34467913 An innovative approach for the non-invasive surveillance of communities and early detection of SARS-CoV-2 via solid waste analysis. This mutation has been detected in five sequences found in the Italian regions of Apulia, Abruzzo, and Veneto, and four of these sequences carry the A222V substitution. 2021 The Science of the total environment Discussion SARS_CoV_2 A222V 149 154 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. Energy-based epitope prediction through the MLCE approach reveals a common theme across variants: the number and surface exposure of potentially immunoreactive regions decrease in S protein mutants compared to the reference D641G. 2021 Journal of chemical information and modeling Discussion SARS_CoV_2 D641G 224 229 S 180 181 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. In fact, N439K RBD forms a new interaction with the human ACE2 receptor (hACE2) and has enhanced affinity for hACE2. 2021 Journal of chemical information and modeling Discussion SARS_CoV_2 N439K 9 14 RBD 15 18 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. In particular, the number of residues defining the epitope located in the long RBD loop (residues 417-503, recognized by many protective Abs) is much lower in mutants 501Y.V2.noDelta, B1.1.28, and N439K (see Figures 2 and 3, Table S2). 2021 Journal of chemical information and modeling Discussion SARS_CoV_2 N439K 197 202 RBD 79 82 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. In the case of the mutation N439K, it has been reported that this variant maintains fitness while evading antibodies immunity. 2021 Journal of chemical information and modeling Discussion SARS_CoV_2 N439K 28 33 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. The E484K mutation is of particular concern due to its location within nAb epitopes, and it has been shown to reduce or eliminate binding to many potent RBD-directed nAbs. 2021 Journal of chemical information and modeling Discussion SARS_CoV_2 E484K 4 9 RBD 153 156 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. The salt bridge at the RBD-hACE2 interface (RBD N439K/hACE2 E329) plausibly adds a strong interaction at the binding interface during viral cell entry. 2021 Journal of chemical information and modeling Discussion SARS_CoV_2 N439K 48 53 RBD;RBD 23;44 26;47 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. Two striking examples are the loss or reduction of epitopes determined by the N439K and E484K mutations. 2021 Journal of chemical information and modeling Discussion SARS_CoV_2 E484K;N439K 88;78 93;83 34468141 SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern. Upon sequence variation, the protein shifts to states characterized by different intramolecular interactions compared to the initial D614G structure; this transition decreases the number of energetically uncoupled substructures available for engaging interactors such as Abs. 2021 Journal of chemical information and modeling Discussion SARS_CoV_2 D614G 133 138 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. For the first time, we showed the positive association of higher anti-S2 IgG levels with the SNV NSP3 D218E. 2021 GeroScience Discussion SARS_CoV_2 D218E 102 107 Nsp3 97 101 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. Furthermore, patients with chronic lung disease infected with SARS-CoV-2 bearing the non-synonymous SNV N E253A appear to have a longer symptom duration. 2021 GeroScience Discussion SARS_CoV_2 E253A 106 111 N 104 105 Chronic lung disease 27 47 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. In particular, the D614G exchange in the S protein has been extensively studied and is postulated to provide a selection advantage through increased viral infectivity. 2021 GeroScience Discussion SARS_CoV_2 D614G 19 24 S 41 42 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. The prediction of taste and smell disorders by the non-synonymous SNV NSP12 Q444H (OR 5.4) without confounders is another example in this study that genetic changes may influence the clinical presentation of COVID-19. 2021 GeroScience Discussion SARS_CoV_2 Q444H 76 81 Nsp12 70 75 COVID-19 208 216 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. We observed four variants present in all samples (ORF1ab F924F, ORF1ab P4715L, S D614G and 5'UTR 241C > T), representing signature variants of the most dominant SARS-CoV-2 type VI strain. 2021 GeroScience Discussion SARS_CoV_2 C241T;D614G;F924F;P4715L 97;81;57;71 105;86;62;77 ORF1ab;5'UTR;S 64;91;79 70;96;80 34468954 Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics. While the occurrence of bronchial secretions was only associated with blood type A, the absence of the non-synonymous SNV ORF3a S177I was a confounder for the appearance of cough. 2021 GeroScience Discussion SARS_CoV_2 S177I 128 133 ORF3a 122 127 34472141 Pseudoephedrine and its derivatives antagonize wild and mutated severe acute respiratory syndrome-CoV-2 viruses through blocking virus invasion and antiinflammatory effect. Recently, a mutation called D614G is relevant to virus transmissibility enhancement and also opens a potential binding pocket at the interface of spike protein (Ostrov, ). 2021 Phytotherapy research Discussion SARS_CoV_2 D614G 28 33 S 146 151 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. In summary, our results suggest that the RBD from the original strain isolated in Wuhan requires lower temperature for optimal interaction with ACE2, whereas the N501Y mutation frees RBD from this requirement. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 N501Y 162 167 RBD;RBD 41;183 44;186 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. The majority of them bound better to ACE2 at physiological temperature, notably for lineages harboring the N501Y mutation (B.1.1.7, B.1.351, and P.1) or the L452R mutation (B.1.617.2 and B.1.429). 2021 The Journal of biological chemistry Discussion SARS_CoV_2 L452R;N501Y 157;107 162;112 34478710 Impact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2. While all emerging variants bound better to ACE2 at low temperature, their sensitivity to cold temperature was less pronounced, especially for those harboring the N501Y mutation. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 N501Y 163 168 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. Additionally, we speculate that the decreased neutralization activities of A475V and E484Q might be due to their resistance to some mAbs. 2021 Frontiers in immunology Discussion SARS_CoV_2 A475V;E484Q 75;85 80;90 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. However, we also found that certain variants with a single amino acid mutation (e.g., A475V and E484Q) might be able to escape neutralization by plasma from COVID-19 recovered patients. 2021 Frontiers in immunology Discussion SARS_CoV_2 A475V;E484Q 86;96 91;101 COVID-19 157 165 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. In paired neutralization analysis of the Wuhan reference and D614G variant pseudoviruses, we found that the D614G variant pseudovirus was more sensitive to neutralization by the convalescent plasma (Figure 5). 2021 Frontiers in immunology Discussion SARS_CoV_2 D614G;D614G 61;108 66;113 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. Previous study revealed that the percentage of RBD "up" conformation in the G614 spike was higher than that in the D614 spike, which might explain that the D614G variant is more infectious while more sensitive to neutralization. 2021 Frontiers in immunology Discussion SARS_CoV_2 D614G 156 161 S;S;RBD 81;120;47 86;125;50 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. The neutralizing activity of mAb B38 against A475V mutant was reduced 10,000 folds when compared with the wild type virus (Figure 6), while the efficacy of mAb 2-4 in neutralizing the E484Q mutant also decreased up to 1,000 folds (Figure 6). 2021 Frontiers in immunology Discussion SARS_CoV_2 A475V;E484Q 45;184 50;189 34484190 Crucial Mutations of Spike Protein on SARS-CoV-2 Evolved to Variant Strains Escaping Neutralization of Convalescent Plasmas and RBD-Specific Monoclonal Antibodies. Therefore, we suspect that D614G and possibly other sensitive variants might not be challenges for current COVID-19 vaccines. 2021 Frontiers in immunology Discussion SARS_CoV_2 D614G 27 32 COVID-19 107 115 34492088 Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination. Although more data are needed to elucidate the evolution of SARS-CoV-2 variants in minks, the independent presence of Y453F in Greek mink farms suggests its positive selection for mink-specific mutations. 2021 PLoS pathogens Discussion SARS_CoV_2 Y453F 118 123 34492088 Outbreaks of SARS-CoV-2 in naturally infected mink farms: Impact, transmission dynamics, genetic patterns, and environmental contamination. Most single-nucleotide polymorphisms (SNPs) found within the S gene were mostly accumulated in the spike protein RBM region, with the mink-specific amino-acid substitution (S-Y453F) being present in all sequenced genomes. 2021 PLoS pathogens Discussion SARS_CoV_2 Y453F 175 180 S;S;S 99;61;173 104;62;174 34495697 A Bifluorescent-Based Assay for the Identification of Neutralizing Antibodies against SARS-CoV-2 Variants of Concern In Vitro and In Vivo. We also generated rSARS-CoV-2 mCherry SA, an mCherry-expressing rSARS-CoV-2 strain containing the K417N, E484K, and N501Y mutations in the RBD of the S glycoprotein of the SA VoC. 2021 Journal of virology Discussion SARS_CoV_2 E484K;K417N;N501Y 105;98;116 110;103;121 S;RBD 150;139 164;142 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. A similar lack of effect of the D614G mutation on titer was also reported in another study using a 21-amino-acid deletion of the Spike protein cytoplasmic tail in VSV pseudovectors. 2021 Journal of virology Discussion SARS_CoV_2 D614G 32 37 S 129 134 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. Finally, we also used the VSV pseudovectors to evaluate the impact of the D614G mutation on infectivity of different cell types and sensitivity to antibody neutralization. 2021 Journal of virology Discussion SARS_CoV_2 D614G 74 79 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. In an alternative model, the D614G mutation could alter the structure and/or stability of the Spike trimer by abrogating the hydrogen bond connecting D614 in the S1 subunit of one monomer with T859 in the S2 subunit of a neighboring monomer. 2021 Journal of virology Discussion SARS_CoV_2 D614G 29 34 S 94 99 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. In summary, we found that although cytoplasmic tail truncations enhance SARS-CoV-2 Spike protein incorporation into both LV and VSV vectors and enhance the titers of unconcentrated vectors, they can also mask the phenotype of the D614G mutation. 2021 Journal of virology Discussion SARS_CoV_2 D614G 230 235 S 83 88 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. Specifically, we found that the impact of the D614G mutation on Spike protein incorporation and vector titer was obscured by the cytoplasmic tail truncation. 2021 Journal of virology Discussion SARS_CoV_2 D614G 46 51 S 64 69 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. The mechanism for enhanced incorporation and/or titer by D614G is not entirely understood, but structural analyses have suggested that it could impact Spike protein structure and stability, both within and between Spike monomers. 2021 Journal of virology Discussion SARS_CoV_2 D614G 57 62 S;S 151;214 156;219 34495700 Cytoplasmic Tail Truncation of SARS-CoV-2 Spike Protein Enhances Titer of Pseudotyped Vectors but Masks the Effect of the D614G Mutation. This is in agreement with the majority of reports testing the impact of the D614G mutation with full-length Spike pseudovectors or SARS-CoV-2 virus against human convalescent serum, serum from convalescent animals, or vaccinated humans or animals. 2021 Journal of virology Discussion SARS_CoV_2 D614G 76 81 S 108 113 34495709 Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. In this study, we observed the emergence of lineage B.1.575.2 with the spike E484K mutation, circulating in Pamplona in association with an outbreak. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 E484K 77 82 S 71 76 34495709 Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. The E484K mutation has been identified in SARS-CoV-2 variants considered VOCs, such as B.1.351, P.1, and B.1.1.7+E484K and in VOI variants, such as B.1.525, B.1.620, and B1.621, among others; therefore, the presence of this mutation should be monitored. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 E484K;E484K 4;113 9;118 34495709 Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. The E484K mutation is considered one of the most important substitutions associated with reduced antibody neutralization potency and efficacy of the SARS-CoV-2 vaccine. 2021 Journal of clinical microbiology Discussion SARS_CoV_2 E484K 4 9 34495709 Emergence of SARS-CoV-2 Variant B.1.575.2, Containing the E484K Mutation in the Spike Protein, in Pamplona, Spain, May to June 2021. This genetic variant includes a mutation in the spike protein (E484K). 2021 Journal of clinical microbiology Discussion SARS_CoV_2 E484K 63 68 S 48 53 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. After Alpha, the second main VOC detected was Beta in October 2020 in the South African population, and it had five main mutations, which were reported to be beneficial for transmission:L18F, K417N, E484K, N501Y and D614G. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G;E484K;K417N;N501Y;L18F 216;199;192;206;186 221;204;197;211;190 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. Alpha, the first VOC initially discovered in September 2020 in the UK population has four main mutations (H69-, V70-, N501Y and D614G) in the spike protein. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G;N501Y 128;118 133;123 S 142 147 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. Further, it was found that the L45R, E484Q and T478K mutations are highly energetically favourable for the spike protein based on the prime energy calculations of the mutated residues. 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484Q;L45R;T478K 37;31;47 42;35;52 S 107 112 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. Further, when the Kappa spike mutant was tried to be neutralized with Pfizer vaccine sera, it was found that E484K conferred a ten-fold reduction in neutralisation, E484Q had a slightly milder yet significant impact, however, with E484Q and L452R combined, there was a statistically significant loss of sensitivity. 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484K;E484Q;E484Q;L452R 109;165;231;241 114;170;236;246 S 24 29 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. In a recent study on B.1.617 lineages, it has been shown that the P681R has highest impact in increasing the fusion activity, followed by E484K and L452R. 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484K;L452R;P681R 138;148;66 143;153;71 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. In a recent study, where 12 monoclonal antibodies were tested for their neutralizing activity against Alpha and Beta variants, it was found that N501Y of Alpha variant modulated interaction of neutralizing antibodies only, while in case of Beta, complete loss of activity was observed in most of the antibodies, mediated by K417N and E484K, in comparison to wildtype. 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484K;K417N;N501Y 334;324;145 339;329;150 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. Several studies including the current one has indicated that N501Y mutation is the main reason behind the increase of Alpha transmission. 2021 International journal of molecular sciences Discussion SARS_CoV_2 N501Y 61 66 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. Similarly, previous studies have reported that L452R, E484Q/K, P681R and T478K might have role in the increased transmissibility, while the molecular level rationale is not clear. 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484Q;E484K;L452R;P681R;T478K 54;54;47;63;73 61;61;52;68;78 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. The B.1.617.1 is characterized by E154K, L452R, E484Q, D614G, P681R, Q1071H mutations in the spike protein. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G;E154K;E484Q;L452R;P681R;Q1071H 55;34;48;41;62;69 60;39;53;46;67;75 S 93 98 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. The comparative MM/GBSA binding energy calculations of N501Y reported here positively correlate with the available experimental absolute binding free energy reported elsewhere. 2021 International journal of molecular sciences Discussion SARS_CoV_2 N501Y 55 60 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. The N501Y and D614G was conserved in both Alpha and Beta VOC and are believed to be crucial mutations for their higher transmission and infectivity. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G;N501Y 14;4 19;9 34502041 Possible Link between Higher Transmissibility of Alpha, Kappa and Delta Variants of SARS-CoV-2 and Increased Structural Stability of Its Spike Protein and hACE2 Affinity. The results of binding free energy calculations suggested that E484Q and N501Y mutations are crucial for increasing the binding affinity. 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484Q;N501Y 63;73 68;78 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. For example, one of the most well-studied and dominant emerging mutations in the spike protein of the SARS-CoV-2 virus is D614G. 2021 Biochimie Discussion SARS_CoV_2 D614G 122 127 S 81 86 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. From all of these results the main superimposition change that happened at the overall 3D structure of the spike protein was due to the presence and effect of D614G only. 2021 Biochimie Discussion SARS_CoV_2 D614G 159 164 S 107 112 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. However, some variants that have destabilized the protein with increased flexibility (e.g., E484K, K417 N, E484Q, Q675P, and Q675H) might impact the virus's ability to escape the antibodies neutralization by changing the antigenicity drift of the protein 3D structure; this is in agreement with a previous study. 2021 Biochimie Discussion SARS_CoV_2 E484K;E484Q;K417N;Q675H;Q675P 92;107;99;125;114 97;112;105;130;119 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. In addition to Cluster B, Cluster D (20A) included Alpha, Beta, Delta, Kappa; the Cluster C 20A/S.L18F or 20A/S.D583E included Gamma, Epsilon, Iota, Eta; and Cluster A included only the 20A/S.Q675H as shown in. 2021 Biochimie Discussion SARS_CoV_2 D583E;L18F;Q675H 112;98;192 117;102;197 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. Interestingly, the mutation 20A/S.Q675H showed a profound superimposition change with up to 20 A even when compared with a reference sequence of clade 20A, as shown in Table 4. 2021 Biochimie Discussion SARS_CoV_2 Q675H 34 39 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. Interestingly, the NMA analysis results show that some variants are stabilizing but with an increased flexibility effect, for example, D080A, A701V, and D614G that might have an impact on improving the viral fitness and transmissibility by increasing its ability to bind with its receptor. 2021 Biochimie Discussion SARS_CoV_2 A701V;D614G 142;153 147;158 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. It is noteworthy that the clade Lambda has a novel deletion, S.Delta247-253, located at the N-terminal domain in addition to L452Q and F490S mutations in the RBD of the spike protein; this might explain why the conformational change in Lambda has included a formation of new a Beta sheet at the RBD. 2021 Biochimie Discussion SARS_CoV_2 F490S;L452Q 135;125 140;130 S;RBD;RBD;N;S 169;158;295;92;61 174;161;298;93;62 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. It is well-noticed that the mutation D614G is found in all clades reported in the Nextstrain database as mentioned in the introduction; this has led us to question if the current emergency use authorization (EUA)-vaccines have taken into consideration the vaccine design to be effective against the D614G as a basal and dominant mutation or even other mutations of interest. 2021 Biochimie Discussion SARS_CoV_2 D614G;D614G 37;299 42;304 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. Moreover, the results from DynaMut thermodynamic predictions indicated 10 variants had destabilized the spike protein (e.g., E484K, K417 N, V1176F, E484Q, Q675P, and Q675H), two of them, the E484K and the V1176F, have been found among Gamma and Theta variants. 2021 Biochimie Discussion SARS_CoV_2 E484K;E484K;E484Q;K417N;Q675H;Q675P;V1176F;V1176F 125;191;148;132;166;155;140;205 130;196;153;138;171;160;146;211 S 104 109 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. On the other hand, the partners C480 with C488, where the mutations E484K and E484Q are located, are both collectively expected to increase the flexibility of the 3D structure of the RBD. 2021 Biochimie Discussion SARS_CoV_2 E484K;E484Q 68;78 73;83 RBD 183 186 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. Previous reports hypothesized that the mutation D614G impacts viral fitness and infectivity. 2021 Biochimie Discussion SARS_CoV_2 D614G 48 53 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The DALI, SuperPose and TM-scores showed that the subclades with D614G have the same structural similarity compared with the single mutation of D614G (clade 20A). 2021 Biochimie Discussion SARS_CoV_2 D614G;D614G 65;144 70;149 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The mutation Q675H located in the Pre-Furin cleavage site in the spike protein, with the highest destabilizing ability, has appeared in Bangladesh in late 2020. 2021 Biochimie Discussion SARS_CoV_2 Q675H 13 18 S 65 70 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The results of MAESTRO in this study revealed the cysteine disulphide partners in the receptor binding domain (RBD); C391 with C525 where the mutations K417 N, N439K, L452R, Y453F, S477F, N501Y, and N501T among the top ten global frequency ranking are located, all collectively are expected to decrease the flexibility of the 3D structure of the RBD of the spike protein due to a notable change in the interatomic interaction. 2021 Biochimie Discussion SARS_CoV_2 K417N;L452R;N439K;N501T;N501Y;S477F;Y453F 152;167;160;199;188;181;174 158;172;165;204;193;186;179 RBD;S;RBD;RBD 86;357;111;346 109;362;114;349 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The results of our analysis on DALI, SuperPose v 1.0 and TM-score servers have revealed that the single dominant mutation the D614G has changed the whole structural similarity matrix (Dali Z-scores). 2021 Biochimie Discussion SARS_CoV_2 D614G 126 131 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The variant N501Y showed the highest frequency in the RBD with around 711234 counts as displayed on the SARS-CoV-2 mutation tracker of genome-wide analysis. 2021 Biochimie Discussion SARS_CoV_2 N501Y 12 17 RBD 54 57 34508827 Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines. The variant Q677H found among Eta variants has the highest stabilizing ability with decreased flexibility which might play a crucial biological function as it is located in the Pre-Furin cleavage site. 2021 Biochimie Discussion SARS_CoV_2 Q677H 12 17 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. Among them, some mutations, such as D614G and N501Y of SARS-CoV-2, T350G of HBV, and C659T of HVP-16, have been proved to play an important role in the viruses, indicating the reliability and effectiveness of AutoVEM2. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 D614G;N501Y 36;46 41;51 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. Besides, the N501Y variants may reduce the effectiveness of antibodies. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 N501Y 13 18 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. From the epidemic trend analysis, it showed that H1-4-1 and H1-4-2 with N501Y mutation on the S protein, which almost completely linked with the other 16 loci, had continued increasing from early December 2020 and became the dominant epidemic haplotypes in the United Kingdom and Europe by late February 2021. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 N501Y 72 77 S 94 95 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. Furthermore, The A2926G mutation we detected has been reported due to a reference genome sequencing error. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 A2926G 17 23 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. Several studies have reported that the N501Y mutant may reduce the neutralizing effect of the convalescent serum, suggesting that the N501Y variants may change neutralization sensitivity to reduce the effectiveness of the vaccine. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 N501Y;N501Y 39;134 44;139 34512928 AutoVEM2: A flexible automated tool to analyze candidate key mutations and epidemic trends for virus. Therefore, we should pay continuous attention to the N501Y mutant, which is almost completely linked with the other 16 loci. 2021 Computational and structural biotechnology journal Discussion SARS_CoV_2 N501Y 53 58 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. A large body of evidence indicates that the Delta variant (bearing the L452R/T478K double mutation) is the most and fastest-spreading variant in Europe and many countries and it will be the dominant one in the coming weeks. 2021 Cureus Discussion SARS_CoV_2 L452R;T478K 71;77 76;82 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. E484Q. 2021 Cureus Discussion SARS_CoV_2 E484Q 0 5 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. However, the Kappa variant (bearing the L452R/E484Q double mutation) or known as B.1.167.1, has raised red flags and led to widespread gene surveillance to look for its prevalence and spread. 2021 Cureus Discussion SARS_CoV_2 L452R;E484Q 40;46 45;51 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. L452R. 2021 Cureus Discussion SARS_CoV_2 L452R 0 5 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. Mutating the leucine residue at position 452 to an arginine seems at first to have no structural/functional effect, given that it occurs in an otherwise solvent-exposed region in the RBD and on the surface of an amphipathic beta-sheet. 2021 Cureus Discussion SARS_CoV_2 L452R 13 59 RBD 183 186 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. T478K. 2021 Cureus Discussion SARS_CoV_2 T478K 0 5 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. The mutant T478K appears to stabilize the receptor binding by forming a strong H-bond with Gln 24 of ACE2. 2021 Cureus Discussion SARS_CoV_2 T478K 11 16 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. The mutation of the glutamate residue at position 484 with glutamine is particularly interesting. 2021 Cureus Discussion SARS_CoV_2 E484Q 20 68 34513478 Probing the Increased Virulence of Severe Acute Respiratory Syndrome Coronavirus 2 B.1.617 (Indian Variant) From Predicted Spike Protein Structure. Variants bearing two of the above-mentioned mutations (L452R/E484Q in Kappa variant or L452R/T478K in Delta variant) do not seem to have structural changes compared to the wild-type spike protein, yet, their effect on the receptor-binding function seems to be enhanced. 2021 Cureus Discussion SARS_CoV_2 L452R;L452R;E484Q;T478K 87;55;61;93 92;60;66;98 S 182 187 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. A primer pair was designed (F3.CoV-2.S and R8.CoV-2.S), which amplified 172 bp-length regions containing the hotspot mutation of D614G within the S gene. 2021 Heliyon Discussion SARS_CoV_2 D614G 129 134 S;S;S 37;52;146 38;53;147 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. Furthermore, the qPCR-HRM method was proposed and is capable of detecting the D614G mutation by reliably distinguishing the D614 and G614 variants. 2021 Heliyon Discussion SARS_CoV_2 D614G 78 83 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. In conclusion, this study suggests that the D614G mutation of SARS-CoV-2 Spike protein can be detected by the qPCR-HRM assay, which will help to rapidly trace the circulating SARS-CoV-2 variants in certain locations. 2021 Heliyon Discussion SARS_CoV_2 D614G 44 49 S 73 78 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. Surveillance for the D614G mutation is important because the variant that contains this mutation, or the G614 variant, is more transmissible and has become the dominant variant of SARS-CoV-2 that has been circulated around the world, including Indonesia. 2021 Heliyon Discussion SARS_CoV_2 D614G 21 26 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. Surveillance of the mutations by DNA sequencing should be performed regularly to determine whether there are other mutations besides D614G, which might affect the HRM results. 2021 Heliyon Discussion SARS_CoV_2 D614G 133 138 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. The G614 variant carried the missense mutation 23403A > G (Reference Sequence = NC_04512.2), which allowed the higher melting temperature, as Guanine (G) base needs 3 hydrogen bonds to form a base pair, whereas Adenine (A) base needs only 2 hydrogen bonds. 2021 Heliyon Discussion SARS_CoV_2 A23403G 47 57 34514180 Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. This study described the qPCR-HRM analysis method as a sensitive method that can reliably detect D614G mutation in the S gene of SARS-CoV-2. 2021 Heliyon Discussion SARS_CoV_2 D614G 97 102 S 119 120 34515998 The first Italian outbreak of SARS-CoV-2 B.1.1.7 lineage in Corzano, Lombardy. Indeed, local restriction measures adopted resulted in a rapid decrease in reported cases of SARS-CoV-2 in Corzano and their efficacy is further attested by the lack of V551F mutation diffusion in the surrounding areas. 2022 Journal of medical virology Discussion SARS_CoV_2 V551F 169 174 34515998 The first Italian outbreak of SARS-CoV-2 B.1.1.7 lineage in Corzano, Lombardy. Of particular interest, the genomic sequencing revealed the presence of the V551F mutation in 5 out of 21 sequences, representing the first and only evidence of this mutation in the B.1.1.7 lineage in Italy. 2022 Journal of medical virology Discussion SARS_CoV_2 V551F 76 81 34515998 The first Italian outbreak of SARS-CoV-2 B.1.1.7 lineage in Corzano, Lombardy. Up to the end of March 2021, only 7 additional SARS-CoV-2 sequences belonging to B.1.1.7 lineage and carrying the V551F mutation were documented worldwide in the GISAID database. 2022 Journal of medical virology Discussion SARS_CoV_2 V551F 114 119 34518554 Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. Although this is present outside the functional region, the proximity of D614G to S1 cleavage site implicates an important change in the local environment. 2021 Scientific reports Discussion SARS_CoV_2 D614G 73 78 34518554 Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. An important substitution (Spike: D614G) was identified in seventeen SARS-CoV-2 sequences in this study. 2021 Scientific reports Discussion SARS_CoV_2 D614G 34 39 S 27 32 34518554 Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. Another important amino acid substitution P323L in RNA dependent RNA polymerase (RdRP) protein was recorded in 16 viral strains sequenced in this study. 2021 Scientific reports Discussion SARS_CoV_2 P323L 42 47 RdRp;RdRP 51;81 79;85 34518554 Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. Another study suggested role of spike protein D614G mutation in increasing dominance and providing structural advantage to the furin cleavage domain. 2021 Scientific reports Discussion SARS_CoV_2 D614G 46 51 S 32 37 34518554 Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. D614G mutation in spike protein is an interesting substitution and has been reported with increased tally. 2021 Scientific reports Discussion SARS_CoV_2 D614G 0 5 S 18 23 34518554 Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. However, experimental and in silico evidence suggests vaccines are unlikely to be affected by D614G mutation in SARS-CoV-2 spike protein. 2021 Scientific reports Discussion SARS_CoV_2 D614G 94 99 S 123 128 34518554 Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. In addition, the key mutation in spike protein (D614G) also involves loss of the charged group. 2021 Scientific reports Discussion SARS_CoV_2 D614G 48 53 S 33 38 34518554 Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. Other notable significance is the P13L variant (C28311T) in the nucleocapsid (N) protein which is one of the most crucial structural components of the SARS-CoV. 2021 Scientific reports Discussion SARS_CoV_2 P13L;C28311T 34;48 38;55 N;N 64;78 76;79 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Antibody titers against the wild-type D614G peaked 1 month after completion of the primary series and subsequently declined over the 5 months before the booster dose. 2021 Nature medicine Discussion SARS_CoV_2 D614G 38 43 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Neutralizing antibody titers against several VOCs (that is, B.1.351, P.1 and B.1.617.2) increased after the booster dose, with titers against several variants approaching or exceeding those measured after the primary series against the wild-type D614G virus. 2021 Nature medicine Discussion SARS_CoV_2 D614G 246 251 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Neutralizing antibody titers against the wild-type D614G virus after a booster dose were up to 4.4-fold higher than peak titers after the primary series. 2021 Nature medicine Discussion SARS_CoV_2 D614G 51 56 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. Of note, significantly higher neutralizing titers against wild-type D614G, B.1.427/B.1.429 and B.1.526 and statistically equivalent titers against B.1.351, P.1 and B.1.617.2 were measured 2 weeks after the booster dose compared to wild-type D614G neutralization measured 1 month after the primary series in participants who received the multivalent mRNA-1273.211 booster. 2021 Nature medicine Discussion SARS_CoV_2 D614G;D614G 68;241 73;246 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. The mRNA platform approach against SARS-CoV-2 VOCs in this trial appears to be effective in developing wild-type and variant-specific booster vaccines, with boosters increasing neutralizing titers against the wild-type D614G virus and against key VOCs and VOIs. 2021 Nature medicine Discussion SARS_CoV_2 D614G 219 224 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. The multivalent mRNA-1273.211 (50 microg) booster yielded a GMT ratio rise >=1 against all VOCs and VOIs 2 weeks after the booster dose versus peak wild-type D614G titers measured 1 month after the primary series vaccination. 2021 Nature medicine Discussion SARS_CoV_2 D614G 158 163 34526698 Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis. This rise was significant for B.1.427/B.1.429 and B.1.526, indicating that variant neutralization GMTs after the booster were higher than peak wild-type D614G virus GMTs after the primary series in the samples from this cohort, potentially increasing breadth of coverage against VOCs or VOIs. 2021 Nature medicine Discussion SARS_CoV_2 D614G 153 158 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. According to the Centers for Disease Control and Prevention (CDC), this variant, which may be associated with an increased risk of death (as much as twice as deadly as the wild type according to Challen and co-workers), is reported to have undergone at least six key mutations, of which only the asparagine tyrosine N501Y ( Figure 2) replacement falls within the binding motif of the RBD of the spike protein. 2022 Chembiochem Discussion SARS_CoV_2 N501Y 316 321 S;RBD 395;384 400;387 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. All spectral changes in this variant have already been dissected above, except for the K417T mutation, which, as expected, has the same effects as the K417N mutation, as shown in Figure 5. 2022 Chembiochem Discussion SARS_CoV_2 K417N;K417T 151;87 156;92 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. Asparagine has an uncharged -NH2 group and is considerably smaller than the -NH3 + charged lysine (Figure 3), then, the K417N replacement eliminates the positive charge and takes the interacting groups apart, effectively replacing the salt bridge with a very weak, long distance interaction according to the bond descriptors in Table 2. 2022 Chembiochem Discussion SARS_CoV_2 K417N 120 125 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. Calculated UV-Vis and CD spectra with environmental effects for the E484K and K417N mutations are shown in Figures 4 and 5 respectively. 2022 Chembiochem Discussion SARS_CoV_2 E484K;K417N 68;78 73;83 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. In fact, the E484K mutation allows the virus to find a much more favorable attachment site at E75, a helix position in ACE2 far from the initial K31 helical position. 2022 Chembiochem Discussion SARS_CoV_2 E484K 13 18 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. In summary, for the B.1.351 variant, despite the specific bonding descriptors listed in Table 2 for the K484 E75 replacement in the mutated virus being weaker than for the K417 D30 interaction in the wild type, the additional N501Y mutation and the conformational freedom gained by the elimination of the K417 D30 salt bridge, result in a larger virus cell affinity. 2022 Chembiochem Discussion SARS_CoV_2 N501Y 230 235 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. In the bonding motif of the RBD, a glutamate lysine E484K mutation defines this variant. 2022 Chembiochem Discussion SARS_CoV_2 E484K 52 57 RBD 28 31 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. Indeed, facilitated by this structural freedom, the E484K mutation (Figure 4) eliminates a relatively weak E484(s) K31(ACE2) interaction and originates one K484(S) E75(ACE2) salt bridge, which according to Table 2, leads to the strongest contact among all mutations studied here (even stronger than the hydrogen bond in the reference water dimer), described by a orbital interaction from the - group in E75 and a - group in K484. 2022 Chembiochem Discussion SARS_CoV_2 E484K 52 57 S;S 112;163 113;164 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. One serine asparagine mutation, S477N (Table 1, Figure 1), was found in the bonding motif of the RBD. 2022 Chembiochem Discussion SARS_CoV_2 S477N 32 37 RBD 97 100 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. Since threonine and asparagine have neutral groups as opposed to the charged - in lysine, and since both are quite smaller than lysine (Figures 3, 5), both K417N and K417T mutations have identical consequences in the ability of both variants to bind to ACE2. 2022 Chembiochem Discussion SARS_CoV_2 K417N;K417T 156;166 161;171 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. The effects of the N501Y mutation were analyzed in section 2.2. 2022 Chembiochem Discussion SARS_CoV_2 N501Y 19 24 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. The N501Y mutation leads to a blue-shifted Deltalambdamax 39 nm due to the replacement of the N501(S) K353 secondary HB by a similar Y501(S) K353 HB and to the newly added aromatic ring which originates fresh transitions. 2022 Chembiochem Discussion SARS_CoV_2 N501Y 4 9 S;S 100;141 101;142 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. The substitution of glutamate by lysine at the 484 position in the spike protein leads to a substantial change, that is, to the formation of the above analyzed K484(S) E75(ACE2) salt bridge. 2022 Chembiochem Discussion SARS_CoV_2 E484K 20 59 S;S 67;165 72;166 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. This results in a considerable increase of the Spike ACE2 affinity, to the point that this mutation alone, with no simultaneous mutations in the RBD, is enough to stabilize the mutated virus cell complex by more than 10 kcal/mol, when compared to the wild type, however, as shown by Khan et al., this affinity it is still lower than the P.1, B.1.351 cases, which contain the additional N501Y and K417N mutations. 2022 Chembiochem Discussion SARS_CoV_2 K417N;N501Y 400;390 405;395 S;RBD 47;147 52;150 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. Thus, under a molecular perspective, the net result of the N501Y mutation is that the collection of new interactions enhances the ability of the mutated virus to attach to host cells. 2022 Chembiochem Discussion SARS_CoV_2 N501Y 59 64 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. Within the RBD of the spike protein, asparagine tyrosine N501Y, lysine asparagine K417N, and glutamic acid lysine E484K mutations are found, with both N501Y and E484K occurring in the binding motif. 2022 Chembiochem Discussion SARS_CoV_2 E484K;E484K;K417N;N501Y;N501Y 114;161;82;57;151 119;166;87;62;156 S;RBD 22;11 27;14 34529328 The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective. Within the RBD, the B.1.351 and P.1 variants have both N501Y and E484K mutations in common, the only difference in this domain is that P.1 may have either the same K417N replacement as in the B.1.351 variant or a K417T mutation. 2022 Chembiochem Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y 65;164;213;55 70;169;218;60 RBD 11 14 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. Our results also indicate that the N501Y mutation affected one antibody binding and decreased its inhibition potency, in agreement with recent observations. 2021 Scientific reports Discussion SARS_CoV_2 N501Y 35 40 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. Recently reported variants B.1.1.7 (United Kingdom), B.1.351 (South Africa) and P.1 (Brazil) share the N501Y mutation within Spike RBD, which was recently associated with increased infectivity. 2021 Scientific reports Discussion SARS_CoV_2 N501Y 103 108 S;RBD 125;131 130;134 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. Surprisingly, although the presence of the E484K mutation did not significantly affect the RBD:ACE2 interaction. 2021 Scientific reports Discussion SARS_CoV_2 E484K 43 48 RBD 91 94 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. The evaluation of several RBD mutations in a competition assay indicated that two mutations, Y453F and N501Y, increased apparent affinity of RBD to ACE2 eight to tenfold compared to wild type RBD. 2021 Scientific reports Discussion SARS_CoV_2 N501Y;Y453F 103;93 108;98 RBD;RBD;RBD 26;141;192 29;144;195 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. The mutations E484K and N501Y are found in the B.1.351 (South Africa) and P.1 (Brazil) variants. 2021 Scientific reports Discussion SARS_CoV_2 E484K;N501Y 14;24 19;29 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. The Y453F mutation was originally identified in a variant isolated from farmed minks. 2021 Scientific reports Discussion SARS_CoV_2 Y453F 4 9 34531417 A bioluminescent and homogeneous SARS-CoV-2 spike RBD and hACE2 interaction assay for antiviral screening and monitoring patient neutralizing antibody levels. To evaluate the effect of these mutations on antibody binding and RBD:ACE2 PPI inhibition, we generated RBD-Fc variants containing the mutations Y453F, N501Y and E484K. 2021 Scientific reports Discussion SARS_CoV_2 E484K;N501Y;Y453F 162;152;145 167;157;150 RBD;RBD 66;104 69;107 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. All of these new variants also harbor the D614G mutation and, therefore, can be expected to cause similarly increased olfactory dysfunction as the G614 virus. 2021 ACS chemical neuroscience Discussion SARS_CoV_2 D614G 42 47 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. Clinically, despite the higher viral load, studies failed to detect an effect of the D614G mutation on the severity of COVID-19, hospitalization rate, or mortality. 2021 ACS chemical neuroscience Discussion SARS_CoV_2 D614G 85 90 COVID-19 119 127 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. For example, the Alpha variant that often also has N501Y, N439K, and Y453F mutations appears to require a deletion (DeltaH69/V70) in the spike protein to maintain optimal cleavage and infectivity. 2021 ACS chemical neuroscience Discussion SARS_CoV_2 N439K;N501Y;Y453F 58;51;69 63;56;74 S 137 142 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. For example, the virus with the N501Y mutation has similar binding to ACE2, while the K417N and the E484K mutants may have slightly increased binding to ACE2. 2021 ACS chemical neuroscience Discussion SARS_CoV_2 E484K;K417N;N501Y 100;86;32 105;91;37 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. Our meta-analysis of studies on South Asians provides a strong case for a role of the D614G virus mutation in anosmia prevalence. 2021 ACS chemical neuroscience Discussion SARS_CoV_2 D614G 86 91 Anosmia 110 117 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. Regarding the molecular mechanism of how the D614G mutation increases infectivity, transmission and possible disease severity, four different mechanisms are currently discussed, as recently reviewed.- These are (1) modulation of the spike protein (by adding an elastase cleavage site or making furin cleavage more efficient); (2) promoting an open conformation of the receptor binding domain that favors ACE2 interaction; (3) increasing spike density and, therefore, facilitating cell entry; and (4) enhancing the stability of the spike protein (stronger retention of S1, less shedding of S1). 2021 ACS chemical neuroscience Discussion SARS_CoV_2 D614G 45 50 RBD;S;S;S 368;233;437;531 391;238;442;536 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. Role of the D614G Mutation for Anosmia:Presumed Molecular Mechanisms. 2021 ACS chemical neuroscience Discussion SARS_CoV_2 D614G 12 17 Anosmia 31 38 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. The cell entry properties of the new virus variants likely will continue to cause chemosensory dysfunction, and otorhinolaryngologists should expect to see such symptoms in COVID-19 patients when the new variants take over, as long as they maintain the D614G mutation, and assuming that the additional mutations do not neutralize their apparent effect on olfaction. 2021 ACS chemical neuroscience Discussion SARS_CoV_2 D614G 253 258 COVID-19 173 181 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. Virus properties affected by the D614G mutation may further have downstream effects on virus entry because of ethnically distinct differences (e.g., in the frequency of the alpha antitrypsin protease inhibitor). 2021 ACS chemical neuroscience Discussion SARS_CoV_2 D614G 33 38 34533304 The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia. Why is the D614G mutation so much more effective in targeting the olfactory epithelium? What are the molecular mechanisms of this mutation? A number of studies have explored consequences of the D614G mutation, both for the clinical phenotype and for the pathophysiology at the molecular level. 2021 ACS chemical neuroscience Discussion SARS_CoV_2 D614G;D614G 11;194 16;199 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. H655Y has been observed by others in vitro, associated with adaption to cats and hamsters antibody escape and, identified in the sequence of super spreaders as well as arising by convergent evolution in circulating lineages (eg., P1 and A.27 lineages). 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 0 5 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. In this study, only N501T and Q498Y changes observed in our data were associated with an increased affinity for ACE-2, while the E484D substitutions has a negative effect on ACE-2 binding in this system. 2021 PLoS pathogens Discussion SARS_CoV_2 E484D;N501T;Q498Y 129;20;30 134;25;35 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. Indeed, we found that SARS-CoV-2 NSP12 E802D were outcompeted by wild type virus in our in vitro assays. 2021 PLoS pathogens Discussion SARS_CoV_2 E802D 39 44 Nsp12 33 38 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. The SARS-CoV-2 NSP12 E802D mutation, similar to the NSP12 F480 mutation in MHV and SARS-CoV-1 does not fall within the active sites, and we propose that this amino acid substitution results in minor structural modification of NSP12 that potentially influences the position of C813 and S814. 2021 PLoS pathogens Discussion SARS_CoV_2 E802D 21 26 Nsp12;Nsp12;Nsp12 15;52;226 20;57;231 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. The SARS-CoVEngl2 RDV-resistant (Rem1p13.5 and Rem2.5p13.5) and the reverse-genetic derived SARS-CoV-2Wu1 NSP12 mutants (rNSP12_E802D & rNSP12_E802A) increased the EC50 by at least 2-fold regardless of the cell type used for the experiments. 2021 PLoS pathogens Discussion SARS_CoV_2 E802A;E802D 143;128 148;133 Nsp12 106 111 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. This is further highlighted by two mutations that arise in vitro; N501T and H655Y, the first within the RDB and the latter outside of the RDB and toward the S1-S2 cleavage site. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y;N501T 76;66 81;71 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. Whereas, in an analysis using the entire spike protein there was an increase the free energy of the RBD-ACE-2 complex with the E484D substitution, resulting in a more infectious virus. 2021 PLoS pathogens Discussion SARS_CoV_2 E484D 127 132 S;RBD 41;100 46;103 34534263 In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. While the phenotypic importances of H655 mutation is unknown, Braun et al., postulated it is unlikely H655Y improves spike fusion efficiency and entry. 2021 PLoS pathogens Discussion SARS_CoV_2 H655Y 102 107 S 117 122 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Consistent with previous reports, the N501Y mutation shared by B.1.1.7, B.1.351, and P.1 variants presented a significant increase for ACE2-Fc binding. 2021 Virology Discussion SARS_CoV_2 N501Y 38 43 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. Interestingly, variants harboring the N501Y mutation displayed improved ACE2 interaction compared to the D614G Spike, independently of the temperature, highlighting the critical impact of this substitution in improving Spike - ACE2 interaction. 2021 Virology Discussion SARS_CoV_2 D614G;N501Y 105;38 110;43 S;S 111;219 116;224 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. While N501Y plays a major role in enhanced transmissibility and infectivity, variants which do not share this mutation have also gained the increased ACE2 binding by harboring other mutations, such as in the B.1.429 lineage, where the L452R showed higher ACE2 binding. 2021 Virology Discussion SARS_CoV_2 L452R;N501Y 235;6 240;11 34536797 Contribution of single mutations to selected SARS-CoV-2 emerging variants spike antigenicity. While the D614G Spike necessitates lower temperature for optimal ACE2 interaction, Spikes from the different VOCs and VOIs seem to bypass this requirement to efficiently interact with ACE2 at higher temperature (37 C). 2021 Virology Discussion SARS_CoV_2 D614G 10 15 S;S 16;83 21;89 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. All three holothurian sulfated glycans studied here exhibited strong binding to S-protein RBD and mutant spike protein N501Y RBD when examined by SPR. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 N501Y 119 124 S;RBD;RBD;S 105;90;125;80 110;93;128;81 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. At the site studied here, the marine glycan building blocks compete against heparin in their interactions with the WT S-protein RBD and its N501Y mutant, showing greater affinity for the S-protein than heparin. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 N501Y 140 145 RBD;S;S 128;118;187 131;119;188 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. Interestingly, these sulfated glycans also show better binding affinity for binding to mutant protein N501Y. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 N501Y 102 107 34537241 Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection. Since the N501Y mutation is critical and has been shown to impart increased infectivity to the virus by tightening its binding with the receptor, these results are highly promising. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 N501Y 10 15 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. B.1.1.7+E484K and B.1.525 vs. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 E484K 8 13 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. Based on local frequency of these variants, parallel or sequential (P681R when L452R present) evaluation can be performed. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 L452R;P681R 79;68 84;73 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. In the absence of SGTF and presence of 501Y and 484K mutations, the H655Y-specific assay proved to be an excellent discriminator between the Beta and Gamma variant (100% concordance for both). 2022 Clinical microbiology and infection Discussion SARS_CoV_2 H655Y 68 73 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. In the E484K assay, the E484Q mutation (e.g. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 E484K;E484Q 7;24 12;29 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. Interestingly, the Eta variant displayed an aberrant Tm at 60.6+-0.2 C (N=6) in the DeltaH69-V70 assay, presumably due to the A67V mutation allocated in the probe-binding site. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 A67V 126 130 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. Regions where the B.1.1.7+E484K variant, the B.1.525 and/or B.1.620 lineage is circulating, might need to perform follow-up detection of the E484K mutation systematically after N501Y assessment to obtain sufficient discrimination (B.1.1.7 vs. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 E484K;N501Y;E484K 141;177;26 146;182;31 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. Similarly, the Lambda variant might display an aberrant Tm in the L452R-specific assay as it harbors the L452Q mutation, but this was not assessed in the current manuscript. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 L452Q;L452R 105;66 110;71 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. The B.1.617 sublineages harbor both L452R and P681R whereas B.1.427/B.1.429 harbors only L452R. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 L452R;L452R;P681R 36;89;46 41;94;51 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. The data obtained by surveillance sequencing during this study showed increasing occurrence of the Delta variant, leading to the incorporation of the P681R and L452R PCRs in the testing algorithm, demonstrating its flexibility. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 L452R;P681R 160;150 165;155 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. The latter can be overcome by inclusion of a K417N/T-specific assay. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 K417N;K417T 45;45 52;52 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. The proposed algorithm uses SGTF as first discriminator, which could be considered a limitation but alternative strategies including the E484K/Q, L452R, P681R/H and H655Y or K417N/T mutations could be used to discriminate between variants without the requirement of the SGTF. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 E484K;E484Q;H655Y;K417N;K417T;L452R;P681H;P681R 137;137;165;174;174;146;153;153 144;144;170;181;181;151;160;160 34537361 Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants. Therefore, follow-up assessment of the L452R and P681R mutations can be performed in the absence of N501Y and E484K. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 E484K;L452R;N501Y;P681R 110;39;100;49 115;44;105;54 34537363 Influence of treatment with neutralizing monoclonal antibodies on the SARS-CoV-2 nasopharyngeal load and quasispecies. However, this study only looked for mutations E484K/Q, F490S and S494P. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 E484K;E484Q;F490S;S494P 46;46;55;65 53;53;60;70 34537363 Influence of treatment with neutralizing monoclonal antibodies on the SARS-CoV-2 nasopharyngeal load and quasispecies. Our analysis of the SARS-CoV-2 spike protein evolution in infected patients treated with mAbs indicated that key mAb activity-reducing mutations (Q493R/K, E484K) appeared in 5 SOT-patients treated with Bamlanivimab/Etesevimab. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 E484K;Q493K;Q493R 155;146;146 160;153;153 S 31 36 34537363 Influence of treatment with neutralizing monoclonal antibodies on the SARS-CoV-2 nasopharyngeal load and quasispecies. Previous in vitro studies showed that mAbs can induce the production of SARS-CoV-2 variants with mutation E484K and/or Q493R/K. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 E484K;Q493K;Q493R 106;119;119 111;126;126 34537363 Influence of treatment with neutralizing monoclonal antibodies on the SARS-CoV-2 nasopharyngeal load and quasispecies. The Q493R mutation has also been reported in one patient with cholangiocarcinoma. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 Q493R 4 9 Cholangiocarcinoma 62 80 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. Both XG81 and XG83 could effectively neutralize against Wuhan, E484Q, A475V, and D614G pseudoviruses. 2021 Frontiers in immunology Discussion SARS_CoV_2 A475V;D614G;E484Q 70;81;63 75;86;68 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. Interestingly, when compared with the originally paired mAbs, the rAb, CB6H-XG83L, effectively enhanced its neutralizing activity against A475V pseudoviruses so as to avoid the immune escape of the mutation (Table 2). 2021 Frontiers in immunology Discussion SARS_CoV_2 A475V 138 143 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. Similarly, the IC50 of CV30 in neutralizing A475V is 3.7 times relative to Wuhan pseudovirus, while the IC50 of P2B-2F6 is 5.4 times targeting E484Q compared to Wuhan pseudovirus. 2021 Frontiers in immunology Discussion SARS_CoV_2 A475V;E484Q 44;143 49;148 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. Since A475V is located within the binding sites of CB6, the IC50 value of A475V pseudovirus is 29.4 times relative to Wuhan pseudovirus. 2021 Frontiers in immunology Discussion SARS_CoV_2 A475V;A475V 6;74 11;79 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. Since some variants, including A475V, E484Q, and D614G, have been reported to show a decreased sensitivity to neutralizing nAbs or an increased infectivity, we next investigated the neutralizing activity of these antibodies against the mutant pseudoviruses. 2021 Frontiers in immunology Discussion SARS_CoV_2 A475V;D614G;E484Q 31;49;38 36;54;43 34539645 Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. The other rAb, S309H-CV30L, also showed a decreased IC50 ratio with a higher potency of neutralization compared with the original CV30 antibody (Table 2). 2021 Frontiers in immunology Discussion SARS_CoV_2 S309H 15 20 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Another mutation was S477I detected in Tangerang, western border of Jakarta. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 S477I 21 26 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Another unique mutation was recorded in this study was Q677H. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 Q677H 55 60 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Based on computational calculation of free energy, the mutation of A352G may contribute high energy, so that this mutation may not have meaning. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 A352G 67 72 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Comparing to the data taken from other continents, the D614G substitution recorded in all random data retrieved. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 D614G 55 60 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. From its origin of East Asia including Wuhan, before entering Indonesia this virus could be spread by adapting and carrying the D614G mutation (known as G clade marker), which may originated and distributed firstly in European and Americans. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 D614G 128 133 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. In 3CLpro, we recorded two mutations, M49I and L50F. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 L50F;M49I 47;38 51;42 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. In Egypt, the Q677H mutation, was detected as the most frequent mutation after D614G. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 D614G;Q677H 79;14 84;19 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. In PLpro, we recorded at least two mutations; P77L and V205I. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 P77L;V205I 46;55 50;60 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. In resume, 14 (fourteen) samples from Jawa Barat, include Bandung contribute 53% to the total result of D614G mutation. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 D614G 104 109 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. It has been reported in January to April, in total 79 samples were submitted and analysed, all of them harbour the D614G mutation. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 D614G 115 120 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Meanwhile, protein spike data from other continents did not show any substitution, but only sample from Asia/India was recorded having mutation in R1039T. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 R1039T 147 153 S 19 24 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Nowadays, the D614G mutation was recognize as globally dominant variant (www.gisaid.org). 2021 Iranian journal of microbiology Discussion SARS_CoV_2 D614G 14 19 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Other mutations that were found uniquely in S1 subunit were A352G and S477I. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 A352G;S477I 60;70 65;75 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Other studies reported this S477 substitution but in different residue S477G and S477R in Egypt. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 S477G;S477R 71;81 76;86 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Since S1 domain mediates attachment of receptor binding to host cell, the substitution of D614G had been demonstrated to be more epidemiologically stable and increase efficiency in the host receptor binding. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 D614G 90 95 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. Since there were no report for residue P77 and V205, the substitution of Pro-77Leu and Val205Ile may not contribute to substrate stability. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 P77L;V205I 73;87 82;96 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. So, then the substitution M49I may not contribute high change in stability, but this assumption still needs to be proven in MD with different inhibitor or even in wet lab. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 M49I 26 30 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. that D614G mutation predominates in the Middle East and North Africa. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 D614G 5 10 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The D614G mutation may play a major role in death rates worldwide. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 D614G 4 9 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The mutation that appeared most frequently was D614G. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 D614G 47 52 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The only possibility calculated was 2-point mutation combination of R355D and K424E that could produce strongest structural stability to the spike protein. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 K424E;R355D 78;68 83;73 S 141 146 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The prevalence of D614G strain over the time in different locations, indicating that changes in this mutation may be related to host infection and the viral transmission. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 D614G 18 23 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The significant functional of Q677H had not been determined clearly, even though this has been described in previous study. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 Q677H 30 35 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The substitution L50F has not been reported to have a major contribution to the catalytic site. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 L50F 17 21 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The substitution of A352G was recorded two samples from Pasuruan, Jawa Timur. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 A352G 20 25 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. The variant mutations in L clade are similar to the first hypothesis of type B formation, where T8782C and C28144T are the markers. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 C28144T;T8782C 107;96 114;102 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. This study showed that D614G mutation, as an issue of the worldwide today, indicated the virus more contagious. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 D614G 23 28 34540148 Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia. This type was derived from type A with two mutations: T8782C and C28144T. 2021 Iranian journal of microbiology Discussion SARS_CoV_2 C28144T;T8782C 65;54 72;60 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. A major characteristic of the African isolates was the high frequency (84.2%) of the A23403G mutation leading to a D614G. 2021 Frontiers in medicine Discussion SARS_CoV_2 A23403G;D614G 85;115 92;120 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. About 65.6% of the viruses belong to clades 20A, 20B, and 20C and non-synonymous mutations leading to two amino acid substitutions, the D614G in the spike and P323L in nsp12, were predominant in most countries. 2021 Frontiers in medicine Discussion SARS_CoV_2 D614G;P323L 136;159 141;164 S;Nsp12 149;168 154;173 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. During the first wave of the epidemic, the strains that circulated derived from Wuhan-Hu-1-like strains (also named the "China" strain), namely clade 20A and 20B, but these viruses already carried the D614G found in Europe and USA. 2021 Frontiers in medicine Discussion SARS_CoV_2 D614G 201 206 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. However, a D614G substitution in the spike has emerged with an increasing prevalence of this variant during the COVID-19 pandemic. 2021 Frontiers in medicine Discussion SARS_CoV_2 D614G 11 16 S 37 42 COVID-19 112 120 34540874 Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. It should be noted, the P323L substitution has been frequently observed in nsp12 in the strain spreading in Africa. 2021 Frontiers in medicine Discussion SARS_CoV_2 P323L 24 29 Nsp12 75 80 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. A triple-mAb cocktail (MA1-MA2-MA5) was developed against the SARS-CoV-2(V367F) isolate. 2021 MedComm Discussion SARS_CoV_2 V367F 73 78 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. Meanwhile, groups I, II, and IV mAbs can be used to prepare triple-mAb cocktails against the SARS-CoV-2(V367F) isolate. 2021 MedComm Discussion SARS_CoV_2 V367F 104 109 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. The majority of the mAbs neutralize the SARS-CoV-2(V367F) pseudovirus equally well, with group II mAbs, such as MA7 and MA8, exhibiting a remarkable neutralizing potency, with IC50 of about 42 pM. 2021 MedComm Discussion SARS_CoV_2 V367F 51 56 34541573 Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant. These data demonstrated that most mAbs neutralize both live and pseudotype SARS-CoV-2 viruses and the SARS-CoV-2(V367F) pseudovirus particle with IC50 values in the subnanomolar range. 2021 MedComm Discussion SARS_CoV_2 V367F 113 118 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. 7A), and hence mutations T478I and S494P do not bring any change to the binding affinity. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 S494P;T478I 35;25 40;30 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. E484K by itself do not have increased expression or do not escape from CC12.1 compared to the wild-type (Table 5). 2021 The Journal of biological chemistry Discussion SARS_CoV_2 E484K 0 5 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Followed by the Gamma variant, Alpha variant N501Y has the most favorable biophysical parameters in terms of increased affinity towards ACE2 and increased escape potential (Table 5). 2021 The Journal of biological chemistry Discussion SARS_CoV_2 N501Y 45 50 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. For example, although E484K and T478I mutations may not escape CC12.1 (Table 4), they may escape other classes of antibodies. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 E484K;T478I 22;32 27;37 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. For example, the triple mutant K417T/E484K/N501Y (Gamma variant) poses a serious threat with many factors, increased protein expression, increased activity and increased antibody escape potential favoring its emergence and persistence. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 K417T;E484K;N501Y 31;37;43 36;42;48 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. For example, when the data in Table 5 is compared between the N501Y (Alpha variant), the triple mutant K417T/E484K/N501Y (Gamma variant) and the Wild-type, increase in ACE2 binding might be significantly determined by the N501Y mutation, since no significant differences were observed in the Kd of ACE2 binding between the N501Y and K417T/E484K/N501Y variants. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 K417T;K417T;N501Y;N501Y;N501Y;E484K;E484K;N501Y;N501Y 103;333;62;222;323;109;339;115;345 108;338;67;227;328;114;344;120;350 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. In fact, E484K binds to CC12.1 with higher affinity, but it is quite likely that this mutation has evolved to show increased immune escape against other neutralizing antibodies. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 E484K 9 14 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Interestingly, E484K and T478I bind with a higher affinity (or lower Kd) to CC12.1 (Table 4). 2021 The Journal of biological chemistry Discussion SARS_CoV_2 E484K;T478I 15;25 20;30 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Most of the mutations in the RBD were noticed during the Fall of 2020, and variant B.1.1.7 with mutation N501Y (Alpha variant) became the first RBD variant to be labelled as a variant of concern (VOC) (https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/). 2021 The Journal of biological chemistry Discussion SARS_CoV_2 N501Y 105 110 RBD;RBD 29;144 32;147 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Other 2 mutants S477N and S494P did not show any difference in their binding affinity to CC12.1. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 S477N;S494P 16;26 21;31 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Our data shows that only 4 out of the 8 mutants (K417N, Y453F, N501Y and the triple mutant K417T/E484K/N501Y) we examined bind to CC12.1 with weaker affinity (or higher Kd) (Table 4). 2021 The Journal of biological chemistry Discussion SARS_CoV_2 K417T;N501Y;Y453F;K417N;E484K;N501Y 91;63;56;49;97;103 96;68;61;54;102;108 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Our data shows that the four mutations Y453F, S477N, T478I and S494P do not impact ACE2 binding. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 S477N;S494P;T478I;Y453F 46;63;53;39 51;68;58;44 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Out of the 8 variants for which complete biophysical data is available in Table 5, only two (N501Y (Alpha variant) and the triple mutant K417T/E484K/N501Y (Gamma variant)) correspond to the variants of concern (VOCs) and the other 6 are classified as variants of interest (VOI). 2021 The Journal of biological chemistry Discussion SARS_CoV_2 K417T;N501Y;E484K;N501Y 137;93;143;149 142;98;148;154 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. The effect of the other two mutations K417T and E484K in the Gamma variant might be to increase its expression and/or to increase immune escape potential. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 E484K;K417T 48;38 53;43 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. The other single site mutation N501Y corresponding to the Alpha variant and the triple mutant K417T/E484K/N501Y corresponding to the Gamma variant show increased binding affinity to ACE2. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 K417T;N501Y;E484K;N501Y 94;31;100;106 99;36;105;111 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. The single site mutant Y453F showed the weakest binding or the highest potential to escape CC12.1 ScFv. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 Y453F 23 28 34543625 Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. Two mutations K417N and E484K show a decrease in ACE2 binding affinity. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 E484K;K417N 24;14 29;19 34544043 Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants. Current data do not demonstrate widespread dissemination of BV-1 or other Q493R-containing variants at this time, but further monitoring may be warranted as increasing rates of vaccination change the competitive fitness landscape for SARS-CoV-2. 2021 The American journal of tropical medicine and hygiene Discussion SARS_CoV_2 Q493R 74 79 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. Furthermore, D614G, due to the higher flexibility, gains an increase in its thermostability as compared to the WT virus. 2022 Saudi journal of biological sciences Discussion SARS_CoV_2 D614G 13 18 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. The observed secondary and 3D structural changes induced by D108G and A249V mutations may have significant implications on the protease activity, which requires further investigations. 2022 Saudi journal of biological sciences Discussion SARS_CoV_2 A249V;D108G 70;60 75;65 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. This is of substantial importance because earlier reports show that spike protein substitution to glycine in D614G mutation increases the flexibility due to the shorter side chain allowing a more efficient cleavage of S protein subunits, which might explain the improved ACE binding affinity. 2022 Saudi journal of biological sciences Discussion SARS_CoV_2 D614G 109 114 S;S 68;218 73;219 34548835 Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. Thus, the alterations observed in the intramolecular interactions in the mutation site, particularly with the D108G, are likely to play an important role in modifying the substrate binding or the protease enzyme preference for deubiquitination and deISGylation activity. 2022 Saudi journal of biological sciences Discussion SARS_CoV_2 D108G 110 115 34549097 Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran. However, the available data from limited sequences from Iran in GSAID shows that frequency of mutation D614G increased from 1 (AK-SARS-27 in this study) in June 2020 to 16 sequences in March 2021 (data checked on March 14, 2021). 2021 Heliyon Discussion SARS_CoV_2 D614G 103 108 34549097 Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran. However, this trend may not have continued, as one study in India has reported that the mutational probability of 11083 G > T which was high in the beginning, decreased to zero in August and September 2020, suggesting that this mutation was not selected in the virus population for further propagation because of lesser efficiency in infection or fitness disadvantage. 2021 Heliyon Discussion SARS_CoV_2 G11083T 114 125 34549097 Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran. It has already been reported that viral genomes of all patients who returned to Australia, New Zealand and Canada from Iran in February 2020 form a distinct monophyletic group defined by the three SNVs (1397 G > A, 28688T > C, 29742 G > T). 2021 Heliyon Discussion SARS_CoV_2 T28688C;G29742T;G1397A 215;227;203 225;238;213 34549097 Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran. Mutation D614G which causes a change in spike region outside of its receptor binding domain became the most predominant form in pandemic from May 2020 globally. 2021 Heliyon Discussion SARS_CoV_2 D614G 9 14 RBD;S 68;40 91;45 34549097 Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran. Only one of the sequenced genomes had the SNV 23403A > G which results in D614G amino acid substitution, but it was not accompanied by three other mutations which are always co-occurring in the same genome. 2021 Heliyon Discussion SARS_CoV_2 A23403G;D614G 46;74 56;79 34549097 Complete genome sequencing and molecular characterization of SARS-COV-2 from COVID-19 cases in Alborz province in Iran. The small size of SARS-CoV-2 genome sequences from Iran hinders the robust analysis of D614G and other mutations at a national level. 2021 Heliyon Discussion SARS_CoV_2 D614G 87 92 34549975 Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. Among VOCs tested, serum-elicited neutralization of the B.1.1.7 (Alpha) variant was comparable to that of D614G; a range of significantly reduced neutralization titers compared to D614G were observed for other VOCs, including the B.1.351 (Beta), P.1 (Gamma), and B.1.617.2 (Delta) variants, with reductions ranging from 2.1-fold to 8.4-fold. 2021 Journal of virology Discussion SARS_CoV_2 D614G;D614G 106;180 111;185 34550770 Discovery and Evaluation of Entry Inhibitors for SARS-CoV-2 and Its Emerging Variants. None of these residues in B.1.351 directly interact with MU-UNMC-2, confirming that the signature mutations of B.1.351 (N501Y) present at the S-RBD/ACE2 interface may not impact the efficacy of this compound. 2021 Journal of virology Discussion SARS_CoV_2 N501Y 120 125 RBD;S 144;142 147;143 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. Case 5 was found to be wild type for these mutations, and was collected before D614G had become the dominant variant in the world. 2021 PeerJ Discussion SARS_CoV_2 D614G 79 84 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. Our current findings are consistent with this observation, in that the viral genome sequences of the SARS-CoV-2 strains from Cases 1-4 harbored both the D614G and P323L mutations. 2021 PeerJ Discussion SARS_CoV_2 D614G;P323L 153;163 158;168 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. Previous studies have shown that the P323L mutation in NSP12 co-evolved with the D614G mutation in S-protein. 2021 PeerJ Discussion SARS_CoV_2 D614G;P323L 81;37 86;42 Nsp12;S 55;99 60;100 34557346 Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America. The D614G SARS-CoV-2 variant appears to have independently arisen and then dispersed throughout multiple geographic regions, including Europe, Latin America, and Asia. 2021 PeerJ Discussion SARS_CoV_2 D614G 4 9 34560289 SARS-CoV-2 B.1.1.7 lineage rapidly spreads and replaces R.1 lineage in Japan: Serial and stationary observation in a community. The B.1.1.7 (Alpha) has N501Y mutation in receptor binding domain of spike protein, binds to the angiotensin-converting enzyme 2 with high affinity and acquires a high transmission rate. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 N501Y 24 29 RBD;S 42;69 65;74 34560289 SARS-CoV-2 B.1.1.7 lineage rapidly spreads and replaces R.1 lineage in Japan: Serial and stationary observation in a community. The R.1 carries the W152L N-terminal domain and E484K in receptor binding domain, which have been shown to be of concern for immune escape, while there are no reports on its transmission potential. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K;W152L 48;20 53;25 RBD;N 57;26 80;27 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. Here we have shown that highly comparable ADCC was elicited against VOC and the D614G reference strain from infected patients. 2021 Signal transduction and targeted therapy Discussion SARS_CoV_2 D614G 80 85 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. In the mouse model, immunization with pseudoviruses of SARS-CoV-2 VOCs (which included B.1.17, B.1.351, and P.1 variants) triggered comparable ADCC levels and in a similar level to that of the D614G reference strain. 2021 Signal transduction and targeted therapy Discussion SARS_CoV_2 D614G 193 198 34561414 Antibody-dependent cellular cytotoxicity response to SARS-CoV-2 in COVID-19 patients. The K417N+E484K+N501Y triple mutant in the B.1.351 variant significantly reduces the neutralizing activity of convalescent and post-vaccination sera. 2021 Signal transduction and targeted therapy Discussion SARS_CoV_2 K417N;E484K;N501Y 4;10;16 9;15;21 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Although the loss of the salt bridge between D614 and K584 is enthalpically unfavorable, it is compensated by other enthalpic gains evidenced by the significantly higher total enthalpy of unfolding DeltaH of S-D614G compared with that of S-D614. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 D614G 210 215 S;S 208;238 209;239 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. In this work, we determined the cryo-EM structure of S-D614G and revealed the high degree of conformational heterogeneity mostly confined within the RBDs. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 D614G 55 60 RBD;S 149;53 153;54 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. The most significant finding is the markedly increased resistance of S-D614G to withstand cold- and heat-induced unfolding. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 D614G 71 76 S 69 70 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. Third, the ability of S-D614G to withstand long-term storage at 4C without unfolding the prefusion state provides a solution to better vaccine designs and formulation without the need to introduce a large number of mutations and disulfide bonds. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 D614G 24 29 S 22 23 34563540 D614G mutation in the SARS-CoV-2 spike protein enhances viral fitness by desensitizing it to temperature-dependent denaturation. We argue that the increased stability of S-D614G could be further attributed to the increased configurational entropy manifested in the higher conformational heterogeneity of the RBDs. 2021 The Journal of biological chemistry Discussion SARS_CoV_2 D614G 43 48 RBD;S 179;41 183;42 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. For instance, N439K, L452R, T478I, and E484D mutations on RBM have significant free energy changes, and they constitute approximately 58% of all mutations on RBD. 2021 Biomolecules Discussion SARS_CoV_2 E484D;L452R;N439K;T478I 39;21;14;28 44;26;19;33 RBD 158 161 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Global data analysis shows that infectivity strengthening and virion stable mutations are on the rise (especially the frequency of S477N, N439K, V483A, and V367F), clearly indicating the natural selection of mutations with stronger transmissibility. 2021 Biomolecules Discussion SARS_CoV_2 N439K;S477N;V367F;V483A 138;131;156;145 143;136;161;150 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. However, the observed rigidity in some parts of RBDs (i.e., non-RBM regions) in N439K and E484K RBDs might compensate for the entropy penalty due to flexibility in the loop Y473-C489. 2021 Biomolecules Discussion SARS_CoV_2 E484K;N439K 90;80 95;85 RBD;RBD 48;96 52;100 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. In contrast, S477N and L452R RBDs showed comparable flexibility to WT RBD in non-RBM regions but higher flexibility in the RBM regions, as well as a loose conformational compactness. 2021 Biomolecules Discussion SARS_CoV_2 L452R;S477N 23;13 28;18 RBD;RBD 29;70 33;73 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. On the other hand, the loop Y473-C489 flexibility was increased in L452R, N439K, and E484K RBDs, and these mutations were associated with higher infectivity and binding affinity to ACE2. 2021 Biomolecules Discussion SARS_CoV_2 E484K;L452R;N439K 85;67;74 90;72;79 RBD 91 95 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Only N501Y RBD showed different loop Y495-Y508 conformations. 2021 Biomolecules Discussion SARS_CoV_2 N501Y 5 10 RBD 11 14 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Our results were consistent with a pervious study that showed that S477N has a destabilizing effect on RBD structure and therefore less prone to develop disease . 2021 Biomolecules Discussion SARS_CoV_2 S477N 67 72 RBD 103 106 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Our results were consistent with a pervious study that showed that S477N has a destabilizing effect on RBD structure and therefore less prone to develop disease. 2021 Biomolecules Discussion SARS_CoV_2 S477N 67 72 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. PCA, FEL, and porcupine plot results suggested that the destabilizing effect could be noticed in the loop Y473-C489 of S477N RBD as compared to WT RBD. 2021 Biomolecules Discussion SARS_CoV_2 S477N 119 124 RBD;RBD 125;147 128;150 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. So far, mutations in non-RBD residues, such as the D614G variant, can populate RBD open conformation rather than closed conformations. 2021 Biomolecules Discussion SARS_CoV_2 D614G 51 56 RBD;RBD 25;79 28;82 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. The mutation of alanine instead of tyrosine at 501 (i.e., N501A) shows an increase in loop Y473-C489 flexibility and conformational compactness according to a related study. 2021 Biomolecules Discussion SARS_CoV_2 N501A;N501A 16;58 50;63 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. The N501Y flexibility in loop Y473-C489 of RBM was comparable to WT RBD; thus, suggesting that tyrosine mutation did not alter neither the loop Y473-C489 flexibility or the whole RBD conformational compactness. 2021 Biomolecules Discussion SARS_CoV_2 N501Y 4 9 RBD;RBD 68;179 71;182 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. Therefore, the N501Y, N439K, and E484K mutations studied in this work have insignificant changes in the overall RBD flexibility. 2021 Biomolecules Discussion SARS_CoV_2 E484K;N439K;N501Y 33;22;15 38;27;20 RBD 112 115 34572486 Mutations of SARS-CoV-2 RBD May Alter Its Molecular Structure to Improve Its Infection Efficiency. This suggests that the higher infectivity of the N501Y variant might be attributed to an improvement in the N501Y RBD conformation and therefore a higher affinity to ACE2 receptor. 2021 Biomolecules Discussion SARS_CoV_2 N501Y;N501Y 49;108 54;113 RBD 114 117 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. Based on the association study between mutations vis-a-vis disease severity and mortality, we selected the mutations, A26194T, C28854T, and C25611A for structural analysis (Table 3). 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 A26194T;C25611A;C28854T 118;140;127 125;147;134 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. For mutation C25611A, a complete change of secondary structure of RNA was observed, resulting in a decrease in positional entropy (blue: high positional entropy, red: low positional entropy) and an increase in base pair probability of the nucleotide bases (blue: low base pair probability, red: high base pair probability) (Figure S3). 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 C25611A 13 20 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. For mutation C28854T (S194L), a change of secondary structure of RNA was observed resulting in an increase in positional entropy (blue: high positional entropy, red: low positional entropy) and a decrease in base pair probability of the nucleotide bases (blue: low base pair probability, red: high base pair probability) (Figure S4). 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 C28854T;S194L 13;22 20;27 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. Nearly 92% and 72% of the cases with mutation A26194T and C26511A were severe compared to an average of 50% severity rate in our cohort. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 A26194T;C26511A 46;58 53;65 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. Of the most frequent mutations seen in our samples, P314L and D614G, seen in more than 60% of the population, is known to form a haplotype along with mutations C3073T and C241T (Table 2). 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 C241T;C3073T;D614G;P314L 171;160;62;52 176;166;67;57 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. Of these three mutations, the C28854T (S194L) variation has already been reported to be associated with highly severe cases. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 C28854T;S194L 30;39 37;44 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. S194L mutation was found in the SR-rich motif of N protein (Figure 7B), which is shown to be important for virus replication. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 S194L 0 5 N 49 50 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. Upon analyzing these mutations for their effect on the protein and RNA secondary structure, it was observed that minor changes in the polarity of the A26194T (T268S) were seen. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 A26194T;T268S 150;159 157;164 34578142 Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. Whereas 38% and 20% of the cases with the mutation A26194T and C28854T were fatal compared to an average mortality rate of 10.5%, which highlights that these mutations are positively correlated with COVID-19 severity and mortality. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 A26194T;C28854T 51;63 58;70 COVID-19 199 207 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. For the Alpha variant, which became dominant in late 2020, it could be shown that the N501Y substitution in S is associated with higher affinity for the ACE2 receptor and higher transmissibility. 2021 Viruses Discussion SARS_CoV_2 N501Y 86 91 S 108 109 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Hence, both substitutions E484K and E484Q might limit the sensitivity of SARS-CoV-2 to neutralizing antibodies. 2021 Viruses Discussion SARS_CoV_2 E484K;E484Q 26;36 31;41 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Imdevimab, classified as a class 3 antibody, binds outside the ACE2-binding site matching the here observed high sensitivity to Kappa and efficient neutralizing of E484K carrying variants Beta and Gamma, as documented recently. 2021 Viruses Discussion SARS_CoV_2 E484K 164 169 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. In this study, we observed a reduced sensitivity of variants carrying L452R towards convalescent and vaccine-elicited sera that was further diminished by substitutions at E484 and T478K in S, respectively (Figure 1). 2021 Viruses Discussion SARS_CoV_2 L452R;T478K 70;180 75;185 S 189 190 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. In this work, we detected a lower capacity of convalescent or vaccine-elicited sera to neutralize the E484Q-carrying variant Kappa matching the previously shown reduced neutralization of variants Beta and Zeta carrying E484K. 2021 Viruses Discussion SARS_CoV_2 E484K;E484Q 219;102 224;107 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Most likely, T478K could affect imdevimab neutralizing capacity, however, more studies are needed to evaluate the impact of T478K on S secondary structure and antibody binding. 2021 Viruses Discussion SARS_CoV_2 T478K;T478K 13;124 18;129 S 133 134 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Specifically, using convalescent but not vaccine-elicited sera Kappa was neutralized 1.5-fold less effective than the T478K-carrying Delta variant. 2021 Viruses Discussion SARS_CoV_2 T478K 118 123 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. The capacity to neutralize the L452R carrying Epsilon lineages was only moderately reduced for casirivimab and imdevimab (Figure 2). 2021 Viruses Discussion SARS_CoV_2 L452R 31 36 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. The global displacement of Alpha and the dominance of Delta since spring 2021 shifted the focus towards L452R-carrying variants Epsilon and in particular the lineage B.1.617. 2021 Viruses Discussion SARS_CoV_2 L452R 104 109 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. The reduced imdevimab susceptibility towards Delta compared to Kappa indicates that T478K, possibly in combination with other mutations found in Delta S, might mediate the observed immune escape. 2021 Viruses Discussion SARS_CoV_2 T478K 84 89 S 151 152 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. The T478K substitution appears more relevant for neutralization by convalescent sera. 2021 Viruses Discussion SARS_CoV_2 T478K 4 9 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. This was in agreement with another recent study demonstrating a >10-fold resistance of Delta towards imdevimab and further receptor binding motif (RBM) binding antibodies suggesting that both the L452R and T478K substitutions reduce the neutralizing activity. 2021 Viruses Discussion SARS_CoV_2 L452R;T478K 196;206 201;211 34578275 Antibody-Mediated Neutralization of Authentic SARS-CoV-2 B.1.617 Variants Harboring L452R and T478K/E484Q. Using pseudoviruses, the L452R substitution was recently described as sensitive to both mAbs casirivimab and imdevimab, but has also been associated with increased viral shedding in vivo and reduced neutralization of RBD- and N-terminal Domain (NTD) antibodies. 2021 Viruses Discussion SARS_CoV_2 L452R 25 30 RBD;N 217;226 220;227 34578354 SARS-CoV-2 Delta Variant Pathogenesis and Host Response in Syrian Hamsters. B.1.617.3 possesses the E484Q mutation, which is a known site in RBD, which can impact the serum neutralization efficiency. 2021 Viruses Discussion SARS_CoV_2 E484Q 24 29 RBD 65 68 34578363 Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India. As per the WHO classification, the Delta variant has been designated as a variant of concern due to increased transmission and higher immune evasion, whereas the other two sub-lineages of B.1.617:namely, B.1.617.1 and B.1.617.3:with E484Q are grouped in VUI. 2021 Viruses Discussion SARS_CoV_2 E484Q 233 238 34578363 Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India. Delta AY.1 and AY.2 are characterized by the presence of the K417N mutation in the spike protein region. 2021 Viruses Discussion SARS_CoV_2 K417N 61 66 S 83 88 34578363 Clinical Characterization and Genomic Analysis of Samples from COVID-19 Breakthrough Infections during the Second Wave among the Various States of India. K417N, E484K, L452R, and E484Q are the mutations known to disrupt receptor-binding domain (RBD) binding capacity, making them more infectious by immune escape against the current vaccines. 2021 Viruses Discussion SARS_CoV_2 E484K;E484Q;L452R;K417N 7;25;14;0 12;30;19;5 RBD 91 94 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Although the lineage P.6 was substituted by the VOC P.1 as the most prevalent lineage in Uruguay since April 2021, the concurrent emergence of Spike mutations Q675H and Q677H in VOIs and/or VOCs circulating worldwide should be closely monitored. 2021 Viruses Discussion SARS_CoV_2 Q675H;Q677H 159;169 164;174 S 143 148 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. An ancestral B.1.1.28 virus carrying mutation Q675H was probably introduced from southeastern Brazil into Montevideo, Uruguay's capital city, and by November 2020 the virus already fixed mutation Q677H and spread across the entire country, originating lineage P.6. 2021 Viruses Discussion SARS_CoV_2 Q675H;Q677H 46;196 51;201 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Consistent with this notion, a recent study that used a reverse genetic system and primary human airway cultures identified mutation S:P681R as a significant determinant for enhanced viral replication fitness of the VOC Delta, and supported that Spike mutations that potentially affect furin cleavage efficiency must be closely monitored for future variant surveillance. 2021 Viruses Discussion SARS_CoV_2 P681R 135 140 S;S 246;133 251;134 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Convergent evolution is a hallmark of positive selection, and we identified the independent appearance of both S:Q675H and S:Q677H in 12 additional SARS-CoV-2 lineages. 2021 Viruses Discussion SARS_CoV_2 Q675H;Q677H 113;125 118;130 S;S 111;123 112;124 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Finally, we hypothesized that the combined presence of amino acid changes S:Q675H + Q677H might have also produced a more transmissible P.6 variant, contributing to the rapid increase in the lineage dominance observed between December 2020 and February 2021. 2021 Viruses Discussion SARS_CoV_2 Q677H;Q675H 84;76 89;81 S 74 75 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. In summary, this study described the emergence and local spread of lineage P.6, a new B.1.1.28-derived lineage carrying Spike mutations Q675H + Q677H, in Uruguay that coincided with the first exponential growth phase of the country's COVID-19 epidemic, which started by November 2020 and lasted until mid-February 2021. 2021 Viruses Discussion SARS_CoV_2 Q675H;Q677H 136;144 141;149 S 120 125 COVID-19 234 242 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Knowing that histidine residues function as pH sensors in other viruses, Q675H and Q677H mutations might also provide some synergic structural changes in the dynamics of the subdomain SD2, enhancing the effects of mutation D614G. 2021 Viruses Discussion SARS_CoV_2 D614G;Q675H;Q677H 223;73;83 228;78;88 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Moreover, mutations close to or at the polybasic cleavage site at the S1/S2 boundary have been reported in several VOCs and VOIs, including: Alpha (S:P681H), Beta (A701V), Delta (P681R), Eta (Q677H), Iota (A701V), Kappa (P681R), and Theta (P.3, P681H). 2021 Viruses Discussion SARS_CoV_2 P681H;A701V;A701V;P681R;P681R;Q677H;P681H 245;164;206;179;221;192;150 250;169;211;184;226;197;155 S 148 149 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Mutations Q675H and Q677H might alter the properties of this nearby protease-cleavage site through changes in the structure conformation, glycosylation, and/or phosphorylation processes already known to have a role in cleavage regulation. 2021 Viruses Discussion SARS_CoV_2 Q675H;Q677H 10;20 15;25 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Notably, another study that developed an innovative model on epidemiological variables integrating the effect of Spike amino acid changes in viral fitness forecasted that mutations Q675H and Q677H could appear in emerging SARS-CoV-2 VOCs in the following months. 2021 Viruses Discussion SARS_CoV_2 Q675H;Q677H 181;191 186;196 S 113 118 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. Recently, the promotion of syncytium formation and virus infectivity has been shown for the D614G mutation, which is known to impact structural and thermodynamic aspects of the Spike and to enhance the protease cleavage, likely by allosterically increasing the binding to furin. 2021 Viruses Discussion SARS_CoV_2 D614G 92 97 S 177 182 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. These observations underscore the importance of future experimental studies to assess the functional impact of Spike mutations Q675H and Q677H on virus infectivity and transmissibility. 2021 Viruses Discussion SARS_CoV_2 Q675H;Q677H 127;137 132;142 S 111 116 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. We are not aware of any experimental assay that assessed the effect of mutations S:Q675H + Q677H on the viral fitness, but independent data indicated that these amino acid changes (either one or both of them) might facilitate viral transmissibility. 2021 Viruses Discussion SARS_CoV_2 Q677H;Q675H 91;83 96;88 S 81 82 34578382 Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay. We propose that simultaneous presence of Spike mutations Q675H and Q677H might confer to lineage P.6 a higher infectivity and increased transmissibility, which, combined with the establishment in the populated metropolitan region, contributed to its swift dissemination in Uruguay. 2021 Viruses Discussion SARS_CoV_2 Q675H;Q677H 57;67 62;72 S 41 46 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. Except for N501Y and K417N, several other amino acid substitutions in MASCp36 were also found in human variants, including L37F in nsp6 and D128Y in N protein. 2021 Nature communications Discussion SARS_CoV_2 D128Y;K417N;L37F;N501Y 140;21;123;11 145;26;127;16 Nsp6;N 131;149 135;150 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. For example, the 501Y.V1 variant firstly detected in the United Kingdom contained the unique N501Y mutation in RBD, and more recent SARS-CoV-2 variants (501Y.V2 and 501Y.V2) contained both N501Y and K417N substitutions in S protein. 2021 Nature communications Discussion SARS_CoV_2 K417N;N501Y;N501Y 199;93;189 204;98;194 RBD;S 111;222 114;223 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. More importantly, Cryo-EM structures of both hACE2 and mACE2 in complex with RBDMASCp25 and RBDMASCp36 define preciously the atomic determinants of the receptor-binding switch: N501Y/Q493H/K417N in MASCp36 formed tight interactions with mACE2 in three patches, respectively, while K417N reduced interaction with hACE2. 2021 Nature communications Discussion SARS_CoV_2 K417N;N501Y;K417N;Q493H 281;177;189;183 286;182;194;188 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. Notably, R32C and D128Y in the N protein deserve special attention. 2021 Nature communications Discussion SARS_CoV_2 D128Y;R32C 18;9 23;13 N 31 32 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. The D128Y mutation in N protein has been well recorded in human variants from D128Y. 2021 Nature communications Discussion SARS_CoV_2 D128Y;D128Y 4;78 9;83 N 22 23 34580297 Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2. The sequentially acquired triple substitutions N501Y/Q493H/K417N in S protein of MASCp36 increased their affinities to mACE2, thus contributed to enhanced infectivity and lethal phenotype mice. 2021 Nature communications Discussion SARS_CoV_2 N501Y;K417N;Q493H 47;59;53 52;64;58 S 68 69 34592572 SARS-CoV-2 spike protein receptor-binding domain N-glycans facilitate viral internalization in respiratory epithelial cells. Notably, with similar glycan compositions, the binding to the receptors or RBD neutralizing antibodies was different among N331Q, N343Q, and N331Q + N343Q. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 N331Q;N331Q;N343Q;N343Q 123;141;130;149 128;146;135;154 RBD 75 78 34592572 SARS-CoV-2 spike protein receptor-binding domain N-glycans facilitate viral internalization in respiratory epithelial cells. The N331 and N343 N-glycosites shared similar glycan composition and relative abundance. 2021 Biochemical and biophysical research communications Discussion SARS_CoV_2 N343N 13 19 N 18 19 34594910 Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. As one of the key mutations of S protein, the D614G mutation has been concerned by many researchers. 2021 China CDC weekly Discussion SARS_CoV_2 D614G 46 51 S 31 32 34594910 Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. Considering the importance of D614G compared with other mutations, a simple and rapid method to detect this mutation is favorable. 2021 China CDC weekly Discussion SARS_CoV_2 D614G 30 35 34594910 Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. D614G mutation was first found in Germany. 2021 China CDC weekly Discussion SARS_CoV_2 D614G 0 5 34594910 Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. Few studies reported D614G detection. 2021 China CDC weekly Discussion SARS_CoV_2 D614G 21 26 34594910 Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. In view of the characteristics of PDRA and further improvement, PDRA will facilitate the detection of D614G mutations in resource-limited settings, particularly in locations where the contamination of the vaccine strain (D614) needs to be monitored and differentiated with non-local circulating strains (G614) in China. 2021 China CDC weekly Discussion SARS_CoV_2 D614G 102 107 34594910 Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. The D614G detection method designed by Hashemi et al., actually detected the mutation to V615V. 2021 China CDC weekly Discussion SARS_CoV_2 D614G;V615V 4;89 9;94 34594910 Development of a PDRA Method for Detection of the D614G Mutation in COVID-19 Virus - Worldwide, 2021. Whole-genome sequencing is a powerful but costly tool to identify D614G mutants, which cannot be applied in primary laboratories for sequencing a large number of samples. 2021 China CDC weekly Discussion SARS_CoV_2 D614G 66 71 34595399 Genomic epidemiological analysis of SARS-CoV-2 household transmission. For example, the B.1.1.7 'Variant of Concern', which is defined by a set of 23 genomic variations including an S:N501Y substitution and deletions at positions 69-70, spread rapidly throughout the United Kingdom from late November 2020 and received significant attention due to evidence supporting increased viral transmissibility and its association with the failure of S gene qPCR targets. 2021 Access microbiology Discussion SARS_CoV_2 N501Y 113 118 S;S 111;370 112;371 34595399 Genomic epidemiological analysis of SARS-CoV-2 household transmission. These include D614G, associated with the B.1 lineage observed in this family cluster, which is now ubiquitous and appears to have a moderate effect on SARS-CoV-2 transmissibility; A222V, present in the 20A.EU1 (B.1.177) cluster which has spread quickly across Europe from Spain and become dominant in Irish sequences; and N439K, a variant for which there is evidence to suggest increased ACE2 receptor binding affinity and immune-escape from neutralising antibodies. 2021 Access microbiology Discussion SARS_CoV_2 A222V;D614G;N439K 180;14;322 185;19;327 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Alpha bound the most efficiently to ACE2, followed by Beta, D614G, and finally Wuhan. 2021 The EMBO journal Discussion SARS_CoV_2 D614G 60 65 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Comparative video microscopy analysis revealed that Alpha S fused the most rapidly, followed by Beta, D614G, and finally Wuhan. 2021 The EMBO journal Discussion SARS_CoV_2 D614G 102 107 S 58 59 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. For instance, the N501Y and D614G mutations drastically increased ACE2 affinity, but only D614G enhanced fusogenicity. 2021 The EMBO journal Discussion SARS_CoV_2 D614G;D614G;N501Y 28;90;18 33;95;23 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. For instance, there was no major difference in the replication kinetics of Alpha and D614G strains in some reports (preprint: Thorne et al,; Touret et al,), whereas others suggested that Alpha may outcompete D614G in a co-infection assay (Touret et al,). 2021 The EMBO journal Discussion SARS_CoV_2 D614G;D614G 85;208 90;213 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Here, we show that Alpha and Beta variants replicate to the same extent as the early D614G strain in different human cell lines and primary airway cells. 2021 The EMBO journal Discussion SARS_CoV_2 D614G 85 90 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. In accordance with our findings, deep sequence binding analysis and in vitro evolution studies suggest the N501Y mutation increases affinity to ACE2 without disturbing antibody neutralization (preprint: Liu et al,; Starr et al,; Zahradnik et al,). 2021 The EMBO journal Discussion SARS_CoV_2 N501Y 107 112 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. In agreement with infection data, transfection of Alpha and Beta S proteins in the absence of any other viral factors, produced significantly more syncytia than D614G, which in turn, fused more than the Wuhan S. 2021 The EMBO journal Discussion SARS_CoV_2 D614G 161 166 S;S 65;209 66;210 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. In contrast, the Beta variant is comprised of several restrictive mutations ( 242-244, K417N, and E484K) and only one mutation that modestly increased fusion (D215G). 2021 The EMBO journal Discussion SARS_CoV_2 E484K;K417N;D215G 98;87;159 103;92;164 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Indeed, the analogous P681R mutation present in B.1.617.2 and B.1.617.3 variants increases S1/S2 cleavage and facilitates syncytia formation (Jiang et al,; preprint: Ferreira et al,). 2021 The EMBO journal Discussion SARS_CoV_2 P681R 22 27 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Moreover, Alpha and Beta induced more cell-cell fusion than D614G. 2021 The EMBO journal Discussion SARS_CoV_2 D614G 60 65 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Some studies proposed that the N501Y mutation may provide a replication advantage, whereas others suggested that N501Y is deleterious (Hou et al,; Frampton et al,; Leung et al,; preprint: Liu et al,). 2021 The EMBO journal Discussion SARS_CoV_2 N501Y;N501Y 31;113 36;118 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The E484K and K417N RBD mutations in the Beta variant may also increase ACE2 affinity, particularly when in conjunction with N501Y (preprint: Nelson et al,; Zahradnik et al,). 2021 The EMBO journal Discussion SARS_CoV_2 E484K;K417N;N501Y 4;14;125 9;19;130 RBD 20 23 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The E484K mutation significantly restricts fusion, but mildly increases ACE2 affinity. 2021 The EMBO journal Discussion SARS_CoV_2 E484K 4 9 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The highly fusogenic Alpha S consists of more mutations that robustly increase fusion (P681H and D1118H) than mutations that decrease fusion ( 69/70). 2021 The EMBO journal Discussion SARS_CoV_2 D1118H;P681H 97;87 103;92 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The K417N substitution, and to a lesser degree 242-244, had a lower affinity to ACE2 and also restricted cell-cell fusion. 2021 The EMBO journal Discussion SARS_CoV_2 K417N 4 9 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. The strongest increase in fusion was elicited by the P681H mutation at the S1/S2 border. 2021 The EMBO journal Discussion SARS_CoV_2 P681H 53 58 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Upon examining the potential of S proteins carrying individual mutations to bind to human monoclonal antibodies, we found that the ones that restrict ( 242-244, K417N) or have no effect on fusogenicity ( Y144) are also not recognized by some mAbs. 2021 The EMBO journal Discussion SARS_CoV_2 K417N 161 166 S 32 33 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. We found that the S protein of the novel variants induced more syncytia formation than the D614G and Wuhan S proteins in human Caco2 cells which express endogenous ACE2 and TMPRSS2. 2021 The EMBO journal Discussion SARS_CoV_2 D614G 91 96 S;S 18;107 19;108 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. We further show that Alpha, Beta, and Delta S proteins more efficiently bind to ACE2 and are more fusogenic than D614G. 2021 The EMBO journal Discussion SARS_CoV_2 D614G 113 118 S 44 45 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. We selected a panel of 4 mAbs that displayed different profiles of binding to Alpha, Beta, D614G, and Wuhan S proteins. 2021 The EMBO journal Discussion SARS_CoV_2 D614G 91 96 S 108 109 34601723 SARS-CoV-2 Alpha, Beta, and Delta variants display enhanced Spike-mediated syncytia formation. Wuhan and D614G were recognized by the three other antibodies, targeting either the NTD or RBD. 2021 The EMBO journal Discussion SARS_CoV_2 D614G 10 15 RBD 91 94 34603303 A Combination Adjuvant for the Induction of Potent Antiviral Immune Responses for a Recombinant SARS-CoV-2 Protein Vaccine. Furthermore, NE/IVT induced antibodies with broader cross-neutralizing capabilities than those generated with NE alone, more effectively neutralizing MA-SARS-CoV-2 which harbors N501Y and H655Y substitutions and a 4aa insertion in S1, supporting the improved quality of the humoral response with the multivalent adjuvant. 2021 Frontiers in immunology Discussion SARS_CoV_2 H655Y;N501Y 188;178 193;183 34603303 A Combination Adjuvant for the Induction of Potent Antiviral Immune Responses for a Recombinant SARS-CoV-2 Protein Vaccine. The ability of NE/IVT to improve cross-variant protection induced with just the S1 subunit, particularly towards a variant with the N501Y mutation shared by several of the highly transmissible variants of concern, supports its potential for improving the breadth of protection of current vaccine candidates. 2021 Frontiers in immunology Discussion SARS_CoV_2 N501Y 132 137 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. Furthermore, the most observed mutations: P4715L in RdRp and D614G in S protein are observed in same viral sequences across all regions. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;P4715L 61;42 66;48 RdRP;S 52;70 56;71 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. Mutations observed in this study in the nsp13 (P5828L and Y5865C) of ORF1ab polyprotein of SARS-CoV-2 which functions as a replicase or helicase corroborate other findings. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 Y5865C;P5828L 58;47 64;53 Helicase;ORF1ab;Nsp13 136;69;40 144;75;45 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. Our study discovered the mutation (P4715L) as being prevalent in Africa (97.20%), South America (91.30%), North America (90.03%), and Europe (89.83%); this was corroborated by other studies which observed the prevalence of the mutation in viral isolates from Europe (especially France, Spain and Greece) and the USA where COVID-19 pandemic transmission is very severe. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P4715L 35 41 COVID-19 322 330 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. The mutation, L3606F, in ORF1ab nsp6 is prevalent in Asia. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 L3606F 14 20 ORF1ab;Nsp6 25;32 31;36 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. The P4715L mutation was first observed in Italy during the sporadic increase in incidence and fatality of COVID-19 in Europe. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P4715L 4 10 COVID-19 106 114 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. This finding is consistent with an earlier study in a genotyping analysis of 588 SARS-CoV-2 strains where P4715L mutation (14408C > T) was reported to be located in a critical protein necessary for RNA replication. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 P4715L;C14408T 106;123 112;133 34606987 Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome. This missense mutation (position 3606 aa; 11083G > T or L3606F) in this report is consistent with other findings as one of the strongest observed homoplasies in their studies. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 G11083T;L3606F 42;56 52;62 34607456 A Combination of Receptor-Binding Domain and N-Terminal Domain Neutralizing Antibodies Limits the Generation of SARS-CoV-2 Spike Neutralization-Escape Mutants. In addition, mutations at N148S, K150R/E, and S151P in the NTD epitope exhibited reductions in sensitivity to three COVID-19 convalescent-phase plasma samples. 2021 mBio Discussion SARS_CoV_2 K150E;K150R;N148S;S151P 33;33;26;46 40;40;31;51 COVID-19 116 124 34607456 A Combination of Receptor-Binding Domain and N-Terminal Domain Neutralizing Antibodies Limits the Generation of SARS-CoV-2 Spike Neutralization-Escape Mutants. Notably, our rVSV-SARS2 neutralization-escape variants (Y145D, K150E, and W152R) were significantly resistant to neutralization by convalescent-phase COVID-19 sera. 2021 mBio Discussion SARS_CoV_2 K150E;W152R;Y145D 63;74;56 68;79;61 COVID-19 150 158 34607456 A Combination of Receptor-Binding Domain and N-Terminal Domain Neutralizing Antibodies Limits the Generation of SARS-CoV-2 Spike Neutralization-Escape Mutants. showed that mutations F140S and G142D or R158S in the NTD confer resistance to two other NTD nAbs. 2021 mBio Discussion SARS_CoV_2 F140S;G142D;R158S 22;32;41 27;37;46 34611654 Molecular switches regulating the potency and immune evasiveness of SARS-CoV-2 spike protein. Several months in the pandemic, a D614G mutation allowed more SARS-CoV-2 spike molecules to open up, a sign that the virus was gaining more potency. 2021 Research square Discussion SARS_CoV_2 D614G 34 39 S 73 78 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. A few commercial kits partially address the detection of these SC-2 variants, but they target general mutations, such as N501Y and E484K in the spike protein, and not variant-specific mutations, such as the N protein D3L substitution or the spike protein 242 to 244 deletion (https://www.seegene.com/assays/rp, http://www.kogene.co.kr/eng/sub/product/covid-19.asp). 2021 Microbiology spectrum Discussion SARS_CoV_2 D3L;E484K;N501Y 217;131;121 220;136;126 S;S;N 144;241;207 149;246;208 COVID-19 351 359 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. Although this mutation can occur independently of other characteristic mutations, such as N501Y, its presence strongly suggests that the examined sample is the B.1.1.7 variant. 2021 Microbiology spectrum Discussion SARS_CoV_2 N501Y 90 95 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. For diagnostic purposes, however, the N501Y mutation is not variant-specific, as it was identified in several variants other than variant B.1.1.7, such as B.1.351 and the P.1 variant. 2021 Microbiology spectrum Discussion SARS_CoV_2 N501Y 38 43 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. Likewise, the reaction that identifies the variant B.1.351 targets mutations that are strongly associated with this variant:D215G and the triple deletion of amino acids 242 to 244. 2021 Microbiology spectrum Discussion SARS_CoV_2 del 242;D215G 145;124 172;129 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. SC-2 variant B.1.1.7 contains numerous synonymous and nonsynonymous mutations, of which the spike gene mutations 69-70del, N501Y, and P681H received most attention due to their potential effect on virus infectivity. 2021 Microbiology spectrum Discussion SARS_CoV_2 N501Y;P681H 123;134 128;139 S 92 97 34612692 Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351. The D3L substitution in the N gene used in our assay is specific to variant B.1.1.7 and was not reported in other major SC-2 lineages. 2021 Microbiology spectrum Discussion SARS_CoV_2 D3L 4 7 N 28 29 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. Another mutation, A570V, was observed within our predicted residues, but did not yet become as widespread as D614G, likely because it did not have substantial evolutionary advantage. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 A570V;D614G 18;109 23;114 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. However, a different mutation at residue 570 (A570D) has indeed appeared in the recently emerged more-contagious B.1.1.7 strain of SARS-CoV-2. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 A570D 46 51 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. However, both experimental and computer simulation studies have already established that D614G, A570D, and a few other mutations transform the dynamics of the RBD and favor an "up" state. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 A570D;D614G 96;89 101;94 RBD 159 162 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. However, we do show that the dihedral angle preference, interaction energy, and hydrogen bonding pattern of concerned residues change significantly due to a D614G mutation. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 157 162 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. In vitro experiments also established that the single point mutation D614G is capable of altering the "down" to "up" conformational dynamics of the spike. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 69 74 S 148 153 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. The D614G mutant prefers the one RBD "up" state 7 times more than the "three-down" configuration, while they are equally likely in the WT strain. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 4 9 RBD 33 36 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. The D614G mutation is currently observed in SARS-CoV-2, and is becoming widespread among infected patients throughout the world. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 4 9 34615730 Distant residues modulate conformational opening in SARS-CoV-2 spike protein. The specific role of the D614G mutation was recently also established by coarse-grained MD study. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D614G 25 30 34615860 Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil. A cautious approach to variants containing E484K and other RBD mutations is warranted whilst our understanding of their individual impact improves. 2021 Nature communications Discussion SARS_CoV_2 E484K 43 48 RBD 59 62 34615860 Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil. E484K (and a similar mutation E484Q) are being rapidly accumulated by lineages across distinct epidemiological and geographic settings and the addition of E484K/Q mutations to existing VOCs (such as Alpha (B.1.1.7)) is associated with evasion of neutralising antibodies. 2021 Nature communications Discussion SARS_CoV_2 E484K;E484Q;E484Q;E484K 155;155;30;0 162;162;35;5 34615860 Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil. However, it is not known what the relative contribution of E484K/Q mutations may have on vaccine efficacy when occurring as part of a constellation of RBD mutations. 2021 Nature communications Discussion SARS_CoV_2 E484K;E484Q 59;59 66;66 RBD 151 154 34615860 Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil. The observation that vaccine efficacy in our trial was preserved for P.2 may indicate that E484K, when occurring as an isolated RBD mutation, may be responsible for minimal reduction in protection. 2021 Nature communications Discussion SARS_CoV_2 E484K 91 96 RBD 128 131 34615860 Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil. The only RBD lineage defining mutation for Zeta (P.2) lineage is the E484K mutation, whilst Gamma (P.1) and Beta (B.1.351) harbour multiple RBD mutations. 2021 Nature communications Discussion SARS_CoV_2 E484K 69 74 RBD;RBD 9;140 12;143 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. Although the Y453F variants resist neutralization by the REGN10933 monoclonal antibodies, our investigation of possible antigenic linear peptides in the spike suggests that the Y453F mutation should not affect the binding of most anti-SARS-CoV-2 neutralizing antibodies. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F;Y453F 13;177 18;182 S 153 158 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. However, it should be emphasized that in these in vitro experiments, most serum/plasma from convalescent COVID-19 patients completely neutralized the Y453F mutants at the lowest dilution tested. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F 150 155 COVID-19 105 113 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. In contradiction with previous assumptions,, reported that the mutation Y453F does not strongly affect serum antibody binding. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F 72 77 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. Indeed, this was demonstrated by in vitro passing of a VSV-SARS-CoV-2 wild type spike in the presence of the RBD-binding REGN10933 monoclonal antibodies which led to the selection of the Y453F mutation conferring resistance to this antibody. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F 187 192 S;RBD 80;109 85;112 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. More recently, the Y453F mutation was reported in a patient with long-term COVID-19. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F 19 24 COVID-19 75 83 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. Of interest is the distribution of the mink SARS-CoV-2 spike sequences within Group 4 into two populations, one bearing only the Y453F and D614G mutations, and the second accumulating many other mutations. 2021 Frontiers in microbiology Discussion SARS_CoV_2 D614G;Y453F 139;129 144;134 S 55 60 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. Taken together these studies indicate that the antigenic pattern of the SARS-CoV-2 spike is complex and that further analyses are therefore required to estimate whether viruses bearing the Y453F mutation might be less impacted by human immune defenses. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F 189 194 S 83 88 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. The only mink-selected mutation affecting the RBD in the SARS-CoV-2 S protein (Y453F) is expected to have implications for viral fitness (ability to infect humans and animals) and transmissibility (by increasing SARS-CoV-2 affinity for the human ACE2), only. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F 79 84 RBD;S 46;68 49;69 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. The selection pressure exerted by the mink immune system was most likely the reason for the selection of the Y453F mutation. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F 109 114 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. This question must, however, continue to be explored because, recently, reported that the Y453F mutation in the SARS-CoV-2 spike protein diminished the in vitro viral entry inhibition by 7/14 human sera/plasma from convalescent COVID-19 patients. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y453F 90 95 S 123 128 COVID-19 228 236 34616371 Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. Very recently, it was reported that viral entry into certain SARS-CoV-2 susceptible cell lines was reduced when the mink-derived Y453F mutation was combined with H69Delta, V70Delta, I692V, and M1229I. 2021 Frontiers in microbiology Discussion SARS_CoV_2 I692V;M1229I;Y453F 182;193;129 187;199;134 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. Although a significant transmission advantage of D614G is found, we notice that the proportion of 614G variant generally increased, while the reproduction number series decreased in March and then remained constant. 2021 BMC infectious diseases Discussion SARS_CoV_2 D614G 49 54 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. Although some recent studies indicate that the D614G mutation is unlikely to undermine the neutralization from current SARS-CoV-2 vaccine candidates, there are also other studies suggest the concerns should be raised oppositely. 2021 BMC infectious diseases Discussion SARS_CoV_2 D614G 47 52 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. Although the variants carrying D614G substitution might be introduced to California from aboard during the first few months of pandemic, the observed changes in SARS-CoV-2 mutations (pt) were likely due to the spread of virus locally after the implementation of strict travel-ban measurements. 2021 BMC infectious diseases Discussion SARS_CoV_2 D614G 31 36 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. As an example, on one hand, the R384G substitution in influenza A/H3N2 virus enhances ability of in-host immune-escape, which indicates an increase in infectivity, but this substitution appears detrimental. 2021 BMC infectious diseases Discussion SARS_CoV_2 R384G 32 37 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. Consistent evidences of the transmission advantage of D614G substitution were also reported in previous literature both statistically and experimentally. 2021 BMC infectious diseases Discussion SARS_CoV_2 D614G 54 59 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. Fourth, this study focuses on exploring the effects on changing the disease transmissibility associated with a single mutation, e.g., D614G, but the real-world biological mechanisms, which are usually more complex, remain uncovered. 2021 BMC infectious diseases Discussion SARS_CoV_2 D614G 134 139 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. Future studies are needed for exploring the mechanisms of how D614G in SARS-CoV-2 affects the transmissibility of COVID-19. 2021 BMC infectious diseases Discussion SARS_CoV_2 D614G 62 67 COVID-19 114 122 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. However, by screening the literature of COVID-19, we find no evidence that GT is varied associated with the D614G substitution in SARS-CoV-2, and thus we presume w to be a fixed distribution. 2021 BMC infectious diseases Discussion SARS_CoV_2 D614G 108 113 COVID-19 40 48 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. On the other hand, the co-mutations of R384G in nucleoprotein (NP) could improve and compensate the viral fitness or functionality of, such that the mutated strains reached fixation rapidly in 1993-1994 flu season. 2021 BMC infectious diseases Discussion SARS_CoV_2 R384G 39 44 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. Our analytical framework can yield an early warning signal in detecting the transmission advantage due to D614G substitution before the mutation reaching dominance on a real-time basis. 2021 BMC infectious diseases Discussion SARS_CoV_2 D614G 106 111 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. Previous analysis implied that the D614G substitution may alter the conformation of spike protein trimer that shifted toward an ACE2 binding-competent state, and thus may functionally improve receptor binding capacity from a theoretical perspective. 2021 BMC infectious diseases Discussion SARS_CoV_2 D614G 35 40 S 84 89 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. The D614G replacement leads to increased infectivity and stability of the virion and is shown to enhance viral replication in human lung epithelial cells. 2021 BMC infectious diseases Discussion SARS_CoV_2 D614G 4 9 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. The D614G substitution increases host cell entry via ACE2 and transmembrane protease serine 2 (TMPRSS2). 2021 BMC infectious diseases Discussion SARS_CoV_2 D614G 4 9 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. The reasons may include that the increase in transmissibility associated with D614G was counteracted by the effects of local non-pharmaceutical interventions that reduced the overall transmission of COVID-19. 2021 BMC infectious diseases Discussion SARS_CoV_2 D614G 78 83 COVID-19 199 207 34620109 Real-time quantification of the transmission advantage associated with a single mutation in pathogen genomes: a case study on the D614G substitution of SARS-CoV-2. The significant increase in transmissibility associated with the D614G substitution is biologically reasonable according to similar findings reported in previous studies. 2021 BMC infectious diseases Discussion SARS_CoV_2 D614G 65 70 34621509 Characterization of SARS-CoV-2 East Java isolate, Indonesia. Thus, the analysis of the SARS-CoV-2 spike gene shows the mutation of D614G that increases SARS-CoV-2 infectivity, whereas the E484D mutation was correlated with human immune serum neutralization resistance. 2021 F1000Research Discussion SARS_CoV_2 D614G;D614G;E484D;E484D 71;70;128;127 76;75;133;132 S 37 42 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). For example, laboratory developed tests for the detection of L484R, E484K and N501Y (alone or in multiplex) in nasopharyngeal swabs specimen were reported earlier this year, demonstrating excellent clinical performance, and provide an even more economical option in laboratories that have the expertise and infrastructure to validate and perform them. 2021 Journal of clinical virology Discussion SARS_CoV_2 E484K;L484R;N501Y 68;61;78 73;66;83 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). However, these results were generated from a limited number of samples and a cross reaction of E484Q with E484K primers and probes has been previously reported. 2021 Journal of clinical virology Discussion SARS_CoV_2 E484K;E484Q 106;95 111;100 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). Interestingly, the 10 specimens discrepant for the E484K target were B.1.627.1 VOCs, which harbor the E484Q mutation. 2021 Journal of clinical virology Discussion SARS_CoV_2 E484K;E484Q 51;102 56;107 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). Seegene has also launched the AllplexSARS-CoV-2 Master assay that can detect the presence of SARS-CoV-2 via the detection of E, N and RdRP genes and the presence of S gene mutations such as HV69/70 deletion, Y144 deletion, E484K, N501Y and P681H. 2021 Journal of clinical virology Discussion SARS_CoV_2 E484K;N501Y;P681H 223;230;240 228;235;245 RdRP;E;N;S 134;125;128;165 138;126;129;166 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). The detection of E484Q mutation was delayed by 6.15 Ct values on average when compared to the RdRP gene, facilitating differentiation from true positive E484K mutations in most cases, in which the Ct value was within 2 cycles. 2021 Journal of clinical virology Discussion SARS_CoV_2 E484K;E484Q 153;17 158;22 RdRP 94 98 34628158 Evaluation of the clinical and analytical performance of the Seegene allplex SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI). This study that included 871 clinical SARS-CoV-2 specimens, demonstrated the high clinical and analytical performance of the Seegene AllplexSARS-CoV-2 Variants I assay for the detection of SARS-CoV-2 viruses containing HV69/70 deletion, E484K and N501Y mutations in the S gene, demonstrating its suitability for clinical testing. 2021 Journal of clinical virology Discussion SARS_CoV_2 E484K;N501Y 237;247 242;252 S 270 271 34630410 A Barcoded Flow Cytometric Assay to Explore the Antibody Responses Against SARS-CoV-2 Spike and Its Variants. In the case of the alpha variant, we provide direct evidence for a stronger ACE2 binding as the N501Y mutated RBD-CD8 chimera is less well expressed yet better recognized by the ACE2-Ig reagent. 2021 Frontiers in immunology Discussion SARS_CoV_2 N501Y 96 101 RBD 110 113 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Based on microsecond-scale MD simulations, we identified a possible link between a non-synonymous mutation, P108S, frequently observed in patients with mild COVID-19 symptoms in Tokyo, and dynamics of the catalytic site in the main protease. 2021 Biophysics and physicobiology Discussion SARS_CoV_2 P108S 108 113 COVID-19 157 165 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. conducted hydrogen deuterium exchange mass spectroscopy (HDX-MS) to examine difference in dynamics between WT and the P108S mutant protease. 2021 Biophysics and physicobiology Discussion SARS_CoV_2 P108S 118 123 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Considering the differences in flexibility of the loop region at the entrance of the catalytic sites we observed between the WT and P108S mutant, the mechanism of drug binding might be different in the mutant from that of the WT main protease. 2021 Biophysics and physicobiology Discussion SARS_CoV_2 P108S 132 137 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Dominant effects of Km suggest that the P108S mutation reduced the enzymatic activity by interfering substrate binding rather than preventing release of the products, in agreement with our results that the loop region at the entrance of the catalytic site stiffened, making the catalytic dyad less accessible. 2021 Biophysics and physicobiology Discussion SARS_CoV_2 P108S 40 45 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Further studies are certainly necessary to quantitively understand relationships between the mutation P108S and physical properties of the main protease, but our findings will immediately inform design of new protease inhibitors. 2021 Biophysics and physicobiology Discussion SARS_CoV_2 P108S 102 107 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Further, our finding that the catalytic dyad became less accessible upon the P108S mutation were visible only after simulations longer than 4 mus. 2021 Biophysics and physicobiology Discussion SARS_CoV_2 P108S 77 82 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. It is also worth mentioning that our calculations dealt only with the P108S mutation, and we did not evaluate other mutations, which were predicted to be functionally neutral, found in patients in a previous study. 2021 Biophysics and physicobiology Discussion SARS_CoV_2 P108S 70 75 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Therefore, considering the prevalence of the mutation in patients, drug binding to the P108S mutant protease should be studied. 2021 Biophysics and physicobiology Discussion SARS_CoV_2 P108S 87 92 34631338 Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Together with P108S, those mutations may also affect physicochemical properties of the main protease. 2021 Biophysics and physicobiology Discussion SARS_CoV_2 P108S 14 19 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. Although we observed no significant difference between the neutralizing activity of sera against B.1.1.7 and D614G in all patients, the values of neutralizing activity against P.1 and B.1.351 were lower than against D614G, and the neutralizing activity against B.1.351 in particular was much lower. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G;D614G 109;216 114;221 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. As one of the potential explanations for this finding, we note that the N501Y substitution (which is common among these 3 variants) may enhance the binding to ACE2, but its antigenic effects are limited, and it may have little effect on the neutralizing activity of the antibodies. 2021 Open forum infectious diseases Discussion SARS_CoV_2 N501Y 72 77 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. However, our present analyses demonstrate that while some sera of individuals showed similar or high neutralizing activity against P.1 compared with those against D614G, the activity against B.1.351 was consistently lower than that against D614G, indicating that B.1.351 might avoid neutralization more effectively by means other than mutations of the RBD, such as amino acid deletions (242-244 del) and substitutions (D80A, R246I) in the N terminal domain (NTD). 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G;D614G;R246I;D80A 163;240;425;419 168;245;430;423 RBD;N 352;439 355;440 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. However, the E484K mutation, which is found both in P.1 and B.1.351 but not in either D614G or B.1.1.7, has been reported to affect the binding of serum polyclonal neutralizing antibodies. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G;E484K 86;13 91;18 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. In the present study, regardless of the patients' infection time (wave) and disease severity, most of their sera had neutralizing activity against the 4 variants (D614G, B.1.1.7, P.1, and B.1.351), although the neutralizing activity values varied. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G 163 168 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. Interestingly, although we observed that the neutralizing activity against the B.1.1.7 variant seemed to be similar to or slightly lower than that against D614G from the first to third waves in Japan, its activity against B.1.1.7 was higher than that against D614G, P.1, and B.1.351 in the fourth wave, indicating an epidemic of B.1.1.7. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G;D614G 155;259 160;264 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. It is suspected that the conventional D614G variant has already been almost completely replaced by B.1.1.7. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G 38 43 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. On the other hand, because P.1 and B.1.351 have similar mutations in their RBD (including E484K, K417T/N, and N501Y), it might be thought that the neutralization of both variants would be affected similarly. 2021 Open forum infectious diseases Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y 90;97;97;110 95;104;104;115 RBD 75 78 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. Our results may suggest that the mutations in B.1.1.7 could cause the conformational change of its spike protein, which affects immune recognition for D614G. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G 151 156 S 99 104 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. Some individuals that showed high neutralizing activity against D614G and B.1.1.7, and also had high activity against P.1 and B.1.351, indicating that individuals infected with D614G or B.1.1.7 also could have the neutralizing antibody against P.1 and B.1.351. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G;D614G 64;177 69;182 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. The correlation between serum neutralization activity against D614G and clinical severity has been described, and our present findings revealed a similar correlation for 3 other variants. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G 62 67 34631915 Cross-Neutralizing Activity Against SARS-CoV-2 Variants in COVID-19 Patients: Comparison of 4 Waves of the Pandemic in Japan. To predict and help prevent the further spread of SARS-CoV-2 infection, it is necessary to determine whether the neutralizing activity in COVID-19 patients infected with the D614G variant has similar activity against the newly emerging variants. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G 174 179 COVID-19;COVID-19 138;50 146;70 34634289 SARS-CoV-2 monoclonal antibodies with therapeutic potential: Broad neutralizing activity and No evidence of antibody-dependent enhancement. Further evidence shows receptor-binding domain (RBD) mutations E484K and combined K417N and N501Y mutations of SARS-CoV-2 B.1.351 and P.1 variants as vulnerabilities to multiple SARS-CoV-2 neutralizing mAbs engaging the RBD domain, and polyclonal Abs from convalescent sera or vaccine-induced immune sera. 2021 Antiviral research Discussion SARS_CoV_2 E484K;K417N;N501Y 63;82;92 68;87;97 RBD;RBD 48;220 51;223 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. Class 2 antibodies interact with the S1-RBD residue E484; as a result, the E484K mutation confers resistance to this class of neutralizing antibodies. 2021 FASEB journal Discussion SARS_CoV_2 E484K 75 80 RBD 40 43 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. Given high correlation between in vitro blocking assays using recombinant proteins and live virus neutralizing potential when performed with the Wuhan variant, it can be expected that some of the VNAR-hFc antibodies would retain their blocking activity when tested against live virus containing N501Y and E484K mutations. 2021 FASEB journal Discussion SARS_CoV_2 E484K;N501Y 305;295 310;300 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. Of the 10 VNAR-hFc antibodies tested against S1-RBD E484K, three showed reduction in EC50 binding but without losing their IC50 blocking activity. 2021 FASEB journal Discussion SARS_CoV_2 E484K 52 57 RBD 48 51 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. Our results showed that the N501Y mutation in S1-RBD had minor effect on binding and blocking ability of the majority of tested VNAR-hFc antibodies. 2021 FASEB journal Discussion SARS_CoV_2 N501Y 28 33 RBD 49 52 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. The clusters share some of the mutations linked with viral escape, including N501Y (Alpha, Beta, and Gamma), E484K (Beta and Gamma) and K417N/T (Beta and Gamma). 2021 FASEB journal Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y 109;136;136;77 114;143;143;82 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. The E484K mutation was reported to abolish one of the salt bridges otherwise formed between ACE2 and S1-RBD. 2021 FASEB journal Discussion SARS_CoV_2 E484K 4 9 RBD 104 107 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. The N501Y mutation was shown by deep mutation scanning to enhance binding affinity to ACE2 and to increase infectivity and virulence in a mouse model. 2021 FASEB journal Discussion SARS_CoV_2 N501Y 4 9 34637549 Single domain shark VNAR antibodies neutralize SARS-CoV-2 infection in vitro. The VNAR-hFc antibodies were also able to block S1-RBD with N501Y or E484K mutations in vitro, thus are expected to retain neutralizing potential toward virus variants that carry those substitutions. 2021 FASEB journal Discussion SARS_CoV_2 E484K;N501Y 69;60 74;65 RBD 51 54 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. 4) through the acquisition of the C14408T mutation. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 C14408T 34 41 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. As already reported, the SS2 cluster did not spread successfully in the EU/EEA; however, the phylogenetic analysis suggests that this cluster evolved in the SS2B through the acquisition of the G11083T mutation. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 G11083T 193 200 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. At the beginning of February, the virus, with this mutation, was present in several European countries; this is supported by the high number of SS4 genomes detected in several European countries that carried the additional C14408T mutation only. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 C14408T 223 230 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. Conversely, the C14408T resulted in the amino acid substitution P > L in the RdRp. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 C14408T 16 23 RdRP 77 81 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. Following its first detection in Europe (EPI_ISL_406862), the SS4 cluster evolved early, acquiring the mutation C14408T. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 C14408T 112 119 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. Furthermore, several mutations in this cluster were restricted to specific countries (e.g., A12790G/C13568T found in genomes from Sweden, G12832A from Austria). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 A12790G;G12832A;C13568T 92;138;100 99;145;107 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. Indeed, C14805T mutation was found in SS2 cluster as well as in almost all the genomes belonging to the SS2B cluster. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 C14805T 8 15 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. Noteworthy, important mutations contributing to the evolutionary success to some strains (i.e., with A23403G) were not present in these unclassified clusters. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 A23403G 101 108 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. On February 21st, 2020, two genomes collected in France that harbored the C14408T, already carried two additional mutations, the C1059T and the G25563T (EPI_ISL_418218, EPI_ISL_429968). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 C1059T;C14408T;G25563T 129;74;144 135;81;151 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. Similarly, the successful spread of the SS1 cluster in Spain appears to be linked to the acquisition of the C14805T mutation. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 C14805T 108 115 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. Taking into account the mutational rate of the SS4 cluster (1.,2 x 10-3, sub/site/year), the first appearance of C14408T mutation may be estimated at molecular level, to February 1st, 2020 (IC95 +- 9). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 C14408T 113 120 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The C14408T and C14805T mutations fall in a region of the ORF1ab gene whose product is the nsp12 protein, the RNA-dependent RNA polymerase (RdRp). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 C14408T;C14805T 4;16 11;23 RdRp;ORF1ab;Nsp12;RdRP 110;58;91;140 138;64;96;144 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The C14408T and the C14805T mutations could have played an important role in the evolution of SARS-CoV-2. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 C14408T;C14805T 4;20 11;27 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The C14805T is a silent mutation that could act to enhance the role of a cis-domain or to act specifically as a cis-site. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 C14805T 4 11 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The mutation rate of SARS-CoV-2 was estimated to be 6.2 x 10-4 sub/site/year; after the acquisition of C14408T and C14805T mutations, the mutation rates in SS4, SS1, and SS2B clusters were estimated to be double, with rates of 1.24 x 10-3, 1.48 x 10-3 and 1.25 x 10-3 sub/site/year values, respectively. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 C14408T;C14805T 103;115 110;122 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. The success of the SS4 cluster is linked to the acquisition of the C14408T; moreover, about 56% of SNVs with frequency >= 1% were related to this cluster, suggesting an acceleration of the mutation rate. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 C14408T 67 74 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. Then the virus evolved into two directions: the first one, through the acquisition of the C1059T and later of G25563T (SS4B), and another one with the triplet A28881G, A28882G and G28883C (SS4C). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 A28881G;A28882G;C1059T;G25563T;G28883C 159;168;90;110;180 166;175;96;117;187 34637920 Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. This cluster harbored the triple A28881G, A28882G and G28883C mutations and, as well as the SS4B, it represents a further step in the evolution of the SS4 cluster. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 A28881G;A28882G;G28883C 33;42;54 40;49;61 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. Additionally, mutation Q498R, besides increasing the affinity with hACE2, was frequently involved in clashes with Abs. 2021 International journal of molecular sciences Discussion SARS_CoV_2 Q498R 23 28 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. An engineered ACE2-rigid-foldon, as a trimeric protein (PDB 7CT5) inhibits eight naturally occurring mutants, including D614G and seven other RBD domain mutants. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G 120 125 RBD 142 145 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. As a result, the energy barrier for the conformational change is reduced and SARS-CoV-2 D614G strains have increased sensitivity to the presence of hACE2, which could be the underlying mechanism for enhanced infectivity observed in these strains. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G 88 93 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. As such, it is hypothesised that the Delta variant emerged mainly as a result of reduced immune recognition and enhanced transmissibility nonrelated with affinity (effects from mutations D614G, P681 and D950N). 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G;D950N 187;203 192;208 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. Crucially, variant Epsilon has additional mutations, S13I and W152C, resulting in severe decrease of neutralization for NTD-directed Abs, due to a new disulphide bond inducing a conformational change. 2021 International journal of molecular sciences Discussion SARS_CoV_2 S13I;W152C 53;62 57;67 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. From all the mutations in prevalent variants by June 2021 worldwide, mutation D614G is the only one located outside the RBD, and therefore with no direct effect in affinity (PDB 7DF4), but nevertheless, causing increased infectivity and transmission. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G 78 83 RBD 120 123 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. Importantly, mutation N501Y is not found in the Delta variant, in contrast with all other variants of concern.Mutation N501Y results in the highest increase in hACE2 affinity conferred by a single RBD mutation. 2021 International journal of molecular sciences Discussion SARS_CoV_2 N501Y;N501Y 22;119 27;124 RBD 197 200 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. Importantly, N501Y and E484K were present, emerged frequently in earlier stages and have already been found in emerging variants, suggesting some predicting potential for possible new variants. 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484K;N501Y 23;13 28;18 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. In general, mutation D614G greatly disturbs the interactions between subunits S1 and S2, due to the weakened interactions established by the side chain of glycine, in comparison with aspartic acid. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G 21 26 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. In the Delta variant, mutations T19R, E156-, F157- and R158G severely affect NTD directed Abs, due to the adoption of an alpha-helical conformation, instead of the original beta-strand. 2021 International journal of molecular sciences Discussion SARS_CoV_2 R158G;T19R 55;32 60;36 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. In the structure with mutation G485R (PDB 7LO4), residue 485, mutating from glycine to arginine, is not directly involved in the hACE2-SARS-CoV-2 S protein interaction, but close to Ab binding epitopes and in a loop region that makes multiple contacts with hACE2. 2021 International journal of molecular sciences Discussion SARS_CoV_2 G485R 31 36 S 146 147 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. L452R has also appeared in variant Epsilon identified in California, reaching a maximum of 20% of new cases in the United States, before variant Delta became prevalent. 2021 International journal of molecular sciences Discussion SARS_CoV_2 L452R 0 5 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. Mutation K417T deletes a salt bridge with D30 from hACE2, potentially leading to a decreased affinity. 2021 International journal of molecular sciences Discussion SARS_CoV_2 K417T 9 14 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. Mutation L452R causes a steric hindrance to Ab binding, retrieved from structure 7CM4, without affecting binding to hACE2 (Figure 10) but causing a greater than 10-fold decrease in neutralization potency for RBD-specific Abs. 2021 International journal of molecular sciences Discussion SARS_CoV_2 L452R 9 14 RBD 208 211 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. Notably, one mutation is common to all prevalent strains worldwide, D614G, associated with increased infectivity, although with no direct effect to the RBD. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G 68 73 RBD 152 155 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. One of the defining characteristics of this variant is the high number of mutations, particularly in the spike protein, with three mutations specific to the RBD (K417T, E484K and N501Y), that lead to a 19-fold increase in affinity compared to the Wuhan strain. 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484K;N501Y;K417T 169;179;162 174;184;167 S;RBD 105;157 110;160 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. Potentially fundamental for immune escape are mutations K417N, and particularly L452R, both affecting Ab binding, and occurring in the RBD. 2021 International journal of molecular sciences Discussion SARS_CoV_2 K417N;L452R 56;80 61;85 RBD 135 138 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. Regarding infectivity, this strain possesses mutation D614G and one mutation in the RBD, T478K. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G;T478K 54;89 59;94 RBD 84 87 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. Regarding natural occurring mutations, two structures are available, a strain with mutation G485R and variant Gamma. 2021 International journal of molecular sciences Discussion SARS_CoV_2 G485R 92 97 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. Some of the mutations present in the optimized RBD are also present in new variants as critical mutations in variants of concern, appearing often and early in the mutagenesis process, particularly mutations N501Y (variants Alpha, Beta and Gamma) and E484K (variants Beta and Gamma). 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484K;N501Y 250;207 255;212 RBD 47 50 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. The increased affinity is due to both mutation E484K, improving the electrostatic complementarity with the negatively charged hACE2, through the change from a carboxylic acid (E) to an amine group (K), and mutation N501Y creating an additional ring stacking interaction, with the change from the short-chained asparagine to the aromatic chained tyrosine (Figure 9). 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484K;N501Y 47;215 52;220 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. The most common mutations appearing in the later phases, suggest that the next variants with increased infectivity might include mutation Q498R or N460K, as they both significantly increase the affinity and emerged late in the optimization process. 2021 International journal of molecular sciences Discussion SARS_CoV_2 N460K;Q498R 147;138 152;143 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. The mutated RBD (PDB 7BH9) presents, among others, eight amino acid changes actively engaged in the interaction with hACE2, namely V445K, N460K, I468T, T470M, S477N, E484K, Q498R and N501Y. 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484K;I468T;N460K;N501Y;Q498R;S477N;T470M;V445K 166;145;138;183;173;159;152;131 171;150;143;188;178;164;157;136 RBD 12 15 34639178 SARS-CoV-2 Virus-Host Interaction: Currently Available Structures and Implications of Variant Emergence on Infectivity and Immune Response. This may suggest that the in vitro process is possibly mimicking natural evolution, and that artificial selection may have important predictive capabilities over new emerging mutations.Considering the main variants in circulation, only one mutation providing a clear survival advantage is located outside the RBD (mutation D614G, discussed in more detail ahead). 2021 International journal of molecular sciences Discussion SARS_CoV_2 D614G 323 328 RBD 309 312 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. 2A,B, Table S2), we considered all possible mutations actually reported at this position in circulating viral variants (i.e., E484A/D/G/K/Q/R/V), and found that all these amino acid variations should confer strong escaping ability to bamlanivimab. 2021 Scientific reports Discussion SARS_CoV_2 E484A;E484D;E484G;E484K;E484Q;E484R;E484V 126;126;126;126;126;126;126 143;143;143;143;143;143;143 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. And this, in turn, support the view that vaccination elicits a natural infection-like antibody response, and that spike variants like E484K may spread as antigenic evolutions of SARS-CoV-2 to efficiently evade this response. 2021 Scientific reports Discussion SARS_CoV_2 E484K 134 139 S 114 119 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. As a conclusive remark concerning the available anti-SARS-CoV-2 vaccines, according to the report by Andreano and Rappuoli published on May 10, 2021 in Nature Medicine the efficacy of the FDA/EMA approved Ad26.COV2-S vaccine (now Janssen COVID-19 Vaccine) and the EMA approved Oxford-AstraZeneca ChAdOx1 (now Vaxzevria) against the variant B.1.351 (South Africa now Beta, with E484K, K417N and N501Y as spike MOIs) decreased from 85 to 57% and from 62 to 10%, respectively. 2021 Scientific reports Discussion SARS_CoV_2 E484K;K417N;N501Y 377;384;394 382;389;399 S;S 403;215 408;216 COVID-19 238 246 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Collier and coworkers very recently reported that the introduction of the E484K mutation in the B.1.1.7 background (to account for the new VOC B.1.1.7 + E484K found in the virus isolated both in UK and in Pennsylvania, USA) led to robust loss of neutralizing activity by 19 out of 31 vaccine-elicited antibodies and mAbs if compared with the decrease in sensitivity conferred by the mutations in B.1.1.7 alone. 2021 Scientific reports Discussion SARS_CoV_2 E484K;E484K 74;153 79;158 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Concerning the alternative LY-CoV016 mAb, the official Lilly's fact sheet reports that SARS-CoV-2 spike mutants showing reduced susceptibility to etesevimab include substitutions K417N, D420N, and N460K/S/T. 2021 Scientific reports Discussion SARS_CoV_2 D420N;K417N;N460K;N460S;N460T 186;179;197;197;197 191;184;206;206;206 S 98 103 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Finally, and in full agreement with Lilly's data, LY-CoV016 is also found to be escaped by all spike N460 variations (N460I/K/S/T). 2021 Scientific reports Discussion SARS_CoV_2 N460I;N460K;N460S;N460T 118;118;118;118 129;129;129;129 S 95 100 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. From a validation standpoint, the E484K mutation is present in a large number of VOC/VOI/VUM:including the lineages B.1.525 (now Eta, firstly reported in Nigeria on 12/20), P.1 (now Gamma) and P.2 (now Zeta, Brazil, 12/20), P.3 (now Theta, The Philippines, 01/21), B.1.351 (now Beta, South Africa, 09/20), B.1.621 (Colombia, 01/2021), and some strains of lineages B.1.1.7 (firstly reported in the United Kingdom on 09/20, now Alpha) and B.1.526 (reported on 11/20 in the city of New York, USA, now Iota):and it is indeed well known to confer substantial loss of sensitivity to neutralizing Abs found in sera of convalescent and vaccinated individuals. 2021 Scientific reports Discussion SARS_CoV_2 E484K 34 39 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. However, L452R is a spike mutation of interest (MOI) present in the VOC lineages B.1.427/B.1.429 (reported in California, USA, on 09/20, now Epsilon), B.1.526.1 (New York City, USA, 10/20, Iota subtype), and in the B1.617.1 (Kappa)/B.1.617.2 (Delta)/B.1.617.3 lineages now rapidly and deadly spreading in India (12/20-02/21), where it is always found along with the D614G substitution. 2021 Scientific reports Discussion SARS_CoV_2 D614G;L452R 366;9 371;14 S 20 25 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Importantly, the L452R mutation is also present in tandem with E484Q, in particular in the B.1.617.1 (Kappa) variant that is responsible for actual disease outbreaks in 49 countries in all six WHO regions. 2021 Scientific reports Discussion SARS_CoV_2 E484Q;L452R 63;17 68;22 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. In addition, in the current study we identify three further single amino acid changes along the primary sequence of SARS-CoV-2 spike protein that:although not reported as current VOC/VOI/VUM:could escape the action of LY-CoV016, that is the T415P and the Y489C/S mutations. 2021 Scientific reports Discussion SARS_CoV_2 T415P;Y489C;Y489S 241;255;255 246;262;262 S 127 132 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. In agreement with this and other evidences, our current computational alanine/mutagenesis study marks K417 and all its reported variants (K417E/N/R/T) as the strongest hot spots in eliciting potential escape to the LY-CoV016 mAb. 2021 Scientific reports Discussion SARS_CoV_2 K417E;K417N;K417R;K417T 138;138;138;138 149;149;149;149 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. In all these cases, the spike E484K mutation appears to be the real key player in reducing neutralization by antibodies induced by the vaccines. 2021 Scientific reports Discussion SARS_CoV_2 E484K 30 35 S 24 29 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. In parallel, the titer neutralizing antibodies induced by the m-RNA vaccines approved by both governmental agencies (i.e., the BNT162b2 Pfizer/BioNTech COVID-19 vaccine/Comirnaty and COVID-19 vaccine Moderna) against the same SARS-CoV-2 variant is reported to decline by 7- to 12 -fold, while no negative effect on neutralization is seen for the B.1.1.7 (Alpha) variant (with N501Y/D614G as spike MOIs). 2021 Scientific reports Discussion SARS_CoV_2 N501Y;D614G 376;382 381;387 S 391 396 COVID-19;COVID-19 152;183 160;191 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. In silico mutagenesis of Q493 and S494 into the circulating variants (Q493H/K/L/R, and S494A/P/R/T) not only confirms Lilly's data about Q493R and S494P as resistant mutations for LY-CoV555 but also predicts a potential role of other substitutions at these two S-protein positions (i.e., Q493K/L and S494A/P/R) in mediating evasion to this mAb. 2021 Scientific reports Discussion SARS_CoV_2 Q493K;Q493L;Q493R;S494A;S494P;S494R;S494A;S494P;S494R;S494T;S494P;Q493L;Q493H;Q493K;Q493R 288;288;137;300;300;300;87;87;87;87;147;70;70;70;70 295;295;142;309;309;309;98;98;98;98;152;81;81;81;81 S 261 262 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Interestingly, the corresponding mutagenesis into all reported variants (F490L/S/V/Y) revealed that only the F490S spike mutant is a potential escapee for LY-CoV555. 2021 Scientific reports Discussion SARS_CoV_2 F490S;F490L;F490S;F490V;F490Y 109;73;73;73;73 114;84;84;84;84 S 115 120 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Moreover, our data also suggest that the co-presence of the E484Q. 2021 Scientific reports Discussion SARS_CoV_2 E484Q 60 65 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Moreover, the E484Q/V/A/G/D mutations have been just described by Chen et al. 2021 Scientific reports Discussion SARS_CoV_2 E484A;E484D;E484G;E484Q;E484V 14;14;14;14;14 27;27;27;27;27 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Of note F490S, although listed in the actual spike circulating mutations, is not a component of any VOC or VOI listed so far. 2021 Scientific reports Discussion SARS_CoV_2 F490S 8 13 S 45 50 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Of note, the K417N and K417T in particular are spike MOIs in the SARS-CoV2 VOC lineages B.1.351 (Beta) and P.1 (Gamma), respectively. 2021 Scientific reports Discussion SARS_CoV_2 K417N;K417T 13;23 18;28 S 47 52 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Our present data support the escaping potential of the L452R viral mutation with respect to bamlanivimab. 2021 Scientific reports Discussion SARS_CoV_2 L452R 55 60 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Remarkably, the spike S494P mutation is a component of the B.1.17 + S494P VOC/VUM identified in United Kingdom in January 2021. 2021 Scientific reports Discussion SARS_CoV_2 S494P;S494P 22;68 27;73 S 16 21 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Similarly, not only the D420N but all reported circulating spike mutations at positions 420 are predicted by our study to be endowed with high LY-CoV016 escaping potential. 2021 Scientific reports Discussion SARS_CoV_2 D420N 24 29 S 59 64 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Spike variants identified in these studies that presented reduced susceptibility to the LY-CoV555 mAb included the following substitutions: E484D/K/Q, F490S, Q493R, and S494P. 2021 Scientific reports Discussion SARS_CoV_2 E484D;E484K;E484Q;F490S;Q493R;S494P 140;140;140;151;158;169 149;149;149;156;163;174 S 0 5 34642465 Molecular rationale for SARS-CoV-2 spike circulating mutations able to escape bamlanivimab and etesevimab monoclonal antibodies. Using a pseudo-virus expressing the spike protein from the B.1.427/B.1.429 (Epsilon) lineages, or the L452R substitution only, however, the researchers at Lilly reported reduced susceptibility to bamlanivimab and etesevimab together of 7.7-fold or 7.4-fold, respectively. 2021 Scientific reports Discussion SARS_CoV_2 L452R 102 107 S 36 41 34644287 Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. Another example of convergent evolution is the single sequence classified as B.1.1.306, which carries not only the mutation E484K inherited from N.9, but also the N501Y variant on the Spike protein gene. 2021 PLoS neglected tropical diseases Discussion SARS_CoV_2 E484K;N501Y 124;163 129;168 S 184 189 34644287 Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. Finally, the third newly-detected convergent event described in this work is the E484K and N439K variants in a sample of B.1.1.29 from Rio Grande do Norte. 2021 PLoS neglected tropical diseases Discussion SARS_CoV_2 E484K;N439K 81;91 86;96 34644287 Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. Indeed, all convergent mutations aforementioned are somehow associated with viral escape from immune system response: N439K has shown to escape immune escape from both polyclonal and monoclonal antibodies; E484K has been associated with escape from both vaccines and previous infections; and N501Y leads to increased binding specificity to the receptor and is associated with high transmissibility while also escaping immune response. 2021 PLoS neglected tropical diseases Discussion SARS_CoV_2 E484K;N439K;N501Y 206;118;292 211;123;297 34644287 Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. N501Y mutation was firstly identified in B.1.1.7 lineage in the United Kingdom and recently detected in the P.1 lineage. 2021 PLoS neglected tropical diseases Discussion SARS_CoV_2 N501Y 0 5 34644287 Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. Previous studies have shown that both N501Y and E484K have independently emerged in patients with persistent infection. 2021 PLoS neglected tropical diseases Discussion SARS_CoV_2 E484K;N501Y 48;38 53;43 34644287 Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. Remarkably, we observed the convergent occurrence of E484K mutation in this new clade. 2021 PLoS neglected tropical diseases Discussion SARS_CoV_2 E484K 53 58 34644287 Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil. The N439K mutation was also first detected at B.1.1.7 samples from the United Kingdom. 2021 PLoS neglected tropical diseases Discussion SARS_CoV_2 N439K 4 9 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. After the onset of the SARS-CoV-2 outbreak, the D614G strain rapidly replaced the original virus strain and became the dominant variant. 2021 Communications biology Discussion SARS_CoV_2 D614G 48 53 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. E484K was found to be the key mutation that caused the most obvious neutralization insensitivity, while B.1.351 was the variant that exhibited the most significant immune escaped. 2021 Communications biology Discussion SARS_CoV_2 E484K 0 5 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Further analysis showed that M1229I may be the key mutation that responsible for the reduced infectivity. 2021 Communications biology Discussion SARS_CoV_2 M1229I 29 35 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Further studies showed that the host cell infectivity of D614G was increased, compared with the original virus, because of mutation-related structure changes. 2021 Communications biology Discussion SARS_CoV_2 D614G 57 62 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Furthermore, a previous study demonstrated increased binding of N501Y to mouse ACE2, which implies differences in host tropism. 2021 Communications biology Discussion SARS_CoV_2 N501Y 64 69 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Here we found that the K417T mutation in the P.1 variant has a similar effect. 2021 Communications biology Discussion SARS_CoV_2 K417T 23 28 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. However, modification of E484K in the RBD led to the most marked change in immune escape. 2021 Communications biology Discussion SARS_CoV_2 E484K 25 30 RBD 38 41 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. However, neutralization analyses of convalescent sera from D614G-, B.1.1.7- and B.1.351-infected patients indicate that B.1.351 variant induced much lower antibody production, compared with other variants. 2021 Communications biology Discussion SARS_CoV_2 D614G 59 64 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. However, variants carrying the E484K mutation had distinct reductions in neutralization susceptibility. 2021 Communications biology Discussion SARS_CoV_2 E484K 31 36 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Moreover, some studies have shown that selective pressure from therapeutic mAbs or convalescent serum could induce E484K or E484Q mutations. 2021 Communications biology Discussion SARS_CoV_2 E484K;E484Q 115;124 120;129 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Moreover, the increased infectivity of L452R mutation and B.1.429 variant were consistent with the reports by Deng et al. 2021 Communications biology Discussion SARS_CoV_2 L452R 39 44 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Our previous study revealed that the K417N mutation in the RBD region of B.1.351 led to the enhanced convalescence sera neutralization activity. 2021 Communications biology Discussion SARS_CoV_2 K417N 37 42 RBD 59 62 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Our results demonstrate that the K417N/T, E484K, and N501Y mutations change host tropism, implying possible transmission of SARS-CoV-2 variants in mice. 2021 Communications biology Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y 42;33;33;53 47;40;40;58 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Six antibodies showed reduced neutralization against N501Y, including mAbs CB6, which was consistent with previous reports. 2021 Communications biology Discussion SARS_CoV_2 N501Y 53 58 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Slightly enhancements of infectivity were observed among most of the tested variants, compared with the D614G reference strain, whereas the B.1.1.298 variants (mink cluster 5) displayed significantly decreased infectivity. 2021 Communications biology Discussion SARS_CoV_2 D614G 104 109 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. The increase in K417N sensitivity to serum neutralization has been discussed in our previous paper. 2021 Communications biology Discussion SARS_CoV_2 K417N 16 21 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. The increased affinity to ACE2 receptors caused by RBD mutations (e.g., E484K, N501Y) or increased cleavage activity by mutations adjusted to the furin site (e.g., P681H) may facilitate the function of enzymes. 2021 Communications biology Discussion SARS_CoV_2 E484K;N501Y;P681H 72;79;164 77;84;169 RBD 51 54 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. The increased neutralization against K417N by antibodies against RBM was also observed in other group. 2021 Communications biology Discussion SARS_CoV_2 K417N 37 42 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. The K417N/T mutation increases the probability of conversion to the open conformation, thus exposing epitopes to neutralizing antibodies, which would increase the likelihood of virus neutralization by sera containing polyclonal antibodies. 2021 Communications biology Discussion SARS_CoV_2 K417N;K417T 4;4 11;11 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. We found that K417N/T, E484K, and N501Y mutations significantly increased the ability of SARS-CoV-2 to infect 293 T cells overexpressing mouse ACE2; variants carrying these mutations (i.e., B.1.1.7, B.1.351, P.1, P.2, B.1.429, B.1.525, B.1.526-2, and B.1.1.318) showed similar changes in infectivity. 2021 Communications biology Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y 23;14;14;34 28;21;21;39 34645933 Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. When TMPRSS2 overexpressed infection was compared to mock 293T-ACE2 cells, the enhancement of infectivity by TMPRSS2 for the P.1 variant was almost fourfold that for the D614G variant. 2021 Communications biology Discussion SARS_CoV_2 D614G 170 175 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Additionally, we show that the E484Q mutation alone can cause LY-CoV555 to lose neutralizing activity as well, which is consistent with the much larger free energy change (DeltaDeltaG) found in MD simulation (Table 1). 2021 Journal of chemical information and modeling Discussion SARS_CoV_2 E484Q 31 36 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Applying both pseudovirions and live virus-based neutralization assays, we demonstrated that LY-CoV555 can neutralize original SARS-CoV-2 virus but completely lost neutralizing activity against the Kappa variant carrying L452R and E484Q mutations. 2021 Journal of chemical information and modeling Discussion SARS_CoV_2 E484Q;L452R 231;221 236;226 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. For example, E484 coordinates N52/S55 (through hydrogen bonds) in the complex of the RBD and the antibody S2M11, and consequently, the mutation E484Q might weaken the complex, which warrants further studies. 2021 Journal of chemical information and modeling Discussion SARS_CoV_2 E484Q 144 149 RBD 85 88 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. In the in silico part of this study, we assumed that LY-CoV555 targets RBD-v at the same epitope, which leads to our conclusion that based on FEP calculations the double mutations L452R and E484Q in the Kappa variant can significantly reduce LY-CoV555's binding affinity to RBD-v. 2021 Journal of chemical information and modeling Discussion SARS_CoV_2 E484Q;L452R 190;180 195;185 RBD;RBD 71;274 74;277 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. It is worth noting that the recent sub-lineage of B.1.617 (dubbed as Delta+) contains the K417N mutation, allowing the virus to escape LY-CoV016 as well. 2021 Journal of chemical information and modeling Discussion SARS_CoV_2 K417N 90 95 34648284 Structure-Function Analysis of Resistance to Bamlanivimab by SARS-CoV-2 Variants Kappa, Delta, and Lambda. Our alchemy FEP calculations show that binding free energy changes for L452R and E484K mutations are 3.04 and 22.22 kcal/mol, respectively, indicating that these two mutations substantially weaken the binding between RBD-v and LY-CoV555 and thus are evasive. 2021 Journal of chemical information and modeling Discussion SARS_CoV_2 E484K;L452R 81;71 86;76 RBD 217 220 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Although additional studies elaborated the importance of the N501Y mutation, we are the first to use N501Y to model emerging SARS-CoV-2 variants in vivo. 2021 Cell reports Discussion SARS_CoV_2 N501Y;N501Y 61;101 66;106 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Although we show that the N501Y variant drives a species switch of SARS-CoV-2 PsVs to the mouse (Figure 1), we are not the first group to show the importance of this point mutation. 2021 Cell reports Discussion SARS_CoV_2 N501Y 26 31 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. As the pandemic continues, SARS-CoV-2 variants with greater immune escape potential, such as those modeled using the N501Y + K417N + E484K + D614G variant PsV, have dominated new COVID-19 cases globally. 2021 Cell reports Discussion SARS_CoV_2 D614G;E484K;K417N;N501Y 141;133;125;117 146;138;130;122 COVID-19 179 187 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Here we demonstrate the ability of N501Y-bearing SARS-CoV-2 variants to model COVID-19 in common laboratory mouse strains. 2021 Cell reports Discussion SARS_CoV_2 N501Y 35 40 COVID-19 78 86 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. In future murine PsV reinfection studies, the N501Y + K417N + E484K + D614G PsV could be used for primary infection, followed by other emerging variant PsVs. 2021 Cell reports Discussion SARS_CoV_2 D614G;E484K;K417N;N501Y 70;62;54;46 75;67;59;51 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. In this study, we demonstrate that the N501Y SARS-CoV-2 variant permits enhanced hACE2 binding, species switch, and subsequent high-level VSV PsV infection in unmodified laboratory mice. 2021 Cell reports Discussion SARS_CoV_2 N501Y 39 44 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. It was first demonstrated in an in vivo passaged preparation of SARS-CoV-2 that possessed murine tropism and carried the N501Y mutation. 2021 Cell reports Discussion SARS_CoV_2 N501Y 121 126 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. It was interesting that there was no significant difference in IgAs' and IgMs' ability to bind the WT versus N501Y + K417N + E484K + D614G variant RBD. 2021 Cell reports Discussion SARS_CoV_2 D614G;E484K;K417N;N501Y 133;125;117;109 138;130;122;114 RBD 147 150 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Our study also supports the possibility that rodents could become infected with variants containing N501Y. 2021 Cell reports Discussion SARS_CoV_2 N501Y 100 105 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. Our study demonstrated that N501Y + K417N + E484K + D614G PsVs can escape antibodies generated by N501Y + D614G PsVs, allowing successful secondary infection in mice. 2021 Cell reports Discussion SARS_CoV_2 D614G;D614G;E484K;K417N;N501Y;N501Y 52;106;44;36;28;98 57;111;49;41;33;103 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. There are many potential explanations for the lower infectivity observed for the Los Angeles variant, including the theory that L452R drives enhanced transmissibility but not necessarily infectivity. 2021 Cell reports Discussion SARS_CoV_2 L452R 128 133 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. This is further supported by our study regarding infectivity of PsVs incorporating mutations found in the India variant because the L452R mutation was also present and did not mediate enhancement of infection compared with the South Africa variant PsV. 2021 Cell reports Discussion SARS_CoV_2 L452R 132 137 34648735 In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential. When exploring the ability of antibodies in both groups of individuals to bind the WT RBD versus N501Y + K417N + E484K + D614G variant RBD, we observed significant ablation of binding to the variant, particularly for IgGs. 2021 Cell reports Discussion SARS_CoV_2 D614G;E484K;K417N;N501Y 121;113;105;97 126;118;110;102 RBD;RBD 86;135 89;138 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. L452R and R346S co-mutations are present in some strains from different lineages in particular a new lineage C.36. 2021 Genome medicine Discussion SARS_CoV_2 R346S;L452R 10;0 15;5 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Our comprehensive escape mutation map based on the natural substitutions of the binding hot spots not only confirms the widely circulating strains carrying important immune escape RBD mutations such as K417N, E484K, and L452R, but also facilitates the identification of new immune escape-enabling mutations that are already present at clinical isolates such as F486L, N450K, F490S, and R346S. 2021 Genome medicine Discussion SARS_CoV_2 E484K;F486L;F490S;K417N;L452R;N450K;R346S 209;361;375;202;220;368;386 214;366;380;207;225;373;391 RBD 180 183 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Our previous study has also demonstrated that the SARS-CoV-2 RBD carrying L452K exhibits enhanced ACE2 binding. 2021 Genome medicine Discussion SARS_CoV_2 L452K 74 79 RBD 61 64 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. S7, the molecular epidemiology analysis as of June 2021 demonstrated that all the four mutations (F486L, N450K, F490S, and R346S) have occurred in the B.1.1.7 linage (Alpha) and F490S has appeared in other lineages of concern such as B.1.617.2 (Delta), B.1.429 (Epsilon), B.1.351 (Beta), and C.37 (Lambda). 2021 Genome medicine Discussion SARS_CoV_2 F490S;F490S;N450K;R346S;F486L 112;178;105;123;98 117;183;110;128;103 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. The substitution L452R was particularly notable, as it also conferred resistance to multiple NAbs and human convalescent plasma. 2021 Genome medicine Discussion SARS_CoV_2 L452R 17 22 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. The valuable information that K417 are essential for multiple prototype VH3-53/3-66 NAb recognition allows us to re-interpret the potential significance of the mutation K417N and K417T present in B.1.351 and P.1. 2021 Genome medicine Discussion SARS_CoV_2 K417N;K417T 169;179 174;184 34649620 Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Therefore, circulating SARS-CoV-2 variants with L452R in the RBD region might be more infectious and less susceptible to NAbs and vaccines than variants without this mutation. 2021 Genome medicine Discussion SARS_CoV_2 L452R 48 53 RBD 61 64 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. AY.2 additionally harbours V70F (unique among delta lineages), A222V (shared with AY.9, AY.10, AY.11, AY.19 and AY.24) and K417N (as for AY.1) K356N and V1228L have also been rarely reported. 2021 Emerging microbes & infections Discussion SARS_CoV_2 A222V;K356N;K417N;V1228L;V70F 63;143;123;153;27 68;148;128;159;31 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. AY.3 additionally harbours E156G. 2021 Emerging microbes & infections Discussion SARS_CoV_2 E156G 27 32 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. AY.3.1 never harbours T95I nor A222V, and harbours F157C and R158G at about 10% frequencies. 2021 Emerging microbes & infections Discussion SARS_CoV_2 A222V;F157C;R158G;T95I 31;51;61;22 36;56;66;26 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. B.1.617.2 is resistant to bamlanivimab and moderately evades convalescent or BNT162b2-elicited sera, which is similar in magnitude to the loss of sensitivity conferred by L452R or E484Q alone. 2021 Emerging microbes & infections Discussion SARS_CoV_2 E484Q;L452R 180;171 185;176 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. Furthermore, P681R mutation significantly augments syncytium formation in Calu-3 cells and hamsters compared to the B.1.617.1 Spike protein, potentially contributing to increased pathogenesis observed in hamsters and infection growth rates observed in humans. 2021 Emerging microbes & infections Discussion SARS_CoV_2 P681R 13 18 S 126 131 34651569 Spike protein evolution in the SARS-CoV-2 Delta variant of concern: a case series from Northern Lombardy. K77T and T95I (typical of B.1.617 v.1), L216F, A222V, and G1124V have also been rarely reported. 2021 Emerging microbes & infections Discussion SARS_CoV_2 A222V;G1124V;L216F;T95I;K77T 47;58;40;9;0 52;64;45;13;4 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. The mutation L452R has been shown to decrease sensitivity to neutralizing antibodies in previous studies, when compared with parental strains, and has been emerging independently by convergent evolution in different lineages like the VOCs B.1.427/B.1.429 (Epsilon) and B.1.617.2 (Delta). 2021 Frontiers in public health Discussion SARS_CoV_2 L452R 13 18 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. This mutation has been increasing in frequency worldwide since November 2020, being the second most frequent mutation up until July 2021, preceded only by N501Y. 2021 Frontiers in public health Discussion SARS_CoV_2 N501Y 155 160 34660520 The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. Through genomic surveillance of lineages circulating in the state of Sao Paulo:Brazil, we detected the circulation of a new lineage of SARS-CoV-2 in the city of Porto Ferreira bearing the L452R mutation as well as other 14 non-synonymous mutations, not found together in other SARS-CoV-2 sequences. 2021 Frontiers in public health Discussion SARS_CoV_2 L452R 188 193 34663909 SARS-CoV-2 promotes RIPK1 activation to facilitate viral propagation. Furthermore, the increased ability of SARS-CoV-2 323L variant to stimulate RIPK1 activation and replicate in the lung organoids also suggests that the NSP12 P323L mutation may contribute to the spread of this SARS-CoV-2 variant around the world. 2021 Cell research Discussion SARS_CoV_2 P323L 157 162 Nsp12 151 156 34663909 SARS-CoV-2 promotes RIPK1 activation to facilitate viral propagation. In addition, since the structural changes in NSP12 introduced by P323L mutation may contribute to the resistance to remesdesivir, RIPK1 inhibition may offer a therapeutic strategy to reduce viral propagation. 2021 Cell research Discussion SARS_CoV_2 P323L 65 70 Nsp12 45 50 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. In this manuscript, we investigate a highly variable motif in SARS-CoV-2 nucleocapsid located at residues 203-205 and characterized the effects of the alpha variant's R203K/G204R double substitution mutation (KR mt) on SARS-CoV-2 infection. 2022 bioRxiv Discussion SARS_CoV_2 R203K;G204R 167;173 172;178 N 73 85 COVID-19 219 239 34671771 Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. Overall, in this study we establish that the KR mt enhances SARS-CoV-2 infection relative to WT, increasing viral fitness in vitro and in vivo, which along with the N501Y mutation, likely selected for the emergence of the alpha variant. 2022 bioRxiv Discussion SARS_CoV_2 N501Y 165 170 COVID-19 60 80 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. 85% of the sequenced SARS-CoV-2 genomes containing N501Y are VOC-202012/01. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 51 56 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Additionally, the difference between general SARS-CoV-2 and N501Y mutation sequence is determined by sequence alignment with NGS technology as shown in Figure 3. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 60 65 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. All genomes containing N501Y sequenced in the UK since September 2020, belong to VOC-202012/01. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 23 28 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Analyses showed that 501Y.V2 spreads faster than variants without N501Y. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 66 71 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. As shown in Figure 2, 10 exact amino acid changes were described for N501Y mutation. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 69 74 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Detection of more than one mutation is necessary for the detection of VOC in South Africa, as 11% of total sequences in South Africa contain N501Y and none of them belong to VOC-202012/01. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 141 146 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Due to significantly raised concerns about the higher transmission rate and the escape from neutralizing antibodies of mutation N501Y, this study focuses on describing of N501Y mutation type in a wide range of nasal swab samples of patients. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y;N501Y 128;171 133;176 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. In other words, all SARS-CoV-2 variants containing N501Y are important in terms of epidemiology and their prevalence should be monitored. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 51 56 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. In particular, the N501Y mutation has exhibited potential risk firstly in the United Kingdom and after a while all over the world. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 19 24 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Moreover, SARS-Cov-2 variants include the two Alpha variants (B.1.1.7, United Kingdom and B.1.1.7 with the additional E484K mutation), the Beta variant (B.1.351, South Africa), and the Gamma variant (P.1, Brazil). 2021 Journal of medical virology Discussion SARS_CoV_2 E484K 118 123 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Moreover, the variant type of N501Y mutations was described as N501 and Y501, respectively. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 30 35 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. N501Y mutation is one of the important mutation types among other types of mutation of SARS-CoV-2 and is also termed with VOC-202012/01. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 0 5 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. studied N501Y transmissibility and based on the results showed that 501Y is estimated to present an R0 1.75 times higher than 501 N, meaning it is 75% more transmissible compared with the 501 N strain. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 8 13 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The Cq values of each variant type of N501Y mutation are also the information about much more positivity. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 38 43 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The Cq values of the variant type of N501Y mutation showed differences among females and males. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 37 42 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The defined mutations were also classified with the variant types of N501Y mutation as N501 and Y501, respectively. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 69 74 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The N501Y is located in the RBM of the CTD and has been found to increase its binding affinity to human ACE2; as mutations in the CTD of the S protein (aa 333-527) are most likely to alter the receptor recognition properties of SARS-CoV-2. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 4 9 S 141 142 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The new variant containing N501Y detected in South Africa is designated 501Y.V2. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 27 32 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The possibility of other mutations increase the transmissibility of the virus in combination with N501Y. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 98 103 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. The variants of the SARS-CoV-2 with an asparagine-to-tyrosine substitution at position 501 (N501Y) in the RBD show enhanced infectivity compared to wild-type. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y;N501Y 39;92 90;97 RBD 106 109 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Therefore, only N501Y screening will be decisive in areas with a low prevalence of VOCs outside of South Africa. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 16 21 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Three mutations in the S protein of the novel variant (N501Y, HV69-70del, and P681H) have potential biological implications. 2021 Journal of medical virology Discussion SARS_CoV_2 P681H;N501Y 78;55 83;60 S 23 24 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. Thus, the N501Y mutation type of SARS-CoV-2 retrospective approach will be created by way of evaluation and analysis of the data in terms of public health. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 10 15 34676574 The evaluation of potential global impact of the N501Y mutation in SARS-COV-2 positive patients. When the Cq results were examined in N501Y mutation results, it was seen that they varied between 0 and 39.86. 2021 Journal of medical virology Discussion SARS_CoV_2 N501Y 37 42 34678071 Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques. Likewise, the only difference observed in our study between B.1.1.7 and D614G was in the innate immune response in the upper, but not lower, respiratory tract. 2021 Science advances Discussion SARS_CoV_2 D614G 72 77 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. As a practical application of the experimental assays provided in this study, we compiled and provided clinical validation for a high-throughput multiplex-assay to specifically screen for B.1.617 lineage variants (delta/kappa) by detecting the L452R, E484Q and P681R single nucleotide polymorphisms, implemented on a fully automated sample-to-result platform. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 E484Q;L452R;P681R 251;244;261 256;249;266 34679517 Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. For example, the recently emerged B.1.617 (first detected in India) lineages feature E484Q (only B.1.617.1/3) and P681R SNPs instead of the more common E484K and P681H. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 E484K;E484Q;P681H;P681R 152;85;162;114 157;90;167;119 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. In addition, the presence of characteristic mutations such as N501Y results in higher infectivity than the parent strain which might be due to a higher binding affinity between the spike protein and ACE2. 2021 Pharmaceuticals (Basel, Switzerland) Discussion SARS_CoV_2 N501Y 62 67 S 181 186 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. To date, several studies indicate that the D614G viral lineage is more infectious than the D614 virus. 2021 Pharmaceuticals (Basel, Switzerland) Discussion SARS_CoV_2 D614G 43 48 34681279 In Vitro Effect of Taraxacum officinale Leaf Aqueous Extract on the Interaction between ACE2 Cell Surface Receptor and SARS-CoV-2 Spike Protein D614 and Four Mutants. We observed stronger binding of the variants D614G and N501Y to the ACE2 surface receptor of human cells, but all tested variants were sensitive to binding inhibition by T. 2021 Pharmaceuticals (Basel, Switzerland) Discussion SARS_CoV_2 D614G;N501Y 45;55 50;60 34683466 SARS-CoV-2 Evolution among Oncological Population: In-Depth Virological Analysis of a Clinical Cohort. Compared with the Wuhan reference strain, all of the samples sequenced in the present study had a single-nucleotide variation (SNV) at positions 241, 3037, 14408 and 23403, the last one corresponding to the D614G amino acid mutation on the S gene. 2021 Microorganisms Discussion SARS_CoV_2 D614G 207 212 S 240 241 34683466 SARS-CoV-2 Evolution among Oncological Population: In-Depth Virological Analysis of a Clinical Cohort. It is considered that minority variants under specific selective pressure may become predominant and provide a fitness advantage, ultimately influencing the epidemic, as seems to have occurred with the D614G mutation. 2021 Microorganisms Discussion SARS_CoV_2 D614G 202 207 34683466 SARS-CoV-2 Evolution among Oncological Population: In-Depth Virological Analysis of a Clinical Cohort. Similarly, in our study, except for D614G, no mutation or minority variants were observed in the S gene coding for the spike protein; most were observed within the ORF1ab gene, which encodes the replication complex responsible for RNA synthesis. 2021 Microorganisms Discussion SARS_CoV_2 D614G 36 41 ORF1ab;S;S 164;119;97 170;124;98 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. All of the 310 helix mutations demonstrated an increase in flexibility, except for R24H MT. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 R24H 83 87 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. All these mutations exhibited a destabilizing effect, except for V121I and V121W (Table 3). 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 V121I;V121W 65;75 70;80 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. However, here, we report that this is a hotspot region for the most frequently occurring mutations (R24C, R24H, R24S, and R24E). 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 R24E;R24H;R24S;R24C 122;106;112;100 126;110;116;104 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. However, R24S and R24A MTs Nsp1 exhibited a stabilizing effect and a gain in flexibility. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 R24A;R24S 18;9 22;13 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. In the current study, we also detected numerous non-synonymous mutations (V121F (n = 14), V121A (n = 1), V121D (n = 1), V121I (n = 13), V121P (n = 1), and V121W (n = 1)). 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 V121A;V121D;V121I;V121P;V121W;V121F 90;105;120;136;155;74 95;110;125;141;160;79 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. Many mutations (R24C, R24H, R24S, R24E, R24V, and R24A) are also present in the 310 helix, among which R24C is present with the highest frequency (n = 1122) in all Nsp1 mutations, with a destabilizing effect. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 R24A;R24C;R24E;R24H;R24S;R24V;R24C 50;103;34;22;28;40;16 54;107;38;26;32;44;20 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. Recently, a genome from Bangladesh was found to have some novel mutations, including V121D, which destabilizes Nsp1, inactivating the antiviral system mediated by type 1 interferons. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 V121D 85 90 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. Recently, four novel mutations have been detected in the genome of SARS-CoV2, among which V121D substitution exhibited a destabilizing effect on Nsp1. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 V121D 90 95 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. Similar to this study, we detected 18 non-synonymous mutations at positions aa 121 to 124, where all variants exhibited a destabilizing effect, except for V121I, V121W, and L122I. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 L122I;V121I;V121W 173;155;162 178;160;167 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. The highest frequency of mutations for R24C (n = 1122) and D48G (n = 881) was detected in SARS-CoV-2 genomic isolates from England; on the contrary, D75E (890) was detected in New Zealand isolates. 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D48G;D75E;R24C 59;149;39 63;153;43 34684233 Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. The most commonly observed mutation was detected at position R24C, present in 310 helices (aa20-35). 2021 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 R24C 61 65 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. Furthermore, we evaluated the role of the Spike mutation D614G using viral vectors and we validated our results with the use of live SARS-CoV-2 virus to demonstrate platelet aggregation and fibrin deposition on the endothelium as the quantifiable phenotypes for thrombosis progression at a shear stress of 25 dyne cm-2 which simulates laminar shear stress on straight portions of the vasculature. 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Discussion SARS_CoV_2 D614G 57 62 S 42 47 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. In addition, we created custom-designed nanoparticles conjugated with hACE2 as a decoy for the SARS-CoV-2 Spike protein, and we demonstrated that Lipo-hACE2 inhibited microthrombosis in the presence of the Spike, the D614G variant and the live SARS-CoV-2. 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Discussion SARS_CoV_2 D614G 217 222 S;S 106;206 111;211 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. In this study, we integrated nanoliposomes, viral vectors, and human whole blood in the microfluidic platform to recapitulate blood coagulation upon exposure to SARS-CoV-2 or Spike mutation (D614G). 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Discussion SARS_CoV_2 D614G 191 196 S 175 180 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. To this end, we recapitulated a microvascular environment to streamline the testing of the Spike protein and a variant (Asp614 Gly substitute in S1) of SARS-CoV-2 in our integrated platform for individualized prediction of microthrombosis. 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Discussion SARS_CoV_2 D614G 120 130 S 91 96 34687279 Rapid Detection and Inhibition of SARS-CoV-2-Spike Mutation-Mediated Microthrombosis. We demonstrated that the presence of Spike D614G is sufficient to recapitulate SARS-CoV-2-mediated inflammation by upregulating cytokine expression (e.g., IL-1, IL-6, IL-15, and TNF-alpha), and chemokines (e.g., MCP1) together with aberrantly elevated level of endothelial markers, such as von Willebrand Factor (vWF), which can potentially be the link for the significant platelet aggregation and fibrin deposition through Toll-like receptor signaling pathway. 2021 Advanced science (Weinheim, Baden-Wurttemberg, Germany) Discussion SARS_CoV_2 D614G 43 48 S 37 42 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. However, although Alpha (E484K) emerged several times independently, it does not seem to spread well - potentially due to the detrimental effect that the E484K mutation can have on binding affinity to human ACE2. 2021 EBioMedicine Discussion SARS_CoV_2 E484K;E484K 154;25 159;30 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. However, S477N has also been described as escape mutation. 2021 EBioMedicine Discussion SARS_CoV_2 S477N 9 14 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. Interestingly, neutralizing activity was similarly reduced for the local Lambda isolate used in the current study which has more extensive changes in the NTD (Delta63-75, Delta246-252) and the RBD (L452Q, E471Q, F490S) compared to the predominant Lambda variant (NTD: G75V, T76I, Delta246-252; RBD: L452Q, F490S). 2021 EBioMedicine Discussion SARS_CoV_2 E471Q;F490S;F490S;G75V;L452Q;T76I;L452Q 205;212;306;268;299;274;198 210;217;311;272;304;278;203 RBD;RBD 193;294 196;297 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. Interestingly, S477N exerted a stronger impact than E484K, which was surprising given the reduction caused by introduction of E484K into the WA1 wild type backbone. 2021 EBioMedicine Discussion SARS_CoV_2 E484K;E484K;S477N 52;126;15 57;131;20 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. The combination of Alpha (which already harbours two deletions in the NTD) with E484K led to a some reduction in neutralizing activity. 2021 EBioMedicine Discussion SARS_CoV_2 E484K 80 85 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. The impact was higher for the Iota isolates that carry, in addition, E484K or S477N substitutions in the RBD. 2021 EBioMedicine Discussion SARS_CoV_2 E484K;S477N 69;78 74;83 RBD 105 108 34688034 Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. The least negative impact on neutralization was seen for Iota variant, which is reasonable since this isolate has very few changes in the spike protein (T95I, D253G and D614G) compared to the wild type WA1 isolate. 2021 EBioMedicine Discussion SARS_CoV_2 D253G;D614G;T95I 159;169;153 164;174;157 S 138 143 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. However, a third of vaccinees showed reduced CD8 recognition of Delta, which harbors the L452R mutation that confers resistance to human leukocyte antigen (HLA)-A*24:02 recognition. 2021 Cell host & microbe Discussion SARS_CoV_2 L452R 89 94 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. However, although Beta infection resulted in the preserved neutralization of D614G, we, like others, noted significant loss of activity against Delta. 2021 Cell host & microbe Discussion SARS_CoV_2 D614G 77 82 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. However, several studies have now characterized the neutralizing activity against VOCs, including Delta, which now dominates globally and shows approximately 4- to 6-fold reduced sensitivity to convalescent plasma, in comparison with D614G. 2021 Cell host & microbe Discussion SARS_CoV_2 D614G 234 239 34688376 Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. Prior exposure to D614G resulted in reduced titers against both Beta and Delta, consistent with previous studies. 2021 Cell host & microbe Discussion SARS_CoV_2 D614G 18 23 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. The clinical evaluation raised concern over rising cases from B.1.617.1 variant from March 2021, and the data analysis also revealed the presence of mutations L452R and E484Q associated with B.1.617.1 variant lineage in samples collected during March 2021. 2022 The Science of the total environment Discussion SARS_CoV_2 E484Q;L452R 169;159 174;164 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. There are mutations found in wastewater such as S:P1140del which was reported in late February from India and earlier only from Africa-Egypt and North America (GISAID -). 2022 The Science of the total environment Discussion SARS_CoV_2 P1140del 50 58 S 48 49 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. We also report a novel mutation NSP13:G206F (NSP13 region). 2022 The Science of the total environment Discussion SARS_CoV_2 G206F 38 43 Nsp13;Nsp13 32;45 37;50 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. WW12 was the most recent sample with maximum mutations recorded and has 12 mutations unique to the sample, in which NSP3:L550del, NSP14:C279F and S:C480R are not yet reported from India (GISAID -). 2022 The Science of the total environment Discussion SARS_CoV_2 C279F;C480R;L550del 136;148;121 141;153;128 Nsp3;S 116;146 120;147 34688738 High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India. WW9 has shown mutation N:R203M and 3'-UTR:29700, while WW11 has shown mutation S:P618R and N:D63G, present in samples collected in March 2021, and absent in sample WWP taken before March. 2022 The Science of the total environment Discussion SARS_CoV_2 D63G;P618R;R203M 93;81;25 97;86;30 N;N;S 23;91;79 24;92;80 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Apart from the N501Y mutation, several amino acid substitutions including K417N, E484K, Q493H/K, and Q498H were also suggested to be critical for SARS-CoV-2 adaptation in murine species. 2021 EBioMedicine Discussion SARS_CoV_2 E484K;K417N;N501Y;Q493H;Q493K;Q498H 81;74;15;88;88;101 86;79;20;95;95;106 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. As demonstrated in the current study, the evolving SARS-CoV-2 variants with the N501Y mutation in spike can now naturally infect mice and rats, and potentially other rodent species. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y 80 85 S 98 103 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Furthermore, we demonstrated that in addition to wildtype Mus musculus, Rattus norvegicus is also susceptible to the N501Y-carrying mutant B.1.1.7. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y 117 122 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. However, direct experimental evidence on whether authentic N501Y VOCs and other emerging variants can infect mice or other murine is still largely lacking. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y 59 64 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. In summary, we demonstrate that B.1.1.7 and other N501Y-carrying SARS-CoV-2 variants have evolved to gain the capability to cross species barrier to infect wildtype murines including mice and rats, which are not considered permissive to WT SARS-CoV-2. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y 50 55 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Substantial evidence has been raised to demonstrate the increased binding between N501Y mutant spike and mACE2 as well as the role of N501Y in mouse-adapted or genetically-engineered SARS-CoV-2 strains in mouse infection. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y;N501Y 82;134 87;139 S 95 100 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. The N501Y mutation contributed to an over 40-fold increase in pseudovirus entry in mACE2 overexpressed cells. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y 4 9 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. Therefore, infection of N501Y-carrying variants in aged mice may represent a more severe disease model with enhanced pathological tissue damage upon virus infection and ultimately succumbed to high-titre inoculum. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y 24 29 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. This is congruous with our observation that B.1.351 replicated to a higher level than B.1.1.7 and P.3 in wildtype mice since B.1.351 carries K417N, E484K in addition to N501Y. 2021 EBioMedicine Discussion SARS_CoV_2 E484K;K417N;N501Y 148;141;169 153;146;174 34689086 Emerging SARS-CoV-2 variants expand species tropism to murines. We have extended these findings to demonstrate that among the four VOCs, only the N501Y-carrying variants infect wildtype mice. 2021 EBioMedicine Discussion SARS_CoV_2 N501Y 82 87 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. In the present study, two B.1.617 sequences from the United States were found to contain the N501Y substitution. 2021 Frontiers in microbiology Discussion SARS_CoV_2 N501Y 93 98 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. N501Y substitution was detected in B.1.1.7 and B.1.351, and it was suggested to be responsible for the enhanced replication in cell and in animal model and for the potentially increased transmission. 2021 Frontiers in microbiology Discussion SARS_CoV_2 N501Y 0 5 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. Since the discovery of the D641G variant in early 2020, the continuous emergence of SARS-CoV-2 variants has attracted increasing attention worldwide. 2021 Frontiers in microbiology Discussion SARS_CoV_2 D641G 27 32 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. The aa substitution of N501Y can potentially enhance the interactions between S-RBD and ACE2, and the variants bearing N501Y were increasingly distributed in more countries in the follow-up monitoring. 2021 Frontiers in microbiology Discussion SARS_CoV_2 N501Y;N501Y 23;119 28;124 RBD;S 80;78 83;79 34691002 Biological Significance of the Genomic Variation and Structural Dynamics of SARS-CoV-2 B.1.617. The substitution of E to Q at aa site 484 lengthened the interaction distance between the original residues (Q484 of RBD and K11 of hACE2) and reduced the interaction between the two other residues (S477 of RBD and Q4 of hACE2), which may have weakened the affinity between the S protein and its receptor and may function in antibody escape. 2021 Frontiers in microbiology Discussion SARS_CoV_2 E484Q 20 41 RBD;RBD;S 117;207;278 120;210;279 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. Conversely, the decreased neutralization of the N501Y mutation observed in our RBD/ACE-2 inhibition assay may stem from a combination of compromised recognition by neutralizing antibodies and the higher affinity RBD/ACE-2 interaction outcompeting antibodies with affinities around the RBDwt/ACE-2 Kd, and thus displacing the fluid-phase equilibrium towards ACE-2-bound RBD and away from antibody-bound RBD. 2021 Frontiers in immunology Discussion SARS_CoV_2 N501Y 48 53 RBD;RBD;RBD;RBD 79;212;369;402 82;215;372;405 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. Instead of carrying the N501Y, all lineages within the B.1.617 variant include a leucine to arginine substitution at position 452 (L452R), that have been shown to increase affinity towards ACE-2, as well as infectivity and resistance to antibody-mediated neutralization in vitro. 2021 Frontiers in immunology Discussion SARS_CoV_2 L452R;N501Y;L452R 81;24;131 129;29;136 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. Interestingly, the same combined E484K/N501Y is found in the VOI B.1.621, originally identified in Colombia, and the P.3 (Theta), identified in the Philippines, but without the 417T or N substitution that likely reduces the overall virus fitness. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;N501Y 33;39 38;44 N 185 186 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. It also needs to be taken into account that while the N501Y is the only RBD mutation in the B.1.1.7 variant, the latter carries other changes in the spike protein:such as deletions in the NTD:that may contribute to its immune evasion properties. 2021 Frontiers in immunology Discussion SARS_CoV_2 N501Y 54 59 S;RBD 149;72 154;75 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. It is also possible that the K417T/N substitution arose by genetic drift after the fixation of the E484K and N501Y mutations and may thus be regarded as a "neutral passenger" during the development of viral diversity. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;K417T;K417N;N501Y 99;29;29;109 104;36;36;114 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. Moreover, the authors showed that adding the K417T/N mutation into an E484K/N501Y background increased the surface expression of the triple mutant, suggesting positive cooperativity between these three mutations. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y 70;45;45;76 75;52;52;81 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. Several studies have shown that the N501Y compromises neutralization by many mAbs, but polyclonal convalescent and vaccine sera remain, for the most part, effective at neutralizing the N501Y-containing B.1.1.7 (alpha) variant. 2021 Frontiers in immunology Discussion SARS_CoV_2 N501Y;N501Y 36;185 41;190 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. Single residue substitutions are normally unlikely to challenge a distributed polyclonal B-cell response, but we observe a significant evasive capacity of the E484K and combined with the N501Y driving a higher RBD/ACE affinity in the low nM range it might challenge established immunity at a low maturation state. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;N501Y 159;187 164;192 RBD 210 213 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. Surprisingly, both convalescent and vaccinated individuals (originally exposed to either the "wild-type" Wuhan strain or the mRNA sequence that translates into wt spike) mediated a better neutralization of the K417T or K417N RBD/ACE-2 compared to wt. 2021 Frontiers in immunology Discussion SARS_CoV_2 K417N;K417T 219;210 224;215 S;RBD 163;225 168;228 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. The E484K did not influence the affinity significantly but had a pronounced increased antibody evasive capacity. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K 4 9 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. The N501Y mutation has been reported in mice to emerge as adaptation after serial passaging of a SARS-CoV-2 clinical isolate and increase its virulence. 2021 Frontiers in immunology Discussion SARS_CoV_2 N501Y 4 9 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. Therefore, the enhanced neutralization of the single 417 RBD constructs could result from the lower K417N/T-RBD/ACE-2 affinity that might allow for a larger pool of RBD antibodies to bind with lower affinity in the 50-70 nM range. 2021 Frontiers in immunology Discussion SARS_CoV_2 K417N;K417T 100;100 105;105 RBD;RBD;RBD 57;108;165 60;111;168 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. To date, the extent to which the N501Y mutation challenges established immunity remains under debate. 2021 Frontiers in immunology Discussion SARS_CoV_2 N501Y 33 38 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. Two other interesting substitutions are found in the RBD of two distinct lineages within the B.1.617 variant (B.1.617.1/B.1.617.3) originated in India, where the glutamic acid in position 484 is changed to glutamine (E484Q) that might drive an evasive potential. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484Q;E484Q 162;217 215;222 RBD 53 56 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. When we assessed the impact of the individual residue substitutions, we found that the N501Y increased the affinity towards ACE-2 ten-fold, whereas the opposite was the case for the lysine substitution at position 417 to either a threonine or an asparagine residue that resulted in a reduced affinity of around three-fold compared to the original wt. 2021 Frontiers in immunology Discussion SARS_CoV_2 N501Y 87 92 34691078 Functional Effects of Receptor-Binding Domain Mutations of SARS-CoV-2 B.1.351 and P.1 Variants. Yeast surface in vitro evolution experiments aimed at increasing ACE-2 affinity have shown that the E484K and N501Y were among the first mutations to be selected and fixed. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;N501Y 100;110 105;115 34695371 Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data. The spike protein is thought to be important for entry of the virus into host cells and Asp614Gly has been implicated in increased cell entry. 2021 The Lancet. Global health Discussion SARS_CoV_2 D614G 88 97 S 4 9 34695371 Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data. There has been considerable interest in the emergence of a variant lineage of SARS-CoV-2 with a non-synonymous mutation resulting in substitution of 614Gly in which a glycine residue was replaced by an aspartate residue at position 614 (Asp614Gly) of the spike protein. 2021 The Lancet. Global health Discussion SARS_CoV_2 D614G 237 246 S 255 260 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. For example, the parent node sequences of C1 containing C2416T/C3037T/C14408T/A23403G/G25563T was reported to be associated with an international business conference in Boston, resulting in extensive international spread and low-level community transmission in Europe. 2021 Genomics, proteomics & bioinformatics Discussion SARS_CoV_2 C2416T;A23403G;C14408T;C3037T;G25563T 56;78;70;63;86 62;85;77;69;93 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. Genomes of another sister cluster C2, harboring the C26735T variant in addition to common signatures of C3037T/C14408T/A23403G/C18877T/G25563T, have been found mainly in Asia (93 genomes as of October 9, 2020). 2021 Genomics, proteomics & bioinformatics Discussion SARS_CoV_2 C26735T;C3037T;A23403G;C14408T;C18877T;G25563T 52;104;119;111;127;135 59;110;126;118;134;142 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. In contrast, we noticed that two of the most frequently observed iSNVs (T14307C and T25406C) in our data were located at positions that were not polymorphic at the population level. 2021 Genomics, proteomics & bioinformatics Discussion SARS_CoV_2 T25406C;T14307C 84;72 91;79 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. On the other hand, the fast transmission ability of C1 virus might be attributed to its characteristic nucleotide mutation G8371T in the coding region for nonstructural protein 3 (nsp3) in ORF1ab. 2021 Genomics, proteomics & bioinformatics Discussion SARS_CoV_2 G8371T 123 129 ORF1ab;Nsp3 189;180 195;184 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. The C2416T/G8371T sub-lineage was likely the first in the C1 cluster imported into Pakistan based on the most recent common ancestor (MRCA) estimation - the median estimated date to MRCA of the C1 cluster was March 10, 2020 (95% CI: March 7-14, 2020). 2021 Genomics, proteomics & bioinformatics Discussion SARS_CoV_2 C2416T;G8371T 4;11 10;17 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. The deep hierarchical structure of C1 indicates an extensive and persistent nation-wide transmission of the virus, which is probably attributed to a signature nucleotide mutation G8371T in the ORF1ab gene. 2021 Genomics, proteomics & bioinformatics Discussion SARS_CoV_2 G8371T 179 185 ORF1ab 193 199 34695600 Genomic Epidemiology of SARS-CoV-2 in Pakistan. To test this possibility, we collected all publicly-released sequences (as of February 22, 2021) with the G8371T mutation and built a haplotype network (Figure S5). 2021 Genomics, proteomics & bioinformatics Discussion SARS_CoV_2 G8371T 106 112 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. One limitation of this study is that besides N501Y, K417N and V1176F, no other key mutations have been addressed. 2021 Viruses Discussion SARS_CoV_2 K417N;N501Y;V1176F 52;45;62 57;50;68 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. Our results indicate that community prevalence of K417N positive SARS-CoV-2 strains such as B1.351 has been low in Vienna during the study period. 2021 Viruses Discussion SARS_CoV_2 K417N 50 55 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. Our results show that the fraction of N501Y positive strain infections increased during the observation period. 2021 Viruses Discussion SARS_CoV_2 N501Y 38 43 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. Prevalence rates of N501Y mutation reported here (up to 68% of weekly positive cases) are lower than prevalence rates reported by the Austrian Agency for Health and Food Safety (74% of weekly positive cases). 2021 Viruses Discussion SARS_CoV_2 N501Y 20 25 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. SARS CoV-2 specific PCR analysis gave a positivity rate of 0.43% and revealed increasing prevalence of N501Y positive virus strains. 2021 Viruses Discussion SARS_CoV_2 N501Y 103 108 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. This observation has been also confirmed for the K417N mutation where official prevalence rates of up to 1.48% have been reported for Vienna. 2021 Viruses Discussion SARS_CoV_2 K417N 49 54 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. Variants carrying the N501Y mutation, such as VOCs B.1.1.7 and B.1.351, were shown to rapidly spread in mainland Europe during early 2021. 2021 Viruses Discussion SARS_CoV_2 N501Y 22 27 34696444 Evolution of SARS-CoV-2 Key Mutations in Vienna Detected by Large Scale Screening Program. Within all 400,730 cases analyzed, we detected only three K417N positive strains. 2021 Viruses Discussion SARS_CoV_2 K417N 58 63 34696495 High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses. Through our Nextstrain thread, we found that the clade for pangolin lineage B that contains certain distant variants covarying with the D614G spike protein mutation had become increasingly prevalent at the early phase of the pandemic in the state of Georgia. 2021 Viruses Discussion SARS_CoV_2 D614G 136 141 S 142 147 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Amino acid change of T478I (polar to nonpolar residue) and E484K (negative- to positive-charge residue) did not contribute to the major shift of the S-D614G structure. 2021 mBio Discussion SARS_CoV_2 E484K;T478I;D614G 59;21;151 64;26;156 S 149 150 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Among these amino acid mutations, S-D614G is the mutation that emerged in January 2020 that allows SARS-CoV-2 to bind to cell receptors, predominantly hACE2, and enter host cells more easily. 2021 mBio Discussion SARS_CoV_2 D614G 36 41 S 34 35 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Aside from the known mutations, we predicted that if SARS-CoV-2 acquires N439S, T478S, or N501K mutations, the virus will attain a chance to infect host cells even more efficiently and with reduced antigenicity. 2021 mBio Discussion SARS_CoV_2 N439S;N501K;T478S 73;90;80 78;95;85 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Despite this, S-D614G continued to be detected in different countries, indicating that SARS-CoV-2 S-D614G mutant was the parental virus seeding across continents and then continued to mutate independently, giving rise to SARS-CoV-2 variants containing additional signature amino acid mutations. 2021 mBio Discussion SARS_CoV_2 D614G;D614G 16;100 21;105 S;S 14;98 15;99 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. Even though both the B.1.1.7 and B.1.351 variants harbor the N501Y mutation, they display a different degree of infectivity and antibody neutralization ability. 2021 mBio Discussion SARS_CoV_2 N501Y 61 66 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. For instance, the B.1.351 variants with an additional L18F mutation resulted in altered S1-NTD and S1-RBD conformation with increased binding affinity to hACE2. 2021 mBio Discussion SARS_CoV_2 L18F 54 58 RBD 102 105 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. From our predictive models, deletion of amino acids 69 to 70 and 144, which are signatures of B.1.1.7 variants, may enhance the infectivity of the virus; however, this may not affect its immunogenicity, while deletion of amino acids 241 to 243, located relatively closer to S1-RBD, found in B.1.351, renders lower immunogenicity and higher binding affinity to hACE2. 2021 mBio Discussion SARS_CoV_2 del 241;del 69 209;28 236;54 RBD 277 280 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. However, T478R/K (polar to positive-charge residue) and E484Q (negative to polar residue) resulted in a shift of S-D614G to a structure resembling that of the prototype, while amino acid change can lead to a change in S protein antigenicity and binding affinity to hACE2. 2021 mBio Discussion SARS_CoV_2 E484Q;T478K;T478R;D614G 56;9;9;115 61;16;16;120 S;S 113;218 114;219 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. N501Y has also been shown to confer increased infectivity. 2021 mBio Discussion SARS_CoV_2 N501Y 0 5 34700382 Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. SARS-CoV-2 K417T/E484K dual mutants resist postvaccination serum neutralization to an extent similar to that of the B.1.351 variant, while N439K mutation arose independently in different countries, facilitating viral attachment to hACE2 and resistance to antibody neutralization. 2021 mBio Discussion SARS_CoV_2 K417T;N439K;E484K 11;139;17 16;144;22 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. A correlation of the amino acid substituted D614G associated with the G-clades and case fatality in the West African countries can only be identified at a marginal level of r = 0.28 (Supplementary Table 1). 2021 Scientific reports Discussion SARS_CoV_2 D614G 44 49 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. found significant correlations between the percentage of D614G and case-fatality on a country by country basis. 2021 Scientific reports Discussion SARS_CoV_2 D614G 57 62 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. The D614G amino acid substitution which was the most relevant change in SARS-CoV-2 in spring 2020 became prevalent in 2021 and was boosted by continuously acquired new mutations agglomerating into new variants. 2021 Scientific reports Discussion SARS_CoV_2 D614G 4 9 34702899 Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa. The question if that correlates with the severity of the disease still needs to be addressed, Brufsky infers it from the higher mortality at the East Coast of USA with predominantly D614G-carrying G-clades compared to the West Coast with the predominant early clades. 2021 Scientific reports Discussion SARS_CoV_2 D614G 182 187 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. Besides this ACE2 variant, the G476S mutation within the RBD region significantly decreased the binding affinity with ACE2 by the change in polar-polar and polar-apolar ICs. 2021 Bioinformatics and biology insights Discussion SARS_CoV_2 G476S 31 36 RBD 57 60 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. Both the T27A and G476S mutations have previously been demonstrated to be associated with reduced SARS-CoV-2 entry. 2021 Bioinformatics and biology insights Discussion SARS_CoV_2 G476S 18 23 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. In addition, Q493L and S477I mutants of spike protein change the ICs and importantly increase the binding affinity of spike protein (RBD) with ACE2. 2021 Bioinformatics and biology insights Discussion SARS_CoV_2 Q493L;S477I 13;23 18;28 S;S;RBD 40;118;133 45;123;136 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. Q493L mutation has previously been predicted to be involved with increased stability of RBD. 2021 Bioinformatics and biology insights Discussion SARS_CoV_2 Q493L 0 5 RBD 88 91 34720581 Prediction of the Effects of Variants and Differential Expression of Key Host Genes ACE2, TMPRSS2, and FURIN in SARS-CoV-2 Pathogenesis: An In Silico Approach. The mutants P681R and R683W within the FURIN cleavage site change the intermolecular interactions and slightly increase the binding of FURIN with spike protein that may facilitate the cleaving. 2021 Bioinformatics and biology insights Discussion SARS_CoV_2 P681R;R683W 12;22 17;27 S 146 151 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Compared with D614G, N501Y.V1 lineage had no significant change in infectivity. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G;N501Y 14;21 19;26 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Finally, we proved that SARS-CoV-2 WT, D614G, N501Y.V1 and N501Y.V2 entry into host cells mainly through endocytosis, while both cathepsin and TMPRSS2 play important roles in virus entry. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G;N501Y;N501Y 39;46;59 44;51;64 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. However, it is reported that there is no significant difference among the stability of N501Y.V1, N501Y.V2 and N501Y.V3 pseudovirus, which is incubated at 33C for a period of time. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y;N501Y;N501Y 87;97;110 92;102;115 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. However, N501Y.V2 lineage, which is more infectious in cell lines, had no substantial differences in spike cleavage than WT and D614G virions, suggesting that the enhanced virus infectivity of N501Y.V2 lineage is not likely due to the difference of S protein cleavage. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G;N501Y;N501Y 128;9;193 133;14;198 S;S 101;249 106;250 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Importantly, we found that N501Y.V1 and N501Y.V2 lineages are more stable than D614G, indicating that the enhanced infectivity of N501Y.V1 and N501Y.V2 lineages in the population may be partly correlated with its higher thermal stability in the host and environment. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G;N501Y;N501Y;N501Y;N501Y 79;27;40;130;143 84;32;45;135;148 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. In 293T-hACE2 cells, the infection efficiency of N501Y.V1 was slightly lower than D614G; however, in cells expressed TMPRSS2, such as 293T-hACE2-TMPRSS2 and Caco-2 cells, its infectivity increased. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G;N501Y 82;49 87;54 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. In December 2020, newly emerging SARS-CoV-2 N501Y.V1 and N501Y.V2 variants are raising concerns in the UK and South Africa respectively, due to the enhancive spread ability of the virus. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y;N501Y 44;57 49;62 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. In the present study, using a VSV-based pseudotyped system, we packaged pseudovirions bearing S protein with combination and single-site mutations of N501Y.V1 and N501Y.V2 variants. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y;N501Y 150;163 155;168 S 94 95 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. In this study, we demonstrated that the infectivity of SARS-CoV-2 N501Y.V2 was increased in susceptible cells, and the enhanced virus infectivity was not likely related to the cleavage of S protein. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y 66 71 S 188 189 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. In this study, we investigated the infectivity, S protein cleavage, thermal stability and drug inhibition properties of the N501Y.V1 and N501Y.V2 lineages. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y;N501Y 124;137 129;142 S 48 49 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Indeed, N501Y.V3 lineage includes three mutations in the RBD region (K417T, E484K and N501Y), and it almost has the same three mutations present in RBD as N501Y.V2 lineage, except for K417N/T substitution. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y;N501Y;N501Y;K417T 76;184;184;8;86;155;69 81;191;191;13;91;160;74 RBD;RBD 57;148 60;151 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Interestingly, the infection efficiency of N501Y.V2 RBD pesudovirus is higher than N501Y.V2, implying the non-RBD S mutations of N501Y.V2 have negative effect on the infection of SARS-CoV-2. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y;N501Y;N501Y 43;83;129 48;88;134 RBD;RBD;S 52;110;114 55;113;115 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. It is believed that mutations of N501Y.V1 and N501Y.V2 variants possibly change their immunogenicity and virus infectivity. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y;N501Y 33;46 38;51 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. It is reported that SARS-CoV-2 D614G mutant has a higher thermal stability than WT virions, and its strong infectivity and transmissibility may be related to the stability of the virus. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G 31 36 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. More importantly, Camostat has a better inhibition effect on N501Y.V1 and N501Y.V2 lineages than D614G in TMPRSS2+ cells, indicating that the priming of N501Y.V1 and N501Y.V2 S protein maybe more dependent on TMPRSS2 activity. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G;N501Y;N501Y;N501Y;N501Y 97;61;74;153;166 102;66;79;158;171 S 175 176 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Moreover, the thermal stability of N501Y.V2 pesudovirus is higher than N501Y.V2 RBD, implying the non-RBD S mutations of N501Y.V2 have positive effect on the thermal stability of SARS-CoV-2. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y;N501Y;N501Y 35;71;121 40;76;126 RBD;RBD;S 80;102;106 83;105;107 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Our results demonstrated that the mutations of N501Y.V2 lineage enhanced the infection efficiency of SARS-CoV-2 in several susceptible cell lines. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y 47 52 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Particularly, the D614G mutation in the spike leads to increased virus infectivity and subsequently spread rapidly in the world, thereby gradually replacing previously circulating lineages. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G 18 23 S 40 45 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Previous studies in mice have shown that N501Y can increase the affinity for the mouse ACE2 receptor, which proves that this new variant can enhance its infectivity in the host. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y 41 46 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Pseudovirion with HV69-70 deletion could enhance the infectivity of the virus, while single-site mutation T716I, A570D, D118H, and A701V caused a modest reduction in viral infectivity. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 A570D;A701V;D118H;T716I 113;131;120;106 118;136;125;111 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Recently, showed that the infectivity of pseudovirions incorporated with N501Y.V2 S proteins was not obviously changed in human cells, while N501Y.V2 RBD mutations slightly but obviously increase the viral infection efficiency, which is consistent with our research. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y;N501Y 73;141 78;146 RBD;S 150;82 153;83 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. reported that pseudovirions with N501Y+K417N or N501Y+E484K exhibited higher infection rates than the N501Y pseudovirion alone. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y;N501Y;N501Y;E484K;K417N 33;48;102;54;39 38;53;107;59;44 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. The effects of single-site mutations of N501Y.V1 and N501Y.V2 lineages on viral infectivity were variable. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y;N501Y 40;53 45;58 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. Therefore, the higher stability of N501Y.V1 and N501Y.V2 lineages may be related to the synergistic effects of different mutations. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y;N501Y 35;48 40;53 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. These results indicate that the infection of N501Y.V1 lineage may be more dependent on TMPRSS2 activity. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y 45 50 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. These three RBD mutations of S protein maybe cause the higher infection efficiency of N501Y.V2 and N501Y.V3 via promoting the binding affinity with ACE2. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y;N501Y 86;99 91;104 RBD;S 12;29 15;30 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. To our surprise, the cleaved S protein band was slightly weakened in particles of N501Y.V1 than WT and D614G ( Figure 1B ). 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G;N501Y 103;82 108;87 S 29 30 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. We compared the cleavage of S protein in WT, D614G, N501Y.V1 and N501Y.V2 RBD pseudovirions. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G;N501Y;N501Y 45;52;65 50;57;70 RBD;S 74;28 77;29 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. We found that several single-site mutations of N501Y.V1 and N501Y.V2 lineages can increase/decrease the thermal stability of pseudovirion. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y;N501Y 47;60 52;65 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. We further evaluated the effect of single-site mutations of N501Y.V1 and N501Y.V2 lineages on the stability of the virus. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y;N501Y 60;73 65;78 34722330 Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity. We further found that SARS-CoV-2 N501Y.V1 and N501Y.V2 mutants are more thermal stable in the host and environment, which may be associated with the rapid transmission of the two variants in the population. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 N501Y;N501Y 33;46 38;51 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. A recent study examining SARS-CoV-2 variants in the rhesus macaque model showed no difference in viral replication nor disease between the D614G and B.1.1.7 variants. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 139 144 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. B.1.1.7 replicated at higher levels in the respiratory tract resulting in lesions that were both more numerous and severe than seen for D614G infected animals. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 136 141 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Consistent with higher levels of viral replication in the URT, shedding of SARS-CoV-2 RNA in both the nose and oropharyngeal cavity was also higher in B.1.1.7 infected animals suggestive of potentially enhanced transmissibility of the B.1.1.7 (Alpha) over the D614G progenitor variant (Figure 1). 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 260 265 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. Following infection with either variant, animals in both groups exhibited minor differences in disease progression but overall disease signs were similar with mild respiratory disease for both B.1.1.7 and D614G variants (Figure 1A,B; Table S1 & S2). 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 205 210 Respiratory Disease 164 183 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. In contrast, D614G replicated at higher levels in the GIT and the associated pathology seen in these animals correlated with this difference in GIT replication. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 13 18 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. In the present study, we have used the AGM intranasal infection model to compare the B.1.1.7 (Alpha) VOC, a variant that emerged in the UK in September of 2020 and then quickly spread throughout the world, with a contemporary D614G progenitor variant, in terms of virus replication, shedding and disease severity. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 226 231 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. SARS-CoV-2 RNA and infectious virus in the LRT tissues were more prevalent in the animals infected with B.1.1.7 compared to D614G, especially at later timepoints suggesting the development of a stronger respiratory component associated with the emerging VOC (Figures 2 and 3). 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 124 129 34724885 UK B.1.1.7 (Alpha) variant exhibits increased respiratory replication and shedding in nonhuman primates. This may indicate that D614G is more suited to replication in the GIT than other variants which is in line with clinical studies conducted in early to mid-2020 that reported GIT symptoms in approximately 15-20% of COVID-19 patients. 2021 Emerging microbes & infections Discussion SARS_CoV_2 D614G 23 28 COVID-19 214 222 34725366 Association between prognostic factors and the outcomes of patients infected with SARS-CoV-2 harboring multiple spike protein mutations. A large-scale analysis of the COVID-19 Genomics UK consortium demonstrated that although D614G mutation is associated with higher viral loads, it is not associated with clinical severity and fatality of COVID-19 patients. 2021 Scientific reports Discussion SARS_CoV_2 D614G 89 94 COVID-19;COVID-19 203;30 211;38 34725366 Association between prognostic factors and the outcomes of patients infected with SARS-CoV-2 harboring multiple spike protein mutations. All our samples, except one, contained the D614G variant. 2021 Scientific reports Discussion SARS_CoV_2 D614G 43 48 34725366 Association between prognostic factors and the outcomes of patients infected with SARS-CoV-2 harboring multiple spike protein mutations. Indeed, almost all viruses circulating globally consist of the D614G mutation. 2021 Scientific reports Discussion SARS_CoV_2 D614G 63 68 34725366 Association between prognostic factors and the outcomes of patients infected with SARS-CoV-2 harboring multiple spike protein mutations. Interestingly, a previous report showed that one variant in non-RBD S protein, V1176F, might lead to RBD-ACE2 binding changes and was associated with a high mortality rate of COVID-19. 2021 Scientific reports Discussion SARS_CoV_2 V1176F 79 85 RBD;RBD;S 64;101;68 67;104;69 COVID-19 175 183 34725366 Association between prognostic factors and the outcomes of patients infected with SARS-CoV-2 harboring multiple spike protein mutations. It has been shown that the D614G mutation was not associated with the COVID-19 illness. 2021 Scientific reports Discussion SARS_CoV_2 D614G 27 32 COVID-19 70 78 34725366 Association between prognostic factors and the outcomes of patients infected with SARS-CoV-2 harboring multiple spike protein mutations. We also observed other S protein mutations in our samples, including L5F, V213A, and S68SR. 2021 Scientific reports Discussion SARS_CoV_2 L5F;V213A 69;74 72;79 S 23 24 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. For the first time in Pakistan, we have also found one significant mutation E484Q in a 52-year-old male patient infected with delta variant (B.1.617.2), traveling back from Bahrain. 2021 Journal of medical virology Discussion SARS_CoV_2 E484Q 76 81 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Furthermore, in two patients a rare spike mutation (about 1%), A879S, was reported. 2021 Journal of medical virology Discussion SARS_CoV_2 A879S 63 68 S 36 41 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. In case of beta variant, one of the patient is having a travel history of the Middle East carried two rare non-synonymous spike mutations, A27S and G181V, having a global prevalence of 5.7% and 0.1%, respectively according to GISAID data (July 31, 2021). 2021 Journal of medical virology Discussion SARS_CoV_2 A27S;G181V 139;148 143;153 S 122 127 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. In one of the sample, K444R mutation was observed that exhibit increased binding affinity to the human ACE2 receptor based on an in silico study. 2021 Journal of medical virology Discussion SARS_CoV_2 K444R 22 27 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. Moreover, in one female patient, a less prevalent spike mutation (about 0.5%), L5F was observed. 2021 Journal of medical virology Discussion SARS_CoV_2 L5F 79 82 S 50 55 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. The E484Q mutation has a prevalence of only 0.1% in B.1.617.2 as of July 31, 2021. 2021 Journal of medical virology Discussion SARS_CoV_2 E484Q 4 9 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. The viruses with the mutations, L452R and E484Q, are more resistant to monoclonal antibodies, including bamlanivimab, and convalescent plasma, and also have a role in increased transmissibility due to enhanced ACE2 binding based on the structural impact of these mutations in the furin cleavage site. 2021 Journal of medical virology Discussion SARS_CoV_2 E484Q;L452R 42;32 47;37 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. This mutation along with D614G had been found to decrease the sensitivity of convalescent sera and thus more likely to evade immune responses. 2021 Journal of medical virology Discussion SARS_CoV_2 D614G 25 30 34726786 Genomic surveillance reveals the detection of SARS-CoV-2 delta, beta, and gamma VOCs during the third wave in Pakistan. This mutation in combination with D614G had demonstrated increased infectivity and enhanced transmissibility. 2021 Journal of medical virology Discussion SARS_CoV_2 D614G 34 39 34728625 Potent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants. Structural analysis of epitopes revealed the potential neutralizing mechanism of neutralizing Abs against B.1.351 carrying the E484K mutation. 2021 Nature communications Discussion SARS_CoV_2 E484K 127 132 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. Additionally, although the nucleotide substitution C>T at position 241 in the 5' UTR was observed in all analysed sequences, its frequency is lower in the rest of the globe, and did not impact in the secondary structure of 5' UTR. 2021 Microbial genomics Discussion SARS_CoV_2 C241T 51 70 5'UTR;5'UTR 78;223 84;229 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. Additionally, the mutation on the position V1176F in the S protein was identified here in 41 % of the sequences from May to September, being also detected in the VOI P.2, identified in Brazil. 2021 Microbial genomics Discussion SARS_CoV_2 V1176F 43 49 S 57 58 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. Additionally, the N protein also showed positive selection pressure in the sites S202C/I and G204R, and the P.2 variant possessed the G204R mutation associated with R203K, which were observed in our data, however, without positive or negative selection. 2021 Microbial genomics Discussion SARS_CoV_2 G204R;G204R;R203K;S202C;S202I 93;134;165;81;81 98;139;170;88;88 N 18 19 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. Another point to take into consideration is that the substitution D614G in the Spike protein was identified in almost 100 % of Brazilian sequences, in both periods, and, according to Zhang and coworkers, it replaced the D614-carrying virus becoming the dominant circulating strain worldwide. 2021 Microbial genomics Discussion SARS_CoV_2 D614G 66 71 S 79 84 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. As was identified here, the presence of this mutation in late 2020 pointed out an increase in 119.2 % prevalence in V1176F, in contrast with the initial months of the pandemic in Brazil, indicating the persistence of this specific mutation possibly to guarantee viral adaptation. 2021 Microbial genomics Discussion SARS_CoV_2 V1176F 116 122 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. Moreover, the variants of concern B.1.351, B.1.427, and B.1.429 feature the T205I substitution, which were identified in 0.69% of our sequences from May to September (Table S1). 2021 Microbial genomics Discussion SARS_CoV_2 T205I 76 81 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. Our results demonstrated that the substitution V1176F is under positive selection, suggesting under these circumstances that it is a P.2 key element of this variant that emerged from Brazil during the period of analysis. 2021 Microbial genomics Discussion SARS_CoV_2 V1176F 47 53 34730486 Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. This can be evidenced by the emergence of the variants P.3 and P.4 in the Philippines and Mexico, respectively, which possess mutations that were identified in the P.2 variant, such as the V1176F. 2021 Microbial genomics Discussion SARS_CoV_2 V1176F 189 195 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. A previous study reported that the Q57H variant could cause dramatic changes in protein structures and decrease the flexibility of domains, thereby enhancing the binding affinities in ORF3a-M and ORF3a-S complexes. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Q57H 35 39 ORF3a;ORF3a;S 184;196;202 189;201;203 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. D614G and S194L were found to be associated with severe outcomes with high frequency worldwide. 2021 Frontiers in microbiology Discussion SARS_CoV_2 S194L;D614G 10;0 15;5 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. For example, R6997P (ORF1Ab), A222V (S), A220V (N), and V30L (ORF10) co-occurred in 0.5% of all cases in July 2020 and exceeded 50% of all cases by January 2021 worldwide. 2021 Frontiers in microbiology Discussion SARS_CoV_2 A220V;A222V;R6997P;V30L 41;30;13;56 46;35;19;60 ORF1ab;N;S 21;48;37 27;49;38 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. For example, the L3606F mutation in non-structural protein 6 (nsp6) was significantly higher in asymptomatic cases (40.19%) than in symptomatic cases (3.39%). 2021 Frontiers in microbiology Discussion SARS_CoV_2 L3606F 17 23 Nsp6 62 66 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. For example, the Q57H variant, which was found to occur in the ORF3a protein, had a higher frequency in severe cases (39.36%) than in asymptomatic cases (10.04%). 2021 Frontiers in microbiology Discussion SARS_CoV_2 Q57H 17 21 ORF3a 63 68 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. M3087I (ORF1Ab), K4576N (ORF1Ab), X5167Y (ORF1Ab), N5542D (ORF1Ab), S5585I (ORF1ab), and A376T (N) co-occurred in 0.8% of all cases in January 2020 to 5.7% of known cases in January 2021 worldwide. 2021 Frontiers in microbiology Discussion SARS_CoV_2 A376T;K4576N;N5542D;S5585I;X5167Y;M3087I 89;17;51;68;34;0 94;23;57;74;40;6 ORF1ab;ORF1ab;ORF1ab;ORF1ab;ORF1ab;N 8;25;42;59;76;96 14;31;48;65;82;97 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. Some of the mutation hotspots identified herein, namely, R203K, G204R, L3930F, and V1176F, were also high in severe cases, but significant statistical differences were not found. 2021 Frontiers in microbiology Discussion SARS_CoV_2 G204R;L3930F;R203K;V1176F 64;71;57;83 69;77;62;89 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. T265I, which is located in non-structural protein 2 (nsp2), has been observed in 13.83% of all cases worldwide. 2021 Frontiers in microbiology Discussion SARS_CoV_2 T265I 0 5 Nsp2 53 57 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. The D614G variant, which was found to occur in the S protein, has been proved to enhance infection and transmission. 2021 Frontiers in microbiology Discussion SARS_CoV_2 D614G 4 9 S 51 52 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. The issue of whether L3606F mutation can weaken the autophagy function of nsp6 requires further study. 2021 Frontiers in microbiology Discussion SARS_CoV_2 L3606F 21 27 Nsp6 74 78 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. The R203K and G204R variants co-occurred in the N protein and caused dramatic changes in protein structure [root mean square deviation (RMSD) >=5.0 A], thus decreasing the flexibility of the domain. 2021 Frontiers in microbiology Discussion SARS_CoV_2 G204R;R203K 14;4 19;9 N 48 49 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. The SNV frequency of D614G, S194L, and Q57H, which was found to be highly distributed in the Alpha, Beta, and Gamma, were higher in severe cases than in asymptomatic cases. 2021 Frontiers in microbiology Discussion SARS_CoV_2 D614G;Q57H;S194L 21;39;28 26;43;33 34733263 Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission. We found that the mutations correlated with asymptomatic outcomes were mainly in ORF1ab and N genes; especially R6997P and V30L mutations occurred together and were correlated with asymptomatic outcome with high prevalence. 2021 Frontiers in microbiology Discussion SARS_CoV_2 R6997P;V30L 112;123 118;127 ORF1ab;N 81;92 87;93 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. A frequent mutation was also present in the M gene - C26801G (L93L) was observed in 21.82% (and 53.4%-43.2% of all uploads from November-December 2020). 2021 Computers in biology and medicine Discussion SARS_CoV_2 C26801G;L93L 53;62 60;66 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. A G23311C (E583D) was predominantly uploaded by the UK (97.1%), so it may be considered with respect to the other UK statistics. 2021 Computers in biology and medicine Discussion SARS_CoV_2 G23311C;E583D 2;11 9;16 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. A mutation in ORF3a (G26144T) that formed a cluster featured by increased age (57) and significantly different male to female ratio (50.46:49.54) has presumably disappeared from the population and was last noted in the uploads in September 2020. 2021 Computers in biology and medicine Discussion SARS_CoV_2 G26144T 21 28 ORF3a 14 19 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. A T26801C mutation in the M gene was not found among mutations with a frequency greater than 0.3%, but our data yielded two mutations in the same position (freq >0.3%): C26801G and C26801T. 2021 Computers in biology and medicine Discussion SARS_CoV_2 C26801G;C26801T;T26801C 169;181;2 176;188;9 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Age-related changes were noted for the mutations in the S (A22255T) and E (T26424C) genes, with characteristic ages of 38 and 62, respectively. 2021 Computers in biology and medicine Discussion SARS_CoV_2 A22255T;T26424C 59;75 66;82 E;S 72;56 73;57 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Also, R203K and G204R in the N gene were found to occur together with high frequency, which is confirmed in our research. 2021 Computers in biology and medicine Discussion SARS_CoV_2 G204R;R203K 16;6 21;11 N 29 30 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Another work states that G251V and G196V might influence virulence, infectivity, ion channel activity, and viral release. 2021 Computers in biology and medicine Discussion SARS_CoV_2 G196V;G251V 35;25 40;30 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. D614G is considered to be more infectious than the ancestral form but not associated with increased disease severity. 2021 Computers in biology and medicine Discussion SARS_CoV_2 D614G 0 5 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Due to the lack of data, only C23929T (Y789Y) and C28311T (P13L) could be considered further. 2021 Computers in biology and medicine Discussion SARS_CoV_2 C23929T;C28311T;P13L;Y789Y 30;50;59;39 37;57;63;44 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. For a T26424C mutation, 97.96% of the sequences were uploaded by the UK, only 47 records were age-filled, most uploaded by the UK, where the mean patient age was 59. 2021 Computers in biology and medicine Discussion SARS_CoV_2 T26424C 6 13 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. For A22255T, 97.31% of the sequences were uploaded by the USA, and the total age-filled records' number for the SNP was 122, most uploaded by the USA. 2021 Computers in biology and medicine Discussion SARS_CoV_2 A22255T 4 11 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. For example, D614G is often considered together with P323L. 2021 Computers in biology and medicine Discussion SARS_CoV_2 D614G;P323L 13;53 18;58 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Four mutations with a frequency greater than 20% featured the N gene: G28881A (R203K), G28882A (R203R), G28883S (R203R), and C28932T (A220V). 2021 Computers in biology and medicine Discussion SARS_CoV_2 C28932T;G28881A;G28882A;G28883S;A220V;R203K;R203R;R203R 125;70;87;104;134;79;96;113 132;77;94;111;139;84;101;118 N 62 63 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. G251V results in the loss of a phosphatidylinositol-specific phospholipase X-box domain and a creation of a serine protease cleavage site. 2021 Computers in biology and medicine Discussion SARS_CoV_2 G251V 0 5 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. G28881A is concomitant with G28882A and G28883S (r = 0.998). 2021 Computers in biology and medicine Discussion SARS_CoV_2 G28882A;G28883S;G28881A 28;40;0 35;47;7 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. However, in the present research G26144T (G251V) was found to create a cluster on its own; the mutation was featured by increased age (57) and an increased proportion of women compared to the general cohort. 2021 Computers in biology and medicine Discussion SARS_CoV_2 G26144T;G251V 33;42 40;47 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. In S, it was C22227T (A222V) with 22.25%. 2021 Computers in biology and medicine Discussion SARS_CoV_2 C22227T;A222V 13;22 20;27 S 3 4 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Interestingly, Q57H and R203K were found to cause substantial changes in protein structures (RMSD >=5.0 A). 2021 Computers in biology and medicine Discussion SARS_CoV_2 Q57H;R203K 15;24 19;29 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Last, one most frequently occurring mutation found in ORF10, G29645T (V30L), was present in 22.03% of uploads in a general group and 44.6% of all uploads from December 2020. 2021 Computers in biology and medicine Discussion SARS_CoV_2 G29645T;V30L 61;70 68;74 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Only three mutations have not been noted in the uploads for some time: G26144T (G251V) and G25979T (G196V) in ORF3a, which were last uploaded around September 2020 and early December 2020, respectively, and a C28836T (S188L) in the N gene, which was last seen around early to middle November. 2021 Computers in biology and medicine Discussion SARS_CoV_2 C28836T;G25979T;G26144T;G196V;G251V;S188L 209;91;71;100;80;218 216;98;78;105;85;223 ORF3a;N 110;232 115;233 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. P13L (mostly uploaded by Singapore in our research, 74% of males), is presumably associated with decreased deaths and significant changes altering the protein structure. 2021 Computers in biology and medicine Discussion SARS_CoV_2 P13L 0 4 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Some mutations (for example, C27964T in ORF8) have been found to have gender dependence with a presumed ratio of 2:1. 2021 Computers in biology and medicine Discussion SARS_CoV_2 C27964T 29 36 ORF8 40 44 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. Some researchers suggest the inability of D614G to cause viral success when presented alone. 2021 Computers in biology and medicine Discussion SARS_CoV_2 D614G 42 47 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. T85I is noted to co-occur with Q57H, and P504L - with Y541C. 2021 Computers in biology and medicine Discussion SARS_CoV_2 P504L;Q57H;Y541C;T85I 41;31;54;0 46;35;59;4 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. The most frequent mutation in the analyzed genes was a mutation in the S gene - A23403G (D614G), which was found in 94.15% of all studied genomes and in 99.9% of genomes uploaded in December 2020. 2021 Computers in biology and medicine Discussion SARS_CoV_2 A23403G;D614G 80;89 87;94 S 71 72 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. The most recent mutation in the current analysis is A28111G (Y73C) in ORF8, which appeared in the uploaded data about early September 2020. 2021 Computers in biology and medicine Discussion SARS_CoV_2 A28111G;Y73C 52;61 59;65 ORF8 70 74 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. The only interesting message was an article stating that this mutation co-mutates with infectivity-enhancing S protein mutations, such as D614G, which cannot yet explain our finding.). 2021 Computers in biology and medicine Discussion SARS_CoV_2 D614G 138 143 S 109 110 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. The ORF3a gene had a G25563T (Q57H) mutation, found in 21.41% of the genomes. 2021 Computers in biology and medicine Discussion SARS_CoV_2 G25563T;Q57H 21;30 28;34 ORF3a 4 9 34735950 Analysis of 329,942 SARS-CoV-2 records retrieved from GISAID database. The subtype may be characterized by four to six additional mutations, with four being a more frequent option (G28881A, G28882A, G28883S, A23403G, A28095T, G25437T). 2021 Computers in biology and medicine Discussion SARS_CoV_2 A23403G;A28095T;G25437T;G28882A;G28883S;G28881A 137;146;155;119;128;110 144;153;162;126;135;117 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. After March 2020, the D614G clade became increasingly prevalent worldwide, expanding from 22 to 42 countries with GH (D614G + Q57H in the NS3) dominant in North America (59.0%). 2021 Infection and drug resistance Discussion SARS_CoV_2 D614G;Q57H;D614G 22;126;118 27;130;123 NS3 138 141 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. Although K417N/T mutations decrease the affinity of RBD for ACE2, they facilitate the immune escape. 2021 Infection and drug resistance Discussion SARS_CoV_2 K417N;K417T 9;9 16;16 RBD 52 55 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. In addition, E484K disrupts antibody neutralization. 2021 Infection and drug resistance Discussion SARS_CoV_2 E484K 13 18 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. It has L452R, T478K, and P681R substitutions in the S protein. 2021 Infection and drug resistance Discussion SARS_CoV_2 L452R;P681R;T478K 7;25;14 12;30;19 S 52 53 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. Our data from March showed that most of the SARS-CoV-2 had mutation particularly in D614G that may be D614G variant previously described. 2021 Infection and drug resistance Discussion SARS_CoV_2 D614G;D614G 84;102 89;107 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. Our study found B.1.1.7 variant with mutation mainly in D614G, N501Y and del 69-70 was prevalent in all five months predominantly in April and May. 2021 Infection and drug resistance Discussion SARS_CoV_2 D614G;N501Y 56;63 61;68 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. The B.1.351 variant has mutation in the RBD of spike protein, namely, K417N, E484K, and N501Y and the P.1 variant has mutation in the spike RBD, namely, K417T, E484K, and N501Y. 2021 Infection and drug resistance Discussion SARS_CoV_2 E484K;E484K;K417N;K417T;N501Y;N501Y 77;160;70;153;88;171 82;165;75;158;93;176 S;S;RBD;RBD 47;134;40;140 52;139;43;143 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. The B.1.427/B.1.429 variants increased transmissibility up to 24% and L452R spike mutation is associated with spike-ACE2 receptor interaction. 2021 Infection and drug resistance Discussion SARS_CoV_2 L452R 70 75 S;S 76;110 81;115 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. The effect of the mutations L452R and T478K on ACE2 binding was also observed as enhanced stabilization of the RBD-ACE2 complex. 2021 Infection and drug resistance Discussion SARS_CoV_2 L452R;T478K 28;38 33;43 RBD 111 114 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. The emergence of new variants was led by the global rise of the D614G mutation in the Wuhan strain identified in China and Germany. 2021 Infection and drug resistance Discussion SARS_CoV_2 D614G 64 69 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. The mutations in the D614G, E484K, N501Y, L452R, P681R, and E484Q are associated with the enhanced transmissibility due to increased affinity with host's ACE2 receptor. 2021 Infection and drug resistance Discussion SARS_CoV_2 D614G;E484K;E484Q;L452R;N501Y;P681R 21;28;60;42;35;49 26;33;65;47;40;54 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. The study identified that spike mutation P681R is a significant determinant for enhanced viral replication fitness of the Delta compared to the Alpha variant. 2021 Infection and drug resistance Discussion SARS_CoV_2 P681R 41 46 S 26 31 34737587 SARS-CoV-2 Variants Detection Using TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assays. This is probably the result of an increased number of open RBDs due to the D614G mutation combined with the N501Y replacement in the hAce2-binding site. 2021 Infection and drug resistance Discussion SARS_CoV_2 D614G;N501Y 75;108 80;113 RBD 59 63 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. Certain studies reported the increment in viral load in the upper respiratory tract (URT) of patients infected with the D614G mutant type virus. 2022 Virus research Discussion SARS_CoV_2 D614G 120 125 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. N501Y mutation in the spike protein of B.1.1.7 mutant viruses was experimentally showed to exert enhanced replication rates in cell lines and human respiratory cells (ex-vivo studies), which might occur through the same mechanism (; Moelling, 2021). 2022 Virus research Discussion SARS_CoV_2 N501Y 0 5 S 22 27 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. Several studies have implied that the D614G mutation in the spike glycoprotein of SARS-CoV-2, being closely located in the receptor-binding domain. 2022 Virus research Discussion SARS_CoV_2 D614G 38 43 S 60 78 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. The spike protein of SARS-CoV-2 is more prone to multiple point mutations, most notable being D614G (Asp614-to-Gly) variant (globally dominant viral form) with increment in transmissibility, infectivity and neutralization susceptibility. 2022 Virus research Discussion SARS_CoV_2 D614G;D614G 94;101 99;114 S 4 9 34740719 Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. Type 2 mutation (S171L) of ORF3a was found in BRA/HIAE-SP03/2020, none other type doesn't exist in Brazilian isolates. 2022 Virus research Discussion SARS_CoV_2 S171L 17 22 ORF3a 27 32 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. For instance, recent experimental work on mutated RBD with E484K has shown a 100-1000 fold increase in antibody dose for C144. 2021 Scientific reports Discussion SARS_CoV_2 E484K 59 64 RBD 50 53 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. On the other hand, for MT2, MT3, and RBD versions involving mutations K417N, L452R, E484K, T478K, and N501Y, the binding energy increased compared to the WT. 2021 Scientific reports Discussion SARS_CoV_2 E484K;K417N;L452R;N501Y;T478K 85;71;78;103;92 90;76;83;108;97 RBD 38 41 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. reported that the binding between SARS2 and ACE2 increases when the following mutations K417N, E484K, L452R, T478K, and N501Y are present, in good agreement with our findings. 2021 Scientific reports Discussion SARS_CoV_2 E484K;K417N;L452R;N501Y;T478K 95;88;102;120;109 100;93;107;125;114 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. Simulations between the RBD and Class I hNAbs indicated that the binding energy increases between MT1 (N501Y) and B38 and C102 compared to WT. 2021 Scientific reports Discussion SARS_CoV_2 N501Y 103 108 RBD 24 27 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. This result is supported by experimental works where N501Y mutation has been found to have a modest effect on the binding of monoclonal antibodies . 2021 Scientific reports Discussion SARS_CoV_2 N501Y 53 58 34741079 Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations. We found that mutation N501Y marginally enhanced the binding energy between RBD and ACE2, while mutations MT2 (E484K/N501Y) MT3 (K417N/E484K/N501Y), and (L452R/T478K) enhanced the binding avidity between RBD and ACE2. 2021 Scientific reports Discussion SARS_CoV_2 N501Y;E484K;K417N;L452R;E484K;N501Y;N501Y;T478K 23;111;129;155;135;117;141;161 28;116;134;160;140;122;146;166 RBD;RBD 76;205 79;208 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. At low target cell ACE2 levels, the relative ability of the different SARS-CoV-2 S glycoproteins to mediate virus entry exhibited the following rank order: P.1, B.1.1.248 > B.1.351 > B.1.1.7 > D614G > D614. 2021 iScience Discussion SARS_CoV_2 D614G 193 198 S 81 96 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. However, we note that, as previously seen, the D614G S is more stable and sheds S1 less at 0 or 4 C than the D614 S, yet these two variants exhibit minimal differences in the rate of decay of infectivity at these temperatures. 2021 iScience Discussion SARS_CoV_2 D614G 47 52 S;S 53;114 54;115 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. In this study, we compared the functional properties of the S glycoproteins of emerging SARS-CoV-2 variants with those of the original/founder D614 strain and the globally dominant D614G variant. 2021 iScience Discussion SARS_CoV_2 D614G 181 186 S 60 75 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. Increased sensitivity to soluble ACE2 has been attributed to the N501Y change found in the RBD of the B.1.1.7, B.1.351, P.1, and B.1.1.248 S glycoproteins. 2021 iScience Discussion SARS_CoV_2 N501Y 65 70 S;RBD 139;91 154;94 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. Incubation on ice or at 4 C led to rapid loss of infectivity of P.1 and B.1.1.248 pseudotypes, in comparison to the D614, D614G, and B.1.351 viruses. 2021 iScience Discussion SARS_CoV_2 D614G 122 127 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. Likewise, the authentic B.1.1.7 SARS-CoV-2 variant exhibited a longer half-life at 4 C than the authentic D614G and P.1 variants. 2021 iScience Discussion SARS_CoV_2 D614G 106 111 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The B.1.1.7, B.1.351, P.1, and B.1.1.248 SARS-CoV-2 variants all evolved from D614G, which exhibits an increase in S stability at low temperatures relative to D614, but is still inactivated functionally by extended exposure to cold. 2021 iScience Discussion SARS_CoV_2 D614G 78 83 S 115 116 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The K417N and E484K changes in the S1 RBD have been shown to contribute to escape from neutralizing antibodies. 2021 iScience Discussion SARS_CoV_2 E484K;K417N 14;4 19;9 RBD 38 41 34746689 Functional differences among the spike glycoproteins of multiple emerging severe acute respiratory syndrome coronavirus 2 variants of concern. The neutralization profile of B.1.1.7 was similar to that of D614 and D614G, whereas B.1.351, P.1, and B.1.1.248 were less sensitive to these antisera. 2021 iScience Discussion SARS_CoV_2 D614G 70 75 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. Despite one of the viruses carrying the D614G mutation and despite this outbreak occurring in an extremely overcrowded area, it appears that only 89/2722 living in the 6,955 square meters (0.007 km2) area of the Bandaranayaka watta were infected. 2021 PloS one Discussion SARS_CoV_2 D614G 40 45 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. Of the two viruses, one carried the D614G mutation in the S protein, which have been associated with higher transmissibility and infectivity. 2021 PloS one Discussion SARS_CoV_2 D614G 36 41 S 58 59 34748557 Transmission dynamics, clinical characteristics and sero-surveillance in the COVID-19 outbreak in a population dense area of Colombo, Sri Lanka April- May 2020. Since this study was carried out from April to May 2020, none of the current SARS-CoV2 variants that are associated with higher transmissibility that are currently emerging from many countries such as the N501Y or the E484K mutation were detected. 2021 PloS one Discussion SARS_CoV_2 E484K;N501Y 218;205 223;210 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Here we demonstrate that the emergence of Y453F in SARS-CoV-2 spike significantly enhanced its interaction with other Mustela ACE2 orthologs:namely ferret and stoat:conferring a potential fitness advantage in Mustela species that could subsequently promote virus transmission and possible risk of animal-adapted virus with genetic alterations to spilling over into humans. 2021 PLoS pathogens Discussion SARS_CoV_2 Y453F 42 47 S 62 67 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. In addition, the miSARS-CoV-2 Y453F spike mutant maintained its ability to interact with human ACE2 and exhibited partial resistance to neutralizing antibodies, potentially explaining the ability of miSARS-CoV-2 to transmit back to humans and subsequent human-human transmission. 2021 PLoS pathogens Discussion SARS_CoV_2 Y453F 30 35 S 36 41 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. In summary, our study suggests that Y453F is an adaptive mutation in SARS-CoV-2 that results in a virus more competent for infection and transmission among mink. 2021 PLoS pathogens Discussion SARS_CoV_2 Y453F 36 41 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. In this study, we demonstrated that the Y453F substitution in the miSARS-CoV-2 spike protein is an adaptive mutation that significantly enhances interaction with mink ACE2 and promotes infection of minks. 2021 PLoS pathogens Discussion SARS_CoV_2 Y453F 40 45 S 79 84 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. It has been shown that the D614G substitution in the SARS-CoV-2 spike can promote virus entry into host cells and enhance infectivity as well as make the mutant virus resistant to neutralizing antibody. 2021 PLoS pathogens Discussion SARS_CoV_2 D614G 27 32 S 64 69 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Moreover, the Y453F substitution does not compromise the ability of the spike protein to utilize human ACE2, explaining at least in part the circulation of the mink-associated virus observed in humans. 2021 PLoS pathogens Discussion SARS_CoV_2 Y453F 14 19 S 72 77 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. Our results showed that miSARS-CoV-2 Y453F spike pseudotyped virions exhibited 3.5-fold resistance to neutralization by convalescent serum (Fig 7A), suggesting Y453F mutation has potentially compromised the natural infection induced humoral immunity. 2021 PLoS pathogens Discussion SARS_CoV_2 Y453F;Y453F 37;160 42;165 S 43 48 34748603 Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption. The Y453F mutation was shown to be an escape mutation for the monoclonal antibody RGN10933. 2021 PLoS pathogens Discussion SARS_CoV_2 Y453F 4 9 34756912 RT-qPCR detection of SARS-CoV-2 mutations S 69-70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples. The relative proportion of B.1.1.7 to WT in wastewater can be estimated using the Sdel and ND3L assays, while N501Y is present in B.1.1.7, B.1.351, and P.1. 2022 The Science of the total environment Discussion SARS_CoV_2 N501Y 110 115 34757638 Changing predominant SARS-CoV-2 lineages drives successive COVID-19 waves in Malaysia, February 2020 to March 2021. A701V is close to the S2' cleavage site which when cleaved leads to spike-mediated membrane fusion, but its significance remains unknown. 2021 Journal of medical virology Discussion SARS_CoV_2 A701V 0 5 Membrane;S 83;68 91;73 34757638 Changing predominant SARS-CoV-2 lineages drives successive COVID-19 waves in Malaysia, February 2020 to March 2021. B.1.524 viruses carry the spike mutations D614G (present in most SARS-CoV-2 viruses) and A701V, which is also found in the VOC B.1.351 and the previously designated variant of interest B.1.526 (iota). 2021 Journal of medical virology Discussion SARS_CoV_2 A701V;D614G 89;42 94;47 S 26 31 34757638 Changing predominant SARS-CoV-2 lineages drives successive COVID-19 waves in Malaysia, February 2020 to March 2021. The mutation D614G, which has become predominant worldwide, is associated with increased cell entry, replication, and transmissibility, possibly by stabilizing the spike receptor-binding domain and enhancing binding to the host cell receptor angiotensin-converting enzyme 2. 2021 Journal of medical virology Discussion SARS_CoV_2 D614G 13 18 S 164 169 34757638 Changing predominant SARS-CoV-2 lineages drives successive COVID-19 waves in Malaysia, February 2020 to March 2021. The nsp12 (RNA-dependent RNA polymerase) P323L mutation present in lineage B.1.524 is almost always associated with D614G; the significance of P323L is also unclear, but it may impact the interaction between nsP12 and nsP8 and affect RNA polymerase activity. 2021 Journal of medical virology Discussion SARS_CoV_2 D614G;P323L;P323L 116;41;143 121;46;148 RdRp;Nsp12;Nsp12;Nsp8 11;4;208;218 39;9;213;222 34757638 Changing predominant SARS-CoV-2 lineages drives successive COVID-19 waves in Malaysia, February 2020 to March 2021. To date, B.1.524 does not contain other spike mutations associated with increased pathogenicity or immune escape, such as K417N, L452R, E484K, and N501Y. 2021 Journal of medical virology Discussion SARS_CoV_2 E484K;K417N;L452R;N501Y 136;122;129;147 141;127;134;152 S 40 45 34758391 SARS-CoV-2 variants with T135I nucleocapsid mutations may affect antigen test performance. observed that a high-frequency co-occurring-mutation ratio (R203K and G204R) destabilized and decreased overall N protein structural flexibility (Rahman et al., 2021). 2022 International journal of infectious diseases Discussion SARS_CoV_2 G204R;R203K 70;60 75;65 N 112 113 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. Among the mutation hotspots only D614G and A701V in the spike protein as well as P4715L and T2015I in ORF1ab are known to have a world-wide prevalence. 2021 PeerJ Discussion SARS_CoV_2 A701V;D614G;P4715L;T2015I 43;33;81;92 48;38;87;98 ORF1ab;S 102;56 108;61 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. One of the LD sets included A23403G (D164G), C14408T and C3037T which were reported to be the most frequent mutations in many parts of the world and also found to be the most frequent mutations in this study. 2021 PeerJ Discussion SARS_CoV_2 A23403G;C14408T;C3037T;D164G 28;45;57;37 35;52;63;42 34760404 Genomic diversity of SARS-CoV-2 in Malaysia. The linkage between D641G in the S gene and P4715L in ORF1ab is consistent with their presence together in >75% of global sequences. 2021 PeerJ Discussion SARS_CoV_2 D641G;P4715L 20;44 25;50 ORF1ab;S 54;33 60;34 34763050 Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation. Besides those sequenced, 11 sequences presented the D614A mutation in GISAID, however, they belong to A.24 from Asia (6 sequences), B.1.1.7 from Europe (4 sequences) and B.1.2 from North American (1 sequence). 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614A 52 57 34763050 Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation. In SARS-CoV-2 some mutations were correlated with advantages, as the increase of rate of transmission (example: D614G mutation and Gamma variant) and decrease neutralizing antibodies. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 112 117 34763050 Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation. Prior to March, the D614G was present in 10% of global sequences, from 1st to March 31, 2020, the detection rate already reached 67% of sequences and, from 1st April to May 18, 2020, the D614G mutations have already been observed in 78% of the sequences . 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;D614G 20;187 25;192 34763050 Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation. The D614G for D614A change has already been identified in July 2020 in three individuals who returning to Korea from Uzbekistan . 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614A;D614G 14;4 19;9 34763050 Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation. The D614G is a relevant Spike mutation observed in early March 2020 . 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 4 9 S 24 29 34763050 Predominance of SARS-CoV-2 P.1 (Gamma) lineage inducing the recent COVID-19 wave in southern Brazil and the finding of an additional S: D614A mutation. This rapid spread and dominancy of sequences with D614G mutation globally, probably is related with the advantage observed in replication efficiency when comparing to D614, which can increase the probability of human-to-human transmission . 2021 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 50 55 34766651 SARS-CoV-2 AY.4.2 variant circulating in Italy: Genomic preliminary insight. This emerging lineage carries two additional mutations in the spike protein (Y145H and A222V), that may have functional importance, in addition to several mutations seen in the Delta variant related to increased risk of disease severity, risk of vaccine escape and higher transmissibility. 2022 Journal of medical virology Discussion SARS_CoV_2 A222V;Y145H 87;77 92;82 S 62 67 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. Between August 2020 and the end of January 2021 the N501T mutation increased in frequency of sequenced isolates in the United States from.01% to.30%, similar to the increase in N501Y mutations. 2021 PLoS pathogens Discussion SARS_CoV_2 N501T;N501Y 52;177 57;182 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. GISAID differentiates COVID-19 into three major clades: Clade S, Clade V and Clade G (originally prevalent in North America, Asia/Europe, and Europe, respectively), based on NS mutations at NS8_L84S, NS3_G251V and S_D614G, respectively. 2021 PLoS pathogens Discussion SARS_CoV_2 D614G;G251V;L84S 216;204;194 221;209;198 NS3;S 200;62 203;63 COVID-19 22 30 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. In addition to the highly prevalent D614G mutation, the mink isolate had a N501T spike mutation, which is uncommon in humans. 2021 PLoS pathogens Discussion SARS_CoV_2 D614G;N501T 36;75 41;80 S 81 86 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. N501T is located in the Receptor Binding Domain (RBD) of the spike glycoprotein, resulting in a moderate increase in ACE2 binding. 2021 PLoS pathogens Discussion SARS_CoV_2 N501T 0 5 RBD;S;RBD 24;61;49 47;79;52 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. S1205L-NSP3, T91M-NSP15, H182Y-NS3, Q289H-N, and A38S-M are rare mutations of unknown significance. 2021 PLoS pathogens Discussion SARS_CoV_2 A38S;H182Y;Q289H;T91M;S1205L 49;25;36;13;0 53;30;41;17;6 Nsp3;NS3;N 7;31;42 11;34;43 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. Success of the P323L/ G614 variant suggests that the P323L mutation adds to the virulence of the G614 spike variant, although without increasing patient mortality. 2021 PLoS pathogens Discussion SARS_CoV_2 P323L;P323L 15;53 20;58 S 102 107 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. The G clade was subsequently divided into GR clade containing N_203-204: RG>KR and GH clade with NS3_Q57H aa substitutions. 2021 PLoS pathogens Discussion SARS_CoV_2 Q57H 101 105 NS3 97 100 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. The NS3_Q57H mutation is common in the USA and is predicted to be deleterious. 2021 PLoS pathogens Discussion SARS_CoV_2 Q57H 8 12 NS3 4 7 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. The P323L-NSP12 mutation in the viral polymerase gene coevolved with the D614G-spike mutation also present in this mink strain to become the most prevalent variant in the world, and this combination is present in 95.4% of whole virus genomes from mink to date. 2021 PLoS pathogens Discussion SARS_CoV_2 D614G;P323L 73;4 78;9 S;Nsp12 79;10 84;15 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. The polyprotein ORF1ab T85I-NPS2 mutation is most common in the USA (56% of phase 2 viruses) and has spread to at least 37 countries during phase 2 of the pandemic. 2021 PLoS pathogens Discussion SARS_CoV_2 T85I 23 27 ORF1ab 16 22 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. The Utah mink did not share other spike RBD mutations Y453F and F486L, which are common in U.S. 2021 PLoS pathogens Discussion SARS_CoV_2 F486L;Y453F 64;54 69;59 S;RBD 34;40 39;43 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. These included five nsp2 aa substitutions (E352Q, A372V, R398C, A405T, and E743V), four in the nsp3 papain-like proteinase domain (P1096L, H1113Y, I1508V, and M1588K) one in the nsp5 3C-like proteinase domain (I3522V), one in the nsp9 RNA/ DNA binding domain (G4177E or R) one in the nsp15 poly(U) specific endoribonuclease domain (A6544T), two in the nsp12 RNA-dependent RNA polymerase domain (M4588I and T5195I), and two in the nsp13 helicase domain (I5582V and A5770D). 2021 PLoS pathogens Discussion SARS_CoV_2 A372V;A405T;A5770D;E743V;H1113Y;I1508V;M1588K;R398C;T5195I;A6544T;E352Q;G4177E;I3522V;I5582V;M4588I;P1096L 50;64;464;75;139;147;159;57;406;332;43;260;210;453;395;131 55;69;470;80;145;153;165;62;412;338;48;266;216;459;401;137 RdRp;Helicase;Nsp13;Nsp12;Nsp2;Nsp3;Nsp5 358;436;430;352;20;95;178 386;444;435;357;24;99;182 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. This unncommon spike RBD N501T mutation from Utah mink has been found in four emergences within three lineages of mink samples. 2021 PLoS pathogens Discussion SARS_CoV_2 N501T 25 30 S;RBD 15;21 20;24 34767598 An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms. With the exception of the common D614G mutation, the Utah mink have none of the multiple spike protein changes found in variants of concern, which the CDC currently lists as WHO label alpha, beta, delta, and gamma strains (Pango lineages B.1.1.7, B.1.351, B.1.617.2, and P.1). 2021 PLoS pathogens Discussion SARS_CoV_2 D614G 33 38 S 89 94 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. An additional limitation is that while we discovered that the alpha/beta/gamma, [D614G] mutation in the S1 protein, which is at some distance from the RBD, raises the KD for ACE2 binding to the RBD, the present data do not reveal the mechanism. 2021 Scientific reports Discussion SARS_CoV_2 D614G 81 86 RBD;RBD 151;194 154;197 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. By contrast, the potency of digitoxin and digoxin in the in vitro ACE2:RBD binding assays depended on the mutations present in the RBD, and on the presence of the [D614G] mutation in the S1 domain. 2021 Scientific reports Discussion SARS_CoV_2 D614G 164 169 RBD;RBD 71;131 74;134 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Certainly infectivity enhancing mutations such as Mink [Y453F], alpha/beta/gamma [N501Y] and beta [E484K] profoundly affect ACE2 binding kinetics. 2021 Scientific reports Discussion SARS_CoV_2 E484K;N501Y;Y453F 99;82;56 104;87;61 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. However, it has been reported that the alpha/beta/gamma, [D614G] mutation increases spike flexibility, and spike density by 4-fivefold. 2021 Scientific reports Discussion SARS_CoV_2 D614G 58 63 S;S 84;107 89;112 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Nonetheless, the inhibition constants for the cardiac glycosides were not significantly affected by the [D614G] mutation. 2021 Scientific reports Discussion SARS_CoV_2 D614G 105 110 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. Not unexpectedly, we also found that mutations in the RBD, specifically Mink [Y453F] and alpha/ beta/gamma [N501Y], significantly increased ACE2 binding affinity, while the beta [E484K] mutation trended towards reduction in ACE2 binding affinity. 2021 Scientific reports Discussion SARS_CoV_2 E484K;N501Y;Y453F 179;108;78 184;113;83 RBD 54 57 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. The alpha/beta/gamma, [D614G] mutation in the S1 protein may be an example of how changes at some distance from the RBD sequence can raise the KD for ACE2 binding to the RBD. 2021 Scientific reports Discussion SARS_CoV_2 D614G 23 28 RBD;RBD 116;170 119;173 34773067 Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration and infectivity in human lung cells. We also validated a previous finding that the alpha/beta/gamma [D614G] mutation, on a part of the spike S1 protein downstream of the RBD, also reduced ACE2 binding affinity to the RBD. 2021 Scientific reports Discussion SARS_CoV_2 D614G 64 69 S;RBD;RBD 98;133;180 103;136;183 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. C21727T and T23815C) had occurred in it, as well as changes elsewhere within the virus genome. 2021 PLoS pathogens Discussion SARS_CoV_2 T23815C;C21727T 12;0 19;7 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. C3792T, C5167T, G10887A, C21727T and T23815C, see Table 2), which were present in the mink viruses from Farm 4 in November, was found in one person in early November. 2021 PLoS pathogens Discussion SARS_CoV_2 C21727T;C5167T;G10887A;T23815C;C3792T 25;8;16;37;0 32;14;23;44;6 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. However, this process of RNA editing is not relevant to the key mutation in the S gene (A22920T), which seems to be an adaptation that occurred during the initial infection of mink, or to the generation of deletions. 2021 PLoS pathogens Discussion SARS_CoV_2 A22920T 88 95 S 80 81 34780574 Infection, recovery and re-infection of farmed mink with SARS-CoV-2. It has been found that there was a cluster of occurrences of SARS-CoV-2 with the DeltaH69/N70 and Y453F changes (as in Farm 4) in the local human population in August. 2021 PLoS pathogens Discussion SARS_CoV_2 Y453F 98 103 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. 2); this could be explained by the presence of two additional mutations in the S protein, T859I and W152R (Table 1), because the presence of mutations at the same positions have been reported independently in the VOIs B.1.526 (Iota) and B.1.429, respectively. 2022 Virus research Discussion SARS_CoV_2 T859I;W152R 90;100 95;105 S 79 80 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Hence, surveillance of emerging lineages with the E484K mutation, and/or other specific genetic markers associated with greater virulence, should be carried out in individuals with previous infection or vaccination. 2022 Virus research Discussion SARS_CoV_2 E484K 50 55 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. In agreement with previous reports, the single E484K mutation was associated with reduced neutralizing activity of convalescent and post-vaccination (Pfizer-BioNTech) sera, against replication-competent SARS-CoV-2, and pseudoviruses. 2022 Virus research Discussion SARS_CoV_2 E484K 47 52 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. It is essential to clarify that it has been reported that variants with the E484K mutation have no alterations in its stability or in host cell entry (M et al., 2021). 2022 Virus research Discussion SARS_CoV_2 E484K 76 81 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Our results suggest that E484K mutation in B.1+L249S+E484K does not affect the viral titer, however it reduces antibody neutralization, when compared to the A.1, B.1.420, B.1.111 lineages, all of them without the E484K mutation. 2022 Virus research Discussion SARS_CoV_2 E484K;E484K;E484K;L249S 25;213;53;47 30;218;58;52 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. Remarkably, the phylogenetic maximum likelihood phylogenetic tree reconstructed in this study grouped the isolates B.1+L249S+E484K and B.1.111-II in the same clade. 2022 Virus research Discussion SARS_CoV_2 E484K;L249S 125;119 130;124 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. The E484K substitution, located at the receptor-binding domain (RBD), is continuously and independently occurring in emerging SARS-CoV-2 VOCs and VOIs across all over the world ("). 2022 Virus research Discussion SARS_CoV_2 E484K 4 9 RBD 64 67 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. This study shows the neutralizing activity of natural infection-elicited antibodies against four SARS-CoV-2 lineages, including B.1+L249S+E484K. 2022 Virus research Discussion SARS_CoV_2 E484K;L249S 138;132 143;137 34780883 Reduced levels of convalescent neutralizing antibodies against SARS-CoV-2 B.1+L249S+E484K lineage. While the MN assays unequivocally evidenced reduced neutralization antibody titers against B1+L249S+E484K in convalescent sera. 2022 Virus research Discussion SARS_CoV_2 E484K;L249S 100;94 105;99 34783635 Identification of the SARS-CoV-2 Delta variant C22995A using a high-resolution melting curve RT-FRET-PCR. A limitation of using the RT-FRET-PCR is that the C22995A mutation which it detects is also present in other variants, but these are only very rarely reported in GISAID (0.006%; 62 / 962,990), and false-positive results would be expected to be very unusual in symptomatic people. 2022 Emerging microbes & infections Discussion SARS_CoV_2 C22995A 50 57 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. All N501Y mutants were detected among fully vaccinated HCPs, half of which failed to generate WGS data due to higher Ct values, a likely consequence of vaccination. 2021 Microbiology spectrum Discussion SARS_CoV_2 N501Y 4 9 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. Although 44% of the strains recovered from fully vaccinated HCPs harbored mutations of concern (6 N501Y and 1 E484K), they were similar in proportion to strains circulating in the community during the same time period. 2021 Microbiology spectrum Discussion SARS_CoV_2 E484K;N501Y 110;98 115;103 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. Extensive polymorphisms in the spike protein have been documented, including N501Y and E484K mutations that are particularly concerning. 2021 Microbiology spectrum Discussion SARS_CoV_2 E484K;N501Y 87;77 92;82 S 31 36 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. In our study, despite an increasing trend in the proportion of N501Y and E484K variants in the overall population. 2021 Microbiology spectrum Discussion SARS_CoV_2 E484K;N501Y 73;63 78;68 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. Other outbreaks have been reported among vaccinated individuals implicating SARS-CoV-2 strains harboring E484K, a noted immune evasion-conferring polymorphism. 2021 Microbiology spectrum Discussion SARS_CoV_2 E484K 105 110 34787439 Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study. Our WGS analysis suggests that N501Y-harboring strains belong to the B1.1.7 lineage and the E484K mutants to the B.1.526 lineage, both highly prevalent lineages in the Northeastern United States. 2021 Microbiology spectrum Discussion SARS_CoV_2 E484K;N501Y 92;31 97;36 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. also found the C29197T mutation to be present in less than 1% of sequences in the NCBI and GISAID databases. 2021 Microbiology spectrum Discussion SARS_CoV_2 C29197T 15 22 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. also identified the C29197T mutation in cases from Ohio and New York, respectively. 2021 Microbiology spectrum Discussion SARS_CoV_2 C29197T 20 27 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. At present, three mutations have been identified in the N gene that likely result in N gene target detection failures in the Xpert assay; C29197T, C29200T, and C29200A. 2021 Microbiology spectrum Discussion SARS_CoV_2 C29197T;C29200A;C29200T 138;160;147 145;167;154 N;N 56;85 57;86 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. Further analysis revealed that the C29197T mutation is present in 77 SARS-CoV-2 lineages, indicating that it is likely the result of spontaneous mutation independent of evolution. 2021 Microbiology spectrum Discussion SARS_CoV_2 C29197T 35 42 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. In this study, the five isolates containing the C29197T mutation were from a cluster of related cases. 2021 Microbiology spectrum Discussion SARS_CoV_2 C29197T 48 55 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. Interestingly, analysis of SNPs in the E gene found the C26340T mutation to be the most frequent. 2021 Microbiology spectrum Discussion SARS_CoV_2 C26340T 56 63 E 39 40 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. It is important to note that in two of the samples containing the C29200T mutation, with two of the lowest E gene CT values, the N gene was detected with very high CT values, >40. 2021 Microbiology spectrum Discussion SARS_CoV_2 C29200T 66 73 E;N 107;129 108;130 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. It was hypothesized that the C29200T mutation in these strains would also negatively affect the Xpert detection of the N gene target. 2021 Microbiology spectrum Discussion SARS_CoV_2 C29200T 29 36 N 119 120 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. The C29197T and C29200T mutations, located within the CDC probe sequence, are likely responsible for the failed detection of the N gene target in the Xpert assay and have the potential to negatively impact detection in other assays which also use this probe sequence. 2021 Microbiology spectrum Discussion SARS_CoV_2 C29197T;C29200T 4;16 11;23 N 129 130 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. The C29197T mutation accounts for approximately 0.01% of all sequences uploaded to the GISAID EpiCoV database as of June 2021. 2021 Microbiology spectrum Discussion SARS_CoV_2 C29197T 4 11 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. The C29200T mutation is widespread, accounting for more than 0.2% of all sequences uploaded to the GISAID EpiCoV database as of September 2020. 2021 Microbiology spectrum Discussion SARS_CoV_2 C29200T 4 11 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. The N gene target sequence was further aligned with all SARS-CoV-2 sequences in the PathWest database, and an additional eight sequences were found to contain a C to T mutation at position 29200, within the CDC probe binding region. 2021 Microbiology spectrum Discussion SARS_CoV_2 C29200T 161 194 N 4 5 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. This can account for the spontaneous appearance of SNPs, and it is therefore not surprising that the C29197T and C29200T mutations are widespread in the GISAID EpiCoV database, occurring in different lineages and in separate transmission chains. 2021 Microbiology spectrum Discussion SARS_CoV_2 C29197T;C29200T 101;113 108;120 34787486 Single-Point Mutations in the N Gene of SARS-CoV-2 Adversely Impact Detection by a Commercial Dual Target Diagnostic Assay. This is indicative of poor amplification or probe efficiency for these two samples, likely a result of the C29200T mutation. 2021 Microbiology spectrum Discussion SARS_CoV_2 C29200T 107 114 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. For example, the lambda (C.37) variant with a unique L452Q substitution has been put into the list of VOIs by WHO in June 2021 and is predominantly circulating in South America. 2021 Microbiology spectrum Discussion SARS_CoV_2 L452Q 53 58 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. However, the L452Q substitution is almost exclusive to the lambda (C.37) variant. 2021 Microbiology spectrum Discussion SARS_CoV_2 L452Q 13 18 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. In addition, L452R mutation in spike protein has already been reported in other variants, including delta (B.1.617.2), epsilon (B.1.429), and kappa (B.1.617.1) variants. 2021 Microbiology spectrum Discussion SARS_CoV_2 L452R 13 18 S 31 36 34787487 CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern. In our study, we developed a CRISPR-Cas12a-based genotyping assay and have approved its feasibility to detect single nucleotide mutations and to distinguish variants of SARS-CoV-2 based on the combination of a series of crRNAs that are specific for the most important and signature mutations, including K417N, L452R/Q, T478K, E484K/Q, and N501Y within the spike protein of SARS-CoV-2. 2021 Microbiology spectrum Discussion SARS_CoV_2 E484K;E484Q;K417N;L452Q;L452R;N501Y;T478K 326;326;303;310;310;339;319 333;333;308;317;317;344;324 S 356 361 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. For example, D614G and P681H are located in the same PCR amplification fragment. 2021 Microbiology spectrum Discussion SARS_CoV_2 D614G;P681H 13;23 18;28 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. In this study, we developed a mPCR-MS minisequencing method that can simultaneously detect 9 mutation types in 7 mutated sites in the RBD of spike proteins HV69-70del (Alpha), N501Y (Alpha, Beta, and Gamma), K417N (Beta), P681H (Alpha), D614G (Alpha, Beta, Gamma, Epsilon, Iota, and Delta), E484K (Beta and Gamma), L452R (Delta and Epsilon), P681R (Delta), and E484Q (B.1.617.1 and B1.617.3) to identify SARS-CoV-2 and its mutated variants. 2021 Microbiology spectrum Discussion SARS_CoV_2 D614G;E484K;E484Q;K417N;L452R;N501Y;P681H;P681R 237;291;361;208;315;176;222;342 242;296;366;213;320;181;227;347 S;RBD 141;134 146;137 34787499 A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology. The detection limit of D614G is 400 copies after MPE extension, while that of P681H/R is only 1,560 copies, indicating that the probe extension efficiency of P681H/R is much lower than that of D614G, which is closely related to the base sequence near the detection site of P681H/R. 2021 Microbiology spectrum Discussion SARS_CoV_2 D614G;D614G;P681H;P681H;P681H;P681R;P681R;P681R 23;193;273;78;158;78;158;273 28;198;280;85;165;85;165;280 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. A genomic surveillance study carried out in the United Kingdom identified the S:E661D mutation in viral genomes; however, they were at an extremely low frequency, because 6 genomes out of 142,859 were identified. 2021 Virology journal Discussion SARS_CoV_2 E661D 80 85 S 78 79 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. A neutralizing antibody activity study using convalescent serum from patients or serum from vaccinated individuals showed a 3-sixfold reduction against the B.1.429 variant, and furthermore, the neutralizing activity of mAbs targeting NTD was completely blocked due to the combined mutations S:S13I and S:W152C in that domain. 2021 Virology journal Discussion SARS_CoV_2 S13I;W152C 293;304 297;309 S;S 291;302 292;303 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. Additional information from the GISAID (GISAID:2021-06-01) showed that the S:W152C mutation emerged 41,272 times (2.38% of all samples with spike sequences) in 39 countries. 2021 Virology journal Discussion SARS_CoV_2 W152C 77 82 S;S 140;75 145;76 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. Although the results show an increase in infectivity close to 20-fold for the D614G/L452R protein, the increase in infectivity for D614G/W152C was fourfold when compared to the S protein containing only the D614G mutation. 2021 Virology journal Discussion SARS_CoV_2 D614G;D614G;D614G;L452R;W152C 78;131;207;84;137 83;136;212;89;142 S 177 178 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. Among the main mutations common between the two groups, we highlight those that occur in the S protein: S:E484K, S:N501Y and S:D614G. 2021 Virology journal Discussion SARS_CoV_2 D614G;E484K;N501Y 127;106;115 132;111;120 S;S;S;S 93;104;113;125 94;105;114;126 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. Analysis of this group of genomes, classified as belonging to the Gamma variant, revealed the presence of an additional mutation in the S protein (S:E661D). 2021 Virology journal Discussion SARS_CoV_2 E661D 149 154 S;S 136;147 137;148 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. Conversely, the phylogenetic analysis revealed clusterization of the Gamma genomes harboring S:E661D mutation as a function of the state from which the samples were collected, indicating that this mutation had not occurred randomly, but this mutation happened systematically in some geographical regions. 2021 Virology journal Discussion SARS_CoV_2 E661D 95 100 S 93 94 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. Despite the amino acid change, the E661D mutation maintained the acidic character of the motif, suggesting that this feature may be important for the function of the protein. 2021 Virology journal Discussion SARS_CoV_2 E661D 35 40 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. For example, the D614G substitution enhanced viral stability and infectivity, and the E484 mutation in the receptor-binding domain (RBD) conferred a partial resistance of SARS-CoV-2 to neutralizing antibodies. 2021 Virology journal Discussion SARS_CoV_2 D614G 17 22 RBD 132 135 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. However, unlike the N.10 variant originally described (N.10-MA), the N.10-PR variant has the S:W152C mutation in addition to the other mutations previously described. 2021 Virology journal Discussion SARS_CoV_2 W152C 95 100 S 93 94 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. However, we also identified some unique substitutions, which were not yet described, for the Gamma variant and Gamma-like-II lineage, and these substitutions in cluded ORF1a:P1213 L and ORF1b:K23240N, which appeared in 45% of the genomes (Additional file 7: Table S2). 2021 Virology journal Discussion SARS_CoV_2 K23240N;P1213L 192;174 199;181 ORF1a 168 173 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. In addition, there are currently 11 Gamma sublines that are accumulating new mutations near the furin cleavage site, among them the E661D described in this work. 2021 Virology journal Discussion SARS_CoV_2 E661D 132 137 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. In comparison, the second state with the highest frequency of the S:E661D mutation was Minas Gerais, with 2.94%. 2021 Virology journal Discussion SARS_CoV_2 E661D 68 73 S 66 67 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. In our study, the E661D mutation appeared at a much higher frequency and occurred in the Gamma variant, which already has a high number of mutations. 2021 Virology journal Discussion SARS_CoV_2 E661D 18 23 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. Notably, the S:E661D mutation was not detected throughout the state of Parana but was observed specifically in northern Parana, as well as in the capital Curitiba, which accounted for nearly 25% of the Gamma variant genomes. 2021 Virology journal Discussion SARS_CoV_2 E661D 15 20 S 13 14 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. On the other hand, they present some unique substitutions: ORF1ab:C8905T, C16954T and A20931G; NSP4:D2980H, intergenic region E/M A26492T and N:P383L. 2021 Virology journal Discussion SARS_CoV_2 A20931G;A26492T;C16954T;C8905T;D2980H;P383L 86;130;74;66;100;144 93;137;81;72;106;149 ORF1ab;Nsp4;N 59;95;142 65;99;143 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. The analysis of the mutations in the first 11 Gamma-like-II genomes from Parana identified 3 of the 4 unique substitutions of the Gamma-like-II lineage (C8905T, C16954T, A26492T) in addition to the N:P383L and ORF1a:D2980H mutations. 2021 Virology journal Discussion SARS_CoV_2 A26492T;C16954T;C8905T;D2980H;P383L 170;161;153;216;200 177;168;159;222;205 ORF1a;N 210;198 215;199 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. The concern with this N.10-PR variant is the emergence of the S:W152C mutation, and several studies have already showed its relevance to the biology of SARS-CoV-2 due to its S protein that has already accumulated important mutations such as S:V445A, S:E484k and S:D614G. 2021 Virology journal Discussion SARS_CoV_2 D614G;V445A;W152C 264;243;64 269;248;69 S;S;S;S;S 62;174;241;250;262 63;175;242;251;263 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. The Gamma-like-II lineage presents 15 of the 22 mutations of the Gamma variant, including the three main mutations in the RBD domain of the S protein: K417T, E484K and N501Y. 2021 Virology journal Discussion SARS_CoV_2 E484K;K417T;N501Y 158;151;168 163;156;173 RBD;S 122;140 125;141 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. The importance of the S:W152C mutation is the fact that the NTD is a target for neutralizing antibodies. 2021 Virology journal Discussion SARS_CoV_2 W152C 24 29 S 22 23 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. The infective capacities of mutations occurring in the B.1.429 variant were investigated using pseudoviruses carrying the D614G mutation together with the L452R or W152C mutations infected in 293 T cells expressing the ACE2 receptor as well as the cofactor TMPRSS2. 2021 Virology journal Discussion SARS_CoV_2 D614G;L452R;W152C 122;155;164 127;160;169 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. The other mutations identified in the B.1.429 variant, with the exception of S:D614G, do not match the N.10-PR variant. 2021 Virology journal Discussion SARS_CoV_2 D614G 79 84 S 77 78 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. The S:W152C mutation was initially described in the VOI B.1.429 (CAL.20C), which was identified in the state of California, United States (Additional file 6: Table S1). 2021 Virology journal Discussion SARS_CoV_2 W152C 6 11 S 4 5 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. The VOI B.1.429, which also has a very important S:L452R mutation, was identified in California, and to date, there are no reports that it has arrived in Brazil. 2021 Virology journal Discussion SARS_CoV_2 L452R 51 56 S 49 50 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. These results suggest that the N.10-PR S:W152C mutation occurred independently in this variant and has no relation with the VOI B.1.429. 2021 Virology journal Discussion SARS_CoV_2 W152C 41 46 S 39 40 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. This hypothesis also justifies the absence of other mutations in the S protein, such as S:T20N, in the Gamma-like-II lineage. 2021 Virology journal Discussion SARS_CoV_2 T20N 90 94 S;S 69;88 70;89 34789293 Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak. We verified the existence of 46 Brazilian Gamma variant genomes with the S:E661D mutation, 20 of which were identified in April 2021. 2021 Virology journal Discussion SARS_CoV_2 E661D 75 80 S 73 74 34790342 On the association between SARS-COV-2 variants and COVID-19 mortality during the second wave of the pandemic in Europe. The proportion of 20A (mutation S:D614G) variant, firstly observed in Europe during the 1st wave of the pandemic (February 2020), was found to be negatively associated with the deaths peak height considering the pre-peak phase of the second wave. 2021 Journal of market access & health policy Discussion SARS_CoV_2 D614G 34 39 S 32 33 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Besides the three DARPin domains binding to three unique epitopes of the spike ectodomain of SARS-CoV-2, that all carry Asp17Leu in their N-Caps, ensovibep is in addition composed of two anti-HSA DARPins for serum half-life extension. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 120 128 S;N 73;138 78;139 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. However, even the investigated DARPin domains aVEGF and aHER2 that possess framework mutations, which are key for their low picomolar binding affinities, still profit from the Asp17Leu mutation. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 176 184 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Importantly, the MD simulations show that Leu at position 17 faces inward and that the Asp17Leu mutation improves the Coulombic and the van-der-Waals interactions by about 3 kcal/mol and 2 kcal/mol, respectively. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 87 95 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Importantly, the observed stability improvement of about 8 C to 16 C (depending on the actual context) that was caused by the N-Cap Asp17Leu mutation proved to be generically applicable to various sequence backgrounds. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 134 142 N 128 129 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Importantly, the Tm value of an N1C variant comprising the N02 N-Cap (instead of N01) was also increased by about 9 C when introducing the Asp17Leu mutation. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 140 148 N 63 64 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Incorporation of the Asp17Leu mutation into existing DARPin binders could increase their thermostability without significantly impacting their target-binding properties. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 21 29 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Interestingly, ensovibep contains the Asp17Leu mutation described herein in three of its five DARPin domains. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 38 46 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Position 17 is located outside of these known paratope regions, and our MD based structural analyses indicate that the overall alteration of the domain structure through the Asp17Leu mutation is marginal. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 174 182 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Quantitative dimension and additive nature of the Asp17Leu improvement. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 50 58 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Second, the Asp17Leu mutation was also beneficial in the context of the improved mut5 C-Cap. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 12 20 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Similarly, the stability improvement of the novel N-Cap mutation Asp17Leu is additive to the stability gain obtained through the known N-Cap mutation Met24Leu (WO'655). 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L;M24L 65;150 73;158 N;N 50;135 51;136 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. The Asp17Leu N-Cap mutation is universally applicable to DARPins. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 4 12 N 13 14 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. The high thermostability (Tm) of 90 C and absence of any tendency for aggregation (up to 85 C) reported for ensovibep may thus be partly explained by the presence of the Asp17Leu mutation. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 172 180 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. The improved N02 N-Cap of WO'655 comprises a Met24Leu mutation when compared with N01 (Table 2), thereby improving the thermostability of DARPin domains. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 M24L 45 53 N 17 18 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Third, Asp17Leu gave a constant improvement when transferred to three different DARPin binders directed against HER2, VEGF, or HSA, indicating that the observed profound improvement is independent of the randomized positions forming the DARPin paratope. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 7 15 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. This general transferability of the Asp17Leu mutation may be because of the fact that all DARPin domains are based on a quasi-identical framework embedding the randomized positions. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 36 44 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. This not only gives clinical validation to the Asp17Leu mutation, but also underscores the importance and reach of the findings outlined here. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 47 55 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Thus, our discovered Asp17Leu improvement adds substantially to other capping repeat improvements described previously. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 21 29 34793836 Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Thus, we do not expect that the N-Cap Asp17Leu change has a significant impact on the target binding of corresponding DARPin domains. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 D17L 38 46 N 32 33 34794434 SARS-CoV-2 exposure in Malawian blood donors: an analysis of seroprevalence and variant dynamics between January 2020 and July 2021. In agreement, our neutralisation data showed that a higher proportion of sera collected from the second wave (February 2021) had neutralising activity against the beta variant than sera from the first wave (June to October 2020), indicating antibody responses driven by infection with the beta variant rather than the original variant (D614G WT). 2021 BMC medicine Discussion SARS_CoV_2 D614G 336 341 34794434 SARS-CoV-2 exposure in Malawian blood donors: an analysis of seroprevalence and variant dynamics between January 2020 and July 2021. It is also noteworthy that 19% of the second wave sera that were positive for antibodies to the SARS-CoV-2 RBD showed no neutralisation against the beta variant or D614G WT, highlighting a disconnect between qualitative antibody detection and functional activity. 2021 BMC medicine Discussion SARS_CoV_2 D614G 164 169 RBD 107 110 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. A worldwide increase in frequency of E484K mutation in the sequences was observed during the second year of pandemic, where reinfection cases were expected to be more common. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 37 42 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Another amino acid position, 417, missing in this fragment, is also important to differentiate Gamma, Beta, Alpha with E484K, and Mu variants. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 119 124 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Approximately one half of the B.1.526 carry the E484K mutation. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 48 53 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Contrary to our expectations, documented cases of reinfection worldwide were not associated with the presence of E484K mutations, even during the period of March-May 2021, when the frequency of this mutation increased significantly. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 113 118 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. However, as in Brazil, the presence of E484K mutation in the suspected reinfection cases may be only the reflection of the high frequency of circulation of Gamma VOC in the country, although, in one case, the infecting virus was not the Gamma VOC and carried the E484K mutation associated with another lineage. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K;E484K 39;263 44;268 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. However, E484K mutation is very frequent in Brazilian sequences, either in the Gamma VOC or in the P.2 or B.1.1.33 lineages. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 9 14 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. However, the smaller fragment used in this study is still useful for us, for an even more rapid detection (in one day) of the most frequent variants circulating in Venezuela, by restriction enzyme analysis to detect E484K and L452R mutations. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K;L452R 216;226 221;231 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. However, this lineage, with or without the E484K mutation, was not more associated with cases of reinfection, when compared to other lineages. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 43 48 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. In our study, from 6 cases of suspected reinfection, all the isolates from the last infection carry the mutation E484K, either belonging to the Gamma VOC or associated with another lineage. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 113 118 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Indeed, these mutations, particularly, E484K one, have emerged in many other lineages, as previously reported. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 39 44 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Specifically, the E484K mutation is associated with antibody evasion in Beta and gamma VOCs, but also in some other lineages. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 18 23 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. The only exception is Brazil, where some reinfection cases were associated with the presence of E484K mutation. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 96 101 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. The presence of any of these mutations does not necessarily mean that a VOC is circulating in a specific country, nor that this isolate will gain the phenotypic advantages provided by these mutations in VOCs, as the increased transmissibility observed for the VOCs due to the N501Y. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 N501Y 276 281 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Three sequences carrying the mutation E484K but not classified as Gamma VOC, belonged to three different lineages: B.1, B.1.111 and B.1.526. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 38 43 34800714 Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela. Thus, the presence of E484K mutation in reinfection cases may be only the reflection of the high frequency of circulation of this mutation in the country. 2021 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 22 27 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. D614G has also been observed to co-occur with Nsp12: P323L, the most common mutation observed in Nsp12. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 P323L;D614G 53;0 58;5 Nsp12;Nsp12 46;97 51;102 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. Several variants observed in the N-terminal domain and the signal peptide (L18F, Y144del, and D253G) have also been shown to decrease the effectiveness of antibodies. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D253G;Y144del;L18F 94;81;75 99;88;79 N 33 34 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The lack of nucleotide information also limits the ability of alignment programs to distinguish between two possible deletions in regions where two or more identical amino acids are adjacent to one another; this causes the spike variant Y144del to be identified as Y145del in some sequences of our analysis. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 Y144del;Y145del 237;265 244;272 S 223 228 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The Nsp7 mutation L71F has been linked to higher mortality rates in several studies, though these studies have yet to enter peer review. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 L71F 18 22 Nsp7 4 8 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The RBD variant N439K, which has been shown to result in antibody evasion, is becoming more common over time. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 N439K 16 21 RBD 4 7 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The spike protein mutation V1176F results in increased stability of the spike protein and has also been associated with higher mortality rates. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 V1176F 27 33 S;S 4;72 9;77 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The study validated previous findings of the predominance of spike: D614G and Nsp12: P323L in the population while uncovering recent increases in the prevalence of new mutations in Nsp12 and the spike protein. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;P323L 68;85 73;90 S;S;Nsp12;Nsp12 61;195;78;181 66;200;83;186 34801754 Longitudinal analysis of SARS-CoV-2 spike and RNA-dependent RNA polymerase protein sequences reveals the emergence and geographic distribution of diverse mutations. The very high prevalence of the D614G mutant in the sequences sampled reflects studies documenting increased viral counts in-vitro as well as higher viral loads in infected individuals. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 32 37 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. In another study, a total of 20 mus MD simulation trajectory of both wild type and D614G mutant provided mechanistic details of the increased occupancy of open state in G614 form. 2021 Current research in structural biology Discussion SARS_CoV_2 D614G 83 88 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Interestingly, prevalent amino acid substitutions such as A222V, Y453F have also been linked with structural perturbations or ACE2 binding. 2021 Current research in structural biology Discussion SARS_CoV_2 A222V;Y453F 58;65 63;70 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Our simulations of the D614G spike variant bound to ACE2 further elaborates on dynamical features with increased compactness in the NTD-RBD region. 2021 Current research in structural biology Discussion SARS_CoV_2 D614G 23 28 S;RBD 29;136 34;139 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. studied the effect of five prevalent RBD mutations (K417N, K417T, N501Y, E484K, and S477N) on RBD-ACE2 interaction and suggested that the N501Y, E484K, and S477N mutations showed increased affinity towards ACE2 binding as compared to the wild type which might enhance transmission. 2021 Current research in structural biology Discussion SARS_CoV_2 E484K;E484K;K417T;N501Y;N501Y;S477N;S477N;K417N 73;145;59;66;138;84;156;52 78;150;64;71;143;89;161;57 RBD;RBD 37;94 40;97 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. The D614G spike has revealed varied interactions within protomer that induce conformational changes within the S1 subunit. 2021 Current research in structural biology Discussion SARS_CoV_2 D614G 4 9 S 10 15 34806033 A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. Utilising a different approach of normal mode analysis, Teruel et al., calculated transition probabilities between the open and closed states, and proposed an increase in open state occupancy for more infectious D614G mutant and a similar effect was proposed on glycine residues (404, 416, 504, and 252) as well as residues K417, D467, and critical N501Y mutation site. 2021 Current research in structural biology Discussion SARS_CoV_2 D614G;N501Y 212;349 217;354 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. Along with the previously found GGG > AAC mutation, our mutational type analysis identify some another multi-nucleotide mutations CC > TT, TG > CA, and AT > TA which are in the top 20 mutational type and should be monitored for the future as the GGG > AAC (R203K and G204R) reported to be associated with the insertion of a lysine in SR domain of N protein which might affect the phosphorylation. 2021 Informatics in medicine unlocked Discussion SARS_CoV_2 G204R;R203K 267;257 272;262 N 347 348 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. Besides D416G, F106F, P314L, and 5' UTR:C241T, our large scale analysis also identify C22227T;L93L (membrane protein), G29645T;A222V (spike protein), G21255C;A199A (NSP16), C28932T;V30L (ORF10), and T445C;A220V (nucleocapsid protein) mutations which are in top 10 mutations found in our investigation and should get importance in evaluating their role in the efficiency of SARS-CoV-2 transmission. 2021 Informatics in medicine unlocked Discussion SARS_CoV_2 C22227T;C28932T;D416G;F106F;G21255C;G29645T;P314L;T445C;C241T;A199A;A220V;A222V;L93L;V30L 86;173;8;15;150;119;22;199;40;158;205;127;94;181 93;180;13;20;157;126;27;204;45;163;210;132;98;185 N;Membrane;5'UTR;S 212;100;33;134 224;108;39;139 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. D1118H, (S194L, and R262H), (M809L, P314L, A8D, and S220G), (A890D, G1433C, and T1456I), R233C, F263S, L111K, (A54T, and A74V), L183A, A316T, V212F, and (L46C, V48G, Q57H, W131R, G172V, Q185H, and Y206S) missense mutations were found to largely decrease the structural stability of the spike, nucleocapsid, RNA-dependent RNA polymerase, NSP3, NSP6, NSP15, NSP4, NSP8, NSP16, NSP13, NSP5, and ORF3a proteins, respectively and suggests that these missense mutations might decrease the infectivity of the virus. 2021 Informatics in medicine unlocked Discussion SARS_CoV_2 A316T;A74V;A8D;F263S;G1433C;G172V;L111K;L183A;P314L;Q185H;Q57H;R233C;R262H;S220G;T1456I;V212F;V48G;W131R;Y206S;A54T;A890D;L46C;M809L;S194L;D1118H 135;121;43;96;68;179;103;128;36;186;166;89;20;52;80;142;160;172;197;111;61;154;29;9;0 140;125;46;101;74;184;108;133;41;191;170;94;25;57;86;147;164;177;202;115;66;158;34;14;6 RdRp;N;S;ORF3a;Nsp13;Nsp3;Nsp4;Nsp8;Nsp5;Nsp6 307;293;286;392;375;337;356;362;382;343 335;305;291;397;380;341;360;366;386;347 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. F106F mutation is found as predominantly occurring silent mutation in NSP3, suggesting a possible role in mRNA processing which might alter the nature of the viral protein. 2021 Informatics in medicine unlocked Discussion SARS_CoV_2 F106F 0 5 Nsp3 70 74 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. In our large scale study, previously reported D614G, and P314L missense mutations are also identified as the most prevalent mutation in the viral genome. 2021 Informatics in medicine unlocked Discussion SARS_CoV_2 D614G;P314L 46;57 51;62 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. Moreover, the 5' UTR:C241T mutation might be associated with the transcription and replication rates of SARS-CoV-2 as it is found to occur most prominently. 2021 Informatics in medicine unlocked Discussion SARS_CoV_2 C241T 21 26 5'UTR 14 20 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. On the contrary, D3L, L5F, and S97I missense mutations were found to largely increase the structural stability of the nucleocapsid, ORF7a, and ORF8 proteins, respectively and suggests that these mutations might increase the viral infectivity. 2021 Informatics in medicine unlocked Discussion SARS_CoV_2 D3L;L5F;S97I 17;22;31 20;25;35 N;ORF7a;ORF8 118;132;143 130;137;147 34812411 Genome-wide identification and prediction of SARS-CoV-2 mutations show an abundance of variants: Integrated study of bioinformatics and deep neural learning. The P314L mutation in RdRp is associated with the D614G mutation and may favor the SARS-CoV-2 by enhancing its transmission ability. 2021 Informatics in medicine unlocked Discussion SARS_CoV_2 D614G;P314L 50;4 55;9 RdRP 22 26 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. However, the infectivity of the T323I mutant was more sensitive to freeze-thawing than that of viruses pseudotyped with the wild-type S glycoprotein. 2022 Journal of virology Discussion SARS_CoV_2 T323I 32 37 S 134 148 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. However, we noted that the infectivity of the C15F mutant virus was compromised after freeze-thawing more than that of the wild-type virus. 2022 Journal of virology Discussion SARS_CoV_2 C15F 46 50 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. Of note, some of the expressed S glycoproteins formed a disulfide bond between Cys 131 and Cys 136 and therefore lacked two of the canonical disulfide bonds (Cys 15-Cys 136 and Cys 131-Cys 166) in the N-terminal domain. 2022 Journal of virology Discussion SARS_CoV_2 C131C;C15C 177;158 188;168 S;N 31;201 46;202 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. On the other hand, even though the S1170F change altered posttranslational modification of the S2 glycoprotein, this mutant exhibited wild-type levels of infectivity and resistance to freeze-thawing. 2022 Journal of virology Discussion SARS_CoV_2 S1170F 35 41 34817202 Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein. We note that these phenotypes were revealed by changing Asn 234 to an alanine residue, completely removing the potential N-linked glycosylation site. 2022 Journal of virology Discussion SARS_CoV_2 N234A 56 77 N 121 122 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Among them, immune escape from mAbs 9G11 and AM180 by Lambda was caused by both L452Q and F490S mutations, with immune escape for F490S being stronger than for L452Q. 2022 Emerging microbes & infections Discussion SARS_CoV_2 F490S;F490S;L452Q;L452Q 90;130;80;160 95;135;85;165 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Furthermore, escape from mAbs X593 and AbG3 by the Lambda variant was caused by both L452Q and F490S mutations. 2022 Emerging microbes & infections Discussion SARS_CoV_2 F490S;L452Q 95;85 100;90 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Furthermore, our findings showed no significant difference in the infection of ACE2 overexpressing cells by Lambda compared with the D614G variant. 2022 Emerging microbes & infections Discussion SARS_CoV_2 D614G 133 138 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. In addition, escape from mAb R126 was caused by both L452Q and F490S mutations, with L452Q exerting a greater effect than F490S. 2022 Emerging microbes & infections Discussion SARS_CoV_2 F490S;F490S;L452Q;L452Q 63;122;53;85 68;127;58;90 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. In addition, our previous studies revealed that escape of the L452R and E484 K mutants from mAbs frequently occurred in conjunction. 2022 Emerging microbes & infections Discussion SARS_CoV_2 E484K;L452R 72;62 78;67 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. In addition, we found a 1.6-fold decrease in the infectivity of G75 V in Vero cells. 2022 Emerging microbes & infections Discussion SARS_CoV_2 G75V 64 69 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. In other words, Lambda's change in infectivity was much less pronounced than that of D614G, which was about 10 times higher than the initial epidemic virus. 2022 Emerging microbes & infections Discussion SARS_CoV_2 D614G 85 90 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. In the present study, we found that the escape of L452Q and F490S mutants from mAbs also appeared concomitantly. 2022 Emerging microbes & infections Discussion SARS_CoV_2 F490S;L452Q 60;50 65;55 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Meanwhile, the infectivity of T859N was decreased 1.3-fold, 1.7-fold, 1.5-fold, and 1.8-fold in Vero, 293T-hACE2, 293T-hACE2-TMPRSS2, and 293T-hACE2-CatL cells, respectively, which is consistent with a previous report. 2022 Emerging microbes & infections Discussion SARS_CoV_2 T859N 30 35 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Our previous study found that the L452R and F490L mutations can cause escape from mAb X593, consistent with the results of the L452Q and F490S mutations in the present study. 2022 Emerging microbes & infections Discussion SARS_CoV_2 F490L;F490S;L452Q;L452R 44;137;127;34 49;142;132;39 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Our previous study showed that both F490 and L452 are located at the binding site of mAb 9G11 to the RBD, and experimentally verified that F490L and L452R mutations can cause escape from mAb 9G11, which is consistent with the results presented here. 2022 Emerging microbes & infections Discussion SARS_CoV_2 F490L;L452R 139;149 144;154 RBD 101 104 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Previous studies showed that L452R increases viral infectivity and fusion, while also promoting viral replication. 2022 Emerging microbes & infections Discussion SARS_CoV_2 L452R 29 34 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Simultaneously, L452R can escape cellular immunity, while neutralizing protection against L452R by mAbs, convalescent sera, and vaccine-induced immune sera is significantly reduced. 2022 Emerging microbes & infections Discussion SARS_CoV_2 L452R;L452R 16;90 21;95 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Taken together, our results suggest that the L452R and L452Q mutations, and the F490S and F490L mutations, have the same effect on immune escape from mAbs. 2022 Emerging microbes & infections Discussion SARS_CoV_2 F490L;F490S;L452Q;L452R 90;80;55;45 95;85;60;50 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. There is only one published study on convalescent sera, which found a 3.3-fold decrease in neutralizing titres against the Lambda variant, a 4.4-fold decrease against L452Q, and a 2.5-fold decrease against F490S. 2022 Emerging microbes & infections Discussion SARS_CoV_2 F490S;L452Q 206;167 211;172 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. Therefore, we hypothesize that the Lambda variant containing the L452Q mutation is highly variable in both infectivity and antigenicity, warranting close monitoring and attention. 2022 Emerging microbes & infections Discussion SARS_CoV_2 L452Q 65 70 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. When the L452Q and F490S mutations occurred, the hydrophobic interface responsible for binding on RBD was broken, resulting in the escape of the Lambda variant from binding to mAb X593 (Figure 3C). 2022 Emerging microbes & infections Discussion SARS_CoV_2 F490S;L452Q 19;9 24;14 RBD 98 101 34818119 Reduced sensitivity of the SARS-CoV-2 Lambda variant to monoclonal antibodies and neutralizing antibodies induced by infection and vaccination. When the mutation of L452Q with F490S occurs, it breaks the original hydrophobic interface. 2022 Emerging microbes & infections Discussion SARS_CoV_2 F490S;L452Q 32;21 37;26 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. At sufficiently high antibody titres, the N439K and N501Y variants' potential evasion advantage might of less immunological importance. 2021 eLife Discussion SARS_CoV_2 N439K;N501Y 42;52 47;57 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Conversely, hyperimmune sera and high-affinity mAbs from mice that received several immunizations with recombinant wt spike or RBD did not show this significant neutralization difference, indicating that a fully established vaccine response will overcome the evasion potential of the N501Y. 2021 eLife Discussion SARS_CoV_2 N501Y 284 289 S;RBD 118;127 123;130 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Even though they numerically deviate from our findings, they conceptually observe increased affinity of the N501Y variant. 2021 eLife Discussion SARS_CoV_2 N501Y 108 113 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. In this study, we present comprehensive biophysical data showing that the single N501Y residue change in the RBD region results in an eightfold increase in the affinity to human ACE-2. 2021 eLife Discussion SARS_CoV_2 N501Y 81 86 RBD 109 112 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Interestingly, one study proposes that the N501Y variant might pose challenges for the MHC class II presentation and the CD4+ T-cell response. 2021 eLife Discussion SARS_CoV_2 N501Y 43 48 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Moreover, our data show a minor but significant immune evasion effect of the N501Y substitution. 2021 eLife Discussion SARS_CoV_2 N501Y 77 82 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. One of these RBD residue changes is N501Y, which has appeared by convergent evolution in three of the so-called VOC: B.1.351 (beta), P.1 (gamma), and the B.1.1.7 (alpha) variant, but interestingly not in the rapidly spreading B.1.617.2 (delta) variant, where other mutations appear to be of importance. 2021 eLife Discussion SARS_CoV_2 N501Y 36 41 RBD 13 16 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. The relative neutralization evasion level from these experiments was WT RBD < N439K < N501Y. 2021 eLife Discussion SARS_CoV_2 N439K;N501Y 78;86 83;91 RBD 72 75 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. Two recent studies, one yet-to-be peer reviewed, have focused on the biophysics of the N501Y variant, reporting affinities ranging from 0.5 nM to undefined sub pM. 2021 eLife Discussion SARS_CoV_2 N501Y 87 92 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. We also did this for the prevalent RBD mutation N439K and we found a twofold affinity increase to ACE-2 and a partial evasion of antibody-mediated neutralization, lending support to a recently published paper. 2021 eLife Discussion SARS_CoV_2 N439K 48 53 RBD 35 38 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. When we did BLI measurements of the 1:1 interaction of N501Y RBD on ACE-2 immobilized sensors, we found a remarkable eightfold affinity increase of the variant (2.2 nM) compared to wt Wuhan RBD (17 nM). 2021 eLife Discussion SARS_CoV_2 N501Y 55 60 RBD;RBD 61;190 64;193 34821555 The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice. When we tested the antibody-mediated inhibition of the wt, N439K, and N501Y RBD interaction with human ACE-2, we found a minor, but significant reduction of the neutralization potency of convalescent sera (n = 140) compatible with the data observed by. 2021 eLife Discussion SARS_CoV_2 N439K;N501Y 59;70 64;75 RBD 76 79 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Although the S protein and N protein, both structural proteins, are located in different parts of a virion, there are many similarities between D614G and R203K/G204R related to the consequences of the virus properties. 2021 Cell host & microbe Discussion SARS_CoV_2 D614G;R203K;G204R 144;154;160 149;159;165 N;S 27;13 28;14 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. In our previous work, we observed the rapid spread of R203K/G204R mutation in the initial four months after the onset of the SARS-CoV-2 pandemic and predicted that these mutations may benefit virus replication based on statistics. 2021 Cell host & microbe Discussion SARS_CoV_2 R203K;G204R 54;60 59;65 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. In summary, we identified the adaptation of the N protein mutations R203K/G204R through thorough in silico evolutionary analyses. 2021 Cell host & microbe Discussion SARS_CoV_2 R203K;G204R 68;74 73;79 N 48 49 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. In this study, we have performed comprehensive statistical analyses of R203K/G204R and confirmed the adaptiveness of the mutations. 2021 Cell host & microbe Discussion SARS_CoV_2 R203K;G204R 71;77 76;82 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Like D614G, R203K/G204R is associated with predominance (Figure 3) and is shared by the rapidly increasing lineages B.1.1.7 and P.1. 2021 Cell host & microbe Discussion SARS_CoV_2 D614G;R203K;G204R 5;12;18 10;17;23 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Other high-infectivity-related mutations, such as D614G and N510Y, also show associations with increases in fitness and disease severity. 2021 Cell host & microbe Discussion SARS_CoV_2 D614G;N510Y 50;60 55;65 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. R203K/G204R increase the sensitivity of virus to neutralizing antibodies, which may be complemented by immune resistance mutations such as N501Y and E484K. 2021 Cell host & microbe Discussion SARS_CoV_2 E484K;N501Y;G204R;R203K 149;139;6;0 154;144;11;5 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. R203K/G204R variants also show increased infectivity and fitness and an association with the severity of disease. 2021 Cell host & microbe Discussion SARS_CoV_2 G204R;R203K 6;0 11;5 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Selection signature for R203K/G204R did not perform consistently across the whole period of the pandemic like D614G. 2021 Cell host & microbe Discussion SARS_CoV_2 D614G;R203K;G204R 110;24;30 115;29;35 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. The G203K/G204R mutant may increase the assembly efficiency of RNP and further increase the assembly efficiency of the virus particle, thus increasing the quality of the virus particle (PFU) instead of the quantity (genomic RNA level) of the virus particle (Figure 5). 2021 Cell host & microbe Discussion SARS_CoV_2 G203K;G204R 4;10 9;15 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. The increases in the infectivity and virulence of R203K/G204R variants could contribute to the increased transmission and mortality of B.1.1.7 and the increased severity of disease associated with P.1. 2021 Cell host & microbe Discussion SARS_CoV_2 R203K;G204R 50;56 55;61 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. The recently evolved Indian lineages B.1.617.1 (Kappa), B.1.617.2 (Delta), and AY.1 (Delta-plus) also carry a point mutation at 28,881, which is a novel N mutation, R203M, instead of R203K/G204R (Table S3A). 2021 Cell host & microbe Discussion SARS_CoV_2 R203K;R203M;G204R 183;165;189 188;170;194 N 153 154 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Using the authentic virus, we proved that R203K/G204R increase viral replication, which enhances the infectivity, fitness, and virulence of SARS-CoV-2. 2021 Cell host & microbe Discussion SARS_CoV_2 R203K;G204R 42;48 47;53 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. We found that the increase in infectivity was due to the promotion of virus replication efficiency, which may have been caused by the change in the local charge of the N protein resulting from the R203K/G204R mutations. 2021 Cell host & microbe Discussion SARS_CoV_2 R203K;G204R 197;203 202;208 N 168 169 34822776 Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. We have performed analyses and experiments on R203K/G204R mutant virus. 2021 Cell host & microbe Discussion SARS_CoV_2 R203K;G204R 46;52 51;57 34822912 Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR. Furthermore, it would also help to monitor mutations of concern such as the E484 K that could arise in the delta variant itself. 2022 Journal of virological methods Discussion SARS_CoV_2 E484K 76 82 34822912 Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR. However, in situations where there is a dominant variant with L452R or N501Y, confirmed by whole genomic sequencing, this would be an easy to use, low-cost assay to rapidly identify the prevalence of VOCs such as delta. 2022 Journal of virological methods Discussion SARS_CoV_2 L452R;N501Y 62;71 67;76 34822912 Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR. However, the SNPs resulting in L452R and K417 mutations is not unique to delta alone and is detected in several variants of interest such as Kappa (B.1.617.1), Epsilon (B.1.427/9) and C.36. 2022 Journal of virological methods Discussion SARS_CoV_2 L452R 31 36 34822912 Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR. In fact, we have recently detected the E484 K mutation in the delta variant itself and the use of this multi-plex RT-q PCR would help us to further monitor the spread of this variants, in a larger sample cohort. 2022 Journal of virological methods Discussion SARS_CoV_2 E484K 39 45 34822912 Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR. In this study, we identified the delta variant in all districts of Sri Lanka, based on the presence of the L425R in the virus. 2022 Journal of virological methods Discussion SARS_CoV_2 L425R 107 112 34822912 Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR. Therefore, this multiplex real-time PCR approach would not be useful to identify emergence of new SARS-CoV-2 variants or to differentiate between the variants which have L425R, N501Y or E484 K, which again is seen in different SARS-CoV-2 variants. 2022 Journal of virological methods Discussion SARS_CoV_2 E484K;L425R;N501Y 186;170;177 192;175;182 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Although the P681R mutant is highly fusogenic, the virus containing the P681R mutation did not necessarily show stronger growth than the parental virus in in vitro cell cultures. 2022 Nature Discussion SARS_CoV_2 P681R;P681R 13;72 18;77 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. An assumption from our observations is that the higher viral fusogenicity driven by the P681R mutation may be associated with the increased transmissibility of the B.1.617.2/Delta variant observed in humans. 2022 Nature Discussion SARS_CoV_2 P681R 88 93 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Consistently, we showed that both the B.1.617.2/Delta variant and the P681R mutant exhibited higher fusogenicity in vitro and enhanced pathogenicity in vivo. 2022 Nature Discussion SARS_CoV_2 P681R 70 75 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. However, the P681R mutation is not specific for the B.1.617.2/Delta variant, and the sublineages related to the B.1.617.2/Delta variant, such as the B.1.617.1 and B.1.617.3 variants, that contain this mutation have not successfully spread in the human population. 2022 Nature Discussion SARS_CoV_2 P681R 13 18 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. However, transmission experiments using the B.1.617.2/Delta variant or P681R-bearing virus in animal models were not performed in this study, and it remains unaddressed why the B.1.617.2/Delta variant has become more predominant than the other VOCs. 2022 Nature Discussion SARS_CoV_2 P681R 71 76 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Importantly, although FCS-deleted SARS-CoV-2 is less pathogenic compared with its parental virus, we revealed that the B.1.617.2/Delta variant and the P681R-harbouring virus exhibit higher pathogenicity. 2022 Nature Discussion SARS_CoV_2 P681R 151 156 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Our data suggest that the greater COVID-19 severity and unusual symptoms caused by the B.1.617.2/Delta variant are due in part to the higher fusogenicity caused by the P681R mutation. 2022 Nature Discussion SARS_CoV_2 P681R 168 173 COVID-19 34 42 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. These findings suggest that enhanced viral fusogenicity, which is triggered by the P681R mutation, is closely associated with viral pathogenicity. 2022 Nature Discussion SARS_CoV_2 P681R 83 88 34823256 Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. We revealed the association of the P681R mutation with these virological features. 2022 Nature Discussion SARS_CoV_2 P681R 35 40 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. A recent study proposed that residue 501 plays a key role in the ability of RaTG13 S to use human ACE2 for viral entry but the reported enhancing effect of changes at position 501 was weaker than that observed for the T403R change analyzed in the present study. 2021 Nature communications Discussion SARS_CoV_2 T403R 218 223 S 83 84 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. However, the previous finding that numerous residues in the SARS-CoV-2 S RBD are involved in the interaction with the human ACE2 orthologue explains why the R403T substitution only moderately reduced SARS-CoV-2 infection. 2021 Nature communications Discussion SARS_CoV_2 R403T 157 162 RBD;S 73;71 76;72 COVID-19 200 220 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. It came as surprise, however, that overexpression of TMPRSS2 only enhanced VSVpp infection mediated by the SARS-CoV-2 but not by the RaTG13 T403R S protein. 2021 Nature communications Discussion SARS_CoV_2 T403R 140 145 S 146 147 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. More importantly, the reverse T403R substitution generally strongly enhanced RaTG13 S-mediated VSVpp infection without affecting protein expression levels. 2021 Nature communications Discussion SARS_CoV_2 T403R 30 35 S 84 85 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Mutation of E37 in ACE2 reduced the levels of WT CoV-2 S-mediated infection to those obtained for the R403T CoV-2 S. 2021 Nature communications Discussion SARS_CoV_2 R403T 102 107 S;S 55;114 56;115 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Mutation of E37A not only abolished the enhancing effect of the T403R change on RaTG13 S-mediated VSVpp infection but also reduced infection mediated by the SARS-CoV-2 S. 2021 Nature communications Discussion SARS_CoV_2 E37A;T403R 12;64 16;69 S;S 87;168 88;169 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Our results demonstrate that a single amino acid change of T403R allows the S protein of RaTG13, one of the closest known bat relatives of SARS-CoV-2, to utilize human ACE2 for viral entry. 2021 Nature communications Discussion SARS_CoV_2 T403R 59 64 S 76 77 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Similar effects were observed for RaTG13 S T403R but not on the WT RaTG13 S suggesting that interaction with ACE2 has a major impact on proteolytic processing. 2021 Nature communications Discussion SARS_CoV_2 T403R 43 48 S;S 41;74 42;75 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. Some individuals show rare polymorphisms of E37K (frequency: 3.27e-5; gnomAD, https://gnomad.broadinstitute.org) in ACE2 which was reported to impair S binding, similar to the E37A mutant analyzed in the present study. 2021 Nature communications Discussion SARS_CoV_2 E37A;E37K 176;44 180;48 S 150 151 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. The strong enhancing effect of the T403R change on RaTG13 S function came as a surprise since five of six different residues proposed to be critical for SARS-CoV-2 S RBD interaction with human ACE2 are not conserved in RaTG13 S. 2021 Nature communications Discussion SARS_CoV_2 T403R 35 40 RBD;S;S;S 166;58;164;226 169;59;165;227 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. This suggests that the interaction between R403 in the S protein and E37 in the ACE2 receptor is relevant for full infectiousness of SARS-CoV-2, although reduced expression levels and incorporation of the R403T mutant CoV-2 S may also contribute. 2021 Nature communications Discussion SARS_CoV_2 R403T 205 210 S;S 55;224 56;225 34824253 Spike residue 403 affects binding of coronavirus spikes to human ACE2. We show that the effect of T403R on RaTG13 S is due to an increased ability to interact with E37 on human ACE2, allowing more efficient receptor binding. 2021 Nature communications Discussion SARS_CoV_2 T403R 27 32 S 43 44 34828410 Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India. Among the non-spike proteins, the kappa variant harbors the R203M mutation at the edge of the Serine/Arginine (SR) rich domain of N protein and shares sequence variations in this mutational hotspot with the alpha (R203M) and beta (T205I) variants. 2021 Genes Discussion SARS_CoV_2 R203M;R203M;T205I 60;214;231 65;219;236 S;N 14;130 19;131 34828410 Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India. By virtue of sharing three critical mutations in the spike protein with the delta variant (L452R, E484Q and P681R), the kappa variant can be considered to be the "bridging variant" that acted as the forerunner of the highly transmissible delta variant that was responsible for the enormity of the second wave in India. 2021 Genes Discussion SARS_CoV_2 E484Q;P681R;L452R 98;108;91 103;113;96 S 53 58 34828410 Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India. Furthermore, L452R mutation is reported to reduce neutralization activity of RBD-specific monoclonal antibodies by 2-3.5 fold. 2021 Genes Discussion SARS_CoV_2 L452R 13 18 RBD 77 80 34828410 Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India. Furthermore, while retaining all the key mutations contained in the kappa variant, the spike protein of the delta variant contains only one additional mutation in the RBD domain (T478K). 2021 Genes Discussion SARS_CoV_2 T478K 179 184 S;RBD 87;167 92;170 34828410 Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India. Likewise, mutation in position 681 is shared with alpha (B.1.1.7) VOC (P681H). 2021 Genes Discussion SARS_CoV_2 P681H 71 76 34828410 Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India. Of the 14 non-synonymous mutations observed across the genome of all the strains belonging to the kappa variant, five are found in the spike protein (E484Q, L452R, P681R, D614G, Q1071H) and among them the first two lie in the receptor binding domain (RBD) and the third one is adjacent to the furin cleavage site (Figure 7). 2021 Genes Discussion SARS_CoV_2 D614G;L452R;P681R;Q1071H;E484Q 171;157;164;178;150 176;162;169;184;155 RBD;S;RBD 226;135;251 249;140;254 34828410 Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India. Several recent structural studies revealed that the variants with L452R and E484Q mutations in the RBD region divulge low binding energy and achieve enhanced stability of interaction with ACE2 receptor compared to the wild type Wuhan strain. 2021 Genes Discussion SARS_CoV_2 E484Q;L452R 76;66 81;71 RBD 99 102 34828410 Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India. Similarly, L452R mutation is reported in epsilon (B.1.427 and B.1.429), which is a variant of concern reported from California. 2021 Genes Discussion SARS_CoV_2 L452R 11 16 34828410 Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India. While the other variants harbor E484K as the substitution, E484Q is observed in the kappa variant and the E484K mutation is associated with reduced susceptibility to the monoclonal antibody bamlanivimab and the combination of bamlanivimab and etesevimab. 2021 Genes Discussion SARS_CoV_2 E484K;E484K;E484Q 32;106;59 37;111;64 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. As the delta variant is currently the dominant strain globally, an Ag-RDT to detect infections with N501Y meta-signature variants will be a powerful tool for disease monitoring and control. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 N501Y 100 105 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. CB6 neutralization is unaffected by the N501Y RBD mutation, consistent with the relative unimportance of this residue to CB6 binding. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 N501Y 40 45 RBD 46 49 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. Detection of the N501Y spike mutation with the 2E8 mAb is an efficient way distinguish delta from variants with the N501Y meta-signature, such as beta, gamma, mu, C.1.2, and novel N501Y-containing variants yet to emerge. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 N501Y;N501Y;N501Y 17;116;180 22;121;185 S 23 28 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. Mutagenesis and modeling experiments suggest that the N501Y mutation will support the evolution of SARS-CoV-2 variants with increased infectivity and resistance to vaccines and therapeutics. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 N501Y 54 59 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. The 2E8 binding site overlaps the CB6 site, yet its binding is not affected by changes at K417, and CB6 binding is largely insensitive to the N501Y change. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 N501Y 142 147 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. The N501Y mutation does not dramatically alter the overall RBD structure. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 N501Y 4 9 RBD 59 62 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. The N501Y mutation has originated independently within multiple viral lineages and is positively selected because it increases infectivity through enhanced ACE2 binding. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 N501Y 4 9 34829439 A Strategy to Detect Emerging Non-Delta SARS-CoV-2 Variants with a Monoclonal Antibody Specific for the N501 Spike Residue. This is attributable to the K417N mutation, which alone reduces affinity 21.9-fold compared to a 13.8-fold reduction from the K417T change. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 K417N;K417T 28;126 33;131 34829998 SARS-CoV-2 Variants, RBD Mutations, Binding Affinity, and Antibody Escape. However, the change from Leucine (L) to arginine (R) at the amino-acid position 452 due to the mutation L452R introduces two hydrogen bond (i.e., the ADD) interactions between E35 and R452 (see Figure 2d,e). 2021 International journal of molecular sciences Discussion SARS_CoV_2 L452R 104 109 34829998 SARS-CoV-2 Variants, RBD Mutations, Binding Affinity, and Antibody Escape. The mutation L452R thus increases the binding affinity between the RBD and the ACE2. 2021 International journal of molecular sciences Discussion SARS_CoV_2 L452R 13 18 RBD 67 70 34833135 Emerging Mutations Potentially Related to SARS-CoV-2 Immune Escape: The Case of a Long-Term Patient. However, previous studies have shown that both S:E484K and deletion in positions S:144 and S:145 have arisen independently multiple times with possible links to long-term infections. 2021 Life (Basel, Switzerland) Discussion SARS_CoV_2 E484K 49 54 S;S;S 47;81;91 48;82;92 34833135 Emerging Mutations Potentially Related to SARS-CoV-2 Immune Escape: The Case of a Long-Term Patient. However, the surveyed SARS-CoV-2 genome, namely B.1.177.51:TS, also harbored three mutations in the S-protein which are not related to lineage B.1.177.51, namely S:V143D, S:del144/145, and S:E484K. 2021 Life (Basel, Switzerland) Discussion SARS_CoV_2 E484K;V143D 191;164 196;169 S;S;S;S 100;162;171;189 101;163;172;190 34833135 Emerging Mutations Potentially Related to SARS-CoV-2 Immune Escape: The Case of a Long-Term Patient. In previous studies, convalescent sera were shown to have a neutralizing efficiency against SARS-CoV-2 strains harboring the S:N501Y and S:E484K mutations, S:69/70 deletion VUI lineage B.1.617 mutations, although a slightly lower response was seen against VUI B.1.617 and S:E484K. 2021 Life (Basel, Switzerland) Discussion SARS_CoV_2 E484K;E484K;N501Y 139;274;127 144;279;132 S;S;S;S 125;137;156;272 126;138;157;273 34833135 Emerging Mutations Potentially Related to SARS-CoV-2 Immune Escape: The Case of a Long-Term Patient. S:E484K has been shown to confer an increased potential to escape the host immune response. 2021 Life (Basel, Switzerland) Discussion SARS_CoV_2 E484K 2 7 S 0 1 34833135 Emerging Mutations Potentially Related to SARS-CoV-2 Immune Escape: The Case of a Long-Term Patient. S:V143D is a rare mutation (<0.5% of genomes in GISAID) and in B.1.177.51:TS occurs as a consequence of the deletion of the six nucleotides leading to del144/145. 2021 Life (Basel, Switzerland) Discussion SARS_CoV_2 V143D 2 7 S 0 1 34833135 Emerging Mutations Potentially Related to SARS-CoV-2 Immune Escape: The Case of a Long-Term Patient. The variation in neutralizing efficiency between convalescent plasma and vaccinated individuals sera was also investigated: both neutralized a S:N501Y mutant strain, while the B.1.351 variant escaped convalescent and vaccine-induced sera. 2021 Life (Basel, Switzerland) Discussion SARS_CoV_2 N501Y 145 150 S 143 144 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. Curcumin inhibited SARS-CoV-2 D614G strain by pre-infection treatment of Vero E6 cells. 2021 Molecules (Basel, Switzerland) Discussion SARS_CoV_2 D614G 30 35 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. In this context, curcumin inhibited the Delta variant up to 99.9%, exhibiting higher selectivity than the obtained for D614G strain, through pre-post infection and co-treatment strategies. 2021 Molecules (Basel, Switzerland) Discussion SARS_CoV_2 D614G 119 124 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. Similar to these reports, our findings indicated that curcumin inhibits SARS-CoV-2 D614G strain which contains the most widespread amino acid change (D614G in the spike protein) carried by more than 99% of the prevalent variants since the beginning of 2020. 2021 Molecules (Basel, Switzerland) Discussion SARS_CoV_2 D614G;D614G 83;150 88;155 S 163 168 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. Taking into account that curcumin exhibited inhibition against D614G strain, through different treatment strategies, this compound was evaluated against infection by the Delta variant which contains mutations in the spike protein (L452R, T478K, P681R, and D614G) associated with an increase in viral infectivity, transmissibility and pathogenicity in individuals infected with SARS-CoV-2 and a decrease in antibody-mediated neutralization. 2021 Molecules (Basel, Switzerland) Discussion SARS_CoV_2 D614G;D614G;P681R;T478K;L452R 63;256;245;238;231 68;261;250;243;236 S 216 221 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. The post-infection treatment results indicates that curcumin can effectively inhibit SARS-CoV-2 D614G strain up to 87%, affecting the post-entry steps of the viral replicative cycle. 2021 Molecules (Basel, Switzerland) Discussion SARS_CoV_2 D614G 96 101 34833991 Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms. This effect could be related to our results obtained by co-treatment which suggest a possible virucidal activity of curcumin against SARS-CoV-2 D614G strain. 2021 Molecules (Basel, Switzerland) Discussion SARS_CoV_2 D614G 144 149 34834983 High Individual Heterogeneity of Neutralizing Activities against the Original Strain and Nine Different Variants of SARS-CoV-2. Due to its key spike protein mutations (L452R and T478K), the Delta variant may induce an immune evasion, similar to the B.1.351.2, P.1, and R.1 variants. 2021 Viruses Discussion SARS_CoV_2 T478K;L452R 50;40 55;45 S 15 20 34834983 High Individual Heterogeneity of Neutralizing Activities against the Original Strain and Nine Different Variants of SARS-CoV-2. This can be seen for the Gamma and Marseille-484K.V1/R.1 variants harbouring the same spike key mutation (E484K), as they show a similar but potential immune escape (with low nAb recognition). 2021 Viruses Discussion SARS_CoV_2 E484K 106 111 S 86 91 34834987 The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City. A study of in silico molecular dynamics on the spike has shown that the distribution of charges in S:T478K is most drastically affected at the site of substitution and its immediate vicinity on the surface of the folded protein. 2021 Viruses Discussion SARS_CoV_2 T478K 101 106 S;S 47;99 52;100 34834987 The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City. Accordingly, the Delta variant (B.1.617.2) carries the S:T478K substitution. 2021 Viruses Discussion SARS_CoV_2 T478K 57 62 S 55 56 34834987 The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City. An in vitro assay with SARS-CoV-2 S:P681H using fluorogenic peptides mimicking the S1/S2 sequence reported an increase in spike cleavage by furin-like proteases but this does not significantly impact viral entry or membrane fusion. 2021 Viruses Discussion SARS_CoV_2 P681H 36 41 Membrane;S;S 215;122;34 223;127;35 34834987 The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City. B.1.1.519 has three substitutions in spike: T478K, P681H, and T732A. 2021 Viruses Discussion SARS_CoV_2 P681H;T478K;T732A 51;44;62 56;49;67 S 37 42 34834987 The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City. Importantly, they also inferred that the Pro323Leu mutation occurred on an Asp614Gly background. 2021 Viruses Discussion SARS_CoV_2 D614G;P323L 75;41 84;50 34834987 The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City. The Alpha (B.1.1.7) and Gamma (P.1) variants (recognized by the WHO as VOCs) carry S:P681H. 2021 Viruses Discussion SARS_CoV_2 P681H 85 90 S 83 84 34834987 The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City. The S:P681H substitution could also be involved in the increased transmissibility of B.1.1.519 in Mexico City. 2021 Viruses Discussion SARS_CoV_2 P681H 6 11 S 4 5 34834987 The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City. The S:P681H substitution is located immediately adjacent to amino acids 682-685, which correspond to a furin cleavage site at the S1/S2 binding site, where the more basic the string of amino acids is, the more effectively furin recognizes and cuts it, also this amino acid sequence serves as a cleavage site for the cellular host serine protease TMPRSS2, it plays an important role in promoting cell fusion, spread and pathogenesis in the infected host. 2021 Viruses Discussion SARS_CoV_2 P681H 6 11 S 4 5 34834987 The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City. The S:T478K substitution is structurally localized in the region of interaction with the human ACE2 receptor. 2021 Viruses Discussion SARS_CoV_2 T478K 6 11 S 4 5 34834987 The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City. They identified that the Pro323Leu mutation in the RNA-dependent RNA polymerase led to the rapid spread of the virus, rather than the previously reported Asp614Gly mutation in the spike glycoprotein. 2021 Viruses Discussion SARS_CoV_2 D614G;P323L 154;25 163;34 RdRp;S 51;180 79;198 34834987 The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City. This substitution could impact B.1.1.519 transmissibility and may help to explain why B.1.1.519 had a transmission advantage over other variants without S:T478K in Mexico City. 2021 Viruses Discussion SARS_CoV_2 T478K 155 160 S 153 154 34835101 Impact of the Double Mutants on Spike Protein of SARS-CoV-2 B.1.617 Lineage on the Human ACE2 Receptor Binding: A Structural Insight. The dual mutations (L452R + E484Q and L452R + T478K) harbored by the novel variants (kappa and delta) were found to be responsible for the higher virulence. 2021 Viruses Discussion SARS_CoV_2 E484Q;L452R;T478K;L452R 28;38;46;20 33;43;51;25 34840498 Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021. An antibody escape is considered as another mutation mechanism like the upcoming form of D614G which can be accelerated by an antigenic drift. 2021 Bulletin of the National Research Centre Discussion SARS_CoV_2 D614G 89 94 34840498 Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021. Based on these recent studies, the virus virulence and the increase of viral loads in COVID-19 patients characterize the occurrence of D614G mutation (Korber et al.; Zhang et al.), while, based on the current available information, the infectivity as well as the receptor binding, fusion activation, or ADE enhancement can be influenced by D614G mutation in several ways (Ulrich et al.; Wang and Zand.; Nidom et al.). 2021 Bulletin of the National Research Centre Discussion SARS_CoV_2 D614G;D614G 135;340 140;345 COVID-19 86 94 34840498 Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021. Besides, recent publications show that one of the most notable amino acid mutations is D614G (Korber et al.; Nidom et al.). 2021 Bulletin of the National Research Centre Discussion SARS_CoV_2 D614G 87 92 34840498 Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021. D614G mutation has been previously speculated in raising an open configuration of S protein that is more advantageous to ACE2 association (Zhang et al.). 2021 Bulletin of the National Research Centre Discussion SARS_CoV_2 D614G 0 5 S 82 83 34840498 Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021. If the sensitivity of neutralizing antibody can be affected by D614G mutation in SARS-CoV-2 or vice versa, then the ADE activity also can be monitored in the SARS-CoV study; thus, D614G can be considered as an intermediate antibody escape which puts people to be more vulnerable for second infections (Cloutier et al.; Zhang et al.; Nidom et al.). 2021 Bulletin of the National Research Centre Discussion SARS_CoV_2 D614G;D614G 63;180 68;185 34840498 Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021. on D614G mutation which discovered that S1 residue 614 is in a close proximity to S2 domain. 2021 Bulletin of the National Research Centre Discussion SARS_CoV_2 D614G 3 8 34840498 Phylogenetic and full-length genome mutation analysis of SARS-CoV-2 in Indonesia prior to COVID-19 vaccination program in 2021. Therefore, SARS-CoV-2 S protein D614G mutation is highly believed in promoting the virion spike density and infectivity and it is also highly speculated that this mutation might be influence further mutations. 2021 Bulletin of the National Research Centre Discussion SARS_CoV_2 D614G 32 37 S;S 90;22 95;23 34841034 Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2. The D614G is present in data referred to humans, for both SARS-CoV-2 and SARS-CoV. 2021 One health (Amsterdam, Netherlands) Discussion SARS_CoV_2 D614G 4 9 34841034 Codon usage, phylogeny and binding energy estimation predict the evolution of SARS-CoV-2. This confirms D614G as a good marker to track viral evolution. 2021 One health (Amsterdam, Netherlands) Discussion SARS_CoV_2 D614G 14 19 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. A missense mutation at 1163 A > T (I120F) causing an isoleucine to phenylalanine shift in the NSP2 was found to be unique in Bangladeshi isolates and persisted at an elevated level (~78.80%). 2021 Current research in microbial sciences Discussion SARS_CoV_2 A1163T;I120F 23;35 33;40 Nsp2 94 98 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. A specific reason to be held accountable behind the unexpectedly high frequency of 1163 A > T mutation of NSP2 is yet to be found. 2021 Current research in microbial sciences Discussion SARS_CoV_2 A1163T 83 93 Nsp2 106 110 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. B.1.1.8, B.1.1.25, B.1.1.70, B.1.1.80, B.1.1.306 and B.1.1.316 lineages were found predominant in our analysis, all carrying D614G, RG203KR, Q675H mutations. 2021 Current research in microbial sciences Discussion SARS_CoV_2 D614G;Q675H 125;141 130;146 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Considering the relation of NSP2 function against low fatality rate in Bangladesh, we predicted that a frequently occurring mutation (1163A > T) in NSP2 protein can be a strong evidence to figure out the reason of low mortality rate in this country. 2021 Current research in microbial sciences Discussion SARS_CoV_2 A1163T 134 143 Nsp2;Nsp2 28;148 32;152 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. In this study the prevalent and important co-mutations (241C > T, 3037C > T, 14408C > T, 23403A > G) which were identified mostly prevailed in the South Asian SARS-CoV-2 isolates and aligned with those identified in the European countries. 2021 Current research in microbial sciences Discussion SARS_CoV_2 C14408T;A23403G;C3037T;C241T 77;89;66;56 87;99;75;64 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. In this study, we found that the 1163 A > T (I120F) mutation was increasing the NSP2 protein stability, confirmed by analyzing deformation energy, atomic fluctuation, difference of Gibbs free energy and vibrational entropy. 2021 Current research in microbial sciences Discussion SARS_CoV_2 A1163T;I120F 33;45 43;50 Nsp2 80 84 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. One investigation has demonstrated that the D614G mutation in the Spike protein is associated with high fatality rates. 2021 Current research in microbial sciences Discussion SARS_CoV_2 D614G 44 49 S 66 71 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Presence of D614G mutation in the first sequenced sample from Bangladesh indicates the presence of this mutation since the inception of COVID-19 infection and transmission in Bangladesh and explains the reason for the dominance of G-clade mutation in Bangladesh. 2021 Current research in microbial sciences Discussion SARS_CoV_2 D614G 12 17 COVID-19 136 144 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. The combination of Spike D614G and Nucleocapsid RG203KR mutations is currently the most eminent in SARS-CoV-2 positive population. 2021 Current research in microbial sciences Discussion SARS_CoV_2 D614G 25 30 N;S 35;19 47;24 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Therefore, a link between high frequency of 1163 A > T (I120F) mutation in NSP2 protein and low mortality rate against the infection rate in Bangladesh can be hypothesized. 2021 Current research in microbial sciences Discussion SARS_CoV_2 A1163T;I120F 44;56 54;61 Nsp2 75 79 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. This finding contradicts with the results of a study conducted in the United States of America, that found the 27964C > T-(S24L) mutation to be more prevalent in females than in males. 2021 Current research in microbial sciences Discussion SARS_CoV_2 C27964T;S24L 111;123 121;127 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Though the G-clade (D614G) mutations originated from China on 24 January 2020, in the next 30 days from the identification of this mutation the rapid transmission of this clade had occurred in the European countries. 2021 Current research in microbial sciences Discussion SARS_CoV_2 D614G 20 25 34841355 A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Unfortunately, information on NSP2 protein of SARS-CoV-2, especially the impact of 1163 A > T (I120F) mutation is very limited. 2021 Current research in microbial sciences Discussion SARS_CoV_2 A1163T;I120F 83;95 93;100 Nsp2 30 34 34842496 A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). Additionally to the key defining-mutations of B.1.5, B.1.1, B.1.177, and B.1.1.7-related viruses, other substitutions such as S943I associated with a reduced Spike stability, or A262S, also observed among mink-derived SARS-CoV-2 variants, have not caught special attention since they were not fixed in any predominant lineage. 2022 Emerging microbes & infections Discussion SARS_CoV_2 A262S;S943I 178;126 183;131 S 158 163 34842496 A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). Also, P681R is shared by other lineages, and it was firstly reported for lineage A.23.1. 2022 Emerging microbes & infections Discussion SARS_CoV_2 P681R 6 11 34842496 A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). Apart from the lineage-defining changes in variants Delta-like, additional substitutions were observed such as T95I, P251L in the N-terminal domain, Q613H and T719I during the following weeks (data not shown). 2022 Emerging microbes & infections Discussion SARS_CoV_2 P251L;Q613H;T719I;T95I 117;149;159;111 122;154;164;115 N 130 131 34842496 A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). Most circulating B-viruses were carrying the amino acid substitution D614G in the Spike, which appeared by the end of March 2020 and is present in most later circulating lineages belonging to GISAID's G clade. 2022 Emerging microbes & infections Discussion SARS_CoV_2 D614G 69 74 S 82 87 34842496 A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). Nonetheless, the prevalence of E484K mutation among other lineages also increased in many countries due to its benefits for SARS-CoV-2, not only for its major transmissibility, but also evading antibody neutralization from host immune response. 2022 Emerging microbes & infections Discussion SARS_CoV_2 E484K 31 36 34842496 A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). The fact that B.1.177 was defined by the acquisition of the A222V mutation in the Spike could also confer a significant advantage to the virus, favouring its rapid selection and dissemination. 2022 Emerging microbes & infections Discussion SARS_CoV_2 A222V 60 65 S 82 87 34842496 A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). The L452R mutation was previously observed in the United States due to the higher circulation of lineages B.1.427 and B.1.429 (variant Epsilon) and related to a partial immune evasion due to the disruption to the RBD binding together with T478K substitution. 2022 Emerging microbes & infections Discussion SARS_CoV_2 L452R;T478K 4;239 9;244 RBD 213 216 34842496 A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). The same activity is described for E484K substitution, shared by B.1.351 and P.1 lineages, and reported during the initial weeks of the third wave in our study, as in other European regions. 2022 Emerging microbes & infections Discussion SARS_CoV_2 E484K 35 40 34842496 A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). Therefore, one of the substitutions of interest and shared by the new variants is N501Y, located at the RBD of Spike, which increases ACE2 binding affinity, and improves the human-to-human transmission. 2022 Emerging microbes & infections Discussion SARS_CoV_2 N501Y 82 87 S;RBD 111;104 116;107 34842496 A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). This emergent variant is carrying mutations in the RBD (L452R and T478K) and in the polybasic region (P681R). 2022 Emerging microbes & infections Discussion SARS_CoV_2 T478K;L452R;P681R 66;56;102 71;61;107 RBD 51 54 34842496 A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). This major predominance of variants carrying this mutation was because D614G improves viral infectivity and viral transmission giving an advantage to virus by relaxing the trimeric Spike structure and facilitating the viral entry to the cell, as previously reported. 2022 Emerging microbes & infections Discussion SARS_CoV_2 D614G 71 76 S 181 186 34842604 Fc-Independent Protection from SARS-CoV-2 Infection by Recombinant Human Monoclonal Antibodies. Indeed, the addition of a third mutation, P329G (LALA-PG), was needed to completely abrogate the binding of antibodies to the FcgammaR. 2021 Antibodies (Basel, Switzerland) Discussion SARS_CoV_2 P329G 42 47 34842604 Fc-Independent Protection from SARS-CoV-2 Infection by Recombinant Human Monoclonal Antibodies. One commonly used set of mutations creating an Fc-null antibody is L234A/L235A (LALA mutations). 2021 Antibodies (Basel, Switzerland) Discussion SARS_CoV_2 L234A;L235A 67;73 72;78 34843105 SARS-CoV-2 Neutralization in Convalescent Plasma and Commercial Lots of Plasma-Derived Immunoglobulin. A further limitation is that the data presented here were generated using the D614G variant close to Wuhan wildtype strain, while the pandemic is currently driven by SARS-CoV-2 variants of concern and interest. 2022 BioDrugs Discussion SARS_CoV_2 D614G 78 83 34843105 SARS-CoV-2 Neutralization in Convalescent Plasma and Commercial Lots of Plasma-Derived Immunoglobulin. While final container neutralization potencies against SARS-CoV-2 (D614G) are strongly increasing, it is of interest how these could translate into anti-SARS-CoV-2 IgG steady-state trough levels in a patient, which is one possible, yet not validated, correlate of immune protection. 2022 BioDrugs Discussion SARS_CoV_2 D614G 67 72 34843105 SARS-CoV-2 Neutralization in Convalescent Plasma and Commercial Lots of Plasma-Derived Immunoglobulin. While neutralizing plasma antibody levels remain to be validated as a correlate of protection in clinical studies, here we reported a rapid increase of SARS-CoV-2 neutralization potency in Octapharma's IVIG/SCIG final containers by means of ELISA and microneutralization testing against SARS-CoV-2 WT (D614G). 2022 BioDrugs Discussion SARS_CoV_2 D614G 302 307 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. Also, a Y414A substitution was tolerated in MHV-A59, but in our study, Y414A prevented the recovery of infectious progeny for MHV strain JHM, which exhibits less robust RNA synthesis and overall replication than MHV-A59. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 Y414A;Y414A 8;71 13;76 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. Strikingly, for MERS-CoV, which does not tolerate ExoN inactivation, two of the N7-MTase mutations (G333A in motif III and H420A in motif VI) abolished detectable ExoN activity in vitro. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 H420A;G333A 123;100 128;105 Exon;Exon 50;163 54;167 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. The results obtained with mutations in motif III (the presumed SAM-binding motif DxGxPxG/A) were a striking example: The viral phenotype for the D-to-A mutant (D331A in SARS-CoV and MERS-CoV and D330A in MHV) ranged from nonviable for SARS-CoV, via severely crippled for MERS-CoV, to wild-type-like for MHV. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 D330A;D331A 195;160 200;165 34845015 Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication. This might explain a stronger (e.g., MERS-CoV mutant F422A) or less dramatic effect in the virus-infected cell compared to what is observed in enzymatic assays. 2021 Proc Natl Acad Sci U S A Discussion SARS_CoV_2 F422A 53 58 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. All of these mutations except V395I were identified at a high read depth by the protease library screen and show convergent strategies for RBD redesigns, even with distinct mutations. 2021 bioRxiv Discussion SARS_CoV_2 V395I 30 35 RBD 139 142 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. Finally, both isoleucine and phenylalanine are slightly preferred over our originally designed I513L mutation in RBD1. 2021 bioRxiv Discussion SARS_CoV_2 I513L 95 100 RBD 113 116 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. The four mutations encoded in the successful design RBD6 were I358F, Y365W, T430I, and I513L. 2021 bioRxiv Discussion SARS_CoV_2 I358F;I513L;T430I;Y365W 62;87;76;69 67;92;81;74 RBD 52 55 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. The mutation T430I removes a buried unsatisfied polar group. 2021 bioRxiv Discussion SARS_CoV_2 T430I 13 18 34845448 Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning. Their choice to more narrowly focus on linoleic acid binding pocket mutations led to the creation of top designs containing only mutation F392W and mutations Y365F, F392W, and V395I, with melting temperatures of 1.9-2.4 C and 3.8-5.3 C above wild type, respectively. 2021 bioRxiv Discussion SARS_CoV_2 F392W;F392W;V395I;Y365F 138;165;176;158 143;170;181;163 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. For example, the Q57H mutant was predicted to bind S protein, whereas the wildtype does not. 2021 bioRxiv Discussion SARS_CoV_2 Q57H 17 21 S 51 52 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. However, our data cannot rule out the possibility that the Q57H mutant may have other effects on viral pathogenesis. 2021 bioRxiv Discussion SARS_CoV_2 Q57H 59 63 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. If this is indeed the case, interruption of the ORF3a protein with the host restriction factor(s) by the DeltaG188 mutation could releases the ORF3a resulting enhanced triggering of host cellular stress and innate immune response leading to stronger cell death. 2021 bioRxiv Discussion SARS_CoV_2 DeltaG188 105 114 ORF3a;ORF3a 48;143 53;148 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. It would be of interest to test whether the Q57H mutant contributes to viral entry. 2021 bioRxiv Discussion SARS_CoV_2 Q57H 44 48 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. One possible explanation for the stronger effect of the DeltaG188 mutant comparted to wildtype is that the wildtype ORF3a effect might be restricted by a host restriction cellular protein(s) through direct protein-protein interaction as shown in other viral infection. 2021 bioRxiv Discussion SARS_CoV_2 DeltaG188 56 65 ORF3a 116 121 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. Our data show that the Q57H mutant activities are comparable to the wildtype ORF3a regarding the induction of cellular oxidative stress, innate immune responses, and apoptosis and necrosis. 2021 bioRxiv Discussion SARS_CoV_2 Q57H 23 27 ORF3a 77 82 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. The DeltaG188 mutant may interrupt the structure of the two antiparallel beta4 and beta5 sheets at the C-terminal end or the inner cavity where it affects ion channel activity or interaction of ORF3a with host cellular proteins. 2021 bioRxiv Discussion SARS_CoV_2 DeltaG188 4 13 ORF3a 194 199 34845452 Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets. The Q57H mutation recently was found in the emerging Beta variant, and the Q57H variant was suspected of contributing to a surge of SARS-CoV-2 infection in Hong Kong. 2021 bioRxiv Discussion SARS_CoV_2 Q57H;Q57H 4;75 8;79 COVID-19 132 152 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. Apart from the abnormal spindle morphology after the N501Y treatment, the present study also found a significant increase of spindle length and plate width after 24 h N501Y treatment in the morphologically normal oocytes. 2021 Reproductive sciences (Thousand Oaks, Calif.) Discussion SARS_CoV_2 N501Y;N501Y 53;167 58;172 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. Collectively, we have demonstrated the adverse effect of SARS-CoV-2 N501Y spike protein on mouse oocytes. 2021 Reproductive sciences (Thousand Oaks, Calif.) Discussion SARS_CoV_2 N501Y 68 73 S 74 79 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. In addition to the N501Y mutant, the effect of highly transmissible variants such as the b.1.617 variant (also named as delta variant) and delta plus variant (AY.1 or B.1.617.2.1) on oogenesis or oocyte maturation warrants further investigations. 2021 Reproductive sciences (Thousand Oaks, Calif.) Discussion SARS_CoV_2 N501Y 19 24 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. Since the spindle assembly of oocyte is associated with embryo development, we postulate that the N501Y mutant may further affect the embryo development. 2021 Reproductive sciences (Thousand Oaks, Calif.) Discussion SARS_CoV_2 N501Y 98 103 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. Taken together, these results suggest that N501Y mutant spike protein was able to affect the oocyte spindle assembly in mouse oocytes. 2021 Reproductive sciences (Thousand Oaks, Calif.) Discussion SARS_CoV_2 N501Y 43 48 S 56 61 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. The present study has demonstrated the abnormal spindle assembly in mouse oocytes after treatment of N501Y mutant spike protein. 2021 Reproductive sciences (Thousand Oaks, Calif.) Discussion SARS_CoV_2 N501Y 101 106 S 114 119 34845669 The N501Y Mutation of SARS-CoV-2 Spike Protein Impairs Spindle Assembly in Mouse Oocytes. Unexpectedly, the N501Y mutant spike protein did not alter the nuclear maturation and mitochondrial distribution during oocyte maturation. 2021 Reproductive sciences (Thousand Oaks, Calif.) Discussion SARS_CoV_2 N501Y 18 23 S 31 36 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. A case exemplifying a similar scenario in which physically close mutations contribute towards an analogous structural solution is provided by the spike protein mutation Q613H. 2021 Microbial genomics Discussion SARS_CoV_2 Q613H 169 174 S 146 151 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. A hypothesis - yet to be tested - is that mutations P323L-D614G reinforce the asymptomatic phenotype, at least in a Mexican genetic background. 2021 Microbial genomics Discussion SARS_CoV_2 P323L;D614G 52;58 57;63 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Additionally, the N:S194L mutation also occurs at a very high frequency (89.9%, N=1270) in lineage B.1.1.289 , isolated in Denmark and shown to co-infect humans and minks. 2021 Microbial genomics Discussion SARS_CoV_2 S194L 20 25 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Also, as far as we are aware, the association of P323L to severity disease has been only tested in symptomatic patients so ours is the first observation of P323L being associated with an asymptomatic phenotype. 2021 Microbial genomics Discussion SARS_CoV_2 P323L;P323L 49;156 54;161 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. In the meantime, the San Luis Potosi E484K-containing variants are different from the closely related and previously reported P.1, P.2 and, recently, P.3 sequences. 2021 Microbial genomics Discussion SARS_CoV_2 E484K 37 42 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. In this case, mutation Q613H defining the emerging lineage A.23.1, from Uganda, may have taken the role of the mutation D614G in B lineages during evolution of A lineages. 2021 Microbial genomics Discussion SARS_CoV_2 D614G;Q613H 120;23 125;28 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Interestingly, S477 has been identified as the most flexible amino acid within the RBM and with the largest number of mutations, which might be stabilized by mutation T478K. 2021 Microbial genomics Discussion SARS_CoV_2 T478K 167 172 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Interestingly, variants of lineage B.1.36.# with mutation N:S194L have been associated with higher mortality in Gujarat, India. 2021 Microbial genomics Discussion SARS_CoV_2 S194L 60 65 N 58 59 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. It is tempting to speculate that these sequences could be related to the origin of the E484K-containing variant B.1.243.1 detected in Arizona, a southern state in the USA that borders the Mexican northern states of Sonora and Chihuahua. 2021 Microbial genomics Discussion SARS_CoV_2 E484K 87 92 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Like variant 20A/478K.V1, the latter VOC includes the mutations T478K and P681H/R. 2021 Microbial genomics Discussion SARS_CoV_2 P681H;P681R;T478K 74;74;64 81;81;69 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Mutations T478K and S477N, involving changes from similar hydroxylated side-chains (T and S) into positively charged basic amino acids (K and N), may have analogous functional roles, reinforcing the ability of the virus to bind to the human ACE2 receptor. 2021 Microbial genomics Discussion SARS_CoV_2 S477N;T478K 20;10 25;15 S 90 91 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. On the one hand, although further data are needed to confirm the E484K-containing sequences detected in San Luis Potosi as VOI, which occurs within a clade dominated by the B.1.243 lineage, our results emphasize the potential of a combined targeted RT-qPCR screening and genome sequencing approach to anticipate epidemiological hotspots. 2021 Microbial genomics Discussion SARS_CoV_2 E484K 65 70 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. On the other hand, 20B/478K.V1, with mutations T478K, P681R/H and T732A in its spike protein, can undoubtedly be classified as a VOI, with the potential to become a VOC. 2021 Microbial genomics Discussion SARS_CoV_2 P681H;P681R;T478K;T732A 54;54;47;66 61;61;52;71 S 79 84 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Our finding of the mutation N:S194L contributes to an additional site for RT-qPCR screening of samples outside of the spike region. 2021 Microbial genomics Discussion SARS_CoV_2 S194L 30 35 S;N 118;28 123;29 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Our finding that symptomatic hosts are associated with a higher proportion of the N:S194L-derived allele relative to the Wuhan allele is particularly intriguing. 2021 Microbial genomics Discussion SARS_CoV_2 S194L 84 89 N 82 83 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. P323L affects the function of the RNA-dependent RNA polymerase, associated with an increase in mutation rate. 2021 Microbial genomics Discussion SARS_CoV_2 P323L 0 5 RdRp 34 62 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. The discrete association of both D614G and P323L to an asymptomatic phenotype could mean that those fixed mutations enhance transmissibility by bypassing an immune response. 2021 Microbial genomics Discussion SARS_CoV_2 D614G;P323L 33;43 38;48 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. The first one is in the flexible loop of the RBD, and includes S477N, T478K and E484K. 2021 Microbial genomics Discussion SARS_CoV_2 E484K;S477N;T478K 80;63;70 85;68;75 RBD 45 48 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. The mutation we identified, N:S194L, is within the central domain composed of intrinsically disordered regions (IDRs), which are conformationally flexible and promiscuous, and are increasingly recognized as important in increased viral transmission. 2021 Microbial genomics Discussion SARS_CoV_2 S194L 30 35 N 28 29 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. The other hotspot is within S1-S2 subdomains, and which includes the furin-like protease cleavage site, and contains D614G, P681H/R and T732A. 2021 Microbial genomics Discussion SARS_CoV_2 D614G;P681H;P681R;T732A 117;124;124;136 122;131;131;141 34846283 Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. These results are in line with data suggesting convergent evolution and global spread of the virus containing the E484K mutation during the pre-vaccination stage. 2021 Microbial genomics Discussion SARS_CoV_2 E484K 114 119 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. During the early pandemic stage, the first concern mutation in spike protein was D614G that appeared and is emerging as an increasingly common variant in the world. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 81 86 S 63 68 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Moreover, sub-haplotype 2C_3 contained three mutations on N protein (N D63G, N R203M, N D377Y). 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D377Y;D63G;R203M 88;71;79 93;75;84 N;N;N;N 58;69;77;86 59;70;78;87 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Notably, sub-haplotype 2C_3 also showed a novel mutation G671S in nsp12 (RNA-dependent RNA polymerase, RdRp) that was the target for the antiviral drug in treatment such as remdesivir in many countries. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 G671S 57 62 RdRp;Nsp12;RdRP 73;66;103 101;71;107 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Notably, sub-haplotypes 2A_3 and 2B_1 had the mutations at K417T, and E484K in the spike was a small proportion in the high partly vaccinated rate group in May 2021, which was found to decrease neutralization of human immune serum and cause severe disease even in patients that have been previously infected. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 E484K;K417T 70;59 75;64 S 83 88 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Of note, the dataset on May 2021, we found a haplotype 2B_5 contained three mutations in nsp3 (S126L, T350I, P822L), one mutation in nsp6 (L75F), one mutation in nsp13 (S259L), three mutations in spike protein (N439K, P681R, G1251V), and one mutation in N (T205I). 2022 Infection, genetics and evolution Discussion SARS_CoV_2 G1251V;P681R;P822L;T350I;L75F;N439K;S126L;S259L;T205I 225;218;109;102;139;211;95;169;257 231;223;114;107;143;216;100;174;262 S;Nsp13;Nsp3;Nsp6;N 196;162;89;133;254 201;167;93;137;255 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Our complete genome sequence dataset of SARS-CoV-2 variants in 2021, sub-haplotype 2A_1 variant had two deleted-amino acids (H69del, V143del) and six amino acid changes in spike protein (N501Y, A570D, P681H, T716I, S982A, D1118H), as demonstrated in many studies that the deleted at position 69-70, N501Y, P681H mutation had increased viral transmissibility. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 A570D;D1118H;N501Y;P681H;P681H;S982A;T716I;V143del;H69del;N501Y 194;222;299;201;306;215;208;133;125;187 199;228;304;206;311;220;213;140;131;192 S 172 177 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Sub-haplotype 2B_4 haplotype contained one mutation in nsp4 L89F, three other mutations in spike protein (L5F, T95I, D253G), one mutation in ORF3a (P42L), one mutation in ORF8 (T11I). 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D253G;L89F;T95I;L5F;P42L;T11I 117;60;111;106;148;177 122;64;115;109;152;181 S;ORF3a;Nsp4;ORF8 91;141;55;171 96;146;59;175 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. Sub-haplotype 2C_3 had three deleted-amino acids (EFR 156,157,158 deleted) six amino acid changes (T19R, L452R, T478K, D614G, P681R, D950N) in spike protein. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;D950N;L452R;P681R;T478K;T19R 119;133;105;126;112;99 124;138;110;131;117;103 S 143 148 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. The amino acid change P681R near the protease cleavage site might relate with the spike protein stability, and the mutations L452RT and 478 K could alter B-cell epitopes of the spike protein to weaken the binding ability of serum or convalescent patients' antibodies and even the transmission. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 P681R 22 27 S;S 82;177 87;182 34848355 Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021. The mutation N501Y happens in one of six essential residues of RBD for the binding capacity of SARS-CoV-2 (L455, F486, Q493, S494, N501, and Y505). 2022 Infection, genetics and evolution Discussion SARS_CoV_2 N501Y 13 18 RBD 63 66 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. Looking at the residue level, a crucial role for the N501Y mutation present in the Alpha, Beta, and Gamma variants was identified, resulting in a significant gain in the stabilization of the RBD:ACE2 interface. 2021 Nature communications Discussion SARS_CoV_2 N501Y 53 58 RBD 191 194 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. Nevertheless, we observed that the Alpha variant being neutralized by the B-41 shares the N501Y mutation with other mutant that escape the neutralization. 2021 Nature communications Discussion SARS_CoV_2 N501Y 90 95 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. Regarding the Kappa variant, mutation of RBD residue 484 (E484Q) plays an important role from energetics point of view. 2021 Nature communications Discussion SARS_CoV_2 E484Q 58 63 RBD 41 44 34848718 Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. This result is consistent with previous observations which suggest that N501Y mutation is unlikely to greatly affect neutralization by most human plasma, although it could contribute to increased viral titer or enhanced transmissibility. 2021 Nature communications Discussion SARS_CoV_2 N501Y 72 77 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. A similar LNA-based approach for the detection of N501Y and HV69/70 has been successfully tested in Canada on 2430 samples. 2021 Analytical chemistry Discussion SARS_CoV_2 N501Y 50 55 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. Using more than one VOC marker enabled us to identify SARS-CoV-2 variants with an unusual combination of mutations, such as the E484K plus the HV69/70 deletion. 2021 Analytical chemistry Discussion SARS_CoV_2 E484K 128 133 34852455 Rapid Identification of SARS-CoV-2 Variants of Concern Using a Portable peakPCR Platform. We designed, tested, and validated three mutation-specific RT-qPCR assays, detecting the E484K and N501Y SNPs as well as the 6-bp deletion affecting HV69/70, all located in the SARS-CoV-2 spike gene. 2021 Analytical chemistry Discussion SARS_CoV_2 E484K;N501Y 89;99 94;104 S 188 193 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Both Alpha and Delta variants have mutations near the classical furin cleavage site (P681H/R). 2022 Emerging microbes & infections Discussion SARS_CoV_2 P681H;P681R 85;85 92;92 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Cell-cell fusion studies suggested that both the K814A site and the 682-686 sites are important for furin-enhanced cell-cell fusion, with the 682-686 sites necessary for furin functioning in donor cells. 2022 Emerging microbes & infections Discussion SARS_CoV_2 K814A 49 54 34856891 A second functional furin site in the SARS-CoV-2 spike protein. However, no significant difference was found between the WT and K809A mutated SARS-CoV when the lung cell line Calu-3 and the human ACE2 transgenic mice were tested (Figure S1B-D). 2022 Emerging microbes & infections Discussion SARS_CoV_2 K809A 64 69 34856891 A second functional furin site in the SARS-CoV-2 spike protein. In addition, E64D is not only the inhibitor of CTSL but also inhibits other cathepsins. 2022 Emerging microbes & infections Discussion SARS_CoV_2 E64D 13 17 34856891 A second functional furin site in the SARS-CoV-2 spike protein. Previous studies suggested that the P681H mutation enhanced the cleavage of S protein by furin, while P681R promoted cell-cell fusion. 2022 Emerging microbes & infections Discussion SARS_CoV_2 P681H;P681R 36;102 41;107 S 76 77 34856891 A second functional furin site in the SARS-CoV-2 spike protein. The K814A single mutation led to a complete loss of the furin-mediated infectivity enhancement, suggesting its important role during furin functioning (Figure 2D). 2022 Emerging microbes & infections Discussion SARS_CoV_2 K814A 4 9 34856891 A second functional furin site in the SARS-CoV-2 spike protein. This enhancement disappeared after the addition of E64D inhibitor, suggesting that DeltaF may enhance the enzyme activity of CTSL. 2022 Emerging microbes & infections Discussion SARS_CoV_2 E64D 51 55 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. Here we show using a RBD containing the mutations T478K and L452R present in the Delta variant that volunteers vaccinated with CoronaVac exhibit reduced blocking antibodies compared to the WT RBD but we report a seropositivity of 78.57% and 55.76% by sVNT and cVNT ( Tables 1 and 2 ), respectively, which suggests that the vaccine confers protection against this variant. 2021 Frontiers in immunology Discussion SARS_CoV_2 L452R;T478K 60;50 65;55 RBD;RBD 21;192 24;195 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. In line with the reports for the Gamma variant, the E484K mutation found in the Beta variant has been identified as the main mutation responsible for this effect as antibodies bind to RBD with less affinity. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K 52 57 RBD 184 187 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. Of note, we used the D614G variant in the cVNT, which exhibits a mutation outside of the RBD and we were able to observe effective neutralization against viral infection in all the subjects evaluated from both vaccination schedules and both age groups ( Figure 2 ). 2021 Frontiers in immunology Discussion SARS_CoV_2 D614G 21 26 RBD 89 92 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. Pseudoviruses carrying the L452R mutation display higher infectivity in cell culture and when incubated with sera from subjects vaccinated with Moderna mRNA-1273 or BNT16b2, as compared to the WT strain. 2021 Frontiers in immunology Discussion SARS_CoV_2 L452R 27 32 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. Similarly, here we report a 4.73 fold reduction compared to the D614G strain using cVNT ( Figure 2 ). 2021 Frontiers in immunology Discussion SARS_CoV_2 D614G 64 69 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. The Delta variant (first identified in India) exhibit the RBD mutations T478K, L452R and P681R and is currently a cause of concern due to its high transmissibility and may even surpass other variants in this regard. 2021 Frontiers in immunology Discussion SARS_CoV_2 L452R;P681R;T478K 79;89;72 84;94;77 RBD 58 61 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. The reduced neutralizing capacities reported against the Gamma variant have been related to the E484K mutation, which promotes the evasion of neutralizing antibodies. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K 96 101 34858404 Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine. These results support that CoronaVac is protective against the D614G variant, which is one of the most prevalent strains worldwide. 2021 Frontiers in immunology Discussion SARS_CoV_2 D614G 63 68 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. Additionally, spike D614G was accompanied by high occurrence of the nsp12 P4715L mutation, and this duo variant which is linked to pathogenicity was observed to be not linked positively to fatality rates in Africa. 2021 Frontiers in genetics Discussion SARS_CoV_2 D614G;P4715L 20;74 25;80 S;Nsp12 14;68 19;73 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. Considering the high occurrence of D614G in spike protein of SARS-CoV-2, several groups have assessed the antigenic peptides and it is reported that the peptide S597-625 is one of the major immuno-dominant in humans. 2021 Frontiers in genetics Discussion SARS_CoV_2 D614G 35 40 S 44 49 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. Earlier reports have also showed that D614G increases the efficiency of cellular entry for the virus across a broad range of human cell types, including cells from lung, liver, and colon. 2021 Frontiers in genetics Discussion SARS_CoV_2 D614G 38 43 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. However, there is still much scope to understand how D614G affects antigenic properties of S protein; whether elastase-2 inhibitors and convalescent serum samples of patients can block infection of D614G variant remains unclear. 2021 Frontiers in genetics Discussion SARS_CoV_2 D614G;D614G 53;198 58;203 S 91 92 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. In addition, it is concurrently seen with other mutations like P681R, L452R, T19R, E156G, T478K. 2021 Frontiers in genetics Discussion SARS_CoV_2 E156G;L452R;P681R;T19R;T478K 83;70;63;77;90 88;75;68;81;95 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. In the current study, we observed that D614G is highly prevalent mutation in the spike protein of genomes from COVID-19 patients of the Gujarat region. 2021 Frontiers in genetics Discussion SARS_CoV_2 D614G 39 44 S 81 86 COVID-19 111 119 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. In the present work, we attempt to report the mutation analysis of spike protein and the antigenic propensity of D614G mutation in the spike protein of the viral isolates from the Gujarat region. 2021 Frontiers in genetics Discussion SARS_CoV_2 D614G 113 118 S;S 67;135 72;140 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. Regions between amino acid 614 and 621 of SARS-CoV-2 spike proteins were also identified as a B cell epitope by different methods and D614G may affect the antigenicity of this region. 2021 Frontiers in genetics Discussion SARS_CoV_2 D614G 134 139 S 53 58 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. Seeing the rise in the cases with D614G mutation and its enhanced transmission, the D614G attracts significant consideration by researchers and healthcare field fellows. 2021 Frontiers in genetics Discussion SARS_CoV_2 D614G;D614G 34;84 39;89 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. The observation that the P681R was the second most prevalent mutation reveals the recent high dominance of the Delta variant in the region. 2021 Frontiers in genetics Discussion SARS_CoV_2 P681R 25 30 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. There are many mutations observed in the amino acid composition of the spike protein but primary data shows that strains with S-D614G are more infectious and exhibit high transmission efficiency. 2021 Frontiers in genetics Discussion SARS_CoV_2 D614G 128 133 S;S 71;126 76;127 34858480 Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India. These had >50% of occurrence in Gujarat whereas at the global level only D614G showed very high occurrence (98.53%) of all sequences and the rest of these formerly mentioned mutations had a frequency of 35-40% globally, lower than that in Gujarat. 2021 Frontiers in genetics Discussion SARS_CoV_2 D614G 73 78 34866979 Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study. All structural genes in our study showed missense mutations except E gene which showed only one silent mutation; N gene showed highest mutations among the structural genes, the most frequent mutations at positions G28881A (S202N), and G28883C (G204R). 2021 Saudi journal of biological sciences Discussion SARS_CoV_2 G28881A;G28883C;G204R;S202N 214;235;244;223 221;242;249;228 E;N 67;113 68;114 34866979 Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study. In alignment with our findings several reports showed that C3037T and C241T changes were the two most frequent mutations, followed by C14408T, A23403G, and T28144C (L84S, ORF8). 2021 Saudi journal of biological sciences Discussion SARS_CoV_2 A23403G;C14408T;C241T;C3037T;T28144C;L84S 143;134;70;59;156;165 150;141;75;65;163;169 ORF8 171 175 34866979 Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study. Interestingly, C1059T is one of most frequent mutation but did not appear in KSA variants. 2021 Saudi journal of biological sciences Discussion SARS_CoV_2 C1059T 15 21 34866979 Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study. It has also been mentioned that persistent mutation in spike protein may indicate that the virus is becoming more effective in human to human transmission, for example, D614G mutation has been reported to enhance infectivity and transmission due to increased interaction with ACE2 receptor present on host cells. 2021 Saudi journal of biological sciences Discussion SARS_CoV_2 D614G 169 174 S 55 60 34866979 Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study. Our study indicated that the SARS-CoV-2 variants isolated in KSA were characterized with coexistence of C241T (UTR region), C3037T (NSP3 gene), C14408T (NSP12) and A23403G (S gene) nucleotide changes, they occur simultaneously in 55 variants out of 58. 2021 Saudi journal of biological sciences Discussion SARS_CoV_2 A23403G;C14408T;C241T;C3037T 164;144;104;124 171;151;109;130 Nsp12;Nsp3;S 153;132;173 158;136;174 34866979 Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study. Our study showed that the mutations at G 25563T, G28881A and G28883C occurred in 33, 23, 22 variants out of 58; according to, these mutations were found highly prevalent among sequences from the Europe, USA and Bangladesh. 2021 Saudi journal of biological sciences Discussion SARS_CoV_2 G25563T;G28881A;G28883C 39;49;61 47;56;68 34866979 Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study. The most frequent mutations in spike gene were A23403G (D614G) followed by C22444T (silent). 2021 Saudi journal of biological sciences Discussion SARS_CoV_2 A23403G;C22444T;D614G 47;75;56 54;82;61 S 31 36 34866979 Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study. These results revealed that SARS-CoV-2 variants isolated in KSA are free from E484K, K417N, N501Y mutations which characterized South African variant and from N501Y which characterized UK variant. 2021 Saudi journal of biological sciences Discussion SARS_CoV_2 E484K;K417N;N501Y;N501Y 78;85;92;159 83;90;97;164 34869681 Arterial and Venous Thrombosis Complicated in COVID-19: A Retrospective Single Center Analysis in Japan. Recently, several reports described the promotion of thrombus formation via the activation of platelets, the induction of tissue factor, or PAI-1 using virus particle of the Wuhan strain or recombinant S1 protein with D614G single mutation. 2021 Frontiers in cardiovascular medicine Discussion SARS_CoV_2 D614G 218 223 34870573 SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity. The 11 083G>T mutation confers an amino acid change from leucine (L) to phenylalanine (F) at the 37th position in the NSP6 protein (L37F). 2021 Microbial genomics Discussion SARS_CoV_2 L37F 132 136 Nsp6 118 122 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. A comparison of surface hydrophobicity of the trimeric spike reference protein with the Asp614Gly mutation over the simulation trajectory indicated surface hydrophobicity changed for both proteins. 2021 PloS one Discussion SARS_CoV_2 D614G 88 97 S 55 60 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. A Consurf analysis indicated that all the mutations were located in variable regions of the protein except for Asp614Gly. 2021 PloS one Discussion SARS_CoV_2 D614G 111 120 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. On the other hand, the Asp614Gly missense mutation, which has been widely detected in different regions of the world, was seen in two (ACUTG-1 and ACUTG-5) out of the genome sequences of 13 patients in our cohort. 2021 PloS one Discussion SARS_CoV_2 D614G 23 32 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. The Asp614Gly mutant exhibited a lower SASA change than the reference protein and the other mutations, especially around the ACE-2 receptor-binding domain, resulting in a more compact region. 2021 PloS one Discussion SARS_CoV_2 D614G 4 13 34871297 Mutational landscape of SARS-CoV-2 genome in Turkey and impact of mutations on spike protein structure. We also performed modeling of the mutations in spike glycoprotein and our analysis indicates that the trimeric spike glycoprotein surface becomes more hydrophilic upon the Ala222Val mutation. 2021 PloS one Discussion SARS_CoV_2 A222V 172 181 S;S 47;111 65;129 34876033 Emergence of SARS-CoV-2 resistance mutations in a patient who received anti-SARS-COV2 spike protein monoclonal antibodies: a case report. Other mutations on the S protein liable to escape mAbs effect have been described, especially K417N and Q493R. 2021 BMC infectious diseases Discussion SARS_CoV_2 K417N;Q493R 94;104 99;109 S 23 24 34876033 Emergence of SARS-CoV-2 resistance mutations in a patient who received anti-SARS-COV2 spike protein monoclonal antibodies: a case report. Variants with an E484K substitution within S glycoprotein can escape acquired immunity, either through prior natural infection or vaccination, at least partially. 2021 BMC infectious diseases Discussion SARS_CoV_2 E484K 17 22 S 43 57 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. On the contrary, we show a significant neutralisation resistance for a Delta variant that acquired the E484K spike mutation. 2021 Euro surveillance Discussion SARS_CoV_2 E484K 103 108 S 109 114 34886943 Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. While Delta variants bearing the E484K mutation occur mostly sporadically, it has now occurred in Delta sub-lineages with sustained clusters according to recent reports from the UK. 2021 Euro surveillance Discussion SARS_CoV_2 E484K 33 38 34886945 Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020. Firstly, we only considered the D614G mutation and simply categorised the sequences on GISAID by aligning the spike protein region that contains the locus. 2021 Euro surveillance Discussion SARS_CoV_2 D614G 32 37 S 110 115 34886945 Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020. The mutant D614G was detected sporadically among local cases in the mainland Chinese provinces Guangdong and Zhejiang after February 2020, but no sustained circulation of G614 clusters had been detected in mainland China until the Xinfadi Market outbreak in Beijing in June 2020. 2021 Euro surveillance Discussion SARS_CoV_2 D614G 11 16 34886945 Estimating the transmission advantage of the D614G mutant strain of SARS-CoV-2, December 2019 to June 2020. We did not consider mutations in other loci that might provide necessary genetic background for D614G and act synergistically to affect the fitness of G614. 2021 Euro surveillance Discussion SARS_CoV_2 D614G 96 101 34888394 A Multidimensional Cross-Sectional Analysis of Coronavirus Disease 2019 Seroprevalence Among a Police Officer Cohort: The PoliCOV-19 Study. Considering that the sampling occurred from 9 February to 9 March, the vast majority of our cohort was exposed to the virus strain harboring the D614G S protein. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G 145 150 S 151 152 34888394 A Multidimensional Cross-Sectional Analysis of Coronavirus Disease 2019 Seroprevalence Among a Police Officer Cohort: The PoliCOV-19 Study. In line with these observations, naturally acquired antibodies demonstrated good neutralization activity against D614G but performed suboptimally against the Alpha variant and poorly against the Beta variant. 2021 Open forum infectious diseases Discussion SARS_CoV_2 D614G 113 118 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. 3, Table S5), which was higher than that of the Cas13-based N501Y detection system (100 copies/muL). 2022 Biosensors & bioelectronics Discussion SARS_CoV_2 N501Y 60 65 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. also utilized a symRNA-Cas12a detection method to distinguish the D614G mutant samples correctly, but merely 5 mutant samples involved. 2022 Biosensors & bioelectronics Discussion SARS_CoV_2 D614G 66 71 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. By introducing a skillful point mutation at the seed region of crRNA, the RT-CORDS can detect the SARS-CoV-2 single-base mutations (N501Y and D614G) with high specificity. 2022 Biosensors & bioelectronics Discussion SARS_CoV_2 D614G;N501Y 142;132 147;137 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. Compared with similar CRISPR-based methods, the accuracy in this study was higher than that of a Cas9-based N501Y detection method (accuracy: 86%). 2022 Biosensors & bioelectronics Discussion SARS_CoV_2 N501Y 108 113 34894625 Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform. The LOD of RT-CORDS with paper strip were up to 10-15 M for N501Y and D614G detection and 10-16 M for 69/70 detection. 2022 Biosensors & bioelectronics Discussion SARS_CoV_2 D614G;N501Y 70;60 75;65 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Also, there were two other sequences sampled from Shiraz in January 2021, which had five specific mutations as indicator of the Alpha variant (D614G, H69del, N501Y, V70del, Y144del) and were clustered along with the Alpha variants in phylogenetic tree; however, these sequences did not contain the other specific mutations of Alpha variant including A570D, D1118H, L699I, P681H, S982A and T716I. 2022 Gene Discussion SARS_CoV_2 A570D;D1118H;H69del;L699I;N501Y;P681H;S982A;T716I;V70del;Y144del;D614G 350;357;150;365;158;372;379;389;165;173;143 355;363;156;370;163;377;384;394;171;180;148 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Currently, the A262T mutation is seen in some variants from different countries with a very low frequency (221 SARS-COV2 sequences in GISAID). 2022 Gene Discussion SARS_CoV_2 A262T 15 20 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Four of nine sequences sampled from Yazd, in addition to indicator mutations of a Delta variant, also have a common E1202Q mutation in the Heptad Repeat (HR2) subdomain, in which glutamine replaces glutamic acid at position 1202. 2022 Gene Discussion SARS_CoV_2 E1202Q;Q1202E 116;179 122;228 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. However, some of the Delta variants in Iran carry an additional mutation, E1202Q in the HR2 subdomain that might confer an advantage to viral/cell membrane fusion process. 2022 Gene Discussion SARS_CoV_2 E1202Q 74 80 Membrane 147 155 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. In NTD, the most commonly detected mutations have been Del I210, EFR156-158G and T19R with the latter possibly disrupting the "super site" on the NTD. 2022 Gene Discussion SARS_CoV_2 T19R 81 85 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. L452R, T478K, N501Y and S477N have been the most frequently detected mutations in RDB. 2022 Gene Discussion SARS_CoV_2 N501Y;S477N;T478K;L452R 14;24;7;0 19;29;12;5 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Moreover, N501Y mutation is among mutations which are located at the boundary between the spike protein and ACE-2 receptor and can influence efficiency of vaccines and drugs targeted the interface of protein-protein interactions. 2022 Gene Discussion SARS_CoV_2 N501Y 10 15 S 90 95 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. None of the Delta variant sequences from Iran (deposited in GISAID and GenBank up to the end of May 2021) carry the K417N mutation, an additional mutation in Delta variant leading to a new Delta sub-lineage referred to as Delta Plus. 2022 Gene Discussion SARS_CoV_2 K417N 116 121 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Notably, N501Y and S477N has also been reported as frequent mutations in this domain in a World-wide assay. 2022 Gene Discussion SARS_CoV_2 N501Y;S477N 9;19 14;24 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Regarding the frequency of E1202Q mutation in Delta variant sequences from Iran, it seems that this mutation might confer an advantage to viral/cell membrane fusion process. 2022 Gene Discussion SARS_CoV_2 E1202Q 27 33 Membrane 149 157 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Ten out of these eleven sequences belonged to spike sequences carrying the mutation D614G (clade G); however, one sequence belonged to the Glade L, having the original amino acid aspartic acid at position 614. 2022 Gene Discussion SARS_CoV_2 D614G 84 89 S 46 51 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. The D614G mutation as the only frequent mutation in the spike protein detected up to now among all the continents, has been the most commonly detected mutation in RBD-Fusion peptide span region in Iranian samples. 2022 Gene Discussion SARS_CoV_2 D614G 4 9 S;RBD 56;163 61;166 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. The mutations D138Y and S477N are the same as those found in the NTD of VOC Gamma (P.1) and RBD of VOI of lota, respectively. 2022 Gene Discussion SARS_CoV_2 D138Y;S477N 14;24 19;29 RBD 92 95 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. The mutations E1202Q and Y144 deletion in combination with delta variant specific mutations might increase the concerns raised about these variants. 2022 Gene Discussion SARS_CoV_2 E1202Q 14 20 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. There was another sequence sampled from Shiraz in Oct 2020 that contained five specific mutations (D138Y, D614G, E484K, K417T, N501Y) as indicator of the Gamma variant (GR/501Y.V3 (P.1+P.1.x)) and was clustered along with the representative Gamma variant spike sequence in phylogenetic tree. 2022 Gene Discussion SARS_CoV_2 D614G;E484K;K417T;N501Y;D138Y 106;113;120;127;99 111;118;125;132;104 S 255 260 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. This analysis determined the sequential prevalence of O, GH, GRY and G clades, the last one being characterized by D614G variant. 2022 Gene Discussion SARS_CoV_2 D614G 115 120 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. This sequence also had an additional mutation S477N in RBD. 2022 Gene Discussion SARS_CoV_2 S477N 46 51 RBD 55 58 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Two out of these four sequences each had another different mutation including I100T and L699I. 2022 Gene Discussion SARS_CoV_2 I100T;L699I 78;88 83;93 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. We also found that the A262T mutation is the most frequent mutation (15 sequences; 8.5% of samples) among the Iranian SARS-COV2 spike sequences sampled from Mar 2020 to Aug 2020; however, this mutation has been disappeared after Aug 2020, probably due to the emergence of new variants. 2022 Gene Discussion SARS_CoV_2 A262T 23 28 S 128 133 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. We also observed triple co-occurring mutations, namely D138Y (in the NTD), S477N (in the RBD) with the well-established D614G mutation (near the furin cleavage site) in three spike sequences from Tehran and Shiraz sampled from Nov 2020 to Jan 2021. 2022 Gene Discussion SARS_CoV_2 D138Y;D614G;S477N 55;120;75 60;125;80 S;RBD 175;89 180;92 34896524 A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. We found the mutation A262T in both spike sequence with the original D614 (8 out of 15) and with the well-established D614G mutation (7 out of 15). 2022 Gene Discussion SARS_CoV_2 A262T;D614G 22;118 27;123 S 36 41 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Another RBD mutation L452R, appeared in Delta variant, made the conformation of the S protein more stable, leading to the increased affinity of the virus to ACE2 receptor. 2022 Journal of infection and public health Discussion SARS_CoV_2 L452R 21 26 RBD;S 8;84 11;85 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Based on non-synonymous mutational analysis, here we revealed the emergence of a novel SARS-CoV-2 lineage B.1.1.526 harboring 11 coexisting mutations in seven different genes including D614G, P681H and V1230L in the S glycoprotein. 2022 Journal of infection and public health Discussion SARS_CoV_2 D614G;P681H;V1230L 185;192;202 190;197;208 S 216 230 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. D614G, the first mutation appeared in the S glycoprotein, was detected in Germany in January 2020 and became the dominant mutation in all the circulating strains worldwide by June 2020. 2022 Journal of infection and public health Discussion SARS_CoV_2 D614G 0 5 S 42 56 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Hamster infected with the D614G variant produces higher infectious virus titers in nasal washes and the trachea, supporting the role of D614G mutation in high transmissibility. 2022 Journal of infection and public health Discussion SARS_CoV_2 D614G;D614G 26;136 31;141 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. However, D614G does not alter S protein binding to ACE2 or neutralization sensitivity to pseudoviruses. 2022 Journal of infection and public health Discussion SARS_CoV_2 D614G 9 14 S 30 31 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. In addition to immune evasion, both K417N and K417T are expected to moderately decrease ACE2-binding affinity of S glycoprotein. 2022 Journal of infection and public health Discussion SARS_CoV_2 K417N;K417T 36;46 41;51 S 113 127 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. In addition, L452R mutation induces the conformational change of RBD and reduces the ability of monoclonal antibodies and convalescent sera to neutralize the virus. 2022 Journal of infection and public health Discussion SARS_CoV_2 L452R 13 18 RBD 65 68 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. In addition, N501Y mutation enabled the virus to infect BALB/c mice, which expanded its host range. 2022 Journal of infection and public health Discussion SARS_CoV_2 N501Y 13 18 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Interestingly, among 129 SARS-CoV-2 strains that encompass the novel lineage B.1.1.526, 27 strains harbor E484K mutation, which described to have role in immune evasion. 2022 Journal of infection and public health Discussion SARS_CoV_2 E484K 106 111 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. It has also been demonstrated that D614G mutation confers higher susceptibility to serum neutralization. 2022 Journal of infection and public health Discussion SARS_CoV_2 D614G 35 40 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. K417N and K417T mutations, detected in the receptor binding domain (RBD) of S glycoprotein of Beta and Gamma variant respectively, have been shown to have potential role in immune escape. 2022 Journal of infection and public health Discussion SARS_CoV_2 K417T;K417N 10;0 15;5 RBD;S;RBD 43;76;68 66;90;71 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. N501Y mutation, shared by the three VOCs Alpha, Beta and Gamma, could enhance the affinity of the S protein with ACE2, especially with the side chains of residues Y41 and K353 of ACE2 [27,]. 2022 Journal of infection and public health Discussion SARS_CoV_2 N501Y 0 5 S 98 99 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Patients infected with the D614G mutant had higher nasopharyngeal viral RNA loads, indicating its role in increased infectivity. 2022 Journal of infection and public health Discussion SARS_CoV_2 D614G 27 32 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Therefore, the novel lineage B.1.1.526 having D614G, P681H, V1230L and E484K mutations in the S glycoprotein is expected to have increased infectivity, high transmissibility, and enhanced immune evasion properties. 2022 Journal of infection and public health Discussion SARS_CoV_2 D614G;E484K;P681H;V1230L 46;71;53;60 51;76;58;66 S 94 108 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Though the role of D614G in increased infectivity and transmissibility is well known, the functional relevance of P681H/R (previously observed in Alpha variant and Delta variant) and V1230L (first detected in this study) is yet to be determined. 2022 Journal of infection and public health Discussion SARS_CoV_2 D614G;P681H;P681R;V1230L 19;114;114;183 24;121;121;189 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. V1230L mutation, not observed previously in other lineage of SAR-CoV-2, is located at the transmembrane (TM) domain of S2 subunit of S glycoprotein. 2022 Journal of infection and public health Discussion SARS_CoV_2 V1230L 0 6 S 133 147 34896696 Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India. Wet lab experiments confirmed that the D614G mutation enhances virus replication in human lung epithelial cells and primary human airway tissues by increasing the infectivity and stability of the virions. 2022 Journal of infection and public health Discussion SARS_CoV_2 D614G 39 44 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. Indeed, it has been shown that the p.N501Y mutation is associated to an augmented affinity to the angiotensin-converting enzyme 2 (ACE2) receptor and an increased transmissibility compared to previous circulating SARS-CoV-2 lineages. 2021 PloS one Discussion SARS_CoV_2 N501Y;N501Y 35;37 42;42 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. Indeed, mRNA based (Moderna, Pfizer-BioNTech), adenoviral based (Vaxzevria, Johnson&Johnson), and protein-based based (Novavax) vaccines are only able to induce a monoclonal response towards the Asp614Gly bearing SARS-CoV-2 Spike protein, therefore a steady acquisition of mutations that could eventually lead to an enhanced fitness should be carefully monitored. 2021 PloS one Discussion SARS_CoV_2 D614G 195 204 S 224 229 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. Nonetheless, the presence of the p.E484K mutation in the B.1.1.7 background has been recently reported, named VOC-21FEB-02 in late March 2021. 2021 PloS one Discussion SARS_CoV_2 E484K;E484K 33;35 40;40 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. Of particular concern is the B.1.1.7 lineage harboring the p.E484K, since it has been demonstrated that it enhances escape from neutralizing antibody inhibition in vitro, and reduces efficacy of the vaccine. 2021 PloS one Discussion SARS_CoV_2 E484K;E484K 59;61 66;66 34905574 Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. p.E484K is a mutation of concern with regards to antigenic change and receptor binding avidity; it is potentially more concerning when combined with N501Y. 2021 PloS one Discussion SARS_CoV_2 N501Y;E484K;E484K 149;2;0 154;7;7 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. A different type of phylogenetic analysis found no support for a selective advantage of any of the variants they tested, including D614G, presumably because their statistical test required the repeated emergence of a variant in order to draw any power. 2021 Nature communications Discussion SARS_CoV_2 D614G 131 136 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. Our analyses point to strong selection favoring D614G and B.1.1.7, some selection favoring B.1.351, and not a global advantage for R.1. 2021 Nature communications Discussion SARS_CoV_2 D614G 48 53 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. Several studies using other methods have similarly found D614G and B.1.1.7 to each have a selective advantage over other variants circulating contemporaneously. 2021 Nature communications Discussion SARS_CoV_2 D614G 57 62 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. That is, the fitness of B.1.1.7 exceeds that of D614G, which itself exceeds the original genotype. 2021 Nature communications Discussion SARS_CoV_2 D614G 48 53 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. Third, the UK has put effort into developing a representative sample of SARS-CoV-2 genomes in their country and the estimates for the selection effects in the UK for D614G and B.1.1.7 are very close and slightly above the population average for these lineages, while being only slightly below average for B.1.351. 2021 Nature communications Discussion SARS_CoV_2 D614G 166 171 34907182 Estimating the strength of selection for new SARS-CoV-2 variants. This means, for example, that the fitness advantage estimated for B.1.1.7 is relative to a background that consists mostly of D614G. 2021 Nature communications Discussion SARS_CoV_2 D614G 126 131 34909634 Severe breakthrough COVID-19 with a heavily mutated variant in a multiple myeloma patient 10 weeks after vaccination. N440K:also absent from the original B.1.628:has been observed in viral passaging experiments in the presence of convalescent plasma and provides additional immune escape in vitro. 2022 Clinical infection in practice Discussion SARS_CoV_2 N440K 0 5 34909634 Severe breakthrough COVID-19 with a heavily mutated variant in a multiple myeloma patient 10 weeks after vaccination. Notably, N440K is also present in the SARS-CoV-2 Omicron variant (B.1.1.529), and has been shown to be associated with breakthrough infections in vivo. 2022 Clinical infection in practice Discussion SARS_CoV_2 N440K 9 14 34909634 Severe breakthrough COVID-19 with a heavily mutated variant in a multiple myeloma patient 10 weeks after vaccination. Of the three nucleocapsid mutations noted in our isolate, S194L has been best characterized, and is associated with poorer clinical outcomes. 2022 Clinical infection in practice Discussion SARS_CoV_2 S194L 58 63 N 13 25 34909634 Severe breakthrough COVID-19 with a heavily mutated variant in a multiple myeloma patient 10 weeks after vaccination. The cause was an extensively mutated B.1.628 SARS-CoV-2 variant, featuring N440K and E484Q spike mutations. 2022 Clinical infection in practice Discussion SARS_CoV_2 E484Q;N440K 85;75 90;80 S 91 96 34909634 Severe breakthrough COVID-19 with a heavily mutated variant in a multiple myeloma patient 10 weeks after vaccination. The E484Q mutation in the RBD, not present in the original B.1.628 isolate, is also present in the kappa variant of interest and thought to confer immune evasion similar to E484K, which alone reduced neutralizing titers by a median of 2.8-fold among recipients of mRNA vaccines for COVID-19. 2022 Clinical infection in practice Discussion SARS_CoV_2 E484K;E484Q 173;4 178;9 RBD 26 29 COVID-19 282 290 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. Notably, clade of Omicron have the identified bearing R346K (15 descendants at the time of this writing) and R346S (5 descendants) and should be monitored closely [Hadfield 2019, ]. 2021 bioRxiv Discussion SARS_CoV_2 R346K;R346S 54;109 59;114 34909771 Insights on the mutational landscape of the SARS-CoV-2 Omicron variant. While mutation combinations such as Q498S and N501Y have been previously shown to epistatically enhance ACE-2 binding, our network analysis suggests that Omicron H505 may also alter the synergistic behavior between these two sites. 2021 bioRxiv Discussion SARS_CoV_2 N501Y;Q498S 46;36 51;41 34909777 Loss of Neutralizing Antibody Response to mRNA Vaccination against SARS-CoV-2 Variants: Differing Kinetics and Strong Boosting by Breakthrough Infection. In this study, we found that all three VOCs consistently had reduced NT50 values compared to D614G at all time points, with Beta showing the most pronounced nAb resistance, followed by Delta. 2021 bioRxiv Discussion SARS_CoV_2 D614G 93 98 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. A substitution at the same site (P681H) is found in Alpha, which evolved independently of Delta and dominated the global infection landscape between January and June 2021. 2021 medRxiv Discussion SARS_CoV_2 P681H 33 38 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. Although Delta shows compromised sensitivity to some RBD and NTD neutralizing antibodies with up to 8-fold reduced sensitivity in vitro to vaccine-induced antibodies compared to D614G viruses (including infectious virus assays), neutralization escape is substantially lower in magnitude as compared to Beta, Gamma, and Mu. 2021 medRxiv Discussion SARS_CoV_2 D614G 178 183 RBD 53 56 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. Efficient spike cleavage (P681H/R) and replicative competence appear to be central checkpoints for SARS-CoV-2's epidemiological success, with Delta being improved compared to Alpha. 2021 medRxiv Discussion SARS_CoV_2 P681H;P681R 26;26 33;33 S 10 15 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. In line with data from other laboratories, the pre-Delta breakthrough infections that we studied in early 2021 displayed a variant distribution similar to infections in unvaccinated individuals, though with signs of a starting sieve effect of neutralizing antibody escape mutations, e.g., E484K. 2021 medRxiv Discussion SARS_CoV_2 E484K 289 294 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. It remains elusive at this time whether spike: S112L, located at the apical part of spike NTD, nsp12: F192V, located distant from nsp12's active site, or the absence of mutations in the cold spot regions play an active role in breakthrough, immune evasion, enhanced transmission, or act as bystander mutations. 2021 medRxiv Discussion SARS_CoV_2 F192V;S112L 102;47 107;52 S;S;Nsp12;Nsp12 40;84;95;130 45;89;100;135 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. Our data suggest that selective adaptation processes might be in process that may eventually lead to the accumulation of mutations (spike S112L, nsp12 F192V) or new (sub)variants (AY.25) under vaccine immune pressure. 2021 medRxiv Discussion SARS_CoV_2 F192V;S112L 151;138 156;143 S;Nsp12 132;145 137;150 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. P681H/R mutations were both detected more frequently among breakthrough infections in our previous study of breakthrough infections in New York when Alpha and Iota variants were dominant regionally, and in this study during the current Delta wave. 2021 medRxiv Discussion SARS_CoV_2 P681H;P681R 0;0 7;7 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. Third, Delta carries the P681R substitution in the spike furin cleavage site, which triggers enhanced S1/S2 cleavage and might explain Delta's increased replication rate in vitro. 2021 medRxiv Discussion SARS_CoV_2 P681R 25 30 S 51 56 34909779 Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York. We observed an uptick of the subvariant AY.25 and the S112L mutation in NTD, which, while still at low numbers, preferentially spread among the vaccinated individuals in our cohort. 2021 medRxiv Discussion SARS_CoV_2 S112L 54 59 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Both mutations characterizing the main import clade, nsp2:K81N and ORF7a:P45L, are nonsynonymous, making this possibility realistic. 2021 medRxiv Discussion SARS_CoV_2 K81N;P45L 58;73 62;77 ORF7a;Nsp2 67;53 72;57 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. By contrast, here we show that the vast majority of Delta SARS-CoV-2 variants that have spread in Russia were genetically similar, carrying the derived nsp2:K81N and ORF7a:P45L changes that are rare outside Russia. 2021 medRxiv Discussion SARS_CoV_2 K81N;P45L 157;172 161;176 ORF7a;Nsp2 166;152 171;156 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Indeed, the nsp2:K81N+ORF7a:P45L combination occurs in 68 out of 80 (85%) of Russian samples obtained in April, but just in 34 out of 6658 (0.5%) of non-Russian samples obtained at that time. 2021 medRxiv Discussion SARS_CoV_2 K81N;P45L 17;28 21;32 ORF7a;Nsp2 22;12 27;16 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Nevertheless, nsp2:K81N+ORF7a:P45L has been observed in four of them (Table S4). 2021 medRxiv Discussion SARS_CoV_2 K81N;P45L 19;30 23;34 ORF7a;Nsp2 24;14 29;18 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. The AY.122+ORF7a:P45L variant started to spread near-simultaneously in Moscow, Saint Petersburg and the remainder of Russia (Table S2), suggesting that if true, this event took place before April 19 in a poorly sampled location within or outside Russia. 2021 medRxiv Discussion SARS_CoV_2 P45L 17 21 ORF7a 11 16 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. The earliest samples carrying the nsp2:K81N+ORF7a:P45L combination are sporadic, and were often deposited months later than collected, suggesting that they could be misdated in GISAID (Table S4). 2021 medRxiv Discussion SARS_CoV_2 K81N;P45L 39;50 43;54 ORF7a;Nsp2 44;34 49;38 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. There is also no evidence that the nsp2:K81N+ORF7a:P45L combination is characterized by an increased rate of spread compared to other Delta variants. 2021 medRxiv Discussion SARS_CoV_2 K81N;P45L 40;51 44;55 ORF7a;Nsp2 45;35 50;39 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Therefore, the high prevalence of the AY.122+ORF7a:P45L lineage in Russia is probably due to chance. 2021 medRxiv Discussion SARS_CoV_2 P45L 51 55 ORF7a 45 50 34909799 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Third, the success of the AY.122+ORF7a:P45L lineage in Russia could arise from an early superspreading event. 2021 medRxiv Discussion SARS_CoV_2 P45L 39 43 ORF7a 33 38 34910734 Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. Another commonest mutation was D614G in mink found in almost 95% of minks. 2021 PloS one Discussion SARS_CoV_2 D614G 31 36 34910734 Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. D614G mutation is a very common variant in human populations worldwide. 2021 PloS one Discussion SARS_CoV_2 D614G 0 5 34910734 Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. The common mutations were Y505H and Y453F in different animal species including dog, cat, lion, tiger, and gorilla. 2021 PloS one Discussion SARS_CoV_2 Y453F;Y505H 36;26 41;31 34910734 Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. The mutation Y453F in spike protein is specific for the mink variant and responsible for displaying a pronounced increase in ACE-2 affinity. 2021 PloS one Discussion SARS_CoV_2 Y453F 13 18 S 22 27 34910734 Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. The Y453F mutation was found in almost half of the sequenced mink strains. 2021 PloS one Discussion SARS_CoV_2 Y453F 4 9 34910734 Spatial epidemiology and genetic diversity of SARS-CoV-2 and related coronaviruses in domestic and wild animals. Y453F was detected in Denmark first in the mink population. 2021 PloS one Discussion SARS_CoV_2 Y453F 0 5 34912372 Hotspot Mutations in SARS-CoV-2. Figure 9 shows the binding affinity between the RBD of Spike protein and human ACE2 protein performed using SSIPe 6 for the four mutations of SARS-CoV-2, viz., L452R, T478K, E484Q, and N501Y, taking place in such domain. 2021 Frontiers in genetics Discussion SARS_CoV_2 E484Q;L452R;N501Y;T478K 175;161;186;168 180;166;191;173 S;RBD 55;48 60;51 34912372 Hotspot Mutations in SARS-CoV-2. For example, in Supplementary Figure S3A, the occurrence of nucleotide change G > A in 71,038 global sequences is almost 45%, while the number of times it occurs in 45 hotspot mutations is two, as is also evident from Table 2. 2021 Frontiers in genetics Discussion SARS_CoV_2 G71A 78 89 34912372 Hotspot Mutations in SARS-CoV-2. For example, the very low DDG value of G25563T shows that there is a decreased protein stability, thereby resulting in a reduction of virus virulence. 2021 Frontiers in genetics Discussion SARS_CoV_2 G25563T 39 46 34912372 Hotspot Mutations in SARS-CoV-2. The DDG value of -0.769 kcal/mol for E484Q indicates that this is a favorable mutation, while DDG values of 1.083, 1.248, and 0.236 kcal/mol for L452R, T478K, and N501Y indicate that these mutations are somewhat unfavorable. 2021 Frontiers in genetics Discussion SARS_CoV_2 E484Q;L452R;N501Y;T478K 37;145;163;152 42;150;168;157 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Besides analysis of various comorbidities, further work is needed to prove that the D614G mutation causes changes in discernible symptom order, as our current analysis is associative. 2021 PLoS computational biology Discussion SARS_CoV_2 D614G 84 89 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. COVID-19 cases in Japan were characterized as the Wuhan reference strain in January and February 2020, but after the first emergence of the virus with the D614G mutation in early March, approximately 90% of COVID-19 cases were caused by the mutated virus. 2021 PLoS computational biology Discussion SARS_CoV_2 D614G 155 160 COVID-19;COVID-19 207;0 215;8 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Due to the prevalence of the D614G mutation in the USA, we hypothesized that this mutation is the cause of the variance between the results of China and the USA. 2021 PLoS computational biology Discussion SARS_CoV_2 D614G 29 34 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. If true, the widespread use of masks could be more important where the D614G and other similar variants predominate. 2021 PLoS computational biology Discussion SARS_CoV_2 D614G 71 76 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Interestingly, the D614G variant has been shown to have a higher probability of transmission, but not a more severe disease, and here our data suggests that symptom order changes as well. 2021 PLoS computational biology Discussion SARS_CoV_2 D614G 19 24 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Our study also included datasets from varying countries for both the Wuhan reference strain and the D614G variant. 2021 PLoS computational biology Discussion SARS_CoV_2 D614G 100 105 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. The results of our model presented here suggests that there is an order of symptom onset and this order changes with the D614G mutation, but how the variant affects the order of GI symptoms among themselves and relative to respiratory symptoms requires further validation, which requires additional data. 2021 PLoS computational biology Discussion SARS_CoV_2 D614G 121 126 Respiratory Disease 223 243 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. These data are consistent with our findings, as these countries have a predominance of the D614G variant. 2021 PLoS computational biology Discussion SARS_CoV_2 D614G 91 96 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. This hypothesis is consistent with a report that suggest the D614G variant causes a higher upper respiratory tract viral load in patients, which implies that the patients might need to cough more and there is more virus spread per cough. 2021 PLoS computational biology Discussion SARS_CoV_2 D614G 61 66 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Thus, our model predicts that the order of symptom onset in COVID-19 patients are most dependent on the D614G mutation and does not change with comorbidities, age, or weather/climate. 2021 PLoS computational biology Discussion SARS_CoV_2 D614G 104 109 COVID-19 60 68 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. Thus, we propose the hypothesis that cough occurring earlier with the D614G variant could contribute to its higher transmissibility, because symptomatic people cough thereby spreading the virus before they are incapacitated with fever. 2021 PLoS computational biology Discussion SARS_CoV_2 D614G 70 75 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. To further test our hypothesis, we analyzed datasets in Japan where the dominant strain changed from the Wuhan reference strain to D614G variant. 2021 PLoS computational biology Discussion SARS_CoV_2 D614G 131 136 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. To test this hypothesis, we analyzed datasets from Hong Kong and Brazil with high incidence of the Wuhan reference strain and the D614G variant, respectively. 2021 PLoS computational biology Discussion SARS_CoV_2 D614G 130 135 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. We performed the analysis again on a Japan dataset that represents data when the Wuhan reference strain was prominent and a later Japan dataset when the D614G variant was prominent, and again our model's predictions were consistent with our hypothesis that symptom order depends on mutation. 2021 PLoS computational biology Discussion SARS_CoV_2 D614G 153 158 34914688 Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant. While others have proposed that SARS-CoV-2 mutation affects olfactory and gustatory symptoms, diarrhea, and COVID-19 pathology, our results suggest that symptom order may be affected by the D614G variant. 2021 PLoS computational biology Discussion SARS_CoV_2 D614G 190 195 COVID-19 108 126 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Although hydrogen bonding with Y453 is possible in both H34 rotamers (Figures S4K-S4P), the dominant rotamer positioning of H34 in the D614G + N501Y + E484K-ACE2 complex enables it to participate in additional favourable intermolecular interactions with Y453 (hydrogen bond + OH/pi) and L455 (CH/pi), yielding estimated interaction energies of -10.29 and -2.75 kcal/mol, respectively. 2021 Cell reports Discussion SARS_CoV_2 D614G;E484K;N501Y 135;151;143 140;156;148 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Although our analysis did not reveal the N501Y mutation to be highly antibody evasive, its presence within the footprint of several neutralizing antibodies may have implications for antibody escape (Figures 4D-4G). 2021 Cell reports Discussion SARS_CoV_2 N501Y 41 46 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Although there are many factors governing viral evolution, these results suggest that the independent evolution of L452R-bearing spikes and N501Y-, K417N/T-, and E484K-bearing spikes may be explained by a lack of synergistic increase in ACE2 binding upon combination of these mutations. 2021 Cell reports Discussion SARS_CoV_2 E484K;K417N;K417T;L452R;N501Y 162;148;148;115;140 167;155;155;120;145 S;S 129;176 135;182 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Although these mutational combinations enable enhanced ACE2 binding compared with wild-type spikes, the increase in ACE2 binding affinity conferred by the L452R mutation in isolation was not preserved. 2021 Cell reports Discussion SARS_CoV_2 L452R 155 160 S 92 98 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. As L452 is distal to the ACE2-RBD interface, it has been previously suggested that the L452R mutation may increase ACE2 affinity via allosteric modulation of the residues promoting the RBD-ACE2 interaction or via electrostatic effects. 2021 Cell reports Discussion SARS_CoV_2 L452R 87 92 RBD;RBD 30;185 33;188 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Consistent with this hypothesis, analysis of deposited spike sequences in the GISAID database reveals that K417N/T mutations do not occur independently of N501Y and E484K mutations (Figure S5D). 2021 Cell reports Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y 165;107;107;155 170;114;114;160 S 55 60 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Given that K417N/T mutations serve to diminish antibody binding at a cost to ACE2 affinity, the conditional presence of ACE2 affinity enhancing mutations may represent a compensatory mutational mechanism. 2021 Cell reports Discussion SARS_CoV_2 K417N;K417T 11;11 18;18 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. In contrast, K417N/T mutations are not a prerequisite for the occurrence of mutations that increase ACE2 affinity (N501Y) or simultaneously increase ACE2 affinity and decrease antibody binding (E484K, L452R) (Figure S5D). 2021 Cell reports Discussion SARS_CoV_2 K417N;K417T;L452R;E484K;N501Y 13;13;201;194;115 20;20;206;199;120 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. It is noteworthy that all VoCs containing K417N/T mutations also contain the N501Y and E484K mutations. 2021 Cell reports Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y 87;42;42;77 92;49;49;82 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. It should be noted that although the intermolecular K31-E484 salt bridge is lost upon inclusion of the E484K mutation, this electrostatic interaction is likely intramolecularly distributed between ACE2 residues E35 and K31, thus limiting the contribution of the K31-E484 interaction with regard to ACE2-RBD binding. 2021 Cell reports Discussion SARS_CoV_2 E484K 103 108 RBD 303 306 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Most important, the E484K mutation was among several mutations selected via in vitro evolution to affinity-maturate the RBD for enhanced ACE2 binding, demonstrating a clear role for increasing ACE2 binding affinity. 2021 Cell reports Discussion SARS_CoV_2 E484K 20 25 RBD 120 123 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Our analyses make use of trimeric HexaPro-stabilized S protein ectodomain constructs, which differ from native S protein trimers by the addition of six stabilizing proline mutations (F817P, A892P, A899P, A942P, K968P, and V969P) and the transmembrane domain replaced with a trimerization motif. 2021 Cell reports Discussion SARS_CoV_2 A892P;A899P;A942P;K968P;V969P;F817P 190;197;204;211;222;183 195;202;209;216;227;188 S;S 53;111 54;112 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Our described effects on ACE2 binding and antibody evasion imparted by VoC/VoI RBD mutations are in agreement with recent reports, with the exception of the enhanced ACE2 affinity conferred by E484K. 2021 Cell reports Discussion SARS_CoV_2 E484K 193 198 RBD 79 82 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Our results demonstrate that individual mutations may be classified as resulting in (1) increased RBD-ACE2 affinity (N501Y), (2) reduced ACE2 affinity and reduced antibody binding (K417N/T), or (3) a simultaneous increase in ACE2 affinity and reduced antibody binding (E484K, L452R). 2021 Cell reports Discussion SARS_CoV_2 L452R;E484K;K417N;K417T;N501Y 276;269;181;181;117 281;274;188;188;122 RBD 98 101 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Recent reports have suggested that the E484K mutation may enhance ACE2 binding via increasing electrostatic complementarity between ACE2 and the RBD, and the structures reported here are consistent with that hypothesis. 2021 Cell reports Discussion SARS_CoV_2 E484K 39 44 RBD 145 148 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. Several studies have reported conflicting data surrounding the effect of E484K on ACE2 binding, where both decreased and increased affinities are observed. 2021 Cell reports Discussion SARS_CoV_2 E484K 73 78 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. The combination of enhanced intermolecular interactions due to the concomitant repositioning of H34 and Q493 in the D614G + N501Y + E484K-ACE2 complex provides structural rationale for the increased ACE2 binding affinity relative to the D614G + N501Y spike. 2021 Cell reports Discussion SARS_CoV_2 D614G;D614G;E484K;N501Y;N501Y 116;237;132;124;245 121;242;137;129;250 S 251 256 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. The combination of the L452R mutation with either Beta or Gamma variant RBD mutations (D614G + N501Y + E484K + K417N/T) did not further increase ACE2 affinity. 2021 Cell reports Discussion SARS_CoV_2 E484K;K417N;K417T;L452R;N501Y;D614G 103;111;111;23;95;87 108;118;118;28;100;92 RBD 72 75 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. The mechanism of H34 rotamer stabilization in response to the E484K mutation remains unclear at present, although the repositioning of Q493 in this structure permits the formation of an intermolecular hydrogen bond with the main chain carbonyl of H34. 2021 Cell reports Discussion SARS_CoV_2 E484K 62 67 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. The S protein-ACE2 BLI study presented here produced modest (0.63-6.69) fold changes in binding for the RBD mutants relative to wild-type (D614G) S protein and may not reflect absolute quantitative changes within the context of live virus infections. 2021 Cell reports Discussion SARS_CoV_2 D614G 139 144 RBD;S;S 104;4;146 107;5;147 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. The structural basis for the observed discrepancies in ACE2 binding between the K417T and K417N mutations remains unclear. 2021 Cell reports Discussion SARS_CoV_2 K417N;K417T 90;80 95;85 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. This may be explained by electrostatic complementarity effects; namely, E484K already introduces complementary electropositivity near the electronegative site on ACE2 (centered at residues E35 and K31), so the addition of further electropositivity at the more distal L452 position (by the addition of L452R) likely does not additionally enhance the S protein-ACE2 electrostatic complementarity. 2021 Cell reports Discussion SARS_CoV_2 E484K;L452R 72;301 77;306 S 349 350 34914928 Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding. We additionally generated novel combinations of RBD mutations by introducing L452R into B.1.351 and P.1 constructs. 2021 Cell reports Discussion SARS_CoV_2 L452R 77 82 RBD 48 51 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Data suggest that N501Y mutant RDB gains few pi-pi stacking and pi-cation interactions during antibody recognition which accounts for less reduction in binding affinity for this mutant with B38 mAB. 2022 International immunopharmacology Discussion SARS_CoV_2 N501Y 18 23 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. However, the E484K mutation diminishes its interaction with Bamlanivimab in vitro. 2022 International immunopharmacology Discussion SARS_CoV_2 E484K 13 18 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. In addition, N501Y mutant lose several additional hydrogen bonding interactions with the B38 mAB. 2022 International immunopharmacology Discussion SARS_CoV_2 N501Y 13 18 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Not only the interaction pattern, but also the N501Y mutation allows stabilization and close packing of the RBD with ACE2 interface. 2022 International immunopharmacology Discussion SARS_CoV_2 N501Y 47 52 RBD 108 111 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. On the other hand, how the E484K mutation alters the ACE2 recognition is yet to be understood at the structural level. 2022 International immunopharmacology Discussion SARS_CoV_2 E484K 27 32 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Previous modeling and simulation studies showed contradicting results for N501Y mutant on ACE2 recognition. 2022 International immunopharmacology Discussion SARS_CoV_2 N501Y 74 79 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Recent data suggest that N501Y mutation does not significantly alter the binding affinity with Bamlanivimab. 2022 International immunopharmacology Discussion SARS_CoV_2 N501Y 25 30 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. recently evaluated the susceptibility of the 28 pseudoviruses expressing many spike single and multiple variations to neutralization by 12 mAbs (11 of them are anti-RBD) and observed that the E484K mutation is resistant to class II mAbs, while in combination with K417N and N501Y it showed resistance to class I and II mAbs. 2022 International immunopharmacology Discussion SARS_CoV_2 E484K;K417N;N501Y 192;264;274 197;269;279 S;RBD 78;165 83;168 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Results obtained from this study provide crucial insight into the efficacy of therapeutic mAbs on SARS-CoV2 variants harboring the E484K and N501Y mutations. 2022 International immunopharmacology Discussion SARS_CoV_2 E484K;N501Y 131;141 136;146 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The E484K mutant RBD loses all the pi-cation interactions in addition to the loss of several hydrogen-bonding interactions with the B38 mAb. 2022 International immunopharmacology Discussion SARS_CoV_2 E484K 4 9 RBD 17 20 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The extensive free energy simulation performed here complements the experimental data and suggests 21 kJ/mol enhancement in ACE2 binding free energy over the wild-type RBD for N501Y mutant. 2022 International immunopharmacology Discussion SARS_CoV_2 N501Y 176 181 RBD 168 171 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The extensive simulation and free energy data suggest that the E484K mutation showed the highest reduction in binding affinity, while N501Y showed a moderate reduction in binding affinity. 2022 International immunopharmacology Discussion SARS_CoV_2 E484K;N501Y 63;134 68;139 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The extensive simulations also reveal that the N501Y mutations change the local interactions involving pi stacking interaction between Tyr501 of RBD and Tyr41 of ACE2. 2022 International immunopharmacology Discussion SARS_CoV_2 N501Y 47 52 RBD 145 148 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The Phe486 of RBD creates a new pi-pi stacking interaction with Tyr83 of ACE2, which is also present in the N501Y RBD-ACE2 complex. 2022 International immunopharmacology Discussion SARS_CoV_2 N501Y 108 113 RBD;RBD 14;114 17;117 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The present study explores the effect of two critical mutations, E484K and N501Y, observed in few recently emerging variants of concern of SARS-CoV2 on host receptor recognition and immune invasion. 2022 International immunopharmacology Discussion SARS_CoV_2 E484K;N501Y 65;75 70;80 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. The structural insights into the loss of epitopic potential of spike RBM upon E484k and N501Y mutation provide a crucial guideline for future therapeutic antibody designing against SARS-CoV2 variants of concerns. 2022 International immunopharmacology Discussion SARS_CoV_2 N501Y 88 93 S 63 68 34915409 E484K and N501Y SARS-CoV 2 spike mutants Increase ACE2 recognition but reduce affinity for neutralizing antibody. Thus it is important to evaluate the effect of both E484K and N501Y mutations on mAbs recognition, particularly against anti-RBD mAbs. 2022 International immunopharmacology Discussion SARS_CoV_2 E484K;N501Y 52;62 57;67 RBD 125 128 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. A total of eight bases in the viral RNA sequence were mutated (referred to as: Gene Bank ID: MW301121) as follows: C241T, C313T, C3037T, C14408T, A23403G, and GGG28881AAC. 2021 Frontiers in medicine Discussion SARS_CoV_2 A23403G;C14408T;C241T;C3037T;C313T;G28881A;G28881C 146;137;115;129;122;159;159 153;144;120;135;127;170;170 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. Although it has been found that SARS-CoV-2 with the D614G mutation in the spike protein can replicate and spread faster than strains without this mutation, interestingly, the P323L mutation has been reported to co-evolve with D614G worldwide, this adaptation of the virus might strengthen SARS-CoV-2 G614 strain replication rates and infectivity. 2021 Frontiers in medicine Discussion SARS_CoV_2 D614G;D614G;P323L 52;226;175 57;231;180 S 74 79 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. In summary, we sequenced and reported the first case of mutations in the genes encoding the spike (D614G) and Nsp12 (P323L) proteins of SARS-CoV-2 in Sichuan Province, China. 2021 Frontiers in medicine Discussion SARS_CoV_2 D614G;P323L 99;117 104;122 S;Nsp12 92;110 97;115 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. Siqi suggested that R203K and G204R mutations could change viral protein structure, binding affinity, and hot spots of the interface, thereby impact on SARS-CoV-2 transmission, diagnosis, and treatment of COVID-19. 2021 Frontiers in medicine Discussion SARS_CoV_2 G204R;R203K 30;20 35;25 COVID-19 205 213 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. These changes translated to four amino acid changes in three proteins: spike (D614G), Nsp12 (P323L), and N protein (R203K and G204R). 2021 Frontiers in medicine Discussion SARS_CoV_2 G204R;D614G;P323L;R203K 126;78;93;116 131;83;98;121 S;Nsp12;N 71;86;105 76;91;106 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. This basically coincides with the time the carrier in our study returned to China, indicating that the SARS-CoV-2 strain introduced to China was originated from Spain, although Spain may not be the first country where the D614G mutation was discovered. 2021 Frontiers in medicine Discussion SARS_CoV_2 D614G 222 227 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. This study showed that from March 12 onwards, the infection caused by SARS-CoV-2 in China could be divided into two parts: the local clade based on Wuhan native sequences and the main clade formed by the D614G mutation and many other different clades. 2021 Frontiers in medicine Discussion SARS_CoV_2 D614G 204 209 34917639 Case Report: Genomic Characteristics of the First Known Case of SARS-CoV-2 Imported From Spain to Sichuan, China. We determined the Sichuan-2020 sequence belongs to haplogroup A2a4 (diagnostic variants: C241T-C3037T-C14408T-A23403G plus characteristic MNP: GGG28881AAC) according to the haplogroup nomenclature of SARS-CoV-2 clades by Gomez-Carballa et al. 2021 Frontiers in medicine Discussion SARS_CoV_2 C241T;G28881A;G28881C;A23403G;C14408T;C3037T 89;143;143;110;102;95 94;154;154;117;109;101 34920116 Zoonotic spill-over of SARS-CoV-2: mink-adapted virus in humans. In an isolate obtained from an asymptomatic farm employee testing positive for SARS-CoV-2, we found four distinguishing mutations in the S gene that gave rise to the mink-adapted variant (G75V, M177T, Y453F, and C1247F) and others. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 C1247F;M177T;Y453F;G75V 212;194;201;188 218;199;206;192 S 137 138 34920116 Zoonotic spill-over of SARS-CoV-2: mink-adapted virus in humans. These new changes include the Y453F mutation, which was previously reported to have emerged in minks during serial passages (e.g., in Denmark and recently Lithuania), and a novel mutation that is not present in any global SARS-CoV-2 isolate, which truncates ORF 7b at position L22. 2022 Clinical microbiology and infection Discussion SARS_CoV_2 Y453F 30 35 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. A significant portion of this is driven by the activation of a public antibody response to N501Y through IgVH4-39 (6/11 N501Y specific mAbs), and the highly similar IgVH4-30 (1/11). 2022 Cell host & microbe Discussion SARS_CoV_2 N501Y;N501Y 91;120 96;125 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Delta differs from Beta by 5 amino acids in the RBD (K417, L452, T478, E484, N501), while Beta and Gamma are antigenically close (1/27 mAbs KO), finally Alpha, which contains the single N501Y mutation, occupies an intermediate position (5/27 mAbs KO). 2022 Cell host & microbe Discussion SARS_CoV_2 N501Y 186 191 RBD 48 51 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. Following Beta infection, there is a marked shift in the profile of the antibody response compared with infection with early pandemic strains (Figures 3H and 3I), with many potent mAbs picking out the three RBD amino acid changes found in Beta; K417N (3/27 mAbs), E484K (6/27 mAbs), and especially N501Y (11/27 mAbs). 2022 Cell host & microbe Discussion SARS_CoV_2 E484K;K417N;N501Y 264;245;298 269;250;303 RBD 207 210 34921776 The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants. This antibody is specific for the Beta variant, and the Fab/NTD complex structure shows how this specificity is achieved, the three-residue deletion in Beta (Delta242-244) causes a conformation change that impacts on the supersite and will likely cause more generalized escape from supersite binders than the individual amino acid changes also found in Beta NTD (D80A, D215G, and R246F). 2022 Cell host & microbe Discussion SARS_CoV_2 D215G;R246F;D80A 369;380;363 374;385;367 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. An interaction analysis revealed that the number of hydrogen bonds and salt bridges (except E341D) also increased in these mutants compared to those in WT (Figures 2-4). 2021 Frontiers in microbiology Discussion SARS_CoV_2 E341D 92 97 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. It was observed that the mutations, in particular Q88H, have a higher binding affinity than WT and even other mutants (Table 1). 2021 Frontiers in microbiology Discussion SARS_CoV_2 Q88H 50 54 34925297 Structural Analysis on the Severe Acute Respiratory Syndrome Coronavirus 2 Non-structural Protein 13 Mutants Revealed Altered Bonding Network With TANK Binding Kinase 1 to Evade Host Immune System. Similarly, the Q88H exhibited the least fluctuation among all the complexes, except in the region between 480 and 550 (Figure 7). 2021 Frontiers in microbiology Discussion SARS_CoV_2 Q88H 15 19 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. For the Alpha (B.1.1.7) and Beta (B.1.351) variants, the del 69-70, del 144, and del 242-244 deletions in NTD and the K417N/T, E484K, and N501Y mutations in RBD have been shown to increase ACE2 binding affinity and evade antibody-mediated immunity. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y 127;118;118;138 132;125;125;143 RBD 157 160 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. It is also possible that the glycan-masking R158N/Y160T in the NTD interacts spatially with the RBD of another S1 monomer to affect the RBD up and down conformational structures. 2021 Frontiers in immunology Discussion SARS_CoV_2 R158N;Y160T 44;50 49;55 RBD;RBD 96;136 99;139 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. It is possible that the glycan-masking Ad-S-R158N/Y160T site which is nearby the N3 loop on NTD ( Supplementary Figure 1 ) can enhance targeting these epitopes to elicit neutralizing antibodies to block the L-SIGN/DC-SIGN receptor binding and/or the interaction between the L-SIGN/DC-SIGN lectin co-receptor with the ACE2 receptor binding for SARS-CoV-2 infection. 2021 Frontiers in immunology Discussion SARS_CoV_2 Y160T;R158N 50;44 55;49 S 42 43 COVID-19 343 363 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. It is possible that the refocused antibodies using the glycan-masking Ad-S-R158N/Y160T antigen may target the NTD neutralizing epitopes in the N3 and N5 loops as recently reported. 2021 Frontiers in immunology Discussion SARS_CoV_2 Y160T;R158N 81;75 86;80 S 73 74 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Only the glycan-masking Ad-S-F135N/N137T and Ad-S-R158N/Y160T in NTD were found to increase the neutralization titers against the Delta (B.1.617.2) variant ( Figure 6D ). 2021 Frontiers in immunology Discussion SARS_CoV_2 N137T;Y160T;F135N;R158N 35;56;29;50 40;61;34;55 S;S 27;48 28;49 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Our present findings demonstrated that the glycan-masking Ad-S-R158N/Y160T in NTD resulted in a 2.8-fold, 6.5-fold, and 4.6-fold increase, respectively, in the IC-50 titers against the Alpha (B.1.1.7), Beta (B.1.351) and Delta (B.1.617.2) variants, respectively. 2021 Frontiers in immunology Discussion SARS_CoV_2 Y160T;R158N 69;63 74;68 S 61 62 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Our results showed that the glycan-masking Ad-S-R158N/Y160T at the N3 loop in the NTD and the glycan-masking Ad-S-N354/K356T at the C-3 loop in the RBD ( Supplementary Figure 1 ) elicited a potent neutralizing antibody response against the Wuhan-Hu-1 ancestral strain ( Figure 3 ). 2021 Frontiers in immunology Discussion SARS_CoV_2 K356T;Y160T;R158N 119;54;48 124;59;53 RBD;S;S 148;46;112 151;47;113 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The glycan-masking Ad-S-D428N in RBD resulted in a 3.0-fold and 2.0-fold increase, respectively, in the IC-50 NT titer against the Alpha (B.1.1.7) and Beta (B.1.351) variants. 2021 Frontiers in immunology Discussion SARS_CoV_2 D428N 24 29 RBD;S 33;22 36;23 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The glycan-masking Ad-S-D428N was nearby the K417N mutation of the Beta (B.1.351) variant in the C7 loop on RBD ( Supplementary Figure 1 ). 2021 Frontiers in immunology Discussion SARS_CoV_2 K417N;D428N 45;24 50;29 RBD;S 108;22 111;23 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The glycan-masking Ad-S-R158N/Y160T site is close to the del 156-157 of the Delta (B.1.617.2) variant and the del 143 and 144V mutation of the Alpha (B.1.1.7) in the N3 loop on NTD ( Supplementary Figure 1 ). 2021 Frontiers in immunology Discussion SARS_CoV_2 Y160T;R158N 30;24 35;29 S 22 23 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. The increased IC-50 NT titers against the Wuhan-Hu-1 ancestral strain by the glycan-masking Ad-S-R158N/Y160T-immunized group correlated with the increased neutralization titers against the Alpha (B.1.1.7), Beta (B.1.351) and Delta (B.1.617.2) variant ( Figures 4 - 6 ). 2021 Frontiers in immunology Discussion SARS_CoV_2 Y160T;R158N 103;97 108;102 S 95 96 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Therefore, only the glycan-masking Ad-S-R158N/Y160T in NTD elicited broadly neutralizing antibody titers against Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2) variants. 2021 Frontiers in immunology Discussion SARS_CoV_2 Y160T;R158N 46;40 51;45 S 38 39 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. Thus, there is a need for further characterization of these glycan-masking mutants, particularly Ad-S-R158N/Y160T and Ad-S-D428N expressed S proteins. 2021 Frontiers in immunology Discussion SARS_CoV_2 Y160T;D428N;R158N 108;123;102 113;128;107 S;S;S 100;121;139 101;122;140 34925381 Glycan Masking of Epitopes in the NTD and RBD of the Spike Protein Elicits Broadly Neutralizing Antibodies Against SARS-CoV-2 Variants. We introduced seven separate N-linked glycosylation sites into the S glycoprotein, S-F135N/N137T, S-R158N/Y160T, Ad-S- N354/K356T, S-N370/A372T, Ad-S-G413N, Ad-S-D428N and S-H519N/P521T, in the NTD and RBD. 2021 Frontiers in immunology Discussion SARS_CoV_2 A372T;K356T;N137T;P521T;Y160T;D428N;F135N;G413N;H519N;R158N 138;124;91;180;106;162;85;150;174;100 143;129;96;185;111;167;90;155;179;105 S;RBD;N;S;S;S;S;S;S;S 67;202;29;83;98;116;131;148;160;172 81;205;30;84;99;117;132;149;161;173 34931119 Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences. Identical binding energies for engineered-ACE2/wild-type-RBD and engineered-ACE2/mutant-RBD complexes reveal that any loss of stabilizing interaction, due to the N501Y substitution, is compensated with novel and equivalent interactions. 2022 International journal of peptide research and therapeutics Discussion SARS_CoV_2 N501Y 162 167 RBD;RBD 57;88 60;91 34931119 Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences. The interactions between the engineered ACE2 and mutant spike protein showed that the N501Y substitution has made structural changes within the RBD and, by extent RBM of the mutant spike protein. 2022 International journal of peptide research and therapeutics Discussion SARS_CoV_2 N501Y 86 91 S;S;RBD 56;181;144 61;186;147 34931119 Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences. The N501Y substitution is the only mutation within the RBD region of the spike protein. 2022 International journal of peptide research and therapeutics Discussion SARS_CoV_2 N501Y 4 9 S;RBD 73;55 78;58 34931119 Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences. Therefore, the structural changes enforced by all ten mutations of the spike protein, compensate for the loss of a hydrogen bond from N501Y substitution. 2022 International journal of peptide research and therapeutics Discussion SARS_CoV_2 N501Y 134 139 S 71 76 34931119 Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences. They also confirmed the key role of N501Y substitution in bending affinity enhancement. 2022 International journal of peptide research and therapeutics Discussion SARS_CoV_2 N501Y 36 41 34931119 Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences. They have demonstrated that N501Y substitution introduces a pi-pi interaction that enhances RBD binding to ACE2 receptor. 2022 International journal of peptide research and therapeutics Discussion SARS_CoV_2 N501Y 28 33 RBD 92 95 34931119 Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences. They have shown that the P681H mutation may increase the spike cleavage by furin-like proteases. 2022 International journal of peptide research and therapeutics Discussion SARS_CoV_2 P681H 25 30 S 57 62 34931119 Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences. We believe that the P681H mutation could be one of the contributing factors to this change. 2022 International journal of peptide research and therapeutics Discussion SARS_CoV_2 P681H 20 25 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. According to several studies, the L18F mutation, also located in the S glycoprotein and present in 16 of our samples, apparently gives a replicative advantage to the Alpha, Beta, and Gamma lineages. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 L18F 34 38 S 69 83 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. Additionally, R203K is within the top five in the United States (top three in the world); G204R ranks in the top six in the United States (top four in the world). 2022 Infection, genetics and evolution Discussion SARS_CoV_2 G204R;R203K 90;14 95;19 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. All of our samples contain the Spike glycoprotein mutation D614G. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 59 64 S 31 49 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. As previously described, R203K mutation may not affect protein function. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 R203K 25 30 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. However, mutation G204R seems to alter protein folding and eventually lead to a functional impact (R.). 2022 Infection, genetics and evolution Discussion SARS_CoV_2 G204R 18 23 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. In our study we found the E484K mutation in a single sample taken in December 2020 from a case with the B.1 lineage, parental lineage of B.1.111. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 26 31 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. Of those, we reported here the following four: Q57H on ORF3a, and R203K, R203R, G204R on N gene. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 G204R;Q57H;R203K;R203R 80;47;66;73 85;51;71;78 ORF3a;N 55;89 60;90 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. Q57H mutation makes the protein unstable, altering apoptosis and, as a result, increasing the viral load in the host cell. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 Q57H 0 4 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. Recently, new evidence from Colombian National Institute of Health, has shown that the mutation E484K is becoming associated with this lineage. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 96 101 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. The finding of E484K is relevant since this mutation has been described in several VOC and VOI, which WHO labeled as Alpha, Beta, Eta, Gamma, and Iota. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 15 20 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. The frequency of Q57H hotspot mutation on ORF3a has been rated among the top three in the United States (top six around the world). 2022 Infection, genetics and evolution Discussion SARS_CoV_2 Q57H 17 21 ORF3a 42 47 34933126 Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia. Three of them, R203K, R203R, and G204R, co-existed in 72 samples, similar to previous reports around the world, suggesting a linkage disequilibrium, which makes functional inferences difficult. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 G204R;R203K;R203R 33;15;22 38;20;27 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Alpha and wt-S614G exhibited similar replication and transmission in hamsters, a model with very high susceptibility and replication efficacy, in which the impact of a marginally fitter SARS-CoV-2 variant may not become apparent. 2022 Nature Discussion SARS_CoV_2 S614G 13 18 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Although the rate of transmission was not high overall (3 out of 8 pairs in ferrets, and 4 out of 8 pairs in hACE2-K18Tg mice), the almost exclusive transmission of Alpha relative to wt-S614G mirrored increased transmission of Alpha in the human population; Alpha has been responsible for more than 90% of infections in most countries in Europe. 2022 Nature Discussion SARS_CoV_2 S614G 186 191 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Because SARS-CoV-2 replicates to lower levels in ferrets and hACE2-KI mice, the inability to detect wt-S614G in some samples from inoculated animals also reflects the limit of detection of the assays using PCR with reverse transcription (RT-PCR) (approximately 103 gc ml-1). 2022 Nature Discussion SARS_CoV_2 S614G 103 108 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Beta showed a higher binding affinity for human ACE2 than its progenitor wt-S614G and an equal level of replication to Alpha and wt-S614G in single infections of AEC cultures and in hACE2-KI mice. 2022 Nature Discussion SARS_CoV_2 S614G;S614G 76;132 81;137 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Here we provide experimental evidence that SARS-CoV-2 Alpha has a clear replication advantage over wt-S614G in ferrets and in two humanized mouse models. 2022 Nature Discussion SARS_CoV_2 S614G 102 107 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. However, Beta replication was outcompeted in direct competition with wt-S614G in vitro and in hACE2-KI mice. 2022 Nature Discussion SARS_CoV_2 S614G 72 77 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. In hACE2-KI mice, higher genome copies and/or titres of Alpha and wt-SAlpha compared with wt-S614G were found in the URT (oropharynx and nose) and olfactory bulb. 2022 Nature Discussion SARS_CoV_2 S614G 93 98 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. In hamsters, wt-S614G and Alpha also outcompeted Beta in relation to replication and transmission to contact animals, in which Beta was outnumbered by one or two orders of magnitude. 2022 Nature Discussion SARS_CoV_2 S614G 16 21 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Increased replication and transmission of wt-SAlpha over wt-S614G were also evident in hACE2-K18Tg mice. 2022 Nature Discussion SARS_CoV_2 S614G 60 65 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Moreover, Alpha was exclusively transmitted to contact animals in competition experiments, in which ferrets and hACE2-K18Tg mice were inoculated with mixtures of Alpha and wt-S614G. 2022 Nature Discussion SARS_CoV_2 S614G 175 180 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. The hamster model might thus resemble the human superspreader scenario, since there is no clear indication of a specific predominance in transmission between two SARS-CoV-2 variants with high fitness levels, such as wt-S614G and Alpha. 2022 Nature Discussion SARS_CoV_2 S614G 219 224 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. Transmission events are rare in mice; however, we observed transmission of Alpha and wt-SAlpha in 50% of the contact hACE2-K18Tg mice and no detection of wt-S614G in any contact mouse. 2022 Nature Discussion SARS_CoV_2 S614G 157 162 34937050 Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta. We have shown that the molecular mechanism underlying the fitness advantage of Alpha in vivo is largely dependent on a few changes in S, including three amino acid deletions (H69, V70 and Y144) and six substitutions (N501Y, A570D, P681H, T716I, S982A and D1118H). 2022 Nature Discussion SARS_CoV_2 A570D;D1118H;P681H;S982A;T716I;N501Y 224;255;231;245;238;217 229;261;236;250;243;222 S 134 135 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. To further differentiate Alpha, Beta, Gamma, and Mu, other mutation sites in the Spike protein like 69-70 deletion or 144 deletion, 242-244 deletion or K417N, R190S or K417T, T95I or R346K can be detected respectively. 2021 PloS one Discussion SARS_CoV_2 K417N;K417T;R190S;R346K;T95I 152;168;159;183;175 157;173;164;188;179 S 81 86 34941928 Chimeric crRNA improves CRISPR-Cas12a specificity in the N501Y mutation detection of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2. We report for the first time that chimeric crRNA can be used to efficiently differentiate N501Y of Alpha, Beta, Gamma, and Mu variants of SARS-CoV-2 from the wild type and other variants. 2021 PloS one Discussion SARS_CoV_2 N501Y 90 95 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. In addition, A105V-infected patients had a lower viral load and increased death rates despite presenting none or fewer morbidities compared to patients lacking this mutation, suggesting increased virulence of A105V mutation. 2021 Biology Discussion SARS_CoV_2 A105V;A105V 13;209 18;214 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. In this study, we applied computational analyses via molecular dynamics simulations of SARS-CoV-2 accessory protein ORF7a mutation, A105V, which was identified as being responsible for the severe clinical form of COVID-19 disease in a set of Romanian patients, suggesting a potential gain-of-function role of this protein. 2021 Biology Discussion SARS_CoV_2 A105V 132 137 ORF7a 116 121 COVID-19 213 229 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. MD analyses (per-residue RMSF) on WT, mutant A105V, and mutant A106V showed that the A105V mutation alters the protein in a specific way, changing the conformational landscape and likely influencing its atomistic interaction potential. 2021 Biology Discussion SARS_CoV_2 A105V;A105V;A106V 45;85;63 50;90;68 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. ORF7a binds to several cellular receptors and interactions partners, and we hypothesize that A105V mutation translates in an ORF7a protein with differential binding affinities, which may lead to a different interaction landscape and more adverse clinical outcome. 2021 Biology Discussion SARS_CoV_2 A105V 93 98 ORF7a;ORF7a 0;125 5;130 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. Our clinical data showed that, compared to controls, patients infected with A105V mutation developed a severe form of the disease, which was associated with higher systemic inflammation and increased damage to the lungs. 2021 Biology Discussion SARS_CoV_2 A105V 76 81 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. The beta-sheet placed at the exterior of the protein core is formed by residues in position 39-56, but also the adjacent 26-30 loop, which undergo the lowest RMSF variance and are highly impacted through allosteric effects of A105V mutation. 2021 Biology Discussion SARS_CoV_2 A105V 226 231 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. The RMSF standard deviation of A105V simulations in the protein core residues was low, reflecting a high structural stability that is suggestive of a highly deterministic behavior and a subtle allosteric effect of the mutation. 2021 Biology Discussion SARS_CoV_2 A105V 31 36 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. These findings corroborate with generally low, but highly variable rates of ORF7a A105V mutations in overall worldwide sequences processed by CoV-GLUE platform (Figure 5), which amounted to 0.12% of all sequences in late 2020. 2021 Biology Discussion SARS_CoV_2 A105V 82 87 ORF7a 76 81 34943191 A Conservative Replacement in the Transmembrane Domain of SARS-CoV-2 ORF7a as a Putative Risk Factor in COVID-19. This may explain the behavior of A105V mutation in causing more severe clinical symptoms even in patients with fewer comorbidities and lower viral load. 2021 Biology Discussion SARS_CoV_2 A105V 33 38 34943523 Low Represented Mutation Clustering in SARS-CoV-2 B.1.1.7 Sublineage Group with Synonymous Mutations in the E Gene. A clear link between a mutation in the E gene and three SNPs (S137L, N439K, and A156S) emerged from surveillance in Eastern Sicily. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 A156S;N439K;S137L 80;69;62 85;74;67 E 39 40 34943523 Low Represented Mutation Clustering in SARS-CoV-2 B.1.1.7 Sublineage Group with Synonymous Mutations in the E Gene. In this sense, unfortunately, there are not many NGS data coming from this area, which is why the cluster composed of S137L, N439K, and A156S is little expressed when comparing data against Northern Europe. 2021 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 A156S;N439K;S137L 136;125;118 141;130;123 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. Although the number of cases is small, it is possible that N501YV-infected patients had characteristics that led to more apparent symptoms. 2021 Journal of clinical medicine Discussion SARS_CoV_2 N501Y 59 64 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. As mentioned, the prevalence of VOCs in Japan during the study period indicates that N501YV-PCR positive strain detected in this study could be thought to be a proxy for the B.1.1.7 lineage. 2021 Journal of clinical medicine Discussion SARS_CoV_2 N501Y 85 90 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. Hence, cases with mutations in other genomic regions may have been included in the N501Y group. 2021 Journal of clinical medicine Discussion SARS_CoV_2 N501Y 83 88 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. In the follow-up of four N501YV-infected patients who were asymptomatic at the time of diagnostic testing, two patients had a fever of over 38C within 0 or 1 day. 2021 Journal of clinical medicine Discussion SARS_CoV_2 N501Y 25 30 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. Prior literature also reported that fever was significantly associated with the N501Y mutant strain in France and the UK. 2021 Journal of clinical medicine Discussion SARS_CoV_2 N501Y 80 85 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. Third, the detection of the N501Y mutation was done by specific real-time RT-PCR testing and not by whole genome analysis. 2021 Journal of clinical medicine Discussion SARS_CoV_2 N501Y 28 33 34945159 Clinical Characteristics of Patients with SARS-CoV-2 N501Y Variants in General Practitioner Clinic in Japan. We add to the literature that fever of 38C or higher was found to be more frequent in those with the N501Y mutant strain. 2021 Journal of clinical medicine Discussion SARS_CoV_2 N501Y 101 106 34953513 Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a 16-week interval between doses. Plasma collected 3 weeks post second dose had significantly lower humoral activities:notably, neutralizing activity against D614G strain and some VOCs/VOIs compared to naive donors receiving the long interval. 2022 Cell host & microbe Discussion SARS_CoV_2 D614G 124 129 34955621 Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor. In the present study, we have investigated the binding interactions of native and three major mutant spike proteins-L452R, T478K and Y501Y to human ACE2 and provided plausible mechanisms of variations in the binding affinity using protein-protein docking and molecular dynamics simulation approaches. 2022 Journal of King Saud University. Science Discussion SARS_CoV_2 T478K;Y501Y;L452R 123;133;116 128;138;121 S 101 106 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. As the E484 residue is a key contact within the epitope of bamlanivimab, E484K and E484Q substitutions greatly attenuate binding of bamlanivimab; however, binding of etesevimab persists, due to its distinct binding epitope. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;E484Q 73;83 78;88 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. By using the drug tolerant E484Q/K spike-RBDs in this investigation, we may be underestimating the overall endogenous spike immune response. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;E484Q 27;27 34;34 S;S;RBD 35;118;41 40;123;45 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. The latter is a variant of concern and has two key mutations in the RBD of spike, E484K and the K417N, and can escape both bamlanivimab and etesevimab recognition and neutralization in vitro. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;K417N 82;96 87;101 S;RBD 75;68 80;71 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. Therefore, we examined changes in antibody titers against the Spike-RBD E484Q protein, in addition to titers against proteins that lie outside of the epitopes of both bamlanivimab and etesevimab (Spike-NTD and NCP). 2021 Frontiers in immunology Discussion SARS_CoV_2 E484Q 72 77 S;S;RBD 62;196;68 67;201;71 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. To assess the effects of mAb treatment on the spectrum of epitopes neutralized, we measured IC50 titers against Spike E484Q, Spike E484K, and the beta variant (B.1.351). 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;E484Q 131;118 136;123 S;S 112;125 117;130 34956222 Endogenous Antibody Responses to SARS-CoV-2 in Patients With Mild or Moderate COVID-19 Who Received Bamlanivimab Alone or Bamlanivimab and Etesevimab Together. We found that serum samples collected from patients who received bamlanivimab treatment were slightly less effective in neutralizing spike E484Q and beta variant compared with placebo (by a factor of 3.1 and 2.9, respectively). 2021 Frontiers in immunology Discussion SARS_CoV_2 E484Q 139 144 S 133 138 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. A previous study performed deep mutation scanning on SARS-CoV-2 identified N501T as a binding affinity enhancer. 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 N501T 75 80 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. By contrast, S432Y and N479M have the minimum binding-energy changes (DeltaDeltaDeltaG) of -1.686 kcal/mol and -1.42 kcal/mol, respectively. 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 N479M;S432Y 23;13 28;18 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. D614G and N501Y are mutations found in the Delta/B.1.617.2 variant of SARS-CoV-2 S protein. 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 N501Y;D614G 10;0 15;5 S 81 82 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. For example, missense mutation S432V on SARS-CoV-1 decreased the binding energy by -0.22 kcal/mol. 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 S432V 31 36 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. However, S432V has a neutral effect on its stability. 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 S432V 9 14 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. However, the Foldx predicted T487Y to weaken the binding affinity between the SARS-CoV-S RBD and hACE2. 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 T487Y 29 34 RBD;S 89;87 92;88 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Interestingly, D600G and T487Y destabilize SARS-CoV-1 S protein, while corresponding D614G and N501Y stabilize SARS-CoV-2 S protein. 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 D600G;D614G;N501Y;T487Y 15;85;95;25 20;90;100;30 S;S 54;122 55;123 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Interestingly, T487N decrease the binding affinity of SARS-CoV-1, while N501T increase the binding affinity of SARS-CoV-2 (Table 1). 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 N501T;T487N 72;15 77;20 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. Meanwhile, on SARS-CoV-2 S RBD, the missense mutation V445S does not affect its binding affinity. 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 V445S 54 59 RBD;S 27;25 30;26 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. The mutation A430S destabilizes SARS-CoV-1 S protein, while the mutation S443A stabilizes SARS-CoV-2 S protein. 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 A430S;S443A 13;73 18;78 S;S 43;101 44;102 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. The top missense mutations decreasing binding affinity are T487Y, T487W, and G488P, with binding-energy changes (DeltaDeltaDeltaG) of 20.018 kcal/mol, 13.42 kcal/mol, and 15.921 kcal/mol, respectively. 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 G488P;T487W;T487Y 77;66;59 82;71;64 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. The two most destabilizing missense mutations are A430W and A430F. 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 A430F;A430W 60;50 65;55 34957216 Computational Saturation Mutagenesis of SARS-CoV-1 Spike Glycoprotein: Stability, Binding Affinity, and Comparison With SARS-CoV-2. The two most stabilizing missense mutations are G981W and T1059F (Figure 3B). 2021 Frontiers in molecular biosciences Discussion SARS_CoV_2 G981W;T1059F 48;58 53;64 34959053 Isolation of SARS-CoV-2 B.1.1.28.2 (P2) variant and pathogenicity comparison with D614G variant in hamster model. Reinfection cases have also been reported with E484K mutation. 2022 Journal of infection and public health Discussion SARS_CoV_2 E484K 47 52 34959053 Isolation of SARS-CoV-2 B.1.1.28.2 (P2) variant and pathogenicity comparison with D614G variant in hamster model. The characteristic spike mutations in P2 lineage are D614G, E484K and V1176F. 2022 Journal of infection and public health Discussion SARS_CoV_2 D614G;E484K;V1176F 53;60;70 58;65;76 S 19 24 34959053 Isolation of SARS-CoV-2 B.1.1.28.2 (P2) variant and pathogenicity comparison with D614G variant in hamster model. These mutations were reported in many VOCs and VOIs which are rapidly spreading worldwide and E484K substitution is known for immune evasion potential. 2022 Journal of infection and public health Discussion SARS_CoV_2 E484K 94 99 34960156 The Impact of Mutations on the Pathogenic and Antigenic Activity of SARS-CoV-2 during the First Wave of the COVID-19 Pandemic: A Comprehensive Immunoinformatics Analysis. A highly mutated amino acid was observed at the position D614G (50%) in the S protein and P323L (49%) in the RdRp protein. 2021 Vaccines Discussion SARS_CoV_2 D614G;P323L 57;90 62;95 RdRP;S 109;76 113;77 34960156 The Impact of Mutations on the Pathogenic and Antigenic Activity of SARS-CoV-2 during the First Wave of the COVID-19 Pandemic: A Comprehensive Immunoinformatics Analysis. Among these mutations, D614G is highly prevalent and associated with greater infectivity of SARS-CoV-2. 2021 Vaccines Discussion SARS_CoV_2 D614G 23 28 34960156 The Impact of Mutations on the Pathogenic and Antigenic Activity of SARS-CoV-2 during the First Wave of the COVID-19 Pandemic: A Comprehensive Immunoinformatics Analysis. Another highly prevalent mutation, P323L in RdRp, was found to be neutral (score = 2). 2021 Vaccines Discussion SARS_CoV_2 P323L 35 40 RdRP 44 48 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. As a result, Q675H mutation is likely to better promote spike S1 unit release and its interaction with human receptor ACE2. 2021 Viruses Discussion SARS_CoV_2 Q675H 13 18 S 56 61 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. At the time of their emergence, neither B.1.1.7 or B.1.617.2 lineage displayed the Q675H mutation. 2021 Viruses Discussion SARS_CoV_2 Q675H 83 88 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Concerning B.1.617.2 lineage, the number of sequences carrying Q675H spike mutation, grows together with the fraction of B.1.617.2 circulating globally. 2021 Viruses Discussion SARS_CoV_2 Q675H 63 68 S 69 74 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. From the end of January 2021 to the end of March 2021, the genomic surveillance program implemented by our laboratory in Brescia, Italy, led us to detect an increased number of SARS-CoV-2 wild-type sequences displaying a Q675H mutation within the polar region of the spike pocket for furin binding. 2021 Viruses Discussion SARS_CoV_2 Q675H 221 226 S 267 272 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Furthermore, B.1.617 lineage carries the P681R mutation in the furin cleavage site, which increases S1/S2 cleavability, thus enhancing the viral fusion to the host cell membrane. 2021 Viruses Discussion SARS_CoV_2 P681R 41 46 Membrane 169 177 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. However, here we underline the finding that, although at a low rate, Q675H spike mutation is described in all the VOCs and it is documented even when the prevalence of each VOC starts to decrease. 2021 Viruses Discussion SARS_CoV_2 Q675H 69 74 S 75 80 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Importantly, this conformation of Q675H has a higher binding affinity than the Q675 ones, since it presents a y-conformation with the three arginine residues alternatively arranged. 2021 Viruses Discussion SARS_CoV_2 Q675H 34 39 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. In particular, Q675H mutation forms an H-bonds network in the polar region delimiting the conformational space of the three arginines side-chain of the recognition motif and improves their proximity to the corresponding binding pockets of the furin. 2021 Viruses Discussion SARS_CoV_2 Q675H 15 20 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. In particular, we found Q675H mutants detected in our laboratory belonged to B.1 and B.1.177 lineages, and in the considered interval of time, they represented 40% of all the wild-type SARS-CoV-2 analyzed sequences. 2021 Viruses Discussion SARS_CoV_2 Q675H 24 29 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. In this study we predicted the effect of the Q675H mutation on the furin enzymatic activity. 2021 Viruses Discussion SARS_CoV_2 Q675H 45 50 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Indeed, similarly to SARS-CoV-2 Q675H mutants, the emergence and rapid spread of a new variant, defined in Nexstrain as 20C-US, was documented in Louisiana and New Mexico (USA). 2021 Viruses Discussion SARS_CoV_2 Q675H 32 37 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Notably, another mutation, the Q675K in the furin cleavage site has been reported, but its role in SARS-CoV-2 evolution still needs to be investigated. 2021 Viruses Discussion SARS_CoV_2 Q675K 31 36 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. On March 2021, we observed in Italy a dramatic decline of the Q675H mutation rate, because of the progressive establishment of B.1.1.7 lineage over any other circulating wild-type lineage. 2021 Viruses Discussion SARS_CoV_2 Q675H 62 67 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. On the other hand, the Q675H mutant is the only one to have also a P1-S1/P4-S4 conformation. 2021 Viruses Discussion SARS_CoV_2 Q675H 23 28 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. On the whole, our analysis suggests that SARS-CoV-2 Q675H spike mutation could enhance its availability to the furin proteolytic cleavage. 2021 Viruses Discussion SARS_CoV_2 Q675H 52 57 S 58 63 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Other studies are necessary to evaluate how the Q675H influences the activity of the other proprotein convertases involved in spike activation. 2021 Viruses Discussion SARS_CoV_2 Q675H 48 53 S 126 131 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Phylogenetic analysis suggest that Q675H mutation occurred by a homoplasy event, leading us to assume that it could be aimed to enhance viral fitness to the human host. 2021 Viruses Discussion SARS_CoV_2 Q675H 35 40 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. The description of Q675H spike mutation in all the VOC could highlight the homoplasy nature of Q675H spike mutation and that the histidine residues near the furin cleavage site could be relevant for SARS-CoV-2 evolution. 2021 Viruses Discussion SARS_CoV_2 Q675H;Q675H 19;95 24;100 S;S 25;101 30;106 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. The functional characterization of Q675H in silico showed that this mutation, located in the P11 position of the polar region of the furin cleavage site, facilitates the binding of the core region to the furin binding pocket. 2021 Viruses Discussion SARS_CoV_2 Q675H 35 40 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Then, the acquisition of Q675H mutation may lead to gain a fitness. 2021 Viruses Discussion SARS_CoV_2 Q675H 25 30 34960779 Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. This variant carries a series of mutations in SARS-CoV-2 genome, among which the spike substitution Q677H, highlighting the crucial role of histidine in the release of SARS-CoV-2 S1 and S2 units operated by furin. 2021 Viruses Discussion SARS_CoV_2 Q677H 100 105 S 81 86 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. For instance, the E484K mutation in the RBD notably described in the Beta and Gamma variants seems to confer resistance to the neutralizing capacity of fully vaccinated individuals. 2021 Viruses Discussion SARS_CoV_2 E484K 18 23 RBD 40 43 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. Interestingly, K417N, L452R, E484K, and E484Q are the mutations known to disrupt receptor-binding domain (RBD) binding capacity, making them more infectious by immune escape against the current vaccines. 2021 Viruses Discussion SARS_CoV_2 E484K;E484Q;K417N;L452R 29;40;15;22 34;45;20;27 RBD 106 109 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. Our pipeline does not allow the determination of the precise sub-lineage of Delta variant, because the differences detected in the S1 domain are not discriminant enough, with an exception for the AY.1 and AY.2 lineages, characterized by the K417N mutation. 2021 Viruses Discussion SARS_CoV_2 K417N 241 246 34960813 Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. The variant belonging to the lineage B1.617.2 was shown to be resistant to the mAb bamlanivimab due to the escape mutation L452R and was also less sensitive to sera from convalescent patients. 2021 Viruses Discussion SARS_CoV_2 L452R 123 128 34966387 A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. Crystal and cryo-EM structural analyses showed that P36-5D2 recognized a highly conserved epitope on RBD, which is accessible in both "up" and "down" conformations and able to withstand the mutated residues K417N, E484K, and N501Y that compromised many neutralizing mAbs, including some approved for EUA. 2021 Frontiers in immunology Discussion SARS_CoV_2 E484K;K417N;N501Y 214;207;225 219;212;230 RBD 101 104 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. A common feature of the Lambda, Delta, and Epsilon variants is a substitution in L452 of the SARS-CoV-2 S protein: the Lambda variant harbors the L452Q mutation, while the Delta and Epsilon variants possess the L452R mutation. 2022 Cell reports Discussion SARS_CoV_2 L452Q;L452R 146;211 151;216 S 104 105 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Because the epitope of COV2-2490 does not overlap the mutations in the NTD of Lambda S (G75V, T76I, and RSYLTPGD246-253N), these mutations would not directly affect the binding affinity of this antibody to S. 2022 Cell reports Discussion SARS_CoV_2 T76I;G75V 94;88 98;92 S;S 85;206 86;207 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Here, we demonstrated that the L452Q mutation increases viral infectivity. 2022 Cell reports Discussion SARS_CoV_2 L452Q 31 36 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. However, in the gain-of-function experiment based on the parental S (Figure 2H), the 3 mutations detected in the Lambda variant, RSYLTPGD246-253N, L452Q, and F490S, can lead to the resistance to vaccine sera. 2022 Cell reports Discussion SARS_CoV_2 F490S;L452Q 158;147 163;152 S 66 67 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. In addition to the aforementioned virological property of the Lambda S via the mutations in its NTD, we revealed that a mutation in its RBD, L452Q, confers 2 virological properties: increase in viral infectivity and evasion from the HLA-A24-restricted cellular immunity. 2022 Cell reports Discussion SARS_CoV_2 L452Q 141 146 RBD;S 136;69 139;70 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. In addition, the L452Q mutation allows evasion of HLA-A24-restricted cellular immunity. 2022 Cell reports Discussion SARS_CoV_2 L452Q 17 22 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. In this study, we demonstrated that 3 mutations, the RSYLTPGD246-253N, L452Q, and F490S mutations, confer resistance to vaccine-induced antiviral humoral immunity. 2022 Cell reports Discussion SARS_CoV_2 F490S;L452Q 82;71 87;76 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Moreover, the T76I and L452Q mutations contribute to enhanced viral infectivity. 2022 Cell reports Discussion SARS_CoV_2 L452Q;T76I 23;14 28;18 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Our investigations using pseudoviruses suggest at least 2 virological features of the S protein of the Lambda variant: increasing viral infectivity (by the T76I and L452Q mutations) and exhibiting resistance to antiviral immunity (by the RSYLTPGD246-253N, L452Q, and F490S mutations). 2022 Cell reports Discussion SARS_CoV_2 F490S;L452Q;L452Q;T76I 267;165;256;156 272;170;261;160 S 86 87 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. The gain-of-function experiment (Figure 2H) suggests the potential of the RSYLTPGD246-253N, L452Q, and F490S mutations to confer resistance to vaccine sera, when the backbone is parental S protein. 2022 Cell reports Discussion SARS_CoV_2 F490S;L452Q 103;92 108;97 S 187 188 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Therefore, it would be reasonable to assume that the L452Q mutation that emerged via the HLA-A24-mediated immune pressure and the acquisition of this mutation to evade HLA-A24-mediated cellular immunity may further contribute to the relatively higher prevalence of the Lambda variant in these countries. 2022 Cell reports Discussion SARS_CoV_2 L452Q 53 58 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. These are reminiscent of our recent study showing that the L452R mutation confers similar virological phenotypes. 2022 Cell reports Discussion SARS_CoV_2 L452R 59 64 34968415 The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Together with our previous observation that the L452R mutation enhances viral infectivity, these results strongly suggest that the relatively higher infectivity of the Lambda, Delta, and Epsilon variants is attributed to the L452Q/R mutation. 2022 Cell reports Discussion SARS_CoV_2 L452Q;L452R;L452R 225;225;48 232;232;53 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. And, in case of N501Y MT, where a substitution of Asparagine to Tyrosine was found in the binding motif of SpikeS1 RBD, which has increased binding affinity with its protein partner as shown by pyDOCKWEB server and ultimately leads to a stable virus-host relationship (Table S8). 2022 Computer methods and programs in biomedicine Discussion SARS_CoV_2 N501Y 16 21 S;RBD 107;115 112;118 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Binding affinity analysis indicated that V367F and V483A MTs binds to host ACE2 protein with maximum binding strength, thus contributing highly infectious activity. 2022 Computer methods and programs in biomedicine Discussion SARS_CoV_2 V367F;V483A 41;51 46;56 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. ED results suggested that, except for N501Y MT, all other MTs were had similar conformational subspace as with WT, while N501Y MT covered larger conformational space. 2022 Computer methods and programs in biomedicine Discussion SARS_CoV_2 N501Y;N501Y 38;121 43;126 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. In case of R408I MT, there is change in overall charge of protein residue (Arginine), which is mutated to the residues having a neutral charge (Isoleucine). 2022 Computer methods and programs in biomedicine Discussion SARS_CoV_2 R408I 11 16 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. In G476S MT, Glycine of WT residues is mutated to Serine which affects the overall flexibility of protein as Glycine is more flexible than Serine. 2022 Computer methods and programs in biomedicine Discussion SARS_CoV_2 G476S 3 8 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. In V367F MT, a nonpolar hydrophobic amino acid has aliphatic side chain (Valine) is mutated to an aromatic hydrophobic residue (Phenylalanine) that enhanced the structural stability of the spike protein, thus facilitating more efficient binding to the host ACE2 receptor as also shown by pyDOCKWEB server (Table S8). 2022 Computer methods and programs in biomedicine Discussion SARS_CoV_2 V367F 3 8 S 189 194 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. In V483A MT Valine, a large hydrophobic protein residue is mutated to Alanine, a small size hydrophobic residue that alters the overall dimension of the protein, thus help in increasing the binding affinity. 2022 Computer methods and programs in biomedicine Discussion SARS_CoV_2 V483A 3 8 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. P-p interaction results suggested that V367F and V483A MTs showed increased binding affinities predicted while R408I, G476S and N501Y MTs exhibited decreased binding affinities. 2022 Computer methods and programs in biomedicine Discussion SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 118;128;111;39;49 123;133;116;44;54 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. Qualities of generated mutant models were verified by inspecting the stereochemical and geometrical properties through different model validation tools and found that all MTs (V367F, R408I, G476S, V483A and N501Y) had good profiles of Ramachandran plots, acceptable scores of ProSA and QMEAN, similar to WT protein, implying that all MTs along with WT had better stereochemical and geometrical properties. 2022 Computer methods and programs in biomedicine Discussion SARS_CoV_2 G476S;N501Y;R408I;V483A;V367F 190;207;183;197;176 195;212;188;202;181 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. RIN results suggested that Tyrosine453 was an important residue in WT and V367F, R408I, G476S, and V483A MTs, while more than one amino acid had role in signalling in N501Y MT. 2022 Computer methods and programs in biomedicine Discussion SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 88;167;81;74;99 93;172;86;79;104 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. RMSD results suggested that WT as well as MT proteins displayed consistent behavior with higher RMSDs were found in V367F, R408I and V483A MTs as compared to WT, G476S and N501Y MTs. 2022 Computer methods and programs in biomedicine Discussion SARS_CoV_2 G476S;N501Y;R408I;V367F;V483A 162;172;123;116;133 167;177;128;121;138 34968787 Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. This led to a decrease in the stability and binding affinity of G476S MT, as noticed during MD simulation and p-p docking. 2022 Computer methods and programs in biomedicine Discussion SARS_CoV_2 G476S 64 69 34981057 SARS-CoV-2 Omicron neutralization by therapeutic antibodies, convalescent sera, and post-mRNA vaccine booster. Here, using the same lentiviral pseudovirus neutralization platform we measured the change in potency of 24 clinical-stage therapeutic antibodies against Omicron compared to WT (D614G) and compared neutralizing antibodies in sera from two well-characterized cohorts of subjects in prospective clinical studies. 2021 bioRxiv Discussion SARS_CoV_2 D614G 178 183 34982509 Engineered small extracellular vesicles displaying ACE2 variants on the surface protect against SARS-CoV-2 infection. Further, D614G S-containing pseudovirus and RBD triple-mutant S-containing pseudovirus exhibited reduced infectivity in the presence of sACE2-loaded sEVs, indicating that accumulated escape mutations of the S protein, which augmented its affinity for ACE2, failed to compromise the efficacy of ACE2-targeting therapeutics (Chan et al.,). 2022 Journal of extracellular vesicles Discussion SARS_CoV_2 D614G 9 14 RBD;S;S;S 44;15;62;207 47;16;63;208 34982509 Engineered small extracellular vesicles displaying ACE2 variants on the surface protect against SARS-CoV-2 infection. The infectivity of WT, D614G, Beta variant, and Delta variant mutant S-containing pseudovirus was compromised by sACE2.v1 and sACE2.v2 sEVs. 2022 Journal of extracellular vesicles Discussion SARS_CoV_2 D614G 23 28 S 69 70 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. A third-dose inoculation with a bivalent NP vaccine significantly boosted the nAb titers against the D614G and B.1.351 strains at almost the same level. 2022 Cell reports Discussion SARS_CoV_2 D614G 101 106 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Although our data support this claim, we show that, after initial prime-boost with the NP vaccine targeting D614G, the nAb titers for the D614G strain will eventually decrease, and the decrease of nAb titers for B.1.351 is even more significant. 2022 Cell reports Discussion SARS_CoV_2 D614G;D614G 108;138 113;143 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Given that SARS-CoV-2 variants with the E484K/Q mutant dominate in many regions of the world and that the bivalent vaccine has a potent capability to boost nAb titers against viral variants, we suggest that it is necessary to develop a bivalent NP vaccine targeting the early strain and B.1.351 strain, which could be sufficient for the current COVID-19 pandemic with the threat of 484K/Q mutants. 2022 Cell reports Discussion SARS_CoV_2 E484K;E484Q 40;40 47;47 COVID-19 345 353 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. In rhesus macaques receiving initial prime-boost inoculation of the D614G-specific NP vaccine, the nAbs for the D614G and viral variants eventually decreased. 2022 Cell reports Discussion SARS_CoV_2 D614G;D614G 68;112 73;117 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. In this study, we developed a bivalent D614G/B.1.351_RBD-NP vaccine to prevent infection with the early strain and viral variants harboring E484K/Q mutants. 2022 Cell reports Discussion SARS_CoV_2 D614G;E484K;E484Q 39;140;140 44;147;147 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Notably, the deterioration rate of the D614G nAb titer is slower after the third dose compared with that after the second dose, suggesting involvement of a stronger memory immune response. 2022 Cell reports Discussion SARS_CoV_2 D614G 39 44 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. Only the D614G/B.1.351_RBD-NP vaccine was evaluated as a third dose. 2022 Cell reports Discussion SARS_CoV_2 D614G 9 14 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The ability of D614G_RBD-NP or B.1.351_RBD-NP to boost immunity against the D614G and B.1.351 strains has not yet been assessed, although cross-protecting nAbs against the viral variants are expected because of the high levels of titers. 2022 Cell reports Discussion SARS_CoV_2 D614G;D614G 76;15 81;20 34990583 A bivalent nanoparticle vaccine exhibits potent cross-protection against the variants of SARS-CoV-2. The nAbs induced by this bivalent vaccine are quite high, and the protection from the authentic D614G and B.1.351 strains in hACE2 mice is complete. 2022 Cell reports Discussion SARS_CoV_2 D614G 96 101 34993157 Clinical, Virological, Immunological, and Genomic Characterization of Asymptomatic and Symptomatic Cases With SARS-CoV-2 Infection in India. It was observed in this study that the three symptomatic patients with high viral load, two of which had severe disease symptoms and died, were infected with the virus possessing the D614G mutation in the spike protein. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G 183 188 S 205 210 34993157 Clinical, Virological, Immunological, and Genomic Characterization of Asymptomatic and Symptomatic Cases With SARS-CoV-2 Infection in India. This also demonstrated that the D614G mutation is mostly associated with higher virus replication efficiency and severe SARS-CoV-2 infection. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G 32 37 COVID-19 120 140 34993157 Clinical, Virological, Immunological, and Genomic Characterization of Asymptomatic and Symptomatic Cases With SARS-CoV-2 Infection in India. This strengthens the previous hypothesis that infectivity rate and enhanced transmission of SARS-CoV-2 is associated with the D614G mutation. 2021 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G 126 131 34998405 Different decay of antibody response and VOC sensitivity in naive and previously infected subjects at 15 weeks following vaccination with BNT162b2. reported that the B.1.1.7 lineage (and B.1.525 lineage) bearing the N501Y single mutation in the RBD was robustly neutralized by vaccine-elicited antibodies from naive subjects, whereas neutralization of the B.351 and P.1 lineages was lower compared to that of the B.1 lineage, although robust. 2022 Journal of translational medicine Discussion SARS_CoV_2 N501Y 68 73 RBD 97 100 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Acquisition of the K417N and A222V mutations by Delta resulted in the emergence of AY.2, which is being associated with an upsurge in COVID-19 infections in the United States. 2022 Archives of virology Discussion SARS_CoV_2 A222V;K417N 29;19 34;24 COVID-19 134 142 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Apart from the mutations of concern described above, V382L (9/55, 16.4%) and N440K (4/55, 7.3%) substitutions were found in the 2021 sequences (Table 1). 2022 Archives of virology Discussion SARS_CoV_2 N440K;V382L 77;53 82;58 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. In in-vitro experiments, an increased binding affinity of the T478K mutant for the ACE2 receptor has been shown. 2022 Archives of virology Discussion SARS_CoV_2 T478K 62 67 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. In two different sequences, E484K was present without any change at position 452 (Table 2). 2022 Archives of virology Discussion SARS_CoV_2 E484K 28 33 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Interestingly, the L452R mutation was maintained. 2022 Archives of virology Discussion SARS_CoV_2 L452R 19 24 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Interestingly, two Indian strains (CD211295-MW969753, CD210761-MZ021503) had a combination of two substitutions, L18F and E484K. 2022 Archives of virology Discussion SARS_CoV_2 E484K;L18F 122;113 127;117 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. It is pertinent to note here that a recent increase in COVID-19 cases in New York, USA, was observed to be due to the introduction of B.1.243 lineage strain with P681H and T478K mutations. 2022 Archives of virology Discussion SARS_CoV_2 P681H;T478K 162;172 167;177 COVID-19 55 63 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. It seems that the spread of SARS-CoV-2 during the first wave of disease in India could be attributed to the replacement of clade L (original Wuhan strain) with clade G, characterized by the spike mutation D614G. 2022 Archives of virology Discussion SARS_CoV_2 D614G 205 210 S 190 195 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. It was shown that the proportion of genomes with the L18F mutation increased from 35% in September to 43% in October and to 52% in November 2020, suggesting that this mutation facilitates virus transmission. 2022 Archives of virology Discussion SARS_CoV_2 L18F 53 57 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Notably, the D614G mutation was shown to enhance the rate of SARS-CoV-2 infection in the upper airway. 2022 Archives of virology Discussion SARS_CoV_2 D614G 13 18 COVID-19 61 81 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Regarding the L452R and E484Q mutations in the Kappa variant, the substitution of a hydrophobic leucine (L) with a hydrophilic arginine (R) is similar to what occurred in the California variant, which was shown to correlate with increased transmissibility and decreased antibody neutralization. 2022 Archives of virology Discussion SARS_CoV_2 E484Q;L452R 24;14 29;19 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The Delta variant is continuously evolving, and a new variant, AY.1 (delta plus, B.1.617.2.1), carrying an additional K417N mutation, is emerging in India and the UK. 2022 Archives of virology Discussion SARS_CoV_2 K417N 118 123 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The E484K variant is of serious concern because of its resistance to some therapeutic monoclonal antibodies and decreased in vitro neutralization by the serum samples from patients infected with the original SARS-CoV-2. 2022 Archives of virology Discussion SARS_CoV_2 E484K 4 9 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The L18F substitution was dominant in England before the emergence of the UK strain. 2022 Archives of virology Discussion SARS_CoV_2 L18F 4 8 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The N440K mutant showed enhanced binding affinity to the human ACE2 receptor and resulted in immune escape from a panel of neutralizing monoclonal antibodies. 2022 Archives of virology Discussion SARS_CoV_2 N440K 4 9 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The N440K mutation was also reported in COVID-19 reinfection cases from northern India. 2022 Archives of virology Discussion SARS_CoV_2 N440K 4 9 COVID-19 40 48 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The prevalence of an RBD variant with N440K was estimated to be 2.1% in India, with ~34% in Andhra Pradesh, a southern Indian state. 2022 Archives of virology Discussion SARS_CoV_2 N440K 38 43 RBD 21 24 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The rapid global spread of the UK variant with P681H and P681R mutations is well known. 2022 Archives of virology Discussion SARS_CoV_2 P681H;P681R 47;57 52;62 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. The role of simultaneous L18F and E484K mutations in virus transmission needs to be evaluated. 2022 Archives of virology Discussion SARS_CoV_2 E484K;L18F 34;25 39;29 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. With the T478I mutation, moderate resistance to neutralization by two monoclonal antibodies and convalescent sera from two COVID-19 patients has been documented. 2022 Archives of virology Discussion SARS_CoV_2 T478I 9 14 COVID-19 123 131 35000004 Emergence of two distinct variants of SARS-CoV-2 and an explosive second wave of COVID-19: the experience of a tertiary care hospital in Pune, India. Within weeks, the virus evolved further, replacing the E484Q mutation with T478K, and this variant was later named the Delta variant. 2022 Archives of virology Discussion SARS_CoV_2 E484Q;T478K 55;75 60;80 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. As lectins have evolved over millions of years to be highly potent and selective, the H84T-BanLec CAR represents an entirely new approach in that it targets aberrant glycosylation patterns in viral proteins. 2021 Frontiers in immunology Discussion SARS_CoV_2 H84T 86 90 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. H84T-BanLec CAR-NK cells promoted a decrease in the number of total cells infected with pseudovirus after two days of culture. 2021 Frontiers in immunology Discussion SARS_CoV_2 H84T 0 4 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. However, the risk of unspecific toxicity secondary to NK cell surface H84T-BanLec binding of glycosylated protein on normal tissues should also be tested using tissue arrays and relevant in vivo model systems. 2021 Frontiers in immunology Discussion SARS_CoV_2 H84T 70 74 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. In this study we show successful generation of CAR-NK cells expressing extracellular H84T-BanLec linked to intracellular activation domains ( Figure 4 ). 2021 Frontiers in immunology Discussion SARS_CoV_2 H84T 85 89 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. It is encouraging that treatment with H84T-BanLec is safe in murine models. 2021 Frontiers in immunology Discussion SARS_CoV_2 H84T 38 42 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. Our findings support the hypothesis that CAR-NK cells expressing H84T-BanLec can mediate SARS-CoV-2 viral clearance. 2021 Frontiers in immunology Discussion SARS_CoV_2 H84T 65 69 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. Taken together with the innate antiviral activity and capability for allogeneic infusion of NK cells, H84T-BanLec CAR-NK cells exhibit favorable characteristics that support further testing. 2021 Frontiers in immunology Discussion SARS_CoV_2 H84T 102 106 35003077 Glycoprotein Targeted CAR-NK Cells for the Treatment of SARS-CoV-2 Infection. Ultimately, investigation of H84T-BanLec CAR-NK cell efficacy against wild-type SARS-CoV-2 virus and in animal models of SARS-CoV-2 infection is needed. 2021 Frontiers in immunology Discussion SARS_CoV_2 H84T 29 33 COVID-19 121 141 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. Around September 2020, genetic variants carrying the p.Asp501Tyr substitution on the S protein of SARS-CoV-2 were first detected in the United Kingdom, and spread to elsewhere globally, such as Brazil, South Africa, and the United States. 2021 Frontiers in public health Discussion SARS_CoV_2 D501Y;D501Y 53;55 64;64 S 85 86 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. Detection of p.Asp501Tyr mutation flags samples that may harbor mutations associated with immune evasion and increased transmissibility. 2021 Frontiers in public health Discussion SARS_CoV_2 D501Y;D501Y 13;15 24;24 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. In addition, 20% of SNP changes occurred in the S gene, such as p.Asp501Tyr, p.Pro681His, and p.Pro681Arg. 2021 Frontiers in public health Discussion SARS_CoV_2 D501Y;P681R;P681H;D501Y;P681R;P681H 64;94;77;66;96;79 75;105;88;75;105;88 S 48 49 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. It is worth mentioning that p.Asp614Gly variant was significantly positively correlated with the clinical severity of patients. 2021 Frontiers in public health Discussion SARS_CoV_2 D614G;D614G 28;30 39;39 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. Previous SARS-CoV-2 studies suggest that the p.Pro681His mutation is associated with enhanced systemic infection and increased membrane fusion. 2021 Frontiers in public health Discussion SARS_CoV_2 P681H;P681H 45;47 56;56 Membrane 127 135 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. The p.Asp501Tyr substitution reduces the neutralization capacity of antibodies generated against wild type virus. 2021 Frontiers in public health Discussion SARS_CoV_2 D501Y;D501Y 4;6 15;15 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. The p.Pro681Arg mutation causes a small increase in proteolytic processing that might have an effect on viral replication, transmissibility, or pathogenic properties. 2021 Frontiers in public health Discussion SARS_CoV_2 P681R;P681R 4;6 15;15 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. The p.Pro681Arg mutation, was first identified in Uganda in September 2020, is designated a variant of interest in Africa and with subsequent spread to other countries. 2021 Frontiers in public health Discussion SARS_CoV_2 P681R;P681R 4;6 15;15 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. The p.Pro681His mutation has unique and emerging characteristics with a significant exponential increase in worldwide frequency. 2021 Frontiers in public health Discussion SARS_CoV_2 P681H;P681H 4;6 15;15 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. The p.Pro681His mutation is the characteristic of the new SARS-CoV-2 variants from the United Kingdom and Nigeria. 2021 Frontiers in public health Discussion SARS_CoV_2 P681H;P681H 4;6 15;15 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. The p.Ser316Thr and p.Lu484Lys variants were significantly negatively correlated with the course of disease. 2021 Frontiers in public health Discussion SARS_CoV_2 S316T;S316T 4;6 15;15 35004593 Analysis of Clinical Characteristics and Virus Strains Variation of Patients Infected With SARS-CoV-2 in Jiangsu Province-A Retrospective Study. The variant p.Asp614Gly is associated with increased viral load in patients with SARS-CoV-2, which may significantly enhance the infectivity and transmissibility of the virus. 2021 Frontiers in public health Discussion SARS_CoV_2 D614G;D614G 12;14 23;23 35007661 A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: Effects on proteolytic cleavage and ACE2 binding. Based on our results, peptide containing the P681R mutant SARS-CoV-2-specific furin motif indeed was more susceptible to cleavage by furin than the wild type site, and fbAB treatment was able to significantly reduce the cleavage percentage. 2022 Immunology letters Discussion SARS_CoV_2 P681R 45 50 35007661 A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: Effects on proteolytic cleavage and ACE2 binding. fbAB demonstrated effective blockage of SARS-CoV-2 wide type and/or P681R S1/S2 furin site cleavage caused by purified furin enzyme, the serine protease trypsin, and human nasal swab specimens. 2022 Immunology letters Discussion SARS_CoV_2 P681R 68 73 35007661 A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: Effects on proteolytic cleavage and ACE2 binding. In contrast, the mutation of P681H (Alpha variant) and P681R (Delta variant) significantly increased viral replication and transmission, largely due to increased cleavage of S1/S2 site by furin enzyme. 2022 Immunology letters Discussion SARS_CoV_2 P681H;P681R 29;55 34;60 35007661 A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: Effects on proteolytic cleavage and ACE2 binding. The P681R mutation is a hallmark of the Delta variant, the dominant strain of the COVID-19 global pandemic, and leads to increased resistance of SARS-CoV-2 to wild type spike vaccine. 2022 Immunology letters Discussion SARS_CoV_2 P681R 4 9 S 169 174 COVID-19 82 90 35007661 A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: Effects on proteolytic cleavage and ACE2 binding. Thus, inhibition of SARS-CoV-2 cleavage of the furin site containing P681R would allow for the reduction of furin site cleavage-based activation of SARS-CoV-2 Delta variant spike protein, thereby decreasing viral binding to ACE2, cell-cell fusion, and viral entry into human cells. 2022 Immunology letters Discussion SARS_CoV_2 P681R 69 74 S 173 178 35008446 Analysis of Immune Escape Variants from Antibody-Based Therapeutics against COVID-19: A Systematic Review. Among 33 patients having positive NPS PCR for an average of 18 days, Voloch et al., observed a distinguishing pattern of mutations over the course of the infection mainly driven by increasing A U and decreasing G A signatures, including spike mutations (V362L, T553I, H655Y, A688V, S691F, S884F, V1176F). 2021 International journal of molecular sciences Discussion SARS_CoV_2 A688V;H655Y;S691F;S884F;T553I;V1176F;V362L 275;268;282;289;261;296;254 280;273;287;294;266;302;259 S 237 242 35008446 Analysis of Immune Escape Variants from Antibody-Based Therapeutics against COVID-19: A Systematic Review. E406W mutation, which causes resistance to REGN-COV-2, has never been reported in GISAID, and other E406 mutations remain exceedingly rare (worldwide, 318 cases of E406Q, 41 cases of E406D, and 2 cases each from USA for E406G, E406A, E406K, and 1 case of E406V out of 4,410,787 sequences deposited in GISAID as of 13 December 2021). 2021 International journal of molecular sciences Discussion SARS_CoV_2 E406A;E406D;E406G;E406K;E406Q;E406V;E406W 227;183;220;234;164;255;0 232;188;225;239;169;260;5 35008446 Analysis of Immune Escape Variants from Antibody-Based Therapeutics against COVID-19: A Systematic Review. In one instance of immune escape associated with CCP, a variant with D796H mutation manifested modestly reduced sensitivity to neutralization by CCP that was associated with reduced infectivity, which was only partly compensated by DeltaHV69-70. 2021 International journal of molecular sciences Discussion SARS_CoV_2 D796H 69 74 35008446 Analysis of Immune Escape Variants from Antibody-Based Therapeutics against COVID-19: A Systematic Review. L452R, which causes resistance to regdanvimab, also became prevalent first in VOI Epsilon and then in VOC Delta (source: Outbreak.info). 2021 International journal of molecular sciences Discussion SARS_CoV_2 L452R 0 5 35008446 Analysis of Immune Escape Variants from Antibody-Based Therapeutics against COVID-19: A Systematic Review. Notably, several mutations have recurred in VOC and VOIs (e.g., E484K found in Beta and Gamma, E484Q found in Delta, or DeltaLHR244-246 found in VOI lambda), raising the possibility that such variants emerged during the treatment of patients (iatrogenic variants), but such inference will likely remain very hard to prove. 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484K;E484Q 64;95 69;100 35008446 Analysis of Immune Escape Variants from Antibody-Based Therapeutics against COVID-19: A Systematic Review. Nothing can be inferred about the fitness of an emerging mutant in the absence of selective pressure, but it is of interest that one variant with the E484K mutant that emerged after bamlanivimab therapy was able to infect multiple household contacts. 2021 International journal of molecular sciences Discussion SARS_CoV_2 E484K 150 155 35008446 Analysis of Immune Escape Variants from Antibody-Based Therapeutics against COVID-19: A Systematic Review. Similarly, Q493R, which causes resistance to bamlanivimab + etesevimab, had only been reported in 244 sequences and Q493K in 138 sequences, before becoming one of the hallmark mutations of VOC Omicron. 2021 International journal of molecular sciences Discussion SARS_CoV_2 Q493K;Q493R 116;11 121;16 35008446 Analysis of Immune Escape Variants from Antibody-Based Therapeutics against COVID-19: A Systematic Review. The same is true for sotrovimab resistance, with E340 and P337 mutations exceedingly rare to date (E340K in 159 sequences worldwide, P337R in 18, P337L in 195, E340A in 105, E340G in 36, P337H in 44, P337T in 90) (source: Outbreak.info). 2021 International journal of molecular sciences Discussion SARS_CoV_2 E340A;E340G;P337H;P337L;P337R;P337T;E340K 160;174;187;146;133;200;99 165;179;192;151;138;205;104 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. 617-India (L452R, E484Q) VoC. 2022 The EPMA journal Discussion SARS_CoV_2 E484Q;L452R 18;11 23;16 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. A similar reduced flexibility might be expected for the RBD of the double mutant S477N_E484K due to the replacement of the Ser 477 with an Asn residue. 2022 The EPMA journal Discussion SARS_CoV_2 S477N;S477N;E484K 81;123;87 86;142;92 RBD 56 59 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Africa (K417N, E484K, N501Y), B.1.427/B.1.429-California (L452R), the B.1.141 (N439K) and the recent B.1. 2022 The EPMA journal Discussion SARS_CoV_2 E484K;N501Y;K417N;L452R;N439K 15;22;8;58;79 20;27;13;63;84 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Also, the B.1.1.7_UK S494P_N501Y_E484K investigated variant shows an important variation in the interactions at the ACE2/RBD interface and a decrease in the calculated interaction energies. 2022 The EPMA journal Discussion SARS_CoV_2 S494P;E484K;N501Y 21;33;27 26;38;32 RBD 121 124 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. By monitoring binding affinity and interaction energies, it appears that the single amino acid replacements N439K (B.1.141 VoC) and E484K (detected in several VoC) cause the most dramatic increase in interaction energies among the investigated single mutants. 2022 The EPMA journal Discussion SARS_CoV_2 E484K;N439K 132;108 137;113 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. In addition, the triple mutant N501Y_E484K_K417T detected in the P.1 Japan/Brazil VoC shows an increase of about 5% in binding affinity that might reflect the greater ability shown by this VoC in escaping antibodies produced as a consequence of SARS-CoV-2 Wuhan-sequence based vaccination. 2022 The EPMA journal Discussion SARS_CoV_2 N501Y;E484K;K417T 31;37;43 36;42;48 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Indeed, while it is expected that mutations at the RBD need to be monitored because those mutations can be responsible for an increase in the binding affinity for the ACE2 receptor, it is matter of debate the increased efficiency in entering host-cells proposed for variants showing supplementary mutations far from the RBD, i.e., D614G or P681H shown by several VoC and other variants of interest or under monitoring (https://www.ecdc.europa.eu/en/covid-19/variants-concern). 2022 The EPMA journal Discussion SARS_CoV_2 D614G;P681H 331;340 336;345 RBD;RBD 51;320 54;323 COVID-19 449 457 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. It can be argued that the limited flexibility introduced by the S494P amino acid replacement decreases the affinity for ACE2 and makes sensitive this VoC to antibodies produced by vaccination, despite of the presence of N501Y and E484K that as single mutants show a higher affinity for the ACE2 receptor. 2022 The EPMA journal Discussion SARS_CoV_2 E484K;N501Y;S494P 230;220;64 235;225;69 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. It is retained that mutations like D614G and P681H, being located in the N-terminal portion of the spike pre-fusion conformation, despite of their relatively great distance from the SARS-CoV-2 spike RBD/ACE2 protein-protein interface, can confer a different flexibility (increased for the D614G mutant and decreased for the P681H mutant) to the entire spike protein, before cleavage events determining the post-fusion conformation, following the spike N-terminal loss. 2022 The EPMA journal Discussion SARS_CoV_2 D614G;D614G;P681H;P681H 35;289;45;324 40;294;50;329 S;S;S;S;RBD;N;N 99;193;352;446;199;73;452 104;198;357;451;202;74;453 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. More in detail we studied the impact of the mutations responsible for the investigated VoC B.1.1.7-UK (carrying the mutations of concern/interest N501Y, S494P, E484K), P.1-Japan/Brazil (K417N/T, E484K, N501Y), B.1.351-S. 2022 The EPMA journal Discussion SARS_CoV_2 E484K;E484K;N501Y;N501Y;S494P;K417N;K417T 160;195;146;202;153;186;186 165;200;151;207;158;193;193 S 218 219 35013687 Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. Through the monitoring of the binding interactions, it is possible to see that H-bonds and hydrophobic interactions among side chains at the protein-protein interface, but also backbone-side chain H-bonds, among the very short-range (< 3.8 A) interactions, can substantially increase or decrease as a consequence of a mutation occurring at the boat-shaped RBM of the SARS-CoV-2 spike RBD, as observed for the single N439K amino acid replacement occurring at the "stern" RBM region, or for the B.1.141 VoC or in the P.1 Japan/Brazil VoC consisting of the triple mutant N501Y_E484K_K417T showing mutations along the entire RBM, with respect to the interactions calculated in the crystallized SARS-CoV-2 spike RBD/ACE2 protein complex (6m0j.pdb) used as a reference structure. 2022 The EPMA journal Discussion SARS_CoV_2 N439K;N501Y;E484K;K417T 416;568;574;580 421;573;579;585 S;S;RBD;RBD 378;701;384;707 383;706;387;710 35014989 COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis. Multiple genomic variants of SARS-CoV-2 were distributed in patients in New England early in the COVID-19 era, mostly from a B.1 sublineage with the spike D614G mutation. 2021 JMIRx med Discussion SARS_CoV_2 D614G 155 160 S 149 154 COVID-19 97 105 35014989 COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis. The predominance of B lineage D614G in our study specimens provided valuable insight into the pace of epidemiological trend and the evolution of the virus early in the COVID-19 era through the New England region. 2021 JMIRx med Discussion SARS_CoV_2 D614G 30 35 COVID-19 168 176 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. A previous study on Indian SARS-CoV-2 isolates reported scores for D614G mutation in S-protein and several mutations across various proteins with their functional impact. 2021 Journal of global infectious diseases Discussion SARS_CoV_2 D614G 67 72 S 85 86 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. A recent study has reported that L54F, D614G and V1176F of S-protein, identified in the study, are correlated with severe clinical outcome. 2021 Journal of global infectious diseases Discussion SARS_CoV_2 D614G;L54F;V1176F 39;33;49 44;37;55 S 59 60 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. Accordingly, in the present study, the observed mutations in the NGS such as N234Y and N603Y and OGS mutations such as S221 L, T323I, T602I and T602 L are found to stabilize the S-protein. 2021 Journal of global infectious diseases Discussion SARS_CoV_2 N234Y;N603Y;S221L;T323I;T602L;T602I 77;87;119;127;144;134 82;92;125;132;150;139 S 178 179 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. Also, glycosylation mutations such as N149G, N165S, and N709K are reported to increase the sensitivity to neutralizing antibodies and the mutation N234Y is found to reduce the neutralization sensitivity to different set of antibodies. 2021 Journal of global infectious diseases Discussion SARS_CoV_2 N149G;N165S;N234Y;N709K 38;45;147;56 43;50;152;61 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. Besides, D614G in combination with other mutations such as D614G+L5F (n = 23), D614G+V341I (n = 1), D614G+D936Y (n = 3), D614G+S939F (n = 9) and D614G+S943T (n = 2) in strains of the present study was demonstrated to have increased infectivity compared to Wuhan-1 strain. 2021 Journal of global infectious diseases Discussion SARS_CoV_2 D614G;D614G;D614G;D614G;D614G;D614G;D936Y;L5F;S939F;S943T;V341I 9;59;79;100;121;145;106;65;127;151;85 14;64;84;105;126;150;111;68;132;156;90 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. Both the predominant G and GR are European clades and the strains of these clades possess the D614G mutation on the S-protein which is more infectious. 2021 Journal of global infectious diseases Discussion SARS_CoV_2 D614G 94 99 S 116 117 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. For instance, D614G appears along with 3 other mutations in 5'UTR, NSP3 and NSP12 that form G clade. 2021 Journal of global infectious diseases Discussion SARS_CoV_2 D614G 14 19 5'UTR;Nsp12;Nsp3 60;76;67 65;81;71 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. In contrast, the report suggested that mutations such as L54F, G431S, E471D, G502R, Q506H, P507S, Y508N, E583D and Q675H could weaken the interaction of S-protein with ACE2 receptor; whereas, N440K, E471Q and G504V could improve the binding affinity. 2021 Journal of global infectious diseases Discussion SARS_CoV_2 E471D;E471Q;E583D;G431S;G502R;G504V;L54F;N440K;P507S;Q506H;Q675H;Y508N 70;199;105;63;77;209;57;192;91;84;115;98 75;204;110;68;82;214;61;197;96;89;120;103 S 153 154 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. It was reported that mutations such as T29I, H49Y, D138Y, E484Q, E484K, A520S, T572I, D614G and H1083Q identified in strains of the study, could increase the stability of S-protein. 2021 Journal of global infectious diseases Discussion SARS_CoV_2 A520S;D138Y;D614G;E484K;E484Q;H1083Q;H49Y;T29I;T572I 72;51;86;65;58;96;45;39;79 77;56;91;70;63;102;49;43;84 S 171 172 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. On the contrary, very few mutations at the NGS (N709K) and OGS (T1077I) were found to decrease the stability of S protein. 2021 Journal of global infectious diseases Discussion SARS_CoV_2 N709K;T1077I 48;64 53;70 S 112 113 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. The first occurrence of L54F was observed in Wuhan in March whereas India reported in April. 2021 Journal of global infectious diseases Discussion SARS_CoV_2 L54F 24 28 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. The glycosylation mutation N1074D has been found to decrease the infectivity. 2021 Journal of global infectious diseases Discussion SARS_CoV_2 N1074D 27 33 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. The origin of D614G mutation was in China during January, 2020 but the occurrence in India was reported in March and became prevalent afterwards. 2021 Journal of global infectious diseases Discussion SARS_CoV_2 D614G 14 19 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. Though D614G is associated with increased infectivity, mutations such as Q239R, T719I, T719S, D839Y, P1263 L, mutations in RBD such as I434K and P521S, and D614G+Q675H are reported to have decreased infectivity. 2021 Journal of global infectious diseases Discussion SARS_CoV_2 D614G;D614G;D839Y;I434K;P1263L;P521S;Q239R;T719I;T719S;Q675H 7;156;94;135;101;145;73;80;87;162 12;161;99;140;108;150;78;85;92;167 RBD 123 126 35017872 Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India. Virulence of SARS-CoV-2 can be associated with mutations in S-protein such as L18F, H69del, V70del, D138Y and Y144del that confer affinity and adhesive properties for better interaction with host cells through surface electrostatic interaction; besides, these mutations are also reported to evade host immune responses against S-protein. 2021 Journal of global infectious diseases Discussion SARS_CoV_2 D138Y;H69del;L18F;V70del;Y144del 100;84;78;92;110 105;90;82;98;117 S;S 60;327 61;328 35018385 Integrin/TGF-beta1 inhibitor GLPG-0187 blocks SARS-CoV-2 Delta and Omicron pseudovirus infection of airway epithelial cells which could attenuate disease severity. In our current study, we found that the Omicron pseudovirus was less capable of infecting the small airway epithelial cells than D614G or Delta variant pseudovirus, and that integrin inhibition effectively blocked D614G, Delta and Omicron pseudovirus infection of the small airway epithelial cells. 2022 medRxiv Discussion SARS_CoV_2 D614G;D614G 129;214 134;219 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. However, when SARS-CoV-2 pseudovirus with the L1197I mutation was incubated with these plasma samples, increased NT50 values were observed. 2022 PLoS pathogens Discussion SARS_CoV_2 L1197I 46 52 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. Interestingly, the spike T323I mutation that also removes an N-glycosylation site, led to a modest reduction in infectivity compared with the other spike mutations that were tested, despite being located in the RBD. 2022 PLoS pathogens Discussion SARS_CoV_2 T323I 25 30 S;S;RBD;N 19;148;211;61 24;153;214;62 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. Moreover, the effect of additional spike mutations that recently emerged in the Delta variant such as the K417N on SRAS-CoV-2 evolution within the host should be examined. 2022 PLoS pathogens Discussion SARS_CoV_2 K417N 106 111 S 35 40 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. SARS-CoV-2 pseudoviruses that carry the L216P or the T323I mutation showed similar sensitivity to plasma samples from vaccinated individuals and to convalescent plasma in comparison with SARS-CoV-2 pseudovirus that expresses an unmutated spike protein. 2022 PLoS pathogens Discussion SARS_CoV_2 L216P;T323I 40;53 45;58 S 238 243 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. This study included individuals who were infected with the D614G variants and two individuals who were infected with the Alpha variant (individual 48552 and 48559). 2022 PLoS pathogens Discussion SARS_CoV_2 D614G 59 64 35020754 SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection. We chose to preform in-depth analysis on the spike mutations that led to the most modest reduction in infectivity, L216P, T323I and L1197I. 2022 PLoS pathogens Discussion SARS_CoV_2 L1197I;L216P;T323I 132;115;122 138;120;127 S 45 50 35026305 SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021. As omicron carries the spike mutations HV69/70 deletion, Y144 deletion, N501Y, and P681H, both Master and Variants I assays should detect it. 2022 Journal of virological methods Discussion SARS_CoV_2 N501Y;P681H 72;83 77;88 S 23 28 35026305 SARS-CoV-2 multiplex RT-PCR to detect variants of concern (VOCs) in Malaysia, between January to May 2021. However, new important variants such as B.1.617.1 (kappa), B.1.617.2 (delta) and B.1.617.3 have subsequently emerged, with mutations such as L452R and P681R that are not detected by these assays, necessitating additional panels. 2022 Journal of virological methods Discussion SARS_CoV_2 L452R;P681R 141;151 146;156 35028838 SARS-CoV-2 phase I transmission and mutability linked to the interplay of climatic variables: a global observation on the pandemic spread. A few mutant forms like S943P was reported on the 13th of April in Belgium, A831V and D839/Y/N/E during April in Europe. 2022 Environmental science and pollution research international Discussion SARS_CoV_2 A831V;S943P 76;24 81;29 35028838 SARS-CoV-2 phase I transmission and mutability linked to the interplay of climatic variables: a global observation on the pandemic spread. D614G mutation hints that the samples prior to March 1 were characteristically represented by the D614 form and there was a slow transition indicating the predominance of G614 during the 15th of March. 2022 Environmental science and pollution research international Discussion SARS_CoV_2 D614G 0 5 35028838 SARS-CoV-2 phase I transmission and mutability linked to the interplay of climatic variables: a global observation on the pandemic spread. The regional variations in meteorological parameters could have resulted in L8V/W in Hong Kong, H49Y in China, and recombination form of S943P in Belgium (Rehman et al.). 2022 Environmental science and pollution research international Discussion SARS_CoV_2 H49Y;L8V;L8W;S943P 96;76;76;137 100;81;81;142 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Among the infectivity assays in this study, of particular interest was our finding that S494P, A520S, and V367F mutations enhance the infectivity of three VOCs in a variety of mammalian susceptible cells as well as ACE2-overexpressing 293T cells of different species. 2022 Journal of medical virology Discussion SARS_CoV_2 A520S;S494P;V367F 95;88;106 100;93;111 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Certain single amino acid changes on the hemagglutinin (HA) of the influenza virus (e.g., HA T135K) create a significant increase in antigenic distance, resulting in a dramatic decrease in vaccine sera neutralization potency. 2022 Journal of medical virology Discussion SARS_CoV_2 T135K 93 98 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Consistently, the complex structure of Gamma-A520S with hACE2 indicates that this residue does not involve receptor binding. 2022 Journal of medical virology Discussion SARS_CoV_2 A520S 45 50 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. For example, variant D614G has rapidly increased in prevalence, replacing the original variant in February 2020. 2022 Journal of medical virology Discussion SARS_CoV_2 D614G 21 26 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Furthermore, a significant decrease in infectivity was found when multiple RBD mutations were aggregated with the possible Alpha, Beta, and Gamma variants compared with the D614G strain. 2022 Journal of medical virology Discussion SARS_CoV_2 D614G 173 178 RBD 75 78 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Furthermore, the elevated infectivity and fusion capability following the combination of the A520S mutation with the Gamma variant was particularly notable. 2022 Journal of medical virology Discussion SARS_CoV_2 A520S 93 98 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. In this study, both convalescent patient sera and different antigens immunized guinea pig sera showed significantly higher levels of neutralization with the D614G + V367F variant than the D614G strain (Figure S2B), suggesting that V367F does not pose a greater threat of increased protective efficacy in the vaccinated population. 2022 Journal of medical virology Discussion SARS_CoV_2 D614G;D614G;V367F;V367F 157;188;165;231 162;193;170;236 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Meanwhile, in the complex structure, a little conformation change of the A520S-residing loop was observed. 2022 Journal of medical virology Discussion SARS_CoV_2 A520S 73 78 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Only two mutations, E484Q and F490S, have increased the number of mutations into the first 10 positions compared to the start of this study in March. 2022 Journal of medical virology Discussion SARS_CoV_2 E484Q;F490S 20;30 25;35 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Previous studies in our laboratory have shown that the V367F mutation in the original strain enhances susceptibility to mAbs and to sera from convalescent individuals. 2022 Journal of medical virology Discussion SARS_CoV_2 V367F 55 60 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The analysis of SARS-CoV-2 sequences uploaded from around the world has shown that certain mutants (e.g., D614G, L18S) predominate over time. 2022 Journal of medical virology Discussion SARS_CoV_2 D614G;L18S 106;113 111;117 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The S494P mutation has been reported to enhance the affinity of RBD to ACE2. 2022 Journal of medical virology Discussion SARS_CoV_2 S494P 4 9 RBD 64 67 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The subsequent Alpha, Beta, and Gamma epidemic variants were all based on the D614G variant, which suggests the predictive value of our studies combining mutations to individual VOCs. 2022 Journal of medical virology Discussion SARS_CoV_2 D614G 78 83 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. The V367F mutation was mainly found in the A.23.1 variant, which appears in Uganda and Vietnam, and has been suggested to enhance viral infectivity by increasing human ACE2 receptor-binding affinity. 2022 Journal of medical virology Discussion SARS_CoV_2 V367F 4 9 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. This may be similar to the D614G mutation, which reduces the affinity with hACE2, S1 subunit is easier to dissociate and fall off after binding, increasing the chance of S2 subunit exposure and thus enhancing the fusion strength. 2022 Journal of medical virology Discussion SARS_CoV_2 D614G 27 32 35032057 Aggregation of high-frequency RBD mutations of SARS-CoV-2 with three VOCs did not cause significant antigenic drift. Thus, the trimeric S with A520S probably possesses more standing RBD, and more readily interacts with the receptor to initiate the infections. 2022 Journal of medical virology Discussion SARS_CoV_2 A520S 26 31 RBD;S 65;19 68;20 35042962 Two short low complexity regions (LCRs) are hallmark sequences of the Delta SARS-CoV-2 variant spike protein. Accordingly, it is possible that the asparagine (N) of the mutation D950N. 2022 Scientific reports Discussion SARS_CoV_2 D950N 68 73 N 49 50 35042962 Two short low complexity regions (LCRs) are hallmark sequences of the Delta SARS-CoV-2 variant spike protein. In vitro experiments and SARS-CoV-2 infections in animal models have demonstrated that the P681R mutation enhances both the fusogenicity and pathogenicity of the virus. 2022 Scientific reports Discussion SARS_CoV_2 P681R 91 96 COVID-19 25 46 35042962 Two short low complexity regions (LCRs) are hallmark sequences of the Delta SARS-CoV-2 variant spike protein. The mutation P681R detected in the Spike LCR-3 (SRRRARSVASQSIIA). 2022 Scientific reports Discussion SARS_CoV_2 P681R 13 18 S 35 40 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. Because the amino acid substitutions E484K and N501Y are present in the beta (B.1.351) and gamma (P.1) variants, and the substitution K417N is found in the beta variant and K417T in the gamma variant, we hypothesized that RAT might not detect both or at least one of these two virus variants. 2021 Frontiers in public health Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y 37;134;173;47 42;139;178;52 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. Furthermore, we observed that RAT sensitivity for detecting ancestral strain of SARS-CoV-2 decreased from 90 to 42.8% with the SARS-CoV-2 variants that carry K417N/T, E484K and N501Y amino acid substitutions, even in the lower Cq range of 20 <= Cq <25. 2021 Frontiers in public health Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y 167;158;158;177 172;165;165;182 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. The low intensity of bands showed for two of the three SARS-CoV-2 variants identified by RAT suggests a decreased specificity for samples with the K417N/T, E484K, and N501Y mutations. 2021 Frontiers in public health Discussion SARS_CoV_2 E484K;K417N;K417T;N501Y 156;147;147;167 161;154;154;172 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. These data further suggest that this rapid antigen test could also fail to detect other variants, such as delta (B.1.617.2), because, in addition of Spike protein mutations, the delta variant also has mutations in the N protein (different to R203K). 2021 Frontiers in public health Discussion SARS_CoV_2 R203K 242 247 S;N 149;218 154;219 35047474 The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants. This kind of detection can explain the low capacity of RAT to detect the variants, which has the substitutions P80R and R203K in the N protein. 2021 Frontiers in public health Discussion SARS_CoV_2 P80R;R203K 111;120 115;125 N 133 134 35047533 Differences in Clinical Characteristics Between Delta Variant and Wild-Type SARS-CoV-2 Infected Patients. Compared to other SARS-CoV-2 strains, the delta variant possesses notable mutations L452R, T478K, and E484Q in the RBD of S protein and P681R in the S1/S2 site. 2021 Frontiers in medicine Discussion SARS_CoV_2 E484Q;L452R;P681R;T478K 102;84;136;91 107;89;141;96 RBD;S 115;122 118;123 35047533 Differences in Clinical Characteristics Between Delta Variant and Wild-Type SARS-CoV-2 Infected Patients. Each of the L452R and E484Q mutations lowered susceptibility to mRNA vaccine-generated antibodies by disrupting the binding between the RBD and hACE2, albeit the combined mutations did not show synergism. 2021 Frontiers in medicine Discussion SARS_CoV_2 E484Q;L452R 22;12 27;17 RBD 136 139 35047533 Differences in Clinical Characteristics Between Delta Variant and Wild-Type SARS-CoV-2 Infected Patients. In addition, D614G mutation has been identified in all the variants of concern (VOCs), i.e., alpha, beta, gamma, and delta variants). 2021 Frontiers in medicine Discussion SARS_CoV_2 D614G 13 18 35047533 Differences in Clinical Characteristics Between Delta Variant and Wild-Type SARS-CoV-2 Infected Patients. Moreover, within S1/S2 site P681R mutation enabled S protein to be less acidic and made furin in the host much easier to cleave, adding viral infectivity and transmissibility. 2021 Frontiers in medicine Discussion SARS_CoV_2 P681R 28 33 S 51 52 35047533 Differences in Clinical Characteristics Between Delta Variant and Wild-Type SARS-CoV-2 Infected Patients. SARS-CoV-2 strains with L452R and E484Q mutations were associated with heightened resistance to antibody neutralization. 2021 Frontiers in medicine Discussion SARS_CoV_2 E484Q;L452R 34;24 39;29 35047533 Differences in Clinical Characteristics Between Delta Variant and Wild-Type SARS-CoV-2 Infected Patients. T478K mutation enhanced the infectivity and augmented the ability of SARS-CoV-2 to escape immune recognition. 2021 Frontiers in medicine Discussion SARS_CoV_2 T478K 0 5 35055023 Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors. All these results further support our conclusion that the D17R mutation is enhancing the binding affinity of miniprotein with RBD. 2022 International journal of molecular sciences Discussion SARS_CoV_2 D17R 58 62 RBD 126 129 35055023 Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors. D17R substitution is further discussed in Section 3.2. 2022 International journal of molecular sciences Discussion SARS_CoV_2 D17R 0 4 35056548 Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan. Although the most important substitution in the lineage is considered to be N501Y in the S protein, P681H is adjacent to the furin cleavage site (A684/R685) and may affect the efficiency of cleavage, which facilitates efficient SARS-CoV-2 transmission and infection. 2022 Microorganisms Discussion SARS_CoV_2 N501Y;P681H 76;100 81;105 S 89 90 35056548 Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan. Around half of the CA strains acquired the P681H substitution, one of the main mutations in the B.1.1.7 lineage, in the S protein (Figure 2 and Figure 3, Table 3). 2022 Microorganisms Discussion SARS_CoV_2 P681H 43 48 S 120 121 35056548 Unique Evolution of SARS-CoV-2 in the Second Large Cruise Ship Cluster in Japan. Therefore, P681H may be the key substitution that enhanced the transmissibility of SARS-CoV-2 on the CA cruise ship; however, whether P681H affects the cleavage of the S protein by furin protease requires further investigation. 2022 Microorganisms Discussion SARS_CoV_2 P681H;P681H 11;134 16;139 S 168 169 35056592 SARS-CoV-2 Evolution and Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIV Immune Suppression. In addition, emergence of resistance SARS-CoV-2 mutations, such as D484Y in RdRp, have been reported following failure of remdesivir treatment in an individual with B-cell immunodeficiency due to lymphocytic leukemia treated by rituximab. 2022 Microorganisms Discussion SARS_CoV_2 D484Y 67 72 RdRP 76 80 Lymphocytic leukemia 196 216 35056592 SARS-CoV-2 Evolution and Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIV Immune Suppression. Interestingly, E484K was already fixed at the first time point, but waned at the second and third time points. 2022 Microorganisms Discussion SARS_CoV_2 E484K 15 20 35056592 SARS-CoV-2 Evolution and Spike-Specific CD4+ T-Cell Response in Persistent COVID-19 with Severe HIV Immune Suppression. The S:E484K mutation alters antibody recognition. 2022 Microorganisms Discussion SARS_CoV_2 E484K 6 11 S 4 5 35060147 SARS-CoV-2 intralineage variation and temporal patterns of COVID-19 risk factors in three cities of southeastern Brazil: Age, sex, and race. Thus, the A33S specific mutation found in ORF3a of P.1 isolates from Maua patients could interfere in the protein activity, increasing pathogenicity and consequently, the number of symptomatic individuals, which could explain the higher number of positive tests in this city during January and February 2021. 2022 Journal of medical virology Discussion SARS_CoV_2 A33S 10 14 ORF3a 42 47 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. However, the P681H in Omicron might be unfavourable to induce fusion. 2022 Emerging microbes & infections Discussion SARS_CoV_2 P681H 13 18 35060426 Drastic decline in sera neutralization against SARS-CoV-2 Omicron variant in Wuhan COVID-19 convalescents. P681R has been demonstrated increased fusion in the Delta variant and is associated with the higher pathogenicity of the Delta variant. 2022 Emerging microbes & infections Discussion SARS_CoV_2 P681R 0 5 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. A similar situation was also present in RBD double mutants, and mutations outside the RBD can also contribute to the increased affinity of the RBD to the ACE2 receptor, such as D614G breakthrough infection by delta strain has been observed in the vaccinated individuals. 2021 Viruses Discussion SARS_CoV_2 D614G 177 182 RBD;RBD;RBD 40;86;143 43;89;146 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. For example, E484K and E484Q substantially increased the binding affinity of N501 and N501Y to the ACE2 receptor. 2021 Viruses Discussion SARS_CoV_2 E484K;E484Q;N501Y 13;23;86 18;28;91 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. In conclusion, our study suggests that the double-mutated RBD in SARS-CoV-2 (L452R/T487K, L452R/E484Q and E484K/N501Y) can cause changes in the RBD structure, enhance RBD binding to the ACE2 receptor, and change antibody binding sites on the RBD. 2021 Viruses Discussion SARS_CoV_2 E484K;L452R;L452R;E484Q;N501Y;T487K 106;90;77;96;112;83 111;95;82;101;117;88 RBD;RBD;RBD;RBD 58;144;167;242 61;147;170;245 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. It has been determined that N501 enhances the RBD binding to ACE2 by maintaining the RBD at open conformation, and that this function can be enhanced by E484K. 2021 Viruses Discussion SARS_CoV_2 E484K 153 158 RBD;RBD 46;85 49;88 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. It has been proposed that higher transmissibility of new SARS-CoV-2 mutant strains can be attributed to the increased affinity of the mutated RBD to the ACE2 receptor in the host cells and that the RBD double mutations can further increase the affinity and enhance the transmissibility, as represented by the SARS-CoV-2 L452R/T478K (delta), L452R/E484Q (kappa), and E484K/N501Y (beta and gamma) strains. 2021 Viruses Discussion SARS_CoV_2 E484K;L452R;L452R;E484Q;N501Y;T478K 366;320;341;347;372;326 371;325;346;352;377;331 RBD;RBD 142;198 145;201 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. It is interesting to note that the binding energy between single mutants (L452R, T478K, E484K, E484Q and N501Y) and double mutants (L452/E484Q, L452/T478K and E484K/N501Y) were at similar levels, indicating that double mutants cause the change in binding energy in a similar way to the single mutants. 2021 Viruses Discussion SARS_CoV_2 E484K;E484K;E484Q;N501Y;T478K;L452R;E484Q;N501Y;T478K 88;159;95;105;81;74;137;165;149 93;164;100;110;86;79;142;170;154 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. N501 is also a mutation hot spot, as reflected by the RBD single mutation N501Y in the alpha strain and RBD double mutation E484K/N501Y in beta and gamma strains. 2021 Viruses Discussion SARS_CoV_2 E484K;N501Y;N501Y 124;74;130 129;79;135 RBD;RBD 54;104 57;107 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. This is reflected by the RBD mutation sequence data in that only 4 (N501Y, L452R, E484K, Y478K) were listed among the top 7 mutation sequences, but E484Q was listed at the 29th position (Supplementary Table S1). 2021 Viruses Discussion SARS_CoV_2 E484K;E484Q;L452R;Y478K;N501Y 82;148;75;89;68 87;153;80;94;73 RBD 25 28 35062205 RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor. We observed that each tested RBD single or double mutation increased the free binding energy between N501 and the ACE2 receptor (Figure 4B), highlighting that N501 can be a key player in enhancing wild-type and mutated RBD binding to ACE2, not only for N501Y but also the mutated residues in other RBD locations, likely through allosteric activity. 2021 Viruses Discussion SARS_CoV_2 N501Y 253 258 RBD;RBD;RBD 29;219;298 32;222;301 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. In fact, variants change the ability of the virus to bind the human receptor ACE2 thus making it more infective, as in the case of the N501Y mutation. 2022 Viruses Discussion SARS_CoV_2 N501Y 135 140 35062327 Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach. In particular, single high-frequency SNPs in SARS-CoV-2 were found on the spike glycoprotein (D614G, 23364 A > G), as well as in the protein encoding for the nucleocapsid (R203K, R202R, and G204R). 2022 Viruses Discussion SARS_CoV_2 A23364G;G204R;R202R;D614G;R203K 101;190;179;94;172 112;195;184;99;177 S;N 74;158 92;170 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. Accordingly, variants harboring the N501Y mutation, such as the Alpha, Beta and Gamma, displayed improved ACE2 interaction compared to the D614G Spike at cold temperature, revealing the crucial role of this mutation in facilitating Spike-ACE2 interaction. 2022 Viruses Discussion SARS_CoV_2 D614G;N501Y 139;36 144;41 S;S 145;232 150;237 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. Finally, we found that Mu and A.2.5 Spikes were recognized by plasma from vaccinated naive and previously-infected individuals, albeit to a lesser extent than D614G S. 2022 Viruses Discussion SARS_CoV_2 D614G 159 164 S;S 36;165 42;166 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. Further, RBD mutants of these indicated SARS-CoV-2 variants interacted with increased affinity to the ACE2 receptor at lower temperature suggesting that lower temperature promotes the thermodynamic stability of the ACE2-Spike-RBD complex whereas some of the mutations, such as N501Y, bypass this requirement. 2022 Viruses Discussion SARS_CoV_2 N501Y 277 282 S;RBD;RBD 220;9;226 225;12;229 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. However, despite harboring this mutation (N501Y), the capacity of the Mu Spike to favor ACE2 binding over the D614G was not observed at cold temperature. 2022 Viruses Discussion SARS_CoV_2 D614G;N501Y 110;42 115;47 S 73 78 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. In line with previous reports, Beta and Delta Spikes showed a significant increase in ACE2-Fc binding, Mu and A.2.5 also bound ACE2 better than D614G but to a lower extent than Beta and Delta Spikes. 2022 Viruses Discussion SARS_CoV_2 D614G 144 149 S;S 46;192 52;198 35062348 Antigenicity of the Mu (B.1.621) and A.2.5 SARS-CoV-2 Spikes. We previously demonstrated that the N501Y mutation significantly impacts ACE2 interaction independently of the temperature. 2022 Viruses Discussion SARS_CoV_2 N501Y 36 41 35062734 Immunogenicity of a Heterologous Prime-Boost COVID-19 Vaccination with mRNA and Inactivated Virus Vaccines Compared with Homologous Vaccination Strategy against SARS-CoV-2 Variants. Both the beta and theta variants contain N501Y and E484K mutations in the S-protein, which enhanced the affinity of ACE2, and immune sera showed decreased activity when the mutations, including N501Y and E484K. 2022 Vaccines Discussion SARS_CoV_2 E484K;E484K;N501Y;N501Y 51;204;41;194 56;209;46;199 S 74 75 35062734 Immunogenicity of a Heterologous Prime-Boost COVID-19 Vaccination with mRNA and Inactivated Virus Vaccines Compared with Homologous Vaccination Strategy against SARS-CoV-2 Variants. The results showed that the vMN titre all decreased for the D614G, beta, theta and delta variants. 2022 Vaccines Discussion SARS_CoV_2 D614G 60 65 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. All lineages have shown P323L mutation in the interface domain of the RdRP region. 2022 Microbial pathogenesis Discussion SARS_CoV_2 P323L 24 29 RdRP 70 74 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Alpha variant B.1.1.7 was found in one case each from vaccine breakthrough, mild and dead patient category showing nonsynonymous mutations of N501Y, A570D, D614G, P681H, T716I, S982A, D1118H and three deletions of H69del, V70del, and Y144del. 2022 Microbial pathogenesis Discussion SARS_CoV_2 A570D;D1118H;D614G;H69del;N501Y;P681H;S982A;T716I;V70del;Y144del 149;184;156;214;142;163;177;170;222;234 154;190;161;220;147;168;182;175;228;241 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Although both mutations increase the basicity of the S1-S2 poly-basic stretch at the furin cleavage site, P681R has inflicted more advantage to the virus by cleaving more efficiently S1/S2 cleavage at the furin site leading to the enhanced entry of the virus into host cells. 2022 Microbial pathogenesis Discussion SARS_CoV_2 P681R 106 111 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Although mutation in membrane gene relatively uncommon, I82T exclusive presence in Delta variant helps in viral host cell attachment, heparin sulfate proteoglycan, protein assembly in conjunction with nucleocapsid(N) and envelope (E) genes, and enhanced glucose transport to provide more rigidity and stability resulting in increased transmissibility and pathogenicity. 2022 Microbial pathogenesis Discussion SARS_CoV_2 I82T 56 60 N;Membrane;E;N 201;21;231;214 213;29;232;215 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. An earlier study also reports that L452R mutation had abolished the neutralizing effect of 14 mAb out of around 35 RBD mAb. 2022 Microbial pathogenesis Discussion SARS_CoV_2 L452R 35 40 RBD 115 118 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. B.1 and its sublineages showing the persistent presence of D614G in their all sublineages of B.1, B.1.1.216, B.1.36.10, B.1.1.306, B.1.1.326, B.1.36.29 and B.1.36.17 confirms its paramount importance in increasing virion spike density and infectivity. 2022 Microbial pathogenesis Discussion SARS_CoV_2 D614G 59 64 S 221 226 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Both L452R and P681R were reported to also aid in escaping the virus from specific monoclonal antibody responses. 2022 Microbial pathogenesis Discussion SARS_CoV_2 L452R;P681R 5;15 10;20 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. D614G mutation earlier reported producing an allosteric conformational change in the furin cleavage site to result in RBD opening. 2022 Microbial pathogenesis Discussion SARS_CoV_2 D614G 0 5 RBD 118 121 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. D614G mutation has been reported earlier as the first mutation adapted by the variants evolved from original Wuhan nCoV. 2022 Microbial pathogenesis Discussion SARS_CoV_2 D614G 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. During 2020 year-end, subsequent to the first predominant mutation of D614G in the prototype variant, many countries have started noticing the first VOC B.1.1.7 variant after it was first reported from London. 2022 Microbial pathogenesis Discussion SARS_CoV_2 D614G 70 75 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Further, P681H in Alpha disrupts the furin cleavage site by changing the Proline to improve the rate of membrane fusion, virus entry, and higher transmissibility, albeit less efficiently than Delta variant manifesting P681R. 2022 Microbial pathogenesis Discussion SARS_CoV_2 P681H;P681R 9;218 14;223 Membrane 104 112 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. It was reported earlier that in T478K, mutated Lysine reduced the gap to the extent of 8.3 A between spike and ACE2 receptor in comparison to wild prototype which with threonine measured as 10 A to eventually enhance the viral affinity with ACE2 resulting in increased viral infectivity. 2022 Microbial pathogenesis Discussion SARS_CoV_2 T478K 32 37 S 101 106 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. L452R has already been earlier reported for escape from antibody immune response as these mutations reduces the antibody binding to mutation variants compared to wild type. 2022 Microbial pathogenesis Discussion SARS_CoV_2 L452R 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. L452R mutation was further reported to help in virus escape from cellular immunity induced with human leukocyte antigen (HLA)-24 to eventually result in increased viral replication and infectivity. 2022 Microbial pathogenesis Discussion SARS_CoV_2 L452R 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. L452R, T478K occurred in the RBD region of the spike protein. 2022 Microbial pathogenesis Discussion SARS_CoV_2 T478K;L452R 7;0 12;5 S;RBD 47;29 52;32 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Mutation of T19R, G142D, T478K, D950 N, and two deletions of F157 and R158 were exclusively seen in the Delta variant, while other mutations namely L452R, D614G, and P681R in Delta variant was also found in other lineages reported in our study. 2022 Microbial pathogenesis Discussion SARS_CoV_2 D614G;D950N;G142D;L452R;P681R;T19R;T478K 155;32;18;148;166;12;25 160;38;23;153;171;16;30 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. N440K mutation, since first detected from the state of Andhra Pradesh, has been reported in around six percent of the nCoV sequenced across India. 2022 Microbial pathogenesis Discussion SARS_CoV_2 N440K 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. N501Y and A570D at critical RBD enhance viral interaction with ACE2 human receptor. 2022 Microbial pathogenesis Discussion SARS_CoV_2 A570D;N501Y 10;0 15;5 RBD 28 31 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. N501Y, A570D, and three deletions are characteristic signature mutations of the Alpha variant. 2022 Microbial pathogenesis Discussion SARS_CoV_2 A570D;N501Y 7;0 12;5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Only B.1.36.29 and B.1.36.17 also showed N440K mutation, which was reported earlier as prone to immune escape. 2022 Microbial pathogenesis Discussion SARS_CoV_2 N440K 41 46 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. P323L leads to stability of the tertiary protein structure of the virus to help in virus successful survival in different geographical conditions. 2022 Microbial pathogenesis Discussion SARS_CoV_2 P323L 0 5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. P681R was seen in Delta, whereas P681H was observed in Alpha variant. 2022 Microbial pathogenesis Discussion SARS_CoV_2 P681H;P681R 33;0 38;5 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. Remarkably, L452R and T478K observed at the critical RBD in Delta variant have specifically been responsible for enhancing ACE2 binding. 2022 Microbial pathogenesis Discussion SARS_CoV_2 L452R;T478K 12;22 17;27 RBD 53 56 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. T19R, G142D, E156G, and two deletions of F157 and R158 located within NTD have altered a recognized monoclonal antibody (mAb) recognition site N1 and N3 loop to helps the virus in escaping antibody response. 2022 Microbial pathogenesis Discussion SARS_CoV_2 E156G;G142D;T19R 13;6;0 18;11;4 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. The combined mutations of L452R and E484Q have already been earlier reported for escape from antibody immune response. 2022 Microbial pathogenesis Discussion SARS_CoV_2 E484Q;L452R 36;26 41;31 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. The detection of D614G in all our reported lineages has strongly suggested that the emergence of all variants of SARS-CoV-2 occurred after the worldwide adaptation and rise of the D614G mutants. 2022 Microbial pathogenesis Discussion SARS_CoV_2 D614G;D614G 17;180 22;185 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. The Kappa variant harbored only four mutations of L452R, E484Q, D614G, and P681R. 2022 Microbial pathogenesis Discussion SARS_CoV_2 D614G;E484Q;L452R;P681R 64;57;50;75 69;62;55;80 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. The two mutations of P681R, D950 N were found close to the S1/S2 cleavage site to enhance viral replication and transmissibility. 2022 Microbial pathogenesis Discussion SARS_CoV_2 D950N;P681R 28;21 34;26 35065253 Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India. The two significant deletions of F157 and R158 and one substitution E156G at NTD antigenic supersite in Delta variant have also been reported as 'surge-associated mutations' to increase infectivity by 10 fold due to mechanism of evading neutralizing antibodies. 2022 Microbial pathogenesis Discussion SARS_CoV_2 E156G 68 73 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. SARS-CoV-2 spike protein substitution D614G variant is suggested to confer higher viral infectivity, efficient replication, mortality rate, and immune system evasion and transmission. 2021 Frontiers in medicine Discussion SARS_CoV_2 D614G 38 43 S 11 16 35071267 Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India. The breakthrough infections showed aa changes at position S:D574Y in the cases of Delta variant, whereas from Kappa variant conserved residue at position 95 (T) suggesting that these variations are unlikely to reduce the ability to protect against COVID-19 infection. 2021 Frontiers in medicine Discussion SARS_CoV_2 D574Y 60 65 S 58 59 COVID-19 248 266 35074352 Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. In the period under study, replacement S477N was one of the most common in the GISAID database, while A522S although frequent was much less common. 2022 Environmental research Discussion SARS_CoV_2 A522S;S477N 102;39 107;44 35074352 Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. Mutation S477N has been described to induce resistance to neutralization by multiple monoclonal antibodies and, in the presence of the S514F replacement, to human immune sera as well. 2022 Environmental research Discussion SARS_CoV_2 S477N;S514F 9;135 14;140 35074352 Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. Mutations T73A and D253N are located in loops N2 and N5, respectively, of the NTD of the S glycoprotein of SARS-CoV-2. 2022 Environmental research Discussion SARS_CoV_2 D253N;T73A 19;10 24;14 S 89 103 35074352 Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. Similarly, mutations S477N and A522S which were present in the same genome molecule, could represent a combination of concern. 2022 Environmental research Discussion SARS_CoV_2 A522S;S477N 31;21 36;26 35074352 Dynamics of SARS-CoV-2 Alpha (B.1.1.7) variant spread: The wastewater surveillance approach. The effect of the combination of the S477N and A522S mutations on the resistance phenotype to immune sera has not yet been elucidated, but it cannot be rule out. 2022 Environmental research Discussion SARS_CoV_2 A522S;S477N 47;37 52;42 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. Among these six SNVs, four nucleotides (c28854, g28881, g28882, g28883) were non-synonymous and code residues S194L, R203K, R203S and G204R, respectively, in Nucleocapsid, and two nucleotides (t19839, a20268) in endoRNase of orf1ab encoded synonymous changes (N73N and L216L, respectively). 2022 Scientific reports Discussion SARS_CoV_2 G204R;L216L;R203K;R203S;S194L;N73N 134;269;117;124;110;260 139;274;122;129;115;264 N;EndoRNAse;ORF1ab 158;212;225 170;221;231 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. It is worth noting that the a23403 (D614G), the only SNV in the spike protein, was found not to associate with the severity of COVID-19 (p = 0.29), implying Spike protein may have a limited role in disease severity. 2022 Scientific reports Discussion SARS_CoV_2 D614G 36 41 S;S 64;157 69;162 COVID-19 127 135 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. The main variant in the endoRNase, N73N, is synonymous which suggests a testable hypotheses concerning potential impact on virus fitness or function. 2022 Scientific reports Discussion SARS_CoV_2 N73N 35 39 EndoRNAse 24 33 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. The mutations R203S and G204R are non-conservative and even the R203K mutation is often observed to function as a non-conservative substitution in many cases, due to the different size of the R versus K residues and the notably different chemical features of the side-chain guanidinium group (arginine) versus the primary amine (lysine). 2022 Scientific reports Discussion SARS_CoV_2 G204R;R203K;R203S 24;64;14 29;69;19 35075180 Mutations in viral nucleocapsid protein and endoRNase are discovered to associate with COVID19 hospitalization risk. The non-synonymous mutations R203K, R203S and G204R in the nucleocapsid protein all occur in the flexible linker region between the N-terminal RNA-binding domain and the C-terminal dimerization domain, and this linker segment is not resolved in any reported cryo-EM or x-ray structures. 2022 Scientific reports Discussion SARS_CoV_2 G204R;R203K;R203S 46;29;36 51;34;41 N;N 59;132 71;133 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. Both E mutations are in the N-terminal part of the protein that is predicted to be on (V5F) or close to (13IACLV) the surface of the virus and the luminal side of endoplasmic reticulum (ER)-Golgi intermediate compartment. 2022 EBioMedicine Discussion SARS_CoV_2 V5F 87 90 E;N 5;28 6;29 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. Our authentic virus approach identified antibody-specific escape mutations in RBD of the Spike protein, S477R and T345N, that directly affect the recognition by the antibodies. 2022 EBioMedicine Discussion SARS_CoV_2 S477R;T345N 104;114 109;119 S;RBD 89;78 94;81 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. The antibodies were oblivious to the E484K mutation, which has been recently shown to endow the S-typed VSV pseudovirus with resistance to several human convalescent sera. 2022 EBioMedicine Discussion SARS_CoV_2 E484K 37 42 S 96 97 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. The AX677 virus contained different mutation in the E protein, the V5F substitution. 2022 EBioMedicine Discussion SARS_CoV_2 V5F 67 70 E 52 53 35078012 Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. We found that the AX677 escape virus carrying the T345N mutation in Spike had greatly reduced fitness in comparison with the parental virus under antibody-free conditions (Figure 5d). 2022 EBioMedicine Discussion SARS_CoV_2 T345N 50 55 S 68 73 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. An in vitro enzymatic assay of recombinant Pro108Ser showed that the Kcat/Km value of the mutant 3CLpro containing Ser108 was 58% lower as compared with that of 3CLpro containing Pro108. 2022 Scientific reports Discussion SARS_CoV_2 P108S 43 52 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Cell-based cytotoxic and replication assays, similar to the ones performed in preclinical studies of PF-07321332, would further validate the direct linkage between reduced viral replication and the P108S mutation in 3CLpro of SARS-CoV-2. 2022 Scientific reports Discussion SARS_CoV_2 P108S 198 203 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. HDX-MS revealed that the substrate binding site is locally impacted by the mutation, leading to a reduced substrate binding affinity, even though the Pro108Ser did not affect the overall structure or association site the SV-AUC and CD spectroscopy sites. 2022 Scientific reports Discussion SARS_CoV_2 P108S 150 159 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Patients in this study cohort who were infected with the virus sub-lineage that carried the Pro108Ser of 3CLpro (N = 87) (which is the main protease in the virus that cleaves the viral polyproteins into individual proteins that exert viral functions) tended to have a milder disease course than those infected with a viral sub-lineage that did not carry this mutation of 3CLpro (N = 85). 2022 Scientific reports Discussion SARS_CoV_2 P108S 92 101 35079088 Pro108Ser mutation of SARS-CoV-2 3CL(pro) reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Thus, despite the distance between the mutation site and the substrate-biding site, Pro108Ser appears to play a critical role in the reduced enzyme activity and may abrogate both the replication potency and pathogenicity of the virus. 2022 Scientific reports Discussion SARS_CoV_2 P108S 84 93 35079901 Trypsin enhances SARS-CoV-2 infection by facilitating viral entry. Although biochemical studies are needed to investigate whether S proteins with the R685S mutation are cleaved, this mutation suggests that proteolytic priming of the S protein might be dispensable for virus replication in vitro. 2022 Archives of virology Discussion SARS_CoV_2 R685S 83 88 S;S 63;166 64;167 35079901 Trypsin enhances SARS-CoV-2 infection by facilitating viral entry. Considering that none of the P10(-) through P50(-) strains induced syncytia formation, the R685S mutation might make the S1/S2 FCS non-functional and, accordingly, prevent fusion at the plasma membrane. 2022 Archives of virology Discussion SARS_CoV_2 R685S 91 96 Membrane 193 201 35079901 Trypsin enhances SARS-CoV-2 infection by facilitating viral entry. Interestingly, all cell-adapted P10(-) through P50(-) strains contained an R685S substitution in the S1/S2 FCS (681PRRAR685), changing this sequence to 681PRRAS685. 2022 Archives of virology Discussion SARS_CoV_2 R685S 75 80 35079901 Trypsin enhances SARS-CoV-2 infection by facilitating viral entry. It is therefore notable that N960I and V961A mutations were identified in S2 of the P20(+) through to P50(+) strains and that additional K849R and Q949R mutations emerged in the S2 fusion domain of P50(+), suggesting that these genetic changes may contribute to cytopathology. 2022 Archives of virology Discussion SARS_CoV_2 K849R;N960I;Q949R;V961A 137;29;147;39 142;34;152;44 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. Although the specific epitope of HB27 is unknown, it is predicted to be concentrated within the RBD region, potentially explaining the observed immune escape by S477N+D614G, and the corresponding single point mutant S477N showed immune escape from mAb 09-7B8. 2022 Archives of virology Discussion SARS_CoV_2 S477N;S477N;D614G 161;216;167 166;221;172 RBD 96 99 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. At present, the S477N mutation accounts for 5.0% of mutant strains circulating in Portugal. 2022 Archives of virology Discussion SARS_CoV_2 S477N 16 21 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. In the current study, the infectivity of B.1.1.7 did not change significantly after addition of the M740V or L216F mutation. 2022 Archives of virology Discussion SARS_CoV_2 L216F;M740V 109;100 114;105 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. In this study, the VSV system was used to construct pseudoviruses harboring high-frequency SARS-CoV-2 mutations circulating in Portugal, including D614G, A222V+D614G, B.1.1.7, D839Y+D614G, P1162R+D614G+A222V, S477N+D614G, and L176F+D614G, as well as mutations found in UK strains, including B.1.1.7+L216F, B.1.1.7+M740V, B.1.258, B.1.258+L1063F, and B.1.258+N751Y. 2022 Archives of virology Discussion SARS_CoV_2 A222V;D614G;D839Y;L176F;P1162R;S477N;A222V;D614G;D614G;D614G;D614G;D614G;L1063F;L216F;M740V;N751Y 154;147;176;226;189;209;202;160;182;196;215;232;338;299;314;358 159;152;181;231;195;214;207;165;187;201;220;237;344;304;319;363 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. Interestingly, for the majority of high-frequency mutant viruses circulating in Portugal (i.e., A222V+D614G, B.1.1.7, D839Y+D614G, P1162R+D614G+A222V, S477N+D614G, and L176F+D614G, but not B.1.1.7 and S477N+D614G), immune escape from the mAbs used in this study was not observed. 2022 Archives of virology Discussion SARS_CoV_2 A222V;D839Y;L176F;P1162R;S477N;S477N;A222V;D614G;D614G;D614G;D614G;D614G;D614G 96;118;168;131;151;201;144;102;124;138;157;174;207 101;123;173;137;156;206;149;107;129;143;162;179;212 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. Previous studies have shown that compared with D614G, the infectivity of B.1.1.7 in cells containing the hACE2 receptor showed no significant difference, which is consistent with the results of this study. 2022 Archives of virology Discussion SARS_CoV_2 D614G 47 52 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. Previous studies have shown that the N501Y mutation affects the antigenicity of the S protein. 2022 Archives of virology Discussion SARS_CoV_2 N501Y 37 42 S 84 85 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. The antigenicity of B.1.1.7 and derived viruses with combined mutations (M740V+B.1.1.7 and L216F+B.1.1.7), and B.1.258 and derived viruses with combined mutations (B.1.258+L1063F and B.1.258+N751Y) differed. 2022 Archives of virology Discussion SARS_CoV_2 L216F;M740V;L1063F;N751Y 91;73;172;191 96;78;178;196 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. The mutant virus B.1.258 (containing the mutations N439K and Delta69-70Del) also exhibits immune escape from the mAb HB27. 2022 Archives of virology Discussion SARS_CoV_2 N439K 51 56 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. The pseudoviruses that exhibited immune escape all contained the N501Y mutation, and the results of this experiment were consistent with the expected results. 2022 Archives of virology Discussion SARS_CoV_2 N501Y 65 70 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. There was no significant difference in infectivity between the Portuguese high-frequency mutants and the D614G mutant pseudovirus (a ratio >4 was defined as a significant difference). 2022 Archives of virology Discussion SARS_CoV_2 D614G 105 110 35083576 Infectivity and antigenicity of pseudoviruses with high-frequency mutations of SARS-CoV-2 identified in Portugal. Therefore, pseudoviruses containing the N501Y mutation will undergo immune escape or a decrease in the protective effects of the mAb will be observed. 2022 Archives of virology Discussion SARS_CoV_2 N501Y 40 45 35090164 Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants. Furthermore, our structural and functional analyses revealed that the G446S mutation might act as a critical antibody escape site, conferring greater resistance to one major class of antibodies bound at the right shoulder of RBD by altering microenvironments at the S-neutralizing antibody-binding interface. 2022 Nature Discussion SARS_CoV_2 G446S 70 75 RBD;S 225;266 228;267 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. Almost all (>=97%) participants who were SARS-CoV-2 naive attained a four-fold rise in neutralising antibody titres to the D614G variant at day 36, regardless of age strata, presence of high-risk medical condition, or antigen dose. 2022 The Lancet. Infectious diseases Discussion SARS_CoV_2 D614G 123 128 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. Among adults who were non-naive in our study, a single injection increased D614G neutralising-antibody titres to concentrations higher than those observed after two injections in adults who were naive and exceeded those measured in the convalescent sera. 2022 The Lancet. Infectious diseases Discussion SARS_CoV_2 D614G 75 80 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. In the phase 3 study, a bivalent AS03-adjuvanted vaccine containing 5 7mu;g D614G antigen and 5 7mu;g beta antigen is being evaluated. 2022 The Lancet. Infectious diseases Discussion SARS_CoV_2 D614G 76 81 35090638 Safety and immunogenicity of an AS03-adjuvanted SARS-CoV-2 recombinant protein vaccine (CoV2 preS dTM) in healthy adults: interim findings from a phase 2, randomised, dose-finding, multicentre study. On the basis of these results, two formulations of the CoV2 preS dTM-AS03 vaccine candidate, a monovalent D614G and a bivalent D614G and a beta variant vaccine, are undergoing efficacy evaluation in phase 3 trials. 2022 The Lancet. Infectious diseases Discussion SARS_CoV_2 D614G;D614G 106;127 111;132 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Another limitation is that only Y453F-containing viruses were followed up for in depth virological study, therefore this work cannot make strong conclusions about the zoonotic potential of the other mink adaptations that often appear, particularly N501T, which has subsequently appeared on several human SARS-CoV-2 variant lineages. 2022 Cell reports Discussion SARS_CoV_2 N501T;Y453F 248;32 253;37 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Except for the Danish mink-adapted SARS-CoV-2 spillback, Y453F is found rarely in humans with very few isolates reported in GISAID and only a single report of the mutation arising in immunocompromised patients - this is despite Y453F having been shown in several studies to enhance human ACE2 binding, in a similar manner to the VOC-associated mutations N501Y or L452R. 2022 Cell reports Discussion SARS_CoV_2 L452R;N501Y;Y453F;Y453F 363;354;57;228 368;359;62;233 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Here, we have demonstrated many VOCs, particularly Alpha/B.1.1.7 as well as those containing L452R (such as Delta/B.1.617.2), could have a fundamental fitness advantage in mink by increasing interaction with mustelid ACE2, compared with previous nonvariant strains. 2022 Cell reports Discussion SARS_CoV_2 L452R 93 98 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. However, Y453F in particular, negatively impacts replication kinetics of SARS-CoV-2 in human cells, potentially explaining why the Danish mink-origin outbreaks did not propagate further following the culling of the mink. 2022 Cell reports Discussion SARS_CoV_2 Y453F 9 14 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. This would suggest that unlike the VOC-associated mutations, such as N501Y, Y453F attenuates viral fitness in human cells, we speculate this could be due to the previously described destabilization of the spike caused by Y453F outweighing any potential increase in human ACE2 binding. 2022 Cell reports Discussion SARS_CoV_2 N501Y;Y453F;Y453F 69;76;221 74;81;226 S 205 210 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. We have shown earlier strains of SARS-CoV-2 are poorly adapted to mustelid ACE2 and therefore quickly gain adaptations, such as Y453F, N501T, or F486L to use mustelid ACE2. 2022 Cell reports Discussion SARS_CoV_2 F486L;N501T;Y453F 145;135;128 150;140;133 35093235 Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. We have shown that, even in the presence of the putative stabilizing NTD deletion, Delta69-70, virus harboring the Y453F substitution was outcompeted by a closely related virus in human cells. 2022 Cell reports Discussion SARS_CoV_2 Y453F 115 120 35095814 A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands. Nevertheless, in late weeks, the additional spike substitution S:Q613H has been detected in an increasing number of genomes belonging to the Delta variant. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Q613H 65 70 S;S 44;63 49;64 35095814 A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands. Since early 2020, lineage A viruses have not been detected which probably reflects an evolutionary advantage of the D614G spike mutation present in all lineage B viruses. 2021 Frontiers in microbiology Discussion SARS_CoV_2 D614G 116 121 S 122 127 35095814 A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands. This lineage is defined by 14 amino acid changes and three deletions, including six amino acid substitutions and two deletions in the spike protein: S:DeltaH69-V70, S:DeltaY144, S:N501Y, S:A570D, S:P681H, S:T716I, S:S982A, and S:D1118H and it has been related with some evolutionary advantages such as an increased transmissibility. 2021 Frontiers in microbiology Discussion SARS_CoV_2 A570D;D1118H;N501Y;P681H;S982A;T716I 189;229;180;198;216;207 194;235;185;203;221;212 S;S;S;S;S;S;S;S;S 134;149;165;178;187;196;205;214;227 139;150;166;179;188;197;206;215;228 35095814 A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands. This lineage, initially named 20E-EU1 variant and characterized by the spike substitution A222V, was identified in Spain in early summer 2020 and rapidly became the dominant lineage in several European countries. 2021 Frontiers in microbiology Discussion SARS_CoV_2 A222V 90 95 S 71 76 35095814 A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands. This mutation is speculated to be important as it occurs at a position neighboring the fitness-enhancing mutation S:D614G. 2021 Frontiers in microbiology Discussion SARS_CoV_2 D614G 116 121 S 114 115 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. All these substitutions were associated with the B.1.1.7 lineage, besides spike N501Y which also characterizes P.1 and B.1.351 lineages, as their corresponding clade nomenclature suggests. 2021 Frontiers in microbiology Discussion SARS_CoV_2 N501Y 80 85 S 74 79 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. Another substitution whose frequency deviated from the global value was spike Y144F, which was again found only in sequences of the B.1.177.75 lineage. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y144F 78 83 S 72 77 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. Globally, spike Y144F substitution was found quite rarely, with only 1,487 GISAID sequences on almost 2 million total depositions (<0.08%), but a significant proportion of this sequences (1.7%) came from Sardinia, indicating a higher prevalence of this mutation in the island. 2021 Frontiers in microbiology Discussion SARS_CoV_2 Y144F 16 21 S 10 15 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. In contrast, no other significantly diffused RdRp substitution was found in our dataset, except for P4717L. 2021 Frontiers in microbiology Discussion SARS_CoV_2 P4717L 100 106 RdRP 45 49 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. In particular, spike A222V, A262S, P272L, T696I, and S884C were significantly more frequent in our dataset. 2021 Frontiers in microbiology Discussion SARS_CoV_2 A222V;A262S;P272L;S884C;T696I 21;28;35;53;42 26;33;40;58;47 S 15 20 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. In the N gene some deviations from the global frequencies were found as well, namely nucleocapsid A220V, which was again found only in B.1.177 and sublineages, or the A156S and S187A substitutions, which were associated with a few samples of the lineages B.1.1.7 and C.16, respectively, and only rarely found worldwide. 2021 Frontiers in microbiology Discussion SARS_CoV_2 A156S;A220V;S187A 167;98;177 172;103;182 N;N 85;7 97;8 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. It emerged that these two synonymous mutations, namely c.14676C > T and c.15279C > T in ORF1ab, are included in the set of SNPs that are used by the Nextclade v0.14.2 algorithm to identify clade 20I. 2021 Frontiers in microbiology Discussion SARS_CoV_2 C14676T;C15279T 55;72 67;84 ORF1ab 88 94 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. It is important to also notice how most of the lineages detected in the III wave were then classified as VOC (B.1.1.7 and B.1.351) or VUM (C.36 + L452R) by the ECDC. 2021 Frontiers in microbiology Discussion SARS_CoV_2 L452R 146 151 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. It was also observed, along with spike D614G, to be more frequent in severely affected COVID-19 patients, compared to a cohort of mildly affected ones. 2021 Frontiers in microbiology Discussion SARS_CoV_2 D614G 39 44 S 33 38 COVID-19 87 95 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. Other substitutions were found in specific lineages, such as spike H69_V70del, Y144del, N501Y, or nucleocapsid S235F. 2021 Frontiers in microbiology Discussion SARS_CoV_2 N501Y;S235F;Y144del 88;111;79 93;116;86 N;S 98;61 110;66 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. RdRp P4715L was associated with a drastic change in protein structure and, possibly, function. 2021 Frontiers in microbiology Discussion SARS_CoV_2 P4715L 5 11 RdRP 0 4 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. Some globally rare (~1% or less) spike substitutions in the RBD were identified, namely R346S, K417N, and N440K. 2021 Frontiers in microbiology Discussion SARS_CoV_2 K417N;N440K;R346S 95;106;88 100;111;93 S;RBD 33;60 38;63 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. Spike N501Y was associated with a slight but significant reduction in neutralization. 2021 Frontiers in microbiology Discussion SARS_CoV_2 N501Y 6 11 S 0 5 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. Spike substitution D614G was associated with enhanced infectivity of SARS-CoV-2, while no significant impact on neutralization with monoclonal antibodies and with sera from convalescent/vaccinated patients was detected. 2021 Frontiers in microbiology Discussion SARS_CoV_2 D614G 19 24 S 0 5 35095827 Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia. The identification of the specific missense mutations for each gene highlighted how some substitutions are ubiquitous, such as spike D614G and RdRp P4715L (also known as P323L). 2021 Frontiers in microbiology Discussion SARS_CoV_2 D614G;P323L;P4715L 133;170;148 138;175;154 S;RdRP 127;143 132;147 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. In the present manuscript, retrospective NGS of SARS-CoV-2 viral genomes revealed a double Spike mutation D614G/S939F in the members of Bangladeshi community located in Ostia as occasional employees. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 D614G;S939F 106;112 111;117 S 91 96 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. peptides to any HLA molecules was affected by S939F mutation when compared to D614G mutation, that, on the contrary, had no impact on the affinity of strongly binding peptides. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 D614G;S939F 78;46 83;51 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Pre-clinical evidence showed that D614G/S939F double Spike mutation was among those mutations that exhibited higher rate of infection. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 D614G;S939F 34;40 39;45 S 53 58 35096288 Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. This led to the evaluation of T cell propensity that resulted slight but significantly modulated upon S939F mutation compared to D614G. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 D614G;S939F 129;102 134;107 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. The Beta and Gamma variants are the most resistant to monoclonal antibodies (mAbs) and convalescent plasma from SARS CoV-2-infected individuals, and the resistance profiles correspond to several deletions in the N-terminal domain and the K417N/T, E484K/Q, and N501Y mutations in the RBD of SARS-CoV-2 Spike protein. 2022 Vaccine Discussion SARS_CoV_2 E484K;E484Q;K417N;K417T;N501Y 247;247;238;238;260 254;254;245;245;265 S;RBD;N 301;283;212 306;286;213 COVID-19 112 131 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. The E484 position was identified as a dominant residue for escape from neutralizing activity by sera from COVID-19 convalescent patients with the E484K mutation in the SARS-CoV-2 Beta variant as the key factor responsible for the reduced neutralization potency of convalescent immune sera and human mAbs. 2022 Vaccine Discussion SARS_CoV_2 E484K 146 151 COVID-19 106 114 35101265 Pan-SARS neutralizing responses after third boost vaccination in non-human primate immunogenicity model. These data further suggest the need for updated vaccine sequences or multivalent formulations for naive individuals, at least to cover those strains with key mutations, such as E484K/Q, which can escape the vaccine-induced antiviral responses. 2022 Vaccine Discussion SARS_CoV_2 E484K;E484Q 177;177 184;184 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Among our samples we initially observed an apparent association between the R203K/G204R mutations and mortality, however, the association was no longer statistically significant when correcting for sampling time. 2022 Nature communications Discussion SARS_CoV_2 R203K;G204R 76;82 81;87 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. In conclusion, our results suggest a major influence of the R203K/G204R mutations on the essential properties and phosphorylation status of SARS-CoV-2 N protein that may lead to increased host response and heightened efficacy of viral infection. 2022 Nature communications Discussion SARS_CoV_2 R203K;G204R 60;66 65;71 N 151 152 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Our COVID-19 patient data allowed to us detect three SNPs:underlying the N protein R203K and G204R mutations:significantly associated with higher viral load. 2022 Nature communications Discussion SARS_CoV_2 G204R;R203K 93;83 98;88 N 73 74 COVID-19 4 12 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. The association of N protein R203K and G204R mutations with higher viral load persists after adjusting for time but not with mortality, suggesting that the mortality rate of severe infections may be influenced by other factors such as changes in treatment regimes as well as the complexities of host response to SARS-CoV-2 infection. 2022 Nature communications Discussion SARS_CoV_2 G204R;R203K 39;29 44;34 N 19 20 COVID-19 312 332 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. The enrichment of glycogen synthase kinase 3 A (GSK3A) with the mutant N protein, could specifically phosphorylate serine 206 in the R203K/G204R mutation background. 2022 Nature communications Discussion SARS_CoV_2 R203K;G204R 133;139 138;144 N 71 72 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. The R203K and G204R mutations are in close proximity to the recently reported RNA-mediated phase-separation domain (aa 210-246) that is involved in viral RNA packaging through phase separation. 2022 Nature communications Discussion SARS_CoV_2 G204R;R203K 14;4 19;9 35105893 SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. We show that the mutant N protein-containing R203K and G204R changes has higher oligomerization and stronger viral RNA-binding ability, suggesting a potential link of these mutations with efficient viral genome packaging. 2022 Nature communications Discussion SARS_CoV_2 G204R;R203K 55;45 60;50 N 24 25 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. Further, while we determined it was outside the scope of the current paper, we did not generate/analyze crystal structures of an escape variant such as RBD-E484K in complex with antibodies N-612-017-01/03 in comparison with N-612-017. 2022 Cell reports Discussion SARS_CoV_2 E484K 156 161 RBD 152 155 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. Our N-612-017 antibody is a class 2 RBD binder similar to bamlanivimab that also displays a loss of activity in the presence of the E484K mutation. 2022 Cell reports Discussion SARS_CoV_2 E484K 132 137 RBD 36 39 35114110 Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. To address this potential loss of efficacy, we used affinity maturation for N-612-017 and quickly identified subclones that restored affinity for both E484K and L452R. 2022 Cell reports Discussion SARS_CoV_2 E484K;L452R 151;161 156;166 35115239 Persistent viral shedding of severe acute respiratory syndrome coronavirus 2 after treatment with bendamustine and rituximab: A case report. In general, the Ct value is often approximately 20 during the early stage of SARS-CoV-2 infection, including that caused by the N501Y variant; the number increases to over 35 approximately two weeks later. 2022 Journal of infection and chemotherapy Discussion SARS_CoV_2 N501Y 128 133 COVID-19 77 97 35123044 Clinical and genomic data of sars-cov-2 detected in maternal-fetal interface during the first wave of infection in Brazil. A critical polymorphic region of this protein is the serine-arginine region located in amino acids 183-206, exactly where the R203K and G204R aa changes locate. 2022 Microbes and infection Discussion SARS_CoV_2 G204R;R203K 136;126 141;131 35123044 Clinical and genomic data of sars-cov-2 detected in maternal-fetal interface during the first wave of infection in Brazil. D614G in Spike S1 subunit, outside the RBD binding site, was found in both sequences of this study. 2022 Microbes and infection Discussion SARS_CoV_2 D614G 0 5 S;RBD 9;39 14;42 35123044 Clinical and genomic data of sars-cov-2 detected in maternal-fetal interface during the first wave of infection in Brazil. F490S was identified in MT21770 sequence. 2022 Microbes and infection Discussion SARS_CoV_2 F490S 0 5 35123044 Clinical and genomic data of sars-cov-2 detected in maternal-fetal interface during the first wave of infection in Brazil. MT21774 also has one NSP3 (V2090G), one Membrane protein (A2S) and two ORF3ab (S253P and Y264N) aa changes in addition to the characteristic mutations reported worldwide for its lineage. 2022 Microbes and infection Discussion SARS_CoV_2 Y264N;A2S;S253P;V2090G 89;58;79;27 94;61;84;33 Membrane;Nsp3 40;21 48;25 35123044 Clinical and genomic data of sars-cov-2 detected in maternal-fetal interface during the first wave of infection in Brazil. Mutation P314L in NSP12 (RdRp) has also been linked to increased viral fitness. 2022 Microbes and infection Discussion SARS_CoV_2 P314L 9 14 Nsp12;RdRP 18;25 23;29 35123044 Clinical and genomic data of sars-cov-2 detected in maternal-fetal interface during the first wave of infection in Brazil. Mutations R203K/G204R in the Nucleocapsid gene, were found in both sequences. 2022 Microbes and infection Discussion SARS_CoV_2 R203K;G204R 10;16 15;21 N 29 41 35123044 Clinical and genomic data of sars-cov-2 detected in maternal-fetal interface during the first wave of infection in Brazil. The presence of both aa changes, D614G in S protein and P314L in NSP12 has been associated with the fast SARS-CoV-2 dissemination worldwide. 2022 Microbes and infection Discussion SARS_CoV_2 D614G;P314L 33;56 38;61 Nsp12;S 65;42 70;43 35123044 Clinical and genomic data of sars-cov-2 detected in maternal-fetal interface during the first wave of infection in Brazil. The V1176F aa change (MT21774 sequence) is located in the short S2 subunit, region involved in viral envelope fusion with cell membrane after ACE2-receptor binding, TMRPSS2 priming and endocytosis. 2022 Microbes and infection Discussion SARS_CoV_2 V1176F 4 10 Membrane 127 135 35123044 Clinical and genomic data of sars-cov-2 detected in maternal-fetal interface during the first wave of infection in Brazil. These other aa changes are located in ORF1ab, specifically in NSP3 (E995D), NSP12 (R240K) and NSP14 (H1897Y) and in ORF7b (V21F), however, no other information about their relevance has been reported in literature. 2022 Microbes and infection Discussion SARS_CoV_2 E995D;H1897Y;R240K;V21F 68;101;83;123 73;107;88;127 ORF1ab;ORF7b;Nsp12;Nsp3 38;116;76;62 44;121;81;66 35123263 The function of SARS-CoV-2 spike protein is impaired by disulfide-bond disruption with mutation at cysteine-488 and by thiol-reactive N-acetyl-cysteine and glutathione. Here, we showed that the C488A spike mutant lost its fusogenic and infectious activities. 2022 Biochemical and biophysical research communications Discussion SARS_CoV_2 C488A 25 30 S 31 36 35126106 Antidepressant and Antipsychotic Drugs Reduce Viral Infection by SARS-CoV-2 and Fluoxetine Shows Antiviral Activity Against the Novel Variants in vitro. Our data suggest that fluoxetine remains effective against the pseudotyped viruses harboring single mutations (N501Y, K417N, E484K), or a triple mutation (N501Y/K417N/E484K) present in beta and gamma variants. 2021 Frontiers in pharmacology Discussion SARS_CoV_2 E484K;K417N;N501Y;N501Y;E484K;K417N 125;118;111;155;167;161 130;123;116;160;172;166 35126106 Antidepressant and Antipsychotic Drugs Reduce Viral Infection by SARS-CoV-2 and Fluoxetine Shows Antiviral Activity Against the Novel Variants in vitro. Recent in vitro studies reported that some of these vaccines remain effective against the variants carrying a set of mutations; however, others have shown decreased effectiveness, particularly to those carrying the E484K mutation. 2021 Frontiers in pharmacology Discussion SARS_CoV_2 E484K 215 220 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. However, we introduced substitution Q57H in D155Y and another variant S171L, and simulated them for 200 ns. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 D155Y;Q57H;S171L 44;36;70 49;40;75 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. In this study, we provide evidence that substitution D155Y changes the intramolecular hydrogen bond formation, salt bridge formation, and disrupts the interaction between ORF3a and caveolin-1. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 D155Y 53 58 ORF3a 171 176 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. On the basis of our in silicostudy, we are currently investigating the effect of D155Y in cell lines. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 D155Y 81 86 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. Only the Q57H-D155Y variant was found to be considerably less stable. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 Q57H;D155Y 9;14 13;19 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. These intragenetic interactions open up the possibility of potential evolutionary links of the substitutions at D155Y with other positively selected loci in the viral genes, subject to demographic variations. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 D155Y 112 117 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. We also checked the structural stability of W131C, W131R, G172C and G172V, which were found in Domain III and VI, respectively. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 G172C;G172V;W131C;W131R 58;68;44;51 63;73;49;56 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. We may hypothesise that the reduced binding affinity of ORF3a to caveolin-1 may be attributed to the structural instability of the D155Y variant. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 D155Y 131 136 ORF3a 56 61 35126886 D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1. We simulated the variants W131C, W131R, G172C and G172V for 200 ns. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 G172C;G172V;W131C;W131R 40;50;26;33 45;55;31;38 35128118 SARS-CoV-2 in Egypt: epidemiology, clinical characterization and bioinformatics analysis. All clades with D614G mutation are characterized by higher transmission, however, clades GH and GR showed higher virulence and significantly showed higher incidence among death or severe cases. 2022 Heliyon Discussion SARS_CoV_2 D614G 16 21 35128118 SARS-CoV-2 in Egypt: epidemiology, clinical characterization and bioinformatics analysis. Further analysis confirmed that all the Egyptian sequences were mutated and carried D614G, V5F, Q57H and G823S mutations. 2022 Heliyon Discussion SARS_CoV_2 D614G;G823S;Q57H;V5F 84;105;96;91 89;110;100;94 35128118 SARS-CoV-2 in Egypt: epidemiology, clinical characterization and bioinformatics analysis. In agreement with this finding, several studies conducted to track the distribution of viral clades in different countries reported the higher prevalence of all clades with D614G mutation. 2022 Heliyon Discussion SARS_CoV_2 D614G 173 178 35128118 SARS-CoV-2 in Egypt: epidemiology, clinical characterization and bioinformatics analysis. In the present study, we investigated 144 SARS-CoV-2sequences for detection of mutations landscape and confirmed that the most predominant subclade of D614G in Egypt was D614G/Q57H/V5F/G823S consistent with the results of Lamptey et al. 2022 Heliyon Discussion SARS_CoV_2 D614G;D614G;G823S;Q57H;V5F 151;170;185;176;181 156;175;190;180;184 35128118 SARS-CoV-2 in Egypt: epidemiology, clinical characterization and bioinformatics analysis. Moreover, the spike proteins (SP) of all Egyptian tested strains (n = 144) are completely identical in that they have a G to D substitution at site 614 compared with the reference strain (NC_045512). 2022 Heliyon Discussion SARS_CoV_2 G614D 120 151 S;S 14;30 19;32 35128118 SARS-CoV-2 in Egypt: epidemiology, clinical characterization and bioinformatics analysis. recorded that the Nsp12 thumb subdomain variant G823S was prevalent in samples collected during August, in Africa. 2022 Heliyon Discussion SARS_CoV_2 G823S 48 53 Nsp12 18 23 35128118 SARS-CoV-2 in Egypt: epidemiology, clinical characterization and bioinformatics analysis. reported that the D614G mutation was the most dominant mutation on the spike glycoprotein in about 84.2% of isolates in Africa, where it was detected in all isolates from Algeria, Morocco, and the Democratic Republic of Congo, and was co-occurred with E_V5F mutation in two Egyptian isolates. 2022 Heliyon Discussion SARS_CoV_2 D614G 18 23 S 71 89 35128118 SARS-CoV-2 in Egypt: epidemiology, clinical characterization and bioinformatics analysis. The D614G/E_V5F mutation was not observed in any other African country. 2022 Heliyon Discussion SARS_CoV_2 D614E;D614G;V5F 4;4;12 9;9;15 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. In contrast, several substitutions were estimated to be less likely to appear in vaccine breakthrough samples, including nucleocapsid mutation P199L (detected in B.1.2, B.1.526, and B.1.596; odds ratio of 0.5; 95% credible interval of 0.24-0.88), and spike mutation D253G (detected in B.1.526; odds ratio of 0.5; 95% credible interval of 0.23-0.89). 2022 mBio Discussion SARS_CoV_2 D253G;P199L 266;143 271;148 N;S 121;251 133;256 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. N501Y is found in several of the VBM, and this substitution is well known to increase affinity of binding for the viral spike protein to the ACE2 receptor, as well as reduce antibody binding to promote immune evasion. 2022 mBio Discussion SARS_CoV_2 N501Y 0 5 S 120 125 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. Recently the N501Y substitution was suggested to be a central feature in a meta-signature of up to 35 mutations which recur in alpha, beta, gamma and other lineages, and which mark a viral fitness peak reflecting optimization for spread in humans. 2022 mBio Discussion SARS_CoV_2 N501Y 13 18 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. The N501Y substitution stood out among point substitutions for enrichment in vaccine breakthroughs. 2022 mBio Discussion SARS_CoV_2 N501Y 4 9 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. The N501Y substitution stood out as particularly associated with vaccine breakthroughs. 2022 mBio Discussion SARS_CoV_2 N501Y 4 9 35130727 SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021. The spike D253G substitution has been implicated in MAb evasion, and nucleocapsid P199L may alter the assembly of SARS-CoV-2 VLPs, functions possibly linked to their depletion in vaccine breakthrough. 2022 mBio Discussion SARS_CoV_2 D253G;P199L 10;82 15;87 N;S 69;4 81;9 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Analysis of the electrostatic surface potential of the ACE2-bound Delta variant S protein is consistent with enhancements in electrostatic complementarity afforded by both the L452R and T478K mutations. 2022 Nature communications Discussion SARS_CoV_2 L452R;T478K 176;186 181;191 S 80 81 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. As S protein cleavage is a crucial step in the pre- to post-fusion transition of the S protein, the P681R mutation likely contributes to the reported increase in Delta variant replication kinetics and viral loads in oropharyngeal and nose/throat swabs of infected individuals. 2022 Nature communications Discussion SARS_CoV_2 P681R 100 105 S;S 3;85 4;86 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Consistent with previous mutational studies that used S proteins with the K417N mutation alone, recent results have demonstrated enhanced immune evasion and decreased ACE2 affinity for the Delta plus (B.1.617.2+) variant relative to Delta (B.1.617.2). 2022 Nature communications Discussion SARS_CoV_2 K417N 74 79 S 54 55 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Finally, the effects of the D950N mutation (Delta) and the Q1071H mutation within the S protein fusion machinery (Kappa), as well as mutations outside of the S protein open-reading frame, have yet to be assessed for their impact on SARS-CoV-2 viral fitness. 2022 Nature communications Discussion SARS_CoV_2 D950N;Q1071H 28;59 33;65 S;S 86;158 87;159 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. For example, the L452R mutation, mutations at position 484 (E484K and E484Q) and mutations within the N3 loop in the NTD (residues 141-156) have all been previously characterised for their antibody-evasive effects in other variants. 2022 Nature communications Discussion SARS_CoV_2 E484Q;L452R;E484K 70;17;60 75;22;65 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. For example, the P681R mutation - found in all B.1.617 sub-lineages - has recently been reported to enhance S protein cleavage and cell-cell fusion. 2022 Nature communications Discussion SARS_CoV_2 P681R 17 22 S 108 109 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. However, an analysis of mutational frequency at position 484 in globally deposited sequences reveals that only E484, K484 and Q484 S protein genotypes have ever been present at >1% of total deposited sequences, suggesting limited mutational flexibility at this position. 2022 Nature communications Discussion SARS_CoV_2 Q484S 126 132 S 131 132 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. However, for the Kappa variant we report an unprecedented head-to-head S trimer dimerisation, likely facilitated by the abrogation of charge-charge repulsion and the additional contacts afforded by the E484Q substitution. 2022 Nature communications Discussion SARS_CoV_2 E484Q 202 207 S 71 72 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. However, given the shared P681R mutation in both Kappa and Delta variants, this mutation alone does not explain the prevalence of the Delta variant over Kappa in India initially and subsequently globally. 2022 Nature communications Discussion SARS_CoV_2 P681R 26 31 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Mutations outside of the RBD have however been demonstrated to influence ACE2 engagement by modulating RBD conformation, such as the D614G and A570D mutations in the B.1 and B.1.1.7 (Alpha variant) lineages respectively. 2022 Nature communications Discussion SARS_CoV_2 A570D;D614G 143;133 148;138 RBD;RBD 25;103 28;106 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Our analyses make use of HexaPro constructs, which differ from native S proteins by the incorporation of six stabilising proline substitutions (F817P, A892P, A899P, A942P, K968P and V969P) and the replacement of the transmembrane domain with a trimerization motif. 2022 Nature communications Discussion SARS_CoV_2 A892P;A899P;A942P;K968P;V969P;F817P 151;158;165;172;182;144 156;163;170;177;187;149 S 70 71 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Our synthetic mutation of Q484I in the Kappa variant background, which also resulted in dimerisation, suggests that the SARS-CoV-2 S protein may be a single amino acid substitution away from exhibiting this dimer-of-trimers phenotype. 2022 Nature communications Discussion SARS_CoV_2 Q484I 26 31 S 131 132 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The consistency of the effects imparted by the K417N substitution, in isolation or when combined with other mutations, consolidates the understanding of naturally selected mutations as mostly independent functional modules at the molecular level. 2022 Nature communications Discussion SARS_CoV_2 K417N 47 52 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The deleterious effect of decreased ACE2 affinity imparted by K417N/T mutation is compensated by N501Y substitution in Beta and Gamma VoCs, but not in Delta plus, potentially rationalising its relatively limited global prevalence. 2022 Nature communications Discussion SARS_CoV_2 K417N;K417T;N501Y 62;62;97 69;69;102 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The Delta plus variant contains the same mutations as the Delta variant, with the addition of a lysine to asparagine substitution at position 417 (K417N). 2022 Nature communications Discussion SARS_CoV_2 K417N;K417N 96;147 145;152 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The K417N mutation is found identically (K417N) and similarly (K417T) in the Beta (B.1.351) and Gamma (P.1) VoCs respectively. 2022 Nature communications Discussion SARS_CoV_2 K417N;K417N;K417T 4;41;63 9;46;68 35136050 Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. The same L452R mutation in the Kappa variant likely did not result in an overall change in ACE2 affinity due to the deleterious effects of a lost electrostatic interaction from the E484Q mutation. 2022 Nature communications Discussion SARS_CoV_2 E484Q;L452R 181;9 186;14 35139271 Final Analysis of Efficacy and Safety of Single-Dose Ad26.COV2.S. Efficacy against severe-critical disease remained higher (74.6%) than efficacy against moderate to severe-critical disease, with a lower point estimate for variants (93.1% efficacy against the reference strain and 71.8% efficacy against non-reference strain lineages, including "other" sequences with the E484K mutation), indicating that Ad26.COV2.S induces higher levels of protection in proportion to the severity of the disease and the nature of the viral mutation. 2022 The New England journal of medicine Discussion SARS_CoV_2 E484K 305 310 35139811 Linked nosocomial COVID-19 outbreak in three facilities for people with intellectual and developmental disabilities due to SARS-CoV-2 variant B.1.1.519 with spike mutation T478K in the Netherlands. Increased infectiousness of the B.1.1.519 variant could explain the high prevalence in Mexico and rapid transmission in our linked outbreak and could be caused by the T478K mutation or P681H which is shared with the B.1.1.7 variant. 2022 BMC infectious diseases Discussion SARS_CoV_2 P681H;T478K 185;167 190;172 35140714 Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. N440K and K444Q can escape against REGN10987, while K417N, N460T, and A475V can successfully escape against LY-CoV016 antibody (AbCellera), currently approved by the FDA for COVID-19 therapy. 2021 Frontiers in immunology Discussion SARS_CoV_2 A475V;K417N;K444Q;N460T;N440K 70;52;10;59;0 75;57;15;64;5 COVID-19 174 182 35140714 Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. Single E406W mutation can lead to the viral escape from both antibodies in REGN-COV2, whereas F486K has been reported to escape REGN10933. 2021 Frontiers in immunology Discussion SARS_CoV_2 E406W;F486K 7;94 12;99 35140714 Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. Sotrovimab could bind to the highly conserved epitope on the RBD, and among the 15 mutations in the RBDOmic, it faces only G339D mutation. 2021 Frontiers in immunology Discussion SARS_CoV_2 G339D 123 128 RBD 61 64 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. Accordingly, N501Y and D138Y substitutions showed increased HLA affinities and may be good targets to trigger CD8+ T cell responses. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D138Y;N501Y 23;13 28;18 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. D3L, P80R, S235F, and T205I, generated more potential epitopes in comparison to the REF peptides. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 P80R;S235F;T205I;D3L 5;11;22;0 9;16;27;3 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. Despite no difference in affinities to HLAs, the D614G that has been related to increased transmissibility displayed half the number of potential binders than 614D, suggesting that lowering the number of potential binders would be permissive to infection due to lower immune recognition and response. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 49 54 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. For instance, E484K substitution has overall less affinity to class I HLA molecules than the respective REF peptides, but no difference in antigenicity scores. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 14 19 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. On the other hand, 501Y substitution has a stronger affinity to the HLA alleles than the REF peptides but, similarly to E484K, are able to escape from antibody recognition. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 120 125 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. This finding is in line with other reports that identified evasion from antibodies associated with E484K and with lineages bearing this mutation, especially the B.1.351. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 E484K 99 104 35149224 In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. To date, there are no studies associating the nsSNVs in protein S such as D80A, P618H, T1027, and T716I with increased transmissibility or immune evasion, since most studies focused on nsSNVs located on the RBD. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D80A;P618H;T716I 74;80;98 78;85;103 RBD;S 207;64 210;65 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. Although sequences carrying S:T1117I from other latitudes could be included, we followed the cases from Costa Rica (lineage B.1.1.389) due to: (i) a local epidemiological interest in which B.1.1.389 represents a big group with a monophyletic origin in a particular geographic location (Costa Rica) with a high prevalence, unlike the other cases; (ii) B.1.1.389 was the only lineage that carries the S:T1117I as a characteristic mutation (a marker for the lineage), while this mutation is not widely found among the genomes of the other lineages (for example, S:T1117I is present in a minority of cases of the B.1.1.7 lineage, although a large number of S:T1117I-carrying genomes are a lineage B.1.1.7); and (iii) the fact of considering a large dataset can create a complex scenario to get conclusive results for the analysis of selection, as found by with >25,000 whole genome sequences from the United Kingdom. 2022 Gene reports Discussion SARS_CoV_2 T1117I;T1117I;T1117I;T1117I 30;401;561;655 36;407;567;661 S;S;S;S 28;399;559;653 29;400;560;654 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. Besides, we analyzed antigenic peptides from spike protein that could be affected by the mutation S:T1117I using immunoinformatics, similar to other approaches. 2022 Gene reports Discussion SARS_CoV_2 T1117I 100 106 S;S 45;98 50;99 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. Eight sites or mutations were under positive/adaptive selection, including S:T1117I. 2022 Gene reports Discussion SARS_CoV_2 T1117I 77 83 S 75 76 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. For both, the WT and the mutated (S:D614 and S:T1117I) spike proteins, the drug was docked in the HR1 region of S2 domain, as reported before. 2022 Gene reports Discussion SARS_CoV_2 T1117I 47 53 S;S;S 55;34;45 60;35;46 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. In addition, our previous work demonstrated that the clinical manifestations of COVID-19 in Costa Rican cases were independent of the SARS-CoV-2 lineages, including no differences for the lineage B.1.1.389 and the mutation S:T1117I. 2022 Gene reports Discussion SARS_CoV_2 T1117I 225 231 S 223 224 COVID-19 80 88 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. Interestingly, S:N501Y and S:D1118H from lineage B.1.1.7 (alpha variant) were also recognized. 2022 Gene reports Discussion SARS_CoV_2 D1118H;N501Y 29;17 35;22 S;S 15;27 16;28 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. No drastic effects were recognized for the region associated with the mutation S:T1117I. 2022 Gene reports Discussion SARS_CoV_2 T1117I 81 87 S 79 80 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. On the other hand, according to the architecture of the spike protein, the S:T1117I is located between the HR1 and HR2 regions of the S2 domain. 2022 Gene reports Discussion SARS_CoV_2 T1117I 77 83 S;S 56;75 61;76 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. Our analysis is the first one with the report of selection for the S:T1117I. 2022 Gene reports Discussion SARS_CoV_2 T1117I 69 75 S 67 68 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. Owed to the key mutation of the B.1.1.389 is the S:T1117I, we thereby analyzed to study the effects of this change on the spike function. 2022 Gene reports Discussion SARS_CoV_2 T1117I 51 57 S;S 122;49 127;50 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. The frequency of genomes carrying the S:T1117I was similar among the clinical profiles. 2022 Gene reports Discussion SARS_CoV_2 T1117I 40 46 S 38 39 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. These results show that the S:T1117I changes the properties of the epitope to be recognized by the immune system. 2022 Gene reports Discussion SARS_CoV_2 T1117I 30 36 S 28 29 35155843 Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica. We started by comparing all the available sequences with the S:T1117I around the world. 2022 Gene reports Discussion SARS_CoV_2 T1117I 63 69 S 61 62 35157870 Detection of SARS-CoV-2 RNA in wastewater, river water, and hospital wastewater of Nepal. The N501Y mutant was detected in a wastewater sample collected from WWTP A on February 3, 2021. 2022 The Science of the total environment Discussion SARS_CoV_2 N501Y 4 9 35162151 Shorter Incubation Period among Unvaccinated Delta Variant Coronavirus Disease 2019 Patients in Japan. Fourth, the Delta variant was mainly confirmed by the L452R mutation. 2022 International journal of environmental research and public health Discussion SARS_CoV_2 L452R 54 59 35162151 Shorter Incubation Period among Unvaccinated Delta Variant Coronavirus Disease 2019 Patients in Japan. However, genome sequencing showed coincidence between the Delta variant and L452R mutation in Japan. 2022 International journal of environmental research and public health Discussion SARS_CoV_2 L452R 76 81 35164548 Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. For example, the Q57H mutant was predicted to bind the S protein, whereas the wild type does not. 2022 mBio Discussion SARS_CoV_2 Q57H 17 21 S 55 56 35164548 Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. However, our data cannot rule out the possibility that the Q57H mutant may have other effects on viral pathogenesis. 2022 mBio Discussion SARS_CoV_2 Q57H 59 63 35164548 Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. It would be of interest to test whether the Q57H mutant contributes to viral entry. 2022 mBio Discussion SARS_CoV_2 Q57H 44 48 35164548 Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. Our data show that the Q57H mutant activities are comparable to those of the wild-type ORF3a regarding the induction of cellular oxidative stress, innate immune responses, and apoptosis and necrosis. 2022 mBio Discussion SARS_CoV_2 Q57H 23 27 ORF3a 87 92 35164548 Genome-Wide Characterization of SARS-CoV-2 Cytopathogenic Proteins in the Search of Antiviral Targets. The Q57H mutation was found recently in the emerging Beta variant, and the Q57H variant was suspected of contributing to a surge of SARS-CoV-2 infection in Hong Kong. 2022 mBio Discussion SARS_CoV_2 Q57H;Q57H 4;75 8;79 COVID-19 132 152 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. By the time this study was performed, SARS-CoV-2 modified its survival strategy by adopting E484K in addition to D614G to confer higher transmissibility (likely complemented with N501Y) and protect S against antibodies. 2022 mBio Discussion SARS_CoV_2 D614G;E484K;N501Y 113;92;179 118;97;184 S 198 199 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. D614G mutation in the S glycoprotein is associated with enhanced transmissibility of SARS-CoV-2 strains. 2022 mBio Discussion SARS_CoV_2 D614G 0 5 S 22 36 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. D614G reduces S1 shedding. 2022 mBio Discussion SARS_CoV_2 D614G 0 5 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. feature an initially worldwide adopted D614G mutation compared to the original Wuhan strain, while three of them contain an E484K mutation (E484K was also later adopted by the Alpha variant according to the World Health Organization [https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/]) and Omicron contains E484A. 2022 mBio Discussion SARS_CoV_2 D614G;E484A;E484K;E484K 39;321;124;140 44;326;129;145 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. For instance, 2C (S383C and D985C) substitutions shift the conformational dynamics toward the three-RBD-down conformation, in complete agreement with the cryo-EM study. 2022 mBio Discussion SARS_CoV_2 D985C;S383C 28;18 33;23 RBD 100 103 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. However, subsequent variants carrying the D614G mutation within S have adopted another strategy. 2022 mBio Discussion SARS_CoV_2 D614G 42 47 S 64 65 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. In addition to D614G, E484K is another mutation adopted by most of the dominating strains, appearing in 3 of the 5 VOCs (Alpha, Beta and Gamma, despite E484A in Omicron), of which the Alpha variant later was similarly observed to adopt E484K according to the World Health Organization. 2022 mBio Discussion SARS_CoV_2 D614G;E484A;E484K;E484K 15;152;22;236 20;157;27;241 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. It could explain why the original Alpha variant, identified in the United Kingdom, did not contain the E484K mutation but has since adopted it. 2022 mBio Discussion SARS_CoV_2 E484K 103 108 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. Moreover, D614G also exhibits more functional spikes on the surface predominately in the hACE2-accessible conformations, which significantly increases the hACE2 binding competence and may contribute to an enhanced transmission rate. 2022 mBio Discussion SARS_CoV_2 D614G 10 15 S 46 52 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. Notably, E484K was also identified as an escape mutation, as it enables the virus to escape host antibody recognition. 2022 mBio Discussion SARS_CoV_2 E484K 9 14 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. Our results suggest that like D614G, E484K achieves this by promoting the S conformation to shift from predominately all-RBD-down hACE2-inaccessible closed state to one/two-RBD-up hACE2-accessible partially open states, thus exposing the RBD and facilitating receptor binding of S. 2022 mBio Discussion SARS_CoV_2 D614G;E484K 30;37 35;42 RBD;RBD;RBD;S;S 121;173;238;74;279 124;176;241;75;280 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. Similar to the case with D614G, emerged E484K-carrying S variants likely promote transmissibility by adopting more dynamics-decelerated or implied stability-enhanced fusion-promoting hACE2-accessible conformations, revealed by our smFRET results. 2022 mBio Discussion SARS_CoV_2 D614G;E484K 25;40 30;45 S 55 56 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. Structural studies have implied E484K as a local destabilizing factor in the structure that disrupts the native conformation of the RBD tip, hindering the binding of some RBD-directed neutralizing antibodies. 2022 mBio Discussion SARS_CoV_2 E484K 32 37 RBD;RBD 132;171 135;174 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. The appearance of both E484K and N501Y mutations appears to increase the hACE2-binding affinity of S. 2022 mBio Discussion SARS_CoV_2 E484K;N501Y 23;33 28;38 S 99 100 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. The coexistence of enhanced transmissibility and reduced hACE2 binding was rationalized by attributing the transmissibility primarily to the effect of D614G substitution on preventing S1 from shedding off on the virion, which consequently increases the number of functional spikes on the viral surface. 2022 mBio Discussion SARS_CoV_2 D614G 151 156 S 274 280 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. The combined effect of D614G on enhancing S-hACE2 binding competence and stabilizing spikes in receptor-accessible conformations may confer the enhanced transmissibility of D614G-bearing SARS-CoV-2 VOCs. 2022 mBio Discussion SARS_CoV_2 D614G;D614G 23;173 28;178 S;S 85;42 91;43 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. The conformational landscape of D614G and E484K carrying S variants is consistent with various groups' structural studies. 2022 mBio Discussion SARS_CoV_2 D614G;E484K 32;42 37;47 S 57 58 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. The controversy of D614G on spike conformations and receptor binding: (i) enhancing conformational flexibility or stability and (ii) lower or higher binding affinity to hACE2. 2022 mBio Discussion SARS_CoV_2 D614G 19 24 S 28 33 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. This characteristic trait indicates that E484K coexisting with N501Y also serves to increase the transmissibility of SARS-CoV-2. 2022 mBio Discussion SARS_CoV_2 E484K;N501Y 41;63 46;68 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. This explanation was supported by observing a disordered-to-ordered transition of a "630 loop" caused by the D614G substitution, which seemingly stabilizes S trimer in the one-RBD-up conformation, preventing premature S1 shedding. 2022 mBio Discussion SARS_CoV_2 D614G 109 114 RBD;S 176;156 179;157 35164561 SARS-CoV-2 Variants Increase Kinetic Stability of Open Spike Conformations as an Evolutionary Strategy. We showed that lentiviruses that contain D614G spike exhibit significant increase in infectivity compared to the original Wuhan strain. 2022 mBio Discussion SARS_CoV_2 D614G 41 46 S 47 52 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. Moreover, the Ministry of Health, Labour and Welfare of Japan uses the real time RT-PCR based screening for N501Y and L452R mutation, such screening cannot identify the other types of mutant variants in contrast to our method. 2022 Scientific reports Discussion SARS_CoV_2 L452R;N501Y 118;108 123;113 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. SARS-CoV-2 having no mutation in the targeted spike region is circulated in Hiroshima until February 2021, after which E484K mutated strains and B.1.1.7 variant became dominant over previously reported strain. 2022 Scientific reports Discussion SARS_CoV_2 E484K 119 124 S 46 51 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. The Omicron variant possess the distinct mutation pattern having both K417N (Delta) and N501Y (Alpha) in the spike region plus E484A and various mutations which can be easily identified by our Sanger Sequencing Strategy (as shown in. 2022 Scientific reports Discussion SARS_CoV_2 E484A;K417N;N501Y 127;70;88 132;75;93 S 109 114 35165301 Mass Screening of SARS-CoV-2 Variants using Sanger Sequencing Strategy in Hiroshima, Japan. The samples collection dates were very closed to one another, and it is believed that the cluster cases were occurred by this N501S mutant variant in Hiroshima during late November to early December 2020. 2022 Scientific reports Discussion SARS_CoV_2 N501S 126 131 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. All together with the epidemiological data showing the significant increase of COVID-19 cases in Indonesia, this pattern may support the indication that D614G variant is a founder effect of SARS-CoV-2 in Indonesia (Gunadi et al.). 2022 International microbiology Discussion SARS_CoV_2 D614G 153 158 COVID-19 79 87 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. Interestingly, all these VOC harbor the D614G mutation, indicating that this mutation is positively selected and subsequently drives the dynamic evolution of SARS-CoV-2 up to this moment (He et al.). 2022 International microbiology Discussion SARS_CoV_2 D614G 40 45 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. Learning from evidence that the FCS region is important and the potential role of D614G as a founder effect of other mutations in this region, further molecular epidemiology surveillance of the FCS region mutations is important, especially in the area where transmission of COVID-19 is still high, such as Indonesia. 2022 International microbiology Discussion SARS_CoV_2 D614G 82 87 COVID-19 274 282 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. One mutation before the polybasic cleavage site within the S gene, PRRAR (681-685 amino acid) motif was identified as S680P which was previously reported by Kim et al. 2022 International microbiology Discussion SARS_CoV_2 S680P 118 123 S 59 60 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. The development of D614G variant may be the consequence of an evolutionary advantage of the D614G mutation in the FCS region of the S protein of SARS-CoV-2 circulating in Indonesia. 2022 International microbiology Discussion SARS_CoV_2 D614G;D614G 19;92 24;97 S 132 133 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. This finding indicated that D614G mutation is an evolutionary advantage for the SARS-CoV-2 transmission in the Special Region of Yogyakarta and Central Java provinces of Indonesia. 2022 International microbiology Discussion SARS_CoV_2 D614G 28 33 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. Thus, D614G mutation provides a selective advantage and increases the transmissibility of SARS-CoV-2 (Harvey et al.). 2022 International microbiology Discussion SARS_CoV_2 D614G 6 11 35165816 Evolutionary dynamics of SARS-CoV-2 circulating in Yogyakarta and Central Java, Indonesia: sequence analysis covering furin cleavage site (FCS) region of the spike protein. We found two other mutations, Q675H and Q677H, which were also reported by Begum et al. 2022 International microbiology Discussion SARS_CoV_2 Q675H;Q677H 30;40 35;45 35166573 Neutralizing antibody responses elicited by SARS-CoV-2 mRNA vaccination wane over time and are boosted by breakthrough infection. In this study, we found that all four VOCs consistently had reduced NT50 values compared to D614G at all time points, with the Omicron variant showing the most pronounced nAb resistance, followed by the Beta and Delta variants. 2022 Science translational medicine Discussion SARS_CoV_2 D614G 92 97 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. 5f, g), suggesting that 8D3 may use an "induced-fit" mechanism unreported previously for SARS-CoV-2 neutralizing antibodies to accommodate the T478K substitution in Delta. 2022 Nature communications Discussion SARS_CoV_2 T478K 143 148 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. In addition, with the T478K substitution, the RBM interaction interface tends to be more positively charged and hydrophilic, beneficial for RBM interaction with the negatively charged ACE2 in related interaction interface. 2022 Nature communications Discussion SARS_CoV_2 T478K 22 27 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Noteworthy, our Delta RBD-1-ACE2 structure showed that the T478K substitution in Delta can stabilize and reshape the RBM loop473-490 by forming a new H-bond with N487 also within this loop. 2022 Nature communications Discussion SARS_CoV_2 T478K 59 64 RBD 22 25 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. Taken together, our study demonstrates that the increased binding to ACE2, mediated by both affinity-enhancing RBM T478K substitution and increased propensity for the receptor-accessible RBD-up states, may contribute to the high infectivity of the Delta variant. 2022 Nature communications Discussion SARS_CoV_2 T478K 115 120 RBD 187 190 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. The Delta variant contains a T478K substitution located near the center of the 8D3 binding footprint. 2022 Nature communications Discussion SARS_CoV_2 T478K 29 34 35169135 Structural basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies. These structures, in combination with 3DVA and biochemical analysis, reveal that the Delta S gains increased binding to ACE2, mediated by both increased propensity for the more RBD-up states and affinity enhancing RBM T478K substitution, thus providing a structural explanation to the enhanced transmissibility and rapid spread of the Delta variant. 2022 Nature communications Discussion SARS_CoV_2 T478K 218 223 RBD;S 177;91 180;92 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. Earlier examinations of emerging mutations in N proteins, going back to June 2020, were necessarily more limited in scope, and while sufficient to examine hot spots and identify key replacements such as R203K/G204R, it was not yet possible to draw conclusions from a survey of the entire mutational landscape. 2022 bioRxiv Discussion SARS_CoV_2 R203K;G204R 203;209 208;214 N 46 47 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. However, even without disulfide bonds, we found a 200-fold enhancement of dimer-dimer self-association in N:G215C, accompanied by augmented co-assembly with NA, which we hypothesize profoundly alters the co-assembly kinetics of ribonucleoprotein particles. 2022 bioRxiv Discussion SARS_CoV_2 G215C 108 113 N 106 107 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. One of these is in the central linker adjacent to the G215 position, where the G215C mutation has quickly outcompeted all other variants in 2021 after its appearance alongside only ORF1ab and ORF7b mutations in the Delta variant. 2022 bioRxiv Discussion SARS_CoV_2 G215C 79 84 ORF1ab;ORF7b 181;192 187;197 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. Our data show that the single mutation G215C causes significantly altered secondary structure; gross differences in hydrodynamic shape indicate altered subunit arrangements; and strongly enhanced protein-protein interactions modulate the formation of quaternary structure. 2022 bioRxiv Discussion SARS_CoV_2 G215C 39 44 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. The potential introduction of disulfide bonds in the N:G215C mutant stabilizing dimer-dimer crosslinks in the linker region would constitute an even more drastic change in the assembly pathway. 2022 bioRxiv Discussion SARS_CoV_2 G215C 55 60 N 53 54 35169797 Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein. We propose that these helices may be essential for higher-order assembly of N-protein and are either stabilized or exposed in the emerging G215C mutant. 2022 bioRxiv Discussion SARS_CoV_2 G215C 139 144 N 76 77 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Additionally, non-VOC lineages carrying the N501Y SNP will be detected and flagged as VOCs incorrectly. 2022 Microbiology spectrum Discussion SARS_CoV_2 N501Y 44 49 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Another group published an rRT-PCR assay to detect only the N501Y SNP and requires a melting curve to confirm the specimens as wild type if the test is negative. 2022 Microbiology spectrum Discussion SARS_CoV_2 N501Y 60 65 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Because our assay only detects the N501Y SNP, new emerging lineages that are of concern that do not carry this SNP, such as B.1.525, and B.1.617.2, which has rapidly become the predominant strain in most countries, including Canada, will be missed (https://cov-lineages.org/global_report_B.1.617.2.html, https://cov-lineages.org/global_report_B.1.525.html). 2022 Microbiology spectrum Discussion SARS_CoV_2 N501Y 35 40 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Due to the high positive percent agreement, any specimen that is N501Y positive can be presumed to be a VOC while awaiting characterization by WGS. 2022 Microbiology spectrum Discussion SARS_CoV_2 N501Y 65 70 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. During the early response to VOCs, positive SARS-COV-2 specimens were screened for the N501Y SNP using the described rRT-PCR assay and then potentially submitted for WGS to confirm VOC identification and determine the VOC lineage. 2022 Microbiology spectrum Discussion SARS_CoV_2 N501Y 87 92 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Early, high-throughput screening with PHO Laboratory's N501Y screening assay provided the possibility of enhanced public health measures to be put in place (e.g., more expanded contact tracing) in an attempt to limit the spread of VOCs in the community during the early phase of emergence of B.1.1.7. 2022 Microbiology spectrum Discussion SARS_CoV_2 N501Y 55 60 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Having this target allows the assay to detect B.1.617.2, an important VOC, and N501Y-containing VOCs, such as B.1.1.7, P.1, and B.1.351. 2022 Microbiology spectrum Discussion SARS_CoV_2 N501Y 79 84 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Here, we describe the validation and implementation of a N501Y SNP rRT-PCR assay to provide rapid screening of SARS-CoV-2-positive specimens for a subset of VOCs. 2022 Microbiology spectrum Discussion SARS_CoV_2 N501Y 57 62 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. In another assay, the RT-PCR multiplex targets include L452R, a SNP in the S gene that is characteristic of the B.1.617.2 (Delta) variant. 2022 Microbiology spectrum Discussion SARS_CoV_2 L452R 55 60 S 75 76 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Ontario implemented screening of all SARS-CoV-2-positive specimens, which can be in excess of 1,000 specimens per day, and the N501Y SNP rRT-PCR assay has allowed us to screen a high volume of specimens. 2022 Microbiology spectrum Discussion SARS_CoV_2 N501Y 127 132 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Other SNP assays have been developed for important S gene SNPs that characterize VOCs, including E484K (P.1, B.1.351), K417N/T (P.1, B.1.351), and L452R (B.1.617.2). 2022 Microbiology spectrum Discussion SARS_CoV_2 E484K;K417N;K417T;L452R 97;119;119;147 102;126;126;152 S 51 52 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Our assay is efficient and clinically validated with a high degree of positive percent agreement (PPA) and negative percent agreement (NPA) for detection of the N501Y SNP compared with Sanger sequencing. 2022 Microbiology spectrum Discussion SARS_CoV_2 N501Y 161 166 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Our assay is not intended for diagnostic purposes but rather as a screening tool to aid with faster identification of VOCs through differentiation of N501 and N501Y. 2022 Microbiology spectrum Discussion SARS_CoV_2 N501Y 159 164 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Our N501Y rRT-PCR assay has been implemented in the province for screening for VOCs. 2022 Microbiology spectrum Discussion SARS_CoV_2 N501Y 4 9 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. Our validation data set contained a small sample size of 71 N501Y-positive specimens. 2022 Microbiology spectrum Discussion SARS_CoV_2 N501Y 60 65 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. that targets the deletion of amino acids 3675 to 3677 in the ORF1a gene as well as the deletion of amino acids 69 to 70 in the S gene. 2022 Microbiology spectrum Discussion SARS_CoV_2 del 3675;del 69 17;87 45;113 ORF1a;S 61;127 66;128 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The assay is also unable to differentiate between VOCs that share the N501Y SNP; therefore, an additional sequencing step is required to delineate the lineage. 2022 Microbiology spectrum Discussion SARS_CoV_2 N501Y 70 75 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. The ORF1a deletion of amino acids 3675 to 3677 is present in B.1.17, B.1.351, and P.1, and the deletion of amino acids 69 to 70 in the S gene is used to differentiate B.1.17 from B.1351 and P.1. 2022 Microbiology spectrum Discussion SARS_CoV_2 del 3675;del 69 10;95 38;121 ORF1a;S 4;135 9;136 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. There were no adverse events from performing the N501Y SNP rRT-PCR assay on study specimens, as individuals had already been classified as having the mutation or not based on previous sequencing. 2022 Microbiology spectrum Discussion SARS_CoV_2 N501Y 49 54 35170989 Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern. When first implemented, specimens positive for SARS-CoV-2 were screened for N501Y and then sequenced with WGS to determine the lineage if N501Y mutation was detected. 2022 Microbiology spectrum Discussion SARS_CoV_2 N501Y;N501Y 76;138 81;143 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. According to our results, most of the P.1 sequences carried the 22 lineage-defining mutations, including the three mutations in the Spike protein, RBD domain (K417T, E484K and N501Y) associated with evasion of the immune system and greater transmissibility. 2022 Microbiology spectrum Discussion SARS_CoV_2 E484K;N501Y;K417T 166;176;159 171;181;164 S;RBD 132;147 137;150 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. Furthermore, 41 (38.7%) sequences presented the D614G mutation in the Spike gene and, after its first description in February 2020, it has been identified in all VOCs. 2022 Microbiology spectrum Discussion SARS_CoV_2 D614G 48 53 S 70 75 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. Moreover, all the P.1 sequences accumulated other important mutations, such as P314L in the ORF1ab and R203K/G204R in the Nucleocapsid gene. 2022 Microbiology spectrum Discussion SARS_CoV_2 P314L;R203K;G204R 79;103;109 84;108;114 N;ORF1ab 122;92 134;98 35171035 Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil. The P.1.2 sublineage carries some different mutations in comparison to the P.1 lineage and it was considered a Variant of Interest (VOI) due to the mutation D155Y in the ORF3a, which results in a low viral affinity to the host caveolin-1 protein, thereby avoiding cell apoptosis and extending the asymptomatic phase of infection. 2022 Microbiology spectrum Discussion SARS_CoV_2 D155Y 157 162 ORF3a 170 175 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. Another factor to consider when assessing risk of point mutations such as the C29197T mutation is that 4 of the 22 C29197T mutants were originally classified as variant B.1.1.222 when run on Pango lineage version 2.3.2 in February and as late as March of 2021. 2022 PloS one Discussion SARS_CoV_2 C29197T;C29197T 78;115 85;122 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. Even after controlling for household clusters, only 1 of the original 22 C29197T mutants was from the same household as another, indicative of significant community spread for this mutation. 2022 PloS one Discussion SARS_CoV_2 C29197T 73 80 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. In fact, national data demonstrated a broad range of proportions of both B.1.1.222 and B.1.1.519 during the months of January-April that likely reflected highly variable local prevalence rates of the C29197T mutation in different regions of the U.S. 2022 PloS one Discussion SARS_CoV_2 C29197T 200 207 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. In the case of the Xpert Xpress SARS-CoV-2 and Xpert Omni SARS-CoV-2 assays, there are three additional point mutations that have been demonstrated to cause NGTF: G29140T, C29200A, and C29200T. 2022 PloS one Discussion SARS_CoV_2 C29200A;C29200T;G29140T 172;185;163 179;192;170 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. Local period prevalence of the C29197T mutation for January, 2021, estimated using local baseline surveillance sampling, was over 3-fold higher (8.5%) than the statewide prevalence (2.5%) during the same time frame, estimated using GISAID data. 2022 PloS one Discussion SARS_CoV_2 C29197T 31 38 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. Our analysis of the C29197T mutation demonstrates that timely genomic sequencing information that is available at the local level is crucial to providing actionable information concerning mutations of public health concern. 2022 PloS one Discussion SARS_CoV_2 C29197T 20 27 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. The independent introduction of the C29197T mutation amongst two different, circulating variants would have made it more difficult to identify trends associated with this particular point mutation using conventional variant tracking methods. 2022 PloS one Discussion SARS_CoV_2 C29197T 36 43 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. This elevated local prevalence rate of the C29197T mutation can be attributed at least in part to a disproportionately large infection cluster of unknown origin of 9 individuals from separate households. 2022 PloS one Discussion SARS_CoV_2 C29197T 43 50 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. This means that a proportion of the B.1.1.222 variants circulating in the state and nationally may have harbored the C29197T mutation as under the previous classification it was not consistent whether B.1.1.222 variants displayed the C29197T mutation or not. 2022 PloS one Discussion SARS_CoV_2 C29197T;C29197T 117;234 124;241 35171960 Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2. When all 22 samples were reprocessed using Pango lineage version 2.4.2 in May 2021, the 4 samples with the C29197T mutation that were originally classified as B.1.1.222 were reclassified as B.1.1.519 and the remaining 18 samples remained classified as B.1.1.519. 2022 PloS one Discussion SARS_CoV_2 C29197T 107 114 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. Fortunately, the vaccinated blood samples, due to their much-elevated RBD antibody levels, were far more effective in neutralizing both the WT and N501Y RBD from binding to ACE. 2022 Scientific reports Discussion SARS_CoV_2 N501Y 147 152 RBD;RBD 70;153 73;156 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. N501Y RBD is central to the investigation as it is the key driver to increased affinity to cell ACE2 receptors. 2022 Scientific reports Discussion SARS_CoV_2 N501Y 0 5 RBD 6 9 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. Other RBD mutations, K417N/T and E484K, either alone or in combinations, have not been evaluated in this study. 2022 Scientific reports Discussion SARS_CoV_2 E484K;K417N;K417T 33;21;21 38;28;28 RBD 6 9 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. Our study showed that not only the mRNA vaccinated plasma has 17-fold higher antibodies than the convalescent antisera, but also 16 time more potential in neutralizing RBD and ACE2 binding of both the original and N501Y mutation that was present in the above studies. 2022 Scientific reports Discussion SARS_CoV_2 N501Y 214 219 RBD 168 171 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. The N501Y mutation, while did not alter the neutralizing antibody binding, presented with a fivefold greater affinity to ACE2, which resulted in a drastically reduced ability of COVID-19 convalescent antisera to neutralize its ACE2 binding. 2022 Scientific reports Discussion SARS_CoV_2 N501Y 4 9 COVID-19 178 186 35173254 mRNA vaccine-induced antibodies more effective than natural immunity in neutralizing SARS-CoV-2 and its high affinity variants. With an average of 16-fold greater potency than convalescent blood, the vaccinated blood samples were more than sufficient to compensate for the fivefold increased affinity of N501Y RBD, resulting in the highly effective inhibition of both the WT and N501Y RBD from binding to ACE2. 2022 Scientific reports Discussion SARS_CoV_2 N501Y;N501Y 176;251 181;256 RBD;RBD 182;257 185;260 35176330 Evolutionary shift from purifying selection towards divergent selection of SARS-CoV2 favors its invasion into multiple human organs. However, did not find any evidence of a particular strain of SARS-CoV2 that has over-infecting ability in the population although convincingly showed the widespread infectivity of this strain in southern USA population,.However, very recently a super-infective b.1.1.7 strain carries a set of spike protein mutations including D614G, N501Y and P681H. 2022 Virus research Discussion SARS_CoV_2 D614G;N501Y;P681H 327;334;344 332;339;349 S 293 298 35176330 Evolutionary shift from purifying selection towards divergent selection of SARS-CoV2 favors its invasion into multiple human organs. It appears that other spike mutations are selected on D614G carrying background to give better adaptability in different geographical places to evade challenging human immune environment. 2022 Virus research Discussion SARS_CoV_2 D614G 54 59 S 22 27 35176330 Evolutionary shift from purifying selection towards divergent selection of SARS-CoV2 favors its invasion into multiple human organs. MW075768) and D614G independently. 2022 Virus research Discussion SARS_CoV_2 D614G 14 19 35176330 Evolutionary shift from purifying selection towards divergent selection of SARS-CoV2 favors its invasion into multiple human organs. P681H resides in the furin cleavage site in this strain predictably with improved function. 2022 Virus research Discussion SARS_CoV_2 P681H 0 5 35176330 Evolutionary shift from purifying selection towards divergent selection of SARS-CoV2 favors its invasion into multiple human organs. This N501Y (AAT->TAT) conversion is believed to provide further stronger K353-501Y attachment to enable more infective power. 2022 Virus research Discussion SARS_CoV_2 N501Y 5 10 35176330 Evolutionary shift from purifying selection towards divergent selection of SARS-CoV2 favors its invasion into multiple human organs. Virulency of SARs-CoV2 is further evidenced by a strain containing D614G mutation believed to be the reason of widespread infection in USA and Europe. 2022 Virus research Discussion SARS_CoV_2 D614G 67 72 35176330 Evolutionary shift from purifying selection towards divergent selection of SARS-CoV2 favors its invasion into multiple human organs. We also detected P681H in a strain (isolated in New Mexico, USA, in September isolate,) in several people (e.g., Acc no. 2022 Virus research Discussion SARS_CoV_2 P681H 17 22 35176330 Evolutionary shift from purifying selection towards divergent selection of SARS-CoV2 favors its invasion into multiple human organs. Y493Q conversion needs mutation in two nucleotides but could occur through a genetic drift. 2022 Virus research Discussion SARS_CoV_2 Y493Q 0 5 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. By controlling for the biological and clinical heterogeneity across data, we provide evidence of both a conserved host immune response to acute viral infection, irrespective of the SARS-CoV-2 variant, and unique responses to variants carrying the E484K escape mutation. 2022 Scientific reports Discussion SARS_CoV_2 E484K 247 252 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. However, the E484K signature is specific and does not merely reflect disease severity as other functional markers, such as ARG1, ORM1, OLR1, LOX-1, CEACAM-8, MDSCs are not part of the signature. 2022 Scientific reports Discussion SARS_CoV_2 E484K 13 18 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Taken together, our study presents a systems view of the longitudinal and molecular immune state of hospitalized COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation throughout the disease. 2022 Scientific reports Discussion SARS_CoV_2 E484K 178 183 COVID-19 113 121 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. This study focused on the Alpha variant and the Alpha variant carrying the E484K escape mutation. 2022 Scientific reports Discussion SARS_CoV_2 E484K 75 80 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Through RNA-seq, a gene-agnostic approach, we identified a module of 48 genes expressed at distinctly higher levels in patients infected with variants carrying the E484K escape mutation as compared to the Alpha variant. 2022 Scientific reports Discussion SARS_CoV_2 E484K 164 169 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. Using the MetaSignature database (https://metasignature.stanford.edu), we determined that the majority of the genes in the E484K module are preferentially expressed in myeloid cells. 2022 Scientific reports Discussion SARS_CoV_2 E484K 123 128 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. While our study helped to provide an understanding of the consequences of the E484K mutation, variants with unforeseen combinations of mutations might invoke additional unique molecular immune responses. 2022 Scientific reports Discussion SARS_CoV_2 E484K 78 83 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. While the molecular understanding underlying the ability of the E484K mutation to contribute to a specific immune signature is incomplete, a distinct and stronger interaction with SARS-CoV-2 receptor ACE2 might contribute. 2022 Scientific reports Discussion SARS_CoV_2 E484K 64 69 35181735 Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module. While variants are characterized by the acquisition of several mutations, our conclusions are, first and foremost, based on the native Alpha variant and an Alpha variant that had acquired the single point mutation resulting in the E484K escape variant. 2022 Scientific reports Discussion SARS_CoV_2 E484K 231 236 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. Additionally, our data demonstrated that a lower antibody response was observed against the Beta variant, and not against the R.1 lineage variant, which indicates that the weak antibody response against the Beta variant was not solely due to the E484K mutation. 2022 Vaccine Discussion SARS_CoV_2 E484K 246 251 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. Moreover, it has been reported that the Delta variant, which harbors the L452R mutation, causes a lower cellular immunity response among Asians who have human leukocyte antigen HLA-A24. 2022 Vaccine Discussion SARS_CoV_2 L452R 73 78 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. Previous reports demonstrated that although the E484K mutation of Beta variants might cause humoral immunity escape, the combination of N501Y and K417N was further associated with a weakened response; this enhances the binding of the spike protein to ACE2 and reduces the binding to antibodies. 2022 Vaccine Discussion SARS_CoV_2 E484K;K417N;N501Y 48;146;136 53;151;141 S 234 239 35183387 The effect of the E484K mutation of SARS-CoV-2 on the neutralizing activity of antibodies from BNT162b2 vaccinated individuals. Therefore, the E484K mutation of R.1 alone did not have a sufficient impact in reducing vaccine response, but the combination of E484K, N501Y, and K417N of Beta strains caused severe depletion of the neutralization effect of vaccinated sera in our study. 2022 Vaccine Discussion SARS_CoV_2 E484K;E484K;K417N;N501Y 15;129;147;136 20;134;152;141 35187580 Impaired detection of omicron by SARS-CoV-2 rapid antigen tests. Since the rapidly spreading BA.2 sub-lineage of omicron carries an additional S413R mutation in the nucleocapsid protein, it is difficult to predict the RAT performance for this VoC. 2022 Medical microbiology and immunology Discussion SARS_CoV_2 S413R 78 83 N 100 112 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. A founder haplotype (Hap A) characterized by 6 major SNVs [D614G in the S gene; P4715L, ntC3037T (F924F) and S5398P in Orf1ab gene; ntC26681T (F53F) in the M gene; and ntC241T in the non-coding UTR region] was found in 36 patients. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 C241T;C26681T;C3037T;P4715L;S5398P;F53F;F924F;D614G 168;132;88;80;109;143;98;59 175;141;96;86;115;147;103;64 ORF1ab;S 119;72 125;73 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. At that time, the spreading of SARS-CoV-2 was characterized by three main differences compared to the Wuhan H1 strain: ntC241T in the 5' untranslated region, D614G in the S gene and, P4715L in the ORF1ab (NSP12) gene. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;C241T;P4715L 158;119;183 163;126;189 ORF1ab;Nsp12;S 197;205;171 203;210;172 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Given the central role of helicase in SARS-CoV-2 replication and its potential as an antiviral drug target, we have searched for the presence of S5398P substitution which was not found in the additional isolates analyzed (data not shown). 2022 Infection, genetics and evolution Discussion SARS_CoV_2 S5398P 145 151 Helicase 26 34 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. In particular, one patient (#6) carried the L5F substitution, which has been shown to be responsible for increased infectivity by promoting protein folding, assembly and secretion of the virus. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 L5F 44 47 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. In particular, patient #4 had two distinct haplotypes, one of which (Hap E, T2648N ORF1ab) was more prevalent at baseline and reduced on day 16. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 T2648N 76 82 ORF1ab 83 89 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. In particular, the D614G SNV is known to increase viral infectivity. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 19 24 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. It is of note that one of the deceased patients (#38) carried a synonymous SNV (A964A, Hap H) in the non-structural protein nsp3 encoded by ORF1ab. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 A964A 80 85 ORF1ab;Nsp3 140;124 146;128 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Notably, our results showed that patient #6, who unfortunately died, carried the L5F in both baseline samples (isolate 18) and follow-up samples (isolate 19) in major and minor haplotypes (67% vs. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 L5F 81 84 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Notably, the D222A substitution was shared by 2 patients (#7 and #25), suggesting a possible close contact between them, possibly supporting the increased infectivity associated with Orf3a mutations. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D222A 13 18 ORF3a 183 188 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Notably, the S5398P (S74P) substitution is located in the ZBD domain of nsp13, which is expected to have disruptive effects on in vitro helicase activity and viral replication. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 S5398P;S74P 13;21 19;25 Helicase;Nsp13 136;72 144;77 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Of the founder mutations, S5398P in ORf1ab falls in the region encoding the nsp13 helicase enzyme and mutation P4715L falls in the region encoding nsp12 (NiRAN-RdRp). 2022 Infection, genetics and evolution Discussion SARS_CoV_2 P4715L;S5398P 111;26 117;32 Helicase;ORF1ab;Nsp13;Nsp12;RdRP 82;36;76;147;160 90;42;81;152;164 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. One patient (#46) carried the M84I substitution within M protein, located in a region closer to the I82T typical of the delta variant, which currently reaches a frequency of 70%, thus suggesting that this substitution may provide some sort of fitness advantage. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 I82T;M84I 100;30 104;34 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Patient #6 carried the L5F mutation in the S protein in both the major and minor viral populations, while the I473I in ORF1ab was only present in a lower viral population (33%). 2022 Infection, genetics and evolution Discussion SARS_CoV_2 I473I;L5F 110;23 115;26 ORF1ab;S 119;43 125;44 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Patient #7 had three haplotypes at baseline (Hap A, Hap B and Hap B.1), which were completely replaced by a single haplotype (Hap B.2) carrying 2 SNVs (L127F and M5983L in ORF3a, respectively) that may enhance viral infectivity as discussed above. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 M5983L;L127F 162;152 168;157 ORF3a 172 177 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Previous reports consider L5F as a kind of positive Darwinian selection in the spike gene of SARS-CoV-2, which clarifies the adaptation mechanism of this virus. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 L5F 26 29 S 79 84 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Specifically, we found mutations of the ORF3a protein that fall in the cysteine-rich domain (L127F) and in the C-terminal domain (Q185K, D222A, V255del), which are known to be involved in ORF3a protein homodimerization, intracellular protein sorting and trafficking. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D222A;V255del;L127F;Q185K 137;144;93;130 142;151;98;135 ORF3a;ORF3a 40;188 45;193 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. Thirty-six of the 46 patients shared a founder haplotype, characterized by the six most common SNVs (ntC241T in the UTR noncoding region; F924F, P4715L, and S5398P in ORF1ab; D614G in the spike protein; and F53F in the N protein), which may have initiated local transmission of infection. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;F53F;F924F;P4715L;S5398P;C241T 175;207;138;145;157;101 180;211;143;151;163;108 ORF1ab;S;N 167;188;219 173;193;220 35189404 Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a nursing home of Southern Italy. This observation suggests that S5398P substitution may be considered a neutral variant emerged in the patients residents at the nursing home that had not spread like more aggressive mutations. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 S5398P 31 37 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. A previous study conducted by our group detected the concurrent emergence of multiple P.1+ lineages bearing NTD deletions (including Delta144 and Delta141-44) in several Brazilian states and the present molecular survey identified the emergence of P.1 lineages with mutations S:N679K and S:P681H/R outside the Amazonas. 2022 Microbiology spectrum Discussion SARS_CoV_2 N679K;P681H;P681R 278;290;290 283;297;297 S;S 276;288 277;289 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Both mutations have been shown to enhance the S1/S2 cleavability by furin-like proteases and mutation S:P681R, but not S:P681H, also enhances viral replication, viral fusion, and cell-cell viral spread in vitro when it occurs in the background of other S mutations. 2022 Microbiology spectrum Discussion SARS_CoV_2 P681H;P681R 121;104 126;109 S;S;S 102;119;253 103;120;254 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Furthermore, cleavage at S1/S2 junction is not only mediated by furin-like proteases, but also by cathepsins and other host proteases, and mutations S:P681H/R may thus affect affinity to one or more different proteases and contribute to the high replication and transmissibility rate of different SARS-CoV-2 lineages. 2022 Microbiology spectrum Discussion SARS_CoV_2 P681H;P681R 151;151 158;158 S 149 150 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. In summary, our study confirms that endemic transmission of SARS-CoV-2 after the second COVID-19 epidemic wave in the Amazonas state has been associated with the continuous evolution of the VOC gamma through the acquisition of either Spike mutations at the S1/S2 junction (N679K or P681H) or NTD deletions that probably increased viral infectivity or resistance against antiviral immunity. 2022 Microbiology spectrum Discussion SARS_CoV_2 P681H;N679K 282;273 287;278 S 234 239 COVID-19 88 96 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. In this study, we demonstrate that the endemic transmission of SARS-CoV-2 after the second COVID-19 epidemic wave in Amazonas in 2021 was associated with the continuous evolution of the VOC gamma through the acquisition of NTD deletions (mainly Delta144 and Delta141-44) or, more frequently, of S1/S2 mutations (P681H and N679K) in the Spike protein. 2022 Microbiology spectrum Discussion SARS_CoV_2 N679K;P681H 322;312 327;317 S 336 341 COVID-19 91 99 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Nevertheless, recent experimental data demonstrate that when introduced individually into a plasmid expressing the wild-type Spike (D614G), mutation N679K undoubtedly increases S1/S2 cleavage. 2022 Microbiology spectrum Discussion SARS_CoV_2 N679K;D614G 149;132 154;137 S 125 130 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Notably, the VOCs Gamma and Omicron also share mutation S:H655Y that was described to enhance S cleavage and might thus function synergistically with mutations S:N679K and S:P681H/R. 2022 Microbiology spectrum Discussion SARS_CoV_2 H655Y;N679K;P681H;P681R 58;162;174;174 63;167;181;181 S;S;S;S 56;94;160;172 57;95;161;173 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. On the other hand, although the Omicron S has mutations that individually enhance furin cleavage (H655Y, N679K, and P681H), experimental evidence revealed that Omicron S is relatively poorly cleaved and exhibits reduced fusogenicity compared with other S variants. 2022 Microbiology spectrum Discussion SARS_CoV_2 N679K;P681H;H655Y 105;116;98 110;121;103 S;S;S 40;168;253 41;169;254 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. One of the most divergent Gamma sequences detected in Brazil was a P.1.4 lineage variant sampled in the Amazonas in October 2021 (EPI_ISL_5621224) that harbors 20 S mutations (eight more than the parental P.1 lineage), including several in common with (Delta144, Q498R, N501Y, H655Y, and N679K) or like (T95N, K417T, and E484K) those detected in Omicron. 2022 Microbiology spectrum Discussion SARS_CoV_2 E484K;H655Y;K417T;N501Y;N679K;Q498R;T95N 321;277;310;270;288;263;304 326;282;315;275;293;268;308 S 163 164 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Our metadynamics simulations predicted that mutation S:N679K might lead to a dramatic enhancement in binding affinity to the furin binding site that was even higher than that predicted for mutations S:P681H/R, supporting that this mutation could contribute to the high replication and transmissibility of lineage P.1.4. 2022 Microbiology spectrum Discussion SARS_CoV_2 N679K;P681H;P681R 55;201;201 60;208;208 S;S 53;199 54;200 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Several P.1 Brazilian sublineages (P.1.6, P.1.7 and P.1.8) have independently acquired mutations S:P681H/R at the multibasic furin motif that were also characteristic of other VOCs (Alpha, Delta, and Omicron) and VOIs (AV.1, B.1.1.318, B.1.617.1, B.1.617.3, and P.3). 2022 Microbiology spectrum Discussion SARS_CoV_2 P681H;P681R 99;99 106;106 S 97 98 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. The major P.1+ lineages circulating outside the Amazonas state were P.1.7 (P.1+P681H), which probably arose in the state of Sao Paulo around mid-February 2021 and is currently detected in at least 10 different states from all country regions; and P.1.8 (P.1+P681R), that probably arose in the state of Rio de Janeiro in early May 2021 and spread to the Southern (Santa Catarina) and Northern (Amazonas) regions. 2022 Microbiology spectrum Discussion SARS_CoV_2 P681H;P681R 79;258 84;263 35196783 Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. The most prevalent Gamma variant in the Amazonas state by July 2021 was the lineage P.1.4 that harbors the mutation S:N679K, a genetic change that was recently observed in the VOC Omicron. 2022 Microbiology spectrum Discussion SARS_CoV_2 N679K 118 123 S 116 117 35196812 Emergency SARS-CoV-2 Variants of Concern: Novel Multiplex Real-Time RT-PCR Assay for Rapid Detection and Surveillance. Our method accurately detected four Omicron mutations on the spike protein (DeltaHV 69/70, K417N, N501Y, P681H) with one pass. 2022 Microbiology spectrum Discussion SARS_CoV_2 K417N;N501Y;P681H 91;98;105 96;103;110 S 61 66 35197485 An adjuvanted subunit SARS-CoV-2 spike protein vaccine provides protection against Covid-19 infection and transmission. A subunit vaccine based on a recombinant spike protein extracellular domain was immunogenic in mice and provided robust protection of Syrian hamsters against infection by wild-type SARS-CoV-2 (D614G) virus in addition to blocking virus transmission to naive contact animals. 2022 NPJ vaccines Discussion SARS_CoV_2 D614G 193 198 S 41 46 35197485 An adjuvanted subunit SARS-CoV-2 spike protein vaccine provides protection against Covid-19 infection and transmission. This translated into only modest protection in response to challenge with heterologous SARS-CoV-2 D614G mutant, with the RBD-immunized hamsters showing significant weight loss and detectable virus in Day 2 nasopharyngeal swabs and Day 3 nasal bulb and lung tissue. 2022 NPJ vaccines Discussion SARS_CoV_2 D614G 98 103 RBD 121 124 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. A reverse genetics system will be utilized to investigate how the A36V mutation influences the pathogenicity of those two variants in a further study. 2022 Frontiers in immunology Discussion SARS_CoV_2 A36V 66 70 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. A22D and A36V substitutions in E took part in multiple mutation pathways to enhance virulence in mice. 2022 Frontiers in immunology Discussion SARS_CoV_2 A36V;A22D 9;0 13;4 E 31 32 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. But for C57MA14, P252L (C10809T) mutation in nsp5 of ORF1 is the only one that differed from BMA8 virus, although both variants have four mutations in ORF1. 2022 Frontiers in immunology Discussion SARS_CoV_2 P252L;C10809T 17;24 22;31 Nsp5 45 49 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. Especially, the spike D614G and N501Y substitutions that are currently prevalent in global SARS-CoV-2 strains exhibit efficient replication in human-to-human transmission, but its effects on viral pathogenesis and transmissibility remain unclear. 2022 Frontiers in immunology Discussion SARS_CoV_2 D614G;N501Y 22;32 27;37 S 16 21 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. Furthermore, A22D and A36V mutations in E protein were firstly reported in our study but not in MA10. 2022 Frontiers in immunology Discussion SARS_CoV_2 A22D;A36V 13;22 17;26 E 40 41 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. Gradually increasing mortality from P0 to P14 can be observed as the increasing ratio of P252L, but other mutations have reached the biggest ration before P10, but lethality was not achieved 100%. 2022 Frontiers in immunology Discussion SARS_CoV_2 P252L 89 94 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. Importantly, BLP expressing S RBD of ancestral SARS-CoV-2 could provide 100% protection to the aged BALB/c and C57BL/6N mice against mouse-adapted virus challenge despite Q498H mutation identified in the S RBD, effectively reducing viral load in the upper and lower respiratory tracts of BALB/c and C57BL/6N mice. 2022 Frontiers in immunology Discussion SARS_CoV_2 Q498H 171 176 RBD;RBD;S;S 30;206;28;204 33;209;29;205 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. In addition, several studies have confirmed that N439K, S477N, E484K, and N501Y mutation resulted in immune escape by developing resistance to the SARS-CoV-2 neutralizing antibody. 2022 Frontiers in immunology Discussion SARS_CoV_2 E484K;N439K;N501Y;S477N 63;49;74;56 68;54;79;61 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. In addition, the mutations in non-structural protein ORF1 including T819I, L1790F, and I65S were speculated to be necessary for viral adaptation in mice because they were concurrently identified in BMA8 and C57MA14. 2022 Frontiers in immunology Discussion SARS_CoV_2 I65S;L1790F;T819I 87;75;68 91;81;73 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. In view of all published mouse-adapted SARS-CoV-2 strains, single mutations at Q498H or R493K and two engineered Q498Y and P499T in RBD could promote viral replication in the lungs of mice. 2022 Frontiers in immunology Discussion SARS_CoV_2 P499T;Q498H;Q498Y;R493K 123;79;113;88 128;84;118;93 RBD 132 135 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. Intriguingly, three mutations including Q493K, Q498Y, and P499T simultaneously occurred in the spike of MA10, while only Q498H mutation was identified in BMA8 and C57MA14. 2022 Frontiers in immunology Discussion SARS_CoV_2 P499T;Q493K;Q498H;Q498Y 58;40;121;47 63;45;126;52 S 95 100 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. Mutations A22D and A36V in E may provide a reasonable explanation that the C57MA14 variant has higher virulence in C57MA14-infected mice compared to BMA8-infected mice. 2022 Frontiers in immunology Discussion SARS_CoV_2 A22D;A36V 10;19 14;23 E 27 28 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. Normally, C57MA14 only has A22D substitution in E, but BMA8 combines A22D and A36V substitutes in its genome. 2022 Frontiers in immunology Discussion SARS_CoV_2 A22D;A22D;A36V 27;69;78 31;73;82 E 48 49 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. Of note, T67A (A12844G) in nsp9 of ORF1 may play a key role in increasing pathogenicity of BMA8, which leads to a higher fatality rate following its proportion gradually increasing from P1 to P4, while another three mutations have reached the highest ratio before P4. 2022 Frontiers in immunology Discussion SARS_CoV_2 T67A;A12844G 9;15 13;22 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. P252L was a non-negligible factor to contribute to the increasing virulence. 2022 Frontiers in immunology Discussion SARS_CoV_2 P252L 0 5 35197985 Characterization of Two Heterogeneous Lethal Mouse-Adapted SARS-CoV-2 Variants Recapitulating Representative Aspects of Human COVID-19. The A36V mutation may be a key factor leading to different pathogenicities of the two mutants in different mouse strains. 2022 Frontiers in immunology Discussion SARS_CoV_2 A36V 4 8 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. In addition, the C297S and S460R variants established additional three and one contacts, respectively, with camostat mesylate (Figure 6). 2022 Life (Basel, Switzerland) Discussion SARS_CoV_2 C297S;S460R 17;27 22;32 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. In contrast, the Q438E and S339F variants improved binding affinities to the S glycoprotein at cleavage sites one and two, respectively. 2022 Life (Basel, Switzerland) Discussion SARS_CoV_2 Q438E;S339F 17;27 22;32 S 77 91 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. Interestingly, although D435Y, S460R and G462D/G462S have low allele frequencies, they are all carried only by the European population. 2022 Life (Basel, Switzerland) Discussion SARS_CoV_2 D435Y;G462D;S460R;G462S 24;41;31;47 29;46;36;52 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. The replacement of serine by a phenylalanine at position 339 increased its hydrophobicity and reduced the length of the polar contact, established to Q872 of the S protein (Figure 4b), and therefore, predicted to increase the binding affinity at cleavage site two. 2022 Life (Basel, Switzerland) Discussion SARS_CoV_2 S339F 19 60 S 162 163 35207518 In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. Thus, the Q438E and S339F variants will likely render individuals harboring these polymorphisms more susceptible to SARS-CoV-2 infection. 2022 Life (Basel, Switzerland) Discussion SARS_CoV_2 Q438E;S339F 10;20 15;25 COVID-19 116 136 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. All assays detect four different mutations, except for the Ultra Variant Catcher kit, which targets the E484 position without distinguishing between E484K and E484Q, and the UltraGene Assay SARS-CoV-2 452R & 484K & 484Q Mutations V1, which is designed for three mutation targets. 2022 Microorganisms Discussion SARS_CoV_2 E484K;E484Q 149;159 154;164 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. For example, nowadays, the diffusion of the new Omicron variant can be quickly monitored by the means of a test identifying one or more of its new and unshared spike mutations (i.e., ins214EPE, S371L and S373P). 2022 Microorganisms Discussion SARS_CoV_2 S371L;S373P 194;204 199;209 S 160 165 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. However, the use of the SARS-CoV-2 Variants II Assay:Allplex for K417N and the COVID-19 Ultra Variant Catcher, SARS-CoV-2 Extended ELITe MGB or Simplexa SARS-CoV-2 Variants Direct for N501Y and E484 mutations can discriminate the Omicron variant from the Delta variant. 2022 Microorganisms Discussion SARS_CoV_2 K417N;N501Y 65;184 70;189 COVID-19 79 87 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. The analyzed real-time RT-PCR assays target three or four of the following amino acid variations: L452R, W152C, K417T, K417N, E484Q, E484K and N501Y. 2022 Microorganisms Discussion SARS_CoV_2 E484K;E484Q;K417N;K417T;L452R;N501Y;W152C 133;126;119;112;98;143;105 138;131;124;117;103;148;110 35208761 Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. These single mutations are shared by two or more variants, except for W152C, which is described only for Epsilon (B.1.427 and B.1.429 lineages). 2022 Microorganisms Discussion SARS_CoV_2 W152C 70 75 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? Comparative genomic analysis of SARS-CoV-2 genomes revealed multiple crucial mutations to the Spike gene including K417N, K417T, E484K, N501Y, A570D, D614G, P681H, T716I, S982A and D1118H, which may aggravate the severity of SARS-CoV-2 more than the wild type variant, and potentially raise the concern of vaccine efficacy against novel strains. 2022 Microorganisms Discussion SARS_CoV_2 A570D;D1118H;D614G;E484K;K417N;K417T;N501Y;P681H;S982A;T716I 143;181;150;129;115;122;136;157;171;164 148;187;155;134;120;127;141;162;176;169 S 94 99 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? Generally, Spike D614G and ORF1b-P314L variants are consistently related and co-occur in all geographic locations with increasing frequency. 2022 Microorganisms Discussion SARS_CoV_2 D614G;P314L 17;33 22;38 S 11 16 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? However, the A23403G mutation leading to the D614G spike (S) variant was found to be located in a heavily glycosylated residue in the viral spike, was implicated in increased infectiveness and allows fast spreading of the virus during the COVID-19 pandemic compared to the wild type variant Wuhan-Hu-1. 2022 Microorganisms Discussion SARS_CoV_2 A23403G;D614G 13;45 20;50 S;S;S 51;140;58 56;145;59 COVID-19 239 247 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? It is worth mentioning that the Spike D614G mutation accompanies other frequent mutation sites in the ORF1ab (NSP3:C3037T, NSP3:T428I and NSP12:C14408T) region, the mutation at position 241 (C241T) targeting the 5'UTR, as well as the mutations at positions 203 and 212 in the Nucleocapsid protein (N:RG203KR, N:G212V), in the receptor binding domain (RBD) of Spike (S:N501Y), and in the ORF3a protein (ORF3a:Q57H). 2022 Microorganisms Discussion SARS_CoV_2 D614G;C241T;C14408T;C3037T;G212V;N501Y;Q57H;T428I 38;191;144;115;311;368;408;128 43;196;151;121;316;373;412;133 RBD;N;ORF1ab;S;S;ORF3a;ORF3a;5'UTR;Nsp12;Nsp3;Nsp3;RBD;N;N;S 326;276;102;32;359;387;402;212;138;110;123;351;298;309;366 349;288;108;37;364;392;407;217;143;114;127;354;299;310;367 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? Moreover, extragenic SNPs in 5' UTR:C241T may also affect the folding of the ssRNA and influence the replication rates of SARS-CoV-2 as it is found to occur most prominently. 2022 Microorganisms Discussion SARS_CoV_2 C241T 36 41 5'UTR 29 35 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? The D614G spike mutation characterizes the G clade and its derivate has spread exponentially across the world and become rapidly the most prevalent lineage worldwide, occurring in over 92% of total analyzed genomes in this study. 2022 Microorganisms Discussion SARS_CoV_2 D614G 4 9 S 10 15 35208920 Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? The P314L mutation in NSP12 (RNA-dependent polymerase) may play a causal role in viral replication, therefore enhancing its transmission ability and infectivity. 2022 Microorganisms Discussion SARS_CoV_2 P314L 4 9 Nsp12 22 27 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Although major concerns have been raised on the emergence of VOC, SARS-CoV-2 beta (B.1.351) and SARS-CoV-2 Delta (B.1.617.2), our analysis of SARS-CoV-2 genomes from the Malaysian population reported two different lineages of D614G variant that are actively dispersed locally. 2022 PloS one Discussion SARS_CoV_2 D614G 226 231 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Although N439K mutation in RBD was first found in already extinct lineage B.1.1.41, a new lineage B.1.258 independently acquired the same amino acid substitution. 2022 PloS one Discussion SARS_CoV_2 N439K 9 14 RBD 27 30 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Based on earlier report, we found that SARS-CoV-2 variant with D614G mutation had been circulating in Pahang since April 2020 and subsequently found elsewhere throughout Malaysia as the infection continues. 2022 PloS one Discussion SARS_CoV_2 D614G 63 68 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. For the record, the earliest study on SARS-CoV-2 virus genomes in Malaysia did not found D614G mutation, even the lineage B.6 that contributes profoundly in the second wave in Malaysia did not harbour D614G mutation in the spike protein. 2022 PloS one Discussion SARS_CoV_2 D614G;D614G 89;201 94;206 S 223 228 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Higher infectivity of the SARS-CoV-2 variants is associated with increased in binding affinity between spike protein and ACE2 due to K417N, E484K, N439K and N501Y mutations in the RBD of the spike protein. 2022 PloS one Discussion SARS_CoV_2 E484K;K417N;N439K;N501Y 140;133;147;157 145;138;152;162 S;S;RBD 103;191;180 108;196;183 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. However, there is no evidence of change in disease severity in a large cohort of patients infected with SARS-CoV-2 harbouring N439K mutation in the spike protein. 2022 PloS one Discussion SARS_CoV_2 N439K 126 131 S 148 153 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. In addition, A701V mutation, adjacent to the furin cleavage site of spike protein subunit S1 and S2, in B.1.524 of Malaysian lineage was also found in SARS-CoV-2 beta (B.1.351) strains and SARS-CoV-2 i B.1.526 (USA). 2022 PloS one Discussion SARS_CoV_2 A701V 13 18 S 68 73 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. In nations with poor containment capability, it was proven that the SARS-CoV-2 mutant lineage G (D614G) was able to replace earlier lineages more efficiently and was associated with a higher degree of disease severity. 2022 PloS one Discussion SARS_CoV_2 D614G 97 102 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. In tracking the distribution of the ten lineages which caused blooming of positive COVID-19 cases in Pahang this year, it appears that all virus collected from Pahang have the same substitution of amino acid at 1233 from Glycine to Cysteine in TM domain of spike protein, not found previously in Malaysia. 2022 PloS one Discussion SARS_CoV_2 G1233C 211 240 S 257 262 COVID-19 83 91 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. It is unknown whether B.1.466.2 (also known as Indonesian lineage) and AU.2 of Malaysian lineage, acquired N439K divergently and/or as a result of convergent evolution. 2022 PloS one Discussion SARS_CoV_2 N439K 107 112 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Moreover, the emergence of more virulent strains such as included in VOC and VOI that harbored the D614G mutation in spike protein suggests that D614G variant had constantly subjected to positive selection pressure. 2022 PloS one Discussion SARS_CoV_2 D614G;D614G 99;145 104;150 S 117 122 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Of concern, N439K mutation promotes evasion of antibody-mediated immunity by conferring resistance against several neutralizing monoclonal antibodies and reduces the activity of some polyclonal sera from patients recovered from infection. 2022 PloS one Discussion SARS_CoV_2 N439K 12 17 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Of the 41 lineages of D614G variants detected in Malaysia since March 2020, 19 lineages have disappeared, leaving 22 lineages still actively spreading in 2021. 2022 PloS one Discussion SARS_CoV_2 D614G 22 27 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Our analysis also suggests, AU.2 is not correlated to B.1.524, as B.1.524 carry different mutations (A701V) in spike protein. 2022 PloS one Discussion SARS_CoV_2 A701V 101 106 S 111 116 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. Our computational analysis predicted A701V with increase protein-protein interaction affinity. 2022 PloS one Discussion SARS_CoV_2 A701V 37 42 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. We believe the effect of G1223C mutation in TM domain deserve further investigations in future functional experiments. 2022 PloS one Discussion SARS_CoV_2 G1223C 25 31 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. We observed that AU.2 is closely related to B.1.4662 (Indonesian lineage), as both lineages carry the same amino acid mutations N439K in RBD and P681R in non RBD regions of spike protein. 2022 PloS one Discussion SARS_CoV_2 N439K;P681R 128;145 133;150 S;RBD;RBD 173;137;158 178;140;161 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. While N501Y mutation alone enhanced spike RBD-ACE2 affinity, combination of K417N, E484K and N501Y mutations in B.1.351 lineage resulted in noticeable conformational changes in RBD when bound to ACE2. 2022 PloS one Discussion SARS_CoV_2 E484K;K417N;N501Y;N501Y 83;76;6;93 88;81;11;98 S;RBD;RBD 36;42;177 41;45;180 35213571 Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. While the significance of G1223C mutation is still unknown, it is well known that spike protein mediates entry of SARS-CoV-2 into target cells through two steps. 2022 PloS one Discussion SARS_CoV_2 G1223C 26 32 S 82 87 35215765 Versatile SARS-CoV-2 Reverse-Genetics Systems for the Study of Antiviral Resistance and Replication. For SARS-CoV, substitutions F480L and V557L (located in the fingers subdomain of the polymerase), were found to be associated with resistance to remdesivir. 2022 Viruses Discussion SARS_CoV_2 F480L;V557L 28;38 33;43 35215765 Versatile SARS-CoV-2 Reverse-Genetics Systems for the Study of Antiviral Resistance and Replication. In addition to position 323, we investigated two other nsp12 polymorphisms representing minor circulating variants, A97V situated in the N-terminal and N491S found in the fingers subdomain of the polymerase domain. 2022 Viruses Discussion SARS_CoV_2 A97V;N491S 116;152 120;157 Nsp12;N 55;137 60;138 35215765 Versatile SARS-CoV-2 Reverse-Genetics Systems for the Study of Antiviral Resistance and Replication. In our study of SARS-CoV-2, these mutations were tolerated and did not revert, but the V557L mutant spread slower and acquired multiple additional mutations in spike after second passage, suggesting that this mutation had a negative impact on fitness. 2022 Viruses Discussion SARS_CoV_2 V557L 87 92 S 160 165 35215765 Versatile SARS-CoV-2 Reverse-Genetics Systems for the Study of Antiviral Resistance and Replication. Our clone already harbors Leucine compared to the Proline found in the Wuhan reference sequence which was described early during the pandemic, and we therefore tested the L323P mutant to confirm remdesivir response was comparable between both variants. 2022 Viruses Discussion SARS_CoV_2 L323P 171 176 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. Although we cannot assess the persistence of the mutation over time, a relapse of COVID-19 was observed about two weeks after the emergence of the Q493R mutation and the patient died. 2022 Viruses Discussion SARS_CoV_2 Q493R 147 152 COVID-19 82 90 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. Although we included a low number of patients, we reported the acquisition of the Q493R mutation after bamlanivimab/etesevimab therapy in a patient with bi-phenotypic acute leukemia, associated with a new rise of the SARS-CoV-2 viral load and a fatal outcome. 2022 Viruses Discussion SARS_CoV_2 Q493R 82 87 B acute lymphoblastic leukemia 153 181 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. However, no rise of the viral load was observed between the two samples, and the patient recovered from COVID-19, suggesting a limited impact of this mutation on immune escape and resistance, similar to the G1204G/E mutation selected with bamlanivimab/etesevimab. 2022 Viruses Discussion SARS_CoV_2 G1204G 207 215 COVID-19 104 112 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. In late 2021, the emergence of the Omicron variant, which harbored, among others, the Q493R mutation in the spike gene, raised fears of a decline in the efficiency of some monoclonal antibody therapies. 2022 Viruses Discussion SARS_CoV_2 Q493R 86 91 S 108 113 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. In that context, we can postulate that Q493R may have taken over the wild amino acid and may have induced a failure of viral clearance. 2022 Viruses Discussion SARS_CoV_2 Q493R 39 44 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. On the other hand, only one of the eight patients under casirivimab/imdevimab therapy developed a mutation in the spike gene, i.e., the E406E/G, which appeared 5 days after mAbs administration; however, its persistence overtime cannot be assessed with a following sample (part of the spike gene sequence was not analyzed). 2022 Viruses Discussion SARS_CoV_2 E406E;E406G 136;136 143;143 S;S 114;284 119;289 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. Our results also corroborate in vitro results observed under selective pressure from bamlanivimab, with the emergence of immune escape mutations, such as E484K and Q493R/K. 2022 Viruses Discussion SARS_CoV_2 E484K;Q493R;Q493K 154;164;164 159;171;171 35215820 Spike Gene Evolution and Immune Escape Mutations in Patients with Mild or Moderate Forms of COVID-19 and Treated with Monoclonal Antibodies Therapies. The Q493R mutation was also identified in a patient with auto-immune disease, but as part of a mixture. 2022 Viruses Discussion SARS_CoV_2 Q493R 4 9 Autoimmune diseases 57 76 35215823 Characterization of a Broadly Neutralizing Monoclonal Antibody against SARS-CoV-2 Variants. Early research on the Omicron variant has shown multiple mutations in the RBM such as N440K, G446S, S477N, T478K, Q493K, G496S, Q498R, N501Y, Y505H, including a mutation residing at amino acid residue E484A, which is associated with reduced binding, as observed with the tested Beta, Kappa, and Gamma variants harboring the exact mutation. 2022 Viruses Discussion SARS_CoV_2 E484A;G446S;G496S;N440K;N501Y;Q493K;Q498R;S477N;T478K;Y505H 201;93;121;86;135;114;128;100;107;142 206;98;126;91;140;119;133;105;112;147 35215823 Characterization of a Broadly Neutralizing Monoclonal Antibody against SARS-CoV-2 Variants. However, a reduced binding efficacy was observed against variants (Beta, Kappa, and Gamma) containing amino acid mutation at E484K or Q (Table 1). 2022 Viruses Discussion SARS_CoV_2 E484K 125 130 35215823 Characterization of a Broadly Neutralizing Monoclonal Antibody against SARS-CoV-2 Variants. The amino acid mutation Y489H has occurred only 46 times in 15 countries and is a highly conserved amino acid residue in the RBM of the RBD (as of 28 November 2021). 2022 Viruses Discussion SARS_CoV_2 Y489H 24 29 RBD 136 139 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Along with P812R in S, BT20.1 carried a mutation in NSP12 (T4685I/T293I), which is the viral RNA-dependent RNA polymerase. 2022 Viruses Discussion SARS_CoV_2 P812R;T4685I;T293I 11;59;66 16;65;71 RdRp;Nsp12;S 93;52;20 121;57;21 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Alternatively, the mutation P812R could functionally achieve the same phenotype as the deletion of the PBCS, although our primary cell infection model, in which PHE was attenuated compared to BT20.1, would suggest that this is not the case. 2022 Viruses Discussion SARS_CoV_2 P812R 28 33 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Although it is possible that P812R confers a similar phenotypic change as the PBCS deletion, it is not likely to be identical, given the clear differences in growth between PHE and BT20.1 in Vero cells and WD-PNECs. 2022 Viruses Discussion SARS_CoV_2 P812R 29 34 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. For D215G and the deletion, these mutations are similar to those in VOCs, such as Alpha and Beta variants. 2022 Viruses Discussion SARS_CoV_2 D215G 4 9 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Given the linkage between P812R and T4685I, further molecular virological work using isogenic viruses generated through reverse genetics is required to ascertain the impact of this mutation in relevant cell models. 2022 Viruses Discussion SARS_CoV_2 P812R;T4685I 26;36 31;42 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. However, what affects the rise in the P812R/NSP12 mutation remains unknown. 2022 Viruses Discussion SARS_CoV_2 P812R 38 43 Nsp12 44 49 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. In addition to the loss of the PBCS, we observed P812R in Spike and T293I in NSP12, although we were not able to associate them with changes in virus growth in WD-PNECs due to a lack of an additional comparable wild-type isolate. 2022 Viruses Discussion SARS_CoV_2 P812R;T293I 49;68 54;73 S;Nsp12 58;77 63;82 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. In PHE, loss of the PBCS occurred, which was not observed in BT20.1, and vice versa regarding P812R and NSP12. 2022 Viruses Discussion SARS_CoV_2 P812R 94 99 Nsp12 104 109 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Interestingly, P812R was observed before, in at least two other studies, associated with a change in Spike activity using infectious SARS-CoV-2 and one using a chimeric vesicular stomatitis virus encoding SARS-CoV-2 Spike. 2022 Viruses Discussion SARS_CoV_2 P812R 15 20 S;S 101;216 106;221 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Investigation of the patterns of SARS-CoV-2 genetic diversity worldwide during outbreaks has already facilitated a genetic-based nomenclature of lineages and has also highlighted the emergence of functionally relevant mutations, such as D614G in Spike and those contained in extant VOCs. 2022 Viruses Discussion SARS_CoV_2 D614G 237 242 S 246 251 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. It was suggested that P812R generated a novel PBCS at the S2' site. 2022 Viruses Discussion SARS_CoV_2 P812R 22 27 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Like previous work, we noted an association of P812R with enhanced cell-to-cell fusion when BT20.1 grown on Vero cells is compared to that grown in WD-PNECs (Figure S3). 2022 Viruses Discussion SARS_CoV_2 P812R 47 52 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. One notable finding of our work, which builds upon previous studies, is that on several occasions for both isolates, we observed a rapid increase in frequency of specific mutations in the PBCS and independently of it (PBCS deletion and P812R in Spike, and T293I in NSP12) to near fixation over the course of a couple of passages in Vero cells. 2022 Viruses Discussion SARS_CoV_2 P812R;T293I 236;256 241;261 S;Nsp12 245;265 250;270 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. P812R is a non-conservative change and rapidly rose to near fixation alongside NSP12 in BT20.1 in Vero cells. 2022 Viruses Discussion SARS_CoV_2 P812R 0 5 Nsp12 79 84 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. Similar changes (including P812R and the NTD deletion) were identified in other studies. 2022 Viruses Discussion SARS_CoV_2 P812R 27 32 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. The fact that identical mutations arise independently (e.g., loss of the PBCS and P812R) is highly suggestive of convergent evolution, perhaps toward a similar phenotype. 2022 Viruses Discussion SARS_CoV_2 P812R 82 87 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. The mutation T4685I arose with P812R, possibly suggesting genetic linkage, although this remains to be determined. 2022 Viruses Discussion SARS_CoV_2 P812R;T4685I 31;13 36;19 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. This is consistent with an effect dependent on viral input or strain or genetic background through epistatic interactions between mutations, such as D614G in Spike. 2022 Viruses Discussion SARS_CoV_2 D614G 149 154 S 158 163 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. We observed three mutations in the NTD in PHE P3 and P4: E180K, D215G and a deletion resulting in the loss of nine amino acids. 2022 Viruses Discussion SARS_CoV_2 D215G;E180K 64;57 69;62 35215919 Comparison of SARS-CoV-2 Evolution in Paediatric Primary Airway Epithelial Cell Cultures Compared with Vero-Derived Cell Lines. While the PBCS, P812R and NSP12 changes were identified in PHE and BT20.1 when grown in Vero cells, these changes did not rise to high frequencies in WD-PNECs. 2022 Viruses Discussion SARS_CoV_2 P812R 16 21 Nsp12 26 31 35215963 Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic. Identified in February 2020, D614G was the first amino acid substitution to be associated with an increase in SARS-CoV-2 transmissibility, which allowed the D614G variant to reach close to 100% global prevalence by mid-2020. 2022 Viruses Discussion SARS_CoV_2 D614G;D614G 29;157 34;162 35215963 Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic. Interestingly, SARS-CoV-2 isolates with the D614G were more susceptible to neutralization by a commercial monoclonal antibody targeting the spike glycoprotein. 2022 Viruses Discussion SARS_CoV_2 D614G 44 49 S 140 158 35215963 Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic. Interestingly, while most of these non-synonymous mutations have not been associated with changes in viral phenotype, the D614G substitution in the spike gene was detected in four SARS-CoV-2 isolates (NZ3, NZ4, NZ5, and NZ7). 2022 Viruses Discussion SARS_CoV_2 D614G 122 127 S 148 153 35215963 Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic. SARS-CoV-2 variants containing the D614G substitution have been shown to have a slight increase in infectivity in Vero-E6, Vero-81, and Huh7 cells; however, here, we showed that the D614G substitution does not confer a clear replicative advantage in Vero or VeroE6/TMPRSS2 cells. 2022 Viruses Discussion SARS_CoV_2 D614G;D614G 35;182 40;187 35215963 Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic. The D614G substitution was also present in the first VOC, Pango lineage B.1.1.7 (VOC Alpha), and has been present in all VOCs identified thus far, including B.1.617.2 (Delta) and B.1.1.529 (Omicron) (, accessed on 6 January 2022). 2022 Viruses Discussion SARS_CoV_2 D614G 4 9 35215963 Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic. The enhanced infectivity and replication fitness of SARS-CoV-2 D614G seems to be more evident in primary human airway cells and the upper respiratory tract of animal models, e.g., hamsters. 2022 Viruses Discussion SARS_CoV_2 D614G 63 68 35215963 Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic. This is similar to previous studies showing a slight increase in susceptibility to neutralization by mAbs and plasma from convalescent or vaccinated individuals, although other studies have shown an increase in resistance to neutralization in viruses carrying the D614G substitution. 2022 Viruses Discussion SARS_CoV_2 D614G 264 269 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. Interestingly, we observed three cases of putative homoplasy, with: (a) C22088T, present in a Polish sequence collected one month later than Vo' outbreak, (b) G11083T, found in several sequences from different countries and lineages, and (c) C21575T, shared by two Vo household members and appearing at a global level only in 2021, as a mutation defining the B.1.526 lineage. 2022 Viruses Discussion SARS_CoV_2 C21575T;C22088T;G11083T 242;72;159 249;79;166 35215992 Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. The sequencing data identified the Vo' Ancestor Haplotype (AH), characterized by the G11083T and G26144T mutations, from which all the other sequenced haplotypes evolved. 2022 Viruses Discussion SARS_CoV_2 G11083T;G26144T 85;97 92;104 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. As indicated in the STAR methods section, all results generated in the current manuscript were done using the Q493R mutation. 2022 Cell reports Discussion SARS_CoV_2 Q493R 110 115 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. Of note, the sequence initially released for the Omicron Spike contained the Q493K substitution, but was then corrected to Q493R. 2022 Cell reports Discussion SARS_CoV_2 Q493K;Q493R 77;123 82;128 S 57 62 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. Previous in vitro studies already showed the association of some of these mutations with increased infectivity, ACE2 interaction (N501Y, P681H), or immune evasion (K417N, N440K, G446S, S477N, E484A/K, Q493R). 2022 Cell reports Discussion SARS_CoV_2 E484A;E484K;G446S;N440K;P681H;Q493R;S477N;K417N;N501Y 192;192;178;171;137;201;185;164;130 199;199;183;176;142;206;190;169;135 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. Since initial studies on Omicron used the Q493K mutation, we verified whether the nature of the residue at 493 (either K or R) impacted plasma recognition or neutralization. 2022 Cell reports Discussion SARS_CoV_2 Q493K 42 47 35216664 SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-week interval between doses. To get a better understanding of the antigenic profile, we compared the antigenicity of the Omicron Spike with those from D614G, Alpha, Beta, Gamma, and Delta VOCs. 2022 Cell reports Discussion SARS_CoV_2 D614G 122 127 S 100 105 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. Additionally, the Y380Q mutation was identified in the S gene, and thus could be associated with the natural history of virus evolution. 2022 Diagnostic microbiology and infectious disease Discussion SARS_CoV_2 Y380Q 18 23 S 55 56 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. Further, a new mutation (Y380Q) was identified, and with C379W modify important properties in the RBD region, which may interfere with the binding of the CR3022, EY6A, H014, S304 neutralizing antibodies (NAbs). 2022 Diagnostic microbiology and infectious disease Discussion SARS_CoV_2 C379W;Y380Q 57;25 62;30 RBD 98 101 35219552 Y380Q novel mutation in receptor-binding domain of SARS-CoV-2 spike protein together with C379W interfere in the neutralizing antibodies interaction. Nonetheless, despite such limitations, a novel mutation (Y380Q) in the RBD region of SARS-CoV-2 spike protein was described. 2022 Diagnostic microbiology and infectious disease Discussion SARS_CoV_2 Y380Q 57 62 S;RBD 96;71 101;74 35223905 Molecular and Epidemiological Characterization of Emerging Immune-Escape Variants of SARS-CoV-2. In particular, only about 15-30% of vaccinees showed potent neutralizing activity against Delta, Delta + E484K + N501Y, and Mu strains. 2022 Frontiers in medicine Discussion SARS_CoV_2 E484K;N501Y 105;113 110;118 35223905 Molecular and Epidemiological Characterization of Emerging Immune-Escape Variants of SARS-CoV-2. The N501Y mutation was common in the strains with reduced efficacy, suggesting that this mutation is a limitation of etesevimab. 2022 Frontiers in medicine Discussion SARS_CoV_2 N501Y 4 9 35223905 Molecular and Epidemiological Characterization of Emerging Immune-Escape Variants of SARS-CoV-2. These strains commonly include the E484K mutation, and this mutation is considered to be a limitation associated with casirivimab, as previously indicated. 2022 Frontiers in medicine Discussion SARS_CoV_2 E484K 35 40 35231807 Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. In this study, we describe the probable emergence of a de novo E484K mutation and subsequent transmission to all members of a household and then onward to additional close interpersonal contacts. 2022 Diagnostic microbiology and infectious disease Discussion SARS_CoV_2 E484K 63 68 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. A23403G (D614G) was observed in West European states in the early stage of the disease and this finding might point towards the source of infection from which it was introduced in India. 2022 Saudi journal of biological sciences Discussion SARS_CoV_2 D614G;A23403G 9;0 14;7 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. Moreover, the present study showed that A23403G (D614G) co-occurred with three other mutations that were C241T, C14408T, and C3037T, a similar pattern of co-existence was reported by, while observed the co-existent of C14408T and A23403G. 2022 Saudi journal of biological sciences Discussion SARS_CoV_2 A23403G;A23403G;C14408T;C14408T;C241T;C3037T;D614G 40;230;112;218;105;125;49 47;237;119;225;110;131;54 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. Our results disagreed with who studied the mutations among SARS-CoV-2 collected from various locations and reported C29095T in the N gene, T28144C in the ORF8 gene, and C8782T in the ORF1ab gene as the most frequent mutations. 2022 Saudi journal of biological sciences Discussion SARS_CoV_2 C29095T;C8782T;T28144C 116;169;139 123;175;146 ORF1ab;ORF8;N 183;154;131 189;158;132 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. Our study showed that the most common synonymous mutation occurred in the non-coding region at the position C241T, followed by several synonymous mutations in ORF1 a/b, at the positions C3037T and C17788T. 2022 Saudi journal of biological sciences Discussion SARS_CoV_2 C17788T;C241T;C3037T 197;108;186 204;113;192 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. Similar results concerning the abundant nonsynonymous mutations at positions C241T and C3037T have been reported by numerous authors. 2022 Saudi journal of biological sciences Discussion SARS_CoV_2 C241T;C3037T 77;87 82;93 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. The most frequent nonsynonymous mutation in our study occurred in the S gene at the position A23403G where A changed to G leading to the replacement of aspartic acid by glycine in position (D614G). 2022 Saudi journal of biological sciences Discussion SARS_CoV_2 A23403G;D614G 93;190 100;195 S 70 71 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. The nonsynonymous mutation G25563T (Q75H) was reported in Bangladesh and USA. 2022 Saudi journal of biological sciences Discussion SARS_CoV_2 G25563T;Q75H 27;36 34;40 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. The second most dominant nonsynonymous mutation occurred in ORF1 a/b at position C14408T which changed the amino acid in RNA-dependent RNA polymerase and may influence the replication rate of the viruses. 2022 Saudi journal of biological sciences Discussion SARS_CoV_2 C14408T 81 88 RdRp 121 149 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. The third common mutation occurred in ORF3a at position G 25563 T (Q75H) followed by a mutation in the N gene at position C28854T (S194L). 2022 Saudi journal of biological sciences Discussion SARS_CoV_2 C28854T;G25563T;Q75H;S194L 122;56;67;131 129;65;71;136 ORF3a;N 38;103 43;104 35233173 In-silico genomic landscape characterization and evolution of SARS-CoV-2 variants isolated in India shows significant drift with high frequency of mutations. They found that C3037T was the most common synonymous mutation and C14408 > T mutation is the second common mutation, observed A23403G (D614G) in 60% of Indian isolate, observed it in 93% out of 77 Indian variants. 2022 Saudi journal of biological sciences Discussion SARS_CoV_2 A23403G;C14408T;C3037T;D614G 127;67;16;136 134;77;22;141 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. Here, we showed preservation of Fc effector function against VOCs both in individuals previously infected with the original D614G variant and in individuals vaccinated with Ad26.COV2.S. 2022 Cell reports. Medicine Discussion SARS_CoV_2 D614G 124 129 S 183 184 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. This is supported by a recent study measuring natural killer (NK) activation, ADCP, ADCD, and ADCC in Ad26.COV2.S vaccinees showing differences of under 2-fold between original D614G and Beta. 2022 Cell reports. Medicine Discussion SARS_CoV_2 D614G 177 182 S 112 113 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. This was despite the fact that the sequence of immunodominant regions of the eliciting immunogens were the same, with only the single D614G mutation differing between them. 2022 Cell reports. Medicine Discussion SARS_CoV_2 D614G 134 139 35233544 SARS-CoV-2 Beta and Delta variants trigger Fc effector function with increased cross-reactivity. We also show subtle differences in the ability of antibodies elicited by either the original D614G or the Ad26.COV2.S vaccine to perform ADCC against Beta. 2022 Cell reports. Medicine Discussion SARS_CoV_2 D614G 93 98 S 116 117 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. Our unsupervised learning strategy reveals that the Omicron variant is now acquiring four new mutations in the spike protein (R346K, A701V, I1081V, N1192S) and five new mutations in nsp3 (V1069I), nsp4 (V94A), the RNA-dependent RNA polymerase (F694Y), ORF3a (L106F) and nucleocapsid phosphoprotein (D343G). 2022 Research square Discussion SARS_CoV_2 A701V;I1081V;N1192S;D343G;F694Y;L106F;R346K;V1069I;V94A 133;140;148;299;244;259;126;188;203 138;146;154;304;249;264;131;194;207 RdRp;N;S;ORF3a;Nsp3;Nsp4 214;270;111;252;182;197 242;282;116;257;186;201 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. The F694Y mutation in the polymerase enzyme occurs at a position that seems likely to impact binding of Remdesivir and related viral inhibitors. 2022 Research square Discussion SARS_CoV_2 F694Y 4 9 35233566 Rapidly Identifying New Coronavirus Mutations of Potential Concern in the Omicron Variant Using an Unsupervised Learning Strategy. The N1192S mutation is located in a spike protein region, the HR2 sequence, that exhibits extremely high conservation across all human coronavirus, presumably due to the importance of this region in the host cell fusion process. 2022 Research square Discussion SARS_CoV_2 N1192S 4 10 S 36 41 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. It is important to note that bat RaTG13 and pangolin GX-P5L, but not Omicron, are antigenically grouped with SARS-CoV-2. 2022 Research square Discussion SARS_CoV_2 P5L 56 59 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. Third, it is clear that Omicron is exceptional in its NAb escape capability when considering that GX-P5L, with twice as many RBD mutations, displayed less degree of NAb escape, suggesting that the emergence of Omicron is likely due to immune selective pressure. 2022 Research square Discussion SARS_CoV_2 P5L 101 104 RBD 125 128 35233568 Differential escape of neutralizing antibodies by SARS-CoV-2 Omicron and pre-emergent sarbecoviruses. This is based on the fact that pre-emergent clade-2 sarbecovirus GX-P5L and RaTG13, which are evolutionarily more distantly related to SARS-CoV-2 than Omicron (Fig 1b), showed less degree of NAb escape than Omicron (Fig 3a-e). 2022 Research square Discussion SARS_CoV_2 P5L 68 71 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. In this analysis, we evaluated the relative impact of earlier N501Y-positive VOC and subsequent Delta VOC infections on severity of infection by age group. 2022 Clinical infectious diseases Discussion SARS_CoV_2 N501Y 62 67 35234859 Age-Specific Changes in Virulence Associated with SARS-CoV-2 Variants of Concern. We found that, as reported previously, Delta VOC infection is more virulent than infection with both N501Y-positive VOC and non-VOC SARS-CoV-2 strains. 2022 Clinical infectious diseases Discussion SARS_CoV_2 N501Y 101 106 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. According to the sequencing data deposited as GISAID (https://www.gisaid.org/) and the analysis on Outbreak.info, the frequency of the 15 aa mutations in the RBD is very dynamic, e.g., K417N, described for the initial Omicron variant to occur in ~35% (status 2021-12-14, 2146 sequences) of all sequenced Omicron isolates, is now retrieved in above 55% of sequenced viruses (status 2022-02-07, 873.492 sequences). 2022 BMC medicine Discussion SARS_CoV_2 K417N 185 190 RBD 158 161 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. Hence, some bioinformatic models predicted an increase in the ACE2 binding affinity of Omicron RBD while other models rejected this scenario and stated: "the Q493R/K mutations, in a combination with K417N and T478K, dramatically reduced the S1 RBD binding by over 100 folds". 2022 BMC medicine Discussion SARS_CoV_2 K417N;Q493K;Q493R;T478K 199;158;158;209 204;165;165;214 RBD;RBD 95;244 98;247 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. One has also to consider that we utilized in our work the originally available sequence with a Q493K mutation, whereas Q493R sequences have been published since. 2022 BMC medicine Discussion SARS_CoV_2 Q493K;Q493R 95;119 100;124 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. S477N, T478K, and E484A were initially at ~47% (status 2021-12-14, 2146 sequences), now instead above 88%, as N501Y (status 2022-02-07, 873.492 sequences). 2022 BMC medicine Discussion SARS_CoV_2 E484A;N501Y;T478K;S477N 18;110;7;0 23;115;12;5 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. Several Omicron RBD mutations are assumed to increase the binding to ACE2: G339D, S477N, T478K, Q493K, and N501Y; others are proposed to be neutral: S371L, S373P, G446S, E484A, Q493R, and Q498R, or are assumed to reduce the binding to ACE2: S375F, K417N, G496S, and Y505H according to yeast display experiments performed by Starr et al. 2022 BMC medicine Discussion SARS_CoV_2 E484A;G339D;G446S;G496S;K417N;N501Y;Q493K;Q493R;Q498R;S371L;S373P;S375F;S477N;T478K;Y505H 170;75;163;255;248;107;96;177;188;149;156;241;82;89;266 175;80;168;260;253;112;101;182;193;154;161;246;87;94;271 RBD 16 19 35236358 Human serum from SARS-CoV-2-vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant. The K417N mutation is a key mutation also in the Beta variant, the T478K mutation instead in the Delta variant, and N501Y in the Alpha, Beta, and Gamma variants. 2022 BMC medicine Discussion SARS_CoV_2 K417N;N501Y;T478K 4;116;67 9;121;72 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. For clinically approved or authorized antibodies, S309 (sotrovimab) retained activity against both BA.1 and BA.1+R346K, but its activity against BA.2 has dropped 27-fold. 2022 Nature Discussion SARS_CoV_2 R346K 113 118 35240676 Antibody evasion properties of SARS-CoV-2 Omicron sublineages. In summary, we have comprehensively evaluated the antigenic properties of two sublineages of the Omicron variant, BA.1+R346K and BA.2, and we believe that our results have important clinical implications. 2022 Nature Discussion SARS_CoV_2 R346K 119 124 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. A possible explanation for this intermediate fitness phenotype could be the acquisition of the N501Y mutation in the absence of D614G. 2022 Nature communications Discussion SARS_CoV_2 D614G;N501Y 128;95 133;100 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. Importantly, B.1.617.2 escaped these antibodies in a similar manner, suggesting that the L452R mutation present in both variants facilitates this escape. 2022 Nature communications Discussion SARS_CoV_2 L452R 89 94 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. In the COVID-19 pandemic, infections are currently dominated by B.1-derived lineages harboring the prominent D614G mutation. 2022 Nature communications Discussion SARS_CoV_2 D614G 109 114 COVID-19 7 15 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. Interestingly, the VOCs B.1.351 and P.1 escaped LY-COV555 and REGN10933 which was likely facilitated by the E484K mutation present in both variants. 2022 Nature communications Discussion SARS_CoV_2 E484K 108 113 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. L18F lies within the first of five loops of the NTD supersite and could contribute to the escape from antibody-mediated immunity as previously suggested. 2022 Nature communications Discussion SARS_CoV_2 L18F 0 4 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. N501Y increases the affinity of the viral S for ACE2 and D614G is thought to prevent premature dissociation of the S trimer leading to a higher infectivity and transmissibility. 2022 Nature communications Discussion SARS_CoV_2 D614G;N501Y 57;0 62;5 S;S 42;115 43;116 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. The root of the pandemic lies in the parental A lineage with the characteristic C8782T and T28144C mutations. 2022 Nature communications Discussion SARS_CoV_2 C8782T;T28144C 80;91 86;98 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. This is in agreement with deep mutational scanning data that showed decreased binding of L452R and LY-COV555. 2022 Nature communications Discussion SARS_CoV_2 L452R 89 94 35241661 Antibody escape and global spread of SARS-CoV-2 lineage A.27. This suggests that L452R and E484K lead to an escape from LY-COV555 and to a partial resistance to either REGN10987 or REGN10933, respectively. 2022 Nature communications Discussion SARS_CoV_2 E484K;L452R 29;19 34;24 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. All nine amino acid changes, namely N440K, S477N, V483A, E484K/Q, F490S, S494L/P, N501Y are associated with immune escape. 2021 Wellcome open research Discussion SARS_CoV_2 E484K;E484Q;F490S;N440K;N501Y;S477N;S494L;S494P;V483A 57;57;66;36;82;43;73;73;50 64;64;71;41;87;48;80;80;55 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. Early in the pandemic, a single mutation in the gene encoding the Spike protein of SARS-CoV-2 resulting in a D614G amino acid change was identified to increase infectivity and transmission, . 2021 Wellcome open research Discussion SARS_CoV_2 D614G 109 114 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. Four viruses in our study have mutations resulting in amino acid changes at this position (Q677H (n=3), Q677P (n=1)) (extended data, S6 ). 2021 Wellcome open research Discussion SARS_CoV_2 Q677P;Q677H 104;91 109;96 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. Only one of the six sequences from the outbreak cluster had the mutation resulting the N440K replacement in the Spike protein ( Figure 2C, extended data S6. 2021 Wellcome open research Discussion SARS_CoV_2 N440K 87 92 S 112 117 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. The immune escape associated amino acid change, N440K has been reported from the states of Andhra Pradesh, Maharashtra, Telangana, and Karnataka, and is also associated with reinfection, . 2021 Wellcome open research Discussion SARS_CoV_2 N440K 48 53 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. The lineage is characterized by the following amino acid replacements- nsp12-P323L(95.38%), S-D614G (93.85%), S-N440K (56.92%), ORF 3a-Q57H (90.77%), ORF 3a-E261*(81.54%), nsp3-T183I (81.54%), nsp16-L126F(80%), N-S2P (72.31%), ORF 8-S97I (72.31%) (extended data, Supplementary Table 7 ). 2021 Wellcome open research Discussion SARS_CoV_2 D614G;E261X;L126F;N440K;P323L;Q57H;S97I;T183I 94;157;199;112;77;135;233;177 99;162;204;117;82;139;237;182 Nsp12;Nsp3;N;S;S 71;172;211;92;110 76;176;212;93;111 35243004 Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka. They occurred singly or in pairs (N440K+F490S) ( Figure 2). 2021 Wellcome open research Discussion SARS_CoV_2 N440K;F490S 34;40 39;45 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. And this may also be why nsp16 MTase activity is not as affected as nsp14 in the H80A variant, because it can only affect nsp16 indirectly through the C77 residue. 2022 Informatics in medicine unlocked Discussion SARS_CoV_2 H80A 81 85 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. Here, we found one candidate, H80R, that is almost 100% likely to have greater than 90% MTase activity, and, hopefully, more than 100%. 2022 Informatics in medicine unlocked Discussion SARS_CoV_2 H80R 30 34 35252541 Optimizing peptide inhibitors of SARS-Cov-2 nsp10/nsp16 methyltransferase predicted through molecular simulation and machine learning. It is not beyond the realm of possibilities that the variant found furthest away from the "low" MTase variants, as well as the wild type, L92Y, may be the variant that has the most potential to increase the affinity for nsp16. 2022 Informatics in medicine unlocked Discussion SARS_CoV_2 L92Y 138 142 35255849 Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. Using this genomic surveillance system, we detected the emergence of a viral strain with a de novo N501Y substitution in the Spike protein. 2022 BMC public health Discussion SARS_CoV_2 N501Y 99 104 S 125 130 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. illustrated an nAb escape event by the Omicron variant, with the K417N, G446S, E484A, Q493K/R, and N440K mutations, involved in antibody escape. 2022 GeroScience Discussion SARS_CoV_2 E484A;G446S;K417N;N440K;Q493K;Q493R 79;72;65;99;86;86 84;77;70;104;93;93 35258772 Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. The significant mutations and features are N501Y (augments the binding between of S-protein and ACE2); D614G (increase infectivity); H655Y (accelerate transmission); N679K (increase viral transmission); and P681H (enhance binding affinity of S-protein) (Table 2). 2022 GeroScience Discussion SARS_CoV_2 D614G;H655Y;N501Y;N679K;P681H 103;133;43;166;207 108;138;48;171;212 S;S 82;242 83;243 35262011 Use of amplicon melt temperature to detect SARS-CoV-2 Lineage B.1.1.7 variant through the G28048T mutation in the ORF 8 gene. The appearance of additional mutations that could reverse the amplicon melt change, such as A28058G represents a limitation to this approach, although this particular SNP has not been detected in any of the full SARS-CoV-2 genomes deposited to date. 2021 Journal of clinical virology plus Discussion SARS_CoV_2 A28058G 92 99 35262011 Use of amplicon melt temperature to detect SARS-CoV-2 Lineage B.1.1.7 variant through the G28048T mutation in the ORF 8 gene. The G28048T mutation (R52I) has not been identified (GSAID; www.gisaid.org) other SARS-CoV-2 lineages so far (April 2021). 2021 Journal of clinical virology plus Discussion SARS_CoV_2 G28048T;R52I 4;22 11;26 35262087 Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites. The accuracies of K417T, E484K, E484Q, and L452R assays were >= 96.4% (Table 3). 2022 medRxiv Discussion SARS_CoV_2 E484K;E484Q;K417T;L452R 25;32;18;43 30;37;23;48 35262087 Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites. To address this, we are validating Spike SNP assays for K417N, N501Y, and G339D. 2022 medRxiv Discussion SARS_CoV_2 G339D;K417N;N501Y 74;56;63 79;61;68 S 35 40 35262087 Identifying SARS-CoV-2 Variants of Concern through saliva-based RT-qPCR by targeting recurrent mutation sites. We did observe low-level amplification from off-target binding in the E484K, K417T, and L452R assays. 2022 medRxiv Discussion SARS_CoV_2 E484K;K417T;L452R 70;77;88 75;82;93 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. Amino acid changes in spike proteins of variants contribute to immune evasion, and it has been suggested that N501Y is associated with increased infectivity, whereas L452R, T478K, and E484K with K417N reduce the interaction of neutralizing antibodies with RBD. 2022 Microbiology spectrum Discussion SARS_CoV_2 E484K;K417N;L452R;N501Y;T478K 184;195;166;110;173 189;200;171;115;178 S;RBD 22;256 27;259 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. However, Eta with slightly reduced neutralization results has solely an E484K substitution, indicating that the E484K substitution alone is not able to substantially decrease the neutralization efficacy of vaccine-induced antibodies. 2022 Microbiology spectrum Discussion SARS_CoV_2 E484K;E484K 72;112 77;117 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. Similar findings have been observed by others, and especially amino acid change E484K in Beta has been linked to immune evasion. 2022 Microbiology spectrum Discussion SARS_CoV_2 E484K 80 85 35262410 Vaccine-Induced Antibody Responses against SARS-CoV-2 Variants-Of-Concern Six Months after the BNT162b2 COVID-19 mRNA Vaccination. We observed similar neutralization titers against D614G, Alpha, and Eta, whereas neutralization of Beta and Delta was reduced or lost 6 months postvaccination. 2022 Microbiology spectrum Discussion SARS_CoV_2 D614G 50 55 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. Herein, we studied three critical RBD mutants L452R, E484Q and L452R-E484Q by implementing the all-atom MD simulations to examine the spike glycoprotein molecular alterations associated with RBD mutations. 2022 3 Biotech Discussion SARS_CoV_2 E484Q;L452R;L452R;E484Q 53;46;63;69 58;51;68;74 S;RBD;RBD 134;34;191 152;37;194 35265451 Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q. To summarize, the study provided a comprehensive view of destabilizing mechanisms on L452R, E484Q and L452R-E484Q of RBD associated with SARS-CoV-2 spike glycoprotein. 2022 3 Biotech Discussion SARS_CoV_2 E484Q;L452R;L452R;E484Q 92;85;102;108 97;90;107;113 S;RBD 148;117 166;120 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. Additionally, the P681R mutation in the spike proteins of Kappa and Delta variants enhanced the spike processing and cell fusion activities. 2022 mBio Discussion SARS_CoV_2 P681R 18 23 S;S 40;96 45;101 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. Our analysis suggests that the immune escape is mainly conferred by the E484Q, T484K, Delta145-146, and E484K mutations: these new variants must be further surveyed to avoid fast spread, and their presence might raise alerts if they might be considered likely to soon contribute to accelerating the spread of the virus in human populations. 2022 mBio Discussion SARS_CoV_2 E484K;E484Q;T484K 104;72;79 109;77;84 35266815 Characterization of SARS-CoV-2 Variants B.1.617.1 (Kappa), B.1.617.2 (Delta), and B.1.618 by Cell Entry and Immune Evasion. Recent studies of infection with the Delta variant bearing P681R showed it could form large syncytia compared to other variants, further indicating that the P681R mutation in the furin cleavage site could enhance viral fusogenicity. 2022 mBio Discussion SARS_CoV_2 P681R;P681R 59;157 64;162 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. For example, the positively selected site T175I (ORF3; Table S1), also referred to as a site where epitopes overlap, the minor allele (isoleucine-I) is found on other continents, indicating that it is recurrent in several lineages in addition to Gamma. 2022 Genetics and molecular biology Discussion SARS_CoV_2 T175I 42 47 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. It is known that a tyrosine (Y) residue at position 501 (located in the receptor-binding domain, RBD, of the S protein), rather than an asparagine (N; present in Wuhan SARS-CoV-2 genome sequence), is present in Alpha, Beta, and Gamma VOCs, potentially creating opportunities for these to become more infectious and partially resistant to therapeutics blocking RBD-ACE2 interactions. 2022 Genetics and molecular biology Discussion SARS_CoV_2 Y501Y 18 56 RBD;RBD;N;S 97;360;148;109 100;363;149;110 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. Other derived lineages also harbor the N501Y mutation, signaling its recurrence. 2022 Genetics and molecular biology Discussion SARS_CoV_2 N501Y 39 44 35266951 Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. VOCs Beta and Gamma share an additional RDB mutation, K417N/T , while UK researchers detected cases of Alpha lineages with the 484K allele, which also characterizes the Beta and Gamma lineages. 2022 Genetics and molecular biology Discussion SARS_CoV_2 K417N;K417T 54;54 61;61 35273335 The SARS-CoV-2 Alpha variant exhibits comparable fitness to the D614G strain in a Syrian hamster model. In another study that used engineered rescued viruses derived from the USA_WA1/2020 strain, the hamster model appeared useful to detect weak fitness advantages and increases in transmissibility of viruses that carry the N501Y and A570D spike mutations. 2022 Communications biology Discussion SARS_CoV_2 A570D;N501Y 230;220 235;225 S 236 241 35273335 The SARS-CoV-2 Alpha variant exhibits comparable fitness to the D614G strain in a Syrian hamster model. Some recent studies regarding transmissibility of Alpha variant or Alpha-like viruses showed a fitness advantage of these viruses on strains carrying D614G spike mutation in the hamster model. 2022 Communications biology Discussion SARS_CoV_2 D614G 150 155 S 156 161 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Although E484 is located outside of ACE2 binding area, E484K mutation can abolish the binding of RBD to some antibodies, including bamlanivimab. 2022 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 E484K 55 60 RBD 97 100 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Beta variant contains nine mutations in SARS-CoV-2 spike protein: D614G, Delta242-Delta244, R246I, K417N, E484K, N501Y, and A701V. 2022 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 A701V;D614G;E484K;K417N;N501Y;R246I 124;66;106;99;113;92 129;71;111;104;118;97 S 51 56 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. However, 50 mug/mL glycyrrhizic acid did not affect the binding between ACE2 and RBD with K417N-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 K417N;E484K;N501Y 90;96;102 95;101;107 RBD 81 84 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. In conclusion, our results suggest that GB-1 could be a candidate for prophylaxis against some variants of SARS-CoV-2 infection through the inhibition of the binding between ACE2 and RBD with mutations (N501Y, E484K, L452R-T478K or K417N-E484K-N501Y). 2022 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 E484K;K417N;L452R;N501Y;E484K;N501Y;T478K 210;232;217;203;238;244;223 215;237;222;208;243;249;228 RBD 183 186 COVID-19 107 127 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. In our results, GB-1 has higher inhibitory ability in the variant with K417N-E484K-N501Y mutation than the variant with K417T-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 K417N;K417T;E484K;E484K;N501Y;N501Y 71;120;77;126;83;132 76;125;82;131;88;137 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. In this study, we discovered that GB-1 blocked the binding between ACE2 and RBD with Wuhan-type or K417N-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 K417N;E484K;N501Y 99;105;111 104;110;116 RBD 76 79 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. It is possible that the other index compounds in black tea of GB-1 could block the binding between ACE2 and RBD with K417N-E484K-N501Y mutation, except glycyrrhizic acid. 2022 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 K417N;E484K;N501Y 117;123;129 122;128;134 RBD 108 111 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Moreover, GB-1 inhibited the binding between ACE2 and RBD with N501Y mutation or E484K mutation, but not K417N mutation. 2022 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 E484K;K417N;N501Y 81;105;63 86;110;68 RBD 54 57 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. Moreover, K417N-E484K-N501Y mutations within RBD of the virus could increase higher binding affinity to ACE2 than the wildtype RBD. 2022 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 K417N;E484K;N501Y 10;16;22 15;21;27 RBD;RBD 45;127 48;130 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The different K417N/T mutations could affect the inhibitory ability of GB-1 on the binding between ACE2 and RBD with K417N-E484K-N501Y mutation or K417T-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 K417N;K417N;K417T;K417T;E484K;E484K;N501Y;N501Y 117;14;14;147;123;153;129;159 122;21;21;152;128;158;134;164 RBD 108 111 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The first characterization report from Haolin Liu and colleagues showed that N501Y mutation increases the binding affinity between spike protein and ACE2. 2022 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 N501Y 77 82 S 131 136 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The previous studies reported that K417N involves in the interaction between spike protein and ACE2. 2022 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 K417N 35 40 S 77 82 35279013 Potential inhibitor for blocking binding between ACE2 and SARS-CoV-2 spike protein with mutations. The previous study reported that desolvation energy, restraints violation energy, Van der Waals energy, electrostatic energy, and buried surface area are different between K417N-E484K-N501Y mutation and K417T-E484K-N501Y mutation. 2022 Biomedicine & pharmacotherapy Discussion SARS_CoV_2 K417N;K417T;E484K;E484K;N501Y;N501Y 172;203;178;209;184;215 177;208;183;214;189;220 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. Cell-mediated immunity might be obtained because few mutations in the T-cell epitope of VOCs are known, although L452R mutation, which is present in some variants (B.1.167 and B.1.427/429), escapes from HLA-24 cell-mediated immunity. 2022 Frontiers in immunology Discussion SARS_CoV_2 L452R 113 118 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. Further follow-up will be needed to confirm whether the specific Nab titer against D614G is maintained or not. 2022 Frontiers in immunology Discussion SARS_CoV_2 D614G 83 88 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The neutralizing titer against D614G significantly decreased in sera of 6-8 months post onset compared to those of 1-3 months post onset ( Figure 3B ). 2022 Frontiers in immunology Discussion SARS_CoV_2 D614G 31 36 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. The purpose of this study was to examine the longevity of Nab activity of COVID-19 convalescent sera against D614G, and their neutralizing breadth against B.1.1.7, P.1, and B.1.351. 2022 Frontiers in immunology Discussion SARS_CoV_2 D614G 109 114 COVID-19 74 82 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. These observations suggested that all participants in this study were likely to be infected with D614G. 2022 Frontiers in immunology Discussion SARS_CoV_2 D614G 97 102 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. This reason might be that weak immune-response against SARS-CoV-2 lead to the low Nab titers of 'patients without pneumonia' against D614G compared to those of 'patients with pneumonia'. 2022 Frontiers in immunology Discussion SARS_CoV_2 D614G 133 138 Pneumonia;Pneumonia 114;175 123;184 35281007 Cross-Neutralizing Breadth and Longevity Against SARS-CoV-2 Variants After Infections. We performed live virus neutralization assays against D614G and three VOCs to assess the Nab titers of COVID-19 convalescent sera. 2022 Frontiers in immunology Discussion SARS_CoV_2 D614G 54 59 COVID-19 103 111 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. For example, less than 0.5% of Q.4 (one of the sublineages for the Alpha variant and reported in December 2020) is known to have an S:P681H mutation. 2022 Applied and environmental microbiology Discussion SARS_CoV_2 P681H 134 139 S 132 133 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. The S:P681H mutation is one of the mutation markers for the Alpha variant. 2022 Applied and environmental microbiology Discussion SARS_CoV_2 P681H 6 11 S 4 5 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. This low-accuracy issue might happen because their primers include sequences for N:A119S, a mutation marker for the Zeta variant (P.2 lineage). 2022 Applied and environmental microbiology Discussion SARS_CoV_2 A119S 83 88 N 81 82 35285246 Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. Thus, if the S:P681H mutation is targeted for the Alpha variant, Q.4 will cause false negatives. 2022 Applied and environmental microbiology Discussion SARS_CoV_2 P681H 15 20 S 13 14 35285705 Specific Detection of SARS-CoV-2 Variants B.1.1.7 (Alpha) and B.1.617.2 (Delta) Using a One-Step Quantitative PCR Assay. The S157del and the Orf8119del reactions showed similar performance in both clinical and wastewater samples and can therefore be used in the current situation where both deletions are unique for the Delta variant. 2022 Microbiology spectrum Discussion SARS_CoV_2 S157del 4 11 35290827 Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. It carries 3 main substitutions, T95I, Y145H and A222V, compared to the parental Delta lineage. 2022 EBioMedicine Discussion SARS_CoV_2 A222V;T95I;Y145H 49;33;39 54;37;44 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. also showed that the Delta variant (containing nucleocapsid: R203M) produced an immensely higher viral load in patients. 2022 Emerging microbes & infections Discussion SARS_CoV_2 R203M 61 66 N 47 59 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Despite a relatively high LOD of RT-LAMP, the analytical sensitivity of this strategy (481 copies/reaction) is adequate to detect the R203M mutation in clinical use. 2022 Emerging microbes & infections Discussion SARS_CoV_2 R203M 134 139 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. found that the R203M mutation allowed Delta to deposit 10 times more mRNA into host cells than the wild-type virus in luciferase experiments, and they further demonstrated that R203M-mutant viruses generated 51 times more infectious virus in a live coronavirus model. 2022 Emerging microbes & infections Discussion SARS_CoV_2 R203M;R203M 15;177 20;182 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. In our study, we selected a signature mutation of the N gene R203M as the detective target, which accounted for 98.6% in the sequenced Delta variants. 2022 Emerging microbes & infections Discussion SARS_CoV_2 R203M 61 66 N 54 55 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. In the absence of Omicron clinical samples, we can reasonably speculate that the R203M primer provides good discrimination between Omicron and Delta. 2022 Emerging microbes & infections Discussion SARS_CoV_2 R203M 81 86 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. In the present study, we first appraised the application of RT-LAMP in identifying globally dominant Delta variants based on R203M discrimination. 2022 Emerging microbes & infections Discussion SARS_CoV_2 R203M 125 130 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. R203M is considered to be potentially destructive to the nucleocapsid protein structure according to the cluster analysis of SNP data. 2022 Emerging microbes & infections Discussion SARS_CoV_2 R203M 0 5 N 57 69 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. Studies have reported that R203M could enhance the adaptability of the Delta variants and significantly bolster their infectiousness. 2022 Emerging microbes & infections Discussion SARS_CoV_2 R203M 27 32 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The appearance of the Omicron variant also implies that SARS-CoV-2 may evolve into more high-risk variants in the future, and the appearance of other variants near the R203M site is beneficial to the ability of the current R203M primer to identify Delta. 2022 Emerging microbes & infections Discussion SARS_CoV_2 R203M;R203M 168;223 173;228 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The genotyping RT-LAMP method was developed by analyzing the significant discrepancy in amplification efficiency of two sets of primers, the Delta-specific R203M primer set and the conserved N gene primer set, in which the R203M primer set was the core part to realize the amplification difference based on SNP discrimination. 2022 Emerging microbes & infections Discussion SARS_CoV_2 R203M;R203M 156;223 161;228 N 191 192 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. The nucleic acid sequence region corresponding to the core primer LF of the R203M primer set in the Omicron variation differs significantly from that of Delta, whereas the conserved primer area has no significant alteration. 2022 Emerging microbes & infections Discussion SARS_CoV_2 R203M 76 81 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. the R203K/G204R mutation). 2022 Emerging microbes & infections Discussion SARS_CoV_2 R203K;G204R 4;10 9;15 35293849 RT-LAMP assay for rapid detection of the R203M mutation in SARS-CoV-2 Delta variant. We found that the R203M primer set had a favorable capability for distinguishing mutations but a moderate amplification ability for the target sequence. 2022 Emerging microbes & infections Discussion SARS_CoV_2 R203M 18 23 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Here, we demonstrated that molecular features of the spike (such as L452R and E484Q), already known to confer fitness, act in concert with alterations in the NTD to enhance spike function further. 2022 Life science alliance Discussion SARS_CoV_2 E484Q;L452R 78;68 83;73 S;S 53;173 58;178 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. One of Delta variant's siblings, a variant called Lambda, also carries changes in the spike NTD, in addition to L452Q, and these alterations have been associated with the virus' higher infectivity and immune evasion ability ( Preprint; Preprint). 2022 Life science alliance Discussion SARS_CoV_2 L452Q 112 117 S 86 91 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. Our observations that E156G/Delta157-158 and L452R/E484Q mutations bearing spike induced large syncytia formation, almost equivalent to that of the ICS-05/03 spike, exemplifies NTD- and RBD-specific changes in promoting cell-cell fusion. 2022 Life science alliance Discussion SARS_CoV_2 E156G;L452R;E484Q 22;45;51 27;50;56 S;S;RBD 75;158;186 80;163;189 35296517 SARS-CoV-2 spike E156G/Delta157-158 mutations contribute to increased infectivity and immune escape. The widespread NTD-specific mutation E156G/ 157-158, which is also shared by delta variant, likely conferred an evolutionary advantage and might underlie vaccine breakthroughs. 2022 Life science alliance Discussion SARS_CoV_2 E156G 37 42 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. 7a) and P812L. 2022 Nature communications Discussion SARS_CoV_2 P812L 8 13 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. A348S is not proximal to the mAb binding sites. 2022 Nature communications Discussion SARS_CoV_2 A348S 0 5 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. E802D is associated with a fitness cost in vitro, which may limit the broader impact of this mutation on the development of secondary resistance during treatment and the risk for primary resistance through transmission of resistant variants. 2022 Nature communications Discussion SARS_CoV_2 E802D 0 5 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. In summary, we identified the de novo emergence of a RDV-resistance mutation, E802D, following initiation of RDV in an immunocompromised patient with persistent SARS-CoV-2 infection. 2022 Nature communications Discussion SARS_CoV_2 E802D 78 83 COVID-19 161 181 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. One week after casirivimab-imdevimab was administered (day 170), we identified a new spike protein mutation, A348S in the RBD domain, which persisted to day 177. 2022 Nature communications Discussion SARS_CoV_2 A348S 109 114 S;RBD 85;122 90;125 35301314 De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Prior to initiation of mAb therapy, two non-synonymous mutations, H655Y. 2022 Nature communications Discussion SARS_CoV_2 H655Y 66 71 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. Also, the mutation E484Q present in our patient is very similar to the 484A present in the Omicron VOC. 2022 Frontiers in microbiology Discussion SARS_CoV_2 E484Q 19 24 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. Mutation E484Q was first identified in variant Kappa (B.1.617.1) and in B.1.617.3 lineage. 2022 Frontiers in microbiology Discussion SARS_CoV_2 E484Q 9 14 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. Mutation T95I is also present in many Delta variants of concern (VOC) sub-lineages and in the Omicron VOC. 2022 Frontiers in microbiology Discussion SARS_CoV_2 T95I 9 13 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. The spike structure showed different changes: (i) a signal peptide mutation, S12F; (ii) two changes in the N-terminal domain, T95I and L141F; and (iii) two changes in the receptor-binding domain, E484Q and S494. 2022 Frontiers in microbiology Discussion SARS_CoV_2 E484Q;L141F;S12F;T95I 196;135;77;126 201;140;81;130 S;N 4;107 9;108 35308337 Emergence of Progressive Mutations in SARS-CoV-2 From a Hematologic Patient With Prolonged Viral Replication. We also identified the T820I and K977Q mutations representing a change in the enzyme substrate preference diminishing the host's ability to recognize the virus. 2022 Frontiers in microbiology Discussion SARS_CoV_2 K977Q;T820I 33;23 38;28 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? also observed the reduced efficacy of the NTD anti-SARS-CoV-2 antibody against the D138Y mutant spike protein. 2022 Frontiers in microbiology Discussion SARS_CoV_2 D138Y 83 88 S 96 101 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? Herein, the mutations D138Y in the spike protein and D144H in the nucleocapsid protein were observed to significantly change the protein folding dynamics, thereby influencing secondary structure formation (Figure 3). 2022 Frontiers in microbiology Discussion SARS_CoV_2 D138Y;D144H 22;53 27;58 N;S 66;35 78;40 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? Moreover, the mutation R203K/G204R was found to display a different protein structure morphology from the control and an enhanced intraviral interaction of R203K/G204R in the N and E proteins in molecular docking and protein structure prediction analysis. 2022 Frontiers in microbiology Discussion SARS_CoV_2 R203K;R203K;G204R;G204R 23;156;29;162 28;161;34;167 E;N 181;175 182;176 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? The mutation D138Y and four other mutations in the S protein have been reported to change the surface potential of the N-terminal domain (NTD) in protein modeling studies. 2022 Frontiers in microbiology Discussion SARS_CoV_2 D138Y 13 18 N;S 119;51 120;52 35308382 Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? We identified a few such low-frequency mutations previously reported with VBT infections (D138Y and H655Y). 2022 Frontiers in microbiology Discussion SARS_CoV_2 H655Y;D138Y 100;90 105;95 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. Only the B.1-C15324T variant dominated throughout the relevant observation period. 2022 Virus evolution Discussion SARS_CoV_2 C15324T 13 20 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. Our ~73 per cent estimate of unreported cases overall (not limited to B.1-C15324T. 2022 Virus evolution Discussion SARS_CoV_2 C15324T 74 81 35310621 Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. Realistically, cases of the B.1-C15324T variant could have been re-introduced from commuters entering Basel. 2022 Virus evolution Discussion SARS_CoV_2 C15324T 32 39 35311662 Reduced DMPC and PMPC in lung surfactant promote SARS-CoV-2 infection in obesity. Importantly, DMPC and PMPC inhibit both wild-type and D614G mutant pseudotyped SARS-CoV-2 infection, suggesting the reduced surfactant DMPC and PMPC may contribute to a higher viral load and potentially severe COVID-19 in obesity. 2022 Metabolism Discussion SARS_CoV_2 D614G 54 59 COVID-19;COVID-19 210;79 218;99 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). In this study, the L452R-RT-LAMP-BART method using a PNA probe correctly identified the L452R spike mutation within 30 min, with an LoD of ~100 copies per reaction. 2022 PloS one Discussion SARS_CoV_2 L452R;L452R 19;88 24;93 S 94 99 35312732 Detection of SARS-CoV-2 and the L452R spike mutation using reverse transcription loop-mediated isothermal amplification plus bioluminescent assay in real-time (RT-LAMP-BART). The B.1.617 variant has a typical point mutation in the RBD protein (L452R) that increases infectivity and resistance to current vaccines. 2022 PloS one Discussion SARS_CoV_2 L452R 69 74 RBD 56 59 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. But, the effects of K417N can be unmasked when present in a spike background that already contains mutations that disrupt binding of some class 2 antibodies, such as E484K or L452R. 2022 bioRxiv Discussion SARS_CoV_2 E484K;K417N;L452R 166;20;175 171;25;180 S 60 65 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. K417N alone has little effect on neutralization in the D614G spike, but reduces neutralization by ~2-3-fold in the Delta background. 2022 bioRxiv Discussion SARS_CoV_2 D614G;K417N 55;0 60;5 S 61 66 35313588 The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes. We also examined how the K417N and E484K mutations (in the class 1 and 2 epitopes, respectively) impact neutralization in the Delta spike background. 2022 bioRxiv Discussion SARS_CoV_2 E484K;K417N 35;25 40;30 S 132 137 35321335 Omicron Variant of SARS-CoV-2 Virus: In Silico Evaluation of the Possible Impact on People Affected by Diabetes Mellitus. In the Omicron variant, Lys417 mutates into an asparagine, preventing the possible non-enzymatic glycation of this residue. 2022 Frontiers in endocrinology Discussion SARS_CoV_2 K417N 24 57 35321335 Omicron Variant of SARS-CoV-2 Virus: In Silico Evaluation of the Possible Impact on People Affected by Diabetes Mellitus. This variation, together with several mutations on Spike-RBD that were linked to an increased affinity for ACE2 (such as S477N, Q498R, and N501Y), is predicted to contribute to an increase in the interactivity between Omicron-Spike-RBD and ACE2 in a hyperglycemic environment. 2022 Frontiers in endocrinology Discussion SARS_CoV_2 N501Y;Q498R;S477N 139;128;121 144;133;126 S;S;RBD;RBD 51;226;57;232 56;231;60;235 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. ACE2 binding to S D614G had an additive effect on the RBD position, pushing the equilibrium further toward the up conformation than either ACE2 binding or the D614G mutation did independently. 2022 eLife Discussion SARS_CoV_2 D614G;D614G 18;159 23;164 RBD;S 54;16 57;17 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Analysis of the dynamics of the unbound D614G variant showed an overall reduction in dynamics as compared to D614, consistent with the increased thermostability of the S trimer with the D614G mutation. 2022 eLife Discussion SARS_CoV_2 D614G;D614G 40;186 45;191 S 168 169 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Here, we have developed and applied an smFRET imaging approach to monitor conformational dynamics of SARS-CoV-2 S from the ancestral Wuhan-1 strain with D614 and the D614G variant (B.1 lineage) during engagement with the ACE2 receptor and mAbs. 2022 eLife Discussion SARS_CoV_2 D614G 166 171 S 112 113 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Like ACE2 binding to the D614 spike, the predominant effect of the D614G mutation was the reduction of the rate of transition to the down conformation. 2022 eLife Discussion SARS_CoV_2 D614G 67 72 S 30 35 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Our data demonstrate that the D614G mutation stabilized the RBD-up conformation, consistent with previous reports, which likely relates to how the mutation enhances infectivity. 2022 eLife Discussion SARS_CoV_2 D614G 30 35 RBD 60 63 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Overall, RBD- and NTD-targeting mAbs had minimal effect on the conformation of the D614G spike. 2022 eLife Discussion SARS_CoV_2 D614G 83 88 S;RBD 89;9 94;12 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Previous studies have shown that D614G does not increase the rate of ACE2 binding to S, as might be expected for a conformational capture-binding mechanism. 2022 eLife Discussion SARS_CoV_2 D614G 33 38 S 85 86 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Residue D614 is distal to the RBD and forms a salt bridge with K854 in the fusion-peptide proximal region, which is lost with the D614G mutation. 2022 eLife Discussion SARS_CoV_2 D614G 130 135 RBD 30 33 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. The similar impacts of D614G and ACE2 binding on the S energetic landscape imply that the mutation provides a fitness advantage by mimicking the effects of receptor binding. 2022 eLife Discussion SARS_CoV_2 D614G 23 28 S 53 54 35323111 Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike. Thus, the D614G mutation permits further stabilization of an intermediate conformation captured by ACE2 binding. 2022 eLife Discussion SARS_CoV_2 D614G 10 15 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. However, the prevalence of the N156K mutation was as low as 0.15% among the global isolates in registered databases in 2009 to 2012 and was 8.2% among Vietnamese isolates in 2010 to 2013. 2022 Tropical medicine and infectious disease Discussion SARS_CoV_2 N156K 31 36 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. Notably, the more recent clade 6B.1A5A + 156K with K209M was also observed, and its time of emergence was inferred to be September 2019 (August to November 2019). 2022 Tropical medicine and infectious disease Discussion SARS_CoV_2 K209M 51 56 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. showed that the N156K mutation altered the binding efficiency of HA-specific antibodies. 2022 Tropical medicine and infectious disease Discussion SARS_CoV_2 N156K 16 21 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. showed that the N156K mutation had reduced the effectiveness of the influenza vaccine. 2022 Tropical medicine and infectious disease Discussion SARS_CoV_2 N156K 16 21 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. The amino acid substitution of N156K in subclade 6B.1A5A + 156K is reported to have a significant impact on vaccine effectiveness. 2022 Tropical medicine and infectious disease Discussion SARS_CoV_2 N156K 31 36 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. Therefore, the present study showed that all of the recent subclades of H1N1pdm, 6B.1A5A + 187V/A, 6B.1A5A + 156K, and 6B.1A5A + 156K with K209M, all of which first emerged between April and September 2019 in countries other than Bangladesh, were also present in Bangladesh in January 2020. 2022 Tropical medicine and infectious disease Discussion SARS_CoV_2 K209M 139 144 35324585 Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. Vaccines using these strains showed better recognition of 6B.1A5A + 156K but poor recognition of other strains, such as 6B.1A5A + 187V/A, which lacks the N156K mutation. 2022 Tropical medicine and infectious disease Discussion SARS_CoV_2 N156K 154 159 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. A single mutation, NSP13_P77L, which is characteristic only in Delta variants, was detected in all genomic sequences in the current study, and may have a destabilizing effect. 2022 Genes Discussion SARS_CoV_2 P77L 25 29 Nsp13 19 24 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Among the structural proteins, the S protein harbored two mutations in the RBD region (L452R and T478K), four in the NTD (T19R, G142D, Delta156-157 and R158del), and one at the furin-cleavage site (P681R) and S2 region (D950N), detected in 12 virus genome sequences (Table 3). 2022 Genes Discussion SARS_CoV_2 G142D;T478K;D950N;L452R;P681R;T19R 128;97;220;87;198;122 133;102;225;92;203;126 RBD;S 75;35 78;36 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. In a more recent study, E156G, Arg158, and Phe-157/del were found, causing rigidity and reduced flexibility, thus providing fitness advantage and immune escape. 2022 Genes Discussion SARS_CoV_2 E156G 24 29 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Mechanistically, the P681R mutation of Delta improved the full-length cleavage of S1 and S2, facilitated the virus cell surface entry and increased infection 16. 2022 Genes Discussion SARS_CoV_2 P681R 21 26 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Mutation G671S in NSP12 detected in the current study has been observed as emerging, present in all 18 isolates, increasing the stability of the protein. 2022 Genes Discussion SARS_CoV_2 G671S 9 14 Nsp12 18 23 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Mutation NSP6_T77A in the current study (Table 2) seems emerging in the current wave. 2022 Genes Discussion SARS_CoV_2 T77A 14 18 Nsp6 9 13 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Mutations spike_K1086Q, spike_E554K, and spike_C1250W were unique to GISAID. 2022 Genes Discussion SARS_CoV_2 C1250W;E554K;K1086Q 47;30;16 53;35;22 S;S;S 10;24;41 15;29;46 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Mutations T478K, T19R, L452R, F157del, E156G, P681R, D614G, R158del, and G142D were the most common, present in all genomics isolates. 2022 Genes Discussion SARS_CoV_2 D614G;E156G;F157del;G142D;L452R;P681R;R158del;T19R;T478K 53;39;30;73;23;46;60;17;10 58;44;37;78;28;51;67;21;15 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. NSP14_A394V is the most common mutation in NSP14 (Table 2), and has a role in one of the positive section sites of virus. 2022 Genes Discussion SARS_CoV_2 A394V 6 11 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Previously, mutation P323L in RdRp was the most common in Pakistani isolates. 2022 Genes Discussion SARS_CoV_2 P323L 21 26 RdRP 30 34 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Recently, a synonymous mutation (F106F) in NSP3 along with other signature mutations exhibited a virus fitness effect. 2022 Genes Discussion SARS_CoV_2 F106F 33 38 Nsp3 43 47 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Similar to this previous study, mutants T19R, E156G, L452R, T478K, and P681R in S protein (Figure 3 and Figure 4) exhibited a stabilizing effect on protein structure, facilitating the binding affinity for more stable interactions with human ACE2. 2022 Genes Discussion SARS_CoV_2 E156G;L452R;P681R;T19R;T478K 46;53;71;40;60 51;58;76;44;65 S 80 81 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The Delta S P681R mutation present at the furin-cleavage site exhibited stabilizing effects (Figure 4), separating the S1 and S2 regions of S protein. 2022 Genes Discussion SARS_CoV_2 P681R 12 17 S;S 10;140 11;141 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The Delta S protein P681R mutation has an important role in the variant replacement of the alpha-to-Delta. 2022 Genes Discussion SARS_CoV_2 P681R 20 25 S 10 11 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The furin-cleavage site plays an important role in viral pathogenesis and mutation analysis revealed that L452R and P681R increase the ACE2 binding and transmissibility. 2022 Genes Discussion SARS_CoV_2 L452R;P681R 106;116 111;121 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The L452R is an antibody-escaping mutation and the virus with this mutant is resistant to convalescent plasma and monoclonal antibody therapy. 2022 Genes Discussion SARS_CoV_2 L452R 4 9 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The NSP6_L37F mutation, which was very common in the earlier infections, were associated with asymptomatic cases. 2022 Genes Discussion SARS_CoV_2 L37F 9 13 Nsp6 4 8 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The T478K is unique to the SARS-CoV2 Delta variant, present in the epitope region of potent neutralizing monoclonal antibodies. 2022 Genes Discussion SARS_CoV_2 T478K 4 9 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The T478K mutation at the RBD region of S protein, fell near the E484K that facilitates antibody escape. 2022 Genes Discussion SARS_CoV_2 E484K;T478K 65;4 70;9 RBD;S 26;40 29;41 35328105 Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. The T478K mutation present in RBD of S protein is involved in interaction with human ACE2. 2022 Genes Discussion SARS_CoV_2 T478K 4 9 RBD;S 30;37 33;38 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. In addition, the K417N mutation appears to increase the neutralisation efficiency compared to the original B.1.617.2. 2022 Frontiers in immunology Discussion SARS_CoV_2 K417N 17 22 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. More recently the K417N mutation was detected in B.1.617.2 in several sequences from Nepal. 2022 Frontiers in immunology Discussion SARS_CoV_2 K417N 18 23 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. One of the first variants, B.1.1.298 also known as the mink variant, contained a unique mutation, Y453F, in the RBD, which was found to enhance ACE2 binding affinity. 2022 Frontiers in immunology Discussion SARS_CoV_2 Y453F 98 103 RBD 112 115 35330908 Neutralisation Hierarchy of SARS-CoV-2 Variants of Concern Using Standardised, Quantitative Neutralisation Assays Reveals a Correlation With Disease Severity; Towards Deciphering Protective Antibody Thresholds. Our results show that convalescent sera from first wave infected individuals were able to neutralise, albeit with reduce titres, B.1.617.1, B.1.617.2 and B.1.617.2 K417N. 2022 Frontiers in immunology Discussion SARS_CoV_2 K417N 164 169 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. A total of five mutations (P681H, P681L, A684S, S686G, V687L) were found to be associated with reduced S protein cleavage, with mutation S686G showing the lowest level of S protein cleavage. 2022 PloS one Discussion SARS_CoV_2 A684S;P681L;S686G;S686G;V687L;P681H 41;34;48;137;55;27 46;39;53;142;60;32 S;S 103;171 104;172 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. Except for mutation S686G, which moderately increased S protein binding to soluble ACE2, no mutation was associated with changes in receptor binding, in keeping with the mutations being located outside the receptor-binding domain (RBD). 2022 PloS one Discussion SARS_CoV_2 S686G 20 25 RBD;S 231;54 234;55 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. In contrast, Lubinski and colleagues and the present study demonstrate that P681H, which is found in the S proteins of the B.1.1.7 and B.1.1.529, does not increase S protein cleavage as well as S protein-driven cell-cell and virus-cell fusion. 2022 PloS one Discussion SARS_CoV_2 P681H 76 81 S;S;S 105;164;194 106;165;195 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. In keeping with the previously suggested scenario that availability of endogenous CTSL may limit CTSL-dependent entry into Calu-3 cells, directed expression of CTSL increased Calu-3 cell entry of mutant S686G and mutant DeltaS1/S2. 2022 PloS one Discussion SARS_CoV_2 S686G 203 208 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. It is interesting to note that variant of concern B.1.617.2 (Delta variant), harbours exchange P681R, which was recently shown to increase S protein cleavage and cell-cell fusion, demonstrating that naturally occurring mutations at the S1/S2 site can augment S protein cleavability and activity. 2022 PloS one Discussion SARS_CoV_2 P681R 95 100 S;S 139;259 140;260 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. The observation that mutation S686G reduced S protein cleavage at S1/S2 with the highest efficiency of all mutations studied indicates that decreased Calu-3 and Caco-2 cell entry of mutant S686G may have been due to reduced TMPRSS2 usage, which is in line with the observations by Lamers and colleagues. 2022 PloS one Discussion SARS_CoV_2 S686G;S686G 30;189 35;194 S 44 45 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. This observation is different to the results reported by Lamers and colleagues, who found that cell-cell fusion driven by mutant S686G is less efficient as compared to WT S. 2022 PloS one Discussion SARS_CoV_2 S686G 129 134 S 171 172 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. Thus, high ACE2 expression levels on our 293T cells may compensate for the reduced cell-cell fusion ability by SARS-CoV-2 S bearing mutation S686G. 2022 PloS one Discussion SARS_CoV_2 S686G 141 146 S 122 123 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. Why mutant S686G showed enhanced interaction with ACE2 is at present unclear but might be due to its RBD adopting a conformation that may favour ACE2 binding, which would be a similar effect as reported for mutation D614G that is also located outside of the RBD. 2022 PloS one Discussion SARS_CoV_2 D614G;S686G 216;11 221;16 RBD;RBD 101;258 104;261 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. With respect to SARS-CoV-2 S protein-driven cell entry, exchange S686G was associated with reduced entry efficiency for the cell lines Calu-3 and Caco-2 while entry into Vero and A549-ACE2 cells was significantly augmented compared to WT SARS-CoV-2 S. 2022 PloS one Discussion SARS_CoV_2 S686G 65 70 S;S 27;249 28;250 35333910 Functional analysis of polymorphisms at the S1/S2 site of SARS-CoV-2 spike protein. With respect to the ability of the SARS-CoV-2 S protein to drive fusion of S protein expressing cells with neighbouring cells, we observed that all mutations, including S686G, were compatible with robust spike protein-induced cell-cell fusion. 2022 PloS one Discussion SARS_CoV_2 S686G 169 174 S;S;S 204;46;75 209;47;76 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). Among the isolates, the N439K substitution was found in three samples. 2022 Microorganisms Discussion SARS_CoV_2 N439K 24 29 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). As for N439K, S477N occurs in the RBD region and seems to confer enhanced binding ability to the ACE2 receptor, but it does not seem to be associated with the loss of neutralizing activities of convalescent serum antibodies. 2022 Microorganisms Discussion SARS_CoV_2 N439K;S477N 7;14 12;19 RBD 34 37 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). Consequently, N439K might evade the immune system either in recovered COVID-19 patients or in vaccinated subjects. 2022 Microorganisms Discussion SARS_CoV_2 N439K 14 19 COVID-19 70 78 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). In contrast, we did not find any differences in the viral load between the N439K and D614G strains. 2022 Microorganisms Discussion SARS_CoV_2 D614G;N439K 85;75 90;80 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). In our cohort, and compared to the D614G strain, the S477N viral load was slightly lower, while no difference in the clinical presentation was observed. 2022 Microorganisms Discussion SARS_CoV_2 D614G;S477N 35;53 40;58 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). In our study, the S477N substitution was detected in one sample, with a frequency of 3.1%, resembling its frequency rate in Europe, which ranges from 4 to 7%. 2022 Microorganisms Discussion SARS_CoV_2 S477N 18 23 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). No significant differences were observed among the clinical outcomes of the three children positive for N439K and the others, confirming the findings reported by Thomson and colleagues, who found no association between this substitution and increases in COVID-19 symptomatology and severity. 2022 Microorganisms Discussion SARS_CoV_2 N439K 104 109 COVID-19 254 262 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). Of note, NGS analysis also revealed the presence of a stop codon in the ORF7a coding region (G58) due to the G/T mutation at nt 27505. 2022 Microorganisms Discussion SARS_CoV_2 G27505T 109 133 ORF7a 72 77 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). The B.1 strain shows the D614G substitution, able to confer moderate advantages in viral infectiveness and transmissibility, compared to the Wuhan-Hu-1 strain. 2022 Microorganisms Discussion SARS_CoV_2 D614G 25 30 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). The N439K substitution occurs in the RBD, the highly variable region of the SARS-CoV-2 spike protein, which interacts with ACE2 receptors for viral entry and is the main target of neutralizing antibodies. 2022 Microorganisms Discussion SARS_CoV_2 N439K 4 9 S;RBD 87;37 92;40 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). The variant carrying the S477N substitution spread in some European countries, with a higher prevalence in France during the summer of 2020 and a frequency of detection ranging from 4-7%. 2022 Microorganisms Discussion SARS_CoV_2 S477N 25 30 35336187 Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy). To the best of our knowledge, this is the first study to report the detection of the N439K substitution in a pediatric population. 2022 Microorganisms Discussion SARS_CoV_2 N439K 85 90 35336868 Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens. reported that even a single mutation such as R346K might be critical for neutralization escape. 2022 Viruses Discussion SARS_CoV_2 R346K 45 50 35336868 Isolation and Genomic Characterization of SARS-CoV-2 Omicron Variant Obtained from Human Clinical Specimens. Spike region of the virus isolated in hamsters revealed L212C amino acid change along with the C25000T nucleotide change compared to clinical specimens. 2022 Viruses Discussion SARS_CoV_2 C25000T;L212C 95;56 102;61 S 0 5 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. Importantly, the P681R mutation reduces the local rigidity, as evidenced by the NN AABP values (Table 1). 2022 Viruses Discussion SARS_CoV_2 P681R 17 22 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. In addition to these intra-protomer interactions, it has been structurally demonstrated that the D614G mutation destroys an inter-protomer hydrogen bond between D614 (chain A) and T859 (chain B). 2022 Viruses Discussion SARS_CoV_2 D614G 97 102 35336872 Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions. The data in Table 1 reveal that D614G and P681R mutations have lower AABP values than the unmutated WT case. 2022 Viruses Discussion SARS_CoV_2 D614G;P681R 32;42 37;47 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. Among samples that were not sequenced or sequences not deposited in GISAID, there is a high risk that the occurrence of this particular lineage is underreported, since the Pangolin lineage assigner ignores the presence/absence of the S:E484Q mutation in the B.1.617.2 lineage. 2022 Viruses Discussion SARS_CoV_2 E484Q 236 241 S 234 235 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. Hence, we propose that sequences of the B.1.617.2 lineage should be actively surveyed for the presence of the S:E484Q mutation. 2022 Viruses Discussion SARS_CoV_2 E484Q 112 117 S 110 111 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. In contrast to this, and as a result of active surveillance regarding this specific combination, some B.1.617.2 + S:E484Q isolates were detected in patients through December 2021 in Sweden. 2022 Viruses Discussion SARS_CoV_2 E484Q 116 121 S 114 115 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. The acquisition of the S:E484Q mutation in the B.1.617.2 lineage was quite recent (first detected 30 January 2021) but is now rapidly spreading, likely due to selective advantage. 2022 Viruses Discussion SARS_CoV_2 E484Q 25 30 S 23 24 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. The emergence of the S:E484Q mutation in B1.617.2 is of particular concern, since it might provide a rapidly spreading VOC with an enhanced ability to evade antibody neutralization even in vaccinated or previously infected individuals (6). 2022 Viruses Discussion SARS_CoV_2 E484Q 23 28 S 21 22 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. This observation is further supported by a 27% increase in the total number of B.1.617.2 + S:E484Q sequences deposited in GISAID within one week (16 to 23 August 2021) (8). 2022 Viruses Discussion SARS_CoV_2 E484Q 93 98 S 91 92 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. We presented a flight-associated transmission event of a newly emerged combination of SARS-CoV-2 lineage B1.617.2 with an S:E484Q point mutation by merging clinical contact tracing with molecular epidemiology. 2022 Viruses Discussion SARS_CoV_2 E484Q 124 129 S 122 123 35336908 In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation. Whether the gain of S:E484Q affects transmissibility remains to be studied. 2022 Viruses Discussion SARS_CoV_2 E484Q 22 27 S 20 21 35336922 Multiorgan and Vascular Tropism of SARS-CoV-2. Henceforth, a potential impact on the protein functions could be suggested concerning the implication of the E654A mutation regarding its interaction with endothelial cell receptors. 2022 Viruses Discussion SARS_CoV_2 E654A 109 114 35336922 Multiorgan and Vascular Tropism of SARS-CoV-2. Moreover, the H655 residue is closed to the E654A mutation, and both are near the furin cleavage site of the spike protein (S1/S2 site) involved in SARS-CoV-2 cell entry. 2022 Viruses Discussion SARS_CoV_2 E654A 44 49 S 109 114 35336922 Multiorgan and Vascular Tropism of SARS-CoV-2. The difference in D614G physicochemical properties has a significant impact on the three-dimensional structure of the spike protein, giving the RBD (Receptor Binding Domain) a more open conformation than the wild type strain (Wuhan-Hu-1) and, therefore, an improvement in virus interaction with the host's cell receptors. 2022 Viruses Discussion SARS_CoV_2 D614G 18 23 RBD;S;RBD 149;118;144 172;123;147 35336922 Multiorgan and Vascular Tropism of SARS-CoV-2. The E654A mutation suggests a significant change in the physicochemical properties of the amino acid sequence, since a glutamic acid (E) is polar and negatively charged with a higher molecular weight (MW = 128 g/mol) compared to an alanine (A), which is nonpolar and uncharged (71 g/mol). 2022 Viruses Discussion SARS_CoV_2 E654A 4 9 35336922 Multiorgan and Vascular Tropism of SARS-CoV-2. The major impact of such changes has already been described for the D614G mutation in which a polar, negatively charged aspartic acid (D) with a higher MW (114 g/mol) is substituted with a nonpolar uncharged glycine (G) with a lower MW (57 g/mol). 2022 Viruses Discussion SARS_CoV_2 D614G 68 73 35336922 Multiorgan and Vascular Tropism of SARS-CoV-2. These mutations have not yet been characterized in the literature; however, position 655 is also mutated in the 20J/501Y.V variant (H655Y) and has been correlated to antibody neutralization escape and to the modulation of the interaction between the spike glycoprotein and ACE2 receptors. 2022 Viruses Discussion SARS_CoV_2 H655Y 132 137 S 250 268 35336922 Multiorgan and Vascular Tropism of SARS-CoV-2. When focusing on the spike protein, signature mutations associated with vascular tropism may be suggested in vena cava (i.e., V341A, E654A and H655R) (Figure 1, Table 1). 2022 Viruses Discussion SARS_CoV_2 E654A;H655R;V341A 133;143;126 138;148;131 S 21 26 35337002 Protective Immunity of the Primary SARS-CoV-2 Infection Reduces Disease Severity Post Re-Infection with Delta Variants in Syrian Hamsters. Comparable cell entry efficiency was reported by a recent study for the Delta sub-lineages with K417N mutation in comparison with the wildtype SARS-CoV-2 with the D614G mutation. 2022 Viruses Discussion SARS_CoV_2 D614G;K417N 163;96 168;101 35337002 Protective Immunity of the Primary SARS-CoV-2 Infection Reduces Disease Severity Post Re-Infection with Delta Variants in Syrian Hamsters. Here, we observed a comparable neutralization efficiency in Delta AY.1-infected hamster sera against the Delta, B.1 and Beta variants, suggesting that the presence of the K417N mutation may not confer an advantage in terms of immune evasion, at least against these variants. 2022 Viruses Discussion SARS_CoV_2 K417N 171 176 35337002 Protective Immunity of the Primary SARS-CoV-2 Infection Reduces Disease Severity Post Re-Infection with Delta Variants in Syrian Hamsters. Similar results of comparable neutralization efficiency of the Delta variant with the K417N mutation and the Delta variant has been reported in pseudo-virus neutralization studies. 2022 Viruses Discussion SARS_CoV_2 K417N 86 91 35337002 Protective Immunity of the Primary SARS-CoV-2 Infection Reduces Disease Severity Post Re-Infection with Delta Variants in Syrian Hamsters. The B.1.351 variant is known worldwide for its immune escape property due to the mutations K417N, E484K and N501Y in the RBD of the spike region. 2022 Viruses Discussion SARS_CoV_2 E484K;K417N;N501Y 98;91;108 103;96;113 S;RBD 132;121 137;124 35337002 Protective Immunity of the Primary SARS-CoV-2 Infection Reduces Disease Severity Post Re-Infection with Delta Variants in Syrian Hamsters. The K417N mutation in the Delta AY.1 variant was found to be critical for neutralization resistance against some potent NAbs against SARS-CoV-2. 2022 Viruses Discussion SARS_CoV_2 K417N 4 9 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. As described above, the A67V + del-HV69-70 and N679K + P681H components of the multiplex assay feature analytic sensitivities similar to currently available diagnostic SARS-CoV-2 tests (e.g., between 30-50 dcp/mL for the cobas SARS-CoV-2 test and can detect relevant sequence variances even in samples with very low viral-RNA loads. 2022 Viruses Discussion SARS_CoV_2 A67V;N679K;P681H 24;47;55 28;52;60 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. In this study, we presented a multiplexed screening assay with three independent targets for the Omicron variant (first: A67V + del-HV69-70, second: E484A, and third: N679K + P681H) and one for the delta variant P681R, thus allowing easy discrimination between these two prevalent lineages. 2022 Viruses Discussion SARS_CoV_2 A67V;E484A;N679K;P681H;P681R 121;149;167;175;212 125;154;172;180;217 35337015 Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants. Of note, the BA.2 subline (sometimes dubbed the "stealth variant") lacks the A67V and del-HV69-70 mutations, thus leading to a negative result for the NTD target, while retaining positivity for E484A and N679K + P681H; a pattern that can be utilized to distinguish contemporary BA.2 from other Omicron sublines. 2022 Viruses Discussion SARS_CoV_2 A67V;E484A;N679K;P681H 77;194;204;212 81;199;209;217 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. 5) indicates that inhibition of heparin binding by S-protein RBD containing the N501Y mutation can be accomplished just by medium-sized oligomeric lengths in order to achieve effective molecular interactions and consequent viral inhibition. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 N501Y 80 85 RBD;S 61;51 64;52 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. 6) has shown that heparin and the BoSG [4S-3S] disaccharide can interact with the S-protein N501Y RBD with similar binding poses between them. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 N501Y 92 97 RBD;S 98;82 101;83 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. Docking of the BoSG disaccharides to the N501Y mutant S-protein helped predict the overall poses of the BoSG derivatives in the binding site close to the 501Y residue and indicated the various possible pairwise mutant-BoSG polar interactions. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 N501Y 41 46 S 54 55 35337800 Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties. Here, we also noticed great selectivity of the BoSG and low MW derivatives towards the SARS-CoV-2 variants that express the N501Y mutation in their S-protein RBD. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 N501Y 124 129 RBD;S 158;148 161;149 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Additionally, the N501Y convergent mutation in these three strains studied has shown a crucial interfacial remolding of the spike-ACE2 complex. 2022 PeerJ Discussion SARS_CoV_2 N501Y 18 23 S 124 129 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Additionally, the results show a frequent loss of attractive connections in these residues, mainly caused by the E484Q mutation. 2022 PeerJ Discussion SARS_CoV_2 E484Q 113 118 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Again, our MD analysis points the local packing alterations with a substitution that similarly removes the charge and shortens the side chain at the position 417 (i.e., the K417T substitution from wt to P1) as an important factor to shift the RBM dynamics and, eventually, stabilize a less antibody complementary conformation. 2022 PeerJ Discussion SARS_CoV_2 K417T 173 178 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Alongside, the L452R alteration creates a highly repulsive interface involving the K106 residue in these models, further producing hydrogen bonds with the Y32 antibody amino acid. 2022 PeerJ Discussion SARS_CoV_2 L452R 15 20 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Also, the beta2'/eta1' loop (residues 497 to 506, in whose center the N501Y substitution occurs), as well the loop alpha1'/beta1' (residues 438 to 450) are local fluctuation hotspots at the RBM and at the RBD as a whole. 2022 PeerJ Discussion SARS_CoV_2 N501Y 70 75 RBD 205 208 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Beta and Gamma have several altered interactions between the spike's 484 residue and ACE's 31 residue, mainly due to the E484K mutation, which accounts for changing from an attractive to a repulsive interaction in this site. 2022 PeerJ Discussion SARS_CoV_2 E484K 121 126 S 61 66 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Concerning antibody modeled interfaces, within the 7CHH model, the BD-368-2 antibody (7CHH) has shown a major loss of attractive interactions in essential residues such as R100 and R102, probably due to the E484Q mutation. 2022 PeerJ Discussion SARS_CoV_2 E484Q 207 212 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Figure 3B depicts the frequent contacts that emerged in the P1 lineage, denoting the E484K mutation in hydrogen bonds with the K31 and E35 human ACE2 residues, alongside the N501Y alteration in hydrophobic interactions with the K353 and Y41 residues. 2022 PeerJ Discussion SARS_CoV_2 E484K;N501Y 85;174 90;179 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Finally, the 417 position (where K417T substitution occurs) is placed at the center of the helix 3,before the RBM and at a less mobile position in. 2022 PeerJ Discussion SARS_CoV_2 K417T 33 38 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Furthermore, it also has gained highly frequent repulsive interactions in these residues caused by the L452R modification. 2022 PeerJ Discussion SARS_CoV_2 L452R 103 108 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. In addition, the MD and PBSA results suggest that the three substitutions in Gamma lineage (K417T, E484K, N501Y) can still intensify this higher complementarity of the RBM to the receptor and lower to the antibodies by shifting the RBD conformational equilibrium. 2022 PeerJ Discussion SARS_CoV_2 E484K;N501Y;K417T 99;106;92 104;111;97 RBD 232 235 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Moreover, the results show a correlation involving a more frequent interaction on the spike-antibody complexes presenting the K417N mutation, which has taken the view of scientists for a more stabilized interface, such as shown by and. 2022 PeerJ Discussion SARS_CoV_2 K417N 126 131 S 86 91 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Our research presents data explaining the convalescent serum neutralization escapability amongst lineages presenting the E484K mutation, alongside the N417K/T alteration, on the viral RBD. 2022 PeerJ Discussion SARS_CoV_2 E484K;N417K;N417T 121;151;151 126;158;158 RBD 184 187 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Subsequently, there have also been alterations such as attractive hydrogen bonds becoming hydrogen bonds in these residues because of E484Q and L452R. 2022 PeerJ Discussion SARS_CoV_2 E484Q;L452R 134;144 139;149 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. The pose of the K417N alteration frequently jeopardizes the monoclonal antibody serum activity for the SARS-CoV-2 infections, being present on the Beta and Gamma strains alongside the E484K mutation. 2022 PeerJ Discussion SARS_CoV_2 E484K;K417N 184;16 189;21 COVID-19 103 124 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. The results provided by the identification and matching of contacts and the molecular docking, amongst the complexes, rebound a persistent breach on the interactivity between the viral RBD and the significant amount of sampled PDB antibodies, chiefly guided by the E484K alteration. 2022 PeerJ Discussion SARS_CoV_2 E484K 265 270 RBD 185 188 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. The spike-ACE2 configuration presents constant affinity-based contacts due to the N501Y mutation on the VOCs examined, clarifying results such as shown by, elucidating this vehement binding affinity present in this complex. 2022 PeerJ Discussion SARS_CoV_2 N501Y 82 87 S 4 9 35341044 E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. Utilizing this real-time tracking of protein interfaces, we have perceived key alterations that cause Delta's clinical characteristics regarding the L452R, P681R, and E484Q spike mutations. 2022 PeerJ Discussion SARS_CoV_2 E484Q;L452R;P681R 167;149;156 172;154;161 S 173 178 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. A distinctive feature of the Delta variant, the S_P681R mutation within the S protein has been correlated to higher fusogenicity, which in turn led to viruses that exhibit enhanced pathogenicity in vivo and greater resistance to neutralizing antibodies compared to the parental virus without this mutation . 2022 PeerJ Discussion SARS_CoV_2 P681R 50 55 S 76 77 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. Although not associated with worse disease severity, the S_D614G change has been implicated in enhanced transmission and higher viral loads . 2022 PeerJ Discussion SARS_CoV_2 D614G 59 64 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. Another substitution at the same position, S_P681H, has also been shown to enhance cleavage of S protein, but did not necessarily result in improved viral entry . 2022 PeerJ Discussion SARS_CoV_2 P681H 45 50 S 95 96 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. For Delta variants, we observed 12 key amino acid changes in spike protein that were mostly similar to other studies, including S_T19R, S_T95I, S_G142D, S_E156-, S_F157-, S_R158G, S_K417N, S_L452R, S_T478K, S_D614G, S_P681R, and S_D950N . 2022 PeerJ Discussion SARS_CoV_2 D614G;D950N;G142D;K417N;L452R;P681R;R158G;T19R;T478K;T95I 209;231;146;182;191;218;173;130;200;138 214;236;151;187;196;223;178;134;205;142 S 61 66 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. However, functional assays showed that the S_P681R substitution on its own is not enough to promote enhanced infectivity and transmissibility associated with variants bearing this mutation . 2022 PeerJ Discussion SARS_CoV_2 P681R 45 50 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. On the other hand, substitutions in the region encoding the spike protein in Indonesian lineages mainly consisted of three key mutations, namely S_D614G, S_N439K and S_P681R. 2022 PeerJ Discussion SARS_CoV_2 D614G;N439K;P681R 147;156;168 152;161;173 S 60 65 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. Similarly, increased infection due to enhanced cleavage of the S protein has also been associated with the presence of S_P681R mutation, leading to improved viral replication efficiency of Delta variant compared to the Alpha variant . 2022 PeerJ Discussion SARS_CoV_2 P681R 121 126 S 63 64 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. The D614G variant is considered to be G clade by GISAID and B.1 clade by the PANGOLIN . 2022 PeerJ Discussion SARS_CoV_2 D614G 4 9 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. The most prevalent amino acid change found in our study was the S_D614G, as 199 out of 202 (99%) genomes were found to carry it. 2022 PeerJ Discussion SARS_CoV_2 D614G 66 71 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. The presence of the S_N439K and S_ P681R substitutions in the Indonesian lineages are important to note, as these mutations have been shown to confer certain advantages for the variants. 2022 PeerJ Discussion SARS_CoV_2 P681R;N439K 35;22 40;27 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. The S_N439K mutation has been associated with a similar level of fitness and virulence to the wild-type virus, whilst potentially conferring a stronger binding affinity to human ACE2 receptor and allowing immune escape from antibody-mediated immunity . 2022 PeerJ Discussion SARS_CoV_2 N439K 6 11 35341058 The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia. Variants carrying the S_D614G mutation have been suggested to benefit from increased binding affinity to its target ACE2 . 2022 PeerJ Discussion SARS_CoV_2 D614G 24 29 35341060 An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. The appearance of the premature stop codon in the ORF8 gene encoding the NS8 (ORF8) protein (Q27stop) not only generates the truncated form of this protein due to the deletion of almost 80% of the ORF8 protein, but also eliminates the whole immunopeptidome associated with this part of protein. 2022 PeerJ Discussion SARS_CoV_2 Q27X 93 100 ORF8;ORF8;ORF8 50;78;197 54;82;201 35341060 An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. The Q27STOP mutation in the ORF8 protein has been discovered to cause 47 distinct truncated ORF8 variations. 2022 PeerJ Discussion SARS_CoV_2 Q27X 4 11 ORF8;ORF8 28;92 32;96 35341060 An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. Within North America, it was reported that one of the top mutations, 27964C>T-(S24L) in the ORF8 protein, has an unusually strong gender dependence. 2022 PeerJ Discussion SARS_CoV_2 C27964T;S24L 69;79 77;83 ORF8 92 96 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. Clinical studies have shown that COVID-19 patients infected with naturally occurring ORF8 deletion or ORF8-L84S variant virus had mild symptoms, suggesting ORF8 as a potential virulence factor that contributes to COVID-19 disease severity. 2022 mBio Discussion SARS_CoV_2 L84S 107 111 ORF8;ORF8;ORF8 85;102;156 89;106;160 COVID-19;COVID-19 33;213 41;229 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. In fact, the L84S variant was unable to induce hIL-17RA/C heterodimerization like the Y42H and E106P mutants. 2022 mBio Discussion SARS_CoV_2 E106P;L84S;Y42H 95;13;86 100;17;90 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. It is also intriguing that the Y42H and E106P mutants showed next to no hIL-17RA binding activity but maintained hIL-17RC binding activity, whereas the I71D and I76D mutants showed similar hIL-17RA binding activity but drastically decreased hIL-17RC binding activity compared to the WT. 2022 mBio Discussion SARS_CoV_2 E106P;I71D;I76D;Y42H 40;152;161;31 45;156;165;35 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. Unlike the ORF8 WT, the naturally occurring ORF8 L84S variant induced neither the heterodimerization of hIL-17RA/C nor the production of proinflammatory factors. 2022 mBio Discussion SARS_CoV_2 L84S 49 53 ORF8;ORF8 11;44 15;48 35343786 Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. While all three variants exhibited reduced binding activity to hIL-17RA, the L84S variant demonstrated the loss of hIL-17RA binding activity as well as the lack of proinflammatory cytokine production activity. 2022 mBio Discussion SARS_CoV_2 L84S 77 81 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. Both the D614G and the delta variants escape from the neutralising antibodies against the original strain, an effect that depends on neutralising antibody titres. 2022 The Lancet. Microbe Discussion SARS_CoV_2 D614G 9 14 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. However, higher neutralising antibody titres against the original strain contributed to the protection from infection of D614G and delta variants in vitro. 2022 The Lancet. Microbe Discussion SARS_CoV_2 D614G 121 126 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. However, the D614G variant enhances infectivity mainly through increasing the stability of the trimer, rather than through more exposed receptor-binding domains. 2022 The Lancet. Microbe Discussion SARS_CoV_2 D614G 13 18 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. Neutralising antibodies against the original strain had a lower ability to neutralise the beta variant than the D614G and delta variants. 2022 The Lancet. Microbe Discussion SARS_CoV_2 D614G 112 117 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. Neutralising antibody responses to the D614G, beta, and delta variants are much poorer than those to the original strain from Wuhan, China. 2022 The Lancet. Microbe Discussion SARS_CoV_2 D614G 39 44 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. Our data showed that neutralising antibodies from individuals who had recovered from natural infection against the original strain are less able to neutralise effectively the D614G, beta, and delta variants. 2022 The Lancet. Microbe Discussion SARS_CoV_2 D614G 175 180 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. The three mutations characterising the beta variant (K417N, E484K, and N501Y) are located at the receptor-binding domain, making the variant resistant to some potent neutralising antibodies. 2022 The Lancet. Microbe Discussion SARS_CoV_2 E484K;N501Y;K417N 60;71;53 65;76;58 35345417 SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study. Third, we evaluated neutralising antibody responses to the D614G, beta, and delta variants, and the cellular responses to the beta variant. 2022 The Lancet. Microbe Discussion SARS_CoV_2 D614G 59 64 35346184 AstraZeneca COVID-19 vaccine induces robust broadly cross-reactive antibody responses in Malawian adults previously infected with SARS-CoV-2. Consistent with these observations, we show that an adenovirus vaccine elevates levels of anti-Spike and anti-RBD antibodies that are cross-reactive against D614G, alpha, beta, gamma, and delta variants in individuals previously infected with SARS-CoV-2. 2022 BMC medicine Discussion SARS_CoV_2 D614G 157 162 S;RBD 95;110 100;113 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. 1B, for the detection of the mutation T22917G, HRM curves of the amplicon from the cDNA reference standard of the RBD Delta variant showed a significant difference from the others. 2022 Biochemical and biophysical research communications Discussion SARS_CoV_2 T22917G 38 45 RBD 114 117 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. Additionally, we attempted HRM analysis of viral RNA without nested PCR, which is the direct HRM analysis of amplicons from RT-PCR by using a primer pair for nested PCR (i.e., "Second G339D forward" and "Second G339D reverse" in Supplementary Table 1). 2022 Biochemical and biophysical research communications Discussion SARS_CoV_2 G339D;G339D 184;211 189;216 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. Despite the fact that there are T22882G and G22898A mutations in the amplicon of the cDNA reference standard of the Omicron variant RBD. 2022 Biochemical and biophysical research communications Discussion SARS_CoV_2 G22898A;T22882G 44;32 51;39 RBD 132 135 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. for the detection of mutation T22917G to confirm the efficacy of the post-nested PCR HRM analysis. 2022 Biochemical and biophysical research communications Discussion SARS_CoV_2 T22917G 30 37 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. Here, we report the detection of G339D and D796Y variations in the SARS-CoV-2 spike protein by HRM analysis of nested PCR amplicons. 2022 Biochemical and biophysical research communications Discussion SARS_CoV_2 D796Y;G339D 43;33 48;38 S 78 83 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. In conclusion, our results clearly indicate that the combination of the first PCR and the second nested PCR is useful for HRM analysis and that the primer pairs for the first PCR and the second nested PCR are valuable for the detection of G339D and D796Y variations. 2022 Biochemical and biophysical research communications Discussion SARS_CoV_2 D796Y;G339D 249;239 254;244 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. In HRM analyses designed to target G339D and D796Y variations (nt G22578A and G23948T), Tm values of amplicon from cDNA reference standard of Omicron variant RBD were 0.4-0.5 C higher than the others (Table 1). 2022 Biochemical and biophysical research communications Discussion SARS_CoV_2 D796Y;G22578A;G23948T;G339D 45;66;78;35 50;73;85;40 RBD 158 161 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. In the case of detection for the D614G variation (mutation A23403G) reported by Gazali et al., the difference in the Tm value was 0.23 C. 2022 Biochemical and biophysical research communications Discussion SARS_CoV_2 A23403G;D614G 59;33 66;38 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. Taken together, these results indicate that HRM analysis after the second amplification by nested PCR can be applied to detect specific G339D (G22578A mutation) and D796Y (G23948T mutation) variations in SARS-CoV-2 Omicron variant-positive specimens. 2022 Biochemical and biophysical research communications Discussion SARS_CoV_2 D796Y;G339D;G22578A;G23948T 165;136;143;172 170;141;150;179 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. The measured normalized and derivative HRM curves of the detection of the D796Y variation (mutation: G23948T) are shown in Supplementary. 2022 Biochemical and biophysical research communications Discussion SARS_CoV_2 D796Y;G23948T 74;101 79;108 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. Therefore, a pair of "Second L452R forward" and "Second L452R reverse" primers was not suitable to detect mutations in RBD nt 22852-22956. 2022 Biochemical and biophysical research communications Discussion SARS_CoV_2 L452R;L452R 29;56 34;61 RBD 119 122 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. This means that the positive effect of the T22882G mutation on the Tm of the amplicon counteracts the negative effect of the G22898A mutation on the Tm of the amplicon. 2022 Biochemical and biophysical research communications Discussion SARS_CoV_2 G22898A;T22882G 125;43 132;50 35349821 High-resolution melting analysis after nested PCR for the detection of SARS-CoV-2 spike protein G339D and D796Y variations. We employed the same primer pair ("Second L452R forward" and "Second L452R reverse" in Supplementary Table 1) as reported by Aoki et al. 2022 Biochemical and biophysical research communications Discussion SARS_CoV_2 L452R;L452R 42;69 47;74 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. A.VOI.V2 harbors R346K, T478R and E484K in the RBD. 2022 Future microbiology Discussion SARS_CoV_2 E484K;R346K;T478R 34;17;24 39;22;29 RBD 47 50 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. Another question is why Beta+R346K did not proliferate despite its immune-escaping capacity. 2022 Future microbiology Discussion SARS_CoV_2 R346K 29 34 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. Beta sub-variant with spike-R346K mutation had remarkable vaccine-escaping capacity prior to Omicron. 2022 Future microbiology Discussion SARS_CoV_2 R346K 28 33 S 22 27 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. Beta+R346K was identified in the Philippines in August 2021. 2022 Future microbiology Discussion SARS_CoV_2 R346K 5 10 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. Imdevimab exhibited efficacy against both Beta+R346K and Mu+K417N. 2022 Future microbiology Discussion SARS_CoV_2 K417N;R346K 60;47 65;52 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. In particular, mRNA-1273 might provide better protection against the Beta+R346K strain, since mRNA-1273 seems more effective than BNT162b2 in general. 2022 Future microbiology Discussion SARS_CoV_2 R346K 74 79 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. It was quite surprising to observe a prominent difference in neutralization titer between Beta+R346K and Mu+K417N, despite their being the same RBD haplotype. 2022 Future microbiology Discussion SARS_CoV_2 K417N;R346K 108;95 113;100 RBD 144 147 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. reported that neutralization efficacy was reduced for the Mu variant harboring R346K, E484K and N501Y in the RBD. 2022 Future microbiology Discussion SARS_CoV_2 E484K;N501Y;R346K 86;96;79 91;101;84 RBD 109 112 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. reported that neutralization titer against the Beta variant, which harbors K417N and E484K, declined substantially compared with the Alpha variant. 2022 Future microbiology Discussion SARS_CoV_2 E484K;K417N 85;75 90;80 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. These neutralization studies led the authors to hypothesize that strains with R346K, K417N and E484K might induce vaccine immune escape. 2022 Future microbiology Discussion SARS_CoV_2 E484K;K417N;R346K 95;85;78 100;90;83 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. Unexpectedly, the Mu sub-variant with spike-K417N, which has a receptor-binding domain mutation identical to that of Beta+R346K, did not exhibit more escaping capability than the regular Mu variant. 2022 Future microbiology Discussion SARS_CoV_2 R346K;K417N 122;44 127;49 S 38 43 35350884 Evasion of vaccine-induced humoral immunity by emerging sub-variants of SARS-CoV-2. Whereas Mu is simple, with one single-nucleotide variant (SNV), T95I, and a deletion, 144_145delinsTSN, Beta harbors three SNVs - D80A, D215G and R246I - and a deletion, 242_244del, as illustrated in Figure 1. 2022 Future microbiology Discussion SARS_CoV_2 D215G;D80A;R246I;T95I 136;130;146;64 141;134;151;68 35369437 Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China. concluded that the D614G mutation enhanced binding affinity for ACE2 while maintaining neutralization susceptibility, increasing cell entry no infiuence on the antigenicity of the S protein. 2022 Frontiers in microbiology Discussion SARS_CoV_2 D614G 19 24 S 180 181 35369437 Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China. D614G mutation can be found in most of our genome sequences, which is consistent with the global variation trend of SARS-CoV-2. 2022 Frontiers in microbiology Discussion SARS_CoV_2 D614G 0 5 35369437 Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China. D614G, in the S protein of SARS-CoV-2, which has emerged as a predominant clade in Europe and was spreading worldwide. 2022 Frontiers in microbiology Discussion SARS_CoV_2 D614G 0 5 S 14 15 35369437 Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China. demonstrated that D614G has enhanced binding to the ACE2, increased replication in human bronchial and nasal airway epithelial cultures and in a human ACE2 knock-in mouse model, and increased replication and transmission in SARS-CoV-2-infected hamster and ferret models. 2022 Frontiers in microbiology Discussion SARS_CoV_2 D614G 18 23 35369437 Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China. Following the D614G mutation, several novel SARS-CoV-2 variants of concern (VOCs) carrying the D614G mutation have emerged rapidly and are associated with large-scale infections worldwide. 2022 Frontiers in microbiology Discussion SARS_CoV_2 D614G;D614G 14;95 19;100 35369437 Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China. The D614G mutation was the beginning of the SARS-CoV-2 mutation. 2022 Frontiers in microbiology Discussion SARS_CoV_2 D614G 4 9 35369437 Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China. Their data explained the global predominance of D614G mutants. 2022 Frontiers in microbiology Discussion SARS_CoV_2 D614G 48 53 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. Consistent with this report, our data showed that ATV also inhibited D614G strain in Caco-2 (EC50 = 7.4 muM), a colorectal epithelial cell line highly permissive for SARS-CoV-2 infection. 2022 Frontiers in microbiology Discussion SARS_CoV_2 D614G 69 74 COVID-19 166 186 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. In the present study, the antiviral effect of atorvastatin against SARS-CoV-2 D614G strain was identified by the treatment of Vero E6 cells at different times of infection. 2022 Frontiers in microbiology Discussion SARS_CoV_2 D614G 78 83 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. In this study, Vero E6 cells were treated with ATV for 48 h after infection, obtaining a reduction of the infectious SARS-CoV-2 D614G particles at all evaluated concentrations. 2022 Frontiers in microbiology Discussion SARS_CoV_2 D614G 128 133 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. Similar to this report, our study demonstrated that ATV inhibited D614G strain at 31.2 muM by pretreating cells for 1 h. 2022 Frontiers in microbiology Discussion SARS_CoV_2 D614G 66 71 35369500 Atorvastatin Effectively Inhibits Ancestral and Two Emerging Variants of SARS-CoV-2 in vitro. The results presented in this article also showed a reduction of the intracellular D614G strain RNA after post-treatment with ATV at 31.2 and 15.6 muM. 2022 Frontiers in microbiology Discussion SARS_CoV_2 D614G 83 88 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. A few mutants' viz.L455Y, Q493N, R408I, Q498Y, F486L, N501T within the RBD region (319-591), and D936Y& A930V within HR1 site (912-984) have also been studied by in silico analysis to investigate the basic structure of spike glycoprotein. 2022 Indian journal of medical microbiology Discussion SARS_CoV_2 A930V;D936Y;F486L;N501T;Q493N;Q498Y;R408I;L455Y 104;97;47;54;26;40;33;19 109;102;52;59;31;45;38;24 S;RBD 219;71 237;74 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. B.1.351 (Beta variant), a variant first encountered in South Africa, is of greater concern as this variant is incompliant to NTD mAbs neutralization, mainly due to E484K mutations. 2022 Indian journal of medical microbiology Discussion SARS_CoV_2 E484K 164 169 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. Comparison of wild with mutant RBD protein, significant RMSD fluctuations were observed in all variants (B.1.617 0.25-0.5 nm, E484K nm 0.25-0.4 nm, F486L 0.2-0.3 nm, K417G 0.2-0.4 nm, L455Y 0.2-0.4 nm, L455Y 0.2-0.4 nm, Q493N 0.2-0.4 nm and R408I 0.25-0.45 nm). 2022 Indian journal of medical microbiology Discussion SARS_CoV_2 E484K;F486L;K417G;L455Y;L455Y;Q493N;R408I 126;148;166;184;202;220;241 131;153;171;189;207;225;246 RBD 31 34 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. D614G, T20N, D138Y, L18F, R190S, and P26S in the NTD and K417T, E484K and N501Y in the RBD region and H655Y within the furin cleavage site. 2022 Indian journal of medical microbiology Discussion SARS_CoV_2 D138Y;E484K;H655Y;K417T;L18F;N501Y;P26S;R190S;T20N;D614G 13;64;102;57;20;74;37;26;7;0 18;69;107;62;24;79;41;31;11;5 RBD 87 90 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. Shared E484K mutation is the main culprit, which emerged in more than 50 lines independently along with B.1.526, recently identified in New York. 2022 Indian journal of medical microbiology Discussion SARS_CoV_2 E484K 7 12 35370005 Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. The mRNA-1273 vaccine's neutralizing activity towards number of variants like B.1.351, B.1.1.7 + E484K, B.1.1.7, P.1, B.1.427/B.1.429, D614G, 20A.EU2, 20E [EU1], N439K-D614G, and previously identified mutant in Denmark mink cluster 5 were identified and found to have the same neutrality level as Wuhan-Hu-1 (D1414). 2022 Indian journal of medical microbiology Discussion SARS_CoV_2 D614G;E484K;N439K;D614G 135;97;162;168 140;102;167;173 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. After the SARS-CoV-2 outbreak, the D614G strain quickly replaced the original strain and became the dominant variant. 2022 Frontiers in immunology Discussion SARS_CoV_2 D614G 35 40 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. Furthermore, 4A8 targets the SARS-CoV-2 NTD domain, and its neutralizing activity can be affected by SARS-CoV-2 Y144del, LAL242-244del, and R246I mutations. 2022 Frontiers in immunology Discussion SARS_CoV_2 R246I;Y144del 140;112 145;119 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. However, in Caco2-hACE2, 293T-hACE2, and 293T-hACE2-TMPRSS2 cells, B.1.1.7, B.1.351, and B.1.617.2 exhibit higher infection efficiency than D614G in shorter incubation time. 2022 Frontiers in immunology Discussion SARS_CoV_2 D614G 140 145 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. In fact, B.1.617.2 contains the P681R mutation, which results in enhanced cleavage of the S protein in cells, which may account for the enhanced infectivity of B.1.617.2 in some susceptible cells. 2022 Frontiers in immunology Discussion SARS_CoV_2 P681R 32 37 S 90 91 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. LY-CoV555 has immune escape against almost all variants except D614G and B.1.17. 2022 Frontiers in immunology Discussion SARS_CoV_2 D614G 63 68 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. Previous studies have shown that the SARS-CoV-2 K417N/T mutation can lead to reduced neutralizing activity of CB6. 2022 Frontiers in immunology Discussion SARS_CoV_2 K417N;K417T 48;48 55;55 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. showed that the fusion activity among D614G, B.1.1.7, B.1.351, P.1, B.1.617.1, and B.1.617.2 had no significant differences when spike and ACE2 were transfected at high levels. 2022 Frontiers in immunology Discussion SARS_CoV_2 D614G 38 43 S 129 134 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. Similar to the neutralizing activity of antibodies, LY-CoV555 had reduced binding capacity for almost all variants except D614G and B.1.17. 2022 Frontiers in immunology Discussion SARS_CoV_2 D614G 122 127 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. Studies show that the D614G substitution leads to the enhancement of viral replication and infectivity in host cells. 2022 Frontiers in immunology Discussion SARS_CoV_2 D614G 22 27 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. The immune escape of some variants against LY-CoV555 may be related to the E484K/A mutation. 2022 Frontiers in immunology Discussion SARS_CoV_2 E484A;E484K 75;75 82;82 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. The P681H, P681R, and Q677H mutation sites in the variants are located near the furin cleavage site, which may affect the cleavage of S protein. 2022 Frontiers in immunology Discussion SARS_CoV_2 P681H;P681R;Q677H 4;11;22 9;16;27 S 134 135 35371108 Multiple SARS-CoV-2 Variants Exhibit Variable Target Cell Infectivity and Ability to Evade Antibody Neutralization. The present study shows that, compared with the D614G strain, the infectivity of most variants was changed in mammalian cells. 2022 Frontiers in immunology Discussion SARS_CoV_2 D614G 48 53 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Alternatively, it could result from imports from multiple undersampled locations such that AY.122 + ORF7a:P45L has reached a high frequency in all of them:but this also seems less likely in the absence of advantage of AY.122 + ORF7a:P45L compared to other Delta variants. 2022 Virus evolution Discussion SARS_CoV_2 P45L;P45L 106;233 110;237 ORF7a;ORF7a 100;227 105;232 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Both mutations characterizing the main PII, nsp2:K81N and ORF7a:P45L, are nonsynonymous, making this possibility realistic. 2022 Virus evolution Discussion SARS_CoV_2 K81N;P45L 49;64 53;68 ORF7a;Nsp2 58;44 63;48 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Both single and repeated importations of the AY.122 + ORF7a:P45L lineage from the same unsampled location(s) are a possibility. 2022 Virus evolution Discussion SARS_CoV_2 P45L 60 64 ORF7a 54 59 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. By contrast, here we show that the vast majority of Delta SARS-CoV-2 variants that have spread in Russia were genetically similar, carrying the derived nsp2:K81N and ORF7a:P45L changes that are rare outside Russia. 2022 Virus evolution Discussion SARS_CoV_2 K81N;P45L 157;172 161;176 ORF7a;Nsp2 166;152 171;156 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. However, AY.122 + ORF7a:P45L was the major variant in all 41 Russian regions with more than five Delta samples by the time of this study (Supplementary Table S2). 2022 Virus evolution Discussion SARS_CoV_2 P45L 24 28 ORF7a 18 23 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Indeed, the nsp2:K81N + ORF7a:P45L combination occurs in 68 out of 80 (85 per cent) of Russian samples obtained in April, but just in 34 out of 6658 (0.5 per cent) of non-Russian samples obtained at that time. 2022 Virus evolution Discussion SARS_CoV_2 K81N;P45L 17;30 21;34 ORF7a;Nsp2 24;12 29;16 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Nevertheless, nsp2:K81N + ORF7a:P45L has been observed in four of them (Supplementary Table S4). 2022 Virus evolution Discussion SARS_CoV_2 K81N;P45L 19;32 23;36 ORF7a;Nsp2 26;14 31;18 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. The AY.122 + ORF7a:P45L variant started to spread near-simultaneously in Moscow, Saint Petersburg, and the remainder of Russia (Supplementary Table S2), suggesting that if true, this event took place before 19 April in a poorly sampled location within or outside Russia. 2022 Virus evolution Discussion SARS_CoV_2 P45L 19 23 ORF7a 13 18 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. The earliest samples carrying the nsp2:K81N + ORF7a:P45L combination are sporadic, and were often deposited months later than collected, suggesting that they could be misdated in GISAID (Supplementary Table S4). 2022 Virus evolution Discussion SARS_CoV_2 K81N;P45L 39;52 43;56 ORF7a;Nsp2 46;34 51;38 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. The latter will require the existence of a region with a high prevalence of AY.122 + ORF7a:P45L before mid-April which would be the source of multiple imports, which seems somewhat unlikely because Russia is about equally well connected with multiple countries and there is no reason for just one to play the predominant role. 2022 Virus evolution Discussion SARS_CoV_2 P45L 91 95 ORF7a 85 90 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. There is also no evidence that the nsp2:K81N + ORF7a:P45L combination is characterized by an increased rate of spread compared to other Delta variants. 2022 Virus evolution Discussion SARS_CoV_2 K81N;P45L 40;53 44;57 ORF7a;Nsp2 47;35 52;39 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Therefore, the high prevalence of the AY.122 + ORF7a:P45L lineage in Russia is probably due to chance. 2022 Virus evolution Discussion SARS_CoV_2 P45L 53 57 ORF7a 47 52 35371558 The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia. Third, the success of the AY.122 + ORF7a:P45L lineage in Russia could arise from an early superspreading event. 2022 Virus evolution Discussion SARS_CoV_2 P45L 41 45 ORF7a 35 40 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. Antigenic cartography analysis suggests that Omicron is antigenically distant from D614G and Delta variants of SARS-CoV-2, but this distance decreased after the 3rd vaccination. 2022 Science translational medicine Discussion SARS_CoV_2 D614G 83 88 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. Changes in antigenic distances after immunizations may reflect the proportion of D614G-specific antibodies and antibodies that cross-neutralize variants. 2022 Science translational medicine Discussion SARS_CoV_2 D614G 81 86 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. Here, using a lentiviral pseudovirus neutralization platform we measured the change in potency of 18 clinical-stage therapeutic antibody products and a DARPin product against Omicron compared to D614G and assessed neutralizing antibodies in serum samples from two well-characterized cohorts of individuals in prospective clinical studies. 2022 Science translational medicine Discussion SARS_CoV_2 D614G 195 200 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. In contrast to Omicron, the antigenic distance between D614G and Delta increased slightly from the 2nd to 3rd immunization. 2022 Science translational medicine Discussion SARS_CoV_2 D614G 55 60 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. Modest or moderate changes in neutralization potency against a new variant relative to D614G may overcome by high therapeutic concentrations. 2022 Science translational medicine Discussion SARS_CoV_2 D614G 87 92 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. Of the antibody products tested here, only the DARPin and two of eighteen clinical-stage therapeutic antibody products retained potency against Omicron that was comparable to D614G. 2022 Science translational medicine Discussion SARS_CoV_2 D614G 175 180 35380448 SARS-CoV-2 BA.1 variant is neutralized by vaccine booster-elicited serum, but evades most convalescent serum and therapeutic antibodies. Some substitutions specific to the Omicron spike protein near the prefusion-stabilizing 2P mutations (K986P and V987P) used in mRNA vaccines could help stabilize conformations that expose shared epitopes between the D614G vaccine antigen and Omicron. 2022 Science translational medicine Discussion SARS_CoV_2 D614G;V987P;K986P 216;112;102 221;117;107 S 43 48 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. A comparative analysis of the parameter RMSF value demonstrated that the recovered mutant protein S194* showed more fluctuations in comparison with the wild type and the protein mutation at the same position associated with the mortality group. 2022 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 S194X 98 103 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. A study by also demonstrated the mutations C241T, F924F, and P4715L to have a similar frequency as D614G in their cohort as well, which shows their co-occurrence in the viral genome. 2022 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 C241T;D614G;F924F;P4715L 43;99;50;61 48;104;55;67 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. A study by reported that the mutation Q57H, which is observed in our mortality patients, is consistently present in high frequency at all the time points. 2022 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 Q57H 38 42 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. Also, the mutation S194L found in the Nucleocapsid gene was a highly significant mutation observed across our cohort and is also associated with mortality. 2022 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 S194L 19 24 N 38 50 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. Although mutation S194L is previously reported to be associated with mortality as seen in our cohort, its effect on the protein structure has not been explored and elucidated. 2022 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 S194L 18 23 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. Another study describes the loss of function of orf3b protein, an accessory protein, due to the truncation of orf3a protein by Q57H mutation. 2022 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 Q57H 127 131 ORF3b;ORF3a 48;110 53;115 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. Furthermore, they also found that the loss of orf3b coincides with the emergence of D614G spike mutation that strikingly correlates with our observation of D614G being present at high frequency in our mortality patients. 2022 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G;D614G 84;156 89;161 ORF3b;S 46;90 51;95 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. Intriguingly, 5/26 significant mutations (C241T, Q57H, F924F, P4715L, D614G) in the mortality patients did not exhibit any frequency flip with a high frequency occurrence observed in the cohort as well as the global level. 2022 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G;F924F;P4715L;Q57H;C241T 70;55;62;49;42 75;60;68;53;47 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. Moreover, a significant frequency flip (p-value = 0.0001) was seen for the five mutations, S2015R, Y789Y, T2016K, S194*, and A4489V, in the recovered with a low global presence, indicating that the mutations associated with COVID-19 recovery are deselected by the virus during its evolution. 2022 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 A4489V;S194X;S2015R;T2016K;Y789Y 125;114;91;106;99 131;119;97;112;104 COVID-19 224 232 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. Moreover, the mutation P4715L in RdRp protein affects the viral replication, and the spike mutation D614G influences the viral interaction with the ACE2 receptor, thereby enhancing the overall fitness of the virus. 2022 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 D614G;P4715L 100;23 105;29 S;RdRP 85;33 90;37 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. The MD simulations performed for the mutations S194* and S194L from the recovered and mortality group, respectively, revealed RMSD values, which was evaluated for both the mutations and the wild-type, implying a state of equilibrium achieved for all the three systems. 2022 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 S194X;S194L 47;57 52;62 35386683 SARS-CoV-2 Mutations and COVID-19 Clinical Outcome: Mutation Global Frequency Dynamics and Structural Modulation Hold the Key. This suggests the instability of the mutation S194* in the recovered group, which is exactly correlating with its low frequency occurrence at the global level as compared to S194L in the mortality group. 2022 Frontiers in cellular and infection microbiology Discussion SARS_CoV_2 S194X;S194L 46;174 51;179 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. Subsequently, in the month of February the D614G mutant entered in North Italy rapidly spreading to the rest of Italy and Europe, determining a different epidemiological profile of the Italian epidemic since then sustained only by B.1 lineage and his descendants. 2022 Scientific reports Discussion SARS_CoV_2 D614G 43 48 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. The introduction in Italy of the D614G variant with a greater transmissibility and its hidden circulation for weeks before the detection of the first cases in Italy could be responsible for the rapid spread of the epidemic in Northern Italy followed by spread to other Italian regions and possibly to the rest of Europe, similar to what was observed for lineage B.1.7.7, firstly predominating in UK and, subsequently, in many other European (and extra-European) countries (eCDC, rapid risk assessment, 15 February 2021). 2022 Scientific reports Discussion SARS_CoV_2 D614G 33 38 35388091 Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. The second phylogeographic scenario involving lineage B.1, showed initially only a few introductions from Asia to Italy and Europe (more precisely defined as Germany in the more detailed country based analysis), of small clusters corresponding to ancestral B.1/19A isolates, characterized by the substitution D614G in the spike protein in the absence of the P314L in the RdRp. 2022 Scientific reports Discussion SARS_CoV_2 D614G;P314L 309;358 314;363 S;RdRP 322;371 327;375 35389264 SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. Thus, we speculate that the S46A nsp5 mutant may result in changes to the position of the side chain at position 46 and further influence the conformation of M49 in the S2 pocket. 2022 Journal of virology Discussion SARS_CoV_2 S46A 28 32 Nsp5 33 37 35396165 A self-amplifying RNA vaccine protects against SARS-CoV-2 (D614G) and Alpha variant of concern (B.1.1.7) in a transmission-challenge hamster model. Using an in vivo contact transmission model in Syrian Golden hamsters, we demonstrated that a prime-boost vaccination with a Wuhan-like spike saRNA vaccine protected against severe disease, measured by weight loss, following infection by exposure to a D614G 'wild type' virus or the Alpha VOC. 2022 Vaccine Discussion SARS_CoV_2 D614G 252 257 S 136 141 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. According to Welkers et al., each of the three mutations (Y453F, F486L, and N501T) results in SARS-CoV-2 infection in minks. 2022 Journal of applied genetics Discussion SARS_CoV_2 F486L;N501T;Y453F 65;76;58 70;81;63 COVID-19 94 114 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Along with these, two other S protein mutations (I692V, M1229I) have been observed in the cluster's 5 variant strains (Larsen). 2022 Journal of applied genetics Discussion SARS_CoV_2 M1229I;I692V 56;49 62;54 S 28 29 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. An additional mutation H182Y within ORF3a was also found in mink sequences from Denmark (Hammer et al.). 2022 Journal of applied genetics Discussion SARS_CoV_2 H182Y 23 28 ORF3a 36 41 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Because of the current pandemic status of SARS-CoV-2 worldwide including Poland and the threat of the most common UK strain B.1.1.7, we decided to answer the question: Is this strain a threat to mink farms in Poland and worldwide? Unfortunately, the D614G is observed in the UK SARS-CoV-2 B.1.1.7 variant. 2022 Journal of applied genetics Discussion SARS_CoV_2 D614G 250 255 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. During our analysis, we have found the F486L mutation in the RaTG13 sequence, but it was observed in only one of the minks, so it seems that this mutation has no essential role in mink infection. 2022 Journal of applied genetics Discussion SARS_CoV_2 F486L 39 44 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. During our analysis, we have observed the presence of the Y453F mutation in 5 out of 13 mink coronavirus isolates from the Netherlands, in 8 out of 12 mink coronavirus isolates from Denmark, and in 2 out of 14 mink coronavirus isolates from Poland. 2022 Journal of applied genetics Discussion SARS_CoV_2 Y453F 58 63 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. From the point of view of the mink infection, the D614G mutation may be important because all minks from Denmark and Poland have this mutation. 2022 Journal of applied genetics Discussion SARS_CoV_2 D614G 50 55 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. have shown that multiple ACE2 residues that differ between human and mink ACE2 interact with the Y453F, F486L, or N501T residues. 2022 Journal of applied genetics Discussion SARS_CoV_2 F486L;N501T;Y453F 104;114;97 109;119;102 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. However, in all sequences stored in GISAD from Polish minks, three mutations were present: G75V, D614G, and C1247F. 2022 Journal of applied genetics Discussion SARS_CoV_2 C1247F;D614G;G75V 108;97;91 114;102;95 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. If any modification of the S protein is needed to infect minks in Poland, one of them (G75V, D614G, and C1247F) enables such infection, and out of these three mutations, only one:the D614G:was observed in the B.1.1.7 variant. 2022 Journal of applied genetics Discussion SARS_CoV_2 C1247F;D614G;D614G;G75V 104;93;183;87 110;98;188;91 S 27 28 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. In addition, the latest SARS-CoV-2 variants that were first reported in India: B.1.617.1, B.1.617.2, and B.1.617.3 have also the D614G mutation (European Centre for Disease Prevention and Control). 2022 Journal of applied genetics Discussion SARS_CoV_2 D614G 129 134 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. Substitution D614G, which is mainly common in humans, is also observed in coronavirus from mink (Hoffmann et al.). 2022 Journal of applied genetics Discussion SARS_CoV_2 D614G 13 18 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. The D614G mutation was detected in 7 out of 13 mink coronavirus isolates from the Netherlands, 12 out of 12 mink coronavirus isolates from Denmark, and 14 out of 14 mink coronavirus isolates from Poland. 2022 Journal of applied genetics Discussion SARS_CoV_2 D614G 4 9 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. The S protein mutation Y453F has been observed in minks from Denmark and the Netherlands. 2022 Journal of applied genetics Discussion SARS_CoV_2 Y453F 23 28 S 4 5 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. The Y453F and N501T mutations were not detected in the RaTG13 sequence, which suggests that this may be a change determining new interspecies infections. 2022 Journal of applied genetics Discussion SARS_CoV_2 N501T;Y453F 14;4 19;9 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. There was only one strain from the Netherlands that does not have either Y453F or D614G but has the F486L mutation. 2022 Journal of applied genetics Discussion SARS_CoV_2 D614G;F486L;Y453F 82;100;73 87;105;78 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. We can conclude that the occurrence of one of the two mutations:D614G or Y453F, is sufficient for the infection of minks by SARS-CoV-2 from humans. 2022 Journal of applied genetics Discussion SARS_CoV_2 Y453F;D614G 73;64 78;69 35396646 The basis of mink susceptibility to SARS-CoV-2 infection. We have found two mutations:the Y453F and D614G, which are common in Western Europe and Poland and allow mink to become infected. 2022 Journal of applied genetics Discussion SARS_CoV_2 D614G;Y453F 42;32 47;37 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Also, D614G variant is found to be more sensitive than the WT in presence of two-pore channel (TPC) blocker tetrandrine (Figure S4). 2022 Cell reports Discussion SARS_CoV_2 D614G 6 11 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. In summary, the enhanced infectivity of the Delta spike compared to Alpha, Beta, and D614G viruses largely results from the increased affinity of the spike protein to Ca2. 2022 Cell reports Discussion SARS_CoV_2 D614G 85 90 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Our study demonstrated that SARS-CoV-2 spike is a dynamic calcium sensor, and D614G mutation and evolved spike strains B.1.1.7, B.1.351, and B.1.617.2 elicit enhanced dynamic calcium sensitivity leading to fast and efficient membrane fusion for entry. 2022 Cell reports Discussion SARS_CoV_2 D614G 78 83 Membrane;S;S 225;39;105 233;44;110 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Remarkably, the WT spike, D614G, and evolved spike variants are sensitive to Ca2+ concentration of 500 muM for fusion, and further increment of Ca2+ concentration does not promote the fusion. 2022 Cell reports Discussion SARS_CoV_2 D614G 26 31 S;S 19;45 24;50 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Therefore, this difference could be due to different potency of these blockers and the high calcium sensitivity of the D614G spike. 2022 Cell reports Discussion SARS_CoV_2 D614G 119 124 S 125 130 35397208 Dynamic Ca(2+) sensitivity stimulates the evolved SARS-CoV-2 spike strain-mediated membrane fusion for enhanced entry. Whereas the effect of verapamil is similar for both the WT and D614G, tetrandrine is especially more potent than verapamil in blocking this TPC channel. 2022 Cell reports Discussion SARS_CoV_2 D614G 63 68 35398519 Immune evasion and chronological decrease in titer of neutralizing antibody against SARS-CoV-2 and its variants of concerns in COVID-19 patients. There are several limitations in this study: first, because most of the participants were infected by the Wuhan-hu-1 strain with or without D614G mutation, we cannot assess immune evasion among other strains, such as the neutralization titers of the Delta variant after infection with the Alpha variant. 2022 Clinical immunology (Orlando, Fla.) Discussion SARS_CoV_2 D614G 140 145 35398602 SARS-CoV-2 infections in mRNA vaccinated individuals are biased for viruses encoding spike E484K and associated with reduced infectious virus loads that correlate with respiratory antiviral IgG levels. Genomic analysis revealed a statistically significant increased representation of lineage B.1.526 as well as the Spike amino acid change S: E484K in genomes from the vaccinated group. 2022 Journal of clinical virology Discussion SARS_CoV_2 E484K 140 145 S;S 113;137 118;138 35398602 SARS-CoV-2 infections in mRNA vaccinated individuals are biased for viruses encoding spike E484K and associated with reduced infectious virus loads that correlate with respiratory antiviral IgG levels. Our data showed a significant association of S: E484K with positives after full vaccination using a well-controlled analysis and a relatively large sample size in a time when the Alpha variant predominated. 2022 Journal of clinical virology Discussion SARS_CoV_2 E484K 48 53 S 45 46 35398602 SARS-CoV-2 infections in mRNA vaccinated individuals are biased for viruses encoding spike E484K and associated with reduced infectious virus loads that correlate with respiratory antiviral IgG levels. Our study shows that the S: E484K is significantly associated with breakthrough cases after vaccination in a well-controlled analysis that used a large cohort of controls from a matched time frame of sample collection. 2022 Journal of clinical virology Discussion SARS_CoV_2 E484K 28 33 S 25 26 35398602 SARS-CoV-2 infections in mRNA vaccinated individuals are biased for viruses encoding spike E484K and associated with reduced infectious virus loads that correlate with respiratory antiviral IgG levels. The S: E484K independently emerged in multiple lineages in distant geographical locations including the Gamma and the Beta and those lineages showed some reduction in neutralization by sera collected from immunized individuals as well as decreased susceptibility to certain therapeutic monoclonal antibodies. 2022 Journal of clinical virology Discussion SARS_CoV_2 E484K 7 12 S 4 5 35398602 SARS-CoV-2 infections in mRNA vaccinated individuals are biased for viruses encoding spike E484K and associated with reduced infectious virus loads that correlate with respiratory antiviral IgG levels. The S: E484K is also present in some strains of lineage B.1.526, a lineage which was significantly associated with positives after vaccination in our cohort, even though in a previous study, it was not reported to associate with positives after vaccination. 2022 Journal of clinical virology Discussion SARS_CoV_2 E484K 7 12 S 4 5 35398602 SARS-CoV-2 infections in mRNA vaccinated individuals are biased for viruses encoding spike E484K and associated with reduced infectious virus loads that correlate with respiratory antiviral IgG levels. Those variants were associated with an increase in transmissibility and in particular the S: E484K substitution was associated with a compromise in the neutralization by monoclonal antibodies rendering this change "of therapeutic concern". 2022 Journal of clinical virology Discussion SARS_CoV_2 E484K 93 98 S 90 91 35401825 Inhibitor screening using microarray identifies the high capacity of neutralizing antibodies to Spike variants in SARS-CoV-2 infection and vaccination. identified a monoclonal antibody (03-1F9) with decreased neutralization activity to the N501Y mutant. 2022 Theranostics Discussion SARS_CoV_2 N501Y 88 93 35401825 Inhibitor screening using microarray identifies the high capacity of neutralizing antibodies to Spike variants in SARS-CoV-2 infection and vaccination. In Cheng's study, 12 monoclonal antibodies showed varying neutralizing levels against the N501Y mutant compared with wild-type SARS-CoV-2. 2022 Theranostics Discussion SARS_CoV_2 N501Y 90 95 35401825 Inhibitor screening using microarray identifies the high capacity of neutralizing antibodies to Spike variants in SARS-CoV-2 infection and vaccination. In comparison, antibodies #21 and #53 did not have any neutralizing activity to 8 and 5 variants, respectively, with 4 overlapped mutations (F456E, N487R, N501Y, Y505C). 2022 Theranostics Discussion SARS_CoV_2 N487R;N501Y;Y505C;F456E 148;155;162;141 153;160;167;146 35401825 Inhibitor screening using microarray identifies the high capacity of neutralizing antibodies to Spike variants in SARS-CoV-2 infection and vaccination. It is possible that N501Y may induce neutralization resistance in the serum from convalescent COVID-19 patients or the N501Y mutant may alter the availability of epitopes that are targeted by the antibodies. 2022 Theranostics Discussion SARS_CoV_2 N501Y;N501Y 20;119 25;124 COVID-19 94 102 35401825 Inhibitor screening using microarray identifies the high capacity of neutralizing antibodies to Spike variants in SARS-CoV-2 infection and vaccination. Moreover, resistance could be enhanced with the combination of E484K/K417N mutations. 2022 Theranostics Discussion SARS_CoV_2 E484K;K417N 63;69 68;74 35401825 Inhibitor screening using microarray identifies the high capacity of neutralizing antibodies to Spike variants in SARS-CoV-2 infection and vaccination. Notably, the N501Y mutation is present in several SARS-CoV-2 lineages and its role in COVID-19 is inconclusive. 2022 Theranostics Discussion SARS_CoV_2 N501Y 13 18 COVID-19 86 94 35401825 Inhibitor screening using microarray identifies the high capacity of neutralizing antibodies to Spike variants in SARS-CoV-2 infection and vaccination. The results are consistent to our data using monoclonal and polyclonal antibodies and the serum from convalescent patients and vaccinees (Figure 4 and 5), suggesting that N501Y/E484K/K417N mutations improve the inhibition of S-ACE2 interactions. 2022 Theranostics Discussion SARS_CoV_2 N501Y;E484K;K417N 171;177;183 176;182;188 S 225 226 35401825 Inhibitor screening using microarray identifies the high capacity of neutralizing antibodies to Spike variants in SARS-CoV-2 infection and vaccination. The S variants tested here contain mutations that were selected from the COVID-19 virus mutation tracker database and literature, including known mutations like N501Y, L452R, K417N, N439K, S477N and S494P, and less publicized mutations (Figure S2). 2022 Theranostics Discussion SARS_CoV_2 K417N;L452R;N439K;N501Y;S477N;S494P 175;168;182;161;189;199 180;173;187;166;194;204 S 4 5 COVID-19 73 81 35401825 Inhibitor screening using microarray identifies the high capacity of neutralizing antibodies to Spike variants in SARS-CoV-2 infection and vaccination. While N501Y is a known loss-of function mutation, 456E, N487R, and Y505C are new resistant mutations that should be assessed further. 2022 Theranostics Discussion SARS_CoV_2 N487R;N501Y;Y505C 56;6;67 61;11;72 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Here, we have characterized an Omicron isolate of BA.1.1 sub lineage with R346K mutation in Syrian hamster model. 2022 EBioMedicine Discussion SARS_CoV_2 R346K 74 79 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. In addition virus isolate used in study also possess R346K mutation which is also present in the Mu variant known for immune escape. 2022 EBioMedicine Discussion SARS_CoV_2 R346K 53 58 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. In comparison to our earlier studies of SARS-CoV-2 variants in Syrian hamster model and also the Delta variant infected group used for comparison, the lung lesions observed with Omicron (R346K) was prominent. 2022 EBioMedicine Discussion SARS_CoV_2 R346K 187 192 Lung diseases 151 163 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. It harbours N501Y, K417N, T478K, E484A which are amino acid substitutions linked with immune escape. 2022 EBioMedicine Discussion SARS_CoV_2 E484A;K417N;N501Y;T478K 33;19;12;26 38;24;17;31 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Moreover, the neutralizing antibodies generated after Omicron (R346K) infection showed substantial reduction or negligible neutralization against other variants like B.1, Alpha, Beta and Delta. 2022 EBioMedicine Discussion SARS_CoV_2 R346K 63 68 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Neutralizing antibodies could be detected from 5th DPI in Omicron (R346K) infected hamsters, which showed an increase in titre on further days similar to other VOCs. 2022 EBioMedicine Discussion SARS_CoV_2 R346K 67 72 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. Our preliminary data suggests that humoral immune response generated by Omicron (R346K) infection may not confer much protection to other currently circulating variants like Delta. 2022 EBioMedicine Discussion SARS_CoV_2 R346K 81 86 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. The disease characteristics of the Omicron (R346K) variant observed here are similar to those reported for other SARS-CoV-2 variants like Alpha, Beta, Kappa and Delta in hamsters by earlier studies except that of the body weight loss. 2022 EBioMedicine Discussion SARS_CoV_2 R346K 44 49 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. The Omicron variant we used in this study had an R346K substitution unlike other studies available in public domain. 2022 EBioMedicine Discussion SARS_CoV_2 R346K 49 54 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. The presented data provides new insight into the neutralization potential and cross protection of Omicron (R346K) variant against other VOCs and suggest that the pathogenicity of the circulating Omicron lineages could differ. 2022 EBioMedicine Discussion SARS_CoV_2 R346K 107 112 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. The serum samples of hamster infected with Omicron (R346K) showed poor neutralization against other VOCs tested like Alpha, Beta and Delta variants. 2022 EBioMedicine Discussion SARS_CoV_2 R346K 52 57 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. We found no evidence that Omicron (R346K) produce less severe lung disease or more predilection to upper respiratory tract in comparison to lung as reported earlier. 2022 EBioMedicine Discussion SARS_CoV_2 R346K 35 40 Lung diseases 62 74 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. We observed limited body weight gain, viral replication in the upper and lower respiratory tract and interstitial pneumonia in Syrian hamsters following infection with the Omicron (R346K) variant. 2022 EBioMedicine Discussion SARS_CoV_2 R346K 181 186 Pneumonia 101 123 35405385 Pathogenicity of SARS-CoV-2 Omicron (R346K) variant in Syrian hamsters and its cross-neutralization with different variants of concern. We observed moderate to severe changes in the lungs of hamsters infected with Omicron (R346K). 2022 EBioMedicine Discussion SARS_CoV_2 R346K 87 92 35409572 Increased Secondary Attack Rate among Unvaccinated Household Contacts of Coronavirus Disease 2019 Patients with Delta Variant in Japan. Last, the Delta and Alpha variants were mainly confirmed by the L452R and N501Y mutations, respectively. 2022 International journal of environmental research and public health Discussion SARS_CoV_2 L452R;N501Y 64;74 69;79 35421378 Efficacy of vaccination and previous infection against the Omicron BA.1 variant in Syrian hamsters. However, unlike the S-614G isolate, the Omicron variant replicated efficiently in the upper respiratory tract (nasal turbinate tissue) in previously infected hamsters. 2022 Cell reports Discussion SARS_CoV_2 S614G 20 26 S 20 21 35421378 Efficacy of vaccination and previous infection against the Omicron BA.1 variant in Syrian hamsters. Previous infection with either early isolate (S-614D or S-614G) resulted in higher spike-specific IgG antibody titers in hamsters when compared to Moderna mRNA-vaccinated animals. 2022 Cell reports Discussion SARS_CoV_2 S614G;S614D 56;46 62;52 S;S;S 83;46;56 88;47;57 35421378 Efficacy of vaccination and previous infection against the Omicron BA.1 variant in Syrian hamsters. This better immune response to a previous infection compared to vaccination prevented replication of both isolates (S-614G and the Omicron variant) after rechallenge in the lungs of previously infected hamsters, demonstrating that both short- and long-term immunity was protective in the lower respiratory tract. 2022 Cell reports Discussion SARS_CoV_2 S614G 116 122 S 116 117 35421378 Efficacy of vaccination and previous infection against the Omicron BA.1 variant in Syrian hamsters. While vaccination of hamsters with the Moderna mRNA vaccine reduced viral loads in the respiratory tissues upon challenge with an early S-614G isolate, the vaccine efficacy was not as pronounced after infection with the Omicron variant. 2022 Cell reports Discussion SARS_CoV_2 S614G 136 142 S 136 137 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. D614G is found in all VOIs and VOCs, and the mutation might be the outcome of a positive selection. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 0 5 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. Finally, we evaluated the comparative receptor binding (hACE2) pattern with the Wuhan strain, VOC B.1.1.7 variant (RBD N501Y mutation), and VOI B.1.617.2 variant of the spike protein (RBD double mutations L452R, E484Q). 2022 Infection, genetics and evolution Discussion SARS_CoV_2 E484Q;L452R;N501Y 212;205;119 217;210;124 S;RBD;RBD 169;115;184 174;118;187 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. N501Y, D614G L452R, and E484Q mutations are reported as significant mutations in different variants in SARS-CoV-2. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;E484Q;L452R;N501Y 7;24;13;0 12;29;18;5 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. One of the significant mutations is D614G which is responsible for infectivity and re-infectivity. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D614G 36 41 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. The L452R mutation, found in the B.1.617.2 variant, is linked with increased transmissibility. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 L452R 4 9 35427787 Comparative genomics, evolutionary epidemiology, and RBD-hACE2 receptor binding pattern in B.1.1.7 (Alpha) and B.1.617.2 (Delta) related to their pandemic response in UK and India. The variant was observed with some significant mutations in spike protein.Comparative genomics assessment of these two variants has revealed specific unique mutations, such as N501Y, D614G L452R, E484Q, and P681R in the S-glycoprotein. 2022 Infection, genetics and evolution Discussion SARS_CoV_2 D614G;E484Q;L452R;N501Y;P681R 183;196;189;176;207 188;201;194;181;212 S;S 220;60 234;65 35430092 Prolonged shedding of infectious viruses with haplotype switches of SARS-CoV-2 in an immunocompromised patient. Both E484Q and S494Q are common mutations in isolates of RBD escape mutants. 2022 Journal of infection and chemotherapy Discussion SARS_CoV_2 E484Q;S494Q 5;15 10;20 RBD 57 60 35430092 Prolonged shedding of infectious viruses with haplotype switches of SARS-CoV-2 in an immunocompromised patient. Further studies on V658I under drug pressure among immunocompromised host are needed. 2022 Journal of infection and chemotherapy Discussion SARS_CoV_2 V658I 19 24 35430092 Prolonged shedding of infectious viruses with haplotype switches of SARS-CoV-2 in an immunocompromised patient. Haplotypes 4 to 7 acquired an additional mutation, E484Q, which is a one of the signature mutations in the kappa variant (B.1.617.1). 2022 Journal of infection and chemotherapy Discussion SARS_CoV_2 E484Q 51 56 35430092 Prolonged shedding of infectious viruses with haplotype switches of SARS-CoV-2 in an immunocompromised patient. In addition, haplotype 7 acquired S494Q. 2022 Journal of infection and chemotherapy Discussion SARS_CoV_2 S494Q 34 39 35430092 Prolonged shedding of infectious viruses with haplotype switches of SARS-CoV-2 in an immunocompromised patient. On the other hand, V658I was observed during the administration of remdesivir (haplotype 2), but disappeared thereafter. 2022 Journal of infection and chemotherapy Discussion SARS_CoV_2 V658I 19 24 35430092 Prolonged shedding of infectious viruses with haplotype switches of SARS-CoV-2 in an immunocompromised patient. P314L (P323L) had been one of the common mutations in PANGON lineage B, and all seven haplotypes in our study possessed the mutation as the background. 2022 Journal of infection and chemotherapy Discussion SARS_CoV_2 P323L;P314L 7;0 12;5 35430092 Prolonged shedding of infectious viruses with haplotype switches of SARS-CoV-2 in an immunocompromised patient. Regarding RdRp, we observed two mutations in nsp12: P314L and V658I. 2022 Journal of infection and chemotherapy Discussion SARS_CoV_2 P314L;V658I 52;62 57;67 Nsp12;RdRP 45;10 50;14 35430092 Prolonged shedding of infectious viruses with haplotype switches of SARS-CoV-2 in an immunocompromised patient. Such transient observation of the haplotype may suggest the emergence of resistant virus, but there had been no report on V658I. 2022 Journal of infection and chemotherapy Discussion SARS_CoV_2 V658I 122 127 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. AM180 and 9G11 lost neutralizing activity to the other seven variants except for D614G, presumably due to the E484 mutation. 2022 MedComm Discussion SARS_CoV_2 D614G 81 86 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Among them, D614G, B.1.640.1, and B.1.630 formed a cluster, C.1.2 and B.1.640.2 formed a cluster, and BA.1, BA.2, and BA.3 formed a cluster. 2022 MedComm Discussion SARS_CoV_2 D614G 12 17 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. In addition, Omicron spike-immunized sera also has a certain protective effect on B.1.630, possibly due to Omicron immunogen containing T478K and E484A. 2022 MedComm Discussion SARS_CoV_2 E484A;T478K 146;136 151;141 S 21 26 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. In addition, the neutralization activity of XGv282 against C.1.2 decreased by 606.8-fold, which was speculated to be related to the Y449H mutation of C.1.2 variant. 2022 MedComm Discussion SARS_CoV_2 Y449H 132 137 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. It was speculated that the BA.1 variant RBD contained G446S and G496S, whereas the BA.2 and BA.3 variants did not contain these two mutations, thus leading to this result. 2022 MedComm Discussion SARS_CoV_2 G446S;G496S 54;64 59;69 RBD 40 43 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Monoclonal antibody 10D12 almost lost protection against Omicron sublineages, presumably related to the K417N mutation, which is consistent with the previous reports. 2022 MedComm Discussion SARS_CoV_2 K417N 104 109 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Our data indicated that D614G, Alpha, Delta, and Mu were similar in immunogenicity, and these sera had significantly reduced protection against Omicron sublineages (Figure S1). 2022 MedComm Discussion SARS_CoV_2 D614G 24 29 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Similarly, the strong neutralization protection of Lambda spike-immunized sera against B.1.630 and B.1.640.1 may be due to the presence of L452Q (B.1.630 containing L452R mutation) and F490S (B.1.640.1 containing F490R mutation but not E484K mutation) in the Lambda immunogen. 2022 MedComm Discussion SARS_CoV_2 E484K;F490R;F490S;L452Q;L452R 236;213;185;139;165 241;218;190;144;170 S 58 63 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Structural analysis showed that the antigenic binding epitope of XGv282 was located at the right shoulder of RBD, whereas the G446S mutation of BA.1 and BA.3 affected the binding of the mAb. 2022 MedComm Discussion SARS_CoV_2 G446S 126 131 RBD 109 112 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Surprisingly, the neutralizing activity of XGv282 against B.1.640.1 was reduced by 89.5-fold, but no significant change against B.1.640.2, presumably due to the additional E484K mutation altering the spatial conformation of the spike protein. 2022 MedComm Discussion SARS_CoV_2 E484K 172 177 S 228 233 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. Surprisingly, these four groups of sera also had poor neutralizing activity against C.1.2 and B.1.640.2, which may be caused by E484K mutation. 2022 MedComm Discussion SARS_CoV_2 E484K 128 133 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. The immunogenicity of Beta, Gamma, and Mu were similar, probably because these three immunogens all contained E484K and N501Y mutations (Figure S1). 2022 MedComm Discussion SARS_CoV_2 E484K;N501Y 110;120 115;125 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. The neutralizing activity of mAb JS016 was reduced due to the N501Y mutation in the variants. 2022 MedComm Discussion SARS_CoV_2 N501Y 62 67 35434713 Antigenicity comparison of SARS-CoV-2 Omicron sublineages with other variants contained multiple mutations in RBD. The strong neutralization protection of Delta spike-immunized sera against B.1.630 may be due to the L452R mutation contained in the Delta immunogen. 2022 MedComm Discussion SARS_CoV_2 L452R 101 106 S 46 51 35434714 Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern. For example, E484K mutations are currently known to affect the neutralization of serum or monoclonal antibodies (mAb) during the recovery period. 2022 MedComm Discussion SARS_CoV_2 E484K 13 18 35434714 Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern. In July 2020, a strain with the spike protein D614G mutation was discovered in Europe and subsequently became the main form of the virus pandemic. 2022 MedComm Discussion SARS_CoV_2 D614G 46 51 S 32 37 35434714 Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern. In the Alpha and Omicron strains, two key deletions, H60V70, are on the epitope, which can affect the immune escape of the S protein (Figure 4F), whereas N501Y and D614G have almost no effect on the antigen score, and the P681 mutation slightly reduces the epitope score and may have a certain impact. 2022 MedComm Discussion SARS_CoV_2 D614G;N501Y 164;154 169;159 S 123 124 35434714 Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern. In the Omicron variant, there are some consistent RBD mutations with previously focused variants (K417N, T478K, and N501Y). 2022 MedComm Discussion SARS_CoV_2 N501Y;T478K;K417N 116;105;98 121;110;103 RBD 50 53 35434714 Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern. Most of the mutations have been shown to reduce Omicron receptor binding, except for G339D, N440K, S447N, and Q498R. 2022 MedComm Discussion SARS_CoV_2 G339D;N440K;Q498R;S447N 85;92;110;99 90;97;115;104 35434714 Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern. S477G, S477N, and S477R occupy a prominent position in mAb escape mutations. 2022 MedComm Discussion SARS_CoV_2 S477N;S477R;S477G 7;18;0 12;23;5 35434714 Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern. Similarly, the combined mutation of K417N and N501Y affects the neutralization of mAb and convalescent serum. 2022 MedComm Discussion SARS_CoV_2 K417N;N501Y 36;46 41;51 35434714 Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern. The N501Y and K417N mutations confer increased and decreased binding affinity to ACE2, respectively. 2022 MedComm Discussion SARS_CoV_2 K417N;N501Y 14;4 19;9 35434714 Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern. The RBD regions of Alpha, Beta, Delta, and Omicron strains are more exposed, and the junction between the variants S protein and the virion has a prominent structure, which may be caused by the D614G mutation. 2022 MedComm Discussion SARS_CoV_2 D614G 194 199 RBD;S 4;115 7;116 35434714 Characteristic analysis of Omicron-included SARS-CoV-2 variants of concern. The same spike proteins, K444E, G446 V, L452R, and F490S, can also evade serum neutralization. 2022 MedComm Discussion SARS_CoV_2 F490S;G446V;K444E;L452R 51;32;25;40 56;38;30;45 S 9 14 35436320 Occurrence of a novel cleavage site for cathepsin G adjacent to the polybasic sequence within the proteolytically sensitive activation loop of the SARS-CoV-2 Omicron variant: The amino acid substitution N679K and P681H of the spike protein. Furthermore, the increased turnover capacity of furin and the fact that furin (CatG) controlled the processing of SARS-CoV-2 N679K P681R (Omicron) peptide in contrast to NE, indicate to target furin and, most likely, CatG with selective protease inhibitors as a logical consequence to interfere with the priming of the S protein. 2022 PloS one Discussion SARS_CoV_2 N679K;P681R 125;131 130;136 S 319 320 35436320 Occurrence of a novel cleavage site for cathepsin G adjacent to the polybasic sequence within the proteolytically sensitive activation loop of the SARS-CoV-2 Omicron variant: The amino acid substitution N679K and P681H of the spike protein. It has been suggested that proline at the position 681 in SARS-CoV-2 allows an addition of O-linked glycans to nearby residues, leading to the creation of a mucin-like domain that shields antigen processing, which is circumvented by the introduction of an arginine residue in SARS-CoV-2 P681R. 2022 PloS one Discussion SARS_CoV_2 P681R 287 292 35436320 Occurrence of a novel cleavage site for cathepsin G adjacent to the polybasic sequence within the proteolytically sensitive activation loop of the SARS-CoV-2 Omicron variant: The amino acid substitution N679K and P681H of the spike protein. Strikingly, the P681R substitution is crucial for viral replication which has been suggested by reverting the P681R substitution to a wild-type P681 of the SARS-CoV-2 (Delta) background. 2022 PloS one Discussion SARS_CoV_2 P681R;P681R 16;110 21;115 35436320 Occurrence of a novel cleavage site for cathepsin G adjacent to the polybasic sequence within the proteolytically sensitive activation loop of the SARS-CoV-2 Omicron variant: The amino acid substitution N679K and P681H of the spike protein. The author hypothesized that furin might be responsible for increased transfection by enhanced priming of the S protein at the P681R substitution (preprint, https://doi.org/10.1101/2021.08.12.456173), which could be explained by our findings of increased SARS-CoV-2 P681R (Delta) substrate turnover by furin. 2022 PloS one Discussion SARS_CoV_2 P681R;P681R 127;266 132;271 S 110 111 35436320 Occurrence of a novel cleavage site for cathepsin G adjacent to the polybasic sequence within the proteolytically sensitive activation loop of the SARS-CoV-2 Omicron variant: The amino acid substitution N679K and P681H of the spike protein. Whether the novel cleavage site performed by CatG for SARS-CoV-2 Omicron peptide, carrying the mutations N679K and P681H, might increase infectivity and transmissibility need to be investigated by a cell-based assay. 2022 PloS one Discussion SARS_CoV_2 N679K;P681H 105;115 110;120 35454022 Unusual N Gene Dropout and Ct Value Shift in Commercial Multiplex PCR Assays Caused by Mutated SARS-CoV-2 Strain. According to the same tool, the frequency of the four amino acid substitutions, R203K, G204R, A208G and M234I, in 9.525.430 sequences available from the GISAID database (as of 29 March 2022, with collection days 2020-1-29, 2020-1-29, 2020-3-3, 2020-1-26 to 2022-3-29) was 44%, 43%, <0.5% and 2%, respectively. 2022 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 A208G;G204R;M234I;R203K 94;87;104;80 99;92;109;85 35454022 Unusual N Gene Dropout and Ct Value Shift in Commercial Multiplex PCR Assays Caused by Mutated SARS-CoV-2 Strain. As far as the A208G amino acid is concerned, it seems to be predominant in (but not unique to) the B.1.1.318 lineage and sub-lineages. 2022 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 A208G 14 19 35454022 Unusual N Gene Dropout and Ct Value Shift in Commercial Multiplex PCR Assays Caused by Mutated SARS-CoV-2 Strain. Sequencing analysis revealed four amino acid mutations (R203K, G204R, A208G, M234I) in the N protein sequence of all our B.1.1.318 isolates. 2022 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 A208G;G204R;M234I;R203K 70;63;77;56 75;68;82;61 N 91 92 35454022 Unusual N Gene Dropout and Ct Value Shift in Commercial Multiplex PCR Assays Caused by Mutated SARS-CoV-2 Strain. The M234I amino acid substitution has also occurred independently in several variants and, when it is coupled with the A376 substitution, may confer to carrying variants the ability to escape detection by commercial antigen tests. 2022 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 M234I 4 9 35454022 Unusual N Gene Dropout and Ct Value Shift in Commercial Multiplex PCR Assays Caused by Mutated SARS-CoV-2 Strain. The R203K and G204R amino acid changes have been found in several variants beside B.1.1.318 and are considered to contribute to increased infectivity and fitness and are related to a severe clinical outcome. 2022 Diagnostics (Basel, Switzerland) Discussion SARS_CoV_2 G204R;R203K 14;4 19;9 35456137 Comparative Evaluation of Six SARS-CoV-2 Real-Time RT-PCR Diagnostic Approaches Shows Substantial Genomic Variant-Dependent Intra- and Inter-Test Variability, Poor Interchangeability of Cycle Threshold and Complementary Turn-Around Times. In addition, variant B.1.258.17 as the main lineage during the second wave, variant A.27 as a rare variant, with mutation N501Y, and variant B.1 (with D614G) as the first main lineage, which caused a substantial part of the first wave of infections in Europe, were included. 2022 Pathogens (Basel, Switzerland) Discussion SARS_CoV_2 D614G;N501Y 151;122 156;127 35458508 Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN and the Neighbouring East Asian Countries: Features, Challenges and Achievements. Of note, the N439K mutation prevalent in the B.1.466.2 variant has been indicated to confer resistance to some monoclonal antibodies and evade some polyclonal ones. 2022 Viruses Discussion SARS_CoV_2 N439K 13 18 35458530 Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice. As Omicron is fast replacing all past VOC, including Delta, which is still prevalent, we chose to compare the neutralising antibody responses of polyclonal mouse antisera generated against these thermotolerant vaccine candidates against Delta, Omicron and a reference isolate used in our previous work (VIC31-D614G). 2022 Viruses Discussion SARS_CoV_2 D614G 309 314 35458530 Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice. Even the Delta variant, with only two mutations in the RBD (L452R and T478K) has significantly reduced antibody neutralisation effects, suggestive of how specific vaccine-derived antibodies can be. 2022 Viruses Discussion SARS_CoV_2 T478K;L452R 70;60 75;65 RBD 55 58 35458530 Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice. In line with recent findings from studies using monoclonal antibodies, mAb cocktails or patient sera, there was a significant reduction in neutralising ability of the serum collected from immunised mice against the Omicron (BA.1.1) variant compared to VIC31-D614G and Delta. 2022 Viruses Discussion SARS_CoV_2 D614G 258 263 35458530 Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice. One highly altered region of the Omicron BA.1.1 RBD occurs along the side face including changes G339D, S371L, S373P, S375F and N440K, which occurs at approximately a 90 degree orientation to the receptor binding face. 2022 Viruses Discussion SARS_CoV_2 G339D;N440K;S371L;S373P;S375F 97;128;104;111;118 102;133;109;116;123 RBD 48 51 35458530 Highly Thermotolerant SARS-CoV-2 Vaccine Elicits Neutralising Antibodies against Delta and Omicron in Mice. The proportional reduction in neutralising antibodies to Omicron (BA.1.1), compared to VIC31-D614G and Delta rather than complete immune evasion, suggests that mouse antibodies directed to very specific epitopes in the Spike protein of the WT virus are being evaded through mutations, while antibodies to other epitopes are still able to provide significant level of virus neutralisation. 2022 Viruses Discussion SARS_CoV_2 D614G 93 98 S 219 224 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. Adding a E484K-RBD mutation to FCS-pseudoviruses, moderately decreased neutralization sensitivity against our sera samples, with no effects on viral infectivity. 2022 Viruses Discussion SARS_CoV_2 E484K 9 14 RBD 15 18 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. FCS mutations include P681H in Alpha and Omicron, A701V in Beta, and P681R in Delta:indicating that the P681 residue plays a critical role in viral fitness. 2022 Viruses Discussion SARS_CoV_2 A701V;P681H;P681R 50;22;69 55;27;74 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. FCS-P681R mutation within the Kappa and Delta SARS-CoV-2 variants augmented syncytium formation, thus contributing to increased infectivity of the UK and SA variants. 2022 Viruses Discussion SARS_CoV_2 P681R 4 9 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. However, RBD-specific mutations like N501Y, E484K, S477N, and L452R K417N, which lay within or close to the binding surface to ACE2, will keep playing key roles in respectively affecting binding of the spike to the receptor or escaping from mAb. 2022 Viruses Discussion SARS_CoV_2 E484K;K417N;L452R;N501Y;S477N 44;68;62;37;51 49;73;67;42;56 S;RBD 202;9 207;12 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. However, upon adding an N501Y RBD mutation, infectivity levels of FCS-exhibiting pseudoviruses were enhanced relative to wild-type SARS-CoV-2. 2022 Viruses Discussion SARS_CoV_2 N501Y 24 29 RBD 30 33 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. In contrast, neutralization sensitivity of single or double FCS/N501Y pseudoviruses against post-vaccinated sera remained similar to wild-type SARS-CoV-2 pseudoviruses (Figure 2). 2022 Viruses Discussion SARS_CoV_2 N501Y 64 69 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. In this study, we used pseudoviruses that express spike proteins from different SARS-CoV-2 variants to monitor the effects of mutations within FCS of either Alpha and Omicron (P681H), Beta and P1 (A701V), and Delta (P681R) on viral infectivity and neutralization sensitivity to post-vaccination sera drawn from fully vaccinated individuals. 2022 Viruses Discussion SARS_CoV_2 A701V;P681H;P681R 197;176;216 202;181;221 S 50 55 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. N501Y L452R, E484K S477S, and T478K distinct RBD mutations potentially compromise the efficacy of administrated vaccines. 2022 Viruses Discussion SARS_CoV_2 E484K;L452R;S477S;T478K;N501Y 13;6;19;30;0 18;11;24;35;5 RBD 45 48 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. Our data showed that, while S477N-RBD mutation alone had no impact on both viral infectivity or neutralizing sensitivity to post vaccination sera, the addition of N501Y or E484K spike mutations enhanced viral infectivity and decreased neutralizing sensitivity to post vaccinated sera (Figure 5). 2022 Viruses Discussion SARS_CoV_2 E484K;N501Y;S477N 172;163;28 177;168;33 S;RBD 178;34 183;37 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. Overall, we conclude that RBD mutations-N501Y and E484K dictate the ability of the virus to efficiently spread, by respectively modulating viral infectivity and ability to resist the humoral response that is induced by vaccination. 2022 Viruses Discussion SARS_CoV_2 E484K;N501Y 50;40 55;45 RBD 26 29 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. Single L452R and T478K RBD mutations moderately impact the neutralization potential, reaching about x2 fold reduction (Figure 4). 2022 Viruses Discussion SARS_CoV_2 L452R;T478K 7;17 12;22 RBD 23 26 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. The same results were obtained when there was a double L452R/T478K RBD mutation. 2022 Viruses Discussion SARS_CoV_2 L452R;T478K 55;61 60;66 RBD 67 70 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. The significance of RBD mutations was also demonstrated with the Lota SARS-CoV-2 that carries S477N/E484K within its spike. 2022 Viruses Discussion SARS_CoV_2 S477N;E484K 94;100 99;105 S;RBD 117;20 122;23 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. These reports demonstrate that spike residues like D614G and N501Y are located at the distal region of the spike RBD and facilitate transitions from a closed to open state of the spike prior to ACE2 binding, enhancing the stability and affinity of the viral spike to its receptor and subsequently affecting viral spread. 2022 Viruses Discussion SARS_CoV_2 D614G;N501Y 51;61 56;66 S;S;S;S;RBD 31;107;179;258;113 36;112;184;263;116 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. These results align with our previous data on Delta SARS-CoV-2 and state that both L452R and T478K combine to equally affect the moderate decrease in neutralizing sensitivity and viral infectivity that is exhibited by Delta SARS-CoV-2 (Figure 4). 2022 Viruses Discussion SARS_CoV_2 L452R;T478K 83;93 88;98 35458533 Functional Analysis of Spike from SARS-CoV-2 Variants Reveals the Role of Distinct Mutations in Neutralization Potential and Viral Infectivity. These results are comparable to the Delta SARS-CoV-2 that carries the complete, L452R/T478K/P681R-Delta RBD mutations. 2022 Viruses Discussion SARS_CoV_2 L452R;P681R;T478K 80;92;86 85;97;91 RBD 104 107 35461042 Increased resistance of SARS-CoV-2 Lambda variant to antibody neutralization. Although the number of samples was limited and all donors were Chinese in this study, we found that the neutralizing activities of convalescent and inactivated vaccine-elicited plasma against SARS-CoV-2 Lambda variant were significantly decreased compared with those against D614G-WT. 2022 Journal of clinical virology Discussion SARS_CoV_2 D614G 275 280 35461042 Increased resistance of SARS-CoV-2 Lambda variant to antibody neutralization. BD-368-2 and C110 totally lost their binding activities to the RBD-L452R, but still maintained some degree of affinity to the RBD-L452Q, suggesting that an arginine at L452 residual might have a greater impact on antibody recognition than the glutamine. 2022 Journal of clinical virology Discussion SARS_CoV_2 L452Q;L452R 130;67 135;72 RBD;RBD 63;126 66;129 35461042 Increased resistance of SARS-CoV-2 Lambda variant to antibody neutralization. The F490S substitution introducing a potential O-linked glycosylation site once appeared in some variants sporadically before it became the characteristic mutation of Lambda. 2022 Journal of clinical virology Discussion SARS_CoV_2 F490S 4 9 35461042 Increased resistance of SARS-CoV-2 Lambda variant to antibody neutralization. The more common mutation at L452 in the RBD was the L452R substitution, which has been found in Epsilon, Kappa, and Delta variants. 2022 Journal of clinical virology Discussion SARS_CoV_2 L452R 52 57 RBD 40 43 35461042 Increased resistance of SARS-CoV-2 Lambda variant to antibody neutralization. The results of site-mutated neutralization assay showed that the mutations in RBD, especially F490S, played an important role in the reduced sensitivity of Lambda variant. 2022 Journal of clinical virology Discussion SARS_CoV_2 F490S 94 99 RBD 78 81 35461042 Increased resistance of SARS-CoV-2 Lambda variant to antibody neutralization. Thus, we performed a head-to-head comparison of the binding affinity of nAbs to the RBD-L452R and RBD-L452Q. 2022 Journal of clinical virology Discussion SARS_CoV_2 L452Q;L452R 102;88 107;93 RBD;RBD 84;98 87;101 35461811 Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. Furthermore, deuterium exchange profiles of K90R, G15S and P132H showed equivalent uptake to wildtype Mpro, and revealed no detectable differences in backbone dynamics. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 G15S;K90R;P132H 50;44;59 54;48;64 35461811 Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. In combination with static high-resolution crystal structures, HDX-MS exchange from the ensemble of solution-phase conformations, provides evidence of equivalent solution-phase backbone dynamics for K90R, G15S and P132H to wildtype and suggests no evidence for influence from crystal lattice packing in the crystal structures. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 G15S;K90R;P132H 205;199;214 209;203;219 35461811 Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. Indeed, the x-ray crystal structures of nirmatrelvir bound to K90R, G15S and P132H Mpro variants shows that, not only is the binding mode of nirmatrelvir indistinguishable to the wildtype Mpro structure, but also that the conformation of the protein is not altered by the mutations, in agreement with the solution-phase data. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 G15S;K90R;P132H 68;62;77 72;66;82 35461811 Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. The K90R, G15S and P132H Mpro mutations exhibited comparable enzymatic properties as compared to wildtype Mpro as evidenced by our determined catalytic efficiencies (kcat/Km). 2022 The Journal of biological chemistry Discussion SARS_CoV_2 G15S;K90R;P132H 10;4;19 14;8;24 35461811 Structural basis for the in vitro efficacy of nirmatrelvir against SARS-CoV-2 variants. We evaluated the catalytic activity and potency of nirmatrelvir against the Mpro mutations observed in the prevalent variants of concern (VOC): Alpha (alpha, B.1.1.7), Beta (beta, B.1.351), and Gamma (gamma, P.1), which harbor a K90R mutation; Lambda (lambda, B.1.1.1.37/C.37) with a G15S mutation and Omicron (omicron, Beta.1.1.529) with a P132H mutation. 2022 The Journal of biological chemistry Discussion SARS_CoV_2 G15S;K90R;P132H 284;229;341 288;233;346 35464398 Case Report: X-Linked SASH3 Deficiency Presenting as a Common Variable Immunodeficiency. Our patient carried the c.505C>T/p.Gln169* variant, which truncates SASH3 protein upstream of the SAM and SH3 domains and leads to a complete absence of the protein. 2022 Frontiers in immunology Discussion SARS_CoV_2 C505T;C505T;N169X 24;26;37 32;32;42 35474907 SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants. Although this site was ultimately selected as aspartate (D) after 12 passages in all cell types, it may be crucial for viral adaptation in host cells; importantly, E484K and E484D have been associated with a protective immune response and viral permissiveness in several host cells. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 E484D;E484K 174;164 179;169 35474907 SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants. An E484D substitution on the spike protein was found in all viruses, including the original isolate used here, compared to the SARS-CoV-2 reference genome (Wuhan-Hu-1, GenBank Accession no. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 E484D 3 8 S 29 34 35474907 SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants. Following the noticeable increase in the D614G mutation in April 2020, the Omicron variant has acquired over 30 mutations, including those found in the Alpha, Beta, Gamma, and Delta variants. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 D614G 41 46 35474907 SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants. For example, Q493R and Q498R substitutions in the RBD were identified in this study and are consistent with key amino acid substitutions in the Omicron variant, which was first reported on November 24, 2021, in South Africa. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 Q493R;Q498R 13;23 18;28 RBD 50 53 35474907 SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants. However, in this experiment, key natural mutations such as D614G were not observed, which could be due to the specific host cells used or the in vitro culture system. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 D614G 59 64 35474907 SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants. In addition, the Y144del and H655Y substitutions reported in this study have naturally arisen in the B.1.1.7 (Alpha), P.1 (Gamma), and B.1.1.529 (Omicron) variants. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 H655Y;Y144del 29;17 34;24 35474907 SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants. The E484D mutation may have been generated in the passaging process, allowing replication in the A549 cells in this study. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 E484D 4 9 35474907 SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants. These selected mutations in the spike protein are also associated with mutations in mouse-adapted SARS-CoV-2 (Q493K and Q498H). 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 Q498H;Q493K 120;110 125;115 S 32 37 35474907 SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants. These SNPs resulted in non-synonymous amino acid substitutions (I76T, H655Y, Q895K, and T1076A on the spike protein; H125Y on the M protein; V5F on the ORF6 protein; L86M on the ORF7a protein; and an eight-amino-acid deletion in the E protein). 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 H125Y;H655Y;L86M;Q895K;T1076A;V5F;I76T 117;70;166;77;88;141;64 122;75;170;82;94;144;68 ORF7a;S;ORF6;E 178;102;152;233 183;107;156;234 35474907 SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants. V5F and L86M substitutions in ORF6 and ORF7a were not observed in viruses passaged in A549 cells. 2022 Computational and structural biotechnology journal Discussion SARS_CoV_2 L86M;V5F 8;0 12;3 ORF7a;ORF6 39;30 44;34 35480056 Safety and Immunogenicity of Inactivated COVID-19 Vaccines Among People Living with HIV in China. However, the GMT for the delta variant was significantly lower than the GMT for the D614G variant in PLWH, which is consistent with Chang Liu's finding that mRNA vaccines induced an antibody response to some variants, but the neutralization of the delta variant was reduced. 2022 Infection and drug resistance Discussion SARS_CoV_2 D614G 84 89 35480056 Safety and Immunogenicity of Inactivated COVID-19 Vaccines Among People Living with HIV in China. SARS-CoV-2 IgG concentrations and neutralizing antibody titers against the D614G and delta variants also declined significantly in PLWH compared to HDs. 2022 Infection and drug resistance Discussion SARS_CoV_2 D614G 75 80 SARS-CoV-2-HIV coinfections 131 135 35480056 Safety and Immunogenicity of Inactivated COVID-19 Vaccines Among People Living with HIV in China. The D614G and delta variants harbor mutations in the RBD, so neutralizing titers to the pseudotyped virus may better show the immune response to the two variants elicited by vaccination than titers of S-RBD-IgG. 2022 Infection and drug resistance Discussion SARS_CoV_2 D614G 4 9 RBD;RBD;S 53;203;201 56;206;202 35480056 Safety and Immunogenicity of Inactivated COVID-19 Vaccines Among People Living with HIV in China. The positive rates of neutralizing antibodies against the D614G virus and SARS-CoV-2 IgG in PLWH were markedly lower than those in HDs. 2022 Infection and drug resistance Discussion SARS_CoV_2 D614G 58 63 SARS-CoV-2-HIV coinfections 92 96 35480056 Safety and Immunogenicity of Inactivated COVID-19 Vaccines Among People Living with HIV in China. We evaluated the differences in neutralizing antibodies to D614G and the delta variant in PLWH. 2022 Infection and drug resistance Discussion SARS_CoV_2 D614G 59 64 SARS-CoV-2-HIV coinfections 90 94